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From: <mor...@us...> - 2010-07-09 11:49:47
|
Revision: 3848
http://ecell.svn.sourceforge.net/ecell/?rev=3848&view=rev
Author: moriyoshi
Date: 2010-07-09 11:49:40 +0000 (Fri, 09 Jul 2010)
Log Message:
-----------
* Forgot to commit.
Modified Paths:
--------------
ecell3/trunk/ecell/dm/FluxDistributionStepper.cpp
Modified: ecell3/trunk/ecell/dm/FluxDistributionStepper.cpp
===================================================================
--- ecell3/trunk/ecell/dm/FluxDistributionStepper.cpp 2010-07-09 11:46:16 UTC (rev 3847)
+++ ecell3/trunk/ecell/dm/FluxDistributionStepper.cpp 2010-07-09 11:49:40 UTC (rev 3848)
@@ -94,7 +94,7 @@
DifferentialStepper::setStepInterval( INF );
}
- ~FluxDistributionStepper()
+ virtual ~FluxDistributionStepper()
{
if ( theUnknownMatrix )
{
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|
|
From: <mor...@us...> - 2010-07-09 11:46:26
|
Revision: 3847
http://ecell.svn.sourceforge.net/ecell/?rev=3847&view=rev
Author: moriyoshi
Date: 2010-07-09 11:46:16 +0000 (Fri, 09 Jul 2010)
Log Message:
-----------
* Add virtual attributes for RTTI production.
Modified Paths:
--------------
ecell3/trunk/ecell/dm/ESSYNSProcessInterface.hpp
ecell3/trunk/ecell/dm/ExpressionProcessBase.hpp
ecell3/trunk/ecell/dm/GillespieProcessInterface.hpp
ecell3/trunk/ecell/dm/QuasiDynamicFluxProcess.hpp
ecell3/trunk/ecell/dm/QuasiDynamicFluxProcessInterface.hpp
Modified: ecell3/trunk/ecell/dm/ESSYNSProcessInterface.hpp
===================================================================
--- ecell3/trunk/ecell/dm/ESSYNSProcessInterface.hpp 2010-07-07 10:59:17 UTC (rev 3846)
+++ ecell3/trunk/ecell/dm/ESSYNSProcessInterface.hpp 2010-07-09 11:46:16 UTC (rev 3847)
@@ -36,6 +36,8 @@
virtual const boost::multi_array< libecs::Real, 2 >& getESSYNSMatrix() = 0;
virtual libecs::Integer getSystemSize() const = 0;
+
+ virtual ~ESSYNSProcessInterface() {}
};
#endif /* __ESSYNSPROCESS_HPP */
Modified: ecell3/trunk/ecell/dm/ExpressionProcessBase.hpp
===================================================================
--- ecell3/trunk/ecell/dm/ExpressionProcessBase.hpp 2010-07-07 10:59:17 UTC (rev 3846)
+++ ecell3/trunk/ecell/dm/ExpressionProcessBase.hpp 2010-07-09 11:46:16 UTC (rev 3847)
@@ -161,7 +161,7 @@
// ; do nothing
}
- ~ExpressionProcessBase()
+ virtual ~ExpressionProcessBase()
{
delete theCompiledCode;
}
Modified: ecell3/trunk/ecell/dm/GillespieProcessInterface.hpp
===================================================================
--- ecell3/trunk/ecell/dm/GillespieProcessInterface.hpp 2010-07-07 10:59:17 UTC (rev 3846)
+++ ecell3/trunk/ecell/dm/GillespieProcessInterface.hpp 2010-07-09 11:46:16 UTC (rev 3847)
@@ -35,6 +35,8 @@
virtual GET_METHOD( libecs::Real, Propensity ) = 0;
virtual libecs::Real getPD( libecs::Variable const* aVariable ) const = 0;
+
+ virtual ~GillespieProcessInterface() {}
};
#endif /* __GILLESPIEPROCESSINTERFACE_HPP */
Modified: ecell3/trunk/ecell/dm/QuasiDynamicFluxProcess.hpp
===================================================================
--- ecell3/trunk/ecell/dm/QuasiDynamicFluxProcess.hpp 2010-07-07 10:59:17 UTC (rev 3846)
+++ ecell3/trunk/ecell/dm/QuasiDynamicFluxProcess.hpp 2010-07-09 11:46:16 UTC (rev 3847)
@@ -56,7 +56,7 @@
theFluxDistributionVector.reserve( 0 );
}
- ~QuasiDynamicFluxProcess()
+ virtual ~QuasiDynamicFluxProcess()
{
; // do nothing
}
Modified: ecell3/trunk/ecell/dm/QuasiDynamicFluxProcessInterface.hpp
===================================================================
--- ecell3/trunk/ecell/dm/QuasiDynamicFluxProcessInterface.hpp 2010-07-07 10:59:17 UTC (rev 3846)
+++ ecell3/trunk/ecell/dm/QuasiDynamicFluxProcessInterface.hpp 2010-07-09 11:46:16 UTC (rev 3847)
@@ -39,6 +39,7 @@
virtual GET_METHOD( libecs::Real, Vmax ) = 0;
+ virtual ~QuasiDynamicFluxProcessInterface() {}
};
#endif /* __QUASIDYNAMICFLUXPROCESSINTERFACE_HPP */
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|
|
From: <mor...@us...> - 2010-07-07 10:59:23
|
Revision: 3846
http://ecell.svn.sourceforge.net/ecell/?rev=3846&view=rev
Author: moriyoshi
Date: 2010-07-07 10:59:17 +0000 (Wed, 07 Jul 2010)
Log Message:
-----------
* Add compatibility check.
Modified Paths:
--------------
ecell3/trunk/ecell/frontend/session-monitor/ecell/ui/osogo/FileSelection.py
Modified: ecell3/trunk/ecell/frontend/session-monitor/ecell/ui/osogo/FileSelection.py
===================================================================
--- ecell3/trunk/ecell/frontend/session-monitor/ecell/ui/osogo/FileSelection.py 2010-07-06 15:30:54 UTC (rev 3845)
+++ ecell3/trunk/ecell/frontend/session-monitor/ecell/ui/osogo/FileSelection.py 2010-07-07 10:59:17 UTC (rev 3846)
@@ -17,7 +17,8 @@
self.cancel_button = self.add_button(gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL)
self.ok_button = self.add_button(gtk.STOCK_OK, gtk.RESPONSE_OK)
self.ok_button.grab_default()
- self.set_alternative_button_order([gtk.RESPONSE_OK, gtk.RESPONSE_CANCEL])
+ if hasattr(self, "set_alternative_button_order"):
+ self.set_alternative_button_order([gtk.RESPONSE_OK, gtk.RESPONSE_CANCEL])
def __set_action(self, action):
gtk.FileChooserDialog.set_action(self, self.actions[action])
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|
|
From: <mor...@us...> - 2010-07-06 15:31:00
|
Revision: 3845
http://ecell.svn.sourceforge.net/ecell/?rev=3845&view=rev
Author: moriyoshi
Date: 2010-07-06 15:30:54 +0000 (Tue, 06 Jul 2010)
Log Message:
-----------
* Let it go.
Modified Paths:
--------------
ecell3/trunk/NEWS
Modified: ecell3/trunk/NEWS
===================================================================
--- ecell3/trunk/NEWS 2010-07-06 15:30:33 UTC (rev 3844)
+++ ecell3/trunk/NEWS 2010-07-06 15:30:54 UTC (rev 3845)
@@ -1,4 +1,4 @@
-ecell-3.2.1: 17-Jun-2010
+ecell-3.2.1: 7-Jul-2010
* Removed DifferentialStepper::initializeStepInterval() in favor of
virtualized Stepper::setStepInterval().
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|
|
From: <mor...@us...> - 2010-07-06 15:30:40
|
Revision: 3844
http://ecell.svn.sourceforge.net/ecell/?rev=3844&view=rev
Author: moriyoshi
Date: 2010-07-06 15:30:33 +0000 (Tue, 06 Jul 2010)
Log Message:
-----------
* That should not be a const reference.
Modified Paths:
--------------
ecell3/trunk/ecell/libecs/PropertySlot.hpp
Modified: ecell3/trunk/ecell/libecs/PropertySlot.hpp
===================================================================
--- ecell3/trunk/ecell/libecs/PropertySlot.hpp 2010-06-29 22:15:12 UTC (rev 3843)
+++ ecell3/trunk/ecell/libecs/PropertySlot.hpp 2010-07-06 15:30:33 UTC (rev 3844)
@@ -338,7 +338,7 @@
}
protected:
- inline void callLoadMethod( T& anObject, typename Param<SlotType>::type const& aValue ) const
+ inline void callLoadMethod( T& anObject, typename Param<SlotType>::type aValue ) const
{
( anObject.*theLoadMethodPtr )( aValue );
}
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|
|
From: <mor...@us...> - 2010-06-29 22:15:19
|
Revision: 3843
http://ecell.svn.sourceforge.net/ecell/?rev=3843&view=rev
Author: moriyoshi
Date: 2010-06-29 22:15:12 +0000 (Tue, 29 Jun 2010)
Log Message:
-----------
* Upstream update.
Modified Paths:
--------------
ecell-build/trunk/pkg/rpm/ecell3.spec
Added Paths:
-----------
ecell-build/trunk/pkg/rpm/ecell-3.2.1-ply-2.3-compat.patch
Added: ecell-build/trunk/pkg/rpm/ecell-3.2.1-ply-2.3-compat.patch
===================================================================
--- ecell-build/trunk/pkg/rpm/ecell-3.2.1-ply-2.3-compat.patch (rev 0)
+++ ecell-build/trunk/pkg/rpm/ecell-3.2.1-ply-2.3-compat.patch 2010-06-29 22:15:12 UTC (rev 3843)
@@ -0,0 +1,30 @@
+diff -ur ecell-3.2.1~/ecell/pyecell/ecell/emparser.py ecell-3.2.1/ecell/pyecell/ecell/emparser.py
+--- ecell-3.2.1~/ecell/pyecell/ecell/emparser.py 2010-01-16 11:23:46.000000000 +0900
++++ ecell-3.2.1/ecell/pyecell/ecell/emparser.py 2010-06-30 01:04:01.000000000 +0900
+@@ -429,8 +429,9 @@
+ def initializePLY(outputdir):
+ lextabmod = LEXTAB.split('.')
+ parsertabmod = PARSERTAB.split('.')
+- lex.lex( lextab=lextabmod[-1], optimize=1, outputdir=os.path.join( outputdir,*lextabmod[:-1] ) )
+- yacc.yacc( tabmodule=parsertabmod[-1], outputdir=os.path.join( outputdir, *parsertabmod[:-1] ) )
++ lex.lex( lextab=lextabmod[-1], optimize=1 )
++ os.rename( lextabmod[-1] + ".py", os.path.join( outputdir, *lextabmod ) )
++ yacc.yacc( tabmodule=parsertabmod[-1], optimize=1, outputdir=os.path.join( outputdir, *parsertabmod[:-1] ) )
+
+ def convertEm2Eml( anEmFileObject, debug=0 ):
+
+diff -ur ecell-3.2.1~/ecell/pyecell/ecell/expressionparser.py ecell-3.2.1/ecell/pyecell/ecell/expressionparser.py
+--- ecell-3.2.1~/ecell/pyecell/ecell/expressionparser.py 2010-01-16 11:23:46.000000000 +0900
++++ ecell-3.2.1/ecell/pyecell/ecell/expressionparser.py 2010-06-30 01:05:38.000000000 +0900
+@@ -315,8 +315,9 @@
+ def initializePLY(outputdir):
+ lextabmod = LEXTAB.split('.')
+ parsertabmod = PARSERTAB.split('.')
+- lex.lex( lextab=lextabmod[-1], optimize=1, outputdir=os.path.join( outputdir,*lextabmod[:-1] ) )
+- yacc.yacc( tabmodule=parsertabmod[-1], outputdir=os.path.join( outputdir, *parsertabmod[:-1] ) )
++ lex.lex( lextab=lextabmod[-1], optimize=1 )
++ os.rename( lextabmod[-1] + ".py", os.path.join( outputdir, *lextabmod ) )
++ yacc.yacc( tabmodule=parsertabmod[-1], optimize=1, outputdir=os.path.join( outputdir, *parsertabmod[:-1] ) )
+
+
+ def isID_Namespace( aVariableID ):
Property changes on: ecell-build/trunk/pkg/rpm/ecell-3.2.1-ply-2.3-compat.patch
___________________________________________________________________
Added: svn:mime-type
+ text/plain
Added: svn:eol-style
+ native
Modified: ecell-build/trunk/pkg/rpm/ecell3.spec
===================================================================
--- ecell-build/trunk/pkg/rpm/ecell3.spec 2010-06-26 05:03:10 UTC (rev 3842)
+++ ecell-build/trunk/pkg/rpm/ecell3.spec 2010-06-29 22:15:12 UTC (rev 3843)
@@ -1,9 +1,12 @@
+%{!?python_sitelib: %define python_sitelib %(python -c "from distutils.sysconfig import get_python_lib; print get_python_lib()")}
+
Summary: E-Cell is a generic software package for cellular modeling and simulation.
Name: ecell3
-Version: 3.1.106
-Release: 2%{?dist}
+Version: 3.2.1
+Release: 1%{?dist}
URL: http://www.e-cell.org/
-Source: ecell-%{version}.tar.gz
+Source: ecell-%{version}.tar.bz2
+Patch0: ecell-3.2.1-ply-2.3-compat.patch
License: GPL
Group: Applications
Packager: Takeshi Sakurada
@@ -14,10 +17,12 @@
Requires: boost >= 1.32.0
Requires: libstdc++
Requires: python >= 2.3
+Requires: python-ply >= 2.3
Requires: glibc
BuildRequires: make
BuildRequires: python-devel
BuildRequires: pygtk2 >= 2.4
+BuildRequires: python-ply >= 2.3
BuildRequires: glibc-devel
BuildRequires: libstdc++-devel
BuildRequires: gcc-c++
@@ -75,22 +80,9 @@
simulation, and analysis of large scale complex systems, particularly focused
on biological details of cellular behavior.
-%package tool-launcher
-Summary: E-Cell Tool Launcher
-Group: Development/Libraries
-Requires: ecell3 = %{version}
-Requires: python >= 2.3
-Requires: pygtk2 >= 2.4
-Requires: gnome-python2-canvas >= 2.4
-
-%description tool-launcher
-E-Cell System is an object-oriented software suite for modeling,
-simulation, and analysis of large scale complex systems, particularly focused
-on biological details of cellular behavior.
-
-
%prep
%setup -n ecell-%{version}
+%patch0 -p1
%ifarch i686
CXXFLAGS="-O2 -mfpmath=sse -msse2 $RPM_OPT_FLAGS" ./configure --prefix=%{_prefix}
@@ -120,6 +112,7 @@
infodir=%{_infodir} \
docdir=%{_datadir}/doc/ecell3 \
install
+rm -rf ${RPM_BUILD_ROOT}/usr/lib/python*
mv ${RPM_BUILD_ROOT}%{_datadir}/doc/ecell3/users-manual .
mv ${RPM_BUILD_ROOT}%{_datadir}/doc/ecell3/api .
mv ${RPM_BUILD_ROOT}%{_datadir}/doc/ecell3/model-editor .
