Examples with MovingBoundarySolverOptions cbit.vcell.solvers.mb.MovingBoundarySolverOptions used on opensource projects

Example 1 with MovingBoundarySolverOptions

use of cbit.vcell.solvers.mb.MovingBoundarySolverOptions in project vcell by virtualcell.

the class XmlReader method getMovingBoundarySolverOptions.

private MovingBoundarySolverOptions getMovingBoundarySolverOptions(SolverTaskDescription solverTaskDesc, Element mbElement) {
    double frontToNodeRatio = parseDoubleWithDefault(mbElement, XMLTags.FrontToNodeRatioTag, MovingBoundarySolverOptions.DEFAULT_FRONT_TO_NODE_RATIO);
    int redistributionFrequency = parseIntWithDefault(mbElement, XMLTags.RedistributionFrequencyTag, MovingBoundarySolverOptions.DEFAULT_REDISTRIBUTION_FREQUENCY);
    RedistributionMode redistributionMode = RedistributionMode.FULL_REDIST;
    Element child = mbElement.getChild(XMLTags.RedistributionModeTag, vcNamespace);
    if (child != null) {
        String text = child.getText();
        redistributionMode = RedistributionMode.valueOf(text);
    }
    RedistributionVersion redistributionVersion = RedistributionVersion.EQUI_BOND_REDISTRIBUTE;
    child = mbElement.getChild(XMLTags.RedistributionVersionTag, vcNamespace);
    if (child != null) {
        String text = child.getText();
        redistributionVersion = RedistributionVersion.valueOf(text);
    }
    ExtrapolationMethod extrapolationMethod = ExtrapolationMethod.NEAREST_NEIGHBOR;
    child = mbElement.getChild(XMLTags.ExtrapolationMethodTag, vcNamespace);
    if (child != null) {
        String text = child.getText();
        extrapolationMethod = ExtrapolationMethod.valueOf(text);
    }
    MovingBoundarySolverOptions mb = new MovingBoundarySolverOptions(frontToNodeRatio, redistributionMode, redistributionVersion, redistributionFrequency, extrapolationMethod);
    return mb;
}

Example 2 with MovingBoundarySolverOptions

use of cbit.vcell.solvers.mb.MovingBoundarySolverOptions in project vcell by virtualcell.

the class Xmlproducer method getXML.

