1 #include <petsc-private/dmpleximpl.h> /*I "petscdmplex.h" I*/ 2 #include <petscsf.h> 3 4 #undef __FUNCT__ 5 #define __FUNCT__ "DMPlexMarkBoundaryFaces" 6 /*@ 7 DMPlexMarkBoundaryFaces - Mark all faces on the boundary 8 9 Not Collective 10 11 Input Parameter: 12 . dm - The original DM 13 14 Output Parameter: 15 . label - The DMLabel marking boundary faces with value 1 16 17 Level: developer 18 19 .seealso: DMLabelCreate(), DMPlexCreateLabel() 20 @*/ 21 PetscErrorCode DMPlexMarkBoundaryFaces(DM dm, DMLabel label) 22 { 23 PetscInt fStart, fEnd, f; 24 PetscErrorCode ierr; 25 26 PetscFunctionBegin; 27 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 28 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 29 for (f = fStart; f < fEnd; ++f) { 30 PetscInt supportSize; 31 32 ierr = DMPlexGetSupportSize(dm, f, &supportSize);CHKERRQ(ierr); 33 if (supportSize == 1) { 34 ierr = DMLabelSetValue(label, f, 1);CHKERRQ(ierr); 35 } 36 } 37 PetscFunctionReturn(0); 38 } 39 40 #undef __FUNCT__ 41 #define __FUNCT__ "DMPlexLabelComplete" 42 /*@ 43 DMPlexLabelComplete - Starting with a label marking points on a surface, we add the transitive closure to the surface 44 45 Input Parameters: 46 + dm - The DM 47 - label - A DMLabel marking the surface points 48 49 Output Parameter: 50 . label - A DMLabel marking all surface points in the transitive closure 51 52 Level: developer 53 54 .seealso: DMPlexLabelCohesiveComplete() 55 @*/ 56 PetscErrorCode DMPlexLabelComplete(DM dm, DMLabel label) 57 { 58 IS valueIS; 59 const PetscInt *values; 60 PetscInt numValues, v; 61 PetscErrorCode ierr; 62 63 PetscFunctionBegin; 64 ierr = DMLabelGetNumValues(label, &numValues);CHKERRQ(ierr); 65 ierr = DMLabelGetValueIS(label, &valueIS);CHKERRQ(ierr); 66 ierr = ISGetIndices(valueIS, &values);CHKERRQ(ierr); 67 for (v = 0; v < numValues; ++v) { 68 IS pointIS; 69 const PetscInt *points; 70 PetscInt numPoints, p; 71 72 ierr = DMLabelGetStratumSize(label, values[v], &numPoints);CHKERRQ(ierr); 73 ierr = DMLabelGetStratumIS(label, values[v], &pointIS);CHKERRQ(ierr); 74 ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); 75 for (p = 0; p < numPoints; ++p) { 76 PetscInt *closure = NULL; 77 PetscInt closureSize, c; 78 79 ierr = DMPlexGetTransitiveClosure(dm, points[p], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 80 for (c = 0; c < closureSize*2; c += 2) { 81 ierr = DMLabelSetValue(label, closure[c], values[v]);CHKERRQ(ierr); 82 } 83 ierr = DMPlexRestoreTransitiveClosure(dm, points[p], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 84 } 85 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 86 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 87 } 88 ierr = ISRestoreIndices(valueIS, &values);CHKERRQ(ierr); 89 ierr = ISDestroy(&valueIS);CHKERRQ(ierr); 90 PetscFunctionReturn(0); 91 } 92 93 #undef __FUNCT__ 94 #define __FUNCT__ "DMPlexShiftPoint_Internal" 95 PETSC_STATIC_INLINE PetscInt DMPlexShiftPoint_Internal(PetscInt p, PetscInt depth, PetscInt depthEnd[], PetscInt depthShift[]) 96 { 97 if (depth < 0) return p; 98 /* Cells */ if (p < depthEnd[depth]) return p; 99 /* Vertices */ if (p < depthEnd[0]) return p + depthShift[depth]; 100 /* Faces */ if (p < depthEnd[depth-1]) return p + depthShift[depth] + depthShift[0]; 101 /* Edges */ return p + depthShift[depth] + depthShift[0] + depthShift[depth-1]; 102 } 103 104 #undef __FUNCT__ 105 #define __FUNCT__ "DMPlexShiftSizes_Internal" 106 static PetscErrorCode DMPlexShiftSizes_Internal(DM dm, PetscInt depthShift[], DM dmNew) 107 { 108 PetscInt *depthEnd; 109 PetscInt depth = 0, d, pStart, pEnd, p; 110 PetscErrorCode ierr; 111 112 PetscFunctionBegin; 113 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 114 if (depth < 0) PetscFunctionReturn(0); 115 ierr = PetscMalloc((depth+1) * sizeof(PetscInt), &depthEnd);CHKERRQ(ierr); 116 /* Step 1: Expand chart */ 117 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 118 for (d = 0; d <= depth; ++d) { 119 pEnd += depthShift[d]; 120 ierr = DMPlexGetDepthStratum(dm, d, NULL, &depthEnd[d]);CHKERRQ(ierr); 121 } 122 ierr = DMPlexSetChart(dmNew, pStart, pEnd);CHKERRQ(ierr); 123 /* Step 2: Set cone and support sizes */ 124 for (d = 0; d <= depth; ++d) { 125 ierr = DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);CHKERRQ(ierr); 126 for (p = pStart; p < pEnd; ++p) { 127 PetscInt newp = DMPlexShiftPoint_Internal(p, depth, depthEnd, depthShift); 128 PetscInt size; 129 130 ierr = DMPlexGetConeSize(dm, p, &size);CHKERRQ(ierr); 131 ierr = DMPlexSetConeSize(dmNew, newp, size);CHKERRQ(ierr); 132 ierr = DMPlexGetSupportSize(dm, p, &size);CHKERRQ(ierr); 133 ierr = DMPlexSetSupportSize(dmNew, newp, size);CHKERRQ(ierr); 134 } 135 } 136 ierr = PetscFree(depthEnd);CHKERRQ(ierr); 137 PetscFunctionReturn(0); 138 } 139 140 #undef __FUNCT__ 141 #define __FUNCT__ "DMPlexShiftPoints_Internal" 142 static PetscErrorCode DMPlexShiftPoints_Internal(DM dm, PetscInt