Actual source code: pragmaticadapt.c
1: #include <petsc/private/dmpleximpl.h>
2: #include <pragmatic/cpragmatic.h>
4: PETSC_EXTERN PetscErrorCode DMAdaptMetric_Pragmatic_Plex(DM dm, Vec vertexMetric, DMLabel bdLabel, DMLabel rgLabel, DM *dmNew)
5: {
6: MPI_Comm comm;
7: const char *bdName = "_boundary_";
8: #if 0
9: DM odm = dm;
10: #endif
11: DM udm, cdm;
12: DMLabel bdLabelFull;
13: const char *bdLabelName;
14: IS bdIS, globalVertexNum;
15: PetscSection coordSection;
16: Vec coordinates;
17: const PetscScalar *coords, *met;
18: const PetscInt *bdFacesFull, *gV;
19: PetscInt *bdFaces, *bdFaceIds, *l2gv;
20: PetscReal *x, *y, *z, *metric;
21: PetscInt *cells;
22: PetscInt dim, cStart, cEnd, numCells, c, coff, vStart, vEnd, numVertices, numLocVertices, v;
23: PetscInt off, maxConeSize, numBdFaces, f, bdSize, i, j, Nd;
24: PetscBool flg, isotropic, uniform;
25: DMLabel bdLabelNew;
26: PetscReal *coordsNew;
27: PetscInt *bdTags;
28: PetscReal *xNew[3] = {NULL, NULL, NULL};
29: PetscInt *cellsNew;
30: PetscInt d, numCellsNew, numVerticesNew;
31: PetscInt numCornersNew, fStart, fEnd;
32: PetscMPIInt numProcs;
34: PetscFunctionBegin;
35: /* Check for FEM adjacency flags */
36: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
37: PetscCallMPI(MPI_Comm_size(comm, &numProcs));
38: if (bdLabel) {
39: PetscCall(PetscObjectGetName((PetscObject)bdLabel, &bdLabelName));
40: PetscCall(PetscStrcmp(bdLabelName, bdName, &flg));
41: PetscCheck(!flg, comm, PETSC_ERR_ARG_WRONG, "\"%s\" cannot be used as label for boundary facets", bdLabelName);
42: }
43: PetscCheck(!rgLabel, comm, PETSC_ERR_ARG_WRONG, "Cannot currently preserve cell tags with Pragmatic");
44: #if 0
45: /* Check for overlap by looking for cell in the SF */
46: if (!overlapped) {
47: PetscCall(DMPlexDistributeOverlap(odm, 1, NULL, &dm));
48: if (!dm) {dm = odm; PetscCall(PetscObjectReference((PetscObject) dm));}
49: }
50: #endif
52: /* Get mesh information */
53: PetscCall(DMGetDimension(dm, &dim));
54: PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd));
55: PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd));
56: PetscCall(DMPlexUninterpolate(dm, &udm));
57: PetscCall(DMPlexGetMaxSizes(udm, &maxConeSize, NULL));
58: numCells = cEnd - cStart;
59: if (numCells == 0) {
60: PetscMPIInt rank;
62: PetscCallMPI(MPI_Comm_rank(comm, &rank));
63: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Cannot perform mesh adaptation because process %d does not own any cells.", rank);
64: }
65: numVertices = vEnd - vStart;
66: PetscCall(PetscCalloc5(numVertices, &x, numVertices, &y, numVertices, &z, numVertices * PetscSqr(dim), &metric, numCells * maxConeSize, &cells));
68: /* Get cell offsets */
69: for (c = 0, coff = 0; c < numCells; ++c) {
70: const PetscInt *cone;
71: PetscInt coneSize, cl;
73: PetscCall(DMPlexGetConeSize(udm, c, &coneSize));
74: PetscCall(DMPlexGetCone(udm, c, &cone));
75: for (cl = 0; cl < coneSize; ++cl) cells[coff++] = cone[cl] - vStart;
76: }
78: /* Get local-to-global vertex map */
79: PetscCall(PetscCalloc1(numVertices, &l2gv));
80: PetscCall(DMPlexGetVertexNumbering(udm, &globalVertexNum));
81: PetscCall(ISGetIndices(globalVertexNum, &gV));
82: for (v = 0, numLocVertices = 0; v < numVertices; ++v) {
83: if (gV[v] >= 0) ++numLocVertices;
84: l2gv[v] = gV[v] < 0 ? -(gV[v] + 1) : gV[v];
85: }
86: PetscCall(ISRestoreIndices(globalVertexNum, &gV));
87: PetscCall(DMDestroy(&udm));
89: /* Get vertex coordinate arrays */
90: PetscCall(DMGetCoordinateDM(dm, &cdm));
