Example 11 with Feature
use of cbit.vcell.model.Feature in project vcell by virtualcell.
the class SpeciesContextSpec method computeApplicableParameterList.
public List<SpeciesContextSpecParameter> computeApplicableParameterList() {
List<SpeciesContextSpecParameter> speciesContextSpecParameterList = new ArrayList<SpeciesContextSpecParameter>();
speciesContextSpecParameterList.add(getInitialConditionParameter());
int dimension = simulationContext.getGeometry().getDimension();
if (!isConstant() && !isWellMixed() && dimension > 0) {
// diffusion
speciesContextSpecParameterList.add(getDiffusionParameter());
}
if (hasTransport()) {
SpeciesContext speciesContext = getSpeciesContext();
if (speciesContext.getStructure() instanceof Membrane) {
// boundary condition
speciesContextSpecParameterList.add(getBoundaryXmParameter());
speciesContextSpecParameterList.add(getBoundaryXpParameter());
speciesContextSpecParameterList.add(getBoundaryYmParameter());
speciesContextSpecParameterList.add(getBoundaryYpParameter());
if (dimension > 2) {
speciesContextSpecParameterList.add(getBoundaryZmParameter());
speciesContextSpecParameterList.add(getBoundaryZpParameter());
}
} else if (speciesContext.getStructure() instanceof Feature) {
// boundary condition
speciesContextSpecParameterList.add(getBoundaryXmParameter());
speciesContextSpecParameterList.add(getBoundaryXpParameter());
if (dimension > 1) {
speciesContextSpecParameterList.add(getBoundaryYmParameter());
speciesContextSpecParameterList.add(getBoundaryYpParameter());
if (dimension > 2) {
speciesContextSpecParameterList.add(getBoundaryZmParameter());
speciesContextSpecParameterList.add(getBoundaryZpParameter());
}
}
// velocity
speciesContextSpecParameterList.add(getVelocityXParameter());
if (dimension > 1) {
speciesContextSpecParameterList.add(getVelocityYParameter());
if (dimension > 2) {
speciesContextSpecParameterList.add(getVelocityZParameter());
}
}
}
}
return speciesContextSpecParameterList;
}
Also used :
ArrayList(java.util.ArrayList)
Membrane(cbit.vcell.model.Membrane)
SpeciesContext(cbit.vcell.model.SpeciesContext)
Feature(cbit.vcell.model.Feature)
Example 12 with Feature
use of cbit.vcell.model.Feature in project vcell by virtualcell.
the class ElectricalCircuitGraph method getCircuitGraph.
/**
* Insert the method's description here.
* Creation date: (2/19/2002 11:24:04 AM)
* @return cbit.vcell.mapping.potential.Graph
* @param simContext cbit.vcell.mapping.SimulationContext
*/
public static Graph getCircuitGraph(SimulationContext simContext, AbstractMathMapping mathMapping) throws ExpressionException {
Graph graph = new Graph();
Model model = simContext.getModel();
//
// add nodes to the graph (one for each Feature)
//
Structure[] structures = model.getStructures();
for (int i = 0; i < structures.length; i++) {
if (structures[i] instanceof Feature) {
graph.addNode(new Node(structures[i].getName(), structures[i]));
}
}
//
// add edges for all current clamp electrodes (always have dependent voltages)
//
ElectricalStimulus[] stimuli = simContext.getElectricalStimuli();
Electrode groundElectrode = simContext.getGroundElectrode();
for (int i = 0; i < stimuli.length; i++) {
ElectricalStimulus stimulus = stimuli[i];
//
// get electrodes
//
Electrode probeElectrode = stimulus.getElectrode();
if (probeElectrode == null) {
throw new RuntimeException("null electrode for electrical stimulus");
}
if (groundElectrode == null) {
throw new RuntimeException("null ground electrode for electrical stimulus");
}
// if (!membraneMapping.getResolved()){
Node groundNode = graph.getNode(groundElectrode.getFeature().getName());
Node probeNode = graph.getNode(probeElectrode.getFeature().getName());
if (stimulus instanceof CurrentDensityClampStimulus) {
CurrentDensityClampStimulus ccStimulus = (CurrentDensityClampStimulus) stimulus;
ElectricalDevice device = new CurrentClampElectricalDevice(ccStimulus, mathMapping);
Edge edge = new Edge(probeNode, groundNode, device);
graph.addEdge(edge);
} else if (stimulus instanceof TotalCurrentClampStimulus) {
TotalCurrentClampStimulus ccStimulus = (TotalCurrentClampStimulus) stimulus;
ElectricalDevice device = new CurrentClampElectricalDevice(ccStimulus, mathMapping);
Edge edge = new Edge(probeNode, groundNode, device);
graph.addEdge(edge);
}
// }
}
//
// add edges for all membranes
//
ElectricalTopology electricalTopology = simContext.getModel().getElectricalTopology();
for (int i = 0; i < structures.length; i++) {
if (structures[i] instanceof Membrane) {
Membrane membrane = (Membrane) structures[i];
MembraneMapping membraneMapping = (MembraneMapping) simContext.getGeometryContext().getStructureMapping(membrane);
Feature positiveFeature = electricalTopology.getPositiveFeature(membrane);
Feature negativeFeature = electricalTopology.getNegativeFeature(membrane);
if (positiveFeature != null && negativeFeature != null) {
Node insideNode = graph.getNode(positiveFeature.getName());
Node outsideNode = graph.getNode(negativeFeature.getName());
//
// getTotalMembraneCurrent() already converts to "outwardCurrent" so that same convention as voltage
//
Expression currentSource = getTotalMembraneCurrent(simContext, membrane, mathMapping);
MembraneElectricalDevice device = new MembraneElectricalDevice(membraneMapping, mathMapping);
device.getParameterFromRole(ElectricalDevice.ROLE_TransmembraneCurrent).setExpression(currentSource);
Edge edge = new Edge(insideNode, outsideNode, device);
graph.addEdge(edge);
}
}
}
//
for (int i = 0; i < stimuli.length; i++) {
ElectricalStimulus stimulus = stimuli[i];
//
// get electrodes
//
Electrode probeElectrode = stimulus.getElectrode();
if (probeElectrode == null) {
throw new RuntimeException("null electrode for electrical stimulus");
}
if (groundElectrode == null) {
throw new RuntimeException("null ground electrode for electrical stimulus");
}
// if (!membraneMapping.getResolved()){
Node groundNode = graph.getNode(groundElectrode.getFeature().getName());
Node probeNode = graph.getNode(probeElectrode.getFeature().getName());
if (stimulus instanceof VoltageClampStimulus) {
VoltageClampStimulus vcStimulus = (VoltageClampStimulus) stimulus;
ElectricalDevice device = new VoltageClampElectricalDevice(vcStimulus, mathMapping);
Edge edge = new Edge(probeNode, groundNode, device);
graph.addEdge(edge);
}
// }
}
// System.out.println(graph);
return graph;
}
Also used :
MembraneMapping(cbit.vcell.mapping.MembraneMapping)
Electrode(cbit.vcell.mapping.Electrode)
Node(cbit.util.graph.Node)
ElectricalTopology(cbit.vcell.model.Model.ElectricalTopology)
CurrentDensityClampStimulus(cbit.vcell.mapping.CurrentDensityClampStimulus)
Feature(cbit.vcell.model.Feature)
TotalCurrentClampStimulus(cbit.vcell.mapping.TotalCurrentClampStimulus)
ElectricalStimulus(cbit.vcell.mapping.ElectricalStimulus)
Graph(cbit.util.graph.Graph)
Expression(cbit.vcell.parser.Expression)
VoltageClampStimulus(cbit.vcell.mapping.VoltageClampStimulus)
Model(cbit.vcell.model.Model)
Membrane(cbit.vcell.model.Membrane)
Structure(cbit.vcell.model.Structure)
Edge(cbit.util.graph.Edge)
Example 13 with Feature
use of cbit.vcell.model.Feature in project vcell by virtualcell.
the class PotentialMapping method getEdges.
/**
* Insert the method's description here.
* Creation date: (3/2/2002 11:10:22 PM)
* @return cbit.vcell.mapping.potential.Edge[]
*/
private Edge[] getEdges(Membrane membrane) {
java.util.Vector<Edge> edgeList = new java.util.Vector<Edge>();
ElectricalTopology electricalTopology = fieldSimContext.getModel().getElectricalTopology();
for (int i = 0; i < fieldEdges.length; i++) {
boolean a1 = ((Feature) fieldEdges[i].getNode1().getData()).compareEqual(electricalTopology.getPositiveFeature(membrane));
boolean a2 = ((Feature) fieldEdges[i].getNode2().getData()).compareEqual(electricalTopology.getNegativeFeature(membrane));
if (a1 && a2) {
edgeList.add(fieldEdges[i]);
}
boolean b1 = ((Feature) fieldEdges[i].getNode2().getData()).compareEqual(electricalTopology.getPositiveFeature(membrane));
boolean b2 = ((Feature) fieldEdges[i].getNode1().getData()).compareEqual(electricalTopology.getNegativeFeature(membrane));
if (b1 && b2) {
edgeList.add(fieldEdges[i]);
}
}
Edge[] edgesForMembrane = new Edge[edgeList.size()];
edgeList.copyInto(edgesForMembrane);
return edgesForMembrane;
}
Also used :
ElectricalTopology(cbit.vcell.model.Model.ElectricalTopology)
Edge(cbit.util.graph.Edge)
Feature(cbit.vcell.model.Feature)
Example 14 with Feature
use of cbit.vcell.model.Feature in project vcell by virtualcell.
the class MathMapping_4_8 method refreshKFluxParameters.
