bind fast invariant expressions for fast systems.

.gitignore

@@ -5,3 +5,4 @@
 /.pydevproject
 /.project
 /.classpath
+/vcell_debug_server.properties

localsolvers/linux32/.gitignore

@@ -0,0 +1,6 @@
+/FiniteVolume
+/NFsim
+/SundialsSolverStandalone
+/VCellStoch
+/libgfortran.so.3
+/smoldyn

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

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

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

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());

vcell-core/src/main/java/cbit/vcell/mapping/vcell_4_8/FastSystemAnalyzer.java

@@ -335,6 +335,7 @@ private void refreshSubstitutedRateExps() throws MathException, ExpressionExcept
 	Enumeration<FastInvariant> 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());

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);
 	}
 }