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

Example 21 with CompartmentSubDomain

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

the class IDAFileWriter method writeEquations.

/**
 * Insert the method's description here.
 * Creation date: (3/8/00 10:31:52 PM)
 */
protected String writeEquations(HashMap<Discontinuity, String> discontinuityNameMap) throws MathException, ExpressionException {
    Simulation simulation = simTask.getSimulation();
    StringBuffer sb = new StringBuffer();
    MathDescription mathDescription = simulation.getMathDescription();
    if (mathDescription.hasFastSystems()) {
        // 
        // define vector of original variables
        // 
        SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
        CompartmentSubDomain subDomain = (CompartmentSubDomain) mathDescription.getSubDomains().nextElement();
        FastSystem fastSystem = subDomain.getFastSystem();
        FastSystemAnalyzer fs_Analyzer = new FastSystemAnalyzer(fastSystem, simSymbolTable);
        int numIndependent = fs_Analyzer.getNumIndependentVariables();
        int systemDim = mathDescription.getStateVariableNames().size();
        int numDependent = systemDim - numIndependent;
        // 
        // get all variables from fast system (dependent and independent)
        // 
        HashSet<String> fastSystemVarHash = new HashSet<String>();
        Enumeration<Variable> dependentfastSystemVarEnum = fs_Analyzer.getDependentVariables();
        while (dependentfastSystemVarEnum.hasMoreElements()) {
            fastSystemVarHash.add(dependentfastSystemVarEnum.nextElement().getName());
        }
        Enumeration<Variable> independentfastSystemVarEnum = fs_Analyzer.getIndependentVariables();
        while (independentfastSystemVarEnum.hasMoreElements()) {
            fastSystemVarHash.add(independentfastSystemVarEnum.nextElement().getName());
        }
        // 
        // get all equations including for variables that are not in the fastSystem (ode equations for "slow system")
        // 
        RationalExpMatrix origInitVector = new RationalExpMatrix(systemDim, 1);
        RationalExpMatrix origSlowRateVector = new RationalExpMatrix(systemDim, 1);
        RationalExpMatrix origVarColumnVector = new RationalExpMatrix(systemDim, 1);
        Enumeration<Equation> enumEquations = subDomain.getEquations();
        int varIndex = 0;
        while (enumEquations.hasMoreElements()) {
            Equation equation = enumEquations.nextElement();
            origVarColumnVector.set_elem(varIndex, 0, new RationalExp(equation.getVariable().getName()));
            Expression rateExpr = equation.getRateExpression();
            rateExpr.bindExpression(varsSymbolTable);
            rateExpr = MathUtilities.substituteFunctions(rateExpr, varsSymbolTable);
            origSlowRateVector.set_elem(varIndex, 0, new RationalExp("(" + rateExpr.flatten().infix() + ")"));
            Expression initExpr = new Expression(equation.getInitialExpression());
            initExpr.substituteInPlace(new Expression("t"), new Expression(0.0));
            initExpr = MathUtilities.substituteFunctions(initExpr, varsSymbolTable).flatten();
            origInitVector.set_elem(varIndex, 0, new RationalExp("(" + initExpr.flatten().infix() + ")"));
            varIndex++;
        }
        // 
        // make symbolic matrix for fast invariants (from FastSystem's fastInvariants as well as a new fast invariant for each variable not included in the fast system.
        // 
        RationalExpMatrix fastInvarianceMatrix = new RationalExpMatrix(numDependent, systemDim);
        int row = 0;
        for (int i = 0; i < origVarColumnVector.getNumRows(); i++) {
            // 
            if (!fastSystemVarHash.contains(origVarColumnVector.get(i, 0).infixString())) {
                fastInvarianceMatrix.set_elem(row, i, RationalExp.ONE);
                row++;
            }
        }
        Enumeration<FastInvariant> enumFastInvariants = fastSystem.getFastInvariants();
        while (enumFastInvariants.hasMoreElements()) {
            FastInvariant fastInvariant = enumFastInvariants.nextElement();
            Expression fastInvariantExpression = fastInvariant.getFunction();
            for (int col = 0; col < systemDim; col++) {
                Expression coeff = fastInvariantExpression.differentiate(origVarColumnVector.get(col, 0).infixString()).flatten();
                coeff = simSymbolTable.substituteFunctions(coeff);
                fastInvarianceMatrix.set_elem(row, col, RationalExpUtils.getRationalExp(coeff));
            }
            row++;
        }
        for (int i = 0; i < systemDim; i++) {
            sb.append("VAR " + origVarColumnVector.get(i, 0).infixString() + " INIT " + origInitVector.get(i, 0).infixString() + ";\n");
        }
        RationalExpMatrix fullMatrix = null;
        RationalExpMatrix inverseFullMatrix = null;
        RationalExpMatrix newSlowRateVector = null;
        try {
            RationalExpMatrix fastMat = ((RationalExpMatrix) fastInvarianceMatrix.transpose().findNullSpace());
            fullMatrix = new RationalExpMatrix(systemDim, systemDim);
            row = 0;
            for (int i = 0; i < fastInvarianceMatrix.getNumRows(); i++) {
                for (int col = 0; col < systemDim; col++) {
                    fullMatrix.set_elem(row, col, fastInvarianceMatrix.get(i, col));
                }
                row++;
            }
            for (int i = 0; i < fastMat.getNumRows(); i++) {
                for (int col = 0; col < systemDim; col++) {
                    fullMatrix.set_elem(row, col, fastMat.get(i, col));
