Examples with NonspatialStochHybridOptions cbit.vcell.solver.NonspatialStochHybridOptions used on opensource projects

Example 1 with NonspatialStochHybridOptions

use of cbit.vcell.solver.NonspatialStochHybridOptions in project vcell by virtualcell.

the class XmlReader method getStochHybridOptions.

/**
 * This method returns a TimeStep object from a XML Element.
 * Creation date: (5/22/2001 11:45:33 AM)
 * @return cbit.vcell.solver.TimeStep
 * @param param org.jdom.Element
 */
private NonspatialStochHybridOptions getStochHybridOptions(Element param) {
    // StochHybridOptions are immutable, so we grab the default values from the default constructor - and read the options which are stored in XML
    NonspatialStochHybridOptions defaultStochHybridOptions = new NonspatialStochHybridOptions();
    double epsilon = defaultStochHybridOptions.getEpsilon();
    double lambda = defaultStochHybridOptions.getLambda();
    double MSRTolerance = defaultStochHybridOptions.getMSRTolerance();
    double SDETDolerance = defaultStochHybridOptions.getSDETolerance();
    if (param.getAttributeValue(XMLTags.HybridEpsilonAttrTag) != null) {
        epsilon = Double.parseDouble(param.getAttributeValue(XMLTags.HybridEpsilonAttrTag));
    }
    if (param.getAttributeValue(XMLTags.HybridLambdaAttrTag) != null) {
        lambda = Double.parseDouble(param.getAttributeValue(XMLTags.HybridLambdaAttrTag));
    }
    if (param.getAttributeValue(XMLTags.HybridMSRToleranceAttrTag) != null) {
        MSRTolerance = Double.parseDouble(param.getAttributeValue(XMLTags.HybridMSRToleranceAttrTag));
    }
    if (param.getAttributeValue(XMLTags.HybridSDEToleranceAttrTag) != null) {
        SDETDolerance = Double.parseDouble(param.getAttributeValue(XMLTags.HybridSDEToleranceAttrTag));
    }
    // **** create a new StochHybridOptions object and return ****
    return new NonspatialStochHybridOptions(epsilon, lambda, MSRTolerance, SDETDolerance);
}

Example 2 with NonspatialStochHybridOptions

use of cbit.vcell.solver.NonspatialStochHybridOptions in project vcell by virtualcell.

the class StochSimOptionsPanel method setNewOptions.

/**
 * Update parameters for stochastic simulations,
 * including using customized seed or not, customized seed, using tractory or histogram, number of trials (for all, and below four paras for hybrid only)
 * Epsilon : minimum number of molecus required for approximation as a continuous Markow process,
 * Lambda : minimum rate of reaction required for approximation to a continuous Markov process,
 * MSR Tolerance : Maximum allowed effect of slow reactions per numerical integration of the SDEs,
 * SDE Tolerance : Maximum allowed value of the drift and diffusion errors
 */
private void setNewOptions() {
    if (!isVisible()) {
        return;
    }
    try {
        NonspatialStochSimOptions stochOpt = getSolverTaskDescription().getStochOpt();
        long numTrials = 1;
        if (getHistogramButton().isSelected()) {
            numTrials = Integer.parseInt(getJTextFieldNumOfTrials().getText());
        }
        boolean bUseCustomSeed = getCustomizedSeedRadioButton().isSelected();
        int customSeed = stochOpt.getCustomSeed();
        if (bUseCustomSeed) {
            customSeed = (Integer.parseInt(getJTextFieldCustomSeed().getText()));
        }
        getSolverTaskDescription().setStochOpt(new NonspatialStochSimOptions(bUseCustomSeed, customSeed, numTrials));
        if (!getSolverTaskDescription().getSolverDescription().equals(SolverDescription.StochGibson)) {
            NonspatialStochHybridOptions stochHybridOpt = getSolverTaskDescription().getStochHybridOpt();
            double epsilon = stochHybridOpt.getEpsilon();
            if (getEpsilonTextField().isEnabled() && getEpsilonTextField().getText().length() > 0) {
                epsilon = Double.parseDouble(getEpsilonTextField().getText());
            }
            double lambda = stochHybridOpt.getLambda();
            if (getLambdaTextField().isEnabled() && getLambdaTextField().getText().length() > 0) {
                lambda = Double.parseDouble(getLambdaTextField().getText());
            }
            double MSRTolerance = stochHybridOpt.getMSRTolerance();
            if (getMSRToleranceTextField().isEnabled() && getMSRToleranceTextField().getText().length() > 0) {
                MSRTolerance = Double.parseDouble(getMSRToleranceTextField().getText());
            }
            double SDETolerance = stochHybridOpt.getSDETolerance();
            if (getSDEToleranceTextField().isEnabled() && getSDEToleranceTextField().getText().length() > 0) {
                SDETolerance = Double.parseDouble(getSDEToleranceTextField().getText());
            }
            getSolverTaskDescription().setStochHybridOpt(new NonspatialStochHybridOptions(epsilon, lambda, MSRTolerance, SDETolerance));
        }
    } catch (Exception e) {
        PopupGenerator.showErrorDialog(this, e.getMessage(), e);
    }
}

Example 3 with NonspatialStochHybridOptions

use of cbit.vcell.solver.NonspatialStochHybridOptions in project vcell by virtualcell.

the class StochSimOptionsPanel method refresh.

