/*
This takes as input the coordinates for each vertex
*/
PetscErrorCode DMPlexBuildCoordinates_Private(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, const double vertexCoords[])
{
PetscSection coordSection;
Vec coordinates;
PetscScalar *coords;
PetscInt coordSize, v, d;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr);
ierr = PetscSectionSetFieldComponents(coordSection, 0, spaceDim);CHKERRQ(ierr);
ierr = PetscSectionSetChart(coordSection, numCells, numCells + numVertices);CHKERRQ(ierr);
for (v = numCells; v < numCells+numVertices; ++v) {
ierr = PetscSectionSetDof(coordSection, v, spaceDim);CHKERRQ(ierr);
ierr = PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);CHKERRQ(ierr);
}
ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr);
ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr);
ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr);
ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr);
ierr = VecSetFromOptions(coordinates);CHKERRQ(ierr);
ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr);
for (v = 0; v < numVertices; ++v) {
for (d = 0; d < spaceDim; ++d) {
coords[v*spaceDim+d] = vertexCoords[v*spaceDim+d];
}
}
ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr);
ierr = VecDestroy(&coordinates);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode DMPlexCopyCoordinates(DM dmA, DM dmB)
{
Vec coordinatesA, coordinatesB;
PetscSection coordSectionA, coordSectionB;
PetscScalar *coordsA, *coordsB;
PetscInt spaceDim, vStartA, vStartB, vEndA, vEndB, coordSizeB, v, d;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMPlexGetDepthStratum(dmA, 0, &vStartA, &vEndA);CHKERRQ(ierr);
ierr = DMPlexGetDepthStratum(dmB, 0, &vStartB, &vEndB);CHKERRQ(ierr);
if ((vEndA-vStartA) != (vEndB-vStartB)) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "The number of vertices in first DM %d != %d in the second DM", vEndA-vStartA, vEndB-vStartB);
ierr = DMPlexGetCoordinateSection(dmA, &coordSectionA);CHKERRQ(ierr);
ierr = DMPlexGetCoordinateSection(dmB, &coordSectionB);CHKERRQ(ierr);
ierr = PetscSectionSetNumFields(coordSectionB, 1);CHKERRQ(ierr);
ierr = PetscSectionGetFieldComponents(coordSectionA, 0, &spaceDim);CHKERRQ(ierr);
ierr = PetscSectionSetFieldComponents(coordSectionB, 0, spaceDim);CHKERRQ(ierr);
ierr = PetscSectionSetChart(coordSectionB, vStartB, vEndB);CHKERRQ(ierr);
for (v = vStartB; v < vEndB; ++v) {
ierr = PetscSectionSetDof(coordSectionB, v, spaceDim);CHKERRQ(ierr);
ierr = PetscSectionSetFieldDof(coordSectionB, v, 0, spaceDim);CHKERRQ(ierr);
}
ierr = PetscSectionSetUp(coordSectionB);CHKERRQ(ierr);
ierr = PetscSectionGetStorageSize(coordSectionB, &coordSizeB);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(dmA, &coordinatesA);CHKERRQ(ierr);
ierr = VecCreate(PetscObjectComm((PetscObject) dmB), &coordinatesB);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) coordinatesB, "coordinates");CHKERRQ(ierr);
ierr = VecSetSizes(coordinatesB, coordSizeB, PETSC_DETERMINE);CHKERRQ(ierr);
ierr = VecSetFromOptions(coordinatesB);CHKERRQ(ierr);
ierr = VecGetArray(coordinatesA, &coordsA);CHKERRQ(ierr);
ierr = VecGetArray(coordinatesB, &coordsB);CHKERRQ(ierr);
for (v = 0; v < vEndB-vStartB; ++v) {
for (d = 0; d < spaceDim; ++d) {
coordsB[v*spaceDim+d] = coordsA[v*spaceDim+d];
}
}
ierr = VecRestoreArray(coordinatesA, &coordsA);CHKERRQ(ierr);
ierr = VecRestoreArray(coordinatesB, &coordsB);CHKERRQ(ierr);
ierr = DMSetCoordinatesLocal(dmB, coordinatesB);CHKERRQ(ierr);