/**
 * This method returns a XML representation of a SolverTaskDescription object.
 * Creation date: (3/2/2001 10:59:55 PM)
 * @return Element
 * @param param cbit.vcell.solver.SolverTaskDescription
 */
private Element getXML(SolverTaskDescription param) {
    Element solvertask = new Element(XMLTags.SolverTaskDescriptionTag);
    // Add Attributes
    if (param.getTaskType() == SolverTaskDescription.TASK_UNSTEADY) {
        solvertask.setAttribute(XMLTags.TaskTypeTag, XMLTags.UnsteadyTag);
    } else if (param.getTaskType() == SolverTaskDescription.TASK_STEADY) {
        solvertask.setAttribute(XMLTags.TaskTypeTag, XMLTags.SteadyTag);
    } else {
        throw new IllegalArgumentException("Unexpected task type:" + param.getTaskType());
    }
    // solvertask.setAttribute(XMLTags.KeepEveryTag, String.valueOf(param.getKeepEvery()));
    // solvertask.setAttribute(XMLTags.KeepAtMostTag, String.valueOf(param.getKeepAtMost()));
    solvertask.setAttribute(XMLTags.UseSymbolicJacobianAttrTag, String.valueOf(param.getUseSymbolicJacobian()));
    // Add timeBounds
    solvertask.addContent(getXML(param.getTimeBounds()));
    // Add timeStep
    solvertask.addContent(getXML(param.getTimeStep()));
    // Add ErrorTolerence
    solvertask.addContent(getXML(param.getErrorTolerance()));
    // Jan 8, 2016 (jim) let getXML(stochOpt) write out the correct stochastic options
    if (param.getStochOpt() != null) {
        solvertask.addContent(getXML(param.getStochOpt(), param.getStochHybridOpt()));
    }
    // Add OutputOptions
    solvertask.addContent(getXML(param.getOutputTimeSpec()));
    // Add sensitivityParameter
    if (param.getSensitivityParameter() != null) {
        solvertask.addContent(getXML(param.getSensitivityParameter()));
    }
    // Add solver name
    solvertask.setAttribute(XMLTags.SolverNameTag, param.getSolverDescription().getDatabaseName());
    // Stop At Spatially Uniform
    ErrorTolerance stopAtSpatiallyUniformErrorTolerance = param.getStopAtSpatiallyUniformErrorTolerance();
    if (stopAtSpatiallyUniformErrorTolerance != null) {
        Element element = new Element(XMLTags.StopAtSpatiallyUniform);
        element.addContent(getXML(stopAtSpatiallyUniformErrorTolerance));
        solvertask.addContent(element);
    }
    boolean bRunParameterScanSerially = param.isSerialParameterScan();
    if (bRunParameterScanSerially) {
        solvertask.setAttribute(XMLTags.RunParameterScanSerially, String.valueOf(bRunParameterScanSerially));
    }
    SmoldynSimulationOptions smoldynSimulationOptions = param.getSmoldynSimulationOptions();
    if (smoldynSimulationOptions != null) {
        solvertask.addContent(getXML(smoldynSimulationOptions));
    }
    NFsimSimulationOptions nfsimSimulationOptions = param.getNFSimSimulationOptions();
    if (nfsimSimulationOptions != null) {
        solvertask.addContent(getXML(nfsimSimulationOptions));
    }
    SundialsPdeSolverOptions sundialsPdeSolverOptions = param.getSundialsPdeSolverOptions();
    if (sundialsPdeSolverOptions != null) {
        solvertask.addContent(getXML(sundialsPdeSolverOptions));
    }
    ChomboSolverSpec chomboSolverSpec = param.getChomboSolverSpec();
    if (chomboSolverSpec != null) {
        Element chomboElement = getXML(chomboSolverSpec);
        solvertask.addContent(chomboElement);
    }
    MovingBoundarySolverOptions mb = param.getMovingBoundarySolverOptions();
    if (mb != null) {
        Element e = getXML(mb);
        solvertask.addContent(e);
    }
    Element numProcessors = new Element(XMLTags.NUM_PROCESSORS);
    numProcessors.setText(Integer.toString(param.getNumProcessors()));
    solvertask.addContent(numProcessors);
    return solvertask;
}

Example 3 with MovingBoundarySolverOptions

use of cbit.vcell.solvers.mb.MovingBoundarySolverOptions in project vcell by virtualcell.

the class SolverTaskDescription method propertyChange.

