#define PETSCDM_DLL #include /*I "petscdmplex.h" I*/ #include #include /*@ DMPlexCreateDoublet - Creates a mesh of two cells of the specified type, optionally with later refinement. Collective on MPI_Comm Input Parameters: + comm - The communicator for the DM object . dim - The spatial dimension . simplex - Flag for simplicial cells, otherwise they are tensor product cells . interpolate - Flag to create intermediate mesh pieces (edges, faces) . refinementUniform - Flag for uniform parallel refinement - refinementLimit - A nonzero number indicates the largest admissible volume for a refined cell Output Parameter: . dm - The DM object Level: beginner .keywords: DM, create .seealso: DMSetType(), DMCreate() @*/ PetscErrorCode DMPlexCreateDoublet(MPI_Comm comm, PetscInt dim, PetscBool simplex, PetscBool interpolate, PetscBool refinementUniform, PetscReal refinementLimit, DM *newdm) { DM dm; PetscInt p; PetscMPIInt rank; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMCreate(comm, &dm);CHKERRQ(ierr); ierr = DMSetType(dm, DMPLEX);CHKERRQ(ierr); ierr = DMSetDimension(dm, dim);CHKERRQ(ierr); ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); switch (dim) { case 2: if (simplex) {ierr = PetscObjectSetName((PetscObject) dm, "triangular");CHKERRQ(ierr);} else {ierr = PetscObjectSetName((PetscObject) dm, "quadrilateral");CHKERRQ(ierr);} break; case 3: if (simplex) {ierr = PetscObjectSetName((PetscObject) dm, "tetrahedral");CHKERRQ(ierr);} else {ierr = PetscObjectSetName((PetscObject) dm, "hexahedral");CHKERRQ(ierr);} break; default: SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %d", dim); } if (rank) { PetscInt numPoints[2] = {0, 0}; ierr = DMPlexCreateFromDAG(dm, 1, numPoints, NULL, NULL, NULL, NULL);CHKERRQ(ierr); } else { switch (dim) { case 2: if (simplex) { PetscInt numPoints[2] = {4, 2}; PetscInt coneSize[6] = {3, 3, 0, 0, 0, 0}; PetscInt cones[6] = {2, 3, 4, 5, 4, 3}; PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0}; PetscScalar vertexCoords[8] = {-0.5, 0.5, 0.0, 0.0, 0.0, 1.0, 0.5, 0.5}; PetscInt markerPoints[8] = {2, 1, 3, 1, 4, 1, 5, 1}; ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); for (p = 0; p < 4; ++p) {ierr = DMSetLabelValue(dm, "marker", markerPoints[p*2], markerPoints[p*2+1]);CHKERRQ(ierr);} } else { PetscInt numPoints[2] = {6, 2}; PetscInt coneSize[8] = {4, 4, 0, 0, 0, 0, 0, 0}; PetscInt cones[8] = {2, 3, 4, 5, 3, 6, 7, 4}; PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; PetscScalar vertexCoords[12] = {-1.0, -0.5, 0.0, -0.5, 0.0, 0.5, -1.0, 0.5, 1.0, -0.5, 1.0, 0.5}; ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); } break; case 3: if (simplex) { PetscInt numPoints[2] = {5, 2}; PetscInt coneSize[7] = {4, 4, 0, 0, 0, 0, 0}; PetscInt cones[8] = {4, 3, 5, 2, 5, 3, 4, 6}; PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; PetscScalar vertexCoords[15] = {-1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 1.0, 0.0, 1.0, 0.0, 0.0}; PetscInt markerPoints[10] = {2, 1, 3, 1, 4, 1, 5, 1, 6, 1}; ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); for (p = 0; p < 5; ++p) {ierr = DMSetLabelValue(dm, "marker", markerPoints[p*2], markerPoints[p*2+1]);CHKERRQ(ierr);} } else { PetscInt numPoints[2] = {12, 2}; PetscInt coneSize[14] = {8, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; PetscInt cones[16] = {2, 3, 4, 5, 6, 7, 8, 9, 5, 4, 10, 11, 7, 12, 13, 8}; PetscInt coneOrientations[16] = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; PetscScalar vertexCoords[36] = {-1.0, -0.5, -0.5, -1.0, 0.5, -0.5, 0.0, 0.5, -0.5, 0.0, -0.5, -0.5, -1.0, -0.5, 0.5, 0.0, -0.5, 0.5, 0.0, 0.5, 0.5, -1.0, 0.5, 0.5, 1.0, 0.5, -0.5, 1.0, -0.5, -0.5, 1.0, -0.5, 0.5, 1.0, 0.5, 0.5}; ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); } break; default: SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %d", dim); } } *newdm = dm; if (refinementLimit > 0.0) { DM rdm; const char *name; ierr = DMPlexSetRefinementUniform(*newdm, PETSC_FALSE);CHKERRQ(ierr); ierr = DMPlexSetRefinementLimit(*newdm, refinementLimit);CHKERRQ(ierr); ierr = DMRefine(*newdm, comm, &rdm);CHKERRQ(ierr); ierr = PetscObjectGetName((PetscObject) *newdm, &name);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) rdm, name);CHKERRQ(ierr); ierr = DMDestroy(newdm);CHKERRQ(ierr); *newdm = rdm; } if (interpolate) { DM idm = NULL; const char *name; ierr = DMPlexInterpolate(*newdm, &idm);CHKERRQ(ierr); ierr = PetscObjectGetName((PetscObject) *newdm, &name);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) idm, name);CHKERRQ(ierr); ierr = DMPlexCopyCoordinates(*newdm, idm);CHKERRQ(ierr); ierr = DMCopyLabels(*newdm, idm);CHKERRQ(ierr); ierr = DMDestroy(newdm);CHKERRQ(ierr); *newdm = idm; } { DM refinedMesh = NULL; DM distributedMesh = NULL; /* Distribute mesh over processes */ ierr = DMPlexDistribute(*newdm, 0, NULL, &distributedMesh);CHKERRQ(ierr); if (distributedMesh) { ierr = DMDestroy(newdm);CHKERRQ(ierr); *newdm = distributedMesh; } if (refinementUniform) { ierr = DMPlexSetRefinementUniform(*newdm, refinementUniform);CHKERRQ(ierr); ierr = DMRefine(*newdm, comm, &refinedMesh);CHKERRQ(ierr); if (refinedMesh) { ierr = DMDestroy(newdm);CHKERRQ(ierr); *newdm = refinedMesh; } } } PetscFunctionReturn(0); } /*@ DMPlexCreateSquareBoundary - Creates a 1D mesh the is the boundary of a square lattice. Collective on MPI_Comm Input Parameters: + comm - The communicator for the DM object . lower - The lower left corner coordinates . upper - The upper right corner coordinates - edges - The number of cells in each direction Output Parameter: . dm - The DM object Note: Here is the numbering returned for 2 cells in each direction: $ 18--5-17--4--16 $ | | | $ 6 10 3 $ | | | $ 19-11-20--9--15 $ | | | $ 7 8 2 $ | | | $ 12--0-13--1--14 Level: beginner .keywords: DM, create .seealso: DMPlexCreateBoxMesh(), DMPlexCreateCubeBoundary(), DMSetType(), DMCreate() @*/ PetscErrorCode DMPlexCreateSquareBoundary(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[]) { const PetscInt numVertices = (edges[0]+1)*(edges[1]+1); const 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)->options,((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);CHKERRQ(ierr); if (markerSeparate) { markerTop = 3; markerBottom = 1; markerRight = 2; markerLeft = 4; } 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 = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); ierr = DMSetLabelValue(dm, "marker", cone[0], markerRight);CHKERRQ(ierr); if (ey == edges[1]-1) { ierr = DMSetLabelValue(dm, "marker", cone[1], markerRight);CHKERRQ(ierr); ierr = DMSetLabelValue(dm, "Face Sets", cone[1], markerRight);CHKERRQ(ierr); } } else if (vx == 0) { ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); ierr = DMSetLabelValue(dm, "marker", cone[0], markerLeft);CHKERRQ(ierr); if (ey == edges[1]-1) { ierr = DMSetLabelValue(dm, "marker", cone[1], markerLeft);CHKERRQ(ierr); ierr = DMSetLabelValue(dm, "Face Sets", 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 = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); ierr = DMSetLabelValue(dm, "marker", cone[0], markerTop);CHKERRQ(ierr); if (ex == edges[0]-1) { ierr = DMSetLabelValue(dm, "marker", cone[1], markerTop);CHKERRQ(ierr); ierr = DMSetLabelValue(dm, "Face Sets", cone[1], markerTop);CHKERRQ(ierr); } } else if (vy == 0) { ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); ierr = DMSetLabelValue(dm, "marker", cone[0], markerBottom);CHKERRQ(ierr); if (ex == edges[0]-1) { ierr = DMSetLabelValue(dm, "marker", cone[1], markerBottom);CHKERRQ(ierr); ierr = DMSetLabelValue(dm, "Face Sets", cone[1], markerBottom);CHKERRQ(ierr); } } } } } ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); ierr = DMPlexStratify(dm);CHKERRQ(ierr); /* Build coordinates */ ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); ierr = PetscSectionSetChart(coordSection, numEdges, numEdges + numVertices);CHKERRQ(ierr); ierr = PetscSectionSetFieldComponents(coordSection, 0, 2);CHKERRQ(ierr); for (v = numEdges; v < numEdges+numVertices; ++v) { ierr = PetscSectionSetDof(coordSection, v, 2);CHKERRQ(ierr); ierr = PetscSectionSetFieldDof(coordSection, v, 0, 2);CHKERRQ(ierr); } ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); ierr = VecSetBlockSize(coordinates, 2);CHKERRQ(ierr); ierr = VecSetType(coordinates,VECSTANDARD);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); } /*@ DMPlexCreateCubeBoundary - Creates a 2D mesh the is the boundary of a cubic lattice. Collective on MPI_Comm Input Parameters: + comm - The communicator for the DM object . lower - The lower left front corner coordinates . upper - The upper right back corner coordinates - edges - The number of cells in each direction Output Parameter: . dm - The DM object Level: beginner .keywords: DM, create .seealso: DMPlexCreateBoxMesh(), DMPlexCreateSquareBoundary(), DMSetType(), DMCreate() @*/ PetscErrorCode DMPlexCreateCubeBoundary(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt faces[]) { PetscInt vertices[3], numVertices; PetscInt numFaces = 2*faces[0]*faces[1] + 2*faces[1]*faces[2] + 2*faces[0]*faces[2]; Vec coordinates; PetscSection coordSection; PetscScalar *coords; PetscInt coordSize; PetscMPIInt rank; PetscInt v, vx, vy, vz; PetscInt voffset, iface=0, cone[4]; 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"); ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr); vertices[0] = faces[0]+1; vertices[1] = faces[1]+1; vertices[2] = faces[2]+1; numVertices = vertices[0]*vertices[1]*vertices[2]; 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 = DMSetLabelValue(dm, "marker", v, 1);CHKERRQ(ierr); } /* Side 0 (Top) */ for (vy = 0; vy < faces[1]; vy++) { for (vx = 0; vx < faces[0]; vx++) { voffset = numFaces + vertices[0]*vertices[1]*(vertices[2]-1) + vy*vertices[0] + vx; cone[0] = voffset; cone[1] = voffset+1; cone[2] = voffset+vertices[0]+1; cone[3] = voffset+vertices[0]; ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); iface++; } } /* Side 1 (Bottom) */ for (vy = 0; vy < faces[1]; vy++) { for (vx = 0; vx < faces[0]; vx++) { voffset = numFaces + vy*(faces[0]+1) + vx; cone[0] = voffset+1; cone[1] = voffset; cone[2] = voffset+vertices[0]; cone[3] = voffset+vertices[0]+1; ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); iface++; } } /* Side 2 (Front) */ for (vz = 0; vz < faces[2]; vz++) { for (vx = 0; vx < faces[0]; vx++) { voffset = numFaces + vz*vertices[0]*vertices[1] + vx; cone[0] = voffset; cone[1] = voffset+1; cone[2] = voffset+vertices[0]*vertices[1]+1; cone[3] = voffset+vertices[0]*vertices[1]; ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); iface++; } } /* Side 3 (Back) */ for (vz = 0; vz < faces[2]; vz++) { for (vx = 0; vx < faces[0]; vx++) { voffset = numFaces + vz*vertices[0]*vertices[1] + vertices[0]*(vertices[1]-1) + vx; cone[0] = voffset+vertices[0]*vertices[1]; cone[1] = voffset+vertices[0]*vertices[1]+1; cone[2] = voffset+1; cone[3] = voffset; ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); iface++; } } /* Side 4 (Left) */ for (vz = 0; vz < faces[2]; vz++) { for (vy = 0; vy < faces[1]; vy++) { voffset = numFaces + vz*vertices[0]*vertices[1] + vy*vertices[0]; cone[0] = voffset; cone[1] = voffset+vertices[0]*vertices[1]; cone[2] = voffset+vertices[0]*vertices[1]+vertices[0]; cone[3] = voffset+vertices[0]; ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); iface++; } } /* Side 5 (Right) */ for (vz = 0; vz < faces[2]; vz++) { for (vy = 0; vy < faces[1]; vy++) { voffset = numFaces + vz*vertices[0]*vertices[1] + vy*vertices[0] + vx; cone[0] = voffset+vertices[0]*vertices[1]; cone[1] = voffset; cone[2] = voffset+vertices[0]; cone[3] = voffset+vertices[0]*vertices[1]+vertices[0]; ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); iface++; } } } ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); ierr = DMPlexStratify(dm);CHKERRQ(ierr); /* Build coordinates */ ierr = DMGetCoordinateSection(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(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); ierr = VecSetBlockSize(coordinates, 3);CHKERRQ(ierr); ierr = VecSetType(coordinates,VECSTANDARD);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); } /*@ DMPlexCreateBoxMesh - Creates a mesh on the tensor product of unit intervals (box) using simplices. Collective on MPI_Comm Input Parameters: + comm - The communicator for the DM object . dim - The spatial dimension . numFaces - Number of faces per dimension - interpolate - Flag to create intermediate mesh pieces (edges, faces) Output Parameter: . dm - The DM object Level: beginner .keywords: DM, create .seealso: DMPlexCreateHexBoxMesh(), DMSetType(), DMCreate() @*/ PetscErrorCode DMPlexCreateBoxMesh(MPI_Comm comm, PetscInt dim, PetscInt numFaces, PetscBool interpolate, DM *dm) { DM boundary; PetscErrorCode ierr; PetscFunctionBegin; PetscValidPointer(dm, 4); ierr = DMCreate(comm, &boundary);CHKERRQ(ierr); PetscValidLogicalCollectiveInt(boundary,dim,2); ierr = DMSetType(boundary, DMPLEX);CHKERRQ(ierr); ierr = DMSetDimension(boundary, dim-1);CHKERRQ(ierr); ierr = DMSetCoordinateDim(boundary, dim);CHKERRQ(ierr); switch (dim) { case 2: { PetscReal lower[2] = {0.0, 0.0}; PetscReal upper[2] = {1.0, 1.0}; PetscInt edges[2]; edges[0] = numFaces; edges[1] = numFaces; ierr = DMPlexCreateSquareBoundary(boundary, lower, upper, edges);CHKERRQ(ierr); break; } case 3: { PetscReal lower[3] = {0.0, 0.0, 0.0}; PetscReal upper[3] = {1.0, 1.0, 1.0}; PetscInt faces[3]; faces[0] = numFaces; faces[1] = numFaces; faces[2] = numFaces; ierr = DMPlexCreateCubeBoundary(boundary, lower, upper, faces);CHKERRQ(ierr); break; } default: SETERRQ1(comm, PETSC_ERR_SUP, "Dimension not supported: %d", dim); } ierr = DMPlexGenerate(boundary, NULL, interpolate, dm);CHKERRQ(ierr); ierr = DMDestroy(&boundary);CHKERRQ(ierr); PetscFunctionReturn(0); } static PetscErrorCode DMPlexCreateCubeMesh_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[], DMBoundaryType bdX, DMBoundaryType bdY, DMBoundaryType bdZ) { DMLabel cutLabel = NULL; PetscInt markerTop = 1, faceMarkerTop = 1; PetscInt markerBottom = 1, faceMarkerBottom = 1; PetscInt markerFront = 1, faceMarkerFront = 1; PetscInt markerBack = 1, faceMarkerBack = 1; PetscInt markerRight = 1, faceMarkerRight = 1; PetscInt markerLeft = 1, faceMarkerLeft = 1; PetscInt dim; PetscBool markerSeparate = PETSC_FALSE, cutMarker = PETSC_FALSE; PetscMPIInt rank; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMGetDimension(dm,&dim);CHKERRQ(ierr); ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr); ierr = DMCreateLabel(dm,"marker");CHKERRQ(ierr); ierr = DMCreateLabel(dm,"Face Sets");CHKERRQ(ierr); if (bdX == DM_BOUNDARY_PERIODIC || bdX == DM_BOUNDARY_TWIST || bdY == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST || bdZ == DM_BOUNDARY_PERIODIC || bdZ == DM_BOUNDARY_TWIST) { ierr = PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_periodic_cut", &cutMarker, NULL);CHKERRQ(ierr); if (cutMarker) {ierr = DMCreateLabel(dm, "periodic_cut");CHKERRQ(ierr); ierr = DMGetLabel(dm, "periodic_cut", &cutLabel);CHKERRQ(ierr);} } switch (dim) { case 2: faceMarkerTop = 3; faceMarkerBottom = 1; faceMarkerRight = 2; faceMarkerLeft = 4; break; case 3: faceMarkerBottom = 1; faceMarkerTop = 2; faceMarkerFront = 3; faceMarkerBack = 4; faceMarkerRight = 5; faceMarkerLeft = 6; break; default: SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Dimension %d not supported",dim); break; } ierr = PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);CHKERRQ(ierr); if (markerSeparate) { markerBottom = faceMarkerBottom; markerTop = faceMarkerTop; markerFront = faceMarkerFront; markerBack = faceMarkerBack; markerRight = faceMarkerRight; markerLeft = faceMarkerLeft; } { const PetscInt numXEdges = !rank ? edges[0] : 0; const PetscInt numYEdges = !rank ? edges[1] : 0; const PetscInt numZEdges = !rank ? edges[2] : 0; const PetscInt numXVertices = !rank ? (bdX == DM_BOUNDARY_PERIODIC || bdX == DM_BOUNDARY_TWIST ? edges[0] : edges[0]+1) : 0; const PetscInt numYVertices = !rank ? (bdY == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST ? edges[1] : edges[1]+1) : 0; const PetscInt numZVertices = !rank ? (bdZ == DM_BOUNDARY_PERIODIC || bdZ == DM_BOUNDARY_TWIST ? edges[2] : edges[2]+1) : 0; const PetscInt numCells = numXEdges*numYEdges*numZEdges; const PetscInt numXFaces = numYEdges*numZEdges; const PetscInt numYFaces = numXEdges*numZEdges; const PetscInt numZFaces = numXEdges*numYEdges; const PetscInt numTotXFaces = numXVertices*numXFaces; const PetscInt numTotYFaces = numYVertices*numYFaces; const PetscInt numTotZFaces = numZVertices*numZFaces; const PetscInt numFaces = numTotXFaces + numTotYFaces + numTotZFaces; const PetscInt numTotXEdges = numXEdges*numYVertices*numZVertices; const PetscInt numTotYEdges = numYEdges*numXVertices*numZVertices; const PetscInt numTotZEdges = numZEdges*numXVertices*numYVertices; const PetscInt numVertices = numXVertices*numYVertices*numZVertices; const PetscInt numEdges = numTotXEdges + numTotYEdges + numTotZEdges; const PetscInt firstVertex = (dim == 2) ? numFaces : numCells; const PetscInt firstXFace = (dim == 2) ? 0 : numCells + numVertices; const PetscInt firstYFace = firstXFace + numTotXFaces; const PetscInt firstZFace = firstYFace + numTotYFaces; const PetscInt firstXEdge = numCells + numFaces + numVertices; const PetscInt firstYEdge = firstXEdge + numTotXEdges; const PetscInt firstZEdge = firstYEdge + numTotYEdges; Vec coordinates; PetscSection coordSection; PetscScalar *coords; PetscInt coordSize; PetscInt v, vx, vy, vz; PetscInt c, f, fx, fy, fz, e, ex, ey, ez; ierr = DMPlexSetChart(dm, 0, numCells+numFaces+numEdges+numVertices);CHKERRQ(ierr); for (c = 0; c < numCells; c++) { ierr = DMPlexSetConeSize(dm, c, 6);CHKERRQ(ierr); } for (f = firstXFace; f < firstXFace+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 cells */ for (fz = 0; fz < numZEdges; ++fz) { for (fy = 0; fy < numYEdges; ++fy) { for (fx = 0; fx < numXEdges; ++fx) { PetscInt cell = (fz*numYEdges + fy)*numXEdges + fx; PetscInt faceB = firstZFace + (fy*numXEdges+fx)*numZVertices + fz; PetscInt faceT = firstZFace + (fy*numXEdges+fx)*numZVertices + ((fz+1)%numZVertices); PetscInt faceF = firstYFace + (fz*numXEdges+fx)*numYVertices + fy; PetscInt faceK = firstYFace + (fz*numXEdges+fx)*numYVertices + ((fy+1)%numYVertices); PetscInt faceL = firstXFace + (fz*numYEdges+fy)*numXVertices + fx; PetscInt faceR = firstXFace + (fz*numYEdges+fy)*numXVertices + ((fx+1)%numXVertices); /* B, T, F, K, R, L */ PetscInt ornt[6] = {-4, 0, 0, -1, 0, -4}; /* ??? */ PetscInt cone[6]; /* no boundary twisting in 3D */ cone[0] = faceB; cone[1] = faceT; cone[2] = faceF; cone[3] = faceK; cone[4] = faceR; cone[5] = faceL; ierr = DMPlexSetCone(dm, cell, cone);CHKERRQ(ierr); ierr = DMPlexSetConeOrientation(dm, cell, ornt);CHKERRQ(ierr); if (bdX != DM_BOUNDARY_NONE && fx == numXEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, cell, 2);CHKERRQ(ierr);} if (bdY != DM_BOUNDARY_NONE && fy == numYEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, cell, 2);CHKERRQ(ierr);} if (bdZ != DM_BOUNDARY_NONE && fz == numZEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, cell, 2);CHKERRQ(ierr);} } } } /* Build x faces */ for (fz = 0; fz < numZEdges; ++fz) { for (fy = 0; fy < numYEdges; ++fy) { for (fx = 0; fx < numXVertices; ++fx) { PetscInt face = firstXFace + (fz*numYEdges+fy)*numXVertices + fx; PetscInt edgeL = firstZEdge + ( fy* numXVertices+fx)*numZEdges + fz; PetscInt edgeR = firstZEdge + (((fy+1)%numYVertices)*numXVertices+fx)*numZEdges + fz; PetscInt edgeB = firstYEdge + ( fz* numXVertices+fx)*numYEdges + fy; PetscInt edgeT = firstYEdge + (((fz+1)%numZVertices)*numXVertices+fx)*numYEdges + fy; PetscInt ornt[4] = {0, 0, -2, -2}; PetscInt cone[4]; if (dim == 3) { /* markers */ if (bdX != DM_BOUNDARY_PERIODIC) { if (fx == numXVertices-1) { ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerRight);CHKERRQ(ierr); ierr = DMSetLabelValue(dm, "marker", face, markerRight);CHKERRQ(ierr); } else if (fx == 0) { ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerLeft);CHKERRQ(ierr); ierr = DMSetLabelValue(dm, "marker", face, markerLeft);CHKERRQ(ierr); } } } cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL; ierr = DMPlexSetCone(dm, face, cone);CHKERRQ(ierr); ierr = DMPlexSetConeOrientation(dm, face, ornt);CHKERRQ(ierr); } } } /* Build y faces */ for (fz = 0; fz < numZEdges; ++fz) { for (fx = 0; fx < numXEdges; ++fx) { for (fy = 0; fy < numYVertices; ++fy) { PetscInt face = firstYFace + (fz*numXEdges+fx)*numYVertices + fy; PetscInt edgeL = firstZEdge + (fy*numXVertices+ fx )*numZEdges + fz; PetscInt edgeR = firstZEdge + (fy*numXVertices+((fx+1)%numXVertices))*numZEdges + fz; PetscInt edgeB = firstXEdge + ( fz *numYVertices+fy)*numXEdges + fx; PetscInt edgeT = firstXEdge + (((fz+1)%numZVertices)*numYVertices+fy)*numXEdges + fx; PetscInt ornt[4] = {0, 0, -2, -2}; PetscInt cone[4]; if (dim == 3) { /* markers */ if (bdY != DM_BOUNDARY_PERIODIC) { if (fy == numYVertices-1) { ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerBack);CHKERRQ(ierr); ierr = DMSetLabelValue(dm, "marker", face, markerBack);CHKERRQ(ierr); } else if (fy == 0) { ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerFront);CHKERRQ(ierr); ierr = DMSetLabelValue(dm, "marker", face, markerFront);CHKERRQ(ierr); } } } cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL; ierr = DMPlexSetCone(dm, face, cone);CHKERRQ(ierr); ierr = DMPlexSetConeOrientation(dm, face, ornt);CHKERRQ(ierr); } } } /* Build z faces */ for (fy = 0; fy < numYEdges; ++fy) { for (fx = 0; fx < numXEdges; ++fx) { for (fz = 0; fz < numZVertices; fz++) { PetscInt face = firstZFace + (fy*numXEdges+fx)*numZVertices + fz; PetscInt edgeL = firstYEdge + (fz*numXVertices+ fx )*numYEdges + fy; PetscInt edgeR = firstYEdge + (fz*numXVertices+((fx+1)%numXVertices))*numYEdges + fy; PetscInt edgeB = firstXEdge + (fz*numYVertices+ fy )*numXEdges + fx; PetscInt edgeT = firstXEdge + (fz*numYVertices+((fy+1)%numYVertices))*numXEdges + fx; PetscInt ornt[4] = {0, 0, -2, -2}; PetscInt cone[4]; if (dim == 2) { if (bdX == DM_BOUNDARY_TWIST && fx == numXEdges-1) {edgeR += numYEdges-1-2*fy; ornt[1] = -2;} if (bdY == DM_BOUNDARY_TWIST && fy == numYEdges-1) {edgeT += numXEdges-1-2*fx; ornt[2] = 0;} if (bdX != DM_BOUNDARY_NONE && fx == numXEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, face, 2);CHKERRQ(ierr);} if (bdY != DM_BOUNDARY_NONE && fy == numYEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, face, 2);CHKERRQ(ierr);} } else { /* markers */ if (bdZ != DM_BOUNDARY_PERIODIC) { if (fz == numZVertices-1) { ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerTop);CHKERRQ(ierr); ierr = DMSetLabelValue(dm, "marker", face, markerTop);CHKERRQ(ierr); } else if (fz == 0) { ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerBottom);CHKERRQ(ierr); ierr = DMSetLabelValue(dm, "marker", face, markerBottom);CHKERRQ(ierr); } } } cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL; ierr = DMPlexSetCone(dm, face, cone);CHKERRQ(ierr); ierr = DMPlexSetConeOrientation(dm, face, ornt);CHKERRQ(ierr); } } } /* Build Z edges*/ for (vy = 0; vy < numYVertices; vy++) { for (vx = 0; vx < numXVertices; vx++) { for (ez = 0; ez < numZEdges; ez++) { const PetscInt edge = firstZEdge + (vy*numXVertices+vx)*numZEdges + ez; const PetscInt vertexB = firstVertex + ( ez *numYVertices+vy)*numXVertices + vx; const PetscInt vertexT = firstVertex + (((ez+1)%numZVertices)*numYVertices+vy)*numXVertices + vx; PetscInt cone[2]; if (dim == 3) { if (bdX != DM_BOUNDARY_PERIODIC) { if (vx == numXVertices-1) { ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); } else if (vx == 0) { ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); } } if (bdY != DM_BOUNDARY_PERIODIC) { if (vy == numYVertices-1) { ierr = DMSetLabelValue(dm, "marker", edge, markerBack);CHKERRQ(ierr); } else if (vy == 0) { ierr = DMSetLabelValue(dm, "marker", edge, markerFront);CHKERRQ(ierr); } } } cone[0] = vertexB; cone[1] = vertexT; ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); } } } /* Build Y edges*/ for (vz = 0; vz < numZVertices; vz++) { for (vx = 0; vx < numXVertices; vx++) { for (ey = 0; ey < numYEdges; ey++) { const PetscInt nextv = (dim == 2 && bdY == DM_BOUNDARY_TWIST && ey == numYEdges-1) ? (numXVertices-vx-1) : (vz*numYVertices+((ey+1)%numYVertices))*numXVertices + vx; const PetscInt edge = firstYEdge + (vz*numXVertices+vx)*numYEdges + ey; const PetscInt vertexF = firstVertex + (vz*numYVertices+ey)*numXVertices + vx; const PetscInt vertexK = firstVertex + nextv; PetscInt cone[2]; cone[0] = vertexF; cone[1] = vertexK; ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); if (dim == 2) { if ((bdX != DM_BOUNDARY_PERIODIC) && (bdX != DM_BOUNDARY_TWIST)) { if (vx == numXVertices-1) { ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerRight);CHKERRQ(ierr); ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); ierr = DMSetLabelValue(dm, "marker", cone[0], markerRight);CHKERRQ(ierr); if (ey == numYEdges-1) { ierr = DMSetLabelValue(dm, "marker", cone[1], markerRight);CHKERRQ(ierr); } } else if (vx == 0) { ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerLeft);CHKERRQ(ierr); ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); ierr = DMSetLabelValue(dm, "marker", cone[0], markerLeft);CHKERRQ(ierr); if (ey == numYEdges-1) { ierr = DMSetLabelValue(dm, "marker", cone[1], markerLeft);CHKERRQ(ierr); } } } else { if (vx == 0 && cutMarker) { ierr = DMLabelSetValue(cutLabel, edge, 1);CHKERRQ(ierr); ierr = DMLabelSetValue(cutLabel, cone[0], 1);CHKERRQ(ierr); if (ey == numYEdges-1) { ierr = DMLabelSetValue(cutLabel, cone[1], 1);CHKERRQ(ierr); } } } } else { if (bdX != DM_BOUNDARY_PERIODIC) { if (vx == numXVertices-1) { ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); } else if (vx == 0) { ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); } } if (bdZ != DM_BOUNDARY_PERIODIC) { if (vz == numZVertices-1) { ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); } else if (vz == 0) { ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); } } } } } } /* Build X edges*/ for (vz = 0; vz < numZVertices; vz++) { for (vy = 0; vy < numYVertices; vy++) { for (ex = 0; ex < numXEdges; ex++) { const PetscInt nextv = (dim == 2 && bdX == DM_BOUNDARY_TWIST && ex == numXEdges-1) ? (numYVertices-vy-1)*numXVertices : (vz*numYVertices+vy)*numXVertices + (ex+1)%numXVertices; const PetscInt edge = firstXEdge + (vz*numYVertices+vy)*numXEdges + ex; const PetscInt vertexL = firstVertex + (vz*numYVertices+vy)*numXVertices + ex; const PetscInt vertexR = firstVertex + nextv; PetscInt cone[2]; cone[0] = vertexL; cone[1] = vertexR; ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); if (dim == 2) { if ((bdY != DM_BOUNDARY_PERIODIC) && (bdY != DM_BOUNDARY_TWIST)) { if (vy == numYVertices-1) { ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerTop);CHKERRQ(ierr); ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); ierr = DMSetLabelValue(dm, "marker", cone[0], markerTop);CHKERRQ(ierr); if (ex == numXEdges-1) { ierr = DMSetLabelValue(dm, "marker", cone[1], markerTop);CHKERRQ(ierr); } } else if (vy == 0) { ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerBottom);CHKERRQ(ierr); ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); ierr = DMSetLabelValue(dm, "marker", cone[0], markerBottom);CHKERRQ(ierr); if (ex == numXEdges-1) { ierr = DMSetLabelValue(dm, "marker", cone[1], markerBottom);CHKERRQ(ierr); } } } else { if (vy == 0 && cutMarker) { ierr = DMLabelSetValue(cutLabel, edge, 1);CHKERRQ(ierr); ierr = DMLabelSetValue(cutLabel, cone[0], 1);CHKERRQ(ierr); if (ex == numXEdges-1) { ierr = DMLabelSetValue(cutLabel, cone[1], 1);CHKERRQ(ierr); } } } } else { if (bdY != DM_BOUNDARY_PERIODIC) { if (vy == numYVertices-1) { ierr = DMSetLabelValue(dm, "marker", edge, markerBack);CHKERRQ(ierr); } else if (vy == 0) { ierr = DMSetLabelValue(dm, "marker", edge, markerFront);CHKERRQ(ierr); } } if (bdZ != DM_BOUNDARY_PERIODIC) { if (vz == numZVertices-1) { ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); } else if (vz == 0) { ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); } } } } } } ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); ierr = DMPlexStratify(dm);CHKERRQ(ierr); /* Build coordinates */ ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr); ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVertices);CHKERRQ(ierr); for (v = firstVertex; v < firstVertex+numVertices; ++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(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); ierr = VecSetBlockSize(coordinates, dim);CHKERRQ(ierr); ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); for (vz = 0; vz < numZVertices; ++vz) { for (vy = 0; vy < numYVertices; ++vy) { for (vx = 0; vx < numXVertices; ++vx) { coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+0] = lower[0] + ((upper[0] - lower[0])/numXEdges)*vx; coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+1] = lower[1] + ((upper[1] - lower[1])/numYEdges)*vy; if (dim == 3) { coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+2] = lower[2] + ((upper[2] - lower[2])/numZEdges)*vz; } } } } ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); ierr = VecDestroy(&coordinates);CHKERRQ(ierr); } PetscFunctionReturn(0); } /*@ DMPlexCreateHexBoxMesh - Creates a mesh on the tensor product of unit intervals (box) using hexahedra. Collective on MPI_Comm Input Parameters: + comm - The communicator for the DM object . dim - The spatial dimension . periodicX - The boundary type for the X direction . periodicY - The boundary type for the Y direction . periodicZ - The boundary type for the Z direction - cells - The number of cells in each direction Output Parameter: . dm - The DM object Note: Here is the numbering returned for 2 cells in each direction: $ 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 Level: beginner .keywords: DM, create .seealso: DMPlexCreateBoxMesh(), DMSetType(), DMCreate() @*/ PetscErrorCode DMPlexCreateHexBoxMesh(MPI_Comm comm, PetscInt dim, const PetscInt cells[], DMBoundaryType periodicX, DMBoundaryType periodicY, DMBoundaryType periodicZ, DM *dm) { PetscInt i; PetscErrorCode ierr; PetscFunctionBegin; PetscValidPointer(dm, 7); ierr = DMCreate(comm, dm);CHKERRQ(ierr); PetscValidLogicalCollectiveInt(*dm,dim,2); ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); switch (dim) { case 2: { PetscReal lower[3] = {0.0, 0.0, 0.0}; PetscReal upper[3] = {1.0, 1.0, 0.0}; PetscInt edges[3]; edges[0] = cells[0]; edges[1] = cells[1]; edges[2] = 0; ierr = DMPlexCreateCubeMesh_Internal(*dm, lower, upper, edges, periodicX, periodicY, DM_BOUNDARY_NONE);CHKERRQ(ierr); if (periodicX == DM_BOUNDARY_PERIODIC || periodicX == DM_BOUNDARY_TWIST || periodicY == DM_BOUNDARY_PERIODIC || periodicY == DM_BOUNDARY_TWIST) { PetscReal L[2]; PetscReal maxCell[2]; DMBoundaryType bdType[2]; bdType[0] = periodicX; bdType[1] = periodicY; for (i = 0; i < dim; i++) { L[i] = upper[i] - lower[i]; maxCell[i] = 1.1 * (L[i] / PetscMax(1,cells[i])); } ierr = DMSetPeriodicity(*dm,maxCell,L,bdType);CHKERRQ(ierr); } break; } case 3: { PetscReal lower[3] = {0.0, 0.0, 0.0}; PetscReal upper[3] = {1.0, 1.0, 1.0}; ierr = DMPlexCreateCubeMesh_Internal(*dm, lower, upper, cells, periodicX, periodicY, periodicZ);CHKERRQ(ierr); if (periodicX == DM_BOUNDARY_PERIODIC || periodicX == DM_BOUNDARY_TWIST || periodicY == DM_BOUNDARY_PERIODIC || periodicY == DM_BOUNDARY_TWIST || periodicZ == DM_BOUNDARY_PERIODIC || periodicZ == DM_BOUNDARY_TWIST) { PetscReal L[3]; PetscReal maxCell[3]; DMBoundaryType bdType[3]; bdType[0] = periodicX; bdType[1] = periodicY; bdType[2] = periodicZ; for (i = 0; i < dim; i++) { L[i] = upper[i] - lower[i]; maxCell[i] = 1.1 * (L[i] / cells[i]); } ierr = DMSetPeriodicity(*dm,maxCell,L,bdType);CHKERRQ(ierr); } break; } default: SETERRQ1(comm, PETSC_ERR_SUP, "Dimension not supported: %d", dim); } PetscFunctionReturn(0); } /*@C DMPlexSetOptionsPrefix - Sets the prefix used for searching for all DM options in the database. Logically Collective on DM Input Parameters: + dm - the DM context - prefix - the prefix to prepend to all option names Notes: A hyphen (-) must NOT be given at the beginning of the prefix name. The first character of all runtime options is AUTOMATICALLY the hyphen. Level: advanced .seealso: SNESSetFromOptions() @*/ PetscErrorCode DMPlexSetOptionsPrefix(DM dm, const char prefix[]) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); ierr = PetscObjectSetOptionsPrefix((PetscObject) dm, prefix);CHKERRQ(ierr); ierr = PetscObjectSetOptionsPrefix((PetscObject) mesh->partitioner, prefix);CHKERRQ(ierr); PetscFunctionReturn(0); } /*@ DMPlexCreateHexCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using hexahedra. Collective on MPI_Comm Input Parameters: + comm - The communicator for the DM object . numRefine - The number of regular refinements to the basic 5 cell structure - periodicZ - The boundary type for the Z direction Output Parameter: . dm - The DM object Note: Here is the output numbering looking from the bottom of the cylinder: $ 17-----14 $ | | $ | 2 | $ | | $ 17-----8-----7-----14 $ | | | | $ | 3 | 0 | 1 | $ | | | | $ 19-----5-----6-----13 $ | | $ | 4 | $ | | $ 19-----13 $ $ and up through the top $ $ 18-----16 $ | | $ | 2 | $ | | $ 18----10----11-----16 $ | | | | $ | 3 | 0 | 1 | $ | | | | $ 20-----9----12-----15 $ | | $ | 4 | $ | | $ 20-----15 Level: beginner .keywords: DM, create .seealso: DMPlexCreateHexBoxMesh(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate() @*/ PetscErrorCode DMPlexCreateHexCylinderMesh(MPI_Comm comm, PetscInt numRefine, DMBoundaryType periodicZ, DM *dm) { const PetscInt dim = 3; PetscInt numCells, numVertices, r; PetscErrorCode ierr; PetscFunctionBegin; PetscValidPointer(dm, 4); if (numRefine < 0) SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Number of refinements %D cannot be negative", numRefine); ierr = DMCreate(comm, dm);CHKERRQ(ierr); ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); /* Create topology */ { PetscInt cone[8], c; numCells = 5; numVertices = 16; if (periodicZ == DM_BOUNDARY_PERIODIC) { numCells *= 3; numVertices = 24; } ierr = DMPlexSetChart(*dm, 0, numCells+numVertices);CHKERRQ(ierr); for (c = 0; c < numCells; c++) {ierr = DMPlexSetConeSize(*dm, c, 8);CHKERRQ(ierr);} ierr = DMSetUp(*dm);CHKERRQ(ierr); if (periodicZ == DM_BOUNDARY_PERIODIC) { cone[0] = 15; cone[1] = 18; cone[2] = 17; cone[3] = 16; cone[4] = 31; cone[5] = 32; cone[6] = 33; cone[7] = 34; ierr = DMPlexSetCone(*dm, 0, cone);CHKERRQ(ierr); cone[0] = 16; cone[1] = 17; cone[2] = 24; cone[3] = 23; cone[4] = 32; cone[5] = 36; cone[6] = 37; cone[7] = 33; /* 22 25 26 21 */ ierr = DMPlexSetCone(*dm, 1, cone);CHKERRQ(ierr); cone[0] = 18; cone[1] = 27; cone[2] = 24; cone[3] = 17; cone[4] = 34; cone[5] = 33; cone[6] = 37; cone[7] = 38; ierr = DMPlexSetCone(*dm, 2, cone);CHKERRQ(ierr); cone[0] = 29; cone[1] = 27; cone[2] = 18; cone[3] = 15; cone[4] = 35; cone[5] = 31; cone[6] = 34; cone[7] = 38; ierr = DMPlexSetCone(*dm, 3, cone);CHKERRQ(ierr); cone[0] = 29; cone[1] = 15; cone[2] = 16; cone[3] = 23; cone[4] = 35; cone[5] = 36; cone[6] = 32; cone[7] = 31; ierr = DMPlexSetCone(*dm, 4, cone);CHKERRQ(ierr); cone[0] = 31; cone[1] = 34; cone[2] = 33; cone[3] = 32; cone[4] = 19; cone[5] = 22; cone[6] = 21; cone[7] = 20; ierr = DMPlexSetCone(*dm, 5, cone);CHKERRQ(ierr); cone[0] = 32; cone[1] = 33; cone[2] = 37; cone[3] = 36; cone[4] = 22; cone[5] = 25; cone[6] = 26; cone[7] = 21; ierr = DMPlexSetCone(*dm, 6, cone);CHKERRQ(ierr); cone[0] = 34; cone[1] = 38; cone[2] = 37; cone[3] = 33; cone[4] = 20; cone[5] = 21; cone[6] = 26; cone[7] = 28; ierr = DMPlexSetCone(*dm, 7, cone);CHKERRQ(ierr); cone[0] = 35; cone[1] = 38; cone[2] = 34; cone[3] = 31; cone[4] = 30; cone[5] = 19; cone[6] = 20; cone[7] = 28; ierr = DMPlexSetCone(*dm, 8, cone);CHKERRQ(ierr); cone[0] = 35; cone[1] = 31; cone[2] = 32; cone[3] = 36; cone[4] = 30; cone[5] = 25; cone[6] = 22; cone[7] = 19; ierr = DMPlexSetCone(*dm, 9, cone);CHKERRQ(ierr); cone[0] = 19; cone[1] = 20; cone[2] = 21; cone[3] = 22; cone[4] = 15; cone[5] = 16; cone[6] = 17; cone[7] = 18; ierr = DMPlexSetCone(*dm, 10, cone);CHKERRQ(ierr); cone[0] = 22; cone[1] = 21; cone[2] = 26; cone[3] = 25; cone[4] = 16; cone[5] = 23; cone[6] = 24; cone[7] = 17; ierr = DMPlexSetCone(*dm, 11, cone);CHKERRQ(ierr); cone[0] = 20; cone[1] = 28; cone[2] = 26; cone[3] = 21; cone[4] = 18; cone[5] = 17; cone[6] = 24; cone[7] = 27; ierr = DMPlexSetCone(*dm, 12, cone);CHKERRQ(ierr); cone[0] = 30; cone[1] = 28; cone[2] = 20; cone[3] = 19; cone[4] = 29; cone[5] = 15; cone[6] = 18; cone[7] = 27; ierr = DMPlexSetCone(*dm, 13, cone);CHKERRQ(ierr); cone[0] = 30; cone[1] = 19; cone[2] = 22; cone[3] = 25; cone[4] = 29; cone[5] = 23; cone[6] = 16; cone[7] = 15; ierr = DMPlexSetCone(*dm, 14, cone);CHKERRQ(ierr); } else { cone[0] = 5; cone[1] = 8; cone[2] = 7; cone[3] = 6; cone[4] = 9; cone[5] = 12; cone[6] = 11; cone[7] = 10; ierr = DMPlexSetCone(*dm, 0, cone);CHKERRQ(ierr); cone[0] = 6; cone[1] = 7; cone[2] = 14; cone[3] = 13; cone[4] = 12; cone[5] = 15; cone[6] = 16; cone[7] = 11; ierr = DMPlexSetCone(*dm, 1, cone);CHKERRQ(ierr); cone[0] = 8; cone[1] = 17; cone[2] = 14; cone[3] = 7; cone[4] = 10; cone[5] = 11; cone[6] = 16; cone[7] = 18; ierr = DMPlexSetCone(*dm, 2, cone);CHKERRQ(ierr); cone[0] = 19; cone[1] = 17; cone[2] = 8; cone[3] = 5; cone[4] = 20; cone[5] = 9; cone[6] = 10; cone[7] = 18; ierr = DMPlexSetCone(*dm, 3, cone);CHKERRQ(ierr); cone[0] = 19; cone[1] = 5; cone[2] = 6; cone[3] = 13; cone[4] = 20; cone[5] = 15; cone[6] = 12; cone[7] = 9; ierr = DMPlexSetCone(*dm, 4, cone);CHKERRQ(ierr); } ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); ierr = DMPlexStratify(*dm);CHKERRQ(ierr); } /* Interpolate */ { DM idm = NULL; ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = idm; } /* Create cube geometry */ { Vec coordinates; PetscSection coordSection; PetscScalar *coords; PetscInt coordSize, v; const PetscReal dis = 1.0/PetscSqrtReal(2.0); const PetscReal ds2 = dis/2.0; /* Build coordinates */ ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr); ierr = PetscSectionSetChart(coordSection, numCells, numCells+numVertices);CHKERRQ(ierr); for (v = numCells; v < numCells+numVertices; ++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(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); ierr = VecSetBlockSize(coordinates, dim);CHKERRQ(ierr); ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); coords[0*dim+0] = -ds2; coords[0*dim+1] = -ds2; coords[0*dim+2] = 0.0; coords[1*dim+0] = ds2; coords[1*dim+1] = -ds2; coords[1*dim+2] = 0.0; coords[2*dim+0] = ds2; coords[2*dim+1] = ds2; coords[2*dim+2] = 0.0; coords[3*dim+0] = -ds2; coords[3*dim+1] = ds2; coords[3*dim+2] = 0.0; coords[4*dim+0] = -ds2; coords[4*dim+1] = -ds2; coords[4*dim+2] = 1.0; coords[5*dim+0] = -ds2; coords[5*dim+1] = ds2; coords[5*dim+2] = 1.0; coords[6*dim+0] = ds2; coords[6*dim+1] = ds2; coords[6*dim+2] = 1.0; coords[7*dim+0] = ds2; coords[7*dim+1] = -ds2; coords[7*dim+2] = 1.0; coords[ 8*dim+0] = dis; coords[ 8*dim+1] = -dis; coords[ 8*dim+2] = 0.0; coords[ 9*dim+0] = dis; coords[ 9*dim+1] = dis; coords[ 9*dim+2] = 0.0; coords[10*dim+0] = dis; coords[10*dim+1] = -dis; coords[10*dim+2] = 1.0; coords[11*dim+0] = dis; coords[11*dim+1] = dis; coords[11*dim+2] = 1.0; coords[12*dim+0] = -dis; coords[12*dim+1] = dis; coords[12*dim+2] = 0.0; coords[13*dim+0] = -dis; coords[13*dim+1] = dis; coords[13*dim+2] = 1.0; coords[14*dim+0] = -dis; coords[14*dim+1] = -dis; coords[14*dim+2] = 0.0; coords[15*dim+0] = -dis; coords[15*dim+1] = -dis; coords[15*dim+2] = 1.0; if (periodicZ == DM_BOUNDARY_PERIODIC) { /* 15 31 19 */ coords[16*dim+0] = -ds2; coords[16*dim+1] = -ds2; coords[16*dim+2] = 0.5; /* 16 32 22 */ coords[17*dim+0] = ds2; coords[17*dim+1] = -ds2; coords[17*dim+2] = 0.5; /* 17 33 21 */ coords[18*dim+0] = ds2; coords[18*dim+1] = ds2; coords[18*dim+2] = 0.5; /* 18 34 20 */ coords[19*dim+0] = -ds2; coords[19*dim+1] = ds2; coords[19*dim+2] = 0.5; /* 29 35 30 */ coords[20*dim+0] = -dis; coords[20*dim+1] = -dis; coords[20*dim+2] = 0.5; /* 23 36 25 */ coords[21*dim+0] = dis; coords[21*dim+1] = -dis; coords[21*dim+2] = 0.5; /* 24 37 26 */ coords[22*dim+0] = dis; coords[22*dim+1] = dis; coords[22*dim+2] = 0.5; /* 27 38 28 */ coords[23*dim+0] = -dis; coords[23*dim+1] = dis; coords[23*dim+2] = 0.5; } ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr); ierr = VecDestroy(&coordinates);CHKERRQ(ierr); } /* Create periodicity */ if (periodicZ == DM_BOUNDARY_PERIODIC || periodicZ == DM_BOUNDARY_TWIST) { PetscReal L[3]; PetscReal maxCell[3]; DMBoundaryType bdType[3]; PetscReal lower[3] = {0.0, 0.0, 0.0}; PetscReal upper[3] = {1.0, 1.0, 1.5}; PetscInt i, numZCells = 3; bdType[0] = DM_BOUNDARY_NONE; bdType[1] = DM_BOUNDARY_NONE; bdType[2] = periodicZ; for (i = 0; i < dim; i++) { L[i] = upper[i] - lower[i]; maxCell[i] = 1.1 * (L[i] / numZCells); } ierr = DMSetPeriodicity(*dm, maxCell, L, bdType);CHKERRQ(ierr); } /* Refine topology */ for (r = 0; r < numRefine; ++r) { DM rdm = NULL; ierr = DMRefine(*dm, comm, &rdm);CHKERRQ(ierr); ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = rdm; } /* Remap geometry to cylinder Interior square: Linear interpolation is correct The other cells all have vertices on rays from the origin. We want to uniformly expand the spacing such that the last vertex is on the unit circle. So the closest and farthest vertices are at distance phi = arctan(y/x) d_close = sqrt(1/8 + 1/4 sin^2(phi)) d_far = sqrt(1/2 + sin^2(phi)) so we remap them using x_new = x_close + (x - x_close) (1 - d_close) / (d_far - d_close) y_new = y_close + (y - y_close) (1 - d_close) / (d_far - d_close) If pi/4 < phi < 3pi/4 or -3pi/4 < phi < -pi/4, then we switch x and y. */ { Vec coordinates; PetscSection coordSection; PetscScalar *coords; PetscInt vStart, vEnd, v; const PetscReal dis = 1.0/PetscSqrtReal(2.0); const PetscReal ds2 = 0.5*dis; ierr = DMPlexGetDepthStratum(*dm, 0, &vStart, &vEnd);CHKERRQ(ierr); ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); ierr = DMGetCoordinatesLocal(*dm, &coordinates);CHKERRQ(ierr); ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); for (v = vStart; v < vEnd; ++v) { PetscReal phi, sinp, cosp, dc, df, x, y, xc, yc; PetscInt off; ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr); if ((PetscAbsScalar(coords[off+0]) <= ds2) && (PetscAbsScalar(coords[off+1]) <= ds2)) continue; x = PetscRealPart(coords[off]); y = PetscRealPart(coords[off+1]); phi = PetscAtan2Real(y, x); sinp = PetscSinReal(phi); cosp = PetscCosReal(phi); if ((PetscAbsReal(phi) > PETSC_PI/4.0) && (PetscAbsReal(phi) < 3.0*PETSC_PI/4.0)) { dc = PetscAbsReal(ds2/sinp); df = PetscAbsReal(dis/sinp); xc = ds2*x/PetscAbsScalar(y); yc = ds2*PetscSignReal(y); } else { dc = PetscAbsReal(ds2/cosp); df = PetscAbsReal(dis/cosp); xc = ds2*PetscSignReal(x); yc = ds2*y/PetscAbsScalar(x); } coords[off+0] = xc + (coords[off+0] - xc)*(1.0 - dc)/(df - dc); coords[off+1] = yc + (coords[off+1] - yc)*(1.0 - dc)/(df - dc); } ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); if (periodicZ == DM_BOUNDARY_PERIODIC || periodicZ == DM_BOUNDARY_TWIST) { ierr = DMLocalizeCoordinates(*dm);CHKERRQ(ierr); } } PetscFunctionReturn(0); } /*@ DMPlexCreateWedgeCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using wedges. Collective on MPI_Comm Input Parameters: + comm - The communicator for the DM object . n - The number of wedges around the origin - interpolate - Create edges and faces Output Parameter: . dm - The DM object Level: beginner .keywords: DM, create .seealso: DMPlexCreateHexCylinderMesh(), DMPlexCreateHexBoxMesh(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate() @*/ PetscErrorCode DMPlexCreateWedgeCylinderMesh(MPI_Comm comm, PetscInt n, PetscBool interpolate, DM *dm) { const PetscInt dim = 3; PetscInt numCells, numVertices; PetscErrorCode ierr; PetscFunctionBegin; PetscValidPointer(dm, 3); if (n < 0) SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Number of wedges %D cannot be negative", n); ierr = DMCreate(comm, dm);CHKERRQ(ierr); ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); /* Create topology */ { PetscInt cone[6], c; numCells = n; numVertices = 2*(n+1); ierr = DMPlexSetChart(*dm, 0, numCells+numVertices);CHKERRQ(ierr); for (c = 0; c < numCells; c++) {ierr = DMPlexSetConeSize(*dm, c, 6);CHKERRQ(ierr);} ierr = DMSetUp(*dm);CHKERRQ(ierr); for (c = 0; c < numCells; c++) { cone[0] = c+n*1; cone[1] = (c+1)%n+n*1; cone[2] = 0+3*n; cone[3] = c+n*2; cone[4] = (c+1)%n+n*2; cone[5] = 1+3*n; ierr = DMPlexSetCone(*dm, c, cone);CHKERRQ(ierr); } ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); ierr = DMPlexStratify(*dm);CHKERRQ(ierr); } /* Interpolate */ if (interpolate) { DM idm = NULL; ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = idm; } /* Create cylinder geometry */ { Vec coordinates; PetscSection coordSection; PetscScalar *coords; PetscInt coordSize, v, c; /* Build coordinates */ ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr); ierr = PetscSectionSetChart(coordSection, numCells, numCells+numVertices);CHKERRQ(ierr); for (v = numCells; v < numCells+numVertices; ++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(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); ierr = VecSetBlockSize(coordinates, dim);CHKERRQ(ierr); ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); for (c = 0; c < numCells; c++) { coords[(c+0*n)*dim+0] = PetscCosReal(2.0*c*PETSC_PI/n); coords[(c+0*n)*dim+1] = PetscSinReal(2.0*c*PETSC_PI/n); coords[(c+0*n)*dim+2] = 1.0; coords[(c+1*n)*dim+0] = PetscCosReal(2.0*c*PETSC_PI/n); coords[(c+1*n)*dim+1] = PetscSinReal(2.0*c*PETSC_PI/n); coords[(c+1*n)*dim+2] = 0.0; } coords[(2*n+0)*dim+0] = 0.0; coords[(2*n+0)*dim+1] = 0.0; coords[(2*n+0)*dim+2] = 1.0; coords[(2*n+1)*dim+0] = 0.0; coords[(2*n+1)*dim+1] = 0.0; coords[(2*n+1)*dim+2] = 0.0; ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr); ierr = VecDestroy(&coordinates);CHKERRQ(ierr); } PetscFunctionReturn(0); } PETSC_STATIC_INLINE PetscReal DiffNormReal(PetscInt dim, const PetscReal x[], const PetscReal y[]) { PetscReal prod = 0.0; PetscInt i; for (i = 0; i < dim; ++i) prod += PetscSqr(x[i] - y[i]); return PetscSqrtReal(prod); } PETSC_STATIC_INLINE PetscReal DotReal(PetscInt dim, const PetscReal x[], const PetscReal y[]) { PetscReal prod = 0.0; PetscInt i; for (i = 0; i < dim; ++i) prod += x[i]*y[i]; return prod; } #undef __FUNCT__ #define __FUNCT__ "DMPlexCreateSphereMesh" /*@ DMPlexCreateSphereMesh - Creates a mesh on the d-dimensional sphere, S^d. Collective on MPI_Comm Input Parameters: . comm - The communicator for the DM object . dim - The dimension - simplex - Use simplices, or tensor product cells Output Parameter: . dm - The DM object Level: beginner .keywords: DM, create .seealso: DMPlexCreateBoxMesh(), DMPlexCreateHexBoxMesh(), DMSetType(), DMCreate() @*/ PetscErrorCode DMPlexCreateSphereMesh(MPI_Comm comm, PetscInt dim, PetscBool simplex, DM *dm) { const PetscInt embedDim = dim+1; PetscSection coordSection; Vec coordinates; PetscScalar *coords; PetscReal *coordsIn; PetscInt numCells, numEdges, numVerts, firstVertex, v, firstEdge, coordSize, d, c, e; PetscMPIInt rank; PetscErrorCode ierr; PetscFunctionBegin; PetscValidPointer(dm, 4); ierr = DMCreate(comm, dm);CHKERRQ(ierr); ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); ierr = DMSetCoordinateDim(*dm, dim+1);CHKERRQ(ierr); ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) *dm), &rank);CHKERRQ(ierr); switch (dim) { case 2: if (simplex) { DM idm = NULL; const PetscReal edgeLen = 2.0/(1.0 + PETSC_PHI); const PetscReal vertex[3] = {0.0, 1.0/(1.0 + PETSC_PHI), PETSC_PHI/(1.0 + PETSC_PHI)}; const PetscInt degree = 5; PetscInt s[3] = {1, 1, 1}; PetscInt cone[3]; PetscInt *graph, p, i, j, k; numCells = !rank ? 20 : 0; numEdges = !rank ? 30 : 0; numVerts = !rank ? 12 : 0; firstVertex = numCells; firstEdge = numCells + numVerts; /* Use icosahedron, which for a unit sphere has coordinates which are all cyclic permutations of (0, \pm 1/\phi+1, \pm \phi/\phi+1) where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge length is then given by 2/\phi = 2 * 2.73606 = 5.47214. */ /* Construct vertices */ ierr = PetscCalloc1(numVerts * embedDim, &coordsIn);CHKERRQ(ierr); for (p = 0, i = 0; p < embedDim; ++p) { for (s[1] = -1; s[1] < 2; s[1] += 2) { for (s[2] = -1; s[2] < 2; s[2] += 2) { for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[(d+p)%embedDim]*vertex[(d+p)%embedDim]; ++i; } } } /* Construct graph */ ierr = PetscCalloc1(numVerts * numVerts, &graph);CHKERRQ(ierr); for (i = 0; i < numVerts; ++i) { for (j = 0, k = 0; j < numVerts; ++j) { if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i*embedDim], &coordsIn[j*embedDim]) - edgeLen) < PETSC_SMALL) {graph[i*numVerts+j] = 1; ++k;} } if (k != degree) SETERRQ3(comm, PETSC_ERR_PLIB, "Invalid icosahedron, vertex %D degree %D != %D", i, k, degree); } /* Build Topology */ ierr = DMPlexSetChart(*dm, 0, numCells+numVerts);CHKERRQ(ierr); for (c = 0; c < numCells; c++) { ierr = DMPlexSetConeSize(*dm, c, embedDim);CHKERRQ(ierr); } ierr = DMSetUp(*dm);CHKERRQ(ierr); /* Allocate space for cones */ /* Cells */ for (i = 0, c = 0; i < numVerts; ++i) { for (j = 0; j < i; ++j) { for (k = 0; k < j; ++k) { if (graph[i*numVerts+j] && graph[j*numVerts+k] && graph[k*numVerts+i]) { cone[0] = firstVertex+i; cone[1] = firstVertex+j; cone[2] = firstVertex+k; /* Check orientation */ { const PetscInt epsilon[3][3][3] = {{{0, 0, 0}, {0, 0, 1}, {0, -1, 0}}, {{0, 0, -1}, {0, 0, 0}, {1, 0, 0}}, {{0, 1, 0}, {-1, 0, 0}, {0, 0, 0}}}; PetscReal normal[3]; PetscInt e, f; for (d = 0; d < embedDim; ++d) { normal[d] = 0.0; for (e = 0; e < embedDim; ++e) { for (f = 0; f < embedDim; ++f) { normal[d] += epsilon[d][e][f]*(coordsIn[j*embedDim+e] - coordsIn[i*embedDim+e])*(coordsIn[k*embedDim+f] - coordsIn[i*embedDim+f]); } } } if (DotReal(embedDim, normal, &coordsIn[i*embedDim]) < 0) {PetscInt tmp = cone[1]; cone[1] = cone[2]; cone[2] = tmp;} } ierr = DMPlexSetCone(*dm, c++, cone);CHKERRQ(ierr); } } } } ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); ierr = DMPlexStratify(*dm);CHKERRQ(ierr); ierr = PetscFree(graph);CHKERRQ(ierr); /* Interpolate mesh */ ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = idm; } else { /* 12-21--13 | | 25 4 24 | | 12-25--9-16--8-24--13 | | | | 23 5 17 0 15 3 22 | | | | 10-20--6-14--7-19--11 | | 20 1 19 | | 10-18--11 | | 23 2 22 | | 12-21--13 */ const PetscReal dist = 1.0/PetscSqrtReal(3.0); PetscInt cone[4], ornt[4]; numCells = !rank ? 6 : 0; numEdges = !rank ? 12 : 0; numVerts = !rank ? 