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

Example 11 with DefaultOutputTimeSpec

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

the class SundialsSolver method writeLogFile.

private void writeLogFile() throws SolverException {
    String logFile = getBaseName() + LOGFILE_EXTENSION;
    String ideDataFileName = new File(getBaseName() + IDA_DATA_EXTENSION).getName();
    PrintWriter pw = null;
    try {
        pw = new PrintWriter(logFile);
        pw.println(IDA_DATA_IDENTIFIER);
        pw.println(IDA_DATA_FORMAT_ID);
        pw.println(ideDataFileName);
        OutputTimeSpec outputTimeSpec = simTask.getSimulation().getSolverTaskDescription().getOutputTimeSpec();
        if (outputTimeSpec.isDefault()) {
            pw.println(KEEP_MOST + " " + ((DefaultOutputTimeSpec) outputTimeSpec).getKeepAtMost());
        }
        pw.close();
    } catch (FileNotFoundException e) {
        e.printStackTrace();
        throw new SolverException(e.getMessage());
    } finally {
        if (pw != null) {
            pw.close();
        }
    }
}

Example 12 with DefaultOutputTimeSpec

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

the class MovingBoundaryFileWriter method gettimeReport.

private Element gettimeReport() {
    Element e = new Element(MBTags.timeReport);
    Element e1 = null;
    OutputTimeSpec outTimeSpec = simTask.getSimulation().getSolverTaskDescription().getOutputTimeSpec();
    if (outTimeSpec instanceof UniformOutputTimeSpec) {
        UniformOutputTimeSpec uniformOutputTimeSpec = (UniformOutputTimeSpec) outTimeSpec;
        double interval = uniformOutputTimeSpec.getOutputTimeStep();
        // hard coded.
        double startTime = 0.0;
        e1 = new Element(MBTags.startTime);
        e1.setText("0");
        e.addContent(e1);
        e1 = new Element(MBTags.interval);
        e1.setText(interval + "");
        e.addContent(e1);
    } else if (outTimeSpec instanceof DefaultOutputTimeSpec) {
        DefaultOutputTimeSpec defaultOutputTimeSpec = (DefaultOutputTimeSpec) outTimeSpec;
        Integer step = defaultOutputTimeSpec.getKeepEvery();
        // hard code
        double startTime = 0.0;
        e1 = new Element(MBTags.startTime);
        e1.setText("0");
        e.addContent(e1);
        e1 = new Element(MBTags.step);
        e1.setText(step.toString());
        e.addContent(e1);
    }
    return e;
}

Example 13 with DefaultOutputTimeSpec

use of cbit.vcell.solver.DefaultOutputTimeSpec 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());
    }
    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);
    }
    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) 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 14 with DefaultOutputTimeSpec

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

the class SimulationWorkspace method getEstimatedNumTimePointsForStoch.

