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

Example 76 with Variable

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

the class XmlReader method getOdeEquation.

/**
 * This method returns an OdeEquation from a XML Element.
 * Creation date: (5/17/2001 3:52:40 PM)
 * @return cbit.vcell.math.OdeEquation
 * @param param org.jdom.Element
 * @exception cbit.vcell.xml.XmlParseException The exception description.
 */
private OdeEquation getOdeEquation(Element param, MathDescription mathDesc) throws XmlParseException {
    // get attributes
    String varname = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    // find reference in the dictionnary
    // try as a VolVariable
    Variable varref = mathDesc.getVariable(varname);
    // Make sure that the reference is not empty!!!
    if (varref == null) {
        throw new XmlParseException("The reference to the variable " + varname + " in a OdeEquation could not be resolved!");
    }
    // get Initial condition
    String temp = param.getChildText(XMLTags.InitialTag, vcNamespace);
    Expression initialexp = null;
    if (temp != null && temp.length() > 0) {
        initialexp = unMangleExpression(temp);
    }
    // Get Rate condition
    temp = param.getChildText(XMLTags.RateTag, vcNamespace);
    Expression rateexp = null;
    if (temp != null && temp.length() > 0) {
        rateexp = unMangleExpression((temp));
    }
    // --- Create the OdeEquation object ---
    OdeEquation odeEquation = new OdeEquation(varref, initialexp, rateexp);
    // add specific solutions expressions
    String solType = param.getAttributeValue(XMLTags.SolutionTypeTag);
    if (solType.equalsIgnoreCase(XMLTags.ExactTypeTag)) {
        String solutionExp = param.getChildText(XMLTags.SolutionExpressionTag, vcNamespace);
        if (solutionExp != null && solutionExp.length() > 0) {
            Expression expression = unMangleExpression(solutionExp);
            odeEquation.setExactSolution(expression);
        }
    }
    return odeEquation;
}

Example 77 with Variable

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

the class XmlReader method getPdeEquation.