@@ -141,8 +134,11 @@
%{_bindir}/ecell3-session-manager
%{_libdir}/libecs.so.*
%{_libdir}/libemc.so.*
-%{_libdir}/ecell-3.1/dms
+%{_libdir}/ecell-3.2/dms
%{_libdir}/python*
+%ifarch x86_64 ppc64 sparc64
+%{python_sitelib}/*
+%endif
%files devel
%defattr(-,root,root)
@@ -150,8 +146,8 @@
%{_bindir}/dmcompile
%{_bindir}/ecell3-dmc
%{_includedir}/dmtool
-%{_includedir}/ecell-3.1
-%{_datadir}/ecell-3.1/dms
+%{_includedir}/ecell-3.2
+%{_datadir}/ecell-3.2/dms
%{_libdir}/libecs.so
%{_libdir}/libecs.la
%{_libdir}/libemc.so
@@ -160,23 +156,23 @@
%files session-monitor
%defattr(-,root,root)
%doc AUTHORS COPYING README
-%{_bindir}/gecell
+%{_sysconfdir}/ecell-3.2/osogo.ini
%{_bindir}/ecell3-session-monitor
-%{_libdir}/ecell-3.1/session-monitor
+%{_libdir}/ecell-3.2/session-monitor
+%{_datadir}/ecell-3.2/session-monitor
%files model-editor
%defattr(-,root,root)
%doc AUTHORS COPYING README model-editor
+%{_sysconfdir}/ecell-3.2/model-editor.ini
%{_bindir}/ecell3-model-editor
-%{_libdir}/ecell-3.1/model-editor
+%{_libdir}/ecell-3.2/model-editor
+%{_datadir}/ecell-3.2/model-editor
-%files tool-launcher
-%defattr(-,root,root)
-%doc AUTHORS COPYING README
-%{_bindir}/ecell3-toollauncher
-%{_libdir}/ecell-3.1/toollauncher
-
%changelog
+* Wed Jun 30 2010 Moriyoshi Koizumi <mo...@ri...>
+- Upstream update.
+
* Tue Feb 05 2008 Moriyoshi Koizumi <mo...@sf...>
- Add pygtk2-libglade to ecell3-model-editor dependencies.
- Add ecell3-session-monitor to ecell3-model-editor dependencies.
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|
|
From: <mar...@us...> - 2010-06-26 05:03:17
|
Revision: 3842
http://ecell.svn.sourceforge.net/ecell/?rev=3842&view=rev
Author: maronnax
Date: 2010-06-26 05:03:10 +0000 (Sat, 26 Jun 2010)
Log Message:
-----------
ecell/libecs/DynamicPriorityQueue.hpp
Modified Paths:
--------------
ecell3/branches/naddy/ecell/libecs/DynamicPriorityQueue.hpp
Modified: ecell3/branches/naddy/ecell/libecs/DynamicPriorityQueue.hpp
===================================================================
--- ecell3/branches/naddy/ecell/libecs/DynamicPriorityQueue.hpp 2010-06-26 01:27:30 UTC (rev 3841)
+++ ecell3/branches/naddy/ecell/libecs/DynamicPriorityQueue.hpp 2010-06-26 05:03:10 UTC (rev 3842)
@@ -57,10 +57,10 @@
public:
- typedef uint64_t ID;
- typedef std::vector< ID > IDVector;
- typedef IDVector::size_type Index;
- typedef IDVector::const_iterator IDIterator;
+ typedef uint64_t ID;
+ typedef std::vector< ID > IDVector;
+ typedef IDVector::size_type Index;
+ typedef IDVector::const_iterator IDIterator;
#if defined( HAVE_UNORDERED_MAP ) || defined( HAVE_TR1_UNORDERED_MAP )
@@ -108,18 +108,18 @@
this->indexMap.clear();
}
- const Index getIndex( const ID id ) const
- {
- IndexMap::const_iterator i = this->indexMap.find( id );
+ const Index getIndex( const ID id ) const
+ {
+ IndexMap::const_iterator i = this->indexMap.find( id );
+
+ if( i == this->indexMap.end() )
+ {
+ throw std::out_of_range( "PersistentIDPolicy::getIndex()" );
+ }
+
+ return (*i).second;
+ }
- if( i == this->indexMap.end() )
- {
- throw std::out_of_range( "PersistentIDPolicy::getIndex()" );
- }
-
- return (*i).second;
- }
-
const ID getIDByIndex( const Index index ) const
{
return this->idVector[ index ];
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|
|
From: <mor...@us...> - 2010-06-26 01:27:36
|
Revision: 3841
http://ecell.svn.sourceforge.net/ecell/?rev=3841&view=rev
Author: moriyoshi
Date: 2010-06-26 01:27:30 +0000 (Sat, 26 Jun 2010)
Log Message:
-----------
* Fix a few more build issues.
Modified Paths:
--------------
ecell3/trunk/ecell/dm/ODEStepper.cpp
ecell3/trunk/ecell/libecs/PropertySlot.hpp
ecell3/trunk/ecell/libecs/Variable.hpp
Modified: ecell3/trunk/ecell/dm/ODEStepper.cpp
===================================================================
--- ecell3/trunk/ecell/dm/ODEStepper.cpp 2010-06-17 06:54:24 UTC (rev 3840)
+++ ecell3/trunk/ecell/dm/ODEStepper.cpp 2010-06-26 01:27:30 UTC (rev 3841)
@@ -139,17 +139,17 @@
Real estimateLocalError( Real const aStepInterval );
void initializeRadauIIA( VariableVector::size_type );
- std::pair< bool, Real > calculateRadauIIA( Real const aStepInterval, Real const aPreviousStepInterval );
- void updateInternalStateRadauIIA( Real const aStepInterval );
+ std::pair< bool, Real > calculateRadauIIA( Real aStepInterval, Real aPreviousStepInterval );
+ void updateInternalStateRadauIIA( Real aStepInterval );
- void initializeTolerance( Real value )
+ void initializeTolerance( libecs::Param<Real>::type value )
{
setTolerance( value ); // AdaptiveDifferentialStepper::
rtoler = 0.1 * pow( getTolerance(), 2.0 / 3.0 );
atoler = rtoler * getAbsoluteToleranceFactor();
}
- void initializeAbsoluteToleranceFactor( Real value )
+ void initializeAbsoluteToleranceFactor( libecs::Param<Real>::type value )
{
setAbsoluteToleranceFactor( value ); // AdaptiveDifferentialStepper::
atoler = rtoler * getAbsoluteToleranceFactor();
@@ -619,7 +619,7 @@
return sqrt( aNorm / ( 3 * theSystemSize ) );
}
-std::pair< bool, Real > ODEStepper::calculateRadauIIA( Real const aStepInterval, Real const aPreviousStepInterval )
+std::pair< bool, Real > ODEStepper::calculateRadauIIA( Real aStepInterval, Real aPreviousStepInterval )
{
Real aNewStepInterval;
Real aNorm( 0. );
Modified: ecell3/trunk/ecell/libecs/PropertySlot.hpp
===================================================================
--- ecell3/trunk/ecell/libecs/PropertySlot.hpp 2010-06-17 06:54:24 UTC (rev 3840)
+++ ecell3/trunk/ecell/libecs/PropertySlot.hpp 2010-06-26 01:27:30 UTC (rev 3841)
@@ -179,8 +179,8 @@
typedef SlotType ( T::* GetMethodPtr )() const;
ConcretePropertySlot( String const& aName,
- const SetMethodPtr aSetMethodPtr,
- const GetMethodPtr aGetMethodPtr )
+ SetMethodPtr aSetMethodPtr,
+ GetMethodPtr aGetMethodPtr )
: theName( aName ),
theType( PropertySlotBase::TypeToTypeCode< SlotType_ >::value ),
theSetMethodPtr( SetMethod( aSetMethodPtr ) ),
Modified: ecell3/trunk/ecell/libecs/Variable.hpp
===================================================================
--- ecell3/trunk/ecell/libecs/Variable.hpp 2010-06-17 06:54:24 UTC (rev 3840)
+++ ecell3/trunk/ecell/libecs/Variable.hpp 2010-06-26 01:27:30 UTC (rev 3841)
@@ -176,7 +176,7 @@
}
- void loadValue( Real aValue )
+ void loadValue( Param<Real>::type aValue )
{
theValue = aValue;
}
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From: <mor...@us...> - 2010-06-17 06:54:30
|
Revision: 3840
http://ecell.svn.sourceforge.net/ecell/?rev=3840&view=rev
Author: moriyoshi
Date: 2010-06-17 06:54:24 +0000 (Thu, 17 Jun 2010)
Log Message:
-----------
* Fix this too.
Modified Paths:
--------------
ecell3/trunk/ecell_version.sh
Modified: ecell3/trunk/ecell_version.sh
===================================================================
--- ecell3/trunk/ecell_version.sh 2010-06-17 06:53:43 UTC (rev 3839)
+++ ecell3/trunk/ecell_version.sh 2010-06-17 06:54:24 UTC (rev 3840)
@@ -1,5 +1,5 @@
ECELL_MAJOR_VERSION=3
ECELL_MINOR_VERSION=2
-ECELL_MICRO_VERSION=0
-ECELL_PACKAGE_REVISION=p2
+ECELL_MICRO_VERSION=1
+ECELL_PACKAGE_REVISION=
ECELL_VERSION_NUMBER=${ECELL_MAJOR_VERSION}.${ECELL_MINOR_VERSION}.${ECELL_MICRO_VERSION}${ECELL_PACKAGE_REVISION}
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From: <mor...@us...> - 2010-06-17 06:53:49
|
Revision: 3839
http://ecell.svn.sourceforge.net/ecell/?rev=3839&view=rev
Author: moriyoshi
Date: 2010-06-17 06:53:43 +0000 (Thu, 17 Jun 2010)
Log Message:
-----------
3.2.1.
Modified Paths:
--------------
ecell3/trunk/NEWS
Modified: ecell3/trunk/NEWS
===================================================================
--- ecell3/trunk/NEWS 2010-05-31 07:38:49 UTC (rev 3838)
+++ ecell3/trunk/NEWS 2010-06-17 06:53:43 UTC (rev 3839)
@@ -1,4 +1,19 @@
+ecell-3.2.1: 17-Jun-2010
+
+ * Removed DifferentialStepper::initializeStepInterval() in favor of
+ virtualized Stepper::setStepInterval().
+
+ * Better compatibility with Fujitsu C++ compiler.
+
+ * Fixed possible segmentation fault that occurs during loading a DM.
+
+ * Removed funky macros derived from UtilLinux.
+
+ * Optimized code in VariableReference.
+
+
ecell-3.2.0p2: 2-Apr-2010
+
* Fixed DataPointVector's python wrapper to have "shape" property that returns
the shape of the array. That is required by TableIO module.
(notified by Erin Rachael Shellman. Thanks.)
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From: <mor...@us...> - 2010-05-31 07:38:56
|
Revision: 3838
http://ecell.svn.sourceforge.net/ecell/?rev=3838&view=rev
Author: moriyoshi
Date: 2010-05-31 07:38:49 +0000 (Mon, 31 May 2010)
Log Message:
-----------
Get LoggerPolicyWindow working. It turned out that it has never been working as expected.
Modified Paths:
--------------
ecell3/trunk/ecell/frontend/session-monitor/ecell/ui/osogo/GtkSessionMonitor.py
ecell3/trunk/ecell/frontend/session-monitor/ecell/ui/osogo/LoggingPolicy.py
ecell3/trunk/ecell/frontend/session-monitor/glade/LoggingPolicy.glade
Modified: ecell3/trunk/ecell/frontend/session-monitor/ecell/ui/osogo/GtkSessionMonitor.py
===================================================================
--- ecell3/trunk/ecell/frontend/session-monitor/ecell/ui/osogo/GtkSessionMonitor.py 2010-05-21 09:42:38 UTC (rev 3837)
+++ ecell3/trunk/ecell/frontend/session-monitor/ecell/ui/osogo/GtkSessionMonitor.py 2010-05-31 07:38:49 UTC (rev 3838)
@@ -532,7 +532,6 @@
"""
saves logging policy into config database
"""
-
self.setParameter( 'logger_min_step', logPolicy[0] )
self.setParameter( 'logger_min_interval', logPolicy[1] )
self.setParameter( 'end_policy' , logPolicy[2] )
Modified: ecell3/trunk/ecell/frontend/session-monitor/ecell/ui/osogo/LoggingPolicy.py
===================================================================
--- ecell3/trunk/ecell/frontend/session-monitor/ecell/ui/osogo/LoggingPolicy.py 2010-05-21 09:42:38 UTC (rev 3837)
+++ ecell3/trunk/ecell/frontend/session-monitor/ecell/ui/osogo/LoggingPolicy.py 2010-05-31 07:38:49 UTC (rev 3838)
@@ -69,7 +69,7 @@
)
self.theSession = aSession
# Sets the return number
- self.___num = CANCEL_PRESSED
+ self.___num = None
# Create the Dialog
self.win = gtk.Dialog("Logging Policy", None, gtk.DIALOG_MODAL)
@@ -113,16 +113,12 @@
# add handlers
self.addHandlers( {
- "on_space_max_toggled" : self.__buttonChosen,
- "on_space_no_limit_toggled" : self.__buttonChosen,
- "on_end_overwrite_toggled" : self.__buttonChosen,
- "on_end_throw_ex_toggled" : self.__buttonChosen,
- "on_log_by_secs_toggled" : self.__buttonChosen,
- "on_log_by_step_toggled" : self.__buttonChosen } )
+ "on_space_max_toggled" : self.__spaceLimitButtonChosen,
+ "on_space_no_limit_toggled" : self.__spaceNoLimitButtonChosen,
+ "on_log_by_secs_toggled" : self.__logBySecsButtonChosen,
+ "on_log_by_step_toggled" : self.__logByStepButtonChosen } )
- gtk.main()
-
def openConfirmWindow(self, aMessage, aTitle, isCancel = 1 ):
""" pops up a modal dialog window
with aTitle (str) as its title
@@ -202,20 +198,21 @@
# ==========================================================================
- def __buttonChosen( self, *args ):
- aName = args[0].get_name()
- if aName == "log_by_secs":
- self['second_entry'].set_sensitive( True )
- self['step_entry'].set_sensitive( False )
- elif aName == "log_by_step":
- self['second_entry'].set_sensitive( False )
- self['step_entry'].set_sensitive( True )
- elif aName == "space_no_limit":
- self['space_entry'].set_sensitive( False )
- elif aName == "spac_max":
- self['space_entry'].set_sensitive( True )
+ def __logBySecsButtonChosen( self, *args ):
+ self['second_entry'].set_sensitive( True )
+ self['step_entry'].set_sensitive( False )
+ def __logByStepButtonChosen( self, *args ):
+ self['second_entry'].set_sensitive( False )
+ self['step_entry'].set_sensitive( True )
+ def __spaceNoLimitButtonChosen( self, *args ):
+ self['space_entry'].set_sensitive( False )
+
+ def __spaceLimitButtonChosen( self, *args ):
+ self['space_entry'].set_sensitive( True )
+
+
# ==========================================================================
def oKButtonClicked( self, *arg ):
"""
@@ -237,7 +234,6 @@
"""
# set the return number
- self.___num = None
self.destroy()
@@ -254,5 +250,4 @@
"""destroy dialog
"""
self.win.hide()
- gtk.mainquit()
Modified: ecell3/trunk/ecell/frontend/session-monitor/glade/LoggingPolicy.glade
===================================================================
--- ecell3/trunk/ecell/frontend/session-monitor/glade/LoggingPolicy.glade 2010-05-21 09:42:38 UTC (rev 3837)
+++ ecell3/trunk/ecell/frontend/session-monitor/glade/LoggingPolicy.glade 2010-05-31 07:38:49 UTC (rev 3838)
@@ -227,7 +227,6 @@
<property name="active">False</property>
<property name="inconsistent">False</property>
<property name="draw_indicator">True</property>
- <signal name="toggled" handler="on_end_throw_ex_toggled" last_modification_time="Sat, 29 May 2004 12:31:19 GMT"/>
</widget>
<packing>
<property name="padding">0</property>
@@ -247,7 +246,6 @@
<property name="inconsistent">False</property>
<property name="draw_indicator">True</property>
<property name="group">end_throw_ex</property>
- <signal name="toggled" handler="on_end_overwrite_toggled" last_modification_time="Sat, 29 May 2004 12:31:26 GMT"/>
</widget>
<packing>
<property name="padding">0</property>
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|
|
From: <mor...@us...> - 2010-05-21 09:42:45
|
Revision: 3837
http://ecell.svn.sourceforge.net/ecell/?rev=3837&view=rev
Author: moriyoshi
Date: 2010-05-21 09:42:38 +0000 (Fri, 21 May 2010)
Log Message:
-----------
Remove initializeStepInterval() in favor of virtualized Stepper::setStepInterval()
Modified Paths:
--------------
ecell3/trunk/ecell/dm/FluxDistributionStepper.cpp
ecell3/trunk/ecell/dm/TauLeapStepper.cpp
ecell3/trunk/ecell/libecs/DifferentialStepper.hpp
ecell3/trunk/ecell/libecs/Stepper.hpp
Modified: ecell3/trunk/ecell/dm/FluxDistributionStepper.cpp
===================================================================
--- ecell3/trunk/ecell/dm/FluxDistributionStepper.cpp 2010-05-21 08:52:11 UTC (rev 3836)
+++ ecell3/trunk/ecell/dm/FluxDistributionStepper.cpp 2010-05-21 09:42:38 UTC (rev 3837)
@@ -91,7 +91,7 @@
Epsilon( 1e-6 ),
theIrreversibleFlag( false )
{
- initializeStepInterval( INF );
+ DifferentialStepper::setStepInterval( INF );
}
~FluxDistributionStepper()
Modified: ecell3/trunk/ecell/dm/TauLeapStepper.cpp
===================================================================
--- ecell3/trunk/ecell/dm/TauLeapStepper.cpp 2010-05-21 08:52:11 UTC (rev 3836)
+++ ecell3/trunk/ecell/dm/TauLeapStepper.cpp 2010-05-21 09:42:38 UTC (rev 3837)
@@ -108,7 +108,7 @@
calculateTau();
- initializeStepInterval( getTau() );
+ DifferentialStepper::setStepInterval( getTau() );
FOR_ALL( GillespieProcessVector, theGillespieProcessVector )
{
Modified: ecell3/trunk/ecell/libecs/DifferentialStepper.hpp
===================================================================
--- ecell3/trunk/ecell/libecs/DifferentialStepper.hpp 2010-05-21 08:52:11 UTC (rev 3836)
+++ ecell3/trunk/ecell/libecs/DifferentialStepper.hpp 2010-05-21 09:42:38 UTC (rev 3837)
@@ -58,10 +58,6 @@
INHERIT_PROPERTIES( Stepper );
// FIXME: load/save ??
