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

Example 51 with SolverException

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

the class SmoldynFileWriter method writeMeshFile.

private void writeMeshFile() throws SolverException {
    FileOutputStream fos = null;
    try {
        polygonMembaneElementMap = new HashMap<Polygon, MembraneElement>();
        cartesianMesh = CartesianMesh.createSimpleCartesianMesh(resampledGeometry, polygonMembaneElementMap);
        // Write Mesh file
        File meshFile = new File(baseFileName + SimDataConstants.MESHFILE_EXTENSION);
        fos = new FileOutputStream(meshFile);
        cartesianMesh.write(new PrintStream(fos));
    } catch (Exception e) {
        e.printStackTrace(System.out);
        throw new SolverException(e.getMessage());
    } finally {
        try {
            if (fos != null) {
                fos.close();
            }
        } catch (IOException e) {
            e.printStackTrace();
        }
    }
}

Example 52 with SolverException

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

the class SmoldynFileWriter method write.

@Override
public void write(String[] parameterNames) throws ExpressionException, MathException, SolverException, DataAccessException, IOException, ImageException, PropertyVetoException, GeometryException {
    init();
    setupMolecules();
    if (bUseMessaging) {
        writeJms(simulation);
    }
    writeRandomSeed();
    writeSpecies();
    writeDiffusions();
    writeGraphicsOpenGL();
    if (simulation.getSolverTaskDescription().getSmoldynSimulationOptions().isUseHighResolutionSample()) {
        try {
            writeHighResVolumeSamples();
        } catch (Exception ex) {
            ex.printStackTrace(System.out);
            throw new SolverException(ex.getMessage() + "\n" + "Problem may be solved by disable \'fast mesh sampling\'. It may take much longer time to complete the simulation." + "\n" + "Select \'Edit Simulation\' -> \'Solver\' -> \'Advanced Solver Options\' -> uncheck \'fast mesh sampling\'.");
        }
    }
    writeSurfaces();
    writeCompartments();
    // needs to be after dim=3 in input file (after geometry is written).
    writeDrifts();
    writeReactions();
    writeMolecules();
    writeSimulationTimes();
    writeRuntimeCommands();
    writeSimulationSettings();
    printWriter.println(SmoldynVCellMapper.SmoldynKeyword.end_file);
// SimulationWriter.write(SimulationJobToSmoldyn.convertSimulationJob(simulationJob, outputFile), printWriter, simulationJob);
}

Example 53 with SolverException

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

the class SmoldynFileWriter method writeWallSurfaces.