/**
 * This method returns a PdeEquation from a XML element.
 * Creation date: (4/26/2001 12:11:14 PM)
 * @return cbit.vcell.math.PdeEquation
 * @param param org.jdom.Element
 * @exception cbit.vcell.xml.XmlParseException The exception description.
 */
private PdeEquation getPdeEquation(Element param, MathDescription mathDesc) throws XmlParseException {
    // Retrieve the variable reference
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    boolean bSteady = false;
    String bSteadyAttr = param.getAttributeValue(XMLTags.SteadyTag);
    if (bSteadyAttr != null && bSteadyAttr.equals("1")) {
        bSteady = true;
    }
    Variable varref = mathDesc.getVariable(name);
    if (varref == null) {
        throw new XmlParseException("The variable " + name + " for a PdeEquation, could not be resolved!");
    }
    PdeEquation pdeEquation = null;
    try {
        // Retrieve the initial expression
        String temp = param.getChildText(XMLTags.InitialTag, vcNamespace);
        Expression initialExp = null;
        if (temp != null && temp.length() > 0) {
            initialExp = unMangleExpression(temp);
        }
        // Retrieve the Rate Expression
        temp = param.getChildText(XMLTags.RateTag, vcNamespace);
        Expression rateExp = null;
        if (temp != null && temp.length() > 0) {
            rateExp = unMangleExpression(temp);
        }
        // Retrieve the diffusion rate expression
        temp = param.getChildText(XMLTags.DiffusionTag, vcNamespace);
        Expression difExp = null;
        if (temp != null && temp.length() > 0) {
            difExp = unMangleExpression(temp);
        }
        // *** Create new PdeEquation object ****
        pdeEquation = new PdeEquation(varref, bSteady, initialExp, rateExp, difExp);
        // ***** *****
        // add specific solutions expressions
        String solType = param.getAttributeValue(XMLTags.SolutionTypeTag);
        if (solType.equalsIgnoreCase(XMLTags.ExactTypeTag)) {
            String solutionExp = param.getChildText(XMLTags.SolutionExpressionTag, vcNamespace);
            if (solutionExp != null && solutionExp.length() > 0) {
                Expression expression = unMangleExpression(solutionExp);
                pdeEquation.setExactSolution(expression);
            }
        }
        // Retrieve Boudaries (if any)
        Element tempelement = param.getChild(XMLTags.BoundariesTag, vcNamespace);
        if (tempelement != null) {
            Expression newexp = null;
            // Xm
            temp = tempelement.getAttributeValue(XMLTags.BoundaryAttrValueXm);
            if (temp != null) {
                newexp = unMangleExpression(temp);
                pdeEquation.setBoundaryXm(newexp);
            }
            // Xp
            temp = tempelement.getAttributeValue(XMLTags.BoundaryAttrValueXp);
            if (temp != null) {
                newexp = unMangleExpression(temp);
                pdeEquation.setBoundaryXp(newexp);
            }
            // Ym
            temp = tempelement.getAttributeValue(XMLTags.BoundaryAttrValueYm);
            if (temp != null) {
                newexp = unMangleExpression(temp);
                pdeEquation.setBoundaryYm(newexp);
            }
            // Yp
            temp = tempelement.getAttributeValue(XMLTags.BoundaryAttrValueYp);
            if (temp != null) {
                newexp = unMangleExpression(temp);
                pdeEquation.setBoundaryYp(newexp);
            }
            // Zm
            temp = tempelement.getAttributeValue(XMLTags.BoundaryAttrValueZm);
            if (temp != null) {
                newexp = unMangleExpression(temp);
                pdeEquation.setBoundaryZm(newexp);
            }
            // Zp
            temp = tempelement.getAttributeValue(XMLTags.BoundaryAttrValueZp);
            if (temp != null) {
                newexp = unMangleExpression(temp);
                pdeEquation.setBoundaryZp(newexp);
            }
        }
        // process BoundaryConditionValues
        {
            Iterator<Element> iterator = param.getChildren(XMLTags.BoundaryConditionValueTag, vcNamespace).iterator();
            if (iterator != null) {
                while (iterator.hasNext()) {
                    tempelement = (Element) iterator.next();
                    try {
                        pdeEquation.addBoundaryConditionValue(getBoundaryConditionValue(tempelement, pdeEquation));
                    } catch (MathException e) {
                        e.printStackTrace();
                        throw new XmlParseException("A MathException was fired when adding a BoundaryConditionValue to the compartmentSubDomain " + name, e);
                    }
                }
            }
        }
        {
            // add Velocity
            Element velocityE = param.getChild(XMLTags.VelocityTag, vcNamespace);
            if (velocityE != null) {
                String tempStr = null;
                boolean dummyVel = true;
                tempStr = velocityE.getAttributeValue(XMLTags.XAttrTag);
                if (tempStr != null) {
                    // all velocity dimensions are optional.
                    pdeEquation.setVelocityX(unMangleExpression(tempStr));
                    if (dummyVel) {
                        dummyVel = false;
                    }
                }
                tempStr = velocityE.getAttributeValue(XMLTags.YAttrTag);
                if (tempStr != null) {
                    pdeEquation.setVelocityY(unMangleExpression(tempStr));
                    if (dummyVel) {
                        dummyVel = false;
                    }
                }
                tempStr = velocityE.getAttributeValue(XMLTags.ZAttrTag);
                if (tempStr != null) {
                    pdeEquation.setVelocityZ(unMangleExpression(tempStr));
                    if (dummyVel) {
                        dummyVel = false;
                    }
                }
                if (dummyVel) {
                    throw new XmlParseException("Void Velocity element found under PDE for: " + name);
                }
            }
        }
        {
            // add Grad
            Element gradElement = param.getChild(XMLTags.GradientTag, vcNamespace);
            if (gradElement != null) {
                String tempStr = null;
                tempStr = gradElement.getAttributeValue(XMLTags.XAttrTag);
                if (tempStr != null) {
                    // all grad dimensions are optional.
                    pdeEquation.setGradientX(unMangleExpression(tempStr));
                }
                tempStr = gradElement.getAttributeValue(XMLTags.YAttrTag);
                if (tempStr != null) {
                    pdeEquation.setGradientY(unMangleExpression(tempStr));
                }
                tempStr = gradElement.getAttributeValue(XMLTags.ZAttrTag);
                if (tempStr != null) {
                    pdeEquation.setGradientZ(unMangleExpression(tempStr));
                }
            }
        }
    } catch (Exception e) {
        e.printStackTrace();
        throw new XmlParseException(e);
    }
    return pdeEquation;
}

Example 78 with Variable

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

the class MathTestingUtilities method substituteWithExactSolution.