                }
                row++;
            }
            inverseFullMatrix = new RationalExpMatrix(systemDim, systemDim);
            inverseFullMatrix.identity();
            RationalExpMatrix copyOfFullMatrix = new RationalExpMatrix(fullMatrix);
            copyOfFullMatrix.gaussianElimination(inverseFullMatrix);
            newSlowRateVector = new RationalExpMatrix(numDependent, 1);
            newSlowRateVector.matmul(fastInvarianceMatrix, origSlowRateVector);
        } catch (MatrixException ex) {
            ex.printStackTrace();
            throw new MathException(ex.getMessage());
        }
        sb.append("TRANSFORM\n");
        for (row = 0; row < systemDim; row++) {
            for (int col = 0; col < systemDim; col++) {
                sb.append(fullMatrix.get(row, col).getConstant().doubleValue() + " ");
            }
            sb.append("\n");
        }
        sb.append("INVERSETRANSFORM\n");
        for (row = 0; row < systemDim; row++) {
            for (int col = 0; col < systemDim; col++) {
                sb.append(inverseFullMatrix.get(row, col).getConstant().doubleValue() + " ");
            }
            sb.append("\n");
        }
        int numDifferential = numDependent;
        int numAlgebraic = numIndependent;
        sb.append("RHS DIFFERENTIAL " + numDifferential + " ALGEBRAIC " + numAlgebraic + "\n");
        int equationIndex = 0;
        while (equationIndex < numDependent) {
            // print row of mass matrix followed by slow rate corresponding to fast invariant
            Expression slowRateExp = new Expression(newSlowRateVector.get(equationIndex, 0).infixString()).flatten();
            slowRateExp.bindExpression(simSymbolTable);
            slowRateExp = MathUtilities.substituteFunctions(slowRateExp, varsSymbolTable).flatten();
            Vector<Discontinuity> v = slowRateExp.getDiscontinuities();
            for (Discontinuity od : v) {
                od = getSubsitutedAndFlattened(od, varsSymbolTable);
                String dname = discontinuityNameMap.get(od);
                if (dname == null) {
                    dname = ROOT_VARIABLE_PREFIX + discontinuityNameMap.size();
                    discontinuityNameMap.put(od, dname);
                }
                slowRateExp.substituteInPlace(od.getDiscontinuityExp(), new Expression("(" + dname + "==1)"));
            }
            sb.append(slowRateExp.infix() + ";\n");
            equationIndex++;
        }
        Enumeration<FastRate> enumFastRates = fastSystem.getFastRates();
        while (enumFastRates.hasMoreElements()) {
            // print the fastRate for this row
            Expression fastRateExp = new Expression(enumFastRates.nextElement().getFunction());
            fastRateExp = MathUtilities.substituteFunctions(fastRateExp, varsSymbolTable).flatten();
            Vector<Discontinuity> v = fastRateExp.getDiscontinuities();
            for (Discontinuity od : v) {
                od = getSubsitutedAndFlattened(od, varsSymbolTable);
                String dname = discontinuityNameMap.get(od);
                if (dname == null) {
                    dname = ROOT_VARIABLE_PREFIX + discontinuityNameMap.size();
                    discontinuityNameMap.put(od, dname);
                }
                fastRateExp.substituteInPlace(od.getDiscontinuityExp(), new Expression("(" + dname + "==1)"));
            }
            sb.append(fastRateExp.flatten().infix() + ";\n");
            equationIndex++;
        }
    } else {
        for (int i = 0; i < getStateVariableCount(); i++) {
            StateVariable stateVar = getStateVariable(i);
            Expression initExpr = new Expression(stateVar.getInitialRateExpression());
            initExpr = MathUtilities.substituteFunctions(initExpr, varsSymbolTable);
            initExpr.substituteInPlace(new Expression("t"), new Expression(0.0));
            sb.append("VAR " + stateVar.getVariable().getName() + " INIT " + initExpr.flatten().infix() + ";\n");
        }
        sb.append("TRANSFORM\n");
        for (int row = 0; row < getStateVariableCount(); row++) {
            for (int col = 0; col < getStateVariableCount(); col++) {
                sb.append((row == col ? 1 : 0) + " ");
            }
            sb.append("\n");
        }
        sb.append("INVERSETRANSFORM\n");
        for (int row = 0; row < getStateVariableCount(); row++) {
            for (int col = 0; col < getStateVariableCount(); col++) {
                sb.append((row == col ? 1 : 0) + " ");
            }
            sb.append("\n");
        }
        sb.append("RHS DIFFERENTIAL " + getStateVariableCount() + " ALGEBRAIC 0\n");
        for (int i = 0; i < getStateVariableCount(); i++) {
            StateVariable stateVar = getStateVariable(i);
            Expression rateExpr = new Expression(stateVar.getRateExpression());
            rateExpr = MathUtilities.substituteFunctions(rateExpr, varsSymbolTable).flatten();
            Vector<Discontinuity> v = rateExpr.getDiscontinuities();
            for (Discontinuity od : v) {
                od = getSubsitutedAndFlattened(od, varsSymbolTable);
                String dname = discontinuityNameMap.get(od);
                if (dname == null) {
                    dname = ROOT_VARIABLE_PREFIX + discontinuityNameMap.size();
                    discontinuityNameMap.put(od, dname);
                }
                rateExpr.substituteInPlace(od.getDiscontinuityExp(), new Expression("(" + dname + "==1)"));
            }
            sb.append(rateExpr.infix() + ";\n");
        }
    }
    return sb.toString();
}

