From a1f6b2300eb2fd80bacf204e9c6a7f2c5241662e Mon Sep 17 00:00:00 2001
From: Dilawar Singh <dilawars@ncbs.res.in>
Date: Thu, 6 Sep 2018 12:13:44 +0530
Subject: [PATCH] Squashed 'moose-core/' changes from 1271dcd74b..d5b330dc02
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
d5b330dc02 Merge pull request #296 from hrani/master
5a606df86c Merge remote-tracking branch 'upstream/master'
ce545cf507 Rdesigneur updates (#295)
9869046490 Merge branch 'master' into master
753b189063 changes made after fixXreacs is moved from python to python/moose for package
5eca1a3620 moved fixXreacs.py from python to python/moose for packaging, changes made to get fixXreacs files
3a519cec39 mooseAddChemSolver and mooseDeleteChemSolver is meant for chemical models only (#292)
9ba0e85532 check for enz parent is done by neighbors['enzDes'] rather than enz.parent and if enzyme parent is not pool then raise an exception
161c475e2c Merge branch 'master' into master
f9d869da24 Merge pull request #294 from upibhalla/master
a76dd524b4 Merge branch 'master' of https://github.com/BhallaLab/moose-core
c0d5ba6d9b Added plot y limits to rdesigneur
5fa7226e60 clean up modelRoot while printing
3c6972aae3 mooseAddChemSolver and mooseDeleteChemSolver is meant for chemical models only, a check is made to see if modelroot has just cube/CylMesh
3790376c3e Merge pull request #291 from BhallaLab/dilawar-patch-2
c52740323a Update README.md
5843c73ab5 Merge pull request #289 from upibhalla/master
e3baee2dce Merge branch 'master' of https://github.com/BhallaLab/moose-core
7a1b0d8ff6 Test xreacs (#287)
869522d04c Merge branch 'master' of https://github.com/BhallaLab/moose-core
bb274ee43c loadmodel with add_delete_chemSolver (#288)
7d563c7c23 Merge branch 'master' of https://github.com/BhallaLab/moose-core
637d2233a1 setting up dsolver and by passing loadModel from moosemodule.cpp to m… (#277)
9f5a2697f6 Merge branch 'master' of https://github.com/BhallaLab/moose-core
3a8489c475 All random number generators are based on c++11 (#280)
8e29d8eaa7 Minor updates to rdesigneur waveplotting
46718b9c04 Added wavePlot option to rdeisgneur.
506067669c Minor fixes to rdesigneur for setting up stims
5ab1a3c621 Merge branch 'master' of https://github.com/BhallaLab/moose-core
ea487f3ee0 Updated rdesigneur so it can handle a chem system with only a dendrite and spine compartment, no PSD.
7c321bfe94 Merge pull request #284 from upibhalla/master
d9bd29c97d Fix for units of permeability of ConcChan, as computed in Dsolve.cpp. Now it is 1/(mM.sec).
3056c917fe Merge branch 'master' of https://github.com/BhallaLab/moose-core
ae8f2336ce Fixed bug with NeuroMesh
9271d0ba22 Fixes to ReadKkit, Dsolve, rdesigneur to handle EndoMesh to insert in neuronal geometries.
f4ba9362e4 Intermediate save of rdesigneur with partial changes for handling endoMesh. Works with old examples, not tested for EndoMeshes
git-subtree-dir: moose-core
git-subtree-split: d5b330dc02ed938fcb7cff95d8ae0e2cd388d0ea
---
.travis/travis_build_linux.sh | 24 +-
.travis/travis_build_osx.sh | 10 +-
AUTHORS | 17 +
AUTHROS | 9 -
CMakeLists.txt | 85 +-
CheckCXXCompiler.cmake | 10 +-
MANIFEST.in | 15 -
README.md | 2 +-
basecode/Id.h | 20 +-
basecode/SparseMatrix.cpp | 4 +-
basecode/global.cpp | 31 +-
basecode/global.h | 29 +-
basecode/main.cpp | 6 +-
basecode/testAsync.cpp | 50 +-
biophysics/Compartment.cpp | 411 ++--
biophysics/Compartment.h | 224 +--
biophysics/CompartmentBase.cpp | 1 -
biophysics/MarkovSolver.cpp | 2 +-
biophysics/Neuron.cpp | 1477 +++++++-------
biophysics/Neuron.h | 270 +--
biophysics/RandSpike.cpp | 316 +--
biophysics/RandSpike.h | 65 +-
biophysics/testBiophysics.cpp | 62 +-
builtins/Table.h | 4 -
builtins/testNSDF.cpp | 2 +-
diffusion/ConcChanInfo.h | 6 +-
diffusion/DiffPoolVec.cpp | 107 +-
diffusion/Dsolve.cpp | 50 +-
.../boost/numeric/bindings/lapack/gees.hpp | 9 +
.../boost/numeric/bindings/lapack/gesvd.hpp | 2 +
.../boost/numeric/bindings/lapack/syev.hpp | 5 +
intfire/CMakeLists.txt | 19 +-
intfire/IntFireBase.cpp | 198 +-
intfire/IntFireBase.h | 80 +-
intfire/LIF.cpp | 96 +-
intfire/LIF.h | 34 +-
kinetics/BufPool.cpp | 62 +-
kinetics/BufPool.h | 36 +-
kinetics/Pool.cpp | 170 +-
kinetics/Pool.h | 124 +-
kinetics/PoolBase.cpp | 518 ++---
kinetics/PoolBase.h | 256 +--
kinetics/ReadKkit.cpp | 26 +-
kinetics/ReadKkit.h | 1 +
kinetics/WriteKkit.cpp | 1041 +++++-----
ksolve/BoostSys.cpp | 7 +-
ksolve/BoostSys.h | 27 +-
ksolve/CMakeLists.txt | 8 +-
ksolve/Gsolve.cpp | 16 +-
ksolve/Gsolve.h | 3 +
ksolve/GssaSystem.h | 63 +-
ksolve/GssaVoxelPools.cpp | 77 +-
ksolve/GssaVoxelPools.h | 6 +-
ksolve/Ksolve.cpp | 12 +-
ksolve/OdeSystem.h | 8 +-
ksolve/SteadyStateBoost.cpp | 3 +-
ksolve/SteadyStateBoost.h | 4 +-
ksolve/SteadyStateGsl.cpp | 1714 +++++++++--------
ksolve/Stoich.cpp | 51 +-
ksolve/Stoich.h | 4 +-
ksolve/VoxelPools.cpp | 341 ++--
ksolve/VoxelPools.h | 10 +-
ksolve/VoxelPoolsBase.cpp | 454 ++---
mesh/NeuroNode.cpp | 2 +
msg/SingleMsg.cpp | 223 ++-
msg/SparseMsg.cpp | 799 ++++----
msg/SparseMsg.h | 217 ++-
pymoose/CMakeLists.txt | 30 +-
pymoose/melement.cpp | 2 +-
pymoose/mfield.cpp | 13 +-
pymoose/moosemodule.cpp | 119 +-
.../chemUtil/add_Delete_ChemicalSolver.py | 228 +--
python/{ => moose}/fixXreacs.py | 0
python/moose/genesis/writeKkit.py | 8 +-
python/moose/moose.py | 49 +-
python/moose/print_utils.py | 2 -
python/rdesigneur/rdesigneur.py | 619 +++---
python/rdesigneur/rdesigneurProtos.py | 4 +-
python/rdesigneur/rmoogli.py | 16 +-
randnum/Binomial.cpp | 388 ----
randnum/Binomial.h | 55 -
randnum/BinomialRng.cpp | 180 --
randnum/BinomialRng.h | 45 -
randnum/CMakeLists.txt | 15 +-
randnum/Definitions.h | 46 +
randnum/Distributions.h | 34 +
randnum/Exponential.cpp | 197 --
randnum/Exponential.h | 48 -
randnum/ExponentialRng.cpp | 146 --
randnum/ExponentialRng.h | 49 -
randnum/Gamma.cpp | 154 --
randnum/Gamma.h | 42 -
randnum/GammaRng.cpp | 139 --
randnum/GammaRng.h | 52 -
randnum/Normal.cpp | 604 ------
randnum/Normal.h | 54 -
randnum/NormalDistribution.hpp | 197 ++
randnum/NormalRng.cpp | 142 --
randnum/NormalRng.h | 44 -
randnum/Poisson.cpp | 232 ---
randnum/Poisson.h | 51 -
randnum/PoissonRng.cpp | 86 -
randnum/PoissonRng.h | 33 -
randnum/Probability.cpp | 26 -
randnum/Probability.h | 40 -
randnum/RNG.h | 64 +-
randnum/RandGenerator.cpp | 162 --
randnum/RandGenerator.h | 48 -
randnum/Uniform.cpp | 125 --
randnum/Uniform.h | 43 -
randnum/UniformRng.cpp | 113 --
randnum/UniformRng.h | 43 -
randnum/mt19937ar.cpp | 258 ---
randnum/randnum.h | 15 -
randnum/test_normal_dist.cpp | 63 +
scheduling/Clock.cpp | 300 +--
shell/Shell.cpp | 2 +-
...aupnerBrunel2012CaPlasticitySynHandler.cpp | 634 +++---
...GraupnerBrunel2012CaPlasticitySynHandler.h | 235 +--
synapse/SimpleSynHandler.h | 2 +
synapse/SynHandlerBase.cpp | 159 +-
synapse/SynHandlerBase.h | 126 +-
synapse/testSynapse.cpp | 1 -
tests/python/OSC_diff_vols.g | 219 +++
tests/python/fixXreacs.py | 194 ++
tests/python/params.py | 88 +-
tests/python/testXchan1.py | 183 ++
tests/python/testXdiff1.py | 174 ++
tests/python/testXenz1.py | 137 ++
tests/python/testXreacs2.py | 61 +
tests/python/testXreacs3.py | 132 ++
tests/python/testXreacs4.py | 114 ++
tests/python/testXreacs4a.py | 114 ++
tests/python/testXreacs5.py | 120 ++
tests/python/testXreacs5a.py | 120 ++
tests/python/testXreacs6.py | 120 ++
tests/python/testXreacs7.py | 137 ++
tests/python/testXreacs8.py | 134 ++
...GraupnerBrunel2012_STDPfromCaPlasticity.py | 228 +++
tests/python/test_Xchan1.py | 153 ++
tests/python/test_Xdiff1.py | 129 ++
tests/python/test_Xenz1.py | 117 ++
tests/python/test_Xreacs2.py | 51 +
tests/python/test_Xreacs3.py | 107 +
tests/python/test_Xreacs4.py | 93 +
tests/python/test_Xreacs4a.py | 94 +
tests/python/test_Xreacs5.py | 101 +
tests/python/test_Xreacs5a.py | 99 +
tests/python/test_Xreacs6.py | 99 +
tests/python/test_Xreacs7.py | 114 ++
tests/python/test_Xreacs8.py | 109 ++
tests/python/test_connectionLists.py | 30 +-
tests/python/test_difshells.py | 29 +-
tests/python/test_kkit.py | 2 +-
tests/python/test_muparser.py | 2 +
tests/python/test_negative_value_flag.py | 2 +-
tests/python/test_neuroml2.py | 51 +-
tests/python/test_random_num.py | 59 +
tests/python/test_rdesigneur.py | 2 +
tests/python/test_utils.py | 10 -
utility/Annotator.cpp | 2 +-
utility/cnpy.cpp | 6 +-
utility/matrix_util.cpp | 4 +-
utility/matrix_util.h | 2 +-
utility/print_function.hpp | 26 +-
utility/strutil.cpp | 130 +-
utility/strutil.h | 14 +-
utility/testing_macros.hpp | 18 +-
utility/utility.h | 28 +-
169 files changed, 10702 insertions(+), 9873 deletions(-)
create mode 100644 AUTHORS
delete mode 100644 AUTHROS
delete mode 100644 MANIFEST.in
rename python/{ => moose}/fixXreacs.py (100%)
delete mode 100644 randnum/Binomial.cpp
delete mode 100644 randnum/Binomial.h
delete mode 100644 randnum/BinomialRng.cpp
delete mode 100644 randnum/BinomialRng.h
create mode 100644 randnum/Definitions.h
create mode 100644 randnum/Distributions.h
delete mode 100644 randnum/Exponential.cpp
delete mode 100644 randnum/Exponential.h
delete mode 100644 randnum/ExponentialRng.cpp
delete mode 100644 randnum/ExponentialRng.h
delete mode 100644 randnum/Gamma.cpp
delete mode 100644 randnum/Gamma.h
delete mode 100644 randnum/GammaRng.cpp
delete mode 100644 randnum/GammaRng.h
delete mode 100644 randnum/Normal.cpp
delete mode 100644 randnum/Normal.h
create mode 100644 randnum/NormalDistribution.hpp
delete mode 100644 randnum/NormalRng.cpp
delete mode 100644 randnum/NormalRng.h
delete mode 100644 randnum/Poisson.cpp
delete mode 100644 randnum/Poisson.h
delete mode 100644 randnum/PoissonRng.cpp
delete mode 100644 randnum/PoissonRng.h
delete mode 100644 randnum/Probability.cpp
delete mode 100644 randnum/Probability.h
delete mode 100644 randnum/RandGenerator.cpp
delete mode 100644 randnum/RandGenerator.h
delete mode 100644 randnum/Uniform.cpp
delete mode 100644 randnum/Uniform.h
delete mode 100644 randnum/UniformRng.cpp
delete mode 100644 randnum/UniformRng.h
delete mode 100644 randnum/mt19937ar.cpp
delete mode 100644 randnum/randnum.h
create mode 100644 randnum/test_normal_dist.cpp
create mode 100644 tests/python/OSC_diff_vols.g
create mode 100644 tests/python/fixXreacs.py
create mode 100644 tests/python/testXchan1.py
create mode 100644 tests/python/testXdiff1.py
create mode 100644 tests/python/testXenz1.py
create mode 100644 tests/python/testXreacs2.py
create mode 100644 tests/python/testXreacs3.py
create mode 100644 tests/python/testXreacs4.py
create mode 100644 tests/python/testXreacs4a.py
create mode 100644 tests/python/testXreacs5.py
create mode 100644 tests/python/testXreacs5a.py
create mode 100644 tests/python/testXreacs6.py
create mode 100644 tests/python/testXreacs7.py
create mode 100644 tests/python/testXreacs8.py
create mode 100644 tests/python/test_GraupnerBrunel2012_STDPfromCaPlasticity.py
create mode 100644 tests/python/test_Xchan1.py
create mode 100644 tests/python/test_Xdiff1.py
create mode 100644 tests/python/test_Xenz1.py
create mode 100644 tests/python/test_Xreacs2.py
create mode 100644 tests/python/test_Xreacs3.py
create mode 100644 tests/python/test_Xreacs4.py
create mode 100644 tests/python/test_Xreacs4a.py
create mode 100644 tests/python/test_Xreacs5.py
create mode 100644 tests/python/test_Xreacs5a.py
create mode 100644 tests/python/test_Xreacs6.py
create mode 100644 tests/python/test_Xreacs7.py
create mode 100644 tests/python/test_Xreacs8.py
create mode 100644 tests/python/test_random_num.py
delete mode 100644 tests/python/test_utils.py
diff --git a/.travis/travis_build_linux.sh b/.travis/travis_build_linux.sh
index 3009af21..a4499d30 100755
--- a/.travis/travis_build_linux.sh
+++ b/.travis/travis_build_linux.sh
@@ -18,13 +18,13 @@
# REVISION: ---
#===============================================================================
-set -e -x
+set -e
+set -x
PYTHON2="/usr/bin/python2"
PYTHON3="/usr/bin/python3"
MAKEFLAGS="-j`nproc`"
-
if [ ! -n "$MAKE" ]; then
MAKE="make -j`nproc`"
else
@@ -42,34 +42,34 @@ if type $PYTHON3 > /dev/null; then $PYTHON3 -m compileall -q . ; fi
echo "Currently in `pwd`"
(
- mkdir -p _GSL_BUILD && cd _GSL_BUILD
+ mkdir -p _GSL_BUILD && cd _GSL_BUILD
cmake -DDEBUG=ON -DPYTHON_EXECUTABLE="$PYTHON2" ..
- $MAKE && ctest --output-on-failure
- sudo make install
+ $MAKE && ctest --output-on-failure -j4
+ sudo make install && cd /tmp
$PYTHON2 -c 'import moose;print(moose.__file__);print(moose.version())'
)
(
# Now with boost.
mkdir -p _BOOST_BUILD && cd _BOOST_BUILD && \
- cmake -DWITH_BOOST=ON -DDEBUG=ON -DQUIET_MODE=ON -DPYTHON_EXECUTABLE="$PYTHON2" ..
- $MAKE && ctest --output-on-failure
+ cmake -DWITH_BOOST_ODE=ON -DDEBUG=ON -DPYTHON_EXECUTABLE="$PYTHON2" ..
+ $MAKE && ctest --output-on-failure -j4
)
# This is only applicable on linux build.
echo "Python3: Removed python2-networkx and install python3"
if type $PYTHON3 > /dev/null; then
- sudo apt-get remove -qq python-networkx
- sudo apt-get install -qq python3-networkx
+ sudo apt-get remove -qq python-networkx || echo "Error with apt"
+ sudo apt-get install -qq python3-networkx || echo "Error with apt"
(
mkdir -p _GSL_BUILD2 && cd _GSL_BUILD2 && \
cmake -DDEBUG=ON -DPYTHON_EXECUTABLE="$PYTHON3" ..
- $MAKE && ctest --output-on-failure
+ $MAKE && ctest --output-on-failure -j4
)
(
mkdir -p _BOOST_BUILD2 && cd _BOOST_BUILD2 && \
- cmake -DWITH_BOOST=ON -DDEBUG=ON -DPYTHON_EXECUTABLE="$PYTHON3" ..
- $MAKE && ctest --output-on-failure
+ cmake -DWITH_BOOST_ODE=ON -DDEBUG=ON -DPYTHON_EXECUTABLE="$PYTHON3" ..
+ $MAKE && ctest --output-on-failure -j4
)
echo "All done"
else
diff --git a/.travis/travis_build_osx.sh b/.travis/travis_build_osx.sh
index 0b446a20..814f6af5 100755
--- a/.travis/travis_build_osx.sh
+++ b/.travis/travis_build_osx.sh
@@ -20,21 +20,23 @@
set -o nounset # Treat unset variables as an error
set -e
+# NOTE: On travis, don't enable -j`nproc` option. It may not compile properly.
+
(
# Make sure not to pick up python from /opt.
PATH=/usr/bin:/usr/local/bin:$PATH
mkdir -p _GSL_BUILD && cd _GSL_BUILD \
- && cmake -DQUIET_MODE=ON -DDEBUG=ON \
+ && cmake -DDEBUG=ON \
-DPYTHON_EXECUTABLE=`which python` ..
- make -j3 && ctest --output-on-failure
+ make && ctest --output-on-failure
cd .. # Now with boost.
mkdir -p _BOOST_BUILD && cd _BOOST_BUILD \
- && cmake -DWITH_BOOST=ON -DDEBUG=ON \
+ && cmake -DWITH_BOOST_ODE=ON -DDEBUG=ON \
-DPYTHON_EXECUTABLE=`which python` ..
- make -j3 && ctest --output-on-failure
+ make && ctest --output-on-failure
cd ..
set +e
diff --git a/AUTHORS b/AUTHORS
new file mode 100644
index 00000000..565695af
--- /dev/null
+++ b/AUTHORS
@@ -0,0 +1,17 @@
+# Active developers
+
+Upinder S. Bhalla Primary Architect, rdesigneur
+HarshaRani. G.V MOOSE Website, SBML support, GUI
+Dilawar Singh Multithreading, GSoC, Packaging, Maintenance, BOOST solvers
+
+# Past developers
+
+Subhasis Ray Python interface, GUI
+Niraj Dudani Neuronal solver
+Aditya Gilra NeuroML support
+Aviral Goel Moogli
+
+# Contributors
+
+Padraid Gleeson NeuroML2 support
+Dharma Teja GPU parallelization using CUDA
diff --git a/AUTHROS b/AUTHROS
deleted file mode 100644
index f568c742..00000000
--- a/AUTHROS
+++ /dev/null
@@ -1,9 +0,0 @@
-Upinder S. Bhalla Primary Architect
-Niraj Dudani Neuronal solver
-Subhasis Ray Python interface
-Aditya Gilra NeuroML support
-Aviral Goel Moogli
-HarshaRani. G.V Designing of Website,read and write SBML and
- Graphical User Interface for moose
-Dilawar Singh Packaging, BOOST solvers
-Dharma Teja GPU parallelization using CUDA
diff --git a/CMakeLists.txt b/CMakeLists.txt
index bd6aaf84..59977a0f 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,18 +1,6 @@
-set(CMAKE_LEGACY_CYGWIN_WIN32 0)
cmake_minimum_required(VERSION 2.8 FATAL_ERROR)
-
-
project(pymoose)
-if(COMMAND cmake_policy)
- cmake_policy(SET CMP0003 NEW)
- cmake_policy(SET CMP0004 NEW)
- if(POLICY CMP0050)
- cmake_policy(SET CMP0050 OLD)
- endif(POLICY CMP0050)
-endif(COMMAND cmake_policy)
-
-
set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake_modules")
include(CheckCXXCompiler.cmake)
include(CheckIncludeFileCXX)
@@ -88,22 +76,24 @@ else()
endif()
################################ CMAKE OPTIONS ##################################
-option(DEBUG "Build with debug support" OFF)
-option(GPROF "Build for profiling using gprof" OFF)
-option(ENABLE_UNIT_TESTS "Enable unit tests (DEBUG should also be ON)" OFF)
-option(WITH_MPI "Enable Openmpi support" OFF)
-option(WITH_BOOST "Use boost library instead of GSL" OFF)
-option(WITH_GSL "Use gsl-library. Alternative is WITH_BOOST" ON)
+option(DEBUG "Build with debug support" OFF)
+option(GPROF "Build for profiling using gprof" OFF)
+option(ENABLE_UNIT_TESTS "Enable unit tests (DEBUG should also be ON)" OFF)
+option(WITH_MPI "Enable Openmpi support" OFF)
+option(WITH_BOOST_ODE "Use boost library ode2 library instead of GSL" OFF)
+option(WITH_GSL "Use gsl-library. Alternative is WITH_BOOST" ON)
option(PARALLELIZED_SOLVERS "Use parallel version of GSOLVE. (alpha)" OFF )
-option(PARALLELIZED_CLOCK "High level parallelization of moose::Clock (alpha)" OFF )
+option(PARALLELIZED_CLOCK "High level parallelization of moose::Clock (alpha)" OFF )
+
+option(USE_PRIVATE_RNG "Stochastic Objects use their private RNG" ON)
############################ BUILD CONFIGURATION #################################
-# Default macros
+# Default definitions.
add_definitions(-DUSE_GENESIS_PARSER)
-if(DEBUG)
+if(DEBUG OR "${CMAKE_BUILD_TYPE}" STREQUAL "Debug")
message(STATUS "Building for Debug/Unit testing")
add_definitions(-DDO_UNIT_TESTS)
set(CMAKE_BUILD_TYPE Debug)
@@ -114,15 +104,22 @@ elseif(ENABLE_UNIT_TESTS)
else()
message(STATUS "Building for Release/No unit tests.")
set(CMAKE_BUILD_TYPE Release)
- add_definitions(-UDO_UNIT_TESTS -DQUIET_MODE -O3)
+ add_definitions(-UDO_UNIT_TESTS -O3 -DDISABLE_DEBUG)
+ # Treat all warnings as errors. Some the warnings are disabled in
+ # CheckCXXCompiler.cmake .
+ add_definitions(-Werror)
endif()
-if(GPROF AND DEBUG)
+if(GPROF AND "${CMAKE_BUILD_TYPE}" STREQUAL "Debug")
message(STATUS "Compiling with profiling with gprof")
add_definitions(-pg)
set(CMAKE_EXE_LINKER_FLAGS_DEBUG "-pg")
endif()
+if(PARALLELIZED_SOLVERS)
+ find_package(Threads)
+endif()
+
################################### TARGETS ####################################
@@ -134,9 +131,10 @@ add_executable(moose.bin basecode/main.cpp)
# default include paths.
include_directories( ${CMAKE_CURRENT_SOURCE_DIR} )
-if(WITH_BOOST)
+# If using BOOST ODE2 library to solve ODE system, then don't use GSL.
+if(WITH_BOOST_ODE)
set(WITH_GSL OFF)
-endif(WITH_BOOST)
+endif(WITH_BOOST_ODE)
include_directories(msg basecode)
@@ -148,6 +146,12 @@ set(STATIC_LIBRARIES "" )
# Collect all shared libraries here.
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
+# 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
if(WITH_GSL)
find_package(GSL 1.16 REQUIRED)
if(NOT GSL_FOUND)
@@ -171,18 +175,14 @@ if(WITH_GSL)
# GSL is also used in RNG (whenever applicable), therefore include paths are
# top level.
include_directories( ${GSL_INCLUDE_DIRS} )
-elseif(WITH_BOOST)
- find_package(Boost 1.44 COMPONENTS system filesystem random REQUIRED)
+elseif(WITH_BOOST_ODE)
+ find_package(Boost 1.44 REQUIRED)
find_package( LAPACK REQUIRED )
- add_definitions( -DUSE_BOOST -UUSE_GSL )
- include_directories( ${Boost_INCLUDE_DIRS} )
- check_include_file_cxx(
- ${Boost_INCLUDE_DIRS}/boost/random/random_device.hpp
- BOOST_RANDOM_DEVICE_EXISTS
- )
- if(BOOST_RANDOM_DEVICE_EXISTS)
- add_definitions(-DBOOST_RANDOM_DEVICE_EXISTS)
- endif(BOOST_RANDOM_DEVICE_EXISTS)
+endif()
+
+# if boost ode is being used, don't use GSL.
+if(WITH_BOOST_ODE)
+ add_definitions(-DUSE_BOOST_ODE -UUSE_GSL)
endif()
@@ -264,10 +264,14 @@ if(WITH_MPI)
endif()
endif(WITH_MPI)
-if(WITH_BOOST)
+if(WITH_BOOST_ODE)
list(APPEND SYSTEM_SHARED_LIBS ${LAPACK_LIBRARIES})
list(APPEND SYSTEM_SHARED_LIBS ${Boost_LIBRARIES})
-endif(WITH_BOOST)
+endif(WITH_BOOST_ODE)
+
+if(PARALLELIZED_SOLVERS)
+ list(APPEND SYSTEM_SHARED_LIBS ${CMAKE_THREAD_LIBS_INIT})
+endif()
# These libraries could be static of dynamic. We need to discrimate between
# these two types because of --whole-archive option. See
@@ -330,7 +334,6 @@ list(APPEND MOOSE_LIBRARIES
msg
benchmarks
shell
- randnum
scheduling
moose_mpi
biophysics
@@ -483,13 +486,13 @@ include( CTest )
# onto the console if a test fails.
set(ENV{CTEST_OUTPUT_ON_FAILURE} ON)
-if(DEBUG)
+if(DEBUG OR "${CMAKE_BUILD_TYPE}" STREQUAL "Debug")
# Run this test in debug mode. In Release mode, this does not do anything.
set(MOOSE_BIN_LOCATION $<TARGET_FILE:moose.bin>)
message(STATUS "Executable moose.bin will be at ${MOOSE_BIN_LOCATION}" )
add_test(NAME moose.bin-raw-run COMMAND moose.bin -u -q)
-endif(DEBUG)
+endif()
## PyMOOSE tests.
set(PYMOOSE_TEST_DIRECTORY ${CMAKE_SOURCE_DIR}/tests/python)
diff --git a/CheckCXXCompiler.cmake b/CheckCXXCompiler.cmake
index 92fbfdfa..f3fe24d9 100644
--- a/CheckCXXCompiler.cmake
+++ b/CheckCXXCompiler.cmake
@@ -5,15 +5,17 @@ CHECK_CXX_COMPILER_FLAG( "-std=c++11" COMPILER_SUPPORTS_CXX11 )
CHECK_CXX_COMPILER_FLAG( "-std=c++0x" COMPILER_SUPPORTS_CXX0X )
CHECK_CXX_COMPILER_FLAG( "-Wno-strict-aliasing" COMPILER_WARNS_STRICT_ALIASING )
-
# Turn warning to error: Not all of the options may be supported on all
# versions of compilers. be careful here.
add_definitions(-Wall
#-Wno-return-type-c-linkage
- -Wno-unused-variable
+ -Wno-unused-variable
-Wno-unused-function
+ -Wno-unused-local-typedefs
#-Wno-unused-private-field
)
+
+
add_definitions(-fPIC)
if(COMPILER_WARNS_STRICT_ALIASING)
add_definitions( -Wno-strict-aliasing )
@@ -32,7 +34,9 @@ if(COMPILER_SUPPORTS_CXX11)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
add_definitions( -DENABLE_CPP11 )
if(APPLE)
- set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++" )
+ #set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++" )
+ message(STATUS "NOTE: Making clang to inline more aggresively" )
+ add_definitions( -mllvm -inline-threshold=1000 )
endif(APPLE)
else(COMPILER_SUPPORTS_CXX11)
add_definitions( -DBOOST_NO_CXX11_SCOPED_ENUMS -DBOOST_NO_SCOPED_ENUMS )
diff --git a/MANIFEST.in b/MANIFEST.in
deleted file mode 100644
index 8572af5e..00000000
--- a/MANIFEST.in
+++ /dev/null
@@ -1,15 +0,0 @@
-global-include *.h
-global-include *.cpp
-global-include *.c
-global-include configure.ac
-global-include *.hpp
-global-include *.cc
-global-include *.py
-global-include CMakeLists.txt
-include README
-graft cmake_modules
-graft gsl
-graft external
-graft Demos
-graft Docs
-prune buildMooseUsingCmake
diff --git a/README.md b/README.md
index dd8e6362..6e5ed75a 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,4 @@
-[](https://travis-ci.org/BhallaLab/moose-core) | [](https://badge.fury.io/py/pymoose)
+[](https://travis-ci.org/BhallaLab/moose-core) | [](https://badge.fury.io/py/pymoose) | [Nightly Linux Build on OBS](https://software.opensuse.org//download.html?project=home%3Amoose&package=pymoose)
This is the core computational engine of [MOOSE simulator](https://github.com/BhallaLab/moose). This repository contains
C++ codebase and python interface called `pymoose`. For more details about MOOSE simulator, visit https://moose.ncbs.res.in .
diff --git a/basecode/Id.h b/basecode/Id.h
index 9aed5e9b..1b877e0b 100644
--- a/basecode/Id.h
+++ b/basecode/Id.h
@@ -174,13 +174,19 @@ private:
static vector< Element* >& elements();
};
-namespace std {
- template <> class hash<Id>{
- public :
- size_t operator()(const Id &x ) const{
- return hash<unsigned int>()( x.value() );
- }
- };
+// User defined hash function.
+// See https://en.cppreference.com/w/cpp/utility/hash for more details.
+namespace std
+{
+ template <>
+ struct hash<Id>
+ {
+ public :
+ size_t operator()(const Id &x ) const
+ {
+ return std::hash<unsigned int>()( x.value() );
+ }
+ };
}
#endif // _ID_H
diff --git a/basecode/SparseMatrix.cpp b/basecode/SparseMatrix.cpp
index b5d2acc4..0f1de408 100644
--- a/basecode/SparseMatrix.cpp
+++ b/basecode/SparseMatrix.cpp
@@ -8,8 +8,6 @@
** See the file COPYING.LIB for the full notice.
**********************************************************************/
-using namespace std;
-
#include <algorithm>
#include <vector>
#include <map>
@@ -17,6 +15,8 @@ using namespace std;
#include <iostream>
#include "SparseMatrix.h"
+using namespace std;
+
const unsigned int SM_MAX_ROWS = 200000;
const unsigned int SM_MAX_COLUMNS = 200000;
diff --git a/basecode/global.cpp b/basecode/global.cpp
index 09ebeaa3..90f82b6b 100644
--- a/basecode/global.cpp
+++ b/basecode/global.cpp
@@ -40,10 +40,9 @@ extern string joinPath( string pathA, string pathB);
extern string fixPath( string path);
extern string dumpStats( int );
-
namespace moose {
- int __rng_seed__ = 0;
+ unsigned long __rng_seed__ = 0;
moose::RNG<double> rng;
@@ -131,29 +130,13 @@ namespace moose {
p = p.substr( 0, pos );
else /* no parent directory to create */
return true;
+
if( p.size() == 0 )
return true;
-#ifdef USE_BOOST
- try
- {
- boost::filesystem::path pdirs( p );
- boost::filesystem::create_directories( pdirs );
- LOG( moose::info, "Created directory " << p );
- return true;
- }
- catch(const boost::filesystem::filesystem_error& e)
- {
- LOG( moose::warning, "create_directories(" << p << ") failed with "
- << e.code().message()
- );
- return false;
- }
-#else /* ----- not USE_BOOST ----- */
string command( "mkdir -p ");
command += p;
int ret = system( command.c_str() );
- cout << "+ Return code " << ret << endl;
struct stat info;
if( stat( p.c_str(), &info ) != 0 )
{
@@ -170,7 +153,6 @@ namespace moose {
LOG( moose::warning, p << " is no directory" );
return false;
}
-#endif /* ----- not USE_BOOST ----- */
return true;
}
@@ -221,4 +203,13 @@ namespace moose {
return string( buffer );
}
+ int getGlobalSeed( )
+ {
+ return __rng_seed__;
+ }
+
+ void setGlobalSeed( int seed )
+ {
+ __rng_seed__ = seed;
+ }
}
diff --git a/basecode/global.h b/basecode/global.h
index 761a310f..1735595d 100644
--- a/basecode/global.h
+++ b/basecode/global.h
@@ -16,14 +16,7 @@
#include <map>
#include <sstream>
-
-#ifdef USE_BOOST
-//#ifdef BOOST_FILESYSTEM_EXISTS
-#include <boost/filesystem.hpp>
-//#endif /* BOOST_FILESYSTEM_EXISTS */
-#endif
-
-#include "randnum/RNG.h" /* Use inbuilt rng */
+#include "../randnum/RNG.h" /* Use inbuilt rng */
#include "../utility/print_function.hpp"
using namespace std;
@@ -70,7 +63,7 @@ namespace moose
* initialize them. By default it is initialized by random_device (see
* global.cpp).
*/
- extern int __rng_seed__;
+ extern unsigned long __rng_seed__;
/**
* @brief Fix a path. For testing purpose.
@@ -183,6 +176,24 @@ namespace moose
*/
string moosePathToUserPath( string path );
+ /* --------------------------------------------------------------------------*/
+ /**
+ * @Synopsis Get the global seed set by call of moose.seed( X )
+ *
+ * @Returns seed (int).
+ */
+ /* ----------------------------------------------------------------------------*/
+ int getGlobalSeed( );
+
+ /* --------------------------------------------------------------------------*/
+ /**
+ * @Synopsis Set the seed for all random generator. When seed of a RNG is
+ * not set, this seed it used. It is set to -1 by default.
+ *
+ * @Param seed
+ */
+ /* ----------------------------------------------------------------------------*/
+ void setGlobalSeed( int seed );
}
#endif /* ----- #ifndef __MOOSE_GLOBAL_INC_ ----- */
diff --git a/basecode/main.cpp b/basecode/main.cpp
index d6b28226..cde0f33d 100644
--- a/basecode/main.cpp
+++ b/basecode/main.cpp
@@ -8,6 +8,7 @@
**********************************************************************/
#include "header.h"
+#include "SparseMatrix.h"
#ifndef WIN32
#include <sys/time.h>
@@ -22,9 +23,8 @@
#include <unistd.h> // for getopt
#endif
#include "../scheduling/Clock.h"
-#include "DiagonalMsg.h"
-#include "SparseMatrix.h"
-#include "SparseMsg.h"
+#include "../msg/DiagonalMsg.h"
+#include "../msg/SparseMsg.h"
#include "../mpi/PostMaster.h"
#ifdef USE_MPI
#include <mpi.h>
diff --git a/basecode/testAsync.cpp b/basecode/testAsync.cpp
index b615611b..3ba2b250 100644
--- a/basecode/testAsync.cpp
+++ b/basecode/testAsync.cpp
@@ -6,47 +6,36 @@
** GNU Lesser General Public License version 2.1
** See the file COPYING.LIB for the full notice.
**********************************************************************/
+#include <stdio.h>
+#include <iomanip>
#include "header.h"
#include "global.h"
-
-#include <stdio.h>
-#include <iomanip>
-#include "../shell/Neutral.h"
-#include "../builtins/Arith.h"
#include "Dinfo.h"
-#include <queue>
-#include "../biophysics/IntFire.h"
+#include "SparseMatrix.h"
+
+#include "../msg/OneToOneMsg.h"
+#include "../msg/SparseMsg.h"
+#include "../msg/SingleMsg.h"
+
#include "../synapse/Synapse.h"
#include "../synapse/SynEvent.h"
#include "../synapse/SynHandlerBase.h"
#include "../synapse/SimpleSynHandler.h"
-#include "SparseMatrix.h"
-#include "SparseMsg.h"
-#include "SingleMsg.h"
-#include "OneToOneMsg.h"
-#include "../scheduling/Clock.h"
#include "../shell/Shell.h"
+#include "../shell/Neutral.h"
+
#include "../mpi/PostMaster.h"
+#include "../scheduling/Clock.h"
+#include "../builtins/Arith.h"
+#include "../biophysics/IntFire.h"
+#include "../randnum/RNG.h"
-#include "randnum/RNG.h"
+#include <queue>
int _seed_ = 0;
-moose::RNG<double> rng_;
-
-void _mtseed_( unsigned int seed )
-{
- _seed_ = seed;
- rng_.setSeed( _seed_ );
-}
-
-double _mtrand_( )
-{
- return rng_.uniform( );
-}
-
void showFields()
{
const Cinfo* nc = Neutral::initCinfo();
@@ -818,7 +807,8 @@ void testSparseMsg()
string arg;
- _mtseed_( 5489UL ); // The default value, but better to be explicit.
+ // The default value, but better to be explicit.
+ moose::setGlobalSeed( 5489UL );
Id sshid = Id::nextId();
Element* t2 = new GlobalDataElement( sshid, sshc, "test2", size );
@@ -838,7 +828,7 @@ void testSparseMsg()
vector< double > temp( size, 0.0 );
for ( unsigned int i = 0; i < size; ++i )
- temp[i] = _mtrand_() * Vmax;
+ temp[i] = moose::mtrand() * Vmax;
bool ret = Field< double >::setVec( cells, "Vm", temp );
assert( ret );
@@ -860,8 +850,8 @@ void testSparseMsg()
Field< unsigned int >::get( id, "numSynapse" );
unsigned int k = i * fieldSize;
for ( unsigned int j = 0; j < numSyn; ++j ) {
- weight[ k + j ] = _mtrand_() * weightMax;
- delay[ k + j ] = _mtrand_() * delayMax;
+ weight[ k + j ] = moose::mtrand() * weightMax;
+ delay[ k + j ] = moose::mtrand() * delayMax;
}
}
ret = Field< double >::setVec( syns, "weight", weight );
diff --git a/biophysics/Compartment.cpp b/biophysics/Compartment.cpp
index dda3ee47..8a137df7 100644
--- a/biophysics/Compartment.cpp
+++ b/biophysics/Compartment.cpp
@@ -7,8 +7,8 @@
** See the file COPYING.LIB for the full notice.
**********************************************************************/
-#include "header.h"
-#include "../randnum/randnum.h"
+#include "../basecode/header.h"
+#include "../basecode/global.h"
#include "CompartmentBase.h"
#include "Compartment.h"
@@ -25,29 +25,29 @@ const double Compartment::EPSILON = 1.0e-15;
*/
const Cinfo* Compartment::initCinfo()
{
- ///////////////////////////////////////////////////////////////////
- // static Finfo* compartmentFinfos[] = { };
-
- static string doc[] =
- {
- "Name", "Compartment",
- "Author", "Upi Bhalla",
- "Description", "Compartment object, for branching neuron models.",
- };
+ ///////////////////////////////////////////////////////////////////
+ // static Finfo* compartmentFinfos[] = { };
+
+ static string doc[] =
+ {
+ "Name", "Compartment",
+ "Author", "Upi Bhalla",
+ "Description", "Compartment object, for branching neuron models.",
+ };
static Dinfo< Compartment > dinfo;
- static Cinfo compartmentCinfo(
- "Compartment",
- CompartmentBase::initCinfo(),
- 0,
- 0,
- // compartmentFinfos,
- // sizeof( compartmentFinfos ) / sizeof( Finfo* ),
- &dinfo,
- doc,
- sizeof(doc)/sizeof(string)
- );
-
- return &compartmentCinfo;
+ static Cinfo compartmentCinfo(
+ "Compartment",
+ CompartmentBase::initCinfo(),
+ 0,
+ 0,
+ // compartmentFinfos,
+ // sizeof( compartmentFinfos ) / sizeof( Finfo* ),
+ &dinfo,
+ doc,
+ sizeof(doc)/sizeof(string)
+ );
+
+ return &compartmentCinfo;
}
static const Cinfo* compartmentCinfo = Compartment::initCinfo();
@@ -60,12 +60,12 @@ const SrcFinfo1< double >* VmOut =
*/
const SrcFinfo1< double >* axialOut =
- dynamic_cast< const SrcFinfo1< double >* > (
- compartmentCinfo->findFinfo( "axialOut" ) );
+ dynamic_cast< const SrcFinfo1< double >* > (
+ compartmentCinfo->findFinfo( "axialOut" ) );
const SrcFinfo2< double, double >* raxialOut =
- dynamic_cast< const SrcFinfo2< double, double >* > (
- compartmentCinfo->findFinfo( "raxialOut" ) );
+ dynamic_cast< const SrcFinfo2< double, double >* > (
+ compartmentCinfo->findFinfo( "raxialOut" ) );
//////////////////////////////////////////////////////////////////
// Here we put the Compartment class functions.
@@ -73,104 +73,104 @@ const SrcFinfo2< double, double >* raxialOut =
Compartment::Compartment()
{
- Vm_ = -0.06;
- Em_ = -0.06;
- Cm_ = 1.0;
- Rm_ = 1.0;
- invRm_ = 1.0;
- Ra_ = 1.0;
- Im_ = 0.0;
+ Vm_ = -0.06;
+ Em_ = -0.06;
+ Cm_ = 1.0;
+ Rm_ = 1.0;
+ invRm_ = 1.0;
+ Ra_ = 1.0;
+ Im_ = 0.0;
lastIm_ = 0.0;
- inject_ = 0.0;
- sumInject_ = 0.0;
- initVm_ = -0.06;
- A_ = 0.0;
- B_ = 0.0;
+ inject_ = 0.0;
+ sumInject_ = 0.0;
+ initVm_ = -0.06;
+ A_ = 0.0;
+ B_ = 0.0;
}
Compartment::~Compartment()
{
- ;
+ ;
}
// Value Field access function definitions.
void Compartment::vSetVm( const Eref& e, double Vm )
{
- Vm_ = Vm;
+ Vm_ = Vm;
}
double Compartment::vGetVm( const Eref& e ) const
{
- return Vm_;
+ return Vm_;
}
void Compartment::vSetEm( const Eref& e, double Em )
{
- Em_ = Em;
+ Em_ = Em;
}
double Compartment::vGetEm( const Eref& e ) const
{
- return Em_;
+ return Em_;
}
void Compartment::vSetCm( const Eref& e, double Cm )
{
- if ( rangeWarning( "Cm", Cm ) ) return;
- Cm_ = Cm;
+ if ( rangeWarning( "Cm", Cm ) ) return;
+ Cm_ = Cm;
}
double Compartment::vGetCm( const Eref& e ) const
{
- return Cm_;
+ return Cm_;
}
void Compartment::vSetRm( const Eref& e, double Rm )
{
- if ( rangeWarning( "Rm", Rm ) ) return;
- Rm_ = Rm;
- invRm_ = 1.0/Rm;
+ if ( rangeWarning( "Rm", Rm ) ) return;
+ Rm_ = Rm;
+ invRm_ = 1.0/Rm;
}
double Compartment::vGetRm( const Eref& e ) const
{
- return Rm_;
+ return Rm_;
}
void Compartment::vSetRa( const Eref& e, double Ra )
{
- if ( rangeWarning( "Ra", Ra ) ) return;
- Ra_ = Ra;
+ if ( rangeWarning( "Ra", Ra ) ) return;
+ Ra_ = Ra;
}
double Compartment::vGetRa( const Eref& e ) const
{
- return Ra_;
+ return Ra_;
}
double Compartment::vGetIm( const Eref& e ) const
{
- return lastIm_;
+ return lastIm_;
}
void Compartment::vSetInject( const Eref& e, double inject )
{
- inject_ = inject;
+ inject_ = inject;
}
double Compartment::vGetInject( const Eref& e ) const
{
- return inject_;
+ return inject_;
}
void Compartment::vSetInitVm( const Eref& e, double initVm )
{
- initVm_ = initVm;
+ initVm_ = initVm;
}
double Compartment::vGetInitVm( const Eref& e ) const
{
- return initVm_;
+ return initVm_;
}
@@ -180,84 +180,88 @@ double Compartment::vGetInitVm( const Eref& e ) const
void Compartment::vProcess( const Eref& e, ProcPtr p )
{
- //cout << "Compartment " << e.id().path() << ":: process: A = " << A_ << ", B = " << B_ << endl;
- A_ += inject_ + sumInject_ + Em_ * invRm_;
- if ( B_ > EPSILON ) {
- double x = exp( -B_ * p->dt / Cm_ );
- Vm_ = Vm_ * x + ( A_ / B_ ) * ( 1.0 - x );
- } else {
- Vm_ += ( A_ - Vm_ * B_ ) * p->dt / Cm_;
- }
- A_ = 0.0;
- B_ = invRm_;
- lastIm_ = Im_;
- Im_ = 0.0;
- sumInject_ = 0.0;
- // Send out Vm to channels, SpikeGens, etc.
- VmOut()->send( e, Vm_ );
-
- // The axial/raxial messages go out in the 'init' phase.
+ //cout << "Compartment " << e.id().path() << ":: process: A = " << A_ << ", B = " << B_ << endl;
+ A_ += inject_ + sumInject_ + Em_ * invRm_;
+ if ( B_ > EPSILON )
+ {
+ double x = exp( -B_ * p->dt / Cm_ );
+ Vm_ = Vm_ * x + ( A_ / B_ ) * ( 1.0 - x );
+ }
+ else
+ {
+ Vm_ += ( A_ - Vm_ * B_ ) * p->dt / Cm_;
+ }
+ A_ = 0.0;
+ B_ = invRm_;
+ lastIm_ = Im_;
+ Im_ = 0.0;
+ sumInject_ = 0.0;
+ // Send out Vm to channels, SpikeGens, etc.
+ VmOut()->send( e, Vm_ );
+
+ // The axial/raxial messages go out in the 'init' phase.
}
void Compartment::vReinit( const Eref& e, ProcPtr p )
{
- Vm_ = initVm_;
- A_ = 0.0;
- B_ = invRm_;
- Im_ = 0.0;
- lastIm_ = 0.0;
- sumInject_ = 0.0;
- dt_ = p->dt;
-
- // Send out the resting Vm to channels, SpikeGens, etc.
- VmOut()->send( e, Vm_ );
+ Vm_ = initVm_;
+ A_ = 0.0;
+ B_ = invRm_;
+ Im_ = 0.0;
+ lastIm_ = 0.0;
+ sumInject_ = 0.0;
+ dt_ = p->dt;
+
+ // Send out the resting Vm to channels, SpikeGens, etc.
+ VmOut()->send( e, Vm_ );
}
void Compartment::vInitProc( const Eref& e, ProcPtr p )
{
- // Send out the axial messages
- axialOut->send( e, Vm_ );
- // Send out the raxial messages
- raxialOut->send( e, Ra_, Vm_ );
+ // Send out the axial messages
+ axialOut->send( e, Vm_ );
+ // Send out the raxial messages
+ raxialOut->send( e, Ra_, Vm_ );
}
void Compartment::vInitReinit( const Eref& e, ProcPtr p )
{
- ; // Nothing happens here
+ ; // Nothing happens here
}
void Compartment::vHandleChannel( const Eref& e, double Gk, double Ek)
{
- A_ += Gk * Ek;
- B_ += Gk;
+ A_ += Gk * Ek;
+ B_ += Gk;
}
void Compartment::vHandleRaxial( double Ra, double Vm)
{
- A_ += Vm / Ra;
- B_ += 1.0 / Ra;
- Im_ += ( Vm - Vm_ ) / Ra;
+ A_ += Vm / Ra;
+ B_ += 1.0 / Ra;
+ Im_ += ( Vm - Vm_ ) / Ra;
}
void Compartment::vHandleAxial( double Vm)
{
- A_ += Vm / Ra_;
- B_ += 1.0 / Ra_;
- Im_ += ( Vm - Vm_ ) / Ra_;
+ A_ += Vm / Ra_;
+ B_ += 1.0 / Ra_;
+ Im_ += ( Vm - Vm_ ) / Ra_;
}
void Compartment::vInjectMsg( const Eref& e, double current)
{
- sumInject_ += current;
- Im_ += current;
+ sumInject_ += current;
+ Im_ += current;
}
void Compartment::vRandInject( const Eref& e, double prob, double current)
{
- if ( mtrand() < prob * dt_ ) {
- sumInject_ += current;
- Im_ += current;
- }
+ if ( moose::mtrand() < prob * dt_ )
+ {
+ sumInject_ += current;
+ Im_ += current;
+ }
}
/////////////////////////////////////////////////////////////////////
@@ -270,39 +274,39 @@ void Compartment::vRandInject( const Eref& e, double prob, double current)
void testCompartment()
{
- unsigned int size = 1;
- Eref sheller( Id().eref() );
- Shell* shell = reinterpret_cast< Shell* >( sheller.data() );
- Id comptId = shell->doCreate("Compartment", Id(), "compt", size);
- assert( Id::isValid(comptId));
- Eref compter = comptId.eref();
- Compartment* c = reinterpret_cast< Compartment* >( comptId.eref().data() );
- ProcInfo p;
- p.dt = 0.002;
- c->setInject( compter, 1.0 );
- c->setRm( compter, 1.0 );
- c->setRa( compter, 0.0025 );
- c->setCm( compter, 1.0 );
- c->setEm( compter, 0.0 );
- c->setVm( compter, 0.0 );
-
- // First, test charging curve for a single compartment
- // We want our charging curve to be a nice simple exponential
- // Vm = 1.0 - 1.0 * exp( - t / 1.0 );
- double delta = 0.0;
- double Vm = 0.0;
- double tau = 1.0;
- double Vmax = 1.0;
- for ( p.currTime = 0.0; p.currTime < 2.0; p.currTime += p.dt )
- {
- Vm = c->getVm( compter );
- double x = Vmax - Vmax * exp( -p.currTime / tau );
- delta += ( Vm - x ) * ( Vm - x );
- c->process( compter, &p );
- }
- assert( delta < 1.0e-6 );
- shell->doDelete(comptId);
- cout << "." << flush;
+ unsigned int size = 1;
+ Eref sheller( Id().eref() );
+ Shell* shell = reinterpret_cast< Shell* >( sheller.data() );
+ Id comptId = shell->doCreate("Compartment", Id(), "compt", size);
+ assert( Id::isValid(comptId));
+ Eref compter = comptId.eref();
+ Compartment* c = reinterpret_cast< Compartment* >( comptId.eref().data() );
+ ProcInfo p;
+ p.dt = 0.002;
+ c->setInject( compter, 1.0 );
+ c->setRm( compter, 1.0 );
+ c->setRa( compter, 0.0025 );
+ c->setCm( compter, 1.0 );
+ c->setEm( compter, 0.0 );
+ c->setVm( compter, 0.0 );
+
+ // First, test charging curve for a single compartment
+ // We want our charging curve to be a nice simple exponential
+ // Vm = 1.0 - 1.0 * exp( - t / 1.0 );
+ double delta = 0.0;
+ double Vm = 0.0;
+ double tau = 1.0;
+ double Vmax = 1.0;
+ for ( p.currTime = 0.0; p.currTime < 2.0; p.currTime += p.dt )
+ {
+ Vm = c->getVm( compter );
+ double x = Vmax - Vmax * exp( -p.currTime / tau );
+ delta += ( Vm - x ) * ( Vm - x );
+ c->process( compter, &p );
+ }
+ assert( delta < 1.0e-6 );
+ shell->doDelete(comptId);
+ cout << "." << flush;
}
// Comment out this define if it takes too long (about 5 seconds on
@@ -319,72 +323,73 @@ void testCompartment()
#include "../shell/Shell.h"
void testCompartmentProcess()
{
- Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
- unsigned int size = 100;
- double Rm = 1.0;
- double Ra = 0.01;
- double Cm = 1.0;
- double dt = 0.01;
- double runtime = 10;
- double lambda = sqrt( Rm / Ra );
-
- Id cid = shell->doCreate( "Compartment", Id(), "compt", size );
- assert( Id::isValid(cid));
- assert( cid.eref().element()->numData() == size );
-
- bool ret = Field< double >::setRepeat( cid, "initVm", 0.0 );
- assert( ret );
- Field< double >::setRepeat( cid, "inject", 0 );
- // Only apply current injection in first compartment
- Field< double >::set( ObjId( cid, 0 ), "inject", 1.0 );
- Field< double >::setRepeat( cid, "Rm", Rm );
- Field< double >::setRepeat( cid, "Ra", Ra );
- Field< double >::setRepeat( cid, "Cm", Cm );
- Field< double >::setRepeat( cid, "Em", 0 );
- Field< double >::setRepeat( cid, "Vm", 0 );
-
- // The diagonal message has a default stride of 1, so it connects
- // successive compartments.
- // Note that the src and dest elements here are identical, so we cannot
- // use a shared message. The messaging system will get confused about
- // direction to send data. So we split up the shared message that we
- // might have used, below, into two individual messages.
- // MsgId mid = shell->doAddMsg( "Diagonal", ObjId( cid ), "raxial", ObjId( cid ), "axial" );
- ObjId mid = shell->doAddMsg( "Diagonal", ObjId( cid ), "axialOut", ObjId( cid ), "handleAxial" );
- assert( !mid.bad());
- // mid = shell->doAddMsg( "Diagonal", ObjId( cid ), "handleRaxial", ObjId( cid ), "raxialOut" );
- mid = shell->doAddMsg( "Diagonal", ObjId( cid ), "raxialOut", ObjId( cid ), "handleRaxial" );
- assert( !mid.bad() );
- // ObjId managerId = Msg::getMsg( mid )->manager().objId();
- // Make the raxial data go from high to lower index compartments.
- Field< int >::set( mid, "stride", -1 );
+ Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
+ unsigned int size = 100;
+ double Rm = 1.0;
+ double Ra = 0.01;
+ double Cm = 1.0;
+ double dt = 0.01;
+ double runtime = 10;
+ double lambda = sqrt( Rm / Ra );
+
+ Id cid = shell->doCreate( "Compartment", Id(), "compt", size );
+ assert( Id::isValid(cid));
+ assert( cid.eref().element()->numData() == size );
+
+ bool ret = Field< double >::setRepeat( cid, "initVm", 0.0 );
+ assert( ret );
+ Field< double >::setRepeat( cid, "inject", 0 );
+ // Only apply current injection in first compartment
+ Field< double >::set( ObjId( cid, 0 ), "inject", 1.0 );
+ Field< double >::setRepeat( cid, "Rm", Rm );
+ Field< double >::setRepeat( cid, "Ra", Ra );
+ Field< double >::setRepeat( cid, "Cm", Cm );
+ Field< double >::setRepeat( cid, "Em", 0 );
+ Field< double >::setRepeat( cid, "Vm", 0 );
+
+ // The diagonal message has a default stride of 1, so it connects
+ // successive compartments.
+ // Note that the src and dest elements here are identical, so we cannot
+ // use a shared message. The messaging system will get confused about
+ // direction to send data. So we split up the shared message that we
+ // might have used, below, into two individual messages.
+ // MsgId mid = shell->doAddMsg( "Diagonal", ObjId( cid ), "raxial", ObjId( cid ), "axial" );
+ ObjId mid = shell->doAddMsg( "Diagonal", ObjId( cid ), "axialOut", ObjId( cid ), "handleAxial" );
+ assert( !mid.bad());
+ // mid = shell->doAddMsg( "Diagonal", ObjId( cid ), "handleRaxial", ObjId( cid ), "raxialOut" );
+ mid = shell->doAddMsg( "Diagonal", ObjId( cid ), "raxialOut", ObjId( cid ), "handleRaxial" );
+ assert( !mid.bad() );
+ // ObjId managerId = Msg::getMsg( mid )->manager().objId();
+ // Make the raxial data go from high to lower index compartments.
+ Field< int >::set( mid, "stride", -1 );
#ifdef DO_SPATIAL_TESTS
- shell->doSetClock( 0, dt );
- shell->doSetClock( 1, dt );
- // Ensure that the inter_compt msgs go between nodes once every dt.
- shell->doSetClock( 9, dt );
-
- shell->doUseClock( "/compt", "init", 0 );
- shell->doUseClock( "/compt", "process", 1 );
-
- shell->doReinit();
- shell->doStart( runtime );
-
- double Vmax = Field< double >::get( ObjId( cid, 0 ), "Vm" );
-
- double delta = 0.0;
- // We measure only the first 50 compartments as later we
- // run into end effects because it is not an infinite cable
- for ( unsigned int i = 0; i < size; i++ ) {
- double Vm = Field< double >::get( ObjId( cid, i ), "Vm" );
- double x = Vmax * exp( - static_cast< double >( i ) / lambda );
- delta += ( Vm - x ) * ( Vm - x );
- // cout << i << " (x, Vm) = ( " << x << ", " << Vm << " )\n";
- }
- assert( delta < 1.0e-5 );
+ shell->doSetClock( 0, dt );
+ shell->doSetClock( 1, dt );
+ // Ensure that the inter_compt msgs go between nodes once every dt.
+ shell->doSetClock( 9, dt );
+
+ shell->doUseClock( "/compt", "init", 0 );
+ shell->doUseClock( "/compt", "process", 1 );
+
+ shell->doReinit();
+ shell->doStart( runtime );
+
+ double Vmax = Field< double >::get( ObjId( cid, 0 ), "Vm" );
+
+ double delta = 0.0;
+ // We measure only the first 50 compartments as later we
+ // run into end effects because it is not an infinite cable
+ for ( unsigned int i = 0; i < size; i++ )
+ {
+ double Vm = Field< double >::get( ObjId( cid, i ), "Vm" );
+ double x = Vmax * exp( - static_cast< double >( i ) / lambda );
+ delta += ( Vm - x ) * ( Vm - x );
+ // cout << i << " (x, Vm) = ( " << x << ", " << Vm << " )\n";
+ }
+ assert( delta < 1.0e-5 );
#endif // DO_SPATIAL_TESTS
- shell->doDelete( cid );
- cout << "." << flush;
+ shell->doDelete( cid );
+ cout << "." << flush;
}
#endif // DO_UNIT_TESTS
diff --git a/biophysics/Compartment.h b/biophysics/Compartment.h
index b5c3de04..af2186bb 100644
--- a/biophysics/Compartment.h
+++ b/biophysics/Compartment.h
@@ -21,117 +21,119 @@ namespace moose
{
class Compartment: public CompartmentBase
{
- public:
- Compartment();
- virtual ~Compartment();
-
- // Value Field access function definitions.
- virtual void vSetVm( const Eref& e, double Vm );
- virtual double vGetVm( const Eref& e ) const;
- virtual void vSetEm( const Eref& e, double Em );
- virtual double vGetEm( const Eref& e ) const;
- virtual void vSetCm( const Eref& e, double Cm );
- virtual double vGetCm( const Eref& e ) const;
- virtual void vSetRm( const Eref& e, double Rm );
- virtual double vGetRm( const Eref& e ) const;
- virtual void vSetRa( const Eref& e, double Ra );
- virtual double vGetRa( const Eref& e ) const;
- virtual double vGetIm( const Eref& e ) const;
- virtual void vSetInject( const Eref& e, double Inject );
- virtual double vGetInject( const Eref& e ) const;
- virtual void vSetInitVm( const Eref& e, double initVm );
- virtual double vGetInitVm( const Eref& e ) const;
-
- // Dest function definitions.
- /**
- * The process function does the object updating and sends out
- * messages to channels, nernsts, and so on.
- */
- void vProcess( const Eref& e, ProcPtr p );
-
- /**
- * The reinit function reinitializes all fields.
- */
- void vReinit( const Eref& e, ProcPtr p );
-
- /**
- * The initProc function is for a second phase of 'process'
- * operations. It sends the axial and raxial messages
- * to other compartments. It has to be executed out of phase
- * with the main process so that all compartments are
- * equivalent and there is no calling order dependence in
- * the results.
- */
- void vInitProc( const Eref& e, ProcPtr p );
-
- /**
- * Empty function to do another reinit step out of phase
- * with the main one. Nothing needs doing there.
- */
- void vInitReinit( const Eref& e, ProcPtr p );
-
- /**
- * handleChannel handles information coming from the channel
- * to the compartment
- */
- void vHandleChannel( const Eref& e, double Gk, double Ek);
-
- /**
- * handleRaxial handles incoming raxial message data.
- */
- void vHandleRaxial( double Ra, double Vm);
-
- /**
- * handleAxial handles incoming axial message data.
- */
- void vHandleAxial( double Vm);
-
- /**
- * Injects a constantly updated current into the compartment.
- * Unlike the 'inject' field, this injected current is
- * applicable only for a single timestep. So this is meant to
- * be used as the destination of a message rather than as a
- * one-time assignment.
- */
- void vInjectMsg( const Eref& e, double current);
-
- /**
- * Injects a constantly updated current into the
- * compartment, with a probability prob. Note that it isn't
- * the current amplitude that is random, it is the presence
- * or absence of the current that is probabilistic.
- */
- void vRandInject( const Eref& e, double prob, double current);
-
- /**
- * Dummy function to act as recipient of 'cable' message,
- * which is just for grouping compartments.
- */
- void cable();
-
-
- /**
- * Initializes the class info.
- */
- static const Cinfo* initCinfo();
- protected:
- double Vm_;
- double initVm_;
- double Em_;
- double Cm_;
- double Rm_;
- double Ra_;
- double Im_;
- double lastIm_;
- double inject_;
- double A_;
- double B_;
- double sumInject_;
-
- private:
- double invRm_;
- double dt_;
- static const double EPSILON;
+public:
+ Compartment();
+ virtual ~Compartment();
+
+ // Value Field access function definitions.
+ virtual void vSetVm( const Eref& e, double Vm );
+ virtual double vGetVm( const Eref& e ) const;
+ virtual void vSetEm( const Eref& e, double Em );
+ virtual double vGetEm( const Eref& e ) const;
+ virtual void vSetCm( const Eref& e, double Cm );
+ virtual double vGetCm( const Eref& e ) const;
+ virtual void vSetRm( const Eref& e, double Rm );
+ virtual double vGetRm( const Eref& e ) const;
+ virtual void vSetRa( const Eref& e, double Ra );
+ virtual double vGetRa( const Eref& e ) const;
+ virtual double vGetIm( const Eref& e ) const;
+ virtual void vSetInject( const Eref& e, double Inject );
+ virtual double vGetInject( const Eref& e ) const;
+ virtual void vSetInitVm( const Eref& e, double initVm );
+ virtual double vGetInitVm( const Eref& e ) const;
+
+ // Dest function definitions.
+ /**
+ * The process function does the object updating and sends out
+ * messages to channels, nernsts, and so on.
+ */
+ void vProcess( const Eref& e, ProcPtr p );
+
+ /**
+ * The reinit function reinitializes all fields.
+ */
+ void vReinit( const Eref& e, ProcPtr p );
+
+ /**
+ * The initProc function is for a second phase of 'process'
+ * operations. It sends the axial and raxial messages
+ * to other compartments. It has to be executed out of phase
+ * with the main process so that all compartments are
+ * equivalent and there is no calling order dependence in
+ * the results.
+ */
+ void vInitProc( const Eref& e, ProcPtr p );
+
+ /**
+ * Empty function to do another reinit step out of phase
+ * with the main one. Nothing needs doing there.
+ */
+ void vInitReinit( const Eref& e, ProcPtr p );
+
+ /**
+ * handleChannel handles information coming from the channel
+ * to the compartment
+ */
+ void vHandleChannel( const Eref& e, double Gk, double Ek);
+
+ /**
+ * handleRaxial handles incoming raxial message data.
+ */
+ void vHandleRaxial( double Ra, double Vm);
+
+ /**
+ * handleAxial handles incoming axial message data.
+ */
+ void vHandleAxial( double Vm);
+
+ /**
+ * Injects a constantly updated current into the compartment.
+ * Unlike the 'inject' field, this injected current is
+ * applicable only for a single timestep. So this is meant to
+ * be used as the destination of a message rather than as a
+ * one-time assignment.
+ */
+ void vInjectMsg( const Eref& e, double current);
+
+ /**
+ * Injects a constantly updated current into the
+ * compartment, with a probability prob. Note that it isn't
+ * the current amplitude that is random, it is the presence
+ * or absence of the current that is probabilistic.
+ */
+ void vRandInject( const Eref& e, double prob, double current);
+
+ /**
+ * Dummy function to act as recipient of 'cable' message,
+ * which is just for grouping compartments.
+ */
+ void cable();
+
+
+ /**
+ * Initializes the class info.
+ */
+ static const Cinfo* initCinfo();
+
+protected:
+ double Vm_;
+ double initVm_;
+ double Em_;
+ double Cm_;
+ double Rm_;
+ double Ra_;
+ double Im_;
+ double lastIm_;
+ double inject_;
+ double A_;
+ double B_;
+ double sumInject_;
+
+private:
+ double invRm_;
+ double dt_;
+ static const double EPSILON;
+
};
}
diff --git a/biophysics/CompartmentBase.cpp b/biophysics/CompartmentBase.cpp
index 1528f54f..795acb5a 100644
--- a/biophysics/CompartmentBase.cpp
+++ b/biophysics/CompartmentBase.cpp
@@ -9,7 +9,6 @@
#include "header.h"
#include "ElementValueFinfo.h"
-#include "../randnum/randnum.h"
#include "CompartmentBase.h"
#include "CompartmentDataHolder.h"
#include "../shell/Wildcard.h"
diff --git a/biophysics/MarkovSolver.cpp b/biophysics/MarkovSolver.cpp
index b5e3ddbb..0c877950 100644
--- a/biophysics/MarkovSolver.cpp
+++ b/biophysics/MarkovSolver.cpp
@@ -85,7 +85,7 @@ Matrix* MarkovSolver::computePadeApproximant( Matrix* Q1,
vector< unsigned int >* swaps = new vector< unsigned int >;
unsigned int n = Q1->size();
unsigned int degree = mCandidates[degreeIndex];
- double *padeCoeffs;
+ double *padeCoeffs = NULL;
Matrix *V = matAlloc(n);
//Vector of Matrix pointers. Each entry is an even power of Q.
diff --git a/biophysics/Neuron.cpp b/biophysics/Neuron.cpp
index 6a5e42d3..aa867591 100644
--- a/biophysics/Neuron.cpp
+++ b/biophysics/Neuron.cpp
@@ -105,455 +105,457 @@ const unsigned int nuParser::numVal = 13;
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
- );
- static ValueFinfo< Neuron, double > RA( "RA",
- "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
- );
- static ValueFinfo< Neuron, double > Em( "Em",
- "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. "
- "Accepts swc and dotp formats at present. "
- "Both these formats require that the appropriate channel "
- "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
- );
-
- 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",
- &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",
- &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 systemwill 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",
- &Neuron::setSpineDistribution,
- &Neuron::getSpineDistribution
- );
-
-
- static ReadOnlyValueFinfo< Neuron, unsigned int > numCompartments(
- "numCompartments",
- "Number of electrical compartments in model. ",
- &Neuron::getNumCompartments
- );
-
- static ReadOnlyValueFinfo< Neuron, unsigned int > numSpines(
- "numSpines",
- "Number of dendritic spines in model. ",
- &Neuron::getNumSpines
- );
-
- static ReadOnlyValueFinfo< Neuron, unsigned int > numBranches(
- "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
- );
-
- static ReadOnlyValueFinfo< Neuron, vector< double > > geomDistFromSoma(
- "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
- );
- 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
- );
-
- 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
- );
-
- 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
- );
-
- 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
- );
-
- 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
- );
-
- 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
- );
-
- 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
- );
-
- /////////////////////////////////////////////////////////////////////
- // 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 )
- );
- 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 )
- );
- 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 )
- );
-
- /*
- static DestFinfo rotateInSpace( "rotateInSpace",
- theta, phi
- static DestFinfo transformInSpace( "transformInSpace",
- transfMatrix(4x4)
- static DestFinfo saveAsNeuroML( "saveAsNeuroML", fname )
- static DestFinfo saveAsDotP( "saveAsDotP", fname )
- static DestFinfo saveAsSwc( "saveAsSwc", fname )
- */
- /////////////////////////////////////////////////////////////////////
- // FieldElement
- /////////////////////////////////////////////////////////////////////
- static FieldElementFinfo< Neuron, Spine > spineFinfo(
- "spine",
- "Field Element for spines. Used to handle dynamic "
- "geometry changes in spines. ",
- Spine::initCinfo(),
- &Neuron::lookupSpine,
- &Neuron::setNumSpines,
- &Neuron::getNumSpines,
- false
- );
-
- /////////////////////////////////////////////////////////////////////
- static Finfo* neuronFinfos[] =
- {
- &RM, // ValueFinfo
- &RA, // ValueFinfo
- &CM, // ValueFinfo
- &Em, // ValueFinfo
- &theta, // ValueFinfo
- &phi, // ValueFinfo
- &sourceFile, // ValueFinfo
- &compartmentLengthInLambdas, // ValueFinfo
- &numCompartments, // ReadOnlyValueFinfo
- &numSpines, // ReadOnlyValueFinfo
- &numBranches, // ReadOnlyValueFinfo
- &pathDistFromSoma, // ReadOnlyValueFinfo
- &geomDistFromSoma, // ReadOnlyValueFinfo
- &elecDistFromSoma, // ReadOnlyValueFinfo
- &compartments, // ReadOnlyValueFinfo
- &channelDistribution, // ValueFinfo
- &passiveDistribution, // ValueFinfo
- &spineDistribution, // ValueFinfo
- // &mechSpec, // ValueFinfo
- // &spineSpecification, // ValueFinfo
- &compartmentsFromExpression, // ReadOnlyLookupValueFinfo
- &valuesFromExpression, // ReadOnlyLookupValueFinfo
- &spinesFromExpression, // ReadOnlyLookupValueFinfo
- &spinesOnCompartment, // ReadOnlyLookupValueFinfo
- &parentCompartmentOfSpine, // ReadOnlyLookupValueFinfo
- &spineIdsFromCompartmentIds, // ReadOnlyLookupValueFinfo
- &buildSegmentTree, // DestFinfo
- &setSpineAndPsdMesh, // DestFinfo
- &setSpineAndPsdDsolve, // DestFinfo
- &spineFinfo, // FieldElementFinfo
- };
- static string doc[] =
- {
- "Name", "Neuron",
- "Author", "C H Chaitanya, Upi Bhalla",
- "Description", "Neuron - Manager for neurons. "
- "Handles high-level specification of distribution of "
- "spines, channels and passive properties. Also manages "
- "spine resizing through a Spine FieldElement. ",
- };
- static Dinfo<Neuron> dinfo;
- static Cinfo neuronCinfo(
- "Neuron",
- Neutral::initCinfo(),
- neuronFinfos, sizeof( neuronFinfos ) / sizeof( Finfo* ),
- &dinfo,
- doc,
- sizeof(doc)/sizeof(string)
- );
-
- return &neuronCinfo;
+ /////////////////////////////////////////////////////////////////////
+ // ValueFinfos
+ /////////////////////////////////////////////////////////////////////
+ static ValueFinfo< Neuron, double > RM( "RM",
+ "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
+ );
+ static ValueFinfo< Neuron, double > CM( "CM",
+ "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
+ );
+ 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. "
+ "Accepts swc and dotp formats at present. "
+ "Both these formats require that the appropriate channel "
+ "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
+ );
+
+ 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",
+ &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",
+ &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 systemwill 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",
+ &Neuron::setSpineDistribution,
+ &Neuron::getSpineDistribution
+ );
+
+
+ static ReadOnlyValueFinfo< Neuron, unsigned int > numCompartments(
+ "numCompartments",
+ "Number of electrical compartments in model. ",
+ &Neuron::getNumCompartments
+ );
+
+ static ReadOnlyValueFinfo< Neuron, unsigned int > numSpines(
+ "numSpines",
+ "Number of dendritic spines in model. ",
+ &Neuron::getNumSpines
+ );
+
+ static ReadOnlyValueFinfo< Neuron, unsigned int > numBranches(
+ "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
+ );
+
+ static ReadOnlyValueFinfo< Neuron, vector< double > > geomDistFromSoma(
+ "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
+ );
+ 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
+ );
+
+ 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
+ );
+
+ 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
+ );
+
+ 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
+ );
+
+ 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
+ );
+
+ 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
+ );
+
+ 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
+ );
+
+ /////////////////////////////////////////////////////////////////////
+ // 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 )
+ );
+ 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 )
+ );
+ 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 )
+ );
+
+ /*
+ static DestFinfo rotateInSpace( "rotateInSpace",
+ theta, phi
+ static DestFinfo transformInSpace( "transformInSpace",
+ transfMatrix(4x4)
+ static DestFinfo saveAsNeuroML( "saveAsNeuroML", fname )
+ static DestFinfo saveAsDotP( "saveAsDotP", fname )
+ static DestFinfo saveAsSwc( "saveAsSwc", fname )
+ */
+ /////////////////////////////////////////////////////////////////////
+ // FieldElement
+ /////////////////////////////////////////////////////////////////////
+ static FieldElementFinfo< Neuron, Spine > spineFinfo(
+ "spine",
+ "Field Element for spines. Used to handle dynamic "
+ "geometry changes in spines. ",
+ Spine::initCinfo(),
+ &Neuron::lookupSpine,
+ &Neuron::setNumSpines,
+ &Neuron::getNumSpines,
+ false
+ );
+
+ /////////////////////////////////////////////////////////////////////
+ static Finfo* neuronFinfos[] =
+ {
+ &RM, // ValueFinfo
+ &RA, // ValueFinfo
+ &CM, // ValueFinfo
+ &Em, // ValueFinfo
+ &theta, // ValueFinfo
+ &phi, // ValueFinfo
+ &sourceFile, // ValueFinfo
+ &compartmentLengthInLambdas, // ValueFinfo
+ &numCompartments, // ReadOnlyValueFinfo
+ &numSpines, // ReadOnlyValueFinfo
+ &numBranches, // ReadOnlyValueFinfo
+ &pathDistFromSoma, // ReadOnlyValueFinfo
+ &geomDistFromSoma, // ReadOnlyValueFinfo
+ &elecDistFromSoma, // ReadOnlyValueFinfo
+ &compartments, // ReadOnlyValueFinfo
+ &channelDistribution, // ValueFinfo
+ &passiveDistribution, // ValueFinfo
+ &spineDistribution, // ValueFinfo
+ // &mechSpec, // ValueFinfo
+ // &spineSpecification, // ValueFinfo
+ &compartmentsFromExpression, // ReadOnlyLookupValueFinfo
+ &valuesFromExpression, // ReadOnlyLookupValueFinfo
+ &spinesFromExpression, // ReadOnlyLookupValueFinfo
+ &spinesOnCompartment, // ReadOnlyLookupValueFinfo
+ &parentCompartmentOfSpine, // ReadOnlyLookupValueFinfo
+ &spineIdsFromCompartmentIds, // ReadOnlyLookupValueFinfo
+ &buildSegmentTree, // DestFinfo
+ &setSpineAndPsdMesh, // DestFinfo
+ &setSpineAndPsdDsolve, // DestFinfo
+ &spineFinfo, // FieldElementFinfo
+ };
+ static string doc[] =
+ {
+ "Name", "Neuron",
+ "Author", "C H Chaitanya, Upi Bhalla",
+ "Description", "Neuron - Manager for neurons. "
+ "Handles high-level specification of distribution of "
+ "spines, channels and passive properties. Also manages "
+ "spine resizing through a Spine FieldElement. ",
+ };
+ static Dinfo<Neuron> dinfo;
+ static Cinfo neuronCinfo(
+ "Neuron",
+ Neutral::initCinfo(),
+ neuronFinfos, sizeof( neuronFinfos ) / sizeof( Finfo* ),
+ &dinfo,
+ doc,
+ sizeof(doc)/sizeof(string)
+ );
+
+ return &neuronCinfo;
}
static const Cinfo* neuronCinfo = Neuron::initCinfo();
////////////////////////////////////////////////////////////////////////
Neuron::Neuron()
- :
- RM_( 1.0 ),
- RA_( 1.0 ),
- CM_( 0.01 ),
- Em_( -0.065 ),
- theta_( 0.0 ),
- phi_( 0.0 ),
- maxP_( 0.0 ),
- maxG_( 0.0 ),
- maxL_( 0.0 ),
- sourceFile_( "" ),
- compartmentLengthInLambdas_( 0.2 ),
- spineEntry_( this )
-{;}
+ :
+ RM_( 1.0 ),
+ RA_( 1.0 ),
+ CM_( 0.01 ),
+ Em_( -0.065 ),
+ theta_( 0.0 ),
+ phi_( 0.0 ),
+ maxP_( 0.0 ),
+ maxG_( 0.0 ),
+ maxL_( 0.0 ),
+ sourceFile_( "" ),
+ compartmentLengthInLambdas_( 0.2 ),
+ spineEntry_( this )
+{
+ ;
+}
// When copying Neuron, we next have to rerun buildSegmentTree() and
// setSpineAndPsdMesh
@@ -633,7 +635,7 @@ static void doClassSpecificMessaging( Shell* shell, Id obj, ObjId compt )
{
// cout << "Added Ca Msg for " << obj.path() << ", name = " << obj.element()->getName() << endl;
ObjId mid = shell->doAddMsg(
- "single", obj, "IkOut", elist[0], "current" );
+ "single", obj, "IkOut", elist[0], "current" );
assert( !mid.bad());
}
}
@@ -988,122 +990,133 @@ vector< ObjId > Neuron::getExprElist( const Eref& e, string line ) const
*/
vector< double > Neuron::getExprVal( const Eref& e, string line ) const
{
- Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
- vector< ObjId > elist;
- vector< double > val;
- unsigned long pos = line.find_first_of( " \t" );
- string path = line.substr( 0, pos );
- string expr = line.substr( pos );
- ObjId oldCwe = shell->getCwe();
- shell->setCwe( e.objId() );
- wildcardFind( path, elist );
- shell->setCwe( oldCwe );
- if ( elist.size() == 0 )
- return val;
- evalExprForElist( elist, expr, val );
- return val;
+ Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
+ vector< ObjId > elist;
+ vector< double > val;
+ unsigned long pos = line.find_first_of( " \t" );
+ string path = line.substr( 0, pos );
+ string expr = line.substr( pos );
+ ObjId oldCwe = shell->getCwe();
+ shell->setCwe( e.objId() );
+ wildcardFind( path, elist );
+ shell->setCwe( oldCwe );
+ if ( elist.size() == 0 )
+ return val;
+ evalExprForElist( elist, expr, val );
+ return val;
}
vector< ObjId > Neuron::getSpinesFromExpression(
- const Eref& e, string line ) const
-{
- unsigned long pos = line.find_first_of( " \t" );
- string path = line.substr( 0, pos );
- string expr = line.substr( pos );
-
- // Look for all compartments that fit the expression.
- vector< ObjId > temp = getExprElist( e, "# " + expr );
- // indexed by segIndex, includes all compts in all spines.
- /*
- vector< vector< Id > > allSpinesPerCompt( segId_.size() );
- for ( unsigned int i = 0; i < spines_.size(); ++i ) {
- assert( allSpinesPerCompt.size() > spineParentSegIndex_[i] );
- vector< Id >& s = allSpinesPerCompt[ spineParentSegIndex_[i] ];
- s.insert( s.end(), spines_[i].begin(), spines_[i].end() );
- }
- */
- vector< ObjId >ret;
- if ( allSpinesPerCompt_.size() == 0 )
- return ret;
- for ( vector< ObjId >::iterator
- i = temp.begin(); i != temp.end(); ++i ) {
- map< Id, unsigned int >::const_iterator si =
- segIndex_.find( i->id );
- assert( si != segIndex_.end() );
- assert( si->second < segId_.size() );
- if ( allSpinesPerCompt_.size() > si->second ) {
- const vector< Id >& s = allSpinesPerCompt_[ si->second ];
- for ( vector< Id >::const_iterator j = s.begin(); j != s.end(); ++j ){
- if ( matchBeforeBrace( *j, path ) )
- ret.push_back( *j );
- }
- }
- }
- return ret;
+ const Eref& e, string line ) const
+{
+ unsigned long pos = line.find_first_of( " \t" );
+ string path = line.substr( 0, pos );
+ string expr = line.substr( pos );
+
+ // Look for all compartments that fit the expression.
+ vector< ObjId > temp = getExprElist( e, "# " + expr );
+ // indexed by segIndex, includes all compts in all spines.
+ /*
+ vector< vector< Id > > allSpinesPerCompt( segId_.size() );
+ for ( unsigned int i = 0; i < spines_.size(); ++i ) {
+ assert( allSpinesPerCompt.size() > spineParentSegIndex_[i] );
+ vector< Id >& s = allSpinesPerCompt[ spineParentSegIndex_[i] ];
+ s.insert( s.end(), spines_[i].begin(), spines_[i].end() );
+ }
+ */
+ vector< ObjId >ret;
+ if ( allSpinesPerCompt_.size() == 0 )
+ return ret;
+ for ( vector< ObjId >::iterator
+ i = temp.begin(); i != temp.end(); ++i )
+ {
+ map< Id, unsigned int >::const_iterator si =
+ segIndex_.find( i->id );
+ assert( si != segIndex_.end() );
+ assert( si->second < segId_.size() );
+ if ( allSpinesPerCompt_.size() > si->second )
+ {
+ const vector< Id >& s = allSpinesPerCompt_[ si->second ];
+ for ( vector< Id >::const_iterator j = s.begin(); j != s.end(); ++j )
+ {
+ if ( matchBeforeBrace( *j, path ) )
+ ret.push_back( *j );
+ }
+ }
+ }
+ return ret;
}
vector< ObjId > Neuron::getSpinesOnCompartment(
- const Eref& e, ObjId compt ) const
-{
- vector< ObjId > ret;
- map< Id, unsigned int >::const_iterator pos =
- segIndex_.find( compt.id );
- if ( pos != segIndex_.end() ) {
- assert( pos->second < allSpinesPerCompt_.size() );
- const vector< Id >& spines = allSpinesPerCompt_[pos->second];
- for ( unsigned int i = 0; i < spines.size(); ++i )
- ret.push_back( spines[i] );
- }
- return ret;
+ const Eref& e, ObjId compt ) const
+{
+ vector< ObjId > ret;
+ map< Id, unsigned int >::const_iterator pos =
+ segIndex_.find( compt.id );
+ if ( pos != segIndex_.end() )
+ {
+ assert( pos->second < allSpinesPerCompt_.size() );
+ const vector< Id >& spines = allSpinesPerCompt_[pos->second];
+ for ( unsigned int i = 0; i < spines.size(); ++i )
+ ret.push_back( spines[i] );
+ }
+ return ret;
}
ObjId Neuron::getParentCompartmentOfSpine(
- const Eref& e, ObjId compt ) const
+ const Eref& e, ObjId compt ) const
{
- for ( unsigned int comptIndex = 0; comptIndex < allSpinesPerCompt_.size(); ++comptIndex ) {
- const vector< Id >& v = allSpinesPerCompt_[comptIndex];
- for ( unsigned int j = 0; j < v.size(); j++ )
- if ( v[j] == compt.id )
- return segId_[ comptIndex ];
- }
- return ObjId();
+ for ( unsigned int comptIndex = 0; comptIndex < allSpinesPerCompt_.size(); ++comptIndex )
+ {
+ const vector< Id >& v = allSpinesPerCompt_[comptIndex];
+ for ( unsigned int j = 0; j < v.size(); j++ )
+ if ( v[j] == compt.id )
+ return segId_[ comptIndex ];
+ }
+ return ObjId();
}
vector< ObjId > Neuron::getSpineIdsFromCompartmentIds(
- const Eref& e, vector< ObjId > compt ) const
-{
- vector< ObjId > ret;
- map< Id, unsigned int > lookupSpine;
- Id spineBase = Id( e.id().value() + 1 );
- for ( unsigned int i = 0; i < spines_.size(); ++i ) {
- for ( vector< Id >::const_iterator j = spines_[i].begin(); j != spines_[i].end(); ++j ) {
- lookupSpine[ *j ] = i;
- }
- }
- // cout << "################## " << lookupSpine.size() << endl;
- for ( map< Id, unsigned int >::const_iterator k = lookupSpine.begin(); k != lookupSpine.end(); ++k ) {
- // cout << "spine[" << k->second << "] has " << k->first.element()->getName() << endl;
- // cout << "spine[" << k->second << "] has " << k->first << endl;
+ const Eref& e, vector< ObjId > compt ) const
+{
+ vector< ObjId > ret;
+ map< Id, unsigned int > lookupSpine;
+ Id spineBase = Id( e.id().value() + 1 );
+ for ( unsigned int i = 0; i < spines_.size(); ++i )
+ {
+ for ( vector< Id >::const_iterator j = spines_[i].begin(); j != spines_[i].end(); ++j )
+ {
+ lookupSpine[ *j ] = i;
+ }
+ }
+ // cout << "################## " << lookupSpine.size() << endl;
+ for ( map< Id, unsigned int >::const_iterator k = lookupSpine.begin(); k != lookupSpine.end(); ++k )
+ {
+ // cout << "spine[" << k->second << "] has " << k->first.element()->getName() << endl;
+ // cout << "spine[" << k->second << "] has " << k->first << endl;
- }
- for ( vector< ObjId >::const_iterator j = compt.begin(); j != compt.end(); ++j )
- {
- // cout << "compt: " << *j << " " << j->element()->getName() << endl;
- map< Id, unsigned int >::const_iterator k = lookupSpine.find( j->id );
- if ( k != lookupSpine.end() ) {
- ret.push_back( ObjId( spineBase, e.dataIndex(), k->second ) );
- // cout << "spine[" << k->second << "] has " << j->element()->getName() << endl;
- } else {
- ret.push_back( ObjId() );
- }
- }
- return ret;
+ }
+ for ( vector< ObjId >::const_iterator j = compt.begin(); j != compt.end(); ++j )
+ {
+ // cout << "compt: " << *j << " " << j->element()->getName() << endl;
+ map< Id, unsigned int >::const_iterator k = lookupSpine.find( j->id );
+ if ( k != lookupSpine.end() )
+ {
+ ret.push_back( ObjId( spineBase, e.dataIndex(), k->second ) );
+ // cout << "spine[" << k->second << "] has " << j->element()->getName() << endl;
+ }
+ else
+ {
+ ret.push_back( ObjId() );
+ }
+ }
+ return ret;
}
void Neuron::buildElist( const Eref& e,
- const vector< string >& line,
- vector< ObjId >& elist,
- vector< double >& val )
+ const vector< string >& line,
+ vector< ObjId >& elist,
+ vector< double >& val )
{
Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
const string& path = line[1];
@@ -1111,7 +1124,7 @@ void Neuron::buildElist( const Eref& e,
ObjId oldCwe = shell->getCwe();
shell->setCwe( e.objId() );
wildcardFind( path, elist );
- sort( elist.begin(), elist.end() );
+ sort( elist.begin(), elist.end() );
shell->setCwe( oldCwe );
evalExprForElist( elist, expr, val );
}
@@ -1286,7 +1299,7 @@ static void fillSegments( vector< SwcSegment >& segs,
comptType = 3; // generic dendrite
}
}
- // cout << "Seg[" << i << "].xy = " << int(x*1e6) << " " << int(y*1e6) << endl;
+ // cout << "Seg[" << i << "].xy = " << int(x*1e6) << " " << int(y*1e6) << endl;
segs.push_back(
SwcSegment( i, comptType, x, y, z, dia/2.0, paIndex ) );
@@ -1350,7 +1363,7 @@ void Neuron::buildSegmentTree( const Eref& e )
{
vector< Id > kids;
Neutral::children( e, kids );
- sort( kids.begin(), kids.end() );
+ sort( kids.begin(), kids.end() );
soma_ = fillSegIndex( kids, segIndex_ );
if ( kids.size() == 0 || soma_ == Id() )
@@ -1769,26 +1782,30 @@ string findArg( const vector<string>& line, const string& field )
/// Add entries into the pos vector for a given compartment i.
static void addPos( unsigned int segIndex, unsigned int eIndex,
- double spacing, double minSpacing,
- double dendLength,
- vector< unsigned int >& seglistIndex,
- vector< unsigned int >& elistIndex,
- vector< double >& pos )
-{
- if ( minSpacing < spacing * 0.1 && minSpacing < 1e-7 )
- minSpacing = spacing * 0.1;
- if ( minSpacing > spacing * 0.5 )
- minSpacing = spacing * 0.5;
- unsigned int n = 1 + dendLength / minSpacing;
- double dx = dendLength / n;
- for( unsigned int i = 0; i < n; ++i ) {
- if ( moose::mtrand() < dx / spacing ) {
- seglistIndex.push_back( segIndex );
- elistIndex.push_back( eIndex );
- pos.push_back( i * dx + dx*0.5 );
- }
- }
+ double spacing, double minSpacing,
+ double dendLength,
+ vector< unsigned int >& seglistIndex,
+ vector< unsigned int >& elistIndex,
+ vector< double >& pos )
+{
+ if ( minSpacing < spacing * 0.1 && minSpacing < 1e-7 )
+ minSpacing = spacing * 0.1;
+ if ( minSpacing > spacing * 0.5 )
+ minSpacing = spacing * 0.5;
+ unsigned int n = 1 + dendLength / minSpacing;
+ double dx = dendLength / n;
+ for( unsigned int i = 0; i < n; ++i )
+ {
+ // Use global RNG.
+ if ( moose::mtrand() < dx / spacing )
+ {
+ seglistIndex.push_back( segIndex );
+ elistIndex.push_back( eIndex );
+ pos.push_back( i * dx + dx*0.5 );
+ }
+ }
}
+
/*
* This version tries to put in Pos using simple increments from the
* start of each compt. Multiple issues including inability to put
@@ -1822,169 +1839,187 @@ static void addPos( unsigned int segIndex, unsigned int eIndex,
*/
void Neuron::makeSpacingDistrib( const vector< ObjId >& elist,
- const vector< double >& val,
- vector< unsigned int >& seglistIndex,
- vector< unsigned int >& elistIndex,
- vector< double >& pos,
- const vector< string >& line ) const
-{
- string distribExpr = findArg( line, "spacingDistrib" );
- pos.resize( 0 );
- elistIndex.resize( 0 );
-
- try {
- nuParser parser( distribExpr );
-
- for ( unsigned int i = 0; i < elist.size(); ++i ) {
- unsigned int j = i * nuParser::numVal;
- if ( val[ j + nuParser::EXPR ] > 0 ) {
- double spacing = val[ j + nuParser::EXPR ];
- double spacingDistrib = parser.eval( val.begin() + j );
- if ( spacingDistrib > spacing || spacingDistrib < 0 ) {
- cout << "Warning: Neuron::makeSpacingDistrib: " <<
- "0 < " << spacingDistrib << " < " << spacing <<
- " fails on " << elist[i].path() << ". Using 0.\n";
- spacingDistrib = 0.0;
- }
- map< Id, unsigned int>::const_iterator
- lookupDend = segIndex_.find( elist[i] );
- if ( lookupDend != segIndex_.end() ) {
- double dendLength = segs_[lookupDend->second].length();
- addPos( lookupDend->second, i,
- spacing, spacingDistrib, dendLength,
- seglistIndex, elistIndex, pos );
- }
- }
- }
- }
- catch ( mu::Parser::exception_type& err )
- {
- cout << err.GetMsg() << endl;
- }
+ const vector< double >& val,
+ vector< unsigned int >& seglistIndex,
+ vector< unsigned int >& elistIndex,
+ vector< double >& pos,
+ const vector< string >& line ) const
+{
+ string distribExpr = findArg( line, "spacingDistrib" );
+ pos.resize( 0 );
+ elistIndex.resize( 0 );
+
+ try
+ {
+ nuParser parser( distribExpr );
+
+ for ( unsigned int i = 0; i < elist.size(); ++i )
+ {
+ unsigned int j = i * nuParser::numVal;
+ if ( val[ j + nuParser::EXPR ] > 0 )
+ {
+ double spacing = val[ j + nuParser::EXPR ];
+ double spacingDistrib = parser.eval( val.begin() + j );
+ if ( spacingDistrib > spacing || spacingDistrib < 0 )
+ {
+ cout << "Warning: Neuron::makeSpacingDistrib: " <<
+ "0 < " << spacingDistrib << " < " << spacing <<
+ " fails on " << elist[i].path() << ". Using 0.\n";
+ spacingDistrib = 0.0;
+ }
+ map< Id, unsigned int>::const_iterator
+ lookupDend = segIndex_.find( elist[i] );
+ if ( lookupDend != segIndex_.end() )
+ {
+ double dendLength = segs_[lookupDend->second].length();
+ addPos( lookupDend->second, i,
+ spacing, spacingDistrib, dendLength,
+ seglistIndex, elistIndex, pos );
+ }
+ }
+ }
+ }
+ catch ( mu::Parser::exception_type& err )
+ {
+ cout << err.GetMsg() << endl;
+ }
}
static void makeAngleDistrib ( const vector< ObjId >& elist,
- const vector< double >& val,
- vector< unsigned int >& elistIndex,
- vector< double >& theta,
- const vector< string >& line )
-{
- string angleExpr = findArg( line, "angle" );
- string angleDistribExpr = findArg( line, "angleDistrib" );
- // I won't bother with rotation and rotation distrb for now.
- // Easy to add, but on reflection they don't make sense.
- theta.clear();
- theta.resize( elistIndex.size(), 0.0 );
-
- try {
- nuParser angleParser( angleExpr );
- nuParser distribParser( angleDistribExpr );
- unsigned int lastIndex = ~0U;
- double angle = 0;
- double angleDistrib = 0;
- for ( unsigned int k = 0; k < elistIndex.size(); ++k ) {
- unsigned int i = elistIndex[k];
- if ( i != lastIndex ) {
- lastIndex = i;
- unsigned int j = i * nuParser::numVal;
- angle = angleParser.eval( val.begin() + j );
- angleDistrib = distribParser.eval( val.begin() + j);
- }
- if ( angleDistrib > 0 )
- theta[k] = angle + ( moose::mtrand() - 0.5 ) * angleDistrib;
- else
- theta[k] = angle;
- }
- }
- catch ( mu::Parser::exception_type& err )
- {
- cout << err.GetMsg() << endl;
- }
+ const vector< double >& val,
+ vector< unsigned int >& elistIndex,
+ vector< double >& theta,
+ const vector< string >& line )
+{
+ string angleExpr = findArg( line, "angle" );
+ string angleDistribExpr = findArg( line, "angleDistrib" );
+ // I won't bother with rotation and rotation distrb for now.
+ // Easy to add, but on reflection they don't make sense.
+ theta.clear();
+ theta.resize( elistIndex.size(), 0.0 );
+
+ try
+ {
+ nuParser angleParser( angleExpr );
+ nuParser distribParser( angleDistribExpr );
+ unsigned int lastIndex = ~0U;
+ double angle = 0;
+ double angleDistrib = 0;
+ for ( unsigned int k = 0; k < elistIndex.size(); ++k )
+ {
+ unsigned int i = elistIndex[k];
+ if ( i != lastIndex )
+ {
+ lastIndex = i;
+ unsigned int j = i * nuParser::numVal;
+ angle = angleParser.eval( val.begin() + j );
+ angleDistrib = distribParser.eval( val.begin() + j);
+ }
+
+ // Use global RNG.
+ if ( angleDistrib > 0 )
+ theta[k] = angle + ( moose::mtrand() - 0.5 ) * angleDistrib;
+ else
+ theta[k] = angle;
+ }
+ }
+ catch ( mu::Parser::exception_type& err )
+ {
+ cout << err.GetMsg() << endl;
+ }
}
static void makeSizeDistrib ( const vector< ObjId >& elist,
- const vector< double >& val,
- vector< unsigned int >& elistIndex,
- vector< double >& size,
- const vector< string >& line )
-{
- string sizeExpr = findArg( line, "size" );
- string sizeDistribExpr = findArg( line, "sizeDistrib" );
- size.clear();
- size.resize( elistIndex.size(), 0.0 );
-
- try {
- nuParser sizeParser( sizeExpr );
- nuParser distribParser( sizeDistribExpr );
- unsigned int lastIndex = ~0U;
- double sz = 1.0;
- double sizeDistrib = 0;
- for ( unsigned int k = 0; k < elistIndex.size(); ++k ) {
- unsigned int i = elistIndex[k];
- if ( i != lastIndex ) {
- lastIndex = i;
- unsigned int j = i * nuParser::numVal;
- sz = sizeParser.eval( val.begin() + j );
- sizeDistrib = distribParser.eval( val.begin() + j);
- }
- if ( sizeDistrib > 0 )
- size[k] = sz + ( moose::mtrand() - 0.5 ) * sizeDistrib;
- else
- size[k] = sz;
- }
- }
- catch ( mu::Parser::exception_type& err )
- {
- cout << err.GetMsg() << endl;
- }
+ const vector< double >& val,
+ vector< unsigned int >& elistIndex,
+ vector< double >& size,
+ const vector< string >& line )
+{
+ string sizeExpr = findArg( line, "size" );
+ string sizeDistribExpr = findArg( line, "sizeDistrib" );
+ size.clear();
+ size.resize( elistIndex.size(), 0.0 );
+
+ try
+ {
+ nuParser sizeParser( sizeExpr );
+ nuParser distribParser( sizeDistribExpr );
+ unsigned int lastIndex = ~0U;
+ double sz = 1.0;
+ double sizeDistrib = 0;
+ for ( unsigned int k = 0; k < elistIndex.size(); ++k )
+ {
+ unsigned int i = elistIndex[k];
+ if ( i != lastIndex )
+ {
+ lastIndex = i;
+ unsigned int j = i * nuParser::numVal;
+ sz = sizeParser.eval( val.begin() + j );
+ sizeDistrib = distribParser.eval( val.begin() + j);
+ }
+
+ // Use global RNG.
+ if ( sizeDistrib > 0 )
+ size[k] = sz + ( moose::mtrand() - 0.5 ) * sizeDistrib;
+ else
+ size[k] = sz;
+ }
+ }
+ catch ( mu::Parser::exception_type& err )
+ {
+ cout << err.GetMsg() << endl;
+ }
}
void Neuron::installSpines( const vector< ObjId >& elist,
- const vector< double >& val, const vector< string >& line )
+ const vector< double >& val, const vector< string >& line )
{
- Id spineProto( "/library/spine" );
+ Id spineProto( "/library/spine" );
- if ( spineProto == Id() ) {
- cout << "Warning: Neuron::installSpines: Unable to find prototype spine: /library/spine\n";
- return;
- }
- // Look up elist index from pos index, since there may be many
- // spines on each segment.
- vector< unsigned int > elistIndex;
- vector< double > pos; // spacing of the new spines along compt.
- vector< double > theta; // Angle of spines
- vector< double > size; // Size scaling of spines
- pos.reserve( elist.size() );
- elistIndex.reserve( elist.size() );
-
- makeSpacingDistrib( elist, val,
- spineParentSegIndex_, elistIndex, pos, line);
- makeAngleDistrib( elist, val, elistIndex, theta, line );
- makeSizeDistrib( elist, val, elistIndex, size, line );
- for ( unsigned int k = 0; k < spineParentSegIndex_.size(); ++k ) {
- unsigned int i = spineParentSegIndex_[k];
- Vec x, y, z;
- coordSystem( soma_, segId_[i], x, y, z );
- spines_.push_back(
- addSpine( segId_[i], spineProto, pos[k], theta[k],
- x, y, z, size[k], k )
- );
- }
- spineToMeshOrdering_.clear();
- spineToMeshOrdering_.resize( spines_.size(), 0 );
- spineStoich_.clear();
- spineStoich_.resize( spines_.size() );
- psdStoich_.clear();
- psdStoich_.resize( spines_.size() );
-
- /// Now fill in allSpinesPerCompt_ vector. First clear it out.
- allSpinesPerCompt_.clear();
- allSpinesPerCompt_.resize(segId_.size() );
- for ( unsigned int i = 0; i < spines_.size(); ++i ) {
- assert( allSpinesPerCompt_.size() > spineParentSegIndex_[i] );
- vector< Id >& s = allSpinesPerCompt_[ spineParentSegIndex_[i] ];
- s.insert( s.end(), spines_[i].begin(), spines_[i].end() );
- }
+ if ( spineProto == Id() )
+ {
+ cout << "Warning: Neuron::installSpines: Unable to find prototype spine: /library/spine\n";
+ return;
+ }
+ // Look up elist index from pos index, since there may be many
+ // spines on each segment.
+ vector< unsigned int > elistIndex;
+ vector< double > pos; // spacing of the new spines along compt.
+ vector< double > theta; // Angle of spines
+ vector< double > size; // Size scaling of spines
+ pos.reserve( elist.size() );
+ elistIndex.reserve( elist.size() );
+
+ makeSpacingDistrib( elist, val,
+ spineParentSegIndex_, elistIndex, pos, line);
+ makeAngleDistrib( elist, val, elistIndex, theta, line );
+ makeSizeDistrib( elist, val, elistIndex, size, line );
+ for ( unsigned int k = 0; k < spineParentSegIndex_.size(); ++k )
+ {
+ unsigned int i = spineParentSegIndex_[k];
+ Vec x, y, z;
+ coordSystem( soma_, segId_[i], x, y, z );
+ spines_.push_back(
+ addSpine( segId_[i], spineProto, pos[k], theta[k],
+ x, y, z, size[k], k )
+ );
+ }
+ spineToMeshOrdering_.clear();
+ spineToMeshOrdering_.resize( spines_.size(), 0 );
+ spineStoich_.clear();
+ spineStoich_.resize( spines_.size() );
+ psdStoich_.clear();
+ psdStoich_.resize( spines_.size() );
+
+ /// Now fill in allSpinesPerCompt_ vector. First clear it out.
+ allSpinesPerCompt_.clear();
+ allSpinesPerCompt_.resize(segId_.size() );
+ for ( unsigned int i = 0; i < spines_.size(); ++i )
+ {
+ assert( allSpinesPerCompt_.size() > spineParentSegIndex_[i] );
+ vector< Id >& s = allSpinesPerCompt_[ spineParentSegIndex_[i] ];
+ s.insert( s.end(), spines_[i].begin(), spines_[i].end() );
+ }
}
////////////////////////////////////////////////////////////////////////
// Interface funcs for spines
@@ -2021,8 +2056,8 @@ void Neuron::scaleBufAndRates( unsigned int spineNum,
double lenScale, double diaScale ) const
{
double volScale = lenScale * diaScale * diaScale;
- if ( doubleEq( volScale, 1.0 ) )
- return;
+ if ( doubleEq( volScale, 1.0 ) )
+ return;
if ( spineStoich_.size() == 0 )
// Perhaps no chem stuff in model, but user could have forgotten
// to assign psd and spine meshes.
@@ -2072,8 +2107,8 @@ void Neuron::scaleHeadDiffusion( unsigned int spineNum,
double len, double dia) const
{
double vol = len * dia * dia * PI * 0.25;
- // Note that the diffusion scale for the PSD uses half the length
- // of the head compartment. I'm explicitly putting this in below.
+ // Note that the diffusion scale for the PSD uses half the length
+ // of the head compartment. I'm explicitly putting this in below.
double diffScale = dia * dia * 0.25 * PI / (len/2.0);
unsigned int meshIndex = spineToMeshOrdering_[ spineNum ];
Id headCompt = Field< Id >::get( headDsolve_, "compartment" );
diff --git a/biophysics/Neuron.h b/biophysics/Neuron.h
index 777c5448..81b72658 100644
--- a/biophysics/Neuron.h
+++ b/biophysics/Neuron.h
@@ -17,141 +17,141 @@
class Neuron
{
- public:
- Neuron();
- Neuron( const Neuron& other );
- void setRM( double v );
- double getRM() const;
- void setRA( double v );
- double getRA() const;
- void setCM( double v );
- double getCM() const;
- void setEm( double v );
- double getEm() const;
- void setTheta( double v );
- double getTheta() const;
- void setPhi( double v );
- double getPhi() const;
- void setSourceFile( string v );
- string getSourceFile() const;
- void setCompartmentLengthInLambdas( double v );
- double getCompartmentLengthInLambdas() const;
- unsigned int getNumCompartments() const;
- unsigned int getNumBranches() const;
- vector< double> getPathDistFromSoma() const;
- vector< double> getGeomDistFromSoma() const;
- vector< double> getElecDistFromSoma() const;
- vector< ObjId > getCompartments() const;
- vector< ObjId > getExprElist( const Eref& e, string line ) const;
- vector< double > getExprVal( const Eref& e, string line ) const;
- vector< ObjId > getSpinesFromExpression(
- const Eref& e, string line ) const;
- vector< ObjId > getSpinesOnCompartment(
- const Eref& e, ObjId compt ) const;
- ObjId getParentCompartmentOfSpine( const Eref& e, ObjId compt )
- const;
- vector< ObjId > getSpineIdsFromCompartmentIds(
- const Eref& e, vector< ObjId > compt ) const;
- void setChannelDistribution( const Eref& e, vector< string > v );
- vector< string > getChannelDistribution( const Eref& e ) const;
- void setPassiveDistribution( const Eref& e, vector< string > v );
- vector< string > getPassiveDistribution( const Eref& e ) const;
- void setSpineDistribution( const Eref& e, vector< string > v );
- vector< string > getSpineDistribution( const Eref& e ) const;
-
- void buildSegmentTree( const Eref& e );
- void setSpineAndPsdMesh( Id spineMesh, Id psdMesh );
- void setSpineAndPsdDsolve( Id spineDsolve, Id psdDsolve );
-
- ///////////////////////////////////////////////////////////////////
- // MechSpec set
- ///////////////////////////////////////////////////////////////////
- void updateSegmentLengths();
- void installSpines( const vector< ObjId >& elist,
- const vector< double >& val, const vector< string >& line );
- void makeSpacingDistrib(
- const vector< ObjId >& elist, const vector< double >& val,
- vector< unsigned int >& seglistIndex,
- vector< unsigned int >& elistIndex,
- vector< double >& pos,
- const vector< string >& line ) const;
- void parseMechSpec( const Eref& e );
- void installMechanism( const string& name,
- const vector< ObjId >& elist, const vector< double >& val,
- const vector< string >& line );
- void buildElist(
- const Eref& e,
- const vector< string >& line, vector< ObjId >& elist,
- vector< double >& val );
-
- void evalExprForElist( const vector< ObjId >& elist,
- const string& expn, vector< double >& val ) const;
-
- ///////////////////////////////////////////////////////////////////
- // Interface for Spine class, used mostly in resizing spines.
- ///////////////////////////////////////////////////////////////////
- Spine* lookupSpine( unsigned int index );
- void setNumSpines( unsigned int num );
- unsigned int getNumSpines() const;
-
- const vector< Id >& spineIds( unsigned int index ) const;
- void scaleBufAndRates( unsigned int spineNum,
- double lenScale, double diaScale ) const;
- void scaleShaftDiffusion( unsigned int spineNum,
- double len, double dia) const;
- void scaleHeadDiffusion( unsigned int spineNum,
- double len, double dia) const;
-
- /**
- * Initializes the class info.
- */
- static const Cinfo* initCinfo();
- private:
- double RM_;
- double RA_;
- double CM_;
- double Em_;
- double theta_;
- double phi_;
- double maxP_; // Maximum value of path dist from soma for this cell
- double maxG_; // Maximum value of geom dist from soma for this cell
- double maxL_; // Maximum value of elec dist from soma for this cell
- Id soma_;
- string sourceFile_;
- double compartmentLengthInLambdas_;
- vector< string > channelDistribution_;
- vector< string > passiveDistribution_;
- vector< string > spineDistribution_;
-
- /// Map to look up Seg index from Id of associated compt.
- map< Id, unsigned int > segIndex_;
- /// Look up seg index of parent compartment, from index of spine.
- vector< unsigned int > spineParentSegIndex_;
- vector< vector< Id > > spines_; /// Id of each compt in each spine.
-
- /// Ids of all spines on each compt, looked up by segIndex of compt.
- vector< vector< Id > > allSpinesPerCompt_;
-
- /// Id of stoich associated with each spine. Typically all the same.
- vector< Id > spineStoich_;
- /// Id of stoich associated with each PSD. Typically all the same.
- vector< Id > psdStoich_;
- /// looks up spine/psd mesh index from FieldIndex of selected spine.
- vector< unsigned int > spineToMeshOrdering_;
-
- Id headDsolve_; /// Id of the Dsolve for the head compt.
- Id psdDsolve_; /// Id of the Dsolve for the PSD compt.
- // looks up spine/psd Dsolve::DiffJunction::VoxelJunction index
- //from FieldIndex of selected spine.
- // Turns out this is the same as spineToMeshOrdering.
- //vector< unsigned int > spineToVoxelJunctionOrdering_;
-
- /// Holder for spine operations. Contains pointer to current Neuron.
- Spine spineEntry_;
-
- vector< Id > segId_; /// Id of compartment in each Seg entry, below.
- vector< SwcSegment > segs_;
- vector< SwcBranch > branches_;
+public:
+ Neuron();
+ Neuron( const Neuron& other );
+ void setRM( double v );
+ double getRM() const;
+ void setRA( double v );
+ double getRA() const;
+ void setCM( double v );
+ double getCM() const;
+ void setEm( double v );
+ double getEm() const;
+ void setTheta( double v );
+ double getTheta() const;
+ void setPhi( double v );
+ double getPhi() const;
+ void setSourceFile( string v );
+ string getSourceFile() const;
+ void setCompartmentLengthInLambdas( double v );
+ double getCompartmentLengthInLambdas() const;
+ unsigned int getNumCompartments() const;
+ unsigned int getNumBranches() const;
+ vector< double> getPathDistFromSoma() const;
+ vector< double> getGeomDistFromSoma() const;
+ vector< double> getElecDistFromSoma() const;
+ vector< ObjId > getCompartments() const;
+ vector< ObjId > getExprElist( const Eref& e, string line ) const;
+ vector< double > getExprVal( const Eref& e, string line ) const;
+ vector< ObjId > getSpinesFromExpression(
+ const Eref& e, string line ) const;
+ vector< ObjId > getSpinesOnCompartment(
+ const Eref& e, ObjId compt ) const;
+ ObjId getParentCompartmentOfSpine( const Eref& e, ObjId compt )
+ const;
+ vector< ObjId > getSpineIdsFromCompartmentIds(
+ const Eref& e, vector< ObjId > compt ) const;
+ void setChannelDistribution( const Eref& e, vector< string > v );
+ vector< string > getChannelDistribution( const Eref& e ) const;
+ void setPassiveDistribution( const Eref& e, vector< string > v );
+ vector< string > getPassiveDistribution( const Eref& e ) const;
+ void setSpineDistribution( const Eref& e, vector< string > v );
+ vector< string > getSpineDistribution( const Eref& e ) const;
+
+ void buildSegmentTree( const Eref& e );
+ void setSpineAndPsdMesh( Id spineMesh, Id psdMesh );
+ void setSpineAndPsdDsolve( Id spineDsolve, Id psdDsolve );
+
+ ///////////////////////////////////////////////////////////////////
+ // MechSpec set
+ ///////////////////////////////////////////////////////////////////
+ void updateSegmentLengths();
+ void installSpines( const vector< ObjId >& elist,
+ const vector< double >& val, const vector< string >& line );
+ void makeSpacingDistrib(
+ const vector< ObjId >& elist, const vector< double >& val,
+ vector< unsigned int >& seglistIndex,
+ vector< unsigned int >& elistIndex,
+ vector< double >& pos,
+ const vector< string >& line ) const;
+ void parseMechSpec( const Eref& e );
+ void installMechanism( const string& name,
+ const vector< ObjId >& elist, const vector< double >& val,
+ const vector< string >& line );
+ void buildElist(
+ const Eref& e,
+ const vector< string >& line, vector< ObjId >& elist,
+ vector< double >& val );
+
+ void evalExprForElist( const vector< ObjId >& elist,
+ const string& expn, vector< double >& val ) const;
+
+ ///////////////////////////////////////////////////////////////////
+ // Interface for Spine class, used mostly in resizing spines.
+ ///////////////////////////////////////////////////////////////////
+ Spine* lookupSpine( unsigned int index );
+ void setNumSpines( unsigned int num );
+ unsigned int getNumSpines() const;
+
+ const vector< Id >& spineIds( unsigned int index ) const;
+ void scaleBufAndRates( unsigned int spineNum,
+ double lenScale, double diaScale ) const;
+ void scaleShaftDiffusion( unsigned int spineNum,
+ double len, double dia) const;
+ void scaleHeadDiffusion( unsigned int spineNum,
+ double len, double dia) const;
+
+ /**
+ * Initializes the class info.
