Examples with BoundaryConditionSpec cbit.vcell.math.SubDomain.BoundaryConditionSpec used on opensource projects

Example 1 with BoundaryConditionSpec

use of cbit.vcell.math.SubDomain.BoundaryConditionSpec in project vcell by virtualcell.

the class Xmlproducer method getXML.

/**
 * This method returns a XML representation of a CompartmentSubDomain object.
 * Creation date: (3/2/2001 1:18:55 PM)
 * @return Element
 * @param param cbit.vcell.math.CompartmentSubDomain
 */
private Element getXML(CompartmentSubDomain param) throws XmlParseException {
    Element compartment = new Element(XMLTags.CompartmentSubDomainTag);
    compartment.setAttribute(XMLTags.NameAttrTag, mangle(param.getName()));
    // Add boundaryType subelements
    Element boundary;
    // Xm
    boundary = new Element(XMLTags.BoundaryTypeTag);
    boundary.setAttribute(XMLTags.BoundaryAttrTag, XMLTags.BoundaryAttrValueXm);
    boundary.setAttribute(XMLTags.BoundaryTypeAttrTag, param.getBoundaryConditionXm().boundaryTypeStringValue());
    compartment.addContent(boundary);
    // Xp
    boundary = new Element(XMLTags.BoundaryTypeTag);
    boundary.setAttribute(XMLTags.BoundaryAttrTag, XMLTags.BoundaryAttrValueXp);
    boundary.setAttribute(XMLTags.BoundaryTypeAttrTag, param.getBoundaryConditionXp().boundaryTypeStringValue());
    compartment.addContent(boundary);
    // Ym
    boundary = new Element(XMLTags.BoundaryTypeTag);
    boundary.setAttribute(XMLTags.BoundaryAttrTag, XMLTags.BoundaryAttrValueYm);
    boundary.setAttribute(XMLTags.BoundaryTypeAttrTag, param.getBoundaryConditionYm().boundaryTypeStringValue());
    compartment.addContent(boundary);
    // Yp
    boundary = new Element(XMLTags.BoundaryTypeTag);
    boundary.setAttribute(XMLTags.BoundaryAttrTag, XMLTags.BoundaryAttrValueYp);
    boundary.setAttribute(XMLTags.BoundaryTypeAttrTag, param.getBoundaryConditionYp().boundaryTypeStringValue());
    compartment.addContent(boundary);
    // Zm
    boundary = new Element(XMLTags.BoundaryTypeTag);
    boundary.setAttribute(XMLTags.BoundaryAttrTag, XMLTags.BoundaryAttrValueZm);
    boundary.setAttribute(XMLTags.BoundaryTypeAttrTag, param.getBoundaryConditionZm().boundaryTypeStringValue());
    compartment.addContent(boundary);
    // Zp
    boundary = new Element(XMLTags.BoundaryTypeTag);
    boundary.setAttribute(XMLTags.BoundaryAttrTag, XMLTags.BoundaryAttrValueZp);
    boundary.setAttribute(XMLTags.BoundaryTypeAttrTag, param.getBoundaryConditionZp().boundaryTypeStringValue());
    compartment.addContent(boundary);
    // add BoundaryConditionSpecs
    for (BoundaryConditionSpec bcs : param.getBoundaryconditionSpecs()) {
        compartment.addContent(getXML(bcs));
    }
    // Add Equations
    Enumeration<Equation> enum1 = param.getEquations();
    while (enum1.hasMoreElements()) {
        Equation equ = enum1.nextElement();
        compartment.addContent(getXML(equ));
    }
    // Add FastSystem
    if (param.getFastSystem() != null) {
        compartment.addContent(getXML(param.getFastSystem()));
    }
    // Add Variable Initial Condition
    for (VarIniCondition varIni : param.getVarIniConditions()) {
        compartment.addContent(getXML(varIni));
    }
    // Add JumpProcesses
    for (JumpProcess jp : param.getJumpProcesses()) {
        compartment.addContent(getXML(jp));
    }
    for (ParticleJumpProcess pjp : param.getParticleJumpProcesses()) {
        compartment.addContent(getXML(pjp));
    }
    for (ParticleProperties pp : param.getParticleProperties()) {
        compartment.addContent(getXML(pp));
    }
    return compartment;
}

