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

Example 6 with NonspatialStochSimOptions

use of cbit.vcell.solver.NonspatialStochSimOptions 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 7 with NonspatialStochSimOptions

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

the class NetCDFWriter method writeHybridInputFile.

/**
 * Write the model to a NetCDF file which serves as an input for stoch hybrid simulator.
 * To write to a NetCDF file is a bit complicated. First, we have to create a NetCDF-3
 * file. And then feed in the data.
 * Creation date: (5/22/2007 5:36:03 PM)
 */
public void writeHybridInputFile(String[] parameterNames) throws Exception, cbit.vcell.parser.ExpressionException, IOException, MathException, InvalidRangeException {
    Simulation simulation = simTask.getSimulation();
    SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
    if (initialize()) {
        // we need to get model and control information first
        NetcdfFileWriteable ncfile = NetcdfFileWriteable.createNew(filename, false);
        // Model info. will be extracted from subDomain of mathDescription
        java.util.Enumeration<SubDomain> e = simulation.getMathDescription().getSubDomains();
        // remember we are dealing with compartmental model here. only 1 subdomain.
        SubDomain subDomain = e.nextElement();
        JumpProcess[] reactions = (JumpProcess[]) subDomain.getJumpProcesses().toArray(new JumpProcess[subDomain.getJumpProcesses().size()]);
        // get species variable names
        Variable[] variables = simSymbolTable.getVariables();
        String[] speciesNames = new String[variables.length];
        for (int i = 0; i < variables.length; i++) speciesNames[i] = variables[i].getName();
        // the probabilities for reactions
        Expression[] probs = new Expression[reactions.length];
        for (int i = 0; i < reactions.length; i++) {
            probs[i] = simSymbolTable.substituteFunctions(reactions[i].getProbabilityRate());
            probs[i] = probs[i].flatten();
        }
        VarIniCondition[] varInis = (VarIniCondition[]) subDomain.getVarIniConditions().toArray(new VarIniCondition[subDomain.getVarIniConditions().size()]);
        // the non-constant stoch variables
        Vector<Variable> vars = new Vector<Variable>();
        for (int i = 0; i < varInis.length; i++) {
            if (varInis[i].getVar() instanceof StochVolVariable) {
                vars.addElement(varInis[i].getVar());
            }
        }
        // get reaction rate law types and rate constants
        ReactionRateLaw[] reactionRateLaws = getReactionRateLaws(probs);
        SolverTaskDescription solverTaskDescription = simulation.getSolverTaskDescription();
        TimeBounds timeBounds = solverTaskDescription.getTimeBounds();
        UniformOutputTimeSpec timeSpec = (UniformOutputTimeSpec) solverTaskDescription.getOutputTimeSpec();
        UniformOutputTimeSpec outputTimeSpec = ((UniformOutputTimeSpec) solverTaskDescription.getOutputTimeSpec());
        NonspatialStochSimOptions stochOpt = solverTaskDescription.getStochOpt();
        // create an empty NetCDF-3 file
        // define dimensions
        /* these sizes must match the buffers allocated in corresponding Fortran code -- see globalvariables.f90
			in numerics Hy3S/src directory */
        Dimension numTrial = ncfile.addDimension("NumTrials", (int) stochOpt.getNumOfTrials());
        Dimension numSpecies = ncfile.addDimension("NumSpecies", vars.size());
        Dimension numReactions = ncfile.addDimension("NumReactions", subDomain.getJumpProcesses().size());
        int outPoints = ((int) ((timeBounds.getEndingTime() - timeBounds.getStartingTime()) / outputTimeSpec.getOutputTimeStep())) + 1;
        Dimension numTimePoints = ncfile.addDimension("NumTimePoints", outPoints);
        Dimension numModels = ncfile.addDimension("NumModels", 1);
        Dimension numMaxDepList = ncfile.addDimension("NumMaxDepList", 6);
        Dimension numMaxStoichList = ncfile.addDimension("NumMaxStoichList", 25);
        Dimension stringLen = ncfile.addDimension("StringLen", 72);
        // define variables
        // jms info
        ArrayList<Dimension> dims = new ArrayList<Dimension>();
        dims.add(stringLen);