+ */
+ static const Cinfo* initCinfo();
+private:
+ double RM_;
+ double RA_;
+ double CM_;
+ double Em_;
+ double theta_;
+ double phi_;
+ double maxP_; // Maximum value of path dist from soma for this cell
+ double maxG_; // Maximum value of geom dist from soma for this cell
+ double maxL_; // Maximum value of elec dist from soma for this cell
+ Id soma_;
+ string sourceFile_;
+ double compartmentLengthInLambdas_;
+ vector< string > channelDistribution_;
+ vector< string > passiveDistribution_;
+ vector< string > spineDistribution_;
+
+ /// Map to look up Seg index from Id of associated compt.
+ map< Id, unsigned int > segIndex_;
+ /// Look up seg index of parent compartment, from index of spine.
+ vector< unsigned int > spineParentSegIndex_;
+ vector< vector< Id > > spines_; /// Id of each compt in each spine.
+
+ /// Ids of all spines on each compt, looked up by segIndex of compt.
+ vector< vector< Id > > allSpinesPerCompt_;
+
+ /// Id of stoich associated with each spine. Typically all the same.
+ vector< Id > spineStoich_;
+ /// Id of stoich associated with each PSD. Typically all the same.
+ vector< Id > psdStoich_;
+ /// looks up spine/psd mesh index from FieldIndex of selected spine.
+ vector< unsigned int > spineToMeshOrdering_;
+
+ Id headDsolve_; /// Id of the Dsolve for the head compt.
+ Id psdDsolve_; /// Id of the Dsolve for the PSD compt.
+ // looks up spine/psd Dsolve::DiffJunction::VoxelJunction index
+ //from FieldIndex of selected spine.
+ // Turns out this is the same as spineToMeshOrdering.
+ //vector< unsigned int > spineToVoxelJunctionOrdering_;
+
+ /// Holder for spine operations. Contains pointer to current Neuron.
+ Spine spineEntry_;
+
+ vector< Id > segId_; /// Id of compartment in each Seg entry, below.
+ vector< SwcSegment > segs_;
+ vector< SwcBranch > branches_;
};
diff --git a/biophysics/RandSpike.cpp b/biophysics/RandSpike.cpp
index 4678970f..57fdf8af 100644
--- a/biophysics/RandSpike.cpp
+++ b/biophysics/RandSpike.cpp
@@ -7,123 +7,127 @@
** See the file COPYING.LIB for the full notice.
**********************************************************************/
-#include "header.h"
-#include "../randnum/randnum.h"
+#include "../basecode/header.h"
+#include "../basecode/global.h"
+
#include "RandSpike.h"
- ///////////////////////////////////////////////////////
- // MsgSrc definitions
- ///////////////////////////////////////////////////////
-static SrcFinfo1< double > *spikeOut() {
- static SrcFinfo1< double > spikeOut( "spikeOut",
- "Sends out a trigger for an event.");
- return &spikeOut;
+///////////////////////////////////////////////////////
+// MsgSrc definitions
+///////////////////////////////////////////////////////
+static SrcFinfo1< double > *spikeOut()
+{
+ static SrcFinfo1< double > spikeOut( "spikeOut",
+ "Sends out a trigger for an event.");
+ return &spikeOut;
}
const Cinfo* RandSpike::initCinfo()
{
- ///////////////////////////////////////////////////////
- // Shared message definitions
- ///////////////////////////////////////////////////////
- static DestFinfo process( "process",
- "Handles process call",
- new ProcOpFunc< RandSpike >( &RandSpike::process ) );
- static DestFinfo reinit( "reinit",
- "Handles reinit call",
- new ProcOpFunc< RandSpike >( &RandSpike::reinit ) );
-
- static Finfo* processShared[] =
- {
- &process, &reinit
- };
-
- static SharedFinfo proc( "proc",
- "Shared message to receive Process message from scheduler",
- processShared, sizeof( processShared ) / sizeof( Finfo* ) );
-
- //////////////////////////////////////////////////////////////////
- // Dest Finfos.
- //////////////////////////////////////////////////////////////////
-
- //////////////////////////////////////////////////////////////////
- // Value Finfos.
- //////////////////////////////////////////////////////////////////
-
- static ValueFinfo< RandSpike, double > rate( "rate",
- "Specifies rate for random spike train. Note that this is"
- "probabilistic, so the instantaneous rate may differ. "
- "If the rate is assigned be message and it varies slowly then "
- "the average firing rate will approach the specified rate",
- &RandSpike::setRate,
- &RandSpike::getRate
- );
- static ValueFinfo< RandSpike, double > refractT( "refractT",
- "Refractory Time.",
- &RandSpike::setRefractT,
- &RandSpike::getRefractT
- );
- static ValueFinfo< RandSpike, double > absRefract( "abs_refract",
- "Absolute refractory time. Synonym for refractT.",
- &RandSpike::setRefractT,
- &RandSpike::getRefractT
- );
- static ValueFinfo< RandSpike, bool > doPeriodic( "doPeriodic",
- "Flag: when false, do Poisson process with specified mean rate.\n"
- "When true, fire periodically at specified rate.\n"
- "Defaults to false. Note that refractory time overrides this: "
- "Rate cannot exceed 1/refractT.",
- &RandSpike::setDoPeriodic,
- &RandSpike::getDoPeriodic
- );
- static ReadOnlyValueFinfo< RandSpike, bool > hasFired( "hasFired",
- "True if RandSpike has just fired",
- &RandSpike::getFired
- );
-
- static Finfo* spikeGenFinfos[] =
- {
- spikeOut(), // SrcFinfo
- &proc, // Shared
- &rate, // Value
- &refractT, // Value
- &absRefract, // Value
- &doPeriodic, // Value
- &hasFired, // ReadOnlyValue
- };
-
- static string doc[] =
- {
- "Name", "RandSpike",
- "Author", "Upi Bhalla",
- "Description", "RandSpike object, generates random or regular "
- "spikes at "
- "specified mean rate. Based closely on GENESIS randspike. "
- };
- static Dinfo< RandSpike > dinfo;
- static Cinfo spikeGenCinfo(
- "RandSpike",
- Neutral::initCinfo(),
- spikeGenFinfos, sizeof( spikeGenFinfos ) / sizeof( Finfo* ),
- &dinfo,
- doc,
- sizeof(doc)/sizeof(string)
- );
-
- return &spikeGenCinfo;
+ ///////////////////////////////////////////////////////
+ // Shared message definitions
+ ///////////////////////////////////////////////////////
+ static DestFinfo process( "process",
+ "Handles process call",
+ new ProcOpFunc< RandSpike >( &RandSpike::process ) );
+ static DestFinfo reinit( "reinit",
+ "Handles reinit call",
+ new ProcOpFunc< RandSpike >( &RandSpike::reinit ) );
+
+ static Finfo* processShared[] =
+ {
+ &process, &reinit
+ };
+
+ static SharedFinfo proc( "proc",
+ "Shared message to receive Process message from scheduler",
+ processShared, sizeof( processShared ) / sizeof( Finfo* ) );
+
+ //////////////////////////////////////////////////////////////////
+ // Dest Finfos.
+ //////////////////////////////////////////////////////////////////
+
+ //////////////////////////////////////////////////////////////////
+ // Value Finfos.
+ //////////////////////////////////////////////////////////////////
+
+ static ValueFinfo< RandSpike, double > rate( "rate",
+ "Specifies rate for random spike train. Note that this is"
+ "probabilistic, so the instantaneous rate may differ. "
+ "If the rate is assigned be message and it varies slowly then "
+ "the average firing rate will approach the specified rate",
+ &RandSpike::setRate,
+ &RandSpike::getRate
+ );
+ static ValueFinfo< RandSpike, double > refractT( "refractT",
+ "Refractory Time.",
+ &RandSpike::setRefractT,
+ &RandSpike::getRefractT
+ );
+ static ValueFinfo< RandSpike, double > absRefract( "abs_refract",
+ "Absolute refractory time. Synonym for refractT.",
+ &RandSpike::setRefractT,
+ &RandSpike::getRefractT
+ );
+ static ValueFinfo< RandSpike, bool > doPeriodic( "doPeriodic",
+ "Flag: when false, do Poisson process with specified mean rate.\n"
+ "When true, fire periodically at specified rate.\n"
+ "Defaults to false. Note that refractory time overrides this: "
+ "Rate cannot exceed 1/refractT.",
+ &RandSpike::setDoPeriodic,
+ &RandSpike::getDoPeriodic
+ );
+ static ReadOnlyValueFinfo< RandSpike, bool > hasFired( "hasFired",
+ "True if RandSpike has just fired",
+ &RandSpike::getFired
+ );
+
+ static Finfo* spikeGenFinfos[] =
+ {
+ spikeOut(), // SrcFinfo
+ &proc, // Shared
+ &rate, // Value
+ &refractT, // Value
+ &absRefract, // Value
+ &doPeriodic, // Value
+ &hasFired, // ReadOnlyValue
+ };
+
+ static string doc[] =
+ {
+ "Name", "RandSpike",
+ "Author", "Upi Bhalla",
+ "Description", "RandSpike object, generates random or regular "
+ "spikes at "
+ "specified mean rate. Based closely on GENESIS randspike. "
+ };
+ static Dinfo< RandSpike > dinfo;
+ static Cinfo spikeGenCinfo(
+ "RandSpike",
+ Neutral::initCinfo(),
+ spikeGenFinfos, sizeof( spikeGenFinfos ) / sizeof( Finfo* ),
+ &dinfo,
+ doc,
+ sizeof(doc)/sizeof(string)
+ );
+
+ return &spikeGenCinfo;
}
static const Cinfo* spikeGenCinfo = RandSpike::initCinfo();
RandSpike::RandSpike()
- :
- rate_( 0.0 ),
- realRate_( 0.0 ),
- refractT_(0.0),
- lastEvent_(0.0),
- threshold_(0.0),
- fired_( false ),
- doPeriodic_( false )
-{;}
+ :
+ rate_( 0.0 ),
+ realRate_( 0.0 ),
+ refractT_(0.0),
+ lastEvent_(0.0),
+ threshold_(0.0),
+ fired_( false ),
+ doPeriodic_( false )
+{
+ ;
+}
//////////////////////////////////////////////////////////////////
// Here we put the RandSpike class functions.
@@ -132,45 +136,49 @@ RandSpike::RandSpike()
// Value Field access function definitions.
void RandSpike::setRate( double rate )
{
- if ( rate < 0.0 ) {
- cout <<"Warning: RandSpike::setRate: Rate must be >= 0. Using 0.\n";
- rate = 0.0;
- }
- rate_ = rate;
- double prob = 1.0 - rate * refractT_;
- if ( prob <= 0.0 ) {
- cout << "Warning: RandSpike::setRate: Rate is too high compared to refractory time\n";
- realRate_ = rate_;
- } else {
- realRate_ = rate_ / prob;
- }
+ if ( rate < 0.0 )
+ {
+ cout <<"Warning: RandSpike::setRate: Rate must be >= 0. Using 0.\n";
+ rate = 0.0;
+ }
+ rate_ = rate;
+ double prob = 1.0 - rate * refractT_;
+ if ( prob <= 0.0 )
+ {
+ cout << "Warning: RandSpike::setRate: Rate is too high compared to refractory time\n";
+ realRate_ = rate_;
+ }
+ else
+ {
+ realRate_ = rate_ / prob;
+ }
}
double RandSpike::getRate() const
{
- return rate_;
+ return rate_;
}
void RandSpike::setRefractT( double val )
{
- refractT_ = val;
+ refractT_ = val;
}
double RandSpike::getRefractT() const
{
- return refractT_;
+ return refractT_;
}
bool RandSpike::getFired() const
{
- return fired_;
+ return fired_;
}
void RandSpike::setDoPeriodic( bool val )
{
- doPeriodic_ = val;
+ doPeriodic_ = val;
}
bool RandSpike::getDoPeriodic() const
{
- return doPeriodic_;
+ return doPeriodic_;
}
@@ -180,35 +188,43 @@ bool RandSpike::getDoPeriodic() const
void RandSpike::process( const Eref& e, ProcPtr p )
{
- if ( refractT_ > p->currTime - lastEvent_ || rate_ <= 0.0 )
- return;
- fired_ = false;
- if (doPeriodic_) {
- if ( (p->currTime - lastEvent_) > 1.0/rate_ ) {
- lastEvent_ = p->currTime;
- spikeOut()->send( e, p->currTime );
- fired_ = true;
- }
- } else {
- double prob = realRate_ * p->dt;
- if ( prob >= 1.0 || prob >= mtrand() )
- {
- lastEvent_ = p->currTime;
- spikeOut()->send( e, p->currTime );
- fired_ = true;
- }
- }
+ if ( refractT_ > p->currTime - lastEvent_ || rate_ <= 0.0 )
+ return;
+
+ fired_ = false;
+ if (doPeriodic_)
+ {
+ if ( (p->currTime - lastEvent_) > 1.0/rate_ )
+ {
+ lastEvent_ = p->currTime;
+ spikeOut()->send( e, p->currTime );
+ fired_ = true;
+ }
+ }
+ else
+ {
+ double prob = realRate_ * p->dt;
+ if ( prob >= 1.0 || prob >= moose::mtrand() )
+ {
+ lastEvent_ = p->currTime;
+ spikeOut()->send( e, p->currTime );
+ fired_ = true;
+ }
+ }
}
// Set it so that first spike is allowed.
void RandSpike::reinit( const Eref& e, ProcPtr p )
{
- if ( rate_ <= 0.0 ) {
- lastEvent_ = 0.0;
- realRate_ = 0.0;
- } else {
- double prob = mtrand();
- double m = 1.0 / rate_;
- lastEvent_ = m * log( prob );
- }
+ if ( rate_ <= 0.0 )
+ {
+ lastEvent_ = 0.0;
+ realRate_ = 0.0;
+ }
+ else
+ {
+ double prob = moose::mtrand();
+ double m = 1.0 / rate_;
+ lastEvent_ = m * log( prob );
+ }
}
diff --git a/biophysics/RandSpike.h b/biophysics/RandSpike.h
index 2a7da3de..682c1911 100644
--- a/biophysics/RandSpike.h
+++ b/biophysics/RandSpike.h
@@ -12,40 +12,41 @@
class RandSpike
{
- public:
+public:
RandSpike();
- //////////////////////////////////////////////////////////////////
- // Field functions.
- //////////////////////////////////////////////////////////////////
- void setRate( double rate );
- double getRate() const;
-
- void setRefractT( double val );
- double getRefractT() const;
-
- void setDoPeriodic( bool val );
- bool getDoPeriodic() const;
-
- bool getFired() const;
-
- //////////////////////////////////////////////////////////////////
- // Message dest functions.
- //////////////////////////////////////////////////////////////////
-
- void process( const Eref& e, ProcPtr p );
- void reinit( const Eref& e, ProcPtr p );
-
- //////////////////////////////////////////////////////////////////
- static const Cinfo* initCinfo();
- private:
- double rate_;
- double realRate_;
- double refractT_;
- double lastEvent_;
- double threshold_;
- bool fired_;
- bool doPeriodic_;
+ //////////////////////////////////////////////////////////////////
+ // Field functions.
+ //////////////////////////////////////////////////////////////////
+ void setRate( double rate );
+ double getRate() const;
+
+ void setRefractT( double val );
+ double getRefractT() const;
+
+ void setDoPeriodic( bool val );
+ bool getDoPeriodic() const;
+
+ bool getFired() const;
+
+ //////////////////////////////////////////////////////////////////
+ // Message dest functions.
+ //////////////////////////////////////////////////////////////////
+
+ void process( const Eref& e, ProcPtr p );
+ void reinit( const Eref& e, ProcPtr p );
+
+ //////////////////////////////////////////////////////////////////
+ static const Cinfo* initCinfo();
+private:
+ double rate_;
+ double realRate_;
+ double refractT_;
+ double lastEvent_;
+ double threshold_;
+ bool fired_;
+ bool doPeriodic_;
+
};
#endif // _RANDSPIKE_H
diff --git a/biophysics/testBiophysics.cpp b/biophysics/testBiophysics.cpp
index c3069e33..e46b3012 100644
--- a/biophysics/testBiophysics.cpp
+++ b/biophysics/testBiophysics.cpp
@@ -8,30 +8,19 @@
**********************************************************************/
-#include "header.h"
+#include "../basecode/header.h"
+#include "../basecode/global.h"
#include "../shell/Shell.h"
-#include "../randnum/randnum.h"
-#include "CompartmentBase.h"
#include "../utility/testing_macros.hpp"
+#include "CompartmentBase.h"
#include "Compartment.h"
-/*
-#include "HHGate.h"
-#include "ChanBase.h"
-#include "HHChannel.h"
-*/
+
extern void testCompartment(); // Defined in Compartment.cpp
extern void testCompartmentProcess(); // Defined in Compartment.cpp
extern void testMarkovRateTable(); //Defined in MarkovRateTable.cpp
extern void testVectorTable(); //Defined in VectorTable.cpp
-/*
-extern void testSpikeGen(); // Defined in SpikeGen.cpp
-extern void testCaConc(); // Defined in CaConc.cpp
-extern void testNernst(); // Defined in Nernst.cpp
-extern void testMarkovSolverBase(); //Defined in MarkovSolverBase.cpp
-extern void testMarkovSolver(); //Defined in MarkovSolver.cpp
-*/
#ifdef DO_UNIT_TESTS
@@ -46,7 +35,7 @@ void testIntFireNetwork( unsigned int runsteps = 5 )
static const double delayMax = 4;
static const double delayMin = 0;
static const double connectionProbability = 0.1;
- static const unsigned int NUM_TOT_SYN = 104576;
+ static const unsigned int NUM_TOT_SYN = 104831;
unsigned int size = 1024;
string arg;
Eref sheller( Id().eref() );
@@ -77,7 +66,9 @@ void testIntFireNetwork( unsigned int runsteps = 5 )
unsigned int nd = syn->totNumLocalField();
if ( Shell::numNodes() == 1 )
- assert( nd == NUM_TOT_SYN );
+ {
+ EXPECT_EQ( nd, NUM_TOT_SYN, "" );
+ }
else if ( Shell::numNodes() == 2 )
assert( nd == 52446 );
else if ( Shell::numNodes() == 3 )
@@ -114,8 +105,11 @@ void testIntFireNetwork( unsigned int runsteps = 5 )
// by multiple threads if the above Set call is not complete.
vector< double > origVm( size, 0.0 );
+
+ // NOTE: From
+ moose::mtseed( 5489UL );
for ( unsigned int i = 0; i < size; ++i )
- origVm[i] = mtrand() * Vmax;
+ origVm[i] = moose::mtrand() * Vmax;
double origVm100 = origVm[100];
double origVm900 = origVm[900];
@@ -146,11 +140,10 @@ void testIntFireNetwork( unsigned int runsteps = 5 )
vector< double > delay( numSynVec[i], 0.0 );
for ( unsigned int j = 0; j < numSynVec[i]; ++j )
{
- weight[i][ j ] = mtrand() * weightMax;
- delay[ j ] = delayMin + mtrand() * ( delayMax - delayMin );
+ weight[i][ j ] = moose::mtrand() * weightMax;
+ delay[ j ] = delayMin + moose::mtrand() * ( delayMax - delayMin );
}
- ret = Field< double >::
- setVec( ObjId( synId, i ), "weight", weight[i] );
+ ret = Field< double >::setVec( ObjId( synId, i ), "weight", weight[i] );
assert( ret );
ret = Field< double >::setVec( ObjId( synId, i ), "delay", delay );
assert( ret );
@@ -218,13 +211,24 @@ void testIntFireNetwork( unsigned int runsteps = 5 )
ASSERT_DOUBLE_EQ("", retVm901, 0.28303358631241327 );
ASSERT_DOUBLE_EQ("", retVm902, 0.0096374021108587178 );
*/
- ASSERT_DOUBLE_EQ("", retVm100, 0.069517018453329804 );
- ASSERT_DOUBLE_EQ("", retVm101, 0.32823493598699577 );
- ASSERT_DOUBLE_EQ("", retVm102, 0.35036493874475361 );
- ASSERT_DOUBLE_EQ("", retVm99, 0.04087358817787364 );
- ASSERT_DOUBLE_EQ("", retVm900, 0.26414663635984065 );
- ASSERT_DOUBLE_EQ("", retVm901, 0.39864519810259352 );
- ASSERT_DOUBLE_EQ("", retVm902, 0.04818717439429359 );
+
+#if 0
+ cout << endl;
+ cout << std::setprecision(12) << retVm100 << endl;
+ cout << std::setprecision(12) << retVm101 << endl;
+ cout << std::setprecision(12) << retVm102 << endl;
+ cout << std::setprecision(11) << retVm99 << endl;
+ cout << std::setprecision(12) << retVm900 << endl;
+ cout << std::setprecision(12) << retVm901 << endl;
+ cout << std::setprecision(12) << retVm902 << endl;
+#endif
+ ASSERT_DOUBLE_EQ("", retVm100, 0.0752853031478);
+ ASSERT_DOUBLE_EQ("", retVm101, 0.226731547886 );
+ ASSERT_DOUBLE_EQ("", retVm102, 0.204294350789 );
+ ASSERT_DOUBLE_EQ("", retVm99, 0.2814616871 );
+ ASSERT_DOUBLE_EQ("", retVm900, 0.194820080944 );
+ ASSERT_DOUBLE_EQ("", retVm901, 0.0490452677121);
+ ASSERT_DOUBLE_EQ("", retVm902, 0.214295483534 );
}
/*
diff --git a/builtins/Table.h b/builtins/Table.h
index 9fb78c8b..34397cde 100644
--- a/builtins/Table.h
+++ b/builtins/Table.h
@@ -10,10 +10,6 @@
#ifndef _TABLE_H
#define _TABLE_H
-
-#if USE_BOOST
-#include <boost/filesystem.hpp>
-#endif /* ----- USE_BOOST ----- */
#include <fstream>
/**
diff --git a/builtins/testNSDF.cpp b/builtins/testNSDF.cpp
index b99782f1..86e1f96f 100644
--- a/builtins/testNSDF.cpp
+++ b/builtins/testNSDF.cpp
@@ -73,7 +73,7 @@ void testCreateStringDataset()
hsize_t size = STR_DSET_LEN;
herr_t status;
HDF5WriterBase writer;
- string h5Filename = std::tmpnam( NULL );
+ string h5Filename = moose::random_string( 10 );
file = H5Fcreate(h5Filename.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
dset = writer.createStringDataset(file, STR_DSET_NAME, size, size);
assert(dset >= 0);
diff --git a/diffusion/ConcChanInfo.h b/diffusion/ConcChanInfo.h
index cd16266b..caf2b6b4 100644
--- a/diffusion/ConcChanInfo.h
+++ b/diffusion/ConcChanInfo.h
@@ -17,14 +17,18 @@ class ConcChanInfo
public:
ConcChanInfo();
ConcChanInfo( unsigned int my, unsigned int other,
- unsigned int chan, double perm )
+ 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;
};
diff --git a/diffusion/DiffPoolVec.cpp b/diffusion/DiffPoolVec.cpp
index cd1da649..d8a9208d 100644
--- a/diffusion/DiffPoolVec.cpp
+++ b/diffusion/DiffPoolVec.cpp
@@ -23,135 +23,140 @@ using namespace std;
* work on in single-compartment models.
*/
DiffPoolVec::DiffPoolVec()
- : id_( 0 ), n_( 1, 0.0 ), nInit_( 1, 0.0 ),
- diffConst_( 1.0e-12 ), motorConst_( 0.0 )
-{;}
+ : id_( 0 ), n_( 1, 0.0 ), nInit_( 1, 0.0 ),
+ diffConst_( 1.0e-12 ), motorConst_( 0.0 )
+{
+ ;
+}
double DiffPoolVec::getNinit( unsigned int voxel ) const
{
- assert( voxel < nInit_.size() );
- return nInit_[ voxel ];
+ assert( voxel < nInit_.size() );
+ return nInit_[ voxel ];
}
void DiffPoolVec::setNinit( unsigned int voxel, double v )
{
- assert( voxel < nInit_.size() );
- nInit_[ voxel ] = v;
+ assert( voxel < nInit_.size() );
+ nInit_[ voxel ] = v;
}
double DiffPoolVec::getN( unsigned int voxel ) const
{
- assert( voxel < n_.size() );
- return n_[ voxel ];
+ assert( voxel < n_.size() );
+ return n_[ voxel ];
}
void DiffPoolVec::setN( unsigned int voxel, double v )
{
- assert( voxel < n_.size() );
- n_[ voxel ] = v;
+ assert( voxel < n_.size() );
+ n_[ voxel ] = v;
}
double DiffPoolVec::getPrev( unsigned int voxel ) const
{
- assert( voxel < n_.size() );
- return prev_[ voxel ];
+ assert( voxel < n_.size() );
+ return prev_[ voxel ];
}
const vector< double >& DiffPoolVec::getNvec() const
{
- return n_;
+ return n_;
}
void DiffPoolVec::setNvec( const vector< double >& vec )
{
- assert( vec.size() == n_.size() );
- n_ = vec;
+ assert( vec.size() == n_.size() );
+ n_ = 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;
- for ( unsigned int i = 0; i < num; ++i )
- *p++ = *q++;
+ assert( start + num <= n_.size() );
+ vector< double >::iterator p = n_.begin() + start;
+ for ( unsigned int i = 0; i < num; ++i )
+ *p++ = *q++;
}
void DiffPoolVec::setPrevVec()
{
- prev_ = n_;
+ prev_ = n_;
}
double DiffPoolVec::getDiffConst() const
{
- return diffConst_;
+ return diffConst_;
}
void DiffPoolVec::setDiffConst( double v )
{
- diffConst_ = v;
+ diffConst_ = v;
}
double DiffPoolVec::getMotorConst() const
{
- return motorConst_;
+ return motorConst_;
}
void DiffPoolVec::setMotorConst( double v )
{
- motorConst_ = v;
+ motorConst_ = v;
}
void DiffPoolVec::setNumVoxels( unsigned int num )
{
- nInit_.resize( num, 0.0 );
- n_.resize( num, 0.0 );
+ nInit_.resize( num, 0.0 );
+ n_.resize( num, 0.0 );
}
unsigned int DiffPoolVec::getNumVoxels() const
{
- return n_.size();
+ return n_.size();
}
void DiffPoolVec::setId( unsigned int id )
{
- id_ = id;
+ id_ = id;
}
unsigned int DiffPoolVec::getId() const
{
- return id_;
+ return id_;
}
void DiffPoolVec::setOps(const vector< Triplet< double > >& ops,
- const vector< double >& diagVal )
+ const vector< double >& diagVal )
{
- if ( ops.size() > 0 ) {
- assert( diagVal.size() == n_.size() );
- ops_ = ops;
- diagVal_ = diagVal;
- } else {
- ops_.clear();
- diagVal_.clear();
- }
+ if ( ops.size() > 0 )
+ {
+ assert( diagVal.size() == n_.size() );
+ ops_ = ops;
+ diagVal_ = diagVal;
+ }
+ else
+ {
+ ops_.clear();
+ diagVal_.clear();
+ }
}
void DiffPoolVec::advance( double dt )
{
- if ( ops_.size() == 0 ) return;
- for ( vector< Triplet< double > >::const_iterator
- i = ops_.begin(); i != ops_.end(); ++i )
- n_[i->c_] -= n_[i->b_] * i->a_;
+ if ( ops_.size() == 0 ) return;
+ for ( vector< Triplet< double > >::const_iterator
+ i = ops_.begin(); 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 )
- *iy++ *= *i;
+ assert( n_.size() == diagVal_.size() );
+ vector< double >::iterator iy = n_.begin();
+ for ( vector< double >::const_iterator
+ i = diagVal_.begin(); i != diagVal_.end(); ++i )
+ *iy++ *= *i;
}
void DiffPoolVec::reinit() // Not called by the clock, but by parent.
{
- assert( n_.size() == nInit_.size() );
- prev_ = n_ = nInit_;
+ assert( n_.size() == nInit_.size() );
+ prev_ = n_ = nInit_;
}
diff --git a/diffusion/Dsolve.cpp b/diffusion/Dsolve.cpp
index d2f27122..ec72a97e 100644
--- a/diffusion/Dsolve.cpp
+++ b/diffusion/Dsolve.cpp
@@ -374,33 +374,30 @@ void Dsolve::calcJnChan( const DiffJunction& jn, Dsolve* other, double dt )
{
// Each jn has some channels
// Each channel has a chanPool, an intPool and an extPool.
- // intPool is on self, extPool is on other, but we have a problem
+ // chanPool and intPool must be on self, extPool is on other. In
+ // cases where the intPool is on other, it attempts to swap the
+ // int and ext pools, but this too could fail
// because the chanPool could be a third compartment, such as the memb
- // If we stipulate it is is on self, that is easy but not general.
+ //
+ // Don't have a solution for this case as yet.
// Other alternative is to have a message to update the N of the chan,
// so it isn't in the domain of the solver at all except for here.
// In which case we will want to point to the Moose object for it.
//
- //
for ( unsigned int i = 0; i < jn.myChannels.size(); ++i ) {
ConcChanInfo& myChan = channels_[ jn.myChannels[i] ];
DiffPoolVec& myDv = pools_[ myChan.myPool ];
DiffPoolVec& otherDv = other->pools_[ myChan.otherPool ];
DiffPoolVec& chanDv = pools_[ myChan.chanPool ];
- /*
- DiffPoolVec& myDv = pools_[ jn.myPools[myChan.myPool] ];
- DiffPoolVec& otherDv =
- other->pools_[ jn.otherPools[myChan.otherPool] ];
- DiffPoolVec& chanDv = pools_[ jn.myPools[myChan.chanPool] ];
- */
for ( vector< VoxelJunction >::const_iterator
j = jn.vj.begin(); j != jn.vj.end(); ++j ) {
double myN = myDv.getN( j->first );
double lastN = myN;
double otherN = otherDv.getN( j->second );
- double perm = myChan.permeability * chanDv.getN( j->first );
+ double chanN = chanDv.getN( j->first );
+ double perm = myChan.permeability * chanN / NA;
myN = integ( myN, perm * myN/j->firstVol,
perm * otherN/j->secondVol, dt );
otherN += lastN - myN; // Mass consv
@@ -433,7 +430,8 @@ void Dsolve::calcOtherJnChan( const DiffJunction& jn, Dsolve* other, double dt )
double myN = myDv.getN( j->first );
double lastN = myN;
double otherN = otherDv.getN( j->second );
- double perm = otherChan.permeability * chanDv.getN(j->second);
+ double chanN = chanDv.getN( j->second );
+ double perm = otherChan.permeability * chanN / NA;
myN = integ( myN, perm * myN/j->firstVol,
perm * otherN/j->secondVol, dt );
otherN += lastN - myN; // Mass consv
@@ -571,18 +569,22 @@ void Dsolve::fillConcChans( const vector< ObjId >& chans )
if (i->element()->getNeighbors( ret, chanPoolFinfo ) == 0 ) return;
ObjId chanPool( ret[0] );
ret.clear();
- /*
- ObjId inPool = i->element()->findCaller( fin );
- ObjId chanPool = i->element()->findCaller( fchan );
- ObjId outPool = i->element()->findCaller( fout );
- */
+ unsigned int outPoolValue = outPool.id.value();
+ bool swapped = false;
if ( !( inPool.bad() or chanPool.bad() ) ) {
unsigned int inPoolIndex = convertIdToPoolIndex( inPool.id );
unsigned int chanPoolIndex = convertIdToPoolIndex(chanPool.id);
- if ( inPoolIndex != ~0U && chanPoolIndex != ~0U ) {
- ConcChanInfo cci( inPoolIndex, outPool.id.value(),
- chanPoolIndex,
- Field< double >::get( *i, "permeability" )
+ if ( inPoolIndex == ~0U ) { // Swap in and out as chan is symm
+ inPoolIndex = convertIdToPoolIndex( outPool.id );
+ outPoolValue = inPool.id.value();
+ swapped = true;
+ }
+ if ( ( inPoolIndex != ~0U) && (chanPoolIndex != ~0U ) ) {
+ ConcChanInfo cci(
+ inPoolIndex, outPoolValue, chanPoolIndex,
+ Field< double >::get( *i, "permeability" ),
+ ////// Fix it below ////////
+ swapped
);
channels_.push_back( cci );
}
@@ -895,19 +897,23 @@ void Dsolve::mapChansBetweenDsolves( DiffJunction& jn, Id self, Id other)
vector< ConcChanInfo >& ch = selfSolve->channels_;
unsigned int outIndex;
for ( unsigned int i = 0; i < ch.size(); ++i ) {
+ unsigned int chanIndex = ch[i].chanPool;
outIndex = otherSolve->convertIdToPoolIndex( ch[i].otherPool );
- if ( outIndex != ~0U ) {
+ if ( (outIndex != ~0U) && (chanIndex != ~0U ) ) {
jn.myChannels.push_back(i);
ch[i].otherPool = outIndex; // replace the Id with the index.
+ ch[i].chanPool = chanIndex; //chanIndex may be on either Dsolve
}
}
// Now set up the other Dsolve.
vector< ConcChanInfo >& ch2 = otherSolve->channels_;
for ( unsigned int i = 0; i < ch2.size(); ++i ) {
+ unsigned int chanIndex = ch2[i].chanPool;
outIndex = selfSolve->convertIdToPoolIndex( ch2[i].otherPool );
- if ( outIndex != ~0U ) {
+ if ( (outIndex != ~0U) && (chanIndex != ~0U) ) {
jn.otherChannels.push_back(i);
ch2[i].otherPool = outIndex; // replace the Id with the index
+ ch2[i].chanPool = chanIndex; //chanIndex may be on either Dsolve
}
}
}
diff --git a/external/boost-numeric-bindings/boost/numeric/bindings/lapack/gees.hpp b/external/boost-numeric-bindings/boost/numeric/bindings/lapack/gees.hpp
index 2c2531c9..472ef367 100644
--- a/external/boost-numeric-bindings/boost/numeric/bindings/lapack/gees.hpp
+++ b/external/boost-numeric-bindings/boost/numeric/bindings/lapack/gees.hpp
@@ -140,7 +140,9 @@ namespace boost { namespace numeric { namespace bindings {
>::value));
#endif
+#ifndef NDEBUG
typedef typename MatrA::value_type value_type ;
+#endif
int const n = traits::matrix_size1 (a);
assert (n == traits::matrix_size2 (a));
@@ -185,7 +187,9 @@ namespace boost { namespace numeric { namespace bindings {
>::value));
#endif
+#ifndef NDEBUG
typedef typename MatrA::value_type value_type ;
+#endif
int const n = traits::matrix_size1 (a);
assert (n == traits::matrix_size2 (a));
@@ -265,7 +269,9 @@ namespace boost { namespace numeric { namespace bindings {
inline
int operator() (char jobvs, MatrA& a, EigVal& w, SchVec& vs, optimal_workspace ) const {
typedef typename MatrA::value_type value_type ;
+#ifndef NDEBUG
typedef typename traits::type_traits< value_type >::real_type real_type ;
+#endif
int n = traits::matrix_size1( a );
@@ -278,7 +284,10 @@ namespace boost { namespace numeric { namespace bindings {
inline
int operator() (char jobvs, MatrA& a, EigVal& w, SchVec& vs, minimal_workspace ) const {
typedef typename MatrA::value_type value_type ;
+
+#ifndef NDEBUG
typedef typename traits::type_traits< value_type >::real_type real_type ;
+#endif
int n = traits::matrix_size1( a );
diff --git a/external/boost-numeric-bindings/boost/numeric/bindings/lapack/gesvd.hpp b/external/boost-numeric-bindings/boost/numeric/bindings/lapack/gesvd.hpp
index 0bb01fdb..eba01080 100644
--- a/external/boost-numeric-bindings/boost/numeric/bindings/lapack/gesvd.hpp
+++ b/external/boost-numeric-bindings/boost/numeric/bindings/lapack/gesvd.hpp
@@ -295,7 +295,9 @@ namespace boost { namespace numeric { namespace bindings {
|| (jobvt == 'A' && traits::leading_dimension (vt) >= n)
|| (jobvt == 'S' && traits::leading_dimension (vt) >= minmn));
#ifndef BOOST_NUMERIC_BINDINGS_POOR_MANS_TRAITS
+#ifndef NDEBUG
typedef typename traits::matrix_traits<MatrA>::value_type val_t;
+#endif
#else
typedef typename MatrA::value_type val_t;
#endif
diff --git a/external/boost-numeric-bindings/boost/numeric/bindings/lapack/syev.hpp b/external/boost-numeric-bindings/boost/numeric/bindings/lapack/syev.hpp
index 5aeaf382..fdd5253b 100644
--- a/external/boost-numeric-bindings/boost/numeric/bindings/lapack/syev.hpp
+++ b/external/boost-numeric-bindings/boost/numeric/bindings/lapack/syev.hpp
@@ -136,7 +136,10 @@ namespace boost { namespace numeric { namespace bindings {
template <typename A, typename W, typename Work>
inline
int syev (char jobz, char uplo, A& a, W& w, detail::workspace1<Work> workspace ) {
+
+#ifndef NDEBUG
typedef typename A::value_type value_type ;
+#endif
return detail::syev(jobz, uplo, a, w, workspace.w_);
} // syev()
@@ -195,7 +198,9 @@ namespace boost { namespace numeric { namespace bindings {
template <typename A, typename W, typename Work>
inline
int syev (char jobz, A& a, W& w, detail::workspace1<Work> workspace ) {
+#ifndef NDEBUG
typedef typename A::value_type value_type ;
+#endif
char uplo = traits::matrix_uplo_tag( a ) ;
#ifndef BOOST_NUMERIC_BINDINGS_NO_STRUCTURE_CHECK
typedef typename traits::matrix_traits<A>::matrix_structure matrix_structure ;
diff --git a/intfire/CMakeLists.txt b/intfire/CMakeLists.txt
index 5ee3c2fb..06435a8e 100644
--- a/intfire/CMakeLists.txt
+++ b/intfire/CMakeLists.txt
@@ -1,14 +1,5 @@
-cmake_minimum_required(VERSION 2.6)
-INCLUDE_DIRECTORIES(../basecode)
-
-ADD_LIBRARY(intfire
- AdExIF.cpp
- AdThreshIF.cpp
- ExIF.cpp
- IntFireBase.cpp
- IzhIF.cpp
- LIF.cpp
- QIF.cpp
- testIntFire.cpp
- )
-
+cmake_minimum_required(VERSION 2.8)
+include_directories(../basecode)
+add_definitions( -std=c++11 )
+file(GLOB SRC *.cpp)
+add_library(intfire ${SRC})
diff --git a/intfire/IntFireBase.cpp b/intfire/IntFireBase.cpp
index a4364db4..7488c54f 100644
--- a/intfire/IntFireBase.cpp
+++ b/intfire/IntFireBase.cpp
@@ -7,97 +7,99 @@
** See the file COPYING.LIB for the full notice.
**********************************************************************/
-#include "header.h"
-#include "ElementValueFinfo.h"
+#include "../basecode/header.h"
+#include "../basecode/ElementValueFinfo.h"
#include "../biophysics/CompartmentBase.h"
#include "../biophysics/Compartment.h"
#include "IntFireBase.h"
using namespace moose;
-SrcFinfo1< double >* IntFireBase::spikeOut() {
- static SrcFinfo1< double > spikeOut(
- "spikeOut",
- "Sends out spike events. The argument is the timestamp of "
- "the spike. "
- );
- return &spikeOut;
+SrcFinfo1< double >* IntFireBase::spikeOut()
+{
+ static SrcFinfo1< double > spikeOut(
+ "spikeOut",
+ "Sends out spike events. The argument is the timestamp of "
+ "the spike. "
+ );
+ return &spikeOut;
}
const Cinfo* IntFireBase::initCinfo()
{
- //////////////////////////////////////////////////////////////
- // Field Definitions
- //////////////////////////////////////////////////////////////
-
- static ElementValueFinfo< IntFireBase, double > thresh(
- "thresh",
- "firing threshold",
- &IntFireBase::setThresh,
- &IntFireBase::getThresh
- );
-
- static ElementValueFinfo< IntFireBase, double > vReset(
- "vReset",
- "voltage is set to vReset after firing",
- &IntFireBase::setVReset,
- &IntFireBase::getVReset
- );
-
- static ElementValueFinfo< IntFireBase, double > refractoryPeriod(
- "refractoryPeriod",
- "Minimum time between successive spikes",
- &IntFireBase::setRefractoryPeriod,
- &IntFireBase::getRefractoryPeriod
- );
-
- static ReadOnlyElementValueFinfo< IntFireBase, double > lastEventTime(
- "lastEventTime",
- "Timestamp of last firing.",
- &IntFireBase::getLastEventTime
- );
-
- static ReadOnlyElementValueFinfo< IntFireBase, bool > hasFired(
- "hasFired",
- "The object has fired within the last timestep",
- &IntFireBase::hasFired
- );
- //////////////////////////////////////////////////////////////
- // MsgDest Definitions
- //////////////////////////////////////////////////////////////
- static DestFinfo activation( "activation",
- "Handles value of synaptic activation arriving on this object",
- new OpFunc1< IntFireBase, double >( &IntFireBase::activation ));
-
- //////////////////////////////////////////////////////////////
-
- static Finfo* intFireFinfos[] = {
- &thresh, // Value
- &vReset, // Value
- &refractoryPeriod, // Value
- &hasFired, // ReadOnlyValue
- &lastEventTime, // ReadOnlyValue
- &activation, // DestFinfo
- IntFireBase::spikeOut() // MsgSrc
- };
-
- static string doc[] =
- {
- "Name", "IntFireBase",
- "Author", "Upi Bhalla",
- "Description", "Base class for Integrate-and-fire compartment.",
- };
+ //////////////////////////////////////////////////////////////
+ // Field Definitions
+ //////////////////////////////////////////////////////////////
+ static ElementValueFinfo< IntFireBase, double > thresh(
+ "thresh",
+ "firing threshold",
+ &IntFireBase::setThresh,
+ &IntFireBase::getThresh
+ );
+
+ static ElementValueFinfo< IntFireBase, double > vReset(
+ "vReset",
+ "voltage is set to vReset after firing",
+ &IntFireBase::setVReset,
+ &IntFireBase::getVReset
+ );
+
+ static ElementValueFinfo< IntFireBase, double > refractoryPeriod(
+ "refractoryPeriod",
+ "Minimum time between successive spikes",
+ &IntFireBase::setRefractoryPeriod,
+ &IntFireBase::getRefractoryPeriod
+ );
+
+ static ReadOnlyElementValueFinfo< IntFireBase, double > lastEventTime(
+ "lastEventTime",
+ "Timestamp of last firing.",
+ &IntFireBase::getLastEventTime
+ );
+
+ static ReadOnlyElementValueFinfo< IntFireBase, bool > hasFired(
+ "hasFired",
+ "The object has fired within the last timestep",
+ &IntFireBase::hasFired
+ );
+ //////////////////////////////////////////////////////////////
+ // MsgDest Definitions
+ //////////////////////////////////////////////////////////////
+ static DestFinfo activation(
+ "activation",
+ "Handles value of synaptic activation arriving on this object",
+ new OpFunc1< IntFireBase, double >( &IntFireBase::activation ));
+
+ //////////////////////////////////////////////////////////////
+
+ static Finfo* intFireFinfos[] =
+ {
+ &thresh, // Value
+ &vReset, // Value
+ &refractoryPeriod, // Value
+ &hasFired, // ReadOnlyValue
+ &lastEventTime, // ReadOnlyValue
+ &activation, // DestFinfo
+ IntFireBase::spikeOut() // MsgSrc
+ };
+
+ static string doc[] =
+ {
+ "Name", "IntFireBase",
+ "Author", "Upi Bhalla",
+ "Description", "Base class for Integrate-and-fire compartment.",
+ };
static ZeroSizeDinfo< int > dinfo;
- static Cinfo intFireBaseCinfo(
- "IntFireBase",
- Compartment::initCinfo(),
- intFireFinfos,
- sizeof( intFireFinfos ) / sizeof (Finfo*),
- &dinfo,
- doc,
- sizeof(doc)/sizeof(string)
- );
-
- return &intFireBaseCinfo;
+ static Cinfo intFireBaseCinfo(
+ "IntFireBase",
+ Compartment::initCinfo(),
+ intFireFinfos,
+ sizeof( intFireFinfos ) / sizeof (Finfo*),
+ &dinfo,
+ doc,
+ sizeof(doc)/sizeof(string)
+ );
+
+ return &intFireBaseCinfo;
}
static const Cinfo* intFireBaseCinfo = IntFireBase::initCinfo();
@@ -107,59 +109,59 @@ static const Cinfo* intFireBaseCinfo = IntFireBase::initCinfo();
//////////////////////////////////////////////////////////////////
IntFireBase::IntFireBase()
- :
- threshold_( 0.0 ),
- vReset_( 0.0 ),
- activation_( 0.0 ),
- refractT_( 0.0 ),
- lastEvent_( 0.0 ),
- fired_( false )
+ :
+ threshold_( 0.0 ),
+ vReset_( 0.0 ),
+ activation_( 0.0 ),
+ refractT_( 0.0 ),
+ lastEvent_( 0.0 ),
+ fired_( false )
{;}
IntFireBase::~IntFireBase()
{
- ;
+ ;
}
// Value Field access function definitions.
void IntFireBase::setThresh( const Eref& e, double val )
{
- threshold_ = val;
+ threshold_ = val;
}
double IntFireBase::getThresh( const Eref& e ) const
{
- return threshold_;
+ return threshold_;
}
void IntFireBase::setVReset( const Eref& e, double val )
{
- vReset_ = val;
+ vReset_ = val;
}
double IntFireBase::getVReset( const Eref& e ) const
{
- return vReset_;
+ return vReset_;
}
void IntFireBase::setRefractoryPeriod( const Eref& e, double val )
{
- refractT_ = val;
+ refractT_ = val;
}
double IntFireBase::getRefractoryPeriod( const Eref& e ) const
{
- return refractT_;
+ return refractT_;
}
double IntFireBase::getLastEventTime( const Eref& e ) const
{
- return lastEvent_;
+ return lastEvent_;
}
bool IntFireBase::hasFired( const Eref& e ) const
{
- return fired_;
+ return fired_;
}
//////////////////////////////////////////////////////////////////
@@ -168,5 +170,5 @@ bool IntFireBase::hasFired( const Eref& e ) const
void IntFireBase::activation( double v )
{
- activation_ += v;
+ activation_ += v;
}
diff --git a/intfire/IntFireBase.h b/intfire/IntFireBase.h
index c17dbdca..bbdc12d5 100644
--- a/intfire/IntFireBase.h
+++ b/intfire/IntFireBase.h
@@ -18,52 +18,52 @@ namespace moose
*/
class IntFireBase: public Compartment
{
- public:
- IntFireBase();
- virtual ~IntFireBase();
+public:
+ IntFireBase();
+ virtual ~IntFireBase();
- // Value Field access function definitions.
- void setThresh( const Eref& e, double val );
- double getThresh( const Eref& e ) const;
- void setVReset( const Eref& e, double val );
- double getVReset( const Eref& e ) const;
- void setRefractoryPeriod( const Eref& e, double val );
- double getRefractoryPeriod( const Eref& e ) const;
- double getLastEventTime( const Eref& e ) const;
- bool hasFired( const Eref& e ) const;
+ // Value Field access function definitions.
+ void setThresh( const Eref& e, double val );
+ double getThresh( const Eref& e ) const;
+ void setVReset( const Eref& e, double val );
+ double getVReset( const Eref& e ) const;
+ void setRefractoryPeriod( const Eref& e, double val );
+ double getRefractoryPeriod( const Eref& e ) const;
+ double getLastEventTime( const Eref& e ) const;
+ bool hasFired( const Eref& e ) const;
- // Dest function definitions.
- /**
- * The process function does the object updating and sends out
- * messages to channels, nernsts, and so on.
- */
- virtual void vProcess( const Eref& e, ProcPtr p ) = 0;
+ // Dest function definitions.
+ /**
+ * The process function does the object updating and sends out
+ * messages to channels, nernsts, and so on.
+ */
+ virtual void vProcess( const Eref& e, ProcPtr p ) = 0;
- /**
- * The reinit function reinitializes all fields.
- */
- virtual void vReinit( const Eref& e, ProcPtr p ) = 0;
+ /**
+ * The reinit function reinitializes all fields.
+ */
+ virtual void vReinit( const Eref& e, ProcPtr p ) = 0;
- /**
- * activation handles information coming from the SynHandler
- * to the intFire.
- */
- void activation( double val );
+ /**
+ * activation handles information coming from the SynHandler
+ * to the intFire.
+ */
+ void activation( double val );
- /// Message src for outgoing spikes.
- static SrcFinfo1< double >* spikeOut();
+ /// Message src for outgoing spikes.
+ static SrcFinfo1< double >* spikeOut();
- /**
- * Initializes the class info.
- */
- static const Cinfo* initCinfo();
- protected:
- double threshold_;
- double vReset_;
- double activation_;
- double refractT_;
- double lastEvent_;
- bool fired_;
+ /**
+ * Initializes the class info.
+ */
+ static const Cinfo* initCinfo();
+protected:
+ double threshold_;
+ double vReset_;
+ double activation_;
+ double refractT_;
+ double lastEvent_;
+ bool fired_;
};
} // namespace
diff --git a/intfire/LIF.cpp b/intfire/LIF.cpp
index 3812583a..f1815ccd 100644
--- a/intfire/LIF.cpp
+++ b/intfire/LIF.cpp
@@ -7,8 +7,8 @@
** See the file COPYING.LIB for the full notice.
**********************************************************************/
-#include "header.h"
-#include "ElementValueFinfo.h"
+#include "../basecode/header.h"
+#include "../basecode/ElementValueFinfo.h"
#include "../biophysics/CompartmentBase.h"
#include "../biophysics/Compartment.h"
#include "IntFireBase.h"
@@ -18,23 +18,23 @@ using namespace moose;
const Cinfo* LIF::initCinfo()
{
- static string doc[] =
- {
- "Name", "LIF",
- "Author", "Upi Bhalla",
- "Description", "Leaky Integrate-and-Fire neuron"
- };
+ static string doc[] =
+ {
+ "Name", "LIF",
+ "Author", "Upi Bhalla",
+ "Description", "Leaky Integrate-and-Fire neuron"
+ };
static Dinfo< LIF > dinfo;
- static Cinfo lifCinfo(
- "LIF",
- IntFireBase::initCinfo(),
- 0, 0,
- &dinfo,
- doc,
- sizeof(doc)/sizeof(string)
- );
+ static Cinfo lifCinfo(
+ "LIF",
+ IntFireBase::initCinfo(),
+ 0, 0,
+ &dinfo,
+ doc,
+ sizeof(doc)/sizeof(string)
+ );
- return &lifCinfo;
+ return &lifCinfo;
}
static const Cinfo* lifCinfo = LIF::initCinfo();
@@ -44,10 +44,14 @@ static const Cinfo* lifCinfo = LIF::initCinfo();
//////////////////////////////////////////////////////////////////
LIF::LIF()
-{;}
+{
+ ;
+}
LIF::~LIF()
-{;}
+{
+ ;
+}
//////////////////////////////////////////////////////////////////
// LIF::Dest function definitions.
@@ -55,37 +59,43 @@ LIF::~LIF()
void LIF::vProcess( const Eref& e, ProcPtr p )
{
- fired_ = false;
- if ( p->currTime < lastEvent_ + refractT_ ) {
- Vm_ = vReset_;
- A_ = 0.0;
- B_ = 1.0 / Rm_;
- sumInject_ = 0.0;
- VmOut()->send( e, Vm_ );
- } else {
+ fired_ = false;
+ if ( p->currTime < lastEvent_ + refractT_ )
+ {
+ Vm_ = vReset_;
+ A_ = 0.0;
+ B_ = 1.0 / Rm_;
+ sumInject_ = 0.0;
+ VmOut()->send( e, Vm_ );
+ }
+ else
+ {
// activation can be a continous variable (graded synapse).
// So integrate it at every time step, thus *dt.
// For a delta-fn synapse, SynHandler-s divide by dt and send activation.
// See: http://www.genesis-sim.org/GENESIS/Hyperdoc/Manual-26.html#synchan
// for this continuous definition of activation.
- Vm_ += activation_ * p->dt;
- activation_ = 0.0;
- if ( Vm_ > threshold_ ) {
- Vm_ = vReset_;
- lastEvent_ = p->currTime;
- fired_ = true;
- spikeOut()->send( e, p->currTime );
- VmOut()->send( e, Vm_ );
- } else {
- Compartment::vProcess( e, p );
- }
- }
+ Vm_ += activation_ * p->dt;
+ activation_ = 0.0;
+ if ( Vm_ > threshold_ )
+ {
+ Vm_ = vReset_;
+ lastEvent_ = p->currTime;
+ fired_ = true;
+ spikeOut()->send( e, p->currTime );
+ VmOut()->send( e, Vm_ );
+ }
+ else
+ {
+ Compartment::vProcess( e, p );
+ }
+ }
}
void LIF::vReinit( const Eref& e, ProcPtr p )
{
- activation_ = 0.0;
- fired_ = false;
- lastEvent_ = -refractT_; // Allow it to fire right away.
- Compartment::vReinit( e, p );
+ activation_ = 0.0;
+ fired_ = false;
+ lastEvent_ = -refractT_; // Allow it to fire right away.
+ Compartment::vReinit( e, p );
}
diff --git a/intfire/LIF.h b/intfire/LIF.h
index 4b15f2c3..6bad5019 100644
--- a/intfire/LIF.h
+++ b/intfire/LIF.h
@@ -13,30 +13,32 @@
namespace moose
{
+
/**
* The IntFire class sets up an integrate-and-fire compartment.
*/
class LIF: public IntFireBase
{
- public:
- LIF();
- virtual ~LIF();
- /**
- * The process function does the object updating and sends out
- * messages to channels, nernsts, and so on.
- */
- void vProcess( const Eref& e, ProcPtr p );
+public:
+ LIF();
+ virtual ~LIF();
+ /**
+ * The process function does the object updating and sends out
+ * messages to channels, nernsts, and so on.
+ */
+ void vProcess( const Eref& e, ProcPtr p );
- /**
- * The reinit function reinitializes all fields.
- */
- void vReinit( const Eref& e, ProcPtr p );
+ /**
+ * The reinit function reinitializes all fields.
+ */
+ void vReinit( const Eref& e, ProcPtr p );
- /**
- * Initializes the class info.
- */
- static const Cinfo* initCinfo();
+ /**
+ * Initializes the class info.
+ */
+ static const Cinfo* initCinfo();
};
+
}
#endif // _LIF_H
diff --git a/kinetics/BufPool.cpp b/kinetics/BufPool.cpp
index 54e18378..a980ffc1 100644
--- a/kinetics/BufPool.cpp
+++ b/kinetics/BufPool.cpp
@@ -7,7 +7,7 @@
** See the file COPYING.LIB for the full notice.
**********************************************************************/
-#include "header.h"
+#include "../basecode/header.h"
#include "PoolBase.h"
#include "Pool.h"
#include "BufPool.h"
@@ -17,28 +17,28 @@
const Cinfo* BufPool::initCinfo()
{
- //////////////////////////////////////////////////////////////
- // Field Definitions
- //////////////////////////////////////////////////////////////
-
- //////////////////////////////////////////////////////////////
- // MsgDest Definitions
- //////////////////////////////////////////////////////////////
-
- //////////////////////////////////////////////////////////////
- // SharedMsg Definitions
- //////////////////////////////////////////////////////////////
-
- static Dinfo< BufPool > dinfo;
- static Cinfo bufPoolCinfo (
- "BufPool",
- Pool::initCinfo(),
- 0,
- 0,
- &dinfo
- );
-
- return &bufPoolCinfo;
+ //////////////////////////////////////////////////////////////
+ // Field Definitions
+ //////////////////////////////////////////////////////////////
+
+ //////////////////////////////////////////////////////////////
+ // MsgDest Definitions
+ //////////////////////////////////////////////////////////////
+
+ //////////////////////////////////////////////////////////////
+ // SharedMsg Definitions
+ //////////////////////////////////////////////////////////////
+
+ static Dinfo< BufPool > dinfo;
+ static Cinfo bufPoolCinfo (
+ "BufPool",
+ Pool::initCinfo(),
+ 0,
+ 0,
+ &dinfo
+ );
+
+ return &bufPoolCinfo;
}
//////////////////////////////////////////////////////////////
@@ -58,24 +58,24 @@ BufPool::~BufPool()
void BufPool::vSetN( const Eref& e, double v )
{
- Pool::vSetN( e, v );
- Pool::vSetNinit( e, v );
+ Pool::vSetN( e, v );
+ Pool::vSetNinit( e, v );
}
void BufPool::vSetNinit( const Eref& e, double v )
{
- vSetN( e, v );
+ vSetN( e, v );
}
void BufPool::vSetConc( const Eref& e, double conc )
{
- double n = NA * conc * lookupVolumeFromMesh( e );
- vSetN( e, n );
+ double n = NA * conc * lookupVolumeFromMesh( e );
+ vSetN( e, n );
}
void BufPool::vSetConcInit( const Eref& e, double conc )
{
- vSetConc( e, conc );
+ vSetConc( e, conc );
}
//////////////////////////////////////////////////////////////
@@ -84,12 +84,12 @@ void BufPool::vSetConcInit( const Eref& e, double conc )
void BufPool::vProcess( const Eref& e, ProcPtr p )
{
- Pool::vReinit( e, p );
+ Pool::vReinit( e, p );
}
void BufPool::vReinit( const Eref& e, ProcPtr p )
{
- Pool::vReinit( e, p );
+ Pool::vReinit( e, p );
}
diff --git a/kinetics/BufPool.h b/kinetics/BufPool.h
index 45b401e7..a0282d9b 100644
--- a/kinetics/BufPool.h
+++ b/kinetics/BufPool.h
@@ -12,28 +12,28 @@
class BufPool: public Pool
{
- public:
- BufPool();
- ~BufPool();
+public:
+ BufPool();
+ ~BufPool();
- //////////////////////////////////////////////////////////////////
- // Field assignment stuff
- //////////////////////////////////////////////////////////////////
- /// The 'get' functions are simply inherited from Pool
- void vSetN( const Eref& e, double v );
- void vSetNinit( const Eref& e, double v );
- void vSetConc( const Eref& e, double v );
- void vSetConcInit( const Eref& e, double v );
+ //////////////////////////////////////////////////////////////////
+ // Field assignment stuff
+ //////////////////////////////////////////////////////////////////
+ /// The 'get' functions are simply inherited from Pool
+ void vSetN( const Eref& e, double v );
+ void vSetNinit( const Eref& e, double v );
+ void vSetConc( const Eref& e, double v );
+ void vSetConcInit( const Eref& e, double v );
- //////////////////////////////////////////////////////////////////
- // Dest funcs
- //////////////////////////////////////////////////////////////////
+ //////////////////////////////////////////////////////////////////
+ // Dest funcs
+ //////////////////////////////////////////////////////////////////
- void vProcess( const Eref& e, ProcPtr p );
- void vReinit( const Eref& e, ProcPtr p );
+ void vProcess( const Eref& e, ProcPtr p );
+ void vReinit( const Eref& e, ProcPtr p );
- static const Cinfo* initCinfo();
- private:
+ static const Cinfo* initCinfo();
+private:
};
#endif // _BUF_POOL_H
diff --git a/kinetics/Pool.cpp b/kinetics/Pool.cpp
index 8b0eb629..b6b448ba 100644
--- a/kinetics/Pool.cpp
+++ b/kinetics/Pool.cpp
@@ -7,8 +7,8 @@
** See the file COPYING.LIB for the full notice.
**********************************************************************/
-#include "header.h"
-#include "ElementValueFinfo.h"
+#include "../basecode/header.h"
+#include "../basecode/ElementValueFinfo.h"
#include "lookupVolumeFromMesh.h"
#include "PoolBase.h"
#include "Pool.h"
@@ -17,41 +17,41 @@
const Cinfo* Pool::initCinfo()
{
- //////////////////////////////////////////////////////////////
- // Field Definitions: All inherited from PoolBase.
- //////////////////////////////////////////////////////////////
- //////////////////////////////////////////////////////////////
- // MsgDest Definitions: All inherited
- //////////////////////////////////////////////////////////////
- //////////////////////////////////////////////////////////////
- // SrcFinfo Definitions: All inherited.
- //////////////////////////////////////////////////////////////
- //////////////////////////////////////////////////////////////
- // SharedMsg Definitions: All inherited.
- //////////////////////////////////////////////////////////////
- static Dinfo< Pool > dinfo;
- static Cinfo poolCinfo (
- "Pool",
- PoolBase::initCinfo(),
- 0,
- 0,
- &dinfo
- );
-
- return &poolCinfo;
+ //////////////////////////////////////////////////////////////
+ // Field Definitions: All inherited from PoolBase.
+ //////////////////////////////////////////////////////////////
+ //////////////////////////////////////////////////////////////
+ // MsgDest Definitions: All inherited
+ //////////////////////////////////////////////////////////////
+ //////////////////////////////////////////////////////////////
+ // SrcFinfo Definitions: All inherited.
+ //////////////////////////////////////////////////////////////
+ //////////////////////////////////////////////////////////////
+ // SharedMsg Definitions: All inherited.
+ //////////////////////////////////////////////////////////////
+ static Dinfo< Pool > dinfo;
+ static Cinfo poolCinfo (
+ "Pool",
+ PoolBase::initCinfo(),
+ 0,
+ 0,
+ &dinfo
+ );
+
+ return &poolCinfo;
}
//////////////////////////////////////////////////////////////
// Class definitions
//////////////////////////////////////////////////////////////
static const Cinfo* poolCinfo = Pool::initCinfo();
-const SrcFinfo1< double >& nOut =
- *dynamic_cast< const SrcFinfo1< double >* >(
- poolCinfo->findFinfo( "nOut" ) );
+
+const SrcFinfo1< double >& nOut = *dynamic_cast<const SrcFinfo1< double >*
+ >(poolCinfo->findFinfo( "nOut"));
Pool::Pool()
- : n_( 0.0 ), nInit_( 0.0 ), diffConst_( 0.0 ), motorConst_( 0.0 ),
- A_( 0.0 ), B_( 0.0 ), species_( 0 )
+ : n_( 0.0 ), nInit_( 0.0 ), diffConst_( 0.0 ), motorConst_( 0.0 ),
+ A_( 0.0 ), B_( 0.0 ), species_( 0 )
{;}
Pool::~Pool()
@@ -67,22 +67,25 @@ Pool::~Pool()
*/
void Pool::vSetIsBuffered( const Eref& e, bool v )
{
- static const Cinfo* bufPoolCinfo = Cinfo::find( "BufPool" );
- if (vGetIsBuffered( e ) == v)
- return;
- if (v) {
- e.element()->replaceCinfo( bufPoolCinfo );
- } else {
- e.element()->replaceCinfo( poolCinfo );
- }
+ static const Cinfo* bufPoolCinfo = Cinfo::find( "BufPool" );
+ if (vGetIsBuffered( e ) == v)
+ return;
+ if (v)
+ {
+ e.element()->replaceCinfo( bufPoolCinfo );
+ }
+ else
+ {
+ e.element()->replaceCinfo( poolCinfo );
+ }
}
bool Pool::vGetIsBuffered( const Eref& e ) const
{
- /// We need this explicit check because when the moose class is
- /// flipped, the internal C++ class isn't.
- /// Inherited by BufPool.
- return e.element()->cinfo()->name() == "BufPool";
+ /// We need this explicit check because when the moose class is
+ /// flipped, the internal C++ class isn't.
+ /// Inherited by BufPool.
+ return e.element()->cinfo()->name() == "BufPool";
}
//////////////////////////////////////////////////////////////
@@ -93,51 +96,54 @@ bool Pool::vGetIsBuffered( const Eref& e ) const
void Pool::vProcess( const Eref& e, ProcPtr p )
{
- // double A = e.sumBuf( aSlot );
- // double B = e.sumBuf( bSlot );
+ // double A = e.sumBuf( aSlot );
+ // double B = e.sumBuf( bSlot );
- if ( n_ > EPSILON && B_ > EPSILON ) {
- double C = exp( -B_ * p->dt / n_ );
- n_ *= C + (A_ / B_ ) * ( 1.0 - C );
- } else {
- n_ += ( A_ - B_ ) * p->dt;
- if ( n_ < 0.0 )
- n_ = 0.0;
- }
+ if ( n_ > EPSILON && B_ > EPSILON )
+ {
+ double C = exp( -B_ * p->dt / n_ );
+ n_ *= C + (A_ / B_ ) * ( 1.0 - C );
+ }
+ else
+ {
+ n_ += ( A_ - B_ ) * p->dt;
+ if ( n_ < 0.0 )
+ n_ = 0.0;
+ }
- A_ = B_ = 0.0;
+ A_ = B_ = 0.0;
- nOut.send( e, n_ );
+ nOut.send( e, n_ );
}
void Pool::vReinit( const Eref& e, ProcPtr p )
{
- A_ = B_ = 0.0;
- n_ = getNinit( e );
+ A_ = B_ = 0.0;
+ n_ = getNinit( e );
- nOut.send( e, n_ );
+ nOut.send( e, n_ );
}
void Pool::vReac( double A, double B )
{
- A_ += A;
- B_ += B;
+ A_ += A;
+ B_ += B;
}
void Pool::vIncrement( double val )
{
- if ( val > 0 )
- A_ += val;
- else
- B_ -= val;
+ if ( val > 0 )
+ A_ += val;
+ else
+ B_ -= val;
}
void Pool::vDecrement( double val )
{
- if ( val < 0 )
- A_ -= val;
- else
- B_ += val;
+ if ( val < 0 )
+ A_ -= val;
+ else
+ B_ += val;
}
void Pool::vnIn( double val)
@@ -149,7 +155,7 @@ void Pool::vnIn( double val)
void Pool::vHandleMolWt( const Eref& e, double v )
{
- ; // Here I should update DiffConst too.
+ ; // Here I should update DiffConst too.
}
//////////////////////////////////////////////////////////////
@@ -158,77 +164,77 @@ void Pool::vHandleMolWt( const Eref& e, double v )
void Pool::vSetN( const Eref& e, double v )
{
- n_ = v;
+ n_ = v;
}
double Pool::vGetN( const Eref& e ) const
{
- return n_;
+ return n_;
}
void Pool::vSetNinit( const Eref& e, double v )
{
- nInit_ = v;
+ nInit_ = v;
}
double Pool::vGetNinit( const Eref& e ) const
{
- return nInit_;
+ return nInit_;
}
// Conc is given in millimolar. Volume is in m^3
void Pool::vSetConc( const Eref& e, double c )
{
- n_ = NA * c * lookupVolumeFromMesh( e );
+ n_ = NA * c * lookupVolumeFromMesh( e );
}
// Returns conc in millimolar.
double Pool::vGetConc( const Eref& e ) const
{
- return (n_ / NA) / lookupVolumeFromMesh( e );
+ return (n_ / NA) / lookupVolumeFromMesh( e );
}
void Pool::vSetConcInit( const Eref& e, double c )
{
- nInit_ = NA * c * lookupVolumeFromMesh( e );
+ nInit_ = NA * c * lookupVolumeFromMesh( e );
}
void Pool::vSetDiffConst( const Eref& e, double v )
{
- diffConst_ = v;
+ diffConst_ = v;
}
double Pool::vGetDiffConst( const Eref& e ) const
{
- return diffConst_;
+ return diffConst_;
}
void Pool::vSetMotorConst( const Eref& e, double v )
{
- motorConst_ = v;
+ motorConst_ = v;
}
double Pool::vGetMotorConst( const Eref& e ) const
{
- return motorConst_;
+ return motorConst_;
}
void Pool::vSetVolume( const Eref& e, double v )
{
- cout << "Warning: Pool::vSetVolume: Operation not permitted. Ignored\n";
+ cout << "Warning: Pool::vSetVolume: Operation not permitted. Ignored\n";
}
double Pool::vGetVolume( const Eref& e ) const
{
- return lookupVolumeFromMesh( e );
+ return lookupVolumeFromMesh( e );
}
void Pool::vSetSpecies( const Eref& e, SpeciesId v )
{
- species_ = v;
+ species_ = v;
}
SpeciesId Pool::vGetSpecies( const Eref& e ) const
{
- return species_;
+ return species_;
}
diff --git a/kinetics/Pool.h b/kinetics/Pool.h
index bc4e8877..51fbc512 100644
--- a/kinetics/Pool.h
+++ b/kinetics/Pool.h
@@ -18,80 +18,80 @@
*/
class Pool: public PoolBase
{
- public:
- Pool();
- ~Pool();
+public:
+ Pool();
+ ~Pool();
- //////////////////////////////////////////////////////////////////
- // Field assignment stuff. All override virtual funcs in the Pool
- // base class.
- //////////////////////////////////////////////////////////////////
+ //////////////////////////////////////////////////////////////////
+ // Field assignment stuff. All override virtual funcs in the Pool
+ // base class.
+ //////////////////////////////////////////////////////////////////
- void vSetN( const Eref& e, double v );
- double vGetN( const Eref& e ) const;
- void vSetNinit( const Eref& e, double v );
- double vGetNinit( const Eref& e ) const;
- void vSetDiffConst( const Eref& e, double v );
- double vGetDiffConst( const Eref& e ) const;
- void vSetMotorConst( const Eref& e, double v );
- double vGetMotorConst( const Eref& e ) const;
+ void vSetN( const Eref& e, double v );
+ double vGetN( const Eref& e ) const;
+ void vSetNinit( const Eref& e, double v );
+ double vGetNinit( const Eref& e ) const;
+ void vSetDiffConst( const Eref& e, double v );
+ double vGetDiffConst( const Eref& e ) const;
+ void vSetMotorConst( const Eref& e, double v );
+ double vGetMotorConst( const Eref& e ) const;
- void vSetConc( const Eref& e, double v );
- double vGetConc( const Eref& e ) const;
- void vSetConcInit( const Eref& e, double v );
- // double vGetConcInit( const Eref& e ) const;
+ void vSetConc( const Eref& e, double v );
+ double vGetConc( const Eref& e ) const;
+ void vSetConcInit( const Eref& e, double v );
+ // double vGetConcInit( const Eref& e ) const;
- /**
- * Volume is usually volume, but we also permit areal density
- * This is obtained by looking up the corresponding spatial mesh
- * entry in the parent compartment. If the message isn't set then
- * it defaults to 1.0.
- */
- void vSetVolume( const Eref& e, double v );
- double vGetVolume( const Eref& e ) const;
+ /**
+ * Volume is usually volume, but we also permit areal density
+ * This is obtained by looking up the corresponding spatial mesh
+ * entry in the parent compartment. If the message isn't set then
+ * it defaults to 1.0.
+ */
+ void vSetVolume( const Eref& e, double v );
+ double vGetVolume( const Eref& e ) const;
- void vSetSpecies( const Eref& e, SpeciesId v );
- SpeciesId vGetSpecies( const Eref& e ) const;
+ void vSetSpecies( const Eref& e, SpeciesId v );
+ SpeciesId vGetSpecies( const Eref& e ) const;
- /**
- * Functions to examine and change class between Pool and BufPool.
- */
- void vSetIsBuffered( const Eref& e, bool v );
- bool vGetIsBuffered( const Eref& e) const;
+ /**
+ * Functions to examine and change class between Pool and BufPool.
+ */
+ void vSetIsBuffered( const Eref& e, bool v );
+ bool vGetIsBuffered( const Eref& e) const;
- //////////////////////////////////////////////////////////////////
- // Dest funcs. These too override virtual funcs in the Pool base
- // class.
- //////////////////////////////////////////////////////////////////
+ //////////////////////////////////////////////////////////////////
+ // Dest funcs. These too override virtual funcs in the Pool base
+ // class.
+ //////////////////////////////////////////////////////////////////
- void vHandleMolWt( const Eref& e, double v );
- void vProcess( const Eref& e, ProcPtr p );
- void vReinit( const Eref& e, ProcPtr p );
- void vReac( double A, double B );
- void vIncrement( double val );
- void vDecrement( double val );
- void vnIn( double val );
+ void vHandleMolWt( const Eref& e, double v );
+ void vProcess( const Eref& e, ProcPtr p );
+ void vReinit( const Eref& e, ProcPtr p );
+ void vReac( double A, double B );
+ void vIncrement( double val );
+ void vDecrement( double val );
+ void vnIn( double val );
- //////////////////////////////////////////////////////////////////
- // Novel Dest funcs not present in Pool base class.
- //////////////////////////////////////////////////////////////////
+ //////////////////////////////////////////////////////////////////
+ // Novel Dest funcs not present in Pool base class.
+ //////////////////////////////////////////////////////////////////
- //////////////////////////////////////////////////////////////////
- static const Cinfo* initCinfo();
- private:
- double n_; /// Number of molecules in pool
- double nInit_; /// initial number of molecules.
- double diffConst_; /// Diffusion constant
- double motorConst_; /// Motor transport constant
- double A_; /// Internal state variables, used only in explict mode
- double B_;
+ //////////////////////////////////////////////////////////////////
+ static const Cinfo* initCinfo();
+private:
+ double n_; /// Number of molecules in pool
+ double nInit_; /// initial number of molecules.
+ double diffConst_; /// Diffusion constant
+ double motorConst_; /// Motor transport constant
+ double A_; /// Internal state variables, used only in explict mode
+ double B_;
- /**
- * System wide identifier for all mol pools that are chemically
- * the same species.
- */
- unsigned int species_;
+ /**
+ * System wide identifier for all mol pools that are chemically
+ * the same species.
+ */
+ unsigned int species_;
};
#endif // _POOL_H
diff --git a/kinetics/PoolBase.cpp b/kinetics/PoolBase.cpp
index f1d7e0f4..b00153f4 100644
--- a/kinetics/PoolBase.cpp
+++ b/kinetics/PoolBase.cpp
@@ -18,201 +18,205 @@ const SpeciesId DefaultSpeciesId = 0;
const Cinfo* PoolBase::initCinfo()
{
- //////////////////////////////////////////////////////////////
- // Field Definitions
- //////////////////////////////////////////////////////////////
- static ElementValueFinfo< PoolBase, double > n(
- "n",
- "Number of molecules in pool",
- &PoolBase::setN,
- &PoolBase::getN
- );
-
- static ElementValueFinfo< PoolBase, double > nInit(
- "nInit",
- "Initial value of number of molecules in pool",
- &PoolBase::setNinit,
- &PoolBase::getNinit
- );
-
- static ElementValueFinfo< PoolBase, double > diffConst(
- "diffConst",
- "Diffusion constant of molecule",
- &PoolBase::setDiffConst,
- &PoolBase::getDiffConst
- );
-
- static ElementValueFinfo< PoolBase, double > motorConst(
- "motorConst",
- "Motor transport rate molecule. + is away from soma, - is "
- "towards soma. Only relevant for ZombiePool subclasses.",
- &PoolBase::setMotorConst,
- &PoolBase::getMotorConst
- );
-
- static ElementValueFinfo< PoolBase, double > conc(
- "conc",
- "Concentration of molecules in this pool",
- &PoolBase::setConc,
- &PoolBase::getConc
- );
-
- static ElementValueFinfo< PoolBase, double > concInit(
- "concInit",
- "Initial value of molecular concentration in pool",
- &PoolBase::setConcInit,
- &PoolBase::getConcInit
- );
-
- static ElementValueFinfo< PoolBase, double > volume(
- "volume",
- "Volume of compartment. Units are SI. "
- "Utility field, the actual volume info is "
- "stored on a volume mesh entry in the parent compartment."
- "This mapping is implicit: the parent compartment must be "
- "somewhere up the element tree, and must have matching mesh "
- "entries. If the compartment isn't"
- "available the volume is just taken as 1",
- &PoolBase::setVolume,
- &PoolBase::getVolume
- );
-
- static ElementValueFinfo< PoolBase, unsigned int > speciesId(
- "speciesId",
- "Species identifier for this mol pool. Eventually link to ontology.",
- &PoolBase::setSpecies,
- &PoolBase::getSpecies
- );
-
- static ElementValueFinfo< PoolBase, bool > isBuffered(
- "isBuffered",
- "Flag: True if Pool is buffered. "
- "In the case of Pool and BufPool the field can be assigned, to "
- "change the type of the Pool object to BufPool, or vice versa. "
- "None of the messages are affected. "
- "This object class flip can only be done in the non-zombified "
- "form of the Pool/BufPool. In Zombies it is read-only.",
- &PoolBase::setIsBuffered,
- &PoolBase::getIsBuffered
- );
-
- //////////////////////////////////////////////////////////////
- // MsgDest Definitions
- //////////////////////////////////////////////////////////////
- static DestFinfo process( "process",
- "Handles process call",
- new ProcOpFunc< PoolBase >( &PoolBase::process ) );
- static DestFinfo reinit( "reinit",
- "Handles reinit call",
- new ProcOpFunc< PoolBase >( &PoolBase::reinit ) );
-
- static DestFinfo reacDest( "reacDest",
- "Handles reaction input",
- new OpFunc2< PoolBase, double, double >( &PoolBase::reac )
- );
-
- static DestFinfo handleMolWt( "handleMolWt",
- "Separate finfo to assign molWt, and consequently diffusion const."
- "Should only be used in SharedMsg with species.",
- new EpFunc1< PoolBase, double >( &PoolBase::handleMolWt )
- );
- //////////////////////////////////////////////////////////////
- // MsgDest Definitions: These three are used for non-reaction
- // calculations involving algebraically defined rate terms.
- //////////////////////////////////////////////////////////////
- static DestFinfo increment( "increment",
- "Increments mol numbers by specified amount. Can be +ve or -ve",
- new OpFunc1< PoolBase, double >( &PoolBase::increment )
- );
-
- static DestFinfo decrement( "decrement",
- "Decrements mol numbers by specified amount. Can be +ve or -ve",
- new OpFunc1< PoolBase, double >( &PoolBase::decrement )
- );
-
- static DestFinfo nIn( "nIn",
- "Assigns the number of molecules in Pool to specified value",
- new OpFunc1< PoolBase, double >( &PoolBase::nIn )
- );
-
- //////////////////////////////////////////////////////////////
- // SrcFinfo Definitions
- //////////////////////////////////////////////////////////////
-
- static SrcFinfo1< double > nOut(
- "nOut",
- "Sends out # of molecules in pool on each timestep"
- );
-
- static SrcFinfo0 requestMolWt(
- "requestMolWt",
- "Requests Species object for mol wt"
- );
-
- //////////////////////////////////////////////////////////////
- // SharedMsg Definitions
- //////////////////////////////////////////////////////////////
- static Finfo* reacShared[] = {
- &reacDest, &nOut
- };
- static SharedFinfo reac( "reac",
- "Connects to reaction",
- reacShared, sizeof( reacShared ) / sizeof( const Finfo* )
- );
- static Finfo* procShared[] = {
- &process, &reinit
- };
- static SharedFinfo proc( "proc",
- "Shared message for process and reinit",
- procShared, sizeof( procShared ) / sizeof( const Finfo* )
- );
-
- static Finfo* speciesShared[] = {
- &requestMolWt, &handleMolWt
- };
-
- static SharedFinfo species( "species",
- "Shared message for connecting to species objects",
- speciesShared, sizeof( speciesShared ) / sizeof ( const Finfo* )
- );
-
- static Finfo* poolFinfos[] = {
- &n, // Value
- &nInit, // Value
- &diffConst, // Value
- &motorConst, // Value
- &conc, // Value
- &concInit, // Value
- &volume, // Readonly Value
- &speciesId, // Value
- &isBuffered, // Value
- &increment, // DestFinfo
- &decrement, // DestFinfo
+ //////////////////////////////////////////////////////////////
+ // Field Definitions
+ //////////////////////////////////////////////////////////////
+ static ElementValueFinfo< PoolBase, double > n(
+ "n",
+ "Number of molecules in pool",
+ &PoolBase::setN,
+ &PoolBase::getN
+ );
+
+ static ElementValueFinfo< PoolBase, double > nInit(
+ "nInit",
+ "Initial value of number of molecules in pool",
+ &PoolBase::setNinit,
+ &PoolBase::getNinit
+ );
+
+ static ElementValueFinfo< PoolBase, double > diffConst(
+ "diffConst",
+ "Diffusion constant of molecule",
+ &PoolBase::setDiffConst,
+ &PoolBase::getDiffConst
+ );
+
+ static ElementValueFinfo< PoolBase, double > motorConst(
+ "motorConst",
+ "Motor transport rate molecule. + is away from soma, - is "
+ "towards soma. Only relevant for ZombiePool subclasses.",
+ &PoolBase::setMotorConst,
+ &PoolBase::getMotorConst
+ );
+
+ static ElementValueFinfo< PoolBase, double > conc(
+ "conc",
+ "Concentration of molecules in this pool",
+ &PoolBase::setConc,
+ &PoolBase::getConc
+ );
+
+ static ElementValueFinfo< PoolBase, double > concInit(
+ "concInit",
+ "Initial value of molecular concentration in pool",
+ &PoolBase::setConcInit,
+ &PoolBase::getConcInit
+ );
+
+ static ElementValueFinfo< PoolBase, double > volume(
+ "volume",
+ "Volume of compartment. Units are SI. "
+ "Utility field, the actual volume info is "
+ "stored on a volume mesh entry in the parent compartment."
+ "This mapping is implicit: the parent compartment must be "
+ "somewhere up the element tree, and must have matching mesh "
+ "entries. If the compartment isn't"
+ "available the volume is just taken as 1",
+ &PoolBase::setVolume,
+ &PoolBase::getVolume
+ );
+
+ static ElementValueFinfo< PoolBase, unsigned int > speciesId(
+ "speciesId",
+ "Species identifier for this mol pool. Eventually link to ontology.",
+ &PoolBase::setSpecies,
+ &PoolBase::getSpecies
+ );
+
+ static ElementValueFinfo< PoolBase, bool > isBuffered(
+ "isBuffered",
+ "Flag: True if Pool is buffered. "
+ "In the case of Pool and BufPool the field can be assigned, to "
+ "change the type of the Pool object to BufPool, or vice versa. "
+ "None of the messages are affected. "
+ "This object class flip can only be done in the non-zombified "
+ "form of the Pool/BufPool. In Zombies it is read-only.",
+ &PoolBase::setIsBuffered,
+ &PoolBase::getIsBuffered
+ );
+
+ //////////////////////////////////////////////////////////////
+ // MsgDest Definitions
+ //////////////////////////////////////////////////////////////
+ static DestFinfo process( "process",
+ "Handles process call",
+ new ProcOpFunc< PoolBase >( &PoolBase::process ) );
+ static DestFinfo reinit( "reinit",
+ "Handles reinit call",
+ new ProcOpFunc< PoolBase >( &PoolBase::reinit ) );
+
+ static DestFinfo reacDest( "reacDest",
+ "Handles reaction input",
+ new OpFunc2< PoolBase, double, double >( &PoolBase::reac )
+ );
+
+ static DestFinfo handleMolWt( "handleMolWt",
+ "Separate finfo to assign molWt, and consequently diffusion const."
+ "Should only be used in SharedMsg with species.",
+ new EpFunc1< PoolBase, double >( &PoolBase::handleMolWt )
+ );
+ //////////////////////////////////////////////////////////////
+ // MsgDest Definitions: These three are used for non-reaction
+ // calculations involving algebraically defined rate terms.
+ //////////////////////////////////////////////////////////////
+ static DestFinfo increment( "increment",
+ "Increments mol numbers by specified amount. Can be +ve or -ve",
+ new OpFunc1< PoolBase, double >( &PoolBase::increment )
+ );
+
+ static DestFinfo decrement( "decrement",
+ "Decrements mol numbers by specified amount. Can be +ve or -ve",
+ new OpFunc1< PoolBase, double >( &PoolBase::decrement )
+ );
+
+ static DestFinfo nIn( "nIn",
+ "Assigns the number of molecules in Pool to specified value",
+ new OpFunc1< PoolBase, double >( &PoolBase::nIn )
+ );
+
+ //////////////////////////////////////////////////////////////
+ // SrcFinfo Definitions
+ //////////////////////////////////////////////////////////////
+
+ static SrcFinfo1< double > nOut(
+ "nOut",
+ "Sends out # of molecules in pool on each timestep"
+ );
+
+ static SrcFinfo0 requestMolWt(
+ "requestMolWt",
+ "Requests Species object for mol wt"
+ );
+
+ //////////////////////////////////////////////////////////////
+ // SharedMsg Definitions
+ //////////////////////////////////////////////////////////////
+ static Finfo* reacShared[] =
+ {
+ &reacDest, &nOut
+ };
+ static SharedFinfo reac( "reac",
+ "Connects to reaction",
+ reacShared, sizeof( reacShared ) / sizeof( const Finfo* )
+ );
+ static Finfo* procShared[] =
+ {
+ &process, &reinit
+ };
+ static SharedFinfo proc( "proc",
+ "Shared message for process and reinit",
+ procShared, sizeof( procShared ) / sizeof( const Finfo* )
+ );
+
+ static Finfo* speciesShared[] =
+ {
+ &requestMolWt, &handleMolWt
+ };
+
+ static SharedFinfo species( "species",
+ "Shared message for connecting to species objects",
+ speciesShared, sizeof( speciesShared ) / sizeof ( const Finfo* )
+ );
+
+ static Finfo* poolFinfos[] =
+ {
+ &n, // Value
+ &nInit, // Value
+ &diffConst, // Value
+ &motorConst, // Value
+ &conc, // Value
+ &concInit, // Value
+ &volume, // Readonly Value
+ &speciesId, // Value
+ &isBuffered, // Value
+ &increment, // DestFinfo
+ &decrement, // DestFinfo
&nIn, // DestFinfo
- &reac, // SharedFinfo
- &proc, // SharedFinfo
- &species, // SharedFinfo
- };
-
- static string doc[] =
- {
- "Name", "PoolBase",
- "Author", "Upi Bhalla",
- "Description", "Abstract base class for pools."
- };
- static ZeroSizeDinfo< int > dinfo;
- static Cinfo poolCinfo (
- "PoolBase",
- Neutral::initCinfo(),
- poolFinfos,
- sizeof( poolFinfos ) / sizeof ( Finfo* ),
- &dinfo,
- doc,
- sizeof( doc )/sizeof( string ),
- true // Ban creation as this is an abstract base class.
- );
-
- return &poolCinfo;
+ &reac, // SharedFinfo
+ &proc, // SharedFinfo
+ &species, // SharedFinfo
+ };
+
+ static string doc[] =
+ {
+ "Name", "PoolBase",
+ "Author", "Upi Bhalla",
+ "Description", "Abstract base class for pools."
+ };
+ static ZeroSizeDinfo< int > dinfo;
+ static Cinfo poolCinfo (
+ "PoolBase",
+ Neutral::initCinfo(),
+ poolFinfos,
+ sizeof( poolFinfos ) / sizeof ( Finfo* ),
+ &dinfo,
+ doc,
+ sizeof( doc )/sizeof( string ),
+ true // Ban creation as this is an abstract base class.
+ );
+
+ return &poolCinfo;
}
//////////////////////////////////////////////////////////////
@@ -222,7 +226,7 @@ static const Cinfo* poolCinfo = PoolBase::initCinfo();
//////////////////////////////////////////////////////////////
PoolBase::PoolBase()
- : concInit_( 0.0 )
+ : concInit_( 0.0 )
{;}
PoolBase::~PoolBase()
@@ -234,37 +238,37 @@ PoolBase::~PoolBase()
void PoolBase::process( const Eref& e, ProcPtr p )
{
- vProcess( e, p );
+ vProcess( e, p );
}
void PoolBase::reinit( const Eref& e, ProcPtr p )
{
- vReinit( e, p );
+ vReinit( e, p );
}
void PoolBase::increment( double val )
{
- vIncrement(val);
+ vIncrement(val);
}
void PoolBase::decrement( double val )
{
- vDecrement( val );
+ vDecrement( val );
}
void PoolBase::nIn( double val)
{
- vnIn(val);
+ vnIn(val);
}
void PoolBase::reac( double A, double B )
{
- vReac( A, B );
+ vReac( A, B );
}
void PoolBase::handleMolWt( const Eref& e, double v )
{
- vHandleMolWt( e, v );
+ vHandleMolWt( e, v );
}
//////////////////////////////////////////////////////////////
@@ -298,92 +302,92 @@ void PoolBase::vnIn( double val)
void PoolBase::setN( const Eref& e, double v )
{
- vSetN( e, v );
+ vSetN( e, v );
}
double PoolBase::getN( const Eref& e ) const
{
- return vGetN( e );
+ return vGetN( e );
}
void PoolBase::setNinit( const Eref& e, double v )
{
- concInit_ = v / ( NA * lookupVolumeFromMesh( e ) );
- vSetNinit( e, v );
+ concInit_ = v / ( NA * lookupVolumeFromMesh( e ) );
+ vSetNinit( e, v );
}
double PoolBase::getNinit( const Eref& e ) const
{
- return vGetNinit( e );
+ return vGetNinit( e );
}
// Conc is given in millimolar. Volume is in m^3
void PoolBase::setConc( const Eref& e, double c )
{
- vSetConc( e, c );
+ vSetConc( e, c );
}
// Returns conc in millimolar.
double PoolBase::getConc( const Eref& e ) const
{
- return vGetConc( e );
+ return vGetConc( e );
}
void PoolBase::setConcInit( const Eref& e, double c )
{
- concInit_ = c;
- vSetConcInit( e, c );
+ concInit_ = c;
+ vSetConcInit( e, c );
}
double PoolBase::vGetConcInit( const Eref& e ) const
{
- return concInit_;
+ return concInit_;
}
double PoolBase::getConcInit( const Eref& e ) const
{
- // return concInit_;
- return vGetConcInit( e );
+ // return concInit_;
+ return vGetConcInit( e );
}
void PoolBase::setDiffConst( const Eref& e, double v )
{
- vSetDiffConst( e, v );
+ vSetDiffConst( e, v );
}
double PoolBase::getDiffConst(const Eref& e ) const
{
- return vGetDiffConst( e );
+ return vGetDiffConst( e );
}
void PoolBase::setMotorConst( const Eref& e, double v )
{
- vSetMotorConst( e, v );
+ vSetMotorConst( e, v );
}
double PoolBase::getMotorConst(const Eref& e ) const
{
- return vGetMotorConst( e );
+ return vGetMotorConst( e );
}
void PoolBase::setVolume( const Eref& e, double v )
{
- vSetVolume( e, v );
+ vSetVolume( e, v );
}
double PoolBase::getVolume( const Eref& e ) const
{
- return vGetVolume( e );
+ return vGetVolume( e );
}
void PoolBase::setSpecies( const Eref& e, unsigned int v )
{
- vSetSpecies( e, v );
+ vSetSpecies( e, v );
}
unsigned int PoolBase::getSpecies( const Eref& e ) const
{
- return vGetSpecies( e );
+ return vGetSpecies( e );
}
/**
@@ -391,12 +395,12 @@ unsigned int PoolBase::getSpecies( const Eref& e ) const
*/
void PoolBase::setIsBuffered( const Eref& e, bool v )
{
- vSetIsBuffered( e, v );
+ vSetIsBuffered( e, v );
}
bool PoolBase::getIsBuffered( const Eref& e ) const
{
- return vGetIsBuffered( e );
+ return vGetIsBuffered( e );
}
//////////////////////////////////////////////////////////////
@@ -409,7 +413,7 @@ void PoolBase::vSetMotorConst( const Eref& e, double v )
double PoolBase::vGetMotorConst(const Eref& e ) const
{
- return 0.0;
+ return 0.0;
}
/// Dummy default function for most pool subclasses.
@@ -424,41 +428,43 @@ void PoolBase::vSetIsBuffered( const Eref& e, bool v )
//////////////////////////////////////////////////////////////
// static func
void PoolBase::zombify( Element* orig, const Cinfo* zClass,
- Id ksolve, Id dsolve )
+ Id ksolve, Id dsolve )
{
- if ( orig->cinfo() == zClass )
- return;
- unsigned int start = orig->localDataStart();
- unsigned int num = orig->numLocalData();
- if ( num == 0 )
- return;
- vector< unsigned int > species( num, 0 );
- vector< double > concInit( num, 0.0 );
- vector< double > diffConst( num, 0.0 );
- vector< double > motorConst( num, 0.0 );
- for ( unsigned int i = 0; i < num; ++i ) {
- Eref er( orig, i + start );
- const PoolBase* pb =
- reinterpret_cast< const PoolBase* >( er.data() );
- species[ i ] = pb->getSpecies( er );
- concInit[ i ] = pb->getConcInit( er );
- diffConst[ i ] = pb->getDiffConst( er );
- motorConst[ i ] = pb->getMotorConst( er );
- }
- orig->zombieSwap( zClass );
- for ( unsigned int i = 0; i < num; ++i ) {
- Eref er( orig, i + start );
- PoolBase* pb = reinterpret_cast< PoolBase* >( er.data() );
- pb->vSetSolver( ksolve, dsolve );
- pb->setSpecies( er, species[i] );
- pb->setConcInit( er, concInit[i] );
- pb->setDiffConst( er, diffConst[i] );
- pb->setMotorConst( er, motorConst[i] );
- }
+ if ( orig->cinfo() == zClass )
+ return;
+ unsigned int start = orig->localDataStart();
+ unsigned int num = orig->numLocalData();
+ if ( num == 0 )
+ return;
+ vector< unsigned int > species( num, 0 );
+ vector< double > concInit( num, 0.0 );
+ vector< double > diffConst( num, 0.0 );
+ vector< double > motorConst( num, 0.0 );
+ for ( unsigned int i = 0; i < num; ++i )
+ {
+ Eref er( orig, i + start );
+ const PoolBase* pb =
+ reinterpret_cast< const PoolBase* >( er.data() );
+ species[ i ] = pb->getSpecies( er );
+ concInit[ i ] = pb->getConcInit( er );
+ diffConst[ i ] = pb->getDiffConst( er );
+ motorConst[ i ] = pb->getMotorConst( er );
+ }
+ orig->zombieSwap( zClass );
+ for ( unsigned int i = 0; i < num; ++i )
+ {
+ Eref er( orig, i + start );
+ PoolBase* pb = reinterpret_cast< PoolBase* >( er.data() );
+ pb->vSetSolver( ksolve, dsolve );
+ pb->setSpecies( er, species[i] );
+ pb->setConcInit( er, concInit[i] );
+ pb->setDiffConst( er, diffConst[i] );
+ pb->setMotorConst( er, motorConst[i] );
+ }
}
// Virtual func: default does nothing.
void PoolBase::vSetSolver( Id ksolve, Id dsolve )
{
- ;
+ ;
}
diff --git a/kinetics/PoolBase.h b/kinetics/PoolBase.h
index b5aaa1b8..20ab0000 100644
--- a/kinetics/PoolBase.h
+++ b/kinetics/PoolBase.h
@@ -29,134 +29,134 @@ extern const SpeciesId DefaultSpeciesId;
*/
class PoolBase
{
- friend void testSyncArray( unsigned int size, unsigned int numThreads,
- unsigned int method );
- friend void checkVal( double time, const PoolBase* m, unsigned int size );
- friend void forceCheckVal( double time, Element* e, unsigned int size );
-
- public:
- PoolBase();
- virtual ~PoolBase();
-
- //////////////////////////////////////////////////////////////////
- // Field assignment stuff: Interface for the Cinfo, hence regular
- // funcs. These internally call the virtual funcs that do the real
- // work.
- //////////////////////////////////////////////////////////////////
- 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;
- void setMotorConst( const Eref& e, double v );
- double getMotorConst( const Eref& e ) const;
-
- void setConc( const Eref& e, double v );
- double getConc( const Eref& e ) const;
- void setConcInit( const Eref& e, double v );
- double getConcInit( const Eref& e ) const;
-
- /**
- * Volume is usually volume, but we also permit areal density
- * This is obtained by looking up the corresponding spatial mesh
- * entry in the parent compartment. If the message isn't set then
- * it defaults to 1.0.
- */
- void setVolume( const Eref& e, double v );
- double getVolume( const Eref& e ) const;
-
- void setSpecies( const Eref& e, SpeciesId v );
- SpeciesId getSpecies( const Eref& e ) const;
- /**
- * Functions to examine and change class between Pool and BufPool.
- */
- void setIsBuffered( const Eref& e, bool v );
- bool getIsBuffered( const Eref& e ) const;
-
- //////////////////////////////////////////////////////////////////
- // Here are the inner virtual funcs for fields.
- // All these are pure virtual
- //////////////////////////////////////////////////////////////////
-
- virtual void vSetN( const Eref& e, double v ) = 0;
- virtual double vGetN( const Eref& e ) const = 0;
- virtual void vSetNinit( const Eref& e, double v ) = 0;
- virtual double vGetNinit( const Eref& e ) const = 0;
- virtual void vSetDiffConst( const Eref& e, double v ) = 0;
- virtual double vGetDiffConst( const Eref& e ) const = 0;
- virtual void vSetMotorConst( const Eref& e, double v );
- virtual double vGetMotorConst( const Eref& e ) const;
-
- virtual void vSetConc( const Eref& e, double v ) = 0;
- virtual double vGetConc( const Eref& e ) const = 0;
- virtual void vSetConcInit( const Eref& e, double v ) = 0;
- virtual double vGetConcInit( const Eref& e ) const;
- virtual double vGetVolume( const Eref& e ) const = 0;
- virtual void vSetVolume( const Eref& e, double v ) = 0;
- virtual void vSetSpecies( const Eref& e, SpeciesId v ) = 0;
- virtual SpeciesId vGetSpecies( const Eref& e ) const = 0;
- /// I put in a default empty function for vSetIsBuffered.
- virtual void vSetIsBuffered( const Eref& e, bool v );
- virtual bool vGetIsBuffered( const Eref& e) const = 0;
- /**
- * Assign whatever info is needed by the zombie based on the
- * solver Element. Encapsulates some unpleasant field extraction,
- * casting, and assignment. Default version of this function does
- * nothing.
- */
- virtual void vSetSolver( Id ksolve, Id dsolve );
-
- //////////////////////////////////////////////////////////////////
- /**
- * zombify is the base function for conversion between pool
- * subclasses. This can be overridden, but should work for most
- * things. This takes the original Element, and without touching
- * its messaging, replaces it with a new data object of the
- * specified zClass. It does the best it can with conversion of
- * fields. Typically needs to be followed by rescheduling and
- * possibly a class-specific function for assigning further
- * zombie fields outside the ken of the PoolBase.
- * The 'solver' argument specifies which objects handle the solver
- * for this conversion. For the Pool this is either or both of
- * a kinetic solver /ksolve/ and a diffusion solver /dsolve/.
- * The term zombie arises because this operation was originally
- * carried out to strip an object of independent function, and
- * replace it with a solver-controlled facsimile.
- */
- static void zombify( Element* original, const Cinfo* zClass,
- Id ksolve, Id dsolve );
-
- //////////////////////////////////////////////////////////////////
- // Dest funcs
- //////////////////////////////////////////////////////////////////
- void process( const Eref& e, ProcPtr p );
- void reinit( const Eref& e, ProcPtr p );
- void reac( double A, double B );
- void handleMolWt( const Eref& e, double v );
- void increment( double val );
- void decrement( double val );
- void nIn( double val );
-
- //////////////////////////////////////////////////////////////////
- // Virtual Dest funcs. Most of these have a generic do-nothing
- // function here, as most of the derived classes don't need to
- // do anything.
- //////////////////////////////////////////////////////////////////
- virtual void vProcess( const Eref& e, ProcPtr p );
- virtual void vReinit( const Eref& e, ProcPtr p );
- virtual void vReac( double A, double B );
- virtual void vHandleMolWt( const Eref& e, double v);
- virtual void vIncrement( double val );
- virtual void vDecrement( double val );
- virtual void vnIn( double val );
-
- //////////////////////////////////////////////////////////////////
- static const Cinfo* initCinfo();
- private:
- double concInit_; /// Initial concentration.
- // We don't store the conc here as this is computed on the fly
- // by derived classes. But the PoolBase::concInit is authoritative.
+ friend void testSyncArray( unsigned int size, unsigned int numThreads,
+ unsigned int method );
+ friend void checkVal( double time, const PoolBase* m, unsigned int size );
+ friend void forceCheckVal( double time, Element* e, unsigned int size );
+
+public:
+ PoolBase();
+ virtual ~PoolBase();
+
+ //////////////////////////////////////////////////////////////////
+ // Field assignment stuff: Interface for the Cinfo, hence regular
+ // funcs. These internally call the virtual funcs that do the real
+ // work.
+ //////////////////////////////////////////////////////////////////
+ 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;
+ void setMotorConst( const Eref& e, double v );
+ double getMotorConst( const Eref& e ) const;
+
+ void setConc( const Eref& e, double v );
+ double getConc( const Eref& e ) const;
+ void setConcInit( const Eref& e, double v );
+ double getConcInit( const Eref& e ) const;
+
+ /**
+ * Volume is usually volume, but we also permit areal density
+ * This is obtained by looking up the corresponding spatial mesh
+ * entry in the parent compartment. If the message isn't set then
+ * it defaults to 1.0.
+ */
+ void setVolume( const Eref& e, double v );
+ double getVolume( const Eref& e ) const;
+
+ void setSpecies( const Eref& e, SpeciesId v );
+ SpeciesId getSpecies( const Eref& e ) const;
+ /**
+ * Functions to examine and change class between Pool and BufPool.
+ */
+ void setIsBuffered( const Eref& e, bool v );
+ bool getIsBuffered( const Eref& e ) const;
+
+ //////////////////////////////////////////////////////////////////
+ // Here are the inner virtual funcs for fields.
+ // All these are pure virtual
+ //////////////////////////////////////////////////////////////////
+
+ virtual void vSetN( const Eref& e, double v ) = 0;
+ virtual double vGetN( const Eref& e ) const = 0;
+ virtual void vSetNinit( const Eref& e, double v ) = 0;
+ virtual double vGetNinit( const Eref& e ) const = 0;
+ virtual void vSetDiffConst( const Eref& e, double v ) = 0;
+ virtual double vGetDiffConst( const Eref& e ) const = 0;
+ virtual void vSetMotorConst( const Eref& e, double v );
+ virtual double vGetMotorConst( const Eref& e ) const;
+
+ virtual void vSetConc( const Eref& e, double v ) = 0;
+ virtual double vGetConc( const Eref& e ) const = 0;
+ virtual void vSetConcInit( const Eref& e, double v ) = 0;
+ virtual double vGetConcInit( const Eref& e ) const;
+ virtual double vGetVolume( const Eref& e ) const = 0;
+ virtual void vSetVolume( const Eref& e, double v ) = 0;
+ virtual void vSetSpecies( const Eref& e, SpeciesId v ) = 0;
+ virtual SpeciesId vGetSpecies( const Eref& e ) const = 0;
+ /// I put in a default empty function for vSetIsBuffered.
+ virtual void vSetIsBuffered( const Eref& e, bool v );
+ virtual bool vGetIsBuffered( const Eref& e) const = 0;
+ /**
+ * Assign whatever info is needed by the zombie based on the
+ * solver Element. Encapsulates some unpleasant field extraction,
+ * casting, and assignment. Default version of this function does
+ * nothing.
+ */
+ virtual void vSetSolver( Id ksolve, Id dsolve );
+
+ //////////////////////////////////////////////////////////////////
+ /**
+ * zombify is the base function for conversion between pool
+ * subclasses. This can be overridden, but should work for most
+ * things. This takes the original Element, and without touching
+ * its messaging, replaces it with a new data object of the
+ * specified zClass. It does the best it can with conversion of
+ * fields. Typically needs to be followed by rescheduling and
+ * possibly a class-specific function for assigning further
+ * zombie fields outside the ken of the PoolBase.
+ * The 'solver' argument specifies which objects handle the solver
+ * for this conversion. For the Pool this is either or both of
+ * a kinetic solver /ksolve/ and a diffusion solver /dsolve/.
+ * The term zombie arises because this operation was originally
+ * carried out to strip an object of independent function, and
+ * replace it with a solver-controlled facsimile.
+ */
+ static void zombify( Element* original, const Cinfo* zClass,
+ Id ksolve, Id dsolve );
+
+ //////////////////////////////////////////////////////////////////
+ // Dest funcs
+ //////////////////////////////////////////////////////////////////
+ void process( const Eref& e, ProcPtr p );
+ void reinit( const Eref& e, ProcPtr p );
+ void reac( double A, double B );
+ void handleMolWt( const Eref& e, double v );
+ void increment( double val );
+ void decrement( double val );
+ void nIn( double val );
+
+ //////////////////////////////////////////////////////////////////
+ // Virtual Dest funcs. Most of these have a generic do-nothing
+ // function here, as most of the derived classes don't need to
+ // do anything.
+ //////////////////////////////////////////////////////////////////
+ virtual void vProcess( const Eref& e, ProcPtr p );
+ virtual void vReinit( const Eref& e, ProcPtr p );
+ virtual void vReac( double A, double B );
+ virtual void vHandleMolWt( const Eref& e, double v);
+ virtual void vIncrement( double val );
+ virtual void vDecrement( double val );
+ virtual void vnIn( double val );
+
+ //////////////////////////////////////////////////////////////////
+ static const Cinfo* initCinfo();
+private:
+ double concInit_; /// Initial concentration.
+ // We don't store the conc here as this is computed on the fly
+ // by derived classes. But the PoolBase::concInit is authoritative.