/**
 * Insert the method's description here.
 * Creation date: (1/24/2003 10:18:14 AM)
 * @return cbit.vcell.parser.Expression
 * @param origExp cbit.vcell.parser.Expression
 * @param subDomain cbit.vcell.math.SubDomain
 */
private static Expression substituteWithExactSolution(Expression origExp, CompartmentSubDomain subDomain, MathDescription exactMathDesc) throws ExpressionException {
    Expression substitutedExp = new Expression(origExp);
    substitutedExp.bindExpression(exactMathDesc);
    substitutedExp = MathUtilities.substituteFunctions(substitutedExp, exactMathDesc);
    substitutedExp.bindExpression(null);
    substitutedExp = substitutedExp.flatten();
    substitutedExp.bindExpression(exactMathDesc);
    String[] symbols = substitutedExp.getSymbols();
    for (int i = 0; i < symbols.length; i++) {
        Variable var = (Variable) substitutedExp.getSymbolBinding(symbols[i]);
        if (var instanceof VolVariable) {
            String exactVarName = var.getName() + "_" + subDomain.getName() + "_exact";
            substitutedExp.substituteInPlace(new Expression(var.getName()), new Expression(exactVarName));
        } else if (var instanceof VolumeRegionVariable || var instanceof MemVariable || var instanceof MembraneRegionVariable || var instanceof FilamentVariable || var instanceof FilamentRegionVariable) {
            throw new RuntimeException("variable substitution not yet implemented for Variable type " + var.getClass().getName() + "(" + var.getName() + ")");
        }
    }
    substitutedExp.bindExpression(null);
    return substitutedExp;
}

Example 79 with Variable

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

the class MathTestingUtilities method comparePDEResults.