ierr = VecDestroy(&coordinatesB);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*
This takes as input the raw Hasse Diagram data
*/
PetscErrorCode DMPlexCreateFromDAG(DM dm, PetscInt depth, const PetscInt numPoints[], const PetscInt coneSize[], const PetscInt cones[], const PetscInt coneOrientations[], const PetscScalar vertexCoords[])
{
Vec coordinates;
PetscSection coordSection;
PetscScalar *coords;
PetscInt coordSize, firstVertex = numPoints[depth], pStart = 0, pEnd = 0, p, v, dim, d, off;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr);
for (d = 0; d <= depth; ++d) pEnd += numPoints[d];
ierr = DMPlexSetChart(dm, pStart, pEnd);CHKERRQ(ierr);
for (p = pStart; p < pEnd; ++p) {
ierr = DMPlexSetConeSize(dm, p, coneSize[p-pStart]);CHKERRQ(ierr);
}
ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */
for (p = pStart, off = 0; p < pEnd; off += coneSize[p-pStart], ++p) {
ierr = DMPlexSetCone(dm, p, &cones[off]);CHKERRQ(ierr);
ierr = DMPlexSetConeOrientation(dm, p, &coneOrientations[off]);CHKERRQ(ierr);
}
ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr);
ierr = DMPlexStratify(dm);CHKERRQ(ierr);
/* Build coordinates */
ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr);
ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr);
ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numPoints[0]);CHKERRQ(ierr);
for (v = firstVertex; v < firstVertex+numPoints[0]; ++v) {
ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr);
ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr);
}
ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr);
ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr);
ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr);
ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr);
ierr = VecSetFromOptions(coordinates);CHKERRQ(ierr);
ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr);
for (v = 0; v < numPoints[0]; ++v) {
PetscInt off;
ierr = PetscSectionGetOffset(coordSection, v+firstVertex, &off);CHKERRQ(ierr);
for (d = 0; d < dim; ++d) {
coords[off+d] = vertexCoords[v*dim+d];
}
}
ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr);
ierr = VecDestroy(&coordinates);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode ChangeCoordinates(DM dm, PetscInt spaceDim, PetscScalar vertexCoords[])
{
PetscSection coordSection;
Vec coordinates;
PetscScalar *coords;
PetscInt vStart, vEnd, v, d, coordSize;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr);
ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr);
ierr = PetscSectionSetFieldComponents(coordSection, 0, spaceDim);CHKERRQ(ierr);
ierr = PetscSectionSetChart(coordSection, vStart, vEnd);CHKERRQ(ierr);
for (v = vStart; v < vEnd; ++v) {
ierr = PetscSectionSetDof(coordSection, v, spaceDim);CHKERRQ(ierr);
ierr = PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);CHKERRQ(ierr);
}
ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr);
ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr);
ierr = VecCreate(PetscObjectComm((PetscObject) dm), &coordinates);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr);
ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr);
ierr = VecSetFromOptions(coordinates);CHKERRQ(ierr);
ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr);
for (v = vStart; v < vEnd; ++v) {
PetscInt off;
ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr);
for (d = 0; d < spaceDim; ++d) {
coords[off+d] = vertexCoords[(v-vStart)*spaceDim+d];
