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

Example 11 with OdeEquation

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

the class XmlReader method getOdeEquation.

/**
 * This method returns an OdeEquation from a XML Element.
 * Creation date: (5/17/2001 3:52:40 PM)
 * @return cbit.vcell.math.OdeEquation
 * @param param org.jdom.Element
 * @exception cbit.vcell.xml.XmlParseException The exception description.
 */
private OdeEquation getOdeEquation(Element param, MathDescription mathDesc) throws XmlParseException {
    // get attributes
    String varname = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    // find reference in the dictionnary
    // try as a VolVariable
    Variable varref = mathDesc.getVariable(varname);
    // Make sure that the reference is not empty!!!
    if (varref == null) {
        throw new XmlParseException("The reference to the variable " + varname + " in a OdeEquation could not be resolved!");
    }
    // get Initial condition
    String temp = param.getChildText(XMLTags.InitialTag, vcNamespace);
    Expression initialexp = null;
    if (temp != null && temp.length() > 0) {
        initialexp = unMangleExpression(temp);
    }
    // Get Rate condition
    temp = param.getChildText(XMLTags.RateTag, vcNamespace);
    Expression rateexp = null;
    if (temp != null && temp.length() > 0) {
        rateexp = unMangleExpression((temp));
    }
    // --- Create the OdeEquation object ---
    OdeEquation odeEquation = new OdeEquation(varref, initialexp, rateexp);
    // add specific solutions expressions
    String solType = param.getAttributeValue(XMLTags.SolutionTypeTag);
    if (solType.equalsIgnoreCase(XMLTags.ExactTypeTag)) {
        String solutionExp = param.getChildText(XMLTags.SolutionExpressionTag, vcNamespace);
        if (solutionExp != null && solutionExp.length() > 0) {
            Expression expression = unMangleExpression(solutionExp);
            odeEquation.setExactSolution(expression);
        }
    }
    return odeEquation;
}

Example 12 with OdeEquation

use of cbit.vcell.math.OdeEquation 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 13 with OdeEquation

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

the class CellQuanVCTranslator method addCompartmentSubDomain.

/**
 * 	addCompartmentSubDomain : we pick the variable name by reading through the mathML.
 * 	Redundancy in variable name with the volume variable?
 */
protected void addCompartmentSubDomain() throws Exception {
    String csdName = sRoot.getAttributeValue(CELLMLTags.name, sAttNamespace);
    CompartmentSubDomain csd = new CompartmentSubDomain(csdName, CompartmentSubDomain.NON_SPATIAL_PRIORITY);
    Iterator<?> compElementIter = sRoot.getChildren(CELLMLTags.COMPONENT, sNamespace).iterator();
    // JDOMTreeWalker walker = new JDOMTreeWalker(sRoot, new ElementFilter(CELLMLTags.COMPONENT));
    Element comp, math;
    String compName, varName, mangledName;
    while (compElementIter.hasNext()) {
        comp = (Element) compElementIter.next();
        compName = comp.getAttributeValue(CELLMLTags.name, sAttNamespace);
        @SuppressWarnings("unchecked") Iterator<Element> mathIter = comp.getChildren(CELLMLTags.MATH, mathns).iterator();
        while (mathIter.hasNext()) {
            math = mathIter.next();
            Element apply, apply2, apply3, ci;
            // allow multiple 'apply' children.
            @SuppressWarnings("unchecked") Iterator<Element> applyIter = math.getChildren(MathMLTags.APPLY, mathns).iterator();
            while (applyIter.hasNext()) {
                apply = applyIter.next();
                @SuppressWarnings("unchecked") ArrayList<Element> list = new ArrayList<Element>(apply.getChildren());
                if (list.size() < 3)
                    continue;
                if (!(list.get(0)).getName().equals(MathMLTags.EQUAL))
                    continue;
                apply2 = list.get(1);
                if (!apply2.getName().equals(MathMLTags.APPLY))
                    continue;
                @SuppressWarnings("unchecked") ArrayList<Element> list2 = new ArrayList<Element>(apply2.getChildren());
                if (list2.size() < 3)
                    continue;
                if (!(list2.get(0)).getName().equals(MathMLTags.DIFFERENTIAL))
                    continue;
                // skip the time variable
                ci = list2.get(2);
                varName = ci.getTextTrim();
                // can be a constant
                apply3 = list.get(2);
                mangledName = nm.getMangledName(compName, varName);
                Element trimmedMath = new Element(CELLMLTags.MATH, mathns).addContent(apply3.detach());
                fixMathMLBug(trimmedMath);
                Expression rateExp = null;
                try {
                    rateExp = (new ExpressionMathMLParser(null)).fromMathML(trimmedMath);
                    rateExp = processMathExp(comp, rateExp);
                    rateExp = rateExp.flatten();
                    nl.mangleString(rateExp.infix());
                } catch (ExpressionException e) {
                    e.printStackTrace(System.out);
                    throw new RuntimeException(e.getMessage());
                }
                Expression initExp = new Expression(getInitial(comp, varName));
                Domain domain = null;
                OdeEquation ode = new OdeEquation(new VolVariable(mangledName, domain), initExp, rateExp);
                csd.addEquation(ode);
            }
        }
    }
    mathDescription.addSubDomain(csd);
}

