1 #include <petsc/private/dmpleximpl.h> /*I "petscdmplex.h" I*/ 2 #include <mmg/libmmg.h> 3 4 PETSC_EXTERN PetscErrorCode DMAdaptMetric_Mmg_Plex(DM dm, Vec vertexMetric, DMLabel bdLabel, DMLabel rgLabel, DM *dmNew) 5 { 6 MPI_Comm comm; 7 const char *bdName = "_boundary_"; 8 const char *rgName = "_regions_"; 9 DM udm, cdm; 10 DMLabel bdLabelFull; 11 const char *bdLabelName, *rgLabelName; 12 IS bdIS; 13 PetscSection coordSection; 14 Vec coordinates; 15 const PetscScalar *coords, *met; 16 const PetscInt *bdFacesFull; 17 PetscInt *bdFaces, *bdFaceIds; 18 PetscReal *vertices, *metric, *verticesNew, gradationFactor; 19 PetscInt *cells, *cellsNew; 20 PetscInt *facesNew, *faceTagsNew; 21 PetscInt *verTags, *cellTags, *verTagsNew, *cellTagsNew; 22 PetscInt *corners, *requiredCells, *requiredVer, *ridges, *requiredFaces; 23 PetscInt dim, cStart, cEnd, numCells, c, coff, vStart, vEnd, numVertices, v; 24 PetscInt off, maxConeSize, numBdFaces, f, bdSize, fStart, fEnd, i, j, k, Neq; 25 PetscInt numCellsNew, numVerticesNew, numCornersNew, numFacesNew; 26 PetscInt verbosity; 27 PetscBool flg, noInsert, noSwap, noMove; 28 DMLabel bdLabelNew, rgLabelNew; 29 MMG5_pMesh mmg_mesh = NULL; 30 MMG5_pSol mmg_metric = NULL; 31 PetscErrorCode ierr; 32 33 PetscFunctionBegin; 34 ierr = PetscObjectGetComm((PetscObject) dm, &comm);CHKERRQ(ierr); 35 if (bdLabel) { 36 ierr = PetscObjectGetName((PetscObject) bdLabel, &bdLabelName);CHKERRQ(ierr); 37 ierr = PetscStrcmp(bdLabelName, bdName, &flg);CHKERRQ(ierr); 38 if (flg) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "\"%s\" cannot be used as label for boundary facets", bdLabelName); 39 } 40 if (rgLabel) { 41 ierr = PetscObjectGetName((PetscObject) rgLabel, &rgLabelName);CHKERRQ(ierr); 42 ierr = PetscStrcmp(rgLabelName, rgName, &flg);CHKERRQ(ierr); 43 if (flg) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "\"%s\" cannot be used as label for element tags", rgLabelName); 44 } 45 46 /* Get mesh information */ 47 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 48 Neq = (dim*(dim+1))/2; 49 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 50 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 51 ierr = DMPlexUninterpolate(dm, &udm);CHKERRQ(ierr); 52 ierr = DMPlexGetMaxSizes(udm, &maxConeSize, NULL);CHKERRQ(ierr); 53 numCells = cEnd - cStart; 54 numVertices = vEnd - vStart; 55 56 /* Get cell offsets */ 57 ierr = PetscMalloc1(numCells*maxConeSize, &cells);CHKERRQ(ierr); 58 for (c = 0, coff = 0; c < numCells; ++c) { 59 const PetscInt *cone; 60 PetscInt coneSize, cl; 61 62 ierr = DMPlexGetConeSize(udm, c, &coneSize);CHKERRQ(ierr); 63 ierr = DMPlexGetCone(udm, c, &cone);CHKERRQ(ierr); 64 for (cl = 0; cl < coneSize; ++cl) cells[coff++] = cone[cl] - vStart + 1; 65 } 66 67 /* Get vertex coordinate array */ 68 ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); 69 ierr = DMGetLocalSection(cdm, &coordSection);CHKERRQ(ierr); 70 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 71 ierr = VecGetArrayRead(coordinates, &coords);CHKERRQ(ierr); 72 ierr = PetscMalloc2(numVertices*Neq, &metric, dim*numVertices, &vertices);CHKERRQ(ierr); 73 for (v = 0; v < vEnd-vStart; ++v) { 74 ierr = PetscSectionGetOffset(coordSection, v+vStart, &off);CHKERRQ(ierr); 