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

Example 1 with NonspatialStochSimOptions

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

the class SimulationSummaryPanel method displayTask.

/**
 * Comment
 */
private void displayTask() {
    SolverTaskDescription solverTaskDescription = getSimulation().getSolverTaskDescription();
    try {
        NonspatialStochSimOptions stochOpt = solverTaskDescription.getStochOpt();
        if (stochOpt != null && stochOpt.getNumOfTrials() > 1) {
            if (stochOpt.isHistogram()) {
                getJLabelOutput().setText("Histogram with " + stochOpt.getNumOfTrials() + " Trials(@last time point)");
            } else {
                getJLabelOutput().setText("Average of " + stochOpt.getNumOfTrials() + " trajectories; " + solverTaskDescription.getOutputTimeSpec().getDescription());
            }
        } else {
            // gcwtodo
            String text = solverTaskDescription.getOutputTimeSpec().getShortDescription();
            if (solverTaskDescription.getSolverDescription().isChomboSolver()) {
                text = "Variable";
                if (solverTaskDescription.getChomboSolverSpec().getTimeIntervalList().size() == 1) {
                    text = "Every " + solverTaskDescription.getChomboSolverSpec().getLastTimeInterval().getOutputTimeStep() + "s";
                }
            } else if (solverTaskDescription.getOutputTimeSpec().isDefault() && !solverTaskDescription.getSolverDescription().isSemiImplicitPdeSolver() && !solverTaskDescription.getSolverDescription().equals(SolverDescription.StochGibson)) {
                text += ", at most " + ((DefaultOutputTimeSpec) solverTaskDescription.getOutputTimeSpec()).getKeepAtMost();
            }
            getJLabelOutput().setText(text);
        }
    } catch (Exception exc) {
        exc.printStackTrace(System.out);
        getJLabelOutput().setText("");
    }
    SolverDescription solverDescription = solverTaskDescription.getSolverDescription();
    try {
        ErrorTolerance errorTolerance = solverTaskDescription.getErrorTolerance();
        TimeStep timeStep = solverTaskDescription.getTimeStep();
        getJLabelRelTol().setText("Rel tol");
        getJLabelAbsTol().setText("Abs tol");
        getJLabel12().setText("Timestep");
        getJLabelRelTol().setEnabled(false);
        getJLabelAbsTol().setEnabled(false);
        getJLabel12().setEnabled(false);
        getJLabel10().setText("Sensitivity Analysis");
        getJLabel10().setEnabled(true);
        if (solverDescription.equals(SolverDescription.StochGibson)) {
            getJLabel12().setEnabled(false);
            getJLabelTimestep().setText("");
        } else if (solverDescription.equals(SolverDescription.NFSim)) {
            TimeBounds tb = solverTaskDescription.getTimeBounds();
            double dtime = tb.getEndingTime() - tb.getStartingTime();
            if (solverTaskDescription.getOutputTimeSpec() instanceof UniformOutputTimeSpec) {
                UniformOutputTimeSpec uots = (UniformOutputTimeSpec) solverTaskDescription.getOutputTimeSpec();
                double interval = uots.getOutputTimeStep();
                int steps = (int) Math.round(dtime / interval);
                getJLabel12().setEnabled(true);
                getJLabel12().setText("Timepoints");
                getJLabelTimestep().setText(steps + "");
            } else if (solverTaskDescription.getOutputTimeSpec() instanceof DefaultOutputTimeSpec) {
                DefaultOutputTimeSpec uots = (DefaultOutputTimeSpec) solverTaskDescription.getOutputTimeSpec();
                getJLabel12().setEnabled(true);
                getJLabel12().setText("End Time");
                getJLabelTimestep().setText(solverTaskDescription.getTimeBounds().getEndingTime() + "");
            } else {
                getJLabel12().setEnabled(false);
                getJLabel12().setText("End Time");
                getJLabelTimestep().setText("na");
            }
            NFsimSimulationOptions nfsso = solverTaskDescription.getNFSimSimulationOptions();
            String utl = "default";
            Integer moleculeDistance = nfsso.getMoleculeDistance();
            if (moleculeDistance != null) {
                utl = moleculeDistance + "";
            }
            getJLabelRelTol().setEnabled(true);
            getJLabelRelTol().setText("Universal Transversal Limit");