private void writeWallSurfaces() throws SolverException {
    GeometrySurfaceDescription geometrySurfaceDescription = resampledGeometry.getGeometrySurfaceDescription();
    GeometrySpec geometrySpec = resampledGeometry.getGeometrySpec();
    SubVolume[] subVolumes = geometrySpec.getSubVolumes();
    printWriter.println("# boundaries");
    Origin origin = geometrySpec.getOrigin();
    Extent extent = geometrySpec.getExtent();
    Coordinate lowWall = new Coordinate(origin.getX(), origin.getY(), origin.getZ());
    Coordinate highWall = new Coordinate(origin.getX() + extent.getX(), origin.getY() + extent.getY(), origin.getZ() + extent.getZ());
    // potential artifact.
    if (bHasNoSurface) {
        SubDomain subDomain0 = mathDesc.getSubDomains().nextElement();
        CompartmentSubDomain compartSubDomain0 = null;
        compartSubDomain0 = (CompartmentSubDomain) subDomain0;
        // x
        if (compartSubDomain0.getBoundaryConditionXm().isPERIODIC()) {
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.boundaries + " 0 " + lowWall.getX() + " " + highWall.getX() + " " + SmoldynVCellMapper.SmoldynKeyword.p);
        } else {
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.low_wall + " 0 " + lowWall.getX() + " " + (compartSubDomain0.getBoundaryConditionXm().isNEUMANN() ? SmoldynVCellMapper.SmoldynKeyword.r : SmoldynVCellMapper.SmoldynKeyword.a));
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.high_wall + " 0 " + highWall.getX() + " " + (compartSubDomain0.getBoundaryConditionXp().isNEUMANN() ? SmoldynVCellMapper.SmoldynKeyword.r : SmoldynVCellMapper.SmoldynKeyword.a));
        }
        if (dimension > 1) {
            // y
            if (compartSubDomain0.getBoundaryConditionYm().isPERIODIC()) {
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.boundaries + " 1 " + lowWall.getY() + " " + highWall.getY() + " " + SmoldynVCellMapper.SmoldynKeyword.p);
            } else {
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.low_wall + " 1 " + lowWall.getY() + " " + (compartSubDomain0.getBoundaryConditionYm().isNEUMANN() ? SmoldynVCellMapper.SmoldynKeyword.r : SmoldynVCellMapper.SmoldynKeyword.a));
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.high_wall + " 1 " + highWall.getY() + " " + (compartSubDomain0.getBoundaryConditionYp().isNEUMANN() ? SmoldynVCellMapper.SmoldynKeyword.r : SmoldynVCellMapper.SmoldynKeyword.a));
            }
            if (dimension > 2) {
                // z
                if (compartSubDomain0.getBoundaryConditionZm().isPERIODIC()) {
                    printWriter.println(SmoldynVCellMapper.SmoldynKeyword.boundaries + " 2 " + lowWall.getZ() + " " + highWall.getZ() + " " + SmoldynVCellMapper.SmoldynKeyword.p);
                } else {
                    printWriter.println(SmoldynVCellMapper.SmoldynKeyword.low_wall + " 2 " + lowWall.getZ() + " " + (compartSubDomain0.getBoundaryConditionZm().isNEUMANN() ? SmoldynVCellMapper.SmoldynKeyword.r : SmoldynVCellMapper.SmoldynKeyword.a));
                    printWriter.println(SmoldynVCellMapper.SmoldynKeyword.high_wall + " 2 " + highWall.getZ() + " " + (compartSubDomain0.getBoundaryConditionZp().isNEUMANN() ? SmoldynVCellMapper.SmoldynKeyword.r : SmoldynVCellMapper.SmoldynKeyword.a));
                }
            }
        }
        printWriter.println();
    } else {
        // x
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.boundaries + " 0 " + lowWall.getX() + " " + highWall.getX());
        if (dimension > 1) {
            // y
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.boundaries + " 1 " + lowWall.getY() + " " + highWall.getY());
            if (dimension > 2) {
                // z
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.boundaries + " 2 " + lowWall.getZ() + " " + highWall.getZ());
            }
        }
        printWriter.println();
        // bounding walls as surfaces
        // have to find boundary condition type
        ISize sampleSize = simulation.getMeshSpecification().getSamplingSize();
        int numX = sampleSize.getX();
        int numY = dimension < 2 ? 1 : sampleSize.getY();
        int numZ = dimension < 3 ? 1 : sampleSize.getZ();
        if (dimension > 2) {
            int[] k_wall = new int[] { 0, numZ - 1 };
            for (int k = 0; k < k_wall.length; k++) {
                for (int j = 0; j < numY; j++) {
                    for (int i = 0; i < numX; i++) {
                        int volIndex = k_wall[k] * numX * numY + j * numX + i;
                        for (SubVolume sv : subVolumes) {
                            // gather all the points in all the regions
                            GeometricRegion[] geometricRegions = geometrySurfaceDescription.getGeometricRegions(sv);
                            RegionInfo[] regionInfos = geometrySurfaceDescription.getRegionImage().getRegionInfos();
                            for (GeometricRegion gr : geometricRegions) {
                                VolumeGeometricRegion vgr = (VolumeGeometricRegion) gr;
                                for (RegionInfo ri : regionInfos) {
                                    if (ri.getRegionIndex() == vgr.getRegionID() && ri.isIndexInRegion(volIndex)) {
                                        boundaryZSubVolumes.add(sv);
                                    }
                                }
                            }
                        }
                    }
                }
            }
        }
        if (dimension > 1) {