};
#endif // _POOL_BASE_H
diff --git a/kinetics/ReadKkit.cpp b/kinetics/ReadKkit.cpp
index 8172ae90..1a2e0776 100644
--- a/kinetics/ReadKkit.cpp
+++ b/kinetics/ReadKkit.cpp
@@ -228,13 +228,13 @@ void setMethod( Shell* s, Id mgr, double simdt, double plotdt,
string simpath2 = mgr.path() + "/##[ISA=StimulusTable]," +
mgr.path() + "/##[ISA=PulseGen]";
string m = lower( method );
-
+ /*
if ( m == "ksolve" || m =="gsl" || m == "gssa" || m == "gsolve" ||
m == "gillespie" || m == "stochastic" )
{
cout << " Warning: Default solver set is Exponential Euler. To set \'gsl\' or \'gssa\' solver use function mooseaddChemSolver(modelpath,\'solverType\')"<<"\n";
}
- /*
+
if ( m == "rk4" ) {
cout << "Warning, not yet implemented. Using rk5 instead\n";
@@ -312,7 +312,7 @@ Id ReadKkit::read(
assert(kinetics != Id());
Id cInfo = s->doCreate( "Annotator", basePath_, "info", 1 );
assert( cInfo != Id() );
- Field< string > ::set(cInfo, "solver", method);
+ Field< string > ::set(cInfo, "solver", "ee");
Field< double > ::set(cInfo, "runtime", maxtime_);
s->doReinit();
return mgr;
@@ -578,6 +578,8 @@ void ReadKkit::objdump( const vector< string >& args)
assignArgs( tableMap_, args );
else if ( args[1] == "stim" )
assignArgs( stimMap_, args );
+ else if ( args[1] == "kchan" )
+ assignArgs( chanMap_, args );
}
void ReadKkit::call( const vector< string >& args)
@@ -1185,9 +1187,11 @@ Id ReadKkit::buildChan( const vector< string >& args )
Id pa = shell_->doFind( head ).id;
assert( pa != Id() );
- cout << "Warning: Kchan not yet supported in MOOSE, creating dummy:\n"
- << " " << clean << "\n";
- Id chan = shell_->doCreate( "Neutral", pa, tail, 1 );
+ // cout << "Warning: Kchan not yet supported in MOOSE, creating dummy:\n" << " " << clean << "\n";
+ //
+ double permeability = atof( args[ chanMap_["perm"] ].c_str() );
+ Id chan = shell_->doCreate( "ConcChan", pa, tail, 1 );
+ Field< double >::set( chan, "permeability", permeability );
assert( chan != Id() );
string chanPath = clean.substr( 10 );
chanIds_[ chanPath ] = chan;
@@ -1346,16 +1350,14 @@ void ReadKkit::addmsg( const vector< string >& args)
if ( args[3] == "REAC" ) {
if ( args[4] == "A" && args[5] == "B" ) {
- // Ignore kchans
if ( chanIds_.find( src ) != chanIds_.end() )
- ; // found a kchan, do nothing
+ innerAddMsg( src, chanIds_, "in", dest, poolIds_, "reac");
else
innerAddMsg( src, reacIds_, "sub", dest, poolIds_, "reac");
}
else if ( args[4] == "B" && args[5] == "A" ) {
- // Ignore kchans
if ( chanIds_.find( src ) != chanIds_.end() )
- ; // found a kchan, do nothing
+ innerAddMsg( src, chanIds_, "out", dest, poolIds_, "reac");
else
// dest pool is product of src reac
innerAddMsg( src, reacIds_, "prd", dest, poolIds_, "reac");
@@ -1387,6 +1389,10 @@ void ReadKkit::addmsg( const vector< string >& args)
else
innerAddMsg( src, mmEnzIds_, "prd", dest, poolIds_, "reac" );
}
+ else if ( args[3] == "NUMCHAN" ) { // Msg from chan pool to concchan
+ if ( chanIds_.find( dest ) != chanIds_.end() )
+ innerAddMsg( src, poolIds_, "nOut", dest, chanIds_, "setNumChan");
+ }
else if ( args[3] == "PLOT" ) { // Time-course output for pool
string head;
string temp;
diff --git a/kinetics/ReadKkit.h b/kinetics/ReadKkit.h
index 8e171fc6..1dae27bf 100644
--- a/kinetics/ReadKkit.h
+++ b/kinetics/ReadKkit.h
@@ -217,6 +217,7 @@ class ReadKkit
map< string, int > groupMap_;
map< string, int > tableMap_;
map< string, int > stimMap_;
+ map< string, int > chanMap_;
map< string, Id > poolIds_;
map< string, Id > reacIds_;
map< string, Id > enzIds_;
diff --git a/kinetics/WriteKkit.cpp b/kinetics/WriteKkit.cpp
index c32b1fa0..3c3bc890 100644
--- a/kinetics/WriteKkit.cpp
+++ b/kinetics/WriteKkit.cpp
@@ -26,255 +26,268 @@
void writeHeader( ofstream& fout,
- double simdt, double plotdt, double maxtime, double defaultVol)
+ double simdt, double plotdt, double maxtime, double defaultVol)
{
- time_t rawtime;
- time( &rawtime );
-
- fout <<
- "//genesis\n"
- "// kkit Version 11 flat dumpfile\n\n";
- fout << "// Saved on " << ctime( &rawtime ) << endl;
- fout << "include kkit {argv 1}\n";
- fout << "FASTDT = " << simdt << endl;
- fout << "SIMDT = " << simdt << endl;
- fout << "CONTROLDT = " << plotdt << endl;
- fout << "PLOTDT = " << plotdt << endl;
- fout << "MAXTIME = " << maxtime << endl;
- fout << "TRANSIENT_TIME = 2\n"
- "VARIABLE_DT_FLAG = 0\n";
- fout << "DEFAULT_VOL = " << defaultVol << endl;
- fout << "VERSION = 11.0\n"
- "setfield /file/modpath value ~/scripts/modules\n"
- "kparms\n\n";
-
- fout <<
- "initdump -version 3 -ignoreorphans 1\n"
- "simobjdump table input output alloced step_mode stepsize x y z\n"
- "simobjdump xtree path script namemode sizescale\n"
- "simobjdump xcoredraw xmin xmax ymin ymax\n"
- "simobjdump xtext editable\n"
- "simobjdump xgraph xmin xmax ymin ymax overlay\n"
- "simobjdump xplot pixflags script fg ysquish do_slope wy\n"
- "simobjdump group xtree_fg_req xtree_textfg_req plotfield expanded movealone \\\n"
- " link savename file version md5sum mod_save_flag x y z\n"
- "simobjdump geometry size dim shape outside xtree_fg_req xtree_textfg_req x y z\n"
- "simobjdump kpool DiffConst CoInit Co n nInit mwt nMin vol slave_enable \\\n"
- " geomname xtree_fg_req xtree_textfg_req x y z\n"
- "simobjdump kreac kf kb notes xtree_fg_req xtree_textfg_req x y z\n"
- "simobjdump kenz CoComplexInit CoComplex nComplexInit nComplex vol k1 k2 k3 \\\n"
- " keepconc usecomplex notes xtree_fg_req xtree_textfg_req link x y z\n"
- "simobjdump stim level1 width1 delay1 level2 width2 delay2 baselevel trig_time \\\n"
- " trig_mode notes xtree_fg_req xtree_textfg_req is_running x y z\n"
- "simobjdump xtab input output alloced step_mode stepsize notes editfunc \\\n"
- " xtree_fg_req xtree_textfg_req baselevel last_x last_y is_running x y z\n"
- "simobjdump kchan perm gmax Vm is_active use_nernst notewriteReacs xtree_fg_req \\\n"
- " xtree_textfg_req x y z\n"
- "simobjdump transport input output alloced step_mode stepsize dt delay clock \\\n"
- " kf xtree_fg_req xtree_textfg_req x y z\n"
- "simobjdump proto x y z\n";
- //"simundump geometry /kinetics/geometry 0 1.6667e-19 3 sphere \"\" white black 0 0 0\n\n";
+ time_t rawtime;
+ time( &rawtime );
+
+ fout <<
+ "//genesis\n"
+ "// kkit Version 11 flat dumpfile\n\n";
+ fout << "// Saved on " << ctime( &rawtime ) << endl;
+ fout << "include kkit {argv 1}\n";
+ fout << "FASTDT = " << simdt << endl;
+ fout << "SIMDT = " << simdt << endl;
+ fout << "CONTROLDT = " << plotdt << endl;
+ fout << "PLOTDT = " << plotdt << endl;
+ fout << "MAXTIME = " << maxtime << endl;
+ fout << "TRANSIENT_TIME = 2\n"
+ "VARIABLE_DT_FLAG = 0\n";
+ fout << "DEFAULT_VOL = " << defaultVol << endl;
+ fout << "VERSION = 11.0\n"
+ "setfield /file/modpath value ~/scripts/modules\n"
+ "kparms\n\n";
+
+ fout <<
+ "initdump -version 3 -ignoreorphans 1\n"
+ "simobjdump table input output alloced step_mode stepsize x y z\n"
+ "simobjdump xtree path script namemode sizescale\n"
+ "simobjdump xcoredraw xmin xmax ymin ymax\n"
+ "simobjdump xtext editable\n"
+ "simobjdump xgraph xmin xmax ymin ymax overlay\n"
+ "simobjdump xplot pixflags script fg ysquish do_slope wy\n"
+ "simobjdump group xtree_fg_req xtree_textfg_req plotfield expanded movealone \\\n"
+ " link savename file version md5sum mod_save_flag x y z\n"
+ "simobjdump geometry size dim shape outside xtree_fg_req xtree_textfg_req x y z\n"
+ "simobjdump kpool DiffConst CoInit Co n nInit mwt nMin vol slave_enable \\\n"
+ " geomname xtree_fg_req xtree_textfg_req x y z\n"
+ "simobjdump kreac kf kb notes xtree_fg_req xtree_textfg_req x y z\n"
+ "simobjdump kenz CoComplexInit CoComplex nComplexInit nComplex vol k1 k2 k3 \\\n"
+ " keepconc usecomplex notes xtree_fg_req xtree_textfg_req link x y z\n"
+ "simobjdump stim level1 width1 delay1 level2 width2 delay2 baselevel trig_time \\\n"
+ " trig_mode notes xtree_fg_req xtree_textfg_req is_running x y z\n"
+ "simobjdump xtab input output alloced step_mode stepsize notes editfunc \\\n"
+ " xtree_fg_req xtree_textfg_req baselevel last_x last_y is_running x y z\n"
+ "simobjdump kchan perm gmax Vm is_active use_nernst notewriteReacs xtree_fg_req \\\n"
+ " xtree_textfg_req x y z\n"
+ "simobjdump transport input output alloced step_mode stepsize dt delay clock \\\n"
+ " kf xtree_fg_req xtree_textfg_req x y z\n"
+ "simobjdump proto x y z\n";
+ //"simundump geometry /kinetics/geometry 0 1.6667e-19 3 sphere \"\" white black 0 0 0\n\n";
}
string trimPath(Id id, Id comptid)
{
- string msgpath = Field <string> :: get(id,"path");
- ObjId compartment(msgpath);
- string path1;
- cout << " trimpath " << msgpath <<endl;
- // triming the string compartment Level
- while( Field<string>::get(compartment,"className") != "CubeMesh"
- && Field<string>::get(compartment,"className") != "CylMesh"
- )
- compartment = Field<ObjId> :: get(compartment, "parent");
- string cmpt = Field < string > :: get(compartment,"name");
- if (cmpt != "kinetics")
- { std::size_t found = msgpath.find(cmpt);
- if (found !=std::string::npos)
- path1 = msgpath.substr(found-1,msgpath.length());
- else
- {
- path1 = msgpath;
-
- }
- }
- else
- { std :: size_t found = msgpath.find(cmpt);
- if (found !=std::string::npos)
- { string pathC = msgpath.substr(found-1,msgpath.length());
- std :: size_t slash = pathC.find('/',found);
- if (slash !=std::string::npos)
- path1 = pathC.substr(slash,pathC.length());
- else
- { path1 = msgpath;
- }
- }
- }
- cout << " path " << path1 << endl;
- return path1;
+ string msgpath = Field <string> :: get(id,"path");
+ ObjId compartment(msgpath);
+ string path1;
+ cout << " trimpath " << msgpath <<endl;
+ // triming the string compartment Level
+ while( Field<string>::get(compartment,"className") != "CubeMesh"
+ && Field<string>::get(compartment,"className") != "CylMesh"
+ )
+ compartment = Field<ObjId> :: get(compartment, "parent");
+ string cmpt = Field < string > :: get(compartment,"name");
+ if (cmpt != "kinetics")
+ {
+ std::size_t found = msgpath.find(cmpt);
+ if (found !=std::string::npos)
+ path1 = msgpath.substr(found-1,msgpath.length());
+ else
+ {
+ path1 = msgpath;
+ }
+ }
+ else
+ {
+ std :: size_t found = msgpath.find(cmpt);
+ if (found !=std::string::npos)
+ {
+ string pathC = msgpath.substr(found-1,msgpath.length());
+ std :: size_t slash = pathC.find('/',found);
+ if (slash !=std::string::npos)
+ path1 = pathC.substr(slash,pathC.length());
+ else
+ {
+ path1 = msgpath;
+ }
+ }
+ }
+ cout << " path " << path1 << endl;
+ return path1;
}
Id getEnzCplx( Id id )
{
- vector < Id > srct = LookupField <string,vector < Id> >::get(id, "neighbors","cplxDest");
- return srct[0];
+ vector < Id > srct = LookupField <string,vector < Id> >::get(id, "neighbors","cplxDest");
+ return srct[0];
}
Id getEnzMol( Id id )
{
- vector < Id > srct = LookupField <string,vector < Id> >::get(id, "neighbors","enzDest");
- return srct[0];
+ vector < Id > srct = LookupField <string,vector < Id> >::get(id, "neighbors","enzDest");
+ return srct[0];
}
void writeEnz( ofstream& fout, Id id,
- string colour, string textcolour,
- double x, double y, Id comptid )
+ string colour, string textcolour,
+ double x, double y, Id comptid )
{
- string path = id.path();
- string comptname = Field < string > :: get(comptid,"name");
- string poolpath = trimPath(id,comptid);
-
-
- double k1 = 0;
- double k2 = 0;
- double k3 = 0;
- double nInit = 0;
- double concInit = 0;
- double n = 0;
- double conc = 0;
- Id enzMol = getEnzMol( id );
- assert( enzMol != Id() );
- double vol = Field< double >::get( enzMol, "volume" ) * NA * 1e-3;
- unsigned int isMichaelisMenten = 0;
- string enzClass = Field < string > :: get(id,"className");
- if (enzClass == "ZombieMMenz" or enzClass == "MMenz")
- { k1 = Field < double > :: get (id,"numKm");
- k3 = Field < double > :: get (id,"kcat");
- k2 = 4.0*k3;
- k1 = (k2 + k3) / k1;
- isMichaelisMenten = 1;
- }
- else if (enzClass == "ZombieEnz" or enzClass == "Enz")
- { k1 = Field< double >::get( id, "k1" );
- k2 = Field< double >::get( id, "k2" );
- k3 = Field< double >::get( id, "k3" );
- Id cplx = getEnzCplx( id );
- assert( cplx != Id() );
- nInit = Field< double >::get( cplx, "nInit" );
- n = Field< double >::get( cplx, "n" );
- concInit = Field< double >::get( cplx, "concInit" );
- conc = Field< double >::get( cplx, "conc" );
- }
- fout << "simundump kenz /kinetics" << poolpath << " 0 " <<
- concInit << " " <<
- conc << " " <<
- nInit << " " <<
- n << " " <<
- vol << " " <<
- k1 << " " <<
- k2 << " " <<
- k3 << " " <<
- 0 << " " <<
- isMichaelisMenten << " " <<
- "\"\"" << " " <<
- colour << " " << textcolour << " \"\"" <<
- " " << x << " " << y << " 0\n";
+ string path = id.path();
+ string comptname = Field < string > :: get(comptid,"name");
+ string poolpath = trimPath(id,comptid);
+
+
+ double k1 = 0;
+ double k2 = 0;
+ double k3 = 0;
+ double nInit = 0;
+ double concInit = 0;
+ double n = 0;
+ double conc = 0;
+ Id enzMol = getEnzMol( id );
+ assert( enzMol != Id() );
+ double vol = Field< double >::get( enzMol, "volume" ) * NA * 1e-3;
+ unsigned int isMichaelisMenten = 0;
+ string enzClass = Field < string > :: get(id,"className");
+ if (enzClass == "ZombieMMenz" or enzClass == "MMenz")
+ {
+ k1 = Field < double > :: get (id,"numKm");
+ k3 = Field < double > :: get (id,"kcat");
+ k2 = 4.0*k3;
+ k1 = (k2 + k3) / k1;
+ isMichaelisMenten = 1;
+ }
+ else if (enzClass == "ZombieEnz" or enzClass == "Enz")
+ {
+ k1 = Field< double >::get( id, "k1" );
+ k2 = Field< double >::get( id, "k2" );
+ k3 = Field< double >::get( id, "k3" );
+ Id cplx = getEnzCplx( id );
+ assert( cplx != Id() );
+ nInit = Field< double >::get( cplx, "nInit" );
+ n = Field< double >::get( cplx, "n" );
+ concInit = Field< double >::get( cplx, "concInit" );
+ conc = Field< double >::get( cplx, "conc" );
+ }
+ fout << "simundump kenz /kinetics" << poolpath << " 0 " <<
+ concInit << " " <<
+ conc << " " <<
+ nInit << " " <<
+ n << " " <<
+ vol << " " <<
+ k1 << " " <<
+ k2 << " " <<
+ k3 << " " <<
+ 0 << " " <<
+ isMichaelisMenten << " " <<
+ "\"\"" << " " <<
+ colour << " " << textcolour << " \"\"" <<
+ " " << x << " " << y << " 0\n";
}
void writeReac( ofstream& fout, Id id,
- string colour, string textcolour,
- double x, double y, Id comptid )
+ string colour, string textcolour,
+ double x, double y, Id comptid )
{
- string reacPar = Field <string> :: get(comptid,"name");
- string reacname = Field<string> :: get(id, "name");
- double kf = Field< double >::get( id, "numKf" );
- double kb = Field< double >::get( id, "numKb" );
-
- unsigned int numSub =
- Field< unsigned int >::get( id, "numSubstrates" );
- unsigned int numPrd =
- Field< unsigned int >::get( id, "numProducts" );
- fout << "simundump kreac /kinetics" << trimPath(id,comptid) << " 0 " <<
- kf << " " << kb << " \"\" " <<
- colour << " " << textcolour << " " << x << " " << y << " 0\n";
+ string reacPar = Field <string> :: get(comptid,"name");
+ string reacname = Field<string> :: get(id, "name");
+ double kf = Field< double >::get( id, "numKf" );
+ double kb = Field< double >::get( id, "numKb" );
+
+ unsigned int numSub =
+ Field< unsigned int >::get( id, "numSubstrates" );
+ unsigned int numPrd =
+ Field< unsigned int >::get( id, "numProducts" );
+ fout << "simundump kreac /kinetics" << trimPath(id,comptid) << " 0 " <<
+ kf << " " << kb << " \"\" " <<
+ colour << " " << textcolour << " " << x << " " << y << " 0\n";
}
unsigned int getSlaveEnable( Id id )
{
- static const Finfo* setNinitFinfo =
- PoolBase::initCinfo()->findFinfo( "set_nInit" );
- static const Finfo* setConcInitFinfo =
- PoolBase::initCinfo()->findFinfo( "set_concInit" );
- unsigned int ret = 0;
- vector< Id > src;
- if ( id.element()->cinfo()->isA( "BufPool" ) ) {
- if ( id.element()->getNeighbors( src, setConcInitFinfo ) > 0 ) {
- ret = 2;
- } else if ( id.element()->getNeighbors( src, setNinitFinfo ) > 0 ){
- ret = 4;
- }
- } else {
- return 0;
- }
- if ( ret == 0 )
- return 4; // Just simple buffered molecule
- if ( src[0].element()->cinfo()->isA( "StimulusTable" ) )
- return ret; // Following a table, this is fine.
+ static const Finfo* setNinitFinfo =
+ PoolBase::initCinfo()->findFinfo( "set_nInit" );
+ static const Finfo* setConcInitFinfo =
+ PoolBase::initCinfo()->findFinfo( "set_concInit" );
+ unsigned int ret = 0;
+ vector< Id > src;
+ if ( id.element()->cinfo()->isA( "BufPool" ) )
+ {
+ if ( id.element()->getNeighbors( src, setConcInitFinfo ) > 0 )
+ {
+ ret = 2;
+ }
+ else if ( id.element()->getNeighbors( src, setNinitFinfo ) > 0 )
+ {
+ ret = 4;
+ }
+ }
+ else
+ {
+ return 0;
+ }
+ if ( ret == 0 )
+ return 4; // Just simple buffered molecule
+ if ( src[0].element()->cinfo()->isA( "StimulusTable" ) )
+ return ret; // Following a table, this is fine.
- // Fallback: I have no idea what sent it the input, assume it is legit.
- return ret;
+ // Fallback: I have no idea what sent it the input, assume it is legit.
+ return ret;
}
void writePool( ofstream& fout, Id id,
- string colour, string textcolour,
- double x, double y, Id comptid,int comptIndex )
+ string colour, string textcolour,
+ double x, double y, Id comptid,int comptIndex )
{
- string poolPar = Field <string> :: get(comptid,"name");
- string pooltype = Field < string > :: get(id,"className");
- double diffConst = Field< double >::get( id, "diffConst" );
- double concInit = Field< double >::get( id, "concInit" );
- //double conc = Field< double >::get( id, "conc" );
- double nInit = Field< double >::get( id, "nInit" );
- //double n = Field< double >::get( id, "n" );
- double volume = Field< double >::get( id, "volume" );
- string geometry;
- stringstream geometryTemp ;
- unsigned int slave_enable = 0;
- if (pooltype == "BufPool" or pooltype == "ZombieBufPool")
- { vector< Id > children = Field< vector< Id > >::get( id, "children" );
- if (children.size() == 0)
- slave_enable = 4;
- for ( vector< Id >::iterator i = children.begin(); i != children.end(); ++i )
- { string funcpath = Field <string> :: get(*i,"path");
- string clsname = Field <string> :: get(*i,"className");
- if (clsname == "Function" or clsname == "ZombieFunction")
- slave_enable = 0;
- else
- slave_enable = 4;
+ string poolPar = Field <string> :: get(comptid,"name");
+ string pooltype = Field < string > :: get(id,"className");
+ double diffConst = Field< double >::get( id, "diffConst" );
+ double concInit = Field< double >::get( id, "concInit" );
+ //double conc = Field< double >::get( id, "conc" );
+ double nInit = Field< double >::get( id, "nInit" );
+ //double n = Field< double >::get( id, "n" );
+ double volume = Field< double >::get( id, "volume" );
+ string geometry;
+ stringstream geometryTemp ;
+ unsigned int slave_enable = 0;
+ if (pooltype == "BufPool" or pooltype == "ZombieBufPool")
+ {
+ vector< Id > children = Field< vector< Id > >::get( id, "children" );
+ if (children.size() == 0)
+ slave_enable = 4;
+ for ( vector< Id >::iterator i = children.begin(); i != children.end(); ++i )
+ {
+ string funcpath = Field <string> :: get(*i,"path");
+ string clsname = Field <string> :: get(*i,"className");
+ if (clsname == "Function" or clsname == "ZombieFunction")
+ slave_enable = 0;
+ else
+ slave_enable = 4;
- }
- }
- if (comptIndex > 0)
- geometryTemp << "/geometry[" << comptIndex <<"]";
- else
- geometryTemp << "/geometry";
-
- // simobjdump kpool DiffConst CoInit Co n nInit mwt nMin vol slave_enable
-
- fout << "simundump kpool /kinetics" << trimPath(id,comptid) << " 0 " <<
- diffConst << " " <<
- 0 << " " <<
- 0 << " " <<
- 0 << " " <<
- nInit << " " <<
- 0 << " " << 0 << " " << // mwt, nMin
- volume * NA * 1e-3 << " " << // volscale
- slave_enable << //GENESIS FIELD HERE.
- " /kinetics"<< geometryTemp.str() << " " <<
- colour << " " << textcolour << " " << x << " " << y << " 0\n";
+ }
+ }
+ if (comptIndex > 0)
+ geometryTemp << "/geometry[" << comptIndex <<"]";
+ else
+ geometryTemp << "/geometry";
+
+ // simobjdump kpool DiffConst CoInit Co n nInit mwt nMin vol slave_enable
+
+ fout << "simundump kpool /kinetics" << trimPath(id,comptid) << " 0 " <<
+ diffConst << " " <<
+ 0 << " " <<
+ 0 << " " <<
+ 0 << " " <<
+ nInit << " " <<
+ 0 << " " << 0 << " " << // mwt, nMin
+ volume * NA * 1e-3 << " " << // volscale
+ slave_enable << //GENESIS FIELD HERE.
+ " /kinetics"<< geometryTemp.str() << " " <<
+ colour << " " << textcolour << " " << x << " " << y << " 0\n";
}
void writePlot( ofstream& fout, Id id,
- string colour, string textcolour,
- double x, double y )
+ string colour, string textcolour,
+ double x, double y )
{
string path = id.path();
size_t pos = path.find( "/graphs" );
@@ -291,143 +304,148 @@ void writePlot( ofstream& fout, Id id,
void writeGui( ofstream& fout )
{
- fout << "simundump xgraph /graphs/conc1 0 0 99 0.001 0.999 0\n"
- "simundump xgraph /graphs/conc2 0 0 100 0 1 0\n"
- "simundump xgraph /moregraphs/conc3 0 0 100 0 1 0\n"
- "simundump xgraph /moregraphs/conc4 0 0 100 0 1 0\n"
- "simundump xcoredraw /edit/draw 0 -6 4 -2 6\n"
- "simundump xtree /edit/draw/tree 0 \\\n"
- " /kinetics/#[],/kinetics/#[]/#[],/kinetics/#[]/#[]/#[][TYPE!=proto],/kinetics/#[]/#[]/#[][TYPE!=linkinfo]/##[] \"edit_elm.D <v>; drag_from_edit.w <d> <S> <x> <y> <z>\" auto 0.6\n"
- "simundump xtext /file/notes 0 1\n";
+ fout << "simundump xgraph /graphs/conc1 0 0 99 0.001 0.999 0\n"
+ "simundump xgraph /graphs/conc2 0 0 100 0 1 0\n"
+ "simundump xgraph /moregraphs/conc3 0 0 100 0 1 0\n"
+ "simundump xgraph /moregraphs/conc4 0 0 100 0 1 0\n"
+ "simundump xcoredraw /edit/draw 0 -6 4 -2 6\n"
+ "simundump xtree /edit/draw/tree 0 \\\n"
+ " /kinetics/#[],/kinetics/#[]/#[],/kinetics/#[]/#[]/#[][TYPE!=proto],/kinetics/#[]/#[]/#[][TYPE!=linkinfo]/##[] \"edit_elm.D <v>; drag_from_edit.w <d> <S> <x> <y> <z>\" auto 0.6\n"
+ "simundump xtext /file/notes 0 1\n";
}
void writeFooter( ofstream& fout )
{
- fout << "\nenddump\n";
- fout << "complete_loading\n";
+ fout << "\nenddump\n";
+ fout << "complete_loading\n";
}
void storeMMenzMsgs( Id enz, vector< string >& msgs, Id comptid )
{
- Id enzparentId = Field <ObjId> :: get(enz,"parent");
- string enzPar = Field <string> :: get(enzparentId,"name");
- string enzName = Field<string> :: get(enz,"name");
-
- vector < Id > srct = LookupField <string,vector < Id> >::get(enz, "neighbors","sub");
- for (vector <Id> :: iterator rsub = srct.begin();rsub != srct.end();rsub++)
- {
- string s = "addmsg /kinetics" + trimPath(*rsub, comptid) + " /kinetics" + trimPath(enz, comptid) + " SUBSTRATE n";
- msgs.push_back( s );
- s = "addmsg /kinetics" + trimPath(enz, comptid) + " /kinetics" + trimPath( *rsub, comptid ) + " REAC sA B";
- msgs.push_back( s );
- }
- vector < Id > prct = LookupField <string,vector < Id> >::get(enz, "neighbors","prd");
- for (vector <Id> :: iterator rprd = prct.begin();rprd != prct.end();rprd++)
- {
- string s = "addmsg /kinetics" + trimPath( enz, comptid ) + " /kinetics" + trimPath(*rprd, comptid) + " MM_PRD pA";
- msgs.push_back( s );
- }
- vector < Id > enzC = LookupField <string,vector < Id> >::get(enz, "neighbors","enzDest");
- for (vector <Id> :: iterator enzCl = enzC.begin();enzCl != enzC.end();enzCl++)
- {
- string s = "addmsg /kinetics" + trimPath( *enzCl, comptid ) + " /kinetics" + trimPath(enz, comptid) + " ENZYME n";
- msgs.push_back( s );
- }
+ Id enzparentId = Field <ObjId> :: get(enz,"parent");
+ string enzPar = Field <string> :: get(enzparentId,"name");
+ string enzName = Field<string> :: get(enz,"name");
+
+ vector < Id > srct = LookupField <string,vector < Id> >::get(enz, "neighbors","sub");
+ for (vector <Id> :: iterator rsub = srct.begin(); rsub != srct.end(); rsub++)
+ {
+ string s = "addmsg /kinetics" + trimPath(*rsub, comptid) + " /kinetics" + trimPath(enz, comptid) + " SUBSTRATE n";
+ msgs.push_back( s );
+ s = "addmsg /kinetics" + trimPath(enz, comptid) + " /kinetics" + trimPath( *rsub, comptid ) + " REAC sA B";
+ msgs.push_back( s );
+ }
+ vector < Id > prct = LookupField <string,vector < Id> >::get(enz, "neighbors","prd");
+ for (vector <Id> :: iterator rprd = prct.begin(); rprd != prct.end(); rprd++)
+ {
+ string s = "addmsg /kinetics" + trimPath( enz, comptid ) + " /kinetics" + trimPath(*rprd, comptid) + " MM_PRD pA";
+ msgs.push_back( s );
+ }
+ vector < Id > enzC = LookupField <string,vector < Id> >::get(enz, "neighbors","enzDest");
+ for (vector <Id> :: iterator enzCl = enzC.begin(); enzCl != enzC.end(); enzCl++)
+ {
+ string s = "addmsg /kinetics" + trimPath( *enzCl, comptid ) + " /kinetics" + trimPath(enz, comptid) + " ENZYME n";
+ msgs.push_back( s );
+ }
}
void storeCplxEnzMsgs( Id enz, vector< string >& msgs, Id comptid )
-{ Id enzparentId = Field <ObjId> :: get(enz,"parent");
- string enzPar = Field <string> :: get(enzparentId,"name");
- string enzName = Field<string> :: get(enz,"name");
-
- vector < Id > srct = LookupField <string,vector < Id> >::get(enz, "neighbors","sub");
- for (vector <Id> :: iterator rsub = srct.begin();rsub != srct.end();rsub++)
- {
- string s = "addmsg /kinetics" + trimPath(*rsub, comptid) + " /kinetics" + trimPath(enz, comptid) + " SUBSTRATE n";
- msgs.push_back( s );
- s = "addmsg /kinetics" + trimPath(enz, comptid) + " /kinetics" + trimPath( *rsub, comptid ) + " REAC sA B";
- msgs.push_back( s );
- }
- vector < Id > prct = LookupField <string,vector < Id> >::get(enz, "neighbors","prd");
- for (vector <Id> :: iterator rprd = prct.begin();rprd != prct.end();rprd++)
- {
- string s = "addmsg /kinetics" + trimPath( enz, comptid ) + " /kinetics" + trimPath(*rprd, comptid) + " MM_PRD pA";
- msgs.push_back( s );
- }
- vector < Id > enzC = LookupField <string,vector < Id> >::get(enz, "neighbors","enzOut");
- for (vector <Id> :: iterator enzCl = enzC.begin();enzCl != enzC.end();enzCl++)
- {
- string s = "addmsg /kinetics" + trimPath( *enzCl, comptid ) + " /kinetics" + trimPath(enz, comptid) + " ENZYME n";
- msgs.push_back( s );
- s = "addmsg /kinetics" + trimPath( enz, comptid ) + " /kinetics" + trimPath(*enzCl, comptid) + " REAC eA B";
- msgs.push_back( s );
- }
+{
+ Id enzparentId = Field <ObjId> :: get(enz,"parent");
+ string enzPar = Field <string> :: get(enzparentId,"name");
+ string enzName = Field<string> :: get(enz,"name");
+
+ vector < Id > srct = LookupField <string,vector < Id> >::get(enz, "neighbors","sub");
+ for (vector <Id> :: iterator rsub = srct.begin(); rsub != srct.end(); rsub++)
+ {
+ string s = "addmsg /kinetics" + trimPath(*rsub, comptid) + " /kinetics" + trimPath(enz, comptid) + " SUBSTRATE n";
+ msgs.push_back( s );
+ s = "addmsg /kinetics" + trimPath(enz, comptid) + " /kinetics" + trimPath( *rsub, comptid ) + " REAC sA B";
+ msgs.push_back( s );
+ }
+ vector < Id > prct = LookupField <string,vector < Id> >::get(enz, "neighbors","prd");
+ for (vector <Id> :: iterator rprd = prct.begin(); rprd != prct.end(); rprd++)
+ {
+ string s = "addmsg /kinetics" + trimPath( enz, comptid ) + " /kinetics" + trimPath(*rprd, comptid) + " MM_PRD pA";
+ msgs.push_back( s );
+ }
+ vector < Id > enzC = LookupField <string,vector < Id> >::get(enz, "neighbors","enzOut");
+ for (vector <Id> :: iterator enzCl = enzC.begin(); enzCl != enzC.end(); enzCl++)
+ {
+ string s = "addmsg /kinetics" + trimPath( *enzCl, comptid ) + " /kinetics" + trimPath(enz, comptid) + " ENZYME n";
+ msgs.push_back( s );
+ s = "addmsg /kinetics" + trimPath( enz, comptid ) + " /kinetics" + trimPath(*enzCl, comptid) + " REAC eA B";
+ msgs.push_back( s );
+ }
}
void storeEnzMsgs( Id enz, vector< string >& msgs, Id comptid )
{
- string enzClass = Field < string > :: get(enz,"className");
- if (enzClass == "ZombieMMenz" or enzClass == "MMenz")
- storeMMenzMsgs(enz, msgs, comptid);
- else
- storeCplxEnzMsgs( enz, msgs, comptid );
+ string enzClass = Field < string > :: get(enz,"className");
+ if (enzClass == "ZombieMMenz" or enzClass == "MMenz")
+ storeMMenzMsgs(enz, msgs, comptid);
+ else
+ storeCplxEnzMsgs( enz, msgs, comptid );
}
void storeReacMsgs( Id reac, vector< string >& msgs, Id comptid )
{
- vector < Id > srct = LookupField <string,vector < Id> >::get(reac, "neighbors","sub");
- for (vector <Id> :: iterator rsub = srct.begin();rsub != srct.end();rsub++)
- { string s = "addmsg /kinetics" + trimPath(*rsub, comptid) + " /kinetics" + trimPath(reac, comptid) + " SUBSTRATE n";
- msgs.push_back( s );
- s = "addmsg /kinetics" + trimPath(reac, comptid) + " /kinetics" + trimPath( *rsub, comptid ) + " REAC A B";
- msgs.push_back( s );
- }
- vector < Id > prct = LookupField <string,vector < Id> >::get(reac, "neighbors","prd");
- for (vector <Id> :: iterator rprd = prct.begin();rprd != prct.end();rprd++)
- { string rpath = Field <string> :: get(reac,"path");
- string cpath = Field <string> :: get(comptid,"path");
- string prdPath = Field <string> :: get(*rprd,"path");
- string s = "addmsg /kinetics" + trimPath( *rprd, comptid ) + " /kinetics" + trimPath(reac, comptid) + " PRODUCT n";
- msgs.push_back( s );
- s = "addmsg /kinetics" + trimPath(reac, comptid) + " /kinetics" + trimPath( *rprd,comptid ) + " REAC B A";
- msgs.push_back( s );
- }
+ vector < Id > srct = LookupField <string,vector < Id> >::get(reac, "neighbors","sub");
+ for (vector <Id> :: iterator rsub = srct.begin(); rsub != srct.end(); rsub++)
+ {
+ string s = "addmsg /kinetics" + trimPath(*rsub, comptid) + " /kinetics" + trimPath(reac, comptid) + " SUBSTRATE n";
+ msgs.push_back( s );
+ s = "addmsg /kinetics" + trimPath(reac, comptid) + " /kinetics" + trimPath( *rsub, comptid ) + " REAC A B";
+ msgs.push_back( s );
+ }
+ vector < Id > prct = LookupField <string,vector < Id> >::get(reac, "neighbors","prd");
+ for (vector <Id> :: iterator rprd = prct.begin(); rprd != prct.end(); rprd++)
+ {
+ string rpath = Field <string> :: get(reac,"path");
+ string cpath = Field <string> :: get(comptid,"path");
+ string prdPath = Field <string> :: get(*rprd,"path");
+ string s = "addmsg /kinetics" + trimPath( *rprd, comptid ) + " /kinetics" + trimPath(reac, comptid) + " PRODUCT n";
+ msgs.push_back( s );
+ s = "addmsg /kinetics" + trimPath(reac, comptid) + " /kinetics" + trimPath( *rprd,comptid ) + " REAC B A";
+ msgs.push_back( s );
+ }
}
void storeFunctionMsgs( Id func, vector< string >& msgs,map < double, pair<Id, int> > & compt_vol )
{
- // Get the msg sources into this Function object.
- ObjId poolPath = Neutral::parent( func.eref() );
- double poolvol = Field < double > :: get(poolPath,"Volume");
- Id poolParentId = compt_vol[poolvol].first;
- string poolParent = Field <string> :: get(compt_vol[poolvol].first,"name");
- Id xi(func.value()+1);
- vector < Id > func_input = LookupField <string,vector < Id> >::get(xi, "neighbors","input");
-
- for (vector <Id> :: iterator funcIp = func_input.begin();funcIp != func_input.end();funcIp++)
- { string funcIp_path = Field < string > :: get(*funcIp,"path");
- double vol = Field < double > :: get(*funcIp,"Volume");
- Id parentId = compt_vol[vol].first;
- string parentname = Field <string> :: get(parentId,"name");
- string s = "addmsg /kinetics" + trimPath(*funcIp, parentId)+ " /kinetics" + trimPath(poolPath,poolParentId) +
- " SUMTOTAL n nInit";
- msgs.push_back(s);
- }
+ // Get the msg sources into this Function object.
+ ObjId poolPath = Neutral::parent( func.eref() );
+ double poolvol = Field < double > :: get(poolPath,"Volume");
+ Id poolParentId = compt_vol[poolvol].first;
+ string poolParent = Field <string> :: get(compt_vol[poolvol].first,"name");
+ Id xi(func.value()+1);
+ vector < Id > func_input = LookupField <string,vector < Id> >::get(xi, "neighbors","input");
+
+ for (vector <Id> :: iterator funcIp = func_input.begin(); funcIp != func_input.end(); funcIp++)
+ {
+ string funcIp_path = Field < string > :: get(*funcIp,"path");
+ double vol = Field < double > :: get(*funcIp,"Volume");
+ Id parentId = compt_vol[vol].first;
+ string parentname = Field <string> :: get(parentId,"name");
+ string s = "addmsg /kinetics" + trimPath(*funcIp, parentId)+ " /kinetics" + trimPath(poolPath,poolParentId) +
+ " SUMTOTAL n nInit";
+ msgs.push_back(s);
+ }
}
void storePlotMsgs( Id tab, vector< string >& msgs, Id pool, string bg, Id comptid)
-{ string tabPath = tab.path();
- string poolPath = Field <string> :: get(pool,"path");
- string poolName = Field <string> :: get(pool,"name");
-
- size_t pos = tabPath.find( "/graphs" );
- if ( pos == string::npos )
- pos = tabPath.find( "/moregraphs" );
- assert( pos != string::npos );
- tabPath = tabPath.substr( pos );
- string s = "addmsg /kinetics" + trimPath( poolPath, comptid) + " " + tabPath +
- " PLOT Co *" + poolName + " *" + bg;
- msgs.push_back( s );
+{
+ string tabPath = tab.path();
+ string poolPath = Field <string> :: get(pool,"path");
+ string poolName = Field <string> :: get(pool,"name");
+
+ size_t pos = tabPath.find( "/graphs" );
+ if ( pos == string::npos )
+ pos = tabPath.find( "/moregraphs" );
+ assert( pos != string::npos );
+ tabPath = tabPath.substr( pos );
+ string s = "addmsg /kinetics" + trimPath( poolPath, comptid) + " " + tabPath +
+ " PLOT Co *" + poolName + " *" + bg;
+ msgs.push_back( s );
}
/**
@@ -436,52 +454,54 @@ void storePlotMsgs( Id tab, vector< string >& msgs, Id pool, string bg, Id compt
*/
double estimateSimTimes( double& simDt, double& plotDt )
{
- double runTime = Field< double >::get( Id( 1 ), "runTime" );
- if ( runTime <= 0 )
- runTime = 100.0;
- vector< double > dts =
- Field< vector< double> >::get( Id( 1 ), "dts" );
-
- simDt = dts[11];
- plotDt = dts[18];
- cout << "estimatesimtimes" << simDt << plotDt;
- if ( plotDt <= 0 )
- plotDt = runTime / 200.0;
- if ( simDt == 0 )
- simDt = 0.01;
- if ( simDt > plotDt )
- simDt = plotDt / 100;
-
- return runTime;
+ double runTime = Field< double >::get( Id( 1 ), "runTime" );
+ if ( runTime <= 0 )
+ runTime = 100.0;
+ vector< double > dts =
+ Field< vector< double> >::get( Id( 1 ), "dts" );
+
+ simDt = dts[11];
+ plotDt = dts[18];
+ cout << "estimatesimtimes" << simDt << plotDt;
+ if ( plotDt <= 0 )
+ plotDt = runTime / 200.0;
+ if ( simDt == 0 )
+ simDt = 0.01;
+ if ( simDt > plotDt )
+ simDt = plotDt / 100;
+
+ return runTime;
}
/// Returns an estimate of the default volume used in the model.
double estimateDefaultVol( Id model )
{
- vector< Id > children =
- Field< vector< Id > >::get( model, "children" );
- vector< double > vols;
- double maxVol = 0;
- for ( vector< Id >::iterator i = children.begin();
- i != children.end(); ++i ) {
- if ( i->element()->cinfo()->isA( "ChemCompt" ) ) {
- double v = Field< double >::get( *i, "volume" );
- if ( i->element()->getName() == "kinetics" )
- return v;
- vols.push_back( v );
- if ( maxVol < v )
- maxVol = v;
- }
- }
- if ( maxVol > 0 )
- return maxVol;
- return 1.0e-15;
+ vector< Id > children =
+ Field< vector< Id > >::get( model, "children" );
+ vector< double > vols;
+ double maxVol = 0;
+ for ( vector< Id >::iterator i = children.begin();
+ i != children.end(); ++i )
+ {
+ if ( i->element()->cinfo()->isA( "ChemCompt" ) )
+ {
+ double v = Field< double >::get( *i, "volume" );
+ if ( i->element()->getName() == "kinetics" )
+ return v;
+ vols.push_back( v );
+ if ( maxVol < v )
+ maxVol = v;
+ }
+ }
+ if ( maxVol > 0 )
+ return maxVol;
+ return 1.0e-15;
}
void writeMsgs( ofstream& fout, const vector< string >& msgs )
{
- for ( vector< string >::const_iterator i = msgs.begin();
- i != msgs.end(); ++i )
- fout << *i << endl;
+ for ( vector< string >::const_iterator i = msgs.begin();
+ i != msgs.end(); ++i )
+ fout << *i << endl;
}
void writeGroup(ofstream& fout,Id model)
{
@@ -489,7 +509,7 @@ void writeGroup(ofstream& fout,Id model)
int x = 10;
int y = 20;
int num = wildcardFind( model.path() + "/##[TYPE=Neutral]", group );
- for ( vector< ObjId >::iterator itr = group.begin(); itr != group.end();itr++)
+ for ( vector< ObjId >::iterator itr = group.begin(); itr != group.end(); itr++)
{
string path = Field<string>::get(*itr,"path");
size_t pos = path.find( "/kinetics" );
@@ -497,149 +517,158 @@ void writeGroup(ofstream& fout,Id model)
{
path = path.substr( pos );
fout << "simundump group " << path << " 0 " <<
- "blue" << " " << "green" << " x 0 0 \"\" defaultfile \\\n";
+ "blue" << " " << "green" << " x 0 0 \"\" defaultfile \\\n";
fout << " defaultfile.g 0 0 0 " << x << " " << y << " 0\n";
}
}
}
void writeKkit( Id model, const string& fname )
-{ ofstream fout( fname.c_str(), ios::out );
- vector< ObjId > chemCompt;
- vector< string > msgs;
- double simDt;
- double plotDt;
-
- double runTime = estimateSimTimes( simDt, plotDt );
- double defaultVol = estimateDefaultVol( model );
- writeHeader( fout, simDt, plotDt, runTime, defaultVol );
- string bg = "cyan";
- string fg = "black";
- double x = 0;
- double y = 0;
-
- map < double, pair<Id, int> > compt_vol;
-
- unsigned int num = wildcardFind( model.path() + "/##[ISA=ChemCompt]", chemCompt );
- if ( num == 0 ) {
- cout << "Warning: writeKkit:: No model found on " << model <<
- endl;
- return;
- }
- for ( vector< ObjId >::iterator itr = chemCompt.begin(); itr != chemCompt.end();itr++)
- {
- vector < unsigned int>dims;
- unsigned int dims_size;
- dims_size = 1;
- unsigned index = 0;
- string comptPath = Field<string>::get(*itr,"path");
- string comptname = Field<string>::get(*itr,"name");
- if (comptname != "kinetics")
- {
- fout << "simundump group /kinetics/" << comptname << " 0 " <<
- "blue" << " " << "green" << " x 0 0 \"\" defaultfile \\\n";
- fout << " defaultfile.g 0 0 0 " << rand() % 10 + 1 << " " << rand() % 10 + 1 << " 0\n";
- }
- double size = Field<double>::get(ObjId(*itr,index),"Volume");
- unsigned int ndim = Field<unsigned int>::get(ObjId(*itr,index),"NumDimensions");
- ostringstream geometry;
- int vecIndex = itr-chemCompt.begin();
- if (vecIndex > 0)
- geometry << "simundump geometry /kinetics" << "/geometry[" << vecIndex <<"] 0 " << size << " " << ndim << " sphere " <<" \"\" white black 0 0 0\n";
- else
- geometry << "simundump geometry /kinetics" << "/geometry 0 " << size << " " << ndim << " sphere " <<" \"\" white black 0 0 0\n";
- fout << geometry.str();
- compt_vol.insert(make_pair(size,make_pair(*itr,vecIndex)));
- } // compartmentclose
- writeGroup(fout, model);
- map<double, pair<Id, int> >::iterator compt;
- for (compt = compt_vol.begin(); compt != compt_vol.end(); compt++)
- {
- string comptPath = Field<string>::get(compt->second.first,"path");
- // Species
- vector< ObjId > Compt_spe;
- wildcardFind(comptPath+"/##[ISA=PoolBase]",Compt_spe);
- int species_size = 1;
- string objname;
- for (vector <ObjId> :: iterator itrp = Compt_spe.begin();itrp != Compt_spe.end();itrp++)
- { string path = Field <string> :: get (*itrp,"path");
- Id enzPoolparent = Field <ObjId> :: get(*itrp,"parent");
- string enzpoolClass = Field <string> :: get(enzPoolparent,"className");
- if (enzpoolClass != "ZombieEnz" or enzpoolClass != "Enz")
- { Id annotaId( path+"/info");
- if ( annotaId != Id() )
- { double x = Field <double> :: get(annotaId,"x");
- double y = Field <double> :: get(annotaId,"y");
- string fg = Field <string> :: get(annotaId,"textColor");
- string bg = Field <string> :: get(annotaId,"color");
- writePool(fout, *itrp,bg,fg,x,y,compt->second.first,compt->second.second);
- }
- }
- } //species is closed
- vector< ObjId > Compt_Func;
- wildcardFind(comptPath+"/##[ISA=Function]",Compt_Func);
- for (vector <ObjId> :: iterator itrF= Compt_Func.begin();itrF != Compt_Func.end();itrF++)
- { storeFunctionMsgs( *itrF, msgs,compt_vol);
- }
- // Reaction
- vector< ObjId > Compt_Reac;
- wildcardFind(comptPath+"/##[ISA=ReacBase]",Compt_Reac);
- for (vector <ObjId> :: iterator itrR= Compt_Reac.begin();itrR != Compt_Reac.end();itrR++)
- {
- string path = Field<string> :: get(*itrR,"path");
- Id annotaId( path+"/info");
- string noteClass = Field<string> :: get(annotaId,"className");
- string notes;
- double x = Field <double> :: get(annotaId,"x");
- double y = Field <double> :: get(annotaId,"y");
- string fg = Field <string> :: get(annotaId,"textColor");
- string bg = Field <string> :: get(annotaId,"color");
- writeReac( fout, *itrR, bg, fg, x, y, compt->second.first);
- storeReacMsgs( *itrR, msgs, compt->second.first );
- }// reaction
- vector< ObjId > Compt_Enz;
- wildcardFind(comptPath+"/##[ISA=EnzBase]",Compt_Enz);
- for (vector <ObjId> :: iterator itrE= Compt_Enz.begin();itrE != Compt_Enz.end();itrE++)
- { string path = Field<string> :: get(*itrE,"path");
- Id annotaId( path+"/info");
- string noteClass = Field<string> :: get(annotaId,"className");
- string notes;
- double x = Field <double> :: get(annotaId,"x");
- double y = Field <double> :: get(annotaId,"y");
- string fg = Field <string> :: get(annotaId,"textColor");
- string bg = Field <string> :: get(annotaId,"color");
- writeEnz( fout, *itrE, bg, fg, x, y, compt->second.first);
- storeEnzMsgs( *itrE, msgs, compt->second.first);
- }// reaction
-
- } //compatment loop
- writeGui ( fout);
-
- /* Table */
-
- vector< ObjId > table;
- wildcardFind(model.path()+"/##[ISA=Table2]",table);
- for (vector <ObjId> :: iterator itrT= table.begin();itrT != table.end();itrT++)
- { string tabPath = Field <string> :: get(*itrT,"path");
- vector < Id > tabSrc = LookupField <string,vector < Id> >::get(*itrT, "neighbors","requestOut");
- for (vector <Id> :: iterator tabItem= tabSrc.begin();tabItem != tabSrc.end();tabItem++)
- { string path = Field <string> :: get(*tabItem,"path");
- double vol = Field < double> :: get (*tabItem,"Volume");
- //Trying to find the compartment name via volume
- //otherwise if we go via parent, sometimes it might
- // get groupname so maped compartment Id and volume
-
- Id parentId = compt_vol[vol].first;
- string parentname = Field <string> :: get(parentId,"name");
- Id annotaId(path+"/info");
- double x = Field <double> :: get(annotaId,"x");
- double y = Field <double> :: get(annotaId,"y");
- string bg = Field <string> :: get(annotaId,"textColor");
- string fg = Field <string> :: get(annotaId,"color");
- writePlot( fout, *itrT, bg, fg, x, y );
- storePlotMsgs( *itrT, msgs,*tabItem,fg, parentId);
+{
+ ofstream fout( fname.c_str(), ios::out );
+ vector< ObjId > chemCompt;
+ vector< string > msgs;
+ double simDt;
+ double plotDt;
+
+ double runTime = estimateSimTimes( simDt, plotDt );
+ double defaultVol = estimateDefaultVol( model );
+ writeHeader( fout, simDt, plotDt, runTime, defaultVol );
+ string bg = "cyan";
+ string fg = "black";
+ double x = 0;
+ double y = 0;
+
+ map < double, pair<Id, int> > compt_vol;
+
+ unsigned int num = wildcardFind( model.path() + "/##[ISA=ChemCompt]", chemCompt );
+ if ( num == 0 )
+ {
+ cout << "Warning: writeKkit:: No model found on " << model <<
+ endl;
+ return;
+ }
+ for ( vector< ObjId >::iterator itr = chemCompt.begin(); itr != chemCompt.end(); itr++)
+ {
+ vector < unsigned int>dims;
+ unsigned int dims_size;
+ dims_size = 1;
+ unsigned index = 0;
+ string comptPath = Field<string>::get(*itr,"path");
+ string comptname = Field<string>::get(*itr,"name");
+ if (comptname != "kinetics")
+ {
+ fout << "simundump group /kinetics/" << comptname << " 0 " <<
+ "blue" << " " << "green" << " x 0 0 \"\" defaultfile \\\n";
+ fout << " defaultfile.g 0 0 0 " << rand() % 10 + 1 << " " << rand() % 10 + 1 << " 0\n";
+ }
+ double size = Field<double>::get(ObjId(*itr,index),"Volume");
+ unsigned int ndim = Field<unsigned int>::get(ObjId(*itr,index),"NumDimensions");
+ ostringstream geometry;
+ int vecIndex = itr-chemCompt.begin();
+ if (vecIndex > 0)
+ geometry << "simundump geometry /kinetics" << "/geometry[" << vecIndex <<"] 0 " << size << " " << ndim << " sphere " <<" \"\" white black 0 0 0\n";
+ else
+ geometry << "simundump geometry /kinetics" << "/geometry 0 " << size << " " << ndim << " sphere " <<" \"\" white black 0 0 0\n";
+ fout << geometry.str();
+ compt_vol.insert(make_pair(size,make_pair(*itr,vecIndex)));
+ } // compartmentclose
+ writeGroup(fout, model);
+ map<double, pair<Id, int> >::iterator compt;
+ for (compt = compt_vol.begin(); compt != compt_vol.end(); compt++)
+ {
+ string comptPath = Field<string>::get(compt->second.first,"path");
+ // Species
+ vector< ObjId > Compt_spe;
+ wildcardFind(comptPath+"/##[ISA=PoolBase]",Compt_spe);
+ int species_size = 1;
+ string objname;
+ for (vector <ObjId> :: iterator itrp = Compt_spe.begin(); itrp != Compt_spe.end(); itrp++)
+ {
+ string path = Field <string> :: get (*itrp,"path");
+ Id enzPoolparent = Field <ObjId> :: get(*itrp,"parent");
+ string enzpoolClass = Field <string> :: get(enzPoolparent,"className");
+ if (enzpoolClass != "ZombieEnz" or enzpoolClass != "Enz")
+ {
+ Id annotaId( path+"/info");
+ if ( annotaId != Id() )
+ {
+ double x = Field <double> :: get(annotaId,"x");
+ double y = Field <double> :: get(annotaId,"y");
+ string fg = Field <string> :: get(annotaId,"textColor");
+ string bg = Field <string> :: get(annotaId,"color");
+ writePool(fout, *itrp,bg,fg,x,y,compt->second.first,compt->second.second);
+ }
+ }
+ } //species is closed
+ vector< ObjId > Compt_Func;
+ wildcardFind(comptPath+"/##[ISA=Function]",Compt_Func);
+ for (vector <ObjId> :: iterator itrF= Compt_Func.begin(); itrF != Compt_Func.end(); itrF++)
+ {
+ storeFunctionMsgs( *itrF, msgs,compt_vol);
+ }
+ // Reaction
+ vector< ObjId > Compt_Reac;
+ wildcardFind(comptPath+"/##[ISA=ReacBase]",Compt_Reac);
+ for (vector <ObjId> :: iterator itrR= Compt_Reac.begin(); itrR != Compt_Reac.end(); itrR++)
+ {
+ string path = Field<string> :: get(*itrR,"path");
+ Id annotaId( path+"/info");
+ string noteClass = Field<string> :: get(annotaId,"className");
+ string notes;
+ double x = Field <double> :: get(annotaId,"x");
+ double y = Field <double> :: get(annotaId,"y");
+ string fg = Field <string> :: get(annotaId,"textColor");
+ string bg = Field <string> :: get(annotaId,"color");
+ writeReac( fout, *itrR, bg, fg, x, y, compt->second.first);
+ storeReacMsgs( *itrR, msgs, compt->second.first );
+ }// reaction
+ vector< ObjId > Compt_Enz;
+ wildcardFind(comptPath+"/##[ISA=EnzBase]",Compt_Enz);
+ for (vector <ObjId> :: iterator itrE= Compt_Enz.begin(); itrE != Compt_Enz.end(); itrE++)
+ {
+ string path = Field<string> :: get(*itrE,"path");
+ Id annotaId( path+"/info");
+ string noteClass = Field<string> :: get(annotaId,"className");
+ string notes;
+ double x = Field <double> :: get(annotaId,"x");
+ double y = Field <double> :: get(annotaId,"y");
+ string fg = Field <string> :: get(annotaId,"textColor");
+ string bg = Field <string> :: get(annotaId,"color");
+ writeEnz( fout, *itrE, bg, fg, x, y, compt->second.first);
+ storeEnzMsgs( *itrE, msgs, compt->second.first);
+ }// reaction
+
+ } //compatment loop
+ writeGui ( fout);
+
+ /* Table */
+
+ vector< ObjId > table;
+ wildcardFind(model.path()+"/##[ISA=Table2]",table);
+ for (vector <ObjId> :: iterator itrT= table.begin(); itrT != table.end(); itrT++)
+ {
+ string tabPath = Field <string> :: get(*itrT,"path");
+ vector < Id > tabSrc = LookupField <string,vector < Id> >::get(*itrT, "neighbors","requestOut");
+ for (vector <Id> :: iterator tabItem= tabSrc.begin(); tabItem != tabSrc.end(); tabItem++)
+ {
+ string path = Field <string> :: get(*tabItem,"path");
+ double vol = Field < double> :: get (*tabItem,"Volume");
+ //Trying to find the compartment name via volume
+ //otherwise if we go via parent, sometimes it might
+ // get groupname so maped compartment Id and volume
+
+ Id parentId = compt_vol[vol].first;
+ string parentname = Field <string> :: get(parentId,"name");
+ Id annotaId(path+"/info");
+ double x = Field <double> :: get(annotaId,"x");
+ double y = Field <double> :: get(annotaId,"y");
+ string bg = Field <string> :: get(annotaId,"textColor");
+ string fg = Field <string> :: get(annotaId,"color");
+ writePlot( fout, *itrT, bg, fg, x, y );
+ storePlotMsgs( *itrT, msgs,*tabItem,fg, parentId);
- }
- }// table
- writeMsgs( fout, msgs );
- writeFooter( fout );
+ }
+ }// table
+ writeMsgs( fout, msgs );
+ writeFooter( fout );
}
diff --git a/ksolve/BoostSys.cpp b/ksolve/BoostSys.cpp
index 4a3faf01..0a6e4eb3 100644
--- a/ksolve/BoostSys.cpp
+++ b/ksolve/BoostSys.cpp
@@ -18,7 +18,7 @@
#include <iostream>
#include "VoxelPools.h"
-#ifdef USE_BOOST
+#ifdef USE_BOOST_ODE
BoostSys::BoostSys( ) : vp( NULL )
{ ; }
@@ -34,5 +34,6 @@ void BoostSys::operator()( const vector_type_ y
VoxelPools::evalRates( y, dydt, t, vp );
}
-#else /* ----- not USE_BOOST ----- */
-#endif /* ----- not USE_BOOST ----- */
+#else /* ----- not USE_BOOST_ODE ----- */
+
+#endif /* ----- not USE_BOOST_ODE ----- */
diff --git a/ksolve/BoostSys.h b/ksolve/BoostSys.h
index 8714b3d4..ae97723a 100644
--- a/ksolve/BoostSys.h
+++ b/ksolve/BoostSys.h
@@ -1,11 +1,10 @@
#ifndef BOOSTSYSTEM_H
#define BOOSTSYSTEM_H
-#ifdef USE_BOOST
+#ifdef USE_BOOST_ODE
#include <vector>
#include <string>
-
#include <boost/numeric/odeint.hpp>
typedef double value_type_;
@@ -34,23 +33,23 @@ class VoxelPools;
*/
class BoostSys
{
- public:
- BoostSys( );
- ~BoostSys();
+public:
+ BoostSys( );
+ ~BoostSys( );
- /* Operator is called by boost ode-solver */
- void operator()( const vector_type_ y , vector_type_& dydt, const double t );
+ /* Operator is called by boost ode-solver */
+ void operator()( const vector_type_ y , vector_type_& dydt, const double t );
- /* Pointer to the arbitrary parameters of the system */
- VoxelPools* vp;
- void* params;
+ /* Pointer to the arbitrary parameters of the system */
+ VoxelPools* vp;
+ void* params;
- double epsAbs;
- double epsRel;
- std::string method;
+ double epsAbs;
+ double epsRel;
+ std::string method;
};
-#endif // USE_BOOST
+#endif // USE_BOOST_ODE
#endif /* end of include guard: BOOSTSYSTEM_H */
diff --git a/ksolve/CMakeLists.txt b/ksolve/CMakeLists.txt
index c26bbcec..f35588de 100644
--- a/ksolve/CMakeLists.txt
+++ b/ksolve/CMakeLists.txt
@@ -1,11 +1,11 @@
-cmake_minimum_required(VERSION 2.6)
+cmake_minimum_required(VERSION 2.8)
include(CheckIncludeFileCXX)
include_directories(../builtins ../basecode ../utility ../kinetics)
include_directories(../ )
include_directories(../mesh)
include_directories(../external/muparser/include )
-IF(WITH_BOOST)
+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
@@ -16,7 +16,7 @@ IF(WITH_BOOST)
include_directories( ../external/boost-numeric-bindings )
elseif(WITH_GSL)
include_directories( ${GSL_INCLUDE_DIRS} )
-endif(WITH_BOOST)
+endif(WITH_BOOST_ODE)
if(PARALLELIZED_SOLVERS)
message( STATUS "Parallel version of KSolve and Gsolve" )
@@ -46,7 +46,7 @@ set(KSOLVE_SRCS
if(WITH_GSL)
list(APPEND KSOLVE_SRCS SteadyStateGsl.cpp )
-elseif(WITH_BOOST)
+elseif(WITH_BOOST_ODE)
list(APPEND KSOLVE_SRCS SteadyStateBoost.cpp )
list(APPEND KSOLVE_SRCS BoostSys.cpp)
endif(WITH_GSL)
diff --git a/ksolve/Gsolve.cpp b/ksolve/Gsolve.cpp
index 25a5c060..c7f5cb8a 100644
--- a/ksolve/Gsolve.cpp
+++ b/ksolve/Gsolve.cpp
@@ -6,10 +6,12 @@
** GNU Lesser General Public License version 2.1
** See the file COPYING.LIB for the full notice.
**********************************************************************/
-#include "header.h"
+#include "../basecode/header.h"
+#include "../basecode/global.h"
-#include "VoxelPoolsBase.h"
#include "../mesh/VoxelJunction.h"
+
+#include "VoxelPoolsBase.h"
#include "XferInfo.h"
#include "ZombiePoolInterface.h"
@@ -21,7 +23,6 @@
#include "GssaSystem.h"
#include "Stoich.h"
#include "GssaVoxelPools.h"
-#include "../randnum/randnum.h"
#include <future>
#include <atomic>
@@ -215,6 +216,11 @@ Gsolve::Gsolve() :
;
}
+Gsolve& Gsolve::operator=(const Gsolve& )
+{
+ return *this;
+}
+
Gsolve::~Gsolve()
{
;
@@ -419,7 +425,9 @@ void Gsolve::process( const Eref& e, ProcPtr p )
*i = round( *i );
#else
double base = floor( *i );
- if ( mtrand() >= (*i - base) )
+
+ // Use global RNG.
+ if ( moose::mtrand() >= (*i - base) )
*i = base;
else
*i = base + 1.0;
diff --git a/ksolve/Gsolve.h b/ksolve/Gsolve.h
index 78f572ab..cb511814 100644
--- a/ksolve/Gsolve.h
+++ b/ksolve/Gsolve.h
@@ -17,6 +17,9 @@ public:
Gsolve();
~Gsolve();
+ // Assignment operator required for c++11
+ Gsolve& operator=(const Gsolve& );
+
//////////////////////////////////////////////////////////////////
// Field assignment stuff
//////////////////////////////////////////////////////////////////
diff --git a/ksolve/GssaSystem.h b/ksolve/GssaSystem.h
index 6c81c513..c1b8ad91 100644
--- a/ksolve/GssaSystem.h
+++ b/ksolve/GssaSystem.h
@@ -18,35 +18,40 @@
class Stoich;
class GssaSystem
{
- public:
- GssaSystem()
- : stoich( 0 ), useRandInit( true ), isReady( false )
- {;}
- vector< vector< unsigned int > > dependency;
- vector< vector< unsigned int > > dependentMathExpn;
- vector< vector< unsigned int > > ratesDependentOnPool;
-
- /// Transpose of stoichiometry matrix.
- KinSparseMatrix transposeN;
- Stoich* stoich;
-
- /**
- * Flag: True when using probabilistic (random) rounding.
- * When initializing the mol# from floating-point Sinit values,
- * we have two options. One is to look at each Sinit, and round
- * to the nearest integer. The other is to look at each Sinit,
- * and probabilistically round up or down depending on the
- * value. For example, if we had a Sinit value of 1.49,
- * this would always be rounded to 1.0 if the flag is false,
- * and would be rounded to 1.0 and 2.0 in the ratio 51:49 if
- * the flag is true.
- */
- bool useRandInit;
-
- /**
- * Flag: True when all initialization is done.
- */
- bool isReady;
+public:
+ GssaSystem()
+ : stoich(0), useRandInit(true), isReady(false), honorMassConservation(true)
+ {;}
+ vector< vector< unsigned int > > dependency;
+ vector< vector< unsigned int > > dependentMathExpn;
+ vector< vector< unsigned int > > ratesDependentOnPool;
+
+ /// Transpose of stoichiometry matrix.
+ KinSparseMatrix transposeN;
+ Stoich* stoich;
+
+ /**
+ * Flag: True when using probabilistic (random) rounding.
+ * When initializing the mol# from floating-point Sinit values,
+ * we have two options. One is to look at each Sinit, and round
+ * to the nearest integer. The other is to look at each Sinit,
+ * and probabilistically round up or down depending on the
+ * value. For example, if we had a Sinit value of 1.49,
+ * this would always be rounded to 1.0 if the flag is false,
+ * and would be rounded to 1.0 and 2.0 in the ratio 51:49 if
+ * the flag is true.
+ */
+ bool useRandInit = true;
+
+ /**
+ * Flag: True when all initialization is done.
+ */
+ bool isReady = false;
+
+ /* When set to true, it makes sure that after rounding number of molecules,
+ * the sum of molecules is does not differ more than 1.0 molecules.
+ */
+ bool honorMassConservation = true;
};
#endif // _GSSA_SYSTEM_H
diff --git a/ksolve/GssaVoxelPools.cpp b/ksolve/GssaVoxelPools.cpp
index 27396430..4128d0a6 100644
--- a/ksolve/GssaVoxelPools.cpp
+++ b/ksolve/GssaVoxelPools.cpp
@@ -48,7 +48,7 @@ const double SAFETY_FACTOR = 1.0 + 1.0e-9;
//////////////////////////////////////////////////////////////
GssaVoxelPools::GssaVoxelPools() :
- VoxelPoolsBase(), t_( 0.0 ), atot_( 0.0 )
+ VoxelPoolsBase(), t_( 0.0 ), atot_( 0.0 )
{ ; }
GssaVoxelPools::~GssaVoxelPools()
@@ -78,15 +78,15 @@ void GssaVoxelPools::updateDependentMathExpn(
g->stoich->funcs( *i )->evalPool( varS(), time );
}
*/
- /*
+ /*
unsigned int numFuncs = g->stoich->getNumFuncs();
for( unsigned int i = 0; i < numFuncs; ++i )
{
g->stoich->funcs( i )->evalPool( varS(), time );
}
- */
- // This function is equivalent to the loop above.
- g->stoich->updateFuncs( varS(), time );
+ */
+ // This function is equivalent to the loop above.
+ g->stoich->updateFuncs( varS(), time );
}
void GssaVoxelPools::updateDependentRates(
@@ -139,7 +139,7 @@ void GssaVoxelPools::setNumReac( unsigned int n )
*/
bool GssaVoxelPools::refreshAtot( const GssaSystem* g )
{
- g->stoich->updateFuncs( varS(), t_ );
+ g->stoich->updateFuncs( varS(), t_ );
updateReacVelocities( g, S(), v_ );
atot_ = 0;
for ( vector< double >::const_iterator
@@ -178,8 +178,8 @@ void GssaVoxelPools::advance( const ProcInfo* p, const GssaSystem* g )
if ( atot_ <= 0.0 ) // reac system is stuck, will not advance.
{
t_ = nextt;
- g->stoich->updateFuncs( varS(), t_ );
- // updateDependentMathExpn( g, 0, t_ );
+ g->stoich->updateFuncs( varS(), t_ );
+ // updateDependentMathExpn( g, 0, t_ );
return;
}
unsigned int rindex = pickReac();
@@ -191,8 +191,8 @@ void GssaVoxelPools::advance( const ProcInfo* p, const GssaSystem* g )
if ( !refreshAtot( g ) ) // Stuck state.
{
t_ = nextt;
- g->stoich->updateFuncs( varS(), t_ );
- // updateDependentMathExpn( g, 0, t_ );
+ g->stoich->updateFuncs( varS(), t_ );
+ // updateDependentMathExpn( g, 0, t_ );
return;
}
// We had a roundoff error, fixed it, but now need to be sure
@@ -208,17 +208,22 @@ void GssaVoxelPools::advance( const ProcInfo* p, const GssaSystem* g )
assert( rindex < v_.size() );
}
+#if ENABLE_CPP11
+ double sign = std::copysign( 1, v_[rindex] );
+#else
double sign = double(v_[rindex] >= 0) - double(0 > v_[rindex] );
+#endif
+
g->transposeN.fireReac( rindex, Svec(), sign );
- numFire_[rindex]++;
+ numFire_[rindex]++;
double r = rng_.uniform();
+
while ( r <= 0.0 )
- {
r = rng_.uniform();
- }
+
t_ -= ( 1.0 / atot_ ) * log( r );
- g->stoich->updateFuncs( varS(), t_ );
+ g->stoich->updateFuncs( varS(), t_ );
// updateDependentMathExpn( g, rindex, t_ );
updateDependentRates( g->dependency[ rindex ], g->stoich );
}
@@ -233,36 +238,66 @@ void GssaVoxelPools::reinit( const GssaSystem* g )
double* n = varS();
- if ( g->useRandInit )
+ if( g->useRandInit )
{
- // round up or down probabilistically depending on fractional
- // num molecules.
+ vector<double> error(numVarPools, 0.0);
+ map<double, vector<Eref>> groupByVal;
+
for ( unsigned int i = 0; i < numVarPools; ++i )
{
- double base = floor( n[i] );
+ error[i] = n[i];
+ double base = std::floor( n[i] );
assert( base >= 0.0 );
double frac = n[i] - base;
- if ( rng_.uniform() > frac )
+ if ( rng_.uniform() >= frac )
n[i] = base;
else
n[i] = base + 1.0;
+
+ error[i] -= n[i];
+
+ //if( true )
+ //{
+ // //NOTE: Thats how I get the name of the pool at this index.
+ // Eref e = g->stoich->getPoolByIndex( i ).eref();
+ // groupByVal[n[i]].push_back( e );
+
+ // // Guess the fix the error.
+ //}
+
+
+ }
+
+ double extra = std::accumulate( error.begin(), error.end(), 0.0 );
+ if( std::abs(extra) > 0.1 )
+ {
+ cout << "WARNING: Extra " << extra
+ << " molecules in system after converting fractional to integer e.g. 1.1 = 1 (~90% of times) or 2 (~10% of times)." << endl;
}
}
else // Just round to the nearest int.
{
for ( unsigned int i = 0; i < numVarPools; ++i )
{
+#if ENABLE_CPP11
+ // 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]);
+#else
n[i] = round( n[i] );
+#endif
}
}
+
t_ = 0.0;
refreshAtot( g );
- numFire_.assign( v_.size(), 0 );
+ numFire_.assign( v_.size(), 0 );
}
vector< unsigned int > GssaVoxelPools::numFire() const
{
- return numFire_;
+ return numFire_;
}
/////////////////////////////////////////////////////////////////////////
diff --git a/ksolve/GssaVoxelPools.h b/ksolve/GssaVoxelPools.h
index 716698a4..b0bc90e5 100644
--- a/ksolve/GssaVoxelPools.h
+++ b/ksolve/GssaVoxelPools.h
@@ -34,7 +34,7 @@ public:
void advance( const ProcInfo* p, const GssaSystem* g );
- vector< unsigned int > numFire() const;
+ vector< unsigned int > numFire() const;
/**
* Cleans out all reac rates and recalculates atot. Needed whenever a
@@ -88,8 +88,8 @@ private:
vector< double > v_;
// Possibly we should put independent RNGS, so save one here.
- // Count how many times each reaction has fired.
- vector< unsigned int > numFire_;
+ // Count how many times each reaction has fired.
+ vector< unsigned int > numFire_;
/**
* @brief RNG.
diff --git a/ksolve/Ksolve.cpp b/ksolve/Ksolve.cpp
index 8b7b5ac9..b55d0d12 100644
--- a/ksolve/Ksolve.cpp
+++ b/ksolve/Ksolve.cpp
@@ -6,7 +6,7 @@
** GNU Lesser General Public License version 2.1
** See the file COPYING.LIB for the full notice.
**********************************************************************/
-#include "header.h"
+#include "../basecode/header.h"
#ifdef USE_GSL
#include <gsl/gsl_errno.h>
#include <gsl/gsl_matrix.h>
@@ -21,7 +21,7 @@
#include "RateTerm.h"
#include "FuncTerm.h"
-#include "SparseMatrix.h"
+#include "../basecode/SparseMatrix.h"
#include "KinSparseMatrix.h"
#include "Stoich.h"
#include "../shell/Shell.h"
@@ -217,7 +217,7 @@ Ksolve::Ksolve()
:
#if USE_GSL
method_( "rk5" ),
-#elif USE_BOOST
+#elif USE_BOOST_ODE
method_( "rk5a" ),
#endif
epsAbs_( 1e-7 ),
@@ -265,7 +265,7 @@ void Ksolve::setMethod( string method )
"' not known, using rk5\n";
method_ = "rk5";
}
-#elif USE_BOOST
+#elif USE_BOOST_ODE
// TODO: Check for boost related methods.
method_ = method;
#endif
@@ -380,7 +380,7 @@ void Ksolve::setStoich( Id stoich )
pools_[i].setStoich( stoichPtr_, &ode );
// pools_[i].setIntDt( ode.initStepSize ); // We're setting it up anyway
}
-#elif USE_BOOST
+#elif USE_BOOST_ODE
ode.dimension = stoichPtr_->getNumAllPools();
ode.boostSys.epsAbs = epsAbs_;
ode.boostSys.epsRel = epsRel_;
@@ -511,7 +511,7 @@ void Ksolve::process( const Eref& e, ProcPtr p )
dsolvePtr_->getBlock( dvalues );
// Second, set the prev_ value in DiffPoolVec
dsolvePtr_->setPrev();
- setBlock( dvalues );
+ setBlock( dvalues );
}
size_t nvPools = pools_.size( );
diff --git a/ksolve/OdeSystem.h b/ksolve/OdeSystem.h
index 0f7e37a6..84e2c72f 100644
--- a/ksolve/OdeSystem.h
+++ b/ksolve/OdeSystem.h
@@ -10,11 +10,11 @@
#ifndef _ODE_SYSTEM_H
#define _ODE_SYSTEM_H
-#if USE_BOOST
+#if USE_BOOST_ODE
#include "BoostSys.h"
#elif USE_GSL
#include <gsl/gsl_odeiv2.h>
-#endif /* ----- not USE_BOOST ----- */
+#endif /* ----- not USE_BOOST_ODE ----- */
class OdeSystem {
public:
@@ -36,11 +36,11 @@ class OdeSystem {
double epsAbs; // Absolute error
double epsRel; // Relative error
-#if USE_BOOST
+#if USE_BOOST_ODE
//BoostSys* pBoostSys;
BoostSys boostSys;
size_t dimension;
-#endif /* ----- USE_BOOST ----- */
+#endif /* ----- USE_BOOST_ODE ----- */
};
#endif // _ODE_SYSTEM_H
diff --git a/ksolve/SteadyStateBoost.cpp b/ksolve/SteadyStateBoost.cpp
index 98e5b210..a96439ba 100644
--- a/ksolve/SteadyStateBoost.cpp
+++ b/ksolve/SteadyStateBoost.cpp
@@ -339,7 +339,6 @@ SteadyState::SteadyState()
solutionStatus_( 0 ),
numFailed_( 0 )
{
- rng.setSeed( moose::__rng_seed__ );
}
SteadyState::~SteadyState()
@@ -1046,7 +1045,7 @@ void SteadyState::fitConservationRules(
double ytot = 0.0;
for ( int k = j; k < lastJ; ++k )
{
- y[k] = rng.uniform( );
+ y[k] = moose::mtrand();
ytot += y[k] * U( i, k );
}
assert( fabs( ytot ) > EPSILON );
diff --git a/ksolve/SteadyStateBoost.h b/ksolve/SteadyStateBoost.h
index 66303a18..7db6b0da 100644
--- a/ksolve/SteadyStateBoost.h
+++ b/ksolve/SteadyStateBoost.h
@@ -125,9 +125,7 @@ private:
unsigned int numFailed_;
VoxelPools pool_;
- moose::RNG<double> rng;
-
-#if USE_BOOST
+#if USE_BOOST_ODE
NonlinearSystem* ss;
#endif
diff --git a/ksolve/SteadyStateGsl.cpp b/ksolve/SteadyStateGsl.cpp
index e8d805d7..295b5256 100644
--- a/ksolve/SteadyStateGsl.cpp
+++ b/ksolve/SteadyStateGsl.cpp
@@ -18,7 +18,9 @@
* Likewise, if you want to carry out a dose-response calculation.
*/
-#include "header.h"
+#include "../basecode/header.h"
+#include "../basecode/global.h"
+
#include "SparseMatrix.h"
#include "KinSparseMatrix.h"
#include "RateTerm.h"
@@ -28,7 +30,6 @@
#include "XferInfo.h"
#include "ZombiePoolInterface.h"
#include "Stoich.h"
-#include "../randnum/randnum.h"
#ifdef USE_GSL
#include <gsl/gsl_errno.h>
@@ -64,249 +65,250 @@ const double SteadyState::DELTA = 1e-6;
*/
struct reac_info
{
- int rank;
- int num_reacs;
- size_t num_mols;
- int nIter;
- double convergenceCriterion;
+ int rank;
+ int num_reacs;
+ size_t num_mols;
+ int nIter;
+ double convergenceCriterion;
- double* T;
- VoxelPools* pool;
- vector< double > nVec;
+ double* T;
+ VoxelPools* pool;
+ vector< double > nVec;
#ifdef USE_GSL
- gsl_matrix* Nr;
- gsl_matrix* gamma;
+ gsl_matrix* Nr;
+ gsl_matrix* gamma;
#endif
};
const Cinfo* SteadyState::initCinfo()
{
- /**
- * This picks up the entire Stoich data structure
- static Finfo* gslShared[] =
- {
- new SrcFinfo( "reinitSrc", Ftype0::global() ),
- new DestFinfo( "assignStoich",
- Ftype1< void* >::global(),
- RFCAST( &SteadyState::assignStoichFunc )
- ),
- new DestFinfo( "setMolN",
- Ftype2< double, unsigned int >::global(),
- RFCAST( &SteadyState::setMolN )
- ),
- new SrcFinfo( "requestYsrc", Ftype0::global() ),
- new DestFinfo( "assignY",
- Ftype1< double* >::global(),
- RFCAST( &SteadyState::assignY )
- ),
- };
- */
-
- /**
- * These are the fields of the SteadyState class
- */
- ///////////////////////////////////////////////////////
- // Field definitions
- ///////////////////////////////////////////////////////
- static ValueFinfo< SteadyState, Id > stoich(
- "stoich",
- "Specify the Id of the stoichiometry system to use",
- &SteadyState::setStoich,
- &SteadyState::getStoich
- );
- static ReadOnlyValueFinfo< SteadyState, bool > badStoichiometry(
- "badStoichiometry",
- "Bool: True if there is a problem with the stoichiometry",
- &SteadyState::badStoichiometry
- );
- static ReadOnlyValueFinfo< SteadyState, bool > isInitialized(
- "isInitialized",
- "True if the model has been initialized successfully",
- &SteadyState::isInitialized
- );
- static ReadOnlyValueFinfo< SteadyState, unsigned int > nIter(
- "nIter",
- "Number of iterations done by steady state solver",
- &SteadyState::getNiter
- );
- static ReadOnlyValueFinfo< SteadyState, string > status(
- "status",
- "Status of solver",
- &SteadyState::getStatus
- );
- static ValueFinfo< SteadyState, unsigned int > maxIter(
- "maxIter",
- "Max permissible number of iterations to try before giving up",
- &SteadyState::setMaxIter,
- &SteadyState::getMaxIter
- );
- static ValueFinfo< SteadyState, double> convergenceCriterion(
- "convergenceCriterion",
- "Fractional accuracy required to accept convergence",
- &SteadyState::setConvergenceCriterion,
- &SteadyState::getConvergenceCriterion
- );
- static ReadOnlyValueFinfo< SteadyState, unsigned int > numVarPools(
- "numVarPools",
- "Number of variable molecules in reaction system.",
- &SteadyState::getNumVarPools
- );
- static ReadOnlyValueFinfo< SteadyState, unsigned int > rank(
- "rank",
- "Number of independent molecules in reaction system",
- &SteadyState::getRank
- );
- static ReadOnlyValueFinfo< SteadyState, unsigned int > stateType(
- "stateType",
- "0: stable; 1: unstable; 2: saddle; 3: osc?; 4: one near-zero eigenvalue; 5: other",
- &SteadyState::getStateType
- );
- static ReadOnlyValueFinfo< SteadyState, unsigned int >
- nNegEigenvalues (
- "nNegEigenvalues",
- "Number of negative eigenvalues: indicates type of solution",
- &SteadyState::getNnegEigenvalues
- );
- static ReadOnlyValueFinfo< SteadyState, unsigned int >
- nPosEigenvalues(
- "nPosEigenvalues",
- "Number of positive eigenvalues: indicates type of solution",
- &SteadyState::getNposEigenvalues
- );
- static ReadOnlyValueFinfo< SteadyState, unsigned int > solutionStatus(
- "solutionStatus",
- "0: Good; 1: Failed to find steady states; "
- "2: Failed to find eigenvalues",
- &SteadyState::getSolutionStatus
- );
- static LookupValueFinfo< SteadyState, unsigned int, double > total(
- "total",
- "Totals table for conservation laws. The exact mapping of"
- "this to various sums of molecules is given by the "
- "conservation matrix, and is currently a bit opaque."
- "The value of 'total' is set to initial conditions when"
- "the 'SteadyState::settle' function is called."
- "Assigning values to the total is a special operation:"
- "it rescales the concentrations of all the affected"
- "molecules so that they are at the specified total."
- "This happens the next time 'settle' is called.",
- &SteadyState::setTotal,
- &SteadyState::getTotal
- );
- static ReadOnlyLookupValueFinfo<
- SteadyState, unsigned int, double > eigenvalues(
- "eigenvalues",
- "Eigenvalues computed for steady state",
- &SteadyState::getEigenvalue
- );
- ///////////////////////////////////////////////////////
- // MsgDest definitions
- ///////////////////////////////////////////////////////
- static DestFinfo setupMatrix( "setupMatrix",
- "This function initializes and rebuilds the matrices used "
- "in the calculation.",
- new OpFunc0< SteadyState >(&SteadyState::setupMatrix)
- );
-
- static DestFinfo settle( "settle",
- "Finds the nearest steady state to the current initial "
- "conditions. This function rebuilds the entire calculation "
- "only if the object has not yet been initialized.",
- new OpFunc0< SteadyState >( &SteadyState::settleFunc )
- );
- static DestFinfo resettle( "resettle",
- "Finds the nearest steady state to the current initial "
- "conditions. This function rebuilds the entire calculation ",
- new OpFunc0< SteadyState >( &SteadyState::resettleFunc )
- );
- static DestFinfo showMatrices( "showMatrices",
- "Utility function to show the matrices derived for the calculations on the reaction system. Shows the Nr, gamma, and total matrices",
- new OpFunc0< SteadyState >( &SteadyState::showMatrices )
- );
- static DestFinfo randomInit( "randomInit",
- "Generate random initial conditions consistent with the mass"
- "conservation rules. Typically invoked in order to scan"
- "states",
- new EpFunc0< SteadyState >(
- &SteadyState::randomizeInitialCondition )
- );
- ///////////////////////////////////////////////////////
- // Shared definitions
- ///////////////////////////////////////////////////////
-
- static Finfo * steadyStateFinfos[] = {
- &stoich, // Value
- &badStoichiometry, // ReadOnlyValue
- &isInitialized, // ReadOnlyValue
- &nIter, // ReadOnlyValue
- &status, // ReadOnlyValue
- &maxIter, // Value
- &convergenceCriterion, // ReadOnlyValue
- &numVarPools, // ReadOnlyValue
- &rank, // ReadOnlyValue
- &stateType, // ReadOnlyValue
- &nNegEigenvalues, // ReadOnlyValue
- &nPosEigenvalues, // ReadOnlyValue
- &solutionStatus, // ReadOnlyValue
- &total, // LookupValue
- &eigenvalues, // ReadOnlyLookupValue
- &setupMatrix, // DestFinfo
- &settle, // DestFinfo
- &resettle, // DestFinfo
- &showMatrices, // DestFinfo
- &randomInit, // DestFinfo
-
-
- };
-
- static string doc[] =
- {
- "Name", "SteadyState",
- "Author", "Upinder S. Bhalla, 2009, updated 2014, NCBS",
- "Description", "SteadyState: works out a steady-state value for "
- "a reaction system. "
- "This class uses the GSL multidimensional root finder algorithms "
- "to find the fixed points closest to the "
- "current molecular concentrations. "
- "When it finds the fixed points, it figures out eigenvalues of "
- "the solution, as a way to help classify the fixed points. "
- "Note that the method finds unstable as well as stable fixed "
- "points.\n "
- "The SteadyState class also provides a utility function "
- "*randomInit()* to "
- "randomly initialize the concentrations, within the constraints "
- "of stoichiometry. This is useful if you are trying to find "
- "the major fixed points of the system. Note that this is "
- "probabilistic. If a fixed point is in a very narrow range of "
- "state space the probability of finding it is small and you "
- "will have to run many iterations with different initial "
- "conditions to find it.\n "
- "The numerical calculations used by the SteadyState solver are "
- "prone to failing on individual calculations. All is not lost, "
- "because the system reports the solutionStatus. "
- "It is recommended that you test this field after every "
- "calculation, so you can simply ignore "
- "cases where it failed and try again with different starting "
- "conditions.\n "
- "Another rule of thumb is that the SteadyState object is more "
- "likely to succeed in finding solutions from a new starting point "
- "if you numerically integrate the chemical system for a short "
- "time (typically under 1 second) before asking it to find the "
- "fixed point. "
- };
-
- static Dinfo< SteadyState > dinfo;
- static Cinfo steadyStateCinfo(
- "SteadyState",
- Neutral::initCinfo(),
- steadyStateFinfos,
- sizeof( steadyStateFinfos )/sizeof(Finfo *),
- &dinfo,
- doc, sizeof( doc ) / sizeof( string )
- );
-
- return &steadyStateCinfo;
+ /**
+ * This picks up the entire Stoich data structure
+ static Finfo* gslShared[] =
+ {
+ new SrcFinfo( "reinitSrc", Ftype0::global() ),
+ new DestFinfo( "assignStoich",
+ Ftype1< void* >::global(),
+ RFCAST( &SteadyState::assignStoichFunc )
+ ),
+ new DestFinfo( "setMolN",
+ Ftype2< double, unsigned int >::global(),
+ RFCAST( &SteadyState::setMolN )
+ ),
+ new SrcFinfo( "requestYsrc", Ftype0::global() ),
+ new DestFinfo( "assignY",
+ Ftype1< double* >::global(),
+ RFCAST( &SteadyState::assignY )
+ ),
+ };
+ */
+
+ /**
+ * These are the fields of the SteadyState class
+ */
+ ///////////////////////////////////////////////////////
+ // Field definitions
+ ///////////////////////////////////////////////////////
+ static ValueFinfo< SteadyState, Id > stoich(
+ "stoich",
+ "Specify the Id of the stoichiometry system to use",
+ &SteadyState::setStoich,
+ &SteadyState::getStoich
+ );
+ static ReadOnlyValueFinfo< SteadyState, bool > badStoichiometry(
+ "badStoichiometry",
+ "Bool: True if there is a problem with the stoichiometry",
+ &SteadyState::badStoichiometry
+ );
+ static ReadOnlyValueFinfo< SteadyState, bool > isInitialized(
+ "isInitialized",
+ "True if the model has been initialized successfully",
+ &SteadyState::isInitialized
+ );
+ static ReadOnlyValueFinfo< SteadyState, unsigned int > nIter(
+ "nIter",
+ "Number of iterations done by steady state solver",
+ &SteadyState::getNiter
+ );
+ static ReadOnlyValueFinfo< SteadyState, string > status(
+ "status",
+ "Status of solver",
+ &SteadyState::getStatus
+ );
+ static ValueFinfo< SteadyState, unsigned int > maxIter(
+ "maxIter",
+ "Max permissible number of iterations to try before giving up",
+ &SteadyState::setMaxIter,
+ &SteadyState::getMaxIter
+ );
+ static ValueFinfo< SteadyState, double> convergenceCriterion(
+ "convergenceCriterion",
+ "Fractional accuracy required to accept convergence",
+ &SteadyState::setConvergenceCriterion,
+ &SteadyState::getConvergenceCriterion
+ );
+ static ReadOnlyValueFinfo< SteadyState, unsigned int > numVarPools(
+ "numVarPools",
+ "Number of variable molecules in reaction system.",
+ &SteadyState::getNumVarPools
+ );
+ static ReadOnlyValueFinfo< SteadyState, unsigned int > rank(
+ "rank",
+ "Number of independent molecules in reaction system",
+ &SteadyState::getRank
+ );
+ static ReadOnlyValueFinfo< SteadyState, unsigned int > stateType(
+ "stateType",
+ "0: stable; 1: unstable; 2: saddle; 3: osc?; 4: one near-zero eigenvalue; 5: other",
+ &SteadyState::getStateType
+ );
+ static ReadOnlyValueFinfo< SteadyState, unsigned int >
+ nNegEigenvalues (
+ "nNegEigenvalues",
+ "Number of negative eigenvalues: indicates type of solution",
+ &SteadyState::getNnegEigenvalues
+ );
+ static ReadOnlyValueFinfo< SteadyState, unsigned int >
+ nPosEigenvalues(
+ "nPosEigenvalues",
+ "Number of positive eigenvalues: indicates type of solution",
+ &SteadyState::getNposEigenvalues
+ );
+ static ReadOnlyValueFinfo< SteadyState, unsigned int > solutionStatus(
+ "solutionStatus",
+ "0: Good; 1: Failed to find steady states; "
+ "2: Failed to find eigenvalues",
+ &SteadyState::getSolutionStatus
+ );
+ static LookupValueFinfo< SteadyState, unsigned int, double > total(
+ "total",
+ "Totals table for conservation laws. The exact mapping of"
+ "this to various sums of molecules is given by the "
+ "conservation matrix, and is currently a bit opaque."
+ "The value of 'total' is set to initial conditions when"
+ "the 'SteadyState::settle' function is called."
+ "Assigning values to the total is a special operation:"
+ "it rescales the concentrations of all the affected"
+ "molecules so that they are at the specified total."
+ "This happens the next time 'settle' is called.",
+ &SteadyState::setTotal,
+ &SteadyState::getTotal
+ );
+ static ReadOnlyLookupValueFinfo<
+ SteadyState, unsigned int, double > eigenvalues(
+ "eigenvalues",
+ "Eigenvalues computed for steady state",
+ &SteadyState::getEigenvalue
+ );
+ ///////////////////////////////////////////////////////
+ // MsgDest definitions
+ ///////////////////////////////////////////////////////
+ static DestFinfo setupMatrix( "setupMatrix",
+ "This function initializes and rebuilds the matrices used "
+ "in the calculation.",
+ new OpFunc0< SteadyState >(&SteadyState::setupMatrix)
+ );
+
+ static DestFinfo settle( "settle",
+ "Finds the nearest steady state to the current initial "
+ "conditions. This function rebuilds the entire calculation "
+ "only if the object has not yet been initialized.",
+ new OpFunc0< SteadyState >( &SteadyState::settleFunc )
+ );
+ static DestFinfo resettle( "resettle",
+ "Finds the nearest steady state to the current initial "
+ "conditions. This function rebuilds the entire calculation ",
+ new OpFunc0< SteadyState >( &SteadyState::resettleFunc )
+ );
+ static DestFinfo showMatrices( "showMatrices",
+ "Utility function to show the matrices derived for the calculations on the reaction system. Shows the Nr, gamma, and total matrices",
+ new OpFunc0< SteadyState >( &SteadyState::showMatrices )
+ );
+ static DestFinfo randomInit( "randomInit",
+ "Generate random initial conditions consistent with the mass"
+ "conservation rules. Typically invoked in order to scan"
+ "states",
+ new EpFunc0< SteadyState >(
+ &SteadyState::randomizeInitialCondition )
+ );
+ ///////////////////////////////////////////////////////
+ // Shared definitions
+ ///////////////////////////////////////////////////////
+
+ static Finfo * steadyStateFinfos[] =
+ {
+ &stoich, // Value
+ &badStoichiometry, // ReadOnlyValue
+ &isInitialized, // ReadOnlyValue
+ &nIter, // ReadOnlyValue
+ &status, // ReadOnlyValue
+ &maxIter, // Value
+ &convergenceCriterion, // ReadOnlyValue
+ &numVarPools, // ReadOnlyValue
+ &rank, // ReadOnlyValue
+ &stateType, // ReadOnlyValue
+ &nNegEigenvalues, // ReadOnlyValue
+ &nPosEigenvalues, // ReadOnlyValue
+ &solutionStatus, // ReadOnlyValue
+ &total, // LookupValue
+ &eigenvalues, // ReadOnlyLookupValue
+ &setupMatrix, // DestFinfo
+ &settle, // DestFinfo
+ &resettle, // DestFinfo
+ &showMatrices, // DestFinfo
+ &randomInit, // DestFinfo
+
+
+ };
+
+ static string doc[] =
+ {
+ "Name", "SteadyState",
+ "Author", "Upinder S. Bhalla, 2009, updated 2014, NCBS",
+ "Description", "SteadyState: works out a steady-state value for "
+ "a reaction system. "
+ "This class uses the GSL multidimensional root finder algorithms "
+ "to find the fixed points closest to the "
+ "current molecular concentrations. "
+ "When it finds the fixed points, it figures out eigenvalues of "
+ "the solution, as a way to help classify the fixed points. "
+ "Note that the method finds unstable as well as stable fixed "
+ "points.\n "
+ "The SteadyState class also provides a utility function "
+ "*randomInit()* to "
+ "randomly initialize the concentrations, within the constraints "
+ "of stoichiometry. This is useful if you are trying to find "
+ "the major fixed points of the system. Note that this is "
+ "probabilistic. If a fixed point is in a very narrow range of "
+ "state space the probability of finding it is small and you "
+ "will have to run many iterations with different initial "
+ "conditions to find it.\n "
+ "The numerical calculations used by the SteadyState solver are "
+ "prone to failing on individual calculations. All is not lost, "
+ "because the system reports the solutionStatus. "
+ "It is recommended that you test this field after every "
+ "calculation, so you can simply ignore "
+ "cases where it failed and try again with different starting "
+ "conditions.\n "
+ "Another rule of thumb is that the SteadyState object is more "
+ "likely to succeed in finding solutions from a new starting point "
+ "if you numerically integrate the chemical system for a short "
+ "time (typically under 1 second) before asking it to find the "
+ "fixed point. "
+ };
+
+ static Dinfo< SteadyState > dinfo;
+ static Cinfo steadyStateCinfo(
+ "SteadyState",
+ Neutral::initCinfo(),
+ steadyStateFinfos,
+ sizeof( steadyStateFinfos )/sizeof(Finfo *),
+ &dinfo,
+ doc, sizeof( doc ) / sizeof( string )
+ );
+
+ return &steadyStateCinfo;
}
static const Cinfo* steadyStateCinfo = SteadyState::initCinfo();
@@ -316,42 +318,42 @@ static const Cinfo* steadyStateCinfo = SteadyState::initCinfo();
///////////////////////////////////////////////////
SteadyState::SteadyState()
- :
- nIter_( 0 ),
- maxIter_( 100 ),
- badStoichiometry_( 0 ),
- status_( "OK" ),
- isInitialized_( 0 ),
- isSetup_( 0 ),
- convergenceCriterion_( 1e-7 ),
+ :
+ nIter_( 0 ),
+ maxIter_( 100 ),
+ badStoichiometry_( 0 ),
+ status_( "OK" ),
+ isInitialized_( 0 ),
+ isSetup_( 0 ),
+ convergenceCriterion_( 1e-7 ),
#ifdef USE_GSL
- LU_( 0 ),
- Nr_( 0 ),
- gamma_( 0 ),
+ LU_( 0 ),
+ Nr_( 0 ),
+ gamma_( 0 ),
#endif
- stoich_(),
- numVarPools_( 0 ),
- nReacs_( 0 ),
- rank_( 0 ),
- reassignTotal_( 0 ),
- nNegEigenvalues_( 0 ),
- nPosEigenvalues_( 0 ),
- stateType_( 0 ),
- solutionStatus_( 0 ),
- numFailed_( 0 )
+ stoich_(),
+ numVarPools_( 0 ),
+ nReacs_( 0 ),
+ rank_( 0 ),
+ reassignTotal_( 0 ),
+ nNegEigenvalues_( 0 ),
+ nPosEigenvalues_( 0 ),
+ stateType_( 0 ),
+ solutionStatus_( 0 ),
+ numFailed_( 0 )
{
- ;
+ ;
}
SteadyState::~SteadyState()
{
#ifdef USE_GSL
- if ( LU_ != 0 )
- gsl_matrix_free( LU_ );
- if ( Nr_ != 0 )
- gsl_matrix_free( Nr_ );
- if ( gamma_ != 0 )
- gsl_matrix_free( gamma_ );
+ if ( LU_ != 0 )
+ gsl_matrix_free( LU_ );
+ if ( Nr_ != 0 )
+ gsl_matrix_free( Nr_ );
+ if ( gamma_ != 0 )
+ gsl_matrix_free( gamma_ );
#endif
}
@@ -359,118 +361,136 @@ SteadyState::~SteadyState()
// Field function definitions
///////////////////////////////////////////////////
-Id SteadyState::getStoich() const {
- return stoich_;
+Id SteadyState::getStoich() const
+{
+ return stoich_;
}
-void SteadyState::setStoich( Id value ) {
- if ( !value.element()->cinfo()->isA( "Stoich" ) ) {
- cout << "Error: SteadyState::setStoich: Must be of Stoich class\n";
- return;
- }
-
- stoich_ = value;
- Stoich* stoichPtr = reinterpret_cast< Stoich* >( value.eref().data());
- numVarPools_ = Field< unsigned int >::get( stoich_, "numVarPools" );
- nReacs_ = Field< unsigned int >::get( stoich_, "numRates" );
- setupSSmatrix();
- double vol = LookupField< unsigned int, double >::get(
- stoichPtr->getCompartment(), "oneVoxelVolume", 0 );
- pool_.setVolume( vol );
- pool_.setStoich( stoichPtr, 0 );
- pool_.updateAllRateTerms( stoichPtr->getRateTerms(),
- stoichPtr->getNumCoreRates() );
- isInitialized_ = 1;
+void SteadyState::setStoich( Id value )
+{
+ if ( !value.element()->cinfo()->isA( "Stoich" ) )
+ {
+ cout << "Error: SteadyState::setStoich: Must be of Stoich class\n";
+ return;
+ }
+
+ stoich_ = value;
+ Stoich* stoichPtr = reinterpret_cast< Stoich* >( value.eref().data());
+ numVarPools_ = Field< unsigned int >::get( stoich_, "numVarPools" );
+ nReacs_ = Field< unsigned int >::get( stoich_, "numRates" );
+ setupSSmatrix();
+ double vol = LookupField< unsigned int, double >::get(
+ stoichPtr->getCompartment(), "oneVoxelVolume", 0 );
+ pool_.setVolume( vol );
+ pool_.setStoich( stoichPtr, 0 );
+ pool_.updateAllRateTerms( stoichPtr->getRateTerms(),
+ stoichPtr->getNumCoreRates() );
+ isInitialized_ = 1;
}
-bool SteadyState::badStoichiometry() const {
- return badStoichiometry_;
+bool SteadyState::badStoichiometry() const
+{
+ return badStoichiometry_;
}
-bool SteadyState::isInitialized() const {
- return isInitialized_;
+bool SteadyState::isInitialized() const
+{
+ return isInitialized_;
}
-unsigned int SteadyState::getNiter() const {
- return nIter_;
+unsigned int SteadyState::getNiter() const
+{
+ return nIter_;
}
-string SteadyState::getStatus() const {
- return status_;
+string SteadyState::getStatus() const
+{
+ return status_;
}
-unsigned int SteadyState::getMaxIter() const {
- return maxIter_;
+unsigned int SteadyState::getMaxIter() const
+{
+ return maxIter_;
}
-void SteadyState::setMaxIter( unsigned int value ) {
- maxIter_ = value;
+void SteadyState::setMaxIter( unsigned int value )
+{
+ maxIter_ = value;
}
-unsigned int SteadyState::getRank() const {
- return rank_;
+unsigned int SteadyState::getRank() const
+{
+ return rank_;
}
-unsigned int SteadyState::getNumVarPools() const {
- return numVarPools_;
+unsigned int SteadyState::getNumVarPools() const
+{
+ return numVarPools_;
}
-unsigned int SteadyState::getStateType() const {
- return stateType_;
+unsigned int SteadyState::getStateType() const
+{
+ return stateType_;
}
-unsigned int SteadyState::getNnegEigenvalues() const {
- return nNegEigenvalues_;
+unsigned int SteadyState::getNnegEigenvalues() const
+{
+ return nNegEigenvalues_;
}
-unsigned int SteadyState::getNposEigenvalues() const {
- return nPosEigenvalues_;
+unsigned int SteadyState::getNposEigenvalues() const
+{
+ return nPosEigenvalues_;
}
-unsigned int SteadyState::getSolutionStatus() const {
- return solutionStatus_;
+unsigned int SteadyState::getSolutionStatus() const
+{
+ return solutionStatus_;
}
-void SteadyState::setConvergenceCriterion( double value ) {
- if ( value > 1e-10 )
- convergenceCriterion_ = value;
- else
- cout << "Warning: Convergence criterion " << value <<
- " too small. Old value " <<
- convergenceCriterion_ << " retained\n";
+void SteadyState::setConvergenceCriterion( double value )
+{
+ if ( value > 1e-10 )
+ convergenceCriterion_ = value;
+ else
+ cout << "Warning: Convergence criterion " << value <<
+ " too small. Old value " <<
+ convergenceCriterion_ << " retained\n";
}
-double SteadyState::getConvergenceCriterion() const {
- return convergenceCriterion_;
+double SteadyState::getConvergenceCriterion() const
+{
+ return convergenceCriterion_;
}
double SteadyState::getTotal( const unsigned int i ) const
{
- if ( i < total_.size() )
- return total_[i];
- cout << "Warning: SteadyState::getTotal: index " << i <<
- " out of range " << total_.size() << endl;
- return 0.0;
+ if ( i < total_.size() )
+ return total_[i];
+ cout << "Warning: SteadyState::getTotal: index " << i <<
+ " out of range " << total_.size() << endl;
+ return 0.0;
}
void SteadyState::setTotal( const unsigned int i, double val )
{
- if ( i < total_.size() ) {
- total_[i] = val;
- reassignTotal_ = 1;
- return;
- }
- cout << "Warning: SteadyState::setTotal: index " << i <<
- " out of range " << total_.size() << endl;
+ if ( i < total_.size() )
+ {
+ total_[i] = val;
+ reassignTotal_ = 1;
+ return;
+ }
+ cout << "Warning: SteadyState::setTotal: index " << i <<
+ " out of range " << total_.size() << endl;
}
double SteadyState::getEigenvalue( const unsigned int i ) const
{
- if ( i < eigenvalues_.size() )
- return eigenvalues_[i];
- cout << "Warning: SteadyState::getEigenvalue: index " << i <<
- " out of range " << eigenvalues_.size() << endl;
- return 0.0;
+ if ( i < eigenvalues_.size() )
+ return eigenvalues_[i];
+ cout << "Warning: SteadyState::getEigenvalue: index " << i <<
+ " out of range " << eigenvalues_.size() << endl;
+ return 0.0;
}
///////////////////////////////////////////////////
@@ -480,16 +500,16 @@ double SteadyState::getEigenvalue( const unsigned int i ) const
// Static func
void SteadyState::setupMatrix()
{
- setupSSmatrix();
+ setupSSmatrix();
}
void SteadyState::settleFunc()
{
- settle( 0 );
+ settle( 0 );
}
void SteadyState::resettleFunc()
{
- settle( 1 );
+ settle( 1 );
}
// Dummy function
@@ -506,8 +526,10 @@ void print_gsl_mat( gsl_matrix* m, const char* name )
{
size_t i, j;
printf( "%s[%lu, %lu] = \n", name, m->size1, m->size2 );
- for (i = 0; i < m->size1; i++) {
- for (j = 0; j < m->size2; j++) {
+ for (i = 0; i < m->size1; i++)
+ {
+ for (j = 0; j < m->size2; j++)
+ {
double x = gsl_matrix_get (m, i, j );
if ( fabs( x ) < 1e-9 ) x = 0;
printf( "%6g", x );
@@ -520,129 +542,140 @@ void print_gsl_mat( gsl_matrix* m, const char* name )
void SteadyState::showMatrices()
{
- if ( !isInitialized_ ) {
- cout << "SteadyState::showMatrices: Sorry, the system is not yet initialized.\n";
- return;
- }
- int numConsv = numVarPools_ - rank_;
- cout << "Totals: ";
- for ( int i = 0; i < numConsv; ++i )
- cout << total_[i] << " ";
- cout << endl;
+ if ( !isInitialized_ )
+ {
+ cout << "SteadyState::showMatrices: Sorry, the system is not yet initialized.\n";
+ return;
+ }
+ int numConsv = numVarPools_ - rank_;
+ cout << "Totals: ";
+ for ( int i = 0; i < numConsv; ++i )
+ cout << total_[i] << " ";
+ cout << endl;
#ifdef USE_GSL
- print_gsl_mat( gamma_, "gamma" );
- print_gsl_mat( Nr_, "Nr" );
- print_gsl_mat( LU_, "LU" );
+ print_gsl_mat( gamma_, "gamma" );
+ print_gsl_mat( Nr_, "Nr" );
+ print_gsl_mat( LU_, "LU" );
#endif
}
void SteadyState::setupSSmatrix()
{
#ifdef USE_GSL
- if ( numVarPools_ == 0 || nReacs_ == 0 )
- return;
-
- int nTot = numVarPools_ + nReacs_;
- gsl_matrix* N = gsl_matrix_calloc (numVarPools_, nReacs_);
- if ( LU_ ) { // Clear out old one.
- gsl_matrix_free( LU_ );
- }
- LU_ = gsl_matrix_calloc (numVarPools_, nTot);
- vector< int > entry = Field< vector< int > >::get(
- stoich_, "matrixEntry" );
- vector< unsigned int > colIndex = Field< vector< unsigned int > >::get(
- stoich_, "columnIndex" );
- vector< unsigned int > rowStart = Field< vector< unsigned int > >::get(
- stoich_, "rowStart" );
-
- // cout << endl << endl;
- for ( unsigned int i = 0; i < numVarPools_; ++i ) {
- gsl_matrix_set (LU_, i, i + nReacs_, 1 );
- unsigned int k = rowStart[i];
- // cout << endl << i << ": ";
- for ( unsigned int j = 0; j < nReacs_; ++j ) {
- double x = 0;
- if ( j == colIndex[k] && k < rowStart[i+1] ) {
- x = entry[k++];
- }
- // cout << " " << x;
- gsl_matrix_set (N, i, j, x);
- gsl_matrix_set (LU_, i, j, x );
- }
- }
- cout << endl << endl;
-
- rank_ = myGaussianDecomp( LU_ );
-
- unsigned int nConsv = numVarPools_ - rank_;
- if ( nConsv == 0 ) {
- cout << "SteadyState::setupSSmatrix(): Number of conserved species == 0. Aborting\n";
- return;
- }
-
- if ( Nr_ ) { // Clear out old one.
- gsl_matrix_free( Nr_ );
- }
- Nr_ = gsl_matrix_calloc ( rank_, nReacs_ );
- // Fill up Nr.
- for ( unsigned int i = 0; i < rank_; i++)
- for ( unsigned int j = i; j < nReacs_; j++)
- gsl_matrix_set (Nr_, i, j, gsl_matrix_get( LU_, i, j ) );
-
- if ( gamma_ ) { // Clear out old one.
- gsl_matrix_free( gamma_ );
- }
- gamma_ = gsl_matrix_calloc (nConsv, numVarPools_ );
-
- // Fill up gamma
- for ( unsigned int i = rank_; i < numVarPools_; ++i )
- for ( unsigned int j = 0; j < numVarPools_; ++j )
- gsl_matrix_set( gamma_, i - rank_, j,
- gsl_matrix_get( LU_, i, j + nReacs_ ) );
-
- // Fill up boundary condition values
- total_.resize( nConsv );
- total_.assign( nConsv, 0.0 );
-
- /*
- cout << "S = (";
- for ( unsigned int j = 0; j < numVarPools_; ++j )
- cout << s_->S()[ j ] << ", ";
- cout << "), Sinit = ( ";
- for ( unsigned int j = 0; j < numVarPools_; ++j )
- cout << s_->Sinit()[ j ] << ", ";
- cout << ")\n";
- */
- Id ksolve = Field< Id >::get( stoich_, "ksolve" );
- vector< double > nVec =
- LookupField< unsigned int, vector< double > >::get(
- ksolve,"nVec", 0 );
-
- if ( nVec.size() >= numVarPools_ ) {
- for ( unsigned int i = 0; i < nConsv; ++i )
- for ( unsigned int j = 0; j < numVarPools_; ++j )
- total_[i] += gsl_matrix_get( gamma_, i, j ) * nVec[ j ];
- isSetup_ = 1;
- } else {
- cout << "Error: SteadyState::setupSSmatrix(): unable to get"
- "pool numbers from ksolve.\n";
- isSetup_ = 0;
- }
-
- gsl_matrix_free( N );
+ if ( numVarPools_ == 0 || nReacs_ == 0 )
+ return;
+
+ int nTot = numVarPools_ + nReacs_;
+ gsl_matrix* N = gsl_matrix_calloc (numVarPools_, nReacs_);
+ if ( LU_ ) // Clear out old one.
+ {
+ gsl_matrix_free( LU_ );
+ }
+ LU_ = gsl_matrix_calloc (numVarPools_, nTot);
+ vector< int > entry = Field< vector< int > >::get(
+ stoich_, "matrixEntry" );
+ vector< unsigned int > colIndex = Field< vector< unsigned int > >::get(
+ stoich_, "columnIndex" );
+ vector< unsigned int > rowStart = Field< vector< unsigned int > >::get(
+ stoich_, "rowStart" );
+
+ // cout << endl << endl;
+ for ( unsigned int i = 0; i < numVarPools_; ++i )
+ {
+ gsl_matrix_set (LU_, i, i + nReacs_, 1 );
+ unsigned int k = rowStart[i];
+ // cout << endl << i << ": ";
+ for ( unsigned int j = 0; j < nReacs_; ++j )
+ {
+ double x = 0;
+ if ( j == colIndex[k] && k < rowStart[i+1] )
+ {
+ x = entry[k++];
+ }
+ // cout << " " << x;
+ gsl_matrix_set (N, i, j, x);
+ gsl_matrix_set (LU_, i, j, x );
+ }
+ }
+ cout << endl << endl;
+
+ rank_ = myGaussianDecomp( LU_ );
+
+ unsigned int nConsv = numVarPools_ - rank_;
+ if ( nConsv == 0 )
+ {
+ cout << "SteadyState::setupSSmatrix(): Number of conserved species == 0. Aborting\n";
+ return;
+ }
+
+ if ( Nr_ ) // Clear out old one.
+ {
+ gsl_matrix_free( Nr_ );
+ }
+ Nr_ = gsl_matrix_calloc ( rank_, nReacs_ );
+ // Fill up Nr.
+ for ( unsigned int i = 0; i < rank_; i++)
+ for ( unsigned int j = i; j < nReacs_; j++)
+ gsl_matrix_set (Nr_, i, j, gsl_matrix_get( LU_, i, j ) );
+
+ if ( gamma_ ) // Clear out old one.
+ {
+ gsl_matrix_free( gamma_ );
+ }
+ gamma_ = gsl_matrix_calloc (nConsv, numVarPools_ );
+
+ // Fill up gamma
+ for ( unsigned int i = rank_; i < numVarPools_; ++i )
+ for ( unsigned int j = 0; j < numVarPools_; ++j )
+ gsl_matrix_set( gamma_, i - rank_, j,
+ gsl_matrix_get( LU_, i, j + nReacs_ ) );
+
+ // Fill up boundary condition values
+ total_.resize( nConsv );
+ total_.assign( nConsv, 0.0 );
+
+ /*
+ cout << "S = (";
+ for ( unsigned int j = 0; j < numVarPools_; ++j )
+ cout << s_->S()[ j ] << ", ";
+ cout << "), Sinit = ( ";
+ for ( unsigned int j = 0; j < numVarPools_; ++j )
+ cout << s_->Sinit()[ j ] << ", ";
+ cout << ")\n";
+ */
+ Id ksolve = Field< Id >::get( stoich_, "ksolve" );
+ vector< double > nVec =
+ LookupField< unsigned int, vector< double > >::get(
+ ksolve,"nVec", 0 );
+
+ if ( nVec.size() >= numVarPools_ )
+ {
+ for ( unsigned int i = 0; i < nConsv; ++i )
+ for ( unsigned int j = 0; j < numVarPools_; ++j )
+ total_[i] += gsl_matrix_get( gamma_, i, j ) * nVec[ j ];
+ isSetup_ = 1;
+ }
+ else
+ {
+ cout << "Error: SteadyState::setupSSmatrix(): unable to get"
+ "pool numbers from ksolve.\n";
+ isSetup_ = 0;
+ }
+
+ gsl_matrix_free( N );
#endif
}
static double op( double x )
{
- return x * x;
+ return x * x;
}
static double invop( double x )
{
- if ( x > 0.0 )
- return sqrt( x );
- return 0.0;
+ if ( x > 0.0 )
+ return sqrt( x );
+ return 0.0;
}
@@ -654,140 +687,153 @@ static double invop( double x )
*/
#ifdef USE_GSL
int iterate( const gsl_multiroot_fsolver_type* st, struct reac_info *ri,
- int maxIter )
+ int maxIter )
{
- int status = 0;
- gsl_vector* x = gsl_vector_calloc( ri->num_mols );
- gsl_multiroot_fsolver *solver =
- gsl_multiroot_fsolver_alloc( st, ri->num_mols );
- gsl_multiroot_function func = {&ss_func, ri->num_mols, ri};
-
- // This gives the starting point for finding the solution
- for ( unsigned int i = 0; i < ri->num_mols; ++i )
- gsl_vector_set( x, i, invop( ri->nVec[i] ) );
-
- gsl_multiroot_fsolver_set( solver, &func, x );
-
- ri->nIter = 0;
- do {
- ri->nIter++;
- status = gsl_multiroot_fsolver_iterate( solver );
- if (status ) break;
- status = gsl_multiroot_test_residual(
- solver->f, ri->convergenceCriterion);
- } while (status == GSL_CONTINUE && ri->nIter < maxIter );
-
- gsl_multiroot_fsolver_free( solver );
- gsl_vector_free( x );
- return status;
+ int status = 0;
+ gsl_vector* x = gsl_vector_calloc( ri->num_mols );
+ gsl_multiroot_fsolver *solver =
+ gsl_multiroot_fsolver_alloc( st, ri->num_mols );
+ gsl_multiroot_function func = {&ss_func, ri->num_mols, ri};
+
+ // This gives the starting point for finding the solution
+ for ( unsigned int i = 0; i < ri->num_mols; ++i )
+ gsl_vector_set( x, i, invop( ri->nVec[i] ) );
+
+ gsl_multiroot_fsolver_set( solver, &func, x );
+
+ ri->nIter = 0;
+ do
+ {
+ ri->nIter++;
+ status = gsl_multiroot_fsolver_iterate( solver );
+ if (status ) break;
+ status = gsl_multiroot_test_residual(
+ solver->f, ri->convergenceCriterion);
+ }
+ while (status == GSL_CONTINUE && ri->nIter < maxIter );
+
+ gsl_multiroot_fsolver_free( solver );
+ gsl_vector_free( x );
+ return status;
}
#endif
void SteadyState::classifyState( const double* T )
{
#ifdef USE_GSL
- // unsigned int nConsv = numVarPools_ - rank_;
- gsl_matrix* J = gsl_matrix_calloc ( numVarPools_, numVarPools_ );
- // double* yprime = new double[ numVarPools_ ];
- // vector< double > yprime( numVarPools_, 0.0 );
- // Generate an approximation to the Jacobean by generating small
- // increments to each of the molecules in the steady state, one
- // at a time, and putting the resultant rate vector into a column
- // of the J matrix.
- // This needs a bit of heuristic to decide what is a 'small' increment.
- // Use the CoInits for this. Stoichiometry shouldn't matter too much.
- // I used the totals from consv rules earlier, but that can have
- // negative values.
- double tot = 0.0;
- Stoich* s = reinterpret_cast< Stoich* >( stoich_.eref().data() );
- vector< double > nVec = LookupField< unsigned int, vector< double > >::get(
- s->getKsolve(), "nVec", 0 );
- for ( unsigned int i = 0; i < numVarPools_; ++i ) {
- tot += nVec[i];
- }
- tot *= DELTA;
-
- vector< double > yprime( nVec.size(), 0.0 );
- // Fill up Jacobian
- for ( unsigned int i = 0; i < numVarPools_; ++i ) {
- double orig = nVec[i];
- if ( isNaN( orig ) ) {
- cout << "Warning: SteadyState::classifyState: orig=nan\n";
- solutionStatus_ = 2; // Steady state OK, eig failed
- gsl_matrix_free ( J );
- return;
- }
- if ( isNaN( tot ) ) {
- cout << "Warning: SteadyState::classifyState: tot=nan\n";
- solutionStatus_ = 2; // Steady state OK, eig failed
- gsl_matrix_free ( J );
- return;
- }
- nVec[i] = orig + tot;
-
- pool_.updateRates( &nVec[0], &yprime[0] );
- nVec[i] = orig;
-
- // Assign the rates for each mol.
- for ( unsigned int j = 0; j < numVarPools_; ++j ) {
- gsl_matrix_set( J, i, j, yprime[j] );
- }
- }
-
- // Jacobian is now ready. Find eigenvalues.
- gsl_vector_complex* vec = gsl_vector_complex_alloc( numVarPools_ );
- gsl_eigen_nonsymm_workspace* workspace =
- gsl_eigen_nonsymm_alloc( numVarPools_ );
- int status = gsl_eigen_nonsymm( J, vec, workspace );
- eigenvalues_.clear();
- eigenvalues_.resize( numVarPools_, 0.0 );
- if ( status != GSL_SUCCESS ) {
- cout << "Warning: SteadyState::classifyState failed to find eigenvalues. Status = " <<
- status << endl;
- solutionStatus_ = 2; // Steady state OK, eig classification failed
- } else { // Eigenvalues are ready. Classify state.
- nNegEigenvalues_ = 0;
- nPosEigenvalues_ = 0;
- for ( unsigned int i = 0; i < numVarPools_; ++i ) {
- gsl_complex z = gsl_vector_complex_get( vec, i );
- double r = GSL_REAL( z );
- nNegEigenvalues_ += ( r < -EPSILON );
- nPosEigenvalues_ += ( r > EPSILON );
- eigenvalues_[i] = r;
- // We have a problem here because numVarPools_ usually > rank
- // This means we have several zero eigenvalues.
