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

Example 1 with SmoldynSimulationOptions

use of cbit.vcell.solver.SmoldynSimulationOptions 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());
        }
        if (solverTaskDesc.isBorderExtrapolationDisabled()) {
            // Set with GUI checkbox in SolverTaskDescriptionAdvancedPanel
            // Tells vcell-solvers/VCell/src/SundialsPdeScheduler.cpp not to extrapolate values at boundaries
            // Read by vcell-solvers/VCell/src/FVSolver.cpp::loadSimulationParameters(...) from file {vcellUserDataDir}/SimID_xxx.fvinput
            printWriter.print(" " + ("" + solverTaskDesc.isBorderExtrapolationDisabled()).toLowerCase());
        }
        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);
    }
    MathDescription md = simulation.getMathDescription();
    if (md.isSpatialHybrid()) {
        SmoldynSimulationOptions smoldynSimulationOptions = simulation.getSolverTaskDescription().getSmoldynSimulationOptions();
        if (smoldynSimulationOptions != null && smoldynSimulationOptions.getSmoldynStepMultiplier() > 1) {
            printWriter.println(FVInputFileKeyword.SMOLDYN_STEP_MULTIPLIER + " " + smoldynSimulationOptions.getSmoldynStepMultiplier());
        }
    }
    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 2 with SmoldynSimulationOptions

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

the class SmoldynFileWriter method writeSimulationTimes.

private void writeSimulationTimes() {
    // write simulation times
    TimeBounds timeBounds = simulation.getSolverTaskDescription().getTimeBounds();
    TimeStep timeStep = simulation.getSolverTaskDescription().getTimeStep();
    printWriter.println("# simulation times");
    printWriter.println(SmoldynVCellMapper.SmoldynKeyword.time_start + " " + timeBounds.getStartingTime());
    printWriter.println(SmoldynVCellMapper.SmoldynKeyword.time_stop + " " + timeBounds.getEndingTime());
    MathDescription md = simulation.getMathDescription();
    if (md.isSpatialHybrid()) {
        SmoldynSimulationOptions smoldynSimulationOptions = simulation.getSolverTaskDescription().getSmoldynSimulationOptions();
        double ts = timeStep.getDefaultTimeStep() * (double) smoldynSimulationOptions.getSmoldynStepMultiplier();
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.time_step + " " + ts);
    } else {
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.time_step + " " + timeStep.getDefaultTimeStep());
    }
    printWriter.println();
}

Example 3 with SmoldynSimulationOptions

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

the class Xmlproducer method getXML.

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

Example 4 with SmoldynSimulationOptions

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

the class XmlReader method getSmoldySimulationOptions.

private SmoldynSimulationOptions getSmoldySimulationOptions(Element smoldySimulationOptionsElement) throws XmlParseException {
    SmoldynSimulationOptions sso = null;
    if (smoldySimulationOptionsElement != null) {
        sso = new SmoldynSimulationOptions();
        String temp = smoldySimulationOptionsElement.getChildText(XMLTags.SmoldynSimulationOptions_accuracy, vcNamespace);
        if (temp != null) {
            sso.setAccuracy(Double.parseDouble(temp));
        }
        temp = smoldySimulationOptionsElement.getChildText(XMLTags.SmoldynSimulationOptions_randomSeed, vcNamespace);
        if (temp != null) {
            sso.setRandomSeed(new Integer(temp));
        }
        temp = smoldySimulationOptionsElement.getChildText(XMLTags.SmoldynSimulationOptions_gaussianTableSize, vcNamespace);
        if (temp != null) {
            try {
                sso.setGaussianTableSize(Integer.parseInt(temp));
            } catch (NumberFormatException e) {
                e.printStackTrace(System.out);
                throw new XmlParseException(e);
            } catch (PropertyVetoException e) {
                e.printStackTrace(System.out);
                throw new XmlParseException(e);
            }
        }
        temp = smoldySimulationOptionsElement.getChildText(XMLTags.SmoldynSimulationOptions_high_res, vcNamespace);
        if (temp != null) {
            sso.setUseHighResolutionSample(new Boolean(temp));
        }
        temp = smoldySimulationOptionsElement.getChildText(XMLTags.SmoldynSimulationOptions_saveParticleFiles, vcNamespace);
        if (temp != null) {
            sso.setSaveParticleLocations(new Boolean(temp));
        }
        temp = smoldySimulationOptionsElement.getChildText(XMLTags.SmoldynSimulationOptions_stepMultiplier, vcNamespace);
        if (temp != null) {
            sso.setSmoldynStepMultiplier(Integer.parseInt(temp));
        }
    }
    return sso;
}

Example 5 with SmoldynSimulationOptions

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

the class SmoldynFileWriter method writeSimulationSettings.

private void writeSimulationSettings() {
    printWriter.println("# simulation settings");
    SmoldynSimulationOptions smoldynSimulationOptions = simulation.getSolverTaskDescription().getSmoldynSimulationOptions();
    printWriter.println(SmoldynVCellMapper.SmoldynKeyword.accuracy + " " + smoldynSimulationOptions.getAccuracy());
    printWriter.println(SmoldynVCellMapper.SmoldynKeyword.gauss_table_size + " " + smoldynSimulationOptions.getGaussianTableSize());
    printWriter.println();
}