Examples with ChomboSolverSpec org.vcell.chombo.ChomboSolverSpec used on opensource projects

Example 6 with ChomboSolverSpec

use of org.vcell.chombo.ChomboSolverSpec in project vcell by virtualcell.

the class SimulationSummaryPanel method displayMesh.

/**
 * Comment
 */
private void displayMesh() {
    try {
        boolean isSpatial = getSimulation().isSpatial();
        getJLabel11().setVisible(isSpatial);
        getJLabelMesh().setVisible(isSpatial);
        labelMeshRefinementTitle.setVisible(isSpatial);
        getJLabelMeshRefinement().setVisible(isSpatial);
        labelFinestMeshTitle.setVisible(isSpatial);
        labelFinestMesh.setVisible(isSpatial);
        labelRefinementRoiTitle.setVisible(isSpatial);
        labelRefinementRoi.setVisible(isSpatial);
        labelViewLevelMeshTitle.setVisible(isSpatial);
        labelViewLevelMesh.setVisible(isSpatial);
        if (getSimulation() != null && getSimulation().getMeshSpecification() != null) {
            ISize samplingSize = getSimulation().getMeshSpecification().getSamplingSize();
            String labelText = "";
            int dimension = getSimulation().getMeshSpecification().getGeometry().getDimension();
            switch(dimension) {
                case 0:
                    {
                        labelText = "error: no mesh expected";
                        break;
                    }
                default:
                    {
                        labelText = GuiUtils.getMeshSizeText(dimension, samplingSize, true) + " elements";
                        break;
                    }
            }
            getJLabelMesh().setText(labelText);
            ChomboSolverSpec chomboSolverSpec = getSimulation().getSolverTaskDescription().getChomboSolverSpec();
            if (getSimulation().getSolverTaskDescription().getSolverDescription().isChomboSolver()) {
                int numRefinementLevels = chomboSolverSpec.getNumRefinementLevels();
                labelMeshRefinementTitle.setVisible(true);
                getJLabelMeshRefinement().setVisible(true);
                labelFinestMeshTitle.setVisible(true);
                labelFinestMesh.setVisible(true);
                ISize finestISize = chomboSolverSpec.getFinestSamplingSize(samplingSize);
                String text = GuiUtils.getMeshSizeText(dimension, finestISize, true);
                labelFinestMesh.setText(text);
                boolean bHasRefinement = numRefinementLevels > 0;
                if (bHasRefinement) {
                    String refinementText = numRefinementLevels + " level(s)";
                    getJLabelMeshRefinement().setText(refinementText);
                    labelRefinementRoiTitle.setVisible(true);
                    labelRefinementRoi.setVisible(true);
                    String roiText = "Membrane ROI(s): " + chomboSolverSpec.getMembraneRefinementRois().size() + "; Volume ROI(s): " + chomboSolverSpec.getVolumeRefinementRois().size() + ";";
                    labelViewLevelMeshTitle.setVisible(true);
                    labelViewLevelMesh.setVisible(true);
                    labelViewLevelMesh.setText(GuiUtils.getMeshSizeText(dimension, chomboSolverSpec.getViewLevelSamplingSize(samplingSize), true));
                    labelRefinementRoi.setText(roiText);
                } else {
                    labelMeshRefinementTitle.setVisible(false);
                    meshRefinementLabel.setVisible(false);
                    labelFinestMeshTitle.setVisible(false);
                    labelFinestMesh.setVisible(false);
                    labelRefinementRoiTitle.setVisible(false);
                    labelRefinementRoi.setVisible(false);
                    labelViewLevelMeshTitle.setVisible(false);
                    labelViewLevelMesh.setVisible(false);
                }
            } else {
                labelMeshRefinementTitle.setVisible(false);
                getJLabelMeshRefinement().setVisible(false);
                labelFinestMesh.setVisible(false);
                labelFinestMeshTitle.setVisible(false);
                labelRefinementRoiTitle.setVisible(false);
                labelRefinementRoi.setVisible(false);
                labelViewLevelMeshTitle.setVisible(false);
                labelViewLevelMesh.setVisible(false);
            }
        }
    } catch (Exception exc) {
        exc.printStackTrace(System.out);
        getJLabelMesh().setText("");
    }
}