private static long getEstimatedNumTimePointsForStoch(SimulationSymbolTable simSymbolTable) {
    Simulation sim = simSymbolTable.getSimulation();
    SolverTaskDescription solverTaskDescription = sim.getSolverTaskDescription();
    TimeBounds tb = solverTaskDescription.getTimeBounds();
    double startTime = tb.getStartingTime();
    double endTime = tb.getEndingTime();
    OutputTimeSpec tSpec = solverTaskDescription.getOutputTimeSpec();
    // hybrid G_E and G_M are fixed time step methods using uniform output time spec
    if (tSpec.isUniform()) {
        double outputTimeStep = ((UniformOutputTimeSpec) tSpec).getOutputTimeStep();
        return (long) ((endTime - startTime) / outputTimeStep);
    }
    double maxProbability = 0;
    SubDomain subDomain = sim.getMathDescription().getSubDomains().nextElement();
    List<VarIniCondition> varInis = subDomain.getVarIniConditions();
    // get all the probability expressions
    ArrayList<Expression> probList = new ArrayList<Expression>();
    for (JumpProcess jp : subDomain.getJumpProcesses()) {
        probList.add(jp.getProbabilityRate());
    }
    // loop through probability expressions
    for (int i = 0; i < probList.size(); i++) {
        try {
            Expression pExp = new Expression(probList.get(i));
            pExp.bindExpression(simSymbolTable);
            pExp = simSymbolTable.substituteFunctions(pExp);
            pExp = pExp.flatten();
            String[] symbols = pExp.getSymbols();
            // substitute stoch vars with it's initial condition expressions
            if (symbols != null) {
                for (int j = 0; symbols != null && j < symbols.length; j++) {
                    for (int k = 0; k < varInis.size(); k++) {
                        if (symbols[j].equals(varInis.get(k).getVar().getName())) {
                            pExp.substituteInPlace(new Expression(symbols[j]), new Expression(varInis.get(k).getIniVal()));
                            break;
                        }
                    }
                }
            }
            pExp = simSymbolTable.substituteFunctions(pExp);
            pExp = pExp.flatten();
            double val = pExp.evaluateConstant();
            if (maxProbability < val) {
                maxProbability = val;
            }
        } catch (ExpressionBindingException e) {
            System.out.println("Cannot estimate the total time points for stochastic simulation!! Due to the reason below...");
            e.printStackTrace();
        } catch (ExpressionException ex) {
            System.out.println("Cannot estimate the total time points for stochastic simulation!! Due to the reason below...");
            ex.printStackTrace();
        } catch (MathException e) {
            System.out.println("Cannot estimate the total time points for stochastic simulation!! Due to the reason below...");
            e.printStackTrace();
        }
    }
    int keepEvery = 1;
    if (tSpec.isDefault()) {
        keepEvery = ((DefaultOutputTimeSpec) tSpec).getKeepEvery();
    }
    // points = (endt-startt)/(t*keepEvery) = (endt - startt)/(keepEvery*1/prob)
    long estimatedPoints = Math.round((tb.getEndingTime() - tb.getStartingTime()) * maxProbability / keepEvery) + 1;
    return estimatedPoints;
}

Example 15 with DefaultOutputTimeSpec

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

the class SimulationWorkspace method checkSimulationParameters.

