diff --git a/.gitignore b/.gitignore index bfc0caef00..066f639f7c 100644 --- a/.gitignore +++ b/.gitignore @@ -5,3 +5,4 @@ /.pydevproject /.project /.classpath +/vcell_debug_server.properties diff --git a/localsolvers/linux32/.gitignore b/localsolvers/linux32/.gitignore new file mode 100644 index 0000000000..2fde56b5e8 --- /dev/null +++ b/localsolvers/linux32/.gitignore @@ -0,0 +1,6 @@ +/FiniteVolume +/NFsim +/SundialsSolverStandalone +/VCellStoch +/libgfortran.so.3 +/smoldyn diff --git a/localsolvers/linux64/.gitignore b/localsolvers/linux64/.gitignore new file mode 100644 index 0000000000..1e6411bcc8 --- /dev/null +++ b/localsolvers/linux64/.gitignore @@ -0,0 +1,17 @@ +/FiniteVolume_x64 +/MovingBoundary_x64 +/NFsim_x64 +/SundialsSolverStandalone_x64 +/VCellStoch_x64 +/libactivemq-cpp.so.19 +/libapr-1.so.0 +/libgfortran.so.3 +/libhdf5.so.8 +/libhdf5_cpp.so.8 +/libquadmath.so.0 +/libzip.so +/libzip.so.3 +/libzip.so.3.0 +/smoldyn_x64 +/testzip +/ziptool diff --git a/localsolvers/mac64/.gitignore b/localsolvers/mac64/.gitignore new file mode 100644 index 0000000000..b3b6172664 --- /dev/null +++ b/localsolvers/mac64/.gitignore @@ -0,0 +1,17 @@ +/FiniteVolume_x64 +/MovingBoundary_x64 +/NFsim_x64 +/SundialsSolverStandalone_x64 +/VCellStoch_x64 +/libgcc_s.1.dylib +/libgfortran.4.dylib +/libhdf5.10.dylib +/libhdf5_cpp.14.dylib +/libquadmath.0.dylib +/libsz.2.dylib +/libzip.3.0.dylib +/libzip.3.dylib +/libzip.dylib +/smoldyn_x64 +/testzip +/ziptool diff --git a/localsolvers/win64/.gitignore b/localsolvers/win64/.gitignore new file mode 100644 index 0000000000..e85205eba2 --- /dev/null +++ b/localsolvers/win64/.gitignore @@ -0,0 +1,18 @@ +/FiniteVolume_x64.exe +/MovingBoundary_x64.exe +/NFsim_x64.exe +/SundialsSolverStandalone_x64.exe +/VCellStoch_x64.exe +/libgcc_s_seh-1.dll +/libgfortran-4.dll +/libhdf5-0.dll +/libhdf5_cpp-0.dll +/libquadmath-0.dll +/libstdc++-6.dll +/libszip.dll +/libwinpthread-1.dll +/libzip.dll +/smoldyn_x64.exe +/testzip.exe +/ziptool.exe +/zlib1.dll diff --git a/vcell-core/src/main/java/cbit/vcell/mapping/FastSystemAnalyzer.java b/vcell-core/src/main/java/cbit/vcell/mapping/FastSystemAnalyzer.java index 4252c68383..b6aa85fde2 100644 --- a/vcell-core/src/main/java/cbit/vcell/mapping/FastSystemAnalyzer.java +++ b/vcell-core/src/main/java/cbit/vcell/mapping/FastSystemAnalyzer.java @@ -337,6 +337,7 @@ private void refreshSubstitutedRateExps() throws MathException, ExpressionExcept while (enum_fi.hasMoreElements()) { FastInvariant fi = enum_fi.nextElement(); Domain domain = new Domain(fastSystem.getSubDomain()); + fi.getFunction().bindExpression(this); PseudoConstant pc = new PseudoConstant(getAvailablePseudoConstantName(),fi.getFunction(),domain); pseudoConstantList.addElement(pc); //System.out.println("FastSystem.refreshSubstitutedRateExps() __C"+i+" = "+fi.getFunction()); diff --git a/vcell-core/src/main/java/cbit/vcell/mapping/vcell_4_8/FastSystemAnalyzer.java b/vcell-core/src/main/java/cbit/vcell/mapping/vcell_4_8/FastSystemAnalyzer.java index 4d9e58dd69..99ec217c19 100644 --- a/vcell-core/src/main/java/cbit/vcell/mapping/vcell_4_8/FastSystemAnalyzer.java +++ b/vcell-core/src/main/java/cbit/vcell/mapping/vcell_4_8/FastSystemAnalyzer.java @@ -335,6 +335,7 @@ private void refreshSubstitutedRateExps() throws MathException, ExpressionExcept Enumeration enum_fi = fastSystem.getFastInvariants(); while (enum_fi.hasMoreElements()) { FastInvariant fi = enum_fi.nextElement(); + fi.getFunction().bindExpression(this); PseudoConstant pc = new PseudoConstant(getAvailablePseudoConstantName(),fi.getFunction(),MathMapping_4_8.nullDomain); pseudoConstantList.addElement(pc); //System.out.println("FastSystem.refreshSubstitutedRateExps() __C"+i+" = "+fi.getFunction()); diff --git a/vcell-core/src/main/java/cbit/vcell/solver/ode/DefaultODESolver.java b/vcell-core/src/main/java/cbit/vcell/solver/ode/DefaultODESolver.java index 7a5b0a93bf..ae678b6264 100644 --- a/vcell-core/src/main/java/cbit/vcell/solver/ode/DefaultODESolver.java +++ b/vcell-core/src/main/java/cbit/vcell/solver/ode/DefaultODESolver.java @@ -576,10 +576,8 @@ protected void integrate() throws SolverException, UserStopException, IOExceptio int keepEvery = ((DefaultOutputTimeSpec)taskDescription.getOutputTimeSpec()).getKeepEvery(); if ((iteration % keepEvery) != 0) updateResultSet(); } - } catch (ExpressionException expressionException) { - throw new SolverException(expressionException.getMessage()); - } catch (MathException mathException) { - throw new SolverException(mathException.getMessage()); + } catch (ExpressionException | MathException e) { + throw new SolverException("Solver failed: "+e.getMessage(),e); } }