diff --git a/moose-core/.travis.yml b/moose-core/.travis.yml
index a88c1f75306724a1614f40053e866de64a8e330c..7a134ba7fc4a69d462617c4e22315e601ab2edfb 100644
--- a/moose-core/.travis.yml
+++ b/moose-core/.travis.yml
@@ -10,6 +10,8 @@ os:
notifications:
email:
recipients:
+ - bhalla@ncbs.res.in
+ - hrani@ncbs.res.in
- dilawar.s.rajput@gmail.com
on_success: change
on_failure: always
@@ -30,6 +32,6 @@ before_script :
script:
- # checking if any python3 incompatible file is in the source tree.
- python2 -m compileall -q .
- - if type python3 -c 'import sys' > /dev/null; then python3 -m compileall -q . ; fi
+ - if type python3 > /dev/null; then python3 -m compileall -q . ; fi
- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then ./.travis/travis_build_osx.sh; fi
- if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then ./.travis/travis_build_linux.sh; fi
diff --git a/moose-core/.travis/travis_build_linux.sh b/moose-core/.travis/travis_build_linux.sh
index cf3399695355795695fe42b8d668b8baa80e2d21..b993e109f7ec82154791414896c6b02e5b7c645c 100755
--- a/moose-core/.travis/travis_build_linux.sh
+++ b/moose-core/.travis/travis_build_linux.sh
@@ -30,8 +30,8 @@ PYTHON3="/usr/bin/python3"
(
# Old makefile based flow.
- python2 -m compileall -q .
- if type $PYTHON3 > /dev/null; then python3 -m compileall -q . ; fi
+ $PYTHON2 -m compileall -q .
+ if type $PYTHON3 > /dev/null; then $PYTHON3 -m compileall -q . ; fi
# Traditional make.
make
## CMAKE based flow
diff --git a/moose-core/biophysics/Neuron.cpp b/moose-core/biophysics/Neuron.cpp
index 002952ac7780ea7d270dce08f1b07fb61c403965..cf30533641f7a385d5f10351cf1c3fd419853809 100644
--- a/moose-core/biophysics/Neuron.cpp
+++ b/moose-core/biophysics/Neuron.cpp
@@ -14,11 +14,10 @@
#include "shell/Wildcard.h"
#include "ReadCell.h"
#include "utility/Vec.h"
-#include "randnum/Normal.h"
-#include "randnum/randnum.h"
#include "SwcSegment.h"
#include "Spine.h"
#include "Neuron.h"
+#include "basecode/global.h"
#include "muParser.h"
@@ -1737,7 +1736,7 @@ static void addPos( unsigned int segIndex, unsigned int eIndex,
unsigned int n = 1 + dendLength / minSpacing;
double dx = dendLength / n;
for( unsigned int i = 0; i < n; ++i ) {
- if ( mtrand() < dx / spacing ) {
+ if ( moose::mtrand() < dx / spacing ) {
seglistIndex.push_back( segIndex );
elistIndex.push_back( eIndex );
pos.push_back( i * dx + dx*0.5 );
@@ -1758,12 +1757,12 @@ static void addPos( unsigned int segIndex, unsigned int eIndex,
{
if ( spacingDistrib > 0.0 ) {
double position = spacing * 0.5 +
- ( mtrand() - 0.5 ) * spacingDistrib;
+ ( moose::mtrand() - 0.5 ) * spacingDistrib;
while ( position < dendLength ) {
seglistIndex.push_back( segIndex );
elistIndex.push_back( eIndex );
pos.push_back( position );
- position += spacing + ( mtrand() - 0.5 ) * spacingDistrib;
+ position += spacing + ( moose::mtrand() - 0.5 ) * spacingDistrib;
}
} else {
for ( double position = spacing * 0.5;
@@ -1846,7 +1845,7 @@ static void makeAngleDistrib ( const vector< ObjId >& elist,
angleDistrib = distribParser.eval( val.begin() + j);
}
if ( angleDistrib > 0 )
- theta[k] = angle + ( mtrand() - 0.5 ) * angleDistrib;
+ theta[k] = angle + ( moose::mtrand() - 0.5 ) * angleDistrib;
else
theta[k] = angle;
}
@@ -1883,7 +1882,7 @@ static void makeSizeDistrib ( const vector< ObjId >& elist,
sizeDistrib = distribParser.eval( val.begin() + j);
}
if ( sizeDistrib > 0 )
- size[k] = sz + ( mtrand() - 0.5 ) * sizeDistrib;