Example 2 with BoundaryConditionSpec

use of cbit.vcell.math.SubDomain.BoundaryConditionSpec in project vcell by virtualcell.

the class PdeEquation method isDummy.

public boolean isDummy(MathSymbolTable simSymbolTable, CompartmentSubDomain thisCompartment) {
    if (!(getVariable() instanceof VolVariable)) {
        return false;
    }
    VolVariable volVar = (VolVariable) getVariable();
    // in any case the initial conditions will be respected.
    if (testZero(simSymbolTable, getRateExpression()) && testZero(simSymbolTable, velocityX) && testZero(simSymbolTable, velocityY) && testZero(simSymbolTable, velocityZ) && testZero(simSymbolTable, gradientX) && testZero(simSymbolTable, gradientY) && testZero(simSymbolTable, gradientZ)) {
        if (testZero(simSymbolTable, diffusionExp)) {
            // zero rate, velocity and diffusion
            return true;
        } else {
            // for non-zero diffusion, look for non zero fluxes or non-uniform initial conditions.
            if (testConstant(simSymbolTable, getInitialExpression()) && testZero(simSymbolTable, boundaryXm) && testZero(simSymbolTable, boundaryXp) && testZero(simSymbolTable, boundaryYm) && testZero(simSymbolTable, boundaryYp) && testZero(simSymbolTable, boundaryZm) && testZero(simSymbolTable, boundaryZp)) {
                // 1. get THIS compartment
                // 2. get all membranes that touch this compartment
                // 3. get jump condition for this variable
                // 4. check either influx or outflux
                Enumeration<SubDomain> subDomainEnum = simSymbolTable.getMathDescription().getSubDomains();
                while (subDomainEnum.hasMoreElements()) {
                    SubDomain subDomain = (SubDomain) subDomainEnum.nextElement();
                    if (subDomain instanceof MembraneSubDomain) {
                        MembraneSubDomain memSubDomain = (MembraneSubDomain) subDomain;
                        if (memSubDomain.getInsideCompartment() == thisCompartment) {
                            JumpCondition jump = memSubDomain.getJumpCondition(volVar);
                            if (jump != null && !testZero(simSymbolTable, jump.getInFluxExpression())) {
                                // non zero jump condition
                                return false;
                            }
                        } else if (memSubDomain.getOutsideCompartment() == thisCompartment) {
                            JumpCondition jump = memSubDomain.getJumpCondition(volVar);
                            if (jump != null && !testZero(simSymbolTable, jump.getOutFluxExpression())) {
                                // non zero jump condition
                                return false;
                            }
                        }
                        // check if BoundaryConditionValue is defined for var on membrane
                        try {
                            BoundaryConditionValue boundaryValue = getBoundaryConditionValue(memSubDomain.getName());
                            if (boundaryValue != null) {
                                Expression boundaryValExpr = boundaryValue.getBoundaryConditionExpression();
                                BoundaryConditionSpec boundarySpec = thisCompartment.getBoundaryConditionSpec(memSubDomain.getName());
                                if (boundarySpec != null) {
                                    boolean bZeroFlux = boundarySpec.getBoundaryConditionType().isNEUMANN() && testZero(simSymbolTable, boundaryValExpr);
                                    boolean bUniformDirichlet = boundarySpec.getBoundaryConditionType().isDIRICHLET() && testZero(simSymbolTable, Expression.add(boundaryValExpr, Expression.negate(getInitialExpression())));
                                    if (!bZeroFlux && !bUniformDirichlet) {
                                        return false;
                                    }
                                }
                            }
                        } catch (ExpressionException e) {
                            e.printStackTrace(System.out);
                        }
                    }
                }
                // check fast system if jump conditions are all zero
                FastSystem fastSystem = thisCompartment.getFastSystem();
                if (fastSystem != null) {
                    Enumeration<FastInvariant> fastInvariants = fastSystem.getFastInvariants();
                    while (fastInvariants.hasMoreElements()) {
                        FastInvariant fi = fastInvariants.nextElement();
                        try {
                            // look for fast invariants that involve only this variable
                            // which means this variable is not affected by fast system
                            Expression exp = new Expression(fi.getFunction());
                            exp.bindExpression(simSymbolTable);
                            exp = exp.flatten();
                            SymbolTableEntry ste = exp.getSymbolBinding(volVar.getName());
                            if (ste != null && exp.getSymbols().length == 1) {
                                return true;
                            }
                        } catch (ExpressionException ex) {
                            ex.printStackTrace(System.out);
                            throw new RuntimeException("PdeEquation::isDummy(), not expected: " + ex.getMessage());
                        }
                    }
                    // the variable is not found to be invariant in this fast system, might be changed by fast system
                    return false;
                }
                // not changed by jump conditions, boundary conditions and fast system even if diffusion rate is non zero
                return true;
            }
        }
    }
    // non zero rate or velocity
    return false;
}

