Examples with SolverTaskDescription cbit.vcell.solver.SolverTaskDescription used on opensource projects

Example 26 with SolverTaskDescription

use of cbit.vcell.solver.SolverTaskDescription in project vcell by virtualcell.

the class StopAtSpatiallyUniformPanel method setSolverTaskDescription.

public void setSolverTaskDescription(SolverTaskDescription newValue) {
    SolverTaskDescription oldValue = solverTaskDescription;
    /* Stop listening for events from the current object */
    if (oldValue != null) {
        oldValue.removePropertyChangeListener(ivjEventHandler);
    }
    solverTaskDescription = newValue;
    /* Listen for events from the new object */
    if (newValue != null) {
        newValue.addPropertyChangeListener(ivjEventHandler);
    }
    solverTaskDescription = newValue;
    firePropertyChange("solverTaskDescription", oldValue, newValue);
    initConnections();
}

Example 27 with SolverTaskDescription

use of cbit.vcell.solver.SolverTaskDescription in project vcell by virtualcell.

the class NFSimSimulationOptionsPanel method setSolverTaskDescription.

public final void setSolverTaskDescription(SolverTaskDescription newValue) {
    SolverTaskDescription oldValue = solverTaskDescription;
    if (oldValue != null) {
        oldValue.removePropertyChangeListener(ivjEventHandler);
    }
    solverTaskDescription = newValue;
    if (newValue != null) {
        newValue.addPropertyChangeListener(ivjEventHandler);
    }
    solverTaskDescription = newValue;
    refresh();
    initConnections();
}

Example 28 with SolverTaskDescription

use of cbit.vcell.solver.SolverTaskDescription in project vcell by virtualcell.

the class SmoldynSimulationOptionsPanel method setSolverTaskDescription.

public final void setSolverTaskDescription(SolverTaskDescription newValue) {
    SolverTaskDescription oldValue = solverTaskDescription;
    if (oldValue != null) {
        oldValue.removePropertyChangeListener(ivjEventHandler);
    }
    solverTaskDescription = newValue;
    if (newValue != null) {
        newValue.addPropertyChangeListener(ivjEventHandler);
    }
    solverTaskDescription = newValue;
    refresh();
    initConnections();
}

Example 29 with SolverTaskDescription

use of cbit.vcell.solver.SolverTaskDescription in project vcell by virtualcell.

the class TestingFrameworkWindowManager method generateTestCriteriaReport.