- PROPERTYSLOT( Real, StepInterval,
- &DifferentialStepper::initializeStepInterval,
- &DifferentialStepper::getStepInterval );
-
PROPERTYSLOT_GET_NO_LOAD_SAVE( Real, NextStepInterval );
PROPERTYSLOT_SET_GET_NO_LOAD_SAVE( Real, TolerableStepInterval );
PROPERTYSLOT_GET_NO_LOAD_SAVE( Integer, Stage );
@@ -118,9 +114,9 @@
return theTolerableStepInterval;
}
- void initializeStepInterval( Real aStepInterval )
+ virtual void setStepInterval( Real aStepInterval )
{
- setStepInterval( aStepInterval );
+ Stepper::setStepInterval( aStepInterval );
setTolerableStepInterval( aStepInterval );
setNextStepInterval( aStepInterval );
}
Modified: ecell3/trunk/ecell/libecs/Stepper.hpp
===================================================================
--- ecell3/trunk/ecell/libecs/Stepper.hpp 2010-05-21 08:52:11 UTC (rev 3836)
+++ ecell3/trunk/ecell/libecs/Stepper.hpp 2010-05-21 09:42:38 UTC (rev 3837)
@@ -146,7 +146,7 @@
@return the step interval of this Stepper
*/
- GET_METHOD( Real, StepInterval )
+ virtual GET_METHOD( Real, StepInterval )
{
const Real aNextTime( getNextTime() );
const Real aCurrentTime( getCurrentTime() );
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|
|
From: <mor...@us...> - 2010-05-21 08:52:17
|
Revision: 3836
http://ecell.svn.sourceforge.net/ecell/?rev=3836&view=rev
Author: moriyoshi
Date: 2010-05-21 08:52:11 +0000 (Fri, 21 May 2010)
Log Message:
-----------
* This doesn't work with FCC for unknown reasons...
Modified Paths:
--------------
ecell3/trunk/ecell/libecs/PropertyInterface.hpp
Modified: ecell3/trunk/ecell/libecs/PropertyInterface.hpp
===================================================================
--- ecell3/trunk/ecell/libecs/PropertyInterface.hpp 2010-05-21 08:51:15 UTC (rev 3835)
+++ ecell3/trunk/ecell/libecs/PropertyInterface.hpp 2010-05-21 08:52:11 UTC (rev 3836)
@@ -144,10 +144,11 @@
registerPropertySlot( PropertySlotBase* aPropertySlotPtr )
{
String const& aName( aPropertySlotPtr->getName() );
- if( findPropertySlot( aName ) != thePropertySlotMap.end() )
+ PropertySlotMapConstIterator i( findPropertySlot( aName ) );
+ if ( i != thePropertySlotMap.end() )
{
// it already exists. take the latter one.
- delete thePropertySlotMap[ aName ];
+ delete ( *i ).second;
thePropertySlotMap.erase( aName );
}
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|
|
From: <mor...@us...> - 2010-05-21 08:51:21
|
Revision: 3835
http://ecell.svn.sourceforge.net/ecell/?rev=3835&view=rev
Author: moriyoshi
Date: 2010-05-21 08:51:15 +0000 (Fri, 21 May 2010)
Log Message:
-----------
* Seems like lt_dlerror() may return NULL.
Modified Paths:
--------------
ecell3/trunk/dmtool/SharedModuleMaker.hpp
Modified: ecell3/trunk/dmtool/SharedModuleMaker.hpp
===================================================================
--- ecell3/trunk/dmtool/SharedModuleMaker.hpp 2010-04-13 09:24:40 UTC (rev 3834)
+++ ecell3/trunk/dmtool/SharedModuleMaker.hpp 2010-05-21 08:51:15 UTC (rev 3835)
@@ -182,17 +182,14 @@
{
break;
}
+ const char* err( lt_dlerror() );
if ( error.empty() )
{
- error = lt_dlerror();
- if ( error.empty() )
- {
- error = "unknown reasons";
- }
+ error = err ? err: "unknown reasons";
}
else
{
- if ( error != lt_dlerror() )
+ if ( !err || error != err )
{
error = "various reasons";
}
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|
|
From: <mor...@us...> - 2010-04-13 09:24:49
|
Revision: 3834
http://ecell.svn.sourceforge.net/ecell/?rev=3834&view=rev
Author: moriyoshi
Date: 2010-04-13 09:24:40 +0000 (Tue, 13 Apr 2010)
Log Message:
-----------
* Remove funky macros derived from UtilLinux.
Modified Paths:
--------------
ecell3/trunk/dmtool/SharedModuleMaker.hpp
ecell3/trunk/dmtool/SharedModuleMakerInterface.hpp
ecell3/trunk/ecell/dm/DAEStepper.cpp
ecell3/trunk/ecell/dm/ESSYNSProcessInterface.hpp
ecell3/trunk/ecell/dm/ESSYNSStepper.cpp
ecell3/trunk/ecell/dm/ExpressionAlgebraicProcess.cpp
ecell3/trunk/ecell/dm/ExpressionAssignmentProcess.cpp
ecell3/trunk/ecell/dm/ExpressionFluxProcess.cpp
ecell3/trunk/ecell/dm/ExpressionProcessBase.hpp
ecell3/trunk/ecell/dm/FixedDAE1Stepper.cpp
ecell3/trunk/ecell/dm/FluxDistributionStepper.cpp
ecell3/trunk/ecell/dm/GMAProcess.cpp
ecell3/trunk/ecell/dm/GillespieProcess.cpp
ecell3/trunk/ecell/dm/GillespieProcess.hpp
ecell3/trunk/ecell/dm/GillespieProcessInterface.hpp
ecell3/trunk/ecell/dm/MassActionFluxProcess.cpp
ecell3/trunk/ecell/dm/ODE23Stepper.cpp
ecell3/trunk/ecell/dm/ODE45Stepper.cpp
ecell3/trunk/ecell/dm/ODEStepper.cpp
ecell3/trunk/ecell/dm/PythonFluxProcess.cpp
ecell3/trunk/ecell/dm/PythonProcess.cpp
ecell3/trunk/ecell/dm/PythonProcessBase.hpp
ecell3/trunk/ecell/dm/QuasiDynamicFluxProcess.cpp
ecell3/trunk/ecell/dm/QuasiDynamicFluxProcess.hpp
ecell3/trunk/ecell/dm/QuasiDynamicFluxProcessInterface.hpp
ecell3/trunk/ecell/dm/SSystemProcess.cpp
ecell3/trunk/ecell/dm/TauLeapProcess.cpp
ecell3/trunk/ecell/dm/TauLeapStepper.cpp
ecell3/trunk/ecell/libecs/AdaptiveDifferentialStepper.hpp
ecell3/trunk/ecell/libecs/ContinuousProcess.hpp
ecell3/trunk/ecell/libecs/DataPoint.cpp
ecell3/trunk/ecell/libecs/DataPoint.hpp
ecell3/trunk/ecell/libecs/DataPointVector.cpp
ecell3/trunk/ecell/libecs/DataPointVector.hpp
ecell3/trunk/ecell/libecs/Defs.hpp.in
ecell3/trunk/ecell/libecs/DifferentialStepper.cpp
ecell3/trunk/ecell/libecs/DifferentialStepper.hpp
ecell3/trunk/ecell/libecs/DiscreteEventStepper.cpp
ecell3/trunk/ecell/libecs/DiscreteEventStepper.hpp
ecell3/trunk/ecell/libecs/DiscreteTimeStepper.hpp
ecell3/trunk/ecell/libecs/EcsObject.cpp
ecell3/trunk/ecell/libecs/EcsObject.hpp
ecell3/trunk/ecell/libecs/EcsObjectMaker.hpp
ecell3/trunk/ecell/libecs/Entity.cpp
ecell3/trunk/ecell/libecs/Entity.hpp
ecell3/trunk/ecell/libecs/EntityType.cpp
ecell3/trunk/ecell/libecs/EntityType.hpp
ecell3/trunk/ecell/libecs/EventScheduler.hpp
ecell3/trunk/ecell/libecs/Exceptions.hpp
ecell3/trunk/ecell/libecs/FullID.cpp
ecell3/trunk/ecell/libecs/FullID.hpp
ecell3/trunk/ecell/libecs/Interpolant.hpp
ecell3/trunk/ecell/libecs/Logger.cpp
ecell3/trunk/ecell/libecs/Logger.hpp
ecell3/trunk/ecell/libecs/LoggerBroker.cpp
ecell3/trunk/ecell/libecs/LoggerBroker.hpp
ecell3/trunk/ecell/libecs/MethodProxy.hpp
ecell3/trunk/ecell/libecs/Model.cpp
ecell3/trunk/ecell/libecs/Model.hpp
ecell3/trunk/ecell/libecs/PassiveStepper.cpp
ecell3/trunk/ecell/libecs/PassiveStepper.hpp
ecell3/trunk/ecell/libecs/PhysicalLogger.cpp
ecell3/trunk/ecell/libecs/PhysicalLogger.hpp
ecell3/trunk/ecell/libecs/Polymorph.hpp
ecell3/trunk/ecell/libecs/Process.cpp
ecell3/trunk/ecell/libecs/Process.hpp
ecell3/trunk/ecell/libecs/ProcessEvent.hpp
ecell3/trunk/ecell/libecs/PropertyInterface.hpp
ecell3/trunk/ecell/libecs/PropertySlot.hpp
ecell3/trunk/ecell/libecs/PropertySlotProxyLoggerAdapter.hpp
ecell3/trunk/ecell/libecs/Stepper.cpp
ecell3/trunk/ecell/libecs/Stepper.hpp
ecell3/trunk/ecell/libecs/StepperEvent.cpp
ecell3/trunk/ecell/libecs/StepperEvent.hpp
ecell3/trunk/ecell/libecs/System.cpp
ecell3/trunk/ecell/libecs/System.hpp
ecell3/trunk/ecell/libecs/SystemStepper.cpp
ecell3/trunk/ecell/libecs/SystemStepper.hpp
ecell3/trunk/ecell/libecs/Util.cpp
ecell3/trunk/ecell/libecs/Util.hpp
ecell3/trunk/ecell/libecs/Variable.cpp
ecell3/trunk/ecell/libecs/Variable.hpp
ecell3/trunk/ecell/libecs/VariableReference.cpp
ecell3/trunk/ecell/libecs/VariableReference.hpp
ecell3/trunk/ecell/libecs/convertTo.hpp
ecell3/trunk/ecell/libecs/scripting/Assembler.cpp
ecell3/trunk/ecell/libecs/scripting/ExpressionCompiler.cpp
ecell3/trunk/ecell/libecs/scripting/ExpressionCompiler.hpp
ecell3/trunk/ecell/libecs/scripting/VirtualMachine.cpp
ecell3/trunk/ecell/libecs/scripting/VirtualMachine.hpp
ecell3/trunk/ecell/libecs/tests/LoggerBroker_test.cpp
ecell3/trunk/ecell/libecs/tests/Model_test.cpp
ecell3/trunk/ecell/libecs/tests/Polymorph_test.cpp
ecell3/trunk/ecell/libemc/LocalSimulatorImplementation.cpp
ecell3/trunk/ecell/libemc/LocalSimulatorImplementation.hpp
ecell3/trunk/ecell/libemc/Simulator.hpp
ecell3/trunk/ecell/libemc/SimulatorImplementation.hpp
ecell3/trunk/ecell/libemc/libemc.hpp
ecell3/trunk/ecell/pyecell/ecell/_ecs.cpp
Modified: ecell3/trunk/dmtool/SharedModuleMaker.hpp
===================================================================
--- ecell3/trunk/dmtool/SharedModuleMaker.hpp 2010-04-07 05:34:30 UTC (rev 3833)
+++ ecell3/trunk/dmtool/SharedModuleMaker.hpp 2010-04-13 09:24:40 UTC (rev 3834)
@@ -54,7 +54,7 @@
}
}
- virtual const std::string getSearchPath() const
+ virtual std::string getSearchPath() const
{
typedef std::set< std::string > StringSet;
std::string retval;
Modified: ecell3/trunk/dmtool/SharedModuleMakerInterface.hpp
===================================================================
--- ecell3/trunk/dmtool/SharedModuleMakerInterface.hpp 2010-04-07 05:34:30 UTC (rev 3833)
+++ ecell3/trunk/dmtool/SharedModuleMakerInterface.hpp 2010-04-13 09:24:40 UTC (rev 3834)
@@ -38,7 +38,7 @@
virtual void setSearchPath( const std::string& path ) = 0;
- virtual const std::string getSearchPath() const = 0;
+ virtual std::string getSearchPath() const = 0;
public:
static const char PATH_SEPARATOR = LT_PATHSEP_CHAR;
Modified: ecell3/trunk/ecell/dm/DAEStepper.cpp
===================================================================
--- ecell3/trunk/ecell/dm/DAEStepper.cpp 2010-04-07 05:34:30 UTC (rev 3833)
+++ ecell3/trunk/ecell/dm/DAEStepper.cpp 2010-04-13 09:24:40 UTC (rev 3834)
@@ -43,10 +43,10 @@
USE_LIBECS;
-DECLARE_VECTOR( Integer, IntVector );
-
LIBECS_DM_CLASS( DAEStepper, DifferentialStepper )
{
+public:
+ typedef std::vector< Integer > IntegerVector;
public:
@@ -67,27 +67,27 @@
DAEStepper( void )
: theSystemSize( -1 ),
- theJacobianMatrix1( NULLPTR ),
- thePermutation1( NULLPTR ),
- theVelocityVector1( NULLPTR ),
- theSolutionVector1( NULLPTR ),
- theJacobianMatrix2( NULLPTR ),
- thePermutation2( NULLPTR ),
- theVelocityVector2( NULLPTR ),
- theSolutionVector2( NULLPTR ),
+ theContinuousVariableVector( 0 ),
+ theJacobianMatrix1( 0 ),
+ thePermutation1( 0 ),
+ theVelocityVector1( 0 ),
+ theSolutionVector1( 0 ),
+ theJacobianMatrix2( 0 ),
+ thePermutation2( 0 ),
+ theVelocityVector2( 0 ),
+ theSolutionVector2( 0 ),
theMaxIterationNumber( 7 ),
+ theStoppingCriterion( 0.0 ),
eta( 1.0 ),
Uround( 1e-10 ),
theAbsoluteTolerance( 1e-6 ),
theRelativeTolerance( 1e-6 ),
- theStoppingCriterion( 0.0 ),
theFirstStepFlag( true ),
theRejectedStepFlag( false ),
- theJacobianCalculateFlag( true ),
theAcceptedError( 0.0 ),
theAcceptedStepInterval( 0.0 ),
- theJacobianRecalculateTheta( 0.001 ),
- theContinuousVariableVector( NULLPTR )
+ theJacobianCalculateFlag( true ),
+ theJacobianRecalculateTheta( 0.001 )
{
const Real pow913( pow( 9.0, 1.0 / 3.0 ) );
@@ -229,7 +229,7 @@
if ( theJacobianMatrix1 )
{
gsl_matrix_free( theJacobianMatrix1 );
- theJacobianMatrix1 = NULLPTR;
+ theJacobianMatrix1 = 0;
}
if ( aSize > 0 )
@@ -242,7 +242,7 @@
if ( thePermutation1 )
{
gsl_permutation_free( thePermutation1 );
- thePermutation1 = NULLPTR;
+ thePermutation1 = 0;
}
if ( aSize > 0 )
@@ -255,7 +255,7 @@
if ( theVelocityVector1 )
{
gsl_vector_free( theVelocityVector1 );
- theVelocityVector1 = NULLPTR;
+ theVelocityVector1 = 0;
}
if ( aSize > 0 )
{
@@ -267,7 +267,7 @@
if ( theSolutionVector1 )
{
gsl_vector_free( theSolutionVector1 );
- theSolutionVector1 = NULLPTR;
+ theSolutionVector1 = 0;
}
if ( aSize > 0 )
{
@@ -281,7 +281,7 @@
if ( theJacobianMatrix2 )
{
gsl_matrix_complex_free( theJacobianMatrix2 );
- theJacobianMatrix2 = NULLPTR;
+ theJacobianMatrix2 = 0;
}
if ( aSize > 0 )
{
@@ -293,7 +293,7 @@
if ( thePermutation2 )
{
gsl_permutation_free( thePermutation2 );
- thePermutation2 = NULLPTR;
+ thePermutation2 = 0;
}
if ( aSize > 0 )
{
@@ -305,7 +305,7 @@
if ( theVelocityVector2 )
{
gsl_vector_complex_free( theVelocityVector2 );
- theVelocityVector2 = NULLPTR;
+ theVelocityVector2 = 0;
}
if ( aSize > 0 )
{
@@ -318,7 +318,7 @@
if ( theSolutionVector2 )
{
gsl_vector_complex_free( theSolutionVector2 );
- theSolutionVector2 = NULLPTR;
+ theSolutionVector2 = 0;
