1 #include <petsc-private/dmpleximpl.h> /*I "petscdmplex.h" I*/ 2 #include <petscsf.h> 3 4 #undef __FUNCT__ 5 #define __FUNCT__ "DMPlexMarkBoundaryFaces" 6 /*@ 7 DMPlexMarkBoundaryFaces - Mark all faces on the boundary 8 9 Not Collective 10 11 Input Parameter: 12 . dm - The original DM 13 14 Output Parameter: 15 . label - The DMLabel marking boundary faces with value 1 16 17 Level: developer 18 19 .seealso: DMLabelCreate(), DMPlexCreateLabel() 20 @*/ 21 PetscErrorCode DMPlexMarkBoundaryFaces(DM dm, DMLabel label) 22 { 23 PetscInt fStart, fEnd, f; 24 PetscErrorCode ierr; 25 26 PetscFunctionBegin; 27 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 28 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 29 for (f = fStart; f < fEnd; ++f) { 30 PetscInt supportSize; 31 32 ierr = DMPlexGetSupportSize(dm, f, &supportSize);CHKERRQ(ierr); 33 if (supportSize == 1) { 34 ierr = DMLabelSetValue(label, f, 1);CHKERRQ(ierr); 35 } 36 } 37 PetscFunctionReturn(0); 38 } 39 40 #undef __FUNCT__ 41 #define __FUNCT__ "DMPlexLabelComplete" 42 /*@ 43 DMPlexLabelComplete - Starting with a label marking points on a surface, we add the transitive closure to the surface 44 45 Input Parameters: 46 + dm - The DM 47 - label - A DMLabel marking the surface points 48 49 Output Parameter: 50 . label - A DMLabel marking all surface points in the transitive closure 51 52 Level: developer 53 54 .seealso: DMPlexLabelCohesiveComplete() 55 @*/ 56 PetscErrorCode DMPlexLabelComplete(DM dm, DMLabel label) 57 { 58 IS valueIS; 59 const PetscInt *values; 60 PetscInt numValues, v; 61 PetscErrorCode ierr; 62 63 PetscFunctionBegin; 64 ierr = DMLabelGetNumValues(label, &numValues);CHKERRQ(ierr); 65 ierr = DMLabelGetValueIS(label, &valueIS);CHKERRQ(ierr); 66 ierr = ISGetIndices(valueIS, &values);CHKERRQ(ierr); 67 for (v = 0; v < numValues; ++v) { 68 IS pointIS; 69 const PetscInt *points; 70 PetscInt numPoints, p; 71 72 ierr = DMLabelGetStratumSize(label, values[v], &numPoints);CHKERRQ(ierr); 73 ierr = DMLabelGetStratumIS(label, values[v], &pointIS);CHKERRQ(ierr); 74 ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); 75 for (p = 0; p < numPoints; ++p) { 76 PetscInt *closure = NULL; 77 PetscInt closureSize, c; 78 79 ierr = DMPlexGetTransitiveClosure(dm, points[p], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 80 for (c = 0; c < closureSize*2; c += 2) { 81 ierr = DMLabelSetValue(label, closure[c], values[v]);CHKERRQ(ierr); 82 } 83 ierr = DMPlexRestoreTransitiveClosure(dm, points[p], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 84 } 85 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 86 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 87 } 88 ierr = ISRestoreIndices(valueIS, &values);CHKERRQ(ierr); 89 ierr = ISDestroy(&valueIS);CHKERRQ(ierr); 90 PetscFunctionReturn(0); 91 } 92 93 #undef __FUNCT__ 94 #define __FUNCT__ "DMPlexShiftPoint_Internal" 95 PETSC_STATIC_INLINE PetscInt DMPlexShiftPoint_Internal(PetscInt p, PetscInt depth, PetscInt depthEnd[], PetscInt depthShift[]) 96 { 97 if (depth < 0) return p; 98 /* Cells */ if (p < depthEnd[depth]) return p; 99 /* Vertices */ if (p < depthEnd[0]) return p + depthShift[depth]; 100 /* Faces */ if (p < depthEnd[depth-1]) return p + depthShift[depth] + depthShift[0]; 101 /* Edges */ return p + depthShift[depth] + depthShift[0] + depthShift[depth-1]; 102 } 103 104 #undef __FUNCT__ 105 #define __FUNCT__ "DMPlexShiftSizes_Internal" 106 static PetscErrorCode DMPlexShiftSizes_Internal(DM dm, PetscInt depthShift[], DM dmNew) 107 { 108 PetscInt *depthEnd; 109 PetscInt depth = 0, d, pStart, pEnd, p; 110 PetscErrorCode ierr; 111 112 PetscFunctionBegin; 113 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 114 if (depth < 0) PetscFunctionReturn(0); 115 ierr = PetscMalloc((depth+1) * sizeof(PetscInt), &depthEnd);CHKERRQ(ierr); 116 /* Step 1: Expand chart */ 117 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 118 for (d = 0; d <= depth; ++d) { 119 pEnd += depthShift[d]; 120 ierr = DMPlexGetDepthStratum(dm, d, NULL, &depthEnd[d]);CHKERRQ(ierr); 121 } 122 ierr = DMPlexSetChart(dmNew, pStart, pEnd);CHKERRQ(ierr); 123 /* Step 2: Set cone and support sizes */ 124 for (d = 0; d <= depth; ++d) { 125 ierr = DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);CHKERRQ(ierr); 126 for (p = pStart; p < pEnd; ++p) { 127 PetscInt newp = DMPlexShiftPoint_Internal(p, depth, depthEnd, depthShift); 128 PetscInt size; 129 130 ierr = DMPlexGetConeSize(dm, p, &size);CHKERRQ(ierr); 131 ierr = DMPlexSetConeSize(dmNew, newp, size);CHKERRQ(ierr); 132 ierr = DMPlexGetSupportSize(dm, p, &size);CHKERRQ(ierr); 133 ierr = DMPlexSetSupportSize(dmNew, newp, size);CHKERRQ(ierr); 134 } 135 } 136 ierr = PetscFree(depthEnd);CHKERRQ(ierr); 137 PetscFunctionReturn(0); 138 } 139 140 #undef __FUNCT__ 141 #define __FUNCT__ "DMPlexShiftPoints_Internal" 142 static PetscErrorCode DMPlexShiftPoints_Internal(DM dm, PetscInt depthShift[], DM dmNew) 143 { 144 PetscInt *depthEnd, *newpoints; 145 PetscInt depth = 0, d, maxConeSize, maxSupportSize, pStart, pEnd, p; 146 PetscErrorCode ierr; 147 148 PetscFunctionBegin; 149 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 150 if (depth < 0) PetscFunctionReturn(0); 151 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize);CHKERRQ(ierr); 152 ierr = PetscMalloc2(depth+1,PetscInt,&depthEnd,PetscMax(maxConeSize, maxSupportSize),PetscInt,&newpoints);CHKERRQ(ierr); 153 for (d = 0; d <= depth; ++d) { 154 ierr = DMPlexGetDepthStratum(dm, d, NULL, &depthEnd[d]);CHKERRQ(ierr); 155 } 156 /* Step 5: Set cones and supports */ 157 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 158 for (p = pStart; p < pEnd; ++p) { 159 const PetscInt *points = NULL, *orientations = NULL; 160 PetscInt size, i, newp = DMPlexShiftPoint_Internal(p, depth, depthEnd, depthShift); 161 162 ierr = DMPlexGetConeSize(dm, p, &size);CHKERRQ(ierr); 163 ierr = DMPlexGetCone(dm, p, &points);CHKERRQ(ierr); 164 ierr = DMPlexGetConeOrientation(dm, p, &orientations);CHKERRQ(ierr); 165 for (i = 0; i < size; ++i) { 166 newpoints[i] = DMPlexShiftPoint_Internal(points[i], depth, depthEnd, depthShift); 167 } 168 ierr = DMPlexSetCone(dmNew, newp, newpoints);CHKERRQ(ierr); 169 ierr = DMPlexSetConeOrientation(dmNew, newp, orientations);CHKERRQ(ierr); 170 ierr = DMPlexGetSupportSize(dm, p, &size);CHKERRQ(ierr); 171 ierr = DMPlexGetSupport(dm, p, &points);CHKERRQ(ierr); 172 for (i = 0; i < size; ++i) { 173 newpoints[i] = DMPlexShiftPoint_Internal(points[i], depth, depthEnd, depthShift); 174 } 175 ierr = DMPlexSetSupport(dmNew, newp, newpoints);CHKERRQ(ierr); 176 } 177 ierr = PetscFree2(depthEnd,newpoints);CHKERRQ(ierr); 178 PetscFunctionReturn(0); 179 } 180 181 #undef __FUNCT__ 182 #define __FUNCT__ "DMPlexShiftCoordinates_Internal" 183 static PetscErrorCode DMPlexShiftCoordinates_Internal(DM dm, PetscInt depthShift[], DM dmNew) 184 { 185 PetscSection coordSection, newCoordSection; 186 Vec coordinates, newCoordinates; 187 PetscScalar *coords, *newCoords; 188 PetscInt *depthEnd, coordSize; 189 PetscInt dim, depth = 0, d, vStart, vEnd, vStartNew, vEndNew, v; 190 PetscErrorCode ierr; 191 192 PetscFunctionBegin; 193 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 194 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 195 ierr = PetscMalloc((depth+1) * sizeof(PetscInt), &depthEnd);CHKERRQ(ierr); 196 for (d = 0; d <= depth; ++d) { 197 ierr = DMPlexGetDepthStratum(dm, d, NULL, &depthEnd[d]);CHKERRQ(ierr); 198 } 199 /* Step 8: Convert coordinates */ 200 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 201 ierr = DMPlexGetDepthStratum(dmNew, 0, &vStartNew, &vEndNew);CHKERRQ(ierr); 202 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 203 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &newCoordSection);CHKERRQ(ierr); 204 ierr = PetscSectionSetNumFields(newCoordSection, 1);CHKERRQ(ierr); 205 ierr = PetscSectionSetFieldComponents(newCoordSection, 0, dim);CHKERRQ(ierr); 206 ierr = PetscSectionSetChart(newCoordSection, vStartNew, vEndNew);CHKERRQ(ierr); 207 for (v = vStartNew; v < vEndNew; ++v) { 208 ierr = PetscSectionSetDof(newCoordSection, v, dim);CHKERRQ(ierr); 209 ierr = PetscSectionSetFieldDof(newCoordSection, v, 0, dim);CHKERRQ(ierr); 210 } 211 ierr = PetscSectionSetUp(newCoordSection);CHKERRQ(ierr); 212 ierr = DMPlexSetCoordinateSection(dmNew, newCoordSection);CHKERRQ(ierr); 213 ierr = PetscSectionGetStorageSize(newCoordSection, &coordSize);CHKERRQ(ierr); 214 ierr = VecCreate(PetscObjectComm((PetscObject)dm), &newCoordinates);CHKERRQ(ierr); 215 ierr = PetscObjectSetName((PetscObject) newCoordinates, "coordinates");CHKERRQ(ierr); 216 ierr = VecSetSizes(newCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 217 ierr = VecSetFromOptions(newCoordinates);CHKERRQ(ierr); 218 ierr = DMSetCoordinatesLocal(dmNew, newCoordinates);CHKERRQ(ierr); 219 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 220 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 221 ierr = VecGetArray(newCoordinates, &newCoords);CHKERRQ(ierr); 222 for (v = vStart; v < vEnd; ++v) { 223 PetscInt dof, off, noff, d; 224 225 ierr = PetscSectionGetDof(coordSection, v, &dof);CHKERRQ(ierr); 226 ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr); 227 ierr = PetscSectionGetOffset(newCoordSection, DMPlexShiftPoint_Internal(v, depth, depthEnd, depthShift), &noff);CHKERRQ(ierr); 228 for (d = 0; d < dof; ++d) { 229 newCoords[noff+d] = coords[off+d]; 230 } 231 } 232 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 233 ierr = VecRestoreArray(newCoordinates, &newCoords);CHKERRQ(ierr); 234 ierr = VecDestroy(&newCoordinates);CHKERRQ(ierr); 235 ierr = PetscSectionDestroy(&newCoordSection);CHKERRQ(ierr); 236 ierr = PetscFree(depthEnd);CHKERRQ(ierr); 237 PetscFunctionReturn(0); 238 } 239 240 #undef __FUNCT__ 241 #define __FUNCT__ "DMPlexShiftSF_Internal" 242 static PetscErrorCode DMPlexShiftSF_Internal(DM dm, PetscInt depthShift[], DM dmNew) 243 { 244 PetscInt *depthEnd; 245 PetscInt depth = 0, d; 246 PetscSF sfPoint, sfPointNew; 247 const PetscSFNode *remotePoints; 248 PetscSFNode *gremotePoints; 249 const PetscInt *localPoints; 250 PetscInt *glocalPoints, *newLocation, *newRemoteLocation; 251 PetscInt numRoots, numLeaves, l, pStart, pEnd, totShift = 0; 252 PetscMPIInt numProcs; 253 PetscErrorCode ierr; 254 255 PetscFunctionBegin; 256 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 257 ierr = PetscMalloc((depth+1) * sizeof(PetscInt), &depthEnd);CHKERRQ(ierr); 258 for (d = 0; d <= depth; ++d) { 259 totShift += depthShift[d]; 260 ierr = DMPlexGetDepthStratum(dm, d, NULL, &depthEnd[d]);CHKERRQ(ierr); 261 } 262 /* Step 9: Convert pointSF */ 263 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)dm), &numProcs);CHKERRQ(ierr); 264 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 265 ierr = DMGetPointSF(dmNew, &sfPointNew);CHKERRQ(ierr); 266 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 267 ierr = PetscSFGetGraph(sfPoint, &numRoots, &numLeaves, &localPoints, &remotePoints);CHKERRQ(ierr); 268 if (numRoots >= 0) { 269 ierr = PetscMalloc2(numRoots,PetscInt,&newLocation,pEnd-pStart,PetscInt,&newRemoteLocation);CHKERRQ(ierr); 270 for (l=0; l<numRoots; l++) newLocation[l] = DMPlexShiftPoint_Internal(l, depth, depthEnd, depthShift); 271 ierr = PetscSFBcastBegin(sfPoint, MPIU_INT, newLocation, newRemoteLocation);CHKERRQ(ierr); 272 ierr = PetscSFBcastEnd(sfPoint, MPIU_INT, newLocation, newRemoteLocation);CHKERRQ(ierr); 273 ierr = PetscMalloc(numLeaves * sizeof(PetscInt), &glocalPoints);CHKERRQ(ierr); 274 ierr = PetscMalloc(numLeaves * sizeof(PetscSFNode), &gremotePoints);CHKERRQ(ierr); 275 for (l = 0; l < numLeaves; ++l) { 276 glocalPoints[l] = DMPlexShiftPoint_Internal(localPoints[l], depth, depthEnd, depthShift); 277 gremotePoints[l].rank = remotePoints[l].rank; 278 gremotePoints[l].index = newRemoteLocation[localPoints[l]]; 279 } 280 ierr = PetscFree2(newLocation,newRemoteLocation);CHKERRQ(ierr); 281 ierr = PetscSFSetGraph(sfPointNew, numRoots + totShift, numLeaves, glocalPoints, PETSC_OWN_POINTER, gremotePoints, PETSC_OWN_POINTER);CHKERRQ(ierr); 282 } 283 ierr = PetscFree(depthEnd);CHKERRQ(ierr); 284 PetscFunctionReturn(0); 285 } 286 287 #undef __FUNCT__ 288 #define __FUNCT__ "DMPlexShiftLabels_Internal" 289 static PetscErrorCode DMPlexShiftLabels_Internal(DM dm, PetscInt depthShift[], DM dmNew) 290 { 291 PetscSF sfPoint; 292 DMLabel vtkLabel, ghostLabel; 293 PetscInt *depthEnd; 294 const PetscSFNode *leafRemote; 295 const PetscInt *leafLocal; 296 PetscInt depth = 0, d, numLeaves, numLabels, l, cStart, cEnd, c, fStart, fEnd, f; 297 PetscMPIInt rank; 298 PetscErrorCode ierr; 299 300 PetscFunctionBegin; 301 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 302 ierr = PetscMalloc((depth+1) * sizeof(PetscInt), &depthEnd);CHKERRQ(ierr); 303 for (d = 0; d <= depth; ++d) { 304 ierr = DMPlexGetDepthStratum(dm, d, NULL, &depthEnd[d]);CHKERRQ(ierr); 305 } 306 /* Step 10: Convert labels */ 307 ierr = DMPlexGetNumLabels(dm, &numLabels);CHKERRQ(ierr); 308 for (l = 0; l < numLabels; ++l) { 309 DMLabel label, newlabel; 310 const char *lname; 311 PetscBool isDepth; 312 IS valueIS; 313 const PetscInt *values; 314 PetscInt numValues, val; 315 316 ierr = DMPlexGetLabelName(dm, l, &lname);CHKERRQ(ierr); 