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 const PetscInt *cells = NULL; 1155 PetscInt numCells, nc; 1156 1157 ++(*numFaces); 1158 for (cl = 0; cl < faceSize; ++cl) { 1159 ierr = DMLabelSetValue(subpointMap, closure[cl], 0);CHKERRQ(ierr); 1160 } 1161 ierr = DMPlexGetJoin(dm, faceSize, closure, &numCells, &cells);CHKERRQ(ierr); 1162 for (nc = 0; nc < numCells; ++nc) { 1163 ierr = DMLabelSetValue(subpointMap, cells[nc], 2);CHKERRQ(ierr); 1164 } 1165 ierr = DMPlexRestoreJoin(dm, faceSize, closure, &numCells, &cells);CHKERRQ(ierr); 1166 } 1167 ierr = DMPlexRestoreTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1168 } 1169 ierr = DMPlexRestoreTransitiveClosure(dm, vertex, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1170 } 1171 if (subvertexIS) { 1172 ierr = ISRestoreIndices(subvertexIS, &subvertices);CHKERRQ(ierr); 1173 } 1174 ierr = ISDestroy(&subvertexIS);CHKERRQ(ierr); 1175 ierr = PetscFree3(pStart,pEnd,pMax);CHKERRQ(ierr); 1176 PetscFunctionReturn(0); 1177 } 1178 1179 #undef __FUNCT__ 1180 #define __FUNCT__ "DMPlexMarkSubmesh_Interpolated" 1181 static PetscErrorCode DMPlexMarkSubmesh_Interpolated(DM dm, DMLabel vertexLabel, PetscInt value, DMLabel subpointMap, DM subdm) 1182 { 1183 IS subvertexIS; 1184 const PetscInt *subvertices; 1185 PetscInt *pStart, *pEnd, *pMax; 1186 PetscInt dim, d, numSubVerticesInitial = 0, v; 1187 PetscErrorCode ierr; 1188 1189 PetscFunctionBegin; 1190 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1191 ierr = PetscMalloc3(dim+1,PetscInt,&pStart,dim+1,PetscInt,&pEnd,dim+1,PetscInt,&pMax);CHKERRQ(ierr); 1192 ierr = DMPlexGetHybridBounds(dm, &pMax[dim], dim>1 ? &pMax[dim-1] : NULL, dim > 2 ? &pMax[1] : NULL, &pMax[0]);CHKERRQ(ierr); 1193 for (d = 0; d <= dim; ++d) { 1194 ierr = DMPlexGetDepthStratum(dm, d, &pStart[d], &pEnd[d]);CHKERRQ(ierr); 1195 if (pMax[d] >= 0) pEnd[d] = PetscMin(pEnd[d], pMax[d]); 1196 } 1197 /* Loop over initial vertices and mark all faces in the collective star() */ 1198 ierr = DMLabelGetStratumIS(vertexLabel, value, &subvertexIS);CHKERRQ(ierr); 1199 if (subvertexIS) { 1200 ierr = ISGetSize(subvertexIS, &numSubVerticesInitial);CHKERRQ(ierr); 1201 ierr = ISGetIndices(subvertexIS, &subvertices);CHKERRQ(ierr); 1202 } 1203 for (v = 0; v < numSubVerticesInitial; ++v) { 1204 const PetscInt vertex = subvertices[v]; 1205 PetscInt *star = NULL; 1206 PetscInt starSize, s, numFaces = 0, f; 1207 1208 ierr = DMPlexGetTransitiveClosure(dm, vertex, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1209 for (s = 0; s < starSize*2; s += 2) { 1210 const PetscInt point = star[s]; 1211 if ((point >= pStart[dim-1]) && (point < pEnd[dim-1])) star[numFaces++] = point; 1212 } 1213 for (f = 0; f < numFaces; ++f) { 1214 const PetscInt face = star[f]; 1215 PetscInt *closure = NULL; 1216 PetscInt closureSize, c; 1217 PetscInt faceLoc; 1218 1219 ierr = DMLabelGetValue(subpointMap, face, &faceLoc);CHKERRQ(ierr); 1220 if (faceLoc == dim-1) continue; 1221 if (faceLoc >= 0) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Face %d has dimension %d in the surface label", face, faceLoc); 1222 ierr = DMPlexGetTransitiveClosure(dm, face, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1223 for (c = 0; c < closureSize*2; c += 2) { 1224 const PetscInt point = closure[c]; 1225 PetscInt vertexLoc; 1226 1227 if ((point >= pStart[0]) && (point < pEnd[0])) { 1228 ierr = DMLabelGetValue(vertexLabel, point, &vertexLoc);CHKERRQ(ierr); 1229 if (vertexLoc != value) break; 1230 } 1231 } 1232 if (c == closureSize*2) { 1233 const PetscInt *support; 1234 PetscInt supportSize, s; 1235 1236 for (c = 0; c < closureSize*2; c += 2) { 1237 const PetscInt point = closure[c]; 1238 1239 for (d = 0; d < dim; ++d) { 1240 if ((point >= pStart[d]) && (point < pEnd[d])) { 1241 ierr = DMLabelSetValue(subpointMap, point, d);CHKERRQ(ierr); 1242 break; 1243 } 1244 } 1245 } 1246 ierr = DMPlexGetSupportSize(dm, face, &supportSize);CHKERRQ(ierr); 1247 ierr = DMPlexGetSupport(dm, face, &support);CHKERRQ(ierr); 1248 for (s = 0; s < supportSize; ++s) { 1249 ierr = DMLabelSetValue(subpointMap, support[s], dim);CHKERRQ(ierr); 1250 } 1251 } 1252 ierr = DMPlexRestoreTransitiveClosure(dm, face, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1253 } 1254 ierr = DMPlexRestoreTransitiveClosure(dm, vertex, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1255 } 1256 if (subvertexIS) { 1257 ierr = ISRestoreIndices(subvertexIS, &subvertices);CHKERRQ(ierr); 1258 } 1259 ierr = ISDestroy(&subvertexIS);CHKERRQ(ierr); 1260 ierr = PetscFree3(pStart,pEnd,pMax);CHKERRQ(ierr); 1261 PetscFunctionReturn(0); 1262 } 1263 1264 #undef __FUNCT__ 1265 #define __FUNCT__ "DMPlexMarkCohesiveSubmesh_Uninterpolated" 1266 static PetscErrorCode DMPlexMarkCohesiveSubmesh_Uninterpolated(DM dm, PetscBool hasLagrange, DMLabel subpointMap, PetscInt *numFaces, PetscInt *nFV, PetscInt *subCells[], DM subdm) 1267 { 1268 const PetscInt *cone; 1269 PetscInt dim, cMax, cEnd, c, p, coneSize; 1270 PetscErrorCode ierr; 1271 1272 PetscFunctionBegin; 1273 *numFaces = 0; 1274 *nFV = 0; 1275 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1276 ierr = DMPlexGetHeightStratum(dm, 0, NULL, &cEnd);CHKERRQ(ierr); 1277 ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); 1278 if (cMax < 0) PetscFunctionReturn(0); 1279 ierr = DMPlexGetConeSize(dm, cMax, &coneSize);CHKERRQ(ierr); 1280 *numFaces = cEnd - cMax; 1281 *nFV = hasLagrange ? coneSize/3 : coneSize/2; 1282 ierr = PetscMalloc(*numFaces *2 * sizeof(PetscInt), subCells);CHKERRQ(ierr); 1283 for (c = cMax; c < cEnd; ++c) { 1284 const PetscInt *cells; 1285 PetscInt numCells; 1286 1287 ierr = DMPlexGetCone(dm, c, &cone);CHKERRQ(ierr); 1288 for (p = 0; p < *nFV; ++p) { 1289 ierr = DMLabelSetValue(subpointMap, cone[p], 0);CHKERRQ(ierr); 1290 } 1291 /* Negative face */ 1292 ierr = DMPlexGetJoin(dm, *nFV, cone, &numCells, &cells);CHKERRQ(ierr); 1293 if (numCells != 2) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive cells should separate two cells"); 1294 for (p = 0; p < numCells; ++p) { 1295 ierr = DMLabelSetValue(subpointMap, cells[p], 2);CHKERRQ(ierr); 1296 (*subCells)[(c-cMax)*2+p] = cells[p]; 1297 } 1298 ierr = DMPlexRestoreJoin(dm, *nFV, cone, &numCells, &cells);CHKERRQ(ierr); 1299 /* Positive face is not included */ 1300 } 1301 PetscFunctionReturn(0); 1302 } 1303 1304 #undef __FUNCT__ 1305 #define __FUNCT__ "DMPlexMarkCohesiveSubmesh_Interpolated" 1306 static PetscErrorCode DMPlexMarkCohesiveSubmesh_Interpolated(DM dm, PetscBool hasLagrange, DMLabel subpointMap, DM subdm) 1307 { 1308 PetscInt *pStart, *pEnd; 1309 PetscInt dim, cMax, cEnd, c, d; 1310 PetscErrorCode ierr; 1311 1312 PetscFunctionBegin; 1313 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1314 ierr = DMPlexGetHeightStratum(dm, 0, NULL, &cEnd);CHKERRQ(ierr); 1315 ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); 1316 if (cMax < 0) PetscFunctionReturn(0); 1317 ierr = PetscMalloc2(dim+1,PetscInt,&pStart,dim+1,PetscInt,&pEnd);CHKERRQ(ierr); 1318 for (d = 0; d <= dim; ++d) { 1319 ierr = DMPlexGetDepthStratum(dm, d, &pStart[d], &pEnd[d]);CHKERRQ(ierr); 1320 } 1321 for (c = cMax; c < cEnd; ++c) { 1322 const PetscInt *cone; 1323 PetscInt *closure = NULL; 1324 PetscInt coneSize, closureSize, cl; 1325 1326 ierr = DMPlexGetConeSize(dm, c, &coneSize);CHKERRQ(ierr); 1327 if (hasLagrange) { 1328 if (coneSize != 3) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive cells should separate two cells"); 1329 } else { 1330 if (coneSize != 2) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive cells should separate two cells"); 1331 } 1332 /* Negative face */ 1333 ierr = DMPlexGetCone(dm, c, &cone);CHKERRQ(ierr); 1334 ierr = DMPlexGetTransitiveClosure(dm, cone[0], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1335 for (cl = 0; cl < closureSize*2; cl += 2) { 1336 const PetscInt point = closure[cl]; 1337 1338 for (d = 0; d <= dim; ++d) { 1339 if ((point >= pStart[d]) && (point < pEnd[d])) { 1340 ierr = DMLabelSetValue(subpointMap, point, d);CHKERRQ(ierr); 1341 break; 1342 } 1343 } 1344 } 1345 ierr = DMPlexRestoreTransitiveClosure(dm, cone[0], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1346 /* Cells -- positive face is not included */ 1347 for (cl = 0; cl < 1; ++cl) { 1348 const PetscInt *support; 1349 PetscInt supportSize, s; 1350 1351 ierr = DMPlexGetSupportSize(dm, cone[cl], &supportSize);CHKERRQ(ierr); 1352 if (supportSize != 2) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive faces should separate two cells"); 1353 ierr = DMPlexGetSupport(dm, cone[cl], &support);CHKERRQ(ierr); 1354 for (s = 0; s < supportSize; ++s) { 1355 ierr = DMLabelSetValue(subpointMap, support[s], dim);CHKERRQ(ierr); 1356 } 1357 } 1358 } 1359 ierr = PetscFree2(pStart, pEnd);CHKERRQ(ierr); 1360 PetscFunctionReturn(0); 1361 } 1362 1363 #undef __FUNCT__ 1364 #define __FUNCT__ "DMPlexGetFaceOrientation" 1365 PetscErrorCode DMPlexGetFaceOrientation(DM dm, PetscInt cell, PetscInt numCorners, PetscInt indices[], PetscInt oppositeVertex, PetscInt origVertices[], PetscInt faceVertices[], PetscBool *posOriented) 1366 { 1367 MPI_Comm comm; 1368 PetscBool posOrient = PETSC_FALSE; 1369 const PetscInt debug = 0; 1370 PetscInt cellDim, faceSize, f; 1371 PetscErrorCode ierr; 1372 1373 PetscFunctionBegin; 1374 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 1375 ierr = DMPlexGetDimension(dm, &cellDim);CHKERRQ(ierr); 1376 if (debug) {PetscPrintf(comm, "cellDim: %d numCorners: %d\n", cellDim, numCorners);CHKERRQ(ierr);} 1377 1378 if (cellDim == numCorners-1) { 1379 /* Simplices */ 1380 faceSize = numCorners-1; 1381 posOrient = !(oppositeVertex%2) ? PETSC_TRUE : PETSC_FALSE; 1382 } else if (cellDim == 1 && numCorners == 3) { 1383 /* Quadratic line */ 1384 faceSize = 1; 1385 posOrient = PETSC_TRUE; 1386 } else if (cellDim == 2 && numCorners == 4) { 1387 /* Quads */ 1388 faceSize = 2; 1389 if ((indices[1] > indices[0]) && (indices[1] - indices[0] == 1)) { 1390 posOrient = PETSC_TRUE; 1391 } else if ((indices[0] == 3) && (indices[1] == 0)) { 1392 posOrient = PETSC_TRUE; 1393 } else { 1394 if (((indices[0] > indices[1]) && (indices[0] - indices[1] == 1)) || ((indices[0] == 0) && (indices[1] == 3))) { 1395 posOrient = PETSC_FALSE; 1396 } else SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid quad crossedge"); 1397 } 1398 } else if (cellDim == 2 && numCorners == 6) { 1399 /* Quadratic triangle (I hate this) */ 1400 /* Edges are determined by the first 2 vertices (corners of edges) */ 1401 const PetscInt faceSizeTri = 3; 1402 PetscInt sortedIndices[3], i, iFace; 1403 PetscBool found = PETSC_FALSE; 1404 PetscInt faceVerticesTriSorted[9] = { 1405 0, 3, 4, /* bottom */ 1406 1, 4, 5, /* right */ 1407 2, 3, 5, /* left */ 1408 }; 1409 PetscInt faceVerticesTri[9] = { 1410 0, 3, 4, /* bottom */ 1411 1, 4, 5, /* right */ 1412 2, 5, 3, /* left */ 1413 }; 1414 1415 faceSize = faceSizeTri; 1416 for (i = 0; i < faceSizeTri; ++i) sortedIndices[i] = indices[i]; 1417 ierr = PetscSortInt(faceSizeTri, sortedIndices);CHKERRQ(ierr); 1418 for (iFace = 0; iFace < 3; ++iFace) { 1419 const PetscInt ii = iFace*faceSizeTri; 1420 PetscInt fVertex, cVertex; 1421 1422 if ((sortedIndices[0] == faceVerticesTriSorted[ii+0]) && 1423 (sortedIndices[1] == faceVerticesTriSorted[ii+1])) { 1424 for (fVertex = 0; fVertex < faceSizeTri; ++fVertex) { 1425 for (cVertex = 0; cVertex < faceSizeTri; ++cVertex) { 1426 if (indices[cVertex] == faceVerticesTri[ii+fVertex]) { 1427 faceVertices[fVertex] = origVertices[cVertex]; 1428 break; 1429 } 1430 } 1431 } 1432 found = PETSC_TRUE; 1433 break; 1434 } 1435 } 1436 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid tri crossface"); 1437 if (posOriented) *posOriented = PETSC_TRUE; 1438 PetscFunctionReturn(0); 1439 } else if (cellDim == 2 && numCorners == 9) { 1440 /* Quadratic quad (I hate this) */ 1441 /* Edges are determined by the first 2 vertices (corners of edges) */ 1442 const PetscInt faceSizeQuad = 3; 1443 PetscInt sortedIndices[3], i, iFace; 1444 PetscBool found = PETSC_FALSE; 1445 PetscInt faceVerticesQuadSorted[12] = { 1446 0, 1, 4, /* bottom */ 1447 1, 2, 5, /* right */ 1448 2, 3, 6, /* top */ 1449 0, 3, 7, /* left */ 1450 }; 1451 PetscInt faceVerticesQuad[12] = { 1452 0, 1, 4, /* bottom */ 1453 1, 2, 5, /* right */ 1454 2, 3, 6, /* top */ 1455 3, 0, 7, /* left */ 1456 }; 1457 1458 faceSize = faceSizeQuad; 1459 for (i = 0; i < faceSizeQuad; ++i) sortedIndices[i] = indices[i]; 1460 ierr = PetscSortInt(faceSizeQuad, sortedIndices);CHKERRQ(ierr); 1461 for (iFace = 0; iFace < 4; ++iFace) { 1462 const PetscInt ii = iFace*faceSizeQuad; 1463 PetscInt fVertex, cVertex; 1464 1465 if ((sortedIndices[0] == faceVerticesQuadSorted[ii+0]) && 1466 (sortedIndices[1] == faceVerticesQuadSorted[ii+1])) { 1467 for (fVertex = 0; fVertex < faceSizeQuad; ++fVertex) { 1468 for (cVertex = 0; cVertex < faceSizeQuad; ++cVertex) { 1469 if (indices[cVertex] == faceVerticesQuad[ii+fVertex]) { 1470 faceVertices[fVertex] = origVertices[cVertex]; 1471 break; 1472 } 1473 } 1474 } 1475 found = PETSC_TRUE; 1476 break; 1477 } 1478 } 1479 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid quad crossface"); 1480 if (posOriented) *posOriented = PETSC_TRUE; 1481 PetscFunctionReturn(0); 1482 } else if (cellDim == 3 && numCorners == 8) { 1483 /* Hexes 1484 A hex is two oriented quads with the normal of the first 1485 pointing up at the second. 1486 1487 7---6 1488 /| /| 1489 4---5 | 1490 | 3-|-2 1491 |/ |/ 1492 0---1 1493 1494 Faces are determined by the first 4 vertices (corners of faces) */ 1495 const PetscInt faceSizeHex = 4; 1496 PetscInt sortedIndices[4], i, iFace; 1497 PetscBool found = PETSC_FALSE; 1498 PetscInt faceVerticesHexSorted[24] = { 1499 0, 1, 2, 3, /* bottom */ 1500 4, 5, 6, 7, /* top */ 1501 0, 1, 4, 5, /* front */ 1502 1, 2, 5, 6, /* right */ 1503 2, 3, 6, 7, /* back */ 1504 0, 3, 4, 7, /* left */ 1505 }; 1506 PetscInt faceVerticesHex[24] = { 1507 3, 2, 1, 0, /* bottom */ 1508 4, 5, 6, 7, /* top */ 1509 0, 1, 5, 4, /* front */ 1510 1, 2, 6, 5, /* right */ 1511 2, 3, 7, 6, /* back */ 1512 3, 0, 4, 7, /* left */ 1513 }; 1514 1515 faceSize = faceSizeHex; 1516 for (i = 0; i < faceSizeHex; ++i) sortedIndices[i] = indices[i]; 1517 ierr = PetscSortInt(faceSizeHex, sortedIndices);CHKERRQ(ierr); 1518 for (iFace = 0; iFace < 6; ++iFace) { 1519 const PetscInt ii = iFace*faceSizeHex; 1520 PetscInt fVertex, cVertex; 1521 1522 if ((sortedIndices[0] == faceVerticesHexSorted[ii+0]) && 1523 (sortedIndices[1] == faceVerticesHexSorted[ii+1]) && 1524 (sortedIndices[2] == faceVerticesHexSorted[ii+2]) && 1525 (sortedIndices[3] == faceVerticesHexSorted[ii+3])) { 1526 for (fVertex = 0; fVertex < faceSizeHex; ++fVertex) { 1527 for (cVertex = 0; cVertex < faceSizeHex; ++cVertex) { 1528 if (indices[cVertex] == faceVerticesHex[ii+fVertex]) { 1529 faceVertices[fVertex] = origVertices[cVertex]; 1530 break; 1531 } 1532 } 1533 } 1534 found = PETSC_TRUE; 1535 break; 1536 } 1537 } 1538 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid hex crossface"); 1539 if (posOriented) *posOriented = PETSC_TRUE; 1540 PetscFunctionReturn(0); 1541 } else if (cellDim == 3 && numCorners == 10) { 1542 /* Quadratic tet */ 1543 /* Faces are determined by the first 3 vertices (corners of faces) */ 1544 const PetscInt faceSizeTet = 6; 1545 PetscInt sortedIndices[6], i, iFace; 1546 PetscBool found = PETSC_FALSE; 1547 PetscInt faceVerticesTetSorted[24] = { 1548 0, 1, 2, 6, 7, 8, /* bottom */ 1549 0, 3, 4, 6, 7, 9, /* front */ 1550 1, 4, 5, 7, 8, 9, /* right */ 1551 2, 3, 5, 6, 8, 9, /* left */ 1552 }; 1553 PetscInt faceVerticesTet[24] = { 1554 0, 1, 2, 6, 7, 8, /* bottom */ 1555 0, 4, 3, 6, 7, 9, /* front */ 1556 1, 5, 4, 7, 8, 9, /* right */ 1557 2, 3, 5, 8, 6, 9, /* left */ 1558 }; 1559 1560 faceSize = faceSizeTet; 1561 for (i = 0; i < faceSizeTet; ++i) sortedIndices[i] = indices[i]; 1562 ierr = PetscSortInt(faceSizeTet, sortedIndices);CHKERRQ(ierr); 1563 for (iFace=0; iFace < 4; ++iFace) { 1564 const PetscInt ii = iFace*faceSizeTet; 1565 PetscInt fVertex, cVertex; 1566 1567 if ((sortedIndices[0] == faceVerticesTetSorted[ii+0]) && 1568 (sortedIndices[1] == faceVerticesTetSorted[ii+1]) && 1569 (sortedIndices[2] == faceVerticesTetSorted[ii+2]) && 1570 (sortedIndices[3] == faceVerticesTetSorted[ii+3])) { 1571 for (fVertex = 0; fVertex < faceSizeTet; ++fVertex) { 1572 for (cVertex = 0; cVertex < faceSizeTet; ++cVertex) { 1573 if (indices[cVertex] == faceVerticesTet[ii+fVertex]) { 1574 faceVertices[fVertex] = origVertices[cVertex]; 1575 break; 1576 } 1577 } 1578 } 1579 found = PETSC_TRUE; 1580 break; 1581 } 1582 } 1583 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid tet crossface"); 1584 if (posOriented) *posOriented = PETSC_TRUE; 1585 PetscFunctionReturn(0); 1586 } else if (cellDim == 3 && numCorners == 27) { 1587 /* Quadratic hexes (I hate this) 1588 A hex is two oriented quads with the normal of the first 1589 pointing up at the second. 1590 1591 7---6 1592 /| /| 1593 4---5 | 1594 | 3-|-2 1595 |/ |/ 1596 0---1 1597 1598 Faces are determined by the first 4 vertices (corners of faces) */ 1599 const PetscInt faceSizeQuadHex = 9; 1600 PetscInt sortedIndices[9], i, iFace; 1601 PetscBool found = PETSC_FALSE; 1602 PetscInt faceVerticesQuadHexSorted[54] = { 1603 0, 1, 2, 3, 8, 9, 10, 11, 24, /* bottom */ 1604 4, 5, 6, 7, 12, 13, 14, 15, 25, /* top */ 1605 0, 1, 4, 5, 8, 12, 16, 17, 22, /* front */ 1606 1, 2, 5, 6, 9, 13, 17, 18, 21, /* right */ 1607 2, 3, 6, 7, 10, 14, 18, 19, 23, /* back */ 1608 0, 3, 4, 7, 11, 15, 16, 19, 20, /* left */ 1609 }; 1610 PetscInt faceVerticesQuadHex[54] = { 1611 3, 2, 1, 0, 10, 9, 8, 11, 24, /* bottom */ 1612 4, 5, 6, 7, 12, 13, 14, 15, 25, /* top */ 1613 0, 1, 5, 4, 8, 17, 12, 16, 22, /* front */ 1614 1, 2, 6, 5, 9, 18, 13, 17, 21, /* right */ 1615 2, 3, 7, 6, 10, 19, 14, 18, 23, /* back */ 1616 3, 0, 4, 7, 11, 16, 15, 19, 20 /* left */ 1617 }; 1618 1619 faceSize = faceSizeQuadHex; 1620 for (i = 0; i < faceSizeQuadHex; ++i) sortedIndices[i] = indices[i]; 1621 ierr = PetscSortInt(faceSizeQuadHex, sortedIndices);CHKERRQ(ierr); 1622 for (iFace = 0; iFace < 6; ++iFace) { 1623 const PetscInt ii = iFace*faceSizeQuadHex; 1624 PetscInt fVertex, cVertex; 1625 1626 if ((sortedIndices[0] == faceVerticesQuadHexSorted[ii+0]) && 1627 (sortedIndices[1] == faceVerticesQuadHexSorted[ii+1]) && 1628 (sortedIndices[2] == faceVerticesQuadHexSorted[ii+2]) && 1629 (sortedIndices[3] == faceVerticesQuadHexSorted[ii+3])) { 1630 for (fVertex = 0; fVertex < faceSizeQuadHex; ++fVertex) { 1631 for (cVertex = 0; cVertex < faceSizeQuadHex; ++cVertex) { 1632 if (indices[cVertex] == faceVerticesQuadHex[ii+fVertex]) { 1633 faceVertices[fVertex] = origVertices[cVertex]; 1634 break; 1635 } 1636 } 1637 } 1638 found = PETSC_TRUE; 1639 break; 1640 } 1641 } 1642 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid hex crossface"); 1643 if (posOriented) *posOriented = PETSC_TRUE; 1644 PetscFunctionReturn(0); 1645 } else SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Unknown cell type for faceOrientation()."); 1646 if (!posOrient) { 1647 if (debug) {ierr = PetscPrintf(comm, " Reversing initial face orientation\n");CHKERRQ(ierr);} 1648 for (f = 0; f < faceSize; ++f) faceVertices[f] = origVertices[faceSize-1 - f]; 1649 } else { 1650 if (debug) {ierr = PetscPrintf(comm, " Keeping initial face orientation\n");CHKERRQ(ierr);} 1651 for (f = 0; f < faceSize; ++f) faceVertices[f] = origVertices[f]; 1652 } 1653 if (posOriented) *posOriented = posOrient; 1654 PetscFunctionReturn(0); 1655 } 1656 1657 #undef __FUNCT__ 1658 #define __FUNCT__ "DMPlexGetOrientedFace" 1659 /* 1660 Given a cell and a face, as a set of vertices, 1661 return the oriented face, as a set of vertices, in faceVertices 1662 The orientation is such that the face normal points out of the cell 1663 */ 1664 PetscErrorCode DMPlexGetOrientedFace(DM dm, PetscInt cell, PetscInt faceSize, const PetscInt face[], PetscInt numCorners, PetscInt indices[], PetscInt origVertices[], PetscInt faceVertices[], PetscBool *posOriented) 1665 { 1666 const PetscInt *cone = NULL; 1667 PetscInt coneSize, v, f, v2; 1668 PetscInt oppositeVertex = -1; 1669 PetscErrorCode ierr; 1670 1671 PetscFunctionBegin; 1672 ierr = DMPlexGetConeSize(dm, cell, &coneSize);CHKERRQ(ierr); 1673 ierr = DMPlexGetCone(dm, cell, &cone);CHKERRQ(ierr); 1674 for (v = 0, v2 = 0; v < coneSize; ++v) { 1675 PetscBool found = PETSC_FALSE; 1676 1677 for (f = 0; f < faceSize; ++f) { 1678 if (face[f] == cone[v]) { 1679 found = PETSC_TRUE; break; 1680 } 1681 } 1682 if (found) { 1683 indices[v2] = v; 1684 origVertices[v2] = cone[v]; 1685 ++v2; 1686 } else { 1687 oppositeVertex = v; 1688 } 1689 } 1690 ierr = DMPlexGetFaceOrientation(dm, cell, numCorners, indices, oppositeVertex, origVertices, faceVertices, posOriented);CHKERRQ(ierr); 1691 PetscFunctionReturn(0); 1692 } 1693 1694 #undef __FUNCT__ 1695 #define __FUNCT__ "DMPlexInsertFace_Internal" 1696 /* 1697 DMPlexInsertFace_Internal - Puts a face into the mesh 1698 1699 Not collective 1700 1701 Input Parameters: 1702 + dm - The DMPlex 1703 . numFaceVertex - The number of vertices in the face 1704 . faceVertices - The vertices in the face for dm 1705 . subfaceVertices - The vertices in the face for subdm 1706 . numCorners - The number of vertices in the cell 1707 . cell - A cell in dm containing the face 1708 . subcell - A cell in subdm containing the face 1709 . firstFace - First face in the mesh 1710 - newFacePoint - Next face in the mesh 1711 1712 Output Parameters: 1713 . newFacePoint - Contains next face point number on input, updated on output 1714 1715 Level: developer 1716 */ 1717 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) 1718 { 1719 MPI_Comm comm; 1720 DM_Plex *submesh = (DM_Plex*) subdm->data; 1721 const PetscInt *faces; 1722 PetscInt numFaces, coneSize; 1723 PetscErrorCode ierr; 1724 1725 PetscFunctionBegin; 1726 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 1727 ierr = DMPlexGetConeSize(subdm, subcell, &coneSize);CHKERRQ(ierr); 1728 if (coneSize != 1) SETERRQ2(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cone size of cell %d is %d != 1", cell, coneSize); 1729 #if 0 1730 /* Cannot