        if (bMessaging) {
            ncfile.addVariable("JMS_BROKER", DataType.CHAR, dims);
            ncfile.addVariable("JMS_USER", DataType.CHAR, dims);
            ncfile.addVariable("JMS_PASSWORD", DataType.CHAR, dims);
            ncfile.addVariable("JMS_QUEUE", DataType.CHAR, dims);
            ncfile.addVariable("JMS_TOPIC", DataType.CHAR, dims);
            ncfile.addVariable("VCELL_USER", DataType.CHAR, dims);
            ncfile.addVariable("SIMULATION_KEY", DataType.INT, new ArrayList<Dimension>());
            ncfile.addVariable("JOB_INDEX", DataType.INT, new ArrayList<Dimension>());
        }
        // scalars
        ncfile.addVariable("TStart", DataType.DOUBLE, new ArrayList<Dimension>());
        ncfile.addVariable("TEnd", DataType.DOUBLE, new ArrayList<Dimension>());
        ncfile.addVariable("SaveTime", DataType.DOUBLE, new ArrayList<Dimension>());
        ncfile.addVariable("Volume", DataType.DOUBLE, new ArrayList<Dimension>());
        ncfile.addVariable("CellGrowthTime", DataType.DOUBLE, new ArrayList<Dimension>());
        ncfile.addVariable("CellGrowthTimeSD", DataType.DOUBLE, new ArrayList<Dimension>());
        ncfile.addVariable("ExpType", DataType.INT, new ArrayList<Dimension>());
        ncfile.addVariable("LastTrial", DataType.INT, new ArrayList<Dimension>());
        ncfile.addVariable("LastModel", DataType.INT, new ArrayList<Dimension>());
        ncfile.addVariable("MaxNumModels", DataType.INT, new ArrayList<Dimension>());
        ncfile.addVariable("NumModels", DataType.INT, new ArrayList<Dimension>());
        // variables with at least 1 dimension
        ArrayList<Dimension> dimspecies = new ArrayList<Dimension>();
        dimspecies.add(numSpecies);
        ArrayList<Dimension> dimreactions = new ArrayList<Dimension>();
        dimreactions.add(numReactions);
        ncfile.addVariable("SpeciesSplitOnDivision", DataType.INT, dimspecies);
        ncfile.addVariable("SaveSpeciesData", DataType.INT, dimspecies);
        ncfile.addVariable("Reaction_Rate_Laws", DataType.INT, dimreactions);
        ncfile.addVariable("Reaction_DListLen", DataType.INT, dimreactions);
        ncfile.addVariable("Reaction_StoichListLen", DataType.INT, dimreactions);
        ncfile.addVariable("Reaction_OptionalData", DataType.INT, dimreactions);
        dims.clear();
        dims.add(numReactions);
        dims.add(numMaxStoichList);
        ncfile.addVariable("Reaction_StoichCoeff", DataType.INT, dims);
        ncfile.addVariable("Reaction_StoichSpecies", DataType.INT, dims);
        dims.clear();
        dims.add(numReactions);
        dims.add(numMaxDepList);
        ncfile.addVariable("Reaction_DepList", DataType.INT, dims);
        dims.clear();
        dims.add(numReactions);
        dims.add(stringLen);
        ncfile.addVariable("Reaction_names", DataType.CHAR, dims);
        dims.clear();
        dims.add(numSpecies);
        dims.add(stringLen);
        ncfile.addVariable("Species_names", DataType.CHAR, dims);
        ncfile.addVariable("SpeciesIC", DataType.INT, dimspecies);
        dims.clear();
        dims.add(numReactions);
        dims.add(numMaxDepList);
        ncfile.addVariable("Reaction_Rate_Constants", DataType.DOUBLE, dims);
        // create the file
        try {
            ncfile.create();
        } catch (IOException ioe) {
            ioe.printStackTrace(System.err);
            throw new IOException("Error creating hybrid file " + filename + ": " + ioe.getMessage());
        }
        // write data to the NetCDF file
        try {
            // write jms info
            if (bMessaging) {
                ArrayChar.D1 jmsString = new ArrayChar.D1(stringLen.getLength());
                String jmshost = PropertyLoader.getRequiredProperty(PropertyLoader.jmsHostExternal);
                // 
                // Used for new REST HTTP messaging api (USE THIS WHEN Hyrbid Solvers are compiled).
                // 
                // String jmsrestport = PropertyLoader.getRequiredProperty(PropertyLoader.jmsRestPortExternal);
                // String jmsurl = jmshost+":"+jmsrestport;
                // 
                // connect to messaging using legacy AMQP protocol instead of new REST api.  Needed for legacy pre-compiled solvers.
