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

Example 46 with Constant

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

the class XmlReader method getSolverTaskDescription.

/**
 * This method returns a SolverTaskDescription Object from a XML Element.
 * Creation date: (5/22/2001 10:51:23 AM)
 * @return cbit.vcell.solver.SolverTaskDescription
 * @param param org.jdom.Element
 * @param simulation cbit.vcell.solver.Simulation
 */
private SolverTaskDescription getSolverTaskDescription(Element param, Simulation simulation) throws XmlParseException {
    // *** create new SolverTaskDescription ***
    SolverTaskDescription solverTaskDesc = new SolverTaskDescription(simulation);
    // Added July 22nd, 2007, used as condition for stochSimOptions or stochHybridOprtions
    SolverDescription sd = null;
    // Retrieve attributes
    String taskType = param.getAttributeValue(XMLTags.TaskTypeTag);
    int keepEvery = -1;
    int keepAtMost = -1;
    if (param.getAttributeValue(XMLTags.KeepEveryTag) != null) {
        keepEvery = Integer.parseInt(param.getAttributeValue(XMLTags.KeepEveryTag));
        keepAtMost = Integer.parseInt(param.getAttributeValue(XMLTags.KeepAtMostTag));
    }
    boolean useSymJacob = new Boolean(param.getAttributeValue(XMLTags.UseSymbolicJacobianAttrTag)).booleanValue();
    String solverName = param.getAttributeValue(XMLTags.SolverNameTag);
    // get sentivity parameter
    Element sensparamElement = param.getChild(XMLTags.ConstantTag, vcNamespace);
    Constant sensitivityparam = null;
    if (sensparamElement != null) {
        sensitivityparam = getConstant(sensparamElement);
    }
    // set Attributes
    try {
        // set solver
        sd = SolverDescription.fromDatabaseName(solverName);
        if (sd == null) {
            System.err.println("====================================== couldn't find solver description name ==========================================");
        }
        solverTaskDesc.setSolverDescription(sd);
        if (taskType.equalsIgnoreCase(XMLTags.UnsteadyTag)) {
            solverTaskDesc.setTaskType(SolverTaskDescription.TASK_UNSTEADY);
        } else if (taskType.equalsIgnoreCase(XMLTags.SteadyTag)) {
            solverTaskDesc.setTaskType(SolverTaskDescription.TASK_STEADY);
        } else {
            throw new XmlParseException("Unexpected task type: " + taskType);
        }
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException("A PropertyVetoException was fired when setting the taskType: " + taskType, e);
    }
    int numProcessors = parseIntWithDefault(param, XMLTags.NUM_PROCESSORS, 1);
    try {
        solverTaskDesc.setNumProcessors(numProcessors);
        solverTaskDesc.setUseSymbolicJacobian(useSymJacob);
        // get TimeBound
        solverTaskDesc.setTimeBounds(getTimeBounds(param.getChild(XMLTags.TimeBoundTag, vcNamespace)));
        // get TimeStep
        solverTaskDesc.setTimeStep(getTimeStep(param.getChild(XMLTags.TimeStepTag, vcNamespace)));
        // get ErrorTolerance
        solverTaskDesc.setErrorTolerance(getErrorTolerance(param.getChild(XMLTags.ErrorToleranceTag, vcNamespace)));
        // get StochSimOptions
        if (simulation != null && simulation.getMathDescription() != null) {
            if (simulation.getMathDescription().isNonSpatialStoch() && param.getChild(XMLTags.StochSimOptionsTag, vcNamespace) != null) {
                // Amended July 22nd, 2007 to read either stochSimOptions or stochHybridOptions