Example 7 with ChomboSolverSpec

use of org.vcell.chombo.ChomboSolverSpec in project vcell by virtualcell.

the class ChomboSolverSpecPanel method updateViewLevel.

private void updateViewLevel() {
    ChomboSolverSpec chomboSolverSpec = simulation.getSolverTaskDescription().getChomboSolverSpec();
    viewLevelComboBox.removeActionListener(eventHandler);
    viewLevelComboBox.removeAllItems();
    viewLevelComboBox.addItem(new Integer(0));
    int numLevels = chomboSolverSpec.getNumRefinementLevels();
    for (int i = 0; i < numLevels; ++i) {
        viewLevelComboBox.addItem(i + 1);
    }
    if (chomboSolverSpec.isFinestViewLevel()) {
        viewLevelFinestRadioButton.setSelected(chomboSolverSpec.isFinestViewLevel());
        viewLevelComboBox.setEnabled(false);
    } else {
        viewLevelUserSelectRadioButton.setSelected(!chomboSolverSpec.isFinestViewLevel());
        viewLevelComboBox.setEnabled(true);
        int viewLevel = chomboSolverSpec.getViewLevel();
        viewLevelComboBox.setSelectedItem(viewLevel);
    }
    viewLevelComboBox.addActionListener(eventHandler);
}

Example 8 with ChomboSolverSpec

use of org.vcell.chombo.ChomboSolverSpec in project vcell by virtualcell.

the class XmlReader method getChomboSolverSpec.

