Examples with CompartmentSubDomain cbit.vcell.math.CompartmentSubDomain used on opensource projects

Example 36 with CompartmentSubDomain

use of cbit.vcell.math.CompartmentSubDomain 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();
}

Example 37 with CompartmentSubDomain

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

the class MovingBoundaryFileWriter method getXMLSubdomain.

private Element getXMLSubdomain(SubDomain sd) throws ExpressionException, MathException {
    Element e = new Element(MBXmlTags.subdomain.name());
    e.setAttribute(MBTags.name, sd.getName());
    if (sd instanceof CompartmentSubDomain) {
        e.setAttribute(MBXmlTags.type.name(), MBXmlTags.volume.name());
    } else if (sd instanceof PointSubDomain) {
        e.setAttribute(MBXmlTags.type.name(), MBXmlTags.point.name());
        Element x = new Element(MBXmlTags.positionX.name());
        setExpression(x, ((PointSubDomain) sd).getPositionX(), VariableDomain.VARIABLEDOMAIN_POINT);
        e.addContent(x);
        Element y = new Element(MBXmlTags.positionY.name());
        setExpression(y, ((PointSubDomain) sd).getPositionY(), VariableDomain.VARIABLEDOMAIN_POINT);
        e.addContent(y);
    }
    return e;
}

Example 38 with CompartmentSubDomain

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

the class MovingBoundaryFileWriter method manageCompartment.

private void manageCompartment(Element e, SubDomain sd) {
    try {
        if (!sd.getEquationCollection().isEmpty()) {
            Element se = getXMLSubdomain(sd);
            if (sd instanceof CompartmentSubDomain || sd instanceof PointSubDomain) {
                for (Equation equation : sd.getEquationCollection()) {
                    System.out.println("add this: " + equation.getVariable().getName());
                    se.addContent(getSpecies(equation));
                }
                e.addContent(se);
            }
        }
    } catch (Exception exc) {
        throw new RuntimeException("error managing compartment", exc);
    }
}

Example 39 with CompartmentSubDomain

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

the class CellQuanVCTranslator method addCompartmentSubDomain.

/**
 * 	addCompartmentSubDomain : we pick the variable name by reading through the mathML.
 * 	Redundancy in variable name with the volume variable?
 */
protected void addCompartmentSubDomain() throws Exception {
    String csdName = sRoot.getAttributeValue(CELLMLTags.name, sAttNamespace);
    CompartmentSubDomain csd = new CompartmentSubDomain(csdName, CompartmentSubDomain.NON_SPATIAL_PRIORITY);
    Iterator<?> compElementIter = sRoot.getChildren(CELLMLTags.COMPONENT, sNamespace).iterator();
    // JDOMTreeWalker walker = new JDOMTreeWalker(sRoot, new ElementFilter(CELLMLTags.COMPONENT));
    Element comp, math;
    String compName, varName, mangledName;
    while (compElementIter.hasNext()) {
        comp = (Element) compElementIter.next();
        compName = comp.getAttributeValue(CELLMLTags.name, sAttNamespace);
        @SuppressWarnings("unchecked") Iterator<Element> mathIter = comp.getChildren(CELLMLTags.MATH, mathns).iterator();
        while (mathIter.hasNext()) {
            math = mathIter.next();
            Element apply, apply2, apply3, ci;
            // allow multiple 'apply' children.
            @SuppressWarnings("unchecked") Iterator<Element> applyIter = math.getChildren(MathMLTags.APPLY, mathns).iterator();
            while (applyIter.hasNext()) {
                apply = applyIter.next();
                @SuppressWarnings("unchecked") ArrayList<Element> list = new ArrayList<Element>(apply.getChildren());
                if (list.size() < 3)
                    continue;
                if (!(list.get(0)).getName().equals(MathMLTags.EQUAL))
                    continue;
                apply2 = list.get(1);
                if (!apply2.getName().equals(MathMLTags.APPLY))
                    continue;
                @SuppressWarnings("unchecked") ArrayList<Element> list2 = new ArrayList<Element>(apply2.getChildren());
                if (list2.size() < 3)
                    continue;
                if (!(list2.get(0)).getName().equals(MathMLTags.DIFFERENTIAL))
                    continue;
                // skip the time variable
                ci = list2.get(2);
                varName = ci.getTextTrim();
                // can be a constant
                apply3 = list.get(2);
                mangledName = nm.getMangledName(compName, varName);
                Element trimmedMath = new Element(CELLMLTags.MATH, mathns).addContent(apply3.detach());
                fixMathMLBug(trimmedMath);
                Expression rateExp = null;
                try {
                    rateExp = (new ExpressionMathMLParser(null)).fromMathML(trimmedMath);
                    rateExp = processMathExp(comp, rateExp);
                    rateExp = rateExp.flatten();
                    nl.mangleString(rateExp.infix());
                } catch (ExpressionException e) {
                    e.printStackTrace(System.out);
                    throw new RuntimeException(e.getMessage());
                }
                Expression initExp = new Expression(getInitial(comp, varName));
                Domain domain = null;
                OdeEquation ode = new OdeEquation(new VolVariable(mangledName, domain), initExp, rateExp);
                csd.addEquation(ode);
            }
        }
    }
    mathDescription.addSubDomain(csd);
}