depthShift[], DM dmNew) 143 { 144 PetscInt *depthEnd, *newpoints; 145 PetscInt depth = 0, d, maxConeSize, maxSupportSize, pStart, pEnd, p; 146 PetscErrorCode ierr; 147 148 PetscFunctionBegin; 149 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 150 if (depth < 0) PetscFunctionReturn(0); 151 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize);CHKERRQ(ierr); 152 ierr = PetscMalloc2(depth+1,PetscInt,&depthEnd,PetscMax(maxConeSize, maxSupportSize),PetscInt,&newpoints);CHKERRQ(ierr); 153 for (d = 0; d <= depth; ++d) { 154 ierr = DMPlexGetDepthStratum(dm, d, NULL, &depthEnd[d]);CHKERRQ(ierr); 155 } 156 /* Step 5: Set cones and supports */ 157 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 158 for (p = pStart; p < pEnd; ++p) { 159 const PetscInt *points = NULL, *orientations = NULL; 160 PetscInt size, i, newp = DMPlexShiftPoint_Internal(p, depth, depthEnd, depthShift); 161 162 ierr = DMPlexGetConeSize(dm, p, &size);CHKERRQ(ierr); 163 ierr = DMPlexGetCone(dm, p, &points);CHKERRQ(ierr); 164 ierr = DMPlexGetConeOrientation(dm, p, &orientations);CHKERRQ(ierr); 165 for (i = 0; i < size; ++i) { 166 newpoints[i] = DMPlexShiftPoint_Internal(points[i], depth, depthEnd, depthShift); 167 } 168 ierr = DMPlexSetCone(dmNew, newp, newpoints);CHKERRQ(ierr); 169 ierr = DMPlexSetConeOrientation(dmNew, newp, orientations);CHKERRQ(ierr); 170 ierr = DMPlexGetSupportSize(dm, p, &size);CHKERRQ(ierr); 171 ierr = DMPlexGetSupport(dm, p, &points);CHKERRQ(ierr); 172 for (i = 0; i < size; ++i) { 173 newpoints[i] = DMPlexShiftPoint_Internal(points[i], depth, depthEnd, depthShift); 174 } 175 ierr = DMPlexSetSupport(dmNew, newp, newpoints);CHKERRQ(ierr); 176 } 177 ierr = PetscFree2(depthEnd,newpoints);CHKERRQ(ierr); 178 PetscFunctionReturn(0); 179 } 180 181 #undef __FUNCT__ 182 #define __FUNCT__ "DMPlexShiftCoordinates_Internal" 183 static PetscErrorCode DMPlexShiftCoordinates_Internal(DM dm, PetscInt depthShift[], DM dmNew) 184 { 185 PetscSection coordSection, newCoordSection; 186 Vec coordinates, newCoordinates; 187 PetscScalar *coords, *newCoords; 188 PetscInt *depthEnd, coordSize; 189 PetscInt dim, depth = 0, d, vStart, vEnd, vStartNew, vEndNew, v; 190 PetscErrorCode ierr; 191 192 PetscFunctionBegin; 193 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 194 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 195 ierr = PetscMalloc((depth+1) * sizeof(PetscInt), &depthEnd);CHKERRQ(ierr); 196 for (d = 0; d <= depth; ++d) { 197 ierr = DMPlexGetDepthStratum(dm, d, NULL, &depthEnd[d]);CHKERRQ(ierr); 198 } 199 /* Step 8: Convert coordinates */ 200 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 201 ierr = DMPlexGetDepthStratum(dmNew, 0, &vStartNew, &vEndNew);CHKERRQ(ierr); 202 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 203 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &newCoordSection);CHKERRQ(ierr); 204 ierr = PetscSectionSetNumFields(newCoordSection, 1);CHKERRQ(ierr); 205 ierr = PetscSectionSetFieldComponents(newCoordSection, 0, dim);CHKERRQ(ierr); 206 ierr = PetscSectionSetChart(newCoordSection, vStartNew, vEndNew);CHKERRQ(ierr); 207 for (v = vStartNew; v < vEndNew; ++v) { 208 ierr = PetscSectionSetDof(newCoordSection, v, dim);CHKERRQ(ierr); 209 ierr = PetscSectionSetFieldDof(newCoordSection, v, 0, dim);CHKERRQ(ierr); 210 } 211 ierr = PetscSectionSetUp(newCoordSection);CHKERRQ(ierr); 212 ierr = DMPlexSetCoordinateSection(dmNew, newCoordSection);CHKERRQ(ierr); 213 ierr = PetscSectionGetStorageSize(newCoordSection, &coordSize);CHKERRQ(ierr); 214 ierr = VecCreate(PetscObjectComm((PetscObject)dm), &newCoordinates);CHKERRQ(ierr); 215 ierr = PetscObjectSetName((PetscObject) newCoordinates, "coordinates");CHKERRQ(ierr); 216 ierr = VecSetSizes(newCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 217 ierr = VecSetFromOptions(newCoordinates);CHKERRQ(ierr); 218 ierr = DMSetCoordinatesLocal(dmNew, newCoordinates);CHKERRQ(ierr); 219 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 220 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 221 ierr = VecGetArray(newCoordinates, &newCoords);CHKERRQ(ierr); 222 for (v = vStart; v < vEnd; ++v) { 223 PetscInt dof, off, noff, d; 224 225 ierr = PetscSectionGetDof(coordSection, v, &dof);CHKERRQ(ierr); 226 ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr); 227 ierr = PetscSectionGetOffset(newCoordSection, DMPlexShiftPoint_Internal(v, depth, depthEnd, depthShift), &noff);CHKERRQ(ierr); 228 for (d = 0; d < dof; ++d) { 229 newCoords[noff+d] = coords[off+d]; 230 } 231 } 232 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 233 ierr = VecRestoreArray(newCoordinates, &newCoords);CHKERRQ(ierr); 234 ierr = VecDestroy(&newCoordinates);CHKERRQ(ierr); 235 ierr = PetscSectionDestroy(&newCoordSection);CHKERRQ(ierr); 236 ierr = PetscFree(depthEnd);CHKERRQ(ierr); 237 PetscFunctionReturn(0); 238 } 239 240 #undef __FUNCT__ 241 #define __FUNCT__ "DMPlexShiftSF_Internal" 