            getJLabelRelTolValue().setText(utl);
            String gml = "default";
            Integer maxMoleculesPerType = nfsso.getMaxMoleculesPerType();
            if (maxMoleculesPerType != null) {
                gml = maxMoleculesPerType + "";
            }
            getJLabelAbsTol().setEnabled(true);
            getJLabelAbsTol().setText("Max # of each " + MolecularType.typeName);
            getJLabelAbsTolValue().setText(gml);
        } else if (solverDescription.isNonSpatialStochasticSolver()) {
            getJLabel12().setEnabled(true);
            getJLabel12().setText("Timestep");
            getJLabelTimestep().setText(timeStep.getDefaultTimeStep() + "s");
        } else if (solverDescription.hasVariableTimestep()) {
            getJLabel12().setEnabled(true);
            getJLabel12().setText("Max timestep");
            getJLabelTimestep().setText(timeStep.getMaximumTimeStep() + "s");
            getJLabelRelTol().setEnabled(true);
            getJLabelRelTolValue().setText("" + errorTolerance.getRelativeErrorTolerance());
            getJLabelAbsTol().setEnabled(true);
            getJLabelAbsTolValue().setText("" + errorTolerance.getAbsoluteErrorTolerance());
        } else {
            getJLabel12().setEnabled(true);
            getJLabel12().setText("Timestep");
            if (solverDescription.isChomboSolver()) {
                String text = "Variable";
                if (solverTaskDescription.getChomboSolverSpec().getTimeIntervalList().size() == 1) {
                    text = solverTaskDescription.getChomboSolverSpec().getLastTimeInterval().getTimeStep() + "s";
                }
                getJLabelTimestep().setText(text);
            } else {
                getJLabelTimestep().setText(timeStep.getDefaultTimeStep() + "s");
            }
            if (solverDescription.isSemiImplicitPdeSolver()) {
                getJLabelRelTol().setEnabled(true);
                getJLabelRelTolValue().setText("" + errorTolerance.getRelativeErrorTolerance());
            } else {
                getJLabelRelTol().setEnabled(false);
                getJLabelRelTolValue().setText("");
            }
            getJLabelAbsTol().setEnabled(false);
            getJLabelAbsTolValue().setText("");
        }
    } catch (Exception exc) {
        exc.printStackTrace(System.out);
        getJLabelTimestep().setText("");
        getJLabelRelTolValue().setText("");
        getJLabelAbsTolValue().setText("");
    }
    try {
        boolean bChomboSolver = solverDescription.isChomboSolver();
        getJLabelTitleNumProcessors().setVisible(bChomboSolver);
        getJLabelNumProcessors().setVisible(bChomboSolver);
        if (bChomboSolver) {
            getJLabelNumProcessors().setText(String.valueOf(solverTaskDescription.getNumProcessors()));
        }
        if (getSimulation().isSpatial() || solverDescription.isNonSpatialStochasticSolver()) {
            getJLabelSensitivity().setVisible(false);
            getJLabel10().setVisible(false);
        } else if (solverDescription.equals(SolverDescription.NFSim)) {
            getJLabel10().setText("On-the-fly observ comp.");
            NFsimSimulationOptions nfsso = solverTaskDescription.getNFSimSimulationOptions();
            boolean goc = nfsso.getObservableComputationOff();
            getJLabelSensitivity().setText(goc + "");
        } else {
            getJLabelSensitivity().setVisible(true);
            getJLabel10().setVisible(true);
            Constant param = solverTaskDescription.getSensitivityParameter();
            if (param == null) {
                getJLabelSensitivity().setText("no");
            } else {
                getJLabelSensitivity().setText(param.getName());
            }
        }
    } catch (Exception exc) {
        exc.printStackTrace(System.out);
        getJLabelSensitivity().setText("");
    }
    if (solverDescription.isNonSpatialStochasticSolver()) {
        getJLabelRelTol().setVisible(false);
        getJLabelAbsTol().setVisible(false);
        getJLabelRelTolValue().setVisible(false);
        getJLabelAbsTolValue().setVisible(false);
    } else {
        getJLabelRelTol().setVisible(true);
        getJLabelAbsTol().setVisible(true);
    }
}

Example 2 with NonspatialStochSimOptions

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

the class StochSimOptionsPanel method refresh.

