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

Example 1 with ChomboSolverSpec

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

the class ChomboSolverSpecPanel method updateDisplay.

private void updateDisplay() {
    if (!simulation.getSolverTaskDescription().getSolverDescription().isChomboSolver()) {
        setVisible(false);
        return;
    }
    setVisible(true);
    ChomboSolverSpec chomboSolverSpec = simulation.getSolverTaskDescription().getChomboSolverSpec();
    maxBoxSizeComboBox.setSelectedItem(chomboSolverSpec.getMaxBoxSize());
    blockFactorComboBox.setSelectedItem(chomboSolverSpec.getBlockFactor());
    fillRatioTextField.setText(chomboSolverSpec.getFillRatio() + "");
    checkBoxTagsGrow.setSelected(chomboSolverSpec.isTagsGrowEnabled());
    updateViewLevel();
    updateFinestInfoPanel();
}

Example 2 with ChomboSolverSpec

use of org.vcell.chombo.ChomboSolverSpec 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 3 with ChomboSolverSpec

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

the class FVSolverStandalone method getChomboCommands.

private Collection<ExecutableCommand> getChomboCommands() {
    assert (isChombo);
    ArrayList<ExecutableCommand> commands = new ArrayList<ExecutableCommand>(2);
    String inputFilename = getInputFilename();
    String executableName = null;
    Simulation simulation = getSimulationJob().getSimulation();
    SolverTaskDescription sTaskDesc = simulation.getSolverTaskDescription();
    final boolean isParallel = sTaskDesc.isParallel();
    int dimension = simulation.getMeshSpecification().getGeometry().getDimension();
    switch(dimension) {
        case 2:
            try {
                executableName = SolverUtilities.getExes(SolverDescription.Chombo)[0].getAbsolutePath();
            } catch (IOException e) {
                throw new RuntimeException("failed to get executable for 2D solver " + SolverDescription.Chombo.getDisplayLabel() + ": " + e.getMessage(), e);
            }
            break;
        case 3:
            try {
                executableName = SolverUtilities.getExes(SolverDescription.Chombo)[1].getAbsolutePath();
            } catch (IOException e) {
                throw new RuntimeException("failed to get executable for 3D solver " + SolverDescription.Chombo.getDisplayLabel() + ": " + e.getMessage(), e);
            }
            break;
        default:
            throw new IllegalArgumentException("VCell Chombo solver does not support " + dimension + "problems");
    }
    if (isParallel) {
        String parallelName = executableName + "parallel";
        ExecutableCommand solve = new ExecutableCommand(new ExecutableCommand.LibraryPath(ResourceUtil.getLocalSolversDirectory().getAbsolutePath()), true, true, parallelName, inputFilename);
        commands.add(solve);
        ChomboSolverSpec css = sTaskDesc.getChomboSolverSpec();
        Objects.requireNonNull(css);
        if (css.isSaveVCellOutput()) {
            ExecutableCommand convertChomboData = new ExecutableCommand(new ExecutableCommand.LibraryPath(ResourceUtil.getLocalSolversDirectory().getAbsolutePath()), true, false, executableName, "-ccd", inputFilename);
            commands.add(convertChomboData);
        }
    } else {
        ExecutableCommand ec = new ExecutableCommand(new ExecutableCommand.LibraryPath(ResourceUtil.getLocalSolversDirectory().getAbsolutePath()), true, false, executableName, inputFilename);
        commands.add(ec);
        primaryCommand = ec;
    }
    return commands;
}

Example 4 with ChomboSolverSpec

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

the class SolverTaskDescription method propertyChange.

/**
 * This method gets called when a bound property is changed.
 * @param evt A PropertyChangeEvent object describing the event source
 *   and the property that has changed.
 */
public void propertyChange(java.beans.PropertyChangeEvent evt) {
    try {
        if (evt.getSource() == this && (evt.getPropertyName().equals(PROPERTY_SOLVER_DESCRIPTION))) {
            SolverDescription solverDescription = getSolverDescription();
            if (solverDescription.equals(SolverDescription.SundialsPDE) || solverDescription.isSemiImplicitPdeSolver() || solverDescription.isGibsonSolver()) {
                TimeBounds timeBounds = getTimeBounds();
                if (!(getOutputTimeSpec() instanceof UniformOutputTimeSpec)) {
                    // set to uniform output if it is not.
                    double outputTime = (timeBounds.getEndingTime() - timeBounds.getStartingTime()) / 20;
                    setOutputTimeSpec(new UniformOutputTimeSpec(outputTime));
                }
                if (solverDescription.equals(SolverDescription.SundialsPDE)) {
                    setErrorTolerance(ErrorTolerance.getDefaultSundialsErrorTolerance());
                    setDefaultTimeStep(TimeStep.getDefaultSundialsTimeStep());
                    if (sundialsPdeSolverOptions == null) {
                        sundialsPdeSolverOptions = new SundialsPdeSolverOptions();
                    }
                } else {
                    sundialsPdeSolverOptions = null;
                    setErrorTolerance(ErrorTolerance.getDefaultSemiImplicitErrorTolerance());
                }
            } else if (!solverDescription.supports(getOutputTimeSpec())) {
                setOutputTimeSpec(solverDescription.createOutputTimeSpec(this));
            }
            if (solverDescription.isNonSpatialStochasticSolver()) {
                if (fieldNonspatialStochOpt == null) {
                    setStochOpt(new NonspatialStochSimOptions());
                } else {
                    setStochOpt(new NonspatialStochSimOptions(fieldNonspatialStochOpt));
                }
                if (!solverDescription.equals(SolverDescription.StochGibson)) {
                    if (fieldNonspatialStochHybridOpt == null) {
                        setStochHybridOpt(new NonspatialStochHybridOptions());
                    }
                }
            } else if (solverDescription.isSpatialStochasticSolver()) {
                setTimeStep(TimeStep.getDefaultSmoldynTimeStep());
                if (smoldynSimulationOptions == null) {
                    smoldynSimulationOptions = new SmoldynSimulationOptions();
                }
            // setSmoldynDefaultTimeStep();
            }
            if (solverDescription.isNFSimSolver()) {
                if (nfsimSimulationOptions == null) {
                    nfsimSimulationOptions = new NFsimSimulationOptions();
                }
            }
            if (solverDescription.isChomboSolver()) {
                if (chomboSolverSpec == null && getSimulation() != null) {
                    chomboSolverSpec = new ChomboSolverSpec(ChomboSolverSpec.getDefaultMaxBoxSize(getSimulation().getMathDescription().getGeometry().getDimension()));
                }
                if (getOutputTimeSpec() == null || !(getOutputTimeSpec() instanceof UniformOutputTimeSpec)) {
                    double outputTime = getTimeBounds().getEndingTime() / 10;
                    setOutputTimeSpec(new UniformOutputTimeSpec(outputTime));
                }
                if (chomboSolverSpec != null && chomboSolverSpec.getTimeIntervalList().size() == 0) {
                    chomboSolverSpec.addTimeInterval(TimeInterval.getDefaultTimeInterval());
                }
            } else {
                chomboSolverSpec = null;
            }
            if (solverDescription.isMovingBoundarySolver()) {
                if (movingBoundarySolverOptions == null && getSimulation() != null) {
                    movingBoundarySolverOptions = new MovingBoundarySolverOptions();
                }
            } else {
                movingBoundarySolverOptions = null;
            }
        }
    } catch (PropertyVetoException e) {
        e.printStackTrace();
    }
}

Example 5 with ChomboSolverSpec

use of org.vcell.chombo.ChomboSolverSpec 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;
}