242 static PetscErrorCode DMPlexShiftSF_Internal(DM dm, PetscInt depthShift[], DM dmNew) 243 { 244 PetscInt *depthEnd; 245 PetscInt depth = 0, d; 246 PetscSF sfPoint, sfPointNew; 247 const PetscSFNode *remotePoints; 248 PetscSFNode *gremotePoints; 249 const PetscInt *localPoints; 250 PetscInt *glocalPoints, *newLocation, *newRemoteLocation; 251 PetscInt numRoots, numLeaves, l, pStart, pEnd, totShift = 0; 252 PetscMPIInt numProcs; 253 PetscErrorCode ierr; 254 255 PetscFunctionBegin; 256 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 257 ierr = PetscMalloc((depth+1) * sizeof(PetscInt), &depthEnd);CHKERRQ(ierr); 258 for (d = 0; d <= depth; ++d) { 259 totShift += depthShift[d]; 260 ierr = DMPlexGetDepthStratum(dm, d, NULL, &depthEnd[d]);CHKERRQ(ierr); 261 } 262 /* Step 9: Convert pointSF */ 263 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)dm), &numProcs);CHKERRQ(ierr); 264 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 265 ierr = DMGetPointSF(dmNew, &sfPointNew);CHKERRQ(ierr); 266 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 267 ierr = PetscSFGetGraph(sfPoint, &numRoots, &numLeaves, &localPoints, &remotePoints);CHKERRQ(ierr); 268 if (numRoots >= 0) { 269 ierr = PetscMalloc2(numRoots,PetscInt,&newLocation,pEnd-pStart,PetscInt,&newRemoteLocation);CHKERRQ(ierr); 270 for (l=0; l<numRoots; l++) newLocation[l] = DMPlexShiftPoint_Internal(l, depth, depthEnd, depthShift); 271 ierr = PetscSFBcastBegin(sfPoint, MPIU_INT, newLocation, newRemoteLocation);CHKERRQ(ierr); 272 ierr = PetscSFBcastEnd(sfPoint, MPIU_INT, newLocation, newRemoteLocation);CHKERRQ(ierr); 273 ierr = PetscMalloc(numLeaves * sizeof(PetscInt), &glocalPoints);CHKERRQ(ierr); 274 ierr = PetscMalloc(numLeaves * sizeof(PetscSFNode), &gremotePoints);CHKERRQ(ierr); 275 for (l = 0; l < numLeaves; ++l) { 276 glocalPoints[l] = DMPlexShiftPoint_Internal(localPoints[l], depth, depthEnd, depthShift); 277 gremotePoints[l].rank = remotePoints[l].rank; 278 gremotePoints[l].index = newRemoteLocation[localPoints[l]]; 279 } 280 ierr = PetscFree2(newLocation,newRemoteLocation);CHKERRQ(ierr); 281 ierr = PetscSFSetGraph(sfPointNew, numRoots + totShift, numLeaves, glocalPoints, PETSC_OWN_POINTER, gremotePoints, PETSC_OWN_POINTER);CHKERRQ(ierr); 282 } 283 ierr = PetscFree(depthEnd);CHKERRQ(ierr); 284 PetscFunctionReturn(0); 285 } 286 287 #undef __FUNCT__ 288 #define __FUNCT__ "DMPlexShiftLabels_Internal" 289 static PetscErrorCode DMPlexShiftLabels_Internal(DM dm, PetscInt depthShift[], DM dmNew) 290 { 291 PetscSF sfPoint; 292 DMLabel vtkLabel, ghostLabel; 293 PetscInt *depthEnd; 294 const PetscSFNode *leafRemote; 295 const PetscInt *leafLocal; 296 PetscInt depth = 0, d, numLeaves, numLabels, l, cStart, cEnd, c, fStart, fEnd, f; 297 PetscMPIInt rank; 298 PetscErrorCode ierr; 299 300 PetscFunctionBegin; 301 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 302 ierr = PetscMalloc((depth+1) * sizeof(PetscInt), &depthEnd);CHKERRQ(ierr); 303 for (d = 0; d <= depth; ++d) { 304 ierr = DMPlexGetDepthStratum(dm, d, NULL, &depthEnd[d]);CHKERRQ(ierr); 305 } 306 /* Step 10: Convert labels */ 307 ierr = DMPlexGetNumLabels(dm, &numLabels);CHKERRQ(ierr); 308 for (l = 0; l < numLabels; ++l) { 309 DMLabel label, newlabel; 310 const char *lname; 311 PetscBool isDepth; 312 IS valueIS; 313 const PetscInt *values; 314 PetscInt numValues, val; 315 316 ierr = DMPlexGetLabelName(dm, l, &lname);CHKERRQ(ierr); 317 ierr = PetscStrcmp(lname, "depth", &isDepth);CHKERRQ(ierr); 318 if (isDepth) continue; 319 ierr = DMPlexCreateLabel(dmNew, lname);CHKERRQ(ierr); 320 ierr = DMPlexGetLabel(dm, lname, &label);CHKERRQ(ierr); 321 ierr = DMPlexGetLabel(dmNew, lname, &newlabel);CHKERRQ(ierr); 322 ierr = DMLabelGetValueIS(label, &valueIS);CHKERRQ(ierr); 323 ierr = ISGetLocalSize(valueIS, &numValues);CHKERRQ(ierr); 324 ierr = ISGetIndices(valueIS, &values);CHKERRQ(ierr); 325 for (val = 0; val < numValues; ++val) { 326 IS pointIS; 327 const PetscInt *points; 328 PetscInt numPoints, p; 329 330 ierr = DMLabelGetStratumIS(label, values[val], &pointIS);CHKERRQ(ierr); 331 ierr = ISGetLocalSize(pointIS, &numPoints);CHKERRQ(ierr); 332 ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); 333 for (p = 0; p < numPoints; ++p) { 334 const PetscInt newpoint = DMPlexShiftPoint_Internal(points[p], depth, depthEnd, depthShift); 335 336 ierr = DMLabelSetValue(newlabel, newpoint, values[val]);CHKERRQ(ierr); 337 } 338 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 339 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 340 } 341 ierr = ISRestoreIndices(valueIS, &values);CHKERRQ(ierr); 342 ierr = ISDestroy(&valueIS);CHKERRQ(ierr); 343 } 344 ierr = PetscFree(depthEnd);CHKERRQ(ierr); 345 /* Step 11: Make label for output (vtk) and to mark ghost points (ghost) */ 346 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr); 347 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 