                solverTaskDesc.setStochOpt(getStochSimOptions(param.getChild(XMLTags.StochSimOptionsTag, vcNamespace)));
                if (sd != null && !sd.equals(SolverDescription.StochGibson)) {
                    solverTaskDesc.setStochHybridOpt(getStochHybridOptions(param.getChild(XMLTags.StochSimOptionsTag, vcNamespace)));
                }
            }
        }
        // get OutputOptions
        if (keepEvery != -1) {
            solverTaskDesc.setOutputTimeSpec(new DefaultOutputTimeSpec(keepEvery, keepAtMost));
        }
        OutputTimeSpec ots = getOutputTimeSpec(param.getChild(XMLTags.OutputOptionsTag, vcNamespace));
        if (ots != null) {
            solverTaskDesc.setOutputTimeSpec(getOutputTimeSpec(param.getChild(XMLTags.OutputOptionsTag, vcNamespace)));
        }
        // set SensitivityParameter
        solverTaskDesc.setSensitivityParameter(sensitivityparam);
        // set StopAtSpatiallyUniform
        Element stopSpatiallyElement = param.getChild(XMLTags.StopAtSpatiallyUniform, vcNamespace);
        if (stopSpatiallyElement != null) {
            Element errTolElement = stopSpatiallyElement.getChild(XMLTags.ErrorToleranceTag, vcNamespace);
            if (errTolElement != null) {
                solverTaskDesc.setStopAtSpatiallyUniformErrorTolerance(getErrorTolerance(errTolElement));
            }
        }
        String runParameterScanSeriallyAttributeValue = param.getAttributeValue(XMLTags.RunParameterScanSerially);
        if (runParameterScanSeriallyAttributeValue != null) {
            solverTaskDesc.setSerialParameterScan(new Boolean(runParameterScanSeriallyAttributeValue).booleanValue());
        }
        Element nfsimSimulationOptionsElement = param.getChild(XMLTags.NFSimSimulationOptions, vcNamespace);
        if (nfsimSimulationOptionsElement != null) {
            NFsimSimulationOptions nfsimSimulationOptions = getNFSimSimulationOptions(nfsimSimulationOptionsElement);
            solverTaskDesc.setNFSimSimulationOptions(nfsimSimulationOptions);
        }
        Element smoldySimulationOptionsElement = param.getChild(XMLTags.SmoldynSimulationOptions, vcNamespace);
        if (smoldySimulationOptionsElement != null) {
            SmoldynSimulationOptions smoldynSimulationOptions = getSmoldySimulationOptions(smoldySimulationOptionsElement);
            solverTaskDesc.setSmoldynSimulationOptions(smoldynSimulationOptions);
        }
        Element sundialsPdeSolverOptionsElement = param.getChild(XMLTags.SundialsSolverOptions, vcNamespace);
        if (sundialsPdeSolverOptionsElement != null) {
            SundialsPdeSolverOptions sundialsPdeSolverOptions = getSundialsPdeSolverOptions(sundialsPdeSolverOptionsElement);
            solverTaskDesc.setSundialsPdeSolverOptions(sundialsPdeSolverOptions);
        }
        Element chomboElement = param.getChild(XMLTags.ChomboSolverSpec, vcNamespace);
        if (chomboElement != null) {
            ChomboSolverSpec chombo = getChomboSolverSpec(solverTaskDesc, chomboElement, simulation.getMathDescription().getGeometry().getDimension());
            solverTaskDesc.setChomboSolverSpec(chombo);
        }
        Element mbElement = param.getChild(XMLTags.MovingBoundarySolverOptionsTag, vcNamespace);
        if (mbElement != null) {
            MovingBoundarySolverOptions mb = getMovingBoundarySolverOptions(solverTaskDesc, mbElement);
            solverTaskDesc.setMovingBoundarySolverOptions(mb);
        }
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException(e);
    }
    return solverTaskDesc;
}

