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

Example 11 with SolverTaskDescription

use of cbit.vcell.solver.SolverTaskDescription 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 12 with SolverTaskDescription

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

the class FiniteVolumeFileWriter method writeChomboSpec.

private void writeChomboSpec() throws ExpressionException, SolverException, PropertyVetoException, ClassNotFoundException, IOException, GeometryException, ImageException {
    if (!bChomboSolver) {
        return;
    }
    GeometrySpec geometrySpec = resampledGeometry.getGeometrySpec();
    int dimension = geometrySpec.getDimension();
    if (dimension == 1) {
        throw new SolverException(simTask.getSimulation().getSolverTaskDescription().getSolverDescription().getDisplayLabel() + " is only supported for simulations with 2D or 3D geometry.");
    }
    Simulation simulation = getSimulationTask().getSimulation();
    SolverTaskDescription solverTaskDescription = simulation.getSolverTaskDescription();
    ChomboSolverSpec chomboSolverSpec = solverTaskDescription.getChomboSolverSpec();
    printWriter.println(FVInputFileKeyword.CHOMBO_SPEC_BEGIN);
    printWriter.println(FVInputFileKeyword.DIMENSION + " " + geometrySpec.getDimension());
    Extent extent = geometrySpec.getExtent();
    Origin origin = geometrySpec.getOrigin();
    ISize isize = simulation.getMeshSpecification().getSamplingSize();
    switch(geometrySpec.getDimension()) {
        case 2:
            printWriter.println(FVInputFileKeyword.MESH_SIZE + " " + isize.getX() + " " + isize.getY());
            printWriter.println(FVInputFileKeyword.DOMAIN_SIZE + " " + extent.getX() + " " + extent.getY());
            printWriter.println(FVInputFileKeyword.DOMAIN_ORIGIN + " " + origin.getX() + " " + origin.getY());
            break;
        case 3:
            printWriter.println(FVInputFileKeyword.MESH_SIZE + " " + isize.getX() + " " + isize.getY() + " " + isize.getZ());
            printWriter.println(FVInputFileKeyword.DOMAIN_SIZE + " " + extent.getX() + " " + extent.getY() + " " + extent.getZ());
            printWriter.println(FVInputFileKeyword.DOMAIN_ORIGIN + " " + origin.getX() + " " + origin.getY() + " " + origin.getZ());
            break;
    }
    List<CompartmentSubDomain> featureList = new ArrayList<CompartmentSubDomain>();
    Enumeration<SubDomain> enum1 = simulation.getMathDescription().getSubDomains();
    while (enum1.hasMoreElements()) {
        SubDomain sd = enum1.nextElement();
        if (sd instanceof CompartmentSubDomain) {
            featureList.add((CompartmentSubDomain) sd);
        }
    }
    int numFeatures = featureList.size();
    CompartmentSubDomain[] features = featureList.toArray(new CompartmentSubDomain[0]);
    int[] phases = new int[numFeatures];
    Arrays.fill(phases, -1);
    phases[numFeatures - 1] = 0;
    int[] numAssigned = new int[] { 1 };
    assignPhases(features, numFeatures - 1, phases, numAssigned);
    Map<String, Integer> subDomainPhaseMap = new HashMap<String, Integer>();
    for (int i = 0; i < phases.length; ++i) {
        if (phases[i] == -1) {
            throw new SolverException("Failed to assign a phase to CompartmentSubdomain '" + features[i].getName() + "'. It might be caused by too coarsh a mesh.");
        }
        subDomainPhaseMap.put(features[i].getName(), phases[i]);
    }
    SubVolume[] subVolumes = geometrySpec.getSubVolumes();
    if (geometrySpec.hasImage()) {
        Geometry geometry = (Geometry) BeanUtils.cloneSerializable(simulation.getMathDescription().getGeometry());
        Geometry simGeometry = geometry;
        VCImage img = geometry.getGeometrySpec().getImage();
        int factor = Math.max(Math.max(img.getNumX(), img.getNumY()), img.getNumZ()) < 512 ? 2 : 1;
