use of cbit.vcell.math.Action in project vcell by virtualcell.
the class StochMathMapping method addJumpProcesses.
private void addJumpProcesses(VariableHash varHash, GeometryClass geometryClass, SubDomain subDomain) throws ExpressionException, ModelException, MappingException, MathException {
// set up jump processes
// get all the reactions from simulation context
// ReactionSpec[] reactionSpecs = simContext.getReactionContext().getReactionSpecs();---need to take a look here!
ModelUnitSystem modelUnitSystem = getSimulationContext().getModel().getUnitSystem();
ReactionSpec[] reactionSpecs = getSimulationContext().getReactionContext().getReactionSpecs();
for (ReactionSpec reactionSpec : reactionSpecs) {
if (reactionSpec.isExcluded()) {
continue;
}
// get the reaction
ReactionStep reactionStep = reactionSpec.getReactionStep();
Kinetics kinetics = reactionStep.getKinetics();
// probability parameter from modelUnitSystem
VCUnitDefinition probabilityParamUnit = modelUnitSystem.getStochasticSubstanceUnit().divideBy(modelUnitSystem.getTimeUnit());
// Different ways to deal with simple reactions and flux reactions
if (// simple reactions
reactionStep instanceof SimpleReaction) {
// check the reaction rate law to see if we need to decompose a reaction(reversible) into two jump processes.
// rate constants are important in calculating the probability rate.
// for Mass Action, we use KForward and KReverse,
// for General Kinetics we parse reaction rate J to see if it is in Mass Action form.
Expression forwardRate = null;
Expression reverseRate = null;
if (kinetics.getKineticsDescription().equals(KineticsDescription.MassAction) || kinetics.getKineticsDescription().equals(KineticsDescription.General)) {
Expression rateExp = new Expression(kinetics.getKineticsParameterFromRole(Kinetics.ROLE_ReactionRate), reactionStep.getNameScope());
Parameter forwardRateParameter = null;
Parameter reverseRateParameter = null;
if (kinetics.getKineticsDescription().equals(KineticsDescription.MassAction)) {
forwardRateParameter = kinetics.getKineticsParameterFromRole(Kinetics.ROLE_KForward);
reverseRateParameter = kinetics.getKineticsParameterFromRole(Kinetics.ROLE_KReverse);
}
MassActionSolver.MassActionFunction maFunc = MassActionSolver.solveMassAction(forwardRateParameter, reverseRateParameter, rateExp, reactionStep);
if (maFunc.getForwardRate() == null && maFunc.getReverseRate() == null) {
throw new MappingException("Cannot generate stochastic math mapping for the reaction:" + reactionStep.getName() + "\nLooking for the rate function according to the form of k1*Reactant1^Stoir1*Reactant2^Stoir2...-k2*Product1^Stoip1*Product2^Stoip2.");
} else {
if (maFunc.getForwardRate() != null) {
forwardRate = maFunc.getForwardRate();
}
if (maFunc.getReverseRate() != null) {
reverseRate = maFunc.getReverseRate();
}
}
} else // if it's macro/microscopic kinetics, we'll have them set up as reactions with only forward rate.
if (kinetics.getKineticsDescription().equals(KineticsDescription.Macroscopic_irreversible) || kinetics.getKineticsDescription().equals(KineticsDescription.Microscopic_irreversible)) {
Expression Kon = getIdentifierSubstitutions(new Expression(reactionStep.getKinetics().getKineticsParameterFromRole(Kinetics.ROLE_KOn), getNameScope()), reactionStep.getKinetics().getKineticsParameterFromRole(Kinetics.ROLE_Binding_Radius).getUnitDefinition(), geometryClass);
if (Kon != null) {
Expression KonCopy = new Expression(Kon);
try {
MassActionSolver.substituteParameters(KonCopy, true).evaluateConstant();
forwardRate = new Expression(Kon);
} catch (ExpressionException e) {
throw new MathException(VCellErrorMessages.getMassActionSolverMessage(reactionStep.getName(), "Problem with Kon parameter in " + reactionStep.getName() + ": '" + KonCopy.infix() + "', " + e.getMessage()));
}
} else {
throw new MathException(VCellErrorMessages.getMassActionSolverMessage(reactionStep.getName(), "Kon parameter of " + reactionStep.getName() + " is null."));
}
}
boolean isForwardRatePresent = false;
boolean isReverseRatePresent = false;
if (forwardRate != null) {
isForwardRatePresent = true;
}
if (reverseRate != null) {
isReverseRatePresent = true;
}
// we process it as forward reaction
if ((isForwardRatePresent)) /*|| ((forwardRate == null) && (reverseRate == null))*/
{
// get jump process name
String jpName = TokenMangler.mangleToSName(reactionStep.getName());
// get probability
Expression exp = null;
// reactions are of mass action form
exp = getProbabilityRate(reactionStep, forwardRate, true);
ProbabilityParameter probParm = null;
try {
probParm = addProbabilityParameter(PARAMETER_PROBABILITYRATE_PREFIX + jpName, exp, PARAMETER_ROLE_P, probabilityParamUnit, reactionStep);
} catch (PropertyVetoException pve) {
pve.printStackTrace();
throw new MappingException(pve.getMessage());
}
// add probability to function or constant
varHash.addVariable(newFunctionOrConstant(getMathSymbol(probParm, geometryClass), getIdentifierSubstitutions(exp, probabilityParamUnit, geometryClass), geometryClass));
JumpProcess jp = new JumpProcess(jpName, new Expression(getMathSymbol(probParm, geometryClass)));
// actions
ReactionParticipant[] reacPart = reactionStep.getReactionParticipants();
for (int j = 0; j < reacPart.length; j++) {
Action action = null;
SpeciesCountParameter spCountParam = getSpeciesCountParameter(reacPart[j].getSpeciesContext());
if (reacPart[j] instanceof Reactant) {
// check if the reactant is a constant. If the species is a constant, there will be no action taken on this species
if (// not a constant
!simContext.getReactionContext().getSpeciesContextSpec(reacPart[j].getSpeciesContext()).isConstant()) {
int stoi = ((Reactant) reacPart[j]).getStoichiometry();
action = Action.createIncrementAction(varHash.getVariable(getMathSymbol(spCountParam, geometryClass)), new Expression(-stoi));
jp.addAction(action);
}
} else if (reacPart[j] instanceof Product) {
// check if the product is a constant. If the product is a constant, there will be no action taken on this species
if (// not a constant
!simContext.getReactionContext().getSpeciesContextSpec(reacPart[j].getSpeciesContext()).isConstant()) {
int stoi = ((Product) reacPart[j]).getStoichiometry();
action = Action.createIncrementAction(varHash.getVariable(getMathSymbol(spCountParam, geometryClass)), new Expression(stoi));
jp.addAction(action);
}
}
}
// add jump process to compartment subDomain
subDomain.addJumpProcess(jp);
}
if (// one more jump process for a reversible reaction
isReverseRatePresent) {
// get jump process name
String jpName = TokenMangler.mangleToSName(reactionStep.getName()) + PARAMETER_PROBABILITY_RATE_REVERSE_SUFFIX;
Expression exp = null;
// reactions are mass actions
exp = getProbabilityRate(reactionStep, reverseRate, false);
ProbabilityParameter probRevParm = null;
try {
probRevParm = addProbabilityParameter(PARAMETER_PROBABILITYRATE_PREFIX + jpName, exp, PARAMETER_ROLE_P_reverse, probabilityParamUnit, reactionStep);
} catch (PropertyVetoException pve) {
pve.printStackTrace();
throw new MappingException(pve.getMessage());
}
// add probability to function or constant
varHash.addVariable(newFunctionOrConstant(getMathSymbol(probRevParm, geometryClass), getIdentifierSubstitutions(exp, probabilityParamUnit, geometryClass), geometryClass));
JumpProcess jp = new JumpProcess(jpName, new Expression(getMathSymbol(probRevParm, geometryClass)));
// actions
ReactionParticipant[] reacPart = reactionStep.getReactionParticipants();
for (int j = 0; j < reacPart.length; j++) {
Action action = null;
SpeciesCountParameter spCountParam = getSpeciesCountParameter(reacPart[j].getSpeciesContext());
if (reacPart[j] instanceof Reactant) {
// check if the reactant is a constant. If the species is a constant, there will be no action taken on this species
if (// not a constant
!simContext.getReactionContext().getSpeciesContextSpec(reacPart[j].getSpeciesContext()).isConstant()) {
int stoi = ((Reactant) reacPart[j]).getStoichiometry();
action = Action.createIncrementAction(varHash.getVariable(getMathSymbol(spCountParam, geometryClass)), new Expression(stoi));
jp.addAction(action);
}
} else if (reacPart[j] instanceof Product) {
// check if the product is a constant. If the product is a constant, there will be no action taken on this species
if (// not a constant
!simContext.getReactionContext().getSpeciesContextSpec(reacPart[j].getSpeciesContext()).isConstant()) {
int stoi = ((Product) reacPart[j]).getStoichiometry();
action = Action.createIncrementAction(varHash.getVariable(getMathSymbol(spCountParam, geometryClass)), new Expression(-stoi));
jp.addAction(action);
}
}
}
// add jump process to compartment subDomain
subDomain.addJumpProcess(jp);
}
// end of if(isForwardRateNonZero), if(isReverseRateNonRate)
} else if (// flux reactions
reactionStep instanceof FluxReaction) {
// we could set jump processes for general flux rate in forms of p1*Sout + p2*Sin
if (kinetics.getKineticsDescription().equals(KineticsDescription.General) || kinetics.getKineticsDescription().equals(KineticsDescription.GeneralPermeability)) {
Expression fluxRate = new Expression(kinetics.getKineticsParameterFromRole(Kinetics.ROLE_ReactionRate), reactionStep.getNameScope());
// we have to pass the math description para to flux solver, coz somehow math description in simulation context is not updated.