/**
 * Insert the method's description here.
 * Creation date: (5/11/2004 2:57:10 PM)
 * @return boolean
 * @param simulation cbit.vcell.solver.Simulation
 */
private static boolean checkSimulationParameters(Simulation simulation, Component parent) {
    SimulationSymbolTable simSymbolTable = new SimulationSymbolTable(simulation, 0);
    String errorMessage = null;
    long maxTimepoints = Simulation.MAX_LIMIT_NON_SPATIAL_TIMEPOINTS;
    long warningTimepoints = Simulation.WARNING_NON_SPATIAL_TIMEPOINTS;
    boolean bSpatial = simulation.isSpatial();
    if (bSpatial) {
        maxTimepoints = Simulation.MAX_LIMIT_SPATIAL_TIMEPOINTS;
        warningTimepoints = Simulation.WARNING_SPATIAL_TIMEPOINTS;
    }
    long maxSizeBytes = megabytesToBytes(Simulation.MAX_LIMIT_0DE_MEGABYTES);
    long warningSizeBytes = megabytesToBytes(Simulation.WARNING_0DE_MEGABYTES);
    if (bSpatial) {
        maxSizeBytes = megabytesToBytes(Simulation.MAX_LIMIT_PDE_MEGABYTES);
        warningSizeBytes = megabytesToBytes(Simulation.WARNING_PDE_MEGABYTES);
    } else if (simulation.getMathDescription().isNonSpatialStoch()) {
        maxSizeBytes = megabytesToBytes(Simulation.MAX_LIMIT_STOCH_MEGABYTES);
        warningSizeBytes = megabytesToBytes(Simulation.WARNING_STOCH_MEGABYTES);
    }
    long expectedNumTimePoints = getExpectedNumTimePoints(simulation);
    long expectedSizeBytes = getExpectedSizeBytes(simSymbolTable);
    // 
    // check for error conditions (hard limits on resources) ... Note: each user should have it's own limits (and quotas).
    // 
    SolverTaskDescription solverTaskDescription = simulation.getSolverTaskDescription();
    SolverDescription solverDescription = solverTaskDescription.getSolverDescription();
    if (expectedNumTimePoints > maxTimepoints) {
        errorMessage = "Errors in Simulation: '" + simulation.getName() + "'!\n" + "The simulation has too many timepoints (" + expectedNumTimePoints + ") to be saved, which has exceeded our limit.\n\n" + "maximum saving timepoints limits are:\n" + "     " + Simulation.MAX_LIMIT_NON_SPATIAL_TIMEPOINTS + " for compartmental simulations\n" + "     " + Simulation.MAX_LIMIT_SPATIAL_TIMEPOINTS + " for spatial simulations\n" + "suggested saving timepoints limits are:\n" + "     " + Simulation.WARNING_NON_SPATIAL_TIMEPOINTS + " for compartmental simulations\n" + "     " + Simulation.WARNING_SPATIAL_TIMEPOINTS + " for spatial simulations\n" + "Try saving fewer timepoints\n" + "If you need to exceed the quota, please contact us";
        // not used for multiple stochastic run
        if (solverTaskDescription.getStochOpt() != null && solverTaskDescription.getStochOpt().getNumOfTrials() > 1) {
            errorMessage = null;
        }
    } else if (expectedSizeBytes > maxSizeBytes) {
        errorMessage = "Errors in Simulation: '" + simulation.getName() + "'!\n" + "The simulation's result dataset (" + CodeUtil.humanBytePrint(expectedSizeBytes) + ") is too large, which has exceeded our limit.\n\n" + "maximum size limits are:\n" + "     " + Simulation.MAX_LIMIT_0DE_MEGABYTES + " MB for compartmental ODE simulations\n" + "     " + Simulation.MAX_LIMIT_PDE_MEGABYTES + " MB for spatial simulations\n" + "     " + Simulation.MAX_LIMIT_STOCH_MEGABYTES + " MB for compartmental stochastic simulations\n" + "suggested size limits are:\n" + "     " + Simulation.WARNING_0DE_MEGABYTES + " MB for compartmental ODE simulations\n" + "     " + Simulation.WARNING_PDE_MEGABYTES + " MB for spatial simulations\n" + "     " + Simulation.WARNING_STOCH_MEGABYTES + " MB for compartmental stochastic simulations\n" + "Try saving fewer timepoints or using a smaller mesh (if spatial)\n" + "If you need to exceed the quota, please contact us";
        // not used for multiple stochastic run
        if (solverTaskDescription.getStochOpt() != null && solverTaskDescription.getStochOpt().getNumOfTrials() > 1) {
            errorMessage = null;
        }
    } else if (simulation.getScanCount() > Simulation.MAX_LIMIT_SCAN_JOBS) {
        errorMessage = "Errors in Simulation: '" + simulation.getName() + "'!\n" + "The simulation generates too many simulations (" + simulation.getScanCount() + ") required for parameter scan, which has exceeded our limit.\n\n" + "maximum number of parameter sets is: " + Simulation.MAX_LIMIT_SCAN_JOBS + " \n" + "suggested limit for number of parameter sets is: " + Simulation.WARNING_SCAN_JOBS + " \n" + "Try choosing fewer parameters or reducing the size of scan for each parameter.";