Example 3 with BoundaryConditionSpec

use of cbit.vcell.math.SubDomain.BoundaryConditionSpec 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 4 with BoundaryConditionSpec

use of cbit.vcell.math.SubDomain.BoundaryConditionSpec in project vcell by virtualcell.

the class FiniteVolumeFileWriter method writeMembrane_jumpConditions.

/**
 *JUMP_CONDITION_BEGIN r
 *INFLUX 0.0;
 *OUTFLUX 0.0;
 *JUMP_CONDITION_END
 * @throws ExpressionException
 * @throws MathException
 */
private void writeMembrane_jumpConditions(MembraneSubDomain msd) throws ExpressionException, MathException {
    Enumeration<JumpCondition> enum1 = msd.getJumpConditions();
    // equations for boundaryValues for inner compartment subdomain
    CompartmentSubDomain innerCompSubDomain = msd.getInsideCompartment();
    Enumeration<Equation> innercompSubDomEqnsEnum = innerCompSubDomain.getEquations();
    while (innercompSubDomEqnsEnum.hasMoreElements()) {
        Equation eqn = innercompSubDomEqnsEnum.nextElement();
        if (eqn instanceof PdeEquation) {
            PdeEquation pdeEqn = (PdeEquation) eqn;
            BoundaryConditionValue boundaryValue = pdeEqn.getBoundaryConditionValue(msd.getName());
            if (boundaryValue != null) {
                // check if the type of BoundaryConditionSpec for this membraneSubDomain (msd) in the (inner) compartmentSubDomain is Flux; if not, it cannot be handled.
                BoundaryConditionSpec bcs = innerCompSubDomain.getBoundaryConditionSpec(msd.getName());
                if (bcs == null) {
                    throw new MathException("No Boundary type specified for '" + msd.getName() + "' in '" + innerCompSubDomain.getName() + "'.");
                }
                if (bcs != null && !bcs.getBoundaryConditionType().compareEqual(BoundaryConditionType.getNEUMANN()) && !bChomboSolver) {
                    throw new MathException("Boundary type '" + bcs.getBoundaryConditionType().boundaryTypeStringValue() + "' for compartmentSubDomain '" + innerCompSubDomain.getName() + "' not handled by the chosen solver. Expecting boundary condition of type 'Flux'.");
                }
                if (pdeEqn.getVariable().getDomain() == null || pdeEqn.getVariable().getDomain().getName().equals(msd.getInsideCompartment().getName())) {
                    printWriter.println("JUMP_CONDITION_BEGIN " + pdeEqn.getVariable().getName());
                    Expression flux = subsituteExpression(boundaryValue.getBoundaryConditionExpression(), VariableDomain.VARIABLEDOMAIN_MEMBRANE);
                    String infix = replaceVolumeVariable(getSimulationTask(), msd, flux);
                    printWriter.println(bcs.getBoundaryConditionType().boundaryTypeStringValue().toUpperCase() + " " + msd.getInsideCompartment().getName() + " " + infix + ";");
                    printWriter.println("JUMP_CONDITION_END");
                    printWriter.println();
                }
            }
        }
    }
    // equations for boundaryValues for outer compartment subdomain
    CompartmentSubDomain outerCompSubDomain = msd.getOutsideCompartment();
    Enumeration<Equation> outerCompSubDomEqnsEnum = outerCompSubDomain.getEquations();