- }
-
- if ( nNegEigenvalues_ == rank_ )
- stateType_ = 0; // Stable
- else if ( nPosEigenvalues_ == rank_ ) // Never see it.
- stateType_ = 1; // Unstable
- else if (nPosEigenvalues_ == 1)
- stateType_ = 2; // Saddle
- else if ( nPosEigenvalues_ >= 2 )
- stateType_ = 3; // putative oscillatory
- else if ( nNegEigenvalues_ == ( rank_ - 1) && nPosEigenvalues_ == 0 )
- stateType_ = 4; // one zero or unclassified eigenvalue. Messy.
- else
- stateType_ = 5; // Other
- }
-
- gsl_vector_complex_free( vec );
- gsl_matrix_free ( J );
- gsl_eigen_nonsymm_free( workspace );
+ // unsigned int nConsv = numVarPools_ - rank_;
+ gsl_matrix* J = gsl_matrix_calloc ( numVarPools_, numVarPools_ );
+ // double* yprime = new double[ numVarPools_ ];
+ // vector< double > yprime( numVarPools_, 0.0 );
+ // Generate an approximation to the Jacobean by generating small
+ // increments to each of the molecules in the steady state, one
+ // at a time, and putting the resultant rate vector into a column
+ // of the J matrix.
+ // This needs a bit of heuristic to decide what is a 'small' increment.
+ // Use the CoInits for this. Stoichiometry shouldn't matter too much.
+ // I used the totals from consv rules earlier, but that can have
+ // negative values.
+ double tot = 0.0;
+ Stoich* s = reinterpret_cast< Stoich* >( stoich_.eref().data() );
+ vector< double > nVec = LookupField< unsigned int, vector< double > >::get(
+ s->getKsolve(), "nVec", 0 );
+ for ( unsigned int i = 0; i < numVarPools_; ++i )
+ {
+ tot += nVec[i];
+ }
+ tot *= DELTA;
+
+ vector< double > yprime( nVec.size(), 0.0 );
+ // Fill up Jacobian
+ for ( unsigned int i = 0; i < numVarPools_; ++i )
+ {
+ double orig = nVec[i];
+ if ( isNaN( orig ) )
+ {
+ cout << "Warning: SteadyState::classifyState: orig=nan\n";
+ solutionStatus_ = 2; // Steady state OK, eig failed
+ gsl_matrix_free ( J );
+ return;
+ }
+ if ( isNaN( tot ) )
+ {
+ cout << "Warning: SteadyState::classifyState: tot=nan\n";
+ solutionStatus_ = 2; // Steady state OK, eig failed
+ gsl_matrix_free ( J );
+ return;
+ }
+ nVec[i] = orig + tot;
+
+ pool_.updateRates( &nVec[0], &yprime[0] );
+ nVec[i] = orig;
+
+ // Assign the rates for each mol.
+ for ( unsigned int j = 0; j < numVarPools_; ++j )
+ {
+ gsl_matrix_set( J, i, j, yprime[j] );
+ }
+ }
+
+ // Jacobian is now ready. Find eigenvalues.
+ gsl_vector_complex* vec = gsl_vector_complex_alloc( numVarPools_ );
+ gsl_eigen_nonsymm_workspace* workspace =
+ gsl_eigen_nonsymm_alloc( numVarPools_ );
+ int status = gsl_eigen_nonsymm( J, vec, workspace );
+ eigenvalues_.clear();
+ eigenvalues_.resize( numVarPools_, 0.0 );
+ if ( status != GSL_SUCCESS )
+ {
+ cout << "Warning: SteadyState::classifyState failed to find eigenvalues. Status = " <<
+ status << endl;
+ solutionStatus_ = 2; // Steady state OK, eig classification failed
+ }
+ else // Eigenvalues are ready. Classify state.
+ {
+ nNegEigenvalues_ = 0;
+ nPosEigenvalues_ = 0;
+ for ( unsigned int i = 0; i < numVarPools_; ++i )
+ {
+ gsl_complex z = gsl_vector_complex_get( vec, i );
+ double r = GSL_REAL( z );
+ nNegEigenvalues_ += ( r < -EPSILON );
+ nPosEigenvalues_ += ( r > EPSILON );
+ eigenvalues_[i] = r;
+ // We have a problem here because numVarPools_ usually > rank
+ // This means we have several zero eigenvalues.
+ }
+
+ if ( nNegEigenvalues_ == rank_ )
+ stateType_ = 0; // Stable
+ else if ( nPosEigenvalues_ == rank_ ) // Never see it.
+ stateType_ = 1; // Unstable
+ else if (nPosEigenvalues_ == 1)
+ stateType_ = 2; // Saddle
+ else if ( nPosEigenvalues_ >= 2 )
+ stateType_ = 3; // putative oscillatory
+ else if ( nNegEigenvalues_ == ( rank_ - 1) && nPosEigenvalues_ == 0 )
+ stateType_ = 4; // one zero or unclassified eigenvalue. Messy.
+ else
+ stateType_ = 5; // Other
+ }
+
+ gsl_vector_complex_free( vec );
+ gsl_matrix_free ( J );
+ gsl_eigen_nonsymm_free( workspace );
#endif
}
static bool isSolutionPositive( const vector< double >& x )
{
- for ( vector< double >::const_iterator
- i = x.begin(); i != x.end(); ++i ) {
- if ( *i < 0.0 ) {
- cout << "Warning: SteadyState iteration gave negative concs\n";
- return false;
- }
- }
- return true;
+ for ( vector< double >::const_iterator
+ i = x.begin(); i != x.end(); ++i )
+ {
+ if ( *i < 0.0 )
+ {
+ cout << "Warning: SteadyState iteration gave negative concs\n";
+ return false;
+ }
+ }
+ return true;
}
/**
@@ -797,76 +843,84 @@ static bool isSolutionPositive( const vector< double >& x )
void SteadyState::settle( bool forceSetup )
{
#ifdef USE_GSL
- gsl_set_error_handler_off();
-
- if ( !isInitialized_ ) {
- cout << "Error: SteadyState object has not been initialized. No calculations done\n";
- return;
- }
- if ( forceSetup || isSetup_ == 0 ) {
- setupSSmatrix();
- }
-
- // Setting up matrices and vectors for the calculation.
- unsigned int nConsv = numVarPools_ - rank_;
- double * T = (double *) calloc( nConsv, sizeof( double ) );
-
- unsigned int i, j;
-
-
- Id ksolve = Field< Id >::get( stoich_, "ksolve" );
- struct reac_info ri;
- ri.rank = rank_;
- ri.num_reacs = nReacs_;
- ri.num_mols = numVarPools_;
- ri.T = T;
- ri.Nr = Nr_;
- ri.gamma = gamma_;
- ri.pool = &pool_;
- ri.nVec =
- LookupField< unsigned int, vector< double > >::get(
- ksolve,"nVec", 0 );
- ri.convergenceCriterion = convergenceCriterion_;
-
- // Fill up boundary condition values
- if ( reassignTotal_ ) { // The user has defined new conservation values.
- for ( i = 0; i < nConsv; ++i )
- T[i] = total_[i];
- reassignTotal_ = 0;
- } else {
- for ( i = 0; i < nConsv; ++i )
- for ( j = 0; j < numVarPools_; ++j )
- T[i] += gsl_matrix_get( gamma_, i, j ) * ri.nVec[ j ];
- total_.assign( T, T + nConsv );
- }
-
- vector< double > repair( numVarPools_, 0.0 );
- for ( unsigned int j = 0; j < numVarPools_; ++j )
- repair[j] = ri.nVec[j];
-
- int status = iterate( gsl_multiroot_fsolver_hybrids, &ri, maxIter_ );
- if ( status ) // It failed. Fall back with the Newton method
- status = iterate( gsl_multiroot_fsolver_dnewton, &ri, maxIter_ );
- status_ = string( gsl_strerror( status ) );
- nIter_ = ri.nIter;
- if ( status == GSL_SUCCESS && isSolutionPositive( ri.nVec ) ) {
- solutionStatus_ = 0; // Good solution
- LookupField< unsigned int, vector< double > >::set(
- ksolve,"nVec", 0, ri.nVec );
- classifyState( T );
- } else {
- cout << "Warning: SteadyState iteration failed, status = " <<
- status_ << ", nIter = " << nIter_ << endl;
- // Repair the mess
- for ( unsigned int j = 0; j < numVarPools_; ++j )
- ri.nVec[j] = repair[j];
- solutionStatus_ = 1; // Steady state failed.
- LookupField< unsigned int, vector< double > >::set(
- ksolve,"nVec", 0, ri.nVec );
- }
-
- // Clean up.
- free( T );
+ gsl_set_error_handler_off();
+
+ if ( !isInitialized_ )
+ {
+ cout << "Error: SteadyState object has not been initialized. No calculations done\n";
+ return;
+ }
+ if ( forceSetup || isSetup_ == 0 )
+ {
+ setupSSmatrix();
+ }
+
+ // Setting up matrices and vectors for the calculation.
+ unsigned int nConsv = numVarPools_ - rank_;
+ double * T = (double *) calloc( nConsv, sizeof( double ) );
+
+ unsigned int i, j;
+
+
+ Id ksolve = Field< Id >::get( stoich_, "ksolve" );
+ struct reac_info ri;
+ ri.rank = rank_;
+ ri.num_reacs = nReacs_;
+ ri.num_mols = numVarPools_;
+ ri.T = T;
+ ri.Nr = Nr_;
+ ri.gamma = gamma_;
+ ri.pool = &pool_;
+ ri.nVec =
+ LookupField< unsigned int, vector< double > >::get(
+ ksolve,"nVec", 0 );
+ ri.convergenceCriterion = convergenceCriterion_;
+
+ // Fill up boundary condition values
+ if ( reassignTotal_ ) // The user has defined new conservation values.
+ {
+ for ( i = 0; i < nConsv; ++i )
+ T[i] = total_[i];
+ reassignTotal_ = 0;
+ }
+ else
+ {
+ for ( i = 0; i < nConsv; ++i )
+ for ( j = 0; j < numVarPools_; ++j )
+ T[i] += gsl_matrix_get( gamma_, i, j ) * ri.nVec[ j ];
+ total_.assign( T, T + nConsv );
+ }
+
+ vector< double > repair( numVarPools_, 0.0 );
+ for ( unsigned int j = 0; j < numVarPools_; ++j )
+ repair[j] = ri.nVec[j];
+
+ int status = iterate( gsl_multiroot_fsolver_hybrids, &ri, maxIter_ );
+ if ( status ) // It failed. Fall back with the Newton method
+ status = iterate( gsl_multiroot_fsolver_dnewton, &ri, maxIter_ );
+ status_ = string( gsl_strerror( status ) );
+ nIter_ = ri.nIter;
+ if ( status == GSL_SUCCESS && isSolutionPositive( ri.nVec ) )
+ {
+ solutionStatus_ = 0; // Good solution
+ LookupField< unsigned int, vector< double > >::set(
+ ksolve,"nVec", 0, ri.nVec );
+ classifyState( T );
+ }
+ else
+ {
+ cout << "Warning: SteadyState iteration failed, status = " <<
+ status_ << ", nIter = " << nIter_ << endl;
+ // Repair the mess
+ for ( unsigned int j = 0; j < numVarPools_; ++j )
+ ri.nVec[j] = repair[j];
+ solutionStatus_ = 1; // Steady state failed.
+ LookupField< unsigned int, vector< double > >::set(
+ ksolve,"nVec", 0, ri.nVec );
+ }
+
+ // Clean up.
+ free( T );
#endif
}
@@ -874,42 +928,48 @@ void SteadyState::settle( bool forceSetup )
#ifdef USE_GSL
int ss_func( const gsl_vector* x, void* params, gsl_vector* f )
{
- struct reac_info* ri = (struct reac_info *)params;
- // Stoich* s = reinterpret_cast< Stoich* >( ri->stoich.eref().data() );
- int num_consv = ri->num_mols - ri->rank;
-
- for ( unsigned int i = 0; i < ri->num_mols; ++i ) {
- double temp = op( gsl_vector_get( x, i ) );
- if ( isNaN( temp ) || isInfinity( temp ) ) {
- return GSL_ERANGE;
- } else {
- ri->nVec[i] = temp;
- }
- }
- vector< double > vels;
- ri->pool->updateReacVelocities( &ri->nVec[0], vels );
- assert( vels.size() == static_cast< unsigned int >( ri->num_reacs ) );
-
- // y = Nr . v
- // Note that Nr is row-echelon: diagonal and above.
- for ( int i = 0; i < ri->rank; ++i ) {
- double temp = 0;
- for ( int j = i; j < ri->num_reacs; ++j )
- temp += gsl_matrix_get( ri->Nr, i, j ) * vels[j];
- gsl_vector_set( f, i, temp );
- }
-
- // dT = gamma.S - T
- for ( int i = 0; i < num_consv; ++i ) {
- double dT = - ri->T[i];
- for ( unsigned int j = 0; j < ri->num_mols; ++j )
- dT += gsl_matrix_get( ri->gamma, i, j) *
- op( gsl_vector_get( x, j ) );
-
- gsl_vector_set( f, i + ri->rank, dT );
- }
-
- return GSL_SUCCESS;
+ struct reac_info* ri = (struct reac_info *)params;
+ // Stoich* s = reinterpret_cast< Stoich* >( ri->stoich.eref().data() );
+ int num_consv = ri->num_mols - ri->rank;
+
+ for ( unsigned int i = 0; i < ri->num_mols; ++i )
+ {
+ double temp = op( gsl_vector_get( x, i ) );
+ if ( isNaN( temp ) || isInfinity( temp ) )
+ {
+ return GSL_ERANGE;
+ }
+ else
+ {
+ ri->nVec[i] = temp;
+ }
+ }
+ vector< double > vels;
+ ri->pool->updateReacVelocities( &ri->nVec[0], vels );
+ assert( vels.size() == static_cast< unsigned int >( ri->num_reacs ) );
+
+ // y = Nr . v
+ // Note that Nr is row-echelon: diagonal and above.
+ for ( int i = 0; i < ri->rank; ++i )
+ {
+ double temp = 0;
+ for ( int j = i; j < ri->num_reacs; ++j )
+ temp += gsl_matrix_get( ri->Nr, i, j ) * vels[j];
+ gsl_vector_set( f, i, temp );
+ }
+
+ // dT = gamma.S - T
+ for ( int i = 0; i < num_consv; ++i )
+ {
+ double dT = - ri->T[i];
+ for ( unsigned int j = 0; j < ri->num_mols; ++j )
+ dT += gsl_matrix_get( ri->gamma, i, j) *
+ op( gsl_vector_get( x, j ) );
+
+ gsl_vector_set( f, i + ri->rank, dT );
+ }
+
+ return GSL_SUCCESS;
}
/**
@@ -923,24 +983,27 @@ int ss_func( const gsl_vector* x, void* params, gsl_vector* f )
*/
void eliminateRowsBelow( gsl_matrix* U, int start, int leftCol )
{
- int numMols = U->size1;
- double pivot = gsl_matrix_get( U, start, leftCol );
- assert( fabs( pivot ) > SteadyState::EPSILON );
- for ( int i = start + 1; i < numMols; ++i ) {
- double factor = gsl_matrix_get( U, i, leftCol );
- if ( fabs ( factor ) > SteadyState::EPSILON ) {
- factor = factor / pivot;
- for ( size_t j = leftCol + 1; j < U->size2; ++j ) {
- double x = gsl_matrix_get( U, i, j );
- double y = gsl_matrix_get( U, start, j );
- x -= y * factor;
- if ( fabs( x ) < SteadyState::EPSILON )
- x = 0.0;
- gsl_matrix_set( U, i, j, x );
- }
- }
- gsl_matrix_set( U, i, leftCol, 0.0 ); // Cleaning up.
- }
+ int numMols = U->size1;
+ double pivot = gsl_matrix_get( U, start, leftCol );
+ assert( fabs( pivot ) > SteadyState::EPSILON );
+ for ( int i = start + 1; i < numMols; ++i )
+ {
+ double factor = gsl_matrix_get( U, i, leftCol );
+ if ( fabs ( factor ) > SteadyState::EPSILON )
+ {
+ factor = factor / pivot;
+ for ( size_t j = leftCol + 1; j < U->size2; ++j )
+ {
+ double x = gsl_matrix_get( U, i, j );
+ double y = gsl_matrix_get( U, start, j );
+ x -= y * factor;
+ if ( fabs( x ) < SteadyState::EPSILON )
+ x = 0.0;
+ gsl_matrix_set( U, i, j, x );
+ }
+ }
+ gsl_matrix_set( U, i, leftCol, 0.0 ); // Cleaning up.
+ }
}
/**
@@ -953,24 +1016,29 @@ void eliminateRowsBelow( gsl_matrix* U, int start, int leftCol )
*/
int reorderRows( gsl_matrix* U, int start, int leftCol )
{
- int leftMostRow = start;
- int numReacs = U->size2 - U->size1;
- int newLeftCol = numReacs;
- for ( size_t i = start; i < U->size1; ++i ) {
- for ( int j = leftCol; j < numReacs; ++j ) {
- if ( fabs( gsl_matrix_get( U, i, j ) ) > SteadyState::EPSILON ){
- if ( j < newLeftCol ) {
- newLeftCol = j;
- leftMostRow = i;
- }
- break;
- }
- }
- }
- if ( leftMostRow != start ) { // swap them.
- gsl_matrix_swap_rows( U, start, leftMostRow );
- }
- return newLeftCol;
+ int leftMostRow = start;
+ int numReacs = U->size2 - U->size1;
+ int newLeftCol = numReacs;
+ for ( size_t i = start; i < U->size1; ++i )
+ {
+ for ( int j = leftCol; j < numReacs; ++j )
+ {
+ if ( fabs( gsl_matrix_get( U, i, j ) ) > SteadyState::EPSILON )
+ {
+ if ( j < newLeftCol )
+ {
+ newLeftCol = j;
+ leftMostRow = i;
+ }
+ break;
+ }
+ }
+ }
+ if ( leftMostRow != start ) // swap them.
+ {
+ gsl_matrix_swap_rows( U, start, leftMostRow );
+ }
+ return newLeftCol;
}
/**
@@ -982,19 +1050,20 @@ int reorderRows( gsl_matrix* U, int start, int leftCol )
*/
int myGaussianDecomp( gsl_matrix* U )
{
- int numMols = U->size1;
- int numReacs = U->size2 - numMols;
- int i;
- // Start out with a nonzero entry at 0,0
- int leftCol = reorderRows( U, 0, 0 );
-
- for ( i = 0; i < numMols - 1; ++i ) {
- eliminateRowsBelow( U, i, leftCol );
- leftCol = reorderRows( U, i + 1, leftCol );
- if ( leftCol == numReacs )
- break;
- }
- return i + 1;
+ int numMols = U->size1;
+ int numReacs = U->size2 - numMols;
+ int i;
+ // Start out with a nonzero entry at 0,0
+ int leftCol = reorderRows( U, 0, 0 );
+
+ for ( i = 0; i < numMols - 1; ++i )
+ {
+ eliminateRowsBelow( U, i, leftCol );
+ leftCol = reorderRows( U, i + 1, leftCol );
+ if ( leftCol == numReacs )
+ break;
+ }
+ return i + 1;
}
//////////////////////////////////////////////////////////////////
@@ -1003,24 +1072,26 @@ int myGaussianDecomp( gsl_matrix* U )
void recalcTotal( vector< double >& tot, gsl_matrix* g, const double* S )
{
- assert( g->size1 == tot.size() );
- for ( unsigned int i = 0; i < g->size1; ++i ) {
- double t = 0.0;
- for ( unsigned int j = 0; j < g->size2; ++j )
- t += gsl_matrix_get( g, i, j ) * S[j];
- tot[ i ] = t;
- }
+ assert( g->size1 == tot.size() );
+ for ( unsigned int i = 0; i < g->size1; ++i )
+ {
+ double t = 0.0;
+ for ( unsigned int j = 0; j < g->size2; ++j )
+ t += gsl_matrix_get( g, i, j ) * S[j];
+ tot[ i ] = t;
+ }
}
#endif // end of long section of functions using GSL
static bool checkAboveZero( const vector< double >& y )
{
- for ( vector< double >::const_iterator
- i = y.begin(); i != y.end(); ++i ) {
- if ( *i < 0.0 )
- return false;
- }
- return true;
+ for ( vector< double >::const_iterator
+ i = y.begin(); i != y.end(); ++i )
+ {
+ if ( *i < 0.0 )
+ return false;
+ }
+ return true;
}
/**
@@ -1030,54 +1101,62 @@ static bool checkAboveZero( const vector< double >& y )
void SteadyState::randomizeInitialCondition( const Eref& me )
{
#ifdef USE_GSL
- Id ksolve = Field< Id >::get( stoich_, "ksolve" );
- vector< double > nVec =
- LookupField< unsigned int, vector< double > >::get(
- ksolve,"nVec", 0 );
- int numConsv = total_.size();
- recalcTotal( total_, gamma_, &nVec[0] );
- // The reorderRows function likes to have an I matrix at the end of
- // numVarPools_, so we provide space for it, although only its first
- // column is used for the total vector.
- gsl_matrix* U = gsl_matrix_calloc ( numConsv, numVarPools_ + numConsv );
- for ( int i = 0; i < numConsv; ++i ) {
- for ( unsigned int j = 0; j < numVarPools_; ++j ) {
- gsl_matrix_set( U, i, j, gsl_matrix_get( gamma_, i, j ) );
- }
- gsl_matrix_set( U, i, numVarPools_, total_[i] );
- }
- // Do the forward elimination
- int rank = myGaussianDecomp( U );
- assert( rank = numConsv );
-
- vector< double > eliminatedTotal( numConsv, 0.0 );
- for ( int i = 0; i < numConsv; ++i ) {
- eliminatedTotal[i] = gsl_matrix_get( U, i, numVarPools_ );
- }
-
- // Put Find a vector Y that fits the consv rules.
- vector< double > y( numVarPools_, 0.0 );
- do {
- fitConservationRules( U, eliminatedTotal, y );
- } while ( !checkAboveZero( y ) );
-
- // Sanity check. Try the new vector with the old gamma and tots
- for ( int i = 0; i < numConsv; ++i ) {
- double tot = 0.0;
- for ( unsigned int j = 0; j < numVarPools_; ++j ) {
- tot += y[j] * gsl_matrix_get( gamma_, i, j );
- }
- assert( fabs( tot - total_[i] ) / tot < EPSILON );
- }
-
- // Put the new values into S.
- // cout << endl;
- for ( unsigned int j = 0; j < numVarPools_; ++j ) {
- nVec[j] = y[j];
- // cout << y[j] << " ";
- }
- LookupField< unsigned int, vector< double > >::set(
- ksolve,"nVec", 0, nVec );
+ Id ksolve = Field< Id >::get( stoich_, "ksolve" );
+ vector< double > nVec =
+ LookupField< unsigned int, vector< double > >::get(
+ ksolve,"nVec", 0 );
+ int numConsv = total_.size();
+ recalcTotal( total_, gamma_, &nVec[0] );
+ // The reorderRows function likes to have an I matrix at the end of
+ // numVarPools_, so we provide space for it, although only its first
+ // column is used for the total vector.
+ gsl_matrix* U = gsl_matrix_calloc ( numConsv, numVarPools_ + numConsv );
+ for ( int i = 0; i < numConsv; ++i )
+ {
+ for ( unsigned int j = 0; j < numVarPools_; ++j )
+ {
+ gsl_matrix_set( U, i, j, gsl_matrix_get( gamma_, i, j ) );
+ }
+ gsl_matrix_set( U, i, numVarPools_, total_[i] );
+ }
+ // Do the forward elimination
+ int rank = myGaussianDecomp( U );
+ assert( rank = numConsv );
+
+ vector< double > eliminatedTotal( numConsv, 0.0 );
+ for ( int i = 0; i < numConsv; ++i )
+ {
+ eliminatedTotal[i] = gsl_matrix_get( U, i, numVarPools_ );
+ }
+
+ // Put Find a vector Y that fits the consv rules.
+ vector< double > y( numVarPools_, 0.0 );
+ do
+ {
+ fitConservationRules( U, eliminatedTotal, y );
+ }
+ while ( !checkAboveZero( y ) );
+
+ // Sanity check. Try the new vector with the old gamma and tots
+ for ( int i = 0; i < numConsv; ++i )
+ {
+ double tot = 0.0;
+ for ( unsigned int j = 0; j < numVarPools_; ++j )
+ {
+ tot += y[j] * gsl_matrix_get( gamma_, i, j );
+ }
+ assert( fabs( tot - total_[i] ) / tot < EPSILON );
+ }
+
+ // Put the new values into S.
+ // cout << endl;
+ for ( unsigned int j = 0; j < numVarPools_; ++j )
+ {
+ nVec[j] = y[j];
+ // cout << y[j] << " ";
+ }
+ LookupField< unsigned int, vector< double > >::set(
+ ksolve,"nVec", 0, nVec );
#endif
}
@@ -1087,36 +1166,43 @@ void SteadyState::randomizeInitialCondition( const Eref& me )
*/
#ifdef USE_GSL
void SteadyState::fitConservationRules(
- gsl_matrix* U, const vector< double >& eliminatedTotal,
- vector< double >&y
- )
+ gsl_matrix* U, const vector< double >& eliminatedTotal,
+ vector< double >&y
+)
{
- int numConsv = total_.size();
- int lastJ = numVarPools_;
- for ( int i = numConsv - 1; i >= 0; --i ) {
- for ( unsigned int j = 0; j < numVarPools_; ++j ) {
- double g = gsl_matrix_get( U, i, j );
- if ( fabs( g ) > EPSILON ) {
- // double ytot = calcTot( g, i, j, lastJ );
- double ytot = 0.0;
- for ( int k = j; k < lastJ; ++k ) {
- y[k] = mtrand();
- ytot += y[k] * gsl_matrix_get( U, i, k );
- }
- assert( fabs( ytot ) > EPSILON );
- double lastYtot = 0.0;
- for ( unsigned int k = lastJ; k < numVarPools_; ++k ) {
- lastYtot += y[k] * gsl_matrix_get( U, i, k );
- }
- double scale = ( eliminatedTotal[i] - lastYtot ) / ytot;
- for ( int k = j; k < lastJ; ++k ) {
- y[k] *= scale;
- }
- lastJ = j;
- break;
- }
- }
- }
+ int numConsv = total_.size();
+ int lastJ = numVarPools_;
+ for ( int i = numConsv - 1; i >= 0; --i )
+ {
+ for ( unsigned int j = 0; j < numVarPools_; ++j )
+ {
+ double g = gsl_matrix_get( U, i, j );
+ if ( fabs( g ) > EPSILON )
+ {
+ // double ytot = calcTot( g, i, j, lastJ );
+ double ytot = 0.0;
+ for ( int k = j; k < lastJ; ++k )
+ {
+ // Use global RNG.
+ y[k] = moose::mtrand();
+ ytot += y[k] * gsl_matrix_get( U, i, k );
+ }
+ assert( fabs( ytot ) > EPSILON );
+ double lastYtot = 0.0;
+ for ( unsigned int k = lastJ; k < numVarPools_; ++k )
+ {
+ lastYtot += y[k] * gsl_matrix_get( U, i, k );
+ }
+ double scale = ( eliminatedTotal[i] - lastYtot ) / ytot;
+ for ( int k = j; k < lastJ; ++k )
+ {
+ y[k] *= scale;
+ }
+ lastJ = j;
+ break;
+ }
+ }
+ }
}
#endif
diff --git a/ksolve/Stoich.cpp b/ksolve/Stoich.cpp
index 45815140..3cd9d902 100644
--- a/ksolve/Stoich.cpp
+++ b/ksolve/Stoich.cpp
@@ -81,9 +81,9 @@ const Cinfo* Stoich::initCinfo()
" This is used to protect the chemical system from going unstable"
" in cases where the numerical integration gives a negative value."
" Typically it is a small negative value but is obviously"
- " physically impossible. In some cases we want to use the "
+ " physically impossible. In some cases we want to use the "
" solvers to handle general systems of equations (not purely "
- " chemical ones), so we have this flag to allow it.",
+ " chemical ones), so we have this flag to allow it.",
&Stoich::setAllowNegative,
&Stoich::getAllowNegative
);
@@ -554,6 +554,17 @@ vector< unsigned int > Stoich::getPoolIdMap() const
return ret;
}
+Id Stoich::getPoolByIndex( unsigned int index ) const
+{
+ map< Id, unsigned int >::const_iterator i;
+ for ( i = poolLookup_.begin(); i != poolLookup_.end(); ++i )
+ {
+ if( i->second == index )
+ return i->first;
+ }
+ return Id();
+}
+
unsigned int Stoich::getNumRates() const
{
return rates_.size();
@@ -594,8 +605,8 @@ const FuncTerm* Stoich::funcs( unsigned int i ) const
bool Stoich::isFuncTarget( unsigned int poolIndex ) const
{
- assert( poolIndex < funcTarget_.size() );
- return ( funcTarget_[poolIndex] != ~0U );
+ assert( poolIndex < funcTarget_.size() );
+ return ( funcTarget_[poolIndex] != ~0U );
}
vector< int > Stoich::getMatrixEntry() const
@@ -935,9 +946,9 @@ void Stoich::resizeArrays()
species_.resize( totNumPools, 0 );
- funcTarget_.clear();
- // Only the pools controlled by a func (targets) have positive indices.
- funcTarget_.resize( totNumPools, ~0 );
+ funcTarget_.clear();
+ // Only the pools controlled by a func (targets) have positive indices.
+ funcTarget_.resize( totNumPools, ~0 );
unsigned int totNumRates =
( reacVec_.size() + offSolverReacVec_.size() ) * (1+useOneWay_) +
@@ -1089,13 +1100,13 @@ void Stoich::installAndUnschedFunc( Id func, Id pool, double volScale )
string expr = Field< string >::get( func, "expr" );
ft->setExpr( expr );
// Tie the output of the FuncTerm to the pool it controls.
- unsigned int targetIndex = convertIdToPoolIndex( pool );
+ unsigned int targetIndex = convertIdToPoolIndex( pool );
ft->setTarget( targetIndex );
ft->setVolScale( volScale );
unsigned int funcIndex = convertIdToFuncIndex( func );
assert( funcIndex != ~0U );
- // funcTarget_ vector tracks which pools are controlled by which func.
- funcTarget_[targetIndex] = funcIndex;
+ // funcTarget_ vector tracks which pools are controlled by which func.
+ funcTarget_[targetIndex] = funcIndex;
funcs_[ funcIndex ] = ft;
}
@@ -1401,8 +1412,9 @@ void Stoich::unZombifyModel()
unZombifyPools();
- vector< Id > temp = reacVec_; temp.insert( temp.end(),
- offSolverReacVec_.begin(), offSolverReacVec_.end() );
+ vector< Id > temp = reacVec_;
+ temp.insert( temp.end(),
+ offSolverReacVec_.begin(), offSolverReacVec_.end() );
for ( vector< Id >::iterator i = temp.begin(); i != temp.end(); ++i )
{
Element* e = i->element();
@@ -1410,8 +1422,9 @@ void Stoich::unZombifyModel()
ReacBase::zombify( e, reacCinfo, Id() );
}
- temp = mmEnzVec_; temp.insert( temp.end(),
- offSolverMMenzVec_.begin(), offSolverMMenzVec_.end() );
+ temp = mmEnzVec_;
+ temp.insert( temp.end(),
+ offSolverMMenzVec_.begin(), offSolverMMenzVec_.end() );
for ( vector< Id >::iterator i = temp.begin(); i != temp.end(); ++i )
{
Element* e = i->element();
@@ -1419,8 +1432,9 @@ void Stoich::unZombifyModel()
EnzBase::zombify( e, mmEnzCinfo, Id() );
}
- temp = enzVec_; temp.insert( temp.end(),
- offSolverEnzVec_.begin(), offSolverEnzVec_.end() );
+ temp = enzVec_;
+ temp.insert( temp.end(),
+ offSolverEnzVec_.begin(), offSolverEnzVec_.end() );
for ( vector< Id >::iterator i = temp.begin(); i != temp.end(); ++i )
{
Element* e = i->element();
@@ -1428,8 +1442,9 @@ void Stoich::unZombifyModel()
CplxEnzBase::zombify( e, enzCinfo, Id() );
}
- temp = poolFuncVec_; temp.insert( temp.end(),
- incrementFuncVec_.begin(), incrementFuncVec_.end() );
+ temp = poolFuncVec_;
+ temp.insert( temp.end(),
+ incrementFuncVec_.begin(), incrementFuncVec_.end() );
for ( vector< Id >::iterator i = temp.begin(); i != temp.end(); ++i )
{
Element* e = i->element();
diff --git a/ksolve/Stoich.h b/ksolve/Stoich.h
index bea3d067..93e63b9f 100644
--- a/ksolve/Stoich.h
+++ b/ksolve/Stoich.h
@@ -91,6 +91,8 @@ class Stoich
*/
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.
@@ -485,7 +487,7 @@ class Stoich
*/
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.
diff --git a/ksolve/VoxelPools.cpp b/ksolve/VoxelPools.cpp
index 64b07be2..38c5e2e7 100644
--- a/ksolve/VoxelPools.cpp
+++ b/ksolve/VoxelPools.cpp
@@ -12,7 +12,7 @@
#include <gsl/gsl_errno.h>
#include <gsl/gsl_matrix.h>
#include <gsl/gsl_odeiv2.h>
-#elif USE_BOOST
+#elif USE_BOOST_ODE
#include <boost/numeric/odeint.hpp>
using namespace boost::numeric;
#endif
@@ -36,17 +36,17 @@ using namespace boost::numeric;
VoxelPools::VoxelPools()
{
#ifdef USE_GSL
- driver_ = 0;
+ driver_ = 0;
#endif
}
VoxelPools::~VoxelPools()
{
- for ( unsigned int i = 0; i < rates_.size(); ++i )
- delete( rates_[i] );
+ for ( unsigned int i = 0; i < rates_.size(); ++i )
+ delete( rates_[i] );
#ifdef USE_GSL
- if ( driver_ )
- gsl_odeiv2_driver_free( driver_ );
+ if ( driver_ )
+ gsl_odeiv2_driver_free( driver_ );
#endif
}
@@ -55,12 +55,12 @@ VoxelPools::~VoxelPools()
//////////////////////////////////////////////////////////////
void VoxelPools::reinit( double dt )
{
- VoxelPoolsBase::reinit();
+ VoxelPoolsBase::reinit();
#ifdef USE_GSL
- if ( !driver_ )
- return;
- gsl_odeiv2_driver_reset( driver_ );
- gsl_odeiv2_driver_reset_hstart( driver_, dt / 10.0 );
+ if ( !driver_ )
+ return;
+ gsl_odeiv2_driver_reset( driver_ );
+ gsl_odeiv2_driver_reset_hstart( driver_, dt / 10.0 );
#endif
}
@@ -68,15 +68,18 @@ void VoxelPools::setStoich( Stoich* s, const OdeSystem* ode )
{
stoichPtr_ = s;
#ifdef USE_GSL
- if ( ode ) {
+ if ( ode )
+ {
sys_ = ode->gslSys;
if ( driver_ )
gsl_odeiv2_driver_free( driver_ );
+
driver_ = gsl_odeiv2_driver_alloc_y_new(
- &sys_, ode->gslStep, ode->initStepSize,
- ode->epsAbs, ode->epsRel );
+ &sys_, ode->gslStep, ode->initStepSize,
+ ode->epsAbs, ode->epsRel
+ );
}
-#elif USE_BOOST
+#elif USE_BOOST_ODE
if( ode )
sys_ = ode->boostSys;
#endif
@@ -88,11 +91,12 @@ void VoxelPools::advance( const ProcInfo* p )
double t = p->currTime - p->dt;
#ifdef USE_GSL
int status = gsl_odeiv2_driver_apply( driver_, &t, p->currTime, varS());
- if ( status != GSL_SUCCESS ) {
+ if ( status != GSL_SUCCESS )
+ {
cout << "Error: VoxelPools::advance: GSL integration error at time "
- << t << "\n";
+ << t << "\n";
cout << "Error info: " << status << ", " <<
- gsl_strerror( status ) << endl;
+ gsl_strerror( status ) << endl;
if ( status == GSL_EMAXITER )
cout << "Max number of steps exceeded\n";
else if ( status == GSL_ENOPROG )
@@ -102,7 +106,7 @@ void VoxelPools::advance( const ProcInfo* p )
assert( 0 );
}
-#elif USE_BOOST
+#elif USE_BOOST_ODE
// NOTE: Make sure to assing vp to BoostSys vp. In next call, it will be used by
@@ -144,126 +148,128 @@ void VoxelPools::advance( const ProcInfo* p )
if( sys_.method == "rk2" )
odeint::integrate_const( rk_midpoint_stepper_type_()
- , sys_ , Svec()
- , p->currTime - p->dt, p->currTime, std::min( p->dt, fixedDt )
- );
+ , sys_ , Svec()
+ , p->currTime - p->dt, p->currTime, std::min( p->dt, fixedDt )
+ );
else if( sys_.method == "rk4" )
odeint::integrate_const( rk4_stepper_type_()
- , sys_ , Svec()
- , p->currTime - p->dt, p->currTime, std::min( p->dt, fixedDt )
- );
+ , sys_ , Svec()
+ , p->currTime - p->dt, p->currTime, std::min( p->dt, fixedDt )
+ );
else if( sys_.method == "rk5")
odeint::integrate_const( rk_karp_stepper_type_()
- , sys_ , Svec()
- , p->currTime - p->dt, p->currTime, std::min( p->dt, fixedDt )
- );
+ , sys_ , Svec()
+ , p->currTime - p->dt, p->currTime, std::min( p->dt, fixedDt )
+ );
else if( sys_.method == "rk5a")
odeint::integrate_adaptive(
- odeint::make_controlled<rk_karp_stepper_type_>( absTol, relTol)
- , sys_
- , Svec()
- , p->currTime - p->dt
- , p->currTime
- , p->dt
- );
+ odeint::make_controlled<rk_karp_stepper_type_>( absTol, relTol)
+ , sys_
+ , Svec()
+ , p->currTime - p->dt
+ , p->currTime
+ , p->dt
+ );
else if ("rk54" == sys_.method )
odeint::integrate_const( rk_karp_stepper_type_()
- , sys_ , Svec()
- , p->currTime - p->dt, p->currTime, std::min( p->dt, fixedDt )
- );
+ , sys_ , Svec()
+ , p->currTime - p->dt, p->currTime, std::min( p->dt, fixedDt )
+ );
else if ("rk54a" == sys_.method )
odeint::integrate_adaptive(
- odeint::make_controlled<rk_karp_stepper_type_>( absTol, relTol )
- , sys_, Svec()
- , p->currTime - p->dt
- , p->currTime
- , p->dt
- );
+ odeint::make_controlled<rk_karp_stepper_type_>( absTol, relTol )
+ , sys_, Svec()
+ , p->currTime - p->dt
+ , p->currTime
+ , p->dt
+ );
else if ("rk5" == sys_.method )
odeint::integrate_const( rk_dopri_stepper_type_()
- , sys_ , Svec()
- , p->currTime - p->dt, p->currTime, std::min( p->dt, fixedDt )
- );
+ , sys_ , Svec()
+ , p->currTime - p->dt, p->currTime, std::min( p->dt, fixedDt )
+ );
else if ("rk5a" == sys_.method )
odeint::integrate_adaptive(
- odeint::make_controlled<rk_dopri_stepper_type_>( absTol, relTol )
- , sys_, Svec()
- , p->currTime - p->dt
- , p->currTime
- , p->dt
- );
+ odeint::make_controlled<rk_dopri_stepper_type_>( absTol, relTol )
+ , sys_, Svec()
+ , p->currTime - p->dt
+ , p->currTime
+ , p->dt
+ );
else if( sys_.method == "rk8" )
odeint::integrate_const( rk_felhberg_stepper_type_()
- , sys_ , Svec()
- , p->currTime - p->dt, p->currTime, std::min( p->dt, fixedDt )
- );
+ , sys_ , Svec()
+ , p->currTime - p->dt, p->currTime, std::min( p->dt, fixedDt )
+ );
else if( sys_.method == "rk8a" )
odeint::integrate_adaptive(
- odeint::make_controlled<rk_felhberg_stepper_type_>( absTol, relTol )
- , sys_, Svec()
- , p->currTime - p->dt
- , p->currTime
- , p->dt
- );
+ odeint::make_controlled<rk_felhberg_stepper_type_>( absTol, relTol )
+ , sys_, Svec()
+ , p->currTime - p->dt
+ , p->currTime
+ , p->dt
+ );
else
odeint::integrate_adaptive(
- odeint::make_controlled<rk_karp_stepper_type_>( absTol, relTol )
- , sys_, Svec()
- , p->currTime - p->dt
- , p->currTime
- , p->dt
- );
+ odeint::make_controlled<rk_karp_stepper_type_>( absTol, relTol )
+ , sys_, Svec()
+ , p->currTime - p->dt
+ , p->currTime
+ , p->dt
+ );
#endif
- if ( !stoichPtr_->getAllowNegative() ) { // clean out negatives
- unsigned int nv = stoichPtr_->getNumVarPools();
- double* vs = varS();
- for ( unsigned int i = 0; i < nv; ++i ) {
- if ( signbit(vs[i]) )
- vs[i] = 0.0;
- }
- }
+ if ( !stoichPtr_->getAllowNegative() ) // clean out negatives
+ {
+ unsigned int nv = stoichPtr_->getNumVarPools();
+ double* vs = varS();
+ for ( unsigned int i = 0; i < nv; ++i )
+ {
+ if ( signbit(vs[i]) )
+ vs[i] = 0.0;
+ }
+ }
}
void VoxelPools::setInitDt( double dt )
{
#ifdef USE_GSL
- gsl_odeiv2_driver_reset_hstart( driver_, dt );
+ gsl_odeiv2_driver_reset_hstart( driver_, dt );
#endif
}
#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 )
+ void* params )
{
- VoxelPools* vp = reinterpret_cast< VoxelPools* >( params );
- // Stoich* s = reinterpret_cast< Stoich* >( params );
- double* q = const_cast< double* >( y ); // Assign the func portion.
-
- // Assign the buffered pools
- // Not possible because this is a static function
- // Not needed because dydt = 0;
- /*
- double* b = q + s->getNumVarPools();
- vector< double >::const_iterator sinit = Sinit_.begin() + s->getNumVarPools();
- for ( unsigned int i = 0; i < s->getNumBufPools(); ++i )
- *b++ = *sinit++;
- */
-
- vp->stoichPtr_->updateFuncs( q, t );
- vp->updateRates( y, dydt );
+ VoxelPools* vp = reinterpret_cast< VoxelPools* >( params );
+ // Stoich* s = reinterpret_cast< Stoich* >( params );
+ double* q = const_cast< double* >( y ); // Assign the func portion.
+
+ // Assign the buffered pools
+ // Not possible because this is a static function
+ // Not needed because dydt = 0;
+ /*
+ double* b = q + s->getNumVarPools();
+ vector< double >::const_iterator sinit = Sinit_.begin() + s->getNumVarPools();
+ for ( unsigned int i = 0; i < s->getNumBufPools(); ++i )
+ *b++ = *sinit++;
+ */
+
+ vp->stoichPtr_->updateFuncs( q, t );
+ vp->updateRates( y, dydt );
#ifdef USE_GSL
- return GSL_SUCCESS;
+ return GSL_SUCCESS;
#else
- return 0;
+ return 0;
#endif
}
-#elif USE_BOOST
+#elif USE_BOOST_ODE
void VoxelPools::evalRates(
const vector_type_& y, vector_type_& dydt, const double t, VoxelPools* vp
- )
+)
{
vp->updateRates( &y[0], &dydt[0] );
}
@@ -274,64 +280,66 @@ void VoxelPools::evalRates(
///////////////////////////////////////////////////////////////////////
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 )
- delete( rates_[i] );
-
- rates_.resize( rates.size() );
- for ( unsigned int i = 0; i < numCoreRates; ++i )
- rates_[i] = rates[i]->copyWithVolScaling( getVolume(), 1, 1 );
- for ( unsigned int i = numCoreRates; i < rates.size(); ++i ) {
- rates_[i] = rates[i]->copyWithVolScaling( getVolume(),
- getXreacScaleSubstrates(i - numCoreRates),
- getXreacScaleProducts(i - numCoreRates ) );
- }
+ // Clear out old rates if any
+ for ( unsigned int i = 0; i < rates_.size(); ++i )
+ delete( rates_[i] );
+
+ rates_.resize( rates.size() );
+ for ( unsigned int i = 0; i < numCoreRates; ++i )
+ rates_[i] = rates[i]->copyWithVolScaling( getVolume(), 1, 1 );
+ for ( unsigned int i = numCoreRates; i < rates.size(); ++i )
+ {
+ rates_[i] = rates[i]->copyWithVolScaling( getVolume(),
+ getXreacScaleSubstrates(i - numCoreRates),
+ getXreacScaleProducts(i - numCoreRates ) );
+ }
}
void VoxelPools::updateRateTerms( const vector< RateTerm* >& rates,
- unsigned int numCoreRates, unsigned int index )
+ unsigned int numCoreRates, unsigned int index )
{
- // During setup or expansion of the reac system, it is possible to
- // call this function before the rates_ term is assigned. Disable.
- if ( index >= rates_.size() )
- 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 );
+ // During setup or expansion of the reac system, it is possible to
+ // call this function before the rates_ term is assigned. Disable.
+ if ( index >= rates_.size() )
+ 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 );
}
void VoxelPools::updateRates( const double* s, double* yprime ) const
{
- const KinSparseMatrix& N = stoichPtr_->getStoichiometryMatrix();
- vector< double > v( N.nColumns(), 0.0 );
- vector< double >::iterator j = v.begin();
- // totVar should include proxyPools only if this voxel uses them
- unsigned int totVar = stoichPtr_->getNumVarPools() +
- stoichPtr_->getNumProxyPools();
- // totVar should include proxyPools if this voxel does not use them
- unsigned int totInvar = stoichPtr_->getNumBufPools();
- assert( N.nColumns() == 0 ||
- N.nRows() == stoichPtr_->getNumAllPools() );
- assert( N.nColumns() == rates_.size() );
-
- for ( vector< RateTerm* >::const_iterator
- i = rates_.begin(); i != rates_.end(); i++) {
- *j++ = (**i)( s );
- assert( !std::isnan( *( j-1 ) ) );
- }
-
- for (unsigned int i = 0; i < totVar; ++i)
- *yprime++ = N.computeRowRate( i , v );
- for (unsigned int i = 0; i < totInvar ; ++i)
- *yprime++ = 0.0;
+ const KinSparseMatrix& N = stoichPtr_->getStoichiometryMatrix();
+ vector< double > v( N.nColumns(), 0.0 );
+ vector< double >::iterator j = v.begin();
+ // totVar should include proxyPools only if this voxel uses them
+ unsigned int totVar = stoichPtr_->getNumVarPools() +
+ stoichPtr_->getNumProxyPools();
+ // totVar should include proxyPools if this voxel does not use them
+ unsigned int totInvar = stoichPtr_->getNumBufPools();
+ assert( N.nColumns() == 0 ||
+ N.nRows() == stoichPtr_->getNumAllPools() );
+ assert( N.nColumns() == rates_.size() );
+
+ for ( vector< RateTerm* >::const_iterator
+ i = rates_.begin(); i != rates_.end(); i++)
+ {
+ *j++ = (**i)( s );
+ assert( !std::isnan( *( j-1 ) ) );
+ }
+
+ for (unsigned int i = 0; i < totVar; ++i)
+ *yprime++ = N.computeRowRate( i , v );
+ for (unsigned int i = 0; i < totInvar ; ++i)
+ *yprime++ = 0.0;
}
/**
@@ -340,28 +348,29 @@ void VoxelPools::updateRates( const double* s, double* yprime ) const
* to analyze velocity.
*/
void VoxelPools::updateReacVelocities(
- const double* s, vector< double >& v ) const
+ const double* s, vector< double >& v ) const
{
- const KinSparseMatrix& N = stoichPtr_->getStoichiometryMatrix();
- assert( N.nColumns() == rates_.size() );
-
- vector< RateTerm* >::const_iterator i;
- v.clear();
- v.resize( rates_.size(), 0.0 );
- vector< double >::iterator j = v.begin();
-
- for ( i = rates_.begin(); i != rates_.end(); i++) {
- *j++ = (**i)( s );
- assert( !std::isnan( *( j-1 ) ) );
- }
+ const KinSparseMatrix& N = stoichPtr_->getStoichiometryMatrix();
+ assert( N.nColumns() == rates_.size() );
+
+ vector< RateTerm* >::const_iterator i;
+ v.clear();
+ v.resize( rates_.size(), 0.0 );
+ vector< double >::iterator j = v.begin();
+
+ for ( i = rates_.begin(); i != rates_.end(); i++)
+ {
+ *j++ = (**i)( s );
+ assert( !std::isnan( *( j-1 ) ) );
+ }
}
/// For debugging: Print contents of voxel pool
void VoxelPools::print() const
{
- cout << "numAllRates = " << rates_.size() <<
- ", numLocalRates= " << stoichPtr_->getNumCoreRates() << endl;
- VoxelPoolsBase::print();
+ cout << "numAllRates = " << rates_.size() <<
+ ", numLocalRates= " << stoichPtr_->getNumCoreRates() << endl;
+ VoxelPoolsBase::print();
}
////////////////////////////////////////////////////////////
@@ -370,8 +379,8 @@ 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/ksolve/VoxelPools.h b/ksolve/VoxelPools.h
index bd1e5ec5..a8f0b4ae 100644
--- a/ksolve/VoxelPools.h
+++ b/ksolve/VoxelPools.h
@@ -14,7 +14,7 @@
#include "OdeSystem.h"
#include "VoxelPoolsBase.h"
-#ifdef USE_BOOST
+#ifdef USE_BOOST_ODE
#include "BoostSys.h"
#endif
@@ -52,15 +52,15 @@ public:
/// Set initial timestep to use by the solver.
void setInitDt( double dt );
-#ifdef USE_GSL /* ----- not USE_BOOST ----- */
+#ifdef USE_GSL /* ----- not USE_BOOST_ODE ----- */
static int gslFunc( double t, const double* y, double *dydt, void* params);
-#elif USE_BOOST
+#elif USE_BOOST_ODE
static void evalRates( const vector_type_& y
, vector_type_& dydt
, const double t
, VoxelPools* vp
);
-#endif /* ----- not USE_BOOST ----- */
+#endif /* ----- not USE_BOOST_ODE ----- */
//////////////////////////////////////////////////////////////////
// Rate manipulation and calculation functions
@@ -102,7 +102,7 @@ private:
#ifdef USE_GSL
gsl_odeiv2_driver* driver_;
gsl_odeiv2_system sys_;
-#elif USE_BOOST
+#elif USE_BOOST_ODE
BoostSys sys_;
#endif
diff --git a/ksolve/VoxelPoolsBase.cpp b/ksolve/VoxelPoolsBase.cpp
index 22831c66..f0261245 100644
--- a/ksolve/VoxelPoolsBase.cpp
+++ b/ksolve/VoxelPoolsBase.cpp
@@ -22,13 +22,14 @@
// Class definitions
//////////////////////////////////////////////////////////////
-VoxelPoolsBase::VoxelPoolsBase()
- :
- stoichPtr_( 0 ),
- S_(1),
- Sinit_(1),
- volume_(1.0)
-{ ; }
+VoxelPoolsBase::VoxelPoolsBase() :
+ stoichPtr_( 0 ),
+ S_(1),
+ Sinit_(1),
+ volume_(1.0)
+{
+ ;
+}
VoxelPoolsBase::~VoxelPoolsBase()
{}
@@ -53,91 +54,93 @@ void VoxelPoolsBase::reinit()
//////////////////////////////////////////////////////////////
const double* VoxelPoolsBase::S() const
{
- return &S_[0];
+ return &S_[0];
}
vector< double >& VoxelPoolsBase::Svec()
{
- return S_;
+ return S_;
}
double* VoxelPoolsBase::varS()
{
- return &S_[0];
+ return &S_[0];
}
const double* VoxelPoolsBase::Sinit() const
{
- return &Sinit_[0];
+ return &Sinit_[0];
}
double* VoxelPoolsBase::varSinit()
{
- return &Sinit_[0];
+ return &Sinit_[0];
}
unsigned int VoxelPoolsBase::size() const
{
- return Sinit_.size();
+ return Sinit_.size();
}
void VoxelPoolsBase::setVolume( double vol )
{
- volume_ = vol;
+ volume_ = vol;
}
double VoxelPoolsBase::getVolume() const
{
- return volume_;
+ return volume_;
}
void VoxelPoolsBase::setVolumeAndDependencies( double vol )
{
- double ratio = vol / volume_;
- volume_ = vol;
- for ( vector< double >::iterator
- i = Sinit_.begin(); i != Sinit_.end(); ++i )
- *i *= ratio;
+ double ratio = vol / volume_;
+ volume_ = vol;
+ for ( vector< double >::iterator
+ i = Sinit_.begin(); i != Sinit_.end(); ++i )
+ *i *= ratio;
- for ( vector< double >::iterator i = S_.begin(); i != S_.end(); ++i )
- *i *= ratio;
+ for ( vector< double >::iterator i = S_.begin(); i != S_.end(); ++i )
+ *i *= ratio;
- // I would like to update the xReacScaleSubstreates and Products here,
- // but I don't know the order of their reactions. So leave it to
- // a subsequent call via Ksolve or Stoich.
+ // I would like to update the xReacScaleSubstreates and Products here,
+ // but I don't know the order of their reactions. So leave it to
+ // a subsequent call via Ksolve or Stoich.
}
void VoxelPoolsBase::scaleVolsBufsRates(
- double ratio, const Stoich* stoichPtr )
-{
- volume_ *= ratio; // Scale vol
- for ( vector< double >::iterator
- i = Sinit_.begin(); i != Sinit_.end(); ++i )
- *i *= ratio; // Scale Bufs
- // Here we also need to set the Ns for the buffered pools.
- unsigned int start = stoichPtr_->getNumVarPools();
- unsigned int end = start + stoichPtr_->getNumBufPools();
- assert( end == Sinit_.size() );
- for ( unsigned int i = start; i < end; ++i ) {
- // Must not reassign pools that are controlled by functions.
- if ( !stoichPtr->isFuncTarget(i) )
- S_[i] = Sinit_[i];
- }
-
- // Scale rates. Start by clearing out old rates if any
- for ( unsigned int i = 0; i < rates_.size(); ++i )
- delete( rates_[i] );
-
- unsigned int numCoreRates = stoichPtr->getNumCoreRates();
- const vector< RateTerm* >& rates = stoichPtr->getRateTerms();
- rates_.resize( rates.size() );
- for ( unsigned int i = 0; i < numCoreRates; ++i )
- rates_[i] = rates[i]->copyWithVolScaling( getVolume(), 1, 1 );
- for ( unsigned int i = numCoreRates; i < rates.size(); ++i ) {
- rates_[i] = rates[i]->copyWithVolScaling( getVolume(),
- getXreacScaleSubstrates(i - numCoreRates),
- getXreacScaleProducts(i - numCoreRates ) );
- }
+ double ratio, const Stoich* stoichPtr )
+{
+ volume_ *= ratio; // Scale vol
+ for ( vector< double >::iterator
+ i = Sinit_.begin(); i != Sinit_.end(); ++i )
+ *i *= ratio; // Scale Bufs
+ // Here we also need to set the Ns for the buffered pools.
+ unsigned int start = stoichPtr_->getNumVarPools();
+ unsigned int end = start + stoichPtr_->getNumBufPools();
+ assert( end == Sinit_.size() );
+ for ( unsigned int i = start; i < end; ++i )
+ {
+ // Must not reassign pools that are controlled by functions.
+ if ( !stoichPtr->isFuncTarget(i) )
+ S_[i] = Sinit_[i];
+ }
+
+ // Scale rates. Start by clearing out old rates if any
+ for ( unsigned int i = 0; i < rates_.size(); ++i )
+ delete( rates_[i] );
+
+ unsigned int numCoreRates = stoichPtr->getNumCoreRates();
+ const vector< RateTerm* >& rates = stoichPtr->getRateTerms();
+ rates_.resize( rates.size() );
+ for ( unsigned int i = 0; i < numCoreRates; ++i )
+ rates_[i] = rates[i]->copyWithVolScaling( getVolume(), 1, 1 );
+ for ( unsigned int i = numCoreRates; i < rates.size(); ++i )
+ {
+ rates_[i] = rates[i]->copyWithVolScaling( getVolume(),
+ getXreacScaleSubstrates(i - numCoreRates),
+ getXreacScaleProducts(i - numCoreRates ) );
+ }
}
//////////////////////////////////////////////////////////////
@@ -146,129 +149,134 @@ void VoxelPoolsBase::scaleVolsBufsRates(
void VoxelPoolsBase::setN( unsigned int i, double v )
{
- S_[i] = v;
- if ( S_[i] < 0.0 )
- S_[i] = 0.0;
+ S_[i] = v;
+ if ( S_[i] < 0.0 )
+ S_[i] = 0.0;
}
double VoxelPoolsBase::getN( unsigned int i ) const
{
- return S_[i];
+ return S_[i];
}
void VoxelPoolsBase::setNinit( unsigned int i, double v )
{
- Sinit_[i] = v;
- if ( Sinit_[i] < 0.0 )
- Sinit_[i] = 0.0;
+ Sinit_[i] = v;
+ if ( Sinit_[i] < 0.0 )
+ Sinit_[i] = 0.0;
}
double VoxelPoolsBase::getNinit( unsigned int i ) const
{
- return Sinit_[i];
+ return Sinit_[i];
}
void VoxelPoolsBase::setDiffConst( unsigned int i, double v )
{
- ; // Do nothing.
+ ; // Do nothing.
}
double VoxelPoolsBase::getDiffConst( unsigned int i ) const
{
- return 0;
+ return 0;
}
//////////////////////////////////////////////////////////////
// Handle cross compartment reactions
//////////////////////////////////////////////////////////////
void VoxelPoolsBase::xferIn(
- const vector< unsigned int >& poolIndex,
- const vector< double >& values,
- const vector< double >& lastValues,
- unsigned int voxelIndex )
+ const vector< unsigned int >& poolIndex,
+ const vector< double >& values,
+ const vector< double >& lastValues,
+ unsigned int voxelIndex )
{
- unsigned int offset = voxelIndex * poolIndex.size();
- vector< double >::const_iterator i = values.begin() + offset;
- vector< double >::const_iterator j = lastValues.begin() + offset;
- for ( vector< unsigned int >::const_iterator
- k = poolIndex.begin(); k != poolIndex.end(); ++k ) {
- S_[*k] += *i++ - *j++;
- }
+ unsigned int offset = voxelIndex * poolIndex.size();
+ vector< double >::const_iterator i = values.begin() + offset;
+ vector< double >::const_iterator j = lastValues.begin() + offset;
+ for ( vector< unsigned int >::const_iterator
+ k = poolIndex.begin(); k != poolIndex.end(); ++k )
+ {
+ S_[*k] += *i++ - *j++;
+ }
}
void VoxelPoolsBase::xferInOnlyProxies(
- const vector< unsigned int >& poolIndex,
- const vector< double >& values,
- unsigned int numProxyPools,
- unsigned int voxelIndex )
-{
- unsigned int offset = voxelIndex * poolIndex.size();
- vector< double >::const_iterator i = values.begin() + offset;
- unsigned int proxyEndIndex = stoichPtr_->getNumVarPools() +
- stoichPtr_->getNumProxyPools();
- for ( vector< unsigned int >::const_iterator
- k = poolIndex.begin(); k != poolIndex.end(); ++k ) {
- // if ( *k >= S_.size() - numProxyPools )
- if ( *k >= stoichPtr_->getNumVarPools() && *k < proxyEndIndex ) {
- // cout << S_[*k] << ", " << Sinit_[*k] << ", " << *i << endl;
- Sinit_[*k] = *i;
- S_[*k] = *i;
- }
- i++;
- }
+ const vector< unsigned int >& poolIndex,
+ const vector< double >& values,
+ unsigned int numProxyPools,
+ unsigned int voxelIndex )
+{
+ unsigned int offset = voxelIndex * poolIndex.size();
+ vector< double >::const_iterator i = values.begin() + offset;
+ unsigned int proxyEndIndex = stoichPtr_->getNumVarPools() +
+ stoichPtr_->getNumProxyPools();
+ for ( vector< unsigned int >::const_iterator
+ k = poolIndex.begin(); k != poolIndex.end(); ++k )
+ {
+ // if ( *k >= S_.size() - numProxyPools )
+ if ( *k >= stoichPtr_->getNumVarPools() && *k < proxyEndIndex )
+ {
+ // cout << S_[*k] << ", " << Sinit_[*k] << ", " << *i << endl;
+ Sinit_[*k] = *i;
+ S_[*k] = *i;
+ }
+ i++;
+ }
}
void VoxelPoolsBase::xferOut(
- unsigned int voxelIndex,
- vector< double >& values,
- const vector< unsigned int >& poolIndex)
+ unsigned int voxelIndex,
+ vector< double >& values,
+ const vector< unsigned int >& poolIndex)
{
- unsigned int offset = voxelIndex * poolIndex.size();
- vector< double >::iterator i = values.begin() + offset;
- for ( vector< unsigned int >::const_iterator
- k = poolIndex.begin(); k != poolIndex.end(); ++k ) {
- *i++ = S_[*k];
- }
+ unsigned int offset = voxelIndex * poolIndex.size();
+ vector< double >::iterator i = values.begin() + offset;
+ for ( vector< unsigned int >::const_iterator
+ k = poolIndex.begin(); k != poolIndex.end(); ++k )
+ {
+ *i++ = S_[*k];
+ }
}
void VoxelPoolsBase::addProxyVoxy(
- unsigned int comptIndex, Id otherComptId, unsigned int voxel )
+ unsigned int comptIndex, Id otherComptId, unsigned int voxel )
{
- if ( comptIndex >= proxyPoolVoxels_.size() ) {
- proxyPoolVoxels_.resize( comptIndex + 1 );
- }
+ if ( comptIndex >= proxyPoolVoxels_.size() )
+ {
+ proxyPoolVoxels_.resize( comptIndex + 1 );
+ }
- proxyPoolVoxels_[comptIndex].push_back( voxel );
- proxyComptMap_[otherComptId] = comptIndex;
+ proxyPoolVoxels_[comptIndex].push_back( voxel );
+ proxyComptMap_[otherComptId] = comptIndex;
}
void VoxelPoolsBase::addProxyTransferIndex(
- unsigned int comptIndex, unsigned int transferIndex )
+ unsigned int comptIndex, unsigned int transferIndex )
{
- if ( comptIndex >= proxyTransferIndex_.size() )
- proxyTransferIndex_.resize( comptIndex + 1 );
- proxyTransferIndex_[comptIndex].push_back( transferIndex );
+ if ( comptIndex >= proxyTransferIndex_.size() )
+ proxyTransferIndex_.resize( comptIndex + 1 );
+ proxyTransferIndex_[comptIndex].push_back( transferIndex );
}
bool VoxelPoolsBase::hasXfer( unsigned int comptIndex ) const
{
- if ( comptIndex >= proxyPoolVoxels_.size() )
- return false;
- return (proxyPoolVoxels_[ comptIndex ].size() > 0);
+ if ( comptIndex >= proxyPoolVoxels_.size() )
+ return false;
+ return (proxyPoolVoxels_[ comptIndex ].size() > 0);
}
bool VoxelPoolsBase::isVoxelJunctionPresent( Id i1, Id i2 ) const
{
- if ( i1 == Id () )
- return false;
- if ( proxyComptMap_.find( i1 ) == proxyComptMap_.end() )
- return false;
- if ( i2 == Id() ) // This is intentionally blank, only one jn.
- return true;
- // If there is an i2 but it isn't on the map, then not connected.
- if ( proxyComptMap_.find( i2 ) == proxyComptMap_.end() )
- return false;
- return true;
+ if ( i1 == Id () )
+ return false;
+ if ( proxyComptMap_.find( i1 ) == proxyComptMap_.end() )
+ return false;
+ if ( i2 == Id() ) // This is intentionally blank, only one jn.
+ return true;
+ // If there is an i2 but it isn't on the map, then not connected.
+ if ( proxyComptMap_.find( i2 ) == proxyComptMap_.end() )
+ return false;
+ return true;
}
////////////////////////////////////////////////////////////////////
@@ -277,32 +285,32 @@ bool VoxelPoolsBase::isVoxelJunctionPresent( Id i1, Id i2 ) const
void VoxelPoolsBase::resetXreacScale( unsigned int size )
{
- xReacScaleSubstrates_.assign( size, 1.0 );
- xReacScaleProducts_.assign( size, 1.0 );
+ xReacScaleSubstrates_.assign( size, 1.0 );
+ xReacScaleProducts_.assign( size, 1.0 );
}
void VoxelPoolsBase::forwardReacVolumeFactor( unsigned int i, double volume )
{
- assert( i < xReacScaleSubstrates_.size() );
- xReacScaleSubstrates_[i] *= volume / getVolume();
- // cout << "forwardReacVolumeFactor[" << i << "] = " << xReacScaleSubstrates_[i] <<endl;
+ assert( i < xReacScaleSubstrates_.size() );
+ xReacScaleSubstrates_[i] *= volume / getVolume();
+ // cout << "forwardReacVolumeFactor[" << i << "] = " << xReacScaleSubstrates_[i] <<endl;
}
void VoxelPoolsBase::backwardReacVolumeFactor( unsigned int i, double volume )
{
- assert( i < xReacScaleProducts_.size() );
- xReacScaleProducts_[i] *= volume / getVolume();
- // cout << "backwardReacVolumeFactor[" << i << "] = "<< xReacScaleProducts_[i] <<endl;
+ assert( i < xReacScaleProducts_.size() );
+ xReacScaleProducts_[i] *= volume / getVolume();
+ // cout << "backwardReacVolumeFactor[" << i << "] = "<< xReacScaleProducts_[i] <<endl;
}
double VoxelPoolsBase::getXreacScaleSubstrates( unsigned int i ) const
{
- return xReacScaleSubstrates_[i];
+ return xReacScaleSubstrates_[i];
}
double VoxelPoolsBase::getXreacScaleProducts( unsigned int i ) const
{
- return xReacScaleProducts_[i];
+ return xReacScaleProducts_[i];
}
/**
@@ -310,88 +318,102 @@ double VoxelPoolsBase::getXreacScaleProducts( unsigned int i ) const
* are not present on current voxel.
*/
void VoxelPoolsBase::filterCrossRateTerms(
- const vector< Id >& offSolverReacs,
- const vector< pair< Id, Id > >& offSolverReacCompts )
-{
- assert (offSolverReacs.size() == offSolverReacCompts.size() );
- // unsigned int numCoreRates = stoichPtr_->getNumCoreRates();
- for ( unsigned int i = 0; i < offSolverReacCompts.size(); ++i ) {
- const pair< Id, Id >& p = offSolverReacCompts[i];
- if ( !isVoxelJunctionPresent( p.first, p.second) ) {
- Id reacId = offSolverReacs[i];
- const Cinfo* reacCinfo = reacId.element()->cinfo();
- unsigned int k = stoichPtr_->convertIdToReacIndex( offSolverReacs[i] );
- // Start by replacing the immediate cross reaction term.
- if ( rates_[k] )
- delete rates_[k];
- rates_[k] = new ExternReac;
- if ( stoichPtr_->getOneWay() ) {
- k++; // Delete the next entry too, it is the reverse reacn.
- assert( k < rates_.size() );
- if ( reacCinfo->isA( "ReacBase" ) ) {
- if ( rates_[k] )
- delete rates_[k];
- rates_[k] = new ExternReac;
- }
- if ( reacCinfo->isA( "CplxEnzBase" ) ) { // Delete next two.
- if ( rates_[k] )
- delete rates_[k];
- rates_[k] = new ExternReac;
- k++;
- assert( k < rates_.size() );
- if ( rates_[k] )
- delete rates_[k];
- rates_[k] = new ExternReac;
- }
- } else {
- if ( reacCinfo->isA( "CplxEnzBase" ) ) { // Delete next one.
- k++;
- assert( k < rates_.size() );
- if ( rates_[k] )
- delete rates_[k];
- rates_[k] = new ExternReac;
- }
- }
- }
- }
+ const vector< Id >& offSolverReacs,
+ const vector< pair< Id, Id > >& offSolverReacCompts )
+{
+ assert (offSolverReacs.size() == offSolverReacCompts.size() );
+ // unsigned int numCoreRates = stoichPtr_->getNumCoreRates();
+ for ( unsigned int i = 0; i < offSolverReacCompts.size(); ++i )
+ {
+ const pair< Id, Id >& p = offSolverReacCompts[i];
+ if ( !isVoxelJunctionPresent( p.first, p.second) )
+ {
+ Id reacId = offSolverReacs[i];
+ const Cinfo* reacCinfo = reacId.element()->cinfo();
+ unsigned int k = stoichPtr_->convertIdToReacIndex( offSolverReacs[i] );
+ // Start by replacing the immediate cross reaction term.
+ if ( rates_[k] )
+ delete rates_[k];
+ rates_[k] = new ExternReac;
+ if ( stoichPtr_->getOneWay() )
+ {
+ k++; // Delete the next entry too, it is the reverse reacn.
+ assert( k < rates_.size() );
+ if ( reacCinfo->isA( "ReacBase" ) )
+ {
+ if ( rates_[k] )
+ delete rates_[k];
+ rates_[k] = new ExternReac;
+ }
+ if ( reacCinfo->isA( "CplxEnzBase" ) ) // Delete next two.
+ {
+ if ( rates_[k] )
+ delete rates_[k];
+ rates_[k] = new ExternReac;
+ k++;
+ assert( k < rates_.size() );
+ if ( rates_[k] )
+ delete rates_[k];
+ rates_[k] = new ExternReac;
+ }
+ }
+ else
+ {
+ if ( reacCinfo->isA( "CplxEnzBase" ) ) // Delete next one.
+ {
+ k++;
+ assert( k < rates_.size() );
+ if ( rates_[k] )
+ delete rates_[k];
+ rates_[k] = new ExternReac;
+ }
+ }
+ }
+ }
}
////////////////////////////////////////////////////////////////////////
void VoxelPoolsBase::print() const
{
- cout << "S_.size=" << S_.size() << ", volume = " << volume_ << endl;
- cout << "proxyPoolsVoxels.size()=" << proxyPoolVoxels_.size() <<
- ", proxyTransferIndex.size()=" << proxyTransferIndex_.size() <<
- endl;
- assert( proxyPoolVoxels_.size() == proxyTransferIndex_.size() );
- for ( unsigned int i = 0; i < proxyPoolVoxels_.size(); ++i ) {
- cout << "ppv[" << i << "]=";
- const vector< unsigned int >& ppv = proxyPoolVoxels_[i];
- for ( unsigned int j = 0; j < ppv.size(); ++j ) {
- cout << " " << ppv[j];
- }
- cout << endl;
- }
- for ( unsigned int i = 0; i < proxyTransferIndex_.size(); ++i ) {
- cout << "pti[" << i << "]=";
- const vector< unsigned int >& pti = proxyTransferIndex_[i];
- for ( unsigned int j = 0; j < pti.size(); ++j ) {
- cout << " " << pti[j];
- }
- cout << endl;
- }
- cout <<
- "xReacScaleSubstrates.size()=" << xReacScaleSubstrates_.size() <<
- ", xReacScaleProducts.size()=" << xReacScaleProducts_.size() <<
- endl;
- assert( xReacScaleSubstrates_.size() == xReacScaleProducts_.size() );
- for ( unsigned int i = 0; i < xReacScaleSubstrates_.size(); ++i ) {
- cout << i << " " << xReacScaleSubstrates_[i] << " " <<
- xReacScaleProducts_[i] << endl;
- }
- cout << "############## RATES ######################\n";
- for ( unsigned int i = 0; i < rates_.size(); ++i ) {
- cout << i << " : " << rates_[i]->getR1() << ", " <<
- rates_[i]->getR2() << endl;
- }
+ cout << "S_.size=" << S_.size() << ", volume = " << volume_ << endl;
+ cout << "proxyPoolsVoxels.size()=" << proxyPoolVoxels_.size() <<
+ ", proxyTransferIndex.size()=" << proxyTransferIndex_.size() <<
+ endl;
+ assert( proxyPoolVoxels_.size() == proxyTransferIndex_.size() );
+ for ( unsigned int i = 0; i < proxyPoolVoxels_.size(); ++i )
+ {
+ cout << "ppv[" << i << "]=";
+ const vector< unsigned int >& ppv = proxyPoolVoxels_[i];
+ for ( unsigned int j = 0; j < ppv.size(); ++j )
+ {
+ cout << " " << ppv[j];
+ }
+ cout << endl;
+ }
+ for ( unsigned int i = 0; i < proxyTransferIndex_.size(); ++i )
+ {
+ cout << "pti[" << i << "]=";
+ const vector< unsigned int >& pti = proxyTransferIndex_[i];
+ for ( unsigned int j = 0; j < pti.size(); ++j )
+ {
+ cout << " " << pti[j];
+ }
+ cout << endl;
+ }
+ cout <<
+ "xReacScaleSubstrates.size()=" << xReacScaleSubstrates_.size() <<
+ ", xReacScaleProducts.size()=" << xReacScaleProducts_.size() <<
+ endl;
+ assert( xReacScaleSubstrates_.size() == xReacScaleProducts_.size() );
+ for ( unsigned int i = 0; i < xReacScaleSubstrates_.size(); ++i )
+ {
+ cout << i << " " << xReacScaleSubstrates_[i] << " " <<
+ xReacScaleProducts_[i] << endl;
+ }
+ cout << "############## RATES ######################\n";
+ for ( unsigned int i = 0; i < rates_.size(); ++i )
+ {
+ cout << i << " : " << rates_[i]->getR1() << ", " <<
+ rates_[i]->getR2() << endl;
+ }
}
diff --git a/mesh/NeuroNode.cpp b/mesh/NeuroNode.cpp
index 9e86634a..9610227b 100644
--- a/mesh/NeuroNode.cpp
+++ b/mesh/NeuroNode.cpp
@@ -533,6 +533,8 @@ void NeuroNode::buildSpinyTree(
void NeuroNode::setParentAndChildren( unsigned int index, int dendParent,
vector< NeuroNode >& nodes, const unordered_map< Id, unsigned int >& dendMap )
{
+ if (dendParent < 0 || static_cast< unsigned int >(dendParent) >= nodes.size() )
+ return;
parent_ = dendParent;
const unordered_map< Id, unsigned int >::const_iterator dendLookup =
dendMap.find( nodes[dendParent].elecCompt_ );
diff --git a/msg/SingleMsg.cpp b/msg/SingleMsg.cpp
index 8286e2e7..c8ba6f00 100644
--- a/msg/SingleMsg.cpp
+++ b/msg/SingleMsg.cpp
@@ -19,48 +19,51 @@ vector< SingleMsg* > SingleMsg::msg_;
/////////////////////////////////////////////////////////////////////
SingleMsg::SingleMsg( const Eref& e1, const Eref& e2, unsigned int msgIndex)
- : Msg( ObjId( managerId_, (msgIndex != 0 ) ? msgIndex: msg_.size() ),
- e1.element(), e2.element() ),
- i1_( e1.dataIndex() ),
- i2_( e2.dataIndex() ),
- f2_( e2.fieldIndex() )
-{
- if ( msgIndex == 0 ) {
- msg_.push_back( this );
- return;
- } else if ( msg_.size() <= msgIndex ) {
- msg_.resize( msgIndex + 1 );
- }
- msg_[ msgIndex ] = this;
+ : Msg( ObjId( managerId_, (msgIndex != 0 ) ? msgIndex: msg_.size() ),
+ e1.element(), e2.element() ),
+ i1_( e1.dataIndex() ),
+ i2_( e2.dataIndex() ),
+ f2_( e2.fieldIndex() )
+{
+ if ( msgIndex == 0 )
+ {
+ msg_.push_back( this );
+ return;
+ }
+ else if ( msg_.size() <= msgIndex )
+ {
+ msg_.resize( msgIndex + 1 );
+ }
+ msg_[ msgIndex ] = this;
}
SingleMsg::~SingleMsg()
{
- assert( mid_.dataIndex < msg_.size() );
- msg_[ mid_.dataIndex ] = 0; // ensure deleted ptr isn't reused.
+ assert( mid_.dataIndex < msg_.size() );
+ msg_[ mid_.dataIndex ] = 0; // ensure deleted ptr isn't reused.
}
Eref SingleMsg::firstTgt( const Eref& src ) const
{
- if ( src.element() == e1_ )
- return Eref( e2_, i2_, f2_ );
- else if ( src.element() == e2_ )
- return Eref( e1_, i1_ );
- return Eref( 0, 0 );
+ if ( src.element() == e1_ )
+ return Eref( e2_, i2_, f2_ );
+ else if ( src.element() == e2_ )
+ return Eref( e1_, i1_ );
+ return Eref( 0, 0 );
}
void SingleMsg::sources( vector< vector< Eref > >& v ) const
{
- v.clear();
- v.resize( e2_->numData() );
- v[i2_].resize( 1, Eref( e1_, i1_ ) );
+ v.clear();
+ v.resize( e2_->numData() );
+ v[i2_].resize( 1, Eref( e1_, i1_ ) );
}
void SingleMsg::targets( vector< vector< Eref > >& v ) const
{
- v.clear();
- v.resize( e1_->numData() );
- v[i1_].resize( 1, Eref( e2_, i2_, f2_ ) );
+ v.clear();
+ v.resize( e1_->numData() );
+ v[i1_].resize( 1, Eref( e2_, i2_, f2_ ) );
}
@@ -77,54 +80,65 @@ bool SingleMsg::isMsgHere( const Qinfo& q ) const
DataId SingleMsg::i1() const
{
- return i1_;
+ return i1_;
}
DataId SingleMsg::i2() const
{
- return i2_;
+ return i2_;
}
Id SingleMsg::managerId() const
{
- return SingleMsg::managerId_;
+ return SingleMsg::managerId_;
}
ObjId SingleMsg::findOtherEnd( ObjId f ) const
{
- if ( f.element() == e1() ) {
- if ( f.dataIndex == i1_ )
- return ObjId( e2()->id(), i2_ );
- } else if ( f.element() == e2() ) {
- if ( f.dataIndex == i2_ )
- return ObjId( e1()->id(), i1_ );
- }
- return ObjId( 0, BADINDEX );
+ if ( f.element() == e1() )
+ {
+ if ( f.dataIndex == i1_ )
+ return ObjId( e2()->id(), i2_ );
+ }
+ else if ( f.element() == e2() )
+ {
+ if ( f.dataIndex == i2_ )
+ return ObjId( e1()->id(), i1_ );
+ }
+ return ObjId( 0, BADINDEX );
}
Msg* SingleMsg::copy( Id origSrc, Id newSrc, Id newTgt,
- FuncId fid, unsigned int b, unsigned int n ) const
-{
- const Element* orig = origSrc.element();
- if ( n <= 1 ) {
- SingleMsg* ret = 0;
- if ( orig == e1() ) {
- ret = new SingleMsg( Eref( newSrc.element(), i1_ ),
- Eref( newTgt.element(), i2_, f2_ ), 0 );
- ret->e1()->addMsgAndFunc( ret->mid(), fid, b );
- } else if ( orig == e2() ) {
- ret = new SingleMsg( Eref( newTgt.element(), i1_ ),
- Eref( newSrc.element(), i2_, f2_ ), 0 );
- ret->e2()->addMsgAndFunc( ret->mid(), fid, b );
- } else {
- assert( 0 );
- }
- return ret;
- } else {
- // Here we need a SliceMsg which goes from one 2-d array to another.
- cout << "Error: SingleMsg::copy: SliceMsg not yet implemented\n";
- return 0;
- }
+ FuncId fid, unsigned int b, unsigned int n ) const
+{
+ const Element* orig = origSrc.element();
+ if ( n <= 1 )
+ {
+ SingleMsg* ret = 0;
+ if ( orig == e1() )
+ {
+ ret = new SingleMsg( Eref( newSrc.element(), i1_ ),
+ Eref( newTgt.element(), i2_, f2_ ), 0 );
+ ret->e1()->addMsgAndFunc( ret->mid(), fid, b );
+ }
+ else if ( orig == e2() )
+ {
+ ret = new SingleMsg( Eref( newTgt.element(), i1_ ),
+ Eref( newSrc.element(), i2_, f2_ ), 0 );
+ ret->e2()->addMsgAndFunc( ret->mid(), fid, b );
+ }
+ else
+ {
+ assert( 0 );
+ }
+ return ret;
+ }
+ else
+ {
+ // Here we need a SliceMsg which goes from one 2-d array to another.
+ cout << "Error: SingleMsg::copy: SliceMsg not yet implemented\n";
+ return 0;
+ }
}
///////////////////////////////////////////////////////////////////////
@@ -133,37 +147,38 @@ Msg* SingleMsg::copy( Id origSrc, Id newSrc, Id newTgt,
const Cinfo* SingleMsg::initCinfo()
{
- ///////////////////////////////////////////////////////////////////
- // Field definitions.
- ///////////////////////////////////////////////////////////////////
- static ValueFinfo< SingleMsg, DataId > index1(
- "i1",
- "Index of source object.",
- &SingleMsg::setI1,
- &SingleMsg::getI1
- );
- static ValueFinfo< SingleMsg, DataId > index2(
- "i2",
- "Index of dest object.",
- &SingleMsg::setI2,
- &SingleMsg::getI2
- );
-
- static Finfo* singleMsgFinfos[] = {
- &index1, // value
- &index2, // value
- };
-
- static Dinfo< short > dinfo;
- static Cinfo singleMsgCinfo (
- "SingleMsg", // name
- Msg::initCinfo(), // base class
- singleMsgFinfos,
- sizeof( singleMsgFinfos ) / sizeof( Finfo* ), // num Fields
- &dinfo
- );
-
- return &singleMsgCinfo;
+ ///////////////////////////////////////////////////////////////////
+ // Field definitions.
+ ///////////////////////////////////////////////////////////////////
+ static ValueFinfo< SingleMsg, DataId > index1(
+ "i1",
+ "Index of source object.",
+ &SingleMsg::setI1,
+ &SingleMsg::getI1
+ );
+ static ValueFinfo< SingleMsg, DataId > index2(
+ "i2",
+ "Index of dest object.",
+ &SingleMsg::setI2,
+ &SingleMsg::getI2
+ );
+
+ static Finfo* singleMsgFinfos[] =
+ {
+ &index1, // value
+ &index2, // value
+ };
+
+ static Dinfo< short > dinfo;
+ static Cinfo singleMsgCinfo (
+ "SingleMsg", // name
+ Msg::initCinfo(), // base class
+ singleMsgFinfos,
+ sizeof( singleMsgFinfos ) / sizeof( Finfo* ), // num Fields
+ &dinfo
+ );
+
+ return &singleMsgCinfo;
}
static const Cinfo* singleMsgCinfo = SingleMsg::initCinfo();
@@ -171,48 +186,48 @@ static const Cinfo* singleMsgCinfo = SingleMsg::initCinfo();
DataId SingleMsg::getI1() const
{
- return i1_;
+ return i1_;
}
void SingleMsg::setI1( DataId di )
{
- i1_ = di;
- e1()->markRewired();
- e2()->markRewired();
+ i1_ = di;
+ e1()->markRewired();
+ e2()->markRewired();
}
DataId SingleMsg::getI2() const
{
- return i2_;
+ return i2_;
}
void SingleMsg::setI2( DataId di )
{
- i2_ = di;
- e1()->markRewired();
- e2()->markRewired();
+ i2_ = di;
+ e1()->markRewired();
+ e2()->markRewired();
}
void SingleMsg::setTargetField( unsigned int f )
{
- f2_ = f;
- e1()->markRewired();
+ f2_ = f;
+ e1()->markRewired();
}
unsigned int SingleMsg::getTargetField() const
{
- return f2_;
+ return f2_;
}
/// Static function for Msg access
unsigned int SingleMsg::numMsg()
{
- return msg_.size();
+ return msg_.size();
}
/// Static function for Msg access
char* SingleMsg::lookupMsg( unsigned int index )
{
- assert( index < msg_.size() );
- return reinterpret_cast< char* >( msg_[index] );
+ assert( index < msg_.size() );
+ return reinterpret_cast< char* >( msg_[index] );
}
diff --git a/msg/SparseMsg.cpp b/msg/SparseMsg.cpp
index 7511aa0f..0196ed30 100644
--- a/msg/SparseMsg.cpp
+++ b/msg/SparseMsg.cpp
@@ -7,11 +7,11 @@
** See the file COPYING.LIB for the full notice.
**********************************************************************/
-#include "header.h"
-#include "SparseMatrix.h"
-#include "SparseMsg.h"
-#include "../randnum/randnum.h"
+#include "../basecode/header.h"
+#include "../basecode/global.h"
#include "../shell/Shell.h"
+#include "../basecode/SparseMatrix.h"
+#include "SparseMsg.h"
// Initializing static variables
Id SparseMsg::managerId_;
@@ -23,34 +23,34 @@ vector< SparseMsg* > SparseMsg::msg_;
const Cinfo* SparseMsg::initCinfo()
{
- ///////////////////////////////////////////////////////////////////
- // Field definitions.
- ///////////////////////////////////////////////////////////////////
- static ReadOnlyValueFinfo< SparseMsg, unsigned int > numRows(
- "numRows",
- "Number of rows in matrix.",
- &SparseMsg::getNumRows
- );
- static ReadOnlyValueFinfo< SparseMsg, unsigned int > numColumns(
- "numColumns",
- "Number of columns in matrix.",
- &SparseMsg::getNumColumns
- );
- static ReadOnlyValueFinfo< SparseMsg, unsigned int > numEntries(
- "numEntries",
- "Number of Entries in matrix.",
- &SparseMsg::getNumEntries
- );
-
- static ValueFinfo< SparseMsg, vector< unsigned int > > connectionList(
- "connectionList",
- "Pairwise specification of connection matrix where each x,y value "
- "represents a connection from src[x] to dest[y]. "
- "The (x,y) entries are ordered in a single vector as \n"
- "(x0, x1,... x_n-1, y0, y1,... y_n-1)\n",
- &SparseMsg::setEntryPairs,
- &SparseMsg::getEntryPairs
- );
+ ///////////////////////////////////////////////////////////////////
+ // Field definitions.
+ ///////////////////////////////////////////////////////////////////
+ static ReadOnlyValueFinfo< SparseMsg, unsigned int > numRows(
+ "numRows",
+ "Number of rows in matrix.",
+ &SparseMsg::getNumRows
+ );
+ static ReadOnlyValueFinfo< SparseMsg, unsigned int > numColumns(
+ "numColumns",
+ "Number of columns in matrix.",
+ &SparseMsg::getNumColumns
+ );
+ static ReadOnlyValueFinfo< SparseMsg, unsigned int > numEntries(
+ "numEntries",
+ "Number of Entries in matrix.",
+ &SparseMsg::getNumEntries
+ );
+
+ static ValueFinfo< SparseMsg, vector< unsigned int > > connectionList(
+ "connectionList",
+ "Pairwise specification of connection matrix where each x,y value "
+ "represents a connection from src[x] to dest[y]. "
+ "The (x,y) entries are ordered in a single vector as \n"
+ "(x0, x1,... x_n-1, y0, y1,... y_n-1)\n",
+ &SparseMsg::setEntryPairs,
+ &SparseMsg::getEntryPairs
+ );
/// Connection matrix entries to manipulate in Python.
static ReadOnlyValueFinfo< SparseMsg, vector< unsigned int > >
@@ -76,106 +76,107 @@ const Cinfo* SparseMsg::initCinfo()
&SparseMsg::getRowStart
);
- static ValueFinfo< SparseMsg, double > probability(
- "probability",
- "connection probability for random connectivity.",
- &SparseMsg::setProbability,
- &SparseMsg::getProbability
- );
+ static ValueFinfo< SparseMsg, double > probability(
+ "probability",
+ "connection probability for random connectivity.",
+ &SparseMsg::setProbability,
+ &SparseMsg::getProbability
+ );
- static ValueFinfo< SparseMsg, long > seed(
- "seed",
- "Random number seed for generating probabilistic connectivity.",
- &SparseMsg::setSeed,
- &SparseMsg::getSeed
- );
+ static ValueFinfo< SparseMsg, unsigned long > seed(
+ "seed",
+ "Random number seed for generating probabilistic connectivity.",
+ &SparseMsg::setSeed,
+ &SparseMsg::getSeed
+ );
////////////////////////////////////////////////////////////////////////
// DestFinfos
////////////////////////////////////////////////////////////////////////
- static DestFinfo setRandomConnectivity( "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 ) );
-
- static DestFinfo unsetEntry( "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 ) );
-
- static DestFinfo transpose( "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 ) );
-
- 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 ) );
-
- 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 ) );
+ static DestFinfo setRandomConnectivity( "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 ) );
+
+ static DestFinfo unsetEntry( "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 ) );
+
+ static DestFinfo transpose( "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 ) );
+
+ 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 ) );
+
+ 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 ) );
////////////////////////////////////////////////////////////////////////
// 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
- };
-
- static Dinfo< short > dinfo;
- static Cinfo sparseMsgCinfo (
- "SparseMsg", // name
- Msg::initCinfo(), // base class
- sparseMsgFinfos,
- sizeof( sparseMsgFinfos ) / sizeof( Finfo* ), // num Fields
- &dinfo
- );
-
- return &sparseMsgCinfo;
+ 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
+ };
+
+ static Dinfo< short > dinfo;
+ static Cinfo sparseMsgCinfo (
+ "SparseMsg", // name
+ Msg::initCinfo(), // base class
+ sparseMsgFinfos,
+ sizeof( sparseMsgFinfos ) / sizeof( Finfo* ), // num Fields
+ &dinfo
+ );
+
+ return &sparseMsgCinfo;
}
static const Cinfo* sparseMsgCinfo = SparseMsg::initCinfo();
@@ -185,41 +186,44 @@ static const Cinfo* sparseMsgCinfo = SparseMsg::initCinfo();
//////////////////////////////////////////////////////////////////
void SparseMsg::setProbability ( double probability )
{
- p_ = probability;
- mtseed( seed_ );
- randomConnect( probability );
+ p_ = probability;
+ randomConnect( probability );
}
double SparseMsg::getProbability ( ) const
{
- return p_;
+ return p_;
}
-void SparseMsg::setSeed ( long seed )
+void SparseMsg::setSeed ( unsigned long seed )
{
- seed_ = seed;
- mtseed( seed_ );
- randomConnect( p_ );
+ if( seed > 0 )
+ seed_ = seed;
+ else
+ seed_ = rd_();
+
+ rng_.seed( seed_ );
+ randomConnect( p_ );
}
-long SparseMsg::getSeed () const
+unsigned long SparseMsg::getSeed () const
{
- return seed_;
+ return seed_;
}
unsigned int SparseMsg::getNumRows() const
{
- return matrix_.nRows();
+ return matrix_.nRows();
}
unsigned int SparseMsg::getNumColumns() const
{
- return matrix_.nColumns();
+ return matrix_.nColumns();
}
unsigned int SparseMsg::getNumEntries() const
{
- return matrix_.nEntries();
+ return matrix_.nEntries();
}
vector< unsigned int > SparseMsg::getMatrixEntry() const
@@ -239,24 +243,25 @@ vector< unsigned int > SparseMsg::getRowStart() const
void SparseMsg::setEntryPairs( vector< unsigned int > v )
{
- vector< unsigned int > src( v.begin(), v.begin() + v.size()/2 );
- vector< unsigned int > dest( v.begin() + v.size()/2, v.end() );
- pairFill( src, dest );
+ vector< unsigned int > src( v.begin(), v.begin() + v.size()/2 );
+ vector< unsigned int > dest( v.begin() + v.size()/2, v.end() );
+ pairFill( src, dest );
}
vector< unsigned int > SparseMsg::getEntryPairs() const
{
- vector< unsigned int > cols = matrix_.colIndex();
- vector< unsigned int > y;
- for ( unsigned int row = 0; row < matrix_.nRows(); ++row ) {
- unsigned int begin = matrix_.rowStart()[row];
- unsigned int end = matrix_.rowStart()[row+1];
- for ( unsigned int j = begin; j < end; ++j )
- y.push_back( row );
- }
- assert( cols.size() == y.size() );
- y.insert( y.end(), cols.begin(), cols.end() );
- return y;
+ vector< unsigned int > cols = matrix_.colIndex();
+ vector< unsigned int > y;
+ for ( unsigned int row = 0; row < matrix_.nRows(); ++row )
+ {
+ unsigned int begin = matrix_.rowStart()[row];
+ unsigned int end = matrix_.rowStart()[row+1];
+ for ( unsigned int j = begin; j < end; ++j )
+ y.push_back( row );
+ }
+ assert( cols.size() == y.size() );
+ y.insert( y.end(), cols.begin(), cols.end() );
+ return y;
}
//////////////////////////////////////////////////////////////////
@@ -265,109 +270,115 @@ vector< unsigned int > SparseMsg::getEntryPairs() const
void SparseMsg::setRandomConnectivity( double probability, long seed )
{
- p_ = probability;
- seed_ = seed;
- mtseed( seed );
- randomConnect( probability );
+ p_ = probability;
+ rng_.seed( seed );
+ randomConnect( probability );
}
void SparseMsg::setEntry(
- unsigned int row, unsigned int column, unsigned int value )
+ unsigned int row, unsigned int column, unsigned int value )
{
- matrix_.set( row, column, value );
+ matrix_.set( row, column, value );
}
void SparseMsg::unsetEntry( unsigned int row, unsigned int column )
{
- matrix_.unset( row, column );
+ matrix_.unset( row, column );
}
void SparseMsg::clear()
{
- matrix_.clear();
+ matrix_.clear();
}
void SparseMsg::transpose()
{
- matrix_.transpose();
- e1()->markRewired();
- e2()->markRewired();
+ matrix_.transpose();
+ e1()->markRewired();
+ e2()->markRewired();
}
void SparseMsg::updateAfterFill()
{
- unsigned int startData = e2_->localDataStart();
- unsigned int endData = startData + e2_->numLocalData();
- SparseMatrix< unsigned int > temp( matrix_);
- temp.transpose();
- for ( unsigned int i = 0; i < temp.nRows(); ++ i ) {
- const unsigned int* colIndex;
- const unsigned int* entry;
- unsigned int num = temp.getRow( i, &entry, &colIndex );
- if ( i >= startData && i < endData ) {
- // Inefficient. Better to do it in one pass after getting
- // the max num
- e2_->resizeField( i - startData, num + 1 );
- }
- }
- e1()->markRewired();
- e2()->markRewired();
+ unsigned int startData = e2_->localDataStart();
+ unsigned int endData = startData + e2_->numLocalData();
+ SparseMatrix< unsigned int > temp( matrix_);
+ temp.transpose();
+ for ( unsigned int i = 0; i < temp.nRows(); ++ i )
+ {
+ const unsigned int* colIndex;
+ const unsigned int* entry;
+ unsigned int num = temp.getRow( i, &entry, &colIndex );
+ if ( i >= startData && i < endData )
+ {
+ // Inefficient. Better to do it in one pass after getting
+ // the max num
+ e2_->resizeField( i - startData, num + 1 );
+ }
+ }
+ e1()->markRewired();
+ e2()->markRewired();
}
void SparseMsg::pairFill( vector< unsigned int > src,
- vector< unsigned int> dest )
-{
- // Sanity check
- vector< unsigned int >::const_iterator i;
- for ( i = src.begin(); i != src.end(); ++i ) {
- if (*i >= e1()->numData() ) {
- cout << "Warning: SparseMsg::pairFill: Src index " << *i <<
- " exceeds Src array size " << e1()->numData() <<
- ". Aborting\n";
- return;
- }
- }
- for ( i = dest.begin(); i != dest.end(); ++i ) {
- if (*i >= e2()->numData() ) {
- cout << "Warning: SparseMsg::pairFill: Dest index " << *i <<
- " exceeds Dest array size " << e2()->numData() <<
- ". Aborting\n";
- return;
- }
- }
-
- vector< unsigned int > numAtDest( dest.size(), 0 );
- vector< unsigned int > fieldIndex( dest.size(), 0 );
- for ( unsigned int i = 0; i < dest.size(); ++i ) {
- fieldIndex[i] = numAtDest[ dest[i] ];
- // Could do on previous line, but clarity
- ++numAtDest[ dest[i] ];
- }
-
- /**
- * We set retainSize flag to true since the # of src/dest objects
- * doesn't change. We can explicitly assign it elsewhere if needed.
- */
- matrix_.tripletFill( src, dest, fieldIndex, true );
- updateAfterFill();
+ vector< unsigned int> dest )
+{
+ // Sanity check
+ vector< unsigned int >::const_iterator i;
+ for ( i = src.begin(); i != src.end(); ++i )
+ {
+ if (*i >= e1()->numData() )
+ {
+ cout << "Warning: SparseMsg::pairFill: Src index " << *i <<
+ " exceeds Src array size " << e1()->numData() <<
+ ". Aborting\n";
+ return;
+ }
+ }
+ for ( i = dest.begin(); i != dest.end(); ++i )
+ {
+ if (*i >= e2()->numData() )
+ {
+ cout << "Warning: SparseMsg::pairFill: Dest index " << *i <<
+ " exceeds Dest array size " << e2()->numData() <<
+ ". Aborting\n";
+ return;
+ }
+ }
+
+ vector< unsigned int > numAtDest( dest.size(), 0 );
+ vector< unsigned int > fieldIndex( dest.size(), 0 );
+ for ( unsigned int i = 0; i < dest.size(); ++i )
+ {
+ fieldIndex[i] = numAtDest[ dest[i] ];
+ // Could do on previous line, but clarity
+ ++numAtDest[ dest[i] ];
+ }
+
+ /**
+ * We set retainSize flag to true since the # of src/dest objects
+ * doesn't change. We can explicitly assign it elsewhere if needed.
+ */
+ matrix_.tripletFill( src, dest, fieldIndex, true );
+ updateAfterFill();
}
void SparseMsg::tripletFill( vector< unsigned int > src,
- vector< unsigned int> destDataIndex,
- vector< unsigned int> destFieldIndex )
+ vector< unsigned int> destDataIndex,
+ vector< unsigned int> destFieldIndex )
{
- // We set retainSize flag to true
- matrix_.tripletFill( src, destDataIndex, destFieldIndex, true );
- updateAfterFill();
+ // We set retainSize flag to true
+ matrix_.tripletFill( src, destDataIndex, destFieldIndex, true );
+ updateAfterFill();
}
void SparseMsg::tripletFill1( vector< unsigned int > v )
{
- unsigned int s3 = v.size() / 3;
- vector< unsigned int > src( v.begin(), v.begin() + s3 );
- vector< unsigned int > dest( v.begin() + s3, v.begin() + 2 * s3 );
- vector< unsigned int > fieldIndex( v.begin() + 2 * s3, v.end() );
- tripletFill( src, dest, fieldIndex );
+ unsigned int s3 = v.size() / 3;
+ vector< unsigned int > src( v.begin(), v.begin() + s3 );
+ vector< unsigned int > dest( v.begin() + s3, v.begin() + 2 * s3 );
+ vector< unsigned int > fieldIndex( v.begin() + 2 * s3, v.end() );
+ tripletFill( src, dest, fieldIndex );
}
//////////////////////////////////////////////////////////////////
@@ -376,59 +387,70 @@ 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 ),
- numThreads_( 1 ),
- nrows_( 0 ),
- p_( 0.0 ), seed_( 0 )
-{
- unsigned int nrows = 0;
- unsigned int ncolumns = 0;
- nrows = e1->numData();
- ncolumns = e2->numData();
- matrix_.setSize( nrows, ncolumns );
- if ( msgIndex == 0 ) {
- msg_.push_back( this );
- } else {
- if ( msg_.size() <= msgIndex )
- msg_.resize( msgIndex + 1 );
- msg_[ msgIndex ] = this;
- }
-
- // cout << Shell::myNode() << ": SparseMsg constructor between " << e1->getName() << " and " << e2->getName() << endl;
+ : Msg( ObjId( managerId_, (msgIndex != 0) ? msgIndex: msg_.size() ),
+ e1, e2 ),
+ numThreads_( 1 ),
+ nrows_( 0 ),
+ p_( 0.0 ), seed_( 0 )
+{
+ unsigned int nrows = 0;
+ unsigned int ncolumns = 0;
+ nrows = e1->numData();
+ ncolumns = e2->numData();
+ matrix_.setSize( nrows, ncolumns );
+ if ( msgIndex == 0 )
+ {
+ msg_.push_back( this );
+ }
+ else
+ {
+ if ( msg_.size() <= msgIndex )
+ msg_.resize( msgIndex + 1 );
+ msg_[ msgIndex ] = this;
+ }
+
+ // cout << Shell::myNode() << ": SparseMsg constructor between " << e1->getName() << " and " << e2->getName() << endl;
+
+ // Init rng with random device.
+ if( seed_ == 0 )
+ rng_.seed( rd_() );
}
SparseMsg::~SparseMsg()
{
- assert( mid_.dataIndex < msg_.size() );
- msg_[ mid_.dataIndex ] = 0; // ensure deleted ptr isn't reused.
+ assert( mid_.dataIndex < msg_.size() );
+ msg_[ mid_.dataIndex ] = 0; // ensure deleted ptr isn't reused.
}
unsigned int rowIndex( const Element* e, const DataId& d )
{
- // FieldDataHandlerBase* fdh = dynamic_cast< FieldDataHandlerBase* >( e->dataHandler() );
+ // FieldDataHandlerBase* fdh = dynamic_cast< FieldDataHandlerBase* >( e->dataHandler() );
- return d;
+ return d;
}
Eref SparseMsg::firstTgt( const Eref& src ) const
{
- if ( matrix_.nEntries() == 0 )
- return Eref( 0, 0 );
-
- if ( src.element() == e1_ ) {
- const unsigned int* fieldIndex;
- const unsigned int* colIndex;
- unsigned int n = matrix_.getRow( src.dataIndex(),
- &fieldIndex, &colIndex );
- if ( n != 0 ) {
- return Eref( e2_, colIndex[0], fieldIndex[0] );
- }
- } else if ( src.element() == e2_ ) {
- return Eref( e1_, 0 );
- }
- return Eref( 0, 0 );
+ if ( matrix_.nEntries() == 0 )
+ return Eref( 0, 0 );
+
+ if ( src.element() == e1_ )
+ {
+ const unsigned int* fieldIndex;
+ const unsigned int* colIndex;
+ unsigned int n = matrix_.getRow( src.dataIndex(),
+ &fieldIndex, &colIndex );
+ if ( n != 0 )
+ {
+ return Eref( e2_, colIndex[0], fieldIndex[0] );
+ }
+ }
+ else if ( src.element() == e2_ )
+ {
+ return Eref( e1_, 0 );
+ }
+ return Eref( 0, 0 );
}
/**
@@ -442,163 +464,184 @@ Eref SparseMsg::firstTgt( const Eref& src ) const
*/
unsigned int SparseMsg::randomConnect( double probability )
{
- unsigned int nRows = matrix_.nRows(); // Sources
- unsigned int nCols = matrix_.nColumns(); // Destinations
- matrix_.clear();
- unsigned int totalSynapses = 0;
- vector< unsigned int > sizes( nCols, 0 );
- unsigned int totSynNum = 0;
- Element* syn = e2_;
- unsigned int startData = syn->localDataStart();
- unsigned int endData = startData + syn->numLocalData();
-
- assert( nCols == syn->numData() );
-
- matrix_.transpose();
- for ( unsigned int i = 0; i < nCols; ++i ) {
- vector< unsigned int > synIndex;
- // This needs to be obtained from current size of syn array.
- // unsigned int synNum = sizes[ i ];
- unsigned int synNum = 0;
- for ( unsigned int j = 0; j < nRows; ++j ) {
- double r = mtrand(); // Want to ensure it is called each time round the loop.
- if ( r < probability ) {
- synIndex.push_back( synNum );
- ++synNum;
- ++totSynNum;
- } else {
- synIndex.push_back( ~0 );
- }
- }
-
- if ( i >= startData && i < endData ) {
- e2_->resizeField( i - startData, synNum );
- }
- totalSynapses += synNum;
- matrix_.addRow( i, synIndex );
- /*
- * This is the correct form, but I need to implement something
- * to check up for target nodes in order to use this.
- if ( i >= startData && i < endData ) {
- e2_->resizeField( i - startData, synNum );
- totalSynapses += synNum;
- matrix_.addRow( i, synIndex );
- } else {
- synIndex.resize( 0 );
- synIndex.assign( nRows, ~0 );
- matrix_.addRow( i, synIndex );
- }
- */
- }
-
- matrix_.transpose();
- // cout << Shell::myNode() << ": sizes.size() = " << sizes.size() << ", ncols = " << nCols << ", startSynapse = " << startSynapse << endl;
- e1()->markRewired();
- e2()->markRewired();
- return totalSynapses;
+ unsigned int nRows = matrix_.nRows(); // Sources
+ unsigned int nCols = matrix_.nColumns(); // Destinations
+ matrix_.clear();
+ unsigned int totalSynapses = 0;
+ vector< unsigned int > sizes( nCols, 0 );
+ unsigned int totSynNum = 0;
+ Element* syn = e2_;
+ unsigned int startData = syn->localDataStart();
+ unsigned int endData = startData + syn->numLocalData();
+
+ assert( nCols == syn->numData() );
+
+ matrix_.transpose();
+ for ( unsigned int i = 0; i < nCols; ++i )
+ {
+ vector< unsigned int > synIndex;
+ // This needs to be obtained from current size of syn array.
+ // unsigned int synNum = sizes[ i ];
+ 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.
+ if ( r < probability )
+ {
+ synIndex.push_back( synNum );
+ ++synNum;
+ ++totSynNum;
+ }
+ else
+ {
+ synIndex.push_back( ~0 );
+ }
+ }
+
+ if ( i >= startData && i < endData )
+ {
+ e2_->resizeField( i - startData, synNum );
+ }
+ totalSynapses += synNum;
+ matrix_.addRow( i, synIndex );
+ /*
+ * This is the correct form, but I need to implement something
+ * to check up for target nodes in order to use this.
+ if ( i >= startData && i < endData ) {
+ e2_->resizeField( i - startData, synNum );
+ totalSynapses += synNum;
+ matrix_.addRow( i, synIndex );
+ } else {
+ synIndex.resize( 0 );
+ synIndex.assign( nRows, ~0 );
+ matrix_.addRow( i, synIndex );
+ }
+ */
+ }
+
+ matrix_.transpose();
+ // cout << Shell::myNode() << ": sizes.size() = " << sizes.size() << ", ncols = " << nCols << ", startSynapse = " << startSynapse << endl;
+ e1()->markRewired();
+ e2()->markRewired();
+ return totalSynapses;
}
Id SparseMsg::managerId() const
{
- return SparseMsg::managerId_;
+ return SparseMsg::managerId_;
}
void SparseMsg::setMatrix( const SparseMatrix< unsigned int >& m )
{
- matrix_ = m;
+ matrix_ = m;
}
SparseMatrix< unsigned int >& SparseMsg::getMatrix( )
{
- return matrix_;
+ return matrix_;
}
ObjId SparseMsg::findOtherEnd( ObjId f ) const
{
- if ( f.element() == e1() ) {
- const unsigned int* entry;
- const unsigned int* colIndex;
- unsigned int num = matrix_.getRow( f.dataIndex, &entry, &colIndex );
- if ( num > 0 ) { // Return the first matching entry.
- return ObjId( e2()->id(), colIndex[0] );
- }
- return ObjId( 0, BADINDEX );
- } else if ( f.element() == e2() ) { // Bad! Slow! Avoid!
- vector< unsigned int > entry;
- vector< unsigned int > rowIndex;
- unsigned int num = matrix_.getColumn( f.dataIndex, entry, rowIndex );
- if ( num > 0 ) { // Return the first matching entry.
- return ObjId( e1()->id(), DataId( rowIndex[0] ) );
- }
- }
- return ObjId( 0, BADINDEX );
+ if ( f.element() == e1() )
+ {
+ const unsigned int* entry;
+ const unsigned int* colIndex;
+ unsigned int num = matrix_.getRow( f.dataIndex, &entry, &colIndex );
+ if ( num > 0 ) // Return the first matching entry.
+ {
+ return ObjId( e2()->id(), colIndex[0] );
+ }
+ return ObjId( 0, BADINDEX );
+ }
+ else if ( f.element() == e2() ) // Bad! Slow! Avoid!
+ {
+ vector< unsigned int > entry;
+ vector< unsigned int > rowIndex;
+ unsigned int num = matrix_.getColumn( f.dataIndex, entry, rowIndex );
+ if ( num > 0 ) // Return the first matching entry.
+ {
+ return ObjId( e1()->id(), DataId( rowIndex[0] ) );
+ }
+ }
+ return ObjId( 0, BADINDEX );
}
Msg* SparseMsg::copy( Id origSrc, Id newSrc, Id newTgt,
- FuncId fid, unsigned int b, unsigned int n ) const
-{
- const Element* orig = origSrc.element();
- if ( n <= 1 ) {
- SparseMsg* ret = 0;
- if ( orig == e1() ) {
- ret = new SparseMsg( newSrc.element(), newTgt.element(), 0 );
- ret->e1()->addMsgAndFunc( ret->mid(), fid, b );
- } else if ( orig == e2() ) {
- ret = new SparseMsg( newTgt.element(), newSrc.element(), 0 );
- ret->e2()->addMsgAndFunc( ret->mid(), fid, b );
- } else {
- assert( 0 );
- }
- ret->setMatrix( matrix_ );
- ret->nrows_ = nrows_;
- return ret;
- } else {
- // Here we need a SliceMsg which goes from one 2-d array to another.
- cout << "Error: SparseMsg::copy: SparseSliceMsg not yet implemented\n";
- return 0;
- }
+ FuncId fid, unsigned int b, unsigned int n ) const
+{
+ const Element* orig = origSrc.element();
+ if ( n <= 1 )
+ {
+ SparseMsg* ret = 0;
+ if ( orig == e1() )
+ {
+ ret = new SparseMsg( newSrc.element(), newTgt.element(), 0 );
+ ret->e1()->addMsgAndFunc( ret->mid(), fid, b );
+ }
+ else if ( orig == e2() )
+ {
+ ret = new SparseMsg( newTgt.element(), newSrc.element(), 0 );
+ ret->e2()->addMsgAndFunc( ret->mid(), fid, b );
+ }
+ else
+ {
+ assert( 0 );
+ }
+ ret->setMatrix( matrix_ );
+ ret->nrows_ = nrows_;
+ return ret;
+ }
+ else
+ {
+ // Here we need a SliceMsg which goes from one 2-d array to another.
+ cout << "Error: SparseMsg::copy: SparseSliceMsg not yet implemented\n";
+ return 0;
+ }
}
void fillErefsFromMatrix(
- const SparseMatrix< unsigned int >& matrix,
- vector< vector < Eref > >& v, Element* e1, Element* e2 )
-{
- v.clear();
- v.resize( e1->numData() );
- assert( e1->numData() == matrix.nRows() );
- assert( e2->numData() == matrix.nColumns() );
- for ( unsigned int i = 0; i < e1->numData(); ++i ) {
- const unsigned int* entry;
- const unsigned int* colIndex;
- unsigned int num = matrix.getRow( i, &entry, &colIndex );
- v[i].resize( num );
- for ( unsigned int j = 0; j < num; ++j ) {
- v[i][j] = Eref( e2, colIndex[j], entry[j] );
- }
- }
+ const SparseMatrix< unsigned int >& matrix,
+ vector< vector < Eref > >& v, Element* e1, Element* e2 )
+{
+ v.clear();
+ v.resize( e1->numData() );
+ assert( e1->numData() == matrix.nRows() );
+ assert( e2->numData() == matrix.nColumns() );
+ for ( unsigned int i = 0; i < e1->numData(); ++i )
+ {
+ const unsigned int* entry;
+ const unsigned int* colIndex;
+ unsigned int num = matrix.getRow( i, &entry, &colIndex );
+ v[i].resize( num );
+ for ( unsigned int j = 0; j < num; ++j )
+ {
+ v[i][j] = Eref( e2, colIndex[j], entry[j] );
+ }
+ }
}
void SparseMsg::sources( vector< vector < Eref > >& v ) const
{
- SparseMatrix< unsigned int > temp( matrix_ );
- temp.transpose();
- fillErefsFromMatrix( temp, v, e2_, e1_ );
+ SparseMatrix< unsigned int > temp( matrix_ );
+ temp.transpose();
+ fillErefsFromMatrix( temp, v, e2_, e1_ );
}
void SparseMsg::targets( vector< vector< Eref > >& v ) const
{
- fillErefsFromMatrix( matrix_, v, e1_, e2_ );
+ fillErefsFromMatrix( matrix_, v, e1_, e2_ );
}
/// Static function for Msg access
unsigned int SparseMsg::numMsg()
{
- return msg_.size();
+ return msg_.size();
}
/// Static function for Msg access
char* SparseMsg::lookupMsg( unsigned int index )
{
- assert( index < msg_.size() );
- return reinterpret_cast< char* >( msg_[index] );
+ assert( index < msg_.size() );
+ return reinterpret_cast< char* >( msg_[index] );
}
diff --git a/msg/SparseMsg.h b/msg/SparseMsg.h
index 3d7ba580..0061a9fe 100644
--- a/msg/SparseMsg.h
+++ b/msg/SparseMsg.h
@@ -10,6 +10,8 @@
#ifndef _SPARSE_MSG_H
#define _SPARSE_MSG_H
+#include "../randnum/RNG.h"
+
/**
* This is a parallelized sparse message.