/**
* Insert the method's description here.
* Creation date: (6/13/2004 8:10:34 AM)
*/
private void refreshKFluxParameters() throws ExpressionException {
MathMapping_4_8.MathMappingParameter[] newMathMappingParameters = (MathMappingParameter[]) fieldMathMappingParameters.clone();
//
for (int i = 0; i < newMathMappingParameters.length; i++) {
if (newMathMappingParameters[i].getRole() == PARAMETER_ROLE_KFLUX) {
newMathMappingParameters = (MathMappingParameter[]) BeanUtils.removeElement(newMathMappingParameters, newMathMappingParameters[i]);
}
}
//
// Add new KFlux Parameters
//
StructureMapping[] structureMappings = simContext.getGeometryContext().getStructureMappings();
StructureTopology structTopology = simContext.getModel().getStructureTopology();
VCUnitDefinition lengthInverseUnit = simContext.getModel().getX().getUnitDefinition().getInverse();
for (int i = 0; i < structureMappings.length; i++) {
if (structureMappings[i] instanceof MembraneMapping && !getResolved(structureMappings[i])) {
MembraneMapping membraneMapping = (MembraneMapping) structureMappings[i];
//
// add "inside" flux correction
//
Expression insideCorrectionExp = getInsideFluxCorrectionExpression(membraneMapping);
insideCorrectionExp.bindExpression(this);
Membrane memMappingMembrane = membraneMapping.getMembrane();
Feature insideFeature = structTopology.getInsideFeature(memMappingMembrane);
String membraneNameWithScope = membraneMapping.getNameScope().getName();
String insideName = "KFlux_" + membraneNameWithScope + "_" + insideFeature.getNameScope().getName();
KFluxParameter insideKFluxParameter = new KFluxParameter(insideName, insideCorrectionExp, lengthInverseUnit, membraneMapping, insideFeature);
newMathMappingParameters = (MathMappingParameter[]) BeanUtils.addElement(newMathMappingParameters, insideKFluxParameter);
//
// add "outside" flux correction
//
Expression outsideCorrectionExp = getOutsideFluxCorrectionExpression(simContext, membraneMapping);
outsideCorrectionExp.bindExpression(this);
Feature outsideFeature = structTopology.getOutsideFeature(memMappingMembrane);
String outsideName = "KFlux_" + membraneNameWithScope + "_" + outsideFeature.getNameScope().getName();
KFluxParameter outsideKFluxParameter = new KFluxParameter(outsideName, outsideCorrectionExp, lengthInverseUnit, membraneMapping, outsideFeature);
newMathMappingParameters = (MathMappingParameter[]) BeanUtils.addElement(newMathMappingParameters, outsideKFluxParameter);
}
}
try {
setMathMapppingParameters(newMathMappingParameters);
} catch (java.beans.PropertyVetoException e) {
e.printStackTrace(System.out);
throw new RuntimeException(e.getMessage());
}
}
Also used :
MembraneMapping(cbit.vcell.mapping.MembraneMapping)
StructureTopology(cbit.vcell.model.Model.StructureTopology)
StructureMapping(cbit.vcell.mapping.StructureMapping)
Feature(cbit.vcell.model.Feature)
PropertyVetoException(java.beans.PropertyVetoException)
VCUnitDefinition(cbit.vcell.units.VCUnitDefinition)
Expression(cbit.vcell.parser.Expression)
Membrane(cbit.vcell.model.Membrane)
Example 15 with Feature
use of cbit.vcell.model.Feature in project vcell by virtualcell.
the class MathMapping_4_8 method refreshMathDescription.
/**
* This method was created in VisualAge.
*/
private void refreshMathDescription() throws MappingException, MatrixException, MathException, ExpressionException, ModelException {
// All sizes must be set for new ODE models and ratios must be set for old ones.
simContext.checkValidity();
//
// temporarily place all variables in a hashtable (before binding) and discarding duplicates (check for equality)
//
VariableHash varHash = new VariableHash();
StructureMapping[] structureMappings = simContext.getGeometryContext().getStructureMappings();
Model model = simContext.getModel();
StructureTopology structTopology = model.getStructureTopology();
//
// verify that all structures are mapped to subvolumes and all subvolumes are mapped to a structure
//
Structure[] structures = simContext.getGeometryContext().getModel().getStructures();
for (int i = 0; i < structures.length; i++) {
StructureMapping sm = simContext.getGeometryContext().getStructureMapping(structures[i]);
if (sm == null || (sm instanceof FeatureMapping && getSubVolume((FeatureMapping) sm) == null)) {
throw new MappingException("model structure '" + structures[i].getName() + "' not mapped to a geometry subdomain");
}
if (sm != null && (sm instanceof MembraneMapping) && ((MembraneMapping) sm).getVolumeFractionParameter() != null) {
Expression volFractExp = ((MembraneMapping) sm).getVolumeFractionParameter().getExpression();
if (volFractExp != null) {
try {
double volFract = volFractExp.evaluateConstant();
if (volFract >= 1.0) {
throw new MappingException("model structure '" + structTopology.getInsideFeature(((MembraneMapping) sm).getMembrane()).getName() + "' has volume fraction >= 1.0");
}
} catch (ExpressionException e) {
}
}
}
}
SubVolume[] subVolumes = simContext.getGeometryContext().getGeometry().getGeometrySpec().getSubVolumes();
for (int i = 0; i < subVolumes.length; i++) {
if (getStructures(subVolumes[i]) == null || getStructures(subVolumes[i]).length == 0) {
throw new MappingException("geometry subdomain '" + subVolumes[i].getName() + "' not mapped from a model structure");
}
}
// deals with model parameters
Hashtable<VolVariable, EventAssignmentInitParameter> eventVolVarHash = new Hashtable<VolVariable, EventAssignmentInitParameter>();
ModelParameter[] modelParameters = model.getModelParameters();
if (simContext.getGeometry().getDimension() == 0) {
//
// global parameters from model (that presently are constants)
//
BioEvent[] bioEvents = simContext.getBioEvents();
ArrayList<SymbolTableEntry> eventAssignTargets = new ArrayList<SymbolTableEntry>();
if (bioEvents != null && bioEvents.length > 0) {
for (BioEvent be : bioEvents) {
for (EventAssignment ea : be.getEventAssignments()) {
if (!eventAssignTargets.contains(ea.getTarget())) {
eventAssignTargets.add(ea.getTarget());
}
}
}
}
for (int j = 0; j < modelParameters.length; j++) {
Expression modelParamExpr = getIdentifierSubstitutions(modelParameters[j].getExpression(), modelParameters[j].getUnitDefinition(), null);
if (eventAssignTargets.contains(modelParameters[j])) {
EventAssignmentInitParameter eap = null;
try {
eap = addEventAssignmentInitParameter(modelParameters[j].getName(), modelParameters[j].getExpression(), PARAMETER_ROLE_EVENTASSIGN_INITCONDN, modelParameters[j].getUnitDefinition());
} catch (PropertyVetoException e) {
e.printStackTrace(System.out);
throw new MappingException(e.getMessage());
}
// varHash.addVariable(newFunctionOrConstant(getMathSymbol(eap, null), modelParamExpr));
VolVariable volVar = new VolVariable(modelParameters[j].getName(), nullDomain);
varHash.addVariable(volVar);
eventVolVarHash.put(volVar, eap);
} else {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(modelParameters[j], null), modelParamExpr));
}
}
} else {
//
for (int pass = 0; pass < 2; pass++) {
for (int j = 0; j < modelParameters.length; j++) {
Hashtable<String, Expression> structMappingVariantsHash = new Hashtable<String, Expression>();
for (int k = 0; k < structureMappings.length; k++) {
String paramVariantName = null;
Expression paramVariantExpr = null;
if (modelParameters[j].getExpression().getSymbols() == null) {
paramVariantName = modelParameters[j].getName();
paramVariantExpr = getIdentifierSubstitutions(modelParameters[j].getExpression(), modelParameters[j].getUnitDefinition(), null);
} else {
paramVariantName = modelParameters[j].getName() + "_" + TokenMangler.fixTokenStrict(structureMappings[k].getStructure().getName());
// if the expression has symbols that do not belong in that structureMapping, do not create the variant.
Expression exp1 = modelParameters[j].getExpression();
Expression flattenedModelParamExpr = substituteGlobalParameters(exp1);
String[] symbols = flattenedModelParamExpr.getSymbols();
boolean bValid = true;
Structure sm_struct = structureMappings[k].getStructure();
if (symbols != null) {
for (int ii = 0; ii < symbols.length; ii++) {
SpeciesContext sc = model.getSpeciesContext(symbols[ii]);
if (sc != null) {
// symbol[ii] is a speciesContext, check its structure with structureMapping[k].structure. If they are the same or
// if it is the adjacent membrane(s), allow variant expression to be created. Else, continue.