317 ierr = PetscStrcmp(lname, "depth", &isDepth);CHKERRQ(ierr); 318 if (isDepth) continue; 319 ierr = DMPlexCreateLabel(dmNew, lname);CHKERRQ(ierr); 320 ierr = DMPlexGetLabel(dm, lname, &label);CHKERRQ(ierr); 321 ierr = DMPlexGetLabel(dmNew, lname, &newlabel);CHKERRQ(ierr); 322 ierr = DMLabelGetValueIS(label, &valueIS);CHKERRQ(ierr); 323 ierr = ISGetLocalSize(valueIS, &numValues);CHKERRQ(ierr); 324 ierr = ISGetIndices(valueIS, &values);CHKERRQ(ierr); 325 for (val = 0; val < numValues; ++val) { 326 IS pointIS; 327 const PetscInt *points; 328 PetscInt numPoints, p; 329 330 ierr = DMLabelGetStratumIS(label, values[val], &pointIS);CHKERRQ(ierr); 331 ierr = ISGetLocalSize(pointIS, &numPoints);CHKERRQ(ierr); 332 ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); 333 for (p = 0; p < numPoints; ++p) { 334 const PetscInt newpoint = DMPlexShiftPoint_Internal(points[p], depth, depthEnd, depthShift); 335 336 ierr = DMLabelSetValue(newlabel, newpoint, values[val]);CHKERRQ(ierr); 337 } 338 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 339 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 340 } 341 ierr = ISRestoreIndices(valueIS, &values);CHKERRQ(ierr); 342 ierr = ISDestroy(&valueIS);CHKERRQ(ierr); 343 } 344 ierr = PetscFree(depthEnd);CHKERRQ(ierr); 345 /* Step 11: Make label for output (vtk) and to mark ghost points (ghost) */ 346 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr); 347 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 348 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 349 ierr = PetscSFGetGraph(sfPoint, NULL, &numLeaves, &leafLocal, &leafRemote);CHKERRQ(ierr); 350 ierr = DMPlexCreateLabel(dmNew, "vtk");CHKERRQ(ierr); 351 ierr = DMPlexCreateLabel(dmNew, "ghost");CHKERRQ(ierr); 352 ierr = DMPlexGetLabel(dmNew, "vtk", &vtkLabel);CHKERRQ(ierr); 353 ierr = DMPlexGetLabel(dmNew, "ghost", &ghostLabel);CHKERRQ(ierr); 354 for (l = 0, c = cStart; l < numLeaves && c < cEnd; ++l, ++c) { 355 for (; c < leafLocal[l] && c < cEnd; ++c) { 356 ierr = DMLabelSetValue(vtkLabel, c, 1);CHKERRQ(ierr); 357 } 358 if (leafLocal[l] >= cEnd) break; 359 if (leafRemote[l].rank == rank) { 360 ierr = DMLabelSetValue(vtkLabel, c, 1);CHKERRQ(ierr); 361 } else { 362 ierr = DMLabelSetValue(ghostLabel, c, 2);CHKERRQ(ierr); 363 } 364 } 365 for (; c < cEnd; ++c) { 366 ierr = DMLabelSetValue(vtkLabel, c, 1);CHKERRQ(ierr); 367 } 368 if (0) { 369 ierr = PetscViewerASCIISynchronizedAllow(PETSC_VIEWER_STDOUT_WORLD, PETSC_TRUE);CHKERRQ(ierr); 370 ierr = DMLabelView(vtkLabel, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 371 ierr = PetscViewerFlush(PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 372 } 373 ierr = DMPlexGetHeightStratum(dmNew, 1, &fStart, &fEnd);CHKERRQ(ierr); 374 for (f = fStart; f < fEnd; ++f) { 375 PetscInt numCells; 376 377 ierr = DMPlexGetSupportSize(dmNew, f, &numCells);CHKERRQ(ierr); 378 if (numCells < 2) { 379 ierr = DMLabelSetValue(ghostLabel, f, 1);CHKERRQ(ierr); 380 } else { 381 const PetscInt *cells = NULL; 382 PetscInt vA, vB; 383 384 ierr = DMPlexGetSupport(dmNew, f, &cells);CHKERRQ(ierr); 385 ierr = DMLabelGetValue(vtkLabel, cells[0], &vA);CHKERRQ(ierr); 386 ierr = DMLabelGetValue(vtkLabel, cells[1], &vB);CHKERRQ(ierr); 387 if (!vA && !vB) {ierr = DMLabelSetValue(ghostLabel, f, 1);CHKERRQ(ierr);} 388 } 389 } 390 if (0) { 391 ierr = PetscViewerASCIISynchronizedAllow(PETSC_VIEWER_STDOUT_WORLD, PETSC_TRUE);CHKERRQ(ierr); 392 ierr = DMLabelView(ghostLabel, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 393 ierr = PetscViewerFlush(PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 394 } 395 PetscFunctionReturn(0); 396 } 397 398 #undef __FUNCT__ 399 #define __FUNCT__ "DMPlexConstructGhostCells_Internal" 400 static PetscErrorCode DMPlexConstructGhostCells_Internal(DM dm, DMLabel label, PetscInt *numGhostCells, DM gdm) 401 { 402 IS valueIS; 403 const PetscInt *values; 404 PetscInt *depthShift; 405 PetscInt depth = 0, numFS, fs, ghostCell, cEnd, c; 406 PetscErrorCode ierr; 407 408 PetscFunctionBegin; 409 /* Count ghost cells */ 410 ierr = DMLabelGetValueIS(label, &valueIS);CHKERRQ(ierr); 411 ierr = ISGetLocalSize(valueIS, &numFS);CHKERRQ(ierr); 412 ierr = ISGetIndices(valueIS, &values);CHKERRQ(ierr); 413 414 *numGhostCells = 0; 415 for (fs = 0; fs < numFS; ++fs) { 416 PetscInt numBdFaces; 417 418 ierr = DMLabelGetStratumSize(label, values[fs], &numBdFaces);CHKERRQ(ierr); 419 420 *numGhostCells += numBdFaces; 421 } 422 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 423 ierr = PetscMalloc((depth+1) * sizeof(PetscInt), &depthShift);CHKERRQ(ierr); 424 ierr = PetscMemzero(depthShift, (depth+1) * sizeof(PetscInt));CHKERRQ(ierr); 425 if (depth >= 0) depthShift[depth] = *numGhostCells; 426 ierr = DMPlexShiftSizes_Internal(dm, depthShift, gdm);CHKERRQ(ierr); 427 /* Step 3: Set cone/support sizes for new points */ 428 ierr = DMPlexGetHeightStratum(dm, 0, NULL, &cEnd);CHKERRQ(ierr); 429 for (c = cEnd; c < cEnd + *numGhostCells; ++c) { 430 ierr = DMPlexSetConeSize(gdm, c, 1);CHKERRQ(ierr); 431 } 432 for (fs = 0; fs < numFS; ++fs) { 433 IS faceIS; 434 const PetscInt *faces; 435 PetscInt numFaces, f; 436 437 ierr = DMLabelGetStratumIS(label, values[fs], &faceIS);CHKERRQ(ierr); 438 ierr = ISGetLocalSize(faceIS, &numFaces);CHKERRQ(ierr); 439 ierr = ISGetIndices(faceIS, &faces);CHKERRQ(ierr); 440 for (f = 0; f < numFaces; ++f) { 441 PetscInt size; 442 443 ierr = DMPlexGetSupportSize(dm, faces[f], &size);CHKERRQ(ierr); 444 if (size != 1) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "DM has boundary face %d with %d support cells", faces[f], size); 445 ierr = DMPlexSetSupportSize(gdm, faces[f] + *numGhostCells, 2);CHKERRQ(ierr); 446 } 447 ierr = ISRestoreIndices(faceIS, &faces);CHKERRQ(ierr); 448 ierr = ISDestroy(&faceIS);CHKERRQ(ierr); 449 } 450 /* Step 4: Setup ghosted DM */ 451 ierr = DMSetUp(gdm);CHKERRQ(ierr); 452 ierr = DMPlexShiftPoints_Internal(dm, depthShift, gdm);CHKERRQ(ierr); 453 /* Step 6: Set cones and supports for new points */ 454 ghostCell = cEnd; 455 for (fs = 0; fs < numFS; ++fs) { 456 IS faceIS; 457 const PetscInt *faces; 458 PetscInt numFaces, f; 459 460 ierr = DMLabelGetStratumIS(label, values[fs], &faceIS);CHKERRQ(ierr); 461 ierr = ISGetLocalSize(faceIS, &numFaces);CHKERRQ(ierr); 462 ierr = ISGetIndices(faceIS, &faces);CHKERRQ(ierr); 463 for (f = 0; f < numFaces; ++f, ++ghostCell) { 464 PetscInt newFace = faces[f] + *numGhostCells; 465 466 ierr = DMPlexSetCone(gdm, ghostCell, &newFace);CHKERRQ(ierr); 467 ierr = DMPlexInsertSupport(gdm, newFace, 1, ghostCell);CHKERRQ(ierr); 468 } 469 ierr = ISRestoreIndices(faceIS, &faces);CHKERRQ(ierr); 470 ierr = ISDestroy(&faceIS);CHKERRQ(ierr); 471 } 472 ierr = ISRestoreIndices(valueIS, &values);CHKERRQ(ierr); 473 ierr = ISDestroy(&valueIS);CHKERRQ(ierr); 474 /* Step 7: Stratify */ 475 ierr = DMPlexStratify(gdm);CHKERRQ(ierr); 476 ierr = DMPlexShiftCoordinates_Internal(dm, depthShift, gdm);CHKERRQ(ierr); 477 ierr = DMPlexShiftSF_Internal(dm, depthShift, gdm);CHKERRQ(ierr); 478 ierr = DMPlexShiftLabels_Internal(dm, depthShift, gdm);CHKERRQ(ierr); 479 ierr = PetscFree(depthShift);CHKERRQ(ierr); 480 PetscFunctionReturn(0); 481 } 482 483 #undef __FUNCT__ 484 #define __FUNCT__ "DMPlexConstructGhostCells" 485 /*@C 486 DMPlexConstructGhostCells - Construct ghost cells which connect to every boundary face 487 488 Collective on dm 489 490 Input Parameters: 491 + dm - The original DM 492 - labelName - The label specifying the boundary faces, or "Face Sets" if this is NULL 493 494 Output Parameters: 495 + numGhostCells - The number of ghost cells added to the DM 496 - dmGhosted - The new DM 497 498 Note: If no label exists of that name, one will be created marking all boundary faces 499 500 Level: developer 501 502 .seealso: DMCreate() 503 */ 504 PetscErrorCode DMPlexConstructGhostCells(DM dm, const char labelName[], PetscInt *numGhostCells, DM *dmGhosted) 505 { 506 DM gdm; 507 DMLabel label; 508 const char *name = labelName ? labelName : "Face Sets"; 509 PetscInt dim; 510 PetscErrorCode ierr; 511 512 PetscFunctionBegin; 513 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 514 PetscValidPointer(numGhostCells, 3); 515 PetscValidPointer(dmGhosted, 4); 516 ierr = DMCreate(PetscObjectComm((PetscObject)dm), &gdm);CHKERRQ(ierr); 517 ierr = DMSetType(gdm, DMPLEX);CHKERRQ(ierr); 518 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 519 ierr = DMPlexSetDimension(gdm, dim);CHKERRQ(ierr); 520 ierr = DMPlexGetLabel(dm, name, &label);CHKERRQ(ierr); 521 if (!label) { 522 /* Get label for boundary faces */ 523 ierr = DMPlexCreateLabel(dm, name);CHKERRQ(ierr); 524 ierr = DMPlexGetLabel(dm, name, &label);CHKERRQ(ierr); 525 ierr = DMPlexMarkBoundaryFaces(dm, label);CHKERRQ(ierr); 526 } 527 ierr = DMPlexConstructGhostCells_Internal(dm, label, numGhostCells, gdm);CHKERRQ(ierr); 528 ierr = DMSetFromOptions(gdm);CHKERRQ(ierr); 529 *dmGhosted = gdm; 530 PetscFunctionReturn(0); 531 } 532 533 #undef __FUNCT__ 534 #define __FUNCT__ "DMPlexConstructCohesiveCells_Internal" 535 static PetscErrorCode DMPlexConstructCohesiveCells_Internal(DM dm, DMLabel label, DM sdm) 536 { 537 MPI_Comm comm; 538 IS valueIS, *pointIS; 539 const PetscInt *values, **splitPoints; 540 PetscSection coordSection; 541 Vec coordinates; 542 PetscScalar *coords; 543 PetscInt *depthShift, *depthOffset, *pMaxNew, *numSplitPoints, *coneNew, *supportNew; 544 PetscInt shift = 100, depth = 0, dep, dim, d, numSP = 0, sp, maxConeSize, maxSupportSize, numLabels, p, v; 545 PetscErrorCode ierr; 546 547 PetscFunctionBegin; 548 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 549 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 550 /* Count split points and add cohesive cells */ 551 if (label) { 552 ierr = DMLabelGetValueIS(label, &valueIS);CHKERRQ(ierr); 553 ierr = ISGetLocalSize(valueIS, &numSP);CHKERRQ(ierr); 554 ierr = ISGetIndices(valueIS, &values);CHKERRQ(ierr); 555 } 556 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 557 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize);CHKERRQ(ierr); 558 ierr = PetscMalloc5(depth+1,PetscInt,&depthShift,depth+1,PetscInt,&depthOffset,depth+1,PetscInt,&pMaxNew,maxConeSize*3,PetscInt,&coneNew,maxSupportSize,PetscInt,&supportNew);CHKERRQ(ierr); 559 ierr = PetscMalloc3(depth+1,IS,&pointIS,depth+1,PetscInt,&numSplitPoints,depth+1,const PetscInt*,&splitPoints);CHKERRQ(ierr); 560 ierr = PetscMemzero(depthShift, (depth+1) * sizeof(PetscInt));CHKERRQ(ierr); 561 for (d = 0; d <= depth; ++d) { 562 ierr = DMPlexGetDepthStratum(dm, d, NULL, &pMaxNew[d]);CHKERRQ(ierr); 563 numSplitPoints[d] = 0; 564 splitPoints[d] = NULL; 565 pointIS[d] = NULL; 566 } 567 for (sp = 0; sp < numSP; ++sp) { 568 const PetscInt dep = values[sp]; 569 570 if ((dep < 0) || (dep > depth)) continue; 571 ierr = DMLabelGetStratumSize(label, dep, &depthShift[dep]);CHKERRQ(ierr); 572 ierr = DMLabelGetStratumIS(label, dep, &pointIS[dep]);CHKERRQ(ierr); 573 if (pointIS[dep]) { 574 ierr = ISGetLocalSize(pointIS[dep], &numSplitPoints[dep]);CHKERRQ(ierr); 575 ierr = ISGetIndices(pointIS[dep], &splitPoints[dep]);CHKERRQ(ierr); 576 } 577 } 578 if (depth >= 0) { 579 /* Calculate number of additional points */ 580 depthShift[depth] = depthShift[depth-1]; /* There is a cohesive cell for every split face */ 581 depthShift[1] += depthShift[0]; /* There is a cohesive edge for every split vertex */ 582 /* Calculate hybrid bound for each dimension */ 583 pMaxNew[0] += depthShift[depth]; 584 if (depth > 1) pMaxNew[dim-1] += depthShift[depth] + depthShift[0]; 585 if (depth > 2) pMaxNew[1] += depthShift[depth] + depthShift[0] + depthShift[dim-1]; 586 587 /* Calculate point offset for each dimension */ 588 depthOffset[depth] = 0; 589 depthOffset[0] = depthOffset[depth] + depthShift[depth]; 590 if (depth > 1) depthOffset[dim-1] = depthOffset[0] + depthShift[0]; 591 if (depth > 2) depthOffset[1] = depthOffset[dim-1] + depthShift[dim-1]; 592 } 593 ierr = DMPlexShiftSizes_Internal(dm, depthShift, sdm);CHKERRQ(ierr); 594 /* Step 3: Set cone/support sizes for new points */ 595 for (dep = 0; dep <= depth; ++dep) { 596 for (p = 0; p < numSplitPoints[dep]; ++p) { 597 const PetscInt oldp = splitPoints[dep][p]; 598 const PetscInt newp = depthOffset[dep] + oldp; 599 const PetscInt splitp = pMaxNew[dep] + p; 600 const PetscInt *support; 601 PetscInt coneSize, supportSize, q, e; 602 603 ierr = DMPlexGetConeSize(dm, oldp, &coneSize);CHKERRQ(ierr); 604 ierr = DMPlexSetConeSize(sdm, splitp, coneSize);CHKERRQ(ierr); 605 ierr = DMPlexGetSupportSize(dm, oldp, &supportSize);CHKERRQ(ierr); 606 ierr = DMPlexSetSupportSize(sdm, splitp, supportSize);CHKERRQ(ierr); 607 if (dep == depth-1) { 608 const PetscInt ccell = pMaxNew[depth] + p; 609 /* Add cohesive cells, they are prisms */ 610 ierr = DMPlexSetConeSize(sdm, ccell, 2 + coneSize);CHKERRQ(ierr); 611 } else if (dep == 0) { 612 const PetscInt cedge = pMaxNew[1] + (depthShift[1] - depthShift[0]) + p; 613 614 ierr = DMPlexGetSupport(dm, oldp, &support);CHKERRQ(ierr); 615 /* Split old vertex: Edges in old split faces and new cohesive edge */ 616 for (e = 0, q = 0; e < supportSize; ++e) { 617 PetscInt val; 618 619 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 