        ISize distanceMapMeshSize = new ISize(img.getNumX() * factor, img.getNumY() * factor, img.getNumZ() * factor);
        Vect3d deltaX = null;
        boolean bCellCentered = false;
        double dx = 0.5;
        double dy = 0.5;
        double dz = 0.5;
        int Nx = distanceMapMeshSize.getX();
        int Ny = distanceMapMeshSize.getY();
        int Nz = distanceMapMeshSize.getZ();
        if (dimension == 2) {
            // pad the 2D image with itself in order to obtain a 3D image used to compute the distance map
            // because the distance map algorithm is 3D only (using distance to triangles)
            byte[] oldPixels = img.getPixels();
            byte[] newPixels = new byte[oldPixels.length * 3];
            System.arraycopy(oldPixels, 0, newPixels, 0, oldPixels.length);
            System.arraycopy(oldPixels, 0, newPixels, oldPixels.length, oldPixels.length);
            System.arraycopy(oldPixels, 0, newPixels, oldPixels.length * 2, oldPixels.length);
            double distX = geometry.getExtent().getX() / img.getNumX();
            double distY = geometry.getExtent().getY() / img.getNumY();
            // we set the distance on the z axis to something that makes sense
            double distZ = Math.max(distX, distY);
            Extent newExtent = new Extent(geometry.getExtent().getX(), geometry.getExtent().getY(), distZ * 3);
            VCImage newImage = new VCImageUncompressed(null, newPixels, newExtent, img.getNumX(), img.getNumY(), 3);
            // copy the pixel classes too
            ArrayList<VCPixelClass> newPixelClasses = new ArrayList<VCPixelClass>();
            for (VCPixelClass origPixelClass : geometry.getGeometrySpec().getImage().getPixelClasses()) {
                SubVolume origSubvolume = geometry.getGeometrySpec().getImageSubVolumeFromPixelValue(origPixelClass.getPixel());
                newPixelClasses.add(new VCPixelClass(null, origSubvolume.getName(), origPixelClass.getPixel()));
            }
            newImage.setPixelClasses(newPixelClasses.toArray(new VCPixelClass[newPixelClasses.size()]));
            simGeometry = new Geometry(geometry, newImage);
            Nz = 3;
        }
        GeometrySpec simGeometrySpec = simGeometry.getGeometrySpec();
        Extent simExtent = simGeometrySpec.getExtent();
        dx = simExtent.getX() / (Nx - 1);
        dy = simExtent.getY() / (Ny - 1);
        dz = simExtent.getZ() / (Nz - 1);
        if (Math.abs(dx - dy) > 0.1 * Math.max(dx, dy)) {
            dx = Math.min(dx, dy);
            dy = dx;
            Nx = (int) (simExtent.getX() / dx + 1);
            Ny = (int) (simExtent.getY() / dx + 1);
            if (dimension == 3) {
                dz = dx;
                Nz = (int) (simExtent.getZ() / dx + 1);
            }
        }
        deltaX = new Vect3d(dx, dy, dz);
        // one more point in each direction
        distanceMapMeshSize = new ISize(Nx + 1, Ny + 1, Nz + 1);
        Extent distanceMapExtent = new Extent(simExtent.getX() + dx, simExtent.getY() + dy, simExtent.getZ() + dz);
        simGeometrySpec.setExtent(distanceMapExtent);
        GeometrySurfaceDescription geoSurfaceDesc = simGeometry.getGeometrySurfaceDescription();
        geoSurfaceDesc.setVolumeSampleSize(distanceMapMeshSize);
        geoSurfaceDesc.updateAll();
        VCImage vcImage = RayCaster.sampleGeometry(simGeometry, distanceMapMeshSize, bCellCentered);
        SubvolumeSignedDistanceMap[] distanceMaps = DistanceMapGenerator.computeDistanceMaps(simGeometry, vcImage, bCellCentered);
        if (dimension == 2) {
            distanceMaps = DistanceMapGenerator.extractMiddleSlice(distanceMaps);
        }
        printWriter.println(FVInputFileKeyword.SUBDOMAINS + " " + simGeometrySpec.getNumSubVolumes() + " " + FVInputFileKeyword.DISTANCE_MAP);