Structure sp_struct = sc.getStructure();
if (sp_struct.compareEqual(sm_struct)) {
bValid = bValid && true;
} else {
// if the 2 structures are not the same, are they adjacent? then 'bValid' is true, else false.
if ((sm_struct instanceof Feature) && (sp_struct instanceof Membrane)) {
Feature sm_feature = (Feature) sm_struct;
Membrane sp_mem = (Membrane) sp_struct;
if (sp_mem.compareEqual(structTopology.getParentStructure(sm_feature)) || (structTopology.getInsideFeature(sp_mem).compareEqual(sm_feature) || structTopology.getOutsideFeature(sp_mem).compareEqual(sm_feature))) {
bValid = bValid && true;
} else {
bValid = bValid && false;
break;
}
} else if ((sm_struct instanceof Membrane) && (sp_struct instanceof Feature)) {
Feature sp_feature = (Feature) sp_struct;
Membrane sm_mem = (Membrane) sm_struct;
if (sm_mem.compareEqual(structTopology.getParentStructure(sp_feature)) || (structTopology.getInsideFeature(sm_mem).compareEqual(sp_feature) || structTopology.getOutsideFeature(sm_mem).compareEqual(sp_feature))) {
bValid = bValid && true;
} else {
bValid = bValid && false;
break;
}
} else {
bValid = bValid && false;
break;
}
}
}
}
}
if (bValid) {
if (pass == 0) {
paramVariantExpr = new Expression("VCELL_TEMPORARY_EXPRESSION_PLACEHOLDER");
} else {
paramVariantExpr = getIdentifierSubstitutions(modelParameters[j].getExpression(), modelParameters[j].getUnitDefinition(), structureMappings[k]);
}
}
}
if (paramVariantExpr != null) {
structMappingVariantsHash.put(paramVariantName, paramVariantExpr);
}
}
globalParamVariantsHash.put(modelParameters[j], structMappingVariantsHash);
}
}
//
for (int j = 0; j < modelParameters.length; j++) {
if (modelParameters[j].getExpression().getSymbols() == null) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(modelParameters[j], null), getIdentifierSubstitutions(modelParameters[j].getExpression(), modelParameters[j].getUnitDefinition(), null)));
} else {
Hashtable<String, Expression> smVariantsHash = globalParamVariantsHash.get(modelParameters[j]);
for (int k = 0; k < structureMappings.length; k++) {
String variantName = modelParameters[j].getName() + "_" + TokenMangler.fixTokenStrict(structureMappings[k].getStructure().getName());
Expression variantExpr = smVariantsHash.get(variantName);
if (variantExpr != null) {
varHash.addVariable(newFunctionOrConstant(variantName, variantExpr));
}
}
}
}
}
//
// gather only those reactionSteps that are not "excluded"
//
ReactionSpec[] reactionSpecs = simContext.getReactionContext().getReactionSpecs();
Vector<ReactionStep> rsList = new Vector<ReactionStep>();
for (int i = 0; i < reactionSpecs.length; i++) {
if (reactionSpecs[i].isExcluded() == false) {
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);
}
}
//
// create new MathDescription (based on simContext's previous MathDescription if possible)
//
MathDescription oldMathDesc = simContext.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(simContext.getName() + "_generated");
}
//
// volume variables
//
Enumeration<SpeciesContextMapping> enum1 = getSpeciesContextMappings();
while (enum1.hasMoreElements()) {
SpeciesContextMapping scm = enum1.nextElement();
if (scm.getVariable() instanceof VolVariable) {
if (!(mathDesc.getVariable(scm.getVariable().getName()) instanceof VolVariable)) {
varHash.addVariable(scm.getVariable());
}
}
}
//
// membrane variables
//
enum1 = getSpeciesContextMappings();
while (enum1.hasMoreElements()) {
SpeciesContextMapping scm = (SpeciesContextMapping) enum1.nextElement();
if (scm.getVariable() instanceof MemVariable) {
varHash.addVariable(scm.getVariable());
}
}
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(simContext.getTemperatureKelvin()), model.getTEMPERATURE().getUnitDefinition(), null)));
//
// only calculate potential if at least one MembraneMapping has CalculateVoltage == true
//
boolean bCalculatePotential = false;
for (int i = 0; i < structureMappings.length; i++) {
if (structureMappings[i] instanceof MembraneMapping) {
if (((MembraneMapping) structureMappings[i]).getCalculateVoltage()) {
bCalculatePotential = true;
}
}
}
// (simContext.getGeometry().getDimension() == 0);
potentialMapping = new PotentialMapping(simContext, this);
potentialMapping.computeMath();
if (bCalculatePotential) {
//
// copy functions for currents and constants for capacitances
//
ElectricalDevice[] devices = potentialMapping.getElectricalDevices();
for (int j = 0; j < devices.length; j++) {
if (devices[j] instanceof MembraneElectricalDevice) {
MembraneElectricalDevice membraneElectricalDevice = (MembraneElectricalDevice) devices[j];
MembraneMapping memMapping = membraneElectricalDevice.getMembraneMapping();
Parameter specificCapacitanceParm = memMapping.getParameterFromRole(MembraneMapping.ROLE_SpecificCapacitance);
varHash.addVariable(new Constant(getMathSymbol(specificCapacitanceParm, memMapping), getIdentifierSubstitutions(specificCapacitanceParm.getExpression(), specificCapacitanceParm.getUnitDefinition(), memMapping)));
ElectricalDevice.ElectricalDeviceParameter transmembraneCurrentParm = membraneElectricalDevice.getParameterFromRole(ElectricalDevice.ROLE_TransmembraneCurrent);
ElectricalDevice.ElectricalDeviceParameter totalCurrentParm = membraneElectricalDevice.getParameterFromRole(ElectricalDevice.ROLE_TotalCurrent);
ElectricalDevice.ElectricalDeviceParameter capacitanceParm = membraneElectricalDevice.getParameterFromRole(ElectricalDevice.ROLE_Capacitance);
if (totalCurrentParm != null && /* totalCurrentDensityParm.getExpression()!=null && */
memMapping.getCalculateVoltage()) {
Expression totalCurrentDensityExp = (totalCurrentParm.getExpression() != null) ? (totalCurrentParm.getExpression()) : (new Expression(0.0));
varHash.addVariable(newFunctionOrConstant(getMathSymbol(totalCurrentParm, membraneElectricalDevice.getMembraneMapping()), getIdentifierSubstitutions(totalCurrentDensityExp, totalCurrentParm.getUnitDefinition(), membraneElectricalDevice.getMembraneMapping())));
}
if (transmembraneCurrentParm != null && transmembraneCurrentParm.getExpression() != null && memMapping.getCalculateVoltage()) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(transmembraneCurrentParm, membraneElectricalDevice.getMembraneMapping()), getIdentifierSubstitutions(transmembraneCurrentParm.getExpression(), transmembraneCurrentParm.getUnitDefinition(), membraneElectricalDevice.getMembraneMapping())));
}
if (capacitanceParm != null && capacitanceParm.getExpression() != null && memMapping.getCalculateVoltage()) {
StructureMappingParameter sizeParameter = membraneElectricalDevice.getMembraneMapping().getSizeParameter();
if (simContext.getGeometry().getDimension() == 0 && (sizeParameter.getExpression() == null || sizeParameter.getExpression().isZero())) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(capacitanceParm, membraneElectricalDevice.getMembraneMapping()), getIdentifierSubstitutions(Expression.mult(memMapping.getNullSizeParameterValue(), specificCapacitanceParm.getExpression()), capacitanceParm.getUnitDefinition(), membraneElectricalDevice.getMembraneMapping())));
} else {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(capacitanceParm, membraneElectricalDevice.getMembraneMapping()), getIdentifierSubstitutions(capacitanceParm.getExpression(), capacitanceParm.getUnitDefinition(), membraneElectricalDevice.getMembraneMapping())));
}
}
//
if (membraneElectricalDevice.getDependentVoltageExpression() == null) {
// is Voltage Independent?
StructureMapping.StructureMappingParameter initialVoltageParm = memMapping.getInitialVoltageParameter();
varHash.addVariable(newFunctionOrConstant(getMathSymbol(initialVoltageParm, memMapping), getIdentifierSubstitutions(initialVoltageParm.getExpression(), initialVoltageParm.getUnitDefinition(), memMapping)));
} else //
// membrane forced potential
//
{
varHash.addVariable(newFunctionOrConstant(getMathSymbol(memMapping.getMembrane().getMembraneVoltage(), memMapping), getIdentifierSubstitutions(membraneElectricalDevice.getDependentVoltageExpression(), memMapping.getMembrane().getMembraneVoltage().getUnitDefinition(), memMapping)));
}
} else if (devices[j] instanceof CurrentClampElectricalDevice) {
CurrentClampElectricalDevice currentClampDevice = (CurrentClampElectricalDevice) devices[j];
// total current = current source (no capacitance)
Parameter totalCurrentParm = currentClampDevice.getParameterFromRole(CurrentClampElectricalDevice.ROLE_TotalCurrent);
Parameter currentParm = currentClampDevice.getParameterFromRole(CurrentClampElectricalDevice.ROLE_TransmembraneCurrent);
// Parameter dependentVoltage = currentClampDevice.getCurrentClampStimulus().getVoltageParameter();
varHash.addVariable(newFunctionOrConstant(getMathSymbol(totalCurrentParm, null), getIdentifierSubstitutions(totalCurrentParm.getExpression(), totalCurrentParm.getUnitDefinition(), null)));
varHash.addVariable(newFunctionOrConstant(getMathSymbol(currentParm, null), getIdentifierSubstitutions(currentParm.getExpression(), currentParm.getUnitDefinition(), null)));
// varHash.addVariable(newFunctionOrConstant(getMathSymbol(dependentVoltage,null),getIdentifierSubstitutions(currentClampDevice.getDependentVoltageExpression(),dependentVoltage.getUnitDefinition(),null)));
//
// add user-defined parameters
//
ElectricalDevice.ElectricalDeviceParameter[] parameters = currentClampDevice.getParameters();
for (int k = 0; k < parameters.length; k++) {
if (parameters[k].getExpression() != null) {
// guards against voltage parameters that are "variable".