Example 22 with CompartmentSubDomain

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

the class SubdomainInfo method write.

public static void write(File file, MathDescription mathDesc) throws IOException, MathException {
    PrintWriter pw = null;
    try {
        pw = new PrintWriter(new FileWriter(file));
        pw.println("# " + VCML.CompartmentSubDomain + " name, handle");
        pw.println("# " + VCML.MembraneSubDomain + " name, inside compartment name, handle, outside compartment name, handle");
        Enumeration<SubDomain> subdomains = mathDesc.getSubDomains();
        while (subdomains.hasMoreElements()) {
            SubDomain sd = subdomains.nextElement();
            if (sd instanceof CompartmentSubDomain) {
                CompartmentSubDomain csd = (CompartmentSubDomain) sd;
                pw.println(VCML.CompartmentSubDomain + ", " + csd.getName() + ", " + mathDesc.getHandle(csd));
            } else if (sd instanceof MembraneSubDomain) {
                MembraneSubDomain msd = (MembraneSubDomain) sd;
                CompartmentSubDomain insideCompartment = msd.getInsideCompartment();
                CompartmentSubDomain outsideCompartment = msd.getOutsideCompartment();
                pw.println(VCML.MembraneSubDomain + ", " + msd.getName() + ", " + insideCompartment.getName() + ", " + mathDesc.getHandle(insideCompartment) + ", " + outsideCompartment.getName() + ", " + mathDesc.getHandle(outsideCompartment));
            }
        }
        pw.close();
    } finally {
        if (pw != null) {
            pw.close();
        }
    }
}

Example 23 with CompartmentSubDomain

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

the class SimulationData method getVarAndFunctionDataIdentifiers.

