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

Example 16 with SolverException

use of cbit.vcell.solver.SolverException 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 17 with SolverException

use of cbit.vcell.solver.SolverException 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 18 with SolverException

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

the class AdamsMoultonFiveSolver method step.

/**
 * Integrate over time step using the forward Euler method (1st order explicit)
 * results must be stored in NumVectors-1 = vector(4);
 *  t is the current time
 *  h is the time step
 */
protected void step(double t, double h) throws SolverException {
    try {
        double[] oldValues = getValueVector(0);
        double[] newValues = getValueVector(1);
        // 
        // update time
        oldValues[getTimeIndex()] = t;
        newValues[getTimeIndex()] = t + h;
        // Predict
        for (int i = 0; i < getStateVariableCount(); i++) {
            int I = getVariableIndex(i);
            newValues[I] = oldValues[I] + h * (55.0 * f[3][I] - 59.0 * f[2][I] + 37.0 * f[1][I] - 9.0 * f[0][I]) / 24.0;
        }
        // Evaluate
        for (int i = 0; i < getStateVariableCount(); i++) {
            f[4][getVariableIndex(i)] = evaluate(newValues, i);
        }
        // Correct
        for (int i = 0; i < getStateVariableCount(); i++) {
            int I = getVariableIndex(i);
            newValues[I] = oldValues[I] + h * (9.0 * f[4][I] + 19.0 * f[3][I] - 5.0 * f[2][I] + 1.0 * f[1][I]) / 24.0;
        }
    } catch (ExpressionException expressionException) {
        throw new SolverException(expressionException.getMessage());
    }
}

Example 19 with SolverException

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

the class CVodeSolverStandalone method initialize.

/**
 *  This method takes the place of the old runUnsteady()...
 */
protected void initialize() throws SolverException {
    fireSolverStarting(SimulationMessage.MESSAGE_SOLVEREVENT_STARTING_INIT);
    super.initialize();
    String inputFilename = getInputFilename();
    setSolverStatus(new SolverStatus(SolverStatus.SOLVER_RUNNING, SimulationMessage.MESSAGE_SOLVER_RUNNING_INPUT_FILE));
    fireSolverStarting(SimulationMessage.MESSAGE_SOLVEREVENT_STARTING_INPUT_FILE);
    PrintWriter pw = null;
    try {
        pw = new java.io.PrintWriter(inputFilename);
        CVodeFileWriter cvodeFileWriter = new CVodeFileWriter(pw, simTask, bMessaging);
        cvodeFileWriter.write();
    } catch (Exception e) {
        setSolverStatus(new SolverStatus(SolverStatus.SOLVER_ABORTED, SimulationMessage.solverAborted("CVODE solver could not generate input file: " + e.getMessage())));
        e.printStackTrace(System.out);
        throw new SolverException("CVODE solver could not generate input file: " + e.getMessage());
    } finally {
        if (pw != null) {
            pw.close();
        }
    }
    setSolverStatus(new SolverStatus(SolverStatus.SOLVER_RUNNING, SimulationMessage.MESSAGE_SOLVER_RUNNING_START));
    setMathExecutable(new MathExecutable(getMathExecutableCommand(), getSaveDirectory()));
}

Example 20 with SolverException

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

the class AbstractJavaSolver method runSolver.

/**
 * Insert the method's description here.
 * Creation date: (6/26/2001 3:08:31 PM)
 */
public void runSolver() {
    try {
        fieldRunning = true;
        setSolverStatus(new SolverStatus(SolverStatus.SOLVER_STARTING, SimulationMessage.MESSAGE_SOLVER_STARTING_INIT));
        fireSolverStarting(SimulationMessage.MESSAGE_SOLVEREVENT_STARTING_INIT);
        initialize();
        setSolverStatus(new SolverStatus(SolverStatus.SOLVER_RUNNING, SimulationMessage.MESSAGE_SOLVER_RUNNING_START));
        fireSolverProgress(getProgress());
        integrate();
        setSolverStatus(new SolverStatus(SolverStatus.SOLVER_FINISHED, SimulationMessage.MESSAGE_SOLVER_FINISHED));
        fireSolverFinished();
    } catch (SolverException integratorException) {
        lg.error(integratorException.getMessage(), integratorException);
        SimulationMessage simulationMessage = SimulationMessage.solverAborted(integratorException.getMessage());
        setSolverStatus(new SolverStatus(SolverStatus.SOLVER_ABORTED, simulationMessage));
        fireSolverAborted(simulationMessage);
    } catch (IOException ioException) {
        lg.error(ioException.getMessage(), ioException);
        SimulationMessage simulationMessage = SimulationMessage.solverAborted(ioException.getMessage());
        setSolverStatus(new SolverStatus(SolverStatus.SOLVER_ABORTED, simulationMessage));
        fireSolverAborted(simulationMessage);
    } catch (UserStopException userStopException) {
        lg.error(userStopException.getMessage(), userStopException);
        setSolverStatus(new SolverStatus(SolverStatus.SOLVER_STOPPED, SimulationMessage.solverStopped(userStopException.getMessage())));
        fireSolverStopped();
    } catch (Exception e) {
        lg.error("AbstractJavaSolver.runSolver() : Caught Throwable instead of SolverException -- THIS EXCEPTION SHOULD NOT HAPPEN!", e);
        SimulationMessage simulationMessage = SimulationMessage.solverAborted(e.getMessage());
        setSolverStatus(new SolverStatus(SolverStatus.SOLVER_ABORTED, simulationMessage));
        fireSolverAborted(simulationMessage);
    } finally {
        fieldRunning = false;
    }
}