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

Example 11 with BoundaryConditionType

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

the class XmlReader method getCompartmentSubDomain.

/**
 * This method returns a CompartmentSubDomain objecy from a XML element.
 * Creation date: (5/17/2001 11:59:45 AM)
 * @return cbit.vcell.math.CompartmentSubDomain
 * @param param org.jdom.Element
 * @exception cbit.vcell.xml.XmlParseException The exception description.
 */
private CompartmentSubDomain getCompartmentSubDomain(Element param, MathDescription mathDesc) throws XmlParseException {
    // get attributes
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    int priority = -1;
    String temp = param.getAttributeValue(XMLTags.PriorityAttrTag);
    if (temp != null) {
        priority = Integer.parseInt(temp);
    }
    // --- create new CompartmentSubDomain ---
    CompartmentSubDomain subDomain = new CompartmentSubDomain(name, priority);
    transcribeComments(param, subDomain);
    // Process BoundaryConditions
    Iterator<Element> iterator = param.getChildren(XMLTags.BoundaryTypeTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element tempelement = (Element) iterator.next();
        // create BoundaryConditionType
        temp = tempelement.getAttributeValue(XMLTags.BoundaryTypeAttrTag);
        BoundaryConditionType bType = new BoundaryConditionType(temp);
        // Process Xm
        if (tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueXm)) {
            subDomain.setBoundaryConditionXm(bType);
        } else if (tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueXp)) {
            // Process Xp
            subDomain.setBoundaryConditionXp(bType);
        } else if (tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueYm)) {
            // Process Ym
            subDomain.setBoundaryConditionYm(bType);
        } else if (tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueYp)) {
            // Process Yp
            subDomain.setBoundaryConditionYp(bType);
        } else if (tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueZm)) {
            // Process Zm
            subDomain.setBoundaryConditionZm(bType);
        } else if (tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueZp)) {
            // Process Zp
            subDomain.setBoundaryConditionZp(bType);
        } else {
            // If not indentified throw an exception!!
            throw new XmlParseException("Unknown BoundaryConditionType: " + tempelement.getAttributeValue(XMLTags.BoundaryAttrTag));
        }
    }
    // process BoundaryConditionSpecs
    iterator = param.getChildren(XMLTags.BoundaryConditionSpecTag, vcNamespace).iterator();
    if (iterator != null) {
        while (iterator.hasNext()) {
            Element tempelement = (Element) iterator.next();
            try {
                subDomain.addBoundaryConditionSpec(getBoundaryConditionSpec(tempelement));
            } catch (MathException e) {
                e.printStackTrace();
                throw new XmlParseException("A MathException was fired when adding a BoundaryConditionSpec to the compartmentSubDomain " + name, e);
            }
        }
    }
    // process OdeEquations
    iterator = param.getChildren(XMLTags.OdeEquationTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element tempelement = (Element) iterator.next();
        try {
            subDomain.addEquation(getOdeEquation(tempelement, mathDesc));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("A MathException was fired when adding an OdeEquation to the compartmentSubDomain " + name, e);
        }
    }
    // process PdeEquations
    iterator = param.getChildren(XMLTags.PdeEquationTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element tempelement = (Element) iterator.next();
        try {
            subDomain.addEquation(getPdeEquation(tempelement, mathDesc));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("A MathException was fired when adding an PdeEquation to the compartmentSubDomain " + name, e);
        }
    }
    // Process VolumeRegionEquation
    iterator = param.getChildren(XMLTags.VolumeRegionEquationTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element tempelement = (Element) iterator.next();
        try {
            subDomain.addEquation(getVolumeRegionEquation(tempelement, mathDesc));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("A MathException was fired when adding a VolumeRegionEquation to the compartmentSubDomain " + name, e);
        }
    }
    // Process Variable initial conditions (added for stochastic algos)