Example 14 with OdeEquation

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

the class DefaultODESolver method createStateVariables.

/**
 * This method was created in VisualAge.
 */
private Vector<StateVariable> createStateVariables() throws MathException, ExpressionException {
    SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
    Simulation sim = simSymbolTable.getSimulation();
    Vector<StateVariable> stateVariables = new Vector<StateVariable>();
    // get Ode's from MathDescription and create ODEStateVariables
    Enumeration<Equation> enum1 = getSubDomain().getEquations();
    while (enum1.hasMoreElements()) {
        Equation equation = enum1.nextElement();
        if (equation instanceof OdeEquation) {
            stateVariables.addElement(new ODEStateVariable((OdeEquation) equation, simSymbolTable));
        } else {
            throw new MathException("encountered non-ode equation, unsupported");
        }
    }
    MathDescription mathDescription = sim.getMathDescription();
    if (rateSensitivity == null) {
        rateSensitivity = new RateSensitivity(mathDescription, mathDescription.getSubDomains().nextElement());
    }
    if (jacobian == null) {
        jacobian = new Jacobian(mathDescription, mathDescription.getSubDomains().nextElement());
    }
    // get Jacobian and RateSensitivities from MathDescription and create SensStateVariables
    for (int v = 0; v < fieldSensVariables.size(); v++) {
        stateVariables.addElement(new SensStateVariable(fieldSensVariables.elementAt(v), rateSensitivity, jacobian, fieldSensVariables, simSymbolTable));
    }
    if (stateVariables.size() == 0) {
        throw new MathException("there are no equations defined");
    }
    return (stateVariables);
}

Example 15 with OdeEquation

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

the class RateSensitivity method parseMathDesc.

/**
 * This method was created by a SmartGuide.
 * @exception java.lang.Exception The exception description.
 */
private void parseMathDesc() throws MathException {
    Vector equationList = new Vector();
    Enumeration enum1 = subDomain.getEquations();
    while (enum1.hasMoreElements()) {
        Equation equ = (Equation) enum1.nextElement();
        if (equ instanceof OdeEquation) {
            equationList.addElement(equ);
        } else {
            throw new MathException("encountered non-ode equation, unsupported");
        }
    }
    Vector constantList = new Vector();
    enum1 = mathDesc.getVariables();
    while (enum1.hasMoreElements()) {
        Variable var = (Variable) enum1.nextElement();
        if (var instanceof Constant) {
            constantList.addElement(var);
        }
    }
    numConstants = constantList.size();
    numRates = equationList.size();
    rates = new Expression[numRates];
    vars = new Variable[numRates];
    consts = new Constant[numConstants];
    for (int i = 0; i < numRates; i++) {
        OdeEquation odeEqu = (OdeEquation) equationList.elementAt(i);
        rates[i] = odeEqu.getRateExpression();
        vars[i] = odeEqu.getVariable();
    }
    for (int i = 0; i < numConstants; i++) {
        consts[i] = (Constant) constantList.elementAt(i);
    }
}