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

Example 66 with MathException

use of cbit.vcell.math.MathException 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 67 with MathException

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

the class MergedData method getSimDataBlock.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.simdata.DataBlock
 * @param user cbit.vcell.server.User
 * @param simID java.lang.String
 */
public SimDataBlock getSimDataBlock(OutputContext outputContext, String varName, double time) throws DataAccessException, IOException {
    VCDataIdentifier vcDataID = getVCDataIdentifierFromDataId(varName);
    if (vcDataID == null) {
        return null;
    }
    DataSetIdentifier varDatasetID = getDataSetIdentifier(varName);
    int actualVarNameIndx = varName.indexOf(".");
    String actualVarName = varName.substring(actualVarNameIndx + 1);
    SimDataBlock simDataBlk = null;
    // 
    if (vcDataID.getID().equals(datasetsIDList[0].getID())) {
        simDataBlk = getDatasetControllerImpl().getSimDataBlock(outputContext, vcDataID, actualVarName, time);
        return simDataBlk;
    } else {
        // TIME INTERPOLATION of datablock
        double[] timeArray = getDatasetControllerImpl().getDataSetTimes(vcDataID);
        boolean bTimesEqual = checkTimeArrays(timeArray);
        double[] timeResampledData = null;
        int timeArrayCounter = 0;
        long lastModified = Long.MIN_VALUE;
        if (bTimesEqual) {
            // If time arrays for both datasets are equal, no need to resample/interpolate in time, just obtain the datablock
            simDataBlk = getDatasetControllerImpl().getSimDataBlock(outputContext, vcDataID, actualVarName, time);
            timeResampledData = simDataBlk.getData();
        } else {
            while ((timeArrayCounter < timeArray.length - 2) && (time > timeArray[timeArrayCounter + 1])) {
                timeArrayCounter++;
            }
            SimDataBlock simDataBlock_1 = getDatasetControllerImpl().getSimDataBlock(outputContext, vcDataID, actualVarName, timeArray[timeArrayCounter]);
            double[] data_1 = simDataBlock_1.getData();
            if ((timeArrayCounter + 1) < (timeArray.length - 1)) {
                SimDataBlock simDataBlock_2 = getDatasetControllerImpl().getSimDataBlock(outputContext, vcDataID, actualVarName, timeArray[timeArrayCounter + 1]);
                lastModified = simDataBlock_2.getPDEDataInfo().getTimeStamp();
                double[] data_2 = simDataBlock_2.getData();
                timeResampledData = new double[data_1.length];
                // 
                for (int m = 0; m < data_1.length; m++) {
                    timeResampledData[m] = data_1[m] + (data_2[m] - data_1[m]) * (time - timeArray[timeArrayCounter]) / (timeArray[timeArrayCounter + 1] - timeArray[timeArrayCounter]);
                }
            } else {
                // past end of array, zero order interpolation
                lastModified = simDataBlock_1.getPDEDataInfo().getTimeStamp();
                timeResampledData = data_1;
            }
        }
        // SPATIAL INTERPOLATION
        CartesianMesh refMesh = null;
        CartesianMesh mesh = null;
        try {
            refMesh = getDatasetControllerImpl().getMesh(datasetsIDList[0]);
            mesh = getDatasetControllerImpl().getMesh(vcDataID);
        } catch (MathException e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Could not get Mesh for reference or given dataID");
        }
        double[] spaceResampledData = null;
        // Check origin and extent of reference and given dataset. If they don't match, cannot resample spatially
        if (!mesh.getExtent().compareEqual(refMesh.getExtent()) || !mesh.getOrigin().compareEqual(refMesh.getOrigin())) {
            throw new RuntimeException("Different origins and/or extents for the 2 geometries. Cannot compare the 2 simulations");
        }
        // Get dimension of geometry for reference and given datasets (using mesh variables!) to use appropriate
        // resampling algorithm. Check if mesh sizes for the 2 datasets are equal, then there is no need to
        // spatially resample the second dataset.
        int dimension = mesh.getGeometryDimension();
        int refDimension = refMesh.getGeometryDimension();
        if (mesh.getSizeX() != refMesh.getSizeX() || mesh.getSizeY() != refMesh.getSizeY() || mesh.getSizeZ() != refMesh.getSizeZ()) {
            if (varDatasetID.getVariableType().equals(VariableType.VOLUME)) {
                if (dimension == 1 && refDimension == 1) {
                    spaceResampledData = MathTestingUtilities.resample1DSpatial(timeResampledData, mesh, refMesh);
                } else if (dimension == 2 && refDimension == 2) {
                    spaceResampledData = MathTestingUtilities.resample2DSpatial(timeResampledData, mesh, refMesh);
                } else if (dimension == 3 && refDimension == 3) {
                    spaceResampledData = MathTestingUtilities.resample3DSpatial(timeResampledData, mesh, refMesh);
                } else {
                    throw new RuntimeException("Comparison of 2 simulations with different geometry dimensions are not handled at this time!");
                }
            } else {
                throw new RuntimeException("spatial resampling for variable type: " + varDatasetID.getVariableType().getTypeName() + " not supported");
            }
        } else {
            // 
            if (varDatasetID.getVariableType().equals(VariableType.MEMBRANE)) {
                // 
                if (membraneIndexMapping == null) {
                    membraneIndexMapping = mesh.getMembraneIndexMapping(refMesh);
                }
                spaceResampledData = new double[timeResampledData.length];
                for (int i = 0; i < timeResampledData.length; i++) {
                    spaceResampledData[i] = timeResampledData[membraneIndexMapping[i]];
                }
            } else {
                // 
                // no reordering needed for other variable types.
                // 
                spaceResampledData = timeResampledData;
            }
        }
        if (simDataBlk != null) {
            lastModified = simDataBlk.getPDEDataInfo().getTimeStamp();
        }
        PDEDataInfo pdeDataInfo = new PDEDataInfo(vcDataID.getOwner(), vcDataID.getID(), varName, time, lastModified);
        if (spaceResampledData != null) {
            return new SimDataBlock(pdeDataInfo, spaceResampledData, varDatasetID.getVariableType());
        } else {
            return null;
        }
    }
}