                // 
                String jmsport = PropertyLoader.getRequiredProperty(PropertyLoader.jmsPortExternal);
                String jmsurl = "failover:(tcp://" + jmshost + ":" + jmsport + ")";
                jmsString.setString(jmsurl);
                ncfile.write("JMS_BROKER", jmsString);
                jmsString.setString(PropertyLoader.getRequiredProperty(PropertyLoader.jmsUser));
                ncfile.write("JMS_USER", jmsString);
                String jmsPassword = PropertyLoader.getSecretValue(PropertyLoader.jmsPasswordValue, PropertyLoader.jmsPasswordFile);
                jmsString.setString(jmsPassword);
                ncfile.write("JMS_PASSWORD", jmsString);
                jmsString.setString(VCellQueue.WorkerEventQueue.getName());
                ncfile.write("JMS_QUEUE", jmsString);
                jmsString.setString(VCellTopic.ServiceControlTopic.getName());
                ncfile.write("JMS_TOPIC", jmsString);
                jmsString.setString(simulation.getVersion().getOwner().getName());
                ncfile.write("VCELL_USER", jmsString);
                ArrayInt.D0 scalarJMS = new ArrayInt.D0();
                scalarJMS.set(Integer.parseInt(simulation.getVersion().getVersionKey() + ""));
                ncfile.write("SIMULATION_KEY", scalarJMS);
                scalarJMS.set(simTask.getSimulationJob().getJobIndex());
                ncfile.write("JOB_INDEX", scalarJMS);
            }
            ArrayDouble.D0 scalarDouble = new ArrayDouble.D0();
            // TStart, TEnd, SaveTime
            if ((timeBounds.getEndingTime() > timeBounds.getStartingTime()) && (outputTimeSpec.getOutputTimeStep() > 0)) {
                scalarDouble.set(timeBounds.getStartingTime());
                ncfile.write("TStart", scalarDouble);
                scalarDouble.set(timeBounds.getEndingTime());
                ncfile.write("TEnd", scalarDouble);
                scalarDouble.set(outputTimeSpec.getOutputTimeStep());
                ncfile.write("SaveTime", scalarDouble);
            } else {
                System.err.println("Time setting error. Ending time smaller than starting time or save interval is not a positive value.");
                throw new RuntimeException("Time setting error. Ending time smaller than starting time or save interval is not a positive value.");
            }
            // Volume
            // we set volume to 1. This model file cannot support multi-compartmental sizes.
            // When writting the rate constants, we must take the volume into account according to the reaction type.
            scalarDouble.set(1);
            ncfile.write("Volume", scalarDouble);
            // CellGrowthTime, CellGrowthTimeSD,
            scalarDouble.set(0);
            ncfile.write("CellGrowthTime", scalarDouble);
            ncfile.write("CellGrowthTimeSD", scalarDouble);
            // ExpType, Last Trial, Last Model, MaxNumModels, NumModels
            ArrayInt.D0 scalarInt = new ArrayInt.D0();
            scalarInt.set(0);
            ncfile.write("LastTrial", scalarInt);
            ncfile.write("LastModel", scalarInt);
            scalarInt.set(1);
            ncfile.write("ExpType", scalarInt);
            ncfile.write("MaxNumModels", scalarInt);
            ncfile.write("NumModels", scalarInt);
            // SpeciesSplitOnDivision
            ArrayInt A1 = new ArrayInt.D1(numSpecies.getLength());
            Index idx = A1.getIndex();
            for (int i = 0; i < numSpecies.getLength(); i++) {
                A1.setInt(idx.set(i), 0);
            }
            ncfile.write("SpeciesSplitOnDivision", new int[1], A1);
            // SaveSpeciesData
            ArrayInt A2 = new ArrayInt.D1(numSpecies.getLength());
            idx = A2.getIndex();
            for (int i = 0; i < numSpecies.getLength(); i++) {
                A2.setInt(idx.set(i), 1);
            }
            ncfile.write("SaveSpeciesData", new int[1], A2);
            // Reaction_Rate_Laws
            ArrayInt A3 = new ArrayInt.D1(numReactions.getLength());
            idx = A3.getIndex();
            for (int i = 0; i < numReactions.getLength(); i++) {
                A3.setInt(idx.set(i), reactionRateLaws[i].getLawType());
            }
            ncfile.write("Reaction_Rate_Laws", new int[1], A3);
            // Reaction_DListLen
            ArrayInt A4 = new ArrayInt.D1(numReactions.getLength());
            idx = A4.getIndex();
            for (int i = 0; i < numReactions.getLength(); i++) {