/**
 * Insert the method's description here.
 * Creation date: (8/18/2003 5:36:47 PM)
 */
private String generateTestCriteriaReport(TestCaseNew testCase, TestCriteriaNew testCriteria, Simulation testSim, TFGenerateReport.VCDocumentAndSimInfo userSelectedRefSimInfo) /*,VCDocument refDoc,VCDocument testDocument*/
{
    if (testSim.getScanCount() != 1) {
        throw new RuntimeException("paramater scan is not supported in Math Testing Framework");
    }
    SimulationSymbolTable simSymbolTable = new SimulationSymbolTable(testSim, 0);
    String simReportStatus = null;
    String simReportStatusMessage = null;
    StringBuffer reportTCBuffer = new StringBuffer();
    VariableComparisonSummary[] failVarSummaries = null;
    VariableComparisonSummary[] allVarSummaries = null;
    double absErr = 0;
    double relErr = 0;
    if (testCriteria != null) {
        absErr = testCriteria.getMaxAbsError().doubleValue();
        relErr = testCriteria.getMaxRelError().doubleValue();
    }
    try {
        VCDocument testDoc = null;
        if (testCase instanceof TestCaseNewMathModel) {
            MathModelInfo mmInfo = ((TestCaseNewMathModel) testCase).getMathModelInfo();
            MathModel mathModel = getRequestManager().getDocumentManager().getMathModel(mmInfo);
            testDoc = mathModel;
        } else if (testCase instanceof TestCaseNewBioModel) {
            TestCaseNewBioModel bioTestCase = (TestCaseNewBioModel) testCase;
            // bioTestCase.
            BioModelInfo bmInfo = bioTestCase.getBioModelInfo();
            BioModel bioModel = getRequestManager().getDocumentManager().getBioModel(bmInfo);
            testDoc = bioModel;
        }
        TFGenerateReport.VCDocumentAndSimInfo refVCDocumentAndSimInfo = null;
        if (userSelectedRefSimInfo == null) {
            SimulationInfo refSimInfo = testCriteria.getRegressionSimInfo();
            if (refSimInfo != null) {
                VCDocument refDoc = null;
                if (testCriteria instanceof TestCriteriaNewMathModel) {
                    MathModelInfo mmInfo = ((TestCriteriaNewMathModel) testCriteria).getRegressionMathModelInfo();
                    MathModel mathModel = getRequestManager().getDocumentManager().getMathModel(mmInfo);
                    refDoc = mathModel;
                } else if (testCriteria instanceof TestCriteriaNewBioModel) {
                    BioModelInfo bmInfo = ((TestCriteriaNewBioModel) testCriteria).getRegressionBioModelInfo();
                    BioModel bioModel = getRequestManager().getDocumentManager().getBioModel(bmInfo);
                    refDoc = bioModel;
                }
                refVCDocumentAndSimInfo = new TFGenerateReport.VCDocumentAndSimInfo(refSimInfo, refDoc);
            }
            reportTCBuffer.append("\t\t" + testSim.getName() + (refVCDocumentAndSimInfo != null ? " (Using TestCrit RegrRefSim)" : "") + " : " + "\n");
        } else {
            refVCDocumentAndSimInfo = userSelectedRefSimInfo;
            reportTCBuffer.append("\t\t" + testSim.getName() + " (Using UserDefined RegrRefSim '" + userSelectedRefSimInfo.getSimInfo().getAuthoritativeVCSimulationIdentifier() + "') : " + "\n");
        }
        if (testCase.getType().equals(TestCaseNew.REGRESSION) && refVCDocumentAndSimInfo == null) {
            reportTCBuffer.append("\t\t\tNo reference SimInfo, SimInfoKey=" + testCriteria.getSimInfo().getVersion().getName() + ". Cannot perform Regression Test!\n");
            simReportStatus = TestCriteriaNew.TCRIT_STATUS_NOREFREGR;
        } else {
            VCDataIdentifier vcdID = new VCSimulationDataIdentifier(testSim.getSimulationInfo().getAuthoritativeVCSimulationIdentifier(), 0);
            DataManager simDataManager = getRequestManager().getDataManager(null, vcdID, testSim.isSpatial());
            double[] timeArray = null;
            // can be histogram, so there won't be time array
            try {
                timeArray = simDataManager.getDataSetTimes();
            } catch (Exception ex) {
                ex.printStackTrace(System.out);
            }
            NonspatialStochSimOptions stochOpt = testSim.getSolverTaskDescription().getStochOpt();
            if ((stochOpt == null || stochOpt.getNumOfTrials() == 1) && (timeArray == null || timeArray.length == 0)) {
                reportTCBuffer.append("\t\t\tNO DATA : Simulation not run yet.\n");
                simReportStatus = TestCriteriaNew.TCRIT_STATUS_NODATA;
            } else {
                // SPATIAL simulation