8 : 0; firstVertex = numCells; firstEdge = numCells + numVerts; /* Build Topology */ ierr = DMPlexSetChart(*dm, 0, numCells+numEdges+numVerts);CHKERRQ(ierr); for (c = 0; c < numCells; c++) { ierr = DMPlexSetConeSize(*dm, c, 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 */ /* Cell 0 */ cone[0] = 14; cone[1] = 15; cone[2] = 16; cone[3] = 17; ierr = DMPlexSetCone(*dm, 0, cone);CHKERRQ(ierr); ornt[0] = 0; ornt[1] = 0; ornt[2] = 0; ornt[3] = 0; ierr = DMPlexSetConeOrientation(*dm, 0, ornt);CHKERRQ(ierr); /* Cell 1 */ cone[0] = 18; cone[1] = 19; cone[2] = 14; cone[3] = 20; ierr = DMPlexSetCone(*dm, 1, cone);CHKERRQ(ierr); ornt[0] = 0; ornt[1] = 0; ornt[2] = -2; ornt[3] = 0; ierr = DMPlexSetConeOrientation(*dm, 1, ornt);CHKERRQ(ierr); /* Cell 2 */ cone[0] = 21; cone[1] = 22; cone[2] = 18; cone[3] = 23; ierr = DMPlexSetCone(*dm, 2, cone);CHKERRQ(ierr); ornt[0] = 0; ornt[1] = 0; ornt[2] = -2; ornt[3] = 0; ierr = DMPlexSetConeOrientation(*dm, 2, ornt);CHKERRQ(ierr); /* Cell 3 */ cone[0] = 19; cone[1] = 22; cone[2] = 24; cone[3] = 15; ierr = DMPlexSetCone(*dm, 3, cone);CHKERRQ(ierr); ornt[0] = -2; ornt[1] = -2; ornt[2] = 0; ornt[3] = -2; ierr = DMPlexSetConeOrientation(*dm, 3, ornt);CHKERRQ(ierr); /* Cell 4 */ cone[0] = 16; cone[1] = 24; cone[2] = 21; cone[3] = 25; ierr = DMPlexSetCone(*dm, 4, cone);CHKERRQ(ierr); ornt[0] = -2; ornt[1] = -2; ornt[2] = -2; ornt[3] = 0; ierr = DMPlexSetConeOrientation(*dm, 4, ornt);CHKERRQ(ierr); /* Cell 5 */ cone[0] = 20; cone[1] = 17; cone[2] = 25; cone[3] = 23; ierr = DMPlexSetCone(*dm, 5, cone);CHKERRQ(ierr); ornt[0] = -2; ornt[1] = -2; ornt[2] = -2; ornt[3] = -2; ierr = DMPlexSetConeOrientation(*dm, 5, ornt);CHKERRQ(ierr); /* Edges */ cone[0] = 6; cone[1] = 7; ierr = DMPlexSetCone(*dm, 14, cone);CHKERRQ(ierr); cone[0] = 7; cone[1] = 8; ierr = DMPlexSetCone(*dm, 15, cone);CHKERRQ(ierr); cone[0] = 8; cone[1] = 9; ierr = DMPlexSetCone(*dm, 16, cone);CHKERRQ(ierr); cone[0] = 9; cone[1] = 6; ierr = DMPlexSetCone(*dm, 17, cone);CHKERRQ(ierr); cone[0] = 10; cone[1] = 11; ierr = DMPlexSetCone(*dm, 18, cone);CHKERRQ(ierr); cone[0] = 11; cone[1] = 7; ierr = DMPlexSetCone(*dm, 19, cone);CHKERRQ(ierr); cone[0] = 6; cone[1] = 10; ierr = DMPlexSetCone(*dm, 20, cone);CHKERRQ(ierr); cone[0] = 12; cone[1] = 13; ierr = DMPlexSetCone(*dm, 21, cone);CHKERRQ(ierr); cone[0] = 13; cone[1] = 11; ierr = DMPlexSetCone(*dm, 22, cone);CHKERRQ(ierr); cone[0] = 10; cone[1] = 12; ierr = DMPlexSetCone(*dm, 23, cone);CHKERRQ(ierr); cone[0] = 13; cone[1] = 8; ierr = DMPlexSetCone(*dm, 24, cone);CHKERRQ(ierr); cone[0] = 12; cone[1] = 9; ierr = DMPlexSetCone(*dm, 25, cone);CHKERRQ(ierr); ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); ierr = DMPlexStratify(*dm);CHKERRQ(ierr); /* Build coordinates */ ierr = PetscCalloc1(numVerts * embedDim, &coordsIn);CHKERRQ(ierr); coordsIn[0*embedDim+0] = -dist; coordsIn[0*embedDim+1] = dist; coordsIn[0*embedDim+2] = -dist; coordsIn[1*embedDim+0] = dist; coordsIn[1*embedDim+1] = dist; coordsIn[1*embedDim+2] = -dist; coordsIn[2*embedDim+0] = dist; coordsIn[2*embedDim+1] = -dist; coordsIn[2*embedDim+2] = -dist; coordsIn[3*embedDim+0] = -dist; coordsIn[3*embedDim+1] = -dist; coordsIn[3*embedDim+2] = -dist; coordsIn[4*embedDim+0] = -dist; coordsIn[4*embedDim+1] = dist; coordsIn[4*embedDim+2] = dist; coordsIn[5*embedDim+0] = dist; coordsIn[5*embedDim+1] = dist; coordsIn[5*embedDim+2] = dist; coordsIn[6*embedDim+0] = -dist; coordsIn[6*embedDim+1] = -dist; coordsIn[6*embedDim+2] = dist; coordsIn[7*embedDim+0] = dist; coordsIn[7*embedDim+1] = -dist; coordsIn[7*embedDim+2] = dist; } break; case 3: if (simplex) { DM idm = NULL; const PetscReal edgeLen = 1.0/PETSC_PHI; const PetscReal vertexA[4] = {0.5, 0.5, 0.5, 0.5}; const PetscReal vertexB[4] = {1.0, 0.0, 0.0, 0.0}; const PetscReal vertexC[4] = {0.5, 0.5*PETSC_PHI, 0.5/PETSC_PHI, 0.0}; const PetscInt degree = 12; PetscInt s[4] = {1, 1, 1}; PetscInt evenPerm[12][4] = {{0, 1, 2, 3}, {0, 2, 3, 1}, {0, 3, 1, 2}, {1, 0, 3, 2}, {1, 2, 0, 3}, {1, 3, 2, 0}, {2, 0, 1, 3}, {2, 1, 3, 0}, {2, 3, 0, 1}, {3, 0, 2, 1}, {3, 1, 0, 2}, {3, 2, 1, 0}}; PetscInt cone[4]; PetscInt *graph, p, i, j, k, l; numCells = !rank ? 600 : 0; numVerts = !rank ? 120 : 0; firstVertex = numCells; /* Use the 600-cell, which for a unit sphere has coordinates which are 1/2 (\pm 1, \pm 1, \pm 1, \pm 1) 16 (\pm 1, 0, 0, 0) all cyclic permutations 8 1/2 (\pm 1, \pm phi, \pm 1/phi, 0) all even permutations 96 where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge length is then given by 1/\phi = 2.73606. http://buzzard.pugetsound.edu/sage-practice/ch03s03.html http://mathworld.wolfram.com/600-Cell.html */ /* Construct vertices */ ierr = PetscCalloc1(numVerts * embedDim, &coordsIn);CHKERRQ(ierr); i = 0; for (s[0] = -1; s[0] < 2; s[0] += 2) { for (s[1] = -1; s[1] < 2; s[1] += 2) { for (s[2] = -1; s[2] < 2; s[2] += 2) { for (s[3] = -1; s[3] < 2; s[3] += 2) { for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[d]*vertexA[d]; ++i; } } } } for (p = 0; p < embedDim; ++p) { s[1] = s[2] = s[3] = 1; for (s[0] = -1; s[0] < 2; s[0] += 2) { for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[(d+p)%embedDim]*vertexB[(d+p)%embedDim]; ++i; } } for (p = 0; p < 12; ++p) { s[3] = 1; for (s[0] = -1; s[0] < 2; s[0] += 2) { for (s[1] = -1; s[1] < 2; s[1] += 2) { for (s[2] = -1; s[2] < 2; s[2] += 2) { for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[evenPerm[p][d]]*vertexC[evenPerm[p][d]]; ++i; } } } } if (i != numVerts) SETERRQ2(comm, PETSC_ERR_PLIB, "Invalid 600-cell, vertices %D != %D", i, numVerts); /* Construct graph */ ierr = PetscCalloc1(numVerts * numVerts, &graph);CHKERRQ(ierr); for (i = 0; i < numVerts; ++i) { for (j = 0, k = 0; j < numVerts; ++j) { if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i*embedDim], &coordsIn[j*embedDim]) - edgeLen) < PETSC_SMALL) {graph[i*numVerts+j] = 1; ++k;} } if (k != degree) SETERRQ3(comm, PETSC_ERR_PLIB, "Invalid 600-cell, vertex %D degree %D != %D", i, k, degree); } /* Build Topology */ ierr = DMPlexSetChart(*dm, 0, numCells+numVerts);CHKERRQ(ierr); for (c = 0; c < numCells; c++) { ierr = DMPlexSetConeSize(*dm, c, embedDim);CHKERRQ(ierr); } ierr = DMSetUp(*dm);CHKERRQ(ierr); /* Allocate space for cones */ /* Cells */ for (i = 0, c = 0; i < numVerts; ++i) { for (j = 0; j < i; ++j) { for (k = 0; k < j; ++k) { for (l = 0; l < k; ++l) { if (graph[i*numVerts+j] && graph[j*numVerts+k] && graph[k*numVerts+i] && graph[l*numVerts+i] && graph[l*numVerts+j] && graph[l*numVerts+k]) { cone[0] = firstVertex+i; cone[1] = firstVertex+j; cone[2] = firstVertex+k; cone[3] = firstVertex+l; /* Check orientation: https://ef.gy/linear-algebra:normal-vectors-in-higher-dimensional-spaces */ { const PetscInt epsilon[4][4][4][4] = {{{{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 1}, { 0, 0, -1, 0}}, {{0, 0, 0, 0}, { 0, 0, 0, -1}, { 0, 0, 0, 0}, { 0, 1, 0, 0}}, {{0, 0, 0, 0}, { 0, 0, 1, 0}, { 0, -1, 0, 0}, { 0, 0, 0, 0}}}, {{{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, -1}, { 0, 0, 1, 0}}, {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, {{0, 0, 0, 1}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, {-1, 0, 0, 0}}, {{0, 0, -1, 0}, { 0, 0, 0, 0}, { 1, 0, 0, 0}, { 0, 0, 0, 0}}}, {{{0, 0, 0, 0}, { 0, 0, 0, 1}, { 0, 0, 0, 0}, { 0, -1, 0, 0}}, {{0, 0, 0, -1}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 1, 0, 0, 0}}, {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, {{0, 1, 0, 0}, {-1, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}}, {{{0, 0, 0, 0}, { 0, 0, -1, 0}, { 0, 1, 0, 0}, { 0, 0, 0, 0}}, {{0, 0, 1, 0}, { 0, 0, 0, 0}, {-1, 0, 0, 0}, { 0, 0, 0, 0}}, {{0, -1, 0, 0}, { 1, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}}}; PetscReal normal[4]; PetscInt e, f, g; for (d = 0; d < embedDim; ++d) { normal[d] = 0.0; for (e = 0; e < embedDim; ++e) { for (f = 0; f < embedDim; ++f) { for (g = 0; g < embedDim; ++g) { normal[d] += epsilon[d][e][f][g]*(coordsIn[j*embedDim+e] - coordsIn[i*embedDim+e])*(coordsIn[k*embedDim+f] - coordsIn[i*embedDim+f])*(coordsIn[l*embedDim+f] - coordsIn[i*embedDim+f]); } } } } if (DotReal(embedDim, normal, &coordsIn[i*embedDim]) < 0) {PetscInt tmp = cone[1]; cone[1] = cone[2]; cone[2] = tmp;} } ierr = DMPlexSetCone(*dm, c++, cone);CHKERRQ(ierr); } } } } } ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); ierr = DMPlexStratify(*dm);CHKERRQ(ierr); ierr = PetscFree(graph);CHKERRQ(ierr); /* Interpolate mesh */ ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = idm; break; } default: SETERRQ1(comm, PETSC_ERR_SUP, "Unsupported dimension for sphere: %D", dim); } /* Create coordinates */ ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); ierr = PetscSectionSetFieldComponents(coordSection, 0, embedDim);CHKERRQ(ierr); ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVerts);CHKERRQ(ierr); for (v = firstVertex; v < firstVertex+numVerts; ++v) { ierr = PetscSectionSetDof(coordSection, v, embedDim);CHKERRQ(ierr); ierr = PetscSectionSetFieldDof(coordSection, v, 0, embedDim);CHKERRQ(ierr); } ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); ierr = VecSetBlockSize(coordinates, embedDim);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); for (v = 0; v < numVerts; ++v) for (d = 0; d < embedDim; ++d) {coords[v*embedDim+d] = coordsIn[v*embedDim+d];} ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr); ierr = VecDestroy(&coordinates);CHKERRQ(ierr); ierr = PetscFree(coordsIn);CHKERRQ(ierr); PetscFunctionReturn(0); } /* External function declarations here */ extern PetscErrorCode DMCreateInterpolation_Plex(DM dmCoarse, DM dmFine, Mat *interpolation, Vec *scaling); extern PetscErrorCode DMCreateInjection_Plex(DM dmCoarse, DM dmFine, Mat *mat); extern PetscErrorCode DMCreateDefaultSection_Plex(DM dm); extern PetscErrorCode DMCreateDefaultConstraints_Plex(DM dm); extern PetscErrorCode DMCreateMatrix_Plex(DM dm, Mat *J); extern PetscErrorCode DMCreateCoordinateDM_Plex(DM dm, DM *cdm); PETSC_INTERN PetscErrorCode DMClone_Plex(DM dm, DM *newdm); extern PetscErrorCode DMSetUp_Plex(DM dm); extern PetscErrorCode DMDestroy_Plex(DM dm); extern PetscErrorCode DMView_Plex(DM dm, PetscViewer viewer); extern PetscErrorCode DMLoad_Plex(DM dm, PetscViewer viewer); extern PetscErrorCode DMCreateSubDM_Plex(DM dm, PetscInt numFields, PetscInt fields[], IS *is, DM *subdm); static PetscErrorCode DMInitialize_Plex(DM dm); /* Replace dm with the contents of dmNew - Share the DM_Plex structure - Share the coordinates - Share the SF */ static PetscErrorCode DMPlexReplace_Static(DM dm, DM dmNew) { PetscSF sf; DM coordDM, coarseDM; Vec coords; const PetscReal *maxCell, *L; const DMBoundaryType *bd; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMGetPointSF(dmNew, &sf);CHKERRQ(ierr); ierr = DMSetPointSF(dm, sf);CHKERRQ(ierr); ierr = DMGetCoordinateDM(dmNew, &coordDM);CHKERRQ(ierr); ierr = DMGetCoordinatesLocal(dmNew, &coords);CHKERRQ(ierr); ierr = DMSetCoordinateDM(dm, coordDM);CHKERRQ(ierr); ierr = DMSetCoordinatesLocal(dm, coords);CHKERRQ(ierr); ierr = DMGetPeriodicity(dm, &maxCell, &L, &bd);CHKERRQ(ierr); if (L) {ierr = DMSetPeriodicity(dmNew, maxCell, L, bd);CHKERRQ(ierr);} ierr = DMDestroy_Plex(dm);CHKERRQ(ierr); ierr = DMInitialize_Plex(dm);CHKERRQ(ierr); dm->data = dmNew->data; ((DM_Plex *) dmNew->data)->refct++; dmNew->labels->refct++; if (!