varHash.addVariable(newFunctionOrConstant(getMathSymbol(parameters[k], null), getIdentifierSubstitutions(parameters[k].getExpression(), parameters[k].getUnitDefinition(), null)));
}
}
} else if (devices[j] instanceof VoltageClampElectricalDevice) {
VoltageClampElectricalDevice voltageClampDevice = (VoltageClampElectricalDevice) devices[j];
// total current = current source (no capacitance)
Parameter totalCurrent = voltageClampDevice.getParameterFromRole(VoltageClampElectricalDevice.ROLE_TotalCurrent);
Parameter totalCurrentParm = voltageClampDevice.getParameterFromRole(VoltageClampElectricalDevice.ROLE_TotalCurrent);
Parameter voltageParm = voltageClampDevice.getParameterFromRole(VoltageClampElectricalDevice.ROLE_Voltage);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(totalCurrent, null), getIdentifierSubstitutions(totalCurrent.getExpression(), totalCurrent.getUnitDefinition(), null)));
varHash.addVariable(newFunctionOrConstant(getMathSymbol(totalCurrentParm, null), getIdentifierSubstitutions(totalCurrentParm.getExpression(), totalCurrentParm.getUnitDefinition(), null)));
varHash.addVariable(newFunctionOrConstant(getMathSymbol(voltageParm, null), getIdentifierSubstitutions(voltageParm.getExpression(), voltageParm.getUnitDefinition(), null)));
//
// add user-defined parameters
//
ElectricalDevice.ElectricalDeviceParameter[] parameters = voltageClampDevice.getParameters();
for (int k = 0; k < parameters.length; k++) {
if (parameters[k].getRole() == ElectricalDevice.ROLE_UserDefined) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(parameters[k], null), getIdentifierSubstitutions(parameters[k].getExpression(), parameters[k].getUnitDefinition(), null)));
}
}
}
}
} else {
//
for (int j = 0; j < structureMappings.length; j++) {
if (structureMappings[j] instanceof MembraneMapping) {
MembraneMapping memMapping = (MembraneMapping) structureMappings[j];
varHash.addVariable(newFunctionOrConstant(getMathSymbol(memMapping.getMembrane().getMembraneVoltage(), memMapping), getIdentifierSubstitutions(memMapping.getInitialVoltageParameter().getExpression(), memMapping.getInitialVoltageParameter().getUnitDefinition(), memMapping)));
}
}
}
//
for (int j = 0; j < structureMappings.length; j++) {
if (structureMappings[j] instanceof MembraneMapping) {
MembraneMapping membraneMapping = (MembraneMapping) structureMappings[j];
Membrane.MembraneVoltage membraneVoltage = membraneMapping.getMembrane().getMembraneVoltage();
ElectricalDevice[] membraneDevices = potentialMapping.getElectricalDevices(membraneMapping.getMembrane());
// ElectricalDevice membraneDevice = null;
for (int i = 0; i < membraneDevices.length; i++) {
if (membraneDevices[i].hasCapacitance() && membraneDevices[i].getDependentVoltageExpression() == null) {
if (membraneMapping.getCalculateVoltage() && bCalculatePotential) {
if (getResolved(membraneMapping)) {
//
if (mathDesc.getVariable(Membrane.MEMBRANE_VOLTAGE_REGION_NAME) == null) {
// varHash.addVariable(new MembraneRegionVariable(MembraneVoltage.MEMBRANE_VOLTAGE_REGION_NAME));
varHash.addVariable(new MembraneRegionVariable(getMathSymbol(membraneVoltage, membraneMapping), nullDomain));
}
} else {
//
// spatially unresolved membrane, and must solve for potential ... make VolVariable for this compartment
//
varHash.addVariable(new VolVariable(getMathSymbol(membraneVoltage, membraneMapping), nullDomain));
}
Parameter initialVoltageParm = membraneMapping.getInitialVoltageParameter();
Variable initVoltageFunction = newFunctionOrConstant(getMathSymbol(initialVoltageParm, membraneMapping), getIdentifierSubstitutions(initialVoltageParm.getExpression(), initialVoltageParm.getUnitDefinition(), membraneMapping));
varHash.addVariable(initVoltageFunction);
} else {
//
// don't calculate voltage, still may need it though
//
Parameter initialVoltageParm = membraneMapping.getInitialVoltageParameter();
Variable voltageFunction = newFunctionOrConstant(getMathSymbol(membraneMapping.getMembrane().getMembraneVoltage(), membraneMapping), getIdentifierSubstitutions(initialVoltageParm.getExpression(), initialVoltageParm.getUnitDefinition(), membraneMapping));
varHash.addVariable(voltageFunction);
}
}
}
}
}
//
for (int j = 0; j < reactionSteps.length; j++) {
ReactionStep rs = reactionSteps[j];
if (simContext.getReactionContext().getReactionSpec(rs).isExcluded()) {
continue;
}
Kinetics.KineticsParameter[] parameters = rs.getKinetics().getKineticsParameters();
StructureMapping sm = simContext.getGeometryContext().getStructureMapping(rs.getStructure());
if (parameters != null) {
for (int i = 0; i < parameters.length; i++) {
if (((parameters[i].getRole() == Kinetics.ROLE_CurrentDensity) || (parameters[i].getRole() == Kinetics.ROLE_LumpedCurrent)) && (parameters[i].getExpression() == null || parameters[i].getExpression().isZero())) {
continue;
}
varHash.addVariable(newFunctionOrConstant(getMathSymbol(parameters[i], sm), getIdentifierSubstitutions(parameters[i].getExpression(), parameters[i].getUnitDefinition(), sm)));
}
}
}
//
// initial constants (either function or constant)
//
SpeciesContextSpec[] speciesContextSpecs = simContext.getReactionContext().getSpeciesContextSpecs();
for (int i = 0; i < speciesContextSpecs.length; i++) {
SpeciesContextSpecParameter initParm = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_InitialConcentration);
if (initParm != null) {
Expression initExpr = new Expression(initParm.getExpression());
StructureMapping sm = simContext.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 = simContext.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), getIdentifierSubstitutions(initExpr, initParm.getUnitDefinition(), sm)));
}
}
//
for (int i = 0; i < speciesContextSpecs.length; i++) {
SpeciesContextMapping scm = getSpeciesContextMapping(speciesContextSpecs[i].getSpeciesContext());
SpeciesContextSpec.SpeciesContextSpecParameter diffParm = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_DiffusionRate);
if (diffParm != null && (scm.isPDERequired())) {
StructureMapping sm = simContext.getGeometryContext().getStructureMapping(speciesContextSpecs[i].getSpeciesContext().getStructure());
varHash.addVariable(newFunctionOrConstant(getMathSymbol(diffParm, sm), getIdentifierSubstitutions(diffParm.getExpression(), diffParm.getUnitDefinition(), sm)));
}
}
//
for (int i = 0; i < speciesContextSpecs.length; i++) {
SpeciesContextSpec.SpeciesContextSpecParameter bc_xm = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_BoundaryValueXm);
StructureMapping sm = simContext.getGeometryContext().getStructureMapping(speciesContextSpecs[i].getSpeciesContext().getStructure());
if (bc_xm != null && (bc_xm.getExpression() != null)) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(bc_xm, sm), getIdentifierSubstitutions(bc_xm.getExpression(), bc_xm.getUnitDefinition(), sm)));
}
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), getIdentifierSubstitutions(bc_xp.getExpression(), bc_xp.getUnitDefinition(), sm)));
}
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), getIdentifierSubstitutions(bc_ym.getExpression(), bc_ym.getUnitDefinition(), sm)));
}
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), getIdentifierSubstitutions(bc_yp.getExpression(), bc_yp.getUnitDefinition(), sm)));
}
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), getIdentifierSubstitutions(bc_zm.getExpression(), bc_zm.getUnitDefinition(), sm)));
}
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), getIdentifierSubstitutions(bc_zp.getExpression(), bc_zp.getUnitDefinition(), sm)));
}
}
//
for (int i = 0; i < speciesContextSpecs.length; i++) {
SpeciesContextSpec.SpeciesContextSpecParameter advection_velX = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_VelocityX);
StructureMapping sm = simContext.getGeometryContext().getStructureMapping(speciesContextSpecs[i].getSpeciesContext().getStructure());
if (advection_velX != null && (advection_velX.getExpression() != null)) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(advection_velX, sm), getIdentifierSubstitutions(advection_velX.getExpression(), advection_velX.getUnitDefinition(), sm)));
}
SpeciesContextSpec.SpeciesContextSpecParameter advection_velY = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_VelocityY);
if (advection_velY != null && (advection_velY.getExpression() != null)) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(advection_velY, sm), getIdentifierSubstitutions(advection_velY.getExpression(), advection_velY.getUnitDefinition(), sm)));
}
SpeciesContextSpec.SpeciesContextSpecParameter advection_velZ = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_VelocityZ);
if (advection_velZ != null && (advection_velZ.getExpression() != null)) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(advection_velZ, sm), getIdentifierSubstitutions(advection_velZ.getExpression(), advection_velZ.getUnitDefinition(), sm)));
}
}
//
// 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(model.getN_PMOLE().getName(), getIdentifierSubstitutions(model.getN_PMOLE().getExpression(), model.getN_PMOLE().getUnitDefinition(), null)));