use this because support() has not been constructed yet */ 1731 ierr = DMPlexGetJoin(subdm, numFaceVertices, subfaceVertices, &numFaces, &faces);CHKERRQ(ierr); 1732 #else 1733 { 1734 PetscInt f; 1735 1736 numFaces = 0; 1737 ierr = DMGetWorkArray(subdm, 1, PETSC_INT, (void**) &faces);CHKERRQ(ierr); 1738 for (f = firstFace; f < *newFacePoint; ++f) { 1739 PetscInt dof, off, d; 1740 1741 ierr = PetscSectionGetDof(submesh->coneSection, f, &dof);CHKERRQ(ierr); 1742 ierr = PetscSectionGetOffset(submesh->coneSection, f, &off);CHKERRQ(ierr); 1743 /* Yes, I know this is quadratic, but I expect the sizes to be <5 */ 1744 for (d = 0; d < dof; ++d) { 1745 const PetscInt p = submesh->cones[off+d]; 1746 PetscInt v; 1747 1748 for (v = 0; v < numFaceVertices; ++v) { 1749 if (subfaceVertices[v] == p) break; 1750 } 1751 if (v == numFaceVertices) break; 1752 } 1753 if (d == dof) { 1754 numFaces = 1; 1755 ((PetscInt*) faces)[0] = f; 1756 } 1757 } 1758 } 1759 #endif 1760 if (numFaces > 1) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Vertex set had %d faces, not one", numFaces); 1761 else if (numFaces == 1) { 1762 /* Add the other cell neighbor for this face */ 1763 ierr = DMPlexSetCone(subdm, subcell, faces);CHKERRQ(ierr); 1764 } else { 1765 PetscInt *indices, *origVertices, *orientedVertices, *orientedSubVertices, v, ov; 1766 PetscBool posOriented; 1767 1768 ierr = DMGetWorkArray(subdm, 4*numFaceVertices * sizeof(PetscInt), PETSC_INT, &orientedVertices);CHKERRQ(ierr); 1769 origVertices = &orientedVertices[numFaceVertices]; 1770 indices = &orientedVertices[numFaceVertices*2]; 1771 orientedSubVertices = &orientedVertices[numFaceVertices*3]; 1772 ierr = DMPlexGetOrientedFace(dm, cell, numFaceVertices, faceVertices, numCorners, indices, origVertices, orientedVertices, &posOriented);CHKERRQ(ierr); 1773 /* TODO: I know that routine should return a permutation, not the indices */ 1774 for (v = 0; v < numFaceVertices; ++v) { 1775 const PetscInt vertex = faceVertices[v], subvertex = subfaceVertices[v]; 1776 for (ov = 0; ov < numFaceVertices; ++ov) { 1777 if (orientedVertices[ov] == vertex) { 1778 orientedSubVertices[ov] = subvertex; 1779 break; 1780 } 1781 } 1782 if (ov == numFaceVertices) SETERRQ1(comm, PETSC_ERR_PLIB, "Could not find face vertex %d in orientated set", vertex); 1783 } 1784 ierr = DMPlexSetCone(subdm, *newFacePoint, orientedSubVertices);CHKERRQ(ierr); 1785 ierr = DMPlexSetCone(subdm, subcell, newFacePoint);CHKERRQ(ierr); 1786 ierr = DMRestoreWorkArray(subdm, 4*numFaceVertices * sizeof(PetscInt), PETSC_INT, &orientedVertices);CHKERRQ(ierr); 1787 ++(*newFacePoint); 1788 } 1789 ierr = DMPlexRestoreJoin(subdm, numFaceVertices, subfaceVertices, &numFaces, &faces);CHKERRQ(ierr); 1790 PetscFunctionReturn(0); 1791 } 1792 1793 #undef __FUNCT__ 1794 #define __FUNCT__ "DMPlexCreateSubmesh_Uninterpolated" 1795 static PetscErrorCode DMPlexCreateSubmesh_Uninterpolated(DM dm, const char vertexLabelName[], PetscInt value, DM subdm) 1796 { 1797 MPI_Comm comm; 1798 DMLabel vertexLabel, subpointMap; 1799 IS subvertexIS, subcellIS; 1800 const PetscInt *subVertices, *subCells; 1801 PetscInt numSubVertices, firstSubVertex, numSubCells; 1802 PetscInt *subface, maxConeSize, numSubFaces, firstSubFace, newFacePoint, nFV; 1803 PetscInt vStart, vEnd, c, f; 1804 PetscErrorCode ierr; 1805 1806 PetscFunctionBegin; 1807 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 1808 /* Create subpointMap which marks the submesh */ 1809 ierr = DMLabelCreate("subpoint_map", &subpointMap);CHKERRQ(ierr); 1810 ierr = DMPlexSetSubpointMap(subdm, subpointMap);CHKERRQ(ierr); 1811 ierr = DMLabelDestroy(&subpointMap);CHKERRQ(ierr); 1812 ierr = DMPlexGetLabel(dm, vertexLabelName, &vertexLabel);CHKERRQ(ierr); 1813 ierr = DMPlexMarkSubmesh_Uninterpolated(dm, vertexLabel, value, subpointMap, &numSubFaces, &nFV, subdm);CHKERRQ(ierr); 1814 /* Setup chart */ 1815 ierr = DMLabelGetStratumSize(subpointMap, 0, &numSubVertices);CHKERRQ(ierr); 1816 ierr = DMLabelGetStratumSize(subpointMap, 2, &numSubCells);CHKERRQ(ierr); 1817 ierr = DMPlexSetChart(subdm, 0, numSubCells+numSubFaces+numSubVertices);CHKERRQ(ierr); 1818 ierr = DMPlexSetVTKCellHeight(subdm, 1);CHKERRQ(ierr); 1819 /* Set cone sizes */ 1820 firstSubVertex = numSubCells; 1821 firstSubFace = numSubCells+numSubVertices; 1822 newFacePoint = firstSubFace; 1823 ierr = DMLabelGetStratumIS(subpointMap, 0, &subvertexIS);CHKERRQ(ierr); 1824 if (subvertexIS) {ierr = ISGetIndices(subvertexIS, &subVertices);CHKERRQ(ierr);} 1825 ierr = DMLabelGetStratumIS(subpointMap, 2, &subcellIS);CHKERRQ(ierr); 1826 if (subcellIS) {ierr = ISGetIndices(subcellIS, &subCells);CHKERRQ(ierr);} 1827 for (c = 0; c < numSubCells; ++c) { 1828 ierr = DMPlexSetConeSize(subdm, c, 1);CHKERRQ(ierr); 1829 } 1830 for (f = firstSubFace; f < firstSubFace+numSubFaces; ++f) { 1831 ierr = DMPlexSetConeSize(subdm, f, nFV);CHKERRQ(ierr); 1832 } 1833 ierr = DMSetUp(subdm);CHKERRQ(ierr); 1834 /* Create face cones */ 1835 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 1836 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, NULL);CHKERRQ(ierr); 1837 ierr = DMGetWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);CHKERRQ(ierr); 1838 for (c = 0; c < numSubCells; ++c) { 1839 const PetscInt cell = subCells[c]; 1840 const PetscInt subcell = c; 1841 PetscInt *closure = NULL; 1842 PetscInt closureSize, cl, numCorners = 0, faceSize = 0; 1843 1844 ierr = DMPlexGetTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1845 for (cl = 0; cl < closureSize*2; cl += 2) { 1846 const PetscInt point = closure[cl]; 1847 PetscInt subVertex; 1848 1849 if ((point >= vStart) && (point < vEnd)) { 1850 ++numCorners; 1851 ierr = PetscFindInt(point, numSubVertices, subVertices, &subVertex);CHKERRQ(ierr); 1852 if (subVertex >= 0) { 1853 closure[faceSize] = point; 1854 subface[faceSize] = firstSubVertex+subVertex; 1855 ++faceSize; 1856 } 1857 } 1858 } 1859 if (faceSize > nFV) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Invalid submesh: Too many vertices %d of an element on the surface", faceSize); 1860 if (faceSize == nFV) { 1861 ierr = DMPlexInsertFace_Internal(dm, subdm, faceSize, closure, subface, numCorners, cell, subcell, firstSubFace, &newFacePoint);CHKERRQ(ierr); 1862 } 1863 ierr = DMPlexRestoreTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1864 } 1865 ierr = DMRestoreWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);CHKERRQ(ierr); 1866 ierr = DMPlexSymmetrize(subdm);CHKERRQ(ierr); 1867 ierr = DMPlexStratify(subdm);CHKERRQ(ierr); 1868 /* Build coordinates */ 1869 { 1870 PetscSection coordSection, subCoordSection; 1871 Vec coordinates, subCoordinates; 1872 PetscScalar *coords, *subCoords; 1873 PetscInt numComp, coordSize, v; 1874 1875 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1876 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 1877 ierr = DMPlexGetCoordinateSection(subdm, &subCoordSection);CHKERRQ(ierr); 1878 ierr = PetscSectionSetNumFields(subCoordSection, 1);CHKERRQ(ierr); 1879 ierr = PetscSectionGetFieldComponents(coordSection, 0, &numComp);CHKERRQ(ierr); 1880 ierr = PetscSectionSetFieldComponents(subCoordSection, 0, numComp);CHKERRQ(ierr); 1881 ierr = PetscSectionSetChart(subCoordSection, firstSubVertex, firstSubVertex+numSubVertices);CHKERRQ(ierr); 1882 for (v = 0; v < numSubVertices; ++v) { 1883 const PetscInt vertex = subVertices[v]; 1884 const