                if (testSim.getMathDescription().isSpatial()) {
                    PDEDataManager pdeDataManager = (PDEDataManager) simDataManager;
                    // Get EXACT solution if test case type is EXACT, Compare with numerical
                    if (testCase.getType().equals(TestCaseNew.EXACT) || testCase.getType().equals(TestCaseNew.EXACT_STEADY)) {
                        SimulationComparisonSummary simCompSummary = MathTestingUtilities.comparePDEResultsWithExact(simSymbolTable, pdeDataManager, testCase.getType(), testCriteria.getMaxAbsError(), testCriteria.getMaxRelError());
                        // Failed var summaries
                        failVarSummaries = simCompSummary.getFailingVariableComparisonSummaries(absErr, relErr);
                        allVarSummaries = simCompSummary.getVariableComparisonSummaries();
                        if (failVarSummaries.length > 0) {
                            simReportStatus = TestCriteriaNew.TCRIT_STATUS_FAILEDVARS;
                            // Failed simulation
                            reportTCBuffer.append("\t\tTolerance test FAILED \n");
                            reportTCBuffer.append("\t\tFailed Variables : \n");
                            for (int m = 0; m < failVarSummaries.length; m++) {
                                reportTCBuffer.append("\t\t\t" + failVarSummaries[m].toShortString() + "\n");
                            }
                        } else {
                            simReportStatus = TestCriteriaNew.TCRIT_STATUS_PASSED;
                            reportTCBuffer.append("\t\tTolerance test PASSED \n");
                        }
                        reportTCBuffer.append("\t\tPassed Variables : \n");
                        // Check if varSummary exists in failed summaries list. If not, simulation passed.
                        for (int m = 0; m < allVarSummaries.length; m++) {
                            if (!BeanUtils.arrayContains(failVarSummaries, allVarSummaries[m])) {
                                reportTCBuffer.append("\t\t\t" + allVarSummaries[m].toShortString() + "\n");
                            }
                        }
                    // Get CONSTRUCTED solution if test case type is CONSTRUCTED, Compare with numerical
                    } else if (testCase.getType().equals(TestCaseNew.CONSTRUCTED)) {
                        SimulationComparisonSummary simCompSummary = MathTestingUtilities.comparePDEResultsWithExact(simSymbolTable, pdeDataManager, testCase.getType(), testCriteria.getMaxAbsError(), testCriteria.getMaxRelError());
                        // Failed var summaries
                        failVarSummaries = simCompSummary.getFailingVariableComparisonSummaries(absErr, relErr);
                        allVarSummaries = simCompSummary.getVariableComparisonSummaries();
                        if (failVarSummaries.length > 0) {
                            simReportStatus = TestCriteriaNew.TCRIT_STATUS_FAILEDVARS;
                            // Failed simulation
                            reportTCBuffer.append("\t\tTolerance test FAILED \n");
                            reportTCBuffer.append("\t\tFailed Variables : \n");
                            for (int m = 0; m < failVarSummaries.length; m++) {
                                reportTCBuffer.append("\t\t\t" + failVarSummaries[m].toShortString() + "\n");
                            }
                        } else {
                            simReportStatus = TestCriteriaNew.TCRIT_STATUS_PASSED;
                            reportTCBuffer.append("\t\tTolerance test PASSED \n");
                        }
                        reportTCBuffer.append("\t\tPassed Variables : \n");
                        // Check if varSummary exists in failed summaries list. If not, simulation passed.
                        for (int m = 0; m < allVarSummaries.length; m++) {
                            if (!BeanUtils.arrayContains(failVarSummaries, allVarSummaries[m])) {
                                reportTCBuffer.append("\t\t\t" + allVarSummaries[m].toShortString() + "\n");
                            }
                        }
                    } else if (testCase.getType().equals(TestCaseNew.REGRESSION)) {
                        Simulation refSim = ((ClientDocumentManager) getRequestManager().getDocumentManager()).getSimulation(refVCDocumentAndSimInfo.getSimInfo());
                        VCDataIdentifier refVcdID = new VCSimulationDataIdentifier(refVCDocumentAndSimInfo.getSimInfo().getAuthoritativeVCSimulationIdentifier(), 0);