varHash.addVariable(new Constant(model.getKMILLIVOLTS().getName(), getIdentifierSubstitutions(model.getKMILLIVOLTS().getExpression(), model.getKMILLIVOLTS().getUnitDefinition(), null)));
varHash.addVariable(new Constant(model.getK_GHK().getName(), getIdentifierSubstitutions(model.getK_GHK().getExpression(), model.getK_GHK().getUnitDefinition(), null)));
//
// geometric functions
//
ModelUnitSystem modelUnitSystem = simContext.getModel().getUnitSystem();
VCUnitDefinition lengthInverseUnit = modelUnitSystem.getLengthUnit().getInverse();
for (int i = 0; i < structureMappings.length; i++) {
StructureMapping sm = structureMappings[i];
Parameter parm = sm.getParameterFromRole(StructureMapping.ROLE_VolumeFraction);
if (parm != null && parm.getExpression() != null && sm.getGeometryClass() instanceof SubVolume) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(parm, sm), getIdentifierSubstitutions(parm.getExpression(), parm.getUnitDefinition(), sm)));
}
parm = sm.getParameterFromRole(StructureMapping.ROLE_SurfaceToVolumeRatio);
if (parm != null && parm.getExpression() != null && sm.getGeometryClass() instanceof SubVolume) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(parm, sm), getIdentifierSubstitutions(parm.getExpression(), parm.getUnitDefinition(), sm)));
}
if (sm instanceof MembraneMapping && !getResolved(sm)) {
MembraneMapping mm = (MembraneMapping) sm;
parm = ((MembraneMapping) sm).getVolumeFractionParameter();
if (parm.getExpression() == null) {
throw new MappingException("volume fraction not specified for feature '" + structTopology.getInsideFeature(mm.getMembrane()).getName() + "', please refer to Structure Mapping in Application '" + simContext.getName() + "'");
}
varHash.addVariable(newFunctionOrConstant(getMathSymbol(parm, sm), getIdentifierSubstitutions(parm.getExpression(), modelUnitSystem.getInstance_DIMENSIONLESS(), sm)));
parm = mm.getSurfaceToVolumeParameter();
if (parm.getExpression() == null) {
throw new MappingException("surface to volume ratio not specified for membrane '" + mm.getMembrane().getName() + "', please refer to Structure Mapping in Application '" + simContext.getName() + "'");
}
varHash.addVariable(newFunctionOrConstant(getMathSymbol(parm, sm), getIdentifierSubstitutions(parm.getExpression(), lengthInverseUnit, sm)));
}
StructureMappingParameter sizeParm = sm.getSizeParameter();
if (sizeParm != null) {
if (simContext.getGeometry().getDimension() == 0) {
if (sizeParm.getExpression() != null) {
try {
double value = sizeParm.getExpression().evaluateConstant();
varHash.addVariable(new Constant(getMathSymbol(sizeParm, sm), new Expression(value)));
} catch (ExpressionException e) {
// varHash.addVariable(new Function(getMathSymbol(parm,sm),getIdentifierSubstitutions(parm.getExpression(),parm.getUnitDefinition(),sm)));
e.printStackTrace(System.out);
throw new MappingException("Size of structure:" + sm.getNameScope().getName() + " cannot be evaluated as constant.");
}
}
} else {
String compartmentName = null;
VCUnitDefinition sizeUnit = sm.getSizeParameter().getUnitDefinition();
String sizeFunctionName = null;
if (sm instanceof MembraneMapping) {
MembraneMapping mm = (MembraneMapping) sm;
if (getResolved(mm)) {
FeatureMapping fm_inside = (FeatureMapping) simContext.getGeometryContext().getStructureMapping(structTopology.getInsideFeature(mm.getMembrane()));
FeatureMapping fm_outside = (FeatureMapping) simContext.getGeometryContext().getStructureMapping(structTopology.getOutsideFeature(mm.getMembrane()));
compartmentName = getSubVolume(fm_inside).getName() + "_" + getSubVolume(fm_outside).getName();
sizeFunctionName = MathFunctionDefinitions.Function_regionArea_current.getFunctionName();
} else {
FeatureMapping fm_inside = (FeatureMapping) simContext.getGeometryContext().getStructureMapping(structTopology.getInsideFeature(mm.getMembrane()));
FeatureMapping fm_outside = (FeatureMapping) simContext.getGeometryContext().getStructureMapping(structTopology.getOutsideFeature(mm.getMembrane()));
if (getSubVolume(fm_inside) == getSubVolume(fm_outside)) {
compartmentName = getSubVolume(fm_inside).getName();
sizeFunctionName = MathFunctionDefinitions.Function_regionVolume_current.getFunctionName();
} else {
throw new RuntimeException("unexpected structure mapping for membrane '" + mm.getMembrane().getName() + "'");
}
}
} else if (sm instanceof FeatureMapping) {
FeatureMapping fm = (FeatureMapping) sm;
compartmentName = getSubVolume(fm).getName();
sizeFunctionName = MathFunctionDefinitions.Function_regionVolume_current.getFunctionName();
} else {
throw new RuntimeException("structure mapping " + sm.getClass().getName() + " not yet supported");
}
Expression totalVolumeCorrection = sm.getStructureSizeCorrection(simContext, this);
Expression sizeFunctionExpression = Expression.function(sizeFunctionName, new Expression[] { new Expression("'" + compartmentName + "'") });
sizeFunctionExpression.bindExpression(mathDesc);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(sizeParm, sm), getIdentifierSubstitutions(Expression.mult(totalVolumeCorrection, sizeFunctionExpression), sizeUnit, sm)));
parm = sm.getParameterFromRole(StructureMapping.ROLE_AreaPerUnitArea);
if (parm != null && parm.getExpression() != null && sm.getGeometryClass() instanceof SurfaceClass) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(parm, sm), getIdentifierSubstitutions(parm.getExpression(), parm.getUnitDefinition(), sm)));
}
parm = sm.getParameterFromRole(StructureMapping.ROLE_AreaPerUnitVolume);
if (parm != null && parm.getExpression() != null && sm.getGeometryClass() instanceof SubVolume) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(parm, sm), getIdentifierSubstitutions(parm.getExpression(), parm.getUnitDefinition(), sm)));
}
parm = sm.getParameterFromRole(StructureMapping.ROLE_VolumePerUnitArea);
if (parm != null && parm.getExpression() != null && sm.getGeometryClass() instanceof SurfaceClass) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(parm, sm), getIdentifierSubstitutions(parm.getExpression(), parm.getUnitDefinition(), sm)));
}
parm = sm.getParameterFromRole(StructureMapping.ROLE_VolumePerUnitVolume);
if (parm != null && parm.getExpression() != null && sm.getGeometryClass() instanceof SubVolume) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(parm, sm), getIdentifierSubstitutions(parm.getExpression(), parm.getUnitDefinition(), sm)));
}
}
}
}
//
for (int i = 0; i < fieldMathMappingParameters.length; i++) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(fieldMathMappingParameters[i], null), getIdentifierSubstitutions(fieldMathMappingParameters[i].getExpression(), fieldMathMappingParameters[i].getUnitDefinition(), null)));
}
//
// functions
//
enum1 = getSpeciesContextMappings();
while (enum1.hasMoreElements()) {
SpeciesContextMapping scm = (SpeciesContextMapping) enum1.nextElement();
if (scm.getVariable() == null && scm.getDependencyExpression() != null) {
StructureMapping sm = simContext.getGeometryContext().getStructureMapping(scm.getSpeciesContext().getStructure());
varHash.addVariable(newFunctionOrConstant(getMathSymbol(scm.getSpeciesContext(), sm), getIdentifierSubstitutions(scm.getDependencyExpression(), scm.getSpeciesContext().getUnitDefinition(), sm)));
}
}
//
// set Variables to MathDescription all at once with the order resolved by "VariableHash"
//
mathDesc.setAllVariables(varHash.getAlphabeticallyOrderedVariables());
//
if (simContext.getGeometryContext().getGeometry() != null) {
try {
mathDesc.setGeometry(simContext.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");
}
//
// volume subdomains
//
subVolumes = simContext.getGeometryContext().getGeometry().getGeometrySpec().getSubVolumes();
VCUnitDefinition timeUnit = modelUnitSystem.getTimeUnit();
for (int j = 0; j < subVolumes.length; j++) {
SubVolume subVolume = (SubVolume) subVolumes[j];
//
// get priority of subDomain
//
int priority;
Feature spatialFeature = getResolvedFeature(subVolume);
if (spatialFeature == null) {
if (simContext.getGeometryContext().getGeometry().getDimension() > 0) {
throw new MappingException("no compartment (in Physiology) is mapped to subdomain '" + subVolume.getName() + "' (in Geometry)");
} else {
priority = CompartmentSubDomain.NON_SPATIAL_PRIORITY;
}
} else {
// now does not have to match spatial feature, *BUT* needs to be unique
priority = j;
}
//
// create subDomain
//
CompartmentSubDomain subDomain = new CompartmentSubDomain(subVolume.getName(), priority);
mathDesc.addSubDomain(subDomain);
//
if (spatialFeature != null) {
FeatureMapping fm = (FeatureMapping) simContext.getGeometryContext().getStructureMapping(spatialFeature);
subDomain.setBoundaryConditionXm(fm.getBoundaryConditionTypeXm());
subDomain.setBoundaryConditionXp(fm.getBoundaryConditionTypeXp());
if (simContext.getGeometry().getDimension() > 1) {
subDomain.setBoundaryConditionYm(fm.getBoundaryConditionTypeYm());
subDomain.setBoundaryConditionYp(fm.getBoundaryConditionTypeYp());
}
if (simContext.getGeometry().getDimension() > 2) {
subDomain.setBoundaryConditionZm(fm.getBoundaryConditionTypeZm());