}
}
ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr);
ierr = VecDestroy(&coordinates);CHKERRQ(ierr);
ierr = DMSetFromOptions(dm);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
void PETSC_STDCALL dmplexgetcoordinatesection_(DM dm,PetscSection *section, int *__ierr ){
*__ierr = DMPlexGetCoordinateSection(
(DM)PetscToPointer((dm) ),section);
}
/*
Simple square boundary:
18--5-17--4--16
| | |
6 10 3
| | |
19-11-20--9--15
| | |
7 8 2
| | |
12--0-13--1--14
*/
PetscErrorCode DMPlexCreateSquareBoundary(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[])
{
PetscInt numVertices = (edges[0]+1)*(edges[1]+1);
PetscInt numEdges = edges[0]*(edges[1]+1) + (edges[0]+1)*edges[1];
PetscInt markerTop = 1;
PetscInt markerBottom = 1;
PetscInt markerRight = 1;
PetscInt markerLeft = 1;
PetscBool markerSeparate = PETSC_FALSE;
Vec coordinates;
PetscSection coordSection;
PetscScalar *coords;
PetscInt coordSize;
PetscMPIInt rank;
PetscInt v, vx, vy;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscOptionsGetBool(((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);CHKERRQ(ierr);
if (markerSeparate) {
markerTop = 1;
markerBottom = 0;
markerRight = 0;
markerLeft = 0;
}
ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr);
if (!rank) {
PetscInt e, ex, ey;
ierr = DMPlexSetChart(dm, 0, numEdges+numVertices);CHKERRQ(ierr);
for (e = 0; e < numEdges; ++e) {
ierr = DMPlexSetConeSize(dm, e, 2);CHKERRQ(ierr);
}
ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */
for (vx = 0; vx <= edges[0]; vx++) {
for (ey = 0; ey < edges[1]; ey++) {
PetscInt edge = vx*edges[1] + ey + edges[0]*(edges[1]+1);
PetscInt vertex = ey*(edges[0]+1) + vx + numEdges;
PetscInt cone[2];
cone[0] = vertex; cone[1] = vertex+edges[0]+1;
ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr);
if (vx == edges[0]) {
ierr = DMPlexSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr);
ierr = DMPlexSetLabelValue(dm, "marker", cone[0], markerRight);CHKERRQ(ierr);
if (ey == edges[1]-1) {
ierr = DMPlexSetLabelValue(dm, "marker", cone[1], markerRight);CHKERRQ(ierr);
}
} else if (vx == 0) {
ierr = DMPlexSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr);
ierr = DMPlexSetLabelValue(dm, "marker", cone[0], markerLeft);CHKERRQ(ierr);
if (ey == edges[1]-1) {
ierr = DMPlexSetLabelValue(dm, "marker", cone[1], markerLeft);CHKERRQ(ierr);
}
}
}
}
for (vy = 0; vy <= edges[1]; vy++) {
for (ex = 0; ex < edges[0]; ex++) {
PetscInt edge = vy*edges[0] + ex;
PetscInt vertex = vy*(edges[0]+1) + ex + numEdges;
PetscInt cone[2];
cone[0] = vertex; cone[1] = vertex+1;
ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr);
if (vy == edges[1]) {
ierr = DMPlexSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr);
ierr = DMPlexSetLabelValue(dm, "marker", cone[0], markerTop);CHKERRQ(ierr);
if (ex == edges[0]-1) {
ierr = DMPlexSetLabelValue(dm, "marker", cone[1], markerTop);CHKERRQ(ierr);
}
} else if (vy == 0) {
ierr = DMPlexSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr);
ierr = DMPlexSetLabelValue(dm, "marker", cone[0], markerBottom);CHKERRQ(ierr);
if (ex == edges[0]-1) {
ierr = DMPlexSetLabelValue(dm, "marker", cone[1], markerBottom);CHKERRQ(ierr);
}
}
}
}
}
ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr);
ierr = DMPlexStratify(dm);CHKERRQ(ierr);
/* Build coordinates */
ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
ierr = PetscSectionSetChart(coordSection, numEdges, numEdges + numVertices);CHKERRQ(ierr);