}
if ( aSize > 0 )
{
@@ -332,7 +332,7 @@
{
const VariableVector::size_type aSize( getReadOnlyVariableOffset() );
Real aNewStepInterval;
- Real aNorm;
+ Real aNorm( 0. );
Real theta( fabs( theJacobianRecalculateTheta ) );
Integer anIterator( 0 );
@@ -609,22 +609,22 @@
aDiscreteProcessOffset( getDiscreteProcessOffset() );
for ( ProcessVector::size_type c( 0 ); c < aDiscreteProcessOffset; c++ )
{
- ProcessPtr aProcess( theProcessVector[ c ] );
+ Process const* const aProcess( theProcessVector[ c ] );
- VariableReferenceVectorCref aVariableReferenceVector(
+ Process::VariableReferenceVector const& aVariableReferenceVector(
aProcess->getVariableReferenceVector() );
- const VariableReferenceVector::size_type
+ const Process::VariableReferenceVector::size_type
aPositiveVariableReferenceOffset(
aProcess->getPositiveVariableReferenceOffset() );
- const VariableReferenceVector::size_type
+ const Process::VariableReferenceVector::size_type
aZeroVariableReferenceOffset(
aProcess->getZeroVariableReferenceOffset() );
const bool aContinuity( aProcess->isContinuous() );
if ( aContinuity )
{
- for ( VariableReferenceVector::size_type i( 0 );
+ for ( Process::VariableReferenceVector::size_type i( 0 );
i < aVariableReferenceVector.size(); i++)
{
if ( i == aZeroVariableReferenceOffset )
@@ -637,7 +637,7 @@
i = aPositiveVariableReferenceOffset;
}
- VariablePtr const aVariable(
+ Variable* const aVariable(
aVariableReferenceVector[ i ].getVariable() );
const VariableVector::size_type anIndex(
getVariableIndex( aVariable ) );
@@ -686,7 +686,7 @@
theDiscreteActivityBuffer[ c - aDiscreteProcessOffset ] );
}
- for ( IntVector::size_type c( 0 );
+ for ( IntegerVector::size_type c( 0 );
c < theContinuousVariableVector.size(); c++ )
{
const std::size_t anIndex( theContinuousVariableVector[ c ] );
@@ -734,7 +734,7 @@
theProcessVector[ c ]->getActivity() );
}
- for ( IntVector::size_type c( 0 );
+ for ( IntegerVector::size_type c( 0 );
c < theContinuousVariableVector.size(); c++ )
{
const std::size_t anIndex( theContinuousVariableVector[ c ] );
@@ -774,7 +774,7 @@
for ( VariableVector::size_type i( 0 ); i < aSize; ++i )
{
- const VariablePtr aVariable( theVariableVector[ i ] );
+ Variable* const aVariable( theVariableVector[ i ] );
const Real aValue( aVariable->getValue() );
aPerturbation = sqrt( Uround * std::max( 1e-5, fabs( aValue ) ) );
@@ -798,7 +798,7 @@
aPerturbation;
}
- for ( IntVector::size_type j( 0 );
+ for ( IntegerVector::size_type j( 0 );
j < theContinuousVariableVector.size(); ++j )
{
// int as VariableVector::size_type
@@ -812,8 +812,6 @@
void setJacobianMatrix( Real const aStepInterval )
{
- VariableVector::size_type aSize( getReadOnlyVariableOffset() );
-
const Real alphah( alpha / aStepInterval );
const Real betah( beta / aStepInterval );
const Real gammah( gamma / aStepInterval );
@@ -832,7 +830,7 @@
}
}
- for ( IntVector::size_type c( 0 );
+ for ( IntegerVector::size_type c( 0 );
c < theContinuousVariableVector.size(); c++ )
{
const std::size_t anIndex( theContinuousVariableVector[ c ] );
@@ -898,14 +896,14 @@
{
const ProcessVector::size_type anIndex(
theContinuousVariableVector.size() + c - aDiscreteProcessOffset );
- const ProcessPtr aProcess( theProcessVector[ c ] );
+ const Process* const aProcess( theProcessVector[ c ] );
aTIF[ anIndex ] = aProcess->getActivity() * 4.3255798900631553510;
aTIF[ anIndex + aSize ] = aProcess->getActivity() * -4.1787185915519047273;
aTIF[ anIndex + aSize*2 ] = aProcess->getActivity() * -0.50287263494578687595;
}
- for ( IntVector::size_type c( 0 );
+ for ( IntegerVector::size_type c( 0 );
c < theContinuousVariableVector.size(); c++ )
{
const std::size_t anIndex( theContinuousVariableVector[ c ] );
@@ -935,14 +933,14 @@
{
const ProcessVector::size_type anIndex(
theContinuousVariableVector.size() + c - aDiscreteProcessOffset );
- const ProcessPtr aProcess( theProcessVector[ c ] );
+ const Process* const aProcess( theProcessVector[ c ] );
aTIF[ anIndex ] += aProcess->getActivity() * 0.33919925181580986954;
aTIF[ anIndex + aSize ] -= aProcess->getActivity() * 0.32768282076106238708;
aTIF[ anIndex + aSize*2 ] += aProcess->getActivity() * 2.5719269498556054292;
}
- for ( IntVector::size_type c( 0 );
+ for ( IntegerVector::size_type c( 0 );
c < theContinuousVariableVector.size(); c++ )
{
const std::size_t anIndex( theContinuousVariableVector[ c ] );
@@ -970,7 +968,7 @@
{
const ProcessVector::size_type anIndex(
theContinuousVariableVector.size() + c - aDiscreteProcessOffset );
- const ProcessPtr aProcess( theProcessVector[ c ] );
+ const Process* const aProcess( theProcessVector[ c ] );
aTIF[ anIndex ] += aProcess->getActivity() * 0.54177053993587487119;
aTIF[ anIndex + aSize ] += aProcess->getActivity() * 0.47662355450055045196;
@@ -983,7 +981,7 @@
gsl_vector_complex_set( theVelocityVector2, anIndex, comp );
}
- for ( IntVector::size_type c( 0 );
+ for ( IntegerVector::size_type c( 0 );
c < theContinuousVariableVector.size(); c++ )
{
const std::size_t anIndex( theContinuousVariableVector[ c ] );
Modified: ecell3/trunk/ecell/dm/ESSYNSProcessInterface.hpp
===================================================================
--- ecell3/trunk/ecell/dm/ESSYNSProcessInterface.hpp 2010-04-07 05:34:30 UTC (rev 3833)
+++ ecell3/trunk/ecell/dm/ESSYNSProcessInterface.hpp 2010-04-13 09:24:40 UTC (rev 3834)
@@ -33,8 +33,6 @@
struct ESSYNSProcessInterface
{
- DECLARE_VECTOR( libecs::Real, RealVector );
-
virtual const boost::multi_array< libecs::Real, 2 >& getESSYNSMatrix() = 0;
virtual libecs::Integer getSystemSize() const = 0;
Modified: ecell3/trunk/ecell/dm/ESSYNSStepper.cpp
===================================================================
--- ecell3/trunk/ecell/dm/ESSYNSStepper.cpp 2010-04-07 05:34:30 UTC (rev 3833)
+++ ecell3/trunk/ecell/dm/ESSYNSStepper.cpp 2010-04-13 09:24:40 UTC (rev 3834)
@@ -61,7 +61,7 @@
}
ESSYNSStepper()
- : theESSYNSProcessPtr( NULLPTR, NULLPTR ), theTaylorOrder( 1 )
+ : theTaylorOrder( 1 ), theESSYNSProcessPtr( 0, 0 )
{
;
}
@@ -95,15 +95,15 @@
theESSYNSMatrix.resize( boost::extents[ theSystemSize + 1 ][ theTaylorOrder + 1 ] );
theIndexVector.resize( theSystemSize );
- VariableReferenceVectorCref aVariableReferenceVectorCref(
+ Process::VariableReferenceVector const& aVariableReferenceVectorCref(
theESSYNSProcessPtr.second->getVariableReferenceVector() );
- for ( VariableReferenceVector::size_type c(
+ for ( Integer c(
theESSYNSProcessPtr.second->getPositiveVariableReferenceOffset() );
c < theSystemSize; ++c )
{
- VariableReferenceCref aVariableReferenceCref( aVariableReferenceVectorCref[ c ] );
- const VariablePtr aVariablePtr( aVariableReferenceCref.getVariable() );
+ VariableReference const& aVariableReferenceCref( aVariableReferenceVectorCref[ c ] );
+ Variable* const aVariablePtr( aVariableReferenceCref.getVariable() );
theIndexVector[ c ] = getVariableIndex( aVariablePtr );
}
@@ -113,8 +113,6 @@
{
const VariableVector::size_type aSize( getReadOnlyVariableOffset() );
- Real aCurrentTime( getCurrentTime() );
-
// write step() function
theESSYNSMatrix = theESSYNSProcessPtr.first->getESSYNSMatrix();
@@ -132,10 +130,10 @@
}
//set value
- for( int c( 0 ); c < aSize; ++c )
+ for( VariableVector::size_type c( 0 ); c < aSize; ++c )
{
const VariableVector::size_type anIndex( theIndexVector[ c ] );
- VariablePtr const aVariable( theVariableVector[ anIndex ] );
+ Variable* const aVariable( theVariableVector[ anIndex ] );
const Real aVelocity( ( exp( (theESSYNSMatrix[c])[0] ) - ( aVariable->getValue() ) ) / aStepInterval );
Modified: ecell3/trunk/ecell/dm/ExpressionAlgebraicProcess.cpp
===================================================================
--- ecell3/trunk/ecell/dm/ExpressionAlgebraicProcess.cpp 2010-04-07 05:34:30 UTC (rev 3833)
+++ ecell3/trunk/ecell/dm/ExpressionAlgebraicProcess.cpp 2010-04-13 09:24:40 UTC (rev 3834)
@@ -59,22 +59,22 @@
}
virtual void defaultSetProperty( libecs::String const& aPropertyName,
- libecs::PolymorphCref aValue )
+ libecs::Polymorph const& aValue )
{
return _LIBECS_MIXIN_CLASS_::defaultSetProperty( aPropertyName, aValue );
}
- virtual const libecs::Polymorph defaultGetProperty( libecs::String const& aPropertyName ) const
+ virtual libecs::Polymorph defaultGetProperty( libecs::String const& aPropertyName ) const
{
return _LIBECS_MIXIN_CLASS_::defaultGetProperty( aPropertyName );
}
- virtual const libecs::StringVector defaultGetPropertyList() const
+ virtual std::vector< libecs::String > defaultGetPropertyList() const
{
return _LIBECS_MIXIN_CLASS_::defaultGetPropertyList();
}
- virtual const libecs::PropertyAttributes
+ virtual libecs::PropertyAttributes
defaultGetPropertyAttributes( libecs::String const& aPropertyName ) const
{
return _LIBECS_MIXIN_CLASS_::defaultGetPropertyAttributes( aPropertyName );
Modified: ecell3/trunk/ecell/dm/ExpressionAssignmentProcess.cpp
===================================================================
--- ecell3/trunk/ecell/dm/ExpressionAssignmentProcess.cpp 2010-04-07 05:34:30 UTC (rev 3833)
+++ ecell3/trunk/ecell/dm/ExpressionAssignmentProcess.cpp 2010-04-13 09:24:40 UTC (rev 3834)
@@ -69,22 +69,22 @@
}
virtual void defaultSetProperty( libecs::String const& aPropertyName,
- libecs::PolymorphCref aValue )
+ libecs::Polymorph const& aValue )
{
return _LIBECS_MIXIN_CLASS_::defaultSetProperty( aPropertyName, aValue );
}
- virtual const libecs::Polymorph defaultGetProperty( libecs::String const& aPropertyName ) const
+ virtual libecs::Polymorph defaultGetProperty( libecs::String const& aPropertyName ) const
{
return _LIBECS_MIXIN_CLASS_::defaultGetProperty( aPropertyName );
}
- virtual const libecs::StringVector defaultGetPropertyList() const
+ virtual std::vector< libecs::String > defaultGetPropertyList() const
{
return _LIBECS_MIXIN_CLASS_::defaultGetPropertyList();
}
- virtual const libecs::PropertyAttributes
+ virtual libecs::PropertyAttributes
defaultGetPropertyAttributes( libecs::String const& aPropertyName ) const
{
return _LIBECS_MIXIN_CLASS_::defaultGetPropertyAttributes( aPropertyName );
@@ -95,7 +95,7 @@
Process::initialize();
_LIBECS_MIXIN_CLASS_::initialize();
- for( VariableReferenceVectorConstIterator i(
+ for( VariableReferenceVector::const_iterator i(
getVariableReferenceVector().begin() );
i != getVariableReferenceVector().end(); ++i )
{
Modified: ecell3/trunk/ecell/dm/ExpressionFluxProcess.cpp
===================================================================
--- ecell3/trunk/ecell/dm/ExpressionFluxProcess.cpp 2010-04-07 05:34:30 UTC (rev 3833)
+++ ecell3/trunk/ecell/dm/ExpressionFluxProcess.cpp 2010-04-13 09:24:40 UTC (rev 3834)
@@ -66,22 +66,22 @@
}
virtual void defaultSetProperty( libecs::String const& aPropertyName,
- libecs::PolymorphCref aValue )
+ libecs::Polymorph const& aValue )
{
return _LIBECS_MIXIN_CLASS_::defaultSetProperty( aPropertyName, aValue );
}
- virtual const libecs::Polymorph defaultGetProperty( libecs::String const& aPropertyName ) const
+ virtual libecs::Polymorph defaultGetProperty( libecs::String const& aPropertyName ) const
{
return _LIBECS_MIXIN_CLASS_::defaultGetProperty( aPropertyName );
}
- virtual const libecs::StringVector defaultGetPropertyList() const
+ virtual std::vector< libecs::String > defaultGetPropertyList() const
{
return _LIBECS_MIXIN_CLASS_::defaultGetPropertyList();
}
- virtual const libecs::PropertyAttributes
+ virtual libecs::PropertyAttributes
defaultGetPropertyAttributes( libecs::String const& aPropertyName ) const
{
return _LIBECS_MIXIN_CLASS_::defaultGetPropertyAttributes( aPropertyName );
Modified: ecell3/trunk/ecell/dm/ExpressionProcessBase.hpp
===================================================================
--- ecell3/trunk/ecell/dm/ExpressionProcessBase.hpp 2010-04-07 05:34:30 UTC (rev 3833)
+++ ecell3/trunk/ecell/dm/ExpressionProcessBase.hpp 2010-04-13 09:24:40 UTC (rev 3834)
@@ -48,12 +48,8 @@
class ExpressionProcessBase
{
protected:
- DECLARE_ASSOCVECTOR(
- libecs::String,