91: PetscCall(DMGetLocalSection(cdm, &coordSection));
92: PetscCall(DMGetCoordinatesLocal(dm, &coordinates));
93: PetscCall(VecGetArrayRead(coordinates, &coords));
94: for (v = vStart; v < vEnd; ++v) {
95: PetscCall(PetscSectionGetOffset(coordSection, v, &off));
96: x[v - vStart] = PetscRealPart(coords[off + 0]);
97: if (dim > 1) y[v - vStart] = PetscRealPart(coords[off + 1]);
98: if (dim > 2) z[v - vStart] = PetscRealPart(coords[off + 2]);
99: }
100: PetscCall(VecRestoreArrayRead(coordinates, &coords));
102: /* Get boundary mesh */
103: PetscCall(DMLabelCreate(PETSC_COMM_SELF, bdName, &bdLabelFull));
104: PetscCall(DMPlexMarkBoundaryFaces(dm, 1, bdLabelFull));
105: PetscCall(DMLabelGetStratumIS(bdLabelFull, 1, &bdIS));
106: PetscCall(DMLabelGetStratumSize(bdLabelFull, 1, &numBdFaces));
107: PetscCall(ISGetIndices(bdIS, &bdFacesFull));
108: for (f = 0, bdSize = 0; f < numBdFaces; ++f) {
109: PetscInt *closure = NULL;
110: PetscInt closureSize, cl;
112: PetscCall(DMPlexGetTransitiveClosure(dm, bdFacesFull[f], PETSC_TRUE, &closureSize, &closure));
113: for (cl = 0; cl < closureSize * 2; cl += 2) {
114: if ((closure[cl] >= vStart) && (closure[cl] < vEnd)) ++bdSize;
115: }
116: PetscCall(DMPlexRestoreTransitiveClosure(dm, bdFacesFull[f], PETSC_TRUE, &closureSize, &closure));
117: }
118: PetscCall(PetscMalloc2(bdSize, &bdFaces, numBdFaces, &bdFaceIds));
119: for (f = 0, bdSize = 0; f < numBdFaces; ++f) {
120: PetscInt *closure = NULL;
121: PetscInt closureSize, cl;
123: PetscCall(DMPlexGetTransitiveClosure(dm, bdFacesFull[f], PETSC_TRUE, &closureSize, &closure));
124: for (cl = 0; cl < closureSize * 2; cl += 2) {
125: if ((closure[cl] >= vStart) && (closure[cl] < vEnd)) bdFaces[bdSize++] = closure[cl] - vStart;
126: }
127: PetscCall(DMPlexRestoreTransitiveClosure(dm, bdFacesFull[f], PETSC_TRUE, &closureSize, &closure));
128: if (bdLabel) PetscCall(DMLabelGetValue(bdLabel, bdFacesFull[f], &bdFaceIds[f]));
129: else bdFaceIds[f] = 1;
130: }
131: PetscCall(ISDestroy(&bdIS));
132: PetscCall(DMLabelDestroy(&bdLabelFull));
134: /* Get metric */
135: PetscCall(VecViewFromOptions(vertexMetric, NULL, "-adapt_metric_view"));
136: PetscCall(VecGetArrayRead(vertexMetric, &met));
137: PetscCall(DMPlexMetricIsIsotropic(dm, &isotropic));
138: PetscCall(DMPlexMetricIsUniform(dm, &uniform));
139: Nd = PetscSqr(dim);
140: for (v = 0; v < vEnd - vStart; ++v) {
141: for (i = 0; i < dim; ++i) {
142: for (j = 0; j < dim; ++j) {
143: if (isotropic) {
144: if (i == j) {
145: if (uniform) metric[Nd * v + dim * i + j] = PetscRealPart(met[0]);
146: else metric[Nd * v + dim * i + j] = PetscRealPart(met[v]);
147: } else metric[Nd * v + dim * i + j] = 0.0;
148: } else metric[Nd * v + dim * i + j] = PetscRealPart(met[Nd * v + dim * i + j]);
149: }
150: }
151: }
152: PetscCall(VecRestoreArrayRead(vertexMetric, &met));
154: #if 0
155: /* Destroy overlap mesh */
156: PetscCall(DMDestroy(&dm));
157: #endif
158: /* Send to Pragmatic and remesh */
159: PetscCall(PetscFPTrapPush(PETSC_FP_TRAP_OFF));
160: switch (dim) {
161: case 2:
162: PetscStackCallExternalVoid("pragmatic_2d_mpi_init", pragmatic_2d_mpi_init(&numVertices, &numCells, cells, x, y, l2gv, numLocVertices, comm));
163: break;
164: case 3:
165: PetscStackCallExternalVoid("pragmatic_3d_mpi_init", pragmatic_3d_mpi_init(&numVertices, &numCells, cells, x, y, z, l2gv, numLocVertices, comm));
166: break;
167: default:
168: SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "No Pragmatic adaptation defined for dimension %" PetscInt_FMT, dim);
