Examples with ExpressionException cbit.vcell.parser.ExpressionException used on opensource projects

Example 66 with ExpressionException

use of cbit.vcell.parser.ExpressionException in project vcell by virtualcell.

the class SimulationSymbolTable method createAnnotatedFunctionsList.

public Vector<AnnotatedFunction> createAnnotatedFunctionsList(MathDescription mathDescription) throws InconsistentDomainException {
    // Get the list of (volVariables) in the simulation. Needed to determine 'type' of  functions
    boolean bSpatial = getSimulation().isSpatial();
    String[] variableNames = null;
    VariableType[] variableTypes = null;
    if (bSpatial) {
        Variable[] allVariables = getVariables();
        Vector<Variable> varVector = new Vector<Variable>();
        for (int i = 0; i < allVariables.length; i++) {
            if ((allVariables[i] instanceof VolVariable) || (allVariables[i] instanceof VolumeRegionVariable) || (allVariables[i] instanceof MemVariable) || (allVariables[i] instanceof MembraneRegionVariable) || (allVariables[i] instanceof FilamentVariable) || (allVariables[i] instanceof FilamentRegionVariable) || (allVariables[i] instanceof PointVariable) || (allVariables[i] instanceof ParticleVariable) || (allVariables[i] instanceof InsideVariable) || (allVariables[i] instanceof OutsideVariable)) {
                varVector.addElement(allVariables[i]);
            } else if (allVariables[i] instanceof Constant || (allVariables[i] instanceof Function)) {
            } else {
                System.err.println("SimulationSymbolTable.createAnnotatedFunctionsList() found unexpected variable type " + allVariables[i].getClass().getSimpleName() + " in spatial simulation");
            }
        }
        variableNames = new String[varVector.size()];
        for (int i = 0; i < variableNames.length; i++) {
            variableNames[i] = varVector.get(i).getName();
        }
        // Lookup table for variableType for each variable in 'variables' array.
        variableTypes = new VariableType[variableNames.length];
        for (int i = 0; i < variableNames.length; i++) {
            variableTypes[i] = VariableType.getVariableType(varVector.get(i));
        }
    }
    // 
    // Bind and substitute functions to simulation before storing them in the '.functions' file
    // 
    Function[] functions = getFunctions();
    Vector<AnnotatedFunction> annotatedFunctionVector = new Vector<AnnotatedFunction>();
    for (int i = 0; i < functions.length; i++) {
        if (isFunctionSaved(functions[i])) {
            String errString = "";
            VariableType funcType = null;
            try {
                Expression substitutedExp = substituteFunctions(functions[i].getExpression());
                substitutedExp.bindExpression(this);
                functions[i].setExpression(substitutedExp.flatten());
            } catch (MathException e) {
                e.printStackTrace(System.out);
                errString = errString + ", " + e.getMessage();
            // throw new RuntimeException(e.getMessage());
            } catch (ExpressionException e) {
                e.printStackTrace(System.out);
                errString = errString + ", " + e.getMessage();
            // throw new RuntimeException(e.getMessage());
            }
            // 
            // get function's data type from the types of it's identifiers
            // 
            funcType = bSpatial ? getFunctionVariableType(functions[i], mathDescription, variableNames, variableTypes, bSpatial) : VariableType.NONSPATIAL;
            AnnotatedFunction annotatedFunc = new AnnotatedFunction(functions[i].getName(), functions[i].getExpression(), functions[i].getDomain(), errString, funcType, FunctionCategory.PREDEFINED);
            annotatedFunctionVector.addElement(annotatedFunc);
        }
    }
    return annotatedFunctionVector;
}

Example 67 with ExpressionException

use of cbit.vcell.parser.ExpressionException 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 68 with ExpressionException

use of cbit.vcell.parser.ExpressionException in project vcell by virtualcell.

the class AdamsMoultonFiveSolver method step.