subDomain.setBoundaryConditionZp(fm.getBoundaryConditionTypeZp());
}
}
//
// create equations
//
VolumeStructureAnalyzer structureAnalyzer = getVolumeStructureAnalyzer(subVolume);
Enumeration<SpeciesContextMapping> enumSCM = getSpeciesContextMappings();
while (enumSCM.hasMoreElements()) {
SpeciesContextMapping scm = enumSCM.nextElement();
//
if (scm.getVariable() instanceof VolVariable && scm.getDependencyExpression() == null) {
SpeciesContext sc = scm.getSpeciesContext();
StructureMapping sm = simContext.getGeometryContext().getStructureMapping(sc.getStructure());
SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec(sc);
VolVariable variable = (VolVariable) scm.getVariable();
Equation equation = null;
if ((scm.isPDERequired()) && sm instanceof FeatureMapping) {
//
if (getSubVolume((FeatureMapping) sm) == subVolume) {
//
// species context belongs to this subDomain
//
Expression initial = new Expression(getMathSymbol(scs.getParameterFromRole(SpeciesContextSpec.ROLE_InitialConcentration), sm));
Expression rate = getIdentifierSubstitutions(scm.getRate(), scm.getSpeciesContext().getUnitDefinition().divideBy(timeUnit), simContext.getGeometryContext().getStructureMapping(sc.getStructure()));
Expression diffusion = new Expression(getMathSymbol(scs.getDiffusionParameter(), sm));
equation = new PdeEquation(variable, initial, rate, diffusion);
((PdeEquation) equation).setBoundaryXm((scs.getBoundaryXmParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryXmParameter(), sm)));
((PdeEquation) equation).setBoundaryXp((scs.getBoundaryXpParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryXpParameter(), sm)));
((PdeEquation) equation).setBoundaryYm((scs.getBoundaryYmParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryYmParameter(), sm)));
((PdeEquation) equation).setBoundaryYp((scs.getBoundaryYpParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryYpParameter(), sm)));
((PdeEquation) equation).setBoundaryZm((scs.getBoundaryZmParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryZmParameter(), sm)));
((PdeEquation) equation).setBoundaryZp((scs.getBoundaryZpParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryZpParameter(), sm)));
((PdeEquation) equation).setVelocityX((scs.getVelocityXParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getVelocityXParameter(), sm)));
((PdeEquation) equation).setVelocityY((scs.getVelocityYParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getVelocityYParameter(), sm)));
((PdeEquation) equation).setVelocityZ((scs.getVelocityZParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getVelocityZParameter(), sm)));
subDomain.replaceEquation(equation);
} else {
Expression initial = new Expression(0.0);
Expression rate = new Expression(0.0);
Expression diffusion = new Expression(getMathSymbol(scs.getDiffusionParameter(), sm));
equation = new PdeEquation(variable, initial, rate, diffusion);
if (subDomain.getEquation(variable) == null) {
subDomain.addEquation(equation);
}
}
} else {
//
// ODE
//
SubVolume mappedSubVolume = null;
if (sm instanceof FeatureMapping) {
mappedSubVolume = getSubVolume((FeatureMapping) sm);
} else if (sm instanceof MembraneMapping) {
// membrane is mapped to that of the inside feature
FeatureMapping featureMapping = (FeatureMapping) simContext.getGeometryContext().getStructureMapping(structTopology.getInsideFeature((Membrane) sm.getStructure()));
mappedSubVolume = getSubVolume(featureMapping);
}
if (mappedSubVolume == subVolume) {
//
// species context belongs to this subDomain
//
Expression initial = new Expression(getMathSymbol(scs.getParameterFromRole(SpeciesContextSpec.ROLE_InitialConcentration), null));
Expression rate = (scm.getRate() == null) ? new Expression(0.0) : getIdentifierSubstitutions(scm.getRate(), scm.getSpeciesContext().getUnitDefinition().divideBy(timeUnit), simContext.getGeometryContext().getStructureMapping(sc.getStructure()));
equation = new OdeEquation(variable, initial, rate);
subDomain.replaceEquation(equation);
} else {
Expression initial = new Expression(0.0);
Expression rate = new Expression(0.0);
equation = new OdeEquation(variable, initial, rate);
if (subDomain.getEquation(variable) == null) {
subDomain.addEquation(equation);
}
}
}
}
}
//
// create fast system (if neccessary)
//
SpeciesContextMapping[] fastSpeciesContextMappings = structureAnalyzer.getFastSpeciesContextMappings();
VCUnitDefinition subDomainUnit = modelUnitSystem.getVolumeConcentrationUnit();
if (fastSpeciesContextMappings != null) {
FastSystem fastSystem = new FastSystem(mathDesc);
for (int i = 0; i < fastSpeciesContextMappings.length; i++) {
SpeciesContextMapping scm = fastSpeciesContextMappings[i];
if (scm.getFastInvariant() == null) {
//
// independant-fast variable, create a fastRate object
//
Expression rate = getIdentifierSubstitutions(scm.getFastRate(), scm.getSpeciesContext().getUnitDefinition().divideBy(timeUnit), simContext.getGeometryContext().getStructureMapping(getResolvedFeature(subVolume)));
FastRate fastRate = new FastRate(rate);
fastSystem.addFastRate(fastRate);
} else {
//
// dependant-fast variable, create a fastInvariant object
//
Expression rate = getIdentifierSubstitutions(scm.getFastInvariant(), subDomainUnit, simContext.getGeometryContext().getStructureMapping(getResolvedFeature(subVolume)));
FastInvariant fastInvariant = new FastInvariant(rate);
fastSystem.addFastInvariant(fastInvariant);
}
}
subDomain.setFastSystem(fastSystem);
// constructor calls the 'refresh' method which constructs depemdency matrix, dependent/independent vars and pseudoconstants, etc.
FastSystemAnalyzer fs_analyzer = new FastSystemAnalyzer(fastSystem, mathDesc);
}
//
// create ode's for voltages to be calculated on unresolved membranes mapped to this subVolume
//
Structure[] localStructures = getStructures(subVolume);
for (int sIndex = 0; sIndex < localStructures.length; sIndex++) {
if (localStructures[sIndex] instanceof Membrane) {
Membrane membrane = (Membrane) localStructures[sIndex];
MembraneMapping membraneMapping = (MembraneMapping) simContext.getGeometryContext().getStructureMapping(membrane);
if (!getResolved(membraneMapping) && membraneMapping.getCalculateVoltage()) {
MembraneElectricalDevice capacitiveDevice = potentialMapping.getCapacitiveDevice(membrane);
if (capacitiveDevice.getDependentVoltageExpression() == null) {
VolVariable vVar = (VolVariable) mathDesc.getVariable(getMathSymbol(capacitiveDevice.getVoltageSymbol(), membraneMapping));
Expression initExp = new Expression(getMathSymbol(capacitiveDevice.getMembraneMapping().getInitialVoltageParameter(), membraneMapping));
subDomain.addEquation(new OdeEquation(vVar, initExp, getIdentifierSubstitutions(potentialMapping.getOdeRHS(capacitiveDevice, this), membrane.getMembraneVoltage().getUnitDefinition().divideBy(timeUnit), membraneMapping)));
} else {
//
//
//
}
}
}
}
}
//
for (int k = 0; k < subVolumes.length; k++) {
SubVolume subVolume = (SubVolume) subVolumes[k];
//
// if there is a spatially resolved membrane surrounding this subVolume, then create a membraneSubDomain
//
structures = getStructures(subVolume);
Membrane membrane = null;
if (structures != null) {
for (int j = 0; j < structures.length; j++) {
if (structures[j] instanceof Membrane && getResolved(simContext.getGeometryContext().getStructureMapping(structures[j]))) {
membrane = (Membrane) structures[j];
}
}
}
if (membrane == null) {
continue;
}
SubVolume outerSubVolume = getSubVolume(((FeatureMapping) simContext.getGeometryContext().getStructureMapping(structTopology.getOutsideFeature(membrane))));
SubVolume innerSubVolume = getSubVolume(((FeatureMapping) simContext.getGeometryContext().getStructureMapping(structTopology.getInsideFeature(membrane))));
if (innerSubVolume != subVolume) {
throw new MappingException("membrane " + membrane.getName() + " improperly mapped to inner subVolume " + innerSubVolume.getName());
}
//
// get priority of subDomain
//
// Feature spatialFeature = simContext.getGeometryContext().getResolvedFeature(subVolume);
// int priority = spatialFeature.getPriority();
//
// create subDomain
//
CompartmentSubDomain outerCompartment = mathDesc.getCompartmentSubDomain(outerSubVolume.getName());
CompartmentSubDomain innerCompartment = mathDesc.getCompartmentSubDomain(innerSubVolume.getName());
SurfaceClass surfaceClass = simContext.getGeometry().getGeometrySurfaceDescription().getSurfaceClass(innerSubVolume, outerSubVolume);
MembraneSubDomain memSubDomain = new MembraneSubDomain(innerCompartment, outerCompartment, surfaceClass.getName());
mathDesc.addSubDomain(memSubDomain);
//
// create equations for membrane-bound molecular species
//
MembraneStructureAnalyzer membraneStructureAnalyzer = getMembraneStructureAnalyzer(membrane);
Enumeration<SpeciesContextMapping> enumSCM = getSpeciesContextMappings();
while (enumSCM.hasMoreElements()) {
SpeciesContextMapping scm = enumSCM.nextElement();
SpeciesContext sc = scm.getSpeciesContext();
SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec(sc);
//