for (v = numEdges; v < numEdges+numVertices; ++v) {
ierr = PetscSectionSetDof(coordSection, v, 2);CHKERRQ(ierr);
}
ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr);
ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr);
ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr);
ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr);
ierr = VecSetFromOptions(coordinates);CHKERRQ(ierr);
ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr);
for (vy = 0; vy <= edges[1]; ++vy) {
for (vx = 0; vx <= edges[0]; ++vx) {
coords[(vy*(edges[0]+1)+vx)*2+0] = lower[0] + ((upper[0] - lower[0])/edges[0])*vx;
coords[(vy*(edges[0]+1)+vx)*2+1] = lower[1] + ((upper[1] - lower[1])/edges[1])*vy;
}
}
ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr);
ierr = VecDestroy(&coordinates);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*
Simple square mesh:
22--8-23--9--24
| | |
13 2 14 3 15
| | |
19--6-20--7--21
| | |
10 0 11 1 12
| | |
16--4-17--5--18
*/
PetscErrorCode DMPlexCreateSquareMesh(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[])
{
PetscInt markerTop = 1;
PetscInt markerBottom = 1;
PetscInt markerRight = 1;
PetscInt markerLeft = 1;
PetscBool markerSeparate = PETSC_FALSE;
PetscMPIInt rank;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);CHKERRQ(ierr);
if (markerSeparate) {
markerTop = 3;
markerBottom = 1;
markerRight = 2;
markerLeft = 4;
}
{
const PetscInt numXEdges = !rank ? edges[0] : 0;
const PetscInt numYEdges = !rank ? edges[1] : 0;
const PetscInt numXVertices = !rank ? edges[0]+1 : 0;
const PetscInt numYVertices = !rank ? edges[1]+1 : 0;
const PetscInt numTotXEdges = numXEdges*numYVertices;
const PetscInt numTotYEdges = numYEdges*numXVertices;
const PetscInt numVertices = numXVertices*numYVertices;
const PetscInt numEdges = numTotXEdges + numTotYEdges;
const PetscInt numFaces = numXEdges*numYEdges;
const PetscInt firstVertex = numFaces;
const PetscInt firstXEdge = numFaces + numVertices;
const PetscInt firstYEdge = numFaces + numVertices + numTotXEdges;
Vec coordinates;
PetscSection coordSection;
PetscScalar *coords;
PetscInt coordSize;
PetscInt v, vx, vy;
PetscInt f, fx, fy, e, ex, ey;
ierr = DMPlexSetChart(dm, 0, numFaces+numEdges+numVertices);CHKERRQ(ierr);
for (f = 0; f < numFaces; ++f) {
ierr = DMPlexSetConeSize(dm, f, 4);CHKERRQ(ierr);
}
for (e = firstXEdge; e < firstXEdge+numEdges; ++e) {
ierr = DMPlexSetConeSize(dm, e, 2);CHKERRQ(ierr);
}
ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */
/* Build faces */
for (fy = 0; fy < numYEdges; fy++) {
for (fx = 0; fx < numXEdges; fx++) {
const PetscInt face = fy*numXEdges + fx;
const PetscInt edgeL = firstYEdge + fx*numYEdges + fy;
const PetscInt edgeB = firstXEdge + fy*numXEdges + fx;
const PetscInt ornt[4] = {0, 0, -2, -2};
PetscInt cone[4];
cone[0] = edgeB; cone[1] = edgeL+numYEdges; cone[2] = edgeB+numXEdges; cone[3] = edgeL;
ierr = DMPlexSetCone(dm, face, cone);CHKERRQ(ierr);
ierr = DMPlexSetConeOrientation(dm, face, ornt);CHKERRQ(ierr);
}
}
/* Build Y edges*/
for (vx = 0; vx < numXVertices; vx++) {
for (ey = 0; ey < numYEdges; ey++) {
const PetscInt edge = firstYEdge + vx*numYEdges + ey;
const PetscInt vertex = firstVertex + ey*numXVertices + vx;
PetscInt cone[2];
cone[0] = vertex; cone[1] = vertex+numXVertices;
ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr);
if (vx == numXVertices-1) {
ierr = DMPlexSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr);