// forward and reverse rate parameters may be null
Parameter forwardRateParameter = null;
Parameter reverseRateParameter = null;
if (kinetics.getKineticsDescription().equals(KineticsDescription.GeneralPermeability)) {
forwardRateParameter = kinetics.getKineticsParameterFromRole(Kinetics.ROLE_Permeability);
reverseRateParameter = kinetics.getKineticsParameterFromRole(Kinetics.ROLE_Permeability);
}
MassActionSolver.MassActionFunction fluxFunc = MassActionSolver.solveMassAction(forwardRateParameter, reverseRateParameter, fluxRate, (FluxReaction) reactionStep);
// create jump process for forward flux if it exists.
Expression rsStructureSize = new Expression(reactionStep.getStructure().getStructureSize(), getNameScope());
VCUnitDefinition probRateUnit = modelUnitSystem.getStochasticSubstanceUnit().divideBy(modelUnitSystem.getAreaUnit()).divideBy(modelUnitSystem.getTimeUnit());
Expression rsRateUnitFactor = getUnitFactor(probRateUnit.divideBy(modelUnitSystem.getFluxReactionUnit()));
if (fluxFunc.getForwardRate() != null && !fluxFunc.getForwardRate().isZero()) {
Expression rate = fluxFunc.getForwardRate();
// get species expression (depend on structure, if mem: Species/mem_Size, if vol: species*KMOLE/vol_size)
if (fluxFunc.getReactants().size() != 1) {
throw new MappingException("Flux " + reactionStep.getName() + " should have only one reactant.");
}
SpeciesContext scReactant = fluxFunc.getReactants().get(0).getSpeciesContext();
Expression scConcExpr = new Expression(getSpeciesConcentrationParameter(scReactant), getNameScope());
Expression probExp = Expression.mult(rate, rsRateUnitFactor, rsStructureSize, scConcExpr);
// jump process name
// +"_reverse";
String jpName = TokenMangler.mangleToSName(reactionStep.getName());
ProbabilityParameter probParm = null;
try {
probParm = addProbabilityParameter(PARAMETER_PROBABILITYRATE_PREFIX + jpName, probExp, PARAMETER_ROLE_P, probabilityParamUnit, reactionStep);
} catch (PropertyVetoException pve) {
pve.printStackTrace();
throw new MappingException(pve.getMessage());
}
// add probability to function or constant
String ms = getMathSymbol(probParm, geometryClass);
Expression is = getIdentifierSubstitutions(probExp, probabilityParamUnit, geometryClass);
Variable nfoc = newFunctionOrConstant(ms, is, geometryClass);
varHash.addVariable(nfoc);
JumpProcess jp = new JumpProcess(jpName, new Expression(getMathSymbol(probParm, geometryClass)));
// actions
Action action = null;
SpeciesContext sc = fluxFunc.getReactants().get(0).getSpeciesContext();
if (!simContext.getReactionContext().getSpeciesContextSpec(sc).isConstant()) {
SpeciesCountParameter spCountParam = getSpeciesCountParameter(sc);
action = Action.createIncrementAction(varHash.getVariable(getMathSymbol(spCountParam, geometryClass)), new Expression(-1));
jp.addAction(action);
}
sc = fluxFunc.getProducts().get(0).getSpeciesContext();
if (!simContext.getReactionContext().getSpeciesContextSpec(sc).isConstant()) {
SpeciesCountParameter spCountParam = getSpeciesCountParameter(sc);
action = Action.createIncrementAction(varHash.getVariable(getMathSymbol(spCountParam, geometryClass)), new Expression(1));
jp.addAction(action);
}
subDomain.addJumpProcess(jp);
}
// create jump process for reverse flux if it exists.
if (fluxFunc.getReverseRate() != null && !fluxFunc.getReverseRate().isZero()) {
// jump process name
String jpName = TokenMangler.mangleToSName(reactionStep.getName()) + PARAMETER_PROBABILITY_RATE_REVERSE_SUFFIX;
Expression rate = fluxFunc.getReverseRate();
// get species expression (depend on structure, if mem: Species/mem_Size, if vol: species*KMOLE/vol_size)
if (fluxFunc.getProducts().size() != 1) {
throw new MappingException("Flux " + reactionStep.getName() + " should have only one product.");
}
SpeciesContext scProduct = fluxFunc.getProducts().get(0).getSpeciesContext();
Expression scConcExpr = new Expression(getSpeciesConcentrationParameter(scProduct), getNameScope());
Expression probExp = Expression.mult(rate, rsRateUnitFactor, rsStructureSize, scConcExpr);
ProbabilityParameter probRevParm = null;
try {
probRevParm = addProbabilityParameter(PARAMETER_PROBABILITYRATE_PREFIX + jpName, probExp, PARAMETER_ROLE_P_reverse, probabilityParamUnit, reactionStep);
} catch (PropertyVetoException pve) {
pve.printStackTrace();
throw new MappingException(pve.getMessage());
}
// add probability to function or constant
varHash.addVariable(newFunctionOrConstant(getMathSymbol(probRevParm, geometryClass), getIdentifierSubstitutions(probExp, probabilityParamUnit, geometryClass), geometryClass));
JumpProcess jp = new JumpProcess(jpName, new Expression(getMathSymbol(probRevParm, geometryClass)));
// actions
Action action = null;
SpeciesContext sc = fluxFunc.getReactants().get(0).getSpeciesContext();
if (!simContext.getReactionContext().getSpeciesContextSpec(sc).isConstant()) {
SpeciesCountParameter spCountParam = getSpeciesCountParameter(sc);
action = Action.createIncrementAction(varHash.getVariable(getMathSymbol(spCountParam, geometryClass)), new Expression(1));
jp.addAction(action);
}
sc = fluxFunc.getProducts().get(0).getSpeciesContext();
if (!simContext.getReactionContext().getSpeciesContextSpec(sc).isConstant()) {
SpeciesCountParameter spCountParam = getSpeciesCountParameter(sc);
action = Action.createIncrementAction(varHash.getVariable(getMathSymbol(spCountParam, geometryClass)), new Expression(-1));
jp.addAction(action);
}
subDomain.addJumpProcess(jp);
}
}
}
// end of if (simplereaction)...else if(fluxreaction)
}
// end of reaction step loop
}
use of cbit.vcell.math.Action in project vcell by virtualcell.
the class ParticleMathMapping method refreshMathDescription.
/**
* This method was created in VisualAge.