PetscInt subvertex = firstSubVertex+v; 1885 PetscInt dof; 1886 1887 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 1888 ierr = PetscSectionSetDof(subCoordSection, subvertex, dof);CHKERRQ(ierr); 1889 ierr = PetscSectionSetFieldDof(subCoordSection, subvertex, 0, dof);CHKERRQ(ierr); 1890 } 1891 ierr = PetscSectionSetUp(subCoordSection);CHKERRQ(ierr); 1892 ierr = PetscSectionGetStorageSize(subCoordSection, &coordSize);CHKERRQ(ierr); 1893 ierr = VecCreate(comm, &subCoordinates);CHKERRQ(ierr); 1894 ierr = VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1895 ierr = VecSetFromOptions(subCoordinates);CHKERRQ(ierr); 1896 if (coordSize) { 1897 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1898 ierr = VecGetArray(subCoordinates, &subCoords);CHKERRQ(ierr); 1899 for (v = 0; v < numSubVertices; ++v) { 1900 const PetscInt vertex = subVertices[v]; 1901 const PetscInt subvertex = firstSubVertex+v; 1902 PetscInt dof, off, sdof, soff, d; 1903 1904 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 1905 ierr = PetscSectionGetOffset(coordSection, vertex, &off);CHKERRQ(ierr); 1906 ierr = PetscSectionGetDof(subCoordSection, subvertex, &sdof);CHKERRQ(ierr); 1907 ierr = PetscSectionGetOffset(subCoordSection, subvertex, &soff);CHKERRQ(ierr); 1908 if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof); 1909 for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d]; 1910 } 1911 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1912 ierr = VecRestoreArray(subCoordinates, &subCoords);CHKERRQ(ierr); 1913 } 1914 ierr = DMSetCoordinatesLocal(subdm, subCoordinates);CHKERRQ(ierr); 1915 ierr = VecDestroy(&subCoordinates);CHKERRQ(ierr); 1916 } 1917 /* Cleanup */ 1918 if (subvertexIS) {ierr = ISRestoreIndices(subvertexIS, &subVertices);CHKERRQ(ierr);} 1919 ierr = ISDestroy(&subvertexIS);CHKERRQ(ierr); 1920 if (subcellIS) {ierr = ISRestoreIndices(subcellIS, &subCells);CHKERRQ(ierr);} 1921 ierr = ISDestroy(&subcellIS);CHKERRQ(ierr); 1922 PetscFunctionReturn(0); 1923 } 1924 1925 #undef __FUNCT__ 1926 #define __FUNCT__ "DMPlexCreateSubmesh_Interpolated" 1927 static PetscErrorCode DMPlexCreateSubmesh_Interpolated(DM dm, const char vertexLabelName[], PetscInt value, DM subdm) 1928 { 1929 MPI_Comm comm; 1930 DMLabel subpointMap, vertexLabel; 1931 IS *subpointIS; 1932 const PetscInt **subpoints; 1933 PetscInt *numSubPoints, *firstSubPoint, *coneNew; 1934 PetscInt totSubPoints = 0, maxConeSize, dim, p, d, v; 1935 PetscErrorCode ierr; 1936 1937 PetscFunctionBegin; 1938 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 1939 /* Create subpointMap which marks the submesh */ 1940 ierr = DMLabelCreate("subpoint_map", &subpointMap);CHKERRQ(ierr); 1941 ierr = DMPlexSetSubpointMap(subdm, subpointMap);CHKERRQ(ierr); 1942 ierr = DMLabelDestroy(&subpointMap);CHKERRQ(ierr); 1943 ierr = DMPlexGetLabel(dm, vertexLabelName, &vertexLabel);CHKERRQ(ierr); 1944 ierr = DMPlexMarkSubmesh_Interpolated(dm, vertexLabel, value, subpointMap, subdm);CHKERRQ(ierr); 1945 /* Setup chart */ 1946 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1947 ierr = PetscMalloc4(dim+1,PetscInt,&numSubPoints,dim+1,PetscInt,&firstSubPoint,dim+1,IS,&subpointIS,dim+1,const PetscInt *,&subpoints);CHKERRQ(ierr); 1948 for (d = 0; d <= dim; ++d) { 1949 ierr = DMLabelGetStratumSize(subpointMap, d, &numSubPoints[d]);CHKERRQ(ierr); 1950 totSubPoints += numSubPoints[d]; 1951 } 1952 ierr = DMPlexSetChart(subdm, 0, totSubPoints);CHKERRQ(ierr); 1953 ierr = DMPlexSetVTKCellHeight(subdm, 1);CHKERRQ(ierr); 1954 /* Set cone sizes */ 1955 firstSubPoint[dim] = 0; 1956 firstSubPoint[0] = firstSubPoint[dim] + numSubPoints[dim]; 1957 if (dim > 1) {firstSubPoint[dim-1] = firstSubPoint[0] + numSubPoints[0];} 1958 if (dim > 2) {firstSubPoint[dim-2] = firstSubPoint[dim-1] + numSubPoints[dim-1];} 1959 for (d = 0; d <= dim; ++d) { 1960 ierr = DMLabelGetStratumIS(subpointMap, d, &subpointIS[d]);CHKERRQ(ierr); 1961 ierr = ISGetIndices(subpointIS[d], &subpoints[d]);CHKERRQ(ierr); 1962 } 1963 for (d = 0; d <= dim; ++d) { 1964 for (p = 0; p < numSubPoints[d]; ++p) { 1965 const PetscInt point = subpoints[d][p]; 1966 const PetscInt subpoint = firstSubPoint[d] + p; 1967 const PetscInt *cone; 1968 PetscInt coneSize, coneSizeNew, c, val; 1969 1970 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 1971 ierr = DMPlexSetConeSize(subdm, subpoint, coneSize);CHKERRQ(ierr); 1972 if (d == dim) { 1973 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 1974 for (c = 0, coneSizeNew = 0; c < coneSize; ++c) { 1975 ierr = DMLabelGetValue(subpointMap, cone[c], &val);CHKERRQ(ierr); 1976 if (val >= 0) coneSizeNew++; 1977 } 1978 ierr = DMPlexSetConeSize(subdm, subpoint, coneSizeNew);CHKERRQ(ierr); 1979 } 1980 } 1981 } 1982 ierr = DMSetUp(subdm);CHKERRQ(ierr); 1983 /* Set cones */ 1984 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, NULL);CHKERRQ(ierr); 1985 ierr = PetscMalloc(maxConeSize * sizeof(PetscInt), &coneNew);CHKERRQ(ierr); 1986 for (d = 0; d <= dim; ++d) { 1987 for (p = 0; p < numSubPoints[d]; ++p) { 1988 const PetscInt point = subpoints[d][p]; 1989 const PetscInt subpoint = firstSubPoint[d] + p; 1990 const PetscInt *cone; 1991 PetscInt coneSize, subconeSize, coneSizeNew, c, subc; 1992 1993 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 1994 ierr = DMPlexGetConeSize(subdm, subpoint, &subconeSize);CHKERRQ(ierr); 1995 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 1996 for (c = 0, coneSizeNew = 0; c < coneSize; ++c) { 1997 ierr = PetscFindInt(cone[c], numSubPoints[d-1], subpoints[d-1], &subc);CHKERRQ(ierr); 1998 if (subc >= 0) coneNew[coneSizeNew++] = firstSubPoint[d-1] + subc; 1999 } 2000 if (coneSizeNew != subconeSize) SETERRQ2(comm, PETSC_ERR_PLIB, "Number of cone points located %d does not match subcone size %d", coneSizeNew, subconeSize); 2001 ierr = DMPlexSetCone(subdm, subpoint, coneNew);CHKERRQ(ierr); 2002 } 2003 } 2004 ierr = PetscFree(coneNew);CHKERRQ(ierr); 2005 ierr = DMPlexSymmetrize(subdm);CHKERRQ(ierr); 2006 ierr = DMPlexStratify(subdm);CHKERRQ(ierr); 2007 /* Build coordinates */ 2008 { 2009 PetscSection coordSection, subCoordSection; 2010 Vec coordinates, subCoordinates; 2011 PetscScalar *coords, *subCoords; 2012 PetscInt numComp, coordSize; 2013 2014 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2015 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 2016 ierr = DMPlexGetCoordinateSection(subdm, &subCoordSection);CHKERRQ(ierr); 2017 ierr = PetscSectionSetNumFields(subCoordSection, 1);CHKERRQ(ierr); 2018 ierr = PetscSectionGetFieldComponents(coordSection, 0, &numComp);CHKERRQ(ierr); 2019 ierr = PetscSectionSetFieldComponents(subCoordSection, 0, numComp);CHKERRQ(ierr); 2020 ierr = PetscSectionSetChart(subCoordSection, firstSubPoint[0], firstSubPoint[0]+numSubPoints[0]);CHKERRQ(ierr); 2021 for (v = 0; v < numSubPoints[0]; ++v) { 2022 const PetscInt vertex = subpoints[0][v]; 2023 const PetscInt subvertex = firstSubPoint[0]+v; 2024 PetscInt dof; 2025 2026 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2027 ierr = PetscSectionSetDof(subCoordSection, subvertex, dof);CHKERRQ(ierr); 2028 ierr = PetscSectionSetFieldDof(subCoordSection, subvertex, 0, dof);CHKERRQ(ierr); 2029 } 2030 ierr = PetscSectionSetUp(subCoordSection);CHKERRQ(ierr); 2031 ierr = PetscSectionGetStorageSize(subCoordSection, &coordSize);CHKERRQ(ierr); 2032 ierr = VecCreate(comm, &subCoordinates);CHKERRQ(ierr); 2033 