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

Example 6 with ErrorTolerance

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

the class SimulationSummaryPanel method displayTask.

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

Example 7 with ErrorTolerance

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

the class StopAtSpatiallyUniformPanel method setNewErrorTolerance.

public void setNewErrorTolerance() {
    double absError = absTolTextField.isEnabled() ? new Double(absTolTextField.getText()).doubleValue() : 1e-9;
    double relError = relTolTextField.isEnabled() ? new Double(relTolTextField.getText()).doubleValue() : 1e-9;
    ErrorTolerance newErrorTol = new ErrorTolerance(absError, relError);
    solverTaskDescription.setStopAtSpatiallyUniformErrorTolerance(newErrorTol);
}

Example 8 with ErrorTolerance

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

the class FiniteVolumeFileWriter method writeSimulationParamters.

/**
 * @param timeFunction
 * @param startTime
 * @param endTime
 * @param rootFinder
 * @param uniqueRootTimes
 * @param bPrintIterations
 * @throws ExpressionException
 *
 * for testing within scrapbook, see below:
 *
 * try {
 *	edu.northwestern.at.utils.math.rootfinders.MonadicFunctionRootFinder rootFinder =
 *//			new edu.northwestern.at.utils.math.rootfinders.Brent();
 *			new edu.northwestern.at.utils.math.rootfinders.Bisection();
 *//			new edu.northwestern.at.utils.math.rootfinders.NewtonRaphson();
 *//			new edu.northwestern.at.utils.math.rootfinders.Secant();
 *	cbit.vcell.parser.SimpleSymbolTable simpleSymbolTable = new cbit.vcell.parser.SimpleSymbolTable(new String[] { "t" });
 *
 *	cbit.vcell.parser.Expression exp = new cbit.vcell.parser.Expression("t-0.56");
 *
 *	exp.bindExpression(simpleSymbolTable);
 *	java.util.TreeSet<Double> rootTimes = new java.util.TreeSet<Double>();
 *	double startTime = 0.0;
 *	double endTime = 100.0;
 *	System.out.print("exp = '"+ exp.infix() + "'");
 *	long currentTimeMS = System.currentTimeMillis();
 *	cbit.vcell.solvers.FiniteVolumeFileWriter.findAllRoots(exp,startTime,endTime,rootFinder,rootTimes,false);
 *	long finalTimeMS = System.currentTimeMillis();
 *	for (double root : rootTimes){
 *		System.out.println("root = "+root);
 *	}
 *	System.out.println("elapsedTime of computation = "+(finalTimeMS-currentTimeMS)+" ms, found " + rootTimes.size() + " roots (not unique)");
 *
 *}catch (Exception e){
 *	e.printStackTrace(System.out);
 *}
 */
/*public static void findAllRoots(Expression timeFunction, double startTime, double endTime, MonadicFunctionRootFinder rootFinder, TreeSet<Double> uniqueRootTimes, boolean bPrintIterations) throws ExpressionException{
	TreeSet<Double> allRootTimes = new TreeSet<Double>();
	final Expression function_exp = new Expression(timeFunction);
	MonadicFunction valueFunction = new MonadicFunction() {
		double[] values = new double[1];
		public double f(double t) {
			values[0] = t;
			try {
				return function_exp.evaluateVector(values);
			} catch (ExpressionException e) {
				e.printStackTrace();
				throw new RuntimeException("expression exception "+e.getMessage());
			}
		}
	};
	
	final Expression derivative_exp = new Expression(timeFunction.differentiate(ReservedVariable.TIME.getName()));
	MonadicFunction derivativeFunction = new MonadicFunction() {
		double[] values = new double[1];
		public double f(double t) {
			values[0] = t;
			try {
				return derivative_exp.evaluateVector(values);
			} catch (ExpressionException e) {
				e.printStackTrace();
				throw new RuntimeException("expression exception "+e.getMessage());
			}
		}
	};
	