    iterator = param.getChildren(XMLTags.VarIniCount_OldTag, vcNamespace).iterator();
    if (iterator != null) {
        while (iterator.hasNext()) {
            Element tempelement = (Element) iterator.next();
            try {
                subDomain.addVarIniCondition(getVarIniCount(tempelement, mathDesc));
            } catch (MathException e) {
                e.printStackTrace();
                throw new XmlParseException("A MathException was fired when adding a variable initial condition to the compartmentSubDomain " + name, e);
            } catch (ExpressionException e) {
                e.printStackTrace();
            }
        }
    }
    iterator = param.getChildren(XMLTags.VarIniCountTag, vcNamespace).iterator();
    if (iterator != null) {
        while (iterator.hasNext()) {
            Element tempelement = (Element) iterator.next();
            try {
                subDomain.addVarIniCondition(getVarIniCount(tempelement, mathDesc));
            } catch (MathException e) {
                e.printStackTrace();
                throw new XmlParseException("A MathException was fired when adding a variable initial condition to the compartmentSubDomain " + name, e);
            } catch (ExpressionException e) {
                e.printStackTrace();
            }
        }
    }
    iterator = param.getChildren(XMLTags.VarIniPoissonExpectedCountTag, vcNamespace).iterator();
    if (iterator != null) {
        while (iterator.hasNext()) {
            Element tempelement = (Element) iterator.next();
            try {
                subDomain.addVarIniCondition(getVarIniPoissonExpectedCount(tempelement, mathDesc));
            } catch (MathException e) {
                e.printStackTrace();
                throw new XmlParseException("A MathException was fired when adding a variable initial condition to the compartmentSubDomain " + name, e);
            } catch (ExpressionException e) {
                e.printStackTrace();
            }
        }
    }
    // 
    // Process JumpProcesses (added for stochastic algos)
    iterator = param.getChildren(XMLTags.JumpProcessTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element tempelement = (Element) iterator.next();
        try {
            subDomain.addJumpProcess(getJumpProcess(tempelement, mathDesc));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("A MathException was fired when adding a jump process to the compartmentSubDomain " + name, e);
        }
    }
    iterator = param.getChildren(XMLTags.ParticleJumpProcessTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element tempelement = (Element) iterator.next();
        try {
            subDomain.addParticleJumpProcess(getParticleJumpProcess(tempelement, mathDesc));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("A MathException was fired when adding a jump process to the compartmentSubDomain " + name, e);
        }
    }
    iterator = param.getChildren(XMLTags.ParticlePropertiesTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element tempelement = (Element) iterator.next();
        try {
            subDomain.addParticleProperties(getParticleProperties(tempelement, mathDesc));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("A MathException was fired when adding a jump process to the compartmentSubDomain " + name, e);
        }
    }
    // process ComputeCentroid "equations"
    iterator = param.getChildren(XMLTags.ComputeCentroidTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element tempelement = (Element) iterator.next();
        try {
            subDomain.addEquation(getComputeCentroid(tempelement, mathDesc));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("A MathException was fired when adding an ComputeCentroid 'equation' to the compartmentSubDomain " + name, e);
        }
    }
    // process ComputeMembraneMetric "equations"
    iterator = param.getChildren(XMLTags.ComputeMembraneMetricTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element tempelement = (Element) iterator.next();
        try {
            subDomain.addEquation(getComputeMembraneMetric(tempelement, mathDesc));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("A MathException was fired when adding an ComputeMembraneMetric 'equation' to the compartmentSubDomain " + name, e);
        }
    }
    // Process the FastSystem (if thre is)
    Element tempelement = param.getChild(XMLTags.FastSystemTag, vcNamespace);
    if (tempelement != null) {
        subDomain.setFastSystem(getFastSystem(tempelement, mathDesc));
    }
    return subDomain;
}