169: }
170: PetscStackCallExternalVoid("pragmatic_set_boundary", pragmatic_set_boundary(&numBdFaces, bdFaces, bdFaceIds));
171: PetscStackCallExternalVoid("pragmatic_set_metric", pragmatic_set_metric(metric));
172: PetscStackCallExternalVoid("pragmatic_adapt", pragmatic_adapt(((DM_Plex *)dm->data)->remeshBd ? 1 : 0));
173: PetscCall(PetscFree(l2gv));
174: PetscCall(PetscFPTrapPop());
176: /* Retrieve mesh from Pragmatic and create new plex */
177: PetscStackCallExternalVoid("pragmatic_get_info_mpi", pragmatic_get_info_mpi(&numVerticesNew, &numCellsNew));
178: PetscCall(PetscMalloc1(numVerticesNew * dim, &coordsNew));
179: switch (dim) {
180: case 2:
181: numCornersNew = 3;
182: PetscCall(PetscMalloc2(numVerticesNew, &xNew[0], numVerticesNew, &xNew[1]));
183: PetscStackCallExternalVoid("pragmatic_get_coords_2d_mpi", pragmatic_get_coords_2d_mpi(xNew[0], xNew[1]));
184: break;
185: case 3:
186: numCornersNew = 4;
187: PetscCall(PetscMalloc3(numVerticesNew, &xNew[0], numVerticesNew, &xNew[1], numVerticesNew, &xNew[2]));
188: PetscStackCallExternalVoid("pragmatic_get_coords_3d_mpi", pragmatic_get_coords_3d_mpi(xNew[0], xNew[1], xNew[2]));
189: break;
190: default:
191: SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "No Pragmatic adaptation defined for dimension %" PetscInt_FMT, dim);
192: }
193: for (v = 0; v < numVerticesNew; ++v) {
194: for (d = 0; d < dim; ++d) coordsNew[v * dim + d] = xNew[d][v];
195: }
196: PetscCall(PetscMalloc1(numCellsNew * (dim + 1), &cellsNew));
197: PetscStackCallExternalVoid("pragmatic_get_elements", pragmatic_get_elements(cellsNew));
198: PetscCall(DMPlexCreateFromCellListParallelPetsc(comm, dim, numCellsNew, numVerticesNew, PETSC_DECIDE, numCornersNew, PETSC_TRUE, cellsNew, dim, coordsNew, NULL, NULL, dmNew));
200: /* Rebuild boundary label */
201: PetscStackCallExternalVoid("pragmatic_get_boundaryTags", pragmatic_get_boundaryTags(&bdTags));
202: PetscCall(DMCreateLabel(*dmNew, bdLabel ? bdLabelName : bdName));
203: PetscCall(DMGetLabel(*dmNew, bdLabel ? bdLabelName : bdName, &bdLabelNew));
204: PetscCall(DMPlexGetHeightStratum(*dmNew, 0, &cStart, &cEnd));
205: PetscCall(DMPlexGetHeightStratum(*dmNew, 1, &fStart, &fEnd));
206: PetscCall(DMPlexGetDepthStratum(*dmNew, 0, &vStart, &vEnd));
207: for (c = cStart; c < cEnd; ++c) {
208: /* Only for simplicial meshes */
209: coff = (c - cStart) * (dim + 1);
211: /* d is the local cell number of the vertex opposite to the face we are marking */
212: for (d = 0; d < dim + 1; ++d) {
213: if (bdTags[coff + d]) {
214: const PetscInt perm[4][4] = {
215: {-1, -1, -1, -1},
216: {-1, -1, -1, -1},
217: {1, 2, 0, -1},
218: {3, 2, 1, 0 }
219: }; /* perm[d] = face opposite */
220: const PetscInt *cone;
222: /* Mark face opposite to this vertex: This pattern is specified in DMPlexGetRawFaces_Internal() */
223: PetscCall(DMPlexGetCone(*dmNew, c, &cone));
224: PetscCall(DMLabelSetValue(bdLabelNew, cone[perm[dim][d]], bdTags[coff + d]));
225: }
226: }
227: }
229: /* Clean up */
230: switch (dim) {
231: case 2:
232: PetscCall(PetscFree2(xNew[0], xNew[1]));
233: break;
234: case 3:
235: PetscCall(PetscFree3(xNew[0], xNew[1], xNew[2]));
236: break;
237: }
238: PetscCall(PetscFree(cellsNew));
239: PetscCall(PetscFree5(x, y, z, metric, cells));
240: PetscCall(PetscFree2(bdFaces, bdFaceIds));
241: PetscCall(PetscFree(coordsNew));
242: PetscStackCallExternalVoid("pragmatic_finalize", pragmatic_finalize());
243: PetscFunctionReturn(PETSC_SUCCESS);
244: }