	RootFinderConvergenceTest convergenceTest = new StandardRootFinderConvergenceTest();
	RootFinderIterationInformation iterationInformation = null;
	if (bPrintIterations){
		iterationInformation = new RootFinderIterationInformation() {				
			public void iterationInformation(double x, double fx, double dfx, int currentIteration) {
				System.out.println(currentIteration+") x="+x+", fx="+fx+", dfx="+dfx);
			}
		};
	}
	int NUM_BRACKETS = 1000;
	double simulationTime = endTime - startTime;
	double tolerance = simulationTime/1e10;
	int maxIter = 1000;
	
	for (int i=0;i<NUM_BRACKETS-1;i++){
		double bracketMin = startTime + simulationTime*i/NUM_BRACKETS;
		double bracketMax = startTime + simulationTime*(i+1)/NUM_BRACKETS;
	
		double root = rootFinder.findRoot(bracketMin, bracketMax, tolerance, maxIter, valueFunction, derivativeFunction, convergenceTest, iterationInformation);
		if (root>startTime && root<endTime && valueFunction.f(root)<=tolerance){
			allRootTimes.add(root);
		}
	}
	double uniqueTolerance = tolerance * 100;
	double lastUniqueRoot = Double.NEGATIVE_INFINITY;
	for (double root : allRootTimes){
		if (root-lastUniqueRoot > uniqueTolerance){
			uniqueRootTimes.add(root);
		}
		lastUniqueRoot = root;
	}