        // not used for multiple stochastic run
        if (simulation.getMathDescription().isNonSpatialStoch() && solverTaskDescription.getStochOpt() != null && solverTaskDescription.getStochOpt().getNumOfTrials() > 1) {
            errorMessage = null;
        }
    } else if (solverDescription.equals(SolverDescription.SundialsPDE)) {
        if (solverTaskDescription.getOutputTimeSpec().isDefault()) {
            DefaultOutputTimeSpec dot = (DefaultOutputTimeSpec) solverTaskDescription.getOutputTimeSpec();
            int maxNumberOfSteps = dot.getKeepEvery() * dot.getKeepAtMost();
            double maximumTimeStep = solverTaskDescription.getTimeStep().getMaximumTimeStep();
            double maxSimTime = maxNumberOfSteps * maximumTimeStep;
            double endingTime = solverTaskDescription.getTimeBounds().getEndingTime();
            if (maxSimTime < endingTime) {
                errorMessage = "Errors in Simulation: '" + simulation.getName() + "'!\n" + "The maximum possible simulation time (keepEvery * maxTimestep * keepAtMost = " + maxSimTime + ") is less than simulation end time (" + endingTime + ").\n\n" + "You have chosen a variable time step solver and specified a maximum number of time steps of " + maxNumberOfSteps + " (keepEvery*keepAtMost).  " + "Actual time steps are often small, but even if all steps were at the maximum time step of " + maximumTimeStep + ", the simulation end time of " + endingTime + " would not be reached. \n\n" + "Either adjust the parameters or choose the \"Output Interval\" option.";
            }
        }
    } else if (simulation.getMathDescription().isNonSpatialStoch() && !(solverDescription.isNonSpatialStochasticSolver())) {
        // to guarantee stochastic model uses stochastic methods and deterministic model uses ODE/PDE methods.
        errorMessage = "Errors in Simulation: '" + simulation.getName() + "'!\n" + "Stochastic simulation(s) must use stochastic solver(s).\n" + solverDescription.getDisplayLabel() + " is not a stochastic solver!";
    } else if (!simulation.getMathDescription().isNonSpatialStoch() && (solverDescription.isNonSpatialStochasticSolver())) {
        errorMessage = "Errors in Simulation: '" + simulation.getName() + "'!\n" + "ODE/PDE simulation(s) must use ODE/PDE solver(s).\n" + solverDescription.getDisplayLabel() + " is not a ODE/PDE solver!";
    } else if (simulation.getSolverTaskDescription().getSolverDescription().isChomboSolver()) {
        MeshSpecification meshSpecification = simulation.getMeshSpecification();
        boolean bCellCentered = simulation.hasCellCenteredMesh();
        if (meshSpecification != null && !meshSpecification.isAspectRatioOK(1e-4, bCellCentered)) {
            errorMessage = "Non uniform spatial step is detected. This will affect the accuracy of the solution.\n\n" + "\u0394x=" + meshSpecification.getDx(bCellCentered) + "\n" + "\u0394y=" + meshSpecification.getDy(bCellCentered) + (meshSpecification.getGeometry().getDimension() < 3 ? "" : "\n\u0394z=" + meshSpecification.getDz(bCellCentered));
        }
    } else {
        errorMessage = null;
    }
    if (errorMessage != null) {
        DialogUtils.showErrorDialog(parent, errorMessage);
        return false;
    } else if (simulation.getSolverTaskDescription().getSolverDescription().isChomboSolver()) {
        Geometry geometry = simulation.getMathDescription().getGeometry();
        ChomboMeshValidator meshValidator = new ChomboMeshValidator(geometry, simulation.getSolverTaskDescription().getChomboSolverSpec());
        ChomboMeshRecommendation chomboMeshRecommendation = meshValidator.computeMeshSpecs();
        boolean bValid = chomboMeshRecommendation.validate();
        if (!bValid) {
            String option = DialogUtils.showWarningDialog(parent, "Error", chomboMeshRecommendation.getErrorMessage(), chomboMeshRecommendation.getDialogOptions(), ChomboMeshRecommendation.optionClose);
            if (ChomboMeshRecommendation.optionSuggestions.equals(option)) {