--(dm->labels->refct)) { DMLabelLink next = dm->labels->next; /* destroy the labels */ while (next) { DMLabelLink tmp = next->next; ierr = DMLabelDestroy(&next->label);CHKERRQ(ierr); ierr = PetscFree(next);CHKERRQ(ierr); next = tmp; } ierr = PetscFree(dm->labels);CHKERRQ(ierr); } dm->labels = dmNew->labels; dm->depthLabel = dmNew->depthLabel; ierr = DMGetCoarseDM(dmNew,&coarseDM);CHKERRQ(ierr); ierr = DMSetCoarseDM(dm,coarseDM);CHKERRQ(ierr); PetscFunctionReturn(0); } /* Swap dm with the contents of dmNew - Swap the DM_Plex structure - Swap the coordinates - Swap the point PetscSF */ static PetscErrorCode DMPlexSwap_Static(DM dmA, DM dmB) { DM coordDMA, coordDMB; Vec coordsA, coordsB; PetscSF sfA, sfB; void *tmp; DMLabelLinkList listTmp; DMLabel depthTmp; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMGetPointSF(dmA, &sfA);CHKERRQ(ierr); ierr = DMGetPointSF(dmB, &sfB);CHKERRQ(ierr); ierr = PetscObjectReference((PetscObject) sfA);CHKERRQ(ierr); ierr = DMSetPointSF(dmA, sfB);CHKERRQ(ierr); ierr = DMSetPointSF(dmB, sfA);CHKERRQ(ierr); ierr = PetscObjectDereference((PetscObject) sfA);CHKERRQ(ierr); ierr = DMGetCoordinateDM(dmA, &coordDMA);CHKERRQ(ierr); ierr = DMGetCoordinateDM(dmB, &coordDMB);CHKERRQ(ierr); ierr = PetscObjectReference((PetscObject) coordDMA);CHKERRQ(ierr); ierr = DMSetCoordinateDM(dmA, coordDMB);CHKERRQ(ierr); ierr = DMSetCoordinateDM(dmB, coordDMA);CHKERRQ(ierr); ierr = PetscObjectDereference((PetscObject) coordDMA);CHKERRQ(ierr); ierr = DMGetCoordinatesLocal(dmA, &coordsA);CHKERRQ(ierr); ierr = DMGetCoordinatesLocal(dmB, &coordsB);CHKERRQ(ierr); ierr = PetscObjectReference((PetscObject) coordsA);CHKERRQ(ierr); ierr = DMSetCoordinatesLocal(dmA, coordsB);CHKERRQ(ierr); ierr = DMSetCoordinatesLocal(dmB, coordsA);CHKERRQ(ierr); ierr = PetscObjectDereference((PetscObject) coordsA);CHKERRQ(ierr); tmp = dmA->data; dmA->data = dmB->data; dmB->data = tmp; listTmp = dmA->labels; dmA->labels = dmB->labels; dmB->labels = listTmp; depthTmp = dmA->depthLabel; dmA->depthLabel = dmB->depthLabel; dmB->depthLabel = depthTmp; PetscFunctionReturn(0); } PetscErrorCode DMSetFromOptions_NonRefinement_Plex(PetscOptionItems *PetscOptionsObject,DM dm) { DM_Plex *mesh = (DM_Plex*) dm->data; PetscErrorCode ierr; PetscFunctionBegin; /* Handle viewing */ ierr = PetscOptionsBool("-dm_plex_print_set_values", "Output all set values info", "DMView", PETSC_FALSE, &mesh->printSetValues, NULL);CHKERRQ(ierr); ierr = PetscOptionsInt("-dm_plex_print_fem", "Debug output level all fem computations", "DMView", 0, &mesh->printFEM, NULL);CHKERRQ(ierr); ierr = PetscOptionsReal("-dm_plex_print_tol", "Tolerance for FEM output", "DMView", mesh->printTol, &mesh->printTol, NULL);CHKERRQ(ierr); /* Point Location */ ierr = PetscOptionsBool("-dm_plex_hash_location", "Use grid hashing for point location", "DMView", PETSC_FALSE, &mesh->useHashLocation, NULL);CHKERRQ(ierr); /* Generation and remeshing */ ierr = PetscOptionsBool("-dm_plex_remesh_bd", "Allow changes to the boundary on remeshing", "DMView", PETSC_FALSE, &mesh->remeshBd, NULL);CHKERRQ(ierr); /* Projection behavior */ ierr = PetscOptionsInt("-dm_plex_max_projection_height", "Maxmimum mesh point height used to project locally", "DMPlexSetMaxProjectionHeight", 0, &mesh->maxProjectionHeight, NULL);CHKERRQ(ierr); ierr = PetscOptionsBool("-dm_plex_regular_refinement", "Use special nested projection algorithm for regular refinement", "DMPlexSetRegularRefinement", mesh->regularRefinement, &mesh->regularRefinement, NULL);CHKERRQ(ierr); ierr = PetscPartitionerSetFromOptions(mesh->partitioner);CHKERRQ(ierr); PetscFunctionReturn(0); } static PetscErrorCode DMSetFromOptions_Plex(PetscOptionItems *PetscOptionsObject,DM dm) { PetscInt refine = 0, coarsen = 0, r; PetscBool isHierarchy; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); ierr = PetscOptionsHead(PetscOptionsObject,"DMPlex Options");CHKERRQ(ierr); /* Handle DMPlex refinement */ ierr = PetscOptionsInt("-dm_refine", "The number of uniform refinements", "DMCreate", refine, &refine, NULL);CHKERRQ(ierr); ierr = PetscOptionsInt("-dm_refine_hierarchy", "The number of uniform refinements", "DMCreate", refine, &refine, &isHierarchy);CHKERRQ(ierr); if (refine) {ierr = DMPlexSetRefinementUniform(dm, PETSC_TRUE);CHKERRQ(ierr);} if (refine && isHierarchy) { DM *dms, coarseDM; ierr = DMGetCoarseDM(dm, &coarseDM);CHKERRQ(ierr); ierr = PetscObjectReference((PetscObject)coarseDM);CHKERRQ(ierr); ierr = PetscMalloc1(refine,&dms);CHKERRQ(ierr); ierr = DMRefineHierarchy(dm, refine, dms);CHKERRQ(ierr); /* Total hack since we do not pass in a pointer */ ierr = DMPlexSwap_Static(dm, dms[refine-1]);CHKERRQ(ierr); if (refine == 1) { ierr = DMSetCoarseDM(dm, dms[0]);CHKERRQ(ierr); ierr = DMPlexSetRegularRefinement(dm, PETSC_TRUE);CHKERRQ(ierr); } else { ierr = DMSetCoarseDM(dm, dms[refine-2]);CHKERRQ(ierr); ierr = DMPlexSetRegularRefinement(dm, PETSC_TRUE);CHKERRQ(ierr); ierr = DMSetCoarseDM(dms[0], dms[refine-1]);CHKERRQ(ierr); ierr = DMPlexSetRegularRefinement(dms[0], PETSC_TRUE);CHKERRQ(ierr); } ierr = DMSetCoarseDM(dms[refine-1], coarseDM);CHKERRQ(ierr); ierr = PetscObjectDereference((PetscObject)coarseDM);CHKERRQ(ierr); /* Free DMs */ for (r = 0; r < refine; ++r) { ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);CHKERRQ(ierr); ierr = DMDestroy(&dms[r]);CHKERRQ(ierr); } ierr = PetscFree(dms);CHKERRQ(ierr); } else { for (r = 0; r < refine; ++r) { DM refinedMesh; ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); ierr = DMRefine(dm, PetscObjectComm((PetscObject) dm), &refinedMesh);CHKERRQ(ierr); /* Total hack since we do not pass in a pointer */ ierr = DMPlexReplace_Static(dm, refinedMesh);CHKERRQ(ierr); ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); ierr = DMDestroy(&refinedMesh);CHKERRQ(ierr); } } /* Handle DMPlex coarsening */ ierr = PetscOptionsInt("-dm_coarsen", "Coarsen the mesh", "DMCreate", coarsen, &coarsen, NULL);CHKERRQ(ierr); ierr = PetscOptionsInt("-dm_coarsen_hierarchy", "The number of coarsenings", "DMCreate", coarsen, &coarsen, &isHierarchy);CHKERRQ(ierr); if (coarsen && isHierarchy) { DM *dms; ierr = PetscMalloc1(coarsen, &dms);CHKERRQ(ierr); ierr = DMCoarsenHierarchy(dm, coarsen, dms);CHKERRQ(ierr); /* Free DMs */ for (r = 0; r < coarsen; ++r) { ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);CHKERRQ(ierr); ierr = DMDestroy(&dms[r]);CHKERRQ(ierr); } ierr = PetscFree(dms);CHKERRQ(ierr); } else { for (r = 0; r < coarsen; ++r) { DM coarseMesh; ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); ierr = DMCoarsen(dm, PetscObjectComm((PetscObject) dm), &coarseMesh);CHKERRQ(ierr); /* Total hack since we do not pass in a pointer */ ierr = DMPlexReplace_Static(dm, coarseMesh);CHKERRQ(ierr); ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); ierr = DMDestroy(&coarseMesh);CHKERRQ(ierr); } } /* Handle */ ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); ierr = PetscOptionsTail();CHKERRQ(ierr); PetscFunctionReturn(0); } static PetscErrorCode DMCreateGlobalVector_Plex(DM dm,Vec *vec) { PetscErrorCode ierr; PetscFunctionBegin; ierr = DMCreateGlobalVector_Section_Private(dm,vec);CHKERRQ(ierr); /* ierr = VecSetOperation(*vec, VECOP_DUPLICATE, (void(*)(void)) VecDuplicate_MPI_DM);CHKERRQ(ierr); */ ierr = VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex);CHKERRQ(ierr); ierr = VecSetOperation(*vec, VECOP_VIEWNATIVE, (void (*)(void)) VecView_Plex_Native);CHKERRQ(ierr); ierr = VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex);CHKERRQ(ierr); ierr = VecSetOperation(*vec, VECOP_LOADNATIVE, (void (*)(void)) VecLoad_Plex_Native);CHKERRQ(ierr); PetscFunctionReturn(0); } static PetscErrorCode DMCreateLocalVector_Plex(DM dm,Vec *vec) { PetscErrorCode ierr; PetscFunctionBegin; ierr = DMCreateLocalVector_Section_Private(dm,vec);CHKERRQ(ierr); ierr = VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex_Local);CHKERRQ(ierr); ierr = VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex_Local);CHKERRQ(ierr); PetscFunctionReturn(0); } static PetscErrorCode DMGetDimPoints_Plex(DM dm, PetscInt dim, PetscInt *pStart, PetscInt *pEnd) { PetscInt depth, d; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); if (depth == 1) { ierr = DMGetDimension(dm, &d);CHKERRQ(ierr); if (dim == 0) {ierr = DMPlexGetDepthStratum(dm, dim, pStart, pEnd);CHKERRQ(ierr);} else if (dim == d) {ierr = DMPlexGetDepthStratum(dm, 1, pStart, pEnd);CHKERRQ(ierr);} else {*pStart = 0; *pEnd = 0;} } else { ierr = DMPlexGetDepthStratum(dm, dim, pStart, pEnd);CHKERRQ(ierr); } PetscFunctionReturn(0); } static PetscErrorCode DMGetNeighors_Plex(DM dm, PetscInt *nranks, const PetscMPIInt *ranks[]) { PetscSF sf; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMGetPointSF(dm, &sf);CHKERRQ(ierr); ierr = PetscSFGetRanks(sf, nranks, ranks, NULL, NULL, NULL);CHKERRQ(ierr); PetscFunctionReturn(0); } static PetscErrorCode DMInitialize_Plex(DM dm) { PetscErrorCode ierr; PetscFunctionBegin; dm->ops->view = DMView_Plex; dm->ops->load = DMLoad_Plex; dm->ops->setfromoptions = DMSetFromOptions_Plex; dm->ops->clone = DMClone_Plex; dm->ops->setup = DMSetUp_Plex; dm->ops->createdefaultsection = DMCreateDefaultSection_Plex; dm->ops->createdefaultconstraints = DMCreateDefaultConstraints_Plex; dm->ops->createglobalvector = DMCreateGlobalVector_Plex; dm->ops->createlocalvector = DMCreateLocalVector_Plex; dm->ops->getlocaltoglobalmapping = NULL; dm->ops->createfieldis = NULL; dm->ops->createcoordinatedm = DMCreateCoordinateDM_Plex; dm->ops->getcoloring = NULL; dm->ops->creatematrix = DMCreateMatrix_Plex; dm->ops->createinterpolation = DMCreateInterpolation_Plex; dm->ops->getaggregates = NULL; dm->ops->getinjection = DMCreateInjection_Plex; dm->ops->refine = DMRefine_Plex; dm->ops->coarsen = DMCoarsen_Plex; dm->ops->refinehierarchy = DMRefineHierarchy_Plex; dm->ops->coarsenhierarchy = DMCoarsenHierarchy_Plex; dm->ops->globaltolocalbegin = NULL; dm->ops->globaltolocalend = NULL; dm->ops->localtoglobalbegin = NULL; dm->ops->localtoglobalend = NULL; dm->ops->destroy = DMDestroy_Plex; dm->ops->createsubdm = DMCreateSubDM_Plex; dm->ops->getdimpoints = DMGetDimPoints_Plex; dm->ops->locatepoints = DMLocatePoints_Plex; dm->ops->projectfunctionlocal = DMProjectFunctionLocal_Plex; dm->ops->projectfunctionlabellocal = DMProjectFunctionLabelLocal_Plex; dm->ops->projectfieldlocal = DMProjectFieldLocal_Plex; dm->ops->projectfieldlabellocal = DMProjectFieldLabelLocal_Plex; dm->ops->computel2diff = DMComputeL2Diff_Plex; dm->ops->computel2gradientdiff = DMComputeL2GradientDiff_Plex; dm->ops->computel2fielddiff = DMComputeL2FieldDiff_Plex; dm->ops->getneighbors = DMGetNeighors_Plex; ierr = PetscObjectComposeFunction((PetscObject)dm,"DMAdaptLabel_C",DMAdaptLabel_Plex);CHKERRQ(ierr); ierr = PetscObjectComposeFunction((PetscObject)dm,"DMPlexInsertBoundaryValues_C",DMPlexInsertBoundaryValues_Plex);CHKERRQ(ierr); PetscFunctionReturn(0); } PETSC_INTERN