/**
 * Insert the method's description here.
 * Creation date: (8/20/2003 12:58:10 PM)
 */
public static SimulationComparisonSummary comparePDEResults(SimulationSymbolTable testSimSymbolTable, PDEDataManager testDataManager, SimulationSymbolTable refSimSymbolTable, PDEDataManager refDataManager, String[] varsToCompare, double absErrorThreshold, double relErrorThreshold, VCDocument refDocument, DataInfoProvider refDataInfoProvider, VCDocument testDocument, DataInfoProvider testDataInfoProvider) throws DataAccessException, ExpressionException {
    java.util.Hashtable<String, DataErrorSummary> tempVarHash = new java.util.Hashtable<String, DataErrorSummary>();
    boolean bTimesEqual = true;
    double[] testTimeArray = testDataManager.getDataSetTimes();
    double[] refTimeArray = refDataManager.getDataSetTimes();
    if (testTimeArray.length != refTimeArray.length) {
        bTimesEqual = false;
    // throw new RuntimeException("Data times for reference and test simulations don't match, cannot compare the two simulations!");
    } else {
        for (int i = 0; i < testTimeArray.length; i++) {
            if (testTimeArray[i] != refTimeArray[i]) {
                bTimesEqual = false;
            }
        }
    }
    // if (!checkSimVars(testSim, refSim)) {
    // //String errorS = "TestVars - ";
    // Variable[] testVars = testSim.getVariables();
    // //for(int i =0;i<vars.length;i+= 1){
    // //errorS+= vars[i].getName()+" ";
    // //}
    // //errorS+=" <<>> RefVars - ";
    // Variable[] refVars = refSim.getVariables();
    // //for(int i =0;i<vars.length;i+= 1){
    // //errorS+= vars[i].getName()+" ";
    // //}
    // throw new RuntimeException(
    // "VarNotMatch testLength="+(testVars != null?testVars.length+"":"null")+" refLength="+(refVars != null?refVars.length+"":"null"));
    // }
    CartesianMesh testMesh = testDataManager.getMesh();
    MathDescription testMathDesc = testSimSymbolTable.getSimulation().getMathDescription();
    // Variable[] refVars = refSim.getVariables();
    MathDescription refMathDesc = refSimSymbolTable.getSimulation().getMathDescription();
    CartesianMesh refMesh = refDataManager.getMesh();
    int[] membraneIndexMapping = null;
    // Get volumeSubdomains from mathDesc/mesh and store in lookupTable for testSimulation
    int testNumVol = testMesh.getSizeX() * testMesh.getSizeY() * testMesh.getSizeZ();
    CompartmentSubDomain[] testVolSubDomainLookup = new CompartmentSubDomain[testNumVol];
    for (int i = 0; i < testNumVol; i++) {
        int subVolumeIndex = testMesh.getSubVolumeFromVolumeIndex(i);
        SubVolume subVolume = testMathDesc.getGeometry().getGeometrySpec().getSubVolume(subVolumeIndex);
        CompartmentSubDomain compSubDomain = testMathDesc.getCompartmentSubDomain(subVolume.getName());
        testVolSubDomainLookup[i] = compSubDomain;
    }
    // Get membraneSubdomains from mathDesc/mesh and store in lookupTable for testSimulation
    int testNumMem = testMesh.getMembraneElements().length;
    MembraneSubDomain[] testMemSubDomainLookup = new MembraneSubDomain[testNumMem];
    for (int i = 0; i < testNumMem; i++) {
        int insideVolIndex = testMesh.getMembraneElements()[i].getInsideVolumeIndex();
        int outsideVolIndex = testMesh.getMembraneElements()[i].getOutsideVolumeIndex();
        MembraneSubDomain memSubDomain = testMathDesc.getMembraneSubDomain(testVolSubDomainLookup[insideVolIndex], testVolSubDomainLookup[outsideVolIndex]);
        testMemSubDomainLookup[i] = memSubDomain;
    }
    // Get volumeSubdomains from mathDesc/mesh and store in lookupTable for refSimulation
    int refNumVol = refMesh.getSizeX() * refMesh.getSizeY() * refMesh.getSizeZ();
    CompartmentSubDomain[] refVolSubDomainLookup = new CompartmentSubDomain[refNumVol];
    for (int i = 0; i < refNumVol; i++) {
        int subVolumeIndex = refMesh.getSubVolumeFromVolumeIndex(i);
        SubVolume subVolume = refMathDesc.getGeometry().getGeometrySpec().getSubVolume(subVolumeIndex);
        CompartmentSubDomain compSubDomain = refMathDesc.getCompartmentSubDomain(subVolume.getName());
        refVolSubDomainLookup[i] = compSubDomain;
    }
    // Get membraneSubdomains from mathDesc/mesh and store in lookupTable for refSimulation
    int refNumMem = refMesh.getMembraneElements().length;
    MembraneSubDomain[] refMemSubDomainLookup = new MembraneSubDomain[refNumMem];
    for (int i = 0; i < refNumMem; i++) {
        int insideVolIndex = refMesh.getMembraneElements()[i].getInsideVolumeIndex();
        int outsideVolIndex = refMesh.getMembraneElements()[i].getOutsideVolumeIndex();
        MembraneSubDomain memSubDomain = refMathDesc.getMembraneSubDomain(refVolSubDomainLookup[insideVolIndex], refVolSubDomainLookup[outsideVolIndex]);
        refMemSubDomainLookup[i] = memSubDomain;
    }
    SimulationComparisonSummary simComparisonSummary = new SimulationComparisonSummary();
    String hashKey = new String("");
    DataErrorSummary tempVar = null;
    DataIdentifier[] refDataIDs = refDataManager.getDataIdentifiers();
    // for each var, do the following :
    for (int i = 0; i < varsToCompare.length; i++) {
        DataIdentifier refDataID = null;
        for (int j = 0; j < refDataIDs.length; j++) {
            if (refDataIDs[j].getName().equals(varsToCompare[i])) {
                refDataID = refDataIDs[j];
                break;
            }