348 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 349 ierr = PetscSFGetGraph(sfPoint, NULL, &numLeaves, &leafLocal, &leafRemote);CHKERRQ(ierr); 350 ierr = DMPlexCreateLabel(dmNew, "vtk");CHKERRQ(ierr); 351 ierr = DMPlexCreateLabel(dmNew, "ghost");CHKERRQ(ierr); 352 ierr = DMPlexGetLabel(dmNew, "vtk", &vtkLabel);CHKERRQ(ierr); 353 ierr = DMPlexGetLabel(dmNew, "ghost", &ghostLabel);CHKERRQ(ierr); 354 for (l = 0, c = cStart; l < numLeaves && c < cEnd; ++l, ++c) { 355 for (; c < leafLocal[l] && c < cEnd; ++c) { 356 ierr = DMLabelSetValue(vtkLabel, c, 1);CHKERRQ(ierr); 357 } 358 if (leafLocal[l] >= cEnd) break; 359 if (leafRemote[l].rank == rank) { 360 ierr = DMLabelSetValue(vtkLabel, c, 1);CHKERRQ(ierr); 361 } else { 362 ierr = DMLabelSetValue(ghostLabel, c, 2);CHKERRQ(ierr); 363 } 364 } 365 for (; c < cEnd; ++c) { 366 ierr = DMLabelSetValue(vtkLabel, c, 1);CHKERRQ(ierr); 367 } 368 if (0) { 369 ierr = PetscViewerASCIISynchronizedAllow(PETSC_VIEWER_STDOUT_WORLD, PETSC_TRUE);CHKERRQ(ierr); 370 ierr = DMLabelView(vtkLabel, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 371 ierr = PetscViewerFlush(PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 372 } 373 ierr = DMPlexGetHeightStratum(dmNew, 1, &fStart, &fEnd);CHKERRQ(ierr); 374 for (f = fStart; f < fEnd; ++f) { 375 PetscInt numCells; 376 377 ierr = DMPlexGetSupportSize(dmNew, f, &numCells);CHKERRQ(ierr); 378 if (numCells < 2) { 379 ierr = DMLabelSetValue(ghostLabel, f, 1);CHKERRQ(ierr); 380 } else { 381 const PetscInt *cells = NULL; 382 PetscInt vA, vB; 383 384 ierr = DMPlexGetSupport(dmNew, f, &cells);CHKERRQ(ierr); 385 ierr = DMLabelGetValue(vtkLabel, cells[0], &vA);CHKERRQ(ierr); 386 ierr = DMLabelGetValue(vtkLabel, cells[1], &vB);CHKERRQ(ierr); 387 if (!vA && !vB) {ierr = DMLabelSetValue(ghostLabel, f, 1);CHKERRQ(ierr);} 388 } 389 } 390 if (0) { 391 ierr = PetscViewerASCIISynchronizedAllow(PETSC_VIEWER_STDOUT_WORLD, PETSC_TRUE);CHKERRQ(ierr); 392 ierr = DMLabelView(ghostLabel, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 393 ierr = PetscViewerFlush(PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 394 } 395 PetscFunctionReturn(0); 396 } 397 398 #undef __FUNCT__ 399 #define __FUNCT__ "DMPlexConstructGhostCells_Internal" 400 static PetscErrorCode DMPlexConstructGhostCells_Internal(DM dm, DMLabel label, PetscInt *numGhostCells, DM gdm) 401 { 402 IS valueIS; 403 const PetscInt *values; 404 PetscInt *depthShift; 405 PetscInt depth = 0, numFS, fs, ghostCell, cEnd, c; 406 PetscErrorCode ierr; 407 408 PetscFunctionBegin; 409 /* Count ghost cells */ 410 ierr = DMLabelGetValueIS(label, &valueIS);CHKERRQ(ierr); 411 ierr = ISGetLocalSize(valueIS, &numFS);CHKERRQ(ierr); 412 ierr = ISGetIndices(valueIS, &values);CHKERRQ(ierr); 413 414 *numGhostCells = 0; 415 for (fs = 0; fs < numFS; ++fs) { 416 PetscInt numBdFaces; 417 418 ierr = DMLabelGetStratumSize(label, values[fs], &numBdFaces);CHKERRQ(ierr); 419 420 *numGhostCells += numBdFaces; 421 } 422 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 423 ierr = PetscMalloc((depth+1) * sizeof(PetscInt), &depthShift);CHKERRQ(ierr); 424 ierr = PetscMemzero(depthShift, (depth+1) * sizeof(PetscInt));CHKERRQ(ierr); 425 if (depth >= 0) depthShift[depth] = *numGhostCells; 426 ierr = DMPlexShiftSizes_Internal(dm, depthShift, gdm);CHKERRQ(ierr); 427 /* Step 3: Set cone/support sizes for new points */ 428 ierr = DMPlexGetHeightStratum(dm, 0, NULL, &cEnd);CHKERRQ(ierr); 429 for (c = cEnd; c < cEnd + *numGhostCells; ++c) { 430 ierr = DMPlexSetConeSize(gdm, c, 1);CHKERRQ(ierr); 431 } 432 for (fs = 0; fs < numFS; ++fs) { 433 IS faceIS; 434 const PetscInt *faces; 435 PetscInt numFaces, f; 436 437 ierr = DMLabelGetStratumIS(label, values[fs], &faceIS);CHKERRQ(ierr); 438 ierr = ISGetLocalSize(faceIS, &numFaces);CHKERRQ(ierr); 439 ierr = ISGetIndices(faceIS, &faces);CHKERRQ(ierr); 440 for (f = 0; f < numFaces; ++f) { 441 PetscInt size; 442 443 ierr = DMPlexGetSupportSize(dm, faces[f], &size);CHKERRQ(ierr); 444 if (size != 1) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "DM has boundary face %d with %d support cells", faces[f], size); 445 ierr = DMPlexSetSupportSize(gdm, faces[f] + *numGhostCells, 2);CHKERRQ(ierr); 446 } 447 ierr = ISRestoreIndices(faceIS, &faces);CHKERRQ(ierr); 448 ierr = ISDestroy(&faceIS);CHKERRQ(ierr); 449 } 450 /* Step 4: Setup ghosted DM */ 451 ierr = DMSetUp(gdm);CHKERRQ(ierr); 452 ierr = DMPlexShiftPoints_Internal(dm, depthShift, gdm);CHKERRQ(ierr); 453 /* Step 6: Set cones and supports for new points */ 454 ghostCell = cEnd; 455 for (fs = 0; fs < numFS; ++fs) { 456 IS faceIS; 457 const PetscInt *faces; 458 PetscInt numFaces, f; 459 460 ierr = DMLabelGetStratumIS(label, values[fs], &faceIS);CHKERRQ(ierr); 461 ierr = ISGetLocalSize(faceIS, &numFaces);CHKERRQ(ierr); 462 ierr = ISGetIndices(faceIS, &faces);CHKERRQ(ierr); 463 for (f = 0; f < numFaces; ++f, ++ghostCell) { 464 