Example 47 with Constant

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

the class XmlReader method getConstant.

/**
 * This method returns a Constant object from a XML element.
 * Creation date: (5/16/2001 1:50:07 PM)
 * @return cbit.vcell.math.Constant
 * @param param org.jdom.Element
 * @exception cbit.vcell.xml.XmlParseException The exception description.
 */
private Constant getConstant(Element param) throws XmlParseException {
    // retrieve values
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    Expression exp = unMangleExpression(param.getText());
    // -- create new constant object ---
    Constant newconstant = new Constant(name, exp);
    transcribeComments(param, newconstant);
    return newconstant;
}

Example 48 with Constant

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

the class XmlReader method addResevedSymbols.

/**
 * This method returns a Kinetics object from a XML Element based on the value of the kinetics type attribute.
 * Creation date: (3/19/2001 4:42:04 PM)
 * @return cbit.vcell.model.Kinetics
 * @param param org.jdom.Element
 */
private void addResevedSymbols(VariableHash varHash, Model model) throws XmlParseException {
    // 
    try {
        // add reserved symbols
        varHash.addVariable(new Constant(model.getPI_CONSTANT().getName(), new Expression(0.0)));
        varHash.addVariable(new Constant(model.getFARADAY_CONSTANT().getName(), new Expression(0.0)));
        varHash.addVariable(new Constant(model.getFARADAY_CONSTANT_NMOLE().getName(), new Expression(0.0)));
        varHash.addVariable(new Constant(model.getGAS_CONSTANT().getName(), new Expression(0.0)));
        varHash.addVariable(new Constant(model.getKMILLIVOLTS().getName(), new Expression(0.0)));
        varHash.addVariable(new Constant(model.getN_PMOLE().getName(), new Expression(0.0)));
        varHash.addVariable(new Constant(model.getKMOLE().getName(), new Expression(0.0)));
        varHash.addVariable(new Constant(model.getTEMPERATURE().getName(), new Expression(0.0)));
        varHash.addVariable(new Constant(model.getK_GHK().getName(), new Expression(0.0)));
        varHash.addVariable(new Constant(model.getTIME().getName(), new Expression(0.0)));
    } catch (MathException e) {
        e.printStackTrace(System.out);
        throw new XmlParseException("error reordering parameters according to dependencies", e);
    }
}

Example 49 with Constant

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

the class SimulationRepresentation method getParameters.

private static ParameterRepresentation[] getParameters(BioModel bioModel, SimulationRep simulationRep) {
    SimulationContext simContext = null;
    for (SimulationContext sc : bioModel.getSimulationContexts()) {
        if (sc.getMathDescription().getKey().equals(simulationRep.getMathKey())) {
            simContext = sc;
            break;
        }
    }
    if (simContext == null) {
        return null;
    }
    // initialize to old mathDescription in case error generating math
    MathDescription mathDesc = simContext.getMathDescription();
    MathMapping mathMapping = simContext.createNewMathMapping();
    MathSymbolMapping mathSymbolMapping = null;
    try {
        mathDesc = mathMapping.getMathDescription();
        mathSymbolMapping = mathMapping.getMathSymbolMapping();
    } catch (Exception e1) {
        System.err.println(e1.getMessage());
    }
    ArrayList<ParameterRepresentation> parameterReps = new ArrayList<ParameterRepresentation>();
    Enumeration<Constant> enumMath = mathDesc.getConstants();
    while (enumMath.hasMoreElements()) {
        Constant constant = enumMath.nextElement();
        if (constant.getExpression().isNumeric()) {
            SymbolTableEntry biologicalSymbolTableEntry = null;
            if (mathSymbolMapping != null) {
                SymbolTableEntry[] stes = mathSymbolMapping.getBiologicalSymbol(constant);
                if (stes != null && stes.length >= 1) {
                    biologicalSymbolTableEntry = stes[0];
                }
            }
            if (biologicalSymbolTableEntry instanceof ReservedSymbol) {
                continue;
            }
            try {
                parameterReps.add(new ParameterRepresentation(constant.getName(), constant.getExpression().evaluateConstant(), biologicalSymbolTableEntry));
            } catch (ExpressionException e) {
                // can't happen, because constant expression is numeric
                e.printStackTrace();
            }
        }
    }
    return parameterReps.toArray(new ParameterRepresentation[0]);
}

Example 50 with Constant

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

the class ConstantArraySpec method createListSpec.

/**
 * Insert the method's description here.
 * Creation date: (9/23/2005 1:33:00 PM)
 * @return cbit.vcell.solver.ConstantArraySpec
 */
public static ConstantArraySpec createListSpec(String name, String[] values) throws cbit.vcell.parser.ExpressionException {
    if (values.length < 2)
        throw new RuntimeException("List must contain at least two values");
    ConstantArraySpec spec = new ConstantArraySpec();
    spec.type = TYPE_LIST;
    spec.name = name;
    spec.constants = new Constant[values.length];
    spec.numValues = values.length;
    for (int i = 0; i < values.length; i++) {
        spec.constants[i] = new Constant(name, new cbit.vcell.parser.Expression(values[i]));
    }
    return spec;
}