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, maxConeSizeNew, maxSupportSizeNew, 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 = DMPlexGetMaxSizes(dmNew, &maxConeSizeNew, &maxSupportSizeNew);CHKERRQ(ierr); 153 ierr = PetscMalloc2(depth+1,PetscInt,&depthEnd,PetscMax(PetscMax(maxConeSize, maxSupportSize), PetscMax(maxConeSizeNew, maxSupportSizeNew)),PetscInt,&newpoints);CHKERRQ(ierr); 154 for (d = 0; d <= depth; ++d) { 155 ierr = DMPlexGetDepthStratum(dm, d, NULL, &depthEnd[d]);CHKERRQ(ierr); 156 } 157 /* Step 5: Set cones and supports */ 158 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 159 for (p = pStart; p < pEnd; ++p) { 160 const PetscInt *points = NULL, *orientations = NULL; 161 PetscInt size,sizeNew, i, newp = DMPlexShiftPoint_Internal(p, depth, depthEnd, depthShift); 162 163 ierr = DMPlexGetConeSize(dm, p, &size);CHKERRQ(ierr); 164 ierr = DMPlexGetCone(dm, p, &points);CHKERRQ(ierr); 165 ierr = DMPlexGetConeOrientation(dm, p, &orientations);CHKERRQ(ierr); 166 for (i = 0; i < size; ++i) { 167 newpoints[i] = DMPlexShiftPoint_Internal(points[i], depth, depthEnd, depthShift); 168 } 169 ierr = DMPlexSetCone(dmNew, newp, newpoints);CHKERRQ(ierr); 170 ierr = DMPlexSetConeOrientation(dmNew, newp, orientations);CHKERRQ(ierr); 171 ierr = DMPlexGetSupportSize(dm, p, &size);CHKERRQ(ierr); 172 ierr = DMPlexGetSupportSize(dmNew, newp, &sizeNew);CHKERRQ(ierr); 173 ierr = DMPlexGetSupport(dm, p, &points);CHKERRQ(ierr); 174 for (i = 0; i < size; ++i) { 175 newpoints[i] = DMPlexShiftPoint_Internal(points[i], depth, depthEnd, depthShift); 176 } 177 for (i = size; i < sizeNew; ++i) newpoints[i] = 0; 178 ierr = DMPlexSetSupport(dmNew, newp, newpoints);CHKERRQ(ierr); 179 } 180 ierr = PetscFree2(depthEnd,newpoints);CHKERRQ(ierr); 181 PetscFunctionReturn(0); 182 } 183 184 #undef __FUNCT__ 185 #define __FUNCT__ "DMPlexShiftCoordinates_Internal" 186 static PetscErrorCode DMPlexShiftCoordinates_Internal(DM dm, PetscInt depthShift[], DM dmNew) 187 { 188 PetscSection coordSection, newCoordSection; 189 Vec coordinates, newCoordinates; 190 PetscScalar *coords, *newCoords; 191 PetscInt *depthEnd, coordSize; 192 PetscInt dim, depth = 0, d, vStart, vEnd, vStartNew, vEndNew, v; 193 PetscErrorCode ierr; 194 195 PetscFunctionBegin; 196 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 197 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 198 ierr = PetscMalloc((depth+1) * sizeof(PetscInt), &depthEnd);CHKERRQ(ierr); 199 for (d = 0; d <= depth; ++d) { 200 ierr = DMPlexGetDepthStratum(dm, d, NULL, &depthEnd[d]);CHKERRQ(ierr); 201 } 202 /* Step 8: Convert coordinates */ 203 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 204 ierr = DMPlexGetDepthStratum(dmNew, 0, &vStartNew, &vEndNew);CHKERRQ(ierr); 205 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 206 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &newCoordSection);CHKERRQ(ierr); 207 ierr = PetscSectionSetNumFields(newCoordSection, 1);CHKERRQ(ierr); 208 ierr = PetscSectionSetFieldComponents(newCoordSection, 0, dim);CHKERRQ(ierr); 209 ierr = PetscSectionSetChart(newCoordSection, vStartNew, vEndNew);CHKERRQ(ierr); 210 for (v = vStartNew; v < vEndNew; ++v) { 211 ierr = PetscSectionSetDof(newCoordSection, v, dim);CHKERRQ(ierr); 212 ierr = PetscSectionSetFieldDof(newCoordSection, v, 0, dim);CHKERRQ(ierr); 213 } 214 ierr = PetscSectionSetUp(newCoordSection);CHKERRQ(ierr); 215 ierr = DMPlexSetCoordinateSection(dmNew, newCoordSection);CHKERRQ(ierr); 216 ierr = PetscSectionGetStorageSize(newCoordSection, &coordSize);CHKERRQ(ierr); 217 ierr = VecCreate(PetscObjectComm((PetscObject)dm), &newCoordinates);CHKERRQ(ierr); 218 ierr = PetscObjectSetName((PetscObject) newCoordinates, "coordinates");CHKERRQ(ierr); 219 ierr = VecSetSizes(newCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 220 ierr = VecSetType(newCoordinates,VECSTANDARD);CHKERRQ(ierr); 221 ierr = DMSetCoordinatesLocal(dmNew, newCoordinates);CHKERRQ(ierr); 222 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 223 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 224 ierr = VecGetArray(newCoordinates, &newCoords);CHKERRQ(ierr); 225 for (v = vStart; v < vEnd; ++v) { 226 PetscInt dof, off, noff, d; 227 228 ierr = PetscSectionGetDof(coordSection, v, &dof);CHKERRQ(ierr); 229 ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr); 230 ierr = PetscSectionGetOffset(newCoordSection, DMPlexShiftPoint_Internal(v, depth, depthEnd, depthShift), &noff);CHKERRQ(ierr); 231 for (d = 0; d < dof; ++d) { 232 newCoords[noff+d] = coords[off+d]; 233 } 234 } 235 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 236 ierr = VecRestoreArray(newCoordinates, &newCoords);CHKERRQ(ierr); 237 ierr = VecDestroy(&newCoordinates);CHKERRQ(ierr); 238 ierr = PetscSectionDestroy(&newCoordSection);CHKERRQ(ierr); 239 ierr = PetscFree(depthEnd);CHKERRQ(ierr); 240 PetscFunctionReturn(0); 241 } 242 243 #undef __FUNCT__ 244 #define __FUNCT__ "DMPlexShiftSF_Internal" 245 static PetscErrorCode DMPlexShiftSF_Internal(DM dm, PetscInt depthShift[], DM dmNew) 246 { 247 PetscInt *depthEnd; 248 PetscInt depth = 0, d; 249 PetscSF sfPoint, sfPointNew; 250 const PetscSFNode *remotePoints; 251 PetscSFNode *gremotePoints; 252 const PetscInt *localPoints; 253 PetscInt *glocalPoints, *newLocation, *newRemoteLocation; 254 PetscInt numRoots, numLeaves, l, pStart, pEnd, totShift = 0; 255 PetscErrorCode ierr; 256 257 PetscFunctionBegin; 258 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 259 ierr = PetscMalloc((depth+1) * sizeof(PetscInt), &depthEnd);CHKERRQ(ierr); 260 for (d = 0; d <= depth; ++d) { 261 totShift += depthShift[d]; 262 ierr = DMPlexGetDepthStratum(dm, d, NULL, &depthEnd[d]);CHKERRQ(ierr); 263 } 264 /* Step 9: Convert pointSF */ 265 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 266 ierr = DMGetPointSF(dmNew, &sfPointNew);CHKERRQ(ierr); 267 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 268 ierr = PetscSFGetGraph(sfPoint, &numRoots, &numLeaves, &localPoints, &remotePoints);CHKERRQ(ierr); 269 if (numRoots >= 0) { 270 ierr = PetscMalloc2(numRoots,PetscInt,&newLocation,pEnd-pStart,PetscInt,&newRemoteLocation);CHKERRQ(ierr); 271 for (l=0; l<numRoots; l++) newLocation[l] = DMPlexShiftPoint_Internal(l, depth, depthEnd, depthShift); 272 ierr = PetscSFBcastBegin(sfPoint, MPIU_INT, newLocation, newRemoteLocation);CHKERRQ(ierr); 273 ierr = PetscSFBcastEnd(sfPoint, MPIU_INT, newLocation, newRemoteLocation);CHKERRQ(ierr); 274 ierr = PetscMalloc(numLeaves * sizeof(PetscInt), &glocalPoints);CHKERRQ(ierr); 275 ierr = PetscMalloc(numLeaves * sizeof(PetscSFNode), &gremotePoints);CHKERRQ(ierr); 276 for (l = 0; l < numLeaves; ++l) { 277 glocalPoints[l] = DMPlexShiftPoint_Internal(localPoints[l], depth, depthEnd, depthShift); 278 gremotePoints[l].rank = remotePoints[l].rank; 279 gremotePoints[l].index = newRemoteLocation[localPoints[l]]; 280 } 281 ierr = PetscFree2(newLocation,newRemoteLocation);CHKERRQ(ierr); 282 ierr = PetscSFSetGraph(sfPointNew, numRoots + totShift, numLeaves, glocalPoints, PETSC_OWN_POINTER, gremotePoints, PETSC_OWN_POINTER);CHKERRQ(ierr); 283 } 284 ierr = PetscFree(depthEnd);CHKERRQ(ierr); 285 PetscFunctionReturn(0); 286 } 287 288 #undef __FUNCT__ 289 #define __FUNCT__ "DMPlexShiftLabels_Internal" 290 static PetscErrorCode DMPlexShiftLabels_Internal(DM dm, PetscInt depthShift[], DM dmNew) 291 { 292 PetscSF sfPoint; 293 DMLabel vtkLabel, ghostLabel; 294 PetscInt *depthEnd; 295 const PetscSFNode *leafRemote; 296 const PetscInt *leafLocal; 297 PetscInt depth = 0, d, numLeaves, numLabels, l, cStart, cEnd, c, fStart, fEnd, f; 298 PetscMPIInt rank; 299 PetscErrorCode ierr; 300 301 PetscFunctionBegin; 302 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 303 ierr = PetscMalloc((depth+1) * sizeof(PetscInt), &depthEnd);CHKERRQ(ierr); 304 for (d = 0; d <= depth; ++d) { 305 ierr = DMPlexGetDepthStratum(dm, d, NULL, &depthEnd[d]);CHKERRQ(ierr); 306 } 307 /* Step 10: Convert labels */ 308 ierr = DMPlexGetNumLabels(dm, &numLabels);CHKERRQ(ierr); 309 for (l = 0; l < numLabels; ++l) { 310 DMLabel label, newlabel; 311 const char *lname; 312 PetscBool isDepth; 313 IS valueIS; 314 const PetscInt *values; 315 PetscInt numValues, val; 316 317 ierr = DMPlexGetLabelName(dm, l, &lname);CHKERRQ(ierr); 318 ierr = PetscStrcmp(lname, "depth", &isDepth);CHKERRQ(ierr); 319 if (isDepth) continue; 320 ierr = DMPlexCreateLabel(dmNew, lname);CHKERRQ(ierr); 321 ierr = DMPlexGetLabel(dm, lname, &label);CHKERRQ(ierr); 322 ierr = DMPlexGetLabel(dmNew, lname, &newlabel);CHKERRQ(ierr); 323 ierr = DMLabelGetValueIS(label, &valueIS);CHKERRQ(ierr); 324 ierr = ISGetLocalSize(valueIS, &numValues);CHKERRQ(ierr); 325 ierr = ISGetIndices(valueIS, &values);CHKERRQ(ierr); 326 for (val = 0; val < numValues; ++val) { 327 IS pointIS; 328 const PetscInt *points; 329 PetscInt numPoints, p; 330 331 ierr = DMLabelGetStratumIS(label, values[val], &pointIS);CHKERRQ(ierr); 332 ierr = ISGetLocalSize(pointIS, &numPoints);CHKERRQ(ierr); 333 ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); 334 for (p = 0; p < numPoints; ++p) { 335 const PetscInt newpoint = DMPlexShiftPoint_Internal(points[p], depth, depthEnd, depthShift); 336 337 ierr = DMLabelSetValue(newlabel, newpoint, values[val]);CHKERRQ(ierr); 338 } 339 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 340 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 341 } 342 ierr = ISRestoreIndices(valueIS, &values);CHKERRQ(ierr); 343 ierr = ISDestroy(&valueIS);CHKERRQ(ierr); 344 } 345 ierr = PetscFree(depthEnd);CHKERRQ(ierr); 346 /* Step 11: Make label for output (vtk) and to mark ghost points (ghost) */ 347 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr); 348 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 349 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 350 ierr = PetscSFGetGraph(sfPoint, NULL, &numLeaves, &leafLocal, &leafRemote);CHKERRQ(ierr); 351 ierr = DMPlexCreateLabel(dmNew, "vtk");CHKERRQ(ierr); 352 ierr = DMPlexCreateLabel(dmNew, "ghost");CHKERRQ(ierr); 353 ierr = DMPlexGetLabel(dmNew, "vtk", &vtkLabel);CHKERRQ(ierr); 354 ierr = DMPlexGetLabel(dmNew, "ghost", &ghostLabel);CHKERRQ(ierr); 355 for (l = 0, c = cStart; l < numLeaves && c < cEnd; ++l, ++c) { 356 for (; c < leafLocal[l] && c < cEnd; ++c) { 357 ierr = DMLabelSetValue(vtkLabel, c, 1);CHKERRQ(ierr); 358 } 359 if (leafLocal[l] >= cEnd) break; 360 if (leafRemote[l].rank == rank) { 361 ierr = DMLabelSetValue(vtkLabel, c, 1);CHKERRQ(ierr); 362 } else { 363 ierr = DMLabelSetValue(ghostLabel, c, 2);CHKERRQ(ierr); 364 } 365 } 366 for (; c < cEnd; ++c) { 367 ierr = DMLabelSetValue(vtkLabel, c, 1);CHKERRQ(ierr); 368 } 369 if (0) { 370 ierr = PetscViewerASCIISynchronizedAllow(PETSC_VIEWER_STDOUT_WORLD, PETSC_TRUE);CHKERRQ(ierr); 371 ierr = DMLabelView(vtkLabel, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 372 ierr = PetscViewerFlush(PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 373 } 374 ierr = DMPlexGetHeightStratum(dmNew, 1, &fStart, &fEnd);CHKERRQ(ierr); 375 for (f = fStart; f < fEnd; ++f) { 376 PetscInt numCells; 377 378 ierr = DMPlexGetSupportSize(dmNew, f, &numCells);CHKERRQ(ierr); 379 if (numCells < 2) { 380 ierr = DMLabelSetValue(ghostLabel, f, 1);CHKERRQ(ierr); 381 } else { 382 const PetscInt *cells = NULL; 383 PetscInt vA, vB; 384 385 ierr = DMPlexGetSupport(dmNew, f, &cells);CHKERRQ(ierr); 386 ierr = DMLabelGetValue(vtkLabel, cells[0], &vA);CHKERRQ(ierr); 387 ierr = DMLabelGetValue(vtkLabel, cells[1], &vB);CHKERRQ(ierr); 388 if (!vA && !vB) {ierr = DMLabelSetValue(ghostLabel, f, 1);CHKERRQ(ierr);} 389 } 390 } 391 if (0) { 392 ierr = PetscViewerASCIISynchronizedAllow(PETSC_VIEWER_STDOUT_WORLD, PETSC_TRUE);CHKERRQ(ierr); 393 ierr = DMLabelView(ghostLabel, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 394 ierr = PetscViewerFlush(PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 395 } 396 PetscFunctionReturn(0); 397 } 398 399 #undef __FUNCT__ 400 #define __FUNCT__ "DMPlexConstructGhostCells_Internal" 401 static PetscErrorCode DMPlexConstructGhostCells_Internal(DM dm, DMLabel label, PetscInt *numGhostCells, DM gdm) 402 { 403 IS valueIS; 404 const PetscInt *values; 405 PetscInt *depthShift; 406 PetscInt depth = 0, numFS, fs, ghostCell, cEnd, c; 407 PetscErrorCode ierr; 408 409 PetscFunctionBegin; 410 /* Count ghost cells */ 411 ierr = DMLabelGetValueIS(label, &valueIS);CHKERRQ(ierr); 412 ierr = ISGetLocalSize(valueIS, &numFS);CHKERRQ(ierr); 413 ierr = ISGetIndices(valueIS, &values);CHKERRQ(ierr); 414 415 *numGhostCells = 0; 416 for (fs = 0; fs < numFS; ++fs) { 417 PetscInt numBdFaces; 418 419 ierr = DMLabelGetStratumSize(label, values[fs], &numBdFaces);CHKERRQ(ierr); 420 421 *numGhostCells += numBdFaces; 422 } 423 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 424 ierr = PetscMalloc((depth+1) * sizeof(PetscInt), &depthShift);CHKERRQ(ierr); 425 ierr = PetscMemzero(depthShift, (depth+1) * sizeof(PetscInt));CHKERRQ(ierr); 426 if (depth >= 0) depthShift[depth] = *numGhostCells; 427 ierr = DMPlexShiftSizes_Internal(dm, depthShift, gdm);CHKERRQ(ierr); 428 /* Step 3: Set cone/support sizes for new points */ 429 ierr = DMPlexGetHeightStratum(dm, 0, NULL, &cEnd);CHKERRQ(ierr); 430 for (c = cEnd; c < cEnd + *numGhostCells; ++c) { 431 ierr = DMPlexSetConeSize(gdm, c, 1);CHKERRQ(ierr); 432 } 433 for (fs = 0; fs < numFS; ++fs) { 434 IS faceIS; 435 const PetscInt *faces; 436 PetscInt numFaces, f; 437 438 ierr = DMLabelGetStratumIS(label, values[fs], &faceIS);CHKERRQ(ierr); 439 ierr = ISGetLocalSize(faceIS, &numFaces);CHKERRQ(ierr); 440 ierr = ISGetIndices(faceIS, &faces);CHKERRQ(ierr); 441 for (f = 0; f < numFaces; ++f) { 442 PetscInt size; 443 444 ierr = DMPlexGetSupportSize(dm, faces[f], &size);CHKERRQ(ierr); 445 if (size != 1) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "DM has boundary face %d with %d support cells", faces[f], size); 446 ierr = DMPlexSetSupportSize(gdm, faces[f] + *numGhostCells, 2);CHKERRQ(ierr); 447 } 448 ierr = ISRestoreIndices(faceIS, &faces);CHKERRQ(ierr); 449 ierr = ISDestroy(&faceIS);CHKERRQ(ierr); 450 } 451 /* Step 4: Setup ghosted DM */ 452 ierr = DMSetUp(gdm);CHKERRQ(ierr); 453 ierr = DMPlexShiftPoints_Internal(dm, depthShift, gdm);CHKERRQ(ierr); 454 /* Step 6: Set cones and supports for new points */ 455 ghostCell = cEnd; 456 for (fs = 0; fs < numFS; ++fs) { 457 IS faceIS; 458 const PetscInt *faces; 459 PetscInt numFaces, f; 460 461 ierr = DMLabelGetStratumIS(label, values[fs], &faceIS);CHKERRQ(ierr); 462 ierr = ISGetLocalSize(faceIS, &numFaces);CHKERRQ(ierr); 463 ierr = ISGetIndices(faceIS, &faces);CHKERRQ(ierr); 464 for (f = 0; f < numFaces; ++f, ++ghostCell) { 465 PetscInt newFace = faces[f] + *numGhostCells; 466 467 ierr = DMPlexSetCone(gdm, ghostCell, &newFace);CHKERRQ(ierr); 468 ierr = DMPlexInsertSupport(gdm, newFace, 1, ghostCell);CHKERRQ(ierr); 469 } 470 ierr = ISRestoreIndices(faceIS, &faces);CHKERRQ(ierr); 471 ierr = ISDestroy(&faceIS);CHKERRQ(ierr); 472 } 473 ierr = ISRestoreIndices(valueIS, &values);CHKERRQ(ierr); 474 ierr = ISDestroy(&valueIS);CHKERRQ(ierr); 475 /* Step 7: Stratify */ 476 ierr = DMPlexStratify(gdm);CHKERRQ(ierr); 477 ierr = DMPlexShiftCoordinates_Internal(dm, depthShift, gdm);CHKERRQ(ierr); 478 ierr = DMPlexShiftSF_Internal(dm, depthShift, gdm);CHKERRQ(ierr); 479 ierr = DMPlexShiftLabels_Internal(dm, depthShift, gdm);CHKERRQ(ierr); 480 ierr = PetscFree(depthShift);CHKERRQ(ierr); 481 PetscFunctionReturn(0); 482 } 483 484 #undef __FUNCT__ 485 #define __FUNCT__ "DMPlexConstructGhostCells" 486 /*@C 487 DMPlexConstructGhostCells - Construct ghost cells which connect to every boundary face 488 489 Collective on dm 490 491 Input Parameters: 492 + dm - The original DM 493 - labelName - The label specifying the boundary faces, or "Face Sets" if this is NULL 494 495 Output Parameters: 496 + numGhostCells - The number of ghost cells added to the DM 497 - dmGhosted - The new DM 498 499 Note: If no label exists of that name, one will be created marking all boundary faces 500 501 Level: developer 502 503 .seealso: DMCreate() 504 */ 505 PetscErrorCode DMPlexConstructGhostCells(DM dm, const char labelName[], PetscInt *numGhostCells, DM *dmGhosted) 506 { 507 DM gdm; 508 DMLabel label; 509 const char *name = labelName ? labelName : "Face Sets"; 510 PetscInt dim; 511 PetscErrorCode ierr; 512 513 PetscFunctionBegin; 514 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 515 PetscValidPointer(numGhostCells, 3); 516 PetscValidPointer(dmGhosted, 4); 517 ierr = DMCreate(PetscObjectComm((PetscObject)dm), &gdm);CHKERRQ(ierr); 518 ierr = DMSetType(gdm, DMPLEX);CHKERRQ(ierr); 519 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 520 ierr = DMPlexSetDimension(gdm, dim);CHKERRQ(ierr); 521 ierr = DMPlexGetLabel(dm, name, &label);CHKERRQ(ierr); 522 if (!label) { 523 /* Get label for boundary faces */ 524 ierr = DMPlexCreateLabel(dm, name);CHKERRQ(ierr); 525 ierr = DMPlexGetLabel(dm, name, &label);CHKERRQ(ierr); 526 ierr = DMPlexMarkBoundaryFaces(dm, label);CHKERRQ(ierr); 527 } 528 ierr = DMPlexConstructGhostCells_Internal(dm, label, numGhostCells, gdm);CHKERRQ(ierr); 529 ierr = DMSetFromOptions(gdm);CHKERRQ(ierr); 530 *dmGhosted = gdm; 531 PetscFunctionReturn(0); 532 } 533 534 #undef __FUNCT__ 535 #define __FUNCT__ "DMPlexConstructCohesiveCells_Internal" 536 /* 537 We are adding two kinds of points here: 538 Replicated: Copies of points which exist in the mesh, such as vertices identified across a fault 539 Hybrid: Entirely new points, such as cohesive cells 540 */ 541 static PetscErrorCode DMPlexConstructCohesiveCells_Internal(DM dm, DMLabel label, DM sdm) 542 { 543 MPI_Comm comm; 544 IS valueIS; 545 PetscInt numSP = 0; /* The number of depths for which we have replicated points */ 546 const PetscInt *values; /* List of depths for which we have replicated points */ 547 IS *pointIS; 548 PetscInt *numSplitPoints; /* The number of replicated points at each depth */ 549 PetscInt *numHybridPoints; /* The number of hybrid points at each depth */ 550 const PetscInt **splitPoints; /* Replicated points for each depth */ 551 PetscSection coordSection; 552 Vec coordinates; 553 PetscScalar *coords; 554 PetscInt depths[4]; /* Depths in the order that plex points are numbered */ 555 PetscInt *depthShift; /* Number of replicated+hybrid points at each depth */ 556 PetscInt *depthOffset; /* Prefix sums of depthShift */ 557 PetscInt *pMaxNew; /* The first replicated point at each depth in the new mesh, hybrids come after this */ 558 PetscInt *coneNew, *coneONew, *supportNew; 559 PetscInt shift = 100, depth = 0, dep, dim, d, sp, maxConeSize, maxSupportSize, maxConeSizeNew, maxSupportSizeNew, numLabels, vStart, vEnd, pEnd, p, v; 560 PetscErrorCode ierr; 561 562 PetscFunctionBegin; 563 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 564 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 565 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 566 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 567 depths[0] = depth; 568 depths[1] = 0; 569 depths[2] = depth-1; 570 depths[3] = 1; 571 /* Count split points and add cohesive cells */ 572 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize);CHKERRQ(ierr); 573 ierr = PetscMalloc3(depth+1,PetscInt,&depthShift,depth+1,PetscInt,&depthOffset,depth+1,PetscInt,&pMaxNew);CHKERRQ(ierr); 574 ierr = PetscMalloc4(depth+1,IS,&pointIS,depth+1,PetscInt,&numSplitPoints,depth+1,PetscInt,&numHybridPoints,depth+1,const PetscInt*,&splitPoints);CHKERRQ(ierr); 575 ierr = PetscMemzero(depthShift, (depth+1) * sizeof(PetscInt));CHKERRQ(ierr); 576 ierr = PetscMemzero(depthOffset, (depth+1) * sizeof(PetscInt));CHKERRQ(ierr); 577 for (d = 0; d <= depth; ++d) { 578 ierr = DMPlexGetDepthStratum(dm, d, NULL, &pMaxNew[d]);CHKERRQ(ierr); 579 numSplitPoints[d] = 0; 580 numHybridPoints[d] = 0; 581 splitPoints[d] = NULL; 582 pointIS[d] = NULL; 583 } 584 if (label) { 585 ierr = DMLabelGetValueIS(label, &valueIS);CHKERRQ(ierr); 586 ierr = ISGetLocalSize(valueIS, &numSP);CHKERRQ(ierr); 587 ierr = ISGetIndices(valueIS, &values);CHKERRQ(ierr); 588 } 589 for (sp = 0; sp < numSP; ++sp) { 590 const PetscInt dep = values[sp]; 591 592 if ((dep < 0) || (dep > depth)) continue; 593 ierr = DMLabelGetStratumIS(label, dep, &pointIS[dep]);CHKERRQ(ierr); 594 if (pointIS[dep]) { 595 ierr = ISGetLocalSize(pointIS[dep], &numSplitPoints[dep]);CHKERRQ(ierr); 596 ierr = ISGetIndices(pointIS[dep], &splitPoints[dep]);CHKERRQ(ierr); 597 } 598 } 599 /* Calculate number of hybrid points */ 600 for (d = 1; d <= depth; ++d) numHybridPoints[d] = numSplitPoints[d-1]; /* There is a hybrid cell/face/edge for every split face/edge/vertex */ 601 for (d = 0; d <= depth; ++d) depthShift[d] = numSplitPoints[d] + numHybridPoints[d]; 602 for (d = 1; d <= depth; ++d) depthOffset[depths[d]] = depthOffset[depths[d-1]] + depthShift[depths[d-1]]; 603 for (d = 0; d <= depth; ++d) pMaxNew[d] += depthOffset[d]; 604 ierr = DMPlexShiftSizes_Internal(dm, depthShift, sdm);CHKERRQ(ierr); 605 /* Step 3: Set cone/support sizes for new points */ 606 for (dep = 0; dep <= depth; ++dep) { 607 for (p = 0; p < numSplitPoints[dep]; ++p) { 608 const PetscInt oldp = splitPoints[dep][p]; 609 const PetscInt newp = oldp + depthOffset[dep]; 610 const PetscInt splitp = p + pMaxNew[dep]; 611 const PetscInt *support; 612 PetscInt coneSize, supportSize, qf, qn, qp, e; 613 614 ierr = DMPlexGetConeSize(dm, oldp, &coneSize);CHKERRQ(ierr); 615 ierr = DMPlexSetConeSize(sdm, splitp, coneSize);CHKERRQ(ierr); 616 ierr = DMPlexGetSupportSize(dm, oldp, &supportSize);CHKERRQ(ierr); 617 ierr = DMPlexSetSupportSize(sdm, splitp, supportSize);CHKERRQ(ierr); 618 if (dep == depth-1) { 619 const PetscInt hybcell = p + pMaxNew[dep+1] + numSplitPoints[dep+1]; 620 621 /* Add cohesive cells, they are prisms */ 622 ierr = DMPlexSetConeSize(sdm, hybcell, 2 + coneSize);CHKERRQ(ierr); 623 } else if (dep == 0) { 624 const PetscInt hybedge = p + pMaxNew[dep+1] + numSplitPoints[dep+1]; 625 626 ierr = DMPlexGetSupport(dm, oldp, &support);CHKERRQ(ierr); 627 for (e = 0, qn = 0, qp = 0, qf = 0; e < supportSize; ++e) { 628 PetscInt val; 629 630 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 631 if (val == 1) ++qf; 632 if ((val == 1) || (val == (shift + 1))) ++qn; 633 if ((val == 1) || (val == -(shift + 1))) ++qp; 634 } 635 /* Split old vertex: Edges into original vertex and new cohesive edge */ 636 ierr = DMPlexSetSupportSize(sdm, newp, qn+1);CHKERRQ(ierr); 637 /* Split new vertex: Edges into split vertex and new cohesive edge */ 638 ierr = DMPlexSetSupportSize(sdm, splitp, qp+1);CHKERRQ(ierr); 639 /* Add hybrid edge */ 640 ierr = DMPlexSetConeSize(sdm, hybedge, 2);CHKERRQ(ierr); 641 ierr = DMPlexSetSupportSize(sdm, hybedge, qf);CHKERRQ(ierr); 642 } else if (dep == dim-2) { 643 const PetscInt hybface = p + pMaxNew[dep+1] + numSplitPoints[dep+1]; 644 645 ierr = DMPlexGetSupport(dm, oldp, &support);CHKERRQ(ierr); 646 for (e = 0, qn = 0, qp = 0, qf = 0; e < supportSize; ++e) { 647 PetscInt val; 648 649 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 650 if (val == dim-1) ++qf; 651 if ((val == dim-1) || (val == (shift + dim-1))) ++qn; 652 if ((val == dim-1) || (val == -(shift + dim-1))) ++qp; 653 } 654 /* Split old edge: Faces into original edge and cohesive face (positive side?) */ 655 ierr = DMPlexSetSupportSize(sdm, newp, qn+1);CHKERRQ(ierr); 656 /* Split new edge: Faces into split edge and cohesive face (negative side?) */ 657 ierr = DMPlexSetSupportSize(sdm, splitp, qp+1);CHKERRQ(ierr); 658 /* Add hybrid face */ 659 ierr = DMPlexSetConeSize(sdm, hybface, 4);CHKERRQ(ierr); 660 ierr = DMPlexSetSupportSize(sdm, hybface, qf);CHKERRQ(ierr); 661 } 662 } 663 } 664 /* Step 4: Setup split DM */ 665 ierr = DMSetUp(sdm);CHKERRQ(ierr); 666 ierr = DMPlexShiftPoints_Internal(dm, depthShift, sdm);CHKERRQ(ierr); 667 ierr = DMPlexGetMaxSizes(sdm, &maxConeSizeNew, &maxSupportSizeNew);CHKERRQ(ierr); 668 ierr = PetscMalloc3(PetscMax(maxConeSize, maxConeSizeNew)*3,PetscInt,&coneNew,PetscMax(maxConeSize, maxConeSizeNew)*3,PetscInt,&coneONew,PetscMax(maxSupportSize, maxSupportSizeNew),PetscInt,&supportNew);CHKERRQ(ierr); 669 /* Step 6: Set cones and supports for new points */ 670 for (dep = 0; dep <= depth; ++dep) { 671 for (p = 0; p < numSplitPoints[dep]; ++p) { 672 const PetscInt oldp = splitPoints[dep][p]; 673 const PetscInt newp = oldp + depthOffset[dep]; 674 const PetscInt splitp = p + pMaxNew[dep]; 675 const PetscInt *cone, *support, *ornt; 676 PetscInt coneSize, supportSize, q, qf, qn, qp, v, e, s; 677 678 ierr = DMPlexGetConeSize(dm, oldp, &coneSize);CHKERRQ(ierr); 679 ierr = DMPlexGetCone(dm, oldp, &cone);CHKERRQ(ierr); 680 ierr = DMPlexGetConeOrientation(dm, oldp, &ornt);CHKERRQ(ierr); 681 ierr = DMPlexGetSupportSize(dm, oldp, &supportSize);CHKERRQ(ierr); 682 ierr = DMPlexGetSupport(dm, oldp, &support);CHKERRQ(ierr); 683 if (dep == depth-1) { 684 const PetscInt hybcell = p + pMaxNew[dep+1] + numSplitPoints[dep+1]; 685 const PetscInt *supportF; 686 687 /* Split face: copy in old face to new face to start */ 688 ierr = DMPlexGetSupport(sdm, newp, &supportF);CHKERRQ(ierr); 689 ierr = DMPlexSetSupport(sdm, splitp, supportF);CHKERRQ(ierr); 690 /* Split old face: old vertices/edges in cone so no change */ 691 /* Split new face: new vertices/edges in cone */ 692 for (q = 0; q < coneSize; ++q) { 693 ierr = PetscFindInt(cone[q], numSplitPoints[dep-1], splitPoints[dep-1], &v);CHKERRQ(ierr); 694 695 coneNew[2+q] = v + pMaxNew[dep-1]; 696 } 697 ierr = DMPlexSetCone(sdm, splitp, &coneNew[2]);CHKERRQ(ierr); 698 ierr = DMPlexSetConeOrientation(sdm, splitp, ornt);CHKERRQ(ierr); 699 /* Face support */ 700 for (s = 0; s < supportSize; ++s) { 701 PetscInt val; 702 703 ierr = DMLabelGetValue(label, support[s], &val);CHKERRQ(ierr); 704 if (val < 0) { 705 /* Split old face: Replace negative side cell with cohesive cell */ 706 ierr = DMPlexInsertSupport(sdm, newp, s, hybcell);CHKERRQ(ierr); 707 } else { 708 /* Split new face: Replace positive side cell with cohesive cell */ 709 ierr = DMPlexInsertSupport(sdm, splitp, s, hybcell);CHKERRQ(ierr); 710 /* Get orientation for cohesive face */ 711 { 712 const PetscInt *ncone, *nconeO; 713 PetscInt nconeSize, nc; 714 715 ierr = DMPlexGetConeSize(dm, support[s], &nconeSize);CHKERRQ(ierr); 716 ierr = DMPlexGetCone(dm, support[s], &ncone);CHKERRQ(ierr); 717 ierr = DMPlexGetConeOrientation(dm, support[s], &nconeO);CHKERRQ(ierr); 718 for (nc = 0; nc < nconeSize; ++nc) { 719 if (ncone[nc] == oldp) { 720 coneONew[0] = nconeO[nc]; 721 break; 722 } 723 } 724 if (nc >= nconeSize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not locate face %d in neighboring cell %d", oldp, support[s]); 725 } 726 } 727 } 728 /* Cohesive cell: Old and new split face, then new cohesive faces */ 729 coneNew[0] = newp; /* Extracted negative side orientation above */ 730 coneNew[1] = splitp; 731 coneONew[1] = coneONew[0]; 732 for (q = 0; q < coneSize; ++q) { 733 coneNew[2+q] += (pMaxNew[dep] - pMaxNew[dep-1]) + numSplitPoints[dep]; 734 coneONew[2+q] = 0; 735 } 736 ierr = DMPlexSetCone(sdm, hybcell, coneNew);CHKERRQ(ierr); 737 ierr = DMPlexSetConeOrientation(sdm, hybcell, coneONew);CHKERRQ(ierr); 738 } else if (dep == 0) { 739 const PetscInt hybedge = p + pMaxNew[dep+1] + numSplitPoints[dep+1]; 740 741 /* Split old vertex: Edges in old split faces and new cohesive edge */ 742 for (e = 0, qn = 0; e < supportSize; ++e) { 743 PetscInt val; 744 745 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 746 if ((val == 1) || (val == (shift + 1))) { 747 supportNew[qn++] = support[e] + depthOffset[dep+1]; 748 } 749 } 750 supportNew[qn] = hybedge; 751 ierr = DMPlexSetSupport(sdm, newp, supportNew);CHKERRQ(ierr); 752 /* Split new vertex: Edges in new split faces and new cohesive edge */ 753 for (e = 0, qp = 0; e < supportSize; ++e) { 754 PetscInt val, edge; 755 756 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 757 if (val == 1) { 758 ierr = PetscFindInt(support[e], numSplitPoints[dep+1], splitPoints[dep+1], &edge);CHKERRQ(ierr); 759 if (edge < 0) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Edge %d is not a split edge", support[e]); 760 supportNew[qp++] = edge + pMaxNew[dep+1]; 761 } else if (val == -(shift + 1)) { 762 supportNew[qp++] = support[e] + depthOffset[dep+1]; 763 } 764 } 765 supportNew[qp] = hybedge; 766 ierr = DMPlexSetSupport(sdm, splitp, supportNew);CHKERRQ(ierr); 767 /* Hybrid edge: Old and new split vertex */ 768 coneNew[0] = newp; 769 coneNew[1] = splitp; 770 ierr = DMPlexSetCone(sdm, hybedge, coneNew);CHKERRQ(ierr); 771 for (e = 0, qf = 0; e < supportSize; ++e) { 772 PetscInt val, edge; 773 774 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 775 if (val == 1) { 776 ierr = PetscFindInt(support[e], numSplitPoints[dep+1], splitPoints[dep+1], &edge);CHKERRQ(ierr); 777 if (edge < 0) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Edge %d is not a split edge", support[e]); 778 supportNew[qf++] = edge + pMaxNew[dep+2] + numSplitPoints[dep+2]; 779 } 780 } 781 ierr = DMPlexSetSupport(sdm, hybedge, supportNew);CHKERRQ(ierr); 782 } else if (dep == dim-2) { 783 const PetscInt hybface = p + pMaxNew[dep+1] + numSplitPoints[dep+1]; 784 785 /* Split old edge: old vertices in cone so no change */ 786 /* Split new edge: new vertices in cone */ 787 for (q = 0; q < coneSize; ++q) { 788 ierr = PetscFindInt(cone[q], numSplitPoints[dep-1], splitPoints[dep-1], &v);CHKERRQ(ierr); 789 790 coneNew[q] = v + pMaxNew[dep-1]; 791 } 792 