Example 12 with BoundaryConditionType

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

the class XmlReader method getBoundaryConditionSpec.

private BoundaryConditionSpec getBoundaryConditionSpec(Element param) throws XmlParseException, MathException {
    // retrieve values
    String boundarySubdomainName = unMangle(param.getAttributeValue(XMLTags.BoundarySubdomainNameTag));
    String boundarySubdomainType = unMangle(param.getAttributeValue(XMLTags.BoundaryTypeTag));
    if (boundarySubdomainName != null && boundarySubdomainType != null) {
        BoundaryConditionSpec bcs = new BoundaryConditionSpec(boundarySubdomainName, new BoundaryConditionType(boundarySubdomainType));
        return bcs;
    }
    return null;
}

Example 13 with BoundaryConditionType

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

the class XmlReader method getFeatureMapping.

/**
 * This method retuns a FeatureMapping object from a XML representation.
 * Creation date: (5/7/2001 4:12:03 PM)
 * @return cbit.vcell.mapping.FeatureMapping
 * @param param org.jdom.Element
 */
private FeatureMapping getFeatureMapping(Element param, SimulationContext simulationContext) throws XmlParseException {
    // Retrieve attributes
    String featurename = unMangle(param.getAttributeValue(XMLTags.FeatureAttrTag));
    String geometryClassName = param.getAttributeValue(XMLTags.SubVolumeAttrTag);
    if (geometryClassName != null) {
        geometryClassName = unMangle(geometryClassName);
    } else {
        geometryClassName = param.getAttributeValue(XMLTags.GeometryClassAttrTag);
        if (geometryClassName != null) {
            geometryClassName = unMangle(geometryClassName);
        }
    }
    Feature featureref = (Feature) simulationContext.getModel().getStructure(featurename);
    if (featureref == null) {
        throw new XmlParseException("The Feature " + featurename + " could not be resolved!");
    }
    // *** Create new Feature Mapping ****
    FeatureMapping feamap = new FeatureMapping(featureref, simulationContext, simulationContext.getModel().getUnitSystem());
    // Set Size
    if (param.getAttributeValue(XMLTags.SizeTag) != null) {
        String size = unMangle(param.getAttributeValue(XMLTags.SizeTag));
        try {
            feamap.getSizeParameter().setExpression(unMangleExpression(size));
        } catch (ExpressionException e) {
            e.printStackTrace(System.out);
            throw new XmlParseException("An expressionException was fired when setting the size Expression " + size + " to a featureMapping!", e);
        }
    } else {
        try {
            feamap.getSizeParameter().setExpression(null);
        } catch (Exception e) {
            e.printStackTrace();
            throw new RuntimeException("unexpected exception while setting structure size: " + e.getMessage());
        }
    }
    // Set Volume/unit_area if it exists
    if (param.getAttributeValue(XMLTags.VolumePerUnitAreaTag) != null) {
        String volPerUnitArea = unMangle(param.getAttributeValue(XMLTags.VolumePerUnitAreaTag));
        try {
            feamap.getVolumePerUnitAreaParameter().setExpression(unMangleExpression(volPerUnitArea));
        } catch (ExpressionException e) {
            e.printStackTrace(System.out);
            throw new XmlParseException("An expressionException was fired when setting the VolumePerUnitArea Expression " + volPerUnitArea + " to a featureMapping!", e);
        }
    }
    // Set Volume/unitVol if it exists
    if (param.getAttributeValue(XMLTags.VolumePerUnitVolumeTag) != null) {
        String volPerUnitVol = unMangle(param.getAttributeValue(XMLTags.VolumePerUnitVolumeTag));
        try {
            feamap.getVolumePerUnitVolumeParameter().setExpression(unMangleExpression(volPerUnitVol));
        } catch (ExpressionException e) {
            e.printStackTrace(System.out);
            throw new XmlParseException("An expressionException was fired when setting the size Expression " + volPerUnitVol + " to a featureMapping!", e);
        }
    }
    if (geometryClassName != null) {
        GeometryClass[] geometryClasses = simulationContext.getGeometry().getGeometryClasses();
        for (int i = 0; i < geometryClasses.length; i++) {
            if (geometryClasses[i].getName().equals(geometryClassName)) {
                try {
                    feamap.setGeometryClass(geometryClasses[i]);
                } catch (PropertyVetoException e) {
                    e.printStackTrace(System.out);
                    throw new XmlParseException("A propertyVetoException was fired when trying to set the subvolume or surface " + geometryClassName + " to a MembraneMapping!", e);
                }
            }
        }
    }
    // Set Boundary conditions
    Element tempElement = param.getChild(XMLTags.BoundariesTypesTag, vcNamespace);
    // Xm
    String temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueXm);
    BoundaryConditionType bct = new BoundaryConditionType(temp);
    feamap.setBoundaryConditionTypeXm(bct);
    // Xp
    temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueXp);
    bct = new BoundaryConditionType(temp);
    feamap.setBoundaryConditionTypeXp(bct);
    // Ym
    temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueYm);
    bct = new BoundaryConditionType(temp);
    feamap.setBoundaryConditionTypeYm(bct);
    // Yp
    temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueYp);
    bct = new BoundaryConditionType(temp);
    feamap.setBoundaryConditionTypeYp(bct);
    // Zm
    temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueZm);
    bct = new BoundaryConditionType(temp);
    feamap.setBoundaryConditionTypeZm(bct);
    // Zp
    temp = tempElement.getAttributeValue(XMLTags.BoundaryAttrValueZp);
    bct = new BoundaryConditionType(temp);
    feamap.setBoundaryConditionTypeZp(bct);
    return feamap;
}