                if (reactionRateLaws[i].getLawType() == ReactionRateLaw.order_0)
                    A4.setInt(idx.set(i), 0);
                else if ((reactionRateLaws[i].getLawType() == ReactionRateLaw.order_1) || (reactionRateLaws[i].getLawType() == ReactionRateLaw.order_2_1substrate) || (reactionRateLaws[i].getLawType() == ReactionRateLaw.order_3_1substrate))
                    A4.setInt(idx.set(i), 1);
                else if ((reactionRateLaws[i].getLawType() == ReactionRateLaw.order_2_2substrate) || (reactionRateLaws[i].getLawType() == ReactionRateLaw.order_3_2substrate))
                    A4.setInt(idx.set(i), 2);
                else if (reactionRateLaws[i].getLawType() == ReactionRateLaw.order_3_3substrate)
                    A4.setInt(idx.set(i), 3);
            }
            ncfile.write("Reaction_DListLen", new int[1], A4);
            // Reaction_StoichListLen
            ArrayInt A5 = new ArrayInt.D1(numReactions.getLength());
            idx = A5.getIndex();
            for (int i = 0; i < numReactions.getLength(); i++) {
                A5.setInt(idx.set(i), reactions[i].getActions().size());
            }
            ncfile.write("Reaction_StoichListLen", new int[1], A5);
            // Reaction_OptionalData
            ArrayInt A6 = new ArrayInt.D1(numReactions.getLength());
            idx = A6.getIndex();
            for (int i = 0; i < numReactions.getLength(); i++) {
                A6.setInt(idx.set(i), 0);
            }
            ncfile.write("Reaction_OptionalData", new int[1], A6);
            // Reaction_StoichCoeff
            ArrayInt A7 = new ArrayInt.D2(numReactions.getLength(), numMaxStoichList.getLength());
            idx = A7.getIndex();
            for (int i = 0; i < numReactions.getLength(); i++) {
                Action[] actions = (Action[]) reactions[i].getActions().toArray(new Action[reactions[i].getActions().size()]);
                for (int j = 0; j < actions.length; j++) {
                    try {
                        actions[j].getOperand().evaluateConstant();
                        int coeff = (int) Math.round(actions[j].getOperand().evaluateConstant());
                        A7.setInt(idx.set(i, j), coeff);
                    } catch (ExpressionException ex) {
                        ex.printStackTrace(System.err);
                        throw new ExpressionException(ex.getMessage());
                    }
                }
            }
            ncfile.write("Reaction_StoichCoeff", new int[2], A7);
            // Reaction_StoichSpecies
            ArrayInt A8 = new ArrayInt.D2(numReactions.getLength(), numMaxStoichList.getLength());
            idx = A8.getIndex();
            for (int i = 0; i < numReactions.getLength(); i++) {
                ArrayList<Action> actions = reactions[i].getActions();
                for (int j = 0; j < actions.size(); j++) {
                    A8.setInt(idx.set(i, j), getVariableIndex(((Action) actions.get(j)).getVar().getName(), vars));
                }
            }
            ncfile.write("Reaction_StoichSpecies", new int[2], A8);
            // Reaction_DepList
            ArrayInt A9 = new ArrayInt.D2(numReactions.getLength(), numMaxDepList.getLength());
            idx = A9.getIndex();
            for (int i = 0; i < numReactions.getLength(); i++) {
                ReactionRateLaw rl = reactionRateLaws[i];
                Hashtable<String, Integer> tem = varInProbOrderHash[i];
                Enumeration<String> varnames = tem.keys();
                if (rl.getLawType() == ReactionRateLaw.order_0) {
                // don't do anything here.
                } else if ((rl.getLawType() == ReactionRateLaw.order_1) || (rl.getLawType() == ReactionRateLaw.order_2_1substrate) || (rl.getLawType() == ReactionRateLaw.order_3_1substrate) || (rl.getLawType() == ReactionRateLaw.order_2_2substrate) || (rl.getLawType() == ReactionRateLaw.order_3_3substrate)) {
                    int j = 0;
                    while (varnames.hasMoreElements()) {
                        String name = varnames.nextElement();
                        A9.setInt(idx.set(i, j), getVariableIndex(name, vars));
                        j++;
                    }
                } else if (rl.getLawType() == ReactionRateLaw.order_3_2substrate) {
                    int order = 0;
                    String highOrderName = "";
                    String lowOrderName = "";
                    // we must make sure to put the higher order species first.
