diff --git a/moose-core/.travis.yml b/moose-core/.travis.yml
index 2f37437c30ae8d941c6062a7d09d5c11eaf0add4..0bf992ae852e4d7031e5c20c1e24123f3f924d5c 100644
--- a/moose-core/.travis.yml
+++ b/moose-core/.travis.yml
@@ -3,10 +3,10 @@ sudo: required
matrix:
include:
- - os : linux
- dist: xenial
- - os : osx
- osx_image: xcode10.1
+ - os: linux
+ dist: xenial
+ - os: osx
+ osx_image: xcode10.2
notifications:
email:
@@ -26,12 +26,6 @@ before_script:
- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then ./.travis/travis_prepare_osx.sh; fi
- if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo ./.travis/travis_prepare_linux.sh; fi
-
-before_script:
-- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then nvm get head || true; fi
-- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then ./.travis/travis_prepare_osx.sh; fi
-- if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo ./.travis/travis_prepare_linux.sh; fi
-
script:
- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then ./.travis/travis_build_osx.sh; fi
- if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then ./.travis/travis_build_linux.sh; fi
diff --git a/moose-core/.travis/travis_build_osx.sh b/moose-core/.travis/travis_build_osx.sh
index bb1fffe0edf851e6cb14dfa32b00470dff05de0b..20d0638e5a19aa955e1d399034e2b3dc394f621a 100755
--- a/moose-core/.travis/travis_build_osx.sh
+++ b/moose-core/.travis/travis_build_osx.sh
@@ -26,23 +26,26 @@ set -e
# Make sure not to pick up python from /opt.
PATH=/usr/local/bin:/usr/bin:$PATH
+ PYTHON3=$(which python3)
+
# Get pylint
- python -m pip install pylint --user
- python -m pip install python-libsbml --user
- python -m pip install pyneuroml --user
+ $PYTHON3 -m pip install pylint --user
+ $PYTHON3 -m pip install python-libsbml --user
+ $PYTHON3 -m pip install pyneuroml --user
mkdir -p _GSL_BUILD && cd _GSL_BUILD \
&& cmake -DDEBUG=ON \
- -DPYTHON_EXECUTABLE=`which python` ..
+ -DPYTHON_EXECUTABLE=$PYTHON3 \
+ ..
make pylint -j3
- make && ctest --output-on-failure -E ".*socket_streamer.*"
+ make && ctest --output-on-failure
cd .. # Now with boost.
mkdir -p _BOOST_BUILD && cd _BOOST_BUILD \
&& cmake -DWITH_BOOST_ODE=ON -DDEBUG=ON \
- -DPYTHON_EXECUTABLE=`which python` ..
+ -DPYTHON_EXECUTABLE=`which python3` ..
- make && ctest --output-on-failure -E ".*socket_streamer.*"
+ make -j4 && ctest --output-on-failure
cd ..
set +e
diff --git a/moose-core/.travis/travis_prepare_osx.sh b/moose-core/.travis/travis_prepare_osx.sh
index d56638ed70f802230d570697cc3d3dc3fdac8bdd..d706e68bb906973a4434c5d5b04a4c4a6b4c28c3 100755
--- a/moose-core/.travis/travis_prepare_osx.sh
+++ b/moose-core/.travis/travis_prepare_osx.sh
@@ -28,17 +28,20 @@ brew install python
brew install numpy
brew install boost
+PYTHON3=$(which python3)
+
#brew outdated python || brew install python
#brew outdated numpy || brew install homebrew/python/numpy
brew unlink numpy && brew link numpy || echo "Failed to link numpy"
# Numpy caveats
-mkdir -p $HOME/Library/Python/2.7/lib/python/site-packages
-echo 'import sys; sys.path.insert(1, "/usr/local/lib/python2.7/site-packages")' >> $HOME/Library/Python/2.7/lib/python/site-packages/homebrew.pth
+#mkdir -p $HOME/Library/Python/2.7/lib/python/site-packages
+#echo 'import sys; sys.path.insert(1, "/usr/local/lib/python2.7/site-packages")' >> $HOME/Library/Python/2.7/lib/python/site-packages/homebrew.pth
# To make sure that we do not pick python from /opt etc.
PATH=/usr/local/bin:/usr/bin:$PATH
# ensurepip
-python -m ensurepip
-python -m pip install matplotlib --user --upgrade
-python -m pip install pyNeuroML libNeuroML --user
-python -m pip install scipy --user
+$PYTHON3 -m ensurepip
+$PYTHON3 -m pip install matplotlib --user --upgrade
+$PYTHON3 -m pip install pyNeuroML libNeuroML --user
+$PYTHON3 -m pip install scipy --user
+$PYTHON3 -m pip install pylint --user
diff --git a/moose-core/CMakeLists.txt b/moose-core/CMakeLists.txt
index 0fa33eb6051be4169d0e3182c1f976a36cfbb95e..35a86c98aebf22674ae3dba8c20972077947ffbc 100644
--- a/moose-core/CMakeLists.txt
+++ b/moose-core/CMakeLists.txt
@@ -4,7 +4,6 @@ project(pymoose)
set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake_modules")
include(CheckCXXCompiler.cmake)
include(CheckIncludeFileCXX)
-include(FindPkgConfig)
# getgit revision number
find_program( GIT_EXEC git )
@@ -78,6 +77,7 @@ option(WITH_BOOST_ODE "Use boost library ode2 library instead of GSL" OFF)
option(WITH_GSL "Use gsl-library. Alternative is WITH_BOOST" ON)
option(PARALLELIZED_CLOCK "High level parallelization of moose::Clock (alpha)" OFF )
option(USE_PRIVATE_RNG "Stochastic Objects use their private RNG" ON)
+option(WITH_ASAN "Use AddressSanitizer in DEBUG mode." OFF)
############################ BUILD CONFIGURATION #################################
@@ -87,7 +87,7 @@ add_definitions(-DUSE_GENESIS_PARSER)
if(DEBUG OR "${CMAKE_BUILD_TYPE}" STREQUAL "Debug")
message(STATUS "Building for Debug/Unit testing")
- add_definitions(-DDO_UNIT_TESTS)
+ add_definitions(-DDO_UNIT_TESTS -O)
set(CMAKE_BUILD_TYPE Debug)
elseif(ENABLE_UNIT_TESTS)
MESSAGE(STATUS "Enabled Unit tests")
@@ -109,8 +109,14 @@ if(GPROF AND "${CMAKE_BUILD_TYPE}" STREQUAL "Debug")
set(CMAKE_EXE_LINKER_FLAGS_DEBUG "-pg")
endif()
-find_package(Threads)
-
+if(WITH_ASAN AND "${CMAKE_BUILD_TYPE}" STREQUAL "Debug")
+ message(STATUS "Compiling with ASAN")
+ set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} \
+ -fno-omit-frame-pointer -fsanitize=leak -fsanitize=address")
+ set(CMAKE_LINKER_FLAGS_DEBUG "${CMAKE_LINKER_FLAGS_DEBUG} \
+ -fno-omit-frame-pointer -fsanitize=leak -fsanitize=address")
+ set(CMAKE_MODULE_LINKER_FLAGS "${CMAKE_MODULE_LINKER_FLAGS} -fsanitize=address")
+endif()
################################### TARGETS ####################################
@@ -132,8 +138,6 @@ if(WITH_BOOST_ODE)
set(WITH_GSL OFF)
endif(WITH_BOOST_ODE)
-include_directories(msg basecode)
-
set_target_properties(libmoose PROPERTIES COMPILE_DEFINITIONS "MOOSE_LIB")
set_target_properties(libmoose PROPERTIES PREFIX "")
@@ -143,11 +147,10 @@ set(STATIC_LIBRARIES "" )
set(SYSTEM_SHARED_LIBS ${LibXML2_LIBRARIES})
# BOOST ode library performs better than GSL and ideally should be made default.
-# Making boost default means that we get rid of gsl. Boost does not have a very
-# good matrix library; it has ublas which is not well maintained and emit a lot
+# Unfortunately Boost does not have a very good matrix library; it has ublas
+# which is not well maintained and emit a lot
# of warning during compilation. Nonetheless, WITH_BOOST_ODE works fine and
-# produce results quicker than GSL. Both boost ode and ublas are in moose source
-# tree ./external/odeint-v2 and ./external/boost-numeric-bindings
+# produce results quicker than GSL.
if(WITH_GSL)
find_package(GSL 1.16 REQUIRED)
if(NOT GSL_FOUND)
@@ -172,13 +175,14 @@ if(WITH_GSL)
# top level.
include_directories( ${GSL_INCLUDE_DIRS} )
elseif(WITH_BOOST_ODE)
- find_package(Boost 1.44 REQUIRED)
- find_package( LAPACK REQUIRED )
+ find_package(Boost 1.53 REQUIRED)
+ find_package(LAPACK REQUIRED)
endif()
# if boost ode is being used, don't use GSL.
if(WITH_BOOST_ODE)
add_definitions(-DUSE_BOOST_ODE -UUSE_GSL)
+ include_directories(${Boost_INCLUDE_DIRS})
endif()
# Openmpi
@@ -202,6 +206,7 @@ if(WITH_BOOST_ODE)
list(APPEND SYSTEM_SHARED_LIBS ${Boost_LIBRARIES})
endif(WITH_BOOST_ODE)
+find_package( Threads )
list(APPEND SYSTEM_SHARED_LIBS ${CMAKE_THREAD_LIBS_INIT})
# These libraries could be static of dynamic. We need to discrimate between
@@ -265,6 +270,7 @@ list(APPEND MOOSE_LIBRARIES
msg
benchmarks
shell
+ randnum
scheduling
moose_mpi
biophysics
@@ -441,6 +447,7 @@ set(PYMOOSE_TEST_DIRECTORY ${CMAKE_SOURCE_DIR}/tests/python)
# Collect all python script in tests folder and run them.
file(GLOB PY_TEST_SCRIPTS "${PYMOOSE_TEST_DIRECTORY}/test_*.py" )
+
# Run python tests.
foreach( _test_script ${PY_TEST_SCRIPTS} )
get_filename_component( _test_name ${_test_script} NAME_WE)
@@ -453,6 +460,36 @@ foreach( _test_script ${PY_TEST_SCRIPTS} )
)
endforeach( )
+# Alpha tests. These should not run by default.
+set(MOOSE_ALPHA_TEST_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/tests/alpha)
+file(GLOB PY_ALPHA_TEST_SCRIPTS "${PYMOOSE_ALPHA_TEST_DIRECTORY}/*.py" )
+foreach( _test_script ${PY_ALPHA_TEST_SCRIPTS} )
+ get_filename_component( _test_name ${_test_script} NAME_WE)
+ add_test( NAME ${_test_name}
+ COMMAND ${PYTHON_EXECUTABLE} ${_test_script}
+ CONFIGURATIONS Devel
+ WORKING_DIRECTORY ${PYMOOSE_ALPHA_TEST_DIRECTORY}
+ )
+ set_tests_properties( ${_test_name}
+ PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}/python"
+ )
+endforeach( )
+
+# Regression and github issues. These should not run by default.
+set(PYMOOSE_ISSUES_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/tests/issues)
+file(GLOB PY_ISSUES_SCRIPTS "${PYMOOSE_ISSUES_DIRECTORY}/*.py" )
+foreach( _test_script ${PY_ISSUES_SCRIPTS} )
+ get_filename_component( _test_name ${_test_script} NAME_WE)
+ add_test( NAME ${_test_name}
+ COMMAND ${PYTHON_EXECUTABLE} ${_test_script}
+ CONFIGURATIONS Devel
+ WORKING_DIRECTORY ${PYMOOSE_ISSUES_DIRECTORY}
+ )
+ set_tests_properties( ${_test_name}
+ PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}/python"
+ )
+endforeach( )
+
# add pylint target.
set(PYSCRIPTS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/python )
file(GLOB_RECURSE PY_SCRIPTS "python/*.py")
@@ -476,4 +513,5 @@ foreach( _py_script ${PY_SCRIPTS} )
endforeach( )
############################ CPACK ######################################
+# This is not maintained anymore since packaging is done using OpenBuildService
include(${CMAKE_CURRENT_SOURCE_DIR}/cmake_moose_cpack.cmake)
diff --git a/moose-core/basecode/FuncOrder.h b/moose-core/basecode/FuncOrder.h
index 03c4bfc17dc83579cb4e433b1d4ae09e58b2780c..b75a8360c736d206584d3687bcff6138eb933360 100644
--- a/moose-core/basecode/FuncOrder.h
+++ b/moose-core/basecode/FuncOrder.h
@@ -13,28 +13,31 @@
class FuncOrder
{
- public:
- FuncOrder()
- : func_( 0 ), index_( 0 )
- {;}
+public:
+ FuncOrder()
+ : func_( 0 ), index_( 0 )
+ {;}
- const OpFunc* func() const {
- return func_;
- }
- unsigned int index() const {
- return index_;
- }
+ const OpFunc* func() const
+ {
+ return func_;
+ }
+ unsigned int index() const
+ {
+ return index_;
+ }
- void set( const OpFunc* func, unsigned int index ) {
- func_ = func;
- index_ = index;
- }
+ void set( const OpFunc* func, unsigned int index )
+ {
+ func_ = func;
+ index_ = index;
+ }
- bool operator<( const FuncOrder& other ) const
- {
- return func_ < other.func_;
- }
- private:
- const OpFunc* func_;
- unsigned int index_;
+ bool operator<( const FuncOrder& other ) const
+ {
+ return func_ < other.func_;
+ }
+private:
+ const OpFunc* func_;
+ unsigned int index_;
};
diff --git a/moose-core/basecode/global.cpp b/moose-core/basecode/global.cpp
index fadf41ef88f76f8586120c6b5a79675bc128f16d..c2c365428e72514f473071606cfbbc5151e798c2 100644
--- a/moose-core/basecode/global.cpp
+++ b/moose-core/basecode/global.cpp
@@ -49,7 +49,7 @@ namespace moose {
{ "HSolve", {0.0, 0} }
};
- moose::RNG<double> rng;
+ moose::RNG rng;
/* Check if path is OK */
int checkPath( const string& path )
@@ -104,6 +104,11 @@ namespace moose {
return moose::rng.uniform( );
}
+ double mtrand( double a, double b )
+ {
+ return (b-a) * mtrand() + a;
+ }
+
// MOOSE suffixes [0] to all elements to path. Remove [0] with null
// character whenever possible. For n > 0, [n] should not be touched. Its
// the user job to take the pain and write the correct path.
diff --git a/moose-core/basecode/global.h b/moose-core/basecode/global.h
index 893c55762c7fe4f1bb51f2496c4346478a1a8de0..3beab75dc583579fce039a8383bb78825ce0511a 100644
--- a/moose-core/basecode/global.h
+++ b/moose-core/basecode/global.h
@@ -56,7 +56,7 @@ extern unsigned int totalTests;
namespace moose
{
- extern moose::RNG<double> rng;
+ extern moose::RNG rng;
extern map<string, valarray<double>> solverProfMap;
@@ -114,6 +114,18 @@ namespace moose
*/
double mtrand( void );
+ /* --------------------------------------------------------------------------*/
+ /**
+ * @Synopsis Overloaded function. Random number between a and b
+ *
+ * @Param a lower limit.
+ * @Param b Upper limit.
+ *
+ * @Returns
+ */
+ /* ----------------------------------------------------------------------------*/
+ double mtrand( double a, double b );
+
/**
* @brief Create a POSIX compatible path from a given string.
* Remove/replace bad characters.
diff --git a/moose-core/biophysics/Compartment.cpp b/moose-core/biophysics/Compartment.cpp
index 8a137df7d39497e5ef7b0d967a59076983751c14..4f7742f7efcb54a04602aa447408958c29c9f031 100644
--- a/moose-core/biophysics/Compartment.cpp
+++ b/moose-core/biophysics/Compartment.cpp
@@ -268,7 +268,7 @@ void Compartment::vRandInject( const Eref& e, double prob, double current)
#ifdef DO_UNIT_TESTS
-#include "header.h"
+#include "../basecode/header.h"
#include "../shell/Shell.h"
//#include "../randnum/randnum.h"
diff --git a/moose-core/biophysics/Neuron.cpp b/moose-core/biophysics/Neuron.cpp
index 4d5993f1676aa1a4fe03ba6719563880115e8ee6..fc72bf01b199090879cfccf7d51d7f049fa1bdec 100644
--- a/moose-core/biophysics/Neuron.cpp
+++ b/moose-core/biophysics/Neuron.cpp
@@ -19,13 +19,13 @@
#include "Neuron.h"
#include "../basecode/global.h"
-#include "../external/muparser/include/muParser.h"
+#include "../builtins/MooseParser.h"
-class nuParser: public mu::Parser
+class nuParser: public MooseParser
{
public:
nuParser( const string& expr ):
- mu::Parser(),
+ MooseParser(),
p(0.0), // geometrical path distance wound through dendrite
g(0.0), // geometrical path distance direct from soma.
L(0.0), // electrical distance arg
@@ -109,40 +109,40 @@ const Cinfo* Neuron::initCinfo()
// ValueFinfos
/////////////////////////////////////////////////////////////////////
static ValueFinfo< Neuron, double > RM( "RM",
- "Membrane resistivity, in ohm.m^2. Default value is 1.0.",
- &Neuron::setRM,
- &Neuron::getRM
- );
+ "Membrane resistivity, in ohm.m^2. Default value is 1.0.",
+ &Neuron::setRM,
+ &Neuron::getRM
+ );
static ValueFinfo< Neuron, double > RA( "RA",
- "Axial resistivity of cytoplasm, in ohm.m. Default value is 1.0.",
- &Neuron::setRA,
- &Neuron::getRA
- );
+ "Axial resistivity of cytoplasm, in ohm.m. Default value is 1.0.",
+ &Neuron::setRA,
+ &Neuron::getRA
+ );
static ValueFinfo< Neuron, double > CM( "CM",
- "Membrane Capacitance, in F/m^2. Default value is 0.01",
- &Neuron::setCM,
- &Neuron::getCM
- );
+ "Membrane Capacitance, in F/m^2. Default value is 0.01",
+ &Neuron::setCM,
+ &Neuron::getCM
+ );
static ValueFinfo< Neuron, double > Em( "Em",
- "Resting membrane potential of compartments, in Volts. "
- "Default value is -0.065.",
- &Neuron::setEm,
- &Neuron::getEm
- );
+ "Resting membrane potential of compartments, in Volts. "
+ "Default value is -0.065.",
+ &Neuron::setEm,
+ &Neuron::getEm
+ );
static ValueFinfo< Neuron, double > theta( "theta",
"Angle to rotate cell geometry, around long axis of neuron. "
"Think Longitude. Units are radians. "
"Default value is zero, which means no rotation. ",
&Neuron::setTheta,
&Neuron::getTheta
- );
+ );
static ValueFinfo< Neuron, double > phi( "phi",
"Angle to rotate cell geometry, around elevation of neuron. "
"Think Latitude. Units are radians. "
"Default value is zero, which means no rotation. ",
&Neuron::setPhi,
&Neuron::getPhi
- );
+ );
static ValueFinfo< Neuron, string > sourceFile( "sourceFile",
"Name of source file from which to load a model. "
@@ -151,317 +151,317 @@ const Cinfo* Neuron::initCinfo()
"definitions should have been loaded into /library. ",
&Neuron::setSourceFile,
&Neuron::getSourceFile
- );
+ );
static ValueFinfo< Neuron, double > compartmentLengthInLambdas(
- "compartmentLengthInLambdas",
- "Units: meters (SI). \n"
- "Electrotonic length to use for the largest compartment in the "
- "model. Used to define subdivision of branches into compartments. "
- "For example, if we set *compartmentLengthInLambdas* to 0.1, "
- "and *lambda* (electrotonic length) is 250 microns, then it "
- "sets the compartment length to 25 microns. Thus a dendritic "
- "branch of 500 microns is subdivided into 20 commpartments. "
- "If the branch is shorter than *compartmentLengthInLambdas*, "
- "then it is not subdivided. "
- "If *compartmentLengthInLambdas* is set to 0 then the original "
- "compartmental structure of the model is preserved. "
- " Note that this routine does NOT merge branches, even if "
- "*compartmentLengthInLambdas* is bigger than the branch. "
- "While all this subdivision is being done, the Neuron class "
- "preserves as detailed a geometry as it can, so it can rebuild "
- "the more detailed version if needed. "
- "Default value of *compartmentLengthInLambdas* is 0. ",
- &Neuron::setCompartmentLengthInLambdas,
- &Neuron::getCompartmentLengthInLambdas
- );
+ "compartmentLengthInLambdas",
+ "Units: meters (SI). \n"
+ "Electrotonic length to use for the largest compartment in the "
+ "model. Used to define subdivision of branches into compartments. "
+ "For example, if we set *compartmentLengthInLambdas* to 0.1, "
+ "and *lambda* (electrotonic length) is 250 microns, then it "
+ "sets the compartment length to 25 microns. Thus a dendritic "
+ "branch of 500 microns is subdivided into 20 commpartments. "
+ "If the branch is shorter than *compartmentLengthInLambdas*, "
+ "then it is not subdivided. "
+ "If *compartmentLengthInLambdas* is set to 0 then the original "
+ "compartmental structure of the model is preserved. "
+ " Note that this routine does NOT merge branches, even if "
+ "*compartmentLengthInLambdas* is bigger than the branch. "
+ "While all this subdivision is being done, the Neuron class "
+ "preserves as detailed a geometry as it can, so it can rebuild "
+ "the more detailed version if needed. "
+ "Default value of *compartmentLengthInLambdas* is 0. ",
+ &Neuron::setCompartmentLengthInLambdas,
+ &Neuron::getCompartmentLengthInLambdas
+ );
static ElementValueFinfo< Neuron, vector< string > >
- channelDistribution(
- "channelDistribution",
- "Specification for distribution of channels, CaConcens and "
- "any other model components that are defined as prototypes and "
- "have to be placed on the electrical compartments.\n"
- "Arguments: proto path field expr [field expr]...\n"
- " Each entry is terminated with an empty string. "
- "The prototype is any object created in */library*, "
- "If a channel matching the prototype name already exists, then "
- "all subsequent operations are applied to the extant channel and "
- "a new one is not created. "
- "The paired arguments are as follows: \n"
- "The *field* argument specifies the name of the parameter "
- "that is to be assigned by the expression.\n"
- "The *expression* argument is a mathematical expression in "
- "the muparser framework, which permits most operations including "
- "trig and transcendental ones. Of course it also handles simple "
- "numerical values like 1.0, 1e-10 and so on. "
- "Available arguments for muParser are:\n"
- " p, g, L, len, dia, maxP, maxG, maxL \n"
- " p: path distance from soma, measured along dendrite, in metres.\n"
- " g: geometrical distance from soma, in metres.\n"
- " L: electrotonic distance (# of lambdas) from soma, along dend. No units.\n"
- " len: length of compartment, in metres.\n"
- " dia: for diameter of compartment, in metres.\n"
- " maxP: Maximum value of *p* for this neuron. \n"
- " maxG: Maximum value of *g* for this neuron. \n"
- " maxL: Maximum value of *L* for this neuron.\n"
- "The expression for the first field must evaluate to > 0 "
- "for the channel to be installed. For example, for "
- "channels, if Field == Gbar, and func( r, L, len, dia) < 0, \n"
- "then the channel is not installed. This feature is typically "
- "used with the sign() or Heaviside H() function to limit range: "
- "for example: H(1 - L) will only put channels closer than "
- "one length constant from the soma, and zero elsewhere. \n"
- "Available fields are: \n"
- "Channels: Gbar (install), Ek \n"
- "CaConcen: shellDia (install), shellFrac (install), tau, min\n"
- "Unless otherwise noted, all fields are scaled appropriately by "
- "the dimensions of their compartment. Thus the channel "
- "maximal conductance Gbar is automatically scaled by the area "
- "of the compartment, and the user does not need to insert this "
- "scaling into the calculations.\n"
- "All parameters are expressed in SI units. Conductance, for "
- "example, is Siemens/sq metre. "
- "\n\n"
- "Some example function forms might be for a channel Gbar: \n"
- " p < 10e-6 ? 400 : 0.0 \n"
- " equivalently, \n"
- " H(10e-6 - p) * 400 \n"
- " equivalently, \n"
- " ( sign(10e-6 - p) + 1) * 200 \n"
- "Each of these forms instruct the function to "
- "set channel Gbar to 400 S/m^2 only within 10 microns path "
- "distance of soma\n"
- "\n"
- " L < 1.0 ? 100 * exp( -L ) : 0.0 \n"
- " ->Set channel Gbar to an exponentially falling function of "
- "electrotonic distance from soma, provided L is under "
- "1.0 lambdas. \n",
+ channelDistribution(
+ "channelDistribution",
+ "Specification for distribution of channels, CaConcens and "
+ "any other model components that are defined as prototypes and "
+ "have to be placed on the electrical compartments.\n"
+ "Arguments: proto path field expr [field expr]...\n"
+ " Each entry is terminated with an empty string. "
+ "The prototype is any object created in */library*, "
+ "If a channel matching the prototype name already exists, then "
+ "all subsequent operations are applied to the extant channel and "
+ "a new one is not created. "
+ "The paired arguments are as follows: \n"
+ "The *field* argument specifies the name of the parameter "
+ "that is to be assigned by the expression.\n"
+ "The *expression* argument is a mathematical expression in "
+ "the muparser framework, which permits most operations including "
+ "trig and transcendental ones. Of course it also handles simple "
+ "numerical values like 1.0, 1e-10 and so on. "
+ "Available arguments for muParser are:\n"
+ " p, g, L, len, dia, maxP, maxG, maxL \n"
+ " p: path distance from soma, measured along dendrite, in metres.\n"
+ " g: geometrical distance from soma, in metres.\n"
+ " L: electrotonic distance (# of lambdas) from soma, along dend. No units.\n"
+ " len: length of compartment, in metres.\n"
+ " dia: for diameter of compartment, in metres.\n"
+ " maxP: Maximum value of *p* for this neuron. \n"
+ " maxG: Maximum value of *g* for this neuron. \n"
+ " maxL: Maximum value of *L* for this neuron.\n"
+ "The expression for the first field must evaluate to > 0 "
+ "for the channel to be installed. For example, for "
+ "channels, if Field == Gbar, and func( r, L, len, dia) < 0, \n"
+ "then the channel is not installed. This feature is typically "
+ "used with the sign() or Heaviside H() function to limit range: "
+ "for example: H(1 - L) will only put channels closer than "
+ "one length constant from the soma, and zero elsewhere. \n"
+ "Available fields are: \n"
+ "Channels: Gbar (install), Ek \n"
+ "CaConcen: shellDia (install), shellFrac (install), tau, min\n"
+ "Unless otherwise noted, all fields are scaled appropriately by "
+ "the dimensions of their compartment. Thus the channel "
+ "maximal conductance Gbar is automatically scaled by the area "
+ "of the compartment, and the user does not need to insert this "
+ "scaling into the calculations.\n"
+ "All parameters are expressed in SI units. Conductance, for "
+ "example, is Siemens/sq metre. "
+ "\n\n"
+ "Some example function forms might be for a channel Gbar: \n"
+ " p < 10e-6 ? 400 : 0.0 \n"
+ " equivalently, \n"
+ " H(10e-6 - p) * 400 \n"
+ " equivalently, \n"
+ " ( sign(10e-6 - p) + 1) * 200 \n"
+ "Each of these forms instruct the function to "
+ "set channel Gbar to 400 S/m^2 only within 10 microns path "
+ "distance of soma\n"
+ "\n"
+ " L < 1.0 ? 100 * exp( -L ) : 0.0 \n"
+ " ->Set channel Gbar to an exponentially falling function of "
+ "electrotonic distance from soma, provided L is under "
+ "1.0 lambdas. \n",
&Neuron::setChannelDistribution,
&Neuron::getChannelDistribution
- );
+ );
static ElementValueFinfo< Neuron, vector< string > >
- passiveDistribution(
- "passiveDistribution",
- "Specification for distribution of passive properties of cell.\n"
- "Arguments: . path field expr [field expr]...\n"
- "Note that the arguments list starts with a period. "
- " Each entry is terminated with an empty string. "
- "The paired arguments are as follows: \n"
- "The *field* argument specifies the name of the parameter "
- "that is to be assigned by the expression.\n"
- "The *expression* argument is a mathematical expression in "
- "the muparser framework, which permits most operations including "
- "trig and transcendental ones. Of course it also handles simple "
- "numerical values like 1.0, 1e-10 and so on. "
- "Available arguments for muParser are:\n"
- " p, g, L, len, dia, maxP, maxG, maxL \n"
- " p: path distance from soma, measured along dendrite, in metres.\n"
- " g: geometrical distance from soma, in metres.\n"
- " L: electrotonic distance (# of lambdas) from soma, along dend. No units.\n"
- " len: length of compartment, in metres.\n"
- " dia: for diameter of compartment, in metres.\n"
- " maxP: Maximum value of *p* for this neuron. \n"
- " maxG: Maximum value of *g* for this neuron. \n"
- " maxL: Maximum value of *L* for this neuron.\n"
- "Available fields are: \n"
- "RM, RA, CM, Rm, Ra, Cm, Em, initVm \n"
- "The first three fields are scaled appropriately by "
- "the dimensions of their compartment. Thus the membrane "
- "resistivity RM (ohms.m^2) is automatically scaled by the area "
- "of the compartment, and the user does not need to insert this "
- "scaling into the calculations to compute Rm."
- "Using the Rm field lets the user directly assign the "
- "membrane resistance (in ohms), presumably using len and dia.\n"
- "Similarly, RA (ohms.m) and CM (Farads/m^2) are specific units "
- "and the actual values for each compartment are assigned by "
- "scaling by length and diameter. Ra (ohms) and Cm (Farads) "
- "require explicit evaluation of the expression. "
- "All parameters are expressed in SI units. Conductance, for "
- "example, is Siemens/sq metre.\n"
- "Note that time these calculations do NOT currently include spines\n",
+ passiveDistribution(
+ "passiveDistribution",
+ "Specification for distribution of passive properties of cell.\n"
+ "Arguments: . path field expr [field expr]...\n"
+ "Note that the arguments list starts with a period. "
+ " Each entry is terminated with an empty string. "
+ "The paired arguments are as follows: \n"
+ "The *field* argument specifies the name of the parameter "
+ "that is to be assigned by the expression.\n"
+ "The *expression* argument is a mathematical expression in "
+ "the muparser framework, which permits most operations including "
+ "trig and transcendental ones. Of course it also handles simple "
+ "numerical values like 1.0, 1e-10 and so on. "
+ "Available arguments for muParser are:\n"
+ " p, g, L, len, dia, maxP, maxG, maxL \n"
+ " p: path distance from soma, measured along dendrite, in metres.\n"
+ " g: geometrical distance from soma, in metres.\n"
+ " L: electrotonic distance (# of lambdas) from soma, along dend. No units.\n"
+ " len: length of compartment, in metres.\n"
+ " dia: for diameter of compartment, in metres.\n"
+ " maxP: Maximum value of *p* for this neuron. \n"
+ " maxG: Maximum value of *g* for this neuron. \n"
+ " maxL: Maximum value of *L* for this neuron.\n"
+ "Available fields are: \n"
+ "RM, RA, CM, Rm, Ra, Cm, Em, initVm \n"
+ "The first three fields are scaled appropriately by "
+ "the dimensions of their compartment. Thus the membrane "
+ "resistivity RM (ohms.m^2) is automatically scaled by the area "
+ "of the compartment, and the user does not need to insert this "
+ "scaling into the calculations to compute Rm."
+ "Using the Rm field lets the user directly assign the "
+ "membrane resistance (in ohms), presumably using len and dia.\n"
+ "Similarly, RA (ohms.m) and CM (Farads/m^2) are specific units "
+ "and the actual values for each compartment are assigned by "
+ "scaling by length and diameter. Ra (ohms) and Cm (Farads) "
+ "require explicit evaluation of the expression. "
+ "All parameters are expressed in SI units. Conductance, for "
+ "example, is Siemens/sq metre.\n"
+ "Note that time these calculations do NOT currently include spines\n",
&Neuron::setPassiveDistribution,
&Neuron::getPassiveDistribution
- );
+ );
static ElementValueFinfo< Neuron, vector< string > >spineDistribution(
- "spineDistribution",
- "Specification for distribution of spines on dendrite. \n"
- "Arguments: proto path spacing expr [field expr]...\n"
- " Each entry is terminated with an empty string. "
- "The *prototype* is any spine object created in */library*, \n"
- "The *path* is the wildcard path of compartments on which to "
- "place the spine.\n"
- "The *spacing* is the spacing of spines, in metres. \n"
- "The *expression* argument is a mathematical expression in "
- "the muparser framework, which permits most operations including "
- "trig and transcendental ones. Of course it also handles simple "
- "numerical values like 1.0, 1e-10 and so on. "
- "The paired arguments are as follows: \n"
- "The *field* argument specifies the name of the parameter "
- "that is to be assigned by the expression.\n"
- "The *expression* argument is a mathematical expression as above. "
- "Available arguments for muParser are:\n"
- " p, g, L, len, dia, maxP, maxG, maxL \n"
- " p: path distance from soma, measured along dendrite, in metres.\n"
- " g: geometrical distance from soma, in metres.\n"
- " L: electrotonic distance (# of lambdas) from soma, along dend. No units.\n"
- " len: length of compartment, in metres.\n"
- " dia: for diameter of compartment, in metres.\n"
- " maxP: Maximum value of *p* for this neuron. \n"
- " maxG: Maximum value of *g* for this neuron. \n"
- " maxL: Maximum value of *L* for this neuron.\n"
- "The expression for the *spacing* field must evaluate to > 0 for "
- "the spine to be installed. For example, if the expresssion is\n"
- " H(1 - L) \n"
- "then the system will only put spines closer than "
- "one length constant from the soma, and zero elsewhere. \n"
- "Available spine parameters are: \n"
- "spacing, minSpacing, size, sizeDistrib "
- "angle, angleDistrib \n"
- "minSpacing sets the granularity of sampling (typically about 0.1*"
- "spacing) for the usual case where spines are spaced randomly. "
- "If minSpacing < 0 then the spines are spaced equally at "
- "'spacing', unless the dendritic segment length is smaller than "
- "'spacing'. In that case it falls back to the regular random "
- "placement method.",
+ "spineDistribution",
+ "Specification for distribution of spines on dendrite. \n"
+ "Arguments: proto path spacing expr [field expr]...\n"
+ " Each entry is terminated with an empty string. "
+ "The *prototype* is any spine object created in */library*, \n"
+ "The *path* is the wildcard path of compartments on which to "
+ "place the spine.\n"
+ "The *spacing* is the spacing of spines, in metres. \n"
+ "The *expression* argument is a mathematical expression in "
+ "the muparser framework, which permits most operations including "
+ "trig and transcendental ones. Of course it also handles simple "
+ "numerical values like 1.0, 1e-10 and so on. "
+ "The paired arguments are as follows: \n"
+ "The *field* argument specifies the name of the parameter "
+ "that is to be assigned by the expression.\n"
+ "The *expression* argument is a mathematical expression as above. "
+ "Available arguments for muParser are:\n"
+ " p, g, L, len, dia, maxP, maxG, maxL \n"
+ " p: path distance from soma, measured along dendrite, in metres.\n"
+ " g: geometrical distance from soma, in metres.\n"
+ " L: electrotonic distance (# of lambdas) from soma, along dend. No units.\n"
+ " len: length of compartment, in metres.\n"
+ " dia: for diameter of compartment, in metres.\n"
+ " maxP: Maximum value of *p* for this neuron. \n"
+ " maxG: Maximum value of *g* for this neuron. \n"
+ " maxL: Maximum value of *L* for this neuron.\n"
+ "The expression for the *spacing* field must evaluate to > 0 for "
+ "the spine to be installed. For example, if the expresssion is\n"
+ " H(1 - L) \n"
+ "then the system will only put spines closer than "
+ "one length constant from the soma, and zero elsewhere. \n"
+ "Available spine parameters are: \n"
+ "spacing, minSpacing, size, sizeDistrib "
+ "angle, angleDistrib \n"
+ "minSpacing sets the granularity of sampling (typically about 0.1*"
+ "spacing) for the usual case where spines are spaced randomly. "
+ "If minSpacing < 0 then the spines are spaced equally at "
+ "'spacing', unless the dendritic segment length is smaller than "
+ "'spacing'. In that case it falls back to the regular random "
+ "placement method.",
&Neuron::setSpineDistribution,
&Neuron::getSpineDistribution
- );
+ );
static ReadOnlyValueFinfo< Neuron, unsigned int > numCompartments(
- "numCompartments",
- "Number of electrical compartments in model. ",
- &Neuron::getNumCompartments
- );
+ "numCompartments",
+ "Number of electrical compartments in model. ",
+ &Neuron::getNumCompartments
+ );
static ReadOnlyValueFinfo< Neuron, unsigned int > numSpines(
- "numSpines",
- "Number of dendritic spines in model. ",
- &Neuron::getNumSpines
- );
+ "numSpines",
+ "Number of dendritic spines in model. ",
+ &Neuron::getNumSpines
+ );
static ReadOnlyValueFinfo< Neuron, unsigned int > numBranches(
- "numBranches",
- "Number of branches in dendrites. ",
- &Neuron::getNumBranches
- );
+ "numBranches",
+ "Number of branches in dendrites. ",
+ &Neuron::getNumBranches
+ );
static ReadOnlyValueFinfo< Neuron, vector< double > > pathDistFromSoma(
- "pathDistanceFromSoma",
- "geometrical path distance of each segment from soma, measured by "
- "threading along the dendrite.",
- &Neuron::getPathDistFromSoma
- );
+ "pathDistanceFromSoma",
+ "geometrical path distance of each segment from soma, measured by "
+ "threading along the dendrite.",
+ &Neuron::getPathDistFromSoma
+ );
static ReadOnlyValueFinfo< Neuron, vector< double > > geomDistFromSoma(
- "geometricalDistanceFromSoma",
- "geometrical distance of each segment from soma.",
- &Neuron::getGeomDistFromSoma
- );
+ "geometricalDistanceFromSoma",
+ "geometrical distance of each segment from soma.",
+ &Neuron::getGeomDistFromSoma
+ );
static ReadOnlyValueFinfo< Neuron, vector< double > > elecDistFromSoma(
- "electrotonicDistanceFromSoma",
- "geometrical distance of each segment from soma, as measured along "
- "the dendrite.",
- &Neuron::getElecDistFromSoma
- );
+ "electrotonicDistanceFromSoma",
+ "geometrical distance of each segment from soma, as measured along "
+ "the dendrite.",
+ &Neuron::getElecDistFromSoma
+ );
static ReadOnlyValueFinfo< Neuron, vector< ObjId > > compartments(
- "compartments",
- "Vector of ObjIds of electrical compartments. Order matches order "
- "of segments, and also matches the order of the electrotonic and "
- "geometricalDistanceFromSoma vectors. ",
- &Neuron::getCompartments
- );
+ "compartments",
+ "Vector of ObjIds of electrical compartments. Order matches order "
+ "of segments, and also matches the order of the electrotonic and "
+ "geometricalDistanceFromSoma vectors. ",
+ &Neuron::getCompartments
+ );
static ReadOnlyLookupElementValueFinfo< Neuron, string, vector< ObjId > >
- compartmentsFromExpression(
- "compartmentsFromExpression",
- "Vector of ObjIds of electrical compartments that match the "
- "'path expression' pair in the argument string.",
- &Neuron::getExprElist
- );
+ compartmentsFromExpression(
+ "compartmentsFromExpression",
+ "Vector of ObjIds of electrical compartments that match the "
+ "'path expression' pair in the argument string.",
+ &Neuron::getExprElist
+ );
static ReadOnlyLookupElementValueFinfo< Neuron, string, vector< double > >
- valuesFromExpression(
- "valuesFromExpression",
- "Vector of values computed for each electrical compartment that "
- "matches the 'path expression' pair in the argument string."
- "This has 13 times the number of entries as # of compartments."
- "For each compartment the entries are: \n"
- "val, p, g, L, len, dia, maxP, maxG, maxL, x, y, z, 0",
- &Neuron::getExprVal
- );
+ valuesFromExpression(
+ "valuesFromExpression",
+ "Vector of values computed for each electrical compartment that "
+ "matches the 'path expression' pair in the argument string."
+ "This has 13 times the number of entries as # of compartments."
+ "For each compartment the entries are: \n"
+ "val, p, g, L, len, dia, maxP, maxG, maxL, x, y, z, 0",
+ &Neuron::getExprVal
+ );
static ReadOnlyLookupElementValueFinfo< Neuron, string, vector< ObjId > >
- spinesFromExpression(
- "spinesFromExpression",
- //"Vector of ObjIds of spines/heads sitting on the electrical "
- //"compartments that match the 'path expression' pair in the "
- //"argument string.",
- "Vector of ObjIds of compartments comprising spines/heads "
- "that match the 'path expression' pair in the "
- "argument string.",
- &Neuron::getSpinesFromExpression
- );
+ spinesFromExpression(
+ "spinesFromExpression",
+ //"Vector of ObjIds of spines/heads sitting on the electrical "
+ //"compartments that match the 'path expression' pair in the "
+ //"argument string.",
+ "Vector of ObjIds of compartments comprising spines/heads "
+ "that match the 'path expression' pair in the "
+ "argument string.",
+ &Neuron::getSpinesFromExpression
+ );
static ReadOnlyLookupElementValueFinfo< Neuron, ObjId,vector< ObjId > >
- spinesOnCompartment(
- "spinesOnCompartment",
- "Vector of ObjIds of spines shafts/heads sitting on the specified "
- "electrical compartment. If each spine has a shaft and a head,"
- "and there are 10 spines on the compartment, there will be 20 "
- "entries in the returned vector, ordered "
- "shaft0, head0, shaft1, head1, ... ",
- &Neuron::getSpinesOnCompartment
- );
+ spinesOnCompartment(
+ "spinesOnCompartment",
+ "Vector of ObjIds of spines shafts/heads sitting on the specified "
+ "electrical compartment. If each spine has a shaft and a head,"
+ "and there are 10 spines on the compartment, there will be 20 "
+ "entries in the returned vector, ordered "
+ "shaft0, head0, shaft1, head1, ... ",
+ &Neuron::getSpinesOnCompartment
+ );
static ReadOnlyLookupElementValueFinfo< Neuron, ObjId, ObjId >
- parentCompartmentOfSpine(
- "parentCompartmentOfSpine",
- "Returns parent compartment of specified spine compartment."
- "Both the spine head or its shaft will return the same parent.",
- &Neuron::getParentCompartmentOfSpine
- );
+ parentCompartmentOfSpine(
+ "parentCompartmentOfSpine",
+ "Returns parent compartment of specified spine compartment."
+ "Both the spine head or its shaft will return the same parent.",
+ &Neuron::getParentCompartmentOfSpine
+ );
static ReadOnlyLookupElementValueFinfo< Neuron, vector< ObjId >, vector< ObjId > >
- spineIdsFromCompartmentIds(
- "spineIdsFromCompartmentIds",
- "Vector of ObjIds of spine entries (FieldElements on this Neuron, "
- "used for scaling) that map to the the specified "
- "electrical compartments. If a bad compartment Id is given, the"
- "corresponding spine entry is the root Id.",
- &Neuron::getSpineIdsFromCompartmentIds
- );
+ spineIdsFromCompartmentIds(
+ "spineIdsFromCompartmentIds",
+ "Vector of ObjIds of spine entries (FieldElements on this Neuron, "
+ "used for scaling) that map to the the specified "
+ "electrical compartments. If a bad compartment Id is given, the"
+ "corresponding spine entry is the root Id.",
+ &Neuron::getSpineIdsFromCompartmentIds
+ );
/////////////////////////////////////////////////////////////////////
// DestFinfos
/////////////////////////////////////////////////////////////////////
static DestFinfo buildSegmentTree( "buildSegmentTree",
- "Build the reference segment tree structure using the child "
- "compartments of the current Neuron. Fills in all the coords and "
- "length constant information into the segments, for later use "
- "when we build reduced compartment trees and channel "
- "distributions. Should only be called once, since subsequent use "
- "on a reduced model will lose the original full cell geometry. ",
- new EpFunc0< Neuron >( &Neuron::buildSegmentTree )
- );
+ "Build the reference segment tree structure using the child "
+ "compartments of the current Neuron. Fills in all the coords and "
+ "length constant information into the segments, for later use "
+ "when we build reduced compartment trees and channel "
+ "distributions. Should only be called once, since subsequent use "
+ "on a reduced model will lose the original full cell geometry. ",
+ new EpFunc0< Neuron >( &Neuron::buildSegmentTree )
+ );
static DestFinfo setSpineAndPsdMesh( "setSpineAndPsdMesh",
- "Assigns the spine and psd mesh to the Neuron. This is used "
- "to build up a mapping from Spine entries on the Neuron to "
- "chem spines and PSDs, so that volume change operations from "
- "the Spine can propagate to the chem systems.",
- new OpFunc2< Neuron, Id, Id >( &Neuron::setSpineAndPsdMesh )
- );
+ "Assigns the spine and psd mesh to the Neuron. This is used "
+ "to build up a mapping from Spine entries on the Neuron to "
+ "chem spines and PSDs, so that volume change operations from "
+ "the Spine can propagate to the chem systems.",
+ new OpFunc2< Neuron, Id, Id >( &Neuron::setSpineAndPsdMesh )
+ );
static DestFinfo setSpineAndPsdDsolve( "setSpineAndPsdDsolve",
- "Assigns the Dsolves used by spine and PSD to the Neuron. "
- "This is used "
- "to handle the rescaling of diffusion rates when spines are "
- "resized. ",
- new OpFunc2< Neuron, Id, Id >( &Neuron::setSpineAndPsdDsolve )
- );
+ "Assigns the Dsolves used by spine and PSD to the Neuron. "
+ "This is used "
+ "to handle the rescaling of diffusion rates when spines are "
+ "resized. ",
+ new OpFunc2< Neuron, Id, Id >( &Neuron::setSpineAndPsdDsolve )
+ );
/*
static DestFinfo rotateInSpace( "rotateInSpace",
diff --git a/moose-core/biophysics/ReadCell.cpp b/moose-core/biophysics/ReadCell.cpp
index d900e5a34475822b9564113a226d1628cb70c527..50f2ef08b47745f61ff385bda8136164ff678c32 100644
--- a/moose-core/biophysics/ReadCell.cpp
+++ b/moose-core/biophysics/ReadCell.cpp
@@ -11,7 +11,6 @@
#include "../shell/Shell.h"
#include "ReadCell.h"
#include "../utility/utility.h"
-#include "../utility/numutil.h"
#include "CompartmentBase.h"
#include "Compartment.h"
#include "SymCompartment.h"
diff --git a/moose-core/builtins/CMakeLists.txt b/moose-core/builtins/CMakeLists.txt
index 8b96a98ede778da45649ed00f064ff603e95576e..9b4e63994ff122dab957b0bc498a18ae925b8a84 100644
--- a/moose-core/builtins/CMakeLists.txt
+++ b/moose-core/builtins/CMakeLists.txt
@@ -51,7 +51,7 @@ set(SRCS
Arith.cpp
Group.cpp
Mstring.cpp
- Func.cpp
+ MooseParser.cpp
Function.cpp
Variable.cpp
InputVariable.cpp
diff --git a/moose-core/builtins/Function.cpp b/moose-core/builtins/Function.cpp
index 3883b699a618a7b2b1e26dcb0dd45cd6b3c7fc03..16ee175ead27092b7df78c1bd61bec0bbdcb6299 100644
--- a/moose-core/builtins/Function.cpp
+++ b/moose-core/builtins/Function.cpp
@@ -1,81 +1,39 @@
-// Function.cpp ---
-//
-// Filename: Function.cpp
// Description: Implementation of a wrapper around muParser.
// Author: Subhasis Ray
// Maintainer: Subhasis Ray
-// Created: Sat May 25 16:35:17 2013 (+0530)
-// Version:
-// Last-Updated: Tue Jun 11 16:49:01 2013 (+0530)
-// By: subha
-// Update #: 619
-// URL:
-// Keywords:
-// Compatibility:
-//
-//
-
-// Commentary:
-//
-//
-//
-//
-
-// Change log:
-//
-//
-//
-//
-// This program is free software; you can redistribute it and/or
-// modify it under the terms of the GNU Lesser General Public License as
-// published by the Free Software Foundation; either version 3, or
-// (at your option) any later version.
-//
-// This program is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-// General Public License for more details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this program; see the file COPYING. If not, write to
-// the Free Software Foundation, Inc., 51 Franklin Street, Fifth
-// Floor, Boston, MA 02110-1301, USA.
-//
-//
-
-// Code:
#include "../basecode/header.h"
#include "../utility/utility.h"
#include "../utility/numutil.h"
-#include "Variable.h"
+#include "../utility/print_function.hpp"
+#include "../builtins/MooseParser.h"
+#include "Variable.h"
#include "Function.h"
-#include "../basecode/ElementValueFinfo.h"
-
-#define PARSER_MAXVARS 100
+#include "../basecode/ElementValueFinfo.h"
static const double TriggerThreshold = 0.0;
static SrcFinfo1<double> *valueOut()
{
static SrcFinfo1<double> valueOut("valueOut",
- "Evaluated value of the function for the current variable values.");
+ "Evaluated value of the function for the current variable values."
+ );
return &valueOut;
}
static SrcFinfo1< double > *derivativeOut()
{
static SrcFinfo1< double > derivativeOut("derivativeOut",
- "Value of derivative of the function for the current variable values");
+ "Value of derivative of the function for the current variable values");
return &derivativeOut;
}
static SrcFinfo1< double > *rateOut()
{
static SrcFinfo1< double > rateOut("rateOut",
- "Value of time-derivative of the function for the current variable values");
+ "Value of time-derivative of the function for the current variable values");
return &rateOut;
}
@@ -123,19 +81,19 @@ const Cinfo * Function::initCinfo()
static ValueFinfo< Function, bool > useTrigger(
"useTrigger",
"When *false*, disables event-driven calculation and turns on "
- "Process-driven calculations. \n"
+ "Process-driven calculations. \n"
"When *true*, enables event-driven calculation and turns off "
- "Process-driven calculations. \n"
- "Defaults to *false*. \n",
+ "Process-driven calculations. \n"
+ "Defaults to *false*. \n",
&Function::setUseTrigger,
&Function::getUseTrigger);
static ValueFinfo< Function, bool > doEvalAtReinit(
"doEvalAtReinit",
"When *false*, disables function evaluation at reinit, and "
- "just emits a value of zero to any message targets. \n"
+ "just emits a value of zero to any message targets. \n"
"When *true*, does a function evaluation at reinit and sends "
- "the computed value to any message targets. \n"
- "Defaults to *false*. \n",
+ "the computed value to any message targets. \n"
+ "Defaults to *false*. \n",
&Function::setDoEvalAtReinit,
&Function::getDoEvalAtReinit);
static ElementValueFinfo< Function, string > expr(
@@ -170,8 +128,9 @@ const Cinfo * Function::initCinfo()
"max var. max of all arguments\n"
"sum var. sum of all arguments\n"
"avg var. mean value of all arguments\n"
+ "rnd 0 rand(), random float between 0 and 1, honors global moose.seed.\n"
"rand 1 rand(seed), random float between 0 and 1, \n"
- " if seed = -1, then a 'random' seed is created.\n"
+ " if seed = -1, then a 'random' seed is used.\n"
"rand2 3 rand(a, b, seed), random float between a and b, \n"
" if seed = -1, a 'random' seed is created using either\n"
" by random_device or by reading system clock\n"
@@ -253,64 +212,64 @@ const Cinfo * Function::initCinfo()
"time, thread, dt and so on. The second entry is a MsgDest "
"for the Reinit operation. It also uses ProcInfo. ",
processShared, sizeof( processShared ) / sizeof( Finfo* )
- );
- /*
- static DestFinfo trigger( "trigger",
- "Handles trigger input. Argument is timestamp of event. This is "
- "compatible with spike events as well as chemical ones. ",
- new OpFunc1< Function, double >( &Function::trigger ) );
- */
+ );
+ /*
+ static DestFinfo trigger( "trigger",
+ "Handles trigger input. Argument is timestamp of event. This is "
+ "compatible with spike events as well as chemical ones. ",
+ new OpFunc1< Function, double >( &Function::trigger ) );
+ */
static Finfo *functionFinfos[] =
- {
- &value,
- &rate,
- &derivative,
- &mode,
- &useTrigger,
- &doEvalAtReinit,
- &expr,
- &numVars,
- &inputs,
- &constants,
- &independent,
- &proc,
- requestOut(),
- valueOut(),
- rateOut(),
- derivativeOut(),
- };
+ {
+ &value,
+ &rate,
+ &derivative,
+ &mode,
+ &useTrigger,
+ &doEvalAtReinit,
+ &expr,
+ &numVars,
+ &inputs,
+ &constants,
+ &independent,
+ &proc,
+ requestOut(),
+ valueOut(),
+ rateOut(),
+ derivativeOut(),
+ };
static string doc[] =
- {
- "Name", "Function",
- "Author", "Subhasis Ray",
- "Description",
- "General purpose function calculator using real numbers.\n"
- "It can parse mathematical expression defining a function and evaluate"
- " it and/or its derivative for specified variable values."
- "You can assign expressions of the form::\n"
- "\n"
- "f(c0, c1, ..., cM, x0, x1, ..., xN, y0,..., yP ) \n"
- "\n"
- " where `ci`'s are constants and `xi`'s and `yi`'s are variables."
-
- "The constants must be defined before setting the expression and"
- " variables are connected via messages. The constants can have any"
- " name, but the variable names must be of the form x{i} or y{i}"
- " where i is increasing integer starting from 0.\n"
- " The variables can be input from other moose objects."
- " Such variables must be named `x{i}` in the expression and the source"
- " field is connected to Function.x[i]'s `input` destination field.\n"
- " In case the input variable is not available as a source field, but is"
- " a value field, then the value can be requested by connecting the"
- " `requestOut` message to the `get{Field}` destination on the target"
- " object. Such variables must be specified in the expression as y{i}"
- " and connecting the messages should happen in the same order as the"
- " y indices.\n"
- " This class handles only real numbers (C-double). Predefined constants"
- " are: pi=3.141592..., e=2.718281..."
- };
+ {
+ "Name", "Function",
+ "Author", "Subhasis Ray",
+ "Description",
+ "General purpose function calculator using real numbers.\n"
+ "It can parse mathematical expression defining a function and evaluate"
+ " it and/or its derivative for specified variable values."
+ "You can assign expressions of the form::\n"
+ "\n"
+ "f(c0, c1, ..., cM, x0, x1, ..., xN, y0,..., yP ) \n"
+ "\n"
+ " where `ci`'s are constants and `xi`'s and `yi`'s are variables."
+
+ "The constants must be defined before setting the expression and"
+ " variables are connected via messages. The constants can have any"
+ " name, but the variable names must be of the form x{i} or y{i}"
+ " where i is increasing integer starting from 0.\n"
+ " The variables can be input from other moose objects."
+ " Such variables must be named `x{i}` in the expression and the source"
+ " field is connected to Function.x[i]'s `input` destination field.\n"
+ " In case the input variable is not available as a source field, but is"
+ " a value field, then the value can be requested by connecting the"
+ " `requestOut` message to the `get{Field}` destination on the target"
+ " object. Such variables must be specified in the expression as y{i}"
+ " and connecting the messages should happen in the same order as the"
+ " y indices.\n"
+ " This class handles only real numbers (C-double). Predefined constants"
+ " are: pi=3.141592..., e=2.718281..."
+ };
static Dinfo< Function > dinfo;
static Cinfo functionCinfo("Function",
@@ -335,9 +294,12 @@ Function::Function(): _t(0.0), _valid(false), _numVar(0), _lastValue(0.0),
//extendMuParser( );
// Adding this default expression by default to avoid complains from GUI
- try{
+ try
+ {
_parser.SetExpr("0");
- } catch (mu::Parser::exception_type &e) {
+ }
+ catch (moose::Parser::exception_type &e)
+ {
_showError(e);
_clearBuffer();
return;
@@ -345,12 +307,13 @@ Function::Function(): _t(0.0), _valid(false), _numVar(0), _lastValue(0.0),
_valid = true;
}
-Function::Function(const Function& rhs): _numVar(rhs._numVar),
+Function::Function(const Function& rhs):
+ _numVar(rhs._numVar),
_lastValue(rhs._lastValue),
_value(rhs._value), _rate(rhs._rate),
_mode(rhs._mode),
_useTrigger( rhs._useTrigger),
- _stoich(0)
+ _stoich(nullptr)
{
static Eref er;
_independent = rhs._independent;
@@ -359,10 +322,12 @@ Function::Function(const Function& rhs): _numVar(rhs._numVar),
//extendMuParser( );
// Copy the constants
- mu::valmap_type cmap = rhs._parser.GetConst();
- if (cmap.size()){
- mu::valmap_type::const_iterator item = cmap.begin();
- for (; item!=cmap.end(); ++item){
+ moose::Parser::valmap_type cmap = rhs._parser.GetConst();
+ if (cmap.size())
+ {
+ moose::Parser::valmap_type::const_iterator item = cmap.begin();
+ for (; item!=cmap.end(); ++item)
+ {
_parser.DefineConst(item->first, item->second);
}
}
@@ -371,11 +336,13 @@ Function::Function(const Function& rhs): _numVar(rhs._numVar),
setExpr(er, rhs.getExpr( er ));
// Copy the values from the var pointers in rhs
assert(_varbuf.size() == rhs._varbuf.size());
- for (unsigned int ii = 0; ii < rhs._varbuf.size(); ++ii){
+ for (unsigned int ii = 0; ii < rhs._varbuf.size(); ++ii)
+ {
_varbuf[ii]->value = rhs._varbuf[ii]->value;
}
assert(_pullbuf.size() == rhs._pullbuf.size());
- for (unsigned int ii = 0; ii < rhs._pullbuf.size(); ++ii){
+ for (unsigned int ii = 0; ii < rhs._pullbuf.size(); ++ii)
+ {
*_pullbuf[ii] = *(rhs._pullbuf[ii]);
}
}
@@ -390,24 +357,28 @@ Function& Function::operator=(const Function rhs)
_rate = rhs._rate;
_independent = rhs._independent;
// Adding pi and e, the defaults are `_pi` and `_e`
- _parser.DefineConst(_T("pi"), (mu::value_type)M_PI);
- _parser.DefineConst(_T("e"), (mu::value_type)M_E);
+ _parser.DefineConst(_T("pi"), (moose::Parser::value_type)M_PI);
+ _parser.DefineConst(_T("e"), (moose::Parser::value_type)M_E);
// Copy the constants
- mu::valmap_type cmap = rhs._parser.GetConst();
- if (cmap.size()){
- mu::valmap_type::const_iterator item = cmap.begin();
- for (; item!=cmap.end(); ++item){
+ moose::Parser::valmap_type cmap = rhs._parser.GetConst();
+ if (cmap.size())
+ {
+ moose::Parser::valmap_type::const_iterator item = cmap.begin();
+ for (; item!=cmap.end(); ++item)
+ {
_parser.DefineConst(item->first, item->second);
}
}
// Copy the values from the var pointers in rhs
setExpr(er, rhs.getExpr( er ));
assert(_varbuf.size() == rhs._varbuf.size());
- for (unsigned int ii = 0; ii < rhs._varbuf.size(); ++ii){
+ for (unsigned int ii = 0; ii < rhs._varbuf.size(); ++ii)
+ {
_varbuf[ii]->value = rhs._varbuf[ii]->value;
}
assert(_pullbuf.size() == rhs._pullbuf.size());
- for (unsigned int ii = 0; ii < rhs._pullbuf.size(); ++ii){
+ for (unsigned int ii = 0; ii < rhs._pullbuf.size(); ++ii)
+ {
*_pullbuf[ii] = *(rhs._pullbuf[ii]);
}
return *this;
@@ -415,8 +386,8 @@ Function& Function::operator=(const Function rhs)
Function::~Function()
{
- _clearBuffer();
- }
+ _clearBuffer();
+}
// do not know what to do about Variables that have already been
// connected by message.
@@ -424,28 +395,28 @@ void Function::_clearBuffer()
{
_numVar = 0;
_parser.ClearVar();
- for (unsigned int ii = 0; ii < _varbuf.size(); ++ii){
- if ( _varbuf[ii] ){
+ for (unsigned int ii = 0; ii < _varbuf.size(); ++ii)
+ {
+ if ( _varbuf[ii] )
+ {
delete _varbuf[ii];
}
}
_varbuf.clear();
- for (unsigned int ii = 0; ii < _pullbuf.size(); ++ii){
- if ( _pullbuf[ii] ){
+ for (unsigned int ii = 0; ii < _pullbuf.size(); ++ii)
+ {
+ if ( _pullbuf[ii] )
+ {
delete _pullbuf[ii];
}
}
_pullbuf.clear();
}
-void Function::_showError(mu::Parser::exception_type &e) const
+void Function::_showError(moose::Parser::exception_type &e) const
{
- cout << "Error occurred in parser.\n"
- << "Message: " << e.GetMsg() << "\n"
- << "Formula: " << e.GetExpr() << "\n"
- << "Token: " << e.GetToken() << "\n"
- << "Position: " << e.GetPos() << "\n"
- << "Error code: " << e.GetCode() << endl;
+ cerr << "Error occurred in parser.\n"
+ << "Message: " << e.GetMsg() << endl;
}
/**
@@ -474,27 +445,33 @@ double * _functionAddVar(const char *name, void *data)
string strname(name);
// Names starting with x are variables, everything else is constant.
- if (strname[0] == 'x')
+ if (name[0] == 'x')
{
int index = atoi(strname.substr(1).c_str());
- if ((unsigned)index >= function->_varbuf.size()){
+ if ((unsigned)index >= function->_varbuf.size())
+ {
function->_varbuf.resize(index+1, 0);
- for (int ii = 0; ii <= index; ++ii){
- if (function->_varbuf[ii] == 0){
+ for (int ii = 0; ii <= index; ++ii)
+ {
+ if (function->_varbuf[ii] == 0)
+ {
function->_varbuf[ii] = new Variable();
}
}
function->_numVar = function->_varbuf.size();
}
ret = &(function->_varbuf[index]->value);
- }
- else if (strname[0] == 'y')
+ }
+ else if (name[0] == 'y')
{
int index = atoi(strname.substr(1).c_str());
- if ((unsigned)index >= function->_pullbuf.size()){
+ if ((unsigned)index >= function->_pullbuf.size())
+ {
function->_pullbuf.resize(index+1, 0 );
- for (int ii = 0; ii <= index; ++ii){
- if (function->_pullbuf[ii] == 0){
+ for (int ii = 0; ii <= index; ++ii)
+ {
+ if (function->_pullbuf[ii] == 0)
+ {
function->_pullbuf[ii] = new double();
}
}
@@ -505,14 +482,14 @@ double * _functionAddVar(const char *name, void *data)
{
ret = &function->_t;
}
- else
+ else
{
- cerr << "Got an undefined symbol: " << name << endl
- << "Variables must be named xi, yi, where i is integer index."
- << " You must define the constants beforehand using LookupField c: c[name]"
- " = value"
- << endl;
- throw mu::ParserError("Undefined constant.");
+ MOOSE_WARN( "Got an undefined symbol: " << strname << ".\n"
+ << "Variables must be named xi, yi, where i is integer index."
+ << " You must define the constants beforehand using LookupField c: c[name]"
+ " = value"
+ );
+ throw moose::Parser::exception_type("Undefined constant.");
}
return ret;
@@ -549,10 +526,13 @@ void Function::innerSetExpr(const Eref& eref, string expr)
_clearBuffer();
_varbuf.resize(_numVar);
// _pullbuf.resize(_num
- mu::varmap_type vars;
- try{
+ moose::Parser::varmap_type vars;
+ try
+ {
_parser.SetExpr(expr);
- } catch (mu::Parser::exception_type &e) {
+ }
+ catch (moose::Parser::exception_type &e)
+ {
cerr << "Error setting expression on: " << eref.objId().path() << endl;
_showError(e);
_clearBuffer();
@@ -560,17 +540,21 @@ void Function::innerSetExpr(const Eref& eref, string expr)
}
// Force variable creation right away. Otherwise numVar does not
// get set properly
- try{
+ try
+ {
_parser.Eval();
_valid = true;
- } catch (mu::Parser::exception_type &e){
+ }
+ catch (moose::Parser::exception_type &e)
+ {
_showError(e);
}
}
string Function::getExpr( const Eref& e ) const
{
- if (!_valid){
+ if (!_valid)
+ {
cout << "Error: " << e.objId().path() << "::getExpr() - invalid parser state" << endl;
return "";
}
@@ -610,13 +594,17 @@ bool Function::getDoEvalAtReinit() const
double Function::getValue() const
{
double value = 0.0;
- if (!_valid){
+ if (!_valid)
+ {
cout << "Error: Function::getValue() - invalid state" << endl;
return value;
}
- try{
+ try
+ {
value = _parser.Eval();
- } catch (mu::Parser::exception_type &e){
+ }
+ catch (moose::Parser::exception_type &e)
+ {
_showError(e);
}
return value;
@@ -624,7 +612,8 @@ double Function::getValue() const
double Function::getRate() const
{
- if (!_valid){
+ if (!_valid)
+ {
cout << "Error: Function::getValue() - invalid state" << endl;
}
return _rate;
@@ -643,7 +632,8 @@ string Function::getIndependent() const
vector< double > Function::getY() const
{
vector < double > ret(_pullbuf.size());
- for (unsigned int ii = 0; ii < ret.size(); ++ii){
+ for (unsigned int ii = 0; ii < ret.size(); ++ii)
+ {
ret[ii] = *_pullbuf[ii];
}
return ret;
@@ -652,16 +642,21 @@ vector< double > Function::getY() const
double Function::getDerivative() const
{
double value = 0.0;
- if (!_valid){
+ if (!_valid)
+ {
cout << "Error: Function::getDerivative() - invalid state" << endl;
return value;
}
- mu::varmap_type variables = _parser.GetVar();
- mu::varmap_type::const_iterator item = variables.find(_independent);
- if (item != variables.end()){
- try{
+ moose::Parser::varmap_type variables = _parser.GetVar();
+ moose::Parser::varmap_type::const_iterator item = variables.find(_independent);
+ if (item != variables.end())
+ {
+ try
+ {
value = _parser.Diff(item->second, *(item->second));
- } catch (mu::Parser::exception_type &e){
+ }
+ catch (moose::Parser::exception_type &e)
+ {
_showError(e);
}
}
@@ -682,10 +677,13 @@ unsigned int Function::getNumVar() const
void Function::setVar(unsigned int index, double value)
{
- cout << "varbuf[" << index << "]->setValue(" << value << ")\n";
- if (index < _varbuf.size()){
+ cout << "varbuf[" << index << "]->setValue(" << value << ")\n";
+ if (index < _varbuf.size())
+ {
_varbuf[index]->setValue(value);
- } else {
+ }
+ else
+ {
cerr << "Function: index " << index << " out of bounds." << endl;
}
}
@@ -693,7 +691,8 @@ void Function::setVar(unsigned int index, double value)
Variable * Function::getVar(unsigned int ii)
{
static Variable dummy;
- if ( ii < _varbuf.size()){
+ if ( ii < _varbuf.size())
+ {
return _varbuf[ii];
}
cout << "Warning: Function::getVar: index: "
@@ -709,105 +708,114 @@ void Function::setConst(string name, double value)
double Function::getConst(string name) const
{
- mu::valmap_type cmap = _parser.GetConst();
- if (cmap.size()){
- mu::valmap_type::const_iterator it = cmap.find(name);
- if (it != cmap.end()){
+ auto cmap = _parser.GetConst();
+ if (cmap.size())
+ {
+ auto it = cmap.find(name);
+ if (it != cmap.end())
return it->second;
- }
}
return 0;
}
void Function::process(const Eref &e, ProcPtr p)
{
- if (!_valid){
+ if (!_valid)
+ {
return;
}
vector < double > databuf;
requestOut()->send(e, &databuf);
for (unsigned int ii = 0;
- (ii < databuf.size()) && (ii < _pullbuf.size());
- ++ii){
+ (ii < databuf.size()) && (ii < _pullbuf.size());
+ ++ii)
+ {
*_pullbuf[ii] = databuf[ii];
}
_t = p->currTime;
_value = getValue();
_rate = (_value - _lastValue) / p->dt;
- if ( _useTrigger && _value < TriggerThreshold ) {
- _lastValue = _value;
- return;
- }
- switch (_mode){
- case 1: {
- valueOut()->send(e, _value);
- break;
- }
- case 2: {
- derivativeOut()->send(e, getDerivative());
- break;
- }
- case 3: {
- rateOut()->send(e, _rate);
- break;
- }
- default: {
- valueOut()->send(e, _value);
- derivativeOut()->send(e, getDerivative());
- rateOut()->send(e, _rate);
- break;
- }
+ if ( _useTrigger && _value < TriggerThreshold )
+ {
+ _lastValue = _value;
+ return;
+ }
+ switch (_mode)
+ {
+ case 1:
+ {
+ valueOut()->send(e, _value);
+ return;
+ }
+ case 2:
+ {
+ derivativeOut()->send(e, getDerivative());
+ return;
+ }
+ case 3:
+ {
+ rateOut()->send(e, _rate);
+ return;
+ }
+ default:
+ {
+ valueOut()->send(e, _value);
+ derivativeOut()->send(e, getDerivative());
+ rateOut()->send(e, _rate);
+ return;
+ }
}
_lastValue = _value;
}
void Function::reinit(const Eref &e, ProcPtr p)
{
- if (!_valid){
+ if (!_valid)
+ {
cout << "Error: Function::reinit() - invalid parser state. Will do nothing." << endl;
return;
}
- if (moose::trim(_parser.GetExpr(), " \t\n\r").length() == 0){
+ if (moose::trim(_parser.GetExpr(), " \t\n\r").length() == 0)
+ {
cout << "Error: no expression set. Will do nothing." << endl;
setExpr(e, "0.0");
_valid = false;
}
_t = p->currTime;
- if (_doEvalAtReinit) {
- _lastValue = _value = getValue();
- } else {
- _lastValue = _value = 0.0;
- }
+ if (_doEvalAtReinit)
+ {
+ _lastValue = _value = getValue();
+ }
+ else
+ {
+ _lastValue = _value = 0.0;
+ }
_rate = 0.0;
- switch (_mode){
- case 1: {
- valueOut()->send(e, _value);
- break;
- }
- case 2: {
- derivativeOut()->send(e, 0.0);
- break;
- }
- case 3: {
- rateOut()->send(e, _rate);
- break;
- }
- default: {
- valueOut()->send(e, _value);
- derivativeOut()->send(e, 0.0);
- rateOut()->send(e, _rate);
- break;
- }
+ switch (_mode)
+ {
+ case 1:
+ {
+ valueOut()->send(e, _value);
+ break;
+ }
+ case 2:
+ {
+ derivativeOut()->send(e, 0.0);
+ break;
+ }
+ case 3:
+ {
+ rateOut()->send(e, _rate);
+ break;
+ }
+ default:
+ {
+ valueOut()->send(e, _value);
+ derivativeOut()->send(e, 0.0);
+ rateOut()->send(e, _rate);
+ break;
+ }
}
}
-#if 0
-mu::value_type Function::muCallbackFMod( mu::value_type a, mu::value_type b)
-{
- cerr << "Callback: " << a << " " << b << endl;
- return fmod(a, b);
-}
-#endif
-
-//
// Function.cpp ends here
diff --git a/moose-core/builtins/Function.h b/moose-core/builtins/Function.h
index 6a9fff3f0ebd8f2cfac2456f50ef9808f0e5a890..8834b51ced8d1c2a756dd5e0d61333496c134c66 100644
--- a/moose-core/builtins/Function.h
+++ b/moose-core/builtins/Function.h
@@ -1,54 +1,9 @@
-// Function.h ---
-//
-// Filename: Function.h
// Description:
// Author: Subhasis Ray
-// Maintainer:
-// Created: Fri May 30 19:34:13 2014 (+0530)
-// Version:
-// Last-Updated:
-// By:
-// Update #: 0
-// URL:
-// Keywords:
-// Compatibility:
-//
-//
-
-// Commentary:
-//
-// A new version of Func with FieldElements to collect data.
-//
-//
-
-// Change log:
-//
-//
-//
-//
-// This program is free software; you can redistribute it and/or
-// modify it under the terms of the GNU General Public License as
-// published by the Free Software Foundation; either version 3, or
-// (at your option) any later version.
-//
-// This program is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-// General Public License for more details.
-//
-// You should have received a copy of the GNU General Public License
-// along with this program; see the file COPYING. If not, write to
-// the Free Software Foundation, Inc., 51 Franklin Street, Fifth
-// Floor, Boston, MA 02110-1301, USA.
-//
-//
-
-// Code:
#ifndef _MOOSE_FUNCTION_H_
#define _MOOSE_FUNCTION_H_
-#include "../external/muparser/include/muParser.h"
/**
Simple function parser and evaluator for MOOSE. This can take a mathematical
@@ -59,7 +14,7 @@ double *_functionAddVar(const char *name, void *data);
class Function
{
- public:
+public:
static const int VARMAX;
Function();
Function(const Function& rhs);
@@ -68,7 +23,6 @@ class Function
void setExpr( const Eref& e, string expr);
string getExpr( const Eref& e ) const;
-
// get a list of variable identifiers.
// this is created by the parser
vector<string> getVars() const;
@@ -88,11 +42,11 @@ class Function
void setMode(unsigned int mode);
unsigned int getMode() const;
- // set/get flag to use trigger mode.
+ // set/get flag to use trigger mode.
void setUseTrigger(bool useTrigger);
bool getUseTrigger() const;
- // set/get flag to do function evaluation at reinit
+ // set/get flag to do function evaluation at reinit
void setDoEvalAtReinit(bool doEvalAtReinit);
bool getDoEvalAtReinit() const;
@@ -109,24 +63,6 @@ class Function
double getDerivative() const;
-#if 0
- /**
- * @brief Extend standard muparser library. This add some binary operators
- * and user-defined functions.
- */
- void extendMuParser( void );
-
- /**
- * @brief callback function for floating point mod-operator.
- *
- * @param a double
- * @param b double
- *
- * @return double using std::fmod(a, b)
- */
- static mu::value_type muCallbackFMod( mu::value_type a, mu::value_type b );
-#endif
-
Function& operator=(const Function rhs);
unsigned int addVar();
@@ -159,18 +95,13 @@ protected:
map< string, double *> _constbuf; // for constants
string _independent; // index of independent variable
- mu::Parser _parser;
+ MooseParser _parser;
void _clearBuffer();
- void _showError(mu::Parser::exception_type &e) const;
+ void _showError(moose::Parser::exception_type &e) const;
// Used by kinetic solvers when this is zombified.
char* _stoich;
};
-
#endif
-
-
-//
-//// Function.h ends here_parser.DefineVar( _T("t"),
diff --git a/moose-core/builtins/HDF5DataWriter.cpp b/moose-core/builtins/HDF5DataWriter.cpp
index 72e43af9ed9b9bc5037db4ec78a3c671585b4539..5f7ba3b93dc99848d9957252dbc31f63665f7f32 100644
--- a/moose-core/builtins/HDF5DataWriter.cpp
+++ b/moose-core/builtins/HDF5DataWriter.cpp
@@ -12,7 +12,7 @@
#include "hdf5.h"
-#include "header.h"
+#include "../basecode/header.h"
#include "../utility/utility.h"
#include "HDF5DataWriter.h"
diff --git a/moose-core/builtins/HDF5WriterBase.cpp b/moose-core/builtins/HDF5WriterBase.cpp
index 747a2d8dd76bd134ef37fde2380ab5bed7bcc88e..8e423524439a08d1512b3ff8439ca41299081f58 100644
--- a/moose-core/builtins/HDF5WriterBase.cpp
+++ b/moose-core/builtins/HDF5WriterBase.cpp
@@ -36,7 +36,7 @@
#include "hdf5.h"
-#include "header.h"
+#include "../basecode/header.h"
#include "../utility/utility.h"
#include "HDF5WriterBase.h"
diff --git a/moose-core/builtins/InputVariable.cpp b/moose-core/builtins/InputVariable.cpp
index b1d47d63a0f6111e32c28f337af93146b5435656..ac018da26dc16139ece178342b0ca2af2e840c74 100644
--- a/moose-core/builtins/InputVariable.cpp
+++ b/moose-core/builtins/InputVariable.cpp
@@ -46,7 +46,7 @@
// Code:
#ifdef USE_HDF5
-#include "header.h"
+#include "../basecode/header.h"
#include "hdf5.h"
#include "NSDFWriter.h"
diff --git a/moose-core/builtins/MooseParser.cpp b/moose-core/builtins/MooseParser.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..b8cdcb74faa6897a15523b9e69552447524705fe
--- /dev/null
+++ b/moose-core/builtins/MooseParser.cpp
@@ -0,0 +1,18 @@
+/***
+ * Description: Class MooseParser.
+ *
+ * Created: 2019-05-30
+
+ * Author: Dilawar Singh <dilawars@ncbs.res.in>
+ * Organization: NCBS Bangalore
+ * License: MIT License
+ */
+
+#include "MooseParser.h"
+
+MooseParser::MooseParser()
+{}
+
+MooseParser::~MooseParser()
+{}
+
diff --git a/moose-core/builtins/MooseParser.h b/moose-core/builtins/MooseParser.h
new file mode 100644
index 0000000000000000000000000000000000000000..cea2c0ae9ff0c2bfa3e5f589c6190f1d3f740bae
--- /dev/null
+++ b/moose-core/builtins/MooseParser.h
@@ -0,0 +1,56 @@
+/***
+ * Description: MooseParser class.
+ *
+ * Created: 2019-05-30
+
+ * Author: Dilawar Singh <dilawars@ncbs.res.in>
+ * Organization: NCBS Bangalore
+ * License: MIT License
+ */
+
+#ifndef MOOSEPARSER_H
+#define MOOSEPARSER_H
+
+#include <map>
+using namespace std;
+
+#include "../external/muparser/include/muParser.h"
+
+namespace moose {
+ namespace Parser {
+
+ struct ParserException : public std::exception
+ {
+ ParserException( const std::string msg ) : msg_(msg) { ; }
+
+ string GetMsg()
+ {
+ return msg_;
+ }
+
+ string msg_;
+ };
+
+ typedef ParserException exception_type;
+
+
+ // These should be same for both muparser and EXPRTK parser.
+ typedef std::map<string, double> valmap_type;
+ typedef std::map<string, double*> varmap_type;
+ typedef double value_type;
+
+ } // namespace Parser
+
+} // namespace moose
+
+class MooseParser : public mu::Parser
+{
+ public:
+ MooseParser();
+ ~MooseParser();
+
+ private:
+ /* data */
+};
+
+#endif /* end of include guard: MOOSEPARSER_H */
diff --git a/moose-core/builtins/NSDFWriter.cpp b/moose-core/builtins/NSDFWriter.cpp
index 1e30dc4d35f4dccc40cee214df2ed0ef52abfa56..16cd787b22090f31e32eb9ae61e0f8f74b6e2bcd 100644
--- a/moose-core/builtins/NSDFWriter.cpp
+++ b/moose-core/builtins/NSDFWriter.cpp
@@ -52,7 +52,7 @@
#include <ctime>
#include <deque>
-#include "header.h"
+#include "../basecode/header.h"
#include "../utility/utility.h"
#include "HDF5WriterBase.h"
diff --git a/moose-core/builtins/Table.cpp b/moose-core/builtins/Table.cpp
index be3702b13cb3cc46b569af8fc4b319d32dbd6268..4721cf05b07a1a4548864975e861ed1e8208445c 100644
--- a/moose-core/builtins/Table.cpp
+++ b/moose-core/builtins/Table.cpp
@@ -16,10 +16,6 @@
#include "../scheduling/Clock.h"
#include "StreamerBase.h"
-// Write to numpy arrays.
-#include "../utility/cnpy.hpp"
-
-
static SrcFinfo1< vector< double >* > *requestOut()
{
static SrcFinfo1< vector< double >* > requestOut(
@@ -63,7 +59,7 @@ const Cinfo* Table::initCinfo()
"useSpikeMode"
, "When set to true, look for spikes in a time-series."
" Normally used for monitoring Vm for action potentials."
- " Could be used for any thresholded event. Default is False."
+ " Could be used for any thresholded event. Default is False."
, &Table::setUseSpikeMode
, &Table::getUseSpikeMode
);
@@ -211,8 +207,8 @@ const Cinfo* Table::initCinfo()
static const Cinfo* tableCinfo = Table::initCinfo();
Table::Table() :
- threshold_( 0.0 ) ,
- lastTime_( 0.0 ) ,
+ threshold_( 0.0 ),
+ lastTime_( 0.0 ),
input_( 0.0 ),
fired_(false),
useSpikeMode_(false),
@@ -258,7 +254,7 @@ void Table::process( const Eref& e, ProcPtr p )
if (useSpikeMode_)
{
- for ( vector< double >::const_iterator i = ret.begin(); i != ret.end(); ++i )
+ for ( auto i = ret.begin(); i != ret.end(); ++i )
spike( *i );
}
else
@@ -270,14 +266,14 @@ void Table::process( const Eref& e, ProcPtr p )
*/
if( useFileStreamer_ )
{
- if( fmod(lastTime_, 5.0) == 0.0 or getVecSize() >= 10000 )
+ if( fmod(lastTime_, 5.0) == 0.0 || getVecSize() >= 10000 )
{
mergeWithTime( data_ );
- StreamerBase::writeToOutFile( outfile_, format_ , "a", data_, columns_ );
+ StreamerBase::writeToOutFile( outfile_, format_, "a", data_, columns_ );
clearAllVecs();
}
+ }
}
-}
void Table::clearAllVecs()
{
@@ -297,8 +293,9 @@ void Table::reinit( const Eref& e, ProcPtr p )
tablePath_ = e.id().path();
unsigned int numTick = e.element()->getTick();
Clock* clk = reinterpret_cast<Clock*>(Id(1).eref().data());
+
dt_ = clk->getTickDt( numTick );
- fired_ = false;
+ fired_ = false;
/** Create the default filepath for this table. */
if( useFileStreamer_ )
@@ -312,8 +309,8 @@ void Table::reinit( const Eref& e, ProcPtr p )
// with rootdit as path.
if( ! outfileIsSet_ )
setOutfile( rootdir_ +
- moose::moosePathToUserPath(tablePath_) + '.' + format_
- );
+ moose::moosePathToUserPath(tablePath_) + '.' + format_
+ );
}
input_ = 0.0;
@@ -324,7 +321,7 @@ void Table::reinit( const Eref& e, ProcPtr p )
if (useSpikeMode_)
{
- for (vector<double>::const_iterator i = ret.begin(); i != ret.end(); ++i )
+ for ( auto i = ret.begin(); i != ret.end(); ++i )
spike( *i );
}
else
@@ -369,8 +366,6 @@ void Table::spike( double v )
//////////////////////////////////////////////////////////////
// Field Definitions
-//////////////////////////////////////////////////////////////
-
void Table::setThreshold( double v )
{
threshold_ = v;
@@ -384,12 +379,12 @@ double Table::getThreshold() const
// Set the format of table to which its data should be written.
void Table::setFormat( string format )
{
- if( format == "csv" or format == "npy" )
+ if( format == "csv" )
format_ = format;
else
LOG( moose::warning
- , "Unsupported format " << format
- << " only npy and csv are supported"
+ , "Unsupported format " << format
+ << " only sv is supported"
);
}
diff --git a/moose-core/builtins/Variable.cpp b/moose-core/builtins/Variable.cpp
index 6233e24853dba9217b6a1a96c0538e059732688f..e68e08ed0e6424b02847987747a4db6f93afbaba 100644
--- a/moose-core/builtins/Variable.cpp
+++ b/moose-core/builtins/Variable.cpp
@@ -1,51 +1,10 @@
-// Variable.cpp ---
-//
-// Filename: Variable.cpp
// Description:
// Author: Subhasis Ray
// Maintainer:
// Created: Fri May 30 19:56:06 2014 (+0530)
-// Version:
-// Last-Updated:
-// By:
-// Update #: 0
-// URL:
-// Keywords:
-// Compatibility:
-//
-//
-
-// Commentary:
-//
-//
-//
-//
-
-// Change log:
-//
-//
-//
-//
-// This program is free software; you can redistribute it and/or
-// modify it under the terms of the GNU General Public License as
-// published by the Free Software Foundation; either version 3, or
-// (at your option) any later version.
-//
-// This program is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-// General Public License for more details.
-//
-// You should have received a copy of the GNU General Public License
-// along with this program; see the file COPYING. If not, write to
-// the Free Software Foundation, Inc., 51 Franklin Street, Fifth
-// Floor, Boston, MA 02110-1301, USA.
-//
-//
-
-// Code:
#include "../basecode/header.h"
+#include "MooseParser.h"
#include "Variable.h"
#include "Function.h"
@@ -56,21 +15,26 @@ const Cinfo * Variable::initCinfo()
"Variable value",
&Variable::setValue,
&Variable::getValue);
+
static DestFinfo input(
"input",
"Handles incoming variable value.",
new EpFunc1< Variable, double >( &Variable::epSetValue ));
- static Finfo * variableFinfos[] = {
+ static Finfo * variableFinfos[] =
+ {
&value,
&input
};
- static string doc[] = {
+ static string doc[] =
+ {
"Name", "Variable",
"Author", "Subhasis Ray",
"Description", "Variable for storing double values. This is used in Function class."
};
+
static Dinfo< Variable > dinfo;
+
static Cinfo variableCinfo("Variable",
Neutral::initCinfo(),
variableFinfos,
@@ -79,41 +43,10 @@ const Cinfo * Variable::initCinfo()
doc,
sizeof(doc) / sizeof(string),
true // is FieldElement, not to be created directly
- );
+ );
+
return & variableCinfo;
}
static const Cinfo * variableCinfo = Variable::initCinfo();
-// This imitates Synapse::addMsgCallback
-// but does not seem to be used anywhere
-// - Subha, Tue Sep 9 19:37:11 IST 2014
-
-void Variable::addMsgCallback(const Eref& e, const string& finfoName, ObjId msg, unsigned int msgLookup)
-{
- /*
- if (finfoName == "input"){
- ObjId pa = Neutral::parent(e);
- Function * fn = reinterpret_cast< Function *>(pa.data());
- unsigned int varNumber = fn->addVar();
- SetGet2<unsigned int, unsigned int>::set(msg, "fieldIndex", msgLookup, varNumber);
- }
- */
-}
-
-// // This imitates Synapse::dropMsgCallback
-// void Variable::dropMsgCallback(
-// const Eref& e, const string& finfoName,
-// ObjId msg, unsigned int msgLookup )
-// {
-// if ( finfoName == "input" ) {
-// ObjId pa = Neutral::parent( e );
-// SynHandlerBase* sh =
-// reinterpret_cast< Function* >( pa.data() );
-// sh->dropVar( msgLookup );
-// }
-// }
-
-
-//
-// Variable.cpp ends here
diff --git a/moose-core/builtins/testNSDF.cpp b/moose-core/builtins/testNSDF.cpp
index 86e1f96f04746ceef3930f771dfec5603679884f..9c40f8ec7380b4782176ca2a0dd19dd5e7e61b22 100644
--- a/moose-core/builtins/testNSDF.cpp
+++ b/moose-core/builtins/testNSDF.cpp
@@ -54,7 +54,7 @@
#include <deque>
#include <cstdio>
-#include "header.h"
+#include "../basecode/header.h"
#include "../utility/utility.h"
#include "HDF5WriterBase.h"
diff --git a/moose-core/diffusion/CMakeLists.txt b/moose-core/diffusion/CMakeLists.txt
index 95c1ebf0fdecf799a88a7c235db02254db015021..7a0509b7c65671e3631b2ef3c58d01b4f6d9bce3 100644
--- a/moose-core/diffusion/CMakeLists.txt
+++ b/moose-core/diffusion/CMakeLists.txt
@@ -1,6 +1,10 @@
cmake_minimum_required(VERSION 2.8)
include( ${CMAKE_CURRENT_SOURCE_DIR}/../CheckCXXCompiler.cmake)
-include_directories(${GSL_INCLUDE_DIRS})
+
+if(WITH_GSL)
+ include_directories(${GSL_INCLUDE_DIRS})
+endif(WITH_GSL)
+
add_library(diffusion
FastMatrixElim.cpp
DiffPoolVec.cpp
diff --git a/moose-core/diffusion/ConcChanInfo.h b/moose-core/diffusion/ConcChanInfo.h
index caf2b6b4d460b897dfd28134069f59f4163d3acf..9aeb984b5dc9c17453ad8acff3457a45ec9a73fb 100644
--- a/moose-core/diffusion/ConcChanInfo.h
+++ b/moose-core/diffusion/ConcChanInfo.h
@@ -14,22 +14,22 @@
*/
class ConcChanInfo
{
- public:
- ConcChanInfo();
- ConcChanInfo( unsigned int my, unsigned int other,
- unsigned int chan, double perm, bool isSwapped )
- : myPool( my ), otherPool( other ), chanPool( chan ),
- swapped( isSwapped ),
- permeability( perm )
- {;}
+public:
+ ConcChanInfo();
+ ConcChanInfo( unsigned int my, unsigned int other,
+ unsigned int chan, double perm, bool isSwapped )
+ : myPool( my ), otherPool( other ), chanPool( chan ),
+ swapped( isSwapped ),
+ permeability( perm )
+ {;}
- unsigned int myPool;
- unsigned int otherPool;
- unsigned int chanPool;
- bool swapped; // Flag records whether myPool/otherPool are
- // swapped wrt inPool/outPool. System expects
- // that inPool should be in same compt as chanPool.
- double permeability;
+ unsigned int myPool;
+ unsigned int otherPool;
+ unsigned int chanPool;
+ bool swapped; // Flag records whether myPool/otherPool are
+ // swapped wrt inPool/outPool. System expects
+ // that inPool should be in same compt as chanPool.
+ double permeability;
};
#endif // _CONC_CHAN_INFO_H
diff --git a/moose-core/diffusion/DiffJunction.h b/moose-core/diffusion/DiffJunction.h
index a4e44d23c88d6e9898a38881cdba23af434784af..957d77d3df6097f9c50bff0b0a986c8a90a639cb 100644
--- a/moose-core/diffusion/DiffJunction.h
+++ b/moose-core/diffusion/DiffJunction.h
@@ -32,19 +32,19 @@
*/
class DiffJunction
{
- public:
- unsigned int otherDsolve;
- vector< unsigned int > myPools;
- vector< unsigned int > otherPools;
+public:
+ unsigned int otherDsolve;
+ vector< unsigned int > myPools;
+ vector< unsigned int > otherPools;
- vector< unsigned int > myXferSrc;
- vector< unsigned int > otherXferDest;
-
- vector< unsigned int > myXferDest;
- vector< unsigned int > otherXferSrc;
+ vector< unsigned int > myXferSrc;
+ vector< unsigned int > otherXferDest;
- vector< unsigned int > myChannels;
- vector< unsigned int > otherChannels;
+ vector< unsigned int > myXferDest;
+ vector< unsigned int > otherXferSrc;
- vector< VoxelJunction > vj;
+ vector< unsigned int > myChannels;
+ vector< unsigned int > otherChannels;
+
+ vector< VoxelJunction > vj;
};
diff --git a/moose-core/diffusion/DiffPoolVec.cpp b/moose-core/diffusion/DiffPoolVec.cpp
index 536d7dd737a48f9354f381661a7231db859699dd..9877c8f0accb7d64448263bdc675dc43c924b4d2 100644
--- a/moose-core/diffusion/DiffPoolVec.cpp
+++ b/moose-core/diffusion/DiffPoolVec.cpp
@@ -71,7 +71,7 @@ void DiffPoolVec::setNvec( const vector< double >& vec )
}
void DiffPoolVec::setNvec( unsigned int start, unsigned int num,
- vector< double >::const_iterator q )
+ vector< double >::const_iterator q )
{
assert( start + num <= n_.size() );
vector< double >::iterator p = n_.begin() + start;
@@ -126,7 +126,7 @@ unsigned int DiffPoolVec::getId() const
}
void DiffPoolVec::setOps(const vector< Triplet< double > >& ops,
- const vector< double >& diagVal )
+ const vector< double >& diagVal )
{
if ( ops.size() > 0 )
{
@@ -144,14 +144,14 @@ void DiffPoolVec::setOps(const vector< Triplet< double > >& ops,
void DiffPoolVec::advance( double dt )
{
if ( ops_.size() == 0 ) return;
- for ( vector< Triplet< double > >::const_iterator
- i = ops_.begin(); i != ops_.end(); ++i )
+
+ for (auto i = ops_.cbegin(); i != ops_.end(); ++i )
n_[i->c_] -= n_[i->b_] * i->a_;
assert( n_.size() == diagVal_.size() );
- vector< double >::iterator iy = n_.begin();
- for ( vector< double >::const_iterator
- i = diagVal_.begin(); i != diagVal_.end(); ++i )
+
+ auto iy = n_.begin();
+ for ( auto i = diagVal_.cbegin(); i != diagVal_.end(); ++i )
*iy++ *= *i;
}
diff --git a/moose-core/diffusion/DiffPoolVec.h b/moose-core/diffusion/DiffPoolVec.h
index 587533eb35d0ba4715f4c7cf54947abb4359edff..ce0b2d0a5e193c6cecabe7a84c427b99c713f8db 100644
--- a/moose-core/diffusion/DiffPoolVec.h
+++ b/moose-core/diffusion/DiffPoolVec.h
@@ -17,50 +17,50 @@
*/
class DiffPoolVec
{
- public:
- DiffPoolVec();
- void process();
- void reinit();
- void advance( double dt );
- double getNinit( unsigned int vox ) const;
- void setNinit( unsigned int vox, double value );
- double getN( unsigned int vox ) const;
- void setN( unsigned int vox, double value );
- double getPrev( unsigned int vox ) const;
+public:
+ DiffPoolVec();
+ void process();
+ void reinit();
+ void advance( double dt );
+ double getNinit( unsigned int vox ) const;
+ void setNinit( unsigned int vox, double value );
+ double getN( unsigned int vox ) const;
+ void setN( unsigned int vox, double value );
+ double getPrev( unsigned int vox ) const;
- double getDiffConst() const;
- void setDiffConst( double value );
+ double getDiffConst() const;
+ void setDiffConst( double value );
- double getMotorConst() const;
- void setMotorConst( double value );
+ double getMotorConst() const;
+ void setMotorConst( double value );
- void setNumVoxels( unsigned int num );
- unsigned int getNumVoxels() const;
+ void setNumVoxels( unsigned int num );
+ unsigned int getNumVoxels() const;
- void setId( unsigned int id );
- unsigned int getId() const;
+ void setId( unsigned int id );
+ unsigned int getId() const;
- /////////////////////////////////////////////////
- /// Used by parent solver to manipulate 'n'
- const vector< double >& getNvec() const;
- /// Used by parent solver to manipulate 'n'
- void setNvec( const vector< double >& n );
- void setNvec( unsigned int start, unsigned int num,
- vector< double >::const_iterator q );
- void setPrevVec(); /// Assigns prev_ = n_
- void setOps( const vector< Triplet< double > >& ops_,
- const vector< double >& diagVal_ ); /// Assign operations.
+ /////////////////////////////////////////////////
+ /// Used by parent solver to manipulate 'n'
+ const vector< double >& getNvec() const;
+ /// Used by parent solver to manipulate 'n'
+ void setNvec( const vector< double >& n );
+ void setNvec( unsigned int start, unsigned int num,
+ vector< double >::const_iterator q );
+ void setPrevVec(); /// Assigns prev_ = n_
+ void setOps( const vector< Triplet< double > >& ops_,
+ const vector< double >& diagVal_ ); /// Assign operations.
- // static const Cinfo* initCinfo();
- private:
- unsigned int id_; /// Integer conversion of Id of pool handled.
- vector< double > n_; /// Number of molecules of pool in each voxel
- vector< double > prev_; /// # molecules of pool on previous timestep
- vector< double > nInit_; /// Boundary condition: Initial 'n'.
- double diffConst_; /// Diffusion const, assumed uniform
- double motorConst_; /// Motor const, ie, transport rate.
- vector< Triplet< double > > ops_;
- vector< double > diagVal_;
+ // static const Cinfo* initCinfo();
+private:
+ unsigned int id_; /// Integer conversion of Id of pool handled.
+ vector< double > n_; /// Number of molecules of pool in each voxel
+ vector< double > prev_; /// # molecules of pool on previous timestep
+ vector< double > nInit_; /// Boundary condition: Initial 'n'.
+ double diffConst_; /// Diffusion const, assumed uniform
+ double motorConst_; /// Motor const, ie, transport rate.
+ vector< Triplet< double > > ops_;
+ vector< double > diagVal_;
};
#endif // _DIFF_POOL_VEC_H
diff --git a/moose-core/diffusion/Dsolve.cpp b/moose-core/diffusion/Dsolve.cpp
index 9f1fc45af0e0e566eec1971ca6060223552f19ef..d65b528accaa6e8bee49ffada64305ac6f139921 100644
--- a/moose-core/diffusion/Dsolve.cpp
+++ b/moose-core/diffusion/Dsolve.cpp
@@ -122,25 +122,26 @@ const Cinfo* Dsolve::initCinfo()
///////////////////////////////////////////////////////
// DestFinfo definitions
- ///////////////////////////////////////////////////////
-
static DestFinfo process( "process",
"Handles process call",
- new ProcOpFunc< Dsolve >( &Dsolve::process ) );
+ new ProcOpFunc< Dsolve >( &Dsolve::process )
+ );
+
static DestFinfo reinit( "reinit",
"Handles reinit call",
- new ProcOpFunc< Dsolve >( &Dsolve::reinit ) );
+ new ProcOpFunc< Dsolve >( &Dsolve::reinit )
+ );
static DestFinfo buildMeshJunctions( "buildMeshJunctions",
"Builds junctions between mesh on current Dsolve, and another"
" Dsolve. The meshes have to be compatible. ",
- new EpFunc1< Dsolve, Id >(
- &Dsolve::buildMeshJunctions ) );
+ new EpFunc1< Dsolve, Id >(&Dsolve::buildMeshJunctions )
+ );
static DestFinfo buildNeuroMeshJunctions( "buildNeuroMeshJunctions",
"Builds junctions between NeuroMesh, SpineMesh and PsdMesh",
- new EpFunc2< Dsolve, Id, Id >(
- &Dsolve::buildNeuroMeshJunctions ) );
+ new EpFunc2< Dsolve, Id, Id >(&Dsolve::buildNeuroMeshJunctions )
+ );
///////////////////////////////////////////////////////
// Shared definitions
@@ -149,10 +150,11 @@ const Cinfo* Dsolve::initCinfo()
{
&process, &reinit
};
+
static SharedFinfo proc( "proc",
- "Shared message for process and reinit",
- procShared, sizeof( procShared ) / sizeof( const Finfo* )
- );
+ "Shared message for process and reinit",
+ procShared, sizeof( procShared ) / sizeof( const Finfo* )
+ );
static Finfo* dsolveFinfos[] =
{
@@ -340,8 +342,8 @@ void Dsolve::calcJnDiff( const DiffJunction& jn, Dsolve* other, double dt)
// different diffusion constants.
double effectiveDiffConst =
sqrt( myDv.getDiffConst() * otherDv.getDiffConst() );
- for ( vector< VoxelJunction >::const_iterator
- j = jn.vj.begin(); j != jn.vj.end(); ++j )
+
+ for (auto j = jn.vj.cbegin(); j != jn.vj.end(); ++j )
{
double myN = myDv.getN( j->first );
double otherN = otherDv.getN( j->second );
@@ -517,11 +519,8 @@ void Dsolve::process( const Eref& e, ProcPtr p )
void Dsolve::reinit( const Eref& e, ProcPtr p )
{
build( p->dt );
- for ( vector< DiffPoolVec >::iterator
- i = pools_.begin(); i != pools_.end(); ++i )
- {
+ for (auto i = pools_.begin(); i != pools_.end(); ++i )
i->reinit();
- }
}
void Dsolve::updateJunctions( double dt )
@@ -1236,11 +1235,10 @@ void Dsolve::setBlock( const vector< double >& values )
for ( unsigned int i = 0; i < numPools; ++i )
{
unsigned int j = i + startPool;
- if ( j >= poolStartIndex_ && j < poolStartIndex_ + numLocalPools_ )
+ if (j >= poolStartIndex_ && j < poolStartIndex_ + numLocalPools_)
{
- vector< double >::const_iterator
- q = values.begin() + 4 + i * numVoxels;
- pools_[ j - poolStartIndex_ ].setNvec( startVoxel, numVoxels, q );
+ auto q = values.cbegin() + 4 + i * numVoxels;
+ pools_[j-poolStartIndex_].setNvec(startVoxel, numVoxels, q);
}
}
}
diff --git a/moose-core/external/muparser/include/muParser.h b/moose-core/external/muparser/include/muParser.h
index 653cd44ab19aa43d09c1f944acb5bafdc3861457..c1baf798461d155417f4af4c436e51c3144e98c5 100644
--- a/moose-core/external/muparser/include/muParser.h
+++ b/moose-core/external/muparser/include/muParser.h
@@ -35,7 +35,7 @@
// Get the random number generator type from here.
#include "../../../randnum/RNG.h"
-extern moose::RNG<double> rng;
+extern moose::RNG rng;
/** \file
\brief Definition of the standard floating point parser.
@@ -107,7 +107,8 @@ namespace mu
static value_type Rand2(value_type, value_type, value_type);
// Random number between 0 and 1, non-deterministic seed.
- static value_type Rand( value_type );
+ static value_type Rand( value_type seed );
+ static value_type Rnd( );
// Prefix operators
// !!! Unary Minus is a MUST if you want to use negative signs !!!
diff --git a/moose-core/external/muparser/src/muParser.cpp b/moose-core/external/muparser/src/muParser.cpp
index 65a1f314e20c1c8a203a0bb09d7a51c91b368e56..2f9321ee147b7b0d3a22ec0b61fb764904bb8e79 100644
--- a/moose-core/external/muparser/src/muParser.cpp
+++ b/moose-core/external/muparser/src/muParser.cpp
@@ -25,6 +25,7 @@
*/
#include "../include/muParser.h"
#include "../include/muParserTemplateMagic.h"
+#include "../../../basecode/global.h"
//--- Standard includes ------------------------------------------------------------------------
#include <cmath>
@@ -51,7 +52,7 @@ namespace mu
{
// Initialize the RNG with random time.
- moose::RNG<double> rng;
+ moose::RNG rng;
//---------------------------------------------------------------------------
// Trigonometric function
@@ -112,10 +113,24 @@ namespace mu
value_type Parser::Fmod(value_type v1, value_type v2) { return fmod(v1, v2); }
value_type Parser::Quot(value_type v1, value_type v2) { return (int)(v1 / v2); }
+ value_type Parser::Rand( value_type seed = -1 )
+ {
+ static bool isSeedSet_ = false;
+
+ if( ! isSeedSet_ )
+ {
+ mu::rng.setSeed( seed );
+ isSeedSet_ = true;
+ }
+ return rng.uniform( ); /* Between 0 and 1 */
+ }
+
// If no seed is given,
- value_type Parser::Rand( value_type seed )
+ value_type Parser::Rnd( )
{
static bool isSeedSet_ = false;
+ // check if global seed is set
+ size_t seed = moose::getGlobalSeed();
if( ! isSeedSet_ )
{
mu::rng.setSeed( seed );
@@ -330,6 +345,7 @@ namespace mu
DefineFun(_T("rint"), Rint);
DefineFun(_T("abs"), Abs);
DefineFun(_T("fmod"), Fmod);
+ DefineFun(_T("rnd"), Rnd);
DefineFun(_T("rand"), Rand);
DefineFun(_T("rand2"), Rand2);
// Functions with variable number of arguments
diff --git a/moose-core/external/odeint-v2/README.md b/moose-core/external/odeint-v2/README.md
deleted file mode 100644
index 49e3a20b5ceb0ebb77ad9eafcc65762cf481e920..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/README.md
+++ /dev/null
@@ -1,3 +0,0 @@
-odeint is a highly flexible library for solving ordinary differential equations.
-
-This version is modified to suit the need of MOOSE simulator.
diff --git a/moose-core/external/odeint-v2/fix-copyright.py b/moose-core/external/odeint-v2/fix-copyright.py
deleted file mode 100755
index 753596e6d4b9ec230609fa82b7df7b46af83d9be..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/fix-copyright.py
+++ /dev/null
@@ -1,73 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-from __future__ import print_function
-from subprocess import check_output as run
-from datetime import datetime
-from itertools import groupby
-from operator import itemgetter
-import re
-import magic
-
-def authors(filename):
- log = run(['git', 'log', '--follow',
- '--date=short','--format=%aN%x09%ad', filename],
- universal_newlines=True)
- for line in log.splitlines():
- author, date = line.split('\t')
- if author != 'fix-copyright.py':
- yield author, datetime.strptime(date, '%Y-%m-%d')
-
-def new_copyright(filename, previous):
- def f():
- au = list(authors(filename))
- alldates = list(map(itemgetter(1), au))
- aup = sorted(au + [(a, None) for a in previous], key=itemgetter(0))
- for author, records in groupby(aup, itemgetter(0)):
- dates = [_f for _f in map(itemgetter(1), records) if _f]
- if not dates: dates = alldates
- start = min(dates)
- end = max(dates)
- fmt = '{0}' if start.year == end.year else '{0}-{1}'
- line = 'Copyright ' + fmt.format(start.year, end.year) + ' ' + author
- key = (start, author)
- yield key, line
- return list(map(itemgetter(1), sorted(f())))
-
-def fix_copyright(filename):
- # Find copyright block in original file
- prefix = set()
- names = []
- lines = []
- with open(filename, 'r') as f:
- content = list(f)
- for i, line in enumerate(content[:15]):
- m = re.match(r'^(?P<prefix>\W*)(\(c\))?\s*?copyright\s*(\(c\))?\s+\d{4}(\s*-\s*\d{4})?\s+(?P<name>.+?)\s*$', line, re.IGNORECASE)
- if m:
- d = m.groupdict()
- prefix.add(d['prefix'])
- lines.append(i)
- names.append(d['name'].strip())
- if len(prefix) != 1:
- print('Not found:', filename)
- return
- prefix = list(prefix)[0]
-
- print(filename)
- new = iter(new_copyright(filename, names))
- with open(filename, 'w') as f:
- for i, line in enumerate(content):
- if i in lines:
- for repl in new:
- print(prefix + repl, file=f)
- else:
- print(line, end=' ', file=f)
- pass
-
-def all_files():
- ls = run(['git', 'ls-files'], universal_newlines=True)
- for filename in ls.splitlines():
- if magic.from_file(filename, mime=True).split('/')[0] == 'text':
- yield filename
-
-for f in all_files():
- fix_copyright(f)
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint.hpp
deleted file mode 100644
index e0100899ca16b4ab831b3e4574bae96ed9059cfe..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint.hpp
+++ /dev/null
@@ -1,84 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint.hpp
-
- [begin_description]
- Forward include for odeint. Includes nearly everything.
- [end_description]
-
- Copyright 2009-2013 Karsten Ahnert
- Copyright 2010-2013 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_HPP_INCLUDED
-
-#include <boost/numeric/odeint/version.hpp>
-#include <boost/numeric/odeint/config.hpp>
-
-// start with ublas wrapper because we need its specializations before including state_wrapper.hpp
-#include <boost/numeric/odeint/util/ublas_wrapper.hpp>
-
-#include <boost/numeric/odeint/stepper/euler.hpp>
-#include <boost/numeric/odeint/stepper/runge_kutta4_classic.hpp>
-#include <boost/numeric/odeint/stepper/runge_kutta4.hpp>
-#include <boost/numeric/odeint/stepper/runge_kutta_cash_karp54.hpp>
-#include <boost/numeric/odeint/stepper/runge_kutta_cash_karp54_classic.hpp>
-#include <boost/numeric/odeint/stepper/runge_kutta_dopri5.hpp>
-#include <boost/numeric/odeint/stepper/runge_kutta_fehlberg78.hpp>
-
-#include <boost/numeric/odeint/stepper/controlled_runge_kutta.hpp>
-
-#include <boost/numeric/odeint/stepper/dense_output_runge_kutta.hpp>
-
-#include <boost/numeric/odeint/stepper/bulirsch_stoer.hpp>
-
-#ifndef __CUDACC__
-/* Bulirsch Stoer with Dense Output does not compile with nvcc
- * because of the binomial library used there which relies on unsupported SSE functions
- */
-#include <boost/numeric/odeint/stepper/bulirsch_stoer_dense_out.hpp>
-#endif
-
-#include <boost/numeric/odeint/stepper/symplectic_euler.hpp>
-#include <boost/numeric/odeint/stepper/symplectic_rkn_sb3a_mclachlan.hpp>
-#include <boost/numeric/odeint/stepper/velocity_verlet.hpp>
-
-#include <boost/numeric/odeint/stepper/adams_bashforth_moulton.hpp>
-
-#include <boost/numeric/odeint/stepper/implicit_euler.hpp>
-#include <boost/numeric/odeint/stepper/rosenbrock4.hpp>
-#include <boost/numeric/odeint/stepper/rosenbrock4_controller.hpp>
-#include <boost/numeric/odeint/stepper/rosenbrock4_dense_output.hpp>
-
-#include <boost/numeric/odeint/algebra/algebra_dispatcher.hpp>
-#include <boost/numeric/odeint/algebra/multi_array_algebra.hpp>
-#include <boost/numeric/odeint/util/multi_array_adaption.hpp>
-/*
- * Including this algebra slows down the compilation time
- */
-// #include <boost/numeric/odeint/algebra/fusion_algebra.hpp>
-
-#include <boost/numeric/odeint/integrate/integrate.hpp>
-#include <boost/numeric/odeint/integrate/integrate_adaptive.hpp>
-#include <boost/numeric/odeint/integrate/integrate_const.hpp>
-#include <boost/numeric/odeint/integrate/integrate_n_steps.hpp>
-#include <boost/numeric/odeint/integrate/integrate_times.hpp>
-
-#include <boost/numeric/odeint/integrate/observer_collection.hpp>
-#include <boost/numeric/odeint/integrate/max_step_checker.hpp>
-
-#include <boost/numeric/odeint/stepper/generation.hpp>
-
-#include <boost/numeric/odeint/iterator/adaptive_iterator.hpp>
-#include <boost/numeric/odeint/iterator/adaptive_time_iterator.hpp>
-#include <boost/numeric/odeint/iterator/const_step_iterator.hpp>
-#include <boost/numeric/odeint/iterator/const_step_time_iterator.hpp>
-
-
-#endif // BOOST_NUMERIC_ODEINT_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/algebra/algebra_dispatcher.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/algebra/algebra_dispatcher.hpp
deleted file mode 100644
index bcae2d3eacf492f8006f67a7c063524197ff7aa3..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/algebra/algebra_dispatcher.hpp
+++ /dev/null
@@ -1,110 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/algebra/algebra_dispatcher.hpp
-
- [begin_description]
- Algebra dispatcher to automatically chose suitable algebra.
- [end_description]
-
- Copyright 2013 Karsten Ahnert
- Copyright 2013 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-#ifndef BOOST_NUMERIC_ODEINT_ALGEBRA_ALGEBRA_DISPATCHER_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_ALGEBRA_ALGEBRA_DISPATCHER_HPP_INCLUDED
-
-#include <boost/numeric/odeint/config.hpp>
-
-#include <complex>
-#include <boost/type_traits/is_floating_point.hpp>
-
-#include <boost/numeric/ublas/vector.hpp>
-#include <boost/numeric/ublas/matrix.hpp>
-
-#include <boost/numeric/odeint/algebra/range_algebra.hpp>
-#include <boost/numeric/odeint/algebra/array_algebra.hpp>
-#include <boost/numeric/odeint/algebra/vector_space_algebra.hpp>
-
-#include <boost/array.hpp>
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-template< class StateType , class Enabler = void >
-struct algebra_dispatcher_sfinae
-{
- // range_algebra is the standard algebra
- typedef range_algebra algebra_type;
-};
-
-template< class StateType >
-struct algebra_dispatcher : algebra_dispatcher_sfinae< StateType > { };
-
-// specialize for array
-template< class T , size_t N >
-struct algebra_dispatcher< boost::array< T , N > >
-{
- typedef array_algebra algebra_type;
-};
-
-//specialize for some integral types
-template< typename T >
-struct algebra_dispatcher_sfinae< T , typename boost::enable_if< typename boost::is_floating_point< T >::type >::type >
-{
- typedef vector_space_algebra algebra_type;
-};
-
-template< typename T >
-struct algebra_dispatcher< std::complex<T> >
-{
- typedef vector_space_algebra algebra_type;
-};
-
-///* think about that again....
-// specialize for ublas vector and matrix types
-template< class T , class A >
-struct algebra_dispatcher< boost::numeric::ublas::vector< T , A > >
-{
- typedef vector_space_algebra algebra_type;
-};
-
-template< class T , class L , class A >
-struct algebra_dispatcher< boost::numeric::ublas::matrix< T , L , A > >
-{
- typedef vector_space_algebra algebra_type;
-};
-//*/
-
-}
-}
-}
-
-#ifdef BOOST_NUMERIC_ODEINT_CXX11
-
-// c++11 mode: specialization for std::array if available
-
-#include <array>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-// specialize for std::array
-template< class T , size_t N >
-struct algebra_dispatcher< std::array< T , N > >
-{
- typedef array_algebra algebra_type;
-};
-
-} } }
-
-#endif
-
-
-#endif
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/algebra/array_algebra.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/algebra/array_algebra.hpp
deleted file mode 100644
index 39b79240adfe9a304bd39d67158912a886b89eb4..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/algebra/array_algebra.hpp
+++ /dev/null
@@ -1,293 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/algebra/array_algebra.hpp
-
- [begin_description]
- Algebra for Arrays. Highly specialized for odeint. Const arguments are
- introduce to work with odeint.
- The Array algebra can be used for Array structures with two template
- parameters:
- Array<T, N>
- [end_description]
-
- Copyright 2011-2013 Mario Mulansky
- Copyright 2011-2012 Karsten Ahnert
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_ALGEBRA_ARRAY_ALGEBRA_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_ALGEBRA_ARRAY_ALGEBRA_HPP_INCLUDED
-
-#include <algorithm>
-#include <boost/array.hpp>
-
-#include <boost/numeric/odeint/algebra/norm_result_type.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-struct array_algebra
-{
- //template< typename T , size_t dim , class Op >
- template < template < typename, size_t > class Array, typename T,
- size_t dim, class Op >
- static void for_each1( Array< T, dim > &s1, Op op )
- {
- for( size_t i=0 ; i<dim ; ++i )
- op( s1[i] );
- }
-
- template < template < typename, size_t > class Array, typename T,
- size_t dim, class Op >
- static void for_each2( Array< T, dim > &s1, const Array< T, dim > &s2,
- Op op )
- {
- for( size_t i=0 ; i<dim ; ++i )
- op( s1[i] , s2[i] );
- }
-
- template < template < typename, size_t > class Array, typename T,
- size_t dim, class Op >
- static void for_each3( Array< T , dim > &s1 ,
- const Array< T , dim > &s2 ,
- const Array< T , dim > &s3 , Op op )
- {
- for( size_t i=0 ; i<dim ; ++i )
- op( s1[i] , s2[i] , s3[i] );
- }
-
- /* different const signature - required for the scale_sum_swap2 operation */
- template < template < typename, size_t > class Array, typename T,
- size_t dim, class Op >
- static void for_each3( Array< T , dim > &s1 ,
- Array< T , dim > &s2 ,
- const Array< T , dim > &s3 , Op op )
- {
- for( size_t i=0 ; i<dim ; ++i )
- op( s1[i] , s2[i] , s3[i] );
- }
-
- template < template < typename, size_t > class Array, typename T,
- size_t dim, class Op >
- static void for_each4( Array< T , dim > &s1 ,
- const Array< T , dim > &s2 ,
- const Array< T , dim > &s3 ,
- const Array< T , dim > &s4 , Op op )
- {
- for( size_t i=0 ; i<dim ; ++i )
- op( s1[i] , s2[i] , s3[i] , s4[i] );
- }
-
- template < template < typename, size_t > class Array, typename T,
- size_t dim, class Op >
- static void for_each5( Array< T , dim > &s1 ,
- const Array< T , dim > &s2 ,
- const Array< T , dim > &s3 ,
- const Array< T , dim > &s4 ,
- const Array< T , dim > &s5 , Op op )
- {
- for( size_t i=0 ; i<dim ; ++i )
- op( s1[i] , s2[i] , s3[i] , s4[i] , s5[i] );
- }
-
- template < template < typename, size_t > class Array, typename T,
- size_t dim, class Op >
- static void for_each6( Array< T , dim > &s1 ,
- const Array< T , dim > &s2 ,
- const Array< T , dim > &s3 ,
- const Array< T , dim > &s4 ,
- const Array< T , dim > &s5 ,
- const Array< T , dim > &s6 , Op op )
- {
- for( size_t i=0 ; i<dim ; ++i )
- op( s1[i] , s2[i] , s3[i] , s4[i] , s5[i] , s6[i] );
- }
-
- template < template < typename, size_t > class Array, typename T,
- size_t dim, class Op >
- static void for_each7( Array< T , dim > &s1 ,
- const Array< T , dim > &s2 ,
- const Array< T , dim > &s3 ,
- const Array< T , dim > &s4 ,
- const Array< T , dim > &s5 ,
- const Array< T , dim > &s6 ,
- const Array< T , dim > &s7 , Op op )
- {
- for( size_t i=0 ; i<dim ; ++i )
- op( s1[i] , s2[i] , s3[i] , s4[i] , s5[i] , s6[i] , s7[i] );
- }
-
- template < template < typename, size_t > class Array, typename T,
- size_t dim, class Op >
- static void for_each8( Array< T , dim > &s1 ,
- const Array< T , dim > &s2 ,
- const Array< T , dim > &s3 ,
- const Array< T , dim > &s4 ,
- const Array< T , dim > &s5 ,
- const Array< T , dim > &s6 ,
- const Array< T , dim > &s7 ,
- const Array< T , dim > &s8 , Op op )
- {
- for( size_t i=0 ; i<dim ; ++i )
- op( s1[i] , s2[i] , s3[i] , s4[i] , s5[i] , s6[i] , s7[i] , s8[i] );
- }
-
- template < template < typename, size_t > class Array, typename T,
- size_t dim, class Op >
- static void for_each9( Array< T , dim > &s1 ,
- const Array< T , dim > &s2 ,
- const Array< T , dim > &s3 ,
- const Array< T , dim > &s4 ,
- const Array< T , dim > &s5 ,
- const Array< T , dim > &s6 ,
- const Array< T , dim > &s7 ,
- const Array< T , dim > &s8 ,
- const Array< T , dim > &s9 , Op op )
- {
- for( size_t i=0 ; i<dim ; ++i )
- op( s1[i] , s2[i] , s3[i] , s4[i] , s5[i] , s6[i] , s7[i] , s8[i] , s9[i] );
- }
-
- template < template < typename, size_t > class Array, typename T,
- size_t dim, class Op >
- static void for_each10( Array< T , dim > &s1 ,
- const Array< T , dim > &s2 ,
- const Array< T , dim > &s3 ,
- const Array< T , dim > &s4 ,
- const Array< T , dim > &s5 ,
- const Array< T , dim > &s6 ,
- const Array< T , dim > &s7 ,
- const Array< T , dim > &s8 ,
- const Array< T , dim > &s9 ,
- const Array< T , dim > &s10 , Op op )
- {
- for( size_t i=0 ; i<dim ; ++i )
- op( s1[i] , s2[i] , s3[i] , s4[i] , s5[i] , s6[i] , s7[i] , s8[i] , s9[i] , s10[i] );
- }
-
- template < template < typename, size_t > class Array, typename T,
- size_t dim, class Op >
- static void for_each11( Array< T , dim > &s1 ,
- const Array< T , dim > &s2 ,
- const Array< T , dim > &s3 ,
- const Array< T , dim > &s4 ,
- const Array< T , dim > &s5 ,
- const Array< T , dim > &s6 ,
- const Array< T , dim > &s7 ,
- const Array< T , dim > &s8 ,
- const Array< T , dim > &s9 ,
- const Array< T , dim > &s10 ,
- const Array< T , dim > &s11 , Op op )
- {
- for( size_t i=0 ; i<dim ; ++i )
- op( s1[i] , s2[i] , s3[i] , s4[i] , s5[i] , s6[i] , s7[i] , s8[i] , s9[i] , s10[i] , s11[i] );
- }
-
- template < template < typename, size_t > class Array, typename T,
- size_t dim, class Op >
- static void for_each12( Array< T , dim > &s1 ,
- const Array< T , dim > &s2 ,
- const Array< T , dim > &s3 ,
- const Array< T , dim > &s4 ,
- const Array< T , dim > &s5 ,
- const Array< T , dim > &s6 ,
- const Array< T , dim > &s7 ,
- const Array< T , dim > &s8 ,
- const Array< T , dim > &s9 ,
- const Array< T , dim > &s10 ,
- const Array< T , dim > &s11 ,
- const Array< T , dim > &s12 , Op op )
- {
- for( size_t i=0 ; i<dim ; ++i )
- op( s1[i] , s2[i] , s3[i] , s4[i] , s5[i] , s6[i] , s7[i] , s8[i] , s9[i] , s10[i] , s11[i] , s12[i] );
- }
-
- template < template < typename, size_t > class Array, typename T,
- size_t dim, class Op >
- static void for_each13( Array< T , dim > &s1 ,
- const Array< T , dim > &s2 ,
- const Array< T , dim > &s3 ,
- const Array< T , dim > &s4 ,
- const Array< T , dim > &s5 ,
- const Array< T , dim > &s6 ,
- const Array< T , dim > &s7 ,
- const Array< T , dim > &s8 ,
- const Array< T , dim > &s9 ,
- const Array< T , dim > &s10 ,
- const Array< T , dim > &s11 ,
- const Array< T , dim > &s12 ,
- const Array< T , dim > &s13 , Op op )
- {
- for( size_t i=0 ; i<dim ; ++i )
- op( s1[i] , s2[i] , s3[i] , s4[i] , s5[i] , s6[i] , s7[i] , s8[i] , s9[i] , s10[i] , s11[i] , s12[i] , s13[i] );
- }
-
- template < template < typename, size_t > class Array, typename T,
- size_t dim, class Op >
- static void for_each14( Array< T , dim > &s1 ,
- const Array< T , dim > &s2 ,
- const Array< T , dim > &s3 ,
- const Array< T , dim > &s4 ,
- const Array< T , dim > &s5 ,
- const Array< T , dim > &s6 ,
- const Array< T , dim > &s7 ,
- const Array< T , dim > &s8 ,
- const Array< T , dim > &s9 ,
- const Array< T , dim > &s10 ,
- const Array< T , dim > &s11 ,
- const Array< T , dim > &s12 ,
- const Array< T , dim > &s13 ,
- const Array< T , dim > &s14 , Op op )
- {
- for( size_t i=0 ; i<dim ; ++i )
- op( s1[i] , s2[i] , s3[i] , s4[i] , s5[i] , s6[i] , s7[i] , s8[i] , s9[i] , s10[i] , s11[i] , s12[i] , s13[i] , s14[i] );
- }
-
- template < template < typename, size_t > class Array, typename T,
- size_t dim, class Op >
- static void for_each15( Array< T , dim > &s1 ,
- const Array< T , dim > &s2 ,
- const Array< T , dim > &s3 ,
- const Array< T , dim > &s4 ,
- const Array< T , dim > &s5 ,
- const Array< T , dim > &s6 ,
- const Array< T , dim > &s7 ,
- const Array< T , dim > &s8 ,
- const Array< T , dim > &s9 ,
- const Array< T , dim > &s10 ,
- const Array< T , dim > &s11 ,
- const Array< T , dim > &s12 ,
- const Array< T , dim > &s13 ,
- const Array< T , dim > &s14 ,
- const Array< T , dim > &s15 , Op op )
- {
- for( size_t i=0 ; i<dim ; ++i )
- op( s1[i] , s2[i] , s3[i] , s4[i] , s5[i] , s6[i] , s7[i] , s8[i] , s9[i] , s10[i] , s11[i] , s12[i] , s13[i] , s14[i] , s15[i] );
- }
-
-
- template < template < typename, size_t > class Array, typename T,
- size_t dim>
- static typename norm_result_type< Array< T , dim > >::type norm_inf( const Array< T , dim > &s )
- {
- BOOST_USING_STD_MAX();
- using std::abs;
- typedef typename norm_result_type< Array< T , dim > >::type result_type;
- result_type init = static_cast< result_type >( 0 );
- for( size_t i=0 ; i<dim ; ++i )
- init = max BOOST_PREVENT_MACRO_SUBSTITUTION ( init , static_cast< result_type >(abs(s[i])) );
- return init;
- }
-
-};
-
-}
-}
-}
-
-#endif // BOOST_NUMERIC_ODEINT_ALGEBRA_ARRAY_ALGEBRA_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/algebra/default_operations.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/algebra/default_operations.hpp
deleted file mode 100644
index b10944fa19cda02bb77090b0358ba639ed40e795..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/algebra/default_operations.hpp
+++ /dev/null
@@ -1,599 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/algebra/default_operations.hpp
-
- [begin_description]
- Default operations. They work with the default numerical types, like float, double, complex< double> ...
- [end_description]
-
- Copyright 2010-2012 Karsten Ahnert
- Copyright 2010-2013 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_ALGEBRA_DEFAULT_OPERATIONS_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_ALGEBRA_DEFAULT_OPERATIONS_HPP_INCLUDED
-
-#include <algorithm>
-
-#include <boost/config.hpp>
-#include <boost/array.hpp>
-
-#include <boost/numeric/odeint/util/unit_helper.hpp>
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-
-/*
- * Notes:
- *
- * * the results structs are needed in order to work with fusion_algebra
- */
-struct default_operations
-{
-
- template< class Fac1 = double >
- struct scale
- {
- const Fac1 m_alpha1;
-
- scale( Fac1 alpha1 ) : m_alpha1( alpha1 ) { }
-
- template< class T1 >
- void operator()( T1 &t1 ) const
- {
- t1 *= m_alpha1;
- }
-
- typedef void result_type;
- };
-
- template< class Fac1 = double >
- struct scale_sum1
- {
- const Fac1 m_alpha1;
-
- scale_sum1( Fac1 alpha1 ) : m_alpha1( alpha1 ) { }
-
- template< class T1 , class T2 >
- void operator()( T1 &t1 , const T2 &t2 ) const
- {
- t1 = m_alpha1 * t2;
- }
-
- typedef void result_type;
- };
-
-
- template< class Fac1 = double , class Fac2 = Fac1 >
- struct scale_sum2
- {
- const Fac1 m_alpha1;
- const Fac2 m_alpha2;
-
- scale_sum2( Fac1 alpha1 , Fac2 alpha2 ) : m_alpha1( alpha1 ) , m_alpha2( alpha2 ) { }
-
- template< class T1 , class T2 , class T3 >
- void operator()( T1 &t1 , const T2 &t2 , const T3 &t3) const
- {
- t1 = m_alpha1 * t2 + m_alpha2 * t3;
- }
-
- typedef void result_type;
- };
-
-
- template< class Fac1 = double , class Fac2 = Fac1 , class Fac3 = Fac2 >
- struct scale_sum3
- {
- const Fac1 m_alpha1;
- const Fac2 m_alpha2;
- const Fac3 m_alpha3;
-
- scale_sum3( Fac1 alpha1 , Fac2 alpha2 , Fac3 alpha3 )
- : m_alpha1( alpha1 ) , m_alpha2( alpha2 ) , m_alpha3( alpha3 ) { }
-
- template< class T1 , class T2 , class T3 , class T4 >
- void operator()( T1 &t1 , const T2 &t2 , const T3 &t3 , const T4 &t4 ) const
- {
- t1 = m_alpha1 * t2 + m_alpha2 * t3 + m_alpha3 * t4;
- }
-
- typedef void result_type;
- };
-
-
- template< class Fac1 = double , class Fac2 = Fac1 , class Fac3 = Fac2 , class Fac4 = Fac3 >
- struct scale_sum4
- {
- const Fac1 m_alpha1;
- const Fac2 m_alpha2;
- const Fac3 m_alpha3;
- const Fac4 m_alpha4;
-
- scale_sum4( Fac1 alpha1 , Fac2 alpha2 , Fac3 alpha3 , Fac4 alpha4 )
- : m_alpha1( alpha1 ) , m_alpha2( alpha2 ) , m_alpha3( alpha3 ) , m_alpha4( alpha4 ) { }
-
- template< class T1 , class T2 , class T3 , class T4 , class T5 >
- void operator()( T1 &t1 , const T2 &t2 , const T3 &t3 , const T4 &t4 , const T5 &t5) const
- {
- t1 = m_alpha1 * t2 + m_alpha2 * t3 + m_alpha3 * t4 + m_alpha4 * t5;
- }
-
- typedef void result_type;
- };
-
-
- template< class Fac1 = double , class Fac2 = Fac1 , class Fac3 = Fac2 , class Fac4 = Fac3 , class Fac5 = Fac4 >
- struct scale_sum5
- {
- const Fac1 m_alpha1;
- const Fac2 m_alpha2;
- const Fac3 m_alpha3;
- const Fac4 m_alpha4;
- const Fac5 m_alpha5;
-
- scale_sum5( Fac1 alpha1 , Fac2 alpha2 , Fac3 alpha3 , Fac4 alpha4 , Fac5 alpha5 )
- : m_alpha1( alpha1 ) , m_alpha2( alpha2 ) , m_alpha3( alpha3 ) , m_alpha4( alpha4 ) , m_alpha5( alpha5 ) { }
-
- template< class T1 , class T2 , class T3 , class T4 , class T5 , class T6 >
- void operator()( T1 &t1 , const T2 &t2 , const T3 &t3 , const T4 &t4 , const T5 &t5 , const T6 &t6) const
- {
- t1 = m_alpha1 * t2 + m_alpha2 * t3 + m_alpha3 * t4 + m_alpha4 * t5 + m_alpha5 * t6;
- }
-
- typedef void result_type;
- };
-
-
- template< class Fac1 = double , class Fac2 = Fac1 , class Fac3 = Fac2 , class Fac4 = Fac3 , class Fac5 = Fac4 , class Fac6 = Fac5 >
- struct scale_sum6
- {
- const Fac1 m_alpha1;
- const Fac2 m_alpha2;
- const Fac3 m_alpha3;
- const Fac4 m_alpha4;
- const Fac5 m_alpha5;
- const Fac6 m_alpha6;
-
- scale_sum6( Fac1 alpha1 , Fac2 alpha2 , Fac3 alpha3 , Fac4 alpha4 , Fac5 alpha5 , Fac6 alpha6 )
- : m_alpha1( alpha1 ) , m_alpha2( alpha2 ) , m_alpha3( alpha3 ) , m_alpha4( alpha4 ) , m_alpha5( alpha5 ) , m_alpha6( alpha6 ){ }
-
- template< class T1 , class T2 , class T3 , class T4 , class T5 , class T6 , class T7 >
- void operator()( T1 &t1 , const T2 &t2 , const T3 &t3 , const T4 &t4 , const T5 &t5 , const T6 &t6 ,const T7 &t7) const
- {
- t1 = m_alpha1 * t2 + m_alpha2 * t3 + m_alpha3 * t4 + m_alpha4 * t5 + m_alpha5 * t6 + m_alpha6 * t7;
- }
-
- typedef void result_type;
- };
-
-
- template< class Fac1 = double , class Fac2 = Fac1 , class Fac3 = Fac2 , class Fac4 = Fac3 , class Fac5 = Fac4 , class Fac6 = Fac5 , class Fac7 = Fac6 >
- struct scale_sum7
- {
- const Fac1 m_alpha1;
- const Fac2 m_alpha2;
- const Fac3 m_alpha3;
- const Fac4 m_alpha4;
- const Fac5 m_alpha5;
- const Fac6 m_alpha6;
- const Fac7 m_alpha7;
-
- scale_sum7( Fac1 alpha1 , Fac2 alpha2 , Fac3 alpha3 , Fac4 alpha4 ,
- Fac5 alpha5 , Fac6 alpha6 , Fac7 alpha7 )
- : m_alpha1( alpha1 ) , m_alpha2( alpha2 ) , m_alpha3( alpha3 ) , m_alpha4( alpha4 ) , m_alpha5( alpha5 ) , m_alpha6( alpha6 ) , m_alpha7( alpha7 ) { }
-
- template< class T1 , class T2 , class T3 , class T4 , class T5 , class T6 , class T7 , class T8 >
- void operator()( T1 &t1 , const T2 &t2 , const T3 &t3 , const T4 &t4 , const T5 &t5 , const T6 &t6 , const T7 &t7 , const T8 &t8 ) const
- {
- t1 = m_alpha1 * t2 + m_alpha2 * t3 + m_alpha3 * t4 + m_alpha4 * t5 + m_alpha5 * t6 + m_alpha6 * t7 + m_alpha7 * t8;
- }
-
- typedef void result_type;
- };
-
-
- template< class Fac1 = double , class Fac2 = Fac1 , class Fac3 = Fac2 , class Fac4 = Fac3 , class Fac5 = Fac4 , class Fac6 = Fac5 , class Fac7 = Fac6 , class Fac8 = Fac7 >
- struct scale_sum8
- {
- const Fac1 m_alpha1;
- const Fac2 m_alpha2;
- const Fac3 m_alpha3;
- const Fac4 m_alpha4;
- const Fac5 m_alpha5;
- const Fac6 m_alpha6;
- const Fac7 m_alpha7;
- const Fac8 m_alpha8;
-
- scale_sum8( Fac1 alpha1 , Fac2 alpha2 , Fac3 alpha3 , Fac4 alpha4 ,
- Fac5 alpha5 , Fac6 alpha6 , Fac7 alpha7 , Fac8 alpha8 )
- : m_alpha1( alpha1 ) , m_alpha2( alpha2 ) , m_alpha3( alpha3 ) , m_alpha4( alpha4 ) , m_alpha5( alpha5 ) , m_alpha6( alpha6 ) , m_alpha7( alpha7 ) , m_alpha8( alpha8 ) { }
-
- template< class T1 , class T2 , class T3 , class T4 , class T5 , class T6 , class T7 , class T8 , class T9 >
- void operator()( T1 &t1 , const T2 &t2 , const T3 &t3 , const T4 &t4 , const T5 &t5 , const T6 &t6 , const T7 &t7 , const T8 &t8 , const T9 &t9 ) const
- {
- t1 = m_alpha1 * t2 + m_alpha2 * t3 + m_alpha3 * t4 + m_alpha4 * t5 + m_alpha5 * t6 + m_alpha6 * t7 + m_alpha7 * t8 + m_alpha8 * t9;
- }
-
- typedef void result_type;
- };
-
- template< class Fac1 = double , class Fac2 = Fac1 , class Fac3 = Fac2 , class Fac4 = Fac3 , class Fac5 = Fac4 , class Fac6 = Fac5 , class Fac7 = Fac6 , class Fac8 = Fac7 , class Fac9 = Fac8 >
- struct scale_sum9
- {
- const Fac1 m_alpha1;
- const Fac2 m_alpha2;
- const Fac3 m_alpha3;
- const Fac4 m_alpha4;
- const Fac5 m_alpha5;
- const Fac6 m_alpha6;
- const Fac7 m_alpha7;
- const Fac8 m_alpha8;
- const Fac9 m_alpha9;
-
- scale_sum9( Fac1 alpha1 , Fac2 alpha2 , Fac3 alpha3 , Fac4 alpha4 ,
- Fac5 alpha5 , Fac6 alpha6 , Fac7 alpha7 , Fac8 alpha8 , Fac9 alpha9 )
- : m_alpha1( alpha1 ) , m_alpha2( alpha2 ) , m_alpha3( alpha3 ) , m_alpha4( alpha4 ) , m_alpha5( alpha5 ) , m_alpha6( alpha6 ) , m_alpha7( alpha7 ) , m_alpha8( alpha8 ) , m_alpha9( alpha9 ) { }
-
- template< class T1 , class T2 , class T3 , class T4 , class T5 , class T6 , class T7 , class T8 , class T9 , class T10 >
- void operator()( T1 &t1 , const T2 &t2 , const T3 &t3 , const T4 &t4 , const T5 &t5 , const T6 &t6 , const T7 &t7 , const T8 &t8 , const T9 &t9 , const T10 &t10 ) const
- {
- t1 = m_alpha1 * t2 + m_alpha2 * t3 + m_alpha3 * t4 + m_alpha4 * t5 + m_alpha5 * t6 + m_alpha6 * t7 + m_alpha7 * t8 + m_alpha8 * t9 + m_alpha9 * t10;
- }
-
- typedef void result_type;
- };
-
- template< class Fac1 = double , class Fac2 = Fac1 , class Fac3 = Fac2 , class Fac4 = Fac3 , class Fac5 = Fac4 , class Fac6 = Fac5 , class Fac7 = Fac6 , class Fac8 = Fac7 , class Fac9 = Fac8 , class Fac10 = Fac9 >
- struct scale_sum10
- {
- const Fac1 m_alpha1;
- const Fac2 m_alpha2;
- const Fac3 m_alpha3;
- const Fac4 m_alpha4;
- const Fac5 m_alpha5;
- const Fac6 m_alpha6;
- const Fac7 m_alpha7;
- const Fac8 m_alpha8;
- const Fac9 m_alpha9;
- const Fac10 m_alpha10;
-
- scale_sum10( Fac1 alpha1 , Fac2 alpha2 , Fac3 alpha3 , Fac4 alpha4 ,
- Fac5 alpha5 , Fac6 alpha6 , Fac7 alpha7 , Fac8 alpha8 , Fac9 alpha9 , Fac10 alpha10 )
- : m_alpha1( alpha1 ) , m_alpha2( alpha2 ) , m_alpha3( alpha3 ) , m_alpha4( alpha4 ) , m_alpha5( alpha5 ) , m_alpha6( alpha6 ) , m_alpha7( alpha7 ) , m_alpha8( alpha8 ) , m_alpha9( alpha9 ) , m_alpha10( alpha10 ) { }
-
- template< class T1 , class T2 , class T3 , class T4 , class T5 , class T6 , class T7 , class T8 , class T9 , class T10 , class T11 >
- void operator()( T1 &t1 , const T2 &t2 , const T3 &t3 , const T4 &t4 , const T5 &t5 , const T6 &t6 , const T7 &t7 , const T8 &t8 , const T9 &t9 , const T10 &t10 , const T11 &t11 ) const
- {
- t1 = m_alpha1 * t2 + m_alpha2 * t3 + m_alpha3 * t4 + m_alpha4 * t5 + m_alpha5 * t6 + m_alpha6 * t7 + m_alpha7 * t8 + m_alpha8 * t9 + m_alpha9 * t10 + m_alpha10 * t11;
- }
-
- typedef void result_type;
- };
-
-
- template< class Fac1 = double , class Fac2 = Fac1 , class Fac3 = Fac2 , class Fac4 = Fac3 , class Fac5 = Fac4 , class Fac6 = Fac5 , class Fac7 = Fac6 , class Fac8 = Fac7 , class Fac9 = Fac8 , class Fac10 = Fac9 , class Fac11 = Fac10 >
- struct scale_sum11
- {
- const Fac1 m_alpha1;
- const Fac2 m_alpha2;
- const Fac3 m_alpha3;
- const Fac4 m_alpha4;
- const Fac5 m_alpha5;
- const Fac6 m_alpha6;
- const Fac7 m_alpha7;
- const Fac8 m_alpha8;
- const Fac9 m_alpha9;
- const Fac10 m_alpha10;
- const Fac11 m_alpha11;
-
- scale_sum11( Fac1 alpha1 , Fac2 alpha2 , Fac3 alpha3 , Fac4 alpha4 ,
- Fac5 alpha5 , Fac6 alpha6 , Fac7 alpha7 , Fac8 alpha8 , Fac9 alpha9 ,
- Fac10 alpha10 , Fac11 alpha11 )
- : m_alpha1( alpha1 ) , m_alpha2( alpha2 ) , m_alpha3( alpha3 ) , m_alpha4( alpha4 ) , m_alpha5( alpha5 ) , m_alpha6( alpha6 ) , m_alpha7( alpha7 ) , m_alpha8( alpha8 ) , m_alpha9( alpha9 ) , m_alpha10( alpha10 ) , m_alpha11( alpha11 ) { }
-
- template< class T1 , class T2 , class T3 , class T4 , class T5 , class T6 , class T7 , class T8 , class T9 , class T10 , class T11 , class T12 >
- void operator()( T1 &t1 , const T2 &t2 , const T3 &t3 , const T4 &t4 , const T5 &t5 , const T6 &t6 , const T7 &t7 , const T8 &t8 , const T9 &t9 , const T10 &t10 , const T11 &t11 , const T12 &t12 ) const
- {
- t1 = m_alpha1 * t2 + m_alpha2 * t3 + m_alpha3 * t4 + m_alpha4 * t5 + m_alpha5 * t6 + m_alpha6 * t7 + m_alpha7 * t8 + m_alpha8 * t9 + m_alpha9 * t10 + m_alpha10 * t11 + m_alpha11 * t12;
- }
-
- typedef void result_type;
- };
-
- template< class Fac1 = double , class Fac2 = Fac1 , class Fac3 = Fac2 , class Fac4 = Fac3 , class Fac5 = Fac4 , class Fac6 = Fac5 , class Fac7 = Fac6 , class Fac8 = Fac7 , class Fac9 = Fac8 , class Fac10 = Fac9 , class Fac11 = Fac10 , class Fac12 = Fac11 >
- struct scale_sum12
- {
- const Fac1 m_alpha1;
- const Fac2 m_alpha2;
- const Fac3 m_alpha3;
- const Fac4 m_alpha4;
- const Fac5 m_alpha5;
- const Fac6 m_alpha6;
- const Fac7 m_alpha7;
- const Fac8 m_alpha8;
- const Fac9 m_alpha9;
- const Fac10 m_alpha10;
- const Fac11 m_alpha11;
- const Fac12 m_alpha12;
-
- scale_sum12( Fac1 alpha1 , Fac2 alpha2 , Fac3 alpha3 , Fac4 alpha4 ,
- Fac5 alpha5 , Fac6 alpha6 , Fac7 alpha7 , Fac8 alpha8 , Fac9 alpha9 ,
- Fac10 alpha10 , Fac11 alpha11 , Fac12 alpha12 )
- : m_alpha1( alpha1 ) , m_alpha2( alpha2 ) , m_alpha3( alpha3 ) , m_alpha4( alpha4 ) , m_alpha5( alpha5 ) , m_alpha6( alpha6 ) , m_alpha7( alpha7 ) , m_alpha8( alpha8 ) , m_alpha9( alpha9 ) , m_alpha10( alpha10 ) , m_alpha11( alpha11 ) , m_alpha12( alpha12 ) { }
-
- template< class T1 , class T2 , class T3 , class T4 , class T5 , class T6 , class T7 , class T8 , class T9 , class T10 , class T11 , class T12 , class T13 >
- void operator()( T1 &t1 , const T2 &t2 , const T3 &t3 , const T4 &t4 , const T5 &t5 , const T6 &t6 , const T7 &t7 , const T8 &t8 , const T9 &t9 , const T10 &t10 , const T11 &t11 , const T12 &t12 , const T13 &t13 ) const
- {
- t1 = m_alpha1 * t2 + m_alpha2 * t3 + m_alpha3 * t4 + m_alpha4 * t5 + m_alpha5 * t6 + m_alpha6 * t7 + m_alpha7 * t8 + m_alpha8 * t9 + m_alpha9 * t10 + m_alpha10 * t11 + m_alpha11 * t12 + m_alpha12 * t13;
- }
-
- typedef void result_type;
- };
-
- template< class Fac1 = double , class Fac2 = Fac1 , class Fac3 = Fac2 , class Fac4 = Fac3 , class Fac5 = Fac4 , class Fac6 = Fac5 , class Fac7 = Fac6 , class Fac8 = Fac7 , class Fac9 = Fac8 , class Fac10 = Fac9 , class Fac11 = Fac10 , class Fac12 = Fac11 , class Fac13 = Fac12 >
- struct scale_sum13
- {
- const Fac1 m_alpha1;
- const Fac2 m_alpha2;
- const Fac3 m_alpha3;
- const Fac4 m_alpha4;
- const Fac5 m_alpha5;
- const Fac6 m_alpha6;
- const Fac7 m_alpha7;
- const Fac8 m_alpha8;
- const Fac9 m_alpha9;
- const Fac10 m_alpha10;
- const Fac11 m_alpha11;
- const Fac12 m_alpha12;
- const Fac13 m_alpha13;
-
- scale_sum13( Fac1 alpha1 , Fac2 alpha2 , Fac3 alpha3 , Fac4 alpha4 ,
- Fac5 alpha5 , Fac6 alpha6 , Fac7 alpha7 , Fac8 alpha8 , Fac9 alpha9 ,
- Fac10 alpha10 , Fac11 alpha11 , Fac12 alpha12 , Fac13 alpha13 )
- : m_alpha1( alpha1 ) , m_alpha2( alpha2 ) , m_alpha3( alpha3 ) , m_alpha4( alpha4 ) , m_alpha5( alpha5 ) , m_alpha6( alpha6 ) , m_alpha7( alpha7 ) , m_alpha8( alpha8 ) , m_alpha9( alpha9 ) , m_alpha10( alpha10 ) , m_alpha11( alpha11 ) , m_alpha12( alpha12 ) , m_alpha13( alpha13 ) { }
-
- template< class T1 , class T2 , class T3 , class T4 , class T5 , class T6 , class T7 , class T8 , class T9 , class T10 , class T11 , class T12 , class T13 , class T14 >
- void operator()( T1 &t1 , const T2 &t2 , const T3 &t3 , const T4 &t4 , const T5 &t5 , const T6 &t6 , const T7 &t7 , const T8 &t8 , const T9 &t9 , const T10 &t10 , const T11 &t11 , const T12 &t12 , const T13 &t13 , const T14 &t14 ) const
- {
- t1 = m_alpha1 * t2 + m_alpha2 * t3 + m_alpha3 * t4 + m_alpha4 * t5 + m_alpha5 * t6 + m_alpha6 * t7 + m_alpha7 * t8 + m_alpha8 * t9 + m_alpha9 * t10 + m_alpha10 * t11 + m_alpha11 * t12 + m_alpha12 * t13 + m_alpha13 * t14;
- }
-
- typedef void result_type;
- };
-
- template< class Fac1 = double , class Fac2 = Fac1 , class Fac3 = Fac2 , class Fac4 = Fac3 , class Fac5 = Fac4 , class Fac6 = Fac5 , class Fac7 = Fac6 , class Fac8 = Fac7 , class Fac9 = Fac8 , class Fac10 = Fac9 , class Fac11 = Fac10 , class Fac12 = Fac11 , class Fac13 = Fac12 , class Fac14 = Fac13 >
- struct scale_sum14
- {
- const Fac1 m_alpha1;
- const Fac2 m_alpha2;
- const Fac3 m_alpha3;
- const Fac4 m_alpha4;
- const Fac5 m_alpha5;
- const Fac6 m_alpha6;
- const Fac7 m_alpha7;
- const Fac8 m_alpha8;
- const Fac9 m_alpha9;
- const Fac10 m_alpha10;
- const Fac11 m_alpha11;
- const Fac12 m_alpha12;
- const Fac13 m_alpha13;
- const Fac14 m_alpha14;
-
- scale_sum14( Fac1 alpha1 , Fac2 alpha2 , Fac3 alpha3 , Fac4 alpha4 ,
- Fac5 alpha5 , Fac6 alpha6 , Fac7 alpha7 , Fac8 alpha8 , Fac9 alpha9 ,
- Fac10 alpha10 , Fac11 alpha11 , Fac12 alpha12 , Fac13 alpha13 , Fac14 alpha14 )
- : m_alpha1( alpha1 ) , m_alpha2( alpha2 ) , m_alpha3( alpha3 ) , m_alpha4( alpha4 ) , m_alpha5( alpha5 ) , m_alpha6( alpha6 ) , m_alpha7( alpha7 ) , m_alpha8( alpha8 ) , m_alpha9( alpha9 ) , m_alpha10( alpha10 ) , m_alpha11( alpha11 ) , m_alpha12( alpha12 ) , m_alpha13( alpha13 ) , m_alpha14( alpha14 ) { }
-
- template< class T1 , class T2 , class T3 , class T4 , class T5 , class T6 , class T7 , class T8 , class T9 , class T10 , class T11 , class T12 , class T13 , class T14 , class T15 >
- void operator()( T1 &t1 , const T2 &t2 , const T3 &t3 , const T4 &t4 , const T5 &t5 , const T6 &t6 , const T7 &t7 , const T8 &t8 , const T9 &t9 , const T10 &t10 , const T11 &t11 , const T12 &t12 , const T13 &t13 , const T14 &t14 , const T15 &t15 ) const
- {
- t1 = m_alpha1 * t2 + m_alpha2 * t3 + m_alpha3 * t4 + m_alpha4 * t5 + m_alpha5 * t6 + m_alpha6 * t7 + m_alpha7 * t8 + m_alpha8 * t9 + m_alpha9 * t10 + m_alpha10 * t11 + m_alpha11 * t12 + m_alpha12 * t13 + m_alpha13 * t14 + m_alpha14 * t15;
- }
-
- typedef void result_type;
- };
-
- template< class Fac1 = double , class Fac2 = Fac1 >
- struct scale_sum_swap2
- {
- const Fac1 m_alpha1;
- const Fac2 m_alpha2;
-
- scale_sum_swap2( Fac1 alpha1 , Fac2 alpha2 ) : m_alpha1( alpha1 ) , m_alpha2( alpha2 ) { }
-
- template< class T1 , class T2 , class T3 >
- void operator()( T1 &t1 , T2 &t2 , const T3 &t3) const
- {
- const T1 tmp( t1 );
- t1 = m_alpha1 * t2 + m_alpha2 * t3;
- t2 = tmp;
- }
-
- typedef void result_type;
- };
-
- /*
- * for usage in for_each2
- *
- * Works with boost::units by eliminating the unit
- */
- template< class Fac1 = double >
- struct rel_error
- {
- const Fac1 m_eps_abs , m_eps_rel , m_a_x , m_a_dxdt;
-
- rel_error( Fac1 eps_abs , Fac1 eps_rel , Fac1 a_x , Fac1 a_dxdt )
- : m_eps_abs( eps_abs ) , m_eps_rel( eps_rel ) , m_a_x( a_x ) , m_a_dxdt( a_dxdt ) { }
-
-
- template< class T1 , class T2 , class T3 >
- void operator()( T3 &t3 , const T1 &t1 , const T2 &t2 ) const
- {
- using std::abs;
- set_unit_value( t3 , abs( get_unit_value( t3 ) ) / ( m_eps_abs + m_eps_rel * ( m_a_x * abs( get_unit_value( t1 ) ) + m_a_dxdt * abs( get_unit_value( t2 ) ) ) ) );
- }
-
- typedef void result_type;
- };
-
-
- /*
- * for usage in for_each3
- *
- * used in the controller for the rosenbrock4 method
- *
- * Works with boost::units by eliminating the unit
- */
- template< class Fac1 = double >
- struct default_rel_error
- {
- const Fac1 m_eps_abs , m_eps_rel ;
-
- default_rel_error( Fac1 eps_abs , Fac1 eps_rel )
- : m_eps_abs( eps_abs ) , m_eps_rel( eps_rel ) { }
-
-
- /*
- * xerr = xerr / ( eps_abs + eps_rel * max( x , x_old ) )
- */
- template< class T1 , class T2 , class T3 >
- void operator()( T3 &t3 , const T1 &t1 , const T2 &t2 ) const
- {
- BOOST_USING_STD_MAX();
- using std::abs;
- Fac1 x1 = abs( get_unit_value( t1 ) ) , x2 = abs( get_unit_value( t2 ) );
- set_unit_value( t3 , abs( get_unit_value( t3 ) ) / ( m_eps_abs + m_eps_rel * max BOOST_PREVENT_MACRO_SUBSTITUTION ( x1 , x2 ) ) );
- }
-
- typedef void result_type;
- };
-
-
-
- /*
- * for usage in reduce
- */
-
- template< class Value >
- struct maximum
- {
- template< class Fac1 , class Fac2 >
- Value operator()( Fac1 t1 , const Fac2 t2 ) const
- {
- using std::abs;
- Value a1 = abs( get_unit_value( t1 ) ) , a2 = abs( get_unit_value( t2 ) );
- return ( a1 < a2 ) ? a2 : a1 ;
- }
-
- typedef Value result_type;
- };
-
-
- template< class Fac1 = double >
- struct rel_error_max
- {
- const Fac1 m_eps_abs , m_eps_rel;
-
- rel_error_max( Fac1 eps_abs , Fac1 eps_rel )
- : m_eps_abs( eps_abs ) , m_eps_rel( eps_rel )
- { }
-
- template< class Res , class T1 , class T2 , class T3 >
- Res operator()( Res r , const T1 &x_old , const T2 &x , const T3 &x_err )
- {
- BOOST_USING_STD_MAX();
- using std::abs;
- Res tmp = abs( get_unit_value( x_err ) ) / ( m_eps_abs + m_eps_rel * max BOOST_PREVENT_MACRO_SUBSTITUTION ( abs( x_old ) , abs( x ) ) );
- return max BOOST_PREVENT_MACRO_SUBSTITUTION ( r , tmp );
- }
- };
-
-
- template< class Fac1 = double >
- struct rel_error_max2
- {
- const Fac1 m_eps_abs , m_eps_rel , m_a_x , m_a_dxdt;
-
- rel_error_max2( Fac1 eps_abs , Fac1 eps_rel , Fac1 a_x , Fac1 a_dxdt )
- : m_eps_abs( eps_abs ) , m_eps_rel( eps_rel ) , m_a_x( a_x ) , m_a_dxdt( a_dxdt )
- { }
-
- template< class Res , class T1 , class T2 , class T3 , class T4 >
- Res operator()( Res r , const T1 &x_old , const T2 &x , const T3 &dxdt_old , const T4 &x_err )
- {
- BOOST_USING_STD_MAX();
- using std::abs;
- Res tmp = abs( get_unit_value( x_err ) ) /
- ( m_eps_abs + m_eps_rel * ( m_a_x * abs( get_unit_value( x_old ) ) + m_a_dxdt * abs( get_unit_value( dxdt_old ) ) ) );
- return max BOOST_PREVENT_MACRO_SUBSTITUTION ( r , tmp );
- }
- };
-
-
-
-
- template< class Fac1 = double >
- struct rel_error_l2
- {
- const Fac1 m_eps_abs , m_eps_rel;
-
- rel_error_l2( Fac1 eps_abs , Fac1 eps_rel )
- : m_eps_abs( eps_abs ) , m_eps_rel( eps_rel )
- { }
-
- template< class Res , class T1 , class T2 , class T3 >
- Res operator()( Res r , const T1 &x_old , const T2 &x , const T3 &x_err )
- {
- BOOST_USING_STD_MAX();
- using std::abs;
- Res tmp = abs( get_unit_value( x_err ) ) / ( m_eps_abs + m_eps_rel * max BOOST_PREVENT_MACRO_SUBSTITUTION ( abs( x_old ) , abs( x ) ) );
- return r + tmp * tmp;
- }
- };
-
-
-
-
- template< class Fac1 = double >
- struct rel_error_l2_2
- {
- const Fac1 m_eps_abs , m_eps_rel , m_a_x , m_a_dxdt;
-
- rel_error_l2_2( Fac1 eps_abs , Fac1 eps_rel , Fac1 a_x , Fac1 a_dxdt )
- : m_eps_abs( eps_abs ) , m_eps_rel( eps_rel ) , m_a_x( a_x ) , m_a_dxdt( a_dxdt )
- { }
-
- template< class Res , class T1 , class T2 , class T3 , class T4 >
- Res operator()( Res r , const T1 &x_old , const T2 &x , const T3 &dxdt_old , const T4 &x_err )
- {
- using std::abs;
- Res tmp = abs( get_unit_value( x_err ) ) /
- ( m_eps_abs + m_eps_rel * ( m_a_x * abs( get_unit_value( x_old ) ) + m_a_dxdt * abs( get_unit_value( dxdt_old ) ) ) );
- return r + tmp * tmp;
- }
- };
-
-
-
-
-
-
-};
-
-
-} // odeint
-} // numeric
-} // boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_ALGEBRA_DEFAULT_OPERATIONS_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/algebra/detail/extract_value_type.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/algebra/detail/extract_value_type.hpp
deleted file mode 100644
index c5246bb6f492d7a3d9e737a3adfcade8ff2873a9..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/algebra/detail/extract_value_type.hpp
+++ /dev/null
@@ -1,52 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/algebra/detail/extract_value_type.hpp
-
- [begin_description]
- Extract true value type from complex types (eg. std::complex)
- [end_description]
-
- Copyright 2013 Karsten Ahnert
- Copyright 2013 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-#ifndef BOOST_NUMERIC_ODEINT_ALGEBRA_DETAIL_EXTRACT_VALUE_TYPE_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_ALGEBRA_DETAIL_EXTRACT_VALUE_TYPE_HPP_INCLUDED
-
-#include <boost/utility.hpp>
-#include <boost/mpl/has_xxx.hpp>
-
-BOOST_MPL_HAS_XXX_TRAIT_DEF(value_type)
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-namespace detail {
-
-template< typename S , typename Enabler = void >
-struct extract_value_type {};
-
-// as long as value_types are defined we go down the value_type chain
-// e.g. returning S::value_type::value_type::value_type
-
-template< typename S >
-struct extract_value_type<S , typename boost::disable_if< has_value_type<S> >::type >
-{
- // no value_type defined, return S
- typedef S type;
-};
-
-template< typename S >
-struct extract_value_type< S , typename boost::enable_if< has_value_type<S> >::type >
-{
- // go down the value_type
- typedef typename extract_value_type< typename S::value_type >::type type;
-};
-
-} } } }
-
-#endif
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/algebra/detail/for_each.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/algebra/detail/for_each.hpp
deleted file mode 100644
index 5387a47db6f2eabec7eeca6f5eede40223636f93..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/algebra/detail/for_each.hpp
+++ /dev/null
@@ -1,165 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/algebra/detail/for_each.hpp
-
- [begin_description]
- Default for_each implementations.
- [end_description]
-
- Copyright 2010-2012 Karsten Ahnert
- Copyright 2011 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_ALGEBRA_DETAIL_FOR_EACH_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_ALGEBRA_DETAIL_FOR_EACH_HPP_INCLUDED
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-namespace detail {
-
-
- template< class Iterator1 , class Operation >
- inline void for_each1( Iterator1 first1 , Iterator1 last1 , Operation op )
- {
- for( ; first1 != last1 ; )
- op( *first1++ );
- }
-
-
- template< class Iterator1 , class Iterator2 , class Operation >
- inline void for_each2( Iterator1 first1 , Iterator1 last1 , Iterator2 first2 , Operation op )
- {
- for( ; first1 != last1 ; )
- op( *first1++ , *first2++ );
- }
-
-
- template< class Iterator1 , class Iterator2 , class Iterator3 , class Operation >
- inline void for_each3( Iterator1 first1 , Iterator1 last1 , Iterator2 first2 , Iterator3 first3, Operation op )
- {
- for( ; first1 != last1 ; )
- op( *first1++ , *first2++ , *first3++ );
- }
-
-
- template< class Iterator1 , class Iterator2 , class Iterator3 , class Iterator4 , class Operation >
- inline void for_each4( Iterator1 first1 , Iterator1 last1 , Iterator2 first2 , Iterator3 first3, Iterator4 first4, Operation op )
- {
- for( ; first1 != last1 ; )
- op( *first1++ , *first2++ , *first3++ , *first4++ );
- }
-
-
- template< class Iterator1 , class Iterator2 , class Iterator3 , class Iterator4 , class Iterator5 , class Operation >
- inline void for_each5( Iterator1 first1 , Iterator1 last1 , Iterator2 first2 , Iterator3 first3,
- Iterator4 first4, Iterator5 first5, Operation op )
- {
- for( ; first1 != last1 ; )
- op( *first1++ , *first2++ , *first3++ , *first4++ , *first5++ );
- }
-
-
- template< class Iterator1 , class Iterator2 , class Iterator3 , class Iterator4 , class Iterator5 , class Iterator6 , class Operation >
- inline void for_each6( Iterator1 first1 , Iterator1 last1 , Iterator2 first2 , Iterator3 first3,
- Iterator4 first4, Iterator5 first5, Iterator6 first6 , Operation op )
- {
- for( ; first1 != last1 ; )
- op( *first1++ , *first2++ , *first3++ , *first4++ , *first5++ , *first6++ );
- }
-
-
- template< class Iterator1 , class Iterator2 , class Iterator3 , class Iterator4 , class Iterator5 , class Iterator6 , class Iterator7 , class Operation >
- inline void for_each7( Iterator1 first1 , Iterator1 last1 , Iterator2 first2 , Iterator3 first3,
- Iterator4 first4, Iterator5 first5, Iterator6 first6 , Iterator7 first7 , Operation op )
- {
- for( ; first1 != last1 ; )
- op( *first1++ , *first2++ , *first3++ , *first4++ , *first5++ , *first6++ , *first7++ );
- }
-
- template< class Iterator1 , class Iterator2 , class Iterator3 , class Iterator4 , class Iterator5 , class Iterator6 , class Iterator7 , class Iterator8 , class Operation >
- inline void for_each8( Iterator1 first1 , Iterator1 last1 , Iterator2 first2 , Iterator3 first3,
- Iterator4 first4, Iterator5 first5, Iterator6 first6 , Iterator7 first7 , Iterator8 first8 , Operation op )
- {
- for( ; first1 != last1 ; )
- op( *first1++ , *first2++ , *first3++ , *first4++ , *first5++ , *first6++ , *first7++ , *first8++ );
- }
-
- template< class Iterator1 , class Iterator2 , class Iterator3 , class Iterator4 , class Iterator5 , class Iterator6 , class Iterator7 , class Iterator8 , class Iterator9 , class Operation >
- inline void for_each9( Iterator1 first1 , Iterator1 last1 , Iterator2 first2 , Iterator3 first3,
- Iterator4 first4, Iterator5 first5, Iterator6 first6 , Iterator7 first7 , Iterator8 first8 ,
- Iterator9 first9 , Operation op )
- {
- for( ; first1 != last1 ; )
- op( *first1++ , *first2++ , *first3++ , *first4++ , *first5++ , *first6++ , *first7++ , *first8++ , *first9++ );
- }
-
- template< class Iterator1 , class Iterator2 , class Iterator3 , class Iterator4 , class Iterator5 , class Iterator6 , class Iterator7 , class Iterator8 , class Iterator9 , class Iterator10 , class Operation >
- inline void for_each10( Iterator1 first1 , Iterator1 last1 , Iterator2 first2 , Iterator3 first3,
- Iterator4 first4, Iterator5 first5, Iterator6 first6 , Iterator7 first7 , Iterator8 first8 ,
- Iterator9 first9 , Iterator10 first10 , Operation op )
- {
- for( ; first1 != last1 ; )
- op( *first1++ , *first2++ , *first3++ , *first4++ , *first5++ , *first6++ , *first7++ , *first8++ , *first9++ , *first10++ );
- }
-
- template< class Iterator1 , class Iterator2 , class Iterator3 , class Iterator4 , class Iterator5 , class Iterator6 , class Iterator7 , class Iterator8 , class Iterator9 , class Iterator10 , class Iterator11 , class Operation >
- inline void for_each11( Iterator1 first1 , Iterator1 last1 , Iterator2 first2 , Iterator3 first3,
- Iterator4 first4, Iterator5 first5, Iterator6 first6 , Iterator7 first7 , Iterator8 first8 ,
- Iterator9 first9 , Iterator10 first10 , Iterator11 first11 , Operation op )
- {
- for( ; first1 != last1 ; )
- op( *first1++ , *first2++ , *first3++ , *first4++ , *first5++ , *first6++ , *first7++ , *first8++ , *first9++ , *first10++ , *first11++ );
- }
-
- template< class Iterator1 , class Iterator2 , class Iterator3 , class Iterator4 , class Iterator5 , class Iterator6 , class Iterator7 , class Iterator8 , class Iterator9 , class Iterator10 , class Iterator11 , class Iterator12 , class Operation >
- inline void for_each12( Iterator1 first1 , Iterator1 last1 , Iterator2 first2 , Iterator3 first3,
- Iterator4 first4, Iterator5 first5, Iterator6 first6 , Iterator7 first7 , Iterator8 first8 ,
- Iterator9 first9 , Iterator10 first10 , Iterator11 first11 , Iterator12 first12 , Operation op )
- {
- for( ; first1 != last1 ; )
- op( *first1++ , *first2++ , *first3++ , *first4++ , *first5++ , *first6++ , *first7++ , *first8++ , *first9++ , *first10++ , *first11++ , *first12++ );
- }
-
- template< class Iterator1 , class Iterator2 , class Iterator3 , class Iterator4 , class Iterator5 , class Iterator6 , class Iterator7 , class Iterator8 , class Iterator9 , class Iterator10 , class Iterator11 , class Iterator12 , class Iterator13 , class Operation >
- inline void for_each13( Iterator1 first1 , Iterator1 last1 , Iterator2 first2 , Iterator3 first3,
- Iterator4 first4, Iterator5 first5, Iterator6 first6 , Iterator7 first7 , Iterator8 first8 ,
- Iterator9 first9 , Iterator10 first10 , Iterator11 first11 , Iterator12 first12 , Iterator13 first13 , Operation op )
- {
- for( ; first1 != last1 ; )
- op( *first1++ , *first2++ , *first3++ , *first4++ , *first5++ , *first6++ , *first7++ , *first8++ , *first9++ , *first10++ , *first11++ , *first12++ , *first13++ );
- }
-
- template< class Iterator1 , class Iterator2 , class Iterator3 , class Iterator4 , class Iterator5 , class Iterator6 , class Iterator7 , class Iterator8 , class Iterator9 , class Iterator10 , class Iterator11 , class Iterator12 , class Iterator13 , class Iterator14 , class Operation >
- inline void for_each14( Iterator1 first1 , Iterator1 last1 , Iterator2 first2 , Iterator3 first3,
- Iterator4 first4, Iterator5 first5, Iterator6 first6 , Iterator7 first7 , Iterator8 first8 ,
- Iterator9 first9 , Iterator10 first10 , Iterator11 first11 , Iterator12 first12 , Iterator13 first13 ,
- Iterator14 first14 , Operation op )
- {
- for( ; first1 != last1 ; )
- op( *first1++ , *first2++ , *first3++ , *first4++ , *first5++ , *first6++ , *first7++ , *first8++ , *first9++ , *first10++ , *first11++ , *first12++ , *first13++ , *first14++ );
- }
-
- template< class Iterator1 , class Iterator2 , class Iterator3 , class Iterator4 , class Iterator5 , class Iterator6 , class Iterator7 , class Iterator8 , class Iterator9 , class Iterator10 , class Iterator11 , class Iterator12 , class Iterator13 , class Iterator14 , class Iterator15 , class Operation >
- inline void for_each15( Iterator1 first1 , Iterator1 last1 , Iterator2 first2 , Iterator3 first3,
- Iterator4 first4, Iterator5 first5, Iterator6 first6 , Iterator7 first7 , Iterator8 first8 ,
- Iterator9 first9 , Iterator10 first10 , Iterator11 first11 , Iterator12 first12 , Iterator13 first13 ,
- Iterator14 first14 , Iterator15 first15 , Operation op )
- {
- for( ; first1 != last1 ; )
- op( *first1++ , *first2++ , *first3++ , *first4++ , *first5++ , *first6++ , *first7++ , *first8++ , *first9++ , *first10++ , *first11++ , *first12++ , *first13++ , *first14++ , *first15++ );
- }
-
-
-} // detail
-} // odeint
-} // numeric
-} // boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_ALGEBRA_DETAIL_FOR_EACH_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/algebra/detail/macros.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/algebra/detail/macros.hpp
deleted file mode 100644
index 9e18a8a2f0f7c98e5b2400861a88bd29c1fb057f..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/algebra/detail/macros.hpp
+++ /dev/null
@@ -1,43 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/algebra/detail/macros.hpp
-
- [begin_description]
- Some macros for type checking.
- [end_description]
-
- Copyright 2010-2012 Karsten Ahnert
- Copyright 2010 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_ALGEBRA_DETAIL_MACROS_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_ALGEBRA_DETAIL_MACROS_HPP_INCLUDED
-
-
-//type traits aren't working with nvcc
-#ifndef __CUDACC__
-#include <boost/type_traits.hpp>
-#include <boost/static_assert.hpp>
-
-#define BOOST_ODEINT_CHECK_CONTAINER_TYPE( Type1 , Type2 ) \
- BOOST_STATIC_ASSERT(( boost::is_same< typename boost::remove_const< Type1 >::type , Type2 >::value ))
-
-#else
-//empty macro for nvcc
-#define BOOST_ODEINT_CHECK_CONTAINER_TYPE( Type1 , Type2 )
-
-#endif // __CUDACC__
-
-
-
-/*
-#define BOOST_ODEINT_CHECK_OPERATION_ARITY( Operation , Arity ) \
- BOOST_STATIC_ASSERT(( boost::function_traits< Operation >::arity == Arity ))
- */
-
-#endif // BOOST_NUMERIC_ODEINT_ALGEBRA_DETAIL_MACROS_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/algebra/detail/norm_inf.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/algebra/detail/norm_inf.hpp
deleted file mode 100644
index 3d32c99bee8ae5669aab81c4d5ef350f7917688d..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/algebra/detail/norm_inf.hpp
+++ /dev/null
@@ -1,45 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/algebra/detail/norm_inf.hpp
-
- [begin_description]
- Default reduce implementation.
- [end_description]
-
- Copyright 2013 Karsten Ahnert
- Copyright 2013 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_ALGEBRA_DETAIL_NORM_INF_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_ALGEBRA_DETAIL_NORM_INF_HPP_INCLUDED
-
-#include <cmath>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-namespace detail {
-
-template< typename Value , class Iterator1 >
-inline Value norm_inf( Iterator1 first1 , Iterator1 last1 , Value init )
-{
- using std::max;
- using std::abs;
- for( ; first1 != last1 ; )
- init = max( init , abs( *first1++ ) );
- return init;
-}
-
-
-} // detail
-} // odeint
-} // numeric
-} // boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_ALGEBRA_DETAIL_NORM_INF_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/algebra/fusion_algebra.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/algebra/fusion_algebra.hpp
deleted file mode 100644
index 0055e5d4de446297e27cadcc34144316f1ee1924..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/algebra/fusion_algebra.hpp
+++ /dev/null
@@ -1,216 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/algebra/fusion_algebra.hpp
-
- [begin_description]
- Algebra for boost::fusion sequences.
- [end_description]
-
- Copyright 2011-2013 Karsten Ahnert
- Copyright 2011-2013 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_ALGEBRA_FUSION_ALGEBRA_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_ALGEBRA_FUSION_ALGEBRA_HPP_INCLUDED
-
-#include <algorithm>
-
-#include <boost/numeric/odeint/config.hpp>
-
-#include <boost/fusion/container/vector.hpp>
-#include <boost/fusion/algorithm/iteration/for_each.hpp>
-#include <boost/fusion/view/zip_view.hpp>
-#include <boost/fusion/functional/generation/make_fused.hpp>
-#include <boost/fusion/algorithm/iteration/accumulate.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-namespace detail {
-
- template< class Value >
- struct fusion_maximum
- {
- template< class Fac1 , class Fac2 >
- Value operator()( Fac1 t1 , const Fac2 t2 ) const
- {
- using std::abs;
- Value a1 = abs( get_unit_value( t1 ) ) , a2 = abs( get_unit_value( t2 ) );
- return ( a1 < a2 ) ? a2 : a1 ;
- }
-
- typedef Value result_type;
- };
-}
-
-/* specialize this if the fundamental numeric type in your fusion sequence is
- * anything else but double (most likely not)
- */
-template< typename Sequence >
-struct fusion_traits {
- typedef double value_type;
-};
-
-struct fusion_algebra
-{
- template< class S1 , class Op >
- static void for_each1( S1 &s1 , Op op )
- {
- boost::fusion::for_each( s1 , op );
- };
-
-
- template< class S1 , class S2 , class Op >
- static void for_each2( S1 &s1 , S2 &s2 , Op op )
- {
- typedef boost::fusion::vector< S1& , S2& > Sequences;
- Sequences sequences( s1 , s2 );
- boost::fusion::for_each( boost::fusion::zip_view< Sequences >( sequences ) , boost::fusion::make_fused( op ) );
- }
-
-
- template< class S1 , class S2 , class S3 , class Op >
- static void for_each3( S1 &s1 , S2 &s2 , S3 &s3 , Op op )
- {
- typedef boost::fusion::vector< S1& , S2& , S3& > Sequences;
- Sequences sequences( s1 , s2 , s3 );
- boost::fusion::for_each( boost::fusion::zip_view< Sequences >( sequences ) , boost::fusion::make_fused( op ) );
- }
-
- template< class S1 , class S2 , class S3 , class S4 , class Op >
- static void for_each4( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , Op op )
- {
- typedef boost::fusion::vector< S1& , S2& , S3& , S4& > Sequences;
- Sequences sequences( s1 , s2 , s3 , s4 );
- boost::fusion::for_each( boost::fusion::zip_view< Sequences >( sequences ) , boost::fusion::make_fused( op ) );
- }
-
-
- template< class S1 , class S2 , class S3 , class S4 , class S5 , class Op >
- static void for_each5( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , Op op )
- {
- typedef boost::fusion::vector< S1& , S2& , S3& , S4& , S5& > Sequences;
- Sequences sequences( s1 , s2 , s3 , s4 , s5 );
- boost::fusion::for_each( boost::fusion::zip_view< Sequences >( sequences ) , boost::fusion::make_fused( op ) );
- }
-
-
- template< class S1 , class S2 , class S3 , class S4 , class S5 , class S6 , class Op >
- static void for_each6( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , Op op )
- {
- typedef boost::fusion::vector< S1& , S2& , S3& , S4& , S5& , S6& > Sequences;
- Sequences sequences( s1 , s2 , s3 , s4 , s5 , s6 );
- boost::fusion::for_each( boost::fusion::zip_view< Sequences >( sequences ) , boost::fusion::make_fused( op ) );
- }
-
-
- template< class S1 , class S2 , class S3 , class S4 , class S5 , class S6 , class S7 , class Op >
- static void for_each7( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , Op op )
- {
- typedef boost::fusion::vector< S1& , S2& , S3& , S4& , S5& , S6& , S7& > Sequences;
- Sequences sequences( s1 , s2 , s3 , s4 , s5 , s6 , s7 );
- boost::fusion::for_each( boost::fusion::zip_view< Sequences >( sequences ) , boost::fusion::make_fused( op ) );
- }
-
-
- template< class S1 , class S2 , class S3 , class S4 , class S5 , class S6 , class S7 , class S8 , class Op >
- static void for_each8( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , S8 &s8 , Op op )
- {
- BOOST_STATIC_ASSERT_MSG( BOOST_FUSION_INVOKE_MAX_ARITY >= 8 , "Macro Parameter BOOST_FUSION_INVOKE_MAX_ARITY to small!" );
- typedef boost::fusion::vector< S1& , S2& , S3& , S4& , S5& , S6& , S7& , S8& > Sequences;
- Sequences sequences( s1 , s2 , s3 , s4 , s5 , s6 , s7 , s8 );
- boost::fusion::for_each( boost::fusion::zip_view< Sequences >( sequences ) , boost::fusion::make_fused( op ) );
- }
-
- template< class S1 , class S2 , class S3 , class S4 , class S5 , class S6 , class S7 , class S8 , class S9 , class Op >
- static void for_each9( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , S8 &s8 , S9 &s9 , Op op )
- {
- BOOST_STATIC_ASSERT_MSG( BOOST_FUSION_INVOKE_MAX_ARITY >= 9 , "Macro Parameter BOOST_FUSION_INVOKE_MAX_ARITY to small!" );
- typedef boost::fusion::vector< S1& , S2& , S3& , S4& , S5& , S6& , S7& , S8& , S9& > Sequences;
- Sequences sequences( s1 , s2 , s3 , s4 , s5 , s6 , s7 , s8 , s9 );
- boost::fusion::for_each( boost::fusion::zip_view< Sequences >( sequences ) , boost::fusion::make_fused( op ) );
- }
-
- template< class S1 , class S2 , class S3 , class S4 , class S5 , class S6 , class S7 , class S8 , class S9 , class S10 , class Op >
- static void for_each10( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , S8 &s8 , S9 &s9 , S10 &s10 , Op op )
- {
- BOOST_STATIC_ASSERT_MSG( BOOST_FUSION_INVOKE_MAX_ARITY >= 10 , "Macro Parameter BOOST_FUSION_INVOKE_MAX_ARITY to small!" );
- typedef boost::fusion::vector< S1& , S2& , S3& , S4& , S5& , S6& , S7& , S8& , S9& , S10& > Sequences;
- Sequences sequences( s1 , s2 , s3 , s4 , s5 , s6 , s7 , s8 , s9 , s10 );
- boost::fusion::for_each( boost::fusion::zip_view< Sequences >( sequences ) , boost::fusion::make_fused( op ) );
- }
-
- template< class S1 , class S2 , class S3 , class S4 , class S5 , class S6 , class S7 , class S8 , class S9 , class S10 , class S11 , class Op >
- static void for_each11( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , S8 &s8 , S9 &s9 , S10 &s10 , S11 &s11 , Op op )
- {
- BOOST_STATIC_ASSERT_MSG( BOOST_FUSION_INVOKE_MAX_ARITY >= 11 , "Macro Parameter BOOST_FUSION_INVOKE_MAX_ARITY to small!" );
- BOOST_STATIC_ASSERT_MSG( BOOST_RESULT_OF_NUM_ARGS >= 11 , "Macro Parameter BOOST_RESULT_OF_NUM_ARGS to small!" );
- typedef boost::fusion::vector< S1& , S2& , S3& , S4& , S5& , S6& , S7& , S8& , S9& , S10& , S11& > Sequences;
- Sequences sequences( s1 , s2 , s3 , s4 , s5 , s6 , s7 , s8 , s9 , s10 , s11 );
- boost::fusion::for_each( boost::fusion::zip_view< Sequences >( sequences ) , boost::fusion::make_fused( op ) );
- }
-
- template< class S1 , class S2 , class S3 , class S4 , class S5 , class S6 , class S7 , class S8 , class S9 , class S10 , class S11 , class S12 , class Op >
- static void for_each12( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , S8 &s8 , S9 &s9 , S10 &s10 , S11 &s11 , S12 &s12 , Op op )
- {
- BOOST_STATIC_ASSERT_MSG( BOOST_FUSION_INVOKE_MAX_ARITY >= 12 , "Macro Parameter BOOST_FUSION_INVOKE_MAX_ARITY to small!" );
- BOOST_STATIC_ASSERT_MSG( BOOST_RESULT_OF_NUM_ARGS >= 12 , "Macro Parameter BOOST_RESULT_OF_NUM_ARGS to small!" );
- typedef boost::fusion::vector< S1& , S2& , S3& , S4& , S5& , S6& , S7& , S8& , S9& , S10& , S11& , S12& > Sequences;
- Sequences sequences( s1 , s2 , s3 , s4 , s5 , s6 , s7 , s8 , s9 , s10 , s11 , s12 );
- boost::fusion::for_each( boost::fusion::zip_view< Sequences >( sequences ) , boost::fusion::make_fused( op ) );
- }
-
- template< class S1 , class S2 , class S3 , class S4 , class S5 , class S6 , class S7 , class S8 , class S9 , class S10 , class S11 , class S12 , class S13 , class Op >
- static void for_each13( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , S8 &s8 , S9 &s9 , S10 &s10 , S11 &s11 , S12 &s12 , S13 &s13 , Op op )
- {
- BOOST_STATIC_ASSERT_MSG( BOOST_FUSION_INVOKE_MAX_ARITY >= 13 , "Macro Parameter BOOST_FUSION_INVOKE_MAX_ARITY to small!" );
- BOOST_STATIC_ASSERT_MSG( BOOST_RESULT_OF_NUM_ARGS >= 13 , "Macro Parameter BOOST_RESULT_OF_NUM_ARGS to small!" );
- typedef boost::fusion::vector< S1& , S2& , S3& , S4& , S5& , S6& , S7& , S8& , S9& , S10& , S11& , S12& , S13& > Sequences;
- Sequences sequences( s1 , s2 , s3 , s4 , s5 , s6 , s7 , s8 , s9 , s10 , s11 , s12 , s13 );
- boost::fusion::for_each( boost::fusion::zip_view< Sequences >( sequences ) , boost::fusion::make_fused( op ) );
- }
-
- template< class S1 , class S2 , class S3 , class S4 , class S5 , class S6 , class S7 , class S8 , class S9 , class S10 , class S11 , class S12 , class S13 , class S14 , class Op >
- static void for_each14( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , S8 &s8 , S9 &s9 , S10 &s10 , S11 &s11 , S12 &s12 , S13 &s13 , S14 &s14 , Op op )
- {
- BOOST_STATIC_ASSERT_MSG( BOOST_FUSION_INVOKE_MAX_ARITY >= 14 , "Macro Parameter BOOST_FUSION_INVOKE_MAX_ARITY to small!" );
- BOOST_STATIC_ASSERT_MSG( BOOST_RESULT_OF_NUM_ARGS >= 14 , "Macro Parameter BOOST_RESULT_OF_NUM_ARGS to small!" );
- typedef boost::fusion::vector< S1& , S2& , S3& , S4& , S5& , S6& , S7& , S8& , S9& , S10& , S11& , S12& , S13& , S14& > Sequences;
- Sequences sequences( s1 , s2 , s3 , s4 , s5 , s6 , s7 , s8 , s9 , s10 , s11 , s12 , s13 , s14 );
- boost::fusion::for_each( boost::fusion::zip_view< Sequences >( sequences ) , boost::fusion::make_fused( op ) );
- }
-
- template< class S1 , class S2 , class S3 , class S4 , class S5 , class S6 , class S7 , class S8 , class S9 , class S10 , class S11 , class S12 , class S13 , class S14 , class S15 , class Op >
- static void for_each15( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , S8 &s8 , S9 &s9 , S10 &s10 , S11 &s11 , S12 &s12 , S13 &s13 , S14 &s14 , S15 &s15 , Op op )
- {
- BOOST_STATIC_ASSERT_MSG( BOOST_FUSION_INVOKE_MAX_ARITY >= 15 , "Macro Parameter BOOST_FUSION_INVOKE_MAX_ARITY to small!" );
- BOOST_STATIC_ASSERT_MSG( BOOST_RESULT_OF_NUM_ARGS >= 15 , "Macro Parameter BOOST_RESULT_OF_NUM_ARGS to small!" );
- typedef boost::fusion::vector< S1& , S2& , S3& , S4& , S5& , S6& , S7& , S8& , S9& , S10& , S11& , S12& , S13& , S14& , S15& > Sequences;
- Sequences sequences( s1 , s2 , s3 , s4 , s5 , s6 , s7 , s8 , s9 , s10 , s11 , s12 , s13 , s14 , s15 );
- boost::fusion::for_each( boost::fusion::zip_view< Sequences >( sequences ) , boost::fusion::make_fused( op ) );
- }
-
- template< class S >
- static typename fusion_traits< S >::value_type norm_inf( const S &s )
- {
- typedef typename fusion_traits< S >::value_type value_type;
- return boost::fusion::accumulate( s , static_cast<value_type>(0) ,
- detail::fusion_maximum<value_type>() );
- }
-
-};
-
-
-
-} // odeint
-} // numeric
-} // boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_ALGEBRA_FUSION_ALGEBRA_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/algebra/fusion_algebra_dispatcher.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/algebra/fusion_algebra_dispatcher.hpp
deleted file mode 100644
index 4bfc5c26ba76f5770377fec5b3decd97d5ba3a26..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/algebra/fusion_algebra_dispatcher.hpp
+++ /dev/null
@@ -1,48 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/algebra/fusion_algebra_dispatcher.hpp
-
- [begin_description]
- tba.
- [end_description]
-
- Copyright 2013 Karsten Ahnert
- Copyright 2013 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
-*/
-
-
-#ifndef BOOST_NUMERIC_ODEINT_ALGEBRA_FUSION_ALGEBRA_DISPATCHER_HPP_DEFINED
-#define BOOST_NUMERIC_ODEINT_ALGEBRA_FUSION_ALGEBRA_DISPATCHER_HPP_DEFINED
-
-#include <boost/numeric/odeint/algebra/fusion_algebra.hpp>
-#include <boost/numeric/odeint/algebra/algebra_dispatcher.hpp>
-
-#include <boost/utility/enable_if.hpp>
-#include <boost/fusion/include/is_sequence.hpp>
-
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-// specialization for fusion sequences
-template< class FusionSequence >
-struct algebra_dispatcher_sfinae< FusionSequence ,
- typename boost::enable_if<
- typename boost::fusion::traits::is_sequence< FusionSequence >::type >::type >
-{
- typedef fusion_algebra algebra_type;
-};
-
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_ALGEBRA_FUSION_ALGEBRA_DISPATCHER_HPP_DEFINED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/algebra/multi_array_algebra.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/algebra/multi_array_algebra.hpp
deleted file mode 100644
index 1f8c41b2eac1e3e43c082240c491b90cd7ff077a..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/algebra/multi_array_algebra.hpp
+++ /dev/null
@@ -1,148 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/algebra/multi_array_algebra.hpp
-
- [begin_description]
- tba.
- [end_description]
-
- Copyright 2009-2012 Karsten Ahnert
- Copyright 2009-2012 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
-*/
-
-
-#ifndef BOOST_NUMERIC_ODEINT_ALGEBRA_MULTI_ARRAY_ALGEBRA_HPP_DEFINED
-#define BOOST_NUMERIC_ODEINT_ALGEBRA_MULTI_ARRAY_ALGEBRA_HPP_DEFINED
-
-
-#include <boost/numeric/odeint/algebra/detail/for_each.hpp>
-#include <boost/numeric/odeint/algebra/detail/norm_inf.hpp>
-#include <boost/numeric/odeint/algebra/norm_result_type.hpp>
-#include <boost/numeric/odeint/algebra/algebra_dispatcher.hpp>
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-// not ready
-struct multi_array_algebra
-{
- template< class S1 , class Op >
- static void for_each1( S1 &s1 , Op op )
- {
- detail::for_each1( s1.data() , s1.data() + s1.num_elements() , op );
- }
-
- template< class S1 , class S2 , class Op >
- static void for_each2( S1 &s1 , S2 &s2 , Op op )
- {
- detail::for_each2( s1.data() , s1.data() + s1.num_elements() , s2.data() , op );
- }
-
- template< class S1 , class S2 , class S3 , class Op >
- static void for_each3( S1 &s1 , S2 &s2 , S3 &s3 , Op op )
- {
- detail::for_each3( s1.data() , s1.data() + s1.num_elements() , s2.data() , s3.data() , op );
- }
-
- template< class S1 , class S2 , class S3 , class S4 , class Op >
- static void for_each4( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , Op op )
- {
- detail::for_each4( s1.data() , s1.data() + s1.num_elements() , s2.data() , s3.data() , s4.data() , op );
- }
-
- template< class S1 , class S2 , class S3 , class S4 , class S5 , class Op >
- static void for_each5( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , Op op )
- {
- detail::for_each5( s1.data() , s1.data() + s1.num_elements() , s2.data() , s3.data() , s4.data() , s5.data() , op );
- }
-
- template< class S1 , class S2 , class S3 , class S4 , class S5 , class S6 , class Op >
- static void for_each6( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , Op op )
- {
- detail::for_each6( s1.data() , s1.data() + s1.num_elements() , s2.data() , s3.data() , s4.data() , s5.data() , s6.data() , op );
- }
-
- template< class S1 , class S2 , class S3 , class S4 , class S5 , class S6 ,class S7 , class Op >
- static void for_each7( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , Op op )
- {
- detail::for_each7( s1.data() , s1.data() + s1.num_elements() , s2.data() , s3.data() , s4.data() , s5.data() , s6.data() , s7.data() , op );
- }
-
- template< class S1 , class S2 , class S3 , class S4 , class S5 , class S6 ,class S7 , class S8 , class Op >
- static void for_each8( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , S8 &s8 , Op op )
- {
- detail::for_each8( s1.data() , s1.data() + s1.num_elements() , s2.data() , s3.data() , s4.data() , s5.data() , s6.data() , s7.data() , s8.data() , op );
- }
-
- template< class S1 , class S2 , class S3 , class S4 , class S5 , class S6 ,class S7 , class S8 , class S9 , class Op >
- static void for_each9( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , S8 &s8 , S9 &s9 , Op op )
- {
- detail::for_each9( s1.data() , s1.data() + s1.num_elements() , s2.data() , s3.data() , s4.data() , s5.data() , s6.data() , s7.data() , s8.data() , s9.data() , op );
- }
-
- template< class S1 , class S2 , class S3 , class S4 , class S5 , class S6 ,class S7 , class S8 , class S9 , class S10 , class Op >
- static void for_each10( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , S8 &s8 , S9 &s9 , S10 &s10 , Op op )
- {
- detail::for_each10( s1.data() , s1.data() + s1.num_elements() , s2.data() , s3.data() , s4.data() , s5.data() , s6.data() , s7.data() , s8.data() , s9.data() , s10.data() , op );
- }
-
- template< class S1 , class S2 , class S3 , class S4 , class S5 , class S6 ,class S7 , class S8 , class S9 , class S10 , class S11 , class Op >
- static void for_each11( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , S8 &s8 , S9 &s9 , S10 &s10 , S11 &s11 , Op op )
- {
- detail::for_each11( s1.data() , s1.data() + s1.num_elements() , s2.data() , s3.data() , s4.data() , s5.data() , s6.data() , s7.data() , s8.data() , s9.data() , s10.data() , s11.data() , op );
- }
-
- template< class S1 , class S2 , class S3 , class S4 , class S5 , class S6 ,class S7 , class S8 , class S9 , class S10 , class S11 , class S12 , class Op >
- static void for_each12( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , S8 &s8 , S9 &s9 , S10 &s10 , S11 &s11 , S12 &s12 , Op op )
- {
- detail::for_each12( s1.data() , s1.data() + s1.num_elements() , s2.data() , s3.data() , s4.data() , s5.data() , s6.data() , s7.data() , s8.data() , s9.data() , s10.data() , s11.data() , s12.data() , op );
- }
-
- template< class S1 , class S2 , class S3 , class S4 , class S5 , class S6 ,class S7 , class S8 , class S9 , class S10 , class S11 , class S12 , class S13 , class Op >
- static void for_each13( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , S8 &s8 , S9 &s9 , S10 &s10 , S11 &s11 , S12 &s12 , S13 &s13 , Op op )
- {
- detail::for_each13( s1.data() , s1.data() + s1.num_elements() , s2.data() , s3.data() , s4.data() , s5.data() , s6.data() , s7.data() , s8.data() , s9.data() , s10.data() , s11.data() , s12.data() , s13.data() , op );
- }
-
- template< class S1 , class S2 , class S3 , class S4 , class S5 , class S6 ,class S7 , class S8 , class S9 , class S10 , class S11 , class S12 , class S13 , class S14 , class Op >
- static void for_each14( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , S8 &s8 , S9 &s9 , S10 &s10 , S11 &s11 , S12 &s12 , S13 &s13 , S14 &s14 , Op op )
- {
- detail::for_each14( s1.data() , s1.data() + s1.num_elements() , s2.data() , s3.data() , s4.data() , s5.data() , s6.data() , s7.data() , s8.data() , s9.data() , s10.data() , s11.data() , s12.data() , s13.data() , s14.data() , op );
- }
-
- template< class S1 , class S2 , class S3 , class S4 , class S5 , class S6 ,class S7 , class S8 , class S9 , class S10 , class S11 , class S12 , class S13 , class S14 , class S15 , class Op >
- static void for_each15( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , S8 &s8 , S9 &s9 , S10 &s10 , S11 &s11 , S12 &s12 , S13 &s13 , S14 &s14 , S15 &s15 , Op op )
- {
- detail::for_each15( s1.data() , s1.data() + s1.num_elements() , s2.data() , s3.data() , s4.data() , s5.data() , s6.data() , s7.data() , s8.data() , s9.data() , s10.data() , s11.data() , s12.data() , s13.data() , s14.data() , s15.data() , op );
- }
-
- template< typename S >
- static typename norm_result_type<S>::type norm_inf( const S &s )
- {
- return detail::norm_inf( s.data() , s.data() + s.num_elements() , static_cast< typename norm_result_type<S>::type >( 0 ) );
- }
-};
-
-// template< class T , size_t N >
-// struct algebra_dispatcher< boost::array< T , N > >
-// {
-// typedef array_algebra algebra_type;
-// };
-
-
-
-
-
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_ALGEBRA_MULTI_ARRAY_ALGEBRA_HPP_DEFINED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/algebra/norm_result_type.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/algebra/norm_result_type.hpp
deleted file mode 100644
index 0e99e8fcc23a31472f38b42df3edd585e2428aa9..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/algebra/norm_result_type.hpp
+++ /dev/null
@@ -1,33 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/algebra/norm_result_type.hpp
-
- [begin_description]
- Calculates the type of the norm_inf operation for container types
- [end_description]
-
- Copyright 2013 Karsten Ahnert
- Copyright 2013 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-#ifndef BOOST_NUMERIC_ODEINT_ALGEBRA_NORM_RESULT_TYPE_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_ALGEBRA_NORM_RESULT_TYPE_HPP_INCLUDED
-
-#include <boost/numeric/odeint/algebra/detail/extract_value_type.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-template< typename S , typename Enabler = void >
-struct norm_result_type {
- typedef typename detail::extract_value_type< S >::type type;
-};
-
-} } }
-
-#endif
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/algebra/operations_dispatcher.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/algebra/operations_dispatcher.hpp
deleted file mode 100644
index 5a0b21bb81a1d9f13bd516af9ad8a77cbdb3e4f6..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/algebra/operations_dispatcher.hpp
+++ /dev/null
@@ -1,41 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/algebra/operations_dispatcher.hpp
-
- [begin_description]
- Operations dispatcher to automatically chose suitable operations.