/**
 * This method gets called when a bound property is changed.
 * @param evt A PropertyChangeEvent object describing the event source
 *   and the property that has changed.
 */
public void propertyChange(java.beans.PropertyChangeEvent evt) {
    try {
        if (evt.getSource() == this && (evt.getPropertyName().equals(PROPERTY_SOLVER_DESCRIPTION))) {
            SolverDescription solverDescription = getSolverDescription();
            if (solverDescription.equals(SolverDescription.SundialsPDE) || solverDescription.isSemiImplicitPdeSolver() || solverDescription.isGibsonSolver()) {
                TimeBounds timeBounds = getTimeBounds();
                if (!(getOutputTimeSpec() instanceof UniformOutputTimeSpec)) {
                    // set to uniform output if it is not.
                    double outputTime = (timeBounds.getEndingTime() - timeBounds.getStartingTime()) / 20;
                    setOutputTimeSpec(new UniformOutputTimeSpec(outputTime));
                }
                if (solverDescription.equals(SolverDescription.SundialsPDE)) {
                    setErrorTolerance(ErrorTolerance.getDefaultSundialsErrorTolerance());
                    setDefaultTimeStep(TimeStep.getDefaultSundialsTimeStep());
                    if (sundialsPdeSolverOptions == null) {
                        sundialsPdeSolverOptions = new SundialsPdeSolverOptions();
                    }
                } else {
                    sundialsPdeSolverOptions = null;
                    setErrorTolerance(ErrorTolerance.getDefaultSemiImplicitErrorTolerance());
                }
            } else if (!solverDescription.supports(getOutputTimeSpec())) {
                setOutputTimeSpec(solverDescription.createOutputTimeSpec(this));
            }
            if (solverDescription.isNonSpatialStochasticSolver()) {
                if (fieldNonspatialStochOpt == null) {
                    setStochOpt(new NonspatialStochSimOptions());
                } else {
                    setStochOpt(new NonspatialStochSimOptions(fieldNonspatialStochOpt));
                }
                if (!solverDescription.equals(SolverDescription.StochGibson)) {
                    if (fieldNonspatialStochHybridOpt == null) {
                        setStochHybridOpt(new NonspatialStochHybridOptions());
                    }
                }
            } else if (solverDescription.isSpatialStochasticSolver()) {
                setTimeStep(TimeStep.getDefaultSmoldynTimeStep());
                if (smoldynSimulationOptions == null) {
                    smoldynSimulationOptions = new SmoldynSimulationOptions();
                }
            // setSmoldynDefaultTimeStep();
            }
            if (solverDescription.isNFSimSolver()) {
                if (nfsimSimulationOptions == null) {
                    nfsimSimulationOptions = new NFsimSimulationOptions();
                }
            }
            if (solverDescription.isChomboSolver()) {
                if (chomboSolverSpec == null && getSimulation() != null) {
                    chomboSolverSpec = new ChomboSolverSpec(ChomboSolverSpec.getDefaultMaxBoxSize(getSimulation().getMathDescription().getGeometry().getDimension()));
                }
                if (getOutputTimeSpec() == null || !(getOutputTimeSpec() instanceof UniformOutputTimeSpec)) {
                    double outputTime = getTimeBounds().getEndingTime() / 10;
                    setOutputTimeSpec(new UniformOutputTimeSpec(outputTime));
                }
                if (chomboSolverSpec != null && chomboSolverSpec.getTimeIntervalList().size() == 0) {
                    chomboSolverSpec.addTimeInterval(TimeInterval.getDefaultTimeInterval());
                }
            } else {
                chomboSolverSpec = null;
            }
            if (solverDescription.isMovingBoundarySolver()) {
                if (movingBoundarySolverOptions == null && getSimulation() != null) {
                    movingBoundarySolverOptions = new MovingBoundarySolverOptions();
                }
            } else {
                movingBoundarySolverOptions = null;
            }
        }
    } catch (PropertyVetoException e) {
        e.printStackTrace();
    }
}

Example 4 with MovingBoundarySolverOptions

use of cbit.vcell.solvers.mb.MovingBoundarySolverOptions in project vcell by virtualcell.

the class XmlReader method getSolverTaskDescription.