                        PDEDataManager refDataManager = (PDEDataManager) getRequestManager().getDataManager(null, refVcdID, refSim.isSpatial());
                        if (refSim.getScanCount() != 1) {
                            throw new RuntimeException("paramater scan is not supported in Math Testing Framework");
                        }
                        SimulationSymbolTable refSimSymbolTable = new SimulationSymbolTable(refSim, 0);
                        String[] varsToCompare = getVariableNamesToCompare(simSymbolTable, refSimSymbolTable);
                        SimulationComparisonSummary simCompSummary = MathTestingUtilities.comparePDEResults(simSymbolTable, pdeDataManager, refSimSymbolTable, refDataManager, varsToCompare, testCriteria.getMaxAbsError(), testCriteria.getMaxRelError(), refVCDocumentAndSimInfo.getVCDocument(), getDataInfoProvider(refVCDocumentAndSimInfo.getVCDocument(), refDataManager.getPDEDataContext(), refSim.getName()), testDoc, getDataInfoProvider(testDoc, pdeDataManager.getPDEDataContext(), testSim.getName()));
                        // Failed var summaries
                        failVarSummaries = simCompSummary.getFailingVariableComparisonSummaries(absErr, relErr);
                        allVarSummaries = simCompSummary.getVariableComparisonSummaries();
                        if (failVarSummaries.length > 0) {
                            simReportStatus = TestCriteriaNew.TCRIT_STATUS_FAILEDVARS;
                            // Failed simulation
                            reportTCBuffer.append("\t\tTolerance test FAILED \n");
                            reportTCBuffer.append("\t\tFailed Variables : \n");
                            for (int m = 0; m < failVarSummaries.length; m++) {
                                reportTCBuffer.append("\t\t\t" + failVarSummaries[m].toShortString() + "\n");
                            }
                        } else {
                            simReportStatus = TestCriteriaNew.TCRIT_STATUS_PASSED;
                            reportTCBuffer.append("\t\tTolerance test PASSED \n");
                        }
                        reportTCBuffer.append("\t\tPassed Variables : \n");
                        // Check if varSummary exists in failed summaries list. If not, simulation passed.
                        for (int m = 0; m < allVarSummaries.length; m++) {
                            if (!BeanUtils.arrayContains(failVarSummaries, allVarSummaries[m])) {
                                reportTCBuffer.append("\t\t\t" + allVarSummaries[m].toShortString() + "\n");
                            }
                        }
                    }
                } else {
                    // NON-SPATIAL CASE
                    ODEDataManager odeDataManager = (ODEDataManager) simDataManager;
                    ODESolverResultSet numericalResultSet = odeDataManager.getODESolverResultSet();
                    // Get EXACT result set if test case type is EXACT, Compare with numerical
                    if (testCase.getType().equals(TestCaseNew.EXACT) || testCase.getType().equals(TestCaseNew.EXACT_STEADY)) {
                        ODESolverResultSet exactResultSet = MathTestingUtilities.getExactResultSet(testSim.getMathDescription(), timeArray, testSim.getSolverTaskDescription().getSensitivityParameter());
                        String[] varsToCompare = getVariableNamesToCompare(simSymbolTable, simSymbolTable);
                        SimulationComparisonSummary simCompSummary_exact = MathTestingUtilities.compareResultSets(numericalResultSet, exactResultSet, varsToCompare, testCase.getType(), testCriteria.getMaxAbsError(), testCriteria.getMaxRelError());
                        // Get all the variable comparison summaries and the failed ones to print out report for EXACT solution comparison.
                        failVarSummaries = simCompSummary_exact.getFailingVariableComparisonSummaries(absErr, relErr);
                        allVarSummaries = simCompSummary_exact.getVariableComparisonSummaries();
                        if (failVarSummaries.length > 0) {
                            simReportStatus = TestCriteriaNew.TCRIT_STATUS_FAILEDVARS;
                            // Failed simulation
                            reportTCBuffer.append("\t\tTolerance test FAILED \n");
                            reportTCBuffer.append("\t\tFailed Variables : \n");
                            for (int m = 0; m < failVarSummaries.length; m++) {