            int[] j_wall = new int[] { 0, numY - 1 };
            for (int k = 0; k < numZ; k++) {
                for (int j = 0; j < j_wall.length; j++) {
                    for (int i = 0; i < numX; i++) {
                        int volIndex = k * numX * numY + j_wall[j] * numX + i;
                        for (SubVolume sv : subVolumes) {
                            // gather all the points in all the regions
                            GeometricRegion[] geometricRegions = geometrySurfaceDescription.getGeometricRegions(sv);
                            RegionInfo[] regionInfos = geometrySurfaceDescription.getRegionImage().getRegionInfos();
                            for (GeometricRegion gr : geometricRegions) {
                                VolumeGeometricRegion vgr = (VolumeGeometricRegion) gr;
                                for (RegionInfo ri : regionInfos) {
                                    if (ri.getRegionIndex() == vgr.getRegionID() && ri.isIndexInRegion(volIndex)) {
                                        boundaryYSubVolumes.add(sv);
                                    }
                                }
                            }
                        }
                    }
                }
            }
        }
        int[] i_wall = new int[] { 0, numX - 1 };
        for (int k = 0; k < numZ; k++) {
            for (int j = 0; j < numY; j++) {
                for (int i = 0; i < i_wall.length; i++) {
                    int volIndex = k * numX * numY + j * numX + i_wall[i];
                    for (SubVolume sv : subVolumes) {
                        // gather all the points in all the regions
                        GeometricRegion[] geometricRegions = geometrySurfaceDescription.getGeometricRegions(sv);
                        RegionInfo[] regionInfos = geometrySurfaceDescription.getRegionImage().getRegionInfos();
                        for (GeometricRegion gr : geometricRegions) {
                            VolumeGeometricRegion vgr = (VolumeGeometricRegion) gr;
                            for (RegionInfo ri : regionInfos) {
                                if (ri.getRegionIndex() == vgr.getRegionID() && ri.isIndexInRegion(volIndex)) {
                                    boundaryXSubVolumes.add(sv);
                                }
                            }
                        }
                    }
                }
            }
        }
        Set<SubVolume> boundarySubVolumes = new HashSet<SubVolume>();
        boundarySubVolumes.addAll(boundaryXSubVolumes);
        boundarySubVolumes.addAll(boundaryYSubVolumes);
        boundarySubVolumes.addAll(boundaryZSubVolumes);
        BoundaryConditionType[] computedBct = new BoundaryConditionType[dimension * 2];
        String[] smoldynBct = new String[dimension * 2];
        String[] wallNames = new String[] { "Xm", "Xp", "Ym", "Yp", "Zm", "Zp" };
        if (boundarySubVolumes.size() >= 1) {
            for (SubVolume sv : boundarySubVolumes) {
                CompartmentSubDomain csd = (CompartmentSubDomain) mathDesc.getSubDomain(sv.getName());
                BoundaryConditionType[] bct = new BoundaryConditionType[] { csd.getBoundaryConditionXm(), csd.getBoundaryConditionXp(), csd.getBoundaryConditionYm(), csd.getBoundaryConditionYp(), csd.getBoundaryConditionZm(), csd.getBoundaryConditionZp() };
                if (computedBct[0] == null) {
                    System.arraycopy(bct, 0, computedBct, 0, dimension * 2);
                    for (int i = 0; i < dimension * 2; i++) {
                        if (computedBct[i].isPERIODIC()) {
                            throw new SolverException("Models with both surfaces and periodic boundary conditions are not supported yet.");
                        }
                        smoldynBct[i] = computedBct[i].isDIRICHLET() ? SmoldynVCellMapper.SmoldynKeyword.absorb.name() : SmoldynVCellMapper.SmoldynKeyword.reflect.name();
                    }
                } else {
                    for (int i = 0; i < dimension * 2; i++) {
                        if (!computedBct[i].compareEqual(bct[i])) {
                            throw new SolverException(wallNames[i] + " wall has different boundary conditions");
                        }
                    }
                }
            }
        }
        printWriter.println("# bounding wall surface");
        // X walls
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.start_surface + " " + VCellSmoldynKeyword.bounding_wall_surface_X);
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.action + " " + SmoldynVCellMapper.SmoldynKeyword.all + "(" + SmoldynVCellMapper.SmoldynKeyword.up + ") " + SmoldynVCellMapper.SmoldynKeyword.both + " " + SmoldynVCellMapper.SmoldynKeyword.reflect);
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.action + " " + SmoldynVCellMapper.SmoldynKeyword.all + " " + SmoldynVCellMapper.SmoldynKeyword.front + " " + smoldynBct[0]);
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.action + " " + SmoldynVCellMapper.SmoldynKeyword.all + " " + SmoldynVCellMapper.SmoldynKeyword.back + " " + smoldynBct[1]);
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.color + " " + SmoldynVCellMapper.SmoldynKeyword.both + " 1 1 1");
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.polygon + " " + SmoldynVCellMapper.SmoldynKeyword.both + " " + SmoldynVCellMapper.SmoldynKeyword.edge);
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.max_panels + " " + SmoldynVCellMapper.SmoldynKeyword.rect + " 2");
        // yz walls