+ size[k] = sz + ( moose::mtrand() - 0.5 ) * sizeDistrib;
else
size[k] = sz;
}
diff --git a/moose-core/kinetics/Pool.cpp b/moose-core/kinetics/Pool.cpp
index 691daf295c3b0242c87743d18ffd54b0883def95..8b8b656148f78c6a0390f22471e05eb29fea80a4 100644
--- a/moose-core/kinetics/Pool.cpp
+++ b/moose-core/kinetics/Pool.cpp
@@ -8,6 +8,7 @@
**********************************************************************/
#include "header.h"
+#include "ElementValueFinfo.h"
#include "lookupVolumeFromMesh.h"
#include "PoolBase.h"
#include "Pool.h"
@@ -19,6 +20,16 @@ const Cinfo* Pool::initCinfo()
//////////////////////////////////////////////////////////////
// Field Definitions: All inherited from PoolBase.
//////////////////////////////////////////////////////////////
+ static ElementValueFinfo< Pool, bool > isBuffered(
+ "isBuffered",
+ "Flag: True if Pool is buffered. This field changes 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.",
+ &Pool::setIsBuffered,
+ &Pool::getIsBuffered
+ );
//////////////////////////////////////////////////////////////
// MsgDest Definitions: All but increment and decrement inherited
@@ -45,9 +56,10 @@ const Cinfo* Pool::initCinfo()
// SharedMsg Definitions: All inherited.
//////////////////////////////////////////////////////////////
static Finfo* poolFinfos[] = {
+ &isBuffered, // ElementValueFinfo
&increment, // DestFinfo
&decrement, // DestFinfo
- &nIn,
+ &nIn, // DestFinfo
};
static Dinfo< Pool > dinfo;
@@ -78,6 +90,33 @@ Pool::Pool()
Pool::~Pool()
{;}
+//////////////////////////////////////////////////////////////
+// Field Definitions
+/**
+ * setIsBuffered is a really nasty operation, made possible only because
+ * BufPool is derived from Pool and has no other fields.
+ * It uses a low-level replaceCinfo call to just change the
+ * identity of the Cinfo used, leaving everything else as is.
+ */
+void Pool::setIsBuffered( const Eref& e, bool v )
+{
+ static const Cinfo* bufPoolCinfo = Cinfo::find( "BufPool" );
+ if (getIsBuffered( e ) == v)
+ return;
+ if (v) {
+ e.element()->replaceCinfo( bufPoolCinfo );
+ } else {
+ e.element()->replaceCinfo( poolCinfo );
+ }
+}
+
+bool Pool::getIsBuffered( const Eref& e ) const
+{
+ return e.element()->cinfo()->name() == "BufPool";
+}
+
+//////////////////////////////////////////////////////////////
+//
//////////////////////////////////////////////////////////////
// MsgDest Definitions
//////////////////////////////////////////////////////////////
diff --git a/moose-core/kinetics/Pool.h b/moose-core/kinetics/Pool.h
index dc45e189b21b7adfd328c21833e7fb03db48ff2f..dec4dfa4f136057f79545254448ff89fa2d53227 100644
--- a/moose-core/kinetics/Pool.h
+++ b/moose-core/kinetics/Pool.h
@@ -53,6 +53,13 @@ class Pool: public PoolBase
void vSetSpecies( const Eref& e, SpeciesId v );
SpeciesId vGetSpecies( 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;
+
//////////////////////////////////////////////////////////////////
// Dest funcs. These too override virtual funcs in the Pool base
// class.
diff --git a/moose-core/pymoose/moosemodule.cpp b/moose-core/pymoose/moosemodule.cpp
index 62a9ea2eb85cc6c16ab8bd9dd145e39eeebc8421..1ac1d91f6c8737b1bca5fc6b3d99b5332a4b0668 100644
--- a/moose-core/pymoose/moosemodule.cpp
+++ b/moose-core/pymoose/moosemodule.cpp
@@ -125,7 +125,7 @@ extern void mooseBenchmarks( unsigned int option );
* themselves. If seed is not set by user, it uses std::random_device to
* initialize itself.