                                reportTCBuffer.append("\t\t\t" + failVarSummaries[m].toShortString() + "\n");
                            }
                        } else {
                            simReportStatus = TestCriteriaNew.TCRIT_STATUS_PASSED;
                            reportTCBuffer.append("\t\tTolerance test PASSED \n");
                        }
                        reportTCBuffer.append("\t\tPassed Variables : \n");
                        // Check if varSummary exists in failed summaries list. If not, simulation passed.
                        for (int m = 0; m < allVarSummaries.length; m++) {
                            if (!BeanUtils.arrayContains(failVarSummaries, allVarSummaries[m])) {
                                reportTCBuffer.append("\t\t\t" + allVarSummaries[m].toShortString() + "\n");
                            }
                        }
                    // Get CONSTRUCTED result set if test case type is CONSTRUCTED , compare with numerical
                    } else if (testCase.getType().equals(TestCaseNew.CONSTRUCTED)) {
                        ODESolverResultSet constructedResultSet = MathTestingUtilities.getConstructedResultSet(testSim.getMathDescription(), timeArray);
                        String[] varsToCompare = getVariableNamesToCompare(simSymbolTable, simSymbolTable);
                        SimulationComparisonSummary simCompSummary_constr = MathTestingUtilities.compareResultSets(numericalResultSet, constructedResultSet, varsToCompare, testCase.getType(), testCriteria.getMaxAbsError(), testCriteria.getMaxRelError());
                        // Get all the variable comparison summaries and the failed ones to print out report for CONSTRUCTED solution comparison.
                        failVarSummaries = simCompSummary_constr.getFailingVariableComparisonSummaries(absErr, relErr);
                        allVarSummaries = simCompSummary_constr.getVariableComparisonSummaries();
                        if (failVarSummaries.length > 0) {
                            simReportStatus = TestCriteriaNew.TCRIT_STATUS_FAILEDVARS;
                            // Failed simulation
                            reportTCBuffer.append("\t\tTolerance test FAILED \n");
                            reportTCBuffer.append("\t\tFailed Variables : \n");
                            for (int m = 0; m < failVarSummaries.length; m++) {
                                reportTCBuffer.append("\t\t\t" + failVarSummaries[m].toShortString() + "\n");
                            }
                        } else {
                            simReportStatus = TestCriteriaNew.TCRIT_STATUS_PASSED;
                            reportTCBuffer.append("\t\tTolerance test PASSED \n");
                        }
                        reportTCBuffer.append("\t\tPassed Variables : \n");
                        // Check if varSummary exists in failed summaries list. If not, simulation passed.
                        for (int m = 0; m < allVarSummaries.length; m++) {
                            if (!BeanUtils.arrayContains(failVarSummaries, allVarSummaries[m])) {
                                reportTCBuffer.append("\t\t\t" + allVarSummaries[m].toShortString() + "\n");
                            }
                        }
                    } else if (testCase.getType().equals(TestCaseNew.REGRESSION)) {
                        Simulation refSim = ((ClientDocumentManager) getRequestManager().getDocumentManager()).getSimulation(testCriteria.getRegressionSimInfo());
                        if (refSim.getScanCount() != 1) {
                            throw new RuntimeException("paramater scan is not supported in Math Testing Framework");
                        }
                        SimulationSymbolTable refSimSymbolTable = new SimulationSymbolTable(refSim, 0);
                        String[] varsToTest = getVariableNamesToCompare(simSymbolTable, refSimSymbolTable);
                        VCDataIdentifier refVcdID = new VCSimulationDataIdentifier(refVCDocumentAndSimInfo.getSimInfo().getAuthoritativeVCSimulationIdentifier(), 0);
                        ODEDataManager refDataManager = (ODEDataManager) getRequestManager().getDataManager(null, refVcdID, refSim.isSpatial());
                        ODESolverResultSet referenceResultSet = refDataManager.getODESolverResultSet();
                        SimulationComparisonSummary simCompSummary_regr = null;
                        int interpolationOrder = 1;