/**
 * This method returns a SolverTaskDescription Object from a XML Element.
 * Creation date: (5/22/2001 10:51:23 AM)
 * @return cbit.vcell.solver.SolverTaskDescription
 * @param param org.jdom.Element
 * @param simulation cbit.vcell.solver.Simulation
 */
private SolverTaskDescription getSolverTaskDescription(Element param, Simulation simulation) throws XmlParseException {
    // *** create new SolverTaskDescription ***
    SolverTaskDescription solverTaskDesc = new SolverTaskDescription(simulation);
    // Added July 22nd, 2007, used as condition for stochSimOptions or stochHybridOprtions
    SolverDescription sd = null;
    // Retrieve attributes
    String taskType = param.getAttributeValue(XMLTags.TaskTypeTag);
    int keepEvery = -1;
    int keepAtMost = -1;
    if (param.getAttributeValue(XMLTags.KeepEveryTag) != null) {
        keepEvery = Integer.parseInt(param.getAttributeValue(XMLTags.KeepEveryTag));
        keepAtMost = Integer.parseInt(param.getAttributeValue(XMLTags.KeepAtMostTag));
    }
    boolean useSymJacob = new Boolean(param.getAttributeValue(XMLTags.UseSymbolicJacobianAttrTag)).booleanValue();
    String solverName = param.getAttributeValue(XMLTags.SolverNameTag);
    // get sentivity parameter
    Element sensparamElement = param.getChild(XMLTags.ConstantTag, vcNamespace);
    Constant sensitivityparam = null;
    if (sensparamElement != null) {
        sensitivityparam = getConstant(sensparamElement);
    }
    // set Attributes
    try {
        // set solver
        sd = SolverDescription.fromDatabaseName(solverName);
        if (sd == null) {
            System.err.println("====================================== couldn't find solver description name ==========================================");
        }
        solverTaskDesc.setSolverDescription(sd);
        if (taskType.equalsIgnoreCase(XMLTags.UnsteadyTag)) {
            solverTaskDesc.setTaskType(SolverTaskDescription.TASK_UNSTEADY);
        } else if (taskType.equalsIgnoreCase(XMLTags.SteadyTag)) {
            solverTaskDesc.setTaskType(SolverTaskDescription.TASK_STEADY);
        } else {
            throw new XmlParseException("Unexpected task type: " + taskType);
        }
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException("A PropertyVetoException was fired when setting the taskType: " + taskType, e);
    }
    int numProcessors = parseIntWithDefault(param, XMLTags.NUM_PROCESSORS, 1);
    try {
        solverTaskDesc.setNumProcessors(numProcessors);
        solverTaskDesc.setUseSymbolicJacobian(useSymJacob);
        // get TimeBound
        solverTaskDesc.setTimeBounds(getTimeBounds(param.getChild(XMLTags.TimeBoundTag, vcNamespace)));
        // get TimeStep
        solverTaskDesc.setTimeStep(getTimeStep(param.getChild(XMLTags.TimeStepTag, vcNamespace)));
        // get ErrorTolerance
        solverTaskDesc.setErrorTolerance(getErrorTolerance(param.getChild(XMLTags.ErrorToleranceTag, vcNamespace)));
        // get StochSimOptions
        if (simulation != null && simulation.getMathDescription() != null) {
            if (simulation.getMathDescription().isNonSpatialStoch() && param.getChild(XMLTags.StochSimOptionsTag, vcNamespace) != null) {
                // Amended July 22nd, 2007 to read either stochSimOptions or stochHybridOptions
                solverTaskDesc.setStochOpt(getStochSimOptions(param.getChild(XMLTags.StochSimOptionsTag, vcNamespace)));