// deals with the visual elements when some selection changes (enable / disable other fields, for example)
private void refresh() {
    if (getSolverTaskDescription() != null) {
        if (!getSolverTaskDescription().getSolverDescription().isNonSpatialStochasticSolver()) {
            setVisible(false);
            return;
        }
    }
    setVisible(true);
    NonspatialStochSimOptions sso = getSolverTaskDescription().getStochOpt();
    long numTrials = sso.getNumOfTrials();
    boolean bHistogram = sso.isHistogram();
    if (numTrials == 1) {
        // 1 trial
        getJTextFieldNumOfTrials().setEnabled(false);
        // getMultiRunButton().setEnabled(false);
        getTrajectoryButton().setSelected(true);
    } else {
        // more than 1 trial
        getJTextFieldNumOfTrials().setEnabled(true);
        // getMultiRunButton().setEnabled(true);
        getJTextFieldNumOfTrials().setText(numTrials + "");
        if (bHistogram) {
            getHistogramButton().setSelected(true);
        } else {
            getMultiRunButton().setSelected(true);
        }
    }
    getMultiRunButton().setEnabled(true);
    getMultiRunButton().setSelected(getMultiRunButton().isSelected() && getSolverTaskDescription().getSolverDescription().equals(SolverDescription.StochGibson));
    getMultiRunButton().setEnabled(getSolverTaskDescription().getSolverDescription().equals(SolverDescription.StochGibson));
    // TODO: temporarily disable the button
    // UNDO THIS WHEN DEVELOPMENT IS COMPLETE
    // getMultiRunButton().setEnabled(false);
    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 3 with NonspatialStochSimOptions

use of cbit.vcell.solver.NonspatialStochSimOptions 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() || getMultiRunButton().isSelected()) {
            numTrials = Integer.parseInt(getJTextFieldNumOfTrials().getText());
        }
        boolean bHistogram = getHistogramButton().isSelected();
        boolean bUseCustomSeed = getCustomizedSeedRadioButton().isSelected();
        int customSeed = stochOpt.getCustomSeed();
        if (bUseCustomSeed) {
            customSeed = (Integer.parseInt(getJTextFieldCustomSeed().getText()));
        }
        NonspatialStochSimOptions nssso = new NonspatialStochSimOptions(bUseCustomSeed, customSeed, numTrials, bHistogram);
        getSolverTaskDescription().setStochOpt(nssso);
        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());
            }
            NonspatialStochHybridOptions nssho = new NonspatialStochHybridOptions(epsilon, lambda, MSRTolerance, SDETolerance);
            getSolverTaskDescription().setStochHybridOpt(nssho);
        }
    } catch (Exception e) {
        PopupGenerator.showErrorDialog(this, e.getMessage(), e);
    }
}

Example 4 with NonspatialStochSimOptions

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

the class StochFileWriter method write.