620 if ((val == 1) || (val == (shift + 1))) ++q; 621 } 622 ierr = DMPlexSetSupportSize(sdm, newp, q+1);CHKERRQ(ierr); 623 /* Split new vertex: Edges in new split faces and new cohesive edge */ 624 for (e = 0, q = 0; e < supportSize; ++e) { 625 PetscInt val; 626 627 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 628 if ((val == 1) || (val == -(shift + 1))) ++q; 629 } 630 ierr = DMPlexSetSupportSize(sdm, splitp, q+1);CHKERRQ(ierr); 631 /* Add cohesive edges */ 632 ierr = DMPlexSetConeSize(sdm, cedge, 2);CHKERRQ(ierr); 633 /* Punt for now on support, you loop over closure, extract faces, check which ones are in the label */ 634 } else if (dep == dim-2) { 635 ierr = DMPlexGetSupport(dm, oldp, &support);CHKERRQ(ierr); 636 /* Split old edge: Faces in positive side cells and old split faces */ 637 for (e = 0, q = 0; e < supportSize; ++e) { 638 PetscInt val; 639 640 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 641 if ((val == dim-1) || (val == (shift + dim-1))) ++q; 642 } 643 ierr = DMPlexSetSupportSize(sdm, newp, q);CHKERRQ(ierr); 644 /* Split new edge: Faces in negative side cells and new split faces */ 645 for (e = 0, q = 0; e < supportSize; ++e) { 646 PetscInt val; 647 648 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 649 if ((val == dim-1) || (val == -(shift + dim-1))) ++q; 650 } 651 ierr = DMPlexSetSupportSize(sdm, splitp, q);CHKERRQ(ierr); 652 } 653 } 654 } 655 /* Step 4: Setup split DM */ 656 ierr = DMSetUp(sdm);CHKERRQ(ierr); 657 ierr = DMPlexShiftPoints_Internal(dm, depthShift, sdm);CHKERRQ(ierr); 658 /* Step 6: Set cones and supports for new points */ 659 for (dep = 0; dep <= depth; ++dep) { 660 for (p = 0; p < numSplitPoints[dep]; ++p) { 661 const PetscInt oldp = splitPoints[dep][p]; 662 const PetscInt newp = depthOffset[dep] + oldp; 663 const PetscInt splitp = pMaxNew[dep] + p; 664 const PetscInt *cone, *support, *ornt; 665 PetscInt coneSize, supportSize, q, v, e, s; 666 667 ierr = DMPlexGetConeSize(dm, oldp, &coneSize);CHKERRQ(ierr); 668 ierr = DMPlexGetCone(dm, oldp, &cone);CHKERRQ(ierr); 669 ierr = DMPlexGetConeOrientation(dm, oldp, &ornt);CHKERRQ(ierr); 670 ierr = DMPlexGetSupportSize(dm, oldp, &supportSize);CHKERRQ(ierr); 671 ierr = DMPlexGetSupport(dm, oldp, &support);CHKERRQ(ierr); 672 if (dep == depth-1) { 673 const PetscInt ccell = pMaxNew[depth] + p; 674 const PetscInt *supportF; 675 676 /* Split face: copy in old face to new face to start */ 677 ierr = DMPlexGetSupport(sdm, newp, &supportF);CHKERRQ(ierr); 678 ierr = DMPlexSetSupport(sdm, splitp, supportF);CHKERRQ(ierr); 679 /* Split old face: old vertices/edges in cone so no change */ 680 /* Split new face: new vertices/edges in cone */ 681 for (q = 0; q < coneSize; ++q) { 682 ierr = PetscFindInt(cone[q], numSplitPoints[dim-2], splitPoints[dim-2], &v);CHKERRQ(ierr); 683 684 coneNew[2+q] = pMaxNew[dim-2] + v; 685 } 686 ierr = DMPlexSetCone(sdm, splitp, &coneNew[2]);CHKERRQ(ierr); 687 ierr = DMPlexSetConeOrientation(sdm, splitp, ornt);CHKERRQ(ierr); 688 /* Cohesive cell: Old and new split face, then new cohesive edges */ 689 coneNew[0] = newp; 690 coneNew[1] = splitp; 691 for (q = 0; q < coneSize; ++q) { 692 coneNew[2+q] = (pMaxNew[1] - pMaxNew[dim-2]) + (depthShift[1] - depthShift[0]) + coneNew[2+q]; 693 } 694 ierr = DMPlexSetCone(sdm, ccell, coneNew);CHKERRQ(ierr); 695 696 697 for (s = 0; s < supportSize; ++s) { 698 PetscInt val; 699 700 ierr = DMLabelGetValue(label, support[s], &val);CHKERRQ(ierr); 701 if (val < 0) { 702 /* Split old face: Replace negative side cell with cohesive cell */ 703 ierr = DMPlexInsertSupport(sdm, newp, s, ccell);CHKERRQ(ierr); 704 } else { 705 /* Split new face: Replace positive side cell with cohesive cell */ 706 ierr = DMPlexInsertSupport(sdm, splitp, s, ccell);CHKERRQ(ierr); 707 } 708 } 709 } else if (dep == 0) { 710 const PetscInt cedge = pMaxNew[1] + (depthShift[1] - depthShift[0]) + p; 711 712 /* Split old vertex: Edges in old split faces and new cohesive edge */ 713 for (e = 0, q = 0; e < supportSize; ++e) { 714 PetscInt val; 715 716 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 717 if ((val == 1) || (val == (shift + 1))) { 718 supportNew[q++] = depthOffset[1] + support[e]; 719 } 720 } 721 supportNew[q] = cedge; 722 723 ierr = DMPlexSetSupport(sdm, newp, supportNew);CHKERRQ(ierr); 724 /* Split new vertex: Edges in new split faces and new cohesive edge */ 725 for (e = 0, q = 0; e < supportSize; ++e) { 726 PetscInt val, edge; 727 728 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 729 if (val == 1) { 730 ierr = PetscFindInt(support[e], numSplitPoints[1], splitPoints[1], &edge);CHKERRQ(ierr); 731 if (edge < 0) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Edge %d is not a split edge", support[e]); 732 supportNew[q++] = pMaxNew[1] + edge; 733 } else if (val == -(shift + 1)) { 734 supportNew[q++] = depthOffset[1] + support[e]; 735 } 736 } 737 supportNew[q] = cedge; 738 ierr = DMPlexSetSupport(sdm, splitp, supportNew);CHKERRQ(ierr); 739 /* Cohesive edge: Old and new split vertex, punting on support */ 740 coneNew[0] = newp; 741 coneNew[1] = splitp; 742 ierr = DMPlexSetCone(sdm, cedge, coneNew);CHKERRQ(ierr); 743 } else if (dep == dim-2) { 744 /* Split old edge: old vertices in cone so no change */ 745 /* Split new edge: new vertices in cone */ 746 for (q = 0; q < coneSize; ++q) { 747 ierr = PetscFindInt(cone[q], numSplitPoints[dim-3], splitPoints[dim-3], &v);CHKERRQ(ierr); 748 749 coneNew[q] = pMaxNew[dim-3] + v; 750 } 751 ierr = DMPlexSetCone(sdm, splitp, coneNew);CHKERRQ(ierr); 752 /* Split old edge: Faces in positive side cells and old split faces */ 753 for (e = 0, q = 0; e < supportSize; ++e) { 754 PetscInt val; 755 756 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 757 if ((val == dim-1) || (val == (shift + dim-1))) { 758 supportNew[q++] = depthOffset[dim-1] + support[e]; 759 } 760 } 761 ierr = DMPlexSetSupport(sdm, newp, supportNew);CHKERRQ(ierr); 762 /* Split new edge: Faces in negative side cells and new split faces */ 763 for (e = 0, q = 0; e < supportSize; ++e) { 764 PetscInt val, face; 765 766 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 767 if (val == dim-1) { 768 ierr = PetscFindInt(support[e], numSplitPoints[dim-1], splitPoints[dim-1], &face);CHKERRQ(ierr); 769 if (face < 0) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Face %d is not a split face", support[e]); 770 supportNew[q++] = pMaxNew[dim-1] + face; 771 } else if (val == -(shift + dim-1)) { 772 supportNew[q++] = depthOffset[dim-1] + support[e]; 773 } 774 } 775 ierr = DMPlexSetSupport(sdm, splitp, supportNew);CHKERRQ(ierr); 776 } 777 } 778 } 779 /* Step 6b: Replace split points in negative side cones */ 780 for (sp = 0; sp < numSP; ++sp) { 781 PetscInt dep = values[sp]; 782 IS pIS; 783 PetscInt numPoints; 784 const PetscInt *points; 785 786 if (dep >= 0) continue; 787 ierr = DMLabelGetStratumIS(label, dep, &pIS);CHKERRQ(ierr); 788 if (!pIS) continue; 789 dep = -dep - shift; 790 ierr = ISGetLocalSize(pIS, &numPoints);CHKERRQ(ierr); 791 ierr = ISGetIndices(pIS, &points);CHKERRQ(ierr); 792 for (p = 0; p < numPoints; ++p) { 793 const PetscInt oldp = points[p]; 794 const PetscInt newp = depthOffset[dep] + oldp; 795 const PetscInt *cone; 796 PetscInt coneSize, c; 797 PetscBool replaced = PETSC_FALSE; 798 799 /* Negative edge: replace split vertex */ 800 /* Negative cell: replace split face */ 801 ierr = DMPlexGetConeSize(sdm, newp, &coneSize);CHKERRQ(ierr); 802 ierr = DMPlexGetCone(sdm, newp, &cone);CHKERRQ(ierr); 803 for (c = 0; c < coneSize; ++c) { 804 const PetscInt coldp = cone[c] - depthOffset[dep-1]; 805 PetscInt csplitp, cp, val; 806 807 ierr = DMLabelGetValue(label, coldp, &val);CHKERRQ(ierr); 808 if (val == dep-1) { 809 ierr = PetscFindInt(coldp, numSplitPoints[dep-1], splitPoints[dep-1], &cp);CHKERRQ(ierr); 810 if (cp < 0) SETERRQ2(comm, PETSC_ERR_ARG_WRONG, "Point %d is not a split point of dimension %d", oldp, dep-1); 811 csplitp = pMaxNew[dep-1] + cp; 812 ierr = DMPlexInsertCone(sdm, newp, c, csplitp);CHKERRQ(ierr); 813 replaced = PETSC_TRUE; 814 } 815 } 816 if (!replaced) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "The cone of point %d does not contain split points", oldp); 817 } 818 ierr = ISRestoreIndices(pIS, &points);CHKERRQ(ierr); 819 ierr = ISDestroy(&pIS);CHKERRQ(ierr); 820 } 821 /* Step 7: Stratify */ 822 ierr = DMPlexStratify(sdm);CHKERRQ(ierr); 823 /* Step 8: Coordinates */ 824 ierr = DMPlexShiftCoordinates_Internal(dm, depthShift, sdm);CHKERRQ(ierr); 825 ierr = DMPlexGetCoordinateSection(sdm, &coordSection);CHKERRQ(ierr); 826 ierr = DMGetCoordinatesLocal(sdm, &coordinates);CHKERRQ(ierr); 827 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 828 for (v = 0; v < (numSplitPoints ? numSplitPoints[0] : 0); ++v) { 829 const PetscInt newp = depthOffset[0] + splitPoints[0][v]; 830 const PetscInt splitp = pMaxNew[0] + v; 831 PetscInt dof, off, soff, d; 832 833 ierr = PetscSectionGetDof(coordSection, newp, &dof);CHKERRQ(ierr); 834 ierr = PetscSectionGetOffset(coordSection, newp, &off);CHKERRQ(ierr); 835 ierr = PetscSectionGetOffset(coordSection, splitp, &soff);CHKERRQ(ierr); 836 for (d = 0; d < dof; ++d) coords[soff+d] = coords[off+d]; 837 } 838 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 839 /* Step 9: SF, if I can figure this out we can split the mesh in parallel */ 840 ierr = DMPlexShiftSF_Internal(dm, depthShift, sdm);CHKERRQ(ierr); 841 /* Step 10: Labels */ 842 ierr = DMPlexShiftLabels_Internal(dm, depthShift, sdm);CHKERRQ(ierr); 843 ierr = DMPlexGetNumLabels(sdm, &numLabels);CHKERRQ(ierr); 844 for (dep = 0; dep <= depth; ++dep) { 845 for (p = 0; p < numSplitPoints[dep]; ++p) { 846 const PetscInt newp = depthOffset[dep] + splitPoints[dep][p]; 847 const PetscInt splitp = pMaxNew[dep] + p; 848 PetscInt l; 849 850 for (l = 0; l < numLabels; ++l) { 851 DMLabel mlabel; 852 const char *lname; 853 PetscInt val; 854 855 ierr = DMPlexGetLabelName(sdm, l, &lname);CHKERRQ(ierr); 856 ierr = DMPlexGetLabel(sdm, lname, &mlabel);CHKERRQ(ierr); 857 ierr = DMLabelGetValue(mlabel, newp, &val);CHKERRQ(ierr); 858 if (val >= 0) { 859 ierr = DMLabelSetValue(mlabel, splitp, val);CHKERRQ(ierr); 860 if (dep == 0) { 861 const PetscInt cedge = pMaxNew[1] + (depthShift[1] - depthShift[0]) + p; 862 ierr = DMLabelSetValue(mlabel, cedge, val);CHKERRQ(ierr); 863 } 864 } 865 } 866 } 867 } 868 for (sp = 0; sp < numSP; ++sp) { 869 const PetscInt dep = values[sp]; 870 871 if ((dep < 0) || (dep > depth)) continue; 872 if (pointIS[dep]) {ierr = ISRestoreIndices(pointIS[dep], &splitPoints[dep]);CHKERRQ(ierr);} 873 ierr = ISDestroy(&pointIS[dep]);CHKERRQ(ierr); 874 } 875 if (label) { 876 ierr = ISRestoreIndices(valueIS, &values);CHKERRQ(ierr); 877 ierr = ISDestroy(&valueIS);CHKERRQ(ierr); 878 } 879 ierr = PetscFree5(depthShift, depthOffset, pMaxNew, coneNew, supportNew);CHKERRQ(ierr); 880 ierr = PetscFree3(pointIS, numSplitPoints, splitPoints);CHKERRQ(ierr); 881 PetscFunctionReturn(0); 882 } 883 884 #undef __FUNCT__ 885 #define __FUNCT__ "DMPlexConstructCohesiveCells" 886 /*@C 887 DMPlexConstructCohesiveCells - Construct cohesive cells which split the face along an internal interface 888 889 Collective on dm 890 891 Input Parameters: 892 + dm - The original DM 893 - labelName - The label specifying the boundary faces (this could be auto-generated) 894 895 Output Parameters: 896 - dmSplit - The new DM 897 898 Level: developer 899 900 .seealso: DMCreate(), DMPlexLabelCohesiveComplete() 901 @*/ 902 PetscErrorCode DMPlexConstructCohesiveCells(DM dm, DMLabel label, DM *dmSplit) 903 { 904 DM sdm; 905 PetscInt dim; 906 PetscErrorCode ierr; 907 908 PetscFunctionBegin; 909 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 910 PetscValidPointer(dmSplit, 4); 911 ierr = DMCreate(PetscObjectComm((PetscObject)dm), &sdm);CHKERRQ(ierr); 912 ierr = DMSetType(sdm, DMPLEX);CHKERRQ(ierr); 913 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 914 ierr = DMPlexSetDimension(sdm, dim);CHKERRQ(ierr); 915 switch (dim) { 916 case 2: 917 case 3: 918 ierr = DMPlexConstructCohesiveCells_Internal(dm, label, sdm);CHKERRQ(ierr); 919 break; 920 default: 921 SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Cannot construct cohesive cells for dimension %d", dim); 922 } 923 *dmSplit = sdm; 924 PetscFunctionReturn(0); 925 } 926 927 #undef __FUNCT__ 928 #define __FUNCT__ "DMPlexLabelCohesiveComplete" 929 /*@ 930 DMPlexLabelCohesiveComplete - Starting with a label marking vertices on an internal surface, we add all other mesh pieces 931 to complete the surface 932 933 Input Parameters: 934 + dm - The DM 935 - label - A DMLabel marking the surface vertices 936 937 Output Parameter: 938 . label - A DMLabel marking all surface points 939 940 Level: developer 941 942 .seealso: DMPlexConstructCohesiveCells(), DMPlexLabelComplete() 943 @*/ 944 PetscErrorCode DMPlexLabelCohesiveComplete(DM dm, DMLabel label) 945 { 946 IS dimIS; 947 const PetscInt *points; 948 PetscInt shift = 100, dim, dep, cStart, cEnd, numPoints, p, val; 949 PetscErrorCode ierr; 950 951 PetscFunctionBegin; 952 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 953 /* Cell orientation for face gives the side of the fault */ 954 ierr = DMLabelGetStratumIS(label, dim-1, &dimIS);CHKERRQ(ierr); 955 if (!dimIS) PetscFunctionReturn(0); 956 ierr = ISGetLocalSize(dimIS, &numPoints);CHKERRQ(ierr); 957 ierr = ISGetIndices(dimIS, &points);CHKERRQ(ierr); 958 for (p = 0; p < numPoints; ++p) { 959 const PetscInt *support; 960 PetscInt supportSize, s; 961 962 ierr = DMPlexGetSupportSize(dm, points[p], &supportSize);CHKERRQ(ierr); 963 if (supportSize != 2) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Split face %d has %d != 2 supports", points[p], supportSize); 964 ierr = DMPlexGetSupport(dm, points[p], &support);CHKERRQ(ierr); 965 for (s = 0; s < supportSize; ++s) { 966 const PetscInt *cone, *ornt; 967 PetscInt coneSize, c; 968 PetscBool pos = PETSC_TRUE; 969 970 ierr = DMPlexGetConeSize(dm, support[s], &coneSize);CHKERRQ(ierr); 971 ierr = DMPlexGetCone(dm, support[s], &cone);CHKERRQ(ierr); 972 ierr = DMPlexGetConeOrientation(dm, support[s], &ornt);CHKERRQ(ierr); 973 for (c = 0; c < coneSize; ++c) { 974 if (cone[c] == points[p]) { 975 if (ornt[c] >= 0) { 976 ierr = DMLabelSetValue(label, support[s], shift+dim);CHKERRQ(ierr); 977 } else { 978 ierr = DMLabelSetValue(label, support[s], -(shift+dim));CHKERRQ(ierr); 979 pos = PETSC_FALSE; 980 } 981 break; 982 } 983 } 984 if (c == coneSize) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Cell split face %d support does not have it in the cone", points[p]); 985 /* Put faces touching the fault in the label */ 986 for (c = 0; c < coneSize; ++c) { 987 const PetscInt point = cone[c]; 988 989 ierr = DMLabelGetValue(label, point, &val);CHKERRQ(ierr); 990 if (val == -1) { 991 PetscInt *closure = NULL; 992 PetscInt closureSize, cl; 993 994 ierr = DMPlexGetTransitiveClosure(dm, point, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 995 for (cl = 0; cl < closureSize*2; cl += 2) { 996 const PetscInt clp = closure[cl]; 997 998 ierr = DMLabelGetValue(label, clp, &val);CHKERRQ(ierr); 999 if ((val >= 0) && (val < dim-1)) { 1000 ierr = DMLabelSetValue(label, point, pos == PETSC_TRUE ? shift+dim-1 : -(shift+dim-1));CHKERRQ(ierr); 1001 break; 1002 } 1003 } 1004 ierr = DMPlexRestoreTransitiveClosure(dm, point, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1005 } 1006 } 1007 } 1008 } 1009 ierr = ISRestoreIndices(dimIS, &points);CHKERRQ(ierr); 1010 ierr = ISDestroy(&dimIS);CHKERRQ(ierr); 1011 /* Search for other cells/faces/edges connected to the fault by a vertex */ 1012 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1013 ierr = DMLabelGetStratumIS(label, 0, &dimIS);CHKERRQ(ierr); 1014 if (!dimIS) PetscFunctionReturn(0); 1015 ierr = ISGetLocalSize(dimIS, &numPoints);CHKERRQ(ierr); 1016 ierr = ISGetIndices(dimIS, &points);CHKERRQ(ierr); 1017 for (p = 0; p < numPoints; ++p) { 1018 PetscInt *star = NULL; 1019 PetscInt starSize, s; 1020 PetscInt again = 1; /* 0: Finished 1: Keep iterating after a change 2: No change */ 1021 1022 /* First mark cells connected to the fault */ 1023 ierr = DMPlexGetTransitiveClosure(dm, points[p], PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1024 while (again) { 1025 if (again > 1) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Could not classify all cells connected to the fault"); 1026 again = 0; 1027 for (s = 0; s < starSize*2; s += 2) { 1028 const PetscInt point = star[s]; 1029 const PetscInt *cone; 1030 PetscInt coneSize, c; 1031 1032 if ((point < cStart) || (point >= cEnd)) continue; 1033 ierr = DMLabelGetValue(label, point, &val);CHKERRQ(ierr); 1034 if (val != -1) continue; 1035 again = 2; 1036 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 1037 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 1038 for (c = 0; c < coneSize; ++c) { 1039 ierr = DMLabelGetValue(label, cone[c], &val);CHKERRQ(ierr); 1040 if (val != -1) { 1041 if (abs(val) < shift) SETERRQ3(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Face %d on cell %d has an invalid label %d", cone[c], point, val); 1042 if (val > 0) { 1043 ierr = DMLabelSetValue(label, point, shift+dim);CHKERRQ(ierr); 1044 } else { 1045 ierr = DMLabelSetValue(label, point, -(shift+dim));CHKERRQ(ierr); 1046 } 1047 again = 1; 1048 break; 1049 } 1050 } 1051 } 1052 } 1053 /* Classify the rest by cell membership */ 1054 for (s = 0; s < starSize*2; s += 2) { 1055 const PetscInt point = star[s]; 1056 1057 ierr = DMLabelGetValue(label, point, &val);CHKERRQ(ierr); 1058 if (val == -1) { 1059 PetscInt *sstar = NULL; 1060 PetscInt sstarSize, ss; 1061 PetscBool marked = PETSC_FALSE; 1062 1063 ierr = DMPlexGetTransitiveClosure(dm, point, PETSC_FALSE, &sstarSize, &sstar);CHKERRQ(ierr); 1064 for (ss = 0; ss < sstarSize*2; ss += 2) { 1065 const PetscInt spoint = sstar[ss]; 1066 1067 if ((spoint < cStart) || (spoint >= cEnd)) continue; 1068 ierr = DMLabelGetValue(label, spoint, &val);CHKERRQ(ierr); 1069 if (val == -1) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Cell %d in star of %d does not have a valid label", spoint, point); 1070 ierr = DMPlexGetLabelValue(dm, "depth", point, &dep);CHKERRQ(ierr); 1071 if (val > 0) { 1072 ierr = DMLabelSetValue(label, point, shift+dep);CHKERRQ(ierr); 1073 } else { 1074 ierr = DMLabelSetValue(label, point, -(shift+dep));CHKERRQ(ierr); 1075 } 1076 marked = PETSC_TRUE; 1077 break; 1078 } 1079 ierr = DMPlexRestoreTransitiveClosure(dm, point, PETSC_FALSE, &sstarSize, &sstar);CHKERRQ(ierr); 1080 if (!marked) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Point %d could not be classified", point); 1081 } 1082 } 1083 ierr = DMPlexRestoreTransitiveClosure(dm, points[p], PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1084 } 1085 ierr = ISRestoreIndices(dimIS, &points);CHKERRQ(ierr); 1086 ierr = ISDestroy(&dimIS);CHKERRQ(ierr); 1087 PetscFunctionReturn(0); 1088 } 1089 1090 #undef __FUNCT__ 1091 #define __FUNCT__ "DMPlexMarkSubmesh_Uninterpolated" 1092 /* Here we need the explicit assumption that: 1093 1094 For any marked cell, the marked vertices constitute a single face 1095 */ 1096 static PetscErrorCode DMPlexMarkSubmesh_Uninterpolated(DM dm, DMLabel vertexLabel, PetscInt value, DMLabel subpointMap, PetscInt *numFaces, PetscInt *nFV, DM subdm) 1097 { 1098 IS subvertexIS; 1099 const PetscInt *subvertices; 1100 PetscInt *pStart, *pEnd, *pMax; 1101 PetscInt depth, dim, d, numSubVerticesInitial = 0, v; 1102 PetscErrorCode ierr; 1103 1104 PetscFunctionBegin; 1105 *numFaces = 0; 1106 *nFV = 0; 1107 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 1108 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1109 ierr = PetscMalloc3(dim+1,PetscInt,&pStart,dim+1,PetscInt,&pEnd,dim+1,PetscInt,&pMax);CHKERRQ(ierr); 1110 ierr = DMPlexGetHybridBounds(dm, &pMax[depth], depth>1 ? &pMax[depth-1] : NULL, depth > 2 ? &pMax[1] : NULL, &pMax[0]);CHKERRQ(ierr); 1111 for (d = 0; d <= depth; ++d) { 1112 ierr = DMPlexGetDepthStratum(dm, d, &pStart[d], &pEnd[d]);CHKERRQ(ierr); 1113 if (pMax[d] >= 0) pEnd[d] = PetscMin(pEnd[d], pMax[d]); 1114 } 1115 /* Loop over initial vertices and mark all faces in the collective star() */ 1116 ierr = DMLabelGetStratumIS(vertexLabel, value, &subvertexIS);CHKERRQ(ierr); 1117 if (subvertexIS) { 1118 ierr = ISGetSize(subvertexIS, &numSubVerticesInitial);CHKERRQ(ierr); 1119 ierr = ISGetIndices(subvertexIS, &subvertices);CHKERRQ(ierr); 1120 } 1121 for (v = 0; v < numSubVerticesInitial; ++v) { 1122 const PetscInt vertex = subvertices[v]; 1123 PetscInt *star = NULL; 1124 PetscInt starSize, s, numCells = 0, c; 1125 1126 ierr = DMPlexGetTransitiveClosure(dm, vertex, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1127 for (s = 0; s < starSize*2; s += 2) { 1128 const PetscInt point = star[s]; 1129 if ((point >= pStart[depth]) && (point < pEnd[depth])) star[numCells++] = point; 1130 } 1131 for (c = 0; c < numCells; ++c) { 1132 const PetscInt cell = star[c]; 1133 PetscInt *closure = NULL; 1134 PetscInt closureSize, cl; 1135 PetscInt cellLoc, numCorners = 0, faceSize = 0; 1136 1137 ierr = DMLabelGetValue(subpointMap, cell, &cellLoc);CHKERRQ(ierr); 1138 if (cellLoc == 2) continue; 1139 if (cellLoc >= 0) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Cell %d has dimension %d in the surface label", cell, cellLoc); 1140 ierr = DMPlexGetTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1141 for (cl = 0; cl < closureSize*2; cl += 2) { 1142 const PetscInt point = closure[cl]; 1143 PetscInt vertexLoc; 1144 1145 if ((point >= pStart[0]) && (point < pEnd[0])) { 1146 ++numCorners; 1147 ierr = DMLabelGetValue(vertexLabel, point, &vertexLoc);CHKERRQ(ierr); 1148 if (vertexLoc == value) closure[faceSize++] = point; 1149 } 1150 } 1151 if (!(*nFV)) {ierr = DMPlexGetNumFaceVertices(dm, dim, numCorners, nFV);CHKERRQ(ierr);} 1152 if (faceSize > *nFV) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Invalid submesh: Too many vertices %d of an element on the surface", faceSize); 1153 if (faceSize == *nFV) { 1154 ++(*numFaces); 1155 for (cl = 0; cl < faceSize; ++cl) { 1156 ierr = DMLabelSetValue(subpointMap, closure[cl], 0);CHKERRQ(ierr); 1157 } 1158 ierr = DMLabelSetValue(subpointMap, cell, 2);CHKERRQ(ierr); 1159 } 1160 ierr = DMPlexRestoreTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1161 } 1162 ierr = DMPlexRestoreTransitiveClosure(dm, vertex, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1163 } 1164 if (subvertexIS) { 1165 ierr = ISRestoreIndices(subvertexIS, &subvertices);CHKERRQ(ierr); 1166 } 1167 ierr = ISDestroy(&subvertexIS);CHKERRQ(ierr); 1168 ierr = PetscFree3(pStart,pEnd,pMax);CHKERRQ(ierr); 1169 PetscFunctionReturn(0); 1170 } 1171 1172 #undef __FUNCT__ 1173 #define __FUNCT__ "DMPlexMarkSubmesh_Interpolated" 1174 static PetscErrorCode DMPlexMarkSubmesh_Interpolated(DM dm, DMLabel vertexLabel, PetscInt value, DMLabel subpointMap, DM subdm) 1175 { 1176 IS subvertexIS; 1177 const PetscInt *subvertices; 1178 PetscInt *pStart, *pEnd, *pMax; 1179 PetscInt dim, d, numSubVerticesInitial = 0, v; 1180 PetscErrorCode ierr; 1181 1182 PetscFunctionBegin; 1183 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1184 ierr = PetscMalloc3(dim+1,PetscInt,&pStart,dim+1,PetscInt,&pEnd,dim+1,PetscInt,&pMax);CHKERRQ(ierr); 1185 ierr = DMPlexGetHybridBounds(dm, &pMax[dim], dim>1 ? &pMax[dim-1] : NULL, dim > 2 ? &pMax[1] : NULL, &pMax[0]);CHKERRQ(ierr); 1186 for (d = 0; d <= dim; ++d) { 1187 ierr = DMPlexGetDepthStratum(dm, d, &pStart[d], &pEnd[d]);CHKERRQ(ierr); 1188 if (pMax[d] >= 0) pEnd[d] = PetscMin(pEnd[d], pMax[d]); 1189 } 1190 /* Loop over initial vertices and mark all faces in the collective star() */ 1191 ierr = DMLabelGetStratumIS(vertexLabel, value, &subvertexIS);CHKERRQ(ierr); 1192 if (subvertexIS) { 1193 ierr = ISGetSize(subvertexIS, &numSubVerticesInitial);CHKERRQ(ierr); 1194 ierr = ISGetIndices(subvertexIS, &subvertices);CHKERRQ(ierr); 1195 } 1196 for (v = 0; v < numSubVerticesInitial; ++v) { 1197 const PetscInt vertex = subvertices[v]; 1198 PetscInt *star = NULL; 1199 PetscInt starSize, s, numFaces = 0, f; 1200 1201 ierr = DMPlexGetTransitiveClosure(dm, vertex, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1202 for (s = 0; s < starSize*2; s += 2) { 1203 const PetscInt point = star[s]; 1204 if ((point >= pStart[dim-1]) && (point < pEnd[dim-1])) star[numFaces++] = point; 1205 } 1206 for (f = 0; f < numFaces; ++f) { 1207 const PetscInt face = star[f]; 1208 PetscInt *closure = NULL; 1209 PetscInt closureSize, c; 1210 PetscInt faceLoc; 1211 1212 ierr = DMLabelGetValue(subpointMap, face, &faceLoc);CHKERRQ(ierr); 1213 if (faceLoc == dim-1) continue; 1214 if (faceLoc >= 0) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Face %d has dimension %d in the surface label", face, faceLoc); 1215 ierr = DMPlexGetTransitiveClosure(dm, face, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1216 for (c = 0; c < closureSize*2; c += 2) { 1217 const PetscInt point = closure[c]; 1218 PetscInt vertexLoc; 1219 1220 if ((point >= pStart[0]) && (point < pEnd[0])) { 1221 ierr = DMLabelGetValue(vertexLabel, point, &vertexLoc);CHKERRQ(ierr); 1222 if (vertexLoc != value) break; 1223 } 1224 } 1225 if (c == closureSize*2) { 1226 const PetscInt *support; 1227 PetscInt supportSize, s; 1228 1229 for (c = 0; c < closureSize*2; c += 2) { 1230 const PetscInt point = closure[c]; 1231 1232 for (d = 0; d < dim; ++d) { 1233 if ((point >= pStart[d]) && (point < pEnd[d])) { 1234 ierr = DMLabelSetValue(subpointMap, point, d);CHKERRQ(ierr); 1235 break; 1236 } 1237 } 1238 } 1239 ierr = DMPlexGetSupportSize(dm, face, &supportSize);CHKERRQ(ierr); 1240 ierr = DMPlexGetSupport(dm, face, &support);CHKERRQ(ierr); 1241 for (s = 0; s < supportSize; ++s) { 1242 ierr = DMLabelSetValue(subpointMap, support[s], dim);CHKERRQ(ierr); 1243 } 1244 } 1245 ierr = DMPlexRestoreTransitiveClosure(dm, face, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1246 } 1247 ierr = DMPlexRestoreTransitiveClosure(dm, vertex, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1248 } 1249 if (subvertexIS) { 1250 ierr = ISRestoreIndices(subvertexIS, &subvertices);CHKERRQ(ierr); 1251 } 1252 ierr = ISDestroy(&subvertexIS);CHKERRQ(ierr); 1253 ierr = PetscFree3(pStart,pEnd,pMax);CHKERRQ(ierr); 1254 PetscFunctionReturn(0); 1255 } 1256 1257 #undef __FUNCT__ 1258 #define __FUNCT__ "DMPlexMarkCohesiveSubmesh_Uninterpolated" 1259 static PetscErrorCode DMPlexMarkCohesiveSubmesh_Uninterpolated(DM