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

Example 96 with Variable

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

the class SimulationSymbolTable method getVariables.

/**
 * Insert the method's description here.
 * Creation date: (5/25/01 11:34:08 AM)
 * @return cbit.vcell.math.Variable[]
 */
public Variable[] getVariables() {
    Vector<Variable> varList = new Vector<Variable>();
    // 
    // get all variables from MathDescription, but replace MathOverrides
    // 
    Enumeration<Variable> enum1 = simulation.getMathDescription().getVariables();
    while (enum1.hasMoreElements()) {
        Variable mathDescriptionVar = enum1.nextElement();
        // 
        if (mathDescriptionVar instanceof Constant) {
            try {
                Constant overriddenConstant = getLocalConstant((Constant) mathDescriptionVar);
                varList.addElement(overriddenConstant);
            } catch (ExpressionException e) {
                e.printStackTrace(System.out);
                throw new RuntimeException("local Constant " + mathDescriptionVar.getName() + " not found for Simulation");
            }
        // 
        // replace all Functions with local Functions that are bound to this Simulation
        // 
        } else if (mathDescriptionVar instanceof Function) {
            try {
                Function overriddenFunction = getLocalFunction((Function) mathDescriptionVar);
                varList.addElement(overriddenFunction);
            } catch (ExpressionException e) {
                e.printStackTrace(System.out);
                throw new RuntimeException("local Function " + mathDescriptionVar.getName() + " not found for Simulation");
            }
        // 
        // pass all other Variables through
        // 
        } else {
            varList.addElement(mathDescriptionVar);
        }
    }
    Variable[] variables = (Variable[]) BeanUtils.getArray(varList, Variable.class);
    return variables;
}

Example 97 with Variable

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

the class SimulationSymbolTable method applyOverrides.

public void applyOverrides(MathDescription newMath) throws ExpressionException, MappingException, MathException {
    // 
    // replace original constants with "Simulation" constants
    // 
    Variable[] newVarArray = (Variable[]) BeanUtils.getArray(newMath.getVariables(), Variable.class);
    for (int i = 0; i < newVarArray.length; i++) {
        if (newVarArray[i] instanceof Constant) {
            Constant origConstant = (Constant) newVarArray[i];
            Constant simConstant = getLocalConstant(origConstant);
            newVarArray[i] = new Constant(origConstant.getName(), new Expression(simConstant.getExpression()));
        }
    }
    newMath.setAllVariables(newVarArray);
}

Example 98 with Variable

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

the class DefaultODESolver method createIdentifiers.

/**
 * This method was created in VisualAge.
 */
private Vector<Variable> createIdentifiers() throws MathException, ExpressionException {
    SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
    // create list of possible identifiers (including reserved x,y,z,t)
    Vector<Variable> identifiers = new Vector<Variable>();
    // add reserved variables x,y,z,t
    identifiers.addElement(ReservedVariable.TIME);
    identifiers.addElement(ReservedVariable.X);
    identifiers.addElement(ReservedVariable.Y);
    identifiers.addElement(ReservedVariable.Z);
    // add regular variables
    Variable[] variables = simSymbolTable.getVariables();
    for (int i = 0; i < variables.length; i++) {
        if (variables[i] instanceof VolVariable) {
            identifiers.addElement(variables[i]);
        }
    }
    // Add sensitivity variables (for sensitivity equations)...
    fieldSensVariables = 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());
                identifiers.addElement(sv);
            }
        }
    }
    // Add pseudoConstants for fast system (if necessary)...
    if (getFastAlgebraicSystem() != null) {
        Enumeration<PseudoConstant> enum1 = fieldFastAlgebraicSystem.getPseudoConstants();
        while (enum1.hasMoreElements()) {
            identifiers.addElement(enum1.nextElement());
        }
    }
    // Assign indices...
    for (int i = 0; i < identifiers.size(); i++) {
        Variable variable = (Variable) identifiers.elementAt(i);
        variable.setIndex(i);
    }
    return (identifiers);
}

Example 99 with Variable

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

Example 100 with Variable

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

the class SundialsSolver method createFunctionList.

public Vector<AnnotatedFunction> createFunctionList() {
    // 
    // add appropriate Function columns to result set
    // 
    Vector<AnnotatedFunction> funcList = super.createFunctionList();
    SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
    if (getSensitivityParameter() != null) {
        try {
            AnnotatedFunction saf = new AnnotatedFunction(getSensitivityParameter().getName(), new Expression(getSensitivityParameter().getConstantValue()), getSensitivityParameter().getDomain(), "", VariableType.NONSPATIAL, FunctionCategory.PREDEFINED);
            if (!funcList.contains(saf)) {
                funcList.add(saf);
            }
            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) {
                        AnnotatedFunction af = new AnnotatedFunction(depSensFnName, depSensFnExpr.flatten(), variables[i].getDomain(), "", VariableType.NONSPATIAL, FunctionCategory.PREDEFINED);
                        funcList.add(af);
                    }
                }
            }
        } 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 funcList;
}