                if (sd != null && !sd.equals(SolverDescription.StochGibson)) {
                    solverTaskDesc.setStochHybridOpt(getStochHybridOptions(param.getChild(XMLTags.StochSimOptionsTag, vcNamespace)));
                }
            }
        }
        // get OutputOptions
        if (keepEvery != -1) {
            solverTaskDesc.setOutputTimeSpec(new DefaultOutputTimeSpec(keepEvery, keepAtMost));
        }
        OutputTimeSpec ots = getOutputTimeSpec(param.getChild(XMLTags.OutputOptionsTag, vcNamespace));
        if (ots != null) {
            solverTaskDesc.setOutputTimeSpec(getOutputTimeSpec(param.getChild(XMLTags.OutputOptionsTag, vcNamespace)));
        }
        // set SensitivityParameter
        solverTaskDesc.setSensitivityParameter(sensitivityparam);
        // set StopAtSpatiallyUniform
        Element stopSpatiallyElement = param.getChild(XMLTags.StopAtSpatiallyUniform, vcNamespace);
        if (stopSpatiallyElement != null) {
            Element errTolElement = stopSpatiallyElement.getChild(XMLTags.ErrorToleranceTag, vcNamespace);
            if (errTolElement != null) {
                solverTaskDesc.setStopAtSpatiallyUniformErrorTolerance(getErrorTolerance(errTolElement));
            }
        }
        String runParameterScanSeriallyAttributeValue = param.getAttributeValue(XMLTags.RunParameterScanSerially);
        if (runParameterScanSeriallyAttributeValue != null) {
            solverTaskDesc.setSerialParameterScan(new Boolean(runParameterScanSeriallyAttributeValue).booleanValue());
        }
        Element nfsimSimulationOptionsElement = param.getChild(XMLTags.NFSimSimulationOptions, vcNamespace);
        if (nfsimSimulationOptionsElement != null) {
            NFsimSimulationOptions nfsimSimulationOptions = getNFSimSimulationOptions(nfsimSimulationOptionsElement);
            solverTaskDesc.setNFSimSimulationOptions(nfsimSimulationOptions);
        }
        Element smoldySimulationOptionsElement = param.getChild(XMLTags.SmoldynSimulationOptions, vcNamespace);
        if (smoldySimulationOptionsElement != null) {
            SmoldynSimulationOptions smoldynSimulationOptions = getSmoldySimulationOptions(smoldySimulationOptionsElement);
            solverTaskDesc.setSmoldynSimulationOptions(smoldynSimulationOptions);
        }
        Element sundialsPdeSolverOptionsElement = param.getChild(XMLTags.SundialsSolverOptions, vcNamespace);
        if (sundialsPdeSolverOptionsElement != null) {
            SundialsPdeSolverOptions sundialsPdeSolverOptions = getSundialsPdeSolverOptions(sundialsPdeSolverOptionsElement);
            solverTaskDesc.setSundialsPdeSolverOptions(sundialsPdeSolverOptions);
        }
        Element chomboElement = param.getChild(XMLTags.ChomboSolverSpec, vcNamespace);
        if (chomboElement != null) {
            ChomboSolverSpec chombo = getChomboSolverSpec(solverTaskDesc, chomboElement, simulation.getMathDescription().getGeometry().getDimension());
            solverTaskDesc.setChomboSolverSpec(chombo);
        }
        Element mbElement = param.getChild(XMLTags.MovingBoundarySolverOptionsTag, vcNamespace);
        if (mbElement != null) {
            MovingBoundarySolverOptions mb = getMovingBoundarySolverOptions(solverTaskDesc, mbElement);
            solverTaskDesc.setMovingBoundarySolverOptions(mb);
        }
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException(e);
    }
    return solverTaskDesc;
}