dm, PetscBool hasLagrange, DMLabel subpointMap, PetscInt *numFaces, PetscInt *nFV, PetscInt *subCells[], DM subdm) 1260 { 1261 const PetscInt *cone; 1262 PetscInt dim, cMax, cEnd, c, p, coneSize; 1263 PetscErrorCode ierr; 1264 1265 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1266 ierr = DMPlexGetHeightStratum(dm, 0, NULL, &cEnd);CHKERRQ(ierr); 1267 ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); 1268 if (cMax < 0) PetscFunctionReturn(0); 1269 ierr = DMPlexGetConeSize(dm, cMax, &coneSize);CHKERRQ(ierr); 1270 *numFaces = cEnd - cMax; 1271 *nFV = hasLagrange ? coneSize/3 : coneSize/2; 1272 ierr = PetscMalloc(*numFaces *2 * sizeof(PetscInt), subCells);CHKERRQ(ierr); 1273 for (c = cMax; c < cEnd; ++c) { 1274 const PetscInt *cells; 1275 PetscInt numCells; 1276 1277 ierr = DMPlexGetCone(dm, c, &cone);CHKERRQ(ierr); 1278 for (p = 0; p < *nFV; ++p) { 1279 ierr = DMLabelSetValue(subpointMap, cone[p], 0);CHKERRQ(ierr); 1280 } 1281 /* Negative face */ 1282 ierr = DMPlexGetJoin(dm, *nFV, cone, &numCells, &cells);CHKERRQ(ierr); 1283 if (numCells != 2) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive cells should separate two cells"); 1284 for (p = 0; p < numCells; ++p) { 1285 ierr = DMLabelSetValue(subpointMap, cells[p], 2);CHKERRQ(ierr); 1286 (*subCells)[(c-cMax)*2+p] = cells[p]; 1287 } 1288 ierr = DMPlexRestoreJoin(dm, *nFV, cone, &numCells, &cells);CHKERRQ(ierr); 1289 /* Positive face is not included */ 1290 } 1291 PetscFunctionReturn(0); 1292 } 1293 1294 #undef __FUNCT__ 1295 #define __FUNCT__ "DMPlexMarkCohesiveSubmesh_Interpolated" 1296 static PetscErrorCode DMPlexMarkCohesiveSubmesh_Interpolated(DM dm, PetscBool hasLagrange, DMLabel subpointMap, DM subdm) 1297 { 1298 PetscInt *pStart, *pEnd; 1299 PetscInt dim, cMax, cEnd, c, d; 1300 PetscErrorCode ierr; 1301 1302 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1303 ierr = DMPlexGetHeightStratum(dm, 0, NULL, &cEnd);CHKERRQ(ierr); 1304 ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); 1305 if (cMax < 0) PetscFunctionReturn(0); 1306 ierr = PetscMalloc2(dim+1,PetscInt,&pStart,dim+1,PetscInt,&pEnd);CHKERRQ(ierr); 1307 for (d = 0; d <= dim; ++d) { 1308 ierr = DMPlexGetDepthStratum(dm, d, &pStart[d], &pEnd[d]);CHKERRQ(ierr); 1309 } 1310 for (c = cMax; c < cEnd; ++c) { 1311 const PetscInt *cone; 1312 PetscInt *closure = NULL; 1313 PetscInt coneSize, closureSize, cl; 1314 1315 ierr = DMPlexGetConeSize(dm, c, &coneSize);CHKERRQ(ierr); 1316 if (hasLagrange) { 1317 if (coneSize != 3) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive cells should separate two cells"); 1318 } else { 1319 if (coneSize != 2) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive cells should separate two cells"); 1320 } 1321 /* Negative face */ 1322 ierr = DMPlexGetCone(dm, c, &cone);CHKERRQ(ierr); 1323 ierr = DMPlexGetTransitiveClosure(dm, cone[0], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1324 for (cl = 0; cl < closureSize*2; cl += 2) { 1325 const PetscInt point = closure[cl]; 1326 1327 for (d = 0; d <= dim; ++d) { 1328 if ((point >= pStart[d]) && (point < pEnd[d])) { 1329 ierr = DMLabelSetValue(subpointMap, point, d);CHKERRQ(ierr); 1330 break; 1331 } 1332 } 1333 } 1334 ierr = DMPlexRestoreTransitiveClosure(dm, cone[0], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1335 /* Cells -- positive face is not included */ 1336 for (cl = 0; cl < 1; ++cl) { 1337 const PetscInt *support; 1338 PetscInt supportSize, s; 1339 1340 ierr = DMPlexGetSupportSize(dm, cone[cl], &supportSize);CHKERRQ(ierr); 1341 if (supportSize != 2) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive faces should separate two cells"); 1342 ierr = DMPlexGetSupport(dm, cone[cl], &support);CHKERRQ(ierr); 1343 for (s = 0; s < supportSize; ++s) { 1344 ierr = DMLabelSetValue(subpointMap, support[s], dim);CHKERRQ(ierr); 1345 } 1346 } 1347 } 1348 ierr = PetscFree2(pStart, pEnd);CHKERRQ(ierr); 1349 PetscFunctionReturn(0); 1350 } 1351 1352 #undef __FUNCT__ 1353 #define __FUNCT__ "DMPlexGetFaceOrientation" 1354 PetscErrorCode DMPlexGetFaceOrientation(DM dm, PetscInt cell, PetscInt numCorners, PetscInt indices[], PetscInt oppositeVertex, PetscInt origVertices[], PetscInt faceVertices[], PetscBool *posOriented) 1355 { 1356 MPI_Comm comm; 1357 PetscBool posOrient = PETSC_FALSE; 1358 const PetscInt debug = 0; 1359 PetscInt cellDim, faceSize, f; 1360 PetscErrorCode ierr; 1361 1362 PetscFunctionBegin; 1363 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 1364 ierr = DMPlexGetDimension(dm, &cellDim);CHKERRQ(ierr); 1365 if (debug) {PetscPrintf(comm, "cellDim: %d numCorners: %d\n", cellDim, numCorners);CHKERRQ(ierr);} 1366 1367 if (cellDim == numCorners-1) { 1368 /* Simplices */ 1369 faceSize = numCorners-1; 1370 posOrient = !(oppositeVertex%2) ? PETSC_TRUE : PETSC_FALSE; 1371 } else if (cellDim == 1 && numCorners == 3) { 1372 /* Quadratic line */ 1373 faceSize = 1; 1374 posOrient = PETSC_TRUE; 1375 } else if (cellDim == 2 && numCorners == 4) { 1376 /* Quads */ 1377 faceSize = 2; 1378 if ((indices[1] > indices[0]) && (indices[1] - indices[0] == 1)) { 1379 posOrient = PETSC_TRUE; 1380 } else if ((indices[0] == 3) && (indices[1] == 0)) { 1381 posOrient = PETSC_TRUE; 1382 } else { 1383 if (((indices[0] > indices[1]) && (indices[0] - indices[1] == 1)) || ((indices[0] == 0) && (indices[1] == 3))) { 1384 posOrient = PETSC_FALSE; 1385 } else SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid quad crossedge"); 1386 } 1387 } else if (cellDim == 2 && numCorners == 6) { 1388 /* Quadratic triangle (I hate this) */ 1389 /* Edges are determined by the first 2 vertices (corners of edges) */ 1390 const PetscInt faceSizeTri = 3; 1391 PetscInt sortedIndices[3], i, iFace; 1392 PetscBool found = PETSC_FALSE; 1393 PetscInt faceVerticesTriSorted[9] = { 1394 0, 3, 4, /* bottom */ 1395 1, 4, 5, /* right */ 1396 2, 3, 5, /* left */ 1397 }; 1398 PetscInt faceVerticesTri[9] = { 1399 0, 3, 4, /* bottom */ 1400 1, 4, 5, /* right */ 1401 2, 5, 3, /* left */ 1402 }; 1403 1404 faceSize = faceSizeTri; 1405 for (i = 0; i < faceSizeTri; ++i) sortedIndices[i] = indices[i]; 1406 ierr = PetscSortInt(faceSizeTri, sortedIndices);CHKERRQ(ierr); 1407 for (iFace = 0; iFace < 3; ++iFace) { 1408 const PetscInt ii = iFace*faceSizeTri; 1409 PetscInt fVertex, cVertex; 1410 1411 if ((sortedIndices[0] == faceVerticesTriSorted[ii+0]) && 1412 (sortedIndices[1] == faceVerticesTriSorted[ii+1])) { 1413 for (fVertex = 0; fVertex < faceSizeTri; ++fVertex) { 1414 for (cVertex = 0; cVertex < faceSizeTri; ++cVertex) { 1415 if (indices[cVertex] == faceVerticesTri[ii+fVertex]) { 1416 faceVertices[fVertex] = origVertices[cVertex]; 1417 break; 1418 } 1419 } 1420 } 1421 found = PETSC_TRUE; 1422 break; 1423 } 1424 } 1425 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid tri crossface"); 1426 if (posOriented) *posOriented = PETSC_TRUE; 1427 PetscFunctionReturn(0); 1428 } else if (cellDim == 2 && numCorners == 9) { 1429 /* Quadratic quad (I hate this) */ 1430 /* Edges are determined by the first 2 vertices (corners of edges) */ 1431 const PetscInt faceSizeQuad = 3; 1432 PetscInt sortedIndices[3], i, iFace; 1433 PetscBool found = PETSC_FALSE; 1434 PetscInt faceVerticesQuadSorted[12] = { 1435 0, 1, 4, /* bottom */ 1436 1, 2, 5, /* right */ 1437 2, 3, 6, /* top */ 1438 0, 3, 7, /* left */ 1439 }; 1440 PetscInt faceVerticesQuad[12] = { 1441 0, 1, 4, /* bottom */ 1442 1, 2, 5, /* right */ 1443 2, 3, 6, /* top */ 1444 3, 0, 7, /* left */ 1445 }; 1446 1447 faceSize = faceSizeQuad; 1448 for (i = 0; i < faceSizeQuad; ++i) sortedIndices[i] = indices[i]; 1449 ierr = PetscSortInt(faceSizeQuad, sortedIndices);CHKERRQ(ierr); 1450 for (iFace = 0; iFace < 4; ++iFace) { 1451 const PetscInt ii = iFace*faceSizeQuad; 1452 PetscInt fVertex, cVertex; 1453 1454 if ((sortedIndices[0] == faceVerticesQuadSorted[ii+0]) && 1455 (sortedIndices[1] == faceVerticesQuadSorted[ii+1])) { 1456 for (fVertex = 0; fVertex < faceSizeQuad; ++fVertex) { 1457 for (cVertex = 0; cVertex < faceSizeQuad; ++cVertex) { 1458 if (indices[cVertex] == faceVerticesQuad[ii+fVertex]) { 1459 faceVertices[fVertex] = origVertices[cVertex]; 1460 break; 1461 } 1462 } 1463 } 1464 found = PETSC_TRUE; 1465 break; 1466 } 1467 } 1468 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid quad crossface"); 1469 if (posOriented) *posOriented = PETSC_TRUE; 1470 PetscFunctionReturn(0); 1471 } else if (cellDim == 3 && numCorners == 8) { 1472 /* Hexes 1473 A hex is two oriented quads with the normal of the first 1474 pointing up at the second. 1475 1476 7---6 1477 /| /| 1478 4---5 | 1479 | 3-|-2 1480 |/ |/ 1481 0---1 1482 1483 Faces are determined by the first 4 vertices (corners of faces) */ 1484 const PetscInt faceSizeHex = 4; 1485 PetscInt sortedIndices[4], i, iFace; 1486 PetscBool found = PETSC_FALSE; 1487 PetscInt faceVerticesHexSorted[24] = { 1488 0, 1, 2, 3, /* bottom */ 1489 4, 5, 6, 7, /* top */ 1490 0, 1, 4, 5, /* front */ 1491 1, 2, 5, 6, /* right */ 1492 2, 3, 6, 7, /* back */ 1493 0, 3, 4, 7, /* left */ 1494 }; 1495 PetscInt faceVerticesHex[24] = { 1496 3, 2, 1, 0, /* bottom */ 1497 4, 5, 6, 7, /* top */ 1498 0, 1, 5, 4, /* front */ 1499 1, 2, 6, 5, /* right */ 1500 2, 3, 7, 6, /* back */ 1501 3, 0, 4, 7, /* left */ 1502 }; 1503 1504 faceSize = faceSizeHex; 1505 for (i = 0; i < faceSizeHex; ++i) sortedIndices[i] = indices[i]; 1506 ierr = PetscSortInt(faceSizeHex, sortedIndices);CHKERRQ(ierr); 1507 for (iFace = 0; iFace < 6; ++iFace) { 1508 const PetscInt ii = iFace*faceSizeHex; 1509 PetscInt fVertex, cVertex; 1510 1511 if ((sortedIndices[0] == faceVerticesHexSorted[ii+0]) && 1512 (sortedIndices[1] == faceVerticesHexSorted[ii+1]) && 1513 (sortedIndices[2] == faceVerticesHexSorted[ii+2]) && 1514 (sortedIndices[3] == faceVerticesHexSorted[ii+3])) { 1515 for (fVertex = 0; fVertex < faceSizeHex; ++fVertex) { 1516 for (cVertex = 0; cVertex < faceSizeHex; ++cVertex) { 1517 if (indices[cVertex] == faceVerticesHex[ii+fVertex]) { 1518 faceVertices[fVertex] = origVertices[cVertex]; 1519 break; 1520 } 1521 } 1522 } 1523 found = PETSC_TRUE; 1524 break; 1525 } 1526 } 1527 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid hex crossface"); 1528 if (posOriented) *posOriented = PETSC_TRUE; 1529 PetscFunctionReturn(0); 1530 } else if (cellDim == 3 && numCorners == 10) { 1531 /* Quadratic tet */ 1532 /* Faces are determined by the first 3 vertices (corners of faces) */ 1533 const PetscInt faceSizeTet = 6; 1534 PetscInt sortedIndices[6], i, iFace; 1535 PetscBool found = PETSC_FALSE; 1536 PetscInt faceVerticesTetSorted[24] = { 1537 0, 1, 2, 6, 7, 8, /* bottom */ 1538 0, 3, 4, 6, 7, 9, /* front */ 1539 1, 4, 5, 7, 8, 9, /* right */ 1540 2, 3, 5, 6, 8, 9, /* left */ 1541 }; 1542 PetscInt faceVerticesTet[24] = { 1543 0, 1, 2, 6, 7, 8, /* bottom */ 1544 0, 4, 3, 6, 7, 9, /* front */ 1545 1, 5, 4, 7, 8, 9, /* right */ 1546 2, 3, 5, 8, 6, 9, /* left */ 1547 }; 1548 1549 faceSize = faceSizeTet; 1550 for (i = 0; i < faceSizeTet; ++i) sortedIndices[i] = indices[i]; 1551 ierr = PetscSortInt(faceSizeTet, sortedIndices);CHKERRQ(ierr); 1552 for (iFace=0; iFace < 4; ++iFace) { 1553 const PetscInt ii = iFace*faceSizeTet; 1554 PetscInt fVertex, cVertex; 1555 1556 if ((sortedIndices[0] == faceVerticesTetSorted[ii+0]) && 1557 (sortedIndices[1] == faceVerticesTetSorted[ii+1]) && 1558 (sortedIndices[2] == faceVerticesTetSorted[ii+2]) && 1559 (sortedIndices[3] == faceVerticesTetSorted[ii+3])) { 1560 for (fVertex = 0; fVertex < faceSizeTet; ++fVertex) { 1561 for (cVertex = 0; cVertex < faceSizeTet; ++cVertex) { 1562 if (indices[cVertex] == faceVerticesTet[ii+fVertex]) { 1563 faceVertices[fVertex] = origVertices[cVertex]; 1564 break; 1565 } 1566 } 1567 } 1568 found = PETSC_TRUE; 1569 break; 1570 } 1571 } 1572 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid tet crossface"); 1573 if (posOriented) *posOriented = PETSC_TRUE; 1574 PetscFunctionReturn(0); 1575 } else if (cellDim == 3 && numCorners == 27) { 1576 /* Quadratic hexes (I hate this) 1577 A hex is two oriented quads with the normal of the first 1578 pointing up at the second. 