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Example 1 with MembraneRandomVariable

use of cbit.vcell.math.MembraneRandomVariable in project vcell by virtualcell.

the class FiniteVolumeFileWriter method writeVariables.

/**
 *# Variables : type name unit time_dependent_flag advection_flag solve_whole_mesh_flag solve_regions
 *VARIABLE_BEGIN
 *VOLUME_ODE rB uM
 *VOLUME_PDE rf uM false false
 *VOLUME_PDE r uM false false
 *VOLUME_ODE rfB uM
 *VARIABLE_END
 * @throws MathException
 * @throws ExpressionException
 * @throws IOException
 */
private void writeVariables() throws MathException, ExpressionException, IOException {
    SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
    printWriter.println("# Variables : type name domain time_dependent_flag advection_flag grad_flag solve_whole_mesh_flag solve_regions");
    printWriter.println(FVInputFileKeyword.VARIABLE_BEGIN);
    MathDescription mathDesc = simSymbolTable.getSimulation().getMathDescription();
    Variable[] vars = simSymbolTable.getVariables();
    ArrayList<RandomVariable> rvList = new ArrayList<RandomVariable>();
    for (int i = 0; i < vars.length; i++) {
        String varName = vars[i].getName();
        String domainName = vars[i].getDomain() == null ? null : vars[i].getDomain().getName();
        if (vars[i] instanceof VolumeRandomVariable || vars[i] instanceof MembraneRandomVariable) {
            rvList.add((RandomVariable) vars[i]);
        } else if (vars[i] instanceof VolVariable) {
            if (bChomboSolver && domainName == null) {
                throw new MathException(simTask.getSimulation().getSolverTaskDescription().getSolverDescription().getDisplayLabel() + " requires that every variable is defined in a single domain");
            }
            VolVariable volVar = (VolVariable) vars[i];
            if (mathDesc.isPDE(volVar)) {
                boolean hasTimeVaryingDiffusionOrAdvection = simSymbolTable.hasTimeVaryingDiffusionOrAdvection(volVar);
                final boolean hasVelocity = mathDesc.hasVelocity(volVar);
                final boolean hasGradient = mathDesc.hasGradient(volVar);
                if (mathDesc.isPdeSteady(volVar)) {
                    printWriter.print("VOLUME_PDE_STEADY ");
                } else {
                    printWriter.print("VOLUME_PDE ");
                }
                printWriter.print(varName + " " + domainName + " " + hasTimeVaryingDiffusionOrAdvection + " " + hasVelocity + " " + hasGradient);
            } else {
                printWriter.print("VOLUME_ODE " + varName + " " + domainName);
            }
            if (domainName == null) {
                Vector<SubDomain> listOfSubDomains = new Vector<SubDomain>();
                int totalNumCompartments = 0;
                Enumeration<SubDomain> subDomainEnum = mathDesc.getSubDomains();
                while (subDomainEnum.hasMoreElements()) {
                    SubDomain subDomain = subDomainEnum.nextElement();
                    if (subDomain instanceof CompartmentSubDomain) {
                        CompartmentSubDomain compartmentSubDomain = (CompartmentSubDomain) subDomain;
                        totalNumCompartments++;
                        Equation varEquation = subDomain.getEquation(vars[i]);
                        if (varEquation != null) {
                            if (!(varEquation instanceof PdeEquation) || !((PdeEquation) varEquation).isDummy(simSymbolTable, compartmentSubDomain)) {
                                listOfSubDomains.add(compartmentSubDomain);
                            }
                        }
                    }
                }
                if ((totalNumCompartments == listOfSubDomains.size()) || (listOfSubDomains.size() == 0 && simTask.getSimulation().getSolverTaskDescription().getSolverDescription().equals(SolverDescription.SundialsPDE))) {
                    printWriter.print(" true");
                } else {
                    printWriter.print(" false");
                    for (int j = 0; j < listOfSubDomains.size(); j++) {
                        CompartmentSubDomain compartmentSubDomain = (CompartmentSubDomain) listOfSubDomains.elementAt(j);
                        printWriter.print(" " + compartmentSubDomain.getName());
                    }
                }
                printWriter.println();
            } else {
                printWriter.println(" false " + domainName);
            }
        } else if (vars[i] instanceof VolumeParticleVariable) {
            printWriter.println(FVInputFileKeyword.VOLUME_PARTICLE + " " + varName + " " + domainName);
        } else if (vars[i] instanceof MembraneParticleVariable) {
            printWriter.println(FVInputFileKeyword.MEMBRANE_PARTICLE + " " + varName + " " + domainName);
        } else if (vars[i] instanceof VolumeRegionVariable) {