                    while (varnames.hasMoreElements()) {
                        lowOrderName = varnames.nextElement();
                        if (tem.get(lowOrderName) > order) {
                            String s = highOrderName;
                            highOrderName = lowOrderName;
                            lowOrderName = s;
                            order = tem.get(highOrderName);
                        }
                    }
                    A9.setInt(idx.set(i, 0), getVariableIndex(highOrderName, vars));
                    A9.setInt(idx.set(i, 1), getVariableIndex(lowOrderName, vars));
                }
            }
            ncfile.write("Reaction_DepList", new int[2], A9);
            // Reaction_names
            ArrayChar A10 = new ArrayChar.D2(numReactions.getLength(), stringLen.getLength());
            for (int i = 0; i < numReactions.getLength(); i++) {
                String name = reactions[i].getName();
                int diff = stringLen.getLength() - name.length();
                if (diff >= 0) {
                    for (int j = 0; j < diff; j++) {
                        name = name + " ";
                    }
                    A10.setString(i, name);
                } else
                    throw new RuntimeException("Name of Reaction:" + name + " is too long. Please shorten to " + stringLen.getLength() + " chars.");
            }
            ncfile.write("Reaction_names", A10);
            // Species_names
            ArrayChar A11 = new ArrayChar.D2(numSpecies.getLength(), stringLen.getLength());
            for (int i = 0; i < numSpecies.getLength(); i++) {
                String name = vars.elementAt(i).getName();
                int diff = stringLen.getLength() - name.length();
                if (diff >= 0) {
                    for (int j = 0; j < diff; j++) {
                        name = name + " ";
                    }
                    A11.setString(i, name);
                } else
                    throw new RuntimeException("Name of Species:" + name + " is too long. Please shorten to " + stringLen.getLength() + " chars.");
            }
            ncfile.write("Species_names", A11);
            // Species Initial Condition (in number of molecules).
            // Species iniCondition are sampled from a poisson distribution(which has a mean of the current iniExp value)
            RandomDataGenerator dist = new RandomDataGenerator();
            if (stochOpt.isUseCustomSeed()) {
                Integer randomSeed = stochOpt.getCustomSeed();
                if (randomSeed != null) {
                    dist.reSeed(randomSeed);
                }
            }
            ArrayLong A12 = new ArrayLong.D1(numSpecies.getLength());
            idx = A12.getIndex();
            for (int i = 0; i < numSpecies.getLength(); i++) {
                try {
                    VarIniCondition varIniCondition = subDomain.getVarIniCondition(vars.elementAt(i));
                    Expression varIniExp = varIniCondition.getIniVal();
                    varIniExp.bindExpression(simSymbolTable);
                    varIniExp = simSymbolTable.substituteFunctions(varIniExp).flatten();
                    double expectedCount = varIniExp.evaluateConstant();
                    long varCount = 0;
                    if (varIniCondition instanceof VarIniCount) {
                        varCount = (long) expectedCount;
                    } else {
                        if (expectedCount > 0) {
                            varCount = dist.nextPoisson(expectedCount);
                        }
                    }
                    A12.setLong(idx.set(i), varCount);
                } catch (ExpressionException ex) {
                    ex.printStackTrace(System.err);
                    throw new ExpressionException(ex.getMessage());
                }
            }
            ncfile.write("SpeciesIC", new int[1], A12);
            // Reaction_Rate_Constants(NumReactions, NumMaxDepList) ;
            ArrayDouble A13 = new ArrayDouble.D2(numReactions.getLength(), numMaxDepList.getLength());
            idx = A13.getIndex();
            for (int i = 0; i < numReactions.getLength(); i++) {
                ReactionRateLaw rl = reactionRateLaws[i];
                A13.setDouble(idx.set(i, 0), rl.getRateConstant());
            }
            ncfile.write("Reaction_Rate_Constants", A13);
        } catch (IOException ioe) {
            ioe.printStackTrace(System.err);
            throw new IOException("Error writing hybrid input file " + filename + ": " + ioe.getMessage());
        } catch (InvalidRangeException ire) {
            ire.printStackTrace(System.err);
            throw new InvalidRangeException("Error writing hybrid input file " + filename + ": " + ire.getMessage());
        }
        try {
            ncfile.close();
        } catch (IOException ioe) {
            throw new IOException("Error closing file " + filename + ". " + ioe.getMessage());
        }
    }
}