1579 1580 7---6 1581 /| /| 1582 4---5 | 1583 | 3-|-2 1584 |/ |/ 1585 0---1 1586 1587 Faces are determined by the first 4 vertices (corners of faces) */ 1588 const PetscInt faceSizeQuadHex = 9; 1589 PetscInt sortedIndices[9], i, iFace; 1590 PetscBool found = PETSC_FALSE; 1591 PetscInt faceVerticesQuadHexSorted[54] = { 1592 0, 1, 2, 3, 8, 9, 10, 11, 24, /* bottom */ 1593 4, 5, 6, 7, 12, 13, 14, 15, 25, /* top */ 1594 0, 1, 4, 5, 8, 12, 16, 17, 22, /* front */ 1595 1, 2, 5, 6, 9, 13, 17, 18, 21, /* right */ 1596 2, 3, 6, 7, 10, 14, 18, 19, 23, /* back */ 1597 0, 3, 4, 7, 11, 15, 16, 19, 20, /* left */ 1598 }; 1599 PetscInt faceVerticesQuadHex[54] = { 1600 3, 2, 1, 0, 10, 9, 8, 11, 24, /* bottom */ 1601 4, 5, 6, 7, 12, 13, 14, 15, 25, /* top */ 1602 0, 1, 5, 4, 8, 17, 12, 16, 22, /* front */ 1603 1, 2, 6, 5, 9, 18, 13, 17, 21, /* right */ 1604 2, 3, 7, 6, 10, 19, 14, 18, 23, /* back */ 1605 3, 0, 4, 7, 11, 16, 15, 19, 20 /* left */ 1606 }; 1607 1608 faceSize = faceSizeQuadHex; 1609 for (i = 0; i < faceSizeQuadHex; ++i) sortedIndices[i] = indices[i]; 1610 ierr = PetscSortInt(faceSizeQuadHex, sortedIndices);CHKERRQ(ierr); 1611 for (iFace = 0; iFace < 6; ++iFace) { 1612 const PetscInt ii = iFace*faceSizeQuadHex; 1613 PetscInt fVertex, cVertex; 1614 1615 if ((sortedIndices[0] == faceVerticesQuadHexSorted[ii+0]) && 1616 (sortedIndices[1] == faceVerticesQuadHexSorted[ii+1]) && 1617 (sortedIndices[2] == faceVerticesQuadHexSorted[ii+2]) && 1618 (sortedIndices[3] == faceVerticesQuadHexSorted[ii+3])) { 1619 for (fVertex = 0; fVertex < faceSizeQuadHex; ++fVertex) { 1620 for (cVertex = 0; cVertex < faceSizeQuadHex; ++cVertex) { 1621 if (indices[cVertex] == faceVerticesQuadHex[ii+fVertex]) { 1622 faceVertices[fVertex] = origVertices[cVertex]; 1623 break; 1624 } 1625 } 1626 } 1627 found = PETSC_TRUE; 1628 break; 1629 } 1630 } 1631 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid hex crossface"); 1632 if (posOriented) *posOriented = PETSC_TRUE; 1633 PetscFunctionReturn(0); 1634 } else SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Unknown cell type for faceOrientation()."); 1635 if (!posOrient) { 1636 if (debug) {ierr = PetscPrintf(comm, " Reversing initial face orientation\n");CHKERRQ(ierr);} 1637 for (f = 0; f < faceSize; ++f) faceVertices[f] = origVertices[faceSize-1 - f]; 1638 } else { 1639 if (debug) {ierr = PetscPrintf(comm, " Keeping initial face orientation\n");CHKERRQ(ierr);} 1640 for (f = 0; f < faceSize; ++f) faceVertices[f] = origVertices[f]; 1641 } 1642 if (posOriented) *posOriented = posOrient; 1643 PetscFunctionReturn(0); 1644 } 1645 1646 #undef __FUNCT__ 1647 #define __FUNCT__ "DMPlexGetOrientedFace" 1648 /* 1649 Given a cell and a face, as a set of vertices, 1650 return the oriented face, as a set of vertices, in faceVertices 1651 The orientation is such that the face normal points out of the cell 1652 */ 1653 PetscErrorCode DMPlexGetOrientedFace(DM dm, PetscInt cell, PetscInt faceSize, const PetscInt face[], PetscInt numCorners, PetscInt indices[], PetscInt origVertices[], PetscInt faceVertices[], PetscBool *posOriented) 1654 { 1655 const PetscInt *cone = NULL; 1656 PetscInt coneSize, v, f, v2; 1657 PetscInt oppositeVertex = -1; 1658 PetscErrorCode ierr; 1659 1660 PetscFunctionBegin; 1661 ierr = DMPlexGetConeSize(dm, cell, &coneSize);CHKERRQ(ierr); 1662 ierr = DMPlexGetCone(dm, cell, &cone);CHKERRQ(ierr); 1663 for (v = 0, v2 = 0; v < coneSize; ++v) { 1664 PetscBool found = PETSC_FALSE; 1665 1666 for (f = 0; f < faceSize; ++f) { 1667 if (face[f] == cone[v]) { 1668 found = PETSC_TRUE; break; 1669 } 1670 } 1671 if (found) { 1672 indices[v2] = v; 1673 origVertices[v2] = cone[v]; 1674 ++v2; 1675 } else { 1676 oppositeVertex = v; 1677 } 1678 } 1679 ierr = DMPlexGetFaceOrientation(dm, cell, numCorners, indices, oppositeVertex, origVertices, faceVertices, posOriented);CHKERRQ(ierr); 1680 PetscFunctionReturn(0); 1681 } 1682 1683 #undef __FUNCT__ 1684 #define __FUNCT__ "DMPlexInsertFace_Internal" 1685 /* 1686 DMPlexInsertFace_Internal - Puts a face into the mesh 1687 1688 Not collective 1689 1690 Input Parameters: 1691 + dm - The DMPlex 1692 . numFaceVertex - The number of vertices in the face 1693 . faceVertices - The vertices in the face for dm 1694 . subfaceVertices - The vertices in the face for subdm 1695 . numCorners - The number of vertices in the cell 1696 . cell - A cell in dm containing the face 1697 . subcell - A cell in subdm containing the face 1698 . firstFace - First face in the mesh 1699 - newFacePoint - Next face in the mesh 1700 1701 Output Parameters: 1702 . newFacePoint - Contains next face point number on input, updated on output 1703 1704 Level: developer 1705 */ 1706 static PetscErrorCode DMPlexInsertFace_Internal(DM dm, DM subdm, PetscInt numFaceVertices, const PetscInt faceVertices[], const PetscInt subfaceVertices[], PetscInt numCorners, PetscInt cell, PetscInt subcell, PetscInt firstFace, PetscInt *newFacePoint) 1707 { 1708 MPI_Comm comm; 1709 DM_Plex *submesh = (DM_Plex*) subdm->data; 1710 const PetscInt *faces; 1711 PetscInt numFaces, coneSize; 1712 PetscErrorCode ierr; 1713 1714 PetscFunctionBegin; 1715 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 1716 ierr = DMPlexGetConeSize(subdm, subcell, &coneSize);CHKERRQ(ierr); 1717 if (coneSize != 1) SETERRQ2(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cone size of cell %d is %d != 1", cell, coneSize); 1718 #if 0 1719 /* Cannot use this because support() has not been constructed yet */ 1720 ierr = DMPlexGetJoin(subdm, numFaceVertices, subfaceVertices, &numFaces, &faces);CHKERRQ(ierr); 1721 #else 1722 { 1723 PetscInt f; 1724 1725 numFaces = 0; 1726 ierr = DMGetWorkArray(subdm, 1, PETSC_INT, (void**) &faces);CHKERRQ(ierr); 1727 for (f = firstFace; f < *newFacePoint; ++f) { 1728 PetscInt dof, off, d; 1729 1730 ierr = PetscSectionGetDof(submesh->coneSection, f, &dof);CHKERRQ(ierr); 1731 ierr = PetscSectionGetOffset(submesh->coneSection, f, &off);CHKERRQ(ierr); 1732 /* Yes, I know this is quadratic, but I expect the sizes to be <5 */ 1733 for (d = 0; d < dof; ++d) { 1734 const PetscInt p = submesh->cones[off+d]; 1735 PetscInt v; 1736 1737 for (v = 0; v < numFaceVertices; ++v) { 1738 if (subfaceVertices[v] == p) break; 1739 } 1740 if (v == numFaceVertices) break; 1741 } 1742 if (d == dof) { 1743 numFaces = 1; 1744 ((PetscInt*) faces)[0] = f; 1745 } 1746 } 1747 } 1748 #endif 1749 if (numFaces > 1) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Vertex set had %d faces, not one", numFaces); 1750 else if (numFaces == 1) { 1751 /* Add the other cell neighbor for this face */ 1752 ierr = DMPlexSetCone(subdm, subcell, faces);CHKERRQ(ierr); 1753 } else { 1754 PetscInt *indices, *origVertices, *orientedVertices, *orientedSubVertices, v, ov; 1755 PetscBool posOriented; 1756 1757 ierr = DMGetWorkArray(subdm, 4*numFaceVertices * sizeof(PetscInt), PETSC_INT, &orientedVertices);CHKERRQ(ierr); 1758 origVertices = &orientedVertices[numFaceVertices]; 1759 indices = &orientedVertices[numFaceVertices*2]; 1760 orientedSubVertices = &orientedVertices[numFaceVertices*3]; 1761 ierr = DMPlexGetOrientedFace(dm, cell, numFaceVertices, faceVertices, numCorners, indices, origVertices, orientedVertices, &posOriented);CHKERRQ(ierr); 1762 /* TODO: I know that routine should return a permutation, not the indices */ 1763 for (v = 0; v < numFaceVertices; ++v) { 1764 const PetscInt vertex = faceVertices[v], subvertex = subfaceVertices[v]; 1765 for (ov = 0; ov < numFaceVertices; ++ov) { 1766 if (orientedVertices[ov] == vertex) { 1767 orientedSubVertices[ov] = subvertex; 1768 break; 1769 } 1770 } 1771 if (ov == numFaceVertices) SETERRQ1(comm, PETSC_ERR_PLIB, "Could not find face vertex %d in orientated set", vertex); 1772 } 1773 ierr = DMPlexSetCone(subdm, *newFacePoint, orientedSubVertices);CHKERRQ(ierr); 1774 ierr = DMPlexSetCone(subdm, subcell, newFacePoint);CHKERRQ(ierr); 1775 ierr = DMRestoreWorkArray(subdm, 4*numFaceVertices * sizeof(PetscInt), PETSC_INT, &orientedVertices);CHKERRQ(ierr); 1776 ++(*newFacePoint); 1777 } 1778 ierr = DMPlexRestoreJoin(subdm, numFaceVertices, subfaceVertices, &numFaces, &faces);CHKERRQ(ierr); 1779 PetscFunctionReturn(0); 1780 } 1781 1782 #undef __FUNCT__ 1783 #define __FUNCT__ "DMPlexCreateSubmesh_Uninterpolated" 1784 static PetscErrorCode DMPlexCreateSubmesh_Uninterpolated(DM dm, const char vertexLabelName[], PetscInt value, DM subdm) 1785 { 1786 MPI_Comm comm; 1787 DMLabel vertexLabel, subpointMap; 1788 IS subvertexIS, subcellIS; 1789 const PetscInt *subVertices, *subCells; 1790 PetscInt numSubVertices, firstSubVertex, numSubCells; 1791 PetscInt *subface, maxConeSize, numSubFaces, firstSubFace, newFacePoint, nFV; 1792 PetscInt vStart, vEnd, c, f; 1793 PetscErrorCode ierr; 1794 1795 PetscFunctionBegin; 1796 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 1797 /* Create subpointMap which marks the submesh */ 1798 ierr = DMLabelCreate("subpoint_map", &subpointMap);CHKERRQ(ierr); 1799 ierr = DMPlexSetSubpointMap(subdm, subpointMap);CHKERRQ(ierr); 1800 ierr = DMLabelDestroy(&subpointMap);CHKERRQ(ierr); 1801 ierr = DMPlexGetLabel(dm, vertexLabelName, &vertexLabel);CHKERRQ(ierr); 1802 ierr = DMPlexMarkSubmesh_Uninterpolated(dm, vertexLabel, value, subpointMap, &numSubFaces, &nFV, subdm);CHKERRQ(ierr); 1803 /* Setup chart */ 1804 ierr = DMLabelGetStratumSize(subpointMap, 0, &numSubVertices);CHKERRQ(ierr); 1805 ierr = DMLabelGetStratumSize(subpointMap, 2, &numSubCells);CHKERRQ(ierr); 1806 ierr = DMPlexSetChart(subdm, 0, numSubCells+numSubFaces+numSubVertices);CHKERRQ(ierr); 1807 ierr = DMPlexSetVTKCellHeight(subdm, 1);CHKERRQ(ierr); 1808 /* Set cone sizes */ 1809 firstSubVertex = numSubCells; 1810 firstSubFace = numSubCells+numSubVertices; 1811 newFacePoint = firstSubFace; 1812 ierr = DMLabelGetStratumIS(subpointMap, 0, &subvertexIS);CHKERRQ(ierr); 1813 if (subvertexIS) {ierr = ISGetIndices(subvertexIS, &subVertices);CHKERRQ(ierr);} 1814 ierr = DMLabelGetStratumIS(subpointMap, 2, &subcellIS);CHKERRQ(ierr); 1815 if (subcellIS) {ierr = ISGetIndices(subcellIS, &subCells);CHKERRQ(ierr);} 1816 for (c = 0; c < numSubCells; ++c) { 1817 ierr = DMPlexSetConeSize(subdm, c, 1);CHKERRQ(ierr); 1818 } 1819 for (f = firstSubFace; f < firstSubFace+numSubFaces; ++f) { 1820 ierr = DMPlexSetConeSize(subdm, f, nFV);CHKERRQ(ierr); 1821 } 1822 ierr = DMSetUp(subdm);CHKERRQ(ierr); 1823 /* Create face cones */ 1824 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 1825 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, NULL);CHKERRQ(ierr); 1826 ierr = DMGetWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);CHKERRQ(ierr); 1827 for (c = 0; c < numSubCells; ++c) { 1828 const PetscInt cell = subCells[c]; 1829 const PetscInt subcell = c; 1830 PetscInt *closure = NULL; 1831 PetscInt closureSize, cl, numCorners = 0, faceSize = 0; 1832 1833 ierr = DMPlexGetTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1834 for (cl = 0; cl < closureSize*2; cl += 2) { 1835 const PetscInt point = closure[cl]; 1836 PetscInt subVertex; 1837 1838 if ((point >= vStart) && (point < vEnd)) { 1839 ++numCorners; 1840 ierr = PetscFindInt(point, numSubVertices, subVertices, &subVertex);CHKERRQ(ierr); 1841 if (subVertex >= 0) { 1842 closure[faceSize] = point; 1843 subface[faceSize] = firstSubVertex+subVertex; 1844 ++faceSize; 1845 } 1846 } 1847 } 1848 if (faceSize > nFV) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Invalid submesh: Too many vertices %d of an element on the surface", faceSize); 1849 if (faceSize == nFV) { 1850 ierr = DMPlexInsertFace_Internal(dm, subdm, faceSize, closure, subface, numCorners, cell, subcell, firstSubFace, &newFacePoint);CHKERRQ(ierr); 1851 } 1852 ierr = DMPlexRestoreTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1853 } 1854 ierr = DMRestoreWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);CHKERRQ(ierr); 1855 ierr = DMPlexSymmetrize(subdm);CHKERRQ(ierr); 1856 ierr = DMPlexStratify(subdm);CHKERRQ(ierr); 1857 /* Build coordinates */ 1858 { 1859 PetscSection coordSection, subCoordSection; 1860 Vec coordinates, subCoordinates; 1861 PetscScalar *coords, *subCoords; 1862 PetscInt coordSize, v; 1863 1864 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1865 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 1866 ierr = DMPlexGetCoordinateSection(subdm, &subCoordSection);CHKERRQ(ierr); 1867 ierr = PetscSectionSetChart(subCoordSection, firstSubVertex, firstSubVertex+numSubVertices);CHKERRQ(ierr); 1868 for (v = 0; v < numSubVertices; ++v) { 1869 const PetscInt vertex = subVertices[v]; 1870 const PetscInt subvertex = firstSubVertex+v; 1871 PetscInt dof; 1872 1873 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 1874 ierr = PetscSectionSetDof(subCoordSection, subvertex, dof);CHKERRQ(ierr); 1875 } 1876 ierr = PetscSectionSetUp(subCoordSection);CHKERRQ(ierr); 1877 ierr = PetscSectionGetStorageSize(subCoordSection, &coordSize);CHKERRQ(ierr); 1878 ierr = VecCreate(comm, &subCoordinates);CHKERRQ(ierr); 1879 ierr = VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1880 ierr = VecSetFromOptions(subCoordinates);CHKERRQ(ierr); 1881 if (coordSize) { 1882 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1883 ierr = VecGetArray(subCoordinates, &subCoords);CHKERRQ(ierr); 1884 for (v = 0; v < numSubVertices; ++v) { 1885 const PetscInt vertex = subVertices[v]; 1886 const PetscInt subvertex = firstSubVertex+v; 1887 PetscInt dof, off, sdof, soff, d; 1888 1889 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 1890 ierr = PetscSectionGetOffset(coordSection, vertex, &off);CHKERRQ(ierr); 1891 ierr = PetscSectionGetDof(subCoordSection, subvertex, &sdof);CHKERRQ(ierr); 1892 ierr = PetscSectionGetOffset(subCoordSection, subvertex, &soff);CHKERRQ(ierr); 1893 if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof); 1894 for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d]; 1895 } 1896 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1897 ierr = VecRestoreArray(subCoordinates, &subCoords);CHKERRQ(ierr); 1898 } 1899 ierr = DMSetCoordinatesLocal(subdm, subCoordinates);CHKERRQ(ierr); 1900 ierr = VecDestroy(&subCoordinates);CHKERRQ(ierr); 1901 } 1902 /* Cleanup */ 1903 if (subvertexIS) {ierr = ISRestoreIndices(subvertexIS, &subVertices);CHKERRQ(ierr);} 1904 ierr = ISDestroy(&subvertexIS);CHKERRQ(ierr); 1905 if (subcellIS) {ierr = ISRestoreIndices(subcellIS, &subCells);CHKERRQ(ierr);} 1906 ierr = ISDestroy(&subcellIS);CHKERRQ(ierr); 1907 PetscFunctionReturn(0); 1908 } 1909 1910 #undef __FUNCT__ 1911 #define __FUNCT__ "DMPlexCreateSubmesh_Interpolated" 1912 static PetscErrorCode DMPlexCreateSubmesh_Interpolated(DM dm, const char vertexLabelName[], PetscInt value, DM subdm) 1913 { 1914 MPI_Comm comm; 1915 DMLabel subpointMap, vertexLabel; 1916 IS *subpointIS; 1917 const PetscInt **subpoints; 1918 PetscInt *numSubPoints, *firstSubPoint, *coneNew; 1919 PetscInt totSubPoints = 0, maxConeSize, dim, p, d, v; 1920 PetscErrorCode ierr; 1921 1922 PetscFunctionBegin; 1923 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 1924 /* Create subpointMap which marks the submesh */ 1925 ierr = DMLabelCreate("subpoint_map", &subpointMap);CHKERRQ(ierr); 1926 ierr = DMPlexSetSubpointMap(subdm, subpointMap);CHKERRQ(ierr); 1927 ierr = DMLabelDestroy(&subpointMap);CHKERRQ(ierr); 1928 ierr = DMPlexGetLabel(dm, vertexLabelName, &vertexLabel);CHKERRQ(ierr); 1929 ierr = DMPlexMarkSubmesh_Interpolated(dm, vertexLabel, value, subpointMap, subdm);CHKERRQ(ierr); 1930 /* Setup chart */ 1931 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1932 ierr = PetscMalloc4(dim+1,PetscInt,&numSubPoints,dim+1,PetscInt,&firstSubPoint,dim+1,IS,&subpointIS,dim+1,const PetscInt *,&subpoints);CHKERRQ(ierr); 1933 for (d = 0; d <= dim; ++d) { 1934 ierr = DMLabelGetStratumSize(subpointMap, d, &numSubPoints[d]);CHKERRQ(ierr); 1935 totSubPoints += numSubPoints[d]; 1936 } 1937 ierr = DMPlexSetChart(subdm, 0, totSubPoints);CHKERRQ(ierr); 1938 ierr = DMPlexSetVTKCellHeight(subdm, 1);CHKERRQ(ierr); 1939 /* Set cone sizes */ 1940 firstSubPoint[dim] = 0; 1941 firstSubPoint[0] = firstSubPoint[dim] + numSubPoints[dim]; 1942 if (dim > 1) {firstSubPoint[dim-1] = firstSubPoint[0] + numSubPoints[0];} 1943 if (dim > 2) {firstSubPoint[dim-2] = firstSubPoint[dim-1] + numSubPoints[dim-1];} 1944 for (d = 0; d <= dim; ++d) { 1945 ierr = DMLabelGetStratumIS(subpointMap, d, &subpointIS[d]);CHKERRQ(ierr); 1946 ierr = ISGetIndices(subpointIS[d], &subpoints[d]);CHKERRQ(ierr); 1947 } 1948 for (d = 0; d <= dim; ++d) { 1949 for (p = 0; p < numSubPoints[d]; ++p) { 1950 const PetscInt point = subpoints[d][p]; 1951 const PetscInt subpoint = firstSubPoint[d] + p; 1952 const PetscInt *cone; 1953 PetscInt coneSize, coneSizeNew, c, val; 1954 1955 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 1956 ierr = DMPlexSetConeSize(subdm, subpoint, coneSize);CHKERRQ(ierr); 1957 if (d == dim) { 1958 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 1959 for (c = 0, coneSizeNew = 0; c < coneSize; ++c) { 1960 ierr = DMLabelGetValue(subpointMap, cone[c], &val);CHKERRQ(ierr); 1961 if (val >= 0) coneSizeNew++; 1962 } 1963 ierr = DMPlexSetConeSize(subdm, subpoint, coneSizeNew);CHKERRQ(ierr); 1964 } 1965 } 1966 } 1967 ierr = DMSetUp(subdm);CHKERRQ(ierr); 1968 /* Set cones */ 1969 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, NULL);CHKERRQ(ierr); 1970 ierr = PetscMalloc(maxConeSize * sizeof(PetscInt), &coneNew);CHKERRQ(ierr); 1971 for (d = 0; d <= dim; ++d) { 1972 for (p = 0; p < numSubPoints[d]; ++p) { 1973 const PetscInt point = subpoints[d][p]; 1974 const PetscInt subpoint = firstSubPoint[d] + p; 1975 const PetscInt *cone; 1976 PetscInt coneSize, subconeSize, coneSizeNew, c, subc; 1977 1978 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 1979 ierr = DMPlexGetConeSize(subdm, subpoint, &subconeSize);CHKERRQ(ierr); 1980 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 1981 for (c = 0, coneSizeNew = 0; c < coneSize; ++c) { 1982 ierr = PetscFindInt(cone[c], numSubPoints[d-1], subpoints[d-1], &subc);CHKERRQ(ierr); 1983 if (subc >= 0) coneNew[coneSizeNew++] = firstSubPoint[d-1] + subc; 1984 } 1985 if (coneSizeNew != subconeSize) SETERRQ2(comm, PETSC_ERR_PLIB, "Number of cone points located %d does not match subcone size %d", coneSizeNew, subconeSize); 1986 ierr = DMPlexSetCone(subdm, subpoint, coneNew);CHKERRQ(ierr); 1987 } 1988 } 1989 ierr = PetscFree(coneNew);CHKERRQ(ierr); 1990 ierr = DMPlexSymmetrize(subdm);CHKERRQ(ierr); 1991 ierr = DMPlexStratify(subdm);CHKERRQ(ierr); 1992 /* Build coordinates */ 1993 { 1994 PetscSection coordSection, subCoordSection; 1995 Vec coordinates, subCoordinates; 1996 PetscScalar *coords, *subCoords; 1997 PetscInt coordSize; 1998 1999 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2000 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 2001 ierr = DMPlexGetCoordinateSection(subdm, &subCoordSection);CHKERRQ(ierr); 2002 ierr = PetscSectionSetChart(subCoordSection, firstSubPoint[0], firstSubPoint[0]+numSubPoints[0]);CHKERRQ(ierr); 2003 for (v = 0; v < numSubPoints[0]; ++v) { 2004 const PetscInt vertex = subpoints[0][v]; 2005 const PetscInt subvertex = firstSubPoint[0]+v; 2006 PetscInt dof; 2007 2008 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2009 ierr = PetscSectionSetDof(subCoordSection, subvertex, dof);CHKERRQ(ierr); 2010 } 2011 ierr = PetscSectionSetUp(subCoordSection);CHKERRQ(ierr); 2012 ierr = PetscSectionGetStorageSize(subCoordSection, &coordSize);CHKERRQ(ierr); 2013 ierr = VecCreate(comm, &subCoordinates);CHKERRQ(ierr); 2014 ierr = VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2015 ierr = VecSetFromOptions(subCoordinates);CHKERRQ(ierr); 2016 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2017 ierr = VecGetArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2018 for (v = 0; v < numSubPoints[0]; ++v) { 2019 const PetscInt vertex = subpoints[0][v]; 2020 const PetscInt subvertex = firstSubPoint[0]+v; 2021 PetscInt dof, off, sdof, soff, d; 2022 2023 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2024 ierr = PetscSectionGetOffset(coordSection, vertex, &off);CHKERRQ(ierr); 2025 ierr = PetscSectionGetDof(subCoordSection, subvertex, &sdof);CHKERRQ(ierr); 2026 ierr = PetscSectionGetOffset(subCoordSection, subvertex, &soff);CHKERRQ(ierr); 2027 if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof); 2028 for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d]; 2029 } 2030 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2031 ierr = VecRestoreArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2032 ierr = DMSetCoordinatesLocal(subdm, subCoordinates);CHKERRQ(ierr); 2033 ierr = VecDestroy(&subCoordinates);CHKERRQ(ierr); 2034 } 2035 /* Cleanup */ 2036 for (d = 0; d <= dim; ++d) { 2037 ierr = ISRestoreIndices(subpointIS[d], &subpoints[d]);CHKERRQ(ierr); 2038 ierr = ISDestroy(&subpointIS[d]);CHKERRQ(ierr); 2039 } 2040 ierr = PetscFree4(numSubPoints,firstSubPoint,subpointIS,subpoints);CHKERRQ(ierr); 2041 PetscFunctionReturn(0); 2042 } 2043 2044 #undef __FUNCT__ 2045 #define __FUNCT__ "DMPlexCreateSubmesh" 2046 /*@C 2047 DMPlexCreateSubmesh - Extract a hypersurface from the mesh using vertices defined by a label 2048 2049 Input Parameters: 2050 + dm - The original mesh 2051 . vertexLabel - The DMLabel marking vertices contained in the surface 2052 - value - The label value to use 2053 2054 Output Parameter: 2055 . subdm - The surface mesh 2056 2057 Note: This function produces a DMLabel mapping original points in the submesh to their depth. This can be obtained using DMPlexGetSubpointMap(). 2058 2059 Level: developer 2060 2061 .seealso: DMPlexGetSubpointMap(), DMPlexGetLabel(), DMLabelSetValue() 2062 @*/ 2063 PetscErrorCode DMPlexCreateSubmesh(DM dm, const char vertexLabel[], PetscInt value, DM *subdm) 2064 { 2065 PetscInt dim, depth; 2066 PetscErrorCode ierr; 2067 2068 PetscFunctionBegin; 2069 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2070 PetscValidCharPointer(vertexLabel, 2); 2071 PetscValidPointer(subdm, 3); 2072 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 2073 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 2074 ierr = DMCreate(PetscObjectComm((PetscObject)dm), subdm);CHKERRQ(ierr); 2075 ierr = DMSetType(*subdm, DMPLEX);CHKERRQ(ierr); 2076 ierr = DMPlexSetDimension(*subdm, dim-1);CHKERRQ(ierr); 2077 if (depth == dim) { 2078 ierr = DMPlexCreateSubmesh_Interpolated(dm, vertexLabel, value, *subdm);CHKERRQ(ierr); 2079 } else { 2080 ierr = DMPlexCreateSubmesh_Uninterpolated(dm, vertexLabel, value, *subdm);CHKERRQ(ierr); 2081 } 2082 PetscFunctionReturn(0); 2083 } 2084 2085 #undef __FUNCT__ 2086 #define __FUNCT__ "DMPlexCreateCohesiveSubmesh_Uninterpolated" 2087 static PetscErrorCode DMPlexCreateCohesiveSubmesh_Uninterpolated(DM dm, PetscBool hasLagrange, DM subdm) 2088 { 2089 MPI_Comm comm; 2090 DMLabel subpointMap; 2091 IS subvertexIS; 2092 const PetscInt *subVertices; 2093 PetscInt numSubVertices, firstSubVertex, numSubCells, *subCells; 2094 PetscInt *subface, maxConeSize, numSubFaces, firstSubFace, newFacePoint, nFV; 2095 PetscInt cMax, c, f; 2096 PetscErrorCode ierr; 2097 2098 PetscFunctionBegin; 2099 ierr = PetscObjectGetComm((PetscObject)dm, &comm);CHKERRQ(ierr); 2100 /* Create subpointMap which marks the submesh */ 2101 ierr = DMLabelCreate("subpoint_map", &subpointMap);CHKERRQ(ierr); 2102 ierr = DMPlexSetSubpointMap(subdm, subpointMap);CHKERRQ(ierr); 2103 ierr = DMLabelDestroy(&subpointMap);CHKERRQ(ierr); 2104 ierr = DMPlexMarkCohesiveSubmesh_Uninterpolated(dm, hasLagrange, subpointMap, &numSubFaces, &nFV, &subCells, subdm);CHKERRQ(ierr); 2105 /* Setup chart */ 2106 ierr = DMLabelGetStratumSize(subpointMap, 0, &numSubVertices);CHKERRQ(ierr); 2107 ierr = DMLabelGetStratumSize(subpointMap, 2, &numSubCells);CHKERRQ(ierr); 2108 ierr = DMPlexSetChart(subdm, 0, numSubCells+numSubFaces+numSubVertices);CHKERRQ(ierr); 2109 ierr = DMPlexSetVTKCellHeight(subdm, 1);CHKERRQ(ierr); 2110 /* Set cone sizes */ 2111 firstSubVertex = numSubCells; 2112 firstSubFace = numSubCells+numSubVertices; 2113 newFacePoint = firstSubFace; 2114 ierr = DMLabelGetStratumIS(subpointMap, 0, &subvertexIS);CHKERRQ(ierr); 2115 if (subvertexIS) {ierr = ISGetIndices(subvertexIS, &subVertices);CHKERRQ(ierr);} 2116 for (c = 0; c < numSubCells; ++c) { 2117 ierr = DMPlexSetConeSize(subdm, c, 1);CHKERRQ(ierr); 2118 } 2119 for (f = firstSubFace; f < firstSubFace+numSubFaces; ++f) { 2120 ierr = DMPlexSetConeSize(subdm, f, nFV);CHKERRQ(ierr); 2121 } 2122 ierr = DMSetUp(subdm);CHKERRQ(ierr); 2123 /* Create face cones */ 2124 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, NULL);CHKERRQ(ierr); 2125 ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); 2126 ierr = DMGetWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);CHKERRQ(ierr); 2127 for (c = 0; c < numSubCells; ++c) { 2128 const PetscInt cell = subCells[c]; 2129 const PetscInt subcell = c; 2130 const PetscInt *cone, *cells; 2131 PetscInt numCells, subVertex, p, v; 2132 2133 if (cell < cMax) continue; 2134 ierr = DMPlexGetCone(dm, cell, &cone);CHKERRQ(ierr); 2135 for (v = 0; v < nFV; ++v) { 2136 ierr = PetscFindInt(cone[v], numSubVertices, subVertices, &subVertex);CHKERRQ(ierr); 2137 subface[v] = firstSubVertex+subVertex; 2138 } 2139 ierr = DMPlexSetCone(subdm, newFacePoint, subface);CHKERRQ(ierr); 2140 ierr = DMPlexSetCone(subdm, subcell, &newFacePoint);CHKERRQ(ierr); 2141 ierr = DMPlexGetJoin(dm, nFV, cone, &numCells, &cells);CHKERRQ(ierr); 2142 if (numCells != 2) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive cells should separate two cells"); 2143 for (p = 0; p < numCells; ++p) { 2144 PetscInt negsubcell; 2145 2146 if (cells[p] >= cMax) continue; 2147 /* I know this is a crap search */ 2148 for (negsubcell = 0; negsubcell < numSubCells; ++negsubcell) { 2149 if (subCells[negsubcell] == cells[p]) break; 2150 } 2151 if (negsubcell == numSubCells) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not find negative face neighbor for cohesive cell %d", cell); 2152 ierr = DMPlexSetCone(subdm, negsubcell, &newFacePoint);CHKERRQ(ierr); 2153 } 2154 ierr = DMPlexRestoreJoin(dm, nFV, cone, &numCells, &cells);CHKERRQ(ierr); 2155 ++newFacePoint; 2156 } 2157 ierr = DMRestoreWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);CHKERRQ(ierr); 2158 ierr = DMPlexSymmetrize(subdm);CHKERRQ(ierr); 2159 ierr = DMPlexStratify(subdm);CHKERRQ(ierr); 2160 /* Build coordinates */ 2161 { 2162 PetscSection coordSection, subCoordSection; 2163 Vec coordinates, subCoordinates; 2164 PetscScalar *coords, *subCoords; 2165 PetscInt coordSize, v; 2166 2167 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2168 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 2169 ierr = DMPlexGetCoordinateSection(subdm, &subCoordSection);CHKERRQ(ierr); 2170 ierr = PetscSectionSetChart(subCoordSection, firstSubVertex, firstSubVertex+numSubVertices);CHKERRQ(ierr); 2171 for (v = 0; v < numSubVertices; ++v) { 2172 const PetscInt vertex = subVertices[v]; 2173 const PetscInt subvertex = firstSubVertex+v; 2174 PetscInt dof; 2175 2176 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2177 ierr = PetscSectionSetDof(subCoordSection, subvertex, dof);CHKERRQ(ierr); 2178 } 2179 ierr = PetscSectionSetUp(subCoordSection);CHKERRQ(ierr); 2180 ierr = PetscSectionGetStorageSize(subCoordSection, &coordSize);CHKERRQ(ierr); 2181 ierr = VecCreate(comm, &subCoordinates);CHKERRQ(ierr); 2182 if (coordSize) { 2183 ierr = VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2184 ierr = VecSetFromOptions(subCoordinates);CHKERRQ(ierr); 2185 