PetscInt newFace = faces[f] + *numGhostCells; 465 466 ierr = DMPlexSetCone(gdm, ghostCell, &newFace);CHKERRQ(ierr); 467 ierr = DMPlexInsertSupport(gdm, newFace, 1, ghostCell);CHKERRQ(ierr); 468 } 469 ierr = ISRestoreIndices(faceIS, &faces);CHKERRQ(ierr); 470 ierr = ISDestroy(&faceIS);CHKERRQ(ierr); 471 } 472 ierr = ISRestoreIndices(valueIS, &values);CHKERRQ(ierr); 473 ierr = ISDestroy(&valueIS);CHKERRQ(ierr); 474 /* Step 7: Stratify */ 475 ierr = DMPlexStratify(gdm);CHKERRQ(ierr); 476 ierr = DMPlexShiftCoordinates_Internal(dm, depthShift, gdm);CHKERRQ(ierr); 477 ierr = DMPlexShiftSF_Internal(dm, depthShift, gdm);CHKERRQ(ierr); 478 ierr = DMPlexShiftLabels_Internal(dm, depthShift, gdm);CHKERRQ(ierr); 479 ierr = PetscFree(depthShift);CHKERRQ(ierr); 480 PetscFunctionReturn(0); 481 } 482 483 #undef __FUNCT__ 484 #define __FUNCT__ "DMPlexConstructGhostCells" 485 /*@C 486 DMPlexConstructGhostCells - Construct ghost cells which connect to every boundary face 487 488 Collective on dm 489 490 Input Parameters: 491 + dm - The original DM 492 - labelName - The label specifying the boundary faces, or "Face Sets" if this is NULL 493 494 Output Parameters: 495 + numGhostCells - The number of ghost cells added to the DM 496 - dmGhosted - The new DM 497 498 Note: If no label exists of that name, one will be created marking all boundary faces 499 500 Level: developer 501 502 .seealso: DMCreate() 503 */ 504 PetscErrorCode DMPlexConstructGhostCells(DM dm, const char labelName[], PetscInt *numGhostCells, DM *dmGhosted) 505 { 506 DM gdm; 507 DMLabel label; 508 const char *name = labelName ? labelName : "Face Sets"; 509 PetscInt dim; 510 PetscErrorCode ierr; 511 512 PetscFunctionBegin; 513 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 514 PetscValidPointer(numGhostCells, 3); 515 PetscValidPointer(dmGhosted, 4); 516 ierr = DMCreate(PetscObjectComm((PetscObject)dm), &gdm);CHKERRQ(ierr); 517 ierr = DMSetType(gdm, DMPLEX);CHKERRQ(ierr); 518 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 519 ierr = DMPlexSetDimension(gdm, dim);CHKERRQ(ierr); 520 ierr = DMPlexGetLabel(dm, name, &label);CHKERRQ(ierr); 521 if (!label) { 522 /* Get label for boundary faces */ 523 ierr = DMPlexCreateLabel(dm, name);CHKERRQ(ierr); 524 ierr = DMPlexGetLabel(dm, name, &label);CHKERRQ(ierr); 525 ierr = DMPlexMarkBoundaryFaces(dm, label);CHKERRQ(ierr); 526 } 527 ierr = DMPlexConstructGhostCells_Internal(dm, label, numGhostCells, gdm);CHKERRQ(ierr); 528 ierr = DMSetFromOptions(gdm);CHKERRQ(ierr); 529 *dmGhosted = gdm; 530 PetscFunctionReturn(0); 531 } 532 533 #undef __FUNCT__ 534 #define __FUNCT__ "DMPlexConstructCohesiveCells_Internal" 535 static PetscErrorCode DMPlexConstructCohesiveCells_Internal(DM dm, DMLabel label, DM sdm) 536 { 537 MPI_Comm comm; 538 IS valueIS, *pointIS; 539 const PetscInt *values, **splitPoints; 540 PetscSection coordSection; 541 Vec coordinates; 542 PetscScalar *coords; 543 PetscInt *depthShift, *depthOffset, *pMaxNew, *numSplitPoints, *coneNew, *supportNew; 544 PetscInt shift = 100, depth = 0, dep, dim, d, numSP = 0, sp, maxConeSize, maxSupportSize, numLabels, p, v; 545 PetscErrorCode ierr; 546 547 PetscFunctionBegin; 548 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 549 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 550 /* Count split points and add cohesive cells */ 551 if (label) { 552 ierr = DMLabelGetValueIS(label, &valueIS);CHKERRQ(ierr); 553 ierr = ISGetLocalSize(valueIS, &numSP);CHKERRQ(ierr); 554 ierr = ISGetIndices(valueIS, &values);CHKERRQ(ierr); 555 } 556 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 557 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize);CHKERRQ(ierr); 558 ierr = PetscMalloc5(depth+1,PetscInt,&depthShift,depth+1,PetscInt,&depthOffset,depth+1,PetscInt,&pMaxNew,maxConeSize*3,PetscInt,&coneNew,maxSupportSize,PetscInt,&supportNew);CHKERRQ(ierr); 559 ierr = PetscMalloc3(depth+1,IS,&pointIS,depth+1,PetscInt,&numSplitPoints,depth+1,const PetscInt*,&splitPoints);CHKERRQ(ierr); 560 ierr = PetscMemzero(depthShift, (depth+1) * sizeof(PetscInt));CHKERRQ(ierr); 561 for (d = 0; d <= depth; ++d) { 562 ierr = DMPlexGetDepthStratum(dm, d, NULL, &pMaxNew[d]);CHKERRQ(ierr); 563 numSplitPoints[d] = 0; 564 splitPoints[d] = NULL; 565 pointIS[d] = NULL; 566 } 567 for (sp = 0; sp < numSP; ++sp) { 568 const PetscInt dep = values[sp]; 569 570 if ((dep < 0) || (dep > depth)) continue; 571 ierr = DMLabelGetStratumSize(label, dep, &depthShift[dep]);CHKERRQ(ierr); 572 ierr = DMLabelGetStratumIS(label, dep, &pointIS[dep]);CHKERRQ(ierr); 573 if (pointIS[dep]) { 574 ierr = ISGetLocalSize(pointIS[dep], &numSplitPoints[dep]);CHKERRQ(ierr); 575 ierr = ISGetIndices(pointIS[dep], &splitPoints[dep]);CHKERRQ(ierr); 576 } 577 } 578 if (depth >= 0) { 579 /* Calculate number of additional points */ 580 depthShift[depth] = depthShift[depth-1]; /* There is a cohesive cell for every split face */ 