*/
private void refreshMathDescription() throws MappingException, MatrixException, MathException, ExpressionException, ModelException {
getSimulationContext().checkValidity();
if (getSimulationContext().getGeometry().getDimension() == 0) {
throw new MappingException("particle math mapping requires spatial geometry - dimension >= 1");
}
StructureMapping[] structureMappings = getSimulationContext().getGeometryContext().getStructureMappings();
for (int i = 0; i < structureMappings.length; i++) {
if (structureMappings[i] instanceof MembraneMapping) {
if (((MembraneMapping) structureMappings[i]).getCalculateVoltage()) {
throw new MappingException("electric potential not yet supported for particle models");
}
}
}
//
// fail if any events
//
BioEvent[] bioEvents = getSimulationContext().getBioEvents();
if (bioEvents != null && bioEvents.length > 0) {
throw new MappingException("events not yet supported for particle-based models");
}
//
// gather only those reactionSteps that are not "excluded"
//
ReactionSpec[] reactionSpecs = getSimulationContext().getReactionContext().getReactionSpecs();
Vector<ReactionStep> rsList = new Vector<ReactionStep>();
for (int i = 0; i < reactionSpecs.length; i++) {
if (reactionSpecs[i].isExcluded() == false) {
if (reactionSpecs[i].isFast()) {
throw new MappingException("fast reactions not supported for particle models");
}
rsList.add(reactionSpecs[i].getReactionStep());
}
}
ReactionStep[] reactionSteps = new ReactionStep[rsList.size()];
rsList.copyInto(reactionSteps);
//
for (int i = 0; i < reactionSteps.length; i++) {
Kinetics.UnresolvedParameter[] unresolvedParameters = reactionSteps[i].getKinetics().getUnresolvedParameters();
if (unresolvedParameters != null && unresolvedParameters.length > 0) {
StringBuffer buffer = new StringBuffer();
for (int j = 0; j < unresolvedParameters.length; j++) {
if (j > 0) {
buffer.append(", ");
}
buffer.append(unresolvedParameters[j].getName());
}
throw new MappingException(reactionSteps[i].getDisplayType() + " '" + reactionSteps[i].getName() + "' contains unresolved identifier(s): " + buffer);
}
}
//
// temporarily place all variables in a hashtable (before binding) and discarding duplicates (check for equality)
//
VariableHash varHash = new VariableHash();
// //
// // verify that all structures are mapped to geometry classes and all geometry classes are mapped to a structure
// //
// Structure structures[] = getSimulationContext().getGeometryContext().getModel().getStructures();
// for (int i = 0; i < structures.length; i++){
// StructureMapping sm = getSimulationContext().getGeometryContext().getStructureMapping(structures[i]);
// if (sm==null || (sm.getGeometryClass() == null)){
// throw new MappingException("model structure '"+structures[i].getName()+"' not mapped to a geometry subdomain");
// }
// if (sm.getUnitSizeParameter()!=null){
// Expression unitSizeExp = sm.getUnitSizeParameter().getExpression();
// if(unitSizeExp != null)
// {
// try {
// double unitSize = unitSizeExp.evaluateConstant();
// if (unitSize != 1.0){
// throw new MappingException("model structure '"+sm.getStructure().getName()+"' unit size = "+unitSize+" != 1.0 ... partial volume or surface mapping not yet supported for particles");
// }
// }catch (ExpressionException e){
// e.printStackTrace(System.out);
// throw new MappingException("couldn't evaluate unit size for model structure '"+sm.getStructure().getName()+"' : "+e.getMessage());
// }
// }
// }
// }
// {
// GeometryClass[] geometryClass = getSimulationContext().getGeometryContext().getGeometry().getGeometryClasses();
// for (int i = 0; i < geometryClass.length; i++){
// Structure[] mappedStructures = getSimulationContext().getGeometryContext().getStructuresFromGeometryClass(geometryClass[i]);
// if (mappedStructures==null || mappedStructures.length==0){
// throw new MappingException("geometryClass '"+geometryClass[i].getName()+"' not mapped from a model structure");
// }
// }
// }
// deals with model parameters
Model model = getSimulationContext().getModel();
ModelUnitSystem modelUnitSystem = model.getUnitSystem();
ModelParameter[] modelParameters = model.getModelParameters();
// populate in globalParameterVariants hashtable
for (int j = 0; j < modelParameters.length; j++) {
Expression modelParamExpr = modelParameters[j].getExpression();
GeometryClass geometryClass = getDefaultGeometryClass(modelParamExpr);
modelParamExpr = getIdentifierSubstitutions(modelParamExpr, modelParameters[j].getUnitDefinition(), geometryClass);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(modelParameters[j], geometryClass), modelParamExpr, geometryClass));
}
//
// create new MathDescription (based on simContext's previous MathDescription if possible)
//
MathDescription oldMathDesc = getSimulationContext().getMathDescription();
mathDesc = null;
if (oldMathDesc != null) {
if (oldMathDesc.getVersion() != null) {
mathDesc = new MathDescription(oldMathDesc.getVersion());
} else {
mathDesc = new MathDescription(oldMathDesc.getName());
}
} else {
mathDesc = new MathDescription(getSimulationContext().getName() + "_generated");
}
//
// volume particle variables
//
Enumeration<SpeciesContextMapping> enum1 = getSpeciesContextMappings();
while (enum1.hasMoreElements()) {
SpeciesContextMapping scm = enum1.nextElement();
if (scm.getVariable() instanceof ParticleVariable) {
if (!(mathDesc.getVariable(scm.getVariable().getName()) instanceof ParticleVariable)) {
varHash.addVariable(scm.getVariable());
}
}
}
varHash.addVariable(new Constant(getMathSymbol(model.getPI_CONSTANT(), null), getIdentifierSubstitutions(model.getPI_CONSTANT().getExpression(), model.getPI_CONSTANT().getUnitDefinition(), null)));
varHash.addVariable(new Constant(getMathSymbol(model.getFARADAY_CONSTANT(), null), getIdentifierSubstitutions(model.getFARADAY_CONSTANT().getExpression(), model.getFARADAY_CONSTANT().getUnitDefinition(), null)));
varHash.addVariable(new Constant(getMathSymbol(model.getFARADAY_CONSTANT_NMOLE(), null), getIdentifierSubstitutions(model.getFARADAY_CONSTANT_NMOLE().getExpression(), model.getFARADAY_CONSTANT_NMOLE().getUnitDefinition(), null)));
varHash.addVariable(new Constant(getMathSymbol(model.getGAS_CONSTANT(), null), getIdentifierSubstitutions(model.getGAS_CONSTANT().getExpression(), model.getGAS_CONSTANT().getUnitDefinition(), null)));
varHash.addVariable(new Constant(getMathSymbol(model.getTEMPERATURE(), null), getIdentifierSubstitutions(new Expression(getSimulationContext().getTemperatureKelvin()), model.getTEMPERATURE().getUnitDefinition(), null)));
//
for (int j = 0; j < structureMappings.length; j++) {
if (structureMappings[j] instanceof MembraneMapping) {
MembraneMapping membraneMapping = (MembraneMapping) structureMappings[j];
GeometryClass geometryClass = membraneMapping.getGeometryClass();
//
// don't calculate voltage, still may need it though
//
Parameter initialVoltageParm = membraneMapping.getInitialVoltageParameter();
Variable voltageFunction = newFunctionOrConstant(getMathSymbol(membraneMapping.getMembrane().getMembraneVoltage(), geometryClass), getIdentifierSubstitutions(initialVoltageParm.getExpression(), initialVoltageParm.getUnitDefinition(), geometryClass), geometryClass);
varHash.addVariable(voltageFunction);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(membraneMapping.getMembrane().getMembraneVoltage(), membraneMapping.getGeometryClass()), getIdentifierSubstitutions(membraneMapping.getInitialVoltageParameter().getExpression(), membraneMapping.getInitialVoltageParameter().getUnitDefinition(), membraneMapping.getGeometryClass()), membraneMapping.getGeometryClass()));
}
}
//
for (int j = 0; j < reactionSteps.length; j++) {
ReactionStep rs = reactionSteps[j];
if (getSimulationContext().getReactionContext().getReactionSpec(rs).isExcluded()) {
continue;
}
Kinetics.KineticsParameter[] parameters = rs.getKinetics().getKineticsParameters();
GeometryClass geometryClass = null;
if (rs.getStructure() != null) {
geometryClass = getSimulationContext().getGeometryContext().getStructureMapping(rs.getStructure()).getGeometryClass();
}
if (parameters != null) {
for (int i = 0; i < parameters.length; i++) {
// Reaction rate, currentDensity, LumpedCurrent and null parameters are not going to displayed in the particle math description.
if (((parameters[i].getRole() == Kinetics.ROLE_CurrentDensity) || (parameters[i].getRole() == Kinetics.ROLE_LumpedCurrent) || (parameters[i].getRole() == Kinetics.ROLE_ReactionRate)) || (parameters[i].getExpression() == null)) {
continue;
}
varHash.addVariable(newFunctionOrConstant(getMathSymbol(parameters[i], geometryClass), getIdentifierSubstitutions(parameters[i].getExpression(), parameters[i].getUnitDefinition(), geometryClass), geometryClass));
}
}
}
//
// initial constants (either function or constant)
//
SpeciesContextSpec[] speciesContextSpecs = getSimulationContext().getReactionContext().getSpeciesContextSpecs();
for (int i = 0; i < speciesContextSpecs.length; i++) {
SpeciesContextSpecParameter initParm = null;
Expression initExpr = null;
if (getSimulationContext().isUsingConcentration()) {
initParm = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_InitialConcentration);
initExpr = new Expression(initParm.getExpression());
// if (speciesContextSpecs[i].getSpeciesContext().getStructure() instanceof Feature) {
// initExpr = Expression.div(initExpr, new Expression(model.getKMOLE, getNameScope())).flatten();
// }
} else {
initParm = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_InitialCount);
initExpr = new Expression(initParm.getExpression());
}
if (initExpr != null) {
StructureMapping sm = getSimulationContext().getGeometryContext().getStructureMapping(speciesContextSpecs[i].getSpeciesContext().getStructure());
String[] symbols = initExpr.getSymbols();
// Check if 'initExpr' has other speciesContexts in its expression, need to replace it with 'spContext_init'
for (int j = 0; symbols != null && j < symbols.length; j++) {
// if symbol is a speciesContext, replacing it with a reference to initial condition for that speciesContext.
SpeciesContext spC = null;
SymbolTableEntry ste = initExpr.getSymbolBinding(symbols[j]);
if (ste instanceof SpeciesContextSpecProxyParameter) {
SpeciesContextSpecProxyParameter spspp = (SpeciesContextSpecProxyParameter) ste;
if (spspp.getTarget() instanceof SpeciesContext) {
spC = (SpeciesContext) spspp.getTarget();
SpeciesContextSpec spcspec = getSimulationContext().getReactionContext().getSpeciesContextSpec(spC);
SpeciesContextSpecParameter spCInitParm = spcspec.getParameterFromRole(SpeciesContextSpec.ROLE_InitialConcentration);
// if initConc param expression is null, try initCount
if (spCInitParm.getExpression() == null) {
spCInitParm = spcspec.getParameterFromRole(SpeciesContextSpec.ROLE_InitialCount);
}
// need to get init condn expression, but can't get it from getMathSymbol() (mapping between bio and math), hence get it as below.