/**
 * Integrate over time step using the forward Euler method (1st order explicit)
 * results must be stored in NumVectors-1 = vector(4);
 *  t is the current time
 *  h is the time step
 */
protected void step(double t, double h) throws SolverException {
    try {
        double[] oldValues = getValueVector(0);
        double[] newValues = getValueVector(1);
        // 
        // update time
        oldValues[getTimeIndex()] = t;
        newValues[getTimeIndex()] = t + h;
        // Predict
        for (int i = 0; i < getStateVariableCount(); i++) {
            int I = getVariableIndex(i);
            newValues[I] = oldValues[I] + h * (55.0 * f[3][I] - 59.0 * f[2][I] + 37.0 * f[1][I] - 9.0 * f[0][I]) / 24.0;
        }
        // Evaluate
        for (int i = 0; i < getStateVariableCount(); i++) {
            f[4][getVariableIndex(i)] = evaluate(newValues, i);
        }
        // Correct
        for (int i = 0; i < getStateVariableCount(); i++) {
            int I = getVariableIndex(i);
            newValues[I] = oldValues[I] + h * (9.0 * f[4][I] + 19.0 * f[3][I] - 5.0 * f[2][I] + 1.0 * f[1][I]) / 24.0;
        }
    } catch (ExpressionException expressionException) {
        throw new SolverException(expressionException.getMessage());
    }
}

Example 69 with ExpressionException

use of cbit.vcell.parser.ExpressionException in project vcell by virtualcell.

the class DefaultODESolver method initialize.

/**
 * This method was created by a SmartGuide.
 * @exception SolverException The exception description.
 */
protected void initialize() throws SolverException {
    SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
    Simulation sim = simSymbolTable.getSimulation();
    try {
        // create a fast system if necessary
        fieldFastAlgebraicSystem = null;
        if (getSubDomain().getFastSystem() != null) {
            fieldFastAlgebraicSystem = new FastAlgebraicSystem(new FastSystemAnalyzer(getSubDomain().getFastSystem(), simSymbolTable));
        }
        // refreshIdentifiers();
        fieldIdentifiers = createIdentifiers();
        fieldSensVariables = createSensitivityVariables();
        // refreshStateVariables();
        fieldStateVariables = createStateVariables();
        // 
        // allocate ValueVectors object
        fieldValueVectors = new ValueVectors(getValueVectorCount(), fieldIdentifiers.size());
        // initialize indexes of variables
        fieldVariableIndexes = new int[getStateVariableCount()];
        for (int i = 0; i < getStateVariableCount(); i++) {
            fieldVariableIndexes[i] = getStateVariable(i).getVariable().getIndex();
        }
        // initialize constants
        double[] initialValues = getValueVector(0);
        for (int i = 0; i < fieldIdentifiers.size(); i++) {
            if (fieldIdentifiers.elementAt(i) instanceof Constant) {
                Constant constant = (Constant) fieldIdentifiers.elementAt(i);
                constant.bind(simSymbolTable);
                if (constant.isConstant()) {
                    // constant.getValue();
                    initialValues[constant.getIndex()] = constant.getExpression().evaluateConstant();
                } else {
                    throw new SolverException("cannot evaluate constant '" + constant.getName() + "' = " + constant.getExpression());
                }
            }
        }
        // initialize variables
        for (int i = 0; i < getStateVariableCount(); i++) {
            initialValues[getVariableIndex(i)] = getStateVariable(i).evaluateIC(initialValues);
        }
        fieldODESolverResultSet = createODESolverResultSet();
        // reset - in the ** default ** solvers we don't pick up from where we left off, we can override that behaviour in integrate() if ever necessary
        fieldCurrentTime = sim.getSolverTaskDescription().getTimeBounds().getStartingTime();
    } catch (ExpressionException expressionException) {
        expressionException.printStackTrace(System.out);
        throw new SolverException(expressionException.getMessage());
    } catch (MathException mathException) {
        mathException.printStackTrace(System.out);
        throw new SolverException(mathException.getMessage());
    }
}

Example 70 with ExpressionException

use of cbit.vcell.parser.ExpressionException 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;
}