}  ---------------------------------JIM's CODE COMMENTTED FOR FUTURE DEVELOPMENT*/
/**
 *# Simulation Parameters
 *SIMULATION_PARAM_BEGIN
 *SOLVER SUNDIALS_PDE_SOLVER 1.0E-7 1.0E-9
 *DISCONTINUITY_TIMES 2 1.0E-4 3.0000000000000003E-4
 *BASE_FILE_NAME c:/Vcell/users/fgao/SimID_31746636_0_
 *ENDING_TIME 4.0E-4
 *KEEP_EVERY ONE_STEP 3
 *KEEP_AT_MOST 1000
 *SIMULATION_PARAM_END
 * @throws MathException
 * @throws ExpressionException
 */
private void writeSimulationParamters() throws ExpressionException, MathException {
    Simulation simulation = simTask.getSimulation();
    SolverTaskDescription solverTaskDesc = simulation.getSolverTaskDescription();
    printWriter.println("# Simulation Parameters");
    printWriter.println(FVInputFileKeyword.SIMULATION_PARAM_BEGIN);
    if (solverTaskDesc.getSolverDescription().equals(SolverDescription.SundialsPDE)) {
        printWriter.print(FVInputFileKeyword.SOLVER + " " + FVInputFileKeyword.SUNDIALS_PDE_SOLVER + " " + solverTaskDesc.getErrorTolerance().getRelativeErrorTolerance() + " " + solverTaskDesc.getErrorTolerance().getAbsoluteErrorTolerance() + " " + solverTaskDesc.getTimeStep().getMaximumTimeStep());
        if (simulation.getMathDescription().hasVelocity()) {
            printWriter.print(" " + solverTaskDesc.getSundialsPdeSolverOptions().getMaxOrderAdvection());
        }
        printWriter.println();
        Vector<Discontinuity> discontinuities = new Vector<Discontinuity>();
        TreeSet<Double> discontinuityTimes = new TreeSet<Double>();
        MathDescription mathDesc = simulation.getMathDescription();
        Enumeration<SubDomain> enum1 = mathDesc.getSubDomains();
        while (enum1.hasMoreElements()) {
            SubDomain sd = enum1.nextElement();
            Enumeration<Equation> enum_equ = sd.getEquations();
            while (enum_equ.hasMoreElements()) {
                Equation equation = enum_equ.nextElement();
                equation.getDiscontinuities(simTask.getSimulationJob().getSimulationSymbolTable(), discontinuities);
            }
        }
        getDiscontinuityTimes(discontinuities, discontinuityTimes);
        if (discontinuityTimes.size() > 0) {
            printWriter.print(FVInputFileKeyword.DISCONTINUITY_TIMES + " " + discontinuityTimes.size());
            for (double d : discontinuityTimes) {
                printWriter.print(" " + d);
            }
            printWriter.println();
        }
    } else if (solverTaskDesc.getSolverDescription().equals(SolverDescription.Chombo)) {
        printWriter.println(FVInputFileKeyword.SOLVER + " " + FVInputFileKeyword.CHOMBO_SEMIIMPLICIT_SOLVER);
    } else if (solverTaskDesc.getSolverDescription().equals(SolverDescription.VCellPetsc)) {
        printWriter.println(FVInputFileKeyword.SOLVER + " " + FVInputFileKeyword.VCELL_PETSC_SOLVER);
    } else {
        printWriter.println(FVInputFileKeyword.SOLVER + " " + FVInputFileKeyword.FV_SOLVER + " " + solverTaskDesc.getErrorTolerance().getRelativeErrorTolerance());
    }
    printWriter.println(FVInputFileKeyword.BASE_FILE_NAME + " " + new File(workingDirectory, simTask.getSimulationJob().getSimulationJobID()).getAbsolutePath());
