Merge pull request #1176 from virtualcell/dan-ss-volume-size-param

We use the GeometricRegion to recover the correct size of the ROLE_Size parameter

vcell-core/src/main/java/cbit/vcell/mapping/LangevinMathMapping.java

@@ -14,6 +14,7 @@
 import java.beans.PropertyVetoException;
 import java.util.*;
 
+import cbit.vcell.geometry.surface.GeometricRegion;
 import org.vcell.model.rbm.ComponentStateDefinition;
 import org.vcell.model.rbm.ComponentStatePattern;
 import org.vcell.model.rbm.MolecularComponent;
@@ -338,15 +339,21 @@ protected void refreshMathDescription() throws MappingException, MatrixException
 		for (int i=0;i<structureMappings.length;i++){
 			StructureMapping sm = structureMappings[i];
 			StructureMapping.StructureMappingParameter parm = sm.getParameterFromRole(StructureMapping.ROLE_Size);
-			if(parm.getExpression() != null)
+			if(parm.getExpression() != null)	// this is the default 50,000 um3 which don't make any sense for Langevin; we don't use it!!!
 			{
 				try {
-					double value = parm.getExpression().evaluateConstant();
-					varHash.addVariable(new Constant(getMathSymbol(parm,sm.getGeometryClass()),new Expression(value)));
-				}catch (ExpressionException e){
-					//varHash.addVariable(new Function(getMathSymbol0(parm,sm),getIdentifierSubstitutions(parm.getExpression(),parm.getUnitDefinition(),sm)));
+					// instead, we use the size of the geometric region
+					GeometricRegion[] grArray = simContext.getGeometry().getGeometrySurfaceDescription().getGeometricRegions(sm.getGeometryClass());
+					if(grArray.length != 1) {
+						throw new RuntimeException("Expecting only one region for GeometryClass '" + sm.getGeometryClass().getName() + "', found: " + grArray.length);
+					}
+					GeometricRegion gr = grArray[0];
+					double value2 = gr.getSize();
+					varHash.addVariable(new Constant(getMathSymbol(parm, sm.getGeometryClass()), new Expression(value2)));
+
+				}catch (Exception e) {
 					e.printStackTrace(System.out);
-					throw new MappingException("Size of structure:"+sm.getNameScope().getName()+" cannot be evaluated as constant.");
+					throw new MappingException("Size of structure:"+sm.getNameScope().getName()+" cannot be evaluated.");
 				}
 			}
 		}