        }
        // 
        // Find REFERENCE variable
        // 
        Variable refVar = getSimVar(refSimSymbolTable, varsToCompare[i]);
        if (refVar == null) {
            // Should only happen if TEST sims were generated 'post-domains' and REFERENCE sims were generated 'pre-domains'
            if (refDataID != null) {
                throw new RuntimeException("Unexpected reference condition: '" + varsToCompare[i] + "' not found in symboltable but was found in dataidentifiers");
            }
            if (testDocument instanceof BioModel) {
                // Only BioModels need to be checked
                // Look in TEST for a speciescontext with matching species name
                System.out.println("ReferenceVariable: using alternate method to find '" + varsToCompare[i] + "'");
                BioModel refBioModel = (BioModel) refDocument;
                BioModel testBioModel = (BioModel) testDocument;
                SpeciesContext testSpeciesContext = testBioModel.getModel().getSpeciesContext(varsToCompare[i]);
                if (testSpeciesContext != null) {
                    refVar = refSimSymbolTable.getVariable(testSpeciesContext.getSpecies().getCommonName());
                    for (int j = 0; j < refDataIDs.length; j++) {
                        if (refDataIDs[j].getName().equals(testSpeciesContext.getSpecies().getCommonName())) {
                            refDataID = refDataIDs[j];
                            break;
                        }
                    }
                }
            }
            if (refVar == null || refDataID == null) {
                Simulation refSim = refSimSymbolTable.getSimulation();
                throw new RuntimeException("The variable " + varsToCompare[i] + " was not found in Simulation (" + refSim.getName() + " " + refSim.getVersion().getDate() + ")\n");
            }
        }
        // 
        // Find TEST variable (assumed to have sims generated with a software version later than REFERENCE)
        // 
        Variable testVar = getSimVar(testSimSymbolTable, varsToCompare[i]);
        if (testVar == null) {
            // Should only happen if TEST sims were generated 'post-domains' and REFERENCE sims were generated 'pre-domains'
            System.out.println("TestVariable: using alternate method to find '" + varsToCompare[i] + "'");
            BioModel testBioModel = (BioModel) testDocument;
            SpeciesContext[] speciesContexts = testBioModel.getModel().getSpeciesContexts();
            boolean bSkip = false;
            for (int j = 0; j < speciesContexts.length; j++) {
                if (speciesContexts[j].getSpecies().getCommonName().equals(varsToCompare[i])) {
                    testVar = testSimSymbolTable.getVariable(speciesContexts[j].getName());
                    if (testVar == null) {
                        throw new RuntimeException("Speciescontext name '" + speciesContexts[j].getName() + "' not found in testsimsymboltable");
                    }
                    // If we got here it means at least one matching speciescontext was found in TEST with
                    // a species name matching varsToCompare[i].  We can skip because the matching speciesconetext
                    // will be used to do a comparison at some point.
                    bSkip = true;
                    break;
                }
            }
            if (bSkip) {
                // these are tested already using full simcontext names
                System.out.println("Skipping '" + varsToCompare[i] + "' as lookup in testSimSymbolTable");
                continue;
            }
            Simulation refSim = refSimSymbolTable.getSimulation();
            throw new RuntimeException("The variable " + varsToCompare[i] + " was not found in Simulation (" + refSim.getName() + " " + refSim.getVersion().getDate() + ")\n");
        }
        // for each time in timeArray. ('t' is used to index the testTimeArray, for interpolation purposes.)
        int t = 0;
        for (int j = 0; j < refTimeArray.length; j++) {
            // get data block from varName, data from datablock
            SimDataBlock refSimDataBlock = refDataManager.getSimDataBlock(refVar.getName(), refTimeArray[j]);
            double[] refData = refSimDataBlock.getData();
            double[] resampledTestData = null;
            if (bTimesEqual) {
                // If time arrays for both sims are equal, no need to resample/interpolate, just obtain the datablock from dataManager
                SimDataBlock testSimDataBlock = testDataManager.getSimDataBlock(testVar.getName(), testTimeArray[j]);
                resampledTestData = testSimDataBlock.getData();
            } else {
                // Time resampling (interpolation) needed.
                while ((t < testTimeArray.length - 2) && (refTimeArray[j] >= testTimeArray[t + 1])) {
                    t++;
                }
                SimDataBlock testSimDataBlock_1 = testDataManager.getSimDataBlock(testVar.getName(), testTimeArray[t]);
                double[] testData_1 = testSimDataBlock_1.getData();
                SimDataBlock testSimDataBlock_2 = testDataManager.getSimDataBlock(testVar.getName(), testTimeArray[t + 1]);
                double[] testData_2 = testSimDataBlock_2.getData();
                resampledTestData = new double[testData_1.length];