ierr = DMPlexSetLabelValue(dm, "marker", cone[0], markerRight);CHKERRQ(ierr);
if (ey == numYEdges-1) {
ierr = DMPlexSetLabelValue(dm, "marker", cone[1], markerRight);CHKERRQ(ierr);
}
} else if (vx == 0) {
ierr = DMPlexSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr);
ierr = DMPlexSetLabelValue(dm, "marker", cone[0], markerLeft);CHKERRQ(ierr);
if (ey == numYEdges-1) {
ierr = DMPlexSetLabelValue(dm, "marker", cone[1], markerLeft);CHKERRQ(ierr);
}
}
}
}
/* Build X edges*/
for (vy = 0; vy < numYVertices; vy++) {
for (ex = 0; ex < numXEdges; ex++) {
const PetscInt edge = firstXEdge + vy*numXEdges + ex;
const PetscInt vertex = firstVertex + vy*numXVertices + ex;
PetscInt cone[2];
cone[0] = vertex; cone[1] = vertex+1;
ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr);
if (vy == numYVertices-1) {
ierr = DMPlexSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr);
ierr = DMPlexSetLabelValue(dm, "marker", cone[0], markerTop);CHKERRQ(ierr);
if (ex == numXEdges-1) {
ierr = DMPlexSetLabelValue(dm, "marker", cone[1], markerTop);CHKERRQ(ierr);
}
} else if (vy == 0) {
ierr = DMPlexSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr);
ierr = DMPlexSetLabelValue(dm, "marker", cone[0], markerBottom);CHKERRQ(ierr);
if (ex == numXEdges-1) {
ierr = DMPlexSetLabelValue(dm, "marker", cone[1], markerBottom);CHKERRQ(ierr);
}
}
}
}
ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr);
ierr = DMPlexStratify(dm);CHKERRQ(ierr);
/* Build coordinates */
ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVertices);CHKERRQ(ierr);
for (v = firstVertex; v < firstVertex+numVertices; ++v) {
ierr = PetscSectionSetDof(coordSection, v, 2);CHKERRQ(ierr);
}
ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr);
ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr);
ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr);
ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr);
ierr = VecSetFromOptions(coordinates);CHKERRQ(ierr);
ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr);
for (vy = 0; vy < numYVertices; ++vy) {
for (vx = 0; vx < numXVertices; ++vx) {
coords[(vy*numXVertices+vx)*2+0] = lower[0] + ((upper[0] - lower[0])/numXEdges)*vx;
coords[(vy*numXVertices+vx)*2+1] = lower[1] + ((upper[1] - lower[1])/numYEdges)*vy;
}
}
ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr);
ierr = VecDestroy(&coordinates);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
/*
Simple cubic boundary:
2-------3
/| /|
6-------7 |
| | | |
| 0-----|-1
|/ |/
4-------5
*/
PetscErrorCode DMPlexCreateCubeBoundary(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt faces[])
{
PetscInt numVertices = (faces[0]+1)*(faces[1]+1)*(faces[2]+1);
PetscInt numFaces = 6;
Vec coordinates;
PetscSection coordSection;
PetscScalar *coords;
PetscInt coordSize;
PetscMPIInt rank;
PetscInt v, vx, vy, vz;
PetscErrorCode ierr;
PetscFunctionBegin;
if ((faces[0] < 1) || (faces[1] < 1) || (faces[2] < 1)) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Must have at least 1 face per side");
if ((faces[0] > 1) || (faces[1] > 1) || (faces[2] > 1)) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Currently can't handle more than 1 face per side");
ierr = PetscMalloc(numVertices*2 * sizeof(PetscReal), &coords);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr);
if (!rank) {
PetscInt f;
ierr = DMPlexSetChart(dm, 0, numFaces+numVertices);CHKERRQ(ierr);
for (f = 0; f < numFaces; ++f) {
ierr = DMPlexSetConeSize(dm, f, 4);CHKERRQ(ierr);
}
ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */
for (v = 0; v < numFaces+numVertices; ++v) {
ierr = DMPlexSetLabelValue(dm, "marker", v, 1);CHKERRQ(ierr);
}
{ /* Side 0 (Front) */
PetscInt cone[4];
cone[0] = numFaces+4; cone[1] = numFaces+5; cone[2] = numFaces+7; cone[3] = numFaces+6;
ierr = DMPlexSetCone(dm, 0, cone);CHKERRQ(ierr);
}
{ /* Side 1 (Back) */
PetscInt cone[4];
cone[0] = numFaces+1; cone[1] = numFaces+0; cone[2] = numFaces+2; cone[3] = numFaces+3;
ierr = DMPlexSetCone(dm, 1, cone);CHKERRQ(ierr);
}
{ /* Side 2 (Bottom) */
PetscInt cone[4];
cone[0] = numFaces+0; cone[1] = numFaces+1; cone[2] = numFaces+5; cone[3] = numFaces+4;
ierr = DMPlexSetCone(dm, 2, cone);CHKERRQ(ierr);
}
{ /* Side 3 (Top) */
PetscInt cone[4];
cone[0] = numFaces+6; cone[1] = numFaces+7; cone[2] = numFaces+3; cone[3] = numFaces+2;
ierr = DMPlexSetCone(dm, 3, cone);CHKERRQ(ierr);
}
{ /* Side 4 (Left) */
PetscInt cone[4];
cone[0] = numFaces+0; cone[1] = numFaces+4; cone[2] = numFaces+6; cone[3] = numFaces+2;
ierr = DMPlexSetCone(dm, 4, cone);CHKERRQ(ierr);
}
{ /* Side 5 (Right) */
PetscInt cone[4];
cone[0] = numFaces+5; cone[1] = numFaces+1; cone[2] = numFaces+3; cone[3] = numFaces+7;
ierr = DMPlexSetCone(dm, 5, cone);CHKERRQ(ierr);
}
}
ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr);
ierr = DMPlexStratify(dm);CHKERRQ(ierr);
/* Build coordinates */
ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
ierr = PetscSectionSetChart(coordSection, numFaces, numFaces + numVertices);CHKERRQ(ierr);
for (v = numFaces; v < numFaces+numVertices; ++v) {
ierr = PetscSectionSetDof(coordSection, v, 3);CHKERRQ(ierr);
}
ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr);
ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr);
ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr);
ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr);
ierr = VecSetFromOptions(coordinates);CHKERRQ(ierr);
ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr);
for (vz = 0; vz <= faces[2]; ++vz) {
for (vy = 0; vy <= faces[1]; ++vy) {
for (vx = 0; vx <= faces[0]; ++vx) {
coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+0] = lower[0] + ((upper[0] - lower[0])/faces[0])*vx;
coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+1] = lower[1] + ((upper[1] - lower[1])/faces[1])*vy;
coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+2] = lower[2] + ((upper[2] - lower[2])/faces[2])*vz;
}
}
}
ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr);
ierr = VecDestroy(&coordinates);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/* Two triangles separated by a zero-volume cell with 6 vertices
5--16--8
/ | | \
11 | | 12
/ | | \
3 0 10 2 14 1 6
\ | | /
9 | | 13
\ | | /
4--15--7
*/
PetscErrorCode CreateSimplexHybrid_2D(MPI_Comm comm, DM dm)
{
Vec coordinates;
PetscSection coordSection;
PetscScalar *coords;
PetscInt numVertices = 0, numEdges = 0, numCells = 0, cMax = PETSC_DETERMINE, fMax = PETSC_DETERMINE;
PetscInt firstVertex, firstEdge, coordSize;
PetscInt v, e;
PetscMPIInt rank;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
if (!rank) {
numVertices = 3 + 3;
numEdges = 6 + 2;
numCells = 3;
cMax = 2;
fMax = 15;
}
firstVertex = numCells;
firstEdge = numCells + numVertices;
ierr = DMPlexSetChart(dm, 0, numCells+numEdges+numVertices);CHKERRQ(ierr);
if (numCells) {
ierr = DMPlexSetConeSize(dm, 0, 3);CHKERRQ(ierr);
ierr = DMPlexSetConeSize(dm, 1, 3);CHKERRQ(ierr);
ierr = DMPlexSetConeSize(dm, 2, 4);CHKERRQ(ierr);
}
