use of cbit.vcell.math.SubDomain in project vcell by virtualcell.
the class SundialsSolver method createStateVariables.
/*
This method was created in Visual Age
*/
private StateVariable[] createStateVariables() throws MathException, ExpressionException {
Vector<StateVariable> stateVariables = new Vector<StateVariable>();
// get Ode's from MathDescription and create ODEStateVariables
SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
MathDescription mathDescription = simSymbolTable.getSimulation().getMathDescription();
Enumeration<Equation> enum1 = ((SubDomain) mathDescription.getSubDomains().nextElement()).getEquations();
while (enum1.hasMoreElements()) {
Equation equation = (Equation) enum1.nextElement();
if (equation instanceof OdeEquation) {
stateVariables.addElement(new ODEStateVariable((OdeEquation) equation, simSymbolTable));
} else {
throw new MathException("encountered non-ode equation, unsupported");
}
}
// Get sensitivity variables
Variable[] variables = simSymbolTable.getVariables();
Vector<SensVariable> sensVariables = new Vector<SensVariable>();
if (getSensitivityParameter() != null) {
for (int i = 0; i < variables.length; i++) {
if (variables[i] instanceof VolVariable) {
VolVariable volVariable = (VolVariable) variables[i];
SensVariable sv = new SensVariable(volVariable, getSensitivityParameter());
sensVariables.addElement(sv);
}
}
}
if (rateSensitivity == null) {
rateSensitivity = new RateSensitivity(mathDescription, mathDescription.getSubDomains().nextElement());
}
if (jacobian == null) {
jacobian = new Jacobian(mathDescription, mathDescription.getSubDomains().nextElement());
}
for (int v = 0; v < sensVariables.size(); v++) {
stateVariables.addElement(new SensStateVariable((SensVariable) sensVariables.elementAt(v), rateSensitivity, jacobian, sensVariables, simSymbolTable));
}
if (stateVariables.size() == 0) {
throw new MathException("there are no equations defined");
}
StateVariable[] stateVars = (StateVariable[]) BeanUtils.getArray(stateVariables, StateVariable.class);
return (stateVars);
}
use of cbit.vcell.math.SubDomain in project vcell by virtualcell.
the class SubdomainInfo method write.
public static void write(File file, MathDescription mathDesc) throws IOException, MathException {
PrintWriter pw = null;
try {
pw = new PrintWriter(new FileWriter(file));
pw.println("# " + VCML.CompartmentSubDomain + " name, handle");
pw.println("# " + VCML.MembraneSubDomain + " name, inside compartment name, handle, outside compartment name, handle");
Enumeration<SubDomain> subdomains = mathDesc.getSubDomains();
while (subdomains.hasMoreElements()) {
SubDomain sd = subdomains.nextElement();
if (sd instanceof CompartmentSubDomain) {
CompartmentSubDomain csd = (CompartmentSubDomain) sd;
pw.println(VCML.CompartmentSubDomain + ", " + csd.getName() + ", " + mathDesc.getHandle(csd));
} else if (sd instanceof MembraneSubDomain) {
MembraneSubDomain msd = (MembraneSubDomain) sd;
CompartmentSubDomain insideCompartment = msd.getInsideCompartment();
CompartmentSubDomain outsideCompartment = msd.getOutsideCompartment();
pw.println(VCML.MembraneSubDomain + ", " + msd.getName() + ", " + insideCompartment.getName() + ", " + mathDesc.getHandle(insideCompartment) + ", " + outsideCompartment.getName() + ", " + mathDesc.getHandle(outsideCompartment));
}
}
pw.close();
} finally {
if (pw != null) {
pw.close();
}
}
}
use of cbit.vcell.math.SubDomain in project vcell by virtualcell.
the class SimulationData method getVarAndFunctionDataIdentifiers.
/**
* This method was created in VisualAge.