                        SolverTaskDescription solverTaskDescription = refSim.getSolverTaskDescription();
                        if (solverTaskDescription.getOutputTimeSpec().isDefault() && ((DefaultOutputTimeSpec) solverTaskDescription.getOutputTimeSpec()).getKeepEvery() == 1) {
                            SolverDescription solverDescription = solverTaskDescription.getSolverDescription();
                            if ((!solverDescription.supportsAll(SolverDescription.DiscontinutiesFeatures)) || !refSim.getMathDescription().hasDiscontinuities()) {
                                interpolationOrder = solverDescription.getTimeOrder();
                            }
                        }
                        simCompSummary_regr = MathTestingUtilities.compareUnEqualResultSets(numericalResultSet, referenceResultSet, varsToTest, testCriteria.getMaxAbsError(), testCriteria.getMaxRelError(), interpolationOrder);
                        // Get all the variable comparison summaries and the failed ones to print out report for CONSTRUCTED solution comparison.
                        failVarSummaries = simCompSummary_regr.getFailingVariableComparisonSummaries(absErr, relErr);
                        allVarSummaries = simCompSummary_regr.getVariableComparisonSummaries();
                        if (failVarSummaries.length > 0) {
                            simReportStatus = TestCriteriaNew.TCRIT_STATUS_FAILEDVARS;
                            // Failed simulation
                            reportTCBuffer.append("\t\tTolerance test FAILED \n");
                            reportTCBuffer.append("\t\tFailed Variables : \n");
                            for (int m = 0; m < failVarSummaries.length; m++) {
                                reportTCBuffer.append("\t\t\t" + failVarSummaries[m].toShortString() + "\n");
                            }
                        } else {
                            simReportStatus = TestCriteriaNew.TCRIT_STATUS_PASSED;
                            reportTCBuffer.append("\t\tTolerance test PASSED \n");
                        }
                        reportTCBuffer.append("\t\tPassed Variables : \n");
                        // Check if varSummary exists in failed summaries list. If not, simulation passed.
                        for (int m = 0; m < allVarSummaries.length; m++) {
                            if (!BeanUtils.arrayContains(failVarSummaries, allVarSummaries[m])) {
                                reportTCBuffer.append("\t\t\t" + allVarSummaries[m].toShortString() + "\n");
                            }
                        }
                    }
                }
            }
        }
    } catch (Throwable e) {
        simReportStatus = TestCriteriaNew.TCRIT_STATUS_RPERROR;
        simReportStatusMessage = e.getClass().getName() + " " + e.getMessage();
        reportTCBuffer.append("\t\t" + simReportStatusMessage + "\n");
        e.printStackTrace(System.out);
    }
    if (userSelectedRefSimInfo == null) {
        try {
            // Remove any test results already present for testCriteria
            RemoveTestResultsOP removeResultsOP = new RemoveTestResultsOP(new BigDecimal[] { testCriteria.getTCritKey() });
            // testResultsOPsVector.add(removeResultsOP);
            getRequestManager().getDocumentManager().doTestSuiteOP(removeResultsOP);
            // Create new AddTestREsultsOP object for the current simulation./testCriteria.
            if (allVarSummaries != null) {
                AddTestResultsOP testResultsOP = new AddTestResultsOP(testCriteria.getTCritKey(), allVarSummaries);
                // testResultsOPsVector.add(testResultsOP);
                // Write the testResults for simulation/TestCriteria into the database ...
                getRequestManager().getDocumentManager().doTestSuiteOP(testResultsOP);
            }
            // Update report status
            updateTCritStatus(testCriteria, simReportStatus, simReportStatusMessage);
        } catch (Throwable e) {
            reportTCBuffer.append("\t\tUpdate DB Results failed. " + e.getClass().getName() + " " + e.getMessage() + "\n");
            try {
                getRequestManager().getDocumentManager().doTestSuiteOP(new EditTestCriteriaOPReportStatus(testCriteria.getTCritKey(), TestCriteriaNew.TCRIT_STATUS_RPERROR, e.getClass().getName() + " " + e.getMessage()));
            } catch (Throwable e2) {
            // Nothing more can be done
            }
        }
    }
    return reportTCBuffer.toString();
}