Expression scsInitExpr = new Expression(spCInitParm, getNameScope());
// scsInitExpr.bindExpression(this);
initExpr.substituteInPlace(new Expression(spC.getName()), scsInitExpr);
}
}
}
// now create the appropriate function for the current speciesContextSpec.
varHash.addVariable(newFunctionOrConstant(getMathSymbol(initParm, sm.getGeometryClass()), getIdentifierSubstitutions(initExpr, initParm.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
}
//
for (int i = 0; i < speciesContextSpecs.length; i++) {
SpeciesContextSpec.SpeciesContextSpecParameter diffParm = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_DiffusionRate);
if (diffParm != null) {
StructureMapping sm = getSimulationContext().getGeometryContext().getStructureMapping(speciesContextSpecs[i].getSpeciesContext().getStructure());
varHash.addVariable(newFunctionOrConstant(getMathSymbol(diffParm, sm.getGeometryClass()), getIdentifierSubstitutions(diffParm.getExpression(), diffParm.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
}
//
for (int i = 0; i < speciesContextSpecs.length; i++) {
SpeciesContextSpec.SpeciesContextSpecParameter bc_xm = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_BoundaryValueXm);
StructureMapping sm = getSimulationContext().getGeometryContext().getStructureMapping(speciesContextSpecs[i].getSpeciesContext().getStructure());
if (bc_xm != null && (bc_xm.getExpression() != null)) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(bc_xm, sm.getGeometryClass()), getIdentifierSubstitutions(bc_xm.getExpression(), bc_xm.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
SpeciesContextSpec.SpeciesContextSpecParameter bc_xp = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_BoundaryValueXp);
if (bc_xp != null && (bc_xp.getExpression() != null)) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(bc_xp, sm.getGeometryClass()), getIdentifierSubstitutions(bc_xp.getExpression(), bc_xp.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
SpeciesContextSpec.SpeciesContextSpecParameter bc_ym = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_BoundaryValueYm);
if (bc_ym != null && (bc_ym.getExpression() != null)) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(bc_ym, sm.getGeometryClass()), getIdentifierSubstitutions(bc_ym.getExpression(), bc_ym.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
SpeciesContextSpec.SpeciesContextSpecParameter bc_yp = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_BoundaryValueYp);
if (bc_yp != null && (bc_yp.getExpression() != null)) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(bc_yp, sm.getGeometryClass()), getIdentifierSubstitutions(bc_yp.getExpression(), bc_yp.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
SpeciesContextSpec.SpeciesContextSpecParameter bc_zm = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_BoundaryValueZm);
if (bc_zm != null && (bc_zm.getExpression() != null)) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(bc_zm, sm.getGeometryClass()), getIdentifierSubstitutions(bc_zm.getExpression(), bc_zm.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
SpeciesContextSpec.SpeciesContextSpecParameter bc_zp = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_BoundaryValueZp);
if (bc_zp != null && (bc_zp.getExpression() != null)) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(bc_zp, sm.getGeometryClass()), getIdentifierSubstitutions(bc_zp.getExpression(), bc_zp.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
}
//
for (int i = 0; i < speciesContextSpecs.length; i++) {
SpeciesContextSpec.SpeciesContextSpecParameter advection_velX = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_VelocityX);
StructureMapping sm = getSimulationContext().getGeometryContext().getStructureMapping(speciesContextSpecs[i].getSpeciesContext().getStructure());
GeometryClass geometryClass = sm.getGeometryClass();
if (advection_velX != null && (advection_velX.getExpression() != null)) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(advection_velX, geometryClass), getIdentifierSubstitutions(advection_velX.getExpression(), advection_velX.getUnitDefinition(), geometryClass), geometryClass));
}
SpeciesContextSpec.SpeciesContextSpecParameter advection_velY = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_VelocityY);
if (advection_velY != null && (advection_velY.getExpression() != null)) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(advection_velY, geometryClass), getIdentifierSubstitutions(advection_velY.getExpression(), advection_velY.getUnitDefinition(), geometryClass), geometryClass));
}
SpeciesContextSpec.SpeciesContextSpecParameter advection_velZ = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_VelocityZ);
if (advection_velZ != null && (advection_velZ.getExpression() != null)) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(advection_velZ, geometryClass), getIdentifierSubstitutions(advection_velZ.getExpression(), advection_velZ.getUnitDefinition(), geometryClass), geometryClass));
}
}
//
// constant species (either function or constant)
//
enum1 = getSpeciesContextMappings();
while (enum1.hasMoreElements()) {
SpeciesContextMapping scm = (SpeciesContextMapping) enum1.nextElement();
if (scm.getVariable() instanceof Constant) {
varHash.addVariable(scm.getVariable());
}
}
//
// conversion factors
//
varHash.addVariable(new Constant(getMathSymbol(model.getKMOLE(), null), getIdentifierSubstitutions(model.getKMOLE().getExpression(), model.getKMOLE().getUnitDefinition(), null)));
varHash.addVariable(new Constant(getMathSymbol(model.getN_PMOLE(), null), getIdentifierSubstitutions(model.getN_PMOLE().getExpression(), model.getN_PMOLE().getUnitDefinition(), null)));
varHash.addVariable(new Constant(getMathSymbol(model.getKMILLIVOLTS(), null), getIdentifierSubstitutions(model.getKMILLIVOLTS().getExpression(), model.getKMILLIVOLTS().getUnitDefinition(), null)));
varHash.addVariable(new Constant(getMathSymbol(model.getK_GHK(), null), getIdentifierSubstitutions(model.getK_GHK().getExpression(), model.getK_GHK().getUnitDefinition(), null)));
//
for (int i = 0; i < structureMappings.length; i++) {
StructureMapping sm = structureMappings[i];
if (getSimulationContext().getGeometry().getDimension() == 0) {
StructureMappingParameter sizeParm = sm.getSizeParameter();
if (sizeParm != null && sizeParm.getExpression() != null) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(sizeParm, sm.getGeometryClass()), getIdentifierSubstitutions(sizeParm.getExpression(), sizeParm.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
} else {
if (sm instanceof MembraneMapping) {
MembraneMapping mm = (MembraneMapping) sm;
StructureMappingParameter volFrac = mm.getVolumeFractionParameter();
if (volFrac != null && volFrac.getExpression() != null) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(volFrac, sm.getGeometryClass()), getIdentifierSubstitutions(volFrac.getExpression(), volFrac.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
StructureMappingParameter surfToVol = mm.getSurfaceToVolumeParameter();
if (surfToVol != null && surfToVol.getExpression() != null) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(surfToVol, sm.getGeometryClass()), getIdentifierSubstitutions(surfToVol.getExpression(), surfToVol.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
}
}
} else {
Parameter parm = sm.getParameterFromRole(StructureMapping.ROLE_AreaPerUnitArea);
if (parm != null && parm.getExpression() != null && sm.getGeometryClass() instanceof SurfaceClass) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(parm, sm.getGeometryClass()), getIdentifierSubstitutions(parm.getExpression(), parm.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
parm = sm.getParameterFromRole(StructureMapping.ROLE_AreaPerUnitVolume);
if (parm != null && parm.getExpression() != null && sm.getGeometryClass() instanceof SubVolume) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(parm, sm.getGeometryClass()), getIdentifierSubstitutions(parm.getExpression(), parm.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
parm = sm.getParameterFromRole(StructureMapping.ROLE_VolumePerUnitArea);
if (parm != null && parm.getExpression() != null && sm.getGeometryClass() instanceof SurfaceClass) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(parm, sm.getGeometryClass()), getIdentifierSubstitutions(parm.getExpression(), parm.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
parm = sm.getParameterFromRole(StructureMapping.ROLE_VolumePerUnitVolume);
if (parm != null && parm.getExpression() != null && sm.getGeometryClass() instanceof SubVolume) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(parm, sm.getGeometryClass()), getIdentifierSubstitutions(parm.getExpression(), parm.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
}
}
//
// functions
//
enum1 = getSpeciesContextMappings();
while (enum1.hasMoreElements()) {
SpeciesContextMapping scm = (SpeciesContextMapping) enum1.nextElement();
if (scm.getVariable() == null && scm.getDependencyExpression() != null) {
StructureMapping sm = getSimulationContext().getGeometryContext().getStructureMapping(scm.getSpeciesContext().getStructure());
Variable dependentVariable = newFunctionOrConstant(getMathSymbol(scm.getSpeciesContext(), sm.getGeometryClass()), getIdentifierSubstitutions(scm.getDependencyExpression(), scm.getSpeciesContext().getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass());