private void refresh() {
    if (getSolverTaskDescription() != null) {
        if (!getSolverTaskDescription().getSolverDescription().isNonSpatialStochasticSolver()) {
            setVisible(false);
            return;
        }
    }
    setVisible(true);
    NonspatialStochSimOptions sso = getSolverTaskDescription().getStochOpt();
    long numTrials = sso.getNumOfTrials();
    if (numTrials == 1) {
        // 1 trial
        getJTextFieldNumOfTrials().setEnabled(false);
        getTrajectoryButton().setSelected(true);
    } else {
        // more than 1 trial
        getJTextFieldNumOfTrials().setEnabled(true);
        getHistogramButton().setSelected(true);
        getJTextFieldNumOfTrials().setText(numTrials + "");
    }
    boolean isUseCustomSeed = sso.isUseCustomSeed();
    int customSeed = sso.getCustomSeed();
    getJTextFieldCustomSeed().setEnabled(isUseCustomSeed);
    if (isUseCustomSeed) {
        getCustomizedSeedRadioButton().setSelected(true);
        getJTextFieldCustomSeed().setEnabled(true);
    } else {
        getRandomSeedRadioButton().setSelected(true);
        getJTextFieldCustomSeed().setEnabled(false);
    }
    getJTextFieldCustomSeed().setText(customSeed + "");
    NonspatialStochHybridOptions hybridOptions = getSolverTaskDescription().getStochHybridOpt();
    boolean bHybrid = hybridOptions != null;
    getEpsilonLabel().setEnabled(bHybrid);
    getEpsilonTextField().setEnabled(bHybrid);
    getLambdaLabel().setEnabled(bHybrid);
    getLambdaTextField().setEnabled(bHybrid);
    getMSRToleranceLabel().setEnabled(bHybrid);
    getMSRToleranceTextField().setEnabled(bHybrid);
    getSDEToleranceLabel().setEnabled(bHybrid);
    getSDEToleranceTextField().setEnabled(bHybrid);
    if (bHybrid) {
        getEpsilonTextField().setText(hybridOptions.getEpsilon() + "");
        getLambdaTextField().setText(hybridOptions.getLambda() + "");
        getMSRToleranceTextField().setText(hybridOptions.getMSRTolerance() + "");
        getSDEToleranceTextField().setText(hybridOptions.getSDETolerance() + "");
        if (!getSolverTaskDescription().getSolverDescription().equals(SolverDescription.HybridMilAdaptive)) {
            getSDEToleranceTextField().setEnabled(false);
        }
    }
}

Example 4 with NonspatialStochHybridOptions

use of cbit.vcell.solver.NonspatialStochHybridOptions in project vcell by virtualcell.

the class HybridSolver method getMathExecutableCommand.

@Override
protected String[] getMathExecutableCommand() {
    String randomNumber = "";
    // if one of the following paras is applied, all the paras in front of it must be set.
    String epsilon = " 100";
    String lambda = " 10";
    String MSR_Tolerance = " 0.01";
    String SDE_Tolerance = " 1e-4";
    String SDE_dt = " 0.1";
    String paraString = "";
    SolverTaskDescription solverTaskDescription = simTask.getSimulation().getSolverTaskDescription();
    NonspatialStochSimOptions stochOpts = solverTaskDescription.getStochOpt();
    NonspatialStochHybridOptions hybridOpts = solverTaskDescription.getStochHybridOpt();
    if (hybridOpts == null) {
        throw new RuntimeException("expecting StochHybridOptions for solver type " + solverTaskDescription.getSolverDescription().getDisplayLabel());
    }
    epsilon = " " + String.valueOf(hybridOpts.getEpsilon());
    lambda = " " + String.valueOf(hybridOpts.getLambda());
    MSR_Tolerance = " " + String.valueOf(hybridOpts.getMSRTolerance());
    if (solverTaskDescription.getSolverDescription().equals(SolverDescription.HybridMilAdaptive))
        SDE_Tolerance = " " + String.valueOf(hybridOpts.getSDETolerance());
    else
        SDE_Tolerance = "";
    SDE_dt = " " + String.valueOf(solverTaskDescription.getTimeStep().getDefaultTimeStep());
    paraString = epsilon + lambda + MSR_Tolerance + SDE_Tolerance + SDE_dt;
    if (stochOpts.isUseCustomSeed())
        randomNumber = " -R " + String.valueOf(stochOpts.getCustomSeed());
    SolverDescription solverDescription = null;
    if (getIntegratorType() == HybridSolver.EMIntegrator) {
        solverDescription = SolverDescription.HybridEuler;
    } else if (getIntegratorType() == HybridSolver.MilsteinIntegrator) {
        solverDescription = SolverDescription.HybridMilstein;
    } else {
        solverDescription = SolverDescription.HybridMilAdaptive;
    }
    String executableName;
    try {
        executableName = SolverUtilities.getExes(SolverDescription.HybridEuler)[0].getAbsolutePath();
    } catch (IOException e) {
        throw new RuntimeException("failed to get executable for solver " + solverDescription.getDisplayLabel() + ": " + e.getMessage(), e);
    }
    ArrayList<String> commandList = new ArrayList<String>();
    commandList.add(executableName);
    commandList.add(getInputFilename());
    String argumentString = paraString.toLowerCase() + randomNumber + " -OV";
    StringTokenizer st = new StringTokenizer(argumentString);
    while (st.hasMoreTokens()) {
        commandList.add(st.nextToken());
    }
    return commandList.toArray(new String[0]);
}