    if (solverTaskDesc.isParallel() && destinationDirectory != null && !destinationDirectory.equals(workingDirectory)) {
        printWriter.println(FVInputFileKeyword.PRIMARY_DATA_DIR + " " + destinationDirectory.getAbsolutePath());
    }
    printWriter.println(FVInputFileKeyword.ENDING_TIME + " " + solverTaskDesc.getTimeBounds().getEndingTime());
    OutputTimeSpec outputTimeSpec = solverTaskDesc.getOutputTimeSpec();
    if (solverTaskDesc.getSolverDescription().isChomboSolver()) {
        List<TimeInterval> timeIntervalList = solverTaskDesc.getChomboSolverSpec().getTimeIntervalList();
        printWriter.println(FVInputFileKeyword.TIME_INTERVALS + " " + timeIntervalList.size());
        for (TimeInterval ti : timeIntervalList) {
            printWriter.println(ti.getEndingTime() + " " + ti.getTimeStep() + " " + ti.getKeepEvery());
        }
    } else if (solverTaskDesc.getSolverDescription().equals(SolverDescription.SundialsPDE)) {
        if (outputTimeSpec.isDefault()) {
            DefaultOutputTimeSpec defaultOutputTimeSpec = (DefaultOutputTimeSpec) outputTimeSpec;
            printWriter.println(FVInputFileKeyword.KEEP_EVERY + " " + FVInputFileKeyword.ONE_STEP + " " + defaultOutputTimeSpec.getKeepEvery());
            printWriter.println(FVInputFileKeyword.KEEP_AT_MOST + " " + defaultOutputTimeSpec.getKeepAtMost());
        } else {
            printWriter.println(FVInputFileKeyword.TIME_STEP + " " + ((UniformOutputTimeSpec) outputTimeSpec).getOutputTimeStep());
            printWriter.println(FVInputFileKeyword.KEEP_EVERY + " 1");
        }
    } else {
        double defaultTimeStep = solverTaskDesc.getTimeStep().getDefaultTimeStep();
        printWriter.println(FVInputFileKeyword.TIME_STEP + " " + defaultTimeStep);
        int keepEvery = 1;
        if (outputTimeSpec.isDefault()) {
            keepEvery = ((DefaultOutputTimeSpec) outputTimeSpec).getKeepEvery();
        } else if (outputTimeSpec.isUniform()) {
            UniformOutputTimeSpec uots = (UniformOutputTimeSpec) outputTimeSpec;
            double ots = uots.getOutputTimeStep();
            keepEvery = (int) Math.round(ots / defaultTimeStep);
        } else {
            throw new RuntimeException("unexpected OutputTime specification type :" + outputTimeSpec.getClass().getName());
        }
        if (keepEvery <= 0) {
            throw new RuntimeException("Output KeepEvery must be a positive integer. Try to change the output option.");
        }
        printWriter.println(FVInputFileKeyword.KEEP_EVERY + " " + keepEvery);
    }
    ErrorTolerance stopAtSpatiallyUniformErrorTolerance = solverTaskDesc.getStopAtSpatiallyUniformErrorTolerance();
    if (stopAtSpatiallyUniformErrorTolerance != null) {
        printWriter.println(FVInputFileKeyword.CHECK_SPATIALLY_UNIFORM + " " + stopAtSpatiallyUniformErrorTolerance.getAbsoluteErrorTolerance() + " " + stopAtSpatiallyUniformErrorTolerance.getRelativeErrorTolerance());
    }
    printWriter.println(FVInputFileKeyword.SIMULATION_PARAM_END);
    printWriter.println();
}