- [end_description]
-
- Copyright 2013 Karsten Ahnert
- Copyright 2013 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-#ifndef BOOST_NUMERIC_ODEINT_ALGEBRA_OPERATIONS_DISPATCHER_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_ALGEBRA_OPERATIONS_DISPATCHER_HPP_INCLUDED
-
-#include <boost/numeric/odeint/algebra/default_operations.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-template< class StateType , class Enabler = void >
-struct operations_dispatcher_sfinae
-{
- typedef default_operations operations_type;
-};
-
-template< class StateType >
-struct operations_dispatcher : operations_dispatcher_sfinae< StateType > {};
-
-// no further specializations required
-
-}
-}
-}
-
-#endif
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/algebra/range_algebra.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/algebra/range_algebra.hpp
deleted file mode 100644
index 3d7695c8127802ba2db00576a76e23a1cf824a23..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/algebra/range_algebra.hpp
+++ /dev/null
@@ -1,142 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/algebra/range_algebra.hpp
-
- [begin_description]
- Default algebra, which works with the most state types, like vector< double >, boost::array< double >, boost::range.
- Internally is uses boost::range to obtain the begin and end iterator of the according sequence.
- [end_description]
-
- Copyright 2010-2013 Karsten Ahnert
- Copyright 2010-2013 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_ALGEBRA_RANGE_ALGEBRA_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_ALGEBRA_RANGE_ALGEBRA_HPP_INCLUDED
-
-#include <boost/range.hpp>
-#include <boost/mpl/size_t.hpp>
-
-#include <boost/numeric/odeint/algebra/detail/macros.hpp>
-#include <boost/numeric/odeint/algebra/detail/for_each.hpp>
-#include <boost/numeric/odeint/algebra/detail/norm_inf.hpp>
-#include <boost/numeric/odeint/algebra/norm_result_type.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-struct range_algebra
-{
- template< class S1 , class Op >
- static void for_each1( S1 &s1 , Op op )
- {
- detail::for_each1( boost::begin( s1 ) , boost::end( s1 ) ,
- op );
- }
-
- template< class S1 , class S2 , class Op >
- static void for_each2( S1 &s1 , S2 &s2 , Op op )
- {
- detail::for_each2( boost::begin( s1 ) , boost::end( s1 ) ,
- boost::begin( s2 ) , op );
- }
-
- template< class S1 , class S2 , class S3 , class Op >
- static void for_each3( S1 &s1 , S2 &s2 , S3 &s3 , Op op )
- {
- detail::for_each3( boost::begin( s1 ) , boost::end( s1 ) , boost::begin( s2 ) , boost::begin( s3 ) , op );
- }
-
- template< class S1 , class S2 , class S3 , class S4 , class Op >
- static void for_each4( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , Op op )
- {
- detail::for_each4( boost::begin( s1 ) , boost::end( s1 ) , boost::begin( s2 ) , boost::begin( s3 ) , boost::begin( s4 ) , op );
- }
-
- template< class S1 , class S2 , class S3 , class S4 , class S5 , class Op >
- static void for_each5( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , Op op )
- {
- detail::for_each5( boost::begin( s1 ) , boost::end( s1 ) , boost::begin( s2 ) , boost::begin( s3 ) , boost::begin( s4 ) , boost::begin( s5 ) , op );
- }
-
- template< class S1 , class S2 , class S3 , class S4 , class S5 , class S6 , class Op >
- static void for_each6( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , Op op )
- {
- detail::for_each6( boost::begin( s1 ) , boost::end( s1 ) , boost::begin( s2 ) , boost::begin( s3 ) , boost::begin( s4 ) , boost::begin( s5 ) , boost::begin( s6 ) , op );
- }
-
- template< class S1 , class S2 , class S3 , class S4 , class S5 , class S6 ,class S7 , class Op >
- static void for_each7( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , Op op )
- {
- detail::for_each7( boost::begin( s1 ) , boost::end( s1 ) , boost::begin( s2 ) , boost::begin( s3 ) , boost::begin( s4 ) , boost::begin( s5 ) , boost::begin( s6 ) , boost::begin( s7 ) , op );
- }
-
- template< class S1 , class S2 , class S3 , class S4 , class S5 , class S6 ,class S7 , class S8 , class Op >
- static void for_each8( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , S8 &s8 , Op op )
- {
- detail::for_each8( boost::begin( s1 ) , boost::end( s1 ) , boost::begin( s2 ) , boost::begin( s3 ) , boost::begin( s4 ) , boost::begin( s5 ) , boost::begin( s6 ) , boost::begin( s7 ) , boost::begin( s8 ) , op );
- }
-
- template< class S1 , class S2 , class S3 , class S4 , class S5 , class S6 ,class S7 , class S8 , class S9 , class Op >
- static void for_each9( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , S8 &s8 , S9 &s9 , Op op )
- {
- detail::for_each9( boost::begin( s1 ) , boost::end( s1 ) , boost::begin( s2 ) , boost::begin( s3 ) , boost::begin( s4 ) , boost::begin( s5 ) , boost::begin( s6 ) , boost::begin( s7 ) , boost::begin( s8 ) , boost::begin( s9 ) , op );
- }
-
- template< class S1 , class S2 , class S3 , class S4 , class S5 , class S6 ,class S7 , class S8 , class S9 , class S10 , class Op >
- static void for_each10( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , S8 &s8 , S9 &s9 , S10 &s10 , Op op )
- {
- detail::for_each10( boost::begin( s1 ) , boost::end( s1 ) , boost::begin( s2 ) , boost::begin( s3 ) , boost::begin( s4 ) , boost::begin( s5 ) , boost::begin( s6 ) , boost::begin( s7 ) , boost::begin( s8 ) , boost::begin( s9 ) , boost::begin( s10 ) , op );
- }
-
- template< class S1 , class S2 , class S3 , class S4 , class S5 , class S6 ,class S7 , class S8 , class S9 , class S10 , class S11 , class Op >
- static void for_each11( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , S8 &s8 , S9 &s9 , S10 &s10 , S11 &s11 , Op op )
- {
- detail::for_each11( boost::begin( s1 ) , boost::end( s1 ) , boost::begin( s2 ) , boost::begin( s3 ) , boost::begin( s4 ) , boost::begin( s5 ) , boost::begin( s6 ) , boost::begin( s7 ) , boost::begin( s8 ) , boost::begin( s9 ) , boost::begin( s10 ) , boost::begin( s11 ) , op );
- }
-
- template< class S1 , class S2 , class S3 , class S4 , class S5 , class S6 ,class S7 , class S8 , class S9 , class S10 , class S11 , class S12 , class Op >
- static void for_each12( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , S8 &s8 , S9 &s9 , S10 &s10 , S11 &s11 , S12 &s12 , Op op )
- {
- detail::for_each12( boost::begin( s1 ) , boost::end( s1 ) , boost::begin( s2 ) , boost::begin( s3 ) , boost::begin( s4 ) , boost::begin( s5 ) , boost::begin( s6 ) , boost::begin( s7 ) , boost::begin( s8 ) , boost::begin( s9 ) , boost::begin( s10 ) , boost::begin( s11 ) , boost::begin( s12 ) , op );
- }
-
- template< class S1 , class S2 , class S3 , class S4 , class S5 , class S6 ,class S7 , class S8 , class S9 , class S10 , class S11 , class S12 , class S13 , class Op >
- static void for_each13( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , S8 &s8 , S9 &s9 , S10 &s10 , S11 &s11 , S12 &s12 , S13 &s13 , Op op )
- {
- detail::for_each13( boost::begin( s1 ) , boost::end( s1 ) , boost::begin( s2 ) , boost::begin( s3 ) , boost::begin( s4 ) , boost::begin( s5 ) , boost::begin( s6 ) , boost::begin( s7 ) , boost::begin( s8 ) , boost::begin( s9 ) , boost::begin( s10 ) , boost::begin( s11 ) , boost::begin( s12 ) , boost::begin( s13 ) , op );
- }
-
- template< class S1 , class S2 , class S3 , class S4 , class S5 , class S6 ,class S7 , class S8 , class S9 , class S10 , class S11 , class S12 , class S13 , class S14 , class Op >
- static void for_each14( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , S8 &s8 , S9 &s9 , S10 &s10 , S11 &s11 , S12 &s12 , S13 &s13 , S14 &s14 , Op op )
- {
- detail::for_each14( boost::begin( s1 ) , boost::end( s1 ) , boost::begin( s2 ) , boost::begin( s3 ) , boost::begin( s4 ) , boost::begin( s5 ) , boost::begin( s6 ) , boost::begin( s7 ) , boost::begin( s8 ) , boost::begin( s9 ) , boost::begin( s10 ) , boost::begin( s11 ) , boost::begin( s12 ) , boost::begin( s13 ) , boost::begin( s14 ) , op );
- }
-
- template< class S1 , class S2 , class S3 , class S4 , class S5 , class S6 ,class S7 , class S8 , class S9 , class S10 , class S11 , class S12 , class S13 , class S14 , class S15 , class Op >
- static void for_each15( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , S8 &s8 , S9 &s9 , S10 &s10 , S11 &s11 , S12 &s12 , S13 &s13 , S14 &s14 , S15 &s15 , Op op )
- {
- detail::for_each15( boost::begin( s1 ) , boost::end( s1 ) , boost::begin( s2 ) , boost::begin( s3 ) , boost::begin( s4 ) , boost::begin( s5 ) , boost::begin( s6 ) , boost::begin( s7 ) , boost::begin( s8 ) , boost::begin( s9 ) , boost::begin( s10 ) , boost::begin( s11 ) , boost::begin( s12 ) , boost::begin( s13 ) , boost::begin( s14 ) , boost::begin( s15 ) , op );
- }
-
- template< typename S >
- static typename norm_result_type<S>::type norm_inf( const S &s )
- {
- return detail::norm_inf( boost::begin( s ) , boost::end( s ) ,
- static_cast< typename norm_result_type<S>::type >( 0 ) );
- }
-
-};
-
-} // odeint
-} // numeric
-} // boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_ALGEBRA_RANGE_ALGEBRA_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/algebra/vector_space_algebra.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/algebra/vector_space_algebra.hpp
deleted file mode 100644
index 17ff007eef09da1457550beae911b5a0272c42d7..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/algebra/vector_space_algebra.hpp
+++ /dev/null
@@ -1,178 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/algebra/vector_space_algebra.hpp
-
- [begin_description]
- An algebra for types which have vector space semantics, hence types on which the operators +,-,* are well defined.
- [end_description]
-
- Copyright 2010-2012 Karsten Ahnert
- Copyright 2010-2013 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_ALGEBRA_VECTOR_SPACE_ALGEBRA_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_ALGEBRA_VECTOR_SPACE_ALGEBRA_HPP_INCLUDED
-
-#include <complex>
-
-#include <boost/type_traits/remove_reference.hpp>
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-/*
- * This class template has to be overload in order to call vector_space_algebra::norm_inf
- */
-template< class State > struct vector_space_norm_inf;
-
-/*
- * Example: instantiation for sole doubles and complex
- */
-template<>
-struct vector_space_norm_inf< double >
-{
- typedef double result_type;
- double operator()( double x ) const
- {
- using std::abs;
- return abs(x);
- }
-};
-
-template<>
-struct vector_space_norm_inf< float >
-{
- typedef float result_type;
- result_type operator()( float x ) const
- {
- using std::abs;
- return abs(x);
- }
-};
-
-template< typename T >
-struct vector_space_norm_inf< std::complex<T> >
-{
- typedef T result_type;
- result_type operator()( std::complex<T> x ) const
- {
- using std::abs;
- return abs( x );
- }
-};
-
-struct vector_space_algebra
-{
- template< class S1 , class Op >
- static void for_each1( S1 &s1 , Op op )
- {
- // ToDo : build checks, that the +-*/ operators are well defined
- op( s1 );
- }
-
- template< class S1 , class S2 , class Op >
- static void for_each2( S1 &s1 , S2 &s2 , Op op )
- {
- op( s1 , s2 );
- }
-
- template< class S1 , class S2 , class S3 , class Op >
- static void for_each3( S1 &s1 , S2 &s2 , S3 &s3 , Op op )
- {
- op( s1 , s2 , s3 );
- }
-
- template< class S1 , class S2 , class S3 , class S4 , class Op >
- static void for_each4( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , Op op )
- {
- op( s1 , s2 , s3 , s4 );
- }
-
- template< class S1 , class S2 , class S3 , class S4 , class S5 , class Op >
- static void for_each5( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , Op op )
- {
- op( s1 , s2 , s3 , s4 , s5 );
- }
-
- template< class S1 , class S2 , class S3 , class S4 , class S5 , class S6 , class Op >
- static void for_each6( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , Op op )
- {
- op( s1 , s2 , s3 , s4 , s5 , s6 );
- }
-
- template< class S1 , class S2 , class S3 , class S4 , class S5 , class S6 ,class S7 , class Op >
- static void for_each7( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , Op op )
- {
- op( s1 , s2 , s3 , s4 , s5 , s6 , s7 );
- }
-
- template< class S1 , class S2 , class S3 , class S4 , class S5 , class S6 ,class S7 , class S8 , class Op >
- static void for_each8( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , S8 &s8 , Op op )
- {
- op( s1 , s2 , s3 , s4 , s5 , s6 , s7 , s8 );
- }
-
- template< class S1 , class S2 , class S3 , class S4 , class S5 , class S6 ,class S7 , class S8 , class S9 , class Op >
- static void for_each9( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , S8 &s8 , S9 &s9 , Op op )
- {
- op( s1 , s2 , s3 , s4 , s5 , s6 , s7 , s8 , s9 );
- }
-
- template< class S1 , class S2 , class S3 , class S4 , class S5 , class S6 ,class S7 , class S8 , class S9 , class S10 , class Op >
- static void for_each10( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , S8 &s8 , S9 &s9 , S10 &s10 , Op op )
- {
- op( s1 , s2 , s3 , s4 , s5 , s6 , s7 , s8 , s9 , s10 );
- }
-
- template< class S1 , class S2 , class S3 , class S4 , class S5 , class S6 ,class S7 , class S8 , class S9 , class S10 , class S11 , class Op >
- static void for_each11( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , S8 &s8 , S9 &s9 , S10 &s10 , S11 &s11 , Op op )
- {
- op( s1 , s2 , s3 , s4 , s5 , s6 , s7 , s8 , s9 , s10 , s11 );
- }
-
- template< class S1 , class S2 , class S3 , class S4 , class S5 , class S6 ,class S7 , class S8 , class S9 , class S10 , class S11 , class S12 , class Op >
- static void for_each12( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , S8 &s8 , S9 &s9 , S10 &s10 , S11 &s11 , S12 &s12 , Op op )
- {
- op( s1 , s2 , s3 , s4 , s5 , s6 , s7 , s8 , s9 , s10 , s11 , s12 );
- }
-
- template< class S1 , class S2 , class S3 , class S4 , class S5 , class S6 ,class S7 , class S8 , class S9 , class S10 , class S11 , class S12 , class S13 , class Op >
- static void for_each13( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , S8 &s8 , S9 &s9 , S10 &s10 , S11 &s11 , S12 &s12 , S13 &s13 , Op op )
- {
- op( s1 , s2 , s3 , s4 , s5 , s6 , s7 , s8 , s9 , s10 , s11 , s12 , s13 );
- }
-
- template< class S1 , class S2 , class S3 , class S4 , class S5 , class S6 ,class S7 , class S8 , class S9 , class S10 , class S11 , class S12 , class S13 , class S14 , class Op >
- static void for_each14( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , S8 &s8 , S9 &s9 , S10 &s10 , S11 &s11 , S12 &s12 , S13 &s13 , S14 &s14 , Op op )
- {
- op( s1 , s2 , s3 , s4 , s5 , s6 , s7 , s8 , s9 , s10 , s11 , s12 , s13 , s14 );
- }
-
- template< class S1 , class S2 , class S3 , class S4 , class S5 , class S6 ,class S7 , class S8 , class S9 , class S10 , class S11 , class S12 , class S13 , class S14 , class S15 , class Op >
- static void for_each15( S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , S8 &s8 , S9 &s9 , S10 &s10 , S11 &s11 , S12 &s12 , S13 &s13 , S14 &s14 , S15 &s15 , Op op )
- {
- op( s1 , s2 , s3 , s4 , s5 , s6 , s7 , s8 , s9 , s10 , s11 , s12 , s13 , s14 , s15 );
- }
-
- template< class S >
- static typename boost::numeric::odeint::vector_space_norm_inf< S >::result_type norm_inf( const S &s )
- {
- boost::numeric::odeint::vector_space_norm_inf< S > n;
- return n( s );
- }
-};
-
-
-} // odeint
-} // numeric
-} // boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_ALGEBRA_VECTOR_SPACE_ALGEBRA_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/config.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/config.hpp
deleted file mode 100644
index f1915825587a3b0520b678142638b3879cd438c4..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/config.hpp
+++ /dev/null
@@ -1,53 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/config.hpp
-
- [begin_description]
- Sets configurations for odeint and used libraries. Should be included before any other odeint library
- [end_description]
-
- Copyright 2011-2012 Mario Mulansky
- Copyright 2011-2012 Karsten Ahnert
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-#ifndef BOOST_NUMERIC_ODEINT_CONFIG_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_CONFIG_HPP_INCLUDED
-
-
-//increase macro variable to allow rk78 scheme
-#ifndef FUSION_MAX_VECTOR_SIZE
-#define FUSION_MAX_VECTOR_SIZE 15
-#endif
-
-
-/*
- * the following definitions are only required if fusion vectors are used as state types
- * in the rk78 scheme
- * they should be defined by the user if required, see e.g. libs/numeric/examples/harmonic_oscillator_units.cpp
- */
-#ifndef BOOST_FUSION_INVOKE_MAX_ARITY
-#define BOOST_FUSION_INVOKE_MAX_ARITY 15
-#endif
-
-#ifndef BOOST_RESULT_OF_NUM_ARGS
-#define BOOST_RESULT_OF_NUM_ARGS 15
-#endif
-
-
-
-
-
-#include <boost/config.hpp>
-
-#if __cplusplus >= 201103L
-#define BOOST_NUMERIC_ODEINT_CXX11 1
-#endif
-
-
-
-
-#endif // BOOST_NUMERIC_ODEINT_CONFIG_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/blaze/blaze_algebra_dispatcher.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/blaze/blaze_algebra_dispatcher.hpp
deleted file mode 100644
index 29bf78621d1ec5e394715c503be29b022d4ce1a9..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/blaze/blaze_algebra_dispatcher.hpp
+++ /dev/null
@@ -1,55 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/external/blaze/blaze_algebra_dispatcher.hpp
-
- [begin_description]
- tba.
- [end_description]
-
- Copyright 2009-2012 Karsten Ahnert
- Copyright 2009-2012 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
-*/
-
-
-#ifndef BOOST_NUMERIC_ODEINT_EXTERNAL_BLAZE_BLAZE_ALGEBRA_DISPATCHER_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_EXTERNAL_BLAZE_BLAZE_ALGEBRA_DISPATCHER_HPP_INCLUDED
-
-#include <boost/numeric/odeint/algebra/algebra_dispatcher.hpp>
-#include <blaze/math/dense/StaticVector.h>
-#include <blaze/math/dense/DynamicVector.h>
-
-
-
-
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-template< typename T , size_t N , bool TF >
-struct algebra_dispatcher< blaze::StaticVector< T , N , TF > >
-{
- typedef vector_space_algebra algebra_type;
-};
-
-template< typename T , bool TF >
-struct algebra_dispatcher< blaze::DynamicVector< T , TF > >
-{
- typedef vector_space_algebra algebra_type;
-};
-
-
-
-
-
-}
-}
-}
-
-
-#endif // BOOST_NUMERIC_ODEINT_EXTERNAL_BLAZE_BLAZE_ALGEBRA_DISPATCHER_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/blaze/blaze_resize.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/blaze/blaze_resize.hpp
deleted file mode 100644
index 50ad3192632c453369aba374c3db9d3901192f58..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/blaze/blaze_resize.hpp
+++ /dev/null
@@ -1,62 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/external/blaze/blaze_resize.hpp
-
- [begin_description]
- tba.
- [end_description]
-
- Copyright 2009-2012 Karsten Ahnert
- Copyright 2009-2012 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
-*/
-
-
-#ifndef BOOST_NUMERIC_ODEINT_EXTERNAL_BLAZE_BLAZE_RESIZE_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_EXTERNAL_BLAZE_BLAZE_RESIZE_HPP_INCLUDED
-
-#include <boost/numeric/odeint/util/is_resizeable.hpp>
-#include <boost/numeric/odeint/util/resize.hpp>
-#include <boost/numeric/odeint/util/same_size.hpp>
-
-#include <blaze/math/dense/DynamicVector.h>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-template< typename T , bool TF >
-struct is_resizeable< blaze::DynamicVector< T , TF > >
-{
- typedef boost::true_type type;
- const static bool value = type::value;
-};
-
-template< typename T1 , bool TF1, typename T2 , bool TF2 >
-struct same_size_impl< blaze::DynamicVector< T1 , TF1 > , blaze::DynamicVector< T2 , TF2 > >
-{
- static bool same_size( const blaze::DynamicVector< T1 , TF1 > &x1 , const blaze::DynamicVector< T2 , TF2 > &x2 )
- {
- return x1.size() == x2.size();
- }
-};
-
-template< typename T1 , bool TF1, typename T2 , bool TF2 >
-struct resize_impl< blaze::DynamicVector< T1 , TF1 > , blaze::DynamicVector< T2 , TF2 > >
-{
- static void resize( blaze::DynamicVector< T1 , TF1 > &x1 , const blaze::DynamicVector< T2 , TF2 > &x2 )
- {
- x1.resize( x2.size() );
- }
-};
-
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_EXTERNAL_BLAZE_BLAZE_RESIZE_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/compute/compute.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/compute/compute.hpp
deleted file mode 100644
index fe04b581e721a1950051146d6ecbec5ad16217ee..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/compute/compute.hpp
+++ /dev/null
@@ -1,27 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/external/compute/compute.hpp
-
- [begin_description]
- includes all headers required for using odeint with Boost.Compute
- [end_description]
-
- Copyright 2009-2013 Karsten Ahnert
- Copyright 2009-2013 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
-*/
-
-
-#ifndef BOOST_NUMERIC_ODEINT_EXTERNAL_COMPUTE_COMPUTE_HPP_DEFINED
-#define BOOST_NUMERIC_ODEINT_EXTERNAL_COMPUTE_COMPUTE_HPP_DEFINED
-
-#include <boost/numeric/odeint/external/compute/compute_algebra.hpp>
-#include <boost/numeric/odeint/external/compute/compute_operations.hpp>
-#include <boost/numeric/odeint/external/compute/compute_algebra_dispatcher.hpp>
-#include <boost/numeric/odeint/external/compute/compute_operations_dispatcher.hpp>
-#include <boost/numeric/odeint/external/compute/compute_resize.hpp>
-
-#endif // BOOST_NUMERIC_ODEINT_EXTERNAL_COMPUTE_COMPUTE_HPP_DEFINED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/compute/compute_algebra.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/compute/compute_algebra.hpp
deleted file mode 100644
index 9cd3912eea68b59a0381016e9a5f568a68ef33c6..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/compute/compute_algebra.hpp
+++ /dev/null
@@ -1,65 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/external/compute/compute_algebra.hpp
-
- [begin_description]
- An algebra for Boost.Compute vectors.
- [end_description]
-
- Copyright 2009-2011 Karsten Ahnert
- Copyright 2009-2011 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_EXTERNAL_COMPUTE_COMPUTE_ALGEBRA_HPP_DEFINED
-#define BOOST_NUMERIC_ODEINT_EXTERNAL_COMPUTE_COMPUTE_ALGEBRA_HPP_DEFINED
-
-#include <boost/preprocessor/repetition.hpp>
-#include <boost/compute.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-struct compute_algebra
-{
-
-#define BOOST_ODEINT_COMPUTE_STATE_PARAM(z, n, unused) \
- StateType ## n &s ## n,
-
-#define BOOST_ODEINT_COMPUTE_ALGEBRA(z, n, unused) \
- template< BOOST_PP_ENUM_PARAMS(n, class StateType), class Operation > \
- static void for_each ## n( \
- BOOST_PP_REPEAT(n, BOOST_ODEINT_COMPUTE_STATE_PARAM, ~) \
- Operation op \
- ) \
- { \
- op( BOOST_PP_ENUM_PARAMS(n, s) ); \
- }
-
-BOOST_PP_REPEAT_FROM_TO(3, 9, BOOST_ODEINT_COMPUTE_ALGEBRA, ~)
-
-#undef BOOST_ODEINT_COMPUTE_ALGEBRA
-#undef BOOST_ODEINT_COMPUTE_STATE_PARAM
-
- template < class S >
- static typename S::value_type norm_inf( const S &s ) {
- typedef typename S::value_type value_type;
-
- BOOST_COMPUTE_FUNCTION(value_type, max_abs, (value_type, value_type),
- {
- return max(_1, fabs(_2));
- });
-
- return boost::compute::accumulate(s.begin(), s.end(), value_type(), max_abs);
- }
-};
-} // odeint
-} // numeric
-} // boost
-
-#endif
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/compute/compute_algebra_dispatcher.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/compute/compute_algebra_dispatcher.hpp
deleted file mode 100644
index 6df360b76d8376a63ac88b867f23d3033e1550f2..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/compute/compute_algebra_dispatcher.hpp
+++ /dev/null
@@ -1,41 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/external/compute/compute_algebra_dispatcher.hpp
-
- [begin_description]
- algebra_dispatcher specialization for Boost.Compute
- [end_description]
-
- Copyright 2009-2013 Karsten Ahnert
- Copyright 2009-2013 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
-*/
-
-
-#ifndef BOOST_NUMERIC_ODEINT_EXTERNAL_COMPUTE_COMPUTE_ALGEBRA_DISPATCHER_HPP_DEFINED
-#define BOOST_NUMERIC_ODEINT_EXTERNAL_COMPUTE_COMPUTE_ALGEBRA_DISPATCHER_HPP_DEFINED
-
-#include <boost/compute/container/vector.hpp>
-
-#include <boost/numeric/odeint/external/compute/compute_algebra.hpp>
-#include <boost/numeric/odeint/algebra/algebra_dispatcher.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-// specialization for Boost.Compute vector
-template< class T , class A >
-struct algebra_dispatcher< boost::compute::vector< T , A > >
-{
- typedef compute_algebra algebra_type;
-};
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-#endif // BOOST_NUMERIC_ODEINT_EXTERNAL_COMPUTE_COMPUTE_ALGEBRA_DISPATCHER_HPP_DEFINED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/compute/compute_operations.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/compute/compute_operations.hpp
deleted file mode 100644
index 58d5f692ffaa2b6c1dd64693dd0ffe8ad406f6af..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/compute/compute_operations.hpp
+++ /dev/null
@@ -1,198 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/external/compute/compute_operations.hpp
-
- [begin_description]
- Operations of Boost.Compute zipped iterators. Is the counterpart of the compute_algebra.
- [end_description]
-
- Copyright 2009-2011 Karsten Ahnert
- Copyright 2009-2011 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_EXTERNAL_COMPUTE_COMPUTE_OPERATIONS_HPP_DEFINED
-#define BOOST_NUMERIC_ODEINT_EXTERNAL_COMPUTE_COMPUTE_OPERATIONS_HPP_DEFINED
-
-#include <boost/preprocessor/repetition.hpp>
-#include <boost/compute.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-struct compute_operations {
-
-#define BOOST_ODEINT_COMPUTE_TEMPL_FAC(z, n, unused) \
- , class Fac ## n = BOOST_PP_CAT(Fac, BOOST_PP_DEC(n))
-
-#define BOOST_ODEINT_COMPUTE_MEMB_FAC(z, n, unused) \
- const Fac ## n m_alpha ## n;
-
-#define BOOST_ODEINT_COMPUTE_PRM_FAC(z, n, unused) \
- BOOST_PP_COMMA_IF(n) const Fac ## n alpha ## n
-
-#define BOOST_ODEINT_COMPUTE_INIT_FAC(z, n, unused) \
- BOOST_PP_COMMA_IF(n) m_alpha ## n (alpha ## n)
-
-#define BOOST_ODEINT_COMPUTE_PRM_STATE(z, n, unused) \
- BOOST_PP_COMMA_IF(n) StateType ## n &s ## n
-
-#define BOOST_ODEINT_COMPUTE_BEGIN_STATE(z, n, unused) \
- BOOST_PP_COMMA_IF( BOOST_PP_DEC(n) ) s ## n.begin()
-
-#define BOOST_ODEINT_COMPUTE_END_STATE(z, n, unused) \
- BOOST_PP_COMMA_IF( BOOST_PP_DEC(n) ) s ## n.end()
-
-#define BOOST_ODEINT_COMPUTE_LAMBDA(z, n, unused) \
- BOOST_PP_EXPR_IF(n, +) m_alpha ## n * bc::lambda::get< n >(bc::_1)
-
-#define BOOST_ODEINT_COMPUTE_OPERATIONS(z, n, unused) \
- template< \
- class Fac0 = double \
- BOOST_PP_REPEAT_FROM_TO(1, n, BOOST_ODEINT_COMPUTE_TEMPL_FAC, ~) \
- > \
- struct scale_sum ## n { \
- BOOST_PP_REPEAT(n, BOOST_ODEINT_COMPUTE_MEMB_FAC, ~) \
- scale_sum ## n( \
- BOOST_PP_REPEAT(n, BOOST_ODEINT_COMPUTE_PRM_FAC, ~) \
- ) \
- : BOOST_PP_REPEAT(n, BOOST_ODEINT_COMPUTE_INIT_FAC, ~) \
- { } \
- template< BOOST_PP_ENUM_PARAMS(BOOST_PP_INC(n), class StateType) > \
- void operator()( \
- BOOST_PP_REPEAT( \
- BOOST_PP_INC(n), \
- BOOST_ODEINT_COMPUTE_PRM_STATE, ~) \
- ) const \
- { \
- namespace bc = boost::compute; \
- bc::transform( \
- bc::make_zip_iterator( \
- boost::make_tuple( \
- BOOST_PP_REPEAT_FROM_TO( \
- 1, BOOST_PP_INC(n), \
- BOOST_ODEINT_COMPUTE_BEGIN_STATE, ~) \
- ) \
- ), \
- bc::make_zip_iterator( \
- boost::make_tuple( \
- BOOST_PP_REPEAT_FROM_TO( \
- 1, BOOST_PP_INC(n), \
- BOOST_ODEINT_COMPUTE_END_STATE, ~) \
- ) \
- ), \
- s0.begin(), \
- BOOST_PP_REPEAT(n, BOOST_ODEINT_COMPUTE_LAMBDA, ~) \
- ); \
- } \
- };
-
-BOOST_PP_REPEAT_FROM_TO(2, 8, BOOST_ODEINT_COMPUTE_OPERATIONS, ~)
-
-#undef BOOST_ODEINT_COMPUTE_TEMPL_FAC
-#undef BOOST_ODEINT_COMPUTE_MEMB_FAC
-#undef BOOST_ODEINT_COMPUTE_PRM_FAC
-#undef BOOST_ODEINT_COMPUTE_INIT_FAC
-#undef BOOST_ODEINT_COMPUTE_PRM_STATE
-#undef BOOST_ODEINT_COMPUTE_BEGIN_STATE
-#undef BOOST_ODEINT_COMPUTE_END_STATE
-#undef BOOST_ODEINT_COMPUTE_LAMBDA
-#undef BOOST_ODEINT_COMPUTE_OPERATIONS
-
- template<class Fac1 = double, class Fac2 = Fac1>
- struct scale_sum_swap2 {
- const Fac1 m_alpha1;
- const Fac2 m_alpha2;
-
- scale_sum_swap2(const Fac1 alpha1, const Fac2 alpha2)
- : m_alpha1(alpha1), m_alpha2(alpha2) { }
-
- template<class State0, class State1, class State2>
- void operator()(State0 &s0, State1 &s1, State2 &s2) const {
- namespace bc = boost::compute;
-
- bc::command_queue &queue = bc::system::default_queue();
- const bc::context &context = queue.get_context();
-
- const char source[] = BOOST_COMPUTE_STRINGIZE_SOURCE(
- kernel void scale_sum_swap2(
- F1 a1, F2 a2,
- global T0 *x0, global T1 *x1, global T2 *x2,
- )
- {
- uint i = get_global_id(0);
- T0 tmp = x0[i];
- x0[i] = a1 * x1[i] + a2 * x2[i];
- x1[i] = tmp;
- }
- );
-
- std::stringstream options;
- options
- << " -DT0=" << bc::type_name<typename State0::value_type>()
- << " -DT1=" << bc::type_name<typename State1::value_type>()
- << " -DT2=" << bc::type_name<typename State2::value_type>()
- << " -DF1=" << bc::type_name<Fac1>()
- << " -DF2=" << bc::type_name<Fac2>();
-
- bc::program program =
- bc::program::build_with_source(source, context, options.str());
-
- bc::kernel kernel(program, "scale_sum_swap2");
- kernel.set_arg(0, m_alpha1);
- kernel.set_arg(1, m_alpha2);
- kernel.set_arg(2, s0.get_buffer());
- kernel.set_arg(3, s1.get_buffer());
- kernel.set_arg(4, s2.get_buffer());
-
- queue.enqueue_1d_range_kernel(kernel, 0, s0.size());
-
- }
- };
-
- template<class Fac1 = double>
- struct rel_error {
- const Fac1 m_eps_abs, m_eps_rel, m_a_x, m_a_dxdt;
-
- rel_error(const Fac1 eps_abs, const Fac1 eps_rel, const Fac1 a_x, const Fac1 a_dxdt)
- : m_eps_abs(eps_abs), m_eps_rel(eps_rel), m_a_x(a_x), m_a_dxdt(a_dxdt) { }
-
-
- template <class State0, class State1, class State2>
- void operator()(State0 &s0, State1 &s1, State2 &s2) const {
- namespace bc = boost::compute;
- using bc::_1;
- using bc::lambda::get;
-
- bc::for_each(
- bc::make_zip_iterator(
- boost::make_tuple(
- s0.begin(),
- s1.begin(),
- s2.begin()
- )
- ),
- bc::make_zip_iterator(
- boost::make_tuple(
- s0.end(),
- s1.end(),
- s2.end()
- )
- ),
- get<0>(_1) = abs( get<0>(_1) ) /
- (m_eps_abs + m_eps_rel * (m_a_x * abs(get<1>(_1) + m_a_dxdt * abs(get<2>(_1)))))
- );
- }
- };
-};
-
-} // odeint
-} // numeric
-} // boost
-
-#endif // BOOST_NUMERIC_ODEINT_EXTERNAL_COMPUTE_COMPUTE_OPERATIONS_HPP_DEFINED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/compute/compute_operations_dispatcher.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/compute/compute_operations_dispatcher.hpp
deleted file mode 100644
index 76df2f37d561a592fe7c80727a074e9b1eaef4fe..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/compute/compute_operations_dispatcher.hpp
+++ /dev/null
@@ -1,44 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/external/compute/compute_operations_dispatcher.hpp
-
- [begin_description]
- operations_dispatcher specialization for Boost.Compute
- [end_description]
-
- Copyright 2009-2013 Karsten Ahnert
- Copyright 2009-2013 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
-*/
-
-
-#ifndef BOOST_NUMERIC_ODEINT_EXTERNAL_COMPUTE_COMPUTE_OPERATIONS_DISPATCHER_HPP_DEFINED
-#define BOOST_NUMERIC_ODEINT_EXTERNAL_COMPUTE_COMPUTE_OPERATIONS_DISPATCHER_HPP_DEFINED
-
-#include <boost/compute/container/vector.hpp>
-
-#include <boost/numeric/odeint/external/compute/compute_operations.hpp>
-#include <boost/numeric/odeint/algebra/operations_dispatcher.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-// specialization for Boost.Compute vector
-template< class T , class A >
-struct operations_dispatcher< boost::compute::vector< T , A > >
-{
- typedef compute_operations operations_type;
-};
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-
-
-#endif // BOOST_NUMERIC_ODEINT_EXTERNAL_COMPUTE_COMPUTE_OPERATIONS_DISPATCHER_HPP_DEFINED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/compute/compute_resize.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/compute/compute_resize.hpp
deleted file mode 100644
index 013a7acc41d6edc5f8c520218990c4bf7555385d..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/compute/compute_resize.hpp
+++ /dev/null
@@ -1,90 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/external/compute/compute_resize.hpp
-
- [begin_description]
- Enable resizing for Boost.Compute vector
- [end_description]
-
- Copyright 2009-2011 Karsten Ahnert
- Copyright 2009-2011 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_EXTERNAL_COMPUTE_COMPUTE_RESIZE_HPP_DEFINED
-#define BOOST_NUMERIC_ODEINT_EXTERNAL_COMPUTE_COMPUTE_RESIZE_HPP_DEFINED
-
-#include <boost/compute/container/vector.hpp>
-
-#include <boost/numeric/odeint/util/copy.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-template< class T, class A >
-struct is_resizeable< boost::compute::vector< T , A > >
-{
- struct type : public boost::true_type { };
- const static bool value = type::value;
-};
-
-template< class T, class A >
-struct same_size_impl< boost::compute::vector< T, A > , boost::compute::vector< T, A > >
-{
- static bool same_size( const boost::compute::vector< T, A > &x , const boost::compute::vector< T, A > &y )
- {
- return x.size() == y.size();
- }
-};
-
-template< class T, class A >
-struct resize_impl< boost::compute::vector< T, A > , boost::compute::vector< T, A > >
-{
- static void resize( boost::compute::vector< T, A > &x , const boost::compute::vector< T, A > &y )
- {
- x.resize( y.size() );
- }
-};
-
-
-template< class Container1, class T, class A >
-struct copy_impl< Container1 , boost::compute::vector< T, A > >
-{
- static void copy( const Container1 &from , boost::compute::vector< T, A > &to )
- {
- boost::compute::copy( boost::begin( from ) , boost::end( from ) , boost::begin( to ) );
- }
-};
-
-template< class T, class A, class Container2 >
-struct copy_impl< boost::compute::vector< T, A > , Container2 >
-{
- static void copy( const boost::compute::vector< T, A > &from , Container2 &to )
- {
- boost::compute::copy( boost::begin( from ) , boost::end( from ) , boost::begin( to ) );
- }
-};
-
-template< class T, class A >
-struct copy_impl< boost::compute::vector< T, A > , boost::compute::vector< T, A > >
-{
- static void copy( const boost::compute::vector< T, A > &from , boost::compute::vector< T, A > &to )
- {
- boost::compute::copy( boost::begin( from ) , boost::end( from ) , boost::begin( to ) );
- }
-};
-
-
-
-
-} // odeint
-} // numeric
-} // boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_EXTERNAL_COMPUTE_COMPUTE_RESIZE_HPP_DEFINED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/eigen/eigen.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/eigen/eigen.hpp
deleted file mode 100644
index 620acae51f2c3e7a1e79826ea0107612e2e70997..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/eigen/eigen.hpp
+++ /dev/null
@@ -1,27 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/external/eigen/eigen.hpp
-
- [begin_description]
- tba.
- [end_description]
-
- Copyright 2009-2012 Karsten Ahnert
- Copyright 2009-2012 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
-*/
-
-
-#ifndef BOOST_NUMERIC_ODEINT_EXTERNAL_EIGEN_EIGEN_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_EXTERNAL_EIGEN_EIGEN_HPP_INCLUDED
-
-
-#include <boost/numeric/odeint/external/eigen/eigen_algebra.hpp>
-#include <boost/numeric/odeint/external/eigen/eigen_algebra_dispatcher.hpp>
-#include <boost/numeric/odeint/external/eigen/eigen_resize.hpp>
-
-
-#endif // BOOST_NUMERIC_ODEINT_EXTERNAL_EIGEN_EIGEN_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/eigen/eigen_algebra.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/eigen/eigen_algebra.hpp
deleted file mode 100644
index 093154decb0cf321e908bd2bc2205e008a61c432..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/eigen/eigen_algebra.hpp
+++ /dev/null
@@ -1,109 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/external/eigen/eigen_algebra.hpp
-
- [begin_description]
- tba.
- [end_description]
-
- Copyright 2013 Christian Shelton
- Copyright 2013 Karsten Ahnert
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
-*/
-
-
-#ifndef BOOST_NUMERIC_ODEINT_EXTERNAL_EIGEN_EIGEN_ALGEBRA_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_EXTERNAL_EIGEN_EIGEN_ALGEBRA_HPP_INCLUDED
-
-#include <Eigen/Dense>
-#include <boost/numeric/odeint/algebra/vector_space_algebra.hpp>
-
-// Necessary routines for Eigen matrices to work with vector_space_algebra
-// from odeint
-// (that is, it lets odeint treat the eigen matrices correctly, knowing
-// how to add, multiply, compute the norm, etc)
-
-namespace Eigen {
-
-
-template<typename D>
-inline const
-typename Eigen::CwiseUnaryOp<
- typename Eigen::internal::scalar_add_op<
- typename Eigen::internal::traits<D>::Scalar>,
- const D >
-operator+(const typename Eigen::MatrixBase<D> &m,
- const typename Eigen::internal::traits<D>::Scalar &s) {
- return Eigen::CwiseUnaryOp<
- typename Eigen::internal::scalar_add_op<
- typename Eigen::internal::traits<D>::Scalar>,
- const D >(m.derived(),Eigen::internal::scalar_add_op<
- typename Eigen::internal::traits<D>::Scalar>(s));
-}
-
-template<typename D>
-inline const
-typename Eigen::CwiseUnaryOp<
- typename Eigen::internal::scalar_add_op<
- typename Eigen::internal::traits<D>::Scalar>,
- const D >
-operator+(const typename Eigen::internal::traits<D>::Scalar &s,
-const typename Eigen::MatrixBase<D> &m) {
- return Eigen::CwiseUnaryOp<
- typename Eigen::internal::scalar_add_op<
- typename Eigen::internal::traits<D>::Scalar>,
- const D >(m.derived(),Eigen::internal::scalar_add_op<
- typename Eigen::internal::traits<D>::Scalar>(s));
-}
-
-
-
-template<typename D1,typename D2>
-inline const
-typename Eigen::CwiseBinaryOp<
- typename Eigen::internal::scalar_quotient_op<
- typename Eigen::internal::traits<D1>::Scalar>,
- const D1, const D2>
-operator/(const Eigen::MatrixBase<D1> &x1, const Eigen::MatrixBase<D2> &x2) {
- return x1.cwiseQuotient(x2);
-}
-
-
-template< typename D >
-inline const
-typename Eigen::CwiseUnaryOp<
- typename Eigen::internal::scalar_abs_op<
- typename Eigen::internal::traits< D >::Scalar > ,
- const D >
-abs( const Eigen::MatrixBase< D > &m ) {
- return m.cwiseAbs();
-}
-
-
-
-} // end Eigen namespace
-
-
-
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-template<typename B,int S1,int S2,int O, int M1, int M2>
-struct vector_space_norm_inf< Eigen::Matrix<B,S1,S2,O,M1,M2> >
-{
- typedef B result_type;
- result_type operator()( const Eigen::Matrix<B,S1,S2,O,M1,M2> &m ) const
- {
- return m.template lpNorm<Eigen::Infinity>();
- }
-};
-
-} } } // end boost::numeric::odeint namespace
-
-#endif // BOOST_NUMERIC_ODEINT_EXTERNAL_EIGEN_EIGEN_ALGEBRA_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/eigen/eigen_algebra_dispatcher.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/eigen/eigen_algebra_dispatcher.hpp
deleted file mode 100644
index 24a258257b10112888540aae8e37fa651b1656bd..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/eigen/eigen_algebra_dispatcher.hpp
+++ /dev/null
@@ -1,49 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/external/eigen/eigen_algebra_dispatcher.hpp
-
- [begin_description]
- tba.
- [end_description]
-
- Copyright 2009-2012 Karsten Ahnert
- Copyright 2009-2012 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
-*/
-
-
-#ifndef BOOST_NUMERIC_ODEINT_EXTERNAL_EIGEN_EIGEN_ALGEBRA_DISPATCHER_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_EXTERNAL_EIGEN_EIGEN_ALGEBRA_DISPATCHER_HPP_INCLUDED
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-template< class Derived >
-struct algebra_dispatcher_sfinae< Derived ,
- typename boost::enable_if< typename boost::is_base_of< Eigen::MatrixBase< Derived > , Derived >::type >::type >
-{
- typedef vector_space_algebra algebra_type;
-};
-
-
-template < class Derived >
-struct algebra_dispatcher_sfinae< Derived ,
- typename boost::enable_if< typename boost::is_base_of< Eigen::ArrayBase< Derived > , Derived >::type >::type >
-{
- typedef vector_space_algebra algebra_type;
-};
-
-
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_EXTERNAL_EIGEN_EIGEN_ALGEBRA_DISPATCHER_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/eigen/eigen_resize.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/eigen/eigen_resize.hpp
deleted file mode 100644
index 4066c866fa97c4736de9010fd34acca847495f7b..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/eigen/eigen_resize.hpp
+++ /dev/null
@@ -1,107 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/external/eigen/eigen_resize.hpp
-
- [begin_description]
- tba.
- [end_description]
-
- Copyright 2013 Ankur Sinha
- Copyright 2013 Karsten Ahnert
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
-*/
-
-
-#ifndef BOOST_NUMERIC_ODEINT_EXTERNAL_EIGEN_EIGEN_RESIZE_HPP_DEFINED
-#define BOOST_NUMERIC_ODEINT_EXTERNAL_EIGEN_EIGEN_RESIZE_HPP_DEFINED
-
-
-#include <boost/numeric/odeint/util/is_resizeable.hpp>
-#include <boost/numeric/odeint/util/resize.hpp>
-#include <boost/numeric/odeint/util/same_size.hpp>
-
-#include <boost/utility/enable_if.hpp>
-#include <boost/type_traits/is_base_of.hpp>
-
-#include <Eigen/Dense>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-
-template< class Derived >
-struct is_resizeable_sfinae< Derived ,
- typename boost::enable_if< typename boost::is_base_of< Eigen::MatrixBase< Derived > , Derived >::type >::type >
-{
- typedef boost::true_type type;
- const static bool value = type::value;
-};
-
-
-template < class Derived >
-struct is_resizeable_sfinae< Derived ,
- typename boost::enable_if< typename boost::is_base_of< Eigen::ArrayBase< Derived > , Derived >::type >::type >
-{
- typedef boost::true_type type;
- const static bool value = type::value;
-};
-
-
-
-template< class Derived >
-struct same_size_impl_sfinae< Derived , Derived ,
- typename boost::enable_if< typename boost::is_base_of< Eigen::MatrixBase< Derived > , Derived >::type >::type >
-{
- static bool same_size( const Eigen::MatrixBase< Derived > &m1 , const Eigen::MatrixBase< Derived > &m2 )
-
- {
- return ( ( m1.innerSize () == m2.innerSize () ) && ( m1.outerSize() == m2.outerSize() ) );
- }
-};
-
-template< class Derived >
-struct same_size_impl_sfinae< Derived , Derived ,
- typename boost::enable_if< typename boost::is_base_of< Eigen::ArrayBase< Derived > , Derived >::type >::type >
-{
- static bool same_size( const Eigen::ArrayBase< Derived > &v1 , const Eigen::ArrayBase< Derived > &v2 )
- {
- return ( ( v1.innerSize () == v2.innerSize () ) && ( v1.outerSize() == v2.outerSize() ) );
- }
-};
-
-
-
-
-template< class Derived >
-struct resize_impl_sfinae< Derived , Derived ,
- typename boost::enable_if< typename boost::is_base_of< Eigen::MatrixBase< Derived > , Derived >::type >::type >
-{
- static void resize( Eigen::MatrixBase< Derived > &m1 , const Eigen::MatrixBase< Derived > &m2 )
- {
- m1.derived().resizeLike(m2);
- }
-};
-
-template< class Derived >
-struct resize_impl_sfinae< Derived , Derived ,
- typename boost::enable_if< typename boost::is_base_of< Eigen::ArrayBase< Derived > , Derived >::type >::type >
-{
- static void resize( Eigen::ArrayBase< Derived > &v1 , const Eigen::ArrayBase< Derived > &v2 )
- {
- v1.derived().resizeLike(v2);
- }
-};
-
-
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_EXTERNAL_EIGEN_EIGEN_RESIZE_HPP_DEFINED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/gsl/gsl_wrapper.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/gsl/gsl_wrapper.hpp
deleted file mode 100644
index a856f6e8a16db90435506d2cc98b396c1b20caea..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/gsl/gsl_wrapper.hpp
+++ /dev/null
@@ -1,229 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/external/gsl/gsl_wrapper.hpp
-
- [begin_description]
- Wrapper for gsl_vector.
- [end_description]
-
- Copyright 2011-2012 Mario Mulansky
- Copyright 2011 Karsten Ahnert
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_EXTERNAL_GSL_GSL_WRAPPER_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_EXTERNAL_GSL_GSL_WRAPPER_HPP_INCLUDED
-
-#include <new>
-
-#include <gsl/gsl_vector.h>
-
-#include <boost/type_traits/integral_constant.hpp>
-#include <boost/range.hpp>
-#include <boost/iterator/iterator_facade.hpp>
-
-
-#include <boost/numeric/odeint/util/state_wrapper.hpp>
-#include <boost/numeric/odeint/util/is_resizeable.hpp>
-#include <boost/numeric/odeint/util/copy.hpp>
-
-class const_gsl_vector_iterator;
-
-/*
- * defines an iterator for gsl_vector
- */
-class gsl_vector_iterator : public boost::iterator_facade< gsl_vector_iterator , double , boost::random_access_traversal_tag >
-{
-public :
-
- gsl_vector_iterator( void ): m_p(0) , m_stride( 0 ) { }
- explicit gsl_vector_iterator( gsl_vector *p ) : m_p( p->data ) , m_stride( p->stride ) { }
- friend gsl_vector_iterator end_iterator( gsl_vector * );
-
-private :
-
- friend class boost::iterator_core_access;
- friend class const_gsl_vector_iterator;
-
- void increment( void ) { m_p += m_stride; }
- void decrement( void ) { m_p -= m_stride; }
- void advance( ptrdiff_t n ) { m_p += n*m_stride; }
- bool equal( const gsl_vector_iterator &other ) const { return this->m_p == other.m_p; }
- bool equal( const const_gsl_vector_iterator &other ) const;
- double& dereference( void ) const { return *m_p; }
-
- double *m_p;
- size_t m_stride;
-};
-
-
-
-/*
- * defines an const iterator for gsl_vector
- */
-class const_gsl_vector_iterator : public boost::iterator_facade< const_gsl_vector_iterator , const double , boost::random_access_traversal_tag >
-{
-public :
-
- const_gsl_vector_iterator( void ): m_p(0) , m_stride( 0 ) { }
- explicit const_gsl_vector_iterator( const gsl_vector *p ) : m_p( p->data ) , m_stride( p->stride ) { }
- const_gsl_vector_iterator( const gsl_vector_iterator &p ) : m_p( p.m_p ) , m_stride( p.m_stride ) { }
-
-private :
-
- friend class boost::iterator_core_access;
- friend class gsl_vector_iterator;
- friend const_gsl_vector_iterator end_iterator( const gsl_vector * );
-
- void increment( void ) { m_p += m_stride; }
- void decrement( void ) { m_p -= m_stride; }
- void advance( ptrdiff_t n ) { m_p += n*m_stride; }
- bool equal( const const_gsl_vector_iterator &other ) const { return this->m_p == other.m_p; }
- bool equal( const gsl_vector_iterator &other ) const { return this->m_p == other.m_p; }
- const double& dereference( void ) const { return *m_p; }
-
- const double *m_p;
- size_t m_stride;
-};
-
-
-bool gsl_vector_iterator::equal( const const_gsl_vector_iterator &other ) const { return this->m_p == other.m_p; }
-
-
-gsl_vector_iterator end_iterator( gsl_vector *x )
-{
- gsl_vector_iterator iter( x );
- iter.m_p += iter.m_stride * x->size;
- return iter;
-}
-
-const_gsl_vector_iterator end_iterator( const gsl_vector *x )
-{
- const_gsl_vector_iterator iter( x );
- iter.m_p += iter.m_stride * x->size;
- return iter;
-}
-
-
-
-
-namespace boost
-{
-template<>
-struct range_mutable_iterator< gsl_vector* >
-{
- typedef gsl_vector_iterator type;
-};
-
-template<>
-struct range_const_iterator< gsl_vector* >
-{
- typedef const_gsl_vector_iterator type;
-};
-} // namespace boost
-
-
-
-
-// template<>
-inline gsl_vector_iterator range_begin( gsl_vector *x )
-{
- return gsl_vector_iterator( x );
-}
-
-// template<>
-inline const_gsl_vector_iterator range_begin( const gsl_vector *x )
-{
- return const_gsl_vector_iterator( x );
-}
-
-// template<>
-inline gsl_vector_iterator range_end( gsl_vector *x )
-{
- return end_iterator( x );
-}
-
-// template<>
-inline const_gsl_vector_iterator range_end( const gsl_vector *x )
-{
- return end_iterator( x );
-}
-
-
-
-
-
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-template<>
-struct is_resizeable< gsl_vector* >
-{
- //struct type : public boost::true_type { };
- typedef boost::true_type type;
- const static bool value = type::value;
-};
-
-template <>
-struct same_size_impl< gsl_vector* , gsl_vector* >
-{
- static bool same_size( const gsl_vector* x , const gsl_vector* y )
- {
- return x->size == y->size;
- }
-};
-
-template <>
-struct resize_impl< gsl_vector* , gsl_vector* >
-{
- static void resize( gsl_vector* &x , const gsl_vector* y )
- {
- gsl_vector_free( x );
- x = gsl_vector_alloc( y->size );
- }
-};
-
-template<>
-struct state_wrapper< gsl_vector* >
-{
- typedef double value_type;
- typedef gsl_vector* state_type;
- typedef state_wrapper< gsl_vector* > state_wrapper_type;
-
- state_type m_v;
-
- state_wrapper( )
- {
- m_v = gsl_vector_alloc( 1 );
- }
-
- state_wrapper( const state_wrapper_type &x )
- {
- resize( m_v , x.m_v );
- gsl_vector_memcpy( m_v , x.m_v );
- }
-
-
- ~state_wrapper()
- {
- gsl_vector_free( m_v );
- }
-
-};
-
-} // odeint
-} // numeric
-} // boost
-
-
-
-
-#endif // BOOST_NUMERIC_ODEINT_EXTERNAL_GSL_GSL_WRAPPER_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/mkl/mkl_operations.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/mkl/mkl_operations.hpp
deleted file mode 100644
index 59ac4b83cb87280398025407e644a54cecfa3ac4..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/mkl/mkl_operations.hpp
+++ /dev/null
@@ -1,181 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/external/mkl/mkl_operations.hpp
-
- [begin_description]
- Wrapper classes for intel math kernel library types.
- Get a free, non-commercial download of MKL at
- http://software.intel.com/en-us/articles/non-commercial-software-download/
- [end_description]
-
- Copyright 2010-2011 Mario Mulansky
- Copyright 2011-2013 Karsten Ahnert
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_EXTERNAL_MKL_MKL_OPERATIONS_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_EXTERNAL_MKL_MKL_OPERATIONS_HPP_INCLUDED
-
-#include <iostream>
-
-#include <mkl_cblas.h>
-#include <boost/numeric/odeint/algebra/default_operations.hpp>
-
-/* exemplary example for writing bindings to the Intel MKL library
- * see test/mkl for how to use mkl with odeint
- * this is a quick and dirty implementation showing the general possibility.
- * It works only with containers based on double and sequential memory allocation.
- */
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-/* only defined for doubles */
-struct mkl_operations
-{
- //template< class Fac1 , class Fac2 > struct scale_sum2;
-
- template< class F1 = double , class F2 = F1 >
- struct scale_sum2
- {
- typedef double Fac1;
- typedef double Fac2;
- const Fac1 m_alpha1;
- const Fac2 m_alpha2;
-
- scale_sum2( const Fac1 alpha1 , const Fac2 alpha2 ) : m_alpha1( alpha1 ) , m_alpha2( alpha2 ) { }
-
- template< class T1 , class T2 , class T3 >
- void operator()( T1 &t1 , const T2 &t2 , const T3 &t3) const
- { // t1 = m_alpha1 * t2 + m_alpha2 * t3;
- // we get Containers that have size() and [i]-access
-
- const int n = t1.size();
- //boost::numeric::odeint::copy( t1 , t3 );
- if( &(t2[0]) != &(t1[0]) )
- {
- cblas_dcopy( n , &(t2[0]) , 1 , &(t1[0]) , 1 );
- }
- cblas_dscal( n , m_alpha1 , &(t1[0]) , 1 );
- cblas_daxpy( n , m_alpha2 , &(t3[0]) , 1 , &(t1[0]) , 1 );
- //daxpby( &n , &m_alpha2 , &(t3[0]) , &one , &m_alpha1 , &(t1[0]) , &one );
- }
- };
-
- template< class F1 = double , class F2 = F1 , class F3 = F2 >
- struct scale_sum3
- {
- typedef double Fac1;
- typedef double Fac2;
- typedef double Fac3;
- const Fac1 m_alpha1;
- const Fac2 m_alpha2;
- const Fac3 m_alpha3;
-
- scale_sum3( const Fac1 alpha1 , const Fac2 alpha2 , const Fac3 alpha3 )
- : m_alpha1( alpha1 ) , m_alpha2( alpha2 ) , m_alpha3( alpha3 ) { }
-
- template< class T1 , class T2 , class T3 , class T4 >
- void operator()( T1 &t1 , const T2 &t2 , const T3 &t3 , const T4 &t4 ) const
- { // t1 = m_alpha1 * t2 + m_alpha2 * t3 + m_alpha3 * t4;
- // we get Containers that have size() and [i]-access
-
- const int n = t1.size();
- //boost::numeric::odeint::copy( t1 , t3 );
- if( &(t2[0]) != &(t1[0]) )
- {
- cblas_dcopy( n , &(t2[0]) , 1 , &(t1[0]) , 1 );
- }
- cblas_dscal( n , m_alpha1 , &(t1[0]) , 1 );
- cblas_daxpy( n , m_alpha2 , &(t3[0]) , 1 , &(t1[0]) , 1 );
- //daxpby( &n , &m_alpha2 , &(t3[0]) , &one , &m_alpha1 , &(t1[0]) , &one );
- cblas_daxpy( n , m_alpha3 , &(t4[0]) , 1 , &(t1[0]) , 1 );
- }
- };
-
- template< class F1 = double , class F2 = F1 , class F3 = F2 , class F4 = F3 >
- struct scale_sum4
- {
- typedef double Fac1;
- typedef double Fac2;
- typedef double Fac3;
- typedef double Fac4;
- const Fac1 m_alpha1;
- const Fac2 m_alpha2;
- const Fac3 m_alpha3;
- const Fac4 m_alpha4;
-
- scale_sum4( const Fac1 alpha1 , const Fac2 alpha2 , const Fac3 alpha3 , const Fac4 alpha4 )
- : m_alpha1( alpha1 ) , m_alpha2( alpha2 ) , m_alpha3( alpha3 ) , m_alpha4( alpha4 ) { }
-
- template< class T1 , class T2 , class T3 , class T4 , class T5 >
- void operator()( T1 &t1 , const T2 &t2 , const T3 &t3 , const T4 &t4 , const T5 &t5 ) const
- { // t1 = m_alpha1 * t2 + m_alpha2 * t3 + m_alpha3 * t4 + m_alpha4 * t5;
- // we get Containers that have size() and [i]-access
-
- const int n = t1.size();
- //boost::numeric::odeint::copy( t1 , t3 );
- if( &(t2[0]) != &(t1[0]) )
- {
- cblas_dcopy( n , &(t2[0]) , 1 , &(t1[0]) , 1 );
- }
-
- cblas_dscal( n , m_alpha1 , &(t1[0]) , 1 );
- cblas_daxpy( n , m_alpha2 , &(t3[0]) , 1 , &(t1[0]) , 1 );
- //daxpby( &n , &m_alpha2 , &(t3[0]) , &one , &m_alpha1 , &(t1[0]) , &one );
- cblas_daxpy( n , m_alpha3 , &(t4[0]) , 1 , &(t1[0]) , 1 );
- cblas_daxpy( n , m_alpha4 , &(t5[0]) , 1 , &(t1[0]) , 1 );
- }
- };
-
-
- template< class F1 = double , class F2 = F1 , class F3 = F2 , class F4 = F3 , class F5 = F4 >
- struct scale_sum5
- {
- typedef double Fac1;
- typedef double Fac2;
- typedef double Fac3;
- typedef double Fac4;
- typedef double Fac5;
- const Fac1 m_alpha1;
- const Fac2 m_alpha2;
- const Fac3 m_alpha3;
- const Fac4 m_alpha4;
- const Fac5 m_alpha5;
-
- scale_sum5( const Fac1 alpha1 , const Fac2 alpha2 , const Fac3 alpha3 , const Fac4 alpha4 , const Fac5 alpha5 )
- : m_alpha1( alpha1 ) , m_alpha2( alpha2 ) , m_alpha3( alpha3 ) , m_alpha4( alpha4 ) , m_alpha5( alpha5 ) { }
-
- template< class T1 , class T2 , class T3 , class T4 , class T5 , class T6 >
- void operator()( T1 &t1 , const T2 &t2 , const T3 &t3 , const T4 &t4 , const T5 &t5 , const T6 &t6 ) const
- { // t1 = m_alpha1 * t2 + m_alpha2 * t3 + m_alpha3 * t4 + m_alpha4 * t5 + m_alpha5 * t6;
- // we get Containers that have size() and [i]-access
-
- const int n = t1.size();
- //boost::numeric::odeint::copy( t1 , t3 );
- if( &(t2[0]) != &(t1[0]) )
- {
- cblas_dcopy( n , &(t2[0]) , 1 , &(t1[0]) , 1 );
- }
-
- cblas_dscal( n , m_alpha1 , &(t1[0]) , 1 );
- cblas_daxpy( n , m_alpha2 , &(t3[0]) , 1 , &(t1[0]) , 1 );
- //daxpby( &n , &m_alpha2 , &(t3[0]) , &one , &m_alpha1 , &(t1[0]) , &one );
- cblas_daxpy( n , m_alpha3 , &(t4[0]) , 1 , &(t1[0]) , 1 );
- cblas_daxpy( n , m_alpha4 , &(t5[0]) , 1 , &(t1[0]) , 1 );
- cblas_daxpy( n , m_alpha5 , &(t6[0]) , 1 , &(t1[0]) , 1 );
- }
- };
-
-};
-
-} // odeint
-} // numeric
-} // boost
-
-#endif // BOOST_NUMERIC_ODEINT_EXTERNAL_MKL_MKL_OPERATIONS_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/mpi/mpi.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/mpi/mpi.hpp
deleted file mode 100644
index 26e1ae991a7eb3e8e5af98a56de119b5a0acb50c..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/mpi/mpi.hpp
+++ /dev/null
@@ -1,25 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/external/mpi/mpi.hpp
-
- [begin_description]
- Wrappers for MPI.
- [end_description]
-
- Copyright 2013 Karsten Ahnert
- Copyright 2013 Mario Mulansky
- Copyright 2013 Pascal Germroth
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_EXTERNAL_MPI_MPI_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_EXTERNAL_MPI_MPI_HPP_INCLUDED
-
-#include <boost/numeric/odeint/external/mpi/mpi_vector_state.hpp>
-#include <boost/numeric/odeint/external/mpi/mpi_nested_algebra.hpp>
-
-#endif
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/mpi/mpi_nested_algebra.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/mpi/mpi_nested_algebra.hpp
deleted file mode 100644
index 5d9022582ac495bdded4535c9341409501c9fda2..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/mpi/mpi_nested_algebra.hpp
+++ /dev/null
@@ -1,62 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/external/mpi/mpi_nested_algebra.hpp
-
- [begin_description]
- Nested parallelized algebra for MPI.
- [end_description]
-
- Copyright 2013 Karsten Ahnert
- Copyright 2013 Mario Mulansky
- Copyright 2013 Pascal Germroth
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_EXTERNAL_MPI_MPI_NESTED_ALGEBRA_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_EXTERNAL_MPI_MPI_NESTED_ALGEBRA_HPP_INCLUDED
-
-#include <boost/numeric/odeint/algebra/norm_result_type.hpp>
-#include <boost/numeric/odeint/util/n_ary_helper.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-/** \brief MPI-parallelized algebra, wrapping another algebra.
- */
-template< class InnerAlgebra >
-struct mpi_nested_algebra
-{
-
-// execute the InnerAlgebra on each node's local data.
-#define BOOST_ODEINT_GEN_BODY(n) \
- InnerAlgebra::for_each##n( \
- BOOST_PP_ENUM_BINARY_PARAMS(n, s, () BOOST_PP_INTERCEPT) , \
- op \
- );
-BOOST_ODEINT_GEN_FOR_EACH(BOOST_ODEINT_GEN_BODY)
-#undef BOOST_ODEINT_GEN_BODY
-
-
- template< class NestedState >
- static typename norm_result_type< typename NestedState::value_type >::type norm_inf( const NestedState &s )
- {
- typedef typename norm_result_type< typename NestedState::value_type >::type result_type;
- // local maximum
- result_type value = InnerAlgebra::norm_inf( s() );
- // global maximum
- return boost::mpi::all_reduce(s.world, value, boost::mpi::maximum<result_type>());
- }
-
-};
-
-
-}
-}
-}
-
-#endif
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/mpi/mpi_state.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/mpi/mpi_state.hpp
deleted file mode 100644
index aba179c09c85715f51960e959b5c74dc428472e6..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/mpi/mpi_state.hpp
+++ /dev/null
@@ -1,113 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/external/mpi/mpi_state.hpp
-
- [begin_description]
- A generic split state, storing partial data on each node.
- [end_description]
-
- Copyright 2013 Karsten Ahnert
- Copyright 2013 Mario Mulansky
- Copyright 2013 Pascal Germroth
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_EXTERNAL_MPI_MPI_STATE_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_EXTERNAL_MPI_MPI_STATE_HPP_INCLUDED
-
-#include <vector>
-#include <algorithm>
-#include <boost/mpi.hpp>
-#include <boost/numeric/odeint/util/copy.hpp>
-#include <boost/numeric/odeint/util/split.hpp>
-#include <boost/numeric/odeint/util/resize.hpp>
-#include <boost/numeric/odeint/util/same_size.hpp>
-#include <boost/numeric/odeint/algebra/algebra_dispatcher.hpp>
-#include <boost/numeric/odeint/external/mpi/mpi_nested_algebra.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-/** \brief A container which has its contents distributed among the nodes.
- */
-template< class InnerState >
-struct mpi_state
-{
- typedef InnerState value_type;
-
- // the node's local data.
- InnerState m_data;
-
- boost::mpi::communicator world;
-
- mpi_state() {}
- mpi_state(boost::mpi::communicator comm) : world(comm) {}
-
- inline InnerState &operator()() { return m_data; }
- inline const InnerState &operator()() const { return m_data; }
-};
-
-
-
-
-template< class InnerState >
-struct is_resizeable< mpi_state< InnerState > >
- : is_resizeable< InnerState > { };
-
-
-template< class InnerState1 , class InnerState2 >
-struct same_size_impl< mpi_state< InnerState1 > , mpi_state< InnerState2 > >
-{
- static bool same_size( const mpi_state< InnerState1 > &x , const mpi_state< InnerState2 > &y )
- {
- const bool local = boost::numeric::odeint::same_size(x(), y());
- return boost::mpi::all_reduce(x.world, local, mpi::bitwise_and<bool>());
- }
-};
-
-
-template< class InnerState1 , class InnerState2 >
-struct resize_impl< mpi_state< InnerState1 > , mpi_state< InnerState2 > >
-{
- static void resize( mpi_state< InnerState1 > &x , const mpi_state< InnerState2 > &y )
- {
- // resize local parts on each node.
- boost::numeric::odeint::resize(x(), y());
- }
-};
-
-
-/** \brief Copy data between mpi_states of same size. */
-template< class InnerState1 , class InnerState2 >
-struct copy_impl< mpi_state< InnerState1 > , mpi_state< InnerState2 > >
-{
- static void copy( const mpi_state< InnerState1 > &from , mpi_state< InnerState2 > &to )
- {
- // copy local parts on each node.
- boost::numeric::odeint::copy(from(), to());
- }
-};
-
-
-
-/** \brief Use `mpi_algebra` for `mpi_state`. */
-template< class InnerState >
-struct algebra_dispatcher< mpi_state< InnerState > >
-{
- typedef mpi_nested_algebra<
- typename algebra_dispatcher< InnerState >::algebra_type
- > algebra_type;
-};
-
-
-}
-}
-}
-
-
-#endif
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/mpi/mpi_vector_state.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/mpi/mpi_vector_state.hpp
deleted file mode 100644
index 096d40a65528bb4014a599da5f6d85a34f2ad62b..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/mpi/mpi_vector_state.hpp
+++ /dev/null
@@ -1,94 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/external/mpi/mpi_vector_state.hpp
-
- [begin_description]
- Copying a container from/to an mpi_state splits/joins it.
- [end_description]
-
- Copyright 2013 Karsten Ahnert
- Copyright 2013 Mario Mulansky
- Copyright 2013 Pascal Germroth
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_EXTERNAL_MPI_MPI_VECTOR_STATE_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_EXTERNAL_MPI_MPI_VECTOR_STATE_HPP_INCLUDED
-
-#include <vector>
-#include <algorithm>
-#include <boost/mpi.hpp>
-#include <boost/numeric/odeint/util/copy.hpp>
-#include <boost/numeric/odeint/util/split_adaptor.hpp>
-#include <boost/numeric/odeint/algebra/algebra_dispatcher.hpp>
-#include <boost/numeric/odeint/external/mpi/mpi_state.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-/** \brief Split data from some container on node 0 to the slaves.
- * Source must be a model of Random Access Range. */
-template< class Source , class InnerState >
-struct split_impl< Source, mpi_state< InnerState >,
- typename boost::enable_if< boost::has_range_const_iterator<Source> >::type >
-{
- typedef typename boost::range_iterator<const Source>::type iterator;
-
- static void split( const Source &from, mpi_state< InnerState > &to )
- {
- std::vector< InnerState > pieces;
- if(to.world.rank() == 0) {
- const size_t num = static_cast<size_t>(to.world.size());
- pieces.resize(num);
- for(size_t i = 0 ; i < num ; i++) {
- iterator_range<iterator> part = detail::make_split_range(from, i, num);
- boost::numeric::odeint::resize(pieces[i], part);
- boost::numeric::odeint::copy(part, pieces[i]);
- }
- }
- // send to nodes
- boost::mpi::scatter(to.world, pieces, to(), 0);
- }
-};
-
-/** \brief Merge data from an mpi_state to some container on node 0.
- * Target must be a model Single Pass Range. */
-template< class Target, class InnerState >
-struct unsplit_impl< mpi_state< InnerState >, Target,
- typename boost::enable_if< boost::has_range_iterator<Target> >::type >
-{
- typedef typename boost::range_iterator<Target>::type iterator;
-
- static void unsplit( const mpi_state< InnerState > &from , Target &to )
- {
- std::vector< InnerState > pieces;
- // send data to root
- boost::mpi::gather(from.world, from(), pieces, 0);
- if(from.world.rank() == 0) {
- // check target size
- size_t total_size = 0;
- for(size_t i = 0 ; i < pieces.size() ; i++)
- total_size += boost::size(pieces[i]);
- BOOST_ASSERT( total_size <= boost::size(to) );
- // copy parts
- iterator out = boost::begin(to);
- for(size_t i = 0 ; i < pieces.size() ; i++)
- out = boost::copy(pieces[i], out);
- }
- }
-};
-
-
-}
-}
-}
-
-
-#endif
-
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/mtl4/implicit_euler_mtl4.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/mtl4/implicit_euler_mtl4.hpp
deleted file mode 100644
index 9950ce1592e53b0f4c478e9c95599ce5749b6b6d..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/mtl4/implicit_euler_mtl4.hpp
+++ /dev/null
@@ -1,162 +0,0 @@
-/*
-[begin_description]
-Modification of the implicit Euler method, works with the MTL4 matrix library only.
-[end_description]
-
-Copyright 2012-2013 Andreas Angelopoulos
-Copyright 2012-2013 Karsten Ahnert
-Copyright 2012-2013 Mario Mulansky
-
-Distributed under the Boost Software License, Version 1.0.
-(See accompanying file LICENSE_1_0.txt or
-copy at http://www.boost.org/LICENSE_1_0.txt)
-*/
-
-
-#ifndef BOOST_NUMERIC_ODEINT_EXTERNAL_IMPLICIT_EULER_MTL4_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_EXTERNAL_IMPLICIT_EULER_MTL4_HPP_INCLUDED
-
-
-#include <utility>
-
-#include <boost/numeric/odeint/util/bind.hpp>
-#include <boost/numeric/odeint/util/unwrap_reference.hpp>
-#include <boost/numeric/odeint/stepper/stepper_categories.hpp>
-
-#include <boost/numeric/odeint/external/mtl4/mtl4_resize.hpp>
-
-#include <boost/numeric/mtl/mtl.hpp>
-#include <boost/numeric/itl/itl.hpp>
-
-
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-template< class ValueType , class Resizer = initially_resizer >
-class implicit_euler_mtl4
-{
-
-public:
-
- typedef ValueType value_type;
- typedef value_type time_type;
- typedef mtl::dense_vector<value_type> state_type;
-
- typedef state_wrapper< state_type > wrapped_state_type;
- typedef state_type deriv_type;
- typedef state_wrapper< deriv_type > wrapped_deriv_type;
- typedef mtl::compressed2D< value_type > matrix_type;
- typedef state_wrapper< matrix_type > wrapped_matrix_type;
-
- typedef Resizer resizer_type;
- typedef stepper_tag stepper_category;
-
- typedef implicit_euler_mtl4< ValueType , Resizer > stepper_type;
-
-
- implicit_euler_mtl4( const value_type epsilon = 1E-6 )
- : m_epsilon( epsilon ) , m_resizer() ,
- m_dxdt() , m_x() ,
- m_identity() , m_jacobi()
- { }
-
-
- template< class System >
- void do_step( System system , state_type &x , time_type t , time_type dt )
- {
- typedef typename odeint::unwrap_reference< System >::type system_type;
- typedef typename odeint::unwrap_reference< typename system_type::first_type >::type deriv_func_type;
- typedef typename odeint::unwrap_reference< typename system_type::second_type >::type jacobi_func_type;
- system_type &sys = system;
- deriv_func_type &deriv_func = sys.first;
- jacobi_func_type &jacobi_func = sys.second;
-
- m_resizer.adjust_size( x , detail::bind(
- &stepper_type::template resize_impl< state_type > , detail::ref( *this ) , detail::_1 ) );
-
- m_identity.m_v = 1;
-
- t += dt;
- m_x.m_v = x;
-
- deriv_func( x , m_dxdt.m_v , t );
- jacobi_func( x , m_jacobi.m_v , t );
-
-
- m_dxdt.m_v *= -dt;
-
- m_jacobi.m_v *= dt;
- m_jacobi.m_v -= m_identity.m_v ;
-
-
-
- // using ilu_0 preconditioning -incomplete LU factorisation
- // itl::pc::diagonal<matrix_type,double> L(m_jacobi.m_v);
- itl::pc::ilu_0<matrix_type> L( m_jacobi.m_v );
-
- solve( m_jacobi.m_v , m_x.m_v , m_dxdt.m_v , L );
- x+= m_x.m_v;
-
-
- }
-
-
- template< class StateType >
- void adjust_size( const StateType &x )
- {
- resize_impl( x );
- }
-
-
-private:
-
-
- /*
- Applying approximate iterative linear solvers
- default solver is Biconjugate gradient stabilized method
- itl::bicgstab(A, x, b, L, iter);
- */
- template < class LinearOperator, class HilbertSpaceX, class HilbertSpaceB, class Preconditioner>
- void solve(const LinearOperator& A, HilbertSpaceX& x, const HilbertSpaceB& b,
- const Preconditioner& L, int max_iteractions =500)
- {
- // Termination criterion: r < 1e-6 * b or N iterations
- itl::basic_iteration< double > iter( b , max_iteractions , 1e-6 );
- itl::bicgstab( A , x , b , L , iter );
-
- }
-
-
- template< class StateIn >
- bool resize_impl( const StateIn &x )
- {
- bool resized = false;
- resized |= adjust_size_by_resizeability( m_dxdt , x , typename is_resizeable<deriv_type>::type() );
- resized |= adjust_size_by_resizeability( m_x , x , typename is_resizeable<state_type>::type() );
- resized |= adjust_size_by_resizeability( m_identity , x , typename is_resizeable<matrix_type>::type() );
- resized |= adjust_size_by_resizeability( m_jacobi , x , typename is_resizeable<matrix_type>::type() );
- return resized;
- }
-
-
-private:
-
- value_type m_epsilon;
- resizer_type m_resizer;
- wrapped_deriv_type m_dxdt;
- wrapped_state_type m_x;
- wrapped_matrix_type m_identity;
- wrapped_matrix_type m_jacobi;
-};
-
-
-} // odeint
-} // numeric
-} // boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_EXTERNAL_IMPLICIT_EULER_MTL4_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/mtl4/mtl4.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/mtl4/mtl4.hpp
deleted file mode 100644
index 9b9ebf71d05302dec0fe44c6813c25262aa3bc8b..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/mtl4/mtl4.hpp
+++ /dev/null
@@ -1,23 +0,0 @@
-/*
- [auto_generated]
- /boost/numeric/odeint/external/mtl4/mtl4.hpp
-
- [begin_description]
- includes all headers required for using mtl4 with odeint
- [end_description]
-
- Copyright 2013 Karsten Ahnert
- Copyright 2013 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-#ifndef BOOST_NUMERIC_ODEINT_EXTERNAL_MTL4_MTL4_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_EXTERNAL_MTL4_MTL4_HPP_INCLUDED
-
-#include <boost/numeric/odeint/external/mtl4/mtl4_algebra_dispatcher.hpp>
-#include <boost/numeric/odeint/external/mtl4/mtl4_resize.hpp>
-
-#endif // BOOST_NUMERIC_ODEINT_EXTERNAL_MTL4_MTL4_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/mtl4/mtl4_algebra_dispatcher.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/mtl4/mtl4_algebra_dispatcher.hpp
deleted file mode 100644
index 8f6bfbe32e93dc58a2390c84d1bb8390371c208c..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/mtl4/mtl4_algebra_dispatcher.hpp
+++ /dev/null
@@ -1,99 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/external/mtl4/mtl4_algebra_dispatcher.hpp
-
- [begin_description]
- specialization of the algebra dispatcher for mtl4
- [end_description]
-
- Copyright 2013 Karsten Ahnert
- Copyright 2013 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-#ifndef BOOST_NUMERIC_ODEINT_MTL4_MTL4_ALGEBRA_DISPATCHER_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_MTL4_MTL4_ALGEBRA_DISPATCHER_HPP_INCLUDED
-
-#include <boost/numeric/mtl/mtl.hpp>
-
-#include <boost/numeric/odeint/algebra/vector_space_algebra.hpp>
-#include <boost/numeric/odeint/algebra/algebra_dispatcher.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-template<typename Value, typename Parameters>
-struct algebra_dispatcher< mtl::dense_vector< Value , Parameters > >
-{
- typedef vector_space_algebra algebra_type;
-};
-
-template<typename Value, typename Parameters>
-struct algebra_dispatcher< mtl::dense2D< Value , Parameters > >
-{
- typedef vector_space_algebra algebra_type;
-};
-
-template<typename Value , size_t BitMask , typename Parameters>
-struct algebra_dispatcher< mtl::morton_dense< Value , BitMask, Parameters > >
-{
- typedef vector_space_algebra algebra_type;
-};
-
-template<typename Value, typename Parameters>
-struct algebra_dispatcher< mtl::compressed2D< Value , Parameters > >
-{
- typedef vector_space_algebra algebra_type;
-};
-
-// specialization of infinity norm calculation
-
-template<typename Value, typename Parameters>
-struct vector_space_norm_inf< mtl::dense_vector< Value , Parameters > >
-{
- typedef Value result_type;
- Value operator()( const mtl::dense_vector< Value , Parameters > &x ) const
- {
- return mtl::infinity_norm(x);
- }
-};
-
-template<typename Value, typename Parameters>
-struct vector_space_norm_inf< mtl::dense2D< Value , Parameters > >
-{
- typedef Value result_type;
- Value operator()( const mtl::dense2D< Value , Parameters > &x ) const
- {
- return mtl::infinity_norm(x);
- }
-};
-
-template<typename Value , size_t BitMask , typename Parameters>
-struct vector_space_norm_inf< mtl::morton_dense< Value , BitMask , Parameters > >
-{
- typedef Value result_type;
- Value operator()( const mtl::morton_dense< Value , BitMask , Parameters > &x ) const
- {
- return mtl::infinity_norm(x);
- }
-};
-
-template<typename Value, typename Parameters>
-struct vector_space_norm_inf< mtl::compressed2D< Value , Parameters > >
-{
- typedef Value result_type;
- Value operator()( const mtl::compressed2D< Value , Parameters > &x ) const
- {
- return mtl::infinity_norm(x);
- }
-};
-
-}
-}
-}
-
-#endif // BOOST_NUMERIC_ODEINT_MTL4_MTL4_ALGEBRA_DISPATCHER_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/mtl4/mtl4_resize.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/mtl4/mtl4_resize.hpp
deleted file mode 100644
index 762283550b48039cbd459e5a411aed94b36331cd..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/mtl4/mtl4_resize.hpp
+++ /dev/null
@@ -1,133 +0,0 @@
-/*
-[begin_description]
-Modification of the implicit Euler method, works with the MTL4 matrix library only.
-[end_description]
-
-Copyright 2012-2013 Andreas Angelopoulos
-Copyright 2012-2013 Karsten Ahnert
-Copyright 2012-2013 Mario Mulansky
-
-Distributed under the Boost Software License, Version 1.0.
-(See accompanying file LICENSE_1_0.txt or
-copy at http://www.boost.org/LICENSE_1_0.txt)
-*/
-
-
-#ifndef BOOST_NUMERIC_ODEINT_EXTERNAL_MTL4_RESIZE_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_EXTERNAL_MTL4_RESIZE_HPP_INCLUDED
-
-#include <boost/numeric/odeint/util/is_resizeable.hpp>
-#include <boost/numeric/odeint/util/resize.hpp>
-#include <boost/numeric/odeint/util/same_size.hpp>
-
-#include <boost/numeric/mtl/vector/dense_vector.hpp>
-#include <boost/numeric/mtl/matrix/dense2D.hpp>
-#include <boost/numeric/mtl/matrix/compressed2D.hpp>
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-template< class Value , class Parameters >
-struct is_resizeable< mtl::dense_vector< Value , Parameters > >
-{
- typedef boost::true_type type;
- const static bool value = type::value;
-};
-
-template< class Value , class Parameters >
-struct is_resizeable< mtl::dense2D< Value , Parameters > >
-{
- typedef boost::true_type type;
- const static bool value = type::value;
-};
-
-template< class Value , class Parameters >
-struct is_resizeable< mtl::compressed2D< Value , Parameters > >
-{
- typedef boost::true_type type;
- const static bool value = type::value;
-};
-
-
-
-
-template< class Value , class Parameters >
-struct same_size_impl< mtl::dense_vector< Value , Parameters > , mtl::dense_vector< Value , Parameters > >
-{
- static bool same_size( const mtl::dense_vector< Value , Parameters > &v1 ,
- const mtl::dense_vector< Value , Parameters > &v2 )
- {
- return mtl::size( v1 ) == mtl::size( v2 );
- }
-};
-
-template< class Value , class Parameters >
-struct resize_impl< mtl::dense_vector< Value , Parameters > , mtl::dense_vector< Value , Parameters > >
-{
- static void resize( mtl::dense_vector< Value , Parameters > &v1 ,
- const mtl::dense_vector< Value , Parameters > &v2 )
- {
- v1.change_dim( mtl::size( v2 ) );
- }
-};
-
-
-
-template< class Value , class MatrixParameters , class VectorParameters >
-struct same_size_impl< mtl::dense2D< Value , MatrixParameters > , mtl::dense_vector< Value , VectorParameters > >
-{
- static bool same_size( const mtl::dense2D< Value , MatrixParameters > &m ,
- const mtl::dense_vector< Value , VectorParameters > &v )
- {
- return ( ( mtl::size( v ) == m.num_cols() ) && ( mtl::size( v ) == m.num_rows() ) );
- }
-};
-
-template< class Value , class MatrixParameters , class VectorParameters >
-struct resize_impl< mtl::dense2D< Value , MatrixParameters > , mtl::dense_vector< Value , VectorParameters > >
-{
- static void resize( mtl::dense2D< Value , MatrixParameters > &m ,
- const mtl::dense_vector< Value , VectorParameters > &v )
- {
- m.change_dim( mtl::size( v ) , mtl::size( v ) , false );
- }
-};
-
-
-
-
-template< class Value , class MatrixParameters , class VectorParameters >
-struct same_size_impl< mtl::compressed2D< Value , MatrixParameters > , mtl::dense_vector< Value , VectorParameters > >
-{
- static bool same_size( const mtl::compressed2D< Value , MatrixParameters > &m ,
- const mtl::dense_vector< Value , VectorParameters > &v )
- {
- return ( ( mtl::size( v ) == m.num_cols() ) && ( mtl::size( v ) == m.num_rows() ) );
- }
-};
-
-template< class Value , class MatrixParameters , class VectorParameters >
-struct resize_impl< mtl::compressed2D< Value , MatrixParameters > , mtl::dense_vector< Value , VectorParameters > >
-{
- static void resize( mtl::compressed2D< Value , MatrixParameters > &m ,
- const mtl::dense_vector< Value , VectorParameters > &v )
- {
- m.change_dim( mtl::size( v ) , mtl::size( v ) );
- }
-};
-
-
-
-
-
-
-
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-#endif // BOOST_NUMERIC_ODEINT_EXTERNAL_MTL4_RESIZE_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/nt2/nt2_algebra_dispatcher.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/nt2/nt2_algebra_dispatcher.hpp
deleted file mode 100644
index 7b82a8b315151a084fbe140ab10154dce734fe44..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/nt2/nt2_algebra_dispatcher.hpp
+++ /dev/null
@@ -1,25 +0,0 @@
-//==============================================================================
-// Copyright 2014 LRI UMR 8623 CNRS/Univ Paris Sud XI
-// Copyright 2014 NumScale SAS
-//
-// Distributed under the Boost Software License, Version 1.0.
-// See accompanying file LICENSE.txt or copy at
-// http://www.boost.org/LICENSE_1_0.txt
-//==============================================================================
-#ifndef BOOST_NUMERIC_ODEINT_EXTERNAL_NT2_NT2_ALGEBRA_DISPATCHER_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_EXTERNAL_NT2_NT2_ALGEBRA_DISPATCHER_HPP_INCLUDED
-
-#include <nt2/core/container/table/table.hpp>
-
-#include <boost/numeric/odeint/algebra/vector_space_algebra.hpp>
-#include <boost/numeric/odeint/algebra/algebra_dispatcher.hpp>
-
-namespace boost { namespace numeric { namespace odeint {
-template<typename T, typename S>
-struct algebra_dispatcher<nt2::container::table<T,S> >
-{
- typedef vector_space_algebra algebra_type;
-};
-} } }
-
-#endif
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/nt2/nt2_copy.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/nt2/nt2_copy.hpp
deleted file mode 100644
index 0fd558843c69dbc2140c0c52df49850856fce053..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/nt2/nt2_copy.hpp
+++ /dev/null
@@ -1,33 +0,0 @@
-//==============================================================================
-// Copyright 2014 LASMEA UMR 6602 CNRS/Univ. Clermont II
-// Copyright 2014 LRI UMR 8623 CNRS/Univ Paris Sud XI
-// Copyright 2014 MetaScale SAS
-//
-// Distributed under the Boost Software License, Version 1.0.
-// See accompanying file LICENSE.txt or copy at
-// http://www.boost.org/LICENSE_1_0.txt
-//==============================================================================
-#ifndef BOOST_NUMERIC_ODEINT_EXTERNAL_NT2_NT2_COPY_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_EXTERNAL_NT2_NT2_COPY_HPP_INCLUDED
-
-#include <nt2/core/container/table/table.hpp>
-
-#include <boost/numeric/odeint/util/copy.hpp>
-
-namespace boost { namespace numeric { namespace odeint {
-
-template<typename T, typename S>
-struct copy_impl< nt2::container::table<T,S>
- , nt2::container::table<T,S>
- >
-{
- static void copy ( const nt2::container::table<T,S> &v1
- , nt2::container::table<T,S> &v2
- )
- {
- v2 = v1;
- }
-};
-} } }
-
-#endif
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/nt2/nt2_norm_inf.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/nt2/nt2_norm_inf.hpp
deleted file mode 100644
index 81f867e35367514b5b0217564c5b2545454d0da1..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/nt2/nt2_norm_inf.hpp
+++ /dev/null
@@ -1,31 +0,0 @@
-//==============================================================================
-// Copyright 2014 LRI UMR 8623 CNRS/Univ Paris Sud XI
-// Copyright 2014 NumScale SAS
-//
-// Distributed under the Boost Software License, Version 1.0.
-// See accompanying file LICENSE.txt or copy at
-// http://www.boost.org/LICENSE_1_0.txt
-//==============================================================================
-#ifndef BOOST_NUMERIC_ODEINT_EXTERNAL_NT2_NT2_NORM_INF_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_EXTERNAL_NT2_NT2_NORM_INF_HPP_INCLUDED
-
-#include <nt2/core/container/table/table.hpp>
-#include <nt2/include/functions/globalmax.hpp>
-#include <nt2/include/functions/abs.hpp>
-
-#include <boost/numeric/odeint/algebra/vector_space_algebra.hpp>
-
-namespace boost { namespace numeric { namespace odeint
-{
- template<typename T, typename S>
- struct vector_space_norm_inf<nt2::container::table<T,S> >
- {
- typedef T result_type;
- result_type operator()(const nt2::container::table<T,S> &v1) const
- {
- return nt2::globalmax(nt2::abs(v1));
- }
- };
-} } }
-
-#endif
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/nt2/nt2_resize.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/nt2/nt2_resize.hpp
deleted file mode 100644
index d9c2359c3ed99b44903ccae7a0abaf6ff5780333..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/nt2/nt2_resize.hpp
+++ /dev/null
@@ -1,52 +0,0 @@
-//==============================================================================
-// Copyright 2014 LRI UMR 8623 CNRS/Univ Paris Sud XI
-// Copyright 2014 NumScale SAS
-//
-// Distributed under the Boost Software License, Version 1.0.
-// See accompanying file LICENSE.txt or copy at
-// http://www.boost.org/LICENSE_1_0.txt
-//==============================================================================
-#ifndef BOOST_NUMERIC_ODEINT_EXTERNAL_NT2_NT2_RESIZE_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_EXTERNAL_NT2_NT2_RESIZE_HPP_INCLUDED
-
-#include <nt2/core/container/table/table.hpp>
-
-#include <boost/numeric/odeint/util/same_size.hpp>
-
-namespace boost { namespace numeric { namespace odeint {
-
-template<typename T, typename S>
-struct is_resizeable< nt2::container::table<T,S> >
-{
- typedef boost::true_type type;
- static const bool value = type::value;
-};
-
-template<typename T, typename S>
-struct same_size_impl< nt2::container::table<T,S>
- , nt2::container::table<T,S>
- >
-{
- static bool same_size ( const nt2::container::table<T,S> &v1
- , const nt2::container::table<T,S> &v2
- )
- {
- return v1.extent() == v2.extent();
- }
-};
-
-template<typename T, typename S>
-struct resize_impl< nt2::container::table<T,S>
- , nt2::container::table<T,S>
- >
-{
- static void resize ( nt2::container::table<T,S> &v1
- , const nt2::container::table<T,S> &v2
- )
- {
- v1.resize( v2.extent() );
- }
-};
-} } }
-
-#endif
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/openmp/openmp.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/openmp/openmp.hpp
deleted file mode 100644
index 0d6fb0b85579cd31721a6d25eb52ead72d62902c..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/openmp/openmp.hpp
+++ /dev/null
@@ -1,31 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/external/openmp/openmp.hpp
-
- [begin_description]
- Wrappers for OpenMP.
- [end_description]
-
- Copyright 2013 Karsten Ahnert
- Copyright 2013 Mario Mulansky
- Copyright 2013 Pascal Germroth
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_EXTERNAL_OPENMP_OPENMP_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_EXTERNAL_OPENMP_OPENMP_HPP_INCLUDED
-
-// level 1: parallel iteration over random access container
-#include <boost/numeric/odeint/external/openmp/openmp_range_algebra.hpp>
-
-// level 2: split range state
-#include <boost/numeric/odeint/external/openmp/openmp_state.hpp>
-
-// level 3: process a random access container of sub-states in parallel
-#include <boost/numeric/odeint/external/openmp/openmp_nested_algebra.hpp>
-
-#endif
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/openmp/openmp_nested_algebra.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/openmp/openmp_nested_algebra.hpp
deleted file mode 100644
index a3d299f0a74238b99edcb45f1fddb99aa6f6c25f..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/openmp/openmp_nested_algebra.hpp
+++ /dev/null
@@ -1,281 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/external/openmp/openmp_nested_algebra.hpp
-
- [begin_description]
- Nested parallelized algebra for OpenMP.
- [end_description]
-
- Copyright 2013 Karsten Ahnert
- Copyright 2013 Mario Mulansky
- Copyright 2013 Pascal Germroth
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_EXTERNAL_OPENMP_OPENMP_NESTED_ALGEBRA_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_EXTERNAL_OPENMP_OPENMP_NESTED_ALGEBRA_HPP_INCLUDED
-
-#include <boost/assert.hpp>
-#include <boost/range.hpp>
-#include <boost/numeric/odeint/algebra/norm_result_type.hpp>
-#include <boost/numeric/odeint/util/n_ary_helper.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-/** \brief OpenMP-parallelized algebra, wrapping another, non-parallelized algebra.
- *
- * NestedState must be a model of Random Access Range, where the elements are sub-states
- * which will be processed in parallel.
- */
-template< class InnerAlgebra >
-struct openmp_nested_algebra
-{
-
-#if __cplusplus >= 201103L // C++11 supports _Pragma
-
-#define BOOST_ODEINT_GEN_LOCAL(z, n, unused) \
- BOOST_ASSERT_MSG( len == boost::size(s ## n), "All nested state ranges must have the same size." ); \
- typename boost::range_iterator<S ## n>::type beg ## n = boost::begin(s ## n);
-#define BOOST_ODEINT_GEN_BODY(n) \
- const size_t len = boost::size(s0); \
- BOOST_PP_REPEAT(n, BOOST_ODEINT_GEN_LOCAL, ~) \
- _Pragma("omp parallel for schedule(runtime)") \
- for( size_t i = 0 ; i < len ; i++ ) \
- InnerAlgebra::for_each##n( \
- BOOST_PP_ENUM_BINARY_PARAMS(n, beg, [i] BOOST_PP_INTERCEPT) , \
- op \
- );
-BOOST_ODEINT_GEN_FOR_EACH(BOOST_ODEINT_GEN_BODY)
-#undef BOOST_ODEINT_GEN_BODY
-#undef BOOST_ODEINT_GEN_LOCAL
-
-#else
-
- template< class S0 , class Op > static void for_each1 ( S0 &s0 , Op op ) {
- const size_t len = boost::size(s0);
- typename boost::range_iterator<S0>::type beg0 = boost::begin(s0);
- #pragma omp parallel for schedule(runtime)
- for( size_t i = 0 ; i < len ; i++ ) InnerAlgebra::for_each1( beg0 [i] , op );
- }
- template< class S0 , class S1 , class Op > static void for_each2 ( S0 &s0 , S1 &s1 , Op op ) {
- const size_t len = boost::size(s0);
- typename boost::range_iterator<S0>::type beg0 = boost::begin(s0);
- typename boost::range_iterator<S1>::type beg1 = boost::begin(s1);
- #pragma omp parallel for schedule(runtime)
- for( size_t i = 0 ; i < len ; i++ ) InnerAlgebra::for_each2( beg0 [i] , beg1 [i] , op );
- }
- template< class S0 , class S1 , class S2 , class Op > static void for_each3 ( S0 &s0 , S1 &s1 , S2 &s2 , Op op ) {
- const size_t len = boost::size(s0);
- typename boost::range_iterator<S0>::type beg0 = boost::begin(s0);
- typename boost::range_iterator<S1>::type beg1 = boost::begin(s1);
- typename boost::range_iterator<S2>::type beg2 = boost::begin(s2);
- #pragma omp parallel for schedule(runtime)
- for( size_t i = 0 ; i < len ; i++ ) InnerAlgebra::for_each3( beg0 [i] , beg1 [i] , beg2 [i] , op );
- }
- template< class S0 , class S1 , class S2 , class S3 , class Op > static void for_each4 ( S0 &s0 , S1 &s1 , S2 &s2 , S3 &s3 , Op op ) {
- const size_t len = boost::size(s0);
- typename boost::range_iterator<S0>::type beg0 = boost::begin(s0);
- typename boost::range_iterator<S1>::type beg1 = boost::begin(s1);
- typename boost::range_iterator<S2>::type beg2 = boost::begin(s2);
- typename boost::range_iterator<S3>::type beg3 = boost::begin(s3);
- #pragma omp parallel for schedule(runtime)
- for( size_t i = 0 ; i < len ; i++ ) InnerAlgebra::for_each4( beg0 [i] , beg1 [i] , beg2 [i] , beg3 [i] , op );
- }
- template< class S0 , class S1 , class S2 , class S3 , class S4 , class Op > static void for_each5 ( S0 &s0 , S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , Op op ) {
- const size_t len = boost::size(s0);
- typename boost::range_iterator<S0>::type beg0 = boost::begin(s0);
- typename boost::range_iterator<S1>::type beg1 = boost::begin(s1);
- typename boost::range_iterator<S2>::type beg2 = boost::begin(s2);
- typename boost::range_iterator<S3>::type beg3 = boost::begin(s3);
- typename boost::range_iterator<S4>::type beg4 = boost::begin(s4);
- #pragma omp parallel for schedule(runtime)
- for( size_t i = 0 ; i < len ; i++ ) InnerAlgebra::for_each5( beg0 [i] , beg1 [i] , beg2 [i] , beg3 [i] , beg4 [i] , op );
- }
- template< class S0 , class S1 , class S2 , class S3 , class S4 , class S5 , class Op > static void for_each6 ( S0 &s0 , S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , Op op ) {
- const size_t len = boost::size(s0);
- typename boost::range_iterator<S0>::type beg0 = boost::begin(s0);
- typename boost::range_iterator<S1>::type beg1 = boost::begin(s1);
- typename boost::range_iterator<S2>::type beg2 = boost::begin(s2);
- typename boost::range_iterator<S3>::type beg3 = boost::begin(s3);
- typename boost::range_iterator<S4>::type beg4 = boost::begin(s4);
- typename boost::range_iterator<S5>::type beg5 = boost::begin(s5);
- #pragma omp parallel for schedule(runtime)
- for( size_t i = 0 ; i < len ; i++ ) InnerAlgebra::for_each6( beg0 [i] , beg1 [i] , beg2 [i] , beg3 [i] , beg4 [i] , beg5 [i] , op );
- }
- template< class S0 , class S1 , class S2 , class S3 , class S4 , class S5 , class S6 , class Op > static void for_each7 ( S0 &s0 , S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , Op op ) {
- const size_t len = boost::size(s0);
- typename boost::range_iterator<S0>::type beg0 = boost::begin(s0);
- typename boost::range_iterator<S1>::type beg1 = boost::begin(s1);
- typename boost::range_iterator<S2>::type beg2 = boost::begin(s2);
- typename boost::range_iterator<S3>::type beg3 = boost::begin(s3);
- typename boost::range_iterator<S4>::type beg4 = boost::begin(s4);
- typename boost::range_iterator<S5>::type beg5 = boost::begin(s5);
- typename boost::range_iterator<S6>::type beg6 = boost::begin(s6);
- #pragma omp parallel for schedule(runtime)
- for( size_t i = 0 ; i < len ; i++ ) InnerAlgebra::for_each7( beg0 [i] , beg1 [i] , beg2 [i] , beg3 [i] , beg4 [i] , beg5 [i] , beg6 [i] , op );
- }
- template< class S0 , class S1 , class S2 , class S3 , class S4 , class S5 , class S6 , class S7 , class Op > static void for_each8 ( S0 &s0 , S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , Op op ) {
- const size_t len = boost::size(s0);
- typename boost::range_iterator<S0>::type beg0 = boost::begin(s0);
- typename boost::range_iterator<S1>::type beg1 = boost::begin(s1);
- typename boost::range_iterator<S2>::type beg2 = boost::begin(s2);
- typename boost::range_iterator<S3>::type beg3 = boost::begin(s3);
- typename boost::range_iterator<S4>::type beg4 = boost::begin(s4);
- typename boost::range_iterator<S5>::type beg5 = boost::begin(s5);
- typename boost::range_iterator<S6>::type beg6 = boost::begin(s6);
- typename boost::range_iterator<S7>::type beg7 = boost::begin(s7);
- #pragma omp parallel for schedule(runtime)
- for( size_t i = 0 ; i < len ; i++ ) InnerAlgebra::for_each8( beg0 [i] , beg1 [i] , beg2 [i] , beg3 [i] , beg4 [i] , beg5 [i] , beg6 [i] , beg7 [i] , op );
- }
- template< class S0 , class S1 , class S2 , class S3 , class S4 , class S5 , class S6 , class S7 , class S8 , class Op > static void for_each9 ( S0 &s0 , S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , S8 &s8 , Op op ) {
- const size_t len = boost::size(s0);
- typename boost::range_iterator<S0>::type beg0 = boost::begin(s0);
- typename boost::range_iterator<S1>::type beg1 = boost::begin(s1);
- typename boost::range_iterator<S2>::type beg2 = boost::begin(s2);
- typename boost::range_iterator<S3>::type beg3 = boost::begin(s3);
- typename boost::range_iterator<S4>::type beg4 = boost::begin(s4);
- typename boost::range_iterator<S5>::type beg5 = boost::begin(s5);
- typename boost::range_iterator<S6>::type beg6 = boost::begin(s6);
- typename boost::range_iterator<S7>::type beg7 = boost::begin(s7);
- typename boost::range_iterator<S8>::type beg8 = boost::begin(s8);
- #pragma omp parallel for schedule(runtime)
- for( size_t i = 0 ; i < len ; i++ ) InnerAlgebra::for_each9( beg0 [i] , beg1 [i] , beg2 [i] , beg3 [i] , beg4 [i] , beg5 [i] , beg6 [i] , beg7 [i] , beg8 [i] , op );
- }
- template< class S0 , class S1 , class S2 , class S3 , class S4 , class S5 , class S6 , class S7 , class S8 , class S9 , class Op > static void for_each10 ( S0 &s0 , S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , S8 &s8 , S9 &s9 , Op op ) {
- const size_t len = boost::size(s0);
- typename boost::range_iterator<S0>::type beg0 = boost::begin(s0);
- typename boost::range_iterator<S1>::type beg1 = boost::begin(s1);
- typename boost::range_iterator<S2>::type beg2 = boost::begin(s2);
- typename boost::range_iterator<S3>::type beg3 = boost::begin(s3);
- typename boost::range_iterator<S4>::type beg4 = boost::begin(s4);
- typename boost::range_iterator<S5>::type beg5 = boost::begin(s5);
- typename boost::range_iterator<S6>::type beg6 = boost::begin(s6);
- typename boost::range_iterator<S7>::type beg7 = boost::begin(s7);
- typename boost::range_iterator<S8>::type beg8 = boost::begin(s8);
- typename boost::range_iterator<S9>::type beg9 = boost::begin(s9);
- #pragma omp parallel for schedule(runtime)
- for( size_t i = 0 ; i < len ; i++ ) InnerAlgebra::for_each10( beg0 [i] , beg1 [i] , beg2 [i] , beg3 [i] , beg4 [i] , beg5 [i] , beg6 [i] , beg7 [i] , beg8 [i] , beg9 [i] , op );
- }
- template< class S0 , class S1 , class S2 , class S3 , class S4 , class S5 , class S6 , class S7 , class S8 , class S9 , class S10 , class Op > static void for_each11 ( S0 &s0 , S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , S8 &s8 , S9 &s9 , S10 &s10 , Op op ) {
- const size_t len = boost::size(s0);
- typename boost::range_iterator<S0>::type beg0 = boost::begin(s0);
- typename boost::range_iterator<S1>::type beg1 = boost::begin(s1);
- typename boost::range_iterator<S2>::type beg2 = boost::begin(s2);
- typename boost::range_iterator<S3>::type beg3 = boost::begin(s3);
- typename boost::range_iterator<S4>::type beg4 = boost::begin(s4);
- typename boost::range_iterator<S5>::type beg5 = boost::begin(s5);
- typename boost::range_iterator<S6>::type beg6 = boost::begin(s6);
- typename boost::range_iterator<S7>::type beg7 = boost::begin(s7);
- typename boost::range_iterator<S8>::type beg8 = boost::begin(s8);
- typename boost::range_iterator<S9>::type beg9 = boost::begin(s9);
- typename boost::range_iterator<S10>::type beg10 = boost::begin(s10);
- #pragma omp parallel for schedule(runtime)
- for( size_t i = 0 ; i < len ; i++ ) InnerAlgebra::for_each11( beg0 [i] , beg1 [i] , beg2 [i] , beg3 [i] , beg4 [i] , beg5 [i] , beg6 [i] , beg7 [i] , beg8 [i] , beg9 [i] , beg10 [i] , op );
- }
- template< class S0 , class S1 , class S2 , class S3 , class S4 , class S5 , class S6 , class S7 , class S8 , class S9 , class S10 , class S11 , class Op > static void for_each12 ( S0 &s0 , S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , S8 &s8 , S9 &s9 , S10 &s10 , S11 &s11 , Op op ) {
- const size_t len = boost::size(s0);
- typename boost::range_iterator<S0>::type beg0 = boost::begin(s0);
- typename boost::range_iterator<S1>::type beg1 = boost::begin(s1);
- typename boost::range_iterator<S2>::type beg2 = boost::begin(s2);
- typename boost::range_iterator<S3>::type beg3 = boost::begin(s3);
- typename boost::range_iterator<S4>::type beg4 = boost::begin(s4);
- typename boost::range_iterator<S5>::type beg5 = boost::begin(s5);
- typename boost::range_iterator<S6>::type beg6 = boost::begin(s6);
- typename boost::range_iterator<S7>::type beg7 = boost::begin(s7);
- typename boost::range_iterator<S8>::type beg8 = boost::begin(s8);
- typename boost::range_iterator<S9>::type beg9 = boost::begin(s9);
- typename boost::range_iterator<S10>::type beg10 = boost::begin(s10);
- typename boost::range_iterator<S11>::type beg11 = boost::begin(s11);
- #pragma omp parallel for schedule(runtime)
- for( size_t i = 0 ; i < len ; i++ ) InnerAlgebra::for_each12( beg0 [i] , beg1 [i] , beg2 [i] , beg3 [i] , beg4 [i] , beg5 [i] , beg6 [i] , beg7 [i] , beg8 [i] , beg9 [i] , beg10 [i] , beg11 [i] , op );
- }
- template< class S0 , class S1 , class S2 , class S3 , class S4 , class S5 , class S6 , class S7 , class S8 , class S9 , class S10 , class S11 , class S12 , class Op > static void for_each13 ( S0 &s0 , S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , S8 &s8 , S9 &s9 , S10 &s10 , S11 &s11 , S12 &s12 , Op op ) {
- const size_t len = boost::size(s0);
- typename boost::range_iterator<S0>::type beg0 = boost::begin(s0);
- typename boost::range_iterator<S1>::type beg1 = boost::begin(s1);
- typename boost::range_iterator<S2>::type beg2 = boost::begin(s2);
- typename boost::range_iterator<S3>::type beg3 = boost::begin(s3);
- typename boost::range_iterator<S4>::type beg4 = boost::begin(s4);
- typename boost::range_iterator<S5>::type beg5 = boost::begin(s5);
- typename boost::range_iterator<S6>::type beg6 = boost::begin(s6);
- typename boost::range_iterator<S7>::type beg7 = boost::begin(s7);
- typename boost::range_iterator<S8>::type beg8 = boost::begin(s8);
- typename boost::range_iterator<S9>::type beg9 = boost::begin(s9);
- typename boost::range_iterator<S10>::type beg10 = boost::begin(s10);
- typename boost::range_iterator<S11>::type beg11 = boost::begin(s11);
- typename boost::range_iterator<S12>::type beg12 = boost::begin(s12);
- #pragma omp parallel for schedule(runtime)
- for( size_t i = 0 ; i < len ; i++ ) InnerAlgebra::for_each13( beg0 [i] , beg1 [i] , beg2 [i] , beg3 [i] , beg4 [i] , beg5 [i] , beg6 [i] , beg7 [i] , beg8 [i] , beg9 [i] , beg10 [i] , beg11 [i] , beg12 [i] , op );
- }
- template< class S0 , class S1 , class S2 , class S3 , class S4 , class S5 , class S6 , class S7 , class S8 , class S9 , class S10 , class S11 , class S12 , class S13 , class Op > static void for_each14 ( S0 &s0 , S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , S8 &s8 , S9 &s9 , S10 &s10 , S11 &s11 , S12 &s12 , S13 &s13 , Op op ) {
- const size_t len = boost::size(s0);
- typename boost::range_iterator<S0>::type beg0 = boost::begin(s0);
- typename boost::range_iterator<S1>::type beg1 = boost::begin(s1);
- typename boost::range_iterator<S2>::type beg2 = boost::begin(s2);
- typename boost::range_iterator<S3>::type beg3 = boost::begin(s3);
- typename boost::range_iterator<S4>::type beg4 = boost::begin(s4);
- typename boost::range_iterator<S5>::type beg5 = boost::begin(s5);
- typename boost::range_iterator<S6>::type beg6 = boost::begin(s6);
- typename boost::range_iterator<S7>::type beg7 = boost::begin(s7);
- typename boost::range_iterator<S8>::type beg8 = boost::begin(s8);
- typename boost::range_iterator<S9>::type beg9 = boost::begin(s9);
- typename boost::range_iterator<S10>::type beg10 = boost::begin(s10);
- typename boost::range_iterator<S11>::type beg11 = boost::begin(s11);
- typename boost::range_iterator<S12>::type beg12 = boost::begin(s12);
- typename boost::range_iterator<S13>::type beg13 = boost::begin(s13);
- #pragma omp parallel for schedule(runtime)
- for( size_t i = 0 ; i < len ; i++ ) InnerAlgebra::for_each14( beg0 [i] , beg1 [i] , beg2 [i] , beg3 [i] , beg4 [i] , beg5 [i] , beg6 [i] , beg7 [i] , beg8 [i] , beg9 [i] , beg10 [i] , beg11 [i] , beg12 [i] , beg13 [i] , op );
- }
- template< class S0 , class S1 , class S2 , class S3 , class S4 , class S5 , class S6 , class S7 , class S8 , class S9 , class S10 , class S11 , class S12 , class S13 , class S14 , class Op > static void for_each15 ( S0 &s0 , S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , S8 &s8 , S9 &s9 , S10 &s10 , S11 &s11 , S12 &s12 , S13 &s13 , S14 &s14 , Op op ) {
- const size_t len = boost::size(s0);
- typename boost::range_iterator<S0>::type beg0 = boost::begin(s0);
- typename boost::range_iterator<S1>::type beg1 = boost::begin(s1);
- typename boost::range_iterator<S2>::type beg2 = boost::begin(s2);
- typename boost::range_iterator<S3>::type beg3 = boost::begin(s3);
- typename boost::range_iterator<S4>::type beg4 = boost::begin(s4);
- typename boost::range_iterator<S5>::type beg5 = boost::begin(s5);
- typename boost::range_iterator<S6>::type beg6 = boost::begin(s6);
- typename boost::range_iterator<S7>::type beg7 = boost::begin(s7);
- typename boost::range_iterator<S8>::type beg8 = boost::begin(s8);
- typename boost::range_iterator<S9>::type beg9 = boost::begin(s9);
- typename boost::range_iterator<S10>::type beg10 = boost::begin(s10);
- typename boost::range_iterator<S11>::type beg11 = boost::begin(s11);
- typename boost::range_iterator<S12>::type beg12 = boost::begin(s12);
- typename boost::range_iterator<S13>::type beg13 = boost::begin(s13);
- typename boost::range_iterator<S14>::type beg14 = boost::begin(s14);
- #pragma omp parallel for schedule(runtime)
- for( size_t i = 0 ; i < len ; i++ ) InnerAlgebra::for_each15( beg0 [i] , beg1 [i] , beg2 [i] , beg3 [i] , beg4 [i] , beg5 [i] , beg6 [i] , beg7 [i] , beg8 [i] , beg9 [i] , beg10 [i] , beg11 [i] , beg12 [i] , beg13 [i] , beg14 [i] , op );
- }
-
-#endif
-
-
- template< class NestedState >
- static typename norm_result_type< typename NestedState::value_type >::type norm_inf( const NestedState &s )
- {
- typedef typename boost::range_iterator<const NestedState>::type iterator;
- typedef typename std::iterator_traits<iterator>::value_type value_type;
- typedef typename norm_result_type<value_type>::type result_type;
- result_type init = static_cast< result_type >( 0 );
- const size_t len = boost::size(s);
- iterator beg = boost::begin(s);
-# pragma omp parallel for reduction(max: init) schedule(dynamic)
- for( size_t i = 0 ; i < len ; i++ )
- init = (std::max)( init , InnerAlgebra::norm_inf( beg[i] ) );
- return init;
- }
-
-};
-
-
-}
-}
-}
-
-#endif
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/openmp/openmp_range_algebra.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/openmp/openmp_range_algebra.hpp
deleted file mode 100644
index 295db647d46c41ccda97cc5133a772a45a403b98..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/openmp/openmp_range_algebra.hpp
+++ /dev/null
@@ -1,276 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/external/openmp/openmp_range_algebra.hpp
-
- [begin_description]
- Range algebra for OpenMP.
- [end_description]
-
- Copyright 2013 Karsten Ahnert
- Copyright 2013 Mario Mulansky
- Copyright 2013 Pascal Germroth
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_EXTERNAL_OPENMP_OPENMP_RANGE_ALGEBRA_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_EXTERNAL_OPENMP_OPENMP_RANGE_ALGEBRA_HPP_INCLUDED
-
-#include <boost/assert.hpp>
-#include <boost/range.hpp>
-#include <boost/numeric/odeint/algebra/norm_result_type.hpp>
-#include <boost/numeric/odeint/util/n_ary_helper.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-/** \brief OpenMP-parallelized range algebra.
- *
- * State must be a model of Random Access Range.
- */
-struct openmp_range_algebra
-{
-
-#if __cplusplus >= 201103L // C++11 supports _Pragma
-
-#define BOOST_ODEINT_GEN_LOCAL(z, n, unused) \
- BOOST_ASSERT_MSG( len == boost::size(s ## n), "All state ranges must have the same size." ); \
- typename boost::range_iterator<S ## n>::type beg ## n = boost::begin(s ## n);
-#define BOOST_ODEINT_GEN_BODY(n) \
- const size_t len = boost::size(s0); \
- BOOST_PP_REPEAT(n, BOOST_ODEINT_GEN_LOCAL, ~) \
- _Pragma("omp parallel for schedule(runtime)") \
- for( size_t i = 0 ; i < len ; i++ ) \
- op( BOOST_PP_ENUM_BINARY_PARAMS(n, beg, [i] BOOST_PP_INTERCEPT) );
-BOOST_ODEINT_GEN_FOR_EACH(BOOST_ODEINT_GEN_BODY)
-#undef BOOST_ODEINT_GEN_BODY
-#undef BOOST_ODEINT_GEN_LOCAL
-
-#else
-
- template< class S0 , class Op > static void for_each1 ( S0 &s0 , Op op ) {
- const size_t len = boost::size(s0);
- typename boost::range_iterator<S0>::type beg0 = boost::begin(s0);
- #pragma omp parallel for schedule(runtime)
- for( size_t i = 0 ; i < len ; i++ ) op( beg0 [i] );
- }
- template< class S0 , class S1 , class Op > static void for_each2 ( S0 &s0 , S1 &s1 , Op op ) {
- const size_t len = boost::size(s0);
- typename boost::range_iterator<S0>::type beg0 = boost::begin(s0);
- typename boost::range_iterator<S1>::type beg1 = boost::begin(s1);
- #pragma omp parallel for schedule(runtime)
- for( size_t i = 0 ; i < len ; i++ ) op( beg0 [i] , beg1 [i] );
- }
- template< class S0 , class S1 , class S2 , class Op > static void for_each3 ( S0 &s0 , S1 &s1 , S2 &s2 , Op op ) {
- const size_t len = boost::size(s0);
- typename boost::range_iterator<S0>::type beg0 = boost::begin(s0);
- typename boost::range_iterator<S1>::type beg1 = boost::begin(s1);
- typename boost::range_iterator<S2>::type beg2 = boost::begin(s2);
- #pragma omp parallel for schedule(runtime)
- for( size_t i = 0 ; i < len ; i++ ) op( beg0 [i] , beg1 [i] , beg2 [i] );
- }
- template< class S0 , class S1 , class S2 , class S3 , class Op > static void for_each4 ( S0 &s0 , S1 &s1 , S2 &s2 , S3 &s3 , Op op ) {
- const size_t len = boost::size(s0);
- typename boost::range_iterator<S0>::type beg0 = boost::begin(s0);
- typename boost::range_iterator<S1>::type beg1 = boost::begin(s1);
- typename boost::range_iterator<S2>::type beg2 = boost::begin(s2);
- typename boost::range_iterator<S3>::type beg3 = boost::begin(s3);
- #pragma omp parallel for schedule(runtime)
- for( size_t i = 0 ; i < len ; i++ ) op( beg0 [i] , beg1 [i] , beg2 [i] , beg3 [i] );
- }
- template< class S0 , class S1 , class S2 , class S3 , class S4 , class Op > static void for_each5 ( S0 &s0 , S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , Op op ) {
- const size_t len = boost::size(s0);
- typename boost::range_iterator<S0>::type beg0 = boost::begin(s0);
- typename boost::range_iterator<S1>::type beg1 = boost::begin(s1);
- typename boost::range_iterator<S2>::type beg2 = boost::begin(s2);
- typename boost::range_iterator<S3>::type beg3 = boost::begin(s3);
- typename boost::range_iterator<S4>::type beg4 = boost::begin(s4);
- #pragma omp parallel for schedule(runtime)
- for( size_t i = 0 ; i < len ; i++ ) op( beg0 [i] , beg1 [i] , beg2 [i] , beg3 [i] , beg4 [i] );
- }
- template< class S0 , class S1 , class S2 , class S3 , class S4 , class S5 , class Op > static void for_each6 ( S0 &s0 , S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , Op op ) {
- const size_t len = boost::size(s0);
- typename boost::range_iterator<S0>::type beg0 = boost::begin(s0);
- typename boost::range_iterator<S1>::type beg1 = boost::begin(s1);
- typename boost::range_iterator<S2>::type beg2 = boost::begin(s2);
- typename boost::range_iterator<S3>::type beg3 = boost::begin(s3);
- typename boost::range_iterator<S4>::type beg4 = boost::begin(s4);
- typename boost::range_iterator<S5>::type beg5 = boost::begin(s5);
- #pragma omp parallel for schedule(runtime)
- for( size_t i = 0 ; i < len ; i++ ) op( beg0 [i] , beg1 [i] , beg2 [i] , beg3 [i] , beg4 [i] , beg5 [i] );
- }
- template< class S0 , class S1 , class S2 , class S3 , class S4 , class S5 , class S6 , class Op > static void for_each7 ( S0 &s0 , S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , Op op ) {
- const size_t len = boost::size(s0);
- typename boost::range_iterator<S0>::type beg0 = boost::begin(s0);
- typename boost::range_iterator<S1>::type beg1 = boost::begin(s1);
- typename boost::range_iterator<S2>::type beg2 = boost::begin(s2);
- typename boost::range_iterator<S3>::type beg3 = boost::begin(s3);
- typename boost::range_iterator<S4>::type beg4 = boost::begin(s4);
- typename boost::range_iterator<S5>::type beg5 = boost::begin(s5);
- typename boost::range_iterator<S6>::type beg6 = boost::begin(s6);
- #pragma omp parallel for schedule(runtime)
- for( size_t i = 0 ; i < len ; i++ ) op( beg0 [i] , beg1 [i] , beg2 [i] , beg3 [i] , beg4 [i] , beg5 [i] , beg6 [i] );
- }
- template< class S0 , class S1 , class S2 , class S3 , class S4 , class S5 , class S6 , class S7 , class Op > static void for_each8 ( S0 &s0 , S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , Op op ) {
- const size_t len = boost::size(s0);
- typename boost::range_iterator<S0>::type beg0 = boost::begin(s0);
- typename boost::range_iterator<S1>::type beg1 = boost::begin(s1);
- typename boost::range_iterator<S2>::type beg2 = boost::begin(s2);
- typename boost::range_iterator<S3>::type beg3 = boost::begin(s3);
- typename boost::range_iterator<S4>::type beg4 = boost::begin(s4);
- typename boost::range_iterator<S5>::type beg5 = boost::begin(s5);
- typename boost::range_iterator<S6>::type beg6 = boost::begin(s6);
- typename boost::range_iterator<S7>::type beg7 = boost::begin(s7);
- #pragma omp parallel for schedule(runtime)
- for( size_t i = 0 ; i < len ; i++ ) op( beg0 [i] , beg1 [i] , beg2 [i] , beg3 [i] , beg4 [i] , beg5 [i] , beg6 [i] , beg7 [i] );
- }
- template< class S0 , class S1 , class S2 , class S3 , class S4 , class S5 , class S6 , class S7 , class S8 , class Op > static void for_each9 ( S0 &s0 , S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , S8 &s8 , Op op ) {
- const size_t len = boost::size(s0);
- typename boost::range_iterator<S0>::type beg0 = boost::begin(s0);
- typename boost::range_iterator<S1>::type beg1 = boost::begin(s1);
- typename boost::range_iterator<S2>::type beg2 = boost::begin(s2);
- typename boost::range_iterator<S3>::type beg3 = boost::begin(s3);
- typename boost::range_iterator<S4>::type beg4 = boost::begin(s4);
- typename boost::range_iterator<S5>::type beg5 = boost::begin(s5);
- typename boost::range_iterator<S6>::type beg6 = boost::begin(s6);
- typename boost::range_iterator<S7>::type beg7 = boost::begin(s7);
- typename boost::range_iterator<S8>::type beg8 = boost::begin(s8);
- #pragma omp parallel for schedule(runtime)
- for( size_t i = 0 ; i < len ; i++ ) op( beg0 [i] , beg1 [i] , beg2 [i] , beg3 [i] , beg4 [i] , beg5 [i] , beg6 [i] , beg7 [i] , beg8 [i] );
- }
- template< class S0 , class S1 , class S2 , class S3 , class S4 , class S5 , class S6 , class S7 , class S8 , class S9 , class Op > static void for_each10 ( S0 &s0 , S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , S8 &s8 , S9 &s9 , Op op ) {
- const size_t len = boost::size(s0);
- typename boost::range_iterator<S0>::type beg0 = boost::begin(s0);
- typename boost::range_iterator<S1>::type beg1 = boost::begin(s1);
- typename boost::range_iterator<S2>::type beg2 = boost::begin(s2);
- typename boost::range_iterator<S3>::type beg3 = boost::begin(s3);
- typename boost::range_iterator<S4>::type beg4 = boost::begin(s4);
- typename boost::range_iterator<S5>::type beg5 = boost::begin(s5);
- typename boost::range_iterator<S6>::type beg6 = boost::begin(s6);
- typename boost::range_iterator<S7>::type beg7 = boost::begin(s7);
- typename boost::range_iterator<S8>::type beg8 = boost::begin(s8);
- typename boost::range_iterator<S9>::type beg9 = boost::begin(s9);
- #pragma omp parallel for schedule(runtime)
- for( size_t i = 0 ; i < len ; i++ ) op( beg0 [i] , beg1 [i] , beg2 [i] , beg3 [i] , beg4 [i] , beg5 [i] , beg6 [i] , beg7 [i] , beg8 [i] , beg9 [i] );
- }
- template< class S0 , class S1 , class S2 , class S3 , class S4 , class S5 , class S6 , class S7 , class S8 , class S9 , class S10 , class Op > static void for_each11 ( S0 &s0 , S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , S8 &s8 , S9 &s9 , S10 &s10 , Op op ) {
- const size_t len = boost::size(s0);
- typename boost::range_iterator<S0>::type beg0 = boost::begin(s0);
- typename boost::range_iterator<S1>::type beg1 = boost::begin(s1);
- typename boost::range_iterator<S2>::type beg2 = boost::begin(s2);
- typename boost::range_iterator<S3>::type beg3 = boost::begin(s3);
- typename boost::range_iterator<S4>::type beg4 = boost::begin(s4);
- typename boost::range_iterator<S5>::type beg5 = boost::begin(s5);
- typename boost::range_iterator<S6>::type beg6 = boost::begin(s6);
- typename boost::range_iterator<S7>::type beg7 = boost::begin(s7);
- typename boost::range_iterator<S8>::type beg8 = boost::begin(s8);
- typename boost::range_iterator<S9>::type beg9 = boost::begin(s9);
- typename boost::range_iterator<S10>::type beg10 = boost::begin(s10);
- #pragma omp parallel for schedule(runtime)
- for( size_t i = 0 ; i < len ; i++ ) op( beg0 [i] , beg1 [i] , beg2 [i] , beg3 [i] , beg4 [i] , beg5 [i] , beg6 [i] , beg7 [i] , beg8 [i] , beg9 [i] , beg10 [i] );
- }
- template< class S0 , class S1 , class S2 , class S3 , class S4 , class S5 , class S6 , class S7 , class S8 , class S9 , class S10 , class S11 , class Op > static void for_each12 ( S0 &s0 , S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , S8 &s8 , S9 &s9 , S10 &s10 , S11 &s11 , Op op ) {
- const size_t len = boost::size(s0);
- typename boost::range_iterator<S0>::type beg0 = boost::begin(s0);
- typename boost::range_iterator<S1>::type beg1 = boost::begin(s1);
- typename boost::range_iterator<S2>::type beg2 = boost::begin(s2);
- typename boost::range_iterator<S3>::type beg3 = boost::begin(s3);
- typename boost::range_iterator<S4>::type beg4 = boost::begin(s4);
- typename boost::range_iterator<S5>::type beg5 = boost::begin(s5);
- typename boost::range_iterator<S6>::type beg6 = boost::begin(s6);
- typename boost::range_iterator<S7>::type beg7 = boost::begin(s7);
- typename boost::range_iterator<S8>::type beg8 = boost::begin(s8);
- typename boost::range_iterator<S9>::type beg9 = boost::begin(s9);
- typename boost::range_iterator<S10>::type beg10 = boost::begin(s10);
- typename boost::range_iterator<S11>::type beg11 = boost::begin(s11);
- #pragma omp parallel for schedule(runtime)
- for( size_t i = 0 ; i < len ; i++ ) op( beg0 [i] , beg1 [i] , beg2 [i] , beg3 [i] , beg4 [i] , beg5 [i] , beg6 [i] , beg7 [i] , beg8 [i] , beg9 [i] , beg10 [i] , beg11 [i] );
- }
- template< class S0 , class S1 , class S2 , class S3 , class S4 , class S5 , class S6 , class S7 , class S8 , class S9 , class S10 , class S11 , class S12 , class Op > static void for_each13 ( S0 &s0 , S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , S8 &s8 , S9 &s9 , S10 &s10 , S11 &s11 , S12 &s12 , Op op ) {
- const size_t len = boost::size(s0);
- typename boost::range_iterator<S0>::type beg0 = boost::begin(s0);
- typename boost::range_iterator<S1>::type beg1 = boost::begin(s1);
- typename boost::range_iterator<S2>::type beg2 = boost::begin(s2);
- typename boost::range_iterator<S3>::type beg3 = boost::begin(s3);
- typename boost::range_iterator<S4>::type beg4 = boost::begin(s4);
- typename boost::range_iterator<S5>::type beg5 = boost::begin(s5);
- typename boost::range_iterator<S6>::type beg6 = boost::begin(s6);
- typename boost::range_iterator<S7>::type beg7 = boost::begin(s7);
- typename boost::range_iterator<S8>::type beg8 = boost::begin(s8);
- typename boost::range_iterator<S9>::type beg9 = boost::begin(s9);
- typename boost::range_iterator<S10>::type beg10 = boost::begin(s10);
- typename boost::range_iterator<S11>::type beg11 = boost::begin(s11);
- typename boost::range_iterator<S12>::type beg12 = boost::begin(s12);
- #pragma omp parallel for schedule(runtime)
- for( size_t i = 0 ; i < len ; i++ ) op( beg0 [i] , beg1 [i] , beg2 [i] , beg3 [i] , beg4 [i] , beg5 [i] , beg6 [i] , beg7 [i] , beg8 [i] , beg9 [i] , beg10 [i] , beg11 [i] , beg12 [i] );
- }
- template< class S0 , class S1 , class S2 , class S3 , class S4 , class S5 , class S6 , class S7 , class S8 , class S9 , class S10 , class S11 , class S12 , class S13 , class Op > static void for_each14 ( S0 &s0 , S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , S8 &s8 , S9 &s9 , S10 &s10 , S11 &s11 , S12 &s12 , S13 &s13 , Op op ) {
- const size_t len = boost::size(s0);
- typename boost::range_iterator<S0>::type beg0 = boost::begin(s0);
- typename boost::range_iterator<S1>::type beg1 = boost::begin(s1);
- typename boost::range_iterator<S2>::type beg2 = boost::begin(s2);
- typename boost::range_iterator<S3>::type beg3 = boost::begin(s3);
- typename boost::range_iterator<S4>::type beg4 = boost::begin(s4);
- typename boost::range_iterator<S5>::type beg5 = boost::begin(s5);
- typename boost::range_iterator<S6>::type beg6 = boost::begin(s6);
- typename boost::range_iterator<S7>::type beg7 = boost::begin(s7);
- typename boost::range_iterator<S8>::type beg8 = boost::begin(s8);
- typename boost::range_iterator<S9>::type beg9 = boost::begin(s9);
- typename boost::range_iterator<S10>::type beg10 = boost::begin(s10);
- typename boost::range_iterator<S11>::type beg11 = boost::begin(s11);
- typename boost::range_iterator<S12>::type beg12 = boost::begin(s12);
- typename boost::range_iterator<S13>::type beg13 = boost::begin(s13);
- #pragma omp parallel for schedule(runtime)
- for( size_t i = 0 ; i < len ; i++ ) op( beg0 [i] , beg1 [i] , beg2 [i] , beg3 [i] , beg4 [i] , beg5 [i] , beg6 [i] , beg7 [i] , beg8 [i] , beg9 [i] , beg10 [i] , beg11 [i] , beg12 [i] , beg13 [i] );
- }
- template< class S0 , class S1 , class S2 , class S3 , class S4 , class S5 , class S6 , class S7 , class S8 , class S9 , class S10 , class S11 , class S12 , class S13 , class S14 , class Op > static void for_each15 ( S0 &s0 , S1 &s1 , S2 &s2 , S3 &s3 , S4 &s4 , S5 &s5 , S6 &s6 , S7 &s7 , S8 &s8 , S9 &s9 , S10 &s10 , S11 &s11 , S12 &s12 , S13 &s13 , S14 &s14 , Op op ) {
- const size_t len = boost::size(s0);
- typename boost::range_iterator<S0>::type beg0 = boost::begin(s0);
- typename boost::range_iterator<S1>::type beg1 = boost::begin(s1);
- typename boost::range_iterator<S2>::type beg2 = boost::begin(s2);
- typename boost::range_iterator<S3>::type beg3 = boost::begin(s3);
- typename boost::range_iterator<S4>::type beg4 = boost::begin(s4);
- typename boost::range_iterator<S5>::type beg5 = boost::begin(s5);
- typename boost::range_iterator<S6>::type beg6 = boost::begin(s6);
- typename boost::range_iterator<S7>::type beg7 = boost::begin(s7);
- typename boost::range_iterator<S8>::type beg8 = boost::begin(s8);
- typename boost::range_iterator<S9>::type beg9 = boost::begin(s9);
- typename boost::range_iterator<S10>::type beg10 = boost::begin(s10);
- typename boost::range_iterator<S11>::type beg11 = boost::begin(s11);
- typename boost::range_iterator<S12>::type beg12 = boost::begin(s12);
- typename boost::range_iterator<S13>::type beg13 = boost::begin(s13);
- typename boost::range_iterator<S14>::type beg14 = boost::begin(s14);
- #pragma omp parallel for schedule(runtime)
- for( size_t i = 0 ; i < len ; i++ ) op( beg0 [i] , beg1 [i] , beg2 [i] , beg3 [i] , beg4 [i] , beg5 [i] , beg6 [i] , beg7 [i] , beg8 [i] , beg9 [i] , beg10 [i] , beg11 [i] , beg12 [i] , beg13 [i] , beg14 [i] );
- }
-
-#endif
-
-
- template< class S >
- static typename norm_result_type< S >::type norm_inf( const S &s )
- {
- using std::max;
- using std::abs;
- typedef typename norm_result_type< S >::type result_type;
- result_type init = static_cast< result_type >( 0 );
- const size_t len = boost::size(s);
- typename boost::range_iterator<const S>::type beg = boost::begin(s);
-# pragma omp parallel for reduction(max: init) schedule(dynamic)
- for( size_t i = 0 ; i < len ; ++i )
- init = max( init , abs( beg[i] ) );
- return init;
- }
-
-};
-
-
-}
-}
-}
-
-#endif
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/openmp/openmp_state.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/openmp/openmp_state.hpp
deleted file mode 100644
index 83bbc19232e3757d55ecd63cfca9e9db70b9901d..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/openmp/openmp_state.hpp
+++ /dev/null
@@ -1,171 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/external/openmp/openmp_state.hpp
-
- [begin_description]
- Wrappers for OpenMP.
- [end_description]
-
- Copyright 2013 Karsten Ahnert
- Copyright 2013 Mario Mulansky
- Copyright 2013 Pascal Germroth
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_EXTERNAL_OPENMP_OPENMP_STATE_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_EXTERNAL_OPENMP_OPENMP_STATE_HPP_INCLUDED
-
-#include <omp.h>
-#include <vector>
-#include <algorithm>
-#include <boost/range/adaptor/sliced.hpp>
-#include <boost/numeric/odeint/util/copy.hpp>
-#include <boost/numeric/odeint/util/split.hpp>
-#include <boost/numeric/odeint/util/resize.hpp>
-#include <boost/numeric/odeint/external/openmp/openmp_nested_algebra.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-/** \brief A container that is split into distinct parts, for threading.
- * Just a wrapper for vector<vector<T>>, use `copy` for splitting/joining.
- */
-template< class T >
-struct openmp_state : public std::vector< std::vector< T > >
-{
- openmp_state() {}
-
- openmp_state(size_t n, const std::vector<T>& val = std::vector<T>())
- : std::vector< std::vector< T > >(n, val) {}
-
- template<class InputIterator>
- openmp_state(InputIterator first, InputIterator last)
- : std::vector< std::vector< T > >(first, last) {}
-
- openmp_state(const std::vector< std::vector< T > > &orig)
- : std::vector< std::vector< T > >(orig) {}
-
-};
-
-
-
-
-template< class T >
-struct is_resizeable< openmp_state< T > > : boost::true_type { };
-
-
-template< class T >
-struct same_size_impl< openmp_state< T > , openmp_state< T > >
-{
- static bool same_size( const openmp_state< T > &x , const openmp_state< T > &y )
- {
- if( x.size() != y.size() ) return false;
- for( size_t i = 0 ; i != x.size() ; i++ )
- if( x[i].size() != y[i].size() ) return false;
- return true;
- }
-};
-
-
-template< class T >
-struct resize_impl< openmp_state< T > , openmp_state< T > >
-{
- static void resize( openmp_state< T > &x , const openmp_state< T > &y )
- {
- x.resize( y.size() );
-# pragma omp parallel for schedule(dynamic)
- for(size_t i = 0 ; i < x.size() ; i++)
- x[i].resize( y[i].size() );
- }
-};
-
-
-/** \brief Copy data between openmp_states of same size. */
-template< class T >
-struct copy_impl< openmp_state< T >, openmp_state< T > >
-{
- static void copy( const openmp_state< T > &from, openmp_state< T > &to )
- {
-# pragma omp parallel for schedule(dynamic)
- for(size_t i = 0 ; i < from.size() ; i++)
- std::copy( from[i].begin() , from[i].end() , to.begin() );
- }
-};
-
-
-
-/** \brief Copy data from some container to an openmp_state and resize it.
- * Target container size will determine number of blocks to split into.
- * If it is empty, it will be resized to the maximum number of OpenMP threads.
- * SourceContainer must support `s::value_type`, `s::const_iterator`, `s.begin()`, `s.end()` and `s.size()`,
- * with Random Access Iterators; i.e. it must be a Random Access Container. */
-template< class SourceContainer >
-struct split_impl< SourceContainer, openmp_state< typename SourceContainer::value_type > >
-{
- static void split( const SourceContainer &from, openmp_state< typename SourceContainer::value_type > &to )
- {
- if(to.size() == 0) to.resize( omp_get_max_threads() );
- const size_t part = from.size() / to.size();
-# pragma omp parallel for schedule(dynamic)
- for(size_t i = 0 ; i < to.size() ; i++) {
- typedef typename SourceContainer::const_iterator it_t;
- const it_t begin = from.begin() + i * part;
- it_t end = begin + part;
- // for cases where from.size() % to.size() > 0
- if(i + 1 == to.size() || end > from.end()) end = from.end();
- to[i].resize(end - begin);
- std::copy(begin, end, to[i].begin());
- }
- }
-};
-
-/** \brief Copy data from an openmp_state to some container and resize it.
- * TargetContainer must support `s::value_type`, `s::iterator`, `s.begin()` and `s.resize(n)`,
- * i.e. it must be a `std::vector`. */
-template< class TargetContainer >
-struct unsplit_impl< openmp_state< typename TargetContainer::value_type >, TargetContainer >
-{
- static void unsplit( const openmp_state< typename TargetContainer::value_type > &from , TargetContainer &to )
- {
- // resize target
- size_t total_size = 0;
- for(size_t i = 0 ; i < from.size() ; i++)
- total_size += from[i].size();
- to.resize( total_size );
- // copy parts
- typename TargetContainer::iterator out = to.begin();
- for(size_t i = 0 ; i < from.size() ; i++)
- out = std::copy(from[i].begin(), from[i].end(), out);
- }
-};
-
-
-
-
-/** \brief OpenMP-parallelized algebra.
- * For use with openmp_state.
- */
-typedef openmp_nested_algebra< range_algebra > openmp_algebra;
-
-
-
-/** \brief Use `openmp_algebra` for `openmp_state`. */
-template< class T >
-struct algebra_dispatcher< openmp_state< T > >
-{
- typedef openmp_algebra algebra_type;
-};
-
-
-}
-}
-}
-
-
-#endif
-
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/thrust/thrust.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/thrust/thrust.hpp
deleted file mode 100644
index 5c4987cfbb1203672cc71dc1f4ec4cecb8dac2e3..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/thrust/thrust.hpp
+++ /dev/null
@@ -1,27 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/external/thrust/thrust.hpp
-
- [begin_description]
- includes all headers required for using odeint with thrust
- [end_description]
-
- Copyright 2013 Karsten Ahnert
- Copyright 2013 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
-*/
-
-
-#ifndef BOOST_NUMERIC_ODEINT_EXTERNAL_THRUST_HPP_DEFINED
-#define BOOST_NUMERIC_ODEINT_EXTERNAL_THRUST_HPP_DEFINED
-
-#include <boost/numeric/odeint/external/thrust/thrust_algebra.hpp>
-#include <boost/numeric/odeint/external/thrust/thrust_operations.hpp>
-#include <boost/numeric/odeint/external/thrust/thrust_algebra_dispatcher.hpp>
-#include <boost/numeric/odeint/external/thrust/thrust_operations_dispatcher.hpp>
-#include <boost/numeric/odeint/external/thrust/thrust_resize.hpp>
-
-#endif // BOOST_NUMERIC_ODEINT_EXTERNAL_THRUST_HPP_DEFINED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/thrust/thrust_algebra.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/thrust/thrust_algebra.hpp
deleted file mode 100644
index f33e86296fd6343f9c48019ed54ae118375eadb3..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/thrust/thrust_algebra.hpp
+++ /dev/null
@@ -1,217 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/external/thrust/thrust_algebra.hpp
-
- [begin_description]
- An algebra for thrusts device_vectors.
- [end_description]
-
- Copyright 2010-2013 Mario Mulansky
- Copyright 2010-2011 Karsten Ahnert
- Copyright 2013 Kyle Lutz
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_EXTERNAL_THRUST_THRUST_ALGEBRA_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_EXTERNAL_THRUST_THRUST_ALGEBRA_HPP_INCLUDED
-
-
-#include <thrust/device_vector.h>
-#include <thrust/for_each.h>
-#include <thrust/iterator/zip_iterator.h>
-
-#include <boost/range.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-namespace detail {
-
- // to use in thrust::reduce
- template< class Value >
- struct maximum
- {
- template< class Fac1 , class Fac2 >
- __host__ __device__
- Value operator()( const Fac1 t1 , const Fac2 t2 ) const
- {
- return ( abs( t1 ) < abs( t2 ) ) ? t2 : t1 ;
- }
-
- typedef Value result_type;
- };
-
-}
-
-
-
-
-/** ToDO extend until for_each14 for rk78 */
-
-/*
- * The const versions are needed for boost.range to work, i.e.
- * it allows you to do
- * for_each1( make_pair( vec1.begin() , vec1.begin() + 10 ) , op );
- */
-
-struct thrust_algebra
-{
- template< class StateType , class Operation >
- static void for_each1( StateType &s , Operation op )
- {
- thrust::for_each( boost::begin(s) , boost::end(s) , op );
- }
-
- template< class StateType1 , class StateType2 , class Operation >
- static void for_each2( StateType1 &s1 , StateType2 &s2 , Operation op )
- {
- thrust::for_each(
- thrust::make_zip_iterator( thrust::make_tuple( boost::begin(s1) ,
- boost::begin(s2) ) ) ,
- thrust::make_zip_iterator( thrust::make_tuple( boost::end(s1) ,
- boost::end(s2) ) ) ,
- op);
- }
-
- template< class StateType1 , class StateType2 , class StateType3 , class Operation >
- static void for_each3( StateType1 &s1 , StateType2 &s2 , StateType3 &s3 , Operation op )
- {
- thrust::for_each(
- thrust::make_zip_iterator( thrust::make_tuple( boost::begin(s1) ,
- boost::begin(s2) ,
- boost::begin(s3) ) ) ,
- thrust::make_zip_iterator( thrust::make_tuple( boost::end(s1) ,
- boost::end(s2) ,
- boost::end(s3) ) ) ,
- op);
- }
-
- template< class StateType1 , class StateType2 , class StateType3 , class StateType4 ,
- class Operation >
- static void for_each4( StateType1 &s1 , StateType2 &s2 , StateType3 &s3 , StateType4 &s4 ,
- Operation op )
- {
- thrust::for_each(
- thrust::make_zip_iterator( thrust::make_tuple( boost::begin(s1) ,
- boost::begin(s2) ,
- boost::begin(s3) ,
- boost::begin(s4) ) ) ,
- thrust::make_zip_iterator( thrust::make_tuple( boost::end(s1) ,
- boost::end(s2) ,
- boost::end(s3) ,
- boost::end(s4) ) ) ,
- op);
- }
-
- template< class StateType1 , class StateType2 , class StateType3 ,
- class StateType4 , class StateType5 ,class Operation >
- static void for_each5( StateType1 &s1 , StateType2 &s2 , StateType3 &s3 , StateType4 &s4 ,
- StateType5 &s5 , Operation op )
- {
- thrust::for_each(
- thrust::make_zip_iterator( thrust::make_tuple( boost::begin(s1) ,
- boost::begin(s2) ,
- boost::begin(s3) ,
- boost::begin(s4) ,
- boost::begin(s5) ) ) ,
- thrust::make_zip_iterator( thrust::make_tuple( boost::end(s1) ,
- boost::end(s2) ,
- boost::end(s3) ,
- boost::end(s4) ,
- boost::end(s5) ) ) ,
- op);
- }
-
- template< class StateType1 , class StateType2 , class StateType3 ,
- class StateType4 , class StateType5 , class StateType6 , class Operation >
- static void for_each6( StateType1 &s1 , StateType2 &s2 , StateType3 &s3 , StateType4 &s4 ,
- StateType5 &s5 , StateType6 &s6 , Operation op )
- {
- thrust::for_each(
- thrust::make_zip_iterator( thrust::make_tuple( boost::begin(s1) ,
- boost::begin(s2) ,
- boost::begin(s3) ,
- boost::begin(s4) ,
- boost::begin(s5) ,
- boost::begin(s6) ) ) ,
- thrust::make_zip_iterator( thrust::make_tuple( boost::end(s1) ,
- boost::end(s2) ,
- boost::end(s3) ,
- boost::end(s4) ,
- boost::end(s5) ,
- boost::end(s6) ) ) ,
- op);
- }
-
- template< class StateType1 , class StateType2 , class StateType3 , class StateType4 ,
- class StateType5 , class StateType6 , class StateType7 , class Operation >
- static void for_each7( StateType1 &s1 , StateType2 &s2 , StateType3 &s3 , StateType4 &s4 ,
- StateType5 &s5 , StateType6 &s6 , StateType7 &s7 , Operation op )
- {
- thrust::for_each(
- thrust::make_zip_iterator( thrust::make_tuple( boost::begin(s1) ,
- boost::begin(s2) ,
- boost::begin(s3) ,
- boost::begin(s4) ,
- boost::begin(s5) ,
- boost::begin(s6) ,
- boost::begin(s7) ) ) ,
- thrust::make_zip_iterator( thrust::make_tuple( boost::end(s1) ,
- boost::end(s2) ,
- boost::end(s3) ,
- boost::end(s4) ,
- boost::end(s5) ,
- boost::end(s6) ,
- boost::end(s7) ) ) ,
- op);
- }
-
- template< class StateType1 , class StateType2 , class StateType3 , class StateType4 ,
- class StateType5 , class StateType6 , class StateType7 , class StateType8 , class Operation >
- static void for_each8( StateType1 &s1 , StateType2 &s2 , StateType3 &s3 , StateType4 &s4 ,
- StateType5 &s5 , StateType6 &s6 , StateType7 &s7 , StateType8 &s8 , Operation op )
- {
- thrust::for_each(
- thrust::make_zip_iterator( thrust::make_tuple( boost::begin(s1) ,
- boost::begin(s2) ,
- boost::begin(s3) ,
- boost::begin(s4) ,
- boost::begin(s5) ,
- boost::begin(s6) ,
- boost::begin(s7) ,
- boost::begin(s8) ) ) ,
- thrust::make_zip_iterator( thrust::make_tuple( boost::end(s1) ,
- boost::end(s2) ,
- boost::end(s3) ,
- boost::end(s4) ,
- boost::end(s5) ,
- boost::end(s6) ,
- boost::end(s7) ,
- boost::end(s8) ) ) ,
- op);
- }
-
- template< class S >
- static typename S::value_type norm_inf( const S &s )
- {
- typedef typename S::value_type value_type;
- return thrust::reduce( boost::begin( s ) , boost::end( s ) ,
- static_cast<value_type>(0) ,
- detail::maximum<value_type>() );
- }
-
-};
-
-
-} // odeint
-} // numeric
-} // boost
-
-
-
-#endif // BOOST_NUMERIC_ODEINT_EXTERNAL_THRUST_THRUST_ALGEBRA_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/thrust/thrust_algebra_dispatcher.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/thrust/thrust_algebra_dispatcher.hpp
deleted file mode 100644
index 09613463501a42f404c5f9ff4dc9e640b22bdde9..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/thrust/thrust_algebra_dispatcher.hpp
+++ /dev/null
@@ -1,107 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/external/thrust/thrust_algebra_dispatcher.hpp
-
- [begin_description]
- algebra_dispatcher specialization for thrust
- [end_description]
-
- Copyright 2013 Karsten Ahnert
- Copyright 2013 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
-*/
-
-
-#ifndef BOOST_NUMERIC_ODEINT_EXTERNAL_THRUST_THRUST_ALGEBRA_DISPATCHER_HPP_DEFINED
-#define BOOST_NUMERIC_ODEINT_EXTERNAL_THRUST_THRUST_ALGEBRA_DISPATCHER_HPP_DEFINED
-
-#include <thrust/host_vector.h>
-#include <thrust/device_vector.h>
-
-#include <boost/numeric/odeint/external/thrust/thrust_algebra.hpp>
-#include <boost/numeric/odeint/algebra/algebra_dispatcher.hpp>
-
-// specializations for the standard thrust containers
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-// specialization for thrust host_vector
-template< class T , class A >
-struct algebra_dispatcher< thrust::host_vector< T , A > >
-{
- typedef thrust_algebra algebra_type;
-};
-
-// specialization for thrust device_vector
-template< class T , class A >
-struct algebra_dispatcher< thrust::device_vector< T , A > >
-{
- typedef thrust_algebra algebra_type;
-};
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-// add support for thrust backend vectors, if available
-
-#include <thrust/version.h>
-
-#if THRUST_VERSION >= 100600
-
-// specialization for thrust cpp vector
-#include <thrust/system/cpp/vector.h>
-namespace boost { namespace numeric { namespace odeint {
- template< class T , class A >
- struct algebra_dispatcher< thrust::cpp::vector< T , A > >
- {
- typedef thrust_algebra algebra_type;
- };
-} } }
-
-// specialization for thrust omp vector
-#ifdef _OPENMP
-#include <thrust/system/omp/vector.h>
-namespace boost { namespace numeric { namespace odeint {
- template< class T , class A >
- struct algebra_dispatcher< thrust::omp::vector< T , A > >
- {
- typedef thrust_algebra algebra_type;
- };
-} } }
-#endif // _OPENMP
-
-// specialization for thrust tbb vector
-#ifdef TBB_VERSION_MAJOR
-#include <thrust/system/tbb/vector.h>
-namespace boost { namespace numeric { namespace odeint {
- template< class T , class A >
- struct algebra_dispatcher< thrust::tbb::vector< T , A > >
- {
- typedef thrust_algebra algebra_type;
- };
-} } }
-#endif // TBB_VERSION_MAJOR
-
-// specialization for thrust cuda vector
-#ifdef __CUDACC__
-#include <thrust/system/cuda/vector.h>
-namespace boost { namespace numeric { namespace odeint {
- template< class T , class A >
- struct algebra_dispatcher< thrust::cuda::vector< T , A > >
- {
- typedef thrust_algebra algebra_type;
- };
-} } }
-#endif // __CUDACC__
-
-#endif // THRUST_VERSION >= 100600
-
-#endif // BOOST_NUMERIC_ODEINT_EXTERNAL_THRUST_THRUST_ALGEBRA_DISPATCHER_HPP_DEFINED
-
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/thrust/thrust_operations.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/thrust/thrust_operations.hpp
deleted file mode 100644
index ce2d372925d8040d74c5d6f3e00d6724548cad8a..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/thrust/thrust_operations.hpp
+++ /dev/null
@@ -1,233 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/external/thrust/thrust_operations.hpp
-
- [begin_description]
- Operations of thrust zipped iterators. Is the counterpart of the thrust_algebra.
- [end_description]
-
- Copyright 2010-2013 Mario Mulansky
- Copyright 2010-2012 Karsten Ahnert
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_EXTERNAL_THRUST_THRUST_OPERATIONS_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_EXTERNAL_THRUST_THRUST_OPERATIONS_HPP_INCLUDED
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-#include <thrust/tuple.h>
-#include <thrust/iterator/zip_iterator.h>
-
-/**ToDo extend to scale_sum13 for rk78 */
-
-struct thrust_operations
-{
- template< class Fac1 = double , class Fac2 = Fac1 >
- struct scale_sum2
- {
- const Fac1 m_alpha1;
- const Fac2 m_alpha2;
-
- scale_sum2( const Fac1 alpha1 , const Fac2 alpha2 )
- : m_alpha1( alpha1 ) , m_alpha2( alpha2 ) { }
-
- template< class Tuple >
- __host__ __device__
- void operator()( Tuple t ) const
- {
- thrust::get<0>(t) = m_alpha1 * thrust::get<1>(t) + m_alpha2 * thrust::get<2>(t);
- }
- };
-
- template< class Fac1 = double , class Fac2 = Fac1 >
- struct scale_sum_swap2
- {
- const Fac1 m_alpha1;
- const Fac2 m_alpha2;
-
- scale_sum_swap2( const Fac1 alpha1 , const Fac2 alpha2 )
- : m_alpha1( alpha1 ) , m_alpha2( alpha2 ) { }
-
- template< class Tuple >
- __host__ __device__
- void operator()( Tuple t ) const
- {
- typename thrust::tuple_element<0,Tuple>::type tmp = thrust::get<0>(t);
- thrust::get<0>(t) = m_alpha1 * thrust::get<1>(t) + m_alpha2 * thrust::get<2>(t);
- thrust::get<1>(t) = tmp;
- }
- };
-
- template< class Fac1 = double , class Fac2 = Fac1 , class Fac3 = Fac2 >
- struct scale_sum3
- {
- const Fac1 m_alpha1;
- const Fac2 m_alpha2;
- const Fac3 m_alpha3;
-
- scale_sum3( const Fac1 alpha1 , const Fac2 alpha2 , const Fac3 alpha3 )
- : m_alpha1( alpha1 ) , m_alpha2( alpha2 ) , m_alpha3( alpha3 ) { }
-
- template< class Tuple >
- __host__ __device__
- void operator()( Tuple t ) const
- {
- thrust::get<0>(t) = m_alpha1 * thrust::get<1>(t) +
- m_alpha2 * thrust::get<2>(t) +
- m_alpha3 * thrust::get<3>(t);
- }
- };
-
-
- template< class Fac1 = double , class Fac2 = Fac1 , class Fac3 = Fac2 , class Fac4 = Fac3 >
- struct scale_sum4
- {
- const Fac1 m_alpha1;
- const Fac2 m_alpha2;
- const Fac3 m_alpha3;
- const Fac4 m_alpha4;
-
- scale_sum4( const Fac1 alpha1 , const Fac2 alpha2 , const Fac3 alpha3 , const Fac4 alpha4 )
- : m_alpha1( alpha1 ) , m_alpha2( alpha2 ) , m_alpha3( alpha3 ) , m_alpha4( alpha4 ){ }
-
- template< class Tuple >
- __host__ __device__
- void operator()( Tuple t ) const
- {
- thrust::get<0>(t) = m_alpha1 * thrust::get<1>(t) +
- m_alpha2 * thrust::get<2>(t) +
- m_alpha3 * thrust::get<3>(t) +
- m_alpha4 * thrust::get<4>(t);
- }
- };
-
-
- template< class Fac1 = double , class Fac2 = Fac1 , class Fac3 = Fac2 ,
- class Fac4 = Fac3 , class Fac5 = Fac4 >
- struct scale_sum5
- {
- const Fac1 m_alpha1;
- const Fac2 m_alpha2;
- const Fac3 m_alpha3;
- const Fac4 m_alpha4;
- const Fac5 m_alpha5;
-
- scale_sum5( const Fac1 alpha1 , const Fac2 alpha2 , const Fac3 alpha3 ,
- const Fac4 alpha4 , const Fac5 alpha5 )
- : m_alpha1( alpha1 ) , m_alpha2( alpha2 ) , m_alpha3( alpha3 ) ,
- m_alpha4( alpha4 ) , m_alpha5( alpha5 ) { }
-
- template< class Tuple >
- __host__ __device__
- void operator()( Tuple t ) const
- {
- thrust::get<0>(t) = m_alpha1 * thrust::get<1>(t) +
- m_alpha2 * thrust::get<2>(t) +
- m_alpha3 * thrust::get<3>(t) +
- m_alpha4 * thrust::get<4>(t) +
- m_alpha5 * thrust::get<5>(t);
- }
- };
-
-
- template< class Fac1 = double , class Fac2 = Fac1 , class Fac3 = Fac2 ,
- class Fac4 = Fac3 , class Fac5 = Fac4 , class Fac6 = Fac5 >
- struct scale_sum6
- {
- const Fac1 m_alpha1;
- const Fac2 m_alpha2;
- const Fac3 m_alpha3;
- const Fac4 m_alpha4;
- const Fac5 m_alpha5;
- const Fac6 m_alpha6;
-
- scale_sum6( const Fac1 alpha1 , const Fac2 alpha2 , const Fac3 alpha3 ,
- const Fac4 alpha4 , const Fac5 alpha5 , const Fac6 alpha6 )
- : m_alpha1( alpha1 ) , m_alpha2( alpha2 ) , m_alpha3( alpha3 ) ,
- m_alpha4( alpha4 ) , m_alpha5( alpha5 ) , m_alpha6( alpha6 ) { }
-
- template< class Tuple >
- __host__ __device__
- void operator()( Tuple t ) const
- {
- thrust::get<0>(t) = m_alpha1 * thrust::get<1>(t) +
- m_alpha2 * thrust::get<2>(t) +
- m_alpha3 * thrust::get<3>(t) +
- m_alpha4 * thrust::get<4>(t) +
- m_alpha5 * thrust::get<5>(t) +
- m_alpha6 * thrust::get<6>(t);
- }
- };
-
-
- template< class Fac1 = double , class Fac2 = Fac1 , class Fac3 = Fac2 , class Fac4 = Fac3 ,
- class Fac5 = Fac4 , class Fac6 = Fac5 , class Fac7 = Fac6 >
- struct scale_sum7
- {
- const Fac1 m_alpha1;
- const Fac2 m_alpha2;
- const Fac3 m_alpha3;
- const Fac4 m_alpha4;
- const Fac5 m_alpha5;
- const Fac6 m_alpha6;
- const Fac7 m_alpha7;
-
- scale_sum7( const Fac1 alpha1 , const Fac2 alpha2 , const Fac3 alpha3 ,
- const Fac4 alpha4 , const Fac5 alpha5 , const Fac6 alpha6 , const Fac7 alpha7 )
- : m_alpha1( alpha1 ) , m_alpha2( alpha2 ) , m_alpha3( alpha3 ) ,
- m_alpha4( alpha4 ) , m_alpha5( alpha5 ) , m_alpha6( alpha6 ) , m_alpha7( alpha7 ) { }
-
- template< class Tuple >
- __host__ __device__
- void operator()( Tuple t ) const
- {
- thrust::get<0>(t) = m_alpha1 * thrust::get<1>(t) +
- m_alpha2 * thrust::get<2>(t) +
- m_alpha3 * thrust::get<3>(t) +
- m_alpha4 * thrust::get<4>(t) +
- m_alpha5 * thrust::get<5>(t) +
- m_alpha6 * thrust::get<6>(t) +
- m_alpha7 * thrust::get<7>(t) ;
- }
- };
-
-
-
-
- template< class Fac1 = double >
- struct rel_error
- {
- const Fac1 m_eps_abs , m_eps_rel , m_a_x , m_a_dxdt;
-
- rel_error( const Fac1 eps_abs , const Fac1 eps_rel , const Fac1 a_x , const Fac1 a_dxdt )
- : m_eps_abs( eps_abs ) , m_eps_rel( eps_rel ) , m_a_x( a_x ) , m_a_dxdt( a_dxdt ) { }
-
-
- template< class Tuple >
- __host__ __device__
- void operator()( Tuple t ) const
- {
- using std::abs;
- thrust::get< 0 >( t ) = abs( thrust::get< 0 >( t ) ) /
- ( m_eps_abs + m_eps_rel * ( m_a_x * abs( thrust::get< 1 >( t ) + m_a_dxdt * abs( thrust::get< 2 >( t ) ) ) ) );
- }
-
- typedef void result_type;
- };
-
-
-};
-
-} // odeint
-} // numeric
-} // boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_EXTERNAL_THRUST_THRUST_OPERATIONS_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/thrust/thrust_operations_dispatcher.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/thrust/thrust_operations_dispatcher.hpp
deleted file mode 100644
index e9b3a6423467d4d153a9269cb1798fa415320796..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/thrust/thrust_operations_dispatcher.hpp
+++ /dev/null
@@ -1,107 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/external/thrust/thrust_operations_dispatcher.hpp
-
- [begin_description]
- operations_dispatcher specialization for thrust
- [end_description]
-
- Copyright 2013-2014 Karsten Ahnert
- Copyright 2013-2014 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
-*/
-
-
-#ifndef BOOST_NUMERIC_ODEINT_EXTERNAL_THRUST_THRUST_OPERATIONS_DISPATCHER_HPP_DEFINED
-#define BOOST_NUMERIC_ODEINT_EXTERNAL_THRUST_THRUST_OPERATIONS_DISPATCHER_HPP_DEFINED
-
-#include <thrust/host_vector.h>
-#include <thrust/device_vector.h>
-
-#include <boost/numeric/odeint/external/thrust/thrust_operations.hpp>
-#include <boost/numeric/odeint/algebra/operations_dispatcher.hpp>
-
-// support for the standard thrust containers
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-// specialization for thrust host_vector
-template< class T , class A >
-struct operations_dispatcher< thrust::host_vector< T , A > >
-{
- typedef thrust_operations operations_type;
-};
-
-// specialization for thrust device_vector
-template< class T , class A >
-struct operations_dispatcher< thrust::device_vector< T , A > >
-{
- typedef thrust_operations operations_type;
-};
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-// add support for thrust backend vectors, if available
-
-#include <thrust/version.h>
-
-#if THRUST_VERSION >= 100600
-
-// specialization for thrust cpp vector
-#include <thrust/system/cpp/vector.h>
-namespace boost { namespace numeric { namespace odeint {
- template< class T , class A >
- struct operations_dispatcher< thrust::cpp::vector< T , A > >
- {
- typedef thrust_operations operations_type;
- };
-} } }
-
-// specialization for thrust omp vector
-#ifdef _OPENMP
-#include <thrust/system/omp/vector.h>
-namespace boost { namespace numeric { namespace odeint {
- template< class T , class A >
- struct operations_dispatcher< thrust::omp::vector< T , A > >
- {
- typedef thrust_operations operations_type;
- };
-} } }
-#endif // _OPENMP
-
-// specialization for thrust tbb vector
-#ifdef TBB_VERSION_MAJOR
-#include <thrust/system/tbb/vector.h>
-namespace boost { namespace numeric { namespace odeint {
- template< class T , class A >
- struct operations_dispatcher< thrust::tbb::vector< T , A > >
- {
- typedef thrust_operations operations_type;
- };
-} } }
-#endif // TBB_VERSION_MAJOR
-
-// specialization for thrust cuda vector
-#ifdef __CUDACC__
-#include <thrust/system/cuda/vector.h>
-namespace boost { namespace numeric { namespace odeint {
- template< class T , class A >
- struct operations_dispatcher< thrust::cuda::vector< T , A > >
- {
- typedef thrust_operations operations_type;
- };
-} } }
-#endif // __CUDACC__
-
-#endif // THRUST_VERSION >= 100600
-
-
-#endif // BOOST_NUMERIC_ODEINT_EXTERNAL_THRUST_THRUST_OPERATIONS_DISPATCHER_HPP_DEFINED
-
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/thrust/thrust_resize.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/thrust/thrust_resize.hpp
deleted file mode 100644
index 2f7f7b23b1d45ee2db726131a4a862e786f1fa4d..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/thrust/thrust_resize.hpp
+++ /dev/null
@@ -1,185 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/external/thrust/thrust_resize.hpp
-
- [begin_description]
- Enable resizing for thrusts device and host_vector.
- [end_description]
-
- Copyright 2010-2014 Mario Mulansky
- Copyright 2010-2011 Karsten Ahnert
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_EXTERNAL_THRUST_THRUST_RESIZE_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_EXTERNAL_THRUST_THRUST_RESIZE_HPP_INCLUDED
-
-#include <boost/range.hpp>
-
-#include <thrust/device_vector.h>
-#include <thrust/host_vector.h>
-#include <thrust/distance.h>
-
-#include <boost/numeric/odeint/util/resize.hpp>
-#include <boost/numeric/odeint/util/same_size.hpp>
-#include <boost/numeric/odeint/util/copy.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-// some macros that define the necessary utilities
-
-#define ODEINT_THRUST_VECTOR_IS_RESIZEABLE( THRUST_VECTOR ) \
-template< class T , class A > \
-struct is_resizeable< THRUST_VECTOR<T,A> > \
-{ \
- struct type : public boost::true_type { }; \
- const static bool value = type::value; \
-}; \
-
-#define ODEINT_TRHUST_VECTOR_RESIZE_IMPL( THRUST_VECTOR ) \
-template< class T, class A > \
-struct resize_impl< THRUST_VECTOR<T,A> , THRUST_VECTOR<T,A> > \
-{ \
- static void resize( THRUST_VECTOR<T,A> &x , \
- const THRUST_VECTOR<T,A> &y ) \
- { \
- x.resize( y.size() ); \
- } \
-}; \
-template< class T, class A, typename Range > \
-struct resize_impl< THRUST_VECTOR<T,A> , Range > \
-{ \
- static void resize( THRUST_VECTOR<T,A> &x , \
- const Range &y ) \
- { \
- x.resize( thrust::distance(boost::begin(y), \
- boost::end(y))); \
- } \
-}; \
-
-
-#define ODEINT_THRUST_SAME_SIZE_IMPL( THRUST_VECTOR ) \
-template< class T , class A > \
-struct same_size_impl< THRUST_VECTOR<T,A> , THRUST_VECTOR<T,A> > \
-{ \
- static bool same_size( const THRUST_VECTOR<T,A> &x , \
- const THRUST_VECTOR<T,A> &y ) \
- { \
- return x.size() == y.size(); \
- } \
-}; \
-template< class T , class A, typename Range > \
-struct same_size_impl< THRUST_VECTOR<T,A> , Range > \
-{ \
- static bool same_size( const THRUST_VECTOR<T,A> &x , \
- const Range &y ) \
- { \
- return x.size() == thrust::distance(boost::begin(y), \
- boost::end(y)); \
- } \
-}; \
-
-
-#define ODEINT_THRUST_COPY_IMPL( THRUST_VECTOR ) \
-template< class Container1 , class T , class A > \
-struct copy_impl< Container1 , THRUST_VECTOR<T,A> > \
-{ \
- static void copy( const Container1 &from , THRUST_VECTOR<T,A> &to ) \
- { \
- thrust::copy( boost::begin( from ) , boost::end( from ) , \
- boost::begin( to ) ); \
- } \
-}; \
- \
-template< class T , class A , class Container2 > \
-struct copy_impl< THRUST_VECTOR<T,A> , Container2 > \
-{ \
- static void copy( const THRUST_VECTOR<T,A> &from , Container2 &to ) \
- { \
- thrust::copy( boost::begin( from ) , boost::end( from ) , \
- boost::begin( to ) ); \
- } \
-}; \
- \
-template< class T , class A > \
-struct copy_impl< THRUST_VECTOR<T,A> , THRUST_VECTOR<T,A> > \
-{ \
- static void copy( const THRUST_VECTOR<T,A> &from , \
- THRUST_VECTOR<T,A> &to ) \
- { \
- thrust::copy( boost::begin( from ) , boost::end( from ) , \
- boost::begin( to ) ); \
- } \
-}; \
-
-// add support for the standard thrust containers
-
-ODEINT_THRUST_VECTOR_IS_RESIZEABLE( thrust::device_vector )
-ODEINT_TRHUST_VECTOR_RESIZE_IMPL( thrust::device_vector )
-ODEINT_THRUST_SAME_SIZE_IMPL( thrust::device_vector )
-ODEINT_THRUST_COPY_IMPL( thrust::device_vector )
-
-
-ODEINT_THRUST_VECTOR_IS_RESIZEABLE( thrust::host_vector )
-ODEINT_TRHUST_VECTOR_RESIZE_IMPL( thrust::host_vector )
-ODEINT_THRUST_SAME_SIZE_IMPL( thrust::host_vector )
-ODEINT_THRUST_COPY_IMPL( thrust::host_vector )
-
-
-} // odeint
-} // numeric
-} // boost
-
-// add support for thrust backend vectors, if available
-
-#include <thrust/version.h>
-
-#if THRUST_VERSION >= 100600
-
-#include <thrust/system/cpp/vector.h>
-namespace boost { namespace numeric { namespace odeint {
- ODEINT_THRUST_VECTOR_IS_RESIZEABLE( thrust::cpp::vector )
- ODEINT_TRHUST_VECTOR_RESIZE_IMPL( thrust::cpp::vector )
- ODEINT_THRUST_SAME_SIZE_IMPL( thrust::cpp::vector )
- ODEINT_THRUST_COPY_IMPL( thrust::cpp::vector )
-} } }
-
-#ifdef _OPENMP
-#include <thrust/system/omp/vector.h>
-namespace boost { namespace numeric { namespace odeint {
- ODEINT_THRUST_VECTOR_IS_RESIZEABLE( thrust::omp::vector )
- ODEINT_TRHUST_VECTOR_RESIZE_IMPL( thrust::omp::vector )
- ODEINT_THRUST_SAME_SIZE_IMPL( thrust::omp::vector )
- ODEINT_THRUST_COPY_IMPL( thrust::omp::vector )
-} } }
-#endif // _OPENMP
-
-#ifdef TBB_VERSION_MAJOR
-#include <thrust/system/tbb/vector.h>
-namespace boost { namespace numeric { namespace odeint {
- ODEINT_THRUST_VECTOR_IS_RESIZEABLE( thrust::tbb::vector )
- ODEINT_TRHUST_VECTOR_RESIZE_IMPL( thrust::tbb::vector )
- ODEINT_THRUST_SAME_SIZE_IMPL( thrust::tbb::vector )
- ODEINT_THRUST_COPY_IMPL( thrust::tbb::vector )
-} } }
-#endif // TBB_VERSION_MAJOR
-
-#ifdef __CUDACC__
-#include <thrust/system/cuda/vector.h>
-namespace boost { namespace numeric { namespace odeint {
- ODEINT_THRUST_VECTOR_IS_RESIZEABLE( thrust::cuda::vector )
- ODEINT_TRHUST_VECTOR_RESIZE_IMPL( thrust::cuda::vector )
- ODEINT_THRUST_SAME_SIZE_IMPL( thrust::cuda::vector )
- ODEINT_THRUST_COPY_IMPL( thrust::cuda::vector )
-} } }
-#endif // __CUDACC__
-
-#endif // THRUST_VERSION >= 100600
-
-#endif // BOOST_NUMERIC_ODEINT_EXTERNAL_THRUST_THRUST_RESIZE_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/vexcl/vexcl.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/vexcl/vexcl.hpp
deleted file mode 100644
index 0a99e27c8a0266e6dae2f1a293abd2dfce5f6802..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/vexcl/vexcl.hpp
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/external/vexcl/vexcl.hpp
-
- [begin_description]
- includes all headers required for using vexcl in odeint
- [end_description]
-
- Copyright 2013 Karsten Ahnert
- Copyright 2013 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
-*/
-
-
-#ifndef BOOST_NUMERIC_ODEINT_EXTERNAL_VEXCL_VEXCL_HPP_DEFINED
-#define BOOST_NUMERIC_ODEINT_EXTERNAL_VEXCL_VEXCL_HPP_DEFINED
-
-#include <boost/numeric/odeint/external/vexcl/vexcl_algebra_dispatcher.hpp>
-#include <boost/numeric/odeint/external/vexcl/vexcl_resize.hpp>
-#include <boost/numeric/odeint/external/vexcl/vexcl_same_instance.hpp>
-#include <boost/numeric/odeint/external/vexcl/vexcl_norm_inf.hpp>
-#include <boost/numeric/odeint/external/vexcl/vexcl_abs.hpp>
-#include <boost/numeric/odeint/external/vexcl/vexcl_copy.hpp>
-
-#endif // BOOST_NUMERIC_ODEINT_EXTERNAL_VEXCL_VEXCL_HPP_DEFINED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/vexcl/vexcl_abs.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/vexcl/vexcl_abs.hpp
deleted file mode 100644
index c5e5c73329c3452ec9a4b8c6c484db846154b381..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/vexcl/vexcl_abs.hpp
+++ /dev/null
@@ -1,61 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/external/vexcl/vexcl_abs.hpp
-
- [begin_description]
- abs() specialization for vexcl
- [end_description]
-
- Copyright 2009-2013 Karsten Ahnert
- Copyright 2009-2013 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
-*/
-
-
-#ifndef BOOST_NUMERIC_ODEINT_EXTERNAL_VEXCL_VEXCL_ABS_HPP_DEFINED
-#define BOOST_NUMERIC_ODEINT_EXTERNAL_VEXCL_VEXCL_ABS_HPP_DEFINED
-
-#include <vexcl/vector.hpp>
-#include <vexcl/multivector.hpp>
-#include <vexcl/operations.hpp>
-
-namespace vex {
-
-template <typename T, size_t N>
-typename std::enable_if<
- std::is_integral<T>::value,
- typename boost::proto::result_of::make_expr<
- boost::proto::tag::function,
- abs_func,
- const vex::multivector<T, N>&
- >::type const
->::type
-abs(const multivector<T, N> &arg) {
- return boost::proto::make_expr<boost::proto::tag::function>(
- abs_func(),
- boost::ref(arg)
- );
-}
-
-template <typename T, size_t N>
-typename std::enable_if<
- !std::is_integral<T>::value,
- typename boost::proto::result_of::make_expr<
- boost::proto::tag::function,
- fabs_func,
- const vex::multivector<T, N>&
- >::type const
->::type
-abs(const multivector<T, N> &arg) {
- return boost::proto::make_expr<boost::proto::tag::function>(
- fabs_func(),
- boost::ref(arg)
- );
-}
-
-} // namespace vex
-
-#endif // BOOST_NUMERIC_ODEINT_EXTERNAL_VEXCL_VEXCL_ABS_HPP_DEFINED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/vexcl/vexcl_algebra_dispatcher.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/vexcl/vexcl_algebra_dispatcher.hpp
deleted file mode 100644
index 95111376de912d6ff34978edc49f72e917e8e37a..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/vexcl/vexcl_algebra_dispatcher.hpp
+++ /dev/null
@@ -1,51 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/external/vexcl/vexcl_algebra_dispatcher.hpp
-
- [begin_description]
- algebra_dispatcher specialization for vexcl
- [end_description]
-
- Copyright 2013 Karsten Ahnert
- Copyright 2013 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
-*/
-
-
-#ifndef BOOST_NUMERIC_ODEINT_EXTERNAL_VEXCL_VEXCL_ALGEBRA_DISPATCHER_HPP_DEFINED
-#define BOOST_NUMERIC_ODEINT_EXTERNAL_VEXCL_VEXCL_ALGEBRA_DISPATCHER_HPP_DEFINED
-
-#include <vexcl/vector.hpp>
-#include <vexcl/multivector.hpp>
-
-#include <boost/numeric/odeint/algebra/vector_space_algebra.hpp>
-#include <boost/numeric/odeint/algebra/algebra_dispatcher.hpp>
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-// specialization for vexcl vector
-template< typename T >
-struct algebra_dispatcher< vex::vector< T > >
-{
- typedef vector_space_algebra algebra_type;
-};
-
-// specialization for vexcl multivector
-template< typename T , size_t N >
-struct algebra_dispatcher< vex::multivector< T , N > >
-{
- typedef vector_space_algebra algebra_type;
-};
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_EXTERNAL_VEXCL_VEXCL_ALGEBRA_DISPATCHER_HPP_DEFINED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/vexcl/vexcl_copy.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/vexcl/vexcl_copy.hpp
deleted file mode 100644
index 6a5afac9faf77019b9a55c4d5735970544dd6885..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/vexcl/vexcl_copy.hpp
+++ /dev/null
@@ -1,55 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/external/vexcl/vexcl_copy.hpp
-
- [begin_description]
- copy_impl specializations for vexcl
- [end_description]
-
- Copyright 2009-2011 Karsten Ahnert
- Copyright 2009-2011 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_EXTERNAL_VEXCL_VEXCL_COPY_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_EXTERNAL_VEXCL_VEXCL_COPY_HPP_INCLUDED
-
-#include <vexcl/vector.hpp>
-#include <vexcl/multivector.hpp>
-
-#include <boost/numeric/odeint/util/copy.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-template< typename T1, typename T2 >
-struct copy_impl< vex::vector<T1>, vex::vector<T2> >
-{
- static void copy( const vex::vector<T1> &from , vex::vector<T2> &to )
- {
- to = from;
- }
-};
-
-template< typename T1, typename T2, size_t N >
-struct copy_impl< vex::multivector<T1, N>, vex::multivector<T2, N> >
-{
- static void copy( const vex::multivector<T1, N> &from , vex::multivector<T2, N> &to )
- {
- to = from;
- }
-};
-
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-
-#endif // BOOST_NUMERIC_ODEINT_EXTERNAL_VEXCL_VEXCL_COPY_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/vexcl/vexcl_norm_inf.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/vexcl/vexcl_norm_inf.hpp
deleted file mode 100644
index a0a62afc04379309b564fd163bac67054bf78bf6..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/vexcl/vexcl_norm_inf.hpp
+++ /dev/null
@@ -1,68 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/external/vexcl/vexcl_norm_inf.hpp
-
- [begin_description]
- vector_space_norm_inf specialization for vexcl
- [end_description]
-
- Copyright 2009-2013 Karsten Ahnert
- Copyright 2009-2013 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
-*/
-
-
-#ifndef BOOST_NUMERIC_ODEINT_EXTERNAL_VEXCL_VEXCL_NORM_INF_HPP_DEFINED
-#define BOOST_NUMERIC_ODEINT_EXTERNAL_VEXCL_VEXCL_NORM_INF_HPP_DEFINED
-
-#include <map>
-#include <algorithm>
-
-#include <vexcl/vector.hpp>
-#include <vexcl/multivector.hpp>
-#include <vexcl/reductor.hpp>
-
-#include <boost/numeric/odeint/algebra/vector_space_algebra.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-// specialization for vexcl vector
-template <typename T>
-struct vector_space_norm_inf< vex::vector<T> > {
- typedef T result_type;
-
- T operator()( const vex::vector<T> &x ) const {
- const auto &max = vex::get_reductor<T, vex::MAX>(x.queue_list());
-
- return max( fabs(x) );
- }
-};
-
-// specialization for vexcl multivector
-template <typename T, size_t N>
-struct vector_space_norm_inf< vex::multivector<T, N> > {
- typedef T result_type;
-
- T operator()( const vex::multivector<T, N> &x ) const {
- const auto &max = vex::get_reductor<T, vex::MAX>(x.queue_list());
-
- // Reducing a multivector results in std::array<T, N>:
- auto m = max( fabs(x) );
-
- // We will need to reduce it even further:
- return *std::max_element(m.begin(), m.end());
- }
-};
-
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_EXTERNAL_VEXCL_VEXCL_NORM_INF_HPP_DEFINED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/vexcl/vexcl_resize.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/vexcl/vexcl_resize.hpp
deleted file mode 100644
index 2d6291edfeb3bee374438285449e135d348b47e0..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/vexcl/vexcl_resize.hpp
+++ /dev/null
@@ -1,94 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/external/vexcl/vexcl_resize.hpp
-
- [begin_description]
- Enable resizing for vexcl vector and multivector.
- [end_description]
-
- Copyright 2012 Karsten Ahnert
- Copyright 2012 Mario Mulansky
- Copyright 2012 Denis Demidov
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_EXTERNAL_VEXCL_VEXCL_RESIZE_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_EXTERNAL_VEXCL_VEXCL_RESIZE_HPP_INCLUDED
-
-#include <vexcl/vector.hpp>
-#include <vexcl/multivector.hpp>
-
-#include <boost/numeric/odeint/util/is_resizeable.hpp>
-#include <boost/numeric/odeint/util/resize.hpp>
-#include <boost/numeric/odeint/util/same_size.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-
-/*
- * specializations for vex::vector< T >
- */
-template< typename T >
-struct is_resizeable< vex::vector< T > > : boost::true_type { };
-
-template< typename T >
-struct resize_impl< vex::vector< T > , vex::vector< T > >
-{
- static void resize( vex::vector< T > &x1 , const vex::vector< T > &x2 )
- {
- x1.resize( x2.queue_list() , x2.size() );
- }
-};
-
-template< typename T >
-struct same_size_impl< vex::vector< T > , vex::vector< T > >
-{
- static bool same_size( const vex::vector< T > &x1 , const vex::vector< T > &x2 )
- {
- return x1.size() == x2.size();
- }
-};
-
-
-
-
-
-/*
- * specializations for vex::multivector< T >
- */
-template< typename T , size_t N >
-struct is_resizeable< vex::multivector< T , N > > : boost::true_type { };
-
-template< typename T , size_t N >
-struct resize_impl< vex::multivector< T , N > , vex::multivector< T , N > >
-{
- static void resize( vex::multivector< T , N > &x1 , const vex::multivector< T , N > &x2 )
- {
- x1.resize( x2.queue_list() , x2.size() );
- }
-};
-
-template< typename T , size_t N >
-struct same_size_impl< vex::multivector< T , N > , vex::multivector< T , N > >
-{
- static bool same_size( const vex::multivector< T , N > &x1 , const vex::multivector< T , N > &x2 )
- {
- return x1.size() == x2.size();
- }
-};
-
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-
-#endif // BOOST_NUMERIC_ODEINT_EXTERNAL_VEXCL_VEXCL_RESIZE_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/vexcl/vexcl_same_instance.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/vexcl/vexcl_same_instance.hpp
deleted file mode 100644
index f5a7378cd8ee287f9f4fdb4b3d9962b98a6d8325..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/vexcl/vexcl_same_instance.hpp
+++ /dev/null
@@ -1,58 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/external/vexcl/vexcl_same_instance.hpp
-
- [begin_description]
- Check if two VexCL containers are the same instance.
- [end_description]
-
- Copyright 2009-2011 Karsten Ahnert
- Copyright 2009-2011 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_EXTERNAL_VEXCL_VEXCL_SAME_INSTANCE_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_EXTERNAL_VEXCL_VEXCL_SAME_INSTANCE_HPP_INCLUDED
-
-#include <vexcl/vector.hpp>
-#include <vexcl/multivector.hpp>
-
-#include <boost/numeric/odeint/util/same_instance.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-template <typename T>
-struct same_instance_impl< vex::vector<T> , vex::vector<T> >
-{
- static bool same_instance( const vex::vector<T> &x1 , const vex::vector<T> &x2 )
- {
- return
- static_cast<const vex::vector<T>*>(&x1) ==
- static_cast<const vex::vector<T>*>(&x2);
- }
-};
-
-template <typename T, size_t N>
-struct same_instance_impl< vex::multivector<T, N> , vex::multivector<T, N> >
-{
- static bool same_instance( const vex::multivector<T, N> &x1 , const vex::multivector<T, N> &x2 )
- {
- return
- static_cast<const vex::multivector<T, N>*>(&x1) ==
- static_cast<const vex::multivector<T, N>*>(&x2);
- }
-};
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-
-#endif // BOOST_NUMERIC_ODEINT_EXTERNAL_VEXCL_VEXCL_SAME_INSTANCE_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/viennacl/viennacl_operations.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/viennacl/viennacl_operations.hpp
deleted file mode 100644
index 662c36a1ed1ffd352168aab7eeb183e782efbf2e..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/viennacl/viennacl_operations.hpp
+++ /dev/null
@@ -1,226 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/external/viennacl_operations.hpp
-
- [begin_description]
- ViennaCL operations.
- [end_description]
-
- Copyright 2012 Denis Demidov
- Copyright 2012 Karsten Ahnert
- Copyright 2012 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_EXTERNAL_VIENNACL_VIENNACL_OPERATIONS_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_EXTERNAL_VIENNACL_VIENNACL_OPERATIONS_HPP_INCLUDED
-
-#include <viennacl/vector.hpp>
-
-#ifdef VIENNACL_WITH_OPENCL
-# include <viennacl/generator/custom_operation.hpp>
-#endif
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-#ifdef VIENNACL_WITH_OPENCL
-struct viennacl_operations
-{
-
- template< class Fac1 = double , class Fac2 = Fac1 >
- struct scale_sum2
- {
- const Fac1 m_alpha1;
- const Fac2 m_alpha2;
-
- scale_sum2( Fac1 alpha1 , Fac2 alpha2 )
- : m_alpha1( alpha1 ) , m_alpha2( alpha2 )
- { }
-
- template< class T1 , class T2 , class T3 >
- void operator()( viennacl::vector<T1> &v1 ,
- const viennacl::vector<T2> &v2 ,
- const viennacl::vector<T3> &v3
- ) const
- {
- using namespace viennacl;
-
- static generator::symbolic_vector <0, T1> sym_v1;
- static generator::symbolic_vector <1, T2> sym_v2;
- static generator::symbolic_vector <2, T3> sym_v3;
- static generator::cpu_symbolic_scalar<3, Fac1> sym_a1;
- static generator::cpu_symbolic_scalar<4, Fac2> sym_a2;
-
- static generator::custom_operation op(
- sym_v1 = sym_a1 * sym_v2
- + sym_a2 * sym_v3,
- "scale_sum2"
- );
-
- ocl::enqueue( op(v1, v2, v3, m_alpha1, m_alpha2) );
- }
-
- typedef void result_type;
- };
-
-
- template< class Fac1 = double , class Fac2 = Fac1 , class Fac3 = Fac2 >
- struct scale_sum3
- {
- const Fac1 m_alpha1;
- const Fac2 m_alpha2;
- const Fac3 m_alpha3;
-
- scale_sum3( Fac1 alpha1 , Fac2 alpha2 , Fac3 alpha3 )
- : m_alpha1( alpha1 ) , m_alpha2( alpha2 ) , m_alpha3( alpha3 )
- { }
-
- template< class T1 , class T2 , class T3 , class T4 >
- void operator()( viennacl::vector<T1> &v1 ,
- const viennacl::vector<T2> &v2 ,
- const viennacl::vector<T3> &v3 ,
- const viennacl::vector<T4> &v4
- ) const
- {
- using namespace viennacl;
-
- static generator::symbolic_vector <0, T1> sym_v1;
- static generator::symbolic_vector <1, T2> sym_v2;
- static generator::symbolic_vector <2, T3> sym_v3;
- static generator::symbolic_vector <3, T4> sym_v4;
- static generator::cpu_symbolic_scalar<4, Fac1> sym_a1;
- static generator::cpu_symbolic_scalar<5, Fac2> sym_a2;
- static generator::cpu_symbolic_scalar<6, Fac3> sym_a3;
-
- static generator::custom_operation op(
- sym_v1 = sym_a1 * sym_v2
- + sym_a2 * sym_v3
- + sym_a3 * sym_v4,
- "scale_sum3"
- );
-
- ocl::enqueue( op(v1, v2, v3, v4, m_alpha1, m_alpha2, m_alpha3) );
- }
-
- typedef void result_type;
- };
-
-
- template< class Fac1 = double , class Fac2 = Fac1 , class Fac3 = Fac2 , class Fac4 = Fac3 >
- struct scale_sum4
- {
- const Fac1 m_alpha1;
- const Fac2 m_alpha2;
- const Fac3 m_alpha3;
- const Fac4 m_alpha4;
-
- scale_sum4( Fac1 alpha1 , Fac2 alpha2 , Fac3 alpha3 , Fac4 alpha4 )
- : m_alpha1( alpha1 ) , m_alpha2( alpha2 ) , m_alpha3( alpha3 ) , m_alpha4( alpha4 ) { }
-
- template< class T1 , class T2 , class T3 , class T4 , class T5 >
- void operator()( viennacl::vector<T1> &v1 ,
- const viennacl::vector<T2> &v2 ,
- const viennacl::vector<T3> &v3 ,
- const viennacl::vector<T4> &v4 ,
- const viennacl::vector<T5> &v5
- ) const
- {
- using namespace viennacl;
-
- static generator::symbolic_vector <0, T1> sym_v1;
- static generator::symbolic_vector <1, T2> sym_v2;
- static generator::symbolic_vector <2, T3> sym_v3;
- static generator::symbolic_vector <3, T4> sym_v4;
- static generator::symbolic_vector <4, T5> sym_v5;
- static generator::cpu_symbolic_scalar<5, Fac1> sym_a1;
- static generator::cpu_symbolic_scalar<6, Fac2> sym_a2;
- static generator::cpu_symbolic_scalar<7, Fac3> sym_a3;
- static generator::cpu_symbolic_scalar<8, Fac4> sym_a4;
-
- static generator::custom_operation op(
- sym_v1 = sym_a1 * sym_v2
- + sym_a2 * sym_v3
- + sym_a3 * sym_v4
- + sym_a4 * sym_v5,
- "scale_sum4"
- );
-
- ocl::enqueue( op(v1, v2, v3, v4, v5,
- m_alpha1, m_alpha2, m_alpha3, m_alpha4) );
- }
-
- typedef void result_type;
- };
-
-
- template< class Fac1 = double , class Fac2 = Fac1 , class Fac3 = Fac2 , class Fac4 = Fac3 , class Fac5 = Fac4 >
- struct scale_sum5
- {
- const Fac1 m_alpha1;
- const Fac2 m_alpha2;
- const Fac3 m_alpha3;
- const Fac4 m_alpha4;
- const Fac5 m_alpha5;
-
- scale_sum5( Fac1 alpha1 , Fac2 alpha2 , Fac3 alpha3 , Fac4 alpha4 , Fac5 alpha5 )
- : m_alpha1( alpha1 ) , m_alpha2( alpha2 ) , m_alpha3( alpha3 ) , m_alpha4( alpha4 ) , m_alpha5( alpha5 ) { }
-
- template< class T1 , class T2 , class T3 , class T4 , class T5 , class T6 >
- void operator()( viennacl::vector<T1> &v1 ,
- const viennacl::vector<T2> &v2 ,
- const viennacl::vector<T3> &v3 ,
- const viennacl::vector<T4> &v4 ,
- const viennacl::vector<T5> &v5 ,
- const viennacl::vector<T6> &v6
- ) const
- {
- using namespace viennacl;
-
- static generator::symbolic_vector < 0, T1> sym_v1;
- static generator::symbolic_vector < 1, T2> sym_v2;
- static generator::symbolic_vector < 2, T3> sym_v3;
- static generator::symbolic_vector < 3, T4> sym_v4;
- static generator::symbolic_vector < 4, T5> sym_v5;
- static generator::symbolic_vector < 5, T6> sym_v6;
- static generator::cpu_symbolic_scalar< 6, Fac1> sym_a1;
- static generator::cpu_symbolic_scalar< 7, Fac2> sym_a2;
- static generator::cpu_symbolic_scalar< 8, Fac3> sym_a3;
- static generator::cpu_symbolic_scalar< 9, Fac4> sym_a4;
- static generator::cpu_symbolic_scalar<10, Fac5> sym_a5;
-
- static generator::custom_operation op(
- sym_v1 = sym_a1 * sym_v2
- + sym_a2 * sym_v3
- + sym_a3 * sym_v4
- + sym_a4 * sym_v5
- + sym_a5 * sym_v6,
- "scale_sum5"
- );
-
- ocl::enqueue( op(v1, v2, v3, v4, v5, v6,
- m_alpha1, m_alpha2, m_alpha3, m_alpha4, m_alpha5) );
- }
-
- typedef void result_type;
- };
-
-
-};
-#else
-struct viennacl_operations : public default_operations {};
-#endif
-
-
-} // odeint
-} // numeric
-} // boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_EXTERNAL_VIENNACL_VIENNACL_OPERATIONS_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/viennacl/viennacl_resize.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/viennacl/viennacl_resize.hpp
deleted file mode 100644
index d3240705be0562b21ef7270508e53c8cce0aafe3..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/external/viennacl/viennacl_resize.hpp
+++ /dev/null
@@ -1,66 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/external/viennacl/viennacl_resize.hpp
-
- [begin_description]
- Enable resizing for viennacl vector.