581 depthShift[1] += depthShift[0]; /* There is a cohesive edge for every split vertex */ 582 /* Calculate hybrid bound for each dimension */ 583 pMaxNew[0] += depthShift[depth]; 584 if (depth > 1) pMaxNew[dim-1] += depthShift[depth] + depthShift[0]; 585 if (depth > 2) pMaxNew[1] += depthShift[depth] + depthShift[0] + depthShift[dim-1]; 586 587 /* Calculate point offset for each dimension */ 588 depthOffset[depth] = 0; 589 depthOffset[0] = depthOffset[depth] + depthShift[depth]; 590 if (depth > 1) depthOffset[dim-1] = depthOffset[0] + depthShift[0]; 591 if (depth > 2) depthOffset[1] = depthOffset[dim-1] + depthShift[dim-1]; 592 } 593 ierr = DMPlexShiftSizes_Internal(dm, depthShift, sdm);CHKERRQ(ierr); 594 /* Step 3: Set cone/support sizes for new points */ 595 for (dep = 0; dep <= depth; ++dep) { 596 for (p = 0; p < numSplitPoints[dep]; ++p) { 597 const PetscInt oldp = splitPoints[dep][p]; 598 const PetscInt newp = depthOffset[dep] + oldp; 599 const PetscInt splitp = pMaxNew[dep] + p; 600 const PetscInt *support; 601 PetscInt coneSize, supportSize, q, e; 602 603 ierr = DMPlexGetConeSize(dm, oldp, &coneSize);CHKERRQ(ierr); 604 ierr = DMPlexSetConeSize(sdm, splitp, coneSize);CHKERRQ(ierr); 605 ierr = DMPlexGetSupportSize(dm, oldp, &supportSize);CHKERRQ(ierr); 606 ierr = DMPlexSetSupportSize(sdm, splitp, supportSize);CHKERRQ(ierr); 607 if (dep == depth-1) { 608 const PetscInt ccell = pMaxNew[depth] + p; 609 /* Add cohesive cells, they are prisms */ 610 ierr = DMPlexSetConeSize(sdm, ccell, 2 + coneSize);CHKERRQ(ierr); 611 } else if (dep == 0) { 612 const PetscInt cedge = pMaxNew[1] + (depthShift[1] - depthShift[0]) + p; 613 614 ierr = DMPlexGetSupport(dm, oldp, &support);CHKERRQ(ierr); 615 /* Split old vertex: Edges in old split faces and new cohesive edge */ 616 for (e = 0, q = 0; e < supportSize; ++e) { 617 PetscInt val; 618 619 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 620 if ((val == 1) || (val == (shift + 1))) ++q; 621 } 622 ierr = DMPlexSetSupportSize(sdm, newp, q+1);CHKERRQ(ierr); 623 /* Split new vertex: Edges in new split faces and new cohesive edge */ 624 for (e = 0, q = 0; e < supportSize; ++e) { 625 PetscInt val; 626 627 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 628 if ((val == 1) || (val == -(shift + 1))) ++q; 629 } 630 ierr = DMPlexSetSupportSize(sdm, splitp, q+1);CHKERRQ(ierr); 631 /* Add cohesive edges */ 632 ierr = DMPlexSetConeSize(sdm, cedge, 2);CHKERRQ(ierr); 633 /* Punt for now on support, you loop over closure, extract faces, check which ones are in the label */ 634 } else if (dep == dim-2) { 635 ierr = DMPlexGetSupport(dm, oldp, &support);CHKERRQ(ierr); 636 /* Split old edge: Faces in positive side cells and old split faces */ 637 for (e = 0, q = 0; e < supportSize; ++e) { 638 PetscInt val; 639 640 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 641 if ((val == dim-1) || (val == (shift + dim-1))) ++q; 642 } 643 ierr = DMPlexSetSupportSize(sdm, newp, q);CHKERRQ(ierr); 644 /* Split new edge: Faces in negative side cells and new split faces */ 645 for (e = 0, q = 0; e < supportSize; ++e) { 646 PetscInt val; 647 648 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 649 if ((val == dim-1) || (val == -(shift + dim-1))) ++q; 650 } 651 ierr = DMPlexSetSupportSize(sdm, splitp, q);CHKERRQ(ierr); 652 } 653 } 654 } 655 /* Step 4: Setup split DM */ 656 ierr = DMSetUp(sdm);CHKERRQ(ierr); 657 ierr = DMPlexShiftPoints_Internal(dm, depthShift, sdm);CHKERRQ(ierr); 658 /* Step 6: Set cones and supports for new points */ 659 for (dep = 0; dep <= depth; ++dep) { 660 for (p = 0; p < numSplitPoints[dep]; ++p) { 661 const PetscInt oldp = splitPoints[dep][p]; 662 const PetscInt newp = depthOffset[dep] + oldp; 663 const PetscInt splitp = pMaxNew[dep] + p; 664 const PetscInt *cone, *support, *ornt; 665 PetscInt coneSize, supportSize, q, v, e, s; 666 667 ierr = DMPlexGetConeSize(dm, oldp, &coneSize);CHKERRQ(ierr); 668 ierr = DMPlexGetCone(dm, oldp, &cone);CHKERRQ(ierr); 669 ierr = DMPlexGetConeOrientation(dm, oldp, &ornt);CHKERRQ(ierr); 670 ierr = DMPlexGetSupportSize(dm, oldp, &supportSize);CHKERRQ(ierr); 671 ierr = DMPlexGetSupport(dm, oldp, &support);CHKERRQ(ierr); 672 if (dep == depth-1) { 673 const PetscInt ccell = pMaxNew[depth] + p; 674 const PetscInt *supportF; 675 676 /* Split face: copy in old face to new face to start */ 677 ierr = DMPlexGetSupport(sdm, newp, &supportF);CHKERRQ(ierr); 678 ierr = DMPlexSetSupport(sdm, splitp, supportF);CHKERRQ(ierr); 679 /* Split old face: old vertices/edges in cone so no change */ 680 /* Split new face: new vertices/edges in cone */ 681 for (q = 0; q < coneSize; ++q) { 682 ierr = PetscFindInt(cone[q], numSplitPoints[dim-2], splitPoints[dim-2], &v);CHKERRQ(ierr); 683 684 coneNew[2+q] = pMaxNew[dim-2] + v; 685 } 686 ierr = DMPlexSetCone(sdm, splitp, &coneNew[2]);CHKERRQ(ierr); 687 ierr = DMPlexSetConeOrientation(sdm, splitp, ornt);CHKERRQ(ierr); 