* It is a general message type optimized for sparse matrix like
@@ -27,6 +29,7 @@
* Synapses, which are array fields of IntFire objects.
* The sparse connectivity maps between the source IntFire and target
* Synapses.
+ *
* The location of the entry in the sparse matrix provides the index of
* the target IntFire.
* The data value in the sparse matrix provides the index of the Synapse
@@ -39,113 +42,117 @@
* BiSparseMsg.
* It can be modified after creation to add or remove message entries.
*/
+
class SparseMsg: public Msg
{
- friend unsigned int Msg::initMsgManagers(); // for initializing Id.
- public:
- SparseMsg( Element* e1, Element* e2, unsigned int msgIndex );
- ~SparseMsg();
-
- Eref firstTgt( const Eref& src ) const;
-
- void sources( vector< vector< Eref > >& v ) const;
- void targets( vector< vector< Eref > >& v ) const;
-
- unsigned int randomConnect( double probability );
-
- Id managerId() const;
-
- ObjId findOtherEnd( ObjId end ) const;
-
- Msg* copy( Id origSrc, Id newSrc, Id newTgt,
- FuncId fid, unsigned int b, unsigned int n ) const;
-
- /**
- * Assigns the whole connection matrix
- */
- void setMatrix( const SparseMatrix< unsigned int >& m );
-
- /**
- * Returns the connection matrix
- */
- SparseMatrix< unsigned int >& getMatrix();
-
- // Uses default addToQ function.
-
- /////////////////////////////////////////////////////////////////
- // Here we define the Element interface functions for SparseMsg
- /////////////////////////////////////////////////////////////////
- void setRandomConnectivity( double probability, long seed );
- double getProbability() const;
- void setProbability( double value );
-
- //
- vector< unsigned int > getMatrixEntry() const;
- vector< unsigned int > getColIndex() const;
- vector< unsigned int > getRowStart() const;
-
- long getSeed() const;
- void setSeed( long value );
-
- vector< unsigned int > getEntryPairs() const;
- void setEntryPairs( vector< unsigned int > entries );
-
- void setEntry( unsigned int row, unsigned int column,
- unsigned int value );
-
- void unsetEntry( unsigned int row, unsigned int column );
-
- // Still need to implement array field gets.
-
- unsigned int getNumRows() const;
- unsigned int getNumColumns() const;
- unsigned int getNumEntries() const;
- void clear();
- void transpose();
-
- /**
- * Fills up the entire message based on pairs of src,dest (i.e.,
- * row,column) values. All filled entries are set to zero.
- */
- void pairFill( vector< unsigned int > src,
- vector< unsigned int> dest );
-
- /**
- * Fills up the entire message based on triplets of
- * src,destDataIndex,destFieldIndex
- */
- void tripletFill( vector< unsigned int > src,
- vector< unsigned int> dest,
- vector< unsigned int > field );
-
- /**
- * Fills up the entire message based on triplets of
- * src,destDataIndex,destFieldIndex, but catenates them all into
- * a single long vector since PyMoose doesn't know how to handle
- * multiple vectors.
- */
- void tripletFill1( vector< unsigned int > entries );
-
- /**
- * Utility function to update all sorts of values after we've
- * rebuilt the matrix.
- */
- void updateAfterFill();
-
- /// Msg lookup functions
- static unsigned int numMsg();
- static char* lookupMsg( unsigned int index );
-
- static const Cinfo* initCinfo();
-
- private:
- SparseMatrix< unsigned int > matrix_;
- unsigned int numThreads_; // Number of threads to partition
- unsigned int nrows_; // The original size of the matrix.
- double p_;
- unsigned long seed_;
- static Id managerId_; // The Element that manages Sparse Msgs.
- static vector< SparseMsg* > msg_;
+ friend unsigned int Msg::initMsgManagers(); // for initializing Id.
+
+public:
+
+ SparseMsg( Element* e1, Element* e2, unsigned int msgIndex );
+ ~SparseMsg();
+
+ Eref firstTgt( const Eref& src ) const;
+
+ void sources( vector< vector< Eref > >& v ) const;
+ void targets( vector< vector< Eref > >& v ) const;
+
+ unsigned int randomConnect( double probability );
+
+ Id managerId() const;
+
+ ObjId findOtherEnd( ObjId end ) const;
+
+ Msg* copy( Id origSrc, Id newSrc, Id newTgt,
+ FuncId fid, unsigned int b, unsigned int n ) const;
+
+ /**
+ * Assigns the whole connection matrix
+ */
+ void setMatrix( const SparseMatrix< unsigned int >& m );
+
+ /**
+ * Returns the connection matrix
+ */
+ SparseMatrix< unsigned int >& getMatrix();
+
+ // Uses default addToQ function.
+
+ // Here we define the Element interface functions for SparseMsg
+ void setRandomConnectivity( double probability, long seed );
+ double getProbability() const;
+ void setProbability( double value );
+
+ vector< unsigned int > getMatrixEntry() const;
+ vector< unsigned int > getColIndex() const;
+ vector< unsigned int > getRowStart() const;
+
+ unsigned long getSeed() const;
+ void setSeed( unsigned long value );
+
+ vector< unsigned int > getEntryPairs() const;
+ void setEntryPairs( vector< unsigned int > entries );
+
+ void setEntry( unsigned int row, unsigned int column,
+ unsigned int value );
+
+ void unsetEntry( unsigned int row, unsigned int column );
+
+ // Still need to implement array field gets.
+ unsigned int getNumRows() const;
+ unsigned int getNumColumns() const;
+ unsigned int getNumEntries() const;
+ void clear();
+ void transpose();
+
+ /**
+ * Fills up the entire message based on pairs of src,dest (i.e.,
+ * row,column) values. All filled entries are set to zero.
+ */
+ void pairFill( vector< unsigned int > src,
+ vector< unsigned int> dest );
+
+ /**
+ * Fills up the entire message based on triplets of
+ * src,destDataIndex,destFieldIndex
+ */
+ void tripletFill( vector< unsigned int > src,
+ vector< unsigned int> dest,
+ vector< unsigned int > field );
+
+ /**
+ * Fills up the entire message based on triplets of
+ * src,destDataIndex,destFieldIndex, but catenates them all into
+ * a single long vector since PyMoose doesn't know how to handle
+ * multiple vectors.
+ */
+ void tripletFill1( vector< unsigned int > entries );
+
+ /**
+ * Utility function to update all sorts of values after we've
+ * rebuilt the matrix.
+ */
+ void updateAfterFill();
+
+ /// Msg lookup functions
+ static unsigned int numMsg();
+ static char* lookupMsg( unsigned int index );
+
+ static const Cinfo* initCinfo();
+
+private:
+ SparseMatrix< unsigned int > matrix_;
+ unsigned int numThreads_; // Number of threads to partition
+ unsigned int nrows_; // The original size of the matrix.
+ double p_;
+ static Id managerId_; // The Element that manages Sparse Msgs.
+ 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_;
};
#endif // _SPARSE_MSG_H
diff --git a/pymoose/CMakeLists.txt b/pymoose/CMakeLists.txt
index b5d118b7..3c69dacd 100644
--- a/pymoose/CMakeLists.txt
+++ b/pymoose/CMakeLists.txt
@@ -1,5 +1,4 @@
-add_definitions(-DPYMOOSE)
-include_directories(../basecode ../msg)
+cmake_minimum_required(VERSION 2.8)
set(PYMOOSE_SRCS
moosemodule.cpp
@@ -7,8 +6,8 @@ set(PYMOOSE_SRCS
mfield.cpp
pymooseinit.cpp
melement.cpp
- test_moosemodule.cpp
PyRun.cpp
+ test_moosemodule.cpp
)
# Build _moose.so in source directory and them copy everything to
@@ -35,15 +34,20 @@ add_definitions(-DUSE_NUMPY)
add_definitions(-DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION)
-execute_process( COMMAND ${PYTHON_EXECUTABLE}-config --includes
- OUTPUT_VARIABLE PYTHON_INCLUDE_FLAGS
- OUTPUT_STRIP_TRAILING_WHITESPACE
- )
-execute_process( COMMAND ${PYTHON_EXECUTABLE}-config --libs
- OUTPUT_VARIABLE PYTHON_LIBRARIES
- OUTPUT_STRIP_TRAILING_WHITESPACE
- )
-message( STATUS "Python include flags: ${PYTHON_INCLUDE_FLAGS}" )
+# make sure the Python.h is found.
+find_package( PythonLibs REQUIRED)
+include_directories( ${PYTHON_INCLUDE_DIRS} )
+
+#execute_process( COMMAND ${PYTHON_EXECUTABLE}-config --includes
+# OUTPUT_VARIABLE PYTHON_INCLUDE_FLAGS
+# OUTPUT_STRIP_TRAILING_WHITESPACE
+# )
+#execute_process( COMMAND ${PYTHON_EXECUTABLE}-config --libs
+# OUTPUT_VARIABLE PYTHON_LIBRARIES
+# OUTPUT_STRIP_TRAILING_WHITESPACE
+# )
+# message( STATUS "Python include flags: ${PYTHON_INCLUDE_FLAGS}" )
+
set_target_properties(_moose PROPERTIES
COMPILE_DEFINITIONS "PYMOOSE"
COMPILE_FLAGS "${PYTHON_INCLUDE_FLAGS}"
@@ -62,7 +66,6 @@ if(HDF5_LIBRARY_DIRS)
set_target_properties( _moose PROPERTIES LINK_FLAGS "-L${HDF5_LIBRARY_DIRS}" )
endif()
-
if(MACOSX)
set(CMAKE_MODULE_LINKER_FLAGS "-undefined dynamic_lookup")
message(STATUS "ADDING some linker flags ${CMAKE_EXE_LINKER_FLAGS}")
@@ -83,7 +86,6 @@ else(MACOSX)
${MOOSE_LIBRARIES}
${STATIC_LIBRARIES}
"-Wl,--no-whole-archive"
- # ${PYTHON_LIBRARIES}
${SYSTEM_SHARED_LIBS}
)
endif(MACOSX)
diff --git a/pymoose/melement.cpp b/pymoose/melement.cpp
index 82856488..47ce0e40 100644
--- a/pymoose/melement.cpp
+++ b/pymoose/melement.cpp
@@ -49,7 +49,7 @@
#include <Python.h>
#include <structmember.h>
-#ifdef USE_BOOST
+#ifdef USE_BOOST_ODE
#include <boost/format.hpp>
#endif
diff --git a/pymoose/mfield.cpp b/pymoose/mfield.cpp
index 7e73f265..9cb2b073 100644
--- a/pymoose/mfield.cpp
+++ b/pymoose/mfield.cpp
@@ -116,11 +116,12 @@ int moose_Field_init(_Field * self, PyObject * args, PyObject * kwargs)
}
self->owner = ((_ObjId*)owner);
Py_INCREF(self->owner);
- ObjId tmp = ((_ObjId*)owner)->oid_;
- size_t size = strlen(fieldName);
- char * name = (char*)calloc(size+1, sizeof(char));
- strncpy(name, fieldName, size);
- self->name = name;
+ self->name = strdup(fieldName);
+ if (!self->name) {
+ PyErr_NoMemory();
+ return -1;
+ }
+
// In earlier version I tried to deallocate the existing
// self->name if it is not NULL. But it turns out that it
// causes a SIGABRT. In any case it should not be an issue as
@@ -316,7 +317,7 @@ PyObject * moose_DestField_call(PyObject * self, PyObject * args,
PyObject * arg = PyTuple_GetItem(args, ii);
Py_INCREF(arg);
PyTuple_SetItem(newargs, ii+1, arg);
- Py_DECREF(arg);
+ //Py_DECREF(arg);
}
// Call ObjId._setDestField with the new arguments
PyObject * ret = moose_ObjId_setDestField(((_Field*)self)->owner, newargs);
diff --git a/pymoose/moosemodule.cpp b/pymoose/moosemodule.cpp
index ae638e18..acf86f02 100644
--- a/pymoose/moosemodule.cpp
+++ b/pymoose/moosemodule.cpp
@@ -20,7 +20,7 @@
#include <exception>
-#if USE_BOOST
+#if USE_BOOST_ODE
#include <boost/format.hpp>
#endif
@@ -2536,66 +2536,6 @@ int defineLookupFinfos(const Cinfo * cinfo)
return 1;
}
-int defineDestFinfos(const Cinfo * cinfo)
-{
- const string& className = cinfo->name();
-#ifndef NDEBUG
- if (verbosity > 1)
- {
- cout << "\tCreating destField attributes for " << className << endl;
- }
-#endif
- vector <PyGetSetDef>& vec = get_getsetdefs()[className];
- /*
- We do not know the final number of user-accessible
- destFinfos as we have to ignore the destFinfos starting
- with get/set. So use a vector instead of C array.
- */
- size_t currIndex = vec.size();
- for (unsigned int ii = 0; ii < cinfo->getNumDestFinfo(); ++ii)
- {
- Finfo * destFinfo = const_cast<Cinfo*>(cinfo)->getDestFinfo(ii);
- const string& name = destFinfo->name();
- /*
- get_{xyz} and set_{xyz} are internal destFinfos for
- accessing valueFinfos. Ignore them.
-
- With the '_' removed from internal get/set for value
- fields, we cannot separate them out. - Subha Fri Jan 31
- 16:43:51 IST 2014
-
- The policy changed in the past and hence the following were commented out.
- - Subha Tue May 26 00:25:28 EDT 2015
- */
- // if (name.find("get") == 0 || name.find("set") == 0){
- // continue;
- // }
- PyGetSetDef destFieldGetSet;
- vec.push_back(destFieldGetSet);
-
- vec[currIndex].name = (char*)calloc(name.size() + 1, sizeof(char));
- strncpy(vec[currIndex].name,
- const_cast<char*>(name.c_str()),
- name.size());
-
- vec[currIndex].doc = (char*) "D_field";
- vec[currIndex].get = (getter)moose_ObjId_get_destField_attr;
- PyObject * args = PyTuple_New(1);
- if (args == NULL)
- {
- cerr << "moosemodule.cpp: defineDestFinfos: Failed to allocate tuple" << endl;
- return 0;
- }
- PyTuple_SetItem(args, 0, PyString_FromString(name.c_str()));
- vec[currIndex].closure = (void*)args;
-
- //LOG( debug, "\tCreated destField " << vec[currIndex].name );
-
- ++currIndex;
- } // ! for
-
- return 1;
-}
int defineClass(PyObject * module_dict, const Cinfo * cinfo)
{
@@ -2770,6 +2710,63 @@ PyObject * moose_ObjId_get_destField_attr(PyObject * self, void * closure)
return (PyObject*)ret;
}
+
+int defineDestFinfos(const Cinfo * cinfo)
+{
+ const string& className = cinfo->name();
+#ifndef NDEBUG
+ if (verbosity > 1)
+ {
+ cout << "\tCreating destField attributes for " << className << endl;
+ }
+#endif
+ vector <PyGetSetDef>& vec = get_getsetdefs()[className];
+ /*
+ We do not know the final number of user-accessible
+ destFinfos as we have to ignore the destFinfos starting
+ with get/set. So use a vector instead of C array.
+ */
+ size_t currIndex = vec.size();
+ for (unsigned int ii = 0; ii < cinfo->getNumDestFinfo(); ++ii)
+ {
+ Finfo * destFinfo = const_cast<Cinfo*>(cinfo)->getDestFinfo(ii);
+ const string& name = destFinfo->name();
+ /*
+ get_{xyz} and set_{xyz} are internal destFinfos for
+ accessing valueFinfos. Ignore them.
+
+ With the '_' removed from internal get/set for value
+ fields, we cannot separate them out. - Subha Fri Jan 31
+ 16:43:51 IST 2014
+
+ The policy changed in the past and hence the following were commented out.
+ - Subha Tue May 26 00:25:28 EDT 2015
+ */
+ // if (name.find("get") == 0 || name.find("set") == 0){
+ // continue;
+ // }
+ PyGetSetDef destFieldGetSet;
+ vec.push_back(destFieldGetSet);
+
+ vec[currIndex].name = strdup(name.c_str());
+ vec[currIndex].doc = (char*) "Destination field";
+ vec[currIndex].get = (getter)moose_ObjId_get_destField_attr;
+ PyObject *args = PyTuple_New(1);
+ if (!args || !vec[currIndex].name) {
+ cerr << "moosemodule.cpp: defineDestFinfos: allocation failed\n";
+ return 0;
+ }
+ PyTuple_SetItem(args, 0, PyString_FromString(name.c_str()));
+ vec[currIndex].closure = (void*)args;
+
+ //LOG( debug, "\tCreated destField " << vec[currIndex].name );
+
+ ++currIndex;
+ } // ! for
+
+ return 1;
+}
+
/**
Try to obtain a LookupField object for a specified
lookupFinfo. The first item in `closure` must be the name of
diff --git a/python/moose/chemUtil/add_Delete_ChemicalSolver.py b/python/moose/chemUtil/add_Delete_ChemicalSolver.py
index cc350ec6..9b11a5c1 100644
--- a/python/moose/chemUtil/add_Delete_ChemicalSolver.py
+++ b/python/moose/chemUtil/add_Delete_ChemicalSolver.py
@@ -1,158 +1,140 @@
# -*- coding: utf-8 -*-
+__author__ = "HarshaRani"
+__credits__ = ["Upi Lab"]
+__license__ = "GPL3"
+__version__ = "1.0.0"
+__maintainer__ = "HarshaRani"
+__email__ = "hrani@ncbs.res.in"
+__status__ = "Development"
+__updated__ = "Sep 03 2018"
+
+
+'''
+mooseAddChemSolver and mooseDeleteChemSolver is for adding and deleting only
+Chemical solver
+'''
+
import moose
-from fixXreacs import fixXreacs
+from moose.fixXreacs import fixXreacs
def positionCompt( compt ):
i = 0
while (i != len(compt)-1):
- #print "PositionCompt ", compt[i+1],compt[i+1].volume, compt[i], compt[i].volume
compt[i+1].x1 += compt[i].x1
compt[i+1].x0 += compt[i].x1
i += 1
-def moosedeleteChemSolver(modelRoot):
- """Delete solvers from Chemical Compartment
+def mooseDeleteChemSolver(modelRoot):
+ """Delete solvers from Chemical Compartment """
- """
- compts = moose.wildcardFind(modelRoot + '/##[ISA=ChemCompt]')
- for compt in compts:
- if moose.exists(compt.path + '/stoich'):
- st = moose.element(compt.path + '/stoich')
- st_ksolve = st.ksolve
- st_dsolve = st.dsolve
-
- moose.delete(st)
- if moose.exists((st_ksolve).path):
- moose.delete(st_ksolve)
- print("KSolver is deleted for modelpath %s " % modelRoot)
- if moose.exists((st_dsolve).path):
- moose.delete(st_dsolve)
- print("DSolver is deleted for modelpath %s " % modelRoot)
- '''
compts = moose.wildcardFind(modelRoot + '/##[ISA=ChemCompt]')
- for compt in compts:
- if moose.exists(compt.path + '/stoich'):
- st = moose.element(compt.path + '/stoich')
- st_ksolve = st.ksolve
- moose.delete(st)
- if moose.exists((st_ksolve).path):
- moose.delete(st_ksolve)
- print("Solver is deleted for modelpath %s " % modelRoot)
-
- '''
-
-def mooseaddChemSolver(modelRoot, solver):
+ if all(isinstance(x, (moose.CubeMesh,moose.CylMesh)) for x in compts):
+ for compt in compts:
+ if moose.exists(compt.path + '/stoich'):
+ st = moose.element(compt.path + '/stoich')
+ st_ksolve = st.ksolve
+ st_dsolve = st.dsolve
+
+ moose.delete(st)
+
+ if moose.exists((st_ksolve).path):
+ print("KSolver is deleted for modelpath %s " % st_ksolve)
+ moose.delete(st_ksolve)
+
+ if moose.exists((st_dsolve).path) and st_dsolve.path != '/':
+ print("DSolver is deleted for modelpath %s " % st_dsolve)
+ moose.delete(st_dsolve)
+ else:
+ return ("mooseDeleteChemSolver is only for deleting Chemical Model solver which has to be `CubeMesh` or `CylMesh` found ",list(set([x.className for x in compts]) - set(['CubeMesh',"CylMesh"])))
+
+def stdSolvertype(solverName):
+ if solverName.lower() in ["gssa","gillespie","stochastic","gsolve"]:
+ return "gssa"
+ elif solverName.lower() in ["gsl","runge kutta","deterministic","ksolve","rungekutta","rk5","rkf","rk"]:
+ return "gsl"
+ elif solverName.lower() in ["ee","exponential euler","exponentialeuler","neutral"]:
+ return "ee"
+ return "ee"
+
+def mooseAddChemSolver(modelRoot, solver):
"""
- Add the solvers to Chemical compartment
+ Add the solvers only if all are Chemical compartment
"""
- compt = moose.wildcardFind(modelRoot + '/##[ISA=ChemCompt]')
- if compt:
- comptinfo = moose.Annotator(moose.element(compt[0]).path + '/info')
- previousSolver = comptinfo.solver
- currentSolver = previousSolver
- if solver == "Gillespie" or solver == "gssa":
- currentSolver = "gssa"
- elif solver == "Runge Kutta" or solver == "gsl":
- currentSolver = "gsl"
- elif solver == "Exponential Euler" or solver == "ee":
- currentSolver = "ee"
-
- if previousSolver != currentSolver:
- # if previousSolver != currentSolver
- comptinfo.solver = currentSolver
- if (moose.exists(compt[0].path + '/stoich')):
- # "A: and stoich exists then delete the stoich add solver"
- deleteSolver(modelRoot)
- setCompartmentSolver(modelRoot, currentSolver)
- return True
- else:
- # " B: stoich doesn't exists then addSolver, this is when object is deleted which delete's the solver "
- # " and solver is also changed, then add addsolver "
- setCompartmentSolver(modelRoot, currentSolver)
- return True
+ compts = moose.wildcardFind(modelRoot + '/##[ISA=ChemCompt]')
+ if all(isinstance(x, (moose.CubeMesh,moose.CylMesh)) for x in compts):
+ if not compts:
+ return ("Atleast one compartment is required ")
+ elif ( len(compts) > 3 ):
+ return ("Warning: setSolverOnCompt Cannot handle " , len(compts) , " chemical compartments\n")
+
else:
- if moose.exists(compt[0].path + '/stoich'):
- # " stoich exist, doing nothing"
- return False
- else:
- # "but stoich doesn't exist,this is when object is deleted which deletes the solver
- # " but solver are not changed, then also call addSolver"
+ comptinfo = moose.Annotator(moose.element(compts[0]).path + '/info')
+
+ previousSolver = stdSolvertype(comptinfo.solver)
+ currentSolver = stdSolvertype(solver)
+
+ if previousSolver != currentSolver:
+ comptinfo.solver = currentSolver
+ if (moose.exists(compts[0].path + '/stoich')):
+ # "A: and stoich exists then delete the stoich add solver"
+ mooseDeleteChemSolver(modelRoot)
setCompartmentSolver(modelRoot, currentSolver)
return True
- return False
+ else:
+ if not moose.exists(compts[0].path + '/stoich'):
+ # " stoich exist, doing nothing"
+ setCompartmentSolver(modelRoot, currentSolver)
+ return True
+ else:
+
+ return ("mooseAddChemSolver is only for adding Chemical Model which has to be `CubeMesh` or `CylMesh` found ",list(set([x.className for x in compts]) - set(['CubeMesh',"CylMesh"])))
def setCompartmentSolver(modelRoot, solver):
- comptlist = dict((c, c.volume) for c in moose.wildcardFind(modelRoot + '/##[ISA=ChemCompt]'))
- comptVol = {}
- compts = []
- vol = [v for k,v in comptlist.items()]
- volumeSort = sorted(vol)
- for k,v in comptlist.items():
- comptVol[k]= v
- for volSor in volumeSort:
- for a,b in comptVol.items():
- if b == volSor:
- compts.append(a)
-
- #compts = [key for key, value in sorted(comptlist.items(), key=lambda (k,v): (v,k))]
- if ( len(compts) == '0'):
- print ("Atleast one compartment is required ")
- return
- else:
- if ( len(compts) > 3 ):
- print ("Warning: setSolverOnCompt Cannot handle " , len(compts) , " chemical compartments\n")
- return;
+ """
+ If Solver type is 'gsl' or 'gssa' do add Solver
+ if 'ee' nothing
- elif (len(compts) >1 ):
- positionCompt(compts)
+ """
+ if solver != 'ee':
+ comptlist = dict((c.volume, c) for c in moose.wildcardFind(modelRoot + '/##[ISA=ChemCompt]'))
+ vollist = sorted(comptlist.keys())
+ compts = [comptlist[key] for key in vollist]
- fixXreacs( modelRoot )
+ #compts = [key for key, value in sorted(comptlist.items(), key=lambda (k,v): (v,k))]
+
+ if (len(compts) >1 ):
+ positionCompt(compts)
+ fixXreacs( modelRoot )
+
+ vollist = sorted(comptlist.keys())
+ compts = [comptlist[key] for key in vollist]
+ #compts = [key for key, value in sorted(comptlist.items(), key=lambda (k,v): (v,k))]
for compt in compts:
if solver != 'ee':
- if (solver == 'gsl') or (solver == 'Runge Kutta'):
+ if (solver == 'gsl'):
ksolve = moose.Ksolve(compt.path + '/ksolve')
- if (solver == 'gssa') or (solver == 'Gillespie'):
+ if (solver == 'gssa') :
ksolve = moose.Gsolve(compt.path + '/gsolve')
-
- dsolve = moose.Dsolve(compt.path+'/dsolve')
+
+ if (len(compts) > 1):
+ dsolve = moose.Dsolve(compt.path+'/dsolve')
+
stoich = moose.Stoich(compt.path + '/stoich')
- stoich.compartment = compt
stoich.ksolve = ksolve
- stoich.dsolve = dsolve
+ if (len(compts) > 1):
+ stoich.dsolve = dsolve
+
+ stoich.compartment = compt
stoich.path = compt.path + "/##"
- ksolveList = moose.wildcardFind(modelRoot+'/##[ISA=Ksolve]')
+
+
dsolveList = moose.wildcardFind(modelRoot+'/##[ISA=Dsolve]')
- stoichList = moose.wildcardFind(modelRoot+'/##[ISA=Stoich]')
-
i = 0
while(i < len(dsolveList)-1):
dsolveList[i+1].buildMeshJunctions(dsolveList[i])
i += 1
-
- print( " Solver is added to model path %s" % modelRoot )
- '''
- compts = moose.wildcardFind(modelRoot + '/##[ISA=ChemCompt]')
- for compt in compts:
- if (solver == 'gsl') or (solver == 'Runge Kutta'):
- ksolve = moose.Ksolve(compt.path + '/ksolve')
- if (solver == 'gssa') or (solver == 'Gillespie'):
- ksolve = moose.Gsolve(compt.path + '/gsolve')
- if (solver != 'ee'):
- stoich = moose.Stoich(compt.path + '/stoich')
- stoich.compartment = compt
- stoich.ksolve = ksolve
- if moose.exists(compt.path):
- stoich.path = compt.path + "/##"
- stoichList = moose.wildcardFind(modelRoot + '/##[ISA=Stoich]')
- if len(stoichList) == 2:
- stoichList[1].buildXreacs(stoichList[0])
- if len(stoichList) == 3:
- stoichList[1].buildXreacs(stoichList[0])
- stoichList[1].buildXreacs(stoichList[2])
-
- for i in stoichList:
- i.filterXreacs()
- print( " Solver is added to model path %s" % modelRoot )
- '''
+ if not modelRoot[:1].startswith('/'):
+ modelRoot ='/'+modelRoot
+ print( " Solver is added to model path `%s` with `%s` solver" % (modelRoot,solver) )
diff --git a/python/fixXreacs.py b/python/moose/fixXreacs.py
similarity index 100%
rename from python/fixXreacs.py
rename to python/moose/fixXreacs.py
diff --git a/python/moose/genesis/writeKkit.py b/python/moose/genesis/writeKkit.py
index c94ca3da..f6bba42b 100644
--- a/python/moose/genesis/writeKkit.py
+++ b/python/moose/genesis/writeKkit.py
@@ -224,9 +224,11 @@ def writeEnz( modelpath,f,sceneitems):
concInit = 0;
n = 0;
conc = 0;
- enzParent = enz.parent
- if (isinstance(enzParent.className,moose.Pool)) or (isinstance(enzParent.className,moose.ZombiePool)):
- print(" raise exception enz doesn't have pool as parent")
+ if len(moose.element(enz).neighbors['enzDest']) == 1:
+ enzParent = moose.element(moose.element(enz).neighbors['enzDest'][0])
+
+ if not (isinstance(enzParent,moose.PoolBase)):
+ print(" raise exception enz doesn't have pool as parent %s",moose.element(enz).path)
return False
else:
vol = enzParent.volume * NA * 1e-3;
diff --git a/python/moose/moose.py b/python/moose/moose.py
index a949e5f4..b9acb706 100644
--- a/python/moose/moose.py
+++ b/python/moose/moose.py
@@ -10,7 +10,7 @@ from contextlib import closing
import warnings
import pydoc
from io import StringIO
-
+from os.path import splitext
import moose
import moose.utils as mu
@@ -62,6 +62,42 @@ except Exception as e:
# Import function from C++ module into moose namespace.
from moose._moose import *
+#`loadModel` is deleted from global import,
+# this is to bypass the call from c++ module which is due to fixXreacs() which is
+# now written in python and readKkit.cpp will not be possible to set/call the solver due to this
+
+del globals()['loadModel']
+
+def loadModel(filename, target,method=None):
+ solverClass = 'Neutral'
+ if method != None:
+ solverClass = method
+ try:
+ f = open(filename,'r')
+ f.close()
+ except IOError as e:
+ print (e)
+ return
+ else:
+ file_name,extension = splitext(filename)
+ if extension in [".swc",".p"]:
+ ret = moose._moose.loadModel(filename,target,"Neutral")
+ elif extension in [".g",".cspace"]:
+ #only if genesis or cspace file, then mooseAddChemSolver is called
+ ret = moose._moose.loadModel(filename,target,"ee")
+
+ method = "ee"
+ if solverClass.lower() in ["gssa","gillespie","stochastic","gsolve"]:
+ method = "gssa"
+ elif solverClass.lower() in ["gsl","runge kutta","deterministic","ksolve","rungekutta","rk5","rkf","rk"]:
+ method = "gsl"
+ elif solverClass.lower() in ["exponential euler","exponentialeuler","neutral"]:
+ method = "ee"
+
+ if method != 'ee':
+ chemError_ = _chemUtil.add_Delete_ChemicalSolver.mooseAddChemSolver(target,method)
+ return ret
+
def version( ):
return VERSION
@@ -149,20 +185,20 @@ def mooseWriteKkit(modelpath, filepath,sceneitems={}):
return _writeKkit.mooseWriteKkit(modelpath, filepath,sceneitems)
-def moosedeleteChemSolver(modelpath):
+def mooseDeleteChemSolver(modelpath):
""" deletes solver on all the compartment and its children.
This is neccesary while created a new moose object on a pre-existing modelpath,\n
- this should be followed by mooseaddChemSolver for add solvers on to compartment to simulate else
+ this should be followed by mooseAddChemSolver for add solvers on to compartment to simulate else
default is Exponential Euler (ee)
"""
if chemImport_:
- return _chemUtil.add_Delete_ChemicalSolver.moosedeleteChemSolver(modelpath)
+ return _chemUtil.add_Delete_ChemicalSolver.mooseDeleteChemSolver(modelpath)
else:
print( chemError_ )
return False
-def mooseaddChemSolver(modelpath, solver):
+def mooseAddChemSolver(modelpath, solver):
""" Add solver on chemical compartment and its children for calculation
keyword arguments:\n
@@ -174,7 +210,8 @@ def mooseaddChemSolver(modelpath, solver):
"""
if chemImport_:
- return _chemUtil.add_Delete_ChemicalSolver.mooseaddChemSolver(modelpath, solver)
+ chemError_ = _chemUtil.add_Delete_ChemicalSolver.mooseAddChemSolver(modelpath, solver)
+ return chemError_
else:
print( chemError_ )
return False
diff --git a/python/moose/print_utils.py b/python/moose/print_utils.py
index 5cc08416..e3406231 100644
--- a/python/moose/print_utils.py
+++ b/python/moose/print_utils.py
@@ -1,6 +1,4 @@
# -*- coding: utf-8 -*-
-# print_utils.py:
-#
# A library with some print functions. Very useful during development.
from __future__ import print_function, division, absolute_import
diff --git a/python/rdesigneur/rdesigneur.py b/python/rdesigneur/rdesigneur.py
index 66a2ea68..aa5b3fce 100644
--- a/python/rdesigneur/rdesigneur.py
+++ b/python/rdesigneur/rdesigneur.py
@@ -23,13 +23,14 @@ import os
import moose
import numpy as np
import math
-import itertools
import sys
import time
+import matplotlib.pyplot as plt
import rdesigneur.rmoogli as rmoogli
from rdesigneur.rdesigneurProtos import *
-import fixXreacs
+from moose.fixXreacs import fixXreacs
+#import fixXreacs
#from . import fixXreacs
#from rdesigneur.rmoogli import *
#import rmoogli
@@ -77,6 +78,8 @@ class rdesigneur:
combineSegments = True,
stealCellFromLibrary = False,
verbose = True,
+ addSomaChemCompt = False, # Put a soma chemCompt on neuroMesh
+ addEndoChemCompt = False, # Put an endo compartment, typically for ER, on each of the NeuroMesh compartments.
diffusionLength= 2e-6,
meshLambda = -1.0, #This is a backward compatibility hack
temperature = 32,
@@ -87,6 +90,7 @@ class rdesigneur:
elecPlotDt = 0.1e-3, # Same default as from MOOSE
funcDt = 0.1e-3, # Used when turnOffElec is False.
# Otherwise system uses chemDt.
+ numWaveFrames = 100, # Number of frames to use for waveplots
cellProto = [],
spineProto = [],
chanProto = [],
@@ -97,8 +101,8 @@ class rdesigneur:
chemDistrib = [],
adaptorList= [],
stimList = [],
- plotList = [],
- moogList = [],
+ plotList = [], # elecpath, geom_expr, object, field, title ['wave' [min max]]
+ moogList = [],
params = None
):
""" Constructor of the rdesigner. This just sets up internal fields
@@ -111,6 +115,8 @@ class rdesigneur:
self.combineSegments = combineSegments
self.stealCellFromLibrary = stealCellFromLibrary
self.verbose = verbose
+ self.addSomaChemCompt = addSomaChemCompt
+ self.addEndoChemCompt = addEndoChemCompt
self.diffusionLength= diffusionLength
if meshLambda > 0.0:
print("Warning: meshLambda argument is deprecated. Please use 'diffusionLength' instead.\nFor now rdesigneur will accept this argument.")
@@ -122,6 +128,7 @@ class rdesigneur:
self.elecPlotDt= elecPlotDt
self.funcDt= funcDt
self.chemPlotDt= chemPlotDt
+ self.numWaveFrames = numWaveFrames
self.cellProtoList = cellProto
self.spineProtoList = spineProto
@@ -136,17 +143,24 @@ class rdesigneur:
self.params = params
self.adaptorList = adaptorList
- self.stimList = stimList
- self.plotList = plotList
- self.saveList = plotList #ADDED BY Sarthak
+ try:
+ self.stimList = [ rstim.convertArg(i) for i in stimList ]
+ self.plotList = [ rplot.convertArg(i) for i in plotList ]
+ self.moogList = [ rmoog.convertArg(i) for i in moogList ]
+ except BuildError as msg:
+ print("Error: rdesigneur: " + msg)
+ quit()
+
+ #self.saveList = plotList #ADDED BY Sarthak
self.saveAs = []
- self.moogList = moogList
self.plotNames = []
+ self.wavePlotNames = []
self.saveNames = []
self.moogNames = []
self.cellPortionElist = []
self.spineComptElist = []
self.tabForXML = []
+ self._endos = []
if not moose.exists( '/library' ):
library = moose.Neutral( '/library' )
@@ -169,16 +183,10 @@ class rdesigneur:
len( self.cellPortionElist ), "compartments.")
if hasattr( self , 'chemid' ):
dmstoich = moose.element( self.dendCompt.path + '/stoich' )
- print("Chem part of model has ",
- self.dendCompt.mesh.num, "dendrite voxels X",
- dmstoich.numAllPools, "pools,\n ")
- if hasattr( self , 'spineCompt' ):
- smstoich = moose.element( self.spineCompt.path + '/stoich')
- pmstoich = moose.element( self.psdCompt.path + '/stoich' )
- print(self.spineCompt.mesh.num, "spine voxels X",
- smstoich.numAllPools, "pools,",
- self.psdCompt.mesh.num, "psd voxels X",
- pmstoich.numAllPools, "pools.")
+ print("Chem part of model has the following compartments: ")
+ for j in moose.wildcardFind( '/model/chem/##[ISA=ChemCompt]'):
+ s = moose.element( j.path + '/stoich' )
+ print( "In {}, {} voxels X {} pools".format( j.name, j.mesh.num, s.numAllPools ) )
def buildModel( self, modelPath = '/model' ):
if moose.exists( modelPath ):
@@ -205,7 +213,6 @@ class rdesigneur:
self._configureClocks()
if self.verbose:
self._printModelStats()
- self._savePlots()
except BuildError as msg:
print("Error: rdesigneur: model build failed:", msg)
@@ -462,10 +469,10 @@ class rdesigneur:
# Here we hack geomExpr to use it for the syn weight. We assume it
# is just a number. In due course
# it should be possible to actually evaluate it according to geom.
- synWeight = float( stimInfo[1] )
+ synWeight = float( stimInfo.geom_expr )
stimObj = []
for i in dendCompts + spineCompts:
- path = i.path + '/' + stimInfo[2] + '/sh/synapse[0]'
+ path = i.path + '/' + stimInfo.relpath + '/sh/synapse[0]'
if moose.exists( path ):
synInput = make_synInput( name='synInput', parent=path )
synInput.doPeriodic = doPeriodic
@@ -478,13 +485,17 @@ class rdesigneur:
# Here we set up the distributions
################################################################
def buildPassiveDistrib( self ):
- # [. path field expr [field expr]...]
+ # [path field expr [field expr]...]
# RM, RA, CM set specific values, per unit area etc.
- # Ra, Ra, Cm set absolute values.
+ # Rm, Ra, Cm set absolute values.
# Also does Em, Ek, initVm
# Expression can use p, g, L, len, dia, maxP, maxG, maxL.
temp = []
for i in self.passiveDistrib:
+ if (len( i ) < 3) or (len(i) %2 != 1):
+ raise BuildError( "buildPassiveDistrib: Need 3 + N*2 arguments, have {}".format( len(i) ) )
+
+ temp.append( '.' )
temp.extend( i )
temp.extend( [""] )
self.elecid.passiveDistribution = temp
@@ -605,22 +616,24 @@ class rdesigneur:
# [ region_wildcard, region_expr, path, field, title]
def _parseComptField( self, comptList, plotSpec, knownFields ):
# Put in stuff to go through fields if the target is a chem object
- field = plotSpec[3]
+ field = plotSpec.field
if not field in knownFields:
print("Warning: Rdesigneur::_parseComptField: Unknown field '{}'".format( field ) )
return (), ""
kf = knownFields[field] # Find the field to decide type.
if ( kf[0] == 'CaConcBase' or kf[0] == 'ChanBase' or kf[0] == 'NMDAChan' or kf[0] == 'VClamp' ):
- objList = self._collapseElistToPathAndClass( comptList, plotSpec[2], kf[0] )
+ objList = self._collapseElistToPathAndClass( comptList, plotSpec.relpath, kf[0] )
return objList, kf[1]
elif (field == 'n' or field == 'conc' or field == 'volume' ):
- path = plotSpec[2]
+ path = plotSpec.relpath
pos = path.find( '/' )
if pos == -1: # Assume it is in the dend compartment.
path = 'dend/' + path
pos = path.find( '/' )
chemCompt = path[:pos]
+ if chemCompt[-5:] == "_endo":
+ chemCompt = chemCompt[0:-5]
cc = moose.element( self.modelPath + '/chem/' + chemCompt)
voxelVec = []
temp = [ self._makeUniqueNameStr( i ) for i in comptList ]
@@ -634,13 +647,13 @@ class rdesigneur:
voxelVec = [i for i in range(len( em ) ) if em[i] in comptSet ]
# Here we collapse the voxelVec into objects to plot.
- allObj = moose.vec( self.modelPath + '/chem/' + plotSpec[2] )
+ allObj = moose.vec( self.modelPath + '/chem/' + plotSpec.relpath )
#print "####### allObj=", self.modelPath + '/chem/' + plotSpec[2]
if len( allObj ) >= len( voxelVec ):
objList = [ allObj[int(j)] for j in voxelVec]
else:
objList = []
- print( "Warning: Rdesigneur::_parseComptField: unknown Object: '", plotSpec[2], "'" )
+ print( "Warning: Rdesigneur::_parseComptField: unknown Object: '", plotSpec.relpath, "'" )
#print "############", chemCompt, len(objList), kf[1]
return objList, kf[1]
@@ -672,7 +685,7 @@ class rdesigneur:
dummy = moose.element( '/' )
k = 0
for i in self.plotList:
- pair = i[0] + " " + i[1]
+ pair = i.elecpath + ' ' + i.geom_expr
dendCompts = self.elecid.compartmentsFromExpression[ pair ]
spineCompts = self.elecid.spinesFromExpression[ pair ]
plotObj, plotField = self._parseComptField( dendCompts, i, knownFields )
@@ -683,15 +696,21 @@ class rdesigneur:
#print( "PlotList: {0}: numobj={1}, field ={2}, nd={3}, ns={4}".format( pair, numPlots, plotField, len( dendCompts ), len( spineCompts ) ) )
if numPlots > 0:
tabname = graphs.path + '/plot' + str(k)
- scale = knownFields[i[3]][2]
- units = knownFields[i[3]][3]
- self.plotNames.append( ( tabname, i[4], k, scale, units, i[3] ) )
+ scale = knownFields[i.field][2]
+ units = knownFields[i.field][3]
+ if i.mode == 'wave':
+ self.wavePlotNames.append( [ tabname, i.title, k, scale, units, i.field, i.ymin, i.ymax ] )
+ else:
+ self.plotNames.append( [ tabname, i.title, k, scale, units, i.field, i.ymin, i.ymax ] )
+ if len( i.saveFile ) > 4 and i.saveFile[-4] == '.xml' or i.saveFile:
+ self.saveNames.append( [ tabname, len(self.saveNames), scale, units, i ] )
+
k += 1
- if i[3] == 'n' or i[3] == 'conc' or i[3] == 'volume' or i[3] == 'Gbar':
+ if i.field == 'n' or i.field == 'conc' or i.field == 'volume' or i.field == 'Gbar':
tabs = moose.Table2( tabname, numPlots )
else:
tabs = moose.Table( tabname, numPlots )
- if i[3] == 'spikeTime':
+ if i.field == 'spikeTime':
tabs.vec.threshold = -0.02 # Threshold for classifying Vm as a spike.
tabs.vec.useSpikeMode = True # spike detect mode on
@@ -719,8 +738,8 @@ class rdesigneur:
moogliBase = moose.Neutral( self.modelPath + '/moogli' )
k = 0
for i in self.moogList:
- kf = knownFields[i[3]]
- pair = i[0] + " " + i[1]
+ kf = knownFields[i.field]
+ pair = i.elecpath + " " + i.geom_expr
dendCompts = self.elecid.compartmentsFromExpression[ pair ]
spineCompts = self.elecid.spinesFromExpression[ pair ]
dendObj, mooField = self._parseComptField( dendCompts, i, knownFields )
@@ -728,13 +747,6 @@ class rdesigneur:
assert( mooField == mooField2 )
mooObj3 = dendObj + spineObj
numMoogli = len( mooObj3 )
- #dendComptMap = self.dendCompt.elecComptMap
- #self.moogliViewer = rmoogli.makeMoogli( self, mooObj3, mooField )
- if len( i ) == 5:
- i.extend( kf[4:6] )
- elif len( i ) == 6:
- i.extend( [kf[5]] )
- #self.moogliViewer = rmoogli.makeMoogli( self, mooObj3, i, kf )
self.moogNames.append( rmoogli.makeMoogli( self, mooObj3, i, kf ) )
@@ -757,8 +769,8 @@ rdesigneur.rmoogli.updateMoogliViewer()
self.display( len( self.moogNames ) + 1 )
def display( self, startIndex = 0 ):
- import matplotlib.pyplot as plt
for i in self.plotNames:
+ # ?, title, fignum, scale, ylabel, wave/spikeTime, ymin, ymax
plt.figure( i[2] + startIndex )
plt.title( i[1] )
plt.xlabel( "Time (s)" )
@@ -776,144 +788,79 @@ rdesigneur.rmoogli.updateMoogliViewer()
t = np.arange( 0, vtab[0].vector.size, 1 ) * vtab[0].dt
for j in vtab:
plt.plot( t, j.vector * i[3] )
- if len( self.moogList ) > 0:
+ if i[6] != i[7]:
+ plt.ylim( i[6], i[7] )
+ if len( self.moogList ) or len( self.wavePlotNames ) > 0:
plt.ion()
+ # Here we build the plots and lines for the waveplots
+ self.initWavePlots( startIndex )
+ if len( self.wavePlotNames ) > 0:
+ for i in range( 3 ):
+ self.displayWavePlots()
plt.show( block=True )
+ self._save()
+
+
+ def initWavePlots( self, startIndex ):
+ self.frameDt = moose.element( '/clock' ).currentTime/self.numWaveFrames
+ for wpn in range( len(self.wavePlotNames) ):
+ i = self.wavePlotNames[wpn]
+ vtab = moose.vec( i[0] )
+ if len( vtab ) < 2:
+ print( "Warning: Waveplot {} abandoned, only {} points".format( i[1], len( vtab ) ) )
+ continue
+ dFrame = len( vtab[0].vector ) / self.numWaveFrames
+ if dFrame < 1:
+ dFrame = 1
+ vpts = np.array( [ [k.vector[j] for j in range( 0, len( k.vector ), dFrame ) ] for k in vtab] ).T * i[3]
+ fig = plt.figure( i[2] + startIndex )
+ ax = fig.add_subplot( 111 )
+ plt.title( i[1] )
+ plt.xlabel( "position (voxels)" )
+ plt.ylabel( i[4] )
+ if i[6] != i[7]:
+ mn = i[6]
+ mx = i[7]
+ else:
+ mn = np.min(vpts)
+ mx = np.max(vpts)
+ if mn/mx < 0.3:
+ mn = 0
+ ax.set_ylim( mn, mx )
+ line, = plt.plot( range( len( vtab ) ), vpts[0] )
+ timeLabel = plt.text( len(vtab ) * 0.05, mn + 0.9*(mx-mn), 'time = 0' )
+ self.wavePlotNames[wpn].append( [fig, line, vpts, timeLabel] )
+ fig.canvas.draw()
+
+ def displayWavePlots( self ):
+ for f in range( self.numWaveFrames ):
+ for i in self.wavePlotNames:
+ wp = i[-1]
+ if len( wp[2] ) > f:
+ wp[1].set_ydata( wp[2][f] )
+ wp[3].set_text( "time = {:.1f}".format(f*self.frameDt) )
+ wp[0].canvas.draw()
+ #plt.pause(0.001)
#This calls the _save function which saves only if the filenames have been specified
- self._save()
################################################################
# Here we get the time-series data and write to various formats
################################################################
#[TO DO] Add NSDF output function
'''
- The author of the functions -- [_savePlots(), _getTimeSeriesTable(), _writeXML(), _writeCSV(), _saveFormats(), _save()] is
+ The original author of the functions -- [_savePlots(), _writeXML(), _writeCSV(), _save()] is
Sarthak Sharma.
Email address: sarthaks442@gmail.com
+ Heavily modified by U.S. Bhalla
'''
-
- def _savePlots( self ):
-
- knownFields = {
- 'Vm':('CompartmentBase', 'getVm', 1000, 'Memb. Potential (mV)' ),
- 'Cm':('CompartmentBase', 'getCm', 1e12, 'Memb. capacitance (pF)' ),
- 'Rm':('CompartmentBase', 'getRm', 1e-9, 'Memb. Res (GOhm)' ),
- 'Ra':('CompartmentBase', 'getRa', 1e-6, 'Axial Res (MOhm)' ),
- 'spikeTime':('CompartmentBase', 'getVm', 1, 'Spike Times (s)'),
- 'Im':('CompartmentBase', 'getIm', 1e9, 'Memb. current (nA)' ),
- 'inject':('CompartmentBase', 'getInject', 1e9, 'inject current (nA)' ),
- 'Gbar':('ChanBase', 'getGbar', 1e9, 'chan max conductance (nS)' ),
- 'modulation':('ChanBase', 'getModulation', 1, 'chan modulation (unitless)' ),
- 'Gk':('ChanBase', 'getGk', 1e9, 'chan conductance (nS)' ),
- 'Ik':('ChanBase', 'getIk', 1e9, 'chan current (nA)' ),
- 'ICa':('NMDAChan', 'getICa', 1e9, 'Ca current (nA)' ),
- 'Ca':('CaConcBase', 'getCa', 1e3, 'Ca conc (uM)' ),
- 'n':('PoolBase', 'getN', 1, '# of molecules'),
- 'conc':('PoolBase', 'getConc', 1000, 'Concentration (uM)' ),
- 'volume':('PoolBase', 'getVolume', 1e18, 'Volume (um^3)' ),
- 'current':('VClamp', 'getCurrent', 1e9, 'Holding Current (nA)')
- }
-
- save_graphs = moose.Neutral( self.modelPath + '/save_graphs' )
- dummy = moose.element( '/' )
- k = 0
-
- for i in self.saveList:
- pair = i[0] + " " + i[1]
- dendCompts = self.elecid.compartmentsFromExpression[ pair ]
- spineCompts = self.elecid.spinesFromExpression[ pair ]
- plotObj, plotField = self._parseComptField( dendCompts, i, knownFields )
- plotObj2, plotField2 = self._parseComptField( spineCompts, i, knownFields )
- assert( plotField == plotField2 )
- plotObj3 = plotObj + plotObj2
- numPlots = sum( i != dummy for i in plotObj3 )
- if numPlots > 0:
- save_tabname = save_graphs.path + '/save_plot' + str(k)
- scale = knownFields[i[3]][2]
- units = knownFields[i[3]][3]
- self.saveNames.append( ( save_tabname, i[4], k, scale, units ) )
- k += 1
- if i[3] == 'n' or i[3] == 'conc' or i[3] == 'volume' or i[3] == 'Gbar':
- save_tabs = moose.Table2( save_tabname, numPlots )
- save_vtabs = moose.vec( save_tabs )
- else:
- save_tabs = moose.Table( save_tabname, numPlots )
- save_vtabs = moose.vec( save_tabs )
- if i[3] == 'spikeTime':
- save_vtabs.threshold = -0.02 # Threshold for classifying Vm as a spike.
- save_vtabs.useSpikeMode = True # spike detect mode on
- q = 0
- for p in [ x for x in plotObj3 if x != dummy ]:
- moose.connect( save_vtabs[q], 'requestOut', p, plotField )
- q += 1
-
- def _getTimeSeriesTable( self ):
-
- '''
- This function gets the list with all the details of the simulation
- required for plotting.
- This function adds flexibility in terms of the details
- we wish to store.
- '''
-
- knownFields = {
- 'Vm':('CompartmentBase', 'getVm', 1000, 'Memb. Potential (mV)' ),
- 'spikeTime':('CompartmentBase', 'getVm', 1, 'Spike Times (s)'),
- 'Im':('CompartmentBase', 'getIm', 1e9, 'Memb. current (nA)' ),
- 'inject':('CompartmentBase', 'getInject', 1e9, 'inject current (nA)' ),
- 'Gbar':('ChanBase', 'getGbar', 1e9, 'chan max conductance (nS)' ),
- 'Gk':('ChanBase', 'getGk', 1e9, 'chan conductance (nS)' ),
- 'Ik':('ChanBase', 'getIk', 1e9, 'chan current (nA)' ),
- 'ICa':('NMDAChan', 'getICa', 1e9, 'Ca current (nA)' ),
- 'Ca':('CaConcBase', 'getCa', 1e3, 'Ca conc (uM)' ),
- 'n':('PoolBase', 'getN', 1, '# of molecules'),
- 'conc':('PoolBase', 'getConc', 1000, 'Concentration (uM)' ),
- 'volume':('PoolBase', 'getVolume', 1e18, 'Volume (um^3)' )
- }
-
- '''
- This takes data from plotList
- saveList is exactly like plotList but with a few additional arguments:
- ->It will have a resolution option, i.e., the number of decimal figures to which the value should be rounded
- ->There is a list of "saveAs" formats
- With saveList, the user will able to set what all details he wishes to be saved.
- '''
-
- for i,ind in enumerate(self.saveNames):
- pair = self.saveList[i][0] + " " + self.saveList[i][1]
- dendCompts = self.elecid.compartmentsFromExpression[ pair ]
- spineCompts = self.elecid.spinesFromExpression[ pair ]
- # Here we get the object details from plotList
- savePlotObj, plotField = self._parseComptField( dendCompts, self.saveList[i], knownFields )
- savePlotObj2, plotField2 = self._parseComptField( spineCompts, self.saveList[i], knownFields )
- savePlotObj3 = savePlotObj + savePlotObj2
-
- rowList = list(ind)
- save_vtab = moose.vec( ind[0] )
- t = np.arange( 0, save_vtab[0].vector.size, 1 ) * save_vtab[0].dt
-
- rowList.append(save_vtab[0].dt)
- rowList.append(t)
- rowList.append([jvec.vector * ind[3] for jvec in save_vtab]) #get values
- rowList.append(self.saveList[i][3])
- rowList.append(filter(lambda obj: obj.path != '/', savePlotObj3)) #this filters out dummy elements
-
- if (type(self.saveList[i][-1])==int):
- rowList.append(self.saveList[i][-1])
- else:
- rowList.append(12)
-
- self.tabForXML.append(rowList)
- rowList = []
-
- timeSeriesTable = self.tabForXML # the list with all the details of plot
- return timeSeriesTable
-
- def _writeXML( self, filename, timeSeriesData ): #to write to XML file
-
- plotData = timeSeriesData
- print("[CAUTION] The '%s' file might be very large if all the compartments are to be saved." % filename)
+ def _writeXML( self, plotData, time, vtab ):
+ tabname = plotData[0]
+ idx = plotData[1]
+ scale = plotData[2]
+ units = plotData[3]
+ rp = plotData[4]
+ filename = rp.saveFile[:-4] + str(idx) + '.xml'
root = etree.Element("TimeSeriesPlot")
parameters = etree.SubElement( root, "parameters" )
if self.params == None:
@@ -926,81 +873,59 @@ rdesigneur.rmoogli.updateMoogliViewer()
#plotData contains all the details of a single plot
title = etree.SubElement( root, "timeSeries" )
- title.set( 'title', str(plotData[1]))
- title.set( 'field', str(plotData[8]))
- title.set( 'scale', str(plotData[3]))
- title.set( 'units', str(plotData[4]))
- title.set( 'dt', str(plotData[5]))
+ title.set( 'title', rp.title)
+ title.set( 'field', rp.field)
+ title.set( 'scale', str(scale) )
+ title.set( 'units', units)
+ title.set( 'dt', str(vtab[0].dt) )
+ res = rp.saveResolution
p = []
- assert(len(plotData[7]) == len(plotData[9]))
-
- res = plotData[10]
- for ind, jvec in enumerate(plotData[7]):
+ for t, v in zip( time, vtab ):
p.append( etree.SubElement( title, "data"))
- p[-1].set( 'path', str(plotData[9][ind].path))
- p[-1].text = ''.join( str(round(value,res)) + ' ' for value in jvec )
-
+ p[-1].set( 'path', v.path )
+ p[-1].text = ''.join( str(round(y,res)) + ' ' for y in v.vector )
tree = etree.ElementTree(root)
tree.write(filename)
- def _writeCSV(self, filename, timeSeriesData):
-
- plotData = timeSeriesData
- dataList = []
- header = []
- time = plotData[6]
- res = plotData[10]
-
- for ind, jvec in enumerate(plotData[7]):
- header.append(plotData[9][ind].path)
- dataList.append([round(value,res) for value in jvec.tolist()])
- dl = [tuple(lst) for lst in dataList]
- rows = zip(tuple(time), *dl)
- header.insert(0, "time")
-
+ def _writeCSV( self, plotData, time, vtab ):
+ tabname = plotData[0]
+ idx = plotData[1]
+ scale = plotData[2]
+ units = plotData[3]
+ rp = plotData[4]
+ filename = rp.saveFile[:-4] + str(idx) + '.csv'
+
+ header = ["time",]
+ valMatrix = [time,]
+ header.extend( [ v.path for v in vtab ] )
+ valMatrix.extend( [ v.vector for v in vtab ] )
+ nv = np.array( valMatrix ).T
with open(filename, 'wb') as f:
writer = csv.writer(f, quoting=csv.QUOTE_MINIMAL)
writer.writerow(header)
- for row in rows:
+ for row in nv:
writer.writerow(row)
##########****SAVING*****###############
- def _saveFormats(self, timeSeriesData, k, *filenames):
- "This takes in the filenames and writes to corresponding format."
- if filenames:
- for filename in filenames:
- for name in filename:
- print (name)
- if name[-4:] == '.xml':
- self._writeXML(name, timeSeriesData)
- print(name, " written")
- elif name[-4:] == '.csv':
- self._writeCSV(name, timeSeriesData)
- print(name, " written")
- else:
- print("not possible")
- pass
- else:
- pass
def _save( self ):
- timeSeriesTable = self._getTimeSeriesTable()
- for i,sList in enumerate(self.saveList):
-
- if (len(sList) >= 6) and (type(sList[5]) != int):
- self.saveAs.extend(filter(lambda fmt: type(fmt)!=int, sList[5:]))
- try:
- timeSeriesData = timeSeriesTable[i]
- except IndexError:
- print("The object to be plotted has all dummy elements.")
- pass
- self._saveFormats(timeSeriesData, i, self.saveAs)
- self.saveAs=[]
+ for i in self.saveNames:
+ tabname = i[0]
+ idx = i[1]
+ scale = i[2]
+ units = i[3]
+ rp = i[4] # The rplot data structure, it has the setup info.
+
+ vtab = moose.vec( tabname )
+ t = np.arange( 0, vtab[0].vector.size, 1 ) * vtab[0].dt
+ ftype = rp.filename[-4:]
+ if ftype == '.xml':
+ self._writeXML( i, t, vtab )
+ elif ftype == '.csv':
+ self._writeCSV( i, t, vtab )
else:
- pass
- else:
- pass
+ print("Save format '{}' not known, please use .csv or .xml".format( ftype ) )
################################################################
# Here we set up the stims
@@ -1008,9 +933,11 @@ rdesigneur.rmoogli.updateMoogliViewer()
def _buildStims( self ):
knownFields = {
'inject':('CompartmentBase', 'setInject'),
- 'Ca':('CaConcBase', 'getCa'),
+ 'Ca':('CaConcBase', 'setCa'),
'n':('PoolBase', 'setN'),
'conc':('PoolBase', 'setConc'),
+ 'nInit':('PoolBase', 'setNinit'),
+ 'concInit':('PoolBase', 'setConcInit'),
'vclamp':('CompartmentBase', 'setInject'),
'randsyn':('SynChan', 'addSpike'),
'periodicsyn':('SynChan', 'addSpike')
@@ -1019,17 +946,17 @@ rdesigneur.rmoogli.updateMoogliViewer()
k = 0
# Stimlist = [path, geomExpr, relPath, field, expr_string]
for i in self.stimList:
- pair = i[0] + " " + i[1]
+ pair = i.elecpath + " " + i.geom_expr
dendCompts = self.elecid.compartmentsFromExpression[ pair ]
spineCompts = self.elecid.spinesFromExpression[ pair ]
#print( "pair = {}, numcompts = {},{} ".format( pair, len( dendCompts), len( spineCompts ) ) )
- if i[3] == 'vclamp':
+ if i.field == 'vclamp':
stimObj3 = self._buildVclampOnCompt( dendCompts, spineCompts, i )
stimField = 'commandIn'
- elif i[3] == 'randsyn':
+ elif i.field == 'randsyn':
stimObj3 = self._buildSynInputOnCompt( dendCompts, spineCompts, i )
stimField = 'setRate'
- elif i[3] == 'periodicsyn':
+ elif i.field == 'periodicsyn':
stimObj3 = self._buildSynInputOnCompt( dendCompts, spineCompts, i, doPeriodic = True )
stimField = 'setRate'
else:
@@ -1042,9 +969,9 @@ rdesigneur.rmoogli.updateMoogliViewer()
funcname = stims.path + '/stim' + str(k)
k += 1
func = moose.Function( funcname )
- func.expr = i[4]
- if i[3] == 'vclamp': # Hack to clean up initial condition
- func.doEvalAtReinit = 1
+ func.expr = i.expr
+ #if i[3] == 'vclamp': # Hack to clean up initial condition
+ func.doEvalAtReinit = 1
for q in stimObj3:
moose.connect( func, 'valueOut', q, stimField )
@@ -1267,6 +1194,7 @@ rdesigneur.rmoogli.updateMoogliViewer()
if len( comptlist ) == 0:
raise BuildError( "validateChem: no compartment on: " + cpath )
+ '''
if len( comptlist ) == 1:
return;
@@ -1276,6 +1204,7 @@ rdesigneur.rmoogli.updateMoogliViewer()
print(cpath, sortedComptlist)
raise BuildError( "validateChem: Require 3 chem compartments, have: " + str( len( sortedComptlist ) ) )
'''
+ '''
if not( sortedComptlist[0].name.lower() == 'dend' and \
sortedComptlist[1].name.lower() == 'spine' and \
sortedComptlist[2].name.lower() == 'psd' ):
@@ -1287,38 +1216,115 @@ rdesigneur.rmoogli.updateMoogliViewer()
#################################################################
+ def _isModelFromKkit( self ):
+ for i in self.chemProtoList:
+ if i[0][-2:] == ".g":
+ return True
+ return False
+
+ def _assignComptNamesFromKkit( self ):
+ '''
+ Algorithm: Identify compts by volume. Assume a couple of standard
+ orders depending on the addSomaChemCompt and addEndoChemCompt
+ flags:\n
+ ascc = 0, aecc = 0: dend, spine, psd.\n
+ ascc = 0, aecc = 1: dend, dend_endo, spine, spine_endo, psd, psd_endo.\n
+ ascc = 1, aecc = 0: soma, dend, spine, psd.\n
+ ascc = 1, aecc = 1: soma, soma_endo, dend, dend_endo, spine, spine_endo, psd, psd_endo.\n
+ In all cases, a shorter list of chem compartments will only fill
+ up the list to the available length.\n
+ soma_endo can be thought of as nucleus.\n
+ psd_endo doesn't really make sense, as peri-synaptic region really
+ needs to talk both to PSD and to spine bulk.
+ '''
+ comptList = moose.wildcardFind( self.chemid.path + '/#[ISA=ChemCompt]' )
+ #print( "comptList = {}".format ( [i.name for i in comptList]) )
+ if len( comptList ) < 2:
+ if comptList[0].name != 'dend':
+ comptList[0].name = 'dend'
+ return comptList
+ if not self._isModelFromKkit():
+ print( "Not isModelfromKkit" )
+ return comptList
+ sortedComptList = sorted( comptList, key=lambda x: -x.volume )
+ if self.addSomaChemCompt:
+ if self.addEndoChemCompt:
+ sortedNames = ["soma", "soma_endo", "dend", "dend_endo", "spine", "spine_endo", "psd", "psd_endo", ]
+ else:
+ sortedNames = ["soma", "dend", "spine","psd"]
+ else:
+ if self.addEndoChemCompt:
+ sortedNames = ["dend", "dend_endo", "spine", "spine_endo", "psd", "psd_endo", ]
+ else:
+ sortedNames = ["dend", "spine","psd"]
+
+ #print( "sortedNames = {}".format( sortedNames ) )
+ for i in range(min( len( sortedComptList ), len( sortedNames ) ) ):
+ #print( "SortedClist= {}".format( sortedComptList[i] ))
+ if sortedComptList[i].name != sortedNames[i]:
+ sortedComptList[i].name = sortedNames[i]
+ return sortedComptList
+
+
def _buildNeuroMesh( self ):
- comptlist = moose.wildcardFind( self.chemid.path + '/#[ISA=ChemCompt]' )
- sortedComptList = sorted( comptlist, key=lambda x: -x.volume )
- # A little juggling here to put the chem pathways onto new meshes.
+ # Address the following cases:
+ # - dend alone
+ # - dend with spine and PSD
+ # - above plus n endo meshes located as per name suffix:
+ # er_1_dend, vesicle_2_spine,
+ # - above plus presyn, e.g.:
+ # er_1_dend, vesicle_2_spine,
+ # - above plus soma
+ # - soma alone
+ # - soma plus n endo meshes
+
self.chemid.name = 'temp_chem'
newChemid = moose.Neutral( self.model.path + '/chem' )
- self.dendCompt = moose.NeuroMesh( newChemid.path + '/dend' )
- self.dendCompt.geometryPolicy = 'cylinder'
- self.dendCompt.separateSpines = 0
- if len( sortedComptList ) == 3:
+ comptlist = self._assignComptNamesFromKkit()
+ comptdict = { i.name:i for i in comptlist }
+ if len(comptdict) == 1 or 'dend' in comptdict:
+ self.dendCompt = moose.NeuroMesh( newChemid.path + '/dend' )
+ self.dendCompt.geometryPolicy = 'cylinder'
+ self.dendCompt.separateSpines = 0
+ self._moveCompt( comptdict['dend'], self.dendCompt )
+ comptdict['dend'] = self.dendCompt
+
+ if 'dend' in comptdict and 'spine' in comptdict:
+ #print( "comptdict = {}".format (comptdict ) )
self.dendCompt.separateSpines = 1
self.spineCompt = moose.SpineMesh( newChemid.path + '/spine' )
moose.connect( self.dendCompt, 'spineListOut', self.spineCompt, 'spineList' )
+ self._moveCompt( comptdict['spine'], self.spineCompt )
+ comptdict['spine'] = self.spineCompt
+ # We need to make a PSD in the spine even if it is uninhabited.
self.psdCompt = moose.PsdMesh( newChemid.path + '/psd' )
moose.connect( self.dendCompt, 'psdListOut', self.psdCompt, 'psdList','OneToOne')
- #Move the old reac systems onto the new compartments.
- self._moveCompt( sortedComptList[0], self.dendCompt )
- if len( sortedComptList ) == 3:
- self._moveCompt( sortedComptList[1], self.spineCompt )
- self._moveCompt( sortedComptList[2], self.psdCompt )
+ if 'psd' in comptdict: # Shift stuff over if any.
+ self._moveCompt( comptdict['psd'], self.psdCompt )
+ comptdict['psd'] = self.psdCompt
+
self.dendCompt.diffLength = self.diffusionLength
self.dendCompt.subTree = self.cellPortionElist
+ for i in comptdict:
+ if len(i) > 5:
+ if i[-5:] == '_endo':
+ endo = moose.EndoMesh( newChemid.path + '/' +i )
+ surround = comptdict[i[0:-5]]
+ self._endos.append( [endo, surround] )
+ #print( "{}****{}".format(i[0:-5], comptdict[i[0:-5]]))
+ self._moveCompt( comptdict[i], endo )
+ comptdict[i] = endo
moose.delete( self.chemid )
self.chemid = newChemid
+
#################################################################
def _configureSolvers( self ) :
if not hasattr( self, 'chemid' ):
return
if not hasattr( self, 'dendCompt' ):
raise BuildError( "configureSolvers: no chem meshes defined." )
- fixXreacs.fixXreacs( self.chemid.path )
+ fixXreacs( self.chemid.path )
dmksolve = moose.Ksolve( self.dendCompt.path + '/ksolve' )
dmdsolve = moose.Dsolve( self.dendCompt.path + '/dsolve' )
dmstoich = moose.Stoich( self.dendCompt.path + '/stoich' )
@@ -1349,6 +1355,8 @@ rdesigneur.rmoogli.updateMoogliViewer()
pmstoich.compartment = self.psdCompt
pmstoich.ksolve = pmksolve
pmstoich.dsolve = pmdsolve
+ if len( moose.wildcardFind( 'self.psdCompt.path/##[ISA=PoolBase]' ) ) == 0:
+ moose.Pool( self.psdCompt.path + '/dummy' )
pmstoich.path = self.psdCompt.path + "/##"
# Here we should test what kind of geom we have to use
@@ -1359,6 +1367,23 @@ rdesigneur.rmoogli.updateMoogliViewer()
# set up the connections so that the spine volume scaling can happen
self.elecid.setSpineAndPsdMesh( self.spineCompt, self.psdCompt)
self.elecid.setSpineAndPsdDsolve( smdsolve, pmdsolve )
+ for i in self._endos:
+ i[0].isMembraneBound = True
+ i[0].surround = i[1]
+ #i[0].elecComptMap = i[1].elecComptMap
+ path = i[0].path
+ #print( "Doing endo {} inside {}".format( path, i[1].path ) )
+ if self.useGssa:
+ eksolve = moose.Gsolve( path + '/ksolve' )
+ else:
+ eksolve = moose.Ksolve( path + '/ksolve' )
+ edsolve = moose.Dsolve( path + '/dsolve' )
+ estoich = moose.Stoich( path + '/stoich' )
+ estoich.compartment = i[0]
+ estoich.ksolve = eksolve
+ estoich.dsolve = edsolve
+ estoich.path = path + "/##"
+ edsolve.buildMeshJunctions( moose.element(i[1].path + '/dsolve' ))
################################################################
def _loadChem( self, fname, chemName ):
@@ -1369,6 +1394,7 @@ rdesigneur.rmoogli.updateMoogliViewer()
print("loadChem: No compartment found in file: ", fname)
return
# Sort comptlist in decreasing order of volume
+ '''
sortedComptlist = sorted( comptlist, key=lambda x: -x.volume )
if ( len( sortedComptlist ) >= 1 ):
sortedComptlist[0].name = 'dend'
@@ -1376,6 +1402,7 @@ rdesigneur.rmoogli.updateMoogliViewer()
sortedComptlist[1].name = 'spine'
if ( len( sortedComptlist ) >= 3 ):
sortedComptlist[2].name = 'psd'
+ '''
################################################################
@@ -1384,6 +1411,7 @@ rdesigneur.rmoogli.updateMoogliViewer()
for i in moose.wildcardFind( a.path + '/#' ):
if ( i.name != 'mesh' ):
moose.move( i, b )
+ #print( "Moving {} {} to {}".format( i.className, i.name, b.name ))
moose.delete( a )
################################################################
def _buildAdaptor( self, meshName, elecRelPath, elecField, \
@@ -1458,3 +1486,94 @@ rdesigneur.rmoogli.updateMoogliViewer()
moose.connect( i[3], 'requestOut', chemVec[j], chemFieldSrc)
msg = moose.connect( i[3], 'output', elObj, elecFieldDest )
+
+#######################################################################
+# Some helper classes, used to define argument lists.
+#######################################################################
+
+class baseplot:
+ def __init__( self,
+ elecpath='soma', geom_expr='1', relpath='.', field='Vm' ):
+ self.elecpath = elecpath
+ self.geom_expr = geom_expr
+ self.relpath = relpath
+ self.field = field
+
+class rplot( baseplot ):
+ def __init__( self,
+ elecpath = 'soma', geom_expr = '1', relpath = '.', field = 'Vm',
+ title = 'Membrane potential',
+ mode = 'time',
+ ymin = 0.0, ymax = 0.0,
+ saveFile = "", saveResolution = 3, show = True ):
+ baseplot.__init__( self, elecpath, geom_expr, relpath, field )
+ self.title = title
+ self.mode = mode # Options: time, wave, wave_still, raster
+ self.ymin = ymin # If ymin == ymax, it autoscales.
+ self.ymax = ymax
+ if len( saveFile ) < 5:
+ self.saveFile = ""
+ else:
+ f = saveFile.split('.')
+ if len(f) < 2 or ( f[-1] != 'xml' and f[-1] != 'csv' ):
+ raise BuildError( "rplot: Filetype is '{}', must be of type .xml or .csv.".format( f[-1] ) )
+ self.saveFile = saveFile
+ self.show = show
+
+ def printme( self ):
+ print( "{}, {}, {}, {}, {}, {}, {}, {}, {}, {}".format(
+ self.elecpath,
+ self.geom_expr, self.relpath, self.field, self.title,
+ self.mode, self.ymin, self.ymax, self.saveFile, self.show ) )
+
+ @staticmethod
+ def convertArg( arg ):
+ if isinstance( arg, rplot ):
+ return arg
+ elif isinstance( arg, list ):
+ return rplot( *arg )
+ else:
+ raise BuildError( "rplot initialization failed" )
+
+class rmoog( baseplot ):
+ def __init__( self,
+ elecpath = 'soma', geom_expr = '1', relpath = '.', field = 'Vm',
+ title = 'Membrane potential',
+ ymin = 0.0, ymax = 0.0,
+ show = True ): # Could put in other display options.
+ baseplot.__init__( self, elecpath, geom_expr, relpath, field )
+ self.title = title
+ self.ymin = ymin # If ymin == ymax, it autoscales.
+ self.ymax = ymax
+ self.show = show
+
+ @staticmethod
+ def convertArg( arg ):
+ if isinstance( arg, rmoog ):
+ return arg
+ elif isinstance( arg, list ):
+ return rmoog( *arg )
+ else:
+ raise BuildError( "rmoog initialization failed" )
+
+ # Stimlist = [path, geomExpr, relPath, field, expr_string]
+class rstim( baseplot ):
+ def __init__( self,
+ elecpath = 'soma', geom_expr = '1', relpath = '.', field = 'inject', expr = '0'):
+ baseplot.__init__( self, elecpath, geom_expr, relpath, field )
+ self.expr = expr
+
+ def printme( self ):
+ print( "{}, {}, {}, {}, {}, {}, {}, {}, {}, {}".format(
+ self.elecpath,
+ self.geom_expr, self.relpath, self.field, self.expr ) )
+
+ @staticmethod
+ def convertArg( arg ):
+ if isinstance( arg, rstim ):
+ return arg
+ elif isinstance( arg, list ):
+ return rstim( *arg )
+ else:
+ raise BuildError( "rstim initialization failed" )
+
diff --git a/python/rdesigneur/rdesigneurProtos.py b/python/rdesigneur/rdesigneurProtos.py
index ec5d7059..920caaba 100644
--- a/python/rdesigneur/rdesigneurProtos.py
+++ b/python/rdesigneur/rdesigneurProtos.py
@@ -757,8 +757,8 @@ def makePassiveHHsoma(name = 'passiveHHsoma', parent='/library'):
if not moose.exists( elecpath ):
elecid = moose.Neuron( elecpath )
dia = 500e-6
- soma = buildComptWrapper( elecid, 'soma', dia, dia, 0.0,
- 0.33333333, 3000, 0.01 )
+ soma = buildCompt( elecid, 'soma', dx = dia, dia = dia, x = 0.0,
+ RM = 0.33333333, RA = 3000, CM = 0.01 )
soma.initVm = -65e-3 # Resting of -65, from HH
soma.Em = -54.4e-3 # 10.6 mV above resting of -65, from HH
else:
diff --git a/python/rdesigneur/rmoogli.py b/python/rdesigneur/rmoogli.py
index f98549c0..16317b56 100644
--- a/python/rdesigneur/rmoogli.py
+++ b/python/rdesigneur/rmoogli.py
@@ -20,21 +20,29 @@ def makeMoogli( rd, mooObj, args, fieldInfo ):
# Cleaner still would be to have the C code give a vector of values
# For now it means something different for chem and elec displays.
#moogliEntry = [elecPath,bool,whichObjToDisplay,FieldToDisplay,titleForDisplay,rangeMin,rangeMax]
- mooField = args[3]
- relObjPath = args[2]
+ mooField = args.field
+ relObjPath = args.relpath
numMoogli = len( mooObj )
+ if args.ymin != args.ymax:
+ ymin = args.ymin
+ ymax = args.ymax
+ else:
+ ymin = fieldInfo[4]
+ ymax = fieldInfo[5]
+ print( "fieldinfo = {}, ymin = {}, ymax = {}".format( fieldInfo, ymin, ymax ))
viewer = moogul.MooView()
if mooField == 'n' or mooField == 'conc':
#moogul.updateDiffCoords( mooObj )
reacSystem = moogul.MooReacSystem( mooObj, fieldInfo,
field = mooField, relativeObj = relObjPath,
- valMin = args[5], valMax = args[6] )
+ valMin = ymin, valMax = ymax )
viewer.addDrawable( reacSystem )
else:
neuron = moogul.MooNeuron( rd.elecid, fieldInfo,
field = mooField, relativeObj = relObjPath,
- valMin = args[5], valMax = args[6] )
+ valMin = ymin, valMax = ymax )
+ print( "min = {}, max = {}".format(ymin, ymax) )
viewer.addDrawable( neuron )
return viewer
diff --git a/randnum/Binomial.cpp b/randnum/Binomial.cpp
deleted file mode 100644
index 2014c283..00000000
--- a/randnum/Binomial.cpp
+++ /dev/null
@@ -1,388 +0,0 @@
-/*******************************************************************
- * File: Binomial.cpp
- * Description:
- * Author: Subhasis Ray
- * E-mail: ray.subhasis@gmail.com
- * Created: 2007-10-28 13:44:46
- ********************************************************************/
-/**********************************************************************
- ** 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 _BINOMIAL_CPP
-#define _BINOMIAL_CPP
-#include <cmath>
-#include "randnum.h"
-#include "utility/numutil.h"
-#include "Binomial.h"
-#include <vector>
-#include <iostream>
-#include <climits>
-using namespace std;
-
-// First 10 entries in lookup table
-const double fc[] = {
- 0.08106146679532726,
- 0.04134069595540929,
- 0.02767792568499834,
- 0.02079067210376509,
- 0.01664469118982119,
- 0.01387612882307075,
- 0.01189670994589177,
- 0.01041126526197209,
- 0.009255462182712733,
- 0.008330563433362871
-};
-
-
-/// Insert first 100 elements in lookup table
-const vector <double> initializeLookupTable()
-{
- static vector <double> table;
-
- for ( int i = 0; i < 10; ++i )
- {
- table.push_back(fc[i]);
- }
- for ( int i = 10; i < 100; ++i )
- {
- double denom = 1.0/(i+1);
- double value = (0.083333333333333333 - (0.002777777777777778 - 0.0007936508*denom*denom)*denom*denom)*denom;
- table.push_back(value);
- }
- return table;
-}
-static const vector <double> lookupTable = initializeLookupTable();
-
-
-
-/**
- retrieve fc value from table or calculate it depending on the value of k
-*/
-inline double getFc(unsigned int k)
-{
- if (lookupTable.size() <= k )
- {
- double denom = 1.0/(k+1);
- return (0.083333333333333333 - (0.002777777777777778 - 0.0007936508*denom*denom)*denom*denom)*denom;
- }
- else
- {
- return lookupTable[k];
- }
-}
-
-/**
- Binomial distribution generator with parameters n and p. p is the
- probability of the favoured outcome, n is the number of trials.
- */
-Binomial::Binomial( long n, double p):n_(n), p_(p)
-{
-
- if (( p < 0 ) || ( p > 1 ))
- {
- cerr << "ERROR: p must be in [0,1] range." << endl;
- p = 0.0;
- return;
- }
- if ( n < 1 )
- {
- cerr << "ERROR: n must be >= 1" << endl;
- return;
- }
-
-
- double tmpMean;
- double tmp;
- isInverted_ = false;
-
-// tmpMean = n*((p < 0.5)? p : (1-p));
-
-// if ((tmpMean > 10.0))
-// {
- // the above can be simplified as: ( saves one floating point comparison, aesthetically pleasing :D )
- if ( n > 20 )
- {
- if( p < 0.5 )
- {
- p_ = p;
- }
- else
- {
- p_ = 1.0 - p;
- isInverted_ = true;
- }
- tmpMean = n*p_;
-
- tmp = sqrt(tmpMean*(1.0 - p_));
- paramC_ = tmpMean + 0.5;
- paramB_ = 1.15 + 2.53*tmp;
- paramA_ = -0.0873 + 0.0248*paramB_ + 0.01*p_;
- paramAlpha_ = (2.83 + 5.1/paramB_)*tmp;
- paramUr_ = 0.43;
- paramVr_ = 0.92 - 4.2/paramB_;
- paramUrVr_ = 0.86*paramVr_;
- paramM_ = floor(tmpMean+p_);
- paramR_ = floor(p_/(1-p_));
- paramNr_ = (n+1)*paramR_;
- paramNpq_ = tmpMean*(1-p_);
- }
- mean_ = n_*p_;
-}
-
-long Binomial::getN() const
-{
- return n_;
-}
-
-double Binomial::getP() const
-{
- if ( isInverted_)
- {
- return 1 - p_;
- }
- else
- {
- return p_;
- }
-}
-
-double Binomial::getMean() const
-{
- if (isInverted_)
- {
- return (n_ - mean_);
- }else{
- return mean_;
- }
-}
-
-double Binomial::getVariance() const
-{
- static double variance = sqrt(n_*p_*(1.0-p_));
- return variance;
-}
-
-/**
- returns the next random number in this distribution as the ratio of
- the number of positive outcomes and the total number of trials.
- This is the most naive implementation. This is ok for small n.
- For large n such that mean > 10, we use BTRD algorithm by Hoermann.
- See documentation of generateTrd() for further detail.
-*/
-double Binomial::getNextSample() const
-{
- double sample = 0;
- if ( p_ == 0 )
- {
- sample = (double)0;
- }
- else if ( isClose<double>(1.0,p_, DBL_EPSILON))
- {
- sample = (double)n_;
- }
- else
- {
- if ( mean_ > 10 )
- {
- sample = isInverted_? n_ - generateTrd(): generateTrd();
- }
- else
- {
- for ( unsigned int i = 0; i < n_; ++i)
- {
- double myRand = mtrand();
- if ( myRand < p_ )
- {
- sample+=1;
- }
- }
- }
-// cerr << "Sample value: " << sample << " " << isInverted_<< endl;
- }
-
- return sample;
-}
-
-/**
- Generate binomially distributed random numbers using transformed
- rejection with decomposition as described in "The Generation of
- Binomial Random Variable" by W Hoermann.
-*/
-double Binomial::generateTrd() const
-{
-
- double varV;
- double varU;
- double varUs;
- double varK;
- double varKm;
- double varF;
- double varNm;
- double varH;
- double varNk;
- double varI;
- double varRho;
- double varT;
-
- while ( true )
- {
- // 1a: generate a uniform random number v
- varV = mtrand();
- if ( varV <= paramUrVr_ )
- {
- // 1b: if v <= urvr then u = v/vr - 0.43
- double varU = varV/paramVr_ - 0.43;
- // 1c: return floor( (2*a/(0.5 - |u|) + b ) * u + c )
- return floor((2*paramA_/(0.5 - fabs(varU)) + paramB_ )*varU+paramC_);
- }
- // 2a: if ( v >= vr ) then generate a uniform random number u in (-0.5,+0.5)
- if ( varV >= paramVr_ )
- {
- varU = mtrand() - 0.5;
- }
- else // 2b: otherwise
- {
- // 2b(i): set u = v/vr - 0.93
- varU = varV/paramVr_ - 0.93;
- // 2b(ii): set u = sign(u)*0.5 - u
- varU = (varU > 0)? 0.5 - varU : - 0.5 - varU;
- // 2b(iii) generate a uniform random number v in (0,vr)
- varV = mtrand()*paramVr_;
- }
- // 3.0a: us = 0.5 - |u|
- varUs = (varU < 0) ? 0.5 + varU : 0.5 - varU;
- // 3.0b: k = floor( ( 2*a/us + b )*u + c )
- varK = floor( (2*paramA_/varUs+paramB_)*varU + paramC_);
- // 3.0c: if k < 0 or k > n go to (1)
- if ( (varK < 0) || ( varK > n_ ))
- {
- continue;
- }
-
- // 3.0d: v = v*alpha/(a/(us*us)+b)
- varV = varV*paramAlpha_/(paramA_/(varUs*varUs) + paramB_ );
- // 3.0e: km = | k - m |
- varKm = ( varK < paramM_)? paramM_ - varK : varK - paramM_;
- // 3.0f: if km > 15 go to 3.2 , else ...
- if ( varKm <= 15 )
- {
- // 3.1: recursive evaluation of f(k)
- // 3.1a: f = 1
- varF = 1;
- // 3.1b: if (m < k)
- if ( paramM_ < varK )
- {
- // 3.1b(i): set i = m
- varI = paramM_;
- // 3.1b(ii): repeat i = i+1, f = f*(nr/i - r) until (i == k).
- while ( varI < varK )
- {
- ++varI;
- varF *= (paramNr_/varI - paramR_);
- }
- }
- else // 3.1c: otherwise ...
- {
- // 3.1c(i) if ( m > k)
- if ( paramM_ > varK )
- {
- // 3.1c(ii): i = k
- varI = varK;
- // 3.1c(ii): repeat i = i+1, v = v*(nr/i - r) until (i == m).
- while ( varI < paramM_)
- {
- ++varI;
- varV *= (paramNr_/varI -paramR_);
- }
- }
- //3.1d: if v <= f return k, otherwise goto (1)
- if ( varV <= varF )
- {
- return varK;
- }
- }
- }
- // 3.2: Squeeze acceptance or rejection
- // 3.2a: v = log(v)
- varV = log(varV);
- // 3.2b: rho = ( km/npq )*(((km/3+0.625)*km + 1/6)/npq+0.5)
- varRho = (varKm/paramNpq_)*(((varKm/3.0+ 0.625)*varKm+0.16666666666666667)/paramNpq_+0.5);
- // 3.2c: t = - km*km/(2*npq)
- varT = -varKm*varKm*0.5/paramNpq_;
- // 3.2d: if ( v < t - rho ) then return k
- if ( varV < ( varT - varRho ))
- {
- return varK;
- }
- // 3.2e: if ( v > t+rho ) then goto (1)
- if ( varV > (varT + varRho))
- {
- continue;
- }
- // 3.3: Set-up for 3.4
- // 3.3a: nm = n - m + 1
- varNm = n_ - paramM_ + 1;
- // 3.3b: h = (m+0.5)*log((m+1)/(r*nm)) + fc(m) + fc(n-m)
- varH = (paramM_ + 0.5)*log((paramM_+1)/(paramR_*varNm)) + getFc((int)paramM_) + getFc((int)(n_-paramM_));
- // 3.4: Final acceptance-rejection test
- // 3.4a: nk = n - k + 1;
- varNk = n_ - varK + 1;
- // 3.4b: if ( v <= h + (n+1)*log(nm/nk) + (k+0.5)*log(nk*r/(k+1)) - fc(k) -fc(n-k) then return k
- if ( varV <= varH + (n_ + 1)*log(varNm/varNk) + ( varK + 0.5)*log(varNk*paramR_/(varK+1)) - getFc((int)varK) - getFc((int)(n_ - varK)))
- {
- return varK;
- }
- // 3.4c: otherwise goto (1)
- }
-}
-
-
-/**
- TODO: what to do to automatically test the quality of the random
- number generation? We can check the mean and variance perhaps?
- We should also check the plot of the distribution manually.
-*/
-void testBinomial()
-{
-
- int trialMin = 2;
- int trialMax = trialMin*1000;
-
- double tmp;
-
-
- for ( int i = trialMin; i < trialMax; i =(int)( i* 1.5) )
- {
- for ( double p = 0.1; p < .95; p += 0.1)
- {
- Binomial b(i, p);
- tmp = 0;
- for ( int j = 0; j < i; ++j )
- {
- tmp += b.getNextSample();
- }
- cerr << "Diff( " << i << "," << p << ") "
- << tmp/i - b.getMean()
- << " [ " << tmp/i << " - " << b.getMean() <<" ]"
- << endl;
- }
- }
-}
-#if 0 // test main
-int main(void)
-{
- testBinomial();
- return 0;
-}
-
-#endif // test main
-
-
-#endif
diff --git a/randnum/Binomial.h b/randnum/Binomial.h
deleted file mode 100644
index 06401f4d..00000000
--- a/randnum/Binomial.h
+++ /dev/null
@@ -1,55 +0,0 @@
-/*******************************************************************
- * File: Binomial.h
- * Description: Implements binomial distribution
- * Author: Subhasis Ray
- * E-mail: ray.subhasis@gmail.com
- * Created: 2007-10-28 13:42:24
- ********************************************************************/
-/**********************************************************************
-** 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 _BINOMIAL_H
-#define _BINOMIAL_H
-#include "Probability.h"
-
-class Binomial:public Probability
-{
- public:
- Binomial(){};
- Binomial( long n, double p);
- long getN() const;
- double getP() const;
- double getMean() const;
- double getVariance() const;
- double getNextSample() const;
-
- private:
- double generateTrd() const;
- bool isInverted_;
-
- unsigned long n_;
- double p_;
- double mean_;
-
- double paramC_;
- double paramB_;
- double paramA_;
- double paramAlpha_;
- double paramUr_;
- double paramVr_;
- double paramUrVr_;
- double paramM_;
- double paramR_;
- double paramNr_;
- double paramNpq_;
-};
-
-
-#endif
diff --git a/randnum/BinomialRng.cpp b/randnum/BinomialRng.cpp
deleted file mode 100644
index 50765b2e..00000000
--- a/randnum/BinomialRng.cpp
+++ /dev/null
@@ -1,180 +0,0 @@
-/*******************************************************************
- * File: BinomialRng.cpp
- * Description:
- * Author: Subhasis Ray
- * E-mail: ray.subhasis@gmail.com
- * Created: 2007-11-08 10:58:01
- ********************************************************************/
-/**********************************************************************
- ** 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 _BINOMIALRNG_CPP
-#define _BINOMIALRNG_CPP
-#include "BinomialRng.h"
-#include "Binomial.h"
-#include "utility/numutil.h"
-#include <cmath>
-extern const Cinfo* initRandGeneratorCinfo();
-
-const Cinfo* BinomialRng::initCinfo()
-{
- static ValueFinfo< BinomialRng, double > n(
- "n",
- "Parameter n of the binomial distribution. In a coin toss experiment,"
- " this is the number of tosses.",
- &BinomialRng::setN,
- &BinomialRng::getN);
- static ValueFinfo < BinomialRng, double > p(
- "p",
- "Parameter p of the binomial distribution. In a coin toss experiment,"
-" this is the probability of one of the two sides of the coin being on"
-" top.",
- &BinomialRng::setP,
- &BinomialRng::getP);
- static Finfo* binomialRngFinfos[] = {
- &n,
- &p,
- };
-
- static string doc[] = {
- "Name", "BinomialRng",
- "Author", "Subhasis Ray",
- "Description", "Binomially distributed random number generator.",
- };
- Dinfo < BinomialRng> dinfo;
- static Cinfo binomialRngCinfo(
- "BinomialRng",
- RandGenerator::initCinfo(),
- binomialRngFinfos,
- sizeof(binomialRngFinfos)/sizeof(Finfo*),
- &dinfo,
- doc,
- sizeof( doc ) / sizeof( string ));
- return &binomialRngCinfo;
-}
-
-
-static const Cinfo* binomialRngCinfo = BinomialRng::initCinfo();
-
-BinomialRng::BinomialRng()
-{
- isNSet_ = false;
- isPSet_ = false;
- isModified_ = true;
-
- n_ = 0;
- p_ = 0;
-}
-
-/**
- Set parameter n ( number of trials for a two-outcome experiment).
- This must be set before the actual generator is instantiated.
- */
-void BinomialRng::setN(double value)
-{
- unsigned long n = (unsigned long)value;
- if ( n <= 0 )
- {
- cerr << "ERROR: BinomialRng::innerSetN - n must be a positive integer." << endl;
- return;
- }
-
- if(!isNSet_)
- {
- isNSet_ = true;
- n_ = n;
- }
- else
- {
- if (n_!= n )
- {
- n_ = n;
- isModified_ = true;
- }
- }
-
- if ( isNSet_ && isPSet_ && isModified_)
- { {
- if ( rng_ )
- {
- delete rng_;
- }
- rng_ = new Binomial((unsigned long)n_,p_);
- isModified_ = false;
- }
- }
-}
-
-/**
- Returns parameter n.
- */
-double BinomialRng::getN() const
-{
- return n_;
-}
-
-/**
- Set parameter p ( the probability of the outcome of interest ).
- This must be set before the actual generator is instantiated.
- */
-void BinomialRng::setP(double p)
-{
- if ( p < 0 || p > 1) {
- cerr << "ERROR: BinomialRng::setP - p must be in (0,1) range." << endl;
- return;
- }
- if ( !isPSet_) {
- p_ = p;
- isPSet_ = true;
- } else {
- if (!isClose< double >(p_,p, DBL_EPSILON)) {
- p_ = p;
- isModified_ = true;
- }
- }
-
- if ( isNSet_ && isPSet_ && isModified_ ){
- if ( rng_ ){
- delete rng_;
- }
- rng_ = new Binomial((long)(n_),p_);
- isModified_ = false;
- }
-}
-
-/**
- returns parameter p.
-*/
-double BinomialRng::getP() const
-{
- return p_;
-}
-
-
-/**
- reports error if one or more of the parameters are not set.
-*/
-void BinomialRng::vReinit( const Eref& e, ProcPtr p)
-{
- if ( isNSet_ ){
- if ( isPSet_ ){
- if ( !rng_ ){
- rng_ = new Binomial((unsigned long)(n_), p_);
- }
- } else {
- cerr << "ERROR: BinomialRng::reinit - first set value of p." << endl;
- }
- } else {
- cerr << "ERROR: BinomialRng::reinit - first set value of n." << endl;
- }
-}
-
-
-#endif
diff --git a/randnum/BinomialRng.h b/randnum/BinomialRng.h
deleted file mode 100644
index df470a51..00000000
--- a/randnum/BinomialRng.h
+++ /dev/null
@@ -1,45 +0,0 @@
-/*******************************************************************
- * File: BinomialRng.h
- * Description:
- * Author: Subhasis Ray
- * E-mail: ray.subhasis@gmail.com
- * Created: 2007-11-08 10:48:59
- ********************************************************************/
-/**********************************************************************
-** 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 _BINOMIALRNG_H
-#define _BINOMIALRNG_H
-
-#include "randnum.h"
-#include "../basecode/header.h"
-#include "RandGenerator.h"
-#include "Binomial.h"
-
-class BinomialRng: public RandGenerator
-{
- public:
- BinomialRng();
- void setN(double n);
- double getN() const;
- void setP(double p);
- double getP() const;
- virtual void vReinit( const Eref& e, ProcPtr p);
-
- static const Cinfo * initCinfo();
- private:
- bool isNSet_;
- unsigned long n_;
- bool isPSet_;
- double p_;
- bool isModified_;
-};
-
-#endif
diff --git a/randnum/CMakeLists.txt b/randnum/CMakeLists.txt
index 343f7f7f..cc4de6b7 100644
--- a/randnum/CMakeLists.txt
+++ b/randnum/CMakeLists.txt
@@ -1,8 +1,11 @@
-file(GLOB random_SRC "*.cpp")
+cmake_minimum_required(VERSION 2.8)
-include_directories(../basecode )
-if(WITH_GSL)
- include_directories(${GSL_INCLUDE_DIRS})
-endif(WITH_GSL)
+if( ${CMAKE_SOURCE_DIR} EQUAL ${CMAKE_CURRENT_SOURCE_DIR} )
+ add_definitions( -std=c++11 -g -Wall )
+endif()
-add_library(randnum ${random_SRC})
+add_executable( normal_dist
+ ${CMAKE_CURRENT_SOURCE_DIR}/test_normal_dist.cpp)
+
+enable_testing()
+add_test( NAME test_normal_dist COMMAND $<TARGET_FILE:normal_dist> )
diff --git a/randnum/Definitions.h b/randnum/Definitions.h
new file mode 100644
index 00000000..19ef33fa
--- /dev/null
+++ b/randnum/Definitions.h
@@ -0,0 +1,46 @@
+/***
+ * Filename: Definitions.h
+ *
+ * Description: Various definitions.
+ *
+ * Version: 0.0.1
+ * Created: 2018-08-04
+
+ * Revision: none
+ *
+ * Author: Dilawar Singh <dilawars@ncbs.res.in>
+ * Organization: NCBS Bangalore
+ *
+ * License: GNU GPL3
+ */
+
+#ifndef DEFINITIONS_H
+#define DEFINITIONS_H
+
+#include <random>
+
+namespace moose {
+
+/* --------------------------------------------------------------------------*/
+/**
+ * @Synopsis MOOSE's random device. Use it from <random>
+ */
+/* ----------------------------------------------------------------------------*/
+typedef std::random_device MOOSE_RANDOM_DEVICE;
+
+/* --------------------------------------------------------------------------*/
+/**
+ * @Synopsis Global random number generator engine. Everywhere we use this
+ * engine.
+ */
+/* ----------------------------------------------------------------------------*/
+typedef std::mersenne_twister_engine< std::uint_fast32_t, 32, 624, 397, 31
+ , 0x9908b0df, 11
+ , 0xffffffff, 7
+ , 0x9d2c5680, 15
+ , 0xefc60000, 18, 1812433253
+ > MOOSE_RNG_DEFAULT_ENGINE;
+
+}
+
+#endif /* end of include guard: DEFINITIONS_H */
diff --git a/randnum/Distributions.h b/randnum/Distributions.h
new file mode 100644
index 00000000..d58fd905
--- /dev/null
+++ b/randnum/Distributions.h
@@ -0,0 +1,34 @@
+/***
+ * Filename: Distributions.h
+ *
+ * Description: All distributions.
+ *
+ * Version: 0.0.1
+ * Created: 2018-08-04
+
+ * Revision: none
+ *
+ * Author: Dilawar Singh <dilawars@ncbs.res.in>
+ * Organization: NCBS Bangalore
+ *
+ * License: GNU GPL2
+ */
+
+#ifndef DISTRIBUTIONS_H
+#define DISTRIBUTIONS_H
+
+#include "NormalDistribution.hpp"
+#include <random>
+
+namespace moose {
+
+ template<typename T=double>
+ using MOOSE_UNIFORM_DISTRIBUTION = std::uniform_real_distribution<T>;
+
+ template<typename T=double>
+ using MOOSE_NORMAL_DISTRIBUTION = moose::normal_distribution<T>;
+
+}
+
+
+#endif /* end of include guard: DISTRIBUTIONS_H */
diff --git a/randnum/Exponential.cpp b/randnum/Exponential.cpp
deleted file mode 100644
index 99f7770d..00000000
--- a/randnum/Exponential.cpp
+++ /dev/null
@@ -1,197 +0,0 @@
-/*******************************************************************
- * File: Exponential.cpp
- * Description:
- * Author: Subhasis Ray
- * E-mail: ray.subhasis@gmail.com
- * Created: 2007-11-01 09:03:51
- ********************************************************************/
-/**********************************************************************
-** 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 _EXPONENTIAL_CPP
-#define _EXPONENTIAL_CPP
-#include "Exponential.h"
-#include "randnum.h"
-#include "utility/numutil.h"
-#include <iostream>
-#include <cmath>
-
-using namespace std;
-
-Exponential::Exponential(double mean):mean_(mean),generator_(&(Exponential::randomMinimization))
-{
-}
-
-Exponential::Exponential(ExponentialGenerator method, double mean):mean_(mean)
-{
- switch(method)
- {
- case LOGARITHMIC:
- generator_ = &(Exponential::logarithmic);
- break;
- default:
- generator_ = &(Exponential::randomMinimization);
- break;
- }
-}
-
-double Exponential::getMean() const
-{
- return mean_;
-}
-
-double Exponential::getVariance() const
-{
- return mean_*mean_;
-}
-
-double Exponential::getNextSample() const
-{
- return generator_(mean_);
-}
-
-
-double Exponential::logarithmic(double mean)
-{
- double uniform = mtrand();
- if ( uniform <= 0 )
- {
- uniform = 1.0e-6;
- }
-
- return - mean*log(uniform);
-}
-
-extern unsigned long genrand_int32(void);
-
-/**
- successive entries in the series
- {Qk} = {(ln2/1! + (ln2)^2/2! + (ln2)^3/3! + ... + (ln2)^k/k!)}
- used in the random minimization algorithm.
- */
-static const double q[] =
-{
- 1.0, // dummy for q[0]
- 0.69314718055994528622676,
- 0.93337368751904603580982,
- 0.98887779618386761892879,
- 0.99849592529149611142003,
- 0.99982928110613900063441,
- 0.99998331641007276449074,
- 0.99999856914387685868917,
- 0.99999989069255590390384,
- 0.99999999247341597730099,
- 0.99999999952832763217003,
- 0.99999999997288147035590 // > 0.99999999953433871269226 = 1 - 2^(-31)
-};
-
-/**
- See Knuth, Vol II Sec 3.4.1 : Algorithm S
- */
-
-double Exponential::randomMinimization(double mean)
-{
- double result;
-
- unsigned long uniform = genrand_int32(); // 1) generate t+1 (=32) bit uniform random binary fraction .b0..bt
- int j = 0;
-
- if ( uniform == 0 )
- {
- uniform = 1;
- }
-
- while (0x80000000 & uniform ) // 1) detect the first 0 bit
- {
- uniform = uniform << 1; // 1a) shift off leading j+1 bits, setting u = .b(j+1) .. b(t)
- ++j;
- }
- uniform = uniform << 1; // 1a)shift off leading j+1 bits, setting u = .b(j+1) .. b(t)
- double uniform_frac = uniform / 4294967296.0;
-
- if ( uniform_frac < LN2 ) // 2) u < ln2?
- {
- result = mean*(j*LN2 + uniform_frac); // x <- mean * ( j * ln2 + u )
- }
- else
- {
- // 3) minimize
- unsigned int k = 2;
- unsigned long v = ~0UL;
- unsigned long u;
-
- while ( ( uniform_frac >= q[k] ))
- {
- k++;
- }
- for ( unsigned int i = 0; i < k; ++i )
- {
- u = genrand_int32();
- if ( u < v )
- {
- v = u;
- }
- }
-
- result = mean*( j + v/4294967296.0 )*LN2;
- }
-
- return result;
-}
-#if 0 // test main
-#include <vector>
-int main(void)
-{
- double mean = .25;
- double sum = 0.0;
- double sd = 0.0;
- vector <unsigned> classes;
- Exponential ex(mean);
- int MAX_SAMPLE = 100000;
- int MAX_CLASSES = 1000;
-
-
- for ( int i = 0; i < MAX_CLASSES; ++i )
- {
- classes.push_back(0);
- }
-
- for ( int i = 0; i < MAX_SAMPLE; ++i )
- {
- double p = ex.getNextSample();//aliasMethod();
- int index = (int)(p*MAX_CLASSES);
-// cout << index << " ] " << p << endl;
-
- if ( index < MAX_CLASSES){
- classes[index]++;
- }
- else
- {
- classes[MAX_CLASSES-1]++;
- }
-
-
- sum += p;
- sd += (p - mean)*(p - mean);
- }
- mean = sum/MAX_SAMPLE;
- sd = sqrt(sd/MAX_SAMPLE);
- cout << "mean = " << mean << " sd = " << sd << endl;
- for ( int i = 0; i < MAX_CLASSES; ++i )
- {
- cout << classes[i] << endl;
- }
-
- return 0;
-}
-#endif // test main
-
-
-#endif
diff --git a/randnum/Exponential.h b/randnum/Exponential.h
deleted file mode 100644
index 7c92e088..00000000
--- a/randnum/Exponential.h
+++ /dev/null
@@ -1,48 +0,0 @@
-/*******************************************************************
- * File: Exponential.h
- * Description:
- * Author: Subhasis Ray
- * E-mail: ray.subhasis@gmail.com
- * Created: 2007-11-01 08:59:47
- ********************************************************************/
-/**********************************************************************
-** 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 _EXPONENTIAL_H
-#define _EXPONENTIAL_H
-#include "Probability.h"
-enum ExponentialGenerator
-{
- LOGARITHMIC,
- RANDOM_MINIMIZATION
-};
-
-
-class Exponential: public Probability
-{
- public:
- Exponential(double mean);
- Exponential( ExponentialGenerator generator, double mean);
-
- double getMean() const;
- double getVariance() const;
- double getNextSample() const;
- private:
- double mean_;
- double (*generator_)(double);
- static double logarithmic(double mean);
- static double randomMinimization(double mean);
-
-
-};
-
-
-
-#endif
diff --git a/randnum/ExponentialRng.cpp b/randnum/ExponentialRng.cpp
deleted file mode 100644
index 9b9bbada..00000000
--- a/randnum/ExponentialRng.cpp
+++ /dev/null
@@ -1,146 +0,0 @@
-/*******************************************************************
- * File: ExponentialRng.cpp
- * Description:
- * Author: Subhasis Ray
- * E-mail: ray.subhasis@gmail.com
- * Created: 2007-11-08 11:33:45
- ********************************************************************/
-/**********************************************************************
-** 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 _EXPONENTIALRNG_CPP
-#define _EXPONENTIALRNG_CPP
-
-#include "RandGenerator.h"
-#include "ExponentialRng.h"
-
-const Cinfo* ExponentialRng::initCinfo()
-{
- static ValueFinfo< ExponentialRng, double > mean(
- "mean",
- "Mean of the exponential distribution.",
- &ExponentialRng::setMean,
- &ExponentialRng::getMean);
-
- static ValueFinfo< ExponentialRng, int > method(
- "method",
- "The algorithm to use for computing the sample. Two methods are"
- " supported: 0 - logarithmic and 1 - random minimization."
- " The logarithmic method is slower (it computes a"
- " logarithm). Default is random minimization. See Knuth, Vol II Sec"
- " 3.4.1 : Algorithm S.",
- &ExponentialRng::setMethod,
- &ExponentialRng::getMethod);
-
- static Finfo* exponentialRngFinfos[] = {
- &mean,
- &method,
- };
-
- static string doc[] = {
- "Name", "ExponentialRng",
- "Author", "Subhasis Ray",
- "Description", "Exponentially distributed random number generator.\n"
- "Exponential distribution with mean k is defined by the probability"
- " density function p(x; k) = k * exp(-k * x) if x >= 0, else 0."
- " By default this class uses the random minimization method"
- " described in Knuth's TAOCP Vol II Sec 3.4.1 (Algorithm S).",
- };
- static Dinfo< ExponentialRng > dinfo;
- static Cinfo exponentialRngCinfo(
- "ExponentialRng",
- RandGenerator::initCinfo(),
- exponentialRngFinfos,
- sizeof(exponentialRngFinfos)/sizeof(Finfo*),
- &dinfo,
- doc,
- sizeof( doc ) / sizeof( string ));
- return &exponentialRngCinfo;
-}
-
-
-static const Cinfo* exponentialRngCinfo = ExponentialRng::initCinfo();
-
-ExponentialRng::ExponentialRng()
-{
- mean_ = 0;
- isMeanSet_ = false;
- method_ = RANDOM_MINIMIZATION;
-}
-/**
- Replaces the same method in base class. Returns the mean as
- stored in this object independent of the actual generator object.
- */
-double ExponentialRng::getMean() const
-{
- return mean_;
-}
-/**
- Sets the mean. Since exponential distribution is defined in terms
- of this parameter, it is stored locally independent of the
- instantiation of the internal generator object.
-*/
-void ExponentialRng::setMean(double mean)
-{
- if ( !rng_ ){
- rng_ = new Exponential(mean);
- isMeanSet_ = true;
- }
-}
-
-/**
- Reports error in case the parameter mean has not been set.
- */
-void ExponentialRng::vReinit(const Eref& e, ProcPtr p)
-{
- Exponential * erng = static_cast<Exponential *>(rng_);
- if (!erng){
- cerr << "ERROR: ExponentialRng::vReinit - mean must be set before using the Exponential distribution generator." << endl;
- }
-}
-
-/**
- Returns the algorithm used for sample generation.
- 0 for logarithmic method.
- 1 for random minimization method.
- */
-int ExponentialRng::getMethod() const
-{
- return method_;
-}
-
-/**
- Sets the algorithm used for sample generation.
- 0 for logarithmic method.
- 1 for random minimization method.
- Default is random minimization.
- */
-void ExponentialRng::setMethod(int method)
-{
- Exponential * erng = static_cast< Exponential * >(rng_);
- if (!erng){
- switch ( method ){
- case 0:
- method_ = LOGARITHMIC;
- break;
- default:
- method_ = RANDOM_MINIMIZATION;
- break;
- }
- } else {
- cerr << "Warning: Will not change method after generator object has been"
- << " created. Method in use:"
- << method << " ("
- << (method == 0? "logarithmic": "random minimization")
- << ")" << endl;
- }
-}
-
-#endif
diff --git a/randnum/ExponentialRng.h b/randnum/ExponentialRng.h
deleted file mode 100644
index 08a8c245..00000000
--- a/randnum/ExponentialRng.h
+++ /dev/null
@@ -1,49 +0,0 @@
-/*******************************************************************
- * File: ExponentialRng.h
- * Description:
- * Author: Subhasis Ray
- * E-mail: ray.subhasis@gmail.com
- * Created: 2007-11-08 11:27:50
- ********************************************************************/
-/**********************************************************************
-** 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 _EXPONENTIALRNG_H
-#define _EXPONENTIALRNG_H
-#include "randnum.h"
-#include "../basecode/header.h"
-#include "RandGenerator.h"
-#include "Exponential.h"
-
-/**
- This is MOOSE wrapper for Exponentially distributed random number generator class, Exponential.
- The default
- */
-class ExponentialRng: public RandGenerator
-{
- public:
- ExponentialRng();
- double getMean() const;
- void setMean(double mean);
- int getMethod() const;
- void setMethod(int method);
- virtual void vReinit( const Eref& e, ProcPtr p);
-
- static const Cinfo* initCinfo();
-
- private:
- double mean_;
- bool isMeanSet_;
- int method_;
-
-};
-
-
-#endif
diff --git a/randnum/Gamma.cpp b/randnum/Gamma.cpp
deleted file mode 100644
index e2eb58ea..00000000
--- a/randnum/Gamma.cpp
+++ /dev/null
@@ -1,154 +0,0 @@
-/*******************************************************************
- * File: Gamma.cpp
- * Description:
- * Author: Subhasis Ray
- * E-mail: ray.subhasis@gmail.com
- * Created: 2007-11-05 18:33:01
- ********************************************************************/
-/**********************************************************************
- ** 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 _GAMMA_CPP
-#define _GAMMA_CPP
-#include <cmath>
-#include "utility/numutil.h"
-#include "Gamma.h"
-#include "Exponential.h"
-#include "randnum.h"
-Gamma::Gamma(double alpha, double theta):alpha_(alpha), theta_(theta)
-{
- if (( alpha < 0 ) || (theta < 0 ))
- {
- cerr << "ERROR: setting parameter of Gamma distribution to negative. Setting both to 1." << endl;
- alpha_ = 1;
- theta_ = 1;
- }
-}
-double Gamma::getAlpha()
-{
- return alpha_;
-}
-
-double Gamma::getTheta()
-{
- return theta_;
-}
-
-double Gamma::getMean() const
-{
- return alpha_*theta_;
-}
-
-double Gamma::getVariance() const
-{
- return alpha_*theta_*theta_;
-}
-
-double Gamma::getNextSample() const
-{
- double result;
-
- if ( alpha_ <= 1 )
- {
- result = gammaSmall();
- }
- else
- {
- result = gammaLarge();
- }
- if ( !isClose< double >(theta_, 1.0, DBL_EPSILON))
- {
- result *= theta_;
- }
-
- return result;
-}
-
-// See Algorithm A in TAOCP by Knuth, Vol 2 ,Section 3.4.1
-double Gamma::gammaLarge() const// alpha > 1
-{
- double result = 0.0;
- // a1. generate candidate
- double yValue;
- double uniformU;
- double uniformV;
- double check;
- double tmp;
-
- while (true)
- {
- uniformU = mtrand();
- yValue = tan(M_PI*uniformU);
- tmp = sqrt(2*alpha_ - 1)*yValue;
-
- result = tmp + alpha_ - 1;
- if (result > 0)
- {
- uniformV = mtrand();
- check = ( 1 + yValue*yValue )*exp((alpha_ - 1.0)*log(result/(alpha_ - 1.0)) - tmp);
- if (uniformV < check )
- {
- return result;
- }
- }
- }
- return result; // silence the compiler
-}
-
-
-// See: TAOCP by Knuth, Vol 2, 3.4.1 Exercise 16
-double Gamma::gammaSmall() const // 0 < alpha < 1
-{
- static Exponential expGen(1.0);
-
- // G1. initialize
- static double p = NATURAL_E/(alpha_+NATURAL_E);
- static double pByE = 1.0/(alpha_+NATURAL_E);
- double uniformU;
- double expSample;
- double xValue = 0.0;
- double qValue;
-
- while ( true )
- {
- // G2. generate G deviate
- uniformU = mtrand();
- expSample = expGen.getNextSample();
- while (expSample == 0 )
- {
- expSample = expGen.getNextSample();
- }
-
- if ( uniformU < p )
- {
- xValue = exp(-expSample/alpha_);
- if ( uniformU < pByE )
- {
- return xValue;
- }
- qValue = p*exp(-xValue);
- }
- else
- {
- xValue = 1 + expSample;
- qValue = p + (1.0-p)*pow(xValue, alpha_ - 1.0);
- }
-
- // G3. reject?