                // 
                for (int m = 0; m < testData_1.length; m++) {
                    resampledTestData[m] = testData_1[m] + (testData_2[m] - testData_1[m]) * (refTimeArray[j] - testTimeArray[t]) / (testTimeArray[t + 1] - testTimeArray[t]);
                }
            }
            // Spatial resampling (interpolation) ...
            double[] spaceResampledData = new double[refData.length];
            if (!testMathDesc.getGeometry().getExtent().compareEqual(refMathDesc.getGeometry().getExtent()) || !testMathDesc.getGeometry().getOrigin().compareEqual(refMathDesc.getGeometry().getOrigin())) {
                throw new RuntimeException("Different origins and/or extents for the 2 geometries. Cannot compare the 2 simulations");
            }
            if (testMesh.getSizeX() != refMesh.getSizeX() || testMesh.getSizeY() != refMesh.getSizeY() || testMesh.getSizeZ() != refMesh.getSizeZ()) {
                if (testVar instanceof VolVariable) {
                    if (testMathDesc.getGeometry().getDimension() == 1 && refMathDesc.getGeometry().getDimension() == 1) {
                        spaceResampledData = resample1DSpatial(resampledTestData, testMesh, refMesh);
                    } else if (testMathDesc.getGeometry().getDimension() == 2 && refMathDesc.getGeometry().getDimension() == 2) {
                        spaceResampledData = resample2DSpatial(resampledTestData, testMesh, refMesh);
                    } else if (testMathDesc.getGeometry().getDimension() == 3 && refMathDesc.getGeometry().getDimension() == 3) {
                        spaceResampledData = resample3DSpatial(resampledTestData, testMesh, refMesh);
                    } else {
                        throw new RuntimeException("Comparison of 2 simulations with different geometry dimensions are not handled at this time!");
                    }
                } else {
                    throw new RuntimeException("spatial resampling for variable type: " + testVar.getClass().getName() + " not supported");
                }
            } else {
                // no space resampling required
                if (testVar instanceof MemVariable) {
                    // 
                    if (membraneIndexMapping == null) {
                        membraneIndexMapping = testMesh.getMembraneIndexMapping(refMesh);
                    }
                    spaceResampledData = new double[resampledTestData.length];
                    for (int k = 0; k < resampledTestData.length; k++) {
                        spaceResampledData[k] = resampledTestData[membraneIndexMapping[k]];
                    }
                } else {
                    // 
                    // no reordering needed for other variable types.
                    // 
                    spaceResampledData = resampledTestData;
                }
            }
            // for each point in data block ...
            testDataInfoProvider.getPDEDataContext().setVariableName(testVar.getName());
            for (int k = 0; k < refData.length; k++) {
                if (!testDataInfoProvider.isDefined(k)) {
                    continue;
                }
                // Determine maxRef, minRef, maxAbsErr for variable
                // SubDomain testSubDomain = null;
                String sn = null;
                VariableType refVarType = refDataID.getVariableType();
                if (refVarType.equals(VariableType.VOLUME)) {
                    // testSubDomain = refVolSubDomainLookup[k];
                    sn = refVolSubDomainLookup[k].getName();
                } else if (refVarType.equals(VariableType.MEMBRANE)) {
                    // testSubDomain = refMemSubDomainLookup[k];
                    sn = refMemSubDomainLookup[k].getName();
                } else if (refVarType.equals(VariableType.MEMBRANE_REGION)) {
                    sn = "MRV_" + i;
                } else if (refVarType.equals(VariableType.VOLUME_REGION)) {
                    sn = "VRV_" + i;
                } else {
                    throw new RuntimeException("Var " + refVar.getName() + " not supported yet!");
                }
                // hashKey = refVar.getName()+":"+testSubDomain.getName();
                hashKey = refVar.getName() + ":" + sn;
                tempVar = tempVarHash.get(hashKey);
                if (tempVar == null) {
                    tempVar = new DataErrorSummary(null);
                    tempVarHash.put(hashKey, tempVar);
                }
                tempVar.addDataValues(refData[k], spaceResampledData[k], refTimeArray[j], k, absErrorThreshold, relErrorThreshold);
            }
        // end for (k)
        }
    // end for (j)
    }
    // end for (i)
    Enumeration<String> enumKeys = tempVarHash.keys();
    while (enumKeys.hasMoreElements()) {
        String key = enumKeys.nextElement();
        DataErrorSummary tempVarSummary = tempVarHash.get(key);
        simComparisonSummary.addVariableComparisonSummary(new VariableComparisonSummary(key, tempVarSummary.getMinRef(), tempVarSummary.getMaxRef(), tempVarSummary.getMaxAbsoluteError(), tempVarSummary.getMaxRelativeError(), tempVarSummary.getL2Norm(), tempVarSummary.getTimeAtMaxAbsoluteError(), tempVarSummary.getIndexAtMaxAbsoluteError(), tempVarSummary.getTimeAtMaxRelativeError(), tempVarSummary.getIndexAtMaxRelativeError()));
    }
    return simComparisonSummary;
}