ierr = DMPlexSetCone(sdm, splitp, coneNew);CHKERRQ(ierr); 793 /* Split old edge: Faces in positive side cells and old split faces */ 794 for (e = 0, q = 0; e < supportSize; ++e) { 795 PetscInt val; 796 797 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 798 if (val == dim-1) { 799 supportNew[q++] = support[e] + depthOffset[dep+1]; 800 } else if (val == (shift + dim-1)) { 801 supportNew[q++] = support[e] + depthOffset[dep+1]; 802 } 803 } 804 supportNew[q++] = p + pMaxNew[dep+1] + numSplitPoints[dep+1]; 805 ierr = DMPlexSetSupport(sdm, newp, supportNew);CHKERRQ(ierr); 806 /* Split new edge: Faces in negative side cells and new split faces */ 807 for (e = 0, q = 0; e < supportSize; ++e) { 808 PetscInt val, face; 809 810 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 811 if (val == dim-1) { 812 ierr = PetscFindInt(support[e], numSplitPoints[dep+1], splitPoints[dep+1], &face);CHKERRQ(ierr); 813 if (face < 0) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Face %d is not a split face", support[e]); 814 supportNew[q++] = face + pMaxNew[dep+1]; 815 } else if (val == -(shift + dim-1)) { 816 supportNew[q++] = support[e] + depthOffset[dep+1]; 817 } 818 } 819 supportNew[q++] = p + pMaxNew[dep+1] + numSplitPoints[dep+1]; 820 ierr = DMPlexSetSupport(sdm, splitp, supportNew);CHKERRQ(ierr); 821 /* Hybrid face */ 822 coneNew[0] = newp; 823 coneNew[1] = splitp; 824 for (v = 0; v < coneSize; ++v) { 825 PetscInt vertex; 826 ierr = PetscFindInt(cone[v], numSplitPoints[dep-1], splitPoints[dep-1], &vertex);CHKERRQ(ierr); 827 if (vertex < 0) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Vertex %d is not a split vertex", support[e]); 828 coneNew[2+v] = vertex + pMaxNew[dep] + numSplitPoints[dep]; 829 } 830 ierr = DMPlexSetCone(sdm, hybface, coneNew);CHKERRQ(ierr); 831 for (e = 0, qf = 0; e < supportSize; ++e) { 832 PetscInt val, face; 833 834 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 835 if (val == dim-1) { 836 ierr = PetscFindInt(support[e], numSplitPoints[dep+1], splitPoints[dep+1], &face);CHKERRQ(ierr); 837 if (face < 0) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Face %d is not a split face", support[e]); 838 supportNew[qf++] = face + pMaxNew[dep+2] + numSplitPoints[dep+2]; 839 } 840 } 841 ierr = DMPlexSetSupport(sdm, hybface, supportNew);CHKERRQ(ierr); 842 } 843 } 844 } 845 /* Step 6b: Replace split points in negative side cones */ 846 for (sp = 0; sp < numSP; ++sp) { 847 PetscInt dep = values[sp]; 848 IS pIS; 849 PetscInt numPoints; 850 const PetscInt *points; 851 852 if (dep >= 0) continue; 853 ierr = DMLabelGetStratumIS(label, dep, &pIS);CHKERRQ(ierr); 854 if (!pIS) continue; 855 dep = -dep - shift; 856 ierr = ISGetLocalSize(pIS, &numPoints);CHKERRQ(ierr); 857 ierr = ISGetIndices(pIS, &points);CHKERRQ(ierr); 858 for (p = 0; p < numPoints; ++p) { 859 const PetscInt oldp = points[p]; 860 const PetscInt newp = depthOffset[dep] + oldp; 861 const PetscInt *cone; 862 PetscInt coneSize, c; 863 /* PetscBool replaced = PETSC_FALSE; */ 864 865 /* Negative edge: replace split vertex */ 866 /* Negative cell: replace split face */ 867 ierr = DMPlexGetConeSize(sdm, newp, &coneSize);CHKERRQ(ierr); 868 ierr = DMPlexGetCone(sdm, newp, &cone);CHKERRQ(ierr); 869 for (c = 0; c < coneSize; ++c) { 870 const PetscInt coldp = cone[c] - depthOffset[dep-1]; 871 PetscInt csplitp, cp, val; 872 873 ierr = DMLabelGetValue(label, coldp, &val);CHKERRQ(ierr); 874 if (val == dep-1) { 875 ierr = PetscFindInt(coldp, numSplitPoints[dep-1], splitPoints[dep-1], &cp);CHKERRQ(ierr); 876 if (cp < 0) SETERRQ2(comm, PETSC_ERR_ARG_WRONG, "Point %d is not a split point of dimension %d", oldp, dep-1); 877 csplitp = pMaxNew[dep-1] + cp; 878 ierr = DMPlexInsertCone(sdm, newp, c, csplitp);CHKERRQ(ierr); 879 /* replaced = PETSC_TRUE; */ 880 } 881 } 882 /* Cells with only a vertex or edge on the submesh have no replacement */ 883 /* if (!replaced) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "The cone of point %d does not contain split points", oldp); */ 884 } 885 ierr = ISRestoreIndices(pIS, &points);CHKERRQ(ierr); 886 ierr = ISDestroy(&pIS);CHKERRQ(ierr); 887 } 888 /* Step 7: Stratify */ 889 ierr = DMPlexStratify(sdm);CHKERRQ(ierr); 890 /* Step 8: Coordinates */ 891 ierr = DMPlexShiftCoordinates_Internal(dm, depthShift, sdm);CHKERRQ(ierr); 892 ierr = DMPlexGetCoordinateSection(sdm, &coordSection);CHKERRQ(ierr); 893 ierr = DMGetCoordinatesLocal(sdm, &coordinates);CHKERRQ(ierr); 894 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 895 for (v = 0; v < (numSplitPoints ? numSplitPoints[0] : 0); ++v) { 896 const PetscInt newp = depthOffset[0] + splitPoints[0][v]; 897 const PetscInt splitp = pMaxNew[0] + v; 898 PetscInt dof, off, soff, d; 899 900 ierr = PetscSectionGetDof(coordSection, newp, &dof);CHKERRQ(ierr); 901 ierr = PetscSectionGetOffset(coordSection, newp, &off);CHKERRQ(ierr); 902 ierr = PetscSectionGetOffset(coordSection, splitp, &soff);CHKERRQ(ierr); 903 for (d = 0; d < dof; ++d) coords[soff+d] = coords[off+d]; 904 } 905 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 906 /* Step 9: SF, if I can figure this out we can split the mesh in parallel */ 907 ierr = DMPlexShiftSF_Internal(dm, depthShift, sdm);CHKERRQ(ierr); 908 /* Step 10: Labels */ 909 ierr = DMPlexShiftLabels_Internal(dm, depthShift, sdm);CHKERRQ(ierr); 910 ierr = DMPlexGetNumLabels(sdm, &numLabels);CHKERRQ(ierr); 911 for (dep = 0; dep <= depth; ++dep) { 912 for (p = 0; p < numSplitPoints[dep]; ++p) { 913 const PetscInt newp = depthOffset[dep] + splitPoints[dep][p]; 914 const PetscInt splitp = pMaxNew[dep] + p; 915 PetscInt l; 916 917 for (l = 0; l < numLabels; ++l) { 918 DMLabel mlabel; 919 const char *lname; 920 PetscInt val; 921 PetscBool isDepth; 922 923 ierr = DMPlexGetLabelName(sdm, l, &lname);CHKERRQ(ierr); 924 ierr = PetscStrcmp(lname, "depth", &isDepth);CHKERRQ(ierr); 925 if (isDepth) continue; 926 ierr = DMPlexGetLabel(sdm, lname, &mlabel);CHKERRQ(ierr); 927 ierr = DMLabelGetValue(mlabel, newp, &val);CHKERRQ(ierr); 928 if (val >= 0) { 929 ierr = DMLabelSetValue(mlabel, splitp, val);CHKERRQ(ierr); 930 #if 0 931 /* Do not put cohesive edges into the label */ 932 if (dep == 0) { 933 const PetscInt cedge = p + pMaxNew[dep+1] + numSplitPoints[dep+1]; 934 ierr = DMLabelSetValue(mlabel, cedge, val);CHKERRQ(ierr); 935 } else if (dep == dim-2) { 936 const PetscInt cface = p + pMaxNew[dep+1] + numSplitPoints[dep+1]; 937 ierr = DMLabelSetValue(mlabel, cface, val);CHKERRQ(ierr); 938 } 939 /* Do not put cohesive faces into the label */ 940 #endif 941 } 942 } 943 } 944 } 945 for (sp = 0; sp < numSP; ++sp) { 946 const PetscInt dep = values[sp]; 947 948 if ((dep < 0) || (dep > depth)) continue; 949 if (pointIS[dep]) {ierr = ISRestoreIndices(pointIS[dep], &splitPoints[dep]);CHKERRQ(ierr);} 950 ierr = ISDestroy(&pointIS[dep]);CHKERRQ(ierr); 951 } 952 if (label) { 953 ierr = ISRestoreIndices(valueIS, &values);CHKERRQ(ierr); 954 ierr = ISDestroy(&valueIS);CHKERRQ(ierr); 955 } 956 for (d = 0; d <= depth; ++d) { 957 ierr = DMPlexGetDepthStratum(sdm, d, NULL, &pEnd);CHKERRQ(ierr); 958 pMaxNew[d] = pEnd - numHybridPoints[d]; 959 } 960 ierr = DMPlexSetHybridBounds(sdm, depth >= 0 ? pMaxNew[depth] : PETSC_DETERMINE, depth>1 ? pMaxNew[depth-1] : PETSC_DETERMINE, depth>2 ? pMaxNew[1] : PETSC_DETERMINE, depth >= 0 ? pMaxNew[0] : PETSC_DETERMINE);CHKERRQ(ierr); 961 ierr = PetscFree3(depthShift, depthOffset, pMaxNew);CHKERRQ(ierr); 962 ierr = PetscFree3(coneNew, coneONew, supportNew);CHKERRQ(ierr); 963 ierr = PetscFree4(pointIS, numSplitPoints, numHybridPoints, splitPoints);CHKERRQ(ierr); 964 PetscFunctionReturn(0); 965 } 966 967 #undef __FUNCT__ 968 #define __FUNCT__ "DMPlexConstructCohesiveCells" 969 /*@C 970 DMPlexConstructCohesiveCells - Construct cohesive cells which split the face along an internal interface 971 972 Collective on dm 973 974 Input Parameters: 975 + dm - The original DM 976 - label - The label specifying the boundary faces (this could be auto-generated) 977 978 Output Parameters: 979 - dmSplit - The new DM 980 981 Level: developer 982 983 .seealso: DMCreate(), DMPlexLabelCohesiveComplete() 984 @*/ 985 PetscErrorCode DMPlexConstructCohesiveCells(DM dm, DMLabel label, DM *dmSplit) 986 { 987 DM sdm; 988 PetscInt dim; 989 PetscErrorCode ierr; 990 991 PetscFunctionBegin; 992 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 993 PetscValidPointer(dmSplit, 3); 994 ierr = DMCreate(PetscObjectComm((PetscObject)dm), &sdm);CHKERRQ(ierr); 995 ierr = DMSetType(sdm, DMPLEX);CHKERRQ(ierr); 996 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 997 ierr = DMPlexSetDimension(sdm, dim);CHKERRQ(ierr); 998 switch (dim) { 999 case 2: 1000 case 3: 1001 ierr = DMPlexConstructCohesiveCells_Internal(dm, label, sdm);CHKERRQ(ierr); 1002 break; 1003 default: 1004 SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Cannot construct cohesive cells for dimension %d", dim); 1005 } 1006 *dmSplit = sdm; 1007 PetscFunctionReturn(0); 1008 } 1009 1010 #undef __FUNCT__ 1011 #define __FUNCT__ "DMPlexLabelCohesiveComplete" 1012 /*@ 1013 DMPlexLabelCohesiveComplete - Starting with a label marking vertices on an internal surface, we add all other mesh pieces 1014 to complete the surface 1015 1016 Input Parameters: 1017 + dm - The DM 1018 . label - A DMLabel marking the surface vertices 1019 . flip - Flag to flip the submesh normal and replace points on the other side 1020 - subdm - The subDM associated with the label, or NULL 1021 1022 Output Parameter: 1023 . label - A DMLabel marking all surface points 1024 1025 Level: developer 1026 1027 .seealso: DMPlexConstructCohesiveCells(), DMPlexLabelComplete() 1028 @*/ 1029 PetscErrorCode DMPlexLabelCohesiveComplete(DM dm, DMLabel label, PetscBool flip, DM subdm) 1030 { 1031 DMLabel depthLabel; 1032 IS dimIS, subpointIS; 1033 const PetscInt *points, *subpoints; 1034 const PetscInt rev = flip ? -1 : 1; 1035 PetscInt shift = 100, dim, dep, cStart, cEnd, numPoints, numSubpoints, p, val; 1036 PetscErrorCode ierr; 1037 1038 PetscFunctionBegin; 1039 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 1040 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1041 if (subdm) { 1042 ierr = DMPlexCreateSubpointIS(subdm, &subpointIS);CHKERRQ(ierr); 1043 if (subpointIS) { 1044 ierr = ISGetLocalSize(subpointIS, &numSubpoints);CHKERRQ(ierr); 1045 ierr = ISGetIndices(subpointIS, &subpoints);CHKERRQ(ierr); 1046 } 1047 } 1048 /* Mark cell on the fault, and its faces which touch the fault: cell orientation for face gives the side of the fault */ 1049 ierr = DMLabelGetStratumIS(label, dim-1, &dimIS);CHKERRQ(ierr); 1050 if (!dimIS) PetscFunctionReturn(0); 1051 ierr = ISGetLocalSize(dimIS, &numPoints);CHKERRQ(ierr); 1052 ierr = ISGetIndices(dimIS, &points);CHKERRQ(ierr); 1053 for (p = 0; p < numPoints; ++p) { /* Loop over fault faces */ 1054 const PetscInt *support; 1055 PetscInt supportSize, s; 1056 1057 ierr = DMPlexGetSupportSize(dm, points[p], &supportSize);CHKERRQ(ierr); 1058 if (supportSize != 2) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Split face %d has %d != 2 supports", points[p], supportSize); 1059 ierr = DMPlexGetSupport(dm, points[p], &support);CHKERRQ(ierr); 1060 for (s = 0; s < supportSize; ++s) { 1061 const PetscInt *cone, *ornt; 1062 PetscInt coneSize, c; 1063 PetscBool pos = PETSC_TRUE; 1064 1065 ierr = DMPlexGetConeSize(dm, support[s], &coneSize);CHKERRQ(ierr); 1066 ierr = DMPlexGetCone(dm, support[s], &cone);CHKERRQ(ierr); 1067 ierr = DMPlexGetConeOrientation(dm, support[s], &ornt);CHKERRQ(ierr); 1068 for (c = 0; c < coneSize; ++c) { 1069 if (cone[c] == points[p]) { 1070 PetscInt o = ornt[c]; 1071 1072 if (subdm) { 1073 const PetscInt *subcone, *subornt; 1074 PetscInt subpoint, subface, subconeSize, sc; 1075 1076 ierr = PetscFindInt(support[s], numSubpoints, subpoints, &subpoint);CHKERRQ(ierr); 1077 ierr = PetscFindInt(points[p], numSubpoints, subpoints, &subface);CHKERRQ(ierr); 1078 ierr = DMPlexGetConeSize(subdm, subpoint, &subconeSize);CHKERRQ(ierr); 1079 ierr = DMPlexGetCone(subdm, subpoint, &subcone);CHKERRQ(ierr); 1080 ierr = DMPlexGetConeOrientation(subdm, subpoint, &subornt);CHKERRQ(ierr); 1081 for (sc = 0; sc < subconeSize; ++sc) { 1082 if (subcone[sc] == subface) { 1083 o = subornt[0]; 1084 break; 1085 } 1086 } 1087 if (sc >= subconeSize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not find point %d in cone for subpoint %d", points[p], subpoint); 1088 } 1089 if (o >= 0) { 1090 ierr = DMLabelSetValue(label, support[s], rev*(shift+dim));CHKERRQ(ierr); 1091 pos = rev > 0 ? PETSC_TRUE : PETSC_FALSE; 1092 } else { 1093 ierr = DMLabelSetValue(label, support[s], -rev*(shift+dim));CHKERRQ(ierr); 1094 pos = rev > 0 ? PETSC_FALSE : PETSC_TRUE; 1095 } 1096 break; 1097 } 1098 } 1099 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]); 1100 /* Put faces touching the fault in the label */ 1101 for (c = 0; c < coneSize; ++c) { 1102 const PetscInt point = cone[c]; 1103 1104 ierr = DMLabelGetValue(label, point, &val);CHKERRQ(ierr); 1105 if (val == -1) { 1106 PetscInt *closure = NULL; 1107 PetscInt closureSize, cl; 1108 1109 ierr = DMPlexGetTransitiveClosure(dm, point, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1110 for (cl = 0; cl < closureSize*2; cl += 2) { 1111 const PetscInt clp = closure[cl]; 1112 1113 ierr = DMLabelGetValue(label, clp, &val);CHKERRQ(ierr); 1114 if ((val >= 0) && (val < dim-1)) { 1115 ierr = DMLabelSetValue(label, point, pos == PETSC_TRUE ? shift+dim-1 : -(shift+dim-1));CHKERRQ(ierr); 1116 break; 1117 } 1118 } 1119 ierr = DMPlexRestoreTransitiveClosure(dm, point, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1120 } 1121 } 1122 } 1123 } 1124 if (subdm) { 1125 if (subpointIS) {ierr = ISRestoreIndices(subpointIS, &subpoints);CHKERRQ(ierr);} 1126 ierr = ISDestroy(&subpointIS);CHKERRQ(ierr); 1127 } 1128 ierr = ISRestoreIndices(dimIS, &points);CHKERRQ(ierr); 1129 ierr = ISDestroy(&dimIS);CHKERRQ(ierr); 1130 /* Search for other cells/faces/edges connected to the fault by a vertex */ 1131 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1132 ierr = DMLabelGetStratumIS(label, 0, &dimIS);CHKERRQ(ierr); 1133 if (!dimIS) PetscFunctionReturn(0); 1134 ierr = ISGetLocalSize(dimIS, &numPoints);CHKERRQ(ierr); 1135 ierr = ISGetIndices(dimIS, &points);CHKERRQ(ierr); 1136 for (p = 0; p < numPoints; ++p) { /* Loop over fault vertices */ 1137 PetscInt *star = NULL; 1138 PetscInt starSize, s; 1139 PetscInt again = 1; /* 0: Finished 1: Keep iterating after a change 2: No change */ 1140 1141 /* All points connected to the fault are inside a cell, so at the top level we will only check cells */ 1142 ierr = DMPlexGetTransitiveClosure(dm, points[p], PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1143 while (again) { 1144 if (again > 1) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Could not classify all cells connected to the fault"); 1145 again = 0; 1146 for (s = 0; s < starSize*2; s += 2) { 1147 const PetscInt point = star[s]; 1148 const PetscInt *cone; 1149 PetscInt coneSize, c; 1150 1151 if ((point < cStart) || (point >= cEnd)) continue; 1152 ierr = DMLabelGetValue(label, point, &val);CHKERRQ(ierr); 1153 if (val != -1) continue; 1154 again = again == 1 ? 