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

Example 36 with MathException

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

the class SundialsSolver method createStateVariables.

/*
	This method was created in Visual Age
*/
private StateVariable[] createStateVariables() throws MathException, ExpressionException {
    Vector<StateVariable> stateVariables = new Vector<StateVariable>();
    // get Ode's from MathDescription and create ODEStateVariables
    SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
    MathDescription mathDescription = simSymbolTable.getSimulation().getMathDescription();
    Enumeration<Equation> enum1 = ((SubDomain) mathDescription.getSubDomains().nextElement()).getEquations();
    while (enum1.hasMoreElements()) {
        Equation equation = (Equation) enum1.nextElement();
        if (equation instanceof OdeEquation) {
            stateVariables.addElement(new ODEStateVariable((OdeEquation) equation, simSymbolTable));
        } else {
            throw new MathException("encountered non-ode equation, unsupported");
        }
    }
    // Get sensitivity variables
    Variable[] variables = simSymbolTable.getVariables();
    Vector<SensVariable> sensVariables = new Vector<SensVariable>();
    if (getSensitivityParameter() != null) {
        for (int i = 0; i < variables.length; i++) {
            if (variables[i] instanceof VolVariable) {
                VolVariable volVariable = (VolVariable) variables[i];
                SensVariable sv = new SensVariable(volVariable, getSensitivityParameter());
                sensVariables.addElement(sv);
            }
        }
    }
    if (rateSensitivity == null) {
        rateSensitivity = new RateSensitivity(mathDescription, mathDescription.getSubDomains().nextElement());
    }
    if (jacobian == null) {
        jacobian = new Jacobian(mathDescription, mathDescription.getSubDomains().nextElement());
    }
    for (int v = 0; v < sensVariables.size(); v++) {
        stateVariables.addElement(new SensStateVariable((SensVariable) sensVariables.elementAt(v), rateSensitivity, jacobian, sensVariables, simSymbolTable));
    }
    if (stateVariables.size() == 0) {
        throw new MathException("there are no equations defined");
    }
    StateVariable[] stateVars = (StateVariable[]) BeanUtils.getArray(stateVariables, StateVariable.class);
    return (stateVars);
}

Example 37 with MathException

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

the class SundialsSolver method getODESolverResultSet.

/**
 * This method was created in VisualAge.
 * @return double[]
 * @param vectorIndex int
 */
public ODESolverResultSet getODESolverResultSet() {
    // 
    // read .ida file
    // 
    ODESolverResultSet odeSolverResultSet = getStateVariableResultSet();
    if (odeSolverResultSet == null) {
        return null;
    }
    // 
    // add appropriate Function columns to result set
    // 
    SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
    Function[] functions = simSymbolTable.getFunctions();
    for (int i = 0; i < functions.length; i++) {
        if (SimulationSymbolTable.isFunctionSaved(functions[i])) {
            Expression exp1 = new Expression(functions[i].getExpression());
            try {
                exp1 = simSymbolTable.substituteFunctions(exp1);
            } catch (MathException e) {
                e.printStackTrace(System.out);
                throw new RuntimeException("Substitute function failed on function " + functions[i].getName() + " " + e.getMessage());
            } catch (ExpressionException e) {
                e.printStackTrace(System.out);
                throw new RuntimeException("Substitute function failed on function " + functions[i].getName() + " " + e.getMessage());
            }
            try {
                FunctionColumnDescription cd = new FunctionColumnDescription(exp1.flatten(), functions[i].getName(), null, functions[i].getName(), false);
                odeSolverResultSet.addFunctionColumn(cd);
            } catch (ExpressionException e) {
                e.printStackTrace(System.out);
            }
        }
    }
    if (getSensitivityParameter() != null) {
        try {
            if (odeSolverResultSet.findColumn(getSensitivityParameter().getName()) == -1) {
                FunctionColumnDescription fcd = new FunctionColumnDescription(new Expression(getSensitivityParameter().getConstantValue()), getSensitivityParameter().getName(), null, getSensitivityParameter().getName(), false);
                odeSolverResultSet.addFunctionColumn(fcd);
            }
            Variable[] variables = simSymbolTable.getVariables();
            StateVariable[] stateVars = createStateVariables();
            for (int i = 0; i < variables.length; i++) {
                if (variables[i] instanceof Function && SimulationSymbolTable.isFunctionSaved((Function) variables[i])) {
                    Function depSensFunction = (Function) variables[i];
                    Expression depSensFnExpr = new Expression(depSensFunction.getExpression());
                    depSensFnExpr = simSymbolTable.substituteFunctions(depSensFnExpr);
                    depSensFnExpr = getFunctionSensitivity(depSensFnExpr, getSensitivityParameter(), stateVars);
                    // depSensFnExpr = depSensFnExpr.flatten(); 	// already bound and flattened in getFunctionSensitivity, no need here.....
                    String depSensFnName = new String("sens_" + depSensFunction.getName() + "_wrt_" + getSensitivityParameter().getName());
                    if (depSensFunction != null) {
                        FunctionColumnDescription cd = new FunctionColumnDescription(depSensFnExpr.flatten(), depSensFnName, getSensitivityParameter().getName(), depSensFnName, false);
                        odeSolverResultSet.addFunctionColumn(cd);
                    }
                }
            }
        } catch (MathException e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Error adding function to resultSet: " + e.getMessage());
        } catch (ExpressionException e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Error adding function to resultSet: " + e.getMessage());
        }
    }
    return odeSolverResultSet;
}

Example 38 with MathException

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

the class CVodeFileWriter method writeEquations.