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2186 ierr = VecGetArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2187 for (v = 0; v < numSubVertices; ++v) { 2188 const PetscInt vertex = subVertices[v]; 2189 const PetscInt subvertex = firstSubVertex+v; 2190 PetscInt dof, off, sdof, soff, d; 2191 2192 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2193 ierr = PetscSectionGetOffset(coordSection, vertex, &off);CHKERRQ(ierr); 2194 ierr = PetscSectionGetDof(subCoordSection, subvertex, &sdof);CHKERRQ(ierr); 2195 ierr = PetscSectionGetOffset(subCoordSection, subvertex, &soff);CHKERRQ(ierr); 2196 if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof); 2197 for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d]; 2198 } 2199 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2200 ierr = VecRestoreArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2201 } 2202 ierr = DMSetCoordinatesLocal(subdm, subCoordinates);CHKERRQ(ierr); 2203 ierr = VecDestroy(&subCoordinates);CHKERRQ(ierr); 2204 } 2205 /* Cleanup */ 2206 if (subvertexIS) {ierr = ISRestoreIndices(subvertexIS, &subVertices);CHKERRQ(ierr);} 2207 ierr = ISDestroy(&subvertexIS);CHKERRQ(ierr); 2208 ierr = PetscFree(subCells);CHKERRQ(ierr); 2209 PetscFunctionReturn(0); 2210 } 2211 2212 #undef __FUNCT__ 2213 #define __FUNCT__ "DMPlexCreateCohesiveSubmesh_Interpolated" 2214 static PetscErrorCode DMPlexCreateCohesiveSubmesh_Interpolated(DM dm, PetscBool hasLagrange, DM subdm) 2215 { 2216 MPI_Comm comm; 2217 DMLabel subpointMap; 2218 IS *subpointIS; 2219 const PetscInt **subpoints; 2220 PetscInt *numSubPoints, *firstSubPoint, *coneNew; 2221 PetscInt totSubPoints = 0, maxConeSize, dim, p, d, v; 2222 PetscErrorCode ierr; 2223 2224 PetscFunctionBegin; 2225 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 2226 /* Create subpointMap which marks the submesh */ 2227 ierr = DMLabelCreate("subpoint_map", &subpointMap);CHKERRQ(ierr); 2228 ierr = DMPlexSetSubpointMap(subdm, subpointMap);CHKERRQ(ierr); 2229 ierr = DMLabelDestroy(&subpointMap);CHKERRQ(ierr); 2230 ierr = DMPlexMarkCohesiveSubmesh_Interpolated(dm, hasLagrange, subpointMap, subdm);CHKERRQ(ierr); 2231 /* Setup chart */ 2232 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 2233 ierr = PetscMalloc4(dim+1,PetscInt,&numSubPoints,dim+1,PetscInt,&firstSubPoint,dim+1,IS,&subpointIS,dim+1,const PetscInt *,&subpoints);CHKERRQ(ierr); 2234 for (d = 0; d <= dim; ++d) { 2235 ierr = DMLabelGetStratumSize(subpointMap, d, &numSubPoints[d]);CHKERRQ(ierr); 2236 totSubPoints += numSubPoints[d]; 2237 } 2238 ierr = DMPlexSetChart(subdm, 0, totSubPoints);CHKERRQ(ierr); 2239 ierr = DMPlexSetVTKCellHeight(subdm, 1);CHKERRQ(ierr); 2240 /* Set cone sizes */ 2241 firstSubPoint[dim] = 0; 2242 firstSubPoint[0] = firstSubPoint[dim] + numSubPoints[dim]; 2243 if (dim > 1) {firstSubPoint[dim-1] = firstSubPoint[0] + numSubPoints[0];} 2244 if (dim > 2) {firstSubPoint[dim-2] = firstSubPoint[dim-1] + numSubPoints[dim-1];} 2245 for (d = 0; d <= dim; ++d) { 2246 ierr = DMLabelGetStratumIS(subpointMap, d, &subpointIS[d]);CHKERRQ(ierr); 2247 ierr = ISGetIndices(subpointIS[d], &subpoints[d]);CHKERRQ(ierr); 2248 } 2249 for (d = 0; d <= dim; ++d) { 2250 for (p = 0; p < numSubPoints[d]; ++p) { 2251 const PetscInt point = subpoints[d][p]; 2252 const PetscInt subpoint = firstSubPoint[d] + p; 2253 const PetscInt *cone; 2254 PetscInt coneSize, coneSizeNew, c, val; 2255 2256 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 2257 ierr = DMPlexSetConeSize(subdm, subpoint, coneSize);CHKERRQ(ierr); 2258 if (d == dim) { 2259 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 2260 for (c = 0, coneSizeNew = 0; c < coneSize; ++c) { 2261 ierr = DMLabelGetValue(subpointMap, cone[c], &val);CHKERRQ(ierr); 2262 if (val >= 0) coneSizeNew++; 2263 } 2264 ierr = DMPlexSetConeSize(subdm, subpoint, coneSizeNew);CHKERRQ(ierr); 2265 } 2266 } 2267 } 2268 ierr = DMSetUp(subdm);CHKERRQ(ierr); 2269 /* Set cones */ 2270 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, NULL);CHKERRQ(ierr); 2271 ierr = PetscMalloc(maxConeSize * sizeof(PetscInt), &coneNew);CHKERRQ(ierr); 2272 for (d = 0; d <= dim; ++d) { 2273 for (p = 0; p < numSubPoints[d]; ++p) { 2274 const PetscInt point = subpoints[d][p]; 2275 const PetscInt subpoint = firstSubPoint[d] + p; 2276 const PetscInt *cone; 2277 PetscInt coneSize, subconeSize, coneSizeNew, c, subc; 2278 2279 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 2280 ierr = DMPlexGetConeSize(subdm, subpoint, &subconeSize);CHKERRQ(ierr); 2281 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 2282 for (c = 0, coneSizeNew = 0; c < coneSize; ++c) { 2283 ierr = PetscFindInt(cone[c], numSubPoints[d-1], subpoints[d-1], &subc);CHKERRQ(ierr); 2284 if (subc >= 0) coneNew[coneSizeNew++] = firstSubPoint[d-1] + subc; 2285 } 2286 if (coneSizeNew != subconeSize) SETERRQ2(comm, PETSC_ERR_PLIB, "Number of cone points located %d does not match subcone size %d", coneSizeNew, subconeSize); 2287 ierr = DMPlexSetCone(subdm, subpoint, coneNew);CHKERRQ(ierr); 2288 } 2289 } 2290 ierr = PetscFree(coneNew);CHKERRQ(ierr); 2291 ierr = DMPlexSymmetrize(subdm);CHKERRQ(ierr); 2292 ierr = DMPlexStratify(subdm);CHKERRQ(ierr); 2293 /* Build coordinates */ 2294 { 2295 PetscSection coordSection, subCoordSection; 2296 Vec coordinates, subCoordinates; 2297 PetscScalar *coords, *subCoords; 2298 PetscInt coordSize; 2299 2300 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2301 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 2302 ierr = DMPlexGetCoordinateSection(subdm, &subCoordSection);CHKERRQ(ierr); 2303 ierr = PetscSectionSetChart(subCoordSection, firstSubPoint[0], firstSubPoint[0]+numSubPoints[0]);CHKERRQ(ierr); 2304 for (v = 0; v < numSubPoints[0]; ++v) { 2305 const PetscInt vertex = subpoints[0][v]; 2306 const PetscInt subvertex = firstSubPoint[0]+v; 2307 PetscInt dof; 2308 2309 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2310 ierr = PetscSectionSetDof(subCoordSection, subvertex, dof);CHKERRQ(ierr); 2311 } 2312 ierr = PetscSectionSetUp(subCoordSection);CHKERRQ(ierr); 2313 ierr = PetscSectionGetStorageSize(subCoordSection, &coordSize);CHKERRQ(ierr); 2314 ierr = VecCreate(comm, &subCoordinates);CHKERRQ(ierr); 2315 ierr = VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2316 ierr = VecSetFromOptions(subCoordinates);CHKERRQ(ierr); 2317 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2318 ierr = VecGetArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2319 for (v = 0; v < numSubPoints[0]; ++v) { 2320 const PetscInt vertex = subpoints[0][v]; 2321 const PetscInt subvertex = firstSubPoint[0]+v; 2322 PetscInt dof, off, sdof, soff, d; 2323 2324 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2325 ierr = PetscSectionGetOffset(coordSection, vertex, &off);CHKERRQ(ierr); 2326 ierr = PetscSectionGetDof(subCoordSection, subvertex, &sdof);CHKERRQ(ierr); 2327 ierr = PetscSectionGetOffset(subCoordSection, subvertex, &soff);CHKERRQ(ierr); 2328 if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof); 2329 for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d]; 2330 } 2331 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2332 ierr = VecRestoreArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2333 ierr = DMSetCoordinatesLocal(subdm, subCoordinates);CHKERRQ(ierr); 2334 ierr = VecDestroy(&subCoordinates);CHKERRQ(ierr); 2335 } 2336 /* Cleanup */ 2337 for (d = 0; d <= dim; ++d) { 2338 ierr = ISRestoreIndices(subpointIS[d], &subpoints[d]);CHKERRQ(ierr); 2339 ierr = ISDestroy(&subpointIS[d]);CHKERRQ(ierr); 2340 } 2341 ierr = PetscFree4(numSubPoints,firstSubPoint,subpointIS,subpoints);CHKERRQ(ierr); 2342 PetscFunctionReturn(0); 2343 } 2344 2345 #undef __FUNCT__ 2346 #define __FUNCT__ "DMPlexCreateCohesiveSubmesh" 2347 /* 2348 DMPlexCreateCohesiveSubmesh - Extract from a mesh with cohesive cells the hypersurface defined by one face of the cells. 2349 2350 Input Parameters: 2351 + dm - The original mesh 2352 - hasLagrange - The mesh has Lagrange unknowns in the cohesive cells 2353 2354 Output Parameter: 2355 . subdm - The surface mesh 2356 2357 Note: This function produces a DMLabel mapping original points in the submesh to their depth. This can be obtained using DMPlexGetSubpointMap(). 2358 2359 Level: developer 2360 2361 .seealso: DMPlexGetSubpointMap(), DMPlexCreateSubmesh() 2362 */ 2363 PetscErrorCode DMPlexCreateCohesiveSubmesh(DM dm, PetscBool hasLagrange, DM *subdm) 2364 { 2365 PetscInt dim, depth; 2366 PetscErrorCode ierr; 2367 2368 PetscFunctionBegin; 2369 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2370 PetscValidPointer(subdm, 3); 2371 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 2372 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 2373 ierr = DMCreate(PetscObjectComm((PetscObject)dm), subdm);CHKERRQ(ierr); 2374 ierr = DMSetType(*subdm, DMPLEX);CHKERRQ(ierr); 2375 ierr = DMPlexSetDimension(*subdm, dim-1);CHKERRQ(ierr); 2376 if (depth == dim) { 2377 ierr = DMPlexCreateCohesiveSubmesh_Interpolated(dm, hasLagrange, *subdm);CHKERRQ(ierr); 2378 } else { 2379 ierr = DMPlexCreateCohesiveSubmesh_Uninterpolated(dm, hasLagrange, *subdm);CHKERRQ(ierr); 2380 } 2381 PetscFunctionReturn(0); 2382 } 2383 2384 #undef __FUNCT__ 2385 #define __FUNCT__ "DMPlexGetSubpointMap" 2386 PetscErrorCode DMPlexGetSubpointMap(DM dm, DMLabel *subpointMap) 2387 { 2388 DM_Plex *mesh = (DM_Plex*) dm->data; 2389 2390 PetscFunctionBegin; 2391 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2392 PetscValidPointer(subpointMap, 2); 2393 *subpointMap = mesh->subpointMap; 2394 PetscFunctionReturn(0); 2395 } 2396 2397 #undef __FUNCT__ 2398 #define __FUNCT__ "DMPlexSetSubpointMap" 2399 /* Note: Should normally not be called by the user, since it is set in DMPlexCreateSubmesh() */ 2400 PetscErrorCode DMPlexSetSubpointMap(DM dm, DMLabel subpointMap) 2401 { 2402 DM_Plex *mesh = (DM_Plex *) dm->data; 2403 PetscErrorCode ierr; 2404 2405 PetscFunctionBegin; 2406 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2407 ierr = DMLabelDestroy(&mesh->subpointMap);CHKERRQ(ierr); 2408 mesh->subpointMap = subpointMap; 2409 ++mesh->subpointMap->refct;CHKERRQ(ierr); 2410 PetscFunctionReturn(0); 2411 } 2412 2413 #undef __FUNCT__ 2414 #define __FUNCT__ "DMPlexCreateSubpointIS" 2415 /* 2416 DMPlexCreateSubpointIS - Creates an IS covering the entire subdm chart with the original points as data 2417 2418 Input Parameter: 2419 . dm - The submesh DM 2420 2421 Output Parameter: 2422 . subpointIS - The IS of all the points from the original mesh in this submesh, or NULL if this is not a submesh 2423 2424 Note: This is IS is guaranteed to be sorted by the construction of the submesh 2425 */ 2426 PetscErrorCode DMPlexCreateSubpointIS(DM dm, IS *subpointIS) 2427 { 2428 MPI_Comm comm; 2429 DMLabel subpointMap; 2430 IS is; 2431 const PetscInt *opoints; 2432 PetscInt *points, *depths; 2433 PetscInt depth, depStart, depEnd, d, pStart, pEnd, p, n, off; 2434 PetscErrorCode ierr; 2435 2436 PetscFunctionBegin; 2437 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2438 PetscValidPointer(subpointIS, 2); 2439 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 2440 *subpointIS = NULL; 2441 ierr = DMPlexGetSubpointMap(dm, &subpointMap);CHKERRQ(ierr); 2442 if (subpointMap) { 2443 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 2444 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 2445 if (pStart) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Submeshes must start the point numbering at 0, not %d", pStart); 2446 ierr = DMGetWorkArray(dm, depth+1, PETSC_INT, &depths);CHKERRQ(ierr); 2447 depths[0] = depth; 2448 depths[1] = 0; 2449 for(d = 2; d <= depth; ++d) {depths[d] = depth+1 - d;} 2450 ierr = PetscMalloc(pEnd * sizeof(PetscInt), &points);CHKERRQ(ierr); 2451 for(d = 0, off = 0; d <= depth; ++d) { 2452 const PetscInt dep = depths[d]; 2453 2454 ierr = DMPlexGetDepthStratum(dm, dep, &depStart, &depEnd);CHKERRQ(ierr); 2455 ierr = DMLabelGetStratumSize(subpointMap, dep, &n);CHKERRQ(ierr); 2456 if (((d < 2) && (depth > 1)) || (d == 1)) { /* Only check vertices and cells for now since the map is broken for others */ 2457 if (n != depEnd-depStart) SETERRQ3(comm, PETSC_ERR_ARG_WRONG, "The number of mapped submesh points %d at depth %d should be %d", n, dep, depEnd-depStart); 2458 } else { 2459 if (!n) { 2460 if (d == 0) { 2461 /* Missing cells */ 2462 for(p = 0; p < depEnd-depStart; ++p, ++off) points[off] = -1; 2463 } else { 2464 /* Missing faces */ 2465 for(p = 0; p < depEnd-depStart; ++p, ++off) points[off] = PETSC_MAX_INT; 2466 } 2467 } 2468 } 2469 if (n) { 2470 ierr = DMLabelGetStratumIS(subpointMap, dep, &is);CHKERRQ(ierr); 2471 ierr = ISGetIndices(is, &opoints);CHKERRQ(ierr); 2472 for(p = 0; p < n; ++p, ++off) points[off] = opoints[p]; 2473 ierr = ISRestoreIndices(is, &opoints);CHKERRQ(ierr); 2474 ierr = ISDestroy(&is);CHKERRQ(ierr); 2475 } 2476 } 2477 ierr = DMRestoreWorkArray(dm, depth+1, PETSC_INT, &depths);CHKERRQ(ierr); 2478 if (off != pEnd) SETERRQ2(comm, PETSC_ERR_ARG_WRONG, "The number of mapped submesh points %d should be %d", off, pEnd); 2479 ierr = ISCreateGeneral(comm, pEnd, points, PETSC_OWN_POINTER, subpointIS);CHKERRQ(ierr); 2480 } 2481 PetscFunctionReturn(0); 2482 } 2483