Examples with ODESolverResultSet cbit.vcell.solver.ode.ODESolverResultSet used on opensource projects

Example 36 with ODESolverResultSet

use of cbit.vcell.solver.ode.ODESolverResultSet in project vcell by virtualcell.

the class AugmentedObjectiveFunction method f.

/**
 * f method comment.
 */
public double f(double[] x) {
    double penalty = 0.0;
    try {
        optSolverCallbacks.setPenaltyMu(new Double(mu));
        penalty = getPenalty(x);
        // }
        if (penalty > 1000) {
            System.out.println("aborting point, penalty = " + penalty);
            return penalty;
        }
        double objFunValue = fobj.f(x) / 1000.0;
        // 
        // send info on evaluation
        // 
        OptSolverCallbacks.EvaluationHolder evaluationHolder = new OptSolverCallbacks.EvaluationHolder((double[]) x.clone(), (penalty + objFunValue));
        ODESolverResultSet resultSet = null;
        optSolverCallbacks.addEvaluation(evaluationHolder, resultSet);
        return penalty + objFunValue;
    } catch (Exception e) {
        e.printStackTrace(System.out);
        System.out.println("penalty = " + penalty);
        if (penalty > 0) {
            System.out.println("too high ... aborting augmentedObjective function");
            return penalty + 1;
        } else {
            throw new cbit.vcell.opt.OptimizationException(e.getMessage(), x);
        }
    }
}

Example 37 with ODESolverResultSet

use of cbit.vcell.solver.ode.ODESolverResultSet in project vcell by virtualcell.

the class PowellOptimizationSolver method solve.

/**
 * Insert the method's description here.
 * Creation date: (3/5/00 11:15:15 PM)
 * @return double[]
 * @param optSpec cbit.vcell.opt.OptimizationSpec
 * @exception java.io.IOException The exception description.
 * @exception cbit.vcell.parser.ExpressionException The exception description.
 * @exception cbit.vcell.opt.OptimizationException The exception description.
 */
public OptimizationResultSet solve(OptimizationSpec os, OptimizationSolverSpec optSolverSpec, OptSolverCallbacks optSolverCallbacks) throws java.io.IOException, cbit.vcell.parser.ExpressionException, OptimizationException {
    final double power = 2.0;
    final double MU_START = 0.1;
    final double MU_END = 100000.0;
    final double MU_STEP = 10.0;
    AugmentedObjectiveFunction augmentedObjFunc = OptUtils.getAugmentedObjectiveFunction(os, power, MU_START, optSolverCallbacks);
    // 
    // initialize starting guess
    // 
    Parameter[] parameters = os.getParameters();
    double[] parameterValues = new double[parameters.length];
    for (int i = 0; i < parameters.length; i++) {
        parameterValues[i] = parameters[i].getInitialGuess();
        System.out.println("initial " + parameters[i].getName() + " = " + parameterValues[i]);
    }
    // 
    // get initial direction set
    // 
    double[][] xi = new double[parameterValues.length][parameterValues.length];
    for (int i = 0; i < parameterValues.length; i++) {
        for (int j = 0; j < parameterValues.length; j++) {
            xi[i][j] = (i == j ? 1.0 : 0.0);
        }
    }
    final double ftol = 1e-6;
    double fret = augmentedObjFunc.f(parameterValues);
    PowellSolver powellSolver = new PowellSolver();
    for (double mu = MU_START; mu <= MU_END; mu *= MU_STEP) {
        try {
            if (optSolverCallbacks.getStopRequested()) {
                break;
            }
            augmentedObjFunc.setMu(mu);
            fret = powellSolver.powell(parameterValues.length, parameterValues, xi, ftol, augmentedObjFunc);
            System.out.println("mu=" + mu + ", function value=" + fret);
            if (augmentedObjFunc.getPenalty(parameterValues) == 0.0) {
                break;
            }
        } catch (Exception ex) {
            ex.printStackTrace();
            break;
        }
    }
    OptimizationStatus optStatus = new OptimizationStatus(OptimizationStatus.NORMAL_TERMINATION, "Normal Termination");
    ODESolverResultSet odeSolverResultSet = null;
    if (optSolverCallbacks.getStopRequested()) {
        optStatus = new OptimizationStatus(OptimizationStatus.STOPPED_BY_USER, "Stopped by user");
    }
    parameterValues = optSolverCallbacks.getBestEvaluation().getParameterValues();
    fret = optSolverCallbacks.getBestEvaluation().getObjectiveFunctionValue();
    odeSolverResultSet = optSolverCallbacks.getBestResultSet();
    for (int i = 0; i < parameters.length; i++) {
        System.out.println("final " + parameters[i].getName() + " = " + parameterValues[i]);
    }
    OptRunResultSet bestResult = new OptRunResultSet(parameterValues, new Double(fret), optSolverCallbacks.getEvaluationCount(), optStatus);
    return new OptimizationResultSet(new OptSolverResultSet(os.getParameterNames(), bestResult), odeSolverResultSet);
}