- libecs::Real,
- std::less<const libecs::String>,
- PropertyMap
- );
+ typedef Loki::AssocVector< libecs::String, libecs::Real,
+ std::less<const libecs::String> > PropertyMap;
private:
class PropertyAccess
@@ -67,7 +63,7 @@
virtual libecs::Real* get( const libecs::String& name )
{
- PropertyMapIterator pos = outer_.thePropertyMap.find( name );
+ PropertyMap::iterator pos = outer_.thePropertyMap.find( name );
return pos == outer_.thePropertyMap.end() ? 0: &(pos->second);
}
@@ -160,7 +156,7 @@
ExpressionProcessBase()
- : theRecompileFlag( true ), theCompiledCode( 0 )
+ : theCompiledCode( 0 ), theRecompileFlag( true )
{
// ; do nothing
}
@@ -182,14 +178,14 @@
}
void defaultSetProperty( libecs::String const& aPropertyName,
- libecs::PolymorphCref aValue )
+ libecs::Polymorph const& aValue )
{
thePropertyMap[ aPropertyName ] = aValue.as< libecs::Real >();
}
- const libecs::Polymorph defaultGetProperty( libecs::String const& aPropertyName ) const
+ libecs::Polymorph defaultGetProperty( libecs::String const& aPropertyName ) const
{
- PropertyMapConstIterator aPropertyMapIterator(
+ PropertyMap::const_iterator aPropertyMapIterator(
thePropertyMap.find( aPropertyName ) );
if ( aPropertyMapIterator != thePropertyMap.end() ) {
@@ -203,9 +199,9 @@
}
}
- const libecs::StringVector defaultGetPropertyList() const
+ std::vector< libecs::String > defaultGetPropertyList() const
{
- libecs::StringVector aVector;
+ std::vector< libecs::String> aVector;
std::transform( thePropertyMap.begin(), thePropertyMap.end(),
std::back_inserter( aVector ),
@@ -214,7 +210,7 @@
return aVector;
}
- const libecs::PropertyAttributes
+ libecs::PropertyAttributes
defaultGetPropertyAttributes( libecs::String const& aPropertyName ) const
{
return libecs::PropertyAttributes( libecs::PropertySlotBase::POLYMORPH,
@@ -239,7 +235,7 @@
theCompiledCode = theCompiler.compileExpression( theExpression );
}
- PropertyMapCref getPropertyMap() const
+ PropertyMap const& getPropertyMap() const
{
return thePropertyMap;
}
@@ -262,7 +258,7 @@
protected:
- PropertyMapRef getPropertyMap()
+ PropertyMap& getPropertyMap()
{
return thePropertyMap;
}
Modified: ecell3/trunk/ecell/dm/FixedDAE1Stepper.cpp
===================================================================
--- ecell3/trunk/ecell/dm/FixedDAE1Stepper.cpp 2010-04-07 05:34:30 UTC (rev 3833)
+++ ecell3/trunk/ecell/dm/FixedDAE1Stepper.cpp 2010-04-13 09:24:40 UTC (rev 3834)
@@ -37,10 +37,10 @@
USE_LIBECS;
-DECLARE_VECTOR( int, IntVector );
-
LIBECS_DM_CLASS( FixedDAE1Stepper, DifferentialStepper )
{
+private:
+ typedef std::vector< Integer > IntegerVector;
public:
@@ -53,16 +53,16 @@
}
FixedDAE1Stepper()
- : theJacobianMatrix( NULLPTR ),
- theVelocityVector( NULLPTR ),
- theSolutionVector( NULLPTR ),
- thePermutation( NULLPTR ),
- theSystemSize( 0 ),
- theTolerance( 1e-10 ),
+ : theSystemSize( 0 ),
thePerturbationRate( 1e-9 ),
- theDependentProcessVector( NULLPTR ),
- theContinuousVariableVector( NULLPTR ),
- theActivityBuffer( NULLPTR )
+ theTolerance( 1e-10 ),
+ theDependentProcessVector( 0 ),
+ theJacobianMatrix( 0 ),
+ theVelocityVector( 0 ),
+ theSolutionVector( 0 ),
+ thePermutation( 0 ),
+ theContinuousVariableVector( 0 ),
+ theActivityBuffer( 0 )
{
; // do nothing
}
@@ -197,7 +197,7 @@
theActivityBuffer[ c ] = theProcessVector[ c ]->getActivity();
}
- for( IntVector::size_type i( 0 );
+ for( IntegerVector::size_type i( 0 );
i < theContinuousVariableVector.size(); ++i )
{
const int anIndex( theContinuousVariableVector[ i ] );
@@ -213,8 +213,6 @@
for( ProcessVector::size_type c( aDiscreteProcessOffset );
c < theProcessVector.size(); ++c )
{
- const Real anActivity( theProcessVector[ c ]->getActivity() );
-
gsl_vector_set( theVelocityVector,
theContinuousVariableVector.size() + c
- aDiscreteProcessOffset,
@@ -240,14 +238,14 @@
for( VariableVector::size_type c( 0 ); c < aReadOnlyVariableOffset;
++c )
{
- VariablePtr const aVariable( theVariableVector[ c ] );
+ Variable* const aVariable( theVariableVector[ c ] );
const Real aValue( aVariable->getValue() );
aVariable->setValue( aValue + aPerturbation );
- FOR_ALL( IntVector, theDependentProcessVector[ c ] )
+ FOR_ALL( IntegerVector, theDependentProcessVector[ c ] )
{
- const Integer anIndex( *i );
+ const VariableVector::size_type anIndex( *i );
theProcessVector[ anIndex ]->fire();
const Real aDifference( theProcessVector[ anIndex ]->getActivity() - theActivityBuffer[ anIndex ] );
@@ -275,7 +273,7 @@
}
}
- for ( IntVector::size_type i( 0 );
+ for ( IntegerVector::size_type i( 0 );
i < theContinuousVariableVector.size(); ++i )
{
// this calculation already includes negative factor
@@ -292,7 +290,7 @@
aVariable->setValue( aValue );
}
- for ( IntVector::size_type c( 0 );
+ for ( IntegerVector::size_type c( 0 );
c < theContinuousVariableVector.size(); c++ )
{
const int anIndex( theContinuousVariableVector[ c ] );
@@ -316,27 +314,27 @@
theContinuousVariableVector.clear();
- IntVector anIndexVector;
- IntVectorConstIterator aWriteVariableIterator;
+ IntegerVector anIndexVector;
+ IntegerVector::const_iterator aWriteVariableIterator;
- ProcessVectorConstIterator anIterator( theProcessVector.begin() );
+ ProcessVector::const_iterator anIterator( theProcessVector.begin() );
for( ProcessVector::size_type c( 0 ); c < theProcessVector.size(); ++c )
{
- VariableReferenceVectorCref aVariableReferenceVector(
+ Process::VariableReferenceVector const& aVariableReferenceVector(
(*anIterator)->getVariableReferenceVector() );
- const VariableReferenceVector::size_type aZeroVariableReferenceOffset(
+ const Process::VariableReferenceVector::size_type aZeroVariableReferenceOffset(
(*anIterator)->getZeroVariableReferenceOffset() );
- const VariableReferenceVector::size_type
+ const Process::VariableReferenceVector::size_type
aPositiveVariableReferenceOffset(
(*anIterator)->getPositiveVariableReferenceOffset() );
anIndexVector.clear();
- for ( VariableReferenceVector::size_type i(
+ for ( Process::VariableReferenceVector::size_type i(
aZeroVariableReferenceOffset );
i != aPositiveVariableReferenceOffset; ++i )
{
- VariablePtr const aVariable(
+ Variable* const aVariable(
aVariableReferenceVector[ i ].getVariable() );
const VariableVector::size_type anIndex(
@@ -352,10 +350,10 @@
}
}
- const IntVector::size_type aNonZeroOffset( anIndexVector.size() );
+ const IntegerVector::size_type aNonZeroOffset( anIndexVector.size() );
const bool aContinuity( (*anIterator)->isContinuous() );
- for( VariableReferenceVector::size_type i( 0 );
+ for( Process::VariableReferenceVector::size_type i( 0 );
i < aVariableReferenceVector.size(); ++i )
{
if ( i == aZeroVariableReferenceOffset )
@@ -367,7 +365,7 @@
i = aPositiveVariableReferenceOffset;
}
- VariablePtr const aVariable(
+ Variable* const aVariable(
aVariableReferenceVector[ i ].getVariable() );
const VariableVector::size_type anIndex(
@@ -393,9 +391,9 @@
}
}
- FOR_ALL( IntVector, anIndexVector )
+ FOR_ALL( IntegerVector, anIndexVector )
{
- for( IntVector::size_type j( aNonZeroOffset );
+ for( IntegerVector::size_type j( aNonZeroOffset );
j != anIndexVector.size(); ++j )
{
const int anIndex( anIndexVector[ j ] );
@@ -438,7 +436,7 @@
for( VariableVector::size_type c( 0 ); c < aReadOnlyVariableOffset;
++c )
{
- VariablePtr const aVariable( theVariableVector[ c ] );
+ Variable* const aVariable( theVariableVector[ c ] );
const Real aDifference( gsl_vector_get( theSolutionVector, c ) );
aVariable->addValue( aDifference );
@@ -459,16 +457,16 @@
Real thePerturbationRate;
Real theTolerance;
- std::vector<IntVector> theDependentProcessVector;
- std::vector<IntVector> theDependentVariableVector;
+ std::vector<IntegerVector> theDependentProcessVector;
+ std::vector<IntegerVector> theDependentVariableVector;
gsl_matrix* theJacobianMatrix;
gsl_vector* theVelocityVector;
gsl_vector* theSolutionVector;
gsl_permutation* thePermutation;
- IntVector theContinuousVariableVector;
- RealVector theActivityBuffer;
+ IntegerVector theContinuousVariableVector;
+ RealVector theActivityBuffer;
};
LIBECS_DM_INIT( FixedDAE1Stepper, Stepper );
Modified: ecell3/trunk/ecell/dm/FluxDistributionStepper.cpp
===================================================================
--- ecell3/trunk/ecell/dm/FluxDistributionStepper.cpp 2010-04-07 05:34:30 UTC (rev 3833)
+++ ecell3/trunk/ecell/dm/FluxDistributionStepper.cpp 2010-04-13 09:24:40 UTC (rev 3834)
@@ -71,7 +71,7 @@
typedef Caster< QuasiDynamicFluxProcessInterface*, Process* > QDFPCaster;
-DECLARE_VECTOR( QDFPCaster::result_type, QuasiDynamicFluxProcessVector );
+typedef std::vector< QDFPCaster::result_type > QuasiDynamicFluxProcessVector;
LIBECS_DM_CLASS( FluxDistributionStepper, DifferentialStepper )
{
@@ -84,12 +84,12 @@
}
FluxDistributionStepper()
- : theUnknownMatrix( NULLPTR ),
- theInverseMatrix( NULLPTR ),
- theVariableVelocityVector( NULLPTR ),
- theFluxVector( NULLPTR ),
- theIrreversibleFlag( false ),
- Epsilon( 1e-6 )
+ : theUnknownMatrix( 0 ),
+ theInverseMatrix( 0 ),
+ theVariableVelocityVector( 0 ),
+ theFluxVector( 0 ),
+ Epsilon( 1e-6 ),
+ theIrreversibleFlag( false )
{
initializeStepInterval( INF );
}
@@ -140,7 +140,7 @@
theMatrixSize = theVariableVector.size();
}
- if( theUnknownMatrix != NULLPTR )
+ if( theUnknownMatrix != 0 )
{
gsl_matrix_free( theUnknownMatrix );
gsl_vector_free( theVariableVelocityVector );
@@ -176,12 +176,12 @@
for( QuasiDynamicFluxProcessVector::size_type i( 0 );
i < aProcessVectorSize; ++i )
{
- VariableReferenceVector aVariableReferenceVector(
+ Process::VariableReferenceVector aVariableReferenceVector(
theQuasiDynamicFluxProcessVector[ i ].first->getFluxDistributionVector() );
- VariableReferenceVector::size_type aVariableReferenceVectorSize(
+ Process::VariableReferenceVector::size_type aVariableReferenceVectorSize(
aVariableReferenceVector.size() );
- for( VariableReferenceVector::size_type j( 0 ); j < aVariableReferenceVectorSize; ++j )
+ for( Process::VariableReferenceVector::size_type j( 0 ); j < aVariableReferenceVectorSize; ++j )
{
gsl_matrix_set( theUnknownMatrix,
theVariableMap.find(
@@ -216,7 +216,7 @@
// generate inverse matrix
//
- if( theInverseMatrix != NULLPTR )
+ if( theInverseMatrix != 0 )
{
gsl_matrix_free( theInverseMatrix );
}
@@ -224,7 +224,7 @@
theInverseMatrix = generateInverse( theUnknownMatrix , theMatrixSize );
}
- virtual void interrupt( StepperPtr const aCaller )
+ virtual void interrupt( Stepper* aCaller )
{
integrate( aCaller->getCurrentTime() );
@@ -276,9 +276,9 @@
if ( gsl_vector_get( theFluxVector, i ) < 0 )
{
aFlag = true;
- VariableReferenceVector aVariableReferenceVector( theQuasiDynamicFluxProcessVector[i].first->getFluxDistributionVector() );
- VariableReferenceVector::size_type aVariableReferenceVectorSize( aVariableReferenceVector.size() );
- for ( VariableReferenceVector::size_type k( 0 ); k < aVariableReferenceVectorSize; ++k )
+ Process::VariableReferenceVector aVariableReferenceVector( theQuasiDynamicFluxProcessVector[i].first->getFluxDistributionVector() );
+ Process::VariableReferenceVector::size_type aVariableReferenceVectorSize( aVariableReferenceVector.size() );
+ for ( Process::VariableReferenceVector::size_type k( 0 ); k < aVariableReferenceVectorSize; ++k )
{
gsl_matrix_set( aTmpUnknownMatrix, theVariableMap.find( aVariableReferenceVector[k].getVariable() )->second, i, 0.0 );
}
@@ -383,7 +383,7 @@
Real Epsilon;
- std::map< VariablePtr, VariableVector::size_type > theVariableMap;
+ std::map< Variable*, VariableVector::size_type > theVariableMap;
std::size_t theMatrixSize;
bool theIrreversibleFlag;
Modified: ecell3/trunk/ecell/dm/GMAProcess.cpp
===================================================================
--- ecell3/trunk/ecell/dm/GMAProcess.cpp 2010-04-07 05:34:30 UTC (rev 3833)
+++ ecell3/trunk/ecell/dm/GMAProcess.cpp 2010-04-13 09:24:40 UTC (rev 3834)
@@ -61,7 +61,7 @@
}
GMAProcess()
- : theSystemSize(0), Order(3)
+ : Order(3), theSystemSize(0)
{
; // do nothing.