Example 9 with ErrorTolerance

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

the class ITextWriter method writeSimulation.

// container can be a chapter or a section of a chapter.
protected void writeSimulation(Section container, Simulation sim) throws DocumentException {
    if (sim == null) {
        return;
    }
    Section simSection = container.addSection(sim.getName(), container.numberDepth() + 1);
    writeMetadata(simSection, sim.getName(), sim.getDescription(), null, "Simulation ");
    // add overriden params
    Table overParamTable = null;
    MathOverrides mo = sim.getMathOverrides();
    if (mo != null) {
        String[] constants = mo.getOverridenConstantNames();
        for (int i = 0; i < constants.length; i++) {
            String actualStr = "", defStr = "";
            Expression tempExp = mo.getDefaultExpression(constants[i]);
            if (tempExp != null) {
                defStr = tempExp.infix();
            }
            if (mo.isScan(constants[i])) {
                actualStr = mo.getConstantArraySpec(constants[i]).toString();
            } else {
                tempExp = mo.getActualExpression(constants[i], 0);
                if (tempExp != null) {
                    actualStr = tempExp.infix();
                }
            }
            if (overParamTable == null) {
                overParamTable = getTable(3, 75, 1, 3, 3);
                overParamTable.setAlignment(Table.ALIGN_LEFT);
                overParamTable.addCell(createCell("Overriden Parameters", getBold(DEF_HEADER_FONT_SIZE), 3, 1, Element.ALIGN_CENTER, true));
                overParamTable.addCell(createHeaderCell("Name", getBold(), 1));
                overParamTable.addCell(createHeaderCell("Actual Value", getBold(), 1));
                overParamTable.addCell(createHeaderCell("Default Value", getBold(), 1));
            }
            overParamTable.addCell(createCell(constants[i], getFont()));
            overParamTable.addCell(createCell(actualStr, getFont()));
            overParamTable.addCell(createCell(defStr, getFont()));
        }
    }
    if (overParamTable != null) {
        simSection.add(overParamTable);
    }
    // add spatial details
    // sim.isSpatial();
    Table meshTable = null;
    MeshSpecification mesh = sim.getMeshSpecification();
    if (mesh != null) {
        Geometry geom = mesh.getGeometry();
        Extent extent = geom.getExtent();
        String extentStr = "(" + extent.getX() + ", " + extent.getY() + ", " + extent.getZ() + ")";
        ISize meshSize = mesh.getSamplingSize();
        String meshSizeStr = "(" + meshSize.getX() + ", " + meshSize.getY() + ", " + meshSize.getZ() + ")";
        meshTable = getTable(2, 75, 1, 3, 3);
        meshTable.setAlignment(Table.ALIGN_LEFT);
        meshTable.addCell(createCell("Geometry Setting", getBold(DEF_HEADER_FONT_SIZE), 2, 1, Element.ALIGN_CENTER, true));
        meshTable.addCell(createCell("Geometry Size (um)", getFont()));
        meshTable.addCell(createCell(extentStr, getFont()));
        meshTable.addCell(createCell("Mesh Size (elements)", getFont()));
        meshTable.addCell(createCell(meshSizeStr, getFont()));
    }
    if (meshTable != null) {
        simSection.add(meshTable);
    }
    // write advanced sim settings
    Table simAdvTable = null;
    SolverTaskDescription solverDesc = sim.getSolverTaskDescription();
    if (solverDesc != null) {
        String solverName = solverDesc.getSolverDescription().getDisplayLabel();
        simAdvTable = getTable(2, 75, 1, 3, 3);
        simAdvTable.setAlignment(Table.ALIGN_LEFT);
        simAdvTable.addCell(createCell("Advanced Settings", getBold(DEF_HEADER_FONT_SIZE), 2, 1, Element.ALIGN_CENTER, true));
        simAdvTable.addCell(createCell("Solver Name", getFont()));
        simAdvTable.addCell(createCell(solverName, getFont()));
        simAdvTable.addCell(createCell("Time Bounds - Starting", getFont()));
        simAdvTable.addCell(createCell("" + solverDesc.getTimeBounds().getStartingTime(), getFont()));
        simAdvTable.addCell(createCell("Time Bounds - Ending", getFont()));
        simAdvTable.addCell(createCell("" + solverDesc.getTimeBounds().getEndingTime(), getFont()));
        simAdvTable.addCell(createCell("Time Step - Min", getFont()));
        simAdvTable.addCell(createCell("" + solverDesc.getTimeStep().getMinimumTimeStep(), getFont()));
        simAdvTable.addCell(createCell("Time Step - Default", getFont()));
        simAdvTable.addCell(createCell("" + solverDesc.getTimeStep().getDefaultTimeStep(), getFont()));
        simAdvTable.addCell(createCell("Time Step - Max", getFont()));
        simAdvTable.addCell(createCell("" + solverDesc.getTimeStep().getMaximumTimeStep(), getFont()));
        ErrorTolerance et = solverDesc.getErrorTolerance();
        if (et != null) {
            simAdvTable.addCell(createCell("Error Tolerance - Absolute", getFont()));
            simAdvTable.addCell(createCell("" + et.getAbsoluteErrorTolerance(), getFont()));
            simAdvTable.addCell(createCell("Error Tolerance - Relative", getFont()));
            simAdvTable.addCell(createCell("" + et.getRelativeErrorTolerance(), getFont()));
        }
        OutputTimeSpec ots = solverDesc.getOutputTimeSpec();
        if (ots.isDefault()) {
            simAdvTable.addCell(createCell("Keep Every", getFont()));
            simAdvTable.addCell(createCell("" + ((DefaultOutputTimeSpec) ots).getKeepEvery(), getFont()));
            simAdvTable.addCell(createCell("Keep At Most", getFont()));
            simAdvTable.addCell(createCell("" + ((DefaultOutputTimeSpec) ots).getKeepAtMost(), getFont()));
        } else if (ots.isUniform()) {
            simAdvTable.addCell(createCell("Output Time Step", getFont()));
            simAdvTable.addCell(createCell("" + ((UniformOutputTimeSpec) ots).getOutputTimeStep(), getFont()));
        } else if (ots.isExplicit()) {
            simAdvTable.addCell(createCell("Output Time Points", getFont()));
            simAdvTable.addCell(createCell("" + ((ExplicitOutputTimeSpec) ots).toCommaSeperatedOneLineOfString(), getFont()));
        }
        simAdvTable.addCell(createCell("Use Symbolic Jacobian (T/F)", getFont()));
        simAdvTable.addCell(createCell((solverDesc.getUseSymbolicJacobian() ? " T " : " F "), getFont()));
        Constant sp = solverDesc.getSensitivityParameter();
        if (sp != null) {
            simAdvTable.addCell(createCell("Sensitivity Analysis Param", getFont()));
            simAdvTable.addCell(createCell(sp.getName(), getFont()));
        }
    }
    if (simAdvTable != null) {
        simSection.add(simAdvTable);
    }
}

Example 10 with ErrorTolerance

use of cbit.vcell.solver.ErrorTolerance 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)
}