Example 30 with SolverTaskDescription

use of cbit.vcell.solver.SolverTaskDescription in project vcell by virtualcell.

the class XmlReader method getSolverTaskDescription.

/**
 * This method returns a SolverTaskDescription Object from a XML Element.
 * Creation date: (5/22/2001 10:51:23 AM)
 * @return cbit.vcell.solver.SolverTaskDescription
 * @param param org.jdom.Element
 * @param simulation cbit.vcell.solver.Simulation
 */
private SolverTaskDescription getSolverTaskDescription(Element param, Simulation simulation) throws XmlParseException {
    // *** create new SolverTaskDescription ***
    SolverTaskDescription solverTaskDesc = new SolverTaskDescription(simulation);
    // Added July 22nd, 2007, used as condition for stochSimOptions or stochHybridOprtions
    SolverDescription sd = null;
    // Retrieve attributes
    String taskType = param.getAttributeValue(XMLTags.TaskTypeTag);
    int keepEvery = -1;
    int keepAtMost = -1;
    if (param.getAttributeValue(XMLTags.KeepEveryTag) != null) {
        keepEvery = Integer.parseInt(param.getAttributeValue(XMLTags.KeepEveryTag));
        keepAtMost = Integer.parseInt(param.getAttributeValue(XMLTags.KeepAtMostTag));
    }
    boolean useSymJacob = new Boolean(param.getAttributeValue(XMLTags.UseSymbolicJacobianAttrTag)).booleanValue();
    String solverName = param.getAttributeValue(XMLTags.SolverNameTag);
    // get sentivity parameter
    Element sensparamElement = param.getChild(XMLTags.ConstantTag, vcNamespace);
    Constant sensitivityparam = null;
    if (sensparamElement != null) {
        sensitivityparam = getConstant(sensparamElement);
    }
    // set Attributes
    try {
        // set solver
        sd = SolverDescription.fromDatabaseName(solverName);
        if (sd == null) {
            System.err.println("====================================== couldn't find solver description name ==========================================");
        }
        solverTaskDesc.setSolverDescription(sd);
        if (taskType.equalsIgnoreCase(XMLTags.UnsteadyTag)) {
            solverTaskDesc.setTaskType(SolverTaskDescription.TASK_UNSTEADY);
        } else if (taskType.equalsIgnoreCase(XMLTags.SteadyTag)) {
            solverTaskDesc.setTaskType(SolverTaskDescription.TASK_STEADY);
        } else {
            throw new XmlParseException("Unexpected task type: " + taskType);
        }
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException("A PropertyVetoException was fired when setting the taskType: " + taskType, e);
    }
    int numProcessors = parseIntWithDefault(param, XMLTags.NUM_PROCESSORS, 1);
    try {
        solverTaskDesc.setNumProcessors(numProcessors);
        solverTaskDesc.setUseSymbolicJacobian(useSymJacob);
        // get TimeBound
        solverTaskDesc.setTimeBounds(getTimeBounds(param.getChild(XMLTags.TimeBoundTag, vcNamespace)));
        // get TimeStep
        solverTaskDesc.setTimeStep(getTimeStep(param.getChild(XMLTags.TimeStepTag, vcNamespace)));
        // get ErrorTolerance
        solverTaskDesc.setErrorTolerance(getErrorTolerance(param.getChild(XMLTags.ErrorToleranceTag, vcNamespace)));
        // get StochSimOptions
        if (simulation != null && simulation.getMathDescription() != null) {
            if (simulation.getMathDescription().isNonSpatialStoch() && param.getChild(XMLTags.StochSimOptionsTag, vcNamespace) != null) {
                // Amended July 22nd, 2007 to read either stochSimOptions or stochHybridOptions