Example 68 with MathException

use of cbit.vcell.math.MathException 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 69 with MathException

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

the class DefaultODESolver method integrate.

/**
 * This method was created by a SmartGuide.
 */
protected void integrate() throws SolverException, UserStopException, IOException {
    try {
        SolverTaskDescription taskDescription = simTask.getSimulation().getSolverTaskDescription();
        double timeStep = taskDescription.getTimeStep().getDefaultTimeStep();
        fieldCurrentTime = taskDescription.getTimeBounds().getStartingTime();
        // before computation begins, settle fast equilibrium
        if (getFastAlgebraicSystem() != null) {
            fieldValueVectors.copyValues(0, 1);
            getFastAlgebraicSystem().initVars(getValueVector(0), getValueVector(1));
            getFastAlgebraicSystem().solveSystem(getValueVector(0), getValueVector(1));
            fieldValueVectors.copyValues(1, 0);
        }
        // check for failure
        check(getValueVector(0));
        updateResultSet();
        // 
        int iteration = 0;
        while (fieldCurrentTime < taskDescription.getTimeBounds().getEndingTime()) {
            checkForUserStop();
            step(fieldCurrentTime, timeStep);
            // update (old = new)
            fieldValueVectors.copyValuesDown();
            // compute fast system
            if (getFastAlgebraicSystem() != null) {
                fieldValueVectors.copyValues(0, 1);
                getFastAlgebraicSystem().initVars(getValueVector(0), getValueVector(1));
                getFastAlgebraicSystem().solveSystem(getValueVector(0), getValueVector(1));
                fieldValueVectors.copyValues(1, 0);
            }
            // check for failure
            check(getValueVector(0));
            // fieldCurrentTime += timeStep;
            iteration++;
            fieldCurrentTime = taskDescription.getTimeBounds().getStartingTime() + iteration * timeStep;
            // Print results if it coincides with a save interval...
            if (taskDescription.getOutputTimeSpec().isDefault()) {
                int keepEvery = ((DefaultOutputTimeSpec) taskDescription.getOutputTimeSpec()).getKeepEvery();
                if ((iteration % keepEvery) == 0) {
                    updateResultSet();
                }
            }
        }
        // store last time point
        if (taskDescription.getOutputTimeSpec().isDefault()) {
            int keepEvery = ((DefaultOutputTimeSpec) taskDescription.getOutputTimeSpec()).getKeepEvery();
            if ((iteration % keepEvery) != 0)
                updateResultSet();
        }
    } catch (ExpressionException | MathException e) {
        throw new SolverException("Solver failed: " + e.getMessage(), e);
    }
}

Example 70 with MathException

use of cbit.vcell.math.MathException 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);
    }
}