* @return java.lang.String[]
*/
public synchronized DataIdentifier[] getVarAndFunctionDataIdentifiers(OutputContext outputContext) throws IOException, DataAccessException {
// Is this zip format?
boolean bIsChombo = false;
try {
bIsChombo = isChombo();
} catch (FileNotFoundException e) {
e.printStackTrace(System.out);
}
File zipFile1 = getZipFile(bIsChombo, null);
File zipFile2 = getZipFile(bIsChombo, 0);
bZipFormat1 = false;
bZipFormat2 = false;
if (zipFile1.exists()) {
bZipFormat1 = true;
} else if (zipFile2.exists()) {
bZipFormat2 = true;
}
refreshLogFile();
if (!isComsol()) {
try {
refreshMeshFile();
} catch (MathException e) {
e.printStackTrace(System.out);
throw new DataAccessException(e.getMessage());
}
}
if (!isRulesData && !getIsODEData() && !isComsol() && dataFilenames != null) {
// read variables only when I have never read the file since variables don't change
if (dataSetIdentifierList.size() == 0) {
File file = getPDEDataFile(0.0);
DataSet dataSet = getPDEDataSet(file, 0.0);
String[] varNames = dataSet.getDataNames();
int[] varTypeInts = dataSet.getVariableTypeIntegers();
if (varNames == null) {
return null;
}
dataSetIdentifierList.clear();
for (int i = 0; i < varNames.length; i++) {
VariableType varType = null;
try {
varType = VariableType.getVariableTypeFromInteger(varTypeInts[i]);
} catch (IllegalArgumentException e) {
if (LG.isEnabledFor(Level.WARN)) {
LG.warn("Exception typing " + varNames[i] + " has unsupported type " + varTypeInts[i] + ": " + e.getMessage());
}
varType = SimulationData.getVariableTypeFromLength(mesh, dataSet.getDataLength(varNames[i]));
}
Domain domain = Variable.getDomainFromCombinedIdentifier(varNames[i]);
String varName = Variable.getNameFromCombinedIdentifier(varNames[i]);
dataSetIdentifierList.addElement(new DataSetIdentifier(varName, varType, domain));
}
refreshDataProcessingOutputInfo(outputContext);
if (dataProcessingOutputInfo != null) {
for (int i = 0; i < dataProcessingOutputInfo.getVariableNames().length; i++) {
if (dataProcessingOutputInfo.getPostProcessDataType(dataProcessingOutputInfo.getVariableNames()[i]).equals(DataProcessingOutputInfo.PostProcessDataType.image)) {
dataSetIdentifierList.addElement(new DataSetIdentifier(dataProcessingOutputInfo.getVariableNames()[i], VariableType.POSTPROCESSING, null));
}
}
}
}
// always read functions file since functions might change
getFunctionDataIdentifiers(outputContext);
}
if ((isRulesData || getIsODEData()) && dataSetIdentifierList.size() == 0) {
ODEDataBlock odeDataBlock = getODEDataBlock();
if (odeDataBlock == null) {
throw new DataAccessException("Results are not availabe yet. Please try again later.");
}
ODESimData odeSimData = odeDataBlock.getODESimData();
int colCount = odeSimData.getColumnDescriptionsCount();
// assume index=0 is time "t"
int DATA_OFFSET = 1;
dataSetIdentifierList.clear();
for (int i = 0; i < (colCount - DATA_OFFSET); i++) {
String varName = odeSimData.getColumnDescriptions(i + DATA_OFFSET).getDisplayName();
// TODO domain
Domain domain = null;
dataSetIdentifierList.addElement(new DataSetIdentifier(varName, VariableType.NONSPATIAL, domain));
}
}
if (isComsol() && dataSetIdentifierList.size() == 0) {
ComsolSimFiles comsolSimFiles = getComsolSimFiles();
if (comsolSimFiles.simTaskXMLFile != null) {
try {
String xmlString = FileUtils.readFileToString(comsolSimFiles.simTaskXMLFile);
SimulationTask simTask = XmlHelper.XMLToSimTask(xmlString);
Enumeration<Variable> variablesEnum = simTask.getSimulation().getMathDescription().getVariables();
while (variablesEnum.hasMoreElements()) {
Variable var = variablesEnum.nextElement();
if (var instanceof VolVariable) {
dataSetIdentifierList.addElement(new DataSetIdentifier(var.getName(), VariableType.VOLUME, var.getDomain()));
} else if (var instanceof MemVariable) {
dataSetIdentifierList.addElement(new DataSetIdentifier(var.getName(), VariableType.MEMBRANE, var.getDomain()));
} else if (var instanceof Function) {
VariableType varType = VariableType.UNKNOWN;