}
@@ -158,7 +158,7 @@
// get theY
Integer anIndex( 0 );
- for ( VariableReferenceVectorConstIterator
+ for ( VariableReferenceVector::const_iterator
i ( thePositiveVariableReferenceIterator );
i != theVariableReferenceVector.end(); ++i )
{
Modified: ecell3/trunk/ecell/dm/GillespieProcess.cpp
===================================================================
--- ecell3/trunk/ecell/dm/GillespieProcess.cpp 2010-04-07 05:34:30 UTC (rev 3833)
+++ ecell3/trunk/ecell/dm/GillespieProcess.cpp 2010-04-13 09:24:40 UTC (rev 3834)
@@ -95,12 +95,12 @@
}
}
-const Real GillespieProcess::getPD( VariablePtr aVariable ) const
+Real GillespieProcess::getPD( Variable const* aVariable ) const
{
return ( this->*theGetPDMethodPtr )( aVariable );
}
-const bool GillespieProcess::isContinuous() const
+bool GillespieProcess::isContinuous() const
{
return true;
}
@@ -131,7 +131,7 @@
Real velocity( getk() * N_A );
velocity *= getSuperSystem()->getSize();
- for( VariableReferenceVectorConstIterator
+ for( VariableReferenceVector::const_iterator
s( theVariableReferenceVector.begin() );
s != theZeroVariableReferenceIterator; ++s )
{
@@ -159,17 +159,17 @@
PROPERTYSLOT_GET_NO_LOAD_SAVE( Integer, Order );
}
-const Real GillespieProcess::getZero() const
+Real GillespieProcess::getZero() const
{
return 0.0;
}
-const Real GillespieProcess::getPD_Zero( VariablePtr aVariable ) const
+Real GillespieProcess::getPD_Zero( Variable const* aVariable ) const
{
return 0.0;
}
-const Real GillespieProcess::getPD_SecondOrder_OneSubstrate( VariablePtr aVariable ) const
+Real GillespieProcess::getPD_SecondOrder_OneSubstrate( Variable const* aVariable ) const
{
if( theVariableReferenceVector[ 0 ].getVariable() == aVariable )
{
@@ -190,12 +190,12 @@
}
}
-const Real GillespieProcess::getMinValue_SecondOrder_OneSubstrate() const
+Real GillespieProcess::getMinValue_SecondOrder_OneSubstrate() const
{
return theVariableReferenceVector[ 0 ].getVariable()->getValue() * 0.5;
}
-const Real GillespieProcess::getPropensity_SecondOrder_OneSubstrate() const
+Real GillespieProcess::getPropensity_SecondOrder_OneSubstrate() const
{
const Real aValue( theVariableReferenceVector[ 0 ].getVariable()->getValue() );
@@ -209,7 +209,7 @@
}
}
-const Real GillespieProcess::getPD_SecondOrder_TwoSubstrates( VariablePtr aVariable ) const
+Real GillespieProcess::getPD_SecondOrder_TwoSubstrates( Variable const* aVariable ) const
{
if ( theVariableReferenceVector[ 0 ].getVariable() == aVariable )
{
@@ -225,7 +225,7 @@
}
}
-const Real GillespieProcess::getPropensity_FirstOrder() const
+Real GillespieProcess::getPropensity_FirstOrder() const
{
const Real aValue( theVariableReferenceVector[ 0 ].getVariable()->getValue() );
@@ -239,12 +239,12 @@
}
}
-const Real GillespieProcess::getMinValue_FirstOrder() const
+Real GillespieProcess::getMinValue_FirstOrder() const
{
return theVariableReferenceVector[ 0 ].getVariable()->getValue();
}
-const Real GillespieProcess::getPD_FirstOrder( VariablePtr aVariable ) const
+Real GillespieProcess::getPD_FirstOrder( Variable const* aVariable ) const
{
if ( theVariableReferenceVector[ 0 ].getVariable() == aVariable )
{
@@ -256,7 +256,7 @@
}
}
-const Real GillespieProcess::getPropensity_SecondOrder_TwoSubstrates() const
+Real GillespieProcess::getPropensity_SecondOrder_TwoSubstrates() const
{
const Real aValue1( theVariableReferenceVector[ 0 ].getVariable()->getValue() );
const Real aValue2( theVariableReferenceVector[ 1 ].getVariable()->getValue() );
@@ -271,7 +271,7 @@
}
}
-const Real GillespieProcess::getMinValue_SecondOrder_TwoSubstrates() const
+Real GillespieProcess::getMinValue_SecondOrder_TwoSubstrates() const
{
const Real aFirstValue( theVariableReferenceVector[ 0 ].getVariable()->getValue() );
const Real aSecondValue( theVariableReferenceVector[ 1 ].getVariable()->getValue() );
@@ -283,7 +283,7 @@
{
theOrder = 0;
- for( libecs::VariableReferenceVectorConstIterator i(
+ for( VariableReferenceVector::const_iterator i(
theVariableReferenceVector.begin() );
i != theVariableReferenceVector.end() ; ++i )
{
Modified: ecell3/trunk/ecell/dm/GillespieProcess.hpp
===================================================================
--- ecell3/trunk/ecell/dm/GillespieProcess.hpp 2010-04-07 05:34:30 UTC (rev 3833)
+++ ecell3/trunk/ecell/dm/GillespieProcess.hpp 2010-04-13 09:24:40 UTC (rev 3834)
@@ -46,7 +46,7 @@
GillespieProcessInterface )
{
typedef libecs::MethodProxy< GillespieProcess, libecs::Real > RealMethodProxy;
- typedef const libecs::Real( GillespieProcess::* PDMethodPtr )( libecs::Variable* ) const;
+ typedef libecs::Real( GillespieProcess::* PDMethodPtr )( libecs::Variable const* ) const;
public:
LIBECS_DM_OBJECT( GillespieProcess, Process );
@@ -65,9 +65,9 @@
GET_METHOD( libecs::Real, Propensity_R );
- virtual const libecs::Real getPD( libecs::Variable* aVariable ) const;
+ virtual libecs::Real getPD( libecs::Variable const* aVariable ) const;
- virtual const bool isContinuous() const;
+ virtual bool isContinuous() const;
// The order of the reaction, i.e. 1 for a unimolecular reaction.
@@ -83,44 +83,43 @@
protected:
- const libecs::Real getZero() const;
+ libecs::Real getZero() const;
- const libecs::Real getPD_Zero( libecs::Variable* aVariable ) const;
+ libecs::Real getPD_Zero( libecs::Variable const* aVariable ) const;
/**
FirstOrder_OneSubstrate
*/
- const libecs::Real getPropensity_FirstOrder() const;
+ libecs::Real getPropensity_FirstOrder() const;
- const libecs::Real getMinValue_FirstOrder() const;
+ libecs::Real getMinValue_FirstOrder() const;
- const libecs::Real getPD_FirstOrder( libecs::Variable* aVariable ) const;
+ libecs::Real getPD_FirstOrder( libecs::Variable const* aVariable ) const;
/**
SecondOrder_TwoSubstrates
*/
- const libecs::Real getPropensity_SecondOrder_TwoSubstrates() const;
+ libecs::Real getPropensity_SecondOrder_TwoSubstrates() const;
- const libecs::Real getMinValue_SecondOrder_TwoSubstrates() const;
+ libecs::Real getMinValue_SecondOrder_TwoSubstrates() const;
- const libecs::Real getPD_SecondOrder_TwoSubstrates( libecs::Variable* aVariable ) const;
+ libecs::Real getPD_SecondOrder_TwoSubstrates( libecs::Variable const* aVariable ) const;
/**
SecondOrder_OneSubstrate
*/
- const libecs::Real getPropensity_SecondOrder_OneSubstrate() const;
+ libecs::Real getPropensity_SecondOrder_OneSubstrate() const;
- const libecs::Real getMinValue_SecondOrder_OneSubstrate() const;
+ libecs::Real getMinValue_SecondOrder_OneSubstrate() const;
- const libecs::Real getPD_SecondOrder_OneSubstrate( libecs::Variable* aVariable ) const;
+ libecs::Real getPD_SecondOrder_OneSubstrate( libecs::Variable const* aVariable ) const;
protected:
- libecs::Real k;
+ libecs::Integer theOrder;
libecs::Real c;
+ libecs::Real k;
- libecs::Integer theOrder;
-
RealMethodProxy theGetPropensityMethodPtr;
RealMethodProxy theGetMinValueMethodPtr;
PDMethodPtr theGetPDMethodPtr; // this should be MethodProxy
Modified: ecell3/trunk/ecell/dm/GillespieProcessInterface.hpp
===================================================================
--- ecell3/trunk/ecell/dm/GillespieProcessInterface.hpp 2010-04-07 05:34:30 UTC (rev 3833)
+++ ecell3/trunk/ecell/dm/GillespieProcessInterface.hpp 2010-04-13 09:24:40 UTC (rev 3834)
@@ -34,7 +34,7 @@
{
virtual GET_METHOD( libecs::Real, Propensity ) = 0;
- virtual const libecs::Real getPD( libecs::Variable* aVariable ) const = 0;
+ virtual libecs::Real getPD( libecs::Variable const* aVariable ) const = 0;
};
#endif /* __GILLESPIEPROCESSINTERFACE_HPP */
Modified: ecell3/trunk/ecell/dm/MassActionFluxProcess.cpp
===================================================================
--- ecell3/trunk/ecell/dm/MassActionFluxProcess.cpp 2010-04-07 05:34:30 UTC (rev 3833)
+++ ecell3/trunk/ecell/dm/MassActionFluxProcess.cpp 2010-04-13 09:24:40 UTC (rev 3834)
@@ -66,7 +66,7 @@
Real velocity( k * N_A );
velocity *= getSuperSystem()->getSize();
- for( VariableReferenceVectorConstIterator s(
+ for( VariableReferenceVector::const_iterator s(
theVariableReferenceVector.begin() );
s != theZeroVariableReferenceIterator; ++s )
{
Modified: ecell3/trunk/ecell/dm/ODE23Stepper.cpp
===================================================================
--- ecell3/trunk/ecell/dm/ODE23Stepper.cpp 2010-04-07 05:34:30 UTC (rev 3833)
+++ ecell3/trunk/ecell/dm/ODE23Stepper.cpp 2010-04-13 09:24:40 UTC (rev 3834)
@@ -85,7 +85,7 @@
for( VariableVector::size_type c( 0 );
c != theVariableVector.size(); ++c )
{
- VariablePtr const aVariable( theVariableVector[ c ] );
+ Variable* const aVariable( theVariableVector[ c ] );
aVariable->setValue( theValueBuffer[ c ] );
aVariable->interIntegrate( aCurrentTime );
Modified: ecell3/trunk/ecell/dm/ODE45Stepper.cpp
===================================================================
--- ecell3/trunk/ecell/dm/ODE45Stepper.cpp 2010-04-07 05:34:30 UTC (rev 3833)
+++ ecell3/trunk/ecell/dm/ODE45Stepper.cpp 2010-04-13 09:24:40 UTC (rev 3834)
@@ -121,7 +121,7 @@
for( VariableVector::size_type c( 0 ); c < aSize; ++c )
{
- VariablePtr const aVariable( theVariableVector[ c ] );
+ Variable* const aVariable( theVariableVector[ c ] );
aVariable->setValue( theTaylorSeries[ 0 ][ c ] * ( 1.0 / 5.0 )
* aStepInterval + theValueBuffer[ c ] );
@@ -131,7 +131,7 @@
{
for( VariableVector::size_type c( 0 ); c < aSize; ++c )
{
- VariablePtr const aVariable( theVariableVector[ c ] );
+ Variable* const aVariable( theVariableVector[ c ] );
// get k1
theTaylorSeries[ 0 ][ c ] = theRungeKuttaBuffer[ 5 ][ c ];
@@ -149,7 +149,7 @@
for ( VariableVector::size_type c( 0 ); c < aSize; ++c )
{
- VariablePtr const aVariable( theVariableVector[ c ] );
+ Variable* const aVariable( theVariableVector[ c ] );
aVariable ->setValue( ( theTaylorSeries[ 0 ][ c ] * ( 3.0 / 40.0 )
+ theRungeKuttaBuffer[ 0 ][ c ] * ( 9.0 / 40.0 ) )
@@ -164,7 +164,7 @@
for( VariableVector::size_type c( 0 ); c < aSize; ++c )
{
- VariablePtr const aVariable( theVariableVector[ c ] );
+ Variable* const aVariable( theVariableVector[ c ] );
aVariable->setValue(
( theTaylorSeries[ 0 ][ c ] * ( 44.0 / 45.0 )
@@ -181,7 +181,7 @@
for( VariableVector::size_type c( 0 ); c < aSize; ++c )
{
- VariablePtr const aVariable( theVariableVector[ c ] );
+ Variable* const aVariable( theVariableVector[ c ] );
aVariable->setValue(
( theTaylorSeries[ 0 ][ c ] * ( 19372.0 / 6561.0 )
@@ -199,7 +199,7 @@
for( VariableVector::size_type c( 0 ); c < aSize; ++c )
{
- VariablePtr const aVariable( theVariableVector[ c ] );
+ Variable* const aVariable( theVariableVector[ c ] );
// temporarily set Y^6
theTaylorSeries[ 1 ][ c ] =
@@ -226,7 +226,7 @@
for( VariableVector::size_type c( 0 ); c < aSize; ++c )
{
- VariablePtr const aVariable( theVariableVector[ c ] );
+ Variable* const aVariable( theVariableVector[ c ] );
theTaylorSeries[ 2 ][ c ] =
theTaylorSeries[ 0 ][ c ] * ( 35.0 / 384.0 )
@@ -256,8 +256,6 @@
for( VariableVector::size_type c( 0 ); c < aSize; ++c )
{
- VariablePtr const aVariable( theVariableVector[ c ] );
-
// calculate error
const Real anEstimatedError(
( theTaylorSeries[ 0 ][ c ] * ( 71.0 / 57600.0 )
Modified: ecell3/trunk/ecell/dm/ODEStepper.cpp
===================================================================
--- ecell3/trunk/ecell/dm/ODEStepper.cpp 2010-04-07 05:34:30 UTC (rev 3833)
+++ ecell3/trunk/ecell/dm/ODEStepper.cpp 2010-04-13 09:24:40 UTC (rev 3834)
@@ -97,7 +97,7 @@
initializeStepper();
}
- const Integer getIntegrationType() const { return isStiff; }
+ Integer getIntegrationType() const { return isStiff; }
SET_METHOD( Real, JacobianRecalculateTheta )
{
@@ -142,14 +142,14 @@
std::pair< bool, Real > calculateRadauIIA( Real const aStepInterval, Real const aPreviousStepInterval );