688 /* Cohesive cell: Old and new split face, then new cohesive edges */ 689 coneNew[0] = newp; 690 coneNew[1] = splitp; 691 for (q = 0; q < coneSize; ++q) { 692 coneNew[2+q] = (pMaxNew[1] - pMaxNew[dim-2]) + (depthShift[1] - depthShift[0]) + coneNew[2+q]; 693 } 694 ierr = DMPlexSetCone(sdm, ccell, coneNew);CHKERRQ(ierr); 695 696 697 for (s = 0; s < supportSize; ++s) { 698 PetscInt val; 699 700 ierr = DMLabelGetValue(label, support[s], &val);CHKERRQ(ierr); 701 if (val < 0) { 702 /* Split old face: Replace negative side cell with cohesive cell */ 703 ierr = DMPlexInsertSupport(sdm, newp, s, ccell);CHKERRQ(ierr); 704 } else { 705 /* Split new face: Replace positive side cell with cohesive cell */ 706 ierr = DMPlexInsertSupport(sdm, splitp, s, ccell);CHKERRQ(ierr); 707 } 708 } 709 } else if (dep == 0) { 710 const PetscInt cedge = pMaxNew[1] + (depthShift[1] - depthShift[0]) + p; 711 712 /* Split old vertex: Edges in old split faces and new cohesive edge */ 713 for (e = 0, q = 0; e < supportSize; ++e) { 714 PetscInt val; 715 716 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 717 if ((val == 1) || (val == (shift + 1))) { 718 supportNew[q++] = depthOffset[1] + support[e]; 719 } 720 } 721 supportNew[q] = cedge; 722 723 ierr = DMPlexSetSupport(sdm, newp, supportNew);CHKERRQ(ierr); 724 /* Split new vertex: Edges in new split faces and new cohesive edge */ 725 for (e = 0, q = 0; e < supportSize; ++e) { 726 PetscInt val, edge; 727 728 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 729 if (val == 1) { 730 ierr = PetscFindInt(support[e], numSplitPoints[1], splitPoints[1], &edge);CHKERRQ(ierr); 731 if (edge < 0) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Edge %d is not a split edge", support[e]); 732 supportNew[q++] = pMaxNew[1] + edge; 733 } else if (val == -(shift + 1)) { 734 supportNew[q++] = depthOffset[1] + support[e]; 735 } 736 } 737 supportNew[q] = cedge; 738 ierr = DMPlexSetSupport(sdm, splitp, supportNew);CHKERRQ(ierr); 739 /* Cohesive edge: Old and new split vertex, punting on support */ 740 coneNew[0] = newp; 741 coneNew[1] = splitp; 742 ierr = DMPlexSetCone(sdm, cedge, coneNew);CHKERRQ(ierr); 743 } else if (dep == dim-2) { 744 /* Split old edge: old vertices in cone so no change */ 745 /* Split new edge: new vertices in cone */ 746 for (q = 0; q < coneSize; ++q) { 747 ierr = PetscFindInt(cone[q], numSplitPoints[dim-3], splitPoints[dim-3], &v);CHKERRQ(ierr); 748 749 coneNew[q] = pMaxNew[dim-3] + v; 750 } 751 ierr = DMPlexSetCone(sdm, splitp, coneNew);CHKERRQ(ierr); 752 /* Split old edge: Faces in positive side cells and old split faces */ 753 for (e = 0, q = 0; e < supportSize; ++e) { 754 PetscInt val; 755 756 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 757 if ((val == dim-1) || (val == (shift + dim-1))) { 758 supportNew[q++] = depthOffset[dim-1] + support[e]; 759 } 760 } 761 ierr = DMPlexSetSupport(sdm, newp, supportNew);CHKERRQ(ierr); 762 /* Split new edge: Faces in negative side cells and new split faces */ 763 for (e = 0, q = 0; e < supportSize; ++e) { 764 PetscInt val, face; 765 766 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 767 if (val == dim-1) { 768 ierr = PetscFindInt(support[e], numSplitPoints[dim-1], splitPoints[dim-1], &face);CHKERRQ(ierr); 769 if (face < 0) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Face %d is not a split face", support[e]); 770 supportNew[q++] = pMaxNew[dim-1] + face; 771 } else if (val == -(shift + dim-1)) { 772 supportNew[q++] = depthOffset[dim-1] + support[e]; 773 } 774 } 775 ierr = DMPlexSetSupport(sdm, splitp, supportNew);CHKERRQ(ierr); 776 } 777 } 778 } 779 /* Step 6b: Replace split points in negative side cones */ 780 for (sp = 0; sp < numSP; ++sp) { 781 PetscInt dep = values[sp]; 782 IS pIS; 783 PetscInt numPoints; 784 const PetscInt *points; 785 786 if (dep >= 0) continue; 787 ierr = DMLabelGetStratumIS(label, dep, &pIS);CHKERRQ(ierr); 788 if (!pIS) continue; 789 dep = -dep - shift; 790 ierr = ISGetLocalSize(pIS, &numPoints);CHKERRQ(ierr); 791 ierr = ISGetIndices(pIS, &points);CHKERRQ(ierr); 792 for (p = 0; p < numPoints; ++p) { 793 const PetscInt oldp = points[p]; 794 const PetscInt newp = depthOffset[dep] + oldp; 795 const PetscInt *cone; 796 PetscInt coneSize, c; 797 PetscBool replaced = PETSC_FALSE; 798 799 /* Negative edge: replace split vertex */ 800 /* Negative cell: replace split face */ 801 ierr = DMPlexGetConeSize(sdm, newp, &coneSize);CHKERRQ(ierr); 802 ierr = DMPlexGetCone(sdm, newp, &cone);CHKERRQ(ierr); 803 for (c = 0; c < coneSize; ++c) { 804 const PetscInt coldp = cone[c] - depthOffset[dep-1]; 805 PetscInt csplitp, cp, val; 806 807 ierr = DMLabelGetValue(label, coldp, &val);CHKERRQ(ierr); 808 if (val == dep-1) { 809 ierr = PetscFindInt(coldp, numSplitPoints[dep-1], splitPoints[dep-1], &cp);CHKERRQ(ierr); 810 if (cp < 0) SETERRQ2(comm, PETSC_ERR_ARG_WRONG, "Point %d is not a split point