                DialogUtils.showInfoDialog(parent, ChomboMeshRecommendation.optionSuggestions, chomboMeshRecommendation.getMeshSuggestions());
            }
        }
        return bValid;
    } else {
        String warningMessage = null;
        // don't check warning message for stochastic multiple trials, let it run.
        if (simulation.getMathDescription().isNonSpatialStoch() && simulation.getSolverTaskDescription().getStochOpt() != null && simulation.getSolverTaskDescription().getStochOpt().getNumOfTrials() > 1) {
            return true;
        }
        // 
        if (expectedNumTimePoints > warningTimepoints) {
            warningMessage = "Warnings from Simulation: '" + simulation.getName() + "'!\n" + "The simulation has large number of saving timepoints (" + expectedNumTimePoints + "), suggested saving timepoints limits are:\n" + "     " + Simulation.WARNING_NON_SPATIAL_TIMEPOINTS + " for compartmental simulations\n" + "     " + Simulation.WARNING_SPATIAL_TIMEPOINTS + " for spatial simulations\n" + "Try saving fewer timepoints";
        } else if (expectedSizeBytes > warningSizeBytes) {
            warningMessage = "Warnings from Simulation: '" + simulation.getName() + "'!\n" + "The simulation has large result dataset (" + (expectedSizeBytes / 1000000L) + "MB), suggested size limits are:\n" + "     " + Simulation.WARNING_0DE_MEGABYTES + " MB for compartmental ODE simulations\n" + "     " + Simulation.WARNING_PDE_MEGABYTES + " MB for spatial simulations\n" + "     " + Simulation.WARNING_STOCH_MEGABYTES + " MB for compartmental stochastic simulations\n" + "Try saving fewer timepoints or using a coarser mesh if spatial.";
        } else if (simulation.getScanCount() > Simulation.WARNING_SCAN_JOBS) {
            warningMessage = "Warnings from Simulation: '" + simulation.getName() + "'!\n" + "The simulation generates a large number of simulations (" + simulation.getScanCount() + ") required for parameter scan.\n" + "maximum number of parameter sets is: " + Simulation.MAX_LIMIT_SCAN_JOBS + " \n" + "suggested limit for the number of parameter sets is: " + Simulation.WARNING_SCAN_JOBS + " \n" + "Try choosing fewer parameters or reducing the size of scan for each parameter.";
        }
        if (solverDescription.equals(SolverDescription.SundialsPDE)) {
            if (solverTaskDescription.getErrorTolerance().getRelativeErrorTolerance() > 1e-4) {
                String msg = "Warnings from Simulation: '" + simulation.getName() + "'!\n" + "Warning: it is not reccomended to use a relative tolerance that is greater than \n1e-4 for " + solverDescription.getDisplayLabel() + ".";
                warningMessage = warningMessage == null ? msg : warningMessage + "\n\n" + msg;
            }
        } else if (solverDescription.isSemiImplicitPdeSolver()) {
            if (solverTaskDescription.getErrorTolerance().getRelativeErrorTolerance() > 1e-8) {
                String msg = "Warnings from Simulation: '" + simulation.getName() + "'!\n" + "Warning: it is not reccomended to use a relative tolerance that is greater than \n1e-8 for " + solverDescription.getDisplayLabel() + ".";
                warningMessage = warningMessage == null ? msg : warningMessage + "\n\n" + msg;
            }
        }
        MeshSpecification meshSpecification = simulation.getMeshSpecification();
        boolean bCellCentered = simulation.hasCellCenteredMesh();
        if (meshSpecification != null && !meshSpecification.isAspectRatioOK(bCellCentered)) {
            warningMessage = (warningMessage == null ? "" : warningMessage + "\n\n") + "Non uniform spatial step is detected. This might affect the accuracy of the solution.\n\n" + "\u0394x=" + meshSpecification.getDx(bCellCentered) + "\n" + "\u0394y=" + meshSpecification.getDy(bCellCentered) + (meshSpecification.getGeometry().getDimension() < 3 ? "" : "\n\u0394z=" + meshSpecification.getDz(bCellCentered));
        }
        if (warningMessage != null) {
            String result = DialogUtils.showWarningDialog(parent, warningMessage + "\n\nDo you want to continue anyway?", new String[] { UserMessage.OPTION_OK, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_OK);
            return (result != null && result.equals(UserMessage.OPTION_OK));
        } else {
            return true;
        }
    }
}