ierr = VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2034 ierr = VecSetFromOptions(subCoordinates);CHKERRQ(ierr); 2035 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2036 ierr = VecGetArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2037 for (v = 0; v < numSubPoints[0]; ++v) { 2038 const PetscInt vertex = subpoints[0][v]; 2039 const PetscInt subvertex = firstSubPoint[0]+v; 2040 PetscInt dof, off, sdof, soff, d; 2041 2042 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2043 ierr = PetscSectionGetOffset(coordSection, vertex, &off);CHKERRQ(ierr); 2044 ierr = PetscSectionGetDof(subCoordSection, subvertex, &sdof);CHKERRQ(ierr); 2045 ierr = PetscSectionGetOffset(subCoordSection, subvertex, &soff);CHKERRQ(ierr); 2046 if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof); 2047 for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d]; 2048 } 2049 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2050 ierr = VecRestoreArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2051 ierr = DMSetCoordinatesLocal(subdm, subCoordinates);CHKERRQ(ierr); 2052 ierr = VecDestroy(&subCoordinates);CHKERRQ(ierr); 2053 } 2054 /* Cleanup */ 2055 for (d = 0; d <= dim; ++d) { 2056 ierr = ISRestoreIndices(subpointIS[d], &subpoints[d]);CHKERRQ(ierr); 2057 ierr = ISDestroy(&subpointIS[d]);CHKERRQ(ierr); 2058 } 2059 ierr = PetscFree4(numSubPoints,firstSubPoint,subpointIS,subpoints);CHKERRQ(ierr); 2060 PetscFunctionReturn(0); 2061 } 2062 2063 #undef __FUNCT__ 2064 #define __FUNCT__ "DMPlexCreateSubmesh" 2065 /*@C 2066 DMPlexCreateSubmesh - Extract a hypersurface from the mesh using vertices defined by a label 2067 2068 Input Parameters: 2069 + dm - The original mesh 2070 . vertexLabel - The DMLabel marking vertices contained in the surface 2071 - value - The label value to use 2072 2073 Output Parameter: 2074 . subdm - The surface mesh 2075 2076 Note: This function produces a DMLabel mapping original points in the submesh to their depth. This can be obtained using DMPlexGetSubpointMap(). 2077 2078 Level: developer 2079 2080 .seealso: DMPlexGetSubpointMap(), DMPlexGetLabel(), DMLabelSetValue() 2081 @*/ 2082 PetscErrorCode DMPlexCreateSubmesh(DM dm, const char vertexLabel[], PetscInt value, DM *subdm) 2083 { 2084 PetscInt dim, depth; 2085 PetscErrorCode ierr; 2086 2087 PetscFunctionBegin; 2088 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2089 PetscValidCharPointer(vertexLabel, 2); 2090 PetscValidPointer(subdm, 3); 2091 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 2092 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 2093 ierr = DMCreate(PetscObjectComm((PetscObject)dm), subdm);CHKERRQ(ierr); 2094 ierr = DMSetType(*subdm, DMPLEX);CHKERRQ(ierr); 2095 ierr = DMPlexSetDimension(*subdm, dim-1);CHKERRQ(ierr); 2096 if (depth == dim) { 2097 ierr = DMPlexCreateSubmesh_Interpolated(dm, vertexLabel, value, *subdm);CHKERRQ(ierr); 2098 } else { 2099 ierr = DMPlexCreateSubmesh_Uninterpolated(dm, vertexLabel, value, *subdm);CHKERRQ(ierr); 2100 } 2101 PetscFunctionReturn(0); 2102 } 2103 2104 #undef __FUNCT__ 2105 #define __FUNCT__ "DMPlexCreateCohesiveSubmesh_Uninterpolated" 2106 static PetscErrorCode DMPlexCreateCohesiveSubmesh_Uninterpolated(DM dm, PetscBool hasLagrange, DM subdm) 2107 { 2108 MPI_Comm comm; 2109 DMLabel subpointMap; 2110 IS subvertexIS; 2111 const PetscInt *subVertices; 2112 PetscInt numSubVertices, firstSubVertex, numSubCells, *subCells; 2113 PetscInt *subface, maxConeSize, numSubFaces, firstSubFace, newFacePoint, nFV; 2114 PetscInt cMax, c, f; 2115 PetscErrorCode ierr; 2116 2117 PetscFunctionBegin; 2118 ierr = PetscObjectGetComm((PetscObject)dm, &comm);CHKERRQ(ierr); 2119 /* Create subpointMap which marks the submesh */ 2120 ierr = DMLabelCreate("subpoint_map", &subpointMap);CHKERRQ(ierr); 2121 ierr = DMPlexSetSubpointMap(subdm, subpointMap);CHKERRQ(ierr); 2122 ierr = DMLabelDestroy(&subpointMap);CHKERRQ(ierr); 2123 ierr = DMPlexMarkCohesiveSubmesh_Uninterpolated(dm, hasLagrange, subpointMap, &numSubFaces, &nFV, &subCells, subdm);CHKERRQ(ierr); 2124 /* Setup chart */ 2125 ierr = DMLabelGetStratumSize(subpointMap, 0, &numSubVertices);CHKERRQ(ierr); 2126 ierr = DMLabelGetStratumSize(subpointMap, 2, &numSubCells);CHKERRQ(ierr); 2127 ierr = DMPlexSetChart(subdm, 0, numSubCells+numSubFaces+numSubVertices);CHKERRQ(ierr); 2128 ierr = DMPlexSetVTKCellHeight(subdm, 1);CHKERRQ(ierr); 2129 /* Set cone sizes */ 2130 firstSubVertex = numSubCells; 2131 firstSubFace = numSubCells+numSubVertices; 2132 newFacePoint = firstSubFace; 2133 ierr = DMLabelGetStratumIS(subpointMap, 0, &subvertexIS);CHKERRQ(ierr); 2134 if (subvertexIS) {ierr = ISGetIndices(subvertexIS, &subVertices);CHKERRQ(ierr);} 2135 for (c = 0; c < numSubCells; ++c) { 2136 ierr = DMPlexSetConeSize(subdm, c, 1);CHKERRQ(ierr); 2137 } 2138 for (f = firstSubFace; f < firstSubFace+numSubFaces; ++f) { 2139 ierr = DMPlexSetConeSize(subdm, f, nFV);CHKERRQ(ierr); 2140 } 2141 ierr = DMSetUp(subdm);CHKERRQ(ierr); 2142 /* Create face cones */ 2143 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, NULL);CHKERRQ(ierr); 2144 ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); 2145 ierr = DMGetWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);CHKERRQ(ierr); 2146 for (c = 0; c < numSubCells; ++c) { 2147 const PetscInt cell = subCells[c]; 2148 const PetscInt subcell = c; 2149 const PetscInt *cone, *cells; 2150 PetscInt numCells, subVertex, p, v; 2151 2152 if (cell < cMax) continue; 2153 ierr = DMPlexGetCone(dm, cell, &cone);CHKERRQ(ierr); 2154 for (v = 0; v < nFV; ++v) { 2155 ierr = PetscFindInt(cone[v], numSubVertices, subVertices, &subVertex);CHKERRQ(ierr); 2156 subface[v] = firstSubVertex+subVertex; 2157 } 2158 ierr = DMPlexSetCone(subdm, newFacePoint, subface);CHKERRQ(ierr); 2159 ierr = DMPlexSetCone(subdm, subcell, &newFacePoint);CHKERRQ(ierr); 2160 ierr = DMPlexGetJoin(dm, nFV, cone, &numCells, &cells);CHKERRQ(ierr); 2161 if (numCells != 2) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive cells should separate two cells"); 2162 for (p = 0; p < numCells; ++p) { 2163 PetscInt negsubcell; 2164 2165 if (cells[p] >= cMax) continue; 2166 /* I know this is a crap search */ 2167 for (negsubcell = 0; negsubcell < numSubCells; ++negsubcell) { 2168 if (subCells[negsubcell] == cells[p]) break; 2169 } 2170 if (negsubcell == numSubCells) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not find negative face neighbor for cohesive cell %d", cell); 2171 ierr = DMPlexSetCone(subdm, negsubcell, &newFacePoint);CHKERRQ(ierr); 2172 } 2173 ierr = DMPlexRestoreJoin(dm, nFV, cone, &numCells, &cells);CHKERRQ(ierr); 2174 ++newFacePoint; 2175 } 2176 ierr = DMRestoreWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);CHKERRQ(ierr); 2177 ierr = DMPlexSymmetrize(subdm);CHKERRQ(ierr); 2178 ierr = DMPlexStratify(subdm);CHKERRQ(ierr); 2179 /* Build coordinates */ 2180 { 2181 PetscSection coordSection, subCoordSection; 2182 Vec coordinates, subCoordinates; 2183 PetscScalar *coords, *subCoords; 2184 PetscInt numComp, coordSize, v; 2185 2186 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2187 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 2188 ierr = DMPlexGetCoordinateSection(subdm, &subCoordSection);CHKERRQ(ierr); 2189 ierr = PetscSectionSetNumFields(subCoordSection, 1);CHKERRQ(ierr); 2190 ierr = PetscSectionGetFieldComponents(coordSection, 0, &numComp);CHKERRQ(ierr); 