private ChomboSolverSpec getChomboSolverSpec(SolverTaskDescription solverTaskDesc, Element element, int dimension) throws XmlParseException {
    int maxBoxSize = parseIntWithDefault(element, XMLTags.MaxBoxSizeTag, ChomboSolverSpec.getDefaultMaxBoxSize(dimension));
    double fillRatio = parseDoubleWithDefault(element, XMLTags.FillRatioTag, ChomboSolverSpec.getDefaultFillRatio());
    boolean bSaveVCellOutput = parseBooleanWithDefault(element, XMLTags.SaveVCellOutput, true);
    boolean bSaveChomboOutput = parseBooleanWithDefault(element, XMLTags.SaveChomboOutput, false);
    Element childElement = element.getChild(XMLTags.RefineRatios, vcNamespace);
    List<Integer> refineRatioList = null;
    if (childElement != null) {
        String text = childElement.getText();
        if (text != null && !text.isEmpty()) {
            StringTokenizer st = new StringTokenizer(text, ",");
            if (st.hasMoreTokens()) {
                refineRatioList = new ArrayList<Integer>();
                while (st.hasMoreElements()) {
                    String token = st.nextToken();
                    if (token != null) {
                        int n = Integer.parseInt(token);
                        refineRatioList.add(n);
                    }
                }
            }
        }
    }
    Integer viewLevel = null;
    try {
        ChomboSolverSpec css = new ChomboSolverSpec(maxBoxSize, fillRatio, viewLevel, bSaveVCellOutput, bSaveChomboOutput, refineRatioList);
        double smallVolfracThreshold = parseDoubleWithDefault(element, XMLTags.SmallVolfracThreshold, 0);
        int blockFactor = parseIntWithDefault(element, XMLTags.BlockFactorTag, ChomboSolverSpec.DEFAULT_BLOCK_FACTOR);
        boolean bActivateFeatureUnderDevelopment = parseBooleanWithDefault(element, XMLTags.ActivateFeatureUnderDevelopment, false);
        css.setSmallVolfracThreshold(smallVolfracThreshold);
        css.setActivateFeatureUnderDevelopment(bActivateFeatureUnderDevelopment);
        css.setBlockFactor(blockFactor);
        int tagsGrow = parseIntWithDefault(element, XMLTags.TagsGrowTag, ChomboSolverSpec.defaultTagsGrow);
        css.setTagsGrow(tagsGrow);
        Element timeBoundsElement = element.getChild(XMLTags.TimeBoundTag, vcNamespace);
        List<Element> timeIntervalElementList = null;
        boolean noTimeBounds = false;
        if (timeBoundsElement == null) {
            noTimeBounds = true;
        } else {
            timeIntervalElementList = timeBoundsElement.getChildren(XMLTags.TimeIntervalTag, vcNamespace);
            if (timeIntervalElementList.size() == 0) {
                noTimeBounds = true;
            }
        }
        if (noTimeBounds) {
            // old format
            double startTime = 0;
            double endTime = solverTaskDesc.getTimeBounds().getEndingTime();
            double timeStep = solverTaskDesc.getTimeStep().getDefaultTimeStep();
            double outputTimeStep = ((UniformOutputTimeSpec) solverTaskDesc.getOutputTimeSpec()).getOutputTimeStep();
            try {
                TimeInterval ti = new TimeInterval(startTime, endTime, timeStep, outputTimeStep);
                css.addTimeInterval(ti);
            } catch (IllegalArgumentException ex) {
                css.addTimeInterval(TimeInterval.getDefaultTimeInterval());
            }
        } else {
            for (Element e : timeIntervalElementList) {
                String s = e.getAttributeValue(XMLTags.StartTimeAttrTag);
                double startTime = Double.valueOf(s);
                s = e.getAttributeValue(XMLTags.EndTimeAttrTag);
                double endTime = Double.valueOf(s);
                s = e.getAttributeValue(XMLTags.TimeStepAttrTag);
                double timeStep = Double.valueOf(s);
                s = e.getAttributeValue(XMLTags.OutputTimeStepAttrTag);
                double outputTimeStep = Double.valueOf(s);
                TimeInterval ti = new TimeInterval(startTime, endTime, timeStep, outputTimeStep);
                css.addTimeInterval(ti);
            }
        }
        Element meshRefineElement = element.getChild(XMLTags.MeshRefinementTag, vcNamespace);
        if (meshRefineElement != null) {
            if (meshRefineElement.getChildren().size() != 0) {
                // in old model, if there is no refinement, set view level to finest
                // only set viewLevel when meshRefinement has children
                Element viewLevelChild = element.getChild(XMLTags.ViewLevelTag, vcNamespace);
                if (viewLevelChild != null) {
                    viewLevel = parseIntWithDefault(element, XMLTags.ViewLevelTag, 0);
                    css.setViewLevel(viewLevel);
                }
            }
            List<Element> levelElementList = meshRefineElement.getChildren(XMLTags.RefinementRoiTag, vcNamespace);
            for (Element levelElement : levelElementList) {
                String levelStr = levelElement.getAttributeValue(XMLTags.RefineRoiLevelAttrTag);
                int level = 1;
                if (levelStr != null) {
                    level = Integer.parseInt(levelStr);
                }
                String type = levelElement.getAttributeValue(XMLTags.RefinementRoiTypeAttrTag);
                RoiType roiType = RoiType.Membrane;
                if (type != null) {
                    try {
                        roiType = RoiType.valueOf(type);
                    } catch (Exception ex) {
                    // ignore
                    }
                }
                Element expElement = levelElement.getChild(XMLTags.ROIExpressionTag, vcNamespace);
                String roiExp = null;
                if (expElement != null) {
                    roiExp = expElement.getText();
                    RefinementRoi roi = new RefinementRoi(roiType, level, roiExp);
                    css.addRefinementRoi(roi);
                }
            }
        }
        return css;
    } catch (ExpressionException e) {
        throw new XmlParseException(e);
    }
}

Example 9 with ChomboSolverSpec

use of org.vcell.chombo.ChomboSolverSpec 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 10 with ChomboSolverSpec

use of org.vcell.chombo.ChomboSolverSpec 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);
    }
}