*-----------------------------------------------------------------------------*/
-void pymoose_mtseed_( unsigned int seed )
+void pymoose_mtseed_( long int seed )
{
moose::mtseed( seed );
}
diff --git a/moose-core/python/moose/__init__.py b/moose-core/python/moose/__init__.py
index a1a77c0ea7e188ed7e3ef16b5cf2e246e7861c1c..2e2f6772607e82d4ad79b68e78782f4c109e5d30 100644
--- a/moose-core/python/moose/__init__.py
+++ b/moose-core/python/moose/__init__.py
@@ -26,8 +26,7 @@ from .moose import *
# Wrapper to get moose version information.
__version__ = moose._moose.__version__
+
VERSION = moose._moose.VERSION
-import chemUtil.add_Delete_ChemicalSolver
-import chemUtil.chemConnectUtil
-import chemUtil.graphUtils
\ No newline at end of file
+# NOTE: No module should be imported here. Use moose.py to write imports.
diff --git a/moose-core/python/moose/chemUtil/add_Delete_ChemicalSolver.py b/moose-core/python/moose/chemUtil/add_Delete_ChemicalSolver.py
index 6d5886f19bd5a003a5a1fa4a960ad5a5b4774809..af9437b92dd886e39e4644a60f15579f3f76d525 100644
--- a/moose-core/python/moose/chemUtil/add_Delete_ChemicalSolver.py
+++ b/moose-core/python/moose/chemUtil/add_Delete_ChemicalSolver.py
@@ -24,11 +24,11 @@ def mooseaddChemSolver(modelRoot, solver):
comptinfo = moose.Annotator(moose.element(compt[0]).path + '/info')
previousSolver = comptinfo.solver
currentSolver = previousSolver
- if solver == "Gillespie":
+ if solver == "Gillespie" or solver == "gssa":
currentSolver = "gssa"
- elif solver == "Runge Kutta":
+ elif solver == "Runge Kutta" or solver == "gsl":
currentSolver = "gsl"
- elif solver == "Exponential Euler":
+ elif solver == "Exponential Euler" or solver == "ee":
currentSolver = "ee"
if previousSolver != currentSolver:
diff --git a/moose-core/randnum/RNG.h b/moose-core/randnum/RNG.h
index 09dbdf05a691d74a36cded4f7012bb33388da654..8fe38b64c1a19168271e8ae627f6d8bddb9a8828 100644
--- a/moose-core/randnum/RNG.h
+++ b/moose-core/randnum/RNG.h
@@ -57,6 +57,14 @@ class RNG
RNG () /* constructor */
{
// Setup a random seed if possible.
+ setRandomSeed( );
+ }
+
+ ~RNG () /* destructor */
+ { ; }
+
+ void setRandomSeed( )
+ {
#if defined(USE_BOOST)
#if defined(BOOST_RANDOM_DEVICE_EXISTS)
boost::random::random_device rd;
@@ -68,12 +76,6 @@ class RNG
#else
mtseed( time(NULL) );
#endif /* ----- not ENABLE_CPP11 ----- */
-
- }
-
- ~RNG () /* destructor */
- {
-
}
/* ==================== ACCESSORS ======================================= */
@@ -83,9 +85,21 @@ class RNG
}
/* ==================== MUTATORS ======================================= */
+ /**
+ * @brief If seed if 0 then set seed to a random number else set seed to
+ * the given number.
+ *
+ * @param seed
+ */
void setSeed( const unsigned long int seed )
{
seed_ = seed;
+ if( seed == 0 )
+ {
+ setRandomSeed( );
+ return;
+ }
+
#if defined(USE_BOOST) || defined(ENABLE_CPP11)
rng_.seed( seed_ );
#else