75 for (i = 0; i < dim; ++i) vertices[dim*v+i] = PetscRealPart(coords[off+i]); 76 } 77 ierr = VecRestoreArrayRead(coordinates, &coords);CHKERRQ(ierr); 78 ierr = DMDestroy(&udm);CHKERRQ(ierr); 79 80 /* Get boundary mesh */ 81 ierr = DMLabelCreate(PETSC_COMM_SELF, bdName, &bdLabelFull);CHKERRQ(ierr); 82 ierr = DMPlexMarkBoundaryFaces(dm, 1, bdLabelFull);CHKERRQ(ierr); 83 ierr = DMLabelGetStratumIS(bdLabelFull, 1, &bdIS);CHKERRQ(ierr); 84 ierr = DMLabelGetStratumSize(bdLabelFull, 1, &numBdFaces);CHKERRQ(ierr); 85 ierr = ISGetIndices(bdIS, &bdFacesFull);CHKERRQ(ierr); 86 for (f = 0, bdSize = 0; f < numBdFaces; ++f) { 87 PetscInt *closure = NULL; 88 PetscInt closureSize, cl; 89 90 ierr = DMPlexGetTransitiveClosure(dm, bdFacesFull[f], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 91 for (cl = 0; cl < closureSize*2; cl += 2) { 92 if ((closure[cl] >= vStart) && (closure[cl] < vEnd)) ++bdSize; 93 } 94 ierr = DMPlexRestoreTransitiveClosure(dm, bdFacesFull[f], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 95 } 96 ierr = PetscMalloc2(bdSize, &bdFaces, numBdFaces, &bdFaceIds);CHKERRQ(ierr); 97 for (f = 0, bdSize = 0; f < numBdFaces; ++f) { 98 PetscInt *closure = NULL; 99 PetscInt closureSize, cl; 100 101 ierr = DMPlexGetTransitiveClosure(dm, bdFacesFull[f], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 102 for (cl = 0; cl < closureSize*2; cl += 2) { 103 if ((closure[cl] >= vStart) && (closure[cl] < vEnd)) bdFaces[bdSize++] = closure[cl] - vStart + 1; 104 } 105 ierr = DMPlexRestoreTransitiveClosure(dm, bdFacesFull[f], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 106 if (bdLabel) {ierr = DMLabelGetValue(bdLabel, bdFacesFull[f], &bdFaceIds[f]);CHKERRQ(ierr);} 107 else {bdFaceIds[f] = 1;} 108 } 109 ierr = ISDestroy(&bdIS);CHKERRQ(ierr); 110 ierr = DMLabelDestroy(&bdLabelFull);CHKERRQ(ierr); 111 112 /* Get cell tags */ 113 ierr = PetscCalloc2(numVertices, &verTags, numCells, &cellTags);CHKERRQ(ierr); 114 if (rgLabel) { 115 for (c = cStart; c < cEnd; ++c) { ierr = DMLabelGetValue(rgLabel, c, &cellTags[c]);CHKERRQ(ierr); } 116 } 117 118 /* Get metric */ 119 ierr = VecViewFromOptions(vertexMetric, NULL, "-adapt_metric_view");CHKERRQ(ierr); 120 ierr = VecGetArrayRead(vertexMetric, &met);CHKERRQ(ierr); 121 for (v = 0; v < (vEnd-vStart); ++v) { 122 for (i = 0, k = 0; i < dim; ++i) { 123 for (j = i; j < dim; ++j) { 124 metric[Neq*v+k] = PetscRealPart(met[dim*dim*v+dim*i+j]); 125 k++; 126 } 127 } 128 } 129 ierr = VecRestoreArrayRead(vertexMetric, &met);CHKERRQ(ierr); 130 131 /* Send mesh to Mmg and remesh */ 132 ierr = DMPlexMetricGetVerbosity(dm, &verbosity);CHKERRQ(ierr); 133 ierr = DMPlexMetricGetGradationFactor(dm, &gradationFactor);CHKERRQ(ierr); 134 ierr = DMPlexMetricNoInsertion(dm, &noInsert);CHKERRQ(ierr); 135 ierr = DMPlexMetricNoSwapping(dm, &noSwap);CHKERRQ(ierr); 136 ierr = DMPlexMetricNoMovement(dm, &noMove);CHKERRQ(ierr); 137 switch (dim) { 138 case 2: 139 ierr = MMG2D_Init_mesh(MMG5_ARG_start, MMG5_ARG_ppMesh, &mmg_mesh, MMG5_ARG_ppMet, &mmg_metric, MMG5_ARG_end); 140 ierr = MMG2D_Set_iparameter(mmg_mesh, mmg_metric, MMG2D_IPARAM_noinsert, noInsert); 141 ierr = MMG2D_Set_iparameter(mmg_mesh, mmg_metric, MMG2D_IPARAM_noswap, noSwap); 