        for (int i = 0; i < subVolumes.length; i++) {
            File distanceMapFile = new File(workingDirectory, getSimulationTask().getSimulationJobID() + "_" + subVolumes[i].getName() + DISTANCE_MAP_FILE_EXTENSION);
            writeDistanceMapFile(deltaX, distanceMaps[i], distanceMapFile);
            int phase = subDomainPhaseMap.get(subVolumes[i].getName());
            printWriter.println(subVolumes[i].getName() + " " + phase + " " + distanceMapFile.getAbsolutePath());
        }
    } else {
        printWriter.println(FVInputFileKeyword.SUBDOMAINS + " " + geometrySpec.getNumSubVolumes());
        Expression[] rvachevExps = convertAnalyticGeometryToRvachevFunction(geometrySpec);
        for (int i = 0; i < subVolumes.length; i++) {
            if (subVolumes[i] instanceof AnalyticSubVolume) {
                String name = subVolumes[i].getName();
                int phase = subDomainPhaseMap.get(name);
                printWriter.println(name + " " + phase + " ");
                printWriter.println(FVInputFileKeyword.IF + " " + rvachevExps[i].infix() + ";");
                printWriter.println(FVInputFileKeyword.USER + " " + ((AnalyticSubVolume) subVolumes[i]).getExpression().infix() + ";");
            }
        }
    }
    printWriter.println(FVInputFileKeyword.MAX_BOX_SIZE + " " + chomboSolverSpec.getMaxBoxSize());
    printWriter.println(FVInputFileKeyword.FILL_RATIO + " " + chomboSolverSpec.getFillRatio());
    printWriter.println(FVInputFileKeyword.RELATIVE_TOLERANCE + " " + simulation.getSolverTaskDescription().getErrorTolerance().getRelativeErrorTolerance());
    printWriter.println(FVInputFileKeyword.SAVE_VCELL_OUTPUT + " " + chomboSolverSpec.isSaveVCellOutput());
    printWriter.println(FVInputFileKeyword.SAVE_CHOMBO_OUTPUT + " " + chomboSolverSpec.isSaveChomboOutput());
    printWriter.println(FVInputFileKeyword.ACTIVATE_FEATURE_UNDER_DEVELOPMENT + " " + chomboSolverSpec.isActivateFeatureUnderDevelopment());
    printWriter.println(FVInputFileKeyword.SMALL_VOLFRAC_THRESHOLD + " " + chomboSolverSpec.getSmallVolfracThreshold());
    printWriter.println(FVInputFileKeyword.BLOCK_FACTOR + " " + chomboSolverSpec.getBlockFactor());
    printWriter.println(FVInputFileKeyword.TAGS_GROW + " " + chomboSolverSpec.getTagsGrow());
    // Refinement
    int numLevels = chomboSolverSpec.getNumRefinementLevels();
    // Refinements #Levels ratio 1, ratio 2, etc
    printWriter.print(FVInputFileKeyword.REFINEMENTS + " " + (numLevels + 1));
    List<Integer> ratios = chomboSolverSpec.getRefineRatioList();
    for (int i : ratios) {
        printWriter.print(" " + i);
    }
    // write last refinement ratio, fake
    printWriter.println(" 2");
    // membrane rois
    List<RefinementRoi> memRios = chomboSolverSpec.getMembraneRefinementRois();
    printWriter.println(FVInputFileKeyword.REFINEMENT_ROIS + " " + RoiType.Membrane + " " + memRios.size());
    for (RefinementRoi roi : memRios) {
        if (roi.getRoiExpression() == null) {
            throw new SolverException("ROI expression cannot be null");
        }
        // level tagsGrow ROIexpression
        printWriter.println(roi.getLevel() + " " + roi.getRoiExpression().infix() + ";");
    }
    List<RefinementRoi> volRios = chomboSolverSpec.getVolumeRefinementRois();
    printWriter.println(FVInputFileKeyword.REFINEMENT_ROIS + " " + RoiType.Volume + " " + volRios.size());
    for (RefinementRoi roi : volRios) {
        if (roi.getRoiExpression() == null) {
            throw new SolverException("ROI expression cannot be null");
        }
        printWriter.println(roi.getLevel() + " " + roi.getRoiExpression().infix() + ";");
    }
    printWriter.println(FVInputFileKeyword.VIEW_LEVEL + " " + chomboSolverSpec.getViewLevel());
    printWriter.println(FVInputFileKeyword.CHOMBO_SPEC_END);
    printWriter.println();
}