Example 80 with Variable

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

the class FiniteVolumeFileWriter method writeCompartment_VarContext.

/**
 * Insert the method's description here.
 * Creation date: (5/9/2005 2:52:48 PM)
 * @throws ExpressionException
 */
private void writeCompartment_VarContext(CompartmentSubDomain volSubDomain) throws ExpressionException {
    Simulation simulation = simTask.getSimulation();
    // 
    // get list of volVariables participating in PDEs (anywhere).
    // 
    Vector<VolVariable> pdeVolVariableList = new Vector<VolVariable>();
    Variable[] variables = simTask.getSimulationJob().getSimulationSymbolTable().getVariables();
    for (int i = 0; i < variables.length; i++) {
        if (variables[i] instanceof VolVariable && simulation.getMathDescription().isPDE((VolVariable) variables[i])) {
            pdeVolVariableList.add((VolVariable) variables[i]);
        }
    }
    Enumeration<Equation> enum_equ = volSubDomain.getEquations();
    while (enum_equ.hasMoreElements()) {
        Equation equation = enum_equ.nextElement();
        // for chombo solver, only write equations for variables that are defined in this compartment
        if (!bChomboSolver || equation.getVariable().getDomain().getName().equals(volSubDomain.getName())) {
            if (equation instanceof VolumeRegionEquation) {
                writeCompartmentRegion_VarContext_Equation(volSubDomain, (VolumeRegionEquation) equation);
            } else if (equation instanceof MeasureEquation) {
                throw new RuntimeException("Measure Equation " + equation.getClass().getSimpleName() + " not yet supported in FiniteVolume solvers");
            } else {
                writeCompartment_VarContext_Equation(volSubDomain, equation);
            }
        }
        if (equation instanceof PdeEquation) {
            pdeVolVariableList.remove(equation.getVariable());
        }
    }
    // 
    if (!bChomboSolver) {
        for (int i = 0; i < pdeVolVariableList.size(); i++) {
            VolVariable volVar = pdeVolVariableList.elementAt(i);
            boolean bSteady = simulation.getMathDescription().isPdeSteady(volVar);
            PdeEquation dummyPdeEquation = new PdeEquation(volVar, bSteady, new Expression(0.0), new Expression(0.0), new Expression(0.0));
            writeCompartment_VarContext_Equation(volSubDomain, dummyPdeEquation);
        }
    }
}