    while (outerCompSubDomEqnsEnum.hasMoreElements()) {
        Equation eqn = outerCompSubDomEqnsEnum.nextElement();
        if (eqn instanceof PdeEquation) {
            PdeEquation pdeEqn = (PdeEquation) eqn;
            BoundaryConditionValue boundaryValue = pdeEqn.getBoundaryConditionValue(msd.getName());
            if (boundaryValue != null) {
                // check if the type of BoundaryConditionSpec for this membraneSubDomain (msd) in the (inner) compartmentSubDomain is Flux; if not, it cannot be handled.
                BoundaryConditionSpec bcs = outerCompSubDomain.getBoundaryConditionSpec(msd.getName());
                if (bcs != null && !bcs.getBoundaryConditionType().compareEqual(BoundaryConditionType.getNEUMANN()) && !bChomboSolver) {
                    throw new MathException("Boundary type '" + bcs.getBoundaryConditionType().boundaryTypeStringValue() + "' for compartmentSubDomain '" + outerCompSubDomain.getName() + "' not handled by the chosen solver. Expecting boundary condition of type 'Flux'.");
                }
                if (pdeEqn.getVariable().getDomain() == null || pdeEqn.getVariable().getDomain().getName().equals(msd.getOutsideCompartment().getName())) {
                    printWriter.println("JUMP_CONDITION_BEGIN " + pdeEqn.getVariable().getName());
                    Expression flux = subsituteExpression(boundaryValue.getBoundaryConditionExpression(), VariableDomain.VARIABLEDOMAIN_MEMBRANE);
                    String infix = replaceVolumeVariable(getSimulationTask(), msd, flux);
                    printWriter.println(bcs.getBoundaryConditionType().boundaryTypeStringValue().toUpperCase() + " " + msd.getOutsideCompartment().getName() + " " + infix + ";");
                    printWriter.println("JUMP_CONDITION_END");
                    printWriter.println();
                }
            }
        }
    }
    while (enum1.hasMoreElements()) {
        JumpCondition jc = enum1.nextElement();
        printWriter.println("JUMP_CONDITION_BEGIN " + jc.getVariable().getName());
        // influx
        if (jc.getVariable().getDomain() == null || jc.getVariable().getDomain().getName().equals(msd.getInsideCompartment().getName())) {
            Expression flux = subsituteExpression(jc.getInFluxExpression(), VariableDomain.VARIABLEDOMAIN_MEMBRANE);
            String infix = replaceVolumeVariable(getSimulationTask(), msd, flux);
            printWriter.println(BoundaryConditionType.NEUMANN_STRING.toUpperCase() + " " + msd.getInsideCompartment().getName() + " " + infix + ";");
        }
        if (jc.getVariable().getDomain() == null || jc.getVariable().getDomain().getName().equals(msd.getOutsideCompartment().getName())) {
            // outflux
            Expression flux = subsituteExpression(jc.getOutFluxExpression(), VariableDomain.VARIABLEDOMAIN_MEMBRANE);
            String infix = replaceVolumeVariable(simTask, msd, flux);
            printWriter.println(BoundaryConditionType.NEUMANN_STRING.toUpperCase() + " " + msd.getOutsideCompartment().getName() + " " + infix + ";");
        }
        printWriter.println("JUMP_CONDITION_END");
        printWriter.println();
    }
}