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

Example 6 with PseudoConstant

use of cbit.vcell.math.PseudoConstant 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 7 with PseudoConstant

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

the class FastAlgebraicSystem method initVars.

/**
 * initVars method comment.
 */
public void initVars(double[] oldValues, double[] newValues) throws ExpressionException, MathException {
    // 
    // calculate C's for invariants
    // 
    Enumeration<PseudoConstant> enum_pc = fs_analyzer.getPseudoConstants();
    while (enum_pc.hasMoreElements()) {
        PseudoConstant pc = enum_pc.nextElement();
        int index = pc.getIndex();
        oldValues[index] = pc.getPseudoExpression().evaluateVector(oldValues);
        newValues[index] = oldValues[index];
    }
}