if ((scm.getVariable() instanceof MemVariable) && scm.getDependencyExpression() == null) {
//
// independant variable, create an equation object
//
Equation equation = null;
MemVariable variable = (MemVariable) scm.getVariable();
MembraneMapping mm = (MembraneMapping) simContext.getGeometryContext().getStructureMapping(sc.getStructure());
if (scm.isPDERequired()) {
//
if (mm.getMembrane() == membrane) {
//
// species context belongs to this subDomain
//
Expression initial = new Expression(getMathSymbol(scs.getParameterFromRole(SpeciesContextSpec.ROLE_InitialConcentration), mm));
Expression rate = getIdentifierSubstitutions(scm.getRate(), scm.getSpeciesContext().getUnitDefinition().divideBy(timeUnit), simContext.getGeometryContext().getStructureMapping(sc.getStructure()));
Expression diffusion = new Expression(getMathSymbol(scs.getDiffusionParameter(), mm));
equation = new PdeEquation(variable, initial, rate, diffusion);
((PdeEquation) equation).setBoundaryXm((scs.getBoundaryXmParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryXmParameter(), mm)));
((PdeEquation) equation).setBoundaryXp((scs.getBoundaryXpParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryXpParameter(), mm)));
((PdeEquation) equation).setBoundaryYm((scs.getBoundaryYmParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryYmParameter(), mm)));
((PdeEquation) equation).setBoundaryYp((scs.getBoundaryYpParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryYpParameter(), mm)));
((PdeEquation) equation).setBoundaryZm((scs.getBoundaryZmParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryZmParameter(), mm)));
((PdeEquation) equation).setBoundaryZp((scs.getBoundaryZpParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryZpParameter(), mm)));
memSubDomain.replaceEquation(equation);
} else {
Expression initial = new Expression(0.0);
Expression rate = new Expression(0.0);
Expression diffusion = new Expression(getMathSymbol(scs.getDiffusionParameter(), mm));
equation = new PdeEquation(variable, initial, rate, diffusion);
if (memSubDomain.getEquation(variable) == null) {
memSubDomain.addEquation(equation);
}
}
} else {
//
if (mm.getMembrane() == membrane) {
//
// species context belongs to this subDomain
//
Expression initial = new Expression(getMathSymbol(scs.getParameterFromRole(SpeciesContextSpec.ROLE_InitialConcentration), null));
Expression rate = getIdentifierSubstitutions(scm.getRate(), scm.getSpeciesContext().getUnitDefinition().divideBy(timeUnit), simContext.getGeometryContext().getStructureMapping(sc.getStructure()));
equation = new OdeEquation(variable, initial, rate);
memSubDomain.replaceEquation(equation);
} else {
Expression initial = new Expression(0.0);
Expression rate = new Expression(0.0);
equation = new OdeEquation(variable, initial, rate);
if (memSubDomain.getEquation(variable) == null) {
memSubDomain.addEquation(equation);
}
}
}
}
}
//
// create dummy jump conditions for all volume variables that diffuse and/or advect
//
Enumeration<SpeciesContextMapping> enum_scm = getSpeciesContextMappings();
while (enum_scm.hasMoreElements()) {
SpeciesContextMapping scm = enum_scm.nextElement();
if (scm.isPDERequired()) {
// Species species = scm.getSpeciesContext().getSpecies();
Variable var = scm.getVariable();
if (var instanceof VolVariable && (scm.isPDERequired())) {
JumpCondition jc = memSubDomain.getJumpCondition((VolVariable) var);
if (jc == null) {
// System.out.println("MathMapping.refreshMathDescription(), adding jump condition for diffusing variable "+var.getName()+" on membrane "+membraneStructureAnalyzer.getMembrane().getName());
jc = new JumpCondition((VolVariable) var);
memSubDomain.addJumpCondition(jc);
}
}
}
}
//
// create jump conditions for any volume variables that bind to membrane or have explicitly defined fluxes
//
ResolvedFlux[] resolvedFluxes = membraneStructureAnalyzer.getResolvedFluxes();
if (resolvedFluxes != null) {
for (int i = 0; i < resolvedFluxes.length; i++) {
Species species = resolvedFluxes[i].getSpecies();
SpeciesContext sc = simContext.getReactionContext().getModel().getSpeciesContext(species, structTopology.getInsideFeature(membraneStructureAnalyzer.getMembrane()));
if (sc == null) {
sc = simContext.getReactionContext().getModel().getSpeciesContext(species, structTopology.getOutsideFeature(membraneStructureAnalyzer.getMembrane()));
}
SpeciesContextMapping scm = getSpeciesContextMapping(sc);
// if (scm.getVariable() instanceof VolVariable && scm.isDiffusing()){
if (scm.getVariable() instanceof VolVariable && ((MembraneStructureAnalyzer.bNoFluxIfFixed || (scm.isPDERequired())))) {
if (MembraneStructureAnalyzer.bNoFluxIfFixed && !scm.isPDERequired()) {
MembraneStructureAnalyzer.bNoFluxIfFixedExercised = true;
}
JumpCondition jc = memSubDomain.getJumpCondition((VolVariable) scm.getVariable());
if (jc == null) {
jc = new JumpCondition((VolVariable) scm.getVariable());
memSubDomain.addJumpCondition(jc);
}
Expression inFlux = getIdentifierSubstitutions(resolvedFluxes[i].inFluxExpression, resolvedFluxes[i].getUnitDefinition(), simContext.getGeometryContext().getStructureMapping(membraneStructureAnalyzer.getMembrane()));
jc.setInFlux(inFlux);
Expression outFlux = getIdentifierSubstitutions(resolvedFluxes[i].outFluxExpression, resolvedFluxes[i].getUnitDefinition(), simContext.getGeometryContext().getStructureMapping(membraneStructureAnalyzer.getMembrane()));
jc.setOutFlux(outFlux);
} else {
throw new MappingException("APPLICATION " + simContext.getName() + " : " + scm.getSpeciesContext().getName() + " has spatially resolved flux at membrane " + membrane.getName() + ", but doesn't diffuse in compartment " + scm.getSpeciesContext().getStructure().getName());
}
}
}
//
// create fast system (if neccessary)
//
SpeciesContextMapping[] fastSpeciesContextMappings = membraneStructureAnalyzer.getFastSpeciesContextMappings();
if (fastSpeciesContextMappings != null) {
FastSystem fastSystem = new FastSystem(mathDesc);
for (int i = 0; i < fastSpeciesContextMappings.length; i++) {
SpeciesContextMapping scm = fastSpeciesContextMappings[i];
if (scm.getFastInvariant() == null) {
//
// independant-fast variable, create a fastRate object
//
VCUnitDefinition rateUnit = scm.getSpeciesContext().getUnitDefinition().divideBy(timeUnit);
MembraneMapping membraneMapping = (MembraneMapping) simContext.getGeometryContext().getStructureMapping(membraneStructureAnalyzer.getMembrane());
FastRate fastRate = new FastRate(getIdentifierSubstitutions(scm.getFastRate(), rateUnit, membraneMapping));
fastSystem.addFastRate(fastRate);
} else {
//
// dependant-fast variable, create a fastInvariant object
//
VCUnitDefinition invariantUnit = scm.getSpeciesContext().getUnitDefinition();
MembraneMapping membraneMapping = (MembraneMapping) simContext.getGeometryContext().getStructureMapping(membraneStructureAnalyzer.getMembrane());
FastInvariant fastInvariant = new FastInvariant(getIdentifierSubstitutions(scm.getFastInvariant(), invariantUnit, membraneMapping));
fastSystem.addFastInvariant(fastInvariant);
}
}
memSubDomain.setFastSystem(fastSystem);
// constructor calls the 'refresh' method which constructs depemdency matrix, dependent/independent vars and pseudoconstants, etc.
FastSystemAnalyzer fs_analyzer = new FastSystemAnalyzer(fastSystem, mathDesc);
}
//
// create Membrane-region equations for potential of this resolved membrane
//
MembraneMapping membraneMapping = (MembraneMapping) simContext.getGeometryContext().getStructureMapping(membrane);
if (membraneMapping.getCalculateVoltage()) {
ElectricalDevice[] membraneDevices = potentialMapping.getElectricalDevices(membrane);
int numCapacitiveDevices = 0;
MembraneElectricalDevice capacitiveDevice = null;
for (int i = 0; i < membraneDevices.length; i++) {
if (membraneDevices[i] instanceof MembraneElectricalDevice) {
numCapacitiveDevices++;
capacitiveDevice = (MembraneElectricalDevice) membraneDevices[i];
}
}
if (numCapacitiveDevices != 1) {
throw new MappingException("expecting 1 capacitive electrical device on graph edge for membrane " + membrane.getName() + ", found '" + numCapacitiveDevices + "'");
}
if (mathDesc.getVariable(getMathSymbol(capacitiveDevice.getVoltageSymbol(), membraneMapping)) instanceof MembraneRegionVariable) {
MembraneRegionVariable vVar = (MembraneRegionVariable) mathDesc.getVariable(getMathSymbol(capacitiveDevice.getVoltageSymbol(), membraneMapping));
Parameter initialVoltageParm = capacitiveDevice.getMembraneMapping().getInitialVoltageParameter();
Expression initExp = getIdentifierSubstitutions(initialVoltageParm.getExpression(), initialVoltageParm.getUnitDefinition(), capacitiveDevice.getMembraneMapping());
MembraneRegionEquation vEquation = new MembraneRegionEquation(vVar, initExp);
vEquation.setMembraneRateExpression(getIdentifierSubstitutions(potentialMapping.getOdeRHS(capacitiveDevice, this), membrane.getMembraneVoltage().getUnitDefinition().divideBy(timeUnit), capacitiveDevice.getMembraneMapping()));
memSubDomain.addEquation(vEquation);
}
}
}
// create equations for event assign targets that are model params/strutureSize, etc.