dependentVariable.setDomain(new Domain(sm.getGeometryClass()));
varHash.addVariable(dependentVariable);
}
}
//
for (int i = 0; i < fieldMathMappingParameters.length; i++) {
if (fieldMathMappingParameters[i] instanceof UnitFactorParameter) {
GeometryClass geometryClass = fieldMathMappingParameters[i].getGeometryClass();
varHash.addVariable(newFunctionOrConstant(getMathSymbol(fieldMathMappingParameters[i], geometryClass), getIdentifierSubstitutions(fieldMathMappingParameters[i].getExpression(), fieldMathMappingParameters[i].getUnitDefinition(), geometryClass), fieldMathMappingParameters[i].getGeometryClass()));
}
}
//
// set Variables to MathDescription all at once with the order resolved by "VariableHash"
//
mathDesc.setAllVariables(varHash.getAlphabeticallyOrderedVariables());
//
if (getSimulationContext().getGeometryContext().getGeometry() != null) {
try {
mathDesc.setGeometry(getSimulationContext().getGeometryContext().getGeometry());
} catch (java.beans.PropertyVetoException e) {
e.printStackTrace(System.out);
throw new MappingException("failure setting geometry " + e.getMessage());
}
} else {
throw new MappingException("geometry must be defined");
}
//
// create subdomains (volume and surfaces)
//
GeometryClass[] geometryClasses = getSimulationContext().getGeometryContext().getGeometry().getGeometryClasses();
for (int k = 0; k < geometryClasses.length; k++) {
if (geometryClasses[k] instanceof SubVolume) {
SubVolume subVolume = (SubVolume) geometryClasses[k];
//
// get priority of subDomain
//
// now does not have to match spatial feature, *BUT* needs to be unique
int priority = k;
//
// create subDomain
//
CompartmentSubDomain subDomain = new CompartmentSubDomain(subVolume.getName(), priority);
mathDesc.addSubDomain(subDomain);
//
// assign boundary condition types
//
StructureMapping[] mappedSMs = getSimulationContext().getGeometryContext().getStructureMappings(subVolume);
FeatureMapping mappedFM = null;
for (int i = 0; i < mappedSMs.length; i++) {
if (mappedSMs[i] instanceof FeatureMapping) {
if (mappedFM != null) {
lg.warn("WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique");
}
mappedFM = (FeatureMapping) mappedSMs[i];
}
}
if (mappedFM != null) {
subDomain.setBoundaryConditionXm(mappedFM.getBoundaryConditionTypeXm());
subDomain.setBoundaryConditionXp(mappedFM.getBoundaryConditionTypeXp());
if (getSimulationContext().getGeometry().getDimension() > 1) {
subDomain.setBoundaryConditionYm(mappedFM.getBoundaryConditionTypeYm());
subDomain.setBoundaryConditionYp(mappedFM.getBoundaryConditionTypeYp());
}
if (getSimulationContext().getGeometry().getDimension() > 2) {
subDomain.setBoundaryConditionZm(mappedFM.getBoundaryConditionTypeZm());
subDomain.setBoundaryConditionZp(mappedFM.getBoundaryConditionTypeZp());
}
}
} else if (geometryClasses[k] instanceof SurfaceClass) {
SurfaceClass surfaceClass = (SurfaceClass) geometryClasses[k];
// determine membrane inside and outside subvolume
// this preserves backward compatibility so that membrane subdomain
// inside and outside correspond to structure hierarchy when present
Pair<SubVolume, SubVolume> ret = DiffEquMathMapping.computeBoundaryConditionSource(model, simContext, surfaceClass);
SubVolume innerSubVolume = ret.one;
SubVolume outerSubVolume = ret.two;
//
// create subDomain
//
CompartmentSubDomain outerCompartment = mathDesc.getCompartmentSubDomain(outerSubVolume.getName());
CompartmentSubDomain innerCompartment = mathDesc.getCompartmentSubDomain(innerSubVolume.getName());
MembraneSubDomain memSubDomain = new MembraneSubDomain(innerCompartment, outerCompartment, surfaceClass.getName());
mathDesc.addSubDomain(memSubDomain);
}
}
//
// create Particle Contexts for all Particle Variables
//
Enumeration<SpeciesContextMapping> enumSCM = getSpeciesContextMappings();
Expression unitFactor = getUnitFactor(modelUnitSystem.getStochasticSubstanceUnit().divideBy(modelUnitSystem.getVolumeSubstanceUnit()));
while (enumSCM.hasMoreElements()) {
SpeciesContextMapping scm = enumSCM.nextElement();
SpeciesContext sc = scm.getSpeciesContext();
StructureMapping sm = getSimulationContext().getGeometryContext().getStructureMapping(sc.getStructure());
SpeciesContextSpec scs = getSimulationContext().getReactionContext().getSpeciesContextSpec(sc);
if (scm.getVariable() instanceof ParticleVariable && scm.getDependencyExpression() == null) {
ParticleVariable particleVariable = (ParticleVariable) scm.getVariable();
//
// initial distribution of particles
//
ArrayList<ParticleInitialCondition> particleInitialConditions = new ArrayList<ParticleInitialCondition>();
ParticleInitialCondition pic = null;
if (getSimulationContext().isUsingConcentration()) {
Expression initialDistribution = scs.getInitialConcentrationParameter().getExpression() == null ? null : new Expression(getMathSymbol(scs.getInitialConcentrationParameter(), sm.getGeometryClass()));
if (particleVariable instanceof VolumeParticleVariable) {
initialDistribution = Expression.mult(initialDistribution, unitFactor);
}
pic = new ParticleInitialConditionConcentration(initialDistribution);
} else {
Expression initialCount = scs.getInitialCountParameter().getExpression() == null ? null : new Expression(getMathSymbol(scs.getInitialCountParameter(), sm.getGeometryClass()));
if (initialCount == null) {
throw new MappingException("initialCount not defined for speciesContext " + scs.getSpeciesContext().getName());
}
Expression locationX = new Expression("u");
Expression locationY = new Expression("u");
Expression locationZ = new Expression("u");
pic = new ParticleInitialConditionCount(initialCount, locationX, locationY, locationZ);
}
particleInitialConditions.add(pic);
//
// diffusion
//
Expression diffusion = new Expression(getMathSymbol(scs.getDiffusionParameter(), sm.getGeometryClass()));
Expression driftXExp = null;
if (scs.getVelocityXParameter().getExpression() != null) {
driftXExp = new Expression(getMathSymbol(scs.getVelocityXParameter(), sm.getGeometryClass()));
} else {
SpatialQuantity[] velX_quantities = scs.getVelocityQuantities(QuantityComponent.X);
if (velX_quantities.length > 0) {
int numRegions = simContext.getGeometry().getGeometrySurfaceDescription().getGeometricRegions(sm.getGeometryClass()).length;
if (velX_quantities.length == 1 && numRegions == 1) {
driftXExp = new Expression(getMathSymbol(velX_quantities[0], sm.getGeometryClass()));
} else {
throw new MappingException("multiple advection velocities enabled set for multiple volume domains ");
}
}
}
Expression driftYExp = null;
if (scs.getVelocityYParameter().getExpression() != null) {
driftYExp = new Expression(getMathSymbol(scs.getVelocityYParameter(), sm.getGeometryClass()));
} else {
SpatialQuantity[] velY_quantities = scs.getVelocityQuantities(QuantityComponent.Y);
if (velY_quantities.length > 0) {
int numRegions = simContext.getGeometry().getGeometrySurfaceDescription().getGeometricRegions(sm.getGeometryClass()).length;
if (velY_quantities.length == 1 && numRegions == 1) {
driftYExp = new Expression(getMathSymbol(velY_quantities[0], sm.getGeometryClass()));
} else {
throw new MappingException("multiple advection velocities enabled set for multiple volume domains ");
}
}
}
Expression driftZExp = null;
if (scs.getVelocityZParameter().getExpression() != null) {
driftZExp = new Expression(getMathSymbol(scs.getVelocityZParameter(), sm.getGeometryClass()));
} else {
SpatialQuantity[] velZ_quantities = scs.getVelocityQuantities(QuantityComponent.Z);
if (velZ_quantities.length > 0) {
int numRegions = simContext.getGeometry().getGeometrySurfaceDescription().getGeometricRegions(sm.getGeometryClass()).length;
if (velZ_quantities.length == 1 && numRegions == 1) {
driftZExp = new Expression(getMathSymbol(velZ_quantities[0], sm.getGeometryClass()));
} else {
throw new MappingException("multiple advection velocities enabled set for multiple volume domains ");
}
}
}
ParticleProperties particleProperties = new ParticleProperties(particleVariable, diffusion, driftXExp, driftYExp, driftZExp, particleInitialConditions);
GeometryClass myGC = sm.getGeometryClass();
if (myGC == null) {
throw new MappingException("Application '" + getSimulationContext().getName() + "'\nGeometry->StructureMapping->(" + sm.getStructure().getTypeName() + ")'" + sm.getStructure().getName() + "' must be mapped to geometry domain.\n(see 'Problems' tab)");
}
SubDomain subDomain = mathDesc.getSubDomain(myGC.getName());
subDomain.addParticleProperties(particleProperties);
}
}
for (ReactionStep reactionStep : reactionSteps) {
Kinetics kinetics = reactionStep.getKinetics();
StructureMapping sm = getSimulationContext().getGeometryContext().getStructureMapping(reactionStep.getStructure());
GeometryClass reactionStepGeometryClass = sm.getGeometryClass();
SubDomain subdomain = mathDesc.getSubDomain(reactionStepGeometryClass.getName());
KineticsParameter reactionRateParameter = null;
if (kinetics instanceof LumpedKinetics) {
reactionRateParameter = ((LumpedKinetics) kinetics).getLumpedReactionRateParameter();
} else {
reactionRateParameter = ((DistributedKinetics) kinetics).getReactionRateParameter();
}
// macroscopic_irreversible/Microscopic_irreversible for bimolecular membrane reactions. They will NOT go through MassAction solver.