/**
 * This method was created in VisualAge.
 * @return java.lang.String[]
 */
public synchronized DataIdentifier[] getVarAndFunctionDataIdentifiers(OutputContext outputContext) throws IOException, DataAccessException {
    // Is this zip format?
    boolean bIsChombo = false;
    try {
        bIsChombo = isChombo();
    } catch (FileNotFoundException e) {
        e.printStackTrace(System.out);
    }
    File zipFile1 = getZipFile(bIsChombo, null);
    File zipFile2 = getZipFile(bIsChombo, 0);
    bZipFormat1 = false;
    bZipFormat2 = false;
    if (zipFile1.exists()) {
        bZipFormat1 = true;
    } else if (zipFile2.exists()) {
        bZipFormat2 = true;
    }
    refreshLogFile();
    if (!isComsol()) {
        try {
            refreshMeshFile();
        } catch (MathException e) {
            e.printStackTrace(System.out);
            throw new DataAccessException(e.getMessage());
        }
    }
    if (!isRulesData && !getIsODEData() && !isComsol() && dataFilenames != null) {
        // read variables only when I have never read the file since variables don't change
        if (dataSetIdentifierList.size() == 0) {
            File file = getPDEDataFile(0.0);
            DataSet dataSet = getPDEDataSet(file, 0.0);
            String[] varNames = dataSet.getDataNames();
            int[] varTypeInts = dataSet.getVariableTypeIntegers();
            if (varNames == null) {
                return null;
            }
            dataSetIdentifierList.clear();
            for (int i = 0; i < varNames.length; i++) {
                VariableType varType = null;
                try {
                    varType = VariableType.getVariableTypeFromInteger(varTypeInts[i]);
                } catch (IllegalArgumentException e) {
                    if (LG.isEnabledFor(Level.WARN)) {
                        LG.warn("Exception typing " + varNames[i] + " has unsupported type " + varTypeInts[i] + ": " + e.getMessage());
                    }
                    varType = SimulationData.getVariableTypeFromLength(mesh, dataSet.getDataLength(varNames[i]));
                }
                Domain domain = Variable.getDomainFromCombinedIdentifier(varNames[i]);
                String varName = Variable.getNameFromCombinedIdentifier(varNames[i]);
                dataSetIdentifierList.addElement(new DataSetIdentifier(varName, varType, domain));
            }
            refreshDataProcessingOutputInfo(outputContext);
            if (dataProcessingOutputInfo != null) {
                for (int i = 0; i < dataProcessingOutputInfo.getVariableNames().length; i++) {
                    if (dataProcessingOutputInfo.getPostProcessDataType(dataProcessingOutputInfo.getVariableNames()[i]).equals(DataProcessingOutputInfo.PostProcessDataType.image)) {
                        dataSetIdentifierList.addElement(new DataSetIdentifier(dataProcessingOutputInfo.getVariableNames()[i], VariableType.POSTPROCESSING, null));
                    }
                }
            }
        }
        // always read functions file since functions might change
        getFunctionDataIdentifiers(outputContext);
    }
    if ((isRulesData || getIsODEData()) && dataSetIdentifierList.size() == 0) {
        ODEDataBlock odeDataBlock = getODEDataBlock();
        if (odeDataBlock == null) {
            throw new DataAccessException("Results are not availabe yet. Please try again later.");
        }
        ODESimData odeSimData = odeDataBlock.getODESimData();
        int colCount = odeSimData.getColumnDescriptionsCount();
        // assume index=0 is time "t"
        int DATA_OFFSET = 1;
        dataSetIdentifierList.clear();
        for (int i = 0; i < (colCount - DATA_OFFSET); i++) {
            String varName = odeSimData.getColumnDescriptions(i + DATA_OFFSET).getDisplayName();
            // TODO domain
            Domain domain = null;
            dataSetIdentifierList.addElement(new DataSetIdentifier(varName, VariableType.NONSPATIAL, domain));