/**
 * Insert the method's description here.
 * Creation date: (3/8/00 10:31:52 PM)
 */
protected String writeEquations(HashMap<Discontinuity, String> discontinuityNameMap) throws MathException, ExpressionException {
    StringBuffer sb = new StringBuffer();
    for (int i = 0; i < getStateVariableCount(); i++) {
        StateVariable stateVar = getStateVariable(i);
        Expression rateExpr = new Expression(stateVar.getRateExpression());
        Expression initExpr = new Expression(stateVar.getInitialRateExpression());
        initExpr = MathUtilities.substituteFunctions(initExpr, varsSymbolTable).flatten();
        initExpr.substituteInPlace(new Expression("t"), new Expression(0.0));
        String[] symbols0 = initExpr.getSymbols();
        if (symbols0 != null) {
            for (String symbol : symbols0) {
                SymbolTableEntry ste = initExpr.getSymbolBinding(symbol);
                if (!ste.equals(ReservedVariable.X) && !ste.equals(ReservedVariable.Y) && !ste.equals(ReservedVariable.Z)) {
                    throw new MathException("Variables are not allowed in initial condition.\nInitial condition of variable:" + stateVar.getVariable().getName() + " has variable(" + symbol + ") in expression.");
                }
            }
        }
        rateExpr = MathUtilities.substituteFunctions(rateExpr, varsSymbolTable).flatten();
        Vector<Discontinuity> v = rateExpr.getDiscontinuities();
        for (Discontinuity od : v) {
            od = getSubsitutedAndFlattened(od, varsSymbolTable);
            String dname = discontinuityNameMap.get(od);
            if (dname == null) {
                dname = ROOT_VARIABLE_PREFIX + discontinuityNameMap.size();
                discontinuityNameMap.put(od, dname);
            }
            rateExpr.substituteInPlace(od.getDiscontinuityExp(), new Expression("(" + dname + "==1)"));
        }
        sb.append("ODE " + stateVar.getVariable().getName() + " INIT " + initExpr.flatten().infix() + ";\n\t RATE " + rateExpr.flatten().infix() + ";\n");
    }
    return sb.toString();
}

Example 39 with MathException

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

the class AdamsMoultonFiveSolver method integrate.

/**
 * This method was created by a SmartGuide.
 *  THIS HAS NOT BEEN UPDATED LIKE ODEIntegrator.integrate () and
 *  RungeKuttaFehlbergIntegrator.integrate()...
 */
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));
        // Evaluate
        for (int i = 0; i < getStateVariableCount(); i++) {
            f[0][getVariableIndex(i)] = evaluate(getValueVector(0), i);
        }
        // check for failure
        check(getValueVector(0));
        updateResultSet();
        // 
        int iteration = 0;
        while (fieldCurrentTime < taskDescription.getTimeBounds().getEndingTime()) {
            checkForUserStop();
            if (iteration < 3) {
                // Take Runge-Kutta step...
                prep(fieldCurrentTime, timeStep);
            } else {
                // Take Adams-Moulton step...
                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));
            if (iteration < 3) {
                for (int i = 0; i < getStateVariableCount(); i++) {
                    f[iteration + 1][getVariableIndex(i)] = evaluate(getValueVector(0), i);
                }
                // check for failure
                check(f[iteration + 1]);
            } else {
                // Evaluate
                for (int i = 0; i < getStateVariableCount(); i++) {
                    f[4][getVariableIndex(i)] = evaluate(getValueVector(0), i);
                }
                // check for failure
                check(f[4]);
                shiftWorkArrays();
            }
            // fieldCurrentTime += timeStep;
            iteration++;
            fieldCurrentTime = taskDescription.getTimeBounds().getStartingTime() + iteration * timeStep;
            // store 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 expressionException) {
        throw new SolverException(expressionException.getMessage());
    } catch (MathException mathException) {
        throw new SolverException(mathException.getMessage());
    }
}

Example 40 with MathException

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

the class XmlReader method getVarIniCount.

/**
 * This method return a VarIniCondition object from a XML element.
 * Creation date: (7/24/2006 5:26:05 PM)
 * @return cbit.vcell.math.VarIniCondition
 * @param param org.jdom.Element
 * @exception cbit.vcell.xml.XmlParseException The exception description.
 */
private VarIniCondition getVarIniCount(Element param, MathDescription md) throws XmlParseException, MathException, ExpressionException {
    // retrieve values
    Expression exp = unMangleExpression(param.getText());
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    Variable var = md.getVariable(name);
    if (var == null) {
        throw new MathFormatException("variable " + name + " not defined");
    }
    if (!(var instanceof StochVolVariable)) {
        throw new MathFormatException("variable " + name + " not a Stochastic Volume Variable");
    }
    try {
        VarIniCondition varIni = new VarIniCount(var, exp);
        return varIni;
    } catch (Exception e) {
        e.printStackTrace();
    }
    return null;
}