- [end_description]
-
- Copyright 2012 Denis Demidov
- Copyright 2012 Karsten Ahnert
- Copyright 2012 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_EXTERNAL_VIENNACL_VIENNACL_RESIZE_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_EXTERNAL_VIENNACL_VIENNACL_RESIZE_HPP_INCLUDED
-
-#include <viennacl/vector.hpp>
-
-#include <boost/numeric/odeint/util/is_resizeable.hpp>
-#include <boost/numeric/odeint/util/resize.hpp>
-#include <boost/numeric/odeint/util/same_size.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-
-/*
- * specializations for viennacl::vector< T >
- */
-template< typename T >
-struct is_resizeable< viennacl::vector< T > > : boost::true_type { };
-
-template< typename T >
-struct resize_impl< viennacl::vector< T > , viennacl::vector< T > >
-{
- static void resize( viennacl::vector< T > &x1 , const viennacl::vector< T > &x2 )
- {
- x1.resize( x2.size() , false );
- }
-};
-
-template< typename T >
-struct same_size_impl< viennacl::vector< T > , viennacl::vector< T > >
-{
- static bool same_size( const viennacl::vector< T > &x1 , const viennacl::vector< T > &x2 )
- {
- return x1.size() == x2.size();
- }
-};
-
-
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-
-#endif // BOOST_NUMERIC_ODEINT_EXTERNAL_VIENNACL_VIENNACL_RESIZE_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/integrate/check_adapter.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/integrate/check_adapter.hpp
deleted file mode 100644
index 3d3ebd6c88d5b60e5c43255f34e9d2df50c31d08..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/integrate/check_adapter.hpp
+++ /dev/null
@@ -1,222 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/integrate/check_adapter.hpp
-
- [begin_description]
- Adapters to add checking facility to stepper and observer
- [end_description]
-
- Copyright 2015 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-#ifndef BOOST_NUMERIC_ODEINT_INTEGRATE_CHECK_ADAPTER_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_INTEGRATE_CHECK_ADAPTER_HPP_INCLUDED
-
-#include <boost/numeric/odeint/stepper/stepper_categories.hpp>
-#include <boost/numeric/odeint/stepper/controlled_step_result.hpp>
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-template<class Stepper, class Checker,
- class StepperCategory = typename base_tag<typename Stepper::stepper_category>::type>
-class checked_stepper;
-
-
-/**
- * \brief Adapter to combine basic stepper and checker.
- */
-template<class Stepper, class Checker>
-class checked_stepper<Stepper, Checker, stepper_tag>
-{
-
-public:
- typedef Stepper stepper_type;
- typedef Checker checker_type;
- // forward stepper typedefs
- typedef typename stepper_type::state_type state_type;
- typedef typename stepper_type::value_type value_type;
- typedef typename stepper_type::deriv_type deriv_type;
- typedef typename stepper_type::time_type time_type;
-
-private:
- stepper_type &m_stepper;
- checker_type &m_checker;
-
-public:
- /**
- * \brief Construct the checked_stepper.
- */
- checked_stepper(stepper_type &stepper, checker_type &checker)
- : m_stepper(stepper), m_checker(checker) { }
-
- /**
- * \brief forward of the do_step method
- */
- template<class System, class StateInOut>
- void do_step(System system, StateInOut &state, const time_type t, const time_type dt)
- {
- // do the step
- m_stepper.do_step(system, state, t, dt);
- // call the checker
- m_checker();
- }
-};
-
-
-/**
- * \brief Adapter to combine controlled stepper and checker.
- */
-template<class ControlledStepper, class Checker>
-class checked_stepper<ControlledStepper, Checker, controlled_stepper_tag>
-{
-
-public:
- typedef ControlledStepper stepper_type;
- typedef Checker checker_type;
- // forward stepper typedefs
- typedef typename stepper_type::state_type state_type;
- typedef typename stepper_type::value_type value_type;
- typedef typename stepper_type::deriv_type deriv_type;
- typedef typename stepper_type::time_type time_type;
-
-private:
- stepper_type &m_stepper;
- checker_type &m_checker;
-
-public:
- /**
- * \brief Construct the checked_stepper.
- */
- checked_stepper(stepper_type &stepper, checker_type &checker)
- : m_stepper(stepper), m_checker(checker) { }
-
- /**
- * \brief forward of the do_step method
- */
- template< class System , class StateInOut >
- controlled_step_result try_step( System system , StateInOut &state , time_type &t , time_type &dt )
- {
- // do the step
- if( m_stepper.try_step(system, state, t, dt) == success )
- {
- // call the checker if step was successful
- m_checker();
- return success;
- } else
- {
- // step failed -> return fail
- return fail;
- }
- }
-};
-
-
-/**
- * \brief Adapter to combine dense out stepper and checker.
- */
-template<class DenseOutStepper, class Checker>
-class checked_stepper<DenseOutStepper, Checker, dense_output_stepper_tag>
-{
-
-public:
- typedef DenseOutStepper stepper_type;
- typedef Checker checker_type;
- // forward stepper typedefs
- typedef typename stepper_type::state_type state_type;
- typedef typename stepper_type::value_type value_type;
- typedef typename stepper_type::deriv_type deriv_type;
- typedef typename stepper_type::time_type time_type;
-
-private:
- stepper_type &m_stepper;
- checker_type &m_checker;
-
-public:
- /**
- * \brief Construct the checked_stepper.
- */
- checked_stepper(stepper_type &stepper, checker_type &checker)
- : m_stepper(stepper), m_checker(checker) { }
-
-
- template< class System >
- std::pair< time_type , time_type > do_step( System system )
- {
- m_checker();
- return m_stepper.do_step(system);
- }
-
- /* provide the remaining dense out stepper interface */
- template< class StateType >
- void initialize( const StateType &x0 , time_type t0 , time_type dt0 )
- { m_stepper.initialize(x0, t0, dt0); }
-
-
- template< class StateOut >
- void calc_state( time_type t , StateOut &x ) const
- { m_stepper.calc_state(t, x); }
-
- template< class StateOut >
- void calc_state( time_type t , const StateOut &x ) const
- { m_stepper.calc_state(t, x); }
-
- const state_type& current_state( void ) const
- { return m_stepper.current_state(); }
-
- time_type current_time( void ) const
- { return m_stepper.current_time(); }
-
- const state_type& previous_state( void ) const
- { return m_stepper.previous_state(); }
-
- time_type previous_time( void ) const
- { return m_stepper.previous_time(); }
-
- time_type current_time_step( void ) const
- { return m_stepper.current_time_step(); }
-
-};
-
-
-/**
- * \brief Adapter to combine observer and checker.
- */
-template<class Observer, class Checker>
-class checked_observer
-{
-public:
- typedef Observer observer_type;
- typedef Checker checker_type;
-
-private:
- observer_type &m_observer;
- checker_type &m_checker;
-
-public:
- checked_observer(observer_type &observer, checker_type &checker)
- : m_observer(observer), m_checker(checker)
- {}
-
- template< class State , class Time >
- void operator()(const State& state, Time t) const
- {
- // call the observer
- m_observer(state, t);
- // reset the checker
- m_checker.reset();
- }
-};
-
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-#endif
\ No newline at end of file
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/integrate/detail/functors.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/integrate/detail/functors.hpp
deleted file mode 100644
index b239217ac4cbc9713ae0b7a93998ebcb4e6bd633..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/integrate/detail/functors.hpp
+++ /dev/null
@@ -1,70 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/integrate/detail/functors.hpp
-
- [begin_description]
- some functors for the iterator based integrate routines
- [end_description]
-
- Copyright 2009-2013 Karsten Ahnert
- Copyright 2009-2013 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_INTEGRATE_DETAIL_FUNCTORS_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_INTEGRATE_DETAIL_FUNCTORS_HPP_INCLUDED
-
-#include <utility>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-namespace detail {
-
-
-template< class Observer >
-struct obs_caller {
-
- size_t &m_n;
- Observer m_obs;
-
- obs_caller( size_t &m , Observer &obs ) : m_n(m) , m_obs( obs ) {}
-
- template< class State , class Time >
- void operator()( std::pair< const State & , const Time & > x )
- {
- typedef typename odeint::unwrap_reference< Observer >::type observer_type;
- observer_type &obs = m_obs;
- obs( x.first , x.second );
- m_n++;
- }
-};
-
-template< class Observer , class Time >
-struct obs_caller_time {
-
- Time &m_t;
- Observer m_obs;
-
- obs_caller_time( Time &t , Observer &obs ) : m_t(t) , m_obs( obs ) {}
-
- template< class State >
- void operator()( std::pair< const State & , const Time & > x )
- {
- typedef typename odeint::unwrap_reference< Observer >::type observer_type;
- observer_type &obs = m_obs;
- obs( x.first , x.second );
- m_t = x.second;
- }
-};
-
-} // namespace detail
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-#endif // BOOST_NUMERIC_ODEINT_INTEGRATE_DETAIL_FUNCTORS_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/integrate/detail/integrate_adaptive.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/integrate/detail/integrate_adaptive.hpp
deleted file mode 100644
index 7516d44087c5ab34242b9d24d320241102f79000..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/integrate/detail/integrate_adaptive.hpp
+++ /dev/null
@@ -1,161 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/integrate/detail/integrate_adaptive.hpp
-
- [begin_description]
- Default Integrate adaptive implementation.
- [end_description]
-
- Copyright 2011-2013 Karsten Ahnert
- Copyright 2011-2015 Mario Mulansky
- Copyright 2012 Christoph Koke
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_INTEGRATE_DETAIL_INTEGRATE_ADAPTIVE_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_INTEGRATE_DETAIL_INTEGRATE_ADAPTIVE_HPP_INCLUDED
-
-#include <stdexcept>
-
-#include <boost/throw_exception.hpp>
-
-#include <boost/numeric/odeint/stepper/stepper_categories.hpp>
-#include <boost/numeric/odeint/stepper/controlled_step_result.hpp>
-#include <boost/numeric/odeint/integrate/max_step_checker.hpp>
-#include <boost/numeric/odeint/integrate/detail/integrate_const.hpp>
-#include <boost/numeric/odeint/util/bind.hpp>
-#include <boost/numeric/odeint/util/unwrap_reference.hpp>
-#include <boost/numeric/odeint/util/copy.hpp>
-
-#include <boost/numeric/odeint/util/detail/less_with_sign.hpp>
-
-
-#include <iostream>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-namespace detail {
-
-// forward declaration
-template< class Stepper , class System , class State , class Time , class Observer >
-size_t integrate_const(
- Stepper stepper , System system , State &start_state ,
- Time start_time , Time end_time , Time dt ,
- Observer observer , stepper_tag );
-
-/*
- * integrate_adaptive for simple stepper is basically an integrate_const + some last step
- */
-template< class Stepper , class System , class State , class Time , class Observer >
-size_t integrate_adaptive(
- Stepper stepper , System system , State &start_state ,
- Time start_time , Time end_time , Time dt ,
- Observer observer , stepper_tag
-)
-{
- size_t steps = detail::integrate_const( stepper , system , start_state , start_time ,
- end_time , dt , observer , stepper_tag() );
- typename odeint::unwrap_reference< Observer >::type &obs = observer;
- typename odeint::unwrap_reference< Stepper >::type &st = stepper;
-
- Time end = start_time + dt*steps;
- if( less_with_sign( end , end_time , dt ) )
- { //make a last step to end exactly at end_time
- st.do_step( system , start_state , end , end_time - end );
- steps++;
- obs( start_state , end_time );
- }
- return steps;
-}
-
-
-/*
- * integrate adaptive for controlled stepper
- */
-template< class Stepper , class System , class State , class Time , class Observer >
-size_t integrate_adaptive(
- Stepper stepper , System system , State &start_state ,
- Time &start_time , Time end_time , Time &dt ,
- Observer observer , controlled_stepper_tag
-)
-{
- typename odeint::unwrap_reference< Observer >::type &obs = observer;
- typename odeint::unwrap_reference< Stepper >::type &st = stepper;
-
- failed_step_checker fail_checker; // to throw a runtime_error if step size adjustment fails
- size_t count = 0;
- while( less_with_sign( start_time , end_time , dt ) )
- {
- obs( start_state , start_time );
- if( less_with_sign( end_time , static_cast<Time>(start_time + dt) , dt ) )
- {
- dt = end_time - start_time;
- }
-
- controlled_step_result res;
- do
- {
- res = st.try_step( system , start_state , start_time , dt );
- fail_checker(); // check number of failed steps
- }
- while( res == fail );
- fail_checker.reset(); // if we reach here, the step was successful -> reset fail checker
-
- ++count;
- }
- obs( start_state , start_time );
- return count;
-}
-
-
-/*
- * integrate adaptive for dense output steppers
- *
- * step size control is used if the stepper supports it
- */
-template< class Stepper , class System , class State , class Time , class Observer >
-size_t integrate_adaptive(
- Stepper stepper , System system , State &start_state ,
- Time start_time , Time end_time , Time dt ,
- Observer observer , dense_output_stepper_tag )
-{
- typename odeint::unwrap_reference< Observer >::type &obs = observer;
- typename odeint::unwrap_reference< Stepper >::type &st = stepper;
-
- size_t count = 0;
- st.initialize( start_state , start_time , dt );
-
- while( less_with_sign( st.current_time() , end_time , st.current_time_step() ) )
- {
- while( less_eq_with_sign( static_cast<Time>(st.current_time() + st.current_time_step()) ,
- end_time ,
- st.current_time_step() ) )
- { //make sure we don't go beyond the end_time
- obs( st.current_state() , st.current_time() );
- st.do_step( system );
- ++count;
- }
- // calculate time step to arrive exactly at end time
- st.initialize( st.current_state() , st.current_time() , static_cast<Time>(end_time - st.current_time()) );
- }
- obs( st.current_state() , st.current_time() );
- // overwrite start_state with the final point
- boost::numeric::odeint::copy( st.current_state() , start_state );
- return count;
-}
-
-
-
-
-} // namespace detail
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_INTEGRATE_DETAIL_INTEGRATE_ADAPTIVE_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/integrate/detail/integrate_const.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/integrate/detail/integrate_const.hpp
deleted file mode 100644
index 52c04a8e13d5916819e4000b419c77e2c44331f4..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/integrate/detail/integrate_const.hpp
+++ /dev/null
@@ -1,167 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/integrate/detail/integrate_const.hpp
-
- [begin_description]
- integrate const implementation
- [end_description]
-
- Copyright 2012-2015 Mario Mulansky
- Copyright 2012 Christoph Koke
- Copyright 2012 Karsten Ahnert
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-#ifndef BOOST_NUMERIC_ODEINT_INTEGRATE_DETAIL_INTEGRATE_CONST_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_INTEGRATE_DETAIL_INTEGRATE_CONST_HPP_INCLUDED
-
-#include <boost/numeric/odeint/util/unwrap_reference.hpp>
-#include <boost/numeric/odeint/stepper/stepper_categories.hpp>
-#include <boost/numeric/odeint/util/unit_helper.hpp>
-#include <boost/numeric/odeint/integrate/detail/integrate_adaptive.hpp>
-
-#include <boost/numeric/odeint/util/detail/less_with_sign.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-namespace detail {
-
-// forward declaration
-template< class Stepper , class System , class State , class Time , class Observer >
-size_t integrate_adaptive(
- Stepper stepper , System system , State &start_state ,
- Time &start_time , Time end_time , Time &dt ,
- Observer observer , controlled_stepper_tag
-);
-
-
-template< class Stepper , class System , class State , class Time , class Observer >
-size_t integrate_const(
- Stepper stepper , System system , State &start_state ,
- Time start_time , Time end_time , Time dt ,
- Observer observer , stepper_tag
-)
-{
-
- typename odeint::unwrap_reference< Observer >::type &obs = observer;
- typename odeint::unwrap_reference< Stepper >::type &st = stepper;
-
- Time time = start_time;
- int step = 0;
- // cast time+dt explicitely in case of expression templates (e.g. multiprecision)
- while( less_eq_with_sign( static_cast<Time>(time+dt) , end_time , dt ) )
- {
- obs( start_state , time );
- st.do_step( system , start_state , time , dt );
- // direct computation of the time avoids error propagation happening when using time += dt
- // we need clumsy type analysis to get boost units working here
- ++step;
- time = start_time + static_cast< typename unit_value_type<Time>::type >(step) * dt;
- }
- obs( start_state , time );
-
- return step;
-}
-
-
-
-template< class Stepper , class System , class State , class Time , class Observer >
-size_t integrate_const(
- Stepper stepper , System system , State &start_state ,
- Time start_time , Time end_time , Time dt ,
- Observer observer , controlled_stepper_tag
-)
-{
- typename odeint::unwrap_reference< Observer >::type &obs = observer;
-
- Time time = start_time;
- const Time time_step = dt;
- int real_steps = 0;
- int step = 0;
-
- while( less_eq_with_sign( static_cast<Time>(time+time_step) , end_time , dt ) )
- {
- obs( start_state , time );
- // integrate_adaptive_checked uses the given checker to throw if an overflow occurs
- real_steps += detail::integrate_adaptive(stepper, system, start_state, time,
- static_cast<Time>(time + time_step), dt,
- null_observer(), controlled_stepper_tag());
- // direct computation of the time avoids error propagation happening when using time += dt
- // we need clumsy type analysis to get boost units working here
- step++;
- time = start_time + static_cast< typename unit_value_type<Time>::type >(step) * time_step;
- }
- obs( start_state , time );
-
- return real_steps;
-}
-
-
-template< class Stepper , class System , class State , class Time , class Observer >
-size_t integrate_const(
- Stepper stepper , System system , State &start_state ,
- Time start_time , Time end_time , Time dt ,
- Observer observer , dense_output_stepper_tag
-)
-{
- typename odeint::unwrap_reference< Observer >::type &obs = observer;
- typename odeint::unwrap_reference< Stepper >::type &st = stepper;
-
- Time time = start_time;
-
- st.initialize( start_state , time , dt );
- obs( start_state , time );
- time += dt;
-
- int obs_step( 1 );
- int real_step( 0 );
-
- while( less_eq_with_sign( static_cast<Time>(time+dt) , end_time , dt ) )
- {
- while( less_eq_with_sign( time , st.current_time() , dt ) )
- {
- st.calc_state( time , start_state );
- obs( start_state , time );
- ++obs_step;
- // direct computation of the time avoids error propagation happening when using time += dt
- // we need clumsy type analysis to get boost units working here
- time = start_time + static_cast< typename unit_value_type<Time>::type >(obs_step) * dt;
- }
- // we have not reached the end, do another real step
- if( less_with_sign( static_cast<Time>(st.current_time()+st.current_time_step()) ,
- end_time ,
- st.current_time_step() ) )
- {
- while( less_eq_with_sign( st.current_time() , time , dt ) )
- {
- st.do_step( system );
- ++real_step;
- }
- }
- else if( less_with_sign( st.current_time() , end_time , st.current_time_step() ) )
- { // do the last step ending exactly on the end point
- st.initialize( st.current_state() , st.current_time() , end_time - st.current_time() );
- st.do_step( system );
- ++real_step;
- }
-
- }
- // last observation, if we are still in observation interval
- // might happen due to finite precision problems when computing the the time
- if( less_eq_with_sign( time , end_time , dt ) )
- {
- st.calc_state( time , start_state );
- obs( start_state , time );
- }
-
- return real_step;
-}
-
-
-} } } }
-
-#endif
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/integrate/detail/integrate_n_steps.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/integrate/detail/integrate_n_steps.hpp
deleted file mode 100644
index 2ef490d5929d52224e3f6825b46f9ab37d2c1f08..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/integrate/detail/integrate_n_steps.hpp
+++ /dev/null
@@ -1,161 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/integrate/detail/integrate_n_steps.hpp
-
- [begin_description]
- integrate steps implementation
- [end_description]
-
- Copyright 2012-2015 Mario Mulansky
- Copyright 2012 Christoph Koke
- Copyright 2012 Karsten Ahnert
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-#ifndef BOOST_NUMERIC_ODEINT_INTEGRATE_DETAIL_INTEGRATE_N_STEPS_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_INTEGRATE_DETAIL_INTEGRATE_N_STEPS_HPP_INCLUDED
-
-#include <boost/numeric/odeint/util/unwrap_reference.hpp>
-#include <boost/numeric/odeint/stepper/stepper_categories.hpp>
-#include <boost/numeric/odeint/integrate/detail/integrate_adaptive.hpp>
-#include <boost/numeric/odeint/util/unit_helper.hpp>
-
-#include <boost/numeric/odeint/util/detail/less_with_sign.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-namespace detail {
-
-// forward declaration
-template< class Stepper , class System , class State , class Time , class Observer >
-size_t integrate_adaptive_checked(
- Stepper stepper , System system , State &start_state ,
- Time &start_time , Time end_time , Time &dt ,
- Observer observer, controlled_stepper_tag
-);
-
-
-/* basic version */
-template< class Stepper , class System , class State , class Time , class Observer>
-Time integrate_n_steps(
- Stepper stepper , System system , State &start_state ,
- Time start_time , Time dt , size_t num_of_steps ,
- Observer observer , stepper_tag )
-{
- typename odeint::unwrap_reference< Observer >::type &obs = observer;
- typename odeint::unwrap_reference< Stepper >::type &st = stepper;
-
- Time time = start_time;
-
- for( size_t step = 0; step < num_of_steps ; ++step )
- {
- obs( start_state , time );
- st.do_step( system , start_state , time , dt );
- // direct computation of the time avoids error propagation happening when using time += dt
- // we need clumsy type analysis to get boost units working here
- time = start_time + static_cast< typename unit_value_type<Time>::type >( step+1 ) * dt;
- }
- obs( start_state , time );
-
- return time;
-}
-
-
-/* controlled version */
-template< class Stepper , class System , class State , class Time , class Observer >
-Time integrate_n_steps(
- Stepper stepper , System system , State &start_state ,
- Time start_time , Time dt , size_t num_of_steps ,
- Observer observer , controlled_stepper_tag )
-{
- typename odeint::unwrap_reference< Observer >::type &obs = observer;
-
- Time time = start_time;
- Time time_step = dt;
-
- for( size_t step = 0; step < num_of_steps ; ++step )
- {
- obs( start_state , time );
- // integrate_adaptive_checked uses the given checker to throw if an overflow occurs
- detail::integrate_adaptive(stepper, system, start_state, time, static_cast<Time>(time + time_step), dt,
- null_observer(), controlled_stepper_tag());
- // direct computation of the time avoids error propagation happening when using time += dt
- // we need clumsy type analysis to get boost units working here
- time = start_time + static_cast< typename unit_value_type<Time>::type >(step+1) * time_step;
- }
- obs( start_state , time );
-
- return time;
-}
-
-
-/* dense output version */
-template< class Stepper , class System , class State , class Time , class Observer >
-Time integrate_n_steps(
- Stepper stepper , System system , State &start_state ,
- Time start_time , Time dt , size_t num_of_steps ,
- Observer observer , dense_output_stepper_tag )
-{
- typename odeint::unwrap_reference< Observer >::type &obs = observer;
- typename odeint::unwrap_reference< Stepper >::type &st = stepper;
-
- Time time = start_time;
- const Time end_time = start_time + static_cast< typename unit_value_type<Time>::type >(num_of_steps) * dt;
-
- st.initialize( start_state , time , dt );
-
- size_t step = 0;
-
- while( step < num_of_steps )
- {
- while( less_with_sign( time , st.current_time() , st.current_time_step() ) )
- {
- st.calc_state( time , start_state );
- obs( start_state , time );
- ++step;
- // direct computation of the time avoids error propagation happening when using time += dt
- // we need clumsy type analysis to get boost units working here
- time = start_time + static_cast< typename unit_value_type<Time>::type >(step) * dt;
- }
-
- // we have not reached the end, do another real step
- if( less_with_sign( static_cast<Time>(st.current_time()+st.current_time_step()) ,
- end_time ,
- st.current_time_step() ) )
- {
- st.do_step( system );
- }
- else if( less_with_sign( st.current_time() , end_time , st.current_time_step() ) )
- { // do the last step ending exactly on the end point
- st.initialize( st.current_state() , st.current_time() , static_cast<Time>(end_time - st.current_time()) );
- st.do_step( system );
- }
- }
-
- // make sure we really end exactly where we should end
- while( st.current_time() < end_time )
- {
- if( less_with_sign( end_time ,
- static_cast<Time>(st.current_time()+st.current_time_step()) ,
- st.current_time_step() ) )
- st.initialize( st.current_state() , st.current_time() , static_cast<Time>(end_time - st.current_time()) );
- st.do_step( system );
- }
-
- // observation at final point
- obs( st.current_state() , end_time );
-
- return time;
-}
-
-
-}
-}
-}
-}
-
-#endif /* BOOST_NUMERIC_ODEINT_INTEGRATE_DETAIL_INTEGRATE_N_STEPS_HPP_INCLUDED */
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/integrate/detail/integrate_times.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/integrate/detail/integrate_times.hpp
deleted file mode 100644
index 2e279904124574979800e1b3a3aee33fc09c32aa..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/integrate/detail/integrate_times.hpp
+++ /dev/null
@@ -1,179 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/integrate/detail/integrate_times.hpp
-
- [begin_description]
- Default integrate times implementation.
- [end_description]
-
- Copyright 2011-2015 Mario Mulansky
- Copyright 2012 Karsten Ahnert
- Copyright 2012 Christoph Koke
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_INTEGRATE_DETAIL_INTEGRATE_TIMES_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_INTEGRATE_DETAIL_INTEGRATE_TIMES_HPP_INCLUDED
-
-#include <stdexcept>
-
-#include <boost/config.hpp>
-#include <boost/throw_exception.hpp>
-#include <boost/numeric/odeint/util/unwrap_reference.hpp>
-#include <boost/numeric/odeint/stepper/controlled_step_result.hpp>
-#include <boost/numeric/odeint/util/detail/less_with_sign.hpp>
-#include <boost/numeric/odeint/integrate/max_step_checker.hpp>
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-namespace detail {
-
-
-
-/*
- * integrate_times for simple stepper
- */
-template<class Stepper, class System, class State, class TimeIterator, class Time, class Observer>
-size_t integrate_times(
- Stepper stepper , System system , State &start_state ,
- TimeIterator start_time , TimeIterator end_time , Time dt ,
- Observer observer , stepper_tag
-)
-{
- typedef typename odeint::unwrap_reference< Stepper >::type stepper_type;
- typedef typename odeint::unwrap_reference< Observer >::type observer_type;
-
- stepper_type &st = stepper;
- observer_type &obs = observer;
- typedef typename unit_value_type<Time>::type time_type;
-
- size_t steps = 0;
- Time current_dt = dt;
- while( true )
- {
- Time current_time = *start_time++;
- obs( start_state , current_time );
- if( start_time == end_time )
- break;
- while( less_with_sign( current_time , static_cast<time_type>(*start_time) , current_dt ) )
- {
- current_dt = min_abs( dt , *start_time - current_time );
- st.do_step( system , start_state , current_time , current_dt );
- current_time += current_dt;
- steps++;
- }
- }
- return steps;
-}
-
-/*
- * integrate_times for controlled stepper
- */
-template< class Stepper , class System , class State , class TimeIterator , class Time , class Observer >
-size_t integrate_times(
- Stepper stepper , System system , State &start_state ,
- TimeIterator start_time , TimeIterator end_time , Time dt ,
- Observer observer , controlled_stepper_tag
-)
-{
- typename odeint::unwrap_reference< Observer >::type &obs = observer;
- typename odeint::unwrap_reference< Stepper >::type &st = stepper;
- typedef typename unit_value_type<Time>::type time_type;
-
- failed_step_checker fail_checker; // to throw a runtime_error if step size adjustment fails
- size_t steps = 0;
- while( true )
- {
- Time current_time = *start_time++;
- obs( start_state , current_time );
- if( start_time == end_time )
- break;
- while( less_with_sign( current_time , static_cast<time_type>(*start_time) , dt ) )
- {
- // adjust stepsize to end up exactly at the observation point
- Time current_dt = min_abs( dt , *start_time - current_time );
- if( st.try_step( system , start_state , current_time , current_dt ) == success )
- {
- ++steps;
- // successful step -> reset the fail counter, see #173
- fail_checker.reset();
- // continue with the original step size if dt was reduced due to observation
- dt = max_abs( dt , current_dt );
- }
- else
- {
- fail_checker(); // check for possible overflow of failed steps in step size adjustment
- dt = current_dt;
- }
- }
- }
- return steps;
-}
-
-/*
- * integrate_times for dense output stepper
- */
-template< class Stepper , class System , class State , class TimeIterator , class Time , class Observer >
-size_t integrate_times(
- Stepper stepper , System system , State &start_state ,
- TimeIterator start_time , TimeIterator end_time , Time dt ,
- Observer observer , dense_output_stepper_tag
-)
-{
- typename odeint::unwrap_reference< Observer >::type &obs = observer;
- typename odeint::unwrap_reference< Stepper >::type &st = stepper;
-
- typedef typename unit_value_type<Time>::type time_type;
-
- if( start_time == end_time )
- return 0;
-
- TimeIterator last_time_iterator = end_time;
- --last_time_iterator;
- Time last_time_point = static_cast<time_type>(*last_time_iterator);
-
- st.initialize( start_state , *start_time , dt );
- obs( start_state , *start_time++ );
-
- size_t count = 0;
- while( start_time != end_time )
- {
- while( ( start_time != end_time ) && less_eq_with_sign( static_cast<time_type>(*start_time) , st.current_time() , st.current_time_step() ) )
- {
- st.calc_state( *start_time , start_state );
- obs( start_state , *start_time );
- start_time++;
- }
-
- // we have not reached the end, do another real step
- if( less_eq_with_sign( st.current_time() + st.current_time_step() ,
- last_time_point ,
- st.current_time_step() ) )
- {
- st.do_step( system );
- ++count;
- }
- else if( start_time != end_time )
- { // do the last step ending exactly on the end point
- st.initialize( st.current_state() , st.current_time() , last_time_point - st.current_time() );
- st.do_step( system );
- ++count;
- }
- }
- return count;
-}
-
-
-} // namespace detail
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_INTEGRATE_DETAIL_INTEGRATE_ADAPTIVE_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/integrate/integrate.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/integrate/integrate.hpp
deleted file mode 100644
index bb380f43b0dbbf07ccb88a965f60e486a99cb3a7..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/integrate/integrate.hpp
+++ /dev/null
@@ -1,133 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/integrate/integrate.hpp
-
- [begin_description]
- Convenience methods which choose the stepper for the current ODE.
- [end_description]
-
- Copyright 2011-2013 Karsten Ahnert
- Copyright 2011-2012 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_INTEGRATE_INTEGRATE_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_INTEGRATE_INTEGRATE_HPP_INCLUDED
-
-#include <boost/utility/enable_if.hpp>
-
-#include <boost/numeric/odeint/stepper/runge_kutta_dopri5.hpp>
-#include <boost/numeric/odeint/stepper/controlled_runge_kutta.hpp>
-#include <boost/numeric/odeint/integrate/null_observer.hpp>
-#include <boost/numeric/odeint/integrate/integrate_adaptive.hpp>
-
-// for has_value_type trait
-#include <boost/numeric/odeint/algebra/detail/extract_value_type.hpp>
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-/*
- * ToDo :
- *
- * determine type of dxdt for units
- *
- */
-template< class System , class State , class Time , class Observer >
-typename boost::enable_if< typename has_value_type<State>::type , size_t >::type
-integrate( System system , State &start_state , Time start_time , Time end_time , Time dt , Observer observer )
-{
- typedef controlled_runge_kutta< runge_kutta_dopri5< State , typename State::value_type , State , Time > > stepper_type;
- return integrate_adaptive( stepper_type() , system , start_state , start_time , end_time , dt , observer );
-}
-
-template< class Value , class System , class State , class Time , class Observer >
-size_t
-integrate( System system , State &start_state , Time start_time , Time end_time , Time dt , Observer observer )
-{
- typedef controlled_runge_kutta< runge_kutta_dopri5< State , Value , State , Time > > stepper_type;
- return integrate_adaptive( stepper_type() , system , start_state , start_time , end_time , dt , observer );
-}
-
-
-
-
-/*
- * the two overloads are needed in order to solve the forwarding problem
- */
-template< class System , class State , class Time >
-size_t integrate( System system , State &start_state , Time start_time , Time end_time , Time dt )
-{
- return integrate( system , start_state , start_time , end_time , dt , null_observer() );
-}
-
-template< class Value , class System , class State , class Time >
-size_t integrate( System system , State &start_state , Time start_time , Time end_time , Time dt )
-{
- return integrate< Value >( system , start_state , start_time , end_time , dt , null_observer() );
-}
-
-
-
-/**
- * \fn integrate( System system , State &start_state , Time start_time , Time end_time , Time dt , Observer observer )
- * \brief Integrates the ODE.
- *
- * Integrates the ODE given by system from start_time to end_time starting
- * with start_state as initial condition and dt as initial time step.
- * This function uses a dense output dopri5 stepper and performs an adaptive
- * integration with step size control, thus dt changes during the integration.
- * This method uses standard error bounds of 1E-6.
- * After each step, the observer is called.
- *
- * \attention A second version of this function template exists which explicitly
- * expects the value type as template parameter, i.e. integrate< double >( sys , x , t0 , t1 , dt , obs );
- *
- * \param system The system function to solve, hence the r.h.s. of the
- * ordinary differential equation.
- * \param start_state The initial state.
- * \param start_time Start time of the integration.
- * \param end_time End time of the integration.
- * \param dt Initial step size, will be adjusted during the integration.
- * \param observer Observer that will be called after each time step.
- * \return The number of steps performed.
- */
-
-
-/**
- * \fn integrate( System system , State &start_state , Time start_time , Time end_time , Time dt )
- * \brief Integrates the ODE without observer calls.
- *
- * Integrates the ODE given by system from start_time to end_time starting
- * with start_state as initial condition and dt as initial time step.
- * This function uses a dense output dopri5 stepper and performs an adaptive
- * integration with step size control, thus dt changes during the integration.
- * This method uses standard error bounds of 1E-6.
- * No observer is called.
- *
- * \attention A second version of this function template exists which explicitly
- * expects the value type as template parameter, i.e. integrate< double >( sys , x , t0 , t1 , dt );
- *
- * \param system The system function to solve, hence the r.h.s. of the
- * ordinary differential equation.
- * \param start_state The initial state.
- * \param start_time Start time of the integration.
- * \param end_time End time of the integration.
- * \param dt Initial step size, will be adjusted during the integration.
- * \return The number of steps performed.
- */
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-
-#endif // BOOST_NUMERIC_ODEINT_INTEGRATE_INTEGRATE_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/integrate/integrate_adaptive.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/integrate/integrate_adaptive.hpp
deleted file mode 100644
index e7d6cf7e861b0a82c834d96ecdb450e523f52aa9..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/integrate/integrate_adaptive.hpp
+++ /dev/null
@@ -1,129 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/integrate/integrate_adaptive.hpp
-
- [begin_description]
- Adaptive integration of ODEs.
- [end_description]
-
- Copyright 2011-2013 Karsten Ahnert
- Copyright 2011-2015 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_INTEGRATE_INTEGRATE_ADAPTIVE_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_INTEGRATE_INTEGRATE_ADAPTIVE_HPP_INCLUDED
-
-#include <boost/type_traits/is_same.hpp>
-
-#include <boost/numeric/odeint/stepper/stepper_categories.hpp>
-#include <boost/numeric/odeint/integrate/null_observer.hpp>
-#include <boost/numeric/odeint/integrate/detail/integrate_adaptive.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-/*
- * the two overloads are needed in order to solve the forwarding problem
- */
-template< class Stepper , class System , class State , class Time , class Observer >
-size_t integrate_adaptive(
- Stepper stepper , System system , State &start_state ,
- Time start_time , Time end_time , Time dt ,
- Observer observer )
-{
- typedef typename odeint::unwrap_reference< Stepper >::type::stepper_category stepper_category;
- return detail::integrate_adaptive(
- stepper , system , start_state ,
- start_time , end_time , dt ,
- observer , stepper_category() );
-
- /*
- * Suggestion for a new extendable version:
- *
- * integrator_adaptive< Stepper , System, State , Time , Observer , typename Stepper::stepper_category > integrator;
- * return integrator.run( stepper , system , start_state , start_time , end_time , dt , observer );
- */
-}
-
-/**
- * \brief Second version to solve the forwarding problem,
- * can be called with Boost.Range as start_state.
- */
-template< class Stepper , class System , class State , class Time , class Observer >
-size_t integrate_adaptive(
- Stepper stepper , System system , const State &start_state ,
- Time start_time , Time end_time , Time dt ,
- Observer observer )
-{
- typedef typename odeint::unwrap_reference< Stepper >::type::stepper_category stepper_category;
- return detail::integrate_adaptive(
- stepper , system , start_state ,
- start_time , end_time , dt ,
- observer , stepper_category() );
-}
-
-
-
-
-/**
- * \brief integrate_adaptive without an observer.
- */
-template< class Stepper , class System , class State , class Time >
-size_t integrate_adaptive(
- Stepper stepper , System system , State &start_state ,
- Time start_time , Time end_time , Time dt )
-{
- return integrate_adaptive( stepper , system , start_state , start_time , end_time , dt , null_observer() );
-}
-
-/**
- * \brief Second version to solve the forwarding problem,
- * can be called with Boost.Range as start_state.
- */
-template< class Stepper , class System , class State , class Time >
-size_t integrate_adaptive(
- Stepper stepper , System system , const State &start_state ,
- Time start_time , Time end_time , Time dt )
-{
- return integrate_adaptive( stepper , system , start_state , start_time , end_time , dt , null_observer() );
-}
-
-
-/************* DOXYGEN ************/
-
- /**
- * \fn integrate_adaptive( Stepper stepper , System system , State &start_state , Time start_time , Time end_time , Time dt , Observer observer )
- * \brief Integrates the ODE with adaptive step size.
- *
- * This function integrates the ODE given by system with the given stepper.
- * The observer is called after each step. If the stepper has no error
- * control, the step size remains constant and the observer is called at
- * equidistant time points t0+n*dt. If the stepper is a ControlledStepper,
- * the step size is adjusted and the observer is called in non-equidistant
- * intervals.
- *
- * \param stepper The stepper to be used for numerical integration.
- * \param system Function/Functor defining the rhs of the ODE.
- * \param start_state The initial condition x0.
- * \param start_time The initial time t0.
- * \param end_time The final integration time tend.
- * \param dt The time step between observer calls, _not_ necessarily the
- * time step of the integration.
- * \param observer Function/Functor called at equidistant time intervals.
- * \return The number of steps performed.
- */
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-
-#endif // BOOST_NUMERIC_ODEINT_INTEGRATE_INTEGRATE_ADAPTIVE_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/integrate/integrate_const.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/integrate/integrate_const.hpp
deleted file mode 100644
index fae683f9782557541983bc1e813ab4a9912b2613..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/integrate/integrate_const.hpp
+++ /dev/null
@@ -1,195 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/integrate/integrate_const.hpp
-
- [begin_description]
- Constant integration of ODEs, meaning that the state of the ODE is observed on constant time intervals.
- The routines makes full use of adaptive and dense-output methods.
- [end_description]
-
- Copyright 2011-2013 Karsten Ahnert
- Copyright 2011-2015 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_INTEGRATE_INTEGRATE_CONST_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_INTEGRATE_INTEGRATE_CONST_HPP_INCLUDED
-
-#include <boost/type_traits/is_same.hpp>
-
-#include <boost/numeric/odeint/stepper/stepper_categories.hpp>
-#include <boost/numeric/odeint/integrate/null_observer.hpp>
-#include <boost/numeric/odeint/integrate/check_adapter.hpp>
-#include <boost/numeric/odeint/integrate/detail/integrate_const.hpp>
-#include <boost/numeric/odeint/integrate/detail/integrate_adaptive.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-/*
- * Integrates with constant time step dt.
- */
-template<class Stepper, class System, class State, class Time, class Observer, class StepOverflowChecker>
-size_t integrate_const(
- Stepper stepper, System system, State &start_state,
- Time start_time, Time end_time, Time dt,
- Observer observer, StepOverflowChecker checker
-) {
- typedef typename odeint::unwrap_reference<Stepper>::type::stepper_category stepper_category;
- // we want to get as fast as possible to the end
- // no overflow checks needed
- if (boost::is_same<null_observer, Observer>::value) {
- return detail::integrate_adaptive(
- stepper, system, start_state,
- start_time, end_time, dt,
- observer, stepper_category());
- }
- else {
- // unwrap references
- typedef typename odeint::unwrap_reference< Stepper >::type stepper_type;
- typedef typename odeint::unwrap_reference< Observer >::type observer_type;
- typedef typename odeint::unwrap_reference< StepOverflowChecker >::type checker_type;
-
- return detail::integrate_const(checked_stepper<stepper_type, checker_type>(stepper, checker),
- system, start_state,
- start_time, end_time, dt,
- checked_observer<observer_type, checker_type>(observer, checker),
- stepper_category());
- }
-}
-
-/**
-* \brief Second version to solve the forwarding problem,
-* can be called with Boost.Range as start_state.
-*/
-template<class Stepper, class System, class State, class Time, class Observer, class StepOverflowChecker >
-size_t integrate_const(
- Stepper stepper, System system, const State &start_state,
- Time start_time, Time end_time, Time dt,
- Observer observer, StepOverflowChecker checker
-) {
- typedef typename odeint::unwrap_reference<Stepper>::type::stepper_category stepper_category;
- // we want to get as fast as possible to the end
-
- if (boost::is_same<null_observer, Observer>::value) {
- return detail::integrate_adaptive(
- stepper, system, start_state,
- start_time, end_time, dt,
- observer, stepper_category());
- }
- else {
- typedef typename odeint::unwrap_reference< Stepper >::type stepper_type;
- typedef typename odeint::unwrap_reference< Observer >::type observer_type;
- typedef typename odeint::unwrap_reference< StepOverflowChecker >::type checker_type;
-
- return detail::integrate_const(checked_stepper<stepper_type, checker_type>(stepper, checker),
- system, start_state,
- start_time, end_time, dt,
- checked_observer<observer_type, checker_type>(observer, checker),
- stepper_category());
- }
-}
-
-
-/**
-* \brief integrate_const without step overflow checker
-*/
-template<class Stepper, class System, class State, class Time, class Observer>
-size_t integrate_const(
- Stepper stepper, System system, State &start_state,
- Time start_time, Time end_time, Time dt, Observer observer)
-{
- typedef typename odeint::unwrap_reference<Stepper>::type::stepper_category stepper_category;
- return detail::integrate_const(stepper, system, start_state,
- start_time, end_time, dt, observer, stepper_category());
-}
-
-/**
-* \brief Second version to solve the forwarding problem,
-* can be called with Boost.Range as start_state.
-*/
-template<class Stepper, class System, class State, class Time, class Observer>
-size_t integrate_const(
- Stepper stepper, System system, const State &start_state,
- Time start_time, Time end_time, Time dt, Observer observer
-) {
- typedef typename odeint::unwrap_reference<Stepper>::type::stepper_category stepper_category;
- return detail::integrate_const(stepper, system, start_state,
- start_time, end_time, dt, observer, stepper_category());
-}
-
-
-/**
-* \brief integrate_const without observer calls
-*/
-template<class Stepper, class System, class State, class Time>
-size_t integrate_const(
- Stepper stepper, System system, State &start_state,
- Time start_time, Time end_time, Time dt
-) {
- return integrate_const(stepper, system, start_state, start_time, end_time, dt, null_observer());
-}
-
-/**
-* \brief Second version to solve the forwarding problem,
-* can be called with Boost.Range as start_state.
-*/
-template<class Stepper, class System, class State, class Time>
-size_t integrate_const(
- Stepper stepper, System system, const State &start_state,
- Time start_time, Time end_time, Time dt
-) {
- return integrate_const(stepper, system, start_state, start_time, end_time, dt, null_observer());
-}
-
-
-
-
-
-
-/********* DOXYGEN *********/
-/**
- * \fn integrate_const( Stepper stepper , System system , State &start_state , Time start_time ,
- * Time end_time , Time dt , Observer observer , StepOverflowChecker checker )
- * \brief Integrates the ODE with constant step size.
- *
- * Integrates the ODE defined by system using the given stepper.
- * This method ensures that the observer is called at constant intervals dt.
- * If the Stepper is a normal stepper without step size control, dt is also
- * used for the numerical scheme. If a ControlledStepper is provided, the
- * algorithm might reduce the step size to meet the error bounds, but it is
- * ensured that the observer is always called at equidistant time points
- * t0 + n*dt. If a DenseOutputStepper is used, the step size also may vary
- * and the dense output is used to call the observer at equidistant time
- * points.
- * If a max_step_checker is provided as StepOverflowChecker, a
- * no_progress_error is thrown if too many steps (default: 500) are performed
- * without progress, i.e. in between observer calls. If no checker is provided,
- * no such overflow check is performed.
- *
- * \param stepper The stepper to be used for numerical integration.
- * \param system Function/Functor defining the rhs of the ODE.
- * \param start_state The initial condition x0.
- * \param start_time The initial time t0.
- * \param end_time The final integration time tend.
- * \param dt The time step between observer calls, _not_ necessarily the
- * time step of the integration.
- * \param observer [optional] Function/Functor called at equidistant time intervals.
- * \param checker [optional] Functor to check for step count overflows, if no
- * checker is provided, no exception is thrown.
- * \return The number of steps performed.
- */
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-
-#endif // BOOST_NUMERIC_ODEINT_INTEGRATE_INTEGRATE_CONST_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/integrate/integrate_n_steps.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/integrate/integrate_n_steps.hpp
deleted file mode 100644
index c95e695193047d521d0ab9fafe508f53ad204d74..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/integrate/integrate_n_steps.hpp
+++ /dev/null
@@ -1,180 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/integrate/integrate_n_steps.hpp
-
- [begin_description]
- Integration of n steps with constant time size. Adaptive and dense-output methods are fully supported.
- [end_description]
-
- Copyright 2011-2013 Karsten Ahnert
- Copyright 2011-2015 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_INTEGRATE_INTEGRATE_N_STEPS_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_INTEGRATE_INTEGRATE_N_STEPS_HPP_INCLUDED
-
-#include <boost/type_traits/is_same.hpp>
-
-#include <boost/numeric/odeint/stepper/stepper_categories.hpp>
-#include <boost/numeric/odeint/integrate/null_observer.hpp>
-#include <boost/numeric/odeint/integrate/detail/integrate_n_steps.hpp>
-#include <boost/numeric/odeint/integrate/check_adapter.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-/*
- * Integrates n steps
- *
- * the two overloads are needed in order to solve the forwarding problem
- */
-template< class Stepper , class System , class State , class Time , class Observer , class StepOverflowChecker >
-Time integrate_n_steps(
- Stepper stepper , System system , State &start_state ,
- Time start_time , Time dt , size_t num_of_steps ,
- Observer observer , StepOverflowChecker checker )
-{
- // unwrap references
- typedef typename odeint::unwrap_reference< Stepper >::type stepper_type;
- typedef typename odeint::unwrap_reference< Observer >::type observer_type;
- typedef typename odeint::unwrap_reference< StepOverflowChecker >::type checker_type;
- typedef typename stepper_type::stepper_category stepper_category;
-
- return detail::integrate_n_steps(
- checked_stepper<stepper_type, checker_type>(stepper, checker),
- system , start_state ,
- start_time , dt , num_of_steps ,
- checked_observer<observer_type, checker_type>(observer, checker),
- stepper_category() );
-}
-
-/**
- * \brief Solves the forwarding problem, can be called with Boost.Range as start_state.
- */
-template< class Stepper , class System , class State , class Time , class Observer , class StepOverflowChecker >
-Time integrate_n_steps(
- Stepper stepper , System system , const State &start_state ,
- Time start_time , Time dt , size_t num_of_steps ,
- Observer observer , StepOverflowChecker checker )
-{
- typedef typename odeint::unwrap_reference< Stepper >::type stepper_type;
- typedef typename odeint::unwrap_reference< Observer >::type observer_type;
- typedef typename odeint::unwrap_reference< StepOverflowChecker >::type checker_type;
- typedef typename stepper_type::stepper_category stepper_category;
-
- return detail::integrate_n_steps(
- checked_stepper<stepper_type, checker_type>(stepper, checker),
- system , start_state ,
- start_time , dt , num_of_steps ,
- checked_observer<observer_type, checker_type>(observer, checker),
- stepper_category() );
-}
-
-
-/**
-* \brief The same function as above, but without checker.
-*/
-template< class Stepper , class System , class State , class Time , class Observer >
-Time integrate_n_steps(
- Stepper stepper , System system , State &start_state ,
- Time start_time , Time dt , size_t num_of_steps , Observer observer )
-{
- typedef typename odeint::unwrap_reference<Stepper>::type::stepper_category stepper_category;
-
- return detail::integrate_n_steps(
- stepper , system , start_state ,
- start_time , dt , num_of_steps ,
- observer , stepper_category() );
-}
-
-/**
-* \brief Solves the forwarding problem, can be called with Boost.Range as start_state.
-*/
-template< class Stepper , class System , class State , class Time , class Observer >
-Time integrate_n_steps(
- Stepper stepper , System system , const State &start_state ,
- Time start_time , Time dt , size_t num_of_steps , Observer observer )
-{
- typedef typename odeint::unwrap_reference<Stepper>::type::stepper_category stepper_category;
-
- return detail::integrate_n_steps(
- stepper , system , start_state ,
- start_time , dt , num_of_steps ,
- observer , stepper_category() );
-}
-
-/**
- * \brief The same function as above, but without observer calls.
- */
-template< class Stepper , class System , class State , class Time >
-Time integrate_n_steps(
- Stepper stepper , System system , State &start_state ,
- Time start_time , Time dt , size_t num_of_steps )
-{
- return integrate_n_steps(stepper, system, start_state, start_time,
- dt, num_of_steps, null_observer());
-}
-
-/**
- * \brief Solves the forwarding problem, can be called with Boost.Range as start_state.
- */
-template< class Stepper , class System , class State , class Time >
-Time integrate_n_steps(
- Stepper stepper , System system , const State &start_state ,
- Time start_time , Time dt , size_t num_of_steps )
-{
- return integrate_n_steps(stepper, system, start_state, start_time,
- dt, num_of_steps, null_observer());
-}
-
-
-
-/************* DOXYGEN *************/
- /**
- * \fn Time integrate_n_steps( Stepper stepper , System system , State &start_state , Time start_time , Time dt , size_t num_of_steps , Observer observer )
- * \brief Integrates the ODE with constant step size.
- *
- * This function is similar to integrate_const. The observer is called at
- * equidistant time intervals t0 + n*dt.
- * If the Stepper is a normal stepper without step size control, dt is also
- * used for the numerical scheme. If a ControlledStepper is provided, the
- * algorithm might reduce the step size to meet the error bounds, but it is
- * ensured that the observer is always called at equidistant time points
- * t0 + n*dt. If a DenseOutputStepper is used, the step size also may vary
- * and the dense output is used to call the observer at equidistant time
- * points. The final integration time is always t0 + num_of_steps*dt.
- * If a max_step_checker is provided as StepOverflowChecker, a
- * no_progress_errror is thrown if too many steps (default: 500) are
- * performed without progress, i.e. in between observer calls. If no
- * checker is provided, no such overflow check is performed.
-
- *
- * \param stepper The stepper to be used for numerical integration.
- * \param system Function/Functor defining the rhs of the ODE.
- * \param start_state The initial condition x0.
- * \param start_time The initial time t0.
- * \param dt The time step between observer calls, _not_ necessarily the
- * time step of the integration.
- * \param num_of_steps Number of steps to be performed
- * \param observer Function/Functor called at equidistant time intervals.
- * \param checker [optional] Functor to check for step count overflows, if no
- * checker is provided, no exception is thrown.
- * \return The number of steps performed.
- */
-
-
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-
-#endif // BOOST_NUMERIC_ODEINT_INTEGRATE_INTEGRATE_N_STEPS_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/integrate/integrate_times.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/integrate/integrate_times.hpp
deleted file mode 100644
index 29662257fc973a8aafab6ef215d83a2a2abf6389..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/integrate/integrate_times.hpp
+++ /dev/null
@@ -1,222 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/integrate/integrate_times.hpp
-
- [begin_description]
- Integration of ODEs with observation at user defined points
- [end_description]
-
- Copyright 2011-2013 Karsten Ahnert
- Copyright 2011-2015 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_INTEGRATE_INTEGRATE_TIMES_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_INTEGRATE_INTEGRATE_TIMES_HPP_INCLUDED
-
-#include <boost/type_traits/is_same.hpp>
-
-#include <boost/range.hpp>
-
-#include <boost/numeric/odeint/stepper/stepper_categories.hpp>
-#include <boost/numeric/odeint/integrate/null_observer.hpp>
-#include <boost/numeric/odeint/integrate/check_adapter.hpp>
-#include <boost/numeric/odeint/integrate/detail/integrate_times.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-/*
- * \brief Integrates while calling the observer at the time points given by sequence [times_start, time_end)
- * the two overloads are needed in order to solve the forwarding problem
- */
-template< class Stepper , class System , class State , class TimeIterator , class Time , class Observer , class StepOverflowChecker >
-size_t integrate_times(
- Stepper stepper , System system , State &start_state ,
- TimeIterator times_start , TimeIterator times_end , Time dt ,
- Observer observer , StepOverflowChecker checker )
-{
- // unwrap references
- typedef typename odeint::unwrap_reference< Stepper >::type stepper_type;
- typedef typename odeint::unwrap_reference< Observer >::type observer_type;
- typedef typename odeint::unwrap_reference< StepOverflowChecker >::type checker_type;
- typedef typename stepper_type::stepper_category stepper_category;
-
- // pass on checked stepper and observer
- // checked_stepper/observer use references internally, so passing by value is fine
- return detail::integrate_times(
- checked_stepper<stepper_type, checker_type>(stepper, checker) ,
- system , start_state ,
- times_start , times_end , dt ,
- checked_observer<observer_type, checker_type>(observer, checker),
- stepper_category() );
-}
-
-/**
- * \brief Solves the forwarding problem, can be called with Boost.Range as start_state.
- */
-template< class Stepper , class System , class State , class TimeIterator , class Time , class Observer , class StepOverflowChecker >
-size_t integrate_times(
- Stepper stepper , System system , const State &start_state ,
- TimeIterator times_start , TimeIterator times_end , Time dt ,
- Observer observer , StepOverflowChecker checker )
-{
- typedef typename odeint::unwrap_reference< Stepper >::type stepper_type;
- typedef typename odeint::unwrap_reference< Observer >::type observer_type;
- typedef typename odeint::unwrap_reference< StepOverflowChecker >::type checker_type;
- typedef typename stepper_type::stepper_category stepper_category;
-
- stepper_type &st = stepper;
- observer_type &obs = observer;
- checker_type &chk = checker;
-
- return detail::integrate_times(
- checked_stepper<stepper_type, checker_type>(stepper, checker) ,
- system , start_state ,
- times_start , times_end , dt ,
- checked_observer<observer_type, checker_type>(observer, checker),
- stepper_category() );
-}
-
-/**
- * \brief The same function as above, but with the observation times given as range.
- */
-template< class Stepper , class System , class State , class TimeRange , class Time , class Observer , class StepOverflowChecker >
-size_t integrate_times(
- Stepper stepper , System system , State &start_state ,
- const TimeRange × , Time dt ,
- Observer observer , StepOverflowChecker checker )
-{
- return integrate_times(
- stepper , system , start_state ,
- boost::begin( times ) , boost::end( times ) , dt , observer , checker );
-}
-
-/**
- * \brief Solves the forwarding problem, can be called with Boost.Range as start_state.
- */
-template< class Stepper , class System , class State , class TimeRange , class Time , class Observer , class StepOverflowChecker >
-size_t integrate_times(
- Stepper stepper , System system , const State &start_state ,
- const TimeRange × , Time dt ,
- Observer observer , StepOverflowChecker checker )
-{
- return integrate_times(
- stepper , system , start_state ,
- boost::begin( times ) , boost::end( times ) , dt , observer , checker );
-}
-
-
-
-
-/*
-* The same functions as above, but without a StepOverflowChecker
-*/
-template< class Stepper , class System , class State , class TimeIterator , class Time , class Observer >
-size_t integrate_times(
- Stepper stepper , System system , State &start_state ,
- TimeIterator times_start , TimeIterator times_end , Time dt ,
- Observer observer )
-{
- typedef typename odeint::unwrap_reference< Stepper >::type::stepper_category stepper_category;
- // simply don't use checked_* adapters
- return detail::integrate_times(
- stepper , system , start_state ,
- times_start , times_end , dt ,
- observer , stepper_category() );
-}
-
-/**
-* \brief Solves the forwarding problem, can be called with Boost.Range as start_state.
-*/
-template< class Stepper , class System , class State , class TimeIterator , class Time , class Observer >
-size_t integrate_times(
- Stepper stepper , System system , const State &start_state ,
- TimeIterator times_start , TimeIterator times_end , Time dt ,
- Observer observer )
-{
- typedef typename odeint::unwrap_reference< Stepper >::type::stepper_category stepper_category;
- return detail::integrate_times(
- stepper , system , start_state ,
- times_start , times_end , dt ,
- observer , stepper_category() );
-}
-
-/**
-* \brief The same function as above, but with the observation times given as range.
-*/
-template< class Stepper , class System , class State , class TimeRange , class Time , class Observer >
-size_t integrate_times(
- Stepper stepper , System system , State &start_state ,
- const TimeRange × , Time dt ,
- Observer observer )
-{
- return integrate_times(
- stepper , system , start_state ,
- boost::begin( times ) , boost::end( times ) , dt , observer );
-}
-
-/**
-* \brief Solves the forwarding problem, can be called with Boost.Range as start_state.
-*/
-template< class Stepper , class System , class State , class TimeRange , class Time , class Observer >
-size_t integrate_times(
- Stepper stepper , System system , const State &start_state ,
- const TimeRange × , Time dt ,
- Observer observer )
-{
- return integrate_times(
- stepper , system , start_state ,
- boost::begin( times ) , boost::end( times ) , dt , observer);
-}
-
-
-/********* DOXYGEN ***********/
-
- /**
- * \fn size_t integrate_times( Stepper stepper , System system , State &start_state , TimeIterator times_start , TimeIterator times_end , Time dt , Observer observer )
- * \brief Integrates the ODE with observer calls at given time points.
- *
- * Integrates the ODE given by system using the given stepper. This function
- * does observer calls at the subsequent time points given by the range
- * times_start, times_end. If the stepper has not step size control, the
- * step size might be reduced occasionally to ensure observer calls exactly
- * at the time points from the given sequence. If the stepper is a
- * ControlledStepper, the step size is adjusted to meet the error bounds,
- * but also might be reduced occasionally to ensure correct observer calls.
- * If a DenseOutputStepper is provided, the dense output functionality is
- * used to call the observer at the given times. The end time of the
- * integration is always *(end_time-1).
- * If a max_step_checker is provided as StepOverflowChecker, a
- * no_progress_error is thrown if too many steps (default: 500) are
- * performed without progress, i.e. in between observer calls. If no
- * checker is provided, no such overflow check is performed.
- *
- * \param stepper The stepper to be used for numerical integration.
- * \param system Function/Functor defining the rhs of the ODE.
- * \param start_state The initial condition x0.
- * \param times_start Iterator to the start time
- * \param times_end Iterator to the end time
- * \param dt The time step between observer calls, _not_ necessarily the
- * time step of the integration.
- * \param observer Function/Functor called at equidistant time intervals.
- * \param checker [optional] Functor to check for step count overflows, if no
- * checker is provided, no exception is thrown.
- * \return The number of steps performed.
- */
-
-
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-
-#endif // BOOST_NUMERIC_ODEINT_INTEGRATE_INTEGRATE_TIMES_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/integrate/max_step_checker.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/integrate/max_step_checker.hpp
deleted file mode 100644
index 6808a57bdbf2318474b0b72395c39c4a9cda2335..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/integrate/max_step_checker.hpp
+++ /dev/null
@@ -1,114 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/integrate/max_step_checker.hpp
-
- [begin_description]
- Throws exception if too many steps are performed.
- [end_description]
-
- Copyright 2015 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_INTEGRATE_MAX_STEP_CHECKER_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_INTEGRATE_MAX_STEP_CHECKER_HPP_INCLUDED
-
-#include <stdexcept>
-#include <cstdio>
-
-#include <boost/throw_exception.hpp>
-#include <boost/numeric/odeint/util/odeint_error.hpp>
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-/**
- * \brief A class for performing overflow checks on the step count in integrate functions.
- *
- * Provide an instance of this class to integrate functions if you want to throw a runtime error if
- * too many steps are performed without progress during the integrate routine.
- */
-class max_step_checker
-{
-public:
-
-protected:
- const int m_max_steps;
- int m_steps;
-
-public:
- /**
- * \brief Construct the max_step_checker.
- * max_steps is the maximal number of iterations allowed before runtime_error is thrown.
- */
- max_step_checker(const int max_steps = 500)
- : m_max_steps(max_steps)
- {
- reset();
- }
-
- /**
- * \brief Resets the max_step_checker by setting the internal counter to 0.
- */
- void reset()
- {
- m_steps = 0;
- }
-
- /**
- * \brief Increases the counter and performs the iteration check
- */
- void operator()(void)
- {
- if( m_steps++ >= m_max_steps )
- {
- char error_msg[200];
- sprintf(error_msg, "Max number of iterations exceeded (%d).", m_max_steps);
- BOOST_THROW_EXCEPTION( no_progress_error(error_msg) );
- }
- }
-};
-
-
-/**
- * \brief A class for performing overflow checks on the failed step count in step size adjustments.
- *
- * Used internally within the dense output stepper and integrate routines.
- */
-class failed_step_checker : public max_step_checker
-{
-
-public:
- /**
- * \brief Construct the failed_step_checker.
- * max_steps is the maximal number of iterations allowed before runtime_error is thrown.
- */
- failed_step_checker(const int max_steps = 500)
- : max_step_checker(max_steps)
- {}
-
- /**
- * \brief Increases the counter and performs the iteration check
- */
- void operator()(void)
- {
- if( m_steps++ >= m_max_steps )
- {
- char error_msg[200];
- sprintf(error_msg, "Max number of iterations exceeded (%d). A new step size was not found.", m_max_steps);
- BOOST_THROW_EXCEPTION( step_adjustment_error(error_msg) );
- }
- }
-};
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-#endif
\ No newline at end of file
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/integrate/null_observer.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/integrate/null_observer.hpp
deleted file mode 100644
index 82b86b4582e2ec4daf94e5b9f27ebb79cbfa777f..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/integrate/null_observer.hpp
+++ /dev/null
@@ -1,38 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/integrate/null_observer.hpp
-
- [begin_description]
- null_observer
- [end_description]
-
- Copyright 2011-2012 Karsten Ahnert
- Copyright 2011-2012 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_INTEGRATE_NULL_OBSERVER_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_INTEGRATE_NULL_OBSERVER_HPP_INCLUDED
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-struct null_observer
-{
- template< class State , class Time >
- void operator()( const State& /* x */ , Time /* t */ ) const
- {
-
- }
-};
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-#endif // BOOST_NUMERIC_ODEINT_INTEGRATE_NULL_OBSERVER_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/integrate/observer_collection.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/integrate/observer_collection.hpp
deleted file mode 100644
index f8c9af8e24f5232fc54a46486128c02c7e45cba8..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/integrate/observer_collection.hpp
+++ /dev/null
@@ -1,56 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/integrate/observer_collection.hpp
-
- [begin_description]
- Collection of observers, which are all called during the evolution of the ODE.
- [end_description]
-
- Copyright 2011-2012 Karsten Ahnert
- Copyright 2011-2012 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_INTEGRATE_OBSERVER_COLLECTION_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_INTEGRATE_OBSERVER_COLLECTION_HPP_INCLUDED
-
-#include <vector>
-
-#include <boost/function.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-template< class State , class Time >
-class observer_collection
-{
-public:
-
- typedef boost::function< void( const State& , const Time& ) > observer_type;
- typedef std::vector< observer_type > collection_type;
-
- void operator()( const State& x , Time t )
- {
- for( size_t i=0 ; i<m_observers.size() ; ++i )
- m_observers[i]( x , t );
- }
-
- collection_type& observers( void ) { return m_observers; }
- const collection_type& observers( void ) const { return m_observers; }
-
-private:
-
- collection_type m_observers;
-};
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_INTEGRATE_OBSERVER_COLLECTION_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/adaptive_iterator.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/adaptive_iterator.hpp
deleted file mode 100644
index d57fe72db0fc18cf0e87e59b5de4c19716c3a7c8..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/adaptive_iterator.hpp
+++ /dev/null
@@ -1,183 +0,0 @@
-
-/*
- [auto_generated]
- boost/numeric/odeint/iterator/adaptive_iterator.hpp
-
- [begin_description]
- Iterator for iterating throught the solution of an ODE with adaptive step size. The dereferenced types containes also the time.
- [end_description]
-
- Copyright 2012-2013 Karsten Ahnert
- Copyright 2012 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_ITERATOR_ADAPTIVE_ITERATOR_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_ITERATOR_ADAPTIVE_ITERATOR_HPP_INCLUDED
-
-#include <boost/numeric/odeint/util/stepper_traits.hpp>
-#include <boost/numeric/odeint/util/unit_helper.hpp>
-#include <boost/numeric/odeint/stepper/stepper_categories.hpp>
-#include <boost/numeric/odeint/stepper/controlled_step_result.hpp>
-#include <boost/numeric/odeint/iterator/impl/adaptive_iterator_impl.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
- /* use the adaptive_iterator_impl with the right tags */
- template< class Stepper , class System , class State
-#ifndef DOXYGEN_SKIP
- , class StepperTag = typename base_tag< typename traits::stepper_category< Stepper >::type >::type
-#endif
- >
- class adaptive_iterator : public adaptive_iterator_impl<
- adaptive_iterator< Stepper , System , State , StepperTag > ,
- Stepper , System , State , detail::ode_state_iterator_tag , StepperTag
- >
- {
- typedef typename traits::time_type< Stepper >::type time_type;
- typedef adaptive_iterator< Stepper , System , State , StepperTag > iterator_type;
-
- public:
- adaptive_iterator( Stepper stepper , System sys , State &s , time_type t_start , time_type t_end , time_type dt )
- : adaptive_iterator_impl< iterator_type , Stepper , System , State , detail::ode_state_iterator_tag , StepperTag >( stepper , sys , s , t_start , t_end , dt )
- {}
-
- adaptive_iterator( Stepper stepper , System sys , State &s )
- : adaptive_iterator_impl< iterator_type , Stepper , System , State , detail::ode_state_iterator_tag , StepperTag >( stepper , sys , s )
- {}
- };
-
-
-
-
- template< class Stepper , class System , class State >
- adaptive_iterator< Stepper , System , State > make_adaptive_iterator_begin(
- Stepper stepper ,
- System system ,
- State &x ,
- typename traits::time_type< Stepper >::type t_start ,
- typename traits::time_type< Stepper >::type t_end ,
- typename traits::time_type< Stepper >::type dt )
- {
- return adaptive_iterator< Stepper , System , State >( stepper , system , x , t_start , t_end , dt );
- }
-
-
- template< class Stepper , class System , class State >
- adaptive_iterator< Stepper , System , State > make_adaptive_iterator_end(
- Stepper stepper ,
- System system ,
- State &x )
- {
- return adaptive_iterator< Stepper , System , State >( stepper , system , x );
- }
-
-
- template< class Stepper , class System , class State >
- std::pair< adaptive_iterator< Stepper , System , State > , adaptive_iterator< Stepper , System , State > >
- make_adaptive_range(
- Stepper stepper ,
- System system ,
- State &x ,
- typename traits::time_type< Stepper >::type t_start ,
- typename traits::time_type< Stepper >::type t_end ,
- typename traits::time_type< Stepper >::type dt )
- {
- return std::make_pair(
- adaptive_iterator< Stepper , System , State >( stepper , system , x , t_start , t_end , dt ) ,
- adaptive_iterator< Stepper , System , State >( stepper , system , x )
- );
- }
-
- /**
- * \class adaptive_iterator
- *
- * \brief ODE Iterator with adaptive step size. The value type of this iterator is the state type of the stepper.
- *
- * Implements an iterator representing the solution of an ODE from t_start
- * to t_end evaluated at steps with an adaptive step size dt.
- * After each iteration the iterator dereferences to the state x at the next
- * time t+dt where dt is controlled by the stepper.
- * This iterator can be used with ControlledSteppers and
- * DenseOutputSteppers and it always makes use of the all the given steppers
- * capabilities. A for_each over such an iterator range behaves similar to
- * the integrate_adaptive routine.
- *
- * adaptive_iterator is a model of single-pass iterator.
- *
- * The value type of this iterator is the state type of the stepper. Hence one can only access the state and not the current time.
- *
- * \tparam Stepper The stepper type which should be used during the iteration.
- * \tparam System The type of the system function (ODE) which should be solved.
- * \tparam State The state type of the ODE.
- */
-
-
-
-
-
-
- /**
- * \fn make_adaptive_iterator_begin( Stepper stepper , System system , State &x ,
- typename traits::time_type< Stepper >::type t_start ,
- typename traits::time_type< Stepper >::type t_end ,
- typename traits::time_type< Stepper >::type dt )
- *
- * \brief Factory function for adaptive_iterator. Constructs a begin iterator.
- *
- * \param stepper The stepper to use during the iteration.
- * \param system The system function (ODE) to solve.
- * \param x The initial state.
- * \param t_start The initial time.
- * \param t_end The end time, at which the iteration should stop.
- * \param dt The initial time step.
- * \returns The adaptive iterator.
- */
-
-
- /**
- * \fn make_adaptive_iterator_end( Stepper stepper , System system , State &x )
- * \brief Factory function for adaptive_iterator. Constructs a end iterator.
- *
- * \param stepper The stepper to use during the iteration.
- * \param system The system function (ODE) to solve.
- * \param x The initial state.
- * \returns The adaptive iterator.
- */
-
-
- /**
- * \fn make_adaptive_range( Stepper stepper , System system , State &x ,
- typename traits::time_type< Stepper >::type t_start ,
- typename traits::time_type< Stepper >::type t_end ,
- typename traits::time_type< Stepper >::type dt )
- *
- * \brief Factory function to construct a single pass range of adaptive iterators. A range is here a pair of adaptive_iterator.
- *
- * \param stepper The stepper to use during the iteration.
- * \param system The system function (ODE) to solve.
- * \param x The initial state.
- * \param t_start The initial time.
- * \param t_end The end time, at which the iteration should stop.
- * \param dt The initial time step.
- * \returns The adaptive range.
- */
-
-
-
-
-
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-
-#endif // BOOST_NUMERIC_ODEINT_ITERATOR_ADAPTIVE_ITERATOR_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/adaptive_time_iterator.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/adaptive_time_iterator.hpp
deleted file mode 100644
index b55b7a744307cf8a706a14d51910946133b9feec..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/adaptive_time_iterator.hpp
+++ /dev/null
@@ -1,175 +0,0 @@
-
-/*
- [auto_generated]
- boost/numeric/odeint/iterator/adaptive_time_iterator.hpp
-
- [begin_description]
- Iterator for iterating throught the solution of an ODE with adaptive step size. The dereferenced types containes also the time.
- [end_description]
-
- Copyright 2012-2013 Karsten Ahnert
- Copyright 2012-2013 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_ITERATOR_ADAPTIVE_TIME_ITERATOR_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_ITERATOR_ADAPTIVE_TIME_ITERATOR_HPP_INCLUDED
-
-
-
-#include <boost/numeric/odeint/stepper/stepper_categories.hpp>
-#include <boost/numeric/odeint/util/stepper_traits.hpp>
-#include <boost/numeric/odeint/iterator/impl/adaptive_iterator_impl.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
- /* use the adaptive_iterator_impl with the right tags */
- template< class Stepper , class System , class State
-#ifndef DOXYGEN_SKIP
- , class StepperTag = typename base_tag< typename traits::stepper_category< Stepper >::type >::type
-#endif
- >
- class adaptive_time_iterator : public adaptive_iterator_impl<
- adaptive_time_iterator< Stepper , System , State , StepperTag > ,
- Stepper , System , State , detail::ode_state_time_iterator_tag , StepperTag
- >
- {
- typedef typename traits::time_type< Stepper >::type time_type;
- typedef adaptive_time_iterator< Stepper , System , State , StepperTag > iterator_type;
-
- public:
- adaptive_time_iterator( Stepper stepper , System sys , State &s , time_type t_start , time_type t_end , time_type dt )
- : adaptive_iterator_impl< iterator_type , Stepper , System , State , detail::ode_state_time_iterator_tag , StepperTag >( stepper , sys , s , t_start , t_end , dt )
- {}
-
- adaptive_time_iterator( Stepper stepper , System sys , State &s )
- : adaptive_iterator_impl< iterator_type , Stepper , System , State , detail::ode_state_time_iterator_tag , StepperTag >( stepper , sys , s )
- {}
- };
-
-
-
-
- template< class Stepper , class System , class State >
- adaptive_time_iterator< Stepper , System , State > make_adaptive_time_iterator_begin(
- Stepper stepper ,
- System system ,
- State &x ,
- typename traits::time_type< Stepper >::type t_start ,
- typename traits::time_type< Stepper >::type t_end ,
- typename traits::time_type< Stepper >::type dt )
- {
- return adaptive_time_iterator< Stepper , System , State >( stepper , system , x , t_start , t_end , dt );
- }
-
- template< class Stepper , class System , class State >
- adaptive_time_iterator< Stepper , System , State > make_adaptive_time_iterator_end(
- Stepper stepper ,
- System system ,
- State &x )
- {
- return adaptive_time_iterator< Stepper , System , State >( stepper , system , x );
- }
-
-
- template< class Stepper , class System , class State >
- std::pair< adaptive_time_iterator< Stepper , System , State > , adaptive_time_iterator< Stepper , System , State > >
- make_adaptive_time_range(
- Stepper stepper ,
- System system ,
- State &x ,
- typename traits::time_type< Stepper >::type t_start ,
- typename traits::time_type< Stepper >::type t_end ,
- typename traits::time_type< Stepper >::type dt )
- {
- return std::make_pair(
- adaptive_time_iterator< Stepper , System , State >( stepper , system , x , t_start , t_end , dt ) ,
- adaptive_time_iterator< Stepper , System , State >( stepper , system , x ) );
- }
-
-
-
- /**
- * \class adaptive_time_iterator
- *
- * \brief ODE Iterator with adaptive step size. The value type of this iterator is a std::pair containing state and time.
- *
- * Implements an iterator representing the solution of an ODE from t_start
- * to t_end evaluated at steps with an adaptive step size dt.
- * After each iteration the iterator dereferences to a pair containing state
- * and time at the next time point t+dt where dt is controlled by the stepper.
- * This iterator can be used with ControlledSteppers and
- * DenseOutputSteppers and it always makes use of the all the given steppers
- * capabilities. A for_each over such an iterator range behaves similar to
- * the integrate_adaptive routine.
- *
- * adaptive_iterator is a model of single-pass iterator.
- *
- * The value type of this iterator is a std::pair of state and time of the stepper.
- *
- * \tparam Stepper The stepper type which should be used during the iteration.
- * \tparam System The type of the system function (ODE) which should be solved.
- * \tparam State The state type of the ODE.
- */
-
-
-
- /**
- * \fn make_adaptive_time_iterator_begin( Stepper stepper , System system , State &x ,
- typename traits::time_type< Stepper >::type t_start ,
- typename traits::time_type< Stepper >::type t_end ,
- typename traits::time_type< Stepper >::type dt )
- *
- * \brief Factory function for adaptive_time_iterator. Constructs a begin iterator.
- *
- * \param stepper The stepper to use during the iteration.
- * \param system The system function (ODE) to solve.
- * \param x The initial state. adaptive_time_iterator stores a reference of s and changes its value during the iteration.
- * \param t_start The initial time.
- * \param t_end The end time, at which the iteration should stop.
- * \param dt The initial time step.
- * \returns The adaptive time iterator.
- */
-
-
- /**
- * \fn make_adaptive_time_iterator_end( Stepper stepper , System system , State &x )
- * \brief Factory function for adaptive_time_iterator. Constructs a end iterator.
- *
- * \param stepper The stepper to use during the iteration.
- * \param system The system function (ODE) to solve.
- * \param x The initial state. adaptive_time_iterator stores a reference of s and changes its value during the iteration.
- * \returns The adaptive time iterator.
- */
-
-
- /**
- * \fn make_adaptive_time_range( Stepper stepper , System system , State &x ,
- typename traits::time_type< Stepper >::type t_start ,
- typename traits::time_type< Stepper >::type t_end ,
- typename traits::time_type< Stepper >::type dt )
- *
- * \brief Factory function to construct a single pass range of adaptive time iterators. A range is here a pair of adaptive_time_iterators.
- *
- * \param stepper The stepper to use during the iteration.
- * \param system The system function (ODE) to solve.
- * \param x The initial state. adaptive_time_iterator stores a reference of s and changes its value during the iteration.
- * \param t_start The initial time.
- * \param t_end The end time, at which the iteration should stop.
- * \param dt The initial time step.
- * \returns The adaptive time range.
- */
-
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_ITERATOR_ADAPTIVE_TIME_ITERATOR_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/const_step_iterator.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/const_step_iterator.hpp
deleted file mode 100644
index f3885b074f205612361db0d94cd23bba60f90c41..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/const_step_iterator.hpp
+++ /dev/null
@@ -1,180 +0,0 @@
-
-/*
- [auto_generated]
- boost/numeric/odeint/iterator/const_step_iterator.hpp
-
- [begin_description]
- Iterator for iterating through the solution of an ODE with constant step size.
- [end_description]
-
- Copyright 2012-2013 Karsten Ahnert
- Copyright 2013 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_ITERATOR_CONST_STEP_ODE_ITERATOR_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_ITERATOR_CONST_STEP_ODE_ITERATOR_HPP_INCLUDED
-
-
-#include <boost/numeric/odeint/util/stepper_traits.hpp>
-#include <boost/numeric/odeint/stepper/stepper_categories.hpp>
-#include <boost/numeric/odeint/iterator/detail/ode_iterator_base.hpp>
-#include <boost/numeric/odeint/iterator/impl/const_step_iterator_impl.hpp>
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
- /* use the const_step_iterator_impl with the right tags */
- template< class Stepper , class System , class State
-#ifndef DOXYGEN_SKIP
- , class StepperTag = typename base_tag< typename traits::stepper_category< Stepper >::type >::type
-#endif
- >
- class const_step_iterator : public const_step_iterator_impl<
- const_step_iterator< Stepper , System , State , StepperTag > ,
- Stepper , System , State , detail::ode_state_iterator_tag , StepperTag
- >
- {
- typedef typename traits::time_type< Stepper >::type time_type;
- typedef const_step_iterator< Stepper , System , State , StepperTag > iterator_type;
-
- public:
- const_step_iterator( Stepper stepper , System sys , State &s , time_type t_start , time_type t_end , time_type dt )
- : const_step_iterator_impl< iterator_type , Stepper , System , State , detail::ode_state_iterator_tag , StepperTag >( stepper , sys , s , t_start , t_end , dt )
- {}
-
- const_step_iterator( Stepper stepper , System sys , State &s )
- : const_step_iterator_impl< iterator_type , Stepper , System , State , detail::ode_state_iterator_tag , StepperTag >( stepper , sys , s )
- {}
- };
-
- /* make functions */
-
- template< class Stepper , class System , class State >
- const_step_iterator< Stepper , System, State > make_const_step_iterator_begin(
- Stepper stepper ,
- System system ,
- State &x ,
- typename traits::time_type< Stepper >::type t_start ,
- typename traits::time_type< Stepper >::type t_end ,
- typename traits::time_type< Stepper >::type dt )
- {
- return const_step_iterator< Stepper , System , State >( stepper , system , x , t_start , t_end , dt );
- }
-
- template< class Stepper , class System , class State >
- const_step_iterator< Stepper , System , State > make_const_step_iterator_end(
- Stepper stepper ,
- System system ,
- State &x )
- {
- return const_step_iterator< Stepper , System , State >( stepper , system , x );
- }
-
- template< class Stepper , class System , class State >
- std::pair< const_step_iterator< Stepper , System , State > , const_step_iterator< Stepper , System , State > >
- make_const_step_range(
- Stepper stepper ,
- System system ,
- State &x ,
- typename traits::time_type< Stepper >::type t_start ,
- typename traits::time_type< Stepper >::type t_end ,
- typename traits::time_type< Stepper >::type dt )
- {
- return std::make_pair(
- const_step_iterator< Stepper , System , State >( stepper , system , x , t_start , t_end , dt ) ,
- const_step_iterator< Stepper , System , State >( stepper , system , x )
- );
- }
-
-
-
- /**
- * \class const_step_iterator
- *
- * \brief ODE Iterator with constant step size. The value type of this iterator is the state type of the stepper.
- *
- * Implements an iterator representing the solution of an ODE from t_start
- * to t_end evaluated at steps with constant step size dt.
- * After each iteration the iterator dereferences to the state x at the next
- * time t+dt.
- * This iterator can be used with Steppers and
- * DenseOutputSteppers and it always makes use of the all the given steppers
- * capabilities. A for_each over such an iterator range behaves similar to
- * the integrate_const routine.
- *
- * const_step_iterator is a model of single-pass iterator.
- *
- * The value type of this iterator is the state type of the stepper. Hence one can only access the state and not the current time.
- *
- * \tparam Stepper The stepper type which should be used during the iteration.
- * \tparam System The type of the system function (ODE) which should be solved.
- * \tparam State The state type of the ODE.
- */
-
-
- /**
- * \fn make_const_step_iterator_begin(
- Stepper stepper ,
- System system ,
- State &x ,
- typename traits::time_type< Stepper >::type t_start ,
- typename traits::time_type< Stepper >::type t_end ,
- typename traits::time_type< Stepper >::type dt )
- *
- * \brief Factory function for const_step_iterator. Constructs a begin iterator.
- *
- * \param stepper The stepper to use during the iteration.
- * \param system The system function (ODE) to solve.
- * \param x The initial state. const_step_iterator stores a reference of s and changes its value during the iteration.
- * \param t_start The initial time.
- * \param t_end The end time, at which the iteration should stop.
- * \param dt The initial time step.
- * \returns The const step iterator.
- */
-
-
- /**
- * \fn make_const_step_iterator_end( Stepper stepper , System system , State &x )
- * \brief Factory function for const_step_iterator. Constructs a end iterator.
- *
- * \param stepper The stepper to use during the iteration.
- * \param system The system function (ODE) to solve.
- * \param x The initial state. const_step_iterator stores a reference of s and changes its value during the iteration.
- * \returns The const_step_iterator.
- */
-
-
- /**
- * \fn make_const_step_range( Stepper stepper , System system , State &x ,
- typename traits::time_type< Stepper >::type t_start ,
- typename traits::time_type< Stepper >::type t_end ,
- typename traits::time_type< Stepper >::type dt )
- *
- * \brief Factory function to construct a single pass range of const step iterators. A range is here a pair
- * of const_step_iterator.
- *
- * \param stepper The stepper to use during the iteration.
- * \param system The system function (ODE) to solve.
- * \param x The initial state. const_step_iterator store a reference of s and changes its value during the iteration.
- * \param t_start The initial time.
- * \param t_end The end time, at which the iteration should stop.
- * \param dt The initial time step.
- * \returns The const step range.
- */
-
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-//#include <boost/numeric/odeint/iterator/impl/const_step_iterator_dense_output_impl.hpp>
-
-#endif // BOOST_NUMERIC_ODEINT_ITERATOR_CONST_STEP_ODE_ITERATOR_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/const_step_time_iterator.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/const_step_time_iterator.hpp
deleted file mode 100644
index cdc6d56fa120606ce519e6798a07bb951ff6fb02..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/const_step_time_iterator.hpp
+++ /dev/null
@@ -1,173 +0,0 @@
-
-/*
- [auto_generated]
- boost/numeric/odeint/iterator/const_step_time_iterator.hpp
-
- [begin_description]
- Iterator for iterating throught the solution of an ODE with constant step size. The dereferences types containes also the time.
- [end_description]
-
- Copyright 2012-2013 Karsten Ahnert
- Copyright 2013 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_ITERATOR_CONST_STEP_TIME_ITERATOR_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_ITERATOR_CONST_STEP_TIME_ITERATOR_HPP_INCLUDED
-
-#include <boost/numeric/odeint/stepper/stepper_categories.hpp>
-#include <boost/numeric/odeint/util/stepper_traits.hpp>
-#include <boost/numeric/odeint/iterator/detail/ode_iterator_base.hpp>
-#include <boost/numeric/odeint/iterator/impl/const_step_iterator_impl.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
- /* use the const_step_iterator_impl with the right tags */
- template< class Stepper , class System , class State
-#ifndef DOXYGEN_SKIP
- , class StepperTag = typename base_tag< typename traits::stepper_category< Stepper >::type >::type
-#endif
- >
- class const_step_time_iterator : public const_step_iterator_impl<
- const_step_time_iterator< Stepper , System , State , StepperTag > ,
- Stepper , System , State , detail::ode_state_time_iterator_tag , StepperTag
- >
- {
- typedef typename traits::time_type< Stepper >::type time_type;
- typedef const_step_time_iterator< Stepper , System , State , StepperTag > iterator_type;
-
- public:
- const_step_time_iterator( Stepper stepper , System sys , State &s , time_type t_start , time_type t_end , time_type dt )
- : const_step_iterator_impl< iterator_type , Stepper , System , State , detail::ode_state_time_iterator_tag , StepperTag >( stepper , sys , s , t_start , t_end , dt )
- {}
-
- const_step_time_iterator( Stepper stepper , System sys , State &s )
- : const_step_iterator_impl< iterator_type , Stepper , System , State , detail::ode_state_time_iterator_tag , StepperTag >( stepper , sys , s )
- {}
- };
-
- template< class Stepper , class System , class State >
- const_step_time_iterator< Stepper , System , State > make_const_step_time_iterator_begin(
- Stepper stepper ,
- System system ,
- State &x ,
- typename traits::time_type< Stepper >::type t_start ,
- typename traits::time_type< Stepper >::type t_end ,
- typename traits::time_type< Stepper >::type dt )
- {
- return const_step_time_iterator< Stepper , System , State >( stepper , system , x , t_start , t_end , dt );
- }
-
- template< class Stepper , class System , class State >
- const_step_time_iterator< Stepper , System , State > make_const_step_time_iterator_end(
- Stepper stepper ,
- System system ,
- State &x )
- {
- return const_step_time_iterator< Stepper , System , State >( stepper , system , x );
- }
-
-
- template< class Stepper , class System , class State >
- std::pair< const_step_time_iterator< Stepper , System , State > , const_step_time_iterator< Stepper , System , State > >
- make_const_step_time_range(
- Stepper stepper ,
- System system ,
- State &x ,
- typename traits::time_type< Stepper >::type t_start ,
- typename traits::time_type< Stepper >::type t_end ,
- typename traits::time_type< Stepper >::type dt )
- {
- return std::make_pair(
- const_step_time_iterator< Stepper , System , State >( stepper , system , x , t_start , t_end , dt ) ,
- const_step_time_iterator< Stepper , System , State >( stepper , system , x ) );
- }
-
- /**
- * \class const_step_time_iterator
- *
- * \brief ODE Iterator with constant step size. The value type of this iterator is a std::pair containing state and time.
- *
- * Implements an iterator representing the solution of an ODE from t_start
- * to t_end evaluated at steps with constant step size dt.
- * After each iteration the iterator dereferences to a pair containing
- * state and time at the next time point t+dt..
- * This iterator can be used with Steppers and
- * DenseOutputSteppers and it always makes use of the all the given steppers
- * capabilities. A for_each over such an iterator range behaves similar to
- * the integrate_const routine.
- *
- * const_step_time_iterator is a model of single-pass iterator.
- *
- * The value type of this iterator is a pair with the state type and time type of the stepper.
- *
- * \tparam Stepper The stepper type which should be used during the iteration.
- * \tparam System The type of the system function (ODE) which should be solved.
- * \tparam State The state type of the ODE.
- */
-
-
- /**
- * \fn make_const_step_time_iterator_begin( Stepper stepper , System system , State &x ,
- typename traits::time_type< Stepper >::type t_start ,
- typename traits::time_type< Stepper >::type t_end ,
- typename traits::time_type< Stepper >::type dt )
- *
- * \brief Factory function for const_step_time_iterator. Constructs a begin iterator.
- *
- * \param stepper The stepper to use during the iteration.
- * \param system The system function (ODE) to solve.
- * \param x The initial state. const_step_time_iterator stores a reference of s and changes its value during the iteration.
- * \param t_start The initial time.
- * \param t_end The end time, at which the iteration should stop.
- * \param dt The initial time step.
- * \returns The const step time iterator.
- */
-
-
- /**
- * \fn make_const_step_time_iterator_end( Stepper stepper , System system , State &x )
- * \brief Factory function for const_step_time_iterator. Constructs a end iterator.
- *
- * \param stepper The stepper to use during the iteration.
- * \param system The system function (ODE) to solve.
- * \param x The initial state. const_step_time_iterator store a reference of s and changes its value during the iteration.
- * \returns The const step time iterator.
- */
-
-
- /**
- * \fn make_const_step_time_range( Stepper stepper , System system , State &x ,
- typename traits::time_type< Stepper >::type t_start ,
- typename traits::time_type< Stepper >::type t_end ,
- typename traits::time_type< Stepper >::type dt)
- *
- * \brief Factory function to construct a single pass range of const_step_time_iterator. A range is here a pair of const_step_time_iterator.
- *
- * \param stepper The stepper to use during the iteration.
- * \param system The system function (ODE) to solve.
- * \param x The initial state. const_step_time_iterator stores a reference of s and changes its value during the iteration.
- * \param t The initial time.
- * \param t_end The end time, at which the iteration should stop.
- * \param dt The initial time step.
- * \returns The const step time range.
- */
-
-
-
-
-
-
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_ITERATOR_CONST_STEP_TIME_ITERATOR_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/detail/ode_iterator_base.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/detail/ode_iterator_base.hpp
deleted file mode 100644
index fcab45fc17951aa7650445ebb7dc7ebc0c66aa52..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/detail/ode_iterator_base.hpp
+++ /dev/null
@@ -1,199 +0,0 @@
-
-/*
- [auto_generated]
- boost/numeric/odeint/iterator/detail/ode_iterator_base.hpp
-
- [begin_description]
- Base class for const_step_iterator and adaptive_iterator.
- [end_description]
-
- Copyright 2012-2013 Karsten Ahnert
- Copyright 2012-2013 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_ITERATOR_DETAIL_ODE_ITERATOR_BASE_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_ITERATOR_DETAIL_ODE_ITERATOR_BASE_HPP_INCLUDED
-
-#include <boost/iterator/iterator_facade.hpp>
-
-#include <boost/numeric/odeint/util/unwrap_reference.hpp>
-#include <boost/numeric/odeint/util/detail/less_with_sign.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-namespace detail {
-
- struct ode_state_iterator_tag {};
- struct ode_state_time_iterator_tag {};
-
- template< class Iterator , class Stepper , class System , class State , typename Tag >
- class ode_iterator_base;
-
-
- /* Specialization for the state iterator that has only state_type as its value_type */
- template< class Iterator , class Stepper , class System , class State >
- class ode_iterator_base< Iterator , Stepper , System , State , ode_state_iterator_tag >
- : public boost::iterator_facade
- <
- Iterator ,
- typename traits::state_type< Stepper >::type const ,
- boost::single_pass_traversal_tag
- >
- {
- private:
-
- typedef Stepper stepper_type;
- typedef System system_type;
- typedef typename boost::numeric::odeint::unwrap_reference< stepper_type >::type unwrapped_stepper_type;
- typedef State state_type;
- typedef typename unwrapped_stepper_type::time_type time_type;
- typedef typename unwrapped_stepper_type::value_type ode_value_type;
-
- public:
-
- ode_iterator_base( stepper_type stepper , system_type sys , time_type t , time_type dt )
- : m_stepper( stepper ) , m_system( sys ) ,
- m_t( t ) , m_dt( dt ) , m_at_end( false )
- { }
-
- ode_iterator_base( stepper_type stepper , system_type sys )
- : m_stepper( stepper ) , m_system( sys ) ,
- m_t() , m_dt() , m_at_end( true )
- { }
-
- // this function is only for testing
- bool same( const ode_iterator_base &iter ) const
- {
- return (
- //( static_cast<Iterator>(*this).get_state() ==
- // static_cast<Iterator>(iter).get_state ) &&
- ( m_t == iter.m_t ) &&
- ( m_dt == iter.m_dt ) &&
- ( m_at_end == iter.m_at_end )
- );
- }
-
-
- protected:
-
- friend class boost::iterator_core_access;
-
- bool equal( ode_iterator_base const& other ) const
- {
- if( m_at_end == other.m_at_end )
- {
- return true;
- }
- else
- {
- return false;
- }
- }
-
- const state_type& dereference() const
- {
- return static_cast<const Iterator*>(this)->get_state();
- }
-
- protected:
-
- stepper_type m_stepper;
- system_type m_system;
- time_type m_t;
- time_type m_dt;
- bool m_at_end;
- };
-
-
-
- /* Specialization for the state-time iterator that has pair<state_type,time_type> as its value_type */
-
- template< class Iterator , class Stepper , class System , class State >
- class ode_iterator_base< Iterator , Stepper , System , State , ode_state_time_iterator_tag >
- : public boost::iterator_facade
- <
- Iterator ,
- std::pair< const State , const typename traits::time_type< Stepper >::type > ,
- boost::single_pass_traversal_tag ,
- std::pair< const State& , const typename traits::time_type< Stepper >::type& >
- >
- {
- private:
-
- typedef Stepper stepper_type;
- typedef System system_type;
- typedef typename boost::numeric::odeint::unwrap_reference< stepper_type >::type unwrapped_stepper_type;
- typedef State state_type;
- typedef typename unwrapped_stepper_type::time_type time_type;
- typedef typename unwrapped_stepper_type::value_type ode_value_type;
-
- public:
-
- ode_iterator_base( stepper_type stepper , system_type sys ,
- time_type t , time_type dt )
- : m_stepper( stepper ) , m_system( sys ) ,
- m_t( t ) , m_dt( dt ) , m_at_end( false )
- { }
-
- ode_iterator_base( stepper_type stepper , system_type sys )
- : m_stepper( stepper ) , m_system( sys ) , m_at_end( true )
- { }
-
- bool same( ode_iterator_base const& iter )
- {
- return (
- //( static_cast<Iterator>(*this).get_state() ==
- // static_cast<Iterator>(iter).get_state ) &&
- ( m_t == iter.m_t ) &&
- ( m_dt == iter.m_dt ) &&
- ( m_at_end == iter.m_at_end )
- );
- }
-
-
- protected:
-
- friend class boost::iterator_core_access;
-
- bool equal( ode_iterator_base const& other ) const
- {
- if( m_at_end == other.m_at_end )
- {
- return true;
- }
- else
- {
- return false;
- }
- }
-
- std::pair< const state_type& , const time_type& > dereference() const
- {
- return std::pair< const state_type & , const time_type & >(
- static_cast<const Iterator*>(this)->get_state() , m_t );
- }
-
- stepper_type m_stepper;
- system_type m_system;
- time_type m_t;
- time_type m_dt;
- bool m_at_end;
-
- };
-
-
-
-} // namespace detail
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-
-#endif // BOOST_NUMERIC_ODEINT_ITERATOR_DETAIL_ODE_ITERATOR_BASE_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/impl/adaptive_iterator_impl.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/impl/adaptive_iterator_impl.hpp
deleted file mode 100644
index e5b4b3cf48a67e1bde8379d240a89d2d7982e84a..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/impl/adaptive_iterator_impl.hpp
+++ /dev/null
@@ -1,253 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/iterator/detail/adaptive_iterator_impl.hpp
-
- [begin_description]
- tba.
- [end_description]
-
- Copyright 2009-2012 Karsten Ahnert
- Copyright 2009-2012 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
-*/
-
-
-#ifndef BOOST_NUMERIC_ODEINT_ITERATOR_DETAIL_ADAPTIVE_ITERATOR_IMPL_HPP_DEFINED
-#define BOOST_NUMERIC_ODEINT_ITERATOR_DETAIL_ADAPTIVE_ITERATOR_IMPL_HPP_DEFINED
-
-#include <boost/utility/enable_if.hpp>
-#include <boost/type_traits/is_same.hpp>
-#include <boost/throw_exception.hpp>
-
-#include <boost/numeric/odeint/util/unit_helper.hpp>
-#include <boost/numeric/odeint/util/copy.hpp>
-#include <boost/numeric/odeint/stepper/controlled_step_result.hpp>
-#include <boost/numeric/odeint/iterator/detail/ode_iterator_base.hpp>
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
- template< class Iterator , class Stepper , class System , class State , typename Tag , typename StepperTag >
- class adaptive_iterator_impl;
-
- /*
- * Specilization for controlled steppers
- */
- /**
- * \brief ODE Iterator with adaptive step size control. The value type of this iterator is the state type of the stepper.
- *
- * Implements an ODE iterator with adaptive step size control. Uses controlled steppers. adaptive_iterator is a model
- * of single-pass iterator.
- *
- * The value type of this iterator is the state type of the stepper. Hence one can only access the state and not the current time.
- *
- * \tparam Stepper The stepper type which should be used during the iteration.
- * \tparam System The type of the system function (ODE) which should be solved.
- */
- template< class Iterator , class Stepper , class System , class State , typename Tag >
- class adaptive_iterator_impl< Iterator , Stepper , System , State , Tag , controlled_stepper_tag >
- : public detail::ode_iterator_base< Iterator , Stepper , System , State , Tag >
- {
- private:
-
-
- typedef Stepper stepper_type;
- typedef System system_type;
- typedef typename boost::numeric::odeint::unwrap_reference< stepper_type >::type unwrapped_stepper_type;
- typedef State state_type;
- typedef typename traits::time_type< stepper_type >::type time_type;
- typedef typename traits::value_type< stepper_type >::type ode_value_type;
- #ifndef DOXYGEN_SKIP
- typedef detail::ode_iterator_base< Iterator , Stepper , System , State , Tag > base_type;
- #endif
-
- public:
-
- /**
- * \brief Constructs an adaptive_iterator. This constructor should be used to construct the begin iterator.
- *
- * \param stepper The stepper to use during the iteration.
- * \param sys The system function (ODE) to solve.
- * \param s The initial state. adaptive_iterator stores a reference of s and changes its value during the iteration.
- * \param t The initial time.
- * \param t_end The end time, at which the iteration should stop.
- * \param dt The initial time step.
- */
- adaptive_iterator_impl( stepper_type stepper , system_type sys , state_type &s , time_type t , time_type t_end , time_type dt )
- : base_type( stepper , sys , t , dt ) , m_t_end( t_end ) , m_state( &s )
- {
- if( detail::less_with_sign( this->m_t_end , this->m_t , this->m_dt ) )
- this->m_at_end = true;
- }
-
- /**
- * \brief Constructs an adaptive_iterator. This constructor should be used to construct the end iterator.
- *
- * \param stepper The stepper to use during the iteration.
- * \param sys The system function (ODE) to solve.
- * \param s The initial state. adaptive_iterator store a reference of s and changes its value during the iteration.
- */
- adaptive_iterator_impl( stepper_type stepper , system_type sys , state_type &s )
- : base_type( stepper , sys ) , m_state( &s ) { }
-
- protected:
-
- friend class boost::iterator_core_access;
-
- void increment()
- {
- if( detail::less_with_sign( this->m_t , this->m_t_end , this->m_dt) )
- {
- if( detail::less_with_sign( this->m_t_end ,
- static_cast<time_type>(this->m_t + this->m_dt) ,
- this->m_dt ) )
- {
- this->m_dt = this->m_t_end - this->m_t;
- }
- unwrapped_stepper_type &stepper = this->m_stepper;
- const size_t max_attempts = 1000;
- size_t trials = 0;
- controlled_step_result res = success;
- do
- {
- res = stepper.try_step( this->m_system , *( this->m_state ) , this->m_t , this->m_dt );
- ++trials;
- }
- while( ( res == fail ) && ( trials < max_attempts ) );
- if( trials == max_attempts )
- {
- BOOST_THROW_EXCEPTION( std::overflow_error( "Adaptive iterator : Maximal number of iterations reached. A step size could not be found." ));
- }
- } else {
- this->m_at_end = true;
- }
- }
- public:
- const state_type& get_state() const
- {
- return *this->m_state;
- }
-
- private:
- time_type m_t_end;
- state_type* m_state;
- };
-
-
-
- /*
- * Specilization for dense outputer steppers
- */
- /**
- * \brief ODE Iterator with adaptive step size control. The value type of this iterator is the state type of the stepper.
- *
- * Implements an ODE iterator with adaptive step size control. Uses dense-output steppers. adaptive_iterator is a model
- * of single-pass iterator.
- *
- * The value type of this iterator is the state type of the stepper. Hence one can only access the state and not the current time.
- *
- * \tparam Stepper The stepper type which should be used during the iteration.
- * \tparam System The type of the system function (ODE) which should be solved.
- */
- template< class Iterator , class Stepper , class System , class State , typename Tag >
- class adaptive_iterator_impl< Iterator , Stepper , System , State , Tag , dense_output_stepper_tag >
- : public detail::ode_iterator_base< Iterator , Stepper , System , State , Tag >
- {
- private:
-
-
- typedef Stepper stepper_type;
- typedef System system_type;
- typedef typename boost::numeric::odeint::unwrap_reference< stepper_type >::type unwrapped_stepper_type;
- typedef State state_type;
- typedef typename traits::time_type< stepper_type >::type time_type;
- typedef typename traits::value_type< stepper_type >::type ode_value_type;
- #ifndef DOXYGEN_SKIP
- typedef detail::ode_iterator_base< Iterator , Stepper , System , State , Tag > base_type;
- #endif
-
-
- public:
-
-
- /**
- * \brief Constructs an adaptive_iterator. This constructor should be used to construct the begin iterator.
- *
- * \param stepper The stepper to use during the iteration.
- * \param sys The system function (ODE) to solve.
- * \param s The initial state.
- * \param t The initial time.
- * \param t_end The end time, at which the iteration should stop.
- * \param dt The initial time step.
- */
- adaptive_iterator_impl( stepper_type stepper , system_type sys , state_type &s , time_type t , time_type t_end , time_type dt )
- : base_type( stepper , sys , t , dt ) , m_t_end( t_end )
- {
- if( detail::less_eq_with_sign( this->m_t , this->m_t_end , this->m_dt ) )
- {
- unwrapped_stepper_type &st = this->m_stepper;
- st.initialize( s , this->m_t , this->m_dt );
- } else {
- this->m_at_end = true;
- }
- }
-
- /**
- * \brief Constructs an adaptive_iterator. This constructor should be used to construct the end iterator.
- *
- * \param stepper The stepper to use during the iteration.
- * \param sys The system function (ODE) to solve.
- * \param s The initial state.
- */
- adaptive_iterator_impl( stepper_type stepper , system_type sys , state_type& /* s */ )
- : base_type( stepper , sys ) { }
-
- protected:
-
- friend class boost::iterator_core_access;
-
- void increment()
- {
- unwrapped_stepper_type &stepper = this->m_stepper;
- if( detail::less_with_sign( this->m_t ,
- this->m_t_end ,
- stepper.current_time_step() ) )
- {
- if( detail::less_with_sign( this->m_t_end ,
- static_cast<time_type>(this->m_t + stepper.current_time_step()) ,
- stepper.current_time_step() ) )
- {
- // make stpper to end exactly at t_end
- stepper.initialize( stepper.current_state() , stepper.current_time() ,
- static_cast<time_type>(this->m_t_end-this->m_t) );
- }
- stepper.do_step( this->m_system );
- this->m_t = stepper.current_time();
- } else { // we have reached t_end
- this->m_at_end = true;
- }
- }
-
- public:
- const state_type& get_state() const
- {
- const unwrapped_stepper_type &stepper = this->m_stepper;
- return stepper.current_state();
- }
-
- private:
- time_type m_t_end;
- };
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_ITERATOR_DETAIL_ADAPTIVE_ITERATOR_IMPL_HPP_DEFINED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/impl/const_step_iterator_impl.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/impl/const_step_iterator_impl.hpp
deleted file mode 100644
index 54b0727485d378e96c014db01163283de741eb60..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/impl/const_step_iterator_impl.hpp
+++ /dev/null
@@ -1,228 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/iterator/detail/const_step_iterator_impl.hpp
-
- [begin_description]
- tba.
- [end_description]
-
- Copyright 2013 Karsten Ahnert
- Copyright 2013 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
-*/
-
-
-#ifndef BOOST_NUMERIC_ODEINT_ITERATOR_DETAIL_CONST_STEP_ITERATOR_IMPL_HPP_DEFINED
-#define BOOST_NUMERIC_ODEINT_ITERATOR_DETAIL_CONST_STEP_ITERATOR_IMPL_HPP_DEFINED
-
-#include <boost/numeric/odeint/iterator/detail/ode_iterator_base.hpp>
-#include <boost/numeric/odeint/util/unit_helper.hpp>
-
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
- template< class Iterator , class Stepper , class System , class State , typename Tag , class StepperTag >
- class const_step_iterator_impl;
-
-
- /*
- * Specilization for steppers and error steppers
- */
- template< class Iterator , class Stepper , class System , class State , typename Tag >
- class const_step_iterator_impl< Iterator , Stepper , System , State , Tag , stepper_tag >
- : public detail::ode_iterator_base< Iterator , Stepper , System , State , Tag >
- {
- private:
-
- typedef Stepper stepper_type;
- typedef System system_type;
- typedef typename boost::numeric::odeint::unwrap_reference< stepper_type >::type unwrapped_stepper_type;
- typedef State state_type;
- typedef typename traits::time_type< stepper_type >::type time_type;
- typedef typename traits::value_type< stepper_type >::type ode_value_type;
- #ifndef DOXYGEN_SKIP
- typedef detail::ode_iterator_base< Iterator , Stepper , System , State , Tag > base_type;
- #endif
-
- public:
-
- /**
- * \brief Constructs a const_step_iterator. This constructor should be used to construct the begin iterator.
- *
- * \param stepper The stepper to use during the iteration.
- * \param sys The system function (ODE) to solve.
- * \param s The initial state. const_step_iterator stores a reference of s and changes its value during the iteration.
- * \param t The initial time.
- * \param t_end The end time, at which the iteration should stop.
- * \param dt The initial time step.
- */
- const_step_iterator_impl( stepper_type stepper , system_type sys , state_type &s , time_type t , time_type t_end , time_type dt )
- : base_type( stepper , sys , t , dt ) , m_t_start( t ) , m_t_end( t_end ) , m_state( &s ) , m_step( 0 )
- {
- if( detail::less_with_sign( this->m_t_end , this->m_t , this->m_dt ) )
- this->m_at_end = true;
- }
-
- /**
- * \brief Constructs a const_step_iterator. This constructor should be used to construct the end iterator.
- *
- * \param stepper The stepper to use during the iteration.
- * \param sys The system function (ODE) to solve.
- * \param s The initial state. const_step_iterator stores a reference of s and changes its value during the iteration.
- */
- const_step_iterator_impl( stepper_type stepper , system_type sys , state_type& /* s */ )
- : base_type( stepper , sys ) { }
-
- protected:
-
- friend class boost::iterator_core_access;
-
- void increment()
- {
- if( detail::less_eq_with_sign( static_cast<time_type>(this->m_t+this->m_dt) ,
- this->m_t_end , this->m_dt ) )
- {
- unwrapped_stepper_type &stepper = this->m_stepper;
- stepper.do_step( this->m_system , *this->m_state , this->m_t , this->m_dt );
- // use integer to compute current time to reduce roundoff errors
- this->m_step++;
- this->m_t = this->m_t_start + static_cast< typename unit_value_type<time_type>::type >(this->m_step)*this->m_dt;
- } else {
- this->m_at_end = true;
- }
- }
-
- public:
- const state_type& get_state() const
- {
- return *m_state;
- }
-
- private:
- time_type m_t_start;
- time_type m_t_end;
- state_type* m_state;
- size_t m_step;
-
- };
-
-
-
- /*
- * Specilization for dense output stepper
- */
- /**
- * \brief ODE Iterator with constant step size. The value type of this iterator is the state type of the stepper.
- *
- * Implements an ODE iterator solving the ODE with constant steps. Uses dense-output steppers.
- * const_step_iterator is a model of single-pass iterator.
- *
- * The value type of this iterator is the state type of the stepper. Hence one can only access the state and not the current time.
- *
- * \tparam Stepper The stepper type which should be used during the iteration.
- * \tparam System The type of the system function (ODE) which should be solved.
- */
- template< class Iterator , class Stepper , class System , class State , typename Tag >
- class const_step_iterator_impl< Iterator , Stepper , System , State , Tag , dense_output_stepper_tag >
- : public detail::ode_iterator_base< Iterator , Stepper , System , State , Tag >
- {
- private:
-
- typedef Stepper stepper_type;
- typedef System system_type;
- typedef typename boost::numeric::odeint::unwrap_reference< stepper_type >::type unwrapped_stepper_type;
- typedef State state_type;
- typedef typename traits::time_type< stepper_type >::type time_type;
- typedef typename traits::value_type< stepper_type >::type ode_value_type;
- #ifndef DOXYGEN_SKIP
- typedef detail::ode_iterator_base< Iterator , Stepper , System , State , Tag > base_type;
- #endif
-
- public:
-
- /**
- * \brief Constructs a const_step_iterator. This constructor should be used to construct the begin iterator.
- *
- * \param stepper The stepper to use during the iteration.
- * \param sys The system function (ODE) to solve.
- * \param s The initial state. const_step_iterator stores a reference of s and changes its value during the iteration.
- * \param t The initial time.
- * \param t_end The end time, at which the iteration should stop.
- * \param dt The initial time step.
- */
- const_step_iterator_impl( stepper_type stepper , system_type sys , state_type &s , time_type t , time_type t_end , time_type dt )
- : base_type( stepper , sys , t , dt ) , m_t_start( t ) , m_t_end( t_end ) , m_state( &s ) , m_step( 0 )
- {
- if( detail::less_eq_with_sign( this->m_t , this->m_t_end , this->m_dt ) )
- {
- unwrapped_stepper_type &st = this->m_stepper;
- st.initialize( * ( this->m_state ) , this->m_t , this->m_dt );
- } else {
- this->m_at_end = true;
- }
- }
-
- /**
- * \brief Constructs a const_step_iterator. This constructor should be used to construct the end iterator.
- *
- * \param stepper The stepper to use during the iteration.
- * \param sys The system function (ODE) to solve.
- * \param s The initial state. const_step_iterator stores a reference of s and changes its value during the iteration.
- */
- const_step_iterator_impl( stepper_type stepper , system_type sys , state_type &s )
- : base_type( stepper , sys ) , m_state( &s )
- {
- }
-
-
-
- protected:
-
- friend class boost::iterator_core_access;
-
- void increment( void )
- {
- if( detail::less_eq_with_sign( static_cast<time_type>(this->m_t+this->m_dt) ,
- this->m_t_end , this->m_dt ) )
- {
- unwrapped_stepper_type &stepper = this->m_stepper;
- // use integer to compute current time to reduce roundoff errors
- this->m_step++;
- this->m_t = this->m_t_start + static_cast< typename unit_value_type<time_type>::type >(this->m_step)*this->m_dt;
- while( detail::less_with_sign( stepper.current_time() , this->m_t ,
- stepper.current_time_step() ) )
- {
- stepper.do_step( this->m_system );
- }
- stepper.calc_state( this->m_t , *( this->m_state ) );
- } else {
- this->m_at_end = true;
- }
- }
-
- public:
- const state_type& get_state() const
- {
- return *m_state;
- }
-
- private:
- time_type m_t_start;
- time_type m_t_end;
- state_type* m_state;
- size_t m_step;
- };
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_ITERATOR_DETAIL_CONST_STEP_ITERATOR_IMPL_HPP_DEFINED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/impl/n_step_iterator_impl.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/impl/n_step_iterator_impl.hpp
deleted file mode 100644
index 6e5b85994e1b3ba090d9895ea8a2b4f0b16b1930..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/impl/n_step_iterator_impl.hpp
+++ /dev/null
@@ -1,239 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/iterator/detail/n_step_iterator_impl.hpp
-
- [begin_description]
- tba.
- [end_description]
-
- Copyright 2009-2013 Karsten Ahnert
- Copyright 2009-2013 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
-*/
-
-
-#ifndef BOOST_NUMERIC_ODEINT_ITERATOR_DETAIL_N_STEP_ITERATOR_IMPL_HPP_DEFINED
-#define BOOST_NUMERIC_ODEINT_ITERATOR_DETAIL_N_STEP_ITERATOR_IMPL_HPP_DEFINED
-
-#include <boost/numeric/odeint/iterator/detail/ode_iterator_base.hpp>
-#include <boost/numeric/odeint/util/unit_helper.hpp>
-
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
- template< class Iterator , class Stepper , class System , class State , typename Tag , class StepperTag >
- class n_step_iterator_impl;
-
-
- /*
- * Specilization for steppers and error steppers
- */
- /**
- * \brief ODE Iterator performing exactly n steps with constant step size. The value type of this iterator is the state type of the stepper.
- *
- * Implements an ODE iterator solving the ODE with constant step size. Uses steppers fulfilling the Stepper concept.
- * n_step_iterator is a model of single-pass iterator.
- *
- * The value type of this iterator is the state type of the stepper. Hence one can only access the state and not the current time.
- *
- * \tparam Stepper The stepper type which should be used during the iteration.
- * \tparam System The type of the system function (ODE) which should be solved.
- */
- template< class Iterator , class Stepper , class System , class State , typename Tag >
- class n_step_iterator_impl< Iterator , Stepper , System , State , Tag , stepper_tag >
- : public detail::ode_iterator_base< Iterator , Stepper , System , State , Tag >
- {
- private:
-
- typedef Stepper stepper_type;
- typedef System system_type;
- typedef typename boost::numeric::odeint::unwrap_reference< stepper_type >::type unwrapped_stepper_type;
- typedef State state_type;
- typedef typename traits::time_type< stepper_type >::type time_type;
- typedef typename traits::value_type< stepper_type >::type ode_value_type;
- #ifndef DOXYGEN_SKIP
- typedef detail::ode_iterator_base< Iterator , Stepper , System , State , Tag > base_type;
- #endif
-
- public:
-
- /**
- * \brief Constructs a n_step_iterator. This constructor should be used to construct the begin iterator.
- *
- * \param stepper The stepper to use during the iteration.
- * \param sys The system function (ODE) to solve.
- * \param s The initial state. const_step_iterator stores a reference of s and changes its value during the iteration.
- * \param t The initial time.
- * \param dt The initial time step.
- * \param num_of_steps the number of steps to be executed.
- */
- n_step_iterator_impl( stepper_type stepper , system_type sys , state_type &s ,
- time_type t , time_type dt , size_t num_of_steps )
- : base_type( stepper , sys , t , dt ) , m_t_start( t ) , m_state( &s ) ,
- m_steps(num_of_steps) , m_step( 0 )
- { }
-
- /**
- * \brief Constructs a const_step_iterator. This constructor should be used to construct the end iterator.
- *
- * \param stepper The stepper to use during the iteration.
- * \param sys The system function (ODE) to solve.
- * \param s The initial state. const_step_iterator stores a reference of s and changes its value during the iteration.
- */
- n_step_iterator_impl( stepper_type stepper , system_type sys , state_type &s )
- : base_type( stepper , sys ) , m_state( &s ) { }
-
- protected:
-
- friend class boost::iterator_core_access;
-
- void increment()
- {
- if( this->m_step < this->m_steps )
- {
- unwrapped_stepper_type &stepper = this->m_stepper;
- stepper.do_step( this->m_system , *this->m_state , this->m_t , this->m_dt );
- // use integer to compute current time to reduce roundoff errors
- this->m_step++;
- this->m_t = this->m_t_start + static_cast< typename unit_value_type<time_type>::type >(this->m_step)*this->m_dt;
- } else {
- this->m_at_end = true;
-
- }
- }
-
- public:
- const state_type& get_state() const
- {
- return *m_state;
- }
-
-
- private:
- time_type m_t_start;
- time_type m_t_end;
- state_type* m_state;
- size_t m_steps;
- size_t m_step;
-
- };
-
-
-
-
- /*
- * Specilization for dense output stepper
- */
- /**
- * \brief ODE Iterator with step-size control and dense output.
- *
- * Implements an ODE iterator solving the ODE with constant steps. Uses dense-output steppers.
- * n_step_iterator is a model of single-pass iterator.
- *
- * The value type of this iterator is the state type of the stepper. Hence one can only access the state and not the current time.
- *
- * \tparam Stepper The stepper type which should be used during the iteration.
- * \tparam System The type of the system function (ODE) which should be solved.
- */
- template< class Iterator , class Stepper , class System , class State , typename Tag >
- class n_step_iterator_impl< Iterator , Stepper , System , State , Tag , dense_output_stepper_tag >
- : public detail::ode_iterator_base< Iterator , Stepper , System , State , Tag >
- {
- private:
-
- typedef Stepper stepper_type;
- typedef System system_type;
- typedef typename boost::numeric::odeint::unwrap_reference< stepper_type >::type unwrapped_stepper_type;
- typedef State state_type;
- typedef typename traits::time_type< stepper_type >::type time_type;
- typedef typename traits::value_type< stepper_type >::type ode_value_type;
- #ifndef DOXYGEN_SKIP
- typedef detail::ode_iterator_base< Iterator , Stepper , System , State , Tag > base_type;
- #endif
-
- public:
-
- /**
- * \brief Constructs a const_step_iterator. This constructor should be used to construct the begin iterator.
- *
- * \param stepper The stepper to use during the iteration.
- * \param sys The system function (ODE) to solve.
- * \param s The initial state. const_step_iterator stores a reference of s and changes its value during the iteration.
- * \param t The initial time.
- * \param dt The initial time step.
- * \param num_of_steps the number of steps to be executed.
- */
- n_step_iterator_impl( stepper_type stepper , system_type sys , state_type &s ,
- time_type t , time_type dt , size_t num_of_steps )
- : base_type( stepper , sys , t , dt ) , m_t_start( t ) , m_state( &s ) ,
- m_steps( num_of_steps ) , m_step( 0 )
- {
- unwrapped_stepper_type &st = this->m_stepper;
- st.initialize( * ( this->m_state ) , this->m_t , this->m_dt );
- }
-
- /**
- * \brief Constructs a const_step_iterator. This constructor should be used to construct the end iterator.
- *
- * \param stepper The stepper to use during the iteration.
- * \param sys The system function (ODE) to solve.
- * \param s The initial state. const_step_iterator stores a reference of s and changes its value during the iteration.
- */
- n_step_iterator_impl( stepper_type stepper , system_type sys , state_type &s )
- : base_type( stepper , sys ) , m_state( &s )
- {
- }
-
-
-
- protected:
-
- friend class boost::iterator_core_access;
-
- void increment( void )
- {
- if( this->m_step < this->m_steps )
- {
- unwrapped_stepper_type &stepper = this->m_stepper;
- // use integer to compute current time to reduce roundoff errors
- this->m_step++;
- this->m_t = this->m_t_start + static_cast< typename unit_value_type<time_type>::type >(this->m_step)*this->m_dt;
- while( detail::less_with_sign( stepper.current_time() , this->m_t ,
- stepper.current_time_step() ) )
- {
- stepper.do_step( this->m_system );
- }
- stepper.calc_state( this->m_t , *( this->m_state ) );
- } else {
- this->m_at_end = true;
- }
- }
-
- public:
- const state_type& get_state() const
- {
- return *m_state;
- }
-
-
- private:
- time_type m_t_start;
- time_type m_t_end;
- state_type* m_state;
- size_t m_steps;
- size_t m_step;
- };
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_ITERATOR_DETAIL_N_STEP_ITERATOR_IMPL_HPP_DEFINED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/impl/times_iterator_impl.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/impl/times_iterator_impl.hpp
deleted file mode 100644
index 7a2b48d829dd286501301c222380452b33801493..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/impl/times_iterator_impl.hpp
+++ /dev/null
@@ -1,371 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/iterator/detail/times_iterator_impl.hpp
-
- [begin_description]
- tba.
- [end_description]
-
- Copyright 2009-2013 Karsten Ahnert
- Copyright 2009-2013 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
-*/
-
-
-#ifndef BOOST_NUMERIC_ODEINT_ITERATOR_DETAIL_TIMES_ITERATOR_IMPL_HPP_DEFINED
-#define BOOST_NUMERIC_ODEINT_ITERATOR_DETAIL_TIMES_ITERATOR_IMPL_HPP_DEFINED
-
-#include <boost/utility/enable_if.hpp>
-#include <boost/type_traits/is_same.hpp>
-#include <boost/throw_exception.hpp>
-
-#include <boost/numeric/odeint/util/unit_helper.hpp>
-#include <boost/numeric/odeint/util/copy.hpp>
-#include <boost/numeric/odeint/stepper/controlled_step_result.hpp>
-#include <boost/numeric/odeint/iterator/detail/ode_iterator_base.hpp>
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
- template< class Iterator , class Stepper , class System , class State , class TimeIterator ,
- typename Tag , typename StepperTag >
- class times_iterator_impl;
-
- /*
- * Specilization for basic steppers
- */
- /**
- * \brief ODE Iterator with constant step size.
- *
- * Implements an ODE iterator with observer calls at predefined times.
- * Uses controlled steppers. times_iterator is a model of single-pass iterator.
- *
- * The value type of this iterator is the state type of the stepper. Hence one can only access the state and not the current time.
- *
- * \tparam Stepper The stepper type which should be used during the iteration.
- * \tparam System The type of the system function (ODE) which should be solved.
- */
- template< class Iterator , class Stepper , class System , class State , class TimeIterator , typename Tag >
- class times_iterator_impl< Iterator , Stepper , System , State , TimeIterator , Tag , stepper_tag >
- : public detail::ode_iterator_base< Iterator , Stepper , System , State , Tag >
- {
- private:
-
-
- typedef Stepper stepper_type;
- typedef System system_type;
- typedef typename boost::numeric::odeint::unwrap_reference< stepper_type >::type unwrapped_stepper_type;
- typedef State state_type;
- typedef TimeIterator time_iterator_type;
- typedef typename traits::time_type< stepper_type >::type time_type;
- typedef typename traits::value_type< stepper_type >::type ode_value_type;
- #ifndef DOXYGEN_SKIP
- typedef detail::ode_iterator_base< Iterator , Stepper , System , State , Tag > base_type;
- #endif
-
- public:
-
- /**
- * \brief Constructs a times_iterator. This constructor should be used to construct the begin iterator.
- *
- * \param stepper The stepper to use during the iteration.
- * \param sys The system function (ODE) to solve.
- * \param s The initial state. adaptive_iterator stores a reference of s and changes its value during the iteration.
- * \param t_start Iterator to the begin of a sequence of time values.
- * \param t_end Iterator to the begin of a sequence of time values.
- * \param dt The (initial) time step.
- */
- times_iterator_impl( stepper_type stepper , system_type sys , state_type &s ,
- time_iterator_type t_start , time_iterator_type t_end , time_type dt )
- : base_type( stepper , sys , *t_start , dt ) ,
- m_t_start( t_start ) , m_t_end( t_end ) , m_state( &s )
- {
- if( t_start == t_end )
- this->m_at_end = true;
- }
-
- /**
- * \brief Constructs an adaptive_iterator. This constructor should be used to construct the end iterator.
- *
- * \param stepper The stepper to use during the iteration.
- * \param sys The system function (ODE) to solve.
- * \param s The initial state. adaptive_iterator store a reference of s and changes its value during the iteration.
- */
- times_iterator_impl( stepper_type stepper , system_type sys , state_type &s )
- : base_type( stepper , sys ) , m_state( &s ) { }
-
- protected:
-
- friend class boost::iterator_core_access;
-
- void increment()
- {
- unwrapped_stepper_type &stepper = this->m_stepper;
- if( ++m_t_start != m_t_end )
- {
- while( detail::less_with_sign( this->m_t , static_cast<time_type>(*m_t_start) , this->m_dt ) )
- {
- const time_type current_dt = detail::min_abs( this->m_dt , static_cast<time_type>(*m_t_start) - this->m_t );
- stepper.do_step( this->m_system , *( this->m_state ) , this->m_t , current_dt );
- this->m_t += current_dt;
- }
-
- } else {
- this->m_at_end = true;
- }
- }
-
- public:
- const state_type& get_state() const
- {
- return *m_state;
- }
-
- private:
- time_iterator_type m_t_start;
- time_iterator_type m_t_end;
- state_type* m_state;
- };
-
-
-
- /*
- * Specilization for controlled steppers
- */
- /**
- * \brief ODE Iterator with adaptive step size control. The value type of this iterator is the state type of the stepper.
- *
- * Implements an ODE iterator with observer calls at predefined times.
- * Uses controlled steppers. times_iterator is a model of single-pass iterator.
- *
- * The value type of this iterator is the state type of the stepper. Hence one can only access the state and not the current time.
- *
- * \tparam Stepper The stepper type which should be used during the iteration.
- * \tparam System The type of the system function (ODE) which should be solved.
- */
- template< class Iterator , class Stepper , class System , class State , class TimeIterator , typename Tag >
- class times_iterator_impl< Iterator , Stepper , System , State , TimeIterator , Tag , controlled_stepper_tag >
- : public detail::ode_iterator_base< Iterator , Stepper , System , State , Tag >
- {
- private:
-
-
- typedef Stepper stepper_type;
- typedef System system_type;
- typedef typename boost::numeric::odeint::unwrap_reference< stepper_type >::type unwrapped_stepper_type;
- typedef State state_type;
- typedef TimeIterator time_iterator_type;
- typedef typename traits::time_type< stepper_type >::type time_type;
- typedef typename traits::value_type< stepper_type >::type ode_value_type;
- #ifndef DOXYGEN_SKIP
- typedef detail::ode_iterator_base< Iterator , Stepper , System , State , Tag > base_type;
- #endif
-
- public:
-
- /**
- * \brief Constructs a times_iterator. This constructor should be used to construct the begin iterator.
- *
- * \param stepper The stepper to use during the iteration.
- * \param sys The system function (ODE) to solve.
- * \param s The initial state. adaptive_iterator stores a reference of s and changes its value during the iteration.
- * \param t_start Iterator to the begin of a sequence of time values.
- * \param t_end Iterator to the begin of a sequence of time values.
- * \param dt The (initial) time step.
- */
- times_iterator_impl( stepper_type stepper , system_type sys , state_type &s ,
- time_iterator_type t_start , time_iterator_type t_end , time_type dt )
- : base_type( stepper , sys , *t_start , dt ) ,
- m_t_start( t_start ) , m_t_end( t_end ) , m_state( &s )
- {
- if( t_start == t_end )
- this->m_at_end = true;
- }
-
- /**
- * \brief Constructs an adaptive_iterator. This constructor should be used to construct the end iterator.
- *
- * \param stepper The stepper to use during the iteration.
- * \param sys The system function (ODE) to solve.
- * \param s The initial state. adaptive_iterator store a reference of s and changes its value during the iteration.
- */
- times_iterator_impl( stepper_type stepper , system_type sys , state_type &s )
- : base_type( stepper , sys ) , m_state( &s ) { }
-
- protected:
-
- friend class boost::iterator_core_access;
-
- void increment()
- {
- if( ++m_t_start != m_t_end )
- {
- while( detail::less_with_sign( this->m_t , static_cast<time_type>(*m_t_start) , this->m_dt ) )
- {
- if( detail::less_with_sign( static_cast<time_type>(*m_t_start) - this->m_t , this->m_dt , this->m_dt ) )
- {
- // we want to end exactly at the time point
- time_type current_dt = static_cast<time_type>(*m_t_start) - this->m_t;
- step_loop( current_dt );
- } else {
- step_loop( this->m_dt );
- }
- }
-
- } else {
- this->m_at_end = true;
- }
- }
-
- private:
- void step_loop( time_type &dt )
- {
- unwrapped_stepper_type &stepper = this->m_stepper;
- const size_t max_attempts = 1000;
- size_t trials = 0;
- controlled_step_result res = success;
- do
- {
- res = stepper.try_step( this->m_system , *( this->m_state ) , this->m_t , dt );
- ++trials;
- }
- while( ( res == fail ) && ( trials < max_attempts ) );
- if( trials == max_attempts )
- {
- BOOST_THROW_EXCEPTION( std::overflow_error( "Adaptive iterator : Maximal number of iterations reached. A step size could not be found." ) );
- }
- }
-
- public:
- const state_type& get_state() const
- {
- return *m_state;
- }
-
-
- private:
- time_iterator_type m_t_start;
- time_iterator_type m_t_end;
- state_type* m_state;
- };
-
-
- /*
- * Specilization for dense outputer steppers
- */
- /**
- * \brief ODE Iterator with step size control and dense output.
- * Implements an ODE iterator with adaptive step size control. Uses dense-output steppers.
- * times_iterator is a model of single-pass iterator.
- *
- * \tparam Stepper The stepper type which should be used during the iteration.
- * \tparam System The type of the system function (ODE) which should be solved.
- */
- template< class Iterator , class Stepper , class System , class State , class TimeIterator , typename Tag >
- class times_iterator_impl< Iterator , Stepper , System , State , TimeIterator , Tag , dense_output_stepper_tag >
- : public detail::ode_iterator_base< Iterator , Stepper , System , State , Tag >
- {
- private:
-
-
- typedef Stepper stepper_type;
- typedef System system_type;
- typedef typename boost::numeric::odeint::unwrap_reference< stepper_type >::type unwrapped_stepper_type;
- typedef State state_type;
- typedef TimeIterator time_iterator_type;
- typedef typename traits::time_type< stepper_type >::type time_type;
- typedef typename traits::value_type< stepper_type >::type ode_value_type;
- #ifndef DOXYGEN_SKIP
- typedef detail::ode_iterator_base< Iterator , Stepper , System , State , Tag > base_type;
- #endif
-
-
- public:
-
-
- /**
- * \brief Constructs a times_iterator. This constructor should be used to construct the begin iterator.
- *
- * \param stepper The stepper to use during the iteration.
- * \param sys The system function (ODE) to solve.
- * \param s The initial state.
- * \param t_start Iterator to the begin of a sequence of time values.
- * \param t_end Iterator to the begin of a sequence of time values.
- * \param dt The (initial) time step.
- */
- times_iterator_impl( stepper_type stepper , system_type sys , state_type &s ,
- time_iterator_type t_start , time_iterator_type t_end , time_type dt )
- : base_type( stepper , sys , *t_start , dt ) ,
- m_t_start( t_start ) , m_t_end( t_end ) , m_final_time( *(t_end-1) ) ,
- m_state( &s )
- {
- if( t_start != t_end )
- {
- unwrapped_stepper_type &st = this->m_stepper;
- st.initialize( *( this->m_state ) , this->m_t , this->m_dt );
- } else {
- this->m_at_end = true;
- }
- }
-
- /**
- * \brief Constructs a times_iterator. This constructor should be used to construct the end iterator.
- *
- * \param stepper The stepper to use during the iteration.
- * \param sys The system function (ODE) to solve.
- * \param s The initial state.
- */
- times_iterator_impl( stepper_type stepper , system_type sys , state_type &s )
- : base_type( stepper , sys ) , m_state( &s ) { }
-
- protected:
-
- friend class boost::iterator_core_access;
-
- void increment()
- {
- unwrapped_stepper_type &st = this->m_stepper;
- if( ++m_t_start != m_t_end )
- {
- this->m_t = static_cast<time_type>(*m_t_start);
- while( detail::less_with_sign( st.current_time() , this->m_t , this->m_dt ) )
- {
- // make sure we don't go beyond the last point
- if( detail::less_with_sign( m_final_time-st.current_time() , st.current_time_step() , st.current_time_step() ) )
- {
- st.initialize( st.current_state() , st.current_time() , m_final_time-st.current_time() );
- }
- st.do_step( this->m_system );
- }
- st.calc_state( this->m_t , *( this->m_state ) );
- } else {
- this->m_at_end = true;
- }
- }
-
- public:
- const state_type& get_state() const
- {
- return *m_state;
- }
-
-
- private:
- time_iterator_type m_t_start;
- time_iterator_type m_t_end;
- time_type m_final_time;
- state_type* m_state;
- };
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_ITERATOR_DETAIL_TIMES_ITERATOR_IMPL_HPP_DEFINED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/integrate/detail/functors.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/integrate/detail/functors.hpp
deleted file mode 100644
index b239217ac4cbc9713ae0b7a93998ebcb4e6bd633..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/integrate/detail/functors.hpp
+++ /dev/null
@@ -1,70 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/integrate/detail/functors.hpp
-
- [begin_description]
- some functors for the iterator based integrate routines
- [end_description]
-
- Copyright 2009-2013 Karsten Ahnert
- Copyright 2009-2013 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_INTEGRATE_DETAIL_FUNCTORS_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_INTEGRATE_DETAIL_FUNCTORS_HPP_INCLUDED
-
-#include <utility>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-namespace detail {
-
-
-template< class Observer >
-struct obs_caller {
-
- size_t &m_n;
- Observer m_obs;
-
- obs_caller( size_t &m , Observer &obs ) : m_n(m) , m_obs( obs ) {}
-
- template< class State , class Time >
- void operator()( std::pair< const State & , const Time & > x )
- {
- typedef typename odeint::unwrap_reference< Observer >::type observer_type;
- observer_type &obs = m_obs;
- obs( x.first , x.second );
- m_n++;
- }
-};
-
-template< class Observer , class Time >
-struct obs_caller_time {
-
- Time &m_t;
- Observer m_obs;
-
- obs_caller_time( Time &t , Observer &obs ) : m_t(t) , m_obs( obs ) {}
-
- template< class State >
- void operator()( std::pair< const State & , const Time & > x )
- {
- typedef typename odeint::unwrap_reference< Observer >::type observer_type;
- observer_type &obs = m_obs;
- obs( x.first , x.second );
- m_t = x.second;
- }
-};
-
-} // namespace detail
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-#endif // BOOST_NUMERIC_ODEINT_INTEGRATE_DETAIL_FUNCTORS_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/integrate/detail/integrate_adaptive.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/integrate/detail/integrate_adaptive.hpp
deleted file mode 100644
index ccbbf497f3ae14162c27ea8a0b3ed28857866de5..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/integrate/detail/integrate_adaptive.hpp
+++ /dev/null
@@ -1,121 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/integrate/detail/integrate_adaptive.hpp
-
- [begin_description]
- Default Integrate adaptive implementation.
- [end_description]
-
- Copyright 2009-2011 Karsten Ahnert
- Copyright 2009-2011 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_INTEGRATE_DETAIL_INTEGRATE_ADAPTIVE_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_INTEGRATE_DETAIL_INTEGRATE_ADAPTIVE_HPP_INCLUDED
-
-#include <stdexcept>
-
-#include <boost/numeric/odeint/stepper/stepper_categories.hpp>
-#include <boost/numeric/odeint/stepper/controlled_step_result.hpp>
-#include <boost/numeric/odeint/iterator/integrate/detail/integrate_const.hpp>
-#include <boost/numeric/odeint/iterator/adaptive_time_iterator.hpp>
-#include <boost/numeric/odeint/iterator/integrate/detail/functors.hpp>
-#include <boost/numeric/odeint/util/bind.hpp>
-#include <boost/numeric/odeint/util/unwrap_reference.hpp>
-#include <boost/numeric/odeint/util/copy.hpp>
-
-#include <boost/numeric/odeint/util/detail/less_with_sign.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-namespace detail {
-
-// forward declaration
-template< class Stepper , class System , class State , class Time , class Observer>
-size_t integrate_const(
- Stepper stepper , System system , State &start_state ,
- Time start_time , Time end_time , Time dt ,
- Observer observer , stepper_tag );
-
-/*
- * integrate_adaptive for simple stepper is basically an integrate_const + some last step
- */
-template< class Stepper , class System , class State , class Time , class Observer >
-size_t integrate_adaptive(
- Stepper stepper , System system , State &start_state ,
- Time start_time , Time end_time , Time dt ,
- Observer observer , stepper_tag
-)
-{
- size_t steps = detail::integrate_const( stepper , system , start_state , start_time ,
- end_time , dt , observer , stepper_tag() );
- typename odeint::unwrap_reference< Observer >::type &obs = observer;
- typename odeint::unwrap_reference< Stepper >::type &st = stepper;
-
- Time end = start_time + dt*steps;
- if( less_with_sign( end , end_time , dt ) )
- { //make a last step to end exactly at end_time
- st.do_step( system , start_state , end , end_time - end );
- steps++;
- obs( start_state , end_time );
- }
- return steps;
-}
-
-
-/*
- * classical integrate adaptive
- */
-template< class Stepper , class System , class State , class Time , class Observer >
-size_t integrate_adaptive(
- Stepper stepper , System system , State &start_state ,
- Time &start_time , Time end_time , Time &dt ,
- Observer observer , controlled_stepper_tag
-)
-{
- size_t obs_calls = 0;
-
- boost::for_each( make_adaptive_time_range( stepper , system , start_state ,
- start_time , end_time , dt ) ,
- obs_caller< Observer >( obs_calls , observer ) );
-
- return obs_calls-1;
-}
-
-
-/*
- * integrate adaptive for dense output steppers
- *
- * step size control is used if the stepper supports it
- */
-template< class Stepper , class System , class State , class Time , class Observer >
-size_t integrate_adaptive(
- Stepper stepper , System system , State &start_state ,
- Time start_time , Time end_time , Time dt ,
- Observer observer , dense_output_stepper_tag )
-{
- size_t obs_calls = 0;
-
- boost::for_each( make_adaptive_time_range( stepper , system , start_state ,
- start_time , end_time , dt ) ,
- obs_caller< Observer >( obs_calls , observer ) );
-
- return obs_calls-1;
-}
-
-
-
-
-} // namespace detail
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_INTEGRATE_DETAIL_INTEGRATE_ADAPTIVE_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/integrate/detail/integrate_const.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/integrate/detail/integrate_const.hpp
deleted file mode 100644
index bdafff2e852b2708f22e9bfacee1feccc213d5c1..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/integrate/detail/integrate_const.hpp
+++ /dev/null
@@ -1,111 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/integrate/detail/integrate_const.hpp
-
- [begin_description]
- integrate const implementation
- [end_description]
-
- Copyright 2009-2012 Karsten Ahnert
- Copyright 2009-2012 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-#ifndef BOOST_NUMERIC_ODEINT_INTEGRATE_DETAIL_INTEGRATE_CONST_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_INTEGRATE_DETAIL_INTEGRATE_CONST_HPP_INCLUDED
-
-#include <boost/range/algorithm/for_each.hpp>
-
-#include <boost/numeric/odeint/util/unwrap_reference.hpp>
-#include <boost/numeric/odeint/stepper/stepper_categories.hpp>
-#include <boost/numeric/odeint/util/unit_helper.hpp>
-#include <boost/numeric/odeint/iterator/const_step_time_iterator.hpp>
-#include <boost/numeric/odeint/iterator/integrate/detail/integrate_adaptive.hpp>
-#include <boost/numeric/odeint/iterator/integrate/detail/functors.hpp>
-#include <boost/numeric/odeint/util/detail/less_with_sign.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-namespace detail {
-
-// forward declaration
-template< class Stepper , class System , class State , class Time , class Observer >
-size_t integrate_adaptive(
- Stepper stepper , System system , State &start_state ,
- Time &start_time , Time end_time , Time &dt ,
- Observer observer , controlled_stepper_tag
-);
-
-
-template< class Stepper , class System , class State , class Time , class Observer >
-size_t integrate_const(
- Stepper stepper , System system , State &start_state ,
- Time start_time , Time end_time , Time dt ,
- Observer observer , stepper_tag
-)
-{
- size_t obs_calls = 0;
-
- boost::for_each( make_const_step_time_range( stepper , system , start_state ,
- start_time , end_time , dt ) ,
- // should we use traits<Stepper>::state_type here instead of State? NO!
- obs_caller< Observer >( obs_calls , observer ) );
-
- // step integration steps gives step+1 observer calls
- return obs_calls-1;
-}
-
-
-
-template< class Stepper , class System , class State , class Time , class Observer >
-size_t integrate_const(
- Stepper stepper , System system , State &start_state ,
- Time start_time , Time end_time , Time dt ,
- Observer observer , controlled_stepper_tag
-)
-{
- typename odeint::unwrap_reference< Observer >::type &obs = observer;
-
- Time time = start_time;
- const Time time_step = dt;
- int step = 0;
-
- while( less_eq_with_sign( static_cast<Time>(time+time_step) , end_time , dt ) )
- {
- obs( start_state , time );
- detail::integrate_adaptive( stepper , system , start_state , time , time+time_step , dt ,
- null_observer() , controlled_stepper_tag() );
- // direct computation of the time avoids error propagation happening when using time += dt
- // we need clumsy type analysis to get boost units working here
- ++step;
- time = start_time + static_cast< typename unit_value_type<Time>::type >(step) * time_step;
- }
- obs( start_state , time );
-
- return step;
-}
-
-
-template< class Stepper , class System , class State , class Time , class Observer >
-size_t integrate_const(
- Stepper stepper , System system , State &start_state ,
- Time start_time , Time end_time , Time dt ,
- Observer observer , dense_output_stepper_tag
-)
-{
- size_t obs_calls = 0;
-
- boost::for_each( make_const_step_time_range( stepper , system , start_state ,
- start_time , end_time , dt ) ,
- obs_caller< Observer >( obs_calls , observer ) );
- return obs_calls-1;
-}
-
-
-} } } }
-
-#endif
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/integrate/detail/integrate_n_steps.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/integrate/detail/integrate_n_steps.hpp
deleted file mode 100644
index f90f8875cefbaf1a712126ae15a4b42d47651398..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/integrate/detail/integrate_n_steps.hpp
+++ /dev/null
@@ -1,107 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/integrate/detail/integrate_n_steps.hpp
-
- [begin_description]
- integrate steps implementation
- [end_description]
-
- Copyright 2009-2012 Karsten Ahnert
- Copyright 2009-2012 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-#ifndef BOOST_NUMERIC_ODEINT_INTEGRATE_DETAIL_INTEGRATE_N_STEPS_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_INTEGRATE_DETAIL_INTEGRATE_N_STEPS_HPP_INCLUDED
-
-#include <boost/numeric/odeint/util/unwrap_reference.hpp>
-#include <boost/numeric/odeint/stepper/stepper_categories.hpp>
-#include <boost/numeric/odeint/iterator/integrate/detail/integrate_adaptive.hpp>
-#include <boost/numeric/odeint/iterator/integrate/detail/functors.hpp>
-#include <boost/numeric/odeint/iterator/n_step_time_iterator.hpp>
-#include <boost/numeric/odeint/util/unit_helper.hpp>
-
-#include <boost/numeric/odeint/util/detail/less_with_sign.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-namespace detail {
-
-// forward declaration
-template< class Stepper , class System , class State , class Time , class Observer >
-size_t integrate_adaptive(
- Stepper stepper , System system , State &start_state ,
- Time &start_time , Time end_time , Time &dt ,
- Observer observer , controlled_stepper_tag
-);
-
-
-/* basic version */
-template< class Stepper , class System , class State , class Time , class Observer>
-Time integrate_n_steps(
- Stepper stepper , System system , State &start_state ,
- Time start_time , Time dt , size_t num_of_steps ,
- Observer observer , stepper_tag )
-{
- // ToDo: is there a better way to extract the final time?
- Time t = start_time; // Assignment is only here to avoid warnings.
- boost::for_each( make_n_step_time_range( stepper , system , start_state ,
- start_time , dt , num_of_steps ) ,
- obs_caller_time< Observer , Time >( t , observer ) );
- return t;
-}
-
-
-/* controlled version */
-template< class Stepper , class System , class State , class Time , class Observer>
-Time integrate_n_steps(
- Stepper stepper , System system , State &start_state ,
- Time start_time , Time dt , size_t num_of_steps ,
- Observer observer , controlled_stepper_tag )
-{
- typename odeint::unwrap_reference< Observer >::type &obs = observer;
-
- Time time = start_time;
- Time time_step = dt;
-
- for( size_t step = 0; step < num_of_steps ; ++step )
- {
- obs( start_state , time );
- detail::integrate_adaptive( stepper , system , start_state , time , static_cast<Time>(time+time_step) , dt ,
- null_observer() , controlled_stepper_tag() );
- // direct computation of the time avoids error propagation happening when using time += dt
- // we need clumsy type analysis to get boost units working here
- time = start_time + static_cast< typename unit_value_type<Time>::type >(step+1) * time_step;
- }
- obs( start_state , time );
-
- return time;
-}
-
-
-/* dense output version */
-template< class Stepper , class System , class State , class Time , class Observer>
-Time integrate_n_steps(
- Stepper stepper , System system , State &start_state ,
- Time start_time , Time dt , size_t num_of_steps ,
- Observer observer , dense_output_stepper_tag )
-{
- // ToDo: is there a better way to extract the final time?
- Time t = start_time; // Assignment is only here to avoid warnings.
- boost::for_each( make_n_step_time_range( stepper , system , start_state ,
- start_time , dt , num_of_steps ) ,
- obs_caller_time< Observer , Time >( t , observer ) );
- return t;
-}
-
-
-}
-}
-}
-}
-
-#endif /* BOOST_NUMERIC_ODEINT_INTEGRATE_DETAIL_INTEGRATE_N_STEPS_HPP_INCLUDED */
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/integrate/detail/integrate_times.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/integrate/detail/integrate_times.hpp
deleted file mode 100644
index bccc7c6b039dd8764c136f6822bbd28dc9bd7723..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/integrate/detail/integrate_times.hpp
+++ /dev/null
@@ -1,67 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/integrate/detail/integrate_times.hpp
-
- [begin_description]
- Default integrate times implementation.
- [end_description]
-
- Copyright 2009-2012 Karsten Ahnert
- Copyright 2009-2012 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_INTEGRATE_DETAIL_INTEGRATE_TIMES_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_INTEGRATE_DETAIL_INTEGRATE_TIMES_HPP_INCLUDED
-
-#include <stdexcept>
-
-#include <boost/config.hpp>
-#include <boost/range/algorithm/for_each.hpp>
-
-#include <boost/numeric/odeint/util/unwrap_reference.hpp>
-#include <boost/numeric/odeint/stepper/controlled_step_result.hpp>
-#include <boost/numeric/odeint/util/detail/less_with_sign.hpp>
-#include <boost/numeric/odeint/iterator/times_time_iterator.hpp>
-#include <boost/numeric/odeint/iterator/integrate/detail/functors.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-namespace detail {
-
-
-
-/*
- * integrate_times for all steppers
- */
-template< class Stepper , class System , class State , class TimeIterator , class Time , class Observer , class StepperTag >
-size_t integrate_times(
- Stepper stepper , System system , State &start_state ,
- TimeIterator start_time , TimeIterator end_time , Time dt ,
- Observer observer , StepperTag
-)
-{
- size_t obs_calls = 0;
-
- boost::for_each( make_times_time_range( stepper , system , start_state ,
- start_time , end_time , dt ) ,
- // should we use traits<Stepper>::state_type here instead of State? NO!
- obs_caller< Observer >( obs_calls , observer ) );
-
- // step integration steps gives step+1 observer calls
- return obs_calls-1;
-}
-
-
-} // namespace detail
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_INTEGRATE_DETAIL_INTEGRATE_ADAPTIVE_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/integrate/integrate.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/integrate/integrate.hpp
deleted file mode 100644
index 5300da2ba159f04d6da84495f5955081825befad..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/integrate/integrate.hpp
+++ /dev/null
@@ -1,111 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/integrate/integrate.hpp
-
- [begin_description]
- Convenience methods which choose the stepper for the current ODE.
- [end_description]
-
- Copyright 2009-2011 Karsten Ahnert
- Copyright 2009-2011 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_INTEGRATE_INTEGRATE_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_INTEGRATE_INTEGRATE_HPP_INCLUDED
-
-#include <boost/utility/enable_if.hpp>
-
-#include <boost/numeric/odeint/stepper/runge_kutta_dopri5.hpp>
-#include <boost/numeric/odeint/stepper/controlled_runge_kutta.hpp>
-#include <boost/numeric/odeint/iterator/integrate/null_observer.hpp>
-#include <boost/numeric/odeint/iterator/integrate/integrate_adaptive.hpp>
-
-// for has_value_type trait
-#include <boost/numeric/odeint/algebra/detail/extract_value_type.hpp>
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-/*
- * ToDo :
- *
- * determine type of dxdt for units
- *
- */
-template< class System , class State , class Time , class Observer >
-typename boost::enable_if< typename has_value_type<State>::type , size_t >::type
-integrate( System system , State &start_state , Time start_time , Time end_time , Time dt , Observer observer )
-{
- typedef controlled_runge_kutta< runge_kutta_dopri5< State , typename State::value_type , State , Time > > stepper_type;
- return integrate_adaptive( stepper_type() , system , start_state , start_time , end_time , dt , observer );
-}
-
-
-
-/*
- * the two overloads are needed in order to solve the forwarding problem
- */
-template< class System , class State , class Time >
-size_t integrate( System system , State &start_state , Time start_time , Time end_time , Time dt )
-{
- return integrate( system , start_state , start_time , end_time , dt , null_observer() );
-}
-
-
-/**
- * \fn integrate( System system , State &start_state , Time start_time , Time end_time , Time dt , Observer observer )
- * \brief Integrates the ODE.
- *
- * Integrates the ODE given by system from start_time to end_time starting
- * with start_state as initial condition and dt as initial time step.
- * This function uses a dense output dopri5 stepper and performs an adaptive
- * integration with step size control, thus dt changes during the integration.
- * This method uses standard error bounds of 1E-6.
- * After each step, the observer is called.
- *
- * \param system The system function to solve, hence the r.h.s. of the
- * ordinary differential equation.
- * \param start_state The initial state.
- * \param start_time Start time of the integration.
- * \param end_time End time of the integration.
- * \param dt Initial step size, will be adjusted during the integration.
- * \param observer Observer that will be called after each time step.
- * \return The number of steps performed.
- */
-
-
-/**
- * \fn integrate( System system , State &start_state , Time start_time , Time end_time , Time dt )
- * \brief Integrates the ODE without observer calls.
- *
- * Integrates the ODE given by system from start_time to end_time starting
- * with start_state as initial condition and dt as initial time step.
- * This function uses a dense output dopri5 stepper and performs an adaptive
- * integration with step size control, thus dt changes during the integration.
- * This method uses standard error bounds of 1E-6.
- * No observer is called.
- *
- * \param system The system function to solve, hence the r.h.s. of the
- * ordinary differential equation.
- * \param start_state The initial state.
- * \param start_time Start time of the integration.
- * \param end_time End time of the integration.
- * \param dt Initial step size, will be adjusted during the integration.
- * \return The number of steps performed.
- */
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-
-#endif // BOOST_NUMERIC_ODEINT_INTEGRATE_INTEGRATE_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/integrate/integrate_adaptive.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/integrate/integrate_adaptive.hpp
deleted file mode 100644
index a8d034d4112d66ed8c196c66fd99d1f72aaab4e9..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/integrate/integrate_adaptive.hpp
+++ /dev/null
@@ -1,129 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/integrate/integrate_adaptive.hpp
-
- [begin_description]
- Adaptive integration of ODEs.
- [end_description]
-
- Copyright 2009-2011 Karsten Ahnert
- Copyright 2009-2011 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_INTEGRATE_INTEGRATE_ADAPTIVE_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_INTEGRATE_INTEGRATE_ADAPTIVE_HPP_INCLUDED
-
-#include <boost/type_traits/is_same.hpp>
-
-#include <boost/numeric/odeint/stepper/stepper_categories.hpp>
-#include <boost/numeric/odeint/iterator/integrate/null_observer.hpp>
-#include <boost/numeric/odeint/iterator/integrate/detail/integrate_adaptive.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-/*
- * the two overloads are needed in order to solve the forwarding problem
- */
-template< class Stepper , class System , class State , class Time , class Observer >
-size_t integrate_adaptive(
- Stepper stepper , System system , State &start_state ,
- Time start_time , Time end_time , Time dt ,
- Observer observer )
-{
- typedef typename odeint::unwrap_reference< Stepper >::type::stepper_category stepper_category;
- return detail::integrate_adaptive(
- stepper , system , start_state ,
- start_time , end_time , dt ,
- observer , stepper_category() );
-
- /*
- * Suggestion for a new extendable version:
- *
- * integrator_adaptive< Stepper , System, State , Time , Observer , typename Stepper::stepper_category > integrator;
- * return integrator.run( stepper , system , start_state , start_time , end_time , dt , observer );
- */
-}
-
-/**
- * \brief Second version to solve the forwarding problem,
- * can be called with Boost.Range as start_state.
- */
-template< class Stepper , class System , class State , class Time , class Observer >
-size_t integrate_adaptive(
- Stepper stepper , System system , const State &start_state ,
- Time start_time , Time end_time , Time dt ,
- Observer observer )
-{
- typedef typename odeint::unwrap_reference< Stepper >::type::stepper_category stepper_category;
- return detail::integrate_adaptive(
- stepper , system , start_state ,
- start_time , end_time , dt ,
- observer , stepper_category() );
-}
-
-
-
-
-/**
- * \brief integrate_adaptive without an observer.
- */
-template< class Stepper , class System , class State , class Time >
-size_t integrate_adaptive(
- Stepper stepper , System system , State &start_state ,
- Time start_time , Time end_time , Time dt )
-{
- return integrate_adaptive( stepper , system , start_state , start_time , end_time , dt , null_observer() );
-}
-
-/**
- * \brief Second version to solve the forwarding problem,
- * can be called with Boost.Range as start_state.
- */
-template< class Stepper , class System , class State , class Time >
-size_t integrate_adaptive(
- Stepper stepper , System system , const State &start_state ,
- Time start_time , Time end_time , Time dt )
-{
- return integrate_adaptive( stepper , system , start_state , start_time , end_time , dt , null_observer() );
-}
-
-
-/************* DOXYGEN ************/
-
- /**
- * \fn integrate_adaptive( Stepper stepper , System system , State &start_state , Time start_time , Time end_time , Time dt , Observer observer )
- * \brief Integrates the ODE with adaptive step size.
- *
- * This function integrates the ODE given by system with the given stepper.
- * The observer is called after each step. If the stepper has no error
- * control, the step size remains constant and the observer is called at
- * equidistant time points t0+n*dt. If the stepper is a ControlledStepper,
- * the step size is adjusted and the observer is called in non-equidistant
- * intervals.
- *
- * \param stepper The stepper to be used for numerical integration.
- * \param system Function/Functor defining the rhs of the ODE.
- * \param start_state The initial condition x0.
- * \param start_time The initial time t0.
- * \param end_time The final integration time tend.
- * \param dt The time step between observer calls, _not_ necessarily the
- * time step of the integration.
- * \param observer Function/Functor called at equidistant time intervals.
- * \return The number of steps performed.
- */
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-
-#endif // BOOST_NUMERIC_ODEINT_INTEGRATE_INTEGRATE_ADAPTIVE_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/integrate/integrate_const.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/integrate/integrate_const.hpp
deleted file mode 100644
index b00024f807aa5ab3b36cbb94ff9a95a7ef105577..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/integrate/integrate_const.hpp
+++ /dev/null
@@ -1,158 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/integrate/integrate_const.hpp
-
- [begin_description]
- Constant integration of ODEs, meaning that the state of the ODE is observed on constant time intervals.
- The routines makes full use of adaptive and dense-output methods.
- [end_description]
-
- Copyright 2009-2011 Karsten Ahnert
- Copyright 2009-2011 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_INTEGRATE_INTEGRATE_CONST_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_INTEGRATE_INTEGRATE_CONST_HPP_INCLUDED
-
-#include <boost/type_traits/is_same.hpp>
-
-#include <boost/numeric/odeint/stepper/stepper_categories.hpp>
-#include <boost/numeric/odeint/iterator/integrate/null_observer.hpp>
-#include <boost/numeric/odeint/iterator/integrate/detail/integrate_const.hpp>
-#include <boost/numeric/odeint/iterator/integrate/detail/integrate_adaptive.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-
-
-
-/*
- * Integrates with constant time step dt.
- */
-template< class Stepper , class System , class State , class Time , class Observer >
-size_t integrate_const(
- Stepper stepper , System system , State &start_state ,
- Time start_time , Time end_time , Time dt ,
- Observer observer
-)
-{
- typedef typename odeint::unwrap_reference< Stepper >::type::stepper_category stepper_category;
- // we want to get as fast as possible to the end
- if( boost::is_same< null_observer , Observer >::value )
- {
- return detail::integrate_adaptive(
- stepper , system , start_state ,
- start_time , end_time , dt ,
- observer , stepper_category() );
- }
- else
- {
- return detail::integrate_const( stepper , system , start_state ,
- start_time , end_time , dt ,
- observer , stepper_category() );
- }
-}
-
-/**
- * \brief Second version to solve the forwarding problem,
- * can be called with Boost.Range as start_state.
- */
-template< class Stepper , class System , class State , class Time , class Observer >
-size_t integrate_const(
- Stepper stepper , System system , const State &start_state ,
- Time start_time , Time end_time , Time dt ,
- Observer observer
-)
-{
- typedef typename odeint::unwrap_reference< Stepper >::type::stepper_category stepper_category;
- // we want to get as fast as possible to the end
- if( boost::is_same< null_observer , Observer >::value )
- {
- return detail::integrate_adaptive(
- stepper , system , start_state ,
- start_time , end_time , dt ,
- observer , stepper_category() );
- }
- else
- {
- return detail::integrate_const( stepper , system , start_state ,
- start_time , end_time , dt ,
- observer , stepper_category() );
- }
-}
-
-
-
-
-
-/**
- * \brief integrate_const without observer calls
- */
-template< class Stepper , class System , class State , class Time >
-size_t integrate_const(
- Stepper stepper , System system , State &start_state ,
- Time start_time , Time end_time , Time dt
-)
-{
- return integrate_const( stepper , system , start_state , start_time , end_time , dt , null_observer() );
-}
-
-/**
- * \brief Second version to solve the forwarding problem,
- * can be called with Boost.Range as start_state.
- */
-template< class Stepper , class System , class State , class Time >
-size_t integrate_const(
- Stepper stepper , System system , const State &start_state ,
- Time start_time , Time end_time , Time dt
-)
-{
- return integrate_const( stepper , system , start_state , start_time , end_time , dt , null_observer() );
-}
-
-
-
-
-
-
-/********* DOXYGEN *********/
- /**
- * \fn integrate_const( Stepper stepper , System system , State &start_state , Time start_time , Time end_time , Time dt , Observer observer )
- * \brief Integrates the ODE with constant step size.
- *
- * Integrates the ODE defined by system using the given stepper.
- * This method ensures that the observer is called at constant intervals dt.
- * If the Stepper is a normal stepper without step size control, dt is also
- * used for the numerical scheme. If a ControlledStepper is provided, the
- * algorithm might reduce the step size to meet the error bounds, but it is
- * ensured that the observer is always called at equidistant time points
- * t0 + n*dt. If a DenseOutputStepper is used, the step size also may vary
- * and the dense output is used to call the observer at equidistant time
- * points.
- *
- * \param stepper The stepper to be used for numerical integration.
- * \param system Function/Functor defining the rhs of the ODE.
- * \param start_state The initial condition x0.
- * \param start_time The initial time t0.
- * \param end_time The final integration time tend.
- * \param dt The time step between observer calls, _not_ necessarily the
- * time step of the integration.
- * \param observer Function/Functor called at equidistant time intervals.
- * \return The number of steps performed.
- */
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-
-#endif // BOOST_NUMERIC_ODEINT_INTEGRATE_INTEGRATE_CONST_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/integrate/integrate_n_steps.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/integrate/integrate_n_steps.hpp
deleted file mode 100644
index d75cb306a372d15fd248c571560afccc26de516c..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/integrate/integrate_n_steps.hpp
+++ /dev/null
@@ -1,125 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/integrate/integrate_n_steps.hpp
-
- [begin_description]
- Integration of n steps with constant time size. Adaptive and dense-output methods are fully supported.
- [end_description]
-
- Copyright 2009-2011 Karsten Ahnert
- Copyright 2009-2011 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_INTEGRATE_INTEGRATE_N_STEPS_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_INTEGRATE_INTEGRATE_N_STEPS_HPP_INCLUDED
-
-#include <boost/type_traits/is_same.hpp>
-
-#include <boost/numeric/odeint/stepper/stepper_categories.hpp>
-#include <boost/numeric/odeint/iterator/integrate/null_observer.hpp>
-#include <boost/numeric/odeint/iterator/integrate/detail/integrate_n_steps.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-/*
- * Integrates n steps
- *
- * the two overloads are needed in order to solve the forwarding problem
- */
-template< class Stepper , class System , class State , class Time , class Observer>
-Time integrate_n_steps(
- Stepper stepper , System system , State &start_state ,
- Time start_time , Time dt , size_t num_of_steps ,
- Observer observer )
-{
- typedef typename odeint::unwrap_reference< Stepper >::type::stepper_category stepper_category;
- return detail::integrate_n_steps(
- stepper , system , start_state ,
- start_time , dt , num_of_steps ,
- observer , stepper_category() );
-}
-
-/**
- * \brief Solves the forwarding problem, can be called with Boost.Range as start_state.
- */
-template< class Stepper , class System , class State , class Time , class Observer >
-Time integrate_n_steps(
- Stepper stepper , System system , const State &start_state ,
- Time start_time , Time dt , size_t num_of_steps ,
- Observer observer )
-{
- typedef typename odeint::unwrap_reference< Stepper >::type::stepper_category stepper_category;
- return detail::integrate_n_steps(
- stepper , system , start_state ,
- start_time , dt , num_of_steps ,
- observer , stepper_category() );
-}
-
-
-/**
- * \brief The same function as above, but without observer calls.
- */
-template< class Stepper , class System , class State , class Time >
-Time integrate_n_steps(
- Stepper stepper , System system , State &start_state ,
- Time start_time , Time dt , size_t num_of_steps )
-{
- return integrate_n_steps( stepper , system , start_state , start_time , dt , num_of_steps , null_observer() );
-}
-
-/**
- * \brief Solves the forwarding problem, can be called with Boost.Range as start_state.
- */
-template< class Stepper , class System , class State , class Time >
-Time integrate_n_steps(
- Stepper stepper , System system , const State &start_state ,
- Time start_time , Time dt , size_t num_of_steps )
-{
- return integrate_n_steps( stepper , system , start_state , start_time , dt , num_of_steps , null_observer() );
-}
-
-
-
-/************* DOXYGEN *************/
- /**
- * \fn Time integrate_n_steps( Stepper stepper , System system , State &start_state , Time start_time , Time dt , size_t num_of_steps , Observer observer )
- * \brief Integrates the ODE with constant step size.
- *
- * This function is similar to integrate_const. The observer is called at
- * equidistant time intervals t0 + n*dt.
- * If the Stepper is a normal stepper without step size control, dt is also
- * used for the numerical scheme. If a ControlledStepper is provided, the
- * algorithm might reduce the step size to meet the error bounds, but it is
- * ensured that the observer is always called at equidistant time points
- * t0 + n*dt. If a DenseOutputStepper is used, the step size also may vary
- * and the dense output is used to call the observer at equidistant time
- * points. The final integration time is always t0 + num_of_steps*dt.
- *
- * \param stepper The stepper to be used for numerical integration.
- * \param system Function/Functor defining the rhs of the ODE.
- * \param start_state The initial condition x0.
- * \param start_time The initial time t0.
- * \param dt The time step between observer calls, _not_ necessarily the
- * time step of the integration.
- * \param num_of_steps Number of steps to be performed
- * \param observer Function/Functor called at equidistant time intervals.
- * \return The number of steps performed.
- */
-
-
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-
-#endif // BOOST_NUMERIC_ODEINT_INTEGRATE_INTEGRATE_N_STEPS_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/integrate/integrate_times.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/integrate/integrate_times.hpp
deleted file mode 100644
index 55101ec9d00b254fbc933d0fba7ac65122188c3b..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/integrate/integrate_times.hpp
+++ /dev/null
@@ -1,133 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/integrate/integrate_times.hpp
-
- [begin_description]
- Integration of ODEs with observation at user defined points
- [end_description]
-
- Copyright 2009-2011 Karsten Ahnert
- Copyright 2009-2011 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_INTEGRATE_INTEGRATE_TIMES_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_INTEGRATE_INTEGRATE_TIMES_HPP_INCLUDED
-
-#include <boost/type_traits/is_same.hpp>
-
-#include <boost/range.hpp>
-
-#include <boost/numeric/odeint/stepper/stepper_categories.hpp>
-#include <boost/numeric/odeint/iterator/integrate/null_observer.hpp>
-#include <boost/numeric/odeint/iterator/integrate/detail/integrate_times.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-/*
- * the two overloads are needed in order to solve the forwarding problem
- */
-template< class Stepper , class System , class State , class TimeIterator , class Time , class Observer >
-size_t integrate_times(
- Stepper stepper , System system , State &start_state ,
- TimeIterator times_start , TimeIterator times_end , Time dt ,
- Observer observer )
-{
- typedef typename odeint::unwrap_reference< Stepper >::type::stepper_category stepper_category;
- return detail::integrate_times(
- stepper , system , start_state ,
- times_start , times_end , dt ,
- observer , stepper_category() );
-}
-
-/**
- * \brief Solves the forwarding problem, can be called with Boost.Range as start_state.
- */
-template< class Stepper , class System , class State , class TimeIterator , class Time , class Observer >
-size_t integrate_times(
- Stepper stepper , System system , const State &start_state ,
- TimeIterator times_start , TimeIterator times_end , Time dt ,
- Observer observer )
-{
- typedef typename odeint::unwrap_reference< Stepper >::type::stepper_category stepper_category;
- return detail::integrate_times(
- stepper , system , start_state ,
- times_start , times_end , dt ,
- observer , stepper_category() );
-}
-
-/**
- * \brief The same function as above, but without observer calls.
- */
-template< class Stepper , class System , class State , class TimeRange , class Time , class Observer >
-size_t integrate_times(
- Stepper stepper , System system , State &start_state ,
- const TimeRange × , Time dt ,
- Observer observer )
-{
- return integrate_times(
- stepper , system , start_state ,
- boost::begin( times ) , boost::end( times ) , dt , observer );
-}
-
-/**
- * \brief Solves the forwarding problem, can be called with Boost.Range as start_state.
- */
-template< class Stepper , class System , class State , class TimeRange , class Time , class Observer >
-size_t integrate_times(
- Stepper stepper , System system , const State &start_state ,
- const TimeRange × , Time dt ,
- Observer observer )
-{
- return integrate_times(
- stepper , system , start_state ,
- boost::begin( times ) , boost::end( times ) , dt , observer );
-}
-
-
-
-
-/********* DOXYGEN ***********/
-
- /**
- * \fn size_t integrate_times( Stepper stepper , System system , State &start_state , TimeIterator times_start , TimeIterator times_end , Time dt , Observer observer )
- * \brief Integrates the ODE with observer calls at given time points.
- *
- * Integrates the ODE given by system using the given stepper. This function
- * does observer calls at the subsequent time points given by the range
- * times_start, times_end. If the stepper has not step size control, the
- * step size might be reduced occasionally to ensure observer calls exactly
- * at the time points from the given sequence. If the stepper is a
- * ControlledStepper, the step size is adjusted to meet the error bounds,
- * but also might be reduced occasionally to ensure correct observer calls.
- * If a DenseOutputStepper is provided, the dense output functionality is
- * used to call the observer at the given times. The end time of the
- * integration is always *(end_time-1).
- *
- * \param stepper The stepper to be used for numerical integration.
- * \param system Function/Functor defining the rhs of the ODE.
- * \param start_state The initial condition x0.
- * \param times_start Iterator to the start time
- * \param times_end Iterator to the end time
- * \param dt The time step between observer calls, _not_ necessarily the
- * time step of the integration.
- * \param observer Function/Functor called at equidistant time intervals.
- * \return The number of steps performed.
- */
-
-
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-
-#endif // BOOST_NUMERIC_ODEINT_INTEGRATE_INTEGRATE_TIMES_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/integrate/null_observer.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/integrate/null_observer.hpp
deleted file mode 100644
index 4d9a070a62d0102f2dcdfe44e224522651417327..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/integrate/null_observer.hpp
+++ /dev/null
@@ -1,38 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/integrate/null_observer.hpp
-
- [begin_description]
- null_observer
- [end_description]
-
- Copyright 2009-2011 Karsten Ahnert
- Copyright 2009-2011 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_INTEGRATE_NULL_OBSERVER_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_INTEGRATE_NULL_OBSERVER_HPP_INCLUDED
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-struct null_observer
-{
- template< class State , class Time >
- void operator()( const State& /* x */ , Time /* t */ ) const
- {
-
- }
-};
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-#endif // BOOST_NUMERIC_ODEINT_INTEGRATE_NULL_OBSERVER_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/integrate/observer_collection.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/integrate/observer_collection.hpp
deleted file mode 100644
index 26101a3afc16fa4061a18f1fe646ba143a2effea..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/integrate/observer_collection.hpp
+++ /dev/null
@@ -1,56 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/integrate/observer_collection.hpp
-
- [begin_description]
- Collection of observers, which are all called during the evolution of the ODE.
- [end_description]
-
- Copyright 2009-2011 Karsten Ahnert
- Copyright 2009-2011 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_INTEGRATE_OBSERVER_COLLECTION_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_INTEGRATE_OBSERVER_COLLECTION_HPP_INCLUDED
-
-#include <vector>
-
-#include <boost/function.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-template< class State , class Time >
-class observer_collection
-{
-public:
-
- typedef boost::function< void( const State& , const Time& ) > observer_type;
- typedef std::vector< observer_type > collection_type;
-
- void operator()( const State& x , Time t )
- {
- for( size_t i=0 ; i<m_observers.size() ; ++i )
- m_observers[i]( x , t );
- }
-
- collection_type& observers( void ) { return m_observers; }
- const collection_type& observers( void ) const { return m_observers; }
-
-private:
-
- collection_type m_observers;
-};
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_INTEGRATE_OBSERVER_COLLECTION_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/n_step_iterator.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/n_step_iterator.hpp
deleted file mode 100644
index c9733107b5e38a4e2d9d2844d3d99970e480bd54..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/n_step_iterator.hpp
+++ /dev/null
@@ -1,168 +0,0 @@
-
-/*
- [auto_generated]
- boost/numeric/odeint/iterator/n_step_iterator.hpp
-
- [begin_description]
- Iterator for iterating through the solution of an ODE with constant step size performing exactly n steps.
- [end_description]
-
- Copyright 2009-2013 Karsten Ahnert
- Copyright 2009-2013 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_ITERATOR_N_STEP_ITERATOR_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_ITERATOR_N_STEP_ITERATOR_HPP_INCLUDED
-
-
-#include <boost/numeric/odeint/util/stepper_traits.hpp>
-#include <boost/numeric/odeint/stepper/stepper_categories.hpp>
-#include <boost/numeric/odeint/iterator/detail/ode_iterator_base.hpp>
-#include <boost/numeric/odeint/iterator/impl/n_step_iterator_impl.hpp>
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
- /* use the n_step_iterator_impl with the right tags */
- template< class Stepper , class System , class State
-#ifndef DOXYGEN_SKIP
- , class StepperTag = typename base_tag< typename traits::stepper_category< Stepper >::type >::type
-#endif
- >
- class n_step_iterator : public n_step_iterator_impl<
- n_step_iterator< Stepper , System , State , StepperTag > ,
- Stepper , System , State , detail::ode_state_iterator_tag , StepperTag
- >
- {
- typedef typename traits::time_type< Stepper >::type time_type;
- typedef n_step_iterator< Stepper , System , State , StepperTag > iterator_type;
-
- public:
- n_step_iterator( Stepper stepper , System sys , State &s , time_type t , time_type dt , size_t num_of_steps )
- : n_step_iterator_impl< iterator_type , Stepper , System , State , detail::ode_state_iterator_tag , StepperTag >( stepper , sys , s , t , dt , num_of_steps )
- {}
-
- n_step_iterator( Stepper stepper , System sys , State &s )
- : n_step_iterator_impl< iterator_type , Stepper , System , State , detail::ode_state_iterator_tag , StepperTag >( stepper , sys , s )
- {}
- };
-
- /* make functions */
-
- template< class Stepper , class System , class State >
- n_step_iterator< Stepper , System, State > make_n_step_iterator_begin(
- Stepper stepper ,
- System system ,
- State &x ,
- typename traits::time_type< Stepper >::type t ,
- typename traits::time_type< Stepper >::type dt ,
- size_t num_of_steps )
- {
- return n_step_iterator< Stepper , System , State >( stepper , system , x , t , dt , num_of_steps );
- }
-
- template< class Stepper , class System , class State >
- n_step_iterator< Stepper , System , State > make_n_step_iterator_end(
- Stepper stepper ,
- System system ,
- State &x )
- {
- return n_step_iterator< Stepper , System , State >( stepper , system , x );
- }
-
- template< class Stepper , class System , class State >
- std::pair< n_step_iterator< Stepper , System , State > , n_step_iterator< Stepper , System , State > >
- make_n_step_range(
- Stepper stepper ,
- System system ,
- State &x ,
- typename traits::time_type< Stepper >::type t ,
- typename traits::time_type< Stepper >::type dt ,
- size_t num_of_steps )
- {
- return std::make_pair(
- n_step_iterator< Stepper , System , State >( stepper , system , x , t , dt , num_of_steps ) ,
- n_step_iterator< Stepper , System , State >( stepper , system , x )
- );
- }
-
-
- /**
- * \class n_step_iterator
- *
- * \brief ODE Iterator with constant step size. The value type of this iterator is the state type of the stepper.
- *
- * Implements an iterator representing the solution of an ODE starting from t
- * with n steps and a constant step size dt.
- * After each iteration the iterator dereferences to the state x at the next
- * time t+dt.
- * This iterator can be used with Steppers and
- * DenseOutputSteppers and it always makes use of the all the given steppers
- * capabilities. A for_each over such an iterator range behaves similar to
- * the integrate_n_steps routine.
- *
- * n_step_iterator is a model of single-pass iterator.
- *
- * The value type of this iterator is the state type of the stepper. Hence one can only access the state and not the current time.
- *
- * \tparam Stepper The stepper type which should be used during the iteration.
- * \tparam System The type of the system function (ODE) which should be solved.
- * \tparam State The state type of the ODE.
- */
-
-
- /**
- * \fn make_n_step_iterator_begin( Stepper stepper , System system , State &x , typename traits::time_type< Stepper >::type t , typename traits::time_type< Stepper >::type dt , size_t num_of_steps )
- *
- * \brief Factory function for n_step_iterator. Constructs a begin iterator.
- *
- * \param stepper The stepper to use during the iteration.
- * \param system The system function (ODE) to solve.
- * \param x The initial state. const_step_iterator stores a reference of s and changes its value during the iteration.
- * \param t The initial time.
- * \param dt The initial time step.
- * \param num_of_steps The number of steps to be executed.
- * \returns The n-step iterator.
- */
-
-
- /**
- * \fn make_n_step_iterator_end( Stepper stepper , System system , State &x )
- * \brief Factory function for n_step_iterator. Constructs an end iterator.
- *
- * \param stepper The stepper to use during the iteration.
- * \param system The system function (ODE) to solve.
- * \param x The initial state. const_step_iterator stores a reference of s and changes its value during the iteration.
- * \returns The const_step_iterator.
- */
-
-
- /**
- * \fn make_n_step_range( Stepper stepper , System system , State &x , typename traits::time_type< Stepper >::type t , typename traits::time_type< Stepper >::type dt , , size_t num_of_steps )
- *
- * \brief Factory function to construct a single pass range of n-step iterators. A range is here a pair
- * of n_step_iterator.
- *
- * \param stepper The stepper to use during the iteration.
- * \param system The system function (ODE) to solve.
- * \param x The initial state. const_step_iterator store a reference of s and changes its value during the iteration.
- * \param t The initial time.
- * \param dt The initial time step.
- * \param num_of_steps The number of steps to be executed.
- * \returns The n-step range.
- */
-
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-#endif // BOOST_NUMERIC_ODEINT_ITERATOR_CONST_N_STEP_ITERATOR_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/n_step_time_iterator.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/n_step_time_iterator.hpp
deleted file mode 100644
index acede2ca3c7534b5ff40793e5fc6dddc5f97f43b..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/n_step_time_iterator.hpp
+++ /dev/null
@@ -1,169 +0,0 @@
-
-/*
- [auto_generated]
- boost/numeric/odeint/iterator/n_step_time_iterator.hpp
-
- [begin_description]
- Iterator for iterating through the solution of an ODE with constant step size performing exactly n steps.
- The dereferenced type contains also the time.
- [end_description]
-
- Copyright 2009-2013 Karsten Ahnert
- Copyright 2009-2013 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_ITERATOR_N_STEP_TIME_ITERATOR_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_ITERATOR_N_STEP_TIME_ITERATOR_HPP_INCLUDED
-
-
-#include <boost/numeric/odeint/util/stepper_traits.hpp>
-#include <boost/numeric/odeint/stepper/stepper_categories.hpp>
-#include <boost/numeric/odeint/iterator/detail/ode_iterator_base.hpp>
-#include <boost/numeric/odeint/iterator/impl/n_step_iterator_impl.hpp>
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
- /* use the n_step_iterator_impl with the right tags */
- template< class Stepper , class System , class State
-#ifndef DOXYGEN_SKIP
- , class StepperTag = typename base_tag< typename traits::stepper_category< Stepper >::type >::type
-#endif
- >
- class n_step_time_iterator : public n_step_iterator_impl<
- n_step_time_iterator< Stepper , System , State , StepperTag > ,
- Stepper , System , State , detail::ode_state_time_iterator_tag , StepperTag
- >
- {
- typedef typename traits::time_type< Stepper >::type time_type;
- typedef n_step_time_iterator< Stepper , System , State , StepperTag > iterator_type;
-
- public:
- n_step_time_iterator( Stepper stepper , System sys , State &s , time_type t , time_type dt , size_t num_of_steps )
- : n_step_iterator_impl< iterator_type , Stepper , System , State , detail::ode_state_time_iterator_tag , StepperTag >( stepper , sys , s , t , dt , num_of_steps )
- {}
-
- n_step_time_iterator( Stepper stepper , System sys , State &s )
- : n_step_iterator_impl< iterator_type , Stepper , System , State , detail::ode_state_time_iterator_tag , StepperTag >( stepper , sys , s )
- {}
- };
-
- /* make functions */
-
- template< class Stepper , class System , class State >
- n_step_time_iterator< Stepper , System, State > make_n_step_time_iterator_begin(
- Stepper stepper ,
- System system ,
- State &x ,
- typename traits::time_type< Stepper >::type t ,
- typename traits::time_type< Stepper >::type dt ,
- size_t num_of_steps )
- {
- return n_step_time_iterator< Stepper , System , State >( stepper , system , x , t , dt , num_of_steps );
- }
-
- template< class Stepper , class System , class State >
- n_step_time_iterator< Stepper , System , State > make_n_step_time_iterator_end(
- Stepper stepper ,
- System system ,
- State &x )
- {
- return n_step_time_iterator< Stepper , System , State >( stepper , system , x );
- }
-
- template< class Stepper , class System , class State >
- std::pair< n_step_time_iterator< Stepper , System , State > , n_step_time_iterator< Stepper , System , State > >
- make_n_step_time_range(
- Stepper stepper ,
- System system ,
- State &x ,
- typename traits::time_type< Stepper >::type t ,
- typename traits::time_type< Stepper >::type dt ,
- size_t num_of_steps )
- {
- return std::make_pair(
- n_step_time_iterator< Stepper , System , State >( stepper , system , x , t , dt , num_of_steps ) ,
- n_step_time_iterator< Stepper , System , State >( stepper , system , x )
- );
- }
-
-
- /**
- * \class n_step_time_iterator
- *
- * \brief ODE Iterator with constant step size. The value type of this iterator is a std::pair containing state and time.
- *
- * Implements an iterator representing the solution of an ODE starting from t
- * with n steps and a constant step size dt.
- * After each iteration the iterator dereferences to a pair of state and time at the next
- * time t+dt.
- * This iterator can be used with Steppers and
- * DenseOutputSteppers and it always makes use of the all the given steppers
- * capabilities. A for_each over such an iterator range behaves similar to
- * the integrate_n_steps routine.
- *
- * n_step_time_iterator is a model of single-pass iterator.
- *
- * The value type of this iterator is pair of state and time.
- *
- * \tparam Stepper The stepper type which should be used during the iteration.
- * \tparam System The type of the system function (ODE) which should be solved.
- * \tparam State The state type of the ODE.
- */
-
-
- /**
- * \fn make_n_step_time_iterator_begin( Stepper stepper , System system , State &x , typename traits::time_type< Stepper >::type t , typename traits::time_type< Stepper >::type dt , size_t num_of_steps )
- *
- * \brief Factory function for n_step_time_iterator. Constructs a begin iterator.
- *
- * \param stepper The stepper to use during the iteration.
- * \param system The system function (ODE) to solve.
- * \param x The initial state. const_step_iterator stores a reference of s and changes its value during the iteration.
- * \param t The initial time.
- * \param dt The initial time step.
- * \param num_of_steps The number of steps to be executed.
- * \returns The n-step iterator.
- */
-
-
- /**
- * \fn make_n_step_time_iterator_end( Stepper stepper , System system , State &x )
- * \brief Factory function for n_step_time_iterator. Constructs an end iterator.
- *
- * \param stepper The stepper to use during the iteration.
- * \param system The system function (ODE) to solve.
- * \param x The initial state. const_step_iterator stores a reference of s and changes its value during the iteration.
- * \returns The const_step_iterator.
- */
-
-
- /**
- * \fn make_n_step_time_range( Stepper stepper , System system , State &x , typename traits::time_type< Stepper >::type t , typename traits::time_type< Stepper >::type dt , size_t num_of_steps )
- *
- * \brief Factory function to construct a single pass range of n-step iterators. A range is here a pair
- * of n_step_time_iterator.
- *
- * \param stepper The stepper to use during the iteration.
- * \param system The system function (ODE) to solve.
- * \param x The initial state. const_step_iterator store a reference of s and changes its value during the iteration.
- * \param t The initial time.
- * \param dt The initial time step.
- * \param num_of_steps The number of steps to be executed.
- * \returns The n-step range.
- */
-
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-#endif // BOOST_NUMERIC_ODEINT_ITERATOR_CONST_N_STEP_TIME_ITERATOR_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/times_iterator.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/times_iterator.hpp
deleted file mode 100644
index dcf5733269f7d12f88cfe446d3aa9b4c78095325..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/times_iterator.hpp
+++ /dev/null
@@ -1,189 +0,0 @@
-
-/*
- [auto_generated]
- boost/numeric/odeint/iterator/times_iterator.hpp
-
- [begin_description]
- Iterator for iterating through the solution of an ODE with oscillator calls at times from a given sequence.
- [end_description]
-
- Copyright 2009-2013 Karsten Ahnert
- Copyright 2009-2013 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_ITERATOR_TIMES_ITERATOR_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_ITERATOR_TIMES_ITERATOR_HPP_INCLUDED
-
-
-#include <boost/numeric/odeint/util/stepper_traits.hpp>
-#include <boost/numeric/odeint/stepper/stepper_categories.hpp>
-#include <boost/numeric/odeint/iterator/detail/ode_iterator_base.hpp>
-#include <boost/numeric/odeint/iterator/impl/times_iterator_impl.hpp>
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
- /* use the times_iterator_impl with the right tags */
- template< class Stepper , class System , class State , class TimeIterator
-#ifndef DOXYGEN_SKIP
- , class StepperTag = typename base_tag< typename traits::stepper_category< Stepper >::type >::type
-#endif
- >
- class times_iterator : public times_iterator_impl<
- times_iterator< Stepper , System , State , TimeIterator , StepperTag > ,
- Stepper , System , State , TimeIterator , detail::ode_state_iterator_tag , StepperTag
- >
- {
- typedef typename traits::time_type< Stepper >::type time_type;
- typedef times_iterator< Stepper , System , State , TimeIterator , StepperTag > iterator_type;
-
- public:
- times_iterator( Stepper stepper , System sys , State &s ,
- TimeIterator t_start , TimeIterator t_end , time_type dt )
- : times_iterator_impl< iterator_type , Stepper , System , State , TimeIterator, detail::ode_state_iterator_tag , StepperTag >( stepper , sys , s , t_start , t_end , dt )
- {}
-
- times_iterator( Stepper stepper , System sys , State &s )
- : times_iterator_impl< iterator_type , Stepper , System , State , TimeIterator , detail::ode_state_iterator_tag , StepperTag >( stepper , sys , s )
- {}
- };
-
- /* make functions */
-
- template< class Stepper , class System , class State , class TimeIterator >
- times_iterator< Stepper , System, State , TimeIterator > make_times_iterator_begin(
- Stepper stepper ,
- System system ,
- State &x ,
- TimeIterator t_start ,
- TimeIterator t_end ,
- typename traits::time_type< Stepper >::type dt )
- {
- return times_iterator< Stepper , System , State , TimeIterator >( stepper , system , x , t_start , t_end , dt );
- }
-
- // ToDo: requires to specifically provide the TimeIterator template parameter, can this be improved?
- template< class TimeIterator , class Stepper , class System , class State >
- times_iterator< Stepper , System , State , TimeIterator > make_times_iterator_end(
- Stepper stepper ,
- System system ,
- State &x )
- //TimeIterator t_end )
- {
- return times_iterator< Stepper , System , State , TimeIterator >( stepper , system , x );
- }
-
- template< class Stepper , class System , class State , class TimeIterator >
- std::pair< times_iterator< Stepper , System , State , TimeIterator > ,
- times_iterator< Stepper , System , State , TimeIterator > >
- make_times_range(
- Stepper stepper ,
- System system ,
- State &x ,
- TimeIterator t_start ,
- TimeIterator t_end ,
- typename traits::time_type< Stepper >::type dt )
- {
- return std::make_pair(
- times_iterator< Stepper , System , State , TimeIterator >( stepper , system , x , t_start , t_end , dt ) ,
- times_iterator< Stepper , System , State , TimeIterator >( stepper , system , x )
- );
- }
-
-
- /**
- * \class times_iterator
- *
- * \brief ODE Iterator with given evaluation points. The value type of this iterator is the state type of the stepper.
- *
- * Implements an iterator representing the solution of an ODE from *t_start
- * to *t_end evaluated at time points given by the sequence t_start to t_end.
- * t_start and t_end are iterators representing a sequence of time points
- * where the solution of the ODE should be evaluated.
- * After each iteration the iterator dereferences to the state x at the next
- * time *t_start++ until t_end is reached.
- * This iterator can be used with Steppers, ControlledSteppers and
- * DenseOutputSteppers and it always makes use of the all the given steppers
- * capabilities. A for_each over such an iterator range behaves similar to
- * the integrate_times routine.
- *
- * times_iterator is a model of single-pass iterator.
- *
- * The value type of this iterator is the state type of the stepper. Hence one can only access the state and not the current time.
- *
- * \tparam Stepper The stepper type which should be used during the iteration.
- * \tparam System The type of the system function (ODE) which should be solved.
- * \tparam State The state type of the ODE.
- * \tparam TimeIterator The iterator type for the sequence of time points.