- if ( uniformU < qValue )
- {
- return xValue;
- }
- }
- return xValue; // silence the compiler
-}
-
-
-#endif
diff --git a/randnum/Gamma.h b/randnum/Gamma.h
deleted file mode 100644
index 2812c762..00000000
--- a/randnum/Gamma.h
+++ /dev/null
@@ -1,42 +0,0 @@
-/*******************************************************************
- * File: Gamma.h
- * Description:
- * Author: Subhasis Ray
- * E-mail: ray.subhasis@gmail.com
- * Created: 2007-11-05 19:22:32
- ********************************************************************/
-/**********************************************************************
-** 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 _GAMMA_H
-#define _GAMMA_H
-#include "Probability.h"
-#include <iostream>
-using namespace std;
-
-class Gamma: public Probability
-{
- public:
- Gamma(double alpha, double theta);
- double getAlpha();
- double getTheta();
- double getMean() const;
- double getVariance() const;
- double getNextSample() const;
- private:
- double alpha_;
- double theta_;
- double gammaSmall() const;
- double gammaLarge() const;
-
-};
-
-
-#endif
diff --git a/randnum/GammaRng.cpp b/randnum/GammaRng.cpp
deleted file mode 100644
index eac78fba..00000000
--- a/randnum/GammaRng.cpp
+++ /dev/null
@@ -1,139 +0,0 @@
-/*******************************************************************
- * File: GammaRng.cpp
- * Description:
- * Author: Subhasis Ray
- * E-mail: ray.subhasis@gmail.com
- * Created: 2007-11-08 11:56:00
- ********************************************************************/
-/**********************************************************************
-** 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 _GAMMARNG_CPP
-#define _GAMMARNG_CPP
-#include "GammaRng.h"
-#include "utility/numutil.h"
-#include <cmath>
-
-const Cinfo* GammaRng::initCinfo()
-{
- static ValueFinfo< GammaRng, double > alpha(
- "alpha",
- "Parameter alpha of the gamma distribution.",
- &GammaRng::setAlpha,
- &GammaRng::getAlpha);
- static ValueFinfo< GammaRng, double > theta(
- "theta",
- "Parameter theta of the Gamma distribution.",
- &GammaRng::setTheta,
- &GammaRng::getTheta);
- static Finfo* gammaRngFinfos[] = {
- &alpha,
- &theta,
- };
-
- static string doc[] = {
- "Name", "GammaRng",
- "Author", "Subhasis Ray",
- "Description", "Gamma distributed random number generator.",
- };
-
- Dinfo < GammaRng > dinfo;
- static Cinfo gammaRngCinfo(
- "GammaRng",
- RandGenerator::initCinfo(),
- gammaRngFinfos,
- sizeof(gammaRngFinfos)/sizeof(Finfo*),
- &dinfo,
- doc,
- sizeof( doc ) / sizeof( string ));
- return &gammaRngCinfo;
-}
-
-
-static const Cinfo* gammaRngCinfo = GammaRng::initCinfo();
-
-GammaRng::GammaRng()
-{
- isAlphaSet_ = false;
- isThetaSet_ = false;
- alpha_ = 1;
- theta_ = 1;
-}
-/**
- returns the shape parameter.
-*/
-double GammaRng::getAlpha() const
-{
- return alpha_;
-}
-/**
- Sets parameter alpha. Also known as the shape parameter.
-*/
-void GammaRng::setAlpha(double alpha)
-{
-
- if (fabs(alpha) < DBL_MIN)
- {
- cerr << "ERROR: Shape parameter alpha must be non-zero." << endl;
- return;
- }
- Gamma * grng = static_cast< Gamma * >(rng_);
- if ( grng ) {
- alpha_ = grng->getAlpha();
- } else {
- alpha_ = alpha;
- isAlphaSet_ = true;
- if ( isThetaSet_ ){
- rng_ = new Gamma(alpha_, theta_);
- }
- }
-}
-/**
- returns the scale parameter.
-*/
-double GammaRng::getTheta()const
-{
- return theta_;
-}
-
-/**
- Sets parameter theta. Also known as the scale parameter.
-*/
-void GammaRng::setTheta(double theta)
-{
-
- if (fabs(theta) < DBL_MIN)
- {
- cerr << "ERROR: Scale parameter theta must be non-zero." << endl;
- return;
- }
- Gamma* grng = static_cast<Gamma*>(rng_);
- if ( grng ){
- theta_ = grng->getTheta();
- } else {
- theta_ = theta;
- isThetaSet_ = true;
- if (isAlphaSet_ ){
- rng_ = new Gamma(alpha_, theta_);
- }
- }
-}
-/**
- reports error if parameters have not been set properly.
-*/
-void GammaRng::vReinit(const Eref& e, ProcPtr p)
-{
- if (! rng_ )
- {
- cerr << "ERROR: GammaRng::vReinit - parameters alpha and theta must be set before using the Gamma distribution generator." << endl;
- }
-}
-
-#endif
diff --git a/randnum/GammaRng.h b/randnum/GammaRng.h
deleted file mode 100644
index 381da44e..00000000
--- a/randnum/GammaRng.h
+++ /dev/null
@@ -1,52 +0,0 @@
-/*******************************************************************
- * File: GammaRng.h
- * Description:
- * Author: Subhasis Ray
- * E-mail: ray.subhasis@gmail.com
- * Created: 2007-11-08 11:53:29
- ********************************************************************/
-/**********************************************************************
-** 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 _GAMMARNG_H
-#define _GAMMARNG_H
-#include "randnum.h"
-#include "basecode/header.h"
-#include "RandGenerator.h"
-#include "Gamma.h"
-
-/**
- This is MOOSE wrapper for Gammaly distributed random number generator class, Gamma.
- The default
- */
-class GammaRng: public RandGenerator
-{
- public:
- GammaRng();
- virtual ~GammaRng() { ; }
- double getAlpha() const;
- double getTheta() const;
- void setAlpha(double alpha);
- void setTheta(double theta);
-
- virtual void vReinit( const Eref& e, ProcPtr p);
-
- static const Cinfo * initCinfo();
-
- private:
- double alpha_;
- double theta_;
-
- bool isAlphaSet_;
- bool isThetaSet_;
-};
-
-
-#endif
diff --git a/randnum/Normal.cpp b/randnum/Normal.cpp
deleted file mode 100644
index 608ce928..00000000
--- a/randnum/Normal.cpp
+++ /dev/null
@@ -1,604 +0,0 @@
-/*******************************************************************
- * File: Normal.cpp
- * Description:
- * Author: Subhasis Ray
- * E-mail: ray.subhasis@gmail.com
- * Created: 2007-10-31 13:48:53
- ********************************************************************/
-/**********************************************************************
- ** 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 _NORMAL_CPP
-#define _NORMAL_CPP
-#include "Normal.h"
-#include "randnum.h"
-#include "../utility/numutil.h"
-#include <cmath>
-#include <iostream>
-using namespace std;
-
-extern unsigned long genrand_int32(void);
-Normal::Normal(double mean, double variance, NormalGenerator method):mean_(mean), variance_(variance), method_(method)
-{
- if (variance <= 0.0 )
- {
- cout << "Warning: cannot set variance <= 0. Setting to 1.0." << endl;
- variance_ = 1.0;
- }
-
- isStandard_ = isClose< double >(0.0, mean, DBL_EPSILON) && isClose < double > (1.0, variance, DBL_EPSILON);
- switch(method)
- {
- case ALIAS:
- generator_ = &(Normal::aliasMethod);
- break;
- case BOX_MUELLER:
- generator_ = &(Normal::BoxMueller);
- break;
-#ifdef USE_GSL
- case ZIGGURAT:
- generator_ = &(Normal::gslZiggurat);
- break;
-#endif
- default:
- cerr << "ERROR: Normal() - generator method# " << method << ". Don't know how to do this. Using alias method."<<endl;
- generator_ = &(Normal::aliasMethod);
- }
-}
-
-double dummy()
-{
- return 0.0;
-}
-
-double Normal::getNextSample() const
-{
- double sd = sqrt(variance_);
- double sample = generator_();
- if (!isStandard_)
- {
- sample = mean_ + sd*sample;
- }
- return sample;
-}
-
-double Normal::getMean() const
-{
- return mean_;
-}
-
-void Normal::setMean( double mean)
-{
- mean_ = mean;
- isStandard_ = isClose< double >(0.0, mean_, DBL_EPSILON) && isClose< double >(1.0, variance_, DBL_EPSILON);
-}
-
-double Normal::getVariance() const
-{
- return variance_;
-}
-
-void Normal::setVariance( double variance )
-{
- if (variance <= 0.0)
- {
- cout << "Warning: cannot set variance < 0." << endl;
- return;
- }
- variance_ = variance;
- isStandard_ = isClose< double > (0.0, mean_, DBL_EPSILON) && isClose< double >(1.0, variance_, DBL_EPSILON);
-}
-
-NormalGenerator Normal::getMethod(void)
-{
- return method_;
-}
-
-void Normal::setMethod(NormalGenerator method)
-{
- method_ = method;
- switch(method)
- {
- case ALIAS:
- generator_ = &(Normal::aliasMethod);
- break;
- case BOX_MUELLER:
- generator_ = &(Normal::BoxMueller);
- break;
-#ifdef USE_GSL
- case ZIGGURAT:
- generator_ = &(Normal::gslZiggurat);
- break;
-#endif
- default:
- cerr << "ERROR: Normal() - generator method# " << method << ". Don't know how to do this. Using alias method."<<endl;
- generator_ = &(Normal::aliasMethod);
- method_ = ALIAS;
- }
-}
-
-#ifdef USE_GSL
-#include <gsl/gsl_rng.h>
-#include <gsl/gsl_randist.h>
-
-double Normal::gslZiggurat()
-{
- static const gsl_rng_type * T;
- static gsl_rng * r;
- static bool inited = false;
- if (!inited)
- {
- /* create a generator chosen by the
- environment variable GSL_RNG_TYPE */
-
- gsl_rng_env_setup();
-
- T = gsl_rng_default;
- r = gsl_rng_alloc (T);
- inited = true;
- }
- return gsl_ran_gaussian_ziggurat(r, 1.0);
-}
-
-#endif // !USE_GSL
-/**
- Very simple but costly implementation
-*/
-double Normal::BoxMueller()
-{
- double result;
- double a, b, r;
- do
- {
- a = 2.0 * mtrand() - 1.0;
- b = 2.0 * mtrand() - 1.0;
- r = a * a + b * b;
- } while ( r >= 1.0 );
- r = sqrt( - 2.0 * log(r) / r );
- result = r * a;
-
- return result;
-}
-/**
- Refer to:
- Eine Alias-Methode zur Stichprohenentnahme aus Normalverteilungen.
- JH Ahrens and U Dieter, 19 89, Computing
-
- We are assuming size of long to be 32 bit
-*/
-
-const unsigned long y[] =
-{
- 200, 199, 199, 198, 197, 196, 195, 193, 192, 190, 188, 186, 184, 181, 179, 176, 173, 170, 167, 164, 161, 157, 154, 151, 147, 143, 140, 136, 132, 128, 125, 121, 117, 113, 110, 106, 102, 98, 95, 91, 88, 84, 81, 77, 74, 71, 68, 64, 61, 59, 56, 53, 50, 48, 45, 43, 40, 38, 36, 34, 32, 30, 28, 27, 25, 23, 22, 20, 19, 18, 17, 15, 14, 13, 12, 11, 11, 10, 9, 8, 8, 7, 6, 6, 5, 5, 4, 4, 4, 3, 3, 3, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
-};
-
-const long a[] =
-{
- 31, 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 27, 26, 25, 24, 23, 22, 21, -1, 19, 19, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1, 0, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1, 0, 51, 50, 49, 48, 47, 46, 45, 44, 43, 42, 41, 40, 39, 38, 37, 36, 35, 34, 33, 32, 31, 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1, 0
-};
-
-const unsigned long q[] =
-{
- 28, 32, 33, 36, 40, 43, 45, 47, 51, 53, 57, 59, 27, 37, 43, 54, 28, 45, 60, 63, 49, 61, 52, 34, 63, 46, 34, 18, 47, 40, 36, 29, 61, 57, 53, 51, 47, 43, 40, 37, 33, 31, 27, 25, 21, 19, 17, 14, 11, 9 , 8, 5, 54, 51, 49, 46, 44, 41, 39, 37, 35, 33, 31, 29, 28, 26, 24, 23, 21, 20, 19, 18, 16, 15, 14, 13, 12, 12, 11, 10, 9, 9, 8, 7, 7, 6, 6, 5, 5, 5, 4, 4, 4, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-};
-const double c = 0.004996971959878404;
-
-const double d = 1.861970434352886050;
-/*********************************************************************************************************************************/
-/* TODO: This implementation has a bug. The sample mean deviates a lot
- * from the generator mean for very small numbers, like 1e-7
- * Need to make sure that this is not due to 32/64 bit incompatibility.
- */
-/*********************************************************************************************************************************/
-double Normal::aliasMethod()
-{
- double result;
-
- unsigned long uniform;
- unsigned long uniform_prime;
- unsigned long x_num;
- unsigned long t_num;
- unsigned long v_num;
-
- unsigned long i_num, k_num, sgn;
-
- while (true)
- {
-
- // 1) u = .B1..B7 (base 256) - we take the little endian approach
- uniform = genrand_int32(); // .B1B2B3B4 - limited by precision
-
- // 1a) s = B1[0]
- sgn = uniform & 0x80000000UL;
- // 1b) B1[0] = 0
- uniform = uniform & 0x7fffffffUL;
-
- // 2) i = B1[1..7]
- i_num = uniform >> 24;
- // 3) k = (B2 ^ B4) and retain least significant 6 bits of k
- k_num = ((uniform >> 16) ^ uniform ) & 0x0000003fUL;
-
- // 4) k <q[i]? goto 7
- if ( k_num >= q[i_num] )
- {
- // 5) i = a[i]
- i_num = a[i_num];
-
- // 5a)i = ~0? goto 11
- if (i_num != ~(0UL))
- {
-
- // 6) B1 = i
- uniform = (uniform & 0x00ffffffUL) | (i_num << (WORD_LENGTH-8));
-
- // 6a) x = 8*u
- x_num = uniform << 3;
-
- // 6b) goto 8 - s = 0? return x: return -x
- // result = x_num/4294967296.0; // convert to double
-// result = (sgn == 0) ? result : -result;
- //return result;
- break;
- }
- }
- else
- {
-
-
- // 7) x = 8*u
- x_num = uniform << 3;
-
- // 7a) if (k <= y[i-1] - y[i]) goto 9
- if (k_num > y[i_num-1] - y[i_num])
- {
- // 8) s = 0? return x: return -x
-// result = x_num/4294967296.0; // convert to double
-// result = (sgn == 0) ? result : -result;
- //return result;
- break;
-
- }
-
- // 9) u' = .B1'..B7' .. using B1-B4 for precision limitation
- uniform_prime = genrand_int32();
- // 9a) t = x*x/2
- t_num = x_num*(x_num/2);
-
- // 9b) v = c*(y[i] + u'*(y[i-1] - y[i] + 1))
- v_num = (unsigned long)(c*(y[i_num] + uniform_prime*(y[i_num - 1] - y[i_num] + 1)));
-
- // 10) v > exp(-t)? goto 1: goto 8
-
-
- if ( testAcceptance(t_num, v_num ))
- {
- result = x_num/4294967296.0; // convert to double
- result = (sgn == 0) ? result : -result;
- //return result;
- break;
-
- }else
- {
- continue;
- }
- }
-
- // 11) u = .B1..B7
- uniform = genrand_int32();
-
- // 11a) u < 1/9? goto 1
- if ( uniform/4294967296.0 < 1.0/9.0)
- {
- continue;
- }
-
- // 12) x = 3.75 + 0.25/u
- unsigned long divider = ((uniform << 24) +
- ((uniform << 16) & 0x00ff0000UL) +
- ((uniform << 8) & 0x0000ff00UL) +
- (uniform & 0x000000ffUL));
-
- x_num = (unsigned long)( 3.75 + (1.0*0x40000000UL)/divider);
- // 12a) t = x*x/2-8, v = d*u*u*u'
- t_num = x_num*x_num/2 - 0x8UL;
- v_num = (unsigned long)(d*uniform*uniform*uniform_prime);
-
- // 12b) goto 10
- // 10) v > exp(-t)? goto 1: goto 8
- if ( testAcceptance(t_num, v_num) )
- {
- // 8)
-// result = x_num/4294967296.0; // convert to double
-// result = (sgn == 0) ? result : -result;
-// return result;
- break;
-
-
- }else // goto 1
- {
- continue;
- }
- }
- // 8)
- result = (sgn == 0) ? x_num/4294967296.0 : -(x_num/4294967296.0);
-
- return result;
-
-}
-/**
- Method to check if v > exp(-t) without doing the exponentiation
- TODO: try to do everything in integer arithmetic
-*/
-bool Normal::testAcceptance(unsigned long t_num, unsigned long v_num)
-{
- bool accept = false;
- bool cont = true;
-
- double t = t_num/4294967296.0;
- double v = v_num/4294967296.0;
-// return (v > exp(-t));
-
- while(cont)
- { // a)
- if ( t >= LN2 )
- {
- // b)
- t = t - LN2;
- v += v;
-
- if ( v > 1 )
- {
- return false;
- }
- else
- {
- continue;
- }
- }
- // c)
- v = v + t - 1;
- if ( v <= 0 )
- {
- return true;
- }
- // d)
- double r = t * t;
- v = v + v - r;
- if ( v > 0)
- {
- return false;
- }
- double c = 3.0;
- // e)
- while(true)
- {
- r *= t;
- v = v * c + r;
- if ( v <= 0)
- {
- return true;
- }
- c += 1.0;
- // f)
- r *= t;
- v = v * c - r;
- if ( v > 0 )
- {
- return false;
- }
- c += 1.0;
- }
- }
- return accept;
-}
-
-/**
- See Knuth, TAOCP Vol 2 Sec 3.4.1
- Algorithm M: The Rectangle-wedge-tail method discovered by G Marsaglia
- TODO: implement it by filling the gaps
-*/
-#if 0
-double algorithmM() // not implemented
-{
- cout << "algorithmM() - not yet implemented." << endl;
- return 0.0;
-
- double result;
- double u;
- int psi;
- // TODO: construct these auxiliary tables.
- static int P[32];
- static int Q[32];
- static int Y[32];
- static int Z[32];
- static int S[32];
- static int D[32];
- static int E[32];
- // M1 [ Get U ]
- // U = (.b0b1b2....bt)2
- u = mtrand();
- // M2 [Rectangle?]
- // psi = b0
- // j = (b1b2b3b4b5)2
- // f = (.b6b7..bt)2
- // if ( f >= Pj ) { X = Yj + f*Zj; goto M9 }
- // else if ( j <= 15, i.e. b1 == 0 ) { X = Sj + f*Qj; goto M9 }
-
- // M3 [ Wedge or tail? ]
- // Now 15 <= j <= 31 and each particular value j occurs with probability pj
- // if ( j == 31 ) goto M7
-
- // M4 [ Get U <= V ]
- // Generate two new uniform deviates, U and V; if U > V, exchange U <-> V
- // Set X =S(j-15) + U/5
-
- // M5 [ Easy case? ]
- // if ( V <= Dj ) goto M9
-
- // M6 [ Another try? ]
- // if ( V > U + Ej * (exp[( S(j-14)^2 - X^2 )/2] - 1 ) ) goto M4
- // else goto M9
-
- // M7 [ Get supertail deviate ]
- // Generate two new independent uniform deviates U and V
- // set X = sqrt(9-2*lnV)
-
- // M8 [ Reject? ]
- // if ( U*X >= 3 ) goto M7
-
- // M9 [ Attach sign ]
- // if ( psi == 1 ) X = -X
-
- return result;
-}
-#endif
-/**
- TODO: Not yet implemented.
-*/
-double algorithmF()
-{
- cout << "algorithmF() - not implemented." << endl;
-
- double result = 0;
- return result;
-}
-
-
-#ifdef DO_UNIT_TESTS
-#include <cassert>
-#include <vector>
-
-void checkMeanVariance(Normal& normalGen, unsigned seqLen)
-{
- vector < double > seq;
- double mean = 0.0;
- for ( unsigned ii = 0; ii < seqLen; ++ii)
- {
- double sample = normalGen.getNextSample();
- seq.push_back(sample);
- mean += sample;
- }
- mean /= seqLen;
- cout << "Testing Normal: " << normalGen.getMethod() << " method for " << seqLen << " samples :: mean set - " << normalGen.getMean() << ", sample mean - " << mean << ". ";
- double variance = 0.0;
- for ( unsigned ii = 0; ii < seqLen; ++ ii)
- {
- variance += (mean - seq[ii]) * (mean - seq[ii]);
- }
- variance /= seqLen;
- cout << "variance set - " << normalGen.getVariance() << ", sample variance - " << variance << endl;
-}
-
-void testNormal()
-{
- // const unsigned SEQ_LEN = 1000;
-
- Normal* normalGen = new Normal();
- // make sure default constructor creates standard normal
- assert(isClose< double >(normalGen->getMean(), 0.0, DBL_EPSILON));
- assert(isClose< double > (normalGen->getVariance(), 1.0, DBL_EPSILON));
- // check if setting method is effective
- normalGen->setMethod(ALIAS);
- assert(normalGen->getMethod() == ALIAS);
- checkMeanVariance(*normalGen, 1000); // check the sample mean and variance for "alias method"
- delete normalGen;
- normalGen = new Normal(100.0, 33.0, BOX_MUELLER);
- assert(normalGen->getMethod() == BOX_MUELLER);
- assert(isClose< double >(normalGen->getMean(), 100.0, DBL_EPSILON));
- assert(isClose(normalGen->getVariance(), 33.0, DBL_EPSILON));
- checkMeanVariance(*normalGen, 1000); // check the sample mean and variance for "Box-Mueller method"
- delete normalGen;
-
- // non standard normal distr.
- normalGen = new Normal();
- normalGen->setMean(-100.0);
- normalGen->setVariance(3.0);
- checkMeanVariance(*normalGen, 1000);
-}
-#if 0 // keep it out of compilation
-void testByte2Double()
-{
- double res;
-
- unsigned char bytes[] =
- {
- 0, 0, 0, 0, 0
- };
- bytes[4] = 0x5;
- res = byte2double(bytes, 5);
- printf("0.0000000005 H = %.20g\n", res);
- bytes[3] = 0x4;
- res = byte2double(bytes, 4);
- printf("0.00000004 H = %.20g\n", res);
- bytes[2] = 0x3;
- res = byte2double(bytes, 3);
- printf("0.000003 H = %.20g\n", res);
- bytes[1] = 0x2;
- res = byte2double(bytes, 2);
- printf("0.0002 H = %.20g\n", res);
- assert(isClose< double >(res, 0.000030517578125));
- bytes[0] = 0x1;
- res = byte2double(bytes, 1);
- printf("0.01 H = %.20g\n", res);
- assert(res == 0.00390625);
- res = byte2double(bytes, 5);
- printf("0.0102030405 in hex = %.20g\n", res);
- assert(isClose< double >(res, 0.0039369473279293742962, 1e-9));// the right comparison is from the same program. Should check for various architectures.
-}
-#endif // #if 0
-#endif // !DO_UNIT_TESTS
-
-#if defined(DO_UNIT_TESTS) && defined(TEST_MAIN)
-// Test main
-
-int main(void)
-{
- double mean = 0.0;
- double sd = 0.0;
- double sum = 0.0;
- int freq [200];
- Normal n(BOX_MUELLER);
-
- for ( int i = 0; i < 200; ++i )
- {
- freq[i] = 0;
- }
-
- for ( int i = 0; i < 10000; ++i )
- {
- double p = n.getNextSample();//aliasMethod();
- int index = (int)(p*100)+99;
- cout << index << " ] " << p << endl;
- if ( index < 0 )
- index = 0;
- else if ( index > 199 )
- index = 199;
-
- freq[index]++;
-
- sum += p;
- sd = p*p;
- }
- mean = sum/1000;
- sd = sd/1000;
- cout << mean << " " << sd << endl;
- for ( int i = 0; i < 200; ++i )
- {
- cout << freq[i] << endl;
- }
-
- testNormal();
-
- return 0;
-}
-#endif // ! define(DO_UNIT_TESTS) && defined(TEST_MAIN)
-
-
-#endif
diff --git a/randnum/Normal.h b/randnum/Normal.h
deleted file mode 100644
index c74cf9bb..00000000
--- a/randnum/Normal.h
+++ /dev/null
@@ -1,54 +0,0 @@
-/*******************************************************************
- * File: Normal.h
- * Description: Generates random numbers with normal
- * distribution.
- * Author: Subhasis Ray
- * E-mail: ray.subhasis@gmail.com
- * Created: 2007-10-30 11:22:51
- ********************************************************************/
-/**********************************************************************
- ** 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 _NORMAL_H
-#define _NORMAL_H
-#include "Probability.h"
-enum NormalGenerator
-{
- ALIAS,
- BOX_MUELLER,
- ZIGGURAT
-};
-
-class Normal : public Probability
-{
-
- public:
- Normal(double mean=0.0, double variance=1.0, NormalGenerator algorithm=ALIAS);
- double getMean() const;
- void setMean(double value);
- double getVariance() const;
- void setVariance( double value );
- NormalGenerator getMethod(void);
- void setMethod(NormalGenerator method);
- double getNextSample() const;
- private:
- double mean_;
- double variance_;
- double (*generator_)();
- bool isStandard_;
- NormalGenerator method_;
- static double BoxMueller();
- static double aliasMethod();
- static double gslZiggurat();
- static bool testAcceptance(unsigned long t, unsigned long v);
-};
-
-
-#endif
diff --git a/randnum/NormalDistribution.hpp b/randnum/NormalDistribution.hpp
new file mode 100644
index 00000000..c79fdf54
--- /dev/null
+++ b/randnum/NormalDistribution.hpp
@@ -0,0 +1,197 @@
+/***
+ * Generates normally distributed numbers. Based on GSL implementation.
+ *
+ * Created: 2018-08-04
+ * Author: Dilawar Singh <dilawars@ncbs.res.in>
+ * Organization: NCBS Bangalore
+ * License: GNU GPL3
+ */
+
+#ifndef NORMALDISTRIBUTION_H
+#define NORMALDISTRIBUTION_H
+
+#include "Definitions.h"
+
+/* position of right-most step */
+#define PARAM_R 3.44428647676
+
+namespace moose {
+namespace details {
+
+/* tabulated values for the heigt of the Ziggurat levels */
+static const double ytab[128] =
+{
+ 1, 0.963598623011, 0.936280813353, 0.913041104253,
+ 0.892278506696, 0.873239356919, 0.855496407634, 0.838778928349,
+ 0.822902083699, 0.807732738234, 0.793171045519, 0.779139726505,
+ 0.765577436082, 0.752434456248, 0.739669787677, 0.727249120285,
+ 0.715143377413, 0.703327646455, 0.691780377035, 0.68048276891,
+ 0.669418297233, 0.65857233912, 0.647931876189, 0.637485254896,
+ 0.62722199145, 0.617132611532, 0.607208517467, 0.597441877296,
+ 0.587825531465, 0.578352913803, 0.569017984198, 0.559815170911,
+ 0.550739320877, 0.541785656682, 0.532949739145, 0.524227434628,
+ 0.515614886373, 0.507108489253, 0.498704867478, 0.490400854812,
+ 0.482193476986, 0.47407993601, 0.466057596125, 0.458123971214,
+ 0.450276713467, 0.442513603171, 0.434832539473, 0.427231532022,
+ 0.419708693379, 0.41226223212, 0.404890446548, 0.397591718955,
+ 0.390364510382, 0.383207355816, 0.376118859788, 0.369097692334,
+ 0.362142585282, 0.355252328834, 0.348425768415, 0.341661801776,
+ 0.334959376311, 0.328317486588, 0.321735172063, 0.31521151497,
+ 0.308745638367, 0.302336704338, 0.29598391232, 0.289686497571,
+ 0.283443729739, 0.27725491156, 0.271119377649, 0.265036493387,
+ 0.259005653912, 0.253026283183, 0.247097833139, 0.241219782932,
+ 0.235391638239, 0.229612930649, 0.223883217122, 0.218202079518,
+ 0.212569124201, 0.206983981709, 0.201446306496, 0.195955776745,
+ 0.190512094256, 0.185114984406, 0.179764196185, 0.174459502324,
+ 0.169200699492, 0.1639876086, 0.158820075195, 0.153697969964,
+ 0.148621189348, 0.143589656295, 0.138603321143, 0.133662162669,
+ 0.128766189309, 0.123915440582, 0.119109988745, 0.114349940703,
+ 0.10963544023, 0.104966670533, 0.100343857232, 0.0957672718266,
+ 0.0912372357329, 0.0867541250127, 0.082318375932, 0.0779304915295,
+ 0.0735910494266, 0.0693007111742, 0.065060233529, 0.0608704821745,
+ 0.056732448584, 0.05264727098, 0.0486162607163, 0.0446409359769,
+ 0.0407230655415, 0.0368647267386, 0.0330683839378, 0.0293369977411,
+ 0.0256741818288, 0.0220844372634, 0.0185735200577, 0.0151490552854,
+ 0.0118216532614, 0.00860719483079, 0.00553245272614, 0.00265435214565
+};
+
+/* tabulated values for 2^24 times x[i]/x[i+1],
+ * used to accept for U*x[i+1]<=x[i] without any floating point operations */
+static const unsigned long ktab[128] =
+{
+ 0, 12590644, 14272653, 14988939,
+ 15384584, 15635009, 15807561, 15933577,
+ 16029594, 16105155, 16166147, 16216399,
+ 16258508, 16294295, 16325078, 16351831,
+ 16375291, 16396026, 16414479, 16431002,
+ 16445880, 16459343, 16471578, 16482744,
+ 16492970, 16502368, 16511031, 16519039,
+ 16526459, 16533352, 16539769, 16545755,
+ 16551348, 16556584, 16561493, 16566101,
+ 16570433, 16574511, 16578353, 16581977,
+ 16585398, 16588629, 16591685, 16594575,
+ 16597311, 16599901, 16602354, 16604679,
+ 16606881, 16608968, 16610945, 16612818,
+ 16614592, 16616272, 16617861, 16619363,
+ 16620782, 16622121, 16623383, 16624570,
+ 16625685, 16626730, 16627708, 16628619,
+ 16629465, 16630248, 16630969, 16631628,
+ 16632228, 16632768, 16633248, 16633671,
+ 16634034, 16634340, 16634586, 16634774,
+ 16634903, 16634972, 16634980, 16634926,
+ 16634810, 16634628, 16634381, 16634066,
+ 16633680, 16633222, 16632688, 16632075,
+ 16631380, 16630598, 16629726, 16628757,
+ 16627686, 16626507, 16625212, 16623794,
+ 16622243, 16620548, 16618698, 16616679,
+ 16614476, 16612071, 16609444, 16606571,
+ 16603425, 16599973, 16596178, 16591995,
+ 16587369, 16582237, 16576520, 16570120,
+ 16562917, 16554758, 16545450, 16534739,
+ 16522287, 16507638, 16490152, 16468907,
+ 16442518, 16408804, 16364095, 16301683,
+ 16207738, 16047994, 15704248, 15472926
+};
+
+/* tabulated values of 2^{-24}*x[i] */
+static const double wtab[128] =
+{
+ 1.62318314817e-08, 2.16291505214e-08, 2.54246305087e-08, 2.84579525938e-08,
+ 3.10340022482e-08, 3.33011726243e-08, 3.53439060345e-08, 3.72152672658e-08,
+ 3.8950989572e-08, 4.05763964764e-08, 4.21101548915e-08, 4.35664624904e-08,
+ 4.49563968336e-08, 4.62887864029e-08, 4.75707945735e-08, 4.88083237257e-08,
+ 5.00063025384e-08, 5.11688950428e-08, 5.22996558616e-08, 5.34016475624e-08,
+ 5.44775307871e-08, 5.55296344581e-08, 5.65600111659e-08, 5.75704813695e-08,
+ 5.85626690412e-08, 5.95380306862e-08, 6.04978791776e-08, 6.14434034901e-08,
+ 6.23756851626e-08, 6.32957121259e-08, 6.42043903937e-08, 6.51025540077e-08,
+ 6.59909735447e-08, 6.68703634341e-08, 6.77413882848e-08, 6.8604668381e-08,
+ 6.94607844804e-08, 7.03102820203e-08, 7.11536748229e-08, 7.1991448372e-08,
+ 7.2824062723e-08, 7.36519550992e-08, 7.44755422158e-08, 7.52952223703e-08,
+ 7.61113773308e-08, 7.69243740467e-08, 7.77345662086e-08, 7.85422956743e-08,
+ 7.93478937793e-08, 8.01516825471e-08, 8.09539758128e-08, 8.17550802699e-08,
+ 8.25552964535e-08, 8.33549196661e-08, 8.41542408569e-08, 8.49535474601e-08,
+ 8.57531242006e-08, 8.65532538723e-08, 8.73542180955e-08, 8.8156298059e-08,
+ 8.89597752521e-08, 8.97649321908e-08, 9.05720531451e-08, 9.138142487e-08,
+ 9.21933373471e-08, 9.30080845407e-08, 9.38259651738e-08, 9.46472835298e-08,
+ 9.54723502847e-08, 9.63014833769e-08, 9.71350089201e-08, 9.79732621669e-08,
+ 9.88165885297e-08, 9.96653446693e-08, 1.00519899658e-07, 1.0138063623e-07,
+ 1.02247952126e-07, 1.03122261554e-07, 1.04003996769e-07, 1.04893609795e-07,
+ 1.05791574313e-07, 1.06698387725e-07, 1.07614573423e-07, 1.08540683296e-07,
+ 1.09477300508e-07, 1.1042504257e-07, 1.11384564771e-07, 1.12356564007e-07,
+ 1.13341783071e-07, 1.14341015475e-07, 1.15355110887e-07, 1.16384981291e-07,
+ 1.17431607977e-07, 1.18496049514e-07, 1.19579450872e-07, 1.20683053909e-07,
+ 1.21808209468e-07, 1.2295639141e-07, 1.24129212952e-07, 1.25328445797e-07,
+ 1.26556042658e-07, 1.27814163916e-07, 1.29105209375e-07, 1.30431856341e-07,
+ 1.31797105598e-07, 1.3320433736e-07, 1.34657379914e-07, 1.36160594606e-07,
+ 1.37718982103e-07, 1.39338316679e-07, 1.41025317971e-07, 1.42787873535e-07,
+ 1.44635331499e-07, 1.4657889173e-07, 1.48632138436e-07, 1.50811780719e-07,
+ 1.53138707402e-07, 1.55639532047e-07, 1.58348931426e-07, 1.61313325908e-07,
+ 1.64596952856e-07, 1.68292495203e-07, 1.72541128694e-07, 1.77574279496e-07,
+ 1.83813550477e-07, 1.92166040885e-07, 2.05295471952e-07, 2.22600839893e-07
+};
+
+} // namespace moose::details
+
+/* --------------------------------------------------------------------------*/
+/**
+ * @Synopsis Get a Normally Distribution value from a given RNG.
+ *
+ * @tparam T
+ */
+/* ----------------------------------------------------------------------------*/
+template<typename T = double>
+class normal_distribution
+{
+
+public:
+
+ normal_distribution( T mean = 0.0, T sigma = 1.0) :
+ mean_(mean), sigma_(sigma)
+ {
+ mean_ = mean;
+ sigma_ = sigma;
+ }
+
+ ~normal_distribution() { ; }
+
+ double operator()( moose::MOOSE_RNG_DEFAULT_ENGINE& r )
+ {
+ unsigned long U=0, sign=0, i=0, j=0;
+ T x=0, y=0;
+
+ while (1)
+ {
+ U = r();
+ i = U & 0x0000007F; /* 7 bit to choose the step */
+ sign = U & 0x00000080; /* 1 bit for the sign */
+ j = U>>8; /* 24 bit for the x-value */
+
+ x = j*details::wtab[i];
+ if (j < details::ktab[i]) break;
+
+ if (i<127)
+ {
+ double y0 = 0, y1 = 0;
+ y0 = details::ytab[i];
+ y1 = details::ytab[i+1];
+ y = y1+(y0-y1)*r();
+ }
+ else
+ {
+ x = PARAM_R - std::log(1.0 - r()) / PARAM_R;
+ y = exp( - PARAM_R*(x-0.5* PARAM_R)) * r();
+ }
+ if (y < std::exp(-0.5*x*x)) break;
+ }
+ return sign ? sigma_*x : -sigma_*x;
+ }
+
+public:
+
+ T mean_;
+ T sigma_;
+};
+
+} // namespace moose
+
+#endif /* end of include guard: NORMALDISTRIBUTION_H */
diff --git a/randnum/NormalRng.cpp b/randnum/NormalRng.cpp
deleted file mode 100644
index e31f636f..00000000
--- a/randnum/NormalRng.cpp
+++ /dev/null
@@ -1,142 +0,0 @@
-/*******************************************************************
- * File: NormalRng.cpp
- * Description: This is the MOOSE front end for class Normal,
- * which generates normally distributed random
- * doubles.
- * Author: Subhasis Ray
- * E-mail: ray.subhasis@gmail.com
- * Created: 2007-11-03 22:07:04
- ********************************************************************/
-/**********************************************************************
-** 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 _NORMALRNG_CPP
-#define _NORMALRNG_CPP
-#include "NormalRng.h"
-#include "Normal.h"
-const Cinfo* NormalRng::initCinfo()
-{
- static ValueFinfo< NormalRng, double > mean(
- "mean",
- "Mean of the normal distribution",
- &NormalRng::setMean,
- &NormalRng::getMean);
- static ValueFinfo< NormalRng, double > variance(
- "variance",
- "Variance of the normal distribution",
- &NormalRng::setVariance,
- &NormalRng::getVariance);
- static ValueFinfo< NormalRng, int > method(
- "method",
- "Algorithm used for computing the sample. The default is 0 = alias"
- " method by Ahrens and Dieter. Other options are: 1 = Box-Mueller method"
- " and 2 = ziggurat method.",
- &NormalRng::setMethod,
- &NormalRng::getMethod);
- static Finfo* normalRngFinfos[] = {
- &mean,
- &variance,
- &method,
- };
-
- static string doc[] = {
- "Name", "NormalRng",
- "Author", "Subhasis Ray",
- "Description", "Normally distributed random number generator.",
- };
- Dinfo< NormalRng > dinfo;
- static Cinfo normalRngCinfo(
- "NormalRng",
- RandGenerator::initCinfo(),
- normalRngFinfos,
- sizeof(normalRngFinfos)/sizeof(Finfo*),
- &dinfo,
- doc,
- sizeof( doc ) / sizeof( string ));
- return &normalRngCinfo;
-}
-
-
-static const Cinfo* normalRngCinfo = NormalRng::initCinfo();
-
-/**
- Set the mean of the internal generator object.
- */
-void NormalRng::setMean(double mean)
-{
- Normal* nrng = static_cast < Normal* >(rng_);
- if (nrng){
- nrng->setMean(mean);
- }
-}
-
-/**
- Since normal distribution is defined in terms of mean and variance, we
- want to store them in order to create the internal generator object.
- */
-void NormalRng::setVariance(double variance)
-{
- if ( variance < 0 )
- {
- cerr << "ERROR: variance cannot be negative." << endl;
- return;
- }
- Normal * nrng = static_cast < Normal* >(rng_);
- if (nrng){
- nrng->setVariance(variance);
- }
-}
-
-/**
- Returns the algorithm used.
- 0 for alias method.
- 1 for BoxMueller method.
- */
-int NormalRng::getMethod() const
-{
- Normal* nrng = static_cast < Normal * > (rng_);
- if (nrng){
- return nrng->getMethod();
- }
- return 0;
-}
-/**
- Set the algorithm to be used.
- 1 for BoxMueller method.
- Anything else for alias method.
- */
-void NormalRng::setMethod(int method)
-{
- Normal* nrng = static_cast <Normal*> (rng_);
- if ( nrng ){
- cout << "Warning: Changing method after generator object has been created. Current method: " << nrng->getMethod() << ". New method: " << method << endl;
- nrng->setMethod((NormalGenerator)method);
- }
-}
-
-void NormalRng::vReinit(const Eref& e, ProcPtr p)
-{
- // do nothing
-}
-
-/**
- By default the method used for normal distribution is alias method
- by Ahrens and Dieter. In order to use some method other than the
- default Alias method, one should call setMethod with a proper
- method index before calling reset ( reinit ). Since different
- methods create different random sequences, the combined sequence
- may not have the intended distribution. By default mean and
- variance are set to 0.0 and 1.0 respectively.
- */
-NormalRng::NormalRng():RandGenerator()
-{
- rng_ = new Normal();
-}
-#endif
diff --git a/randnum/NormalRng.h b/randnum/NormalRng.h
deleted file mode 100644
index 55e100d2..00000000
--- a/randnum/NormalRng.h
+++ /dev/null
@@ -1,44 +0,0 @@
-/*******************************************************************
- * File: NormalRng.h
- * Description:
- * Author: Subhasis Ray
- * E-mail: ray.subhasis@gmail.com
- * Created: 2007-11-05 10:19:18
- ********************************************************************/
-/**********************************************************************
-** 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 _NORMALRNG_H
-#define _NORMALRNG_H
-#include "randnum.h"
-#include "basecode/header.h"
-#include "RandGenerator.h"
-#include "Normal.h"
-
-/**
- This is MOOSE wrapper for normally distributed random number generator class, Normal.
- The default
- */
-class NormalRng: public RandGenerator
-{
- public:
- NormalRng();
- virtual ~NormalRng() { ; }
- void setMean(double mean);
- void setVariance(double variance);
- void setMethod(int method);
- int getMethod() const;
- virtual void vReinit( const Eref& e, ProcPtr p);
-
- static const Cinfo * initCinfo();
-};
-
-
-#endif
diff --git a/randnum/Poisson.cpp b/randnum/Poisson.cpp
deleted file mode 100644
index fe06c4e3..00000000
--- a/randnum/Poisson.cpp
+++ /dev/null
@@ -1,232 +0,0 @@
-/*******************************************************************
- * File: Poisson.cpp
- * Description:
- * Author: Subhasis Ray
- * E-mail: ray.subhasis@gmail.com
- * Created: 2007-11-01 16:09:38
- ********************************************************************/
-/**********************************************************************
-** This program is part of 'MOOSE', the
-** Messaging Object Oriented Simulation Environment,
-** also known as GENESIS 3 base code.
-** copyright (C) 2003-2010 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.
-**********************************************************************/
-/******************************************************************
- * Some of the functions have been copied/adapted from stochastic
- * library package by Agner Fog, published under GPL.
- * Refer to http://www.agner.org/random/ for more information.
- ******************************************************************/
-#ifndef _POISSON_CPP
-#define _POISSON_CPP
-#include "Poisson.h"
-#include "randnum.h"
-#include "utility/numutil.h"
-#include "Gamma.h"
-#include "Binomial.h"
-#include <cmath>
-#include <iostream>
-
-using namespace std;
-
-Poisson::Poisson(double mean):mean_(mean), gammaGen_(NULL) //, binomialGen_(NULL)
- , generator_(NULL)
-{
- /* replicates setMean */
- if (mean <= 0.0)
- {
- cerr << "ERROR: Poisson::setMean - mean must be positive. Setting to 1.0" << endl;
- mean_ = 1.0;
- }
- if ( mean_ < 17)
- {
- generator_ = Poisson::poissonSmall;
- mValue_ = exp(-mean_);
- }
- else
- {
- generator_ = Poisson::poissonLarge;
- mValue_ = floor(0.875*mean_);
- if (gammaGen_)
- {
- delete gammaGen_;
- }
- gammaGen_ = new Gamma(mValue_, 1.0);
- }
-}
-
-Poisson::~Poisson()
-{
- if (gammaGen_)
- {
- delete gammaGen_;
- }
-}
-
-
-void Poisson::setMean(double mean)
-{
- if (mean <= 0.0)
- {
- cerr << "ERROR: Poisson::setMean - mean must be positive. Setting to 1.0" << endl;
- mean_ = 1.0;
- }
- if ( mean_ < 17)
- {
- generator_ = Poisson::poissonSmall;
- mValue_ = exp(-mean_);
- }
- else
- {
- generator_ = Poisson::poissonLarge;
- mValue_ = floor(0.875*mean_);
- if (gammaGen_)
- {
- delete gammaGen_;
- }
- gammaGen_ = new Gamma(mValue_, 1.0);
- }
-}
-
-double Poisson::getMean() const
-{
- return mean_;
-}
-
-double Poisson::getVariance() const
-{
- return mean_;
-}
-
-double Poisson::getNextSample() const
-{
- if (!generator_)
- {
- cerr << "ERROR: Poisson::getNextSample() - generator function is NULL" << endl;
- return 0.0;
- }
- return generator_(*this);
-}
-
-/**
- Poisson distributed random number generator when mean is small.
- See: TAOCP by Knuth, Volume 2, Section 3.4.1
- */
-double Poisson::poissonSmall(const Poisson& poisson)
-{
- double product = 1.0;
-
- int i = 0;
- while ( product > poisson.mValue_ )
- {
- product *= mtrand();
- ++i;
- }
- return i;
-}
-
-/**
- Poisson distributed random number generator when mean is large.
- See: TAOCP by Knuth, Volume 2, Section 3.4.1
- */
-/* //replaced by cleaner version
- double Poisson::poissonLarge() const
-{
-
- // generate X with the gamma distribution of order floor(alpha*mu)
- // where alpha is a suitable constant
- static double m_value = floor(0.875*mean_); // alpha = 7/8 = 0.875 is a good value according to Ahrens and Dieter
- static Gamma gammaGen(m_value, 1.0);
- double n_value;
-
- double x_value = gammaGen.getNextSample();
-
- if ( x_value < mean_ )
- {
- Poisson poissonGen(mean_ - x_value);
- n_value = m_value + poissonGen.getNextSample();
- }
- else
- {
- Binomial binomialGen((long)m_value-1,mean_/x_value);
- n_value = binomialGen.getNextSample();
- }
-
- return n_value;
-}
-*/
- // WATCH OUT: this is recursive. look for better alternative.
-double Poisson::poissonLarge(const Poisson& poisson)
-{
- double xValue = poisson.gammaGen_->getNextSample();
- if (xValue < poisson.mean_)
- {
- Poisson poissonGen(poisson.mean_ - xValue);
- return poisson.mValue_ + poissonGen.getNextSample();
- }
- Binomial binomialGen((long)poisson.mValue_ - 1, poisson.mean_/xValue);
- return binomialGen.getNextSample();
-}
-
-#ifdef TEST_MAIN
-
-#include <vector>
-#include <algorithm>
-#include <cstdlib>
-int main(int argc, char **argv)
-{
- double mean = 4;
-
- if (argc > 1)
- mean = atof(argv[1]);
-
-
- double sum = 0.0;
- double sd = 0.0;
- vector <double> samples;
- Poisson poisson(mean);
- int MAX_SAMPLE = 100000;
- unsigned index;
-
-
- cout << "epsilon = " << getMachineEpsilon() << endl;
- for ( int i = 0; i < MAX_SAMPLE; ++i )
- {
- double p = poisson.getNextSample();//aliasMethod();
- samples.push_back(p);
-
- sum += p;
- sd += (p - mean)*(p - mean);
- }
- mean = sum/MAX_SAMPLE;
- sd = sqrt(sd/MAX_SAMPLE);
- cout << "mean = " << mean << " sd = " << sd << endl;
- sort(samples.begin(), samples.end());
-
- unsigned i = 0;
- unsigned start = 0;
- index = 0;
-
- while ( i < samples.size() )
- {
- int count = 0;
-
- while( ( i < samples.size() ) && (samples[i] == samples[start] ))
- {
- ++count;
- ++i;
- }
- while( index < samples[start])
- {
- cout << index++ << " " << 0 << endl;
- }
-
- cout << index++ << " " << count << endl;
- start = i;
- }
- return 0;
-}
-#endif // test main
-#endif
diff --git a/randnum/Poisson.h b/randnum/Poisson.h
deleted file mode 100644
index 985bd56f..00000000
--- a/randnum/Poisson.h
+++ /dev/null
@@ -1,51 +0,0 @@
-/*******************************************************************
- * File: Poisson.h
- * Description:
- * Author: Subhasis Ray
- * E-mail: ray.subhasis@gmail.com
- * Created: 2007-11-02 09:43:47
- ********************************************************************/
-/**********************************************************************
-** 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 _POISSON_H
-#define _POISSON_H
-
-#include "Probability.h"
-#include "Gamma.h"
-#include "Binomial.h"
-
-class Poisson;
-
-typedef double (Poisson::*PoissonGenerator)() const;
-
-#define CALL_POSSON_GENERATOR(object,ptrToMember) ((object).*(ptrToMember))
-
-class Poisson:public Probability
-{
- public:
- Poisson(double mean=1.0);
- ~Poisson();
-
- void setMean(double mean);
- double getMean() const;
- double getVariance() const;
- double getNextSample() const;
- private:
- double mean_;
- static double poissonSmall(const Poisson&);
- static double poissonLarge(const Poisson&);
- Gamma* gammaGen_;
- //Binomial* binomialGen_;
- double (*generator_)(const Poisson&);
- double mValue_;
-};
-
-#endif
diff --git a/randnum/PoissonRng.cpp b/randnum/PoissonRng.cpp
deleted file mode 100644
index b8ac5b5c..00000000
--- a/randnum/PoissonRng.cpp
+++ /dev/null
@@ -1,86 +0,0 @@
-/*******************************************************************
- * File: PoissonRng.cpp
- * Description:
- * Author: Subhasis Ray
- * E-mail: ray.subhasis@gmail.com
- * Created: 2007-11-08 09:53:32
- * Updated: 2014-09-29
- ********************************************************************/
-/**********************************************************************
-** 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 _POISSONRNG_CPP
-#define _POISSONRNG_CPP
-#include "../basecode/header.h"
-#include "PoissonRng.h"
-
-const Cinfo* PoissonRng::initCinfo()
-{
- static ValueFinfo< PoissonRng, double > mean(
- "mean",
- "Mean of the Poisson distribution.",
- &PoissonRng::setMean,
- &PoissonRng::getMean);
- static Finfo* poissonRngFinfos[] = {
- &mean,
- };
- static string doc[] = {
- "Name", "PoissonRng",
- "Author", "Subhasis Ray",
- "Description", "Poisson distributed random number generator.",
- };
- static Dinfo< PoissonRng > dinfo;
- static Cinfo poissonRngCinfo(
- "PoissonRng",
- RandGenerator::initCinfo(),
- poissonRngFinfos,
- sizeof(poissonRngFinfos)/sizeof(Finfo*),
- &dinfo,
- doc,
- sizeof( doc ) / sizeof( string ));
-
- return &poissonRngCinfo;
-}
-
-
-static const Cinfo* poissonRngCinfo = PoissonRng::initCinfo();
-
-PoissonRng::PoissonRng()
-{
- //do nothing. should not try to get mean
-}
-
-/**
- Sets the mean. Since poisson distribution is defined in terms of
- the rate parameter or the mean, it is mandatory to set this before
- using the generator.
-*/
-void PoissonRng::setMean(double mean)
-{
- Poisson * prng = static_cast<Poisson*>(rng_);
- if ( !prng ){
- rng_ = new Poisson(mean);
- } else {
- prng->setMean(mean);
- }
-}
-/**
- reports error in case the parameter mean has not been set.
-*/
-void PoissonRng::vReinit(const Eref& e, ProcPtr p)
-{
- if ( !rng_ )
- {
- cerr << "ERROR: PoissonRng::vReinit - mean must be set before using the Poisson distribution generator." << endl;
- }
-}
-
-
-#endif
diff --git a/randnum/PoissonRng.h b/randnum/PoissonRng.h
deleted file mode 100644
index 119276b7..00000000
--- a/randnum/PoissonRng.h
+++ /dev/null
@@ -1,33 +0,0 @@
-/*******************************************************************
- * File: PoissonRng.h
- * Description:
- * Author: Subhasis Ray
- * E-mail: ray.subhasis@gmail.com
- * Created: 2007-11-07 16:22:35
- ********************************************************************/
-/**********************************************************************
-** 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 _POISSONRNG_H
-#define _POISSONRNG_H
-#include "Poisson.h"
-#include "RandGenerator.h"
-class PoissonRng:public RandGenerator
-{
- public:
- PoissonRng();
- virtual ~PoissonRng() { ; }
- void setMean(double mean);
- virtual void vReinit(const Eref& e, ProcPtr p);
- static const Cinfo * initCinfo();
-};
-
-
-#endif
diff --git a/randnum/Probability.cpp b/randnum/Probability.cpp
deleted file mode 100644
index c7ad7da7..00000000
--- a/randnum/Probability.cpp
+++ /dev/null
@@ -1,26 +0,0 @@
-/*******************************************************************
- * File: Probability.cpp
- * Description:
- * Author: Subhasis Ray
- * E-mail: ray.subhasis@gmail.com
- * Created: 2007-10-28 13:35:39
- ********************************************************************/
-/**********************************************************************
-** 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 _PROBABILITY_CPP
-#define _PROBABILITY_CPP
-#include "Probability.h"
-
-//const Cinfo* initProbabilityCinfo
-// TODO: implement some tests for generated distributions
-// Kolmogorov-Smirnov test in particular
-
-#endif
diff --git a/randnum/Probability.h b/randnum/Probability.h
deleted file mode 100644
index 61c5acf5..00000000
--- a/randnum/Probability.h
+++ /dev/null
@@ -1,40 +0,0 @@
-/*******************************************************************
- * File: Probability.h
- * Description: This is base class for various probability
- * distribution generator classes.
- * Author: Subhasis Ray
- * E-mail: ray.subhasis@gmail.com
- * Created: 2007-10-28 13:30:41
- ********************************************************************/
-/**********************************************************************
-** 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 _PROBABILITY_H
-#define _PROBABILITY_H
-
-
-/**
- Base class for implementing various probability distributions.
- */
-class Probability
-{
- public:
- virtual ~Probability(){};
-
- virtual double getMean() const =0;
- virtual double getVariance()const =0;
- virtual double getNextSample()const =0;
-
- private:
-// long double mean_; // TODO : do we really need this?
-// long double variance_;// TODO : do we really need this?
-};
-
-#endif
diff --git a/randnum/RNG.h b/randnum/RNG.h
index 9eb1639e..758e599b 100644
--- a/randnum/RNG.h
+++ b/randnum/RNG.h
@@ -19,29 +19,17 @@
#ifndef __RNG_INC
#define __RNG_INC
-#ifdef USE_BOOST
-
-#include <boost/random.hpp>
-#include <boost/random/uniform_01.hpp>
-
-#if defined(BOOST_RANDOM_DEVICE_EXISTS)
-#include <boost/random/random_device.hpp>
-#endif // BOOST_RANDOM_DEVICE_EXISTS
-#else /* ----- not USE_BOOST ----- */
-#include <ctime>
-#include "randnum.h"
-#endif /* ----- not USE_BOOST ----- */
-
#include <limits>
#include <iostream>
-
-#ifdef ENABLE_CPP11
#include <random>
-#endif
+
+#include "Definitions.h"
+#include "Distributions.h"
using namespace std;
-namespace moose {
+namespace moose
+{
/*
* =====================================================================================
@@ -65,17 +53,8 @@ class RNG
void setRandomSeed( )
{
-#if defined(USE_BOOST)
-#if defined(BOOST_RANDOM_DEVICE_EXISTS)
- boost::random::random_device rd;
- setSeed( rd() );
-#endif
-#elif defined(ENABLE_CPP11)
- std::random_device rd;
- setSeed( rd() );
-#else
- mtseed( time(NULL) );
-#endif /* ----- not ENABLE_CPP11 ----- */
+ MOOSE_RANDOM_DEVICE rd_;
+ setSeed( rd_() );
}
/* ==================== ACCESSORS ======================================= */
@@ -91,20 +70,15 @@ class RNG
*
* @param seed
*/
- void setSeed( const unsigned long int seed )
+ void setSeed( const unsigned long seed )
{
seed_ = seed;
if( seed == 0 )
{
- setRandomSeed( );
- return;
+ MOOSE_RANDOM_DEVICE rd_;
+ seed_ = rd_();
}
-
-#if defined(USE_BOOST) || defined(ENABLE_CPP11)
rng_.seed( seed_ );
-#else
- mtseed( seed_ );
-#endif
}
/**
@@ -115,11 +89,7 @@ class RNG
*/
T uniform( const T a, const T b)
{
-#if defined(USE_BOOST) || defined(ENABLE_CPP11)
return ( b - a ) * dist_( rng_ ) + a;
-#else
- return (b-a) * mtrand() + a;
-#endif
}
/**
@@ -130,11 +100,7 @@ class RNG
*/
T uniform( void )
{
-#if defined(USE_BOOST) || defined(ENABLE_CPP11)
return dist_( rng_ );
-#else
- return mtrand();
-#endif
}
@@ -143,17 +109,11 @@ class RNG
T res_;
T seed_;
-#if USE_BOOST
- boost::random::mt19937 rng_;
- boost::random::uniform_01<T> dist_;
-#elif ENABLE_CPP11
- std::mt19937 rng_;
- std::uniform_real_distribution<> dist_;
-#endif /* ----- not ENABLE_CPP11 ----- */
+ moose::MOOSE_RNG_DEFAULT_ENGINE rng_;
+ moose::MOOSE_UNIFORM_DISTRIBUTION<double> dist_;
}; /* ----- end of template class RNG ----- */
-
} /* namespace moose ends */
#endif /* ----- #ifndef __RNG_INC ----- */
diff --git a/randnum/RandGenerator.cpp b/randnum/RandGenerator.cpp
deleted file mode 100644
index 7bd80f35..00000000
--- a/randnum/RandGenerator.cpp
+++ /dev/null
@@ -1,162 +0,0 @@
-/*******************************************************************
- * File: RandGenerator.cpp
- * Description: Interface class for MOOSE to access various
- * random number generator.
- * Author: Subhasis Ray
- * E-mail: ray.subhasis@gmail.com
- * Created: 2007-11-03 21:48:17
- ********************************************************************/
-/**********************************************************************
- ** 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 _RANDGENERATOR_CPP
-#define _RANDGENERATOR_CPP
-
-#include "../basecode/header.h"
-#include "RandGenerator.h"
-
-static SrcFinfo1< double >* output()
-{
- static SrcFinfo1< double > output(
- "output",
- "Generated random number.");
- return &output;
-}
-
-const Cinfo * RandGenerator::initCinfo()
-{
- //////////////////////////////////////////////////////////////
- // MsgDest Definitions
- //////////////////////////////////////////////////////////////
- static DestFinfo process(
- "process",
- "Handles process call, updates internal time stamp.",
- new ProcOpFunc< RandGenerator >( &RandGenerator::process ));
- static DestFinfo reinit(
- "reinit",
- "Handles reinit call.",
- new ProcOpFunc< RandGenerator >( &RandGenerator::reinit ));
- //////////////////////////////////////////////////////////////
- // SharedMsg Definitions
- //////////////////////////////////////////////////////////////
- static Finfo* procShared[] = {
- &process, &reinit
- };
- static SharedFinfo proc(
- "proc",
- "Shared message for process and reinit",
- procShared, sizeof( procShared ) / sizeof( const Finfo* ));
-
- //////////////////////////////////////////////////////////////
- // ValueFinfo Definitions
- //////////////////////////////////////////////////////////////
-
- static ReadOnlyValueFinfo<RandGenerator, double> sample(
- "sample",
- "Generated pseudorandom number.",
- &RandGenerator::getSample);
- static ReadOnlyValueFinfo< RandGenerator, double > mean(
- "mean",
- "Mean of the distribution.",
- &RandGenerator::getMean);
- static ReadOnlyValueFinfo<RandGenerator, double> variance(
- "variance",
- "Variance of the distribution.",
- &RandGenerator::getVariance);
-
- static Finfo * randGeneratorFinfos[] = {
- &sample,
- &mean,
- &variance,
- output(),
- &proc,
- };
-
- static string doc[] = {
- "Name", "RandGenerator",
- "Author", "Subhasis Ray",
- "Description", "Base class for random number generators for sampling various"
- " probability distributions. This class should not be used"
- " directly. Instead, its subclasses named after specific distributions"
- " should be used.",
- };
-
- static Dinfo< RandGenerator > dinfo;
- static Cinfo randGeneratorCinfo(
- "RandGenerator",
- Neutral::initCinfo(),
- randGeneratorFinfos,
- sizeof(randGeneratorFinfos)/sizeof(Finfo*),
- &dinfo,
- doc,
- sizeof( doc ) / sizeof( string ));
-
- return &randGeneratorCinfo;
-}
-
-static const Cinfo * randGeneratorCinfo = RandGenerator::initCinfo();
-
-RandGenerator::RandGenerator()
-{
- sample_ = 0.0;
- rng_ = NULL;
-}
-
-RandGenerator::~RandGenerator()
-{
- if (rng_)
- {
- delete rng_;
- rng_ = NULL;
- }
-}
-
-double RandGenerator::getMean() const
-{
- if (rng_)
- {
- return rng_->getMean();
- }
- return 0.0;
-}
-
-double RandGenerator::getVariance() const
-{
- if (rng_)
- {
- return rng_->getVariance();
- }
- return 0.0;
-}
-
-double RandGenerator::getSample() const
-{
- return sample_;
-}
-
-void RandGenerator::process( const Eref& e, ProcPtr p )
-{
- if (rng_){
- sample_ = rng_->getNextSample();
- output()->send(e, sample_);
- }
-}
-
-void RandGenerator::reinit(const Eref& e, ProcPtr p)
-{
- vReinit(e, p);
-}
-
-void RandGenerator::vReinit(const Eref& e, ProcPtr p)
-{
- cerr << "RandGenerator::vReinit() - this function should never be reached. Guilty party: " << e.id().path() << endl;
-}
-
-#endif
diff --git a/randnum/RandGenerator.h b/randnum/RandGenerator.h
deleted file mode 100644
index 7e37b716..00000000
--- a/randnum/RandGenerator.h
+++ /dev/null
@@ -1,48 +0,0 @@
-/*******************************************************************
- * File: RandGenerator.h
- * Description:
- * Author: Subhasis Ray
- * E-mail: ray.subhasis@gmail.com
- * Created: 2007-11-07 16:25:08
- ********************************************************************/
-/**********************************************************************
-** 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 _RANDGENERATOR_H
-#define _RANDGENERATOR_H
-
-#include "randnum.h"
-#include "basecode/header.h"
-#include "Probability.h"
-
-/**
- This class is a moose interface to underlying random number
- generators (which is an instance of Probability class).
- */
-class RandGenerator
-{
- public:
- RandGenerator();
- virtual ~RandGenerator();
- double getMean() const;
- double getVariance() const;
- double getSample() const;
- void process( const Eref& e, ProcPtr info);
- void reinit( const Eref& e, ProcPtr info);
- virtual void vReinit( const Eref& e, ProcPtr info);
-
- static const Cinfo * initCinfo();
- protected:
- Probability* rng_;
- double sample_;
-};
-
-
-#endif
diff --git a/randnum/Uniform.cpp b/randnum/Uniform.cpp
deleted file mode 100644
index 1b9fb8bf..00000000
--- a/randnum/Uniform.cpp
+++ /dev/null
@@ -1,125 +0,0 @@
-/*******************************************************************
- * File: Uniform.cpp
- * Description:
- * Author: Subhasis Ray
- * E-mail: ray.subhasis@gmail.com
- * Created: 2008-02-21 17:12:55
- ********************************************************************/
-/**********************************************************************
-** 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 _UNIFORM_CPP
-#define _UNIFORM_CPP
-
-#include <cassert>
-#include <iostream>
-#include <vector>
-
-#include "Uniform.h"
-#include "randnum.h"
-#include "utility/numutil.h"
-using namespace std;
-
-Uniform::Uniform()
-{
- min_ = 0.0;
- max_ = 1.0;
-}
-Uniform::Uniform(double min, double max)
-{
- if ( min >= max )
- {
- cerr << "ERROR: specified lowerbound is greater than upper bound." << endl;
- min_ = 0.0;
- max_ = 1.0;
- return;
- }
-
- min_ = min;
- max_ = max;
-}
-double Uniform::getMean() const
-{
- return (max_ + min_) / 2.0;
-}
-double Uniform::getVariance()const
-{
- return (max_- min_) * (max_ - min_)/12.0;
-}
-double Uniform::getMin() const
-{
- return min_;
-}
-double Uniform::getMax() const
-{
- return max_;
-}
-void Uniform::setMin(double min)
-{
- min_ = min;
-}
-void Uniform::setMax(double max)
-{
- max_ = max;
-}
-double Uniform::getNextSample() const
-{
- assert( max_ > min_ );
- return mtrand()*(max_-min_)+min_;
-}
-
-#ifdef DO_UNIT_TESTS
-void doTest(double min, double max, unsigned count)
-{
- Uniform rng;
-
- rng.setMin(min);
- rng.setMax(max);
- assert(isClose<double>(min, rng.getMin(), DBL_EPSILON));
- assert(isClose<double>(max, rng.getMax(), DBL_EPSILON));
- vector <double> seq;
- double mean = 0.0;
-
-
- for (unsigned ii = 0; ii < count; ++ii )
- {
- double sample;
- sample = rng.getNextSample();
- mean += sample;
- seq.push_back(sample);
- }
- mean /= count;
- double var = 0.0;
- for(unsigned ii = 0; ii <seq.size(); ++ii)
- {
- var += (mean - seq[ii]) * (mean - seq[ii]);
- }
- var = var / count;
- cout << "theoretical mean: " << rng.getMean() << ", sample mean: " << mean << ", theoretical var: " << rng.getVariance() << ", sample var: " << var << ", sample size: " << count << endl;
-
-}
-
-void testUniform()
-{
- cout << "testUniform(): testing uniform rng.\n";
- doTest(-10.0, 10.0, 1000);
- doTest(1e-10, 1.1e-10, 1000);
-}
-
-#endif // DO_UNIT_TESTS
-#if defined( TEST_MAIN ) && defined(DO_UNIT_TESTS)
-int main(void)
-{
- testUniform();
-}
-
-#endif // !defined( TEST_MAIN ) && defined(DO_UNIT_TESTS)
-
-#endif
diff --git a/randnum/Uniform.h b/randnum/Uniform.h
deleted file mode 100644
index 3073fb82..00000000
--- a/randnum/Uniform.h
+++ /dev/null
@@ -1,43 +0,0 @@
-/*******************************************************************
- * File: Uniform.h
- * Description:
- * Author: Subhasis Ray
- * E-mail: ray.subhasis@gmail.com
- * Created: 2008-02-21 17:09:54
- ********************************************************************/
-/**********************************************************************
-** 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 _UNIFORM_H
-#define _UNIFORM_H
-
-#include "Probability.h"
-
-class Uniform: public Probability
-{
- public:
- Uniform();
- Uniform(double min, double max);
- double getMean() const;
- double getVariance() const;
- double getNextSample() const;
- double getMin() const;
- double getMax() const;
- void setMin(double min);
- void setMax(double max);
-
- private:
- double min_;
- double max_;
-
-};
-
-
-#endif
diff --git a/randnum/UniformRng.cpp b/randnum/UniformRng.cpp
deleted file mode 100644
index 15630b7c..00000000
--- a/randnum/UniformRng.cpp
+++ /dev/null
@@ -1,113 +0,0 @@
-/*******************************************************************
- * File: UniformRng.cpp
- * Description:
- * Author: Subhasis Ray
- * E-mail: ray.subhasis@gmail.com
- * Created: 2008-02-01 11:30:20
- ********************************************************************/
-/**********************************************************************
-** 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 _UNIFORMRNG_CPP
-#define _UNIFORMRNG_CPP
-#include "../basecode/header.h"
-#include "randnum.h"
-#include "UniformRng.h"
-#include "Uniform.h"
-
-const Cinfo* UniformRng::initCinfo()
-{
- static ValueFinfo< UniformRng, double > min(
- "min",
- "The lower bound on the numbers generated ",
- &UniformRng::setMin,
- &UniformRng::getMin);
- static ValueFinfo< UniformRng, double > max(
- "max",
- "The upper bound on the numbers generated",
- &UniformRng::setMax,
- &UniformRng::getMax);
-
- static Finfo * uniformRngFinfos[] = {
- &min,
- &max,
- };
- static string doc[] =
- {
- "Name", "UniformRng",
- "Author", "Subhasis Ray",
- "Description", "Generates pseudorandom number from a unform distribution.",
- };
- static Dinfo< UniformRng > dinfo;
- static Cinfo uniformRngCinfo(
- "UniformRng",
- RandGenerator::initCinfo(),
- uniformRngFinfos,
- sizeof( uniformRngFinfos ) / sizeof( Finfo* ),
- &dinfo,
- doc,
- sizeof( doc ) / sizeof( string ));
- return &uniformRngCinfo;
-}
-
-static const Cinfo* uniformRngCinfo = UniformRng::initCinfo();
-
-double UniformRng::getMin()const
-{
- Uniform * urng = static_cast< Uniform * >(rng_);
- if (urng){
- return urng->getMin();
- }
- return 0.0;
-}
-
-double UniformRng::getMax() const
-{
- Uniform * urng = static_cast< Uniform * >(rng_);
- if (urng){
- return urng->getMax();
- }
- return 0.0;
-}
-
-void UniformRng::setMin(double min)
-{
- Uniform * urng = static_cast<Uniform *> (rng_);
- if (urng){
- urng->setMin(min);
- }
-}
-
-void UniformRng::setMax(double max)
-{
- Uniform * urng = static_cast<Uniform *> (rng_);
- if (urng){
- urng->setMax(max);
- }
-}
-
-UniformRng::UniformRng():RandGenerator()
-{
- rng_ = new Uniform();
-}
-
-void UniformRng::vReinit(const Eref& e, ProcPtr p)
-{
- ; /* no use */
-}
-
-#ifdef DO_UNIT_TESTS
-void testUniformRng()
-{
- cout << "testUniformRng(): yet to be implemented" << endl;
-}
-
-#endif
-#endif
diff --git a/randnum/UniformRng.h b/randnum/UniformRng.h
deleted file mode 100644
index da4d4af0..00000000
--- a/randnum/UniformRng.h
+++ /dev/null
@@ -1,43 +0,0 @@
-/*******************************************************************
- * File: UniformRng.h
- * Description:
- * Author: Subhasis Ray
- * E-mail: ray.subhasis@gmail.com
- * Created: 2008-02-01 11:52:48
- ********************************************************************/
-/**********************************************************************
-** 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 _UNIFORMRNG_H
-#define _UNIFORMRNG_H
-
-#include "randnum.h"
-#include "RandGenerator.h"
-
-class UniformRng: public RandGenerator
-{
- public:
- UniformRng();
- virtual ~UniformRng() { ; }
- double getMin() const;
- double getMax() const;
- void setMin(double min);
- void setMax(double max);
- virtual void vReinit(const Eref& e, ProcPtr p);
-
- static const Cinfo * initCinfo();
- private:
- double min_;
- double max_;
-};
-
-
-
-#endif
diff --git a/randnum/mt19937ar.cpp b/randnum/mt19937ar.cpp
deleted file mode 100644
index 3becb14a..00000000
--- a/randnum/mt19937ar.cpp
+++ /dev/null
@@ -1,258 +0,0 @@
-/*
- A C-program for MT19937, with initialization improved 2002/1/26.
- Coded by Takuji Nishimura and Makoto Matsumoto.
-
- Before using, initialize the state by using init_genrand(seed)
- or init_by_array(init_key, key_length).
-
- Copyright (C) 1997 - 2002, Makoto Matsumoto and Takuji Nishimura,
- All rights reserved.
-
- Redistribution and use in source and binary forms, with or without
- modification, are permitted provided that the following conditions
- are met:
-
- 1. Redistributions of source code must retain the above copyright
- notice, this list of conditions and the following disclaimer.
-
- 2. Redistributions in binary form must reproduce the above copyright
- notice, this list of conditions and the following disclaimer in the
- documentation and/or other materials provided with the distribution.
-
- 3. The names of its contributors may not be used to endorse or promote
- products derived from this software without specific prior written
- permission.
-
- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
- "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
- LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
- A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
- CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
- EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
- PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
- PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
- LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
- NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
- SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-
- Any feedback is very welcome.
- http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/emt.html
- email: m-mat @ math.sci.hiroshima-u.ac.jp (remove space)
-*/
-
-/* Modified slightly for use in MOOSE by Upi Bhalla, NCBS, 2004 */
-#ifdef _WIN32
-#include <Winsock2.h>
-#else
-#define _BSD_SOURCE
-#include <sys/time.h>
-#endif
-#include <stdlib.h>
-#include "randnum.h"
-/* Period parameters */
-#define N 624
-#define M 397
-#define MATRIX_A 0x9908b0dfUL /* constant vector a */
-#define UPPER_MASK 0x80000000UL /* most significant w-r bits */
-#define LOWER_MASK 0x7fffffffUL /* least significant r bits */
-
-static unsigned long mt[N]; /* the array for the state vector */
-static int mti=N+1; /* mti==N+1 means mt[N] is not initialized */
-
-/* initializes mt[N] with a seed */
-void init_genrand(unsigned long s)
-{
- mt[0]= s & 0xffffffffUL;
- for (mti=1; mti<N; mti++) {
- mt[mti] =
- (1812433253UL * (mt[mti-1] ^ (mt[mti-1] >> 30)) + mti);
- /* See Knuth TAOCP Vol2. 3rd Ed. P.106 for multiplier. */
- /* In the previous versions, MSBs of the seed affect */
- /* only MSBs of the array mt[]. */
- /* 2002/01/09 modified by Makoto Matsumoto */
- mt[mti] &= 0xffffffffUL;
- /* for >32 bit machines */
- }
-}
-
-//Add code for gettimeofday
-#ifdef _WIN32
- int gettimeofday( struct timeval* tv, void* timezone ) {
- FILETIME time;
- double timed;
-
- GetSystemTimeAsFileTime( &time );
-
- // Apparently Win32 has units of 1e-7 sec (tenths of microsecs)
- // 4294967296 is 2^32, to shift high word over
- // 11644473600 is the number of seconds between
- // the Win32 epoch 1601-Jan-01 and the Unix epoch 1970-Jan-01
- // Tests found floating point to be 10x faster than 64bit int math.
-
- timed = ((time.dwHighDateTime * 4294967296e-7) - 11644473600.0) +
- (time.dwLowDateTime * 1e-7);
-
- tv->tv_sec = (long) timed;
- tv->tv_usec = (long) ((timed - tv->tv_sec) * 1e6);
-
- return 0;
- }
-#endif
-
-
-
-
-
-/* initialize by an array with array-length */
-/* init_key is the array for initializing keys */
-/* key_length is its length */
-/* slight change for C++, 2004/2/26 */
-void init_by_array(long int init_key[], int key_length)
-{
- int i, j, k;
- init_genrand(19650218UL);
- i=1; j=0;
- k = (N>key_length ? N : key_length);
- for (; k; k--) {
- mt[i] = (mt[i] ^ ((mt[i-1] ^ (mt[i-1] >> 30)) * 1664525UL))
- + init_key[j] + j; /* non linear */
- mt[i] &= 0xffffffffUL; /* for WORDSIZE > 32 machines */
- i++; j++;
- if (i>=N) { mt[0] = mt[N-1]; i=1; }
- if (j>=key_length) j=0;
- }
- for (k=N-1; k; k--) {
- mt[i] = (mt[i] ^ ((mt[i-1] ^ (mt[i-1] >> 30)) * 1566083941UL))
- - i; /* non linear */
- mt[i] &= 0xffffffffUL; /* for WORDSIZE > 32 machines */
- i++;
- if (i>=N) { mt[0] = mt[N-1]; i=1; }
- }
-
- mt[0] = 0x80000000UL; /* MSB is 1; assuring non-zero initial array */
-}
-
-/* generates a random number on [0,0xffffffff]-interval */
-unsigned long genrand_int32(void)
-{
- unsigned long y;
- static unsigned long mag01[2]={0x0UL, MATRIX_A};
- /* mag01[x] = x * MATRIX_A for x=0,1 */
-
- if (mti >= N) { /* generate N words at one time */
- int kk;
-
- if (mti == N+1) /* if init_genrand() has not been called, */
- init_genrand(5489UL); /* a default initial seed is used */
-
- for (kk=0;kk<N-M;kk++) {
- y = (mt[kk]&UPPER_MASK)|(mt[kk+1]&LOWER_MASK);
- mt[kk] = mt[kk+M] ^ (y >> 1) ^ mag01[y & 0x1UL];
- }
- for (;kk<N-1;kk++) {
- y = (mt[kk]&UPPER_MASK)|(mt[kk+1]&LOWER_MASK);
- mt[kk] = mt[kk+(M-N)] ^ (y >> 1) ^ mag01[y & 0x1UL];
- }
- y = (mt[N-1]&UPPER_MASK)|(mt[0]&LOWER_MASK);
- mt[N-1] = mt[M-1] ^ (y >> 1) ^ mag01[y & 0x1UL];
-
- mti = 0;
- }
-
- y = mt[mti++];
-
- /* Tempering */
- y ^= (y >> 11);
- y ^= (y << 7) & 0x9d2c5680UL;
- y ^= (y << 15) & 0xefc60000UL;
- y ^= (y >> 18);
-
- return y;
-}
-#if 0
-/* generates a random number on [0,0x7fffffff]-interval */
-long genrand_int31(void)
-{
- return (long)(genrand_int32()>>1);
-}
-
-/* generates a random number on [0,1]-real-interval */
-double genrand_real1(void)
-{
- return genrand_int32()*(1.0/4294967295.0);
- /* divided by 2^32-1 */
-}
-
-/* generates a random number on [0,1)-real-interval */
-double genrand_real2(void)
-{
- return genrand_int32()*(1.0/4294967296.0);
- /* divided by 2^32 */
-}
-
-/* generates a random number on (0,1)-real-interval */
-double genrand_real3(void)
-{
- return (((double)genrand_int32()) + 0.5)*(1.0/4294967296.0);
- /* divided by 2^32 */
-}
-
-/* generates a random number on [0,1) with 53-bit resolution*/
-double genrand_res53(void)
-{
- unsigned long a=genrand_int32()>>5, b=genrand_int32()>>6;
- return(a*67108864.0+b)*(1.0/9007199254740992.0);
-}
-/* These real versions are due to Isaku Wada, 2002/01/09 added */
-
-/*
-int main(void)
-{
- int i;
- unsigned long init[4]={0x123, 0x234, 0x345, 0x456}, length=4;
- init_by_array(init, length);
- printf("1000 outputs of genrand_int32()\n");
- for (i=0; i<1000; i++) {
- printf("%10lu ", genrand_int32());
- if (i%5==4) printf("\n");
- }
- printf("\n1000 outputs of genrand_real2()\n");
- for (i=0; i<1000; i++) {
- printf("%10.8f ", genrand_real2());
- if (i%5==4) printf("\n");
- }
- return 0;
-}
-*/
-#endif
-
-void mtseed(long seed = 0)
-{
- struct timeval tv;
-
- if (seed == 0) {
- char* hostname = getenv("HOST");
- gettimeofday(&tv, NULL);
- if (hostname != NULL) {
- for (int i = 0; *hostname; hostname++, i++){
- tv.tv_usec += *hostname * i * i * 16;
- }
- }
- long int init[2] = {tv.tv_sec, tv.tv_usec};
- long int length = 2;
- init_by_array(init, length);
- } else {
- // unsigned long init[1] = {seed};
- // unsigned long length = 1;
- // init_by_array(init, length);
- init_genrand( seed );
- }
-}
-
-/* generates a random number on [0,1)-real-interval */
-double mtrand(void)
-{
- return genrand_int32()*(1.0/4294967296.0);
- /* divided by 2^32 */
-}
diff --git a/randnum/randnum.h b/randnum/randnum.h
deleted file mode 100644
index 5af4abda..00000000
--- a/randnum/randnum.h
+++ /dev/null
@@ -1,15 +0,0 @@
-/**********************************************************************
-** This program is part of 'MOOSE', the
-** Messaging Object Oriented Simulation Environment,
-** copyright (C) 2003-2004 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.
-** Development of this software was supported by
-** Biophase Simulations Inc, http://www.bpsims.com
-** See the file BIOPHASE.INFO for details.
-**********************************************************************/
-extern double mtrand(void);
-extern void mtseed(long seed);
-extern unsigned long genrand_int32(void);
-
diff --git a/randnum/test_normal_dist.cpp b/randnum/test_normal_dist.cpp
new file mode 100644
index 00000000..101a5454
--- /dev/null
+++ b/randnum/test_normal_dist.cpp
@@ -0,0 +1,63 @@
+/***
+ * Filename: test_normal_dist.cpp
+ *
+ * Description: test script.
+ *
+ * Version: 0.0.1
+ * Created: 2018-08-04
+
+ * Revision: none
+ *
+ * Author: Dilawar Singh <dilawars@ncbs.res.in>
+ * Organization: NCBS Bangalore
+ *
+ * License: GNU GPL2
+ */
+
+
+#include <iostream>
+#include <map>
+#include <iomanip>
+
+#include "Distributions.h"
+#include "../utility/testing_macros.hpp"
+
+
+int test_normal_dist( )
+{
+
+ moose::MOOSE_RANDOM_DEVICE rd;
+ moose::MOOSE_RNG_DEFAULT_ENGINE gen;
+ gen.seed( 10 );
+
+ moose::MOOSE_NORMAL_DISTRIBUTION<double> d(0, 1);
+
+ std::map<int, int> hist{};
+ std::vector<double> dist;
+ for(int n=0; n<100000; ++n)
+ {
+ double x = d(gen);
+ dist.push_back( x );
+ ++hist[ std::round(x) ];
+ }
+
+ for(auto p : hist) {
+ std::cout << std::setw(2)
+ << p.first << ' ' << std::string(p.second/200, '*') << '\n';
+ }
+
+ ASSERT_DOUBLE_EQ( "NORMALDIST", hist[-3], 542 );
+ ASSERT_DOUBLE_EQ( "NORMALDIST", hist[-2], 5987 );
+ ASSERT_DOUBLE_EQ( "NORMALDIST", hist[-1], 24262 );
+ ASSERT_DOUBLE_EQ( "NORMALDIST", hist[0], 38236 );
+ ASSERT_DOUBLE_EQ( "NORMALDIST", hist[1], 24386 );
+ ASSERT_DOUBLE_EQ( "NORMALDIST", hist[2], 6071 );
+
+ return 0;
+}
+
+int main(int argc, const char *argv[])
+{
+ test_normal_dist();
+ return 0;
+}
diff --git a/scheduling/Clock.cpp b/scheduling/Clock.cpp
index dc45989f..aad5c066 100644
--- a/scheduling/Clock.cpp
+++ b/scheduling/Clock.cpp
@@ -30,25 +30,25 @@
*
* The system works like this:
* 1. Assign times to each Tick. This is divided by dt_ and the rounded
- * value is used for the integral multiple. Zero means the tick is not
- * scheduled.
+ * value is used for the integral multiple. Zero means the tick is not
+ * scheduled.
* 2. The process call goes through all active ticks in order every
- * timestep. Each Tick increments its counter and decides if it is
- * time to fire.
+ * timestep. Each Tick increments its counter and decides if it is
+ * time to fire.
* 4. The Reinit call goes through all active ticks in order, just once.
* 5. We connect up the Ticks to their target objects.
* 6. We begin the simulation by calling 'start' or 'step' on the Clock.
- * 'step' executes exactly one timestep (of the minimum dt_),
- * visiting all ticks as above..
- * 'start' executes an integral number of such timesteps.
+ * 'step' executes exactly one timestep (of the minimum dt_),
+ * visiting all ticks as above..
+ * 'start' executes an integral number of such timesteps.
* 7. To interrupt the simulation at some intermediate time, call 'stop'.
- * This lets the system complete its current step.
+ * This lets the system complete its current step.
* 8. To restart the simulation from where it left off, use the same
- * 'start' or 'step' function on the Clock. As all the ticks
- * retain their state, the simulation can resume smoothly.
+ * 'start' or 'step' function on the Clock. As all the ticks
+ * retain their state, the simulation can resume smoothly.
*/
-#include "header.h"
+#include "../basecode/header.h"
#include "Clock.h"
#include "../utility/numutil.h"
#include "../utility/print_function.hpp"
@@ -259,52 +259,52 @@ const Cinfo* Clock::initCinfo()
static Finfo* clockFinfos[] =
{
// Fields
- &dt, // Value
- &runTime, // ReadOnlyValue
- ¤tTime, // ReadOnlyValue
- &nsteps, // ReadOnlyValue
- &numTicks, // ReadOnlyValue
- &stride, // ReadOnlyValue
- ¤tStep, // ReadOnlyValue
- &dts, // ReadOnlyValue
- &isRunning, // ReadOnlyValue
- &tickStep, // LookupValue
- &tickDt, // LookupValue
- &defaultTick, // ReadOnlyLookupValue
- &clockControl, // Shared
- finished(), // Src
- procs[0], // Src
- procs[1], // Src
- procs[2], // Src
- procs[3], // Src
- procs[4], // Src
- procs[5], // Src
- procs[6], // Src
- procs[7], // Src
- procs[8], // Src
- procs[9], // Src
- procs[10], // Src
- procs[11], // Src
- procs[12], // Src
- procs[13], // Src
- procs[14], // Src
- procs[15], // Src
- procs[16], // Src
- procs[17], // Src
- procs[18], // Src
- procs[19], // Src
- procs[20], // Src
- procs[21], // Src
- procs[22], // Src
- procs[23], // Src
- procs[24], // Src
- procs[25], // Src
- procs[26], // Src
- procs[27], // Src
- procs[28], // Src
- procs[29], // Src
- procs[30], // Src
- procs[31], // Src
+ &dt, // Value
+ &runTime, // ReadOnlyValue
+ ¤tTime, // ReadOnlyValue
+ &nsteps, // ReadOnlyValue
+ &numTicks, // ReadOnlyValue
+ &stride, // ReadOnlyValue
+ ¤tStep, // ReadOnlyValue
+ &dts, // ReadOnlyValue
+ &isRunning, // ReadOnlyValue
+ &tickStep, // LookupValue
+ &tickDt, // LookupValue
+ &defaultTick, // ReadOnlyLookupValue
+ &clockControl, // Shared
+ finished(), // Src
+ procs[0], // Src
+ procs[1], // Src
+ procs[2], // Src
+ procs[3], // Src
+ procs[4], // Src
+ procs[5], // Src
+ procs[6], // Src
+ procs[7], // Src
+ procs[8], // Src
+ procs[9], // Src
+ procs[10], // Src
+ procs[11], // Src
+ procs[12], // Src
+ procs[13], // Src
+ procs[14], // Src
+ procs[15], // Src
+ procs[16], // Src
+ procs[17], // Src
+ procs[18], // Src
+ procs[19], // Src
+ procs[20], // Src
+ procs[21], // Src
+ procs[22], // Src
+ procs[23], // Src
+ procs[24], // Src
+ procs[25], // Src
+ procs[26], // Src
+ procs[27], // Src
+ procs[28], // Src
+ procs[29], // Src
+ procs[30], // Src
+ procs[31], // Src
};
static string doc[] =
@@ -360,79 +360,79 @@ const Cinfo* Clock::initCinfo()
" STDPSynHandler 1 50e-6\n"
" GraupnerBrunel2012CaPlasticitySynHandler 1 50e-6\n"
" SeqSynHandler 1 50e-6\n"
- " CaConc 1 50e-6\n"
- " CaConcBase 1 50e-6\n"
- " DifShell 1 50e-6\n"
- " DifShellBase 1 50e-6\n"
- " MMPump 1 50e-6\n"
- " DifBuffer 1 50e-6\n"
- " DifBufferBase 1 50e-6\n"
- " MgBlock 1 50e-6\n"
- " Nernst 1 50e-6\n"
- " RandSpike 1 50e-6\n"
- " ChanBase 2 50e-6\n"
- " IntFire 2 50e-6\n"
- " IntFireBase 2 50e-6\n"
- " LIF 2 50e-6\n"
- " QIF 2 50e-6\n"
- " ExIF 2 50e-6\n"
- " AdExIF 2 50e-6\n"
- " AdThreshIF 2 50e-6\n"
- " IzhIF 2 50e-6\n"
- " IzhikevichNrn 2 50e-6\n"
- " SynChan 2 50e-6\n"
- " NMDAChan 2 50e-6\n"
- " GapJunction 2 50e-6\n"
- " HHChannel 2 50e-6\n"
- " HHChannel2D 2 50e-6\n"
- " Leakage 2 50e-6\n"
- " MarkovChannel 2 50e-6\n"
- " MarkovGslSolver 2 50e-6\n"
- " MarkovRateTable 2 50e-6\n"
- " MarkovSolver 2 50e-6\n"
- " MarkovSolverBase 2 50e-6\n"
- " RC 2 50e-6\n"
- " Compartment (init) 3 50e-6\n"
- " CompartmentBase (init ) 3 50e-6\n"
- " SymCompartment (init) 3 50e-6\n"
- " Compartment 4 50e-6\n"
- " CompartmentBase 4 50e-6\n"
- " SymCompartment 4 50e-6\n"
- " SpikeGen 5 50e-6\n"
- " HSolve 6 50e-6\n"
- " SpikeStats 7 50e-6\n"
- " Table 8 0.1e-3\n"
- " TimeTable 8 0.1e-3\n"
-
- " Dsolve 10 0.01\n"
- " Adaptor 11 0.1\n"
- " Func 12 0.1\n"
- " Function 12 0.1\n"
- " Arith 12 0.1\n"
- " BufPool 13 0.1\n"
- " Pool 13 0.1\n"
- " PoolBase 13 0.1\n"
- " CplxEnzBase 14 0.1\n"
- " Enz 14 0.1\n"
- " EnzBase 14 0.1\n"
- " MMenz 14 0.1\n"
- " Reac 14 0.1\n"
- " ReacBase 14 0.1\n"
- " Gsolve (init) 15 0.1\n"
- " Ksolve (init) 15 0.1\n"
- " Gsolve 16 0.1\n"
- " Ksolve 16 0.1\n"
- " Stats 17 0.1\n"
- " Table2 18 1\n"
- " Streamer 19 10\n"
-
- " HDF5DataWriter 30 1\n"
- " HDF5WriterBase 30 1\n"
- " NSDFWriter 30 1\n"
- " PyRun 30 1\n"
- " PostMaster 31 0.01\n"
- " \n"
- " Note that the other classes are not scheduled at all.",
+ " CaConc 1 50e-6\n"
+ " CaConcBase 1 50e-6\n"
+ " DifShell 1 50e-6\n"
+ " DifShellBase 1 50e-6\n"
+ " MMPump 1 50e-6\n"
+ " DifBuffer 1 50e-6\n"
+ " DifBufferBase 1 50e-6\n"
+ " MgBlock 1 50e-6\n"
+ " Nernst 1 50e-6\n"
+ " RandSpike 1 50e-6\n"
+ " ChanBase 2 50e-6\n"
+ " IntFire 2 50e-6\n"
+ " IntFireBase 2 50e-6\n"
+ " LIF 2 50e-6\n"
+ " QIF 2 50e-6\n"
+ " ExIF 2 50e-6\n"
+ " AdExIF 2 50e-6\n"
+ " AdThreshIF 2 50e-6\n"
+ " IzhIF 2 50e-6\n"
+ " IzhikevichNrn 2 50e-6\n"
+ " SynChan 2 50e-6\n"
+ " NMDAChan 2 50e-6\n"
+ " GapJunction 2 50e-6\n"
+ " HHChannel 2 50e-6\n"
+ " HHChannel2D 2 50e-6\n"
+ " Leakage 2 50e-6\n"
+ " MarkovChannel 2 50e-6\n"
+ " MarkovGslSolver 2 50e-6\n"
+ " MarkovRateTable 2 50e-6\n"
+ " MarkovSolver 2 50e-6\n"
+ " MarkovSolverBase 2 50e-6\n"
+ " RC 2 50e-6\n"
+ " Compartment (init) 3 50e-6\n"
+ " CompartmentBase (init ) 3 50e-6\n"
+ " SymCompartment (init) 3 50e-6\n"
+ " Compartment 4 50e-6\n"
+ " CompartmentBase 4 50e-6\n"
+ " SymCompartment 4 50e-6\n"
+ " SpikeGen 5 50e-6\n"
+ " HSolve 6 50e-6\n"
+ " SpikeStats 7 50e-6\n"
+ " Table 8 0.1e-3\n"
+ " TimeTable 8 0.1e-3\n"
+
+ " Dsolve 10 0.01\n"
+ " Adaptor 11 0.1\n"
+ " Func 12 0.1\n"
+ " Function 12 0.1\n"
+ " Arith 12 0.1\n"
+ " BufPool 13 0.1\n"
+ " Pool 13 0.1\n"
+ " PoolBase 13 0.1\n"
+ " CplxEnzBase 14 0.1\n"
+ " Enz 14 0.1\n"
+ " EnzBase 14 0.1\n"
+ " MMenz 14 0.1\n"
+ " Reac 14 0.1\n"
+ " ReacBase 14 0.1\n"
+ " Gsolve (init) 15 0.1\n"
+ " Ksolve (init) 15 0.1\n"
+ " Gsolve 16 0.1\n"
+ " Ksolve 16 0.1\n"
+ " Stats 17 0.1\n"
+ " Table2 18 1\n"
+ " Streamer 19 10\n"
+
+ " HDF5DataWriter 30 1\n"
+ " HDF5WriterBase 30 1\n"
+ " NSDFWriter 30 1\n"
+ " PyRun 30 1\n"
+ " PostMaster 31 0.01\n"
+ " \n"
+ " Note that the other classes are not scheduled at all.",
};
static Dinfo< Clock > dinfo;
@@ -662,7 +662,7 @@ void Clock::innerReportClock() const
cout << "Dts= ";
for ( unsigned int i = 0; i < ticks_.size(); ++i )
{
- cout << "tick[" << i << "] = " << ticks_[i] << " " <<
+ cout << "tick[" << i << "] = " << ticks_[i] << " " <<
ticks_[i] * dt_ << endl;
}
cout << endl;
@@ -834,24 +834,24 @@ void Clock::handleReinit( const Eref& e )
* Useful function, only I don't need it yet. Was implemented for Dsolve
double Dsolve::findDt( const Eref& e )
{
- // Here is the horrible stuff to traverse the message to get the dt.
- const Finfo* f = Dsolve::initCinfo()->findFinfo( "reinit" );
- const DestFinfo* df = dynamic_cast< const DestFinfo* >( f );
- assert( df );
- unsigned int fid = df->getFid();
- ObjId caller = e.element()->findCaller( fid );
- const Msg* m = Msg::getMsg( caller );
- assert( m );
- vector< string > src = m->getSrcFieldsOnE1();
- assert( src.size() > 0 );
- string temp = src[0].substr( src[0].length() - 1 ); // reinitxx
- unsigned int tick = atoi( temp.c_str() );
- assert( tick < 10 );
- Id clock( 1 );
- assert( clock.element() == m->e1() );
- double dt = LookupField< unsigned int, double >::
- get( clock, "tickDt", tick );
- return dt;
+ // Here is the horrible stuff to traverse the message to get the dt.
+ const Finfo* f = Dsolve::initCinfo()->findFinfo( "reinit" );
+ const DestFinfo* df = dynamic_cast< const DestFinfo* >( f );
+ assert( df );
+ unsigned int fid = df->getFid();
+ ObjId caller = e.element()->findCaller( fid );
+ const Msg* m = Msg::getMsg( caller );
+ assert( m );
+ vector< string > src = m->getSrcFieldsOnE1();
+ assert( src.size() > 0 );
+ string temp = src[0].substr( src[0].length() - 1 ); // reinitxx
+ unsigned int tick = atoi( temp.c_str() );
+ assert( tick < 10 );
+ Id clock( 1 );
+ assert( clock.element() == m->e1() );
+ double dt = LookupField< unsigned int, double >::
+ get( clock, "tickDt", tick );
+ return dt;
}
*/
@@ -1027,7 +1027,7 @@ void Clock::buildDefaultTick()
defaultDt_[19] = 10; // For Streamer
// 20-29 are not assigned.
- defaultDt_[30] = 1; // For the HDF writer
+ defaultDt_[30] = 1; // For the HDF writer
defaultDt_[31] = 0.01; // For the postmaster.
}
diff --git a/shell/Shell.cpp b/shell/Shell.cpp
index e29b318a..775092c6 100644
--- a/shell/Shell.cpp
+++ b/shell/Shell.cpp
@@ -341,7 +341,7 @@ void Shell::doStart( double runtime, bool notify )
*-----------------------------------------------------------------------------*/
vector< ObjId > streamers;
wildcardFind( "/##[TYPE=Streamer]", streamers );
- LOG( moose::debug, "total streamers " << streamers.size( ) );
+ // LOG( moose::debug, "total streamers " << streamers.size( ) );
for( vector<ObjId>::const_iterator itr = streamers.begin()
; itr != streamers.end(); itr++ )
{
diff --git a/synapse/GraupnerBrunel2012CaPlasticitySynHandler.cpp b/synapse/GraupnerBrunel2012CaPlasticitySynHandler.cpp
index 835dc72b..7f78996d 100644
--- a/synapse/GraupnerBrunel2012CaPlasticitySynHandler.cpp
+++ b/synapse/GraupnerBrunel2012CaPlasticitySynHandler.cpp
@@ -7,22 +7,22 @@
** See the file COPYING.LIB for the full notice.
**********************************************************************/
-#include <queue>
-#include "header.h"
+#include "../basecode/header.h"
#include "Synapse.h"
#include "SynEvent.h" // only using the SynEvent class from this
#include "SynHandlerBase.h"
-#include "../randnum/Normal.h" // generate normal randum numbers for noisy weight update
#include "GraupnerBrunel2012CaPlasticitySynHandler.h"
+#include <queue>
+
const Cinfo* GraupnerBrunel2012CaPlasticitySynHandler::initCinfo()
{
- static string doc[] =
- {
- "Name", "GraupnerBrunel2012CaPlasticitySynHandler",
- "Author", "Aditya Gilra",
- "Description",
- "The GraupnerBrunel2012CaPlasticitySynHandler handles synapses"
+ static string doc[] =
+ {
+ "Name", "GraupnerBrunel2012CaPlasticitySynHandler",
+ "Author", "Aditya Gilra",
+ "Description",
+ "The GraupnerBrunel2012CaPlasticitySynHandler handles synapses"
"with Ca-based plasticity as per Higgins et al. 2014 and Graupner and Brunel 2012."
"Note 1:"
" Here, Ca ('chemical Ca') is updated only at each pre-spike, pre-spike+delayD and post-spike!"
@@ -43,8 +43,8 @@ const Cinfo* GraupnerBrunel2012CaPlasticitySynHandler::initCinfo()
" in its own electrical compartment (=spine),"
" only then can you have an 'electrical Ca'"
" corresponding to the 'chemical Ca'."
- "Three priority queues are used to manage pre, post, and pre+delayD spikes."
- };
+ "Three priority queues are used to manage pre, post, and pre+delayD spikes."
+ };
static ValueFinfo< GraupnerBrunel2012CaPlasticitySynHandler, double > Ca(
"Ca",
@@ -54,81 +54,81 @@ const Cinfo* GraupnerBrunel2012CaPlasticitySynHandler::initCinfo()
"when a pre- or post- spike has occured, or at time delayD after a pre-spike."
"Do not use it to control a Ca dependent current, etc."
"See notes in the class Description: all pre-synapses get updated via the same post-synaptic Ca.",
- &GraupnerBrunel2012CaPlasticitySynHandler::setCa,
- &GraupnerBrunel2012CaPlasticitySynHandler::getCa
+ &GraupnerBrunel2012CaPlasticitySynHandler::setCa,
+ &GraupnerBrunel2012CaPlasticitySynHandler::getCa
);
static ValueFinfo< GraupnerBrunel2012CaPlasticitySynHandler, double > CaInit(
"CaInit",
"CaInit is the initial value for Ca",
- &GraupnerBrunel2012CaPlasticitySynHandler::setCaInit,
- &GraupnerBrunel2012CaPlasticitySynHandler::getCaInit
+ &GraupnerBrunel2012CaPlasticitySynHandler::setCaInit,
+ &GraupnerBrunel2012CaPlasticitySynHandler::getCaInit
);
static ValueFinfo< GraupnerBrunel2012CaPlasticitySynHandler, double > tauCa(
"tauCa",
"tauCa is the time constant for decay of Ca",
- &GraupnerBrunel2012CaPlasticitySynHandler::setTauCa,
- &GraupnerBrunel2012CaPlasticitySynHandler::getTauCa
+ &GraupnerBrunel2012CaPlasticitySynHandler::setTauCa,
+ &GraupnerBrunel2012CaPlasticitySynHandler::getTauCa
);
static ValueFinfo< GraupnerBrunel2012CaPlasticitySynHandler, double > tauSyn(
"tauSyn",
"tauSyn is the time constant for synaptic weight evolution equation",
- &GraupnerBrunel2012CaPlasticitySynHandler::setTauSyn,
- &GraupnerBrunel2012CaPlasticitySynHandler::getTauSyn
+ &GraupnerBrunel2012CaPlasticitySynHandler::setTauSyn,
+ &GraupnerBrunel2012CaPlasticitySynHandler::getTauSyn
);
static ValueFinfo< GraupnerBrunel2012CaPlasticitySynHandler, double > CaPre(
"CaPre",
"CaPre is added to Ca on every pre-spike",
- &GraupnerBrunel2012CaPlasticitySynHandler::setCaPre,
- &GraupnerBrunel2012CaPlasticitySynHandler::getCaPre
+ &GraupnerBrunel2012CaPlasticitySynHandler::setCaPre,
+ &GraupnerBrunel2012CaPlasticitySynHandler::getCaPre
);
static ValueFinfo< GraupnerBrunel2012CaPlasticitySynHandler, double > CaPost(
"CaPost",
"CaPost is added to Ca on every post-spike",
- &GraupnerBrunel2012CaPlasticitySynHandler::setCaPost,
- &GraupnerBrunel2012CaPlasticitySynHandler::getCaPost
+ &GraupnerBrunel2012CaPlasticitySynHandler::setCaPost,
+ &GraupnerBrunel2012CaPlasticitySynHandler::getCaPost
);
static ValueFinfo< GraupnerBrunel2012CaPlasticitySynHandler, double > delayD(
"delayD",
"Time delay D after pre-spike, when Ca is increased by Capre."
" delayD represents NMDA rise time.",
- &GraupnerBrunel2012CaPlasticitySynHandler::setDelayD,
- &GraupnerBrunel2012CaPlasticitySynHandler::getDelayD
+ &GraupnerBrunel2012CaPlasticitySynHandler::setDelayD,
+ &GraupnerBrunel2012CaPlasticitySynHandler::getDelayD
);
static ValueFinfo< GraupnerBrunel2012CaPlasticitySynHandler, double > gammaP(
"gammaP",
"gammaP is the potentiation factor for synaptic weight increase if Ca>thetaP",
- &GraupnerBrunel2012CaPlasticitySynHandler::setGammaP,
- &GraupnerBrunel2012CaPlasticitySynHandler::getGammaP
+ &GraupnerBrunel2012CaPlasticitySynHandler::setGammaP,
+ &GraupnerBrunel2012CaPlasticitySynHandler::getGammaP
);
static ValueFinfo< GraupnerBrunel2012CaPlasticitySynHandler, double > gammaD(
"gammaD",
"gammaD is the depression factor for synaptic weight decrease if Ca>thetaD",
- &GraupnerBrunel2012CaPlasticitySynHandler::setGammaD,
- &GraupnerBrunel2012CaPlasticitySynHandler::getGammaD
+ &GraupnerBrunel2012CaPlasticitySynHandler::setGammaD,
+ &GraupnerBrunel2012CaPlasticitySynHandler::getGammaD
);
static ValueFinfo< GraupnerBrunel2012CaPlasticitySynHandler, double > thetaP(
"thetaP",
"Potentiation threshold for Ca"
"User must ensure thetaP>thetaD, else simulation results will be wrong.",
- &GraupnerBrunel2012CaPlasticitySynHandler::setThetaP,
- &GraupnerBrunel2012CaPlasticitySynHandler::getThetaP
+ &GraupnerBrunel2012CaPlasticitySynHandler::setThetaP,
+ &GraupnerBrunel2012CaPlasticitySynHandler::getThetaP
);
static ValueFinfo< GraupnerBrunel2012CaPlasticitySynHandler, double > thetaD(
"thetaD",
"Depression threshold for Ca"
"User must ensure thetaP>thetaD, else simulation results will be wrong.",
- &GraupnerBrunel2012CaPlasticitySynHandler::setThetaD,
- &GraupnerBrunel2012CaPlasticitySynHandler::getThetaD
+ &GraupnerBrunel2012CaPlasticitySynHandler::setThetaD,
+ &GraupnerBrunel2012CaPlasticitySynHandler::getThetaD
);
static ValueFinfo< GraupnerBrunel2012CaPlasticitySynHandler, bool > bistable(
@@ -136,36 +136,36 @@ const Cinfo* GraupnerBrunel2012CaPlasticitySynHandler::initCinfo()
"If true, the synapse is bistable as in GraupnerBrunel2012 paper."
"The effect of potential on the weight update is usually ignorable"
" if Ca is above thetaP and thetaD most of the time.",
- &GraupnerBrunel2012CaPlasticitySynHandler::setBistable,
- &GraupnerBrunel2012CaPlasticitySynHandler::getBistable
+ &GraupnerBrunel2012CaPlasticitySynHandler::setBistable,
+ &GraupnerBrunel2012CaPlasticitySynHandler::getBistable
);
static ValueFinfo< GraupnerBrunel2012CaPlasticitySynHandler, bool > noisy(
"noisy",
"If true, turn noise on as per noiseSD",
- &GraupnerBrunel2012CaPlasticitySynHandler::setNoisy,
- &GraupnerBrunel2012CaPlasticitySynHandler::getNoisy
+ &GraupnerBrunel2012CaPlasticitySynHandler::setNoisy,
+ &GraupnerBrunel2012CaPlasticitySynHandler::getNoisy
);
static ValueFinfo< GraupnerBrunel2012CaPlasticitySynHandler, double > noiseSD(
"noiseSD",
"Standard deviation of noise added to Ca",
- &GraupnerBrunel2012CaPlasticitySynHandler::setNoiseSD,
- &GraupnerBrunel2012CaPlasticitySynHandler::getNoiseSD
+ &GraupnerBrunel2012CaPlasticitySynHandler::setNoiseSD,
+ &GraupnerBrunel2012CaPlasticitySynHandler::getNoiseSD
);
static ValueFinfo< GraupnerBrunel2012CaPlasticitySynHandler, double > weightMax(
"weightMax",
"An upper bound on the weight",
- &GraupnerBrunel2012CaPlasticitySynHandler::setWeightMax,
- &GraupnerBrunel2012CaPlasticitySynHandler::getWeightMax
+ &GraupnerBrunel2012CaPlasticitySynHandler::setWeightMax,
+ &GraupnerBrunel2012CaPlasticitySynHandler::getWeightMax
);
static ValueFinfo< GraupnerBrunel2012CaPlasticitySynHandler, double > weightMin(
"weightMin",
"A lower bound on the weight",
- &GraupnerBrunel2012CaPlasticitySynHandler::setWeightMin,
- &GraupnerBrunel2012CaPlasticitySynHandler::getWeightMin
+ &GraupnerBrunel2012CaPlasticitySynHandler::setWeightMin,
+ &GraupnerBrunel2012CaPlasticitySynHandler::getWeightMin
);
static ValueFinfo< GraupnerBrunel2012CaPlasticitySynHandler, double > weightScale(
@@ -173,237 +173,281 @@ const Cinfo* GraupnerBrunel2012CaPlasticitySynHandler::initCinfo()
"Scale all pre-synaptic weights by weightScale before adding to activation (default 1.0)"
"In the terminology of the paper Higgins et al 2012, weight is synaptic efficacy,"
"while weightScale*weight is what finally is added to activation variable.",
- &GraupnerBrunel2012CaPlasticitySynHandler::setWeightScale,
- &GraupnerBrunel2012CaPlasticitySynHandler::getWeightScale
+ &GraupnerBrunel2012CaPlasticitySynHandler::setWeightScale,
+ &GraupnerBrunel2012CaPlasticitySynHandler::getWeightScale
);
- static DestFinfo addPostSpike( "addPostSpike",
+ static DestFinfo addPostSpike(
+ "addPostSpike",
"Handles arriving spike messages from post-synaptic neuron, inserts into postEvent queue.",
new EpFunc1< GraupnerBrunel2012CaPlasticitySynHandler, \
- double >( &GraupnerBrunel2012CaPlasticitySynHandler::addPostSpike ) );
-
- static FieldElementFinfo< SynHandlerBase, Synapse > synFinfo(
- "synapse",
- "Sets up field Elements for synapse",
- Synapse::initCinfo(),
- &SynHandlerBase::getSynapse,
- &SynHandlerBase::setNumSynapses,
- &SynHandlerBase::getNumSynapses
- );
-
- static Finfo* GraupnerBrunel2012CaPlasticitySynHandlerFinfos[] = {
- &synFinfo, // FieldElement
- &addPostSpike, // DestFinfo
- &Ca, // Field
- &CaInit, // Field
- &tauCa, // Field
- &tauSyn, // Field
- &CaPre, // Field
- &CaPost, // Field
- &delayD, // Field
- &thetaP, // Field
- &thetaD, // Field
- &gammaP, // Field
- &gammaD, // Field
- &weightMax, // Field
- &weightMin, // Field
- &weightScale, // Field
- &noisy, // Field
- &noiseSD, // Field
- &bistable // Field
- };
-
- static Dinfo< GraupnerBrunel2012CaPlasticitySynHandler > dinfo;
- static Cinfo synHandlerCinfo (
- "GraupnerBrunel2012CaPlasticitySynHandler",
- SynHandlerBase::initCinfo(),
- GraupnerBrunel2012CaPlasticitySynHandlerFinfos,
- sizeof( GraupnerBrunel2012CaPlasticitySynHandlerFinfos ) / sizeof ( Finfo* ),
- &dinfo,
- doc,
- sizeof( doc ) / sizeof( string )
- );
-
- return &synHandlerCinfo;
+ double >( &GraupnerBrunel2012CaPlasticitySynHandler::addPostSpike ) );
+
+ static FieldElementFinfo< SynHandlerBase, Synapse > synFinfo(
+ "synapse",
+ "Sets up field Elements for synapse",
+ Synapse::initCinfo(),
+ &SynHandlerBase::getSynapse,
+ &SynHandlerBase::setNumSynapses,
+ &SynHandlerBase::getNumSynapses
+ );
+
+ static Finfo* GraupnerBrunel2012CaPlasticitySynHandlerFinfos[] =
+ {
+ &synFinfo, // FieldElement
+ &addPostSpike, // DestFinfo
+ &Ca, // Field
+ &CaInit, // Field
+ &tauCa, // Field
+ &tauSyn, // Field
+ &CaPre, // Field
+ &CaPost, // Field
+ &delayD, // Field
+ &thetaP, // Field
+ &thetaD, // Field
+ &gammaP, // Field
+ &gammaD, // Field
+ &weightMax, // Field
+ &weightMin, // Field
+ &weightScale, // Field
+ &noisy, // Field
+ &noiseSD, // Field
+ &bistable // Field
+ };
+
+ static Dinfo< GraupnerBrunel2012CaPlasticitySynHandler > dinfo;
+ static Cinfo synHandlerCinfo (
+ "GraupnerBrunel2012CaPlasticitySynHandler",
+ SynHandlerBase::initCinfo(),
+ GraupnerBrunel2012CaPlasticitySynHandlerFinfos,
+ sizeof( GraupnerBrunel2012CaPlasticitySynHandlerFinfos ) / sizeof ( Finfo* ),
+ &dinfo,
+ doc,
+ sizeof( doc ) / sizeof( string )
+ );
+
+ return &synHandlerCinfo;
}
static const Cinfo* GraupnerBrunel2012CaPlasticitySynHandlerCinfo =\
- GraupnerBrunel2012CaPlasticitySynHandler::initCinfo();
+ GraupnerBrunel2012CaPlasticitySynHandler::initCinfo();
GraupnerBrunel2012CaPlasticitySynHandler::GraupnerBrunel2012CaPlasticitySynHandler()
{
- Ca_ = 0.0;
- CaInit_ = 0.0;
- tauCa_ = 1.0;
- tauSyn_ = 1.0;
- CaPre_ = 0.0;
- CaPost_ = 0.0;
- thetaD_ = 0.0;
- thetaP_ = 0.0;
- gammaD_ = 0.0;
- gammaP_ = 0.0;
- delayD_ = 0.0;
- weightMin_ = 0.0;
- weightMax_ = 0.0;
+ Ca_ = 0.0;
+ CaInit_ = 0.0;
+ tauCa_ = 1.0;
+ tauSyn_ = 1.0;
+ CaPre_ = 0.0;
+ CaPost_ = 0.0;
+ thetaD_ = 0.0;
+ thetaP_ = 0.0;
+ gammaD_ = 0.0;
+ gammaP_ = 0.0;
+ delayD_ = 0.0;
+ weightMin_ = 0.0;
+ weightMax_ = 0.0;
weightScale_ = 1.0;
- noisy_ = false;
- noiseSD_ = 0.0;
- bistable_ = true;
- normalGenerator_.setMethod(BOX_MUELLER); // the default ALIAS method is 1000x slower!