                solverTaskDesc.setStochOpt(getStochSimOptions(param.getChild(XMLTags.StochSimOptionsTag, vcNamespace)));
                if (sd != null && !sd.equals(SolverDescription.StochGibson)) {
                    solverTaskDesc.setStochHybridOpt(getStochHybridOptions(param.getChild(XMLTags.StochSimOptionsTag, vcNamespace)));
                }
            }
        }
        // get OutputOptions
        if (keepEvery != -1) {
            solverTaskDesc.setOutputTimeSpec(new DefaultOutputTimeSpec(keepEvery, keepAtMost));
        }
        OutputTimeSpec ots = getOutputTimeSpec(param.getChild(XMLTags.OutputOptionsTag, vcNamespace));
        if (ots != null) {
            solverTaskDesc.setOutputTimeSpec(getOutputTimeSpec(param.getChild(XMLTags.OutputOptionsTag, vcNamespace)));
        }
        // set SensitivityParameter
        solverTaskDesc.setSensitivityParameter(sensitivityparam);
        // set StopAtSpatiallyUniform
        Element stopSpatiallyElement = param.getChild(XMLTags.StopAtSpatiallyUniform, vcNamespace);
        if (stopSpatiallyElement != null) {
            Element errTolElement = stopSpatiallyElement.getChild(XMLTags.ErrorToleranceTag, vcNamespace);
            if (errTolElement != null) {
                solverTaskDesc.setStopAtSpatiallyUniformErrorTolerance(getErrorTolerance(errTolElement));
            }
        }
        String runParameterScanSeriallyAttributeValue = param.getAttributeValue(XMLTags.RunParameterScanSerially);
        if (runParameterScanSeriallyAttributeValue != null) {
            solverTaskDesc.setSerialParameterScan(new Boolean(runParameterScanSeriallyAttributeValue).booleanValue());
        }
        Element nfsimSimulationOptionsElement = param.getChild(XMLTags.NFSimSimulationOptions, vcNamespace);
        if (nfsimSimulationOptionsElement != null) {
            NFsimSimulationOptions nfsimSimulationOptions = getNFSimSimulationOptions(nfsimSimulationOptionsElement);
            solverTaskDesc.setNFSimSimulationOptions(nfsimSimulationOptions);
        }
        Element smoldySimulationOptionsElement = param.getChild(XMLTags.SmoldynSimulationOptions, vcNamespace);
        if (smoldySimulationOptionsElement != null) {
            SmoldynSimulationOptions smoldynSimulationOptions = getSmoldySimulationOptions(smoldySimulationOptionsElement);
            solverTaskDesc.setSmoldynSimulationOptions(smoldynSimulationOptions);
        }
        Element sundialsPdeSolverOptionsElement = param.getChild(XMLTags.SundialsSolverOptions, vcNamespace);
        if (sundialsPdeSolverOptionsElement != null) {
            SundialsPdeSolverOptions sundialsPdeSolverOptions = getSundialsPdeSolverOptions(sundialsPdeSolverOptionsElement);
            solverTaskDesc.setSundialsPdeSolverOptions(sundialsPdeSolverOptions);
        }
        Element chomboElement = param.getChild(XMLTags.ChomboSolverSpec, vcNamespace);
        if (chomboElement != null) {
            ChomboSolverSpec chombo = getChomboSolverSpec(solverTaskDesc, chomboElement, simulation.getMathDescription().getGeometry().getDimension());
            solverTaskDesc.setChomboSolverSpec(chombo);
        }
        Element mbElement = param.getChild(XMLTags.MovingBoundarySolverOptionsTag, vcNamespace);
        if (mbElement != null) {
            MovingBoundarySolverOptions mb = getMovingBoundarySolverOptions(solverTaskDesc, mbElement);
            solverTaskDesc.setMovingBoundarySolverOptions(mb);
        }
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException(e);
    }
    return solverTaskDesc;
}