for(e = firstEdge; e < firstEdge+numEdges; ++e) {
ierr = DMPlexSetConeSize(dm, e, 2);CHKERRQ(ierr);
}
ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */
ierr = DMPlexSetHybridBounds(dm, cMax, PETSC_DETERMINE, fMax, PETSC_DETERMINE);CHKERRQ(ierr); /* Indicate a hybrid mesh */
/* Build cells */
if (numCells > 0) {
const PetscInt cone[3] = {9, 10, 11};
const PetscInt ornt[3] = {0, 0, 0};
const PetscInt cell = 0;
ierr = DMPlexSetCone(dm, cell, cone);CHKERRQ(ierr);
ierr = DMPlexSetConeOrientation(dm, cell, ornt);CHKERRQ(ierr);
}
if (numCells > 1) {
const PetscInt cone[3] = {12, 14, 13};
const PetscInt ornt[3] = { 0, -2, 0};
const PetscInt cell = 1;
ierr = DMPlexSetCone(dm, cell, cone);CHKERRQ(ierr);
ierr = DMPlexSetConeOrientation(dm, cell, ornt);CHKERRQ(ierr);
}
if (numCells > 2) {
const PetscInt cone[4] = {10, 14, 15, 16};
const PetscInt ornt[4] = { 0, 0, 0, 0};
const PetscInt cell = 2;
ierr = DMPlexSetCone(dm, cell, cone);CHKERRQ(ierr);
ierr = DMPlexSetConeOrientation(dm, cell, ornt);CHKERRQ(ierr);
}
/* Build edges*/
if (numEdges > 0) {
const PetscInt cone[2] = {3, 4};
const PetscInt edge = 9;
ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr);
ierr = DMPlexSetLabelValue(dm, "marker", edge, 1);CHKERRQ(ierr);
}
if (numEdges > 1) {
const PetscInt cone[2] = {4, 5};
const PetscInt edge = 10;
ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr);
}
if (numEdges > 2) {
const PetscInt cone[2] = {5, 3};
const PetscInt edge = 11;
ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr);
ierr = DMPlexSetLabelValue(dm, "marker", edge, 1);CHKERRQ(ierr);
}
if (numEdges > 3) {
const PetscInt cone[2] = {6, 8};
const PetscInt edge = 12;
ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr);
ierr = DMPlexSetLabelValue(dm, "marker", edge, 1);CHKERRQ(ierr);
}
if (numEdges > 4) {
const PetscInt cone[2] = {7, 6};
const PetscInt edge = 13;
ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr);
ierr = DMPlexSetLabelValue(dm, "marker", edge, 1);CHKERRQ(ierr);
}
if (numEdges > 5) {
const PetscInt cone[2] = {7, 8};
const PetscInt edge = 14;
ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr);
}
if (numEdges > 6) {
const PetscInt cone[2] = {4, 7};
const PetscInt edge = 15;
ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr);
}
if (numEdges > 7) {
const PetscInt cone[2] = {5, 8};
const PetscInt edge = 16;
ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr);
}
ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr);
ierr = DMPlexStratify(dm);CHKERRQ(ierr);
/* Build coordinates */
ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVertices);CHKERRQ(ierr);
for(v = firstVertex; v < firstVertex+numVertices; ++v) {
ierr = PetscSectionSetDof(coordSection, v, 2);CHKERRQ(ierr);
}
ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr);
ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr);
ierr = VecCreate(((PetscObject) dm)->comm, &coordinates);CHKERRQ(ierr);
ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr);
ierr = VecSetFromOptions(coordinates);CHKERRQ(ierr);
ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr);
if (numVertices) {
coords[0] = -0.5; coords[1] = 0.5;
coords[2] = -0.2; coords[3] = 0.0;
coords[4] = -0.2; coords[5] = 1.0;
coords[6] = 0.5; coords[7] = 0.5;
coords[8] = 0.2; coords[9] = 0.0;
coords[10] = 0.2; coords[11] = 1.0;
}
ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr);
ierr = VecDestroy(&coordinates);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