142 ierr = MMG2D_Set_iparameter(mmg_mesh, mmg_metric, MMG2D_IPARAM_nomove, noMove); 143 ierr = MMG2D_Set_iparameter(mmg_mesh, mmg_metric, MMG2D_IPARAM_verbose, verbosity); 144 ierr = MMG2D_Set_dparameter(mmg_mesh, mmg_metric, MMG2D_DPARAM_hgrad, gradationFactor); 145 ierr = MMG2D_Set_meshSize(mmg_mesh, numVertices, numCells, 0, numBdFaces); 146 ierr = MMG2D_Set_vertices(mmg_mesh, vertices, verTags); 147 ierr = MMG2D_Set_triangles(mmg_mesh, cells, cellTags); 148 ierr = MMG2D_Set_edges(mmg_mesh, bdFaces, bdFaceIds); 149 ierr = MMG2D_Set_solSize(mmg_mesh, mmg_metric, MMG5_Vertex, numVertices, MMG5_Tensor); 150 ierr = MMG2D_Set_tensorSols(mmg_metric, metric); 151 ierr = MMG2D_mmg2dlib(mmg_mesh, mmg_metric); 152 break; 153 case 3: 154 ierr = MMG3D_Init_mesh(MMG5_ARG_start, MMG5_ARG_ppMesh, &mmg_mesh, MMG5_ARG_ppMet, &mmg_metric, MMG5_ARG_end); 155 ierr = MMG3D_Set_iparameter(mmg_mesh, mmg_metric, MMG3D_IPARAM_noinsert, noInsert); 156 ierr = MMG3D_Set_iparameter(mmg_mesh, mmg_metric, MMG3D_IPARAM_noswap, noSwap); 157 ierr = MMG3D_Set_iparameter(mmg_mesh, mmg_metric, MMG3D_IPARAM_nomove, noMove); 158 ierr = MMG3D_Set_iparameter(mmg_mesh, mmg_metric, MMG3D_IPARAM_verbose, verbosity); 159 ierr = MMG3D_Set_dparameter(mmg_mesh, mmg_metric, MMG3D_DPARAM_hgrad, gradationFactor); 160 ierr = MMG3D_Set_meshSize(mmg_mesh, numVertices, numCells, 0, numBdFaces, 0, 0); 161 ierr = MMG3D_Set_vertices(mmg_mesh, vertices, verTags); 162 ierr = MMG3D_Set_tetrahedra(mmg_mesh, cells, cellTags); 163 ierr = MMG3D_Set_triangles(mmg_mesh, bdFaces, bdFaceIds); 164 ierr = MMG3D_Set_solSize(mmg_mesh, mmg_metric, MMG5_Vertex, numVertices, MMG5_Tensor); 165 ierr = MMG3D_Set_tensorSols(mmg_metric, metric); 166 ierr = MMG3D_mmg3dlib(mmg_mesh, mmg_metric); 167 break; 168 default: SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "No Mmg adaptation defined for dimension %D", dim); 169 } 170 171 /* Retrieve mesh from Mmg and create new Plex*/ 172 switch (dim) { 173 case 2: 174 numCornersNew = 3; 175 ierr = MMG2D_Get_meshSize(mmg_mesh, &numVerticesNew, &numCellsNew, 0, &numFacesNew); 176 ierr = PetscMalloc4(2*numVerticesNew, &verticesNew, numVerticesNew, &verTagsNew, numVerticesNew, &corners, numVerticesNew, &requiredVer);CHKERRQ(ierr); 177 ierr = PetscMalloc3(3*numCellsNew, &cellsNew, numCellsNew, &cellTagsNew, numCellsNew, &requiredCells);CHKERRQ(ierr); 178 ierr = PetscMalloc4(2*numFacesNew, &facesNew, numFacesNew, &faceTagsNew, numFacesNew, &ridges, numFacesNew, &requiredFaces);CHKERRQ(ierr); 179 ierr = MMG2D_Get_vertices(mmg_mesh, verticesNew, verTagsNew, corners, requiredVer); 180 ierr = MMG2D_Get_triangles(mmg_mesh, cellsNew, cellTagsNew, requiredCells); 181 ierr = MMG2D_Get_edges(mmg_mesh, facesNew, faceTagsNew, ridges, requiredFaces); 182 break; 183 case 3: 184 numCornersNew = 4; 185 ierr = MMG3D_Get_meshSize(mmg_mesh, &numVerticesNew, &numCellsNew, 0, &numFacesNew, 0, 0); 186 ierr = PetscMalloc4(3*numVerticesNew, &verticesNew, numVerticesNew, &verTagsNew, numVerticesNew, &corners, numVerticesNew, &requiredVer);CHKERRQ(ierr); 187 ierr = PetscMalloc3(4*numCellsNew, &cellsNew, numCellsNew, &cellTagsNew, numCellsNew, &requiredCells);CHKERRQ(ierr); 188 ierr = PetscMalloc4(3*numFacesNew, &facesNew, numFacesNew, &faceTagsNew, numFacesNew, &ridges, numFacesNew, &requiredFaces);CHKERRQ(ierr); 189 ierr = MMG3D_Get_vertices(mmg_mesh, verticesNew, verTagsNew, corners, requiredVer); 190 ierr = MMG3D_Get_tetrahedra(mmg_mesh, cellsNew, cellTagsNew, requiredCells); 191 ierr = MMG3D_Get_triangles(mmg_mesh, facesNew, faceTagsNew, requiredFaces); 192 break; 193 default: SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "No Mmg adaptation defined for dimension %D", dim); 194 } 195 for (i = 0; i < (dim+1)*numCellsNew; i++) cellsNew[i] -= 1; 196 for (i = 0; i < dim*numFacesNew; i++) facesNew[i] -= 1; 197 ierr = DMPlexCreateFromCellListParallelPetsc(comm, dim, numCellsNew, numVerticesNew, PETSC_DECIDE, numCornersNew, PETSC_TRUE, cellsNew, dim, verticesNew, NULL, NULL, dmNew);CHKERRQ(ierr); 198 switch (dim) { 199 case 2: 200 ierr = MMG2D_Free_all(MMG5_ARG_start, MMG5_ARG_ppMesh, &mmg_mesh, MMG5_ARG_ppMet, &mmg_metric, MMG5_ARG_end); 201 break; 202 case 3: 203 ierr = MMG3D_Free_all(MMG5_ARG_start, MMG5_ARG_ppMesh, &mmg_mesh, MMG5_ARG_ppMet, &mmg_metric, MMG5_ARG_end); 204 break; 205 default: SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "No Mmg adaptation defined for dimension %D", dim); 206 } 207 208 /* Rebuild boundary labels */ 209 ierr = DMCreateLabel(*dmNew, bdLabel ? bdLabelName : bdName);CHKERRQ(ierr); 210 ierr = DMGetLabel(*dmNew, bdLabel ? bdLabelName : bdName, &bdLabelNew);CHKERRQ(ierr); 211 ierr = DMPlexGetHeightStratum(*dmNew, 1, &fStart, &fEnd);CHKERRQ(ierr); 212 ierr = DMPlexGetDepthStratum(*dmNew, 0, &vStart, &vEnd);CHKERRQ(ierr); 213 for (i = 0; i < numFacesNew; i++) { 214 PetscInt numCoveredPoints, numFaces = 0, facePoints[3]; 215 const PetscInt *coveredPoints = NULL; 216 217 for (j = 0; j < dim; ++j) facePoints[j] = facesNew[i*dim+j]+vStart; 218 ierr = DMPlexGetFullJoin(*dmNew, dim, facePoints, &numCoveredPoints, &coveredPoints);CHKERRQ(ierr); 219 for (j = 0; j < numCoveredPoints; ++j) { 220 if (coveredPoints[j] >= fStart && coveredPoints[j] < fEnd) { 221 numFaces++; 222 f = j; 223 } 224 } 225 if (numFaces != 1) SETERRQ2(comm, PETSC_ERR_ARG_OUTOFRANGE, "%d vertices cannot define more than 1 facet (%d)", dim, numFaces); 226 ierr = DMLabelSetValue(bdLabelNew, coveredPoints[f], faceTagsNew[i]);CHKERRQ(ierr); 227 ierr = DMPlexRestoreJoin(*dmNew, dim, facePoints, &numCoveredPoints, &coveredPoints);CHKERRQ(ierr); 228 } 229 230 /* Rebuild cell labels */ 231 ierr = DMCreateLabel(*dmNew, rgLabel ? rgLabelName : rgName);CHKERRQ(ierr); 232 ierr = DMGetLabel(*dmNew, rgLabel ? rgLabelName : rgName, &rgLabelNew);CHKERRQ(ierr); 233 for (c = cStart; c < cEnd; ++c) { ierr = DMLabelSetValue(rgLabelNew, c, cellTagsNew[c-cStart]);CHKERRQ(ierr); } 234 235 /* Clean up */ 236 ierr = PetscFree(cells);CHKERRQ(ierr); 237 ierr = PetscFree2(metric, vertices);CHKERRQ(ierr); 238 ierr = PetscFree2(bdFaces, bdFaceIds);CHKERRQ(ierr); 239 ierr = PetscFree2(verTags, cellTags);CHKERRQ(ierr); 240 ierr = PetscFree4(verticesNew, verTagsNew, corners, requiredVer);CHKERRQ(ierr); 241 ierr = PetscFree3(cellsNew, cellTagsNew, requiredCells);CHKERRQ(ierr); 242 ierr = PetscFree4(facesNew, faceTagsNew, ridges, requiredFaces);CHKERRQ(ierr); 243 PetscFunctionReturn(0); 244 } 245