- */
-
-
-
- /**
- * \fn make_times_iterator_begin( Stepper stepper ,
- System system ,
- State &x ,
- TimeIterator t_start ,
- TimeIterator t_end ,
- typename traits::time_type< Stepper >::type dt )
- *
- * \brief Factory function for times_iterator. Constructs a begin iterator.
- *
- * \param stepper The stepper to use during the iteration.
- * \param system The system function (ODE) to solve.
- * \param x The initial state. const_step_iterator stores a reference of s and changes its value during the iteration.
- * \param t_start Begin iterator of the sequence of evaluation time points.
- * \param t_end End iterator of the sequence of evaluation time points.
- * \param dt The initial time step.
- * \returns The times iterator.
- */
-
-
- /**
- * \fn make_times_iterator_end( Stepper stepper , System system , State &x )
- * \brief Factory function for times_iterator. Constructs an end iterator.
- *
- * \tparam TimesIterator The iterator type of the time sequence, must be specifically provided.
- *
- * \param stepper The stepper to use during the iteration.
- * \param system The system function (ODE) to solve.
- * \param x The initial state. const_step_iterator stores a reference of s and changes its value during the iteration.
- * \returns The times iterator.
- *
- * This function needs the TimeIterator type specifically defined as a
- * template parameter.
- */
-
-
- /**
- * \fn make_times_range( Stepper stepper , System system , State &x ,
- TimeIterator t_start ,
- TimeIterator t_end ,
- typename traits::time_type< Stepper >::type dt )
- *
- * \brief Factory function to construct a single pass range of times iterators. A range is here a pair
- * of times_iterator.
- *
- * \param stepper The stepper to use during the iteration.
- * \param system The system function (ODE) to solve.
- * \param x The initial state. const_step_iterator store a reference of s and changes its value during the iteration.
- * \param t_start Begin iterator of the sequence of evaluation time points.
- * \param t_end End iterator of the sequence of evaluation time points.
- * \param dt The initial time step.
- * \returns The times iterator range.
- */
-
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-#endif // BOOST_NUMERIC_ODEINT_ITERATOR_TIMES_ITERATOR_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/times_time_iterator.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/times_time_iterator.hpp
deleted file mode 100644
index 1935d053ffc1c5a8a38ee442d8da443ec6426dc4..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/iterator/times_time_iterator.hpp
+++ /dev/null
@@ -1,193 +0,0 @@
-
-/*
- [auto_generated]
- boost/numeric/odeint/iterator/times_time_iterator.hpp
-
- [begin_description]
- Iterator for iterating through the solution of an ODE with oscillator calls at times from a given sequence.
- The dereferenced type contains also the time.
- [end_description]
-
- Copyright 2009-2013 Karsten Ahnert
- Copyright 2009-2013 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_ITERATOR_TIMES_TIME_ITERATOR_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_ITERATOR_TIMES_TIME_ITERATOR_HPP_INCLUDED
-
-
-#include <boost/numeric/odeint/util/stepper_traits.hpp>
-#include <boost/numeric/odeint/stepper/stepper_categories.hpp>
-#include <boost/numeric/odeint/iterator/detail/ode_iterator_base.hpp>
-#include <boost/numeric/odeint/iterator/impl/times_iterator_impl.hpp>
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
- /* use the times_iterator_impl with the right tags */
- template< class Stepper , class System , class State , class TimeIterator
-#ifndef DOXYGEN_SKIP
- , class StepperTag = typename base_tag< typename traits::stepper_category< Stepper >::type >::type
-#endif
- >
- class times_time_iterator : public times_iterator_impl<
- times_time_iterator< Stepper , System , State , TimeIterator , StepperTag > ,
- Stepper , System , State , TimeIterator , detail::ode_state_time_iterator_tag , StepperTag
- >
- {
- typedef typename traits::time_type< Stepper >::type time_type;
- typedef times_time_iterator< Stepper , System , State , TimeIterator , StepperTag > iterator_type;
-
- public:
- times_time_iterator( Stepper stepper , System sys , State &s ,
- TimeIterator t_start , TimeIterator t_end , time_type dt )
- : times_iterator_impl< iterator_type , Stepper , System , State , TimeIterator, detail::ode_state_time_iterator_tag , StepperTag >( stepper , sys , s , t_start , t_end , dt )
- {}
-
- times_time_iterator( Stepper stepper , System sys , State &s )
- : times_iterator_impl< iterator_type , Stepper , System , State , TimeIterator , detail::ode_state_time_iterator_tag , StepperTag >( stepper , sys , s )
- {}
- };
-
- /* make functions */
-
- template< class Stepper , class System , class State , class TimeIterator >
- times_time_iterator< Stepper , System, State , TimeIterator > make_times_time_iterator_begin(
- Stepper stepper ,
- System system ,
- State &x ,
- TimeIterator t_start ,
- TimeIterator t_end ,
- typename traits::time_type< Stepper >::type dt )
- {
- return times_time_iterator< Stepper , System , State , TimeIterator >( stepper , system , x , t_start , t_end , dt );
- }
-
- // ToDo: requires to specifically provide the TimeIterator template parameter, can this be improved?
- template< class TimeIterator , class Stepper , class System , class State >
- times_time_iterator< Stepper , System , State , TimeIterator > make_times_time_iterator_end(
- Stepper stepper ,
- System system ,
- State &x )
- //TimeIterator t_end )
- {
- return times_time_iterator< Stepper , System , State , TimeIterator >( stepper , system , x );
- }
-
- template< class Stepper , class System , class State , class TimeIterator >
- std::pair< times_time_iterator< Stepper , System , State , TimeIterator > ,
- times_time_iterator< Stepper , System , State , TimeIterator > >
- make_times_time_range(
- Stepper stepper ,
- System system ,
- State &x ,
- TimeIterator t_start ,
- TimeIterator t_end ,
- typename traits::time_type< Stepper >::type dt )
- {
- return std::make_pair(
- times_time_iterator< Stepper , System , State , TimeIterator >( stepper , system , x , t_start , t_end , dt ) ,
- times_time_iterator< Stepper , System , State , TimeIterator >( stepper , system , x )
- );
- }
-
-
-
-
-
- /**
- * \class times_time_iterator
- *
- * \brief ODE Iterator with given evaluation points. The value type of this iterator is a std::pair containing state and time.
- *
- * Implements an iterator representing the solution of an ODE from *t_start
- * to *t_end evaluated at time points given by the sequence t_start to t_end.
- * t_start and t_end are iterators representing a sequence of time points
- * where the solution of the ODE should be evaluated.
- * After each iteration the iterator dereferences to a pair with the state
- * and the time at the next evaluation point *t_start++ until t_end is reached.
- * This iterator can be used with Steppers, ControlledSteppers and
- * DenseOutputSteppers and it always makes use of the all the given steppers
- * capabilities. A for_each over such an iterator range behaves similar to
- * the integrate_times routine.
- *
- * times_time_iterator is a model of single-pass iterator.
- *
- * The value type of this iterator is a pair of state and time type.
- *
- * \tparam Stepper The stepper type which should be used during the iteration.
- * \tparam System The type of the system function (ODE) which should be solved.
- * \tparam State The state type of the ODE.
- * \tparam TimeIterator The iterator type for the sequence of time points.
- */
-
-
-
- /**
- * \fn make_times_time_iterator_begin( Stepper stepper ,
- System system ,
- State &x ,
- TimeIterator t_start ,
- TimeIterator t_end ,
- typename traits::time_type< Stepper >::type dt )
- *
- * \brief Factory function for times_time_iterator. Constructs a begin iterator.
- *
- * \param stepper The stepper to use during the iteration.
- * \param system The system function (ODE) to solve.
- * \param x The initial state. const_step_iterator stores a reference of s and changes its value during the iteration.
- * \param t_start Begin iterator of the sequence of evaluation time points.
- * \param t_end End iterator of the sequence of evaluation time points.
- * \param dt The initial time step.
- * \returns The times_time iterator.
- */
-
-
- /**
- * \fn make_times_time_iterator_end( Stepper stepper , System system , State &x )
- * \brief Factory function for times_time_iterator. Constructs an end iterator.
- *
- * \tparam TimesIterator The iterator type of the time sequence, must be specifically provided.
- *
- * \param stepper The stepper to use during the iteration.
- * \param system The system function (ODE) to solve.
- * \param x The initial state. const_step_iterator stores a reference of s and changes its value during the iteration.
- * \returns The times_time iterator.
- *
- * This function needs the TimeIterator type specifically defined as a
- * template parameter.
- */
-
-
- /**
- * \fn make_times_time_range( Stepper stepper , System system , State &x ,
- TimeIterator t_start ,
- TimeIterator t_end ,
- typename traits::time_type< Stepper >::type dt )
- *
- * \brief Factory function to construct a single pass range of times_time iterators. A range is here a pair
- * of times_iterator.
- *
- * \param stepper The stepper to use during the iteration.
- * \param system The system function (ODE) to solve.
- * \param x The initial state. const_step_iterator store a reference of s and changes its value during the iteration.
- * \param t_start Begin iterator of the sequence of evaluation time points.
- * \param t_end End iterator of the sequence of evaluation time points.
- * \param dt The initial time step.
- * \returns The times_time iterator range.
- */
-
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-#endif // BOOST_NUMERIC_ODEINT_ITERATOR_TIMES_TIME_ITERATOR_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/adams_bashforth.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/adams_bashforth.hpp
deleted file mode 100644
index 47c3b939ee89cdf378a5e9d620b73534013f3f5f..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/adams_bashforth.hpp
+++ /dev/null
@@ -1,420 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/adams_bashforth.hpp
-
- [begin_description]
- Implementaton of the Adam-Bashforth method a multistep method used for the predictor step in the
- Adams-Bashforth-Moulton method.
- [end_description]
-
- Copyright 2011-2013 Karsten Ahnert
- Copyright 2011-2013 Mario Mulansky
- Copyright 2012 Christoph Koke
- Copyright 2013 Pascal Germroth
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_ADAMS_BASHFORTH_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_ADAMS_BASHFORTH_HPP_INCLUDED
-
-#include <boost/static_assert.hpp>
-
-#include <boost/numeric/odeint/util/bind.hpp>
-#include <boost/numeric/odeint/util/unwrap_reference.hpp>
-
-#include <boost/numeric/odeint/algebra/range_algebra.hpp>
-#include <boost/numeric/odeint/algebra/default_operations.hpp>
-#include <boost/numeric/odeint/algebra/algebra_dispatcher.hpp>
-#include <boost/numeric/odeint/algebra/operations_dispatcher.hpp>
-
-#include <boost/numeric/odeint/util/state_wrapper.hpp>
-#include <boost/numeric/odeint/util/is_resizeable.hpp>
-#include <boost/numeric/odeint/util/resizer.hpp>
-
-#include <boost/numeric/odeint/stepper/stepper_categories.hpp>
-#include <boost/numeric/odeint/stepper/runge_kutta4.hpp>
-#include <boost/numeric/odeint/stepper/extrapolation_stepper.hpp>
-
-#include <boost/numeric/odeint/stepper/base/algebra_stepper_base.hpp>
-
-#include <boost/numeric/odeint/stepper/detail/adams_bashforth_coefficients.hpp>
-#include <boost/numeric/odeint/stepper/detail/adams_bashforth_call_algebra.hpp>
-#include <boost/numeric/odeint/stepper/detail/rotating_buffer.hpp>
-
-#include <boost/mpl/arithmetic.hpp>
-#include <boost/mpl/min_max.hpp>
-#include <boost/mpl/equal_to.hpp>
-
-namespace mpl = boost::mpl;
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
- using mpl::int_;
-
- /* if N >= 4, returns the smallest even number > N, otherwise returns 4 */
- template < int N >
- struct order_helper
- : mpl::max< typename mpl::eval_if<
- mpl::equal_to< mpl::modulus< int_< N >, int_< 2 > >,
- int_< 0 > >,
- int_< N >, int_< N + 1 > >::type,
- int_< 4 > >::type
- { };
-
-template<
-size_t Steps ,
-class State ,
-class Value = double ,
-class Deriv = State ,
-class Time = Value ,
-class Algebra = typename algebra_dispatcher< State >::algebra_type ,
-class Operations = typename operations_dispatcher< State >::operations_type ,
-class Resizer = initially_resizer ,
-class InitializingStepper = extrapolation_stepper< order_helper<Steps>::value,
- State, Value, Deriv, Time,
- Algebra, Operations, Resizer >
->
-class adams_bashforth : public algebra_stepper_base< Algebra , Operations >
-{
-
-#ifndef DOXYGEN_SKIP
- BOOST_STATIC_ASSERT(( Steps > 0 ));
- BOOST_STATIC_ASSERT(( Steps < 9 ));
-#endif
-
-public :
-
- typedef State state_type;
- typedef state_wrapper< state_type > wrapped_state_type;
- typedef Value value_type;
- typedef Deriv deriv_type;
- typedef state_wrapper< deriv_type > wrapped_deriv_type;
- typedef Time time_type;
- typedef Resizer resizer_type;
- typedef stepper_tag stepper_category;
-
- typedef InitializingStepper initializing_stepper_type;
-
- typedef algebra_stepper_base< Algebra , Operations > algebra_stepper_base_type;
- typedef typename algebra_stepper_base_type::algebra_type algebra_type;
- typedef typename algebra_stepper_base_type::operations_type operations_type;
-#ifndef DOXYGEN_SKIP
- typedef adams_bashforth< Steps , State , Value , Deriv , Time , Algebra , Operations , Resizer , InitializingStepper > stepper_type;
-#endif
- static const size_t steps = Steps;
-
-
-
- typedef unsigned short order_type;
- static const order_type order_value = steps;
-
- typedef detail::rotating_buffer< wrapped_deriv_type , steps > step_storage_type;
-
-
-
- order_type order( void ) const { return order_value; }
-
- adams_bashforth( const algebra_type &algebra = algebra_type() )
- : algebra_stepper_base_type( algebra ) ,
- m_step_storage() , m_resizer() , m_coefficients() ,
- m_steps_initialized( 0 ) , m_initializing_stepper()
- { }
-
-
-
- /*
- * Version 1 : do_step( system , x , t , dt );
- *
- * solves the forwarding problem
- */
- template< class System , class StateInOut >
- void do_step( System system , StateInOut &x , time_type t , time_type dt )
- {
- do_step( system , x , t , x , dt );
- }
-
- /**
- * \brief Second version to solve the forwarding problem, can be called with Boost.Range as StateInOut.
- */
- template< class System , class StateInOut >
- void do_step( System system , const StateInOut &x , time_type t , time_type dt )
- {
- do_step( system , x , t , x , dt );
- }
-
-
-
- /*
- * Version 2 : do_step( system , in , t , out , dt );
- *
- * solves the forwarding problem
- */
-
- template< class System , class StateIn , class StateOut >
- void do_step( System system , const StateIn &in , time_type t , StateOut &out , time_type dt )
- {
- do_step_impl( system , in , t , out , dt );
- }
-
- /**
- * \brief Second version to solve the forwarding problem, can be called with Boost.Range as StateOut.
- */
- template< class System , class StateIn , class StateOut >
- void do_step( System system , const StateIn &in , time_type t , const StateOut &out , time_type dt )
- {
- do_step_impl( system , in , t , out , dt );
- }
-
-
- template< class StateType >
- void adjust_size( const StateType &x )
- {
- resize_impl( x );
- }
-
- const step_storage_type& step_storage( void ) const
- {
- return m_step_storage;
- }
-
- step_storage_type& step_storage( void )
- {
- return m_step_storage;
- }
-
- template< class ExplicitStepper , class System , class StateIn >
- void initialize( ExplicitStepper explicit_stepper , System system , StateIn &x , time_type &t , time_type dt )
- {
- typename odeint::unwrap_reference< ExplicitStepper >::type &stepper = explicit_stepper;
- typename odeint::unwrap_reference< System >::type &sys = system;
-
- m_resizer.adjust_size( x , detail::bind( &stepper_type::template resize_impl<StateIn> , detail::ref( *this ) , detail::_1 ) );
-
- for( size_t i=0 ; i+1<steps ; ++i )
- {
- if( i != 0 ) m_step_storage.rotate();
- sys( x , m_step_storage[0].m_v , t );
- stepper.do_step_dxdt_impl( system, x, m_step_storage[0].m_v, t,
- dt );
- t += dt;
- }
- m_steps_initialized = steps;
- }
-
- template< class System , class StateIn >
- void initialize( System system , StateIn &x , time_type &t , time_type dt )
- {
- initialize( detail::ref( m_initializing_stepper ) , system , x , t , dt );
- }
-
- void reset( void )
- {
- m_steps_initialized = 0;
- }
-
- bool is_initialized( void ) const
- {
- return m_steps_initialized >= ( steps - 1 );
- }
-
- const initializing_stepper_type& initializing_stepper( void ) const { return m_initializing_stepper; }
-
- initializing_stepper_type& initializing_stepper( void ) { return m_initializing_stepper; }
-
-private:
-
- template< class System , class StateIn , class StateOut >
- void do_step_impl( System system , const StateIn &in , time_type t , StateOut &out , time_type dt )
- {
- typename odeint::unwrap_reference< System >::type &sys = system;
- if( m_resizer.adjust_size( in , detail::bind( &stepper_type::template resize_impl<StateIn> , detail::ref( *this ) , detail::_1 ) ) )
- {
- m_steps_initialized = 0;
- }
-
- if( m_steps_initialized + 1 < steps )
- {
- if( m_steps_initialized != 0 ) m_step_storage.rotate();
- sys( in , m_step_storage[0].m_v , t );
- m_initializing_stepper.do_step_dxdt_impl(
- system, in, m_step_storage[0].m_v, t, out, dt );
- ++m_steps_initialized;
- }
- else
- {
- m_step_storage.rotate();
- sys( in , m_step_storage[0].m_v , t );
- detail::adams_bashforth_call_algebra< steps , algebra_type , operations_type >()( this->m_algebra , in , out , m_step_storage , m_coefficients , dt );
- }
- }
-
-
- template< class StateIn >
- bool resize_impl( const StateIn &x )
- {
- bool resized( false );
- for( size_t i=0 ; i<steps ; ++i )
- {
- resized |= adjust_size_by_resizeability( m_step_storage[i] , x , typename is_resizeable<deriv_type>::type() );
- }
- return resized;
- }
-
- step_storage_type m_step_storage;
- resizer_type m_resizer;
- detail::adams_bashforth_coefficients< value_type , steps > m_coefficients;
- size_t m_steps_initialized;
- initializing_stepper_type m_initializing_stepper;
-
-};
-
-
-/***** DOXYGEN *****/
-
-/**
- * \class adams_bashforth
- * \brief The Adams-Bashforth multistep algorithm.
- *
- * The Adams-Bashforth method is a multi-step algorithm with configurable step
- * number. The step number is specified as template parameter Steps and it
- * then uses the result from the previous Steps steps. See also
- * <a href="http://en.wikipedia.org/wiki/Linear_multistep_method">en.wikipedia.org/wiki/Linear_multistep_method</a>.
- * Currently, a maximum of Steps=8 is supported.
- * The method is explicit and fulfills the Stepper concept. Step size control
- * or continuous output are not provided.
- *
- * This class derives from algebra_base and inherits its interface via
- * CRTP (current recurring template pattern). For more details see
- * algebra_stepper_base.
- *
- * \tparam Steps The number of steps (maximal 8).
- * \tparam State The state type.
- * \tparam Value The value type.
- * \tparam Deriv The type representing the time derivative of the state.
- * \tparam Time The time representing the independent variable - the time.
- * \tparam Algebra The algebra type.
- * \tparam Operations The operations type.
- * \tparam Resizer The resizer policy type.
- * \tparam InitializingStepper The stepper for the first two steps.
- */
-
- /**
- * \fn adams_bashforth::adams_bashforth( const algebra_type &algebra )
- * \brief Constructs the adams_bashforth class. This constructor can be used as a default
- * constructor if the algebra has a default constructor.
- * \param algebra A copy of algebra is made and stored.
- */
-
- /**
- * \fn order_type adams_bashforth::order( void ) const
- * \brief Returns the order of the algorithm, which is equal to the number of steps.
- * \return order of the method.
- */
-
- /**
- * \fn void adams_bashforth::do_step( System system , StateInOut &x , time_type t , time_type dt )
- * \brief This method performs one step. It transforms the result in-place.
- *
- * \param system The system function to solve, hence the r.h.s. of the ordinary differential equation. It must fulfill the
- * Simple System concept.
- * \param x The state of the ODE which should be solved. After calling do_step the result is updated in x.
- * \param t The value of the time, at which the step should be performed.
- * \param dt The step size.
- */
-
- /**
- * \fn void adams_bashforth::do_step( System system , const StateIn &in , time_type t , StateOut &out , time_type dt )
- * \brief The method performs one step with the stepper passed by Stepper. The state of the ODE is updated out-of-place.
- *
- * \param system The system function to solve, hence the r.h.s. of the ODE. It must fulfill the
- * Simple System concept.
- * \param in The state of the ODE which should be solved. in is not modified in this method
- * \param t The value of the time, at which the step should be performed.
- * \param out The result of the step is written in out.
- * \param dt The step size.
- */
-
- /**
- * \fn void adams_bashforth::adjust_size( const StateType &x )
- * \brief Adjust the size of all temporaries in the stepper manually.
- * \param x A state from which the size of the temporaries to be resized is deduced.
- */
-
-
- /**
- * \fn const step_storage_type& adams_bashforth::step_storage( void ) const
- * \brief Returns the storage of intermediate results.
- * \return The storage of intermediate results.
- */
-
- /**
- * \fn step_storage_type& adams_bashforth::step_storage( void )
- * \brief Returns the storage of intermediate results.
- * \return The storage of intermediate results.
- */
-
- /**
- * \fn void adams_bashforth::initialize( ExplicitStepper explicit_stepper , System system , StateIn &x , time_type &t , time_type dt )
- * \brief Initialized the stepper. Does Steps-1 steps with the explicit_stepper to fill the buffer.
- * \param explicit_stepper the stepper used to fill the buffer of previous step results
- * \param system The system function to solve, hence the r.h.s. of the ordinary differential equation. It must fulfill the
- * Simple System concept.
- * \param x The state of the ODE which should be solved. After calling do_step the result is updated in x.
- * \param t The value of the time, at which the step should be performed.
- * \param dt The step size.
- */
-
- /**
- * \fn void adams_bashforth::initialize( System system , StateIn &x , time_type &t , time_type dt )
- * \brief Initialized the stepper. Does Steps-1 steps with an internal instance of InitializingStepper to fill the buffer.
- * \note The state x and time t are updated to the values after Steps-1 initial steps.
- * \param system The system function to solve, hence the r.h.s. of the ordinary differential equation. It must fulfill the
- * Simple System concept.
- * \param x The initial state of the ODE which should be solved, updated in this method.
- * \param t The initial value of the time, updated in this method.
- * \param dt The step size.
- */
-
- /**
- * \fn void adams_bashforth::reset( void )
- * \brief Resets the internal buffer of the stepper.
- */
-
- /**
- * \fn bool adams_bashforth::is_initialized( void ) const
- * \brief Returns true if the stepper has been initialized.
- * \return bool true if stepper is initialized, false otherwise
- */
-
- /**
- * \fn const initializing_stepper_type& adams_bashforth::initializing_stepper( void ) const
- * \brief Returns the internal initializing stepper instance.
- * \return initializing_stepper
- */
-
- /**
- * \fn const initializing_stepper_type& adams_bashforth::initializing_stepper( void ) const
- * \brief Returns the internal initializing stepper instance.
- * \return initializing_stepper
- */
-
- /**
- * \fn initializing_stepper_type& adams_bashforth::initializing_stepper( void )
- * \brief Returns the internal initializing stepper instance.
- * \return initializing_stepper
- */
-
-} // odeint
-} // numeric
-} // boost
-
-
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_ADAMS_BASHFORTH_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/adams_bashforth_moulton.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/adams_bashforth_moulton.hpp
deleted file mode 100644
index c7b487fb13ac0fac27254196f469fb282664abce..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/adams_bashforth_moulton.hpp
+++ /dev/null
@@ -1,314 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/adams_bashforth_moulton.hpp
-
- [begin_description]
- Implementation of the Adams-Bashforth-Moulton method, a predictor-corrector multistep method.
- [end_description]
-
- Copyright 2011-2013 Karsten Ahnert
- Copyright 2011-2013 Mario Mulansky
- Copyright 2012 Christoph Koke
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_ADAMS_BASHFORTH_MOULTON_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_ADAMS_BASHFORTH_MOULTON_HPP_INCLUDED
-
-
-#include <boost/numeric/odeint/util/bind.hpp>
-
-#include <boost/numeric/odeint/stepper/stepper_categories.hpp>
-#include <boost/numeric/odeint/algebra/range_algebra.hpp>
-#include <boost/numeric/odeint/algebra/default_operations.hpp>
-#include <boost/numeric/odeint/algebra/algebra_dispatcher.hpp>
-#include <boost/numeric/odeint/algebra/operations_dispatcher.hpp>
-
-#include <boost/numeric/odeint/util/state_wrapper.hpp>
-#include <boost/numeric/odeint/util/resizer.hpp>
-
-#include <boost/numeric/odeint/stepper/adams_bashforth.hpp>
-#include <boost/numeric/odeint/stepper/adams_moulton.hpp>
-
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-template<
-size_t Steps ,
-class State ,
-class Value = double ,
-class Deriv = State ,
-class Time = Value ,
-class Algebra = typename algebra_dispatcher< State >::algebra_type ,
-class Operations = typename operations_dispatcher< State >::operations_type ,
-class Resizer = initially_resizer,
-class InitializingStepper = runge_kutta4< State , Value , Deriv , Time , Algebra , Operations, Resizer >
->
-class adams_bashforth_moulton
-{
-
-#ifndef DOXYGEN_SKIP
- BOOST_STATIC_ASSERT(( Steps > 0 ));
- BOOST_STATIC_ASSERT(( Steps < 9 ));
-#endif
-
-public :
-
- typedef State state_type;
- typedef state_wrapper< state_type > wrapped_state_type;
- typedef Value value_type;
- typedef Deriv deriv_type;
- typedef state_wrapper< deriv_type > wrapped_deriv_type;
- typedef Time time_type;
- typedef Algebra algebra_type;
- typedef Operations operations_type;
- typedef Resizer resizer_type;
- typedef stepper_tag stepper_category;
- typedef InitializingStepper initializing_stepper_type;
-
- static const size_t steps = Steps;
-#ifndef DOXYGEN_SKIP
- typedef adams_bashforth< steps , state_type , value_type , deriv_type , time_type , algebra_type , operations_type , resizer_type, initializing_stepper_type > adams_bashforth_type;
- typedef adams_moulton< steps , state_type , value_type , deriv_type , time_type , algebra_type , operations_type , resizer_type > adams_moulton_type;
- typedef adams_bashforth_moulton< steps , state_type , value_type , deriv_type , time_type , algebra_type , operations_type , resizer_type , initializing_stepper_type> stepper_type;
-#endif //DOXYGEN_SKIP
- typedef unsigned short order_type;
- static const order_type order_value = steps;
-
- /** \brief Constructs the adams_bashforth class. */
- adams_bashforth_moulton( void )
- : m_adams_bashforth() , m_adams_moulton( m_adams_bashforth.algebra() )
- , m_x() , m_resizer()
- { }
-
- adams_bashforth_moulton( const algebra_type &algebra )
- : m_adams_bashforth( algebra ) , m_adams_moulton( m_adams_bashforth.algebra() )
- , m_x() , m_resizer()
- { }
-
- order_type order( void ) const { return order_value; }
-
- template< class System , class StateInOut >
- void do_step( System system , StateInOut &x , time_type t , time_type dt )
- {
- do_step_impl1( system , x , t , dt );
- }
-
- /**
- * \brief Second version to solve the forwarding problem, can be called with Boost.Range as StateInOut.
- */
- template< class System , class StateInOut >
- void do_step( System system , const StateInOut &x , time_type t , time_type dt )
- {
- do_step_impl1( system , x , t , dt );
- }
-
- template< class System , class StateIn , class StateOut >
- void do_step( System system , const StateIn &in , time_type t , const StateOut &out , time_type dt )
- {
- do_step_impl2( system , in , t , out , dt );
- }
-
- /**
- * \brief Second version to solve the forwarding problem, can be called with Boost.Range as StateOut.
- */
- template< class System , class StateIn , class StateOut >
- void do_step( System system , const StateIn &in , time_type t , StateOut &out , time_type dt )
- {
- do_step_impl2( system , in ,t , out , dt );
- }
-
-
- template< class StateType >
- void adjust_size( const StateType &x )
- {
- m_adams_bashforth.adjust_size( x );
- m_adams_moulton.adjust_size( x );
- resize_impl( x );
- }
-
-
- template< class ExplicitStepper , class System , class StateIn >
- void initialize( ExplicitStepper explicit_stepper , System system , StateIn &x , time_type &t , time_type dt )
- {
- m_adams_bashforth.initialize( explicit_stepper , system , x , t , dt );
- }
-
-
- template< class System , class StateIn >
- void initialize( System system , StateIn &x , time_type &t , time_type dt )
- {
- m_adams_bashforth.initialize( system , x , t , dt );
- }
-
-
- void reset(void)
- {
- m_adams_bashforth.reset();
- }
-
-
-
-private:
-
- template< typename System , typename StateInOut >
- void do_step_impl1( System system , StateInOut &x , time_type t , time_type dt )
- {
- if( m_adams_bashforth.is_initialized() )
- {
- m_resizer.adjust_size( x , detail::bind( &stepper_type::template resize_impl< StateInOut > , detail::ref( *this ) , detail::_1 ) );
- m_adams_bashforth.do_step( system , x , t , m_x.m_v , dt );
- m_adams_moulton.do_step( system , x , m_x.m_v , t+dt , x , dt , m_adams_bashforth.step_storage() );
- }
- else
- {
- m_adams_bashforth.do_step( system , x , t , dt );
- }
- }
-
- template< typename System , typename StateIn , typename StateInOut >
- void do_step_impl2( System system , StateIn const &in , time_type t , StateInOut & out , time_type dt )
- {
- if( m_adams_bashforth.is_initialized() )
- {
- m_resizer.adjust_size( in , detail::bind( &stepper_type::template resize_impl< StateInOut > , detail::ref( *this ) , detail::_1 ) );
- m_adams_bashforth.do_step( system , in , t , m_x.m_v , dt );
- m_adams_moulton.do_step( system , in , m_x.m_v , t+dt , out , dt , m_adams_bashforth.step_storage() );
- }
- else
- {
- m_adams_bashforth.do_step( system , in , t , out , dt );
- }
- }
-
-
- template< class StateIn >
- bool resize_impl( const StateIn &x )
- {
- return adjust_size_by_resizeability( m_x , x , typename is_resizeable< state_type >::type() );
- }
-
- adams_bashforth_type m_adams_bashforth;
- adams_moulton_type m_adams_moulton;
- wrapped_state_type m_x;
- resizer_type m_resizer;
-};
-
-
-/********* DOXYGEN ********/
-
-/**
- * \class adams_bashforth_moulton
- * \brief The Adams-Bashforth-Moulton multistep algorithm.
- *
- * The Adams-Bashforth method is a multi-step predictor-corrector algorithm
- * with configurable step number. The step number is specified as template
- * parameter Steps and it then uses the result from the previous Steps steps.
- * See also
- * <a href="http://en.wikipedia.org/wiki/Linear_multistep_method">en.wikipedia.org/wiki/Linear_multistep_method</a>.
- * Currently, a maximum of Steps=8 is supported.
- * The method is explicit and fulfills the Stepper concept. Step size control
- * or continuous output are not provided.
- *
- * This class derives from algebra_base and inherits its interface via
- * CRTP (current recurring template pattern). For more details see
- * algebra_stepper_base.
- *
- * \tparam Steps The number of steps (maximal 8).
- * \tparam State The state type.
- * \tparam Value The value type.
- * \tparam Deriv The type representing the time derivative of the state.
- * \tparam Time The time representing the independent variable - the time.
- * \tparam Algebra The algebra type.
- * \tparam Operations The operations type.
- * \tparam Resizer The resizer policy type.
- * \tparam InitializingStepper The stepper for the first two steps.
- */
-
- /**
- * \fn adams_bashforth_moulton::adams_bashforth_moulton( const algebra_type &algebra )
- * \brief Constructs the adams_bashforth class. This constructor can be used as a default
- * constructor if the algebra has a default constructor.
- * \param algebra A copy of algebra is made and stored.
- */
-
- /**
- * \fn adams_bashforth_moulton::order( void ) const
- * \brief Returns the order of the algorithm, which is equal to the number of steps+1.
- * \return order of the method.
- */
-
- /**
- * \fn adams_bashforth_moulton::do_step( System system , StateInOut &x , time_type t , time_type dt )
- * \brief This method performs one step. It transforms the result in-place.
- *
- * \param system The system function to solve, hence the r.h.s. of the ordinary differential equation. It must fulfill the
- * Simple System concept.
- * \param x The state of the ODE which should be solved. After calling do_step the result is updated in x.
- * \param t The value of the time, at which the step should be performed.
- * \param dt The step size.
- */
-
-
- /**
- * \fn adams_bashforth_moulton::do_step( System system , const StateIn &in , time_type t , const StateOut &out , time_type dt )
- * \brief The method performs one step with the stepper passed by Stepper. The state of the ODE is updated out-of-place.
- *
- * \param system The system function to solve, hence the r.h.s. of the ODE. It must fulfill the
- * Simple System concept.
- * \param in The state of the ODE which should be solved. in is not modified in this method
- * \param t The value of the time, at which the step should be performed.
- * \param out The result of the step is written in out.
- * \param dt The step size.
- */
-
- /**
- * \fn adams_bashforth_moulton::adjust_size( const StateType &x )
- * \brief Adjust the size of all temporaries in the stepper manually.
- * \param x A state from which the size of the temporaries to be resized is deduced.
- */
-
- /**
- * \fn adams_bashforth_moulton::initialize( ExplicitStepper explicit_stepper , System system , StateIn &x , time_type &t , time_type dt )
- * \brief Initialized the stepper. Does Steps-1 steps with the explicit_stepper to fill the buffer.
- * \note The state x and time t are updated to the values after Steps-1 initial steps.
- * \param explicit_stepper the stepper used to fill the buffer of previous step results
- * \param system The system function to solve, hence the r.h.s. of the ordinary differential equation. It must fulfill the
- * Simple System concept.
- * \param x The initial state of the ODE which should be solved, updated after in this method.
- * \param t The initial time, updated in this method.
- * \param dt The step size.
- */
-
- /**
- * \fn adams_bashforth_moulton::initialize( System system , StateIn &x , time_type &t , time_type dt )
- * \brief Initialized the stepper. Does Steps-1 steps using the standard initializing stepper
- * of the underlying adams_bashforth stepper.
- * \param system The system function to solve, hence the r.h.s. of the ordinary differential equation. It must fulfill the
- * Simple System concept.
- * \param x The state of the ODE which should be solved. After calling do_step the result is updated in x.
- * \param t The value of the time, at which the step should be performed.
- * \param dt The step size.
- */
-
- /**
- * \fn adams_bashforth_moulton::reset( void )
- * \brief Resets the internal buffers of the stepper.
- */
-
-
-} // odeint
-} // numeric
-} // boost
-
-
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_ADAMS_BASHFORTH_MOULTON_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/adams_moulton.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/adams_moulton.hpp
deleted file mode 100644
index 05b42777355be822ecb34a300207fb2c8c254c79..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/adams_moulton.hpp
+++ /dev/null
@@ -1,201 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/adams_moulton.hpp
-
- [begin_description]
- Implementation of the Adams-Moulton method. This is method is not a real stepper, it is more a helper class
- which computes the corrector step in the Adams-Bashforth-Moulton method.
- [end_description]
-
- Copyright 2011-2012 Karsten Ahnert
- Copyright 2011-2013 Mario Mulansky
- Copyright 2012 Christoph Koke
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_ADAMS_MOULTON_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_ADAMS_MOULTON_HPP_INCLUDED
-
-
-#include <boost/numeric/odeint/util/bind.hpp>
-
-#include <boost/numeric/odeint/algebra/range_algebra.hpp>
-#include <boost/numeric/odeint/algebra/default_operations.hpp>
-#include <boost/numeric/odeint/algebra/algebra_dispatcher.hpp>
-#include <boost/numeric/odeint/algebra/operations_dispatcher.hpp>
-
-#include <boost/numeric/odeint/util/state_wrapper.hpp>
-#include <boost/numeric/odeint/util/is_resizeable.hpp>
-#include <boost/numeric/odeint/util/resizer.hpp>
-
-#include <boost/numeric/odeint/stepper/stepper_categories.hpp>
-#include <boost/numeric/odeint/stepper/runge_kutta4_classic.hpp>
-
-#include <boost/numeric/odeint/stepper/detail/adams_moulton_call_algebra.hpp>
-#include <boost/numeric/odeint/stepper/detail/adams_moulton_coefficients.hpp>
-#include <boost/numeric/odeint/stepper/detail/rotating_buffer.hpp>
-
-
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-/*
- * Static implicit Adams-Moulton multistep-solver without step size control and without dense output.
- */
-template<
-size_t Steps ,
-class State ,
-class Value = double ,
-class Deriv = State ,
-class Time = Value ,
-class Algebra = typename algebra_dispatcher< State >::algebra_type ,
-class Operations = typename operations_dispatcher< State >::operations_type ,
-class Resizer = initially_resizer
->
-class adams_moulton
-{
-private:
-
-
-public :
-
- typedef State state_type;
- typedef state_wrapper< state_type > wrapped_state_type;
- typedef Value value_type;
- typedef Deriv deriv_type;
- typedef state_wrapper< deriv_type > wrapped_deriv_type;
- typedef Time time_type;
- typedef Algebra algebra_type;
- typedef Operations operations_type;
- typedef Resizer resizer_type;
- typedef stepper_tag stepper_category;
-
- typedef adams_moulton< Steps , State , Value , Deriv , Time , Algebra , Operations , Resizer > stepper_type;
-
- static const size_t steps = Steps;
-
- typedef unsigned short order_type;
- static const order_type order_value = steps + 1;
-
- typedef detail::rotating_buffer< wrapped_deriv_type , steps > step_storage_type;
-
- adams_moulton( )
- : m_coefficients() , m_dxdt() , m_resizer() ,
- m_algebra_instance() , m_algebra( m_algebra_instance )
- { }
-
- adams_moulton( algebra_type &algebra )
- : m_coefficients() , m_dxdt() , m_resizer() ,
- m_algebra_instance() , m_algebra( algebra )
- { }
-
- adams_moulton& operator=( const adams_moulton &stepper )
- {
- m_dxdt = stepper.m_dxdt;
- m_resizer = stepper.m_resizer;
- m_algebra = stepper.m_algebra;
- return *this;
- }
-
- order_type order( void ) const { return order_value; }
-
-
- /*
- * Version 1 : do_step( system , x , t , dt , buf );
- *
- * solves the forwarding problem
- */
- template< class System , class StateInOut , class StateIn , class ABBuf >
- void do_step( System system , StateInOut &x , StateIn const & pred , time_type t , time_type dt , const ABBuf &buf )
- {
- do_step( system , x , pred , t , x , dt , buf );
- }
-
- template< class System , class StateInOut , class StateIn , class ABBuf >
- void do_step( System system , const StateInOut &x , StateIn const & pred , time_type t , time_type dt , const ABBuf &buf )
- {
- do_step( system , x , pred , t , x , dt , buf );
- }
-
-
-
- /*
- * Version 2 : do_step( system , in , t , out , dt , buf );
- *
- * solves the forwarding problem
- */
- template< class System , class StateIn , class PredIn , class StateOut , class ABBuf >
- void do_step( System system , const StateIn &in , const PredIn &pred , time_type t , StateOut &out , time_type dt , const ABBuf &buf )
- {
- do_step_impl( system , in , pred , t , out , dt , buf );
- }
-
- template< class System , class StateIn , class PredIn , class StateOut , class ABBuf >
- void do_step( System system , const StateIn &in , const PredIn &pred , time_type t , const StateOut &out , time_type dt , const ABBuf &buf )
- {
- do_step_impl( system , in , pred , t , out , dt , buf );
- }
-
-
-
- template< class StateType >
- void adjust_size( const StateType &x )
- {
- resize_impl( x );
- }
-
- algebra_type& algebra()
- { return m_algebra; }
-
- const algebra_type& algebra() const
- { return m_algebra; }
-
-
-private:
-
-
- template< class System , class StateIn , class PredIn , class StateOut , class ABBuf >
- void do_step_impl( System system , const StateIn &in , const PredIn &pred , time_type t , StateOut &out , time_type dt , const ABBuf &buf )
- {
- typename odeint::unwrap_reference< System >::type &sys = system;
- m_resizer.adjust_size( in , detail::bind( &stepper_type::template resize_impl<StateIn> , detail::ref( *this ) , detail::_1 ) );
- sys( pred , m_dxdt.m_v , t );
- detail::adams_moulton_call_algebra< steps , algebra_type , operations_type >()( m_algebra , in , out , m_dxdt.m_v , buf , m_coefficients , dt );
- }
-
-
- template< class StateIn >
- bool resize_impl( const StateIn &x )
- {
- return adjust_size_by_resizeability( m_dxdt , x , typename is_resizeable<deriv_type>::type() );
- }
-
-
- const detail::adams_moulton_coefficients< value_type , steps > m_coefficients;
- wrapped_deriv_type m_dxdt;
- resizer_type m_resizer;
-
-protected:
-
- algebra_type m_algebra_instance;
- algebra_type &m_algebra;
-};
-
-
-
-
-} // odeint
-} // numeric
-} // boost
-
-
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_ADAMS_MOULTON_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/base/algebra_stepper_base.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/base/algebra_stepper_base.hpp
deleted file mode 100644
index 66c2b84a81f26e791664d437b24389625142ff10..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/base/algebra_stepper_base.hpp
+++ /dev/null
@@ -1,91 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/base/algebra_stepper_base.hpp
-
- [begin_description]
- Base class for all steppers with an algebra and operations.
- [end_description]
-
- Copyright 2012-2013 Karsten Ahnert
- Copyright 2012 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_BASE_ALGEBRA_STEPPER_BASE_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_BASE_ALGEBRA_STEPPER_BASE_HPP_INCLUDED
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-template< class Algebra , class Operations >
-class algebra_stepper_base
-{
-public:
-
- typedef Algebra algebra_type;
- typedef Operations operations_type;
-
- algebra_stepper_base( const algebra_type &algebra = algebra_type() )
- : m_algebra( algebra ) { }
-
- algebra_type& algebra()
- {
- return m_algebra;
- }
-
- const algebra_type& algebra() const
- {
- return m_algebra;
- }
-
-protected:
-
- algebra_type m_algebra;
-};
-
-
-/******* DOXYGEN *******/
-
-/**
- * \class algebra_stepper_base
- * \brief Base class for all steppers with algebra and operations.
- *
- * This class serves a base class for all steppers with algebra and operations. It holds the
- * algebra and provides access to the algebra. The operations are not instantiated, since they are
- * static classes inside the operations class.
- *
- * \tparam Algebra The type of the algebra. Must fulfill the Algebra Concept, at least partially to work
- * with the stepper.
- * \tparam Operations The type of the operations. Must fulfill the Operations Concept, at least partially
- * to work with the stepper.
- */
-
- /**
- * \fn algebra_stepper_base::algebra_stepper_base( const algebra_type &algebra = algebra_type() )
- * \brief Constructs a algebra_stepper_base and creates the algebra. This constructor can be used as a default
- * constructor if the algebra has a default constructor.
- * \param algebra The algebra_stepper_base stores and uses a copy of algebra.
- */
-
- /**
- * \fn algebra_type& algebra_stepper_base::algebra()
- * \return A reference to the algebra which is held by this class.
- */
-
- /**
- * \fn const algebra_type& algebra_stepper_base::algebra() const
- * \return A const reference to the algebra which is held by this class.
- */
-
-} // odeint
-} // numeric
-} // boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_BASE_ALGEBRA_STEPPER_BASE_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/base/explicit_error_stepper_base.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/base/explicit_error_stepper_base.hpp
deleted file mode 100644
index bb6ea3d0a716eaa5162b8745adc9e91075657619..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/base/explicit_error_stepper_base.hpp
+++ /dev/null
@@ -1,588 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/base/explicit_error_stepper_base.hpp
-
- [begin_description]
- Base class for all explicit Runge Kutta stepper which are also error steppers.
- [end_description]
-
- Copyright 2010-2013 Karsten Ahnert
- Copyright 2010-2012 Mario Mulansky
- Copyright 2012 Christoph Koke
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_BASE_EXPLICIT_ERROR_STEPPER_BASE_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_BASE_EXPLICIT_ERROR_STEPPER_BASE_HPP_INCLUDED
-
-#include <boost/utility/enable_if.hpp>
-#include <boost/type_traits/is_same.hpp>
-
-
-#include <boost/numeric/odeint/util/bind.hpp>
-#include <boost/numeric/odeint/util/unwrap_reference.hpp>
-#include <boost/numeric/odeint/util/state_wrapper.hpp>
-#include <boost/numeric/odeint/util/is_resizeable.hpp>
-#include <boost/numeric/odeint/util/resizer.hpp>
-
-#include <boost/numeric/odeint/stepper/stepper_categories.hpp>
-
-#include <boost/numeric/odeint/stepper/base/algebra_stepper_base.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-/*
- * base class for explicit stepper and error steppers
- * models the stepper AND the error stepper concept
- *
- * this class provides the following do_step variants:
- * do_step( sys , x , t , dt )
- * do_step( sys , x , dxdt , t , dt )
- * do_step( sys , in , t , out , dt )
- * do_step( sys , in , dxdt , t , out , dt )
- * do_step( sys , x , t , dt , xerr )
- * do_step( sys , x , dxdt , t , dt , xerr )
- * do_step( sys , in , t , out , dt , xerr )
- * do_step( sys , in , dxdt , t , out , dt , xerr )
- */
-template<
-class Stepper ,
-unsigned short Order ,
-unsigned short StepperOrder ,
-unsigned short ErrorOrder ,
-class State ,
-class Value ,
-class Deriv ,
-class Time ,
-class Algebra ,
-class Operations ,
-class Resizer
->
-class explicit_error_stepper_base : public algebra_stepper_base< Algebra , Operations >
-{
-public:
-
- typedef algebra_stepper_base< Algebra , Operations > algebra_stepper_base_type;
- typedef typename algebra_stepper_base_type::algebra_type algebra_type;
-
-
- typedef State state_type;
- typedef Value value_type;
- typedef Deriv deriv_type;
- typedef Time time_type;
- typedef Resizer resizer_type;
- typedef Stepper stepper_type;
- typedef explicit_error_stepper_tag stepper_category;
- #ifndef DOXYGEN_SKIP
- typedef state_wrapper< state_type > wrapped_state_type;
- typedef state_wrapper< deriv_type > wrapped_deriv_type;
- typedef explicit_error_stepper_base< Stepper , Order , StepperOrder , ErrorOrder ,
- State , Value , Deriv , Time , Algebra , Operations , Resizer > internal_stepper_base_type;
- #endif
-
- typedef unsigned short order_type;
- static const order_type order_value = Order;
- static const order_type stepper_order_value = StepperOrder;
- static const order_type error_order_value = ErrorOrder;
-
-
- explicit_error_stepper_base( const algebra_type &algebra = algebra_type() )
- : algebra_stepper_base_type( algebra )
- { }
-
- order_type order( void ) const
- {
- return order_value;
- }
-
- order_type stepper_order( void ) const
- {
- return stepper_order_value;
- }
-
- order_type error_order( void ) const
- {
- return error_order_value;
- }
-
-
-
- /*
- * Version 1 : do_step( sys , x , t , dt )
- *
- * the two overloads are needed in order to solve the forwarding problem
- */
- template< class System , class StateInOut >
- void do_step( System system , StateInOut &x , time_type t , time_type dt )
- {
- do_step_v1( system , x , t , dt );
- }
-
- /**
- * \brief Second version to solve the forwarding problem, can be called with Boost.Range as StateInOut.
- */
- template< class System , class StateInOut >
- void do_step( System system , const StateInOut &x , time_type t , time_type dt )
- {
- do_step_v1( system , x , t , dt );
- }
-
-
-
- /*
- * Version 2 : do_step( sys , x , dxdt , t , dt )
- *
- * this version does not solve the forwarding problem, boost.range can not be used
- *
- * the disable is needed to avoid ambiguous overloads if state_type = time_type
- */
- template< class System , class StateInOut , class DerivIn >
- typename boost::disable_if< boost::is_same< DerivIn , time_type > , void >::type
- do_step( System system , StateInOut &x , const DerivIn &dxdt , time_type t , time_type dt )
- {
- this->stepper().do_step_impl( system , x , dxdt , t , x , dt );
- }
-
-
- /*
- * named Version 2: do_step_dxdt_impl( sys , in , dxdt , t , dt )
- *
- * this version is needed when this stepper is used for initializing
- * multistep stepper like adams-bashforth. Hence we provide an explicitely
- * named version that is not disabled. Meant for internal use only.
- */
- template < class System, class StateInOut, class DerivIn >
- void do_step_dxdt_impl( System system, StateInOut &x, const DerivIn &dxdt,
- time_type t, time_type dt )
- {
- this->stepper().do_step_impl( system , x , dxdt , t , x , dt );
- }
-
-
-
- /*
- * Version 3 : do_step( sys , in , t , out , dt )
- *
- * this version does not solve the forwarding problem, boost.range can not be used
- *
- * the disable is needed to avoid ambiguous overloads if state_type = time_type
- */
- template< class System , class StateIn , class StateOut >
- typename boost::disable_if< boost::is_same< StateIn , time_type > , void >::type
- do_step( System system , const StateIn &in , time_type t , StateOut &out , time_type dt )
- {
- typename odeint::unwrap_reference< System >::type &sys = system;
- m_resizer.adjust_size( in , detail::bind( &internal_stepper_base_type::template resize_impl<StateIn> , detail::ref( *this ) , detail::_1 ) );
- sys( in , m_dxdt.m_v ,t );
- this->stepper().do_step_impl( system , in , m_dxdt.m_v , t , out , dt );
- }
-
- /*
- * Version 4 :do_step( sys , in , dxdt , t , out , dt )
- *
- * this version does not solve the forwarding problem, boost.range can not be used
- *
- * the disable is needed to avoid ambiguous overloads if state_type = time_type
- */
- template< class System , class StateIn , class DerivIn , class StateOut >
- typename boost::disable_if< boost::is_same< DerivIn , time_type > , void >::type
- do_step( System system , const StateIn &in , const DerivIn &dxdt , time_type t , StateOut &out , time_type dt )
- {
- this->stepper().do_step_impl( system , in , dxdt , t , out , dt );
- }
-
- /*
- * named Version 4: do_step_dxdt_impl( sys , in , dxdt , t , out, dt )
- *
- * this version is needed when this stepper is used for initializing
- * multistep stepper like adams-bashforth. Hence we provide an explicitely
- * named version that is not disabled. Meant for internal use only.
- */
- template < class System, class StateIn, class DerivIn, class StateOut >
- void do_step_dxdt_impl( System system, const StateIn &in,
- const DerivIn &dxdt, time_type t, StateOut &out,
- time_type dt )
- {
- this->stepper().do_step_impl( system , in , dxdt , t , out , dt );
- }
-
- /*
- * Version 5 :do_step( sys , x , t , dt , xerr )
- *
- * the two overloads are needed in order to solve the forwarding problem
- */
- template< class System , class StateInOut , class Err >
- void do_step( System system , StateInOut &x , time_type t , time_type dt , Err &xerr )
- {
- do_step_v5( system , x , t , dt , xerr );
- }
-
- /**
- * \brief Second version to solve the forwarding problem, can be called with Boost.Range as StateInOut.
- */
- template< class System , class StateInOut , class Err >
- void do_step( System system , const StateInOut &x , time_type t , time_type dt , Err &xerr )
- {
- do_step_v5( system , x , t , dt , xerr );
- }
-
-
- /*
- * Version 6 :do_step( sys , x , dxdt , t , dt , xerr )
- *
- * this version does not solve the forwarding problem, boost.range can not be used
- *
- * the disable is needed to avoid ambiguous overloads if state_type = time_type
- */
- template< class System , class StateInOut , class DerivIn , class Err >
- typename boost::disable_if< boost::is_same< DerivIn , time_type > , void >::type
- do_step( System system , StateInOut &x , const DerivIn &dxdt , time_type t , time_type dt , Err &xerr )
- {
- this->stepper().do_step_impl( system , x , dxdt , t , x , dt , xerr );
- }
-
-
- /*
- * Version 7 : do_step( sys , in , t , out , dt , xerr )
- *
- * this version does not solve the forwarding problem, boost.range can not be used
- */
- template< class System , class StateIn , class StateOut , class Err >
- void do_step( System system , const StateIn &in , time_type t , StateOut &out , time_type dt , Err &xerr )
- {
- typename odeint::unwrap_reference< System >::type &sys = system;
- m_resizer.adjust_size( in , detail::bind( &internal_stepper_base_type::template resize_impl<StateIn> , detail::ref( *this ) , detail::_1 ) );
- sys( in , m_dxdt.m_v ,t );
- this->stepper().do_step_impl( system , in , m_dxdt.m_v , t , out , dt , xerr );
- }
-
-
- /*
- * Version 8 : do_step( sys , in , dxdt , t , out , dt , xerr )
- *
- * this version does not solve the forwarding problem, boost.range can not be used
- */
- template< class System , class StateIn , class DerivIn , class StateOut , class Err >
- void do_step( System system , const StateIn &in , const DerivIn &dxdt , time_type t , StateOut &out , time_type dt , Err &xerr )
- {
- this->stepper().do_step_impl( system , in , dxdt , t , out , dt , xerr );
- }
-
- template< class StateIn >
- void adjust_size( const StateIn &x )
- {
- resize_impl( x );
- }
-
-
-
-private:
-
- template< class System , class StateInOut >
- void do_step_v1( System system , StateInOut &x , time_type t , time_type dt )
- {
- typename odeint::unwrap_reference< System >::type &sys = system;
- m_resizer.adjust_size( x , detail::bind( &internal_stepper_base_type::template resize_impl<StateInOut> , detail::ref( *this ) , detail::_1 ) );
- sys( x , m_dxdt.m_v , t );
- this->stepper().do_step_impl( system , x , m_dxdt.m_v , t , x , dt );
- }
-
- template< class System , class StateInOut , class Err >
- void do_step_v5( System system , StateInOut &x , time_type t , time_type dt , Err &xerr )
- {
- typename odeint::unwrap_reference< System >::type &sys = system;
- m_resizer.adjust_size( x , detail::bind( &internal_stepper_base_type::template resize_impl<StateInOut> , detail::ref( *this ) , detail::_1 ) );
- sys( x , m_dxdt.m_v ,t );
- this->stepper().do_step_impl( system , x , m_dxdt.m_v , t , x , dt , xerr );
- }
-
- template< class StateIn >
- bool resize_impl( const StateIn &x )
- {
- return adjust_size_by_resizeability( m_dxdt , x , typename is_resizeable<deriv_type>::type() );
- }
-
- stepper_type& stepper( void )
- {
- return *static_cast< stepper_type* >( this );
- }
-
- const stepper_type& stepper( void ) const
- {
- return *static_cast< const stepper_type* >( this );
- }
-
-
- resizer_type m_resizer;
-
-protected:
-
- wrapped_deriv_type m_dxdt;
-};
-
-
-
-
-/******** DOXYGEN *******/
-
-/**
- * \class explicit_error_stepper_base
- * \brief Base class for explicit steppers with error estimation. This class can used with
- * controlled steppers for step size control.
- *
- * This class serves as the base class for all explicit steppers with algebra and operations. In contrast to
- * explicit_stepper_base it also estimates the error and can be used in a controlled stepper to provide
- * step size control.
- *
- * \note This stepper provides `do_step` methods with and without error estimation. It has therefore three orders,
- * one for the order of a step if the error is not estimated. The other two orders are the orders of the step and
- * the error step if the error estimation is performed.
- *
- * explicit_error_stepper_base is used as the interface in a CRTP (currently recurring template
- * pattern). In order to work correctly the parent class needs to have a method
- * `do_step_impl( system , in , dxdt_in , t , out , dt , xerr )`.
- * explicit_error_stepper_base derives from algebra_stepper_base.
- *
- * explicit_error_stepper_base provides several overloaded `do_step` methods, see the list below. Only two of them
- * are needed to fulfill the Error Stepper concept. The other ones are for convenience and for performance. Some
- * of them simply update the state out-of-place, while other expect that the first derivative at `t` is passed to the
- * stepper.
- *
- * - `do_step( sys , x , t , dt )` - The classical `do_step` method needed to fulfill the Error Stepper concept. The
- * state is updated in-place. A type modelling a Boost.Range can be used for x.
- * - `do_step( sys , x , dxdt , t , dt )` - This method updates the state in-place, but the derivative at the point `t`
- * must be explicitly passed in `dxdt`.
- * - `do_step( sys , in , t , out , dt )` - This method updates the state out-of-place, hence the result of the step
- * is stored in `out`.
- * - `do_step( sys , in , dxdt , t , out , dt )` - This method update the state out-of-place and expects that the
- * derivative at the point `t` is explicitly passed in `dxdt`. It is a combination of the two `do_step` methods
- * above.
- * - `do_step( sys , x , t , dt , xerr )` - This `do_step` method is needed to fulfill the Error Stepper concept. The
- * state is updated in-place and an error estimate is calculated. A type modelling a Boost.Range can be used for x.
- * - `do_step( sys , x , dxdt , t , dt , xerr )` - This method updates the state in-place, but the derivative at the
- * point `t` must be passed in `dxdt`. An error estimate is calculated.
- * - `do_step( sys , in , t , out , dt , xerr )` - This method updates the state out-of-place and estimates the error
- * during the step.
- * - `do_step( sys , in , dxdt , t , out , dt , xerr )` - This methods updates the state out-of-place and estimates
- * the error during the step. Furthermore, the derivative at `t` must be passed in `dxdt`.
- *
- * \note The system is always passed as value, which might result in poor performance if it contains data. In this
- * case it can be used with `boost::ref` or `std::ref`, for example `stepper.do_step( boost::ref( sys ) , x , t , dt );`
- *
- * \note The time `t` is not advanced by the stepper. This has to done manually, or by the appropriate `integrate`
- * routines or `iterator`s.
- *
- * \tparam Stepper The stepper on which this class should work. It is used via CRTP, hence explicit_stepper_base
- * provides the interface for the Stepper.
- * \tparam Order The order of a stepper if the stepper is used without error estimation.
- * \tparam StepperOrder The order of a step if the stepper is used with error estimation. Usually Order and StepperOrder have
- * the same value.
- * \tparam ErrorOrder The order of the error step if the stepper is used with error estimation.
- * \tparam State The state type for the stepper.
- * \tparam Value The value type for the stepper. This should be a floating point type, like float,
- * double, or a multiprecision type. It must not necessary be the value_type of the State. For example
- * the State can be a `vector< complex< double > >` in this case the Value must be double.
- * The default value is double.
- * \tparam Deriv The type representing time derivatives of the state type. It is usually the same type as the
- * state type, only if used with Boost.Units both types differ.
- * \tparam Time The type representing the time. Usually the same type as the value type. When Boost.Units is
- * used, this type has usually a unit.
- * \tparam Algebra The algebra type which must fulfill the Algebra Concept.
- * \tparam Operations The type for the operations which must fulfill the Operations Concept.
- * \tparam Resizer The resizer policy class.
- */
-
-
- /**
- * \fn explicit_error_stepper_base::explicit_error_stepper_base( const algebra_type &algebra = algebra_type() )
- *
- * \brief Constructs a explicit_error_stepper_base class. This constructor can be used as a default
- * constructor if the algebra has a default constructor.
- * \param algebra A copy of algebra is made and stored inside explicit_stepper_base.
- */
-
- /**
- * \fn explicit_error_stepper_base::order( void ) const
- * \return Returns the order of the stepper if it used without error estimation.
- */
-
- /**
- * \fn explicit_error_stepper_base::stepper_order( void ) const
- * \return Returns the order of a step if the stepper is used without error estimation.
- */
-
- /**
- * \fn explicit_error_stepper_base::error_order( void ) const
- * \return Returns the order of an error step if the stepper is used without error estimation.
- */
-
- /**
- * \fn explicit_error_stepper_base::do_step( System system , StateInOut &x , time_type t , time_type dt )
- * \brief This method performs one step. It transforms the result in-place.
- *
- * \param system The system function to solve, hence the r.h.s. of the ordinary differential equation. It must fulfill the
- * Simple System concept.
- * \param x The state of the ODE which should be solved. After calling do_step the result is updated in x.
- * \param t The value of the time, at which the step should be performed.
- * \param dt The step size.
- */
-
- /**
- * \fn explicit_error_stepper_base::do_step( System system , StateInOut &x , const DerivIn &dxdt , time_type t , time_type dt )
- * \brief The method performs one step with the stepper passed by Stepper. Additionally to the other method
- * the derivative of x is also passed to this method. It is supposed to be used in the following way:
- *
- * \code
- * sys( x , dxdt , t );
- * stepper.do_step( sys , x , dxdt , t , dt );
- * \endcode
- *
- * The result is updated in place in x. This method is disabled if Time and Deriv are of the same type. In this
- * case the method could not be distinguished from other `do_step` versions.
- *
- * \note This method does not solve the forwarding problem.
- *
- * \param system The system function to solve, hence the r.h.s. of the ODE. It must fulfill the
- * Simple System concept.
- * \param x The state of the ODE which should be solved. After calling do_step the result is updated in x.
- * \param dxdt The derivative of x at t.
- * \param t The value of the time, at which the step should be performed.
- * \param dt The step size.
- */
-
- /**
- * \fn explicit_error_stepper_base::do_step( System system , const StateIn &in , time_type t , StateOut &out , time_type dt )
- * \brief The method performs one step with the stepper passed by Stepper. The state of the ODE is updated out-of-place.
- * This method is disabled if StateIn and Time are the same type. In this case the method can not be distinguished from
- * other `do_step` variants.
- * \note This method does not solve the forwarding problem.
- *
- * \param system The system function to solve, hence the r.h.s. of the ODE. It must fulfill the
- * Simple System concept.
- * \param in The state of the ODE which should be solved. in is not modified in this method
- * \param t The value of the time, at which the step should be performed.
- * \param out The result of the step is written in out.
- * \param dt The step size.
- */
-
-
- /**
- * \fn explicit_error_stepper_base::do_step( System system , const StateIn &in , const DerivIn &dxdt , time_type t , StateOut &out , time_type dt )
- * \brief The method performs one step with the stepper passed by Stepper. The state of the ODE is updated out-of-place.
- * Furthermore, the derivative of x at t is passed to the stepper. It is supposed to be used in the following way:
- *
- * \code
- * sys( in , dxdt , t );
- * stepper.do_step( sys , in , dxdt , t , out , dt );
- * \endcode
- *
- * This method is disabled if DerivIn and Time are of same type.
- *
- * \note This method does not solve the forwarding problem.
- *
- * \param system The system function to solve, hence the r.h.s. of the ODE. It must fulfill the
- * Simple System concept.
- * \param in The state of the ODE which should be solved. in is not modified in this method
- * \param dxdt The derivative of x at t.
- * \param t The value of the time, at which the step should be performed.
- * \param out The result of the step is written in out.
- * \param dt The step size.
- */
-
- /**
- * \fn explicit_error_stepper_base::do_step( System system , StateInOut &x , time_type t , time_type dt , Err &xerr )
- * \brief The method performs one step with the stepper passed by Stepper and estimates the error. The state of the ODE
- * is updated in-place.
- *
- * \param system The system function to solve, hence the r.h.s. of the ODE. It must fulfill the
- * Simple System concept.
- * \param x The state of the ODE which should be solved. x is updated by this method.
- * \param t The value of the time, at which the step should be performed.
- * \param dt The step size.
- * \param xerr The estimation of the error is stored in xerr.
- */
-
- /**
- * \fn explicit_error_stepper_base::do_step( System system , StateInOut &x , const DerivIn &dxdt , time_type t , time_type dt , Err &xerr )
- * \brief The method performs one step with the stepper passed by Stepper. Additionally to the other method
- * the derivative of x is also passed to this method. It is supposed to be used in the following way:
- *
- * \code
- * sys( x , dxdt , t );
- * stepper.do_step( sys , x , dxdt , t , dt , xerr );
- * \endcode
- *
- * The result is updated in place in x. This method is disabled if Time and DerivIn are of the same type. In this
- * case the method could not be distinguished from other `do_step` versions.
- *
- * \note This method does not solve the forwarding problem.
- *
- * \param system The system function to solve, hence the r.h.s. of the ODE. It must fulfill the
- * Simple System concept.
- * \param x The state of the ODE which should be solved. After calling do_step the result is updated in x.
- * \param dxdt The derivative of x at t.
- * \param t The value of the time, at which the step should be performed.
- * \param dt The step size.
- * \param xerr The error estimate is stored in xerr.
- */
-
- /**
- * \fn explicit_error_stepper_base::do_step( System system , const StateIn &in , time_type t , StateOut &out , time_type dt , Err &xerr )
- * \brief The method performs one step with the stepper passed by Stepper. The state of the ODE is updated out-of-place.
- * Furthermore, the error is estimated.
- *
- * \note This method does not solve the forwarding problem.
- *
- * \param system The system function to solve, hence the r.h.s. of the ODE. It must fulfill the
- * Simple System concept.
- * \param in The state of the ODE which should be solved. in is not modified in this method
- * \param t The value of the time, at which the step should be performed.
- * \param out The result of the step is written in out.
- * \param dt The step size.
- * \param xerr The error estimate.
- */
-
-
- /**
- * \fn explicit_error_stepper_base::do_step( System system , const StateIn &in , const DerivIn &dxdt , time_type t , StateOut &out , time_type dt , Err &xerr )
- * \brief The method performs one step with the stepper passed by Stepper. The state of the ODE is updated out-of-place.
- * Furthermore, the derivative of x at t is passed to the stepper and the error is estimated. It is supposed to be used in the following way:
- *
- * \code
- * sys( in , dxdt , t );
- * stepper.do_step( sys , in , dxdt , t , out , dt );
- * \endcode
- *
- * This method is disabled if DerivIn and Time are of same type.
- *
- * \note This method does not solve the forwarding problem.
- *
- * \param system The system function to solve, hence the r.h.s. of the ODE. It must fulfill the
- * Simple System concept.
- * \param in The state of the ODE which should be solved. in is not modified in this method
- * \param dxdt The derivative of x at t.
- * \param t The value of the time, at which the step should be performed.
- * \param out The result of the step is written in out.
- * \param dt The step size.
- * \param xerr The error estimate.
- */
-
-
- /**
- * \fn explicit_error_stepper_base::adjust_size( const StateIn &x )
- * \brief Adjust the size of all temporaries in the stepper manually.
- * \param x A state from which the size of the temporaries to be resized is deduced.
- */
-
-} // odeint
-} // numeric
-} // boost
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_BASE_EXPLICIT_ERROR_STEPPER_BASE_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/base/explicit_error_stepper_fsal_base.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/base/explicit_error_stepper_fsal_base.hpp
deleted file mode 100644
index 34381eaf27460414083dbcb1a8eb3bdfeeb9abe5..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/base/explicit_error_stepper_fsal_base.hpp
+++ /dev/null
@@ -1,677 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/base/explicit_error_stepper_fsal_base.hpp
-
- [begin_description]
- Base class for all explicit first-same-as-last Runge Kutta steppers.
- [end_description]
-
- Copyright 2010-2013 Karsten Ahnert
- Copyright 2010-2012 Mario Mulansky
- Copyright 2012 Christoph Koke
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_BASE_EXPLICIT_ERROR_STEPPER_FSAL_BASE_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_BASE_EXPLICIT_ERROR_STEPPER_FSAL_BASE_HPP_INCLUDED
-
-#include <boost/utility/enable_if.hpp>
-#include <boost/type_traits/is_same.hpp>
-
-
-#include <boost/numeric/odeint/util/bind.hpp>
-#include <boost/numeric/odeint/util/unwrap_reference.hpp>
-#include <boost/numeric/odeint/util/state_wrapper.hpp>
-#include <boost/numeric/odeint/util/is_resizeable.hpp>
-#include <boost/numeric/odeint/util/resizer.hpp>
-#include <boost/numeric/odeint/util/copy.hpp>
-
-#include <boost/numeric/odeint/stepper/stepper_categories.hpp>
-
-#include <boost/numeric/odeint/stepper/base/algebra_stepper_base.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-/*
- * base class for explicit stepper and error steppers with the fsal property
- * models the stepper AND the error stepper fsal concept
- *
- * this class provides the following do_step overloads
- * do_step( sys , x , t , dt )
- * do_step( sys , x , dxdt , t , dt )
- * do_step( sys , in , t , out , dt )
- * do_step( sys , in , dxdt_in , t , out , dxdt_out , dt )
- * do_step( sys , x , t , dt , xerr )
- * do_step( sys , x , dxdt , t , dt , xerr )
- * do_step( sys , in , t , out , dt , xerr )
- * do_step( sys , in , dxdt_in , t , out , dxdt_out , dt , xerr )
- */
-template<
-class Stepper ,
-unsigned short Order ,
-unsigned short StepperOrder ,
-unsigned short ErrorOrder ,
-class State ,
-class Value ,
-class Deriv ,
-class Time ,
-class Algebra ,
-class Operations ,
-class Resizer
->
-class explicit_error_stepper_fsal_base : public algebra_stepper_base< Algebra , Operations >
-{
-public:
-
- typedef algebra_stepper_base< Algebra , Operations > algebra_stepper_base_type;
- typedef typename algebra_stepper_base_type::algebra_type algebra_type;
-
- typedef State state_type;
- typedef Value value_type;
- typedef Deriv deriv_type;
- typedef Time time_type;
- typedef Resizer resizer_type;
- typedef Stepper stepper_type;
- typedef explicit_error_stepper_fsal_tag stepper_category;
-
- #ifndef DOXYGEN_SKIP
- typedef state_wrapper< state_type > wrapped_state_type;
- typedef state_wrapper< deriv_type > wrapped_deriv_type;
- typedef explicit_error_stepper_fsal_base< Stepper , Order , StepperOrder , ErrorOrder ,
- State , Value , Deriv , Time , Algebra , Operations , Resizer > internal_stepper_base_type;
- #endif
-
-
- typedef unsigned short order_type;
- static const order_type order_value = Order;
- static const order_type stepper_order_value = StepperOrder;
- static const order_type error_order_value = ErrorOrder;
-
- explicit_error_stepper_fsal_base( const algebra_type &algebra = algebra_type() )
- : algebra_stepper_base_type( algebra ) , m_first_call( true )
- { }
-
- order_type order( void ) const
- {
- return order_value;
- }
-
- order_type stepper_order( void ) const
- {
- return stepper_order_value;
- }
-
- order_type error_order( void ) const
- {
- return error_order_value;
- }
-
-
- /*
- * version 1 : do_step( sys , x , t , dt )
- *
- * the two overloads are needed in order to solve the forwarding problem
- */
- template< class System , class StateInOut >
- void do_step( System system , StateInOut &x , time_type t , time_type dt )
- {
- do_step_v1( system , x , t , dt );
- }
-
- /**
- * \brief Second version to solve the forwarding problem, can be called with Boost.Range as StateInOut.
- */
- template< class System , class StateInOut >
- void do_step( System system , const StateInOut &x , time_type t , time_type dt )
- {
- do_step_v1( system , x , t , dt );
- }
-
-
- /*
- * version 2 : do_step( sys , x , dxdt , t , dt )
- *
- * this version does not solve the forwarding problem, boost.range can not be used
- *
- * the disable is needed to avoid ambiguous overloads if state_type = time_type
- */
- template< class System , class StateInOut , class DerivInOut >
- typename boost::disable_if< boost::is_same< StateInOut , time_type > , void >::type
- do_step( System system , StateInOut &x , DerivInOut &dxdt , time_type t , time_type dt )
- {
- m_first_call = true;
- this->stepper().do_step_impl( system , x , dxdt , t , x , dxdt , dt );
- }
-
-
- /*
- * named Version 2: do_step_dxdt_impl( sys , in , dxdt , t , dt )
- *
- * this version is needed when this stepper is used for initializing
- * multistep stepper like adams-bashforth. Hence we provide an explicitely
- * named version that is not disabled. Meant for internal use only.
- */
- template< class System , class StateInOut , class DerivInOut >
- void do_step_dxdt_impl( System system , StateInOut &x , DerivInOut &dxdt , time_type t , time_type dt )
- {
- m_first_call = true;
- this->stepper().do_step_impl( system , x , dxdt , t , x , dxdt , dt );
- }
-
- /*
- * version 3 : do_step( sys , in , t , out , dt )
- *
- * this version does not solve the forwarding problem, boost.range can not
- * be used.
- *
- * the disable is needed to avoid ambiguous overloads if
- * state_type = time_type
- */
- template< class System , class StateIn , class StateOut >
- typename boost::disable_if< boost::is_same< StateIn , time_type > , void >::type
- do_step( System system , const StateIn &in , time_type t , StateOut &out , time_type dt )
- {
- if( m_resizer.adjust_size( in , detail::bind( &internal_stepper_base_type::template resize_impl< StateIn > , detail::ref( *this ) , detail::_1 ) ) || m_first_call )
- {
- initialize( system , in , t );
- }
- this->stepper().do_step_impl( system , in , m_dxdt.m_v , t , out , m_dxdt.m_v , dt );
- }
-
-
- /*
- * version 4 : do_step( sys , in , dxdt_in , t , out , dxdt_out , dt )
- *
- * this version does not solve the forwarding problem, boost.range can not be used
- */
- template< class System, class StateIn, class DerivIn, class StateOut,
- class DerivOut >
- void do_step( System system, const StateIn &in, const DerivIn &dxdt_in,
- time_type t, StateOut &out, DerivOut &dxdt_out, time_type dt )
- {
- m_first_call = true;
- this->stepper().do_step_impl( system, in, dxdt_in, t, out, dxdt_out,
- dt );
- }
-
-
-
-
-
- /*
- * version 5 : do_step( sys , x , t , dt , xerr )
- *
- * the two overloads are needed in order to solve the forwarding problem
- */
- template< class System , class StateInOut , class Err >
- void do_step( System system , StateInOut &x , time_type t , time_type dt , Err &xerr )
- {
- do_step_v5( system , x , t , dt , xerr );
- }
-
- /**
- * \brief Second version to solve the forwarding problem, can be called with Boost.Range as StateInOut.
- */
- template< class System , class StateInOut , class Err >
- void do_step( System system , const StateInOut &x , time_type t , time_type dt , Err &xerr )
- {
- do_step_v5( system , x , t , dt , xerr );
- }
-
-
- /*
- * version 6 : do_step( sys , x , dxdt , t , dt , xerr )
- *
- * this version does not solve the forwarding problem, boost.range can not be used
- *
- * the disable is needed to avoid ambiguous overloads if state_type = time_type
- */
- template< class System , class StateInOut , class DerivInOut , class Err >
- typename boost::disable_if< boost::is_same< StateInOut , time_type > , void >::type
- do_step( System system , StateInOut &x , DerivInOut &dxdt , time_type t , time_type dt , Err &xerr )
- {
- m_first_call = true;
- this->stepper().do_step_impl( system , x , dxdt , t , x , dxdt , dt , xerr );
- }
-
-
-
-
- /*
- * version 7 : do_step( sys , in , t , out , dt , xerr )
- *
- * this version does not solve the forwarding problem, boost.range can not be used
- */
- template< class System , class StateIn , class StateOut , class Err >
- void do_step( System system , const StateIn &in , time_type t , StateOut &out , time_type dt , Err &xerr )
- {
- if( m_resizer.adjust_size( in , detail::bind( &internal_stepper_base_type::template resize_impl< StateIn > , detail::ref( *this ) , detail::_1 ) ) || m_first_call )
- {
- initialize( system , in , t );
- }
- this->stepper().do_step_impl( system , in , m_dxdt.m_v , t , out , m_dxdt.m_v , dt , xerr );
- }
-
-
- /*
- * version 8 : do_step( sys , in , dxdt_in , t , out , dxdt_out , dt , xerr )
- *
- * this version does not solve the forwarding problem, boost.range can not be used
- */
- template< class System , class StateIn , class DerivIn , class StateOut , class DerivOut , class Err >
- void do_step( System system , const StateIn &in , const DerivIn &dxdt_in , time_type t ,
- StateOut &out , DerivOut &dxdt_out , time_type dt , Err &xerr )
- {
- m_first_call = true;
- this->stepper().do_step_impl( system , in , dxdt_in , t , out , dxdt_out , dt , xerr );
- }
-
- template< class StateIn >
- void adjust_size( const StateIn &x )
- {
- resize_impl( x );
- }
-
- void reset( void )
- {
- m_first_call = true;
- }
-
- template< class DerivIn >
- void initialize( const DerivIn &deriv )
- {
- boost::numeric::odeint::copy( deriv , m_dxdt.m_v );
- m_first_call = false;
- }
-
- template< class System , class StateIn >
- void initialize( System system , const StateIn &x , time_type t )
- {
- typename odeint::unwrap_reference< System >::type &sys = system;
- sys( x , m_dxdt.m_v , t );
- m_first_call = false;
- }
-
- bool is_initialized( void ) const
- {
- return ! m_first_call;
- }
-
-
-
-private:
-
- template< class System , class StateInOut >
- void do_step_v1( System system , StateInOut &x , time_type t , time_type dt )
- {
- if( m_resizer.adjust_size( x , detail::bind( &internal_stepper_base_type::template resize_impl< StateInOut > , detail::ref( *this ) , detail::_1 ) ) || m_first_call )
- {
- initialize( system , x , t );
- }
- this->stepper().do_step_impl( system , x , m_dxdt.m_v , t , x , m_dxdt.m_v , dt );
- }
-
- template< class System , class StateInOut , class Err >
- void do_step_v5( System system , StateInOut &x , time_type t , time_type dt , Err &xerr )
- {
- if( m_resizer.adjust_size( x , detail::bind( &internal_stepper_base_type::template resize_impl< StateInOut > , detail::ref( *this ) , detail::_1 ) ) || m_first_call )
- {
- initialize( system , x , t );
- }
- this->stepper().do_step_impl( system , x , m_dxdt.m_v , t , x , m_dxdt.m_v , dt , xerr );
- }
-
- template< class StateIn >
- bool resize_impl( const StateIn &x )
- {
- return adjust_size_by_resizeability( m_dxdt , x , typename is_resizeable<deriv_type>::type() );
- }
-
-
- stepper_type& stepper( void )
- {
- return *static_cast< stepper_type* >( this );
- }
-
- const stepper_type& stepper( void ) const
- {
- return *static_cast< const stepper_type* >( this );
- }
-
-
- resizer_type m_resizer;
- bool m_first_call;
-
-protected:
-
-
- wrapped_deriv_type m_dxdt;
-};
-
-
-/******* DOXYGEN *******/
-
-/**
- * \class explicit_error_stepper_fsal_base
- * \brief Base class for explicit steppers with error estimation and stepper fulfilling the FSAL (first-same-as-last)
- * property. This class can be used with controlled steppers for step size control.
- *
- * This class serves as the base class for all explicit steppers with algebra and operations and which fulfill the FSAL
- * property. In contrast to explicit_stepper_base it also estimates the error and can be used in a controlled stepper
- * to provide step size control.
- *
- * The FSAL property means that the derivative of the system at t+dt is already used in the current step going from
- * t to t +dt. Therefore, some more do_steps method can be introduced and the controlled steppers can explicitly make use
- * of this property.
- *
- * \note This stepper provides `do_step` methods with and without error estimation. It has therefore three orders,
- * one for the order of a step if the error is not estimated. The other two orders are the orders of the step and
- * the error step if the error estimation is performed.
- *
- * explicit_error_stepper_fsal_base is used as the interface in a CRTP (currently recurring template
- * pattern). In order to work correctly the parent class needs to have a method
- * `do_step_impl( system , in , dxdt_in , t , out , dxdt_out , dt , xerr )`.
- * explicit_error_stepper_fsal_base derives from algebra_stepper_base.
- *
- * This class can have an intrinsic state depending on the explicit usage of the `do_step` method. This means that some
- * `do_step` methods are expected to be called in order. For example the `do_step( sys , x , t , dt , xerr )` will keep track
- * of the derivative of `x` which is the internal state. The first call of this method is recognized such that one
- * does not explicitly initialize the internal state, so it is safe to use this method like
- *
- * \code
- * stepper_type stepper;
- * stepper.do_step( sys , x , t , dt , xerr );
- * stepper.do_step( sys , x , t , dt , xerr );
- * stepper.do_step( sys , x , t , dt , xerr );
- * \endcode
- *
- * But it is unsafe to call this method with different system functions after each other. Do do so, one must initialize the
- * internal state with the `initialize` method or reset the internal state with the `reset` method.
- *
- * explicit_error_stepper_fsal_base provides several overloaded `do_step` methods, see the list below. Only two of them are needed
- * to fulfill the Error Stepper concept. The other ones are for convenience and for better performance. Some of them
- * simply update the state out-of-place, while other expect that the first derivative at `t` is passed to the stepper.
- *
- * - `do_step( sys , x , t , dt )` - The classical `do_step` method needed to fulfill the Error Stepper concept. The
- * state is updated in-place. A type modelling a Boost.Range can be used for x.
- * - `do_step( sys , x , dxdt , t , dt )` - This method updates the state x and the derivative dxdt in-place. It is expected
- * that dxdt has the value of the derivative of x at time t.
- * - `do_step( sys , in , t , out , dt )` - This method updates the state out-of-place, hence the result of the step
- * is stored in `out`.
- * - `do_step( sys , in , dxdt_in , t , out , dxdt_out , dt )` - This method updates the state and the derivative
- * out-of-place. It expects that the derivative at the point `t` is explicitly passed in `dxdt_in`.
- * - `do_step( sys , x , t , dt , xerr )` - This `do_step` method is needed to fulfill the Error Stepper concept. The
- * state is updated in-place and an error estimate is calculated. A type modelling a Boost.Range can be used for x.
- * - `do_step( sys , x , dxdt , t , dt , xerr )` - This method updates the state and the derivative in-place. It is assumed
- * that the dxdt has the value of the derivative of x at time t. An error estimate is calculated.
- * - `do_step( sys , in , t , out , dt , xerr )` - This method updates the state out-of-place and estimates the error
- * during the step.
- * - `do_step( sys , in , dxdt_in , t , out , dxdt_out , dt , xerr )` - This methods updates the state and the derivative
- * out-of-place and estimates the error during the step. It is assumed the dxdt_in is derivative of in at time t.
- *
- * \note The system is always passed as value, which might result in poor performance if it contains data. In this
- * case it can be used with `boost::ref` or `std::ref`, for example `stepper.do_step( boost::ref( sys ) , x , t , dt );`
- *
- * \note The time `t` is not advanced by the stepper. This has to done manually, or by the appropriate `integrate`
- * routines or `iterator`s.
- *
- * \tparam Stepper The stepper on which this class should work. It is used via CRTP, hence explicit_stepper_base
- * provides the interface for the Stepper.
- * \tparam Order The order of a stepper if the stepper is used without error estimation.
- * \tparam StepperOrder The order of a step if the stepper is used with error estimation. Usually Order and StepperOrder have
- * the same value.
- * \tparam ErrorOrder The order of the error step if the stepper is used with error estimation.
- * \tparam State The state type for the stepper.
- * \tparam Value The value type for the stepper. This should be a floating point type, like float,
- * double, or a multiprecision type. It must not necessary be the value_type of the State. For example
- * the State can be a `vector< complex< double > >` in this case the Value must be double.
- * The default value is double.
- * \tparam Deriv The type representing time derivatives of the state type. It is usually the same type as the
- * state type, only if used with Boost.Units both types differ.
- * \tparam Time The type representing the time. Usually the same type as the value type. When Boost.Units is
- * used, this type has usually a unit.
- * \tparam Algebra The algebra type which must fulfill the Algebra Concept.
- * \tparam Operations The type for the operations which must fulfill the Operations Concept.
- * \tparam Resizer The resizer policy class.
- */
-
-
-
- /**
- * \fn explicit_error_stepper_fsal_base::explicit_error_stepper_fsal_base( const algebra_type &algebra )
- * \brief Constructs a explicit_stepper_fsal_base class. This constructor can be used as a default
- * constructor if the algebra has a default constructor.
- * \param algebra A copy of algebra is made and stored inside explicit_stepper_base.
- */
-
-
- /**
- * \fn explicit_error_stepper_fsal_base::order( void ) const
- * \return Returns the order of the stepper if it used without error estimation.
- */
-
- /**
- * \fn explicit_error_stepper_fsal_base::stepper_order( void ) const
- * \return Returns the order of a step if the stepper is used without error estimation.
- */
-
-
- /**
- * \fn explicit_error_stepper_fsal_base::error_order( void ) const
- * \return Returns the order of an error step if the stepper is used without error estimation.
- */
-
- /**
- * \fn explicit_error_stepper_fsal_base::do_step( System system , StateInOut &x , time_type t , time_type dt )
- * \brief This method performs one step. It transforms the result in-place.
- *
- * \note This method uses the internal state of the stepper.
- *
- * \param system The system function to solve, hence the r.h.s. of the ordinary differential equation. It must fulfill the
- * Simple System concept.
- * \param x The state of the ODE which should be solved. After calling do_step the result is updated in x.
- * \param t The value of the time, at which the step should be performed.
- * \param dt The step size.
- */
-
-
- /**
- * \fn explicit_error_stepper_fsal_base::do_step( System system , StateInOut &x , DerivInOut &dxdt , time_type t , time_type dt )
- * \brief The method performs one step with the stepper passed by Stepper. Additionally to the other methods
- * the derivative of x is also passed to this method. Therefore, dxdt must be evaluated initially:
- *
- * \code
- * ode( x , dxdt , t );
- * for( ... )
- * {
- * stepper.do_step( ode , x , dxdt , t , dt );
- * t += dt;
- * }
- * \endcode
- *
- * \note This method does NOT use the initial state, since the first derivative is explicitly passed to this method.
- *
- * The result is updated in place in x as well as the derivative dxdt. This method is disabled if
- * Time and StateInOut are of the same type. In this case the method could not be distinguished from other `do_step`
- * versions.
- *
- * \note This method does not solve the forwarding problem.
- *
- * \param system The system function to solve, hence the r.h.s. of the ODE. It must fulfill the
- * Simple System concept.
- * \param x The state of the ODE which should be solved. After calling do_step the result is updated in x.
- * \param dxdt The derivative of x at t. After calling `do_step` dxdt is updated to the new value.
- * \param t The value of the time, at which the step should be performed.
- * \param dt The step size.
- */
-
- /**
- * \fn explicit_error_stepper_fsal_base::do_step( System system , const StateIn &in , time_type t , StateOut &out , time_type dt )
- * \brief The method performs one step with the stepper passed by Stepper. The state of the ODE is updated out-of-place.
- * This method is disabled if StateIn and Time are the same type. In this case the method can not be distinguished from
- * other `do_step` variants.
- *
- * \note This method uses the internal state of the stepper.
- *
- * \note This method does not solve the forwarding problem.
- *
- * \param system The system function to solve, hence the r.h.s. of the ODE. It must fulfill the
- * Simple System concept.
- * \param in The state of the ODE which should be solved. in is not modified in this method
- * \param t The value of the time, at which the step should be performed.
- * \param out The result of the step is written in out.
- * \param dt The step size.
- */
-
- /**
- * \fn explicit_error_stepper_fsal_base::do_step( System system , const StateIn &in , const DerivIn &dxdt_in , time_type t , StateOut &out , DerivOut &dxdt_out , time_type dt )
- * \brief The method performs one step with the stepper passed by Stepper. The state of the ODE is updated out-of-place.
- * Furthermore, the derivative of x at t is passed to the stepper and updated by the stepper to its new value at
- * t+dt.
- *
- * \note This method does not solve the forwarding problem.
- *
- * \note This method does NOT use the internal state of the stepper.
- *
- * \param system The system function to solve, hence the r.h.s. of the ODE. It must fulfill the
- * Simple System concept.
- * \param in The state of the ODE which should be solved. in is not modified in this method
- * \param dxdt_in The derivative of x at t.
- * \param t The value of the time, at which the step should be performed.
- * \param out The result of the step is written in out.
- * \param dxdt_out The updated derivative of `out` at `t+dt`.
- * \param dt The step size.
- */
-
- /**
- * \fn explicit_error_stepper_fsal_base::do_step( System system , StateInOut &x , time_type t , time_type dt , Err &xerr )
- * \brief The method performs one step with the stepper passed by Stepper and estimates the error. The state of the ODE
- * is updated in-place.
- *
- *
- * \note This method uses the internal state of the stepper.
- *
- * \param system The system function to solve, hence the r.h.s. of the ODE. It must fulfill the
- * Simple System concept.
- * \param x The state of the ODE which should be solved. x is updated by this method.
- * \param t The value of the time, at which the step should be performed.
- * \param dt The step size.
- * \param xerr The estimation of the error is stored in xerr.
- */
-
- /**
- * \fn explicit_error_stepper_fsal_base::do_step( System system , StateInOut &x , DerivInOut &dxdt , time_type t , time_type dt , Err &xerr )
- * \brief The method performs one step with the stepper passed by Stepper. Additionally to the other method
- * the derivative of x is also passed to this method and updated by this method.
- *
- * \note This method does NOT use the internal state of the stepper.
- *
- * The result is updated in place in x. This method is disabled if Time and Deriv are of the same type. In this
- * case the method could not be distinguished from other `do_step` versions. This method is disabled if StateInOut and
- * Time are of the same type.
- *
- * \note This method does NOT use the internal state of the stepper.
- *
- * \note This method does not solve the forwarding problem.
- *
- * \param system The system function to solve, hence the r.h.s. of the ODE. It must fulfill the
- * Simple System concept.
- * \param x The state of the ODE which should be solved. After calling do_step the result is updated in x.
- * \param dxdt The derivative of x at t. After calling `do_step` this value is updated to the new value at `t+dt`.
- * \param t The value of the time, at which the step should be performed.
- * \param dt The step size.
- * \param xerr The error estimate is stored in xerr.
- */
-
-
- /**
- * \fn explicit_error_stepper_fsal_base::do_step( System system , const StateIn &in , time_type t , StateOut &out , time_type dt , Err &xerr )
- * \brief The method performs one step with the stepper passed by Stepper. The state of the ODE is updated out-of-place.
- * Furthermore, the error is estimated.
- *
- * \note This method uses the internal state of the stepper.
- *
- * \note This method does not solve the forwarding problem.
- *
- * \param system The system function to solve, hence the r.h.s. of the ODE. It must fulfill the
- * Simple System concept.
- * \param in The state of the ODE which should be solved. in is not modified in this method
- * \param t The value of the time, at which the step should be performed.
- * \param out The result of the step is written in out.
- * \param dt The step size.
- * \param xerr The error estimate.
- */
-
- /**
- * \fn explicit_error_stepper_fsal_base::do_step( System system , const StateIn &in , const DerivIn &dxdt_in , time_type t , StateOut &out , DerivOut &dxdt_out , time_type dt , Err &xerr )
- * \brief The method performs one step with the stepper passed by Stepper. The state of the ODE is updated out-of-place.
- * Furthermore, the derivative of x at t is passed to the stepper and the error is estimated.
- *
- * \note This method does NOT use the internal state of the stepper.
- *
- * \note This method does not solve the forwarding problem.
- *
- * \param system The system function to solve, hence the r.h.s. of the ODE. It must fulfill the
- * Simple System concept.
- * \param in The state of the ODE which should be solved. in is not modified in this method
- * \param dxdt_in The derivative of x at t.
- * \param t The value of the time, at which the step should be performed.
- * \param out The result of the step is written in out.
- * \param dxdt_out The new derivative at `t+dt` is written into this variable.
- * \param dt The step size.
- * \param xerr The error estimate.
- */
-
- /**
- * \fn explicit_error_stepper_fsal_base::adjust_size( const StateIn &x )
- * \brief Adjust the size of all temporaries in the stepper manually.
- * \param x A state from which the size of the temporaries to be resized is deduced.
- */
-
- /**
- * \fn explicit_error_stepper_fsal_base::reset( void )
- * \brief Resets the internal state of this stepper. After calling this method it is safe to use all
- * `do_step` method without explicitly initializing the stepper.
- */
-
- /**
- * \fn explicit_error_stepper_fsal_base::initialize( const DerivIn &deriv )
- * \brief Initializes the internal state of the stepper.
- * \param deriv The derivative of x. The next call of `do_step` expects that the derivative of `x` passed to `do_step`
- * has the value of `deriv`.
- */
-
- /**
- * \fn explicit_error_stepper_fsal_base::initialize( System system , const StateIn &x , time_type t )
- * \brief Initializes the internal state of the stepper.
- *
- * This method is equivalent to
- * \code
- * Deriv dxdt;
- * system( x , dxdt , t );
- * stepper.initialize( dxdt );
- * \endcode
- *
- * \param system The system function for the next calls of `do_step`.
- * \param x The current state of the ODE.
- * \param t The current time of the ODE.
- */
-
- /**
- * \fn explicit_error_stepper_fsal_base::is_initialized( void ) const
- * \brief Returns if the stepper is already initialized. If the stepper is not initialized, the first
- * call of `do_step` will initialize the state of the stepper. If the stepper is already initialized
- * the system function can not be safely exchanged between consecutive `do_step` calls.
- */
-
-} // odeint
-} // numeric
-} // boost
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_BASE_EXPLICIT_ERROR_STEPPER_FSAL_BASE_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/base/explicit_stepper_base.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/base/explicit_stepper_base.hpp
deleted file mode 100644
index 4dca52572973871ab20f278cd31192e8c6919a2a..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/base/explicit_stepper_base.hpp
+++ /dev/null
@@ -1,415 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/base/explicit_stepper_base.hpp
-
- [begin_description]
- Base class for all explicit Runge Kutta steppers.
- [end_description]
-
- Copyright 2010-2013 Karsten Ahnert
- Copyright 2010-2012 Mario Mulansky
- Copyright 2012 Christoph Koke
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_BASE_EXPLICIT_STEPPER_BASE_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_BASE_EXPLICIT_STEPPER_BASE_HPP_INCLUDED
-
-
-#include <boost/utility/enable_if.hpp>
-#include <boost/type_traits/is_same.hpp>
-
-#include <boost/numeric/odeint/util/bind.hpp>
-#include <boost/numeric/odeint/util/unwrap_reference.hpp>
-
-#include <boost/numeric/odeint/util/state_wrapper.hpp>
-#include <boost/numeric/odeint/util/resizer.hpp>
-#include <boost/numeric/odeint/util/is_resizeable.hpp>
-
-#include <boost/numeric/odeint/stepper/stepper_categories.hpp>
-
-#include <boost/numeric/odeint/stepper/base/algebra_stepper_base.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-/*
- * base class for explicit steppers
- * models the stepper concept
- *
- * this class provides the following overloads
- * do_step( sys , x , t , dt )
- * do_step( sys , in , t , out , dt )
- * do_step( sys , x , dxdt_in , t , dt )
- * do_step( sys , in , dxdt_in , t , out , dt )
- */
-
-template<
-class Stepper ,
-unsigned short Order ,
-class State ,
-class Value ,
-class Deriv ,
-class Time ,
-class Algebra ,
-class Operations ,
-class Resizer
->
-class explicit_stepper_base : public algebra_stepper_base< Algebra , Operations >
-{
-public:
-
- #ifndef DOXYGEN_SKIP
- typedef explicit_stepper_base< Stepper , Order , State , Value , Deriv , Time , Algebra , Operations , Resizer > internal_stepper_base_type;
- #endif // DOXYGEN_SKIP
-
-
- typedef State state_type;
- typedef Value value_type;
- typedef Deriv deriv_type;
- typedef Time time_type;
- typedef Resizer resizer_type;
- typedef Stepper stepper_type;
- typedef stepper_tag stepper_category;
- typedef algebra_stepper_base< Algebra , Operations > algebra_stepper_base_type;
- typedef typename algebra_stepper_base_type::algebra_type algebra_type;
- typedef typename algebra_stepper_base_type::operations_type operations_type;
- typedef unsigned short order_type;
-
- #ifndef DOXYGEN_SKIP
- typedef state_wrapper< state_type > wrapped_state_type;
- typedef state_wrapper< deriv_type > wrapped_deriv_type;
- #endif // DOXYGEN_SKIP
-
-
- static const order_type order_value = Order;
-
-
- explicit_stepper_base( const algebra_type &algebra = algebra_type() )
- : algebra_stepper_base_type( algebra )
- { }
-
- /**
- * \return Returns the order of the stepper.
- */
- order_type order( void ) const
- {
- return order_value;
- }
-
-
- /*
- * Version 1 : do_step( sys , x , t , dt )
- *
- * the two overloads are needed in order to solve the forwarding problem
- */
- template< class System , class StateInOut >
- void do_step( System system , StateInOut &x , time_type t , time_type dt )
- {
- do_step_v1( system , x , t , dt );
- }
-
- /**
- * \brief Second version to solve the forwarding problem, can be called with Boost.Range as StateInOut.
- */
- template< class System , class StateInOut >
- void do_step( System system , const StateInOut &x , time_type t , time_type dt )
- {
- do_step_v1( system , x , t , dt );
- }
-
- /*
- * Version 2 : do_step( sys , x , dxdt , t , dt )
- *
- * this version does not solve the forwarding problem, boost.range can not be used
- *
- * the disable is needed to avoid ambiguous overloads if state_type = time_type
- */
- template< class System , class StateInOut , class DerivIn >
- typename boost::disable_if< boost::is_same< DerivIn , time_type > , void >::type
- do_step( System system , StateInOut &x , const DerivIn &dxdt , time_type t , time_type dt )
- {
- this->stepper().do_step_impl( system , x , dxdt , t , x , dt );
- }
-
-
- /*
- * named Version 2: do_step_dxdt_impl( sys , in , dxdt , t , dt )
- *
- * this version is needed when this stepper is used for initializing
- * multistep stepper like adams-bashforth. Hence we provide an explicitely
- * named version that is not disabled. Meant for internal use only.
- */
- template < class System, class StateInOut, class DerivIn >
- void do_step_dxdt_impl( System system, StateInOut &x, const DerivIn &dxdt,
- time_type t, time_type dt )
- {
- this->stepper().do_step_impl( system , x , dxdt , t , x , dt );
- }
-
-
- /*
- * Version 3 : do_step( sys , in , t , out , dt )
- *
- * this version does not solve the forwarding problem, boost.range can not be used
- */
- template< class System , class StateIn , class StateOut >
- void do_step( System system , const StateIn &in , time_type t , StateOut &out , time_type dt )
- {
- typename odeint::unwrap_reference< System >::type &sys = system;
- m_resizer.adjust_size( in , detail::bind( &internal_stepper_base_type::template resize_impl<StateIn> , detail::ref( *this ) , detail::_1 ) );
- sys( in , m_dxdt.m_v ,t );
- this->stepper().do_step_impl( system , in , m_dxdt.m_v , t , out , dt );
- }
-
-
- /*
- * Version 4 : do_step( sys , in , dxdt , t , out , dt )
- *
- * this version does not solve the forwarding problem, boost.range can not be used
- */
- template< class System , class StateIn , class DerivIn , class StateOut >
- void do_step( System system , const StateIn &in , const DerivIn &dxdt , time_type t , StateOut &out , time_type dt )
- {
- this->stepper().do_step_impl( system , in , dxdt , t , out , dt );
- }
-
-
- /*
- * named Version 4: do_step_dxdt_impl( sys , in , dxdt , t , out, dt )
- *
- * this version is needed when this stepper is used for initializing
- * multistep stepper like adams-bashforth. Hence we provide an explicitely
- * named version. Meant for internal use only.
- */
- template < class System, class StateIn, class DerivIn, class StateOut >
- void do_step_dxdt_impl( System system, const StateIn &in,
- const DerivIn &dxdt, time_type t, StateOut &out,
- time_type dt )
- {
- this->stepper().do_step_impl( system , in , dxdt , t , out , dt );
- }
-
- template< class StateIn >
- void adjust_size( const StateIn &x )
- {
- resize_impl( x );
- }
-
-private:
-
- stepper_type& stepper( void )
- {
- return *static_cast< stepper_type* >( this );
- }
-
- const stepper_type& stepper( void ) const
- {
- return *static_cast< const stepper_type* >( this );
- }
-
-
- template< class StateIn >
- bool resize_impl( const StateIn &x )
- {
- return adjust_size_by_resizeability( m_dxdt , x , typename is_resizeable<deriv_type>::type() );
- }
-
-
- template< class System , class StateInOut >
- void do_step_v1( System system , StateInOut &x , time_type t , time_type dt )
- {
- typename odeint::unwrap_reference< System >::type &sys = system;
- m_resizer.adjust_size( x , detail::bind( &internal_stepper_base_type::template resize_impl< StateInOut > , detail::ref( *this ) , detail::_1 ) );
- sys( x , m_dxdt.m_v ,t );
- this->stepper().do_step_impl( system , x , m_dxdt.m_v , t , x , dt );
- }
-
-
- resizer_type m_resizer;
-
-protected:
-
- wrapped_deriv_type m_dxdt;
-};
-
-
-/******* DOXYGEN *********/
-
-/**
- * \class explicit_stepper_base
- * \brief Base class for explicit steppers without step size control and without dense output.
- *
- * This class serves as the base class for all explicit steppers with algebra and operations.
- * Step size control and error estimation as well as dense output are not provided. explicit_stepper_base
- * is used as the interface in a CRTP (currently recurring template pattern). In order to work
- * correctly the parent class needs to have a method `do_step_impl( system , in , dxdt_in , t , out , dt )`.
- * This is method is used by explicit_stepper_base. explicit_stepper_base derives from
- * algebra_stepper_base. An example how this class can be used is
- *
- * \code
- * template< class State , class Value , class Deriv , class Time , class Algebra , class Operations , class Resizer >
- * class custom_euler : public explicit_stepper_base< 1 , State , Value , Deriv , Time , Algebra , Operations , Resizer >
- * {
- * public:
- *
- * typedef explicit_stepper_base< 1 , State , Value , Deriv , Time , Algebra , Operations , Resizer > base_type;
- *
- * custom_euler( const Algebra &algebra = Algebra() ) { }
- *
- * template< class Sys , class StateIn , class DerivIn , class StateOut >
- * void do_step_impl( Sys sys , const StateIn &in , const DerivIn &dxdt , Time t , StateOut &out , Time dt )
- * {
- * m_algebra.for_each3( out , in , dxdt , Operations::scale_sum2< Value , Time >( 1.0 , dt );
- * }
- *
- * template< class State >
- * void adjust_size( const State &x )
- * {
- * base_type::adjust_size( x );
- * }
- * };
- * \endcode
- *
- * For the Stepper concept only the `do_step( sys , x , t , dt )` needs to be implemented. But this class
- * provides additional `do_step` variants since the stepper is explicit. These methods can be used to increase
- * the performance in some situation, for example if one needs to analyze `dxdt` during each step. In this case
- * one can use
- *
- * \code
- * sys( x , dxdt , t );
- * stepper.do_step( sys , x , dxdt , t , dt ); // the value of dxdt is used here
- * t += dt;
- * \endcode
- *
- * In detail explicit_stepper_base provides the following `do_step` variants
- * - `do_step( sys , x , t , dt )` - The classical `do_step` method needed to fulfill the Stepper concept. The state is updated in-place.
- * A type modelling a Boost.Range can be used for x.
- * - `do_step( sys , in , t , out , dt )` - This method updates the state out-of-place, hence the result of the step is stored in `out`.
- * - `do_step( sys , x , dxdt , t , dt )` - This method updates the state in-place, but the derivative at the point `t` must be
- * explicitly passed in `dxdt`. For an example see the code snippet above.
- * - `do_step( sys , in , dxdt , t , out , dt )` - This method update the state out-of-place and expects that the derivative at the point
- * `t` is explicitly passed in `dxdt`. It is a combination of the two `do_step` methods above.
- *
- * \note The system is always passed as value, which might result in poor performance if it contains data. In this case it can be used with `boost::ref`
- * or `std::ref`, for example `stepper.do_step( boost::ref( sys ) , x , t , dt );`
- *
- * \note The time `t` is not advanced by the stepper. This has to done manually, or by the appropriate `integrate` routines or `iterator`s.
- *
- * \tparam Stepper The stepper on which this class should work. It is used via CRTP, hence explicit_stepper_base
- * provides the interface for the Stepper.
- * \tparam Order The order of the stepper.
- * \tparam State The state type for the stepper.
- * \tparam Value The value type for the stepper. This should be a floating point type, like float,
- * double, or a multiprecision type. It must not necessary be the value_type of the State. For example
- * the State can be a `vector< complex< double > >` in this case the Value must be double.
- * The default value is double.
- * \tparam Deriv The type representing time derivatives of the state type. It is usually the same type as the
- * state type, only if used with Boost.Units both types differ.
- * \tparam Time The type representing the time. Usually the same type as the value type. When Boost.Units is
- * used, this type has usually a unit.
- * \tparam Algebra The algebra type which must fulfill the Algebra Concept.
- * \tparam Operations The type for the operations which must fulfill the Operations Concept.
- * \tparam Resizer The resizer policy class.
- */
-
-
- /**
- * \fn explicit_stepper_base::explicit_stepper_base( const algebra_type &algebra )
- * \brief Constructs a explicit_stepper_base class. This constructor can be used as a default
- * constructor if the algebra has a default constructor.
- * \param algebra A copy of algebra is made and stored inside explicit_stepper_base.
- */
-
- /**
- * \fn explicit_stepper_base::order_type order( void ) const
- * \return Returns the order of the stepper.
- */
-
- /**
- * \fn explicit_stepper_base::do_step( System system , StateInOut &x , time_type t , time_type dt )
- * \brief This method performs one step. It transforms the result in-place.
- *
- * \param system The system function to solve, hence the r.h.s. of the ordinary differential equation. It must fulfill the
- * Simple System concept.
- * \param x The state of the ODE which should be solved. After calling do_step the result is updated in x.
- * \param t The value of the time, at which the step should be performed.
- * \param dt The step size.
- */
-
-
- /**
- * \fn explicit_stepper_base::do_step( System system , StateInOut &x , const DerivIn &dxdt , time_type t , time_type dt )
-
- * \brief The method performs one step. Additionally to the other method
- * the derivative of x is also passed to this method. It is supposed to be used in the following way:
- *
- * \code
- * sys( x , dxdt , t );
- * stepper.do_step( sys , x , dxdt , t , dt );
- * \endcode
- *
- * The result is updated in place in x. This method is disabled if Time and Deriv are of the same type. In this
- * case the method could not be distinguished from other `do_step` versions.
- *
- * \note This method does not solve the forwarding problem.
- *
- * \param system The system function to solve, hence the r.h.s. of the ODE. It must fulfill the
- * Simple System concept.
- * \param x The state of the ODE which should be solved. After calling do_step the result is updated in x.
- * \param dxdt The derivative of x at t.
- * \param t The value of the time, at which the step should be performed.
- * \param dt The step size.
- */
-
- /**
- * \fn void explicit_stepper_base::do_step( System system , const StateIn &in , time_type t , StateOut &out , time_type dt )
- * \brief The method performs one step. The state of the ODE is updated out-of-place.
- * \note This method does not solve the forwarding problem.
- *
- * \param system The system function to solve, hence the r.h.s. of the ODE. It must fulfill the
- * Simple System concept.
- * \param in The state of the ODE which should be solved. in is not modified in this method
- * \param t The value of the time, at which the step should be performed.
- * \param out The result of the step is written in out.
- * \param dt The step size.
- */
-
- /**
- * \fn void explicit_stepper_base::do_step( System system , const StateIn &in , const DerivIn &dxdt , time_type t , StateOut &out , time_type dt )
- * \brief The method performs one step. The state of the ODE is updated out-of-place.
- * Furthermore, the derivative of x at t is passed to the stepper.
- * It is supposed to be used in the following way:
- *
- * \code
- * sys( in , dxdt , t );
- * stepper.do_step( sys , in , dxdt , t , out , dt );
- * \endcode
- *
- * \note This method does not solve the forwarding problem.
- *
- * \param system The system function to solve, hence the r.h.s. of the ODE. It must fulfill the
- * Simple System concept.
- * \param in The state of the ODE which should be solved. in is not modified in this method
- * \param dxdt The derivative of x at t.
- * \param t The value of the time, at which the step should be performed.
- * \param out The result of the step is written in out.
- * \param dt The step size.
- */
-
- /**
- * \fn void explicit_stepper_base::adjust_size( const StateIn &x )
- * \brief Adjust the size of all temporaries in the stepper manually.
- * \param x A state from which the size of the temporaries to be resized is deduced.
- */
-
-} // odeint
-} // numeric
-} // boost
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_BASE_EXPLICIT_STEPPER_BASE_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/base/symplectic_rkn_stepper_base.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/base/symplectic_rkn_stepper_base.hpp
deleted file mode 100644
index e026b068c6610d6200ba655a825a6f27e4754671..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/base/symplectic_rkn_stepper_base.hpp
+++ /dev/null
@@ -1,431 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/base/symplectic_rkn_stepper_base.hpp
-
- [begin_description]
- Base class for symplectic Runge-Kutta-Nystrom steppers.
- [end_description]
-
- Copyright 2011-2013 Karsten Ahnert
- Copyright 2011-2013 Mario Mulansky
- Copyright 2012 Christoph Koke
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_BASE_SYMPLECTIC_RKN_STEPPER_BASE_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_BASE_SYMPLECTIC_RKN_STEPPER_BASE_HPP_INCLUDED
-
-#include <boost/array.hpp>
-
-#include <boost/numeric/odeint/util/bind.hpp>
-#include <boost/numeric/odeint/util/unwrap_reference.hpp>
-
-#include <boost/numeric/odeint/util/copy.hpp>
-#include <boost/numeric/odeint/util/is_pair.hpp>
-
-#include <boost/numeric/odeint/util/state_wrapper.hpp>
-#include <boost/numeric/odeint/util/resizer.hpp>
-
-#include <boost/numeric/odeint/stepper/stepper_categories.hpp>
-
-#include <boost/numeric/odeint/stepper/base/algebra_stepper_base.hpp>
-
-
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-template<
-size_t NumOfStages ,
-unsigned short Order ,
-class Coor ,
-class Momentum ,
-class Value ,
-class CoorDeriv ,
-class MomentumDeriv ,
-class Time ,
-class Algebra ,
-class Operations ,
-class Resizer
->
-class symplectic_nystroem_stepper_base : public algebra_stepper_base< Algebra , Operations >
-{
-
-public:
-
- typedef algebra_stepper_base< Algebra , Operations > algebra_stepper_base_type;
- typedef typename algebra_stepper_base_type::algebra_type algebra_type;
- typedef typename algebra_stepper_base_type::operations_type operations_type;
-
- const static size_t num_of_stages = NumOfStages;
- typedef Coor coor_type;
- typedef Momentum momentum_type;
- typedef std::pair< coor_type , momentum_type > state_type;
- typedef CoorDeriv coor_deriv_type;
- typedef state_wrapper< coor_deriv_type> wrapped_coor_deriv_type;
- typedef MomentumDeriv momentum_deriv_type;
- typedef state_wrapper< momentum_deriv_type > wrapped_momentum_deriv_type;
- typedef std::pair< coor_deriv_type , momentum_deriv_type > deriv_type;
- typedef Value value_type;
- typedef Time time_type;
- typedef Resizer resizer_type;
- typedef stepper_tag stepper_category;
-
- #ifndef DOXYGEN_SKIP
- typedef symplectic_nystroem_stepper_base< NumOfStages , Order , Coor , Momentum , Value ,
- CoorDeriv , MomentumDeriv , Time , Algebra , Operations , Resizer > internal_stepper_base_type;
- #endif
- typedef unsigned short order_type;
-
- static const order_type order_value = Order;
-
- typedef boost::array< value_type , num_of_stages > coef_type;
-
- symplectic_nystroem_stepper_base( const coef_type &coef_a , const coef_type &coef_b , const algebra_type &algebra = algebra_type() )
- : algebra_stepper_base_type( algebra ) , m_coef_a( coef_a ) , m_coef_b( coef_b ) ,
- m_dqdt_resizer() , m_dpdt_resizer() , m_dqdt() , m_dpdt()
- { }
-
-
- order_type order( void ) const
- {
- return order_value;
- }
-
- /*
- * Version 1 : do_step( system , x , t , dt )
- *
- * This version does not solve the forwarding problem, boost.range can not be used.
- */
- template< class System , class StateInOut >
- void do_step( System system , const StateInOut &state , time_type t , time_type dt )
- {
- typedef typename odeint::unwrap_reference< System >::type system_type;
- do_step_impl( system , state , t , state , dt , typename is_pair< system_type >::type() );
- }
-
- /**
- * \brief Same function as above. It differs only in a different const specifier in order
- * to solve the forwarding problem, can be used with Boost.Range.
- */
- template< class System , class StateInOut >
- void do_step( System system , StateInOut &state , time_type t , time_type dt )
- {
- typedef typename odeint::unwrap_reference< System >::type system_type;
- do_step_impl( system , state , t , state , dt , typename is_pair< system_type >::type() );
- }
-
-
-
-
- /*
- * Version 2 : do_step( system , q , p , t , dt );
- *
- * For Convenience
- *
- * The two overloads are needed in order to solve the forwarding problem.
- */
- template< class System , class CoorInOut , class MomentumInOut >
- void do_step( System system , CoorInOut &q , MomentumInOut &p , time_type t , time_type dt )
- {
- do_step( system , std::make_pair( detail::ref( q ) , detail::ref( p ) ) , t , dt );
- }
-
- /**
- * \brief Same function as do_step( system , q , p , t , dt ). It differs only in a different const specifier in order
- * to solve the forwarding problem, can be called with Boost.Range.
- */
- template< class System , class CoorInOut , class MomentumInOut >
- void do_step( System system , const CoorInOut &q , const MomentumInOut &p , time_type t , time_type dt )
- {
- do_step( system , std::make_pair( detail::ref( q ) , detail::ref( p ) ) , t , dt );
- }
-
-
-
-
-
- /*
- * Version 3 : do_step( system , in , t , out , dt )
- *
- * The forwarding problem is not solved in this version
- */
- template< class System , class StateIn , class StateOut >
- void do_step( System system , const StateIn &in , time_type t , StateOut &out , time_type dt )
- {
- typedef typename odeint::unwrap_reference< System >::type system_type;
- do_step_impl( system , in , t , out , dt , typename is_pair< system_type >::type() );
- }
-
-
- template< class StateType >
- void adjust_size( const StateType &x )
- {
- resize_dqdt( x );
- resize_dpdt( x );
- }
-
- /** \brief Returns the coefficients a. */
- const coef_type& coef_a( void ) const { return m_coef_a; }
-
- /** \brief Returns the coefficients b. */
- const coef_type& coef_b( void ) const { return m_coef_b; }
-
-private:
-
- // stepper for systems with function for dq/dt = f(p) and dp/dt = -f(q)
- template< class System , class StateIn , class StateOut >
- void do_step_impl( System system , const StateIn &in , time_type /* t */ , StateOut &out , time_type dt , boost::mpl::true_ )
- {
- typedef typename odeint::unwrap_reference< System >::type system_type;
- typedef typename odeint::unwrap_reference< typename system_type::first_type >::type coor_deriv_func_type;
- typedef typename odeint::unwrap_reference< typename system_type::second_type >::type momentum_deriv_func_type;
- system_type &sys = system;
- coor_deriv_func_type &coor_func = sys.first;
- momentum_deriv_func_type &momentum_func = sys.second;
-
- typedef typename odeint::unwrap_reference< StateIn >::type state_in_type;
- typedef typename odeint::unwrap_reference< typename state_in_type::first_type >::type coor_in_type;
- typedef typename odeint::unwrap_reference< typename state_in_type::second_type >::type momentum_in_type;
- const state_in_type &state_in = in;
- const coor_in_type &coor_in = state_in.first;
- const momentum_in_type &momentum_in = state_in.second;
-
- typedef typename odeint::unwrap_reference< StateOut >::type state_out_type;
- typedef typename odeint::unwrap_reference< typename state_out_type::first_type >::type coor_out_type;
- typedef typename odeint::unwrap_reference< typename state_out_type::second_type >::type momentum_out_type;
- state_out_type &state_out = out;
- coor_out_type &coor_out = state_out.first;
- momentum_out_type &momentum_out = state_out.second;
-
- m_dqdt_resizer.adjust_size( coor_in , detail::bind( &internal_stepper_base_type::template resize_dqdt< coor_in_type > , detail::ref( *this ) , detail::_1 ) );
- m_dpdt_resizer.adjust_size( momentum_in , detail::bind( &internal_stepper_base_type::template resize_dpdt< momentum_in_type > , detail::ref( *this ) , detail::_1 ) );
-
- // ToDo: check sizes?
-
- for( size_t l=0 ; l<num_of_stages ; ++l )
- {
- if( l == 0 )
- {
- coor_func( momentum_in , m_dqdt.m_v );
- this->m_algebra.for_each3( coor_out , coor_in , m_dqdt.m_v ,
- typename operations_type::template scale_sum2< value_type , time_type >( 1.0 , m_coef_a[l] * dt ) );
- momentum_func( coor_out , m_dpdt.m_v );
- this->m_algebra.for_each3( momentum_out , momentum_in , m_dpdt.m_v ,
- typename operations_type::template scale_sum2< value_type , time_type >( 1.0 , m_coef_b[l] * dt ) );
- }
- else
- {
- coor_func( momentum_out , m_dqdt.m_v );
- this->m_algebra.for_each3( coor_out , coor_out , m_dqdt.m_v ,
- typename operations_type::template scale_sum2< value_type , time_type >( 1.0 , m_coef_a[l] * dt ) );
- momentum_func( coor_out , m_dpdt.m_v );
- this->m_algebra.for_each3( momentum_out , momentum_out , m_dpdt.m_v ,
- typename operations_type::template scale_sum2< value_type , time_type >( 1.0 , m_coef_b[l] * dt ) );
- }
- }
- }
-
-
- // stepper for systems with only function dp /dt = -f(q), dq/dt = p, time not required but still expected for compatibility reasons
- template< class System , class StateIn , class StateOut >
- void do_step_impl( System system , const StateIn &in , time_type /* t */ , StateOut &out , time_type dt , boost::mpl::false_ )
- {
- typedef typename odeint::unwrap_reference< System >::type momentum_deriv_func_type;
- momentum_deriv_func_type &momentum_func = system;
-
- typedef typename odeint::unwrap_reference< StateIn >::type state_in_type;
- typedef typename odeint::unwrap_reference< typename state_in_type::first_type >::type coor_in_type;
- typedef typename odeint::unwrap_reference< typename state_in_type::second_type >::type momentum_in_type;
- const state_in_type &state_in = in;
- const coor_in_type &coor_in = state_in.first;
- const momentum_in_type &momentum_in = state_in.second;
-
- typedef typename odeint::unwrap_reference< StateOut >::type state_out_type;
- typedef typename odeint::unwrap_reference< typename state_out_type::first_type >::type coor_out_type;
- typedef typename odeint::unwrap_reference< typename state_out_type::second_type >::type momentum_out_type;
- state_out_type &state_out = out;
- coor_out_type &coor_out = state_out.first;
- momentum_out_type &momentum_out = state_out.second;
-
-
- // m_dqdt not required when called with momentum_func only - don't resize
- // m_dqdt_resizer.adjust_size( coor_in , detail::bind( &internal_stepper_base_type::template resize_dqdt< coor_in_type > , detail::ref( *this ) , detail::_1 ) );
- m_dpdt_resizer.adjust_size( momentum_in , detail::bind( &internal_stepper_base_type::template resize_dpdt< momentum_in_type > , detail::ref( *this ) , detail::_1 ) );
-
-
- // ToDo: check sizes?
-
- // step 0
- this->m_algebra.for_each3( coor_out , coor_in , momentum_in ,
- typename operations_type::template scale_sum2< value_type , time_type >( 1.0 , m_coef_a[0] * dt ) );
- momentum_func( coor_out , m_dpdt.m_v );
- this->m_algebra.for_each3( momentum_out , momentum_in , m_dpdt.m_v ,
- typename operations_type::template scale_sum2< value_type , time_type >( 1.0 , m_coef_b[0] * dt ) );
-
- for( size_t l=1 ; l<num_of_stages ; ++l )
- {
- this->m_algebra.for_each3( coor_out , coor_out , momentum_out ,
- typename operations_type::template scale_sum2< value_type , time_type >( 1.0 , m_coef_a[l] * dt ) );
- momentum_func( coor_out , m_dpdt.m_v );
- this->m_algebra.for_each3( momentum_out , momentum_out , m_dpdt.m_v ,
- typename operations_type::template scale_sum2< value_type , time_type >( 1.0 , m_coef_b[l] * dt ) );
- }
- }
-
- template< class StateIn >
- bool resize_dqdt( const StateIn &x )
- {
- return adjust_size_by_resizeability( m_dqdt , x , typename is_resizeable<coor_deriv_type>::type() );
- }
-
- template< class StateIn >
- bool resize_dpdt( const StateIn &x )
- {
- return adjust_size_by_resizeability( m_dpdt , x , typename is_resizeable<momentum_deriv_type>::type() );
- }
-
-
- const coef_type m_coef_a;
- const coef_type m_coef_b;
-
- resizer_type m_dqdt_resizer;
- resizer_type m_dpdt_resizer;
- wrapped_coor_deriv_type m_dqdt;
- wrapped_momentum_deriv_type m_dpdt;
-
-};
-
-/********* DOXYGEN *********/
-
-/**
- * \class symplectic_nystroem_stepper_base
- * \brief Base class for all symplectic steppers of Nystroem type.
- *
- * This class is the base class for the symplectic Runge-Kutta-Nystroem steppers. Symplectic steppers are usually
- * used to solve Hamiltonian systems and they conserve the phase space volume, see
- * <a href="http://en.wikipedia.org/wiki/Symplectic_integrator">en.wikipedia.org/wiki/Symplectic_integrator</a>.
- * Furthermore, the energy is conserved
- * in average. In detail this class of steppers can be used to solve separable Hamiltonian systems which can be written
- * in the form H(q,p) = H1(p) + H2(q). q is usually called the coordinate, while p is the momentum. The equations of motion
- * are dq/dt = dH1/dp, dp/dt = -dH2/dq.
- *
- * ToDo : add formula for solver and explanation of the coefficients
- *
- * symplectic_nystroem_stepper_base uses odeints algebra and operation system. Step size and error estimation are not
- * provided for this class of solvers. It derives from algebra_stepper_base. Several `do_step` variants are provided:
- *
- * - `do_step( sys , x , t , dt )` - The classical `do_step` method. The sys can be either a pair of function objects
- * for the coordinate or the momentum part or one function object for the momentum part. `x` is a pair of coordinate
- * and momentum. The state is updated in-place.
- * - `do_step( sys , q , p , t , dt )` - This method is similar to the method above with the difference that the coordinate
- * and the momentum are passed explicitly and not packed into a pair.
- * - `do_step( sys , x_in , t , x_out , dt )` - This method transforms the state out-of-place. `x_in` and `x_out` are here pairs
- * of coordinate and momentum.
- *
- * \tparam NumOfStages Number of stages.
- * \tparam Order The order of the stepper.
- * \tparam Coor The type representing the coordinates q.
- * \tparam Momentum The type representing the coordinates p.
- * \tparam Value The basic value type. Should be something like float, double or a high-precision type.
- * \tparam CoorDeriv The type representing the time derivative of the coordinate dq/dt.
- * \tparam MomemtnumDeriv The type representing the time derivative of the momentum dp/dt.
- * \tparam Time The type representing the time t.
- * \tparam Algebra The algebra.
- * \tparam Operations The operations.
- * \tparam Resizer The resizer policy.
- */
-
- /**
- * \fn symplectic_nystroem_stepper_base::symplectic_nystroem_stepper_base( const coef_type &coef_a , const coef_type &coef_b , const algebra_type &algebra )
- * \brief Constructs a symplectic_nystroem_stepper_base class. The parameters of the specific Nystroem method and the
- * algebra have to be passed.
- * \param coef_a The coefficients a.
- * \param coef_b The coefficients b.
- * \param algebra A copy of algebra is made and stored inside explicit_stepper_base.
- */
-
- /**
- * \fn symplectic_nystroem_stepper_base::order( void ) const
- * \return Returns the order of the stepper.
- */
-
- /**
- * \fn symplectic_nystroem_stepper_base::do_step( System system , const StateInOut &state , time_type t , time_type dt )
- * \brief This method performs one step. The system can be either a pair of two function object
- * describing the momentum part and the coordinate part or one function object describing only
- * the momentum part. In this case the coordinate is assumed to be trivial dq/dt = p. The state
- * is updated in-place.
- *
- * \note boost::ref or std::ref can be used for the system as well as for the state. So, it is correct
- * to write `stepper.do_step( make_pair( std::ref( fq ) , std::ref( fp ) ) , make_pair( std::ref( q ) , std::ref( p ) ) , t , dt )`.
- *
- * \note This method solves the forwarding problem.
- *
- * \param system The system, can be represented as a pair of two function object or one function object. See above.
- * \param state The state of the ODE. It is a pair of Coor and Momentum. The state is updated in-place, therefore, the
- * new value of the state will be written into this variable.
- * \param t The time of the ODE. It is not advanced by this method.
- * \param dt The time step.
- */
-
- /**
- * \fn symplectic_nystroem_stepper_base::do_step( System system , CoorInOut &q , MomentumInOut &p , time_type t , time_type dt )
- * \brief This method performs one step. The system can be either a pair of two function object
- * describing the momentum part and the coordinate part or one function object describing only
- * the momentum part. In this case the coordinate is assumed to be trivial dq/dt = p. The state
- * is updated in-place.
- *
- * \note boost::ref or std::ref can be used for the system. So, it is correct
- * to write `stepper.do_step( make_pair( std::ref( fq ) , std::ref( fp ) ) , q , p , t , dt )`.
- *
- * \note This method solves the forwarding problem.
- *
- * \param system The system, can be represented as a pair of two function object or one function object. See above.
- * \param q The coordinate of the ODE. It is updated in-place. Therefore, the new value of the coordinate will be written
- * into this variable.
- * \param p The momentum of the ODE. It is updated in-place. Therefore, the new value of the momentum will be written info
- * this variable.
- * \param t The time of the ODE. It is not advanced by this method.
- * \param dt The time step.
- */
-
- /**
- * \fn symplectic_nystroem_stepper_base::do_step( System system , const StateIn &in , time_type t , StateOut &out , time_type dt )
- * \brief This method performs one step. The system can be either a pair of two function object
- * describing the momentum part and the coordinate part or one function object describing only
- * the momentum part. In this case the coordinate is assumed to be trivial dq/dt = p. The state
- * is updated out-of-place.
- *
- * \note boost::ref or std::ref can be used for the system. So, it is correct
- * to write `stepper.do_step( make_pair( std::ref( fq ) , std::ref( fp ) ) , x_in , t , x_out , dt )`.
- *
- * \note This method NOT solve the forwarding problem.
- *
- * \param system The system, can be represented as a pair of two function object or one function object. See above.
- * \param in The state of the ODE, which is a pair of coordinate and momentum. The state is updated out-of-place, therefore the
- * new value is written into out
- * \param t The time of the ODE. It is not advanced by this method.
- * \param out The new state of the ODE.
- * \param dt The time step.
- */
-
- /**
- * \fn symplectic_nystroem_stepper_base::adjust_size( const StateType &x )
- * \brief Adjust the size of all temporaries in the stepper manually.
- * \param x A state from which the size of the temporaries to be resized is deduced.
- */
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_BASE_SYMPLECTIC_RKN_STEPPER_BASE_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/bulirsch_stoer.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/bulirsch_stoer.hpp
deleted file mode 100644
index 0f5553fdd248aed8b883334f16c819f45c428a94..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/bulirsch_stoer.hpp
+++ /dev/null
@@ -1,642 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/bulirsch_stoer.hpp
-
- [begin_description]
- Implementation of the Burlish-Stoer method. As described in
- Ernst Hairer, Syvert Paul Norsett, Gerhard Wanner
- Solving Ordinary Differential Equations I. Nonstiff Problems.
- Springer Series in Comput. Mathematics, Vol. 8, Springer-Verlag 1987, Second revised edition 1993.
- [end_description]
-
- Copyright 2011-2013 Mario Mulansky
- Copyright 2011-2013 Karsten Ahnert
- Copyright 2012 Christoph Koke
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
-*/
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_BULIRSCH_STOER_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_BULIRSCH_STOER_HPP_INCLUDED
-
-
-#include <iostream>
-
-#include <algorithm>
-
-#include <boost/config.hpp> // for min/max guidelines
-
-#include <boost/numeric/odeint/util/bind.hpp>
-#include <boost/numeric/odeint/util/unwrap_reference.hpp>
-
-#include <boost/numeric/odeint/stepper/controlled_runge_kutta.hpp>
-#include <boost/numeric/odeint/stepper/modified_midpoint.hpp>
-#include <boost/numeric/odeint/stepper/controlled_step_result.hpp>
-#include <boost/numeric/odeint/algebra/range_algebra.hpp>
-#include <boost/numeric/odeint/algebra/default_operations.hpp>
-#include <boost/numeric/odeint/algebra/algebra_dispatcher.hpp>
-#include <boost/numeric/odeint/algebra/operations_dispatcher.hpp>
-
-#include <boost/numeric/odeint/util/state_wrapper.hpp>
-#include <boost/numeric/odeint/util/is_resizeable.hpp>
-#include <boost/numeric/odeint/util/resizer.hpp>
-#include <boost/numeric/odeint/util/unit_helper.hpp>
-#include <boost/numeric/odeint/util/detail/less_with_sign.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-template<
- class State ,
- class Value = double ,
- class Deriv = State ,
- class Time = Value ,
- class Algebra = typename algebra_dispatcher< State >::algebra_type ,
- class Operations = typename operations_dispatcher< State >::operations_type ,
- class Resizer = initially_resizer
- >
-class bulirsch_stoer {
-
-public:
-
- typedef State state_type;
- typedef Value value_type;
- typedef Deriv deriv_type;
- typedef Time time_type;
- typedef Algebra algebra_type;
- typedef Operations operations_type;
- typedef Resizer resizer_type;
-#ifndef DOXYGEN_SKIP
- typedef state_wrapper< state_type > wrapped_state_type;
- typedef state_wrapper< deriv_type > wrapped_deriv_type;
- typedef controlled_stepper_tag stepper_category;
-
- typedef bulirsch_stoer< State , Value , Deriv , Time , Algebra , Operations , Resizer > controlled_error_bs_type;
-
- typedef typename inverse_time< time_type >::type inv_time_type;
-
- typedef std::vector< value_type > value_vector;
- typedef std::vector< time_type > time_vector;
- typedef std::vector< inv_time_type > inv_time_vector; //should be 1/time_type for boost.units
- typedef std::vector< value_vector > value_matrix;
- typedef std::vector< size_t > int_vector;
- typedef std::vector< wrapped_state_type > state_table_type;
-#endif //DOXYGEN_SKIP
- const static size_t m_k_max = 8;
-
- bulirsch_stoer(
- value_type eps_abs = 1E-6 , value_type eps_rel = 1E-6 ,
- value_type factor_x = 1.0 , value_type factor_dxdt = 1.0 ,
- time_type max_dt = static_cast<time_type>(0))
- : m_error_checker( eps_abs , eps_rel , factor_x, factor_dxdt ) , m_midpoint() ,
- m_last_step_rejected( false ) , m_first( true ) ,
- m_max_dt(max_dt) ,
- m_interval_sequence( m_k_max+1 ) ,
- m_coeff( m_k_max+1 ) ,
- m_cost( m_k_max+1 ) ,
- m_facmin_table( m_k_max+1 ) ,
- m_table( m_k_max ) ,
- STEPFAC1( 0.65 ) , STEPFAC2( 0.94 ) , STEPFAC3( 0.02 ) , STEPFAC4( 4.0 ) , KFAC1( 0.8 ) , KFAC2( 0.9 )
- {
- BOOST_USING_STD_MIN();
- BOOST_USING_STD_MAX();
- /* initialize sequence of stage numbers and work */
- for( unsigned short i = 0; i < m_k_max+1; i++ )
- {
- m_interval_sequence[i] = 2 * (i+1);
- if( i == 0 )
- m_cost[i] = m_interval_sequence[i];
- else
- m_cost[i] = m_cost[i-1] + m_interval_sequence[i];
- m_coeff[i].resize(i);
- m_facmin_table[i] = pow BOOST_PREVENT_MACRO_SUBSTITUTION( STEPFAC3 , static_cast< value_type >(1) / static_cast< value_type >( 2*i+1 ) );
- for( size_t k = 0 ; k < i ; ++k )
- {
- const value_type r = static_cast< value_type >( m_interval_sequence[i] ) / static_cast< value_type >( m_interval_sequence[k] );
- m_coeff[i][k] = 1.0 / ( r*r - static_cast< value_type >( 1.0 ) ); // coefficients for extrapolation
- }
- }
- reset();
- }
-
-
- /*
- * Version 1 : try_step( sys , x , t , dt )
- *
- * The overloads are needed to solve the forwarding problem
- */
- template< class System , class StateInOut >
- controlled_step_result try_step( System system , StateInOut &x , time_type &t , time_type &dt )
- {
- return try_step_v1( system , x , t, dt );
- }
-
- /**
- * \brief Second version to solve the forwarding problem, can be used with Boost.Range as StateInOut.
- */
- template< class System , class StateInOut >
- controlled_step_result try_step( System system , const StateInOut &x , time_type &t , time_type &dt )
- {
- return try_step_v1( system , x , t, dt );
- }
-
- /*
- * Version 2 : try_step( sys , x , dxdt , t , dt )
- *
- * this version does not solve the forwarding problem, boost.range can not be used
- */
- template< class System , class StateInOut , class DerivIn >
- controlled_step_result try_step( System system , StateInOut &x , const DerivIn &dxdt , time_type &t , time_type &dt )
- {
- m_xnew_resizer.adjust_size( x , detail::bind( &controlled_error_bs_type::template resize_m_xnew< StateInOut > , detail::ref( *this ) , detail::_1 ) );
- controlled_step_result res = try_step( system , x , dxdt , t , m_xnew.m_v , dt );
- if( res == success )
- {
- boost::numeric::odeint::copy( m_xnew.m_v , x );
- }
- return res;
- }
-
- /*
- * Version 3 : try_step( sys , in , t , out , dt )
- *
- * this version does not solve the forwarding problem, boost.range can not be used
- */
- template< class System , class StateIn , class StateOut >
- typename boost::disable_if< boost::is_same< StateIn , time_type > , controlled_step_result >::type
- try_step( System system , const StateIn &in , time_type &t , StateOut &out , time_type &dt )
- {
- typename odeint::unwrap_reference< System >::type &sys = system;
- m_dxdt_resizer.adjust_size( in , detail::bind( &controlled_error_bs_type::template resize_m_dxdt< StateIn > , detail::ref( *this ) , detail::_1 ) );
- sys( in , m_dxdt.m_v , t );
- return try_step( system , in , m_dxdt.m_v , t , out , dt );
- }
-
-
- /*
- * Full version : try_step( sys , in , dxdt_in , t , out , dt )
- *
- * contains the actual implementation
- */
- template< class System , class StateIn , class DerivIn , class StateOut >
- controlled_step_result try_step( System system , const StateIn &in , const DerivIn &dxdt , time_type &t , StateOut &out , time_type &dt )
- {
- if( m_max_dt != static_cast<time_type>(0) && detail::less_with_sign(m_max_dt, dt, dt) )
- {
- // given step size is bigger then max_dt
- // set limit and return fail
- dt = m_max_dt;
- return fail;
- }
-
- BOOST_USING_STD_MIN();
- BOOST_USING_STD_MAX();
-
- static const value_type val1( 1.0 );
-
- if( m_resizer.adjust_size( in , detail::bind( &controlled_error_bs_type::template resize_impl< StateIn > , detail::ref( *this ) , detail::_1 ) ) )
- {
- reset(); // system resized -> reset
- }
-
- if( dt != m_dt_last )
- {
- reset(); // step size changed from outside -> reset
- }
-
- bool reject( true );
-
- time_vector h_opt( m_k_max+1 );
- inv_time_vector work( m_k_max+1 );
-
- time_type new_h = dt;
-
- /* m_current_k_opt is the estimated current optimal stage number */
- for( size_t k = 0 ; k <= m_current_k_opt+1 ; k++ )
- {
- /* the stage counts are stored in m_interval_sequence */
- m_midpoint.set_steps( m_interval_sequence[k] );
- if( k == 0 )
- {
- m_midpoint.do_step( system , in , dxdt , t , out , dt );
- /* the first step, nothing more to do */
- }
- else
- {
- m_midpoint.do_step( system , in , dxdt , t , m_table[k-1].m_v , dt );
- extrapolate( k , m_table , m_coeff , out );
- // get error estimate
- m_algebra.for_each3( m_err.m_v , out , m_table[0].m_v ,
- typename operations_type::template scale_sum2< value_type , value_type >( val1 , -val1 ) );
- const value_type error = m_error_checker.error( m_algebra , in , dxdt , m_err.m_v , dt );
- h_opt[k] = calc_h_opt( dt , error , k );
- work[k] = static_cast<value_type>( m_cost[k] ) / h_opt[k];
-
- if( (k == m_current_k_opt-1) || m_first )
- { // convergence before k_opt ?
- if( error < 1.0 )
- {
- //convergence
- reject = false;
- if( (work[k] < KFAC2*work[k-1]) || (m_current_k_opt <= 2) )
- {
- // leave order as is (except we were in first round)
- m_current_k_opt = min BOOST_PREVENT_MACRO_SUBSTITUTION( static_cast<int>(m_k_max)-1 , max BOOST_PREVENT_MACRO_SUBSTITUTION( 2 , static_cast<int>(k)+1 ) );
- new_h = h_opt[k];
- new_h *= static_cast<value_type>( m_cost[k+1] ) / static_cast<value_type>( m_cost[k] );
- } else {
- m_current_k_opt = min BOOST_PREVENT_MACRO_SUBSTITUTION( static_cast<int>(m_k_max)-1 , max BOOST_PREVENT_MACRO_SUBSTITUTION( 2 , static_cast<int>(k) ) );
- new_h = h_opt[k];
- }
- break;
- }
- else if( should_reject( error , k ) && !m_first )
- {
- reject = true;
- new_h = h_opt[k];
- break;
- }
- }
- if( k == m_current_k_opt )
- { // convergence at k_opt ?
- if( error < 1.0 )
- {
- //convergence
- reject = false;
- if( (work[k-1] < KFAC2*work[k]) )
- {
- m_current_k_opt = max BOOST_PREVENT_MACRO_SUBSTITUTION( 2 , static_cast<int>(m_current_k_opt)-1 );
- new_h = h_opt[m_current_k_opt];
- }
- else if( (work[k] < KFAC2*work[k-1]) && !m_last_step_rejected )
- {
- m_current_k_opt = min BOOST_PREVENT_MACRO_SUBSTITUTION( static_cast<int>(m_k_max-1) , static_cast<int>(m_current_k_opt)+1 );
- new_h = h_opt[k];
- new_h *= static_cast<value_type>(m_cost[m_current_k_opt])/static_cast<value_type>(m_cost[k]);
- } else
- new_h = h_opt[m_current_k_opt];
- break;
- }
- else if( should_reject( error , k ) )
- {
- reject = true;
- new_h = h_opt[m_current_k_opt];
- break;
- }
- }
- if( k == m_current_k_opt+1 )
- { // convergence at k_opt+1 ?
- if( error < 1.0 )
- { //convergence
- reject = false;
- if( work[k-2] < KFAC2*work[k-1] )
- m_current_k_opt = max BOOST_PREVENT_MACRO_SUBSTITUTION( 2 , static_cast<int>(m_current_k_opt)-1 );
- if( (work[k] < KFAC2*work[m_current_k_opt]) && !m_last_step_rejected )
- m_current_k_opt = min BOOST_PREVENT_MACRO_SUBSTITUTION( static_cast<int>(m_k_max)-1 , static_cast<int>(k) );
- new_h = h_opt[m_current_k_opt];
- } else
- {
- reject = true;
- new_h = h_opt[m_current_k_opt];
- }
- break;
- }
- }
- }
-
- if( !reject )
- {
- t += dt;
- }
-
- if( !m_last_step_rejected || boost::numeric::odeint::detail::less_with_sign(new_h, dt, dt) )
- {
- // limit step size
- if( m_max_dt != static_cast<time_type>(0) )
- {
- new_h = detail::min_abs(m_max_dt, new_h);
- }
- m_dt_last = new_h;
- dt = new_h;
- }
-
- m_last_step_rejected = reject;
- m_first = false;
-
- if( reject )
- return fail;
- else
- return success;
- }
-
- /** \brief Resets the internal state of the stepper */
- void reset()
- {
- m_first = true;
- m_last_step_rejected = false;
- // crude estimate of optimal order
- m_current_k_opt = 4;
- /* no calculation because log10 might not exist for value_type!
- const value_type logfact( -log10( max BOOST_PREVENT_MACRO_SUBSTITUTION( eps_rel , static_cast< value_type >(1.0E-12) ) ) * 0.6 + 0.5 );
- m_current_k_opt = max BOOST_PREVENT_MACRO_SUBSTITUTION( static_cast<value_type>( 1 ) , min BOOST_PREVENT_MACRO_SUBSTITUTION( static_cast<value_type>( m_k_max-1 ) , logfact ));
- */
- }
-
-
- /* Resizer methods */
-
- template< class StateIn >
- void adjust_size( const StateIn &x )
- {
- resize_m_dxdt( x );
- resize_m_xnew( x );
- resize_impl( x );
- m_midpoint.adjust_size( x );
- }
-
-
-private:
-
- template< class StateIn >
- bool resize_m_dxdt( const StateIn &x )
- {
- return adjust_size_by_resizeability( m_dxdt , x , typename is_resizeable<deriv_type>::type() );
- }
-
- template< class StateIn >
- bool resize_m_xnew( const StateIn &x )
- {
- return adjust_size_by_resizeability( m_xnew , x , typename is_resizeable<state_type>::type() );
- }
-
- template< class StateIn >
- bool resize_impl( const StateIn &x )
- {
- bool resized( false );
- for( size_t i = 0 ; i < m_k_max ; ++i )
- resized |= adjust_size_by_resizeability( m_table[i] , x , typename is_resizeable<state_type>::type() );
- resized |= adjust_size_by_resizeability( m_err , x , typename is_resizeable<state_type>::type() );
- return resized;
- }
-
-
- template< class System , class StateInOut >
- controlled_step_result try_step_v1( System system , StateInOut &x , time_type &t , time_type &dt )
- {
- typename odeint::unwrap_reference< System >::type &sys = system;
- m_dxdt_resizer.adjust_size( x , detail::bind( &controlled_error_bs_type::template resize_m_dxdt< StateInOut > , detail::ref( *this ) , detail::_1 ) );
- sys( x , m_dxdt.m_v ,t );
- return try_step( system , x , m_dxdt.m_v , t , dt );
- }
-
-
- template< class StateInOut >
- void extrapolate( size_t k , state_table_type &table , const value_matrix &coeff , StateInOut &xest )
- /* polynomial extrapolation, see http://www.nr.com/webnotes/nr3web21.pdf
- uses the obtained intermediate results to extrapolate to dt->0
- */
- {
- static const value_type val1 = static_cast< value_type >( 1.0 );
- for( int j=k-1 ; j>0 ; --j )
- {
- m_algebra.for_each3( table[j-1].m_v , table[j].m_v , table[j-1].m_v ,
- typename operations_type::template scale_sum2< value_type , value_type >( val1 + coeff[k][j] , -coeff[k][j] ) );
- }
- m_algebra.for_each3( xest , table[0].m_v , xest ,
- typename operations_type::template scale_sum2< value_type , value_type >( val1 + coeff[k][0] , -coeff[k][0]) );
- }
-
- time_type calc_h_opt( time_type h , value_type error , size_t k ) const
- /* calculates the optimal step size for a given error and stage number */
- {
- BOOST_USING_STD_MIN();
- BOOST_USING_STD_MAX();
- using std::pow;
- value_type expo( 1.0/(2*k+1) );
- value_type facmin = m_facmin_table[k];
- value_type fac;
- if (error == 0.0)
- fac=1.0/facmin;
- else
- {
- fac = STEPFAC2 / pow BOOST_PREVENT_MACRO_SUBSTITUTION( error / STEPFAC1 , expo );
- fac = max BOOST_PREVENT_MACRO_SUBSTITUTION( static_cast<value_type>(facmin/STEPFAC4) , min BOOST_PREVENT_MACRO_SUBSTITUTION( static_cast<value_type>(1.0/facmin) , fac ) );
- }
- return h*fac;
- }
-
- controlled_step_result set_k_opt( size_t k , const inv_time_vector &work , const time_vector &h_opt , time_type &dt )
- /* calculates the optimal stage number */
- {
- if( k == 1 )
- {
- m_current_k_opt = 2;
- return success;
- }
- if( (work[k-1] < KFAC1*work[k]) || (k == m_k_max) )
- { // order decrease
- m_current_k_opt = k-1;
- dt = h_opt[ m_current_k_opt ];
- return success;
- }
- else if( (work[k] < KFAC2*work[k-1]) || m_last_step_rejected || (k == m_k_max-1) )
- { // same order - also do this if last step got rejected
- m_current_k_opt = k;
- dt = h_opt[ m_current_k_opt ];
- return success;
- }
- else
- { // order increase - only if last step was not rejected
- m_current_k_opt = k+1;
- dt = h_opt[ m_current_k_opt-1 ] * m_cost[ m_current_k_opt ] / m_cost[ m_current_k_opt-1 ] ;
- return success;
- }
- }
-
- bool in_convergence_window( size_t k ) const
- {
- if( (k == m_current_k_opt-1) && !m_last_step_rejected )
- return true; // decrease stepsize only if last step was not rejected
- return ( (k == m_current_k_opt) || (k == m_current_k_opt+1) );
- }
-
- bool should_reject( value_type error , size_t k ) const
- {
- if( k == m_current_k_opt-1 )
- {
- const value_type d = m_interval_sequence[m_current_k_opt] * m_interval_sequence[m_current_k_opt+1] /
- (m_interval_sequence[0]*m_interval_sequence[0]);
- //step will fail, criterion 17.3.17 in NR
- return ( error > d*d );
- }
- else if( k == m_current_k_opt )
- {
- const value_type d = m_interval_sequence[m_current_k_opt] / m_interval_sequence[0];
- return ( error > d*d );
- } else
- return error > 1.0;
- }
-
- default_error_checker< value_type, algebra_type , operations_type > m_error_checker;
- modified_midpoint< state_type , value_type , deriv_type , time_type , algebra_type , operations_type , resizer_type > m_midpoint;
-
- bool m_last_step_rejected;
- bool m_first;
-
- time_type m_dt_last;
- time_type m_t_last;
- time_type m_max_dt;
-
- size_t m_current_k_opt;
-
- algebra_type m_algebra;
-
- resizer_type m_dxdt_resizer;
- resizer_type m_xnew_resizer;
- resizer_type m_resizer;
-
- wrapped_state_type m_xnew;
- wrapped_state_type m_err;
- wrapped_deriv_type m_dxdt;
-
- int_vector m_interval_sequence; // stores the successive interval counts
- value_matrix m_coeff;
- int_vector m_cost; // costs for interval count
- value_vector m_facmin_table; // for precomputed facmin to save pow calls
-
- state_table_type m_table; // sequence of states for extrapolation
-
- value_type STEPFAC1 , STEPFAC2 , STEPFAC3 , STEPFAC4 , KFAC1 , KFAC2;
-};
-
-
-/******** DOXYGEN ********/
-/**
- * \class bulirsch_stoer
- * \brief The Bulirsch-Stoer algorithm.
- *
- * The Bulirsch-Stoer is a controlled stepper that adjusts both step size
- * and order of the method. The algorithm uses the modified midpoint and
- * a polynomial extrapolation compute the solution.
- *
- * \tparam State The state type.
- * \tparam Value The value type.
- * \tparam Deriv The type representing the time derivative of the state.
- * \tparam Time The time representing the independent variable - the time.
- * \tparam Algebra The algebra type.
- * \tparam Operations The operations type.
- * \tparam Resizer The resizer policy type.
- */
-
- /**
- * \fn bulirsch_stoer::bulirsch_stoer( value_type eps_abs , value_type eps_rel , value_type factor_x , value_type factor_dxdt )
- * \brief Constructs the bulirsch_stoer class, including initialization of
- * the error bounds.
- *
- * \param eps_abs Absolute tolerance level.
- * \param eps_rel Relative tolerance level.
- * \param factor_x Factor for the weight of the state.
- * \param factor_dxdt Factor for the weight of the derivative.
- */
-
- /**
- * \fn bulirsch_stoer::try_step( System system , StateInOut &x , time_type &t , time_type &dt )
- * \brief Tries to perform one step.
- *
- * This method tries to do one step with step size dt. If the error estimate
- * is to large, the step is rejected and the method returns fail and the
- * step size dt is reduced. If the error estimate is acceptably small, the
- * step is performed, success is returned and dt might be increased to make
- * the steps as large as possible. This method also updates t if a step is
- * performed. Also, the internal order of the stepper is adjusted if required.
- *
- * \param system The system function to solve, hence the r.h.s. of the ODE.
- * It must fulfill the Simple System concept.
- * \param x The state of the ODE which should be solved. Overwritten if
- * the step is successful.
- * \param t The value of the time. Updated if the step is successful.
- * \param dt The step size. Updated.
- * \return success if the step was accepted, fail otherwise.
- */
-
- /**
- * \fn bulirsch_stoer::try_step( System system , StateInOut &x , const DerivIn &dxdt , time_type &t , time_type &dt )
- * \brief Tries to perform one step.
- *
- * This method tries to do one step with step size dt. If the error estimate
- * is to large, the step is rejected and the method returns fail and the
- * step size dt is reduced. If the error estimate is acceptably small, the
- * step is performed, success is returned and dt might be increased to make
- * the steps as large as possible. This method also updates t if a step is
- * performed. Also, the internal order of the stepper is adjusted if required.
- *
- * \param system The system function to solve, hence the r.h.s. of the ODE.
- * It must fulfill the Simple System concept.
- * \param x The state of the ODE which should be solved. Overwritten if
- * the step is successful.
- * \param dxdt The derivative of state.
- * \param t The value of the time. Updated if the step is successful.
- * \param dt The step size. Updated.
- * \return success if the step was accepted, fail otherwise.
- */
-
- /**
- * \fn bulirsch_stoer::try_step( System system , const StateIn &in , time_type &t , StateOut &out , time_type &dt )
- * \brief Tries to perform one step.
- *
- * \note This method is disabled if state_type=time_type to avoid ambiguity.
- *
- * This method tries to do one step with step size dt. If the error estimate
- * is to large, the step is rejected and the method returns fail and the
- * step size dt is reduced. If the error estimate is acceptably small, the
- * step is performed, success is returned and dt might be increased to make
- * the steps as large as possible. This method also updates t if a step is
- * performed. Also, the internal order of the stepper is adjusted if required.
- *
- * \param system The system function to solve, hence the r.h.s. of the ODE.
- * It must fulfill the Simple System concept.
- * \param in The state of the ODE which should be solved.
- * \param t The value of the time. Updated if the step is successful.
- * \param out Used to store the result of the step.
- * \param dt The step size. Updated.
- * \return success if the step was accepted, fail otherwise.
- */
-
-
- /**
- * \fn bulirsch_stoer::try_step( System system , const StateIn &in , const DerivIn &dxdt , time_type &t , StateOut &out , time_type &dt )
- * \brief Tries to perform one step.
- *
- * This method tries to do one step with step size dt. If the error estimate
- * is to large, the step is rejected and the method returns fail and the
- * step size dt is reduced. If the error estimate is acceptably small, the
- * step is performed, success is returned and dt might be increased to make
- * the steps as large as possible. This method also updates t if a step is
- * performed. Also, the internal order of the stepper is adjusted if required.
- *
- * \param system The system function to solve, hence the r.h.s. of the ODE.
- * It must fulfill the Simple System concept.
- * \param in The state of the ODE which should be solved.
- * \param dxdt The derivative of state.
- * \param t The value of the time. Updated if the step is successful.
- * \param out Used to store the result of the step.
- * \param dt The step size. Updated.
- * \return success if the step was accepted, fail otherwise.
- */
-
-
- /**
- * \fn bulirsch_stoer::adjust_size( const StateIn &x )
- * \brief Adjust the size of all temporaries in the stepper manually.
- * \param x A state from which the size of the temporaries to be resized is deduced.
- */
-
-}
-}
-}
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_BULIRSCH_STOER_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/bulirsch_stoer_dense_out.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/bulirsch_stoer_dense_out.hpp
deleted file mode 100644
index e74a2641c92f892efca674d033645cfe345c5963..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/bulirsch_stoer_dense_out.hpp
+++ /dev/null
@@ -1,838 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/bulirsch_stoer_dense_out.hpp
-
- [begin_description]
- Implementaiton of the Burlish-Stoer method with dense output
- [end_description]
-
- Copyright 2011-2015 Mario Mulansky
- Copyright 2011-2013 Karsten Ahnert
- Copyright 2012 Christoph Koke
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_BULIRSCH_STOER_DENSE_OUT_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_BULIRSCH_STOER_DENSE_OUT_HPP_INCLUDED
-
-
-#include <iostream>
-
-#include <algorithm>
-
-#include <boost/config.hpp> // for min/max guidelines
-
-#include <boost/numeric/odeint/util/bind.hpp>
-
-#include <boost/math/special_functions/binomial.hpp>
-
-#include <boost/numeric/odeint/stepper/controlled_runge_kutta.hpp>
-#include <boost/numeric/odeint/stepper/modified_midpoint.hpp>
-#include <boost/numeric/odeint/stepper/controlled_step_result.hpp>
-#include <boost/numeric/odeint/algebra/range_algebra.hpp>
-#include <boost/numeric/odeint/algebra/default_operations.hpp>
-#include <boost/numeric/odeint/algebra/algebra_dispatcher.hpp>
-#include <boost/numeric/odeint/algebra/operations_dispatcher.hpp>
-
-#include <boost/numeric/odeint/util/state_wrapper.hpp>
-#include <boost/numeric/odeint/util/is_resizeable.hpp>
-#include <boost/numeric/odeint/util/resizer.hpp>
-#include <boost/numeric/odeint/util/unit_helper.hpp>
-
-#include <boost/numeric/odeint/integrate/max_step_checker.hpp>
-
-#include <boost/type_traits.hpp>
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-template<
- class State ,
- class Value = double ,
- class Deriv = State ,
- class Time = Value ,
- class Algebra = typename algebra_dispatcher< State >::algebra_type ,
- class Operations = typename operations_dispatcher< State >::operations_type ,
- class Resizer = initially_resizer
- >
-class bulirsch_stoer_dense_out {
-
-
-public:
-
- typedef State state_type;
- typedef Value value_type;
- typedef Deriv deriv_type;
- typedef Time time_type;
- typedef Algebra algebra_type;
- typedef Operations operations_type;
- typedef Resizer resizer_type;
- typedef dense_output_stepper_tag stepper_category;
-#ifndef DOXYGEN_SKIP
- typedef state_wrapper< state_type > wrapped_state_type;
- typedef state_wrapper< deriv_type > wrapped_deriv_type;
-
- typedef bulirsch_stoer_dense_out< State , Value , Deriv , Time , Algebra , Operations , Resizer > controlled_error_bs_type;
-
- typedef typename inverse_time< time_type >::type inv_time_type;
-
- typedef std::vector< value_type > value_vector;
- typedef std::vector< time_type > time_vector;
- typedef std::vector< inv_time_type > inv_time_vector; //should be 1/time_type for boost.units
- typedef std::vector< value_vector > value_matrix;
- typedef std::vector< size_t > int_vector;
- typedef std::vector< wrapped_state_type > state_vector_type;
- typedef std::vector< wrapped_deriv_type > deriv_vector_type;
- typedef std::vector< deriv_vector_type > deriv_table_type;
-#endif //DOXYGEN_SKIP
-
- const static size_t m_k_max = 8;
-
-
-
- bulirsch_stoer_dense_out(
- value_type eps_abs = 1E-6 , value_type eps_rel = 1E-6 ,
- value_type factor_x = 1.0 , value_type factor_dxdt = 1.0 ,
- time_type max_dt = static_cast<time_type>(0) ,
- bool control_interpolation = false )
- : m_error_checker( eps_abs , eps_rel , factor_x, factor_dxdt ) ,
- m_max_dt(max_dt) ,
- m_control_interpolation( control_interpolation) ,
- m_last_step_rejected( false ) , m_first( true ) ,
- m_current_state_x1( true ) ,
- m_error( m_k_max ) ,
- m_interval_sequence( m_k_max+1 ) ,
- m_coeff( m_k_max+1 ) ,
- m_cost( m_k_max+1 ) ,
- m_facmin_table( m_k_max+1 ) ,
- m_table( m_k_max ) ,
- m_mp_states( m_k_max+1 ) ,
- m_derivs( m_k_max+1 ) ,
- m_diffs( 2*m_k_max+2 ) ,
- STEPFAC1( 0.65 ) , STEPFAC2( 0.94 ) , STEPFAC3( 0.02 ) , STEPFAC4( 4.0 ) , KFAC1( 0.8 ) , KFAC2( 0.9 )
- {
- BOOST_USING_STD_MIN();
- BOOST_USING_STD_MAX();
-
- for( unsigned short i = 0; i < m_k_max+1; i++ )
- {
- /* only this specific sequence allows for dense output */
- m_interval_sequence[i] = 2 + 4*i; // 2 6 10 14 ...
- m_derivs[i].resize( m_interval_sequence[i] );
- if( i == 0 )
- {
- m_cost[i] = m_interval_sequence[i];
- } else
- {
- m_cost[i] = m_cost[i-1] + m_interval_sequence[i];
- }
- m_facmin_table[i] = pow BOOST_PREVENT_MACRO_SUBSTITUTION( STEPFAC3 , static_cast< value_type >(1) / static_cast< value_type >( 2*i+1 ) );
- m_coeff[i].resize(i);
- for( size_t k = 0 ; k < i ; ++k )
- {
- const value_type r = static_cast< value_type >( m_interval_sequence[i] ) / static_cast< value_type >( m_interval_sequence[k] );
- m_coeff[i][k] = 1.0 / ( r*r - static_cast< value_type >( 1.0 ) ); // coefficients for extrapolation
- }
- // crude estimate of optimal order
-
- m_current_k_opt = 4;
- /* no calculation because log10 might not exist for value_type!
- const value_type logfact( -log10( max BOOST_PREVENT_MACRO_SUBSTITUTION( eps_rel , static_cast< value_type >( 1.0E-12 ) ) ) * 0.6 + 0.5 );
- m_current_k_opt = max BOOST_PREVENT_MACRO_SUBSTITUTION( 1 , min BOOST_PREVENT_MACRO_SUBSTITUTION( static_cast<int>( m_k_max-1 ) , static_cast<int>( logfact ) ));
- */
- }
- int num = 1;
- for( int i = 2*(m_k_max)+1 ; i >=0 ; i-- )
- {
- m_diffs[i].resize( num );
- num += (i+1)%2;
- }
- }
-
- template< class System , class StateIn , class DerivIn , class StateOut , class DerivOut >
- controlled_step_result try_step( System system , const StateIn &in , const DerivIn &dxdt , time_type &t , StateOut &out , DerivOut &dxdt_new , time_type &dt )
- {
- if( m_max_dt != static_cast<time_type>(0) && detail::less_with_sign(m_max_dt, dt, dt) )
- {
- // given step size is bigger then max_dt
- // set limit and return fail
- dt = m_max_dt;
- return fail;
- }
-
- BOOST_USING_STD_MIN();
- BOOST_USING_STD_MAX();
- using std::pow;
-
- static const value_type val1( 1.0 );
-
- bool reject( true );
-
- time_vector h_opt( m_k_max+1 );
- inv_time_vector work( m_k_max+1 );
-
- m_k_final = 0;
- time_type new_h = dt;
-
- //std::cout << "t=" << t <<", dt=" << dt << ", k_opt=" << m_current_k_opt << ", first: " << m_first << std::endl;
-
- for( size_t k = 0 ; k <= m_current_k_opt+1 ; k++ )
- {
- m_midpoint.set_steps( m_interval_sequence[k] );
- if( k == 0 )
- {
- m_midpoint.do_step( system , in , dxdt , t , out , dt , m_mp_states[k].m_v , m_derivs[k]);
- }
- else
- {
- m_midpoint.do_step( system , in , dxdt , t , m_table[k-1].m_v , dt , m_mp_states[k].m_v , m_derivs[k] );
- extrapolate( k , m_table , m_coeff , out );
- // get error estimate
- m_algebra.for_each3( m_err.m_v , out , m_table[0].m_v ,
- typename operations_type::template scale_sum2< value_type , value_type >( val1 , -val1 ) );
- const value_type error = m_error_checker.error( m_algebra , in , dxdt , m_err.m_v , dt );
- h_opt[k] = calc_h_opt( dt , error , k );
- work[k] = static_cast<value_type>( m_cost[k] ) / h_opt[k];
-
- m_k_final = k;
-
- if( (k == m_current_k_opt-1) || m_first )
- { // convergence before k_opt ?
- if( error < 1.0 )
- {
- //convergence
- reject = false;
- if( (work[k] < KFAC2*work[k-1]) || (m_current_k_opt <= 2) )
- {
- // leave order as is (except we were in first round)
- m_current_k_opt = min BOOST_PREVENT_MACRO_SUBSTITUTION( static_cast<int>(m_k_max)-1 , max BOOST_PREVENT_MACRO_SUBSTITUTION( 2 , static_cast<int>(k)+1 ) );
- new_h = h_opt[k] * static_cast<value_type>( m_cost[k+1] ) / static_cast<value_type>( m_cost[k] );
- } else {
- m_current_k_opt = min BOOST_PREVENT_MACRO_SUBSTITUTION( static_cast<int>(m_k_max)-1 , max BOOST_PREVENT_MACRO_SUBSTITUTION( 2 , static_cast<int>(k) ) );
- new_h = h_opt[k];
- }
- break;
- }
- else if( should_reject( error , k ) && !m_first )
- {
- reject = true;
- new_h = h_opt[k];
- break;
- }
- }
- if( k == m_current_k_opt )
- { // convergence at k_opt ?
- if( error < 1.0 )
- {
- //convergence
- reject = false;
- if( (work[k-1] < KFAC2*work[k]) )
- {
- m_current_k_opt = max BOOST_PREVENT_MACRO_SUBSTITUTION( 2 , static_cast<int>(m_current_k_opt)-1 );
- new_h = h_opt[m_current_k_opt];
- }
- else if( (work[k] < KFAC2*work[k-1]) && !m_last_step_rejected )
- {
- m_current_k_opt = min BOOST_PREVENT_MACRO_SUBSTITUTION( static_cast<int>(m_k_max)-1 , static_cast<int>(m_current_k_opt)+1 );
- new_h = h_opt[k]*static_cast<value_type>( m_cost[m_current_k_opt] ) / static_cast<value_type>( m_cost[k] );
- } else
- new_h = h_opt[m_current_k_opt];
- break;
- }
- else if( should_reject( error , k ) )
- {
- reject = true;
- new_h = h_opt[m_current_k_opt];
- break;
- }
- }
- if( k == m_current_k_opt+1 )
- { // convergence at k_opt+1 ?
- if( error < 1.0 )
- { //convergence
- reject = false;
- if( work[k-2] < KFAC2*work[k-1] )
- m_current_k_opt = max BOOST_PREVENT_MACRO_SUBSTITUTION( 2 , static_cast<int>(m_current_k_opt)-1 );
- if( (work[k] < KFAC2*work[m_current_k_opt]) && !m_last_step_rejected )
- m_current_k_opt = min BOOST_PREVENT_MACRO_SUBSTITUTION( static_cast<int>(m_k_max)-1 , static_cast<int>(k) );
- new_h = h_opt[m_current_k_opt];
- } else
- {
- reject = true;
- new_h = h_opt[m_current_k_opt];
- }
- break;
- }
- }
- }
-
- if( !reject )
- {
-
- //calculate dxdt for next step and dense output
- typename odeint::unwrap_reference< System >::type &sys = system;
- sys( out , dxdt_new , t+dt );
-
- //prepare dense output
- value_type error = prepare_dense_output( m_k_final , in , dxdt , out , dxdt_new , dt );
-
- if( error > static_cast<value_type>(10) ) // we are not as accurate for interpolation as for the steps
- {
- reject = true;
- new_h = dt * pow BOOST_PREVENT_MACRO_SUBSTITUTION( error , static_cast<value_type>(-1)/(2*m_k_final+2) );
- } else {
- t += dt;
- }
- }
- //set next stepsize
- if( !m_last_step_rejected || (new_h < dt) )
- {
- // limit step size
- if( m_max_dt != static_cast<time_type>(0) )
- {
- new_h = detail::min_abs(m_max_dt, new_h);
- }
- dt = new_h;
- }
-
- m_last_step_rejected = reject;
- if( reject )
- return fail;
- else
- return success;
- }
-
- template< class StateType >
- void initialize( const StateType &x0 , const time_type &t0 , const time_type &dt0 )
- {
- m_resizer.adjust_size( x0 , detail::bind( &controlled_error_bs_type::template resize_impl< StateType > , detail::ref( *this ) , detail::_1 ) );
- boost::numeric::odeint::copy( x0 , get_current_state() );
- m_t = t0;
- m_dt = dt0;
- reset();
- }
-
-
- /* =======================================================
- * the actual step method that should be called from outside (maybe make try_step private?)
- */
- template< class System >
- std::pair< time_type , time_type > do_step( System system )
- {
- if( m_first )
- {
- typename odeint::unwrap_reference< System >::type &sys = system;
- sys( get_current_state() , get_current_deriv() , m_t );
- }
-
- failed_step_checker fail_checker; // to throw a runtime_error if step size adjustment fails
- controlled_step_result res = fail;
- m_t_last = m_t;
- while( res == fail )
- {
- res = try_step( system , get_current_state() , get_current_deriv() , m_t , get_old_state() , get_old_deriv() , m_dt );
- m_first = false;
- fail_checker(); // check for overflow of failed steps
- }
- toggle_current_state();
- return std::make_pair( m_t_last , m_t );
- }
-
- /* performs the interpolation from a calculated step */
- template< class StateOut >
- void calc_state( time_type t , StateOut &x ) const
- {
- do_interpolation( t , x );
- }
-
- const state_type& current_state( void ) const
- {
- return get_current_state();
- }
-
- time_type current_time( void ) const
- {
- return m_t;
- }
-
- const state_type& previous_state( void ) const
- {
- return get_old_state();
- }
-
- time_type previous_time( void ) const
- {
- return m_t_last;
- }
-
- time_type current_time_step( void ) const
- {
- return m_dt;
- }
-
- /** \brief Resets the internal state of the stepper. */
- void reset()
- {
- m_first = true;
- m_last_step_rejected = false;
- }
-
- template< class StateIn >
- void adjust_size( const StateIn &x )
- {
- resize_impl( x );
- m_midpoint.adjust_size( x );
- }
-
-
-private:
-
- template< class StateInOut , class StateVector >
- void extrapolate( size_t k , StateVector &table , const value_matrix &coeff , StateInOut &xest , size_t order_start_index = 0 )
- //polynomial extrapolation, see http://www.nr.com/webnotes/nr3web21.pdf
- {
- static const value_type val1( 1.0 );
- for( int j=k-1 ; j>0 ; --j )
- {
- m_algebra.for_each3( table[j-1].m_v , table[j].m_v , table[j-1].m_v ,
- typename operations_type::template scale_sum2< value_type , value_type >( val1 + coeff[k + order_start_index][j + order_start_index] ,
- -coeff[k + order_start_index][j + order_start_index] ) );
- }
- m_algebra.for_each3( xest , table[0].m_v , xest ,
- typename operations_type::template scale_sum2< value_type , value_type >( val1 + coeff[k + order_start_index][0 + order_start_index] ,
- -coeff[k + order_start_index][0 + order_start_index]) );
- }
-
-
- template< class StateVector >
- void extrapolate_dense_out( size_t k , StateVector &table , const value_matrix &coeff , size_t order_start_index = 0 )
- //polynomial extrapolation, see http://www.nr.com/webnotes/nr3web21.pdf
- {
- // result is written into table[0]
- static const value_type val1( 1.0 );
- for( int j=k ; j>1 ; --j )
- {
- m_algebra.for_each3( table[j-1].m_v , table[j].m_v , table[j-1].m_v ,
- typename operations_type::template scale_sum2< value_type , value_type >( val1 + coeff[k + order_start_index][j + order_start_index - 1] ,
- -coeff[k + order_start_index][j + order_start_index - 1] ) );
- }
- m_algebra.for_each3( table[0].m_v , table[1].m_v , table[0].m_v ,
- typename operations_type::template scale_sum2< value_type , value_type >( val1 + coeff[k + order_start_index][order_start_index] ,
- -coeff[k + order_start_index][order_start_index]) );
- }
-
- time_type calc_h_opt( time_type h , value_type error , size_t k ) const
- {
- BOOST_USING_STD_MIN();
- BOOST_USING_STD_MAX();
- using std::pow;
-
- value_type expo = static_cast<value_type>(1)/(m_interval_sequence[k-1]);
- value_type facmin = m_facmin_table[k];
- value_type fac;
- if (error == 0.0)
- fac = static_cast<value_type>(1)/facmin;
- else
- {
- fac = STEPFAC2 / pow BOOST_PREVENT_MACRO_SUBSTITUTION( error / STEPFAC1 , expo );
- fac = max BOOST_PREVENT_MACRO_SUBSTITUTION( static_cast<value_type>( facmin/STEPFAC4 ) , min BOOST_PREVENT_MACRO_SUBSTITUTION( static_cast<value_type>(static_cast<value_type>(1)/facmin) , fac ) );
- }
- return h*fac;
- }
-
- bool in_convergence_window( size_t k ) const
- {
- if( (k == m_current_k_opt-1) && !m_last_step_rejected )
- return true; // decrease order only if last step was not rejected
- return ( (k == m_current_k_opt) || (k == m_current_k_opt+1) );
- }
-
- bool should_reject( value_type error , size_t k ) const
- {
- if( k == m_current_k_opt-1 )
- {
- const value_type d = m_interval_sequence[m_current_k_opt] * m_interval_sequence[m_current_k_opt+1] /
- (m_interval_sequence[0]*m_interval_sequence[0]);
- //step will fail, criterion 17.3.17 in NR
- return ( error > d*d );
- }
- else if( k == m_current_k_opt )
- {
- const value_type d = m_interval_sequence[m_current_k_opt+1] / m_interval_sequence[0];
- return ( error > d*d );
- } else
- return error > 1.0;
- }
-
- template< class StateIn1 , class DerivIn1 , class StateIn2 , class DerivIn2 >
- value_type prepare_dense_output( int k , const StateIn1 &x_start , const DerivIn1 &dxdt_start ,
- const StateIn2 & /* x_end */ , const DerivIn2 & /*dxdt_end */ , time_type dt )
- /* k is the order to which the result was approximated */
- {
-
- /* compute the coefficients of the interpolation polynomial
- * we parametrize the interval t .. t+dt by theta = -1 .. 1
- * we use 2k+3 values at the interval center theta=0 to obtain the interpolation coefficients
- * the values are x(t+dt/2) and the derivatives dx/dt , ... d^(2k+2) x / dt^(2k+2) at the midpoints
- * the derivatives are approximated via finite differences
- * all values are obtained from interpolation of the results from the increasing orders of the midpoint calls
- */
-
- // calculate finite difference approximations to derivatives at the midpoint
- for( int j = 0 ; j<=k ; j++ )
- {
- /* not working with boost units... */
- const value_type d = m_interval_sequence[j] / ( static_cast<value_type>(2) * dt );
- value_type f = 1.0; //factor 1/2 here because our interpolation interval has length 2 !!!
- for( int kappa = 0 ; kappa <= 2*j+1 ; ++kappa )
- {
- calculate_finite_difference( j , kappa , f , dxdt_start );
- f *= d;
- }
-
- if( j > 0 )
- extrapolate_dense_out( j , m_mp_states , m_coeff );
- }
-
- time_type d = dt/2;
-
- // extrapolate finite differences
- for( int kappa = 0 ; kappa<=2*k+1 ; kappa++ )
- {
- for( int j=1 ; j<=(k-kappa/2) ; ++j )
- extrapolate_dense_out( j , m_diffs[kappa] , m_coeff , kappa/2 );
-
- // extrapolation results are now stored in m_diffs[kappa][0]
-
- // divide kappa-th derivative by kappa because we need these terms for dense output interpolation
- m_algebra.for_each1( m_diffs[kappa][0].m_v , typename operations_type::template scale< time_type >( static_cast<time_type>(d) ) );
-
- d *= dt/(2*(kappa+2));
- }
-
- // dense output coefficients a_0 is stored in m_mp_states[0], a_i for i = 1...2k are stored in m_diffs[i-1][0]
-
- // the error is just the highest order coefficient of the interpolation polynomial
- // this is because we use only the midpoint theta=0 as support for the interpolation (remember that theta = -1 .. 1)
-
- value_type error = 0.0;
- if( m_control_interpolation )
- {
- boost::numeric::odeint::copy( m_diffs[2*k+1][0].m_v , m_err.m_v );
- error = m_error_checker.error( m_algebra , x_start , dxdt_start , m_err.m_v , dt );
- }
-
- return error;
- }
-
- template< class DerivIn >
- void calculate_finite_difference( size_t j , size_t kappa , value_type fac , const DerivIn &dxdt )
- {
- const int m = m_interval_sequence[j]/2-1;
- if( kappa == 0) // no calculation required for 0th derivative of f
- {
- m_algebra.for_each2( m_diffs[0][j].m_v , m_derivs[j][m].m_v ,
- typename operations_type::template scale_sum1< value_type >( fac ) );
- }
- else
- {
- // calculate the index of m_diffs for this kappa-j-combination
- const int j_diffs = j - kappa/2;
-
- m_algebra.for_each2( m_diffs[kappa][j_diffs].m_v , m_derivs[j][m+kappa].m_v ,
- typename operations_type::template scale_sum1< value_type >( fac ) );
- value_type sign = -1.0;
- int c = 1;
- //computes the j-th order finite difference for the kappa-th derivative of f at t+dt/2 using function evaluations stored in m_derivs
- for( int i = m+static_cast<int>(kappa)-2 ; i >= m-static_cast<int>(kappa) ; i -= 2 )
- {
- if( i >= 0 )
- {
- m_algebra.for_each3( m_diffs[kappa][j_diffs].m_v , m_diffs[kappa][j_diffs].m_v , m_derivs[j][i].m_v ,
- typename operations_type::template scale_sum2< value_type , value_type >( 1.0 ,
- sign * fac * boost::math::binomial_coefficient< value_type >( kappa , c ) ) );
- }
- else
- {
- m_algebra.for_each3( m_diffs[kappa][j_diffs].m_v , m_diffs[kappa][j_diffs].m_v , dxdt ,
- typename operations_type::template scale_sum2< value_type , value_type >( 1.0 , sign * fac ) );
- }
- sign *= -1;
- ++c;
- }
- }
- }
-
- template< class StateOut >
- void do_interpolation( time_type t , StateOut &out ) const
- {
- // interpolation polynomial is defined for theta = -1 ... 1
- // m_k_final is the number of order-iterations done for the last step - it governs the order of the interpolation polynomial
- const value_type theta = 2 * get_unit_value( (t - m_t_last) / (m_t - m_t_last) ) - 1;
- // we use only values at interval center, that is theta=0, for interpolation
- // our interpolation polynomial is thus of order 2k+2, hence we have 2k+3 terms
-
- boost::numeric::odeint::copy( m_mp_states[0].m_v , out );
- // add remaining terms: x += a_1 theta + a2 theta^2 + ... + a_{2k} theta^{2k}
- value_type theta_pow( theta );
- for( size_t i=0 ; i<=2*m_k_final+1 ; ++i )
- {
- m_algebra.for_each3( out , out , m_diffs[i][0].m_v ,
- typename operations_type::template scale_sum2< value_type >( static_cast<value_type>(1) , theta_pow ) );
- theta_pow *= theta;
- }
- }
-
- /* Resizer methods */
- template< class StateIn >
- bool resize_impl( const StateIn &x )
- {
- bool resized( false );
-
- resized |= adjust_size_by_resizeability( m_x1 , x , typename is_resizeable<state_type>::type() );
- resized |= adjust_size_by_resizeability( m_x2 , x , typename is_resizeable<state_type>::type() );
- resized |= adjust_size_by_resizeability( m_dxdt1 , x , typename is_resizeable<state_type>::type() );
- resized |= adjust_size_by_resizeability( m_dxdt2 , x , typename is_resizeable<state_type>::type() );
- resized |= adjust_size_by_resizeability( m_err , x , typename is_resizeable<state_type>::type() );
-
- for( size_t i = 0 ; i < m_k_max ; ++i )
- resized |= adjust_size_by_resizeability( m_table[i] , x , typename is_resizeable<state_type>::type() );
- for( size_t i = 0 ; i < m_k_max+1 ; ++i )
- resized |= adjust_size_by_resizeability( m_mp_states[i] , x , typename is_resizeable<state_type>::type() );
- for( size_t i = 0 ; i < m_k_max+1 ; ++i )
- for( size_t j = 0 ; j < m_derivs[i].size() ; ++j )
- resized |= adjust_size_by_resizeability( m_derivs[i][j] , x , typename is_resizeable<deriv_type>::type() );
- for( size_t i = 0 ; i < 2*m_k_max+2 ; ++i )
- for( size_t j = 0 ; j < m_diffs[i].size() ; ++j )
- resized |= adjust_size_by_resizeability( m_diffs[i][j] , x , typename is_resizeable<deriv_type>::type() );
-
- return resized;
- }
-
-
- state_type& get_current_state( void )
- {
- return m_current_state_x1 ? m_x1.m_v : m_x2.m_v ;
- }
-
- const state_type& get_current_state( void ) const
- {
- return m_current_state_x1 ? m_x1.m_v : m_x2.m_v ;
- }
-
- state_type& get_old_state( void )
- {
- return m_current_state_x1 ? m_x2.m_v : m_x1.m_v ;
- }
-
- const state_type& get_old_state( void ) const
- {
- return m_current_state_x1 ? m_x2.m_v : m_x1.m_v ;
- }
-
- deriv_type& get_current_deriv( void )
- {
- return m_current_state_x1 ? m_dxdt1.m_v : m_dxdt2.m_v ;
- }
-
- const deriv_type& get_current_deriv( void ) const
- {
- return m_current_state_x1 ? m_dxdt1.m_v : m_dxdt2.m_v ;
- }
-
- deriv_type& get_old_deriv( void )
- {
- return m_current_state_x1 ? m_dxdt2.m_v : m_dxdt1.m_v ;
- }
-
- const deriv_type& get_old_deriv( void ) const
- {
- return m_current_state_x1 ? m_dxdt2.m_v : m_dxdt1.m_v ;
- }
-
-
- void toggle_current_state( void )
- {
- m_current_state_x1 = ! m_current_state_x1;
- }
-
-
-
- default_error_checker< value_type, algebra_type , operations_type > m_error_checker;
- modified_midpoint_dense_out< state_type , value_type , deriv_type , time_type , algebra_type , operations_type , resizer_type > m_midpoint;
-
- time_type m_max_dt;
-
- bool m_control_interpolation;
-
- bool m_last_step_rejected;
- bool m_first;
-
- time_type m_t;
- time_type m_dt;
- time_type m_dt_last;
- time_type m_t_last;
-
- size_t m_current_k_opt;
- size_t m_k_final;
-
- algebra_type m_algebra;
-
- resizer_type m_resizer;
-
- wrapped_state_type m_x1 , m_x2;
- wrapped_deriv_type m_dxdt1 , m_dxdt2;
- wrapped_state_type m_err;
- bool m_current_state_x1;
-
-
-
- value_vector m_error; // errors of repeated midpoint steps and extrapolations
- int_vector m_interval_sequence; // stores the successive interval counts
- value_matrix m_coeff;
- int_vector m_cost; // costs for interval count
- value_vector m_facmin_table; // for precomputed facmin to save pow calls
-
- state_vector_type m_table; // sequence of states for extrapolation
-
- //for dense output:
- state_vector_type m_mp_states; // sequence of approximations of x at distance center
- deriv_table_type m_derivs; // table of function values
- deriv_table_type m_diffs; // table of function values
-
- //wrapped_state_type m_a1 , m_a2 , m_a3 , m_a4;
-
- value_type STEPFAC1 , STEPFAC2 , STEPFAC3 , STEPFAC4 , KFAC1 , KFAC2;
-};
-
-
-
-/********** DOXYGEN **********/
-
-/**
- * \class bulirsch_stoer_dense_out
- * \brief The Bulirsch-Stoer algorithm.
- *
- * The Bulirsch-Stoer is a controlled stepper that adjusts both step size
- * and order of the method. The algorithm uses the modified midpoint and
- * a polynomial extrapolation compute the solution. This class also provides
- * dense output facility.
- *
- * \tparam State The state type.
- * \tparam Value The value type.
- * \tparam Deriv The type representing the time derivative of the state.
- * \tparam Time The time representing the independent variable - the time.
- * \tparam Algebra The algebra type.
- * \tparam Operations The operations type.
- * \tparam Resizer The resizer policy type.
- */
-
- /**
- * \fn bulirsch_stoer_dense_out::bulirsch_stoer_dense_out( value_type eps_abs , value_type eps_rel , value_type factor_x , value_type factor_dxdt , bool control_interpolation )
- * \brief Constructs the bulirsch_stoer class, including initialization of
- * the error bounds.
- *
- * \param eps_abs Absolute tolerance level.
- * \param eps_rel Relative tolerance level.
- * \param factor_x Factor for the weight of the state.
- * \param factor_dxdt Factor for the weight of the derivative.
- * \param control_interpolation Set true to additionally control the error of
- * the interpolation.
- */
-
- /**
- * \fn bulirsch_stoer_dense_out::try_step( System system , const StateIn &in , const DerivIn &dxdt , time_type &t , StateOut &out , DerivOut &dxdt_new , time_type &dt )
- * \brief Tries to perform one step.
- *
- * This method tries to do one step with step size dt. If the error estimate
- * is to large, the step is rejected and the method returns fail and the
- * step size dt is reduced. If the error estimate is acceptably small, the
- * step is performed, success is returned and dt might be increased to make
- * the steps as large as possible. This method also updates t if a step is
- * performed. Also, the internal order of the stepper is adjusted if required.
- *
- * \param system The system function to solve, hence the r.h.s. of the ODE.
- * It must fulfill the Simple System concept.
- * \param in The state of the ODE which should be solved.
- * \param dxdt The derivative of state.
- * \param t The value of the time. Updated if the step is successful.
- * \param out Used to store the result of the step.
- * \param dt The step size. Updated.
- * \return success if the step was accepted, fail otherwise.
- */
-
- /**
- * \fn bulirsch_stoer_dense_out::initialize( const StateType &x0 , const time_type &t0 , const time_type &dt0 )
- * \brief Initializes the dense output stepper.
- *
- * \param x0 The initial state.
- * \param t0 The initial time.
- * \param dt0 The initial time step.
- */
-
- /**
- * \fn bulirsch_stoer_dense_out::do_step( System system )
- * \brief Does one time step. This is the main method that should be used to
- * integrate an ODE with this stepper.
- * \note initialize has to be called before using this method to set the
- * initial conditions x,t and the stepsize.
- * \param system The system function to solve, hence the r.h.s. of the
- * ordinary differential equation. It must fulfill the Simple System concept.
- * \return Pair with start and end time of the integration step.
- */
-
- /**
- * \fn bulirsch_stoer_dense_out::calc_state( time_type t , StateOut &x ) const
- * \brief Calculates the solution at an intermediate point within the last step
- * \param t The time at which the solution should be calculated, has to be
- * in the current time interval.
- * \param x The output variable where the result is written into.
- */
-
- /**
- * \fn bulirsch_stoer_dense_out::current_state( void ) const
- * \brief Returns the current state of the solution.
- * \return The current state of the solution x(t).
- */
-
- /**
- * \fn bulirsch_stoer_dense_out::current_time( void ) const
- * \brief Returns the current time of the solution.
- * \return The current time of the solution t.
- */
-
- /**
- * \fn bulirsch_stoer_dense_out::previous_state( void ) const
- * \brief Returns the last state of the solution.
- * \return The last state of the solution x(t-dt).
- */
-
- /**
- * \fn bulirsch_stoer_dense_out::previous_time( void ) const
- * \brief Returns the last time of the solution.
- * \return The last time of the solution t-dt.
- */
-
- /**
- * \fn bulirsch_stoer_dense_out::current_time_step( void ) const
- * \brief Returns the current step size.
- * \return The current step size.
- */
-
- /**
- * \fn bulirsch_stoer_dense_out::adjust_size( const StateIn &x )
- * \brief Adjust the size of all temporaries in the stepper manually.
- * \param x A state from which the size of the temporaries to be resized is deduced.
- */
-
-}
-}
-}
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_BULIRSCH_STOER_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/controlled_runge_kutta.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/controlled_runge_kutta.hpp
deleted file mode 100644
index 2c0bef62131316932ec3c4a5c7f6d3e005b12f27..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/controlled_runge_kutta.hpp
+++ /dev/null
@@ -1,1014 +0,0 @@
-/* [auto_generated]
- boost/numeric/odeint/stepper/controlled_runge_kutta.hpp
-
- [begin_description]
- The default controlled stepper which can be used with all explicit Runge-Kutta error steppers.
- [end_description]
-
- Copyright 2010-2013 Karsten Ahnert
- Copyright 2010-2015 Mario Mulansky
- Copyright 2012 Christoph Koke
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_CONTROLLED_RUNGE_KUTTA_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_CONTROLLED_RUNGE_KUTTA_HPP_INCLUDED
-
-
-
-#include <cmath>
-
-#include <boost/config.hpp>
-#include <boost/utility/enable_if.hpp>
-#include <boost/type_traits/is_same.hpp>
-
-#include <boost/numeric/odeint/util/bind.hpp>
-#include <boost/numeric/odeint/util/unwrap_reference.hpp>
-#include <boost/numeric/odeint/util/copy.hpp>
-
-#include <boost/numeric/odeint/util/state_wrapper.hpp>
-#include <boost/numeric/odeint/util/is_resizeable.hpp>
-#include <boost/numeric/odeint/util/resizer.hpp>
-#include <boost/numeric/odeint/util/detail/less_with_sign.hpp>
-
-#include <boost/numeric/odeint/algebra/range_algebra.hpp>
-#include <boost/numeric/odeint/algebra/default_operations.hpp>
-#include <boost/numeric/odeint/algebra/algebra_dispatcher.hpp>
-
-#include <boost/numeric/odeint/stepper/controlled_step_result.hpp>
-#include <boost/numeric/odeint/stepper/stepper_categories.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-template
-<
-class Value ,
-class Algebra ,
-class Operations
->
-class default_error_checker
-{
-public:
-
- typedef Value value_type;
- typedef Algebra algebra_type;
- typedef Operations operations_type;
-
- default_error_checker(
- value_type eps_abs = static_cast< value_type >( 1.0e-6 ) ,
- value_type eps_rel = static_cast< value_type >( 1.0e-6 ) ,
- value_type a_x = static_cast< value_type >( 1 ) ,
- value_type a_dxdt = static_cast< value_type >( 1 ))
- : m_eps_abs( eps_abs ) , m_eps_rel( eps_rel ) , m_a_x( a_x ) , m_a_dxdt( a_dxdt )
- { }
-
-
- template< class State , class Deriv , class Err, class Time >
- value_type error( const State &x_old , const Deriv &dxdt_old , Err &x_err , Time dt ) const
- {
- return error( algebra_type() , x_old , dxdt_old , x_err , dt );
- }
-
- template< class State , class Deriv , class Err, class Time >
- value_type error( algebra_type &algebra , const State &x_old , const Deriv &dxdt_old , Err &x_err , Time dt ) const
- {
- using std::abs;
- // this overwrites x_err !
- algebra.for_each3( x_err , x_old , dxdt_old ,
- typename operations_type::template rel_error< value_type >( m_eps_abs , m_eps_rel , m_a_x , m_a_dxdt * abs(get_unit_value( dt )) ) );
-
- // value_type res = algebra.reduce( x_err ,
- // typename operations_type::template maximum< value_type >() , static_cast< value_type >( 0 ) );
- return algebra.norm_inf( x_err );
- }
-
-private:
-
- value_type m_eps_abs;
- value_type m_eps_rel;
- value_type m_a_x;
- value_type m_a_dxdt;
-
-};
-
-
-template< typename Value, typename Time >
-class default_step_adjuster
-{
-public:
- typedef Time time_type;
- typedef Value value_type;
-
- default_step_adjuster(const time_type max_dt=static_cast<time_type>(0))
- : m_max_dt(max_dt)
- {}
-
-
- time_type decrease_step(time_type dt, const value_type error, const int error_order) const
- {
- // returns the decreased time step
- BOOST_USING_STD_MIN();
- BOOST_USING_STD_MAX();
- using std::pow;
-
- dt *= max
- BOOST_PREVENT_MACRO_SUBSTITUTION(
- static_cast<value_type>( static_cast<value_type>(9) / static_cast<value_type>(10) *
- pow(error, static_cast<value_type>(-1) / (error_order - 1))),
- static_cast<value_type>( static_cast<value_type>(1) / static_cast<value_type> (5)));
- if(m_max_dt != static_cast<time_type >(0))
- // limit to maximal stepsize even when decreasing
- dt = detail::min_abs(dt, m_max_dt);
- return dt;
- }
-
- time_type increase_step(time_type dt, value_type error, const int stepper_order) const
- {
- // returns the increased time step
- BOOST_USING_STD_MIN();
- BOOST_USING_STD_MAX();
- using std::pow;
-
- // adjust the size if dt is smaller than max_dt (providede max_dt is not zero)
- if(error < 0.5)
- {
- // error should be > 0
- error = max BOOST_PREVENT_MACRO_SUBSTITUTION (
- static_cast<value_type>( pow( static_cast<value_type>(5.0) , -static_cast<value_type>(stepper_order) ) ) ,
- error);
- time_type dt_old = dt;
- //error too small - increase dt and keep the evolution and limit scaling factor to 5.0
- dt *= static_cast<value_type>(9)/static_cast<value_type>(10) *
- pow(error, static_cast<value_type>(-1) / stepper_order);
- if(m_max_dt != static_cast<time_type >(0))
- // limit to maximal stepsize
- dt = detail::min_abs(dt, m_max_dt);
- }
- return dt;
- }
-
- bool check_step_size_limit(const time_type dt)
- {
- if(m_max_dt != static_cast<time_type >(0))
- return detail::less_eq_with_sign(dt, m_max_dt, dt);
- return true;
- }
-
- time_type get_max_dt() { return m_max_dt; }
-
-private:
- time_type m_max_dt;
-};
-
-
-
-/*
- * error stepper category dispatcher
- */
-template<
-class ErrorStepper ,
-class ErrorChecker = default_error_checker< typename ErrorStepper::value_type ,
- typename ErrorStepper::algebra_type ,
- typename ErrorStepper::operations_type > ,
-class StepAdjuster = default_step_adjuster< typename ErrorStepper::value_type ,
- typename ErrorStepper::time_type > ,
-class Resizer = typename ErrorStepper::resizer_type ,
-class ErrorStepperCategory = typename ErrorStepper::stepper_category
->
-class controlled_runge_kutta ;
-
-
-
-/*
- * explicit stepper version
- *
- * this class introduces the following try_step overloads
- * try_step( sys , x , t , dt )
- * try_step( sys , x , dxdt , t , dt )
- * try_step( sys , in , t , out , dt )
- * try_step( sys , in , dxdt , t , out , dt )
- */
-/**
- * \brief Implements step size control for Runge-Kutta steppers with error
- * estimation.