Example 14 with BoundaryConditionType

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

the class XmlReader method getMembraneSubDomain.

/**
 * This method returns a MembraneSubDomain object from a XML Element.
 * Creation date: (5/18/2001 4:23:30 PM)
 * @return cbit.vcell.math.MembraneSubDomain
 * @param param org.jdom.Element
 * @exception cbit.vcell.xml.XmlParseException The exception description.
 */
@SuppressWarnings("unchecked")
private MembraneSubDomain getMembraneSubDomain(Element param, MathDescription mathDesc) throws XmlParseException {
    // no need to do anything with the 'Name' attribute : constructor of MembraneSubDomain creates name from inside/outside compartmentSubDomains.
    // String msdName = unMangle( param.getAttributeValue(XMLTags.NameAttrTag) );
    // if ( msdName != null) {
    // }
    // get compartmentSubDomain references
    // inside
    String name = unMangle(param.getAttributeValue(XMLTags.InsideCompartmentTag));
    CompartmentSubDomain insideRef = (CompartmentSubDomain) mathDesc.getCompartmentSubDomain(name);
    if (insideRef == null) {
        throw new XmlParseException("The reference to the inside CompartmentSubDomain " + name + ", could not be resolved!");
    }
    // outside
    name = unMangle(param.getAttributeValue(XMLTags.OutsideCompartmentTag));
    CompartmentSubDomain outsideRef = (CompartmentSubDomain) mathDesc.getCompartmentSubDomain(name);
    if (outsideRef == null) {
        throw new XmlParseException("The reference to the outside CompartmentSubDomain " + name + ", could not be resolved!");
    }
    // *** create new Membrane SubDomain ***
    SubVolume insideSubVolume = mathDesc.getGeometry().getGeometrySpec().getSubVolume(insideRef.getName());
    SubVolume outsideSubVolume = mathDesc.getGeometry().getGeometrySpec().getSubVolume(outsideRef.getName());
    SurfaceClass surfaceClass = mathDesc.getGeometry().getGeometrySurfaceDescription().getSurfaceClass(insideSubVolume, outsideSubVolume);
    MembraneSubDomain subDomain = new MembraneSubDomain(insideRef, outsideRef, surfaceClass.getName());
    transcribeComments(param, subDomain);
    // Process BoundaryConditions
    Iterator<Element> iterator = param.getChildren(XMLTags.BoundaryTypeTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element tempelement = (Element) iterator.next();
        // create BoundaryConditionType
        String temp = tempelement.getAttributeValue(XMLTags.BoundaryTypeAttrTag);
        BoundaryConditionType bType = new BoundaryConditionType(temp);
        // Process Xm
        if (tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueXm)) {
            subDomain.setBoundaryConditionXm(bType);
        } else if (tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueXp)) {
            // Process Xp
            subDomain.setBoundaryConditionXp(bType);
        } else if (tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueYm)) {
            // Process Ym
            subDomain.setBoundaryConditionYm(bType);
        } else if (tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueYp)) {
            // Process Yp
            subDomain.setBoundaryConditionYp(bType);
        } else if (tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueZm)) {
            // Process Zm
            subDomain.setBoundaryConditionZm(bType);
        } else if (tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueZp)) {
            // Process Zp
            subDomain.setBoundaryConditionZp(bType);
        } else {
            // If not indentified throw an exception!!
            throw new XmlParseException("Unknown BoundaryConditionType: " + tempelement.getAttributeValue(XMLTags.BoundaryAttrTag));
        }
    }
    // Add OdeEquations