        }
    }
    if (isComsol() && dataSetIdentifierList.size() == 0) {
        ComsolSimFiles comsolSimFiles = getComsolSimFiles();
        if (comsolSimFiles.simTaskXMLFile != null) {
            try {
                String xmlString = FileUtils.readFileToString(comsolSimFiles.simTaskXMLFile);
                SimulationTask simTask = XmlHelper.XMLToSimTask(xmlString);
                Enumeration<Variable> variablesEnum = simTask.getSimulation().getMathDescription().getVariables();
                while (variablesEnum.hasMoreElements()) {
                    Variable var = variablesEnum.nextElement();
                    if (var instanceof VolVariable) {
                        dataSetIdentifierList.addElement(new DataSetIdentifier(var.getName(), VariableType.VOLUME, var.getDomain()));
                    } else if (var instanceof MemVariable) {
                        dataSetIdentifierList.addElement(new DataSetIdentifier(var.getName(), VariableType.MEMBRANE, var.getDomain()));
                    } else if (var instanceof Function) {
                        VariableType varType = VariableType.UNKNOWN;
                        if (var.getDomain() != null && var.getDomain().getName() != null) {
                            SubDomain subDomain = simTask.getSimulation().getMathDescription().getSubDomain(var.getDomain().getName());
                            if (subDomain instanceof CompartmentSubDomain) {
                                varType = VariableType.VOLUME;
                            } else if (subDomain instanceof MembraneSubDomain) {
                                varType = VariableType.MEMBRANE;
                            } else if (subDomain instanceof FilamentSubDomain) {
                                throw new RuntimeException("filament subdomains not supported");
                            } else if (subDomain instanceof PointSubDomain) {
                                varType = VariableType.POINT_VARIABLE;
                            }
                        }
                        dataSetIdentifierList.addElement(new DataSetIdentifier(var.getName(), varType, var.getDomain()));
                    } else if (var instanceof Constant) {
                        System.out.println("ignoring Constant " + var.getName());
                    } else if (var instanceof InsideVariable) {
                        System.out.println("ignoring InsideVariable " + var.getName());
                    } else if (var instanceof OutsideVariable) {
                        System.out.println("ignoring OutsideVariable " + var.getName());
                    } else {
                        throw new RuntimeException("unexpected variable " + var.getName() + " of type " + var.getClass().getName());
                    }
                }
            } catch (XmlParseException | ExpressionException e) {
                e.printStackTrace();
                throw new RuntimeException("failed to read sim task file, msg: " + e.getMessage(), e);
            }
        }
    }
    DataIdentifier[] dis = new DataIdentifier[dataSetIdentifierList.size()];
    for (int i = 0; i < dataSetIdentifierList.size(); i++) {
        DataSetIdentifier dsi = (DataSetIdentifier) dataSetIdentifierList.elementAt(i);
        String displayName = dsi.getName();
        if (dsi.isFunction()) {
            AnnotatedFunction f = null;
            for (int j = 0; j < annotatedFunctionList.size(); j++) {
                AnnotatedFunction function = (AnnotatedFunction) annotatedFunctionList.elementAt(j);
                if (function.getName().equals(dsi.getName())) {
                    f = function;
                    break;
                }
            }
            if (f != null) {
                displayName = f.getDisplayName();
            }
        }
        dis[i] = new DataIdentifier(dsi.getName(), dsi.getVariableType(), dsi.getDomain(), dsi.isFunction(), displayName);
    }
    return dis;
}