Example 5 with MovingBoundarySolverOptions

use of cbit.vcell.solvers.mb.MovingBoundarySolverOptions in project vcell by virtualcell.

the class SolverTaskDescription method readVCML.

// private void setSmoldynDefaultTimeStep() throws PropertyVetoException {
// if (fieldSimulation != null) {
// SmoldynTimeStepVars smoldynTimeStepVars = RunSims.computeMaxSmoldynTimeStep(fieldSimulation);
// double maxDt = smoldynTimeStepVars.getMaxDt();
// setTimeStep(new TimeStep(maxDt, maxDt, maxDt));
// }
// }
/**
 * Insert the method's description here.
 * Creation date: (10/24/00 3:45:12 PM)
 * @return java.lang.String
 */
public void readVCML(CommentStringTokenizer tokens) throws DataAccessException {
    // 
    // read format as follows: (OUT OF DATE)
    // 
    // SolverTaskDescription {
    // TaskType Unsteady
    // MaxTime 1
    // SolverDescription "Runga-Kutta Fehlberg"
    // UseSymbolicJacobian false
    // TimeBounds {
    // StartingTime	0.0
    // EndingTime		0.0
    // }
    // TimeStep {
    // DefaultTimeStep		0.0
    // MinimumTimeStep		0.0
    // MaximumTimeStep		0.0
    // }
    // ErrorTolerance {
    // AbsoluteErrorTolerance 1e-8
    // RelativeErrorTolerance 1e-4
    // }
    // StochSimOptions {
    // UseCustomSeed	false
    // CustomSeed	0
    // NumOfTrials	1
    // if Hybrid, we have following four more
    // Epsilon 100
    // Lambda 10
    // MSRTolerance 0.01
    // SDETolerance 1e-4
    // }
    // 
    // or
    // 
    // StochSimOptions {
    // UseCustomSeed	false
    // CustomSeed	0
    // NumOfTrials	1
    // }
    // StochHybridOptions {
    // Epsilon 100
    // Lambda 10
    // MSRTolerance 0.01
    // SDETolerance 1e-4
    // }
    // StopAtSpatiallyUniform {
    // AbsoluteErrorTolerance	1e-8
    // RelativeErrorTolerance 1e-4
    // }
    // KeepEvery 1
    // KeepAtMost	1000
    // OR
    // OutputOptions {
    // KeepEvery 1
    // KeepAtMost 1000
    // }
    // OR
    // OutputOptions {
    // OutputTimeStep 0.5
    // }
    // OR
    // OutputOptions {
    // OutputTimes 0.1,0.3,0.4,... (comma separated list, no spaces or linefeeds between numbers in list)
    // }
    // 
    // SensitivityParameter {
    // Constant k1 39.0;
    // }
    // RunParameterScanSerially false
    // }
    // 
    // 
    int keepEvery = -1;
    int keepAtMost = -1;
    SolverDescription sd = null;
    try {
        String token = tokens.nextToken();
        if (token.equalsIgnoreCase(VCML.SolverTaskDescription)) {
            token = tokens.nextToken();
            if (!token.equalsIgnoreCase(VCML.BeginBlock)) {
                throw new DataAccessException("unexpected token " + token + " expecting " + VCML.BeginBlock);
            }
        }
        while (tokens.hasMoreTokens()) {
            token = tokens.nextToken();
            lg.debug(token);
            if (token.equalsIgnoreCase(VCML.EndBlock)) {
                lg.debug("end block");
                break;
            }
            if (token.equalsIgnoreCase(VCML.TaskType)) {
                token = tokens.nextToken();
                if (token.equals(VCML.TaskType_Unsteady)) {
                    setTaskType(TASK_UNSTEADY);
                } else if (token.equals(VCML.TaskType_Steady)) {
                    setTaskType(TASK_STEADY);
                } else {
                    throw new DataAccessException("unexpected " + VCML.TaskType + " = " + token);
                }
                continue;
            }
            if (token.equalsIgnoreCase(VCML.SolverDescription)) {
                token = tokens.nextToken();
                // 
                try {
                    sd = SolverDescription.fromDatabaseName(token);
                    setSolverDescription(sd);
                } catch (java.beans.PropertyVetoException e) {
                    e.printStackTrace(System.out);
                }
                continue;
            }
            if (token.equalsIgnoreCase(VCML.UseSymbolicJacobian)) {
                token = tokens.nextToken();
                setUseSymbolicJacobian((new Boolean(token)).booleanValue());
                continue;
            }
            // code allows us to read the old format.
            if (token.equalsIgnoreCase(VCML.MaxTime)) {
                token = tokens.nextToken();
                // double dummyMaxTime = Double.parseDouble(token);
                continue;
            }
            if (token.equalsIgnoreCase(VCML.TimeBounds)) {
                getTimeBounds().readVCML(tokens);
                continue;
            }
            if (token.equalsIgnoreCase(VCML.TimeStep)) {
                getTimeStep().readVCML(tokens);
                continue;
            }
            if (token.equalsIgnoreCase(VCML.ErrorTolerance)) {
                getErrorTolerance().readVCML(tokens);
                continue;
            }
            if (token.equalsIgnoreCase(VCML.NFSimSimulationOptions)) {
                getNFSimSimulationOptions().readVCML(tokens);
                continue;
            }
            if (token.equalsIgnoreCase(VCML.StochSimOptions)) {
                boolean useCustomSeed = false;
                int customSeed = -1;
                long numOfTrials = 1;
                Double epsilon = null;
                Double lambda = null;
                Double MSRTolerance = null;
                Double SDETolerance = null;
                token = tokens.nextToken();
                if (!token.equalsIgnoreCase(VCML.BeginBlock)) {
                    throw new DataAccessException("unexpected token " + token + " expecting " + VCML.BeginBlock);