if (kinetics.getKineticsDescription().equals(KineticsDescription.Macroscopic_irreversible) || kinetics.getKineticsDescription().equals(KineticsDescription.Microscopic_irreversible)) {
Expression radiusExp = getIdentifierSubstitutions(reactionStep.getKinetics().getKineticsParameterFromRole(Kinetics.ROLE_Binding_Radius).getExpression(), modelUnitSystem.getBindingRadiusUnit(), reactionStepGeometryClass);
if (radiusExp != null) {
Expression expCopy = new Expression(radiusExp);
try {
MassActionSolver.substituteParameters(expCopy, true).evaluateConstant();
} catch (ExpressionException e) {
throw new MathException(VCellErrorMessages.getMassActionSolverMessage(reactionStep.getName(), "Problem in binding radius of " + reactionStep.getName() + ": '" + radiusExp.infix() + "', " + e.getMessage()));
}
} else {
throw new MathException(VCellErrorMessages.getMassActionSolverMessage(reactionStep.getName(), "Binding radius of " + reactionStep.getName() + " is null."));
}
List<ParticleVariable> reactantParticles = new ArrayList<ParticleVariable>();
List<ParticleVariable> productParticles = new ArrayList<ParticleVariable>();
List<Action> forwardActions = new ArrayList<Action>();
for (ReactionParticipant rp : reactionStep.getReactionParticipants()) {
SpeciesContext sc = rp.getSpeciesContext();
SpeciesContextSpec scs = getSimulationContext().getReactionContext().getSpeciesContextSpec(sc);
GeometryClass scGeometryClass = getSimulationContext().getGeometryContext().getStructureMapping(sc.getStructure()).getGeometryClass();
String varName = getMathSymbol(sc, scGeometryClass);
Variable var = mathDesc.getVariable(varName);
if (var instanceof ParticleVariable) {
ParticleVariable particle = (ParticleVariable) var;
if (rp instanceof Reactant) {
reactantParticles.add(particle);
if (!scs.isConstant() && !scs.isForceContinuous()) {
for (int i = 0; i < Math.abs(rp.getStoichiometry()); i++) {
if (radiusExp != null) {
forwardActions.add(Action.createDestroyAction(particle));
}
}
}
} else if (rp instanceof Product) {
productParticles.add(particle);
if (!scs.isConstant() && !scs.isForceContinuous()) {
for (int i = 0; i < Math.abs(rp.getStoichiometry()); i++) {
if (radiusExp != null) {
forwardActions.add(Action.createCreateAction(particle));
}
}
}
}
} else {
throw new MappingException("particle variable '" + varName + "' not found");
}
}
JumpProcessRateDefinition bindingRadius = new InteractionRadius(radiusExp);
// get jump process name
String jpName = TokenMangler.mangleToSName(reactionStep.getName());
// only for NFSim/Rules for now.
ProcessSymmetryFactor processSymmetryFactor = null;
if (forwardActions.size() > 0) {
ParticleJumpProcess forwardProcess = new ParticleJumpProcess(jpName, reactantParticles, bindingRadius, forwardActions, processSymmetryFactor);
subdomain.addParticleJumpProcess(forwardProcess);
}
} else // other type of reactions
{
/* check the reaction rate law to see if we need to decompose a reaction(reversible) into two jump processes.
rate constants are important in calculating the probability rate.
for Mass Action, we use KForward and KReverse,
for General Kinetics we parse reaction rate J to see if it is in Mass Action form.
*/
Expression forwardRate = null;
Expression reverseRate = null;
// Using the MassActionFunction to write out the math description
MassActionSolver.MassActionFunction maFunc = null;
if (kinetics.getKineticsDescription().equals(KineticsDescription.MassAction) || kinetics.getKineticsDescription().equals(KineticsDescription.General) || kinetics.getKineticsDescription().equals(KineticsDescription.GeneralPermeability)) {
Expression rateExp = kinetics.getKineticsParameterFromRole(Kinetics.ROLE_ReactionRate).getExpression();
Parameter forwardRateParameter = null;
Parameter reverseRateParameter = null;
if (kinetics.getKineticsDescription().equals(KineticsDescription.MassAction)) {
forwardRateParameter = kinetics.getKineticsParameterFromRole(Kinetics.ROLE_KForward);
reverseRateParameter = kinetics.getKineticsParameterFromRole(Kinetics.ROLE_KReverse);
} else if (kinetics.getKineticsDescription().equals(KineticsDescription.GeneralPermeability)) {
forwardRateParameter = kinetics.getKineticsParameterFromRole(Kinetics.ROLE_Permeability);
reverseRateParameter = kinetics.getKineticsParameterFromRole(Kinetics.ROLE_Permeability);
}
maFunc = MassActionSolver.solveMassAction(forwardRateParameter, reverseRateParameter, rateExp, reactionStep);
if (maFunc.getForwardRate() == null && maFunc.getReverseRate() == null) {
throw new MappingException("Cannot generate stochastic math mapping for the reaction:" + reactionStep.getName() + "\nLooking for the rate function according to the form of k1*Reactant1^Stoir1*Reactant2^Stoir2...-k2*Product1^Stoip1*Product2^Stoip2.");
} else {
if (maFunc.getForwardRate() != null) {
forwardRate = maFunc.getForwardRate();
}
if (maFunc.getReverseRate() != null) {
reverseRate = maFunc.getReverseRate();
}
}
}
if (maFunc != null) {
// if the reaction has forward rate (Mass action,HMMs), or don't have either forward or reverse rate (some other rate laws--like general)
// we process it as forward reaction
List<ParticleVariable> reactantParticles = new ArrayList<ParticleVariable>();
List<ParticleVariable> productParticles = new ArrayList<ParticleVariable>();
List<Action> forwardActions = new ArrayList<Action>();
List<Action> reverseActions = new ArrayList<Action>();
List<ReactionParticipant> reactants = maFunc.getReactants();
List<ReactionParticipant> products = maFunc.getProducts();
for (ReactionParticipant rp : reactants) {
SpeciesContext sc = rp.getSpeciesContext();
SpeciesContextSpec scs = getSimulationContext().getReactionContext().getSpeciesContextSpec(sc);
GeometryClass scGeometryClass = getSimulationContext().getGeometryContext().getStructureMapping(sc.getStructure()).getGeometryClass();
String varName = getMathSymbol(sc, scGeometryClass);
Variable var = mathDesc.getVariable(varName);
if (var instanceof ParticleVariable) {
ParticleVariable particle = (ParticleVariable) var;
reactantParticles.add(particle);
if (!scs.isConstant() && !scs.isForceContinuous()) {
for (int i = 0; i < Math.abs(rp.getStoichiometry()); i++) {
if (forwardRate != null) {
forwardActions.add(Action.createDestroyAction(particle));
}
if (reverseRate != null) {
reverseActions.add(Action.createCreateAction(particle));
}
}
}
} else {
throw new MappingException("particle variable '" + varName + "' not found");
}
}
for (ReactionParticipant rp : products) {
SpeciesContext sc = rp.getSpeciesContext();
SpeciesContextSpec scs = getSimulationContext().getReactionContext().getSpeciesContextSpec(sc);
GeometryClass scGeometryClass = getSimulationContext().getGeometryContext().getStructureMapping(sc.getStructure()).getGeometryClass();
String varName = getMathSymbol(sc, scGeometryClass);
Variable var = mathDesc.getVariable(varName);
if (var instanceof ParticleVariable) {
ParticleVariable particle = (ParticleVariable) var;
productParticles.add(particle);
if (!scs.isConstant() && !scs.isForceContinuous()) {
for (int i = 0; i < Math.abs(rp.getStoichiometry()); i++) {
if (forwardRate != null) {
forwardActions.add(Action.createCreateAction(particle));
}
if (reverseRate != null) {
reverseActions.add(Action.createDestroyAction(particle));
}
}
}
} else {
throw new MappingException("particle variable '" + varName + "' not found");
}
}
//
// There are two unit conversions required:
//
// 1) convert entire reaction rate from vcell reaction units to Smoldyn units (molecules/lengthunit^dim/timeunit)
// (where dim is 2 for membrane reactions and 3 for volume reactions)
//
// for forward rates:
// 2) convert each reactant from Smoldyn units (molecules/lengthunit^dim) to VCell units
// (where dim is 2 for membrane reactants and 3 for volume reactants)
//
// or
//
// for reverse rates:
// 2) convert each product from Smoldyn units (molecules/lengthunit^dim) to VCell units
// (where dim is 2 for membrane products and 3 for volume products)
//
RationalNumber reactionLocationDim = new RationalNumber(reactionStep.getStructure().getDimension());
VCUnitDefinition timeUnit = modelUnitSystem.getTimeUnit();
VCUnitDefinition smoldynReactionSizeUnit = modelUnitSystem.getLengthUnit().raiseTo(reactionLocationDim);
VCUnitDefinition smoldynSubstanceUnit = modelUnitSystem.getStochasticSubstanceUnit();
VCUnitDefinition smoldynReactionRateUnit = smoldynSubstanceUnit.divideBy(smoldynReactionSizeUnit).divideBy(timeUnit);
VCUnitDefinition vcellReactionRateUnit = reactionRateParameter.getUnitDefinition();
VCUnitDefinition reactionUnitFactor = smoldynReactionRateUnit.divideBy(vcellReactionRateUnit);
if (forwardRate != null) {
VCUnitDefinition smoldynReactantsUnit = modelUnitSystem.getInstance_DIMENSIONLESS();
// start with factor to translate entire reaction rate.