Example 24 with CompartmentSubDomain

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

the class MathDebuggerPanel method main.

public static void main(java.lang.String[] args) {
    try {
        javax.swing.JFrame frame = new javax.swing.JFrame();
        MathDebuggerPanel aMathDebuggerPanel;
        aMathDebuggerPanel = new MathDebuggerPanel();
        frame.setContentPane(aMathDebuggerPanel);
        frame.setTitle("Math Descriptions Comparator");
        frame.setSize(aMathDebuggerPanel.getSize());
        frame.addWindowListener(new java.awt.event.WindowAdapter() {

            public void windowClosing(java.awt.event.WindowEvent e) {
                System.exit(0);
            }
        });
        MathModel mathModel1 = new MathModel(null);
        mathModel1.setName("math1");
        Geometry geometry1 = new Geometry("geo", 0);
        MathDescription mathDesc1 = mathModel1.getMathDescription();
        mathDesc1.setGeometry(geometry1);
        mathDesc1.addSubDomain(new CompartmentSubDomain("Compartment", CompartmentSubDomain.NON_SPATIAL_PRIORITY));
        MathModel mathModel2 = new MathModel(null);
        mathModel2.setName("math2");
        Geometry geometry2 = new Geometry("geo", 0);
        MathDescription mathDesc2 = mathModel2.getMathDescription();
        mathDesc2.setGeometry(geometry2);
        mathDesc2.addSubDomain(new CompartmentSubDomain("Compartment", CompartmentSubDomain.NON_SPATIAL_PRIORITY));
        aMathDebuggerPanel.setMathModel1(mathModel1);
        aMathDebuggerPanel.setMathModel2(mathModel2);
        frame.setSize(1500, 800);
        frame.setVisible(true);
    } catch (Throwable exception) {
        System.err.println("Exception occurred in main() of javax.swing.JPanel");
        exception.printStackTrace(System.out);
    }
}

Example 25 with CompartmentSubDomain

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

the class MatlabOdeFileCoder method write_V6_MFile.