- *
- * This class implements the step size control for standard Runge-Kutta
- * steppers with error estimation.
- *
- * \tparam ErrorStepper The stepper type with error estimation, has to fulfill the ErrorStepper concept.
- * \tparam ErrorChecker The error checker
- * \tparam Resizer The resizer policy type.
- */
-template<
-class ErrorStepper,
-class ErrorChecker,
-class StepAdjuster,
-class Resizer
->
-class controlled_runge_kutta< ErrorStepper , ErrorChecker , StepAdjuster, Resizer ,
- explicit_error_stepper_tag >
-{
-
-public:
-
- typedef ErrorStepper stepper_type;
- typedef typename stepper_type::state_type state_type;
- typedef typename stepper_type::value_type value_type;
- typedef typename stepper_type::deriv_type deriv_type;
- typedef typename stepper_type::time_type time_type;
- typedef typename stepper_type::algebra_type algebra_type;
- typedef typename stepper_type::operations_type operations_type;
- typedef Resizer resizer_type;
- typedef ErrorChecker error_checker_type;
- typedef StepAdjuster step_adjuster_type;
- typedef explicit_controlled_stepper_tag stepper_category;
-
-#ifndef DOXYGEN_SKIP
- typedef typename stepper_type::wrapped_state_type wrapped_state_type;
- typedef typename stepper_type::wrapped_deriv_type wrapped_deriv_type;
-
- typedef controlled_runge_kutta< ErrorStepper , ErrorChecker , StepAdjuster ,
- Resizer , explicit_error_stepper_tag > controlled_stepper_type;
-#endif //DOXYGEN_SKIP
-
-
- /**
- * \brief Constructs the controlled Runge-Kutta stepper.
- * \param error_checker An instance of the error checker.
- * \param stepper An instance of the underlying stepper.
- */
- controlled_runge_kutta(
- const error_checker_type &error_checker = error_checker_type( ) ,
- const step_adjuster_type &step_adjuster = step_adjuster_type() ,
- const stepper_type &stepper = stepper_type( )
- )
- : m_stepper(stepper), m_error_checker(error_checker) , m_step_adjuster(step_adjuster)
- { }
-
-
-
- /*
- * Version 1 : try_step( sys , x , t , dt )
- *
- * The overloads are needed to solve the forwarding problem
- */
- /**
- * \brief Tries to perform one step.
- *
- * This method tries to do one step with step size dt. If the error estimate
- * is to large, the step is rejected and the method returns fail and the
- * step size dt is reduced. If the error estimate is acceptably small, the
- * step is performed, success is returned and dt might be increased to make
- * the steps as large as possible. This method also updates t if a step is
- * performed.
- *
- * \param system The system function to solve, hence the r.h.s. of the ODE. It must fulfill the
- * Simple System concept.
- * \param x The state of the ODE which should be solved. Overwritten if
- * the step is successful.
- * \param t The value of the time. Updated if the step is successful.
- * \param dt The step size. Updated.
- * \return success if the step was accepted, fail otherwise.
- */
- template< class System , class StateInOut >
- controlled_step_result try_step( System system , StateInOut &x , time_type &t , time_type &dt )
- {
- return try_step_v1( system , x , t, dt );
- }
-
- /**
- * \brief Tries to perform one step. Solves the forwarding problem and
- * allows for using boost range as state_type.
- *
- * This method tries to do one step with step size dt. If the error estimate
- * is to large, the step is rejected and the method returns fail and the
- * step size dt is reduced. If the error estimate is acceptably small, the
- * step is performed, success is returned and dt might be increased to make
- * the steps as large as possible. This method also updates t if a step is
- * performed.
- *
- * \param system The system function to solve, hence the r.h.s. of the ODE. It must fulfill the
- * Simple System concept.
- * \param x The state of the ODE which should be solved. Overwritten if
- * the step is successful. Can be a boost range.
- * \param t The value of the time. Updated if the step is successful.
- * \param dt The step size. Updated.
- * \return success if the step was accepted, fail otherwise.
- */
- template< class System , class StateInOut >
- controlled_step_result try_step( System system , const StateInOut &x , time_type &t , time_type &dt )
- {
- return try_step_v1( system , x , t, dt );
- }
-
-
-
- /*
- * Version 2 : try_step( sys , x , dxdt , t , dt )
- *
- * this version does not solve the forwarding problem, boost.range can not be used
- */
- /**
- * \brief Tries to perform one step.
- *
- * This method tries to do one step with step size dt. If the error estimate
- * is to large, the step is rejected and the method returns fail and the
- * step size dt is reduced. If the error estimate is acceptably small, the
- * step is performed, success is returned and dt might be increased to make
- * the steps as large as possible. This method also updates t if a step is
- * performed.
- *
- * \param system The system function to solve, hence the r.h.s. of the ODE. It must fulfill the
- * Simple System concept.
- * \param x The state of the ODE which should be solved. Overwritten if
- * the step is successful.
- * \param dxdt The derivative of state.
- * \param t The value of the time. Updated if the step is successful.
- * \param dt The step size. Updated.
- * \return success if the step was accepted, fail otherwise.
- */
- template< class System , class StateInOut , class DerivIn >
- controlled_step_result try_step( System system , StateInOut &x , const DerivIn &dxdt , time_type &t , time_type &dt )
- {
- m_xnew_resizer.adjust_size( x , detail::bind( &controlled_runge_kutta::template resize_m_xnew_impl< StateInOut > , detail::ref( *this ) , detail::_1 ) );
- controlled_step_result res = try_step( system , x , dxdt , t , m_xnew.m_v , dt );
- if( res == success )
- {
- boost::numeric::odeint::copy( m_xnew.m_v , x );
- }
- return res;
- }
-
- /*
- * Version 3 : try_step( sys , in , t , out , dt )
- *
- * this version does not solve the forwarding problem, boost.range can not be used
- *
- * the disable is needed to avoid ambiguous overloads if state_type = time_type
- */
- /**
- * \brief Tries to perform one step.
- *
- * \note This method is disabled if state_type=time_type to avoid ambiguity.
- *
- * This method tries to do one step with step size dt. If the error estimate
- * is to large, the step is rejected and the method returns fail and the
- * step size dt is reduced. If the error estimate is acceptably small, the
- * step is performed, success is returned and dt might be increased to make
- * the steps as large as possible. This method also updates t if a step is
- * performed.
- *
- * \param system The system function to solve, hence the r.h.s. of the ODE. It must fulfill the
- * Simple System concept.
- * \param in The state of the ODE which should be solved.
- * \param t The value of the time. Updated if the step is successful.
- * \param out Used to store the result of the step.
- * \param dt The step size. Updated.
- * \return success if the step was accepted, fail otherwise.
- */
- template< class System , class StateIn , class StateOut >
- typename boost::disable_if< boost::is_same< StateIn , time_type > , controlled_step_result >::type
- try_step( System system , const StateIn &in , time_type &t , StateOut &out , time_type &dt )
- {
- typename odeint::unwrap_reference< System >::type &sys = system;
- m_dxdt_resizer.adjust_size( in , detail::bind( &controlled_runge_kutta::template resize_m_dxdt_impl< StateIn > , detail::ref( *this ) , detail::_1 ) );
- sys( in , m_dxdt.m_v , t );
- return try_step( system , in , m_dxdt.m_v , t , out , dt );
- }
-
-
- /*
- * Version 4 : try_step( sys , in , dxdt , t , out , dt )
- *
- * this version does not solve the forwarding problem, boost.range can not be used
- */
- /**
- * \brief Tries to perform one step.
- *
- * This method tries to do one step with step size dt. If the error estimate
- * is to large, the step is rejected and the method returns fail and the
- * step size dt is reduced. If the error estimate is acceptably small, the
- * step is performed, success is returned and dt might be increased to make
- * the steps as large as possible. This method also updates t if a step is
- * performed.
- *
- * \param system The system function to solve, hence the r.h.s. of the ODE. It must fulfill the
- * Simple System concept.
- * \param in The state of the ODE which should be solved.
- * \param dxdt The derivative of state.
- * \param t The value of the time. Updated if the step is successful.
- * \param out Used to store the result of the step.
- * \param dt The step size. Updated.
- * \return success if the step was accepted, fail otherwise.
- */
- template< class System , class StateIn , class DerivIn , class StateOut >
- controlled_step_result try_step( System system , const StateIn &in , const DerivIn &dxdt , time_type &t , StateOut &out , time_type &dt )
- {
- if( !m_step_adjuster.check_step_size_limit(dt) )
- {
- // given dt was above step size limit - adjust and return fail;
- dt = m_step_adjuster.get_max_dt();
- return fail;
- }
-
- m_xerr_resizer.adjust_size( in , detail::bind( &controlled_runge_kutta::template resize_m_xerr_impl< StateIn > , detail::ref( *this ) , detail::_1 ) );
-
- // do one step with error calculation
- m_stepper.do_step( system , in , dxdt , t , out , dt , m_xerr.m_v );
-
- value_type max_rel_err = m_error_checker.error( m_stepper.algebra() , in , dxdt , m_xerr.m_v , dt );
-
- if( max_rel_err > 1.0 )
- {
- // error too big, decrease step size and reject this step
- dt = m_step_adjuster.decrease_step(dt, max_rel_err, m_stepper.error_order());
- return fail;
- } else
- {
- // otherwise, increase step size and accept
- t += dt;
- dt = m_step_adjuster.increase_step(dt, max_rel_err, m_stepper.stepper_order());
- return success;
- }
- }
-
- /**
- * \brief Adjust the size of all temporaries in the stepper manually.
- * \param x A state from which the size of the temporaries to be resized is deduced.
- */
- template< class StateType >
- void adjust_size( const StateType &x )
- {
- resize_m_xerr_impl( x );
- resize_m_dxdt_impl( x );
- resize_m_xnew_impl( x );
- m_stepper.adjust_size( x );
- }
-
- /**
- * \brief Returns the instance of the underlying stepper.
- * \returns The instance of the underlying stepper.
- */
- stepper_type& stepper( void )
- {
- return m_stepper;
- }
-
- /**
- * \brief Returns the instance of the underlying stepper.
- * \returns The instance of the underlying stepper.
- */
- const stepper_type& stepper( void ) const
- {
- return m_stepper;
- }
-
-private:
-
-
- template< class System , class StateInOut >
- controlled_step_result try_step_v1( System system , StateInOut &x , time_type &t , time_type &dt )
- {
- typename odeint::unwrap_reference< System >::type &sys = system;
- m_dxdt_resizer.adjust_size( x , detail::bind( &controlled_runge_kutta::template resize_m_dxdt_impl< StateInOut > , detail::ref( *this ) , detail::_1 ) );
- sys( x , m_dxdt.m_v ,t );
- return try_step( system , x , m_dxdt.m_v , t , dt );
- }
-
- template< class StateIn >
- bool resize_m_xerr_impl( const StateIn &x )
- {
- return adjust_size_by_resizeability( m_xerr , x , typename is_resizeable<state_type>::type() );
- }
-
- template< class StateIn >
- bool resize_m_dxdt_impl( const StateIn &x )
- {
- return adjust_size_by_resizeability( m_dxdt , x , typename is_resizeable<deriv_type>::type() );
- }
-
- template< class StateIn >
- bool resize_m_xnew_impl( const StateIn &x )
- {
- return adjust_size_by_resizeability( m_xnew , x , typename is_resizeable<state_type>::type() );
- }
-
-
-
- stepper_type m_stepper;
- error_checker_type m_error_checker;
- step_adjuster_type m_step_adjuster;
-
- resizer_type m_dxdt_resizer;
- resizer_type m_xerr_resizer;
- resizer_type m_xnew_resizer;
-
- wrapped_deriv_type m_dxdt;
- wrapped_state_type m_xerr;
- wrapped_state_type m_xnew;
-};
-
-
-
-
-
-
-
-
-
-
-/*
- * explicit stepper fsal version
- *
- * the class introduces the following try_step overloads
- * try_step( sys , x , t , dt )
- * try_step( sys , in , t , out , dt )
- * try_step( sys , x , dxdt , t , dt )
- * try_step( sys , in , dxdt_in , t , out , dxdt_out , dt )
- */
-/**
- * \brief Implements step size control for Runge-Kutta FSAL steppers with
- * error estimation.
- *
- * This class implements the step size control for FSAL Runge-Kutta
- * steppers with error estimation.
- *
- * \tparam ErrorStepper The stepper type with error estimation, has to fulfill the ErrorStepper concept.
- * \tparam ErrorChecker The error checker
- * \tparam Resizer The resizer policy type.
- */
-template<
-class ErrorStepper ,
-class ErrorChecker ,
-class StepAdjuster ,
-class Resizer
->
-class controlled_runge_kutta< ErrorStepper , ErrorChecker , StepAdjuster , Resizer , explicit_error_stepper_fsal_tag >
-{
-
-public:
-
- typedef ErrorStepper stepper_type;
- typedef typename stepper_type::state_type state_type;
- typedef typename stepper_type::value_type value_type;
- typedef typename stepper_type::deriv_type deriv_type;
- typedef typename stepper_type::time_type time_type;
- typedef typename stepper_type::algebra_type algebra_type;
- typedef typename stepper_type::operations_type operations_type;
- typedef Resizer resizer_type;
- typedef ErrorChecker error_checker_type;
- typedef StepAdjuster step_adjuster_type;
- typedef explicit_controlled_stepper_fsal_tag stepper_category;
-
-#ifndef DOXYGEN_SKIP
- typedef typename stepper_type::wrapped_state_type wrapped_state_type;
- typedef typename stepper_type::wrapped_deriv_type wrapped_deriv_type;
-
- typedef controlled_runge_kutta< ErrorStepper , ErrorChecker , StepAdjuster , Resizer , explicit_error_stepper_tag > controlled_stepper_type;
-#endif // DOXYGEN_SKIP
-
- /**
- * \brief Constructs the controlled Runge-Kutta stepper.
- * \param error_checker An instance of the error checker.
- * \param stepper An instance of the underlying stepper.
- */
- controlled_runge_kutta(
- const error_checker_type &error_checker = error_checker_type() ,
- const step_adjuster_type &step_adjuster = step_adjuster_type() ,
- const stepper_type &stepper = stepper_type()
- )
- : m_stepper( stepper ) , m_error_checker( error_checker ) , m_step_adjuster(step_adjuster) ,
- m_first_call( true )
- { }
-
- /*
- * Version 1 : try_step( sys , x , t , dt )
- *
- * The two overloads are needed in order to solve the forwarding problem
- */
- /**
- * \brief Tries to perform one step.
- *
- * This method tries to do one step with step size dt. If the error estimate
- * is to large, the step is rejected and the method returns fail and the
- * step size dt is reduced. If the error estimate is acceptably small, the
- * step is performed, success is returned and dt might be increased to make
- * the steps as large as possible. This method also updates t if a step is
- * performed.
- *
- * \param system The system function to solve, hence the r.h.s. of the ODE. It must fulfill the
- * Simple System concept.
- * \param x The state of the ODE which should be solved. Overwritten if
- * the step is successful.
- * \param t The value of the time. Updated if the step is successful.
- * \param dt The step size. Updated.
- * \return success if the step was accepted, fail otherwise.
- */
- template< class System , class StateInOut >
- controlled_step_result try_step( System system , StateInOut &x , time_type &t , time_type &dt )
- {
- return try_step_v1( system , x , t , dt );
- }
-
-
- /**
- * \brief Tries to perform one step. Solves the forwarding problem and
- * allows for using boost range as state_type.
- *
- * This method tries to do one step with step size dt. If the error estimate
- * is to large, the step is rejected and the method returns fail and the
- * step size dt is reduced. If the error estimate is acceptably small, the
- * step is performed, success is returned and dt might be increased to make
- * the steps as large as possible. This method also updates t if a step is
- * performed.
- *
- * \param system The system function to solve, hence the r.h.s. of the ODE. It must fulfill the
- * Simple System concept.
- * \param x The state of the ODE which should be solved. Overwritten if
- * the step is successful. Can be a boost range.
- * \param t The value of the time. Updated if the step is successful.
- * \param dt The step size. Updated.
- * \return success if the step was accepted, fail otherwise.
- */
- template< class System , class StateInOut >
- controlled_step_result try_step( System system , const StateInOut &x , time_type &t , time_type &dt )
- {
- return try_step_v1( system , x , t , dt );
- }
-
-
-
- /*
- * Version 2 : try_step( sys , in , t , out , dt );
- *
- * This version does not solve the forwarding problem, boost::range can not be used.
- *
- * The disabler is needed to solve ambiguous overloads
- */
- /**
- * \brief Tries to perform one step.
- *
- * \note This method is disabled if state_type=time_type to avoid ambiguity.
- *
- * This method tries to do one step with step size dt. If the error estimate
- * is to large, the step is rejected and the method returns fail and the
- * step size dt is reduced. If the error estimate is acceptably small, the
- * step is performed, success is returned and dt might be increased to make
- * the steps as large as possible. This method also updates t if a step is
- * performed.
- *
- * \param system The system function to solve, hence the r.h.s. of the ODE. It must fulfill the
- * Simple System concept.
- * \param in The state of the ODE which should be solved.
- * \param t The value of the time. Updated if the step is successful.
- * \param out Used to store the result of the step.
- * \param dt The step size. Updated.
- * \return success if the step was accepted, fail otherwise.
- */
- template< class System , class StateIn , class StateOut >
- typename boost::disable_if< boost::is_same< StateIn , time_type > , controlled_step_result >::type
- try_step( System system , const StateIn &in , time_type &t , StateOut &out , time_type &dt )
- {
- if( m_dxdt_resizer.adjust_size( in , detail::bind( &controlled_runge_kutta::template resize_m_dxdt_impl< StateIn > , detail::ref( *this ) , detail::_1 ) ) || m_first_call )
- {
- initialize( system , in , t );
- }
- return try_step( system , in , m_dxdt.m_v , t , out , dt );
- }
-
-
- /*
- * Version 3 : try_step( sys , x , dxdt , t , dt )
- *
- * This version does not solve the forwarding problem, boost::range can not be used.
- */
- /**
- * \brief Tries to perform one step.
- *
- * This method tries to do one step with step size dt. If the error estimate
- * is to large, the step is rejected and the method returns fail and the
- * step size dt is reduced. If the error estimate is acceptably small, the
- * step is performed, success is returned and dt might be increased to make
- * the steps as large as possible. This method also updates t if a step is
- * performed.
- *
- * \param system The system function to solve, hence the r.h.s. of the ODE. It must fulfill the
- * Simple System concept.
- * \param x The state of the ODE which should be solved. Overwritten if
- * the step is successful.
- * \param dxdt The derivative of state.
- * \param t The value of the time. Updated if the step is successful.
- * \param dt The step size. Updated.
- * \return success if the step was accepted, fail otherwise.
- */
- template< class System , class StateInOut , class DerivInOut >
- controlled_step_result try_step( System system , StateInOut &x , DerivInOut &dxdt , time_type &t , time_type &dt )
- {
- m_xnew_resizer.adjust_size( x , detail::bind( &controlled_runge_kutta::template resize_m_xnew_impl< StateInOut > , detail::ref( *this ) , detail::_1 ) );
- m_dxdt_new_resizer.adjust_size( x , detail::bind( &controlled_runge_kutta::template resize_m_dxdt_new_impl< StateInOut > , detail::ref( *this ) , detail::_1 ) );
- controlled_step_result res = try_step( system , x , dxdt , t , m_xnew.m_v , m_dxdtnew.m_v , dt );
- if( res == success )
- {
- boost::numeric::odeint::copy( m_xnew.m_v , x );
- boost::numeric::odeint::copy( m_dxdtnew.m_v , dxdt );
- }
- return res;
- }
-
-
- /*
- * Version 4 : try_step( sys , in , dxdt_in , t , out , dxdt_out , dt )
- *
- * This version does not solve the forwarding problem, boost::range can not be used.
- */
- /**
- * \brief Tries to perform one step.
- *
- * This method tries to do one step with step size dt. If the error estimate
- * is to large, the step is rejected and the method returns fail and the
- * step size dt is reduced. If the error estimate is acceptably small, the
- * step is performed, success is returned and dt might be increased to make
- * the steps as large as possible. This method also updates t if a step is
- * performed.
- *
- * \param system The system function to solve, hence the r.h.s. of the ODE. It must fulfill the
- * Simple System concept.
- * \param in The state of the ODE which should be solved.
- * \param dxdt The derivative of state.
- * \param t The value of the time. Updated if the step is successful.
- * \param out Used to store the result of the step.
- * \param dt The step size. Updated.
- * \return success if the step was accepted, fail otherwise.
- */
- template< class System , class StateIn , class DerivIn , class StateOut , class DerivOut >
- controlled_step_result try_step( System system , const StateIn &in , const DerivIn &dxdt_in , time_type &t ,
- StateOut &out , DerivOut &dxdt_out , time_type &dt )
- {
- if( !m_step_adjuster.check_step_size_limit(dt) )
- {
- // given dt was above step size limit - adjust and return fail;
- dt = m_step_adjuster.get_max_dt();
- return fail;
- }
-
- m_xerr_resizer.adjust_size( in , detail::bind( &controlled_runge_kutta::template resize_m_xerr_impl< StateIn > , detail::ref( *this ) , detail::_1 ) );
-
- //fsal: m_stepper.get_dxdt( dxdt );
- //fsal: m_stepper.do_step( sys , x , dxdt , t , dt , m_x_err );
- m_stepper.do_step( system , in , dxdt_in , t , out , dxdt_out , dt , m_xerr.m_v );
-
- // this potentially overwrites m_x_err! (standard_error_checker does, at least)
- value_type max_rel_err = m_error_checker.error( m_stepper.algebra() , in , dxdt_in , m_xerr.m_v , dt );
-
- if( max_rel_err > 1.0 )
- {
- // error too big, decrease step size and reject this step
- dt = m_step_adjuster.decrease_step(dt, max_rel_err, m_stepper.error_order());
- return fail;
- }
- // otherwise, increase step size and accept
- t += dt;
- dt = m_step_adjuster.increase_step(dt, max_rel_err, m_stepper.stepper_order());
- return success;
- }
-
-
- /**
- * \brief Resets the internal state of the underlying FSAL stepper.
- */
- void reset( void )
- {
- m_first_call = true;
- }
-
- /**
- * \brief Initializes the internal state storing an internal copy of the derivative.
- *
- * \param deriv The initial derivative of the ODE.
- */
- template< class DerivIn >
- void initialize( const DerivIn &deriv )
- {
- boost::numeric::odeint::copy( deriv , m_dxdt.m_v );
- m_first_call = false;
- }
-
- /**
- * \brief Initializes the internal state storing an internal copy of the derivative.
- *
- * \param system The system function to solve, hence the r.h.s. of the ODE. It must fulfill the
- * Simple System concept.
- * \param x The initial state of the ODE which should be solved.
- * \param t The initial time.
- */
- template< class System , class StateIn >
- void initialize( System system , const StateIn &x , time_type t )
- {
- typename odeint::unwrap_reference< System >::type &sys = system;
- sys( x , m_dxdt.m_v , t );
- m_first_call = false;
- }
-
- /**
- * \brief Returns true if the stepper has been initialized, false otherwise.
- *
- * \return true, if the stepper has been initialized, false otherwise.
- */
- bool is_initialized( void ) const
- {
- return ! m_first_call;
- }
-
-
- /**
- * \brief Adjust the size of all temporaries in the stepper manually.
- * \param x A state from which the size of the temporaries to be resized is deduced.
- */
- template< class StateType >
- void adjust_size( const StateType &x )
- {
- resize_m_xerr_impl( x );
- resize_m_dxdt_impl( x );
- resize_m_dxdt_new_impl( x );
- resize_m_xnew_impl( x );
- }
-
-
- /**
- * \brief Returns the instance of the underlying stepper.
- * \returns The instance of the underlying stepper.
- */
- stepper_type& stepper( void )
- {
- return m_stepper;
- }
-
- /**
- * \brief Returns the instance of the underlying stepper.
- * \returns The instance of the underlying stepper.
- */
- const stepper_type& stepper( void ) const
- {
- return m_stepper;
- }
-
-
-
-private:
-
-
- template< class StateIn >
- bool resize_m_xerr_impl( const StateIn &x )
- {
- return adjust_size_by_resizeability( m_xerr , x , typename is_resizeable<state_type>::type() );
- }
-
- template< class StateIn >
- bool resize_m_dxdt_impl( const StateIn &x )
- {
- return adjust_size_by_resizeability( m_dxdt , x , typename is_resizeable<deriv_type>::type() );
- }
-
- template< class StateIn >
- bool resize_m_dxdt_new_impl( const StateIn &x )
- {
- return adjust_size_by_resizeability( m_dxdtnew , x , typename is_resizeable<deriv_type>::type() );
- }
-
- template< class StateIn >
- bool resize_m_xnew_impl( const StateIn &x )
- {
- return adjust_size_by_resizeability( m_xnew , x , typename is_resizeable<state_type>::type() );
- }
-
-
- template< class System , class StateInOut >
- controlled_step_result try_step_v1( System system , StateInOut &x , time_type &t , time_type &dt )
- {
- if( m_dxdt_resizer.adjust_size( x , detail::bind( &controlled_runge_kutta::template resize_m_dxdt_impl< StateInOut > , detail::ref( *this ) , detail::_1 ) ) || m_first_call )
- {
- initialize( system , x , t );
- }
- return try_step( system , x , m_dxdt.m_v , t , dt );
- }
-
-
- stepper_type m_stepper;
- error_checker_type m_error_checker;
- step_adjuster_type m_step_adjuster;
-
- resizer_type m_dxdt_resizer;
- resizer_type m_xerr_resizer;
- resizer_type m_xnew_resizer;
- resizer_type m_dxdt_new_resizer;
-
- wrapped_deriv_type m_dxdt;
- wrapped_state_type m_xerr;
- wrapped_state_type m_xnew;
- wrapped_deriv_type m_dxdtnew;
- bool m_first_call;
-};
-
-
-/********** DOXYGEN **********/
-
-/**** DEFAULT ERROR CHECKER ****/
-
-/**
- * \class default_error_checker
- * \brief The default error checker to be used with Runge-Kutta error steppers
- *
- * This class provides the default mechanism to compare the error estimates
- * reported by Runge-Kutta error steppers with user defined error bounds.
- * It is used by the controlled_runge_kutta steppers.
- *
- * \tparam Value The value type.
- * \tparam Time The time type.
- * \tparam Algebra The algebra type.
- * \tparam Operations The operations type.
- */
-
- /**
- * \fn default_error_checker( value_type eps_abs , value_type eps_rel , value_type a_x , value_type a_dxdt ,
- * time_type max_dt)
- * \brief Constructs the error checker.
- *
- * The error is calculated as follows: ????
- *
- * \param eps_abs Absolute tolerance level.
- * \param eps_rel Relative tolerance level.
- * \param a_x Factor for the weight of the state.
- * \param a_dxdt Factor for the weight of the derivative.
- * \param max_dt Maximum allowed step size.
- */
-
- /**
- * \fn error( const State &x_old , const Deriv &dxdt_old , Err &x_err , time_type dt ) const
- * \brief Calculates the error level.
- *
- * If the returned error level is greater than 1, the estimated error was
- * larger than the permitted error bounds and the step should be repeated
- * with a smaller step size.
- *
- * \param x_old State at the beginning of the step.
- * \param dxdt_old Derivative at the beginning of the step.
- * \param x_err Error estimate.
- * \param dt Time step.
- * \return error
- */
-
- /**
- * \fn error( algebra_type &algebra , const State &x_old , const Deriv &dxdt_old , Err &x_err , time_type dt ) const
- * \brief Calculates the error level using a given algebra.
- *
- * If the returned error level is greater than 1, the estimated error was
- * larger than the permitted error bounds and the step should be repeated
- * with a smaller step size.
- *
- * \param algebra The algebra used for calculation of the error.
- * \param x_old State at the beginning of the step.
- * \param dxdt_old Derivative at the beginning of the step.
- * \param x_err Error estimate.
- * \param dt Time step.
- * \return error
- */
-
- /**
- * \fn time_type decrease_step(const time_type dt, const value_type error, const int error_order)
- * \brief Returns a decreased step size based on the given error and order
- *
- * Calculates a new smaller step size based on the given error and its order.
- *
- * \param dt The old step size.
- * \param error The computed error estimate.
- * \param error_order The error order of the stepper.
- * \return dt_new The new, reduced step size.
- */
-
- /**
- * \fn time_type increase_step(const time_type dt, const value_type error, const int error_order)
- * \brief Returns an increased step size based on the given error and order.
- *
- * Calculates a new bigger step size based on the given error and its order. If max_dt != 0, the
- * new step size is limited to max_dt.
- *
- * \param dt The old step size.
- * \param error The computed error estimate.
- * \param error_order The order of the stepper.
- * \return dt_new The new, increased step size.
- */
-
-
-} // odeint
-} // numeric
-} // boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_CONTROLLED_RUNGE_KUTTA_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/controlled_step_result.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/controlled_step_result.hpp
deleted file mode 100644
index 7f17726c570ee2f53da8e17476f3f227a24b0b7d..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/controlled_step_result.hpp
+++ /dev/null
@@ -1,42 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/controlled_step_result.hpp
-
- [begin_description]
- Defines the result type for all controlled stepper.
- [end_description]
-
- Copyright 2011-2013 Karsten Ahnert
- Copyright 2012 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_CONTROLLED_STEP_RESULT_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_CONTROLLED_STEP_RESULT_HPP_INCLUDED
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-/**
- * \enum controlled_step_result
- *
- * \brief Enum representing the return values of the controlled steppers.
- */
-typedef enum
-{
- success , /**< The trial step was successful, hence the state and the time have been advanced. */
- fail /**< The step was not successful and might possibly be repeated with a small step size. */
-} controlled_step_result;
-
-} // namespace odeint
-} // numeric
-} // boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_CONTROLLED_STEP_RESULT_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/dense_output_runge_kutta.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/dense_output_runge_kutta.hpp
deleted file mode 100644
index 0b69f70370f71fad37e405593e81cdd0bdc80d46..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/dense_output_runge_kutta.hpp
+++ /dev/null
@@ -1,476 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/dense_output_runge_kutta.hpp
-
- [begin_description]
- Implementation of the Dense-output stepper for all steppers. Note, that this class does
- not computes the result but serves as an interface.
- [end_description]
-
- Copyright 2011-2013 Karsten Ahnert
- Copyright 2011-2015 Mario Mulansky
- Copyright 2012 Christoph Koke
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_DENSE_OUTPUT_RUNGE_KUTTA_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_DENSE_OUTPUT_RUNGE_KUTTA_HPP_INCLUDED
-
-
-#include <utility>
-#include <stdexcept>
-
-#include <boost/throw_exception.hpp>
-
-#include <boost/numeric/odeint/util/bind.hpp>
-
-#include <boost/numeric/odeint/util/copy.hpp>
-
-#include <boost/numeric/odeint/util/state_wrapper.hpp>
-#include <boost/numeric/odeint/util/is_resizeable.hpp>
-#include <boost/numeric/odeint/util/resizer.hpp>
-
-#include <boost/numeric/odeint/stepper/controlled_step_result.hpp>
-#include <boost/numeric/odeint/stepper/stepper_categories.hpp>
-
-#include <boost/numeric/odeint/integrate/max_step_checker.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-template< class Stepper , class StepperCategory = typename Stepper::stepper_category >
-class dense_output_runge_kutta;
-
-
-/**
- * \brief The class representing dense-output Runge-Kutta steppers.
- * \note In this stepper, the initialize method has to be called before using
- * the do_step method.
- *
- * The dense-output functionality allows to interpolate the solution between
- * subsequent integration points using intermediate results obtained during the
- * computation. This version works based on a normal stepper without step-size
- * control.
- *
- *
- * \tparam Stepper The stepper type of the underlying algorithm.
- */
-template< class Stepper >
-class dense_output_runge_kutta< Stepper , stepper_tag >
-{
-
-public:
-
- /*
- * We do not need all typedefs.
- */
- typedef Stepper stepper_type;
- typedef typename stepper_type::state_type state_type;
- typedef typename stepper_type::wrapped_state_type wrapped_state_type;
- typedef typename stepper_type::value_type value_type;
- typedef typename stepper_type::deriv_type deriv_type;
- typedef typename stepper_type::wrapped_deriv_type wrapped_deriv_type;
- typedef typename stepper_type::time_type time_type;
- typedef typename stepper_type::algebra_type algebra_type;
- typedef typename stepper_type::operations_type operations_type;
- typedef typename stepper_type::resizer_type resizer_type;
- typedef dense_output_stepper_tag stepper_category;
- typedef dense_output_runge_kutta< Stepper > dense_output_stepper_type;
-
-
- /**
- * \brief Constructs the dense_output_runge_kutta class. An instance of the
- * underlying stepper can be provided.
- * \param stepper An instance of the underlying stepper.
- */
- dense_output_runge_kutta( const stepper_type &stepper = stepper_type() )
- : m_stepper( stepper ) , m_resizer() ,
- m_x1() , m_x2() , m_current_state_x1( true ) ,
- m_t() , m_t_old() , m_dt()
- { }
-
-
- /**
- * \brief Initializes the stepper. Has to be called before do_step can be
- * used to set the initial conditions and the step size.
- * \param x0 The initial state of the ODE which should be solved.
- * \param t0 The initial time, at which the step should be performed.
- * \param dt0 The step size.
- */
- template< class StateType >
- void initialize( const StateType &x0 , time_type t0 , time_type dt0 )
- {
- m_resizer.adjust_size( x0 , detail::bind( &dense_output_stepper_type::template resize_impl< StateType > , detail::ref( *this ) , detail::_1 ) );
- boost::numeric::odeint::copy( x0 , get_current_state() );
- m_t = t0;
- m_dt = dt0;
- }
-
- /**
- * \brief Does one time step.
- * \note initialize has to be called before using this method to set the
- * initial conditions x,t and the stepsize.
- * \param system The system function to solve, hence the r.h.s. of the ordinary differential equation. It must fulfill the
- * Simple System concept.
- * \return Pair with start and end time of the integration step.
- */
- template< class System >
- std::pair< time_type , time_type > do_step( System system )
- {
- m_stepper.do_step( system , get_current_state() , m_t , get_old_state() , m_dt );
- m_t_old = m_t;
- m_t += m_dt;
- toggle_current_state();
- return std::make_pair( m_t_old , m_dt );
- }
-
- /*
- * The next two overloads are needed to solve the forwarding problem
- */
-
- /**
- * \brief Calculates the solution at an intermediate point.
- * \param t The time at which the solution should be calculated, has to be
- * in the current time interval.
- * \param x The output variable where the result is written into.
- */
- template< class StateOut >
- void calc_state( time_type t , StateOut &x ) const
- {
- if( t == current_time() )
- {
- boost::numeric::odeint::copy( get_current_state() , x );
- }
- m_stepper.calc_state( x , t , get_old_state() , m_t_old , get_current_state() , m_t );
- }
-
- /**
- * \brief Calculates the solution at an intermediate point. Solves the forwarding problem
- * \param t The time at which the solution should be calculated, has to be
- * in the current time interval.
- * \param x The output variable where the result is written into, can be a boost range.
- */
- template< class StateOut >
- void calc_state( time_type t , const StateOut &x ) const
- {
- m_stepper.calc_state( x , t , get_old_state() , m_t_old , get_current_state() , m_t );
- }
-
- /**
- * \brief Adjust the size of all temporaries in the stepper manually.
- * \param x A state from which the size of the temporaries to be resized is deduced.
- */
- template< class StateType >
- void adjust_size( const StateType &x )
- {
- resize_impl( x );
- m_stepper.stepper().resize( x );
- }
-
- /**
- * \brief Returns the current state of the solution.
- * \return The current state of the solution x(t).
- */
- const state_type& current_state( void ) const
- {
- return get_current_state();
- }
-
- /**
- * \brief Returns the current time of the solution.
- * \return The current time of the solution t.
- */
- time_type current_time( void ) const
- {
- return m_t;
- }
-
- /**
- * \brief Returns the last state of the solution.
- * \return The last state of the solution x(t-dt).
- */
- const state_type& previous_state( void ) const
- {
- return get_old_state();
- }
-
- /**
- * \brief Returns the last time of the solution.
- * \return The last time of the solution t-dt.
- */
- time_type previous_time( void ) const
- {
- return m_t_old;
- }
-
- /**
- * \brief Returns the current time step.
- * \return dt.
- */
- time_type current_time_step( void ) const
- {
- return m_dt;
- }
-
-
-private:
-
- state_type& get_current_state( void )
- {
- return m_current_state_x1 ? m_x1.m_v : m_x2.m_v ;
- }
-
- const state_type& get_current_state( void ) const
- {
- return m_current_state_x1 ? m_x1.m_v : m_x2.m_v ;
- }
-
- state_type& get_old_state( void )
- {
- return m_current_state_x1 ? m_x2.m_v : m_x1.m_v ;
- }
-
- const state_type& get_old_state( void ) const
- {
- return m_current_state_x1 ? m_x2.m_v : m_x1.m_v ;
- }
-
- void toggle_current_state( void )
- {
- m_current_state_x1 = ! m_current_state_x1;
- }
-
-
- template< class StateIn >
- bool resize_impl( const StateIn &x )
- {
- bool resized = false;
- resized |= adjust_size_by_resizeability( m_x1 , x , typename is_resizeable<state_type>::type() );
- resized |= adjust_size_by_resizeability( m_x2 , x , typename is_resizeable<state_type>::type() );
- return resized;
- }
-
-
- stepper_type m_stepper;
- resizer_type m_resizer;
- wrapped_state_type m_x1 , m_x2;
- bool m_current_state_x1; // if true, the current state is m_x1
- time_type m_t , m_t_old , m_dt;
-
-};
-
-
-
-
-
-/**
- * \brief The class representing dense-output Runge-Kutta steppers with FSAL property.
- *
- * The interface is the same as for dense_output_runge_kutta< Stepper , stepper_tag >.
- * This class provides dense output functionality based on methods with step size controlled
- *
- *
- * \tparam Stepper The stepper type of the underlying algorithm.
- */
-template< class Stepper >
-class dense_output_runge_kutta< Stepper , explicit_controlled_stepper_fsal_tag >
-{
-public:
-
- /*
- * We do not need all typedefs.
- */
- typedef Stepper controlled_stepper_type;
-
- typedef typename controlled_stepper_type::stepper_type stepper_type;
- typedef typename stepper_type::state_type state_type;
- typedef typename stepper_type::wrapped_state_type wrapped_state_type;
- typedef typename stepper_type::value_type value_type;
- typedef typename stepper_type::deriv_type deriv_type;
- typedef typename stepper_type::wrapped_deriv_type wrapped_deriv_type;
- typedef typename stepper_type::time_type time_type;
- typedef typename stepper_type::algebra_type algebra_type;
- typedef typename stepper_type::operations_type operations_type;
- typedef typename stepper_type::resizer_type resizer_type;
- typedef dense_output_stepper_tag stepper_category;
- typedef dense_output_runge_kutta< Stepper > dense_output_stepper_type;
-
-
- dense_output_runge_kutta( const controlled_stepper_type &stepper = controlled_stepper_type() )
- : m_stepper( stepper ) , m_resizer() ,
- m_current_state_x1( true ) ,
- m_x1() , m_x2() , m_dxdt1() , m_dxdt2() ,
- m_t() , m_t_old() , m_dt() ,
- m_is_deriv_initialized( false )
- { }
-
-
- template< class StateType >
- void initialize( const StateType &x0 , time_type t0 , time_type dt0 )
- {
- m_resizer.adjust_size( x0 , detail::bind( &dense_output_stepper_type::template resize< StateType > , detail::ref( *this ) , detail::_1 ) );
- boost::numeric::odeint::copy( x0 , get_current_state() );
- m_t = t0;
- m_dt = dt0;
- m_is_deriv_initialized = false;
- }
-
- template< class System >
- std::pair< time_type , time_type > do_step( System system )
- {
- if( !m_is_deriv_initialized )
- {
- typename odeint::unwrap_reference< System >::type &sys = system;
- sys( get_current_state() , get_current_deriv() , m_t );
- m_is_deriv_initialized = true;
- }
-
- failed_step_checker fail_checker; // to throw a runtime_error if step size adjustment fails
- controlled_step_result res = fail;
- m_t_old = m_t;
- do
- {
- res = m_stepper.try_step( system , get_current_state() , get_current_deriv() , m_t ,
- get_old_state() , get_old_deriv() , m_dt );
- fail_checker(); // check for overflow of failed steps
- }
- while( res == fail );
- toggle_current_state();
- return std::make_pair( m_t_old , m_t );
- }
-
-
- /*
- * The two overloads are needed in order to solve the forwarding problem.
- */
- template< class StateOut >
- void calc_state( time_type t , StateOut &x ) const
- {
- m_stepper.stepper().calc_state( t , x , get_old_state() , get_old_deriv() , m_t_old ,
- get_current_state() , get_current_deriv() , m_t );
- }
-
- template< class StateOut >
- void calc_state( time_type t , const StateOut &x ) const
- {
- m_stepper.stepper().calc_state( t , x , get_old_state() , get_old_deriv() , m_t_old ,
- get_current_state() , get_current_deriv() , m_t );
- }
-
-
- template< class StateIn >
- bool resize( const StateIn &x )
- {
- bool resized = false;
- resized |= adjust_size_by_resizeability( m_x1 , x , typename is_resizeable<state_type>::type() );
- resized |= adjust_size_by_resizeability( m_x2 , x , typename is_resizeable<state_type>::type() );
- resized |= adjust_size_by_resizeability( m_dxdt1 , x , typename is_resizeable<deriv_type>::type() );
- resized |= adjust_size_by_resizeability( m_dxdt2 , x , typename is_resizeable<deriv_type>::type() );
- return resized;
- }
-
-
- template< class StateType >
- void adjust_size( const StateType &x )
- {
- resize( x );
- m_stepper.stepper().resize( x );
- }
-
- const state_type& current_state( void ) const
- {
- return get_current_state();
- }
-
- time_type current_time( void ) const
- {
- return m_t;
- }
-
- const state_type& previous_state( void ) const
- {
- return get_old_state();
- }
-
- time_type previous_time( void ) const
- {
- return m_t_old;
- }
-
- time_type current_time_step( void ) const
- {
- return m_dt;
- }
-
-
-private:
-
- state_type& get_current_state( void )
- {
- return m_current_state_x1 ? m_x1.m_v : m_x2.m_v ;
- }
-
- const state_type& get_current_state( void ) const
- {
- return m_current_state_x1 ? m_x1.m_v : m_x2.m_v ;
- }
-
- state_type& get_old_state( void )
- {
- return m_current_state_x1 ? m_x2.m_v : m_x1.m_v ;
- }
-
- const state_type& get_old_state( void ) const
- {
- return m_current_state_x1 ? m_x2.m_v : m_x1.m_v ;
- }
-
- deriv_type& get_current_deriv( void )
- {
- return m_current_state_x1 ? m_dxdt1.m_v : m_dxdt2.m_v ;
- }
-
- const deriv_type& get_current_deriv( void ) const
- {
- return m_current_state_x1 ? m_dxdt1.m_v : m_dxdt2.m_v ;
- }
-
- deriv_type& get_old_deriv( void )
- {
- return m_current_state_x1 ? m_dxdt2.m_v : m_dxdt1.m_v ;
- }
-
- const deriv_type& get_old_deriv( void ) const
- {
- return m_current_state_x1 ? m_dxdt2.m_v : m_dxdt1.m_v ;
- }
-
-
- void toggle_current_state( void )
- {
- m_current_state_x1 = ! m_current_state_x1;
- }
-
-
- controlled_stepper_type m_stepper;
- resizer_type m_resizer;
- bool m_current_state_x1;
- wrapped_state_type m_x1 , m_x2;
- wrapped_deriv_type m_dxdt1 , m_dxdt2;
- time_type m_t , m_t_old , m_dt;
- bool m_is_deriv_initialized;
-
-};
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_DENSE_OUTPUT_RUNGE_KUTTA_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/detail/adams_bashforth_call_algebra.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/detail/adams_bashforth_call_algebra.hpp
deleted file mode 100644
index cc279abbe0eb574e1a67a7ac608169e287cb84e5..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/detail/adams_bashforth_call_algebra.hpp
+++ /dev/null
@@ -1,151 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/detail/adams_bashforth_call_algebra.hpp
-
- [begin_description]
- Algebra caller for the Adams Bashforth stepper.
- [end_description]
-
- Copyright 2011-2012 Karsten Ahnert
- Copyright 2011 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_DETAIL_ADAMS_BASHFORTH_CALL_ALGEBRA_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_DETAIL_ADAMS_BASHFORTH_CALL_ALGEBRA_HPP_INCLUDED
-
-#include <boost/assert.hpp>
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-namespace detail {
-
-template< size_t Step , class Algebra , class Operations >
-struct adams_bashforth_call_algebra;
-
-template< class Algebra , class Operations >
-struct adams_bashforth_call_algebra< 1 , Algebra , Operations >
-{
- template< class StateIn , class StateOut , class StepStorage , class Coefficients , class Time >
- void operator()( Algebra &algebra , const StateIn &in , StateOut &out , const StepStorage &steps , const Coefficients &coef , Time dt ) const
- {
- typedef typename Coefficients::value_type value_type;
- algebra.for_each3( out , in , steps[0].m_v , typename Operations::template scale_sum2< value_type , Time >( 1.0 , dt * coef[0] ) );
- }
-};
-
-
-template< class Algebra , class Operations >
-struct adams_bashforth_call_algebra< 2 , Algebra , Operations >
-{
- template< class StateIn , class StateOut , class StepStorage , class Coefficients , class Time >
- void operator()( Algebra &algebra , const StateIn &in , StateOut &out , const StepStorage &steps , const Coefficients &coef , Time dt ) const
- {
- typedef typename Coefficients::value_type value_type;
- algebra.for_each4( out , in , steps[0].m_v , steps[1].m_v ,
- typename Operations::template scale_sum3< value_type , Time , Time >( 1.0 , dt * coef[0] , dt * coef[1] ) );
- }
-};
-
-
-template< class Algebra , class Operations >
-struct adams_bashforth_call_algebra< 3 , Algebra , Operations >
-{
- template< class StateIn , class StateOut , class StepStorage , class Coefficients , class Time >
- void operator()( Algebra &algebra , const StateIn &in , StateOut &out , const StepStorage &steps , const Coefficients &coef , Time dt ) const
- {
- typedef typename Coefficients::value_type value_type;
- algebra.for_each5( out , in , steps[0].m_v , steps[1].m_v , steps[2].m_v ,
- typename Operations::template scale_sum4< value_type , Time , Time , Time >( 1.0 , dt * coef[0] , dt * coef[1] , dt * coef[2] ) );
- }
-};
-
-
-template< class Algebra , class Operations >
-struct adams_bashforth_call_algebra< 4 , Algebra , Operations >
-{
- template< class StateIn , class StateOut , class StepStorage , class Coefficients , class Time >
- void operator()( Algebra &algebra , const StateIn &in , StateOut &out , const StepStorage &steps , const Coefficients &coef , Time dt ) const
- {
- typedef typename Coefficients::value_type value_type;
- algebra.for_each6( out , in , steps[0].m_v , steps[1].m_v , steps[2].m_v , steps[3].m_v ,
- typename Operations::template scale_sum5< value_type , Time , Time , Time >(
- 1.0 , dt * coef[0] , dt * coef[1] , dt * coef[2] , dt * coef[3] ) );
- }
-};
-
-
-template< class Algebra , class Operations >
-struct adams_bashforth_call_algebra< 5 , Algebra , Operations >
-{
- template< class StateIn , class StateOut , class StepStorage , class Coefficients , class Time >
- void operator()( Algebra &algebra , const StateIn &in , StateOut &out , const StepStorage &steps , const Coefficients &coef , Time dt ) const
- {
- typedef typename Coefficients::value_type value_type;
- algebra.for_each7( out , in , steps[0].m_v , steps[1].m_v , steps[2].m_v , steps[3].m_v , steps[4].m_v ,
- typename Operations::template scale_sum6< value_type , Time , Time , Time , Time >(
- 1.0 , dt * coef[0] , dt * coef[1] , dt * coef[2] , dt * coef[3] , dt * coef[4] ) );
- }
-};
-
-
-template< class Algebra , class Operations >
-struct adams_bashforth_call_algebra< 6 , Algebra , Operations >
-{
- template< class StateIn , class StateOut , class StepStorage , class Coefficients , class Time >
- void operator()( Algebra &algebra , const StateIn &in , StateOut &out , const StepStorage &steps , const Coefficients &coef , Time dt ) const
- {
- typedef typename Coefficients::value_type value_type;
- algebra.for_each8( out , in , steps[0].m_v , steps[1].m_v , steps[2].m_v , steps[3].m_v , steps[4].m_v , steps[5].m_v ,
- typename Operations::template scale_sum7< value_type , Time , Time , Time , Time , Time >(
- 1.0 , dt * coef[0] , dt * coef[1] , dt * coef[2] , dt * coef[3] , dt * coef[4] , dt * coef[5] ) );
- }
-};
-
-
-template< class Algebra , class Operations >
-struct adams_bashforth_call_algebra< 7 , Algebra , Operations >
-{
- template< class StateIn , class StateOut , class StepStorage , class Coefficients , class Time >
- void operator()( Algebra &algebra , const StateIn &in , StateOut &out , const StepStorage &steps , const Coefficients &coef , Time dt ) const
- {
- //BOOST_ASSERT( false ); // not implemented
- typedef typename Coefficients::value_type value_type;
- algebra.for_each9( out , in , steps[0].m_v , steps[1].m_v , steps[2].m_v , steps[3].m_v , steps[4].m_v , steps[5].m_v , steps[6].m_v ,
- typename Operations::template scale_sum8< value_type , Time , Time , Time , Time , Time , Time >(
- 1.0 , dt * coef[0] , dt * coef[1] , dt * coef[2] , dt * coef[3] , dt * coef[4] , dt * coef[5] , dt * coef[6] ) );
- }
-};
-
-
-template< class Algebra , class Operations >
-struct adams_bashforth_call_algebra< 8 , Algebra , Operations >
-{
- template< class StateIn , class StateOut , class StepStorage , class Coefficients , class Time >
- void operator()( Algebra &algebra , const StateIn &in , StateOut &out , const StepStorage &steps , const Coefficients &coef , Time dt ) const
- {
- //BOOST_ASSERT( false ); // not implemented
- typedef typename Coefficients::value_type value_type;
- algebra.for_each10( out , in , steps[0].m_v , steps[1].m_v , steps[2].m_v , steps[3].m_v , steps[4].m_v , steps[5].m_v , steps[6].m_v , steps[7].m_v ,
- typename Operations::template scale_sum9< value_type , Time , Time , Time , Time , Time , Time , Time >(
- 1.0 , dt * coef[0] , dt * coef[1] , dt * coef[2] , dt * coef[3] , dt * coef[4] , dt * coef[5] , dt * coef[6] , dt * coef[7] ) );
- }
-};
-
-
-
-
-} // detail
-} // odeint
-} // numeric
-} // boost
-
-
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_DETAIL_ADAMS_BASHFORTH_CALL_ALGEBRA_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/detail/adams_bashforth_coefficients.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/detail/adams_bashforth_coefficients.hpp
deleted file mode 100644
index 26a9f9a6b46980803d72e683896569c08b62b53c..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/detail/adams_bashforth_coefficients.hpp
+++ /dev/null
@@ -1,168 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/detail/adams_bashforth_coefficients.hpp
-
- [begin_description]
- Definition of the coefficients for the Adams-Bashforth method.
- [end_description]
-
- Copyright 2011-2012 Karsten Ahnert
- Copyright 2011-2012 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_DETAIL_ADAMS_BASHFORTH_COEFFICIENTS_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_DETAIL_ADAMS_BASHFORTH_COEFFICIENTS_HPP_INCLUDED
-
-#include <boost/array.hpp>
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-namespace detail {
-
-template< class Value , size_t Steps >
-class adams_bashforth_coefficients ;
-
-template< class Value >
-class adams_bashforth_coefficients< Value , 1 > : public boost::array< Value , 1 >
-{
-public:
- adams_bashforth_coefficients( void )
- : boost::array< Value , 1 >()
- {
- (*this)[0] = static_cast< Value >( 1 );
- }
-};
-
-
-template< class Value >
-class adams_bashforth_coefficients< Value , 2 > : public boost::array< Value , 2 >
-{
-public:
- adams_bashforth_coefficients( void )
- : boost::array< Value , 2 >()
- {
- (*this)[0] = static_cast< Value >( 3 ) / static_cast< Value >( 2 );
- (*this)[1] = -static_cast< Value >( 1 ) / static_cast< Value >( 2 );
- }
-};
-
-
-template< class Value >
-class adams_bashforth_coefficients< Value , 3 > : public boost::array< Value , 3 >
-{
-public:
- adams_bashforth_coefficients( void )
- : boost::array< Value , 3 >()
- {
- (*this)[0] = static_cast< Value >( 23 ) / static_cast< Value >( 12 );
- (*this)[1] = -static_cast< Value >( 4 ) / static_cast< Value >( 3 );
- (*this)[2] = static_cast< Value >( 5 ) / static_cast< Value >( 12 );
- }
-};
-
-
-template< class Value >
-class adams_bashforth_coefficients< Value , 4 > : public boost::array< Value , 4 >
-{
-public:
- adams_bashforth_coefficients( void )
- : boost::array< Value , 4 >()
- {
- (*this)[0] = static_cast< Value >( 55 ) / static_cast< Value >( 24 );
- (*this)[1] = -static_cast< Value >( 59 ) / static_cast< Value >( 24 );
- (*this)[2] = static_cast< Value >( 37 ) / static_cast< Value >( 24 );
- (*this)[3] = -static_cast< Value >( 3 ) / static_cast< Value >( 8 );
- }
-};
-
-
-template< class Value >
-class adams_bashforth_coefficients< Value , 5 > : public boost::array< Value , 5 >
-{
-public:
- adams_bashforth_coefficients( void )
- : boost::array< Value , 5 >()
- {
- (*this)[0] = static_cast< Value >( 1901 ) / static_cast< Value >( 720 );
- (*this)[1] = -static_cast< Value >( 1387 ) / static_cast< Value >( 360 );
- (*this)[2] = static_cast< Value >( 109 ) / static_cast< Value >( 30 );
- (*this)[3] = -static_cast< Value >( 637 ) / static_cast< Value >( 360 );
- (*this)[4] = static_cast< Value >( 251 ) / static_cast< Value >( 720 );
- }
-};
-
-
-template< class Value >
-class adams_bashforth_coefficients< Value , 6 > : public boost::array< Value , 6 >
-{
-public:
- adams_bashforth_coefficients( void )
- : boost::array< Value , 6 >()
- {
- (*this)[0] = static_cast< Value >( 4277 ) / static_cast< Value >( 1440 );
- (*this)[1] = -static_cast< Value >( 2641 ) / static_cast< Value >( 480 );
- (*this)[2] = static_cast< Value >( 4991 ) / static_cast< Value >( 720 );
- (*this)[3] = -static_cast< Value >( 3649 ) / static_cast< Value >( 720 );
- (*this)[4] = static_cast< Value >( 959 ) / static_cast< Value >( 480 );
- (*this)[5] = -static_cast< Value >( 95 ) / static_cast< Value >( 288 );
- }
-};
-
-
-template< class Value >
-class adams_bashforth_coefficients< Value , 7 > : public boost::array< Value , 7 >
-{
-public:
- adams_bashforth_coefficients( void )
- : boost::array< Value , 7 >()
- {
- (*this)[0] = static_cast< Value >( 198721 ) / static_cast< Value >( 60480 );
- (*this)[1] = -static_cast< Value >( 18637 ) / static_cast< Value >( 2520 );
- (*this)[2] = static_cast< Value >( 235183 ) / static_cast< Value >( 20160 );
- (*this)[3] = -static_cast< Value >( 10754 ) / static_cast< Value >( 945 );
- (*this)[4] = static_cast< Value >( 135713 ) / static_cast< Value >( 20160 );
- (*this)[5] = -static_cast< Value >( 5603 ) / static_cast< Value >( 2520 );
- (*this)[6] = static_cast< Value >( 19087 ) / static_cast< Value >( 60480 );
- }
-};
-
-
-template< class Value >
-class adams_bashforth_coefficients< Value , 8 > : public boost::array< Value , 8 >
-{
-public:
- adams_bashforth_coefficients( void )
- : boost::array< Value , 8 >()
- {
- (*this)[0] = static_cast< Value >( 16083 ) / static_cast< Value >( 4480 );
- (*this)[1] = -static_cast< Value >( 1152169 ) / static_cast< Value >( 120960 );
- (*this)[2] = static_cast< Value >( 242653 ) / static_cast< Value >( 13440 );
- (*this)[3] = -static_cast< Value >( 296053 ) / static_cast< Value >( 13440 );
- (*this)[4] = static_cast< Value >( 2102243 ) / static_cast< Value >( 120960 );
- (*this)[5] = -static_cast< Value >( 115747 ) / static_cast< Value >( 13440 );
- (*this)[6] = static_cast< Value >( 32863 ) / static_cast< Value >( 13440 );
- (*this)[7] = -static_cast< Value >( 5257 ) / static_cast< Value >( 17280 );
- }
-};
-
-
-
-
-
-
-
-} // detail
-} // odeint
-} // numeric
-} // boost
-
-
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_DETAIL_ADAMS_BASHFORTH_COEFFICIENTS_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/detail/adams_moulton_call_algebra.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/detail/adams_moulton_call_algebra.hpp
deleted file mode 100644
index 7ed79d2e15070224b34892dd9cd02088cd67fcbe..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/detail/adams_moulton_call_algebra.hpp
+++ /dev/null
@@ -1,148 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/detail/adams_moulton_call_algebra.hpp
-
- [begin_description]
- Algebra caller for the Adams Moulton method.
- [end_description]
-
- Copyright 2011-2012 Karsten Ahnert
- Copyright 2011 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_DETAIL_ADAMS_MOULTON_CALL_ALGEBRA_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_DETAIL_ADAMS_MOULTON_CALL_ALGEBRA_HPP_INCLUDED
-
-#include <boost/assert.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-namespace detail {
-
-template< size_t Step , class Algebra , class Operations >
-struct adams_moulton_call_algebra;
-
-template< class Algebra , class Operations >
-struct adams_moulton_call_algebra< 1 , Algebra , Operations >
-{
- template< class StateIn , class StateOut , class DerivIn , class StepStorage , class Coefficients , class Time >
- void operator()( Algebra &algebra , const StateIn &in , StateOut &out , const DerivIn &dxdt , const StepStorage& /* steps */ , const Coefficients &coef , Time dt ) const
- {
- typedef typename Coefficients::value_type value_type;
- algebra.for_each3( out , in , dxdt , typename Operations::template scale_sum2< value_type , Time >( 1.0 , dt * coef[0] ) );
- }
-};
-
-
-template< class Algebra , class Operations >
-struct adams_moulton_call_algebra< 2 , Algebra , Operations >
-{
- template< class StateIn , class StateOut , class DerivIn , class StepStorage , class Coefficients , class Time >
- void operator()( Algebra &algebra , const StateIn &in , StateOut &out , const DerivIn &dxdt , const StepStorage &steps , const Coefficients &coef , Time dt ) const
- {
- typedef typename Coefficients::value_type value_type;
- algebra.for_each4( out , in , dxdt , steps[0].m_v ,
- typename Operations::template scale_sum3< value_type , Time , Time >( 1.0 , dt * coef[0] , dt * coef[1] ) );
- }
-};
-
-
-template< class Algebra , class Operations >
-struct adams_moulton_call_algebra< 3 , Algebra , Operations >
-{
- template< class StateIn , class StateOut , class DerivIn , class StepStorage , class Coefficients , class Time >
- void operator()( Algebra &algebra , const StateIn &in , StateOut &out , const DerivIn &dxdt , const StepStorage &steps , const Coefficients &coef , Time dt ) const
- {
- typedef typename Coefficients::value_type value_type;
- algebra.for_each5( out , in , dxdt , steps[0].m_v , steps[1].m_v ,
- typename Operations::template scale_sum4< value_type , Time , Time >( 1.0 , dt * coef[0] , dt * coef[1] , dt * coef[2] ) );
- }
-};
-
-
-template< class Algebra , class Operations >
-struct adams_moulton_call_algebra< 4 , Algebra , Operations >
-{
- template< class StateIn , class StateOut , class DerivIn , class StepStorage , class Coefficients , class Time >
- void operator()( Algebra &algebra , const StateIn &in , StateOut &out , const DerivIn &dxdt , const StepStorage &steps , const Coefficients &coef , Time dt ) const
- {
- typedef typename Coefficients::value_type value_type;
- algebra.for_each6( out , in , dxdt , steps[0].m_v , steps[1].m_v , steps[2].m_v ,
- typename Operations::template scale_sum5< value_type , Time , Time , Time >(
- 1.0 , dt * coef[0] , dt * coef[1] , dt * coef[2] , dt * coef[3] ) );
- }
-};
-
-
-template< class Algebra , class Operations >
-struct adams_moulton_call_algebra< 5 , Algebra , Operations >
-{
- template< class StateIn , class StateOut , class DerivIn , class StepStorage , class Coefficients , class Time >
- void operator()( Algebra &algebra , const StateIn &in , StateOut &out , const DerivIn &dxdt , const StepStorage &steps , const Coefficients &coef , Time dt ) const
- {
- typedef typename Coefficients::value_type value_type;
- algebra.for_each7( out , in , dxdt , steps[0].m_v , steps[1].m_v , steps[2].m_v , steps[3].m_v ,
- typename Operations::template scale_sum6< value_type , Time , Time , Time , Time >(
- 1.0 , dt * coef[0] , dt * coef[1] , dt * coef[2] , dt * coef[3] , dt * coef[4] ) );
- }
-};
-
-
-template< class Algebra , class Operations >
-struct adams_moulton_call_algebra< 6 , Algebra , Operations >
-{
- template< class StateIn , class StateOut , class DerivIn , class StepStorage , class Coefficients , class Time >
- void operator()( Algebra &algebra , const StateIn &in , StateOut &out , const DerivIn &dxdt , const StepStorage &steps , const Coefficients &coef , Time dt ) const
- {
- typedef typename Coefficients::value_type value_type;
- algebra.for_each8( out , in , dxdt , steps[0].m_v , steps[1].m_v , steps[2].m_v , steps[3].m_v , steps[4].m_v ,
- typename Operations::template scale_sum7< value_type , Time , Time , Time , Time , Time >(
- 1.0 , dt * coef[0] , dt * coef[1] , dt * coef[2] , dt * coef[3] , dt * coef[4] , dt * coef[5] ) );
- }
-};
-
-
-template< class Algebra , class Operations >
-struct adams_moulton_call_algebra< 7 , Algebra , Operations >
-{
- template< class StateIn , class StateOut , class DerivIn , class StepStorage , class Coefficients , class Time >
- void operator()( Algebra &algebra , const StateIn &in , StateOut &out , const DerivIn &dxdt , const StepStorage &steps , const Coefficients &coef , Time dt ) const
- {
- typedef typename Coefficients::value_type value_type;
- algebra.for_each9( out , in , dxdt , steps[0].m_v , steps[1].m_v , steps[2].m_v , steps[3].m_v , steps[4].m_v , steps[5].m_v ,
- typename Operations::template scale_sum8< value_type , Time , Time , Time , Time , Time , Time >(
- 1.0 , dt * coef[0] , dt * coef[1] , dt * coef[2] , dt * coef[3] , dt * coef[4] , dt * coef[5] , dt * coef[6] ) );
- }
-};
-
-
-template< class Algebra , class Operations >
-struct adams_moulton_call_algebra< 8 , Algebra , Operations >
-{
- template< class StateIn , class StateOut , class DerivIn , class StepStorage , class Coefficients , class Time >
- void operator()( Algebra &algebra , const StateIn &in , StateOut &out , const DerivIn &dxdt , const StepStorage &steps , const Coefficients &coef , Time dt ) const
- {
- typedef typename Coefficients::value_type value_type;
- algebra.for_each10( out , in , dxdt , steps[0].m_v , steps[1].m_v , steps[2].m_v , steps[3].m_v , steps[4].m_v , steps[5].m_v , steps[6].m_v ,
- typename Operations::template scale_sum9< value_type , Time , Time , Time , Time , Time , Time , Time >(
- 1.0 , dt * coef[0] , dt * coef[1] , dt * coef[2] , dt * coef[3] , dt * coef[4] , dt * coef[5] , dt * coef[6] , dt * coef[7] ) );
- }
-};
-
-
-
-
-} // detail
-} // odeint
-} // numeric
-} // boost
-
-
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_DETAIL_ADAMS_MOULTON_CALL_ALGEBRA_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/detail/adams_moulton_coefficients.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/detail/adams_moulton_coefficients.hpp
deleted file mode 100644
index 8047fa8ae108b59c2d1b9665b89bd71aadd8c441..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/detail/adams_moulton_coefficients.hpp
+++ /dev/null
@@ -1,168 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/detail/adams_moulton_coefficients.hpp
-
- [begin_description]
- Coefficients for the Adams Moulton method.
- [end_description]
-
- Copyright 2011-2012 Karsten Ahnert
- Copyright 2011-2012 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_DETAIL_ADAMS_MOULTON_COEFFICIENTS_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_DETAIL_ADAMS_MOULTON_COEFFICIENTS_HPP_INCLUDED
-
-
-#include <boost/array.hpp>
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-namespace detail {
-
-template< class Value , size_t Steps >
-class adams_moulton_coefficients ;
-
-template< class Value >
-class adams_moulton_coefficients< Value , 1 > : public boost::array< Value , 1 >
-{
-public:
- adams_moulton_coefficients( void )
- : boost::array< Value , 1 >()
- {
- (*this)[0] = static_cast< Value >( 1 );
- }
-};
-
-
-template< class Value >
-class adams_moulton_coefficients< Value , 2 > : public boost::array< Value , 2 >
-{
-public:
- adams_moulton_coefficients( void )
- : boost::array< Value , 2 >()
- {
- (*this)[0] = static_cast< Value >( 1 ) / static_cast< Value >( 2 );
- (*this)[1] = static_cast< Value >( 1 ) / static_cast< Value >( 2 );
- }
-};
-
-
-template< class Value >
-class adams_moulton_coefficients< Value , 3 > : public boost::array< Value , 3 >
-{
-public:
- adams_moulton_coefficients( void )
- : boost::array< Value , 3 >()
- {
- (*this)[0] = static_cast< Value >( 5 ) / static_cast< Value >( 12 );
- (*this)[1] = static_cast< Value >( 2 ) / static_cast< Value >( 3 );
- (*this)[2] = -static_cast< Value >( 1 ) / static_cast< Value >( 12 );
- }
-};
-
-
-template< class Value >
-class adams_moulton_coefficients< Value , 4 > : public boost::array< Value , 4 >
-{
-public:
- adams_moulton_coefficients( void )
- : boost::array< Value , 4 >()
- {
- (*this)[0] = static_cast< Value >( 3 ) / static_cast< Value >( 8 );
- (*this)[1] = static_cast< Value >( 19 ) / static_cast< Value >( 24 );
- (*this)[2] = -static_cast< Value >( 5 ) / static_cast< Value >( 24 );
- (*this)[3] = static_cast< Value >( 1 ) / static_cast< Value >( 24 );
- }
-};
-
-
-template< class Value >
-class adams_moulton_coefficients< Value , 5 > : public boost::array< Value , 5 >
-{
-public:
- adams_moulton_coefficients( void )
- : boost::array< Value , 5 >()
- {
- (*this)[0] = static_cast< Value >( 251 ) / static_cast< Value >( 720 );
- (*this)[1] = static_cast< Value >( 323 ) / static_cast< Value >( 360 );
- (*this)[2] = -static_cast< Value >( 11 ) / static_cast< Value >( 30 );
- (*this)[3] = static_cast< Value >( 53 ) / static_cast< Value >( 360 );
- (*this)[4] = -static_cast< Value >( 19 ) / static_cast< Value >( 720 );
- }
-};
-
-
-template< class Value >
-class adams_moulton_coefficients< Value , 6 > : public boost::array< Value , 6 >
-{
-public:
- adams_moulton_coefficients( void )
- : boost::array< Value , 6 >()
- {
- (*this)[0] = static_cast< Value >( 95 ) / static_cast< Value >( 288 );
- (*this)[1] = static_cast< Value >( 1427 ) / static_cast< Value >( 1440 );
- (*this)[2] = -static_cast< Value >( 133 ) / static_cast< Value >( 240 );
- (*this)[3] = static_cast< Value >( 241 ) / static_cast< Value >( 720 );
- (*this)[4] = -static_cast< Value >( 173 ) / static_cast< Value >( 1440 );
- (*this)[5] = static_cast< Value >( 3 ) / static_cast< Value >( 160 );
- }
-};
-
-template< class Value >
-class adams_moulton_coefficients< Value , 7 > : public boost::array< Value , 7 >
-{
-public:
- adams_moulton_coefficients( void )
- : boost::array< Value , 7 >()
- {
- (*this)[0] = static_cast< Value >( 19087 ) / static_cast< Value >( 60480 );
- (*this)[1] = static_cast< Value >( 2713 ) / static_cast< Value >( 2520 );
- (*this)[2] = -static_cast< Value >( 15487 ) / static_cast< Value >( 20160 );
- (*this)[3] = static_cast< Value >( 586 ) / static_cast< Value >( 945 );
- (*this)[4] = -static_cast< Value >( 6737 ) / static_cast< Value >( 20160 );
- (*this)[5] = static_cast< Value >( 263 ) / static_cast< Value >( 2520 );
- (*this)[6] = -static_cast< Value >( 863 ) / static_cast< Value >( 60480 );
- }
-};
-
-
-template< class Value >
-class adams_moulton_coefficients< Value , 8 > : public boost::array< Value , 8 >
-{
-public:
- adams_moulton_coefficients( void )
- : boost::array< Value , 8 >()
- {
- (*this)[0] = static_cast< Value >( 5257 ) / static_cast< Value >( 17280 );
- (*this)[1] = static_cast< Value >( 139849 ) / static_cast< Value >( 120960 );
- (*this)[2] = -static_cast< Value >( 4511 ) / static_cast< Value >( 4480 );
- (*this)[3] = static_cast< Value >( 123133 ) / static_cast< Value >( 120960 );
- (*this)[4] = -static_cast< Value >( 88547 ) / static_cast< Value >( 120960 );
- (*this)[5] = static_cast< Value >( 1537 ) / static_cast< Value >( 4480 );
- (*this)[6] = -static_cast< Value >( 11351 ) / static_cast< Value >( 120960 );
- (*this)[7] = static_cast< Value >( 275 ) / static_cast< Value >( 24192 );
- }
-};
-
-
-
-
-
-
-
-} // detail
-} // odeint
-} // numeric
-} // boost
-
-
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_DETAIL_ADAMS_MOULTON_COEFFICIENTS_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/detail/generic_rk_algorithm.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/detail/generic_rk_algorithm.hpp
deleted file mode 100644
index ab74b24ee2a3c7af3e142668809cbba8a4cfb3b4..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/detail/generic_rk_algorithm.hpp
+++ /dev/null
@@ -1,247 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/detail/generic_rk_algorithm.hpp
-
- [begin_description]
- Implementation of the generic Runge-Kutta method.
- [end_description]
-
- Copyright 2011-2013 Mario Mulansky
- Copyright 2011-2012 Karsten Ahnert
- Copyright 2012 Christoph Koke
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_DETAIL_GENERIC_RK_ALGORITHM_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_DETAIL_GENERIC_RK_ALGORITHM_HPP_INCLUDED
-
-#include <boost/static_assert.hpp>
-
-#include <boost/mpl/vector.hpp>
-#include <boost/mpl/push_back.hpp>
-#include <boost/mpl/for_each.hpp>
-#include <boost/mpl/range_c.hpp>
-#include <boost/mpl/copy.hpp>
-#include <boost/mpl/size_t.hpp>
-
-#include <boost/fusion/algorithm.hpp>
-#include <boost/fusion/iterator.hpp>
-#include <boost/fusion/mpl.hpp>
-#include <boost/fusion/sequence.hpp>
-
-#include <boost/array.hpp>
-
-#include <boost/numeric/odeint/algebra/range_algebra.hpp>
-#include <boost/numeric/odeint/algebra/default_operations.hpp>
-#include <boost/numeric/odeint/stepper/detail/generic_rk_call_algebra.hpp>
-#include <boost/numeric/odeint/stepper/detail/generic_rk_operations.hpp>
-#include <boost/numeric/odeint/util/bind.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-namespace detail {
-
-template< class T , class Constant >
-struct array_wrapper
-{
- typedef const typename boost::array< T , Constant::value > type;
-};
-
-template< class T , size_t i >
-struct stage
-{
- T c;
- boost::array< T , i > a;
-};
-
-
-template< class T , class Constant >
-struct stage_wrapper
-{
- typedef stage< T , Constant::value > type;
-};
-
-
-template<
-size_t StageCount,
-class Value ,
-class Algebra ,
-class Operations
->
-class generic_rk_algorithm {
-
-public:
- typedef mpl::range_c< size_t , 1 , StageCount > stage_indices;
-
- typedef typename boost::fusion::result_of::as_vector
- <
- typename boost::mpl::copy
- <
- stage_indices ,
- boost::mpl::inserter
- <
- boost::mpl::vector0< > ,
- boost::mpl::push_back< boost::mpl::_1 , array_wrapper< Value , boost::mpl::_2 > >
- >
- >::type
- >::type coef_a_type;
-
- typedef boost::array< Value , StageCount > coef_b_type;
- typedef boost::array< Value , StageCount > coef_c_type;
-
- typedef typename boost::fusion::result_of::as_vector
- <
- typename boost::mpl::push_back
- <
- typename boost::mpl::copy
- <
- stage_indices,
- boost::mpl::inserter
- <
- boost::mpl::vector0<> ,
- boost::mpl::push_back< boost::mpl::_1 , stage_wrapper< Value , boost::mpl::_2 > >
- >
- >::type ,
- stage< Value , StageCount >
- >::type
- >::type stage_vector_base;
-
-
- struct stage_vector : public stage_vector_base
- {
- struct do_insertion
- {
- stage_vector_base &m_base;
- const coef_a_type &m_a;
- const coef_c_type &m_c;
-
- do_insertion( stage_vector_base &base , const coef_a_type &a , const coef_c_type &c )
- : m_base( base ) , m_a( a ) , m_c( c ) { }
-
- template< class Index >
- void operator()( Index ) const
- {
- //boost::fusion::at< Index >( m_base ) = stage< double , Index::value+1 , intermediate_stage >( m_c[ Index::value ] , boost::fusion::at< Index >( m_a ) );
- boost::fusion::at< Index >( m_base ).c = m_c[ Index::value ];
- boost::fusion::at< Index >( m_base ).a = boost::fusion::at< Index >( m_a );
- }
- };
-
- struct print_butcher
- {
- const stage_vector_base &m_base;
- std::ostream &m_os;
-
- print_butcher( const stage_vector_base &base , std::ostream &os )
- : m_base( base ) , m_os( os )
- { }
-
- template<class Index>
- void operator()(Index) const {
- m_os << boost::fusion::at<Index>(m_base).c << " | ";
- for( size_t i=0 ; i<Index::value ; ++i )
- m_os << boost::fusion::at<Index>(m_base).a[i] << " ";
- m_os << std::endl;
- }
- };
-
-
- stage_vector( const coef_a_type &a , const coef_b_type &b , const coef_c_type &c )
- {
- typedef boost::mpl::range_c< size_t , 0 , StageCount-1 > indices;
- boost::mpl::for_each< indices >( do_insertion( *this , a , c ) );
- boost::fusion::at_c< StageCount - 1 >( *this ).c = c[ StageCount - 1 ];
- boost::fusion::at_c< StageCount - 1 >( *this ).a = b;
- }
-
- void print( std::ostream &os ) const
- {
- typedef boost::mpl::range_c< size_t , 0 , StageCount > indices;
- boost::mpl::for_each< indices >( print_butcher( *this , os ) );
- }
- };
-
-
-
- template< class System , class StateIn , class StateTemp , class DerivIn , class Deriv ,
- class StateOut , class Time >
- struct calculate_stage
- {
- Algebra &algebra;
- System &system;
- const StateIn &x;
- StateTemp &x_tmp;
- StateOut &x_out;
- const DerivIn &dxdt;
- Deriv *F;
- Time t;
- Time dt;
-
- calculate_stage( Algebra &_algebra , System &_system , const StateIn &_x , const DerivIn &_dxdt , StateOut &_out ,
- StateTemp &_x_tmp , Deriv *_F , Time _t , Time _dt )
- : algebra( _algebra ) , system( _system ) , x( _x ) , x_tmp( _x_tmp ) , x_out( _out) , dxdt( _dxdt ) , F( _F ) , t( _t ) , dt( _dt )
- {}
-
-
- template< typename T , size_t stage_number >
- void inline operator()( stage< T , stage_number > const &stage ) const
- //typename stage_fusion_wrapper< T , mpl::size_t< stage_number > , intermediate_stage >::type const &stage ) const
- {
- if( stage_number > 1 )
- {
-#ifdef BOOST_MSVC
-#pragma warning( disable : 4307 34 )
-#endif
- system( x_tmp , F[stage_number-2].m_v , t + stage.c * dt );
-#ifdef BOOST_MSVC
-#pragma warning( default : 4307 34 )
-#endif
- }
- //std::cout << stage_number-2 << ", t': " << t + stage.c * dt << std::endl;
-
- if( stage_number < StageCount )
- detail::template generic_rk_call_algebra< stage_number , Algebra >()( algebra , x_tmp , x , dxdt , F ,
- detail::generic_rk_scale_sum< stage_number , Operations , Value , Time >( stage.a , dt) );
- // algebra_type::template for_eachn<stage_number>( x_tmp , x , dxdt , F ,
- // typename operations_type::template scale_sumn< stage_number , time_type >( stage.a , dt ) );
- else
- detail::template generic_rk_call_algebra< stage_number , Algebra >()( algebra , x_out , x , dxdt , F ,
- detail::generic_rk_scale_sum< stage_number , Operations , Value , Time >( stage.a , dt ) );
- // algebra_type::template for_eachn<stage_number>( x_out , x , dxdt , F ,
- // typename operations_type::template scale_sumn< stage_number , time_type >( stage.a , dt ) );
- }
-
- };
-
- generic_rk_algorithm( const coef_a_type &a , const coef_b_type &b , const coef_c_type &c )
- : m_stages( a , b , c )
- { }
-
- template< class System , class StateIn , class DerivIn , class Time , class StateOut , class StateTemp , class Deriv >
- void inline do_step( Algebra &algebra , System system , const StateIn &in , const DerivIn &dxdt ,
- Time t , StateOut &out , Time dt ,
- StateTemp &x_tmp , Deriv F[StageCount-1] ) const
- {
- typedef typename odeint::unwrap_reference< System >::type unwrapped_system_type;
- unwrapped_system_type &sys = system;
- boost::fusion::for_each( m_stages , calculate_stage<
- unwrapped_system_type , StateIn , StateTemp , DerivIn , Deriv , StateOut , Time >
- ( algebra , sys , in , dxdt , out , x_tmp , F , t , dt ) );
- }
-
-private:
- stage_vector m_stages;
-};
-
-
-}
-}
-}
-}
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_DETAIL_GENERIC_RK_ALGORITHM_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/detail/generic_rk_call_algebra.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/detail/generic_rk_call_algebra.hpp
deleted file mode 100644
index 0249d86405ba92dfd60691583c1ea630867eed01..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/detail/generic_rk_call_algebra.hpp
+++ /dev/null
@@ -1,263 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/detail/generic_rk_call_algebra.hpp
-
- [begin_description]
- Algebra caller for the generic Runge-Kutta methods.
- [end_description]
-
- Copyright 2011-2012 Mario Mulansky
- Copyright 2011-2012 Karsten Ahnert
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_DETAIL_GENERIC_RK_CALL_ALGEBRA_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_DETAIL_GENERIC_RK_CALL_ALGEBRA_HPP_INCLUDED
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-namespace detail {
-
-template< size_t StageNumber , class Algebra >
-struct generic_rk_call_algebra;
-
-template< class Algebra >
-struct generic_rk_call_algebra< 1 , Algebra >
-{
- typedef Algebra algebra_type;
-
- template< class S1 , class S2 , class S3 , class S4 , class Op>
- void operator()( algebra_type &algebra , S1 &s1 , S2 &s2 , S3 &s3 , S4 * /* s4_array */ , Op op ) const
- {
- algebra.for_each3( s1 , s2 , s3 , op );
- }
-
- template< class S1 , class S2 , class S4 , class Op>
- void operator()( algebra_type &algebra , S1 &s1 , S2 &s2 , S4 * /* s4_array */ , Op op ) const
- {
- algebra.for_each2( s1 , s2 , op );
- }
-};
-
-template< class Algebra >
-struct generic_rk_call_algebra< 2 , Algebra >
-{
- template< class S1 , class S2 , class S3 , class S4 , class Op>
- void operator()( Algebra &algebra , S1 &s1 , S2 &s2 , S3 &s3 , S4 s4_array[1] , Op op ) const
- {
- algebra.for_each4( s1 , s2 , s3 , s4_array[0].m_v , op );
- }
-
- template< class S1 , class S2 , class S4 , class Op>
- void operator()( Algebra &algebra , S1 &s1 , S2 &s2 , S4 s4_array[1] , Op op ) const
- {
- algebra.for_each3( s1 , s2 , s4_array[0].m_v , op );
- }
-};
-
-
-template< class Algebra >
-struct generic_rk_call_algebra< 3 , Algebra >
-{
- template< class S1 , class S2 , class S3 , class S4 , class Op>
- void operator()( Algebra &algebra , S1 &s1 , S2 &s2 , S3 &s3 , S4 s4_array[2] , Op op ) const
- {
- algebra.for_each5( s1 , s2 , s3 , s4_array[0].m_v , s4_array[1].m_v , op );
- }
-
- template< class S1 , class S2 , class S4 , class Op>
- void operator()( Algebra &algebra , S1 &s1 , S2 &s2 , S4 s4_array[2] , Op op ) const
- {
- algebra.for_each4( s1 , s2 , s4_array[0].m_v , s4_array[1].m_v , op );
- }
-};
-
-
-template< class Algebra >
-struct generic_rk_call_algebra< 4 , Algebra >
-{
- template< class S1 , class S2 , class S3 , class S4 , class Op>
- void operator()( Algebra &algebra , S1 &s1 , S2 &s2 , S3 &s3 , S4 s4_array[3] , Op op ) const
- {
- algebra.for_each6( s1 , s2 , s3 , s4_array[0].m_v , s4_array[1].m_v , s4_array[2].m_v , op );
- }
-
- template< class S1 , class S2 , class S4 , class Op>
- void operator()( Algebra &algebra , S1 &s1 , S2 &s2 , S4 s4_array[3] , Op op ) const
- {
- algebra.for_each5( s1 , s2 , s4_array[0].m_v , s4_array[1].m_v , s4_array[2].m_v , op );
- }
-};
-
-
-template< class Algebra >
-struct generic_rk_call_algebra< 5 , Algebra >
-{
- template< class S1 , class S2 , class S3 , class S4 , class Op>
- void operator()( Algebra &algebra , S1 &s1 , S2 &s2 , S3 &s3 , S4 s4_array[4] , Op op ) const
- {
- algebra.for_each7( s1 , s2 , s3 , s4_array[0].m_v , s4_array[1].m_v , s4_array[2].m_v , s4_array[3].m_v , op );
- }
-
- template< class S1 , class S2 , class S4 , class Op>
- void operator()( Algebra &algebra , S1 &s1 , S2 &s2 , S4 s4_array[4] , Op op ) const
- {
- algebra.for_each6( s1 , s2 , s4_array[0].m_v , s4_array[1].m_v , s4_array[2].m_v , s4_array[3].m_v , op );
- }
-};
-
-template< class Algebra >
-struct generic_rk_call_algebra< 6 , Algebra >
-{
- template< class S1 , class S2 , class S3 , class S4 , class Op>
- void operator()( Algebra &algebra , S1 &s1 , S2 &s2 , S3 &s3 , S4 s4_array[5] , Op op ) const
- {
- algebra.for_each8( s1 , s2 , s3 , s4_array[0].m_v , s4_array[1].m_v , s4_array[2].m_v , s4_array[3].m_v , s4_array[4].m_v , op );
- }
-
- template< class S1 , class S2 , class S4 , class Op>
- void operator()( Algebra &algebra , S1 &s1 , S2 &s2 , S4 s4_array[5] , Op op ) const
- {
- algebra.for_each7( s1 , s2 , s4_array[0].m_v , s4_array[1].m_v , s4_array[2].m_v , s4_array[3].m_v , s4_array[4].m_v , op );
- }
-};
-
-template< class Algebra >
-struct generic_rk_call_algebra< 7 , Algebra >
-{
- template< class S1 , class S2 , class S3 , class S4 , class Op>
- void operator()( Algebra &algebra , S1 &s1 , S2 &s2 , S3 &s3 , S4 s4_array[6] , Op op ) const
- {
- algebra.for_each9( s1 , s2 , s3 , s4_array[0].m_v , s4_array[1].m_v , s4_array[2].m_v , s4_array[3].m_v , s4_array[4].m_v ,
- s4_array[5].m_v , op );
- }
-
- template< class S1 , class S2 , class S4 , class Op>
- void operator()( Algebra &algebra , S1 &s1 , S2 &s2 , S4 s4_array[6] , Op op ) const
- {
- algebra.for_each8( s1 , s2 , s4_array[0].m_v , s4_array[1].m_v , s4_array[2].m_v , s4_array[3].m_v , s4_array[4].m_v ,
- s4_array[5].m_v , op );
- }
-};
-
-template< class Algebra >
-struct generic_rk_call_algebra< 8 , Algebra >
-{
- template< class S1 , class S2 , class S3 , class S4 , class Op>
- void operator()( Algebra &algebra , S1 &s1 , S2 &s2 , S3 &s3 , S4 s4_array[7] , Op op ) const
- {
- algebra.for_each10( s1 , s2 , s3 , s4_array[0].m_v , s4_array[1].m_v , s4_array[2].m_v , s4_array[3].m_v , s4_array[4].m_v ,
- s4_array[5].m_v , s4_array[6].m_v , op );
- }
-
- template< class S1 , class S2 , class S4 , class Op>
- void operator()( Algebra &algebra , S1 &s1 , S2 &s2 , S4 s4_array[7] , Op op ) const
- {
- algebra.for_each9( s1 , s2 , s4_array[0].m_v , s4_array[1].m_v , s4_array[2].m_v , s4_array[3].m_v , s4_array[4].m_v ,
- s4_array[5].m_v , s4_array[6].m_v , op );
- }
-};
-
-template< class Algebra >
-struct generic_rk_call_algebra< 9 , Algebra >
-{
- template< class S1 , class S2 , class S3 , class S4 , class Op>
- void operator()( Algebra &algebra , S1 &s1 , S2 &s2 , S3 &s3 , S4 s4_array[8] , Op op ) const
- {
- algebra.for_each11( s1 , s2 , s3 , s4_array[0].m_v , s4_array[1].m_v , s4_array[2].m_v , s4_array[3].m_v , s4_array[4].m_v ,
- s4_array[5].m_v , s4_array[6].m_v , s4_array[7].m_v , op );
- }
-
- template< class S1 , class S2 , class S4 , class Op>
- void operator()( Algebra &algebra , S1 &s1 , S2 &s2 , S4 s4_array[8] , Op op ) const
- {
- algebra.for_each10( s1 , s2 , s4_array[0].m_v , s4_array[1].m_v , s4_array[2].m_v , s4_array[3].m_v , s4_array[4].m_v ,
- s4_array[5].m_v , s4_array[6].m_v , s4_array[7].m_v , op );
- }
-};
-
-template< class Algebra >
-struct generic_rk_call_algebra< 10 , Algebra >
-{
- template< class S1 , class S2 , class S3 , class S4 , class Op>
- void operator()( Algebra &algebra , S1 &s1 , S2 &s2 , S3 &s3 , S4 s4_array[9] , Op op ) const
- {
- algebra.for_each12( s1 , s2 , s3 , s4_array[0].m_v , s4_array[1].m_v , s4_array[2].m_v , s4_array[3].m_v , s4_array[4].m_v ,
- s4_array[5].m_v , s4_array[6].m_v , s4_array[7].m_v , s4_array[8].m_v , op );
- }
-
- template< class S1 , class S2 , class S4 , class Op>
- void operator()( Algebra &algebra , S1 &s1 , S2 &s2 , S4 s4_array[9] , Op op ) const
- {
- algebra.for_each11( s1 , s2 , s4_array[0].m_v , s4_array[1].m_v , s4_array[2].m_v , s4_array[3].m_v , s4_array[4].m_v ,
- s4_array[5].m_v , s4_array[6].m_v , s4_array[7].m_v , s4_array[8].m_v , op );
- }
-};
-
-
-template< class Algebra >
-struct generic_rk_call_algebra< 11 , Algebra >
-{
- template< class S1 , class S2 , class S3 , class S4 , class Op>
- void operator()( Algebra &algebra , S1 &s1 , S2 &s2 , S3 &s3 , S4 s4_array[10] , Op op ) const
- {
- algebra.for_each13( s1 , s2 , s3 , s4_array[0].m_v , s4_array[1].m_v , s4_array[2].m_v , s4_array[3].m_v , s4_array[4].m_v ,
- s4_array[5].m_v , s4_array[6].m_v , s4_array[7].m_v , s4_array[8].m_v , s4_array[9].m_v , op );
- }
-
- template< class S1 , class S2 , class S4 , class Op>
- void operator()( Algebra &algebra , S1 &s1 , S2 &s2 , S4 s4_array[10] , Op op ) const
- {
- algebra.for_each12( s1 , s2 , s4_array[0].m_v , s4_array[1].m_v , s4_array[2].m_v , s4_array[3].m_v , s4_array[4].m_v ,
- s4_array[5].m_v , s4_array[6].m_v , s4_array[7].m_v , s4_array[8].m_v , s4_array[9].m_v , op );
- }
-};
-
-template< class Algebra >
-struct generic_rk_call_algebra< 12 , Algebra >
-{
- template< class S1 , class S2 , class S3 , class S4 , class Op>
- void operator()( Algebra &algebra , S1 &s1 , S2 &s2 , S3 &s3 , S4 s4_array[11] , Op op ) const
- {
- algebra.for_each14( s1 , s2 , s3 , s4_array[0].m_v , s4_array[1].m_v , s4_array[2].m_v , s4_array[3].m_v , s4_array[4].m_v ,
- s4_array[5].m_v , s4_array[6].m_v , s4_array[7].m_v , s4_array[8].m_v , s4_array[9].m_v , s4_array[10].m_v , op );
- }
-
- template< class S1 , class S2 , class S4 , class Op>
- void operator()( Algebra &algebra , S1 &s1 , S2 &s2 , S4 s4_array[11] , Op op ) const
- {
- algebra.for_each13( s1 , s2 , s4_array[0].m_v , s4_array[1].m_v , s4_array[2].m_v , s4_array[3].m_v , s4_array[4].m_v ,
- s4_array[5].m_v , s4_array[6].m_v , s4_array[7].m_v , s4_array[8].m_v , s4_array[9].m_v , s4_array[10].m_v , op );
- }
-};
-
-template< class Algebra >
-struct generic_rk_call_algebra< 13 , Algebra >
-{
- template< class S1 , class S2 , class S3 , class S4 , class Op>
- void operator()( Algebra &algebra , S1 &s1 , S2 &s2 , S3 &s3 , S4 s4_array[12] , Op op ) const
- {
- algebra.for_each15( s1 , s2 , s3 , s4_array[0].m_v , s4_array[1].m_v , s4_array[2].m_v , s4_array[3].m_v , s4_array[4].m_v ,
- s4_array[5].m_v , s4_array[6].m_v , s4_array[7].m_v , s4_array[8].m_v , s4_array[9].m_v , s4_array[10].m_v , s4_array[11].m_v , op );
- }
-
- template< class S1 , class S2 , class S4 , class Op>
- void operator()( Algebra &algebra , S1 &s1 , S2 &s2 , S4 s4_array[12] , Op op ) const
- {
- algebra.for_each14( s1 , s2 , s4_array[0].m_v , s4_array[1].m_v , s4_array[2].m_v , s4_array[3].m_v , s4_array[4].m_v ,
- s4_array[5].m_v , s4_array[6].m_v , s4_array[7].m_v , s4_array[8].m_v , s4_array[9].m_v , s4_array[10].m_v , s4_array[11].m_v , op );
- }
-};
-
-}
-}
-}
-}
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_DETAIL_GENERIC_RK_CALL_ALGEBRA_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/detail/generic_rk_operations.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/detail/generic_rk_operations.hpp
deleted file mode 100644
index 2cce3f4d0bdc5bc975543597800bf0b4c8450762..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/detail/generic_rk_operations.hpp
+++ /dev/null
@@ -1,252 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/detail/generic_rk_operations.hpp
-
- [begin_description]
- Operations caller for the generic Runge Kutta method.
- [end_description]
-
- Copyright 2011 Mario Mulansky
- Copyright 2011-2012 Karsten Ahnert
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_DETAIL_GENERIC_RK_OPERATIONS_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_DETAIL_GENERIC_RK_OPERATIONS_HPP_INCLUDED
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-namespace detail {
-
-template< size_t StageNumber , class Operations , class Fac , class Time >
-struct generic_rk_scale_sum;
-
-template< class Operations , class Fac , class Time >
-struct generic_rk_scale_sum< 1 , Operations , Fac , Time > : public Operations::template scale_sum2< Fac , Time >
-{
- generic_rk_scale_sum( const boost::array<Fac,1> &a , Time dt ) : Operations::template scale_sum2< Fac , Time >( 1.0 , a[0]*dt )
- { }
-
- typedef void result_type;
-};
-
-
-template< class Operations , class Fac , class Time >
-struct generic_rk_scale_sum< 2 , Operations , Fac , Time > : public Operations::template scale_sum3< Fac , Time >
-{
- generic_rk_scale_sum( const boost::array<Fac,2> &a , Time dt )
- : Operations::template scale_sum3< Fac , Time >( 1.0 , a[0]*dt , a[1]*dt )
- { }
-
- typedef void result_type;
-};
-
-template< class Operations , class Fac , class Time >
-struct generic_rk_scale_sum< 3 , Operations , Fac , Time > : public Operations::template scale_sum4< Fac , Time >
-{
- generic_rk_scale_sum( const boost::array<Fac,3> &a , Time dt )
- : Operations::template scale_sum4< Fac , Time >( 1.0 , a[0]*dt , a[1]*dt , a[2]*dt )
- { }
-
- typedef void result_type;
-};
-
-template< class Operations , class Fac , class Time >
-struct generic_rk_scale_sum< 4 , Operations , Fac , Time > : public Operations::template scale_sum5< Fac , Time >
-{
- generic_rk_scale_sum( const boost::array<Fac,4> &a , Time dt )
- : Operations::template scale_sum5< Fac , Time >( 1.0 , a[0]*dt , a[1]*dt , a[2]*dt , a[3]*dt )
- { }
-
- typedef void result_type;
-};
-
-template< class Operations , class Fac , class Time >
-struct generic_rk_scale_sum< 5 , Operations , Fac , Time > : public Operations::template scale_sum6< Fac , Time >
-{
- generic_rk_scale_sum( const boost::array<Fac,5> &a , Time dt )
- : Operations::template scale_sum6< Fac , Time >( 1.0 , a[0]*dt , a[1]*dt , a[2]*dt , a[3]*dt , a[4]*dt )
- { }
-
- typedef void result_type;
-};
-
-template< class Operations , class Fac , class Time >
-struct generic_rk_scale_sum< 6 , Operations , Fac , Time > : public Operations::template scale_sum7< Fac , Time >
-{
- generic_rk_scale_sum( const boost::array<Fac,6> &a , Time dt )
- : Operations::template scale_sum7< Fac , Time >( 1.0 , a[0]*dt , a[1]*dt , a[2]*dt , a[3]*dt , a[4]*dt , a[5]*dt )
- { }
-
- typedef void result_type;
-};
-
-template< class Operations , class Fac , class Time >
-struct generic_rk_scale_sum< 7 , Operations , Fac , Time > : public Operations::template scale_sum8< Fac , Time >
-{
- generic_rk_scale_sum( const boost::array<Fac,7> &a , Time dt )
- : Operations::template scale_sum8< Fac , Time >( 1.0 , a[0]*dt , a[1]*dt , a[2]*dt , a[3]*dt , a[4]*dt , a[5]*dt , a[6]*dt )
- { }
-
- typedef void result_type;
-};
-
-template< class Operations , class Fac , class Time >
-struct generic_rk_scale_sum< 8 , Operations , Fac , Time > : public Operations::template scale_sum9< Fac , Time >
-{
- generic_rk_scale_sum( const boost::array<Fac,8> &a , Time dt )
- : Operations::template scale_sum9< Fac , Time >( 1.0 , a[0]*dt , a[1]*dt , a[2]*dt , a[3]*dt , a[4]*dt ,
- a[5]*dt , a[6]*dt , a[7]*dt )
- { }
-
- typedef void result_type;
-};
-
-template< class Operations , class Fac , class Time >
-struct generic_rk_scale_sum< 9 , Operations , Fac , Time > : public Operations::template scale_sum10< Fac , Time >
-{
- generic_rk_scale_sum( const boost::array<Fac,9> &a , Time dt )
- : Operations::template scale_sum10< Fac , Time >( 1.0 , a[0]*dt , a[1]*dt , a[2]*dt , a[3]*dt , a[4]*dt ,
- a[5]*dt , a[6]*dt , a[7]*dt , a[8]*dt )
- { }
-
- typedef void result_type;
-};
-
-template< class Operations , class Fac , class Time >
-struct generic_rk_scale_sum< 10 , Operations , Fac , Time > : public Operations::template scale_sum11< Fac , Time >
-{
- generic_rk_scale_sum( const boost::array<Fac,10> &a , Time dt )
- : Operations::template scale_sum11< Fac , Time >( 1.0 , a[0]*dt , a[1]*dt , a[2]*dt , a[3]*dt , a[4]*dt ,
- a[5]*dt , a[6]*dt , a[7]*dt , a[8]*dt , a[9]*dt )
- { }
-
- typedef void result_type;
-};
-
-template< class Operations , class Fac , class Time >
-struct generic_rk_scale_sum< 11 , Operations , Fac , Time > : public Operations::template scale_sum12< Fac , Time >
-{
- generic_rk_scale_sum( const boost::array<Fac,11> &a , Time dt )
- : Operations::template scale_sum12< Fac , Time >( 1.0 , a[0]*dt , a[1]*dt , a[2]*dt , a[3]*dt , a[4]*dt ,
- a[5]*dt , a[6]*dt , a[7]*dt , a[8]*dt , a[9]*dt , a[10]*dt )
- { }
-
- typedef void result_type;
-};
-
-template< class Operations , class Fac , class Time >
-struct generic_rk_scale_sum< 12 , Operations , Fac , Time > : public Operations::template scale_sum13< Fac , Time >
-{
- generic_rk_scale_sum( const boost::array<Fac,12> &a , Time dt )
- : Operations::template scale_sum13< Fac , Time >( 1.0 , a[0]*dt , a[1]*dt , a[2]*dt , a[3]*dt , a[4]*dt ,
- a[5]*dt , a[6]*dt , a[7]*dt , a[8]*dt , a[9]*dt , a[10]*dt , a[11]*dt )
- { }
-
- typedef void result_type;
-};
-
-template< class Operations , class Fac , class Time >
-struct generic_rk_scale_sum< 13 , Operations , Fac , Time > : public Operations::template scale_sum14< Fac , Time >
-{
- generic_rk_scale_sum( const boost::array<Fac,13> &a , Time dt )
- : Operations::template scale_sum14< Fac , Time >( 1.0 , a[0]*dt , a[1]*dt , a[2]*dt , a[3]*dt , a[4]*dt ,
- a[5]*dt , a[6]*dt , a[7]*dt , a[8]*dt , a[9]*dt , a[10]*dt , a[11]*dt , a[12]*dt )
- { }
-
- typedef void result_type;
-};
-
-
-// for error estimates
-template< size_t StageNumber , class Operations , class Fac , class Time >
-struct generic_rk_scale_sum_err;
-
-template< class Operations , class Fac , class Time >
-struct generic_rk_scale_sum_err< 1 , Operations , Fac , Time > : public Operations::template scale_sum1< Time >
-{
- generic_rk_scale_sum_err( const boost::array<Fac,1> &a , Time dt ) : Operations::template scale_sum1< Time >( a[0]*dt )
- { }
-
- typedef void result_type;
-};
-
-
-template< class Operations , class Fac , class Time >
-struct generic_rk_scale_sum_err< 2 , Operations , Fac , Time > : public Operations::template scale_sum2< Time >
-{
- generic_rk_scale_sum_err( const boost::array<Fac,2> &a , Time dt )
- : Operations::template scale_sum2< Time >( a[0]*dt , a[1]*dt )
- { }
-
- typedef void result_type;
-};
-
-template< class Operations , class Fac , class Time >
-struct generic_rk_scale_sum_err< 3 , Operations , Fac , Time > : public Operations::template scale_sum3< Time >
-{
- generic_rk_scale_sum_err( const boost::array<Fac,3> &a , Time dt )
- : Operations::template scale_sum3< Time >( a[0]*dt , a[1]*dt , a[2]*dt )
- { }
-
- typedef void result_type;
-};
-
-template< class Operations , class Fac , class Time >
-struct generic_rk_scale_sum_err< 4 , Operations , Fac , Time > : public Operations::template scale_sum4< Time >
-{
- generic_rk_scale_sum_err( const boost::array<Fac,4> &a , Time dt )
- : Operations::template scale_sum4< Time >( a[0]*dt , a[1]*dt , a[2]*dt , a[3]*dt )
- { }
-
- typedef void result_type;
-};
-
-template< class Operations , class Fac , class Time >
-struct generic_rk_scale_sum_err< 5 , Operations , Fac , Time > : public Operations::template scale_sum5< Fac >
-{
- generic_rk_scale_sum_err( const boost::array<Fac,5> &a , Time dt )
- : Operations::template scale_sum5< Time >( a[0]*dt , a[1]*dt , a[2]*dt , a[3]*dt , a[4]*dt )
- { }
-
- typedef void result_type;
-};
-
-
-template< class Operations , class Fac , class Time >
-struct generic_rk_scale_sum_err< 6 , Operations , Fac , Time > : public Operations::template scale_sum6< Time >
-{
- generic_rk_scale_sum_err( const boost::array<Fac,6> &a , Time dt )
- : Operations::template scale_sum6< Time >( a[0]*dt , a[1]*dt , a[2]*dt , a[3]*dt , a[4]*dt , a[5]*dt )
- { }
-
- typedef void result_type;
-};
-
-
-// for rk87
-template< class Operations , class Fac , class Time >
-struct generic_rk_scale_sum_err< 13 , Operations , Fac , Time > : public Operations::template scale_sum13< Time >
-{
- generic_rk_scale_sum_err( const boost::array<Fac,13> &a , Time dt )
- : Operations::template scale_sum13< Time >( a[0]*dt , a[1]*dt , a[2]*dt , a[3]*dt , a[4]*dt , a[5]*dt ,
- a[6]*dt , a[7]*dt , a[8]*dt , a[9]*dt , a[10]*dt , a[11]*dt , a[12]*dt )
- { }
-
- typedef void result_type;
-};
-
-
-}
-}
-}
-}
-
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_DETAIL_GENERIC_RK_OPERATIONS_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/detail/rotating_buffer.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/detail/rotating_buffer.hpp
deleted file mode 100644
index 2338afd94a22bbd262e9587aab72fd466842dcf2..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/detail/rotating_buffer.hpp
+++ /dev/null
@@ -1,84 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/detail/rotating_buffer.hpp
-
- [begin_description]
- Implemetation of a rotating (cyclic) buffer for use in the Adam Bashforth stepper
- [end_description]
-
- Copyright 2011 Karsten Ahnert
- Copyright 2011 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_DETAIL_ROTATING_BUFFER_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_DETAIL_ROTATING_BUFFER_HPP_INCLUDED
-
-#include <boost/array.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-namespace detail {
-
-template< class T , size_t N >
-class rotating_buffer
-{
-public:
-
- typedef T value_type;
- const static size_t dim = N;
-
- rotating_buffer( void ) : m_first( 0 )
- { }
-
- size_t size( void ) const
- {
- return dim;
- }
-
- value_type& operator[]( size_t i )
- {
- return m_data[ get_index( i ) ];
- }
-
- const value_type& operator[]( size_t i ) const
- {
- return m_data[ get_index( i ) ];
- }
-
- void rotate( void )
- {
- if( m_first == 0 )
- m_first = dim-1;
- else
- --m_first;
- }
-
-protected:
-
- value_type m_data[N];
-
-private:
-
- size_t get_index( size_t i ) const
- {
- return ( ( i + m_first ) % dim );
- }
-
- size_t m_first;
-
-};
-
-
-} // detail
-} // odeint
-} // numeric
-} // boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_DETAIL_ROTATING_BUFFER_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/euler.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/euler.hpp
deleted file mode 100644
index 4941379d6c64de2f8980102e40fc29f6a5f612a1..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/euler.hpp
+++ /dev/null
@@ -1,166 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/euler.hpp
-
- [begin_description]
- Implementation of the classical explicit Euler stepper. This method is really simple and should only
- be used for demonstration purposes.
- [end_description]
-
- Copyright 2010-2013 Karsten Ahnert
- Copyright 2010-2013 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_EULER_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_EULER_HPP_INCLUDED
-
-
-#include <boost/numeric/odeint/stepper/base/explicit_stepper_base.hpp>
-#include <boost/numeric/odeint/util/resizer.hpp>
-#include <boost/numeric/odeint/algebra/range_algebra.hpp>
-#include <boost/numeric/odeint/algebra/default_operations.hpp>
-#include <boost/numeric/odeint/algebra/algebra_dispatcher.hpp>
-#include <boost/numeric/odeint/algebra/operations_dispatcher.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-template<
-class State ,
-class Value = double ,
-class Deriv = State ,
-class Time = Value ,
-class Algebra = typename algebra_dispatcher< State >::algebra_type ,
-class Operations = typename operations_dispatcher< State >::operations_type ,
-class Resizer = initially_resizer
->
-#ifndef DOXYGEN_SKIP
-class euler
-: public explicit_stepper_base<
- euler< State , Value , Deriv , Time , Algebra , Operations , Resizer > ,
- 1 , State , Value , Deriv , Time , Algebra , Operations , Resizer >
-#else
-class euler : public explicit_stepper_base
-#endif
-{
-public :
-
- #ifndef DOXYGEN_SKIP
- typedef explicit_stepper_base< euler< State , Value , Deriv , Time , Algebra , Operations , Resizer > , 1 , State , Value , Deriv , Time , Algebra , Operations , Resizer > stepper_base_type;
- #else
- typedef explicit_stepper_base< euler< ... > , ... > stepper_base_type;
- #endif
- typedef typename stepper_base_type::state_type state_type;
- typedef typename stepper_base_type::value_type value_type;
- typedef typename stepper_base_type::deriv_type deriv_type;
- typedef typename stepper_base_type::time_type time_type;
- typedef typename stepper_base_type::algebra_type algebra_type;
- typedef typename stepper_base_type::operations_type operations_type;
- typedef typename stepper_base_type::resizer_type resizer_type;
-
- #ifndef DOXYGEN_SKIP
- typedef typename stepper_base_type::stepper_type stepper_type;
- typedef typename stepper_base_type::wrapped_state_type wrapped_state_type;
- typedef typename stepper_base_type::wrapped_deriv_type wrapped_deriv_type;
- #endif
-
-
- euler( const algebra_type &algebra = algebra_type() ) : stepper_base_type( algebra )
- { }
-
- template< class System , class StateIn , class DerivIn , class StateOut >
- void do_step_impl( System /* system */ , const StateIn &in , const DerivIn &dxdt , time_type /* t */ , StateOut &out , time_type dt )
- {
- stepper_base_type::m_algebra.for_each3( out , in , dxdt ,
- typename operations_type::template scale_sum2< value_type , time_type >( 1.0 , dt ) );
-
- }
-
- template< class StateOut , class StateIn1 , class StateIn2 >
- void calc_state( StateOut &x , time_type t , const StateIn1 &old_state , time_type t_old , const StateIn2 & /*current_state*/ , time_type /* t_new */ ) const
- {
- const time_type delta = t - t_old;
- stepper_base_type::m_algebra.for_each3( x , old_state , stepper_base_type::m_dxdt.m_v ,
- typename operations_type::template scale_sum2< value_type , time_type >( 1.0 , delta ) );
- }
-
- template< class StateType >
- void adjust_size( const StateType &x )
- {
- stepper_base_type::adjust_size( x );
- }
-};
-
-
-
-/********** DOXYGEN ***********/
-
-/**
- * \class euler
- * \brief An implementation of the Euler method.
- *
- * The Euler method is a very simply solver for ordinary differential equations. This method should not be used
- * for real applications. It is only useful for demonstration purposes. Step size control is not provided but
- * trivial continuous output is available.
- *
- * This class derives from explicit_stepper_base and inherits its interface via CRTP (current recurring template pattern),
- * see explicit_stepper_base
- *
- * \tparam State The state type.
- * \tparam Value The value type.
- * \tparam Deriv The type representing the time derivative of the state.
- * \tparam Time The time representing the independent variable - the time.
- * \tparam Algebra The algebra type.
- * \tparam Operations The operations type.
- * \tparam Resizer The resizer policy type.
- */
-
- /**
- * \fn euler::euler( const algebra_type &algebra )
- * \brief Constructs the euler class. This constructor can be used as a default
- * constructor of the algebra has a default constructor.
- * \param algebra A copy of algebra is made and stored inside explicit_stepper_base.
- */
-
- /**
- * \fn euler::do_step_impl( System system , const StateIn &in , const DerivIn &dxdt , time_type t , StateOut &out , time_type dt )
- * \brief This method performs one step. The derivative `dxdt` of `in` at the time `t` is passed to the method.
- * The result is updated out of place, hence the input is in `in` and the output in `out`.
- * Access to this step functionality is provided by explicit_stepper_base and
- * `do_step_impl` should not be called directly.
- *
- * \param system The system function to solve, hence the r.h.s. of the ODE. It must fulfill the
- * Simple System concept.
- * \param in The state of the ODE which should be solved. in is not modified in this method
- * \param dxdt The derivative of x at t.
- * \param t The value of the time, at which the step should be performed.
- * \param out The result of the step is written in out.
- * \param dt The step size.
- */
-
-
- /**
- * \fn euler::calc_state( StateOut &x , time_type t , const StateIn1 &old_state , time_type t_old , const StateIn2 ¤t_state , time_type t_new ) const
- * \brief This method is used for continuous output and it calculates the state `x` at a time `t` from the
- * knowledge of two states `old_state` and `current_state` at time points `t_old` and `t_new`.
- */
-
- /**
- * \fn euler::adjust_size( const StateType &x )
- * \brief Adjust the size of all temporaries in the stepper manually.
- * \param x A state from which the size of the temporaries to be resized is deduced.
- */
-
-} // odeint
-} // numeric
-} // boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_EULER_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/explicit_error_generic_rk.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/explicit_error_generic_rk.hpp
deleted file mode 100644
index cf028d8b07fb87d3b86d95acb02765b7caae8a37..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/explicit_error_generic_rk.hpp
+++ /dev/null
@@ -1,255 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/explicit_error_generic_rk.hpp
-
- [begin_description]
- Implementation of the generic Runge Kutta error stepper. Base class for many RK error steppers.
- [end_description]
-
- Copyright 2011-2013 Mario Mulansky
- Copyright 2011-2013 Karsten Ahnert
- Copyright 2012 Christoph Koke
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_EXPLICIT_ERROR_GENERIC_RK_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_EXPLICIT_ERROR_GENERIC_RK_HPP_INCLUDED
-
-#include <boost/numeric/odeint/stepper/base/explicit_error_stepper_base.hpp>
-
-#include <boost/numeric/odeint/algebra/default_operations.hpp>
-#include <boost/numeric/odeint/algebra/range_algebra.hpp>
-#include <boost/numeric/odeint/algebra/algebra_dispatcher.hpp>
-#include <boost/numeric/odeint/algebra/operations_dispatcher.hpp>
-#include <boost/numeric/odeint/stepper/detail/generic_rk_algorithm.hpp>
-#include <boost/numeric/odeint/stepper/detail/generic_rk_call_algebra.hpp>
-#include <boost/numeric/odeint/stepper/detail/generic_rk_operations.hpp>
-
-#include <boost/numeric/odeint/util/state_wrapper.hpp>
-#include <boost/numeric/odeint/util/is_resizeable.hpp>
-#include <boost/numeric/odeint/util/resizer.hpp>
-
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-template<
-size_t StageCount,
-size_t Order,
-size_t StepperOrder ,
-size_t ErrorOrder ,
-class State ,
-class Value = double ,
-class Deriv = State ,
-class Time = Value ,
-class Algebra = typename algebra_dispatcher< State >::algebra_type ,
-class Operations = typename operations_dispatcher< State >::operations_type ,
-class Resizer = initially_resizer
->
-#ifndef DOXYGEN_SKIP
-class explicit_error_generic_rk
-: public explicit_error_stepper_base<
- explicit_error_generic_rk< StageCount , Order , StepperOrder , ErrorOrder , State ,
- Value , Deriv , Time , Algebra , Operations , Resizer > ,
- Order , StepperOrder , ErrorOrder , State , Value , Deriv , Time , Algebra ,
- Operations , Resizer >
-#else
-class explicit_error_generic_rk : public explicit_error_stepper_base
-#endif
-{
-
-public:
-#ifndef DOXYGEN_SKIP
- typedef explicit_error_stepper_base<
- explicit_error_generic_rk< StageCount , Order , StepperOrder , ErrorOrder , State ,
- Value , Deriv , Time , Algebra , Operations , Resizer > ,
- Order , StepperOrder , ErrorOrder , State , Value , Deriv , Time , Algebra ,
- Operations , Resizer > stepper_base_type;
-#else
- typedef explicit_stepper_base< ... > stepper_base_type;
-#endif
- typedef typename stepper_base_type::state_type state_type;
- typedef typename stepper_base_type::wrapped_state_type wrapped_state_type;
- typedef typename stepper_base_type::value_type value_type;
- typedef typename stepper_base_type::deriv_type deriv_type;
- typedef typename stepper_base_type::wrapped_deriv_type wrapped_deriv_type;
- typedef typename stepper_base_type::time_type time_type;
- typedef typename stepper_base_type::algebra_type algebra_type;
- typedef typename stepper_base_type::operations_type operations_type;
- typedef typename stepper_base_type::resizer_type resizer_type;
-#ifndef DOXYGEN_SKIP
- typedef explicit_error_generic_rk< StageCount , Order , StepperOrder , ErrorOrder , State ,
- Value , Deriv , Time , Algebra , Operations , Resizer > stepper_type;
-#endif
- typedef detail::generic_rk_algorithm< StageCount , Value , Algebra , Operations > rk_algorithm_type;
-
- typedef typename rk_algorithm_type::coef_a_type coef_a_type;
- typedef typename rk_algorithm_type::coef_b_type coef_b_type;
- typedef typename rk_algorithm_type::coef_c_type coef_c_type;
-
- static const size_t stage_count = StageCount;
-
-private:
-
-
-public:
-
- // we use an explicit_generic_rk to do the normal rk step
- // and add a separate calculation of the error estimate afterwards
- explicit_error_generic_rk( const coef_a_type &a ,
- const coef_b_type &b ,
- const coef_b_type &b2 ,
- const coef_c_type &c ,
- const algebra_type &algebra = algebra_type() )
- : stepper_base_type( algebra ) , m_rk_algorithm( a , b , c ) , m_b2( b2 )
- { }
-
-
- template< class System , class StateIn , class DerivIn , class StateOut , class Err >
- void do_step_impl( System system , const StateIn &in , const DerivIn &dxdt ,
- time_type t , StateOut &out , time_type dt , Err &xerr )
- {
- // normal step
- do_step_impl( system , in , dxdt , t , out , dt );
-
- // additionally, perform the error calculation
- detail::template generic_rk_call_algebra< StageCount , algebra_type >()( stepper_base_type::m_algebra ,
- xerr , dxdt , m_F , detail::generic_rk_scale_sum_err< StageCount , operations_type , value_type , time_type >( m_b2 , dt) );
- }
-
-
- template< class System , class StateIn , class DerivIn , class StateOut >
- void do_step_impl( System system , const StateIn &in , const DerivIn &dxdt ,
- time_type t , StateOut &out , time_type dt )
- {
- m_resizer.adjust_size( in , detail::bind( &stepper_type::template resize_impl< StateIn > , detail::ref( *this ) , detail::_1 ) );
-
- // actual calculation done in generic_rk.hpp
- m_rk_algorithm.do_step( stepper_base_type::m_algebra , system , in , dxdt , t , out , dt , m_x_tmp.m_v , m_F );
- }
-
-
- template< class StateIn >
- void adjust_size( const StateIn &x )
- {
- resize_impl( x );
- stepper_base_type::adjust_size( x );
- }
-
-
-private:
-
- template< class StateIn >
- bool resize_impl( const StateIn &x )
- {
- bool resized( false );
- resized |= adjust_size_by_resizeability( m_x_tmp , x , typename is_resizeable<state_type>::type() );
- for( size_t i = 0 ; i < StageCount-1 ; ++i )
- {
- resized |= adjust_size_by_resizeability( m_F[i] , x , typename is_resizeable<deriv_type>::type() );
- }
- return resized;
- }
-
-
- rk_algorithm_type m_rk_algorithm;
- coef_b_type m_b2;
-
- resizer_type m_resizer;
-
- wrapped_state_type m_x_tmp;
- wrapped_deriv_type m_F[StageCount-1];
-
-};
-
-
-/********* DOXYGEN *********/
-
-/**
- * \class explicit_error_generic_rk
- * \brief A generic implementation of explicit Runge-Kutta algorithms with error estimation. This class is as a
- * base class for all explicit Runge-Kutta steppers with error estimation.
- *
- * This class implements the explicit Runge-Kutta algorithms with error estimation in a generic way.
- * The Butcher tableau is passed to the stepper which constructs the stepper scheme with the help of a
- * template-metaprogramming algorithm. ToDo : Add example!
- *
- * This class derives explicit_error_stepper_base which provides the stepper interface.
- *
- * \tparam StageCount The number of stages of the Runge-Kutta algorithm.
- * \tparam Order The order of a stepper if the stepper is used without error estimation.
- * \tparam StepperOrder The order of a step if the stepper is used with error estimation. Usually Order and StepperOrder have
- * the same value.
- * \tparam ErrorOrder The order of the error step if the stepper is used with error estimation.
- * \tparam State The type representing the state of the ODE.
- * \tparam Value The floating point type which is used in the computations.
- * \tparam Time The type representing the independent variable - the time - of the ODE.
- * \tparam Algebra The algebra type.
- * \tparam Operations The operations type.
- * \tparam Resizer The resizer policy type.
- */
-
-
- /**
- * \fn explicit_error_generic_rk::explicit_error_generic_rk( const coef_a_type &a , const coef_b_type &b , const coef_b_type &b2 , const coef_c_type &c , const algebra_type &algebra )
- * \brief Constructs the explicit_error_generik_rk class with the given parameters a, b, b2 and c. See examples section for details on the coefficients.
- *
- * \param a Triangular matrix of parameters b in the Butcher tableau.
- * \param b Last row of the butcher tableau.
- * \param b2 Parameters for lower-order evaluation to estimate the error.
- * \param c Parameters to calculate the time points in the Butcher tableau.
- * \param algebra A copy of algebra is made and stored inside explicit_stepper_base.
- */
-
-
- /**
- * \fn explicit_error_generic_rk::do_step_impl( System system , const StateIn &in , const DerivIn &dxdt , time_type t , StateOut &out , time_type dt , Err &xerr )
- * \brief This method performs one step. The derivative `dxdt` of `in` at the time `t` is passed to the method.
- * The result is updated out-of-place, hence the input is in `in` and the output in `out`. Futhermore, an
- * estimation of the error is stored in `xerr`. `do_step_impl` is used by explicit_error_stepper_base.
- *
- * \param system The system function to solve, hence the r.h.s. of the ODE. It must fulfill the
- * Simple System concept.
- * \param in The state of the ODE which should be solved. in is not modified in this method
- * \param dxdt The derivative of x at t.
- * \param t The value of the time, at which the step should be performed.
- * \param out The result of the step is written in out.
- * \param dt The step size.
- * \param xerr The result of the error estimation is written in xerr.
- */
-
- /**
- * \fn explicit_error_generic_rk::do_step_impl( System system , const StateIn &in , const DerivIn &dxdt , time_type t , StateOut &out , time_type dt )
- * \brief This method performs one step. The derivative `dxdt` of `in` at the time `t` is passed to the method.
- * The result is updated out-of-place, hence the input is in `in` and the output in `out`.
- * Access to this step functionality is provided by explicit_stepper_base and
- * `do_step_impl` should not be called directly.
- *
- * \param system The system function to solve, hence the r.h.s. of the ODE. It must fulfill the
- * Simple System concept.
- * \param in The state of the ODE which should be solved. in is not modified in this method
- * \param dxdt The derivative of x at t.
- * \param t The value of the time, at which the step should be performed.
- * \param out The result of the step is written in out.
- * \param dt The step size.
- */
-
- /**
- * \fn explicit_error_generic_rk::adjust_size( const StateIn &x )
- * \brief Adjust the size of all temporaries in the stepper manually.
- * \param x A state from which the size of the temporaries to be resized is deduced.
- */
-
-}
-}
-}
-
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_EXPLICIT_ERROR_GENERIC_RK_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/explicit_generic_rk.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/explicit_generic_rk.hpp
deleted file mode 100644
index 620c8b733f22be53eefce5abb79f7ee32c31aa70..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/explicit_generic_rk.hpp
+++ /dev/null
@@ -1,246 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/explicit_generic_rk.hpp
-
- [begin_description]
- Implementation of the generic Runge-Kutta steppers. This is the base class for many Runge-Kutta steppers.
- [end_description]
-
- Copyright 2011-2013 Mario Mulansky
- Copyright 2011-2013 Karsten Ahnert
- Copyright 2012 Christoph Koke
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_EXPLICIT_GENERIC_RK_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_EXPLICIT_GENERIC_RK_HPP_INCLUDED
-
-
-#include <boost/array.hpp>
-
-
-#include <boost/numeric/odeint/stepper/base/explicit_stepper_base.hpp>
-#include <boost/numeric/odeint/algebra/range_algebra.hpp>
-#include <boost/numeric/odeint/algebra/default_operations.hpp>
-#include <boost/numeric/odeint/algebra/algebra_dispatcher.hpp>
-#include <boost/numeric/odeint/algebra/operations_dispatcher.hpp>
-#include <boost/numeric/odeint/stepper/detail/generic_rk_algorithm.hpp>
-
-#include <boost/numeric/odeint/util/state_wrapper.hpp>
-#include <boost/numeric/odeint/util/is_resizeable.hpp>
-#include <boost/numeric/odeint/util/resizer.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-//forward declarations
-
-#ifndef DOXYGEN_SKIP
-template<
-size_t StageCount,
-size_t Order,
-class State ,
-class Value = double ,
-class Deriv = State ,
-class Time = Value ,
-class Algebra = typename algebra_dispatcher< State >::algebra_type ,
-class Operations = typename operations_dispatcher< State >::operations_type ,
-class Resizer = initially_resizer
->
-class explicit_generic_rk;
-
-
-struct stage_vector;
-
-template< class T , class Constant >
-struct array_wrapper
-{
- typedef const typename boost::array< T , Constant::value > type;
-};
-
-template< class T , size_t i >
-struct stage
-{
- T c;
- boost::array< T , i > a;
-};
-
-
-template< class T , class Constant >
-struct stage_wrapper
-{
- typedef stage< T , Constant::value > type;
-};
-#endif
-
-
-template<
-size_t StageCount,
-size_t Order,
-class State ,
-class Value ,
-class Deriv ,
-class Time ,
-class Algebra ,
-class Operations ,
-class Resizer
->
-#ifndef DOXYGEN_SKIP
-class explicit_generic_rk : public explicit_stepper_base<
-explicit_generic_rk< StageCount , Order , State , Value , Deriv , Time , Algebra , Operations , Resizer > ,
-Order , State , Value , Deriv , Time , Algebra , Operations , Resizer >
-#else
-class explicit_generic_rk : public explicit_stepper_base
-#endif
-{
-
-public:
-
- #ifndef DOXYGEN_SKIP
- typedef explicit_stepper_base<
- explicit_generic_rk< StageCount , Order , State , Value , Deriv ,Time , Algebra , Operations , Resizer > ,
- Order , State , Value , Deriv , Time , Algebra ,
- Operations , Resizer > stepper_base_type;
- #else
- typedef explicit_stepper_base< ... > stepper_base_type;
- #endif
-
- typedef typename stepper_base_type::state_type state_type;
- typedef typename stepper_base_type::wrapped_state_type wrapped_state_type;
- typedef typename stepper_base_type::value_type value_type;
- typedef typename stepper_base_type::deriv_type deriv_type;
- typedef typename stepper_base_type::wrapped_deriv_type wrapped_deriv_type;
- typedef typename stepper_base_type::time_type time_type;
- typedef typename stepper_base_type::algebra_type algebra_type;
- typedef typename stepper_base_type::operations_type operations_type;
- typedef typename stepper_base_type::resizer_type resizer_type;
-
- #ifndef DOXYGEN_SKIP
- typedef explicit_generic_rk< StageCount , Order , State , Value , Deriv ,Time , Algebra , Operations , Resizer > stepper_type;
- #endif
-
- typedef detail::generic_rk_algorithm< StageCount , Value , Algebra , Operations > rk_algorithm_type;
-
- typedef typename rk_algorithm_type::coef_a_type coef_a_type;
- typedef typename rk_algorithm_type::coef_b_type coef_b_type;
- typedef typename rk_algorithm_type::coef_c_type coef_c_type;
-
- #ifndef DOXYGEN_SKIP
- static const size_t stage_count = StageCount;
- #endif
-
-public:
-
- explicit_generic_rk( const coef_a_type &a , const coef_b_type &b , const coef_c_type &c ,
- const algebra_type &algebra = algebra_type() )
- : stepper_base_type( algebra ) , m_rk_algorithm( a , b , c )
- { }
-
-
- template< class System , class StateIn , class DerivIn , class StateOut >
- void do_step_impl( System system , const StateIn &in , const DerivIn &dxdt ,
- time_type t , StateOut &out , time_type dt )
- {
- m_resizer.adjust_size( in , detail::bind( &stepper_type::template resize_impl< StateIn > , detail::ref( *this ) , detail::_1 ) );
-
- // actual calculation done in generic_rk.hpp
- m_rk_algorithm.do_step( stepper_base_type::m_algebra , system , in , dxdt , t , out , dt , m_x_tmp.m_v , m_F );
- }
-
- template< class StateIn >
- void adjust_size( const StateIn &x )
- {
- resize_impl( x );
- stepper_base_type::adjust_size( x );
- }
-
-private:
-
- template< class StateIn >
- bool resize_impl( const StateIn &x )
- {
- bool resized( false );
- resized |= adjust_size_by_resizeability( m_x_tmp , x , typename is_resizeable<state_type>::type() );
- for( size_t i = 0 ; i < StageCount-1 ; ++i )
- {
- resized |= adjust_size_by_resizeability( m_F[i] , x , typename is_resizeable<deriv_type>::type() );
- }
- return resized;
- }
-
-
- rk_algorithm_type m_rk_algorithm;
-
- resizer_type m_resizer;
-
- wrapped_state_type m_x_tmp;
- wrapped_deriv_type m_F[StageCount-1];
-
-};
-
-
-
-/*********** DOXYGEN *************/
-
-/**
- * \class explicit_generic_rk
- * \brief A generic implementation of explicit Runge-Kutta algorithms. This class is as a base class
- * for all explicit Runge-Kutta steppers.
- *
- * This class implements the explicit Runge-Kutta algorithms without error estimation in a generic way.
- * The Butcher tableau is passed to the stepper which constructs the stepper scheme with the help of a
- * template-metaprogramming algorithm. ToDo : Add example!
- *
- * This class derives explicit_stepper_base which provides the stepper interface.
- *
- * \tparam StageCount The number of stages of the Runge-Kutta algorithm.
- * \tparam Order The order of the stepper.
- * \tparam State The type representing the state of the ODE.
- * \tparam Value The floating point type which is used in the computations.
- * \tparam Time The type representing the independent variable - the time - of the ODE.
- * \tparam Algebra The algebra type.
- * \tparam Operations The operations type.
- * \tparam Resizer The resizer policy type.
- */
-
- /**
- * \fn explicit_generic_rk::explicit_generic_rk( const coef_a_type &a , const coef_b_type &b , const coef_c_type &c , const algebra_type &algebra )
- * \brief Constructs the explicit_generic_rk class. See examples section for details on the coefficients.
- * \param a Triangular matrix of parameters b in the Butcher tableau.
- * \param b Last row of the butcher tableau.
- * \param c Parameters to calculate the time points in the Butcher tableau.
- * \param algebra A copy of algebra is made and stored inside explicit_stepper_base.
- */
-
- /**
- * \fn explicit_generic_rk::do_step_impl( System system , const StateIn &in , const DerivIn &dxdt , time_type t , StateOut &out , time_type dt )
- * \brief This method performs one step. The derivative `dxdt` of `in` at the time `t` is passed to the method.
- * The result is updated out of place, hence the input is in `in` and the output in `out`.
- * Access to this step functionality is provided by explicit_stepper_base and
- * `do_step_impl` should not be called directly.
- *
- * \param system The system function to solve, hence the r.h.s. of the ODE. It must fulfill the
- * Simple System concept.
- * \param in The state of the ODE which should be solved. in is not modified in this method
- * \param dxdt The derivative of x at t.
- * \param t The value of the time, at which the step should be performed.
- * \param out The result of the step is written in out.
- * \param dt The step size.
- */
-
-
- /**
- * \fn explicit_generic_rk::adjust_size( const StateIn &x )
- * \brief Adjust the size of all temporaries in the stepper manually.
- * \param x A state from which the size of the temporaries to be resized is deduced.
- */
-
-}
-}
-}
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_EXPLICIT_GENERIC_RK_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/extrapolation_stepper.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/extrapolation_stepper.hpp
deleted file mode 100644
index 3b688e958baf15d005d9b4d5d7d1a2e4c64f6982..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/extrapolation_stepper.hpp
+++ /dev/null
@@ -1,293 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/extrapolation_stepper.hpp
-
- [begin_description]
- extrapolation stepper
- [end_description]
-
- Copyright 2009-2015 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
-*/
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_EXTRAPOLATION_STEPPER_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_EXTRAPOLATION_STEPPER_HPP_INCLUDED
-
-#include <iostream>
-
-#include <algorithm>
-
-#include <boost/config.hpp> // for min/max guidelines
-#include <boost/static_assert.hpp>
-
-#include <boost/numeric/odeint/util/bind.hpp>
-#include <boost/numeric/odeint/util/unwrap_reference.hpp>
-
-#include <boost/numeric/odeint/stepper/base/explicit_error_stepper_base.hpp>
-#include <boost/numeric/odeint/stepper/modified_midpoint.hpp>
-#include <boost/numeric/odeint/stepper/controlled_step_result.hpp>
-#include <boost/numeric/odeint/algebra/range_algebra.hpp>
-#include <boost/numeric/odeint/algebra/default_operations.hpp>
-#include <boost/numeric/odeint/algebra/algebra_dispatcher.hpp>
-#include <boost/numeric/odeint/algebra/operations_dispatcher.hpp>
-
-#include <boost/numeric/odeint/util/state_wrapper.hpp>
-#include <boost/numeric/odeint/util/is_resizeable.hpp>
-#include <boost/numeric/odeint/util/resizer.hpp>
-#include <boost/numeric/odeint/util/unit_helper.hpp>
-#include <boost/numeric/odeint/util/detail/less_with_sign.hpp>
-
-namespace boost
-{
-namespace numeric
-{
-namespace odeint
-{
-
-template < unsigned short Order, class State, class Value = double,
- class Deriv = State, class Time = Value,
- class Algebra = typename algebra_dispatcher< State >::algebra_type,
- class Operations =
- typename operations_dispatcher< State >::operations_type,
- class Resizer = initially_resizer >
-#ifndef DOXYGEN_SKIP
-class extrapolation_stepper
- : public explicit_error_stepper_base<
- extrapolation_stepper< Order, State, Value, Deriv, Time, Algebra,
- Operations, Resizer >,
- Order, Order, Order - 2, State, Value, Deriv, Time, Algebra,
- Operations, Resizer >
-#else
-class extrapolation_stepper : public explicit_error_stepper_base
-#endif
-{
-
- private:
- // check for Order being odd
- BOOST_STATIC_ASSERT_MSG(
- ( ( Order % 2 ) == 0 ) && ( Order > 2 ),
- "extrapolation_stepper requires even Order larger than 2" );
-
- public:
-#ifndef DOXYGEN_SKIP
- typedef explicit_error_stepper_base<
- extrapolation_stepper< Order, State, Value, Deriv, Time, Algebra,
- Operations, Resizer >,
- Order, Order, Order - 2, State, Value, Deriv, Time, Algebra, Operations,
- Resizer > stepper_base_type;
-#else
- typedef explicit_error_stepper_base< extrapolation_stepper< ... >, ... >
- stepper_base_type;
-#endif
-
- typedef typename stepper_base_type::state_type state_type;
- typedef typename stepper_base_type::value_type value_type;
- typedef typename stepper_base_type::deriv_type deriv_type;
- typedef typename stepper_base_type::time_type time_type;
- typedef typename stepper_base_type::algebra_type algebra_type;
- typedef typename stepper_base_type::operations_type operations_type;
- typedef typename stepper_base_type::resizer_type resizer_type;
-
-#ifndef DOXYGEN_SKIP
- typedef typename stepper_base_type::stepper_type stepper_type;
- typedef typename stepper_base_type::wrapped_state_type wrapped_state_type;
- typedef typename stepper_base_type::wrapped_deriv_type wrapped_deriv_type;
-
- typedef std::vector< value_type > value_vector;
- typedef std::vector< value_vector > value_matrix;
- typedef std::vector< size_t > int_vector;
- typedef std::vector< wrapped_state_type > state_table_type;
- typedef modified_midpoint< state_type, value_type, deriv_type, time_type,
- algebra_type, operations_type,
- resizer_type > midpoint_stepper_type;
-
-#endif // DOXYGEN_SKIP
-
- typedef unsigned short order_type;
- static const order_type order_value = stepper_base_type::order_value;
- static const order_type stepper_order_value =
- stepper_base_type::stepper_order_value;
- static const order_type error_order_value =
- stepper_base_type::error_order_value;
-
- const static size_t m_k_max = ( order_value - 2 ) / 2;
-
- extrapolation_stepper( const algebra_type &algebra = algebra_type() )
- : stepper_base_type( algebra ), m_interval_sequence( m_k_max + 1 ),
- m_coeff( m_k_max + 1 ), m_table( m_k_max )
- {
- for ( unsigned short i = 0; i < m_k_max + 1; i++ )
- {
- m_interval_sequence[i] = 2 * ( i + 1 );
- m_coeff[i].resize( i );
- for ( size_t k = 0; k < i; ++k )
- {
- const value_type r =
- static_cast< value_type >( m_interval_sequence[i] ) /
- static_cast< value_type >( m_interval_sequence[k] );
- m_coeff[i][k] =
- static_cast< value_type >( 1 ) /
- ( r * r - static_cast< value_type >(
- 1 ) ); // coefficients for extrapolation
- }
- }
- }
-
- template < class System, class StateIn, class DerivIn, class StateOut,
- class Err >
- void do_step_impl( System system, const StateIn &in, const DerivIn &dxdt,
- time_type t, StateOut &out, time_type dt, Err &xerr )
- {
- // std::cout << "dt: " << dt << std::endl;
- // normal step
- do_step_impl( system, in, dxdt, t, out, dt );
-
- static const value_type val1( 1.0 );
- // additionally, perform the error calculation
- stepper_base_type::m_algebra.for_each3(
- xerr, out, m_table[0].m_v,
- typename operations_type::template scale_sum2<
- value_type, value_type >( val1, -val1 ) );
- }
-
- template < class System, class StateInOut, class DerivIn, class Err >
- void do_step_impl_io( System system, StateInOut &inout, const DerivIn &dxdt,
- time_type t, time_type dt, Err &xerr )
- {
- // normal step
- do_step_impl_io( system, inout, dxdt, t, dt );
-
- static const value_type val1( 1.0 );
- // additionally, perform the error calculation
- stepper_base_type::m_algebra.for_each3(
- xerr, inout, m_table[0].m_v,
- typename operations_type::template scale_sum2<
- value_type, value_type >( val1, -val1 ) );
- }
-
- template < class System, class StateIn, class DerivIn, class StateOut >
- void do_step_impl( System system, const StateIn &in, const DerivIn &dxdt,
- time_type t, StateOut &out, time_type dt )
- {
- m_resizer.adjust_size(
- in, detail::bind( &stepper_type::template resize_impl< StateIn >,
- detail::ref( *this ), detail::_1 ) );
- size_t k = 0;
- m_midpoint.set_steps( m_interval_sequence[k] );
- m_midpoint.do_step( system, in, dxdt, t, out, dt );
- for ( k = 1; k <= m_k_max; ++k )
- {
- m_midpoint.set_steps( m_interval_sequence[k] );
- m_midpoint.do_step( system, in, dxdt, t, m_table[k - 1].m_v, dt );
- extrapolate( k, m_table, m_coeff, out );
- }
- }
-
- template < class System, class StateInOut, class DerivIn >
- void do_step_impl_io( System system, StateInOut &inout, const DerivIn &dxdt,
- time_type t, time_type dt )
- {
- // special care for inout
- m_xout_resizer.adjust_size(
- inout,
- detail::bind( &stepper_type::template resize_m_xout< StateInOut >,
- detail::ref( *this ), detail::_1 ) );
- do_step_impl( system, inout, dxdt, t, m_xout.m_v, dt );
- boost::numeric::odeint::copy( m_xout.m_v, inout );
- }
-
- template < class System, class StateInOut, class DerivIn >
- void do_step_dxdt_impl( System system, StateInOut &x, const DerivIn &dxdt,
- time_type t, time_type dt )
- {
- do_step_impl_io( system , x , dxdt , t , dt );
- }
-
- template < class System, class StateIn, class DerivIn, class StateOut >
- void do_step_dxdt_impl( System system, const StateIn &in,
- const DerivIn &dxdt, time_type t, StateOut &out,
- time_type dt )
- {
- do_step_impl( system , in , dxdt , t , out , dt );
- }
-
-
- template < class StateIn > void adjust_size( const StateIn &x )
- {
- resize_impl( x );
- m_midpoint.adjust_size( x );
- }
-
- private:
- template < class StateIn > bool resize_impl( const StateIn &x )
- {
- bool resized( false );
- for ( size_t i = 0; i < m_k_max; ++i )
- resized |= adjust_size_by_resizeability(
- m_table[i], x, typename is_resizeable< state_type >::type() );
- return resized;
- }
-
- template < class StateIn > bool resize_m_xout( const StateIn &x )
- {
- return adjust_size_by_resizeability(
- m_xout, x, typename is_resizeable< state_type >::type() );
- }
-
- template < class StateInOut >
- void extrapolate( size_t k, state_table_type &table,
- const value_matrix &coeff, StateInOut &xest )
- /* polynomial extrapolation, see http://www.nr.com/webnotes/nr3web21.pdf
- uses the obtained intermediate results to extrapolate to dt->0
- */
- {
- static const value_type val1 = static_cast< value_type >( 1.0 );
-
- for ( int j = k - 1; j > 0; --j )
- {
- stepper_base_type::m_algebra.for_each3(
- table[j - 1].m_v, table[j].m_v, table[j - 1].m_v,
- typename operations_type::template scale_sum2<
- value_type, value_type >( val1 + coeff[k][j],
- -coeff[k][j] ) );
- }
- stepper_base_type::m_algebra.for_each3(
- xest, table[0].m_v, xest,
- typename operations_type::template scale_sum2<
- value_type, value_type >( val1 + coeff[k][0], -coeff[k][0] ) );
- }
-
- private:
- midpoint_stepper_type m_midpoint;
-
- resizer_type m_resizer;
- resizer_type m_xout_resizer;
-
- int_vector m_interval_sequence; // stores the successive interval counts
- value_matrix m_coeff;
-
- wrapped_state_type m_xout;
- state_table_type m_table; // sequence of states for extrapolation
-};
-
-/******** DOXYGEN *******/
-
-/**
- * \class extrapolation_stepper
- * \brief Extrapolation stepper with configurable order, and error estimation.
- *
- * The extrapolation stepper is a stepper with error estimation and configurable
- * order. The order is given as template parameter and needs to be an _odd_
- * number. The stepper is based on several executions of the modified midpoint
- * method and a Richardson extrapolation. This is essentially the same technique
- * as for bulirsch_stoer, but without the variable order.
- *
- * \note The Order parameter has to be an even number greater 2.
- */
-}
-}
-}
-#endif
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/generation.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/generation.hpp
deleted file mode 100644
index 90ad2b9a76f500b74b961d40ad2ba8968fc07287..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/generation.hpp
+++ /dev/null
@@ -1,36 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/generation.hpp
-
- [begin_description]
- Forward header for the factory functions. Includes all files from the generation directory.
- [end_description]
-
- Copyright 2011 Karsten Ahnert
- Copyright 2011 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_GENERATION_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_GENERATION_HPP_INCLUDED
-
-#include <boost/numeric/odeint/stepper/generation/make_controlled.hpp>
-#include <boost/numeric/odeint/stepper/generation/make_dense_output.hpp>
-
-#include <boost/numeric/odeint/stepper/generation/generation_controlled_runge_kutta.hpp>
-#include <boost/numeric/odeint/stepper/generation/generation_dense_output_runge_kutta.hpp>
-
-#include <boost/numeric/odeint/stepper/generation/generation_runge_kutta_cash_karp54_classic.hpp>
-#include <boost/numeric/odeint/stepper/generation/generation_runge_kutta_cash_karp54.hpp>
-#include <boost/numeric/odeint/stepper/generation/generation_runge_kutta_dopri5.hpp>
-#include <boost/numeric/odeint/stepper/generation/generation_runge_kutta_fehlberg78.hpp>
-
-
-#include <boost/numeric/odeint/stepper/generation/generation_rosenbrock4.hpp>
-
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_GENERATION_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/generation/generation_controlled_runge_kutta.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/generation/generation_controlled_runge_kutta.hpp
deleted file mode 100644
index bad2bedfef11a61f4923acd34f42969b33328f30..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/generation/generation_controlled_runge_kutta.hpp
+++ /dev/null
@@ -1,61 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/generation/generation_controlled_runge_kutta.hpp
-
- [begin_description]
- Specialization of the controller factory for the controlled_runge_kutta class.
- [end_description]
-
- Copyright 2011-2012 Karsten Ahnert
- Copyright 2011-2012 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_GENERATION_GENERATION_CONTROLLED_RUNGE_KUTTA_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_GENERATION_GENERATION_CONTROLLED_RUNGE_KUTTA_HPP_INCLUDED
-
-#include <boost/numeric/odeint/stepper/controlled_runge_kutta.hpp>
-#include <boost/numeric/odeint/stepper/generation/make_controlled.hpp>
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-// controller factory for controlled_runge_kutta
-template< class Stepper >
-struct controller_factory< Stepper , controlled_runge_kutta< Stepper > >
-{
- typedef Stepper stepper_type;
- typedef controlled_runge_kutta< stepper_type > controller_type;
- typedef typename controller_type::error_checker_type error_checker_type;
- typedef typename controller_type::step_adjuster_type step_adjuster_type;
- typedef typename stepper_type::value_type value_type;
- typedef typename stepper_type::value_type time_type;
-
- controller_type operator()( value_type abs_error , value_type rel_error , const stepper_type &stepper )
- {
- return controller_type( error_checker_type( abs_error , rel_error ) ,
- step_adjuster_type() , stepper );
- }
-
- controller_type operator()( value_type abs_error , value_type rel_error ,
- time_type max_dt, const stepper_type &stepper )
- {
- return controller_type( error_checker_type( abs_error , rel_error ) ,
- step_adjuster_type(max_dt) , stepper );
- }
-};
-
-
-} // odeint
-} // numeric
-} // boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_GENERATION_GENERATION_CONTROLLED_RUNGE_KUTTA_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/generation/generation_dense_output_runge_kutta.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/generation/generation_dense_output_runge_kutta.hpp
deleted file mode 100644
index 276358a12e525e0dfad996e870b3b4bcce70bf88..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/generation/generation_dense_output_runge_kutta.hpp
+++ /dev/null
@@ -1,65 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/generation/generation_dense_output_runge_kutta.hpp
-
- [begin_description]
- Specialization of the controller factory for the dense_output_runge_kutta class.
- [end_description]
-
- Copyright 2011-2012 Karsten Ahnert
- Copyright 2011-2012 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_GENERATION_GENERATION_DENSE_OUTPUT_RUNGE_KUTTA_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_GENERATION_GENERATION_DENSE_OUTPUT_RUNGE_KUTTA_HPP_INCLUDED
-
-#include <boost/numeric/odeint/stepper/controlled_runge_kutta.hpp>
-#include <boost/numeric/odeint/stepper/dense_output_runge_kutta.hpp>
-#include <boost/numeric/odeint/stepper/generation/make_dense_output.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-// controller factory for controlled_runge_kutta
-template< class Stepper >
-struct dense_output_factory< Stepper , dense_output_runge_kutta< controlled_runge_kutta< Stepper > > >
-{
- typedef Stepper stepper_type;
- typedef controlled_runge_kutta< stepper_type > controller_type;
- typedef typename controller_type::error_checker_type error_checker_type;
- typedef typename controller_type::step_adjuster_type step_adjuster_type;
- typedef typename stepper_type::value_type value_type;
- typedef typename stepper_type::time_type time_type;
- typedef dense_output_runge_kutta< controller_type > dense_output_type;
-
- dense_output_type operator()( value_type abs_error , value_type rel_error , const stepper_type &stepper )
- {
- return dense_output_type( controller_type( error_checker_type( abs_error , rel_error ) ,
- step_adjuster_type() , stepper ) );
- }
-
- dense_output_type operator()( value_type abs_error , value_type rel_error ,
- time_type max_dt , const stepper_type &stepper )
- {
- return dense_output_type(
- controller_type( error_checker_type( abs_error , rel_error) ,
- step_adjuster_type( max_dt ) , stepper ) );
- }
-};
-
-
-
-
-
-} // odeint
-} // numeric
-} // boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_GENERATION_GENERATION_DENSE_OUTPUT_RUNGE_KUTTA_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/generation/generation_rosenbrock4.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/generation/generation_rosenbrock4.hpp
deleted file mode 100644
index 366cb5e9c4979547a6b61ce9388df015164f65c9..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/generation/generation_rosenbrock4.hpp
+++ /dev/null
@@ -1,79 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/generation/generation_rosenbrock4.hpp
-
- [begin_description]
- Enable the factory functions for the controller and the dense output of the Rosenbrock4 method.
- [end_description]
-
- Copyright 2011-2012 Karsten Ahnert
- Copyright 2011-2012 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_GENERATION_GENERATION_ROSENBROCK4_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_GENERATION_GENERATION_ROSENBROCK4_HPP_INCLUDED
-
-#include <boost/numeric/odeint/stepper/rosenbrock4.hpp>
-#include <boost/numeric/odeint/stepper/rosenbrock4_controller.hpp>
-#include <boost/numeric/odeint/stepper/rosenbrock4_dense_output.hpp>
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-template< class Value , class Coefficients , class Resize >
-struct get_controller< rosenbrock4< Value , Coefficients , Resize > >
-{
- typedef rosenbrock4< Value , Coefficients , Resize > stepper_type;
- typedef rosenbrock4_controller< stepper_type > type;
-};
-
-
-
-template< class Value , class Coefficients , class Resize >
-struct get_dense_output< rosenbrock4< Value , Coefficients , Resize > >
-{
- typedef rosenbrock4< Value , Coefficients , Resize > stepper_type;
- typedef rosenbrock4_controller< stepper_type > controller_type;
- typedef rosenbrock4_dense_output< controller_type > type;
-};
-
-
-
-// controller factory for controlled_runge_kutta
-template< class Stepper >
-struct dense_output_factory< Stepper , rosenbrock4_dense_output< rosenbrock4_controller< Stepper > > >
-{
- typedef Stepper stepper_type;
- typedef rosenbrock4_controller< stepper_type > controller_type;
- typedef typename stepper_type::value_type value_type;
- typedef typename stepper_type::time_type time_type;
- typedef rosenbrock4_dense_output< controller_type > dense_output_type;
-
- dense_output_type operator()( value_type abs_error , value_type rel_error , const stepper_type &stepper )
- {
- return dense_output_type( controller_type( abs_error , rel_error , stepper ) );
- }
-
- dense_output_type operator()( value_type abs_error , value_type rel_error ,
- time_type max_dt, const stepper_type &stepper )
- {
- return dense_output_type( controller_type( abs_error , rel_error , max_dt , stepper ) );
- }
-};
-
-
-
-} // odeint
-} // numeric
-} // boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_GENERATION_GENERATION_ROSENBROCK4_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/generation/generation_runge_kutta_cash_karp54.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/generation/generation_runge_kutta_cash_karp54.hpp
deleted file mode 100644
index 24ae54799e56e72dcce3987842d414c5d956a99f..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/generation/generation_runge_kutta_cash_karp54.hpp
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/generation/generation_runge_kutta_cash_karp54.hpp
-
- [begin_description]
- Enable the factory functions for the controller and the dense output of the Runge-Kutta-Cash-Karp 54 method.
- [end_description]
-
- Copyright 2011 Karsten Ahnert
- Copyright 2011 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_GENERATION_GENERATION_RUNGE_KUTTA_CASH_KARP54_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_GENERATION_GENERATION_RUNGE_KUTTA_CASH_KARP54_HPP_INCLUDED
-
-#include <boost/numeric/odeint/stepper/controlled_runge_kutta.hpp>
-#include <boost/numeric/odeint/stepper/runge_kutta_cash_karp54.hpp>
-#include <boost/numeric/odeint/stepper/generation/make_controlled.hpp>
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-// Specializations for runge_kutta_cash_karp54
-template< class State , class Value , class Deriv , class Time , class Algebra , class Operations , class Resize >
-struct get_controller< runge_kutta_cash_karp54< State , Value , Deriv , Time , Algebra , Operations , Resize > >
-{
- typedef runge_kutta_cash_karp54< State , Value , Deriv , Time , Algebra , Operations , Resize > stepper_type;
- typedef controlled_runge_kutta< stepper_type > type;
-};
-
-
-
-
-
-} // odeint
-} // numeric
-} // boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_GENERATION_GENERATION_RUNGE_KUTTA_CASH_KARP54_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/generation/generation_runge_kutta_cash_karp54_classic.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/generation/generation_runge_kutta_cash_karp54_classic.hpp
deleted file mode 100644
index 1cc0f91d7f3507fc21b9537e0baa9f506a37b2fa..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/generation/generation_runge_kutta_cash_karp54_classic.hpp
+++ /dev/null
@@ -1,48 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/generation/generation_runge_kutta_cash_karp54_classic.hpp
-
- [begin_description]
- Enable the factory functions for the controller and the dense output of the
- Runge-Kutta-Cash-Karp 54 method with the classical implementation.
- [end_description]
-
- Copyright 2011 Karsten Ahnert
- Copyright 2011 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_GENERATION_GENERATION_RUNGE_KUTTA_CASH_KARP54_CLASSIC_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_GENERATION_GENERATION_RUNGE_KUTTA_CASH_KARP54_CLASSIC_HPP_INCLUDED
-
-#include <boost/numeric/odeint/stepper/controlled_runge_kutta.hpp>
-#include <boost/numeric/odeint/stepper/runge_kutta_cash_karp54_classic.hpp>
-#include <boost/numeric/odeint/stepper/generation/make_controlled.hpp>
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-// Specializations for runge_kutta_cash_karp54
-template< class State , class Value , class Deriv , class Time , class Algebra , class Operations , class Resize >
-struct get_controller< runge_kutta_cash_karp54_classic< State , Value , Deriv , Time , Algebra , Operations , Resize > >
-{
- typedef runge_kutta_cash_karp54_classic< State , Value , Deriv , Time , Algebra , Operations , Resize > stepper_type;
- typedef controlled_runge_kutta< stepper_type > type;
-};
-
-
-
-
-} // odeint
-} // numeric
-} // boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_GENERATION_GENERATION_RUNGE_KUTTA_CASH_KARP54_CLASSIC_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/generation/generation_runge_kutta_dopri5.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/generation/generation_runge_kutta_dopri5.hpp
deleted file mode 100644
index 1a607f39277854e2cc5cd65d855e75a17a53108d..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/generation/generation_runge_kutta_dopri5.hpp
+++ /dev/null
@@ -1,56 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/generation/generation_runge_kutta_dopri5.hpp
-
- [begin_description]
- Enable the factory functions for the controller and the dense output of the Runge-Kutta-Dormand-Prince5 method.
- [end_description]
-
- Copyright 2011 Karsten Ahnert
- Copyright 2011 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_GENERATION_GENERATION_RUNGE_KUTTA_DOPRI5_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_GENERATION_GENERATION_RUNGE_KUTTA_DOPRI5_HPP_INCLUDED
-
-#include <boost/numeric/odeint/stepper/controlled_runge_kutta.hpp>
-#include <boost/numeric/odeint/stepper/dense_output_runge_kutta.hpp>
-#include <boost/numeric/odeint/stepper/runge_kutta_dopri5.hpp>
-#include <boost/numeric/odeint/stepper/generation/make_controlled.hpp>
-#include <boost/numeric/odeint/stepper/generation/make_dense_output.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-template< class State , class Value , class Deriv , class Time , class Algebra , class Operations , class Resize >
-struct get_controller< runge_kutta_dopri5< State , Value , Deriv , Time , Algebra , Operations , Resize > >
-{
- typedef runge_kutta_dopri5< State , Value , Deriv , Time , Algebra , Operations , Resize > stepper_type;
- typedef controlled_runge_kutta< stepper_type > type;
-};
-
-
-template< class State , class Value , class Deriv , class Time , class Algebra , class Operations , class Resize >
-struct get_dense_output< runge_kutta_dopri5< State , Value , Deriv , Time , Algebra , Operations , Resize > >
-{
- typedef runge_kutta_dopri5< State , Value , Deriv , Time , Algebra , Operations , Resize > stepper_type;
- typedef controlled_runge_kutta< stepper_type > controller_type;
- typedef dense_output_runge_kutta< controller_type > type;
-};
-
-
-
-
-} // odeint
-} // numeric
-} // boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_GENERATION_GENERATION_RUNGE_KUTTA_DOPRI5_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/generation/generation_runge_kutta_fehlberg78.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/generation/generation_runge_kutta_fehlberg78.hpp
deleted file mode 100644
index d89343bf44cd164845444e980338ca5335808ee1..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/generation/generation_runge_kutta_fehlberg78.hpp
+++ /dev/null
@@ -1,46 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/generation/generation_runge_kutta_fehlberg78.hpp
-
- [begin_description]
- Enable the factory functions for the controller and the dense output of the Runge-Kutta-Fehlberg 78 method.
- [end_description]
-
- Copyright 2011 Karsten Ahnert
- Copyright 2011 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_GENERATION_GENERATION_RUNGE_KUTTA_FEHLBERG78_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_GENERATION_GENERATION_RUNGE_KUTTA_FEHLBERG78_HPP_INCLUDED
-
-#include <boost/numeric/odeint/stepper/controlled_runge_kutta.hpp>
-#include <boost/numeric/odeint/stepper/runge_kutta_fehlberg78.hpp>
-#include <boost/numeric/odeint/stepper/generation/make_controlled.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-template< class State , class Value , class Deriv , class Time , class Algebra , class Operations , class Resize >
-struct get_controller< runge_kutta_fehlberg78< State , Value , Deriv , Time , Algebra , Operations , Resize > >
-{
- typedef runge_kutta_fehlberg78< State , Value , Deriv , Time , Algebra , Operations , Resize > stepper_type;
- typedef controlled_runge_kutta< stepper_type > type;
-};
-
-
-
-
-
-} // odeint
-} // numeric
-} // boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_GENERATION_GENERATION_RUNGE_KUTTA_FEHLBERG78_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/generation/make_controlled.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/generation/make_controlled.hpp
deleted file mode 100644
index 61bc8f19204ac21f58c101120066a716f5d4cca3..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/generation/make_controlled.hpp
+++ /dev/null
@@ -1,103 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/generation/make_controlled.hpp
-
- [begin_description]
- Factory function to simplify the creation of controlled steppers from error steppers.
- [end_description]
-
- Copyright 2011-2012 Karsten Ahnert
- Copyright 2011-2012 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_GENERATION_MAKE_CONTROLLED_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_GENERATION_MAKE_CONTROLLED_HPP_INCLUDED
-
-
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-
-// default template for the controller
-template< class Stepper > struct get_controller { };
-
-
-
-// default controller factory
-template< class Stepper , class Controller >
-struct controller_factory
-{
- Controller operator()(
- typename Stepper::value_type abs_error ,
- typename Stepper::value_type rel_error ,
- const Stepper &stepper )
- {
- return Controller( abs_error , rel_error , stepper );
- }
-
- Controller operator()(
- typename Stepper::value_type abs_error ,
- typename Stepper::value_type rel_error ,
- typename Stepper::time_type max_dt ,
- const Stepper &stepper )
- {
- return Controller( abs_error , rel_error , max_dt, stepper );
- }
-};
-
-
-
-
-namespace result_of
-{
- template< class Stepper >
- struct make_controlled
- {
- typedef typename get_controller< Stepper >::type type;
- };
-}
-
-
-template< class Stepper >
-typename result_of::make_controlled< Stepper >::type make_controlled(
- typename Stepper::value_type abs_error ,
- typename Stepper::value_type rel_error ,
- const Stepper & stepper = Stepper() )
-{
- typedef Stepper stepper_type;
- typedef typename result_of::make_controlled< stepper_type >::type controller_type;
- typedef controller_factory< stepper_type , controller_type > factory_type;
- factory_type factory;
- return factory( abs_error , rel_error , stepper );
-}
-
-
-template< class Stepper >
-typename result_of::make_controlled< Stepper >::type make_controlled(
- typename Stepper::value_type abs_error ,
- typename Stepper::value_type rel_error ,
- typename Stepper::time_type max_dt ,
- const Stepper & stepper = Stepper() )
-{
- typedef Stepper stepper_type;
- typedef typename result_of::make_controlled< stepper_type >::type controller_type;
- typedef controller_factory< stepper_type , controller_type > factory_type;
- factory_type factory;
- return factory( abs_error , rel_error , max_dt, stepper );
-}
-
-} // odeint
-} // numeric
-} // boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_GENERATION_MAKE_CONTROLLED_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/generation/make_dense_output.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/generation/make_dense_output.hpp
deleted file mode 100644
index fff3590525e14f691fc44940e5a33695e4207576..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/generation/make_dense_output.hpp
+++ /dev/null
@@ -1,100 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/generation/make_dense_output.hpp
-
- [begin_description]
- Factory function to simplify the creation of dense output steppers from error steppers.
- [end_description]
-
- Copyright 2011-2012 Karsten Ahnert
- Copyright 2011-2012 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_GENERATION_MAKE_DENSE_OUTPUT_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_GENERATION_MAKE_DENSE_OUTPUT_HPP_INCLUDED
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-// default template for the dense output
-template< class Stepper > struct get_dense_output { };
-
-
-
-// default dense output factory
-template< class Stepper , class DenseOutput >
-struct dense_output_factory
-{
- DenseOutput operator()(
- typename Stepper::value_type abs_error ,
- typename Stepper::value_type rel_error ,
- const Stepper &stepper )
- {
- return DenseOutput( abs_error , rel_error , stepper );
- }
-
- DenseOutput operator()(
- typename Stepper::value_type abs_error ,
- typename Stepper::value_type rel_error ,
- typename Stepper::time_type max_dt ,
- const Stepper &stepper )
- {
- return DenseOutput( abs_error , rel_error , max_dt , stepper );
- }
-};
-
-
-
-namespace result_of
-{
- template< class Stepper >
- struct make_dense_output
- {
- typedef typename get_dense_output< Stepper >::type type;
- };
-}
-
-
-
-template< class Stepper >
-typename result_of::make_dense_output< Stepper >::type make_dense_output(
- typename Stepper::value_type abs_error ,
- typename Stepper::value_type rel_error ,
- const Stepper &stepper = Stepper() )
-{
- typedef Stepper stepper_type;
- typedef typename result_of::make_dense_output< stepper_type >::type dense_output_type;
- typedef dense_output_factory< stepper_type , dense_output_type > factory_type;
- factory_type factory;
- return factory( abs_error , rel_error , stepper );
-}
-
-
-template< class Stepper >
-typename result_of::make_dense_output< Stepper >::type make_dense_output(
- typename Stepper::value_type abs_error ,
- typename Stepper::value_type rel_error ,
- typename Stepper::time_type max_dt ,
- const Stepper &stepper = Stepper() )
-{
- typedef Stepper stepper_type;
- typedef typename result_of::make_dense_output< stepper_type >::type dense_output_type;
- typedef dense_output_factory< stepper_type , dense_output_type > factory_type;
- factory_type factory;
- return factory( abs_error , rel_error , max_dt, stepper );
-}
-
-
-} // odeint
-} // numeric
-} // boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_GENERATION_MAKE_DENSE_OUTPUT_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/implicit_euler.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/implicit_euler.hpp
deleted file mode 100644
index 24a56e93c383b7e9f6223daf267dc69afcffaafc..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/implicit_euler.hpp
+++ /dev/null
@@ -1,170 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/implicit_euler.hpp
-
- [begin_description]
- Impementation of the implicit Euler method. Works with ublas::vector as state type.
- [end_description]
-
- Copyright 2010-2012 Mario Mulansky
- Copyright 2010-2012 Karsten Ahnert
- Copyright 2012 Christoph Koke
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_IMPLICIT_EULER_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_IMPLICIT_EULER_HPP_INCLUDED
-
-
-#include <utility>
-
-#include <boost/numeric/odeint/util/bind.hpp>
-#include <boost/numeric/odeint/util/unwrap_reference.hpp>
-#include <boost/numeric/odeint/stepper/stepper_categories.hpp>
-
-#include <boost/numeric/odeint/util/ublas_wrapper.hpp>
-#include <boost/numeric/odeint/util/is_resizeable.hpp>
-#include <boost/numeric/odeint/util/resizer.hpp>
-
-#include <boost/numeric/ublas/vector.hpp>
-#include <boost/numeric/ublas/matrix.hpp>
-#include <boost/numeric/ublas/lu.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-
-
-
-
-
-
-template< class ValueType , class Resizer = initially_resizer >
-class implicit_euler
-{
-
-public:
-
- typedef ValueType value_type;
- typedef value_type time_type;
- typedef boost::numeric::ublas::vector< value_type > state_type;
- typedef state_wrapper< state_type > wrapped_state_type;
- typedef state_type deriv_type;
- typedef state_wrapper< deriv_type > wrapped_deriv_type;
- typedef boost::numeric::ublas::matrix< value_type > matrix_type;
- typedef state_wrapper< matrix_type > wrapped_matrix_type;
- typedef boost::numeric::ublas::permutation_matrix< size_t > pmatrix_type;
- typedef state_wrapper< pmatrix_type > wrapped_pmatrix_type;
- typedef Resizer resizer_type;
- typedef stepper_tag stepper_category;
- typedef implicit_euler< ValueType , Resizer > stepper_type;
-
- implicit_euler( value_type epsilon = 1E-6 )
- : m_epsilon( epsilon )
- { }
-
-
- template< class System >
- void do_step( System system , state_type &x , time_type t , time_type dt )
- {
- typedef typename odeint::unwrap_reference< System >::type system_type;
- typedef typename odeint::unwrap_reference< typename system_type::first_type >::type deriv_func_type;
- typedef typename odeint::unwrap_reference< typename system_type::second_type >::type jacobi_func_type;
- system_type &sys = system;
- deriv_func_type &deriv_func = sys.first;
- jacobi_func_type &jacobi_func = sys.second;
-
- m_resizer.adjust_size( x , detail::bind( &stepper_type::template resize_impl<state_type> , detail::ref( *this ) , detail::_1 ) );
-
- for( size_t i=0 ; i<x.size() ; ++i )
- m_pm.m_v[i] = i;
-
- t += dt;
-
- // apply first Newton step
- deriv_func( x , m_dxdt.m_v , t );
-
- m_b.m_v = dt * m_dxdt.m_v;
-
- jacobi_func( x , m_jacobi.m_v , t );
- m_jacobi.m_v *= dt;
- m_jacobi.m_v -= boost::numeric::ublas::identity_matrix< value_type >( x.size() );
-
- solve( m_b.m_v , m_jacobi.m_v );
-
- m_x.m_v = x - m_b.m_v;
-
- // iterate Newton until some precision is reached
- // ToDo: maybe we should apply only one Newton step -> linear implicit one-step scheme
- while( boost::numeric::ublas::norm_2( m_b.m_v ) > m_epsilon )
- {
- deriv_func( m_x.m_v , m_dxdt.m_v , t );
- m_b.m_v = x - m_x.m_v + dt*m_dxdt.m_v;
-
- // simplified version, only the first Jacobian is used
- // jacobi( m_x , m_jacobi , t );
- // m_jacobi *= dt;
- // m_jacobi -= boost::numeric::ublas::identity_matrix< value_type >( x.size() );
-
- solve( m_b.m_v , m_jacobi.m_v );
-
- m_x.m_v -= m_b.m_v;
- }
- x = m_x.m_v;
- }
-
- template< class StateType >
- void adjust_size( const StateType &x )
- {
- resize_impl( x );
- }
-
-
-private:
-
- template< class StateIn >
- bool resize_impl( const StateIn &x )
- {
- bool resized = false;
- resized |= adjust_size_by_resizeability( m_dxdt , x , typename is_resizeable<deriv_type>::type() );
- resized |= adjust_size_by_resizeability( m_x , x , typename is_resizeable<state_type>::type() );
- resized |= adjust_size_by_resizeability( m_b , x , typename is_resizeable<deriv_type>::type() );
- resized |= adjust_size_by_resizeability( m_jacobi , x , typename is_resizeable<matrix_type>::type() );
- resized |= adjust_size_by_resizeability( m_pm , x , typename is_resizeable<pmatrix_type>::type() );
- return resized;
- }
-
-
- void solve( state_type &x , matrix_type &m )
- {
- int res = boost::numeric::ublas::lu_factorize( m , m_pm.m_v );
- if( res != 0 ) exit(0);
- boost::numeric::ublas::lu_substitute( m , m_pm.m_v , x );
- }
-
-private:
-
- value_type m_epsilon;
- resizer_type m_resizer;
- wrapped_deriv_type m_dxdt;
- wrapped_state_type m_x;
- wrapped_deriv_type m_b;
- wrapped_matrix_type m_jacobi;
- wrapped_pmatrix_type m_pm;
-
-
-};
-
-
-} // odeint
-} // numeric
-} // boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_IMPLICIT_EULER_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/modified_midpoint.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/modified_midpoint.hpp
deleted file mode 100644
index af0c522ff2df1618760326dd4e202a460f8ae842..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/modified_midpoint.hpp
+++ /dev/null
@@ -1,315 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/modified_midpoint.hpp
-
- [begin_description]
- Modified midpoint method for the use in Burlish-Stoer stepper.
- [end_description]
-
- Copyright 2011-2013 Mario Mulansky
- Copyright 2011-2013 Karsten Ahnert
- Copyright 2012 Christoph Koke
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_MODIFIED_MIDPOINT_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_MODIFIED_MIDPOINT_HPP_INCLUDED
-
-#include <vector>
-
-#include <boost/numeric/odeint/stepper/base/explicit_stepper_base.hpp>
-#include <boost/numeric/odeint/util/resizer.hpp>
-#include <boost/numeric/odeint/util/is_resizeable.hpp>
-#include <boost/numeric/odeint/algebra/range_algebra.hpp>
-#include <boost/numeric/odeint/algebra/default_operations.hpp>
-#include <boost/numeric/odeint/algebra/algebra_dispatcher.hpp>
-#include <boost/numeric/odeint/algebra/operations_dispatcher.hpp>
-#include <boost/numeric/odeint/util/copy.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-template<
-class State ,
-class Value = double ,
-class Deriv = State ,
-class Time = Value ,
-class Algebra = typename algebra_dispatcher< State >::algebra_type ,
-class Operations = typename operations_dispatcher< State >::operations_type ,
-class Resizer = initially_resizer
->
-#ifndef DOXYGEN_SKIP
-class modified_midpoint
-: public explicit_stepper_base<
- modified_midpoint< State , Value , Deriv , Time , Algebra , Operations , Resizer > ,
- 2 , State , Value , Deriv , Time , Algebra , Operations , Resizer >
-#else
-class modified_midpoint : public explicit_stepper_base
-#endif
-{
-
-public :
-
- typedef explicit_stepper_base<
- modified_midpoint< State , Value , Deriv , Time , Algebra , Operations , Resizer > ,
- 2 , State , Value , Deriv , Time , Algebra , Operations , Resizer > stepper_base_type;
-
- typedef typename stepper_base_type::state_type state_type;
- typedef typename stepper_base_type::wrapped_state_type wrapped_state_type;
- typedef typename stepper_base_type::value_type value_type;
- typedef typename stepper_base_type::deriv_type deriv_type;
- typedef typename stepper_base_type::wrapped_deriv_type wrapped_deriv_type;
- typedef typename stepper_base_type::time_type time_type;
- typedef typename stepper_base_type::algebra_type algebra_type;
- typedef typename stepper_base_type::operations_type operations_type;
- typedef typename stepper_base_type::resizer_type resizer_type;
- typedef typename stepper_base_type::stepper_type stepper_type;
-
-
- modified_midpoint( unsigned short steps = 2 , const algebra_type &algebra = algebra_type() )
- : stepper_base_type( algebra ) , m_steps( steps )
- { }
-
- template< class System , class StateIn , class DerivIn , class StateOut >
- void do_step_impl( System system , const StateIn &in , const DerivIn &dxdt , time_type t , StateOut &out , time_type dt )
- {
- static const value_type val1 = static_cast< value_type >( 1 );
- static const value_type val05 = static_cast< value_type >( 1 ) / static_cast< value_type >( 2 );
-
- m_resizer.adjust_size( in , detail::bind( &stepper_type::template resize_impl< StateIn > , detail::ref( *this ) , detail::_1 ) );
-
- const time_type h = dt / static_cast<value_type>( m_steps );
- const time_type h2 = static_cast<value_type>(2) * h;
-
- typename odeint::unwrap_reference< System >::type &sys = system;
-
- time_type th = t + h;
-
- // m_x1 = x + h*dxdt
- stepper_base_type::m_algebra.for_each3( m_x1.m_v , in , dxdt ,
- typename operations_type::template scale_sum2< value_type , time_type >( val1 , h ) );
-
- sys( m_x1.m_v , m_dxdt.m_v , th );
-
- boost::numeric::odeint::copy( in , m_x0.m_v );
-
- unsigned short i = 1;
- while( i != m_steps )
- {
- // general step
- //tmp = m_x1; m_x1 = m_x0 + h2*m_dxdt; m_x0 = tmp
- stepper_base_type::m_algebra.for_each3( m_x1.m_v , m_x0.m_v , m_dxdt.m_v ,
- typename operations_type::template scale_sum_swap2< value_type , time_type >( val1 , h2 ) );
- th += h;
- sys( m_x1.m_v , m_dxdt.m_v , th);
- i++;
- }
-
- // last step
- // x = 0.5*( m_x0 + m_x1 + h*m_dxdt )
- stepper_base_type::m_algebra.for_each4( out , m_x0.m_v , m_x1.m_v , m_dxdt.m_v ,
- typename operations_type::template scale_sum3< value_type , value_type , time_type >( val05 , val05 , val05*h ) );
- }
-
-
- void set_steps( unsigned short steps )
- { m_steps = steps; }
-
-
- unsigned short steps( void ) const
- { return m_steps; }
-
-
- template< class StateIn >
- void adjust_size( const StateIn &x )
- {
- resize_impl( x );
- stepper_base_type::adjust_size( x );
- }
-
-private:
-
- template< class StateIn >
- bool resize_impl( const StateIn &x )
- {
- bool resized( false );
- resized |= adjust_size_by_resizeability( m_x0 , x , typename is_resizeable<state_type>::type() );
- resized |= adjust_size_by_resizeability( m_x1 , x , typename is_resizeable<state_type>::type() );
- resized |= adjust_size_by_resizeability( m_dxdt , x , typename is_resizeable<deriv_type>::type() );
- return resized;
- }
-
-
- unsigned short m_steps;
-
- resizer_type m_resizer;
-
- wrapped_state_type m_x0;
- wrapped_state_type m_x1;
- wrapped_deriv_type m_dxdt;
-
-};
-
-
-/* Modified midpoint which stores derivatives and state at dt/2 in some external storage for later usage in dense output calculation
- * This Stepper is for use in Bulirsch Stoer only. It DOES NOT meet any stepper concept.
- */
-template<
-class State ,
-class Value = double ,
-class Deriv = State ,
-class Time = Value ,
-class Algebra = typename algebra_dispatcher< State >::algebra_type ,
-class Operations = typename operations_dispatcher< State >::operations_type ,
-class Resizer = initially_resizer
->
-class modified_midpoint_dense_out
-{
-
-public :
-
- typedef State state_type;
- typedef Value value_type;
- typedef Deriv deriv_type;
- typedef Time time_type;
- typedef Algebra algebra_type;
- typedef Operations operations_type;
- typedef Resizer resizer_type;
- typedef state_wrapper< state_type > wrapped_state_type;
- typedef state_wrapper< deriv_type > wrapped_deriv_type;
-
- typedef modified_midpoint_dense_out< State , Value , Deriv , Time , Algebra , Operations , Resizer > stepper_type;
- typedef std::vector< wrapped_deriv_type > deriv_table_type;
-
- modified_midpoint_dense_out( unsigned short steps = 2 , const algebra_type &algebra = algebra_type() )
- : m_algebra( algebra ) , m_steps( steps )
- { }
-
- /*
- * performs a modified midpoint step with m_steps intermediate points
- * stores approximation for x(t+dt/2) in x_mp and all evaluated function results in derivs
- *
- */
-
- template< class System , class StateIn , class DerivIn , class StateOut >
- void do_step( System system , const StateIn &in , const DerivIn &dxdt , time_type t , StateOut &out , time_type dt ,
- state_type &x_mp , deriv_table_type &derivs )
- {
-
- static const value_type val1 = static_cast< value_type >( 1 );
- static const value_type val05 = static_cast< value_type >( 1 ) / static_cast< value_type >( 2 );
-
- m_resizer.adjust_size( in , detail::bind( &stepper_type::template resize< StateIn > , detail::ref( *this ) , detail::_1 ) );
-
- const time_type h = dt / static_cast<value_type>( m_steps );
- const time_type h2 = static_cast<value_type>( 2 ) * h;
-
- typename odeint::unwrap_reference< System >::type &sys = system;
-
- time_type th = t + h;
-
- // m_x1 = x + h*dxdt
- m_algebra.for_each3( m_x1.m_v , in , dxdt ,
- typename operations_type::template scale_sum2< value_type , time_type >( val1 , h ) );
-
- if( m_steps == 2 )
- // result of first step already gives approximation at the center of the interval
- boost::numeric::odeint::copy( m_x1.m_v , x_mp );
-
- sys( m_x1.m_v , derivs[0].m_v , th );
-
- boost::numeric::odeint::copy( in , m_x0.m_v );
-
- unsigned short i = 1;
- while( i != m_steps )
- {
- // general step
- //tmp = m_x1; m_x1 = m_x0 + h2*m_dxdt; m_x0 = tmp
- m_algebra.for_each3( m_x1.m_v , m_x0.m_v , derivs[i-1].m_v ,
- typename operations_type::template scale_sum_swap2< value_type , time_type >( val1 , h2 ) );
- if( i == m_steps/2-1 )
- // save approximation at the center of the interval
- boost::numeric::odeint::copy( m_x1.m_v , x_mp );
-
- th += h;
- sys( m_x1.m_v , derivs[i].m_v , th);
- i++;
- }
-
- // last step
- // x = 0.5*( m_x0 + m_x1 + h*m_dxdt )
- m_algebra.for_each4( out , m_x0.m_v , m_x1.m_v , derivs[m_steps-1].m_v ,
- typename operations_type::template scale_sum3< value_type , value_type , time_type >( val05 , val05 , val05*h ) );
- }
-
-
- void set_steps( unsigned short steps )
- { m_steps = steps; }
-
-
- unsigned short steps( void ) const
- { return m_steps; }
-
-
- template< class StateIn >
- bool resize( const StateIn &x )
- {
- bool resized( false );
- resized |= adjust_size_by_resizeability( m_x0 , x , typename is_resizeable<state_type>::type() );
- resized |= adjust_size_by_resizeability( m_x1 , x , typename is_resizeable<state_type>::type() );
- return resized;
- }
-
- template< class StateIn >
- void adjust_size( const StateIn &x )
- {
- resize( x );
- }
-
-private:
-
- algebra_type m_algebra;
-
- unsigned short m_steps;
-
- resizer_type m_resizer;
-
- wrapped_state_type m_x0;
- wrapped_state_type m_x1;
-
-};
-
-
-
-/********** DOXYGEN ***********/
-
-/**
- * \class modified_midpoint
- *
- * Implementation of the modified midpoint method with a configurable
- * number of intermediate steps. This class is used by the Bulirsch-Stoer
- * algorithm and is not meant for direct usage.
- */
-
-
-/**
- * \class modified_midpoint_dense_out
- *
- * Implementation of the modified midpoint method with a configurable
- * number of intermediate steps. This class is used by the dense output
- * Bulirsch-Stoer algorithm and is not meant for direct usage.
- * \note This stepper is for internal use only and does not meet
- * any stepper concept.
- */
-
-
-}
-}
-}
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_MODIFIED_MIDPOINT_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/rosenbrock4.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/rosenbrock4.hpp
deleted file mode 100644
index 564577c8fc41ccfebdfc329683411b5f500d659d..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/rosenbrock4.hpp
+++ /dev/null
@@ -1,346 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/rosenbrock4.hpp
-
- [begin_description]
- Implementation of the Rosenbrock 4 method for solving stiff ODEs. Note, that a
- controller and a dense-output stepper exist for this method,
- [end_description]
-
- Copyright 2011-2013 Karsten Ahnert
- Copyright 2011-2012 Mario Mulansky
- Copyright 2012 Christoph Koke
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_ROSENBROCK4_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_ROSENBROCK4_HPP_INCLUDED
-
-
-#include <boost/numeric/odeint/util/bind.hpp>
-#include <boost/numeric/odeint/util/unwrap_reference.hpp>
-#include <boost/numeric/ublas/vector.hpp>
-#include <boost/numeric/ublas/matrix.hpp>
-#include <boost/numeric/ublas/lu.hpp>
-
-#include <boost/numeric/odeint/stepper/stepper_categories.hpp>
-
-#include <boost/numeric/odeint/util/ublas_wrapper.hpp>
-#include <boost/numeric/odeint/util/is_resizeable.hpp>
-#include <boost/numeric/odeint/util/resizer.hpp>
-
-#include <boost/numeric/ublas/vector.hpp>
-#include <boost/numeric/ublas/matrix.hpp>
-#include <boost/numeric/ublas/lu.hpp>
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-/*
- * ToDo:
- *
- * 2. Interfacing for odeint, check if controlled_error_stepper can be used
- * 3. dense output
- */
-
-
-
-template< class Value >
-struct default_rosenbrock_coefficients
-{
- typedef Value value_type;
- typedef unsigned short order_type;
-
- default_rosenbrock_coefficients( void )
- : gamma ( static_cast< value_type >( 0.25 ) ) ,
- d1 ( static_cast< value_type >( 0.25 ) ) ,
- d2 ( static_cast< value_type >( -0.1043 ) ) ,
- d3 ( static_cast< value_type >( 0.1035 ) ) ,
- d4 ( static_cast< value_type >( 0.3620000000000023e-01 ) ) ,
- c2 ( static_cast< value_type >( 0.386 ) ) ,
- c3 ( static_cast< value_type >( 0.21 ) ) ,
- c4 ( static_cast< value_type >( 0.63 ) ) ,
- c21 ( static_cast< value_type >( -0.5668800000000000e+01 ) ) ,
- a21 ( static_cast< value_type >( 0.1544000000000000e+01 ) ) ,
- c31 ( static_cast< value_type >( -0.2430093356833875e+01 ) ) ,
- c32 ( static_cast< value_type >( -0.2063599157091915e+00 ) ) ,
- a31 ( static_cast< value_type >( 0.9466785280815826e+00 ) ) ,
- a32 ( static_cast< value_type >( 0.2557011698983284e+00 ) ) ,
- c41 ( static_cast< value_type >( -0.1073529058151375e+00 ) ) ,
- c42 ( static_cast< value_type >( -0.9594562251023355e+01 ) ) ,
- c43 ( static_cast< value_type >( -0.2047028614809616e+02 ) ) ,
- a41 ( static_cast< value_type >( 0.3314825187068521e+01 ) ) ,
- a42 ( static_cast< value_type >( 0.2896124015972201e+01 ) ) ,
- a43 ( static_cast< value_type >( 0.9986419139977817e+00 ) ) ,
- c51 ( static_cast< value_type >( 0.7496443313967647e+01 ) ) ,
- c52 ( static_cast< value_type >( -0.1024680431464352e+02 ) ) ,
- c53 ( static_cast< value_type >( -0.3399990352819905e+02 ) ) ,
- c54 ( static_cast< value_type >( 0.1170890893206160e+02 ) ) ,
- a51 ( static_cast< value_type >( 0.1221224509226641e+01 ) ) ,
- a52 ( static_cast< value_type >( 0.6019134481288629e+01 ) ) ,
- a53 ( static_cast< value_type >( 0.1253708332932087e+02 ) ) ,
- a54 ( static_cast< value_type >( -0.6878860361058950e+00 ) ) ,
- c61 ( static_cast< value_type >( 0.8083246795921522e+01 ) ) ,
- c62 ( static_cast< value_type >( -0.7981132988064893e+01 ) ) ,
- c63 ( static_cast< value_type >( -0.3152159432874371e+02 ) ) ,
- c64 ( static_cast< value_type >( 0.1631930543123136e+02 ) ) ,
- c65 ( static_cast< value_type >( -0.6058818238834054e+01 ) ) ,
- d21 ( static_cast< value_type >( 0.1012623508344586e+02 ) ) ,
- d22 ( static_cast< value_type >( -0.7487995877610167e+01 ) ) ,
- d23 ( static_cast< value_type >( -0.3480091861555747e+02 ) ) ,
- d24 ( static_cast< value_type >( -0.7992771707568823e+01 ) ) ,
- d25 ( static_cast< value_type >( 0.1025137723295662e+01 ) ) ,
- d31 ( static_cast< value_type >( -0.6762803392801253e+00 ) ) ,
- d32 ( static_cast< value_type >( 0.6087714651680015e+01 ) ) ,
- d33 ( static_cast< value_type >( 0.1643084320892478e+02 ) ) ,
- d34 ( static_cast< value_type >( 0.2476722511418386e+02 ) ) ,
- d35 ( static_cast< value_type >( -0.6594389125716872e+01 ) )
- {}
-
- const value_type gamma;
- const value_type d1 , d2 , d3 , d4;
- const value_type c2 , c3 , c4;
- const value_type c21 ;
- const value_type a21;
- const value_type c31 , c32;
- const value_type a31 , a32;
- const value_type c41 , c42 , c43;
- const value_type a41 , a42 , a43;
- const value_type c51 , c52 , c53 , c54;
- const value_type a51 , a52 , a53 , a54;
- const value_type c61 , c62 , c63 , c64 , c65;
- const value_type d21 , d22 , d23 , d24 , d25;
- const value_type d31 , d32 , d33 , d34 , d35;
-
- static const order_type stepper_order = 4;
- static const order_type error_order = 3;
-};
-
-
-
-template< class Value , class Coefficients = default_rosenbrock_coefficients< Value > , class Resizer = initially_resizer >
-class rosenbrock4
-{
-private:
-
-public:
-
- typedef Value value_type;
- typedef boost::numeric::ublas::vector< value_type > state_type;
- typedef state_type deriv_type;
- typedef value_type time_type;
- typedef boost::numeric::ublas::matrix< value_type > matrix_type;
- typedef boost::numeric::ublas::permutation_matrix< size_t > pmatrix_type;
- typedef Resizer resizer_type;
- typedef Coefficients rosenbrock_coefficients;
- typedef stepper_tag stepper_category;
- typedef unsigned short order_type;
-
- typedef state_wrapper< state_type > wrapped_state_type;
- typedef state_wrapper< deriv_type > wrapped_deriv_type;
- typedef state_wrapper< matrix_type > wrapped_matrix_type;
- typedef state_wrapper< pmatrix_type > wrapped_pmatrix_type;
-
- typedef rosenbrock4< Value , Coefficients , Resizer > stepper_type;
-
- const static order_type stepper_order = rosenbrock_coefficients::stepper_order;
- const static order_type error_order = rosenbrock_coefficients::error_order;
-
- rosenbrock4( void )
- : m_resizer() , m_x_err_resizer() ,
- m_jac() , m_pm() ,
- m_dfdt() , m_dxdt() , m_dxdtnew() ,
- m_g1() , m_g2() , m_g3() , m_g4() , m_g5() ,
- m_cont3() , m_cont4() , m_xtmp() , m_x_err() ,
- m_coef()
- { }
-
-
- order_type order() const { return stepper_order; }
-
- template< class System >
- void do_step( System system , const state_type &x , time_type t , state_type &xout , time_type dt , state_type &xerr )
- {
- // get the system and jacobi function
- typedef typename odeint::unwrap_reference< System >::type system_type;
- typedef typename odeint::unwrap_reference< typename system_type::first_type >::type deriv_func_type;
- typedef typename odeint::unwrap_reference< typename system_type::second_type >::type jacobi_func_type;
- system_type &sys = system;
- deriv_func_type &deriv_func = sys.first;
- jacobi_func_type &jacobi_func = sys.second;
-
- const size_t n = x.size();
-
- m_resizer.adjust_size( x , detail::bind( &stepper_type::template resize_impl<state_type> , detail::ref( *this ) , detail::_1 ) );
-
- for( size_t i=0 ; i<n ; ++i )
- m_pm.m_v( i ) = i;
-
- deriv_func( x , m_dxdt.m_v , t );
- jacobi_func( x , m_jac.m_v , t , m_dfdt.m_v );
-
- m_jac.m_v *= -1.0;
- m_jac.m_v += 1.0 / m_coef.gamma / dt * boost::numeric::ublas::identity_matrix< value_type >( n );
- boost::numeric::ublas::lu_factorize( m_jac.m_v , m_pm.m_v );
-
- for( size_t i=0 ; i<n ; ++i )
- m_g1.m_v[i] = m_dxdt.m_v[i] + dt * m_coef.d1 * m_dfdt.m_v[i];
- boost::numeric::ublas::lu_substitute( m_jac.m_v , m_pm.m_v , m_g1.m_v );
-
-
- for( size_t i=0 ; i<n ; ++i )
- m_xtmp.m_v[i] = x[i] + m_coef.a21 * m_g1.m_v[i];
- deriv_func( m_xtmp.m_v , m_dxdtnew.m_v , t + m_coef.c2 * dt );
- for( size_t i=0 ; i<n ; ++i )
- m_g2.m_v[i] = m_dxdtnew.m_v[i] + dt * m_coef.d2 * m_dfdt.m_v[i] + m_coef.c21 * m_g1.m_v[i] / dt;
- boost::numeric::ublas::lu_substitute( m_jac.m_v , m_pm.m_v , m_g2.m_v );
-
-
- for( size_t i=0 ; i<n ; ++i )
- m_xtmp.m_v[i] = x[i] + m_coef.a31 * m_g1.m_v[i] + m_coef.a32 * m_g2.m_v[i];
- deriv_func( m_xtmp.m_v , m_dxdtnew.m_v , t + m_coef.c3 * dt );
- for( size_t i=0 ; i<n ; ++i )
- m_g3.m_v[i] = m_dxdtnew.m_v[i] + dt * m_coef.d3 * m_dfdt.m_v[i] + ( m_coef.c31 * m_g1.m_v[i] + m_coef.c32 * m_g2.m_v[i] ) / dt;
- boost::numeric::ublas::lu_substitute( m_jac.m_v , m_pm.m_v , m_g3.m_v );
-
-
- for( size_t i=0 ; i<n ; ++i )
- m_xtmp.m_v[i] = x[i] + m_coef.a41 * m_g1.m_v[i] + m_coef.a42 * m_g2.m_v[i] + m_coef.a43 * m_g3.m_v[i];
- deriv_func( m_xtmp.m_v , m_dxdtnew.m_v , t + m_coef.c4 * dt );
- for( size_t i=0 ; i<n ; ++i )
- m_g4.m_v[i] = m_dxdtnew.m_v[i] + dt * m_coef.d4 * m_dfdt.m_v[i] + ( m_coef.c41 * m_g1.m_v[i] + m_coef.c42 * m_g2.m_v[i] + m_coef.c43 * m_g3.m_v[i] ) / dt;
- boost::numeric::ublas::lu_substitute( m_jac.m_v , m_pm.m_v , m_g4.m_v );
-
-
- for( size_t i=0 ; i<n ; ++i )
- m_xtmp.m_v[i] = x[i] + m_coef.a51 * m_g1.m_v[i] + m_coef.a52 * m_g2.m_v[i] + m_coef.a53 * m_g3.m_v[i] + m_coef.a54 * m_g4.m_v[i];
- deriv_func( m_xtmp.m_v , m_dxdtnew.m_v , t + dt );
- for( size_t i=0 ; i<n ; ++i )
- m_g5.m_v[i] = m_dxdtnew.m_v[i] + ( m_coef.c51 * m_g1.m_v[i] + m_coef.c52 * m_g2.m_v[i] + m_coef.c53 * m_g3.m_v[i] + m_coef.c54 * m_g4.m_v[i] ) / dt;
- boost::numeric::ublas::lu_substitute( m_jac.m_v , m_pm.m_v , m_g5.m_v );
-
- for( size_t i=0 ; i<n ; ++i )
- m_xtmp.m_v[i] += m_g5.m_v[i];
- deriv_func( m_xtmp.m_v , m_dxdtnew.m_v , t + dt );
- for( size_t i=0 ; i<n ; ++i )
- xerr[i] = m_dxdtnew.m_v[i] + ( m_coef.c61 * m_g1.m_v[i] + m_coef.c62 * m_g2.m_v[i] + m_coef.c63 * m_g3.m_v[i] + m_coef.c64 * m_g4.m_v[i] + m_coef.c65 * m_g5.m_v[i] ) / dt;
- boost::numeric::ublas::lu_substitute( m_jac.m_v , m_pm.m_v , xerr );
-
- for( size_t i=0 ; i<n ; ++i )
- xout[i] = m_xtmp.m_v[i] + xerr[i];
- }
-
- template< class System >
- void do_step( System system , state_type &x , time_type t , time_type dt , state_type &xerr )
- {
- do_step( system , x , t , x , dt , xerr );
- }
-
- /*
- * do_step without error output - just calls above functions with and neglects the error estimate
- */
- template< class System >
- void do_step( System system , const state_type &x , time_type t , state_type &xout , time_type dt )
- {
- m_x_err_resizer.adjust_size( x , detail::bind( &stepper_type::template resize_x_err<state_type> , detail::ref( *this ) , detail::_1 ) );
- do_step( system , x , t , xout , dt , m_x_err.m_v );
- }
-
- template< class System >
- void do_step( System system , state_type &x , time_type t , time_type dt )
- {
- m_x_err_resizer.adjust_size( x , detail::bind( &stepper_type::template resize_x_err<state_type> , detail::ref( *this ) , detail::_1 ) );
- do_step( system , x , t , dt , m_x_err.m_v );
- }
-
- void prepare_dense_output()
- {
- const size_t n = m_g1.m_v.size();
- for( size_t i=0 ; i<n ; ++i )
- {
- m_cont3.m_v[i] = m_coef.d21 * m_g1.m_v[i] + m_coef.d22 * m_g2.m_v[i] + m_coef.d23 * m_g3.m_v[i] + m_coef.d24 * m_g4.m_v[i] + m_coef.d25 * m_g5.m_v[i];
- m_cont4.m_v[i] = m_coef.d31 * m_g1.m_v[i] + m_coef.d32 * m_g2.m_v[i] + m_coef.d33 * m_g3.m_v[i] + m_coef.d34 * m_g4.m_v[i] + m_coef.d35 * m_g5.m_v[i];
- }
- }
-
-
- void calc_state( time_type t , state_type &x ,
- const state_type &x_old , time_type t_old ,
- const state_type &x_new , time_type t_new )
- {
- const size_t n = m_g1.m_v.size();
- time_type dt = t_new - t_old;
- time_type s = ( t - t_old ) / dt;
- time_type s1 = 1.0 - s;
- for( size_t i=0 ; i<n ; ++i )
- x[i] = x_old[i] * s1 + s * ( x_new[i] + s1 * ( m_cont3.m_v[i] + s * m_cont4.m_v[i] ) );
- }
-
-
-
- template< class StateType >
- void adjust_size( const StateType &x )
- {
- resize_impl( x );
- resize_x_err( x );
- }
-
-
-protected:
-
- template< class StateIn >
- bool resize_impl( const StateIn &x )
- {
- bool resized = false;
- resized |= adjust_size_by_resizeability( m_dxdt , x , typename is_resizeable<deriv_type>::type() );
- resized |= adjust_size_by_resizeability( m_dfdt , x , typename is_resizeable<deriv_type>::type() );
- resized |= adjust_size_by_resizeability( m_dxdtnew , x , typename is_resizeable<deriv_type>::type() );
- resized |= adjust_size_by_resizeability( m_xtmp , x , typename is_resizeable<state_type>::type() );
- resized |= adjust_size_by_resizeability( m_g1 , x , typename is_resizeable<state_type>::type() );
- resized |= adjust_size_by_resizeability( m_g2 , x , typename is_resizeable<state_type>::type() );
- resized |= adjust_size_by_resizeability( m_g3 , x , typename is_resizeable<state_type>::type() );
- resized |= adjust_size_by_resizeability( m_g4 , x , typename is_resizeable<state_type>::type() );
- resized |= adjust_size_by_resizeability( m_g5 , x , typename is_resizeable<state_type>::type() );
- resized |= adjust_size_by_resizeability( m_cont3 , x , typename is_resizeable<state_type>::type() );
- resized |= adjust_size_by_resizeability( m_cont4 , x , typename is_resizeable<state_type>::type() );
- resized |= adjust_size_by_resizeability( m_jac , x , typename is_resizeable<matrix_type>::type() );
- resized |= adjust_size_by_resizeability( m_pm , x , typename is_resizeable<pmatrix_type>::type() );
- return resized;
- }
-
- template< class StateIn >
- bool resize_x_err( const StateIn &x )
- {
- return adjust_size_by_resizeability( m_x_err , x , typename is_resizeable<state_type>::type() );
- }
-
-private:
-
-
- resizer_type m_resizer;
- resizer_type m_x_err_resizer;
-
- wrapped_matrix_type m_jac;
- wrapped_pmatrix_type m_pm;
- wrapped_deriv_type m_dfdt , m_dxdt , m_dxdtnew;
- wrapped_state_type m_g1 , m_g2 , m_g3 , m_g4 , m_g5;
- wrapped_state_type m_cont3 , m_cont4;
- wrapped_state_type m_xtmp;
- wrapped_state_type m_x_err;
-
- const rosenbrock_coefficients m_coef;
-};
-
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_ROSENBROCK4_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/rosenbrock4_controller.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/rosenbrock4_controller.hpp
deleted file mode 100644
index e361a1addf9ae49e76d877afb60123c1235132e3..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/rosenbrock4_controller.hpp
+++ /dev/null
@@ -1,240 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/rosenbrock4_controller.hpp
-
- [begin_description]
- Controller for the Rosenbrock4 method.