VCUnitDefinition forwardUnitFactor = reactionUnitFactor;
//
for (ReactionParticipant reactant : maFunc.getReactants()) {
VCUnitDefinition vcellReactantUnit = reactant.getSpeciesContext().getUnitDefinition();
boolean bForceContinuous = simContext.getReactionContext().getSpeciesContextSpec(reactant.getSpeciesContext()).isForceContinuous();
VCUnitDefinition smoldynReactantUnit = null;
if (bForceContinuous) {
// reactant is continuous (vcell units)
smoldynReactantUnit = reactant.getSpeciesContext().getUnitDefinition();
} else {
// reactant is a particle (smoldyn units)
RationalNumber reactantLocationDim = new RationalNumber(reactant.getStructure().getDimension());
VCUnitDefinition smoldynReactantSize = modelUnitSystem.getLengthUnit().raiseTo(reactantLocationDim);
smoldynReactantUnit = smoldynSubstanceUnit.divideBy(smoldynReactantSize);
}
// keep track of units of all reactants
smoldynReactantsUnit = smoldynReactantsUnit.multiplyBy(smoldynReactantUnit);
RationalNumber reactantStoichiometry = new RationalNumber(reactant.getStoichiometry());
VCUnitDefinition reactantUnitFactor = (vcellReactantUnit.divideBy(smoldynReactantUnit)).raiseTo(reactantStoichiometry);
// accumulate unit factors for all reactants
forwardUnitFactor = forwardUnitFactor.multiplyBy(reactantUnitFactor);
}
forwardRate = Expression.mult(forwardRate, getUnitFactor(forwardUnitFactor));
VCUnitDefinition smoldynExpectedForwardRateUnit = smoldynReactionRateUnit.divideBy(smoldynReactantsUnit);
// get probability
Expression exp = getIdentifierSubstitutions(forwardRate, smoldynExpectedForwardRateUnit, reactionStepGeometryClass).flatten();
JumpProcessRateDefinition partRateDef = new MacroscopicRateConstant(exp);
// create particle jump process
String jpName = TokenMangler.mangleToSName(reactionStep.getName());
// only for NFSim/Rules for now.
ProcessSymmetryFactor processSymmetryFactor = null;
if (forwardActions.size() > 0) {
ParticleJumpProcess forwardProcess = new ParticleJumpProcess(jpName, reactantParticles, partRateDef, forwardActions, processSymmetryFactor);
subdomain.addParticleJumpProcess(forwardProcess);
}
}
// end of forward rate not null
if (reverseRate != null) {
VCUnitDefinition smoldynProductsUnit = modelUnitSystem.getInstance_DIMENSIONLESS();
// start with factor to translate entire reaction rate.
VCUnitDefinition reverseUnitFactor = reactionUnitFactor;
//
for (ReactionParticipant product : maFunc.getProducts()) {
VCUnitDefinition vcellProductUnit = product.getSpeciesContext().getUnitDefinition();
boolean bForceContinuous = simContext.getReactionContext().getSpeciesContextSpec(product.getSpeciesContext()).isForceContinuous();
VCUnitDefinition smoldynProductUnit = null;
if (bForceContinuous) {
smoldynProductUnit = product.getSpeciesContext().getUnitDefinition();
} else {
RationalNumber productLocationDim = new RationalNumber(product.getStructure().getDimension());
VCUnitDefinition smoldynProductSize = modelUnitSystem.getLengthUnit().raiseTo(productLocationDim);
smoldynProductUnit = smoldynSubstanceUnit.divideBy(smoldynProductSize);
}
// keep track of units of all products
smoldynProductsUnit = smoldynProductsUnit.multiplyBy(smoldynProductUnit);
RationalNumber productStoichiometry = new RationalNumber(product.getStoichiometry());
VCUnitDefinition productUnitFactor = (vcellProductUnit.divideBy(smoldynProductUnit)).raiseTo(productStoichiometry);
// accumulate unit factors for all products
reverseUnitFactor = reverseUnitFactor.multiplyBy(productUnitFactor);
}
reverseRate = Expression.mult(reverseRate, getUnitFactor(reverseUnitFactor));
VCUnitDefinition smoldynExpectedReverseRateUnit = smoldynReactionRateUnit.divideBy(smoldynProductsUnit);
// get probability
Expression exp = getIdentifierSubstitutions(reverseRate, smoldynExpectedReverseRateUnit, reactionStepGeometryClass).flatten();
JumpProcessRateDefinition partProbRate = new MacroscopicRateConstant(exp);
// get jump process name
String jpName = TokenMangler.mangleToSName(reactionStep.getName() + "_reverse");
// only for NFSim/Rules for now.
ProcessSymmetryFactor processSymmetryFactor = null;
if (reverseActions.size() > 0) {
ParticleJumpProcess reverseProcess = new ParticleJumpProcess(jpName, productParticles, partProbRate, reverseActions, processSymmetryFactor);
subdomain.addParticleJumpProcess(reverseProcess);
}
}
// end of reverse rate not null
}
// end of maFunc not null
}
// end of reaction step for loop
}
//
for (int i = 0; i < fieldMathMappingParameters.length; i++) {
if (fieldMathMappingParameters[i] instanceof UnitFactorParameter) {
GeometryClass geometryClass = fieldMathMappingParameters[i].getGeometryClass();
Variable variable = newFunctionOrConstant(getMathSymbol(fieldMathMappingParameters[i], geometryClass), getIdentifierSubstitutions(fieldMathMappingParameters[i].getExpression(), fieldMathMappingParameters[i].getUnitDefinition(), geometryClass), fieldMathMappingParameters[i].getGeometryClass());
if (mathDesc.getVariable(variable.getName()) == null) {
mathDesc.addVariable(variable);
}
}
}
if (!mathDesc.isValid()) {
lg.warn(mathDesc.getVCML_database());
throw new MappingException("generated an invalid mathDescription: " + mathDesc.getWarning());
}
if (lg.isDebugEnabled()) {
System.out.println("]]]]]]]]]]]]]]]]]]]]]] VCML string begin ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]");
System.out.println(mathDesc.getVCML());
System.out.println("]]]]]]]]]]]]]]]]]]]]]] VCML string end ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]");
}
}
use of cbit.vcell.math.Action in project vcell by virtualcell.
the class RulebasedMathMapping method addParticleJumpProcesses.
private void addParticleJumpProcesses(VariableHash varHash, GeometryClass geometryClass, SubDomain subDomain, HashMap<SpeciesPattern, VolumeParticleSpeciesPattern> speciesPatternMap) throws ExpressionException, MappingException, MathException, PropertyVetoException {
ArrayList<ReactionRule> rrList = new ArrayList<>();
for (ReactionRuleSpec rrSpec : getSimulationContext().getReactionContext().getReactionRuleSpecs()) {
if (!rrSpec.isExcluded()) {
rrList.add(rrSpec.getReactionRule());
}
}
for (ReactionRule reactionRule : rrList) {
String jpName = TokenMangler.mangleToSName(reactionRule.getName());
ArrayList<ParticleVariable> reactantParticles = new ArrayList<ParticleVariable>();
for (ReactantPattern reactantSpeciesPattern : reactionRule.getReactantPatterns()) {
reactantParticles.add(speciesPatternMap.get(reactantSpeciesPattern.getSpeciesPattern()));
}
ArrayList<ParticleVariable> productParticles = new ArrayList<ParticleVariable>();
for (ProductPattern productSpeciesPattern : reactionRule.getProductPatterns()) {
productParticles.add(speciesPatternMap.get(productSpeciesPattern.getSpeciesPattern()));
}
ArrayList<Action> forwardActions = new ArrayList<Action>();
ArrayList<Action> reverseActions = new ArrayList<Action>();
for (ParticleVariable reactant : reactantParticles) {
forwardActions.add(new Action(reactant, Action.ACTION_DESTROY, new Expression(1.0)));
reverseActions.add(new Action(reactant, Action.ACTION_CREATE, new Expression(1.0)));
}
for (ParticleVariable product : productParticles) {
forwardActions.add(new Action(product, Action.ACTION_CREATE, new Expression(1.0)));
reverseActions.add(new Action(product, Action.ACTION_DESTROY, new Expression(1.0)));
}
RbmKineticLaw kinetics = reactionRule.getKineticLaw();
if (kinetics.getRateLawType() == RbmKineticLaw.RateLawType.MassAction) {
boolean constantMassActionKineticCoefficients = true;
StringBuffer errorMessage = new StringBuffer();
Parameter forward_rateParameter = kinetics.getLocalParameter(RbmKineticLawParameterType.MassActionForwardRate);
Expression substitutedForwardRate = MathUtilities.substituteModelParameters(forward_rateParameter.getExpression(), reactionRule.getNameScope().getScopedSymbolTable());
if (!substitutedForwardRate.flatten().isNumeric()) {
errorMessage.append("flattened Kf for reactionRule(" + reactionRule.getName() + ") is not numeric, exp = '" + substitutedForwardRate.flatten().infix() + "'");
constantMassActionKineticCoefficients = false;
}
if (reactionRule.isReversible()) {
Parameter reverse_rateParameter = kinetics.getLocalParameter(RbmKineticLawParameterType.MassActionReverseRate);
if (reverse_rateParameter == null || reverse_rateParameter.getExpression() == null) {
throw new MappingException("reverse rate constant for reaction rule " + reactionRule.getName() + " is missing");
}
Expression substitutedReverseRate = MathUtilities.substituteModelParameters(reverse_rateParameter.getExpression(), reactionRule.getNameScope().getScopedSymbolTable());
if (!substitutedReverseRate.flatten().isNumeric()) {
errorMessage.append("flattened Kr for reactionRule(" + reactionRule.getName() + ") is not numeric, exp = '" + substitutedReverseRate.flatten().infix() + "'");
constantMassActionKineticCoefficients = false;
}
}
if (constantMassActionKineticCoefficients) {
addStrictMassActionParticleJumpProcess(varHash, geometryClass, subDomain, reactionRule, jpName, reactantParticles, productParticles, forwardActions, reverseActions);
} else {
throw new MappingException("not mass action: " + errorMessage.toString());
// addGeneralParticleJumpProcess(varHash, geometryClass, subDomain,
// reactionRule, jpName,
// reactantParticles, productParticles,
// forwardActions, reverseActions);
}
} else {
throw new MappingException("rule-based math generation unsupported for Kinetic Law: " + kinetics.getRateLawType());
}
}
// end reactionRules
}
use of cbit.vcell.math.Action in project vcell by virtualcell.
the class StochFileWriter method write.