/**
 * Insert the method's description here.
 * Creation date: (3/8/00 10:31:52 PM)
 */
public void write_V6_MFile(java.io.PrintWriter pw, String functionName) throws MathException, ExpressionException {
    MathDescription mathDesc = simulation.getMathDescription();
    if (!mathDesc.isValid()) {
        throw new MathException("invalid math description\n" + mathDesc.getWarning());
    }
    if (mathDesc.isSpatial()) {
        throw new MathException("spatial math description, cannot create ode file");
    }
    if (mathDesc.hasFastSystems()) {
        throw new MathException("math description contains algebraic constraints, cannot create .m file");
    }
    // 
    // print function declaration
    // 
    pw.println("function [T,Y,yinit,param, allNames, allValues] = " + functionName + "(argTimeSpan,argYinit,argParam)");
    pw.println("% [T,Y,yinit,param] = " + functionName + "(argTimeSpan,argYinit,argParam)");
    pw.println("%");
    pw.println("% input:");
    pw.println("%     argTimeSpan is a vector of start and stop times (e.g. timeSpan = [0 10.0])");
    pw.println("%     argYinit is a vector of initial conditions for the state variables (optional)");
    pw.println("%     argParam is a vector of values for the parameters (optional)");
    pw.println("%");
    pw.println("% output:");
    pw.println("%     T is the vector of times");
    pw.println("%     Y is the vector of state variables");
    pw.println("%     yinit is the initial conditions that were used");
    pw.println("%     param is the parameter vector that was used");
    pw.println("%     allNames is the output solution variable names");
    pw.println("%     allValues is the output solution variable values corresponding to the names");
    pw.println("%");
    pw.println("%     example of running this file: [T,Y,yinit,param,allNames,allValues] = myMatlabFunc; <-(your main function name)");
    pw.println("%");
    VariableHash varHash = new VariableHash();
    for (Variable var : simulationSymbolTable.getVariables()) {
        varHash.addVariable(var);
    }
    Variable[] variables = varHash.getTopologicallyReorderedVariables();
    CompartmentSubDomain subDomain = (CompartmentSubDomain) mathDesc.getSubDomains().nextElement();
    // 
    // collect "true" constants (Constants without identifiers)
    // 
    // 
    // collect "variables" (VolVariables only)
    // 
    // 
    // collect "functions" (Functions and Constants with identifiers)
    // 
    Vector<Constant> constantList = new Vector<Constant>();
    Vector<VolVariable> volVarList = new Vector<VolVariable>();
    Vector<Variable> functionList = new Vector<Variable>();
    for (int i = 0; i < variables.length; i++) {
        if (variables[i] instanceof Constant) {
            Constant constant = (Constant) variables[i];
            String[] symbols = constant.getExpression().getSymbols();
            if (symbols == null || symbols.length == 0) {
                constantList.addElement(constant);
            } else {
                functionList.add(constant);
            }
        } else if (variables[i] instanceof VolVariable) {
            volVarList.addElement((VolVariable) variables[i]);
        } else if (variables[i] instanceof Function) {
            functionList.addElement(variables[i]);
        }
    }
    Constant[] constants = (Constant[]) BeanUtils.getArray(constantList, Constant.class);
    VolVariable[] volVars = (VolVariable[]) BeanUtils.getArray(volVarList, VolVariable.class);
    Variable[] functions = (Variable[]) BeanUtils.getArray(functionList, Variable.class);
    int numVars = volVarList.size() + functionList.size();
    String varNamesForStringArray = "";
    String varNamesForValueArray = "";
    for (Variable var : volVarList) {
        varNamesForStringArray = varNamesForStringArray + "'" + var.getName() + "';";
        varNamesForValueArray = varNamesForValueArray + var.getName() + " ";
    }
    for (Variable func : functionList) {
        varNamesForStringArray = varNamesForStringArray + "'" + func.getName() + "';";
        varNamesForValueArray = varNamesForValueArray + func.getName() + " ";
    }
    pw.println("");
    pw.println("%");
    pw.println("% Default time span");
    pw.println("%");
    double beginTime = 0.0;
    double endTime = simulation.getSolverTaskDescription().getTimeBounds().getEndingTime();
    pw.println("timeSpan = [" + beginTime + " " + endTime + "];");
    pw.println("");
    pw.println("% output variable lengh and names");
    pw.println("numVars = " + numVars + ";");
    pw.println("allNames = {" + varNamesForStringArray + "};");
    pw.println("");
    pw.println("if nargin >= 1");
    pw.println("\tif length(argTimeSpan) > 0");
    pw.println("\t\t%");
    pw.println("\t\t% TimeSpan overridden by function arguments");
    pw.println("\t\t%");
    pw.println("\t\ttimeSpan = argTimeSpan;");
    pw.println("\tend");
    pw.println("end");
    pw.println("%");
    pw.println("% Default Initial Conditions");
    pw.println("%");
    pw.println("yinit = [");
    for (int j = 0; j < volVars.length; j++) {
        Expression initial = subDomain.getEquation(volVars[j]).getInitialExpression();
        double defaultInitialCondition = 0;
        try {