    iterator = param.getChildren(XMLTags.OdeEquationTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element tempElement = (Element) iterator.next();
        OdeEquation odeEquation = getOdeEquation(tempElement, mathDesc);
        try {
            subDomain.addEquation(odeEquation);
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("A MathException was fired when adding an OdeEquation to a MembraneSubDomain!", e);
        }
    }
    // process PdeEquations
    iterator = param.getChildren(XMLTags.PdeEquationTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element tempElement = (Element) iterator.next();
        try {
            subDomain.addEquation(getPdeEquation(tempElement, mathDesc));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("A MathException was fired when adding an PdeEquation to the MembraneSubDomain " + name, e);
        }
    }
    // Add JumpConditions
    iterator = param.getChildren(XMLTags.JumpConditionTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element tempElement = (Element) iterator.next();
        try {
            subDomain.addJumpCondition(getJumpCondition(tempElement, mathDesc));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("A MathException was fired when adding a JumpCondition to a MembraneSubDomain!", e);
        }
    }
    // Add the FastSystem (if any)
    Element tempElement = param.getChild(XMLTags.FastSystemTag, vcNamespace);
    if (tempElement != null) {
        subDomain.setFastSystem(getFastSystem(tempElement, mathDesc));
    }
    // add MembraneRegionEquation
    iterator = param.getChildren(XMLTags.MembraneRegionEquationTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempElement = (Element) iterator.next();
        try {
            subDomain.addEquation(getMembraneRegionEquation(tempElement, mathDesc));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("A MathException was fired when adding a MembraneRegionEquation to a MEmbraneSubDomain!", e);
        }
    }
    iterator = param.getChildren(XMLTags.ParticleJumpProcessTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element tempelement = (Element) iterator.next();
        try {
            subDomain.addParticleJumpProcess(getParticleJumpProcess(tempelement, mathDesc));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("A MathException was fired when adding a jump process to the MembraneSubDomain " + name, e);
        }
    }
    iterator = param.getChildren(XMLTags.ParticlePropertiesTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element tempelement = (Element) iterator.next();
        try {
            subDomain.addParticleProperties(getParticleProperties(tempelement, mathDesc));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("A MathException was fired when adding a jump process to the MembraneSubDomain " + name, e);
        }
    }
    // process ComputeNormal "equations"
    iterator = param.getChildren(XMLTags.ComputeNormalTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element tempelement = (Element) iterator.next();
        try {
            subDomain.addEquation(getComputeNormal(tempelement, mathDesc));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("A MathException was fired when adding an ComputeNormal 'equation' to the MembraneSubDomain " + name, e);
        }
    }
    Element velElem = param.getChild(XMLTags.VelocityTag, vcNamespace);
    setMembraneSubdomainVelocity(velElem, XMLTags.XAttrTag, subDomain::setVelocityX);
    setMembraneSubdomainVelocity(velElem, XMLTags.YAttrTag, subDomain::setVelocityY);
    return subDomain;
}

Example 15 with BoundaryConditionType

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

the class FiniteVolumeFileWriter method writeMembrane_VarContext_Equation.