                }
                while (tokens.hasMoreTokens()) {
                    token = tokens.nextToken();
                    if (token.equalsIgnoreCase(VCML.EndBlock)) {
                        break;
                    }
                    if (token.equalsIgnoreCase(VCML.UseCustomSeed)) {
                        token = tokens.nextToken();
                        useCustomSeed = Boolean.parseBoolean(token);
                        continue;
                    }
                    if (token.equalsIgnoreCase(VCML.CustomSeed)) {
                        token = tokens.nextToken();
                        int val1 = Integer.parseInt(token);
                        if (val1 < 0) {
                            throw new DataAccessException("unexpected token " + token + ", seed is required to be an unsigned interger. ");
                        } else {
                            customSeed = val1;
                        }
                        continue;
                    }
                    if (token.equalsIgnoreCase(VCML.NumOfTrials)) {
                        token = tokens.nextToken();
                        int val2 = Integer.parseInt(token);
                        if (val2 < 1) {
                            throw new DataAccessException("unexpected token " + token + ", num of trials is requied to be at least 1. ");
                        } else {
                            numOfTrials = val2;
                        }
                        continue;
                    }
                    // 
                    if (token.equalsIgnoreCase(VCML.Epsilon)) {
                        token = tokens.nextToken();
                        double val3 = Double.parseDouble(token);
                        if (val3 < 1)
                            throw new DataAccessException("unexpected token " + token + ", Minimum number of molecue is requied to be greater than or equal to 1. ");
                        else
                            epsilon = val3;
                        continue;
                    }
                    if (token.equalsIgnoreCase(VCML.Lambda)) {
                        token = tokens.nextToken();
                        double val4 = Double.parseDouble(token);
                        if (val4 <= 0)
                            throw new DataAccessException("unexpected token " + token + ", num of trials is requied to be greater than 0. ");
                        else
                            lambda = val4;
                        continue;
                    }
                    if (token.equalsIgnoreCase(VCML.MSRTolerance)) {
                        token = tokens.nextToken();
                        double val5 = Double.parseDouble(token);
                        if (val5 <= 0)
                            throw new DataAccessException("unexpected token " + token + ", Maximum allowed effect of slow reactions is requied to be greater than 0. ");
                        else
                            MSRTolerance = val5;
                        continue;
                    }
                    if (token.equalsIgnoreCase(VCML.SDETolerance)) {
                        token = tokens.nextToken();
                        double val6 = Double.parseDouble(token);
                        if (val6 <= 0)
                            throw new DataAccessException("unexpected token " + token + ", SDE allowed value of drift and diffusion errors is requied to be greater than 0. ");
                        else
                            SDETolerance = val6;
                        continue;
                    }
                    throw new DataAccessException("unexpected identifier " + token);
                }
                if (getSimulation() != null && getSimulation().getMathDescription() != null) {
                    if (getSimulation().getMathDescription().isNonSpatialStoch()) {
                        setStochOpt(new NonspatialStochSimOptions(useCustomSeed, customSeed, numOfTrials));
                        if (epsilon != null && lambda != null && MSRTolerance != null && SDETolerance != null) {
                            setStochHybridOpt(new NonspatialStochHybridOptions(epsilon, lambda, MSRTolerance, SDETolerance));
                        }
                    } else {
                        setStochOpt(null);
                    }
                }
                continue;
            }
            if (token.equalsIgnoreCase(VCML.StochHybridOptions)) {
                Double epsilon = null;
                Double lambda = null;
                Double MSRTolerance = null;
                Double SDETolerance = null;
                token = tokens.nextToken();
                if (!token.equalsIgnoreCase(VCML.BeginBlock)) {
                    throw new DataAccessException("unexpected token " + token + " expecting " + VCML.BeginBlock);
                }
                while (tokens.hasMoreTokens()) {
                    token = tokens.nextToken();
                    if (token.equalsIgnoreCase(VCML.EndBlock)) {
                        break;
                    }
                    if (token.equalsIgnoreCase(VCML.Epsilon)) {
                        token = tokens.nextToken();
                        double val3 = Double.parseDouble(token);
                        if (val3 < 1)
                            throw new DataAccessException("unexpected token " + token + ", Minimum number of molecue is requied to be greater than or equal to 1. ");
                        else
                            epsilon = val3;