1 : 2; 1155 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 1156 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 1157 for (c = 0; c < coneSize; ++c) { 1158 ierr = DMLabelGetValue(label, cone[c], &val);CHKERRQ(ierr); 1159 if (val != -1) { 1160 const PetscInt *ccone; 1161 PetscInt cconeSize, cc, side; 1162 1163 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); 1164 if (val > 0) side = 1; 1165 else side = -1; 1166 ierr = DMLabelSetValue(label, point, side*(shift+dim));CHKERRQ(ierr); 1167 /* Mark cell faces which touch the fault */ 1168 ierr = DMPlexGetConeSize(dm, point, &cconeSize);CHKERRQ(ierr); 1169 ierr = DMPlexGetCone(dm, point, &ccone);CHKERRQ(ierr); 1170 for (cc = 0; cc < cconeSize; ++cc) { 1171 PetscInt *closure = NULL; 1172 PetscInt closureSize, cl; 1173 1174 ierr = DMLabelGetValue(label, ccone[cc], &val);CHKERRQ(ierr); 1175 if (val != -1) continue; 1176 ierr = DMPlexGetTransitiveClosure(dm, ccone[cc], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1177 for (cl = 0; cl < closureSize*2; cl += 2) { 1178 const PetscInt clp = closure[cl]; 1179 1180 ierr = DMLabelGetValue(label, clp, &val);CHKERRQ(ierr); 1181 if (val == -1) continue; 1182 ierr = DMLabelSetValue(label, ccone[cc], side*(shift+dim-1));CHKERRQ(ierr); 1183 break; 1184 } 1185 ierr = DMPlexRestoreTransitiveClosure(dm, ccone[cc], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1186 } 1187 again = 1; 1188 break; 1189 } 1190 } 1191 } 1192 } 1193 /* Classify the rest by cell membership */ 1194 for (s = 0; s < starSize*2; s += 2) { 1195 const PetscInt point = star[s]; 1196 1197 ierr = DMLabelGetValue(label, point, &val);CHKERRQ(ierr); 1198 if (val == -1) { 1199 PetscInt *sstar = NULL; 1200 PetscInt sstarSize, ss; 1201 PetscBool marked = PETSC_FALSE; 1202 1203 ierr = DMPlexGetTransitiveClosure(dm, point, PETSC_FALSE, &sstarSize, &sstar);CHKERRQ(ierr); 1204 for (ss = 0; ss < sstarSize*2; ss += 2) { 1205 const PetscInt spoint = sstar[ss]; 1206 1207 if ((spoint < cStart) || (spoint >= cEnd)) continue; 1208 ierr = DMLabelGetValue(label, spoint, &val);CHKERRQ(ierr); 1209 if (val == -1) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Cell %d in star of %d does not have a valid label", spoint, point); 1210 ierr = DMLabelGetValue(depthLabel, point, &dep);CHKERRQ(ierr); 1211 if (val > 0) { 1212 ierr = DMLabelSetValue(label, point, shift+dep);CHKERRQ(ierr); 1213 } else { 1214 ierr = DMLabelSetValue(label, point, -(shift+dep));CHKERRQ(ierr); 1215 } 1216 marked = PETSC_TRUE; 1217 break; 1218 } 1219 ierr = DMPlexRestoreTransitiveClosure(dm, point, PETSC_FALSE, &sstarSize, &sstar);CHKERRQ(ierr); 1220 if (!marked) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Point %d could not be classified", point); 1221 } 1222 } 1223 ierr = DMPlexRestoreTransitiveClosure(dm, points[p], PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1224 } 1225 ierr = ISRestoreIndices(dimIS, &points);CHKERRQ(ierr); 1226 ierr = ISDestroy(&dimIS);CHKERRQ(ierr); 1227 PetscFunctionReturn(0); 1228 } 1229 1230 #undef __FUNCT__ 1231 #define __FUNCT__ "DMPlexCreateHybridMesh" 1232 /*@C 1233 DMPlexCreateHybridMesh - Create a mesh with hybrid cells along an internal interface 1234 1235 Collective on dm 1236 1237 Input Parameters: 1238 + dm - The original DM 1239 - labelName - The label specifying the interface vertices 1240 1241 Output Parameters: 1242 + hybridLabel - The label fully marking the interface 1243 - dmHybrid - The new DM 1244 1245 Level: developer 1246 1247 .seealso: DMPlexConstructCohesiveCells(), DMPlexLabelCohesiveComplete(), DMCreate() 1248 @*/ 1249 PetscErrorCode DMPlexCreateHybridMesh(DM dm, DMLabel label, DMLabel *hybridLabel, DM *dmHybrid) 1250 { 1251 DM idm; 1252 DMLabel subpointMap, hlabel; 1253 PetscInt dim; 1254 PetscErrorCode ierr; 1255 1256 PetscFunctionBegin; 1257 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1258 if (hybridLabel) PetscValidPointer(hybridLabel, 3); 1259 PetscValidPointer(dmHybrid, 4); 1260 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1261 ierr = DMPlexCreateSubmesh(dm, label, 1, &idm);CHKERRQ(ierr); 1262 ierr = DMPlexOrient(idm);CHKERRQ(ierr); 1263 ierr = DMPlexGetSubpointMap(idm, &subpointMap);CHKERRQ(ierr); 1264 ierr = DMLabelDuplicate(subpointMap, &hlabel);CHKERRQ(ierr); 1265 ierr = DMLabelClearStratum(hlabel, dim);CHKERRQ(ierr); 1266 ierr = DMPlexLabelCohesiveComplete(dm, hlabel, PETSC_FALSE, idm);CHKERRQ(ierr); 1267 ierr = DMDestroy(&idm);CHKERRQ(ierr); 1268 ierr = DMPlexConstructCohesiveCells(dm, hlabel, dmHybrid);CHKERRQ(ierr); 1269 if (hybridLabel) *hybridLabel = hlabel; 1270 else {ierr = DMLabelDestroy(&hlabel);CHKERRQ(ierr);} 1271 PetscFunctionReturn(0); 1272 } 1273 1274 #undef __FUNCT__ 1275 #define __FUNCT__ "DMPlexMarkSubmesh_Uninterpolated" 1276 /* Here we need the explicit assumption that: 1277 1278 For any marked cell, the marked vertices constitute a single face 1279 */ 1280 static PetscErrorCode DMPlexMarkSubmesh_Uninterpolated(DM dm, DMLabel vertexLabel, PetscInt value, DMLabel subpointMap, PetscInt *numFaces, PetscInt *nFV, DM subdm) 1281 { 1282 IS subvertexIS = NULL; 1283 const PetscInt *subvertices; 1284 PetscInt *pStart, *pEnd, *pMax, pSize; 1285 PetscInt depth, dim, d, numSubVerticesInitial = 0, v; 1286 PetscErrorCode ierr; 1287 1288 PetscFunctionBegin; 1289 *numFaces = 0; 1290 *nFV = 0; 1291 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 1292 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1293 pSize = PetscMax(depth, dim) + 1; 1294 ierr = PetscMalloc3(pSize,PetscInt,&pStart,pSize,PetscInt,&pEnd,pSize,PetscInt,&pMax);CHKERRQ(ierr); 1295 ierr = DMPlexGetHybridBounds(dm, depth >= 0 ? &pMax[depth] : NULL, depth>1 ? &pMax[depth-1] : NULL, depth>2 ? &pMax[1] : NULL, &pMax[0]);CHKERRQ(ierr); 1296 for (d = 0; d <= depth; ++d) { 1297 ierr = DMPlexGetDepthStratum(dm, d, &pStart[d], &pEnd[d]);CHKERRQ(ierr); 1298 if (pMax[d] >= 0) pEnd[d] = PetscMin(pEnd[d], pMax[d]); 1299 } 1300 /* Loop over initial vertices and mark all faces in the collective star() */ 1301 if (vertexLabel) {ierr = DMLabelGetStratumIS(vertexLabel, value, &subvertexIS);CHKERRQ(ierr);} 1302 if (subvertexIS) { 1303 ierr = ISGetSize(subvertexIS, &numSubVerticesInitial);CHKERRQ(ierr); 1304 ierr = ISGetIndices(subvertexIS, &subvertices);CHKERRQ(ierr); 1305 } 1306 for (v = 0; v < numSubVerticesInitial; ++v) { 1307 const PetscInt vertex = subvertices[v]; 1308 PetscInt *star = NULL; 1309 PetscInt starSize, s, numCells = 0, c; 1310 1311 ierr = DMPlexGetTransitiveClosure(dm, vertex, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1312 for (s = 0; s < starSize*2; s += 2) { 1313 const PetscInt point = star[s]; 1314 if ((point >= pStart[depth]) && (point < pEnd[depth])) star[numCells++] = point; 1315 } 1316 for (c = 0; c < numCells; ++c) { 1317 const PetscInt cell = star[c]; 1318 PetscInt *closure = NULL; 1319 PetscInt closureSize, cl; 1320 PetscInt cellLoc, numCorners = 0, faceSize = 0; 1321 1322 ierr = DMLabelGetValue(subpointMap, cell, &cellLoc);CHKERRQ(ierr); 1323 if (cellLoc == 2) continue; 1324 if (cellLoc >= 0) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Cell %d has dimension %d in the surface label", cell, cellLoc); 1325 ierr = DMPlexGetTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1326 for (cl = 0; cl < closureSize*2; cl += 2) { 1327 const PetscInt point = closure[cl]; 1328 PetscInt vertexLoc; 1329 1330 if ((point >= pStart[0]) && (point < pEnd[0])) { 1331 ++numCorners; 1332 ierr = DMLabelGetValue(vertexLabel, point, &vertexLoc);CHKERRQ(ierr); 1333 if (vertexLoc == value) closure[faceSize++] = point; 1334 } 1335 } 1336 if (!(*nFV)) {ierr = DMPlexGetNumFaceVertices(dm, dim, numCorners, nFV);CHKERRQ(ierr);} 1337 if (faceSize > *nFV) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Invalid submesh: Too many vertices %d of an element on the surface", faceSize); 1338 if (faceSize == *nFV) { 1339 const PetscInt *cells = NULL; 1340 PetscInt numCells, nc; 1341 1342 ++(*numFaces); 1343 for (cl = 0; cl < faceSize; ++cl) { 1344 ierr = DMLabelSetValue(subpointMap, closure[cl], 0);CHKERRQ(ierr); 1345 } 1346 ierr = DMPlexGetJoin(dm, faceSize, closure, &numCells, &cells);CHKERRQ(ierr); 1347 for (nc = 0; nc < numCells; ++nc) { 1348 ierr = DMLabelSetValue(subpointMap, cells[nc], 2);CHKERRQ(ierr); 1349 } 1350 ierr = DMPlexRestoreJoin(dm, faceSize, closure, &numCells, &cells);CHKERRQ(ierr); 1351 } 1352 ierr = DMPlexRestoreTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1353 } 1354 ierr = DMPlexRestoreTransitiveClosure(dm, vertex, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1355 } 1356 if (subvertexIS) { 1357 ierr = ISRestoreIndices(subvertexIS, &subvertices);CHKERRQ(ierr); 1358 } 1359 ierr = ISDestroy(&subvertexIS);CHKERRQ(ierr); 1360 ierr = PetscFree3(pStart,pEnd,pMax);CHKERRQ(ierr); 1361 PetscFunctionReturn(0); 1362 } 1363 1364 #undef __FUNCT__ 1365 #define __FUNCT__ "DMPlexMarkSubmesh_Interpolated" 1366 static PetscErrorCode DMPlexMarkSubmesh_Interpolated(DM dm, DMLabel vertexLabel, PetscInt value, DMLabel subpointMap, DM subdm) 1367 { 1368 IS subvertexIS; 1369 const PetscInt *subvertices; 1370 PetscInt *pStart, *pEnd, *pMax; 1371 PetscInt dim, d, numSubVerticesInitial = 0, v; 1372 PetscErrorCode ierr; 1373 1374 PetscFunctionBegin; 1375 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1376 ierr = PetscMalloc3(dim+1,PetscInt,&pStart,dim+1,PetscInt,&pEnd,dim+1,PetscInt,&pMax);CHKERRQ(ierr); 1377 ierr = DMPlexGetHybridBounds(dm, &pMax[dim], dim>1 ? &pMax[dim-1] : NULL, dim > 2 ? &pMax[1] : NULL, &pMax[0]);CHKERRQ(ierr); 1378 for (d = 0; d <= dim; ++d) { 1379 ierr = DMPlexGetDepthStratum(dm, d, &pStart[d], &pEnd[d]);CHKERRQ(ierr); 1380 if (pMax[d] >= 0) pEnd[d] = PetscMin(pEnd[d], pMax[d]); 1381 } 1382 /* Loop over initial vertices and mark all faces in the collective star() */ 1383 ierr = DMLabelGetStratumIS(vertexLabel, value, &subvertexIS);CHKERRQ(ierr); 1384 if (subvertexIS) { 1385 ierr = ISGetSize(subvertexIS, &numSubVerticesInitial);CHKERRQ(ierr); 1386 ierr = ISGetIndices(subvertexIS, &subvertices);CHKERRQ(ierr); 1387 } 1388 for (v = 0; v < numSubVerticesInitial; ++v) { 1389 const PetscInt vertex = subvertices[v]; 1390 PetscInt *star = NULL; 1391 PetscInt starSize, s, numFaces = 0, f; 1392 1393 ierr = DMPlexGetTransitiveClosure(dm, vertex, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1394 for (s = 0; s < starSize*2; s += 2) { 1395 const PetscInt point = star[s]; 1396 if ((point >= pStart[dim-1]) && (point < pEnd[dim-1])) star[numFaces++] = point; 1397 } 1398 for (f = 0; f < numFaces; ++f) { 1399 const PetscInt face = star[f]; 1400 PetscInt *closure = NULL; 1401 PetscInt closureSize, c; 1402 PetscInt faceLoc; 1403 1404 ierr = DMLabelGetValue(subpointMap, face, &faceLoc);CHKERRQ(ierr); 1405 if (faceLoc == dim-1) continue; 1406 if (faceLoc >= 0) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Face %d has dimension %d in the surface label", face, faceLoc); 1407 ierr = DMPlexGetTransitiveClosure(dm, face, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1408 for (c = 0; c < closureSize*2; c += 2) { 1409 const PetscInt point = closure[c]; 1410 PetscInt vertexLoc; 1411 1412 if ((point >= pStart[0]) && (point < pEnd[0])) { 1413 ierr = DMLabelGetValue(vertexLabel, point, &vertexLoc);CHKERRQ(ierr); 1414 if (vertexLoc != value) break; 1415 } 1416 } 1417 if (c == closureSize*2) { 1418 const PetscInt *support; 1419 PetscInt supportSize, s; 1420 1421 for (c = 0; c < closureSize*2; c += 2) { 1422 const PetscInt point = closure[c]; 1423 1424 for (d = 0; d < dim; ++d) { 1425 if ((point >= pStart[d]) && (point < pEnd[d])) { 1426 ierr = DMLabelSetValue(subpointMap, point, d);CHKERRQ(ierr); 1427 break; 1428 } 1429 } 1430 } 1431 ierr = DMPlexGetSupportSize(dm, face, &supportSize);CHKERRQ(ierr); 1432 ierr = DMPlexGetSupport(dm, face, &support);CHKERRQ(ierr); 1433 for (s = 0; s < supportSize; ++s) { 1434 ierr = DMLabelSetValue(subpointMap, support[s], dim);CHKERRQ(ierr); 1435 } 1436 } 1437 ierr = DMPlexRestoreTransitiveClosure(dm, face, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1438 } 1439 ierr = DMPlexRestoreTransitiveClosure(dm, vertex, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1440 } 1441 if (subvertexIS) { 1442 ierr = ISRestoreIndices(subvertexIS, &subvertices);CHKERRQ(ierr); 1443 } 1444 ierr = ISDestroy(&subvertexIS);CHKERRQ(ierr); 1445 ierr = PetscFree3(pStart,pEnd,pMax);CHKERRQ(ierr); 1446 PetscFunctionReturn(0); 1447 } 1448 1449 #undef __FUNCT__ 1450 #define __FUNCT__ "DMPlexMarkCohesiveSubmesh_Uninterpolated" 1451 static PetscErrorCode DMPlexMarkCohesiveSubmesh_Uninterpolated(DM dm, PetscBool hasLagrange, const char labelname[], PetscInt value, DMLabel subpointMap, PetscInt *numFaces, PetscInt *nFV, PetscInt *subCells[], DM subdm) 1452 { 1453 DMLabel label = NULL; 1454 const PetscInt *cone; 1455 PetscInt dim, cMax, cEnd, c, subc = 0, p, coneSize; 1456 PetscErrorCode ierr; 1457 1458 PetscFunctionBegin; 1459 *numFaces = 0; 1460 *nFV = 0; 1461 if (labelname) {ierr = DMPlexGetLabel(dm, labelname, &label);CHKERRQ(ierr);} 1462 *subCells = NULL; 1463 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1464 ierr = DMPlexGetHeightStratum(dm, 0, NULL, &cEnd);CHKERRQ(ierr); 1465 ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); 1466 if (cMax < 0) PetscFunctionReturn(0); 1467 if (label) { 1468 for (c = cMax; c < cEnd; ++c) { 1469 PetscInt val; 1470 1471 ierr = DMLabelGetValue(label, c, &val);CHKERRQ(ierr); 1472 if (val == value) { 1473 ++(*numFaces); 1474 ierr = DMPlexGetConeSize(dm, c, &coneSize);CHKERRQ(ierr); 1475 } 1476 } 1477 } else { 1478 *numFaces = cEnd - cMax; 1479 ierr = DMPlexGetConeSize(dm, cMax, &coneSize);CHKERRQ(ierr); 1480 } 1481 *nFV = hasLagrange ? coneSize/3 : coneSize/2; 1482 ierr = PetscMalloc(*numFaces *2 * sizeof(PetscInt), subCells);CHKERRQ(ierr); 1483 for (c = cMax; c < cEnd; ++c) { 1484 const PetscInt *cells; 1485 PetscInt numCells; 1486 1487 if (label) { 1488 PetscInt val; 1489 1490 ierr = DMLabelGetValue(label, c, &val);CHKERRQ(ierr); 1491 if (val != value) continue; 1492 } 1493 ierr = DMPlexGetCone(dm, c, &cone);CHKERRQ(ierr); 1494 for (p = 0; p < *nFV; ++p) { 1495 ierr = DMLabelSetValue(subpointMap, cone[p], 0);CHKERRQ(ierr); 1496 } 1497 /* Negative face */ 1498 ierr = DMPlexGetJoin(dm, *nFV, cone, &numCells, &cells);CHKERRQ(ierr); 1499 /* Not true in parallel 1500 if (numCells != 2) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive cells should separate two cells"); */ 1501 for (p = 0; p < numCells; ++p) { 1502 ierr = DMLabelSetValue(subpointMap, cells[p], 2);CHKERRQ(ierr); 1503 (*subCells)[subc++] = cells[p]; 1504 } 1505 ierr = DMPlexRestoreJoin(dm, *nFV, cone, &numCells, &cells);CHKERRQ(ierr); 1506 /* Positive face is not included */ 1507 } 1508 PetscFunctionReturn(0); 1509 } 1510 1511 #undef __FUNCT__ 1512 #define __FUNCT__ "DMPlexMarkCohesiveSubmesh_Interpolated" 1513 static PetscErrorCode DMPlexMarkCohesiveSubmesh_Interpolated(DM dm, PetscBool hasLagrange, const char labelname[], PetscInt value, DMLabel subpointMap, DM subdm) 1514 { 1515 DMLabel label = NULL; 1516 PetscInt *pStart, *pEnd; 1517 PetscInt dim, cMax, cEnd, c, d; 1518 PetscErrorCode ierr; 1519 1520 PetscFunctionBegin; 1521 if (labelname) {ierr = DMPlexGetLabel(dm, labelname, &label);CHKERRQ(ierr);} 1522 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1523 ierr = DMPlexGetHeightStratum(dm, 0, NULL, &cEnd);CHKERRQ(ierr); 1524 ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); 1525 if (cMax < 0) PetscFunctionReturn(0); 1526 ierr = PetscMalloc2(dim+1,PetscInt,&pStart,dim+1,PetscInt,&pEnd);CHKERRQ(ierr); 1527 for (d = 0; d <= dim; ++d) { 1528 ierr = DMPlexGetDepthStratum(dm, d, &pStart[d], &pEnd[d]);CHKERRQ(ierr); 1529 } 1530 for (c = cMax; c < cEnd; ++c) { 1531 const PetscInt *cone; 1532 PetscInt *closure = NULL; 1533 PetscInt coneSize, closureSize, cl; 1534 1535 if (label) { 1536 PetscInt val; 1537 1538 ierr = DMLabelGetValue(label, c, &val);CHKERRQ(ierr); 1539 if (val != value) continue; 1540 } 1541 ierr = DMPlexGetConeSize(dm, c, &coneSize);CHKERRQ(ierr); 1542 if (hasLagrange) { 1543 if (coneSize != 3) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive cells should separate two cells"); 1544 } else { 1545 if (coneSize != 2) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive cells should separate two cells"); 1546 } 1547 /* Negative face */ 1548 ierr = DMPlexGetCone(dm, c, &cone);CHKERRQ(ierr); 1549 ierr = DMPlexGetTransitiveClosure(dm, cone[0], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1550 for (cl = 0; cl < closureSize*2; cl += 2) { 1551 const PetscInt point = closure[cl]; 1552 1553 for (d = 0; d <= dim; ++d) { 1554 if ((point >= pStart[d]) && (point < pEnd[d])) { 1555 ierr = DMLabelSetValue(subpointMap, point, d);CHKERRQ(ierr); 1556 break; 1557 } 1558 } 1559 } 1560 ierr = DMPlexRestoreTransitiveClosure(dm, cone[0], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1561 /* Cells -- positive face is not included */ 1562 for (cl = 0; cl < 1; ++cl) { 1563 const PetscInt *support; 1564 PetscInt supportSize, s; 1565 1566 ierr = DMPlexGetSupportSize(dm, cone[cl], &supportSize);CHKERRQ(ierr); 1567 if (supportSize != 2) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive faces should separate two cells"); 1568 ierr = DMPlexGetSupport(dm, cone[cl], &support);CHKERRQ(ierr); 1569 for (s = 0; s < supportSize; ++s) { 1570 ierr = DMLabelSetValue(subpointMap, support[s], dim);CHKERRQ(ierr); 1571 } 1572 } 1573 } 1574 ierr = PetscFree2(pStart, pEnd);CHKERRQ(ierr); 1575 PetscFunctionReturn(0); 1576 } 1577 1578 #undef __FUNCT__ 1579 #define __FUNCT__ "DMPlexGetFaceOrientation" 1580 PetscErrorCode DMPlexGetFaceOrientation(DM dm, PetscInt cell, PetscInt numCorners, PetscInt indices[], PetscInt oppositeVertex, PetscInt origVertices[], PetscInt faceVertices[], PetscBool *posOriented) 1581 { 1582 MPI_Comm comm; 1583 PetscBool posOrient = PETSC_FALSE; 1584 const PetscInt debug = 0; 1585 PetscInt cellDim, faceSize, f; 1586 PetscErrorCode ierr; 1587 1588 PetscFunctionBegin; 1589 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 1590 ierr = DMPlexGetDimension(dm, &cellDim);CHKERRQ(ierr); 1591 if (debug) {PetscPrintf(comm, "cellDim: %d numCorners: %d\n", cellDim, numCorners);CHKERRQ(ierr);} 1592 1593 if (cellDim == 1 && numCorners == 2) { 1594 /* Triangle */ 1595 faceSize = numCorners-1; 1596 posOrient = !(oppositeVertex%2) ? PETSC_TRUE : PETSC_FALSE; 1597 } else if (cellDim == 2 && numCorners == 3) { 1598 /* Triangle */ 1599 faceSize = numCorners-1; 1600 posOrient = !(oppositeVertex%2) ? PETSC_TRUE : PETSC_FALSE; 1601 } else if (cellDim == 3 && numCorners == 4) { 1602 /* Tetrahedron */ 1603 faceSize = numCorners-1; 1604 posOrient = (oppositeVertex%2) ? PETSC_TRUE : PETSC_FALSE; 1605 } else if (cellDim == 1 && numCorners == 3) { 1606 /* Quadratic line */ 1607 faceSize = 1; 1608 posOrient = PETSC_TRUE; 1609 } else if (cellDim == 2 && numCorners == 4) { 1610 /* Quads */ 1611 faceSize = 2; 1612 if ((indices[1] > indices[0]) && (indices[1] - indices[0] == 1)) { 1613 posOrient = PETSC_TRUE; 1614 } else if ((indices[0] == 3) && (indices[1] == 0)) { 1615 posOrient = PETSC_TRUE; 1616 } else { 1617 if (((indices[0] > indices[1]) && (indices[0] - indices[1] == 1)) || ((indices[0] == 0) && (indices[1] == 3))) { 1618 posOrient = PETSC_FALSE; 1619 } else SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid quad crossedge"); 1620 } 1621 } else if (cellDim == 2 && numCorners == 6) { 1622 /* Quadratic triangle (I hate this) */ 1623 /* Edges are determined by the first 2 vertices (corners of edges) */ 1624 const PetscInt faceSizeTri = 3; 1625 PetscInt sortedIndices[3], i, iFace; 1626 PetscBool found = PETSC_FALSE; 1627 PetscInt faceVerticesTriSorted[9] = { 1628 0, 3, 4, /* bottom */ 1629 1, 4, 5, /* right */ 1630 2, 3, 5, /* left */ 1631 }; 1632 PetscInt faceVerticesTri[9] = { 1633 0, 3, 4, /* bottom */ 1634 1, 4, 5, /* right */ 1635 2, 5, 3, /* left */ 1636 }; 1637 1638 faceSize = faceSizeTri; 1639 for (i = 0; i < faceSizeTri; ++i) sortedIndices[i] = indices[i]; 1640 ierr = PetscSortInt(faceSizeTri, sortedIndices);CHKERRQ(ierr); 1641 for (iFace = 0; iFace < 3; ++iFace) { 1642 const PetscInt ii = iFace*faceSizeTri; 1643 PetscInt fVertex, cVertex; 1644 1645 if ((sortedIndices[0] == faceVerticesTriSorted[ii+0]) && 1646 (sortedIndices[1] == faceVerticesTriSorted[ii+1])) { 1647 for (fVertex = 0; fVertex < faceSizeTri; ++fVertex) { 1648 for (cVertex = 0; cVertex < faceSizeTri; ++cVertex) { 1649 if (indices[cVertex] == faceVerticesTri[ii+fVertex]) { 1650 faceVertices[fVertex] = origVertices[cVertex]; 1651 break; 1652 } 1653 } 1654 } 1655 found = PETSC_TRUE; 1656 break; 1657 } 1658 } 1659 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid tri crossface"); 1660 if (posOriented) *posOriented = PETSC_TRUE; 1661 PetscFunctionReturn(0); 1662 } else if (cellDim == 2 && numCorners == 9) { 1663 /* Quadratic quad (I hate this) */ 1664 /* Edges are determined by the first 2 vertices (corners of edges) */ 1665 const PetscInt faceSizeQuad = 3; 1666 PetscInt sortedIndices[3], i, iFace; 1667 PetscBool found = PETSC_FALSE; 1668 PetscInt faceVerticesQuadSorted[12] = { 1669 0, 1, 4, /* bottom */ 1670 1, 2, 5, /* right */ 1671 2, 3, 6, /* top */ 1672 0, 3, 7, /* left */ 1673 }; 1674 PetscInt faceVerticesQuad[12] = { 1675 0, 1, 4, /* bottom */ 1676 1, 2, 5, /* right */ 1677 2, 3, 6, /* top */ 1678 3, 0, 7, /* left */ 1679 }; 1680 1681 faceSize = faceSizeQuad; 1682 for (i = 0; i < faceSizeQuad; ++i) sortedIndices[i] = indices[i]; 1683 ierr = PetscSortInt(faceSizeQuad, sortedIndices);CHKERRQ(ierr); 1684 for (iFace = 0; iFace < 4; ++iFace) { 1685 const PetscInt ii = iFace*faceSizeQuad; 1686 PetscInt fVertex, cVertex; 1687 1688 if ((sortedIndices[0] == faceVerticesQuadSorted[ii+0]) && 1689 (sortedIndices[1] == faceVerticesQuadSorted[ii+1])) { 1690 for (fVertex = 0; fVertex < faceSizeQuad; ++fVertex) { 1691 for (cVertex = 0; cVertex < faceSizeQuad; ++cVertex) { 1692 if (indices[cVertex] == faceVerticesQuad[ii+fVertex]) { 1693 faceVertices[fVertex] = origVertices[cVertex]; 1694 break; 1695 } 1696 } 1697 } 1698 found = PETSC_TRUE; 1699 break; 1700 } 1701 } 1702 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid quad crossface"); 1703 if (posOriented) *posOriented = PETSC_TRUE; 1704 PetscFunctionReturn(0); 1705 } else if (cellDim == 3 && numCorners == 8) { 1706 /* Hexes 1707 A hex is two oriented quads with the normal of the first 1708 pointing up at the second. 1709 1710 7---6 1711 /| /| 1712 4---5 | 1713 | 1-|-2 1714 |/ |/ 1715 0---3 1716 1717 Faces are determined by the first 4 vertices (corners of faces) */ 1718 const PetscInt faceSizeHex = 4; 1719 PetscInt sortedIndices[4], i, iFace; 1720 PetscBool found = PETSC_FALSE; 1721 PetscInt faceVerticesHexSorted[24] = { 1722 0, 1, 2, 3, /* bottom */ 1723 4, 5, 6, 7, /* top */ 1724 0, 3, 4, 5, /* front */ 1725 2, 3, 5, 6, /* right */ 1726 1, 2, 6, 7, /* back */ 1727 0, 1, 4, 7, /* left */ 1728 }; 1729 PetscInt faceVerticesHex[24] = { 1730 1, 2, 3, 0, /* bottom */ 1731 4, 5, 6, 7, /* top */ 1732 0, 3, 5, 4, /* front */ 1733 3, 2, 6, 5, /* right */ 1734 2, 1, 7, 6, /* back */ 1735 1, 0, 4, 7, /* left */ 1736 }; 1737 1738 faceSize = faceSizeHex; 1739 for (i = 0; i < faceSizeHex; ++i) sortedIndices[i] = indices[i]; 1740 ierr = PetscSortInt(faceSizeHex, sortedIndices);CHKERRQ(ierr); 1741 for (iFace = 0; iFace < 6; ++iFace) { 1742 const PetscInt ii = iFace*faceSizeHex; 1743 PetscInt fVertex, cVertex; 1744 1745 if ((sortedIndices[0] == faceVerticesHexSorted[ii+0]) && 1746 (sortedIndices[1] == faceVerticesHexSorted[ii+1]) && 1747 (sortedIndices[2] == faceVerticesHexSorted[ii+2]) && 1748 (sortedIndices[3] == faceVerticesHexSorted[ii+3])) { 1749 for (fVertex = 0; fVertex < faceSizeHex; ++fVertex) { 1750 for (cVertex = 0; cVertex < faceSizeHex; ++cVertex) { 1751 if (indices[cVertex] == faceVerticesHex[ii+fVertex]) { 1752 faceVertices[fVertex] = origVertices[cVertex]; 1753 break; 1754 } 1755 } 1756 } 1757 found = PETSC_TRUE; 1758 break; 1759 } 1760 } 1761 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid hex crossface"); 1762 if (posOriented) *posOriented = PETSC_TRUE; 1763 PetscFunctionReturn(0); 1764 } else if (cellDim == 3 && numCorners == 10) { 1765 /* Quadratic tet */ 1766 /* Faces are determined by the first 3 vertices (corners of faces) */ 1767 const PetscInt faceSizeTet = 6; 1768 PetscInt sortedIndices[6], i, iFace; 1769 PetscBool found = PETSC_FALSE; 1770 PetscInt faceVerticesTetSorted[24] = { 1771 0, 1, 2, 6, 7, 8, /* bottom */ 1772 0, 3, 4, 6, 7, 9, /* front */ 1773 1, 4, 5, 7, 8, 9, /* right */ 1774 2, 3, 5, 6, 8, 9, /* left */ 1775 }; 1776 PetscInt faceVerticesTet[24] = { 1777 0, 1, 2, 6, 7, 8, /* bottom */ 1778 0, 4, 3, 6, 7, 9, /* front */ 1779 1, 5, 4, 7, 8, 9, /* right */ 1780 2, 3, 5, 8, 6, 9, /* left */ 1781 }; 1782 1783 faceSize = faceSizeTet; 1784 for (i = 0; i < faceSizeTet; ++i) sortedIndices[i] = indices[i]; 1785 ierr = PetscSortInt(faceSizeTet, sortedIndices);CHKERRQ(ierr); 1786 for (iFace=0; iFace < 4; ++iFace) { 1787 const PetscInt ii = iFace*faceSizeTet; 1788 PetscInt fVertex, cVertex; 1789 1790 if ((sortedIndices[0] == faceVerticesTetSorted[ii+0]) && 1791 (sortedIndices[1] == faceVerticesTetSorted[ii+1]) && 1792 (sortedIndices[2] == faceVerticesTetSorted[ii+2]) && 1793 (sortedIndices[3] == faceVerticesTetSorted[ii+3])) { 1794 for (fVertex = 0; fVertex < faceSizeTet; ++fVertex) { 1795 for (cVertex = 0; cVertex < faceSizeTet; ++cVertex) { 1796 if (indices[cVertex] == faceVerticesTet[ii+fVertex]) { 1797 faceVertices[fVertex] = origVertices[cVertex]; 1798 break; 1799 } 1800 } 1801 } 1802 found = PETSC_TRUE; 1803 break; 1804 } 1805 } 1806 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid tet crossface"); 1807 if (posOriented) *posOriented = PETSC_TRUE; 1808 PetscFunctionReturn(0); 1809 } else if (cellDim == 3 && numCorners == 27) { 1810 /* Quadratic hexes (I hate this) 1811 A hex is two oriented quads with the normal of the first 1812 pointing up at the second. 1813 1814 7---6 1815 /| /| 1816 4---5 | 1817 | 3-|-2 1818 |/ |/ 1819 0---1 1820 1821 Faces are determined by the first 4 vertices (corners of faces) */ 1822 const PetscInt faceSizeQuadHex = 9; 1823 PetscInt sortedIndices[9], i, iFace; 1824 PetscBool found = PETSC_FALSE; 1825 PetscInt faceVerticesQuadHexSorted[54] = { 1826 0, 1, 2, 3, 8, 9, 10, 11, 24, /* bottom */ 1827 4, 5, 6, 7, 12, 13, 14, 15, 25, /* top */ 1828 0, 1, 4, 5, 8, 12, 16, 17, 22, /* front */ 1829 1, 2, 5, 6, 9, 13, 17, 18, 21, /* right */ 1830 2, 3, 6, 7, 10, 14, 18, 19, 23, /* back */ 1831 0, 3, 4, 7, 11, 15, 16, 19, 20, /* left */ 1832 }; 1833 PetscInt faceVerticesQuadHex[54] = { 1834 3, 2, 1, 0, 10, 9, 8, 11, 24, /* bottom */ 1835 4, 5, 6, 7, 12, 13, 14, 15, 25, /* top */ 1836 0, 1, 5, 4, 8, 17, 12, 16, 22, /* front */ 1837 1, 2, 6, 5, 9, 18, 13, 17, 21, /* right */ 1838 2, 3, 7, 6, 10, 19, 14, 18, 23, /* back */ 1839 3, 0, 4, 7, 11, 16, 15, 19, 20 /* left */ 1840 }; 1841 1842 faceSize = faceSizeQuadHex; 1843 for (i = 0; i < faceSizeQuadHex; ++i) sortedIndices[i] = indices[i]; 1844 ierr = PetscSortInt(faceSizeQuadHex, sortedIndices);CHKERRQ(ierr); 1845 for (iFace = 0; iFace < 6; ++iFace) { 1846 const PetscInt ii = iFace*faceSizeQuadHex; 1847 PetscInt fVertex, cVertex; 1848 1849 if ((sortedIndices[0] == faceVerticesQuadHexSorted[ii+0]) && 1850 (sortedIndices[1] == faceVerticesQuadHexSorted[ii+1]) && 1851 (sortedIndices[2] == faceVerticesQuadHexSorted[ii+2]) && 1852 (sortedIndices[3] == faceVerticesQuadHexSorted[ii+3])) { 1853 for (fVertex = 0; fVertex < faceSizeQuadHex; ++fVertex) { 1854 for (cVertex = 0; cVertex < faceSizeQuadHex; ++cVertex) { 1855 if (indices[cVertex] == faceVerticesQuadHex[ii+fVertex]) { 1856 faceVertices[fVertex] = origVertices[cVertex]; 1857 break; 1858 } 1859 } 1860 } 1861 found = PETSC_TRUE; 1862 break; 1863 } 1864 } 1865 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid hex crossface"); 1866 if (posOriented) *posOriented = PETSC_TRUE; 1867 PetscFunctionReturn(0); 1868 } else SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Unknown cell type for faceOrientation()."); 1869 if (!posOrient) { 1870 if (debug) {ierr = PetscPrintf(comm, " Reversing initial face orientation\n");CHKERRQ(ierr);} 1871 for (f = 0; f < faceSize; ++f) faceVertices[f] = origVertices[faceSize-1 - f]; 1872 } else { 1873 if (debug) {ierr = PetscPrintf(comm, " Keeping initial face orientation\n");CHKERRQ(ierr);} 1874 for (f = 0; f < faceSize; ++f) faceVertices[f] = origVertices[f]; 1875 } 1876 if (posOriented) *posOriented = posOrient; 1877 PetscFunctionReturn(0); 1878 } 1879 1880 #undef __FUNCT__ 1881 #define __FUNCT__ "DMPlexGetOrientedFace" 1882 /* 1883 Given a cell and a face, as a set of vertices, 1884 return the oriented face, as a set of vertices, in faceVertices 1885 The orientation is such that the face normal points out of the cell 1886 */ 1887 PetscErrorCode DMPlexGetOrientedFace(DM dm, PetscInt cell, PetscInt