void updateInternalStateRadauIIA( Real const aStepInterval );
- void initializeTolerance( RealParam value )
+ void initializeTolerance( Real value )
{
setTolerance( value ); // AdaptiveDifferentialStepper::
rtoler = 0.1 * pow( getTolerance(), 2.0 / 3.0 );
atoler = rtoler * getAbsoluteToleranceFactor();
}
- void initializeAbsoluteToleranceFactor( RealParam value )
+ void initializeAbsoluteToleranceFactor( Real value )
{
setAbsoluteToleranceFactor( value ); // AdaptiveDifferentialStepper::
atoler = rtoler * getAbsoluteToleranceFactor();
@@ -196,7 +196,7 @@
Real theJacobianRecalculateTheta;
Real theSpectralRadius;
- UnsignedInteger theStiffnessCounter, theRejectedStepCounter;
+ Integer theStiffnessCounter, theRejectedStepCounter;
Integer CheckIntervalCount, SwitchingCount;
bool theFirstStepFlag, theJacobianCalculateFlag;
@@ -210,30 +210,30 @@
ODEStepper::ODEStepper()
: theSystemSize( -1 ),
- theJacobianMatrix1( NULLPTR ),
- thePermutation1( NULLPTR ),
- theVelocityVector1( NULLPTR ),
- theSolutionVector1( NULLPTR ),
- theJacobianMatrix2( NULLPTR ),
- thePermutation2( NULLPTR ),
- theVelocityVector2( NULLPTR ),
- theSolutionVector2( NULLPTR ),
+ theJacobianMatrix1( 0 ),
+ thePermutation1( 0 ),
+ theVelocityVector1( 0 ),
+ theSolutionVector1( 0 ),
+ theJacobianMatrix2( 0 ),
+ thePermutation2( 0 ),
+ theVelocityVector2( 0 ),
+ theSolutionVector2( 0 ),
theMaxIterationNumber( 7 ),
+ theStoppingCriterion( 0.0 ),
eta( 1.0 ),
Uround( 1e-10 ),
- theStoppingCriterion( 0.0 ),
- theFirstStepFlag( true ),
- theRejectedStepCounter( 0 ),
- theJacobianCalculateFlag( true ),
+ rtoler( 1e-6 ),
+ atoler( 1e-6 ),
theAcceptedError( 0.0 ),
theAcceptedStepInterval( 0.0 ),
theJacobianRecalculateTheta( 0.001 ),
- rtoler( 1e-6 ),
- atoler( 1e-6 ),
theSpectralRadius( 0.0 ),
theStiffnessCounter( 0 ),
+ theRejectedStepCounter( 0 ),
CheckIntervalCount( 100 ),
SwitchingCount( 20 ),
+ theFirstStepFlag( true ),
+ theJacobianCalculateFlag( true ),
isStiff( true )
{
const Real pow913( pow( 9.0, 1.0 / 3.0 ) );
@@ -405,7 +405,7 @@
for ( VariableVector::size_type i( 0 ); i < theSystemSize; ++i )
{
- const VariablePtr aVariable1( theVariableVector[ i ] );
+ Variable* const aVariable1( theVariableVector[ i ] );
const Real aValue( aVariable1->getValue() );
aPerturbation = sqrt( Uround * std::max( 1e-5, fabs( aValue ) ) );
@@ -416,8 +416,6 @@
for ( VariableVector::size_type j( 0 ); j < theSystemSize; ++j )
{
- const VariablePtr aVariable2( theVariableVector[ j ] );
-
theJacobian[ j ][ i ] =
- ( theW[ 4 ][ j ] - theW[ 3 ][ j ] ) / aPerturbation;
}
@@ -627,7 +625,7 @@
Real aNorm( 0. );
Real theta( fabs( theJacobianRecalculateTheta ) );
- UnsignedInteger anIterator( 0 );
+ Integer anIterator( 0 );
if ( !isInterrupted )
{
@@ -982,7 +980,7 @@
for( VariableVector::size_type c( 0 ); c < theSystemSize; ++c )
{
- VariablePtr const aVariable( theVariableVector[ c ] );
+ Variable* const aVariable( theVariableVector[ c ] );
aVariable->setValue( theTaylorSeries[ 0 ][ c ] * ( 1.0 / 5.0 )
* aStepInterval
@@ -993,7 +991,7 @@
{
for( VariableVector::size_type c( 0 ); c < theSystemSize; ++c )
{
- VariablePtr const aVariable( theVariableVector[ c ] );
+ Variable* const aVariable( theVariableVector[ c ] );
// get k1
theTaylorSeries[ 0 ][ c ] = theW[ 5 ][ c ];
@@ -1011,7 +1009,7 @@
for( VariableVector::size_type c( 0 ); c < theSystemSize; ++c )
{
- VariablePtr const aVariable( theVariableVector[ c ] );
+ Variable* const aVariable( theVariableVector[ c ] );
aVariable->setValue( ( theTaylorSeries[ 0 ][ c ] * ( 3.0 / 40.0 )
+ theW[ 0 ][ c ] * ( 9.0 / 40.0 ) )
@@ -1026,7 +1024,7 @@
for( VariableVector::size_type c( 0 ); c < theSystemSize; ++c )
{
- VariablePtr const aVariable( theVariableVector[ c ] );
+ Variable* const aVariable( theVariableVector[ c ] );
aVariable->setValue( ( theTaylorSeries[ 0 ][ c ] * ( 44.0 / 45.0 )
- theW[ 0 ][ c ] * ( 56.0 / 15.0 )
@@ -1042,7 +1040,7 @@
for( VariableVector::size_type c( 0 ); c < theSystemSize; ++c )
{
- VariablePtr const aVariable( theVariableVector[ c ] );
+ Variable* const aVariable( theVariableVector[ c ] );
aVariable->setValue( ( theTaylorSeries[ 0 ][ c ] * ( 19372.0 / 6561.0 )
- theW[ 0 ][ c ] * ( 25360.0 / 2187.0 )
@@ -1059,7 +1057,7 @@
for( VariableVector::size_type c( 0 ); c < theSystemSize; ++c )
{
- VariablePtr const aVariable( theVariableVector[ c ] );
+ Variable* const aVariable( theVariableVector[ c ] );
// temporarily set Y^6
theTaylorSeries[ 1 ][ c ] = theTaylorSeries[ 0 ][ c ] * ( 9017.0 / 3168.0 )
@@ -1085,7 +1083,7 @@
for ( VariableVector::size_type c( 0 ); c < theSystemSize; ++c )
{
- VariablePtr const aVariable( theVariableVector[ c ] );
+ Variable* const aVariable( theVariableVector[ c ] );
theTaylorSeries[ 2 ][ c ] =
theTaylorSeries[ 0 ][ c ] * ( 35.0 / 384.0 )
@@ -1114,8 +1112,6 @@
for( VariableVector::size_type c( 0 ); c < theSystemSize; ++c )
{
- VariablePtr const aVariable( theVariableVector[ c ] );
-
// calculate error
const Real anEstimatedError(
( theTaylorSeries[ 0 ][ c ] * ( 71.0 / 57600.0 )
Modified: ecell3/trunk/ecell/dm/PythonFluxProcess.cpp
===================================================================
--- ecell3/trunk/ecell/dm/PythonFluxProcess.cpp 2010-04-07 05:34:30 UTC (rev 3833)
+++ ecell3/trunk/ecell/dm/PythonFluxProcess.cpp 2010-04-13 09:24:40 UTC (rev 3834)
@@ -77,22 +77,22 @@
}
virtual void defaultSetProperty( libecs::String const& aPropertyName,
- libecs::PolymorphCref aValue )
+ libecs::Polymorph const& aValue )
{
return _LIBECS_MIXIN_CLASS_::defaultSetProperty( aPropertyName, aValue );
}
- virtual const libecs::Polymorph defaultGetProperty( libecs::String const& aPropertyName ) const
+ virtual libecs::Polymorph defaultGetProperty( libecs::String const& aPropertyName ) const
{
return _LIBECS_MIXIN_CLASS_::defaultGetProperty( aPropertyName );
}
- virtual const libecs::StringVector defaultGetPropertyList() const
+ virtual std::vector< libecs::String > defaultGetPropertyList() const
{
return _LIBECS_MIXIN_CLASS_::defaultGetPropertyList();
}
- virtual const libecs::PropertyAttributes
+ virtual libecs::PropertyAttributes
defaultGetPropertyAttributes( libecs::String const& aPropertyName ) const
{
return _LIBECS_MIXIN_CLASS_...
[truncated message content] |
|
From: <mor...@us...> - 2010-04-07 05:34:37
|
Revision: 3833
http://ecell.svn.sourceforge.net/ecell/?rev=3833&view=rev
Author: moriyoshi
Date: 2010-04-07 05:34:30 +0000 (Wed, 07 Apr 2010)
Log Message:
-----------
Remove unnecessary code.
Modified Paths:
--------------
ecell3/trunk/ecell/frontend/session-monitor/ecell/ui/osogo/opengui.py
Modified: ecell3/trunk/ecell/frontend/session-monitor/ecell/ui/osogo/opengui.py
===================================================================
--- ecell3/trunk/ecell/frontend/session-monitor/ecell/ui/osogo/opengui.py 2010-04-02 09:47:14 UTC (rev 3832)
+++ ecell3/trunk/ecell/frontend/session-monitor/ecell/ui/osogo/opengui.py 2010-04-07 05:34:30 UTC (rev 3833)
@@ -124,8 +124,6 @@
# creates an instance of GtkSession and
# creates MainWindow instance
# -------------------------------------
- aSimulator = ecell.ecs.Simulator()
- aSimulator.setDMSearchPath( aSimulator.DM_SEARCH_PATH_SEPARATOR.join( config.dm_path ) )
aSession = GtkSessionMonitor()
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mor...@us...> - 2010-04-02 09:47:21
|
Revision: 3832
http://ecell.svn.sourceforge.net/ecell/?rev=3832&view=rev
Author: moriyoshi
Date: 2010-04-02 09:47:14 +0000 (Fri, 02 Apr 2010)
Log Message:
-----------
* aNorm must be initialized before passing it to std::max()
Modified Paths:
--------------
ecell3/trunk/ecell/dm/ODEStepper.cpp
Modified: ecell3/trunk/ecell/dm/ODEStepper.cpp
===================================================================
--- ecell3/trunk/ecell/dm/ODEStepper.cpp 2010-04-02 07:46:55 UTC (rev 3831)
+++ ecell3/trunk/ecell/dm/ODEStepper.cpp 2010-04-02 09:47:14 UTC (rev 3832)
@@ -624,7 +624,7 @@
std::pair< bool, Real > ODEStepper::calculateRadauIIA( Real const aStepInterval, Real const aPreviousStepInterval )
{
Real aNewStepInterval;
- Real aNorm;
+ Real aNorm( 0. );
Real theta( fabs( theJacobianRecalculateTheta ) );
UnsignedInteger anIterator( 0 );
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mor...@us...> - 2010-04-02 07:47:01
|
Revision: 3831
http://ecell.svn.sourceforge.net/ecell/?rev=3831&view=rev
Author: moriyoshi
Date: 2010-04-02 07:46:55 +0000 (Fri, 02 Apr 2010)
Log Message:
-----------
* Prevent unnecessary copy generation of VariableReference
Modified Paths:
--------------
ecell3/trunk/ecell/dm/MassActionFluxProcess.cpp
Modified: ecell3/trunk/ecell/dm/MassActionFluxProcess.cpp
===================================================================
--- ecell3/trunk/ecell/dm/MassActionFluxProcess.cpp 2010-04-02 07:41:58 UTC (rev 3830)
+++ ecell3/trunk/ecell/dm/MassActionFluxProcess.cpp 2010-04-02 07:46:55 UTC (rev 3831)
@@ -70,7 +70,7 @@
theVariableReferenceVector.begin() );
s != theZeroVariableReferenceIterator; ++s )
{
- VariableReference aVariableReference( *s );
+ VariableReference const& aVariableReference( *s );
Integer aCoefficient( aVariableReference.getCoefficient() );
do
{
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mor...@us...> - 2010-04-02 07:42:04
|
Revision: 3830
http://ecell.svn.sourceforge.net/ecell/?rev=3830&view=rev
Author: moriyoshi
Date: 2010-04-02 07:41:58 +0000 (Fri, 02 Apr 2010)
Log Message:
-----------
* rule files for lucid
Added Paths:
-----------
ecell-build/trunk/pkg/deb/ubuntu.lucid/
ecell-build/trunk/pkg/deb/ubuntu.lucid/changelog
Removed Paths:
-------------
ecell-build/trunk/pkg/deb/ubuntu.lucid/changelog
Property changes on: ecell-build/trunk/pkg/deb/ubuntu.lucid
___________________________________________________________________
Added: svn:mergeinfo
+
Deleted: ecell-build/trunk/pkg/deb/ubuntu.lucid/changelog
===================================================================
--- ecell-build/trunk/pkg/deb/ubuntu.karmic/changelog 2010-02-11 04:19:44 UTC (rev 3821)
+++ ecell-build/trunk/pkg/deb/ubuntu.lucid/changelog 2010-04-02 07:41:58 UTC (rev 3830)
@@ -1,48 +0,0 @@
-ecell (3.2.0p1-1) karmic; urgency=low
-
- * Upstream update.
-
- -- Moriyoshi Koizumi <mo...@sf...> Fri, 5 Feb 2009 17:15:42 +0900
-
-ecell (3.1.107-1) jaunty; urgency=low
-
- * Upstream update.
-
- -- Moriyoshi Koizumi <mo...@sf...> Wed, 24 Jun 2008 13:24:12 +0900
-
-ecell (3.1.106-3) jaunty; urgency=low
-
- * Reflect versioning scheme changes of libsbml packages.
-
- -- Moriyoshi Koizumi <mo...@sf...> Wed, 18 Jun 2008 18:24:12 +0900
-
-ecell (3.1.106-2) jaunty; urgency=low
-
- * Fix dependencies between packages.
-
- -- Moriyoshi Koizumi <mo...@sf...> Tue, 05 Feb 2008 17:12:24 +0900
-
-ecell (3.1.106-1) jaunty; urgency=low
-
- * Upstream update.
-
- -- Moriyoshi Koizumi <mo...@sf...> Mon, 04 Feb 2008 17:33:57 +0900
-
-ecell (3.1.106-0rc2-2) jaunty; urgency=low
-
- * Fix ecell3.doc-base to specify users-manual instead of README.
-
- -- Moriyoshi Koizumi <mo...@sf...> Tue, 25 Dec 2007 19:59:02 +0900
-
-ecell (3.1.106-0rc2-1) jaunty; urgency=low
-
- * Upstream update.
-
- -- Moriyoshi Koizumi <mo...@sf...> Fri, 21 Dec 2007 02:57:00 +0900
-
-ecell (3.1.106-0rc1-1) unstable; urgency=low
-
- * Initial release
-
- -- Moriyoshi Koizumi <mo...@sf...> Sat, 15 Dec 2007 07:44:09 +0900
-
Copied: ecell-build/trunk/pkg/deb/ubuntu.lucid/changelog (from rev 3829, ecell-build/trunk/pkg/deb/ubuntu.karmic/changelog)
===================================================================
--- ecell-build/trunk/pkg/deb/ubuntu.lucid/changelog (rev 0)
+++ ecell-build/trunk/pkg/deb/ubuntu.lucid/changelog 2010-04-02 07:41:58 UTC (rev 3830)
@@ -0,0 +1,54 @@
+ecell (3.2.0p2-1) lucid; urgency=low
+
+ * Upstream update.