        switch(dimension) {
            case 1:
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.panel + " " + SmoldynVCellMapper.SmoldynKeyword.rect + " +0 " + lowWall.getX());
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.panel + " " + SmoldynVCellMapper.SmoldynKeyword.rect + " -0 " + highWall.getX());
                break;
            case 2:
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.panel + " " + SmoldynVCellMapper.SmoldynKeyword.rect + " +0 " + lowWall.getX() + " " + lowWall.getY() + " " + extent.getY());
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.panel + " " + SmoldynVCellMapper.SmoldynKeyword.rect + " -0 " + highWall.getX() + " " + lowWall.getY() + " " + extent.getY());
                break;
            case 3:
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.panel + " " + SmoldynVCellMapper.SmoldynKeyword.rect + " +0 " + lowWall.getX() + " " + lowWall.getY() + " " + lowWall.getZ() + " " + extent.getY() + " " + extent.getZ());
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.panel + " " + SmoldynVCellMapper.SmoldynKeyword.rect + " -0 " + highWall.getX() + " " + lowWall.getY() + " " + lowWall.getZ() + " " + extent.getY() + " " + extent.getZ());
                break;
        }
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.end_surface);
        printWriter.println();
        if (dimension > 1) {
            // Y walls
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.start_surface + " " + VCellSmoldynKeyword.bounding_wall_surface_Y);
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.action + " " + SmoldynVCellMapper.SmoldynKeyword.all + "(" + SmoldynVCellMapper.SmoldynKeyword.up + ") " + SmoldynVCellMapper.SmoldynKeyword.both + " " + SmoldynVCellMapper.SmoldynKeyword.reflect);
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.action + " " + SmoldynVCellMapper.SmoldynKeyword.all + " " + SmoldynVCellMapper.SmoldynKeyword.front + " " + smoldynBct[2]);
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.action + " " + SmoldynVCellMapper.SmoldynKeyword.all + " " + SmoldynVCellMapper.SmoldynKeyword.back + " " + smoldynBct[3]);
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.color + " " + SmoldynVCellMapper.SmoldynKeyword.both + " 1 1 1");
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.polygon + " " + SmoldynVCellMapper.SmoldynKeyword.both + " " + SmoldynVCellMapper.SmoldynKeyword.edge);
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.max_panels + " " + SmoldynVCellMapper.SmoldynKeyword.rect + " 2");
            // xz walls
            switch(dimension) {
                case 2:
                    printWriter.println(SmoldynVCellMapper.SmoldynKeyword.panel + " " + SmoldynVCellMapper.SmoldynKeyword.rect + " +1 " + lowWall.getX() + " " + lowWall.getY() + " " + extent.getX());
                    printWriter.println(SmoldynVCellMapper.SmoldynKeyword.panel + " " + SmoldynVCellMapper.SmoldynKeyword.rect + " -1 " + lowWall.getX() + " " + highWall.getY() + " " + extent.getX());
                    break;
                case 3:
                    printWriter.println(SmoldynVCellMapper.SmoldynKeyword.panel + " " + SmoldynVCellMapper.SmoldynKeyword.rect + " +1 " + lowWall.getX() + " " + lowWall.getY() + " " + lowWall.getZ() + " " + extent.getX() + " " + extent.getZ());
                    printWriter.println(SmoldynVCellMapper.SmoldynKeyword.panel + " " + SmoldynVCellMapper.SmoldynKeyword.rect + " -1 " + lowWall.getX() + " " + highWall.getY() + " " + lowWall.getZ() + " " + extent.getX() + " " + extent.getZ());
                    break;
            }
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.end_surface);
            printWriter.println();
            if (dimension > 2) {
                // Z walls
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.start_surface + " " + VCellSmoldynKeyword.bounding_wall_surface_Z);
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.action + " " + SmoldynVCellMapper.SmoldynKeyword.all + "(" + SmoldynVCellMapper.SmoldynKeyword.up + ") " + SmoldynVCellMapper.SmoldynKeyword.both + " " + SmoldynVCellMapper.SmoldynKeyword.reflect);
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.action + " " + SmoldynVCellMapper.SmoldynKeyword.all + " " + SmoldynVCellMapper.SmoldynKeyword.front + " " + smoldynBct[4]);
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.action + " " + SmoldynVCellMapper.SmoldynKeyword.all + " " + SmoldynVCellMapper.SmoldynKeyword.back + " " + smoldynBct[5]);
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.color + " " + SmoldynVCellMapper.SmoldynKeyword.both + " 1 1 1");
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.polygon + " " + SmoldynVCellMapper.SmoldynKeyword.both + " " + SmoldynVCellMapper.SmoldynKeyword.edge);
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.max_panels + " " + SmoldynVCellMapper.SmoldynKeyword.rect + " 2");
                // xy walls
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.panel + " " + SmoldynVCellMapper.SmoldynKeyword.rect + " +2 " + lowWall.getX() + " " + lowWall.getY() + " " + lowWall.getZ() + " " + extent.getX() + " " + extent.getY());
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.panel + " " + SmoldynVCellMapper.SmoldynKeyword.rect + " -2 " + lowWall.getX() + " " + lowWall.getY() + " " + highWall.getZ() + " " + extent.getX() + " " + extent.getY());
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.end_surface);
                printWriter.println();
            }
        }
    }
}