faceSize, const PetscInt face[], PetscInt numCorners, PetscInt indices[], PetscInt origVertices[], PetscInt faceVertices[], PetscBool *posOriented) 1888 { 1889 const PetscInt *cone = NULL; 1890 PetscInt coneSize, v, f, v2; 1891 PetscInt oppositeVertex = -1; 1892 PetscErrorCode ierr; 1893 1894 PetscFunctionBegin; 1895 ierr = DMPlexGetConeSize(dm, cell, &coneSize);CHKERRQ(ierr); 1896 ierr = DMPlexGetCone(dm, cell, &cone);CHKERRQ(ierr); 1897 for (v = 0, v2 = 0; v < coneSize; ++v) { 1898 PetscBool found = PETSC_FALSE; 1899 1900 for (f = 0; f < faceSize; ++f) { 1901 if (face[f] == cone[v]) { 1902 found = PETSC_TRUE; break; 1903 } 1904 } 1905 if (found) { 1906 indices[v2] = v; 1907 origVertices[v2] = cone[v]; 1908 ++v2; 1909 } else { 1910 oppositeVertex = v; 1911 } 1912 } 1913 ierr = DMPlexGetFaceOrientation(dm, cell, numCorners, indices, oppositeVertex, origVertices, faceVertices, posOriented);CHKERRQ(ierr); 1914 PetscFunctionReturn(0); 1915 } 1916 1917 #undef __FUNCT__ 1918 #define __FUNCT__ "DMPlexInsertFace_Internal" 1919 /* 1920 DMPlexInsertFace_Internal - Puts a face into the mesh 1921 1922 Not collective 1923 1924 Input Parameters: 1925 + dm - The DMPlex 1926 . numFaceVertex - The number of vertices in the face 1927 . faceVertices - The vertices in the face for dm 1928 . subfaceVertices - The vertices in the face for subdm 1929 . numCorners - The number of vertices in the cell 1930 . cell - A cell in dm containing the face 1931 . subcell - A cell in subdm containing the face 1932 . firstFace - First face in the mesh 1933 - newFacePoint - Next face in the mesh 1934 1935 Output Parameters: 1936 . newFacePoint - Contains next face point number on input, updated on output 1937 1938 Level: developer 1939 */ 1940 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) 1941 { 1942 MPI_Comm comm; 1943 DM_Plex *submesh = (DM_Plex*) subdm->data; 1944 const PetscInt *faces; 1945 PetscInt numFaces, coneSize; 1946 PetscErrorCode ierr; 1947 1948 PetscFunctionBegin; 1949 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 1950 ierr = DMPlexGetConeSize(subdm, subcell, &coneSize);CHKERRQ(ierr); 1951 if (coneSize != 1) SETERRQ2(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cone size of cell %d is %d != 1", cell, coneSize); 1952 #if 0 1953 /* Cannot use this because support() has not been constructed yet */ 1954 ierr = DMPlexGetJoin(subdm, numFaceVertices, subfaceVertices, &numFaces, &faces);CHKERRQ(ierr); 1955 #else 1956 { 1957 PetscInt f; 1958 1959 numFaces = 0; 1960 ierr = DMGetWorkArray(subdm, 1, PETSC_INT, (void **) &faces);CHKERRQ(ierr); 1961 for (f = firstFace; f < *newFacePoint; ++f) { 1962 PetscInt dof, off, d; 1963 1964 ierr = PetscSectionGetDof(submesh->coneSection, f, &dof);CHKERRQ(ierr); 1965 ierr = PetscSectionGetOffset(submesh->coneSection, f, &off);CHKERRQ(ierr); 1966 /* Yes, I know this is quadratic, but I expect the sizes to be <5 */ 1967 for (d = 0; d < dof; ++d) { 1968 const PetscInt p = submesh->cones[off+d]; 1969 PetscInt v; 1970 1971 for (v = 0; v < numFaceVertices; ++v) { 1972 if (subfaceVertices[v] == p) break; 1973 } 1974 if (v == numFaceVertices) break; 1975 } 1976 if (d == dof) { 1977 numFaces = 1; 1978 ((PetscInt*) faces)[0] = f; 1979 } 1980 } 1981 } 1982 #endif 1983 if (numFaces > 1) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Vertex set had %d faces, not one", numFaces); 1984 else if (numFaces == 1) { 1985 /* Add the other cell neighbor for this face */ 1986 ierr = DMPlexSetCone(subdm, subcell, faces);CHKERRQ(ierr); 1987 } else { 1988 PetscInt *indices, *origVertices, *orientedVertices, *orientedSubVertices, v, ov; 1989 PetscBool posOriented; 1990 1991 ierr = DMGetWorkArray(subdm, 4*numFaceVertices * sizeof(PetscInt), PETSC_INT, &orientedVertices);CHKERRQ(ierr); 1992 origVertices = &orientedVertices[numFaceVertices]; 1993 indices = &orientedVertices[numFaceVertices*2]; 1994 orientedSubVertices = &orientedVertices[numFaceVertices*3]; 1995 ierr = DMPlexGetOrientedFace(dm, cell, numFaceVertices, faceVertices, numCorners, indices, origVertices, orientedVertices, &posOriented);CHKERRQ(ierr); 1996 /* TODO: I know that routine should return a permutation, not the indices */ 1997 for (v = 0; v < numFaceVertices; ++v) { 1998 const PetscInt vertex = faceVertices[v], subvertex = subfaceVertices[v]; 1999 for (ov = 0; ov < numFaceVertices; ++ov) { 2000 if (orientedVertices[ov] == vertex) { 2001 orientedSubVertices[ov] = subvertex; 2002 break; 2003 } 2004 } 2005 if (ov == numFaceVertices) SETERRQ1(comm, PETSC_ERR_PLIB, "Could not find face vertex %d in orientated set", vertex); 2006 } 2007 ierr = DMPlexSetCone(subdm, *newFacePoint, orientedSubVertices);CHKERRQ(ierr); 2008 ierr = DMPlexSetCone(subdm, subcell, newFacePoint);CHKERRQ(ierr); 2009 ierr = DMRestoreWorkArray(subdm, 4*numFaceVertices * sizeof(PetscInt), PETSC_INT, &orientedVertices);CHKERRQ(ierr); 2010 ++(*newFacePoint); 2011 } 2012 #if 0 2013 ierr = DMPlexRestoreJoin(subdm, numFaceVertices, subfaceVertices, &numFaces, &faces);CHKERRQ(ierr); 2014 #else 2015 ierr = DMRestoreWorkArray(subdm, 1, PETSC_INT, (void **) &faces);CHKERRQ(ierr); 2016 #endif 2017 PetscFunctionReturn(0); 2018 } 2019 2020 #undef __FUNCT__ 2021 #define __FUNCT__ "DMPlexCreateSubmesh_Uninterpolated" 2022 static PetscErrorCode DMPlexCreateSubmesh_Uninterpolated(DM dm, DMLabel vertexLabel, PetscInt value, DM subdm) 2023 { 2024 MPI_Comm comm; 2025 DMLabel subpointMap; 2026 IS subvertexIS, subcellIS; 2027 const PetscInt *subVertices, *subCells; 2028 PetscInt numSubVertices, firstSubVertex, numSubCells; 2029 PetscInt *subface, maxConeSize, numSubFaces = 0, firstSubFace, newFacePoint, nFV = 0; 2030 PetscInt vStart, vEnd, c, f; 2031 PetscErrorCode ierr; 2032 2033 PetscFunctionBegin; 2034 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 2035 /* Create subpointMap which marks the submesh */ 2036 ierr = DMLabelCreate("subpoint_map", &subpointMap);CHKERRQ(ierr); 2037 ierr = DMPlexSetSubpointMap(subdm, subpointMap);CHKERRQ(ierr); 2038 ierr = DMLabelDestroy(&subpointMap);CHKERRQ(ierr); 2039 if (vertexLabel) {ierr = DMPlexMarkSubmesh_Uninterpolated(dm, vertexLabel, value, subpointMap, &numSubFaces, &nFV, subdm);CHKERRQ(ierr);} 2040 /* Setup chart */ 2041 ierr = DMLabelGetStratumSize(subpointMap, 0, &numSubVertices);CHKERRQ(ierr); 2042 ierr = DMLabelGetStratumSize(subpointMap, 2, &numSubCells);CHKERRQ(ierr); 2043 ierr = DMPlexSetChart(subdm, 0, numSubCells+numSubFaces+numSubVertices);CHKERRQ(ierr); 2044 ierr = DMPlexSetVTKCellHeight(subdm, 1);CHKERRQ(ierr); 2045 /* Set cone sizes */ 2046 firstSubVertex = numSubCells; 2047 firstSubFace = numSubCells+numSubVertices; 2048 newFacePoint = firstSubFace; 2049 ierr = DMLabelGetStratumIS(subpointMap, 0, &subvertexIS);CHKERRQ(ierr); 2050 if (subvertexIS) {ierr = ISGetIndices(subvertexIS, &subVertices);CHKERRQ(ierr);} 2051 ierr = DMLabelGetStratumIS(subpointMap, 2, &subcellIS);CHKERRQ(ierr); 2052 if (subcellIS) {ierr = ISGetIndices(subcellIS, &subCells);CHKERRQ(ierr);} 2053 for (c = 0; c < numSubCells; ++c) { 2054 ierr = DMPlexSetConeSize(subdm, c, 1);CHKERRQ(ierr); 2055 } 2056 for (f = firstSubFace; f < firstSubFace+numSubFaces; ++f) { 2057 ierr = DMPlexSetConeSize(subdm, f, nFV);CHKERRQ(ierr); 2058 } 2059 ierr = DMSetUp(subdm);CHKERRQ(ierr); 2060 /* Create face cones */ 2061 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 2062 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, NULL);CHKERRQ(ierr); 2063 ierr = DMGetWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);CHKERRQ(ierr); 2064 for (c = 0; c < numSubCells; ++c) { 2065 const PetscInt cell = subCells[c]; 2066 const PetscInt subcell = c; 2067 PetscInt *closure = NULL; 2068 PetscInt closureSize, cl, numCorners = 0, faceSize = 0; 2069 2070 ierr = DMPlexGetTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 2071 for (cl = 0; cl < closureSize*2; cl += 2) { 2072 const PetscInt point = closure[cl]; 2073 PetscInt subVertex; 2074 2075 if ((point >= vStart) && (point < vEnd)) { 2076 ++numCorners; 2077 ierr = PetscFindInt(point, numSubVertices, subVertices, &subVertex);CHKERRQ(ierr); 2078 if (subVertex >= 0) { 2079 closure[faceSize] = point; 2080 subface[faceSize] = firstSubVertex+subVertex; 2081 ++faceSize; 2082 } 2083 } 2084 } 2085 if (faceSize > nFV) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Invalid submesh: Too many vertices %d of an element on the surface", faceSize); 2086 if (faceSize == nFV) { 2087 ierr = DMPlexInsertFace_Internal(dm, subdm, faceSize, closure, subface, numCorners, cell, subcell, firstSubFace, &newFacePoint);CHKERRQ(ierr); 2088 } 2089 ierr = DMPlexRestoreTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 2090 } 2091 ierr = DMRestoreWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);CHKERRQ(ierr); 2092 ierr = DMPlexSymmetrize(subdm);CHKERRQ(ierr); 2093 ierr = DMPlexStratify(subdm);CHKERRQ(ierr); 2094 /* Build coordinates */ 2095 { 2096 PetscSection coordSection, subCoordSection; 2097 Vec coordinates, subCoordinates; 2098 PetscScalar *coords, *subCoords; 2099 PetscInt numComp, coordSize, v; 2100 2101 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2102 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 2103 ierr = DMPlexGetCoordinateSection(subdm, &subCoordSection);CHKERRQ(ierr); 2104 ierr = PetscSectionSetNumFields(subCoordSection, 1);CHKERRQ(ierr); 2105 ierr = PetscSectionGetFieldComponents(coordSection, 0, &numComp);CHKERRQ(ierr); 2106 ierr = PetscSectionSetFieldComponents(subCoordSection, 0, numComp);CHKERRQ(ierr); 2107 ierr = PetscSectionSetChart(subCoordSection, firstSubVertex, firstSubVertex+numSubVertices);CHKERRQ(ierr); 2108 for (v = 0; v < numSubVertices; ++v) { 2109 const PetscInt vertex = subVertices[v]; 2110 const PetscInt subvertex = firstSubVertex+v; 2111 PetscInt dof; 2112 2113 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2114 ierr = PetscSectionSetDof(subCoordSection, subvertex, dof);CHKERRQ(ierr); 2115 ierr = PetscSectionSetFieldDof(subCoordSection, subvertex, 0, dof);CHKERRQ(ierr); 2116 } 2117 ierr = PetscSectionSetUp(subCoordSection);CHKERRQ(ierr); 2118 ierr = PetscSectionGetStorageSize(subCoordSection, &coordSize);CHKERRQ(ierr); 2119 ierr = VecCreate(comm, &subCoordinates);CHKERRQ(ierr); 2120 ierr = VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2121 ierr = VecSetType(subCoordinates,VECSTANDARD);CHKERRQ(ierr); 2122 if (coordSize) { 2123 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2124 ierr = VecGetArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2125 for (v = 0; v < numSubVertices; ++v) { 2126 const PetscInt vertex = subVertices[v]; 2127 const PetscInt subvertex = firstSubVertex+v; 2128 PetscInt dof, off, sdof, soff, d; 2129 2130 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2131 ierr = PetscSectionGetOffset(coordSection, vertex, &off);CHKERRQ(ierr); 2132 ierr = PetscSectionGetDof(subCoordSection, subvertex, &sdof);CHKERRQ(ierr); 2133 ierr = PetscSectionGetOffset(subCoordSection, subvertex, &soff);CHKERRQ(ierr); 2134 if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof); 2135 for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d]; 2136 } 2137 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2138 ierr = VecRestoreArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2139 } 2140 ierr = DMSetCoordinatesLocal(subdm, subCoordinates);CHKERRQ(ierr); 2141 ierr = VecDestroy(&subCoordinates);CHKERRQ(ierr); 2142 } 2143 /* Cleanup */ 2144 if (subvertexIS) {ierr = ISRestoreIndices(subvertexIS, &subVertices);CHKERRQ(ierr);} 2145 ierr = ISDestroy(&subvertexIS);CHKERRQ(ierr); 2146 if (subcellIS) {ierr = ISRestoreIndices(subcellIS, &subCells);CHKERRQ(ierr);} 2147 ierr = ISDestroy(&subcellIS);CHKERRQ(ierr); 2148 PetscFunctionReturn(0); 2149 } 2150 2151 #undef __FUNCT__ 2152 #define __FUNCT__ "DMPlexCreateSubmesh_Interpolated" 2153 static PetscErrorCode DMPlexCreateSubmesh_Interpolated(DM dm, DMLabel vertexLabel, PetscInt value, DM subdm) 2154 { 2155 MPI_Comm comm; 2156 DMLabel subpointMap; 2157 IS *subpointIS; 2158 const PetscInt **subpoints; 2159 PetscInt *numSubPoints, *firstSubPoint, *coneNew, *coneONew; 2160 PetscInt totSubPoints = 0, maxConeSize, dim, p, d, v; 2161 PetscErrorCode ierr; 2162 2163 PetscFunctionBegin; 2164 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 2165 /* Create subpointMap which marks the submesh */ 2166 ierr = DMLabelCreate("subpoint_map", &subpointMap);CHKERRQ(ierr); 2167 ierr = DMPlexSetSubpointMap(subdm, subpointMap);CHKERRQ(ierr); 2168 ierr = DMLabelDestroy(&subpointMap);CHKERRQ(ierr); 2169 if (vertexLabel) {ierr = DMPlexMarkSubmesh_Interpolated(dm, vertexLabel, value, subpointMap, subdm);CHKERRQ(ierr);} 2170 /* Setup chart */ 2171 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 2172 ierr = PetscMalloc4(dim+1,PetscInt,&numSubPoints,dim+1,PetscInt,&firstSubPoint,dim+1,IS,&subpointIS,dim+1,const PetscInt *,&subpoints);CHKERRQ(ierr); 2173 for (d = 0; d <= dim; ++d) { 2174 ierr = DMLabelGetStratumSize(subpointMap, d, &numSubPoints[d]);CHKERRQ(ierr); 2175 totSubPoints += numSubPoints[d]; 2176 } 2177 ierr = DMPlexSetChart(subdm, 0, totSubPoints);CHKERRQ(ierr); 2178 ierr = DMPlexSetVTKCellHeight(subdm, 1);CHKERRQ(ierr); 2179 /* Set cone sizes */ 2180 firstSubPoint[dim] = 0; 2181 firstSubPoint[0] = firstSubPoint[dim] + numSubPoints[dim]; 2182 if (dim > 1) {firstSubPoint[dim-1] = firstSubPoint[0] + numSubPoints[0];} 2183 if (dim > 2) {firstSubPoint[dim-2] = firstSubPoint[dim-1] + numSubPoints[dim-1];} 2184 for (d = 0; d <= dim; ++d) { 2185 ierr = DMLabelGetStratumIS(subpointMap, d, &subpointIS[d]);CHKERRQ(ierr); 2186 ierr = ISGetIndices(subpointIS[d], &subpoints[d]);CHKERRQ(ierr); 2187 } 2188 for (d = 0; d <= dim; ++d) { 2189 for (p = 0; p < numSubPoints[d]; ++p) { 2190 const PetscInt point = subpoints[d][p]; 2191 const PetscInt subpoint = firstSubPoint[d] + p; 2192 const PetscInt *cone; 2193 PetscInt coneSize, coneSizeNew, c, val; 2194 2195 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 2196 ierr = DMPlexSetConeSize(subdm, subpoint, coneSize);CHKERRQ(ierr); 2197 if (d == dim) { 2198 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 2199 for (c = 0, coneSizeNew = 0; c < coneSize; ++c) { 2200 ierr = DMLabelGetValue(subpointMap, cone[c], &val);CHKERRQ(ierr); 2201 if (val >= 0) coneSizeNew++; 2202 } 2203 ierr = DMPlexSetConeSize(subdm, subpoint, coneSizeNew);CHKERRQ(ierr); 2204 } 2205 } 2206 } 2207 ierr = DMSetUp(subdm);CHKERRQ(ierr); 2208 /* Set cones */ 2209 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, NULL);CHKERRQ(ierr); 2210 ierr = PetscMalloc2(maxConeSize,PetscInt,&coneNew,maxConeSize,PetscInt,&coneONew);CHKERRQ(ierr); 2211 for (d = 0; d <= dim; ++d) { 2212 for (p = 0; p < numSubPoints[d]; ++p) { 2213 const PetscInt