            printWriter.println("VOLUME_REGION " + varName + " " + domainName);
        } else if (vars[i] instanceof MemVariable) {
            if (bChomboSolver && domainName == null) {
                throw new MathException(simTask.getSimulation().getSolverTaskDescription().getSolverDescription().getDisplayLabel() + " requires that every variable is defined in a single domain");
            }
            MemVariable memVar = (MemVariable) vars[i];
            if (mathDesc.isPDE(memVar)) {
                printWriter.println("MEMBRANE_PDE " + varName + " " + domainName + " " + simSymbolTable.hasTimeVaryingDiffusionOrAdvection(memVar));
            } else {
                printWriter.println("MEMBRANE_ODE " + varName + " " + domainName);
            }
        } else if (vars[i] instanceof MembraneRegionVariable) {
            printWriter.println("MEMBRANE_REGION " + varName + " " + domainName);
        } else if (vars[i] instanceof FilamentVariable) {
            throw new RuntimeException("Filament application not supported yet");
        }
    }
    int numRandomVariables = rvList.size();
    if (numRandomVariables > 0) {
        ISize samplingSize = simTask.getSimulation().getMeshSpecification().getSamplingSize();
        String[] varNameArr = new String[numRandomVariables];
        VariableType[] varTypeArr = new VariableType[numRandomVariables];
        double[][] dataArr = new double[numRandomVariables][];
        for (int i = 0; i < numRandomVariables; i++) {
            RandomVariable rv = rvList.get(i);
            varNameArr[i] = rv.getName();
            int numRandomNumbers = 0;
            if (rv instanceof VolumeRandomVariable) {
                printWriter.print("VOLUME_RANDOM");
                varTypeArr[i] = VariableType.VOLUME;
                numRandomNumbers = samplingSize.getXYZ();
            } else if (rv instanceof MembraneRandomVariable) {
                printWriter.print("MEMBRANE_RANDOM");
                varTypeArr[i] = VariableType.MEMBRANE;
                numRandomNumbers = resampledGeometry.getGeometrySurfaceDescription().getSurfaceCollection().getTotalPolygonCount();
            } else {
                throw new RuntimeException("Unknown RandomVariable type");
            }
            printWriter.println(" " + varNameArr[i]);
            dataArr[i] = generateRandomNumbers(rv, numRandomNumbers);
        }
        File rvFile = new File(workingDirectory, simTask.getSimulationJobID() + RANDOM_VARIABLE_FILE_EXTENSION);
        DataSet.writeNew(rvFile, varNameArr, varTypeArr, samplingSize, dataArr);
    }
    printWriter.println(FVInputFileKeyword.VARIABLE_END);
    printWriter.println();
}
Also used : FilamentVariable(cbit.vcell.math.FilamentVariable) VolVariable(cbit.vcell.math.VolVariable) ReservedVariable(cbit.vcell.math.ReservedVariable) ParameterVariable(cbit.vcell.math.ParameterVariable) RandomVariable(cbit.vcell.math.RandomVariable) VolumeRandomVariable(cbit.vcell.math.VolumeRandomVariable) MembraneRegionVariable(cbit.vcell.math.MembraneRegionVariable) VolumeParticleVariable(cbit.vcell.math.VolumeParticleVariable) MembraneRandomVariable(cbit.vcell.math.MembraneRandomVariable) VolumeRegionVariable(cbit.vcell.math.VolumeRegionVariable) MembraneParticleVariable(cbit.vcell.math.MembraneParticleVariable) MemVariable(cbit.vcell.math.MemVariable) Variable(cbit.vcell.math.Variable) MembraneRegionVariable(cbit.vcell.math.MembraneRegionVariable) MathDescription(cbit.vcell.math.MathDescription) ISize(org.vcell.util.ISize) ArrayList(java.util.ArrayList) MembraneRandomVariable(cbit.vcell.math.MembraneRandomVariable) RandomVariable(cbit.vcell.math.RandomVariable) VolumeRandomVariable(cbit.vcell.math.VolumeRandomVariable) MembraneRandomVariable(cbit.vcell.math.MembraneRandomVariable) CompartmentSubDomain(cbit.vcell.math.CompartmentSubDomain) SubDomain(cbit.vcell.math.SubDomain) MembraneSubDomain(cbit.vcell.math.MembraneSubDomain) PdeEquation(cbit.vcell.math.PdeEquation) VolumeRegionVariable(cbit.vcell.math.VolumeRegionVariable) MemVariable(cbit.vcell.math.MemVariable) MembraneParticleVariable(cbit.vcell.math.MembraneParticleVariable) Vector(java.util.Vector) Enumeration(java.util.Enumeration) VariableType(cbit.vcell.math.VariableType) VolVariable(cbit.vcell.math.VolVariable) SimulationSymbolTable(cbit.vcell.solver.SimulationSymbolTable) MeasureEquation(cbit.vcell.math.MeasureEquation) PdeEquation(cbit.vcell.math.PdeEquation) VolumeRegionEquation(cbit.vcell.math.VolumeRegionEquation) MembraneRegionEquation(cbit.vcell.math.MembraneRegionEquation) Equation(cbit.vcell.math.Equation) MathException(cbit.vcell.math.MathException) CompartmentSubDomain(cbit.vcell.math.CompartmentSubDomain) VolumeParticleVariable(cbit.vcell.math.VolumeParticleVariable) VolumeRandomVariable(cbit.vcell.math.VolumeRandomVariable) FilamentVariable(cbit.vcell.math.FilamentVariable) File(java.io.File)