- [end_description]
-
- Copyright 2011-2012 Karsten Ahnert
- Copyright 2011-2012 Mario Mulansky
- Copyright 2012 Christoph Koke
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_ROSENBROCK4_CONTROLLER_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_ROSENBROCK4_CONTROLLER_HPP_INCLUDED
-
-#include <boost/config.hpp>
-#include <boost/numeric/odeint/util/bind.hpp>
-
-#include <boost/numeric/odeint/stepper/controlled_step_result.hpp>
-#include <boost/numeric/odeint/stepper/stepper_categories.hpp>
-
-#include <boost/numeric/odeint/util/copy.hpp>
-#include <boost/numeric/odeint/util/is_resizeable.hpp>
-#include <boost/numeric/odeint/util/detail/less_with_sign.hpp>
-
-#include <boost/numeric/odeint/stepper/rosenbrock4.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-template< class Stepper >
-class rosenbrock4_controller
-{
-private:
-
-
-public:
-
- typedef Stepper stepper_type;
- typedef typename stepper_type::value_type value_type;
- typedef typename stepper_type::state_type state_type;
- typedef typename stepper_type::wrapped_state_type wrapped_state_type;
- typedef typename stepper_type::time_type time_type;
- typedef typename stepper_type::deriv_type deriv_type;
- typedef typename stepper_type::wrapped_deriv_type wrapped_deriv_type;
- typedef typename stepper_type::resizer_type resizer_type;
- typedef controlled_stepper_tag stepper_category;
-
- typedef rosenbrock4_controller< Stepper > controller_type;
-
-
- rosenbrock4_controller( value_type atol = 1.0e-6 , value_type rtol = 1.0e-6 ,
- const stepper_type &stepper = stepper_type() )
- : m_stepper( stepper ) , m_atol( atol ) , m_rtol( rtol ) ,
- m_max_dt( static_cast<time_type>(0) ) ,
- m_first_step( true ) , m_err_old( 0.0 ) , m_dt_old( 0.0 ) ,
- m_last_rejected( false )
- { }
-
- rosenbrock4_controller( value_type atol, value_type rtol, time_type max_dt,
- const stepper_type &stepper = stepper_type() )
- : m_stepper( stepper ) , m_atol( atol ) , m_rtol( rtol ) , m_max_dt( max_dt ) ,
- m_first_step( true ) , m_err_old( 0.0 ) , m_dt_old( 0.0 ) ,
- m_last_rejected( false )
- { }
-
- value_type error( const state_type &x , const state_type &xold , const state_type &xerr )
- {
- BOOST_USING_STD_MAX();
- using std::abs;
- using std::sqrt;
-
- const size_t n = x.size();
- value_type err = 0.0 , sk = 0.0;
- for( size_t i=0 ; i<n ; ++i )
- {
- sk = m_atol + m_rtol * max BOOST_PREVENT_MACRO_SUBSTITUTION ( abs( xold[i] ) , abs( x[i] ) );
- err += xerr[i] * xerr[i] / sk / sk;
- }
- return sqrt( err / value_type( n ) );
- }
-
- value_type last_error( void ) const
- {
- return m_err_old;
- }
-
-
-
-
- template< class System >
- boost::numeric::odeint::controlled_step_result
- try_step( System sys , state_type &x , time_type &t , time_type &dt )
- {
- m_xnew_resizer.adjust_size( x , detail::bind( &controller_type::template resize_m_xnew< state_type > , detail::ref( *this ) , detail::_1 ) );
- boost::numeric::odeint::controlled_step_result res = try_step( sys , x , t , m_xnew.m_v , dt );
- if( res == success )
- {
- boost::numeric::odeint::copy( m_xnew.m_v , x );
- }
- return res;
- }
-
-
- template< class System >
- boost::numeric::odeint::controlled_step_result
- try_step( System sys , const state_type &x , time_type &t , state_type &xout , time_type &dt )
- {
- if( m_max_dt != static_cast<time_type>(0) && detail::less_with_sign(m_max_dt, dt, dt) )
- {
- // given step size is bigger then max_dt
- // set limit and return fail
- dt = m_max_dt;
- return fail;
- }
-
- BOOST_USING_STD_MIN();
- BOOST_USING_STD_MAX();
- using std::pow;
-
- static const value_type safe = 0.9 , fac1 = 5.0 , fac2 = 1.0 / 6.0;
-
- m_xerr_resizer.adjust_size( x , detail::bind( &controller_type::template resize_m_xerr< state_type > , detail::ref( *this ) , detail::_1 ) );
-
- m_stepper.do_step( sys , x , t , xout , dt , m_xerr.m_v );
- value_type err = error( xout , x , m_xerr.m_v );
-
- value_type fac = max BOOST_PREVENT_MACRO_SUBSTITUTION (
- fac2 , min BOOST_PREVENT_MACRO_SUBSTITUTION (
- fac1 ,
- static_cast< value_type >( pow( err , 0.25 ) / safe ) ) );
- value_type dt_new = dt / fac;
- if ( err <= 1.0 )
- {
- if( m_first_step )
- {
- m_first_step = false;
- }
- else
- {
- value_type fac_pred = ( m_dt_old / dt ) * pow( err * err / m_err_old , 0.25 ) / safe;
- fac_pred = max BOOST_PREVENT_MACRO_SUBSTITUTION (
- fac2 , min BOOST_PREVENT_MACRO_SUBSTITUTION ( fac1 , fac_pred ) );
- fac = max BOOST_PREVENT_MACRO_SUBSTITUTION ( fac , fac_pred );
- dt_new = dt / fac;
- }
-
- m_dt_old = dt;
- m_err_old = max BOOST_PREVENT_MACRO_SUBSTITUTION ( static_cast< value_type >( 0.01 ) , err );
- if( m_last_rejected )
- dt_new = ( dt >= 0.0 ?
- min BOOST_PREVENT_MACRO_SUBSTITUTION ( dt_new , dt ) :
- max BOOST_PREVENT_MACRO_SUBSTITUTION ( dt_new , dt ) );
- t += dt;
- // limit step size to max_dt
- if( m_max_dt != static_cast<time_type>(0) )
- {
- dt = detail::min_abs(m_max_dt, dt_new);
- } else {
- dt = dt_new;
- }
- m_last_rejected = false;
- return success;
- }
- else
- {
- dt = dt_new;
- m_last_rejected = true;
- return fail;
- }
- }
-
-
- template< class StateType >
- void adjust_size( const StateType &x )
- {
- resize_m_xerr( x );
- resize_m_xnew( x );
- }
-
-
-
- stepper_type& stepper( void )
- {
- return m_stepper;
- }
-
- const stepper_type& stepper( void ) const
- {
- return m_stepper;
- }
-
-
-
-
-private:
-
- template< class StateIn >
- bool resize_m_xerr( const StateIn &x )
- {
- return adjust_size_by_resizeability( m_xerr , x , typename is_resizeable<state_type>::type() );
- }
-
- template< class StateIn >
- bool resize_m_xnew( const StateIn &x )
- {
- return adjust_size_by_resizeability( m_xnew , x , typename is_resizeable<state_type>::type() );
- }
-
-
- stepper_type m_stepper;
- resizer_type m_xerr_resizer;
- resizer_type m_xnew_resizer;
- wrapped_state_type m_xerr;
- wrapped_state_type m_xnew;
- value_type m_atol , m_rtol;
- time_type m_max_dt;
- bool m_first_step;
- value_type m_err_old , m_dt_old;
- bool m_last_rejected;
-};
-
-
-
-
-
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_ROSENBROCK4_CONTROLLER_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/rosenbrock4_dense_output.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/rosenbrock4_dense_output.hpp
deleted file mode 100644
index 72ef437476b99b50763b6c12aadf89db2e6c2265..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/rosenbrock4_dense_output.hpp
+++ /dev/null
@@ -1,199 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/rosenbrock4_dense_output.hpp
-
- [begin_description]
- Dense output for Rosenbrock 4.
- [end_description]
-
- Copyright 2011-2012 Karsten Ahnert
- Copyright 2011-2015 Mario Mulansky
- Copyright 2012 Christoph Koke
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_ROSENBROCK4_DENSE_OUTPUT_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_ROSENBROCK4_DENSE_OUTPUT_HPP_INCLUDED
-
-
-#include <utility>
-
-#include <boost/numeric/odeint/util/bind.hpp>
-
-#include <boost/numeric/odeint/stepper/rosenbrock4_controller.hpp>
-#include <boost/numeric/odeint/util/is_resizeable.hpp>
-
-#include <boost/numeric/odeint/integrate/max_step_checker.hpp>
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-template< class ControlledStepper >
-class rosenbrock4_dense_output
-{
-
-public:
-
- typedef ControlledStepper controlled_stepper_type;
- typedef typename controlled_stepper_type::stepper_type stepper_type;
- typedef typename stepper_type::value_type value_type;
- typedef typename stepper_type::state_type state_type;
- typedef typename stepper_type::wrapped_state_type wrapped_state_type;
- typedef typename stepper_type::time_type time_type;
- typedef typename stepper_type::deriv_type deriv_type;
- typedef typename stepper_type::wrapped_deriv_type wrapped_deriv_type;
- typedef typename stepper_type::resizer_type resizer_type;
- typedef dense_output_stepper_tag stepper_category;
-
- typedef rosenbrock4_dense_output< ControlledStepper > dense_output_stepper_type;
-
- rosenbrock4_dense_output( const controlled_stepper_type &stepper = controlled_stepper_type() )
- : m_stepper( stepper ) ,
- m_x1() , m_x2() ,
- m_current_state_x1( true ) ,
- m_t() , m_t_old() , m_dt()
- {
- }
-
-
-
- template< class StateType >
- void initialize( const StateType &x0 , time_type t0 , time_type dt0 )
- {
- m_resizer.adjust_size( x0 , detail::bind( &dense_output_stepper_type::template resize_impl< StateType > , detail::ref( *this ) , detail::_1 ) );
- get_current_state() = x0;
- m_t = t0;
- m_dt = dt0;
- }
-
- template< class System >
- std::pair< time_type , time_type > do_step( System system )
- {
- failed_step_checker fail_checker; // to throw a runtime_error if step size adjustment fails
- controlled_step_result res = fail;
- m_t_old = m_t;
- do
- {
- res = m_stepper.try_step( system , get_current_state() , m_t , get_old_state() , m_dt );
- fail_checker(); // check for overflow of failed steps
- }
- while( res == fail );
- m_stepper.stepper().prepare_dense_output();
- this->toggle_current_state();
- return std::make_pair( m_t_old , m_t );
- }
-
-
- /*
- * The two overloads are needed in order to solve the forwarding problem.
- */
- template< class StateOut >
- void calc_state( time_type t , StateOut &x )
- {
- m_stepper.stepper().calc_state( t , x , get_old_state() , m_t_old , get_current_state() , m_t );
- }
-
- template< class StateOut >
- void calc_state( time_type t , const StateOut &x )
- {
- m_stepper.stepper().calc_state( t , x , get_old_state() , m_t_old , get_current_state() , m_t );
- }
-
-
- template< class StateType >
- void adjust_size( const StateType &x )
- {
- m_stepper.adjust_size( x );
- resize_impl( x );
- }
-
-
-
-
- const state_type& current_state( void ) const
- {
- return get_current_state();
- }
-
- time_type current_time( void ) const
- {
- return m_t;
- }
-
- const state_type& previous_state( void ) const
- {
- return get_old_state();
- }
-
- time_type previous_time( void ) const
- {
- return m_t_old;
- }
-
- time_type current_time_step( void ) const
- {
- return m_dt;
- }
-
-
-
-
-private:
-
- state_type& get_current_state( void )
- {
- return m_current_state_x1 ? m_x1.m_v : m_x2.m_v ;
- }
-
- const state_type& get_current_state( void ) const
- {
- return m_current_state_x1 ? m_x1.m_v : m_x2.m_v ;
- }
-
- state_type& get_old_state( void )
- {
- return m_current_state_x1 ? m_x2.m_v : m_x1.m_v ;
- }
-
- const state_type& get_old_state( void ) const
- {
- return m_current_state_x1 ? m_x2.m_v : m_x1.m_v ;
- }
-
- void toggle_current_state( void )
- {
- m_current_state_x1 = ! m_current_state_x1;
- }
-
-
- template< class StateIn >
- bool resize_impl( const StateIn &x )
- {
- bool resized = false;
- resized |= adjust_size_by_resizeability( m_x1 , x , typename is_resizeable<state_type>::type() );
- resized |= adjust_size_by_resizeability( m_x2 , x , typename is_resizeable<state_type>::type() );
- return resized;
- }
-
-
- controlled_stepper_type m_stepper;
- resizer_type m_resizer;
- wrapped_state_type m_x1 , m_x2;
- bool m_current_state_x1;
- time_type m_t , m_t_old , m_dt;
-};
-
-
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_ROSENBROCK4_DENSE_OUTPUT_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/runge_kutta4.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/runge_kutta4.hpp
deleted file mode 100644
index c0c4e166fe8947daa6af2bf572f3c5710b18751c..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/runge_kutta4.hpp
+++ /dev/null
@@ -1,181 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/runge_kutta4.hpp
-
- [begin_description]
- Implementation of the classical Runge-Kutta stepper with the generic stepper.
- [end_description]
-
- Copyright 2011-2013 Mario Mulansky
- Copyright 2011-2013 Karsten Ahnert
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_RUNGE_KUTTA4_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_RUNGE_KUTTA4_HPP_INCLUDED
-
-
-
-
-#include <boost/fusion/container/vector.hpp>
-#include <boost/fusion/container/generation/make_vector.hpp>
-
-#include <boost/numeric/odeint/stepper/explicit_generic_rk.hpp>
-#include <boost/numeric/odeint/algebra/range_algebra.hpp>
-#include <boost/numeric/odeint/algebra/default_operations.hpp>
-#include <boost/numeric/odeint/algebra/algebra_dispatcher.hpp>
-#include <boost/numeric/odeint/algebra/operations_dispatcher.hpp>
-
-#include <boost/array.hpp>
-
-#include <boost/numeric/odeint/util/resizer.hpp>
-
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-#ifndef DOXYGEN_SKIP
-template< class Value = double >
-struct rk4_coefficients_a1 : boost::array< Value , 1 >
-{
- rk4_coefficients_a1( void )
- {
- (*this)[0] = static_cast< Value >( 1 ) / static_cast< Value >( 2 );
- }
-};
-
-template< class Value = double >
-struct rk4_coefficients_a2 : boost::array< Value , 2 >
-{
- rk4_coefficients_a2( void )
- {
- (*this)[0] = static_cast<Value>(0);
- (*this)[1] = static_cast< Value >( 1 ) / static_cast< Value >( 2 );
- }
-};
-
-
-template< class Value = double >
-struct rk4_coefficients_a3 : boost::array< Value , 3 >
-{
- rk4_coefficients_a3( void )
- {
- (*this)[0] = static_cast<Value>(0);
- (*this)[1] = static_cast<Value>(0);
- (*this)[2] = static_cast<Value>(1);
- }
-};
-
-template< class Value = double >
-struct rk4_coefficients_b : boost::array< Value , 4 >
-{
- rk4_coefficients_b( void )
- {
- (*this)[0] = static_cast<Value>(1)/static_cast<Value>(6);
- (*this)[1] = static_cast<Value>(1)/static_cast<Value>(3);
- (*this)[2] = static_cast<Value>(1)/static_cast<Value>(3);
- (*this)[3] = static_cast<Value>(1)/static_cast<Value>(6);
- }
-};
-
-template< class Value = double >
-struct rk4_coefficients_c : boost::array< Value , 4 >
-{
- rk4_coefficients_c( void )
- {
- (*this)[0] = static_cast<Value>(0);
- (*this)[1] = static_cast< Value >( 1 ) / static_cast< Value >( 2 );
- (*this)[2] = static_cast< Value >( 1 ) / static_cast< Value >( 2 );
- (*this)[3] = static_cast<Value>(1);
- }
-};
-#endif
-
-
-
-template<
-class State ,
-class Value = double ,
-class Deriv = State ,
-class Time = Value ,
-class Algebra = typename algebra_dispatcher< State >::algebra_type ,
-class Operations = typename operations_dispatcher< State >::operations_type ,
-class Resizer = initially_resizer
->
-#ifndef DOXYGEN_SKIP
-class runge_kutta4 : public explicit_generic_rk< 4 , 4 , State , Value , Deriv , Time ,
-Algebra , Operations , Resizer >
-#else
-class runge_kutta4 : public explicit_generic_rk
-#endif
-{
-
-public:
-
-#ifndef DOXYGEN_SKIP
- typedef explicit_generic_rk< 4 , 4 , State , Value , Deriv , Time ,
- Algebra , Operations , Resizer > stepper_base_type;
-#endif
- typedef typename stepper_base_type::state_type state_type;
- typedef typename stepper_base_type::value_type value_type;
- typedef typename stepper_base_type::deriv_type deriv_type;
- typedef typename stepper_base_type::time_type time_type;
- typedef typename stepper_base_type::algebra_type algebra_type;
- typedef typename stepper_base_type::operations_type operations_type;
- typedef typename stepper_base_type::resizer_type resizer_type;
-
- #ifndef DOXYGEN_SKIP
- typedef typename stepper_base_type::wrapped_state_type wrapped_state_type;
- typedef typename stepper_base_type::wrapped_deriv_type wrapped_deriv_type;
- typedef typename stepper_base_type::stepper_type stepper_type;
- #endif
-
- runge_kutta4( const algebra_type &algebra = algebra_type() ) : stepper_base_type(
- boost::fusion::make_vector( rk4_coefficients_a1<Value>() , rk4_coefficients_a2<Value>() , rk4_coefficients_a3<Value>() ) ,
- rk4_coefficients_b<Value>() , rk4_coefficients_c<Value>() , algebra )
- { }
-
-};
-
-/**
- * \class runge_kutta4
- * \brief The classical Runge-Kutta stepper of fourth order.
- *
- * The Runge-Kutta method of fourth order is one standard method for
- * solving ordinary differential equations and is widely used, see also
- * <a href="http://en.wikipedia.org/wiki/Runge%E2%80%93Kutta_methods">en.wikipedia.org/wiki/Runge-Kutta_methods</a>
- * The method is explicit and fulfills the Stepper concept. Step size control
- * or continuous output are not provided.
- *
- * This class derives from explicit_stepper_base and inherits its interface via CRTP (current recurring template pattern).
- * Furthermore, it derivs from explicit_generic_rk which is a generic Runge-Kutta algorithm. For more details see
- * explicit_stepper_base and explicit_generic_rk.
- *
- * \tparam State The state type.
- * \tparam Value The value type.
- * \tparam Deriv The type representing the time derivative of the state.
- * \tparam Time The time representing the independent variable - the time.
- * \tparam Algebra The algebra type.
- * \tparam Operations The operations type.
- * \tparam Resizer The resizer policy type.
- */
-
-/**
- * \fn runge_kutta4::runge_kutta4( const algebra_type &algebra = algebra_type() )
- * \brief Constructs the runge_kutta4 class. This constructor can be used as a default
- * constructor if the algebra has a default constructor.
- * \param algebra A copy of algebra is made and stored inside explicit_stepper_base.
- */
-
-}
-}
-}
-
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_RUNGE_KUTTA4_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/runge_kutta4_classic.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/runge_kutta4_classic.hpp
deleted file mode 100644
index 215448c74cbbab61f28925f5f932766481a36d7f..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/runge_kutta4_classic.hpp
+++ /dev/null
@@ -1,232 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/runge_kutta4_classic.hpp
-
- [begin_description]
- Implementation for the classical Runge Kutta stepper.
- [end_description]
-
- Copyright 2010-2013 Karsten Ahnert
- Copyright 2010-2013 Mario Mulansky
- Copyright 2012 Christoph Koke
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_RUNGE_KUTTA4_CLASSIC_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_RUNGE_KUTTA4_CLASSIC_HPP_INCLUDED
-
-
-
-#include <boost/numeric/odeint/stepper/base/explicit_stepper_base.hpp>
-#include <boost/numeric/odeint/algebra/range_algebra.hpp>
-#include <boost/numeric/odeint/algebra/default_operations.hpp>
-#include <boost/numeric/odeint/algebra/algebra_dispatcher.hpp>
-#include <boost/numeric/odeint/algebra/operations_dispatcher.hpp>
-
-#include <boost/numeric/odeint/util/state_wrapper.hpp>
-#include <boost/numeric/odeint/util/is_resizeable.hpp>
-#include <boost/numeric/odeint/util/resizer.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-template<
-class State ,
-class Value = double ,
-class Deriv = State ,
-class Time = Value ,
-class Algebra = typename algebra_dispatcher< State >::algebra_type ,
-class Operations = typename operations_dispatcher< State >::operations_type ,
-class Resizer = initially_resizer
->
-#ifndef DOXYGEN_SKIP
-class runge_kutta4_classic
-: public explicit_stepper_base<
- runge_kutta4_classic< State , Value , Deriv , Time , Algebra , Operations , Resizer > ,
- 4 , State , Value , Deriv , Time , Algebra , Operations , Resizer >
-#else
-class runge_kutta4_classic : public explicit_stepper_base
-#endif
-{
-
-public :
-
- #ifndef DOXYGEN_SKIP
- typedef explicit_stepper_base<
- runge_kutta4_classic< State , Value , Deriv , Time , Algebra , Operations , Resizer > ,
- 4 , State , Value , Deriv , Time , Algebra , Operations , Resizer > stepper_base_type;
- #else
- typedef explicit_stepper_base< runge_kutta4_classic< ... > , ... > stepper_base_type;
- #endif
-
- typedef typename stepper_base_type::state_type state_type;
- typedef typename stepper_base_type::value_type value_type;
- typedef typename stepper_base_type::deriv_type deriv_type;
- typedef typename stepper_base_type::time_type time_type;
- typedef typename stepper_base_type::algebra_type algebra_type;
- typedef typename stepper_base_type::operations_type operations_type;
- typedef typename stepper_base_type::resizer_type resizer_type;
-
- #ifndef DOXYGEN_SKIP
- typedef typename stepper_base_type::stepper_type stepper_type;
- typedef typename stepper_base_type::wrapped_state_type wrapped_state_type;
- typedef typename stepper_base_type::wrapped_deriv_type wrapped_deriv_type;
- #endif // DOXYGEN_SKIP
-
-
-
- runge_kutta4_classic( const algebra_type &algebra = algebra_type() ) : stepper_base_type( algebra )
- { }
-
-
- template< class System , class StateIn , class DerivIn , class StateOut >
- void do_step_impl( System system , const StateIn &in , const DerivIn &dxdt , time_type t , StateOut &out , time_type dt )
- {
- // ToDo : check if size of in,dxdt,out are equal?
-
- static const value_type val1 = static_cast< value_type >( 1 );
-
- m_resizer.adjust_size( in , detail::bind( &stepper_type::template resize_impl< StateIn > , detail::ref( *this ) , detail::_1 ) );
-
- typename odeint::unwrap_reference< System >::type &sys = system;
-
- const time_type dh = dt / static_cast< value_type >( 2 );
- const time_type th = t + dh;
-
- // dt * dxdt = k1
- // m_x_tmp = x + dh*dxdt
- stepper_base_type::m_algebra.for_each3( m_x_tmp.m_v , in , dxdt ,
- typename operations_type::template scale_sum2< value_type , time_type >( val1 , dh ) );
-
-
- // dt * m_dxt = k2
- sys( m_x_tmp.m_v , m_dxt.m_v , th );
-
- // m_x_tmp = x + dh*m_dxt
- stepper_base_type::m_algebra.for_each3( m_x_tmp.m_v , in , m_dxt.m_v ,
- typename operations_type::template scale_sum2< value_type , time_type >( val1 , dh ) );
-
-
- // dt * m_dxm = k3
- sys( m_x_tmp.m_v , m_dxm.m_v , th );
- //m_x_tmp = x + dt*m_dxm
- stepper_base_type::m_algebra.for_each3( m_x_tmp.m_v , in , m_dxm.m_v ,
- typename operations_type::template scale_sum2< value_type , time_type >( val1 , dt ) );
-
-
- // dt * m_dxh = k4
- sys( m_x_tmp.m_v , m_dxh.m_v , t + dt );
-
- //x += dt/6 * ( m_dxdt + m_dxt + val2*m_dxm )
- time_type dt6 = dt / static_cast< value_type >( 6 );
- time_type dt3 = dt / static_cast< value_type >( 3 );
- stepper_base_type::m_algebra.for_each6( out , in , dxdt , m_dxt.m_v , m_dxm.m_v , m_dxh.m_v ,
- typename operations_type::template scale_sum5< value_type , time_type , time_type , time_type , time_type >( 1.0 , dt6 , dt3 , dt3 , dt6 ) );
-
- // x += dt/6 * m_dxdt + dt/3 * m_dxt )
- // stepper_base_type::m_algebra.for_each4( out , in , dxdt , m_dxt.m_v ,
- // typename operations_type::template scale_sum3< value_type , time_type , time_type >( 1.0 , dt6 , dt3 ) );
- // // x += dt/3 * m_dxm + dt/6 * m_dxh )
- // stepper_base_type::m_algebra.for_each4( out , out , m_dxm.m_v , m_dxh.m_v ,
- // typename operations_type::template scale_sum3< value_type , time_type , time_type >( 1.0 , dt3 , dt6 ) );
-
- }
-
- template< class StateType >
- void adjust_size( const StateType &x )
- {
- resize_impl( x );
- stepper_base_type::adjust_size( x );
- }
-
-private:
-
- template< class StateIn >
- bool resize_impl( const StateIn &x )
- {
- bool resized = false;
- resized |= adjust_size_by_resizeability( m_x_tmp , x , typename is_resizeable<state_type>::type() );
- resized |= adjust_size_by_resizeability( m_dxm , x , typename is_resizeable<deriv_type>::type() );
- resized |= adjust_size_by_resizeability( m_dxt , x , typename is_resizeable<deriv_type>::type() );
- resized |= adjust_size_by_resizeability( m_dxh , x , typename is_resizeable<deriv_type>::type() );
- return resized;
- }
-
-
- resizer_type m_resizer;
-
- wrapped_deriv_type m_dxt;
- wrapped_deriv_type m_dxm;
- wrapped_deriv_type m_dxh;
- wrapped_state_type m_x_tmp;
-
-};
-
-
-/********* DOXYGEN *********/
-
-/**
- * \class runge_kutta4_classic
- * \brief The classical Runge-Kutta stepper of fourth order.
- *
- * The Runge-Kutta method of fourth order is one standard method for
- * solving ordinary differential equations and is widely used, see also
- * <a href="http://en.wikipedia.org/wiki/Runge%E2%80%93Kutta_methods">en.wikipedia.org/wiki/Runge-Kutta_methods</a>
- * The method is explicit and fulfills the Stepper concept. Step size control
- * or continuous output are not provided. This class implements the method directly, hence the
- * generic Runge-Kutta algorithm is not used.
- *
- * This class derives from explicit_stepper_base and inherits its interface via
- * CRTP (current recurring template pattern). For more details see
- * explicit_stepper_base.
- *
- * \tparam State The state type.
- * \tparam Value The value type.
- * \tparam Deriv The type representing the time derivative of the state.
- * \tparam Time The time representing the independent variable - the time.
- * \tparam Algebra The algebra type.
- * \tparam Operations The operations type.
- * \tparam Resizer The resizer policy type.
- */
-
- /**
- * \fn runge_kutta4_classic::runge_kutta4_classic( const algebra_type &algebra )
- * \brief Constructs the runge_kutta4_classic class. This constructor can be used as a default
- * constructor if the algebra has a default constructor.
- * \param algebra A copy of algebra is made and stored inside explicit_stepper_base.
- */
-
-
- /**
- * \fn runge_kutta4_classic::do_step_impl( System system , const StateIn &in , const DerivIn &dxdt , time_type t , StateOut &out , time_type dt )
- * \brief This method performs one step. The derivative `dxdt` of `in` at the time `t` is passed to the method.
- * The result is updated out of place, hence the input is in `in` and the output in `out`.
- * Access to this step functionality is provided by explicit_stepper_base and
- * `do_step_impl` should not be called directly.
- *
- * \param system The system function to solve, hence the r.h.s. of the ODE. It must fulfill the
- * Simple System concept.
- * \param in The state of the ODE which should be solved. in is not modified in this method
- * \param dxdt The derivative of x at t.
- * \param t The value of the time, at which the step should be performed.
- * \param out The result of the step is written in out.
- * \param dt The step size.
- */
-
- /**
- * \fn runge_kutta4_classic::adjust_size( const StateType &x )
- * \brief Adjust the size of all temporaries in the stepper manually.
- * \param x A state from which the size of the temporaries to be resized is deduced.
- */
-
-} // odeint
-} // numeric
-} // boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_RUNGE_KUTTA4_CLASSIC_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/runge_kutta_cash_karp54.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/runge_kutta_cash_karp54.hpp
deleted file mode 100644
index 74734e6f193e2d864590ff18f400983c6b284fe3..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/runge_kutta_cash_karp54.hpp
+++ /dev/null
@@ -1,231 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/runge_kutta_cash_karp54.hpp
-
- [begin_description]
- Implementation of the Runge Kutta Cash Karp 5(4) method. It uses the generic error stepper.
- [end_description]
-
- Copyright 2011-2013 Mario Mulansky
- Copyright 2011-2013 Karsten Ahnert
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
-*/
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_RUNGE_KUTTA_CASH_KARP54_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_RUNGE_KUTTA_CASH_KARP54_HPP_INCLUDED
-
-#include <boost/fusion/container/vector.hpp>
-#include <boost/fusion/container/generation/make_vector.hpp>
-
-#include <boost/numeric/odeint/stepper/explicit_error_generic_rk.hpp>
-#include <boost/numeric/odeint/algebra/range_algebra.hpp>
-#include <boost/numeric/odeint/algebra/default_operations.hpp>
-#include <boost/numeric/odeint/algebra/algebra_dispatcher.hpp>
-#include <boost/numeric/odeint/algebra/operations_dispatcher.hpp>
-
-#include <boost/numeric/odeint/util/state_wrapper.hpp>
-#include <boost/numeric/odeint/util/is_resizeable.hpp>
-#include <boost/numeric/odeint/util/resizer.hpp>
-
-#include <boost/array.hpp>
-
-
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-#ifndef DOXYGEN_SKIP
-template< class Value = double >
-struct rk54_ck_coefficients_a1 : boost::array< Value , 1 >
-{
- rk54_ck_coefficients_a1( void )
- {
- (*this)[0] = static_cast< Value >( 1 )/static_cast< Value >( 5 );
- }
-};
-
-template< class Value = double >
-struct rk54_ck_coefficients_a2 : boost::array< Value , 2 >
-{
- rk54_ck_coefficients_a2( void )
- {
- (*this)[0] = static_cast<Value>( 3 )/static_cast<Value>( 40 );
- (*this)[1] = static_cast<Value>( 9 )/static_cast<Value>( 40 );
- }
-};
-
-
-template< class Value = double >
-struct rk54_ck_coefficients_a3 : boost::array< Value , 3 >
-{
- rk54_ck_coefficients_a3( void )
- {
- (*this)[0] = static_cast<Value>( 3 )/static_cast<Value>( 10 );
- (*this)[1] = static_cast<Value>( -9 )/static_cast<Value>( 10 );
- (*this)[2] = static_cast<Value>( 6 )/static_cast<Value>( 5 );
- }
-};
-
-template< class Value = double >
-struct rk54_ck_coefficients_a4 : boost::array< Value , 4 >
-{
- rk54_ck_coefficients_a4( void )
- {
- (*this)[0] = static_cast<Value>( -11 )/static_cast<Value>( 54 );
- (*this)[1] = static_cast<Value>( 5 )/static_cast<Value>( 2 );
- (*this)[2] = static_cast<Value>( -70 )/static_cast<Value>( 27 );
- (*this)[3] = static_cast<Value>( 35 )/static_cast<Value>( 27 );
- }
-};
-
-template< class Value = double >
-struct rk54_ck_coefficients_a5 : boost::array< Value , 5 >
-{
- rk54_ck_coefficients_a5( void )
- {
- (*this)[0] = static_cast<Value>( 1631 )/static_cast<Value>( 55296 );
- (*this)[1] = static_cast<Value>( 175 )/static_cast<Value>( 512 );
- (*this)[2] = static_cast<Value>( 575 )/static_cast<Value>( 13824 );
- (*this)[3] = static_cast<Value>( 44275 )/static_cast<Value>( 110592 );
- (*this)[4] = static_cast<Value>( 253 )/static_cast<Value>( 4096 );
- }
-};
-
-template< class Value = double >
-struct rk54_ck_coefficients_b : boost::array< Value , 6 >
-{
- rk54_ck_coefficients_b( void )
- {
- (*this)[0] = static_cast<Value>( 37 )/static_cast<Value>( 378 );
- (*this)[1] = static_cast<Value>( 0 );
- (*this)[2] = static_cast<Value>( 250 )/static_cast<Value>( 621 );
- (*this)[3] = static_cast<Value>( 125 )/static_cast<Value>( 594 );
- (*this)[4] = static_cast<Value>( 0 );
- (*this)[5] = static_cast<Value>( 512 )/static_cast<Value>( 1771 );
- }
-};
-
-template< class Value = double >
-struct rk54_ck_coefficients_db : boost::array< Value , 6 >
-{
- rk54_ck_coefficients_db( void )
- {
- (*this)[0] = static_cast<Value>( 37 )/static_cast<Value>( 378 ) - static_cast<Value>( 2825 )/static_cast<Value>( 27648 );
- (*this)[1] = static_cast<Value>( 0 );
- (*this)[2] = static_cast<Value>( 250 )/static_cast<Value>( 621 ) - static_cast<Value>( 18575 )/static_cast<Value>( 48384 );
- (*this)[3] = static_cast<Value>( 125 )/static_cast<Value>( 594 ) - static_cast<Value>( 13525 )/static_cast<Value>( 55296 );
- (*this)[4] = static_cast<Value>( -277 )/static_cast<Value>( 14336 );
- (*this)[5] = static_cast<Value>( 512 )/static_cast<Value>( 1771 ) - static_cast<Value>( 1 )/static_cast<Value>( 4 );
- }
-};
-
-
-template< class Value = double >
-struct rk54_ck_coefficients_c : boost::array< Value , 6 >
-{
- rk54_ck_coefficients_c( void )
- {
- (*this)[0] = static_cast<Value>(0);
- (*this)[1] = static_cast<Value>( 1 )/static_cast<Value>( 5 );
- (*this)[2] = static_cast<Value>( 3 )/static_cast<Value>( 10 );
- (*this)[3] = static_cast<Value>( 3 )/static_cast<Value>( 5 );
- (*this)[4] = static_cast<Value>( 1 );
- (*this)[5] = static_cast<Value>( 7 )/static_cast<Value>( 8 );
- }
-};
-#endif
-
-
-template<
- class State ,
- class Value = double ,
- class Deriv = State ,
- class Time = Value ,
- class Algebra = typename algebra_dispatcher< State >::algebra_type ,
- class Operations = typename operations_dispatcher< State >::operations_type ,
- class Resizer = initially_resizer
- >
-#ifndef DOXYGEN_SKIP
-class runge_kutta_cash_karp54 : public explicit_error_generic_rk< 6 , 5 , 5 , 4 ,
- State , Value , Deriv , Time , Algebra , Operations , Resizer >
-#else
-class runge_kutta_cash_karp54 : public explicit_error_generic_rk
-#endif
-{
-
-public:
-#ifndef DOXYGEN_SKIP
- typedef explicit_error_generic_rk< 6 , 5 , 5 , 4 , State , Value , Deriv , Time ,
- Algebra , Operations , Resizer > stepper_base_type;
-#endif
- typedef typename stepper_base_type::state_type state_type;
- typedef typename stepper_base_type::value_type value_type;
- typedef typename stepper_base_type::deriv_type deriv_type;
- typedef typename stepper_base_type::time_type time_type;
- typedef typename stepper_base_type::algebra_type algebra_type;
- typedef typename stepper_base_type::operations_type operations_type;
- typedef typename stepper_base_type::resizer_type resizer_typ;
-
- #ifndef DOXYGEN_SKIP
- typedef typename stepper_base_type::stepper_type stepper_type;
- typedef typename stepper_base_type::wrapped_state_type wrapped_state_type;
- typedef typename stepper_base_type::wrapped_deriv_type wrapped_deriv_type;
- #endif
-
-
- runge_kutta_cash_karp54( const algebra_type &algebra = algebra_type() ) : stepper_base_type(
- boost::fusion::make_vector( rk54_ck_coefficients_a1<Value>() ,
- rk54_ck_coefficients_a2<Value>() ,
- rk54_ck_coefficients_a3<Value>() ,
- rk54_ck_coefficients_a4<Value>() ,
- rk54_ck_coefficients_a5<Value>() ) ,
- rk54_ck_coefficients_b<Value>() , rk54_ck_coefficients_db<Value>() , rk54_ck_coefficients_c<Value>() ,
- algebra )
- { }
-};
-
-
-/********** DOXYGEN **********/
-
-/**
- * \class runge_kutta_cash_karp54
- * \brief The Runge-Kutta Cash-Karp method.
- *
- * The Runge-Kutta Cash-Karp method is one of the standard methods for
- * solving ordinary differential equations, see
- * <a href="http://en.wikipedia.org/wiki/Cash%E2%80%93Karp_methods">en.wikipedia.org/wiki/Cash-Karp_methods</a>.
- * The method is explicit and fulfills the Error Stepper concept. Step size control
- * is provided but continuous output is not available for this method.
- *
- * This class derives from explicit_error_stepper_base and inherits its interface via CRTP (current recurring template pattern).
- * Furthermore, it derivs from explicit_error_generic_rk which is a generic Runge-Kutta algorithm with error estimation.
- * For more details see explicit_error_stepper_base and explicit_error_generic_rk.
- *
- * \tparam State The state type.
- * \tparam Value The value type.
- * \tparam Deriv The type representing the time derivative of the state.
- * \tparam Time The time representing the independent variable - the time.
- * \tparam Algebra The algebra type.
- * \tparam Operations The operations type.
- * \tparam Resizer The resizer policy type.
- */
-
-
- /**
- * \fn runge_kutta_cash_karp54::runge_kutta_cash_karp54( const algebra_type &algebra )
- * \brief Constructs the runge_kutta_cash_karp54 class. This constructor can be used as a default
- * constructor if the algebra has a default constructor.
- * \param algebra A copy of algebra is made and stored inside explicit_stepper_base.
- */
-}
-}
-}
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_RUNGE_KUTTA_CASH_KARP54_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/runge_kutta_cash_karp54_classic.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/runge_kutta_cash_karp54_classic.hpp
deleted file mode 100644
index 7600d6efc8b02b77f5bc3b5a47b279797b600e1b..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/runge_kutta_cash_karp54_classic.hpp
+++ /dev/null
@@ -1,289 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/runge_kutta_cash_karp54_classic.hpp
-
- [begin_description]
- Classical implementation of the Runge-Kutta Cash-Karp 5(4) method.
- [end_description]
-
- Copyright 2010-2013 Mario Mulansky
- Copyright 2010-2013 Karsten Ahnert
- Copyright 2012 Christoph Koke
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_RUNGE_KUTTA_CASH_KARP54_CLASSIC_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_RUNGE_KUTTA_CASH_KARP54_CLASSIC_HPP_INCLUDED
-
-
-#include <boost/numeric/odeint/util/bind.hpp>
-
-#include <boost/numeric/odeint/stepper/base/explicit_error_stepper_base.hpp>
-#include <boost/numeric/odeint/algebra/range_algebra.hpp>
-#include <boost/numeric/odeint/algebra/default_operations.hpp>
-#include <boost/numeric/odeint/algebra/algebra_dispatcher.hpp>
-#include <boost/numeric/odeint/algebra/operations_dispatcher.hpp>
-#include <boost/numeric/odeint/stepper/stepper_categories.hpp>
-#include <boost/numeric/odeint/util/state_wrapper.hpp>
-#include <boost/numeric/odeint/util/is_resizeable.hpp>
-#include <boost/numeric/odeint/util/resizer.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-
-
-template<
-class State ,
-class Value = double ,
-class Deriv = State ,
-class Time = Value ,
-class Algebra = typename algebra_dispatcher< State >::algebra_type ,
-class Operations = typename operations_dispatcher< State >::operations_type ,
-class Resizer = initially_resizer
->
-#ifndef DOXYGEN_SKIP
-class runge_kutta_cash_karp54_classic
-: public explicit_error_stepper_base<
- runge_kutta_cash_karp54_classic< State , Value , Deriv , Time , Algebra , Operations , Resizer > ,
- 5 , 5 , 4 , State , Value , Deriv , Time , Algebra , Operations , Resizer >
-#else
-class runge_kutta_cash_karp54_classic : public explicit_error_stepper_base
-#endif
-{
-
-
-public :
-
- #ifndef DOXYGEN_SKIP
- typedef explicit_error_stepper_base<
- runge_kutta_cash_karp54_classic< State , Value , Deriv , Time , Algebra , Operations , Resizer > ,
- 5 , 5 , 4 , State , Value , Deriv , Time , Algebra , Operations , Resizer > stepper_base_type;
- #else
- typedef explicit_error_stepper_base< runge_kutta_cash_karp54_classic< ... > , ... > stepper_base_type;
- #endif
-
- typedef typename stepper_base_type::state_type state_type;
- typedef typename stepper_base_type::value_type value_type;
- typedef typename stepper_base_type::deriv_type deriv_type;
- typedef typename stepper_base_type::time_type time_type;
- typedef typename stepper_base_type::algebra_type algebra_type;
- typedef typename stepper_base_type::operations_type operations_type;
- typedef typename stepper_base_type::resizer_type resizer_type;
-
- #ifndef DOXYGEN_SKIP
- typedef typename stepper_base_type::wrapped_state_type wrapped_state_type;
- typedef typename stepper_base_type::wrapped_deriv_type wrapped_deriv_type;
- typedef typename stepper_base_type::stepper_type stepper_type;
- #endif
-
-
- runge_kutta_cash_karp54_classic( const algebra_type &algebra = algebra_type() ) : stepper_base_type( algebra )
- { }
-
-
-
- template< class System , class StateIn , class DerivIn , class StateOut , class Err >
- void do_step_impl( System system , const StateIn &in , const DerivIn &dxdt , time_type t , StateOut &out , time_type dt , Err &xerr )
- {
- const value_type c1 = static_cast<value_type> ( 37 ) / static_cast<value_type>( 378 );
- const value_type c3 = static_cast<value_type> ( 250 ) / static_cast<value_type>( 621 );
- const value_type c4 = static_cast<value_type> ( 125 ) / static_cast<value_type>( 594 );
- const value_type c6 = static_cast<value_type> ( 512 ) / static_cast<value_type>( 1771 );
-
- const value_type dc1 = c1 - static_cast<value_type> ( 2825 ) / static_cast<value_type>( 27648 );
- const value_type dc3 = c3 - static_cast<value_type> ( 18575 ) / static_cast<value_type>( 48384 );
- const value_type dc4 = c4 - static_cast<value_type> ( 13525 ) / static_cast<value_type>( 55296 );
- const value_type dc5 = static_cast<value_type> ( -277 ) / static_cast<value_type>( 14336 );
- const value_type dc6 = c6 - static_cast<value_type> ( 1 ) / static_cast<value_type> ( 4 );
-
- do_step_impl( system , in , dxdt , t , out , dt );
-
- //error estimate
- stepper_base_type::m_algebra.for_each6( xerr , dxdt , m_k3.m_v , m_k4.m_v , m_k5.m_v , m_k6.m_v ,
- typename operations_type::template scale_sum5< time_type , time_type , time_type , time_type , time_type >( dt*dc1 , dt*dc3 , dt*dc4 , dt*dc5 , dt*dc6 ));
-
- }
-
-
-
- template< class System , class StateIn , class DerivIn , class StateOut >
- void do_step_impl( System system , const StateIn &in , const DerivIn &dxdt , time_type t , StateOut &out , time_type dt )
- {
- const value_type a2 = static_cast<value_type> ( 1 ) / static_cast<value_type> ( 5 );
- const value_type a3 = static_cast<value_type> ( 3 ) / static_cast<value_type> ( 10 );
- const value_type a4 = static_cast<value_type> ( 3 ) / static_cast<value_type> ( 5 );
- const value_type a5 = static_cast<value_type> ( 1 );
- const value_type a6 = static_cast<value_type> ( 7 ) / static_cast<value_type> ( 8 );
-
- const value_type b21 = static_cast<value_type> ( 1 ) / static_cast<value_type> ( 5 );
- const value_type b31 = static_cast<value_type> ( 3 ) / static_cast<value_type>( 40 );
- const value_type b32 = static_cast<value_type> ( 9 ) / static_cast<value_type>( 40 );
- const value_type b41 = static_cast<value_type> ( 3 ) / static_cast<value_type> ( 10 );
- const value_type b42 = static_cast<value_type> ( -9 ) / static_cast<value_type> ( 10 );
- const value_type b43 = static_cast<value_type> ( 6 ) / static_cast<value_type> ( 5 );
- const value_type b51 = static_cast<value_type> ( -11 ) / static_cast<value_type>( 54 );
- const value_type b52 = static_cast<value_type> ( 5 ) / static_cast<value_type> ( 2 );
- const value_type b53 = static_cast<value_type> ( -70 ) / static_cast<value_type>( 27 );
- const value_type b54 = static_cast<value_type> ( 35 ) / static_cast<value_type>( 27 );
- const value_type b61 = static_cast<value_type> ( 1631 ) / static_cast<value_type>( 55296 );
- const value_type b62 = static_cast<value_type> ( 175 ) / static_cast<value_type>( 512 );
- const value_type b63 = static_cast<value_type> ( 575 ) / static_cast<value_type>( 13824 );
- const value_type b64 = static_cast<value_type> ( 44275 ) / static_cast<value_type>( 110592 );
- const value_type b65 = static_cast<value_type> ( 253 ) / static_cast<value_type>( 4096 );
-
- const value_type c1 = static_cast<value_type> ( 37 ) / static_cast<value_type>( 378 );
- const value_type c3 = static_cast<value_type> ( 250 ) / static_cast<value_type>( 621 );
- const value_type c4 = static_cast<value_type> ( 125 ) / static_cast<value_type>( 594 );
- const value_type c6 = static_cast<value_type> ( 512 ) / static_cast<value_type>( 1771 );
-
- typename odeint::unwrap_reference< System >::type &sys = system;
-
- m_resizer.adjust_size( in , detail::bind( &stepper_type::template resize_impl<StateIn> , detail::ref( *this ) , detail::_1 ) );
-
- //m_x1 = x + dt*b21*dxdt
- stepper_base_type::m_algebra.for_each3( m_x_tmp.m_v , in , dxdt ,
- typename operations_type::template scale_sum2< value_type , time_type >( 1.0 , dt*b21 ) );
-
- sys( m_x_tmp.m_v , m_k2.m_v , t + dt*a2 );
- // m_x_tmp = x + dt*b31*dxdt + dt*b32*m_x2
- stepper_base_type::m_algebra.for_each4( m_x_tmp.m_v , in , dxdt , m_k2.m_v ,
- typename operations_type::template scale_sum3< value_type , time_type , time_type >( 1.0 , dt*b31 , dt*b32 ));
-
- sys( m_x_tmp.m_v , m_k3.m_v , t + dt*a3 );
- // m_x_tmp = x + dt * (b41*dxdt + b42*m_x2 + b43*m_x3)
- stepper_base_type::m_algebra.for_each5( m_x_tmp.m_v , in , dxdt , m_k2.m_v , m_k3.m_v ,
- typename operations_type::template scale_sum4< value_type , time_type , time_type , time_type >( 1.0 , dt*b41 , dt*b42 , dt*b43 ));
-
- sys( m_x_tmp.m_v, m_k4.m_v , t + dt*a4 );
- stepper_base_type::m_algebra.for_each6( m_x_tmp.m_v , in , dxdt , m_k2.m_v , m_k3.m_v , m_k4.m_v ,
- typename operations_type::template scale_sum5< value_type , time_type , time_type , time_type , time_type >( 1.0 , dt*b51 , dt*b52 , dt*b53 , dt*b54 ));
-
- sys( m_x_tmp.m_v , m_k5.m_v , t + dt*a5 );
- stepper_base_type::m_algebra.for_each7( m_x_tmp.m_v , in , dxdt , m_k2.m_v , m_k3.m_v , m_k4.m_v , m_k5.m_v ,
- typename operations_type::template scale_sum6< value_type , time_type , time_type , time_type , time_type , time_type >( 1.0 , dt*b61 , dt*b62 , dt*b63 , dt*b64 , dt*b65 ));
-
- sys( m_x_tmp.m_v , m_k6.m_v , t + dt*a6 );
- stepper_base_type::m_algebra.for_each6( out , in , dxdt , m_k3.m_v , m_k4.m_v , m_k6.m_v ,
- typename operations_type::template scale_sum5< value_type , time_type , time_type , time_type , time_type >( 1.0 , dt*c1 , dt*c3 , dt*c4 , dt*c6 ));
-
- }
-
- /**
- * \brief Adjust the size of all temporaries in the stepper manually.
- * \param x A state from which the size of the temporaries to be resized is deduced.
- */
- template< class StateIn >
- void adjust_size( const StateIn &x )
- {
- resize_impl( x );
- stepper_base_type::adjust_size( x );
- }
-
-private:
-
- template< class StateIn >
- bool resize_impl( const StateIn &x )
- {
- bool resized = false;
- resized |= adjust_size_by_resizeability( m_x_tmp , x , typename is_resizeable<state_type>::type() );
- resized |= adjust_size_by_resizeability( m_k2 , x , typename is_resizeable<deriv_type>::type() );
- resized |= adjust_size_by_resizeability( m_k3 , x , typename is_resizeable<deriv_type>::type() );
- resized |= adjust_size_by_resizeability( m_k4 , x , typename is_resizeable<deriv_type>::type() );
- resized |= adjust_size_by_resizeability( m_k5 , x , typename is_resizeable<deriv_type>::type() );
- resized |= adjust_size_by_resizeability( m_k6 , x , typename is_resizeable<deriv_type>::type() );
- return resized;
- }
-
-
- wrapped_state_type m_x_tmp;
- wrapped_deriv_type m_k2, m_k3, m_k4, m_k5, m_k6;
- resizer_type m_resizer;
-
-};
-
-
-
-/************ DOXYGEN *************/
-
-/**
- * \class runge_kutta_cash_karp54_classic
- * \brief The Runge-Kutta Cash-Karp method implemented without the generic Runge-Kutta algorithm.
- *
- * The Runge-Kutta Cash-Karp method is one of the standard methods for
- * solving ordinary differential equations, see
- * <a href="http://en.wikipedia.org/wiki/Cash%E2%80%93Karp_method">en.wikipedia.org/wiki/Cash-Karp_method</a>.
- * The method is explicit and fulfills the Error Stepper concept. Step size control
- * is provided but continuous output is not available for this method.
- *
- * This class derives from explicit_error_stepper_base and inherits its interface via CRTP (current recurring
- * template pattern). This class implements the method directly, hence the generic Runge-Kutta algorithm is not used.
- *
- * \tparam State The state type.
- * \tparam Value The value type.
- * \tparam Deriv The type representing the time derivative of the state.
- * \tparam Time The time representing the independent variable - the time.
- * \tparam Algebra The algebra type.
- * \tparam Operations The operations type.
- * \tparam Resizer The resizer policy type.
- */
-
-
- /**
- * \fn runge_kutta_cash_karp54_classic::runge_kutta_cash_karp54_classic( const algebra_type &algebra )
- * \brief Constructs the runge_kutta_cash_karp54_classic class. This constructor can be used as a default
- * constructor if the algebra has a default constructor.
- * \param algebra A copy of algebra is made and stored inside explicit_stepper_base.
- */
-
-
- /**
- * \fn runge_kutta_cash_karp54_classic::do_step_impl( System system , const StateIn &in , const DerivIn &dxdt , time_type t , StateOut &out , time_type dt , Err &xerr )
- * \brief This method performs one step. The derivative `dxdt` of `in` at the time `t` is passed to the method.
- *
- * The result is updated out-of-place, hence the input is in `in` and the output in `out`. Futhermore, an
- * estimation of the error is stored in `xerr`.
- * Access to this step functionality is provided by explicit_error_stepper_base and
- * `do_step_impl` should not be called directly.
-
- *
- * \param system The system function to solve, hence the r.h.s. of the ODE. It must fulfill the
- * Simple System concept.
- * \param in The state of the ODE which should be solved. in is not modified in this method
- * \param dxdt The derivative of x at t.
- * \param t The value of the time, at which the step should be performed.
- * \param out The result of the step is written in out.
- * \param dt The step size.
- * \param xerr The result of the error estimation is written in xerr.
- */
-
- /**
- * \fn runge_kutta_cash_karp54_classic::do_step_impl( System system , const StateIn &in , const DerivIn &dxdt , time_type t , StateOut &out , time_type dt )
- * \brief This method performs one step. The derivative `dxdt` of `in` at the time `t` is passed to the method.
- * The result is updated out-of-place, hence the input is in `in` and the output in `out`.
- * Access to this step functionality is provided by explicit_error_stepper_base and
- * `do_step_impl` should not be called directly.
- *
- * \param system The system function to solve, hence the r.h.s. of the ODE. It must fulfill the
- * Simple System concept.
- * \param in The state of the ODE which should be solved. in is not modified in this method
- * \param dxdt The derivative of x at t.
- * \param t The value of the time, at which the step should be performed.
- * \param out The result of the step is written in out.
- * \param dt The step size.
- */
-
-} // odeint
-} // numeric
-} // boost
-
-
-
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_RUNGE_KUTTA_CASH_KARP54_CLASSIC_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/runge_kutta_dopri5.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/runge_kutta_dopri5.hpp
deleted file mode 100644
index 5d1b1159093961a2113f354cdd2240d3afd91758..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/runge_kutta_dopri5.hpp
+++ /dev/null
@@ -1,403 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/runge_kutta_dopri5.hpp
-
- [begin_description]
- Implementation of the Dormand-Prince 5(4) method. This stepper can also be used with the dense-output controlled stepper.
- [end_description]
-
- Copyright 2010-2013 Karsten Ahnert
- Copyright 2010-2013 Mario Mulansky
- Copyright 2012 Christoph Koke
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_RUNGE_KUTTA_DOPRI5_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_RUNGE_KUTTA_DOPRI5_HPP_INCLUDED
-
-
-#include <boost/numeric/odeint/util/bind.hpp>
-
-#include <boost/numeric/odeint/stepper/base/explicit_error_stepper_fsal_base.hpp>
-#include <boost/numeric/odeint/algebra/range_algebra.hpp>
-#include <boost/numeric/odeint/algebra/default_operations.hpp>
-#include <boost/numeric/odeint/algebra/algebra_dispatcher.hpp>
-#include <boost/numeric/odeint/algebra/operations_dispatcher.hpp>
-#include <boost/numeric/odeint/stepper/stepper_categories.hpp>
-
-#include <boost/numeric/odeint/util/state_wrapper.hpp>
-#include <boost/numeric/odeint/util/is_resizeable.hpp>
-#include <boost/numeric/odeint/util/resizer.hpp>
-#include <boost/numeric/odeint/util/same_instance.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-
-template<
-class State ,
-class Value = double ,
-class Deriv = State ,
-class Time = Value ,
-class Algebra = typename algebra_dispatcher< State >::algebra_type ,
-class Operations = typename operations_dispatcher< State >::operations_type ,
-class Resizer = initially_resizer
->
-class runge_kutta_dopri5
-#ifndef DOXYGEN_SKIP
-: public explicit_error_stepper_fsal_base<
- runge_kutta_dopri5< State , Value , Deriv , Time , Algebra , Operations , Resizer > ,
- 5 , 5 , 4 , State , Value , Deriv , Time , Algebra , Operations , Resizer >
-#else
-: public explicit_error_stepper_fsal_base
-#endif
-{
-
-public :
-
- #ifndef DOXYGEN_SKIP
- typedef explicit_error_stepper_fsal_base<
- runge_kutta_dopri5< State , Value , Deriv , Time , Algebra , Operations , Resizer > ,
- 5 , 5 , 4 , State , Value , Deriv , Time , Algebra , Operations , Resizer > stepper_base_type;
- #else
- typedef explicit_error_stepper_fsal_base< runge_kutta_dopri5< ... > , ... > stepper_base_type;
- #endif
-
- typedef typename stepper_base_type::state_type state_type;
- typedef typename stepper_base_type::value_type value_type;
- typedef typename stepper_base_type::deriv_type deriv_type;
- typedef typename stepper_base_type::time_type time_type;
- typedef typename stepper_base_type::algebra_type algebra_type;
- typedef typename stepper_base_type::operations_type operations_type;
- typedef typename stepper_base_type::resizer_type resizer_type;
-
- #ifndef DOXYGEN_SKIP
- typedef typename stepper_base_type::stepper_type stepper_type;
- typedef typename stepper_base_type::wrapped_state_type wrapped_state_type;
- typedef typename stepper_base_type::wrapped_deriv_type wrapped_deriv_type;
- #endif // DOXYGEN_SKIP
-
-
- runge_kutta_dopri5( const algebra_type &algebra = algebra_type() ) : stepper_base_type( algebra )
- { }
-
-
- template< class System , class StateIn , class DerivIn , class StateOut , class DerivOut >
- void do_step_impl( System system , const StateIn &in , const DerivIn &dxdt_in , time_type t ,
- StateOut &out , DerivOut &dxdt_out , time_type dt )
- {
- const value_type a2 = static_cast<value_type> ( 1 ) / static_cast<value_type>( 5 );
- const value_type a3 = static_cast<value_type> ( 3 ) / static_cast<value_type> ( 10 );
- const value_type a4 = static_cast<value_type> ( 4 ) / static_cast<value_type> ( 5 );
- const value_type a5 = static_cast<value_type> ( 8 )/static_cast<value_type> ( 9 );
-
- const value_type b21 = static_cast<value_type> ( 1 ) / static_cast<value_type> ( 5 );
-
- const value_type b31 = static_cast<value_type> ( 3 ) / static_cast<value_type>( 40 );
- const value_type b32 = static_cast<value_type> ( 9 ) / static_cast<value_type>( 40 );
-
- const value_type b41 = static_cast<value_type> ( 44 ) / static_cast<value_type> ( 45 );
- const value_type b42 = static_cast<value_type> ( -56 ) / static_cast<value_type> ( 15 );
- const value_type b43 = static_cast<value_type> ( 32 ) / static_cast<value_type> ( 9 );
-
- const value_type b51 = static_cast<value_type> ( 19372 ) / static_cast<value_type>( 6561 );
- const value_type b52 = static_cast<value_type> ( -25360 ) / static_cast<value_type> ( 2187 );
- const value_type b53 = static_cast<value_type> ( 64448 ) / static_cast<value_type>( 6561 );
- const value_type b54 = static_cast<value_type> ( -212 ) / static_cast<value_type>( 729 );
-
- const value_type b61 = static_cast<value_type> ( 9017 ) / static_cast<value_type>( 3168 );
- const value_type b62 = static_cast<value_type> ( -355 ) / static_cast<value_type>( 33 );
- const value_type b63 = static_cast<value_type> ( 46732 ) / static_cast<value_type>( 5247 );
- const value_type b64 = static_cast<value_type> ( 49 ) / static_cast<value_type>( 176 );
- const value_type b65 = static_cast<value_type> ( -5103 ) / static_cast<value_type>( 18656 );
-
- const value_type c1 = static_cast<value_type> ( 35 ) / static_cast<value_type>( 384 );
- const value_type c3 = static_cast<value_type> ( 500 ) / static_cast<value_type>( 1113 );
- const value_type c4 = static_cast<value_type> ( 125 ) / static_cast<value_type>( 192 );
- const value_type c5 = static_cast<value_type> ( -2187 ) / static_cast<value_type>( 6784 );
- const value_type c6 = static_cast<value_type> ( 11 ) / static_cast<value_type>( 84 );
-
- typename odeint::unwrap_reference< System >::type &sys = system;
-
- m_k_x_tmp_resizer.adjust_size( in , detail::bind( &stepper_type::template resize_k_x_tmp_impl<StateIn> , detail::ref( *this ) , detail::_1 ) );
-
- //m_x_tmp = x + dt*b21*dxdt
- stepper_base_type::m_algebra.for_each3( m_x_tmp.m_v , in , dxdt_in ,
- typename operations_type::template scale_sum2< value_type , time_type >( 1.0 , dt*b21 ) );
-
- sys( m_x_tmp.m_v , m_k2.m_v , t + dt*a2 );
- // m_x_tmp = x + dt*b31*dxdt + dt*b32*m_k2
- stepper_base_type::m_algebra.for_each4( m_x_tmp.m_v , in , dxdt_in , m_k2.m_v ,
- typename operations_type::template scale_sum3< value_type , time_type , time_type >( 1.0 , dt*b31 , dt*b32 ));
-
- sys( m_x_tmp.m_v , m_k3.m_v , t + dt*a3 );
- // m_x_tmp = x + dt * (b41*dxdt + b42*m_k2 + b43*m_k3)
- stepper_base_type::m_algebra.for_each5( m_x_tmp.m_v , in , dxdt_in , m_k2.m_v , m_k3.m_v ,
- typename operations_type::template scale_sum4< value_type , time_type , time_type , time_type >( 1.0 , dt*b41 , dt*b42 , dt*b43 ));
-
- sys( m_x_tmp.m_v, m_k4.m_v , t + dt*a4 );
- stepper_base_type::m_algebra.for_each6( m_x_tmp.m_v , in , dxdt_in , m_k2.m_v , m_k3.m_v , m_k4.m_v ,
- typename operations_type::template scale_sum5< value_type , time_type , time_type , time_type , time_type >( 1.0 , dt*b51 , dt*b52 , dt*b53 , dt*b54 ));
-
- sys( m_x_tmp.m_v , m_k5.m_v , t + dt*a5 );
- stepper_base_type::m_algebra.for_each7( m_x_tmp.m_v , in , dxdt_in , m_k2.m_v , m_k3.m_v , m_k4.m_v , m_k5.m_v ,
- typename operations_type::template scale_sum6< value_type , time_type , time_type , time_type , time_type , time_type >( 1.0 , dt*b61 , dt*b62 , dt*b63 , dt*b64 , dt*b65 ));
-
- sys( m_x_tmp.m_v , m_k6.m_v , t + dt );
- stepper_base_type::m_algebra.for_each7( out , in , dxdt_in , m_k3.m_v , m_k4.m_v , m_k5.m_v , m_k6.m_v ,
- typename operations_type::template scale_sum6< value_type , time_type , time_type , time_type , time_type , time_type >( 1.0 , dt*c1 , dt*c3 , dt*c4 , dt*c5 , dt*c6 ));
-
- // the new derivative
- sys( out , dxdt_out , t + dt );
- }
-
-
-
- template< class System , class StateIn , class DerivIn , class StateOut , class DerivOut , class Err >
- void do_step_impl( System system , const StateIn &in , const DerivIn &dxdt_in , time_type t ,
- StateOut &out , DerivOut &dxdt_out , time_type dt , Err &xerr )
- {
- const value_type c1 = static_cast<value_type> ( 35 ) / static_cast<value_type>( 384 );
- const value_type c3 = static_cast<value_type> ( 500 ) / static_cast<value_type>( 1113 );
- const value_type c4 = static_cast<value_type> ( 125 ) / static_cast<value_type>( 192 );
- const value_type c5 = static_cast<value_type> ( -2187 ) / static_cast<value_type>( 6784 );
- const value_type c6 = static_cast<value_type> ( 11 ) / static_cast<value_type>( 84 );
-
- const value_type dc1 = c1 - static_cast<value_type> ( 5179 ) / static_cast<value_type>( 57600 );
- const value_type dc3 = c3 - static_cast<value_type> ( 7571 ) / static_cast<value_type>( 16695 );
- const value_type dc4 = c4 - static_cast<value_type> ( 393 ) / static_cast<value_type>( 640 );
- const value_type dc5 = c5 - static_cast<value_type> ( -92097 ) / static_cast<value_type>( 339200 );
- const value_type dc6 = c6 - static_cast<value_type> ( 187 ) / static_cast<value_type>( 2100 );
- const value_type dc7 = static_cast<value_type>( -1 ) / static_cast<value_type> ( 40 );
-
- /* ToDo: copy only if &dxdt_in == &dxdt_out ? */
- if( same_instance( dxdt_in , dxdt_out ) )
- {
- m_dxdt_tmp_resizer.adjust_size( in , detail::bind( &stepper_type::template resize_dxdt_tmp_impl<StateIn> , detail::ref( *this ) , detail::_1 ) );
- boost::numeric::odeint::copy( dxdt_in , m_dxdt_tmp.m_v );
- do_step_impl( system , in , dxdt_in , t , out , dxdt_out , dt );
- //error estimate
- stepper_base_type::m_algebra.for_each7( xerr , m_dxdt_tmp.m_v , m_k3.m_v , m_k4.m_v , m_k5.m_v , m_k6.m_v , dxdt_out ,
- typename operations_type::template scale_sum6< time_type , time_type , time_type , time_type , time_type , time_type >( dt*dc1 , dt*dc3 , dt*dc4 , dt*dc5 , dt*dc6 , dt*dc7 ) );
-
- }
- else
- {
- do_step_impl( system , in , dxdt_in , t , out , dxdt_out , dt );
- //error estimate
- stepper_base_type::m_algebra.for_each7( xerr , dxdt_in , m_k3.m_v , m_k4.m_v , m_k5.m_v , m_k6.m_v , dxdt_out ,
- typename operations_type::template scale_sum6< time_type , time_type , time_type , time_type , time_type , time_type >( dt*dc1 , dt*dc3 , dt*dc4 , dt*dc5 , dt*dc6 , dt*dc7 ) );
-
- }
-
- }
-
-
- /*
- * Calculates Dense-Output for Dopri5
- *
- * See Hairer, Norsett, Wanner: Solving Ordinary Differential Equations, Nonstiff Problems. I, p.191/192
- *
- * y(t+theta) = y(t) + h * sum_i^7 b_i(theta) * k_i
- *
- * A = theta^2 * ( 3 - 2 theta )
- * B = theta^2 * ( theta - 1 )
- * C = theta^2 * ( theta - 1 )^2
- * D = theta * ( theta - 1 )^2
- *
- * b_1( theta ) = A * b_1 - C * X1( theta ) + D
- * b_2( theta ) = 0
- * b_3( theta ) = A * b_3 + C * X3( theta )
- * b_4( theta ) = A * b_4 - C * X4( theta )
- * b_5( theta ) = A * b_5 + C * X5( theta )
- * b_6( theta ) = A * b_6 - C * X6( theta )
- * b_7( theta ) = B + C * X7( theta )
- *
- * An alternative Method is described in:
- *
- * www-m2.ma.tum.de/homepages/simeon/numerik3/kap3.ps
- */
- template< class StateOut , class StateIn1 , class DerivIn1 , class StateIn2 , class DerivIn2 >
- void calc_state( time_type t , StateOut &x ,
- const StateIn1 &x_old , const DerivIn1 &deriv_old , time_type t_old ,
- const StateIn2 & /* x_new */ , const DerivIn2 &deriv_new , time_type t_new ) const
- {
- const value_type b1 = static_cast<value_type> ( 35 ) / static_cast<value_type>( 384 );
- const value_type b3 = static_cast<value_type> ( 500 ) / static_cast<value_type>( 1113 );
- const value_type b4 = static_cast<value_type> ( 125 ) / static_cast<value_type>( 192 );
- const value_type b5 = static_cast<value_type> ( -2187 ) / static_cast<value_type>( 6784 );
- const value_type b6 = static_cast<value_type> ( 11 ) / static_cast<value_type>( 84 );
-
- const time_type dt = ( t_new - t_old );
- const value_type theta = ( t - t_old ) / dt;
- const value_type X1 = static_cast< value_type >( 5 ) * ( static_cast< value_type >( 2558722523LL ) - static_cast< value_type >( 31403016 ) * theta ) / static_cast< value_type >( 11282082432LL );
- const value_type X3 = static_cast< value_type >( 100 ) * ( static_cast< value_type >( 882725551 ) - static_cast< value_type >( 15701508 ) * theta ) / static_cast< value_type >( 32700410799LL );
- const value_type X4 = static_cast< value_type >( 25 ) * ( static_cast< value_type >( 443332067 ) - static_cast< value_type >( 31403016 ) * theta ) / static_cast< value_type >( 1880347072LL ) ;
- const value_type X5 = static_cast< value_type >( 32805 ) * ( static_cast< value_type >( 23143187 ) - static_cast< value_type >( 3489224 ) * theta ) / static_cast< value_type >( 199316789632LL );
- const value_type X6 = static_cast< value_type >( 55 ) * ( static_cast< value_type >( 29972135 ) - static_cast< value_type >( 7076736 ) * theta ) / static_cast< value_type >( 822651844 );
- const value_type X7 = static_cast< value_type >( 10 ) * ( static_cast< value_type >( 7414447 ) - static_cast< value_type >( 829305 ) * theta ) / static_cast< value_type >( 29380423 );
-
- const value_type theta_m_1 = theta - static_cast< value_type >( 1 );
- const value_type theta_sq = theta * theta;
- const value_type A = theta_sq * ( static_cast< value_type >( 3 ) - static_cast< value_type >( 2 ) * theta );
- const value_type B = theta_sq * theta_m_1;
- const value_type C = theta_sq * theta_m_1 * theta_m_1;
- const value_type D = theta * theta_m_1 * theta_m_1;
-
- const value_type b1_theta = A * b1 - C * X1 + D;
- const value_type b3_theta = A * b3 + C * X3;
- const value_type b4_theta = A * b4 - C * X4;
- const value_type b5_theta = A * b5 + C * X5;
- const value_type b6_theta = A * b6 - C * X6;
- const value_type b7_theta = B + C * X7;
-
- // const state_type &k1 = *m_old_deriv;
- // const state_type &k3 = dopri5().m_k3;
- // const state_type &k4 = dopri5().m_k4;
- // const state_type &k5 = dopri5().m_k5;
- // const state_type &k6 = dopri5().m_k6;
- // const state_type &k7 = *m_current_deriv;
-
- stepper_base_type::m_algebra.for_each8( x , x_old , deriv_old , m_k3.m_v , m_k4.m_v , m_k5.m_v , m_k6.m_v , deriv_new ,
- typename operations_type::template scale_sum7< value_type , time_type , time_type , time_type , time_type , time_type , time_type >( 1.0 , dt * b1_theta , dt * b3_theta , dt * b4_theta , dt * b5_theta , dt * b6_theta , dt * b7_theta ) );
- }
-
-
- template< class StateIn >
- void adjust_size( const StateIn &x )
- {
- resize_k_x_tmp_impl( x );
- resize_dxdt_tmp_impl( x );
- stepper_base_type::adjust_size( x );
- }
-
-
-private:
-
- template< class StateIn >
- bool resize_k_x_tmp_impl( const StateIn &x )
- {
- bool resized = false;
- resized |= adjust_size_by_resizeability( m_x_tmp , x , typename is_resizeable<state_type>::type() );
- resized |= adjust_size_by_resizeability( m_k2 , x , typename is_resizeable<deriv_type>::type() );
- resized |= adjust_size_by_resizeability( m_k3 , x , typename is_resizeable<deriv_type>::type() );
- resized |= adjust_size_by_resizeability( m_k4 , x , typename is_resizeable<deriv_type>::type() );
- resized |= adjust_size_by_resizeability( m_k5 , x , typename is_resizeable<deriv_type>::type() );
- resized |= adjust_size_by_resizeability( m_k6 , x , typename is_resizeable<deriv_type>::type() );
- return resized;
- }
-
- template< class StateIn >
- bool resize_dxdt_tmp_impl( const StateIn &x )
- {
- return adjust_size_by_resizeability( m_dxdt_tmp , x , typename is_resizeable<deriv_type>::type() );
- }
-
-
-
- wrapped_state_type m_x_tmp;
- wrapped_deriv_type m_k2 , m_k3 , m_k4 , m_k5 , m_k6 ;
- wrapped_deriv_type m_dxdt_tmp;
- resizer_type m_k_x_tmp_resizer;
- resizer_type m_dxdt_tmp_resizer;
-};
-
-
-
-/************* DOXYGEN ************/
-/**
- * \class runge_kutta_dopri5
- * \brief The Runge-Kutta Dormand-Prince 5 method.
- *
- * The Runge-Kutta Dormand-Prince 5 method is a very popular method for solving ODEs, see
- * <a href=""></a>.
- * The method is explicit and fulfills the Error Stepper concept. Step size control
- * is provided but continuous output is available which make this method favourable for many applications.
- *
- * This class derives from explicit_error_stepper_fsal_base and inherits its interface via CRTP (current recurring
- * template pattern). The method possesses the FSAL (first-same-as-last) property. See
- * explicit_error_stepper_fsal_base for more details.
- *
- * \tparam State The state type.
- * \tparam Value The value type.
- * \tparam Deriv The type representing the time derivative of the state.
- * \tparam Time The time representing the independent variable - the time.
- * \tparam Algebra The algebra type.
- * \tparam Operations The operations type.
- * \tparam Resizer The resizer policy type.
- */
-
-
- /**
- * \fn runge_kutta_dopri5::runge_kutta_dopri5( const algebra_type &algebra )
- * \brief Constructs the runge_kutta_dopri5 class. This constructor can be used as a default
- * constructor if the algebra has a default constructor.
- * \param algebra A copy of algebra is made and stored inside explicit_stepper_base.
- */
-
- /**
- * \fn runge_kutta_dopri5::do_step_impl( System system , const StateIn &in , const DerivIn &dxdt_in , time_type t , StateOut &out , DerivOut &dxdt_out , time_type dt )
- * \brief This method performs one step. The derivative `dxdt_in` of `in` at the time `t` is passed to the
- * method. The result is updated out-of-place, hence the input is in `in` and the output in `out`. Furthermore,
- * the derivative is update out-of-place, hence the input is assumed to be in `dxdt_in` and the output in
- * `dxdt_out`.
- * Access to this step functionality is provided by explicit_error_stepper_fsal_base and
- * `do_step_impl` should not be called directly.
- *
- * \param system The system function to solve, hence the r.h.s. of the ODE. It must fulfill the
- * Simple System concept.
- * \param in The state of the ODE which should be solved. in is not modified in this method
- * \param dxdt_in The derivative of x at t. dxdt_in is not modified by this method
- * \param t The value of the time, at which the step should be performed.
- * \param out The result of the step is written in out.
- * \param dxdt_out The result of the new derivative at time t+dt.
- * \param dt The step size.
- */
-
- /**
- * \fn runge_kutta_dopri5::do_step_impl( System system , const StateIn &in , const DerivIn &dxdt_in , time_type t , StateOut &out , DerivOut &dxdt_out , time_type dt , Err &xerr )
- * \brief This method performs one step. The derivative `dxdt_in` of `in` at the time `t` is passed to the
- * method. The result is updated out-of-place, hence the input is in `in` and the output in `out`. Furthermore,
- * the derivative is update out-of-place, hence the input is assumed to be in `dxdt_in` and the output in
- * `dxdt_out`.
- * Access to this step functionality is provided by explicit_error_stepper_fsal_base and
- * `do_step_impl` should not be called directly.
- * An estimation of the error is calculated.
- *
- * \param system The system function to solve, hence the r.h.s. of the ODE. It must fulfill the
- * Simple System concept.
- * \param in The state of the ODE which should be solved. in is not modified in this method
- * \param dxdt_in The derivative of x at t. dxdt_in is not modified by this method
- * \param t The value of the time, at which the step should be performed.
- * \param out The result of the step is written in out.
- * \param dxdt_out The result of the new derivative at time t+dt.
- * \param dt The step size.
- * \param xerr An estimation of the error.
- */
-
- /**
- * \fn runge_kutta_dopri5::calc_state( time_type t , StateOut &x , const StateIn1 &x_old , const DerivIn1 &deriv_old , time_type t_old , const StateIn2 & , const DerivIn2 &deriv_new , time_type t_new ) const
- * \brief This method is used for continuous output and it calculates the state `x` at a time `t` from the
- * knowledge of two states `old_state` and `current_state` at time points `t_old` and `t_new`. It also uses
- * internal variables to calculate the result. Hence this method must be called after two successful `do_step`
- * calls.
- */
-
- /**
- * \fn runge_kutta_dopri5::adjust_size( const StateIn &x )
- * \brief Adjust the size of all temporaries in the stepper manually.
- * \param x A state from which the size of the temporaries to be resized is deduced.
- */
-
-} // odeint
-} // numeric
-} // boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_RUNGE_KUTTA_DOPRI5_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/runge_kutta_fehlberg78.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/runge_kutta_fehlberg78.hpp
deleted file mode 100644
index 956b5b62e18d6ee38431c0073432f157ba84abf5..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/runge_kutta_fehlberg78.hpp
+++ /dev/null
@@ -1,374 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/runge_kutta_fehlberg87.hpp
-
- [begin_description]
- Implementation of the Runge-Kutta-Fehlberg stepper with the generic stepper.
- [end_description]
-
- Copyright 2011-2013 Mario Mulansky
- Copyright 2012-2013 Karsten Ahnert
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_RUNGE_KUTTA_FEHLBERG87_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_RUNGE_KUTTA_FEHLBERG87_HPP_INCLUDED
-
-
-#include <boost/fusion/container/vector.hpp>
-#include <boost/fusion/container/generation/make_vector.hpp>
-
-#include <boost/numeric/odeint/stepper/explicit_error_generic_rk.hpp>
-#include <boost/numeric/odeint/algebra/range_algebra.hpp>
-#include <boost/numeric/odeint/algebra/default_operations.hpp>
-#include <boost/numeric/odeint/algebra/algebra_dispatcher.hpp>
-#include <boost/numeric/odeint/algebra/operations_dispatcher.hpp>
-
-#include <boost/array.hpp>
-
-#include <boost/numeric/odeint/util/state_wrapper.hpp>
-#include <boost/numeric/odeint/util/is_resizeable.hpp>
-#include <boost/numeric/odeint/util/resizer.hpp>
-
-
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-#ifndef DOXYGEN_SKIP
-template< class Value = double >
-struct rk78_coefficients_a1 : boost::array< Value , 1 >
-{
- rk78_coefficients_a1( void )
- {
- (*this)[0] = static_cast< Value >( 2 )/static_cast< Value >( 27 );
- }
-};
-
-template< class Value = double >
-struct rk78_coefficients_a2 : boost::array< Value , 2 >
-{
- rk78_coefficients_a2( void )
- {
- (*this)[0] = static_cast< Value >( 1 )/static_cast< Value >( 36 );
- (*this)[1] = static_cast< Value >( 1 )/static_cast< Value >( 12 );
- }
-};
-
-
-template< class Value = double >
-struct rk78_coefficients_a3 : boost::array< Value , 3 >
-{
- rk78_coefficients_a3( void )
- {
- (*this)[0] = static_cast< Value >( 1 )/static_cast< Value >( 24 );
- (*this)[1] = static_cast< Value >( 0 );
- (*this)[2] = static_cast< Value >( 1 )/static_cast< Value >( 8 );
- }
-};
-
-template< class Value = double >
-struct rk78_coefficients_a4 : boost::array< Value , 4 >
-{
- rk78_coefficients_a4( void )
- {
- (*this)[0] = static_cast< Value >( 5 )/static_cast< Value >( 12 );
- (*this)[1] = static_cast< Value >( 0 );
- (*this)[2] = static_cast< Value >( -25 )/static_cast< Value >( 16 );
- (*this)[3] = static_cast< Value >( 25 )/static_cast< Value >( 16 );
- }
-};
-
-template< class Value = double >
-struct rk78_coefficients_a5 : boost::array< Value , 5 >
-{
- rk78_coefficients_a5( void )
- {
- (*this)[0] = static_cast< Value >( 1 )/static_cast< Value >( 20 );
- (*this)[1] = static_cast< Value >( 0 );
- (*this)[2] = static_cast< Value >( 0 );
- (*this)[3] = static_cast< Value >( 1 )/static_cast< Value >( 4 );
- (*this)[4] = static_cast< Value >( 1 )/static_cast< Value >( 5 );
- }
-};
-
-
-template< class Value = double >
-struct rk78_coefficients_a6 : boost::array< Value , 6 >
-{
- rk78_coefficients_a6( void )
- {
- (*this)[0] = static_cast< Value >( -25 )/static_cast< Value >( 108 );
- (*this)[1] = static_cast< Value >( 0 );
- (*this)[2] = static_cast< Value >( 0 );
- (*this)[3] = static_cast< Value >( 125 )/static_cast< Value >( 108 );
- (*this)[4] = static_cast< Value >( -65 )/static_cast< Value >( 27 );
- (*this)[5] = static_cast< Value >( 125 )/static_cast< Value >( 54 );
- }
-};
-
-template< class Value = double >
-struct rk78_coefficients_a7 : boost::array< Value , 7 >
-{
- rk78_coefficients_a7( void )
- {
- (*this)[0] = static_cast< Value >( 31 )/static_cast< Value >( 300 );
- (*this)[1] = static_cast< Value >( 0 );
- (*this)[2] = static_cast< Value >( 0 );
- (*this)[3] = static_cast< Value >( 0 );
- (*this)[4] = static_cast< Value >( 61 )/static_cast< Value >( 225 );
- (*this)[5] = static_cast< Value >( -2 )/static_cast< Value >( 9 );
- (*this)[6] = static_cast< Value >( 13 )/static_cast< Value >( 900 );
- }
-};
-
-template< class Value = double >
-struct rk78_coefficients_a8 : boost::array< Value , 8 >
-{
- rk78_coefficients_a8( void )
- {
- (*this)[0] = static_cast< Value >( 2 );
- (*this)[1] = static_cast< Value >( 0 );
- (*this)[2] = static_cast< Value >( 0 );
- (*this)[3] = static_cast< Value >( -53 )/static_cast< Value >( 6 );
- (*this)[4] = static_cast< Value >( 704 )/static_cast< Value >( 45 );
- (*this)[5] = static_cast< Value >( -107 )/static_cast< Value >( 9 );
- (*this)[6] = static_cast< Value >( 67 )/static_cast< Value >( 90 );
- (*this)[7] = static_cast< Value >( 3 );
- }
-};
-
-template< class Value = double >
-struct rk78_coefficients_a9 : boost::array< Value , 9 >
-{
- rk78_coefficients_a9( void )
- {
- (*this)[0] = static_cast< Value >( -91 )/static_cast< Value >( 108 );
- (*this)[1] = static_cast< Value >( 0 );
- (*this)[2] = static_cast< Value >( 0 );
- (*this)[3] = static_cast< Value >( 23 )/static_cast< Value >( 108 );
- (*this)[4] = static_cast< Value >( -976 )/static_cast< Value >( 135 );
- (*this)[5] = static_cast< Value >( 311 )/static_cast< Value >( 54 );
- (*this)[6] = static_cast< Value >( -19 )/static_cast< Value >( 60 );
- (*this)[7] = static_cast< Value >( 17 )/static_cast< Value >( 6 );
- (*this)[8] = static_cast< Value >( -1 )/static_cast< Value >( 12 );
- }
-};
-
-template< class Value = double >
-struct rk78_coefficients_a10 : boost::array< Value , 10 >
-{
- rk78_coefficients_a10( void )
- {
- (*this)[0] = static_cast< Value >( 2383 )/static_cast< Value >( 4100 );
- (*this)[1] = static_cast< Value >( 0 );
- (*this)[2] = static_cast< Value >( 0 );
- (*this)[3] = static_cast< Value >( -341 )/static_cast< Value >( 164 );
- (*this)[4] = static_cast< Value >( 4496 )/static_cast< Value >( 1025 );
- (*this)[5] = static_cast< Value >( -301 )/static_cast< Value >( 82 );
- (*this)[6] = static_cast< Value >( 2133 )/static_cast< Value >( 4100 );
- (*this)[7] = static_cast< Value >( 45 )/static_cast< Value >( 82 );
- (*this)[8] = static_cast< Value >( 45 )/static_cast< Value >( 164 );
- (*this)[9] = static_cast< Value >( 18 )/static_cast< Value >( 41 );
- }
-};
-
-template< class Value = double >
-struct rk78_coefficients_a11 : boost::array< Value , 11 >
-{
- rk78_coefficients_a11( void )
- {
- (*this)[0] = static_cast< Value >( 3 )/static_cast< Value >( 205 );
- (*this)[1] = static_cast< Value >( 0 );
- (*this)[2] = static_cast< Value >( 0 );
- (*this)[3] = static_cast< Value >( 0 );
- (*this)[4] = static_cast< Value >( 0 );
- (*this)[5] = static_cast< Value >( -6 )/static_cast< Value >( 41 );
- (*this)[6] = static_cast< Value >( -3 )/static_cast< Value >( 205 );
- (*this)[7] = static_cast< Value >( -3 )/static_cast< Value >( 41 );
- (*this)[8] = static_cast< Value >( 3 )/static_cast< Value >( 41 );
- (*this)[9] = static_cast< Value >( 6 )/static_cast< Value >( 41 );
- (*this)[10] = static_cast< Value >( 0 );
- }
-};
-
-template< class Value = double >
-struct rk78_coefficients_a12 : boost::array< Value , 12 >
-{
- rk78_coefficients_a12( void )
- {
- (*this)[0] = static_cast< Value >( -1777 )/static_cast< Value >( 4100 );
- (*this)[1] = static_cast< Value >( 0 );
- (*this)[2] = static_cast< Value >( 0 );
- (*this)[3] = static_cast< Value >( -341 )/static_cast< Value >( 164 );
- (*this)[4] = static_cast< Value >( 4496 )/static_cast< Value >( 1025 );
- (*this)[5] = static_cast< Value >( -289 )/static_cast< Value >( 82 );
- (*this)[6] = static_cast< Value >( 2193 )/static_cast< Value >( 4100 );
- (*this)[7] = static_cast< Value >( 51 )/static_cast< Value >( 82 );
- (*this)[8] = static_cast< Value >( 33 )/static_cast< Value >( 164 );
- (*this)[9] = static_cast< Value >( 12 )/static_cast< Value >( 41 );
- (*this)[10] = static_cast< Value >( 0 );
- (*this)[11] = static_cast< Value >( 1 );
- }
-};
-
-template< class Value = double >
-struct rk78_coefficients_b : boost::array< Value , 13 >
-{
- rk78_coefficients_b( void )
- {
- (*this)[0] = static_cast< Value >( 0 );
- (*this)[1] = static_cast< Value >( 0 );
- (*this)[2] = static_cast< Value >( 0 );
- (*this)[3] = static_cast< Value >( 0 );
- (*this)[4] = static_cast< Value >( 0 );
- (*this)[5] = static_cast< Value >( 34 )/static_cast<Value>( 105 );
- (*this)[6] = static_cast< Value >( 9 )/static_cast<Value>( 35 );
- (*this)[7] = static_cast< Value >( 9 )/static_cast<Value>( 35 );
- (*this)[8] = static_cast< Value >( 9 )/static_cast<Value>( 280 );
- (*this)[9] = static_cast< Value >( 9 )/static_cast<Value>( 280 );
- (*this)[10] = static_cast< Value >( 0 );
- (*this)[11] = static_cast< Value >( 41 )/static_cast<Value>( 840 );
- (*this)[12] = static_cast< Value >( 41 )/static_cast<Value>( 840 );
- }
-};
-
-template< class Value = double >
-struct rk78_coefficients_db : boost::array< Value , 13 >
-{
- rk78_coefficients_db( void )
- {
- (*this)[0] = static_cast< Value >( 0 ) - static_cast< Value >( 41 )/static_cast<Value>( 840 );
- (*this)[1] = static_cast< Value >( 0 );
- (*this)[2] = static_cast< Value >( 0 );
- (*this)[3] = static_cast< Value >( 0 );
- (*this)[4] = static_cast< Value >( 0 );
- (*this)[5] = static_cast< Value >( 0 );
- (*this)[6] = static_cast< Value >( 0 );
- (*this)[7] = static_cast< Value >( 0 );
- (*this)[8] = static_cast< Value >( 0 );
- (*this)[9] = static_cast< Value >( 0 );
- (*this)[10] = static_cast< Value >( 0 ) - static_cast< Value >( 41 )/static_cast<Value>( 840 );
- (*this)[11] = static_cast< Value >( 41 )/static_cast<Value>( 840 );
- (*this)[12] = static_cast< Value >( 41 )/static_cast<Value>( 840 );
- }
-};
-
-
-template< class Value = double >
-struct rk78_coefficients_c : boost::array< Value , 13 >
-{
- rk78_coefficients_c( void )
- {
- (*this)[0] = static_cast< Value >( 0 );
- (*this)[1] = static_cast< Value >( 2 )/static_cast< Value >( 27 );
- (*this)[2] = static_cast< Value >( 1 )/static_cast< Value >( 9 );
- (*this)[3] = static_cast< Value >( 1 )/static_cast<Value>( 6 );
- (*this)[4] = static_cast< Value >( 5 )/static_cast<Value>( 12 );
- (*this)[5] = static_cast< Value >( 1 )/static_cast<Value>( 2 );
- (*this)[6] = static_cast< Value >( 5 )/static_cast<Value>( 6 );
- (*this)[7] = static_cast< Value >( 1 )/static_cast<Value>( 6 );
- (*this)[8] = static_cast< Value >( 2 )/static_cast<Value>( 3 );
- (*this)[9] = static_cast< Value >( 1 )/static_cast<Value>( 3 );
- (*this)[10] = static_cast< Value >( 1 );
- (*this)[11] = static_cast< Value >( 0 );
- (*this)[12] = static_cast< Value >( 1 );
- }
-};
-#endif // DOXYGEN_SKIP
-
-
-
-
-
-template<
-class State ,
-class Value = double ,
-class Deriv = State ,
-class Time = Value ,
-class Algebra = typename algebra_dispatcher< State >::algebra_type ,
-class Operations = typename operations_dispatcher< State >::operations_type ,
-class Resizer = initially_resizer
->
-#ifndef DOXYGEN_SKIP
-class runge_kutta_fehlberg78 : public explicit_error_generic_rk< 13 , 8 , 8 , 7 , State , Value , Deriv , Time ,
-Algebra , Operations , Resizer >
-#else
-class runge_kutta_fehlberg78 : public explicit_error_generic_rk
-#endif
-{
-
-public:
-#ifndef DOXYGEN_SKIP
- typedef explicit_error_generic_rk< 13 , 8 , 8 , 7 , State , Value , Deriv , Time ,
- Algebra , Operations , Resizer > stepper_base_type;
-#endif
- typedef typename stepper_base_type::state_type state_type;
- typedef typename stepper_base_type::value_type value_type;
- typedef typename stepper_base_type::deriv_type deriv_type;
- typedef typename stepper_base_type::time_type time_type;
- typedef typename stepper_base_type::algebra_type algebra_type;
- typedef typename stepper_base_type::operations_type operations_type;
- typedef typename stepper_base_type::resizer_type resizer_type;
-
- #ifndef DOXYGEN_SKIP
- typedef typename stepper_base_type::stepper_type stepper_type;
- typedef typename stepper_base_type::wrapped_state_type wrapped_state_type;
- typedef typename stepper_base_type::wrapped_deriv_type wrapped_deriv_type;
- #endif // DOXYGEN_SKIP
-
-
- runge_kutta_fehlberg78( const algebra_type &algebra = algebra_type() ) : stepper_base_type(
- boost::fusion::make_vector( rk78_coefficients_a1<Value>() , rk78_coefficients_a2<Value>() , rk78_coefficients_a3<Value>() ,
- rk78_coefficients_a4<Value>() , rk78_coefficients_a5<Value>() , rk78_coefficients_a6<Value>() ,
- rk78_coefficients_a7<Value>() , rk78_coefficients_a8<Value>() , rk78_coefficients_a9<Value>() ,
- rk78_coefficients_a10<Value>() , rk78_coefficients_a11<Value>() , rk78_coefficients_a12<Value>() ) ,
- rk78_coefficients_b<Value>() , rk78_coefficients_db<Value>() , rk78_coefficients_c<Value>() , algebra )
- { }
-};
-
-
-
-/************* DOXYGEN *************/
-
-/**
- * \class runge_kutta_fehlberg78
- * \brief The Runge-Kutta Fehlberg 78 method.
- *
- * The Runge-Kutta Fehlberg 78 method is a standard method for high-precision applications.
- * The method is explicit and fulfills the Error Stepper concept. Step size control
- * is provided but continuous output is not available for this method.
- *
- * This class derives from explicit_error_stepper_base and inherits its interface via CRTP (current recurring template pattern).
- * Furthermore, it derivs from explicit_error_generic_rk which is a generic Runge-Kutta algorithm with error estimation.
- * For more details see explicit_error_stepper_base and explicit_error_generic_rk.
- *
- * \tparam State The state type.
- * \tparam Value The value type.
- * \tparam Deriv The type representing the time derivative of the state.
- * \tparam Time The time representing the independent variable - the time.
- * \tparam Algebra The algebra type.
- * \tparam Operations The operations type.
- * \tparam Resizer The resizer policy type.
- */
-
-
- /**
- * \fn runge_kutta_fehlberg78::runge_kutta_fehlberg78( const algebra_type &algebra )
- * \brief Constructs the runge_kutta_cash_fehlberg78 class. This constructor can be used as a default
- * constructor if the algebra has a default constructor.
- * \param algebra A copy of algebra is made and stored inside explicit_stepper_base.
- */
-
-}
-}
-}
-
-#endif //BOOST_NUMERIC_ODEINT_STEPPER_RUNGE_KUTTA_FEHLBERG87_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/stepper_categories.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/stepper_categories.hpp
deleted file mode 100644
index 9bc5372344f95348f90b86ba8a1df38b7e52c818..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/stepper_categories.hpp
+++ /dev/null
@@ -1,68 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/stepper_categories.hpp
-
- [begin_description]
- Definition of all stepper categories.
- [end_description]
-
- Copyright 2010-2011 Mario Mulansky
- Copyright 2010-2012 Karsten Ahnert
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_STEPPER_CATEGORIES_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_STEPPER_CATEGORIES_HPP_INCLUDED
-
-#include <boost/type_traits/integral_constant.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-/*
- * Tags to specify stepper types
- *
- * These tags are used by integrate() to choose which integration method is used
- */
-
-struct stepper_tag {};
-// struct explicit_stepper_tag : stepper_tag {};
-// struct implicit_stepper_tag : stepper_tag {};
-
-
-struct error_stepper_tag : stepper_tag {};
-struct explicit_error_stepper_tag : error_stepper_tag {};
-struct explicit_error_stepper_fsal_tag : error_stepper_tag {};
-
-struct controlled_stepper_tag {};
-struct explicit_controlled_stepper_tag : controlled_stepper_tag {};
-struct explicit_controlled_stepper_fsal_tag : controlled_stepper_tag {};
-
-struct dense_output_stepper_tag {};
-
-
-template< class tag > struct base_tag ;
-template< > struct base_tag< stepper_tag > { typedef stepper_tag type; };
-template< > struct base_tag< error_stepper_tag > { typedef stepper_tag type; };
-template< > struct base_tag< explicit_error_stepper_tag > { typedef stepper_tag type; };
-template< > struct base_tag< explicit_error_stepper_fsal_tag > { typedef stepper_tag type; };
-
-template< > struct base_tag< controlled_stepper_tag > { typedef controlled_stepper_tag type; };
-template< > struct base_tag< explicit_controlled_stepper_tag > { typedef controlled_stepper_tag type; };
-template< > struct base_tag< explicit_controlled_stepper_fsal_tag > { typedef controlled_stepper_tag type; };
-
-template< > struct base_tag< dense_output_stepper_tag > { typedef dense_output_stepper_tag type; };
-
-
-} // odeint
-} // numeric
-} // boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_STEPPER_CATEGORIES_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/symplectic_euler.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/symplectic_euler.hpp
deleted file mode 100644
index bd40860b0b4b5bf6b2764c53ff285c2748e6e556..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/symplectic_euler.hpp
+++ /dev/null
@@ -1,136 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/symplectic_euler.hpp
-
- [begin_description]
- Implementation of the symplectic Euler for separable Hamiltonian systems.
- [end_description]
-
- Copyright 2011-2013 Karsten Ahnert
- Copyright 2011-2013 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_SYMPLECTIC_EULER_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_SYMPLECTIC_EULER_HPP_INCLUDED
-
-
-#include <boost/numeric/odeint/stepper/base/symplectic_rkn_stepper_base.hpp>
-
-#include <boost/numeric/odeint/algebra/range_algebra.hpp>
-#include <boost/numeric/odeint/algebra/default_operations.hpp>
-#include <boost/numeric/odeint/algebra/algebra_dispatcher.hpp>
-#include <boost/numeric/odeint/algebra/operations_dispatcher.hpp>
-
-#include <boost/array.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-#ifndef DOXYGEN_SKIP
-namespace detail {
-namespace symplectic_euler_coef {
-
-template< class Value >
-struct coef_a_type : public boost::array< Value , 1 >
-{
- coef_a_type( void )
- {
- (*this)[0] = static_cast< Value >( 1 );
- }
-};
-
-template< class Value >
-struct coef_b_type : public boost::array< Value , 1 >
-{
- coef_b_type( void )
- {
- (*this)[0] = static_cast< Value >( 1 );
- }
-};
-
-} // namespace symplectic_euler_coef
-} // namespace detail
-#endif
-
-
-
-template<
-class Coor ,
-class Momentum = Coor ,
-class Value = double ,
-class CoorDeriv = Coor ,
-class MomentumDeriv = Coor ,
-class Time = Value ,
-class Algebra = typename algebra_dispatcher< Coor >::algebra_type ,
-class Operations = typename operations_dispatcher< Coor >::operations_type ,
-class Resizer = initially_resizer
->
-#ifndef DOXYGEN_SKIP
-class symplectic_euler :
-public symplectic_nystroem_stepper_base
-<
-1 , 1 ,
-Coor , Momentum , Value , CoorDeriv , MomentumDeriv , Time , Algebra , Operations , Resizer
->
-#else
-class symplectic_euler : public symplectic_nystroem_stepper_base
-#endif
-{
-public:
-
-#ifndef DOXYGEN_SKIP
- typedef symplectic_nystroem_stepper_base<
- 1 , 1 , Coor , Momentum , Value , CoorDeriv , MomentumDeriv , Time , Algebra , Operations , Resizer > stepper_base_type;
-#endif
- typedef typename stepper_base_type::algebra_type algebra_type;
- typedef typename stepper_base_type::value_type value_type;
-
-
- symplectic_euler( const algebra_type &algebra = algebra_type() )
- : stepper_base_type( detail::symplectic_euler_coef::coef_a_type< value_type >() ,
- detail::symplectic_euler_coef::coef_b_type< value_type >() ,
- algebra )
- { }
-};
-
-
-/*************** DOXYGEN ***************/
-
-/**
- * \class symplectic_euler
- * \brief Implementation of the symplectic Euler method.
- *
- * The method is of first order and has one stage. It is described HERE.
- *
- * \tparam Order The order of the stepper.
- * \tparam Coor The type representing the coordinates q.
- * \tparam Momentum The type representing the coordinates p.
- * \tparam Value The basic value type. Should be something like float, double or a high-precision type.
- * \tparam CoorDeriv The type representing the time derivative of the coordinate dq/dt.
- * \tparam MomemtnumDeriv The type representing the time derivative of the momentum dp/dt.
- * \tparam Time The type representing the time t.
- * \tparam Algebra The algebra.
- * \tparam Operations The operations.
- * \tparam Resizer The resizer policy.
- */
-
- /**
- * \fn symplectic_euler::symplectic_euler( const algebra_type &algebra )
- * \brief Constructs the symplectic_euler. This constructor can be used as a default
- * constructor if the algebra has a default constructor.
- * \param algebra A copy of algebra is made and stored inside explicit_stepper_base.
- */
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_SYMPLECTIC_EULER_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/symplectic_rkn_sb3a_m4_mclachlan.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/symplectic_rkn_sb3a_m4_mclachlan.hpp
deleted file mode 100644
index b33773e2f701cbdc5b2a945dfb5ebed848ad07ed..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/symplectic_rkn_sb3a_m4_mclachlan.hpp
+++ /dev/null
@@ -1,160 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/symplectic_rkn_sb3a_m4_mclachlan.hpp
-
- [begin_description]
- tba.
- [end_description]
-
- Copyright 2012-2013 Karsten Ahnert
- Copyright 2012-2013 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
-*/
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_SYMPLECTIC_RKN_SB3A_M4_MCLACHLAN_HPP_DEFINED
-#define BOOST_NUMERIC_ODEINT_STEPPER_SYMPLECTIC_RKN_SB3A_M4_MCLACHLAN_HPP_DEFINED
-
-#include <boost/numeric/odeint/algebra/default_operations.hpp>
-#include <boost/numeric/odeint/algebra/algebra_dispatcher.hpp>
-#include <boost/numeric/odeint/algebra/operations_dispatcher.hpp>
-
-#include <boost/numeric/odeint/util/resizer.hpp>
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-#ifndef DOXYGEN_SKIP
-namespace detail {
-namespace symplectic_rkn_sb3a_m4_mclachlan {
-
- /*
- exp( a1 t A ) exp( b1 t B )
- exp( a2 t A ) exp( b2 t B )
- exp( a3 t A )
- exp( b2 t B ) exp( a2 t A )
- exp( b1 t B ) exp( a1 t A )
- */
-
-
-
- template< class Value >
- struct coef_a_type : public boost::array< Value , 5 >
- {
- coef_a_type( void )
- {
- using std::sqrt;
-
- Value z = sqrt( static_cast< Value >( 7 ) / static_cast< Value >( 8 ) ) / static_cast< Value >( 3 );
- (*this)[0] = static_cast< Value >( 1 ) / static_cast< Value >( 2 ) - z ;
- (*this)[1] = static_cast< Value >( -1 ) / static_cast< Value >( 3 ) + z ;
- (*this)[2] = static_cast< Value >( 2 ) / static_cast< Value >( 3 );
- (*this)[3] = (*this)[1];
- (*this)[4] = (*this)[0];
- }
- };
-
- template< class Value >
- struct coef_b_type : public boost::array< Value , 5 >
- {
- coef_b_type( void )
- {
- (*this)[0] = static_cast< Value >( 1 );
- (*this)[1] = static_cast< Value >( -1 ) / static_cast< Value >( 2 );
- (*this)[2] = (*this)[1];
- (*this)[3] = (*this)[0];
- (*this)[4] = static_cast< Value >( 0 );
- }
- };
-
-} // namespace symplectic_rkn_sb3a_m4_mclachlan
-} // namespace detail
-#endif // DOXYGEN_SKIP
-
-
-
-
-template<
- class Coor ,
- class Momentum = Coor ,
- class Value = double ,
- class CoorDeriv = Coor ,
- class MomentumDeriv = Coor ,
- class Time = Value ,
- class Algebra = typename algebra_dispatcher< Coor >::algebra_type ,
- class Operations = typename operations_dispatcher< Coor >::operations_type ,
- class Resizer = initially_resizer
- >
-#ifndef DOXYGEN_SKIP
-class symplectic_rkn_sb3a_m4_mclachlan :
- public symplectic_nystroem_stepper_base
-<
- 5 , 4 ,
- Coor , Momentum , Value , CoorDeriv , MomentumDeriv , Time , Algebra , Operations , Resizer
- >
-#else
-class symplectic_rkn_sb3a_m4_mclachlan : public symplectic_nystroem_stepper_base
-#endif
-{
-public:
-#ifndef DOXYGEN_SKIP
- typedef symplectic_nystroem_stepper_base
- <
- 5 , 4 ,
- Coor , Momentum , Value , CoorDeriv , MomentumDeriv , Time , Algebra , Operations , Resizer
- > stepper_base_type;
-#endif
- typedef typename stepper_base_type::algebra_type algebra_type;
- typedef typename stepper_base_type::value_type value_type;
-
-
- symplectic_rkn_sb3a_m4_mclachlan( const algebra_type &algebra = algebra_type() )
- : stepper_base_type(
- detail::symplectic_rkn_sb3a_m4_mclachlan::coef_a_type< value_type >() ,
- detail::symplectic_rkn_sb3a_m4_mclachlan::coef_b_type< value_type >() ,
- algebra )
- { }
-};
-
-
-/***************** DOXYGEN ***************/
-
-/**
- * \class symplectic_rkn_sb3a_m4_mclachlan
- * \brief Implementation of the symmetric B3A Runge-Kutta Nystroem method of fifth order.
- *
- * The method is of fourth order and has five stages. It is described HERE. This method can be used
- * with multiprecision types since the coefficients are defined analytically.
- *
- * ToDo: add reference to paper.
- *
- * \tparam Order The order of the stepper.
- * \tparam Coor The type representing the coordinates q.
- * \tparam Momentum The type representing the coordinates p.
- * \tparam Value The basic value type. Should be something like float, double or a high-precision type.
- * \tparam CoorDeriv The type representing the time derivative of the coordinate dq/dt.
- * \tparam MomemtnumDeriv The type representing the time derivative of the momentum dp/dt.
- * \tparam Time The type representing the time t.
- * \tparam Algebra The algebra.
- * \tparam Operations The operations.
- * \tparam Resizer The resizer policy.
- */
-
- /**
- * \fn symplectic_rkn_sb3a_m4_mclachlan::symplectic_rkn_sb3a_m4_mclachlan( const algebra_type &algebra )
- * \brief Constructs the symplectic_rkn_sb3a_m4_mclachlan. This constructor can be used as a default
- * constructor if the algebra has a default constructor.
- * \param algebra A copy of algebra is made and stored inside explicit_stepper_base.
- */
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_SYMPLECTIC_RKN_SB3A_M4_MCLACHLAN_HPP_DEFINED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/symplectic_rkn_sb3a_mclachlan.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/symplectic_rkn_sb3a_mclachlan.hpp
deleted file mode 100644
index 5a23b3081d354c0964f5008d6261f0ee89442d1c..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/symplectic_rkn_sb3a_mclachlan.hpp
+++ /dev/null
@@ -1,162 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/symplectic_rkn_sb3a_mclachlan.hpp
-
- [begin_description]
- Implementation of the symplectic MacLachlan stepper for separable Hamiltonian system.
- [end_description]
-
- Copyright 2011-2013 Karsten Ahnert
- Copyright 2011-2013 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
-*/
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_SYMPLECTIC_RKN_SB3A_MCLACHLAN_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_SYMPLECTIC_RKN_SB3A_MCLACHLAN_HPP_INCLUDED
-
-
-#include <boost/numeric/odeint/stepper/base/symplectic_rkn_stepper_base.hpp>
-
-#include <boost/numeric/odeint/algebra/range_algebra.hpp>
-#include <boost/numeric/odeint/algebra/default_operations.hpp>
-#include <boost/numeric/odeint/algebra/algebra_dispatcher.hpp>
-#include <boost/numeric/odeint/algebra/operations_dispatcher.hpp>
-
-#include <boost/numeric/odeint/util/resizer.hpp>
-
-#include <boost/array.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-#ifndef DOXYGEN_SKIP
-namespace detail {
-namespace symplectic_rkn_sb3a_mclachlan {
-
- /*
- exp( a1 t A ) exp( b1 t B )
- exp( a2 t A ) exp( b2 t B )
- exp( a3 t A ) exp( b3 t B ) exp( a3 t A )
- exp( b2 t B ) exp( a2 t A )
- exp( b1 t B ) exp( a1 t A )
- */
-
- template< class Value >
- struct coef_a_type : public boost::array< Value , 6 >
- {
- coef_a_type( void )
- {
- (*this)[0] = static_cast< Value >( 0.40518861839525227722 );
- (*this)[1] = static_cast< Value >( -0.28714404081652408900 );
- (*this)[2] = static_cast< Value >( 1 ) / static_cast< Value >( 2 ) - ( (*this)[0] + (*this)[1] );
- (*this)[3] = (*this)[2];
- (*this)[4] = (*this)[1];
- (*this)[5] = (*this)[0];
-
- }
- };
-
- template< class Value >
- struct coef_b_type : public boost::array< Value , 6 >
- {
- coef_b_type( void )
- {
- (*this)[0] = static_cast< Value >( -3 ) / static_cast< Value >( 73 );
- (*this)[1] = static_cast< Value >( 17 ) / static_cast< Value >( 59 );
- (*this)[2] = static_cast< Value >( 1 ) - static_cast< Value >( 2 ) * ( (*this)[0] + (*this)[1] );
- (*this)[3] = (*this)[1];
- (*this)[4] = (*this)[0];
- (*this)[5] = static_cast< Value >( 0 );
- }
- };
-
-} // namespace symplectic_rkn_sb3a_mclachlan
-} // namespace detail
-#endif // DOXYGEN_SKIP
-
-
-
-template<
- class Coor ,
- class Momentum = Coor ,
- class Value = double ,
- class CoorDeriv = Coor ,
- class MomentumDeriv = Coor ,
- class Time = Value ,
- class Algebra = typename algebra_dispatcher< Coor >::algebra_type ,
- class Operations = typename operations_dispatcher< Coor >::operations_type ,
- class Resizer = initially_resizer
- >
-#ifndef DOXYGEN_SKIP
-class symplectic_rkn_sb3a_mclachlan :
- public symplectic_nystroem_stepper_base
-<
- 6 , 4 ,
- Coor , Momentum , Value , CoorDeriv , MomentumDeriv , Time , Algebra , Operations , Resizer
- >
-#else
-class symplectic_rkn_sb3a_mclachlan : public symplectic_nystroem_stepper_base
-#endif
-{
-public:
-#ifndef DOXYGEN_SKIP
- typedef symplectic_nystroem_stepper_base
- <
- 6 , 4 ,
- Coor , Momentum , Value , CoorDeriv , MomentumDeriv , Time , Algebra , Operations , Resizer
- > stepper_base_type;
-#endif
- typedef typename stepper_base_type::algebra_type algebra_type;
- typedef typename stepper_base_type::value_type value_type;
-
-
- symplectic_rkn_sb3a_mclachlan( const algebra_type &algebra = algebra_type() )
- : stepper_base_type(
- detail::symplectic_rkn_sb3a_mclachlan::coef_a_type< value_type >() ,
- detail::symplectic_rkn_sb3a_mclachlan::coef_b_type< value_type >() ,
- algebra )
- { }
-};
-
-
-/************* DOXYGEN ***********/
-
-/**
- * \class symplectic_rkn_sb3a_mclachlan
- * \brief Implement of the symmetric B3A method of Runge-Kutta-Nystroem method of sixth order.
- *
- * The method is of fourth order and has six stages. It is described HERE. This method cannot be used
- * with multiprecision types since the coefficients are not defined analytically.
- *
- * ToDo Add reference to the paper.
- *
- * \tparam Order The order of the stepper.
- * \tparam Coor The type representing the coordinates q.
- * \tparam Momentum The type representing the coordinates p.
- * \tparam Value The basic value type. Should be something like float, double or a high-precision type.
- * \tparam CoorDeriv The type representing the time derivative of the coordinate dq/dt.
- * \tparam MomemtnumDeriv The type representing the time derivative of the momentum dp/dt.
- * \tparam Time The type representing the time t.
- * \tparam Algebra The algebra.
- * \tparam Operations The operations.
- * \tparam Resizer The resizer policy.
- */
-
- /**
- * \fn symplectic_rkn_sb3a_mclachlan::symplectic_rkn_sb3a_mclachlan( const algebra_type &algebra )
- * \brief Constructs the symplectic_rkn_sb3a_mclachlan. This constructor can be used as a default
- * constructor if the algebra has a default constructor.
- * \param algebra A copy of algebra is made and stored inside explicit_stepper_base.
- */
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_SYMPLECTIC_RKN_SB3A_MCLACHLAN_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/velocity_verlet.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/velocity_verlet.hpp
deleted file mode 100644
index 6868aad87edd06e18ce8542917d6f7a92cb59aec..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/stepper/velocity_verlet.hpp
+++ /dev/null
@@ -1,381 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/stepper/velocity_verlet.hpp
-
- [begin_description]
- tba.
- [end_description]
-
- Copyright 2009-2012 Karsten Ahnert
- Copyright 2009-2012 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
-*/
-
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_VELOCITY_VERLET_HPP_DEFINED
-#define BOOST_NUMERIC_ODEINT_STEPPER_VELOCITY_VERLET_HPP_DEFINED
-
-#include <boost/numeric/odeint/stepper/base/algebra_stepper_base.hpp>
-#include <boost/numeric/odeint/stepper/stepper_categories.hpp>
-
-#include <boost/numeric/odeint/algebra/algebra_dispatcher.hpp>
-#include <boost/numeric/odeint/algebra/operations_dispatcher.hpp>
-#include <boost/numeric/odeint/util/resizer.hpp>
-#include <boost/numeric/odeint/util/state_wrapper.hpp>
-#include <boost/numeric/odeint/util/unwrap_reference.hpp>
-
-#include <boost/numeric/odeint/util/bind.hpp>
-#include <boost/numeric/odeint/util/copy.hpp>
-#include <boost/numeric/odeint/util/resizer.hpp>
-// #include <boost/numeric/odeint/util/is_pair.hpp>
-// #include <boost/array.hpp>
-
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-
-template <
- class Coor ,
- class Velocity = Coor ,
- class Value = double ,
- class Acceleration = Coor ,
- class Time = Value ,
- class TimeSq = Time ,
- class Algebra = typename algebra_dispatcher< Coor >::algebra_type ,
- class Operations = typename operations_dispatcher< Coor >::operations_type ,
- class Resizer = initially_resizer
- >
-class velocity_verlet : public algebra_stepper_base< Algebra , Operations >
-{
-public:
-
- typedef algebra_stepper_base< Algebra , Operations > algebra_stepper_base_type;
- typedef typename algebra_stepper_base_type::algebra_type algebra_type;
- typedef typename algebra_stepper_base_type::operations_type operations_type;
-
- typedef Coor coor_type;
- typedef Velocity velocity_type;
- typedef Acceleration acceleration_type;
- typedef std::pair< coor_type , velocity_type > state_type;
- typedef std::pair< velocity_type , acceleration_type > deriv_type;
- typedef state_wrapper< acceleration_type > wrapped_acceleration_type;
- typedef Value value_type;
- typedef Time time_type;
- typedef TimeSq time_square_type;
- typedef Resizer resizer_type;
- typedef stepper_tag stepper_category;
-
- typedef unsigned short order_type;
-
- static const order_type order_value = 1;
-
- /**
- * \return Returns the order of the stepper.
- */
- order_type order( void ) const
- {
- return order_value;
- }
-
-
- velocity_verlet( const algebra_type & algebra = algebra_type() )
- : algebra_stepper_base_type( algebra ) , m_first_call( true )
- , m_a1() , m_a2() , m_current_a1( true ) { }
-
-
- template< class System , class StateInOut >
- void do_step( System system , StateInOut & x , time_type t , time_type dt )
- {
- do_step_v1( system , x , t , dt );
- }
-
-
- template< class System , class StateInOut >
- void do_step( System system , const StateInOut & x , time_type t , time_type dt )
- {
- do_step_v1( system , x , t , dt );
- }
-
-
- template< class System , class CoorIn , class VelocityIn , class AccelerationIn ,
- class CoorOut , class VelocityOut , class AccelerationOut >
- void do_step( System system , CoorIn const & qin , VelocityIn const & pin , AccelerationIn const & ain ,
- CoorOut & qout , VelocityOut & pout , AccelerationOut & aout , time_type t , time_type dt )
- {
- const value_type one = static_cast< value_type >( 1.0 );
- const value_type one_half = static_cast< value_type >( 0.5 );
-
- algebra_stepper_base_type::m_algebra.for_each4(
- qout , qin , pin , ain ,
- typename operations_type::template scale_sum3< value_type , time_type , time_square_type >( one , one * dt , one_half * dt * dt ) );
-
- typename odeint::unwrap_reference< System >::type & sys = system;
-
- sys( qout , pin , aout , t + dt );
-
- algebra_stepper_base_type::m_algebra.for_each4(
- pout , pin , ain , aout ,
- typename operations_type::template scale_sum3< value_type , time_type , time_type >( one , one_half * dt , one_half * dt ) );
- }
-
-
- template< class StateIn >
- void adjust_size( const StateIn & x )
- {
- if( resize_impl( x ) )
- m_first_call = true;
- }
-
- void reset( void )
- {
- m_first_call = true;
- }
-
-
- /**
- * \fn velocity_verlet::initialize( const AccelerationIn &qin )
- * \brief Initializes the internal state of the stepper.
- * \param deriv The acceleration of x. The next call of `do_step` expects that the acceleration of `x` passed to `do_step`
- * has the value of `qin`.
- */
- template< class AccelerationIn >
- void initialize( const AccelerationIn & ain )
- {
- // alloc a
- m_resizer.adjust_size( ain ,
- detail::bind( &velocity_verlet::template resize_impl< AccelerationIn > ,
- detail::ref( *this ) , detail::_1 ) );
- boost::numeric::odeint::copy( ain , get_current_acc() );
- m_first_call = false;
- }
-
-
- template< class System , class CoorIn , class VelocityIn >
- void initialize( System system , const CoorIn & qin , const VelocityIn & pin , time_type t )
- {
- m_resizer.adjust_size( qin ,
- detail::bind( &velocity_verlet::template resize_impl< CoorIn > ,
- detail::ref( *this ) , detail::_1 ) );
- initialize_acc( system , qin , pin , t );
- }
-
- bool is_initialized( void ) const
- {
- return ! m_first_call;
- }
-
-
-private:
-
- template< class System , class CoorIn , class VelocityIn >
- void initialize_acc( System system , const CoorIn & qin , const VelocityIn & pin , time_type t )
- {
- typename odeint::unwrap_reference< System >::type & sys = system;
- sys( qin , pin , get_current_acc() , t );
- m_first_call = false;
- }
-
- template< class System , class StateInOut >
- void do_step_v1( System system , StateInOut & x , time_type t , time_type dt )
- {
- typedef typename odeint::unwrap_reference< StateInOut >::type state_in_type;
- typedef typename odeint::unwrap_reference< typename state_in_type::first_type >::type coor_in_type;
- typedef typename odeint::unwrap_reference< typename state_in_type::second_type >::type momentum_in_type;
-
- typedef typename boost::remove_reference< coor_in_type >::type xyz_type;
- state_in_type & statein = x;
- coor_in_type & qinout = statein.first;
- momentum_in_type & pinout = statein.second;
-
- // alloc a
- if( m_resizer.adjust_size( qinout ,
- detail::bind( &velocity_verlet::template resize_impl< xyz_type > ,
- detail::ref( *this ) , detail::_1 ) )
- || m_first_call )
- {
- initialize_acc( system , qinout , pinout , t );
- }
-
- // check first
- do_step( system , qinout , pinout , get_current_acc() , qinout , pinout , get_old_acc() , t , dt );
- toggle_current_acc();
- }
-
- template< class StateIn >
- bool resize_impl( const StateIn & x )
- {
- bool resized = false;
- resized |= adjust_size_by_resizeability( m_a1 , x , typename is_resizeable< acceleration_type >::type() );
- resized |= adjust_size_by_resizeability( m_a2 , x , typename is_resizeable< acceleration_type >::type() );
- return resized;
- }
-
- acceleration_type & get_current_acc( void )
- {
- return m_current_a1 ? m_a1.m_v : m_a2.m_v ;
- }
-
- const acceleration_type & get_current_acc( void ) const
- {
- return m_current_a1 ? m_a1.m_v : m_a2.m_v ;
- }
-
- acceleration_type & get_old_acc( void )
- {
- return m_current_a1 ? m_a2.m_v : m_a1.m_v ;
- }
-
- const acceleration_type & get_old_acc( void ) const
- {
- return m_current_a1 ? m_a2.m_v : m_a1.m_v ;
- }
-
- void toggle_current_acc( void )
- {
- m_current_a1 = ! m_current_a1;
- }
-
- resizer_type m_resizer;
- bool m_first_call;
- wrapped_acceleration_type m_a1 , m_a2;
- bool m_current_a1;
-};
-
-/**
- * \class velocity_verlet
- * \brief The Velocity-Verlet algorithm.
- *
- * <a href="http://en.wikipedia.org/wiki/Verlet_integration" >The Velocity-Verlet algorithm</a> is a method for simulation of molecular dynamics systems. It solves the ODE
- * a=f(r,v',t) where r are the coordinates, v are the velocities and a are the accelerations, hence v = dr/dt, a=dv/dt.
- *
- * \tparam Coor The type representing the coordinates.
- * \tparam Velocity The type representing the velocities.
- * \tparam Value The type value type.
- * \tparam Acceleration The type representing the acceleration.
- * \tparam Time The time representing the independent variable - the time.
- * \tparam TimeSq The time representing the square of the time.
- * \tparam Algebra The algebra.
- * \tparam Operations The operations type.
- * \tparam Resizer The resizer policy type.
- */
-
-
- /**
- * \fn velocity_verlet::velocity_verlet( const algebra_type &algebra )
- * \brief Constructs the velocity_verlet class. This constructor can be used as a default
- * constructor if the algebra has a default constructor.
- * \param algebra A copy of algebra is made and stored.
- */
-
-
- /**
- * \fn velocity_verlet::do_step( System system , StateInOut &x , time_type t , time_type dt )
- * \brief This method performs one step. It transforms the result in-place.
- *
- * It can be used like
- * \code
- * pair< coordinates , velocities > state;
- * stepper.do_step( sys , x , t , dt );
- * \endcode
- *
- * \param system The system function to solve, hence the r.h.s. of the ordinary differential equation. It must fulfill the
- * Second Order System concept.
- * \param x The state of the ODE which should be solved. The state is pair of Coor and Velocity.
- * \param t The value of the time, at which the step should be performed.
- * \param dt The step size.
- */
-
- /**
- * \fn velocity_verlet::do_step( System system , const StateInOut &x , time_type t , time_type dt )
- * \brief This method performs one step. It transforms the result in-place.
- *
- * It can be used like
- * \code
- * pair< coordinates , velocities > state;
- * stepper.do_step( sys , x , t , dt );
- * \endcode
- *
- * \param system The system function to solve, hence the r.h.s. of the ordinary differential equation. It must fulfill the
- * Second Order System concept.
- * \param x The state of the ODE which should be solved. The state is pair of Coor and Velocity.
- * \param t The value of the time, at which the step should be performed.
- * \param dt The step size.
- */
-
-
-
- /**
- * \fn velocity_verlet::do_step( System system , CoorIn const & qin , VelocityIn const & pin , AccelerationIn const & ain , CoorOut & qout , VelocityOut & pout , AccelerationOut & aout , time_type t , time_type dt )
- * \brief This method performs one step. It transforms the result in-place. Additionally to the other methods
- * the coordinates, velocities and accelerations are passed directly to do_step and they are transformed out-of-place.
- *
- * It can be used like
- * \code
- * coordinates qin , qout;
- * velocities pin , pout;
- * accelerations ain, aout;
- * stepper.do_step( sys , qin , pin , ain , qout , pout , aout , t , dt );
- * \endcode
- *
- * \param system The system function to solve, hence the r.h.s. of the ordinary differential equation. It must fulfill the
- * Second Order System concept.
- * \param x The state of the ODE which should be solved. The state is pair of Coor and Velocity.
- * \param t The value of the time, at which the step should be performed.
- * \param dt The step size.
- */
-
-
- /**
- * \fn void velocity_verlet::adjust_size( const StateIn &x )
- * \brief Adjust the size of all temporaries in the stepper manually.
- * \param x A state from which the size of the temporaries to be resized is deduced.
- */
-
-
- /**
- * \fn velocity_verlet::reset( void )
- * \brief Resets the internal state of this stepper. After calling this method it is safe to use all
- * `do_step` method without explicitly initializing the stepper.
- */
-
-
-
- /**
- * \fn velocity_verlet::initialize( System system , const CoorIn &qin , const VelocityIn &pin , time_type t )
- * \brief Initializes the internal state of the stepper.
- *
- * This method is equivalent to
- * \code
- * Acceleration a;
- * system( qin , pin , a , t );
- * stepper.initialize( a );
- * \endcode
- *
- * \param system The system function for the next calls of `do_step`.
- * \param qin The current coordinates of the ODE.
- * \param pin The current velocities of the ODE.
- * \param t The current time of the ODE.
- */
-
-
- /**
- * \fn velocity_verlet::is_initialized()
- * \returns Returns if the stepper is initialized.
- */
-
-
-
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_VELOCITY_VERLET_HPP_DEFINED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/bind.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/bind.hpp
deleted file mode 100644
index ead0fc0e98fa52368be2c85fc69c971f8bbcf621..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/bind.hpp
+++ /dev/null
@@ -1,101 +0,0 @@
-/*
- * [begin_description]
- * Boost bind pull the placeholders, _1, _2, ... into global
- * namespace. This can conflict with the C++03 TR1 and C++11
- * std::placeholders. This header provides a workaround for
- * this problem.
- * [end_description]
- *
- * Copyright 2012 Christoph Koke
- * Copyright 2012 Karsten Ahnert
- *
- * Distributed under the Boost Software License, Version 1.0.
- * (See accompanying file LICENSE_1_0.txt or
- * copy at http://www.boost.org/LICENSE_1_0.txt)
- * */
-
-#ifndef BOOST_NUMERIC_ODEINT_UTIL_BIND_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_UTIL_BIND_HPP_INCLUDED
-
-
-#include <boost/numeric/odeint/config.hpp>
-
-
-#if BOOST_NUMERIC_ODEINT_CXX11
- #include <functional>
-#else
-#define BOOST_BIND_NO_PLACEHOLDERS
-#include <boost/bind.hpp>
-#endif
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-namespace detail {
-
-#if BOOST_NUMERIC_ODEINT_CXX11
-
-using ::std::bind;
-using namespace ::std::placeholders;
-
-
-#else
-
-// unnamed namespace to avoid multiple declarations (#138)
-namespace {
-using ::boost::bind;
-boost::arg<1> _1;
-boost::arg<2> _2;
-}
-// using ::boost::bind;
-// using ::_1;
-// using ::_2;
-
-#endif
-
-}
-}
-}
-}
-
-
-
-
-
-/*
-
-// the following is the suggested way. Unfortunately it does not work with all compilers.
-
-#ifdef BOOST_NO_CXX11_HDR_FUNCTIONAL
-#include <boost/bind.hpp>
-#else
-#include <functional>
-#endif
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-namespace detail {
-
-
-#ifdef BOOST_NO_CXX11_HDR_FUNCTIONAL
-
-using ::boost::bind;
-using ::_1;
-using ::_2;
-
-#else
-
-using ::std::bind;
-using namespace ::std::placeholders;
-
-#endif
-
-
-}
-}
-}
-}*/
-
-#endif // BOOST_NUMERIC_ODEINT_UTIL_BIND_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/copy.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/copy.hpp
deleted file mode 100644
index 161f135534783c9c08d55d1d95e278a66883c326..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/copy.hpp
+++ /dev/null
@@ -1,87 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/util/copy.hpp
-
- [begin_description]
- Copy abstraction for the usage in the steppers.
- [end_description]
-
- Copyright 2011-2012 Karsten Ahnert
- Copyright 2011-2012 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_UTIL_COPY_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_UTIL_COPY_HPP_INCLUDED
-
-
-#include <boost/range/algorithm/copy.hpp>
-
-#include <boost/utility/enable_if.hpp>
-
-#include <boost/numeric/odeint/util/detail/is_range.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-namespace detail {
-
- template< class Container1 , class Container2 >
- void do_copying( const Container1 &from , Container2 &to , boost::mpl::true_ )
- {
- boost::range::copy( from , boost::begin( to ) );
- }
-
- template< class Container1 , class Container2 >
- void do_copying( const Container1 &from , Container2 &to , boost::mpl::false_ )
- {
- to = from;
- }
-
-} // namespace detail
-
-
-
-/*
- * Default implementation of the copy operation used the assign operator
- * gsl_vector must copied differently
- */
-template< class Container1 , class Container2 , class Enabler = void >
-struct copy_impl_sfinae
-{
- static void copy( const Container1 &from , Container2 &to )
- {
- typedef typename boost::numeric::odeint::detail::is_range< Container1 >::type is_range_type;
- detail::do_copying( from , to , is_range_type() );
- }
-
-};
-
-template< class Container1, class Container2 >
-struct copy_impl
-{
- static void copy( const Container1 &from , Container2 &to )
- {
- copy_impl_sfinae< Container1 , Container2 >::copy( from , to );
- }
-};
-
-// ToDo: allow also to copy INTO a range, not only from a range! Needs "const Container2 &to"
-template< class Container1 , class Container2 >
-void copy( const Container1 &from , Container2 &to )
-{
- copy_impl< Container1 , Container2 >::copy( from , to );
-}
-
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_UTIL_COPY_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/detail/is_range.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/detail/is_range.hpp
deleted file mode 100644
index a1768554119c1644c1f8275d1b8777a6d73260e9..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/detail/is_range.hpp
+++ /dev/null
@@ -1,134 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/util/detail/is_range.hpp
-
- [begin_description]
- is_range implementation. Taken from the boost::range library.
- [end_description]
-
- Copyright 2011-2013 Karsten Ahnert
- Copyright 2011-2013 Thorsten Ottosen
-
-
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_UTIL_DETAIL_IS_RANGE_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_UTIL_DETAIL_IS_RANGE_HPP_INCLUDED
-
-
-#if defined(_MSC_VER) && (_MSC_VER >= 1200)
-# pragma once
-#endif
-
-#include <cstddef>
-#include <boost/range/config.hpp>
-#include <boost/mpl/has_xxx.hpp>
-#include <boost/mpl/bool.hpp>
-#include <boost/mpl/and.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-
-namespace range_detail
-{
-BOOST_MPL_HAS_XXX_TRAIT_DEF(iterator)
- BOOST_MPL_HAS_XXX_TRAIT_DEF(const_iterator)
-}
-
-namespace detail
-{
-
-template< typename Range >
-struct is_range : boost::mpl::and_<range_detail::has_iterator<Range>, range_detail::has_const_iterator<Range> >
-{
-};
-
-//////////////////////////////////////////////////////////////////////////
-// pair
-//////////////////////////////////////////////////////////////////////////
-
-template< typename iteratorT >
-struct is_range< std::pair<iteratorT,iteratorT> > : boost::mpl::true_
-{
-};
-
-template< typename iteratorT >
-struct is_range< const std::pair<iteratorT,iteratorT> > : boost::mpl::true_
-{
-};
-
-//////////////////////////////////////////////////////////////////////////
-// array
-//////////////////////////////////////////////////////////////////////////
-
-template< typename elementT, std::size_t sz >
-struct is_range< elementT[sz] > : boost::mpl::true_
-{
-};
-
-template< typename elementT, std::size_t sz >
-struct is_range< const elementT[sz] > : boost::mpl::true_
-{
-};
-
-//////////////////////////////////////////////////////////////////////////
-// string
-//////////////////////////////////////////////////////////////////////////
-
-template<>
-struct is_range< char* > : boost::mpl::true_
-{
-};
-
-template<>
-struct is_range< wchar_t* > : boost::mpl::true_
-{
-};
-
-template<>
-struct is_range< const char* > : boost::mpl::true_
-{
-};
-
-template<>
-struct is_range< const wchar_t* > : boost::mpl::true_
-{
-};
-
-template<>
-struct is_range< char* const > : boost::mpl::true_
-{
-};
-
-template<>
-struct is_range< wchar_t* const > : boost::mpl::true_
-{
-};
-
-template<>
-struct is_range< const char* const > : boost::mpl::true_
-{
-};
-
-template<>
-struct is_range< const wchar_t* const > : boost::mpl::true_
-{
-};
-
-} // namespace detail
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-
-#endif // BOOST_NUMERIC_ODEINT_UTIL_DETAIL_IS_RANGE_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/detail/less_with_sign.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/detail/less_with_sign.hpp
deleted file mode 100644
index 3ffa7ca179252479dd5e1ac075c69fe9f40ccd10..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/detail/less_with_sign.hpp
+++ /dev/null
@@ -1,78 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/util/detail/less_with_sign.hpp
-
- [begin_description]
- Helper function to compare times taking into account the sign of dt
- [end_description]
-
- Copyright 2012-2015 Mario Mulansky
- Copyright 2012 Karsten Ahnert
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-#ifndef BOOST_NUMERIC_ODEINT_INTEGRATE_DETAIL_LESS_WITH_SIGN_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_INTEGRATE_DETAIL_LESS_WITH_SIGN_HPP_INCLUDED
-
-#include <limits>
-
-#include <boost/numeric/odeint/util/unit_helper.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-namespace detail {
-
-/**
- * return t1 < t2 if dt > 0 and t1 > t2 if dt < 0 with epsilon accuracy
- */
-template< typename T >
-bool less_with_sign( T t1 , T t2 , T dt )
-{
- if( get_unit_value(dt) > 0 )
- //return t1 < t2;
- return t2-t1 > std::numeric_limits<T>::epsilon();
- else
- //return t1 > t2;
- return t1-t2 > std::numeric_limits<T>::epsilon();
-}
-
-/**
- * return t1 <= t2 if dt > 0 and t1 => t2 if dt < 0 with epsilon accuracy
- */
-template< typename T >
-bool less_eq_with_sign( T t1 , T t2 , T dt )
-{
- if( get_unit_value(dt) > 0 )
- return t1-t2 <= std::numeric_limits<T>::epsilon();
- else
- return t2-t1 <= std::numeric_limits<T>::epsilon();
-}
-
-template< typename T >
-T min_abs( T t1 , T t2 )
-{
- BOOST_USING_STD_MIN();
- BOOST_USING_STD_MAX();
- if( get_unit_value(t1)>0 )
- return min BOOST_PREVENT_MACRO_SUBSTITUTION ( t1 , t2 );
- else
- return max BOOST_PREVENT_MACRO_SUBSTITUTION ( t1 , t2 );
-}
-
-template< typename T >
-T max_abs( T t1 , T t2 )
-{
- BOOST_USING_STD_MIN();
- BOOST_USING_STD_MAX();
- if( get_unit_value(t1)>0 )
- return max BOOST_PREVENT_MACRO_SUBSTITUTION ( t1 , t2 );
- else
- return min BOOST_PREVENT_MACRO_SUBSTITUTION ( t1 , t2 );
-}
-} } } }
-
-#endif
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/is_pair.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/is_pair.hpp
deleted file mode 100644
index 1827840fe2b84b9bb2ad242baf0f26398869b905..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/is_pair.hpp
+++ /dev/null
@@ -1,45 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/util/is_pair.hpp
-
- [begin_description]
- Metafunction to determine if a type is a std::pair<>.
- [end_description]
-
- Copyright 2011 Karsten Ahnert
- Copyright 2011 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_UTIL_IS_PAIR_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_UTIL_IS_PAIR_HPP_INCLUDED
-
-
-#include <boost/mpl/bool.hpp>
-#include <utility>
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-template< class T >
-struct is_pair : public boost::mpl::false_
-{
-};
-
-template< class T1 , class T2 >
-struct is_pair< std::pair< T1 , T2 > > : public boost::mpl::true_
-{
-};
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_UTIL_IS_PAIR_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/is_resizeable.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/is_resizeable.hpp
deleted file mode 100644
index 6db42183227702ba775be13ffc11dc63dbf49c3c..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/is_resizeable.hpp
+++ /dev/null
@@ -1,83 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/util/is_resizeable.hpp
-
- [begin_description]
- Metafunction to determine if a state type can resized. For usage in the steppers.
- [end_description]
-
- Copyright 2011-2012 Karsten Ahnert
- Copyright 2011 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_UTIL_IS_RESIZEABLE_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_UTIL_IS_RESIZEABLE_HPP_INCLUDED
-
-
-#include <vector>
-
-#include <boost/type_traits/integral_constant.hpp>
-#include <boost/type_traits/remove_reference.hpp>
-#include <boost/fusion/include/front.hpp>
-#include <boost/fusion/include/is_sequence.hpp>
-
-#include <boost/mpl/find_if.hpp>
-#include <boost/mpl/end.hpp>
-#include <boost/mpl/placeholders.hpp>
-#include <boost/mpl/if.hpp>
-#include <boost/type_traits/is_same.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-/*
- * by default any type is not resizable
- */
-template< typename Container , typename Enabler = void >
-struct is_resizeable_sfinae : boost::false_type {};
-
-template< typename Container >
-struct is_resizeable : is_resizeable_sfinae< Container > {};
-
-
-
-/*
- * specialization for std::vector
- */
-template< class V, class A >
-struct is_resizeable< std::vector< V , A > > : boost::true_type {};
-
-
-/*
- * sfinae specialization for fusion sequences
- */
-template< typename FusionSequence >
-struct is_resizeable_sfinae<
- FusionSequence ,
- typename boost::enable_if< typename boost::fusion::traits::is_sequence< FusionSequence >::type >::type >
-{
- typedef typename boost::mpl::find_if< FusionSequence , is_resizeable< boost::mpl::_1 > >::type iter;
- typedef typename boost::mpl::end< FusionSequence >::type last;
-
- typedef typename boost::mpl::if_< boost::is_same< iter , last > , boost::false_type , boost::true_type >::type type;
- const static bool value = type::value;
-};
-
-
-
-
-
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-
-#endif // BOOST_NUMERIC_ODEINT_UTIL_IS_RESIZEABLE_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/multi_array_adaption.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/multi_array_adaption.hpp
deleted file mode 100644
index a7c35fe2cff3f97968f1443cd65130f69f49d029..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/multi_array_adaption.hpp
+++ /dev/null
@@ -1,130 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/util/multi_array_adaption.hpp
-
- [begin_description]
- tba.
- [end_description]
-
- Copyright 2009-2012 Karsten Ahnert
- Copyright 2009-2012 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
-*/
-
-
-#ifndef BOOST_NUMERIC_ODEINT_UTIL_MULTI_ARRAY_ADAPTION_HPP_DEFINED
-#define BOOST_NUMERIC_ODEINT_UTIL_MULTI_ARRAY_ADAPTION_HPP_DEFINED
-
-
-
-#include <boost/numeric/odeint/util/is_resizeable.hpp>
-#include <boost/numeric/odeint/util/resize.hpp>
-#include <boost/numeric/odeint/util/same_size.hpp>
-
-#include <boost/mpl/and.hpp>
-#include <boost/mpl/bool.hpp>
-#include <boost/multi_array.hpp>
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-template< typename T >
-struct is_multi_array
-{
- typedef boost::false_type type;
- const static bool value = type::value;
-};
-
-template< typename T >
-struct is_resizeable_multi_array
-{
- typedef boost::false_type type;
- const static bool value = type::value;
-};
-
-
-
-template< typename V , size_t Dim , typename A >
-struct is_multi_array< boost::multi_array< V , Dim , A > >
-{
- typedef boost::true_type type;
- const static bool value = type::value;
-};
-
-template< typename V , size_t Dim , typename A >
-struct is_resizeable_multi_array< boost::multi_array< V , Dim , A > >
-{
- typedef boost::true_type type;
- const static bool value = type::value;
-};
-
-
-
-
-template< typename T >
-struct is_resizeable_sfinae< T , typename boost::enable_if< typename is_resizeable_multi_array< T >::type >::type >
-{
- typedef boost::true_type type;
- const static bool value = type::value;
-};
-
-
-
-
-
-template< typename T1 , typename T2 >
-struct same_size_impl_sfinae< T1 , T2 ,
- typename boost::enable_if<
- typename boost::mpl::and_<
- is_multi_array< T1 > ,
- is_multi_array< T2 > ,
- boost::mpl::bool_< T1::dimensionality == T2::dimensionality >
- >::type
- >::type >
-{
- static bool same_size( T1 const &x1 , T2 const &x2 )
- {
- for( size_t i=0 ; i<T1::dimensionality ; ++i )
- {
- if( x1.shape()[i] != x2.shape()[i] ) return false;
- if( x1.index_bases()[i] != x2.index_bases()[i] ) return false;
- }
- return true;
- }
-};
-
-
-template< typename T1 , typename T2 >
-struct resize_impl_sfinae< T1 , T2 ,
- typename boost::enable_if<
- typename boost::mpl::and_<
- is_resizeable_multi_array< T1 > ,
- is_multi_array< T2 > ,
- boost::mpl::bool_< T1::dimensionality == T2::dimensionality >
- >::type
- >::type >
-{
- static void resize( T1 &x1 , const T2 &x2 )
- {
- boost::array< int , T1::dimensionality > extents;
- for( size_t i=0 ; i<T1::dimensionality ; ++i ) extents[i] = x2.shape()[i];
- x1.resize( extents );
- boost::array< int , T1::dimensionality > origins;
- for( size_t i=0 ; i<T1::dimensionality ; ++i ) origins[i] = x2.index_bases()[i];
- x1.reindex( origins );
- }
-};
-
-
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_UTIL_MULTI_ARRAY_ADAPTION_HPP_DEFINED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/n_ary_helper.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/n_ary_helper.hpp
deleted file mode 100644
index 61380742074812e6b30a38290600ea4d547e8514..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/n_ary_helper.hpp
+++ /dev/null
@@ -1,96 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/util/n_ary_helper.hpp
-
- Macros to generate scale_sumN and for_eachN functors.
-
- Copyright 2013 Karsten Ahnert
- Copyright 2013 Mario Mulansky
- Copyright 2013 Pascal Germroth
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-#ifndef BOOST_NUMERIC_ODEINT_UTIL_N_ARY_HELPER_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_UTIL_N_ARY_HELPER_HPP_INCLUDED
-
-#include <boost/preprocessor/repetition.hpp>
-
-// like BOOST_PP_ENUM_SHIFTED but with a comma in front like _TRAILING
-#define BOOST_ODEINT_ENUM_TRAILING_SHIFTED_PARAMS(count, param) \
- BOOST_PP_COMMA_IF(BOOST_PP_DEC(count)) \
- BOOST_PP_ENUM_SHIFTED_PARAMS(count, param)
-
-#define BOOST_ODEINT_ENUM_TRAILING_SHIFTED_BINARY_PARAMS(count, p1, p2) \
- BOOST_PP_COMMA_IF(BOOST_PP_DEC(count)) \
- BOOST_PP_ENUM_SHIFTED_BINARY_PARAMS(count, p1, p2)
-
-// like BOOST_PP_ENUM_SHIFTED_BINARY_PARAMS(n, p1, p2) but p2 is shifted left.
-// generate "p1 ## 0 = p2, p1 ## 1 = p3 ## 0, p1 ## 2 = p3 ## 1"
-#define BOOST_ODEINT_ENUM_LSHIFTED_BINARY_PARAMS(count, p1, p2, p3) \
- BOOST_PP_ENUM(count, BOOST_ODEINT_ENUM_LSHIFTED_BINARY_PARAMS_, (p1, p2, p3))
-#define BOOST_ODEINT_ENUM_LSHIFTED_BINARY_PARAMS_(z, n, data) \
- BOOST_PP_CAT(BOOST_PP_TUPLE_ELEM(3, 0, data), n) \
- BOOST_PP_IF(n, \
- BOOST_PP_CAT(BOOST_PP_TUPLE_ELEM(3, 2, data), BOOST_PP_DEC(n)), \
- BOOST_PP_TUPLE_ELEM(3, 1, data))
-
-// like BOOST_PP_ENUM_BINARY_PARAMS(n, p1, p2) but with statements.
-// "p1 ## 0 p2 ## 0 ; p1 ## 1 p2 ## 1 ; ..."
-#define BOOST_ODEINT_ENUM_BINARY_STATEMENTS(count, p1, p2) \
- BOOST_PP_REPEAT(count, BOOST_ODEINT_ENUM_BINARY_STATEMENTS_, (p1, p2))
-#define BOOST_ODEINT_ENUM_BINARY_STATEMENTS_(z, n, data) \
- BOOST_PP_CAT(BOOST_PP_TUPLE_ELEM(2, 0, data), n) \
- BOOST_PP_CAT(BOOST_PP_TUPLE_ELEM(2, 1, data), n) ;
-
-// like BOOST_PP_ENUM_BINARY_PARAMS(n, p1, p2) but p2 is in parens.
-// "p1 ## 0 (p2 ## 0) , p1 ## 1 (p2 ## 1) , ..."
-#define BOOST_ODEINT_ENUM_UNARY_CALLS(count, p1, p2) \
- BOOST_PP_ENUM(count, BOOST_ODEINT_ENUM_UNARY_CALLS_, (p1, p2))
-#define BOOST_ODEINT_ENUM_SHIFTED_UNARY_CALLS(count, p1, p2) \
- BOOST_PP_ENUM_SHIFTED(count, BOOST_ODEINT_ENUM_UNARY_CALLS_, (p1, p2))
-#define BOOST_ODEINT_ENUM_TRAILING_SHIFTED_UNARY_CALLS(count, p1, p2) \
- BOOST_PP_COMMA_IF(BOOST_PP_DEC(count)) \
- BOOST_PP_ENUM_SHIFTED(count, BOOST_ODEINT_ENUM_UNARY_CALLS_, (p1, p2))
-#define BOOST_ODEINT_ENUM_UNARY_CALLS_(z, n, data) \
- BOOST_PP_CAT(BOOST_PP_TUPLE_ELEM(2, 0, data), n) \
- ( BOOST_PP_CAT(BOOST_PP_TUPLE_ELEM(2, 1, data), n) )
-
-
-// maximum arity + 1 for scale_sum and for_each
-#define BOOST_ODEINT_N_ARY_MAX 16
-
-
-// generate scale_sum1 to scale_sumN, operator body generated by macro(N)
-#define BOOST_ODEINT_GEN_SCALE_SUM(macro) \
- BOOST_PP_REPEAT_FROM_TO(1, BOOST_ODEINT_N_ARY_MAX, BOOST_ODEINT_GEN_SCALE_SUM_, macro)
-#define BOOST_ODEINT_GEN_SCALE_SUM_(z, n, macro) \
- template< BOOST_ODEINT_ENUM_LSHIFTED_BINARY_PARAMS(n, class Fac, = double, = Fac) > \
- struct BOOST_PP_CAT(scale_sum, n) \
- { \
- BOOST_ODEINT_ENUM_BINARY_STATEMENTS(n, const Fac, m_alpha) \
- \
- BOOST_PP_CAT(scale_sum, n) \
- ( BOOST_PP_ENUM_BINARY_PARAMS(n, Fac, alpha) ) \
- : BOOST_ODEINT_ENUM_UNARY_CALLS(n, m_alpha, alpha) {} \
- \
- template< BOOST_PP_ENUM_PARAMS(BOOST_PP_INC(n), class T) > \
- void operator()( T0 &t0 \
- BOOST_ODEINT_ENUM_TRAILING_SHIFTED_BINARY_PARAMS(BOOST_PP_INC(n), const T, &t) \
- ) const \
- { macro(n) } \
- typedef void result_type; \
- };
-
-// generate for_each1 to for_eachN, body generated by macro(N)
-#define BOOST_ODEINT_GEN_FOR_EACH(macro) \
- BOOST_PP_REPEAT_FROM_TO(1, BOOST_ODEINT_N_ARY_MAX, BOOST_ODEINT_GEN_FOR_EACH_, macro)
-#define BOOST_ODEINT_GEN_FOR_EACH_(z, n, macro) \
- template< BOOST_PP_ENUM_PARAMS(n, class S) , class Op > \
- static void for_each##n ( BOOST_PP_ENUM_BINARY_PARAMS(n, S, &s) , Op op ) \
- { macro(n) }
-
-
-#endif
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/odeint_error.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/odeint_error.hpp
deleted file mode 100644
index 312e5b1afa7485baca946f89f3e1eb7b36f448d2..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/odeint_error.hpp
+++ /dev/null
@@ -1,77 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/util/odeint_error.hpp
-
- [begin_description]
- Runtime Exceptions thrown by odeint
- [end_description]
-
- Copyright 2015 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
-*/
-
-
-#ifndef BOOST_NUMERIC_ODEINT_UTIL_ODEINT_ERROR_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_UTIL_ODEINT_ERROR_HPP_INCLUDED
-
-#include <stdexcept>
-#include <string>
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-/**
- * \brief Runtime error thrown by odeint
- */
-class odeint_error : public std::runtime_error
-{
-public:
- odeint_error(const std::string &s)
- : std::runtime_error(s)
- { }
-};
-
-
-/**
- * \brief Runtime error thrown from integrate routines
- *
- * This Error occures when too many iterations are performed in between two
- * observer calls in the integrate routines.
- */
-class no_progress_error : public odeint_error
-{
-public:
- no_progress_error(const std::string &s)
- : odeint_error(s)
- { }
-};
-
-
-/**
- * \brief Runtime error thrown during stepsize adjustment
- *
- * This Error occures when too many iterations are performed without finding
- * an appropriate new step size. This usually indicates non-continuous points
- * in the ODE.
- */
-class step_adjustment_error : public odeint_error
-{
-public:
- step_adjustment_error(const std::string &s)
- : odeint_error(s)
- { }
-};
-
-}
-}
-}
-
-
-
-#endif // BOOST_NUMERIC_ODEINT_UTIL_ODEINT_ERROR_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/resize.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/resize.hpp
deleted file mode 100644
index 75e9eff448a167a40488f6d51c4685937eb19f20..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/resize.hpp
+++ /dev/null
@@ -1,118 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/util/state_wrapper.hpp
-
- [begin_description]
- State wrapper for the state type in all stepper. The state wrappers are responsible for construction,
- destruction, copying construction, assignment and resizing.
- [end_description]
-
- Copyright 2011-2013 Karsten Ahnert
- Copyright 2011 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_UTIL_RESIZE_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_UTIL_RESIZE_HPP_INCLUDED
-
-#include <boost/range.hpp>
-
-#include <boost/utility/enable_if.hpp>
-#include <boost/fusion/include/is_sequence.hpp>
-#include <boost/fusion/include/zip_view.hpp>
-#include <boost/fusion/include/vector.hpp>
-#include <boost/fusion/include/make_fused.hpp>
-#include <boost/fusion/include/for_each.hpp>
-
-#include <boost/numeric/odeint/util/is_resizeable.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-template< class StateOut , class StateIn , class Enabler = void >
-struct resize_impl_sfinae
-{
- static void resize( StateOut &x1 , const StateIn &x2 )
- {
- x1.resize( boost::size( x2 ) );
- }
-};
-
-// resize function
-// standard implementation relies on boost.range and resize member function
-template< class StateOut , class StateIn >
-struct resize_impl
-{
- static void resize( StateOut &x1 , const StateIn &x2 )
- {
- resize_impl_sfinae< StateOut , StateIn >::resize( x1 , x2 );
- }
-};
-
-
-// do not overload or specialize this function, specialize resize_impl<> instead
-template< class StateOut , class StateIn >
-void resize( StateOut &x1 , const StateIn &x2 )
-{
- resize_impl< StateOut , StateIn >::resize( x1 , x2 );
-}
-
-
-namespace detail {
-
- struct resizer
- {
- typedef void result_type;
-
- template< class StateOut , class StateIn >
- void operator()( StateOut &x1 , const StateIn &x2 ) const
- {
- resize_op( x1 , x2 , typename is_resizeable< StateOut >::type() );
- }
-
- template< class StateOut , class StateIn >
- void resize_op( StateOut &x1 , const StateIn &x2 , boost::true_type ) const
- {
- resize( x1 , x2 );
- }
-
- template< class StateOut , class StateIn >
- void resize_op( StateOut &x1 , const StateIn &x2 , boost::false_type ) const
- {
- }
-
- };
-} // namespace detail
-
-
-/*
- * specialization for fusion sequences
- */
-template< class FusionSeq >
-struct resize_impl_sfinae< FusionSeq , FusionSeq ,
- typename boost::enable_if< typename boost::fusion::traits::is_sequence< FusionSeq >::type >::type >
-{
- static void resize( FusionSeq &x1 , const FusionSeq &x2 )
- {
- typedef boost::fusion::vector< FusionSeq& , const FusionSeq& > Sequences;
- Sequences sequences( x1 , x2 );
- boost::fusion::for_each( boost::fusion::zip_view< Sequences >( sequences ) , boost::fusion::make_fused( detail::resizer() ) );
- }
-};
-
-
-
-
-}
-}
-}
-
-
-
-#endif // BOOST_NUMERIC_ODEINT_UTIL_RESIZE_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/resizer.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/resizer.hpp
deleted file mode 100644
index fd969ec3b95cb62e99afa60a0b621a77a4f3822d..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/resizer.hpp
+++ /dev/null
@@ -1,93 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/util/resizer.hpp
-
- [begin_description]
- Implementation of the resizers.
- [end_description]
-
- Copyright 2011-2012 Mario Mulansky
- Copyright 2011 Karsten Ahnert
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_UTIL_RESIZER_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_UTIL_RESIZER_HPP_INCLUDED
-
-
-#include <boost/numeric/odeint/util/is_resizeable.hpp>
-#include <boost/numeric/odeint/util/same_size.hpp>
-#include <boost/numeric/odeint/util/resize.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-template< class ResizeWrappedState , class State >
-bool adjust_size_by_resizeability( ResizeWrappedState &x , const State &y , boost::true_type )
-{
- if ( !same_size( x.m_v , y ) )
- {
- resize( x.m_v , y );
- return true;
- }
- else
- return false;
-}
-
-template< class ResizeWrappedState , class State >
-bool adjust_size_by_resizeability( ResizeWrappedState & /* x */ , const State & /* y */ , boost::false_type )
-{
- return false;
-}
-
-struct always_resizer
-{
- template< class State , class ResizeFunction >
- bool adjust_size( const State &x , ResizeFunction f )
- {
- return f( x );
- }
-};
-
-
-struct initially_resizer
-{
-
- bool m_initialized;
-
- initially_resizer() : m_initialized( false )
- { }
-
- template< class State , class ResizeFunction >
- bool adjust_size( const State &x , ResizeFunction f )
- {
- if( !m_initialized )
- {
- m_initialized = true;
- return f( x );
- } else
- return false;
- }
-};
-
-
-struct never_resizer
-{
- template< class State , class ResizeFunction >
- bool adjust_size( const State &x , ResizeFunction f )
- {
- return false;
- }
-};
-
-
-}
-}
-}
-
-#endif // BOOST_NUMERIC_ODEINT_UTIL_RESIZER_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/same_instance.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/same_instance.hpp
deleted file mode 100644
index 0d47b79ac03bc353b6a501dd3cfeae928768266d..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/same_instance.hpp
+++ /dev/null
@@ -1,56 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/util/same_instance.hpp
-
- [begin_description]
- Basic check if two variables are the same instance
- [end_description]
-
- Copyright 2012 Karsten Ahnert
- Copyright 2012 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_UTIL_SAME_INSTANCE_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_UTIL_SAME_INSTANCE_HPP_INCLUDED
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-template< class T1 , class T2 , class Enabler=void >
-struct same_instance_impl
-{
- static bool same_instance( const T1& /* x1 */ , const T2& /* x2 */ )
- {
- return false;
- }
-};
-
-template< class T >
-struct same_instance_impl< T , T >
-{
- static bool same_instance( const T &x1 , const T &x2 )
- {
- // check pointers
- return (&x1 == &x2);
- }
-};
-
-
-template< class T1 , class T2 >
-bool same_instance( const T1 &x1 , const T2 &x2 )
-{
- return same_instance_impl< T1 , T2 >::same_instance( x1 , x2 );
-}
-
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-#endif
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/same_size.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/same_size.hpp
deleted file mode 100644
index a11e30abd5bcf9a827ebd5910834b3795d25aca5..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/same_size.hpp
+++ /dev/null
@@ -1,115 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/util/state_wrapper.hpp
-
- [begin_description]
- State wrapper for the state type in all stepper. The state wrappers are responsible for construction,
- destruction, copying construction, assignment and resizing.
- [end_description]
-
- Copyright 2011-2013 Karsten Ahnert
- Copyright 2011 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_UTIL_SAME_SIZE_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_UTIL_SAME_SIZE_HPP_INCLUDED
-
-#include <boost/numeric/odeint/util/is_resizeable.hpp>
-
-#include <boost/utility/enable_if.hpp>
-#include <boost/fusion/include/is_sequence.hpp>
-#include <boost/fusion/include/zip_view.hpp>
-#include <boost/fusion/include/vector.hpp>
-#include <boost/fusion/include/make_fused.hpp>
-#include <boost/fusion/include/all.hpp>
-
-#include <boost/range.hpp>
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-template< typename State1 , typename State2 , class Enabler = void >
-struct same_size_impl_sfinae
-{
- static bool same_size( const State1 &x1 , const State2 &x2 )
- {
- return ( boost::size( x1 ) == boost::size( x2 ) );
- }
-
-};
-
-// same_size function
-// standard implementation relies on boost.range
-template< class State1 , class State2 >
-struct same_size_impl
-{
- static bool same_size( const State1 &x1 , const State2 &x2 )
- {
- return same_size_impl_sfinae< State1 , State2 >::same_size( x1 , x2 );
- }
-};
-
-
-// do not overload or specialize this function, specialize resize_impl<> instead
-template< class State1 , class State2 >
-bool same_size( const State1 &x1 , const State2 &x2 )
-{
- return same_size_impl< State1 , State2 >::same_size( x1 , x2 );
-}
-
-namespace detail {
-
-struct same_size_fusion
-{
- typedef bool result_type;
-
- template< class S1 , class S2 >
- bool operator()( const S1 &x1 , const S2 &x2 ) const
- {
- return same_size_op( x1 , x2 , typename is_resizeable< S1 >::type() );
- }
-
- template< class S1 , class S2 >
- bool same_size_op( const S1 &x1 , const S2 &x2 , boost::true_type ) const
- {
- return same_size( x1 , x2 );
- }
-
- template< class S1 , class S2 >
- bool same_size_op( const S1 &x1 , const S2 &x2 , boost::false_type ) const
- {
- return true;
- }
-};
-
-} // namespace detail
-
-
-
-template< class FusionSeq >
-struct same_size_impl_sfinae< FusionSeq , FusionSeq , typename boost::enable_if< typename boost::fusion::traits::is_sequence< FusionSeq >::type >::type >
-{
- static bool same_size( const FusionSeq &x1 , const FusionSeq &x2 )
- {
- typedef boost::fusion::vector< const FusionSeq& , const FusionSeq& > Sequences;
- Sequences sequences( x1 , x2 );
- return boost::fusion::all( boost::fusion::zip_view< Sequences >( sequences ) ,
- boost::fusion::make_fused( detail::same_size_fusion() ) );
- }
-};
-
-
-}
-}
-}
-
-
-
-#endif // BOOST_NUMERIC_ODEINT_UTIL_SAME_SIZE_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/split.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/split.hpp
deleted file mode 100644
index ba9875a49a0e7d9f0186f8711b28a88f285cb319..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/split.hpp
+++ /dev/null
@@ -1,64 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/util/split.hpp
-
- [begin_description]
- Split abstraction for parallel backends.
- [end_description]
-
- Copyright 2013 Karsten Ahnert
- Copyright 2013 Mario Mulansky
- Copyright 2013 Pascal Germroth
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_UTIL_SPLIT_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_UTIL_SPLIT_HPP_INCLUDED
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-/*
- * No default implementation of the split operation
- */
-template< class Container1, class Container2 , class Enabler = void >
-struct split_impl
-{
- static void split( const Container1 &from , Container2 &to );
-};
-
-template< class Container1 , class Container2 >
-void split( const Container1 &from , Container2 &to )
-{
- split_impl< Container1 , Container2 >::split( from , to );
-}
-
-
-/*
- * No default implementation of the unsplit operation
- */
-template< class Container1, class Container2 , class Enabler = void >
-struct unsplit_impl
-{
- static void unsplit( const Container1 &from , Container2 &to );
-};
-
-template< class Container1 , class Container2 >
-void unsplit( const Container1 &from , Container2 &to )
-{
- unsplit_impl< Container1 , Container2 >::unsplit( from , to );
-}
-
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_UTIL_COPY_HPP_INCLUDED
-
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/split_adaptor.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/split_adaptor.hpp
deleted file mode 100644
index cf0d6238147ada11f9a2511b4490ea0e17255bce..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/split_adaptor.hpp
+++ /dev/null
@@ -1,102 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/util/split_adaptor.hpp
-
- [begin_description]
- A range adaptor which returns even-sized slices.
- [end_description]
-
- Copyright 2013 Karsten Ahnert
- Copyright 2013 Mario Mulansky
- Copyright 2013 Pascal Germroth
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_UTIL_SPLIT_ADAPTOR_INCLUDED
-#define BOOST_NUMERIC_ODEINT_UTIL_SPLIT_ADAPTOR_INCLUDED
-
-#include <boost/range/adaptor/argument_fwd.hpp>
-#include <boost/range/size_type.hpp>
-#include <boost/range/iterator_range.hpp>
-#include <algorithm>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-namespace detail {
-
-/** \brief Returns the begin and end offset for a sub-range */
-inline std::pair<std::size_t, std::size_t>
-split_offsets( std::size_t total_length, std::size_t index, std::size_t parts )
-{
- BOOST_ASSERT( parts > 0 );
- BOOST_ASSERT( index < parts );
- const std::size_t
- slice = total_length / parts,
- partial = total_length % parts,
- lo = (std::min)(index, partial),
- hi = (std::max<std::ptrdiff_t>)(0, index - partial),
- begin_offset = lo * (slice + 1) + hi * slice,
- length = slice + (index < partial ? 1 : 0),
- end_offset = begin_offset + length;
- return std::make_pair( begin_offset, end_offset );
-}
-
-/** \brief Return the sub-range `index` from a range which is split into `parts`.
- *
- * For example, splitting a range into three about equal-sized sub-ranges:
- * \code
- * sub0 = make_split_range(rng, 0, 3);
- * sub1 = rng | split(1, 3);
- * sub2 = rng | split(2, 3);
- * \endcode
- */
-template< class RandomAccessRange >
-inline iterator_range< typename range_iterator<RandomAccessRange>::type >
-make_split_range( RandomAccessRange& rng, std::size_t index, std::size_t parts )
-{
- const std::pair<std::size_t, std::size_t> off = split_offsets(boost::size(rng), index, parts);
- return make_iterator_range( boost::begin(rng) + off.first, boost::begin(rng) + off.second );
-}
-
-template< class RandomAccessRange >
-inline iterator_range< typename range_iterator<const RandomAccessRange>::type >
-make_split_range( const RandomAccessRange& rng, std::size_t index, std::size_t parts )
-{
- const std::pair<std::size_t, std::size_t> off = split_offsets(boost::size(rng), index, parts);
- return make_iterator_range( boost::begin(rng) + off.first, boost::begin(rng) + off.second );
-}
-
-
-struct split
-{
- split(std::size_t index, std::size_t parts)
- : index(index), parts(parts) {}
- std::size_t index, parts;
-};
-
-template< class RandomAccessRange >
-inline iterator_range< typename range_iterator<RandomAccessRange>::type >
-operator|( RandomAccessRange& rng, const split& f )
-{
- return make_split_range( rng, f.index, f.parts );
-}
-
-template< class RandomAccessRange >
-inline iterator_range< typename range_iterator<const RandomAccessRange>::type >
-operator|( const RandomAccessRange& rng, const split& f )
-{
- return make_split_range( rng, f.index, f.parts );
-}
-
-
-}
-}
-}
-}
-
-#endif
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/state_wrapper.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/state_wrapper.hpp
deleted file mode 100644
index 10f8ecde3123e6b3c58751619eceedd61ee19020..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/state_wrapper.hpp
+++ /dev/null
@@ -1,50 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/util/state_wrapper.hpp
-
- [begin_description]
- State wrapper for the state type in all stepper. The state wrappers are responsible for construction,
- destruction, copying construction, assignment and resizing.
- [end_description]
-
- Copyright 2011-2012 Mario Mulansky
- Copyright 2011-2013 Karsten Ahnert
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_UTIL_STATE_WRAPPER_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_UTIL_STATE_WRAPPER_HPP_INCLUDED
-
-
-#include <boost/type_traits/integral_constant.hpp>
-
-#include <boost/numeric/odeint/util/is_resizeable.hpp>
-#include <boost/numeric/odeint/util/resize.hpp>
-#include <boost/numeric/odeint/util/same_size.hpp>
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-template< class V , class Enabler = void >
-struct state_wrapper
-{
- typedef state_wrapper< V > state_wrapper_type;
-
- V m_v;
-};
-
-
-}
-}
-}
-
-
-
-#endif // BOOST_NUMERIC_ODEINT_UTIL_STATE_WRAPPER_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/stepper_traits.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/stepper_traits.hpp
deleted file mode 100644
index 5d1d31ae6af566da06d99b32ec885a8607e30259..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/stepper_traits.hpp
+++ /dev/null
@@ -1,63 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/util/stepper_traits.hpp
-
- [begin_description]
- tba.
- [end_description]
-
- Copyright 2013 Karsten Ahnert
- Copyright 2013 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
-*/
-
-
-#ifndef BOOST_NUMERIC_ODEINT_UTIL_STEPPER_TRAITS_HPP_DEFINED
-#define BOOST_NUMERIC_ODEINT_UTIL_STEPPER_TRAITS_HPP_DEFINED
-
-#include <boost/numeric/odeint/util/unwrap_reference.hpp>
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-namespace traits {
-
-template< class Stepper >
-struct state_type
-{
- typedef typename boost::numeric::odeint::unwrap_reference< Stepper >::type stepper_type;
- typedef typename stepper_type::state_type type;
-};
-
-template< class Stepper >
-struct time_type
-{
- typedef typename boost::numeric::odeint::unwrap_reference< Stepper >::type stepper_type;
- typedef typename stepper_type::time_type type;
-};
-
-template< class Stepper >
-struct stepper_category
-{
- typedef typename boost::numeric::odeint::unwrap_reference< Stepper >::type stepper_type;
- typedef typename stepper_type::stepper_category type;
-};
-
-template< class Stepper >
-struct value_type
-{
- typedef typename boost::numeric::odeint::unwrap_reference< Stepper >::type stepper_type;
- typedef typename stepper_type::value_type type;
-};
-
-} // namespace traits
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_UTIL_STEPPER_TRAITS_HPP_DEFINED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/ublas_matrix_expression.patch b/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/ublas_matrix_expression.patch
deleted file mode 100644
index 4e8ac6c96462cdd66c1e62fbab688276beeb66b0..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/ublas_matrix_expression.patch
+++ /dev/null
@@ -1,6 +0,0 @@
-3390,3392c3390
-< typename enable_if< is_convertible<typename E1::value_type , T2>,
-< typename matrix_binary_scalar2_traits<E1, const T2, scalar_divides<typename E1::value_type, T2> >::result_type
-< > ::result_type
----
-> typename matrix_binary_scalar2_traits<E1, const T2, scalar_divides<typename E1::value_type, T2> >::result_type
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/ublas_wrapper.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/ublas_wrapper.hpp
deleted file mode 100644
index c8facfc46b4e8f03f4cd6ea956ca5e4dd89cdaae..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/ublas_wrapper.hpp
+++ /dev/null
@@ -1,297 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/util/ublas_wrapper.hpp
-
- [begin_description]
- Resizing for ublas::vector and ublas::matrix
- [end_description]
-
- Copyright 2011-2013 Mario Mulansky
- Copyright 2011-2013 Karsten Ahnert
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_UTIL_UBLAS_WRAPPER_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_UTIL_UBLAS_WRAPPER_HPP_INCLUDED
-
-
-#include <boost/type_traits/integral_constant.hpp>
-#include <boost/numeric/ublas/vector.hpp>
-#include <boost/numeric/ublas/matrix.hpp>
-#include <boost/numeric/ublas/lu.hpp>
-#include <boost/numeric/ublas/vector_expression.hpp>
-#include <boost/numeric/ublas/matrix_expression.hpp>
-
-#include <boost/numeric/odeint/algebra/vector_space_algebra.hpp>
-#include <boost/numeric/odeint/algebra/default_operations.hpp>
-
-#include <boost/numeric/odeint/util/is_resizeable.hpp>
-#include <boost/numeric/odeint/util/state_wrapper.hpp>
-
-
-/* extend ublas by a few operations */
-
-/* map norm_inf onto reduce( v , default_operations::maximum ) */
-namespace boost { namespace numeric { namespace odeint {
-
- template< typename T , typename A >
- struct vector_space_norm_inf< boost::numeric::ublas::vector<T,A> >
- {
- typedef T result_type;
-
- result_type operator()( const boost::numeric::ublas::vector<T,A> &x ) const
- {
- return boost::numeric::ublas::norm_inf( x );
- }
- };
-
-
- template< class T , class L , class A >
- struct vector_space_norm_inf< boost::numeric::ublas::matrix<T,L,A> >
- {
- typedef T result_type;
-
- result_type operator()( const boost::numeric::ublas::matrix<T,L,A> &x ) const
- {
- return boost::numeric::ublas::norm_inf( x );
- }
- };
-} } }
-
-/* additional operations:
- * abs( v )
- * v / w
- * a + v
- */
-namespace boost { namespace numeric { namespace ublas {
-
-
- // elementwise abs - calculates absolute values of the elements
- template<class T>
- struct scalar_abs: public scalar_unary_functor<T> {
- typedef typename scalar_unary_functor<T>::value_type value_type;
- typedef typename scalar_unary_functor<T>::argument_type argument_type;
- typedef typename scalar_unary_functor<T>::result_type result_type;
-
- static BOOST_UBLAS_INLINE
- result_type apply (argument_type t) {
- using std::abs;
- return abs (t);
- }
- };
-
-
- // (abs v) [i] = abs (v [i])
- template<class E>
- BOOST_UBLAS_INLINE
- typename vector_unary_traits<E, scalar_abs<typename E::value_type> >::result_type
- abs (const vector_expression<E> &e) {
- typedef typename vector_unary_traits<E, scalar_abs<typename E::value_type> >::expression_type expression_type;
- return expression_type (e ());
- }
-
- // (abs m) [i] = abs (m [i])
- template<class E>
- BOOST_UBLAS_INLINE
- typename matrix_unary1_traits<E, scalar_abs<typename E::value_type> >::result_type
- abs (const matrix_expression<E> &e) {
- typedef typename matrix_unary1_traits<E, scalar_abs<typename E::value_type> >::expression_type expression_type;
- return expression_type (e ());
- }
-
-
- // elementwise division (v1 / v2) [i] = v1 [i] / v2 [i]
- template<class E1, class E2>
- BOOST_UBLAS_INLINE
- typename vector_binary_traits<E1, E2, scalar_divides<typename E1::value_type,
- typename E2::value_type> >::result_type
- operator / (const vector_expression<E1> &e1,
- const vector_expression<E2> &e2) {
- typedef typename vector_binary_traits<E1, E2, scalar_divides<typename E1::value_type,
- typename E2::value_type> >::expression_type expression_type;
- return expression_type (e1 (), e2 ());
- }
-
-
- // elementwise division (m1 / m2) [i] = m1 [i] / m2 [i]
- template<class E1, class E2>
- BOOST_UBLAS_INLINE
- typename matrix_binary_traits<E1, E2, scalar_divides<typename E1::value_type,
- typename E2::value_type> >::result_type
- operator / (const matrix_expression<E1> &e1,
- const matrix_expression<E2> &e2) {
- typedef typename matrix_binary_traits<E1, E2, scalar_divides<typename E1::value_type,
- typename E2::value_type> >::expression_type expression_type;
- return expression_type (e1 (), e2 ());
- }
-
- // addition with scalar
- // (t + v) [i] = t + v [i]
- template<class T1, class E2>
- BOOST_UBLAS_INLINE
- typename enable_if< is_convertible<T1, typename E2::value_type >,
- typename vector_binary_scalar1_traits<const T1, E2, scalar_plus<T1, typename E2::value_type> >::result_type
- >::type
- operator + (const T1 &e1,
- const vector_expression<E2> &e2) {
- typedef typename vector_binary_scalar1_traits<const T1, E2, scalar_plus<T1, typename E2::value_type> >::expression_type expression_type;
- return expression_type (e1, e2 ());
- }
-
- // addition with scalar
- // (t + m) [i] = t + m [i]
- template<class T1, class E2>
- BOOST_UBLAS_INLINE
- typename enable_if< is_convertible<T1, typename E2::value_type >,
- typename matrix_binary_scalar1_traits<const T1, E2, scalar_plus<T1, typename E2::value_type> >::result_type
- >::type
- operator + (const T1 &e1,
- const matrix_expression<E2> &e2) {
- typedef typename matrix_binary_scalar1_traits<const T1, E2, scalar_plus<T1, typename E2::value_type> >::expression_type expression_type;
- return expression_type (e1, e2 ());
- }
-
-} } }
-
-
-
-
-/* add resize functionality */
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-/*
- * resizeable specialization for boost::numeric::ublas::vector
- */
-template< class T , class A >
-struct is_resizeable< boost::numeric::ublas::vector< T , A > >
-{
- typedef boost::true_type type;
- const static bool value = type::value;
-};
-
-
-/*
- * resizeable specialization for boost::numeric::ublas::matrix
- */
-template< class T , class L , class A >
-struct is_resizeable< boost::numeric::ublas::matrix< T , L , A > >
-{
- typedef boost::true_type type;
- const static bool value = type::value;
-};
-
-
-/*
- * resizeable specialization for boost::numeric::ublas::permutation_matrix
- */
-template< class T , class A >
-struct is_resizeable< boost::numeric::ublas::permutation_matrix< T , A > >
-{
- typedef boost::true_type type;
- const static bool value = type::value;
-};
-
-
-// specialization for ublas::matrix
-// same size and resize specialization for matrix-matrix resizing
-template< class T , class L , class A , class T2 , class L2 , class A2 >
-struct same_size_impl< boost::numeric::ublas::matrix< T , L , A > , boost::numeric::ublas::matrix< T2 , L2 , A2 > >
-{
- static bool same_size( const boost::numeric::ublas::matrix< T , L , A > &m1 ,
- const boost::numeric::ublas::matrix< T2 , L2 , A2 > &m2 )
- {
- return ( ( m1.size1() == m2.size1() ) && ( m1.size2() == m2.size2() ) );
- }
-};
-
-template< class T , class L , class A , class T2 , class L2 , class A2 >
-struct resize_impl< boost::numeric::ublas::matrix< T , L , A > , boost::numeric::ublas::matrix< T2 , L2 , A2 > >
-{
- static void resize( boost::numeric::ublas::matrix< T , L , A > &m1 ,
- const boost::numeric::ublas::matrix< T2 , L2 , A2 > &m2 )
- {
- m1.resize( m2.size1() , m2.size2() );
- }
-};
-
-
-
-// same size and resize specialization for matrix-vector resizing
-template< class T , class L , class A , class T_V , class A_V >
-struct same_size_impl< boost::numeric::ublas::matrix< T , L , A > , boost::numeric::ublas::vector< T_V , A_V > >
-{
- static bool same_size( const boost::numeric::ublas::matrix< T , L , A > &m ,
- const boost::numeric::ublas::vector< T_V , A_V > &v )
- {
- return ( ( m.size1() == v.size() ) && ( m.size2() == v.size() ) );
- }
-};
-
-template< class T , class L , class A , class T_V , class A_V >
-struct resize_impl< boost::numeric::ublas::matrix< T , L , A > , boost::numeric::ublas::vector< T_V , A_V > >
-{
- static void resize( boost::numeric::ublas::matrix< T , L , A > &m ,
- const boost::numeric::ublas::vector< T_V , A_V > &v )
- {
- m.resize( v.size() , v.size() );
- }
-};
-
-
-
-// specialization for ublas::permutation_matrix
-// same size and resize specialization for matrix-vector resizing
-template< class T , class A , class T_V , class A_V >
-struct same_size_impl< boost::numeric::ublas::permutation_matrix< T , A > ,
- boost::numeric::ublas::vector< T_V , A_V > >
-{
- static bool same_size( const boost::numeric::ublas::permutation_matrix< T , A > &m ,
- const boost::numeric::ublas::vector< T_V , A_V > &v )
- {
- return ( m.size() == v.size() ); // && ( m.size2() == v.size() ) );
- }
-};
-
-template< class T , class A , class T_V , class A_V >
-struct resize_impl< boost::numeric::ublas::vector< T_V , A_V > ,
- boost::numeric::ublas::permutation_matrix< T , A > >
-{
- static void resize( const boost::numeric::ublas::vector< T_V , A_V > &v,
- boost::numeric::ublas::permutation_matrix< T , A > &m )
- {
- m.resize( v.size() , v.size() );
- }
-};
-
-
-
-
-
-
-
-template< class T , class A >
-struct state_wrapper< boost::numeric::ublas::permutation_matrix< T , A > > // with resizing
-{
- typedef boost::numeric::ublas::permutation_matrix< T , A > state_type;
- typedef state_wrapper< state_type > state_wrapper_type;
-
- state_type m_v;
-
- state_wrapper() : m_v( 1 ) // permutation matrix constructor requires a size, choose 1 as default
- { }
-
-};
-
-
-
-
-} } }
-
-
-#endif // BOOST_NUMERIC_ODEINT_UTIL_UBLAS_WRAPPER_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/unit_helper.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/unit_helper.hpp
deleted file mode 100644
index 2e6a38c5c040f0e72d06b2d2d7daabf6d22ee030..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/unit_helper.hpp
+++ /dev/null
@@ -1,151 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/util/unit_helper.hpp
-
- [begin_description]
- Get and set the value of a unit.
- [end_description]
-
- Copyright 2012-2013 Karsten Ahnert
- Copyright 2012-2013 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
-*/
-
-
-#ifndef BOOST_NUMERIC_ODEINT_UTIL_UNIT_HELPER_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_UTIL_UNIT_HELPER_HPP_INCLUDED
-
-
-#ifndef __CUDACC__
-#include <boost/units/quantity.hpp>
-#include <boost/units/get_dimension.hpp>
-#include <boost/units/get_system.hpp>
-#endif
-
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-namespace detail {
-
- template<class T , class Enabler = void >
- struct get_unit_value_impl
- {
- static T value(const T &t)
- {
- return t;
- }
- typedef T result_type;
- };
-
-#ifndef __CUDACC__
- template<class Unit , class T>
- struct get_unit_value_impl< boost::units::quantity< Unit , T> >
- {
- static T value( const boost::units::quantity< Unit , T> &t )
- {
- return t.value();
- }
- typedef T result_type;
- };
-#endif
-
-
-
-
-
- template<class T , class V , class Enabler = void >
- struct set_unit_value_impl
- {
- static void set_value(T &t , const V &v)
- {
- t = v;
- }
- };
-
-#ifndef __CUDACC__
- template<class Unit , class T , class V>
- struct set_unit_value_impl<boost::units::quantity<Unit , T> , V>
- {
- static void set_value(boost::units::quantity<Unit , T> &t , const V &v)
- {
- t = boost::units::quantity<Unit , T>::from_value(v);
- }
- };
-#endif
-
-
-
-} // namespace detail
-
-
- template<class T>
- typename detail::get_unit_value_impl<T>::result_type get_unit_value(const T &t)
- {
- return detail::get_unit_value_impl<T>::value(t);
- }
-
-
- template<class T , class V>
- void set_unit_value(T &t , const V &v)
- {
- return detail::set_unit_value_impl<T , V>::set_value(t , v);
- }
-
-
-
- template< class T >
- struct unit_value_type
- {
- typedef T type;
- };
-
-#ifndef __CUDACC__
- template< class Unit , class Y >
- struct unit_value_type< boost::units::quantity< Unit , Y > >
- {
- typedef Y type;
- };
-#endif
-
-
-
-
-
-
-
-
-
-
- template< typename Time >
- struct inverse_time
- {
- typedef Time type;
- };
-
-#ifndef __CUDACC__
- template< typename Unit , typename Value >
- struct inverse_time< boost::units::quantity< Unit , Value > >
- {
- typedef boost::units::quantity< Unit , Value > time_type;
- typedef typename boost::units::get_dimension< time_type >::type dimension;
- typedef typename boost::units::get_system< time_type >::type system;
- typedef typename boost::mpl::divides< boost::units::dimensionless_type , dimension >::type inv_dimension;
- typedef boost::units::unit< inv_dimension , system > inv_unit;
- typedef boost::units::quantity< inv_unit , Value > type;
- };
-#endif
-
-
-} // namespace odeint
-} // namespace numeric
-} // namespace boost
-
-
-#endif // BOOST_NUMERIC_ODEINT_UTIL_UNIT_HELPER_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/unwrap_reference.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/unwrap_reference.hpp
deleted file mode 100644
index be93dc0ed2505eb176b5b26c4eb48d1161f07732..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/util/unwrap_reference.hpp
+++ /dev/null
@@ -1,166 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/util/unwrap_reference.hpp
-
- [begin_description]
- unwrap_reference
- [end_description]
-
- Copyright 2012-2013 Karsten Ahnert
- Copyright 2012-2013 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-
-#ifndef BOOST_NUMERIC_ODEINT_UTIL_UNWRAP_REFERENCE_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_UTIL_UNWRAP_REFERENCE_HPP_INCLUDED
-
-
-#include <boost/numeric/odeint/config.hpp>
-
-
-#if BOOST_NUMERIC_ODEINT_CXX11
-#include <functional>
-#else
-#include <boost/ref.hpp>
-#endif
-
-namespace boost {
-
-#if BOOST_NUMERIC_ODEINT_CXX11
-template<typename T> struct reference_wrapper;
-
-template<typename T> struct unwrap_reference;
-#endif
-
-namespace numeric {
-namespace odeint {
-
-
-#if BOOST_NUMERIC_ODEINT_CXX11
-
-template<typename T>
-struct unwrap_reference
-{
- typedef typename std::remove_reference<T>::type type;
-};
-
-template<typename T>
-struct unwrap_reference< std::reference_wrapper<T> >
-{
- typedef typename std::remove_reference<T>::type type;
-};
-
-template<typename T>
-struct unwrap_reference< boost::reference_wrapper<T> >
-{
- typedef typename boost::unwrap_reference<T>::type type;
-};
-
-#else
-
-using ::boost::unwrap_reference;
-
-#endif
-
-namespace detail
-{
-
-#if BOOST_NUMERIC_ODEINT_CXX11
-
-using ::std::ref;
-
-#else
-
-using ::boost::ref;
-
-#endif
-}
-
-}
-}
-}
-
-
-
-/*
- *
- * the following is the suggested way, but unfortunately it does not work with all compilers.
- */
-
-/*
-
-#include <boost/config.hpp>
-
-
-#ifdef BOOST_NO_CXX11_HDR_FUNCTIONAL
-#include <boost/ref.hpp>
-#else
-#include <functional>
-#endif
-
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-
-#ifndef BOOST_NO_CXX11_HDR_FUNCTIONAL
-
-template<typename T>
-struct unwrap_reference
-{
- typedef typename std::remove_reference<T>::type type;
-};
-
-template<typename T>
-struct unwrap_reference< std::reference_wrapper<T> >
-{
- typedef typename std::remove_reference<T>::type type;
-};
-
-template<typename T>
-struct unwrap_reference< boost::reference_wrapper<T> >
-{
- typedef typename boost::unwrap_reference<T>::type type;
-};
-
-#else
-
-using ::boost::unwrap_reference;
-
-#endif
-
-}
-}
-}
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-namespace detail {
-
-
-#ifndef BOOST_NO_CXX11_HDR_FUNCTIONAL
-
-using ::std::ref;
-
-#else
-
-using ::boost::ref;
-
-#endif
-
-
-}
-}
-}
-}
-
-*/
-
-#endif // BOOST_NUMERIC_ODEINT_UTIL_UNWRAP_REFERENCE_HPP_INCLUDED
diff --git a/moose-core/external/odeint-v2/include/boost/numeric/odeint/version.hpp b/moose-core/external/odeint-v2/include/boost/numeric/odeint/version.hpp
deleted file mode 100644
index 379c9065992b39d3754d27add9d78bc4d6516c9f..0000000000000000000000000000000000000000
--- a/moose-core/external/odeint-v2/include/boost/numeric/odeint/version.hpp
+++ /dev/null
@@ -1,55 +0,0 @@
-/*
- [auto_generated]
- boost/numeric/odeint/version.hpp
-
- [begin_description]
- Defines the current version of odeint.
- [end_description]
-
- Copyright 2011-2012 Karsten Ahnert
- Copyright 2011-2012 Mario Mulansky
-
- Distributed under the Boost Software License, Version 1.0.