2191 ierr = PetscSectionSetFieldComponents(subCoordSection, 0, numComp);CHKERRQ(ierr); 2192 ierr = PetscSectionSetChart(subCoordSection, firstSubVertex, firstSubVertex+numSubVertices);CHKERRQ(ierr); 2193 for (v = 0; v < numSubVertices; ++v) { 2194 const PetscInt vertex = subVertices[v]; 2195 const PetscInt subvertex = firstSubVertex+v; 2196 PetscInt dof; 2197 2198 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2199 ierr = PetscSectionSetDof(subCoordSection, subvertex, dof);CHKERRQ(ierr); 2200 ierr = PetscSectionSetFieldDof(subCoordSection, subvertex, 0, dof);CHKERRQ(ierr); 2201 } 2202 ierr = PetscSectionSetUp(subCoordSection);CHKERRQ(ierr); 2203 ierr = PetscSectionGetStorageSize(subCoordSection, &coordSize);CHKERRQ(ierr); 2204 ierr = VecCreate(comm, &subCoordinates);CHKERRQ(ierr); 2205 if (coordSize) { 2206 ierr = VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2207 ierr = VecSetFromOptions(subCoordinates);CHKERRQ(ierr); 2208 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2209 ierr = VecGetArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2210 for (v = 0; v < numSubVertices; ++v) { 2211 const PetscInt vertex = subVertices[v]; 2212 const PetscInt subvertex = firstSubVertex+v; 2213 PetscInt dof, off, sdof, soff, d; 2214 2215 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2216 ierr = PetscSectionGetOffset(coordSection, vertex, &off);CHKERRQ(ierr); 2217 ierr = PetscSectionGetDof(subCoordSection, subvertex, &sdof);CHKERRQ(ierr); 2218 ierr = PetscSectionGetOffset(subCoordSection, subvertex, &soff);CHKERRQ(ierr); 2219 if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof); 2220 for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d]; 2221 } 2222 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2223 ierr = VecRestoreArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2224 } 2225 ierr = DMSetCoordinatesLocal(subdm, subCoordinates);CHKERRQ(ierr); 2226 ierr = VecDestroy(&subCoordinates);CHKERRQ(ierr); 2227 } 2228 /* Cleanup */ 2229 if (subvertexIS) {ierr = ISRestoreIndices(subvertexIS, &subVertices);CHKERRQ(ierr);} 2230 ierr = ISDestroy(&subvertexIS);CHKERRQ(ierr); 2231 ierr = PetscFree(subCells);CHKERRQ(ierr); 2232 PetscFunctionReturn(0); 2233 } 2234 2235 #undef __FUNCT__ 2236 #define __FUNCT__ "DMPlexCreateCohesiveSubmesh_Interpolated" 2237 static PetscErrorCode DMPlexCreateCohesiveSubmesh_Interpolated(DM dm, PetscBool hasLagrange, DM subdm) 2238 { 2239 MPI_Comm comm; 2240 DMLabel subpointMap; 2241 IS *subpointIS; 2242 const PetscInt **subpoints; 2243 PetscInt *numSubPoints, *firstSubPoint, *coneNew; 2244 PetscInt totSubPoints = 0, maxConeSize, dim, p, d, v; 2245 PetscErrorCode ierr; 2246 2247 PetscFunctionBegin; 2248 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 2249 /* Create subpointMap which marks the submesh */ 2250 ierr = DMLabelCreate("subpoint_map", &subpointMap);CHKERRQ(ierr); 2251 ierr = DMPlexSetSubpointMap(subdm, subpointMap);CHKERRQ(ierr); 2252 ierr = DMLabelDestroy(&subpointMap);CHKERRQ(ierr); 2253 ierr = DMPlexMarkCohesiveSubmesh_Interpolated(dm, hasLagrange, subpointMap, subdm);CHKERRQ(ierr); 2254 /* Setup chart */ 2255 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 2256 ierr = PetscMalloc4(dim+1,PetscInt,&numSubPoints,dim+1,PetscInt,&firstSubPoint,dim+1,IS,&subpointIS,dim+1,const PetscInt *,&subpoints);CHKERRQ(ierr); 2257 for (d = 0; d <= dim; ++d) { 2258 ierr = DMLabelGetStratumSize(subpointMap, d, &numSubPoints[d]);CHKERRQ(ierr); 2259 totSubPoints += numSubPoints[d]; 2260 } 2261 ierr = DMPlexSetChart(subdm, 0, totSubPoints);CHKERRQ(ierr); 2262 ierr = DMPlexSetVTKCellHeight(subdm, 1);CHKERRQ(ierr); 2263 /* Set cone sizes */ 2264 firstSubPoint[dim] = 0; 2265 firstSubPoint[0] = firstSubPoint[dim] + numSubPoints[dim]; 2266 if (dim > 1) {firstSubPoint[dim-1] = firstSubPoint[0] + numSubPoints[0];} 2267 if (dim > 2) {firstSubPoint[dim-2] = firstSubPoint[dim-1] + numSubPoints[dim-1];} 2268 for (d = 0; d <= dim; ++d) { 2269 ierr = DMLabelGetStratumIS(subpointMap, d, &subpointIS[d]);CHKERRQ(ierr); 2270 ierr = ISGetIndices(subpointIS[d], &subpoints[d]);CHKERRQ(ierr); 2271 } 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, coneSizeNew, c, val; 2278 2279 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 2280 ierr = DMPlexSetConeSize(subdm, subpoint, coneSize);CHKERRQ(ierr); 2281 if (d == dim) { 2282 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 2283 for (c = 0, coneSizeNew = 0; c < coneSize; ++c) { 2284 ierr = DMLabelGetValue(subpointMap, cone[c], &val);CHKERRQ(ierr); 2285 if (val >= 0) coneSizeNew++; 2286 } 2287 ierr = DMPlexSetConeSize(subdm, subpoint, coneSizeNew);CHKERRQ(ierr); 2288 } 2289 } 2290 } 2291 ierr = DMSetUp(subdm);CHKERRQ(ierr); 2292 /* Set cones */ 2293 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, NULL);CHKERRQ(ierr); 2294 ierr = PetscMalloc(maxConeSize * sizeof(PetscInt), &coneNew);CHKERRQ(ierr); 2295 for (d = 0; d <= dim; ++d) { 2296 for (p = 0; p < numSubPoints[d]; ++p) { 2297 const PetscInt point = subpoints[d][p]; 2298 const PetscInt subpoint = firstSubPoint[d] + p; 2299 const PetscInt *cone; 2300 PetscInt coneSize, subconeSize, coneSizeNew, c, subc; 2301 2302 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 2303 ierr = DMPlexGetConeSize(subdm, subpoint, &subconeSize);CHKERRQ(ierr); 2304 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 2305 for (c = 0, coneSizeNew = 0; c < coneSize; ++c) { 2306 ierr = PetscFindInt(cone[c], numSubPoints[d-1], subpoints[d-1], &subc);CHKERRQ(ierr); 2307 if (subc >= 0) coneNew[coneSizeNew++] = firstSubPoint[d-1] + subc; 2308 } 2309 if (coneSizeNew != subconeSize) SETERRQ2(comm, PETSC_ERR_PLIB, "Number of cone points located %d does not match subcone size %d", coneSizeNew, subconeSize); 2310 ierr = DMPlexSetCone(subdm, subpoint, coneNew);CHKERRQ(ierr); 2311 } 2312 } 2313 ierr = PetscFree(coneNew);CHKERRQ(ierr); 2314 ierr = DMPlexSymmetrize(subdm);CHKERRQ(ierr); 2315 ierr = DMPlexStratify(subdm);CHKERRQ(ierr); 2316 /* Build coordinates */ 2317 { 2318 PetscSection coordSection, subCoordSection; 2319 Vec coordinates, subCoordinates; 2320 PetscScalar *coords, *subCoords; 2321 PetscInt numComp, coordSize; 2322 2323 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2324 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 2325 ierr = DMPlexGetCoordinateSection(subdm, &subCoordSection);CHKERRQ(ierr); 2326 ierr = PetscSectionSetNumFields(subCoordSection, 1);CHKERRQ(ierr); 2327 ierr = PetscSectionGetFieldComponents(coordSection, 0, &numComp);CHKERRQ(ierr); 2328 ierr = PetscSectionSetFieldComponents(subCoordSection, 0, numComp);CHKERRQ(ierr); 2329 ierr = PetscSectionSetChart(subCoordSection, firstSubPoint[0], firstSubPoint[0]+numSubPoints[0]);CHKERRQ(ierr); 2330 for (v = 0; v < numSubPoints[0]; ++v) { 2331 const PetscInt vertex = subpoints[0][v]; 2332 const PetscInt subvertex = firstSubPoint[0]+v; 2333 PetscInt dof; 2334 2335 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2336 ierr = PetscSectionSetDof(subCoordSection, subvertex, dof);CHKERRQ(ierr); 2337 ierr = PetscSectionSetFieldDof(subCoordSection, subvertex, 0, dof);CHKERRQ(ierr); 2338 } 2339 ierr = PetscSectionSetUp(subCoordSection);CHKERRQ(ierr); 2340 ierr = PetscSectionGetStorageSize(subCoordSection, &coordSize);CHKERRQ(ierr); 2341 ierr = VecCreate(comm, &subCoordinates);CHKERRQ(ierr); 2342 ierr = VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2343 ierr = VecSetFromOptions(subCoordinates);CHKERRQ(ierr); 2344 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2345 ierr = VecGetArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2346 for (v = 0; v < numSubPoints[0]; ++v) { 2347 const PetscInt vertex = subpoints[0][v]; 2348 const PetscInt subvertex = firstSubPoint[0]+v; 2349 PetscInt dof, off, sdof, soff, d; 2350 2351 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2352 ierr = PetscSectionGetOffset(coordSection, vertex, &off);CHKERRQ(ierr); 2353 ierr = PetscSectionGetDof(subCoordSection, subvertex, &sdof);CHKERRQ(ierr); 2354 ierr = PetscSectionGetOffset(subCoordSection, subvertex, &soff);CHKERRQ(ierr); 2355 if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof); 2356 for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d]; 2357 } 2358 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2359 ierr = VecRestoreArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2360 ierr = DMSetCoordinatesLocal(subdm, subCoordinates);CHKERRQ(ierr); 2361 ierr = VecDestroy(&subCoordinates);CHKERRQ(ierr); 2362 } 2363 /* Cleanup */ 2364 for (d = 0; d <= dim; ++d) { 2365 ierr = ISRestoreIndices(subpointIS[d], &subpoints[d]);CHKERRQ(ierr); 2366 ierr = ISDestroy(&subpointIS[d]);CHKERRQ(ierr); 2367 } 2368 ierr = PetscFree4(numSubPoints,firstSubPoint,subpointIS,subpoints);CHKERRQ(ierr); 2369 PetscFunctionReturn(0); 2370 } 2371 2372 #undef __FUNCT__ 2373 #define __FUNCT__ "DMPlexCreateCohesiveSubmesh" 2374 /* 2375 DMPlexCreateCohesiveSubmesh - Extract from a mesh with cohesive cells the hypersurface defined by one face of the cells. 2376 2377 Input Parameters: 2378 + dm - The original mesh 2379 - hasLagrange - The mesh has Lagrange unknowns in the cohesive cells 2380 2381 Output Parameter: 2382 . subdm - The surface mesh 2383 2384 Note: This function produces a DMLabel mapping original points in the submesh to their depth. This can be obtained using DMPlexGetSubpointMap(). 2385 2386 Level: developer 2387 2388 .seealso: DMPlexGetSubpointMap(), DMPlexCreateSubmesh() 2389 */ 2390 PetscErrorCode DMPlexCreateCohesiveSubmesh(DM dm, PetscBool hasLagrange, DM *subdm) 2391 { 2392 PetscInt dim, depth; 2393 PetscErrorCode ierr; 2394 2395 PetscFunctionBegin; 2396 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2397 PetscValidPointer(subdm, 3); 2398 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 2399 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 2400 ierr = DMCreate(PetscObjectComm((PetscObject)dm), subdm);CHKERRQ(ierr); 2401 ierr = DMSetType(*subdm, DMPLEX);CHKERRQ(ierr); 2402 ierr = DMPlexSetDimension(*subdm, dim-1);CHKERRQ(ierr); 2403 if (depth == dim) { 2404 ierr = DMPlexCreateCohesiveSubmesh_Interpolated(dm, hasLagrange, *subdm);CHKERRQ(ierr); 2405 } else { 2406 ierr = DMPlexCreateCohesiveSubmesh_Uninterpolated(dm, hasLagrange, *subdm);CHKERRQ(ierr); 2407 } 2408 PetscFunctionReturn(0); 2409 } 2410 2411 #undef __FUNCT__ 2412 #define __FUNCT__ "DMPlexGetSubpointMap" 2413 /*@ 2414 DMPlexGetSubpointMap - Returns a DMLabel with point dimension as values 2415 2416 Input Parameter: 2417 . dm - The submesh DM 2418 2419 Output Parameter: 2420 . subpointMap - The DMLabel of all the points from the original mesh in this submesh, or NULL if this is not a submesh 2421 2422 Level: developer 2423 2424 .seealso: DMPlexCreateSubmesh(), DMPlexCreateSubpointIS() 2425 @*/ 2426 PetscErrorCode DMPlexGetSubpointMap(DM dm, DMLabel *subpointMap) 2427 { 2428 DM_Plex *mesh = (DM_Plex*) dm->data; 2429 2430 PetscFunctionBegin; 2431 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2432 PetscValidPointer(subpointMap, 2); 2433 *subpointMap = mesh->subpointMap; 2434 PetscFunctionReturn(0); 2435 } 2436 2437 #undef __FUNCT__ 2438 #define __FUNCT__ "DMPlexSetSubpointMap" 2439 /* Note: Should normally not be called by the user, since it is set in DMPlexCreateSubmesh() */ 2440 PetscErrorCode DMPlexSetSubpointMap(DM dm, DMLabel subpointMap) 2441 { 2442 DM_Plex *mesh = (DM_Plex *) dm->data; 2443 DMLabel tmp; 2444 PetscErrorCode ierr; 2445 2446 PetscFunctionBegin; 2447 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2448 tmp = mesh->subpointMap; 2449 mesh->subpointMap = subpointMap; 2450 ++mesh->subpointMap->refct; 2451 ierr = DMLabelDestroy(&tmp);CHKERRQ(ierr); 2452 PetscFunctionReturn(0); 2453 } 2454 2455 #undef __FUNCT__ 2456 #define __FUNCT__ "DMPlexCreateSubpointIS" 2457 /*@ 2458 DMPlexCreateSubpointIS - Creates an IS covering the entire subdm chart with the original points as data 2459 2460 Input Parameter: 2461 . dm - The submesh DM 2462 2463 Output Parameter: 2464 . subpointIS - The IS of all the points from the original mesh in this submesh, or NULL if this is not a submesh 2465 2466 Note: This is IS is guaranteed to be sorted by the construction of the submesh 2467 2468 Level: developer 2469 2470 .seealso: DMPlexCreateSubmesh(), DMPlexGetSubpointMap() 2471 @*/ 2472 PetscErrorCode DMPlexCreateSubpointIS(DM dm, IS *subpointIS) 2473 { 2474 MPI_Comm comm; 2475 DMLabel subpointMap; 2476 IS is; 2477 const PetscInt *opoints; 2478 PetscInt *points, *depths; 2479 PetscInt depth, depStart, depEnd, d, pStart, pEnd, p, n, off; 2480 PetscErrorCode ierr; 2481 2482 PetscFunctionBegin; 2483 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2484 PetscValidPointer(subpointIS, 2); 2485 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 2486 *subpointIS = NULL; 2487 ierr = DMPlexGetSubpointMap(dm, &subpointMap);CHKERRQ(ierr); 2488 if (subpointMap) { 2489 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 2490 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 2491 if (pStart) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Submeshes must start the point numbering at 0, not %d", pStart); 2492 ierr = DMGetWorkArray(dm, depth+1, PETSC_INT, &depths);CHKERRQ(ierr); 2493 depths[0] = depth; 2494 depths[1] = 0; 2495 for(d = 2; d <= depth; ++d) {depths[d] = depth+1 - d;} 2496 ierr = PetscMalloc(pEnd * sizeof(PetscInt), &points);CHKERRQ(ierr); 2497 for(d = 0, off = 0; d <= depth; ++d) { 2498 const PetscInt dep = depths[d]; 2499 2500 ierr = DMPlexGetDepthStratum(dm, dep, &depStart, &depEnd);CHKERRQ(ierr); 2501 ierr = DMLabelGetStratumSize(subpointMap, dep, &n);CHKERRQ(ierr); 2502 if (((d < 2) && (depth > 1)) || (d == 1)) { /* Only check vertices and cells for now since the map is broken for others */ 2503 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); 2504 } else { 2505 if (!n) { 2506 if (d == 0) { 2507 /* Missing cells */ 2508 for(p = 0; p < depEnd-depStart; ++p, ++off) points[off] = -1; 2509 } else { 2510 /* Missing faces */ 2511 for(p = 0; p < depEnd-depStart; ++p, ++off) points[off] = PETSC_MAX_INT; 2512 } 2513 } 2514 } 2515 if (n) { 2516 ierr = DMLabelGetStratumIS(subpointMap, dep, &is);CHKERRQ(ierr); 2517 ierr = ISGetIndices(is, &opoints);CHKERRQ(ierr); 2518 for(p = 0; p < n; ++p, ++off) points[off] = opoints[p]; 2519 ierr = ISRestoreIndices(is, &opoints);CHKERRQ(ierr); 2520 ierr = ISDestroy(&is);CHKERRQ(ierr); 2521 } 2522 } 2523 ierr = DMRestoreWorkArray(dm, depth+1, PETSC_INT, &depths);CHKERRQ(ierr); 2524 if (off != pEnd) SETERRQ2(comm, PETSC_ERR_ARG_WRONG, "The number of mapped submesh points %d should be %d", off, pEnd); 2525 ierr = ISCreateGeneral(comm, pEnd, points, PETSC_OWN_POINTER, subpointIS);CHKERRQ(ierr); 2526 } 2527 PetscFunctionReturn(0); 2528 } 2529