/**
* Write the model to a text file which serves as an input for Stochastic simulation engine.
* Creation date: (6/22/2006 5:37:26 PM)
*/
public void write(String[] parameterNames) throws Exception, ExpressionException {
Simulation simulation = simTask.getSimulation();
SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
initialize();
if (bUseMessaging) {
writeJMSParamters();
}
// Write control information
printWriter.println("<control>");
cbit.vcell.solver.SolverTaskDescription solverTaskDescription = simulation.getSolverTaskDescription();
cbit.vcell.solver.TimeBounds timeBounds = solverTaskDescription.getTimeBounds();
cbit.vcell.solver.OutputTimeSpec outputTimeSpec = solverTaskDescription.getOutputTimeSpec();
ErrorTolerance errorTolerance = solverTaskDescription.getErrorTolerance();
NonspatialStochSimOptions stochOpt = solverTaskDescription.getStochOpt();
printWriter.println("STARTING_TIME" + "\t" + timeBounds.getStartingTime());
printWriter.println("ENDING_TIME " + "\t" + timeBounds.getEndingTime());
// pw.println("MAX_ITERATION"+"\t"+outputTimeSpec.getKeepAtMost());
printWriter.println("TOLERANCE " + "\t" + errorTolerance.getAbsoluteErrorTolerance());
if (outputTimeSpec.isDefault()) {
printWriter.println("SAMPLE_INTERVAL" + "\t" + ((DefaultOutputTimeSpec) outputTimeSpec).getKeepEvery());
printWriter.println("MAX_SAVE_POINTS" + "\t" + ((DefaultOutputTimeSpec) outputTimeSpec).getKeepAtMost());
} else if (outputTimeSpec.isUniform()) {
printWriter.println("SAVE_PERIOD" + "\t" + ((UniformOutputTimeSpec) outputTimeSpec).getOutputTimeStep());
}
printWriter.println("NUM_TRIAL" + "\t" + solverTaskDescription.getStochOpt().getNumOfTrials());
if (stochOpt.isUseCustomSeed()) {
printWriter.println("SEED" + "\t" + stochOpt.getCustomSeed());
} else {
// we generate our own random seed
RandomDataGenerator rdg = new RandomDataGenerator();
int randomSeed = rdg.nextInt(1, Integer.MAX_VALUE);
printWriter.println("SEED" + "\t" + randomSeed);
}
printWriter.println("</control>");
printWriter.println();
// write model information
// Model info. will be extracted from subDomain of mathDescription
Enumeration<SubDomain> e = simulation.getMathDescription().getSubDomains();
SubDomain subDomain = null;
if (e.hasMoreElements()) {
subDomain = e.nextElement();
}
if (subDomain != null) {
printWriter.println("<model>");
// variables
printWriter.println("<discreteVariables>");
// Species iniCondition (if in concentration) is sampled from a poisson distribution(which has a mean of the current iniExp value)
// There is only one subDomain for compartmental model
List<VarIniCondition> varInis = subDomain.getVarIniConditions();
if ((varInis != null) && (varInis.size() > 0)) {
RandomDataGenerator dist = new RandomDataGenerator();
if (simulation.getSolverTaskDescription().getStochOpt().isUseCustomSeed()) {
Integer randomSeed = simulation.getSolverTaskDescription().getStochOpt().getCustomSeed();
if (randomSeed != null) {
dist.reSeed(randomSeed);
}
}
printWriter.println("TotalVars" + "\t" + varInis.size());
for (VarIniCondition varIniCondition : varInis) {
try {
Expression iniExp = varIniCondition.getIniVal();
iniExp.bindExpression(simSymbolTable);
iniExp = simSymbolTable.substituteFunctions(iniExp).flatten();
double expectedCount = iniExp.evaluateConstant();
// 1000 mill
final Integer limit = 1000000000;
if (limit < expectedCount) {
String eMessage = "The Initial count for Species '" + varIniCondition.getVar().getName() + "' is " + BigDecimal.valueOf(expectedCount).toBigInteger() + "\n";
eMessage += "which is higher than the internal vCell limit of " + limit + ".\n";
eMessage += "Please reduce the Initial Condition value for this Species or reduce the compartment size.";
throw new MathFormatException(eMessage);
}
long varCount = 0;
if (varIniCondition instanceof VarIniCount) {
varCount = (long) expectedCount;
} else {
if (expectedCount > 0) {
varCount = dist.nextPoisson(expectedCount);
}
}
// System.out.println("expectedCount: " + expectedCount + ", varCount: " + varCount);
printWriter.println(varIniCondition.getVar().getName() + "\t" + varCount);
} catch (ExpressionException ex) {
ex.printStackTrace();
throw new MathFormatException("variable " + varIniCondition.getVar().getName() + "'s initial condition is required to be a constant.");
}
}
} else
printWriter.println("TotalVars" + "\t" + "0");
printWriter.println("</discreteVariables>");
printWriter.println();
// jump processes
printWriter.println("<jumpProcesses>");
List<JumpProcess> jumpProcesses = subDomain.getJumpProcesses();
if ((jumpProcesses != null) && (jumpProcesses.size() > 0)) {
printWriter.println("TotalProcesses" + "\t" + jumpProcesses.size());
for (int i = 0; i < jumpProcesses.size(); i++) {
printWriter.println(jumpProcesses.get(i).getName());
}
} else
printWriter.println("TotalProcesses" + "\t" + "0");
printWriter.println("</jumpProcesses>");
printWriter.println();
// process description
printWriter.println("<processDesc>");
if ((jumpProcesses != null) && (jumpProcesses.size() > 0)) {
printWriter.println("TotalDescriptions" + "\t" + jumpProcesses.size());
for (int i = 0; i < jumpProcesses.size(); i++) {
JumpProcess temProc = (JumpProcess) jumpProcesses.get(i);
// jump process name
printWriter.println("JumpProcess" + "\t" + temProc.getName());
Expression probExp = temProc.getProbabilityRate();
try {
probExp.bindExpression(simSymbolTable);
probExp = simSymbolTable.substituteFunctions(probExp).flatten();
if (!isValidProbabilityExpression(probExp)) {
throw new MathFormatException("probability rate in jump process " + temProc.getName() + " has illegal symbols(should only contain variable names).");
}
} catch (cbit.vcell.parser.ExpressionException ex) {
ex.printStackTrace();
throw new cbit.vcell.parser.ExpressionException("Binding math description error in probability rate in jump process " + temProc.getName() + ". Some symbols can not be resolved.");
}
// Expression temp = replaceVarIniInProbability(probExp);
// Propensity
printWriter.println("\t" + "Propensity" + "\t" + probExp.infix());
// effects
printWriter.println("\t" + "Effect" + "\t" + temProc.getActions().size());
for (int j = 0; j < temProc.getActions().size(); j++) {
printWriter.print("\t\t" + ((Action) temProc.getActions().get(j)).getVar().getName() + "\t" + ((Action) temProc.getActions().get(j)).getOperation());
printWriter.println("\t" + ((Action) temProc.getActions().get(j)).evaluateOperand());
printWriter.println();
}
// dependencies
Vector<String> dependencies = getDependencies(temProc, jumpProcesses);
if ((dependencies != null) && (dependencies.size() > 0)) {
printWriter.println("\t" + "DependentProcesses" + "\t" + dependencies.size());
for (int j = 0; j < dependencies.size(); j++) printWriter.println("\t\t" + dependencies.elementAt(j));
} else
printWriter.println("\t" + "DependentProcesses" + "\t" + "0");
printWriter.println();
}
} else
printWriter.println("TotalDescriptions" + "\t" + "0");
printWriter.println("</processDesc>");
printWriter.println("</model>");
}
// if (subDomain != null)
}
use of cbit.vcell.math.Action in project vcell by virtualcell.
the class StochFileWriter method getDependencies.
/**
* Find all the dependent processes for a given process.
* Creation date: (6/28/2006 4:16:55 PM)
*/
private Vector<String> getDependencies(JumpProcess process, List<JumpProcess> processList) throws Exception {
Vector<String> result = new Vector<String>();
// get affected vars in the given process.
String[] affectedVars = new String[process.getActions().size()];
for (int i = 0; i < process.getActions().size(); i++) {
affectedVars[i] = ((Action) process.getActions().get(i)).getVar().getName();
}
if (affectedVars.length > 0) {
// go through all the processes to find dependants
for (int i = 0; i < processList.size(); i++) {
if (// to avoid comparing with it's own
!process.compareEqual(processList.get(i))) {
Expression probExp = processList.get(i).getProbabilityRate();
probExp = simTask.getSimulationJob().getSimulationSymbolTable().substituteFunctions(probExp).flatten();
String[] vars = probExp.getSymbols();
if ((vars != null) && (vars.length > 0)) {
if (hasCommonElement(affectedVars, vars)) {
result.addElement(processList.get(i).getName());
}
}
}
}
}
return result;
}
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