- (See accompanying file LICENSE_1_0.txt or
- copy at http://www.boost.org/LICENSE_1_0.txt)
- */
-
-#ifndef BOOST_NUMERIC_ODEINT_VERSION_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_VERSION_HPP_INCLUDED
-
-#include <string>
-#include <sstream>
-
-
-#define ODEINT_MAJOR_VERSION 2
-#define ODEINT_MINOR_VERSION 2
-#define ODEINT_PATCH_LEVEL 0
-#define ODEINT_VERSION ( ODEINT_MAJOR_VERSION * 100000 + ODEINT_MINOR_VERSION * 100 + ODEINT_PATCH_LEVEL )
-
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-namespace version {
-
-const int major = ODEINT_MAJOR_VERSION ;
-const int minor = ODEINT_MINOR_VERSION ;
-const int patch_level = ODEINT_PATCH_LEVEL ;
-
-}
-
-inline std::string get_version_string( void )
-{
- std::ostringstream str;
- str << "v" << version::major << "." << version::minor;
- if( version::patch_level != 0 ) str << "_" << version::patch_level;
- return str.str();
-}
-
-
-}
-}
-}
-
-#endif // BOOST_NUMERIC_ODEINT_VERSION_HPP_INCLUDED
diff --git a/moose-core/hsolve/HSolve.cpp b/moose-core/hsolve/HSolve.cpp
index 5d04a7775fc8d7eff00e38d0f20f411f32a6f2fc..b9151d9820809d03b2695a29be6274539e9d9785 100644
--- a/moose-core/hsolve/HSolve.cpp
+++ b/moose-core/hsolve/HSolve.cpp
@@ -304,7 +304,6 @@ void HSolve::setSeed( Id seed )
<< "' is not derived from type 'Compartment'." << endl;
return;
}
-
seed_ = seed;
}
diff --git a/moose-core/hsolve/HSolveActive.cpp b/moose-core/hsolve/HSolveActive.cpp
index ecb48c4baac39b1c5322a74080d0af635cbbefd6..e2ddd770f094b36aca42ae5c8abde456d4f6fe2f 100644
--- a/moose-core/hsolve/HSolveActive.cpp
+++ b/moose-core/hsolve/HSolveActive.cpp
@@ -59,11 +59,9 @@ void HSolveActive::step( ProcPtr info )
HSolvePassive::backwardSubstitute();
advanceCalcium();
advanceSynChans( info );
-
sendValues( info );
sendSpikes( info );
-
- prevExtCurr_ = externalCurrent_;
+ prevExtCurr_ = externalCurrent_;
externalCurrent_.assign( externalCurrent_.size(), 0.0 );
}
diff --git a/moose-core/hsolve/ZombieCompartment.h b/moose-core/hsolve/ZombieCompartment.h
index e4ef5ca4ccdcb03f4fdfb6ca14a7258be7d6134f..dd8472681d84e9826499a87c4e8b763e903a1612 100644
--- a/moose-core/hsolve/ZombieCompartment.h
+++ b/moose-core/hsolve/ZombieCompartment.h
@@ -144,7 +144,7 @@ private:
void copyFields( moose::Compartment* c );
- moose::RNG<double> rng;
+ moose::RNG rng;
};
diff --git a/moose-core/ksolve/CMakeLists.txt b/moose-core/ksolve/CMakeLists.txt
index f5124aab4ce889bb72bd829c759c7b33d6248af8..8dd567a73b87e89867f0300aa524b9edcf3b5a88 100644
--- a/moose-core/ksolve/CMakeLists.txt
+++ b/moose-core/ksolve/CMakeLists.txt
@@ -3,26 +3,17 @@ include(CheckIncludeFileCXX)
include( ${CMAKE_CURRENT_SOURCE_DIR}/../CheckCXXCompiler.cmake)
if(WITH_BOOST)
- find_package(Boost REQUIRED COMPONENTS thread)
+ find_package(Boost 1.53 REQUIRED COMPONENTS thread)
add_definitions( -DUSE_BOOST_ASYNC )
- if("${CMAKE_BUILD_TYPE}" STREQUAL "Release")
- add_definitions( -UBOOST_UBLAS_TYPE_CHECK )
- else()
- add_definitions( -DBOOST_UBLAS_TYPE_CHECK )
- endif()
set(WITH_BOOST_ODE ON)
include_directories( ${Boost_INCLUDE_DIRS} )
+ # This is still not part of official bindings.
+ include_directories(${CMAKE_CURRENT_SOURCE_DIR}/../external/boost-numeric-bindings)
endif()
IF(WITH_BOOST_ODE)
- check_include_file_cxx( ${Boost_INCLUDE_DIRS}/boost/numeric/odeint.hpp
- ODEINT_EXISTS)
- # If boost distribution does not have its own odeint library, use the
- # private one.
- if(NOT ODEINT_EXISTS)
- include_directories( ../external/odeint-v2/include )
- endif(NOT ODEINT_EXISTS)
- include_directories( ../external/boost-numeric-bindings )
+ include_directories(${Boost_INCLUDE_DIRS})
+ include_directories(${CMAKE_CURRENT_SOURCE_DIR}/../external/boost-numeric-bindings)
elseif(WITH_GSL)
include_directories( ${GSL_INCLUDE_DIRS} )
endif(WITH_BOOST_ODE)
diff --git a/moose-core/ksolve/FuncTerm.cpp b/moose-core/ksolve/FuncTerm.cpp
index c8690071379ac127444a64d4dd7064af889959f7..527744f7055116f16e3f0cdb768f133389284da6 100644
--- a/moose-core/ksolve/FuncTerm.cpp
+++ b/moose-core/ksolve/FuncTerm.cpp
@@ -23,7 +23,6 @@
#include <sstream>
using namespace std;
-#include "../external/muparser/include/muParser.h"
#include "FuncTerm.h"
#include "../utility/numutil.h"
diff --git a/moose-core/ksolve/FuncTerm.h b/moose-core/ksolve/FuncTerm.h
index fe735278adad1f6ba3c1feec04023df5fa313ec7..71bf2de7255580fe3967e309b5f9bcdc42cdb176 100644
--- a/moose-core/ksolve/FuncTerm.h
+++ b/moose-core/ksolve/FuncTerm.h
@@ -10,7 +10,7 @@
#ifndef _FUNC_TERM_H
#define _FUNC_TERM_H
-#include "../external/muparser/include/muParser.h"
+#include "../builtins/MooseParser.h"
class FuncTerm
{
@@ -44,7 +44,7 @@ class FuncTerm
double* args_;
// Look up reactants in the S vec.
vector< unsigned int > reactantIndex_;
- mu::Parser parser_;
+ MooseParser parser_;
string expr_;
/**
* Scale factor to account for pool volume if we are assigning conc
@@ -53,6 +53,7 @@ class FuncTerm
*/
double volScale_;
unsigned int target_; /// Index of the entity to be updated by Func
+
};
#endif // _FUNC_TERM_H
diff --git a/moose-core/ksolve/Gsolve.cpp b/moose-core/ksolve/Gsolve.cpp
index 332005a696dbabebf08f98d0a60b46c62548450a..4b31deec508dfde94aabb6b3e5c0dd55d481e9d7 100644
--- a/moose-core/ksolve/Gsolve.cpp
+++ b/moose-core/ksolve/Gsolve.cpp
@@ -10,6 +10,7 @@
#include "../basecode/global.h"
#include "../mesh/VoxelJunction.h"
+#include "../utility/print_function.hpp"
#include "VoxelPoolsBase.h"
#include "XferInfo.h"
@@ -42,6 +43,14 @@
#define SIMPLE_ROUNDING 0
+// When set use std::async rather than std::thread
+// TODO: Profiling.
+#define USING_ASYNC 1
+
+#if USING_ASYNC
+#define THREAD_LAUNCH_POLICY std::launch::async
+#endif
+
const unsigned int OFFNODE = ~0;
const Cinfo* Gsolve::initCinfo()
@@ -138,10 +147,7 @@ const Cinfo* Gsolve::initCinfo()
&Gsolve::getNumFire
);
- ///////////////////////////////////////////////////////
// DestFinfo definitions
- ///////////////////////////////////////////////////////
-
static DestFinfo process( "process",
"Handles process call",
new ProcOpFunc< Gsolve >( &Gsolve::process ) );
@@ -163,13 +169,12 @@ const Cinfo* Gsolve::initCinfo()
"Handles initReinit call from Clock",
new ProcOpFunc< Gsolve >( &Gsolve::initReinit ) );
- ///////////////////////////////////////////////////////
// Shared definitions
- ///////////////////////////////////////////////////////
static Finfo* procShared[] =
{
&process, &reinit
};
+
static SharedFinfo proc( "proc",
"Shared message for process and reinit",
procShared, sizeof( procShared ) / sizeof( const Finfo* )
@@ -227,10 +232,11 @@ Gsolve::Gsolve() :
pools_( 1 ),
startVoxel_( 0 ),
dsolve_(),
- dsolvePtr_( 0 ),
+ dsolvePtr_(nullptr),
useClockedUpdate_( false )
{
- ;
+ // Initialize with global seed.
+ rng_.setSeed(moose::getGlobalSeed());
}
Gsolve& Gsolve::operator=(const Gsolve& )
@@ -257,8 +263,7 @@ void Gsolve::setCompartment( Id compt )
if ( ( compt.element()->cinfo()->isA( "ChemCompt" ) ) )
{
compartment_ = compt;
- vector< double > vols =
- Field< vector< double > >::get( compt, "voxelVolume" );
+ vector< double > vols = Field< vector< double > >::get( compt, "voxelVolume" );
if ( vols.size() > 0 )
{
pools_.resize( vols.size() );
@@ -336,7 +341,7 @@ void Gsolve::setNvec( unsigned int voxel, vector< double > nVec )
double* s = pools_[voxel].varS();
for ( unsigned int i = 0; i < nVec.size(); ++i )
{
- s[i] = round( nVec[i] );
+ s[i] = std::round( nVec[i] );
if ( s[i] < 0.0 )
s[i] = 0.0;
}
@@ -402,45 +407,25 @@ void Gsolve::process( const Eref& e, ProcPtr p )
// one would use a stochastic (integral) diffusion method with
// the GSSA, but in mixed models it may be more complicated.
vector< double >::iterator i = dvalues.begin() + 4;
-
for ( ; i != dvalues.end(); ++i )
{
- // cout << *i << " " << round( *i ) << " ";
#if SIMPLE_ROUNDING
- *i = round( *i );
+ *i = std::round( *i );
#else
- double base = floor( *i );
-
- // Use global RNG.
- if ( moose::mtrand() >= (*i - base) )
- *i = base;
- else
- *i = base + 1.0;
+ // *i = approximateWithInteger_debug(__FUNCTION__, *i, rng_);
+ *i = approximateWithInteger(*i, rng_);
#endif
}
setBlock( dvalues );
}
- // Third: Fix the rates if we have had any diffusion or xreacs
- // happening. This is very inefficient at this point, need to fix.
if ( dsolvePtr_ )
{
for ( auto i = pools_.begin(); i != pools_.end(); ++i )
i->refreshAtot( &sys_ );
}
- // Fourth, update the mol #s.
- // First we advance the simulation.
- size_t nvPools = pools_.size( );
-
- // Third, do the numerical integration for all reactions.
- size_t grainSize = max( (size_t)1, min( nvPools, nvPools / numThreads_));
-
- // Make sure that we cover all the pools.
- while( (numThreads_ * grainSize) < nvPools )
- grainSize += 1;
-
- if( 1 == numThreads_ || 1 == nvPools )
+ if( 1 == numThreads_ || 1 == pools_.size())
{
if( numThreads_ > 1 )
{
@@ -448,7 +433,7 @@ void Gsolve::process( const Eref& e, ProcPtr p )
numThreads_ = 1;
}
- for ( size_t i = 0; i < nvPools; i++ )
+ for ( size_t i = 0; i < pools_.size(); i++ )
pools_[i].advance( p, &sys_ );
}
else
@@ -457,20 +442,36 @@ void Gsolve::process( const Eref& e, ProcPtr p )
* Somewhat complicated computation to compute the number of threads. 1
* thread per (at least) voxel pool is ideal situation.
*-----------------------------------------------------------------------------*/
+#if USING_ASYNC
+ vector<std::future<size_t>> vecFutures;
+ for (size_t i = 0; i < numThreads_; i++)
+ vecFutures.push_back(
+ std::async( THREAD_LAUNCH_POLICY
+ , [this, i, p](){
+ return this->advance_chunk(i*this->grainSize_, (i+1)*this->grainSize_, p);
+ })
+ );
+ // Block in same order
+ size_t tot = 0;
+ for (auto& fut : vecFutures) tot += fut.get();
+ // We have processed all the pools.
+ assert( tot >= pools_.size() );
+#else
vector<std::thread> vecThreads;
-
for (size_t i = 0; i < numThreads_; i++)
{
// Use lambda. It is roughly 10% faster than std::bind and does not
// involve copying data.
- std::thread t(
- [this, i, grainSize, p](){ this->advance_chunk(i*grainSize, (i+1)*grainSize, p); }
- );
- vecThreads.push_back( std::move(t) );
+ vecThreads.push_back(
+ std::thread(
+ [this, i, p](){ this->advance_chunk(i*this->grainSize_, (i+1)*this->grainSize_, p); }
+ )
+ );
}
for( auto &v : vecThreads )
v.join();
+#endif
}
@@ -483,20 +484,38 @@ void Gsolve::process( const Eref& e, ProcPtr p )
}
else
{
+#if USING_ASYNC
+ vector<std::future<size_t>> vecFutures;
+ for (size_t i = 0; i < numThreads_; i++)
+ vecFutures.push_back(
+ std::async( THREAD_LAUNCH_POLICY
+ , [this, i, p](){
+ return this->recalcTimeChunk(i*this->grainSize_, (i+1)*this->grainSize_, p);
+ })
+ );
+ // Block in same order
+ size_t tot = 0;
+ for (auto& fut : vecFutures) tot += fut.get();
+ assert( tot >= pools_.size() ); // We have processed all the pools.
+#else
vector<std::thread> vecThreads;
for (size_t i = 0; i < numThreads_; i++)
{
// Use lambda. It is roughly 10% faster than std::bind and does not
// involve copying data.
- std::thread t(
- [this, i, grainSize, p](){ this->recalcTimeChunk(i*grainSize, (i+1)*grainSize, p); }
- );
- vecThreads.push_back( std::move(t) );
+ vecThreads.push_back(
+ std::thread(
+ [this, i, p](){
+ this->recalcTimeChunk(i*this->grainSize_, (i+1)*this->grainSize_, p);
+ }
+ )
+ );
}
-
for( auto &v : vecThreads )
v.join();
+#endif
+
}
}
@@ -518,38 +537,54 @@ void Gsolve::process( const Eref& e, ProcPtr p )
}
}
-void Gsolve::recalcTimeChunk( const size_t begin, const size_t end, ProcPtr p)
+size_t Gsolve::recalcTimeChunk( const size_t begin, const size_t end, ProcPtr p)
{
- for (size_t i = begin; i < std::min(pools_.size(), end); i++)
+ assert( begin >= std::min(pools_.size(), end));
+
+ size_t tot = 0;
+ for (size_t i = begin; i < std::min(pools_.size(), end); i++) {
+ tot += 1;
pools_[i].recalcTime( &sys_, p->currTime );
+ }
+ return tot;
}
-void Gsolve::advance_chunk( const size_t begin, const size_t end, ProcPtr p )
+size_t Gsolve::advance_chunk( const size_t begin, const size_t end, ProcPtr p )
{
+ assert( begin <= std::min(end, pools_.size()) );
+ size_t tot = 0;
for (size_t i = begin; i < std::min(end, pools_.size() ); i++)
+ {
pools_[i].advance( p, &sys_ );
+ tot += 1;
+ }
+ return tot;
}
void Gsolve::reinit( const Eref& e, ProcPtr p )
{
if ( !stoichPtr_ )
return;
+
if ( !sys_.isReady )
rebuildGssaSystem();
+
// First reinit concs.
- for ( vector< GssaVoxelPools >::iterator
- i = pools_.begin(); i != pools_.end(); ++i )
- {
+ for (auto i = pools_.begin(); i != pools_.end(); ++i )
i->reinit( &sys_ );
- }
+
// Second, update the atots.
- for ( vector< GssaVoxelPools >::iterator
- i = pools_.begin(); i != pools_.end(); ++i )
- {
+ for ( auto i = pools_.begin(); i != pools_.end(); ++i )
i->refreshAtot( &sys_ );
- }
- if( 1 < getNumThreads( ) )
+ // LoadBalancing. Recompute the optimal number of threads.
+ size_t nvPools = pools_.size( );
+ grainSize_ = (size_t) std::ceil((double)nvPools / (double)numThreads_);
+ assert( grainSize_ * numThreads_ >= nvPools);
+ numThreads_ = nvPools / grainSize_;
+ MOOSE_DEBUG( "Grain size is " << grainSize_ << ". Num threads " << numThreads_);
+
+ if(1 < getNumThreads())
cout << "Info: Setting up threaded gsolve with " << getNumThreads( )
<< " threads. " << endl;
}
@@ -564,10 +599,9 @@ void Gsolve::initReinit( const Eref& e, ProcPtr p )
{
if ( !stoichPtr_ )
return;
- for ( unsigned int i = 0 ; i < pools_.size(); ++i )
- {
+
+ for( size_t i = 0 ; i < pools_.size(); ++i )
pools_[i].reinit( &sys_ );
- }
}
//////////////////////////////////////////////////////////////
// Solver setup
@@ -858,11 +892,8 @@ void Gsolve::makeReacDepsUnique()
vector< unsigned int >::iterator k = dep.begin();
/// STL stuff follows, with the usual weirdness.
- vector< unsigned int >::iterator pos =
- unique( dep.begin(), dep.end() );
+ vector<unsigned int>::iterator pos = unique( dep.begin(), dep.end() );
dep.resize( pos - dep.begin() );
- /*
- */
}
}
@@ -877,7 +908,7 @@ unsigned int Gsolve::getPoolIndex( const Eref& e ) const
unsigned int Gsolve::getVoxelIndex( const Eref& e ) const
{
unsigned int ret = e.dataIndex();
- if ( ret < startVoxel_ || ret >= startVoxel_ + pools_.size() )
+ if ( (ret < startVoxel_) || (ret >= startVoxel_ + pools_.size()))
return OFFNODE;
return ret - startVoxel_;
}
@@ -892,8 +923,7 @@ void Gsolve::setDsolve( Id dsolve )
else if ( dsolve.element()->cinfo()->isA( "Dsolve" ) )
{
dsolve_ = dsolve;
- dsolvePtr_ = reinterpret_cast< ZombiePoolInterface* >(
- dsolve.eref().data() );
+ dsolvePtr_ = reinterpret_cast<ZombiePoolInterface*>(dsolve.eref().data());
}
else
{
@@ -923,7 +953,7 @@ void Gsolve::setN( const Eref& e, double v )
}
else
{
- pools_[vox].setN( getPoolIndex( e ), round( v ) );
+ pools_[vox].setN( getPoolIndex( e ), std::round( v ) );
}
}
}
diff --git a/moose-core/ksolve/Gsolve.h b/moose-core/ksolve/Gsolve.h
index 7eb1275c3bf6d01b79d0c5295fc46fca8d2d9696..594b560751e4f6e11e7cdb257eaebffae92c10ed 100644
--- a/moose-core/ksolve/Gsolve.h
+++ b/moose-core/ksolve/Gsolve.h
@@ -10,7 +10,10 @@
#ifndef _GSOLVE_H
#define _GSOLVE_H
+#include "../randnum/RNG.h"
+
class Stoich;
+
class Gsolve: public ZombiePoolInterface
{
public:
@@ -30,6 +33,7 @@ public:
unsigned int getNumLocalVoxels() const;
unsigned int getNumAllVoxels() const;
+
/**
* Assigns the number of voxels used in the entire reac-diff
* system. Note that fewer than this may be used on any given node.
@@ -70,8 +74,7 @@ public:
void fillMmEnzDep();
void fillPoolFuncDep();
void fillIncrementFuncDep();
- void insertMathDepReacs( unsigned int mathDepIndex,
- unsigned int firedReac );
+ void insertMathDepReacs(unsigned int mathDepIndex, unsigned int firedReac);
void makeReacDepsUnique();
//////////////////////////////////////////////////////////////////
@@ -109,8 +112,8 @@ public:
void updateRateTerms( unsigned int index );
// Function for multithreading.
- void advance_chunk( const size_t begin, const size_t end, ProcPtr p );
- void recalcTimeChunk( const size_t begin, const size_t end, ProcPtr p);
+ size_t advance_chunk( const size_t begin, const size_t end, ProcPtr p );
+ size_t recalcTimeChunk( const size_t begin, const size_t end, ProcPtr p);
//////////////////////////////////////////////////////////////////
/// Flag: returns true if randomized round to integers is done.
@@ -134,9 +137,13 @@ private:
* @brief Number of threads to use when parallel version of Gsolve is
* used.
*/
- unsigned int numThreads_;
+ size_t numThreads_;
+ size_t grainSize_;
GssaSystem sys_;
+
+ moose::RNG rng_;
+
/**
* Each VoxelPools entry handles all the pools in a single voxel.
* Each entry knows how to update itself in order to complete
diff --git a/moose-core/ksolve/GssaVoxelPools.cpp b/moose-core/ksolve/GssaVoxelPools.cpp
index a12d693e86eb89ca71a496d4629075ea3fb04b76..85c4b6b3278e66db8f76eafce18cbb549484550a 100644
--- a/moose-core/ksolve/GssaVoxelPools.cpp
+++ b/moose-core/ksolve/GssaVoxelPools.cpp
@@ -39,13 +39,10 @@
*/
const double SAFETY_FACTOR = 1.0 + 1.0e-9;
-//////////////////////////////////////////////////////////////
-// Class definitions
-//////////////////////////////////////////////////////////////
-GssaVoxelPools::GssaVoxelPools() :
- VoxelPoolsBase(), t_( 0.0 ), atot_( 0.0 )
-{ ; }
+// Class definitions
+GssaVoxelPools::GssaVoxelPools(): VoxelPoolsBase(), t_( 0.0 ), atot_( 0.0 )
+{;}
GssaVoxelPools::~GssaVoxelPools()
{
@@ -88,15 +85,14 @@ void GssaVoxelPools::updateDependentMathExpn(
void GssaVoxelPools::updateDependentRates(
const vector< unsigned int >& deps, const Stoich* stoich )
{
- for ( vector< unsigned int >::const_iterator
- i = deps.begin(); i != deps.end(); ++i )
+ for ( auto i = deps.cbegin(); i != deps.end(); ++i )
{
atot_ -= fabs( v_[ *i ] );
- // atot_ += ( v[ *i ] = ( *rates_[ *i ] )( S() );
atot_ += fabs( v_[ *i ] = getReacVelocity( *i, S() ) );
}
}
+
unsigned int GssaVoxelPools::pickReac()
{
double r = rng_.uniform( ) * atot_;
@@ -108,8 +104,7 @@ unsigned int GssaVoxelPools::pickReac()
// of overhead in managing the tree.
// Slepoy, Thompson and Plimpton 2008
// report a linear time version.
- for ( vector< double >::const_iterator
- i = v_.begin(); i != v_.end(); ++i )
+ for ( auto i = v_.cbegin(); i != v_.end(); ++i )
{
if ( r < ( sum += fabs( *i ) ) )
{
@@ -138,15 +133,14 @@ bool GssaVoxelPools::refreshAtot( const GssaSystem* g )
g->stoich->updateFuncs( varS(), t_ );
updateReacVelocities( g, S(), v_ );
atot_ = 0;
- for ( vector< double >::const_iterator
- i = v_.begin(); i != v_.end(); ++i )
+ for ( auto i = v_.cbegin(); i != v_.cend(); ++i )
atot_ += fabs(*i);
+
atot_ *= SAFETY_FACTOR;
+
// Check if the system is in a stuck state. If so, terminate.
if ( atot_ <= 0.0 )
- {
return false;
- }
return true;
}
@@ -175,7 +169,6 @@ void GssaVoxelPools::advance( const ProcInfo* p, const GssaSystem* g )
{
t_ = nextt;
g->stoich->updateFuncs( varS(), t_ );
- // updateDependentMathExpn( g, 0, t_ );
return;
}
unsigned int rindex = pickReac();
@@ -188,7 +181,6 @@ void GssaVoxelPools::advance( const ProcInfo* p, const GssaSystem* g )
{
t_ = nextt;
g->stoich->updateFuncs( varS(), t_ );
- // updateDependentMathExpn( g, 0, t_ );
return;
}
// We had a roundoff error, fixed it, but now need to be sure
@@ -210,68 +202,49 @@ void GssaVoxelPools::advance( const ProcInfo* p, const GssaSystem* g )
numFire_[rindex]++;
double r = rng_.uniform();
-
while ( r <= 0.0 )
r = rng_.uniform();
t_ -= ( 1.0 / atot_ ) * log( r );
g->stoich->updateFuncs( varS(), t_ );
- // updateDependentMathExpn( g, rindex, t_ );
updateDependentRates( g->dependency[ rindex ], g->stoich );
}
}
void GssaVoxelPools::reinit( const GssaSystem* g )
{
- rng_.setSeed( moose::__rng_seed__ );
+ rng_.setSeed( moose::getGlobalSeed() );
VoxelPoolsBase::reinit(); // Assigns S = Sinit;
unsigned int numVarPools = g->stoich->getNumVarPools();
g->stoich->updateFuncs( varS(), 0 );
double* n = varS();
- double totalN = 0;
+ double error = 0.0;
+ double _prev = 0.0;
if( g->useRandInit )
{
- vector<double> error(numVarPools, 0.0);
map<double, vector<Eref>> groupByVal;
-
for ( unsigned int i = 0; i < numVarPools; ++i )
{
- error[i] = n[i];
- double base = std::floor( n[i] );
- assert( base >= 0.0 );
- totalN += n[i];
- double frac = n[i] - base;
- if ( rng_.uniform() >= frac )
- n[i] = base;
- else
- n[i] = base + 1.0;
-
- error[i] -= n[i];
+ _prev = n[i];
+ n[i] = approximateWithInteger(_prev, rng_);
+ error += (_prev - n[i]);
}
- double extra = std::accumulate( error.begin(), error.end(), 0.0 );
-
// Show warning to user if extra molecules in the system after
// converting flots to integer is larger 1%.
- if( std::abs(extra) / totalN > 0.01 )
+ if( std::abs(error) >= 1.0 )
{
- cout << "Warn: Extra " << extra
- << " molecules in system after converting fractional to integer e.g. 1.1 becomes "
- " 1 roughly 90% of times or 2 roughly 10% of times."
- << endl;
+ MOOSE_WARN( "Extra " << error
+ << " molecules in system after converting fractional to integer."
+ );
}
}
else // Just round to the nearest int.
{
for ( unsigned int i = 0; i < numVarPools; ++i )
- {
- // Just like rint but does not raise exception.
- // See http://en.cppreference.com/w/cpp/numeric/math/nearbyint for
- // details.
- n[i] = std::nearbyint(n[i]);
- }
+ n[i] = std::round(n[i]);
}
t_ = 0.0;
@@ -347,10 +320,7 @@ double GssaVoxelPools::getReacVelocity(
unsigned int r, const double* s ) const
{
double v = rates_[r]->operator()( s );
- // assert( v >= 0.0 );
return v;
-
- // return rates_[r]->operator()( s );
}
void GssaVoxelPools::setStoich( const Stoich* stoichPtr )
@@ -362,47 +332,25 @@ void GssaVoxelPools::setStoich( const Stoich* stoichPtr )
void GssaVoxelPools::setVolumeAndDependencies( double vol )
{
VoxelPoolsBase::setVolumeAndDependencies( vol );
- updateAllRateTerms( stoichPtr_->getRateTerms(),
- stoichPtr_->getNumCoreRates() );
+ updateAllRateTerms(stoichPtr_->getRateTerms(), stoichPtr_->getNumCoreRates());
}
-//////////////////////////////////////////////////////////////
// Handle cross compartment reactions
-//////////////////////////////////////////////////////////////
-
-/*
- * Not sure if we need it. Hold off for now.
-static double integralTransfer( double propensity )
-{
- double t= floor( propensity );
- if ( rng_.uniform() < propensity - t )
- return t + 1;
- return t;
-}
-*/
-
-void GssaVoxelPools::xferIn( XferInfo& xf,
- unsigned int voxelIndex, const GssaSystem* g )
+void GssaVoxelPools::xferIn( XferInfo& xf, unsigned int voxelIndex, const GssaSystem* g )
{
unsigned int offset = voxelIndex * xf.xferPoolIdx.size();
- vector< double >::const_iterator i = xf.values.begin() + offset;
- vector< double >::const_iterator j = xf.lastValues.begin() + offset;
- vector< double >::iterator m = xf.subzero.begin() + offset;
+ auto i = xf.values.cbegin() + offset;
+ auto j = xf.lastValues.cbegin() + offset;
+ auto m = xf.subzero.begin() + offset;
double* s = varS();
- bool hasChanged = false;
- for ( vector< unsigned int >::const_iterator
- k = xf.xferPoolIdx.begin(); k != xf.xferPoolIdx.end(); ++k )
+
+ for ( auto k = xf.xferPoolIdx.cbegin(); k != xf.xferPoolIdx.end(); ++k )
{
double& x = s[*k];
- // cout << x << " i = " << *i << *j << " m = " << *m << endl;
double dx = *i++ - *j++;
- double base = floor( dx );
- if ( rng_.uniform() >= (dx - base) )
- x += base;
- else
- x += base + 1.0;
+ // x += approximateWithInteger_debug(__FUNCTION__, dx, rng_);
+ x += approximateWithInteger(dx, rng_);
- // x += round( *i++ - *j );
if ( x < *m )
{
*m -= x;
@@ -413,23 +361,13 @@ void GssaVoxelPools::xferIn( XferInfo& xf,
x -= *m;
*m = 0;
}
- /*
- double y = fabs( x - *j );
- // hasChanged |= ( fabs( x - *j ) < 0.1 ); // they are all integers.
- hasChanged |= ( y > 0.1 ); // they are all integers.
- */
- // j++;
m++;
}
// If S has changed, then I should update rates of all affected reacs.
// Go through stoich matrix to find affected reacs for each mol
// Store in list, since some may be hit more than once in this func.
// When done, go through and update all affected ones.
- /*
- if ( hasChanged ) {
- refreshAtot( g );
- }
- */
+
// Does this fix the problem of negative concs?
refreshAtot( g );
}
diff --git a/moose-core/ksolve/GssaVoxelPools.h b/moose-core/ksolve/GssaVoxelPools.h
index b0bc90e5c20487ae5e2ddfb7da0fa6893c6b520f..01ca327518eaea981e417fcb62fc78e71ba6405b 100644
--- a/moose-core/ksolve/GssaVoxelPools.h
+++ b/moose-core/ksolve/GssaVoxelPools.h
@@ -19,17 +19,17 @@ public:
virtual ~GssaVoxelPools();
-
- //////////////////////////////////////////////////////////////////
// Solver interface functions
- //////////////////////////////////////////////////////////////////
void advance( const ProcInfo* p );
+
void recalcTime( const GssaSystem* g, double currTime );
- void updateDependentMathExpn(
- const GssaSystem* g, unsigned int rindex, double time );
- void updateDependentRates(
- const vector< unsigned int >& deps, const Stoich* stoich );
+
+ void updateDependentMathExpn( const GssaSystem* g, unsigned int rindex, double time );
+
+ void updateDependentRates( const vector< unsigned int >& deps, const Stoich* stoich );
+
unsigned int pickReac();
+
void setNumReac( unsigned int n );
void advance( const ProcInfo* p, const GssaSystem* g );
@@ -94,8 +94,7 @@ private:
/**
* @brief RNG.
*/
- moose::RNG<double> rng_;
-
+ moose::RNG rng_;
};
#endif // _GSSA_VOXEL_POOLS_H
diff --git a/moose-core/ksolve/KinSparseMatrix.cpp b/moose-core/ksolve/KinSparseMatrix.cpp
index 0ff7676b840924c27b238222d903a6e73b55748d..8716f48e62874f1ee66b337697d32110381c0992 100644
--- a/moose-core/ksolve/KinSparseMatrix.cpp
+++ b/moose-core/ksolve/KinSparseMatrix.cpp
@@ -166,7 +166,7 @@ void makeVecUnique( vector< unsigned int >& v )
#ifdef DO_UNIT_TESTS
-#include "header.h"
+#include "../basecode/header.h"
void testKinSparseMatrix()
{
diff --git a/moose-core/ksolve/Ksolve.cpp b/moose-core/ksolve/Ksolve.cpp
index a072b4c0461110ef058dd7bbe60205df14bef1a2..e81b4d8f7a3fb8e9ec0537b9facf06204f047de7 100644
--- a/moose-core/ksolve/Ksolve.cpp
+++ b/moose-core/ksolve/Ksolve.cpp
@@ -140,36 +140,33 @@ const Cinfo* Ksolve::initCinfo()
);
- ///////////////////////////////////////////////////////
// DestFinfo definitions
- ///////////////////////////////////////////////////////
-
static DestFinfo process( "process",
- "Handles process call from Clock",
- new ProcOpFunc< Ksolve >( &Ksolve::process )
- );
+ "Handles process call from Clock",
+ new ProcOpFunc< Ksolve >( &Ksolve::process )
+ );
static DestFinfo reinit( "reinit",
- "Handles reinit call from Clock",
- new ProcOpFunc< Ksolve >( &Ksolve::reinit )
- );
+ "Handles reinit call from Clock",
+ new ProcOpFunc< Ksolve >( &Ksolve::reinit )
+ );
static DestFinfo initProc( "initProc",
- "Handles initProc call from Clock",
- new ProcOpFunc< Ksolve >( &Ksolve::initProc )
- );
+ "Handles initProc call from Clock",
+ new ProcOpFunc< Ksolve >( &Ksolve::initProc )
+ );
static DestFinfo initReinit( "initReinit",
- "Handles initReinit call from Clock",
- new ProcOpFunc< Ksolve >( &Ksolve::initReinit )
- );
+ "Handles initReinit call from Clock",
+ new ProcOpFunc< Ksolve >( &Ksolve::initReinit )
+ );
static DestFinfo voxelVol( "voxelVol",
- "Handles updates to all voxels. Comes from parent "
- "ChemCompt object.",
- new OpFunc1< Ksolve, vector< double > >(
- &Ksolve::updateVoxelVol )
- );
+ "Handles updates to all voxels. Comes from parent "
+ "ChemCompt object.",
+ new OpFunc1< Ksolve, vector< double > >(
+ &Ksolve::updateVoxelVol )
+ );
///////////////////////////////////////////////////////
// Shared definitions
@@ -180,11 +177,11 @@ const Cinfo* Ksolve::initCinfo()
};
static SharedFinfo proc( "proc",
- "Shared message for process and reinit. These are used for "
- "all regular Ksolve calculations including interfacing with "
- "the diffusion calculations by a Dsolve.",
- procShared, sizeof( procShared ) / sizeof( const Finfo* )
- );
+ "Shared message for process and reinit. These are used for "
+ "all regular Ksolve calculations including interfacing with "
+ "the diffusion calculations by a Dsolve.",
+ procShared, sizeof( procShared ) / sizeof( const Finfo* )
+ );
static Finfo* initShared[] =
{
@@ -192,10 +189,10 @@ const Cinfo* Ksolve::initCinfo()
};
static SharedFinfo init( "init",
- "Shared message for initProc and initReinit. This is used"
- " when the system has cross-compartment reactions. ",
- initShared, sizeof( initShared ) / sizeof( const Finfo* )
- );
+ "Shared message for initProc and initReinit. This is used"
+ " when the system has cross-compartment reactions. ",
+ initShared, sizeof( initShared ) / sizeof( const Finfo* )
+ );
static Finfo* ksolveFinfos[] =
{
@@ -242,7 +239,7 @@ Ksolve::Ksolve()
pools_( 1 ),
startVoxel_( 0 ),
dsolve_(),
- dsolvePtr_( 0 )
+ dsolvePtr_( nullptr )
{
;
}
@@ -419,20 +416,19 @@ void Ksolve::setDsolve( Id dsolve )
{
if ( dsolve == Id () )
{
- dsolvePtr_ = 0;
+ dsolvePtr_ = nullptr;
dsolve_ = Id();
}
else if ( dsolve.element()->cinfo()->isA( "Dsolve" ) )
{
dsolve_ = dsolve;
- dsolvePtr_ = reinterpret_cast< ZombiePoolInterface* >(
- dsolve.eref().data() );
+ dsolvePtr_ = reinterpret_cast<ZombiePoolInterface*>(dsolve.eref().data());
}
else
{
- cout << "Warning: Ksolve::setDsolve: Object '" << dsolve.path() <<
- "' should be class Dsolve, is: " <<
- dsolve.element()->cinfo()->name() << endl;
+ cout << "Warning: Ksolve::setDsolve: Object '" << dsolve.path()
+ << "' should be class Dsolve, is: "
+ << dsolve.element()->cinfo()->name() << endl;
}
}
@@ -508,8 +504,6 @@ double Ksolve::getEstimatedDt() const
//////////////////////////////////////////////////////////////
void Ksolve::process( const Eref& e, ProcPtr p )
{
-
-
if ( isBuilt_ == false )
return;
diff --git a/moose-core/ksolve/Ksolve.h b/moose-core/ksolve/Ksolve.h
index f4b9327ae9ba7e5e271065c88e543139234eada4..89b87cd76b79c1d15f672d6d94a403cc1d5377de 100644
--- a/moose-core/ksolve/Ksolve.h
+++ b/moose-core/ksolve/Ksolve.h
@@ -45,7 +45,6 @@ public:
Id getDsolve() const;
void setDsolve( Id dsolve ); /// Inherited from ZombiePoolInterface.
-
unsigned int getNumLocalVoxels() const;
unsigned int getNumAllVoxels() const;
/**
@@ -79,30 +78,25 @@ public:
void reinit( const Eref& e, ProcPtr p );
void initProc( const Eref& e, ProcPtr p );
void initReinit( const Eref& e, ProcPtr p );
+
/**
* Handles request to change volumes of voxels in this Ksolve, and
* all cascading effects of this. At this point it won't handle
* change in size of voxel array.
*/
void updateVoxelVol( vector< double > vols );
- //////////////////////////////////////////////////////////////////
- // Utility for SrcFinfo
- //////////////////////////////////////////////////////////////////
- //////////////////////////////////////////////////////////////////
// Solver interface functions
- //////////////////////////////////////////////////////////////////
unsigned int getPoolIndex( const Eref& e ) const;
unsigned int getVoxelIndex( const Eref& e ) const;
- //////////////////////////////////////////////////////////////////
// ZombiePoolInterface inherited functions
- //////////////////////////////////////////////////////////////////
-
void setN( const Eref& e, double v );
double getN( const Eref& e ) const;
+
void setNinit( const Eref& e, double v );
double getNinit( const Eref& e ) const;
+
void setDiffConst( const Eref& e, double v );
double getDiffConst( const Eref& e ) const;
diff --git a/moose-core/ksolve/SteadyStateBoost.cpp b/moose-core/ksolve/SteadyStateBoost.cpp
index 98b671541edf292518cc1d70a90b38d936df6920..6282bfb55eef818a905b9d0ba31feb16648314c2 100644
--- a/moose-core/ksolve/SteadyStateBoost.cpp
+++ b/moose-core/ksolve/SteadyStateBoost.cpp
@@ -22,10 +22,10 @@
*/
-#include "header.h"
-#include "global.h"
-#include "SparseMatrix.h"
-#include "KinSparseMatrix.h"
+#include "../basecode/header.h"
+#include "../basecode/global.h"
+#include "../basecode/SparseMatrix.h"
+#include "../ksolve/KinSparseMatrix.h"
#include "RateTerm.h"
#include "FuncTerm.h"
#include "VoxelPoolsBase.h"
diff --git a/moose-core/ksolve/SteadyStateGsl.cpp b/moose-core/ksolve/SteadyStateGsl.cpp
index eaec6d07ed115ed92fb4ec8cb9a4329a404412e6..e01e1ffde6a6ca6c7c6ad856b7323c4bb18012b3 100644
--- a/moose-core/ksolve/SteadyStateGsl.cpp
+++ b/moose-core/ksolve/SteadyStateGsl.cpp
@@ -21,7 +21,7 @@
#include "../basecode/header.h"
#include "../basecode/global.h"
-#include "SparseMatrix.h"
+#include "../basecode/SparseMatrix.h"
#include "KinSparseMatrix.h"
#include "RateTerm.h"
#include "FuncTerm.h"
diff --git a/moose-core/ksolve/Stoich.cpp b/moose-core/ksolve/Stoich.cpp
index 62959a2a31054298d017972fe535b2f510c44dd2..504f8ec10b3d94a45c10a21c874c13f2ec9ee947 100644
--- a/moose-core/ksolve/Stoich.cpp
+++ b/moose-core/ksolve/Stoich.cpp
@@ -260,8 +260,8 @@ Stoich::Stoich()
ksolve_(), // Must be reassigned to build stoich system.
dsolve_(), // Must be assigned if diffusion is planned.
compartment_(), // Must be assigned if diffusion is planned.
- kinterface_( 0 ),
- dinterface_( 0 ),
+ kinterface_( nullptr ),
+ dinterface_( nullptr ),
rates_( 0 ), // No RateTerms yet.
// uniqueVols_( 1, 1.0 ),
numVoxels_( 1 ),
@@ -395,8 +395,7 @@ void Stoich::setElist( const Eref& e, const vector< ObjId >& elist )
// kinterface_->setNumPools( n );
kinterface_->setStoich( e.id() );
Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
- shell->doAddMsg( "Single",
- compartment_, "voxelVolOut", ksolve_, "voxelVol" );
+ shell->doAddMsg( "Single", compartment_, "voxelVolOut", ksolve_, "voxelVol" );
}
if ( dinterface_ )
{
@@ -421,20 +420,16 @@ string Stoich::getPath( const Eref& e ) const
void Stoich::setKsolve( Id ksolve )
{
ksolve_ = Id();
- kinterface_ = 0;
- if ( ! (
- ksolve.element()->cinfo()->isA( "Ksolve" ) ||
- ksolve.element()->cinfo()->isA( "Gsolve" )
- )
- )
+ kinterface_ = nullptr;
+ if ( ! ( ksolve.element()->cinfo()->isA( "Ksolve" ) || ksolve.element()->cinfo()->isA( "Gsolve" )))
{
cout << "Error: Stoich::setKsolve: invalid class assigned,"
" should be either Ksolve or Gsolve\n";
return;
}
+
ksolve_ = ksolve;
- kinterface_ = reinterpret_cast< ZombiePoolInterface* >(
- ksolve.eref().data() );
+ kinterface_ = reinterpret_cast< ZombiePoolInterface* >(ksolve.eref().data());
if ( ksolve.element()->cinfo()->isA( "Gsolve" ) )
setOneWay( true );
@@ -452,18 +447,14 @@ void Stoich::setDsolve( Id dsolve )
{
dsolve_ = Id();
dinterface_ = 0;
- if ( ! (
- dsolve.element()->cinfo()->isA( "Dsolve" )
- )
- )
+ if (not (dsolve.element()->cinfo()->isA("Dsolve") ))
{
cout << "Error: Stoich::setDsolve: invalid class assigned,"
" should be Dsolve\n";
return;
}
dsolve_ = dsolve;
- dinterface_ = reinterpret_cast< ZombiePoolInterface* >(
- dsolve.eref().data() );
+ dinterface_ = reinterpret_cast<ZombiePoolInterface*>(dsolve.eref().data());
}
Id Stoich::getDsolve() const
@@ -473,12 +464,9 @@ Id Stoich::getDsolve() const
void Stoich::setCompartment( Id compartment )
{
- if ( ! (
- compartment.element()->cinfo()->isA( "ChemCompt" )
- )
- )
+ if (! (compartment.element()->cinfo()->isA( "ChemCompt" )))
{
- cout << "Error: Stoich::setCompartment: invalid class assigned,"
+ cerr << "Error: Stoich::setCompartment: invalid class assigned,"
" should be ChemCompt or derived class\n";
return;
}
@@ -493,8 +481,7 @@ void Stoich::setCompartment( Id compartment )
double bigVol = vols.back();
assert( bigVol > 0.0 );
temp.push_back( vols[0] / bigVol );
- for ( vector< double >::iterator
- i = vols.begin(); i != vols.end(); ++i )
+ for ( auto i = vols.begin(); i != vols.end(); ++i )
{
if ( !doubleEq( temp.back(), *i / bigVol ) )
temp.push_back( *i / bigVol );
@@ -535,8 +522,8 @@ vector< unsigned int > Stoich::getPoolIdMap() const
unsigned int minId = 1000000;
unsigned int maxId = 0;
unsigned int maxIndex = 0;
- map< Id, unsigned int >::const_iterator i;
- for ( i = poolLookup_.begin(); i != poolLookup_.end(); ++i )
+
+ for (auto i = poolLookup_.cbegin(); i != poolLookup_.end(); ++i )
{
unsigned int j = i->first.value();
if ( j < minId ) minId = j;
@@ -544,7 +531,7 @@ vector< unsigned int > Stoich::getPoolIdMap() const
if ( maxIndex < i->second ) maxIndex = i->second;
}
vector< unsigned int > ret( maxId - minId + 2, ~0U );
- for ( i = poolLookup_.begin(); i != poolLookup_.end(); ++i )
+ for (auto i = poolLookup_.cbegin(); i != poolLookup_.end(); ++i )
{
unsigned int j = i->first.value() - minId;
ret[j] = i->second;
@@ -1475,9 +1462,7 @@ unsigned int Stoich::convertIdToReacIndex( Id id ) const
{
map< Id, unsigned int >::const_iterator i = rateTermLookup_.find( id );
if ( i != rateTermLookup_.end() )
- {
return i->second;
- }
return ~0U;
}
@@ -1678,8 +1663,7 @@ void Stoich::installMMenz( Id enzId, const vector< Id >& enzMols,
return;
vector< Id > subCompt;
vector< Id > dummy;
- for ( vector< Id >::const_iterator
- i = subs.begin(); i != subs.end(); ++i )
+ for( auto i = subs.cbegin(); i != subs.end(); ++i )
subCompt.push_back( getCompt( *i ).id );
subComptVec_.push_back( subCompt );
prdComptVec_.push_back( dummy );
@@ -2117,15 +2101,9 @@ const vector< Id >& Stoich::offSolverPoolMap( Id compt ) const
// s is the array of pools, S_[meshIndex][0]
void Stoich::updateFuncs( double* s, double t ) const
{
- for ( vector< FuncTerm* >::const_iterator i = funcs_.begin();
- i != funcs_.end(); ++i )
- {
+ for ( auto i = funcs_.cbegin(); i != funcs_.end(); ++i )
if ( *i )
- {
(*i)->evalPool( s, t );
- // s holds arguments and also result location
- }
- }
}
/**
diff --git a/moose-core/ksolve/Stoich.h b/moose-core/ksolve/Stoich.h
index 93e63b9f79fa7a0b344bb3d85638773206db74d6..2b273613809098e2731941211de43da884d09956 100644
--- a/moose-core/ksolve/Stoich.h
+++ b/moose-core/ksolve/Stoich.h
@@ -48,680 +48,680 @@
class Stoich
{
- public:
- Stoich();
- ~Stoich();
-
- //////////////////////////////////////////////////////////////////
- // Field assignment stuff
- //////////////////////////////////////////////////////////////////
-
- void setOneWay( bool v );
- bool getOneWay() const;
-
- // Flag that defines permission for pool values to go negative.
- void setAllowNegative( bool v );
- bool getAllowNegative() const;
-
- /// Returns number of local pools that are updated by solver
- unsigned int getNumVarPools() const;
-
- /// Returns number of local buffered pools.
- unsigned int getNumBufPools() const;
-
- /**
- * Returns total number of pools. Includes the pools whose
- * actual calculations happen on another solver, but are given a
- * proxy here in order to handle cross-compartment reactions.
- */
- unsigned int getNumAllPools() const;
-
- /**
- * Returns number of proxy pools here for
- * cross-compartment reactions
- */
- unsigned int getNumProxyPools() const;
-
- /**
- * Map to look up the index of the pool from its Id.
- * poolIndex = poolIdMap[ Id::value() - poolOffset ]
- * where the poolOffset is the smallest Id::value.
- * poolOffset is passed back as the last entry of this vector.
- * Any Ids that are not pools return EMPTY=~0.
- */
- vector< unsigned int > getPoolIdMap() const;
-
- Id getPoolByIndex( unsigned int index ) const;
-
- /**
- * Take the provided wildcard path to build the list of elements
- * managed by this solver.
- */
- void setPath( const Eref& e, string path );
- string getPath( const Eref& e ) const;
-
- /// assigns kinetic solver: Ksovle or GSSAsolve.
- void setKsolve( Id v );
- Id getKsolve() const;
-
- /// assigns diffusion solver: Dsovle or a Gillespie voxel stepper
- void setDsolve( Id v );
- Id getDsolve() const;
-
- /// assigns compartment occupied by Stoich.
- void setCompartment( Id v );
- Id getCompartment() const;
-
- /**
- * Utility function to return # of rates_ entries. This includes
- * the cross-solver reactions.
- */
- unsigned int getNumRates() const;
-
- /**
- * Utility function to return # of core rates for reacs which are
- * entirely located on current compartment, including all reactants
- */
- unsigned int getNumCoreRates() const;
-
- /// Utility function to return a rates_ entry
- const RateTerm* rates( unsigned int i ) const;
-
- /// Returns a reference to the entire rates_ vector.
- const vector< RateTerm* >& getRateTerms() const;
-
- unsigned int getNumFuncs() const;
- const FuncTerm* funcs( unsigned int i ) const;
- /// Returns true if the specified pool is controlled by a func
- bool isFuncTarget( unsigned int poolIndex ) const;
-
- vector< int > getMatrixEntry() const;
- vector< unsigned int > getColIndex() const;
- vector< unsigned int > getRowStart() const;
-
- vector< Id > getProxyPools( Id i ) const;
-
- /**
- * getStatus(): Flag to track status of Stoich object.
- * -1: No path yet assigned.
- * 0: Success
- * 1: Warning: Missing reactant in Reac or Enz
- * 2: Warning: Missing substrate in MMenz
- * 4: Warning: Compartment not defined
- * 8: Warning: Neither Ksolve nor Dsolve defined
- * 16: Warning: No objects found on path
- */
- int getStatus() const;
- //////////////////////////////////////////////////////////////////
- // Model traversal and building functions
- //////////////////////////////////////////////////////////////////
- /**
- * Internal function which sets up the model based on the provided
- * elist of all elements managed by this solver.
- */
- void setElist( const Eref& e, const vector< ObjId >& elist );
-
- /**
- * Scans through elist to find any reactions that connect to
- * pools not located on solver. Removes these reactions from the
- * elist and maintains Ids of the affected reactions, and their
- * off-solver pools, in offSolverReacs_ and offSolverPools_.
- */
- void locateOffSolverReacs( Id myCompt, vector< Id >& elist );
-
- /**
- * Builds the objMap vector, which maps all Ids to
- * the internal indices for pools and reacs that are used in the
- * solver. In addition to the elist, it also scans through the
- * offSolverPools and offSolverReacs to build the map.
- void allocateObjMap( const vector< Id >& elist );
- */
-
- /// Using the computed array sizes, now allocate space for them.
- void resizeArrays();
- /// Identifies and allocates objects in the Stoich.
- void allocateModelObject( Id id );
- /// Calculate sizes of all arrays, and allocate them.
- void allocateModel( const vector< Id >& elist );
-
- /// Functions to build the maps between Ids and internal indices
- void buildPoolLookup();
- void buildRateTermLookup();
- void buildFuncLookup();
-
- /**
- * This function is used when the stoich class is employed by a
- * Gsolver for doing stochastic calculations.
- * Here we fix the issue of having a single substrate at
- * more than first order. As the first molecule of the substrate is
- * consumed, the number is depleted by one and so its forward rate
- * is reduced. And so on. This also protects against going negative
- * in mol number or concentration.
- */
- void convertRatesToStochasticForm();
-
- /// Used to handle run-time size updates for spines.
- void scaleBufsAndRates( unsigned int index, double volScale );
-
- //////////////////////////////////////////////////////////////////
- // Zombification functions.
- //////////////////////////////////////////////////////////////////
-
- /**
- * zombifyModel marches through the specified id list and
- * converts all entries into zombies. The first arg e is the
- * Eref of the Stoich itself.
- */
- void zombifyModel( const Eref& e, const vector< Id >& elist );
-
- /**
- * Converts back to ExpEuler type basic kinetic Elements.
- */
- void unZombifyModel();
-
- /// unZombifies Pools. Helper for unZombifyModel.
- void unZombifyPools();
-
- void zombifyChemCompt( Id compt );
-
- /**
- * Utility function to find if incoming message assigns N or conc,
- * and to appropriately zombify the function and set up its
- * parameters including volume scaling.
- */
- Id zombifyPoolFuncWithScaling( Id pool );
-
- unsigned int convertIdToReacIndex( Id id ) const;
- unsigned int convertIdToPoolIndex( Id id ) const;
- unsigned int convertIdToFuncIndex( Id id ) const;
-
- /// Utility function to make a half reac and return the rate term.
- ZeroOrder* makeHalfReaction(
- double rate, const vector< Id >& reactants );
-
- /*
- * This takes the specified Reac and its substrate and product
- * list, and installs them into the Stoich. It also builds up the
- * vectors to store which compartment each substrate/product
- * belongs to, needed for cross-reaction computations.
- * This is the high-level interface function.
- */
- void installReaction( Id reacId,
- const vector< Id >& subs, const vector< Id >& prds );
- /*
- * This takes the specified subs and prds belonging
- * to the specified Reac, and builds them into the Stoich.
- * It is a low-level function used internally.
- */
- unsigned int innerInstallReaction( Id reacId,
- const vector< Id >& subs, const vector< Id >& prds );
-
- /**
- * This takes the baseclass for an MMEnzyme and builds the
- * MMenz into the Stoich.
- */
- void installMMenz( Id enzId, const vector< Id >& enzMolId,
- const vector< Id >& subs, const vector< Id >& prds );
- /**
- * This is the inner function to do the installation.
- */
- void installMMenz( MMEnzymeBase* meb, unsigned int rateIndex,
- const vector< Id >& subs, const vector< Id >& prds );
-
- /*
- * This takes the specified Reac and its substrate and product
- * list, and installs them into the Stoich. This is the high-level
- * interface function.
- */
- void installEnzyme( Id enzId, Id enzMolId, Id cplxId,
- const vector< Id >& subs, const vector< Id >& prds );
- /**
- * This takes the forward, backward and product formation half-reacs
- * belonging to the specified Enzyme, and builds them into the
- * Stoich. This is the low-level function.
- */
- void installEnzyme( ZeroOrder* r1, ZeroOrder* r2, ZeroOrder* r3,
- Id enzId, Id enzMolId, const vector< Id >& prds );
-
- /// This is used when the enzyme lacks sub or prd.
- void installDummyEnzyme( Id enzId, Id enzMolId);
-
- /**
- * This installs a FuncTerm, which evaluates a function to specify
- * the conc of the specific pool. The pool is a BufPool.
- */
- void installAndUnschedFunc( Id func, Id pool, double volScale );
-
- /**
- * This installs a FuncRate, which evaluates a function to specify
- * the rate of change of conc of the specific pool.
- * The pool is a Pool.
- */
- void installAndUnschedFuncRate( Id func, Id pool );
-
- /**
- * This installs a FuncReac, which evaluates a function to specify
- * the rate (Kf) of the specified reaction.
- */
- void installAndUnschedFuncReac( Id func, Id reac );
-
- //////////////////////////////////////////////////////////////////
-
- /**
- * Returns SpeciesId of specified pool
- */
- unsigned int getSpecies( unsigned int poolIndex ) const;
-
- /**
- * Assigns SpeciesId of specified pool
- */
- void setSpecies( unsigned int poolIndex, unsigned int s );
-
- /**
- * Sets the forward rate v (given in millimoloar concentration units)
- * for the specified reaction throughout the compartment in which the
- * reaction lives. Internally the stoich uses #/voxel units so this
- * involves querying the volume subsystem about volumes for each
- * voxel, and scaling accordingly.
- */
- void setReacKf( const Eref& e, double v ) const;
-
- /**
- * Sets the reverse rate v (given in millimoloar concentration units)
- * for the specified reaction throughout the compartment in which the
- * reaction lives. Internally the stoich uses #/voxel units so this
- * involves querying the volume subsystem about volumes for each
- * voxel, and scaling accordingly.
- */
- void setReacKb( const Eref& e, double v ) const;
-
- /**
- * Sets the Km for MMenz, using appropriate volume conversion to
- * go from the argument (in millimolar) to #/voxel.
- * This may do the assignment among many voxels containing the enz
- * in case there are different volumes.
- */
- void setMMenzKm( const Eref& e, double v ) const;
- double getMMenzNumKm( const Eref& e ) const;
-
- /**
- * Sets the kcat for MMenz. No conversions needed.
- */
- void setMMenzKcat( const Eref& e, double v ) const;
- double getMMenzKcat( const Eref& e ) const;
-
- /**
- * Sets the rate v (given in millimoloar concentration units)
- * for the forward enzyme reaction of binding substrate to enzyme.
- * Does this throughout the compartment in which the
- * enzyme lives. Internally the stoich uses #/voxel units so this
- * involves querying the volume subsystem about volumes for each
- * voxel, and scaling accordingly.
- */
- void setEnzK1( const Eref& e, double v ) const;
- double getEnzNumK1( const Eref& e ) const;
-
- /// Set rate k2 (1/sec) for enzyme
- void setEnzK2( const Eref& e, double v ) const;
- /// Get rate k2 (1/sec) for enzyme
- double getEnzK2( const Eref& e ) const;
-
- /// Set rate k3 (1/sec) for enzyme
- void setEnzK3( const Eref& e, double v ) const;
- /// Get rate k3, aka kcat, for enzyme
- double getEnzK3( const Eref& e ) const;
-
- /**
- * Returns the internal rate in #/voxel, for R1, for the specified
- * Eref.
- */
- double getR1( const Eref& e ) const;
- /**
- * Returns internal rate R1 in #/voxel, for the rate term
- * following the one directly referred to by the Eref e. Enzymes
- * define multiple successive rate terms, so we look up the first,
- * and then select one after it.
- */
- double getR1offset1( const Eref& e ) const;
- /**
- * Returns internal rate R1 in #/voxel, for the rate term
- * two after the one directly referred to by the Eref e. Enzymes
- * define multiple successive rate terms, so we look up the first,
- * and then select the second one after it.
- */
- double getR1offset2( const Eref& e ) const;
-
- /**
- * Returns the internal rate in #/voxel, for R2, for the specified
- * reacIndex and voxel index. In some cases R2 is undefined, and it
- * then returns 0.
- */
- double getR2( const Eref& e ) const;
-
- /**
- * Sets the arithmetic expression used in a FuncRate or FuncReac
- */
- void setFunctionExpr( const Eref& e, string expr );
-
- /**
- * This function scans all reacs and enzymes and recalculates the
- * internal rate terms depending on the reference terms stored in
- * the original chemical object.
- */
- void updateRatesAfterRemesh();
-
- /// Utility function, prints out N_, used for debugging
- void print() const;
-
- /// Another utility function, prints out all Kf, kf, Kb, kb.
- void printRates() const;
- //////////////////////////////////////////////////////////////////
- // Utility funcs for numeric calculations
- //////////////////////////////////////////////////////////////////
-
- /**
- * Updates the yprime array, rate of change of each molecule
- * The volIndex specifies which set of rates to use, since the
- * rates are volume dependent.
- * Moved to VoxelPools
- void updateRates( const double* s, double* yprime,
- unsigned int volIndex ) const;
- */
-
- /**
- * Computes the velocity of each reaction, vel.
- * The volIndex specifies which set of rates to use, since the
- * rates are volume dependent.
- */
- void updateReacVelocities( const double* s, vector< double >& vel,
- unsigned int volIndex ) const;
-
- /// Updates the function values, within s.
- void updateFuncs( double* s, double t ) const;
-
- /// Updates the rates for cross-compartment reactions.
- /*
- void updateJunctionRates( const double* s,
- const vector< unsigned int >& reacTerms, double* yprime );
- */
-
- /**
- * Get the rate for a single reaction specified by r, as per all
- * the mol numbers in s.
- double getReacVelocity( unsigned int r, const double* s,
- unsigned int volIndex ) const;
- */
-
- /// Returns the stoich matrix. Used by gsolve.
- const KinSparseMatrix& getStoichiometryMatrix() const;
- //////////////////////////////////////////////////////////////////
- // Access functions for cross-node reactions.
- //////////////////////////////////////////////////////////////////
- const vector< Id >& getOffSolverPools() const;
-
- /**
- * List all the compartments to which the current compt is coupled,
- * by cross-compartment reactions. Self not included.
- */
- vector< Id > getOffSolverCompts() const;
-
- /**
- * Looks up the vector of pool Ids originating from the specified
- * compartment, that are represented on this compartment as proxies.
- */
- const vector< Id >& offSolverPoolMap( Id compt ) const;
-
- /**
- * Returns the index of the matching volume,
- * which is also the index into the RateTerm vector.
- unsigned int indexOfMatchingVolume( double vol ) const;
- */
-
- //////////////////////////////////////////////////////////////////
- static const unsigned int PoolIsNotOnSolver;
- static const Cinfo* initCinfo();
- private:
- /**
- * True if the stoich matrix is set up to handle only one-way
- * reactions, as is needed in the case of the Gillespie algorithm.
- */
- bool useOneWay_;
-
- /**
- * True if pools are permitted to take negative concentrations.
- * This may happen if solver is handling a general equation system
- * that is not constrained by chemical rules.
- * Defaults to False, so that we cannot have negative concs.
- */
- bool allowNegative_;
-
- string path_;
-
- /// This contains the Id of the Kinetic solver.
- Id ksolve_;
-
- /// This contains the Id of the Diffusion solver. Optional.
- Id dsolve_;
-
- /// Contains Id of compartment holding reac system. Optional
- Id compartment_;
-
- /// Pointer for ksolve
- ZombiePoolInterface* kinterface_;
- /// Pointer for dsolve
- ZombiePoolInterface* dinterface_;
-
- /**
- * Lookup from each molecule to its Species identifer
- * This will eventually be tied into an ontology reference.
- */
- vector< unsigned int > species_;
-
- /**
- * The RateTerms handle the update operations for reaction rate v_.
- * This is the master vector of RateTerms, and it is scaled to
- * a volume such that the 'n' units and the conc units are
- * identical.
- * Duplicates of this vector are made in each voxel with a different
- * volume. The duplicates have rates scaled as per volume.
- * The RateTerms vector also includes reactions that have
- * off-compartment products. These need special volume scaling
- * involving all the interactiong compartments.
- */
- vector< RateTerm* > rates_;
-
- /**
- * This tracks the unique volumes handled by the reac system.
- * Maps one-to-one with the vector of vector of RateTerms.
- vector< double > uniqueVols_;
- */
-
- /// Number of voxels in reac system.
- unsigned int numVoxels_;
-
- /// The FuncTerms handle mathematical ops on mol levels.
- vector< FuncTerm* > funcs_;
-
- /// N_ is the stoichiometry matrix. All pools * all reac terms.
- KinSparseMatrix N_;
-
- /**
- * Maps Ids to objects in the S_, RateTerm, and FuncTerm vectors.
- * There will be holes in this map, but look up is very fast.
- * The calling Id must know what it wants to find: all it
- * gets back is an integer.
- * The alternative is to have multiple maps, but that is slower.
- * Assume no arrays. Each Pool/reac etc must be a unique
- * Element. Later we'll deal with diffusion.
- */
- // vector< unsigned int > objMap_;
- /**
- * Minor efficiency: We will usually have a set of objects that are
- * nearly contiguous in the map. May as well start with the first of
- * them.
- */
- // unsigned int objMapStart_;
- //
- ///////////////////////////////////////////////////////////
- // Here we have the vectors of the different kinds of objects
- // managed by the Stoich
- ///////////////////////////////////////////////////////////
-
- /**
- * Vector of variablePool Ids.
- */
- vector< Id > varPoolVec_;
-
- /**
- * Vector of bufPool Ids.
- */
- vector< Id > bufPoolVec_;
-
- /**
- * These are pools that were not in the original scope of the
- * solver, but have to be brought in because they are reactants
- * of one or more of the offSolverReacs.
- */
- vector< Id > offSolverPoolVec_;
-
- /**
- * Vector of reaction ids.
- */
- vector< Id > reacVec_;
- vector< Id > offSolverReacVec_;
-
- /**
- * Map back from enz index to Id. Needed to unzombify
- */
- vector< Id > enzVec_;
- vector< Id > offSolverEnzVec_;
-
- /**
- * Map back from enz index to Id. Needed to unzombify
- */
- vector< Id > mmEnzVec_;
- vector< Id > offSolverMMenzVec_;
-
- /**
- * Vector of funcs controlling pool number, that is N.
- */
- vector< Id > poolFuncVec_;
-
- /**
- * vector tracks which pool is controlled by which func.
- * Unused entries are flagged by ~0.
- * funcTarget_[ poolIndex ] == funcIndex
- */
- vector< unsigned int > funcTarget_;
-
- /**
- * Vector of funcs controlling pool increment, that is dN/dt
- * This is handled as a rateTerm.
- */
- vector< Id > incrementFuncVec_;
-
- /**
- * Vector of funcs controlling reac rate, that is numKf
- * This is handled as a rateTerm.
- */
- vector< Id > reacFuncVec_;
-
- ///////////////////////////////////////////////////////////////
- // Here we have maps to look up objects from their ids.
- ///////////////////////////////////////////////////////////////
- map< Id, unsigned int > poolLookup_;
- map< Id, unsigned int > rateTermLookup_;
- map< Id, unsigned int > funcLookup_;
-
- /**
- * Number of variable molecules that the solver deals with,
- * that are local to the solver.
- *
- */
- // unsigned int numVarPools_;
-
- /**
- * Number of variable molecules that the solver deals with,
- * including the proxy molecules which belong in other compartments.
- *
- unsigned int totVarPools_;
- */
-
- /**
- * Number of buffered molecules
- */
- // unsigned int numBufPools_;
-
- /**
- * Looks up the rate term from the Id for a reac, enzyme, or func.
- map< Id, unsigned int > rateTermLookup_;
- */
-
- /**
- * Number functions, currently only the ones controlling molecule
- * numbers, like sumtotals.
- unsigned int numFunctions_;
- */
-
- /**
- * Number of reactions in the solver model. This includes
- * conversion reactions A + B <---> C
- * enzyme reactions E + S <---> E.S ---> E + P
- * and MM enzyme reactions rate = E.S.kcat / ( Km + S )
- * The enzyme reactions count as two reaction steps.
- unsigned int numReac_;
- */
-
- /**
- * Flag to track status of Stoich object.
- * -1: No path yet assigned.
- * 0: Success
- * 1: Warning: Missing reactant in Reac or Enz
- * 2: Warning: Missing substrate in MMenz
- * 4: Warning: Compartment not defined
- * 8: Warning: Neither Ksolve nore Dsolve defined
- */
- int status_;
-
- //////////////////////////////////////////////////////////////////
- // Off-solver stuff
- //////////////////////////////////////////////////////////////////
-
- /**
- * Map of vectors of Ids of offSolver pools.
- * Each map entry contains the vector of Ids of proxy pools
- * coming from the specified compartment.
- * In use, the junction will copy the pool indices over for
- * data transfer.
- */
- map< Id, vector< Id > > offSolverPoolMap_;
-
- /**
- * Tracks the reactions that go off the current solver.
- vector< Id > offSolverReacs_;
- */
-
- /**
- * Which compartment(s) does the off solver reac connect to?
- * Usually it is just one, in which case the second id is Id()
- */
- vector< pair< Id, Id > > offSolverReacCompts_;
- vector< pair< Id, Id > > offSolverEnzCompts_;
- vector< pair< Id, Id > > offSolverMMenzCompts_;
-
- /**
- * subComptVec_[rateTermIndex][substrate#]: Identifies compts
- * for each substrate for each cross-compartment RateTerm in
- * the rates_vector.
- */
- vector< vector< Id > > subComptVec_;
-
- /**
- * prdComptVec_[rateTermIndex][product#]: Identifies compts
- * for each product for each cross-compartment RateTerm in
- * the rates_vector.
- */
- vector< vector< Id > > prdComptVec_;
+public:
+ Stoich();
+ ~Stoich();
+
+ //////////////////////////////////////////////////////////////////
+ // Field assignment stuff
+ //////////////////////////////////////////////////////////////////
+
+ void setOneWay( bool v );
+ bool getOneWay() const;
+
+ // Flag that defines permission for pool values to go negative.
+ void setAllowNegative( bool v );
+ bool getAllowNegative() const;
+
+ /// Returns number of local pools that are updated by solver
+ unsigned int getNumVarPools() const;
+
+ /// Returns number of local buffered pools.
+ unsigned int getNumBufPools() const;
+
+ /**
+ * Returns total number of pools. Includes the pools whose
+ * actual calculations happen on another solver, but are given a
+ * proxy here in order to handle cross-compartment reactions.
+ */
+ unsigned int getNumAllPools() const;
+
+ /**
+ * Returns number of proxy pools here for
+ * cross-compartment reactions
+ */
+ unsigned int getNumProxyPools() const;
+
+ /**
+ * Map to look up the index of the pool from its Id.
+ * poolIndex = poolIdMap[ Id::value() - poolOffset ]
+ * where the poolOffset is the smallest Id::value.
+ * poolOffset is passed back as the last entry of this vector.
+ * Any Ids that are not pools return EMPTY=~0.
+ */
+ vector< unsigned int > getPoolIdMap() const;
+
+ Id getPoolByIndex( unsigned int index ) const;
+
+ /**
+ * Take the provided wildcard path to build the list of elements
+ * managed by this solver.
+ */
+ void setPath( const Eref& e, string path );
+ string getPath( const Eref& e ) const;
+
+ /// assigns kinetic solver: Ksovle or GSSAsolve.
+ void setKsolve( Id v );
+ Id getKsolve() const;
+
+ /// assigns diffusion solver: Dsovle or a Gillespie voxel stepper
+ void setDsolve( Id v );
+ Id getDsolve() const;
+
+ /// assigns compartment occupied by Stoich.
+ void setCompartment( Id v );
+ Id getCompartment() const;
+
+ /**
+ * Utility function to return # of rates_ entries. This includes
+ * the cross-solver reactions.
+ */
+ unsigned int getNumRates() const;
+
+ /**
+ * Utility function to return # of core rates for reacs which are
+ * entirely located on current compartment, including all reactants
+ */
+ unsigned int getNumCoreRates() const;
+
+ /// Utility function to return a rates_ entry
+ const RateTerm* rates( unsigned int i ) const;
+
+ /// Returns a reference to the entire rates_ vector.
+ const vector< RateTerm* >& getRateTerms() const;
+
+ unsigned int getNumFuncs() const;
+ const FuncTerm* funcs( unsigned int i ) const;
+ /// Returns true if the specified pool is controlled by a func
+ bool isFuncTarget( unsigned int poolIndex ) const;
+
+ vector< int > getMatrixEntry() const;
+ vector< unsigned int > getColIndex() const;
+ vector< unsigned int > getRowStart() const;
+
+ vector< Id > getProxyPools( Id i ) const;
+
+ /**
+ * getStatus(): Flag to track status of Stoich object.
+ * -1: No path yet assigned.
+ * 0: Success
+ * 1: Warning: Missing reactant in Reac or Enz
+ * 2: Warning: Missing substrate in MMenz
+ * 4: Warning: Compartment not defined
+ * 8: Warning: Neither Ksolve nor Dsolve defined
+ * 16: Warning: No objects found on path
+ */
+ int getStatus() const;
+ //////////////////////////////////////////////////////////////////
+ // Model traversal and building functions
+ //////////////////////////////////////////////////////////////////
+ /**
+ * Internal function which sets up the model based on the provided
+ * elist of all elements managed by this solver.
+ */
+ void setElist( const Eref& e, const vector< ObjId >& elist );
+
+ /**
+ * Scans through elist to find any reactions that connect to
+ * pools not located on solver. Removes these reactions from the
+ * elist and maintains Ids of the affected reactions, and their
+ * off-solver pools, in offSolverReacs_ and offSolverPools_.
+ */
+ void locateOffSolverReacs( Id myCompt, vector< Id >& elist );
+
+ /**
+ * Builds the objMap vector, which maps all Ids to
+ * the internal indices for pools and reacs that are used in the
+ * solver. In addition to the elist, it also scans through the
+ * offSolverPools and offSolverReacs to build the map.
+ void allocateObjMap( const vector< Id >& elist );
+ */
+
+ /// Using the computed array sizes, now allocate space for them.
+ void resizeArrays();
+ /// Identifies and allocates objects in the Stoich.
+ void allocateModelObject( Id id );
+ /// Calculate sizes of all arrays, and allocate them.
+ void allocateModel( const vector< Id >& elist );
+
+ /// Functions to build the maps between Ids and internal indices
+ void buildPoolLookup();
+ void buildRateTermLookup();
+ void buildFuncLookup();
+
+ /**
+ * This function is used when the stoich class is employed by a
+ * Gsolver for doing stochastic calculations.
+ * Here we fix the issue of having a single substrate at
+ * more than first order. As the first molecule of the substrate is
+ * consumed, the number is depleted by one and so its forward rate
+ * is reduced. And so on. This also protects against going negative
+ * in mol number or concentration.
+ */
+ void convertRatesToStochasticForm();
+
+ /// Used to handle run-time size updates for spines.
+ void scaleBufsAndRates( unsigned int index, double volScale );
+
+ //////////////////////////////////////////////////////////////////
+ // Zombification functions.
+ //////////////////////////////////////////////////////////////////
+
+ /**
+ * zombifyModel marches through the specified id list and
+ * converts all entries into zombies. The first arg e is the
+ * Eref of the Stoich itself.
+ */
+ void zombifyModel( const Eref& e, const vector< Id >& elist );
+
+ /**
+ * Converts back to ExpEuler type basic kinetic Elements.
+ */
+ void unZombifyModel();
+
+ /// unZombifies Pools. Helper for unZombifyModel.
+ void unZombifyPools();
+
+ void zombifyChemCompt( Id compt );
+
+ /**
+ * Utility function to find if incoming message assigns N or conc,
+ * and to appropriately zombify the function and set up its
+ * parameters including volume scaling.
+ */
+ Id zombifyPoolFuncWithScaling( Id pool );
+
+ unsigned int convertIdToReacIndex( Id id ) const;
+ unsigned int convertIdToPoolIndex( Id id ) const;
+ unsigned int convertIdToFuncIndex( Id id ) const;
+
+ /// Utility function to make a half reac and return the rate term.
+ ZeroOrder* makeHalfReaction(
+ double rate, const vector< Id >& reactants );
+
+ /*
+ * This takes the specified Reac and its substrate and product
+ * list, and installs them into the Stoich. It also builds up the
+ * vectors to store which compartment each substrate/product
+ * belongs to, needed for cross-reaction computations.
+ * This is the high-level interface function.
+ */
+ void installReaction( Id reacId,
+ const vector< Id >& subs, const vector< Id >& prds );
+ /*
+ * This takes the specified subs and prds belonging
+ * to the specified Reac, and builds them into the Stoich.
+ * It is a low-level function used internally.
+ */
+ unsigned int innerInstallReaction( Id reacId,
+ const vector< Id >& subs, const vector< Id >& prds );
+
+ /**
+ * This takes the baseclass for an MMEnzyme and builds the
+ * MMenz into the Stoich.
+ */
+ void installMMenz( Id enzId, const vector< Id >& enzMolId,
+ const vector< Id >& subs, const vector< Id >& prds );
+ /**
+ * This is the inner function to do the installation.
+ */
+ void installMMenz( MMEnzymeBase* meb, unsigned int rateIndex,
+ const vector< Id >& subs, const vector< Id >& prds );
+
+ /*
+ * This takes the specified Reac and its substrate and product
+ * list, and installs them into the Stoich. This is the high-level
+ * interface function.
+ */
+ void installEnzyme( Id enzId, Id enzMolId, Id cplxId,
+ const vector< Id >& subs, const vector< Id >& prds );
+ /**
+ * This takes the forward, backward and product formation half-reacs
+ * belonging to the specified Enzyme, and builds them into the
+ * Stoich. This is the low-level function.
+ */
+ void installEnzyme( ZeroOrder* r1, ZeroOrder* r2, ZeroOrder* r3,
+ Id enzId, Id enzMolId, const vector< Id >& prds );
+
+ /// This is used when the enzyme lacks sub or prd.
+ void installDummyEnzyme( Id enzId, Id enzMolId);
+
+ /**
+ * This installs a FuncTerm, which evaluates a function to specify
+ * the conc of the specific pool. The pool is a BufPool.
+ */
+ void installAndUnschedFunc( Id func, Id pool, double volScale );
+
+ /**
+ * This installs a FuncRate, which evaluates a function to specify
+ * the rate of change of conc of the specific pool.
+ * The pool is a Pool.
+ */
+ void installAndUnschedFuncRate( Id func, Id pool );
+
+ /**
+ * This installs a FuncReac, which evaluates a function to specify
+ * the rate (Kf) of the specified reaction.
+ */
+ void installAndUnschedFuncReac( Id func, Id reac );
+
+ //////////////////////////////////////////////////////////////////
+
+ /**
+ * Returns SpeciesId of specified pool
+ */
+ unsigned int getSpecies( unsigned int poolIndex ) const;
+
+ /**
+ * Assigns SpeciesId of specified pool
+ */
+ void setSpecies( unsigned int poolIndex, unsigned int s );
+
+ /**
+ * Sets the forward rate v (given in millimoloar concentration units)
+ * for the specified reaction throughout the compartment in which the
+ * reaction lives. Internally the stoich uses #/voxel units so this
+ * involves querying the volume subsystem about volumes for each
+ * voxel, and scaling accordingly.
+ */
+ void setReacKf( const Eref& e, double v ) const;
+
+ /**
+ * Sets the reverse rate v (given in millimoloar concentration units)
+ * for the specified reaction throughout the compartment in which the
+ * reaction lives. Internally the stoich uses #/voxel units so this
+ * involves querying the volume subsystem about volumes for each
+ * voxel, and scaling accordingly.
+ */
+ void setReacKb( const Eref& e, double v ) const;
+
+ /**
+ * Sets the Km for MMenz, using appropriate volume conversion to
+ * go from the argument (in millimolar) to #/voxel.
+ * This may do the assignment among many voxels containing the enz
+ * in case there are different volumes.
+ */
+ void setMMenzKm( const Eref& e, double v ) const;
+ double getMMenzNumKm( const Eref& e ) const;
+
+ /**
+ * Sets the kcat for MMenz. No conversions needed.
+ */
+ void setMMenzKcat( const Eref& e, double v ) const;
+ double getMMenzKcat( const Eref& e ) const;
+
+ /**
+ * Sets the rate v (given in millimoloar concentration units)
+ * for the forward enzyme reaction of binding substrate to enzyme.
+ * Does this throughout the compartment in which the
+ * enzyme lives. Internally the stoich uses #/voxel units so this
+ * involves querying the volume subsystem about volumes for each
+ * voxel, and scaling accordingly.
+ */
+ void setEnzK1( const Eref& e, double v ) const;
+ double getEnzNumK1( const Eref& e ) const;
+
+ /// Set rate k2 (1/sec) for enzyme
+ void setEnzK2( const Eref& e, double v ) const;
+ /// Get rate k2 (1/sec) for enzyme
+ double getEnzK2( const Eref& e ) const;
+
+ /// Set rate k3 (1/sec) for enzyme
+ void setEnzK3( const Eref& e, double v ) const;
+ /// Get rate k3, aka kcat, for enzyme
+ double getEnzK3( const Eref& e ) const;
+
+ /**
+ * Returns the internal rate in #/voxel, for R1, for the specified
+ * Eref.
+ */
+ double getR1( const Eref& e ) const;
+ /**
+ * Returns internal rate R1 in #/voxel, for the rate term
+ * following the one directly referred to by the Eref e. Enzymes
+ * define multiple successive rate terms, so we look up the first,
+ * and then select one after it.
+ */
+ double getR1offset1( const Eref& e ) const;
+ /**
+ * Returns internal rate R1 in #/voxel, for the rate term
+ * two after the one directly referred to by the Eref e. Enzymes
+ * define multiple successive rate terms, so we look up the first,
+ * and then select the second one after it.
+ */
+ double getR1offset2( const Eref& e ) const;
+
+ /**
+ * Returns the internal rate in #/voxel, for R2, for the specified
+ * reacIndex and voxel index. In some cases R2 is undefined, and it
+ * then returns 0.
+ */
+ double getR2( const Eref& e ) const;
+
+ /**
+ * Sets the arithmetic expression used in a FuncRate or FuncReac
+ */
+ void setFunctionExpr( const Eref& e, string expr );
+
+ /**
+ * This function scans all reacs and enzymes and recalculates the
+ * internal rate terms depending on the reference terms stored in
+ * the original chemical object.
+ */
+ void updateRatesAfterRemesh();
+
+ /// Utility function, prints out N_, used for debugging
+ void print() const;
+
+ /// Another utility function, prints out all Kf, kf, Kb, kb.
+ void printRates() const;
+ //////////////////////////////////////////////////////////////////
+ // Utility funcs for numeric calculations
+ //////////////////////////////////////////////////////////////////
+
+ /**
+ * Updates the yprime array, rate of change of each molecule
+ * The volIndex specifies which set of rates to use, since the
+ * rates are volume dependent.
+ * Moved to VoxelPools
+ void updateRates( const double* s, double* yprime,
+ unsigned int volIndex ) const;
+ */
+
+ /**
+ * Computes the velocity of each reaction, vel.
+ * The volIndex specifies which set of rates to use, since the
+ * rates are volume dependent.
+ */
+ void updateReacVelocities( const double* s, vector< double >& vel,
+ unsigned int volIndex ) const;
+
+ /// Updates the function values, within s.
+ void updateFuncs( double* s, double t ) const;
+
+ /// Updates the rates for cross-compartment reactions.
+ /*
+ void updateJunctionRates( const double* s,
+ const vector< unsigned int >& reacTerms, double* yprime );
+ */
+
+ /**
+ * Get the rate for a single reaction specified by r, as per all
+ * the mol numbers in s.
+ double getReacVelocity( unsigned int r, const double* s,
+ unsigned int volIndex ) const;
+ */
+
+ /// Returns the stoich matrix. Used by gsolve.
+ const KinSparseMatrix& getStoichiometryMatrix() const;
+ //////////////////////////////////////////////////////////////////
+ // Access functions for cross-node reactions.
+ //////////////////////////////////////////////////////////////////
+ const vector< Id >& getOffSolverPools() const;
+
+ /**
+ * List all the compartments to which the current compt is coupled,
+ * by cross-compartment reactions. Self not included.
+ */
+ vector< Id > getOffSolverCompts() const;
+
+ /**
+ * Looks up the vector of pool Ids originating from the specified
+ * compartment, that are represented on this compartment as proxies.
+ */
+ const vector< Id >& offSolverPoolMap( Id compt ) const;
+
+ /**
+ * Returns the index of the matching volume,
+ * which is also the index into the RateTerm vector.
+ unsigned int indexOfMatchingVolume( double vol ) const;
+ */
+
+ //////////////////////////////////////////////////////////////////
+ static const unsigned int PoolIsNotOnSolver;
+ static const Cinfo* initCinfo();
+private:
+ /**
+ * True if the stoich matrix is set up to handle only one-way
+ * reactions, as is needed in the case of the Gillespie algorithm.
+ */
+ bool useOneWay_;
+
+ /**
+ * True if pools are permitted to take negative concentrations.
+ * This may happen if solver is handling a general equation system
+ * that is not constrained by chemical rules.
+ * Defaults to False, so that we cannot have negative concs.
+ */
+ bool allowNegative_;
+
+ string path_;
+
+ /// This contains the Id of the Kinetic solver.
+ Id ksolve_;
+
+ /// This contains the Id of the Diffusion solver. Optional.
+ Id dsolve_;
+
+ /// Contains Id of compartment holding reac system. Optional
+ Id compartment_;
+
+ /// Pointer for ksolve
+ ZombiePoolInterface* kinterface_;
+ /// Pointer for dsolve
+ ZombiePoolInterface* dinterface_;
+
+ /**
+ * Lookup from each molecule to its Species identifer
+ * This will eventually be tied into an ontology reference.
+ */
+ vector< unsigned int > species_;
+
+ /**
+ * The RateTerms handle the update operations for reaction rate v_.
+ * This is the master vector of RateTerms, and it is scaled to
+ * a volume such that the 'n' units and the conc units are
+ * identical.
+ * Duplicates of this vector are made in each voxel with a different
+ * volume. The duplicates have rates scaled as per volume.
+ * The RateTerms vector also includes reactions that have
+ * off-compartment products. These need special volume scaling
+ * involving all the interactiong compartments.
+ */
+ vector< RateTerm* > rates_;
+
+ /**
+ * This tracks the unique volumes handled by the reac system.
+ * Maps one-to-one with the vector of vector of RateTerms.
+ vector< double > uniqueVols_;
+ */
+
+ /// Number of voxels in reac system.
+ unsigned int numVoxels_;
+
+ /// The FuncTerms handle mathematical ops on mol levels.
+ vector< FuncTerm* > funcs_;
+
+ /// N_ is the stoichiometry matrix. All pools * all reac terms.
+ KinSparseMatrix N_;
+
+ /**
+ * Maps Ids to objects in the S_, RateTerm, and FuncTerm vectors.
+ * There will be holes in this map, but look up is very fast.
+ * The calling Id must know what it wants to find: all it
+ * gets back is an integer.
+ * The alternative is to have multiple maps, but that is slower.
+ * Assume no arrays. Each Pool/reac etc must be a unique
+ * Element. Later we'll deal with diffusion.
+ */
+ // vector< unsigned int > objMap_;
+ /**
+ * Minor efficiency: We will usually have a set of objects that are
+ * nearly contiguous in the map. May as well start with the first of
+ * them.
+ */
+ // unsigned int objMapStart_;
+ //
+ ///////////////////////////////////////////////////////////
+ // Here we have the vectors of the different kinds of objects
+ // managed by the Stoich
+ ///////////////////////////////////////////////////////////
+
+ /**
+ * Vector of variablePool Ids.
+ */
+ vector< Id > varPoolVec_;
+
+ /**
+ * Vector of bufPool Ids.
+ */
+ vector< Id > bufPoolVec_;
+
+ /**
+ * These are pools that were not in the original scope of the
+ * solver, but have to be brought in because they are reactants
+ * of one or more of the offSolverReacs.
+ */
+ vector< Id > offSolverPoolVec_;
+
+ /**
+ * Vector of reaction ids.
+ */
+ vector< Id > reacVec_;
+ vector< Id > offSolverReacVec_;
+
+ /**
+ * Map back from enz index to Id. Needed to unzombify
+ */
+ vector< Id > enzVec_;
+ vector< Id > offSolverEnzVec_;
+
+ /**
+ * Map back from enz index to Id. Needed to unzombify
+ */
+ vector< Id > mmEnzVec_;
+ vector< Id > offSolverMMenzVec_;
+
+ /**
+ * Vector of funcs controlling pool number, that is N.
+ */
+ vector< Id > poolFuncVec_;
+
+ /**
+ * vector tracks which pool is controlled by which func.
+ * Unused entries are flagged by ~0.
+ * funcTarget_[ poolIndex ] == funcIndex
+ */
+ vector< unsigned int > funcTarget_;
+
+ /**
+ * Vector of funcs controlling pool increment, that is dN/dt
+ * This is handled as a rateTerm.
+ */
+ vector< Id > incrementFuncVec_;
+
+ /**
+ * Vector of funcs controlling reac rate, that is numKf
+ * This is handled as a rateTerm.
+ */
+ vector< Id > reacFuncVec_;
+
+ ///////////////////////////////////////////////////////////////
+ // Here we have maps to look up objects from their ids.
+ ///////////////////////////////////////////////////////////////
+ map< Id, unsigned int > poolLookup_;
+ map< Id, unsigned int > rateTermLookup_;
+ map< Id, unsigned int > funcLookup_;
+
+ /**
+ * Number of variable molecules that the solver deals with,
+ * that are local to the solver.
+ *
+ */
+ // unsigned int numVarPools_;
+
+ /**
+ * Number of variable molecules that the solver deals with,
+ * including the proxy molecules which belong in other compartments.
+ *
+ unsigned int totVarPools_;
+ */
+
+ /**
+ * Number of buffered molecules
+ */
+ // unsigned int numBufPools_;
+
+ /**
+ * Looks up the rate term from the Id for a reac, enzyme, or func.
+ map< Id, unsigned int > rateTermLookup_;
+ */
+
+ /**
+ * Number functions, currently only the ones controlling molecule
+ * numbers, like sumtotals.
+ unsigned int numFunctions_;
+ */
+
+ /**
+ * Number of reactions in the solver model. This includes
+ * conversion reactions A + B <---> C
+ * enzyme reactions E + S <---> E.S ---> E + P
+ * and MM enzyme reactions rate = E.S.kcat / ( Km + S )
+ * The enzyme reactions count as two reaction steps.
+ unsigned int numReac_;
+ */
+
+ /**
+ * Flag to track status of Stoich object.
+ * -1: No path yet assigned.
+ * 0: Success
+ * 1: Warning: Missing reactant in Reac or Enz
+ * 2: Warning: Missing substrate in MMenz
+ * 4: Warning: Compartment not defined
+ * 8: Warning: Neither Ksolve nore Dsolve defined
+ */
+ int status_;
+
+ //////////////////////////////////////////////////////////////////
+ // Off-solver stuff
+ //////////////////////////////////////////////////////////////////
+
+ /**
+ * Map of vectors of Ids of offSolver pools.
+ * Each map entry contains the vector of Ids of proxy pools
+ * coming from the specified compartment.
+ * In use, the junction will copy the pool indices over for
+ * data transfer.
+ */
+ map< Id, vector< Id > > offSolverPoolMap_;
+
+ /**
+ * Tracks the reactions that go off the current solver.
+ vector< Id > offSolverReacs_;
+ */
+
+ /**
+ * Which compartment(s) does the off solver reac connect to?
+ * Usually it is just one, in which case the second id is Id()
+ */
+ vector< pair< Id, Id > > offSolverReacCompts_;
+ vector< pair< Id, Id > > offSolverEnzCompts_;
+ vector< pair< Id, Id > > offSolverMMenzCompts_;
+
+ /**
+ * subComptVec_[rateTermIndex][substrate#]: Identifies compts
+ * for each substrate for each cross-compartment RateTerm in
+ * the rates_vector.
+ */
+ vector< vector< Id > > subComptVec_;
+
+ /**
+ * prdComptVec_[rateTermIndex][product#]: Identifies compts
+ * for each product for each cross-compartment RateTerm in
+ * the rates_vector.
+ */
+ vector< vector< Id > > prdComptVec_;
};
#endif // _STOICH_H
diff --git a/moose-core/ksolve/VoxelPools.cpp b/moose-core/ksolve/VoxelPools.cpp
index dd797fd3f248ba09288b665ce083a25fbb80fe12..cf16e42375e814e19d7cba1445ceaf1d7b37d4b1 100644
--- a/moose-core/ksolve/VoxelPools.cpp
+++ b/moose-core/ksolve/VoxelPools.cpp
@@ -113,8 +113,6 @@ void VoxelPools::advance( const ProcInfo* p )
#elif USE_BOOST_ODE
/*-----------------------------------------------------------------------------
- NOTE: 04/21/2016 11:31:42 AM
-
We need to call updateFuncs here (unlike in GSL solver) because there
is no way we can update const vector_type_& y in evalRatesUsingBoost
function. In gsl implmentation one could do it, because const_cast can
@@ -144,19 +142,21 @@ void VoxelPools::advance( const ProcInfo* p )
// https://www.boost.org/doc/libs/1_68_0/libs/numeric/odeint/doc/html/boost_numeric_odeint/odeint_in_detail/steppers.html#boost_numeric_odeint.odeint_in_detail.steppers.explicit_steppers
// Describe system to be used in boost solver calls.
- auto sys = [this](const vector_type_& dy, vector_type_& dydt, const double t) {
- VoxelPools::evalRates(this, dy, dydt); };
+ auto sys = [this](const vector_type_& dy, vector_type_& dydt, const double t)
+ {
+ VoxelPools::evalRates(this, dy, dydt);
+ };
// This is usually the default method. It works well in practice. Tested
// with steady-state solver. Closest to GSL rk5 .
if( method_ == "rk5" || method_ == "gsl" || method_ == "boost" )
- odeint::integrate_adaptive(
- make_dense_output( epsAbs_, epsRel_, odeint::runge_kutta_dopri5<vector_type_>() )
- , sys , Svec() , p->currTime - p->dt , p->currTime , p->dt
+ odeint::integrate_adaptive(
+ make_dense_output( epsAbs_, epsRel_, odeint::runge_kutta_dopri5<vector_type_>() )
+ , sys, Svec(), p->currTime - p->dt, p->currTime, p->dt
);
else if( method_ == "rk5a" || method_ == "adaptive" )
odeint::integrate_adaptive( odeint::make_controlled<rk_dopri_stepper_type_>( epsAbs_, epsRel_ )
- , sys , Svec() , p->currTime - p->dt , p->currTime, p->dt );
+ , sys, Svec(), p->currTime - p->dt, p->currTime, p->dt );
else if( method_ == "rk2" )
odeint::integrate_const( rk_midpoint_stepper_type_()
, sys, Svec(), p->currTime - p->dt, p->currTime, p->dt);
@@ -165,26 +165,26 @@ void VoxelPools::advance( const ProcInfo* p )
, sys, Svec(), p->currTime - p->dt, p->currTime, p->dt );
else if ("rk54" == method_ )
odeint::integrate_const( rk_karp_stepper_type_()
- , sys , Svec() , p->currTime - p->dt, p->currTime, p->dt);
+ , sys, Svec(), p->currTime - p->dt, p->currTime, p->dt);
else if ("rkck" == method_ )
odeint::integrate_adaptive( odeint::make_controlled<rk_karp_stepper_type_>( epsAbs_, epsRel_ )
, sys, Svec(), p->currTime - p->dt, p->currTime, p->dt);
else if( method_ == "rk8" )
odeint::integrate_const( rk_felhberg_stepper_type_()
- , sys, Svec(), p->currTime - p->dt, p->currTime, p->dt);
+ , sys, Svec(), p->currTime - p->dt, p->currTime, p->dt);
else if( method_ == "rk8a" )
odeint::integrate_adaptive( rk_felhberg_stepper_type_()
- , sys, Svec(), p->currTime - p->dt, p->currTime, p->dt);
+ , sys, Svec(), p->currTime - p->dt, p->currTime, p->dt);
else
{
cerr << "Ksolve: Unknow method " << method_ << ", using default!" << endl;
odeint::integrate_const(
- make_dense_output( epsAbs_, epsRel_, odeint::runge_kutta_dopri5<vector_type_>() )
- , sys , Svec() , p->currTime - p->dt , p->currTime , p->dt
+ make_dense_output( epsAbs_, epsRel_, odeint::runge_kutta_dopri5<vector_type_>() )
+ , sys, Svec(), p->currTime - p->dt, p->currTime, p->dt
);
}
-
#endif
+
if ( !stoichPtr_->getAllowNegative() ) // clean out negatives
{
unsigned int nv = stoichPtr_->getNumVarPools();
@@ -205,12 +205,10 @@ void VoxelPools::setInitDt( double dt )
}
#ifdef USE_GSL
-// static func. This is the function that goes into the Gsl solver.
-int VoxelPools::gslFunc( double t, const double* y, double *dydt,
- void* params )
+// static func. This goes into the Gsl solver.
+int VoxelPools::gslFunc(double t, const double* y, double *dydt, void* params)
{
VoxelPools* vp = reinterpret_cast< VoxelPools* >( params );
- // Stoich* s = reinterpret_cast< Stoich* >( params );
double* q = const_cast< double* >( y ); // Assign the func portion.
vp->stoichPtr_->updateFuncs( q, t );
vp->updateRates( y, dydt );
@@ -235,7 +233,7 @@ void VoxelPools::evalRates( VoxelPools* vp, const vector_type_& y, vector_type_
///////////////////////////////////////////////////////////////////////
void VoxelPools::updateAllRateTerms( const vector< RateTerm* >& rates,
- unsigned int numCoreRates )
+ unsigned int numCoreRates )
{
// Clear out old rates if any
for ( unsigned int i = 0; i < rates_.size(); ++i )
@@ -249,8 +247,9 @@ void VoxelPools::updateAllRateTerms( const vector< RateTerm* >& rates,
for ( unsigned int i = numCoreRates; i < rates.size(); ++i )
{
rates_[i] = rates[i]->copyWithVolScaling( getVolume(),
- getXreacScaleSubstrates(i - numCoreRates),
- getXreacScaleProducts(i - numCoreRates ) );
+ getXreacScaleSubstrates(i-numCoreRates),
+ getXreacScaleProducts(i-numCoreRates)
+ );
}
}
@@ -263,13 +262,14 @@ void VoxelPools::updateRateTerms( const vector< RateTerm* >& rates,
return;
delete( rates_[index] );
if ( index >= numCoreRates )
+ {
rates_[index] = rates[index]->copyWithVolScaling(
getVolume(),
getXreacScaleSubstrates(index - numCoreRates),
getXreacScaleProducts(index - numCoreRates ) );
+ }
else
- rates_[index] = rates[index]->copyWithVolScaling(
- getVolume(), 1.0, 1.0 );
+ rates_[index] = rates[index]->copyWithVolScaling(getVolume(), 1.0, 1.0);
}
void VoxelPools::updateRates( const double* s, double* yprime ) const
@@ -335,8 +335,7 @@ void VoxelPools::print() const
*/
void VoxelPools::setVolumeAndDependencies( double vol )
{
- VoxelPoolsBase::setVolumeAndDependencies( vol );
- updateAllRateTerms( stoichPtr_->getRateTerms(),
- stoichPtr_->getNumCoreRates() );
+ VoxelPoolsBase::setVolumeAndDependencies(vol);
+ updateAllRateTerms(stoichPtr_->getRateTerms(), stoichPtr_->getNumCoreRates());
}
diff --git a/moose-core/ksolve/ZombieFunction.cpp b/moose-core/ksolve/ZombieFunction.cpp
index 48a218990b6dffe3be174bb49c7e3a143389c70f..e7b5e9ac47df5011cc6c635ad5c81d750ca2f791 100644
--- a/moose-core/ksolve/ZombieFunction.cpp
+++ b/moose-core/ksolve/ZombieFunction.cpp
@@ -10,7 +10,9 @@
#include "../basecode/header.h"
#include "../basecode/ElementValueFinfo.h"
+#include "../builtins/MooseParser.h"
#include "../builtins/Variable.h"
+#include "../builtins/MooseParser.h"
#include "../builtins/Function.h"
#include "ZombieFunction.h"
diff --git a/moose-core/ksolve/ZombiePoolInterface.cpp b/moose-core/ksolve/ZombiePoolInterface.cpp
index 62a50f9f13058ba0378d572bcfdd612ec6c6032a..a4ebf8c4ca0a3b54e550b19fbc93f0754591767c 100644
--- a/moose-core/ksolve/ZombiePoolInterface.cpp
+++ b/moose-core/ksolve/ZombiePoolInterface.cpp
@@ -30,12 +30,12 @@
#include "../mesh/ChemCompt.h"
ZombiePoolInterface::ZombiePoolInterface()
- : stoich_(), compartment_(),
- isBuilt_( false )
+ : stoich_(), compartment_(), isBuilt_(false)
{;}
void ZombiePoolInterface::updateJunctions( double dt )
{;}
+
void ZombiePoolInterface::setPrev()
{;}
@@ -52,15 +52,13 @@ void ZombiePoolInterface::setCompartment( Id compt )
if ( compt.element()->cinfo()->isA( "ChemCompt" ) )
{
compartment_ = compt;
- vector< double > vols =
- Field< vector < double > >::get( compt, "voxelVolume" );
- if ( vols.size() > 0 )
+ vector<double> vols = Field<vector<double>>::get( compt, "voxelVolume" );
+
+ if (vols.size() > 0)
{
setNumAllVoxels( vols.size() );
for ( unsigned int i = 0; i < vols.size(); ++i )
- {
pools(i)->setVolume( vols[i] );
- }
}
}
}
diff --git a/moose-core/mesh/ChemCompt.cpp b/moose-core/mesh/ChemCompt.cpp
index b8961f1d9a8b968ced95b0565269a000f5209cdb..b1d32598d805a42d97fef21a32201e6e70e20c71 100644
--- a/moose-core/mesh/ChemCompt.cpp
+++ b/moose-core/mesh/ChemCompt.cpp
@@ -14,179 +14,182 @@
#include "MeshEntry.h"
#include "ChemCompt.h"
-SrcFinfo1< vector< double > >* ChemCompt::voxelVolOut() {
- static SrcFinfo1< vector< double > > voxelVolOut( "voxelVolOut",
- "Sends updated voxel volume out to Ksolve, Gsolve, and Dsolve."
- "Used to request a recalculation of rates and of initial numbers."
- );
- return &voxelVolOut;
+SrcFinfo1< vector< double > >* ChemCompt::voxelVolOut()
+{
+ static SrcFinfo1< vector< double > > voxelVolOut( "voxelVolOut",
+ "Sends updated voxel volume out to Ksolve, Gsolve, and Dsolve."
+ "Used to request a recalculation of rates and of initial numbers."
+ );
+ return &voxelVolOut;
}
const Cinfo* ChemCompt::initCinfo()
{
- //////////////////////////////////////////////////////////////
- // Field Definitions
- //////////////////////////////////////////////////////////////
- static ElementValueFinfo< ChemCompt, double > volume(
- "volume",
- "Volume of entire chemical domain."
- "Assigning this only works if the chemical compartment has"
- "only a single voxel. Otherwise ignored."
- "This function goes through all objects below this on the"
- "tree, and rescales their molecule #s and rates as per the"
- "volume change. This keeps concentration the same, and also"
- "maintains rates as expressed in volume units.",
- &ChemCompt::setEntireVolume,
- &ChemCompt::getEntireVolume
- );
-
- static ReadOnlyValueFinfo< ChemCompt, vector< double > >
- voxelVolume(
- "voxelVolume",
- "Vector of volumes of each of the voxels.",
- &ChemCompt::getVoxelVolume
- );
-
- static ReadOnlyValueFinfo< ChemCompt, vector< double > >
- voxelMidpoint(
- "voxelMidpoint",
- "Vector of midpoint coordinates of each of the voxels. The "
- "size of this vector is 3N, where N is the number of voxels. "
- "The first N entries are for x, next N for y, last N are z. ",
- &ChemCompt::getVoxelMidpoint
- );
-
- static LookupElementValueFinfo<
- ChemCompt, unsigned int, double >
- oneVoxelVolume(
- "oneVoxelVolume",
- "Volume of specified voxel.",
- &ChemCompt::setOneVoxelVolume,
- &ChemCompt::getOneVoxelVolume
- );
-
- static ReadOnlyValueFinfo< ChemCompt, unsigned int > numDimensions(
- "numDimensions",
- "Number of spatial dimensions of this compartment. Usually 3 or 2",
- &ChemCompt::getDimensions
- );
-
- static ReadOnlyLookupValueFinfo< ChemCompt, unsigned int, vector< double > > stencilRate(
- "stencilRate",
- "vector of diffusion rates in the stencil for specified voxel."
- "The identity of the coupled voxels is given by the partner "
- "field 'stencilIndex'."
- "Returns an empty vector for non-voxelized compartments.",
- &ChemCompt::getStencilRate
- );
-
- static ReadOnlyLookupValueFinfo< ChemCompt, unsigned int, vector< unsigned int > > stencilIndex(
- "stencilIndex",
- "vector of voxels diffusively coupled to the specified voxel."
- "The diffusion rates into the coupled voxels is given by the "
- "partner field 'stencilRate'."
- "Returns an empty vector for non-voxelized compartments.",
- &ChemCompt::getStencilIndex
- );
-
- static ValueFinfo< ChemCompt, bool > isMembraneBound(
- "isMembraneBound",
- "Flag, set to True for meshes where each voxel is membrane "
- "bound. \n"
- "NeuroMesh and SpineMesh are false. \n"
- "CubeMesh, CylMesh, and EndoMesh can be either. If they are "
- "membrane bound they can still interact via channels and "
- "cross-compartment reactions. ",
- &ChemCompt::setIsMembraneBound,
- &ChemCompt::getIsMembraneBound
- );
-
- //////////////////////////////////////////////////////////////
- // MsgDest Definitions
- //////////////////////////////////////////////////////////////
-
- static DestFinfo buildDefaultMesh( "buildDefaultMesh",
- "Tells ChemCompt derived class to build a default mesh with the"
- "specified volume and number of meshEntries.",
- new EpFunc2< ChemCompt, double, unsigned int >(
- &ChemCompt::buildDefaultMesh )
- );
-
- static DestFinfo setVolumeNotRates( "setVolumeNotRates",
- "Changes volume but does not notify any child objects."
- "Only works if the ChemCompt has just one voxel."
- "This function will invalidate any concentration term in"
- "the model. If you don't know why you would want to do this,"
- "then you shouldn't use this function.",
- new OpFunc1< ChemCompt, double >(
- &ChemCompt::setVolumeNotRates )
- );
-
- static DestFinfo handleNodeInfo( "handleNodeInfo",
- "Tells ChemCompt how many nodes and threads per node it is "
- "allowed to use. Triggers a return meshSplitOut message.",
- new EpFunc2< ChemCompt, unsigned int, unsigned int >(
- &ChemCompt::handleNodeInfo )
- );
-
- static DestFinfo resetStencil( "resetStencil",
- "Resets the diffusion stencil to the core stencil that only "
- "includes the within-mesh diffusion. This is needed prior to "
- "building up the cross-mesh diffusion through junctions.",
- new OpFunc0< ChemCompt >(
- &ChemCompt::resetStencil )
- );
-
-
- //////////////////////////////////////////////////////////////
- // Field Elements
- //////////////////////////////////////////////////////////////
-
- static FieldElementFinfo< ChemCompt, MeshEntry > entryFinfo(
- "mesh",
- "Field Element for mesh entries",
- MeshEntry::initCinfo(),
- &ChemCompt::lookupEntry,
- &ChemCompt::setNumEntries,
- &ChemCompt::getNumEntries,
- false
- );
-
- static Finfo* chemMeshFinfos[] = {
- &volume, // Value
- &voxelVolume, // ReadOnlyLookupValue
- &voxelMidpoint, // ReadOnlyLookupValue
- &oneVoxelVolume, // ReadOnlyLookupValue
- &numDimensions, // ReadOnlyValue
- &stencilRate, // ReadOnlyLookupValue
- &stencilIndex, // ReadOnlyLookupValue
- &isMembraneBound, // Value
- voxelVolOut(), // SrcFinfo
- &buildDefaultMesh, // DestFinfo
- &setVolumeNotRates, // DestFinfo
- &resetStencil, // DestFinfo
- &entryFinfo, // FieldElementFinfo
- };
-
- static string doc[] = {
- "Name", "ChemCompt",
- "Author", "Upi Bhalla",
- "Description", "Pure virtual base class for chemical compartments"
-
- };
- static Dinfo< short > dinfo;
- static Cinfo chemMeshCinfo (
- "ChemCompt",
- Neutral::initCinfo(),
- chemMeshFinfos,
- sizeof( chemMeshFinfos ) / sizeof ( Finfo* ),
- &dinfo,
- doc,
- sizeof(doc)/sizeof( string ),
- true // This is a base class, not be be created directly.
- );
-
- return &chemMeshCinfo;
+ //////////////////////////////////////////////////////////////
+ // Field Definitions
+ //////////////////////////////////////////////////////////////
+ static ElementValueFinfo< ChemCompt, double > volume(
+ "volume",
+ "Volume of entire chemical domain."
+ "Assigning this only works if the chemical compartment has"
+ "only a single voxel. Otherwise ignored."
+ "This function goes through all objects below this on the"
+ "tree, and rescales their molecule #s and rates as per the"
+ "volume change. This keeps concentration the same, and also"
+ "maintains rates as expressed in volume units.",
+ &ChemCompt::setEntireVolume,
+ &ChemCompt::getEntireVolume
+ );
+
+ static ReadOnlyValueFinfo< ChemCompt, vector< double > >
+ voxelVolume(
+ "voxelVolume",
+ "Vector of volumes of each of the voxels.",
+ &ChemCompt::getVoxelVolume
+ );
+
+ static ReadOnlyValueFinfo< ChemCompt, vector< double > >
+ voxelMidpoint(
+ "voxelMidpoint",
+ "Vector of midpoint coordinates of each of the voxels. The "
+ "size of this vector is 3N, where N is the number of voxels. "
+ "The first N entries are for x, next N for y, last N are z. ",
+ &ChemCompt::getVoxelMidpoint
+ );
+
+ static LookupElementValueFinfo<
+ ChemCompt, unsigned int, double >
+ oneVoxelVolume(
+ "oneVoxelVolume",
+ "Volume of specified voxel.",
+ &ChemCompt::setOneVoxelVolume,
+ &ChemCompt::getOneVoxelVolume
+ );
+
+ static ReadOnlyValueFinfo< ChemCompt, unsigned int > numDimensions(
+ "numDimensions",
+ "Number of spatial dimensions of this compartment. Usually 3 or 2",
+ &ChemCompt::getDimensions
+ );
+
+ static ReadOnlyLookupValueFinfo< ChemCompt, unsigned int, vector< double > > stencilRate(
+ "stencilRate",
+ "vector of diffusion rates in the stencil for specified voxel."
+ "The identity of the coupled voxels is given by the partner "
+ "field 'stencilIndex'."
+ "Returns an empty vector for non-voxelized compartments.",
+ &ChemCompt::getStencilRate
+ );
+
+ static ReadOnlyLookupValueFinfo< ChemCompt, unsigned int, vector< unsigned int > > stencilIndex(
+ "stencilIndex",
+ "vector of voxels diffusively coupled to the specified voxel."
+ "The diffusion rates into the coupled voxels is given by the "
+ "partner field 'stencilRate'."
+ "Returns an empty vector for non-voxelized compartments.",
+ &ChemCompt::getStencilIndex
+ );
+
+ static ValueFinfo< ChemCompt, bool > isMembraneBound(
+ "isMembraneBound",
+ "Flag, set to True for meshes where each voxel is membrane "
+ "bound. \n"
+ "NeuroMesh and SpineMesh are false. \n"
+ "CubeMesh, CylMesh, and EndoMesh can be either. If they are "
+ "membrane bound they can still interact via channels and "
+ "cross-compartment reactions. ",
+ &ChemCompt::setIsMembraneBound,
+ &ChemCompt::getIsMembraneBound
+ );
+
+ //////////////////////////////////////////////////////////////
+ // MsgDest Definitions
+ //////////////////////////////////////////////////////////////
+
+ static DestFinfo buildDefaultMesh( "buildDefaultMesh",
+ "Tells ChemCompt derived class to build a default mesh with the"
+ "specified volume and number of meshEntries.",
+ new EpFunc2< ChemCompt, double, unsigned int >(
+ &ChemCompt::buildDefaultMesh )
+ );
+
+ static DestFinfo setVolumeNotRates( "setVolumeNotRates",
+ "Changes volume but does not notify any child objects."
+ "Only works if the ChemCompt has just one voxel."
+ "This function will invalidate any concentration term in"
+ "the model. If you don't know why you would want to do this,"
+ "then you shouldn't use this function.",
+ new OpFunc1< ChemCompt, double >(
+ &ChemCompt::setVolumeNotRates )
+ );
+
+ static DestFinfo handleNodeInfo( "handleNodeInfo",
+ "Tells ChemCompt how many nodes and threads per node it is "
+ "allowed to use. Triggers a return meshSplitOut message.",
+ new EpFunc2< ChemCompt, unsigned int, unsigned int >(
+ &ChemCompt::handleNodeInfo )
+ );
+
+ static DestFinfo resetStencil( "resetStencil",
+ "Resets the diffusion stencil to the core stencil that only "
+ "includes the within-mesh diffusion. This is needed prior to "
+ "building up the cross-mesh diffusion through junctions.",
+ new OpFunc0< ChemCompt >(
+ &ChemCompt::resetStencil )
+ );
+
+
+ //////////////////////////////////////////////////////////////
+ // Field Elements
+ //////////////////////////////////////////////////////////////
+
+ static FieldElementFinfo< ChemCompt, MeshEntry > entryFinfo(
+ "mesh",
+ "Field Element for mesh entries",
+ MeshEntry::initCinfo(),
+ &ChemCompt::lookupEntry,
+ &ChemCompt::setNumEntries,
+ &ChemCompt::getNumEntries,
+ false
+ );
+
+ static Finfo* chemMeshFinfos[] =
+ {
+ &volume, // Value
+ &voxelVolume, // ReadOnlyLookupValue
+ &voxelMidpoint, // ReadOnlyLookupValue
+ &oneVoxelVolume, // ReadOnlyLookupValue
+ &numDimensions, // ReadOnlyValue
+ &stencilRate, // ReadOnlyLookupValue
+ &stencilIndex, // ReadOnlyLookupValue
+ &isMembraneBound, // Value
+ voxelVolOut(), // SrcFinfo
+ &buildDefaultMesh, // DestFinfo
+ &setVolumeNotRates, // DestFinfo
+ &resetStencil, // DestFinfo
+ &entryFinfo, // FieldElementFinfo
+ };
+
+ static string doc[] =
+ {
+ "Name", "ChemCompt",
+ "Author", "Upi Bhalla",
+ "Description", "Pure virtual base class for chemical compartments"
+
+ };
+ static Dinfo< short > dinfo;
+ static Cinfo chemMeshCinfo (
+ "ChemCompt",
+ Neutral::initCinfo(),
+ chemMeshFinfos,
+ sizeof( chemMeshFinfos ) / sizeof ( Finfo* ),
+ &dinfo,
+ doc,
+ sizeof(doc)/sizeof( string ),
+ true // This is a base class, not be be created directly.
+ );
+
+ return &chemMeshCinfo;
}
//////////////////////////////////////////////////////////////
@@ -196,21 +199,21 @@ const Cinfo* ChemCompt::initCinfo()
static const Cinfo* chemMeshCinfo = ChemCompt::initCinfo();
ChemCompt::ChemCompt()
- :
- entry_( this ),
- isMembraneBound_( false )
+ :
+ entry_( this ),
+ isMembraneBound_( false )
{
- ;
+ ;
}
ChemCompt::~ChemCompt()
{
- /*
- for ( unsigned int i = 0; i < stencil_.size(); ++i ) {
- if ( stencil_[i] )
- delete stencil_[i];
- }
- */
+ /*
+ for ( unsigned int i = 0; i < stencil_.size(); ++i ) {
+ if ( stencil_[i] )
+ delete stencil_[i];
+ }
+ */
}
//////////////////////////////////////////////////////////////
@@ -218,21 +221,21 @@ ChemCompt::~ChemCompt()
//////////////////////////////////////////////////////////////
void ChemCompt::buildDefaultMesh( const Eref& e,
- double volume, unsigned int numEntries )
+ double volume, unsigned int numEntries )
{
- this->innerBuildDefaultMesh( e, volume, numEntries );
+ this->innerBuildDefaultMesh( e, volume, numEntries );
}
void ChemCompt::handleNodeInfo( const Eref& e,
- unsigned int numNodes, unsigned int numThreads )
+ unsigned int numNodes, unsigned int numThreads )
{
- // Pass it down to derived classes along with the SrcFinfo
- innerHandleNodeInfo( e, numNodes, numThreads );
+ // Pass it down to derived classes along with the SrcFinfo
+ innerHandleNodeInfo( e, numNodes, numThreads );
}
void ChemCompt::resetStencil()
{
- this->innerResetStencil();
+ this->innerResetStencil();
}
//////////////////////////////////////////////////////////////
@@ -241,125 +244,141 @@ void ChemCompt::resetStencil()
void ChemCompt::setEntireVolume( const Eref& e, double volume )
{
- // If the reac system is not solved, then explicitly do scaling
- vector< ObjId > tgtVec =
- e.element()->getMsgTargets( e.dataIndex(), voxelVolOut() );
- if ( tgtVec.size() == 0 ) {
- vector< double > childConcs;
- getChildConcs( e, childConcs );
- if ( vSetVolumeNotRates( volume ) ) {
- setChildConcs( e, childConcs, 0 );
- }
- } else {
- vSetVolumeNotRates( volume );
- voxelVolOut()->send( e, this->vGetVoxelVolume() );
- }
+ // If the reac system is not solved, then explicitly do scaling
+ vector< ObjId > tgtVec =
+ e.element()->getMsgTargets( e.dataIndex(), voxelVolOut() );
+ if ( tgtVec.size() == 0 )
+ {
+ vector< double > childConcs;
+ getChildConcs( e, childConcs );
+ if ( vSetVolumeNotRates( volume ) )
+ {
+ setChildConcs( e, childConcs, 0 );
+ }
+ }
+ else
+ {
+ vSetVolumeNotRates( volume );
+ voxelVolOut()->send( e, this->vGetVoxelVolume() );
+ }
}
double ChemCompt::getEntireVolume( const Eref& e ) const
{
- return vGetEntireVolume();
+ return vGetEntireVolume();
}
-void ChemCompt::getChildConcs( const Eref& e, vector< double >& childConcs )
- const
+void ChemCompt::getChildConcs( const Eref& e, vector< double >& childConcs ) const
{
- vector< Id > kids;
- Neutral::children( e, kids );
- for ( vector < Id >::iterator i = kids.begin(); i != kids.end(); ++i )
- {
- if ( i->element()->cinfo()->isA( "PoolBase" ) ) {
- childConcs.push_back( Field< double >::get( *i, "conc" ) );
- childConcs.push_back( Field< double >::get( *i, "concInit" ) );
- } else if ( i->element()->cinfo()->isA( "ReacBase" ) ) {
- childConcs.push_back( Field< double >::get( *i, "Kf" ) );
- childConcs.push_back( Field< double >::get( *i, "Kb" ) );
- } else if ( i->element()->cinfo()->isA( "EnzBase" ) ) {
- childConcs.push_back( Field< double >::get( *i, "Km" ) );
- } else if ( i->element()->cinfo()->isA( "ChemCompt" ) ) {
- // Do NOT traverse into child ChemCompts, they look after their
- // own volumes.
- continue;
- }
- getChildConcs( i->eref(), childConcs );
- }
+ vector< Id > kids;
+ Neutral::children( e, kids );
+ for ( vector < Id >::iterator i = kids.begin(); i != kids.end(); ++i )
+ {
+ if ( i->element()->cinfo()->isA( "PoolBase" ) )
+ {
+ childConcs.push_back( Field< double >::get( *i, "conc" ) );
+ childConcs.push_back( Field< double >::get( *i, "concInit" ) );
+ }
+ else if ( i->element()->cinfo()->isA( "ReacBase" ) )
+ {
+ childConcs.push_back( Field< double >::get( *i, "Kf" ) );
+ childConcs.push_back( Field< double >::get( *i, "Kb" ) );
+ }
+ else if ( i->element()->cinfo()->isA( "EnzBase" ) )
+ {
+ childConcs.push_back( Field< double >::get( *i, "Km" ) );
+ }
+ else if ( i->element()->cinfo()->isA( "ChemCompt" ) )
+ {
+ // Do NOT traverse into child ChemCompts, they look after their
+ // own volumes.
+ continue;
+ }
+ getChildConcs( i->eref(), childConcs );
+ }
}
unsigned int ChemCompt::setChildConcs( const Eref& e,
- const vector< double >& conc, unsigned int start ) const
+ const vector< double >& conc, unsigned int start) const
{
- vector< Id > kids;
- Neutral::children( e, kids );
- for ( vector < Id >::iterator i = kids.begin(); i != kids.end(); ++i )
- {
- if ( i->element()->cinfo()->isA( "PoolBase" ) ) {
- Field< double >::set( *i, "conc", conc[ start++ ] );
- Field< double >::set( *i, "concInit", conc[start++] );
- } else if ( i->element()->cinfo()->isA( "ReacBase" ) ) {
- Field< double >::set( *i, "Kf", conc[ start++ ] );
- Field< double >::set( *i, "Kb", conc[ start++ ] );
- } else if ( i->element()->cinfo()->isA( "EnzBase" ) ) {
- Field< double >::set( *i, "Km", conc[ start++ ] );
- } else if ( i->element()->cinfo()->isA( "ChemCompt" ) ) {
- // Do NOT traverse into child ChemCompts, they look after their
- // own volumes.
- continue;
- }
- start = setChildConcs( i->eref(), conc, start );
- }
- return start;
+ vector< Id > kids;
+ Neutral::children( e, kids );
+ for ( vector < Id >::iterator i = kids.begin(); i != kids.end(); ++i )
+ {
+ if ( i->element()->cinfo()->isA( "PoolBase" ) )
+ {
+ Field< double >::set( *i, "conc", conc[ start++ ] );
+ Field< double >::set( *i, "concInit", conc[start++] );
+ }
+ else if ( i->element()->cinfo()->isA( "ReacBase" ) )
+ {
+ Field< double >::set( *i, "Kf", conc[ start++ ] );
+ Field< double >::set( *i, "Kb", conc[ start++ ] );
+ }
+ else if ( i->element()->cinfo()->isA( "EnzBase" ) )
+ {
+ Field< double >::set( *i, "Km", conc[ start++ ] );
+ }
+ else if ( i->element()->cinfo()->isA( "ChemCompt" ) )
+ {
+ // Do NOT traverse into child ChemCompts, they look after their
+ // own volumes.
+ continue;
+ }
+ start = setChildConcs( i->eref(), conc, start );
+ }
+ return start;
}
vector< double > ChemCompt::getVoxelVolume() const
{
- return this->vGetVoxelVolume();
+ return this->vGetVoxelVolume();
}
vector< double > ChemCompt::getVoxelMidpoint() const
{
- return this->vGetVoxelMidpoint();
+ return this->vGetVoxelMidpoint();
}
double ChemCompt::getOneVoxelVolume( const Eref& e, unsigned int dataIndex ) const
{
- return this->getMeshEntryVolume( dataIndex );
+ return this->getMeshEntryVolume( dataIndex );
}
-void ChemCompt::setOneVoxelVolume( const Eref& e, unsigned int dataIndex,
- double volume )
+void ChemCompt::setOneVoxelVolume( const Eref& e, unsigned int dataIndex, double volume )
{
- this->setMeshEntryVolume( dataIndex, volume );
+ this->setMeshEntryVolume( dataIndex, volume );
}
// A virtual function, meant to be overridden.
void ChemCompt::setMeshEntryVolume( unsigned int dataIndex, double volume )
{
- cout << "Warning: ChemCompt::setMeshEntryVolume: Undefined except for PSD and spine mesh.\n";
+ cout << "Warning: ChemCompt::setMeshEntryVolume: Undefined except for PSD and spine mesh.\n";
}
unsigned int ChemCompt::getDimensions() const
{
- return this->innerGetDimensions();
+ return this->innerGetDimensions();
}
vector< double > ChemCompt::getStencilRate( unsigned int row ) const
{
- return this->innerGetStencilRate( row );
+ return this->innerGetStencilRate( row );
}
vector< unsigned int > ChemCompt::getStencilIndex( unsigned int row ) const
{
- return this->getNeighbors( row );
+ return this->getNeighbors( row );
}
bool ChemCompt::getIsMembraneBound() const
{
- return isMembraneBound_;
+ return isMembraneBound_;
}
void ChemCompt::setIsMembraneBound( bool v )
{
- isMembraneBound_ = v;
+ isMembraneBound_ = v;
}
@@ -369,7 +388,7 @@ void ChemCompt::setIsMembraneBound( bool v )
void ChemCompt::setVolumeNotRates( double volume )
{
- vSetVolumeNotRates( volume ); // Pass on to derived classes.
+ vSetVolumeNotRates( volume ); // Pass on to derived classes.
}
//////////////////////////////////////////////////////////////
@@ -378,18 +397,18 @@ void ChemCompt::setVolumeNotRates( double volume )
MeshEntry* ChemCompt::lookupEntry( unsigned int index )
{
- return &entry_;
+ return &entry_;
}
void ChemCompt::setNumEntries( unsigned int num )
{
- this->innerSetNumEntries( num );
- // cout << "Warning: ChemCompt::setNumEntries: No effect. Use subclass-specific functions\nto build or resize mesh.\n";
+ this->innerSetNumEntries( num );
+ // cout << "Warning: ChemCompt::setNumEntries: No effect. Use subclass-specific functions\nto build or resize mesh.\n";
}
unsigned int ChemCompt::getNumEntries() const
{
- return this->innerGetNumEntries();
+ return this->innerGetNumEntries();
}
@@ -399,21 +418,22 @@ unsigned int ChemCompt::getNumEntries() const
//////////////////////////////////////////////////////////////
void ChemCompt::buildJunction( ChemCompt* other, vector< VoxelJunction >& ret)
{
- matchMeshEntries( other, ret );
- extendStencil( other, ret );
+ matchMeshEntries( other, ret );
+ extendStencil( other, ret );
}
void ChemCompt::flipRet( vector< VoxelJunction >& ret ) const
{
- vector< VoxelJunction >::iterator i;
- for ( i = ret.begin(); i != ret.end(); ++i ) {
- unsigned int temp = i->first;
- i->first = i->second;
- i->second = temp;
- double vol = i->firstVol;
- i->firstVol = i->secondVol;
- i->secondVol = vol;
- }
+ vector< VoxelJunction >::iterator i;
+ for ( i = ret.begin(); i != ret.end(); ++i )
+ {
+ unsigned int temp = i->first;
+ i->first = i->second;
+ i->second = temp;
+ double vol = i->firstVol;
+ i->firstVol = i->secondVol;
+ i->secondVol = vol;
+ }
}
////////////////////////////////////////////////////////////////////////
@@ -421,5 +441,5 @@ void ChemCompt::flipRet( vector< VoxelJunction >& ret ) const
double ChemCompt::distance( double x, double y, double z )
{
- return sqrt( x * x + y * y + z * z );
+ return sqrt(x*x + y*y + z*z);
}
diff --git a/moose-core/mesh/CubeMesh.cpp b/moose-core/mesh/CubeMesh.cpp
index d50507437ff4d32d50aea6d83d4d48efeb67c3de..3d19d32be2abc7ccc3e5eb116b5c508ae007c919 100644
--- a/moose-core/mesh/CubeMesh.cpp
+++ b/moose-core/mesh/CubeMesh.cpp
@@ -30,223 +30,224 @@ typedef pair< unsigned int, unsigned int > PII;
const Cinfo* CubeMesh::initCinfo()
{
- //////////////////////////////////////////////////////////////
- // Field Definitions
- //////////////////////////////////////////////////////////////
- static ValueFinfo< CubeMesh, double > x0(
- "x0",
- "X coord of one end",
- &CubeMesh::setX0,
- &CubeMesh::getX0
- );
- static ValueFinfo< CubeMesh, double > y0(
- "y0",
- "Y coord of one end",
- &CubeMesh::setY0,
- &CubeMesh::getY0
- );
- static ValueFinfo< CubeMesh, double > z0(
- "z0",
- "Z coord of one end",
- &CubeMesh::setZ0,
- &CubeMesh::getZ0
- );
- static ValueFinfo< CubeMesh, double > x1(
- "x1",
- "X coord of other end",
- &CubeMesh::setX1,
- &CubeMesh::getX1
- );
- static ValueFinfo< CubeMesh, double > y1(
- "y1",
- "Y coord of other end",
- &CubeMesh::setY1,
- &CubeMesh::getY1
- );
- static ValueFinfo< CubeMesh, double > z1(
- "z1",
- "Z coord of other end",
- &CubeMesh::setZ1,
- &CubeMesh::getZ1
- );
-
- static ValueFinfo< CubeMesh, double > dx(
- "dx",
- "X size for mesh",
- &CubeMesh::setDx,
- &CubeMesh::getDx
- );
- static ValueFinfo< CubeMesh, double > dy(
- "dy",
- "Y size for mesh",
- &CubeMesh::setDy,
- &CubeMesh::getDy
- );
- static ValueFinfo< CubeMesh, double > dz(
- "dz",
- "Z size for mesh",
- &CubeMesh::setDz,
- &CubeMesh::getDz
- );
-
- static ValueFinfo< CubeMesh, unsigned int > nx(
- "nx",
- "Number of subdivisions in mesh in X",
- &CubeMesh::setNx,
- &CubeMesh::getNx
- );
- static ValueFinfo< CubeMesh, unsigned int > ny(
- "ny",
- "Number of subdivisions in mesh in Y",
- &CubeMesh::setNy,
- &CubeMesh::getNy
- );
- static ValueFinfo< CubeMesh, unsigned int > nz(
- "nz",
- "Number of subdivisions in mesh in Z",
- &CubeMesh::setNz,
- &CubeMesh::getNz
- );
-
- static ValueFinfo< CubeMesh, bool > isToroid(
- "isToroid",
- "Flag. True when the mesh should be toroidal, that is,"
- "when going beyond the right face brings us around to the"
- "left-most mesh entry, and so on. If we have nx, ny, nz"
- "entries, this rule means that the coordinate (x, ny, z)"
- "will map onto (x, 0, z). Similarly,"
- "(-1, y, z) -> (nx-1, y, z)"
- "Default is false",
- &CubeMesh::setIsToroid,
- &CubeMesh::getIsToroid
- );
-
- static ValueFinfo< CubeMesh, bool > preserveNumEntries(
- "preserveNumEntries",
- "Flag. When it is true, the numbers nx, ny, nz remain"
- "unchanged when x0, x1, y0, y1, z0, z1 are altered. Thus"
- "dx, dy, dz would change instead. When it is false, then"
- "dx, dy, dz remain the same and nx, ny, nz are altered."
- "Default is true",
- &CubeMesh::setPreserveNumEntries,
- &CubeMesh::getPreserveNumEntries
- );
-
- static ValueFinfo< CubeMesh, bool > alwaysDiffuse(
- "alwaysDiffuse",
- "Flag. When it is true, the mesh matches up sequential "
- "mesh entries for diffusion and chmestry. This is regardless "
- "of spatial location, and is guaranteed to set up at least "
- "the home reaction system"
- "Default is false",
- &CubeMesh::setAlwaysDiffuse,
- &CubeMesh::getAlwaysDiffuse
- );
-
- static ElementValueFinfo< CubeMesh, vector< double > > coords(
- "coords",
- "Set all the coords of the cuboid at once. Order is:"
- "x0 y0 z0 x1 y1 z1 dx dy dz"
- "When this is done, it recalculates the numEntries since "
- "dx, dy and dz are given explicitly."
- "As a special hack, you can leave out dx, dy and dz and use "
- "a vector of size 6. In this case the operation assumes that "
- "nx, ny and nz are to be preserved and dx, dy and dz will "
- "be recalculated. ",
- &CubeMesh::setCoords,
- &CubeMesh::getCoords
- );
-
- static ValueFinfo< CubeMesh, vector< unsigned int > > meshToSpace(
- "meshToSpace",
- "Array in which each mesh entry stores spatial (cubic) index",
- &CubeMesh::setMeshToSpace,
- &CubeMesh::getMeshToSpace
- );
-
- static ValueFinfo< CubeMesh, vector< unsigned int > > spaceToMesh(
- "spaceToMesh",
- "Array in which each space index (obtained by linearizing "
- "the xyz coords) specifies which meshIndex is present."
- "In many cases the index will store the EMPTY flag if there is"
- "no mesh entry at that spatial location",
- &CubeMesh::setSpaceToMesh,
- &CubeMesh::getSpaceToMesh
- );
-
- static ValueFinfo< CubeMesh, vector< unsigned int > > surface(
- "surface",
- "Array specifying surface of arbitrary volume within the "
- "CubeMesh. All entries must fall within the cuboid. "
- "Each entry of the array is a spatial index obtained by "
- "linearizing the ix, iy, iz coordinates within the cuboid. "
- "So, each entry == ( iz * ny + iy ) * nx + ix"
- "Note that the voxels listed on the surface are WITHIN the "
- "volume of the CubeMesh object",
- &CubeMesh::setSurface,
- &CubeMesh::getSurface
- );
-
- //////////////////////////////////////////////////////////////
- // MsgDest Definitions
- //////////////////////////////////////////////////////////////
-
- static DestFinfo buildMesh( "buildMesh",
- "Build cubical mesh for geom surface specified by Id, using"
- "specified x y z coords as an inside point in mesh",
- new OpFunc4< CubeMesh, Id, double, double, double >(
- &CubeMesh::buildMesh )
- );
-
- //////////////////////////////////////////////////////////////
- // Field Elements
- //////////////////////////////////////////////////////////////
-
- static Finfo* cubeMeshFinfos[] = {
- &isToroid, // Value
- &preserveNumEntries, // Value
- &alwaysDiffuse, // Value
- &x0, // Value
- &y0, // Value
- &z0, // Value
- &x1, // Value
- &y1, // Value
- &z1, // Value
- &dx, // Value
- &dy, // Value
- &dz, // Value
- &nx, // Value
- &ny, // Value
- &nz, // Value
- &coords, // Value
- &meshToSpace, // Value
- &spaceToMesh, // Value
- &surface, // Value
- };
-
- static string doc[] =
- {
- "Name", "CubeMesh",
- "Author", "Upi Bhalla",
- "Description", "Chemical compartment with cuboid grid. "
- "Defaults to a cube of size 10 microns, with mesh size "
- "also 10 microns, so that there is just 1 cubic voxel. "
- "These defaults are similar to that of a typical cell. "
- "Can be configured to have different x,y,z dimensions and "
- "also different dx,dy,dz voxel sizes. ",
- };
- static Dinfo< CubeMesh > dinfo;
- static Cinfo cubeMeshCinfo (
- "CubeMesh",
- ChemCompt::initCinfo(),
- cubeMeshFinfos,
- sizeof( cubeMeshFinfos ) / sizeof ( Finfo* ),
- &dinfo,
- doc,
+ //////////////////////////////////////////////////////////////
+ // Field Definitions
+ //////////////////////////////////////////////////////////////
+ static ValueFinfo< CubeMesh, double > x0(
+ "x0",
+ "X coord of one end",
+ &CubeMesh::setX0,
+ &CubeMesh::getX0
+ );
+ static ValueFinfo< CubeMesh, double > y0(
+ "y0",
+ "Y coord of one end",
+ &CubeMesh::setY0,
+ &CubeMesh::getY0
+ );
+ static ValueFinfo< CubeMesh, double > z0(
+ "z0",
+ "Z coord of one end",
+ &CubeMesh::setZ0,
+ &CubeMesh::getZ0
+ );
+ static ValueFinfo< CubeMesh, double > x1(
+ "x1",
+ "X coord of other end",
+ &CubeMesh::setX1,
+ &CubeMesh::getX1
+ );
+ static ValueFinfo< CubeMesh, double > y1(
+ "y1",
+ "Y coord of other end",
+ &CubeMesh::setY1,
+ &CubeMesh::getY1
+ );
+ static ValueFinfo< CubeMesh, double > z1(
+ "z1",
+ "Z coord of other end",
+ &CubeMesh::setZ1,
+ &CubeMesh::getZ1
+ );
+
+ static ValueFinfo< CubeMesh, double > dx(
+ "dx",
+ "X size for mesh",
+ &CubeMesh::setDx,
+ &CubeMesh::getDx
+ );
+ static ValueFinfo< CubeMesh, double > dy(
+ "dy",
+ "Y size for mesh",
+ &CubeMesh::setDy,
+ &CubeMesh::getDy
+ );
+ static ValueFinfo< CubeMesh, double > dz(
+ "dz",
+ "Z size for mesh",
+ &CubeMesh::setDz,
+ &CubeMesh::getDz
+ );
+
+ static ValueFinfo< CubeMesh, unsigned int > nx(
+ "nx",
+ "Number of subdivisions in mesh in X",
+ &CubeMesh::setNx,
+ &CubeMesh::getNx
+ );
+ static ValueFinfo< CubeMesh, unsigned int > ny(
+ "ny",
+ "Number of subdivisions in mesh in Y",
+ &CubeMesh::setNy,
+ &CubeMesh::getNy
+ );
+ static ValueFinfo< CubeMesh, unsigned int > nz(
+ "nz",
+ "Number of subdivisions in mesh in Z",
+ &CubeMesh::setNz,
+ &CubeMesh::getNz
+ );
+
+ static ValueFinfo< CubeMesh, bool > isToroid(
+ "isToroid",
+ "Flag. True when the mesh should be toroidal, that is,"
+ "when going beyond the right face brings us around to the"
+ "left-most mesh entry, and so on. If we have nx, ny, nz"
+ "entries, this rule means that the coordinate (x, ny, z)"
+ "will map onto (x, 0, z). Similarly,"
+ "(-1, y, z) -> (nx-1, y, z)"
+ "Default is false",
+ &CubeMesh::setIsToroid,
+ &CubeMesh::getIsToroid
+ );
+
+ static ValueFinfo< CubeMesh, bool > preserveNumEntries(
+ "preserveNumEntries",
+ "Flag. When it is true, the numbers nx, ny, nz remain"
+ "unchanged when x0, x1, y0, y1, z0, z1 are altered. Thus"
+ "dx, dy, dz would change instead. When it is false, then"
+ "dx, dy, dz remain the same and nx, ny, nz are altered."
+ "Default is true",
+ &CubeMesh::setPreserveNumEntries,
+ &CubeMesh::getPreserveNumEntries
+ );
+
+ static ValueFinfo< CubeMesh, bool > alwaysDiffuse(
+ "alwaysDiffuse",
+ "Flag. When it is true, the mesh matches up sequential "
+ "mesh entries for diffusion and chmestry. This is regardless "
+ "of spatial location, and is guaranteed to set up at least "
+ "the home reaction system"
+ "Default is false",
+ &CubeMesh::setAlwaysDiffuse,
+ &CubeMesh::getAlwaysDiffuse
+ );
+
+ static ElementValueFinfo< CubeMesh, vector< double > > coords(
+ "coords",
+ "Set all the coords of the cuboid at once. Order is:"
+ "x0 y0 z0 x1 y1 z1 dx dy dz"
+ "When this is done, it recalculates the numEntries since "
+ "dx, dy and dz are given explicitly."
+ "As a special hack, you can leave out dx, dy and dz and use "
+ "a vector of size 6. In this case the operation assumes that "
+ "nx, ny and nz are to be preserved and dx, dy and dz will "
+ "be recalculated. ",
+ &CubeMesh::setCoords,
+ &CubeMesh::getCoords
+ );
+
+ static ValueFinfo< CubeMesh, vector< unsigned int > > meshToSpace(
+ "meshToSpace",
+ "Array in which each mesh entry stores spatial (cubic) index",
+ &CubeMesh::setMeshToSpace,
+ &CubeMesh::getMeshToSpace
+ );
+
+ static ValueFinfo< CubeMesh, vector< unsigned int > > spaceToMesh(
+ "spaceToMesh",
+ "Array in which each space index (obtained by linearizing "
+ "the xyz coords) specifies which meshIndex is present."
+ "In many cases the index will store the EMPTY flag if there is"
+ "no mesh entry at that spatial location",
+ &CubeMesh::setSpaceToMesh,
+ &CubeMesh::getSpaceToMesh
+ );
+
+ static ValueFinfo< CubeMesh, vector< unsigned int > > surface(
+ "surface",
+ "Array specifying surface of arbitrary volume within the "
+ "CubeMesh. All entries must fall within the cuboid. "
+ "Each entry of the array is a spatial index obtained by "
+ "linearizing the ix, iy, iz coordinates within the cuboid. "
+ "So, each entry == ( iz * ny + iy ) * nx + ix"
+ "Note that the voxels listed on the surface are WITHIN the "
+ "volume of the CubeMesh object",
+ &CubeMesh::setSurface,
+ &CubeMesh::getSurface
+ );
+
+ //////////////////////////////////////////////////////////////
+ // MsgDest Definitions
+ //////////////////////////////////////////////////////////////
+
+ static DestFinfo buildMesh( "buildMesh",
+ "Build cubical mesh for geom surface specified by Id, using"
+ "specified x y z coords as an inside point in mesh",
+ new OpFunc4< CubeMesh, Id, double, double, double >(
+ &CubeMesh::buildMesh )
+ );
+
+ //////////////////////////////////////////////////////////////
+ // Field Elements
+ //////////////////////////////////////////////////////////////
+
+ static Finfo* cubeMeshFinfos[] =
+ {
+ &isToroid, // Value
+ &preserveNumEntries, // Value
+ &alwaysDiffuse, // Value
+ &x0, // Value
+ &y0, // Value
+ &z0, // Value
+ &x1, // Value
+ &y1, // Value
+ &z1, // Value
+ &dx, // Value
+ &dy, // Value
+ &dz, // Value
+ &nx, // Value
+ &ny, // Value
+ &nz, // Value
+ &coords, // Value
+ &meshToSpace, // Value
+ &spaceToMesh, // Value
+ &surface, // Value
+ };
+
+ static string doc[] =
+ {
+ "Name", "CubeMesh",
+ "Author", "Upi Bhalla",
+ "Description", "Chemical compartment with cuboid grid. "
+ "Defaults to a cube of size 10 microns, with mesh size "
+ "also 10 microns, so that there is just 1 cubic voxel. "
+ "These defaults are similar to that of a typical cell. "
+ "Can be configured to have different x,y,z dimensions and "
+ "also different dx,dy,dz voxel sizes. ",
+ };
+ static Dinfo< CubeMesh > dinfo;
+ static Cinfo cubeMeshCinfo (
+ "CubeMesh",
+ ChemCompt::initCinfo(),
+ cubeMeshFinfos,
+ sizeof( cubeMeshFinfos ) / sizeof ( Finfo* ),
+ &dinfo,
+ doc,
sizeof(doc)/sizeof(string)
- );
+ );
- return &cubeMeshCinfo;
+ return &cubeMeshCinfo;
}
//////////////////////////////////////////////////////////////
@@ -259,31 +260,31 @@ static const Cinfo* cubeMeshCinfo = CubeMesh::initCinfo();
// Class stuff.
//////////////////////////////////////////////////////////////////
CubeMesh::CubeMesh()
- :
- isToroid_( 0 ),
- preserveNumEntries_( 1 ),
- alwaysDiffuse_( false ),
- x0_( 0.0 ),
- y0_( 0.0 ),
- z0_( 0.0 ),
- x1_( 10e-6 ),
- y1_( 10e-6 ),
- z1_( 10e-6 ),
- dx_( 10e-6 ),
- dy_( 10e-6 ),
- dz_( 10e-6 ),
- nx_( 1 ),
- ny_( 1 ),
- nz_( 1 ),
- m2s_( 1, 0 ),
- s2m_( 1, 0 )
-{
- updateCoords();
+ :
+ isToroid_( 0 ),
+ preserveNumEntries_( 1 ),
+ alwaysDiffuse_( false ),
+ x0_( 0.0 ),
+ y0_( 0.0 ),
+ z0_( 0.0 ),
+ x1_( 10e-6 ),
+ y1_( 10e-6 ),
+ z1_( 10e-6 ),
+ dx_( 10e-6 ),
+ dy_( 10e-6 ),
+ dz_( 10e-6 ),
+ nx_( 1 ),
+ ny_( 1 ),
+ nz_( 1 ),
+ m2s_( 1, 0 ),
+ s2m_( 1, 0 )
+{
+ updateCoords();
}
CubeMesh::~CubeMesh()
{
- ;
+ ;
}
//////////////////////////////////////////////////////////////////
@@ -293,86 +294,92 @@ CubeMesh::~CubeMesh()
// Swaps x0 and x1 if x0 > x1
void swapIfBackward( double& x0, double& x1 )
{
- if ( x0 > x1 ) {
- double temp = x0;
- x0 = x1;
- x1 = temp;
- }
+ if ( x0 > x1 )
+ {
+ double temp = x0;
+ x0 = x1;
+ x1 = temp;
+ }
}
void CubeMesh::fillTwoDimSurface()
{
- unsigned int size = nx_ * ny_ * nz_;
- if ( nx_ == 1 ) {
- for ( unsigned int j = 0; j < ny_; ++j )
- surface_.push_back( j );
- for ( unsigned int j = size - ny_; j < size; ++j )
- surface_.push_back( j );
- for ( unsigned int i = 1; i < nz_ - 1; ++i )
- surface_.push_back( i * ny_ );
- for ( unsigned int i = 1; i < nz_ - 1; ++i )
- surface_.push_back( ny_ - 1 + i * ny_ );
- } else if ( ny_ == 1 ) {
- for ( unsigned int k = 0; k < nx_; ++k )
- surface_.push_back( k );
- for ( unsigned int k = size - nx_; k < size; ++k )
- surface_.push_back( k );
- for ( unsigned int i = 1; i < nz_ - 1; ++i )
- surface_.push_back( i * nx_ );
- for ( unsigned int i = 1; i < nz_ - 1; ++i )
- surface_.push_back( nx_ - 1 + i * nx_ );
- } else if ( nz_ == 1 ) {
- for ( unsigned int k = 0; k < nx_; ++k )
- surface_.push_back( k );
- for ( unsigned int k = size - nx_; k < size; ++k )
- surface_.push_back( k );
- for ( unsigned int j = 1; j < ny_ - 1; ++j )
- surface_.push_back( j * nx_ );
- for ( unsigned int j = 1; j < ny_ - 1; ++j )
- surface_.push_back( j * nx_ + nx_ - 1 );
- }
- // Ah, C++ STL. Look on my works, ye mighty, and despair.
- sort( surface_.begin(), surface_.end() );
- surface_.erase( unique( surface_.begin(), surface_.end() ),
- surface_.end() );
+ unsigned int size = nx_ * ny_ * nz_;
+ if ( nx_ == 1 )
+ {
+ for ( unsigned int j = 0; j < ny_; ++j )
+ surface_.push_back( j );
+ for ( unsigned int j = size - ny_; j < size; ++j )
+ surface_.push_back( j );
+ for ( unsigned int i = 1; i < nz_ - 1; ++i )
+ surface_.push_back( i * ny_ );
+ for ( unsigned int i = 1; i < nz_ - 1; ++i )
+ surface_.push_back( ny_ - 1 + i * ny_ );
+ }
+ else if ( ny_ == 1 )
+ {
+ for ( unsigned int k = 0; k < nx_; ++k )
+ surface_.push_back( k );
+ for ( unsigned int k = size - nx_; k < size; ++k )
+ surface_.push_back( k );
+ for ( unsigned int i = 1; i < nz_ - 1; ++i )
+ surface_.push_back( i * nx_ );
+ for ( unsigned int i = 1; i < nz_ - 1; ++i )
+ surface_.push_back( nx_ - 1 + i * nx_ );
+ }
+ else if ( nz_ == 1 )
+ {
+ for ( unsigned int k = 0; k < nx_; ++k )
+ surface_.push_back( k );
+ for ( unsigned int k = size - nx_; k < size; ++k )
+ surface_.push_back( k );
+ for ( unsigned int j = 1; j < ny_ - 1; ++j )
+ surface_.push_back( j * nx_ );
+ for ( unsigned int j = 1; j < ny_ - 1; ++j )
+ surface_.push_back( j * nx_ + nx_ - 1 );
+ }
+ // Ah, C++ STL. Look on my works, ye mighty, and despair.
+ sort( surface_.begin(), surface_.end() );
+ surface_.erase( unique( surface_.begin(), surface_.end() ),
+ surface_.end() );
}
void CubeMesh::fillThreeDimSurface() // Need to fix duplicate points.
{
- unsigned int size = nx_ * ny_ * nz_;
- // z == 0 plane
- for ( unsigned int j = 0; j < ny_; ++j )
- for ( unsigned int k = 0; k < nx_; ++k )
- surface_.push_back( j * nx_ + k );
- // z == nz_-1 plane
- unsigned int offset = size - nx_ * ny_;
- for ( unsigned int j = 0; j < ny_; ++j )
- for ( unsigned int k = 0; k < nx_; ++k )
- surface_.push_back( offset + j * nx_ + k );
-
- // y == 0 plane
- for ( unsigned int i = 0; i < nz_; ++i )
- for ( unsigned int k = 0; k < nx_; ++k )
- surface_.push_back( i * nx_ * ny_ + k );
- // y == ny_-1 plane
- offset = nx_ * ( ny_ - 1 );
- for ( unsigned int i = 0; i < nz_; ++i )
- for ( unsigned int k = 0; k < nx_; ++k )
- surface_.push_back( offset + i * nx_ * ny_ + k );
-
- // x == 0 plane
- for ( unsigned int i = 0; i < nz_; ++i )
- for ( unsigned int j = 0; j < ny_; ++j )
- surface_.push_back( ( i * ny_ + j ) * nx_ );
- // x == nx_-1 plane
- offset = nx_ - 1;
- for ( unsigned int i = 0; i < nz_; ++i )
- for ( unsigned int j = 0; j < ny_; ++j )
- surface_.push_back( offset + ( i * ny_ + j ) * nx_ );
-
- sort( surface_.begin(), surface_.end() );
- surface_.erase( unique( surface_.begin(), surface_.end() ),
- surface_.end() );
+ unsigned int size = nx_ * ny_ * nz_;
+ // z == 0 plane
+ for ( unsigned int j = 0; j < ny_; ++j )
+ for ( unsigned int k = 0; k < nx_; ++k )
+ surface_.push_back( j * nx_ + k );
+ // z == nz_-1 plane
+ unsigned int offset = size - nx_ * ny_;
+ for ( unsigned int j = 0; j < ny_; ++j )
+ for ( unsigned int k = 0; k < nx_; ++k )
+ surface_.push_back( offset + j * nx_ + k );
+
+ // y == 0 plane
+ for ( unsigned int i = 0; i < nz_; ++i )
+ for ( unsigned int k = 0; k < nx_; ++k )
+ surface_.push_back( i * nx_ * ny_ + k );
+ // y == ny_-1 plane
+ offset = nx_ * ( ny_ - 1 );
+ for ( unsigned int i = 0; i < nz_; ++i )
+ for ( unsigned int k = 0; k < nx_; ++k )
+ surface_.push_back( offset + i * nx_ * ny_ + k );
+
+ // x == 0 plane
+ for ( unsigned int i = 0; i < nz_; ++i )
+ for ( unsigned int j = 0; j < ny_; ++j )
+ surface_.push_back( ( i * ny_ + j ) * nx_ );
+ // x == nx_-1 plane
+ offset = nx_ - 1;
+ for ( unsigned int i = 0; i < nz_; ++i )
+ for ( unsigned int j = 0; j < ny_; ++j )
+ surface_.push_back( offset + ( i * ny_ + j ) * nx_ );
+
+ sort( surface_.begin(), surface_.end() );
+ surface_.erase( unique( surface_.begin(), surface_.end() ),
+ surface_.end() );
}
/**
@@ -383,310 +390,317 @@ void CubeMesh::fillThreeDimSurface() // Need to fix duplicate points.
*/
void CubeMesh::updateCoords()
{
- swapIfBackward( x0_, x1_ );
- swapIfBackward( y0_, y1_ );
- swapIfBackward( z0_, z1_ );
- if ( preserveNumEntries_ ) {
- dx_ = ( x1_ - x0_ ) / nx_;
- dy_ = ( y1_ - y0_ ) / ny_;
- dz_ = ( z1_ - z0_ ) / nz_;
- } else {
- nx_ = round( (x1_ - x0_) / dx_ );
- ny_ = round( (y1_ - y0_) / dy_ );
- nz_ = round( (z1_ - z0_) / dz_ );
-
- if ( nx_ == 0 ) nx_ = 1;
- if ( ny_ == 0 ) ny_ = 1;
- if ( nz_ == 0 ) nz_ = 1;
- }
-
- /// Temporarily fill out the whole cube for m2s and s2m. These
- // will change for none-cube geometries.
- unsigned int size = nx_ * ny_ * nz_;
- m2s_.resize( size );
- s2m_.resize( size );
- for ( unsigned int i = 0; i < size; ++i ) {
- m2s_[i] = s2m_[i] = i;
- }
-
- // Fill out surface vector
- surface_.resize( 0 );
- /*
- if ( numDims() == 0 ) {
- surface_.push_back( 0 );
- } else if ( numDims() == 1 ) {
- surface_.push_back( 0 );
- if ( size > 1 )
- surface_.push_back( size - 1 );
- } else if ( numDims() == 2 ) {
- fillTwoDimSurface();
- } else if ( numDims() == 3 ) {
- fillThreeDimSurface();
- }
- */
- fillThreeDimSurface();
-
- // volume_ = ( x1_ - x0_ ) * ( y1_ - y0_ ) * ( z1_ - z0_ );
- assert( size >= 0 );
-
- buildStencil();
+ swapIfBackward( x0_, x1_ );
+ swapIfBackward( y0_, y1_ );
+ swapIfBackward( z0_, z1_ );
+ if ( preserveNumEntries_ )
+ {
+ dx_ = ( x1_ - x0_ ) / nx_;
+ dy_ = ( y1_ - y0_ ) / ny_;
+ dz_ = ( z1_ - z0_ ) / nz_;
+ }
+ else
+ {
+ nx_ = round( (x1_ - x0_) / dx_ );
+ ny_ = round( (y1_ - y0_) / dy_ );
+ nz_ = round( (z1_ - z0_) / dz_ );
+
+ if ( nx_ == 0 ) nx_ = 1;
+ if ( ny_ == 0 ) ny_ = 1;
+ if ( nz_ == 0 ) nz_ = 1;
+ }
+
+ /// Temporarily fill out the whole cube for m2s and s2m. These
+ // will change for none-cube geometries.
+ unsigned int size = nx_ * ny_ * nz_;
+ m2s_.resize( size );
+ s2m_.resize( size );
+ for ( unsigned int i = 0; i < size; ++i )
+ {
+ m2s_[i] = s2m_[i] = i;
+ }
+
+ // Fill out surface vector
+ surface_.resize( 0 );
+ /*
+ if ( numDims() == 0 ) {
+ surface_.push_back( 0 );
+ } else if ( numDims() == 1 ) {
+ surface_.push_back( 0 );
+ if ( size > 1 )
+ surface_.push_back( size - 1 );
+ } else if ( numDims() == 2 ) {
+ fillTwoDimSurface();
+ } else if ( numDims() == 3 ) {
+ fillThreeDimSurface();
+ }
+ */
+ fillThreeDimSurface();
+
+ // volume_ = ( x1_ - x0_ ) * ( y1_ - y0_ ) * ( z1_ - z0_ );
+ assert( size >= 0 );
+
+ buildStencil();
}
void CubeMesh::setX0( double v )
{
- x0_ = v;
- updateCoords();
+ x0_ = v;
+ updateCoords();
}
double CubeMesh::getX0() const
{
- return x0_;
+ return x0_;
}
void CubeMesh::setY0( double v )
{
- y0_ = v;
- updateCoords();
+ y0_ = v;
+ updateCoords();
}
double CubeMesh::getY0() const
{
- return y0_;
+ return y0_;
}
void CubeMesh::setZ0( double v )
{
- z0_ = v;
- updateCoords();
+ z0_ = v;
+ updateCoords();
}
double CubeMesh::getZ0() const
{
- return z0_;
+ return z0_;
}
void CubeMesh::setX1( double v )
{
- x1_ = v;
- updateCoords();
+ x1_ = v;
+ updateCoords();
}
double CubeMesh::getX1() const
{
- return x1_;
+ return x1_;
}
void CubeMesh::setY1( double v )
{
- y1_ = v;
- updateCoords();
+ y1_ = v;
+ updateCoords();
}
double CubeMesh::getY1() const
{
- return y1_;
+ return y1_;
}
void CubeMesh::setZ1( double v )
{
- z1_ = v;
- updateCoords();
+ z1_ = v;
+ updateCoords();
}
double CubeMesh::getZ1() const
{
- return z1_;
+ return z1_;
}
void CubeMesh::setDx( double v )
{
- dx_ = v;
- updateCoords();
+ dx_ = v;
+ updateCoords();
}
double CubeMesh::getDx() const
{
- return dx_;
+ return dx_;
}
void CubeMesh::setDy( double v )
{
- dy_ = v;
- updateCoords();
+ dy_ = v;
+ updateCoords();
}
double CubeMesh::getDy() const
{
- return dy_;
+ return dy_;
}
void CubeMesh::setDz( double v )
{
- dz_ = v;
- updateCoords();
+ dz_ = v;
+ updateCoords();
}
double CubeMesh::getDz() const
{
- return dz_;
+ return dz_;
}
void CubeMesh::setNx( unsigned int v )
{
- nx_ = v;
- updateCoords();
+ nx_ = v;
+ updateCoords();
}
unsigned int CubeMesh::getNx() const
{
- return nx_;
+ return nx_;
}
void CubeMesh::setNy( unsigned int v )
{
- ny_ = v;
- updateCoords();
+ ny_ = v;
+ updateCoords();
}
unsigned int CubeMesh::getNy() const
{
- return ny_;
+ return ny_;
}
void CubeMesh::setNz( unsigned int v )
{
- nz_ = v;
- updateCoords();
+ nz_ = v;
+ updateCoords();
}
unsigned int CubeMesh::getNz() const
{
- return nz_;
+ return nz_;
}
void CubeMesh::setIsToroid( bool v )
{
- isToroid_ = v;
+ isToroid_ = v;
}
bool CubeMesh::getIsToroid() const
{
- return isToroid_;
+ return isToroid_;
}
void CubeMesh::setPreserveNumEntries( bool v )
{
- preserveNumEntries_ = v;
+ preserveNumEntries_ = v;
}
bool CubeMesh::getPreserveNumEntries() const
{
- return preserveNumEntries_;
+ return preserveNumEntries_;
}
void CubeMesh::setAlwaysDiffuse( bool v )
{
- alwaysDiffuse_ = v;
+ alwaysDiffuse_ = v;
}
bool CubeMesh::getAlwaysDiffuse() const
{
- // alwaysDiffuse is normally false.
- return alwaysDiffuse_;
+ // alwaysDiffuse is normally false.
+ return alwaysDiffuse_;
}
void CubeMesh::innerSetCoords( const vector< double >& v)
{
- if ( v.size() < 6 )
- return;
+ if ( v.size() < 6 )
+ return;
- x0_ = v[0];
- y0_ = v[1];
- z0_ = v[2];
+ x0_ = v[0];
+ y0_ = v[1];
+ z0_ = v[2];
- x1_ = v[3];
- y1_ = v[4];
- z1_ = v[5];
+ x1_ = v[3];
+ y1_ = v[4];
+ z1_ = v[5];
- bool temp = preserveNumEntries_;
- if ( v.size() >= 9 ) {
- dx_ = v[6];
- dy_ = v[7];
- dz_ = v[8];
- preserveNumEntries_ = 0;
- } else {
- preserveNumEntries_ = 1;
- }
- updateCoords();
- preserveNumEntries_ = temp;
+ bool temp = preserveNumEntries_;
+ if ( v.size() >= 9 )
+ {
+ dx_ = v[6];
+ dy_ = v[7];
+ dz_ = v[8];
+ preserveNumEntries_ = 0;
+ }
+ else
+ {
+ preserveNumEntries_ = 1;
+ }
+ updateCoords();
+ preserveNumEntries_ = temp;
}
void CubeMesh::setCoords( const Eref& e, vector< double > v)
{
- // double oldVol = getMeshEntryVolume( 0 );
- innerSetCoords( v );
- ChemCompt::voxelVolOut()->send( e, vGetVoxelVolume() );
+ // double oldVol = getMeshEntryVolume( 0 );
+ innerSetCoords( v );
+ ChemCompt::voxelVolOut()->send( e, vGetVoxelVolume() );
}
vector< double > CubeMesh::getCoords( const Eref& e ) const
{
- vector< double > ret( 9 );
+ vector< double > ret( 9 );
- ret[0] = x0_;
- ret[1] = y0_;
- ret[2] = z0_;
+ ret[0] = x0_;
+ ret[1] = y0_;
+ ret[2] = z0_;
- ret[3] = x1_;
- ret[4] = y1_;
- ret[5] = z1_;
+ ret[3] = x1_;
+ ret[4] = y1_;
+ ret[5] = z1_;
- ret[6] = dx_;
- ret[7] = dy_;
- ret[8] = dz_;
+ ret[6] = dx_;
+ ret[7] = dy_;
+ ret[8] = dz_;
- return ret;
+ return ret;
}
void CubeMesh::setMeshToSpace( vector< unsigned int > v )
{
- m2s_ = v;
- deriveS2mFromM2s();
+ m2s_ = v;
+ deriveS2mFromM2s();
}
vector< unsigned int > CubeMesh::getMeshToSpace() const
{
- return m2s_;
+ return m2s_;
}
void CubeMesh::setSpaceToMesh( vector< unsigned int > v )
{
- s2m_ = v;
- deriveM2sFromS2m();
+ s2m_ = v;
+ deriveM2sFromS2m();
}
vector< unsigned int > CubeMesh::getSpaceToMesh() const
{
- return s2m_;
+ return s2m_;
}
void CubeMesh::setSurface( vector< unsigned int > v )
{
- surface_ = v;
+ surface_ = v;
}
vector< unsigned int > CubeMesh::getSurface() const
{
- return surface_;
+ return surface_;
}
unsigned int CubeMesh::innerGetDimensions() const
{
- return 3;
+ return 3;
}
@@ -696,7 +710,7 @@ unsigned int CubeMesh::innerGetDimensions() const
void CubeMesh::buildMesh( Id geom, double x, double y, double z )
{
- ;
+ ;
}
/**
@@ -705,62 +719,65 @@ void CubeMesh::buildMesh( Id geom, double x, double y, double z )
* the nearest cube
*/
void CubeMesh::innerBuildDefaultMesh( const Eref& e,
- double volume, unsigned int numEntries )
-{
- double approxN = numEntries;
- approxN = pow( approxN, 1.0 / 3.0 );
- unsigned int smaller = floor( approxN );
- unsigned int bigger = ceil( approxN );
- unsigned int numSide;
- if ( smaller != bigger ) {
- numSide = smaller;
- } else {
- unsigned int smallerVol = smaller * smaller * smaller;
- unsigned int biggerVol = bigger * bigger * bigger;
- if ( numEntries - smallerVol < biggerVol - numEntries )
- numSide = smaller;
- else
- numSide = bigger;
- }
- double side = pow( volume, 1.0 / 3.0 );
- vector< double > coords( 9, side );
- coords[0] = coords[1] = coords[2] = 0;
- coords[6] = coords[7] = coords[8] = side / numSide;
- nx_ = ny_ = nz_ = numSide;
- setCoords( e, coords );
+ double volume, unsigned int numEntries )
+{
+ double approxN = numEntries;
+ approxN = pow( approxN, 1.0 / 3.0 );
+ unsigned int smaller = floor( approxN );
+ unsigned int bigger = ceil( approxN );
+ unsigned int numSide;
+ if ( smaller != bigger )
+ {
+ numSide = smaller;
+ }
+ else
+ {
+ unsigned int smallerVol = smaller * smaller * smaller;
+ unsigned int biggerVol = bigger * bigger * bigger;
+ if ( numEntries - smallerVol < biggerVol - numEntries )
+ numSide = smaller;
+ else
+ numSide = bigger;
+ }
+ double side = pow( volume, 1.0 / 3.0 );
+ vector< double > coords( 9, side );
+ coords[0] = coords[1] = coords[2] = 0;
+ coords[6] = coords[7] = coords[8] = side / numSide;
+ nx_ = ny_ = nz_ = numSide;
+ setCoords( e, coords );
}
/// More inherited virtual funcs: request comes in for mesh stats
void CubeMesh::innerHandleRequestMeshStats( const Eref& e,
- const SrcFinfo2< unsigned int, vector< double > >* meshStatsFinfo )
+ const SrcFinfo2< unsigned int, vector< double > >* meshStatsFinfo )
{
- vector< double > meshVolumes( 1, dx_ * dy_ * dz_ );
- meshStatsFinfo->send( e, nx_ * ny_ * nz_, meshVolumes);
+ vector< double > meshVolumes( 1, dx_ * dy_ * dz_ );
+ meshStatsFinfo->send( e, nx_ * ny_ * nz_, meshVolumes);
}
/// Generate node decomposition of mesh, send it out along
/// meshSplitFinfo msg
void CubeMesh::innerHandleNodeInfo(
- const Eref& e,
- unsigned int numNodes, unsigned int numThreads )
-{
- /*
- unsigned int numEntries = nx_ * ny_ * nz_ ;
- vector< double > vols( numEntries, dx_ * dy_ * dz_ );
- vector< unsigned int > localEntries( numEntries );
- vector< vector< unsigned int > > outgoingEntries;
- vector< vector< unsigned int > > incomingEntries;
- double oldvol = getMeshEntryVolume( 0 );
- meshSplit()->send( e,
- oldvol,
- vols, localEntries,
- outgoingEntries, incomingEntries );
- */
+ const Eref& e,
+ unsigned int numNodes, unsigned int numThreads )
+{
+ /*
+ unsigned int numEntries = nx_ * ny_ * nz_ ;
+ vector< double > vols( numEntries, dx_ * dy_ * dz_ );
+ vector< unsigned int > localEntries( numEntries );
+ vector< vector< unsigned int > > outgoingEntries;
+ vector< vector< unsigned int > > incomingEntries;
+ double oldvol = getMeshEntryVolume( 0 );
+ meshSplit()->send( e,
+ oldvol,
+ vols, localEntries,
+ outgoingEntries, incomingEntries );
+ */
}
double CubeMesh::vGetEntireVolume() const
{
- return fabs( (x1_ - x0_) * (y1_ - y0_) * (z1_ - z0_) );
+ return fabs( (x1_ - x0_) * (y1_ - y0_) * (z1_ - z0_) );
}
@@ -771,116 +788,117 @@ double CubeMesh::vGetEntireVolume() const
/// Virtual function to return MeshType of specified entry.
unsigned int CubeMesh::getMeshType( unsigned int fid ) const
{
- return CUBOID;
+ return CUBOID;
}
/// Virtual function to return dimensions of specified entry.
unsigned int CubeMesh::getMeshDimensions( unsigned int fid ) const
{
- return 3;
+ return 3;
}
/// Virtual function to return volume of mesh Entry.
double CubeMesh::getMeshEntryVolume( unsigned int fid ) const
{
- return dx_ * dy_ * dz_;
+ return dx_ * dy_ * dz_;
}
/// Virtual function to return volume of mesh Entry, including
// for diffusively coupled voxels from other solvers.
double CubeMesh::extendedMeshEntryVolume( unsigned int fid ) const
{
- if ( fid >= m2s_.size() ) {
- return MeshCompt::extendedMeshEntryVolume( fid - m2s_.size() );
- }
- return dx_ * dy_ * dz_;
+ if ( fid >= m2s_.size() )
+ {
+ return MeshCompt::extendedMeshEntryVolume( fid - m2s_.size() );
+ }
+ return dx_ * dy_ * dz_;
}
/// Virtual function to return coords of mesh Entry.
/// For Cuboid mesh, coords are x1y1z1 x2y2z2
vector< double > CubeMesh::getCoordinates( unsigned int fid ) const
{
- assert( fid < m2s_.size() );
- unsigned int spaceIndex = m2s_[fid];
+ assert( fid < m2s_.size() );
+ unsigned int spaceIndex = m2s_[fid];
- unsigned int ix = spaceIndex % nx_;
- unsigned int iy = (spaceIndex / nx_) % ny_;
- unsigned int iz = (spaceIndex / ( nx_ * ny_ )) % nz_;
+ unsigned int ix = spaceIndex % nx_;
+ unsigned int iy = (spaceIndex / nx_) % ny_;
+ unsigned int iz = (spaceIndex / ( nx_ * ny_ )) % nz_;
- vector< double > ret( 6 );
- ret[0] = x0_ + ix * dx_;
- ret[1] = y0_ + iy * dy_;
- ret[2] = z0_ + iz * dz_;
+ vector< double > ret( 6 );
+ ret[0] = x0_ + ix * dx_;
+ ret[1] = y0_ + iy * dy_;
+ ret[2] = z0_ + iz * dz_;
- ret[3] = x0_ + ix * dx_ + dx_;
- ret[4] = y0_ + iy * dy_ + dx_;
- ret[5] = z0_ + iz * dz_ + dx_;
+ ret[3] = x0_ + ix * dx_ + dx_;
+ ret[4] = y0_ + iy * dy_ + dx_;
+ ret[5] = z0_ + iz * dz_ + dx_;
- return ret;
+ return ret;
}
unsigned int CubeMesh::neighbor( unsigned int spaceIndex,
- int dx, int dy, int dz ) const
+ int dx, int dy, int dz ) const
{
- int ix = spaceIndex % nx_;
- int iy = (spaceIndex / nx_) % ny_;
- int iz = (spaceIndex / ( nx_ * ny_ )) % nz_;
+ int ix = spaceIndex % nx_;
+ int iy = (spaceIndex / nx_) % ny_;
+ int iz = (spaceIndex / ( nx_ * ny_ )) % nz_;
- ix += dx;
- iy += dy;
- iz += dz;
+ ix += dx;
+ iy += dy;
+ iz += dz;
- if ( ix < 0 || ix >= static_cast< int >( nx_ ) )
- return EMPTY;
- if ( iy < 0 || iy >= static_cast< int >( ny_ ) )
- return EMPTY;
- if ( iz < 0 || iz >= static_cast< int >( nz_ ) )
- return EMPTY;
+ if ( ix < 0 || ix >= static_cast< int >( nx_ ) )
+ return EMPTY;
+ if ( iy < 0 || iy >= static_cast< int >( ny_ ) )
+ return EMPTY;
+ if ( iz < 0 || iz >= static_cast< int >( nz_ ) )
+ return EMPTY;
- unsigned int nIndex = ( ( iz * ny_ ) + iy ) * nx_ + ix;
+ unsigned int nIndex = ( ( iz * ny_ ) + iy ) * nx_ + ix;
- return s2m_[nIndex];
+ return s2m_[nIndex];
}
/// Virtual function to return diffusion X-section area for each neighbor
vector< double > CubeMesh::getDiffusionArea( unsigned int fid ) const
{
- assert( fid < m2s_.size() );
+ assert( fid < m2s_.size() );
- vector< double > ret;
- unsigned int spaceIndex = m2s_[fid];
+ vector< double > ret;
+ unsigned int spaceIndex = m2s_[fid];
- unsigned int nIndex = neighbor( spaceIndex, 0, 0, 1 );
- if ( nIndex != EMPTY )
- ret.push_back( dx_ * dy_ );
+ unsigned int nIndex = neighbor( spaceIndex, 0, 0, 1 );
+ if ( nIndex != EMPTY )
+ ret.push_back( dx_ * dy_ );
- nIndex = neighbor( spaceIndex, 0, 0, -1 );
- if ( nIndex != EMPTY )
- ret.push_back( dx_ * dy_ );
+ nIndex = neighbor( spaceIndex, 0, 0, -1 );
+ if ( nIndex != EMPTY )
+ ret.push_back( dx_ * dy_ );
- nIndex = neighbor( spaceIndex, 0, 1, 0 );
- if ( nIndex != EMPTY )
- ret.push_back( dz_ * dx_ );
+ nIndex = neighbor( spaceIndex, 0, 1, 0 );
+ if ( nIndex != EMPTY )
+ ret.push_back( dz_ * dx_ );
- nIndex = neighbor( spaceIndex, 0, -1, 0 );
- if ( nIndex != EMPTY )
- ret.push_back( dz_ * dx_ );
+ nIndex = neighbor( spaceIndex, 0, -1, 0 );
+ if ( nIndex != EMPTY )
+ ret.push_back( dz_ * dx_ );
- nIndex = neighbor( spaceIndex, 1, 0, 0 );
- if ( nIndex != EMPTY )
- ret.push_back( dy_ * dz_ );
+ nIndex = neighbor( spaceIndex, 1, 0, 0 );
+ if ( nIndex != EMPTY )
+ ret.push_back( dy_ * dz_ );
- nIndex = neighbor( spaceIndex, -1, 0, 0 );
- if ( nIndex != EMPTY )
- ret.push_back( dy_ * dz_ );
+ nIndex = neighbor( spaceIndex, -1, 0, 0 );
+ if ( nIndex != EMPTY )
+ ret.push_back( dy_ * dz_ );
- return ret;
+ return ret;
}
/// Virtual function to return scale factor for diffusion. 1 here.
vector< double > CubeMesh::getDiffusionScaling( unsigned int fid ) const
{
- return vector< double >( 6, 1.0 );
+ return vector< double >( 6, 1.0 );
}
//////////////////////////////////////////////////////////////////
@@ -890,7 +908,7 @@ vector< double > CubeMesh::getDiffusionScaling( unsigned int fid ) const
*/
unsigned int CubeMesh::innerGetNumEntries() const
{
- return m2s_.size();
+ return m2s_.size();
}
/**
@@ -898,159 +916,170 @@ unsigned int CubeMesh::innerGetNumEntries() const
*/
void CubeMesh::innerSetNumEntries( unsigned int n )
{
- cout << "Warning: CubeMesh::innerSetNumEntries is readonly.\n";
+ cout << "Warning: CubeMesh::innerSetNumEntries is readonly.\n";
}
// We assume this is linear diffusion for now. Fails for 2 or 3-D diffusion
vector< unsigned int > CubeMesh::getParentVoxel() const
{
- unsigned int numEntries = innerGetNumEntries();
- vector< unsigned int > ret( numEntries );
- if ( numEntries > 0 )
- ret[0] = static_cast< unsigned int >( -1 );
- for (unsigned int i = 1; i < numEntries; ++i )
- ret[i] = i-1;
+ unsigned int numEntries = innerGetNumEntries();
+ vector< unsigned int > ret( numEntries );
+ if ( numEntries > 0 )
+ ret[0] = static_cast< unsigned int >( -1 );
+ for (unsigned int i = 1; i < numEntries; ++i )
+ ret[i] = i-1;
- return ret;
+ return ret;
}
const vector< double >& CubeMesh::vGetVoxelVolume() const
{
- static vector< double > vol;
- vol.clear();
- vol.resize( nx_ * ny_ * nz_, dx_ * dy_ * dz_ );
- return vol;
+ static vector< double > vol;
+ vol.clear();
+ vol.resize( nx_ * ny_ * nz_, dx_ * dy_ * dz_ );
+ return vol;
}
const vector< double >& CubeMesh::vGetVoxelMidpoint() const
{
- static vector< double > midpoint;
- midpoint.resize( m2s_.size() * 3 );
- for ( unsigned int i = 0; i < m2s_.size(); ++i ) // x coords. Lowest.
- midpoint[i] = x0_ + ( 0.5 + (m2s_[i] % nx_ ) ) * dx_;
- for ( unsigned int i = 0; i < m2s_.size(); ++i ) { // y coords. Middle.
- unsigned int k = i + m2s_.size();
- midpoint[k] = y0_ + ( 0.5 + ( (m2s_[i] / nx_) % ny_ ) ) * dy_;
- }
- for ( unsigned int i = 0; i < m2s_.size(); ++i ) { // z coords. Top.
- unsigned int k = i + m2s_.size() * 2;
- midpoint[k] = z0_ + ( 0.5 + ( m2s_[i] / ( nx_ * ny_ ) ) ) * dz_;
- }
- return midpoint;
+ static vector< double > midpoint;
+ midpoint.resize( m2s_.size() * 3 );
+ for ( unsigned int i = 0; i < m2s_.size(); ++i ) // x coords. Lowest.
+ midpoint[i] = x0_ + ( 0.5 + (m2s_[i] % nx_ ) ) * dx_;
+ for ( unsigned int i = 0; i < m2s_.size(); ++i ) // y coords. Middle.
+ {
+ unsigned int k = i + m2s_.size();
+ midpoint[k] = y0_ + ( 0.5 + ( (m2s_[i] / nx_) % ny_ ) ) * dy_;
+ }
+ for ( unsigned int i = 0; i < m2s_.size(); ++i ) // z coords. Top.
+ {
+ unsigned int k = i + m2s_.size() * 2;
+ midpoint[k] = z0_ + ( 0.5 + ( m2s_[i] / ( nx_ * ny_ ) ) ) * dz_;
+ }
+ return midpoint;
}
const vector< double >& CubeMesh::getVoxelArea() const
{
- static vector< double > area;
- if ( nx_ * ny_ == 1 )
- area.resize( nz_, dx_ * dy_ );
- else if ( nx_ * nz_ == 1 )
- area.resize( ny_, dx_ * dz_ );
- else if ( ny_ * nz_ == 1 )
- area.resize( nx_, dy_ * dz_ );
- else
- area.resize( nx_, dy_ * dz_ ); // Just put in a number.
- assert( area.size() == nx_ * ny_ * nz_ );
- return area;
+ static vector< double > area;
+ if ( nx_ * ny_ == 1 )
+ area.resize( nz_, dx_ * dy_ );
+ else if ( nx_ * nz_ == 1 )
+ area.resize( ny_, dx_ * dz_ );
+ else if ( ny_ * nz_ == 1 )
+ area.resize( nx_, dy_ * dz_ );
+ else
+ area.resize( nx_, dy_ * dz_ ); // Just put in a number.
+ assert( area.size() == nx_ * ny_ * nz_ );
+ return area;
}
const vector< double >& CubeMesh::getVoxelLength() const
{
- static vector< double > length;
- if ( dx_ > dy_ && dx_ > dz_ )
- length.assign( innerGetNumEntries(), dx_ );
- else if ( dy_ > dz_ )
- length.assign( innerGetNumEntries(), dy_ );
- else
- length.assign( innerGetNumEntries(), dz_ );
- return length;
+ static vector< double > length;
+ if ( dx_ > dy_ && dx_ > dz_ )
+ length.assign( innerGetNumEntries(), dx_ );
+ else if ( dy_ > dz_ )
+ length.assign( innerGetNumEntries(), dy_ );
+ else
+ length.assign( innerGetNumEntries(), dz_ );
+ return length;
}
bool CubeMesh::vSetVolumeNotRates( double vol )
{
- // Leave x0,y0.z0 and nx,ny,nz the same. Do NOT update any rates.
- double oldvol = vGetEntireVolume();
- double linscale = pow( vol / oldvol , 1.0 / 3.0 );
- dx_ *= linscale;
- dy_ *= linscale;
- dz_ *= linscale;
- x1_ = x0_ + dx_;
- y1_ = y0_ + dy_;
- z1_ = z0_ + dz_;
+ // Leave x0,y0.z0 and nx,ny,nz the same. Do NOT update any rates.
+ double oldvol = vGetEntireVolume();
+ double linscale = pow( vol / oldvol, 1.0 / 3.0 );
+ dx_ *= linscale;
+ dy_ *= linscale;
+ dz_ *= linscale;
+ x1_ = x0_ + dx_;
+ y1_ = y0_ + dy_;
+ z1_ = z0_ + dz_;
- return true;
+ return true;
}
//////////////////////////////////////////////////////////////////
bool CubeMesh::isInsideCuboid( double x, double y, double z ) const
{
- return ( x >= x0_ && x < x1_ && y >= y0_ && y < y1_ &&
- z >= z0_ && z < z1_ );
+ return ( x >= x0_ && x < x1_ && y >= y0_ && y < y1_ &&
+ z >= z0_ && z < z1_ );
}
bool CubeMesh::isInsideSpheroid( double x, double y, double z ) const
{
- double cx = ( x0_ + x1_ ) / 2.0;
- double cy = ( y0_ + y1_ ) / 2.0;
- double cz = ( z0_ + z1_ ) / 2.0;
+ double cx = ( x0_ + x1_ ) / 2.0;
+ double cy = ( y0_ + y1_ ) / 2.0;
+ double cz = ( z0_ + z1_ ) / 2.0;
- double rx = ( x - cx ) / fabs( x1_ - x0_ ) / 2.0;
- double ry = ( y - cy ) / fabs( y1_ - y0_ ) / 2.0;
- double rz = ( z - cz ) / fabs( z1_ - z0_ ) / 2.0;
+ double rx = ( x - cx ) / fabs( x1_ - x0_ ) / 2.0;
+ double ry = ( y - cy ) / fabs( y1_ - y0_ ) / 2.0;
+ double rz = ( z - cz ) / fabs( z1_ - z0_ ) / 2.0;
- return ( ( rx * rx + ry * ry + rz * rz ) < 1.0 );
+ return ( ( rx * rx + ry * ry + rz * rz ) < 1.0 );
}
void CubeMesh::fillSpaceToMeshLookup()
{
- static const unsigned int flag = EMPTY;
- unsigned int num = 0;
- unsigned int q = 0;
- m2s_.clear();
- s2m_.resize( nx_ * ny_ * nz_, flag );
- for( unsigned int k = 0; k < nz_; ++k ) {
- double z = k * dz_ + z0_;
- for( unsigned int j = 0; j < ny_; ++j ) {
- double y = j * dy_ + y0_;
- for( unsigned int i = 0; i < nx_; ++i ) {
- double x = i * dx_ + x0_;
- if ( isInsideCuboid( x, y, z ) ) {
- s2m_[q] = num;
- m2s_.push_back( q );
- ++num;
- } else {
- s2m_[q] = flag;
- }
- ++q;
- }
- }
- }
- assert( m2s_.size() == num );
+ static const unsigned int flag = EMPTY;
+ unsigned int num = 0;
+ unsigned int q = 0;
+ m2s_.clear();
+ s2m_.resize( nx_ * ny_ * nz_, flag );
+ for( unsigned int k = 0; k < nz_; ++k )
+ {
+ double z = k * dz_ + z0_;
+ for( unsigned int j = 0; j < ny_; ++j )
+ {
+ double y = j * dy_ + y0_;
+ for( unsigned int i = 0; i < nx_; ++i )
+ {
+ double x = i * dx_ + x0_;
+ if ( isInsideCuboid( x, y, z ) )
+ {
+ s2m_[q] = num;
+ m2s_.push_back( q );
+ ++num;
+ }
+ else
+ {
+ s2m_[q] = flag;
+ }
+ ++q;
+ }
+ }
+ }
+ assert( m2s_.size() == num );
}
// Reads off s2m to build m2s.
void CubeMesh::deriveM2sFromS2m()
{
- m2s_.clear();
- assert( s2m_.size() == nx_ * ny_ * nz_ );
- for ( unsigned int i = 0; i < s2m_.size(); ++i ) {
- if ( s2m_[i] != EMPTY ) {
- m2s_.push_back( i );
- assert( m2s_.size() == s2m_[i] + 1 );
- }
- }
- buildStencil();
+ m2s_.clear();
+ assert( s2m_.size() == nx_ * ny_ * nz_ );
+ for ( unsigned int i = 0; i < s2m_.size(); ++i )
+ {
+ if ( s2m_[i] != EMPTY )
+ {
+ m2s_.push_back( i );
+ assert( m2s_.size() == s2m_[i] + 1 );
+ }
+ }
+ buildStencil();
}
void CubeMesh::deriveS2mFromM2s()
{
- s2m_.clear();
- s2m_.resize( nx_ * ny_ * nz_, EMPTY );
- for ( unsigned int i = 0; i < m2s_.size(); ++i ) {
- s2m_[ m2s_[i] ] = i;
- }
- buildStencil();
+ s2m_.clear();
+ s2m_.resize( nx_ * ny_ * nz_, EMPTY );
+ for ( unsigned int i = 0; i < m2s_.size(); ++i )
+ {
+ s2m_[ m2s_[i] ] = i;
+ }
+ buildStencil();
}
// This is a general version of the function, just relies on the
@@ -1059,222 +1088,235 @@ void CubeMesh::deriveS2mFromM2s()
void CubeMesh::buildStencil()
{
- static const unsigned int flag = EMPTY;
-
-
- // fillSpaceToMeshLookup();
- unsigned int num = m2s_.size();
- setStencilSize( num, num );
- for ( unsigned int i = 0; i < num; ++i ) {
- unsigned int q = m2s_[i];
- unsigned int ix = q % nx_;
- unsigned int iy = ( q / nx_ ) % ny_;
- unsigned int iz = ( q / ( nx_ * ny_ ) ) % nz_;
- vector< double > entry;
- vector< unsigned int > colIndex;
- vector< Ecol > e;
-
- if ( ix > 0 && s2m_[q-1] != flag ) {
- e.push_back( Ecol( dy_ * dz_ / dx_, s2m_[q-1] ) );
- }
- if ( ( ix < nx_ - 1 ) && s2m_[q+1] != flag ) {
- e.push_back( Ecol( dy_ * dz_ / dx_, s2m_[q+1] ) );
- }
- if ( iy > 0 && s2m_[ q-nx_ ] != flag ) {
- assert( q >= nx_ );
- e.push_back( Ecol( dx_ * dz_ / dy_, s2m_[q-nx_] ) );
- }
- if ( iy < ny_ - 1 && s2m_[ q+nx_ ] != flag ) {
- assert( q+nx_ < s2m_.size() );
- e.push_back( Ecol( dx_ * dz_ / dy_, s2m_[q+nx_] ) );
- }
- if ( iz > 0 && s2m_[ q - nx_*ny_ ] != flag ) {
- assert( q >= nx_ * ny_ );
- e.push_back( Ecol( dx_ * dy_ / dz_, s2m_[q - nx_ * ny_] ) );
- }
- if ( iz < nz_ - 1 && s2m_[ q + nx_*ny_ ] ) {
- assert( q+nx_ < s2m_.size() );
- e.push_back( Ecol( dx_ * dy_ / dz_, s2m_[q + nx_ * ny_] ) );
- }
- sort( e.begin(), e.end() );
- for ( vector< Ecol >::iterator j = e.begin(); j != e.end(); ++j ) {
- entry.push_back( j->e_ );
- colIndex.push_back( j->col_ );
- }
- addRow( i, entry, colIndex );
- }
- innerResetStencil();
+ static const unsigned int flag = EMPTY;
+
+
+ // fillSpaceToMeshLookup();
+ unsigned int num = m2s_.size();
+ setStencilSize( num, num );
+ for ( unsigned int i = 0; i < num; ++i )
+ {
+ unsigned int q = m2s_[i];
+ unsigned int ix = q % nx_;
+ unsigned int iy = ( q / nx_ ) % ny_;
+ unsigned int iz = ( q / ( nx_ * ny_ ) ) % nz_;
+ vector< double > entry;
+ vector< unsigned int > colIndex;
+ vector< Ecol > e;
+
+ if ( ix > 0 && s2m_[q-1] != flag )
+ {
+ e.push_back( Ecol( dy_ * dz_ / dx_, s2m_[q-1] ) );
+ }
+ if ( ( ix < nx_ - 1 ) && s2m_[q+1] != flag )
+ {
+ e.push_back( Ecol( dy_ * dz_ / dx_, s2m_[q+1] ) );
+ }
+ if ( iy > 0 && s2m_[ q-nx_ ] != flag )
+ {
+ assert( q >= nx_ );
+ e.push_back( Ecol( dx_ * dz_ / dy_, s2m_[q-nx_] ) );
+ }
+ if ( iy < ny_ - 1 && s2m_[ q+nx_ ] != flag )
+ {
+ assert( q+nx_ < s2m_.size() );
+ e.push_back( Ecol( dx_ * dz_ / dy_, s2m_[q+nx_] ) );
+ }
+ if ( iz > 0 && s2m_[ q - nx_*ny_ ] != flag )
+ {
+ assert( q >= nx_ * ny_ );
+ e.push_back( Ecol( dx_ * dy_ / dz_, s2m_[q - nx_ * ny_] ) );
+ }
+ if ( iz < nz_ - 1 && s2m_[ q + nx_*ny_ ] )
+ {
+ assert( q+nx_ < s2m_.size() );
+ e.push_back( Ecol( dx_ * dy_ / dz_, s2m_[q + nx_ * ny_] ) );
+ }
+ sort( e.begin(), e.end() );
+ for ( vector< Ecol >::iterator j = e.begin(); j != e.end(); ++j )
+ {
+ entry.push_back( j->e_ );
+ colIndex.push_back( j->col_ );
+ }
+ addRow( i, entry, colIndex );
+ }
+ innerResetStencil();
}
//////////////////////////////////////////////////////////////////
const vector< unsigned int >& CubeMesh::surface() const
{
- return surface_;
+ return surface_;
}
// For now: Just brute force through the surface list.
// Surface list applies only if 2 or 3 D.
-void CubeMesh::matchMeshEntries( const ChemCompt* other,
- vector< VoxelJunction >& ret ) const
-{
- const CubeMesh* cm = dynamic_cast< const CubeMesh* >( other );
-
- if ( cm ) {
- if ( alwaysDiffuse_ )
- matchAllEntries( cm, ret );
- else
- matchCubeMeshEntries( cm, ret );
- /*
- if ( compareMeshSpacing( cm ) == 0 ) { // Equal spacing.
- matchSameSpacing( cm, ret );
- } else if ( compareMeshSpacing( cm ) == -1 ) { // self is finer
- cout << "Warning:CubeMesh::matchMeshEntries: cannot yet handle unequal meshes\n";
- } else { // other is finer.
- cout << "Warning:CubeMesh::matchMeshEntries: cannot yet handle unequal meshes\n";
- }
- */
- return;
- }
- const EndoMesh* em = dynamic_cast< const EndoMesh* >( other );
- if ( em ) {
+void CubeMesh::matchMeshEntries(const ChemCompt* other, vector< VoxelJunction >& ret) const
+{
+ const CubeMesh* cm = dynamic_cast< const CubeMesh* >( other );
+
+ if ( cm )
+ {
+ if ( alwaysDiffuse_ )
+ matchAllEntries( cm, ret );
+ else
+ matchCubeMeshEntries( cm, ret );
+ /*
+ if ( compareMeshSpacing( cm ) == 0 ) { // Equal spacing.
+ matchSameSpacing( cm, ret );
+ } else if ( compareMeshSpacing( cm ) == -1 ) { // self is finer
+ cout << "Warning:CubeMesh::matchMeshEntries: cannot yet handle unequal meshes\n";
+ } else { // other is finer.
+ cout << "Warning:CubeMesh::matchMeshEntries: cannot yet handle unequal meshes\n";
+ }
+ */
+ return;
+ }
+ const EndoMesh* em = dynamic_cast< const EndoMesh* >( other );
+ if ( em )
+ {
em->matchMeshEntries( this, ret );
flipRet( ret );
- return;
- }
- cout << "Warning:CubeMesh::matchMeshEntries: cannot yet handle Neuro or Cyl meshes.\n";
+ return;
+ }
+ cout << "Warning:CubeMesh::matchMeshEntries: cannot yet handle Neuro or Cyl meshes.\n";
}
unsigned int CubeMesh::numDims() const
{
- return ( ( nx_ > 1 ) + ( ny_ > 1 ) + ( nz_ > 1 ) );
+ return ( ( nx_ > 1 ) + ( ny_ > 1 ) + ( nz_ > 1 ) );
}
void CubeMesh::indexToSpace( unsigned int index,
- double& x, double& y, double& z ) const
+ double& x, double& y, double& z ) const
{
- assert ( index < nx_ * ny_ * nz_ );
+ assert ( index < nx_ * ny_ * nz_ );
- // index = m2s_[index];
- unsigned int ix = index % nx_;
- index /= nx_;
- unsigned int iy = index % ny_;
- index /= ny_;
- unsigned int iz = index % nz_;
+ // index = m2s_[index];
+ unsigned int ix = index % nx_;
+ index /= nx_;
+ unsigned int iy = index % ny_;
+ index /= ny_;
+ unsigned int iz = index % nz_;
- x = x0_ + ix * dx_ + dx_ * 0.5;
- y = y0_ + iy * dy_ + dy_ * 0.5;
- z = z0_ + iz * dz_ + dz_ * 0.5;
+ x = x0_ + ix * dx_ + dx_ * 0.5;
+ y = y0_ + iy * dy_ + dy_ * 0.5;
+ z = z0_ + iz * dz_ + dz_ * 0.5;
}
unsigned int CubeMesh::spaceToIndex( double x, double y, double z ) const
{
- if ( x > x0_ && x < x1_ && y > y0_ && y < y1_ && z > z0_ && z < z1_ )
- {
- unsigned int ix = ( x - x0_ ) / dx_;
- unsigned int iy = ( y - y0_ ) / dy_;
- unsigned int iz = ( z - z0_ ) / dz_;
- unsigned int index = ( iz * ny_ + iy ) * nx_ + ix;
- unsigned int innerIndex = s2m_[ index ];
- return innerIndex;
- }
- return EMPTY;
+ if ( x > x0_ && x < x1_ && y > y0_ && y < y1_ && z > z0_ && z < z1_ )
+ {
+ unsigned int ix = ( x - x0_ ) / dx_;
+ unsigned int iy = ( y - y0_ ) / dy_;
+ unsigned int iz = ( z - z0_ ) / dz_;
+ unsigned int index = ( iz * ny_ + iy ) * nx_ + ix;
+ unsigned int innerIndex = s2m_[ index ];
+ return innerIndex;
+ }
+ return EMPTY;
}
double CubeMesh::nearest( double x, double y, double z,
- unsigned int& index ) const
-{
- if ( x > x0_ && x < x1_ && y > y0_ && y < y1_ && z > z0_ && z < z1_ )
- {
- unsigned int ix = ( x - x0_ ) / dx_;
- unsigned int iy = ( y - y0_ ) / dy_;
- unsigned int iz = ( z - z0_ ) / dz_;
- index = ( iz * ny_ + iy ) * nx_ + ix;
- unsigned int innerIndex = s2m_[ index ];
- if ( innerIndex != EMPTY ) { // Inside filled volume
- index = innerIndex;
- double tx = x0_ + ix * dx_ + dx_ * 0.5;
- double ty = y0_ + iy * dy_ + dy_ * 0.5;
- double tz = z0_ + iz * dz_ + dz_ * 0.5;
- return distance( x - tx, y - ty, z - tz );
- } else { // Outside volume. Look over surface for nearest.