PetscErrorCode DMClone_Plex(DM dm, DM *newdm) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscErrorCode ierr; PetscFunctionBegin; mesh->refct++; (*newdm)->data = mesh; ierr = PetscObjectChangeTypeName((PetscObject) *newdm, DMPLEX);CHKERRQ(ierr); ierr = DMInitialize_Plex(*newdm);CHKERRQ(ierr); PetscFunctionReturn(0); } /*MC DMPLEX = "plex" - A DM object that encapsulates an unstructured mesh, or CW Complex, which can be expressed using a Hasse Diagram. In the local representation, Vecs contain all unknowns in the interior and shared boundary. This is specified by a PetscSection object. Ownership in the global representation is determined by ownership of the underlying DMPlex points. This is specified by another PetscSection object. Level: intermediate .seealso: DMType, DMPlexCreate(), DMCreate(), DMSetType() M*/ PETSC_EXTERN PetscErrorCode DMCreate_Plex(DM dm) { DM_Plex *mesh; PetscInt unit, d; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); ierr = PetscNewLog(dm,&mesh);CHKERRQ(ierr); dm->dim = 0; dm->data = mesh; mesh->refct = 1; ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->coneSection);CHKERRQ(ierr); mesh->maxConeSize = 0; mesh->cones = NULL; mesh->coneOrientations = NULL; ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->supportSection);CHKERRQ(ierr); mesh->maxSupportSize = 0; mesh->supports = NULL; mesh->refinementUniform = PETSC_TRUE; mesh->refinementLimit = -1.0; mesh->facesTmp = NULL; mesh->tetgenOpts = NULL; mesh->triangleOpts = NULL; ierr = PetscPartitionerCreate(PetscObjectComm((PetscObject)dm), &mesh->partitioner);CHKERRQ(ierr); mesh->remeshBd = PETSC_FALSE; mesh->subpointMap = NULL; for (unit = 0; unit < NUM_PETSC_UNITS; ++unit) mesh->scale[unit] = 1.0; mesh->regularRefinement = PETSC_FALSE; mesh->depthState = -1; mesh->globalVertexNumbers = NULL; mesh->globalCellNumbers = NULL; mesh->anchorSection = NULL; mesh->anchorIS = NULL; mesh->createanchors = NULL; mesh->computeanchormatrix = NULL; mesh->parentSection = NULL; mesh->parents = NULL; mesh->childIDs = NULL; mesh->childSection = NULL; mesh->children = NULL; mesh->referenceTree = NULL; mesh->getchildsymmetry = NULL; for (d = 0; d < 8; ++d) mesh->hybridPointMax[d] = PETSC_DETERMINE; mesh->vtkCellHeight = 0; mesh->useCone = PETSC_FALSE; mesh->useClosure = PETSC_TRUE; mesh->useAnchors = PETSC_FALSE; mesh->maxProjectionHeight = 0; mesh->printSetValues = PETSC_FALSE; mesh->printFEM = 0; mesh->printTol = 1.0e-10; ierr = DMInitialize_Plex(dm);CHKERRQ(ierr); PetscFunctionReturn(0); } /*@ DMPlexCreate - Creates a DMPlex object, which encapsulates an unstructured mesh, or CW complex, which can be expressed using a Hasse Diagram. Collective on MPI_Comm Input Parameter: . comm - The communicator for the DMPlex object Output Parameter: . mesh - The DMPlex object Level: beginner .keywords: DMPlex, create @*/ PetscErrorCode DMPlexCreate(MPI_Comm comm, DM *mesh) { PetscErrorCode ierr; PetscFunctionBegin; PetscValidPointer(mesh,2); ierr = DMCreate(comm, mesh);CHKERRQ(ierr); ierr = DMSetType(*mesh, DMPLEX);CHKERRQ(ierr); PetscFunctionReturn(0); } /* This takes as input the common mesh generator output, a list of the vertices for each cell, but vertex numbers are global and an SF is built for them */ static PetscErrorCode DMPlexBuildFromCellList_Parallel_Private(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const int cells[], PetscSF *sfVert) { PetscSF sfPoint; PetscLayout vLayout; PetscHashI vhash; PetscSFNode *remoteVerticesAdj, *vertexLocal, *vertexOwner, *remoteVertex; const PetscInt *vrange; PetscInt numVerticesAdj, off, *verticesAdj, numVerticesGhost = 0, *localVertex, *cone, c, p, v, g; PETSC_UNUSED PetscHashIIter ret, iter; PetscMPIInt rank, size; PetscErrorCode ierr; PetscFunctionBegin; ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRQ(ierr); ierr = MPI_Comm_size(PetscObjectComm((PetscObject) dm), &size);CHKERRQ(ierr); /* Partition vertices */ ierr = PetscLayoutCreate(PetscObjectComm((PetscObject) dm), &vLayout);CHKERRQ(ierr); ierr = PetscLayoutSetLocalSize(vLayout, numVertices);CHKERRQ(ierr); ierr = PetscLayoutSetBlockSize(vLayout, 1);CHKERRQ(ierr); ierr = PetscLayoutSetUp(vLayout);CHKERRQ(ierr); ierr = PetscLayoutGetRanges(vLayout, &vrange);CHKERRQ(ierr); /* Count vertices and map them to procs */ PetscHashICreate(vhash); for (c = 0; c < numCells; ++c) { for (p = 0; p < numCorners; ++p) { PetscHashIPut(vhash, cells[c*numCorners+p], ret, iter); } } PetscHashISize(vhash, numVerticesAdj); ierr = PetscMalloc1(numVerticesAdj, &verticesAdj);CHKERRQ(ierr); off = 0; ierr = PetscHashIGetKeys(vhash, &off, verticesAdj);CHKERRQ(ierr); if (off != numVerticesAdj) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid number of local vertices %D should be %D", off, numVerticesAdj); ierr = PetscSortInt(numVerticesAdj, verticesAdj);CHKERRQ(ierr); ierr = PetscMalloc1(numVerticesAdj, &remoteVerticesAdj);CHKERRQ(ierr); for (v = 0; v < numVerticesAdj; ++v) { const PetscInt gv = verticesAdj[v]; PetscInt vrank; ierr = PetscFindInt(gv, size+1, vrange, &vrank);CHKERRQ(ierr); vrank = vrank < 0 ? -(vrank+2) : vrank; remoteVerticesAdj[v].index = gv - vrange[vrank]; remoteVerticesAdj[v].rank = vrank; } /* Create cones */ ierr = DMPlexSetChart(dm, 0, numCells+numVerticesAdj);CHKERRQ(ierr); for (c = 0; c < numCells; ++c) {ierr = DMPlexSetConeSize(dm, c, numCorners);CHKERRQ(ierr);} ierr = DMSetUp(dm);CHKERRQ(ierr); ierr = DMGetWorkArray(dm, numCorners, PETSC_INT, &cone);CHKERRQ(ierr); for (c = 0; c < numCells; ++c) { for (p = 0; p < numCorners; ++p) { const PetscInt gv = cells[c*numCorners+p]; PetscInt lv; ierr = PetscFindInt(gv, numVerticesAdj, verticesAdj, &lv);CHKERRQ(ierr); if (lv < 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Could not find global vertex %D in local connectivity", gv); cone[p] = lv+numCells; } ierr = DMPlexSetCone(dm, c, cone);CHKERRQ(ierr); } ierr = DMRestoreWorkArray(dm, numCorners, PETSC_INT, &cone);CHKERRQ(ierr); /* Create SF for vertices */ ierr = PetscSFCreate(PetscObjectComm((PetscObject)dm), sfVert);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) *sfVert, "Vertex Ownership SF");CHKERRQ(ierr); ierr = PetscSFSetFromOptions(*sfVert);CHKERRQ(ierr); ierr = PetscSFSetGraph(*sfVert, numVertices, numVerticesAdj, NULL, PETSC_OWN_POINTER, remoteVerticesAdj, PETSC_OWN_POINTER);CHKERRQ(ierr); ierr = PetscFree(verticesAdj);CHKERRQ(ierr); /* Build pointSF */ ierr = PetscMalloc2(numVerticesAdj, &vertexLocal, numVertices, &vertexOwner);CHKERRQ(ierr); for (v = 0; v < numVerticesAdj; ++v) {vertexLocal[v].index = v+numCells; vertexLocal[v].rank = rank;} for (v = 0; v < numVertices; ++v) {vertexOwner[v].index = -1; vertexOwner[v].rank = -1;} ierr = PetscSFReduceBegin(*sfVert, MPIU_2INT, vertexLocal, vertexOwner, MPI_MAXLOC);CHKERRQ(ierr); ierr = PetscSFReduceEnd(*sfVert, MPIU_2INT, vertexLocal, vertexOwner, MPI_MAXLOC);CHKERRQ(ierr); for (v = 0; v < numVertices; ++v) if (vertexOwner[v].rank < 0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Global vertex %d on rank %d was unclaimed", v + vrange[rank], rank); ierr = PetscSFBcastBegin(*sfVert, MPIU_2INT, vertexOwner, vertexLocal);CHKERRQ(ierr); ierr = PetscSFBcastEnd(*sfVert, MPIU_2INT, vertexOwner, vertexLocal);CHKERRQ(ierr); for (v = 0; v < numVerticesAdj; ++v) if (vertexLocal[v].rank != rank) ++numVerticesGhost; ierr = PetscMalloc1(numVerticesGhost, &localVertex);CHKERRQ(ierr); ierr = PetscMalloc1(numVerticesGhost, &remoteVertex);CHKERRQ(ierr); for (v = 0, g = 0; v < numVerticesAdj; ++v) { if (vertexLocal[v].rank != rank) { localVertex[g] = v+numCells; remoteVertex[g].index = vertexLocal[v].index; remoteVertex[g].rank = vertexLocal[v].rank; ++g; } } ierr = PetscFree2(vertexLocal, vertexOwner);CHKERRQ(ierr); if (g != numVerticesGhost) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid number of vertex ghosts %D should be %D", g, numVerticesGhost); ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) sfPoint, "point SF");CHKERRQ(ierr); ierr = PetscSFSetGraph(sfPoint, numCells+numVerticesAdj, numVerticesGhost, localVertex, PETSC_OWN_POINTER, remoteVertex, PETSC_OWN_POINTER);CHKERRQ(ierr); ierr = PetscLayoutDestroy(&vLayout);CHKERRQ(ierr); PetscHashIDestroy(vhash); /* Fill in the rest of the topology structure */ ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); ierr = DMPlexStratify(dm);CHKERRQ(ierr); PetscFunctionReturn(0); } /* This takes as input the coordinates for each owned vertex */ static PetscErrorCode DMPlexBuildCoordinates_Parallel_Private(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numV, PetscSF sfVert, const PetscReal vertexCoords[]) { PetscSection coordSection; Vec coordinates; PetscScalar *coords; PetscInt numVertices, numVerticesAdj, coordSize, v; PetscErrorCode ierr; PetscFunctionBegin; ierr = PetscSFGetGraph(sfVert, &numVertices, &numVerticesAdj, NULL, NULL);CHKERRQ(ierr); ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); ierr = PetscSectionSetFieldComponents(coordSection, 0, spaceDim);CHKERRQ(ierr); ierr = PetscSectionSetChart(coordSection, numCells, numCells + numVerticesAdj);CHKERRQ(ierr); for (v = numCells; v < numCells+numVerticesAdj; ++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 = VecSetBlockSize(coordinates, spaceDim);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); { MPI_Datatype coordtype; /* Need a temp buffer for coords if we have complex/single */ ierr = MPI_Type_contiguous(spaceDim, MPIU_SCALAR, &coordtype);CHKERRQ(ierr); ierr = MPI_Type_commit(&coordtype);CHKERRQ(ierr); #if defined(PETSC_USE_COMPLEX) { PetscScalar *svertexCoords; PetscInt i; ierr = PetscMalloc1(numV*spaceDim,&svertexCoords);CHKERRQ(ierr); for (i=0; icoordinateDM) { DM ncdm; PetscSection cs; PetscInt pEnd = -1; ierr = DMGetDefaultSection(rdm->coordinateDM, &cs);CHKERRQ(ierr); if (cs) {ierr = PetscSectionGetChart(cs, NULL, &pEnd);CHKERRQ(ierr);} if (pEnd >= 0) { ierr = DMClone(rdm->coordinateDM, &ncdm);CHKERRQ(ierr); ierr = DMSetDefaultSection(ncdm, cs);CHKERRQ(ierr); ierr = DMSetCoordinateDM(*refdm, ncdm);CHKERRQ(ierr); ierr = DMDestroy(&ncdm);CHKERRQ(ierr); } } ierr = DMGetCoordinatesLocal(rdm, &coords);CHKERRQ(ierr); if (coords) { ierr = DMSetCoordinatesLocal(*refdm, coords);CHKERRQ(ierr); } else { ierr = DMGetCoordinates(rdm, &coords);CHKERRQ(ierr); if (coords) {ierr = DMSetCoordinates(*refdm, coords);CHKERRQ(ierr);} } ierr = DMDestroy(&rdm);CHKERRQ(ierr); PetscFunctionReturn(0); }