Example 2 with MembraneRandomVariable

use of cbit.vcell.math.MembraneRandomVariable in project vcell by virtualcell.

the class XmlReader method getRandomVariable.

private RandomVariable getRandomVariable(Element param) throws XmlParseException {
    // get attributes
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    Element element = param.getChild(XMLTags.RandomVariableSeedTag, vcNamespace);
    Expression seed = null;
    if (element != null) {
        seed = unMangleExpression(element.getText());
    }
    Distribution dist = null;
    element = param.getChild(XMLTags.UniformDistributionTag, vcNamespace);
    if (element != null) {
        dist = getUniformDistribution(element);
    }
    element = param.getChild(XMLTags.GaussianDistributionTag, vcNamespace);
    if (element != null) {
        dist = getGaussianDistribution(element);
    }
    String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag));
    Domain domain = null;
    if (domainStr != null) {
        domain = new Domain(domainStr);
    }
    RandomVariable var = null;
    if (param.getName().equals(XMLTags.VolumeRandomVariableTag)) {
        var = new VolumeRandomVariable(name, seed, dist, domain);
    } else if (param.getName().equals(XMLTags.MembraneRandomVariableTag)) {
        var = new MembraneRandomVariable(name, seed, dist, domain);
    } else {
        throw new XmlParseException(param.getName() + " is not supported!");
    }
    transcribeComments(param, var);
    return var;
}
Also used : Expression(cbit.vcell.parser.Expression) Element(org.jdom.Element) UniformDistribution(cbit.vcell.math.UniformDistribution) Distribution(cbit.vcell.math.Distribution) GaussianDistribution(cbit.vcell.math.GaussianDistribution) VolumeRandomVariable(cbit.vcell.math.VolumeRandomVariable) MembraneRandomVariable(cbit.vcell.math.MembraneRandomVariable) RandomVariable(cbit.vcell.math.RandomVariable) VolumeRandomVariable(cbit.vcell.math.VolumeRandomVariable) MembraneRandomVariable(cbit.vcell.math.MembraneRandomVariable) MembraneSubDomain(cbit.vcell.math.MembraneSubDomain) CompartmentSubDomain(cbit.vcell.math.CompartmentSubDomain) FilamentSubDomain(cbit.vcell.math.FilamentSubDomain) PointSubDomain(cbit.vcell.math.PointSubDomain) Domain(cbit.vcell.math.Variable.Domain)

Aggregations

CompartmentSubDomain (cbit.vcell.math.CompartmentSubDomain)2 MembraneRandomVariable (cbit.vcell.math.MembraneRandomVariable)2 MembraneSubDomain (cbit.vcell.math.MembraneSubDomain)2 RandomVariable (cbit.vcell.math.RandomVariable)2 VolumeRandomVariable (cbit.vcell.math.VolumeRandomVariable)2 Distribution (cbit.vcell.math.Distribution)1 Equation (cbit.vcell.math.Equation)1 FilamentSubDomain (cbit.vcell.math.FilamentSubDomain)1 FilamentVariable (cbit.vcell.math.FilamentVariable)1 GaussianDistribution (cbit.vcell.math.GaussianDistribution)1 MathDescription (cbit.vcell.math.MathDescription)1 MathException (cbit.vcell.math.MathException)1 MeasureEquation (cbit.vcell.math.MeasureEquation)1 MemVariable (cbit.vcell.math.MemVariable)1 MembraneParticleVariable (cbit.vcell.math.MembraneParticleVariable)1 MembraneRegionEquation (cbit.vcell.math.MembraneRegionEquation)1 MembraneRegionVariable (cbit.vcell.math.MembraneRegionVariable)1 ParameterVariable (cbit.vcell.math.ParameterVariable)1 PdeEquation (cbit.vcell.math.PdeEquation)1 PointSubDomain (cbit.vcell.math.PointSubDomain)1