Set<VolVariable> hashKeySet = eventVolVarHash.keySet();
Iterator<VolVariable> volVarsIter = hashKeySet.iterator();
// working under teh assumption that we are dealing with non-spatial math, hence only one compartment domain!
SubDomain subDomain = mathDesc.getSubDomains().nextElement();
while (volVarsIter.hasNext()) {
VolVariable volVar = volVarsIter.next();
EventAssignmentInitParameter eap = eventVolVarHash.get(volVar);
Expression rateExpr = new Expression(0.0);
Equation equation = new OdeEquation(volVar, new Expression(getMathSymbol(eap, null)), rateExpr);
subDomain.addEquation(equation);
}
// events - add events to math desc and odes for event assignments that have parameters as target variables
BioEvent[] bioevents = simContext.getBioEvents();
if (bioevents != null && bioevents.length > 0) {
for (BioEvent be : bioevents) {
// transform the bioEvent trigger/delay to math Event
Expression mathTriggerExpr = getIdentifierSubstitutions(be.generateTriggerExpression(), modelUnitSystem.getInstance_DIMENSIONLESS(), null);
Delay mathDelay = null;
if (be.getParameter(BioEventParameterType.TriggerDelay) != null) {
boolean bUseValsFromTriggerTime = be.getUseValuesFromTriggerTime();
Expression mathDelayExpr = getIdentifierSubstitutions(be.getParameter(BioEventParameterType.TriggerDelay).getExpression(), timeUnit, null);
mathDelay = new Delay(bUseValsFromTriggerTime, mathDelayExpr);
}
// now deal with (bio)event Assignment translation to math EventAssignment
ArrayList<EventAssignment> eventAssignments = be.getEventAssignments();
ArrayList<Event.EventAssignment> mathEventAssignmentsList = new ArrayList<Event.EventAssignment>();
for (EventAssignment ea : eventAssignments) {
SymbolTableEntry ste = simContext.getEntry(ea.getTarget().getName());
VCUnitDefinition eventAssignVarUnit = ste.getUnitDefinition();
Variable variable = varHash.getVariable(ste.getName());
Event.EventAssignment mathEA = new Event.EventAssignment(variable, getIdentifierSubstitutions(ea.getAssignmentExpression(), eventAssignVarUnit, null));
mathEventAssignmentsList.add(mathEA);
}
// use the translated trigger, delay and event assignments to create (math) event
Event mathEvent = new Event(be.getName(), mathTriggerExpr, mathDelay, mathEventAssignmentsList);
mathDesc.addEvent(mathEvent);
}
}
if (!mathDesc.isValid()) {
throw new MappingException("generated an invalid mathDescription: " + mathDesc.getWarning());
}
// System.out.println("]]]]]]]]]]]]]]]]]]]]]] VCML string begin ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]");
// System.out.println(mathDesc.getVCML());
// System.out.println("]]]]]]]]]]]]]]]]]]]]]] VCML string end ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]");
}
Also used :
MembraneMapping(cbit.vcell.mapping.MembraneMapping)
MembraneSubDomain(cbit.vcell.math.MembraneSubDomain)
ArrayList(java.util.ArrayList)
SpeciesContext(cbit.vcell.model.SpeciesContext)
StructureMappingParameter(cbit.vcell.mapping.StructureMapping.StructureMappingParameter)
Feature(cbit.vcell.model.Feature)
MemVariable(cbit.vcell.math.MemVariable)
KineticsParameter(cbit.vcell.model.Kinetics.KineticsParameter)
SubVolume(cbit.vcell.geometry.SubVolume)
Vector(java.util.Vector)
SpeciesContextSpecParameter(cbit.vcell.mapping.SpeciesContextSpec.SpeciesContextSpecParameter)
StructureTopology(cbit.vcell.model.Model.StructureTopology)
ReactionSpec(cbit.vcell.mapping.ReactionSpec)
FastInvariant(cbit.vcell.math.FastInvariant)
PropertyVetoException(java.beans.PropertyVetoException)
VCUnitDefinition(cbit.vcell.units.VCUnitDefinition)
FastSystem(cbit.vcell.math.FastSystem)
CompartmentSubDomain(cbit.vcell.math.CompartmentSubDomain)
ReactionStep(cbit.vcell.model.ReactionStep)
MembraneRegionEquation(cbit.vcell.math.MembraneRegionEquation)
SurfaceClass(cbit.vcell.geometry.SurfaceClass)
VariableHash(cbit.vcell.math.VariableHash)
StructureMapping(cbit.vcell.mapping.StructureMapping)
FeatureMapping(cbit.vcell.mapping.FeatureMapping)
Structure(cbit.vcell.model.Structure)
ModelUnitSystem(cbit.vcell.model.ModelUnitSystem)
Hashtable(java.util.Hashtable)
StructureMappingParameter(cbit.vcell.mapping.StructureMapping.StructureMappingParameter)
Expression(cbit.vcell.parser.Expression)
Model(cbit.vcell.model.Model)
ProxyParameter(cbit.vcell.model.ProxyParameter)
StructureMappingParameter(cbit.vcell.mapping.StructureMapping.StructureMappingParameter)
Parameter(cbit.vcell.model.Parameter)
KineticsParameter(cbit.vcell.model.Kinetics.KineticsParameter)
SpeciesContextSpecProxyParameter(cbit.vcell.mapping.SpeciesContextSpec.SpeciesContextSpecProxyParameter)
LocalParameter(cbit.vcell.mapping.ParameterContext.LocalParameter)
ModelParameter(cbit.vcell.model.Model.ModelParameter)
SpeciesContextSpecParameter(cbit.vcell.mapping.SpeciesContextSpec.SpeciesContextSpecParameter)
BioEvent(cbit.vcell.mapping.BioEvent)
Event(cbit.vcell.math.Event)
BioEvent(cbit.vcell.mapping.BioEvent)
MembraneRegionVariable(cbit.vcell.math.MembraneRegionVariable)
MathDescription(cbit.vcell.math.MathDescription)
SpeciesContextMapping(cbit.vcell.mapping.SpeciesContextMapping)
SpeciesContextSpec(cbit.vcell.mapping.SpeciesContextSpec)
ExpressionException(cbit.vcell.parser.ExpressionException)
Delay(cbit.vcell.math.Event.Delay)
MappingException(cbit.vcell.mapping.MappingException)
PropertyVetoException(java.beans.PropertyVetoException)
PdeEquation(cbit.vcell.math.PdeEquation)
CompartmentSubDomain(cbit.vcell.math.CompartmentSubDomain)
SubDomain(cbit.vcell.math.SubDomain)
MembraneSubDomain(cbit.vcell.math.MembraneSubDomain)
Species(cbit.vcell.model.Species)
SpeciesContextSpecParameter(cbit.vcell.mapping.SpeciesContextSpec.SpeciesContextSpecParameter)
EventAssignment(cbit.vcell.mapping.BioEvent.EventAssignment)
VolVariable(cbit.vcell.math.VolVariable)
ModelParameter(cbit.vcell.model.Model.ModelParameter)
OdeEquation(cbit.vcell.math.OdeEquation)
JumpCondition(cbit.vcell.math.JumpCondition)
MembraneRegionVariable(cbit.vcell.math.MembraneRegionVariable)
VolVariable(cbit.vcell.math.VolVariable)
MemVariable(cbit.vcell.math.MemVariable)
Variable(cbit.vcell.math.Variable)
SpeciesContextSpecProxyParameter(cbit.vcell.mapping.SpeciesContextSpec.SpeciesContextSpecProxyParameter)
Constant(cbit.vcell.math.Constant)
SymbolTableEntry(cbit.vcell.parser.SymbolTableEntry)
Membrane(cbit.vcell.model.Membrane)
EventAssignment(cbit.vcell.mapping.BioEvent.EventAssignment)
OdeEquation(cbit.vcell.math.OdeEquation)
MembraneRegionEquation(cbit.vcell.math.MembraneRegionEquation)
PdeEquation(cbit.vcell.math.PdeEquation)
Equation(cbit.vcell.math.Equation)
FastRate(cbit.vcell.math.FastRate)
Aggregations
Feature (cbit.vcell.model.Feature)71
Membrane (cbit.vcell.model.Membrane)50
Structure (cbit.vcell.model.Structure)36
Expression (cbit.vcell.parser.Expression)29
SpeciesContext (cbit.vcell.model.SpeciesContext)25
PropertyVetoException (java.beans.PropertyVetoException)18
Model (cbit.vcell.model.Model)16
StructureTopology (cbit.vcell.model.Model.StructureTopology)16
SimpleReaction (cbit.vcell.model.SimpleReaction)15
SubVolume (cbit.vcell.geometry.SubVolume)14
MembraneMapping (cbit.vcell.mapping.MembraneMapping)14
SurfaceClass (cbit.vcell.geometry.SurfaceClass)13
FeatureMapping (cbit.vcell.mapping.FeatureMapping)13
ExpressionException (cbit.vcell.parser.ExpressionException)13
FluxReaction (cbit.vcell.model.FluxReaction)12
ReactionStep (cbit.vcell.model.ReactionStep)12
KeyValue (org.vcell.util.document.KeyValue)12
BioModel (cbit.vcell.biomodel.BioModel)11
StructureMapping (cbit.vcell.mapping.StructureMapping)11
ModelUnitSystem (cbit.vcell.model.ModelUnitSystem)11