point = subpoints[d][p]; 2214 const PetscInt subpoint = firstSubPoint[d] + p; 2215 const PetscInt *cone, *ornt; 2216 PetscInt coneSize, subconeSize, coneSizeNew, c, subc; 2217 2218 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 2219 ierr = DMPlexGetConeSize(subdm, subpoint, &subconeSize);CHKERRQ(ierr); 2220 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 2221 ierr = DMPlexGetConeOrientation(dm, point, &ornt);CHKERRQ(ierr); 2222 for (c = 0, coneSizeNew = 0; c < coneSize; ++c) { 2223 ierr = PetscFindInt(cone[c], numSubPoints[d-1], subpoints[d-1], &subc);CHKERRQ(ierr); 2224 if (subc >= 0) { 2225 coneNew[coneSizeNew] = firstSubPoint[d-1] + subc; 2226 coneONew[coneSizeNew] = ornt[c]; 2227 ++coneSizeNew; 2228 } 2229 } 2230 if (coneSizeNew != subconeSize) SETERRQ2(comm, PETSC_ERR_PLIB, "Number of cone points located %d does not match subcone size %d", coneSizeNew, subconeSize); 2231 ierr = DMPlexSetCone(subdm, subpoint, coneNew);CHKERRQ(ierr); 2232 ierr = DMPlexSetConeOrientation(subdm, subpoint, coneONew);CHKERRQ(ierr); 2233 } 2234 } 2235 ierr = PetscFree2(coneNew,coneONew);CHKERRQ(ierr); 2236 ierr = DMPlexSymmetrize(subdm);CHKERRQ(ierr); 2237 ierr = DMPlexStratify(subdm);CHKERRQ(ierr); 2238 /* Build coordinates */ 2239 { 2240 PetscSection coordSection, subCoordSection; 2241 Vec coordinates, subCoordinates; 2242 PetscScalar *coords, *subCoords; 2243 PetscInt numComp, coordSize; 2244 2245 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2246 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 2247 ierr = DMPlexGetCoordinateSection(subdm, &subCoordSection);CHKERRQ(ierr); 2248 ierr = PetscSectionSetNumFields(subCoordSection, 1);CHKERRQ(ierr); 2249 ierr = PetscSectionGetFieldComponents(coordSection, 0, &numComp);CHKERRQ(ierr); 2250 ierr = PetscSectionSetFieldComponents(subCoordSection, 0, numComp);CHKERRQ(ierr); 2251 ierr = PetscSectionSetChart(subCoordSection, firstSubPoint[0], firstSubPoint[0]+numSubPoints[0]);CHKERRQ(ierr); 2252 for (v = 0; v < numSubPoints[0]; ++v) { 2253 const PetscInt vertex = subpoints[0][v]; 2254 const PetscInt subvertex = firstSubPoint[0]+v; 2255 PetscInt dof; 2256 2257 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2258 ierr = PetscSectionSetDof(subCoordSection, subvertex, dof);CHKERRQ(ierr); 2259 ierr = PetscSectionSetFieldDof(subCoordSection, subvertex, 0, dof);CHKERRQ(ierr); 2260 } 2261 ierr = PetscSectionSetUp(subCoordSection);CHKERRQ(ierr); 2262 ierr = PetscSectionGetStorageSize(subCoordSection, &coordSize);CHKERRQ(ierr); 2263 ierr = VecCreate(comm, &subCoordinates);CHKERRQ(ierr); 2264 ierr = VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2265 ierr = VecSetType(subCoordinates,VECSTANDARD);CHKERRQ(ierr); 2266 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2267 ierr = VecGetArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2268 for (v = 0; v < numSubPoints[0]; ++v) { 2269 const PetscInt vertex = subpoints[0][v]; 2270 const PetscInt subvertex = firstSubPoint[0]+v; 2271 PetscInt dof, off, sdof, soff, d; 2272 2273 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2274 ierr = PetscSectionGetOffset(coordSection, vertex, &off);CHKERRQ(ierr); 2275 ierr = PetscSectionGetDof(subCoordSection, subvertex, &sdof);CHKERRQ(ierr); 2276 ierr = PetscSectionGetOffset(subCoordSection, subvertex, &soff);CHKERRQ(ierr); 2277 if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof); 2278 for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d]; 2279 } 2280 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2281 ierr = VecRestoreArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2282 ierr = DMSetCoordinatesLocal(subdm, subCoordinates);CHKERRQ(ierr); 2283 ierr = VecDestroy(&subCoordinates);CHKERRQ(ierr); 2284 } 2285 /* Cleanup */ 2286 for (d = 0; d <= dim; ++d) { 2287 ierr = ISRestoreIndices(subpointIS[d], &subpoints[d]);CHKERRQ(ierr); 2288 ierr = ISDestroy(&subpointIS[d]);CHKERRQ(ierr); 2289 } 2290 ierr = PetscFree4(numSubPoints,firstSubPoint,subpointIS,subpoints);CHKERRQ(ierr); 2291 PetscFunctionReturn(0); 2292 } 2293 2294 #undef __FUNCT__ 2295 #define __FUNCT__ "DMPlexCreateSubmesh" 2296 /*@ 2297 DMPlexCreateSubmesh - Extract a hypersurface from the mesh using vertices defined by a label 2298 2299 Input Parameters: 2300 + dm - The original mesh 2301 . vertexLabel - The DMLabel marking vertices contained in the surface 2302 - value - The label value to use 2303 2304 Output Parameter: 2305 . subdm - The surface mesh 2306 2307 Note: This function produces a DMLabel mapping original points in the submesh to their depth. This can be obtained using DMPlexGetSubpointMap(). 2308 2309 Level: developer 2310 2311 .seealso: DMPlexGetSubpointMap(), DMPlexGetLabel(), DMLabelSetValue() 2312 @*/ 2313 PetscErrorCode DMPlexCreateSubmesh(DM dm, DMLabel vertexLabel, PetscInt value, DM *subdm) 2314 { 2315 PetscInt dim, depth; 2316 PetscErrorCode ierr; 2317 2318 PetscFunctionBegin; 2319 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2320 PetscValidPointer(subdm, 3); 2321 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 2322 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 2323 ierr = DMCreate(PetscObjectComm((PetscObject)dm), subdm);CHKERRQ(ierr); 2324 ierr = DMSetType(*subdm, DMPLEX);CHKERRQ(ierr); 2325 ierr = DMPlexSetDimension(*subdm, dim-1);CHKERRQ(ierr); 2326 if (depth == dim) { 2327 ierr = DMPlexCreateSubmesh_Interpolated(dm, vertexLabel, value, *subdm);CHKERRQ(ierr); 2328 } else { 2329 ierr = DMPlexCreateSubmesh_Uninterpolated(dm, vertexLabel, value, *subdm);CHKERRQ(ierr); 2330 } 2331 PetscFunctionReturn(0); 2332 } 2333 2334 #undef __FUNCT__ 2335 #define __FUNCT__ "DMPlexFilterPoint_Internal" 2336 PETSC_STATIC_INLINE PetscInt DMPlexFilterPoint_Internal(PetscInt point, PetscInt firstSubPoint, PetscInt numSubPoints, const PetscInt subPoints[]) 2337 { 2338 PetscInt subPoint; 2339 PetscErrorCode ierr; 2340 2341 ierr = PetscFindInt(point, numSubPoints, subPoints, &subPoint); if (ierr < 0) return ierr; 2342 return subPoint < 0 ? subPoint : firstSubPoint+subPoint; 2343 } 2344 2345 #undef __FUNCT__ 2346 #define __FUNCT__ "DMPlexCreateCohesiveSubmesh_Uninterpolated" 2347 static PetscErrorCode DMPlexCreateCohesiveSubmesh_Uninterpolated(DM dm, PetscBool hasLagrange, const char label[], PetscInt value, DM subdm) 2348 { 2349 MPI_Comm comm; 2350 DMLabel subpointMap; 2351 IS subvertexIS; 2352 const PetscInt *subVertices; 2353 PetscInt numSubVertices, firstSubVertex, numSubCells, *subCells = NULL; 2354 PetscInt *subface, maxConeSize, numSubFaces, firstSubFace, newFacePoint, nFV; 2355 PetscInt cMax, c, f; 2356 PetscErrorCode ierr; 2357 2358 PetscFunctionBegin; 2359 ierr = PetscObjectGetComm((PetscObject)dm, &comm);CHKERRQ(ierr); 2360 /* Create subpointMap which marks the submesh */ 2361 ierr = DMLabelCreate("subpoint_map", &subpointMap);CHKERRQ(ierr); 2362 ierr = DMPlexSetSubpointMap(subdm, subpointMap);CHKERRQ(ierr); 2363 ierr = DMLabelDestroy(&subpointMap);CHKERRQ(ierr); 2364 ierr = DMPlexMarkCohesiveSubmesh_Uninterpolated(dm, hasLagrange, label, value, subpointMap, &numSubFaces, &nFV, &subCells, subdm);CHKERRQ(ierr); 2365 /* Setup chart */ 2366 ierr = DMLabelGetStratumSize(subpointMap, 0, &numSubVertices);CHKERRQ(ierr); 2367 ierr = DMLabelGetStratumSize(subpointMap, 2, &numSubCells);CHKERRQ(ierr); 2368 ierr = DMPlexSetChart(subdm, 0, numSubCells+numSubFaces+numSubVertices);CHKERRQ(ierr); 2369 ierr = DMPlexSetVTKCellHeight(subdm, 1);CHKERRQ(ierr); 2370 /* Set cone sizes */ 2371 firstSubVertex = numSubCells; 2372 firstSubFace = numSubCells+numSubVertices; 2373 newFacePoint = firstSubFace; 2374 ierr = DMLabelGetStratumIS(subpointMap, 0, &subvertexIS);CHKERRQ(ierr); 2375 if (subvertexIS) {ierr = ISGetIndices(subvertexIS, &subVertices);CHKERRQ(ierr);} 2376 for (c = 0; c < numSubCells; ++c) { 2377 ierr = DMPlexSetConeSize(subdm, c, 1);CHKERRQ(ierr); 2378 } 2379 for (f = firstSubFace; f < firstSubFace+numSubFaces; ++f) { 2380 ierr = DMPlexSetConeSize(subdm, f, nFV);CHKERRQ(ierr); 2381 } 2382 ierr = DMSetUp(subdm);CHKERRQ(ierr); 2383 /* Create face cones */ 2384 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, NULL);CHKERRQ(ierr); 2385 ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); 2386 ierr = DMGetWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);CHKERRQ(ierr); 2387 for (c = 0; c < numSubCells; ++c) { 2388 const PetscInt cell = subCells[c]; 2389 const PetscInt subcell = c; 2390 const PetscInt *cone, *cells; 2391 PetscInt numCells, subVertex, p, v; 2392 2393 if (cell < cMax) continue; 2394 ierr = DMPlexGetCone(dm, cell, &cone);CHKERRQ(ierr); 2395 for (v = 0; v < nFV; ++v) { 2396 ierr = PetscFindInt(cone[v], numSubVertices, subVertices, &subVertex);CHKERRQ(ierr); 2397 subface[v] = firstSubVertex+subVertex; 2398 } 2399 ierr = DMPlexSetCone(subdm, newFacePoint, subface);CHKERRQ(ierr); 2400 ierr = DMPlexSetCone(subdm, subcell, &newFacePoint);CHKERRQ(ierr); 2401 ierr = DMPlexGetJoin(dm, nFV, cone, &numCells, &cells);CHKERRQ(ierr); 2402 /* Not true in parallel 2403 if (numCells != 2) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive cells should separate two cells"); */ 2404 for (p = 0; p < numCells; ++p) { 2405 PetscInt negsubcell; 2406 2407 if (cells[p] >= cMax) continue; 2408 /* I know this is a crap search */ 2409 for (negsubcell = 0; negsubcell < numSubCells; ++negsubcell) { 2410 if (subCells[negsubcell] == cells[p]) break; 2411 } 2412 if (negsubcell == numSubCells) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not find negative face neighbor for cohesive cell %d", cell); 2413 ierr = DMPlexSetCone(subdm, negsubcell, &newFacePoint);CHKERRQ(ierr); 2414 } 2415 ierr = DMPlexRestoreJoin(dm, nFV, cone, &numCells, &cells);CHKERRQ(ierr); 2416 ++newFacePoint; 2417 } 2418 ierr = DMRestoreWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);CHKERRQ(ierr); 2419 ierr = DMPlexSymmetrize(subdm);CHKERRQ(ierr); 2420 ierr = DMPlexStratify(subdm);CHKERRQ(ierr); 2421 /* Build coordinates */ 2422 { 2423 PetscSection coordSection, subCoordSection; 2424 Vec coordinates, subCoordinates; 2425 PetscScalar *coords, *subCoords; 2426 PetscInt numComp, coordSize, v; 2427 2428 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2429 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 2430 ierr = DMPlexGetCoordinateSection(subdm, &subCoordSection);CHKERRQ(ierr); 2431 ierr = PetscSectionSetNumFields(subCoordSection, 1);CHKERRQ(ierr); 2432 ierr = PetscSectionGetFieldComponents(coordSection, 0, &numComp);CHKERRQ(ierr); 2433 ierr = PetscSectionSetFieldComponents(subCoordSection, 0, numComp);CHKERRQ(ierr); 2434 ierr = PetscSectionSetChart(subCoordSection, firstSubVertex, firstSubVertex+numSubVertices);CHKERRQ(ierr); 2435 for (v = 0; v < numSubVertices; ++v) { 2436 const PetscInt vertex = subVertices[v]; 2437 const PetscInt subvertex = firstSubVertex+v; 2438 PetscInt dof; 2439 2440 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2441 ierr = PetscSectionSetDof(subCoordSection, subvertex, dof);CHKERRQ(ierr); 2442 ierr = PetscSectionSetFieldDof(subCoordSection, subvertex, 0, dof);CHKERRQ(ierr); 2443 } 2444 ierr = PetscSectionSetUp(subCoordSection);CHKERRQ(ierr); 2445 ierr = PetscSectionGetStorageSize(subCoordSection, &coordSize);CHKERRQ(ierr); 2446 ierr = VecCreate(comm, &subCoordinates);CHKERRQ(ierr); 2447 ierr = VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2448 ierr = VecSetType(subCoordinates,VECSTANDARD);CHKERRQ(ierr); 2449 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2450 ierr = VecGetArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2451 for (v = 0; v < numSubVertices; ++v) { 2452 const PetscInt vertex = subVertices[v]; 2453 const PetscInt subvertex = firstSubVertex+v; 2454 PetscInt dof, off, sdof, soff, d; 2455 2456 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2457 ierr = PetscSectionGetOffset(coordSection, vertex, &off);CHKERRQ(ierr); 2458 ierr = PetscSectionGetDof(subCoordSection, subvertex, &sdof);CHKERRQ(ierr); 2459 ierr = PetscSectionGetOffset(subCoordSection, subvertex, &soff);CHKERRQ(ierr); 2460 if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof); 2461 for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d]; 2462 } 2463 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2464 ierr = VecRestoreArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2465 ierr = DMSetCoordinatesLocal(subdm, subCoordinates);CHKERRQ(ierr); 2466 ierr = VecDestroy(&subCoordinates);CHKERRQ(ierr); 2467 } 2468 /* Build SF */ 2469 CHKMEMQ; 2470 { 2471 PetscSF sfPoint, sfPointSub; 2472 const PetscSFNode *remotePoints; 2473 PetscSFNode *sremotePoints, *newLocalPoints, *newOwners; 2474 const PetscInt *localPoints; 2475 PetscInt *slocalPoints; 2476 PetscInt numRoots, numLeaves, numSubRoots = numSubCells+numSubFaces+numSubVertices, numSubLeaves = 0, l, sl, ll, pStart, pEnd, p, vStart, vEnd; 2477 PetscMPIInt rank; 2478 2479 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRQ(ierr); 2480 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 2481 ierr = DMGetPointSF(subdm, &sfPointSub);CHKERRQ(ierr); 2482 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 2483 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 2484 ierr = PetscSFGetGraph(sfPoint, &numRoots, &numLeaves, &localPoints, &remotePoints);CHKERRQ(ierr); 2485 if (numRoots >= 0) { 2486 /* Only vertices should be shared */ 2487 ierr = PetscMalloc2(pEnd-pStart,PetscSFNode,&newLocalPoints,numRoots,PetscSFNode,&newOwners);CHKERRQ(ierr); 2488 for (p = 0; p < pEnd-pStart; ++p) { 2489 newLocalPoints[p].rank = -2; 2490 newLocalPoints[p].index = -2; 2491 } 2492 /* Set subleaves */ 2493 for (l = 0; l < numLeaves; ++l) { 2494 const PetscInt point = localPoints[l]; 2495 const PetscInt subPoint = DMPlexFilterPoint_Internal(point, firstSubVertex, numSubVertices, subVertices); 2496 2497 if ((point < vStart) && (point >= vEnd)) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Should not be mapping anything but vertices, %d", point); 2498 if (subPoint < 0) continue; 2499 newLocalPoints[point-pStart].rank = rank; 2500 newLocalPoints[point-pStart].index = subPoint; 2501 ++numSubLeaves; 2502 } 2503 /* Must put in owned subpoints */ 2504 for (p = pStart; p < pEnd; ++p) { 2505 const PetscInt subPoint = DMPlexFilterPoint_Internal(p, firstSubVertex, numSubVertices, subVertices); 2506 2507 if (subPoint < 0) { 2508 newOwners[p-pStart].rank = -3; 2509 newOwners[p-pStart].index = -3; 2510 } else { 2511 newOwners[p-pStart].rank = rank; 2512 newOwners[p-pStart].index = subPoint; 2513 } 2514 } 2515 ierr = PetscSFReduceBegin(sfPoint, MPIU_2INT, newLocalPoints, newOwners, MPI_MAXLOC);CHKERRQ(ierr); 2516 ierr = PetscSFReduceEnd(sfPoint, MPIU_2INT, newLocalPoints, newOwners, MPI_MAXLOC);CHKERRQ(ierr); 2517 ierr = PetscSFBcastBegin(sfPoint, MPIU_2INT, newOwners, newLocalPoints);CHKERRQ(ierr); 2518 ierr = PetscSFBcastEnd(sfPoint, MPIU_2INT, newOwners, newLocalPoints);CHKERRQ(ierr); 2519 ierr = PetscMalloc(numSubLeaves * sizeof(PetscInt), &slocalPoints);CHKERRQ(ierr); 2520 ierr = PetscMalloc(numSubLeaves * sizeof(PetscSFNode), &sremotePoints);CHKERRQ(ierr); 2521 for (l = 0, sl = 0, ll = 0; l < numLeaves; ++l) { 2522 const PetscInt point = localPoints[l]; 2523 const PetscInt subPoint = DMPlexFilterPoint_Internal(point, firstSubVertex, numSubVertices, subVertices); 2524 2525 if (subPoint < 0) continue; 2526 if (newLocalPoints[point].rank == rank) {++ll; continue;} 2527 slocalPoints[sl] = subPoint; 2528 sremotePoints[sl].rank = newLocalPoints[point].rank; 2529 sremotePoints[sl].index = newLocalPoints[point].index; 2530 if (sremotePoints[sl].rank < 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid remote rank for local point %d", point); 2531 if (sremotePoints[sl].index < 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid remote subpoint for local point %d", point); 2532 ++sl; 2533 } 2534 ierr = PetscFree2(newLocalPoints,newOwners);CHKERRQ(ierr); 2535 if (sl + ll != numSubLeaves) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Mismatch in number of subleaves %d + %d != %d", sl, ll, numSubLeaves); 2536 ierr = PetscSFSetGraph(sfPointSub, numSubRoots, sl, slocalPoints, PETSC_OWN_POINTER, sremotePoints, PETSC_OWN_POINTER);CHKERRQ(ierr); 2537 } 2538 } 2539 CHKMEMQ; 2540 /* Cleanup */ 2541 if (subvertexIS) {ierr = ISRestoreIndices(subvertexIS, &subVertices);CHKERRQ(ierr);} 2542 ierr = ISDestroy(&subvertexIS);CHKERRQ(ierr); 2543 ierr = PetscFree(subCells);CHKERRQ(ierr); 2544 PetscFunctionReturn(0); 2545 } 2546 2547 #undef __FUNCT__ 2548 #define __FUNCT__ "DMPlexCreateCohesiveSubmesh_Interpolated" 2549 static PetscErrorCode DMPlexCreateCohesiveSubmesh_Interpolated(DM dm, PetscBool hasLagrange, const char label[], PetscInt value, DM subdm) 2550 { 2551 MPI_Comm comm; 2552 DMLabel subpointMap; 2553 IS *subpointIS; 2554 const PetscInt **subpoints; 2555 PetscInt *numSubPoints, *firstSubPoint, *coneNew; 2556 PetscInt totSubPoints = 0, maxConeSize, dim, p, d, v; 2557 PetscErrorCode ierr; 2558 2559 PetscFunctionBegin; 2560 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 2561 /* Create subpointMap which marks the submesh */ 2562 ierr = DMLabelCreate("subpoint_map", &subpointMap);CHKERRQ(ierr); 2563 ierr = DMPlexSetSubpointMap(subdm, subpointMap);CHKERRQ(ierr); 2564 ierr = DMLabelDestroy(&subpointMap);CHKERRQ(ierr); 2565 ierr = DMPlexMarkCohesiveSubmesh_Interpolated(dm, hasLagrange, label, value, subpointMap, subdm);CHKERRQ(ierr); 2566 /* Setup chart */ 2567 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 2568 ierr = PetscMalloc4(dim+1,PetscInt,&numSubPoints,dim+1,PetscInt,&firstSubPoint,dim+1,IS,&subpointIS,dim+1,const PetscInt *,&subpoints);CHKERRQ(ierr); 2569 for (d = 0; d <= dim; ++d) { 2570 ierr = DMLabelGetStratumSize(subpointMap, d, &numSubPoints[d]);CHKERRQ(ierr); 2571 totSubPoints += numSubPoints[d]; 2572 } 2573 ierr = DMPlexSetChart(subdm, 0, totSubPoints);CHKERRQ(ierr); 2574 ierr = DMPlexSetVTKCellHeight(subdm, 1);CHKERRQ(ierr); 2575 /* Set cone sizes */ 2576 firstSubPoint[dim] = 0; 2577 firstSubPoint[0] = firstSubPoint[dim] + numSubPoints[dim]; 2578 if (dim > 1) {firstSubPoint[dim-1] = firstSubPoint[0] + numSubPoints[0];} 2579 if (dim > 2) {firstSubPoint[dim-2] = firstSubPoint[dim-1] + numSubPoints[dim-1];} 2580 for (d = 0; d <= dim; ++d) { 2581 ierr = DMLabelGetStratumIS(subpointMap, d, &subpointIS[d]);CHKERRQ(ierr); 2582 ierr = ISGetIndices(subpointIS[d], &subpoints[d]);CHKERRQ(ierr); 2583 } 2584 for (d = 0; d <= dim; ++d) { 2585 for (p = 0; p < numSubPoints[d]; ++p) { 2586 const PetscInt point = subpoints[d][p]; 2587 const PetscInt subpoint = firstSubPoint[d] + p; 2588 const PetscInt *cone; 2589 PetscInt coneSize, coneSizeNew, c, val; 2590 2591 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 2592 ierr = DMPlexSetConeSize(subdm, subpoint, coneSize);CHKERRQ(ierr); 2593 if (d == dim) { 2594 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 2595 for (c = 0, coneSizeNew = 0; c < coneSize; ++c) { 2596 ierr = DMLabelGetValue(subpointMap, cone[c], &val);CHKERRQ(ierr); 2597 if (val >= 0) coneSizeNew++; 2598 } 2599 ierr = DMPlexSetConeSize(subdm, subpoint, coneSizeNew);CHKERRQ(ierr); 2600 } 2601 } 2602 } 2603 ierr = DMSetUp(subdm);CHKERRQ(ierr); 2604 /* Set cones */ 2605 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, NULL);CHKERRQ(ierr); 2606 ierr = PetscMalloc(maxConeSize * sizeof(PetscInt), &coneNew);CHKERRQ(ierr); 2607 for (d = 0; d <= dim; ++d) { 2608 for (p = 0; p < numSubPoints[d]; ++p) { 2609 const PetscInt point = subpoints[d][p]; 2610 const PetscInt subpoint = firstSubPoint[d] + p; 2611 const PetscInt *cone; 2612 PetscInt coneSize, subconeSize, coneSizeNew, c, subc; 2613 2614 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 2615 ierr = DMPlexGetConeSize(subdm, subpoint, &subconeSize);CHKERRQ(ierr); 2616 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 2617 for (c = 0, coneSizeNew = 0; c < coneSize; ++c) { 2618 ierr = PetscFindInt(cone[c], numSubPoints[d-1], subpoints[d-1], &subc);CHKERRQ(ierr); 2619 if (subc >= 0) coneNew[coneSizeNew++] = firstSubPoint[d-1] + subc; 2620 } 2621 if (coneSizeNew != subconeSize) SETERRQ2(comm, PETSC_ERR_PLIB, "Number of cone points located %d does not match subcone size %d", coneSizeNew, subconeSize); 2622 ierr = DMPlexSetCone(subdm, subpoint, coneNew);CHKERRQ(ierr); 2623 } 2624 } 2625 ierr = PetscFree(coneNew);CHKERRQ(ierr); 2626 ierr = DMPlexSymmetrize(subdm);CHKERRQ(ierr); 2627 ierr = DMPlexStratify(subdm);CHKERRQ(ierr); 2628 /* Build coordinates */ 2629 { 2630 PetscSection coordSection, subCoordSection; 2631 Vec coordinates, subCoordinates; 2632 PetscScalar *coords, *subCoords; 2633 PetscInt numComp, coordSize; 2634 2635 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2636 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 2637 ierr = DMPlexGetCoordinateSection(subdm, &subCoordSection);CHKERRQ(ierr); 2638 ierr = PetscSectionSetNumFields(subCoordSection, 1);CHKERRQ(ierr); 2639 ierr = PetscSectionGetFieldComponents(coordSection, 0, &numComp);CHKERRQ(ierr); 2640 ierr = PetscSectionSetFieldComponents(subCoordSection, 0, numComp);CHKERRQ(ierr); 2641 ierr = PetscSectionSetChart(subCoordSection, firstSubPoint[0], firstSubPoint[0]+numSubPoints[0]);CHKERRQ(ierr); 2642 for (v = 0; v < numSubPoints[0]; ++v) { 2643 const PetscInt vertex = subpoints[0][v]; 2644 const PetscInt subvertex = firstSubPoint[0]+v; 2645 PetscInt dof; 2646 2647 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2648 ierr = PetscSectionSetDof(subCoordSection, subvertex, dof);CHKERRQ(ierr); 2649 ierr = PetscSectionSetFieldDof(subCoordSection, subvertex, 0, dof);CHKERRQ(ierr); 2650 } 2651 ierr = PetscSectionSetUp(subCoordSection);CHKERRQ(ierr); 2652 ierr = PetscSectionGetStorageSize(subCoordSection, &coordSize);CHKERRQ(ierr); 2653 ierr = VecCreate(comm, &subCoordinates);CHKERRQ(ierr); 2654 ierr = VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2655 ierr = VecSetType(subCoordinates,VECSTANDARD);CHKERRQ(ierr); 2656 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2657 ierr = VecGetArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2658 for (v = 0; v < numSubPoints[0]; ++v) { 2659 const PetscInt vertex = subpoints[0][v]; 2660 const PetscInt subvertex = firstSubPoint[0]+v; 2661 PetscInt dof, off, sdof, soff, d; 2662 2663 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2664 ierr = PetscSectionGetOffset(coordSection, vertex, &off);CHKERRQ(ierr); 2665 ierr = PetscSectionGetDof(subCoordSection, subvertex, &sdof);CHKERRQ(ierr); 2666 ierr = PetscSectionGetOffset(subCoordSection, subvertex, &soff);CHKERRQ(ierr); 2667 if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof); 2668 for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d]; 2669 } 2670 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2671 ierr = VecRestoreArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2672 ierr = DMSetCoordinatesLocal(subdm, subCoordinates);CHKERRQ(ierr); 2673 ierr = VecDestroy(&subCoordinates);CHKERRQ(ierr); 2674 } 2675 /* Cleanup */ 2676 for (d = 0; d <= dim; ++d) { 2677 ierr = ISRestoreIndices(subpointIS[d], &subpoints[d]);CHKERRQ(ierr); 2678 ierr = ISDestroy(&subpointIS[d]);CHKERRQ(ierr); 2679 } 2680 ierr = PetscFree4(numSubPoints,firstSubPoint,subpointIS,subpoints);CHKERRQ(ierr); 2681 PetscFunctionReturn(0); 2682 } 2683 2684 #undef __FUNCT__ 2685 #define __FUNCT__ "DMPlexCreateCohesiveSubmesh" 2686 /* 2687 DMPlexCreateCohesiveSubmesh - Extract from a mesh with cohesive cells the hypersurface defined by one face of the cells. Optionally, a Label an be given to restrict the cells. 2688 2689 Input Parameters: 2690 + dm - The original mesh 2691 . hasLagrange - The mesh has Lagrange unknowns in the cohesive cells 2692 . label - A label name, or PETSC_NULL 2693 - value - A label value 2694 2695 Output Parameter: 2696 . subdm - The surface mesh 2697 2698 Note: This function produces a DMLabel mapping original points in the submesh to their depth. This can be obtained using DMPlexGetSubpointMap(). 2699 2700 Level: developer 2701 2702 .seealso: DMPlexGetSubpointMap(), DMPlexCreateSubmesh() 2703 */ 2704 PetscErrorCode DMPlexCreateCohesiveSubmesh(DM dm, PetscBool hasLagrange, const char label[], PetscInt value, DM *subdm) 2705 { 2706 PetscInt dim, depth; 2707 PetscErrorCode ierr; 2708 2709 PetscFunctionBegin; 2710 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2711 PetscValidPointer(subdm, 5); 2712 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 2713 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 2714 ierr = DMCreate(PetscObjectComm((PetscObject)dm), subdm);CHKERRQ(ierr); 2715 ierr = DMSetType(*subdm, DMPLEX);CHKERRQ(ierr); 2716 ierr = DMPlexSetDimension(*subdm, dim-1);CHKERRQ(ierr); 2717 if (depth == dim) { 2718 ierr = DMPlexCreateCohesiveSubmesh_Interpolated(dm, hasLagrange, label, value, *subdm);CHKERRQ(ierr); 2719 } else { 2720 ierr = DMPlexCreateCohesiveSubmesh_Uninterpolated(dm, hasLagrange, label, value, *subdm);CHKERRQ(ierr); 2721 } 2722 PetscFunctionReturn(0); 2723 } 2724 2725 #undef __FUNCT__ 2726 #define __FUNCT__ "DMPlexGetSubpointMap" 2727 /*@ 2728 DMPlexGetSubpointMap - Returns a DMLabel with point dimension as values 2729 2730 Input Parameter: 2731 . dm - The submesh DM 2732 2733 Output Parameter: 2734 . subpointMap - The DMLabel of all the points from the original mesh in this submesh, or NULL if this is not a submesh 2735 2736 Level: developer 2737 2738 .seealso: DMPlexCreateSubmesh(), DMPlexCreateSubpointIS() 2739 @*/ 2740 PetscErrorCode DMPlexGetSubpointMap(DM dm, DMLabel *subpointMap) 2741 { 2742 DM_Plex *mesh = (DM_Plex*) dm->data; 2743 2744 PetscFunctionBegin; 2745 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2746 PetscValidPointer(subpointMap, 2); 2747 *subpointMap = mesh->subpointMap; 2748 PetscFunctionReturn(0); 2749 } 2750 2751 #undef __FUNCT__ 2752 #define __FUNCT__ "DMPlexSetSubpointMap" 2753 /* Note: Should normally not be called by the user, since it is set in DMPlexCreateSubmesh() */ 2754 PetscErrorCode DMPlexSetSubpointMap(DM dm, DMLabel subpointMap) 2755 { 2756 DM_Plex *mesh = (DM_Plex *) dm->data; 2757 DMLabel tmp; 2758 PetscErrorCode ierr; 2759 2760 PetscFunctionBegin; 2761 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2762 tmp = mesh->subpointMap; 2763 mesh->subpointMap = subpointMap; 2764 ++mesh->subpointMap->refct; 2765 ierr = DMLabelDestroy(&tmp);CHKERRQ(ierr); 2766 PetscFunctionReturn(0); 2767 } 2768 2769 #undef __FUNCT__ 2770 #define __FUNCT__ "DMPlexCreateSubpointIS" 2771 /*@ 2772 DMPlexCreateSubpointIS - Creates an IS covering the entire subdm chart with the original points as data 2773 2774 Input Parameter: 2775 . dm - The submesh DM 2776 2777 Output Parameter: 2778 . subpointIS - The IS of all the points from the original mesh in this submesh, or NULL if this is not a submesh 2779 2780 Note: This is IS is guaranteed to be sorted by the construction of the submesh 2781 2782 Level: developer 2783 2784 .seealso: DMPlexCreateSubmesh(), DMPlexGetSubpointMap() 2785 @*/ 2786 PetscErrorCode DMPlexCreateSubpointIS(DM dm, IS *subpointIS) 2787 { 2788 MPI_Comm comm; 2789 DMLabel subpointMap; 2790 IS is; 2791 const PetscInt *opoints; 2792 PetscInt *points, *depths; 2793 PetscInt depth, depStart, depEnd, d, pStart, pEnd, p, n, off; 2794 PetscErrorCode ierr; 2795 2796 PetscFunctionBegin; 2797 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2798 PetscValidPointer(subpointIS, 2); 2799 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 2800 *subpointIS = NULL; 2801 ierr = DMPlexGetSubpointMap(dm, &subpointMap);CHKERRQ(ierr); 2802 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 2803 if (subpointMap && depth >= 0) { 2804 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 2805 if (pStart) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Submeshes must start the point numbering at 0, not %d", pStart); 2806 ierr = DMGetWorkArray(dm, depth+1, PETSC_INT, &depths);CHKERRQ(ierr); 2807 depths[0] = depth; 2808 depths[1] = 0; 2809 for(d = 2; d <= depth; ++d) {depths[d] = depth+1 - d;} 2810 ierr = PetscMalloc(pEnd * sizeof(PetscInt), &points);CHKERRQ(ierr); 2811 for(d = 0, off = 0; d <= depth; ++d) { 2812 const PetscInt dep = depths[d]; 2813 2814 ierr = DMPlexGetDepthStratum(dm, dep, &depStart, &depEnd);CHKERRQ(ierr); 2815 ierr = DMLabelGetStratumSize(subpointMap, dep, &n);CHKERRQ(ierr); 2816 if (((d < 2) && (depth > 1)) || (d == 1)) { /* Only check vertices and cells for now since the map is broken for others */ 2817 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); 2818 } else { 2819 if (!n) { 2820 if (d == 0) { 2821 /* Missing cells */ 2822 for(p = 0; p < depEnd-depStart; ++p, ++off) points[off] = -1; 2823 } else { 2824 /* Missing faces */ 2825 for(p = 0; p < depEnd-depStart; ++p, ++off) points[off] = PETSC_MAX_INT; 2826 } 2827 } 2828 } 2829 if (n) { 2830 ierr = DMLabelGetStratumIS(subpointMap, dep, &is);CHKERRQ(ierr); 2831 ierr = ISGetIndices(is, &opoints);CHKERRQ(ierr); 2832 for(p = 0; p < n; ++p, ++off) points[off] = opoints[p]; 2833 ierr = ISRestoreIndices(is, &opoints);CHKERRQ(ierr); 2834 ierr = ISDestroy(&is);CHKERRQ(ierr); 2835 } 2836 } 2837 ierr = DMRestoreWorkArray(dm, depth+1, PETSC_INT, &depths);CHKERRQ(ierr); 2838 if (off != pEnd) SETERRQ2(comm, PETSC_ERR_ARG_WRONG, "The number of mapped submesh points %d should be %d", off, pEnd); 2839 ierr = ISCreateGeneral(PETSC_COMM_SELF, pEnd, points, PETSC_OWN_POINTER, subpointIS);CHKERRQ(ierr); 2840 } 2841 PetscFunctionReturn(0); 2842 } 2843