Example 40 with CompartmentSubDomain

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

the class SimulationData method getChomboFiles.

@Override
public ChomboFiles getChomboFiles() throws IOException, XmlParseException, ExpressionException {
    if (chomboFileIterationIndices == null) {
        throw new RuntimeException("SimulationData.chomboFileIterationIndices is null, can't process Chombo HDF5 files");
    }
    if (!(getVcDataId() instanceof VCSimulationDataIdentifier)) {
        throw new RuntimeException("SimulationData.getVcDataId() is not a VCSimulationDataIdentifier (type is " + getVcDataId().getClass().getName() + "), can't process chombo HDF5 files");
    }
    VCSimulationDataIdentifier vcDataID = (VCSimulationDataIdentifier) getVcDataId();
    String expectedMeshfile = vcDataID.getID() + ".mesh.hdf5";
    File meshFile = amplistorHelper.getFile(expectedMeshfile);
    ChomboFiles chomboFiles = new ChomboFiles(vcDataID.getSimulationKey(), vcDataID.getJobIndex(), meshFile);
    String simtaskFilePath = vcDataID.getID() + "_0.simtask.xml";
    File simtaskFile = amplistorHelper.getFile(simtaskFilePath);
    if (!simtaskFile.exists()) {
        throw new RuntimeException("Chombo dataset mission .simtask.xml file, please rerun");
    }
    String xmlString = FileUtils.readFileToString(simtaskFile);
    SimulationTask simTask = XmlHelper.XMLToSimTask(xmlString);
    if (!simTask.getSimulation().getSolverTaskDescription().getChomboSolverSpec().isSaveChomboOutput() && !simTask.getSimulation().getSolverTaskDescription().isParallel()) {
        throw new RuntimeException("Export of Chombo simulations to VTK requires chombo data, select 'Chombo' data format in simulation solver options and rerun simulation.");
    }
    CartesianMeshChombo chomboMesh = (CartesianMeshChombo) mesh;
    FeaturePhaseVol[] featurePhaseVols = chomboMesh.getFeaturePhaseVols();
    for (int timeIndex : chomboFileIterationIndices) {
        if (featurePhaseVols == null) {
            // for old format which doesn't have featurephasevols, we need to try ivol up to 20 for each feature
            Enumeration<SubDomain> subdomainEnum = simTask.getSimulation().getMathDescription().getSubDomains();
            while (subdomainEnum.hasMoreElements()) {
                SubDomain subDomain = subdomainEnum.nextElement();
                if (subDomain instanceof CompartmentSubDomain) {
                    for (int ivol = 0; ivol < 20; ++ivol) {
                        // can be many vol, let us try 20
                        findChomboFeatureVolFile(chomboFiles, vcDataID, subDomain.getName(), ivol, timeIndex);
                    }
                }
            }
        } else {
            // note: some feature + ivol doesn't have a file if there are no variables defined in that feature
            for (FeaturePhaseVol pfv : featurePhaseVols) {
                findChomboFeatureVolFile(chomboFiles, vcDataID, pfv.feature, pfv.ivol, timeIndex);
            }
        }
    }
    return chomboFiles;
}