if (var.getDomain() != null && var.getDomain().getName() != null) {
SubDomain subDomain = simTask.getSimulation().getMathDescription().getSubDomain(var.getDomain().getName());
if (subDomain instanceof CompartmentSubDomain) {
varType = VariableType.VOLUME;
} else if (subDomain instanceof MembraneSubDomain) {
varType = VariableType.MEMBRANE;
} else if (subDomain instanceof FilamentSubDomain) {
throw new RuntimeException("filament subdomains not supported");
} else if (subDomain instanceof PointSubDomain) {
varType = VariableType.POINT_VARIABLE;
}
}
dataSetIdentifierList.addElement(new DataSetIdentifier(var.getName(), varType, var.getDomain()));
} else if (var instanceof Constant) {
System.out.println("ignoring Constant " + var.getName());
} else if (var instanceof InsideVariable) {
System.out.println("ignoring InsideVariable " + var.getName());
} else if (var instanceof OutsideVariable) {
System.out.println("ignoring OutsideVariable " + var.getName());
} else {
throw new RuntimeException("unexpected variable " + var.getName() + " of type " + var.getClass().getName());
}
}
} catch (XmlParseException | ExpressionException e) {
e.printStackTrace();
throw new RuntimeException("failed to read sim task file, msg: " + e.getMessage(), e);
}
}
}
DataIdentifier[] dis = new DataIdentifier[dataSetIdentifierList.size()];
for (int i = 0; i < dataSetIdentifierList.size(); i++) {
DataSetIdentifier dsi = (DataSetIdentifier) dataSetIdentifierList.elementAt(i);
String displayName = dsi.getName();
if (dsi.isFunction()) {
AnnotatedFunction f = null;
for (int j = 0; j < annotatedFunctionList.size(); j++) {
AnnotatedFunction function = (AnnotatedFunction) annotatedFunctionList.elementAt(j);
if (function.getName().equals(dsi.getName())) {
f = function;
break;
}
}
if (f != null) {
displayName = f.getDisplayName();
}
}
dis[i] = new DataIdentifier(dsi.getName(), dsi.getVariableType(), dsi.getDomain(), dsi.isFunction(), displayName);
}
return dis;
}
use of cbit.vcell.math.SubDomain in project vcell by virtualcell.
the class NetCDFWriter method initialize.
/**
* Extract infomation from simulation to write hybrid input file.
* Validate the information. If it is valid, a true value will be return.
* The function will be called by writeHybridInputFile().
* Creation date: (5/22/2007 3:59:34 PM)
* @return boolean
*/
public boolean initialize() throws Exception {
Simulation simulation = simTask.getSimulation();
// check variables
if (!simulation.getMathDescription().getVariables().hasMoreElements()) {
throw new MathException("Stochastic model has no variable.");
}
// check subDomain
SubDomain subDomain = null;
Enumeration<SubDomain> e = simulation.getMathDescription().getSubDomains();
if (e.hasMoreElements()) {
subDomain = e.nextElement();
} else
throw new MathException("There is no sub domain.");
// check jump processes
if (subDomain.getJumpProcesses().size() < 1) {
throw new MathException("Stochastic model has no jump process.");
}
return true;
}
use of cbit.vcell.math.SubDomain in project vcell by virtualcell.
the class StochFileWriter method initialize.
/**
* Get infomation for stochasic input file.
* Validate the information. If it is valid, a true value will be return.
* The function will be called by writeStochInputFile().
* Creation date: (6/23/2006 3:59:34 PM)
* @return boolean
*/
public void initialize() throws Exception {
Simulation simulation = simTask.getSimulation();
// check variables
if (!simulation.getMathDescription().getVariables().hasMoreElements()) {
throw new MathException("Stochastic model has no variable.");
}
// check subDomain
SubDomain subDomain = null;
Enumeration<SubDomain> e = simulation.getMathDescription().getSubDomains();
if (e.hasMoreElements()) {
subDomain = e.nextElement();
} else
throw new MathException("There is no sub domain.");
// check jump processes
if (subDomain.getJumpProcesses().size() < 1) {
throw new MathException("Stochastic model has no jump process.");
}
}
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