+ noisy_ = false;
+ noiseSD_ = 0.0;
+ bistable_ = true;
+ seed_ = 0;
+ dist_ = moose::MOOSE_NORMAL_DISTRIBUTION<double>{0, 1};
+ reinitSeed();
+
+ // std::cout << " Mean " << dist_.mean() << " std " << dist_.stddev() << std::endl;
}
GraupnerBrunel2012CaPlasticitySynHandler::~GraupnerBrunel2012CaPlasticitySynHandler()
-{ ; }
+{
+}
+
+void GraupnerBrunel2012CaPlasticitySynHandler::reinitSeed( void )
+{
+ if( 0 == seed_ )
+ seed_ = moose::getGlobalSeed();
+
+ if( 0 == seed_ )
+ seed_ = rd_();
+
+ MOOSE_DEBUG( "Seed is set to " << seed_ );
+ rng_.seed( seed_ );
+}
-GraupnerBrunel2012CaPlasticitySynHandler& GraupnerBrunel2012CaPlasticitySynHandler::operator=\
- ( const GraupnerBrunel2012CaPlasticitySynHandler& ssh)
+GraupnerBrunel2012CaPlasticitySynHandler&
+ GraupnerBrunel2012CaPlasticitySynHandler::operator=(
+ const GraupnerBrunel2012CaPlasticitySynHandler& ssh
+ )
{
- synapses_ = ssh.synapses_;
- for ( vector< Synapse >::iterator
- i = synapses_.begin(); i != synapses_.end(); ++i )
- i->setHandler( this );
+ synapses_ = ssh.synapses_;
+ for ( vector< Synapse >::iterator
+ i = synapses_.begin(); i != synapses_.end(); ++i )
+ i->setHandler( this );
- // For no apparent reason, priority queues don't have a clear operation.
- while( !events_.empty() )
- events_.pop();
- while( !delayDPreEvents_.empty() )
- events_.pop();
- while( !postEvents_.empty() )
- postEvents_.pop();
+ // For no apparent reason, priority queues don't have a clear operation.
+ while( !events_.empty() )
+ events_.pop();
+ while( !delayDPreEvents_.empty() )
+ events_.pop();
+ while( !postEvents_.empty() )
+ postEvents_.pop();
- return *this;
+ return *this;
}
void GraupnerBrunel2012CaPlasticitySynHandler::vSetNumSynapses( const unsigned int v )
{
- unsigned int prevSize = synapses_.size();
- synapses_.resize( v );
- for ( unsigned int i = prevSize; i < v; ++i )
- synapses_[i].setHandler( this );
+ unsigned int prevSize = synapses_.size();
+ synapses_.resize( v );
+ for ( unsigned int i = prevSize; i < v; ++i )
+ synapses_[i].setHandler( this );
}
unsigned int GraupnerBrunel2012CaPlasticitySynHandler::vGetNumSynapses() const
{
- return synapses_.size();
+ return synapses_.size();
}
Synapse* GraupnerBrunel2012CaPlasticitySynHandler::vGetSynapse( unsigned int i )
{
- static Synapse dummy;
- if ( i < synapses_.size() )
- return &synapses_[i];
- cout << "Warning: GraupnerBrunel2012CaPlasticitySynHandler::getSynapse: index: " << i <<
- " is out of range: " << synapses_.size() << endl;
- return &dummy;
+ static Synapse dummy;
+ if ( i < synapses_.size() )
+ return &synapses_[i];
+ cout << "Warning: GraupnerBrunel2012CaPlasticitySynHandler::getSynapse: index: " << i <<
+ " is out of range: " << synapses_.size() << endl;
+ return &dummy;
}
void GraupnerBrunel2012CaPlasticitySynHandler::addSpike(
- unsigned int index, double time, double weight )
+ unsigned int index, double time, double weight )
{
- assert( index < synapses_.size() );
- events_.push( PreSynEvent( index, time, weight ) );
- delayDPreEvents_.push( PreSynEvent( index, time+delayD_, weight ) );
+ assert( index < synapses_.size() );
+ events_.push( PreSynEvent( index, time, weight ) );
+ delayDPreEvents_.push( PreSynEvent( index, time+delayD_, weight ) );
}
-double GraupnerBrunel2012CaPlasticitySynHandler::getTopSpike(
- unsigned int index ) const
+double GraupnerBrunel2012CaPlasticitySynHandler::getTopSpike(
+ unsigned int index ) const
{
- if ( events_.empty() )
- return 0.0;
- return events_.top().time;
+ if ( events_.empty() )
+ return 0.0;
+ return events_.top().time;
}
void GraupnerBrunel2012CaPlasticitySynHandler::addPostSpike( const Eref& e, double time )
{
- postEvents_.push( PostSynEvent( time ) );
+ postEvents_.push( PostSynEvent( time ) );
}
weightFactors GraupnerBrunel2012CaPlasticitySynHandler::updateCaWeightFactors( double currTime )
{
- double CaOld = Ca_;
- double deltaT = currTime-lastCaUpdateTime_;
- // Update Ca, but CaPre and CaPost are added in vProcess()
- Ca_ *= exp(-deltaT/tauCa_);
- lastCaUpdateTime_ = currTime;
- weightFactors wUp; // by default all are set to 0.0
-
- // calculate/approximate time spent above potentiation and depression thresholds
- // see pg 13 of Higgins et al | October 2014 | Volume 10 | Issue 10 | e1003834 | PLOS Comp Biol
- // starting from bottom condition, going upwards in the algorithm given in above paper
- if (CaOld <= thetaD_) {
- } else if (CaOld <= thetaP_) {
- //cout << "tD<Caold<tP" << "\n";
- if (Ca_ <= thetaD_) {
- wUp.tD = tauCa_*log(CaOld/thetaD_);
- //cout << "Ca<tD" << "\n";
- } else {
- wUp.tD = deltaT;
- //cout << "Ca>tD" << "\n";
- }
- } else {
- //cout << "Caold>tP" << "\n";
- if (Ca_ <= thetaD_) {
- wUp.tP = tauCa_*log(CaOld/thetaP_);
- wUp.tD = tauCa_*log(thetaP_/thetaD_);
- //cout << "Ca<tD" << "\n";
- //cout << "Caold = " << CaOld << "thetaP = " << thetaP_ << "\n";
- } else if (Ca_ <= thetaP_) {
- wUp.tP = tauCa_*log(CaOld/thetaP_);
- wUp.tD = deltaT - wUp.tP;
- //cout << "Ca<tP" << "\n";
- } else {
- wUp.tP = deltaT;
- //cout << "Ca>tP" << "\n";
- }
+ double CaOld = Ca_;
+ double deltaT = currTime-lastCaUpdateTime_;
+ // Update Ca, but CaPre and CaPost are added in vProcess()
+ Ca_ *= exp(-deltaT/tauCa_);
+ lastCaUpdateTime_ = currTime;
+ weightFactors wUp; // by default all are set to 0.0
+
+ // calculate/approximate time spent above potentiation and depression thresholds
+ // see pg 13 of Higgins et al | October 2014 | Volume 10 | Issue 10 | e1003834 | PLOS Comp Biol
+ // starting from bottom condition, going upwards in the algorithm given in above paper
+ if (CaOld <= thetaD_)
+ {
+ }
+ else if (CaOld <= thetaP_)
+ {
+ //cout << "tD<Caold<tP" << "\n";
+ if (Ca_ <= thetaD_)
+ {
+ wUp.tD = tauCa_*log(CaOld/thetaD_);
+ //cout << "Ca<tD" << "\n";
+ }
+ else
+ {
+ wUp.tD = deltaT;
+ //cout << "Ca>tD" << "\n";
+ }
+ }
+ else
+ {
+ //cout << "Caold>tP" << "\n";
+ if (Ca_ <= thetaD_)
+ {
+ wUp.tP = tauCa_*log(CaOld/thetaP_);
+ wUp.tD = tauCa_*log(thetaP_/thetaD_);
+ //cout << "Ca<tD" << "\n";
+ //cout << "Caold = " << CaOld << "thetaP = " << thetaP_ << "\n";
+ }
+ else if (Ca_ <= thetaP_)
+ {
+ wUp.tP = tauCa_*log(CaOld/thetaP_);
+ wUp.tD = deltaT - wUp.tP;
+ //cout << "Ca<tP" << "\n";
+ }
+ else
+ {
+ wUp.tP = deltaT;
+ //cout << "Ca>tP" << "\n";
+ }
+ }
+ wUp.t0 = deltaT - wUp.tP - wUp.tD;
+
+ // Depending on tP and tD, I return A,B,C factors for weight update
+ // (see page 13 of Higgins et al 2014).
+ // A,B,C,D,E are used to compute the weight change for one or multiple synapses
+ // A is weight independent, B,D are weight dependent and C,E are accumulated noise
+ if (wUp.tP > 0)
+ {
+ double gPgD = gammaP_+gammaD_;
+ wUp.A = gammaP_/gPgD*(1.0-exp(-wUp.tP*gPgD/tauSyn_));
+ wUp.B = exp(-wUp.tP*gPgD/tauSyn_);
+ if (noisy_)
+ {
+ wUp.C = noiseSD_ * dist_(rng_) *
+ sqrt( ( 1.0-exp(-2*gPgD*wUp.tP/tauSyn_) ) / gPgD );
+ // cout << " A = " << wUp.A << " B = " << wUp.B << " C = " << wUp.C << "\n";
}
- wUp.t0 = deltaT - wUp.tP - wUp.tD;
-
- // Depending on tP and tD, I return A,B,C factors for weight update
- // (see page 13 of Higgins et al 2014).
- // A,B,C,D,E are used to compute the weight change for one or multiple synapses
- // A is weight independent, B,D are weight dependent and C,E are accumulated noise
- if (wUp.tP > 0) {
- double gPgD = gammaP_+gammaD_;
- wUp.A = gammaP_/gPgD*(1.0-exp(-wUp.tP*gPgD/tauSyn_));
- wUp.B = exp(-wUp.tP*gPgD/tauSyn_);
- if (noisy_) {
- wUp.C = noiseSD_ * normalGenerator_.getNextSample() *
- sqrt( ( 1.0-exp(-2*gPgD*wUp.tP/tauSyn_) ) / gPgD );
- //cout << "A = " << wUp.A << " B = " << wUp.B << " C = " << wUp.C << "\n";
- } else {
- wUp.C = 0.0;
- }
+ else
+ {
+ wUp.C = 0.0;
}
+ }
- if (wUp.tD > 0) {
- wUp.D = exp(-wUp.tD*gammaD_/tauSyn_);
- if (noisy_) {
- wUp.E = noiseSD_ * normalGenerator_.getNextSample() *
- sqrt( ( 1.0-exp(-2*gammaD_*wUp.tD/tauSyn_) ) / 2.0/gammaD_ );
- //cout << "D = " << wUp.D << " E = " << wUp.E << "\n";
- } else{
- wUp.E = 0.0;
- }
+ if (wUp.tD > 0)
+ {
+ wUp.D = exp(-wUp.tD*gammaD_/tauSyn_);
+ if (noisy_)
+ {
+ wUp.E = noiseSD_ * dist_( rng_ ) *
+ sqrt( ( 1.0-exp(-2*gammaD_*wUp.tD/tauSyn_) ) / 2.0/gammaD_ );
+ //cout << "D = " << wUp.D << " E = " << wUp.E << "\n";
+ }
+ else
+ {
+ wUp.E = 0.0;
}
+ }
- //cout << currTime << " tD = " << wUp.tD << " tP = " << wUp.tP << "\n";
- // tP, tD, A, B, C, D, E of wUp
- // are set to 0.0 by default in struct constructor
- return wUp; // return by value, i.e. copies the struct, so wUp going out of scope doesn't matter
- // malloc and returning pointer is more expensive for small structs
- // see: http://stackoverflow.com/questions/9590827/is-it-safe-to-return-a-struct-in-c-c
+ //cout << currTime << " tD = " << wUp.tD << " tP = " << wUp.tP << "\n";
+ // tP, tD, A, B, C, D, E of wUp
+ // are set to 0.0 by default in struct constructor
+ return wUp; // return by value, i.e. copies the struct, so wUp going out of scope doesn't matter
+ // malloc and returning pointer is more expensive for small structs
+ // see: http://stackoverflow.com/questions/9590827/is-it-safe-to-return-a-struct-in-c-c
}
void GraupnerBrunel2012CaPlasticitySynHandler::updateWeight( Synapse* synPtr, weightFactors *wFacPtr )
{
double newWeight = synPtr->getWeight();
//cout << " oldweight = " << newWeight << "\n";
- if (wFacPtr->tP > 0.0) {
+ if (wFacPtr->tP > 0.0)
+ {
newWeight = wFacPtr->A + wFacPtr->B*newWeight + wFacPtr->C;
//cout << " midweight = " << newWeight << "\n";
}
- if (wFacPtr->tD > 0.0) {
+ if (wFacPtr->tD > 0.0)
+ {
newWeight = wFacPtr->D*newWeight + wFacPtr->E; // update the weight again
//cout << " newweight = " << newWeight << "\n";
}
@@ -411,12 +455,16 @@ void GraupnerBrunel2012CaPlasticitySynHandler::updateWeight( Synapse* synPtr, we
// potential is usually ignorable when t0 is small,
// i.e. Ca is mostly above thetaD or thetaP
//cout << "before bistable newWeight = " << newWeight << "\n";
- if (bistable_) {
+ if (bistable_)
+ {
double chi0 = pow((newWeight-0.5),2.0) / (newWeight*(newWeight-1));
double weightDeviation = 0.5*sqrt( 1.0 + 1.0/(chi0*exp(wFacPtr->t0/2.0/tauSyn_)-1.0) );
- if (newWeight<0.5) {
+ if (newWeight<0.5)
+ {
newWeight = 0.5 - weightDeviation;
- } else {
+ }
+ else
+ {
newWeight = 0.5 + weightDeviation;
}
}
@@ -432,18 +480,19 @@ void GraupnerBrunel2012CaPlasticitySynHandler::updateWeight( Synapse* synPtr, we
void GraupnerBrunel2012CaPlasticitySynHandler::vProcess( const Eref& e, ProcPtr p )
{
- double activation = 0.0;
+ double activation = 0.0;
double currTime = p->currTime;
bool CaFactorsUpdated = false; // Ca-decay and weight Factors updation is done only once
- // if any pre-spike, pre-spike+delayD or post-spike occurs
- // Ca is bumped by CaPre and CaPost on
- // pre-spike+delayD and post-spike respectively
- // At the end, if any event above occurred,
- // change all pre-synaptic weights based on Ca
+ // if any pre-spike, pre-spike+delayD or post-spike occurs
+ // Ca is bumped by CaPre and CaPost on
+ // pre-spike+delayD and post-spike respectively
+ // At the end, if any event above occurred,
+ // change all pre-synaptic weights based on Ca
weightFactors wFacs;
// process pre-synaptic spike events for activation, Ca and weight update
- while( !events_.empty() && events_.top().time <= currTime ) {
+ while( !events_.empty() && events_.top().time <= currTime )
+ {
PreSynEvent currEvent = events_.top();
unsigned int synIndex = currEvent.synIndex;
@@ -472,56 +521,63 @@ void GraupnerBrunel2012CaPlasticitySynHandler::vProcess( const Eref& e, ProcPtr
// need to send it divided by dt.
// Can connect activation to SynChan (double exp)
// or to LIF as an impulse to voltage.
- //activation += currEvent.weight * weightScale_ / p->dt;
+ //activation += currEvent.weight * weightScale_ / p->dt;
activation += currSynPtr->getWeight() * weightScale_ / p->dt;
// update only once for this time-step if an event occurs
- if (!CaFactorsUpdated) {
+ if (!CaFactorsUpdated)
+ {
// update Ca and weightFactors
wFacs = updateCaWeightFactors( currTime );
CaFactorsUpdated = true;
}
- events_.pop();
- }
- if ( activation != 0.0 )
- SynHandlerBase::activationOut()->send( e, activation );
+ events_.pop();
+ }
+ if ( activation != 0.0 )
+ SynHandlerBase::activationOut()->send( e, activation );
// process delayed pre-synaptic spike events for Ca and weight update
// delayD after pre-spike accounts for NMDA rise time
- while( !delayDPreEvents_.empty() && delayDPreEvents_.top().time <= currTime ) {
+ while( !delayDPreEvents_.empty() && delayDPreEvents_.top().time <= currTime )
+ {
// Update Ca, and add CaPre
// update only once for this time-step if an event occurs
- if (!CaFactorsUpdated) {
+ if (!CaFactorsUpdated)
+ {
// update Ca and weightFactors
wFacs = updateCaWeightFactors( currTime );
CaFactorsUpdated = true;
}
Ca_ += CaPre_;
- delayDPreEvents_.pop();
- }
+ delayDPreEvents_.pop();
+ }
// process post-synaptic spike events for Ca and weight update
- while( !postEvents_.empty() && postEvents_.top().time <= currTime ) {
+ while( !postEvents_.empty() && postEvents_.top().time <= currTime )
+ {
// update Ca, then add CaPost
// update only once for this time-step if an event occurs
- if (!CaFactorsUpdated) {
+ if (!CaFactorsUpdated)
+ {
// update Ca and weightFactors
wFacs = updateCaWeightFactors( currTime );
CaFactorsUpdated = true;
}
Ca_ += CaPost_;
- postEvents_.pop();
- }
+ postEvents_.pop();
+ }
// If any event has happened, update all pre-synaptic weights
// If you want individual Ca for each pre-synapse
// create individual SynHandlers for each
- if (CaFactorsUpdated) {
+ if (CaFactorsUpdated)
+ {
// Change weight of all synapses
- for (unsigned int i=0; i<synapses_.size(); i++) {
+ for (unsigned int i=0; i<synapses_.size(); i++)
+ {
// Warning, coder! 'Synapse currSyn = synapses_[i];' is wrong,
// it creates a new, shallow-copied object.
// We want only to point to the same object.
@@ -534,199 +590,199 @@ void GraupnerBrunel2012CaPlasticitySynHandler::vProcess( const Eref& e, ProcPtr
void GraupnerBrunel2012CaPlasticitySynHandler::vReinit( const Eref& e, ProcPtr p )
{
- // For no apparent reason, priority queues don't have a clear operation.
- while( !events_.empty() )
- events_.pop();
- while( !delayDPreEvents_.empty() )
- events_.pop();
- while( !postEvents_.empty() )
- postEvents_.pop();
+ // For no apparent reason, priority queues don't have a clear operation.
+ while( !events_.empty() )
+ events_.pop();
+ while( !delayDPreEvents_.empty() )
+ events_.pop();
+ while( !postEvents_.empty() )
+ postEvents_.pop();
Ca_ = CaInit_;
}
unsigned int GraupnerBrunel2012CaPlasticitySynHandler::addSynapse()
{
- unsigned int newSynIndex = synapses_.size();
- synapses_.resize( newSynIndex + 1 );
- synapses_[newSynIndex].setHandler( this );
- return newSynIndex;
+ unsigned int newSynIndex = synapses_.size();
+ synapses_.resize( newSynIndex + 1 );
+ synapses_[newSynIndex].setHandler( this );
+ return newSynIndex;
}
void GraupnerBrunel2012CaPlasticitySynHandler::dropSynapse( unsigned int msgLookup )
{
- assert( msgLookup < synapses_.size() );
- synapses_[msgLookup].setWeight( -1.0 );
+ assert( msgLookup < synapses_.size() );
+ synapses_[msgLookup].setWeight( -1.0 );
}
void GraupnerBrunel2012CaPlasticitySynHandler::setCa( const double v )
{
- Ca_ = v;
+ Ca_ = v;
}
double GraupnerBrunel2012CaPlasticitySynHandler::getCa() const
{
- return Ca_;
+ return Ca_;
}
void GraupnerBrunel2012CaPlasticitySynHandler::setCaInit( const double v )
{
- CaInit_ = v;
+ CaInit_ = v;
}
double GraupnerBrunel2012CaPlasticitySynHandler::getCaInit() const
{
- return CaInit_;
+ return CaInit_;
}
void GraupnerBrunel2012CaPlasticitySynHandler::setCaPre( const double v )
{
- CaPre_ = v;
+ CaPre_ = v;
}
double GraupnerBrunel2012CaPlasticitySynHandler::getCaPre() const
{
- return CaPre_;
+ return CaPre_;
}
void GraupnerBrunel2012CaPlasticitySynHandler::setCaPost( const double v )
{
- CaPost_ = v;
+ CaPost_ = v;
}
double GraupnerBrunel2012CaPlasticitySynHandler::getCaPost() const
{
- return CaPost_;
+ return CaPost_;
}
void GraupnerBrunel2012CaPlasticitySynHandler::setThetaP( const double v )
{
- thetaP_ = v;
+ thetaP_ = v;
}
double GraupnerBrunel2012CaPlasticitySynHandler::getThetaP() const
{
- return thetaP_;
+ return thetaP_;
}
void GraupnerBrunel2012CaPlasticitySynHandler::setThetaD( const double v )
{
- thetaD_ = v;
+ thetaD_ = v;
}
double GraupnerBrunel2012CaPlasticitySynHandler::getThetaD() const
{
- return thetaD_;
+ return thetaD_;
}
void GraupnerBrunel2012CaPlasticitySynHandler::setGammaD( const double v )
{
- gammaD_ = v;
+ gammaD_ = v;
}
double GraupnerBrunel2012CaPlasticitySynHandler::getGammaD() const
{
- return gammaD_;
+ return gammaD_;
}
void GraupnerBrunel2012CaPlasticitySynHandler::setGammaP( const double v )
{
- gammaP_ = v;
+ gammaP_ = v;
}
double GraupnerBrunel2012CaPlasticitySynHandler::getGammaP() const
{
- return gammaP_;
+ return gammaP_;
}
void GraupnerBrunel2012CaPlasticitySynHandler::setDelayD( const double v )
{
- delayD_ = v;
+ delayD_ = v;
}
double GraupnerBrunel2012CaPlasticitySynHandler::getDelayD() const
{
- return delayD_;
+ return delayD_;
}
void GraupnerBrunel2012CaPlasticitySynHandler::setTauCa( const double v )
{
- if ( rangeWarning( "tauCa", v ) ) return;
- tauCa_ = v;
+ if ( rangeWarning( "tauCa", v ) ) return;
+ tauCa_ = v;
}
double GraupnerBrunel2012CaPlasticitySynHandler::getTauCa() const
{
- return tauCa_;
+ return tauCa_;
}
void GraupnerBrunel2012CaPlasticitySynHandler::setTauSyn( const double v )
{
- if ( rangeWarning( "tauSyn", v ) ) return;
- tauSyn_ = v;
+ if ( rangeWarning( "tauSyn", v ) ) return;
+ tauSyn_ = v;
}
double GraupnerBrunel2012CaPlasticitySynHandler::getTauSyn() const
{
- return tauSyn_;
+ return tauSyn_;
}
void GraupnerBrunel2012CaPlasticitySynHandler::setNoisy( const bool v )
{
- noisy_ = v;
+ noisy_ = v;
}
bool GraupnerBrunel2012CaPlasticitySynHandler::getNoisy() const
{
- return noisy_;
+ return noisy_;
}
void GraupnerBrunel2012CaPlasticitySynHandler::setNoiseSD( const double v )
{
- noiseSD_ = v;
+ noiseSD_ = v;
}
double GraupnerBrunel2012CaPlasticitySynHandler::getNoiseSD() const
{
- return noiseSD_;
+ return noiseSD_;
}
void GraupnerBrunel2012CaPlasticitySynHandler::setBistable( const bool v )
{
- bistable_ = v;
+ bistable_ = v;
}
bool GraupnerBrunel2012CaPlasticitySynHandler::getBistable() const
{
- return bistable_;
+ return bistable_;
}
void GraupnerBrunel2012CaPlasticitySynHandler::setWeightMax( const double v )
{
- weightMax_ = v;
+ weightMax_ = v;
}
double GraupnerBrunel2012CaPlasticitySynHandler::getWeightMax() const
{
- return weightMax_;
+ return weightMax_;
}
void GraupnerBrunel2012CaPlasticitySynHandler::setWeightMin( const double v )
{
- weightMin_ = v;
+ weightMin_ = v;
}
double GraupnerBrunel2012CaPlasticitySynHandler::getWeightMin() const
{
- return weightMin_;
+ return weightMin_;
}
void GraupnerBrunel2012CaPlasticitySynHandler::setWeightScale( const double v )
{
- weightScale_ = v;
+ weightScale_ = v;
}
double GraupnerBrunel2012CaPlasticitySynHandler::getWeightScale() const
{
- return weightScale_;
+ return weightScale_;
}
diff --git a/synapse/GraupnerBrunel2012CaPlasticitySynHandler.h b/synapse/GraupnerBrunel2012CaPlasticitySynHandler.h
index f7888602..936d9e10 100644
--- a/synapse/GraupnerBrunel2012CaPlasticitySynHandler.h
+++ b/synapse/GraupnerBrunel2012CaPlasticitySynHandler.h
@@ -10,55 +10,20 @@
#ifndef _GRAUPNER_BRUNEL_2012_CA_PLASTICITY_SYN_HANDLER_H
#define _GRAUPNER_BRUNEL_2012_CA_PLASTICITY_SYN_HANDLER_H
-/*
-class PreSynEvent: public SynEvent
-{
- public:
- PreSynEvent()
- : SynEvent(), // call the parent constructor with default args
- // by default calls without args, so no need really
- synIndex( 0 )
- {}
-
- PreSynEvent( unsigned int i, double t, double w )
- : SynEvent(t,w),// call the parent constructor with given args
- synIndex( i )
- {;}
-
- unsigned int synIndex;
-};
-
-class PostSynEvent
-{
- public:
- PostSynEvent()
- : time( 0.0 )
- {;}
-
- PostSynEvent( double t )
- : time( t )
- {;}
+#include "../basecode/global.h"
+#include "../randnum/RNG.h"
- double time;
-};
+#include <queue>
-struct ComparePostSynEvent
-{
- bool operator()(const PostSynEvent& lhs, const PostSynEvent& rhs) const
- {
- // Note that this is backwards. We want the smallest timestamp
- // on the top of the events priority_queue.
- return lhs.time > rhs.time;
- }
-};
-*/
+using namespace std;
// see pg 13 of Higgins et al | October 2014 | Volume 10 | Issue 10 | e1003834 | PLOS Comp Biol
// tP and tD are times spent above potentiation and depression thresholds
// Depending on tP and tD, I return A,B,C factors for weight update (see pg 13 ref above)
// A,B,C are used to compute the weight change for one or multiple synapses
// A is weight independent, B,D are weight dependent and C,E are accumulated noise
-struct weightFactors {
+struct weightFactors
+{
weightFactors() : tP(0.0), tD(0.0), A(0.0), B(0.0), C(0.0), D(0.0), E(0.0) {};
double tP; // time spent above potentiation threshold (thetaP) between two events
double tD; // time spent between depression and potentiation thresholds between two events
@@ -77,94 +42,106 @@ struct weightFactors {
*/
class GraupnerBrunel2012CaPlasticitySynHandler: public SynHandlerBase
{
- public:
- GraupnerBrunel2012CaPlasticitySynHandler();
- ~GraupnerBrunel2012CaPlasticitySynHandler();
- GraupnerBrunel2012CaPlasticitySynHandler& operator \
- = ( const GraupnerBrunel2012CaPlasticitySynHandler& other );
-
- ////////////////////////////////////////////////////////////////
- // Inherited virtual functions from SynHandlerBase
- ////////////////////////////////////////////////////////////////
- void vSetNumSynapses( unsigned int num );
- unsigned int vGetNumSynapses() const;
- Synapse* vGetSynapse( unsigned int i );
- void vProcess( const Eref& e, ProcPtr p );
- void vReinit( const Eref& e, ProcPtr p );
- /// Adds a new synapse, returns its index.
- unsigned int addSynapse();
- void dropSynapse( unsigned int droppedSynNumber );
- void addSpike( unsigned int index, double time, double weight );
- double getTopSpike( unsigned int index ) const;
- ////////////////////////////////////////////////////////////////
- void addPostSpike( const Eref& e, double time );
-
- void setCa( double v );
- double getCa() const;
- void setCaInit( double v );
- double getCaInit() const;
- void setTauCa( double v );
- double getTauCa() const;
- void setTauSyn( double v );
- double getTauSyn() const;
- void setNoiseSD( double v );
- double getNoiseSD() const;
- void setNoisy( bool v );
- bool getNoisy() const;
- void setBistable( bool v );
- bool getBistable() const;
-
- void setCaPre( double v );
- double getCaPre() const;
- void setCaPost( double v );
- double getCaPost() const;
- void setDelayD( double v );
- double getDelayD() const;
-
- void setThetaD( double v );
- double getThetaD() const;
- void setThetaP( double v );
- double getThetaP() const;
- void setGammaD( double v );
- double getGammaD() const;
- void setGammaP( double v );
- double getGammaP() const;
-
- void setWeightMax( double v );
- double getWeightMax() const;
- void setWeightMin( double v );
- double getWeightMin() const;
- void setWeightScale( double v );
- double getWeightScale() const;
-
- weightFactors updateCaWeightFactors( double currTime );
- void updateWeight( Synapse* synPtr, weightFactors *wFacPtr );
-
- static const Cinfo* initCinfo();
- private:
- vector< Synapse > synapses_;
- priority_queue< PreSynEvent, vector< PreSynEvent >, CompareSynEvent > events_;
- priority_queue< PreSynEvent, vector< PreSynEvent >, CompareSynEvent > delayDPreEvents_;
- priority_queue< PostSynEvent, vector< PostSynEvent >, ComparePostSynEvent > postEvents_;
- double Ca_;
- double CaInit_;
- double tauCa_;
- double tauSyn_;
- double CaPre_;
- double CaPost_;
- double delayD_;
- bool noisy_;
- double noiseSD_;
- bool bistable_;
- double thetaD_;
- double thetaP_;
- double gammaD_;
- double gammaP_;
- double weightMax_;
- double weightMin_;
- double weightScale_;
- double lastCaUpdateTime_;
- Normal normalGenerator_;
+public:
+ GraupnerBrunel2012CaPlasticitySynHandler();
+ ~GraupnerBrunel2012CaPlasticitySynHandler();
+ GraupnerBrunel2012CaPlasticitySynHandler& operator=(
+ const GraupnerBrunel2012CaPlasticitySynHandler& other );
+
+ ////////////////////////////////////////////////////////////////
+ // Inherited virtual functions from SynHandlerBase
+ ////////////////////////////////////////////////////////////////
+ void vSetNumSynapses( unsigned int num );
+ unsigned int vGetNumSynapses() const;
+ Synapse* vGetSynapse( unsigned int i );
+ void vProcess( const Eref& e, ProcPtr p );
+ void vReinit( const Eref& e, ProcPtr p );
+ /// Adds a new synapse, returns its index.
+ unsigned int addSynapse();
+ void dropSynapse( unsigned int droppedSynNumber );
+ void addSpike( unsigned int index, double time, double weight );
+ double getTopSpike( unsigned int index ) const;
+ ////////////////////////////////////////////////////////////////
+ void addPostSpike( const Eref& e, double time );
+
+ void setCa( double v );
+ double getCa() const;
+ void setCaInit( double v );
+ double getCaInit() const;
+ void setTauCa( double v );
+ double getTauCa() const;
+ void setTauSyn( double v );
+ double getTauSyn() const;
+ void setNoiseSD( double v );
+ double getNoiseSD() const;
+ void setNoisy( bool v );
+ bool getNoisy() const;
+ void setBistable( bool v );
+ bool getBistable() const;
+
+ void setCaPre( double v );
+ double getCaPre() const;
+ void setCaPost( double v );
+ double getCaPost() const;
+ void setDelayD( double v );
+ double getDelayD() const;
+
+ void setThetaD( double v );
+ double getThetaD() const;
+ void setThetaP( double v );
+ double getThetaP() const;
+ void setGammaD( double v );
+ double getGammaD() const;
+ void setGammaP( double v );
+ double getGammaP() const;
+
+ void setWeightMax( double v );
+ double getWeightMax() const;
+ void setWeightMin( double v );
+ double getWeightMin() const;
+ void setWeightScale( double v );
+ double getWeightScale() const;
+
+ weightFactors updateCaWeightFactors( double currTime );
+ void updateWeight( Synapse* synPtr, weightFactors *wFacPtr );
+
+ void reinitSeed( );
+
+ static const Cinfo* initCinfo();
+
+private:
+
+ vector< Synapse > synapses_;
+
+ priority_queue< PreSynEvent, vector< PreSynEvent >, CompareSynEvent > events_;
+ priority_queue< PreSynEvent, vector< PreSynEvent >, CompareSynEvent > delayDPreEvents_;
+ priority_queue< PostSynEvent, vector< PostSynEvent >, ComparePostSynEvent > postEvents_;
+
+ double Ca_;
+ double CaInit_;
+ double tauCa_;
+ double tauSyn_;
+ double CaPre_;
+ double CaPost_;
+ double delayD_;
+ bool noisy_;
+ double noiseSD_;
+ bool bistable_;
+ double thetaD_;
+ double thetaP_;
+ double gammaD_;
+ double gammaP_;
+ double weightMax_;
+ double weightMin_;
+ double weightScale_;
+ double lastCaUpdateTime_;
+
+ // NormalRng normalGenerator_;
+ unsigned long seed_;
+ moose::MOOSE_RANDOM_DEVICE rd_;
+ moose::MOOSE_NORMAL_DISTRIBUTION<double> dist_;
+ moose::MOOSE_RNG_DEFAULT_ENGINE rng_;
+
};
#endif // _GRAUPNER_BRUNEL_2012_CA_PLASTICITY_SYN_HANDLER_H
diff --git a/synapse/SimpleSynHandler.h b/synapse/SimpleSynHandler.h
index 22ee6c90..687d8862 100644
--- a/synapse/SimpleSynHandler.h
+++ b/synapse/SimpleSynHandler.h
@@ -10,6 +10,8 @@
#ifndef _SIMPLE_SYN_HANDLER_H
#define _SIMPLE_SYN_HANDLER_H
+#include <queue>
+
/*
class SynEvent
{
diff --git a/synapse/SynHandlerBase.cpp b/synapse/SynHandlerBase.cpp
index 3c30a30b..6c325145 100644
--- a/synapse/SynHandlerBase.cpp
+++ b/synapse/SynHandlerBase.cpp
@@ -13,13 +13,14 @@
static const double RANGE = 1.0e-15;
-SrcFinfo1< double >* SynHandlerBase::activationOut() {
- static SrcFinfo1< double > activationOut(
- "activationOut",
- "Sends out level of activation on all synapses converging to "
- "this SynHandler"
- );
- return &activationOut;
+SrcFinfo1< double >* SynHandlerBase::activationOut()
+{
+ static SrcFinfo1< double > activationOut(
+ "activationOut",
+ "Sends out level of activation on all synapses converging to "
+ "this SynHandler"
+ );
+ return &activationOut;
}
/**
@@ -29,60 +30,61 @@ SrcFinfo1< double >* SynHandlerBase::activationOut() {
*/
const Cinfo* SynHandlerBase::initCinfo()
{
- static ValueFinfo< SynHandlerBase, unsigned int > numSynapses(
- "numSynapses",
- "Number of synapses on SynHandler. Duplicate field for num_synapse",
- &SynHandlerBase::setNumSynapses,
- &SynHandlerBase::getNumSynapses
- );
- //////////////////////////////////////////////////////////////////////
- static DestFinfo process( "process",
- "Handles 'process' call. Checks if any spike events are due for"
- "handling at this timestep, and does learning rule stuff if needed",
- new ProcOpFunc< SynHandlerBase >(& SynHandlerBase::process ) );
- static DestFinfo reinit( "reinit",
- "Handles 'reinit' call. Initializes all the synapses.",
- new ProcOpFunc< SynHandlerBase >(& SynHandlerBase::reinit ) );
-
- static Finfo* processShared[] =
- {
- &process, &reinit
- };
- static SharedFinfo proc( "proc",
- "Shared Finfo to receive Process messages from the clock.",
- processShared, sizeof( processShared ) / sizeof( Finfo* )
- );
-
- //////////////////////////////////////////////////////////////////////
- static Finfo* synHandlerFinfos[] = {
- &numSynapses, // Value
- activationOut(), // SrcFinfo
- &proc, // SharedFinfo
- };
-
- static string doc[] =
- {
- "Name", "SynHandlerBase",
- "Author", "Upi Bhalla",
- "Description",
- "Base class for handling synapse arrays converging onto a given "
- "channel or integrate-and-fire neuron. This class provides the "
- "interface for channels/intFires to connect to a range of synapse "
- "types, including simple synapses, synapses with different "
- "plasticity rules, and variants yet to be implemented. "
- };
- static ZeroSizeDinfo< int > dinfo;
- static Cinfo synHandlerCinfo (
- "SynHandlerBase",
- Neutral::initCinfo(),
- synHandlerFinfos,
- sizeof( synHandlerFinfos ) / sizeof ( Finfo* ),
- &dinfo,
- doc,
- sizeof( doc ) / sizeof( string )
- );
-
- return &synHandlerCinfo;
+ static ValueFinfo< SynHandlerBase, unsigned int > numSynapses(
+ "numSynapses",
+ "Number of synapses on SynHandler. Duplicate field for num_synapse",
+ &SynHandlerBase::setNumSynapses,
+ &SynHandlerBase::getNumSynapses
+ );
+ //////////////////////////////////////////////////////////////////////
+ static DestFinfo process( "process",
+ "Handles 'process' call. Checks if any spike events are due for"
+ "handling at this timestep, and does learning rule stuff if needed",
+ new ProcOpFunc< SynHandlerBase >(& SynHandlerBase::process ) );
+ static DestFinfo reinit( "reinit",
+ "Handles 'reinit' call. Initializes all the synapses.",
+ new ProcOpFunc< SynHandlerBase >(& SynHandlerBase::reinit ) );
+
+ static Finfo* processShared[] =
+ {
+ &process, &reinit
+ };
+ static SharedFinfo proc( "proc",
+ "Shared Finfo to receive Process messages from the clock.",
+ processShared, sizeof( processShared ) / sizeof( Finfo* )
+ );
+
+ //////////////////////////////////////////////////////////////////////
+ static Finfo* synHandlerFinfos[] =
+ {
+ &numSynapses, // Value
+ activationOut(), // SrcFinfo
+ &proc, // SharedFinfo
+ };
+
+ static string doc[] =
+ {
+ "Name", "SynHandlerBase",
+ "Author", "Upi Bhalla",
+ "Description",
+ "Base class for handling synapse arrays converging onto a given "
+ "channel or integrate-and-fire neuron. This class provides the "
+ "interface for channels/intFires to connect to a range of synapse "
+ "types, including simple synapses, synapses with different "
+ "plasticity rules, and variants yet to be implemented. "
+ };
+ static ZeroSizeDinfo< int > dinfo;
+ static Cinfo synHandlerCinfo (
+ "SynHandlerBase",
+ Neutral::initCinfo(),
+ synHandlerFinfos,
+ sizeof( synHandlerFinfos ) / sizeof ( Finfo* ),
+ &dinfo,
+ doc,
+ sizeof( doc ) / sizeof( string )
+ );
+
+ return &synHandlerCinfo;
}
static const Cinfo* synHandlerCinfo = SynHandlerBase::initCinfo();
@@ -90,44 +92,49 @@ static const Cinfo* synHandlerCinfo = SynHandlerBase::initCinfo();
////////////////////////////////////////////////////////////////////////
SynHandlerBase::SynHandlerBase()
-{ ; }
+{
+ ;
+}
SynHandlerBase::~SynHandlerBase()
-{ ; }
+{
+ ;
+}
void SynHandlerBase::setNumSynapses( unsigned int num )
{
- vSetNumSynapses( num );
+ vSetNumSynapses( num );
}
unsigned int SynHandlerBase::getNumSynapses() const
{
- return vGetNumSynapses();
+ return vGetNumSynapses();
}
Synapse* SynHandlerBase::getSynapse( unsigned int i )
{
- return vGetSynapse( i );
+ return vGetSynapse( i );
}
void SynHandlerBase::process( const Eref& e, ProcPtr p )
{
- vProcess( e, p );
+ vProcess( e, p );
}
void SynHandlerBase::reinit( const Eref& e, ProcPtr p )
{
- vReinit( e, p );
+ vReinit( e, p );
}
bool SynHandlerBase::rangeWarning( const string& field, double value )
{
- if ( value < RANGE ) {
- cout << "Warning: Ignored attempt to set " << field <<
- " of SynHandler " <<
- // c->target().e->name() <<
- " to less than " << RANGE << endl;
- return 1;
- }
- return 0;
+ if ( value < RANGE )
+ {
+ cout << "Warning: Ignored attempt to set " << field <<
+ " of SynHandler " <<
+ // c->target().e->name() <<
+ " to less than " << RANGE << endl;
+ return 1;
+ }
+ return 0;
}
diff --git a/synapse/SynHandlerBase.h b/synapse/SynHandlerBase.h
index e3b3a383..d0d3d43a 100644
--- a/synapse/SynHandlerBase.h
+++ b/synapse/SynHandlerBase.h
@@ -21,77 +21,79 @@ class Synapse;
*/
class SynHandlerBase
{
- public:
- SynHandlerBase();
- virtual ~SynHandlerBase();
+public:
+ SynHandlerBase();
+ virtual ~SynHandlerBase();
- ////////////////////////////////////////////////////////////////
- // Field assignment stuff.
- ////////////////////////////////////////////////////////////////
+ ////////////////////////////////////////////////////////////////
+ // Field assignment stuff.
+ ////////////////////////////////////////////////////////////////
- /**
- * Resizes the synapse storage
- */
- void setNumSynapses( unsigned int num );
+ /**
+ * Resizes the synapse storage
+ */
+ void setNumSynapses( unsigned int num );
- /**
- * Returns number of synapses defined.
- */
- unsigned int getNumSynapses() const;
+ /**
+ * Returns number of synapses defined.
+ */
+ unsigned int getNumSynapses() const;
- /**
- * Gets specified synapse
- */
- Synapse* getSynapse( unsigned int i );
- ////////////////////////////////////////////////////////////////
+ /**
+ * Gets specified synapse
+ */
+ Synapse* getSynapse( unsigned int i );
+ ////////////////////////////////////////////////////////////////
- void process( const Eref& e, ProcPtr p );
- void reinit( const Eref& e, ProcPtr p );
+ void process( const Eref& e, ProcPtr p );
+ void reinit( const Eref& e, ProcPtr p );
- /**
- * A utility function to check for assignment to fields that
- * must be > 0
- */
- bool rangeWarning( const string& field, double value );
+ /**
+ * A utility function to check for assignment to fields that
+ * must be > 0
+ */
+ bool rangeWarning( const string& field, double value );
- ////////////////////////////////////////////////////////////////
- /**
- * Adds a new synapse, returns its index. This is
- * triggered by addMsg of inputs to the child synapse. The
- * SynHandler has to ensure that we have enough synapses allocated
- * to handle the new message, and the return value is used so that
- * the new message knows the fieldIndex to send the message to.
- */
- virtual unsigned int addSynapse() = 0;
+ ////////////////////////////////////////////////////////////////
+ /**
+ * Adds a new synapse, returns its index. This is
+ * triggered by addMsg of inputs to the child synapse. The
+ * SynHandler has to ensure that we have enough synapses allocated
+ * to handle the new message, and the return value is used so that
+ * the new message knows the fieldIndex to send the message to.
+ */
+ virtual unsigned int addSynapse() = 0;
- /**
- * Drops an existing synapse, triggered by deleteMsg of an input
- * to the child synapse. This is a little messy because we can't
- * change the indices of the other synapses. The Handler has to
- * figure out how to handle the 'holes' in its array of synapses.
- */
- virtual void dropSynapse( unsigned int droppedSynNumber ) = 0;
+ /**
+ * Drops an existing synapse, triggered by deleteMsg of an input
+ * to the child synapse. This is a little messy because we can't
+ * change the indices of the other synapses. The Handler has to
+ * figure out how to handle the 'holes' in its array of synapses.
+ */
+ virtual void dropSynapse( unsigned int droppedSynNumber ) = 0;
+
+ /**
+ * Record arrival of a new spike event. The 'time' is time for
+ * eventual arrival of the spike, and is typically well in the
+ * future. The index specifies which synapse the spike came to.
+ */
+ virtual void addSpike(
+ unsigned int index, double time, double weight ) = 0;
+ virtual double getTopSpike( unsigned int index ) const = 0;
+ ////////////////////////////////////////////////////////////////
+ // Virtual func definitions for fields.
+ ////////////////////////////////////////////////////////////////
+ virtual void vSetNumSynapses( unsigned int num ) = 0;
+ virtual unsigned int vGetNumSynapses() const = 0;
+ virtual Synapse* vGetSynapse( unsigned int i ) = 0;
+ virtual void vProcess( const Eref& e, ProcPtr p ) = 0;
+ virtual void vReinit( const Eref& e, ProcPtr p ) = 0;
+ ////////////////////////////////////////////////////////////////
+ static SrcFinfo1< double >* activationOut();
+ static const Cinfo* initCinfo();
+
+private:
- /**
- * Record arrival of a new spike event. The 'time' is time for
- * eventual arrival of the spike, and is typically well in the
- * future. The index specifies which synapse the spike came to.
- */
- virtual void addSpike(
- unsigned int index, double time, double weight ) = 0;
- virtual double getTopSpike( unsigned int index ) const = 0;
- ////////////////////////////////////////////////////////////////
- // Virtual func definitions for fields.
- ////////////////////////////////////////////////////////////////
- virtual void vSetNumSynapses( unsigned int num ) = 0;
- virtual unsigned int vGetNumSynapses() const = 0;
- virtual Synapse* vGetSynapse( unsigned int i ) = 0;
- virtual void vProcess( const Eref& e, ProcPtr p ) = 0;
- virtual void vReinit( const Eref& e, ProcPtr p ) = 0;
- ////////////////////////////////////////////////////////////////
- static SrcFinfo1< double >* activationOut();
- static const Cinfo* initCinfo();
- private:
};
#endif // _SYN_HANDLER_BASE_H
diff --git a/synapse/testSynapse.cpp b/synapse/testSynapse.cpp
index 600d7ff3..427f08b1 100644
--- a/synapse/testSynapse.cpp
+++ b/synapse/testSynapse.cpp
@@ -18,7 +18,6 @@
#include "RollingMatrix.h"
#include "SeqSynHandler.h"
#include "../shell/Shell.h"
-#include "../randnum/randnum.h"
double doCorrel( RollingMatrix& rm, vector< vector< double >> & kernel )
{
diff --git a/tests/python/OSC_diff_vols.g b/tests/python/OSC_diff_vols.g
new file mode 100644
index 00000000..d7166be2
--- /dev/null
+++ b/tests/python/OSC_diff_vols.g
@@ -0,0 +1,219 @@
+//genesis
+// kkit Version 11 flat dumpfile
+
+// Saved on Tue Jan 21 14:05:52 2014
+
+include kkit {argv 1}
+
+FASTDT = 0.0001
+SIMDT = 0.005
+CONTROLDT = 5
+PLOTDT = 10
+MAXTIME = 2500
+TRANSIENT_TIME = 2
+VARIABLE_DT_FLAG = 1
+DEFAULT_VOL = 1e-20
+VERSION = 11.0
+setfield /file/modpath value /home2/bhalla/scripts/modules
+kparms
+
+//genesis
+
+initdump -version 3 -ignoreorphans 1
+simobjdump doqcsinfo filename accessname accesstype transcriber developer \
+ citation species tissue cellcompartment methodology sources \
+ model_implementation model_validation x y z
+simobjdump table input output alloced step_mode stepsize x y z
+simobjdump xtree path script namemode sizescale
+simobjdump xcoredraw xmin xmax ymin ymax
+simobjdump xtext editable
+simobjdump xgraph xmin xmax ymin ymax overlay
+simobjdump xplot pixflags script fg ysquish do_slope wy
+simobjdump group xtree_fg_req xtree_textfg_req plotfield expanded movealone \
+ link savename file version md5sum mod_save_flag x y z
+simobjdump geometry size dim shape outside xtree_fg_req xtree_textfg_req x y \
+ z
+simobjdump kpool DiffConst CoInit Co n nInit mwt nMin vol slave_enable \
+ geomname xtree_fg_req xtree_textfg_req x y z
+simobjdump kreac kf kb notes xtree_fg_req xtree_textfg_req x y z
+simobjdump kenz CoComplexInit CoComplex nComplexInit nComplex vol k1 k2 k3 \
+ keepconc usecomplex notes xtree_fg_req xtree_textfg_req link x y z
+simobjdump stim level1 width1 delay1 level2 width2 delay2 baselevel trig_time \
+ trig_mode notes xtree_fg_req xtree_textfg_req is_running x y z
+simobjdump xtab input output alloced step_mode stepsize notes editfunc \
+ xtree_fg_req xtree_textfg_req baselevel last_x last_y is_running x y z
+simobjdump kchan perm gmax Vm is_active use_nernst notes xtree_fg_req \
+ xtree_textfg_req x y z
+simobjdump transport input output alloced step_mode stepsize dt delay clock \
+ kf xtree_fg_req xtree_textfg_req x y z
+simobjdump proto x y z
+simobjdump text str
+simundump geometry /kinetics/geometry 0 9.9998e-20 3 sphere "" white black 0 \
+ 0 0
+simundump geometry /kinetics/geometry[1] 0 9.9998e-21 3 sphere "" white black \
+ 0 0 0
+simundump geometry /kinetics/geometry[2] 0 1e-20 3 sphere "" white black 0 0 \
+ 0
+simundump text /kinetics/notes 0 ""
+call /kinetics/notes LOAD \
+""
+simundump text /kinetics/geometry/notes 0 ""
+call /kinetics/geometry/notes LOAD \
+""
+simundump text /kinetics/geometry[1]/notes 0 ""
+call /kinetics/geometry[1]/notes LOAD \
+""
+simundump text /kinetics/geometry[2]/notes 0 ""
+call /kinetics/geometry[2]/notes LOAD \
+""
+simundump kreac /kinetics/exo 0 0.005 0 "" white black 3 9 0
+simundump text /kinetics/exo/notes 0 ""
+call /kinetics/exo/notes LOAD \
+""
+simundump kreac /kinetics/endo 0 0.01 0 "" white black -6 11 0
+simundump text /kinetics/endo/notes 0 ""
+call /kinetics/endo/notes LOAD \
+""
+simundump group /kinetics/B 0 yellow black x 0 0 "" Bulk defaultfile.g 0 0 0 \
+ -7 6 0
+simundump text /kinetics/B/notes 0 ""
+call /kinetics/B/notes LOAD \
+""
+simundump kpool /kinetics/B/P 0 0 0.1 0.1 0.6 0.6 0 0 6 0 /kinetics/geometry \
+ 4 yellow -2 2 0
+simundump text /kinetics/B/P/notes 0 ""
+call /kinetics/B/P/notes LOAD \
+""
+simundump kenz /kinetics/B/P/kenz 0 0 0 0 0 6 16.667 4 1 0 0 "" red 4 "" -2 0 \
+ 0
+simundump text /kinetics/B/P/kenz/notes 0 ""
+call /kinetics/B/P/kenz/notes LOAD \
+""
+simundump kreac /kinetics/B/basal 0 0.01 0 "" white yellow -4 -4 0
+simundump text /kinetics/B/basal/notes 0 ""
+call /kinetics/B/basal/notes LOAD \
+""
+simundump kpool /kinetics/B/M 0 0 0 0 0 0 0 0 6 0 /kinetics/geometry 62 \
+ yellow -5 7 0
+simundump text /kinetics/B/M/notes 0 ""
+call /kinetics/B/M/notes LOAD \
+""
+simundump kpool /kinetics/B/M* 0 0 0 0 0 0 0 0 6 0 /kinetics/geometry 28 \
+ yellow 2 2 0
+simundump text /kinetics/B/M*/notes 0 ""
+call /kinetics/B/M*/notes LOAD \
+""
+simundump kenz /kinetics/B/M*/kenz 0 0 0 0 0 59.999 0.41667 2 0.5 0 0 "" red \
+ 28 "" 1 6 0
+simundump text /kinetics/B/M*/kenz/notes 0 ""
+call /kinetics/B/M*/kenz/notes LOAD \
+""
+simundump group /kinetics/A 0 16 black x 0 0 "" PSD defaultfile.g 0 0 0 -5 16 \
+ 0
+simundump text /kinetics/A/notes 0 ""
+call /kinetics/A/notes LOAD \
+""
+simundump kreac /kinetics/A/basal 0 0.01 0 "" white 16 -1 8 0
+simundump text /kinetics/A/basal/notes 0 ""
+call /kinetics/A/basal/notes LOAD \
+""
+simundump kpool /kinetics/A/Stot 0 0 0 1.75 21 0 0 0 12 0 \
+ /kinetics/geometry[2] 41 16 0 24 0
+simundump text /kinetics/A/Stot/notes 0 ""
+call /kinetics/A/Stot/notes LOAD \
+""
+simundump kpool /kinetics/A/P 0 0 0.049999 0.049999 0.59999 0.59999 0 0 12 0 \
+ /kinetics/geometry[1] 3 16 -1 11 0
+simundump text /kinetics/A/P/notes 0 ""
+call /kinetics/A/P/notes LOAD \
+""
+simundump kenz /kinetics/A/P/kenz 0 0 0 0 0 5.9999 16.667 4 1 0 0 "" red 3 "" \
+ -1 13 0
+simundump text /kinetics/A/P/kenz/notes 0 ""
+call /kinetics/A/P/kenz/notes LOAD \
+""
+simundump kpool /kinetics/A/M* 0 0 0 0 0 0 0 0 12 0 /kinetics/geometry 47 16 \
+ 4 19 0
+simundump text /kinetics/A/M*/notes 0 ""
+call /kinetics/A/M*/notes LOAD \
+""
+simundump kenz /kinetics/A/M*/kenz 0 0 0 0 0 5.9999 0.41667 2 0.5 0 0 "" red \
+ 57 "" -1 18 0
+simundump text /kinetics/A/M*/kenz/notes 0 ""
+call /kinetics/A/M*/kenz/notes LOAD \
+""
+simundump kpool /kinetics/A/M 0 0 1.75 1.75 21 21 0 0 12 0 /kinetics/geometry \
+ 53 16 -4 17 0
+simundump text /kinetics/A/M/notes 0 ""
+call /kinetics/A/M/notes LOAD \
+""
+simundump xgraph /graphs/conc1 0 0 2500 0.001 3 0
+simundump xgraph /graphs/conc2 0 0 2500 0 5 0
+simundump xplot /graphs/conc1/M.Co 3 524288 \
+ "delete_plot.w <s> <d>; edit_plot.D <w>" 53 0 0 1
+simundump xplot /graphs/conc1/M*.Co 3 524288 \
+ "delete_plot.w <s> <d>; edit_plot.D <w>" 47 0 0 1
+simundump xplot /graphs/conc2/M.Co 3 524288 \
+ "delete_plot.w <s> <d>; edit_plot.D <w>" 62 0 0 1
+simundump xplot /graphs/conc2/M*.Co 3 524288 \
+ "delete_plot.w <s> <d>; edit_plot.D <w>" 28 0 0 1
+simundump xgraph /moregraphs/conc3 0 0 2500 0 1 0
+simundump xgraph /moregraphs/conc4 0 0 2500 0 1 0
+simundump xcoredraw /edit/draw 0 -9 6 -6 26
+simundump xtree /edit/draw/tree 0 \
+ /kinetics/#[],/kinetics/#[]/#[],/kinetics/#[]/#[]/#[][TYPE!=proto],/kinetics/#[]/#[]/#[][TYPE!=linkinfo]/##[] \
+ "edit_elm.D <v>; drag_from_edit.w <d> <S> <x> <y> <z>" auto 0.6
+simundump xtext /file/notes 0 1
+xtextload /file/notes \
+"21 Jan 2014." \
+"Using " \
+"different volumes for the two compartments, based on OSC_Cspace.g"
+addmsg /kinetics/B/M* /kinetics/exo SUBSTRATE n
+addmsg /kinetics/A/M* /kinetics/exo PRODUCT n
+addmsg /kinetics/A/M /kinetics/endo SUBSTRATE n
+addmsg /kinetics/B/M /kinetics/endo PRODUCT n
+addmsg /kinetics/B/P/kenz /kinetics/B/P REAC eA B
+addmsg /kinetics/B/P /kinetics/B/P/kenz ENZYME n
+addmsg /kinetics/B/M* /kinetics/B/P/kenz SUBSTRATE n
+addmsg /kinetics/B/M /kinetics/B/basal SUBSTRATE n
+addmsg /kinetics/B/M* /kinetics/B/basal PRODUCT n
+addmsg /kinetics/B/basal /kinetics/B/M REAC A B
+addmsg /kinetics/B/P/kenz /kinetics/B/M MM_PRD pA
+addmsg /kinetics/B/M*/kenz /kinetics/B/M REAC sA B
+addmsg /kinetics/endo /kinetics/B/M REAC B A
+addmsg /kinetics/B/basal /kinetics/B/M* REAC B A
+addmsg /kinetics/B/P/kenz /kinetics/B/M* REAC sA B
+addmsg /kinetics/B/M*/kenz /kinetics/B/M* REAC eA B
+addmsg /kinetics/B/M*/kenz /kinetics/B/M* MM_PRD pA
+addmsg /kinetics/exo /kinetics/B/M* REAC A B
+addmsg /kinetics/B/M* /kinetics/B/M*/kenz ENZYME n
+addmsg /kinetics/B/M /kinetics/B/M*/kenz SUBSTRATE n
+addmsg /kinetics/A/M /kinetics/A/basal SUBSTRATE n
+addmsg /kinetics/A/M* /kinetics/A/basal PRODUCT n
+addmsg /kinetics/A/M /kinetics/A/Stot SUMTOTAL n nInit
+addmsg /kinetics/A/M* /kinetics/A/Stot SUMTOTAL n nInit
+addmsg /kinetics/A/M*/kenz /kinetics/A/Stot SUMTOTAL nComplex nComplexInit
+addmsg /kinetics/A/P/kenz /kinetics/A/Stot SUMTOTAL nComplex nComplexInit
+addmsg /kinetics/A/M*/kenz /kinetics/A/Stot SUMTOTAL nComplex nComplexInit
+addmsg /kinetics/A/P/kenz /kinetics/A/P REAC eA B
+addmsg /kinetics/A/P /kinetics/A/P/kenz ENZYME n
+addmsg /kinetics/A/M* /kinetics/A/P/kenz SUBSTRATE n
+addmsg /kinetics/A/M*/kenz /kinetics/A/M* MM_PRD pA
+addmsg /kinetics/A/P/kenz /kinetics/A/M* REAC sA B
+addmsg /kinetics/A/basal /kinetics/A/M* REAC B A
+addmsg /kinetics/A/M*/kenz /kinetics/A/M* REAC eA B
+addmsg /kinetics/exo /kinetics/A/M* REAC B A
+addmsg /kinetics/A/M /kinetics/A/M*/kenz SUBSTRATE n
+addmsg /kinetics/A/M* /kinetics/A/M*/kenz ENZYME n
+addmsg /kinetics/A/M*/kenz /kinetics/A/M REAC sA B
+addmsg /kinetics/A/P/kenz /kinetics/A/M MM_PRD pA
+addmsg /kinetics/A/basal /kinetics/A/M REAC A B
+addmsg /kinetics/endo /kinetics/A/M REAC A B
+addmsg /kinetics/A/M /graphs/conc1/M.Co PLOT Co *M.Co *53
+addmsg /kinetics/A/M* /graphs/conc1/M*.Co PLOT Co *M*.Co *47
+addmsg /kinetics/B/M /graphs/conc2/M.Co PLOT Co *M.Co *62
+addmsg /kinetics/B/M* /graphs/conc2/M*.Co PLOT Co *M*.Co *28
+enddump
+// End of dump
+
+complete_loading
diff --git a/tests/python/fixXreacs.py b/tests/python/fixXreacs.py
new file mode 100644
index 00000000..7a68ed9b
--- /dev/null
+++ b/tests/python/fixXreacs.py
@@ -0,0 +1,194 @@
+# -*- coding: utf-8 -*-
+####################################################################
+# fixXreacs.py
+# The program is meant to take a model and reconfigure any cross-compartment
+# reactions so that they are split into portions on either side coupled
+# either by diffusion, or by a reaction-driven translocation process.
+#
+# Copyright (C) Upinder S. Bhalla 2018
+# This program is free software. It is licensed under the terms of
+# GPL version 3 or later at your discretion.
+# This program carries no warranty whatsoever.
+####################################################################
+
+
+import sys
+import moose
+
+msgSeparator = "_xMsg_"
+
+def findCompt( elm ):
+ elm = moose.element( elm )
+ pa = elm.parent
+ while pa.path != '/':
+ if moose.Neutral(pa).isA[ 'ChemCompt' ]:
+ return pa.path
+ pa = pa.parent
+ print( 'Error: No compartment parent found for ' + elm.path )
+ return '/'
+
+# http://stackoverflow.com/q/3844948/
+def checkEqual(lst):
+ return not lst or lst.count(lst[0]) == len(lst)
+
+def findXreacs( basepath, reacType ):
+ reacs = moose.wildcardFind( basepath + '/##[ISA=' + reacType + 'Base]' )
+ ret = []
+ for i in reacs:
+ reacc = findCompt( i )
+ subs = i.neighbors['subOut']
+ prds = i.neighbors['prdOut']
+ subc = [findCompt(j) for j in subs]
+ prdc = [findCompt(j) for j in prds]
+
+ enzc = []
+ if reacType == 'Enz':
+ enzc = [reacc]
+ if not checkEqual( subc + prdc + enzc ):
+ ret.append( [i, reacc, subs, subc, prds, prdc ])
+ return ret
+
+def removeEnzFromPool( pool ):
+ kids = moose.wildcardFind( pool.path + "/#" )
+ for i in kids:
+ if i.isA[ 'EnzBase' ]:
+ moose.delete( i )
+ elif i.isA[ 'Function' ]:
+ moose.delete( i )
+
+# If a pool is not in the same compt as reac, make a proxy in the reac
+# compt, connect it up, and disconnect the one in the old compt.
+def proxify( reac, reacc, direction, pool, poolc ):
+ reacc_elm = moose.element( reacc )
+ reac_elm = moose.element( reac )
+ # Preserve the rates which were set up for the x-compt reacn
+ #moose.showfield( reac )
+ dupname = pool.name + '_xfer_' + moose.element(poolc).name
+ #print "#############", pool, dupname, poolc
+ if moose.exists( reacc + '/' + dupname ):
+ duppool = moose.element( reacc + '/' + dupname )
+ else:
+ # This also deals with cases where the duppool is buffered.
+ duppool = moose.copy(pool, reacc_elm, dupname )
+ duppool.diffConst = 0 # diffusion only happens in original compt
+ removeEnzFromPool( duppool )
+ disconnectReactant( reac, pool, duppool )
+ moose.connect( reac, direction, duppool, 'reac' )
+ #moose.showfield( reac )
+ #moose.showmsg( reac )
+
+def enzProxify( enz, enzc, direction, pool, poolc ):
+ if enzc == poolc:
+ return
+ enze = moose.element( enz )
+ # kcat and k2 are indept of volume, just time^-1
+ km = enze.numKm
+ proxify( enz, enzc, direction, pool, poolc )
+ enze.numKm = km
+
+def reacProxify( reac, reacc, direction, pool, poolc ):
+ if reacc == poolc:
+ return
+ reac_elm = moose.element( reac )
+ kf = reac_elm.numKf
+ kb = reac_elm.numKb
+ proxify( reac, reacc, direction, pool, poolc )
+ reac_elm.numKf = kf
+ reac_elm.numKb = kb
+
+def identifyMsg( src, srcOut, dest ):
+ if src.isA[ 'ReacBase' ] or src.isA[ 'EnzBase' ]:
+ if srcOut == 'subOut':
+ return msgSeparator + src.path + ' sub ' + dest.path + ' reac'
+ if srcOut == 'prdOut':
+ return msgSeparator + src.path + ' prd ' + dest.path + ' reac'
+ return ''
+
+def disconnectReactant( reacOrEnz, reactant, duppool ):
+ outMsgs = reacOrEnz.msgOut
+ infoPath = duppool.path + '/info'
+ if moose.exists( infoPath ):
+ info = moose.element( infoPath )
+ else:
+ info = moose.Annotator( infoPath )
+
+ #moose.le( reactant )
+ notes = ""
+ #moose.showmsg( reacOrEnz )
+ for i in outMsgs:
+ #print "killing msg from {} to {}\nfor {} and {}".format( reacOrEnz.path, reactant.path, i.srcFieldsOnE1[0], i.srcFieldsOnE2[0] )
+ if i.e1 == reactant:
+ msgStr = identifyMsg( i.e2, i.e2.srcFieldsOnE2[0], i.e1 )
+ if len( msgStr ) > 0:
+ notes += msgStr
+ moose.delete( i )
+ elif i.e2 == reactant:
+ msgStr = identifyMsg( i.e1[0], i.srcFieldsOnE1[0], i.e2[0] )
+ if len( msgStr ) > 0:
+ notes += msgStr
+ moose.delete( i )
+ #print "MSGS to rebuild:", notes
+ info.notes += notes
+
+def fixXreacs( basepath ):
+ xr = findXreacs( basepath, 'Reac' )
+ xe = findXreacs( basepath, 'Enz' )
+
+ for i in (xr):
+ reac, reacc, subs, subc, prds, prdc = i
+ for j in range( len( subs )):
+ reacProxify( reac, reacc, 'sub', subs[j], subc[j] )
+ for j in range( len( prds )):
+ reacProxify( reac, reacc, 'prd', prds[j], prdc[j] )
+
+ for i in (xe):
+ reac, reacc, subs, subc, prds, prdc = i
+ for j in range( len( subs )):
+ enzProxify( reac, reacc, 'sub', subs[j], subc[j] )
+ for j in range( len( prds )):
+ enzProxify( reac, reacc, 'prd', prds[j], prdc[j] )
+
+#####################################################################
+
+def getOldRates( msgs ):
+ if len( msgs ) > 1 :
+ m1 = msgs[1].split( msgSeparator )[0]
+ elm = moose.element( m1.split( ' ' )[0] )
+ if elm.isA[ 'ReacBase' ]:
+ return [elm.numKf, elm.numKb]
+ elif elm.isA[ 'EnzBase' ]:
+ return [elm.numKm,]
+ print( "Warning: getOldRates did not have any messages" )
+ return [0,]
+
+def restoreOldRates( oldRates, msgs ):
+ #print oldRates, msgs
+ if len( msgs ) > 1 :
+ m1 = msgs[1].split( msgSeparator )[0]
+ elm = moose.element( m1.split( ' ' )[0] )
+ if elm.isA[ 'ReacBase' ]:
+ elm.numKf = oldRates[0]
+ elm.numKb = oldRates[1]
+ elif elm.isA[ 'enzBase' ]:
+ elm.numKm = oldRates[0]
+
+
+
+def restoreXreacs( basepath ):
+ proxyInfo = moose.wildcardFind( basepath + "/##/#_xfer_#/info" )
+ for i in proxyInfo:
+ msgs = i.notes.split( msgSeparator )
+ oldRates = getOldRates( msgs )
+ #print( "Deleting {}".format( i.parent.path ) )
+ #print msgs
+ moose.delete( i.parent )
+ for j in msgs:
+ if len( j ) > 0:
+ args = j.split( ' ' )
+ assert( len( args ) == 4 )
+ #moose.showfield( args[0] )
+ moose.connect( args[0], args[1], args[2], args[3] )
+ #print( "Reconnecting {}".format( args ) )
+ #moose.showfield( args[0] )
+ restoreOldRates( oldRates, msgs )
+
diff --git a/tests/python/params.py b/tests/python/params.py
index 1feacecc..bd3bacae 100644
--- a/tests/python/params.py
+++ b/tests/python/params.py
@@ -1,27 +1,63 @@
# -*- coding: utf-8 -*-
-t_stop = 10
-dend_diameter = 2.2627398e-6
-dend_length = 1.131369936e-6
-Cm = 4.021231698e-12
-Rm = 1865100032
-Em = -0.07100000232
-Vm_0 = -0.0705
-dt = 50e-6
-spines_no = 0
-difshell_no = 2
-difshell_name = "Ca_shell"
-Ca_basal = 50e-6
-Ca_initial = Ca_basal*200
-dca = 200.0e-12
-difbuff_no = 1
-difbuff_name = "Buff"
-btotal = 80.0e-3
-kf = 0.028e6
-kb = 19.6
-d = 66e-12
-inject = 0.1e-9
-gbar = 1
-#MMpump
-km = 0.3e-3
-kcat = 85e-22
-pumps = 1
+"""params.py
+
+Parameters used in this model
+
+These parameters are from paper Miller et. al. "The stability of CaMKII
+switch"
+
+"""
+
+__author__ = "Dilawar Singh"
+__copyright__ = "Copyright 2015, Dilawar Singh and NCBS Bangalore"
+__credits__ = ["NCBS Bangalore"]
+__license__ = "GNU GPL"
+__version__ = "1.0.0"
+__maintainer__ = "Dilawar Singh"
+__email__ = "dilawars@ncbs.res.in"
+__status__ = "Development"
+
+
+run_time = 30
+N_CaMK = 10
+N_PP1 = 100
+num_switch = 1
+voxel_length = 125e-9
+num_voxels = 1
+
+diff_consts = { 'x' : 1e-13, 'y' : 1e-13, 'pp1' : 1e-13 }
+
+conc_i1_free = 0.1e-3
+act_CaN = 1.0
+act_PKA = 1.0
+
+# Michaelis constant of protein phosphatase.
+# 0.4 um to 2.0 uM have been used. Miller uses 0.2 um. The switch shows
+# bistability of these ranges. We have taken the largest Km (or slowest) first
+# step in dephosphorylation.
+K_M = 10e-3
+k_2 = 10.0
+
+# Hill coefficientfor Ca++ activation of CaMKII
+K_H1 = 0.7e-3
+K_H2 = 0.3e-3
+
+k_1 = 1.5
+k_3 = 100e3
+k_4 = 0.001
+K_I = 1e-6
+
+rate_loosex = 0.1
+rate_loosey = 0.1
+rate_gainx = 1
+rate_gainy = 1
+
+turnover_rate = 1/(30*3600.0)
+v_1 = 1.268e-5
+v_2 = 4.36e-3
+phosphatase_inhibit = 280.0
+vi = phosphatase_inhibit
+
+## Calcium input expression.
+ca_basal = 80e-6
+ca_expr = "(fmod(t,4)<2)?{0}:({0}*(1+0.5*rand(-1)))".format( ca_basal )
diff --git a/tests/python/testXchan1.py b/tests/python/testXchan1.py
new file mode 100644
index 00000000..1bcc130b
--- /dev/null
+++ b/tests/python/testXchan1.py
@@ -0,0 +1,183 @@
+# -*- coding: utf-8 -*-
+#########################################################################
+## This program is part of 'MOOSE', the
+## Messaging Object Oriented Simulation Environment.
+## Copyright (C) 2014 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.
+## Here test ConcChan. We set up a channel and a pump and run two tests.
+## First we have zero flux through the pump and check that the conc
+## equalizes on both sides of the membrane. Then we change the Kf of
+## the pump to a value designed to give twice the conc In as Out.
+## The system is a 1-voxel cyl compt and an internal endoMesh, having a
+## volume = 1/8 of the cylinder.
+## \
+## COMPT: s ----> / s :ENDO
+## s =chan= s
+## \
+##
+## This becomes:
+## \
+## COMPT: s ----> s_xfer_endo / s :ENDO
+## s =chan= s
+## \
+##
+#########################################################################
+
+import math
+import numpy as np
+import matplotlib.pyplot as plt
+import matplotlib.image as mpimg
+import moose
+print( '[INFO ] Using moose from %s, %s' % (moose.__file__, moose.version()) )
+import fixXreacs
+
+def makeModel():
+ # create container for model
+ num = 1 # number of compartments
+ model = moose.Neutral( '/model' )
+ compartment = moose.CylMesh( '/model/compartment' )
+ compartment.x1 = 1.0e-6 # Set it to a 1 micron single-voxel cylinder
+
+ # create molecules and reactions
+ s = moose.Pool( '/model/compartment/s' )
+ rXfer = moose.Reac( '/model/compartment/rXfer' )
+ #####################################################################
+ # Put in endo compartment. Add molecule s
+ endo = moose.EndoMesh( '/model/endo' )
+ # Note that the chanPool must be on the 'In' compartment.
+ #chanPool = moose.Pool( '/model/compartment/chanPool' )
+ #chan = moose.ConcChan( '/model/compartment/chanPool/chan' )
+ chanPool = moose.Pool( '/model/endo/chanPool' )
+ chan = moose.ConcChan( '/model/endo/chanPool/chan' )
+ endo.isMembraneBound = True
+ endo.surround = compartment
+ es = moose.Pool( '/model/endo/s' )
+ #####################################################################
+ moose.connect( rXfer, 'sub', s, 'reac' )
+ moose.connect( rXfer, 'prd', es, 'reac' )
+ moose.connect( chanPool, 'nOut', chan, 'setNumChan' )
+ moose.connect( chan, 'out', s, 'reac' )
+ moose.connect( chan, 'in', es, 'reac' )
+ volRatio = compartment.volume / endo.volume
+ rXfer.Kf = 0.0 # 0.02/sec
+ rXfer.Kb = 0.0 #
+ s.concInit = 0.001
+ chanPool.nInit = 1000.0
+ # Flux (#/s) = permeability * N * (#out/vol_out - #in/vol_in)
+ chan.permeability = 0.1 * chanPool.volume / chanPool.nInit
+
+ #####################################################################
+ fixXreacs.fixXreacs( '/model' )
+ #fixXreacs.restoreXreacs( '/model' )
+ #fixXreacs.fixXreacs( '/model' )
+ #####################################################################
+
+ # Make solvers
+ ksolve = moose.Ksolve( '/model/compartment/ksolve' )
+ dsolve = moose.Dsolve( '/model/dsolve' )
+ eksolve = moose.Ksolve( '/model/endo/ksolve' )
+ eksolve.method = 'gsl'
+ edsolve = moose.Dsolve( '/model/endo/dsolve' )
+
+ stoich = moose.Stoich( '/model/compartment/stoich' )
+ stoich.compartment = compartment
+ stoich.ksolve = ksolve
+ stoich.dsolve = dsolve
+ stoich.path = "/model/compartment/##"
+ assert( dsolve.numPools == 2 )
+
+ estoich = moose.Stoich( '/model/endo/stoich' )
+ estoich.compartment = endo
+ estoich.ksolve = eksolve
+ estoich.dsolve = edsolve
+ estoich.path = "/model/endo/##"
+ assert( edsolve.numPools == 2 )
+
+ edsolve.buildMeshJunctions( dsolve )
+
+ plot1 = moose.Table2( '/model/plot1' )
+ plot2 = moose.Table2( '/model/plot2' )
+ plot3 = moose.Table2( '/model/plot3' )
+ moose.connect( '/model/plot1', 'requestOut', s, 'getN' )
+ moose.connect( '/model/plot2', 'requestOut', es, 'getN' )
+ moose.connect( '/model/plot3', 'requestOut', '/model/compartment/s_xfer_endo', 'getN' )
+ plot4 = moose.Table2( '/model/plot4' )
+ plot5 = moose.Table2( '/model/plot5' )
+ plot6 = moose.Table2( '/model/plot6' )
+ moose.connect( '/model/plot4', 'requestOut', s, 'getConc' )
+ moose.connect( '/model/plot5', 'requestOut', es, 'getConc' )
+ moose.connect( '/model/plot6', 'requestOut', '/model/compartment/s_xfer_endo', 'getConc' )
+
+def doPlot( ax, i, label ):
+ scale = 1
+ if i > 3:
+ scale = 1000 # Just to plot in uM.
+ plot1 = '/model/plot' + str(i)
+ plot2 = '/model/plot' + str(i+1)
+ plot3 = '/model/plot' + str(i+2)
+ plt.ylabel( label )
+ plt.xlabel( 'time(s)' )
+ v1 = moose.element(plot1).vector * scale
+ v2 = moose.element(plot2).vector * scale
+ v3 = moose.element(plot3).vector * scale
+ ax.plot( v1, label='s' )
+ ax.plot( v2, 'x',label='es' )
+ ax.plot( v3, label='xfer' )
+ ax.plot( np.array( v1 ) + np.array( v2 ), label='sum' )
+ plt.legend()
+
+
+def almostEq( a, b ):
+ #print a, b, (a-b)/(a+b)
+ return abs(a-b)/(a+b) < 5e-5
+
+def main( standalone = False ):
+ runtime = 100
+ displayInterval = 2
+ makeModel()
+ for i in range( 10, 18 ):
+ moose.setClock( i, 0.01 )
+ moose.reinit()
+ moose.start( runtime )
+ s = moose.element( '/model/compartment/s' )
+ es = moose.element( '/model/endo/s' )
+ assert almostEq( s.conc, es.conc ), 'Asserting %g=%g' % (s.conc, es.conc)
+ # We go for concEndo = 2x concOut. Then
+ # We already know volIn = volOut/8
+ # #in/volIn = 2x #out/volOut
+ # #in/volIn = 2x #out/(8*volIn)
+ # so #in = #out/4
+ # From consv, #in + #out = nInit
+ # so 5/4#out = nInit =>
+ # #out = 0.8*nInit; #in = 0.2*nInit
+ #
+ # flux = perm * nChan * (0.8nInit/volOut - 0.2nInit/(volOut/8) ) =
+ # perm * (nChan*nInit/volOut) * (0.8 - 0.2*8) =
+ # perm * (nChan*nInit/volOut) * (-0.8)
+ #
+ # This has to be balanced by flux = numKf * nOut = numKf * 0.8 * nInit
+ # So 0.8*numKf*nInit = 0.8*perm*nChan*nInit/volOut
+
+ # Note that chan.permeability = 0.1*chanPool.volume / chanPool.nInit
+
+ # so numKf = perm*nChan/volOut = (0.1*volIn/nChan)*nChan/volOut=0.1/8
+ #
+ rXfer = moose.element( '/model/compartment/rXfer' )
+ rXfer.numKf = 0.1/8.0
+ moose.start( runtime )
+ assert( almostEq( 2 * s.conc, es.conc ) )
+
+ if standalone:
+ fig = plt.figure( figsize=(12,10) )
+ ax1 = fig.add_subplot(211)
+ doPlot( ax1, 1, '# of molecules' )
+ ax2 = fig.add_subplot(212)
+ doPlot( ax2, 4, 'conc (uM)' )
+ plt.show()
+ moose.delete( '/model' )
+
+# Run the 'main' if this script is executed standalone.
+if __name__ == '__main__':
+ main( standalone = True )
diff --git a/tests/python/testXdiff1.py b/tests/python/testXdiff1.py
new file mode 100644
index 00000000..bbf73e87
--- /dev/null
+++ b/tests/python/testXdiff1.py
@@ -0,0 +1,174 @@
+# -*- coding: utf-8 -*-
+#########################################################################
+## This program is part of 'MOOSE', the
+## Messaging Object Oriented Simulation Environment.
+## Copyright (C) 2014 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.
+## Here test diffusion across a junction. We set up a pump and change its
+## rate to do a check on the calculation of the diffusion rate separate
+## from the verification that diffusion gives equal concs on either side.
+## The system is a ## 1-voxel cyl compt and an internal endoMesh,
+## having a volume = 1/8 of the parent cylinder..
+## \
+## COMPT: s ----> / s :ENDO
+## s =diffn= s
+## \
+##
+## This becomes:
+## \
+## COMPT: s ----> s_xfer_endo / s :ENDO
+# s =diffn= s
+## \
+##
+#########################################################################
+
+
+import math
+import numpy as np
+import matplotlib.pyplot as plt
+import matplotlib.image as mpimg
+import moose
+import fixXreacs
+
+diffConst = 1e-16
+
+def makeModel():
+ # create container for model
+ num = 1 # number of compartments
+ model = moose.Neutral( '/model' )
+ compartment = moose.CylMesh( '/model/compartment' )
+ compartment.x1 = 1.0e-6 # Set it to a 1 micron single-voxel cylinder
+
+ # create molecules and reactions
+ s = moose.Pool( '/model/compartment/s' )
+ rXfer = moose.Reac( '/model/compartment/rXfer' )
+ #####################################################################
+ # Put in endo compartment. Add molecule s
+ endo = moose.EndoMesh( '/model/endo' )
+ endo.isMembraneBound = False
+ endo.surround = compartment
+ es = moose.Pool( '/model/endo/s' )
+ #####################################################################
+ moose.connect( rXfer, 'sub', s, 'reac' )
+ moose.connect( rXfer, 'prd', es, 'reac' )
+ volRatio = compartment.volume / endo.volume
+ #print( "Volume ratio = {}".format( volRatio ) )
+ rXfer.Kf = 0.0 # 0.02/sec
+ rXfer.Kb = 0.0 #
+ s.concInit = 0.001
+ s.diffConst = diffConst
+ es.diffConst = diffConst
+
+ #####################################################################
+ fixXreacs.fixXreacs( '/model' )
+ #fixXreacs.restoreXreacs( '/model' )
+ #fixXreacs.fixXreacs( '/model' )
+ #####################################################################
+
+ # Make solvers
+ ksolve = moose.Ksolve( '/model/compartment/ksolve' )
+ dsolve = moose.Dsolve( '/model/dsolve' )
+ eksolve = moose.Ksolve( '/model/endo/ksolve' )
+ edsolve = moose.Dsolve( '/model/endo/dsolve' )
+
+ stoich = moose.Stoich( '/model/compartment/stoich' )
+ stoich.compartment = compartment
+ stoich.ksolve = ksolve
+ stoich.dsolve = dsolve
+ stoich.path = "/model/compartment/##"
+ assert( dsolve.numPools == 2 )
+
+ estoich = moose.Stoich( '/model/endo/stoich' )
+ estoich.compartment = endo
+ estoich.ksolve = eksolve
+ estoich.dsolve = edsolve
+ estoich.path = "/model/endo/##"
+ assert( edsolve.numPools == 1 )
+
+ edsolve.buildMeshJunctions( dsolve )
+
+ plot1 = moose.Table2( '/model/plot1' )
+ plot2 = moose.Table2( '/model/plot2' )
+ plot3 = moose.Table2( '/model/plot3' )
+ moose.connect( '/model/plot1', 'requestOut', s, 'getN' )
+ moose.connect( '/model/plot2', 'requestOut', es, 'getN' )
+ moose.connect( '/model/plot3', 'requestOut', '/model/compartment/s_xfer_endo', 'getN' )
+ plot4 = moose.Table2( '/model/plot4' )
+ plot5 = moose.Table2( '/model/plot5' )
+ plot6 = moose.Table2( '/model/plot6' )
+ moose.connect( '/model/plot4', 'requestOut', s, 'getConc' )
+ moose.connect( '/model/plot5', 'requestOut', es, 'getConc' )
+ moose.connect( '/model/plot6', 'requestOut', '/model/compartment/s_xfer_endo', 'getConc' )
+
+def doPlot( ax, i, label ):
+ scale = 1
+ if i > 3:
+ scale = 1000 # Just to plot in uM.
+ plot1 = '/model/plot' + str(i)
+ plot2 = '/model/plot' + str(i+1)
+ plot3 = '/model/plot' + str(i+2)
+ plt.ylabel( label )
+ plt.xlabel( 'time(s)' )
+ v1 = moose.element(plot1).vector * scale
+ v2 = moose.element(plot2).vector * scale
+ v3 = moose.element(plot3).vector * scale
+ ax.plot( v1, label='s' )
+ ax.plot( v2, 'x',label='es' )
+ ax.plot( v3, label='xfer' )
+ ax.plot( np.array( v1 ) + np.array( v2 ), label='sum' )
+ plt.legend()
+
+
+def almostEq( a, b ):
+ #print a, b, (a-b)/(a+b)
+ return abs(a-b)/(a+b) < 5e-5
+
+def main( standalone = False ):
+ runtime = 100
+ makeModel()
+ for i in range( 10, 18 ):
+ moose.setClock( i, 0.01 )
+ moose.reinit()
+ moose.start( runtime )
+ s = moose.element( '/model/compartment/s' )
+ es = moose.element( '/model/endo/s' )
+ assert( almostEq( s.conc, es.conc ) )
+ # We go for concEndo = 2x concOut. Then
+ # We already know volIn = volOut/8
+ # #in/volIn = 2x #out/volOut
+ # #in/volIn = 2x #out/(8*volIn)
+ # so #in = #out/4
+ # From consv, #in + #out = nInit
+ # so 5/4#out = nInit =>
+ # #out = 0.8*nInit; #in = 0.2*nInit
+ #
+ # Diffn flux = D * (xa/L) * (0.8nInit/volOut - 0.2nInit/(volOut/8) )
+ # = -D * (xa/L) * (nInit/volOut) * 0.8
+ # We can obtain xa and L from the endo/mesh
+ #
+ # This has to be balanced by flux = numKf * nOut = numKf * 0.8 * nInit
+ # So 0.8*numKf*nInit = 0.8*(D.Xa/L)*(nInit/volOut)
+ # So numKf = D.Xa/(L*volOut)
+ #
+ rXfer = moose.element( '/model/compartment/rXfer' )
+ endo = moose.element( '/model/endo' )
+ compt = moose.element( '/model/compartment' )
+ endoA = endo.aScale * pow( compt.volume, endo.aPower )
+ rXfer.numKf = 2.0*diffConst*endoA/(compt.r0*compt.volume)
+ moose.start( runtime )
+ assert( almostEq( 2 * s.conc, es.conc ) )
+
+ if standalone:
+ fig = plt.figure( figsize=(12,10) )
+ ax1 = fig.add_subplot(211)
+ doPlot( ax1, 1, '# of molecules' )
+ ax2 = fig.add_subplot(212)
+ doPlot( ax2, 4, 'conc (uM)' )
+ plt.show()
+ moose.delete( '/model' )
+
+# Run the 'main' if this script is executed standalone.
+if __name__ == '__main__':
+ main( standalone = True )
diff --git a/tests/python/testXenz1.py b/tests/python/testXenz1.py
new file mode 100644
index 00000000..b359d44e
--- /dev/null
+++ b/tests/python/testXenz1.py
@@ -0,0 +1,137 @@
+# -*- coding: utf-8 -*-
+#########################################################################
+## This program is part of 'MOOSE', the
+## Messaging Object Oriented Simulation Environment.
+## Copyright (C) 2014 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.
+##
+## Endo / Compartment
+## \
+## sub--enz-/-----> prd
+## sub<-----\----- prd
+## /
+#########################################################################
+
+
+import math
+import numpy as np
+import matplotlib.pyplot as plt
+import matplotlib.image as mpimg
+import moose
+import fixXreacs
+
+subInit = 0.002
+eInit = 0.001
+Km = 0.001
+kcat = 0.2
+Kf = 0.1
+
+def makeModel():
+ # create container for model
+ num = 1 # number of compartments
+ model = moose.Neutral( '/model' )
+ compartment = moose.CylMesh( '/model/compartment' )
+ compartment.x1 = 1.0e-6 # Set it to a 1 micron single-voxel cylinder
+
+ # create molecules and reactions
+ prd = moose.Pool( '/model/compartment/prd' )
+ rXfer = moose.Reac( '/model/compartment/rXfer' )
+ #####################################################################
+ # Put in endo compartment. Add molecule s
+ endo = moose.EndoMesh( '/model/endo' )
+ endo.isMembraneBound = True
+ endo.surround = compartment
+ sub = moose.Pool( '/model/endo/sub' )
+ enzPool = moose.Pool( '/model/endo/enzPool' )
+ enzPool.concInit = eInit
+ enz = moose.MMenz( '/model/endo/enzPool/enz' )
+ #####################################################################
+ moose.connect( enz, 'sub', sub, 'reac' )
+ moose.connect( enz, 'prd', prd, 'reac' )
+ moose.connect( enzPool, 'nOut', enz, 'enzDest' )
+ moose.connect( rXfer, 'sub', prd, 'reac' )
+ moose.connect( rXfer, 'prd', sub, 'reac' )
+ rXfer.Kf = Kf # 0.04/sec
+ rXfer.Kb = 0.0 # 0.02/sec
+ enz.Km = Km
+ enz.kcat = kcat
+ # v = es.kcat/(s+Km)
+ # v = Kf * conc.
+ #####################################################################
+ fixXreacs.fixXreacs( '/model' )
+ fixXreacs.restoreXreacs( '/model' )
+ fixXreacs.fixXreacs( '/model' )
+ #####################################################################
+
+ # Make solvers
+ ksolve = moose.Ksolve( '/model/compartment/ksolve' )
+ dsolve = moose.Dsolve( '/model/dsolve' )
+ eksolve = moose.Ksolve( '/model/endo/ksolve' )
+ edsolve = moose.Dsolve( '/model/endo/dsolve' )
+
+ stoich = moose.Stoich( '/model/compartment/stoich' )
+ stoich.compartment = compartment
+ stoich.ksolve = ksolve
+ stoich.dsolve = dsolve
+ stoich.path = "/model/compartment/##"
+ assert( dsolve.numPools == 2 )
+ sub.vec.concInit = subInit
+ enzPool.vec.concInit = eInit
+
+ estoich = moose.Stoich( '/model/endo/stoich' )
+ estoich.compartment = endo
+ estoich.ksolve = eksolve
+ estoich.dsolve = edsolve
+ estoich.path = "/model/endo/##"
+ assert( edsolve.numPools == 3 )
+
+ edsolve.buildMeshJunctions( dsolve )
+
+ plot1 = moose.Table2( '/model/plot1' )
+ plot2 = moose.Table2( '/model/plot2' )
+ moose.connect( '/model/plot1', 'requestOut', sub, 'getN' )
+ moose.connect( '/model/plot2', 'requestOut', prd, 'getN' )
+ plot3 = moose.Table2( '/model/plot3' )
+ plot4 = moose.Table2( '/model/plot4' )
+ moose.connect( '/model/plot3', 'requestOut', sub, 'getConc' )
+ moose.connect( '/model/plot4', 'requestOut', prd, 'getConc' )
+
+def doPlot( ax, plot1, plot2, label ):
+ plt.ylabel( label )
+ plt.xlabel( 'time(s)' )
+ v1 = moose.element(plot1).vector
+ v2 = moose.element(plot2).vector
+ ax.plot( v1, label='sub' )
+ ax.plot( v2, label='prd' )
+ ax.plot( np.array( v1 ) + np.array( v2 ), label='sum' )
+ plt.legend()
+
+def almostEq( a, b ):
+ #print a, b, (a-b)/(a+b)
+ return abs(a-b)/(a+b) < 5e-5
+
+def main( standalone = False ):
+ for i in range( 10, 18 ):
+ moose.setClock( i, 0.001 )
+ runtime = 100
+ displayInterval = 2
+ makeModel()
+ moose.reinit()
+ moose.start( runtime )
+ assert( almostEq( moose.element( 'model/compartment/prd' ).n,
+ moose.element( '/model/endo/sub' ).n ) )
+
+ if standalone:
+ fig = plt.figure( figsize=(12,10) )
+ ax1 = fig.add_subplot(211)
+ doPlot( ax1, '/model/plot1', '/model/plot2', '# of molecules' )
+ ax2 = fig.add_subplot(212)
+ doPlot( ax2, '/model/plot3', '/model/plot4', 'conc (mM)' )
+ plt.show()
+ moose.delete( '/model' )
+
+# Run the 'main' if this script is executed standalone.
+if __name__ == '__main__':
+ main( standalone = True )
diff --git a/tests/python/testXreacs2.py b/tests/python/testXreacs2.py
new file mode 100644
index 00000000..289c2b24
--- /dev/null
+++ b/tests/python/testXreacs2.py
@@ -0,0 +1,61 @@
+# -*- coding: utf-8 -*-
+import os
+import matplotlib as mpl
+import matplotlib.pyplot as plt
+mpl.rcParams['text.usetex'] = False
+import moose
+import numpy as np
+import fixXreacs
+
+def countCrossings( plot, thresh ):
+ vec = moose.element( plot ).vector
+ #print (vec[:-1] < thresh)
+ return sum( (vec[:-1] < thresh) * (vec[1:] >= thresh ) )
+
+def main( standalone = False ):
+ mfile = os.path.join( os.path.dirname( __file__), 'OSC_diff_vols.g' )
+ runtime = 4000.0
+ modelId = moose.loadModel( mfile, 'model', 'ee' )
+ kin = moose.element( '/model/kinetics' )
+ compt1 = moose.element( '/model/compartment_1' )
+ compt1.x1 += kin.x1
+ compt1.x0 += kin.x1
+ fixXreacs.fixXreacs( '/model' )
+ #fixXreacs.restoreXreacs( '/model' )
+ #fixXreacs.fixXreacs( '/model' )
+
+ ks1 = moose.Ksolve( '/model/kinetics/ksolve' )
+ ds1 = moose.Dsolve( '/model/kinetics/dsolve' )
+ s1 = moose.Stoich( '/model/kinetics/stoich' )
+ s1.compartment = moose.element( '/model/kinetics' )
+ s1.ksolve = ks1
+ s1.dsolve = ds1
+ s1.path = '/model/kinetics/##'
+
+ ks2 = moose.Ksolve( '/model/compartment_1/ksolve' )
+ ds2 = moose.Dsolve( '/model/compartment_1/dsolve' )
+ s2 = moose.Stoich( '/model/compartment_1/stoich' )
+ s2.compartment = moose.element( '/model/compartment_1' )
+ s2.ksolve = ks2
+ s2.dsolve = ds2
+ s2.path = '/model/compartment_1/##'
+
+ ds2.buildMeshJunctions( ds1 )
+
+ moose.reinit()
+ moose.start( runtime )
+ # I don't have an analytic way to assess oscillations
+ assert( countCrossings( '/model/graphs/conc2/M.Co', 0.001 ) == 4 )
+
+ if standalone:
+ # Display all plots.
+ for x in moose.wildcardFind( '/model/#graphs/conc#/#' ):
+ t = np.arange( 0, x.vector.size, 1 ) * x.dt
+ plt.plot( t, x.vector, label=x.name )
+ plt.legend()
+ plt.show()
+ moose.delete( '/model' )
+
+# Run the 'main' if this script is executed standalone.
+if __name__ == '__main__':
+ main( standalone = True )
diff --git a/tests/python/testXreacs3.py b/tests/python/testXreacs3.py
new file mode 100644
index 00000000..4e5ef170
--- /dev/null
+++ b/tests/python/testXreacs3.py
@@ -0,0 +1,132 @@
+# -*- coding: utf-8 -*-
+#########################################################################
+## This program is part of 'MOOSE', the
+## Messaging Object Oriented Simulation Environment.
+## Copyright (C) 2014 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.
+## Here we set up equal Kf and Kb in a reversible reaction across a
+## 1-voxel cyl compt and an internal endoMesh, having a smaller volume.
+## \
+## COMPT: s <===> / s :ENDO
+## \
+##
+## This becomes:
+## \
+## COMPT: s <===> s_xfer_endo / s :ENDO
+## \
+##
+#########################################################################
+
+
+import math
+import numpy as np
+import matplotlib.pyplot as plt
+import matplotlib.image as mpimg
+import moose
+import fixXreacs
+
+def makeModel():
+ # create container for model
+ num = 1 # number of compartments
+ model = moose.Neutral( '/model' )
+ compartment = moose.CylMesh( '/model/compartment' )
+ compartment.x1 = 1.0e-6 # Set it to a 1 micron single-voxel cylinder
+
+ # create molecules and reactions
+ s = moose.Pool( '/model/compartment/s' )
+ rXfer = moose.Reac( '/model/compartment/rXfer' )
+ #####################################################################
+ # Put in endo compartment. Add molecule s
+ endo = moose.EndoMesh( '/model/endo' )
+ endo.isMembraneBound = True
+ endo.surround = compartment
+ es = moose.Pool( '/model/endo/s' )
+ #####################################################################
+ moose.connect( rXfer, 'sub', s, 'reac' )
+ moose.connect( rXfer, 'prd', es, 'reac' )
+ volRatio = compartment.volume / endo.volume
+ rXfer.Kf = 0.02 # 0.01/sec
+ rXfer.Kb = 0.02 # 1/sec
+
+ #####################################################################
+ fixXreacs.fixXreacs( '/model' )
+ fixXreacs.restoreXreacs( '/model' )
+ fixXreacs.fixXreacs( '/model' )
+ #####################################################################
+
+ # Make solvers
+ ksolve = moose.Ksolve( '/model/compartment/ksolve' )
+ dsolve = moose.Dsolve( '/model/dsolve' )
+ eksolve = moose.Ksolve( '/model/endo/ksolve' )
+ edsolve = moose.Dsolve( '/model/endo/dsolve' )
+
+ stoich = moose.Stoich( '/model/compartment/stoich' )
+ stoich.compartment = compartment
+ stoich.ksolve = ksolve
+ stoich.dsolve = dsolve
+ stoich.path = "/model/compartment/##"
+ assert( dsolve.numPools == 2 )
+ s.vec.concInit = [1]*num
+
+ estoich = moose.Stoich( '/model/endo/stoich' )
+ estoich.compartment = endo
+ estoich.ksolve = eksolve
+ estoich.dsolve = edsolve
+ estoich.path = "/model/endo/##"
+ assert( edsolve.numPools == 1 )
+
+ edsolve.buildMeshJunctions( dsolve )
+
+ plot1 = moose.Table2( '/model/plot1' )
+ plot2 = moose.Table2( '/model/plot2' )
+ plot3 = moose.Table2( '/model/plot3' )
+ moose.connect( '/model/plot1', 'requestOut', s, 'getN' )
+ moose.connect( '/model/plot2', 'requestOut', es, 'getN' )
+ moose.connect( '/model/plot3', 'requestOut', '/model/compartment/s_xfer_endo', 'getN' )
+ plot4 = moose.Table2( '/model/plot4' )
+ plot5 = moose.Table2( '/model/plot5' )
+ plot6 = moose.Table2( '/model/plot6' )
+ moose.connect( '/model/plot4', 'requestOut', s, 'getConc' )
+ moose.connect( '/model/plot5', 'requestOut', es, 'getConc' )
+ moose.connect( '/model/plot6', 'requestOut', '/model/compartment/s_xfer_endo', 'getConc' )
+
+def doPlot( ax, i, label ):
+ plot1 = '/model/plot' + str(i)
+ plot2 = '/model/plot' + str(i+1)
+ plot3 = '/model/plot' + str(i+2)
+ plt.ylabel( label )
+ plt.xlabel( 'time(s)' )
+ v1 = moose.element(plot1).vector
+ v2 = moose.element(plot2).vector
+ v3 = moose.element(plot3).vector
+ ax.plot( v1, label='s' )
+ ax.plot( v2, 'x',label='es' )
+ ax.plot( v3, label='xfer' )
+ ax.plot( np.array( v1 ) + np.array( v2 ), label='sum' )
+ plt.legend()
+
+def almostEq( a, b ):
+ return abs(a-b)/(a+b) < 5e-5
+
+def main( standalone = False ):
+ runtime = 100
+ makeModel()
+ moose.reinit()
+ moose.start( runtime )
+ assert( almostEq( moose.element( 'model/compartment/s' ).conc,
+ moose.element( '/model/endo/s' ).conc ) )
+
+ if standalone:
+ fig = plt.figure( figsize=(12,10) )
+ ax1 = fig.add_subplot(211)
+ doPlot( ax1, 1, '# of molecules' )
+ ax2 = fig.add_subplot(212)
+ doPlot( ax2, 4, 'conc (mM)' )
+ plt.show()
+ moose.delete( '/model' )
+
+# Run the 'main' if this script is executed standalone.
+if __name__ == '__main__':
+ main( standalone = True )
diff --git a/tests/python/testXreacs4.py b/tests/python/testXreacs4.py
new file mode 100644
index 00000000..4fd44007
--- /dev/null
+++ b/tests/python/testXreacs4.py
@@ -0,0 +1,114 @@
+# -*- coding: utf-8 -*-
+#########################################################################
+## This program is part of 'MOOSE', the
+## Messaging Object Oriented Simulation Environment.
+## Copyright (C) 2014 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.
+#########################################################################
+
+
+import math
+import numpy as np
+import matplotlib.pyplot as plt
+import matplotlib.image as mpimg
+import moose
+import fixXreacs
+
+def makeModel():
+ # create container for model
+ num = 1 # number of compartments
+ model = moose.Neutral( '/model' )
+ compartment = moose.CylMesh( '/model/compartment' )
+ compartment.x1 = 1.0e-6 # Set it to a 1 micron single-voxel cylinder
+
+ # create molecules and reactions
+ s = moose.Pool( '/model/compartment/s' )
+ rXfer = moose.Reac( '/model/compartment/rXfer' )
+ #####################################################################
+ # Put in endo compartment. Add molecule s
+ endo = moose.EndoMesh( '/model/endo' )
+ endo.isMembraneBound = True
+ endo.surround = compartment
+ es = moose.Pool( '/model/endo/s' )
+ #####################################################################
+ moose.connect( rXfer, 'sub', s, 'reac' )
+ moose.connect( rXfer, 'prd', es, 'reac' )
+ volRatio = compartment.volume / endo.volume
+ rXfer.Kf = 0.04 # 0.04/sec
+ rXfer.Kb = 0.02 # 0.02/sec
+
+ #####################################################################
+ fixXreacs.fixXreacs( '/model' )
+ #fixXreacs.restoreXreacs( '/model' )
+ #fixXreacs.fixXreacs( '/model' )
+ #####################################################################
+
+ # Make solvers
+ ksolve = moose.Ksolve( '/model/compartment/ksolve' )
+ dsolve = moose.Dsolve( '/model/dsolve' )
+ eksolve = moose.Ksolve( '/model/endo/ksolve' )
+ edsolve = moose.Dsolve( '/model/endo/dsolve' )
+
+ stoich = moose.Stoich( '/model/compartment/stoich' )
+ stoich.compartment = compartment
+ stoich.ksolve = ksolve
+ stoich.dsolve = dsolve
+ stoich.path = "/model/compartment/##"
+ assert( dsolve.numPools == 2 )
+ s.vec.concInit = [1]*num
+
+ estoich = moose.Stoich( '/model/endo/stoich' )
+ estoich.compartment = endo
+ estoich.ksolve = eksolve
+ estoich.dsolve = edsolve
+ estoich.path = "/model/endo/##"
+ assert( edsolve.numPools == 1 )
+
+ edsolve.buildMeshJunctions( dsolve )
+
+ plot1 = moose.Table2( '/model/plot1' )
+ plot2 = moose.Table2( '/model/plot2' )
+ moose.connect( '/model/plot1', 'requestOut', s, 'getN' )
+ moose.connect( '/model/plot2', 'requestOut', es, 'getN' )
+ plot3 = moose.Table2( '/model/plot3' )
+ plot4 = moose.Table2( '/model/plot4' )
+ moose.connect( '/model/plot3', 'requestOut', s, 'getConc' )
+ moose.connect( '/model/plot4', 'requestOut', es, 'getConc' )
+
+def doPlot( ax, plot1, plot2, label ):
+ plt.ylabel( label )
+ plt.xlabel( 'time(s)' )
+ v1 = moose.element(plot1).vector
+ v2 = moose.element(plot2).vector
+ ax.plot( v1, label='s' )
+ ax.plot( v2, label='es' )
+ ax.plot( np.array( v1 ) + np.array( v2 ), label='sum' )
+ plt.legend()
+
+def almostEq( a, b ):
+ return abs(a-b)/(a+b) < 5e-5
+
+def main( standalone = False ):
+ runtime = 100
+ displayInterval = 2
+ makeModel()
+ moose.reinit()
+ moose.start( runtime )
+ assert( almostEq( 2.0 * moose.element( 'model/compartment/s' ).conc,
+ moose.element( '/model/endo/s' ).conc ) )
+
+ if standalone:
+ fig = plt.figure( figsize=(12,10) )
+ ax1 = fig.add_subplot(211)
+ doPlot( ax1, '/model/plot1', '/model/plot2', '# of molecules' )
+ ax2 = fig.add_subplot(212)
+ doPlot( ax2, '/model/plot3', '/model/plot4', 'conc (mM)' )
+ plt.show()
+
+ moose.delete( '/model' )
+
+# Run the 'main' if this script is executed standalone.
+if __name__ == '__main__':
+ main( standalone = True )
diff --git a/tests/python/testXreacs4a.py b/tests/python/testXreacs4a.py
new file mode 100644
index 00000000..2fe009e9
--- /dev/null
+++ b/tests/python/testXreacs4a.py
@@ -0,0 +1,114 @@
+# -*- coding: utf-8 -*-
+#########################################################################
+## This program is part of 'MOOSE', the
+## Messaging Object Oriented Simulation Environment.
+## Copyright (C) 2014 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.
+#########################################################################
+
+
+import math
+import numpy as np
+import matplotlib.pyplot as plt
+import matplotlib.image as mpimg
+import moose
+import fixXreacs
+
+def makeModel():
+ # create container for model
+ num = 1 # number of compartments
+ model = moose.Neutral( '/model' )
+ compartment = moose.CylMesh( '/model/compartment' )
+ compartment.x1 = 1.0e-6 # Set it to a 1 micron single-voxel cylinder
+
+ # create molecules and reactions
+ s = moose.Pool( '/model/compartment/s' )
+ #####################################################################
+ # Put in endo compartment. Add molecule s
+ endo = moose.EndoMesh( '/model/endo' )
+ endo.isMembraneBound = True
+ endo.surround = compartment
+ es = moose.Pool( '/model/endo/s' )
+ rXfer = moose.Reac( '/model/endo/rXfer' )
+ #####################################################################
+ moose.connect( rXfer, 'sub', s, 'reac' )
+ moose.connect( rXfer, 'prd', es, 'reac' )
+ volRatio = compartment.volume / endo.volume
+ rXfer.Kf = 0.04 # 0.04/sec
+ rXfer.Kb = 0.02 # 0.02/sec
+
+ #####################################################################
+ fixXreacs.fixXreacs( '/model' )
+ #fixXreacs.restoreXreacs( '/model' )
+ #fixXreacs.fixXreacs( '/model' )
+ #####################################################################
+
+ # Make solvers
+ ksolve = moose.Ksolve( '/model/compartment/ksolve' )
+ dsolve = moose.Dsolve( '/model/dsolve' )
+ eksolve = moose.Ksolve( '/model/endo/ksolve' )
+ edsolve = moose.Dsolve( '/model/endo/dsolve' )
+
+ stoich = moose.Stoich( '/model/compartment/stoich' )
+ stoich.compartment = compartment
+ stoich.ksolve = ksolve
+ stoich.dsolve = dsolve
+ stoich.path = "/model/compartment/##"
+ assert( dsolve.numPools == 1 )
+ s.vec.concInit = [1]*num
+
+ estoich = moose.Stoich( '/model/endo/stoich' )
+ estoich.compartment = endo
+ estoich.ksolve = eksolve
+ estoich.dsolve = edsolve
+ estoich.path = "/model/endo/##"
+ assert( edsolve.numPools == 2 )
+
+ edsolve.buildMeshJunctions( dsolve )
+
+ plot1 = moose.Table2( '/model/plot1' )
+ plot2 = moose.Table2( '/model/plot2' )
+ moose.connect( '/model/plot1', 'requestOut', s, 'getN' )
+ moose.connect( '/model/plot2', 'requestOut', es, 'getN' )
+ plot3 = moose.Table2( '/model/plot3' )
+ plot4 = moose.Table2( '/model/plot4' )
+ moose.connect( '/model/plot3', 'requestOut', s, 'getConc' )
+ moose.connect( '/model/plot4', 'requestOut', es, 'getConc' )
+
+def doPlot( ax, plot1, plot2, label ):
+ plt.ylabel( label )
+ plt.xlabel( 'time(s)' )
+ v1 = moose.element(plot1).vector
+ v2 = moose.element(plot2).vector
+ ax.plot( v1, label='s' )
+ ax.plot( v2, label='es' )
+ ax.plot( np.array( v1 ) + np.array( v2 ), label='sum' )
+ plt.legend()
+
+def almostEq( a, b ):
+ return abs(a-b)/(a+b) < 5e-5
+
+def main( standalone = False ):
+ runtime = 200
+ displayInterval = 2
+ makeModel()
+ moose.reinit()
+ moose.start( runtime )
+ assert( almostEq( 2.0 * moose.element( 'model/compartment/s' ).conc,
+ moose.element( '/model/endo/s' ).conc ) )
+
+ if standalone:
+ fig = plt.figure( figsize=(12,10) )
+ ax1 = fig.add_subplot(211)
+ doPlot( ax1, '/model/plot1', '/model/plot2', '# of molecules' )
+ ax2 = fig.add_subplot(212)
+ doPlot( ax2, '/model/plot3', '/model/plot4', 'conc (mM)' )
+ plt.show()
+ moose.delete( '/model' )
+
+
+# Run the 'main' if this script is executed standalone.
+if __name__ == '__main__':
+ main( standalone = True )
diff --git a/tests/python/testXreacs5.py b/tests/python/testXreacs5.py
new file mode 100644
index 00000000..e46bc459
--- /dev/null
+++ b/tests/python/testXreacs5.py
@@ -0,0 +1,120 @@
+# -*- coding: utf-8 -*-
+#########################################################################
+## This program is part of 'MOOSE', the
+## Messaging Object Oriented Simulation Environment.
+## Copyright (C) 2014 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.
+#########################################################################
+
+
+import math
+import numpy as np
+import matplotlib.pyplot as plt
+import matplotlib.image as mpimg
+import moose
+import fixXreacs
+
+def makeModel():
+ # create container for model
+ num = 1 # number of compartments
+ model = moose.Neutral( '/model' )
+ compartment = moose.CylMesh( '/model/compartment' )
+ compartment.x1 = 1.0e-6 # Set it to a 1 micron single-voxel cylinder
+
+ # create molecules and reactions
+ s = moose.Pool( '/model/compartment/s' )
+ rXfer = moose.Reac( '/model/compartment/rXfer' )
+ #####################################################################
+ # Put in endo compartment. Add molecule s
+ endo = moose.EndoMesh( '/model/endo' )
+ endo.isMembraneBound = True
+ endo.surround = compartment
+ es = moose.Pool( '/model/endo/s' )
+ erXfer = moose.Reac( '/model/endo/erXfer' )
+ #####################################################################
+ moose.connect( erXfer, 'sub', es, 'reac' )
+ moose.connect( erXfer, 'prd', s, 'reac' )
+ moose.connect( rXfer, 'sub', s, 'reac' )
+ moose.connect( rXfer, 'prd', es, 'reac' )
+ rXfer.Kf = 0.04 # 0.04/sec
+ rXfer.Kb = 0.0 # 0.00/sec
+ erXfer.Kf = 0.16 # 0.16/sec
+ erXfer.Kb = 0.0 # 0.00/sec
+
+ #####################################################################
+ fixXreacs.fixXreacs( '/model' )
+ fixXreacs.restoreXreacs( '/model' )
+ fixXreacs.fixXreacs( '/model' )
+ #####################################################################
+
+ # Make solvers
+ ksolve = moose.Ksolve( '/model/compartment/ksolve' )
+ dsolve = moose.Dsolve( '/model/dsolve' )
+ eksolve = moose.Ksolve( '/model/endo/ksolve' )
+ edsolve = moose.Dsolve( '/model/endo/dsolve' )
+
+ stoich = moose.Stoich( '/model/compartment/stoich' )
+ stoich.compartment = compartment
+ stoich.ksolve = ksolve
+ stoich.dsolve = dsolve
+ stoich.path = "/model/compartment/##"
+ assert( dsolve.numPools == 2 )
+ s.vec.concInit = [1]*num
+
+ estoich = moose.Stoich( '/model/endo/stoich' )
+ estoich.compartment = endo
+ estoich.ksolve = eksolve
+ estoich.dsolve = edsolve
+ estoich.path = "/model/endo/##"
+ assert( edsolve.numPools == 2 )
+
+ edsolve.buildMeshJunctions( dsolve )
+
+ plot1 = moose.Table2( '/model/plot1' )
+ plot2 = moose.Table2( '/model/plot2' )
+ moose.connect( '/model/plot1', 'requestOut', s, 'getN' )
+ moose.connect( '/model/plot2', 'requestOut', es, 'getN' )
+ plot3 = moose.Table2( '/model/plot3' )
+ plot4 = moose.Table2( '/model/plot4' )
+ moose.connect( '/model/plot3', 'requestOut', s, 'getConc' )
+ moose.connect( '/model/plot4', 'requestOut', es, 'getConc' )
+
+def doPlot( ax, plot1, plot2, label ):
+ plt.ylabel( label )
+ plt.xlabel( 'time(s)' )
+ v1 = moose.element(plot1).vector
+ v2 = moose.element(plot2).vector
+ ax.plot( v1, label='s' )
+ ax.plot( v2, label='es' )
+ ax.plot( np.array( v1 ) + np.array( v2 ), label='sum' )
+ plt.legend()
+
+def almostEq( a, b ):
+ #print a, b, (a-b)/(a+b)
+ return abs(a-b)/(a+b) < 5e-5
+
+def main( standalone = False ):
+ for i in range( 10, 18):
+ moose.setClock( i, 0.001 )
+ runtime = 100
+ makeModel()
+ moose.reinit()
+ moose.start( runtime )
+
+ assert( almostEq( 2.0 * moose.element( 'model/compartment/s' ).conc,
+ moose.element( '/model/endo/s' ).conc ) )
+
+ if standalone:
+ fig = plt.figure( figsize=(12,10) )
+ ax1 = fig.add_subplot(211)
+ doPlot( ax1, '/model/plot1', '/model/plot2', '# of molecules' )
+ ax2 = fig.add_subplot(212)
+ doPlot( ax2, '/model/plot3', '/model/plot4', 'conc (mM)' )
+ plt.show()
+ moose.delete( '/model' )
+
+# Run the 'main' if this script is executed standalone.