+
+ -- Moriyoshi Koizumi <mo...@sf...> Fri, 2 Apr 2010 15:53:42 +0900
+
+ecell (3.2.0p1-1) lucid; urgency=low
+
+ * Upstream update.
+
+ -- Moriyoshi Koizumi <mo...@sf...> Fri, 5 Feb 2010 17:15:42 +0900
+
+ecell (3.1.107-1) jaunty; urgency=low
+
+ * Upstream update.
+
+ -- Moriyoshi Koizumi <mo...@sf...> Wed, 24 Jun 2008 13:24:12 +0900
+
+ecell (3.1.106-3) jaunty; urgency=low
+
+ * Reflect versioning scheme changes of libsbml packages.
+
+ -- Moriyoshi Koizumi <mo...@sf...> Wed, 18 Jun 2008 18:24:12 +0900
+
+ecell (3.1.106-2) jaunty; urgency=low
+
+ * Fix dependencies between packages.
+
+ -- Moriyoshi Koizumi <mo...@sf...> Tue, 05 Feb 2008 17:12:24 +0900
+
+ecell (3.1.106-1) jaunty; urgency=low
+
+ * Upstream update.
+
+ -- Moriyoshi Koizumi <mo...@sf...> Mon, 04 Feb 2008 17:33:57 +0900
+
+ecell (3.1.106-0rc2-2) jaunty; urgency=low
+
+ * Fix ecell3.doc-base to specify users-manual instead of README.
+
+ -- Moriyoshi Koizumi <mo...@sf...> Tue, 25 Dec 2007 19:59:02 +0900
+
+ecell (3.1.106-0rc2-1) jaunty; urgency=low
+
+ * Upstream update.
+
+ -- Moriyoshi Koizumi <mo...@sf...> Fri, 21 Dec 2007 02:57:00 +0900
+
+ecell (3.1.106-0rc1-1) unstable; urgency=low
+
+ * Initial release
+
+ -- Moriyoshi Koizumi <mo...@sf...> Sat, 15 Dec 2007 07:44:09 +0900
+
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|
|
From: <mor...@us...> - 2010-04-02 07:14:28
|
Revision: 3829
http://ecell.svn.sourceforge.net/ecell/?rev=3829&view=rev
Author: moriyoshi
Date: 2010-04-02 07:14:22 +0000 (Fri, 02 Apr 2010)
Log Message:
-----------
* Update.
Modified Paths:
--------------
ecell-build/trunk/pkg/deb/debian.lenny/changelog
ecell-build/trunk/pkg/deb/ubuntu.jaunty/changelog
ecell-build/trunk/pkg/deb/ubuntu.karmic/changelog
Modified: ecell-build/trunk/pkg/deb/debian.lenny/changelog
===================================================================
--- ecell-build/trunk/pkg/deb/debian.lenny/changelog 2010-04-02 06:48:30 UTC (rev 3828)
+++ ecell-build/trunk/pkg/deb/debian.lenny/changelog 2010-04-02 07:14:22 UTC (rev 3829)
@@ -1,3 +1,9 @@
+ecell (3.2.0p2-1) lenny; urgency=low
+
+ * Upstream update.
+
+ -- Moriyoshi Koizumi <mo...@sf...> Fri, 2 Apr 2010 15:53:42 +0900
+
ecell (3.2.0p1-1) lenny; urgency=low
* Upstream update.
@@ -2,3 +8,3 @@
- -- Moriyoshi Koizumi <mo...@sf...> Fri, 5 Feb 2009 17:15:42 +0900
+ -- Moriyoshi Koizumi <mo...@sf...> Fri, 5 Feb 2010 17:15:42 +0900
Modified: ecell-build/trunk/pkg/deb/ubuntu.jaunty/changelog
===================================================================
--- ecell-build/trunk/pkg/deb/ubuntu.jaunty/changelog 2010-04-02 06:48:30 UTC (rev 3828)
+++ ecell-build/trunk/pkg/deb/ubuntu.jaunty/changelog 2010-04-02 07:14:22 UTC (rev 3829)
@@ -1,3 +1,9 @@
+ecell (3.2.0p2-1) jaunty; urgency=low
+
+ * Upstream update.
+
+ -- Moriyoshi Koizumi <mo...@sf...> Fri, 2 Apr 2010 15:53:42 +0900
+
ecell (3.2.0p1-1) jaunty; urgency=low
* Upstream update.
@@ -2,3 +8,3 @@
- -- Moriyoshi Koizumi <mo...@sf...> Fri, 5 Feb 2009 17:15:42 +0900
+ -- Moriyoshi Koizumi <mo...@sf...> Fri, 5 Feb 2010 17:15:42 +0900
Modified: ecell-build/trunk/pkg/deb/ubuntu.karmic/changelog
===================================================================
--- ecell-build/trunk/pkg/deb/ubuntu.karmic/changelog 2010-04-02 06:48:30 UTC (rev 3828)
+++ ecell-build/trunk/pkg/deb/ubuntu.karmic/changelog 2010-04-02 07:14:22 UTC (rev 3829)
@@ -1,3 +1,9 @@
+ecell (3.2.0p2-1) karmic; urgency=low
+
+ * Upstream update.
+
+ -- Moriyoshi Koizumi <mo...@sf...> Fri, 2 Apr 2010 15:53:42 +0900
+
ecell (3.2.0p1-1) karmic; urgency=low
* Upstream update.
@@ -2,3 +8,3 @@
- -- Moriyoshi Koizumi <mo...@sf...> Fri, 5 Feb 2009 17:15:42 +0900
+ -- Moriyoshi Koizumi <mo...@sf...> Fri, 5 Feb 2010 17:15:42 +0900
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|
|
From: <mor...@us...> - 2010-04-02 06:48:37
|
Revision: 3828
http://ecell.svn.sourceforge.net/ecell/?rev=3828&view=rev
Author: moriyoshi
Date: 2010-04-02 06:48:30 +0000 (Fri, 02 Apr 2010)
Log Message:
-----------
Shipping patchlevel 2
Modified Paths:
--------------
ecell3/trunk/NEWS
ecell3/trunk/ecell_version.sh
Modified: ecell3/trunk/NEWS
===================================================================
--- ecell3/trunk/NEWS 2010-03-31 10:27:39 UTC (rev 3827)
+++ ecell3/trunk/NEWS 2010-04-02 06:48:30 UTC (rev 3828)
@@ -1,3 +1,9 @@
+ecell-3.2.0p2: 2-Apr-2010
+ * Fixed DataPointVector's python wrapper to have "shape" property that returns
+ the shape of the array. That is required by TableIO module.
+ (notified by Erin Rachael Shellman. Thanks.)
+
+
ecell-3.2.0p1: 9-Feb-2010
* Fixed the build system so that resource files for the GUI tools are
Modified: ecell3/trunk/ecell_version.sh
===================================================================
--- ecell3/trunk/ecell_version.sh 2010-03-31 10:27:39 UTC (rev 3827)
+++ ecell3/trunk/ecell_version.sh 2010-04-02 06:48:30 UTC (rev 3828)
@@ -1,5 +1,5 @@
ECELL_MAJOR_VERSION=3
ECELL_MINOR_VERSION=2
ECELL_MICRO_VERSION=0
-ECELL_PACKAGE_REVISION=p1
+ECELL_PACKAGE_REVISION=p2
ECELL_VERSION_NUMBER=${ECELL_MAJOR_VERSION}.${ECELL_MINOR_VERSION}.${ECELL_MICRO_VERSION}${ECELL_PACKAGE_REVISION}
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|
|
From: <mor...@us...> - 2010-03-31 10:27:45
|
Revision: 3827
http://ecell.svn.sourceforge.net/ecell/?rev=3827&view=rev
Author: moriyoshi
Date: 2010-03-31 10:27:39 +0000 (Wed, 31 Mar 2010)
Log Message:
-----------
* Add "shape" property to DataPointVector class for the sake of compatibility.
(required by TableIO).
Modified Paths:
--------------
ecell3/trunk/ecell/pyecell/ecell/_ecs.cpp
Modified: ecell3/trunk/ecell/pyecell/ecell/_ecs.cpp
===================================================================
--- ecell3/trunk/ecell/pyecell/ecell/_ecs.cpp 2010-02-17 17:39:43 UTC (rev 3826)
+++ ecell3/trunk/ecell/pyecell/ecell/_ecs.cpp 2010-03-31 10:27:39 UTC (rev 3827)
@@ -663,6 +663,14 @@
return new DataPointVectorWrapper( aVector );
}
+ static PyObject* __get__shape( DataPointVectorWrapper* self )
+ {
+ PyObject* retval( PyTuple_New( 2 ) );
+ PyTuple_SET_ITEM( retval, 0, PyLong_FromUnsignedLong( self->theVector->getSize() ) );
+ PyTuple_SET_ITEM( retval, 1, PyLong_FromUnsignedLong( theNumOfElemsPerEntry ) );
+ return retval;
+ }
+
static void __dealloc__( DataPointVectorWrapper* self )
{
delete self;
@@ -915,6 +923,7 @@
template< typename Tdp_ >
PyGetSetDef DataPointVectorWrapper< Tdp_ >::__getset__[] = {
{ const_cast< char* >( "__array_struct__" ), (getter)&DataPointVectorWrapper::__get___array__struct, NULL },
+ { const_cast< char* >( "shape" ), (getter)&DataPointVectorWrapper::__get__shape, NULL },
{ NULL }
};
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|
From: <mor...@us...> - 2010-02-17 17:39:49
|
Revision: 3826
http://ecell.svn.sourceforge.net/ecell/?rev=3826&view=rev
Author: moriyoshi
Date: 2010-02-17 17:39:43 +0000 (Wed, 17 Feb 2010)
Log Message:
-----------
* Merge from trunk.
Modified Paths:
--------------
ecell3/branches/ecell-3.1/build/msvc/buildhelper.js
Property Changed:
----------------
ecell3/branches/ecell-3.1/
Property changes on: ecell3/branches/ecell-3.1
___________________________________________________________________
Modified: svn:mergeinfo
- /ecell3/branches/ecell-3.1:3677,3694
/ecell3/branches/ecell-3.2:3372,3467,3481,3562,3568,3572,3585,3592,3598-3599,3608,3615,3619-3620,3625,3688-3692,3697,3699-3700,3702,3704,3706,3708-3710,3713,3715,3721,3726,3734-3735,3748,3750,3752-3754,3758,3760,3762,3781,3789-3791,3802,3804,3807-3809
+ /ecell3/branches/ecell-3.1:3677,3694
/ecell3/branches/ecell-3.2:3372,3467,3481,3562,3568,3572,3585,3592,3598-3599,3608,3615,3619-3620,3625,3688-3692,3697,3699-3700,3702,3704,3706,3708-3710,3713,3715,3721,3726,3734-3735,3748,3750,3752-3754,3758,3760,3762,3781,3789-3791,3802,3804,3807-3809
/ecell3/trunk:3825
Modified: ecell3/branches/ecell-3.1/build/msvc/buildhelper.js
===================================================================
--- ecell3/branches/ecell-3.1/build/msvc/buildhelper.js 2010-02-17 17:32:29 UTC (rev 3825)
+++ ecell3/branches/ecell-3.1/build/msvc/buildhelper.js 2010-02-17 17:39:43 UTC (rev 3826)
@@ -107,7 +107,7 @@
WScript.Echo("Creating launcher script " + script_file_name);
var scr = '';
scr += '@ECHO OFF\n';
- scr += 'SET PWD=%~dp0\n';
+ scr += 'SET PWD=%~dps0\n';
scr += 'IF "%ECELL_HOME%" == "" SET ECELL_HOME=%PWD%\\..\n';
scr += 'SET PYTHONPATH=%PYTHONPATH%;%ECELL_HOME%\\lib\\site-packages\n';
scr += 'SET PATH=%PWD%;%PATH%\n';
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|
From: <mor...@us...> - 2010-02-17 17:32:35
|
Revision: 3825
http://ecell.svn.sourceforge.net/ecell/?rev=3825&view=rev
Author: moriyoshi
Date: 2010-02-17 17:32:29 +0000 (Wed, 17 Feb 2010)
Log Message:
-----------
* Take account of pathnames that contain spaces
Modified Paths:
--------------
ecell3/trunk/build/msvc/buildhelper.js
Modified: ecell3/trunk/build/msvc/buildhelper.js
===================================================================
--- ecell3/trunk/build/msvc/buildhelper.js 2010-02-12 04:40:14 UTC (rev 3824)
+++ ecell3/trunk/build/msvc/buildhelper.js 2010-02-17 17:32:29 UTC (rev 3825)
@@ -108,7 +108,7 @@
var scr = '';
scr += '@ECHO OFF\n';
scr += 'SETLOCAL\n';
- scr += 'SET PWD=%~dp0\n';
+ scr += 'SET PWD=%~dps0\n';
scr += 'IF "%ECELL_HOME%" == "" SET ECELL_HOME=%PWD%\\..\n';
scr += 'SET PYTHONPATH=%PYTHONPATH%;%ECELL_HOME%\\lib\\site-packages\n';
scr += 'SET PATH=%PWD%;%PATH%\n';
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From: <ka...@us...> - 2010-02-12 04:40:22
|
Revision: 3824
http://ecell.svn.sourceforge.net/ecell/?rev=3824&view=rev
Author: kaizu
Date: 2010-02-12 04:40:14 +0000 (Fri, 12 Feb 2010)
Log Message:
-----------
Adding the logistic map model
Modified Paths:
--------------
ecell3/branches/kaizu/ecell-3.1/doc/samples/Makefile.am
Added Paths:
-----------
ecell3/branches/kaizu/ecell-3.1/doc/samples/logistic/
ecell3/branches/kaizu/ecell-3.1/doc/samples/logistic/logistic.em
Modified: ecell3/branches/kaizu/ecell-3.1/doc/samples/Makefile.am
===================================================================
--- ecell3/branches/kaizu/ecell-3.1/doc/samples/Makefile.am 2010-02-11 09:45:52 UTC (rev 3823)
+++ ecell3/branches/kaizu/ecell-3.1/doc/samples/Makefile.am 2010-02-12 04:40:14 UTC (rev 3824)
@@ -15,6 +15,7 @@
session_manager \
boolean \
simple \
+ logistic \
tauleap
EXTRA_DIST = $(SAMPLES)
Added: ecell3/branches/kaizu/ecell-3.1/doc/samples/logistic/logistic.em
===================================================================
--- ecell3/branches/kaizu/ecell-3.1/doc/samples/logistic/logistic.em (rev 0)
+++ ecell3/branches/kaizu/ecell-3.1/doc/samples/logistic/logistic.em 2010-02-12 04:40:14 UTC (rev 3824)
@@ -0,0 +1,19 @@
+Stepper DiscreteTimeStepper( DTS01 )
+{
+ StepInterval 1.0;
+}
+
+System System( / )
+{
+ StepperID DTS01;
+
+ Variable Variable( X ) { Value 0.5; }
+# Variable Variable( X ) { Value 0.0; }
+
+ Process ExpressionAssignmentProcess( R )
+ {
+ a 0.0;
+ Expression "a * X.Value * (1.0 - X.Value)";
+ VariableReferenceList [X :.:X +1];
+ }
+}
Property changes on: ecell3/branches/kaizu/ecell-3.1/doc/samples/logistic/logistic.em
___________________________________________________________________
Added: svn:mime-type
+ text/plain
Added: svn:eol-style
+ native
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