Example 13 with SolverTaskDescription

use of cbit.vcell.solver.SolverTaskDescription 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 14 with SolverTaskDescription

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

the class AdamsMoultonFiveSolver method integrate.

/**
 * This method was created by a SmartGuide.
 *  THIS HAS NOT BEEN UPDATED LIKE ODEIntegrator.integrate () and
 *  RungeKuttaFehlbergIntegrator.integrate()...
 */
protected void integrate() throws SolverException, UserStopException, IOException {
    try {
        SolverTaskDescription taskDescription = simTask.getSimulation().getSolverTaskDescription();
        double timeStep = taskDescription.getTimeStep().getDefaultTimeStep();
        fieldCurrentTime = taskDescription.getTimeBounds().getStartingTime();
        // before computation begins, settle fast equilibrium
        if (getFastAlgebraicSystem() != null) {
            fieldValueVectors.copyValues(0, 1);
            getFastAlgebraicSystem().initVars(getValueVector(0), getValueVector(1));
            getFastAlgebraicSystem().solveSystem(getValueVector(0), getValueVector(1));
            fieldValueVectors.copyValues(1, 0);
        }
        // check for failure
        check(getValueVector(0));
        // Evaluate
        for (int i = 0; i < getStateVariableCount(); i++) {
            f[0][getVariableIndex(i)] = evaluate(getValueVector(0), i);
        }
        // check for failure
        check(getValueVector(0));
        updateResultSet();
        // 
        int iteration = 0;
        while (fieldCurrentTime < taskDescription.getTimeBounds().getEndingTime()) {
            checkForUserStop();
            if (iteration < 3) {
                // Take Runge-Kutta step...
                prep(fieldCurrentTime, timeStep);
            } else {
                // Take Adams-Moulton step...
                step(fieldCurrentTime, timeStep);
            }
            // update (old = new)
            fieldValueVectors.copyValuesDown();
            // compute fast system
            if (getFastAlgebraicSystem() != null) {
                fieldValueVectors.copyValues(0, 1);
                getFastAlgebraicSystem().initVars(getValueVector(0), getValueVector(1));
                getFastAlgebraicSystem().solveSystem(getValueVector(0), getValueVector(1));
                fieldValueVectors.copyValues(1, 0);
            }
            // check for failure
            check(getValueVector(0));
            if (iteration < 3) {
                for (int i = 0; i < getStateVariableCount(); i++) {
                    f[iteration + 1][getVariableIndex(i)] = evaluate(getValueVector(0), i);
                }
                // check for failure
                check(f[iteration + 1]);
            } else {
                // Evaluate
                for (int i = 0; i < getStateVariableCount(); i++) {
                    f[4][getVariableIndex(i)] = evaluate(getValueVector(0), i);
                }
                // check for failure
                check(f[4]);
                shiftWorkArrays();
            }
            // fieldCurrentTime += timeStep;
            iteration++;
            fieldCurrentTime = taskDescription.getTimeBounds().getStartingTime() + iteration * timeStep;
            // store results if it coincides with a save interval
            if (taskDescription.getOutputTimeSpec().isDefault()) {
                int keepEvery = ((DefaultOutputTimeSpec) taskDescription.getOutputTimeSpec()).getKeepEvery();
                if ((iteration % keepEvery) == 0)
                    updateResultSet();
            }
        }
        // store last time point
        if (taskDescription.getOutputTimeSpec().isDefault()) {
            int keepEvery = ((DefaultOutputTimeSpec) taskDescription.getOutputTimeSpec()).getKeepEvery();
            if ((iteration % keepEvery) == 0)
                updateResultSet();
        }
    } catch (ExpressionException expressionException) {
        throw new SolverException(expressionException.getMessage());
    } catch (MathException mathException) {
        throw new SolverException(mathException.getMessage());
    }
}

Example 15 with SolverTaskDescription

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

the class OdeFileWriter method createStateVariables.

private void createStateVariables() throws Exception {
    Simulation simulation = simTask.getSimulation();
    MathDescription mathDescription = simulation.getMathDescription();
    SolverTaskDescription solverTaskDescription = simulation.getSolverTaskDescription();
    // get Ode's from MathDescription and create ODEStateVariables
    Enumeration<Equation> enum1 = mathDescription.getSubDomains().nextElement().getEquations();
    SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
    while (enum1.hasMoreElements()) {
        Equation equation = enum1.nextElement();
        if (equation instanceof OdeEquation) {
            fieldStateVariables.addElement(new ODEStateVariable((OdeEquation) equation, simSymbolTable));
        } else {
            throw new MathException("encountered non-ode equation, unsupported");
        }
    }
    // Get sensitivity variables
    Variable[] variables = simSymbolTable.getVariables();
    Vector<SensVariable> sensVariables = new Vector<SensVariable>();
    Constant sensitivityParameter = solverTaskDescription.getSensitivityParameter();
    if (sensitivityParameter != null) {
        Constant origSensParam = sensitivityParameter;
        Constant overriddenSensParam = (Constant) simSymbolTable.getVariable(origSensParam.getName());
        for (int i = 0; i < variables.length; i++) {
            if (variables[i] instanceof VolVariable) {
                VolVariable volVariable = (VolVariable) variables[i];
                SensVariable sv = new SensVariable(volVariable, overriddenSensParam);
                sensVariables.addElement(sv);
            }
        }
    }
    if (rateSensitivity == null) {
        rateSensitivity = new RateSensitivity(mathDescription, mathDescription.getSubDomains().nextElement());
    }
    if (jacobian == null) {
        jacobian = new Jacobian(mathDescription, mathDescription.getSubDomains().nextElement());
    }
    // get Jacobian and RateSensitivities from MathDescription and create SensStateVariables
    for (int v = 0; v < sensVariables.size(); v++) {
        fieldStateVariables.addElement(new SensStateVariable(sensVariables.elementAt(v), rateSensitivity, jacobian, sensVariables, simSymbolTable));
    }
}