/**
 *EQUATION_BEGIN rf
 *INITIAL 5.0;
 *RATE ( - ((0.02 * ( - rB - rfB + (20.0 * ((x > -3.0) && (x < 3.0) && (y > -5.0) && (y < 5.0))) + _VCell_FieldData_0) * rf) - (0.1 * rfB)) - (50.0 * rf * ((x > -5.0) && (x < 5.0) && (y > -5.0) && (y < 5.0))));
 *DIFFUSION 10.0;
 *BOUNDARY_XM 5.0;
 *BOUNDARY_XP 5.0;
 *BOUNDARY_YM 5.0;
 *BOUNDARY_YP 5.0;
 *EQUATION_END
 * @throws ExpressionException
 * @throws MathException
 */
private void writeMembrane_VarContext_Equation(MembraneSubDomain memSubDomain, Equation equation) throws ExpressionException, MathException {
    printWriter.println("EQUATION_BEGIN " + equation.getVariable().getName());
    printWriter.println("INITIAL " + subsituteExpression(equation.getInitialExpression(), VariableDomain.VARIABLEDOMAIN_MEMBRANE).infix() + ";");
    Expression rateExpression = subsituteExpression(equation.getRateExpression(), VariableDomain.VARIABLEDOMAIN_MEMBRANE);
    printWriter.println("RATE " + replaceVolumeVariable(simTask, memSubDomain, rateExpression) + ";");
    if (bChomboSolver && equation.getExactSolution() != null) {
        printWriter.println(FVInputFileKeyword.EXACT + " " + subsituteExpression(equation.getExactSolution(), VariableDomain.VARIABLEDOMAIN_VOLUME).infix() + ";");
    }
    if (equation instanceof PdeEquation) {
        printWriter.println("DIFFUSION " + subsituteExpression(((PdeEquation) equation).getDiffusionExpression(), VariableDomain.VARIABLEDOMAIN_MEMBRANE).infix() + ";");
        PdeEquation pde = (PdeEquation) equation;
        BoundaryConditionType[] bctypes = new BoundaryConditionType[] { memSubDomain.getInsideCompartment().getBoundaryConditionXm(), memSubDomain.getInsideCompartment().getBoundaryConditionXp(), memSubDomain.getInsideCompartment().getBoundaryConditionYm(), memSubDomain.getInsideCompartment().getBoundaryConditionYp(), memSubDomain.getInsideCompartment().getBoundaryConditionZm(), memSubDomain.getInsideCompartment().getBoundaryConditionZp() };
        writeBoundaryValues(bctypes, pde, VariableDomain.VARIABLEDOMAIN_MEMBRANE);
    }
    // if (simulation.getSolverTaskDescription().getSolverDescription().equals(SolverDescription.SundialsPDE)) {
    // StringBuffer rateDerivativeString = new StringBuffer();
    // Variable[] vars = simulation.getVariables();
    // int count = 0;
    // for (Variable var : vars) {
    // if (var instanceof MemVariable) {
    // Expression exp = rateExpression.differentiate(var.getName());
    // rateDerivativeString.append(exp.flatten().infix() + ";\n");
    // count ++;
    // }
    // }
    // printWriter.println("RATE_DERIVATIVES " + count);
    // printWriter.print(rateDerivativeString);
    // }
    printWriter.println("EQUATION_END");
    printWriter.println();
}