            initial.bindExpression(mathDesc);
            defaultInitialCondition = initial.evaluateConstant();
            pw.println("\t" + defaultInitialCondition + ";\t\t% yinit(" + (j + 1) + ") is the initial condition for '" + cbit.vcell.parser.SymbolUtils.getEscapedTokenMatlab(volVars[j].getName()) + "'");
        } catch (ExpressionException e) {
            e.printStackTrace(System.out);
            pw.println("\t" + initial.infix_Matlab() + ";\t\t% yinit(" + (j + 1) + ") is the initial condition for '" + cbit.vcell.parser.SymbolUtils.getEscapedTokenMatlab(volVars[j].getName()) + "'");
        // throw new RuntimeException("error evaluating initial condition for variable "+volVars[j].getName());
        }
    }
    pw.println("];");
    pw.println("if nargin >= 2");
    pw.println("\tif length(argYinit) > 0");
    pw.println("\t\t%");
    pw.println("\t\t% initial conditions overridden by function arguments");
    pw.println("\t\t%");
    pw.println("\t\tyinit = argYinit;");
    pw.println("\tend");
    pw.println("end");
    pw.println("%");
    pw.println("% Default Parameters");
    pw.println("%   constants are only those \"Constants\" from the Math Description that are just floating point numbers (no identifiers)");
    pw.println("%   note: constants of the form \"A_init\" are really initial conditions and are treated in \"yinit\"");
    pw.println("%");
    pw.println("param = [");
    int paramIndex = 0;
    for (int i = 0; i < constants.length; i++) {
        pw.println("\t" + constants[i].getExpression().infix_Matlab() + ";\t\t% param(" + (paramIndex + 1) + ") is '" + cbit.vcell.parser.SymbolUtils.getEscapedTokenMatlab(constants[i].getName()) + "'");
        paramIndex++;
    }
    pw.println("];");
    pw.println("if nargin >= 3");
    pw.println("\tif length(argParam) > 0");
    pw.println("\t\t%");
    pw.println("\t\t% parameter values overridden by function arguments");
    pw.println("\t\t%");
    pw.println("\t\tparam = argParam;");
    pw.println("\tend");
    pw.println("end");
    pw.println("%");
    pw.println("% invoke the integrator");
    pw.println("%");
    pw.println("[T,Y] = ode15s(@f,timeSpan,yinit,odeset('OutputFcn',@odeplot),param,yinit);");
    pw.println("");
    pw.println("% get the solution");
    pw.println("all = zeros(size(T), numVars);");
    pw.println("for i = 1:size(T)");
    pw.println("\tall(i,:) = getRow(T(i), Y(i,:), yinit, param);");
    pw.println("end");
    pw.println("");
    pw.println("allValues = all;");
    pw.println("end");
    // get row data for solution
    pw.println("");
    pw.println("% -------------------------------------------------------");
    pw.println("% get row data");
    pw.println("function rowValue = getRow(t,y,y0,p)");
    // 
    // print volVariables (in order and assign to var vector)
    // 
    pw.println("\t% State Variables");
    for (int i = 0; i < volVars.length; i++) {
        pw.println("\t" + cbit.vcell.parser.SymbolUtils.getEscapedTokenMatlab(volVars[i].getName()) + " = y(" + (i + 1) + ");");
    }
    // 
    // print constants
    // 
    pw.println("\t% Constants");
    paramIndex = 0;
    for (int i = 0; i < constants.length; i++) {
        pw.println("\t" + cbit.vcell.parser.SymbolUtils.getEscapedTokenMatlab(constants[i].getName()) + " = p(" + (paramIndex + 1) + ");");
        paramIndex++;
    }
    // 
    // print variables
    // 
    pw.println("\t% Functions");
    for (int i = 0; i < functions.length; i++) {
        pw.println("\t" + cbit.vcell.parser.SymbolUtils.getEscapedTokenMatlab(functions[i].getName()) + " = " + functions[i].getExpression().infix_Matlab() + ";");
    }
    pw.println("");
    pw.println("\trowValue = [" + varNamesForValueArray + "];");
    pw.println("end");
    // 
    // print ode-rate
    // 
    pw.println("");
    pw.println("% -------------------------------------------------------");
    pw.println("% ode rate");
    pw.println("function dydt = f(t,y,p,y0)");
    // 
    // print volVariables (in order and assign to var vector)
    // 
    pw.println("\t% State Variables");
    for (int i = 0; i < volVars.length; i++) {
        pw.println("\t" + cbit.vcell.parser.SymbolUtils.getEscapedTokenMatlab(volVars[i].getName()) + " = y(" + (i + 1) + ");");
    }
    // 
    // print constants
    // 
    pw.println("\t% Constants");
    paramIndex = 0;
    for (int i = 0; i < constants.length; i++) {
        pw.println("\t" + cbit.vcell.parser.SymbolUtils.getEscapedTokenMatlab(constants[i].getName()) + " = p(" + (paramIndex + 1) + ");");
        paramIndex++;
    }
    // 
    // print variables
    // 
    pw.println("\t% Functions");
    for (int i = 0; i < functions.length; i++) {
        pw.println("\t" + cbit.vcell.parser.SymbolUtils.getEscapedTokenMatlab(functions[i].getName()) + " = " + functions[i].getExpression().infix_Matlab() + ";");
    }
    pw.println("\t% Rates");
    pw.println("\tdydt = [");
    for (int i = 0; i < volVars.length; i++) {
        pw.println("\t\t" + subDomain.getEquation(volVars[i]).getRateExpression().infix_Matlab() + ";    % rate for " + cbit.vcell.parser.SymbolUtils.getEscapedTokenMatlab(volVars[i].getName()));
    }
    pw.println("\t];");
    pw.println("end");
}