- double rmin = 1e99;
- for ( vector< unsigned int >::const_iterator
- i = surface_.begin(); i != surface_.end(); ++i )
- {
- double tx, ty, tz;
- indexToSpace( *i, tx, ty, tz );
- double r = distance( tx - x, ty - y, tz - z );
- if ( rmin > r ) {
- rmin = r;
- index = *i;
- }
- }
- return -rmin; // Negative distance indicates xyz is outside vol
- }
- }
- // Should really figure out nearest corner anyway.
- index = 0;
- return -1.0;
+ unsigned int& index ) const
+{
+ if ( x > x0_ && x < x1_ && y > y0_ && y < y1_ && z > z0_ && z < z1_ )
+ {
+ unsigned int ix = ( x - x0_ ) / dx_;
+ unsigned int iy = ( y - y0_ ) / dy_;
+ unsigned int iz = ( z - z0_ ) / dz_;
+ index = ( iz * ny_ + iy ) * nx_ + ix;
+ unsigned int innerIndex = s2m_[ index ];
+ if ( innerIndex != EMPTY ) // Inside filled volume
+ {
+ index = innerIndex;
+ double tx = x0_ + ix * dx_ + dx_ * 0.5;
+ double ty = y0_ + iy * dy_ + dy_ * 0.5;
+ double tz = z0_ + iz * dz_ + dz_ * 0.5;
+ return distance( x - tx, y - ty, z - tz );
+ }
+ else // Outside volume. Look over surface for nearest.
+ {
+ double rmin = 1e99;
+ for ( vector< unsigned int >::const_iterator
+ i = surface_.begin(); i != surface_.end(); ++i )
+ {
+ double tx, ty, tz;
+ indexToSpace( *i, tx, ty, tz );
+ double r = distance( tx - x, ty - y, tz - z );
+ if ( rmin > r )
+ {
+ rmin = r;
+ index = *i;
+ }
+ }
+ return -rmin; // Negative distance indicates xyz is outside vol
+ }
+ }
+ // Should really figure out nearest corner anyway.
+ index = 0;
+ return -1.0;
}
int CubeMesh::compareMeshSpacing( const CubeMesh* other ) const
{
- if ( doubleApprox( dx_, other->dx_ ) &&
- doubleApprox( dy_, other->dy_ ) &&
- doubleApprox( dz_, other->dz_ ) )
- return 0; // equal
+ if ( doubleApprox( dx_, other->dx_ ) &&
+ doubleApprox( dy_, other->dy_ ) &&
+ doubleApprox( dz_, other->dz_ ) )
+ return 0; // equal
- if ( dx_ >= other->dx_ &&
- dy_ >= other->dy_ &&
- dz_ >= other->dz_ )
- return 1; // bigger
+ if ( dx_ >= other->dx_ &&
+ dy_ >= other->dy_ &&
+ dz_ >= other->dz_ )
+ return 1; // bigger
- if ( dx_ <= other->dx_ &&
- dy_ <= other->dy_ &&
- dz_ <= other->dz_ )
- return -1; // smaller than other.
+ if ( dx_ <= other->dx_ &&
+ dy_ <= other->dy_ &&
+ dz_ <= other->dz_ )
+ return -1; // smaller than other.
- cout << "Warning: CubeMesh::compareMeshSpacing: inconsistent spacing\n";
- return 0;
+ cout << "Warning: CubeMesh::compareMeshSpacing: inconsistent spacing\n";
+ return 0;
}
void CubeMesh::defineIntersection( const CubeMesh* other,
- double& xmin, double &xmax,
- double& ymin, double &ymax,
- double& zmin, double &zmax )
- const
-{
- const double meshSlop = 0.2;
- xmin = ( x0_ > other->x0_ ) ? x0_ : other->x0_;
- xmax = ( x1_ < other->x1_ ) ? x1_ : other->x1_;
- ymin = ( y0_ > other->y0_ ) ? y0_ : other->y0_;
- ymax = ( y1_ < other->y1_ ) ? y1_ : other->y1_;
- zmin = ( z0_ > other->z0_ ) ? z0_ : other->z0_;
- zmax = ( z1_ < other->z1_ ) ? z1_ : other->z1_;
- // Align to coarser mesh
- double temp = ( xmin - x0_) / dx_;
- if ( temp - floor( temp ) > meshSlop )
- xmin = floor( temp ) * dx_;
- temp = ( ymin - y0_) / dy_;
- if ( temp - floor( temp ) > meshSlop )
- ymin = floor( temp ) * dy_;
- temp = ( zmin - z0_) / dz_;
- if ( temp - floor( temp ) > meshSlop )
- zmin = floor( temp ) * dz_;
-
- // Provide 1 voxel padding all around.
- xmin -= dx_;
- xmax += dx_;
- ymin -= dy_;
- ymax += dy_;
- zmin -= dz_;
- zmax += dz_;
- swapIfBackward( xmin, xmax );
- swapIfBackward( ymin, ymax );
- swapIfBackward( zmin, zmax );
+ double& xmin, double &xmax,
+ double& ymin, double &ymax,
+ double& zmin, double &zmax )
+const
+{
+ const double meshSlop = 0.2;
+ xmin = ( x0_ > other->x0_ ) ? x0_ : other->x0_;
+ xmax = ( x1_ < other->x1_ ) ? x1_ : other->x1_;
+ ymin = ( y0_ > other->y0_ ) ? y0_ : other->y0_;
+ ymax = ( y1_ < other->y1_ ) ? y1_ : other->y1_;
+ zmin = ( z0_ > other->z0_ ) ? z0_ : other->z0_;
+ zmax = ( z1_ < other->z1_ ) ? z1_ : other->z1_;
+ // Align to coarser mesh
+ double temp = ( xmin - x0_) / dx_;
+ if ( temp - floor( temp ) > meshSlop )
+ xmin = floor( temp ) * dx_;
+ temp = ( ymin - y0_) / dy_;
+ if ( temp - floor( temp ) > meshSlop )
+ ymin = floor( temp ) * dy_;
+ temp = ( zmin - z0_) / dz_;
+ if ( temp - floor( temp ) > meshSlop )
+ zmin = floor( temp ) * dz_;
+
+ // Provide 1 voxel padding all around.
+ xmin -= dx_;
+ xmax += dx_;
+ ymin -= dy_;
+ ymax += dy_;
+ zmin -= dz_;
+ zmax += dz_;
+ swapIfBackward( xmin, xmax );
+ swapIfBackward( ymin, ymax );
+ swapIfBackward( zmin, zmax );
}
/**
@@ -1293,44 +1335,44 @@ void CubeMesh::defineIntersection( const CubeMesh* other,
*/
void setAbut( PII& voxel, unsigned int meshIndex, unsigned int axis )
{
- if ( voxel.second == CubeMesh::SURFACE ) // Don't touch surface voxels.
- return;
- if ( voxel.second == CubeMesh::EMPTY )
- voxel = PII( meshIndex, axis );
- else // 1 or more indices are already here.
- voxel.second = CubeMesh::MULTI;
+ if ( voxel.second == CubeMesh::SURFACE ) // Don't touch surface voxels.
+ return;
+ if ( voxel.second == CubeMesh::EMPTY )
+ voxel = PII( meshIndex, axis );
+ else // 1 or more indices are already here.
+ voxel.second = CubeMesh::MULTI;
}
void setIntersectVoxel(
- vector< PII >& intersect,
- unsigned int ix, unsigned int iy, unsigned int iz,
- unsigned int nx, unsigned int ny, unsigned int nz,
- unsigned int meshIndex )
-{
- assert( ix < nx && iy < ny && iz < nz );
- unsigned int index = ( iz * ny + iy ) * nx + ix;
- assert( index < intersect.size() );
- intersect[index] = PII( meshIndex, CubeMesh::SURFACE );
- if ( ix > 0 )
- setAbut( intersect[ (iz*ny + iy) * nx + ix-1 ], meshIndex,
- CubeMesh::ABUTX );
- if ( ix + 1 < nx )
- setAbut( intersect[ (iz*ny + iy) * nx + ix+1 ], meshIndex,
- CubeMesh::ABUTX );
-
- if ( iy > 0 )
- setAbut( intersect[ ( iz*ny + iy-1 ) * nx + ix ], meshIndex,
- CubeMesh::ABUTY);
- if ( iy + 1 < ny )
- setAbut( intersect[ ( iz*ny + iy+1 ) * nx + ix ], meshIndex,
- CubeMesh::ABUTY);
-
- if ( iz > 0 )
- setAbut( intersect[ ( (iz-1)*ny + iy ) * nx + ix ], meshIndex,
- CubeMesh::ABUTZ);
- if ( iz + 1 < nz )
- setAbut( intersect[ ( (iz+1)*ny + iy ) * nx + ix ], meshIndex,
- CubeMesh::ABUTZ);
+ vector< PII >& intersect,
+ unsigned int ix, unsigned int iy, unsigned int iz,
+ unsigned int nx, unsigned int ny, unsigned int nz,
+ unsigned int meshIndex )
+{
+ assert( ix < nx && iy < ny && iz < nz );
+ unsigned int index = ( iz * ny + iy ) * nx + ix;
+ assert( index < intersect.size() );
+ intersect[index] = PII( meshIndex, CubeMesh::SURFACE );
+ if ( ix > 0 )
+ setAbut( intersect[ (iz*ny + iy) * nx + ix-1 ], meshIndex,
+ CubeMesh::ABUTX );
+ if ( ix + 1 < nx )
+ setAbut( intersect[ (iz*ny + iy) * nx + ix+1 ], meshIndex,
+ CubeMesh::ABUTX );
+
+ if ( iy > 0 )
+ setAbut( intersect[ ( iz*ny + iy-1 ) * nx + ix ], meshIndex,
+ CubeMesh::ABUTY);
+ if ( iy + 1 < ny )
+ setAbut( intersect[ ( iz*ny + iy+1 ) * nx + ix ], meshIndex,
+ CubeMesh::ABUTY);
+
+ if ( iz > 0 )
+ setAbut( intersect[ ( (iz-1)*ny + iy ) * nx + ix ], meshIndex,
+ CubeMesh::ABUTZ);
+ if ( iz + 1 < nz )
+ setAbut( intersect[ ( (iz+1)*ny + iy ) * nx + ix ], meshIndex,
+ CubeMesh::ABUTZ);
}
@@ -1346,224 +1388,249 @@ void setIntersectVoxel(
* field of the VoxelJunction. 0 = x; 1 = y; 2 = z.
*/
void checkAbut(
- const vector< PII >& intersect,
- unsigned int ix, unsigned int iy, unsigned int iz,
- unsigned int nx, unsigned int ny, unsigned int nz,
- unsigned int meshIndex,
- vector< VoxelJunction >& ret
- )
-{
- unsigned int index = ( iz * ny + iy ) * nx + ix;
- unsigned int localFlag = intersect[index].second;
-
- if ( localFlag == CubeMesh::EMPTY || localFlag == CubeMesh::SURFACE )
- return; // Nothing to put into the ret vector
- if ( localFlag == CubeMesh::ABUTX ) {
- ret.push_back(
- VoxelJunction( intersect[index].first, meshIndex, 0 ));
- } else if ( localFlag == CubeMesh::ABUTY ) {
- ret.push_back(
- VoxelJunction( intersect[index].first, meshIndex, 1 ));
- } else if ( localFlag == CubeMesh::ABUTZ ) {
- ret.push_back(
- VoxelJunction( intersect[index].first, meshIndex, 2 ));
- } else if ( localFlag == CubeMesh::MULTI ) { // go through all 6 cases.
- if ( ix > 0 ) {
- index = ( iz * ny + iy ) * nx + ix - 1;
- if ( intersect[index].second == CubeMesh::SURFACE )
- ret.push_back(
- VoxelJunction( intersect[index].first, meshIndex, 0 ));
- }
- if ( ix + 1 < nx ) {
- index = ( iz * ny + iy ) * nx + ix + 1;
- if ( intersect[index].second == CubeMesh::SURFACE )
- ret.push_back(
- VoxelJunction( intersect[index].first, meshIndex, 0 ));
- }
- if ( iy > 0 ) {
- index = ( iz * ny + iy -1 ) * nx + ix;
- if ( intersect[index].second == CubeMesh::SURFACE )
- ret.push_back(
- VoxelJunction( intersect[index].first, meshIndex, 1 ));
- }
- if ( iy + 1 < ny ) {
- index = ( iz * ny + iy + 1 ) * nx + ix;
- if ( intersect[index].second == CubeMesh::SURFACE )
- ret.push_back(
- VoxelJunction( intersect[index].first, meshIndex, 1 ));
- }
- if ( iz > 0 ) {
- index = ( (iz-1) * ny + iy ) * nx + ix;
- if ( intersect[index].second == CubeMesh::SURFACE )
- ret.push_back(
- VoxelJunction( intersect[index].first, meshIndex, 2 ));
- }
- if ( iz + 1 < nz ) {
- index = ( (iz+1) * ny + iy ) * nx + ix;
- if ( intersect[index].second == CubeMesh::SURFACE )
- ret.push_back(
- VoxelJunction( intersect[index].first, meshIndex, 2 ));
- }
- }
+ const vector< PII >& intersect,
+ unsigned int ix, unsigned int iy, unsigned int iz,
+ unsigned int nx, unsigned int ny, unsigned int nz,
+ unsigned int meshIndex,
+ vector< VoxelJunction >& ret
+)
+{
+ unsigned int index = ( iz * ny + iy ) * nx + ix;
+ unsigned int localFlag = intersect[index].second;
+
+ if ( localFlag == CubeMesh::EMPTY || localFlag == CubeMesh::SURFACE )
+ return; // Nothing to put into the ret vector
+ if ( localFlag == CubeMesh::ABUTX )
+ {
+ ret.push_back(
+ VoxelJunction( intersect[index].first, meshIndex, 0 ));
+ }
+ else if ( localFlag == CubeMesh::ABUTY )
+ {
+ ret.push_back(
+ VoxelJunction( intersect[index].first, meshIndex, 1 ));
+ }
+ else if ( localFlag == CubeMesh::ABUTZ )
+ {
+ ret.push_back(
+ VoxelJunction( intersect[index].first, meshIndex, 2 ));
+ }
+ else if ( localFlag == CubeMesh::MULTI ) // go through all 6 cases.
+ {
+ if ( ix > 0 )
+ {
+ index = ( iz * ny + iy ) * nx + ix - 1;
+ if ( intersect[index].second == CubeMesh::SURFACE )
+ ret.push_back(
+ VoxelJunction( intersect[index].first, meshIndex, 0 ));
+ }
+ if ( ix + 1 < nx )
+ {
+ index = ( iz * ny + iy ) * nx + ix + 1;
+ if ( intersect[index].second == CubeMesh::SURFACE )
+ ret.push_back(
+ VoxelJunction( intersect[index].first, meshIndex, 0 ));
+ }
+ if ( iy > 0 )
+ {
+ index = ( iz * ny + iy -1 ) * nx + ix;
+ if ( intersect[index].second == CubeMesh::SURFACE )
+ ret.push_back(
+ VoxelJunction( intersect[index].first, meshIndex, 1 ));
+ }
+ if ( iy + 1 < ny )
+ {
+ index = ( iz * ny + iy + 1 ) * nx + ix;
+ if ( intersect[index].second == CubeMesh::SURFACE )
+ ret.push_back(
+ VoxelJunction( intersect[index].first, meshIndex, 1 ));
+ }
+ if ( iz > 0 )
+ {
+ index = ( (iz-1) * ny + iy ) * nx + ix;
+ if ( intersect[index].second == CubeMesh::SURFACE )
+ ret.push_back(
+ VoxelJunction( intersect[index].first, meshIndex, 2 ));
+ }
+ if ( iz + 1 < nz )
+ {
+ index = ( (iz+1) * ny + iy ) * nx + ix;
+ if ( intersect[index].second == CubeMesh::SURFACE )
+ ret.push_back(
+ VoxelJunction( intersect[index].first, meshIndex, 2 ));
+ }
+ }
}
void CubeMesh::assignVoxels( vector< PII >& intersect,
- double xmin, double xmax,
- double ymin, double ymax,
- double zmin, double zmax
- ) const
-{
- unsigned int nx = 0.5 + ( xmax - xmin ) / dx_;
- unsigned int ny = 0.5 + ( ymax - ymin ) / dy_;
- unsigned int nz = 0.5 + ( zmax - zmin ) / dz_;
- // offset terms for nx, ny, nz from coord system for coarser grid.
- // Note that these can go negative if the intersect grid goes past
- // the coarse grid.
- int ox = round( ( xmin - x0_ ) / dx_ );
- int oy = round( ( ymin - y0_ ) / dy_ );
- int oz = round( ( zmin - z0_ ) / dz_ );
-
- // Scan through mesh surface using coarser grid, assign cuboid voxels
- for ( vector< unsigned int >::const_iterator i = surface_.begin();
- i != surface_.end(); ++i ) {
- unsigned int index = *i;
- double x, y, z;
- indexToSpace( index, x, y, z );
- if ( x >= xmin && x <= xmax && y >= ymin && y <= ymax &&
- z >= zmin && z <= zmax ) {
- int ix = index % nx_ - ox;
- assert( ix >= 0 );
- unsigned int uix = ix;
- index /= nx_;
- int iy = index % ny_ - oy;
- assert( iy >= 0 );
- unsigned int uiy = iy;
- index /= ny_;
- int iz = index % nz_ - oz;
- assert( iz >= 0 );
- unsigned int uiz = iz;
- unsigned int meshIndex = s2m_[ *i ];
-
- setIntersectVoxel( intersect, uix, uiy, uiz, nx, ny, nz,
- meshIndex );
- }
- }
+ double xmin, double xmax,
+ double ymin, double ymax,
+ double zmin, double zmax
+ ) const
+{
+ unsigned int nx = 0.5 + ( xmax - xmin ) / dx_;
+ unsigned int ny = 0.5 + ( ymax - ymin ) / dy_;
+ unsigned int nz = 0.5 + ( zmax - zmin ) / dz_;
+ // offset terms for nx, ny, nz from coord system for coarser grid.
+ // Note that these can go negative if the intersect grid goes past
+ // the coarse grid.
+ int ox = round( ( xmin - x0_ ) / dx_ );
+ int oy = round( ( ymin - y0_ ) / dy_ );
+ int oz = round( ( zmin - z0_ ) / dz_ );
+
+ // Scan through mesh surface using coarser grid, assign cuboid voxels
+ for ( vector< unsigned int >::const_iterator i = surface_.begin();
+ i != surface_.end(); ++i )
+ {
+ unsigned int index = *i;
+ double x, y, z;
+ indexToSpace( index, x, y, z );
+ if ( x >= xmin && x <= xmax && y >= ymin && y <= ymax &&
+ z >= zmin && z <= zmax )
+ {
+ int ix = index % nx_ - ox;
+ assert( ix >= 0 );
+ unsigned int uix = ix;
+ index /= nx_;
+ int iy = index % ny_ - oy;
+ assert( iy >= 0 );
+ unsigned int uiy = iy;
+ index /= ny_;
+ int iz = index % nz_ - oz;
+ assert( iz >= 0 );
+ unsigned int uiz = iz;
+ unsigned int meshIndex = s2m_[ *i ];
+
+ setIntersectVoxel( intersect, uix, uiy, uiz, nx, ny, nz,
+ meshIndex );
+ }
+ }
}
void CubeMesh::matchCubeMeshEntries( const CubeMesh* other,
- vector< VoxelJunction >& ret ) const
-{
- // Flip meshes if the current grid is finer.
- // There are still problems here because a finer grid will end
- // up with 2 levels deep defined as being abutting.
- if ( compareMeshSpacing( other ) == -1 ) {
- other->matchMeshEntries( this, ret );
- flipRet( ret );
- return;
- }
- ret.resize( 0 );
- // Define intersecting cuboid
- double xmin, xmax, ymin, ymax, zmin, zmax;
- defineIntersection( other, xmin, xmax, ymin, ymax, zmin, zmax );
-
- // Allocate intersecting cuboid
- unsigned int nx = 0.5 + ( xmax - xmin ) / dx_;
- unsigned int ny = 0.5 + ( ymax - ymin ) / dy_;
- unsigned int nz = 0.5 + ( zmax - zmin ) / dz_;
- vector< PII > intersect( nx * ny * nz, PII( EMPTY, EMPTY ) );
- assignVoxels( intersect, xmin, xmax, ymin, ymax, zmin, zmax );
-
- // Scan through finer mesh surface, check for occupied voxels.
- for ( vector< unsigned int >::const_iterator i =
- other->surface_.begin();
- i != other->surface_.end(); ++i ) {
- double x, y, z;
- other->indexToSpace( *i, x, y, z );
- if ( x >= xmin && x <= xmax && y >= ymin && y <= ymax &&
- z >= zmin && z <= zmax ) {
- unsigned int ix = ( x - xmin ) / dx_;
- unsigned int iy = ( y - ymin ) / dy_;
- unsigned int iz = ( z - zmin ) / dz_;
- unsigned int meshIndex = other->s2m_[ *i ];
- checkAbut( intersect, ix, iy, iz, nx, ny, nz, meshIndex, ret );
- }
- }
-
- // Scan through the VoxelJunctions and populate their diffScale field
- setDiffScale( other, ret );
- // Scan through the VoxelJunctions and populate their volume field
- setJunctionVol( other, ret );
- sort( ret.begin(), ret.end() );
+ vector< VoxelJunction >& ret ) const
+{
+ // Flip meshes if the current grid is finer.
+ // There are still problems here because a finer grid will end
+ // up with 2 levels deep defined as being abutting.
+ if ( compareMeshSpacing( other ) == -1 )
+ {
+ other->matchMeshEntries( this, ret );
+ flipRet( ret );
+ return;
+ }
+ ret.resize( 0 );
+ // Define intersecting cuboid
+ double xmin, xmax, ymin, ymax, zmin, zmax;
+ defineIntersection( other, xmin, xmax, ymin, ymax, zmin, zmax );
+
+ // Allocate intersecting cuboid
+ unsigned int nx = 0.5 + ( xmax - xmin ) / dx_;
+ unsigned int ny = 0.5 + ( ymax - ymin ) / dy_;
+ unsigned int nz = 0.5 + ( zmax - zmin ) / dz_;
+ vector< PII > intersect( nx * ny * nz, PII( EMPTY, EMPTY ) );
+ assignVoxels( intersect, xmin, xmax, ymin, ymax, zmin, zmax );
+
+ // Scan through finer mesh surface, check for occupied voxels.
+ for ( vector< unsigned int >::const_iterator i =
+ other->surface_.begin();
+ i != other->surface_.end(); ++i )
+ {
+ double x, y, z;
+ other->indexToSpace( *i, x, y, z );
+ if ( x >= xmin && x <= xmax && y >= ymin && y <= ymax &&
+ z >= zmin && z <= zmax )
+ {
+ unsigned int ix = ( x - xmin ) / dx_;
+ unsigned int iy = ( y - ymin ) / dy_;
+ unsigned int iz = ( z - zmin ) / dz_;
+ unsigned int meshIndex = other->s2m_[ *i ];
+ checkAbut( intersect, ix, iy, iz, nx, ny, nz, meshIndex, ret );
+ }
+ }
+
+ // Scan through the VoxelJunctions and populate their diffScale field
+ setDiffScale( other, ret );
+ // Scan through the VoxelJunctions and populate their volume field
+ setJunctionVol( other, ret );
+ sort( ret.begin(), ret.end() );
}
/**
* Version that assumes all voxels are in contact and able to diffuse
* with matching voxels on other mesh
*/
-void CubeMesh::matchAllEntries( const CubeMesh* other,
- vector< VoxelJunction >& ret ) const
+void CubeMesh::matchAllEntries(const CubeMesh* other, vector<VoxelJunction>& ret) const
{
- ret.clear();
- unsigned int min = m2s_.size();
- if ( min > other->m2s_.size() )
- min = other->m2s_.size();
- ret.resize( min );
- for ( unsigned int i = 0; i < min; ++i ) {
- ret[i] = VoxelJunction( i, i );
- }
+ ret.clear();
+ unsigned int min = m2s_.size();
+ if ( min > other->m2s_.size() )
+ min = other->m2s_.size();
+ ret.resize( min );
+ for ( unsigned int i = 0; i < min; ++i )
+ {
+ ret[i] = VoxelJunction( i, i );
+ }
}
void CubeMesh::matchCylMeshEntries( const ChemCompt* other,
- vector< VoxelJunction >& ret ) const
+ vector< VoxelJunction >& ret ) const
{
- other->matchMeshEntries( this, ret );
- flipRet( ret );
+ other->matchMeshEntries( this, ret );
+ flipRet( ret );
}
void CubeMesh::setDiffScale( const CubeMesh* other,
- vector< VoxelJunction >& ret ) const
-{
-
- for ( vector< VoxelJunction >::iterator i = ret.begin();
- i != ret.end(); ++i )
- {
- if ( doubleEq( i->diffScale, 0 ) ) { // Junction across x plane
- double selfXA = dy_ * dz_;
- double otherXA = other->dy_ * other->dz_;
- if ( selfXA <= otherXA )
- i->diffScale = 2 * selfXA / ( dx_ + other->dx_ );
- else
- i->diffScale = 2 * otherXA / ( dx_ + other->dx_ );
- } else if ( doubleEq( i->diffScale, 1 ) ) { // across y plane
- double selfXA = dx_ * dz_;
- double otherXA = other->dx_ * other->dz_;
- if ( selfXA <= otherXA )
- i->diffScale = 2 * selfXA / ( dy_ + other->dy_ );
- else
- i->diffScale = 2 * otherXA / ( dy_ + other->dy_ );
- } else if ( doubleEq( i->diffScale, 2 ) ) { // across z plane
- double selfXA = dx_ * dy_;
- double otherXA = other->dx_ * other->dy_;
- if ( selfXA <= otherXA )
- i->diffScale = 2 * selfXA / ( dz_ + other->dz_ );
- else
- i->diffScale = 2 * otherXA / ( dz_ + other->dz_ );
- } else {
- assert( 0 );
- }
- }
+ vector< VoxelJunction >& ret ) const
+{
+
+ for ( vector< VoxelJunction >::iterator i = ret.begin();
+ i != ret.end(); ++i )
+ {
+ if ( doubleEq( i->diffScale, 0 ) ) // Junction across x plane
+ {
+ double selfXA = dy_ * dz_;
+ double otherXA = other->dy_ * other->dz_;
+ if ( selfXA <= otherXA )
+ i->diffScale = 2 * selfXA / ( dx_ + other->dx_ );
+ else
+ i->diffScale = 2 * otherXA / ( dx_ + other->dx_ );
+ }
+ else if ( doubleEq( i->diffScale, 1 ) ) // across y plane
+ {
+ double selfXA = dx_ * dz_;
+ double otherXA = other->dx_ * other->dz_;
+ if ( selfXA <= otherXA )
+ i->diffScale = 2 * selfXA / ( dy_ + other->dy_ );
+ else
+ i->diffScale = 2 * otherXA / ( dy_ + other->dy_ );
+ }
+ else if ( doubleEq( i->diffScale, 2 ) ) // across z plane
+ {
+ double selfXA = dx_ * dy_;
+ double otherXA = other->dx_ * other->dy_;
+ if ( selfXA <= otherXA )
+ i->diffScale = 2 * selfXA / ( dz_ + other->dz_ );
+ else
+ i->diffScale = 2 * otherXA / ( dz_ + other->dz_ );
+ }
+ else
+ {
+ assert( 0 );
+ }
+ }
}
void CubeMesh::setJunctionVol( const CubeMesh* other,
- vector< VoxelJunction >& ret ) const
+ vector< VoxelJunction >& ret ) const
{
- double myVol = dx_ * dy_ * dz_;
- double otherVol = other->dx_ * other->dy_ * other->dz_;
- for ( vector< VoxelJunction >::iterator i = ret.begin();
- i != ret.end(); ++i )
- {
- i->firstVol = myVol;
- i->secondVol = otherVol;
- }
+ double myVol = dx_ * dy_ * dz_;
+ double otherVol = other->dx_ * other->dy_ * other->dz_;
+ for ( vector< VoxelJunction >::iterator i = ret.begin();
+ i != ret.end(); ++i )
+ {
+ i->firstVol = myVol;
+ i->secondVol = otherVol;
+ }
}
diff --git a/moose-core/mesh/CylMesh.cpp b/moose-core/mesh/CylMesh.cpp
index e0057529e42134e4eb5a445372f958caecfa9e84..3f467d949a2085be24c19f7a1d53b2bfb09996aa 100644
--- a/moose-core/mesh/CylMesh.cpp
+++ b/moose-core/mesh/CylMesh.cpp
@@ -13,78 +13,78 @@
#include "../utility/Vec.h"
#include "Boundary.h"
#include "MeshEntry.h"
-// #include "Stencil.h"
#include "ChemCompt.h"
#include "MeshCompt.h"
#include "CubeMesh.h"
#include "CylBase.h"
#include "NeuroNode.h"
-// #include "NeuroStencil.h"
#include "NeuroMesh.h"
#include "CylMesh.h"
#include "EndoMesh.h"
#include "../utility/numutil.h"
+#include "../utility/testing_macros.hpp"
+
const Cinfo* CylMesh::initCinfo()
{
- //////////////////////////////////////////////////////////////
- // Field Definitions
- //////////////////////////////////////////////////////////////
- static ElementValueFinfo< CylMesh, double > x0(
+ //////////////////////////////////////////////////////////////
+ // Field Definitions
+ //////////////////////////////////////////////////////////////
+ static ElementValueFinfo< CylMesh, double > x0(
"x0",
"x coord of one end",
&CylMesh::setX0,
&CylMesh::getX0
- );
- static ElementValueFinfo< CylMesh, double > y0(
+ );
+ static ElementValueFinfo< CylMesh, double > y0(
"y0",
"y coord of one end",
&CylMesh::setY0,
&CylMesh::getY0
- );
- static ElementValueFinfo< CylMesh, double > z0(
+ );
+ static ElementValueFinfo< CylMesh, double > z0(
"z0",
"z coord of one end",
&CylMesh::setZ0,
&CylMesh::getZ0
- );
- static ElementValueFinfo< CylMesh, double > r0(
+ );
+ static ElementValueFinfo< CylMesh, double > r0(
"r0",
"Radius of one end",
&CylMesh::setR0,
&CylMesh::getR0
- );
- static ElementValueFinfo< CylMesh, double > x1(
+ );
+ static ElementValueFinfo< CylMesh, double > x1(
"x1",
"x coord of other end",
&CylMesh::setX1,
&CylMesh::getX1
- );
- static ElementValueFinfo< CylMesh, double > y1(
+ );
+ static ElementValueFinfo< CylMesh, double > y1(
"y1",
"y coord of other end",
&CylMesh::setY1,
&CylMesh::getY1
- );
- static ElementValueFinfo< CylMesh, double > z1(
+ );
+ static ElementValueFinfo< CylMesh, double > z1(
"z1",
"z coord of other end",
&CylMesh::setZ1,
&CylMesh::getZ1
- );
- static ElementValueFinfo< CylMesh, double > r1(
+ );
+ static ElementValueFinfo< CylMesh, double > r1(
"r1",
"Radius of other end",
&CylMesh::setR1,
&CylMesh::getR1
- );
- static ElementValueFinfo< CylMesh, vector< double > > coords(
+ );
+ static ElementValueFinfo< CylMesh, vector< double > > coords(
"coords",
"All the coords as a single vector: x0 y0 z0 x1 y1 z1 r0 r1 diffLength",
&CylMesh::setCoords,
&CylMesh::getCoords
- );
+ );
- static ElementValueFinfo< CylMesh, double > diffLength(
+ static ElementValueFinfo< CylMesh, double > diffLength(
"diffLength",
"Length constant to use for subdivisions"
"The system will attempt to subdivide using compartments of"
@@ -95,27 +95,27 @@ const Cinfo* CylMesh::initCinfo()
"totLength/numEntries",
&CylMesh::setDiffLength,
&CylMesh::getDiffLength
- );
+ );
- static ReadOnlyValueFinfo< CylMesh, unsigned int > numDiffCompts(
+ static ReadOnlyValueFinfo< CylMesh, unsigned int > numDiffCompts(
"numDiffCompts",
"Number of diffusive compartments in model",
&CylMesh::innerGetNumEntries
- );
+ );
- static ReadOnlyValueFinfo< CylMesh, double > totLength(
+ static ReadOnlyValueFinfo< CylMesh, double > totLength(
"totLength",
"Total length of cylinder",
&CylMesh::getTotLength
- );
+ );
- //////////////////////////////////////////////////////////////
- // MsgDest Definitions
- //////////////////////////////////////////////////////////////
+ //////////////////////////////////////////////////////////////
+ // MsgDest Definitions
+ //////////////////////////////////////////////////////////////
- //////////////////////////////////////////////////////////////
- // Field Elements
- //////////////////////////////////////////////////////////////
+ //////////////////////////////////////////////////////////////
+ // Field Elements
+ //////////////////////////////////////////////////////////////
static Finfo* cylMeshFinfos[] = {
&x0, // Value
@@ -166,8 +166,7 @@ static const Cinfo* cylMeshCinfo = CylMesh::initCinfo();
//////////////////////////////////////////////////////////////////
// Class stuff.
//////////////////////////////////////////////////////////////////
-CylMesh::CylMesh()
- :
+CylMesh::CylMesh() :
numEntries_( 100 ),
useCaps_( 0 ),
isToroid_( false ),
@@ -205,14 +204,14 @@ CylMesh::~CylMesh()
void CylMesh::updateCoords( const Eref& e, const vector< double >& concs )
{
double temp = sqrt(
- ( x1_ - x0_ ) * ( x1_ - x0_ ) +
- ( y1_ - y0_ ) * ( y1_ - y0_ ) +
- ( z1_ - z0_ ) * ( z1_ - z0_ )
- );
+ ( x1_ - x0_ ) * ( x1_ - x0_ ) +
+ ( y1_ - y0_ ) * ( y1_ - y0_ ) +
+ ( z1_ - z0_ ) * ( z1_ - z0_ )
+ );
if ( doubleEq( temp, 0.0 ) ) {
cout << "Error: CylMesh::updateCoords:\n"
- "total length of compartment = 0 with these parameters\n";
+ "total length of compartment = 0 with these parameters\n";
return;
}
totLen_ = temp;
@@ -290,18 +289,19 @@ double CylMesh::getR0( const Eref& e ) const
void CylMesh::setX1( const Eref& e, double v )
{
- size_t numVoxels = (v - x0_) / diffLength_;
- if( numVoxels > SM_MAX_COLUMNS )
+ x1_ = v;
+ size_t numVoxels = (x1_ - x0_) / diffLength_;
+ if( numVoxels >= SM_MAX_COLUMNS)
{
- cout << "Warn: Compartment is too big. With diffusion-length of " << diffLength_
- << " total " << numVoxels << " would be generated which is larger than maximum "
- << SM_MAX_COLUMNS << " allowed. Ignoring .." << endl;
- return;
+ diffLength_ = (x1_-x0_)/(SM_MAX_COLUMNS-1);
+ MOOSE_WARN( "Too many voxels (" << numVoxels << ") would be created"
+ << " for current length " << (x1_ - x0_) << " and diffLength "
+ << diffLength_ << " (maximum " << SM_MAX_COLUMNS << " voxels allowed)."
+ << " Rescaling diffLength of compartment to " << diffLength_ << ". "
+ );
}
-
vector< double > childConcs;
getChildConcs( e, childConcs );
- x1_ = v;
updateCoords( e, childConcs );
}
@@ -400,9 +400,18 @@ vector< double > CylMesh::getCoords( const Eref& e ) const
void CylMesh::setDiffLength( const Eref& e, double v )
{
+ diffLength_ = v;
+ size_t numVoxels = (size_t) ((x1_-x0_)/diffLength_);
+ if( numVoxels >= SM_MAX_COLUMNS )
+ {
+ x1_ = x0_ + diffLength_ * (SM_MAX_COLUMNS - 1);
+ MOOSE_WARN( "Too many voxels (" << numVoxels << ") would be created "
+ << "for diffLength of " << diffLength_
+ << " (maximum " << SM_MAX_COLUMNS << " allowed). "
+ << " Changing compartment length to " << (x1_ - x0_) << ".");
+ }
vector< double > childConcs;
getChildConcs( e, childConcs );
- diffLength_ = v;
updateCoords( e, childConcs );
}
@@ -485,7 +494,7 @@ unsigned int CylMesh::getMeshDimensions( unsigned int fid ) const
/// Virtual function to return volume of mesh Entry.
double CylMesh::getMeshEntryVolume( unsigned int fid ) const
{
- double len0 = diffLength_ * 2 * r0_ / ( r0_ + r1_ );
+ double len0 = diffLength_ * 2 * r0_ / ( r0_ + r1_ );
double ri = r0_ + (fid + 0.5) * rSlope_;
double leni = len0 + ( fid + 0.5 ) * lenSlope_;
@@ -498,15 +507,15 @@ double CylMesh::getMeshEntryVolume( unsigned int fid ) const
vector< double > CylMesh::getCoordinates( unsigned int fid ) const
{
vector< double > ret(10, 0.0);
- double len0 = diffLength_ * 2 * r0_ / ( r0_ + r1_ );
- // double len0 = diffLength_ * 2 * ( r0_ + rSlope_ / 0.5) / ( r0_ + r1_ );
+ double len0 = diffLength_ * 2 * r0_ / ( r0_ + r1_ );
+ // double len0 = diffLength_ * 2 * ( r0_ + rSlope_ / 0.5) / ( r0_ + r1_ );
double lenStart = len0 + lenSlope_ * 0.5;
double axialStart = fid * lenStart + ( ( fid * (fid - 1 ) )/2 ) * lenSlope_;
- // fid * totLen_/numEntries_ + (fid - frac ) * lenSlope_;
+ // fid * totLen_/numEntries_ + (fid - frac ) * lenSlope_;
double axialEnd =
(fid + 1) * lenStart + ( ( fid * (fid + 1 ) )/2 ) * lenSlope_;
- // (fid + 1) * totLen_/numEntries_ + (fid - frac + 1.0) * lenSlope_;
+ // (fid + 1) * totLen_/numEntries_ + (fid - frac + 1.0) * lenSlope_;
ret[0] = x0_ + (x1_ - x0_ ) * axialStart/totLen_;
ret[1] = y0_ + (y1_ - y0_ ) * axialStart/totLen_;
@@ -591,30 +600,30 @@ double CylMesh::extendedMeshEntryVolume( unsigned int fid ) const
/// More inherited virtual funcs: request comes in for mesh stats
void CylMesh::innerHandleRequestMeshStats( const Eref& e,
const SrcFinfo2< unsigned int, vector< double > >* meshStatsFinfo
- )
+ )
{
vector< double > ret( vGetEntireVolume() / numEntries_ ,1 );
meshStatsFinfo->send( e, 1, ret );
}
void CylMesh::innerHandleNodeInfo(
- const Eref& e,
- unsigned int numNodes, unsigned int numThreads )
+ const Eref& e,
+ unsigned int numNodes, unsigned int numThreads )
{
- /*
- unsigned int numEntries = numEntries_;
- vector< double > vols( numEntries, volume_ / numEntries );
- vector< unsigned int > localEntries( numEntries );
- vector< vector< unsigned int > > outgoingEntries;
- vector< vector< unsigned int > > incomingEntries;
- */
/*
- double oldvol = getMeshEntryVolume( 0 );
- meshSplit()->send( e,
- oldvol,
- vols, localEntries,
- outgoingEntries, incomingEntries );
- */
+ unsigned int numEntries = numEntries_;
+ vector< double > vols( numEntries, volume_ / numEntries );
+ vector< unsigned int > localEntries( numEntries );
+ vector< vector< unsigned int > > outgoingEntries;
+ vector< vector< unsigned int > > incomingEntries;
+ */
+ /*
+ double oldvol = getMeshEntryVolume( 0 );
+ meshSplit()->send( e,
+ oldvol,
+ vols, localEntries,
+ outgoingEntries, incomingEntries );
+ */
}
//////////////////////////////////////////////////////////////////
@@ -634,7 +643,7 @@ void CylMesh::innerSetNumEntries( unsigned int n )
static const unsigned int WayTooLarge = 1000000;
if ( n == 0 || n > WayTooLarge ) {
cout << "Warning: CylMesh::innerSetNumEntries( " << n <<
- " ): out of range\n";
+ " ): out of range\n";
return;
}
assert( n > 0 );
@@ -648,7 +657,7 @@ void CylMesh::innerSetNumEntries( unsigned int n )
void CylMesh::innerBuildDefaultMesh( const Eref& e,
- double volume, unsigned int numEntries )
+ double volume, unsigned int numEntries )
{
/// Single voxel cylinder with diameter = length.
/// vol = volume = pi.r^2.len.
@@ -749,21 +758,21 @@ bool CylMesh::vSetVolumeNotRates( double volume )
void CylMesh::transmitChange( const Eref& e )
{
- /*
- Id meshEntry( e.id().value() + 1 );
- assert(
- meshEntry.eref().data() == reinterpret_cast< char* >( lookupEntry( 0 ) )
- );
- double oldvol = getMeshEntryVolume( 0 );
- unsigned int totalNumEntries = numEntries_;
- unsigned int localNumEntries = totalNumEntries;
- unsigned int startEntry = 0;
- vector< unsigned int > localIndices( localNumEntries ); // empty
- for ( unsigned int i = 0; i < localNumEntries; ++i )
- localIndices[i] = i;
- vector< double > vols( localNumEntries, volume_ / numEntries_ );
- vector< vector< unsigned int > > outgoingEntries; // [node#][Entry#]
- vector< vector< unsigned int > > incomingEntries; // [node#][Entry#]
+ /*
+ Id meshEntry( e.id().value() + 1 );
+ assert(
+ meshEntry.eref().data() == reinterpret_cast< char* >( lookupEntry( 0 ) )
+ );
+ double oldvol = getMeshEntryVolume( 0 );
+ unsigned int totalNumEntries = numEntries_;
+ unsigned int localNumEntries = totalNumEntries;
+ unsigned int startEntry = 0;
+ vector< unsigned int > localIndices( localNumEntries ); // empty
+ for ( unsigned int i = 0; i < localNumEntries; ++i )
+ localIndices[i] = i;
+ vector< double > vols( localNumEntries, volume_ / numEntries_ );
+ vector< vector< unsigned int > > outgoingEntries; // [node#][Entry#]
+ vector< vector< unsigned int > > incomingEntries; // [node#][Entry#]
// This function updates the size of the FieldDataHandler for the
// MeshEntries.
@@ -771,21 +780,21 @@ void CylMesh::transmitChange( const Eref& e )
FieldDataHandlerBase* fdh = dynamic_cast< FieldDataHandlerBase* >( dh );
assert( fdh );
if ( totalNumEntries > fdh->getMaxFieldEntries() ) {
- fdh->setMaxFieldEntries( localNumEntries );
+ fdh->setMaxFieldEntries( localNumEntries );
}
// This message tells the Stoich about the new mesh, and also about
// how it communicates with other nodes.
meshSplit()->fastSend( e,
- oldvol,
- vols, localIndices,
- outgoingEntries, incomingEntries );
+ oldvol,
+ vols, localIndices,
+ outgoingEntries, incomingEntries );
// This func goes down to the MeshEntry to tell all the pools and
// Reacs to deal with the new mesh. They then update the stoich.
lookupEntry( 0 )->triggerRemesh( meshEntry.eref(),
- oldvol, startEntry, localIndices, vols );
- */
+ oldvol, startEntry, localIndices, vols );
+ */
}
//////////////////////////////////////////////////////////////////
@@ -834,7 +843,7 @@ void CylMesh::buildStencil()
//////////////////////////////////////////////////////////////////
void CylMesh::matchMeshEntries( const ChemCompt* other,
- vector< VoxelJunction >& ret ) const
+ vector< VoxelJunction >& ret ) const
{
// This is seriously ugly, and what virtual funcs were meant to handle.
// Dirty hack for now.
@@ -861,14 +870,14 @@ void CylMesh::matchMeshEntries( const ChemCompt* other,
return;
}
cout << "Warning:CylMesh::matchMeshEntries: " <<
- " unknown mesh type\n";
+ " unknown mesh type\n";
}
// Look for end-to-end diffusion, not sideways for now.
// Very straightforward but tedious because of the different permutations.
// Could readily add cylinder side to other end.
void CylMesh::matchCylMeshEntries( const CylMesh* other,
-vector< VoxelJunction >& ret ) const
+ vector< VoxelJunction >& ret ) const
{
const double EPSILON = 1e-3;
ret.clear();
@@ -877,13 +886,13 @@ vector< VoxelJunction >& ret ) const
// within the radius of the disk. The subsequent calculations are the
// same though.
double dr1 = // startOfSelf-to-startOfOther
- distance(x0_ - other->x0_, y0_ - other->y0_, z0_ - other->z0_ );
+ distance(x0_ - other->x0_, y0_ - other->y0_, z0_ - other->z0_ );
double dr2 = // endOfSelf-to-endOfOther
- distance(x1_ - other->x1_, y1_ - other->y1_, z1_ - other->z1_ );
+ distance(x1_ - other->x1_, y1_ - other->y1_, z1_ - other->z1_ );
double dr3 = // endOfSelf-to-startOfOther
- distance(x1_ - other->x0_, y1_ - other->y0_, z1_ - other->z0_ );
+ distance(x1_ - other->x0_, y1_ - other->y0_, z1_ - other->z0_ );
double dr4 = // startOfSelf-to-endOfOther
- distance(x0_ - other->x1_, y0_ - other->y1_, z0_ - other->z1_ );
+ distance(x0_ - other->x1_, y0_ - other->y1_, z0_ - other->z1_ );
if ( dr1 <= dr2 && dr1 <= dr3 && dr1 <= dr4 ) {
if ( ( dr1/totLen_ < EPSILON && dr1/other->totLen_ < EPSILON ) ) {
@@ -892,7 +901,7 @@ vector< VoxelJunction >& ret ) const
xda = 2 * r0_ * r0_ * PI / ( diffLength_ + other->diffLength_ );
else
xda = 2 * other->r0_ * other->r0_ * PI /
- ( diffLength_ + other->diffLength_ );
+ ( diffLength_ + other->diffLength_ );
ret.push_back( VoxelJunction( 0, 0, xda ) );
ret.back().first = 0;
ret.back().second = 0;
@@ -906,7 +915,7 @@ vector< VoxelJunction >& ret ) const
xda = 2 * r1_ * r1_ * PI / ( diffLength_ + other->diffLength_ );
else
xda = 2 * other->r1_ * other->r1_ * PI /
- ( diffLength_ + other->diffLength_ );
+ ( diffLength_ + other->diffLength_ );
ret.push_back( VoxelJunction( numEntries_ - 1,
other->numEntries_ - 1, xda ) );
ret.back().first = numEntries_;
@@ -921,7 +930,7 @@ vector< VoxelJunction >& ret ) const
xda = 2 * r1_ * r1_ * PI / ( diffLength_ + other->diffLength_ );
else
xda = 2 * other->r0_ * other->r0_ * PI /
- ( diffLength_ + other->diffLength_ );
+ ( diffLength_ + other->diffLength_ );
ret.push_back( VoxelJunction( numEntries_ - 1, 0, xda ) );
ret.back().first = numEntries_ - 1;
ret.back().second = 0;
@@ -935,7 +944,7 @@ vector< VoxelJunction >& ret ) const
xda = 2 * r0_ * r0_ * PI / ( diffLength_ + other->diffLength_ );
else
xda = 2 * other->r1_ * other->r1_ * PI /
- ( diffLength_ + other->diffLength_ );
+ ( diffLength_ + other->diffLength_ );
ret.push_back( VoxelJunction( 0, other->numEntries_ - 1, xda ));
ret.back().first = 0;
ret.back().second = other->numEntries_ - 1;
@@ -962,10 +971,10 @@ double CylMesh::selectGridVolume( double h ) const
}
void fillPointsOnCircle(
- const Vec& u, const Vec& v, const Vec& q,
- double h, double r, vector< double >& area,
- const CubeMesh* other
- )
+ const Vec& u, const Vec& v, const Vec& q,
+ double h, double r, vector< double >& area,
+ const CubeMesh* other
+ )
{
// fine-tune the h spacing so it is integral around circle.
// This will cause small errors in area estimate but they will
@@ -990,7 +999,7 @@ void fillPointsOnCircle(
}
void CylMesh::matchCubeMeshEntries( const CubeMesh* other,
-vector< VoxelJunction >& ret ) const
+ vector< VoxelJunction >& ret ) const
{
const double EPSILON = 1e-18;
Vec a( x1_ - x0_, y1_ - y0_, z1_ - z0_ );
@@ -1014,8 +1023,8 @@ vector< VoxelJunction >& ret ) const
// get radius of cylinder at this point.
double r = r0_ + ( m * h + h / 2.0 ) * rSlope_;
fillPointsOnCircle( u, v, Vec( q0, q1, q2 ),
- h, r, area, other );
- }
+ h, r, area, other );
+ }
// Go through all cubeMesh entries and compute diffusion
// cross-section. Assume this is through a membrane, so the
// only factor relevant is area. Not the distance.
@@ -1028,12 +1037,12 @@ vector< VoxelJunction >& ret ) const
}
void CylMesh::matchNeuroMeshEntries( const NeuroMesh* other,
-vector< VoxelJunction >& ret ) const
+ vector< VoxelJunction >& ret ) const
{
}
void CylMesh::indexToSpace( unsigned int index,
- double& x, double& y, double& z ) const
+ double& x, double& y, double& z ) const
{
if ( index < numEntries_ ) {
double k = ( index + 0.5 ) / static_cast< double >( numEntries_ );
@@ -1044,15 +1053,15 @@ void CylMesh::indexToSpace( unsigned int index,
}
static double dotprd ( double x0, double y0, double z0,
- double x1, double y1, double z1 )
+ double x1, double y1, double z1 )
{
- return x0 * x1 + y0 * y1 + z0 * z1;
+ return x0 * x1 + y0 * y1 + z0 * z1;
}
// this is the function that does the actual calculation.
double CylMesh::nearest( double x, double y, double z,
- double& linePos, double& r ) const
+ double& linePos, double& r ) const
{
// Consider r0 = x0,y0,z0 and r1 = x1, y1, z1, and r = x,y,z.
// Fraction along cylinder = k
@@ -1066,8 +1075,8 @@ double CylMesh::nearest( double x, double y, double z,
double dist = distance( x1_ - x0_, y1_ - y0_, z1_ - z0_ );
double k = dotprd(
- x1_ - x0_, y1_ - y0_, z1_ - z0_,
- x - x0_, y - y0_, z - z0_ ) / ( dist * dist );
+ x1_ - x0_, y1_ - y0_, z1_ - z0_,
+ x - x0_, y - y0_, z - z0_ ) / ( dist * dist );
// x2, y2, z2 are the coords of the nearest point.
double x2 = k * (x1_ - x0_) + x0_;
@@ -1082,7 +1091,7 @@ double CylMesh::nearest( double x, double y, double z,
// This function returns the index.
double CylMesh::nearest( double x, double y, double z,
- unsigned int& index ) const
+ unsigned int& index ) const
{
double k = 0.0;
double r;
@@ -1104,40 +1113,40 @@ double CylMesh::nearest( double x, double y, double z,
/*
-bool isOnSurface( double x, double y, double z,
- double dx, double dy, double dz,
- unsigned int &index, double& adx )
-{
- double len = distance( x1_ - x0_, y1_ - y0_, z1_ - z0_ );
- double k = dotprd(
- x1_ - x0_, y1_ - y0_, z1_ - z0_,
- x - x0_, y - y0_, z - z0_ ) / len;
-
- // x2, y2, z2 are the coords of the nearest point.
- double x2 = k * (x1_ - x0_) + x0_;
- double y2 = k * (y1_ - y0_) + y0_;
- double z2 = k * (z1_ - z0_) + z0_;
-
- double ret = distance( x - x2, y - y2, z - z2 );
-
- double cubeRange = sqrt(dx*dx + dy*dy + dz*dz);
-
- // Now we check if the distance is definitely too far off for the
- // passed in point
- if ( k < -dx/2 || k > len + dx/2 ) // past the end.
- return false;
-
- double ri = k * rSlope_; // local cylinder radius.
-
- if ( ret > ri + cubeRange || ret < ri - cubeRange )
- return false;
-
- // OK, now we need to find the plane of intersection of the cylinder
- // with the cuboid. To make it easier, assume it is flat. We already
- // know the vector from the middle of the cuboid to the nearest
- // cylinder point. Treat it as the normal to the intersection plane.
- // We need: : is the plane inside the cube?
- // What is the area of the plane till its intersection with the cube?
+ bool isOnSurface( double x, double y, double z,
+ double dx, double dy, double dz,
+ unsigned int &index, double& adx )
+ {
+ double len = distance( x1_ - x0_, y1_ - y0_, z1_ - z0_ );
+ double k = dotprd(
+ x1_ - x0_, y1_ - y0_, z1_ - z0_,
+ x - x0_, y - y0_, z - z0_ ) / len;
+
+// x2, y2, z2 are the coords of the nearest point.
+double x2 = k * (x1_ - x0_) + x0_;
+double y2 = k * (y1_ - y0_) + y0_;
+double z2 = k * (z1_ - z0_) + z0_;
+
+double ret = distance( x - x2, y - y2, z - z2 );
+
+double cubeRange = sqrt(dx*dx + dy*dy + dz*dz);
+
+// Now we check if the distance is definitely too far off for the
+// passed in point
+if ( k < -dx/2 || k > len + dx/2 ) // past the end.
+return false;
+
+double ri = k * rSlope_; // local cylinder radius.
+
+if ( ret > ri + cubeRange || ret < ri - cubeRange )
+return false;
+
+// OK, now we need to find the plane of intersection of the cylinder
+// with the cuboid. To make it easier, assume it is flat. We already
+// know the vector from the middle of the cuboid to the nearest
+// cylinder point. Treat it as the normal to the intersection plane.
+// We need: : is the plane inside the cube?
+// What is the area of the plane till its intersection with the cube?
}
diff --git a/moose-core/mesh/CylMesh.h b/moose-core/mesh/CylMesh.h
index 7014e643eabc6674cd8f7aca44ee08b4f7f16a40..8d782679d559caf405c84f6d5d248042ed02746e 100644
--- a/moose-core/mesh/CylMesh.h
+++ b/moose-core/mesh/CylMesh.h
@@ -18,175 +18,177 @@
*/
class CylMesh: public MeshCompt
{
- public:
- CylMesh();
- ~CylMesh();
- //////////////////////////////////////////////////////////////////
- // Utility func
- //////////////////////////////////////////////////////////////////
- /**
- * Recomputes all local coordinate and meshing data following
- * a change in any of the coord parameters
- */
-
- void updateCoords( const Eref& e, const vector< double >& childConcs );
-
- //////////////////////////////////////////////////////////////////
- // Field assignment stuff
- //////////////////////////////////////////////////////////////////
-
- void setX0( const Eref& e, double v );
- double getX0( const Eref& e ) const;
- void setY0( const Eref& e, double v );
- double getY0( const Eref& e ) const;
- void setZ0( const Eref& e, double v );
- double getZ0( const Eref& e ) const;
- void setR0( const Eref& e, double v );
- double getR0( const Eref& e ) const;
-
- void setX1( const Eref& e, double v );
- double getX1( const Eref& e ) const;
- void setY1( const Eref& e, double v );
- double getY1( const Eref& e ) const;
- void setZ1( const Eref& e, double v );
- double getZ1( const Eref& e ) const;
- void setR1( const Eref& e, double v );
- double getR1( const Eref& e ) const;
-
- void innerSetCoords( const Eref& e, const vector< double >& v);
- void setCoords( const Eref& e, vector< double > v );
- vector< double > getCoords( const Eref& e ) const;
-
- void setDiffLength( const Eref& e, double v );
- double getDiffLength( const Eref& e ) const;
-
- double getTotLength() const;
-
- unsigned int innerGetDimensions() const;
-
- //////////////////////////////////////////////////////////////////
- // FieldElement assignment stuff for MeshEntries
- //////////////////////////////////////////////////////////////////
-
- /// Virtual function to return MeshType of specified entry.
- unsigned int getMeshType( unsigned int fid ) const;
- /// Virtual function to return dimensions of specified entry.
- unsigned int getMeshDimensions( unsigned int fid ) const;
- /// Virtual function to return volume of mesh Entry.
- double getMeshEntryVolume( unsigned int fid ) const;
- /// Virtual function to return coords of mesh Entry.
- vector< double > getCoordinates( unsigned int fid ) const;
- /// Virtual function to return diffusion X-section area
- vector< double > getDiffusionArea( unsigned int fid ) const;
- /// Virtual function to return scale factor for diffusion. 1 here.
- vector< double > getDiffusionScaling( unsigned int fid ) const;
- /// Volume of mesh Entry including abutting diff-coupled voxels
- double extendedMeshEntryVolume( unsigned int fid ) const;
-
- //////////////////////////////////////////////////////////////////
-
- /**
- * Inherited virtual func. Returns number of MeshEntry in array
- */
- unsigned int innerGetNumEntries() const;
- /// Inherited virtual func.
- void innerSetNumEntries( unsigned int n );
-
- /// Inherited virtual, do nothing for now.
- vector< unsigned int > getParentVoxel() const;
- const vector< double >& vGetVoxelVolume() const;
- const vector< double >& vGetVoxelMidpoint() const;
- const vector< double >& getVoxelArea() const;
- const vector< double >& getVoxelLength() const;
-
- /// Inherited virtual. Returns entire volume of compartment.
- double vGetEntireVolume() const;
-
- /// Inherited virtual. Resizes len and dia of each voxel.
- bool vSetVolumeNotRates( double volume );
- //////////////////////////////////////////////////////////////////
- // Dest funcs
- //////////////////////////////////////////////////////////////////
-
- /// Virtual func to make a mesh with specified Volume and numEntries
- void innerBuildDefaultMesh( const Eref& e,
- double volume, unsigned int numEntries );
-
- void innerHandleRequestMeshStats(
- const Eref& e,
- const SrcFinfo2< unsigned int, vector< double > >*
- meshStatsFinfo
- );
-
- void innerHandleNodeInfo(
- const Eref& e,
- unsigned int numNodes, unsigned int numThreads );
-
- void transmitChange( const Eref& e );
-
- void buildStencil();
-
- //////////////////////////////////////////////////////////////////
- // inherited virtual funcs for Boundary
- //////////////////////////////////////////////////////////////////
-
- void matchMeshEntries( const ChemCompt* other,
- vector< VoxelJunction > & ret ) const;
-
- double nearest( double x, double y, double z,
- unsigned int& index ) const;
-
- double nearest( double x, double y, double z,
- double& linePos, double& r ) const;
-
- void indexToSpace( unsigned int index,
- double& x, double& y, double& z ) const;
-
- //////////////////////////////////////////////////////////////////
- // Inner specific functions needed by matchMeshEntries.
- //////////////////////////////////////////////////////////////////
- void matchCylMeshEntries( const CylMesh* other,
- vector< VoxelJunction >& ret ) const;
- void matchCubeMeshEntries( const CubeMesh* other,
- vector< VoxelJunction >& ret ) const;
- void matchNeuroMeshEntries( const NeuroMesh* other,
- vector< VoxelJunction >& ret ) const;
-
- // Selects a grid volume for generating intersection with CubeMesh.
- double selectGridVolume( double h ) const;
-
- //////////////////////////////////////////////////////////////////
-
- static const Cinfo* initCinfo();
-
- private:
- unsigned int numEntries_; // Number of subdivisions to use
- bool useCaps_; // Flag: Should the ends have hemispherical caps?
- bool isToroid_; // Flag: Should the ends loop around mathemagically?
-
- double x0_; /// coords
- double y0_; /// coords
- double z0_; /// coords
-
- double x1_; /// coords
- double y1_; /// coords
- double z1_; /// coords
-
- double r0_; /// Radius at one end
- double r1_; /// Radius at other end
-
- double diffLength_; /// Length constant for diffusion. Equal to dx.
-
- /**
- * surfaceGranularity_ decides how finely to subdivide DiffLength
- * or cubic mesh side, when computing surface area of intersections
- * between them when diffusing. Defaults to 0.1
- */
- double surfaceGranularity_;
-
- double totLen_; /// Utility value: Total length of cylinder
- double rSlope_; /// Utility value: dr/dx
- double lenSlope_; /// Utility value: dlen/dx
+public:
+ CylMesh();
+ ~CylMesh();
+ //////////////////////////////////////////////////////////////////
+ // Utility func
+ //////////////////////////////////////////////////////////////////
+ /**
+ * Recomputes all local coordinate and meshing data following
+ * a change in any of the coord parameters
+ */
+
+ void updateCoords( const Eref& e, const std::vector< double >& childConcs );
+
+ //////////////////////////////////////////////////////////////////
+ // Field assignment stuff
+ //////////////////////////////////////////////////////////////////
+
+ void setX0( const Eref& e, double v );
+ double getX0( const Eref& e ) const;
+ void setY0( const Eref& e, double v );
+ double getY0( const Eref& e ) const;
+ void setZ0( const Eref& e, double v );
+ double getZ0( const Eref& e ) const;
+ void setR0( const Eref& e, double v );
+ double getR0( const Eref& e ) const;
+
+ void setX1( const Eref& e, double v );
+ double getX1( const Eref& e ) const;
+ void setY1( const Eref& e, double v );
+ double getY1( const Eref& e ) const;
+ void setZ1( const Eref& e, double v );
+ double getZ1( const Eref& e ) const;
+ void setR1( const Eref& e, double v );
+ double getR1( const Eref& e ) const;
+
+ void innerSetCoords( const Eref& e, const std::vector< double >& v);
+ void setCoords( const Eref& e, std::vector< double > v );
+ std::vector< double > getCoords( const Eref& e ) const;
+
+ void setDiffLength( const Eref& e, double v );
+ double getDiffLength( const Eref& e ) const;
+
+ double getTotLength() const;
+
+ unsigned int innerGetDimensions() const;
+
+ //////////////////////////////////////////////////////////////////
+ // FieldElement assignment stuff for MeshEntries
+ //////////////////////////////////////////////////////////////////
+
+ /// Virtual function to return MeshType of specified entry.
+ unsigned int getMeshType( unsigned int fid ) const;
+ /// Virtual function to return dimensions of specified entry.
+ unsigned int getMeshDimensions( unsigned int fid ) const;
+ /// Virtual function to return volume of mesh Entry.
+ double getMeshEntryVolume( unsigned int fid ) const;
+ /// Virtual function to return coords of mesh Entry.
+ std::vector< double > getCoordinates( unsigned int fid ) const;
+ /// Virtual function to return diffusion X-section area
+ std::vector< double > getDiffusionArea( unsigned int fid ) const;
+ /// Virtual function to return scale factor for diffusion. 1 here.
+ std::vector< double > getDiffusionScaling( unsigned int fid ) const;
+ /// Volume of mesh Entry including abutting diff-coupled voxels
+ double extendedMeshEntryVolume( unsigned int fid ) const;
+
+ //////////////////////////////////////////////////////////////////
+
+ /**
+ * Inherited virtual func. Returns number of MeshEntry in array
+ */
+ unsigned int innerGetNumEntries() const;
+ /// Inherited virtual func.
+ void innerSetNumEntries( unsigned int n );
+
+ /// Inherited virtual, do nothing for now.
+ std::vector< unsigned int > getParentVoxel() const;
+ const std::vector< double >& vGetVoxelVolume() const;
+ const std::vector< double >& vGetVoxelMidpoint() const;
+ const std::vector< double >& getVoxelArea() const;
+ const std::vector< double >& getVoxelLength() const;
+
+ /// Inherited virtual. Returns entire volume of compartment.
+ double vGetEntireVolume() const;
+
+ /// Inherited virtual. Resizes len and dia of each voxel.
+ bool vSetVolumeNotRates( double volume );
+
+ //////////////////////////////////////////////////////////////////
+ // Dest funcs
+ //////////////////////////////////////////////////////////////////
+
+ /// Virtual func to make a mesh with specified Volume and numEntries
+ void innerBuildDefaultMesh( const Eref& e,
+ double volume, unsigned int numEntries
+ );
+
+ void innerHandleRequestMeshStats(
+ const Eref& e,
+ const SrcFinfo2< unsigned int, std::vector< double > >*
+ meshStatsFinfo
+ );
+
+ void innerHandleNodeInfo(
+ const Eref& e,
+ unsigned int numNodes, unsigned int numThreads );
+
+ void transmitChange( const Eref& e );
+
+ void buildStencil();
+
+ //////////////////////////////////////////////////////////////////
+ // inherited virtual funcs for Boundary
+ //////////////////////////////////////////////////////////////////
+
+ void matchMeshEntries( const ChemCompt* other,
+ std::vector< VoxelJunction > & ret ) const;
+
+ double nearest( double x, double y, double z,
+ unsigned int& index ) const;
+
+ double nearest( double x, double y, double z,
+ double& linePos, double& r ) const;
+
+ void indexToSpace( unsigned int index,
+ double& x, double& y, double& z ) const;
+
+ //////////////////////////////////////////////////////////////////
+ // Inner specific functions needed by matchMeshEntries.
+ //////////////////////////////////////////////////////////////////
+ void matchCylMeshEntries( const CylMesh* other,
+ std::vector< VoxelJunction >& ret ) const;
+ void matchCubeMeshEntries( const CubeMesh* other,
+ std::vector< VoxelJunction >& ret ) const;
+ void matchNeuroMeshEntries( const NeuroMesh* other,
+ std::vector< VoxelJunction >& ret ) const;
+
+ // Selects a grid volume for generating intersection with CubeMesh.
+ double selectGridVolume( double h ) const;
+
+ //////////////////////////////////////////////////////////////////
+
+ static const Cinfo* initCinfo();
+
+private:
+ unsigned int numEntries_; // Number of subdivisions to use
+ bool useCaps_; // Flag: Should the ends have hemispherical caps?
+ bool isToroid_; // Flag: Should the ends loop around mathemagically?
+
+ double x0_; /// coords
+ double y0_; /// coords
+ double z0_; /// coords
+
+ double x1_; /// coords
+ double y1_; /// coords
+ double z1_; /// coords
+
+ double r0_; /// Radius at one end
+ double r1_; /// Radius at other end
+
+ double diffLength_; /// Length constant for diffusion. Equal to dx.
+
+ /**
+ * surfaceGranularity_ decides how finely to subdivide DiffLength
+ * or cubic mesh side, when computing surface area of intersections
+ * between them when diffusing. Defaults to 0.1
+ */
+ double surfaceGranularity_;
+
+ double totLen_; /// Utility value: Total length of cylinder
+ double rSlope_; /// Utility value: dr/dx
+ double lenSlope_; /// Utility value: dlen/dx
};
#endif // _CYL_MESH_H
diff --git a/moose-core/mesh/VoxelJunction.h b/moose-core/mesh/VoxelJunction.h
index 4c92a3e95da34c3d58c572a8574cab06f691b855..0a938f850a88595b312b9249c292878d4c749339 100644
--- a/moose-core/mesh/VoxelJunction.h
+++ b/moose-core/mesh/VoxelJunction.h
@@ -17,31 +17,31 @@
*/
class VoxelJunction
{
- public:
- VoxelJunction( unsigned int f, unsigned int s, double d = 1.0 )
- : first( f ), second( s ),
- firstVol( 0 ), secondVol( 0 ),
- diffScale( d )
- {;}
- VoxelJunction()
- : first( ~0 ), second( ~0 ), firstVol( 0 ), secondVol( 0 ),
- diffScale( 1.0 )
- {;}
+public:
+ VoxelJunction( unsigned int f, unsigned int s, double d = 1.0 )
+ : first( f ), second( s ),
+ firstVol( 0 ), secondVol( 0 ),
+ diffScale( d )
+ {;}
+ VoxelJunction()
+ : first( ~0 ), second( ~0 ), firstVol( 0 ), secondVol( 0 ),
+ diffScale( 1.0 )
+ {;}
- // Used for sorting.
- bool operator<( const VoxelJunction& other ) const
- {
- if ( first < other.first ) return 1;
- if ( first > other.first ) return 0;
- if ( second < other.second ) return 1;
- return 0;
- }
+ // Used for sorting.
+ bool operator<( const VoxelJunction& other ) const
+ {
+ if ( first < other.first ) return 1;
+ if ( first > other.first ) return 0;
+ if ( second < other.second ) return 1;
+ return 0;
+ }
- unsigned int first; /// MeshIndex for first compartment
- unsigned int second; /// MeshIndex for second compartment
- double firstVol;
- double secondVol;
- double diffScale; /// smaller of the cross-section areas / diffLen
+ unsigned int first; /// MeshIndex for first compartment
+ unsigned int second; /// MeshIndex for second compartment
+ double firstVol;
+ double secondVol;
+ double diffScale; /// smaller of the cross-section areas / diffLen
};
#endif // _VOXEL_JUNCTION_H
diff --git a/moose-core/msg/Msg.cpp b/moose-core/msg/Msg.cpp
index f260365224c18cfcb1a0f423f7ac3d64ba46adbe..96f7978fcf3a794a9028fc9b84b689ac3dd5df70 100644
--- a/moose-core/msg/Msg.cpp
+++ b/moose-core/msg/Msg.cpp
@@ -28,37 +28,38 @@ bool Msg::lastTrump_ = false;
const Msg* Msg::lastMsg_ = 0;
Msg::Msg( ObjId mid, Element* e1, Element* e2 )
- : mid_( mid), e1_( e1 ), e2_( e2 )
+ : mid_( mid), e1_( e1 ), e2_( e2 )
{
- e1->addMsg( mid_ );
- e2->addMsg( mid_ );
- lastMsg_ = this;
+ e1->addMsg( mid_ );
+ e2->addMsg( mid_ );
+ lastMsg_ = this;
}
Msg::~Msg()
{
- if ( !lastTrump_ ) {
- e1_->dropMsg( mid_ );
- e2_->dropMsg( mid_ );
- }
-
- /*
- if ( mid_ > 1 )
- garbageMsg_.push_back( mid_ );
- */
+ if ( !lastTrump_ )
+ {
+ e1_->dropMsg( mid_ );
+ e2_->dropMsg( mid_ );
+ }
+
+ /*
+ if ( mid_ > 1 )
+ garbageMsg_.push_back( mid_ );
+ */
}
// Static func
void Msg::deleteMsg( ObjId mid )
{
- const Msg* msg = getMsg( mid );
- delete( msg );
+ const Msg* msg = getMsg( mid );
+ delete( msg );
}
// Static func
const Msg* Msg::getMsg( ObjId m )
{
- return reinterpret_cast< const Msg* >( m.data() );
+ return reinterpret_cast< const Msg* >( m.data() );
}
/**
@@ -66,7 +67,7 @@ const Msg* Msg::getMsg( ObjId m )
*/
Id Msg::getE1() const
{
- return e1_->id();
+ return e1_->id();
}
/**
@@ -74,83 +75,99 @@ Id Msg::getE1() const
*/
Id Msg::getE2() const
{
- return e2_->id();
+ return e2_->id();
}
vector< string > Msg::getSrcFieldsOnE1() const
{
- vector< pair< BindIndex, FuncId > > ids;
- vector< string > ret;
-
- e1_->getFieldsOfOutgoingMsg( mid_, ids );
-
- for ( unsigned int i = 0; i < ids.size(); ++i ) {
- string name = e1_->cinfo()->srcFinfoName( ids[i].first );
- if ( name == "" ) {
- cout << "Error: Msg::getSrcFieldsOnE1: Failed to find field on msg " <<
- e1_->getName() << "-->" << e2_->getName() << endl;
- } else {
- ret.push_back( name );
- }
- }
- return ret;
+ vector< pair< BindIndex, FuncId > > ids;
+ vector< string > ret;
+
+ e1_->getFieldsOfOutgoingMsg( mid_, ids );
+
+ for ( unsigned int i = 0; i < ids.size(); ++i )
+ {
+ string name = e1_->cinfo()->srcFinfoName( ids[i].first );
+ if ( name == "" )
+ {
+ cout << "Error: Msg::getSrcFieldsOnE1: Failed to find field on msg " <<
+ e1_->getName() << "-->" << e2_->getName() << endl;
+ }
+ else
+ {
+ ret.push_back( name );
+ }
+ }
+ return ret;
}
vector< string > Msg::getDestFieldsOnE2() const
{
- vector< pair< BindIndex, FuncId > > ids;
- vector< string > ret;
-
- e1_->getFieldsOfOutgoingMsg( mid_, ids );
-
- for ( unsigned int i = 0; i < ids.size(); ++i ) {
- string name = e2_->cinfo()->destFinfoName( ids[i].second );
- if ( name == "" ) {
- cout << "Error: Msg::getDestFieldsOnE2: Failed to find field on msg " <<
- e1_->getName() << "-->" << e2_->getName() << endl;
- } else {
- ret.push_back( name );
- }
- }
- return ret;
+ vector< pair< BindIndex, FuncId > > ids;
+ vector< string > ret;
+
+ e1_->getFieldsOfOutgoingMsg( mid_, ids );
+
+ for ( unsigned int i = 0; i < ids.size(); ++i )
+ {
+ string name = e2_->cinfo()->destFinfoName( ids[i].second );
+ if ( name == "" )
+ {
+ cout << "Error: Msg::getDestFieldsOnE2: Failed to find field on msg " <<
+ e1_->getName() << "-->" << e2_->getName() << endl;
+ }
+ else
+ {
+ ret.push_back( name );
+ }
+ }
+ return ret;
}
vector< string > Msg::getSrcFieldsOnE2() const
{
- vector< pair< BindIndex, FuncId > > ids;
- vector< string > ret;
-
- e2_->getFieldsOfOutgoingMsg( mid_, ids );
-
- for ( unsigned int i = 0; i < ids.size(); ++i ) {
- string name = e2_->cinfo()->srcFinfoName( ids[i].first );
- if ( name == "" ) {
- cout << "Error: Msg::getSrcFieldsOnE2: Failed to find field on msg " <<
- e1_->getName() << "-->" << e2_->getName() << endl;
- } else {
- ret.push_back( name );
- }
- }
- return ret;
+ vector< pair< BindIndex, FuncId > > ids;
+ vector< string > ret;
+
+ e2_->getFieldsOfOutgoingMsg( mid_, ids );
+
+ for ( unsigned int i = 0; i < ids.size(); ++i )
+ {
+ string name = e2_->cinfo()->srcFinfoName( ids[i].first );
+ if ( name == "" )
+ {
+ cout << "Error: Msg::getSrcFieldsOnE2: Failed to find field on msg " <<
+ e1_->getName() << "-->" << e2_->getName() << endl;
+ }
+ else
+ {
+ ret.push_back( name );
+ }
+ }
+ return ret;
}
vector< string > Msg::getDestFieldsOnE1() const
{
- vector< pair< BindIndex, FuncId > > ids;
- vector< string > ret;
-
- e2_->getFieldsOfOutgoingMsg( mid_, ids );
-
- for ( unsigned int i = 0; i < ids.size(); ++i ) {
- string name = e1_->cinfo()->destFinfoName( ids[i].second );
- if ( name == "" ) {
- cout << "Error: Msg::getDestFieldsOnE1: Failed to find field on msg " <<
- e1_->getName() << "-->" << e2_->getName() << endl;
- } else {
- ret.push_back( name );
- }
- }
- return ret;
+ vector< pair< BindIndex, FuncId > > ids;
+ vector< string > ret;
+
+ e2_->getFieldsOfOutgoingMsg( mid_, ids );
+
+ for ( unsigned int i = 0; i < ids.size(); ++i )
+ {
+ string name = e1_->cinfo()->destFinfoName( ids[i].second );
+ if ( name == "" )
+ {
+ cout << "Error: Msg::getDestFieldsOnE1: Failed to find field on msg " <<
+ e1_->getName() << "-->" << e2_->getName() << endl;
+ }
+ else
+ {
+ ret.push_back( name );
+ }
+ }
+ return ret;
}
ObjId Msg::getAdjacent(ObjId obj) const
@@ -164,70 +181,71 @@ ObjId Msg::getAdjacent(ObjId obj) const
const Cinfo* Msg::initCinfo()
{
- ///////////////////////////////////////////////////////////////////
- // Field definitions.
- ///////////////////////////////////////////////////////////////////
- static ReadOnlyValueFinfo< Msg, Id > e1(
- "e1",
- "Id of source Element.",
- &Msg::getE1
- );
- static ReadOnlyValueFinfo< Msg, Id > e2(
- "e2",
- "Id of source Element.",
- &Msg::getE2
- );
-
- static ReadOnlyValueFinfo< Msg, vector< string > > srcFieldsOnE1(
- "srcFieldsOnE1",
- "Names of SrcFinfos for messages going from e1 to e2. There are"
- "matching entries in the destFieldsOnE2 vector",
- &Msg::getSrcFieldsOnE1
- );
- static ReadOnlyValueFinfo< Msg, vector< string > > destFieldsOnE2(
- "destFieldsOnE2",
- "Names of DestFinfos for messages going from e1 to e2. There are"
- "matching entries in the srcFieldsOnE1 vector",
- &Msg::getDestFieldsOnE2
- );
- static ReadOnlyValueFinfo< Msg, vector< string > > srcFieldsOnE2(
- "srcFieldsOnE2",
- "Names of SrcFinfos for messages going from e2 to e1. There are"
- "matching entries in the destFieldsOnE1 vector",
- &Msg::getSrcFieldsOnE2
- );
- static ReadOnlyValueFinfo< Msg, vector< string > > destFieldsOnE1(
- "destFieldsOnE1",
- "Names of destFinfos for messages going from e2 to e1. There are"
- "matching entries in the srcFieldsOnE2 vector",
- &Msg::getDestFieldsOnE1
- );
-
- static ReadOnlyLookupValueFinfo< Msg, ObjId, ObjId > adjacent(
- "adjacent",
- "The element adjacent to the specified element",
- &Msg::getAdjacent);
-
- static Finfo* msgFinfos[] = {
- &e1, // readonly value
- &e2, // readonly value
- &srcFieldsOnE1, // readonly value
- &destFieldsOnE2, // readonly value
- &srcFieldsOnE2, // readonly value
- &destFieldsOnE1, // readonly value
- &adjacent, // readonly lookup value
- };
-
- static Cinfo msgCinfo (
- "Msg", // name
- Neutral::initCinfo(), // base class
- msgFinfos,
- sizeof( msgFinfos ) / sizeof( Finfo* ), // num Fields
- 0
- // new Dinfo< Msg >()
- );
-
- return &msgCinfo;
+ ///////////////////////////////////////////////////////////////////
+ // Field definitions.
+ ///////////////////////////////////////////////////////////////////
+ static ReadOnlyValueFinfo< Msg, Id > e1(
+ "e1",
+ "Id of source Element.",
+ &Msg::getE1
+ );
+ static ReadOnlyValueFinfo< Msg, Id > e2(
+ "e2",
+ "Id of source Element.",
+ &Msg::getE2
+ );
+
+ static ReadOnlyValueFinfo< Msg, vector< string > > srcFieldsOnE1(
+ "srcFieldsOnE1",
+ "Names of SrcFinfos for messages going from e1 to e2. There are"
+ "matching entries in the destFieldsOnE2 vector",
+ &Msg::getSrcFieldsOnE1
+ );
+ static ReadOnlyValueFinfo< Msg, vector< string > > destFieldsOnE2(
+ "destFieldsOnE2",
+ "Names of DestFinfos for messages going from e1 to e2. There are"
+ "matching entries in the srcFieldsOnE1 vector",
+ &Msg::getDestFieldsOnE2
+ );
+ static ReadOnlyValueFinfo< Msg, vector< string > > srcFieldsOnE2(
+ "srcFieldsOnE2",
+ "Names of SrcFinfos for messages going from e2 to e1. There are"
+ "matching entries in the destFieldsOnE1 vector",
+ &Msg::getSrcFieldsOnE2
+ );
+ static ReadOnlyValueFinfo< Msg, vector< string > > destFieldsOnE1(
+ "destFieldsOnE1",
+ "Names of destFinfos for messages going from e2 to e1. There are"
+ "matching entries in the srcFieldsOnE2 vector",
+ &Msg::getDestFieldsOnE1
+ );
+
+ static ReadOnlyLookupValueFinfo< Msg, ObjId, ObjId > adjacent(
+ "adjacent",
+ "The element adjacent to the specified element",
+ &Msg::getAdjacent);
+
+ static Finfo* msgFinfos[] =
+ {
+ &e1, // readonly value
+ &e2, // readonly value
+ &srcFieldsOnE1, // readonly value
+ &destFieldsOnE2, // readonly value
+ &srcFieldsOnE2, // readonly value
+ &destFieldsOnE1, // readonly value
+ &adjacent, // readonly lookup value
+ };
+
+ static Cinfo msgCinfo (
+ "Msg", // name
+ Neutral::initCinfo(), // base class
+ msgFinfos,
+ sizeof( msgFinfos ) / sizeof( Finfo* ), // num Fields
+ 0
+ // new Dinfo< Msg >()
+ );
+
+ return &msgCinfo;
}
static const Cinfo* msgCinfo = Msg::initCinfo();
@@ -235,77 +253,82 @@ static const Cinfo* msgCinfo = Msg::initCinfo();
// Static func. Returns the index to use for msgIndex.
unsigned int Msg::initMsgManagers()
{
- Dinfo< short > dummyDinfo;
-
- // This is to be the parent of all the msg managers.
- msgManagerId_ = Id::nextId();
- new GlobalDataElement(
- msgManagerId_, Neutral::initCinfo(), "Msgs", 1 );
-
- SingleMsg::managerId_ = Id::nextId();
- new MsgElement( SingleMsg::managerId_, SingleMsg::initCinfo(),
- "singleMsg", &SingleMsg::numMsg, &SingleMsg::lookupMsg );
-
- OneToOneMsg::managerId_ = Id::nextId();
- new MsgElement( OneToOneMsg::managerId_, OneToOneMsg::initCinfo(),
- "oneToOneMsg", &OneToOneMsg::numMsg, &OneToOneMsg::lookupMsg );
-
- OneToAllMsg::managerId_ = Id::nextId();
- new MsgElement( OneToAllMsg::managerId_, OneToAllMsg::initCinfo(),
- "oneToAllMsg", &OneToAllMsg::numMsg, &OneToAllMsg::lookupMsg );
-
- DiagonalMsg::managerId_ = Id::nextId();
- new MsgElement( DiagonalMsg::managerId_, DiagonalMsg::initCinfo(),
- "diagonalMsg", &DiagonalMsg::numMsg, &DiagonalMsg::lookupMsg );
-
- SparseMsg::managerId_ = Id::nextId();
- new MsgElement( SparseMsg::managerId_, SparseMsg::initCinfo(),
- "sparseMsg", &SparseMsg::numMsg, &SparseMsg::lookupMsg );
-
- OneToOneDataIndexMsg::managerId_ = Id::nextId();
- new MsgElement( OneToOneDataIndexMsg::managerId_,
- OneToOneDataIndexMsg::initCinfo(),
- "oneToOneDataIndexMsg",
- &OneToOneDataIndexMsg::numMsg,
- &OneToOneDataIndexMsg::lookupMsg );
-
- // Do the 'adopt' only after all the message managers exist - we need
- // the OneToAll manager for the adoption messages themselves.
- assert( OneToAllMsg::numMsg() == 0 );
- unsigned int n = 1;
- Shell::adopt( Id(), msgManagerId_, n++ );
- Shell::adopt( msgManagerId_, SingleMsg::managerId_, n++ );
- Shell::adopt( msgManagerId_, OneToOneMsg::managerId_, n++ );
- Shell::adopt( msgManagerId_, OneToAllMsg::managerId_, n++ );
- Shell::adopt( msgManagerId_, DiagonalMsg::managerId_, n++ );
- Shell::adopt( msgManagerId_, SparseMsg::managerId_, n++ );
-
- return n;
+ Dinfo< short > dummyDinfo;
+
+ // This is to be the parent of all the msg managers.
+ msgManagerId_ = Id::nextId();
+ new GlobalDataElement(
+ msgManagerId_, Neutral::initCinfo(), "Msgs", 1 );
+
+ SingleMsg::managerId_ = Id::nextId();
+ new MsgElement( SingleMsg::managerId_, SingleMsg::initCinfo(),
+ "singleMsg", &SingleMsg::numMsg, &SingleMsg::lookupMsg );
+
+ OneToOneMsg::managerId_ = Id::nextId();
+ new MsgElement( OneToOneMsg::managerId_, OneToOneMsg::initCinfo(),
+ "oneToOneMsg", &OneToOneMsg::numMsg, &OneToOneMsg::lookupMsg );
+
+ OneToAllMsg::managerId_ = Id::nextId();
+ new MsgElement( OneToAllMsg::managerId_, OneToAllMsg::initCinfo(),
+ "oneToAllMsg", &OneToAllMsg::numMsg, &OneToAllMsg::lookupMsg );
+
+ DiagonalMsg::managerId_ = Id::nextId();
+ new MsgElement( DiagonalMsg::managerId_, DiagonalMsg::initCinfo(),
+ "diagonalMsg", &DiagonalMsg::numMsg, &DiagonalMsg::lookupMsg );
+
+ SparseMsg::managerId_ = Id::nextId();
+ new MsgElement( SparseMsg::managerId_, SparseMsg::initCinfo(),
+ "sparseMsg", &SparseMsg::numMsg, &SparseMsg::lookupMsg );
+
+ OneToOneDataIndexMsg::managerId_ = Id::nextId();
+ new MsgElement( OneToOneDataIndexMsg::managerId_,
+ OneToOneDataIndexMsg::initCinfo(),
+ "oneToOneDataIndexMsg",
+ &OneToOneDataIndexMsg::numMsg,
+ &OneToOneDataIndexMsg::lookupMsg );
+
+ // Do the 'adopt' only after all the message managers exist - we need
+ // the OneToAll manager for the adoption messages themselves.
+ assert( OneToAllMsg::numMsg() == 0 );
+ unsigned int n = 1;
+ Shell::adopt( Id(), msgManagerId_, n++ );
+ Shell::adopt( msgManagerId_, SingleMsg::managerId_, n++ );
+ Shell::adopt( msgManagerId_, OneToOneMsg::managerId_, n++ );
+ Shell::adopt( msgManagerId_, OneToAllMsg::managerId_, n++ );
+ Shell::adopt( msgManagerId_, DiagonalMsg::managerId_, n++ );
+ Shell::adopt( msgManagerId_, SparseMsg::managerId_, n++ );
+
+ return n;
}
void Msg::clearAllMsgs()
{
- lastTrump_ = true;
- for ( unsigned int i = 0; i < SingleMsg::numMsg(); ++i ) {
- Msg* m = reinterpret_cast< Msg* >( SingleMsg::lookupMsg( i ) );
- if ( m ) delete m;
- }
- for ( unsigned int i = 0; i < OneToOneMsg::numMsg(); ++i ) {
- Msg* m = reinterpret_cast< Msg* >( OneToOneMsg::lookupMsg( i ) );
- if ( m ) delete m;
- }
- for ( unsigned int i = 0; i < OneToAllMsg::numMsg(); ++i ) {
- Msg* m = reinterpret_cast< Msg* >( OneToAllMsg::lookupMsg( i ) );
- if ( m ) delete m;
- }
- for ( unsigned int i = 0; i < DiagonalMsg::numMsg(); ++i ) {
- Msg* m = reinterpret_cast< Msg* >( DiagonalMsg::lookupMsg( i ) );
- if ( m ) delete m;
- }
- for ( unsigned int i = 0; i < SparseMsg::numMsg(); ++i ) {
- Msg* m = reinterpret_cast< Msg* >( SparseMsg::lookupMsg( i ) );
- if ( m ) delete m;
- }
+ lastTrump_ = true;
+ for ( unsigned int i = 0; i < SingleMsg::numMsg(); ++i )
+ {
+ Msg* m = reinterpret_cast< Msg* >( SingleMsg::lookupMsg( i ) );
+ if ( m ) delete m;
+ }
+ for ( unsigned int i = 0; i < OneToOneMsg::numMsg(); ++i )
+ {
+ Msg* m = reinterpret_cast< Msg* >( OneToOneMsg::lookupMsg( i ) );
+ if ( m ) delete m;
+ }
+ for ( unsigned int i = 0; i < OneToAllMsg::numMsg(); ++i )
+ {
+ Msg* m = reinterpret_cast< Msg* >( OneToAllMsg::lookupMsg( i ) );
+ if ( m ) delete m;
+ }
+ for ( unsigned int i = 0; i < DiagonalMsg::numMsg(); ++i )
+ {
+ Msg* m = reinterpret_cast< Msg* >( DiagonalMsg::lookupMsg( i ) );
+ if ( m ) delete m;
+ }
+ for ( unsigned int i = 0; i < SparseMsg::numMsg(); ++i )
+ {
+ Msg* m = reinterpret_cast< Msg* >( SparseMsg::lookupMsg( i ) );
+ if ( m ) delete m;
+ }
}
/**
@@ -314,10 +337,10 @@ void Msg::clearAllMsgs()
*/
const Msg* Msg::lastMsg()
{
- return lastMsg_;
+ return lastMsg_;
}
bool Msg::isLastTrump()
{
- return lastTrump_;
+ return lastTrump_;
}
diff --git a/moose-core/msg/SparseMsg.cpp b/moose-core/msg/SparseMsg.cpp
index 0196ed30df92d83c61b7802f9615d1e557583778..a43d78c5897b9c0efa004643ac4d571471bde385 100644
--- a/moose-core/msg/SparseMsg.cpp
+++ b/moose-core/msg/SparseMsg.cpp
@@ -83,7 +83,7 @@ const Cinfo* SparseMsg::initCinfo()
&SparseMsg::getProbability
);
- static ValueFinfo< SparseMsg, unsigned long > seed(
+ static ValueFinfo< SparseMsg, int > seed(
"seed",
"Random number seed for generating probabilistic connectivity.",
&SparseMsg::setSeed,
@@ -95,95 +95,91 @@ const Cinfo* SparseMsg::initCinfo()
////////////////////////////////////////////////////////////////////////
static DestFinfo setRandomConnectivity( "setRandomConnectivity",
- "Assigns connectivity with specified probability and seed",
- new OpFunc2< SparseMsg, double, long >(
- &SparseMsg::setRandomConnectivity ) );
+ "Assigns connectivity with specified probability and seed",
+ new OpFunc2< SparseMsg, double, long >(
+ &SparseMsg::setRandomConnectivity ) );
static DestFinfo setEntry( "setEntry",
- "Assigns single row,column value",
- new OpFunc3< SparseMsg, unsigned int, unsigned int, unsigned int >(
- &SparseMsg::setEntry ) );
+ "Assigns single row,column value",
+ new OpFunc3< SparseMsg, unsigned int, unsigned int, unsigned int >(
+ &SparseMsg::setEntry ) );
static DestFinfo unsetEntry( "unsetEntry",
- "Clears single row,column entry",
- new OpFunc2< SparseMsg, unsigned int, unsigned int >(
- &SparseMsg::unsetEntry ) );
+ "Clears single row,column entry",
+ new OpFunc2< SparseMsg, unsigned int, unsigned int >(
+ &SparseMsg::unsetEntry ) );
static DestFinfo clear( "clear",
- "Clears out the entire matrix",
- new OpFunc0< SparseMsg >(
- &SparseMsg::clear ) );
+ "Clears out the entire matrix",
+ new OpFunc0< SparseMsg >(
+ &SparseMsg::clear ) );
static DestFinfo transpose( "transpose",
- "Transposes the sparse matrix",
- new OpFunc0< SparseMsg >(
- &SparseMsg::transpose ) );
+ "Transposes the sparse matrix",
+ new OpFunc0< SparseMsg >(
+ &SparseMsg::transpose ) );
static DestFinfo pairFill( "pairFill",
- "Fills entire matrix using pairs of (x,y) indices to indicate "
- "presence of a connection. If the target is a FieldElement it"
- "automagically assigns FieldIndices.",
- new OpFunc2< SparseMsg,
- vector< unsigned int >, vector< unsigned int> >(
- &SparseMsg::pairFill ) );
+ "Fills entire matrix using pairs of (x,y) indices to indicate "
+ "presence of a connection. If the target is a FieldElement it"
+ "automagically assigns FieldIndices.",
+ new OpFunc2< SparseMsg,
+ vector< unsigned int >, vector< unsigned int> >(
+ &SparseMsg::pairFill ) );
static DestFinfo tripletFill( "tripletFill",
- "Fills entire matrix using triplets of (x,y,fieldIndex) to fully "
- "specify every connection in the sparse matrix.",
- new OpFunc3< SparseMsg,
- vector< unsigned int >, vector< unsigned int>,
- vector< unsigned int > >(
- &SparseMsg::tripletFill ) );
+ "Fills entire matrix using triplets of (x,y,fieldIndex) to fully "
+ "specify every connection in the sparse matrix.",
+ new OpFunc3< SparseMsg,
+ vector< unsigned int >, vector< unsigned int>,
+ vector< unsigned int > >(
+ &SparseMsg::tripletFill ) );
static DestFinfo tripletFill1( "tripletFill1",
- "Single contiguous array to fill entire connection matrix using "
- "triplets of (x,y, fieldindex) ordered as \n"
- "(x0, x1,... xn-1, y0, y1,... yn-1, fi0, fi1,... fi_n-1)\n",
- new OpFunc1< SparseMsg, vector< unsigned int > >(
- &SparseMsg::tripletFill1 ) );
+ "Single contiguous array to fill entire connection matrix using "
+ "triplets of (x,y, fieldindex) ordered as \n"
+ "(x0, x1,... xn-1, y0, y1,... yn-1, fi0, fi1,... fi_n-1)\n",
+ new OpFunc1< SparseMsg, vector< unsigned int > >(
+ &SparseMsg::tripletFill1 ) );
-////////////////////////////////////////////////////////////////////////
-// Assemble it all.
-////////////////////////////////////////////////////////////////////////
+ // Assemble it all.
static Finfo* sparseMsgFinfos[] =
{
- &numRows, // readonly value
- &numColumns, // readonly value
- &numEntries, // readonly value
- &connectionList, // value
- &matrixEntry, // ReadOnlyValue
- &columnIndex, // ReadOnlyValue
- &rowStart, // ReadOnlyValue
- &probability, // value
- &seed, // value
- &setRandomConnectivity, // dest
- &setEntry, // dest
- &unsetEntry, //dest
- &clear, //dest
- &transpose, //dest
- &pairFill, //dest
- &tripletFill, //dest
- &tripletFill1, //dest
+ &numRows, // readonly value
+ &numColumns, // readonly value
+ &numEntries, // readonly value
+ &connectionList, // value
+ &matrixEntry, // ReadOnlyValue
+ &columnIndex, // ReadOnlyValue
+ &rowStart, // ReadOnlyValue
+ &probability, // value
+ &seed, // value
+ &setRandomConnectivity, // dest
+ &setEntry, // dest
+ &unsetEntry, // dest
+ &clear, // dest
+ &transpose, // dest
+ &pairFill, // dest
+ &tripletFill, // dest
+ &tripletFill1, // dest
};
static Dinfo< short > dinfo;
static Cinfo sparseMsgCinfo (
- "SparseMsg", // name
- Msg::initCinfo(), // base class
- sparseMsgFinfos,
- sizeof( sparseMsgFinfos ) / sizeof( Finfo* ), // num Fields
- &dinfo
- );
+ "SparseMsg", // name
+ Msg::initCinfo(), // base class
+ sparseMsgFinfos,
+ sizeof( sparseMsgFinfos ) / sizeof( Finfo* ), // num Fields
+ &dinfo
+ );
return &sparseMsgCinfo;
}
static const Cinfo* sparseMsgCinfo = SparseMsg::initCinfo();
-//////////////////////////////////////////////////////////////////
-// Value Fields
-//////////////////////////////////////////////////////////////////
+// Value Fields
void SparseMsg::setProbability ( double probability )
{
p_ = probability;
@@ -195,18 +191,15 @@ double SparseMsg::getProbability ( ) const
return p_;
}
-void SparseMsg::setSeed ( unsigned long seed )
+void SparseMsg::setSeed (int seed)
{
- if( seed > 0 )
- seed_ = seed;
- else
- seed_ = rd_();
-
- rng_.seed( seed_ );
- randomConnect( p_ );
+ seed_ = seed;
+ if( seed_ >= 0)
+ rng_.setSeed((size_t)seed_);
+ randomConnect(p_);
}
-unsigned long SparseMsg::getSeed () const
+int SparseMsg::getSeed () const
{
return seed_;
}
@@ -271,7 +264,7 @@ vector< unsigned int > SparseMsg::getEntryPairs() const
void SparseMsg::setRandomConnectivity( double probability, long seed )
{
p_ = probability;
- rng_.seed( seed );
+ rng_.setSeed( seed );
randomConnect( probability );
}
@@ -387,11 +380,11 @@ void SparseMsg::tripletFill1( vector< unsigned int > v )
SparseMsg::SparseMsg( Element* e1, Element* e2, unsigned int msgIndex )
- : Msg( ObjId( managerId_, (msgIndex != 0) ? msgIndex: msg_.size() ),
- e1, e2 ),
+ : Msg(ObjId( managerId_, (msgIndex != 0) ? msgIndex: msg_.size() ), e1, e2),
numThreads_( 1 ),
nrows_( 0 ),
- p_( 0.0 ), seed_( 0 )
+ p_( 0.0 ),
+ seed_(-1)
{
unsigned int nrows = 0;
unsigned int ncolumns = 0;
@@ -411,9 +404,10 @@ SparseMsg::SparseMsg( Element* e1, Element* e2, unsigned int msgIndex )
// cout << Shell::myNode() << ": SparseMsg constructor between " << e1->getName() << " and " << e2->getName() << endl;
- // Init rng with random device.
- if( seed_ == 0 )
- rng_.seed( rd_() );
+ // Init rng with global seed if any.
+ seed_ = moose::getGlobalSeed();
+ if(seed_ >= 0)
+ setSeed(seed_);
}
SparseMsg::~SparseMsg()
@@ -485,7 +479,7 @@ unsigned int SparseMsg::randomConnect( double probability )
unsigned int synNum = 0;
for ( unsigned int j = 0; j < nRows; ++j )
{
- double r = dist_( rng_ ); // Want to ensure it is called each time round the loop.
+ double r = rng_.uniform(); // Want to ensure it is called each time round the loop.
if ( r < probability )
{
synIndex.push_back( synNum );
diff --git a/moose-core/msg/SparseMsg.h b/moose-core/msg/SparseMsg.h
index 0061a9fe4f30d183667fa19b17e2992c40599fee..17bfe7c8245f6723990e13ae6a0291db2a0ee5f2 100644
--- a/moose-core/msg/SparseMsg.h
+++ b/moose-core/msg/SparseMsg.h
@@ -87,8 +87,8 @@ public:
vector< unsigned int > getColIndex() const;
vector< unsigned int > getRowStart() const;
- unsigned long getSeed() const;
- void setSeed( unsigned long value );
+ int getSeed() const;
+ void setSeed( int value );
vector< unsigned int > getEntryPairs() const;
void setEntryPairs( vector< unsigned int > entries );
@@ -149,10 +149,8 @@ private:
static vector< SparseMsg* > msg_;
// RNG.
- unsigned long seed_;
- moose::MOOSE_RANDOM_DEVICE rd_;
- moose::MOOSE_RNG_DEFAULT_ENGINE rng_;
- moose::MOOSE_UNIFORM_DISTRIBUTION<double> dist_;
+ int seed_;
+ moose::RNG rng_;
};
#endif // _SPARSE_MSG_H
diff --git a/moose-core/pymoose/moosemodule.cpp b/moose-core/pymoose/moosemodule.cpp
index affdc78f65e3c2006ee607e00a13f9fa1d6168a4..96e37d66f9f9df55d42c6cea1c2f8352b6f26870 100644
--- a/moose-core/pymoose/moosemodule.cpp
+++ b/moose-core/pymoose/moosemodule.cpp
@@ -1555,7 +1555,7 @@ PyObject * moose_move(PyObject * dummy, PyObject * args)
PyDoc_STRVAR(moose_delete_documentation,
"delete(obj)->None\n"
"\n"
- "Delete the underlying moose object. This does not delete any of the\n"
+ "Delete the underlying moose object(s). This does not delete any of the\n"
"Python objects referring to this vec but does invalidate them. Any\n"
"attempt to access them will raise a ValueError.\n"
"\n"
@@ -1577,10 +1577,7 @@ PyObject * moose_delete(PyObject * dummy, PyObject * args)
{
return NULL;
}
- // if (!PyObject_IsInstance(obj, (PyObject*)&IdType)){
- // PyErr_SetString(PyExc_TypeError, "vec instance expected");
- // return NULL;
- // }
+
ObjId oid_;
if (PyObject_IsInstance(obj, (PyObject*)&IdType))
{
@@ -1598,13 +1595,14 @@ PyObject * moose_delete(PyObject * dummy, PyObject * args)
}
else
{
- PyErr_SetString(PyExc_ValueError, "cannot delete moose shell.");
- return NULL;
+ PyErr_WarnEx(PyExc_RuntimeWarning, "Cannot delete moose shell.", 1);
+ Py_RETURN_NONE;;
}
+
if (oid_ == ObjId())
{
- PyErr_SetString(PyExc_ValueError, "cannot delete moose shell.");
- return NULL;
+ PyErr_WarnEx(PyExc_RuntimeWarning, "Cannot delete moose shell.", 1);
+ Py_RETURN_NONE;
}
if ( oid_.bad() )
{
@@ -3252,14 +3250,14 @@ PyMODINIT_FUNC MODINIT(_moose)
clock_t defclasses_end = clock();
- LOG( moose::info, "`Time to define moose classes:"
+ LOG( moose::debug, "`Time to define moose classes:"
<< (defclasses_end - defclasses_start) * 1.0 /CLOCKS_PER_SEC
);
//PyGILState_Release(gstate);
clock_t modinit_end = clock();
- LOG( moose::info, "`Time to initialize module:"
+ LOG( moose::debug, "`Time to initialize module:"
<< (modinit_end - modinit_start) * 1.0 /CLOCKS_PER_SEC
);
diff --git a/moose-core/python/moose/genesis/writeKkit.py b/moose-core/python/moose/genesis/writeKkit.py
index 009f229911812e95e84ddc660050070ec855a699..27eaf50dda9b956a7f3f05f61be28f94e7878cef 100644
--- a/moose-core/python/moose/genesis/writeKkit.py
+++ b/moose-core/python/moose/genesis/writeKkit.py
@@ -664,7 +664,7 @@ def getColorCheck(color,GENESIS_COLOR_SEQUENCE):
index = color
return index
elif isinstance(color, tuple):
- color =[int(x) for x in color[0:3]]
+ color = [int(x) for x in color[0:3]]
index = nearestColorIndex(color, GENESIS_COLOR_SEQUENCE)
return index
elif isinstance(color, int):
@@ -832,4 +832,4 @@ if __name__ == "__main__":
if written:
print(" file written to ",output)
else:
- print(" could be written to kkit format")
\ No newline at end of file
+ print(" could be written to kkit format")
diff --git a/moose-core/python/moose/moose_test.py b/moose-core/python/moose/moose_test.py
index 362a590e1c731d5d6ed8a23c06ee3e2d3e428b50..78f2f921a397939368aae8e72e1b3437229ea3fb 100644
--- a/moose-core/python/moose/moose_test.py
+++ b/moose-core/python/moose/moose_test.py
@@ -4,7 +4,7 @@ Test MOOSE installation with moose-examples.
"""
-from __future__ import print_function
+from __future__ import print_function, division
__author__ = "Dilawar Singh"
__copyright__ = "Copyright 2016, Dilawar Singh"
@@ -102,8 +102,8 @@ def init_test_dir( ):
os.chdir( test_dir_ )
def suitable_for_testing( script ):
- with open( script ) as f:
- txt = f.read( )
+ with open(script, 'r', encoding='utf8') as f:
+ txt = f.read()
if not re.search( r'main\(\s*\)', txt ):
_logger.debug( 'Script %s does not contain main( )' % script )
return False, 'main( ) not found'
diff --git a/moose-core/python/moose/utils.py b/moose-core/python/moose/utils.py
index 17c262d81c1b6637512525585af2080ab4270fa6..a5aba9518e9fcdfb5c6f2e417d59d13f26123e53 100644
--- a/moose-core/python/moose/utils.py
+++ b/moose-core/python/moose/utils.py
@@ -521,7 +521,7 @@ def assignDefaultTicks(modelRoot='/model', dataRoot='/data', solver='hsolve'):
def stepRun(simtime, steptime, verbose=True, logger=None):
"""Run the simulation in steps of `steptime` for `simtime`."""
- clock = moose.Clock('/clock')
+ clock = moose.element('/clock')
if verbose:
msg = 'Starting simulation for %g' % (simtime)
if logger is None:
diff --git a/moose-core/randnum/CMakeLists.txt b/moose-core/randnum/CMakeLists.txt
index cc4de6b76f7791ed222525d41f499689770447dc..a926912a02e9e63b9d96f8562e2b07d32d025a5b 100644
--- a/moose-core/randnum/CMakeLists.txt
+++ b/moose-core/randnum/CMakeLists.txt
@@ -1,11 +1,10 @@
cmake_minimum_required(VERSION 2.8)
-if( ${CMAKE_SOURCE_DIR} EQUAL ${CMAKE_CURRENT_SOURCE_DIR} )
- add_definitions( -std=c++11 -g -Wall )
-endif()
-
add_executable( normal_dist
- ${CMAKE_CURRENT_SOURCE_DIR}/test_normal_dist.cpp)
+ ${CMAKE_CURRENT_SOURCE_DIR}/test_normal_dist.cpp
+ )
+
+add_library(randnum RNG.cpp)
enable_testing()
add_test( NAME test_normal_dist COMMAND $<TARGET_FILE:normal_dist> )
diff --git a/moose-core/randnum/RNG.cpp b/moose-core/randnum/RNG.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..6fa4857907f0ee791db71496a7b74908a3157c93
--- /dev/null
+++ b/moose-core/randnum/RNG.cpp
@@ -0,0 +1,75 @@
+/***
+ * Description: Random number generator.
+ *
+ * Created: 2019-05-26
+
+ * Author: Dilawar Singh <dilawars@ncbs.res.in>
+ * Organization: NCBS Bangalore
+ * License: MIT License
+ */
+
+#include "RNG.h"
+
+namespace moose {
+
+RNG::RNG () /* constructor */
+{
+ // Setup a random seed if possible.
+ setRandomSeed( );
+}
+
+RNG::~RNG () /* destructor */
+{ ; }
+
+void RNG::setRandomSeed( )
+{
+ MOOSE_RANDOM_DEVICE rd_;
+ setSeed( rd_() );
+}
+
+double RNG::getSeed( void )
+{
+ return seed_;
+}
+
+/**
+ * @brief If seed if 0 then set seed to a random number else set seed to
+ * the given number.
+ *
+ * @param seed
+ */
+void RNG::setSeed( const unsigned long seed )
+{
+ seed_ = seed;
+ if( seed == 0 )
+ {
+ MOOSE_RANDOM_DEVICE rd_;
+ seed_ = rd_();
+ }
+ rng_.seed( seed_ );
+}
+
+/**
+ * @brief Generate a uniformly distributed random number between a and b.
+ *
+ * @param a Lower limit (inclusive)
+ * @param b Upper limit (inclusive).
+ */
+double RNG::uniform( const double a, const double b)
+{
+ return ( b - a ) * dist_( rng_ ) + a;
+}
+
+/**
+ * @brief Return a uniformly distributed random number between 0 and 1
+ * (exclusive).
+ *
+ * @return randum number.
+ */
+double RNG::uniform( void )
+{
+ return dist_( rng_ );
+}
+
+}
+
diff --git a/moose-core/randnum/RNG.h b/moose-core/randnum/RNG.h
index 758e599ba4ea21f666607e2a0d54bfed1f635e30..711a769a28d4049301c92a12301a67cdab186a79 100644
--- a/moose-core/randnum/RNG.h
+++ b/moose-core/randnum/RNG.h
@@ -22,6 +22,7 @@
#include <limits>
#include <iostream>
#include <random>
+#include <cassert>
#include "Definitions.h"
#include "Distributions.h"
@@ -30,7 +31,6 @@ using namespace std;
namespace moose
{
-
/*
* =====================================================================================
* Class: RNG
@@ -38,76 +38,28 @@ namespace moose
* =====================================================================================
*/
-template < typename T >
class RNG
{
public:
- RNG () /* constructor */
- {
- // Setup a random seed if possible.
- setRandomSeed( );
- }
-
- ~RNG () /* destructor */
- { ; }
+ RNG ();
+ ~RNG();
- void setRandomSeed( )
- {
- MOOSE_RANDOM_DEVICE rd_;
- setSeed( rd_() );
- }
+ void setRandomSeed( );
/* ==================== ACCESSORS ======================================= */
- T getSeed( void )
- {
- return seed_;
- }
-
- /* ==================== MUTATORS ======================================= */
- /**
- * @brief If seed if 0 then set seed to a random number else set seed to
- * the given number.
- *
- * @param seed
- */
- void setSeed( const unsigned long seed )
- {
- seed_ = seed;
- if( seed == 0 )
- {
- MOOSE_RANDOM_DEVICE rd_;
- seed_ = rd_();
- }
- rng_.seed( seed_ );
- }
-
- /**
- * @brief Generate a uniformly distributed random number between a and b.
- *
- * @param a Lower limit (inclusive)
- * @param b Upper limit (inclusive).
- */
- T uniform( const T a, const T b)
- {
- return ( b - a ) * dist_( rng_ ) + a;
- }
-
- /**
- * @brief Return a uniformly distributed random number between 0 and 1
- * (exclusive).
- *
- * @return randum number.
- */
- T uniform( void )
- {
- return dist_( rng_ );
- }
+ double getSeed( void );
+
+ void setSeed( const unsigned long seed );
+
+ double uniform( const double a, const double b);
+
+ double uniform( void );
private:
/* ==================== DATA MEMBERS ======================================= */
- T res_;
- T seed_;
+ double res_;
+ size_t seed_;
moose::MOOSE_RNG_DEFAULT_ENGINE rng_;
moose::MOOSE_UNIFORM_DISTRIBUTION<double> dist_;
diff --git a/moose-core/scheduling/Clock.cpp b/moose-core/scheduling/Clock.cpp
index e407bb63883ae39be46dc6eb7a15d2fa81be2d0b..aa7feb29e2fed635d349dc2df835ad862a67b7ee 100644
--- a/moose-core/scheduling/Clock.cpp
+++ b/moose-core/scheduling/Clock.cpp
@@ -49,9 +49,8 @@
*/
#include "../basecode/header.h"
-#include "Clock.h"
-#include "../utility/numutil.h"
#include "../utility/print_function.hpp"
+#include "Clock.h"
#if PARALLELIZE_CLOCK_USING_CPP11_ASYNC
#include <future>
diff --git a/moose-core/signeur/testSigNeur.cpp b/moose-core/signeur/testSigNeur.cpp
index 9ea85ed4e250cf736a0e2fd425383911385c4fdf..4e0a7f6f4b11211402439facbe9968e8efc9bfca 100644
--- a/moose-core/signeur/testSigNeur.cpp
+++ b/moose-core/signeur/testSigNeur.cpp
@@ -9,7 +9,7 @@
**********************************************************************/
#ifdef DO_UNIT_TESTS
-#include "header.h"
+#include "../basecode/header.h"
#include "Adaptor.h"
#include "../shell/Shell.h"
#include "../shell/Wildcard.h"
diff --git a/moose-core/synapse/SeqSynHandler.cpp b/moose-core/synapse/SeqSynHandler.cpp
index 7a0056dd94bb5ee8b7b0e12d8abb625fdfad1e99..da94fc4299d1bbf2bc6142ef7208f0084b1275c5 100644
--- a/moose-core/synapse/SeqSynHandler.cpp
+++ b/moose-core/synapse/SeqSynHandler.cpp
@@ -15,7 +15,7 @@
#include "SynHandlerBase.h"
#include "RollingMatrix.h"
#include "SeqSynHandler.h"
-#include "../external/muparser/include/muParser.h"
+#include "../builtins/MooseParser.h"
const Cinfo* SeqSynHandler::initCinfo()
{
diff --git a/moose-core/synapse/testSynapse.cpp b/moose-core/synapse/testSynapse.cpp
index 427f08b1c7a541411e5f7085a2b72d85e1dedf4f..d7f32b300d877a9056d20e267d47c82bee5ae6fb 100644
--- a/moose-core/synapse/testSynapse.cpp
+++ b/moose-core/synapse/testSynapse.cpp
@@ -10,7 +10,7 @@
#ifdef DO_UNIT_TESTS
#include <queue>
-#include "header.h"
+#include "../basecode/header.h"
#include "Synapse.h"
#include "SynEvent.h"
#include "SynHandlerBase.h"
diff --git a/moose-core/tests/alpha/ex7.6_func_controls_reac_rate.py b/moose-core/tests/alpha/ex7.6_func_controls_reac_rate.py
new file mode 100644
index 0000000000000000000000000000000000000000..b8c8fb4c64b3f80d9014633108baba45a55eaf1d
--- /dev/null
+++ b/moose-core/tests/alpha/ex7.6_func_controls_reac_rate.py
@@ -0,0 +1,67 @@
+########################################################################
+# This example illustrates how a function can be used to control a reaction
+# rate. This kind of calculation is appropriate when we need to link
+# different kinds of physical processses with chemical reactions, for
+# example, membrane curvature with molecule accumulation. The use of
+# functions to modify reaction rates should be avoided in purely chemical
+# systems since they obscure the underlying chemistry, and do not map
+# cleanly to stochastic calculations.
+#
+# In this example we simply have a molecule C that controls the forward
+# rate of a reaction that converts A to B. C is a function of location
+# on the cylinder, and is fixed. In more elaborate computations we could
+# have a function of multiple molecules, some of which could be changing and
+# others could be buffered.
+#
+# Copyright (C) Upinder S. Bhalla NCBS 2018
+# Released under the terms of the GNU Public License V3.
+########################################################################
+
+import numpy as np
+import moose
+import pylab
+import rdesigneur as rd
+
+
+def makeFuncRate():
+ model = moose.Neutral( '/library' )
+ model = moose.Neutral( '/library/chem' )
+ compt = moose.CubeMesh( '/library/chem/compt' )
+ compt.volume = 1e-15
+ A = moose.Pool( '/library/chem/compt/A' )
+ B = moose.Pool( '/library/chem/compt/B' )
+ C = moose.Pool( '/library/chem/compt/C' )
+ reac = moose.Reac( '/library/chem/compt/reac' )
+ func = moose.Function( '/library/chem/compt/reac/func' )
+ func.x.num = 1
+ func.expr = "(x0/1e8)^2"
+ moose.connect( C, 'nOut', func.x[0], 'input' )
+ moose.connect( func, 'valueOut', reac, 'setNumKf' )
+ moose.connect( reac, 'sub', A, 'reac' )
+ moose.connect( reac, 'prd', B, 'reac' )
+
+ A.concInit = 1
+ B.concInit = 0
+ C.concInit = 0
+ reac.Kb = 1
+
+
+makeFuncRate()
+
+rdes = rd.rdesigneur(
+ turnOffElec = True,
+ #This subdivides the 50-micron cylinder into 2 micron voxels
+ diffusionLength = 2e-6,
+ cellProto = [['somaProto', 'soma', 5e-6, 50e-6]],
+ chemProto = [['chem', 'chem']],
+ chemDistrib = [['chem', 'soma', 'install', '1' ]],
+ plotList = [['soma', '1', 'dend/A', 'conc', 'A conc', 'wave'],
+ ['soma', '1', 'dend/C', 'conc', 'C conc', 'wave']],
+)
+rdes.buildModel()
+
+C = moose.element( '/model/chem/dend/C' )
+C.vec.concInit = [ 1+np.sin(x/5.0) for x in range( len(C.vec) ) ]
+moose.reinit()
+moose.start(10)
+rdes.display()
diff --git a/moose-core/tests/alpha/function.py b/moose-core/tests/alpha/function.py
new file mode 100644
index 0000000000000000000000000000000000000000..1dc982bf35ccbc05152413dd221e54abd2bd02e9
--- /dev/null
+++ b/moose-core/tests/alpha/function.py
@@ -0,0 +1,160 @@
+# function.py ---
+
+import numpy as np
+import sys
+import moose
+
+simtime = 1.0
+plot_ = False
+if plot_:
+ import matplotlib.pyplot as plt
+
+def example():
+ """Function objects can be used to evaluate expressions with arbitrary
+ number of variables and constants. We can assign expression of the
+ form::
+
+ f(c0, c1, ..., cM, x0, x1, ..., xN, y0,..., yP )
+
+ where `c_i`'s are constants and `x_i`'s and `y_i`'s are variables.
+
+ The constants must be defined before setting the expression and
+ variables are connected via messages. The constants can have any
+ name, but the variable names must be of the form x{i} or y{i}
+ where i is increasing integer starting from 0.
+
+ The `x_i`'s are field elements and you have to set their number
+ first (function.x.num = N). Then you can connect any source field
+ sending out double to the 'input' destination field of the
+ `x[i]`.
+
+ The `y_i`'s are useful when the required variable is a value field
+ and is not available as a source field. In that case you connect
+ the `requestOut` source field of the function element to the
+ `get{Field}` destination field on the target element. The `y_i`'s
+ are automatically added on connecting. Thus, if you call::
+
+ moose.connect(function, 'requestOut', a, 'getSomeField')
+ moose.connect(function, 'requestOut', b, 'getSomeField')
+
+ then ``a.someField`` will be assigned to ``y0`` and
+ ``b.someField`` will be assigned to ``y1``.
+
+ In this example we evaluate the expression: ``z = c0 * exp(c1 *
+ x0) * cos(y0)``
+
+ with x0 ranging from -1 to +1 and y0 ranging from -pi to
+ +pi. These values are stored in two stimulus tables called xtab
+ and ytab respectively, so that at each timestep the next values of
+ x0 and y0 are assigned to the function.
+
+ Along with the value of the expression itself we also compute its
+ derivative with respect to y0 and its derivative with respect to
+ time (rate). The former uses a five-point stencil for the
+ numerical differentiation and has a glitch at y=0. The latter uses
+ backward difference divided by dt.
+
+ Unlike Func class, the number of variables and constants are
+ unlimited in Function and you can set all the variables via
+ messages.
+
+ """
+ demo = moose.Neutral('/model')
+ function = moose.Function('/model/function')
+ function.c['c0'] = 1.0
+ function.c['c1'] = 2.0
+ function.x.num = 1
+ function.expr = 'c0 * exp(c1*x0) * cos(y0) + sin(t)'
+ # mode 0 - evaluate function value, derivative and rate
+ # mode 1 - just evaluate function value,
+ # mode 2 - evaluate derivative,
+ # mode 3 - evaluate rate
+ function.mode = 0
+ function.independent = 'y0'
+ nsteps = 10000
+ xarr = np.linspace(0.0, 1.0, nsteps)
+ # Stimulus tables allow you to store sequences of numbers which
+ # are delivered via the 'output' message at each time step. This
+ # is a placeholder and in real scenario you will be using any
+ # sourceFinfo that sends out a double value.
+ input_x = moose.StimulusTable('/xtab')
+ input_x.vector = xarr
+ input_x.startTime = 0.0
+ input_x.stepPosition = xarr[0]
+ input_x.stopTime = simtime
+ moose.connect(input_x, 'output', function.x[0], 'input')
+
+ yarr = np.linspace(-np.pi, np.pi, nsteps)
+ input_y = moose.StimulusTable('/ytab')
+ input_y.vector = yarr
+ input_y.startTime = 0.0
+ input_y.stepPosition = yarr[0]
+ input_y.stopTime = simtime
+ moose.connect(function, 'requestOut', input_y, 'getOutputValue')
+
+ # data recording
+ result = moose.Table('/ztab')
+ moose.connect(result, 'requestOut', function, 'getValue')
+ derivative = moose.Table('/zprime')
+ moose.connect(derivative, 'requestOut', function, 'getDerivative')
+ rate = moose.Table('/dz_by_dt')
+ moose.connect(rate, 'requestOut', function, 'getRate')
+ x_rec = moose.Table('/xrec')
+ moose.connect(x_rec, 'requestOut', input_x, 'getOutputValue')
+ y_rec = moose.Table('/yrec')
+ moose.connect(y_rec, 'requestOut', input_y, 'getOutputValue')
+
+ dt = simtime/nsteps
+ for ii in range(32):
+ moose.setClock(ii, dt)
+ moose.reinit()
+ moose.start(simtime)
+
+ # Uncomment the following lines and the import matplotlib.pyplot as plt on top
+ # of this file to display the plot.
+ if plot_:
+ plt.plot(x_rec.vector, result.vector, 'r-', label='z = {}'.format(function.expr))
+ plt.subplot(4,1,1)
+ z = function.c['c0'] * np.exp(function.c['c1'] * xarr) * np.cos(yarr) + np.sin(np.arange(len(xarr)) * dt)
+ zz = result.vector[1:]
+ err = z[1:] - zz[1:]
+ assert (np.abs(err) <= 0.05).all(), err
+ assert (np.mean(err) <= 0.001), np.mean(err)
+
+ if plot_:
+ plt.plot(xarr, z, 'b--', label='numpy computed')
+ plt.xlabel('x')
+ plt.ylabel('z')
+ plt.legend()
+
+ if plot_:
+ plt.subplot(4,1,2)
+ plt.plot(y_rec.vector, derivative.vector, 'r-', label='dz/dy0')
+ # derivatives computed by putting x values in the analytical formula
+ dzdy = function.c['c0'] * np.exp(function.c['c1'] * xarr) * (- np.sin(yarr))
+ err = np.abs(dzdy - derivative.vector[1:])
+ assert (err < 1e-2).all(), err
+ assert (np.mean(err) < 1e-3), np.mean(err)
+
+ if plot_:
+ plt.plot(yarr, dzdy, 'b--', label='numpy computed')
+ plt.xlabel('y')
+ plt.ylabel('dz/dy')
+ plt.legend()
+
+ if plot_:
+ plt.subplot(4,1,3)
+ # *** BEWARE *** The first two entries are spurious. Entry 0 is
+ # *** from reinit sending out the defaults. Entry 2 is because
+ # *** there is no lastValue for computing real forward difference.
+ plt.plot(np.arange(2, len(rate.vector), 1) * dt, rate.vector[2:], 'r-', label='dz/dt')
+ dzdt = np.diff(z)/dt
+ plt.plot(np.arange(0, len(dzdt), 1.0) * dt, dzdt, 'b--', label='numpy computed')
+ plt.xlabel('t')
+ plt.ylabel('dz/dt')
+ plt.legend()
+ plt.tight_layout()
+ plt.show()
+
+if __name__ == '__main__':
+ example()
diff --git a/moose-core/tests/python/test_socket_streamer_multitab.py b/moose-core/tests/alpha/test_socket_streamer_multitab.py
similarity index 100%
rename from moose-core/tests/python/test_socket_streamer_multitab.py
rename to moose-core/tests/alpha/test_socket_streamer_multitab.py
diff --git a/moose-core/tests/python/test_socket_streamer_uds.py b/moose-core/tests/alpha/test_socket_streamer_uds.py
similarity index 100%
rename from moose-core/tests/python/test_socket_streamer_uds.py
rename to moose-core/tests/alpha/test_socket_streamer_uds.py
diff --git a/moose-core/tests/issues/issue_239.py b/moose-core/tests/issues/issue_239.py
new file mode 100644
index 0000000000000000000000000000000000000000..be0576b3a04b045637079229d51ef319bf7fb577
--- /dev/null
+++ b/moose-core/tests/issues/issue_239.py
@@ -0,0 +1,41 @@
+import moose
+print( 'Using moose from %s' % moose.__file__)
+
+modelRoot = moose.Neutral('/model')
+compt = moose.CubeMesh('/model/kinetics')
+p1 = moose.BufPool('/model/kinetics/Ca')
+function = moose.Function('/model/kinetics/Ca/func')
+#function out to pool
+moose.connect( function, 'valueOut', p1 ,'setConc' )
+#input pools to be connected to fuction
+S1 = moose.BufPool( '/model/kinetics/s1' )
+S2 = moose.BufPool( '/model/kinetics/s2' )
+
+initiexpr = function.expr
+#S1 connected to function
+numVariables = function.numVars
+expr = ""
+expr = (function.expr+'+'+'x'+str(numVariables))
+expr = expr.lstrip("0 +")
+expr = expr.replace(" ","")
+function.expr = expr
+s1msg = moose.connect( S1, 'nOut', function.x[numVariables], 'input' )
+#S2 connected to function
+numVariables = function.numVars
+expr = ""
+expr = (function.expr+'+'+'x'+str(numVariables))
+expr = expr.lstrip("0 +")
+expr = expr.replace(" ","")
+function.expr = expr
+s2msg = moose.connect( S2, 'nOut', function.x[numVariables], 'input' )
+
+compts = moose.wildcardFind(modelRoot.path+'/##[ISA=ChemCompt]')
+solver = 'gsl'
+moose.mooseAddChemSolver('/model',solver)
+moose.mooseDeleteChemSolver('/model')
+
+#moose.delete(s1msg)
+#moose.delete(s2msg)
+#deleting the function
+#moose.delete(function) #deleting this will not cause seg fault
+print(function.expr) #function's expr still has the expression which is causing the problem
diff --git a/moose-core/tests/issues/issue_47.py b/moose-core/tests/issues/issue_47.py
index d2d6d964d4a5fe8710efa78e4aaf471d1f61ae34..b1d682d6517edc1e26a8aca84c6611a6c42506aa 100644
--- a/moose-core/tests/issues/issue_47.py
+++ b/moose-core/tests/issues/issue_47.py
@@ -1,8 +1,14 @@
# -*- coding: utf-8 -*-
# Issue 47 on moose-core
import moose
+import os
+sdir = os.path.dirname( __file__ )
print( '[INFO] Using moose from %s' % moose.__file__ )
-# moose.loadModel('../data/acc94.g','/acc94','gsl')
-moose.loadModel('../data/acc94.g','/acc94','gssa')
-moose.reinit()
-moose.run( 10 )
+print( '[WONTFIX] See https://github.com/BhallaLab/moose-core/issues/47')
+if False:
+ moose.loadModel(os.path.join(sdir,'../data/acc94.g'),'/acc94','gsl')
+ #moose.loadModel(os.path.join(sdir,'../data/acc94.g'),'/acc94','gssa')
+ moose.reinit()
+ moose.start( 10 )
+else:
+ quit(0)
diff --git a/moose-core/tests/issues/issue_93.py b/moose-core/tests/issues/issue_93.py
index 3a043308b70628164b4820ab5c9f33b9b0eafd85..4c4722428005ca55fdb9a40a4daf77c3a03d8891 100644
--- a/moose-core/tests/issues/issue_93.py
+++ b/moose-core/tests/issues/issue_93.py
@@ -2,7 +2,7 @@
# Issue #93 on moose-core
import numpy as np
-import pylab as pl
+import matplotlib.pyplot as plt
import moose
import os
import sys
@@ -13,7 +13,7 @@ d = os.path.split( os.path.abspath( __file__ ) )[0]
def loadAndRun(solver=True):
simtime = 500e-3
- model = moose.loadModel('../data/h10.CNG.swc', '/cell')
+ model = moose.loadModel(os.path.join(d, '../data/h10.CNG.swc'), '/cell')
comp = moose.element('/cell/apical_e_177_0')
soma = moose.element('/cell/soma')
for i in range(10):
@@ -40,20 +40,18 @@ def loadAndRun(solver=True):
return vec
def main( ):
- print( '[INFO] See the detailed issue in %s/hsolve' % d )
- quit()
eeVec = loadAndRun( False )
hsolveVec = loadAndRun( True )
clk = moose.Clock( '/clock' )
print( '[DEBUG] Total entries %s' % len( eeVec ))
- t = pl.linspace(0, clk.currentTime, len( eeVec ))
- pl.plot(t, eeVec, label = 'ee' )
- pl.plot( t, hsolveVec, label = 'hsolve' )
+ t = np.linspace(0, clk.currentTime, len( eeVec ))
+ plt.plot(t, eeVec, label = 'ee' )
+ plt.plot( t, hsolveVec, label = 'hsolve' )
outfile = '%s.png' % sys.argv[0]
- pl.legend( )
- pl.savefig( outfile )
+ plt.legend( )
+ plt.savefig( outfile )
print( '[INFO] Wrote results to %s' % outfile )
- pl.show()
+ return 1
if __name__ == '__main__':
main()
diff --git a/moose-core/tests/python/test_Xreacs2.py b/moose-core/tests/python/test_Xreacs2.py
index 2fb36cfb16f05a3e4669b6f201f30867330a25f1..c02a2cc3f32d1ac593cfe1b1661697b5d4be81b3 100644
--- a/moose-core/tests/python/test_Xreacs2.py
+++ b/moose-core/tests/python/test_Xreacs2.py
@@ -1,7 +1,7 @@
# -*- coding: utf-8 -*-
import os
-import sys
import moose
+print( "[INFO ] Using moose from %s" % moose.__file__ )
import numpy as np
import moose.fixXreacs as fixXreacs
diff --git a/moose-core/tests/python/test_expr_parser.py b/moose-core/tests/python/test_expr_parser.py
new file mode 100644
index 0000000000000000000000000000000000000000..fabbc28e40cfb8ebfb51b61d3c171d085d0af20f
--- /dev/null
+++ b/moose-core/tests/python/test_expr_parser.py
@@ -0,0 +1,346 @@
+# -*- coding: utf-8 -*-
+"""test_muparser.py:
+
+odified from https://elifesciences.org/articles/25827
+Fig4.py
+"""
+import sys
+import re
+import numpy as np
+import moose
+import rdesigneur as rd
+print( "[INFO ] Using moose from %s" % moose.__file__ )
+
+def parseExpr( expr, params, hasCa ):
+ if hasCa:
+ expr = expr.replace( 'Ca', 'x0' )
+ expr = expr.replace( 'A', 'x1' )
+ expr = expr.replace( 'B', 'x2' )
+ else:
+ expr = expr.replace( 'Ca', 'x0' ) # happens in the negFF model
+ expr = expr.replace( 'A', 'x0' ) # This is the usual case.
+ expr = expr.replace( 'B', 'x1' )
+
+ parts = re.split( 'k', expr )
+ ret = parts[0]
+ for i in parts[1:]:
+ ret += str( params[ 'k' + i[:2] ] )
+ ret += i[2:]
+
+ if hasCa:
+ return 'x3*( ' + ret + ')'
+ else:
+ return 'x2*( ' + ret + ')'
+
+def makeChemProto( name, Aexpr, Bexpr, params ):
+ sw = params['stimWidth']
+ diffLength = params['diffusionLength']
+ dca = params['diffConstA'] * diffLength * diffLength
+ dcb = params['diffConstB'] * diffLength * diffLength
+
+ # Objects
+ chem = moose.Neutral( '/library/' + name )
+ compt = moose.CubeMesh( '/library/' + name + '/' + name )
+ A = moose.Pool( compt.path + '/A' )
+ B = moose.Pool( compt.path + '/B' )
+ Z = moose.BufPool( compt.path + '/Z' )
+ Ca = moose.BufPool( compt.path + '/Ca' )
+ phase = moose.BufPool( compt.path + '/phase' )
+ vel = moose.BufPool( compt.path + '/vel' )
+ ampl = moose.BufPool( compt.path + '/ampl' )
+ Adot = moose.Function( A.path + '/Adot' )
+ Bdot = moose.Function( B.path + '/Bdot' )
+ CaStim = moose.Function( Ca.path + '/CaStim' )
+ A.diffConst = dca
+ B.diffConst = dcb
+
+ # Equations
+
+ Adot.expr = parseExpr( Aexpr, params, True )
+ Bdot.expr = parseExpr( Bexpr, params, False )
+ CaStim.expr = 'x2 * exp( -((x0 - t)^2)/(2* ' + str(sw*sw) + ') )'
+
+ #print Adot.expr
+ #print Bdot.expr
+ #print CaStim.expr
+
+ # Connections
+ Adot.x.num = 4
+ moose.connect( Ca, 'nOut', Adot.x[0], 'input' )
+ moose.connect( A, 'nOut', Adot.x[1], 'input' )
+ moose.connect( B, 'nOut', Adot.x[2], 'input' )
+ moose.connect( Z, 'nOut', Adot.x[3], 'input' )
+ moose.connect( Adot, 'valueOut', A, 'increment' )
+
+ Bdot.x.num = 3
+ if name[:5] == 'negFF':
+ moose.connect( Ca, 'nOut', Bdot.x[0], 'input' )
+ print('Doing special msg')
+ else:
+ moose.connect( A, 'nOut', Bdot.x[0], 'input' )
+ moose.connect( B, 'nOut', Bdot.x[1], 'input' )
+ moose.connect( Z, 'nOut', Bdot.x[2], 'input' )
+ moose.connect( Bdot, 'valueOut', B, 'increment' )
+
+ CaStim.x.num = 3
+ moose.connect( phase, 'nOut', CaStim.x[0], 'input' )
+ moose.connect( vel, 'nOut', CaStim.x[1], 'input' )
+ moose.connect( ampl, 'nOut', CaStim.x[2], 'input' )
+ moose.connect( CaStim, 'valueOut', Ca, 'setN' )
+
+ return compt
+
+
+def makeBis( args = None ):
+ params = {
+ 'k0a':0.1, # Constant
+ 'k1a':-5.0, # Coeff for A
+ 'k2a':5.0, # Coeff for A^2
+ 'k3a':-1.0, # Coeff for A^3
+ 'k4a':10.0, # turnon of A by A and Ca
+ 'k5a':-5.0, # Turnoff of A by B
+ 'k1b':0.01, # turnon of B by A
+ 'k2b':-0.01, # Decay rate of B
+ 'diffusionLength':1.0e-6, # Diffusion characteristic length, used as voxel length too.
+ 'dendDiameter': 10e-6, # Diameter of section of dendrite in model
+ 'dendLength': 100e-6, # Length of section of dendrite in model
+ 'diffConstA':5.0, # Diffusion constant of A
+ 'diffConstB':2.0, # Diffusion constant of B
+ 'stimWidth' :1.0, # Stimulus width in seconds
+ 'stimAmplitude':1.0, # Stimulus amplitude, arb units. From FHN review
+ 'blankVoxelsAtEnd':10, # of voxels to leave blank at end of cylinder
+ 'preStimTime':10.0, # Time to run before turning on stimulus.
+ 'postStimTime':40.0, # Time to run after stimulus. ~3x decay time
+ 'settleTime':20.0, # Settling time of response, after stimulus.
+ # To include in analysis of total response over
+ # entire dendrite.
+ 'fnumber':1, # Number to append to fname
+ }
+
+ for i in args:
+ params[i] = args[i]
+
+ makeChemProto( 'bis',
+ 'k0a + k1a*A + k2a*A*A + k3a*A*A*A + k4a*Ca*A/(1+A+10*B) + k5a*A*B',
+ 'k1b*A*A + k2b*B',
+ params )
+ return params
+
+def makeFHN( args = None ):
+ params = {
+ 'k_t':2.5, # Time-const.
+ 'k_a':0.7, # Coeff1
+ 'k_b':0.8, # Coeff2
+ 'kxa': 2.0, # Offset for V for FHN eqns.
+ 'kxb': 0.8, # Offset for W for FHN eqns.
+ 'diffusionLength':1.0e-6, # Diffusion characteristic length, used as voxel length too.
+ 'dendDiameter': 10e-6, # Diameter of section of dendrite in model
+ 'dendLength': 100e-6, # Length of section of dendrite in model
+ 'diffConstA':7.5, # Diffusion constant of A
+ 'diffConstB':5.0, # Diffusion constant of B
+ 'stimWidth' :1.0, # Stimulus width in seconds
+ 'stimAmplitude':0.4, # Stimulus amplitude, arb units. From FHN review
+ 'blankVoxelsAtEnd':10, # of voxels to leave blank at end of cylinder
+ 'preStimTime':10.0, # Time to run before turning on stimulus.
+ 'postStimTime':40.0, # Time to run after stimulus. ~3x decay time
+ 'settleTime':20.0, # Settling time of response, after stimulus.
+ # To include in analysis of total response over
+ # entire dendrite.
+ 'fnumber': 1, # Number to append to fname
+ }
+
+ for i in args:
+ params[i] = args[i]
+
+ makeChemProto( 'fhn',
+ '5.0*(A - kxa - (A-kxa)^3/3 - (B-kxb) + Ca)',
+ '(A-kxa + k_a - k_b*(B-kxb))/k_t',
+ params )
+ # We do this to get the system to settle at the start.
+ B = moose.element( '/library/fhn/fhn/B' )
+ B.nInit = 0.2
+ return params
+
+
+def makeNegFB( args = None ):
+ params = {
+ 'k1a':-0.1, # Coeff for decay of A, slow.
+ 'k2a':-0.2, # Coeff for turnoff of A by B, medium.
+ 'k3a':10.0, # turnon of A by Ca, fast.
+ 'k1b':0.2, # turnon of B by A, medium
+ 'k2b':-0.1, # Decay rate of B, slow
+ 'diffusionLength':1.0e-6, # Diffusion characteristic length, used as voxel length too.
+ 'dendDiameter': 10e-6, # Diameter of section of dendrite in model
+ 'dendLength': 100e-6, # Length of section of dendrite in model
+ 'diffConstA':0.5, # Diffusion constant of A
+ 'diffConstB':1.0, # Diffusion constant of B
+ 'stimWidth' :1.0, # Stimulus width in seconds
+ 'stimAmplitude':1.0, # Stimulus amplitude, arb units. From FHN review
+ 'blankVoxelsAtEnd':10, #of voxels to leave blank at end of cylinder
+ 'preStimTime':10.0, # Time to run before turning on stimulus.
+ 'postStimTime':40.0, # Time to run after stimulus. ~3x decay time
+ 'settleTime':20.0, # Settling time of response, after stimulus.
+ # To include in analysis of total response over
+ # entire dendrite.
+ 'fnumber':1, # Number to append to fname
+ }
+
+ for i in args:
+ params[i] = args[i]
+
+ makeChemProto( 'negFB',
+ 'k1a*A + k2a*A*B + k3a*Ca',
+ 'k1b*A + k2b*B',
+ params )
+ return params
+
+# Was negFF2 in earlier versions of abstrModelEqns
+def makeNegFF( args = None ):
+ params = {
+ 'k1a':-0.1, # Coeff for decay of A, slow.
+ 'k2a':-0.01, # Coeff for turnoff of A by B, medium.
+ 'k3a':10.0, # turnon of A by Ca, fast.
+ 'k4a':40.0, # amount of B inhibition of turnon of A by Ca.
+ 'k1b':2.0, # turnon of B by Ca, medium
+ 'k2b':-0.05, # Decay rate of B, slow
+ 'diffusionLength':1.0e-6, # Diffusion characteristic length, used as voxel length too.
+ 'dendDiameter': 10e-6, # Diameter of section of dendrite in model
+ 'dendLength': 100e-6, # Length of section of dendrite in model
+ 'diffConstA':0.02, # Diffusion constant of A
+ 'diffConstB':0.4, # Diffusion constant of B
+ 'stimWidth' :1.0, # Stimulus width in seconds
+ 'stimAmplitude':10.0, # Stimulus amplitude, arb units. From FHN review
+ 'blankVoxelsAtEnd':10, # of voxels to leave blank at end of cylinder
+ 'preStimTime':10.0, # Time to run before turning on stimulus.
+ 'postStimTime':40.0, # Time to run after stimulus. ~3x decay time
+ 'settleTime':20.0, # Settling time of response, after stimulus.
+ # To include in analysis of total response over
+ # entire dendrite.
+ 'fnumber':1, # Number to append to fname
+ }
+
+ for i in args:
+ params[i] = args[i]
+
+ makeChemProto( 'negFF',
+ 'k1a*A + k2a*A*B + k3a*Ca/(1+k4a*B*B)',
+ 'k1b*Ca + k2b*B',
+ params )
+
+ return params
+
+
+def singleCompt( name, params ):
+ print('=============')
+ print('[INFO] Making compartment %s' % name)
+ mod = moose.copy( '/library/' + name + '/' + name, '/model' )
+ A = moose.element( mod.path + '/A' )
+ Z = moose.element( mod.path + '/Z' )
+ Z.nInit = 1
+ Ca = moose.element( mod.path + '/Ca' )
+ CaStim = moose.element( Ca.path + '/CaStim' )
+
+ print( '\n\n[INFO] CaStim %s' % CaStim.path )
+ runtime = params['preStimTime'] + params['postStimTime']
+ steptime = 50
+ CaStim.expr += '+x2*(t>100+'+str(runtime)+')*(t<100+'+str(runtime+steptime)+ ')'
+ print("[INFO] CaStim.expr = %s" % CaStim.expr)
+ tab = moose.Table2( '/model/' + name + '/Atab' )
+ ampl = moose.element( mod.path + '/ampl' )
+ phase = moose.element( mod.path + '/phase' )
+ moose.connect( tab, 'requestOut', A, 'getN' )
+ ampl.nInit = params['stimAmplitude'] * 1
+ phase.nInit = params['preStimTime']
+
+ ksolve = moose.Ksolve( mod.path + '/ksolve' )
+ stoich = moose.Stoich( mod.path + '/stoich' )
+ stoich.compartment = mod
+ stoich.ksolve = ksolve
+ stoich.path = mod.path + '/##'
+
+ print( 'REINIT AND START' )
+ moose.reinit()
+ runtime += 100 + steptime*2
+ moose.start( runtime )
+ t = np.arange( 0, runtime + 1e-9, tab.dt )
+ return name, t, tab.vector
+
+
+def runPanelDEFG( name, dist, seqDt, numSpine, seq, stimAmpl ):
+ preStim = 10.0
+ blanks = 20
+ rdes = rd.rdesigneur(
+ useGssa = False,
+ turnOffElec = True,
+ chemPlotDt = 0.1,
+ diffusionLength = 1e-6,
+ cellProto = [['cell', 'soma']],
+ chemProto = [['dend', name]],
+ chemDistrib = [['dend', 'soma', 'install', '1' ]],
+ plotList = [['soma', '1', 'dend' + '/A', 'n', '# of A']],
+ )
+ rdes.buildModel()
+ A = moose.vec( '/model/chem/dend/A' )
+ Z = moose.vec( '/model/chem/dend/Z' )
+ print(moose.element( '/model/chem/dend/A/Adot' ).expr)
+ print(moose.element( '/model/chem/dend/B/Bdot' ).expr)
+ print(moose.element( '/model/chem/dend/Ca/CaStim' ).expr)
+ phase = moose.vec( '/model/chem/dend/phase' )
+ ampl = moose.vec( '/model/chem/dend/ampl' )
+ vel = moose.vec( '/model/chem/dend/vel' )
+ vel.nInit = 1e-6 * seqDt
+ ampl.nInit = stimAmpl
+ stride = int( dist ) / numSpine
+ phase.nInit = 10000
+ Z.nInit = 0
+ for j in range( numSpine ):
+ k = int( blanks + j * stride )
+ Z[k].nInit = 1
+ phase[k].nInit = preStim + seq[j] * seqDt
+
+ moose.reinit()
+ runtime = 50
+ snapshot = preStim + seqDt * (numSpine - 0.8)
+ print(snapshot)
+ moose.start( snapshot )
+ avec = moose.vec( '/model/chem/dend/A' ).n
+ moose.start( runtime - snapshot )
+ tvec = []
+ for i in range( 5 ):
+ tab = moose.element( '/model/graphs/plot0[' + str( blanks + i * stride ) + ']' )
+ dt = tab.dt
+ tvec.append( tab.vector )
+ moose.delete( '/model' )
+ return dt, tvec, avec
+
+def makePassiveSoma( name, length, diameter ):
+ elecid = moose.Neuron( '/library/' + name )
+ dend = moose.Compartment( elecid.path + '/soma' )
+ dend.diameter = diameter
+ dend.length = length
+ dend.x = length
+ return elecid
+
+def run():
+ panelC = []
+ panelCticks = []
+ panelC.append( singleCompt( 'negFB', makeNegFB( [] ) ) )
+ panelC.append( singleCompt( 'negFF', makeNegFF( [] ) ) )
+ panelC.append( singleCompt( 'fhn', makeFHN( [] ) ) )
+ panelC.append( singleCompt( 'bis', makeBis( [] ) ) )
+ panelCticks.append( np.arange( 0, 15.00001, 5 ) )
+ panelCticks.append( np.arange( 0, 1.50001, 0.5 ) )
+ panelCticks.append( np.arange( 0, 5.00002, 1 ) )
+ panelCticks.append( np.arange( 0, 5.00002, 1 ) )
+ moose.delete( '/model' )
+ for i in zip( panelC, panelCticks, list(range( len( panelC ))) ):
+ plotPos = i[2] + 5
+ doty = i[1][-1] * 0.95
+ print('doty', doty )
+ print( '[INFO] Run is over')
+
+if __name__ == '__main__':
+ moose.Neutral( '/library' )
+ moose.Neutral( '/model' )
+ run()
+ print( 'All done' )
diff --git a/moose-core/tests/python/test_function.py b/moose-core/tests/python/test_function.py
index 3ba99164289c2b5d23cba7419de448700c846567..79e9453424d3de6a46981f8b618d1c07647e26b8 100644
--- a/moose-core/tests/python/test_function.py
+++ b/moose-core/tests/python/test_function.py
@@ -1,69 +1,37 @@
# -*- coding: utf-8 -*-
# test_function.py ---
-#
# Filename: test_function.py
# Description:
# Author: subha
-# Maintainer:
+# Maintainer: Dilawar Singh <diawars@ncbs.res.in>
# Created: Sat Mar 28 19:34:20 2015 (-0400)
# Version:
-# Last-Updated:
-# By:
-# Update #: 0
-# URL:
-# Keywords:
-# Compatibility:
-#
-#
-# Commentary:
-#
-#
-#
-#
-
-# Change log:
-#
-#
-#
-#
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License as
-# published by the Free Software Foundation; either version 3, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-# General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program; see the file COPYING. If not, write to
-# the Free Software Foundation, Inc., 51 Franklin Street, Fifth
-# Floor, Boston, MA 02110-1301, USA.
-#
-#
-
-# Code:
-"""Check variable ordering - bug #161"""
from __future__ import print_function
-
import numpy as np
import moose
+print( "[INFO ] Using moose %s form %s" % (moose.version(), moose.__file__) )
+
+def create_func( funcname, expr ):
+ f = moose.Function( funcname )
+ f.expr = expr
+ t = moose.Table( funcname + 'tab' )
+ moose.connect( t, 'requestOut', f, 'getValue' )
+ moose.setClock( f.tick, 0.1)
+ moose.setClock( t.tick, 0.1)
+ return f, t
def test_var_order():
"""The y values are one step behind the x values because of
scheduling sequences"""
+ moose.delete( '/' )
nsteps = 5
simtime = nsteps
dt = 1.0
# fn0 = moose.Function('/fn0')
- # fn0.x.num = 2
- # fn0.expr = 'x0 + x1'
- # fn0.mode = 1
fn1 = moose.Function('/fn1')
fn1.x.num = 2
- fn1.expr = 'y1 + y0 + x1 + x0'
+ fn1.expr = 'y1+y0+x1+x0'
fn1.mode = 1
inputs = np.arange(0, nsteps+1, 1.0)
x0 = moose.StimulusTable('/x0')
@@ -90,6 +58,8 @@ def test_var_order():
y1.startTime = 0.0
y1.stopTime = simtime
y1.stepPosition = 0.0
+ # print( fn1, type(fn1) )
+ # print( moose.showmsg(fn1.x) )
moose.connect(x0, 'output', fn1.x[0], 'input')
moose.connect(x1, 'output', fn1.x[1], 'input')
moose.connect(fn1, 'requestOut', y0, 'getOutputValue')
@@ -100,12 +70,54 @@ def test_var_order():
moose.setClock(ii, dt)
moose.reinit()
moose.start(simtime)
- for ii in range(len(z1.vector)):
- print(ii, z1.vector[ii])
+ expected = [0, 1.1, 2.211, 3.322, 4.433, 5.544]
+ assert np.allclose(z1.vector, expected), "Excepted %s, got %s" % (expected, z1.vector )
+ print( 'Passed order vars' )
-if __name__ == '__main__':
- test_var_order()
+def test_t( ):
+ f, t = create_func( 'funct', 't/2.0')
+ moose.reinit()
+ moose.start(1)
+ y = t.vector
+ d = np.diff( y[1:] )
+ assert np.mean(d) == d[0]
+ print( 'Passed t/2' )
+def test_trig( ):
+ f, t = create_func('func2', '(sin(t)^2+cos(t)^2)-1')
+ moose.reinit()
+ moose.start( 1 )
+ y = t.vector
+ print(y)
+ assert np.isclose(np.mean(y), 0.0), np.mean(y)
+ assert np.isclose(np.std(y), 0.0), np.std(y)
+ print( 'Passed sin^2 x + cos^x=1' )
-#
-# test_function.py ends here
+def test_rand( ):
+ moose.seed( 10 )
+ f, t = create_func( 'random', 'rnd()')
+ moose.reinit()
+ moose.start(1)
+ expected = [0.49458993, 0.44301495, 0.58332174, 0.70920801, 0.26360285,
+ 0.68381843, 0.33607158, 0.19812181, 0.87761494, 0.54088093,
+ 0.41366738]
+ assert np.isclose(t.vector, expected ).all(), t.vector
+ print( 'Passed test random' )
+
+def test_fmod( ):
+ f, t = create_func( 'fmod', 'fmod(t, 2)' )
+ moose.reinit()
+ moose.start( 20 )
+ y = t.vector
+ assert (np.fmod(y, 2) == y).all()
+ assert(np.isclose(np.max(y), 1.9)), np.max(y)
+ assert(np.isclose(np.min(y), 0.0)), np.min(y)
+ print('Passed fmod(t,2)')
+
+
+if __name__ == '__main__':
+ test_var_order()
+ test_t()
+ test_trig()
+ test_rand()
+ test_fmod()
diff --git a/moose-core/tests/python/test_function_chemsys.py b/moose-core/tests/python/test_function_chemsys.py
new file mode 100644
index 0000000000000000000000000000000000000000..fabbc28e40cfb8ebfb51b61d3c171d085d0af20f
--- /dev/null
+++ b/moose-core/tests/python/test_function_chemsys.py
@@ -0,0 +1,346 @@
+# -*- coding: utf-8 -*-
+"""test_muparser.py:
+
+odified from https://elifesciences.org/articles/25827
+Fig4.py
+"""
+import sys
+import re
+import numpy as np
+import moose
+import rdesigneur as rd
+print( "[INFO ] Using moose from %s" % moose.__file__ )
+
+def parseExpr( expr, params, hasCa ):
+ if hasCa:
+ expr = expr.replace( 'Ca', 'x0' )
+ expr = expr.replace( 'A', 'x1' )
+ expr = expr.replace( 'B', 'x2' )
+ else:
+ expr = expr.replace( 'Ca', 'x0' ) # happens in the negFF model
+ expr = expr.replace( 'A', 'x0' ) # This is the usual case.
+ expr = expr.replace( 'B', 'x1' )
+
+ parts = re.split( 'k', expr )
+ ret = parts[0]
+ for i in parts[1:]:
+ ret += str( params[ 'k' + i[:2] ] )
+ ret += i[2:]
+
+ if hasCa:
+ return 'x3*( ' + ret + ')'
+ else:
+ return 'x2*( ' + ret + ')'
+
+def makeChemProto( name, Aexpr, Bexpr, params ):
+ sw = params['stimWidth']
+ diffLength = params['diffusionLength']
+ dca = params['diffConstA'] * diffLength * diffLength
+ dcb = params['diffConstB'] * diffLength * diffLength
+
+ # Objects
+ chem = moose.Neutral( '/library/' + name )
+ compt = moose.CubeMesh( '/library/' + name + '/' + name )
+ A = moose.Pool( compt.path + '/A' )
+ B = moose.Pool( compt.path + '/B' )
+ Z = moose.BufPool( compt.path + '/Z' )
+ Ca = moose.BufPool( compt.path + '/Ca' )
+ phase = moose.BufPool( compt.path + '/phase' )
+ vel = moose.BufPool( compt.path + '/vel' )
+ ampl = moose.BufPool( compt.path + '/ampl' )
+ Adot = moose.Function( A.path + '/Adot' )
+ Bdot = moose.Function( B.path + '/Bdot' )
+ CaStim = moose.Function( Ca.path + '/CaStim' )
+ A.diffConst = dca
+ B.diffConst = dcb
+
+ # Equations
+
+ Adot.expr = parseExpr( Aexpr, params, True )
+ Bdot.expr = parseExpr( Bexpr, params, False )
+ CaStim.expr = 'x2 * exp( -((x0 - t)^2)/(2* ' + str(sw*sw) + ') )'
+
+ #print Adot.expr
+ #print Bdot.expr
+ #print CaStim.expr
+
+ # Connections
+ Adot.x.num = 4
+ moose.connect( Ca, 'nOut', Adot.x[0], 'input' )
+ moose.connect( A, 'nOut', Adot.x[1], 'input' )
+ moose.connect( B, 'nOut', Adot.x[2], 'input' )
+ moose.connect( Z, 'nOut', Adot.x[3], 'input' )
+ moose.connect( Adot, 'valueOut', A, 'increment' )
+
+ Bdot.x.num = 3
+ if name[:5] == 'negFF':
+ moose.connect( Ca, 'nOut', Bdot.x[0], 'input' )
+ print('Doing special msg')
+ else:
+ moose.connect( A, 'nOut', Bdot.x[0], 'input' )
+ moose.connect( B, 'nOut', Bdot.x[1], 'input' )
+ moose.connect( Z, 'nOut', Bdot.x[2], 'input' )
+ moose.connect( Bdot, 'valueOut', B, 'increment' )
+
+ CaStim.x.num = 3
+ moose.connect( phase, 'nOut', CaStim.x[0], 'input' )
+ moose.connect( vel, 'nOut', CaStim.x[1], 'input' )
+ moose.connect( ampl, 'nOut', CaStim.x[2], 'input' )
+ moose.connect( CaStim, 'valueOut', Ca, 'setN' )
+
+ return compt
+
+
+def makeBis( args = None ):
+ params = {
+ 'k0a':0.1, # Constant
+ 'k1a':-5.0, # Coeff for A
+ 'k2a':5.0, # Coeff for A^2
+ 'k3a':-1.0, # Coeff for A^3
+ 'k4a':10.0, # turnon of A by A and Ca
+ 'k5a':-5.0, # Turnoff of A by B
+ 'k1b':0.01, # turnon of B by A
+ 'k2b':-0.01, # Decay rate of B
+ 'diffusionLength':1.0e-6, # Diffusion characteristic length, used as voxel length too.
+ 'dendDiameter': 10e-6, # Diameter of section of dendrite in model
+ 'dendLength': 100e-6, # Length of section of dendrite in model
+ 'diffConstA':5.0, # Diffusion constant of A
+ 'diffConstB':2.0, # Diffusion constant of B
+ 'stimWidth' :1.0, # Stimulus width in seconds
+ 'stimAmplitude':1.0, # Stimulus amplitude, arb units. From FHN review
+ 'blankVoxelsAtEnd':10, # of voxels to leave blank at end of cylinder
+ 'preStimTime':10.0, # Time to run before turning on stimulus.
+ 'postStimTime':40.0, # Time to run after stimulus. ~3x decay time
+ 'settleTime':20.0, # Settling time of response, after stimulus.
+ # To include in analysis of total response over
+ # entire dendrite.
+ 'fnumber':1, # Number to append to fname
+ }
+
+ for i in args:
+ params[i] = args[i]
+
+ makeChemProto( 'bis',
+ 'k0a + k1a*A + k2a*A*A + k3a*A*A*A + k4a*Ca*A/(1+A+10*B) + k5a*A*B',
+ 'k1b*A*A + k2b*B',
+ params )
+ return params
+
+def makeFHN( args = None ):
+ params = {
+ 'k_t':2.5, # Time-const.
+ 'k_a':0.7, # Coeff1
+ 'k_b':0.8, # Coeff2
+ 'kxa': 2.0, # Offset for V for FHN eqns.
+ 'kxb': 0.8, # Offset for W for FHN eqns.
+ 'diffusionLength':1.0e-6, # Diffusion characteristic length, used as voxel length too.
+ 'dendDiameter': 10e-6, # Diameter of section of dendrite in model
+ 'dendLength': 100e-6, # Length of section of dendrite in model
+ 'diffConstA':7.5, # Diffusion constant of A
+ 'diffConstB':5.0, # Diffusion constant of B
+ 'stimWidth' :1.0, # Stimulus width in seconds
+ 'stimAmplitude':0.4, # Stimulus amplitude, arb units. From FHN review
+ 'blankVoxelsAtEnd':10, # of voxels to leave blank at end of cylinder
+ 'preStimTime':10.0, # Time to run before turning on stimulus.
+ 'postStimTime':40.0, # Time to run after stimulus. ~3x decay time
+ 'settleTime':20.0, # Settling time of response, after stimulus.
+ # To include in analysis of total response over
+ # entire dendrite.
+ 'fnumber': 1, # Number to append to fname
+ }
+
+ for i in args:
+ params[i] = args[i]
+
+ makeChemProto( 'fhn',
+ '5.0*(A - kxa - (A-kxa)^3/3 - (B-kxb) + Ca)',
+ '(A-kxa + k_a - k_b*(B-kxb))/k_t',
+ params )
+ # We do this to get the system to settle at the start.
+ B = moose.element( '/library/fhn/fhn/B' )
+ B.nInit = 0.2
+ return params
+
+
+def makeNegFB( args = None ):
+ params = {
+ 'k1a':-0.1, # Coeff for decay of A, slow.
+ 'k2a':-0.2, # Coeff for turnoff of A by B, medium.
+ 'k3a':10.0, # turnon of A by Ca, fast.
+ 'k1b':0.2, # turnon of B by A, medium
+ 'k2b':-0.1, # Decay rate of B, slow
+ 'diffusionLength':1.0e-6, # Diffusion characteristic length, used as voxel length too.
+ 'dendDiameter': 10e-6, # Diameter of section of dendrite in model
+ 'dendLength': 100e-6, # Length of section of dendrite in model
+ 'diffConstA':0.5, # Diffusion constant of A
+ 'diffConstB':1.0, # Diffusion constant of B
+ 'stimWidth' :1.0, # Stimulus width in seconds
+ 'stimAmplitude':1.0, # Stimulus amplitude, arb units. From FHN review
+ 'blankVoxelsAtEnd':10, #of voxels to leave blank at end of cylinder
+ 'preStimTime':10.0, # Time to run before turning on stimulus.
+ 'postStimTime':40.0, # Time to run after stimulus. ~3x decay time
+ 'settleTime':20.0, # Settling time of response, after stimulus.
+ # To include in analysis of total response over
+ # entire dendrite.
+ 'fnumber':1, # Number to append to fname
+ }
+
+ for i in args:
+ params[i] = args[i]
+
+ makeChemProto( 'negFB',
+ 'k1a*A + k2a*A*B + k3a*Ca',
+ 'k1b*A + k2b*B',
+ params )
+ return params
+
+# Was negFF2 in earlier versions of abstrModelEqns
+def makeNegFF( args = None ):
+ params = {
+ 'k1a':-0.1, # Coeff for decay of A, slow.
+ 'k2a':-0.01, # Coeff for turnoff of A by B, medium.
+ 'k3a':10.0, # turnon of A by Ca, fast.
+ 'k4a':40.0, # amount of B inhibition of turnon of A by Ca.
+ 'k1b':2.0, # turnon of B by Ca, medium
+ 'k2b':-0.05, # Decay rate of B, slow
+ 'diffusionLength':1.0e-6, # Diffusion characteristic length, used as voxel length too.
+ 'dendDiameter': 10e-6, # Diameter of section of dendrite in model
+ 'dendLength': 100e-6, # Length of section of dendrite in model
+ 'diffConstA':0.02, # Diffusion constant of A
+ 'diffConstB':0.4, # Diffusion constant of B
+ 'stimWidth' :1.0, # Stimulus width in seconds
+ 'stimAmplitude':10.0, # Stimulus amplitude, arb units. From FHN review
+ 'blankVoxelsAtEnd':10, # of voxels to leave blank at end of cylinder
+ 'preStimTime':10.0, # Time to run before turning on stimulus.
+ 'postStimTime':40.0, # Time to run after stimulus. ~3x decay time
+ 'settleTime':20.0, # Settling time of response, after stimulus.
+ # To include in analysis of total response over
+ # entire dendrite.
+ 'fnumber':1, # Number to append to fname
+ }
+
+ for i in args:
+ params[i] = args[i]
+
+ makeChemProto( 'negFF',
+ 'k1a*A + k2a*A*B + k3a*Ca/(1+k4a*B*B)',
+ 'k1b*Ca + k2b*B',
+ params )
+
+ return params
+
+
+def singleCompt( name, params ):
+ print('=============')
+ print('[INFO] Making compartment %s' % name)
+ mod = moose.copy( '/library/' + name + '/' + name, '/model' )
+ A = moose.element( mod.path + '/A' )
+ Z = moose.element( mod.path + '/Z' )
+ Z.nInit = 1
+ Ca = moose.element( mod.path + '/Ca' )
+ CaStim = moose.element( Ca.path + '/CaStim' )
+
+ print( '\n\n[INFO] CaStim %s' % CaStim.path )
+ runtime = params['preStimTime'] + params['postStimTime']
+ steptime = 50
+ CaStim.expr += '+x2*(t>100+'+str(runtime)+')*(t<100+'+str(runtime+steptime)+ ')'
+ print("[INFO] CaStim.expr = %s" % CaStim.expr)
+ tab = moose.Table2( '/model/' + name + '/Atab' )
+ ampl = moose.element( mod.path + '/ampl' )
+ phase = moose.element( mod.path + '/phase' )
+ moose.connect( tab, 'requestOut', A, 'getN' )
+ ampl.nInit = params['stimAmplitude'] * 1
+ phase.nInit = params['preStimTime']
+
+ ksolve = moose.Ksolve( mod.path + '/ksolve' )
+ stoich = moose.Stoich( mod.path + '/stoich' )
+ stoich.compartment = mod
+ stoich.ksolve = ksolve
+ stoich.path = mod.path + '/##'
+
+ print( 'REINIT AND START' )
+ moose.reinit()
+ runtime += 100 + steptime*2
+ moose.start( runtime )
+ t = np.arange( 0, runtime + 1e-9, tab.dt )
+ return name, t, tab.vector
+
+
+def runPanelDEFG( name, dist, seqDt, numSpine, seq, stimAmpl ):
+ preStim = 10.0
+ blanks = 20
+ rdes = rd.rdesigneur(
+ useGssa = False,
+ turnOffElec = True,
+ chemPlotDt = 0.1,
+ diffusionLength = 1e-6,
+ cellProto = [['cell', 'soma']],
+ chemProto = [['dend', name]],
+ chemDistrib = [['dend', 'soma', 'install', '1' ]],
+ plotList = [['soma', '1', 'dend' + '/A', 'n', '# of A']],
+ )
+ rdes.buildModel()
+ A = moose.vec( '/model/chem/dend/A' )
+ Z = moose.vec( '/model/chem/dend/Z' )
+ print(moose.element( '/model/chem/dend/A/Adot' ).expr)
+ print(moose.element( '/model/chem/dend/B/Bdot' ).expr)
+ print(moose.element( '/model/chem/dend/Ca/CaStim' ).expr)
+ phase = moose.vec( '/model/chem/dend/phase' )
+ ampl = moose.vec( '/model/chem/dend/ampl' )
+ vel = moose.vec( '/model/chem/dend/vel' )
+ vel.nInit = 1e-6 * seqDt
+ ampl.nInit = stimAmpl
+ stride = int( dist ) / numSpine
+ phase.nInit = 10000
+ Z.nInit = 0
+ for j in range( numSpine ):
+ k = int( blanks + j * stride )
+ Z[k].nInit = 1
+ phase[k].nInit = preStim + seq[j] * seqDt
+
+ moose.reinit()
+ runtime = 50
+ snapshot = preStim + seqDt * (numSpine - 0.8)
+ print(snapshot)
+ moose.start( snapshot )
+ avec = moose.vec( '/model/chem/dend/A' ).n
+ moose.start( runtime - snapshot )
+ tvec = []
+ for i in range( 5 ):
+ tab = moose.element( '/model/graphs/plot0[' + str( blanks + i * stride ) + ']' )
+ dt = tab.dt
+ tvec.append( tab.vector )
+ moose.delete( '/model' )
+ return dt, tvec, avec
+
+def makePassiveSoma( name, length, diameter ):
+ elecid = moose.Neuron( '/library/' + name )
+ dend = moose.Compartment( elecid.path + '/soma' )
+ dend.diameter = diameter
+ dend.length = length
+ dend.x = length
+ return elecid
+
+def run():
+ panelC = []
+ panelCticks = []
+ panelC.append( singleCompt( 'negFB', makeNegFB( [] ) ) )
+ panelC.append( singleCompt( 'negFF', makeNegFF( [] ) ) )
+ panelC.append( singleCompt( 'fhn', makeFHN( [] ) ) )
+ panelC.append( singleCompt( 'bis', makeBis( [] ) ) )
+ panelCticks.append( np.arange( 0, 15.00001, 5 ) )
+ panelCticks.append( np.arange( 0, 1.50001, 0.5 ) )
+ panelCticks.append( np.arange( 0, 5.00002, 1 ) )
+ panelCticks.append( np.arange( 0, 5.00002, 1 ) )
+ moose.delete( '/model' )
+ for i in zip( panelC, panelCticks, list(range( len( panelC ))) ):
+ plotPos = i[2] + 5
+ doty = i[1][-1] * 0.95
+ print('doty', doty )
+ print( '[INFO] Run is over')
+
+if __name__ == '__main__':
+ moose.Neutral( '/library' )
+ moose.Neutral( '/model' )
+ run()
+ print( 'All done' )
diff --git a/moose-core/tests/python/test_function_controls_reac_rate.py b/moose-core/tests/python/test_function_controls_reac_rate.py
new file mode 100644
index 0000000000000000000000000000000000000000..0c885b3823b606b532a8479f0a671748a886544f
--- /dev/null
+++ b/moose-core/tests/python/test_function_controls_reac_rate.py
@@ -0,0 +1,87 @@
+########################################################################
+# This example illustrates how a function can be used to control a reaction
+# rate. This kind of calculation is appropriate when we need to link
+# different kinds of physical processses with chemical reactions, for
+# example, membrane curvature with molecule accumulation. The use of
+# functions to modify reaction rates should be avoided in purely chemical
+# systems since they obscure the underlying chemistry, and do not map
+# cleanly to stochastic calculations.
+#
+# In this example we simply have a molecule C that controls the forward
+# rate of a reaction that converts A to B. C is a function of location
+# on the cylinder, and is fixed. In more elaborate computations we could
+# have a function of multiple molecules, some of which could be changing and
+# others could be buffered.
+#
+# Copyright (C) Upinder S. Bhalla NCBS 2018
+# Released under the terms of the GNU Public License V3.
+########################################################################
+
+import numpy as np
+import moose
+import pylab
+import rdesigneur as rd
+
+plot_ = False
+
+def makeFuncRate():
+ model = moose.Neutral( '/library' )
+ model = moose.Neutral( '/library/chem' )
+ compt = moose.CubeMesh( '/library/chem/compt' )
+ compt.volume = 1e-15
+ A = moose.Pool( '/library/chem/compt/A' )
+ B = moose.Pool( '/library/chem/compt/B' )
+ C = moose.Pool( '/library/chem/compt/C' )
+ reac = moose.Reac( '/library/chem/compt/reac' )
+ func = moose.Function( '/library/chem/compt/reac/func' )
+ func.x.num = 1
+ func.expr = "(x0/1e8)^2"
+ moose.connect( C, 'nOut', func.x[0], 'input' )
+ moose.connect( func, 'valueOut', reac, 'setNumKf' )
+ moose.connect( reac, 'sub', A, 'reac' )
+ moose.connect( reac, 'prd', B, 'reac' )
+
+ A.concInit = 1
+ B.concInit = 0
+ C.concInit = 0
+ reac.Kb = 1
+
+def test():
+ makeFuncRate()
+
+ rdes = rd.rdesigneur(
+ turnOffElec = True,
+ #This subdivides the 50-micron cylinder into 2 micron voxels
+ diffusionLength = 2e-6,
+ cellProto = [['somaProto', 'soma', 5e-6, 50e-6]],
+ chemProto = [['chem', 'chem']],
+ chemDistrib = [['chem', 'soma', 'install', '1' ]],
+ plotList = [['soma', '1', 'dend/A', 'conc', 'A conc', 'wave'],
+ ['soma', '1', 'dend/C', 'conc', 'C conc', 'wave']],
+ )
+ rdes.buildModel()
+
+ C = moose.element( '/model/chem/dend/C' )
+ C.vec.concInit = [ 1+np.sin(x/5.0) for x in range( len(C.vec) ) ]
+ moose.reinit()
+ moose.start(10)
+ if plot_:
+ rdes.display()
+ ts = moose.wildcardFind( '/##[TYPE=Table2]')
+ mat = []
+ for t in ts:
+ if 'plot1' in t.path:
+ mat.append(t.vector)
+ mat = np.matrix(mat)
+ exMean, exStd = 1.1619681711817156, 0.6944155817587526
+ assert np.isclose( np.mean(mat), exMean), mp.mean(mat)
+ assert np.isclose( np.std(mat), exStd), mp.std(mat)
+ assert( np.isclose(np.mean(mat, axis=0), exMean).all() )
+ assert( np.isclose(np.std(mat, axis=0), exStd).all() )
+ assert( np.isclose(0.0, np.std(mat, axis=1)).all())
+
+def main():
+ test()
+
+if __name__ == '__main__':
+ main()
diff --git a/moose-core/tests/python/test_function_derivative.py b/moose-core/tests/python/test_function_derivative.py
new file mode 100644
index 0000000000000000000000000000000000000000..c2e1dc81eda91250db52c82a3892c1c6c7ba3d5c
--- /dev/null
+++ b/moose-core/tests/python/test_function_derivative.py
@@ -0,0 +1,160 @@
+# function.py ---
+
+import numpy as np
+import sys
+import moose
+
+simtime = 1.0
+plot_ = False
+if plot_:
+ import matplotlib.pyplot as plt
+
+def example():
+ """Function objects can be used to evaluate expressions with arbitrary
+ number of variables and constants. We can assign expression of the
+ form::
+
+ f(c0, c1, ..., cM, x0, x1, ..., xN, y0,..., yP )
+
+ where `c_i`'s are constants and `x_i`'s and `y_i`'s are variables.
+
+ The constants must be defined before setting the expression and
+ variables are connected via messages. The constants can have any
+ name, but the variable names must be of the form x{i} or y{i}
+ where i is increasing integer starting from 0.
+
+ The `x_i`'s are field elements and you have to set their number
+ first (function.x.num = N). Then you can connect any source field
+ sending out double to the 'input' destination field of the
+ `x[i]`.
+
+ The `y_i`'s are useful when the required variable is a value field
+ and is not available as a source field. In that case you connect
+ the `requestOut` source field of the function element to the
+ `get{Field}` destination field on the target element. The `y_i`'s
+ are automatically added on connecting. Thus, if you call::
+
+ moose.connect(function, 'requestOut', a, 'getSomeField')
+ moose.connect(function, 'requestOut', b, 'getSomeField')
+
+ then ``a.someField`` will be assigned to ``y0`` and
+ ``b.someField`` will be assigned to ``y1``.
+
+ In this example we evaluate the expression: ``z = c0 * exp(c1 *
+ x0) * cos(y0)``
+
+ with x0 ranging from -1 to +1 and y0 ranging from -pi to
+ +pi. These values are stored in two stimulus tables called xtab
+ and ytab respectively, so that at each timestep the next values of
+ x0 and y0 are assigned to the function.
+
+ Along with the value of the expression itself we also compute its
+ derivative with respect to y0 and its derivative with respect to
+ time (rate). The former uses a five-point stencil for the
+ numerical differentiation and has a glitch at y=0. The latter uses
+ backward difference divided by dt.
+
+ Unlike Func class, the number of variables and constants are
+ unlimited in Function and you can set all the variables via
+ messages.
+
+ """
+ demo = moose.Neutral('/model')
+ function = moose.Function('/model/function')
+ function.c['c0'] = 1.0
+ function.c['c1'] = 2.0
+ function.x.num = 1
+ function.expr = 'c0 * exp(c1*x0) * cos(y0) + sin(t)'
+ # mode 0 - evaluate function value, derivative and rate
+ # mode 1 - just evaluate function value,
+ # mode 2 - evaluate derivative,
+ # mode 3 - evaluate rate
+ function.mode = 0
+ function.independent = 'y0'
+ nsteps = 1000
+ xarr = np.linspace(0.0, 1.0, nsteps)
+ # Stimulus tables allow you to store sequences of numbers which
+ # are delivered via the 'output' message at each time step. This
+ # is a placeholder and in real scenario you will be using any
+ # sourceFinfo that sends out a double value.
+ input_x = moose.StimulusTable('/xtab')
+ input_x.vector = xarr
+ input_x.startTime = 0.0
+ input_x.stepPosition = xarr[0]
+ input_x.stopTime = simtime
+ moose.connect(input_x, 'output', function.x[0], 'input')
+
+ yarr = np.linspace(-np.pi, np.pi, nsteps)
+ input_y = moose.StimulusTable('/ytab')
+ input_y.vector = yarr
+ input_y.startTime = 0.0
+ input_y.stepPosition = yarr[0]
+ input_y.stopTime = simtime
+ moose.connect(function, 'requestOut', input_y, 'getOutputValue')
+
+ # data recording
+ result = moose.Table('/ztab')
+ moose.connect(result, 'requestOut', function, 'getValue')
+ derivative = moose.Table('/zprime')
+ moose.connect(derivative, 'requestOut', function, 'getDerivative')
+ rate = moose.Table('/dz_by_dt')
+ moose.connect(rate, 'requestOut', function, 'getRate')
+ x_rec = moose.Table('/xrec')
+ moose.connect(x_rec, 'requestOut', input_x, 'getOutputValue')
+ y_rec = moose.Table('/yrec')
+ moose.connect(y_rec, 'requestOut', input_y, 'getOutputValue')
+
+ dt = simtime/nsteps
+ for ii in range(32):
+ moose.setClock(ii, dt)
+ moose.reinit()
+ moose.start(simtime)
+
+ # Uncomment the following lines and the import matplotlib.pyplot as plt on top
+ # of this file to display the plot.
+ if plot_:
+ plt.plot(x_rec.vector, result.vector, 'r-', label='z = {}'.format(function.expr))
+ plt.subplot(4,1,1)
+ z = function.c['c0'] * np.exp(function.c['c1'] * xarr) * np.cos(yarr) + np.sin(np.arange(len(xarr)) * dt)
+ zz = result.vector[1:]
+ err = z[1:] - zz[1:]
+ assert (np.abs(err) <= 0.05).all(), err[err > 0.05]
+ assert (np.mean(err) <= 0.001), np.mean(err)
+
+ if plot_:
+ plt.plot(xarr, z, 'b--', label='numpy computed')
+ plt.xlabel('x')
+ plt.ylabel('z')
+ plt.legend()
+
+ if plot_:
+ plt.subplot(4,1,2)
+ plt.plot(y_rec.vector, derivative.vector, 'r-', label='dz/dy0')
+ # derivatives computed by putting x values in the analytical formula
+ dzdy = function.c['c0'] * np.exp(function.c['c1'] * xarr) * (- np.sin(yarr))
+ err = np.abs(dzdy - derivative.vector[1:])
+ assert (err < 0.05).all(), (err[err>1e-2])
+ assert (np.mean(err) < 1e-2), np.mean(err)
+
+ if plot_:
+ plt.plot(yarr, dzdy, 'b--', label='numpy computed')
+ plt.xlabel('y')
+ plt.ylabel('dz/dy')
+ plt.legend()
+
+ if plot_:
+ plt.subplot(4,1,3)
+ # *** BEWARE *** The first two entries are spurious. Entry 0 is
+ # *** from reinit sending out the defaults. Entry 2 is because
+ # *** there is no lastValue for computing real forward difference.
+ plt.plot(np.arange(2, len(rate.vector), 1) * dt, rate.vector[2:], 'r-', label='dz/dt')
+ dzdt = np.diff(z)/dt
+ plt.plot(np.arange(0, len(dzdt), 1.0) * dt, dzdt, 'b--', label='numpy computed')
+ plt.xlabel('t')
+ plt.ylabel('dz/dt')
+ plt.legend()
+ plt.tight_layout()
+ plt.show()
+
+if __name__ == '__main__':
+ example()
diff --git a/moose-core/tests/python/test_gsolve_parallel.py b/moose-core/tests/python/test_gsolve_parallel.py
index e7887ce853fa66ef033565d9f46272bedb1189fd..056762b47bd9885e6417741e87f96f36fb63fb97 100644
--- a/moose-core/tests/python/test_gsolve_parallel.py
+++ b/moose-core/tests/python/test_gsolve_parallel.py
@@ -2,8 +2,14 @@ import numpy as np
import moose
print( '[INFO] Using moose from %s' % moose.__file__ )
import time
+
+# Does not guarantee thread determinism in multithreaded Gsolve/Ksolve.
moose.seed( 10 )
+def printCompt(compt):
+ print( 'x0=%s, x1=%s, diffLength=%s, numDiffCompt=%d' % (compt.x0, compt.x1,
+ compt.diffLength, compt.numDiffCompts))
+
def main( nT ):
"""
This example implements a reaction-diffusion like system which is
@@ -14,25 +20,22 @@ def main( nT ):
uses a reaction plus a function object to control its rates.
"""
print( 'Using %d threads' % nT )
-
dt = 0.1
-
# define the geometry
compt = moose.CylMesh( '/cylinder' )
compt.r0 = compt.r1 = 100e-9
- compt.x1 = 200e-9
+ compt.x1 = 200e-09
compt.diffLength = 0.2e-9
- assert( compt.numDiffCompts == compt.x1/compt.diffLength )
+ assert( compt.numDiffCompts == compt.x1/compt.diffLength)
#define the molecule. Its geometry is defined by its parent volume, cylinder
c = moose.Pool( '/cylinder/pool' )
c.diffConst = 1e-13 # define diffusion constant
-
# Here we set up a function calculation
func = moose.Function( '/cylinder/pool/func' )
- func.expr = "(-x0 * (30e-9 - x0) * (100e-9 - x0))*0.0001"
- func.x.num = 1 #specify number of input variables.
+ func.expr = "(-x0*(30e-9-x0)*(100e-9-x0))*0.0001"
+ # func.x.num = 1 #specify number of input variables.
#Connect the molecules to the func
moose.connect( c, 'nOut', func.x[0], 'input' )
@@ -45,6 +48,7 @@ def main( nT ):
ksolve.numThreads = nT
except Exception as e:
print( 'OLD MOOSE. Does not support multithreading' )
+
dsolve = moose.Dsolve( '/cylinder/dsolve' )
stoich = moose.Stoich( '/cylinder/stoich' )
stoich.compartment = compt
@@ -62,16 +66,32 @@ def main( nT ):
runtime = updateDt * 10
t1 = time.time()
res = []
+ clk = moose.element( '/clock' )
for t in range( 0, runtime-1, updateDt ):
- moose.start( updateDt )
y = c.vec.n
- res.append( (np.mean(y), np.std(y)) )
+ s = np.sum(y)
+ v = (np.mean(y), np.max(y), np.min(y), s)
+ print(v)
+ res.append(v)
+ moose.start( updateDt )
+ currTime = clk.currentTime
- expected = [(9.0, 0.0), (6.0, 0.0), (5.0, 0.0), (3.0, 0.0), (2.0, 0.0),
- (2.0, 0.0), (2.0, 0.0), (1.0, 0.0), (1.0, 0.0), (1.0, 0.0)]
- print(("Time = ", time.time() - t1))
- print( res )
- assert res == expected
+ # One molecule here and there because thread launching has undeterministic
+ # characteristics. Even after setting moose.seed; we may not see same
+ # numbers on all platfroms.
+ expected = [
+ (1000.0, 1000.0, 1000.0, 1000000.0)
+ , (9.908, 10.0, 8.0, 9908.0)
+ , (6.869, 7.0, 6.0, 6869.0)
+ , (5.354, 6.0, 5.0, 5354.0)
+ , (4.562, 5.0, 4.0, 4562.0)
+ , (3.483, 4.0, 3.0, 3483.0)
+ , (3.043, 4.0, 3.0, 3043.0)
+ , (2.261, 3.0, 2.0, 2261.0)
+ , (1.967, 2.0, 1.0, 1967.0)
+ , (1.997, 2.0, 1.0, 1997.0) ]
+ print("Time = ", time.time() - t1)
+ assert np.isclose(res, expected, atol=1, rtol=1).all(), "Got %s, expected %s" % (res, expected)
if __name__ == '__main__':
import sys
diff --git a/moose-core/tests/python/test_moose_attribs.py b/moose-core/tests/python/test_moose_attribs.py
index b10a2b30a4be8e81e56307da6cffcbaa6f793f07..3c8746b77341c835369cb1ea03950917af7d1ff6 100644
--- a/moose-core/tests/python/test_moose_attribs.py
+++ b/moose-core/tests/python/test_moose_attribs.py
@@ -18,7 +18,7 @@ attribs = ['AdExIF', 'AdThreshIF', 'Adaptor', 'Annotator', 'Arith', 'BufPool',
'Compartment', 'CompartmentBase', 'ConcChan', 'CplxEnzBase', 'CubeMesh',
'CylMesh', 'DestField', 'DiagonalMsg', 'DifBuffer', 'DifBufferBase',
'DifShell', 'DifShellBase', 'DiffAmp', 'Dsolve', 'ElementField',
- 'EndoMesh', 'Enz', 'EnzBase', 'ExIF', 'Finfo', 'Func', 'Function',
+ 'EndoMesh', 'Enz', 'EnzBase', 'ExIF', 'Finfo', 'Function',
'GapJunction', 'GraupnerBrunel2012CaPlasticitySynHandler', 'Group',
'Gsolve', 'HHChannel', 'HHChannel2D', 'HHChannelBase', 'HHGate',
'HHGate2D', 'HSolve', 'INFINITE', 'IntFire', 'IntFireBase', 'Interpol',
diff --git a/moose-core/tests/python/test_table_streaming_support.py b/moose-core/tests/python/test_table_streaming_support.py
index 42b0b83b8e002ce04276708da97b9f3d3f682b77..73341865479d0aa3863e8e59de1cc7eba5d754bf 100644
--- a/moose-core/tests/python/test_table_streaming_support.py
+++ b/moose-core/tests/python/test_table_streaming_support.py
@@ -64,15 +64,10 @@ def test( ):
print( ' MOOSE is done' )
# Now read the numpy and csv and check the results.
- a = np.load( '_tables/compt/a/tabA.npy' )
+ a = np.loadtxt( '_tables/compt/a/tabA.csv', skiprows=1 )
b = np.load( 'table2.npy' )
c = np.loadtxt( 'tablec.csv', skiprows=1 )
- print( a )
- print( b )
- print( c )
- print(a['time'])
- print(b['time'])
- assert len(a['time']) == len(a['/compt/a/tabA'])
+ assert (len(a) == len(b) == len(c))
def main( ):
test( )
diff --git a/moose-core/utility/Annotator.cpp b/moose-core/utility/Annotator.cpp
index f2df4aa1fa2dd436f4e5937e1321fa213a970101..e8b91b817bf0898c6ade81f118ac3b062acd320a 100644
--- a/moose-core/utility/Annotator.cpp
+++ b/moose-core/utility/Annotator.cpp
@@ -129,7 +129,7 @@ const Cinfo* Annotator::initCinfo()
static const Cinfo* annotatorCinfo = Annotator::initCinfo();
Annotator::Annotator()
- : x_( 0.0 ), y_( 0.0 ), z_( 0.0 ), width_( 0.0 ), height_( 0.0 ),
+ : x_( 0.0 ), y_( 0.0 ), z_( 0.0 ), height_(0.0), width_( 0.0 ),
notes_( "" ), color_( "white" ), textColor_( "black" ),
icon_( "sphere" ),solver_( "ee"),runtime_(100.0),dirpath_(""),modeltype_("")
{
diff --git a/moose-core/utility/numutil.cpp b/moose-core/utility/numutil.cpp
index 240b125f8d888e1889566e5d50ed27c4625b2e01..10b0419560b45e6880b524a144dbd338def3fe6e 100644
--- a/moose-core/utility/numutil.cpp
+++ b/moose-core/utility/numutil.cpp
@@ -5,24 +5,10 @@
* E-mail: ray dot subhasis at gmail dot com
* Created: 2007-11-02 11:46:40
********************************************************************/
-/**********************************************************************
- ** This program is part of 'MOOSE', the
- ** Messaging Object Oriented Simulation Environment,
- ** also known as GENESIS 3 base code.
- ** copyright (C) 2003-2013 Upinder S. Bhalla. and NCBS
- ** It is made available under the terms of the
- ** GNU Lesser General Public License version 2.1
- ** See the file COPYING.LIB for the full notice.
- **********************************************************************/
-#ifndef _NUMUTIL_CPP
-#define _NUMUTIL_CPP
-
-#ifdef ENABLE_CPP11
-#include <ctgmath>
-#else /* ----- not ENABLE_CPP11 ----- */
#include <cmath>
-#endif /* ----- not ENABLE_CPP11 ----- */
+#include "../randnum/RNG.h"
+#include "numutil.h"
bool almostEqual(float x, float y, float epsilon)
{
@@ -61,4 +47,27 @@ bool almostEqual(long double x, long double y, long double epsilon)
}
}
-#endif
+double approximateWithInteger_debug(const char* name, const double x, moose::RNG& rng)
+{
+ static size_t n = 0;
+ n += 1;
+ cerr << name << ' ' << ':' << x;
+ auto y = approximateWithInteger(x, rng);
+ cout << ' ' << y << ", ";
+ if( std::fmod(n, 4) == 0)
+ cerr << endl;
+ return y;
+}
+
+double approximateWithInteger(const double x, moose::RNG& rng)
+{
+ assert(x >= 0.0);
+ double xf = std::floor(x);
+ double base = x - xf;
+ if( base == 0.0)
+ return x;
+ if( rng.uniform() < base)
+ return xf+1.0;
+ return xf;
+}
+
diff --git a/moose-core/utility/numutil.h b/moose-core/utility/numutil.h
index 01ed6e2abbe4c3669533dbed425c64b576235433..b20bba5f51d72d80f982226e23af3e7a68746e00 100644
--- a/moose-core/utility/numutil.h
+++ b/moose-core/utility/numutil.h
@@ -5,15 +5,6 @@
* E-mail: ray dot subhasis at gmail dot com
* Created: 2007-11-02 11:47:21
********************************************************************/
-/**********************************************************************
- ** This program is part of 'MOOSE', the
- ** Messaging Object Oriented Simulation Environment,
- ** also known as GENESIS 3 base code.
- ** copyright (C) 2003-2005 Upinder S. Bhalla. and NCBS
- ** It is made available under the terms of the
- ** GNU General Public License version 2
- ** See the file COPYING.LIB for the full notice.
- **********************************************************************/
#ifndef _NUMUTIL_H
#define _NUMUTIL_H
@@ -21,14 +12,9 @@
#include <cmath>
#include <cfloat>
#include <limits>
+#include "../randnum/RNG.h"
-const int WORD_LENGTH = 32; // number of bits in a word - check for portability
-const double LN2 = 0.69314718055994528622676;
-const unsigned long LN2BYTES = 0xB1721814;
-const double NATURAL_E = 2.718281828459045;
-
-//extern const double getMachineEpsilon();
-//extern const double EPSILON;
+#include "../randnum/RNG.h"
#ifndef M_PI
#define M_PI 3.14159265358979323846
@@ -85,10 +71,7 @@ bool almostEqual(float x, float y, float epsilon = FLT_EPSILON);
bool almostEqual(double x, double y, double epsilon = DBL_EPSILON);
bool almostEqual(long double x, long double y, long double epsilon = LDBL_EPSILON);
-// round, isinf and isnan are not defined in VC++ or Borland C++
-#if defined(__TURBOC__) || defined(__BORLANDC__) || defined(_MSC_VER)
-#define isinf(param) !_finite(param)
-#define isnan(param) _isnan(param)
-#define round(param) floor(param+0.5)
-#endif
+double approximateWithInteger(const double x, moose::RNG& rng);
+double approximateWithInteger_debug(const char* name, const double x, moose::RNG& rng);
+
#endif
diff --git a/moose-core/utility/print_function.hpp b/moose-core/utility/print_function.hpp
index 9d389a0669f17c43cf3606715bd0cf621beac3c3..e7ec0b908628ec6834170ccccf3fd078bd4bb7e9 100644
--- a/moose-core/utility/print_function.hpp
+++ b/moose-core/utility/print_function.hpp
@@ -32,6 +32,7 @@
#include <iomanip>
#include <ctime>
#include <algorithm>
+#include <cstring>
#define T_RESET "\033[0m"
#define T_BLACK "\033[30m" /* Black */
@@ -62,12 +63,17 @@ using namespace std;
#ifndef NDEBUG
#define MOOSE_DEBUG( a ) { \
stringstream ss; ss << a; \
- cout << "DEBUG: " << __FILENAME__ << ":" << __LINE__ << "| " << ss.str(); \
+ cout << "DEBUG: " << __FILENAME__ << ":" << __LINE__ << " " << ss.str() << std::endl; \
}
#else
#define MOOSE_DEBUG( a ) {}
#endif
+#define MOOSE_WARN( a ) { \
+ stringstream ss; ss << a; \
+ moose::showWarn( ss.str() ); \
+ }
+
namespace moose {
/**
@@ -147,7 +153,7 @@ namespace moose {
return ss.str();
}
- // Not print it when built for release.
+ // Not print it when built for release.
inline string debugPrint(string msg, string prefix = "DEBUG"
, string color=T_RESET, unsigned debugLevel = 0
)