/**
 * Write the model to a text file which serves as an input for Stochastic simulation engine.
 * Creation date: (6/22/2006 5:37:26 PM)
 */
public void write(String[] parameterNames) throws Exception, ExpressionException {
    Simulation simulation = simTask.getSimulation();
    SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
    initialize();
    if (bUseMessaging) {
        writeJMSParamters();
    }
    // Write control information
    printWriter.println("<control>");
    cbit.vcell.solver.SolverTaskDescription solverTaskDescription = simulation.getSolverTaskDescription();
    cbit.vcell.solver.TimeBounds timeBounds = solverTaskDescription.getTimeBounds();
    cbit.vcell.solver.OutputTimeSpec outputTimeSpec = solverTaskDescription.getOutputTimeSpec();
    ErrorTolerance errorTolerance = solverTaskDescription.getErrorTolerance();
    NonspatialStochSimOptions stochOpt = solverTaskDescription.getStochOpt();
    printWriter.println("STARTING_TIME" + "\t" + timeBounds.getStartingTime());
    printWriter.println("ENDING_TIME " + "\t" + timeBounds.getEndingTime());
    // pw.println("MAX_ITERATION"+"\t"+outputTimeSpec.getKeepAtMost());
    printWriter.println("TOLERANCE " + "\t" + errorTolerance.getAbsoluteErrorTolerance());
    if (outputTimeSpec.isDefault()) {
        printWriter.println("SAMPLE_INTERVAL" + "\t" + ((DefaultOutputTimeSpec) outputTimeSpec).getKeepEvery());
        printWriter.println("MAX_SAVE_POINTS" + "\t" + ((DefaultOutputTimeSpec) outputTimeSpec).getKeepAtMost());
    } else if (outputTimeSpec.isUniform()) {
        printWriter.println("SAVE_PERIOD" + "\t" + ((UniformOutputTimeSpec) outputTimeSpec).getOutputTimeStep());
        // need to overwrite limit hardcoded in C++
        double savePoints = (timeBounds.getEndingTime() - timeBounds.getStartingTime()) / ((UniformOutputTimeSpec) outputTimeSpec).getOutputTimeStep();
        printWriter.println("MAX_SAVE_POINTS" + "\t" + (Math.ceil(savePoints) + 1));
    }
    // boolean isMultiTrial = !solverTaskDescription.getStochOpt().isHistogram() &&
    // solverTaskDescription.getStochOpt().getNumOfTrials() > 1;
    // //Multi-trial 'NUM_TRIAL' handled by slurm array within .slurm.sh script
    // printWriter.println("NUM_TRIAL"+"\t"+(isMultiTrial?1:solverTaskDescription.getStochOpt().getNumOfTrials()));
    printWriter.println("NUM_TRIAL" + "\t" + solverTaskDescription.getStochOpt().getNumOfTrials());
    if (stochOpt.isUseCustomSeed()) {
        printWriter.println("SEED" + "\t" + stochOpt.getCustomSeed());
    } else {
        // we generate our own random seed
        RandomDataGenerator rdg = new RandomDataGenerator();
        int randomSeed = rdg.nextInt(1, Integer.MAX_VALUE);
        printWriter.println("SEED" + "\t" + randomSeed);
    }
    if (isMultiTrialNonHisto) {
        printWriter.println("BMULTIBUTNOTHISTO" + "\t" + "1");
    }
    printWriter.println("</control>");
    printWriter.println();
    // write model information
    // Model info. will be extracted from subDomain of mathDescription
    Enumeration<SubDomain> e = simulation.getMathDescription().getSubDomains();
    SubDomain subDomain = null;
    if (e.hasMoreElements()) {
        subDomain = e.nextElement();
    }
    if (subDomain != null) {
        printWriter.println("<model>");
        // variables
        printWriter.println("<discreteVariables>");
        // Species iniCondition (if in concentration) is sampled from a poisson distribution(which has a mean of the current iniExp value)
        // There is only one subDomain for compartmental model
        List<VarIniCondition> varInis = subDomain.getVarIniConditions();
        if ((varInis != null) && (varInis.size() > 0)) {
            RandomDataGenerator dist = new RandomDataGenerator();
            if (simulation.getSolverTaskDescription().getStochOpt().isUseCustomSeed()) {
                Integer randomSeed = simulation.getSolverTaskDescription().getStochOpt().getCustomSeed();
                if (randomSeed != null) {
                    dist.reSeed(randomSeed);
                }
            }
            printWriter.println("TotalVars" + "\t" + varInis.size());
            for (VarIniCondition varIniCondition : varInis) {
                try {
                    Expression iniExp = varIniCondition.getIniVal();
                    iniExp.bindExpression(simSymbolTable);
                    iniExp = simSymbolTable.substituteFunctions(iniExp).flatten();
                    double expectedCount = iniExp.evaluateConstant();
                    // 1000 mill
                    final Integer limit = 1000000000;
                    if (limit < expectedCount) {
                        String eMessage = "The Initial count for Species '" + varIniCondition.getVar().getName() + "' is " + BigDecimal.valueOf(expectedCount).toBigInteger() + "\n";