+if __name__ == '__main__':
+ main( standalone = True )
diff --git a/tests/python/testXreacs5a.py b/tests/python/testXreacs5a.py
new file mode 100644
index 00000000..330419ea
--- /dev/null
+++ b/tests/python/testXreacs5a.py
@@ -0,0 +1,120 @@
+# -*- coding: utf-8 -*-
+#########################################################################
+## This program is part of 'MOOSE', the
+## Messaging Object Oriented Simulation Environment.
+## Copyright (C) 2014 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.
+#########################################################################
+
+
+import math
+import numpy as np
+import matplotlib.pyplot as plt
+import matplotlib.image as mpimg
+import moose
+import fixXreacs
+
+def makeModel():
+ # create container for model
+ num = 1 # number of compartments
+ model = moose.Neutral( '/model' )
+ compartment = moose.CylMesh( '/model/compartment' )
+ compartment.x1 = 1.0e-6 # Set it to a 1 micron single-voxel cylinder
+
+ # create molecules and reactions
+ s = moose.Pool( '/model/compartment/s' )
+ rXfer = moose.Reac( '/model/compartment/rXfer' )
+ #####################################################################
+ # Put in endo compartment. Add molecule s
+ endo = moose.EndoMesh( '/model/endo' )
+ endo.isMembraneBound = True
+ endo.surround = compartment
+ es = moose.Pool( '/model/endo/s' )
+ erXfer = moose.Reac( '/model/compartment/erXfer' )
+ #####################################################################
+ moose.connect( erXfer, 'sub', es, 'reac' )
+ moose.connect( erXfer, 'prd', s, 'reac' )
+ moose.connect( rXfer, 'sub', s, 'reac' )
+ moose.connect( rXfer, 'prd', es, 'reac' )
+ rXfer.Kf = 0.04 # 0.04/sec
+ rXfer.Kb = 0.0 # 0.02/sec
+ erXfer.Kf = 0.02 # 0.04/sec
+ erXfer.Kb = 0.0 # 0.02/sec
+
+ #####################################################################
+ fixXreacs.fixXreacs( '/model' )
+ fixXreacs.restoreXreacs( '/model' )
+ fixXreacs.fixXreacs( '/model' )
+ #####################################################################
+ rx = moose.element( '/model/compartment/rXfer' )
+ erx = moose.element( '/model/compartment/erXfer' )
+
+ # Make solvers
+ ksolve = moose.Ksolve( '/model/compartment/ksolve' )
+ dsolve = moose.Dsolve( '/model/dsolve' )
+ eksolve = moose.Ksolve( '/model/endo/ksolve' )
+ edsolve = moose.Dsolve( '/model/endo/dsolve' )
+
+ stoich = moose.Stoich( '/model/compartment/stoich' )
+ stoich.compartment = compartment
+ stoich.ksolve = ksolve
+ stoich.dsolve = dsolve
+ stoich.path = "/model/compartment/##"
+ assert( dsolve.numPools == 2 )
+ s.vec.concInit = [1]*num
+
+ estoich = moose.Stoich( '/model/endo/stoich' )
+ estoich.compartment = endo
+ estoich.ksolve = eksolve
+ estoich.dsolve = edsolve
+ estoich.path = "/model/endo/##"
+ assert( edsolve.numPools == 1 )
+
+ edsolve.buildMeshJunctions( dsolve )
+
+ plot1 = moose.Table2( '/model/plot1' )
+ plot2 = moose.Table2( '/model/plot2' )
+ moose.connect( '/model/plot1', 'requestOut', s, 'getN' )
+ moose.connect( '/model/plot2', 'requestOut', es, 'getN' )
+ plot3 = moose.Table2( '/model/plot3' )
+ plot4 = moose.Table2( '/model/plot4' )
+ moose.connect( '/model/plot3', 'requestOut', s, 'getConc' )
+ moose.connect( '/model/plot4', 'requestOut', es, 'getConc' )
+
+def doPlot( ax, plot1, plot2, label ):
+ plt.ylabel( label )
+ plt.xlabel( 'time(s)' )
+ v1 = moose.element(plot1).vector
+ v2 = moose.element(plot2).vector
+ ax.plot( v1, label='s' )
+ ax.plot( v2, label='es' )
+ ax.plot( np.array( v1 ) + np.array( v2 ), label='sum' )
+ plt.legend()
+
+def almostEq( a, b ):
+ return abs(a-b)/(a+b) < 5e-5
+
+def main( standalone = False ):
+ runtime = 200
+ displayInterval = 2
+ makeModel()
+ moose.reinit()
+ moose.start( runtime )
+
+ assert( almostEq( 2.0 * moose.element( 'model/compartment/s' ).n,
+ moose.element( '/model/endo/s' ).n ) )
+
+ if standalone:
+ fig = plt.figure( figsize=(12,10) )
+ ax1 = fig.add_subplot(211)
+ doPlot( ax1, '/model/plot1', '/model/plot2', '# of molecules' )
+ ax2 = fig.add_subplot(212)
+ doPlot( ax2, '/model/plot3', '/model/plot4', 'conc (mM)' )
+ plt.show()
+ moose.delete( '/model' )
+
+# Run the 'main' if this script is executed standalone.
+if __name__ == '__main__':
+ main( standalone = True )
diff --git a/tests/python/testXreacs6.py b/tests/python/testXreacs6.py
new file mode 100644
index 00000000..7edb514d
--- /dev/null
+++ b/tests/python/testXreacs6.py
@@ -0,0 +1,120 @@
+# -*- coding: utf-8 -*-
+#########################################################################
+## This program is part of 'MOOSE', the
+## Messaging Object Oriented Simulation Environment.
+## Copyright (C) 2018 Upinder S. Bhalla. and NCBS
+## It is made available under the terms of the
+## GNU General Public License version 3 or later.
+## See the file COPYING.LIB for the full notice.
+#########################################################################
+
+
+import math
+import numpy as np
+import matplotlib.pyplot as plt
+import matplotlib.image as mpimg
+import moose
+import fixXreacs
+
+def makeModel():
+ # create container for model
+ num = 1 # number of compartments
+ model = moose.Neutral( '/model' )
+ compartment = moose.CylMesh( '/model/compartment' )
+ compartment.x1 = 1.0e-6 # Set it to a 1 micron single-voxel cylinder
+
+ # create molecules and reactions
+ s = moose.Pool( '/model/compartment/s' )
+ t = moose.Pool( '/model/compartment/t' )
+ rXfer = moose.Reac( '/model/compartment/rXfer' )
+ #####################################################################
+ # Put in endo compartment. Add molecule s
+ endo = moose.EndoMesh( '/model/endo' )
+ endo.isMembraneBound = True
+ endo.surround = compartment
+ es = moose.Pool( '/model/endo/s' )
+ et = moose.Pool( '/model/endo/t' )
+ #####################################################################
+ moose.connect( rXfer, 'sub', s, 'reac' )
+ moose.connect( rXfer, 'sub', t, 'reac' )
+ moose.connect( rXfer, 'prd', es, 'reac' )
+ moose.connect( rXfer, 'prd', et, 'reac' )
+ rXfer.Kf = 0.02 # 0.02/mM/sec
+ rXfer.Kb = 0.02 # 0.02/mM/sec
+
+ #####################################################################
+ fixXreacs.fixXreacs( '/model' )
+ #fixXreacs.restoreXreacs( '/model' )
+ #fixXreacs.fixXreacs( '/model' )
+ #####################################################################
+ # Make solvers
+ ksolve = moose.Ksolve( '/model/compartment/ksolve' )
+ dsolve = moose.Dsolve( '/model/dsolve' )
+ eksolve = moose.Ksolve( '/model/endo/ksolve' )
+ edsolve = moose.Dsolve( '/model/endo/dsolve' )
+
+ stoich = moose.Stoich( '/model/compartment/stoich' )
+ stoich.compartment = compartment
+ stoich.ksolve = ksolve
+ stoich.dsolve = dsolve
+ stoich.path = "/model/compartment/##"
+ assert( dsolve.numPools == 4 )
+ s.vec.concInit = [1]*num
+ t.vec.concInit = [1]*num
+
+ estoich = moose.Stoich( '/model/endo/stoich' )
+ estoich.compartment = endo
+ estoich.ksolve = eksolve
+ estoich.dsolve = edsolve
+ estoich.path = "/model/endo/##"
+ assert( edsolve.numPools == 2 )
+
+ edsolve.buildMeshJunctions( dsolve )
+
+ plot1 = moose.Table2( '/model/plot1' )
+ plot2 = moose.Table2( '/model/plot2' )
+ moose.connect( '/model/plot1', 'requestOut', s, 'getN' )
+ moose.connect( '/model/plot2', 'requestOut', es, 'getN' )
+ plot3 = moose.Table2( '/model/plot3' )
+ plot4 = moose.Table2( '/model/plot4' )
+ moose.connect( '/model/plot3', 'requestOut', s, 'getConc' )
+ moose.connect( '/model/plot4', 'requestOut', es, 'getConc' )
+
+def doPlot( ax, plot1, plot2, label ):
+ plt.ylabel( label )
+ plt.xlabel( 'time(s)' )
+ v1 = moose.element(plot1).vector
+ v2 = moose.element(plot2).vector
+ ax.plot( v1, label='s' )
+ ax.plot( v2, label='es' )
+ ax.plot( np.array( v1 ) + np.array( v2 ), label='sum' )
+ plt.legend()
+
+def almostEq( a, b ):
+ #print a, b, (a-b)/(a+b)
+ return abs(a-b)/(a+b) < 5e-5
+
+def main( standalone = False ):
+ for i in range( 10, 18):
+ moose.setClock( i, 0.01 )
+ runtime = 100
+ displayInterval = 2
+ makeModel()
+ moose.reinit()
+ moose.start( runtime )
+
+ assert( almostEq( moose.element( 'model/compartment/s' ).conc,
+ moose.element( '/model/endo/s' ).conc ) )
+
+ if standalone:
+ fig = plt.figure( figsize=(12,10) )
+ ax1 = fig.add_subplot(211)
+ doPlot( ax1, '/model/plot1', '/model/plot2', '# of molecules' )
+ ax2 = fig.add_subplot(212)
+ doPlot( ax2, '/model/plot3', '/model/plot4', 'conc (mM)' )
+ plt.show()
+ moose.delete( '/model' )
+
+# Run the 'main' if this script is executed standalone.
+if __name__ == '__main__':
+ main( standalone = True )
diff --git a/tests/python/testXreacs7.py b/tests/python/testXreacs7.py
new file mode 100644
index 00000000..b55de268
--- /dev/null
+++ b/tests/python/testXreacs7.py
@@ -0,0 +1,137 @@
+# -*- coding: utf-8 -*-
+#########################################################################
+## This program is part of 'MOOSE', the
+## Messaging Object Oriented Simulation Environment.
+## Copyright (C) 2018 Upinder S. Bhalla. and NCBS
+## It is made available under the terms of the
+## GNU General Public License version 3 or later.
+## See the file COPYING.LIB for the full notice.
+##
+## This file makes u + t <=====> s where u is in a different compt from t,s
+#########################################################################
+
+
+import math
+import numpy as np
+import matplotlib.pyplot as plt
+import matplotlib.image as mpimg
+import moose
+import fixXreacs
+
+def makeModel():
+ # create container for model
+ num = 1 # number of compartments
+ model = moose.Neutral( '/model' )
+ compartment = moose.CylMesh( '/model/compartment' )
+ compartment.x1 = 1.0e-6 # Set it to a 1 micron single-voxel cylinder
+
+ # create molecules and reactions
+ u = moose.Pool( '/model/compartment/u' )
+ #####################################################################
+ # Put in endo compartment. Add molecule s
+ endo = moose.EndoMesh( '/model/endo' )
+ endo.isMembraneBound = True
+ endo.surround = compartment
+ rXfer = moose.Reac( '/model/endo/rXfer' )
+ et = moose.Pool( '/model/endo/t' )
+ es = moose.Pool( '/model/endo/s' )
+ #####################################################################
+ moose.connect( rXfer, 'sub', u, 'reac' )
+ moose.connect( rXfer, 'sub', et, 'reac' )
+ moose.connect( rXfer, 'prd', es, 'reac' )
+ u.concInit = 1.0
+ et.concInit = 1.0
+
+ #####################################################################
+ # [u0] = 1 in compt, [t0] = 1 in endo, [s0] = 0
+ # [u] + [s]/8 = [u0] ; [t] + [s] = [t0]; nu + ns = nu0, nt + ns = nt0
+ # At equil, numKf*nu*nt = numKb*ns
+ # Express all # in terms of ns.
+ # nu = nu0-ns; nt = nt0-ns Also, nu0 = 8*nt0
+ # So numKf*(nu0-ns)*(nt0-ns) = numKb*ns
+ # Target level is nt = ns = nt0/2
+ # So numKf*( 8nt0 - nt0/2)*nt0/2 = numKb*nt0/2
+ # So 7.5*nt0 = numKb/numKf
+ rXfer.numKb = 0.1
+ rXfer.numKf = 0.1/(7.5 * et.nInit)
+ #print( "Rates = {}, {}".format( rXfer.Kf, rXfer.Kb ))
+ #####################################################################
+ fixXreacs.fixXreacs( '/model' )
+ #fixXreacs.restoreXreacs( '/model' )
+ #fixXreacs.fixXreacs( '/model' )
+ #####################################################################
+
+ # Make solvers
+ ksolve = moose.Ksolve( '/model/compartment/ksolve' )
+ dsolve = moose.Dsolve( '/model/compartment/dsolve' )
+ eksolve = moose.Ksolve( '/model/endo/ksolve' )
+ edsolve = moose.Dsolve( '/model/endo/dsolve' )
+
+ stoich = moose.Stoich( '/model/compartment/stoich' )
+ stoich.compartment = compartment
+ stoich.ksolve = ksolve
+ stoich.dsolve = dsolve
+ stoich.path = "/model/compartment/##"
+ assert( dsolve.numPools == 1 )
+
+ estoich = moose.Stoich( '/model/endo/stoich' )
+ estoich.compartment = endo
+ estoich.ksolve = eksolve
+ estoich.dsolve = edsolve
+ estoich.path = "/model/endo/##"
+ assert( edsolve.numPools == 3 )
+
+ edsolve.buildMeshJunctions( dsolve )
+
+ plot1 = moose.Table2( '/model/plot1' )
+ plot2 = moose.Table2( '/model/plot2' )
+ plot3 = moose.Table2( '/model/plot3' )
+ moose.connect( '/model/plot1', 'requestOut', u, 'getN' )
+ moose.connect( '/model/plot2', 'requestOut', et, 'getN' )
+ moose.connect( '/model/plot3', 'requestOut', es, 'getN' )
+ plot4 = moose.Table2( '/model/plot4' )
+ plot5 = moose.Table2( '/model/plot5' )
+ plot6 = moose.Table2( '/model/plot6' )
+ moose.connect( '/model/plot4', 'requestOut', u, 'getConc' )
+ moose.connect( '/model/plot5', 'requestOut', et, 'getConc' )
+ moose.connect( '/model/plot6', 'requestOut', es, 'getConc' )
+
+def doPlot( ax, i, label ):
+ plt.ylabel( label )
+ plt.xlabel( 'time(s)' )
+ v1 = moose.element('/model/plot' + str(i)).vector
+ v2 = moose.element('/model/plot' + str(i+1)).vector
+ v3 = moose.element('/model/plot' + str(i+2)).vector
+ ax.plot( v1, label='u' )
+ ax.plot( v2, label='et' )
+ ax.plot( v3, label='es' )
+ ax.plot( np.array( v1 ) + np.array( v3 ), label='sum' )
+ plt.legend()
+
+def almostEq( a, b ):
+ #print a, b, (a-b)/(a+b)
+ return abs(a-b)/(a+b) < 5e-5
+
+def main( standalone = False ):
+ runtime = 100
+ displayInterval = 2
+ makeModel()
+ moose.reinit()
+ moose.start( runtime )
+
+ assert( almostEq( moose.element( 'model/endo/t' ).conc,
+ moose.element( '/model/endo/s' ).conc ) )
+
+ if standalone:
+ fig = plt.figure( figsize=(12,10) )
+ ax1 = fig.add_subplot(211)
+ doPlot( ax1, 1, '# of molecules' )
+ ax2 = fig.add_subplot(212)
+ doPlot( ax2, 4, 'conc (mM)' )
+ plt.show()
+
+ moose.delete( '/model' )
+
+# Run the 'main' if this script is executed standalone.
+if __name__ == '__main__':
+ main( standalone = True )
diff --git a/tests/python/testXreacs8.py b/tests/python/testXreacs8.py
new file mode 100644
index 00000000..58dc5cf4
--- /dev/null
+++ b/tests/python/testXreacs8.py
@@ -0,0 +1,134 @@
+# -*- coding: utf-8 -*-
+#########################################################################
+## This program is part of 'MOOSE', the
+## Messaging Object Oriented Simulation Environment.
+## Copyright (C) 2014 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.
+## Here we set up equal Kf and Kb in a reversible reaction across a
+## 1-voxel cyl compt and an internal endoMesh, having a smaller volume.
+## \
+## COMPT: 2 s <===> / 2 s :ENDO
+## \
+##
+## This becomes:
+## \
+## COMPT: 2 s <===> 2 s_xfer_endo / 2s :ENDO
+## \
+##
+#########################################################################
+
+
+import math
+import numpy as np
+import matplotlib.pyplot as plt
+import matplotlib.image as mpimg
+import moose
+import fixXreacs
+
+def makeModel():
+ # create container for model
+ num = 1 # number of compartments
+ model = moose.Neutral( '/model' )
+ compartment = moose.CylMesh( '/model/compartment' )
+ compartment.x1 = 1.0e-6 # Set it to a 1 micron single-voxel cylinder
+
+ # create molecules and reactions
+ s = moose.Pool( '/model/compartment/s' )
+ rXfer = moose.Reac( '/model/compartment/rXfer' )
+ #####################################################################
+ # Put in endo compartment. Add molecule s
+ endo = moose.EndoMesh( '/model/endo' )
+ endo.isMembraneBound = True
+ endo.surround = compartment
+ es = moose.Pool( '/model/endo/s' )
+ #####################################################################
+ moose.connect( rXfer, 'sub', s, 'reac' )
+ moose.connect( rXfer, 'sub', s, 'reac' )
+ moose.connect( rXfer, 'prd', es, 'reac' )
+ moose.connect( rXfer, 'prd', es, 'reac' )
+ rXfer.Kf = 0.01 # 0.01/sec
+ rXfer.Kb = 0.01 # 0.01/sec
+
+ #####################################################################
+ fixXreacs.fixXreacs( '/model' )
+ fixXreacs.restoreXreacs( '/model' )
+ fixXreacs.fixXreacs( '/model' )
+ #####################################################################
+
+ # Make solvers
+ ksolve = moose.Ksolve( '/model/compartment/ksolve' )
+ dsolve = moose.Dsolve( '/model/dsolve' )
+ eksolve = moose.Ksolve( '/model/endo/ksolve' )
+ edsolve = moose.Dsolve( '/model/endo/dsolve' )
+
+ stoich = moose.Stoich( '/model/compartment/stoich' )
+ stoich.compartment = compartment
+ stoich.ksolve = ksolve
+ stoich.dsolve = dsolve
+ stoich.path = "/model/compartment/##"
+ assert( dsolve.numPools == 2 )
+ s.vec.concInit = [1]*num
+
+ estoich = moose.Stoich( '/model/endo/stoich' )
+ estoich.compartment = endo
+ estoich.ksolve = eksolve
+ estoich.dsolve = edsolve
+ estoich.path = "/model/endo/##"
+ assert( edsolve.numPools == 1 )
+
+ edsolve.buildMeshJunctions( dsolve )
+
+ plot1 = moose.Table2( '/model/plot1' )
+ plot2 = moose.Table2( '/model/plot2' )
+ plot3 = moose.Table2( '/model/plot3' )
+ moose.connect( '/model/plot1', 'requestOut', s, 'getN' )
+ moose.connect( '/model/plot2', 'requestOut', es, 'getN' )
+ moose.connect( '/model/plot3', 'requestOut', '/model/compartment/s_xfer_endo', 'getN' )
+ plot4 = moose.Table2( '/model/plot4' )
+ plot5 = moose.Table2( '/model/plot5' )
+ plot6 = moose.Table2( '/model/plot6' )
+ moose.connect( '/model/plot4', 'requestOut', s, 'getConc' )
+ moose.connect( '/model/plot5', 'requestOut', es, 'getConc' )
+ moose.connect( '/model/plot6', 'requestOut', '/model/compartment/s_xfer_endo', 'getConc' )
+
+def doPlot( ax, i, label ):
+ plot1 = '/model/plot' + str(i)
+ plot2 = '/model/plot' + str(i+1)
+ plot3 = '/model/plot' + str(i+2)
+ plt.ylabel( label )
+ plt.xlabel( 'time(s)' )
+ v1 = moose.element(plot1).vector
+ v2 = moose.element(plot2).vector
+ v3 = moose.element(plot3).vector
+ ax.plot( v1, label='s' )
+ ax.plot( v2, 'x',label='es' )
+ ax.plot( v3, label='xfer' )
+ ax.plot( np.array( v1 ) + np.array( v2 ), label='sum' )
+ plt.legend()
+
+def almostEq( a, b ):
+ return abs(a-b)/(a+b) < 5e-5
+
+def main( standalone = False ):
+ runtime = 100
+ makeModel()
+ moose.reinit()
+ moose.start( runtime )
+ assert( almostEq( moose.element( 'model/compartment/s' ).conc,
+ moose.element( '/model/endo/s' ).conc ) )
+
+ if standalone:
+ fig = plt.figure( figsize=(12,10) )
+ ax1 = fig.add_subplot(211)
+ doPlot( ax1, 1, '# of molecules' )
+ ax2 = fig.add_subplot(212)
+ doPlot( ax2, 4, 'conc (mM)' )
+ plt.show()
+ moose.delete( '/model' )
+
+
+# Run the 'main' if this script is executed standalone.
+if __name__ == '__main__':
+ main( standalone = True )
diff --git a/tests/python/test_GraupnerBrunel2012_STDPfromCaPlasticity.py b/tests/python/test_GraupnerBrunel2012_STDPfromCaPlasticity.py
new file mode 100644
index 00000000..73aa8c9e
--- /dev/null
+++ b/tests/python/test_GraupnerBrunel2012_STDPfromCaPlasticity.py
@@ -0,0 +1,228 @@
+# -*- coding: utf-8 -*-
+# This script is modified version of GraupnerBrunel2012 model by Aditya Gilra.
+# Modification is following:
+# - Added global seed.
+# - Removed some messages.
+# - Added assertion.
+#
+# NOTE: This script is used for testing random number generators on various
+# platform. This should not be used in any tutorial or scientific demo.
+
+import matplotlib as mpl
+mpl.use('Agg')
+import moose
+print( 'Using moose from %s' % moose.__file__ )
+import numpy as np
+
+moose.seed( 10 )
+
+def main():
+ """
+ Simulate a pseudo-STDP protocol and plot the STDP kernel
+ that emerges from Ca plasticity of Graupner and Brunel 2012.
+
+ Author: Aditya Gilra, NCBS, Bangalore, October, 2014.
+ """
+
+ # ###########################################
+ # Neuron models
+ # ###########################################
+
+ ## Leaky integrate and fire neuron
+ Vrest = -65e-3 # V # resting potential
+ Vt_base = -45e-3 # V # threshold
+ Vreset = -55e-3 # V # in current steps, Vreset is same as pedestal
+ R = 1e8 # Ohm
+ tau = 10e-3 # s
+ refrT = 2e-3 # s
+
+ # ###########################################
+ # Initialize neuron group
+ # ###########################################
+
+ ## two neurons: index 0 will be presynaptic, 1 will be postsynaptic
+ network = moose.LIF( 'network', 2 );
+ moose.le( '/network' )
+ network.vec.Em = Vrest
+ network.vec.thresh = Vt_base
+ network.vec.refractoryPeriod = refrT
+ network.vec.Rm = R
+ network.vec.vReset = Vreset
+ network.vec.Cm = tau/R
+ network.vec.inject = 0.
+ network.vec.initVm = Vrest
+
+ tauCa = 20e-3
+ tauSyn = 150.0
+ CaPre = 1.0
+ CaPost = 2.0
+ delayD = 13.7e-3
+ thetaD = 1.0
+ thetaP = 1.3
+ gammaD = 200.0
+ gammaP = 321.808
+ J = 5e-3 # V
+ weight = 0.5
+ bistable = True
+
+ syn = moose.GraupnerBrunel2012CaPlasticitySynHandler( '/network/syn' )
+ syn.numSynapses = 1
+ moose.connect( syn, 'activationOut', network.vec[1], 'activation' )
+
+ # synapse from presynaptic neuron
+ moose.connect( network.vec[0],'spikeOut', syn.synapse[0], 'addSpike')
+
+ # post-synaptic spikes also needed for STDP
+ moose.connect( network.vec[1], 'spikeOut', syn, 'addPostSpike')
+
+ syn.synapse[0].delay = 0.0
+ syn.synapse[0].weight = weight
+ syn.CaInit = 0.0
+ syn.tauCa = tauCa
+ syn.tauSyn = tauSyn
+ syn.CaPre = CaPre
+ syn.CaPost = CaPost
+ syn.delayD = delayD
+ syn.thetaD = thetaD
+ syn.thetaP = thetaP
+ syn.gammaD = gammaD
+ syn.gammaP = gammaP
+ syn.weightScale = J
+ syn.weightMax = 1.0
+ syn.weightMin = 0.
+
+ syn.noisy = True
+ syn.noiseSD = 1.3333
+ syn.bistable = bistable
+
+ # ###########################################
+ # Setting up tables
+ # ###########################################
+
+ Vms = moose.Table( '/plotVms', 2 )
+ moose.connect( network, 'VmOut', Vms, 'input', 'OneToOne')
+ spikes = moose.Table( '/plotSpikes', 2 )
+ moose.connect( network, 'spikeOut', spikes, 'input', 'OneToOne')
+ CaTable = moose.Table( '/plotCa', 1 )
+ moose.connect( CaTable, 'requestOut', syn, 'getCa')
+ WtTable = moose.Table( '/plotWeight', 1 )
+ moose.connect( WtTable, 'requestOut', syn.synapse[0], 'getWeight')
+
+ dt = 1e-3
+ moose.useClock( 0, '/network/syn', 'process' )
+ moose.useClock( 1, '/network', 'process' )
+ moose.useClock( 2, '/plotSpikes', 'process' )
+ moose.useClock( 3, '/plotVms', 'process' )
+ moose.useClock( 3, '/plotCa', 'process' )
+ moose.useClock( 3, '/plotWeight', 'process' )
+ moose.setClock( 0, dt )
+ moose.setClock( 1, dt )
+ moose.setClock( 2, dt )
+ moose.setClock( 3, dt )
+ moose.setClock( 9, dt )
+ moose.reinit()
+
+ # function to make the aPlus and aMinus settle to equilibrium values
+ settletime = 10e-3 # s
+ def reset_settle():
+ """ Call this between every pre-post pair
+ to reset the neurons and make them settle to rest.
+ """
+ syn.synapse[0].weight = weight
+ syn.Ca = 0.0
+ moose.start(settletime)
+ # Ca gets a jump at pre-spike+delayD
+ # So this event can occur during settletime
+ # So set Ca and weight once more after settletime
+ syn.synapse[0].weight = weight
+ syn.Ca = 0.0
+
+ # function to inject a sharp current pulse to make neuron spike
+ # immediately at a given time step
+ def make_neuron_spike(nrnidx,I=1e-7,duration=1e-3):
+ """ Inject a brief current pulse to
+ make a neuron spike
+ """
+ network.vec[nrnidx].inject = I
+ moose.start(duration)
+ network.vec[nrnidx].inject = 0.
+
+ dwlist_neg = []
+ ddt = 10e-3 # s
+ # since CaPlasticitySynHandler is event based
+ # multiple pairs are needed for Ca to be registered above threshold
+ # Values from Fig 2, last line of legend
+ numpairs = 60 # number of spike parts per deltat
+ t_between_pairs = 1.0 # time between each spike pair
+ t_extent = 100e-3 # s # STDP kernel extent,
+ # t_extent > t_between_pairs/2 inverts pre-post pairing!
+ # dt = tpost - tpre
+ # negative dt corresponds to post before pre
+ print('-----------------------------------------------')
+ for deltat in np.arange(t_extent,0.0,-ddt):
+ reset_settle()
+ for i in range(numpairs):
+ # post neuron spike
+ make_neuron_spike(1)
+ moose.start(deltat)
+ # pre neuron spike after deltat
+ make_neuron_spike(0)
+ moose.start(t_between_pairs) # weight changes after pre-spike+delayD
+ # must run for at least delayD after pre-spike
+ dw = ( syn.synapse[0].weight - weight ) / weight
+ print(('post before pre, dt = %1.3f s, dw/w = %1.3f'%(-deltat,dw)))
+ dwlist_neg.append(dw)
+
+ print('-----------------------------------------------')
+ # positive dt corresponds to pre before post
+ dwlist_pos = []
+ for deltat in np.arange(ddt,t_extent+ddt,ddt):
+ reset_settle()
+ for i in range(numpairs):
+ # pre neuron spike
+ make_neuron_spike(0)
+ moose.start(deltat)
+ # post neuron spike after deltat
+ make_neuron_spike(1)
+ moose.start(t_between_pairs)
+ dw = ( syn.synapse[0].weight - weight ) / weight
+ print(('pre before post, dt = %1.3f s, dw/w = %1.3f'%(deltat,dw)))
+ dwlist_pos.append(dw)
+
+ Vmseries0 = Vms.vec[0].vector
+ numsteps = len(Vmseries0)
+
+ for t in spikes.vec[0].vector:
+ Vmseries0[int(t/dt)-1] = 30e-3 # V
+
+ Vmseries1 = Vms.vec[1].vector
+
+ for t in spikes.vec[1].vector:
+ Vmseries1[int(t/dt)-1] = 30e-3 # V
+
+ timeseries = np.linspace(0.,200*numsteps*dt,numsteps)
+
+ # STDP curve
+ up, sp = np.mean( dwlist_pos ), np.std( dwlist_pos )
+ un, sn = np.mean( dwlist_neg ), np.std( dwlist_neg )
+
+ expected = [0.32476025611655324, 0.22658173497286094,
+ 0.02706212384326734, -0.2176119329016457, -0.17349820098625146,
+ -0.049000627347906, 0.10942145078777199, 0.015381955378225953,
+ 0.004742824127517586, -0.12298343312253879]
+ assert np.isclose(dwlist_pos[1:], expected[1:]).all(), "Got %s \nexpected %s" % (dwlist_pos, expected)
+
+ expected = [-0.07871282492831622, 0.11915009122888964,
+ -0.028510348966579557, 0.11812233585111875, 0.05098143255634335,
+ -0.2303047508248669, 0.18033418630802123, -0.019377885225611347,
+ -0.06038610826728241, 0.06575882890278106]
+ assert np.isclose(dwlist_neg[1:], expected[1:]).all(), "Got %s\nexpected %s" % (dwlist_neg,
+ expected)
+
+
+ got = (up, sp)
+ expNew = (0.014485615086785508, 0.16206703949072981)
+ assert np.isclose(got, expNew).all(), 'Expected: %s, Got: %s' % (str(expNew), str(got))
+
+if __name__ == '__main__':
+ main()
diff --git a/tests/python/test_Xchan1.py b/tests/python/test_Xchan1.py
new file mode 100644
index 00000000..35fc56f6
--- /dev/null
+++ b/tests/python/test_Xchan1.py
@@ -0,0 +1,153 @@
+#########################################################################
+## This program is part of 'MOOSE', the
+## Messaging Object Oriented Simulation Environment.
+## Copyright (C) 2014 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.
+## Here test ConcChan. We set up a channel and a pump and run two tests.
+## First we have zero flux through the pump and check that the conc
+## equalizes on both sides of the membrane. Then we change the Kf of
+## the pump to a value designed to give twice the conc In as Out.
+## The system is a 1-voxel cyl compt and an internal endoMesh, having a
+## volume = 1/8 of the cylinder.
+## \
+## COMPT: s ----> / s :ENDO
+## s =chan= s
+## \
+##
+## This becomes:
+## \
+## COMPT: s ----> s_xfer_endo / s :ENDO
+## s =chan= s
+## \
+##
+#########################################################################
+
+
+import math
+import numpy as np
+import moose
+import fixXreacs
+
+def makeModel():
+ # create container for model
+ num = 1 # number of compartments
+ model = moose.Neutral( '/model' )
+ compartment = moose.CylMesh( '/model/compartment' )
+ compartment.x1 = 1.0e-6 # Set it to a 1 micron single-voxel cylinder
+
+ # create molecules and reactions
+ s = moose.Pool( '/model/compartment/s' )
+ rXfer = moose.Reac( '/model/compartment/rXfer' )
+ #####################################################################
+ # Put in endo compartment. Add molecule s
+ endo = moose.EndoMesh( '/model/endo' )
+ # Note that the chanPool must be on the 'In' compartment.
+ #chanPool = moose.Pool( '/model/compartment/chanPool' )
+ #chan = moose.ConcChan( '/model/compartment/chanPool/chan' )
+ chanPool = moose.Pool( '/model/endo/chanPool' )
+ chan = moose.ConcChan( '/model/endo/chanPool/chan' )
+ endo.isMembraneBound = True
+ endo.surround = compartment
+ es = moose.Pool( '/model/endo/s' )
+ #####################################################################
+ moose.connect( rXfer, 'sub', s, 'reac' )
+ moose.connect( rXfer, 'prd', es, 'reac' )
+ moose.connect( chanPool, 'nOut', chan, 'setNumChan' )
+ moose.connect( chan, 'out', s, 'reac' )
+ moose.connect( chan, 'in', es, 'reac' )
+ volRatio = compartment.volume / endo.volume
+ rXfer.Kf = 0.0 # 0.02/sec
+ rXfer.Kb = 0.0 #
+ s.concInit = 0.001
+ chanPool.nInit = 1000.0
+ # Flux (mM/s) = permeability * N * (conc_out - conc_in )
+ chan.permeability = 0.1 * chanPool.volume * 6.022e23 / chanPool.nInit
+
+ #####################################################################
+ fixXreacs.fixXreacs( '/model' )
+ #fixXreacs.restoreXreacs( '/model' )
+ #fixXreacs.fixXreacs( '/model' )
+ #####################################################################
+
+ # Make solvers
+ ksolve = moose.Ksolve( '/model/compartment/ksolve' )
+ dsolve = moose.Dsolve( '/model/dsolve' )
+ eksolve = moose.Ksolve( '/model/endo/ksolve' )
+ edsolve = moose.Dsolve( '/model/endo/dsolve' )
+
+ stoich = moose.Stoich( '/model/compartment/stoich' )
+ stoich.compartment = compartment
+ stoich.ksolve = ksolve
+ stoich.dsolve = dsolve
+ stoich.path = "/model/compartment/##"
+ assert( dsolve.numPools == 2 )
+
+ estoich = moose.Stoich( '/model/endo/stoich' )
+ estoich.compartment = endo
+ estoich.ksolve = eksolve
+ estoich.dsolve = edsolve
+ estoich.path = "/model/endo/##"
+ assert( edsolve.numPools == 2 )
+
+ edsolve.buildMeshJunctions( dsolve )
+
+ plot1 = moose.Table2( '/model/plot1' )
+ plot2 = moose.Table2( '/model/plot2' )
+ plot3 = moose.Table2( '/model/plot3' )
+ moose.connect( '/model/plot1', 'requestOut', s, 'getN' )
+ moose.connect( '/model/plot2', 'requestOut', es, 'getN' )
+ moose.connect( '/model/plot3', 'requestOut', '/model/compartment/s_xfer_endo', 'getN' )
+ plot4 = moose.Table2( '/model/plot4' )
+ plot5 = moose.Table2( '/model/plot5' )
+ plot6 = moose.Table2( '/model/plot6' )
+ moose.connect( '/model/plot4', 'requestOut', s, 'getConc' )
+ moose.connect( '/model/plot5', 'requestOut', es, 'getConc' )
+ moose.connect( '/model/plot6', 'requestOut', '/model/compartment/s_xfer_endo', 'getConc' )
+
+
+def almostEq( a, b ):
+ #print a, b, (a-b)/(a+b)
+ return abs(a-b)/(a+b) < 5e-5
+
+def main( standalone = False ):
+ runtime = 100
+ displayInterval = 2
+ makeModel()
+ for i in range( 10, 18 ):
+ moose.setClock( i, 0.01 )
+ moose.reinit()
+ moose.start( runtime )
+ s = moose.element( '/model/compartment/s' )
+ es = moose.element( '/model/endo/s' )
+ assert( almostEq( s.conc, es.conc ) )
+ # We go for concEndo = 2x concOut. Then
+ # We already know volIn = volOut/8
+ # #in/volIn = 2x #out/volOut
+ # #in/volIn = 2x #out/(8*volIn)
+ # so #in = #out/4
+ # From consv, #in + #out = nInit
+ # so 5/4#out = nInit =>
+ # #out = 0.8*nInit; #in = 0.2*nInit
+ #
+ # flux = perm * nChan * (0.8nInit/volOut - 0.2nInit/(volOut/8) ) =
+ # perm * (nChan*nInit/volOut) * (0.8 - 0.2*8) =
+ # perm * (nChan*nInit/volOut) * (-0.8)
+ #
+ # This has to be balanced by flux = numKf * nOut = numKf * 0.8 * nInit
+ # So 0.8*numKf*nInit = 0.8*perm*nChan*nInit/volOut
+
+ # Note that chan.permeability = 0.1*chanPool.volume / chanPool.nInit
+
+ # so numKf = perm*nChan/volOut = (0.1*volIn/nChan)*nChan/volOut=0.1/8
+ #
+ rXfer = moose.element( '/model/compartment/rXfer' )
+ rXfer.numKf = 0.1/8.0
+ moose.start( runtime )
+ assert( almostEq( 2 * s.conc, es.conc ) )
+ moose.delete( '/model' )
+
+# Run the 'main' if this script is executed standalone.
+if __name__ == '__main__':
+ main( standalone = True )
diff --git a/tests/python/test_Xdiff1.py b/tests/python/test_Xdiff1.py
new file mode 100644
index 00000000..fc9df5d8
--- /dev/null
+++ b/tests/python/test_Xdiff1.py
@@ -0,0 +1,129 @@
+# -*- coding: utf-8 -*-
+#########################################################################
+## This program is part of 'MOOSE', the
+## Messaging Object Oriented Simulation Environment.
+## Copyright (C) 2014 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.
+## Here test diffusion across a junction. We set up a pump and change its
+## rate to do a check on the calculation of the diffusion rate separate
+## from the verification that diffusion gives equal concs on either side.
+## The system is a ## 1-voxel cyl compt and an internal endoMesh,
+## having a volume = 1/8 of the parent cylinder..
+## \
+## COMPT: s ----> / s :ENDO
+## s =diffn= s
+## \
+##
+## This becomes:
+## \
+## COMPT: s ----> s_xfer_endo / s :ENDO
+# s =diffn= s
+## \
+##
+#########################################################################
+
+
+import math
+import numpy as np
+import moose
+print( '[INFO] Using moose from %s, %s' % (moose.__file__, moose.version()) )
+import fixXreacs
+
+diffConst = 1e-16
+
+def makeModel():
+ # create container for model
+ num = 1 # number of compartments
+ model = moose.Neutral( '/model' )
+ compartment = moose.CylMesh( '/model/compartment' )
+ compartment.x1 = 1.0e-6 # Set it to a 1 micron single-voxel cylinder
+
+ # create molecules and reactions
+ s = moose.Pool( '/model/compartment/s' )
+ rXfer = moose.Reac( '/model/compartment/rXfer' )
+ #####################################################################
+ # Put in endo compartment. Add molecule s
+ endo = moose.EndoMesh( '/model/endo' )
+ endo.isMembraneBound = False
+ endo.surround = compartment
+ es = moose.Pool( '/model/endo/s' )
+ #####################################################################
+ moose.connect( rXfer, 'sub', s, 'reac' )
+ moose.connect( rXfer, 'prd', es, 'reac' )
+ volRatio = compartment.volume / endo.volume
+ #print( "Volume ratio = {}".format( volRatio ) )
+ rXfer.Kf = 0.0 # 0.02/sec
+ rXfer.Kb = 0.0 #
+ s.concInit = 0.001
+ s.diffConst = diffConst
+ es.diffConst = diffConst
+
+ #####################################################################
+ fixXreacs.fixXreacs( '/model' )
+ #fixXreacs.restoreXreacs( '/model' )
+ #fixXreacs.fixXreacs( '/model' )
+ #####################################################################
+
+ # Make solvers
+ ksolve = moose.Ksolve( '/model/compartment/ksolve' )
+ dsolve = moose.Dsolve( '/model/dsolve' )
+ eksolve = moose.Ksolve( '/model/endo/ksolve' )
+ edsolve = moose.Dsolve( '/model/endo/dsolve' )
+
+ stoich = moose.Stoich( '/model/compartment/stoich' )
+ stoich.compartment = compartment
+ stoich.ksolve = ksolve
+ stoich.dsolve = dsolve
+ stoich.path = "/model/compartment/##"
+ assert( dsolve.numPools == 2 )
+
+ estoich = moose.Stoich( '/model/endo/stoich' )
+ estoich.compartment = endo
+ estoich.ksolve = eksolve
+ estoich.dsolve = edsolve
+ estoich.path = "/model/endo/##"
+ assert( edsolve.numPools == 1 )
+
+ edsolve.buildMeshJunctions( dsolve )
+
+ plot1 = moose.Table2( '/model/plot1' )
+ plot2 = moose.Table2( '/model/plot2' )
+ plot3 = moose.Table2( '/model/plot3' )
+ moose.connect( '/model/plot1', 'requestOut', s, 'getN' )
+ moose.connect( '/model/plot2', 'requestOut', es, 'getN' )
+ moose.connect( '/model/plot3', 'requestOut', '/model/compartment/s_xfer_endo', 'getN' )
+ plot4 = moose.Table2( '/model/plot4' )
+ plot5 = moose.Table2( '/model/plot5' )
+ plot6 = moose.Table2( '/model/plot6' )
+ moose.connect( '/model/plot4', 'requestOut', s, 'getConc' )
+ moose.connect( '/model/plot5', 'requestOut', es, 'getConc' )
+ moose.connect( '/model/plot6', 'requestOut', '/model/compartment/s_xfer_endo', 'getConc' )
+
+def almostEq( a, b ):
+ # print( a, b, (a-b)/(a+b) )
+ return abs(a-b)/(a+b) < 6e-5
+
+def main( standalone = False ):
+ runtime = 100
+ makeModel()
+ for i in range( 10, 18 ):
+ moose.setClock( i, 0.01 )
+ moose.reinit()
+ moose.start( runtime, 1 )
+ s = moose.element( '/model/compartment/s' )
+ es = moose.element( '/model/endo/s' )
+ assert( almostEq( s.conc, es.conc ) )
+ rXfer = moose.element( '/model/compartment/rXfer' )
+ endo = moose.element( '/model/endo' )
+ compt = moose.element( '/model/compartment' )
+ endoA = endo.aScale * pow( compt.volume, endo.aPower )
+ rXfer.numKf = 2.0*diffConst*endoA/(compt.r0*compt.volume)
+ moose.start( runtime )
+ assert almostEq( 2 * s.conc, es.conc ), "%g=?%g" % (2*s.conc, es.conc)
+ moose.delete( '/model' )
+
+# Run the 'main' if this script is executed standalone.
+if __name__ == '__main__':
+ main( standalone = True )
diff --git a/tests/python/test_Xenz1.py b/tests/python/test_Xenz1.py
new file mode 100644
index 00000000..c7463ad4
--- /dev/null
+++ b/tests/python/test_Xenz1.py
@@ -0,0 +1,117 @@
+# -*- coding: utf-8 -*-
+#########################################################################
+## This program is part of 'MOOSE', the
+## Messaging Object Oriented Simulation Environment.
+## Copyright (C) 2014 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.
+##
+## Endo / Compartment
+## \
+## sub--enz-/-----> prd
+## sub<-----\----- prd
+## /
+#########################################################################
+
+
+import math
+import numpy as np
+import moose
+import fixXreacs
+
+subInit = 0.002
+eInit = 0.001
+Km = 0.001
+kcat = 0.2
+Kf = 0.1
+
+def makeModel():
+ # create container for model
+ num = 1 # number of compartments
+ model = moose.Neutral( '/model' )
+ compartment = moose.CylMesh( '/model/compartment' )
+ compartment.x1 = 1.0e-6 # Set it to a 1 micron single-voxel cylinder
+
+ # create molecules and reactions
+ prd = moose.Pool( '/model/compartment/prd' )
+ rXfer = moose.Reac( '/model/compartment/rXfer' )
+ #####################################################################
+ # Put in endo compartment. Add molecule s
+ endo = moose.EndoMesh( '/model/endo' )
+ endo.isMembraneBound = True
+ endo.surround = compartment
+ sub = moose.Pool( '/model/endo/sub' )
+ enzPool = moose.Pool( '/model/endo/enzPool' )
+ enzPool.concInit = eInit
+ enz = moose.MMenz( '/model/endo/enzPool/enz' )
+ #####################################################################
+ moose.connect( enz, 'sub', sub, 'reac' )
+ moose.connect( enz, 'prd', prd, 'reac' )
+ moose.connect( enzPool, 'nOut', enz, 'enzDest' )
+ moose.connect( rXfer, 'sub', prd, 'reac' )
+ moose.connect( rXfer, 'prd', sub, 'reac' )
+ rXfer.Kf = Kf # 0.04/sec
+ rXfer.Kb = 0.0 # 0.02/sec
+ enz.Km = Km
+ enz.kcat = kcat
+ # v = es.kcat/(s+Km)
+ # v = Kf * conc.
+ #####################################################################
+ fixXreacs.fixXreacs( '/model' )
+ fixXreacs.restoreXreacs( '/model' )
+ fixXreacs.fixXreacs( '/model' )
+ #####################################################################
+
+ # Make solvers
+ ksolve = moose.Ksolve( '/model/compartment/ksolve' )
+ dsolve = moose.Dsolve( '/model/dsolve' )
+ eksolve = moose.Ksolve( '/model/endo/ksolve' )
+ edsolve = moose.Dsolve( '/model/endo/dsolve' )
+
+ stoich = moose.Stoich( '/model/compartment/stoich' )
+ stoich.compartment = compartment
+ stoich.ksolve = ksolve
+ stoich.dsolve = dsolve
+ stoich.path = "/model/compartment/##"
+ assert( dsolve.numPools == 2 )
+ sub.vec.concInit = subInit
+ enzPool.vec.concInit = eInit
+
+ estoich = moose.Stoich( '/model/endo/stoich' )
+ estoich.compartment = endo
+ estoich.ksolve = eksolve
+ estoich.dsolve = edsolve
+ estoich.path = "/model/endo/##"
+ assert( edsolve.numPools == 3 )
+
+ edsolve.buildMeshJunctions( dsolve )
+
+ plot1 = moose.Table2( '/model/plot1' )
+ plot2 = moose.Table2( '/model/plot2' )
+ moose.connect( '/model/plot1', 'requestOut', sub, 'getN' )
+ moose.connect( '/model/plot2', 'requestOut', prd, 'getN' )
+ plot3 = moose.Table2( '/model/plot3' )
+ plot4 = moose.Table2( '/model/plot4' )
+ moose.connect( '/model/plot3', 'requestOut', sub, 'getConc' )
+ moose.connect( '/model/plot4', 'requestOut', prd, 'getConc' )
+
+def almostEq( a, b ):
+ #print a, b, (a-b)/(a+b)
+ return abs(a-b)/(a+b) < 5e-5
+
+def main( standalone = False ):
+ for i in range( 10, 18 ):
+ moose.setClock( i, 0.001 )
+ runtime = 100
+ displayInterval = 2
+ makeModel()
+ moose.reinit()
+ moose.start( runtime )
+ assert( almostEq( moose.element( 'model/compartment/prd' ).n,
+ moose.element( '/model/endo/sub' ).n ) )
+ moose.delete( '/model' )
+
+# Run the 'main' if this script is executed standalone.
+if __name__ == '__main__':
+ main( standalone = True )
diff --git a/tests/python/test_Xreacs2.py b/tests/python/test_Xreacs2.py
new file mode 100644
index 00000000..1b1e7302
--- /dev/null
+++ b/tests/python/test_Xreacs2.py
@@ -0,0 +1,51 @@
+# -*- coding: utf-8 -*-
+import os
+import sys
+import moose
+import numpy as np
+import fixXreacs
+
+def countCrossings( plot, thresh ):
+ vec = moose.element( plot ).vector
+ #print (vec[:-1] < thresh)
+ return sum( (vec[:-1] < thresh) * (vec[1:] >= thresh ) )
+
+def main( standalone = False ):
+ mfile = os.path.join( os.path.dirname( __file__), 'OSC_diff_vols.g' )
+ runtime = 4000.0
+ modelId = moose.loadModel( mfile, 'model', 'ee' )
+ kin = moose.element( '/model/kinetics' )
+ compt1 = moose.element( '/model/compartment_1' )
+ compt1.x1 += kin.x1
+ compt1.x0 += kin.x1
+ fixXreacs.fixXreacs( '/model' )
+ #fixXreacs.restoreXreacs( '/model' )
+ #fixXreacs.fixXreacs( '/model' )
+
+ ks1 = moose.Ksolve( '/model/kinetics/ksolve' )
+ ds1 = moose.Dsolve( '/model/kinetics/dsolve' )
+ s1 = moose.Stoich( '/model/kinetics/stoich' )
+ s1.compartment = moose.element( '/model/kinetics' )
+ s1.ksolve = ks1
+ s1.dsolve = ds1
+ s1.path = '/model/kinetics/##'
+
+ ks2 = moose.Ksolve( '/model/compartment_1/ksolve' )
+ ds2 = moose.Dsolve( '/model/compartment_1/dsolve' )
+ s2 = moose.Stoich( '/model/compartment_1/stoich' )
+ s2.compartment = moose.element( '/model/compartment_1' )
+ s2.ksolve = ks2
+ s2.dsolve = ds2
+ s2.path = '/model/compartment_1/##'
+
+ ds2.buildMeshJunctions( ds1 )
+
+ moose.reinit()
+ moose.start( runtime )
+ # I don't have an analytic way to assess oscillations
+ assert( countCrossings( '/model/graphs/conc2/M.Co', 0.001 ) == 4 )
+ moose.delete( '/model' )
+
+# Run the 'main' if this script is executed standalone.
+if __name__ == '__main__':
+ main( standalone = True )
diff --git a/tests/python/test_Xreacs3.py b/tests/python/test_Xreacs3.py
new file mode 100644
index 00000000..53cd7600
--- /dev/null
+++ b/tests/python/test_Xreacs3.py
@@ -0,0 +1,107 @@
+# -*- coding: utf-8 -*-
+#########################################################################
+## This program is part of 'MOOSE', the
+## Messaging Object Oriented Simulation Environment.
+## Copyright (C) 2014 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.
+## Here we set up equal Kf and Kb in a reversible reaction across a
+## 1-voxel cyl compt and an internal endoMesh, having a smaller volume.
+## \
+## COMPT: s <===> / s :ENDO
+## \
+##
+## This becomes:
+## \
+## COMPT: s <===> s_xfer_endo / s :ENDO
+## \
+##
+#########################################################################
+
+
+import math
+import numpy as np
+import moose
+import fixXreacs
+
+def makeModel():
+ # create container for model
+ num = 1 # number of compartments
+ model = moose.Neutral( '/model' )
+ compartment = moose.CylMesh( '/model/compartment' )
+ compartment.x1 = 1.0e-6 # Set it to a 1 micron single-voxel cylinder
+
+ # create molecules and reactions
+ s = moose.Pool( '/model/compartment/s' )
+ rXfer = moose.Reac( '/model/compartment/rXfer' )
+ #####################################################################
+ # Put in endo compartment. Add molecule s
+ endo = moose.EndoMesh( '/model/endo' )
+ endo.isMembraneBound = True
+ endo.surround = compartment
+ es = moose.Pool( '/model/endo/s' )
+ #####################################################################
+ moose.connect( rXfer, 'sub', s, 'reac' )
+ moose.connect( rXfer, 'prd', es, 'reac' )
+ volRatio = compartment.volume / endo.volume
+ rXfer.Kf = 0.02 # 0.01/sec
+ rXfer.Kb = 0.02 # 1/sec
+
+ #####################################################################
+ fixXreacs.fixXreacs( '/model' )
+ fixXreacs.restoreXreacs( '/model' )
+ fixXreacs.fixXreacs( '/model' )
+ #####################################################################
+
+ # Make solvers
+ ksolve = moose.Ksolve( '/model/compartment/ksolve' )
+ dsolve = moose.Dsolve( '/model/dsolve' )
+ eksolve = moose.Ksolve( '/model/endo/ksolve' )
+ edsolve = moose.Dsolve( '/model/endo/dsolve' )
+
+ stoich = moose.Stoich( '/model/compartment/stoich' )
+ stoich.compartment = compartment
+ stoich.ksolve = ksolve
+ stoich.dsolve = dsolve
+ stoich.path = "/model/compartment/##"
+ assert( dsolve.numPools == 2 )
+ s.vec.concInit = [1]*num
+
+ estoich = moose.Stoich( '/model/endo/stoich' )
+ estoich.compartment = endo
+ estoich.ksolve = eksolve
+ estoich.dsolve = edsolve
+ estoich.path = "/model/endo/##"
+ assert( edsolve.numPools == 1 )
+
+ edsolve.buildMeshJunctions( dsolve )
+
+ plot1 = moose.Table2( '/model/plot1' )
+ plot2 = moose.Table2( '/model/plot2' )
+ plot3 = moose.Table2( '/model/plot3' )
+ moose.connect( '/model/plot1', 'requestOut', s, 'getN' )
+ moose.connect( '/model/plot2', 'requestOut', es, 'getN' )
+ moose.connect( '/model/plot3', 'requestOut', '/model/compartment/s_xfer_endo', 'getN' )
+ plot4 = moose.Table2( '/model/plot4' )
+ plot5 = moose.Table2( '/model/plot5' )
+ plot6 = moose.Table2( '/model/plot6' )
+ moose.connect( '/model/plot4', 'requestOut', s, 'getConc' )
+ moose.connect( '/model/plot5', 'requestOut', es, 'getConc' )
+ moose.connect( '/model/plot6', 'requestOut', '/model/compartment/s_xfer_endo', 'getConc' )
+
+def almostEq( a, b ):
+ return abs(a-b)/(a+b) < 5e-5
+
+def main( standalone = False ):
+ runtime = 100
+ makeModel()
+ moose.reinit()
+ moose.start( runtime )
+ assert( almostEq( moose.element( 'model/compartment/s' ).conc,
+ moose.element( '/model/endo/s' ).conc ) )
+ moose.delete( '/model' )
+
+# Run the 'main' if this script is executed standalone.
+if __name__ == '__main__':
+ main( standalone = True )
diff --git a/tests/python/test_Xreacs4.py b/tests/python/test_Xreacs4.py
new file mode 100644
index 00000000..c655e4e5
--- /dev/null
+++ b/tests/python/test_Xreacs4.py
@@ -0,0 +1,93 @@
+# -*- coding: utf-8 -*-
+#########################################################################
+## This program is part of 'MOOSE', the
+## Messaging Object Oriented Simulation Environment.
+## Copyright (C) 2014 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.
+#########################################################################
+
+
+import math
+import numpy as np
+import moose
+import fixXreacs
+
+def makeModel():
+ # create container for model
+ num = 1 # number of compartments
+ model = moose.Neutral( '/model' )
+ compartment = moose.CylMesh( '/model/compartment' )
+ compartment.x1 = 1.0e-6 # Set it to a 1 micron single-voxel cylinder
+
+ # create molecules and reactions
+ s = moose.Pool( '/model/compartment/s' )
+ rXfer = moose.Reac( '/model/compartment/rXfer' )
+ #####################################################################
+ # Put in endo compartment. Add molecule s
+ endo = moose.EndoMesh( '/model/endo' )
+ endo.isMembraneBound = True
+ endo.surround = compartment
+ es = moose.Pool( '/model/endo/s' )
+ #####################################################################
+ moose.connect( rXfer, 'sub', s, 'reac' )
+ moose.connect( rXfer, 'prd', es, 'reac' )
+ volRatio = compartment.volume / endo.volume
+ rXfer.Kf = 0.04 # 0.04/sec
+ rXfer.Kb = 0.02 # 0.02/sec
+
+ #####################################################################
+ fixXreacs.fixXreacs( '/model' )
+ #fixXreacs.restoreXreacs( '/model' )
+ #fixXreacs.fixXreacs( '/model' )
+ #####################################################################
+
+ # Make solvers
+ ksolve = moose.Ksolve( '/model/compartment/ksolve' )
+ dsolve = moose.Dsolve( '/model/dsolve' )
+ eksolve = moose.Ksolve( '/model/endo/ksolve' )
+ edsolve = moose.Dsolve( '/model/endo/dsolve' )
+
+ stoich = moose.Stoich( '/model/compartment/stoich' )
+ stoich.compartment = compartment
+ stoich.ksolve = ksolve
+ stoich.dsolve = dsolve
+ stoich.path = "/model/compartment/##"
+ assert( dsolve.numPools == 2 )
+ s.vec.concInit = [1]*num
+
+ estoich = moose.Stoich( '/model/endo/stoich' )
+ estoich.compartment = endo
+ estoich.ksolve = eksolve
+ estoich.dsolve = edsolve
+ estoich.path = "/model/endo/##"
+ assert( edsolve.numPools == 1 )
+
+ edsolve.buildMeshJunctions( dsolve )
+
+ plot1 = moose.Table2( '/model/plot1' )
+ plot2 = moose.Table2( '/model/plot2' )
+ moose.connect( '/model/plot1', 'requestOut', s, 'getN' )
+ moose.connect( '/model/plot2', 'requestOut', es, 'getN' )
+ plot3 = moose.Table2( '/model/plot3' )
+ plot4 = moose.Table2( '/model/plot4' )
+ moose.connect( '/model/plot3', 'requestOut', s, 'getConc' )
+ moose.connect( '/model/plot4', 'requestOut', es, 'getConc' )
+
+def almostEq( a, b ):
+ return abs(a-b)/(a+b) < 5e-5
+
+def main( standalone = False ):
+ runtime = 100
+ displayInterval = 2
+ makeModel()
+ moose.reinit()
+ moose.start( runtime )
+ assert( almostEq( 2.0 * moose.element( 'model/compartment/s' ).conc,
+ moose.element( '/model/endo/s' ).conc ) )
+ moose.delete( '/model' )
+
+# Run the 'main' if this script is executed standalone.
+if __name__ == '__main__':
+ main( standalone = True )
diff --git a/tests/python/test_Xreacs4a.py b/tests/python/test_Xreacs4a.py
new file mode 100644
index 00000000..73c6d547
--- /dev/null
+++ b/tests/python/test_Xreacs4a.py
@@ -0,0 +1,94 @@
+# -*- coding: utf-8 -*-
+#########################################################################
+## This program is part of 'MOOSE', the
+## Messaging Object Oriented Simulation Environment.
+## Copyright (C) 2014 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.
+#########################################################################
+
+
+import math
+import numpy as np
+import moose
+import fixXreacs
+
+def makeModel():
+ # create container for model
+ num = 1 # number of compartments
+ model = moose.Neutral( '/model' )
+ compartment = moose.CylMesh( '/model/compartment' )
+ compartment.x1 = 1.0e-6 # Set it to a 1 micron single-voxel cylinder
+
+ # create molecules and reactions
+ s = moose.Pool( '/model/compartment/s' )
+ #####################################################################
+ # Put in endo compartment. Add molecule s
+ endo = moose.EndoMesh( '/model/endo' )
+ endo.isMembraneBound = True
+ endo.surround = compartment
+ es = moose.Pool( '/model/endo/s' )
+ rXfer = moose.Reac( '/model/endo/rXfer' )
+ #####################################################################
+ moose.connect( rXfer, 'sub', s, 'reac' )
+ moose.connect( rXfer, 'prd', es, 'reac' )
+ volRatio = compartment.volume / endo.volume
+ rXfer.Kf = 0.04 # 0.04/sec
+ rXfer.Kb = 0.02 # 0.02/sec
+
+ #####################################################################
+ fixXreacs.fixXreacs( '/model' )
+ #fixXreacs.restoreXreacs( '/model' )
+ #fixXreacs.fixXreacs( '/model' )
+ #####################################################################
+
+ # Make solvers
+ ksolve = moose.Ksolve( '/model/compartment/ksolve' )
+ dsolve = moose.Dsolve( '/model/dsolve' )
+ eksolve = moose.Ksolve( '/model/endo/ksolve' )
+ edsolve = moose.Dsolve( '/model/endo/dsolve' )
+
+ stoich = moose.Stoich( '/model/compartment/stoich' )
+ stoich.compartment = compartment
+ stoich.ksolve = ksolve
+ stoich.dsolve = dsolve
+ stoich.path = "/model/compartment/##"
+ assert( dsolve.numPools == 1 )
+ s.vec.concInit = [1]*num
+
+ estoich = moose.Stoich( '/model/endo/stoich' )
+ estoich.compartment = endo
+ estoich.ksolve = eksolve
+ estoich.dsolve = edsolve
+ estoich.path = "/model/endo/##"
+ assert( edsolve.numPools == 2 )
+
+ edsolve.buildMeshJunctions( dsolve )
+
+ plot1 = moose.Table2( '/model/plot1' )
+ plot2 = moose.Table2( '/model/plot2' )
+ moose.connect( '/model/plot1', 'requestOut', s, 'getN' )
+ moose.connect( '/model/plot2', 'requestOut', es, 'getN' )
+ plot3 = moose.Table2( '/model/plot3' )
+ plot4 = moose.Table2( '/model/plot4' )
+ moose.connect( '/model/plot3', 'requestOut', s, 'getConc' )
+ moose.connect( '/model/plot4', 'requestOut', es, 'getConc' )
+
+def almostEq( a, b ):
+ return abs(a-b)/(a+b) < 5e-5
+
+def main( standalone = False ):
+ runtime = 200
+ displayInterval = 2
+ makeModel()
+ moose.reinit()
+ moose.start( runtime )
+ assert( almostEq( 2.0 * moose.element( 'model/compartment/s' ).conc,
+ moose.element( '/model/endo/s' ).conc ) )
+ moose.delete( '/model' )
+
+
+# Run the 'main' if this script is executed standalone.
+if __name__ == '__main__':
+ main( standalone = True )
diff --git a/tests/python/test_Xreacs5.py b/tests/python/test_Xreacs5.py
new file mode 100644
index 00000000..4dde2a47
--- /dev/null
+++ b/tests/python/test_Xreacs5.py
@@ -0,0 +1,101 @@
+# -*- coding: utf-8 -*-
+#########################################################################
+## This program is part of 'MOOSE', the
+## Messaging Object Oriented Simulation Environment.
+## Copyright (C) 2014 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.
+#########################################################################
+
+
+import math
+import numpy as np
+import moose
+import fixXreacs
+
+def makeModel():
+ # create container for model
+ num = 1 # number of compartments
+ model = moose.Neutral( '/model' )
+ compartment = moose.CylMesh( '/model/compartment' )
+ compartment.x1 = 1.0e-6 # Set it to a 1 micron single-voxel cylinder
+
+ # create molecules and reactions
+ s = moose.Pool( '/model/compartment/s' )
+ rXfer = moose.Reac( '/model/compartment/rXfer' )
+ #####################################################################
+ # Put in endo compartment. Add molecule s
+ endo = moose.EndoMesh( '/model/endo' )
+ endo.isMembraneBound = True
+ endo.surround = compartment
+ es = moose.Pool( '/model/endo/s' )
+ erXfer = moose.Reac( '/model/endo/erXfer' )
+ #####################################################################
+ moose.connect( erXfer, 'sub', es, 'reac' )
+ moose.connect( erXfer, 'prd', s, 'reac' )
+ moose.connect( rXfer, 'sub', s, 'reac' )
+ moose.connect( rXfer, 'prd', es, 'reac' )
+ rXfer.Kf = 0.04 # 0.04/sec
+ rXfer.Kb = 0.0 # 0.00/sec
+ erXfer.Kf = 0.16 # 0.16/sec
+ erXfer.Kb = 0.0 # 0.00/sec
+
+ #####################################################################
+ fixXreacs.fixXreacs( '/model' )
+ fixXreacs.restoreXreacs( '/model' )
+ fixXreacs.fixXreacs( '/model' )
+ #####################################################################
+
+ # Make solvers
+ ksolve = moose.Ksolve( '/model/compartment/ksolve' )
+ dsolve = moose.Dsolve( '/model/dsolve' )
+ eksolve = moose.Ksolve( '/model/endo/ksolve' )
+ edsolve = moose.Dsolve( '/model/endo/dsolve' )
+
+ stoich = moose.Stoich( '/model/compartment/stoich' )
+ stoich.compartment = compartment
+ stoich.ksolve = ksolve
+ stoich.dsolve = dsolve
+ stoich.path = "/model/compartment/##"
+ assert( dsolve.numPools == 2 )
+ s.vec.concInit = [1]*num
+
+ estoich = moose.Stoich( '/model/endo/stoich' )
+ estoich.compartment = endo
+ estoich.ksolve = eksolve
+ estoich.dsolve = edsolve
+ estoich.path = "/model/endo/##"
+ assert( edsolve.numPools == 2 )
+
+ edsolve.buildMeshJunctions( dsolve )
+
+ plot1 = moose.Table2( '/model/plot1' )
+ plot2 = moose.Table2( '/model/plot2' )
+ moose.connect( '/model/plot1', 'requestOut', s, 'getN' )
+ moose.connect( '/model/plot2', 'requestOut', es, 'getN' )
+ plot3 = moose.Table2( '/model/plot3' )
+ plot4 = moose.Table2( '/model/plot4' )
+ moose.connect( '/model/plot3', 'requestOut', s, 'getConc' )
+ moose.connect( '/model/plot4', 'requestOut', es, 'getConc' )
+
+def almostEq( a, b ):
+ #print a, b, (a-b)/(a+b)
+ return abs(a-b)/(a+b) < 5e-5
+
+def main( standalone = False ):
+ for i in range( 10, 18):
+ moose.setClock( i, 0.001 )
+ runtime = 100
+ makeModel()
+ moose.reinit()
+ moose.start( runtime )
+
+ assert( almostEq( 2.0 * moose.element( 'model/compartment/s' ).conc,
+ moose.element( '/model/endo/s' ).conc ) )
+
+ moose.delete( '/model' )
+
+# Run the 'main' if this script is executed standalone.
+if __name__ == '__main__':
+ main( standalone = True )
diff --git a/tests/python/test_Xreacs5a.py b/tests/python/test_Xreacs5a.py
new file mode 100644
index 00000000..126f9182
--- /dev/null
+++ b/tests/python/test_Xreacs5a.py
@@ -0,0 +1,99 @@
+# -*- coding: utf-8 -*-
+#########################################################################
+## This program is part of 'MOOSE', the
+## Messaging Object Oriented Simulation Environment.
+## Copyright (C) 2014 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.
+#########################################################################
+
+
+import math
+import numpy as np
+import moose
+import fixXreacs
+
+def makeModel():
+ # create container for model
+ num = 1 # number of compartments
+ model = moose.Neutral( '/model' )
+ compartment = moose.CylMesh( '/model/compartment' )
+ compartment.x1 = 1.0e-6 # Set it to a 1 micron single-voxel cylinder
+
+ # create molecules and reactions
+ s = moose.Pool( '/model/compartment/s' )
+ rXfer = moose.Reac( '/model/compartment/rXfer' )
+ #####################################################################
+ # Put in endo compartment. Add molecule s
+ endo = moose.EndoMesh( '/model/endo' )
+ endo.isMembraneBound = True
+ endo.surround = compartment
+ es = moose.Pool( '/model/endo/s' )
+ erXfer = moose.Reac( '/model/compartment/erXfer' )
+ #####################################################################
+ moose.connect( erXfer, 'sub', es, 'reac' )
+ moose.connect( erXfer, 'prd', s, 'reac' )
+ moose.connect( rXfer, 'sub', s, 'reac' )
+ moose.connect( rXfer, 'prd', es, 'reac' )
+ rXfer.Kf = 0.04 # 0.04/sec
+ rXfer.Kb = 0.0 # 0.02/sec
+ erXfer.Kf = 0.02 # 0.04/sec
+ erXfer.Kb = 0.0 # 0.02/sec
+
+ #####################################################################
+ fixXreacs.fixXreacs( '/model' )
+ fixXreacs.restoreXreacs( '/model' )
+ fixXreacs.fixXreacs( '/model' )
+ #####################################################################
+ rx = moose.element( '/model/compartment/rXfer' )
+ erx = moose.element( '/model/compartment/erXfer' )
+
+ # Make solvers
+ ksolve = moose.Ksolve( '/model/compartment/ksolve' )
+ dsolve = moose.Dsolve( '/model/dsolve' )
+ eksolve = moose.Ksolve( '/model/endo/ksolve' )
+ edsolve = moose.Dsolve( '/model/endo/dsolve' )
+
+ stoich = moose.Stoich( '/model/compartment/stoich' )
+ stoich.compartment = compartment
+ stoich.ksolve = ksolve
+ stoich.dsolve = dsolve
+ stoich.path = "/model/compartment/##"
+ assert( dsolve.numPools == 2 )
+ s.vec.concInit = [1]*num
+
+ estoich = moose.Stoich( '/model/endo/stoich' )
+ estoich.compartment = endo
+ estoich.ksolve = eksolve
+ estoich.dsolve = edsolve
+ estoich.path = "/model/endo/##"
+ assert( edsolve.numPools == 1 )
+
+ edsolve.buildMeshJunctions( dsolve )
+
+ plot1 = moose.Table2( '/model/plot1' )
+ plot2 = moose.Table2( '/model/plot2' )
+ moose.connect( '/model/plot1', 'requestOut', s, 'getN' )
+ moose.connect( '/model/plot2', 'requestOut', es, 'getN' )
+ plot3 = moose.Table2( '/model/plot3' )
+ plot4 = moose.Table2( '/model/plot4' )
+ moose.connect( '/model/plot3', 'requestOut', s, 'getConc' )
+ moose.connect( '/model/plot4', 'requestOut', es, 'getConc' )
+
+def almostEq( a, b ):
+ return abs(a-b)/(a+b) < 5e-5
+
+def main( standalone = False ):
+ runtime = 200
+ displayInterval = 2
+ makeModel()
+ moose.reinit()
+ moose.start( runtime )
+ assert( almostEq( 2.0 * moose.element( 'model/compartment/s' ).n,
+ moose.element( '/model/endo/s' ).n ) )
+ moose.delete( '/model' )
+
+# Run the 'main' if this script is executed standalone.
+if __name__ == '__main__':
+ main( standalone = True )
diff --git a/tests/python/test_Xreacs6.py b/tests/python/test_Xreacs6.py
new file mode 100644
index 00000000..35f21c5b
--- /dev/null
+++ b/tests/python/test_Xreacs6.py
@@ -0,0 +1,99 @@
+# -*- coding: utf-8 -*-
+#########################################################################
+## This program is part of 'MOOSE', the
+## Messaging Object Oriented Simulation Environment.
+## Copyright (C) 2018 Upinder S. Bhalla. and NCBS
+## It is made available under the terms of the
+## GNU General Public License version 3 or later.
+## See the file COPYING.LIB for the full notice.
+#########################################################################
+
+
+import math
+import numpy as np
+import moose
+import fixXreacs
+
+def makeModel():
+ # create container for model
+ num = 1 # number of compartments
+ model = moose.Neutral( '/model' )
+ compartment = moose.CylMesh( '/model/compartment' )
+ compartment.x1 = 1.0e-6 # Set it to a 1 micron single-voxel cylinder
+
+ # create molecules and reactions
+ s = moose.Pool( '/model/compartment/s' )
+ t = moose.Pool( '/model/compartment/t' )
+ rXfer = moose.Reac( '/model/compartment/rXfer' )
+ #####################################################################
+ # Put in endo compartment. Add molecule s
+ endo = moose.EndoMesh( '/model/endo' )
+ endo.isMembraneBound = True
+ endo.surround = compartment
+ es = moose.Pool( '/model/endo/s' )
+ et = moose.Pool( '/model/endo/t' )
+ #####################################################################
+ moose.connect( rXfer, 'sub', s, 'reac' )
+ moose.connect( rXfer, 'sub', t, 'reac' )
+ moose.connect( rXfer, 'prd', es, 'reac' )
+ moose.connect( rXfer, 'prd', et, 'reac' )
+ rXfer.Kf = 0.02 # 0.02/mM/sec
+ rXfer.Kb = 0.02 # 0.02/mM/sec
+
+ #####################################################################
+ fixXreacs.fixXreacs( '/model' )
+ #fixXreacs.restoreXreacs( '/model' )
+ #fixXreacs.fixXreacs( '/model' )
+ #####################################################################
+ # Make solvers
+ ksolve = moose.Ksolve( '/model/compartment/ksolve' )
+ dsolve = moose.Dsolve( '/model/dsolve' )
+ eksolve = moose.Ksolve( '/model/endo/ksolve' )
+ edsolve = moose.Dsolve( '/model/endo/dsolve' )
+
+ stoich = moose.Stoich( '/model/compartment/stoich' )
+ stoich.compartment = compartment
+ stoich.ksolve = ksolve
+ stoich.dsolve = dsolve
+ stoich.path = "/model/compartment/##"
+ assert( dsolve.numPools == 4 )
+ s.vec.concInit = [1]*num
+ t.vec.concInit = [1]*num
+
+ estoich = moose.Stoich( '/model/endo/stoich' )
+ estoich.compartment = endo
+ estoich.ksolve = eksolve
+ estoich.dsolve = edsolve
+ estoich.path = "/model/endo/##"
+ assert( edsolve.numPools == 2 )
+
+ edsolve.buildMeshJunctions( dsolve )
+
+ plot1 = moose.Table2( '/model/plot1' )
+ plot2 = moose.Table2( '/model/plot2' )
+ moose.connect( '/model/plot1', 'requestOut', s, 'getN' )
+ moose.connect( '/model/plot2', 'requestOut', es, 'getN' )
+ plot3 = moose.Table2( '/model/plot3' )
+ plot4 = moose.Table2( '/model/plot4' )
+ moose.connect( '/model/plot3', 'requestOut', s, 'getConc' )
+ moose.connect( '/model/plot4', 'requestOut', es, 'getConc' )
+
+def almostEq( a, b ):
+ #print a, b, (a-b)/(a+b)
+ return abs(a-b)/(a+b) < 5e-5
+
+def main( standalone = False ):
+ for i in range( 10, 18):
+ moose.setClock( i, 0.01 )
+ runtime = 100
+ displayInterval = 2
+ makeModel()
+ moose.reinit()
+ moose.start( runtime )
+ assert( almostEq( moose.element( 'model/compartment/s' ).conc,
+ moose.element( '/model/endo/s' ).conc ) )
+ moose.delete( '/model' )
+
+# Run the 'main' if this script is executed standalone.
+if __name__ == '__main__':
+ main( standalone = True )
diff --git a/tests/python/test_Xreacs7.py b/tests/python/test_Xreacs7.py
new file mode 100644
index 00000000..913a7a1c
--- /dev/null
+++ b/tests/python/test_Xreacs7.py
@@ -0,0 +1,114 @@
+# -*- coding: utf-8 -*-
+#########################################################################
+## This program is part of 'MOOSE', the
+## Messaging Object Oriented Simulation Environment.
+## Copyright (C) 2018 Upinder S. Bhalla. and NCBS
+## It is made available under the terms of the
+## GNU General Public License version 3 or later.
+## See the file COPYING.LIB for the full notice.
+##
+## This file makes u + t <=====> s where u is in a different compt from t,s
+#########################################################################
+
+
+import math
+import numpy as np
+import moose
+import fixXreacs
+
+def makeModel():
+ # create container for model
+ num = 1 # number of compartments
+ model = moose.Neutral( '/model' )
+ compartment = moose.CylMesh( '/model/compartment' )
+ compartment.x1 = 1.0e-6 # Set it to a 1 micron single-voxel cylinder
+
+ # create molecules and reactions
+ u = moose.Pool( '/model/compartment/u' )
+ #####################################################################
+ # Put in endo compartment. Add molecule s
+ endo = moose.EndoMesh( '/model/endo' )
+ endo.isMembraneBound = True
+ endo.surround = compartment
+ rXfer = moose.Reac( '/model/endo/rXfer' )
+ et = moose.Pool( '/model/endo/t' )
+ es = moose.Pool( '/model/endo/s' )
+ #####################################################################
+ moose.connect( rXfer, 'sub', u, 'reac' )
+ moose.connect( rXfer, 'sub', et, 'reac' )
+ moose.connect( rXfer, 'prd', es, 'reac' )
+ u.concInit = 1.0
+ et.concInit = 1.0
+
+ #####################################################################
+ # [u0] = 1 in compt, [t0] = 1 in endo, [s0] = 0
+ # [u] + [s]/8 = [u0] ; [t] + [s] = [t0]; nu + ns = nu0, nt + ns = nt0
+ # At equil, numKf*nu*nt = numKb*ns
+ # Express all # in terms of ns.
+ # nu = nu0-ns; nt = nt0-ns Also, nu0 = 8*nt0
+ # So numKf*(nu0-ns)*(nt0-ns) = numKb*ns
+ # Target level is nt = ns = nt0/2
+ # So numKf*( 8nt0 - nt0/2)*nt0/2 = numKb*nt0/2
+ # So 7.5*nt0 = numKb/numKf
+ rXfer.numKb = 0.1
+ rXfer.numKf = 0.1/(7.5 * et.nInit)
+ #print( "Rates = {}, {}".format( rXfer.Kf, rXfer.Kb ))
+ #####################################################################
+ fixXreacs.fixXreacs( '/model' )
+ #fixXreacs.restoreXreacs( '/model' )
+ #fixXreacs.fixXreacs( '/model' )
+ #####################################################################
+
+ # Make solvers
+ ksolve = moose.Ksolve( '/model/compartment/ksolve' )
+ dsolve = moose.Dsolve( '/model/compartment/dsolve' )
+ eksolve = moose.Ksolve( '/model/endo/ksolve' )
+ edsolve = moose.Dsolve( '/model/endo/dsolve' )
+
+ stoich = moose.Stoich( '/model/compartment/stoich' )
+ stoich.compartment = compartment
+ stoich.ksolve = ksolve
+ stoich.dsolve = dsolve
+ stoich.path = "/model/compartment/##"
+ assert( dsolve.numPools == 1 )
+
+ estoich = moose.Stoich( '/model/endo/stoich' )
+ estoich.compartment = endo
+ estoich.ksolve = eksolve
+ estoich.dsolve = edsolve
+ estoich.path = "/model/endo/##"
+ assert( edsolve.numPools == 3 )
+
+ edsolve.buildMeshJunctions( dsolve )
+
+ plot1 = moose.Table2( '/model/plot1' )
+ plot2 = moose.Table2( '/model/plot2' )
+ plot3 = moose.Table2( '/model/plot3' )
+ moose.connect( '/model/plot1', 'requestOut', u, 'getN' )
+ moose.connect( '/model/plot2', 'requestOut', et, 'getN' )
+ moose.connect( '/model/plot3', 'requestOut', es, 'getN' )
+ plot4 = moose.Table2( '/model/plot4' )
+ plot5 = moose.Table2( '/model/plot5' )
+ plot6 = moose.Table2( '/model/plot6' )
+ moose.connect( '/model/plot4', 'requestOut', u, 'getConc' )
+ moose.connect( '/model/plot5', 'requestOut', et, 'getConc' )
+ moose.connect( '/model/plot6', 'requestOut', es, 'getConc' )
+
+def almostEq( a, b ):
+ #print a, b, (a-b)/(a+b)
+ return abs(a-b)/(a+b) < 5e-5
+
+def main( standalone = False ):
+ runtime = 100
+ displayInterval = 2
+ makeModel()
+ moose.reinit()
+ moose.start( runtime )
+
+ assert( almostEq( moose.element( 'model/endo/t' ).conc,
+ moose.element( '/model/endo/s' ).conc ) )
+ moose.delete( '/model' )
+
+# Run the 'main' if this script is executed standalone.
+if __name__ == '__main__':
+ main( standalone = True )
diff --git a/tests/python/test_Xreacs8.py b/tests/python/test_Xreacs8.py
new file mode 100644
index 00000000..15bb0f01
--- /dev/null
+++ b/tests/python/test_Xreacs8.py
@@ -0,0 +1,109 @@
+# -*- coding: utf-8 -*-
+#########################################################################
+## This program is part of 'MOOSE', the
+## Messaging Object Oriented Simulation Environment.
+## Copyright (C) 2014 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.
+## Here we set up equal Kf and Kb in a reversible reaction across a
+## 1-voxel cyl compt and an internal endoMesh, having a smaller volume.
+## \
+## COMPT: 2 s <===> / 2 s :ENDO
+## \
+##
+## This becomes:
+## \
+## COMPT: 2 s <===> 2 s_xfer_endo / 2s :ENDO
+## \
+##
+#########################################################################
+
+
+import math
+import numpy as np
+import moose
+import fixXreacs
+
+def makeModel():
+ # create container for model
+ num = 1 # number of compartments
+ model = moose.Neutral( '/model' )
+ compartment = moose.CylMesh( '/model/compartment' )
+ compartment.x1 = 1.0e-6 # Set it to a 1 micron single-voxel cylinder
+
+ # create molecules and reactions
+ s = moose.Pool( '/model/compartment/s' )
+ rXfer = moose.Reac( '/model/compartment/rXfer' )
+ #####################################################################
+ # Put in endo compartment. Add molecule s
+ endo = moose.EndoMesh( '/model/endo' )
+ endo.isMembraneBound = True
+ endo.surround = compartment
+ es = moose.Pool( '/model/endo/s' )
+ #####################################################################
+ moose.connect( rXfer, 'sub', s, 'reac' )
+ moose.connect( rXfer, 'sub', s, 'reac' )
+ moose.connect( rXfer, 'prd', es, 'reac' )
+ moose.connect( rXfer, 'prd', es, 'reac' )
+ rXfer.Kf = 0.01 # 0.01/sec
+ rXfer.Kb = 0.01 # 0.01/sec
+
+ #####################################################################
+ fixXreacs.fixXreacs( '/model' )
+ fixXreacs.restoreXreacs( '/model' )
+ fixXreacs.fixXreacs( '/model' )
+ #####################################################################
+
+ # Make solvers
+ ksolve = moose.Ksolve( '/model/compartment/ksolve' )
+ dsolve = moose.Dsolve( '/model/dsolve' )
+ eksolve = moose.Ksolve( '/model/endo/ksolve' )
+ edsolve = moose.Dsolve( '/model/endo/dsolve' )
+
+ stoich = moose.Stoich( '/model/compartment/stoich' )
+ stoich.compartment = compartment
+ stoich.ksolve = ksolve
+ stoich.dsolve = dsolve
+ stoich.path = "/model/compartment/##"
+ assert( dsolve.numPools == 2 )
+ s.vec.concInit = [1]*num
+
+ estoich = moose.Stoich( '/model/endo/stoich' )
+ estoich.compartment = endo
+ estoich.ksolve = eksolve
+ estoich.dsolve = edsolve
+ estoich.path = "/model/endo/##"
+ assert( edsolve.numPools == 1 )
+
+ edsolve.buildMeshJunctions( dsolve )
+
+ plot1 = moose.Table2( '/model/plot1' )
+ plot2 = moose.Table2( '/model/plot2' )
+ plot3 = moose.Table2( '/model/plot3' )
+ moose.connect( '/model/plot1', 'requestOut', s, 'getN' )
+ moose.connect( '/model/plot2', 'requestOut', es, 'getN' )
+ moose.connect( '/model/plot3', 'requestOut', '/model/compartment/s_xfer_endo', 'getN' )
+ plot4 = moose.Table2( '/model/plot4' )
+ plot5 = moose.Table2( '/model/plot5' )
+ plot6 = moose.Table2( '/model/plot6' )
+ moose.connect( '/model/plot4', 'requestOut', s, 'getConc' )
+ moose.connect( '/model/plot5', 'requestOut', es, 'getConc' )
+ moose.connect( '/model/plot6', 'requestOut', '/model/compartment/s_xfer_endo', 'getConc' )
+
+def almostEq( a, b ):
+ return abs(a-b)/(a+b) < 5e-5
+
+def main( standalone = False ):
+ runtime = 100
+ makeModel()
+ moose.reinit()
+ moose.start( runtime )
+ assert( almostEq( moose.element( 'model/compartment/s' ).conc,
+ moose.element( '/model/endo/s' ).conc ) )
+ moose.delete( '/model' )
+
+
+# Run the 'main' if this script is executed standalone.
+if __name__ == '__main__':
+ main( standalone = True )
diff --git a/tests/python/test_connectionLists.py b/tests/python/test_connectionLists.py
index 057cd5a4..fcd77867 100644
--- a/tests/python/test_connectionLists.py
+++ b/tests/python/test_connectionLists.py
@@ -66,8 +66,14 @@ def makeGlobalBalanceNetwork():
inhibMatrix.setRandomConnectivity(
params['stimToInhProb'], params['stimToInhSeed'] )
cl = inhibMatrix.connectionList
- expectedCl = [ 1,4,13,13,26,42,52,56,80,82,95,97,4,9,0,9,4,8,0,6,1,6,6,7]
- assert list(cl) == expectedCl, "Expected %s, got %s" % (expectedCl, cl )
+
+ # This can change when random-number generator changes.
+ # This was before we used c++11 <random> to generate random numbers. This
+ # test has changes on Tuesday 31 July 2018 11:12:35 AM IST
+ # expectedCl = [ 1,4,13,13,26,42,52,56,80,82,95,97,4,9,0,9,4,8,0,6,1,6,6,7]
+ expectedCl=[0,6,47,50,56,67,98,2,0,3,5,4,8,3]
+
+ assert list(cl) == expectedCl, "Expected %s, got %s" % (expectedCl, cl)
temp = moose.connect( stim, 'spikeOut', ov, 'addSpike', 'Sparse' )
excMatrix = moose.element( temp )
@@ -80,7 +86,9 @@ def makeGlobalBalanceNetwork():
params['inhToOutProb'], params['inhToOutSeed'] )
# print("ConnMtxEntries: ", inhibMatrix.numEntries, excMatrix.numEntries, negFFMatrix.numEntries)
- assert (12, 57, 48) == (inhibMatrix.numEntries, excMatrix.numEntries, negFFMatrix.numEntries)
+ got = (inhibMatrix.numEntries, excMatrix.numEntries, negFFMatrix.numEntries)
+ expected = (7, 62, 55)
+ assert expected == got, "Expected %s, Got %s" % (expected,got)
cl = negFFMatrix.connectionList
numInhSyns = [ ]
@@ -93,7 +101,9 @@ def makeGlobalBalanceNetwork():
if i.synapse.num > 0:
i.synapse.weight = params['wtStimToInh']
- assert numInhSyns == [2,1,0,0,2,0,3,1,1,2]
+ # expected = [2,1,0,0,2,0,3,1,1,2]
+ expected = [1, 0, 1, 2, 1, 1, 0, 0, 1, 0]
+ assert numInhSyns == expected, "Expected %s, got %s" % (expected,numInhSyns)
for i in moose.vec( outsyn ):
nov += i.synapse.num
@@ -105,12 +115,12 @@ def makeGlobalBalanceNetwork():
if i.synapse.num > 0:
i.synapse.weight = params['wtInhToOut']
- # print("SUMS: ", sum( iv.numField ), sum( ov.numField ), sum( oiv.numField ))
- assert [4,49,9] == [sum( iv.numField ), sum( ov.numField ), sum( oiv.numField )]
- # print("SUMS2: ", niv, nov, noiv)
- assert [12,57,48] == [ niv, nov, noiv ]
- # print("SUMS3: ", sum( insyn.vec.numSynapses ), sum( outsyn.vec.numSynapses ), sum( outInhSyn.vec.numSynapses ))
- assert [12, 57, 48 ] == [ sum( insyn.vec.numSynapses ), sum( outsyn.vec.numSynapses ), sum( outInhSyn.vec.numSynapses ) ]
+ print("SUMS: ", sum( iv.numField ), sum( ov.numField ), sum( oiv.numField ))
+ assert [1, 64, 25] == [sum( iv.numField ), sum( ov.numField ), sum( oiv.numField )]
+ print("SUMS2: ", niv, nov, noiv)
+ assert [7, 62, 55] == [ niv, nov, noiv ]
+ print("SUMS3: ", sum( insyn.vec.numSynapses ), sum( outsyn.vec.numSynapses ), sum( outInhSyn.vec.numSynapses ))
+ assert [7,62,55] == [ sum( insyn.vec.numSynapses ), sum( outsyn.vec.numSynapses ), sum( outInhSyn.vec.numSynapses ) ]
# print(oiv.numField)
# print(insyn.vec[1].synapse.num)
diff --git a/tests/python/test_difshells.py b/tests/python/test_difshells.py
index 4ba00d8a..d9e29fe5 100644
--- a/tests/python/test_difshells.py
+++ b/tests/python/test_difshells.py
@@ -1,10 +1,36 @@
# -*- coding: utf-8 -*-
import moose
+print( 'Using moose from %s. VERSION=%s' % (moose.__file__, moose.__version__) )
import numpy as np
import chan_proto
import param_chan
-from params import *
+t_stop = 10
+dend_diameter = 2.2627398e-6
+dend_length = 1.131369936e-6
+Cm = 4.021231698e-12
+Rm = 1865100032
+Em = -0.07100000232
+Vm_0 = -0.0705
+dt = 50e-6
+spines_no = 0
+difshell_no = 2
+difshell_name = "Ca_shell"
+Ca_basal = 50e-6
+Ca_initial = Ca_basal*200
+dca = 200.0e-12
+difbuff_no = 1
+difbuff_name = "Buff"
+btotal = 80.0e-3
+kf = 0.028e6
+kb = 19.6
+d = 66e-12
+inject = 0.1e-9
+gbar = 1
+#MMpump
+km = 0.3e-3
+kcat = 85e-22
+pumps = 1
def linoid(x, param):
den = (param[2] + np.exp((V + param[3]) / param[4]))
@@ -93,7 +119,6 @@ def addOneChan(chanpath, gbar,comp):
moose.connect(chan, "channelOut", comp, "handleChannel")
return chan
-
if __name__ == '__main__':
lib = moose.Neutral('/library')
for tick in range(0, 7):
diff --git a/tests/python/test_kkit.py b/tests/python/test_kkit.py
index ba194d63..0b7c3758 100644
--- a/tests/python/test_kkit.py
+++ b/tests/python/test_kkit.py
@@ -24,7 +24,7 @@ def main():
if ( len( sys.argv ) == 4 ):
solver = sys.argv[3]
modelId = moose.loadModel( mfile, 'model')
- moose.mooseaddChemSolver('model',solver)
+ moose.mooseAddChemSolver('model',solver)
# Increase volume so that the stochastic solver gssa
# gives an interesting output
diff --git a/tests/python/test_muparser.py b/tests/python/test_muparser.py
index 7adf0e26..d5f92311 100644
--- a/tests/python/test_muparser.py
+++ b/tests/python/test_muparser.py
@@ -8,6 +8,8 @@ Modified from https://elifesciences.org/articles/25827 , Fig4.py
import sys
import os
import numpy as np
+import matplotlib as mpl
+mpl.use('Agg')
import sys
import numpy as np
import moose
diff --git a/tests/python/test_negative_value_flag.py b/tests/python/test_negative_value_flag.py
index 7b073975..70861540 100644
--- a/tests/python/test_negative_value_flag.py
+++ b/tests/python/test_negative_value_flag.py
@@ -36,7 +36,7 @@ def main():
solver = sys.argv[3]
modelId = moose.loadModel( mfile, 'model')
- moose.mooseaddChemSolver('model',solver)
+ moose.mooseAddChemSolver('model',solver)
moose.element( '/model/kinetics/neuroNOS/nNOS.arg' ).concInit = 0.1
moose.reinit()
moose.start( runtime )
diff --git a/tests/python/test_neuroml2.py b/tests/python/test_neuroml2.py
index 5155515d..8460c092 100644
--- a/tests/python/test_neuroml2.py
+++ b/tests/python/test_neuroml2.py
@@ -1,43 +1,7 @@
# -*- coding: utf-8 -*-
# test_neurom2.py, modified from run_cell.py
-# Description:
-# Author:
# Maintainer: P Gleeson, Dilawar Singh
-# Version:
-# 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.
-#
-#
-
+# This test is not robust.
# Code:
from __future__ import absolute_import, print_function, division
@@ -49,7 +13,7 @@ import os
import numpy as np
SCRIPT_DIR = os.path.dirname( os.path.realpath( __file__ ) )
-
+
def run( nogui = True ):
global SCRIPT_DIR
filename = os.path.join(SCRIPT_DIR, 'test_files/passiveCell.nml' )
@@ -57,26 +21,25 @@ def run( nogui = True ):
nml = moose.mooseReadNML2( filename )
if not nml:
mu.warn( "Failed to parse NML2 file" )
- return
+ return
assert nml, "Expecting NML2 object"
msoma = nml.getComp(nml.doc.networks[0].populations[0].id,0,0)
data = moose.Neutral('/data')
pg = nml.getInput('pulseGen1')
-
+
inj = moose.Table('%s/pulse' % (data.path))
moose.connect(inj, 'requestOut', pg, 'getOutputValue')
-
-
+
vm = moose.Table('%s/Vm' % (data.path))
moose.connect(vm, 'requestOut', msoma, 'getVm')
-
+
simtime = 150e-3
moose.reinit()
moose.start(simtime)
print("Finished simulation!")
t = np.linspace(0, simtime, len(vm.vector))
- yvec = vm.vector
+ yvec = vm.vector
injvec = inj.vector * 1e12
m1, u1 = np.mean( yvec ), np.std( yvec )
m2, u2 = np.mean( injvec ), np.std( injvec )
diff --git a/tests/python/test_random_num.py b/tests/python/test_random_num.py
new file mode 100644
index 00000000..9be47e93
--- /dev/null
+++ b/tests/python/test_random_num.py
@@ -0,0 +1,59 @@
+# -*- coding: utf-8 -*-
+"""test_random_num.py:
+
+"""
+
+__author__ = "Dilawar Singh"
+__copyright__ = "Copyright 2017-, Dilawar Singh"
+__version__ = "1.0.0"
+__maintainer__ = "Dilawar Singh"
+__email__ = "dilawars@ncbs.res.in"
+__status__ = "Development"
+
+import sys
+import os
+import numpy as np
+import moose
+
+try:
+ reload
+except NameError:
+ # Python 3
+ from imp import reload
+
+def unequal():
+ rand1, rand2 = [], []
+ N = 10
+ for i in range( N ):
+ x = moose.rand()
+ rand1.append( x )
+ reload( moose )
+ for i in range( N ):
+ x = moose.rand()
+ rand2.append( x )
+
+ assert not np.equal( rand1, rand2 ).all()
+
+def equal():
+ rand1, rand2 = [], []
+ N = 10
+ moose.seed( 10 )
+ for i in range( N ):
+ x = moose.rand()
+ rand1.append( x )
+
+ reload( moose )
+ moose.seed( 10 )
+ for i in range( N ):
+ x = moose.rand()
+ rand2.append( x )
+
+ assert np.equal( rand1, rand2 ).all()
+
+def main( ):
+ unequal()
+ equal()
+
+if __name__ == '__main__':
+ main()
+
diff --git a/tests/python/test_rdesigneur.py b/tests/python/test_rdesigneur.py
index 2972a3c0..f53ac93f 100644
--- a/tests/python/test_rdesigneur.py
+++ b/tests/python/test_rdesigneur.py
@@ -11,6 +11,8 @@ __status__ = "Development"
import sys
import os
+import matplotlib as mpl
+mpl.use('Agg')
import numpy as np
import moose
import rdesigneur as rd
diff --git a/tests/python/test_utils.py b/tests/python/test_utils.py
deleted file mode 100644
index a57633b8..00000000
--- a/tests/python/test_utils.py
+++ /dev/null
@@ -1,10 +0,0 @@
-# -*- coding: utf-8 -*-
-import moose
-import moose.utils as mu
-
-def main( ):
- print( dir( mu ) )
- mu.info( 'Hellow' )
-
-if __name__ == '__main__':
- main()
diff --git a/utility/Annotator.cpp b/utility/Annotator.cpp
index 184ab6b6..8dca2186 100644
--- a/utility/Annotator.cpp
+++ b/utility/Annotator.cpp
@@ -118,7 +118,7 @@ static const Cinfo* annotatorCinfo = Annotator::initCinfo();
Annotator::Annotator()
: x_( 0.0 ), y_( 0.0 ), z_( 0.0 ),
notes_( "" ), color_( "white" ), textColor_( "black" ),
- icon_( "sphere" ),solver_( "gsl"),runtime_(100.0),dirpath_(""),modeltype_("")
+ icon_( "sphere" ),solver_( "ee"),runtime_(100.0),dirpath_(""),modeltype_("")
{
;
}
diff --git a/utility/cnpy.cpp b/utility/cnpy.cpp
index 4acc6558..131df10c 100644
--- a/utility/cnpy.cpp
+++ b/utility/cnpy.cpp
@@ -85,7 +85,11 @@ bool is_valid_numpy_file( FILE* fp )
{
assert( fp );
char buffer[__pre__size__];
- fread( buffer, sizeof(char), __pre__size__, fp );
+ size_t nr = fread( buffer, sizeof(char), __pre__size__, fp );
+
+ if( 0 == nr )
+ return false;
+
bool equal = true;
// Check for equality
for(size_t i = 0; i < __pre__size__; i++ )
diff --git a/utility/matrix_util.cpp b/utility/matrix_util.cpp
index 7db63a81..fecb4a4b 100644
--- a/utility/matrix_util.cpp
+++ b/utility/matrix_util.cpp
@@ -17,7 +17,7 @@
* =====================================================================================
*/
-#ifdef USE_BOOST
+#ifdef USE_BOOST_ODE
#include "matrix_util.h"
@@ -119,4 +119,4 @@ unsigned int rankUsingBoost( ublas::matrix<value_type>& U )
return i + 1;
}
-#endif /* ----- not USE_BOOST ----- */
+#endif /* ----- not USE_BOOST_ODE ----- */
diff --git a/utility/matrix_util.h b/utility/matrix_util.h
index 9b232abb..092dd0c3 100644
--- a/utility/matrix_util.h
+++ b/utility/matrix_util.h
@@ -19,7 +19,7 @@
#ifndef matrix_util_INC
#define matrix_util_INC
-#ifdef USE_BOOST
+#ifdef USE_BOOST_ODE
#include <boost/numeric/ublas/matrix.hpp>
#include "boost/numeric/bindings/lapack/lapack.hpp"
diff --git a/utility/print_function.hpp b/utility/print_function.hpp
index 5a1863ad..d3a9e888 100644
--- a/utility/print_function.hpp
+++ b/utility/print_function.hpp
@@ -53,8 +53,22 @@
using namespace std;
-namespace moose {
+/* --------------------------------------------------------------------------*/
+/**
+ * @Synopsis Macros
+ */
+/* ----------------------------------------------------------------------------*/
+#define __FILENAME__ (strrchr(__FILE__, '/') ? strrchr(__FILE__, '/') + 1 : __FILE__)
+#ifdef NDEBUG
+#define MOOSE_DEBUG( a ) { \
+ stringstream ss; ss << a; \
+ cout << "DEBUG: " << __FILENAME__ << ":" << __LINE__ << "| " << ss.str(); \
+ }
+#else
+#define MOOSE_DEBUG( a ) {}
+#endif
+namespace moose {
/**
* @brief Enumerate type for debug and log.
@@ -134,6 +148,7 @@ namespace moose {
return ss.str();
}
+ // Not print it when built for release.
inline string debugPrint(string msg, string prefix = "DEBUG"
, string color=T_RESET, unsigned debugLevel = 0
)
@@ -211,6 +226,15 @@ namespace moose {
moose::__dump__(msg, moose::warning );
}
+ inline void showDebug( const string msg )
+ {
+#ifdef DISABLE_DEBUG
+
+#else
+ moose::__dump__(msg, moose::debug );
+#endif
+ }
+
inline void showError( string msg )
{
moose::__dump__( msg, moose::error );
diff --git a/utility/strutil.cpp b/utility/strutil.cpp
index 399d2d71..da5ee41f 100644
--- a/utility/strutil.cpp
+++ b/utility/strutil.cpp
@@ -12,38 +12,39 @@
using namespace std;
-namespace moose {
+namespace moose
+{
// Adapted from code available on oopweb.com
-void tokenize(
- const string& str,
- const string& delimiters,
- vector< string >& tokens )
+void tokenize( const string& str, const string& delimiters, vector< string >& tokens )
{
- // Token boundaries
- string::size_type begin = str.find_first_not_of( delimiters, 0 );
- string::size_type end = str.find_first_of( delimiters, begin );
-
- while ( string::npos != begin || string::npos != end )
- {
- // Found a token, add it to the vector.
- tokens.push_back( str.substr( begin, end - begin ) );
-
- // Update boundaries
- begin = str.find_first_not_of( delimiters, end );
- end = str.find_first_of( delimiters, begin );
- }
+ // Token boundaries
+ string::size_type begin = str.find_first_not_of( delimiters, 0 );
+ string::size_type end = str.find_first_of( delimiters, begin );
+
+ while ( string::npos != begin || string::npos != end )
+ {
+ // Found a token, add it to the vector.
+ tokens.push_back( str.substr( begin, end - begin ) );
+
+ // Update boundaries
+ begin = str.find_first_not_of( delimiters, end );
+ end = str.find_first_of( delimiters, begin );
+ }
}
string& clean_type_name(string& arg)
{
- for (size_t pos = arg.find(' '); pos != string::npos; pos = arg.find(' ')){
+ for (size_t pos = arg.find(' '); pos != string::npos; pos = arg.find(' '))
+ {
arg.replace(pos, 1, 1, '_');
}
- for (size_t pos = arg.find('<'); pos != string::npos; pos = arg.find('<')){
+ for (size_t pos = arg.find('<'); pos != string::npos; pos = arg.find('<'))
+ {
arg.replace(pos, 1, 1, '_');
}
- for (size_t pos = arg.find('>'); pos != string::npos; pos = arg.find('>')){
+ for (size_t pos = arg.find('>'); pos != string::npos; pos = arg.find('>'))
+ {
arg.replace(pos, 1, 1, '_');
}
return arg;
@@ -72,20 +73,16 @@ std::string fix(const std::string userPath, const string& delimiters)
string trimmedPath = trim(userPath, delimiters);
string fixedPath;
+ char prev = 0;
// In this loop, we check if there are more than one '/' together. If yes,
// then accept only first one and reject other.
for(unsigned int i = 0; i < trimmedPath.size(); ++i)
{
const char c = trimmedPath[i];
- if('/' == c)
- {
- if('/' != fixedPath[fixedPath.size()-1])
- fixedPath.push_back(c);
- }
- else
+ if(c != '/' || c != prev)
fixedPath.push_back(c);
-
+ prev = c;
}
return fixedPath;
}
@@ -94,36 +91,36 @@ int testTrim()
{
std::string testStrings [] =
- {
- " space at beginning",
- "space at end ",
- " space at both sides ",
- "\ttab at beginning",
- "tab at end\t",
- "\ttab at both sides\t",
- "\nnewline at beginning",
- "newline at end\n",
- "\nnewline at both sides\n",
- "\n\tnewline and tab at beginning",
- "space and tab at end \t",
- " \rtab and return at both sides \r"
- };
+ {
+ " space at beginning",
+ "space at end ",
+ " space at both sides ",
+ "\ttab at beginning",
+ "tab at end\t",
+ "\ttab at both sides\t",
+ "\nnewline at beginning",
+ "newline at end\n",
+ "\nnewline at both sides\n",
+ "\n\tnewline and tab at beginning",
+ "space and tab at end \t",
+ " \rtab and return at both sides \r"
+ };
std::string results[] =
- {
- "space at beginning",
- "space at end",
- "space at both sides",
- "tab at beginning",
- "tab at end",
- "tab at both sides",
- "newline at beginning",
- "newline at end",
- "newline at both sides",
- "newline and tab at beginning",
- "space and tab at end",
- "tab and return at both sides"
- };
+ {
+ "space at beginning",
+ "space at end",
+ "space at both sides",
+ "tab at beginning",
+ "tab at end",
+ "tab at both sides",
+ "newline at beginning",
+ "newline at end",
+ "newline at both sides",
+ "newline and tab at beginning",
+ "space and tab at end",
+ "tab and return at both sides"
+ };
bool success = true;
@@ -140,7 +137,8 @@ int testTrim()
bool endswith(const string & full, const string & ending)
{
- if (full.length() < ending.length()){
+ if (full.length() < ending.length())
+ {
return false;
}
return (0 == full.compare(full.length() - ending.length(), ending.length(), ending));
@@ -159,4 +157,22 @@ int strncasecmp( const string& a, const string& b, size_t n)
return 0;
}
+// This function is modification of this solution:
+// https://stackoverflow.com/a/440240/1805129
+string random_string( const unsigned len )
+{
+ static const char alphanum[] =
+ "0123456789"
+ "ABCDEFGHIJKLMNOPQRSTUVWXYZ"
+ "abcdefghijklmnopqrstuvwxyz";
+
+ string s(len, '_' );
+ for (unsigned i = 0; i < len; ++i)
+ {
+ s[i] = alphanum[rand() % (sizeof(alphanum) - 1)];
+ }
+
+ return s;
+}
+
}
diff --git a/utility/strutil.h b/utility/strutil.h
index d6f48bfd..a5b1760b 100644
--- a/utility/strutil.h
+++ b/utility/strutil.h
@@ -48,16 +48,10 @@ namespace moose
*/
int strncasecmp( const std::string& a, const std::string& b, size_t n);
-
- // TODO: other std::string utilities to add
- // /** Trim leading and trailing whitespace and replace convert any two or more consecutive whitespace inside the std::string by a single 'blank' character. */
- // std::string fulltrim(std::string& myString) const;
- // /** Convert to uppercase */
- // std::string upcase(std::string& myString) const;
- // /** Convert to lowercase */
- // std::string downcase(std::string & myString);
- // Maybe a implement regular expression search - reinventing wheel - but no standard way without using some bloated library.
-
+ /**
+ * Generate random string of given length.
+ */
+ std::string random_string( const unsigned size );
}
#endif //_STRINGUTIL_H
diff --git a/utility/testing_macros.hpp b/utility/testing_macros.hpp
index 5d55dffc..87189889 100644
--- a/utility/testing_macros.hpp
+++ b/utility/testing_macros.hpp
@@ -47,7 +47,7 @@ static ostringstream assertStream;
assertStream.str(""); \
LOCATION( assertStream ); \
assertStream << msg << endl; \
- __dump__(assertStream.str(), "EXPECT_FAILURE"); \
+ moose::__dump__(assertStream.str(), moose::failed); \
}
#define EXPECT_FALSE( condition, msg) \
@@ -55,7 +55,7 @@ static ostringstream assertStream;
assertStream.str(""); \
LOCATION( assertStream ); \
assertStream << msg << endl; \
- __dump__(assertStream.str(), "EXPECT_FAILURE"); \
+ moose::__dump__(assertStream.str(), moose::failed); \
}
#define EXPECT_EQ(a, b, token) \
@@ -64,7 +64,7 @@ static ostringstream assertStream;
LOCATION(assertStream) \
assertStream << "Expected " << b << ", received " << a ; \
assertStream << token; \
- __dump__(assertStream.str(), "EXPECT_FAILURE"); \
+ moose::__dump__(assertStream.str(), moose::failed); \
}
#define EXPECT_NEQ(a, b, token) \
@@ -73,7 +73,7 @@ static ostringstream assertStream;
LOCATION(assertStream); \
assertStream << "Not expected " << a << endl; \
assertStream << token << endl; \
- __dump__(assertStream.str(), "EXPECT_FAILURE"); \
+ moose::__dump__(assertStream.str(), moose::failed); \
}
#define EXPECT_GT(a, b, token) \
@@ -82,7 +82,7 @@ static ostringstream assertStream;
LOCATION(assertStream); \
assertStream << "Expected greater than " << a << ", received " << b << endl; \
assertStream << token << endl; \
- __dump__(assertStream.str(), "EXPECT_FAILURE"); \
+ moose::__dump__(assertStream.str(), moose::failed); \
}
#define EXPECT_GTE(a, b, token) \
@@ -92,7 +92,7 @@ static ostringstream assertStream;
assertStream << "Expected greater than or equal to " << a \
<< ", received " << b << endl; \
assertStream << token << endl; \
- __dump__(assertStream.str(), "EXPECT_FAILURE"); \
+ moose::__dump__(assertStream.str(), moose::failed); \
}
#define EXPECT_LT(a, b, token) \
@@ -101,7 +101,7 @@ static ostringstream assertStream;
LOCATION(assertStream); \
assertStream << "Expected less than " << a << ", received " << b << endl; \
assertStream << token << endl; \
- __dump__(assertStream.str(), "EXPECT_FAILURE"); \
+ moose::__dump__(assertStream.str(), moose::failed); \
}
#define EXPECT_LTE(a, b, token) \
@@ -111,7 +111,7 @@ static ostringstream assertStream;
assertStream << "Expected less than or equal to " << a \
<< ", received " << b << endl; \
assertStream << token << endl; \
- __dump__(assertStream.str(), "EXPECT_FAILURE"); \
+ moose::__dump__(assertStream.str(), moose::failed); \
}
#define ASSERT_TRUE( condition, msg) \
@@ -150,7 +150,7 @@ static ostringstream assertStream;
if(! doubleEq(a, b) ) { \
assertStream.str(""); \
LOCATION(assertStream); \
- assertStream << "Expected " << b << ", received " << a << endl; \
+ assertStream << "Expected " << std::fixed << b << ", received " << a << endl; \
assertStream << token; \
moose::__dump__(assertStream.str(), moose::failed); \
throw std::runtime_error( "float equality test failed" ); \
diff --git a/utility/utility.h b/utility/utility.h
index 303de277..4d551018 100644
--- a/utility/utility.h
+++ b/utility/utility.h
@@ -1,7 +1,5 @@
// utility.h ---
-//
-// Filename: utility.h
-// Description:
+// Description: Some utility function.
// Author: Subhasis Ray
// Maintainer:
// Copyright (C) 2010 Subhasis Ray, all rights reserved.
@@ -10,29 +8,14 @@
// Last-Updated: Tue Jul 23 12:48:17 2013 (+0530)
// By: subha
// Update #: 19
-// URL:
-// Keywords:
-// Compatibility:
-//
-//
-
-// Commentary:
-//
-//
-//
-//
-
-// Change log:
-//
-//
-//
-
-// Code:
#ifndef _UTILITY_H
+
#include "strutil.h"
-namespace moose {
+// See types.cpp file for definitions.
+namespace moose
+{
char shortType(std::string type);
char innerType(char typecode);
@@ -55,6 +38,5 @@ namespace moose {
#endif // !_UTILITY_H
-
//
// utility.h ends here
--
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