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

Example 46 with Variable

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

the class Jacobian 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 variableList = new Vector();
    enum1 = mathDesc.getVariables();
    while (enum1.hasMoreElements()) {
        Variable var = (Variable) enum1.nextElement();
        if (var instanceof VolVariable) {
            variableList.addElement(var);
        }
    }
    if (equationList.size() != variableList.size()) {
        throw new MathException("there are " + equationList.size() + " equations and " + variableList.size() + " variables");
    }
    numVariables = variableList.size();
    rates = new Expression[numVariables];
    vars = new VolVariable[numVariables];
    for (int i = 0; i < numVariables; i++) {
        OdeEquation odeEqu = (OdeEquation) equationList.elementAt(i);
        rates[i] = odeEqu.getRateExpression();
        vars[i] = (VolVariable) odeEqu.getVariable();
    }
}

Example 47 with Variable

use of cbit.vcell.math.Variable 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 48 with Variable

use of cbit.vcell.math.Variable 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 49 with Variable

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

the class OdeFileWriter method createStateVariables.

private void createStateVariables() throws Exception {
    Simulation simulation = simTask.getSimulation();
    MathDescription mathDescription = simulation.getMathDescription();
    SolverTaskDescription solverTaskDescription = simulation.getSolverTaskDescription();
    // get Ode's from MathDescription and create ODEStateVariables
    Enumeration<Equation> enum1 = mathDescription.getSubDomains().nextElement().getEquations();
    SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
    while (enum1.hasMoreElements()) {
        Equation equation = enum1.nextElement();
        if (equation instanceof OdeEquation) {
            fieldStateVariables.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>();
    Constant sensitivityParameter = solverTaskDescription.getSensitivityParameter();
    if (sensitivityParameter != null) {
        Constant origSensParam = sensitivityParameter;
        Constant overriddenSensParam = (Constant) simSymbolTable.getVariable(origSensParam.getName());
        for (int i = 0; i < variables.length; i++) {
            if (variables[i] instanceof VolVariable) {
                VolVariable volVariable = (VolVariable) variables[i];
                SensVariable sv = new SensVariable(volVariable, overriddenSensParam);
                sensVariables.addElement(sv);
            }
        }
    }
    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 < sensVariables.size(); v++) {
        fieldStateVariables.addElement(new SensStateVariable(sensVariables.elementAt(v), rateSensitivity, jacobian, sensVariables, simSymbolTable));
    }
}

Example 50 with Variable

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

the class MovingBoundaryFileWriter method flattenExpression.

private Expression flattenExpression(Expression ex, VariableDomain varDomain) throws ExpressionException, MathException {
    SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
    Variable normalX = new Variable("normalX", null) {

        public boolean compareEqual(Matchable object, boolean bIgnoreMissingDomains) {
            return false;
        }

        public String getVCML() throws MathException {
            return null;
        }
    };
    Variable normalY = new Variable("normalY", null) {

        public boolean compareEqual(Matchable object, boolean bIgnoreMissingDomains) {
            return false;
        }

        public String getVCML() throws MathException {
            return null;
        }
    };
    SymbolTable augmentedSymbolTable = new SymbolTable() {

        @Override
        public SymbolTableEntry getEntry(String identifierString) {
            if (identifierString.equals(normalX.getName())) {
                return normalX;
            }
            if (identifierString.equals(normalY.getName())) {
                return normalY;
            }
            return simSymbolTable.getEntry(identifierString);
        }

        @Override
        public void getEntries(Map<String, SymbolTableEntry> entryMap) {
            simSymbolTable.getEntries(entryMap);
            entryMap.put(normalX.getName(), normalX);
            entryMap.put(normalY.getName(), normalY);
        }
    };
    ex = new Expression(ex);
    ex.bindExpression(augmentedSymbolTable);
    Expression flattended = MathUtilities.substituteFunctions(ex, augmentedSymbolTable).flatten();
    Expression substituted = SolverUtilities.substituteSizeAndNormalFunctions(flattended, varDomain).flatten();
    return substituted;
// return simSymbolTable.substituteFunctions(ex).flatten().infix();
}