                        continue;
                    }
                    if (token.equalsIgnoreCase(VCML.Lambda)) {
                        token = tokens.nextToken();
                        double val4 = Double.parseDouble(token);
                        if (val4 <= 0)
                            throw new DataAccessException("unexpected token " + token + ", num of trials is requied to be greater than 0. ");
                        else
                            lambda = val4;
                        continue;
                    }
                    if (token.equalsIgnoreCase(VCML.MSRTolerance)) {
                        token = tokens.nextToken();
                        double val5 = Double.parseDouble(token);
                        if (val5 <= 0)
                            throw new DataAccessException("unexpected token " + token + ", Maximum allowed effect of slow reactions is requied to be greater than 0. ");
                        else
                            MSRTolerance = val5;
                        continue;
                    }
                    if (token.equalsIgnoreCase(VCML.SDETolerance)) {
                        token = tokens.nextToken();
                        double val6 = Double.parseDouble(token);
                        if (val6 <= 0)
                            throw new DataAccessException("unexpected token " + token + ", SDE allowed value of drift and diffusion errors is requied to be greater than 0. ");
                        else
                            SDETolerance = val6;
                        continue;
                    }
                    throw new DataAccessException("unexpected identifier " + token);
                }
                if (getSimulation() != null && getSimulation().getMathDescription() != null) {
                    if (getSimulation().getMathDescription().isNonSpatialStoch()) {
                        if (epsilon != null && lambda != null && MSRTolerance != null && SDETolerance != null) {
                            setStochHybridOpt(new NonspatialStochHybridOptions(epsilon, lambda, MSRTolerance, SDETolerance));
                        }
                    }
                }
                continue;
            }
            if (token.equalsIgnoreCase(VCML.OutputOptions)) {
                fieldOutputTimeSpec = OutputTimeSpec.readVCML(tokens);
                continue;
            }
            if (token.equalsIgnoreCase(VCML.KeepEvery)) {
                token = tokens.nextToken();
                keepEvery = Integer.parseInt(token);
                continue;
            }
            if (token.equalsIgnoreCase(VCML.KeepAtMost)) {
                token = tokens.nextToken();
                keepAtMost = Integer.parseInt(token);
                continue;
            }
            if (token.equalsIgnoreCase(VCML.SensitivityParameter)) {
                token = tokens.nextToken();
                if (!token.equalsIgnoreCase(VCML.BeginBlock)) {
                    throw new DataAccessException("unexpected token " + token + " expecting " + VCML.BeginBlock);
                }
                token = tokens.nextToken();
                if (!token.equalsIgnoreCase(VCML.Constant)) {
                    throw new DataAccessException("unexpected token " + token + " expecting " + VCML.Constant);
                }
                String name = tokens.nextToken();
                Expression exp = MathFunctionDefinitions.fixFunctionSyntax(tokens);
                Constant constant = new Constant(name, exp);
                setSensitivityParameter(constant);
                token = tokens.nextToken();
                if (!token.equalsIgnoreCase(VCML.EndBlock)) {
                    throw new DataAccessException("unexpected token " + token + " expecting " + VCML.EndBlock);
                }
                continue;
            }
            if (token.equalsIgnoreCase(VCML.StopAtSpatiallyUniform)) {
                token = tokens.nextToken();
                stopAtSpatiallyUniformErrorTolerance = ErrorTolerance.getDefaultSpatiallyUniformErrorTolerance();
                stopAtSpatiallyUniformErrorTolerance.readVCML(tokens);
            } else if (token.equalsIgnoreCase(VCML.RunParameterScanSerially)) {
                token = tokens.nextToken();
                setSerialParameterScan((new Boolean(token)).booleanValue());
            } else if (token.equalsIgnoreCase(VCML.SmoldynSimulationOptions)) {
                setSmoldynSimulationOptions(new SmoldynSimulationOptions(tokens));
            } else if (token.equalsIgnoreCase(VCML.SundialsSolverOptions)) {
                setSundialsPdeSolverOptions(new SundialsPdeSolverOptions(tokens));
            } else if (token.equalsIgnoreCase(VCML.ChomboSolverSpec)) {
                chomboSolverSpec = new ChomboSolverSpec(tokens);
            } else if (token.equalsIgnoreCase(VCML.NUM_PROCESSORS)) {
                token = tokens.nextToken();
                numProcessors = Integer.parseInt(token);
            } else if (token.equalsIgnoreCase(VCML.MovingBoundarySolverOptions)) {
                movingBoundarySolverOptions = new MovingBoundarySolverOptions(tokens);
            } else {
                throw new DataAccessException("unexpected identifier " + token);
            }
        }
    } catch (Throwable e) {
        e.printStackTrace(System.out);
        throw new DataAccessException("line #" + (tokens.lineIndex() + 1) + " Exception: " + e.getMessage());
    }
    if (keepEvery != -1) {
        fieldOutputTimeSpec = new DefaultOutputTimeSpec(keepEvery, keepAtMost);
    }
}