                        eMessage += "which is higher than the internal vCell limit of " + limit + ".\n";
                        eMessage += "Please reduce the Initial Condition value for this Species or reduce the compartment size.";
                        throw new MathFormatException(eMessage);
                    }
                    long varCount = 0;
                    if (varIniCondition instanceof VarIniCount) {
                        varCount = (long) Math.round(expectedCount);
                    } else {
                        if (expectedCount > 0) {
                            varCount = dist.nextPoisson(expectedCount);
                        }
                    }
                    // System.out.println("expectedCount: " + expectedCount + ", varCount: " + varCount);
                    printWriter.println(varIniCondition.getVar().getName() + "\t" + varCount);
                } catch (ExpressionException ex) {
                    ex.printStackTrace();
                    throw new MathFormatException("variable " + varIniCondition.getVar().getName() + "'s initial condition is required to be a constant.");
                }
            }
        } else
            printWriter.println("TotalVars" + "\t" + "0");
        printWriter.println("</discreteVariables>");
        printWriter.println();
        // jump processes
        printWriter.println("<jumpProcesses>");
        List<JumpProcess> jumpProcesses = subDomain.getJumpProcesses();
        if ((jumpProcesses != null) && (jumpProcesses.size() > 0)) {
            printWriter.println("TotalProcesses" + "\t" + jumpProcesses.size());
            for (int i = 0; i < jumpProcesses.size(); i++) {
                printWriter.println(jumpProcesses.get(i).getName());
            }
        } else
            printWriter.println("TotalProcesses" + "\t" + "0");
        printWriter.println("</jumpProcesses>");
        printWriter.println();
        // process description
        printWriter.println("<processDesc>");
        if ((jumpProcesses != null) && (jumpProcesses.size() > 0)) {
            printWriter.println("TotalDescriptions" + "\t" + jumpProcesses.size());
            for (int i = 0; i < jumpProcesses.size(); i++) {
                JumpProcess temProc = (JumpProcess) jumpProcesses.get(i);
                // jump process name
                printWriter.println("JumpProcess" + "\t" + temProc.getName());
                Expression probExp = temProc.getProbabilityRate();
                try {
                    probExp.bindExpression(simSymbolTable);
                    probExp = simSymbolTable.substituteFunctions(probExp).flatten();
                    if (!isValidProbabilityExpression(probExp)) {
                        throw new MathFormatException("probability rate in jump process " + temProc.getName() + " has illegal symbols(should only contain variable names).");
                    }
                } catch (cbit.vcell.parser.ExpressionException ex) {
                    ex.printStackTrace();
                    throw new cbit.vcell.parser.ExpressionException("Binding math description error in probability rate in jump process " + temProc.getName() + ". Some symbols can not be resolved.");
                }
                // Expression temp = replaceVarIniInProbability(probExp);
                // Propensity
                printWriter.println("\t" + "Propensity" + "\t" + probExp.infix());
                // effects
                printWriter.println("\t" + "Effect" + "\t" + temProc.getActions().size());
                for (int j = 0; j < temProc.getActions().size(); j++) {
                    printWriter.print("\t\t" + ((Action) temProc.getActions().get(j)).getVar().getName() + "\t" + ((Action) temProc.getActions().get(j)).getOperation());
                    printWriter.println("\t" + ((Action) temProc.getActions().get(j)).evaluateOperand());
                    printWriter.println();
                }
                // dependencies
                Vector<String> dependencies = getDependencies(temProc, jumpProcesses);
                if ((dependencies != null) && (dependencies.size() > 0)) {
                    printWriter.println("\t" + "DependentProcesses" + "\t" + dependencies.size());
                    for (int j = 0; j < dependencies.size(); j++) printWriter.println("\t\t" + dependencies.elementAt(j));
                } else
                    printWriter.println("\t" + "DependentProcesses" + "\t" + "0");
                printWriter.println();
            }
        } else
            printWriter.println("TotalDescriptions" + "\t" + "0");
        printWriter.println("</processDesc>");
        printWriter.println("</model>");
    }
// if (subDomain != null)
}

Example 5 with NonspatialStochSimOptions

use of cbit.vcell.solver.NonspatialStochSimOptions 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]);
}