of dimension %d", oldp, dep-1); 811 csplitp = pMaxNew[dep-1] + cp; 812 ierr = DMPlexInsertCone(sdm, newp, c, csplitp);CHKERRQ(ierr); 813 replaced = PETSC_TRUE; 814 } 815 } 816 if (!replaced) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "The cone of point %d does not contain split points", oldp); 817 } 818 ierr = ISRestoreIndices(pIS, &points);CHKERRQ(ierr); 819 ierr = ISDestroy(&pIS);CHKERRQ(ierr); 820 } 821 /* Step 7: Stratify */ 822 ierr = DMPlexStratify(sdm);CHKERRQ(ierr); 823 /* Step 8: Coordinates */ 824 ierr = DMPlexShiftCoordinates_Internal(dm, depthShift, sdm);CHKERRQ(ierr); 825 ierr = DMPlexGetCoordinateSection(sdm, &coordSection);CHKERRQ(ierr); 826 ierr = DMGetCoordinatesLocal(sdm, &coordinates);CHKERRQ(ierr); 827 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 828 for (v = 0; v < (numSplitPoints ? numSplitPoints[0] : 0); ++v) { 829 const PetscInt newp = depthOffset[0] + splitPoints[0][v]; 830 const PetscInt splitp = pMaxNew[0] + v; 831 PetscInt dof, off, soff, d; 832 833 ierr = PetscSectionGetDof(coordSection, newp, &dof);CHKERRQ(ierr); 834 ierr = PetscSectionGetOffset(coordSection, newp, &off);CHKERRQ(ierr); 835 ierr = PetscSectionGetOffset(coordSection, splitp, &soff);CHKERRQ(ierr); 836 for (d = 0; d < dof; ++d) coords[soff+d] = coords[off+d]; 837 } 838 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 839 /* Step 9: SF, if I can figure this out we can split the mesh in parallel */ 840 ierr = DMPlexShiftSF_Internal(dm, depthShift, sdm);CHKERRQ(ierr); 841 /* Step 10: Labels */ 842 ierr = DMPlexShiftLabels_Internal(dm, depthShift, sdm);CHKERRQ(ierr); 843 ierr = DMPlexGetNumLabels(sdm, &numLabels);CHKERRQ(ierr); 844 for (dep = 0; dep <= depth; ++dep) { 845 for (p = 0; p < numSplitPoints[dep]; ++p) { 846 const PetscInt newp = depthOffset[dep] + splitPoints[dep][p]; 847 const PetscInt splitp = pMaxNew[dep] + p; 848 PetscInt l; 849 850 for (l = 0; l < numLabels; ++l) { 851 DMLabel mlabel; 852 const char *lname; 853 PetscInt val; 854 855 ierr = DMPlexGetLabelName(sdm, l, &lname);CHKERRQ(ierr); 856 ierr = DMPlexGetLabel(sdm, lname, &mlabel);CHKERRQ(ierr); 857 ierr = DMLabelGetValue(mlabel, newp, &val);CHKERRQ(ierr); 858 if (val >= 0) { 859 ierr = DMLabelSetValue(mlabel, splitp, val);CHKERRQ(ierr); 860 if (dep == 0) { 861 const PetscInt cedge = pMaxNew[1] + (depthShift[1] - depthShift[0]) + p; 862 ierr = DMLabelSetValue(mlabel, cedge, val);CHKERRQ(ierr); 863 } 864 } 865 } 866 } 867 } 868 for (sp = 0; sp < numSP; ++sp) { 869 const PetscInt dep = values[sp]; 870 871 if ((dep < 0) || (dep > depth)) continue; 872 if (pointIS[dep]) {ierr = ISRestoreIndices(pointIS[dep], &splitPoints[dep]);CHKERRQ(ierr);} 873 ierr = ISDestroy(&pointIS[dep]);CHKERRQ(ierr); 874 } 875 if (label) { 876 ierr = ISRestoreIndices(valueIS, &values);CHKERRQ(ierr); 877 ierr = ISDestroy(&valueIS);CHKERRQ(ierr); 878 } 879 ierr = PetscFree5(depthShift, depthOffset, pMaxNew, coneNew, supportNew);CHKERRQ(ierr); 880 ierr = PetscFree3(pointIS, numSplitPoints, splitPoints);CHKERRQ(ierr); 881 PetscFunctionReturn(0); 882 } 883 884 #undef __FUNCT__ 885 #define __FUNCT__ "DMPlexConstructCohesiveCells" 886 /*@C 887 DMPlexConstructCohesiveCells - Construct cohesive cells which split the face along an internal interface 888 889 Collective on dm 890 891 Input Parameters: 892 + dm - The original DM 893 - labelName - The label specifying the boundary faces (this could be auto-generated) 894 895 Output Parameters: 896 - dmSplit - The new DM 897 898 Level: developer 899 900 .seealso: DMCreate(), DMPlexLabelCohesiveComplete() 901 @*/ 902 PetscErrorCode DMPlexConstructCohesiveCells(DM dm, DMLabel label, DM *dmSplit) 903 { 904 DM sdm; 905 PetscInt dim; 906 PetscErrorCode ierr; 907 908 PetscFunctionBegin; 909 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 910 PetscValidPointer(dmSplit, 4); 911 ierr = DMCreate(PetscObjectComm((PetscObject)dm), &sdm);CHKERRQ(ierr); 912 ierr = DMSetType(sdm, DMPLEX);CHKERRQ(ierr); 913 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 914 ierr = DMPlexSetDimension(sdm, dim);CHKERRQ(ierr); 915 switch (dim) { 916 case 2: 917 case 3: 918 ierr = DMPlexConstructCohesiveCells_Internal(dm, label, sdm);CHKERRQ(ierr); 919 break; 920 default: 921 SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Cannot construct cohesive cells for dimension %d", dim); 922 } 923 *dmSplit = sdm; 924 PetscFunctionReturn(0); 925 } 926 927 #undef __FUNCT__ 928 #define __FUNCT__ "DMPlexLabelCohesiveComplete" 929 /*@ 930 DMPlexLabelCohesiveComplete - Starting with a label marking vertices on an internal surface, we add all other mesh pieces 931 to complete the surface 932 933 Input Parameters: 934 + dm - The DM 935 - label - A DMLabel marking the surface vertices 936 937 Output Parameter: 938 . label - A DMLabel marking all surface points 939 940 Level: developer 941 942 .seealso: DMPlexConstructCohesiveCells(), DMPlexLabelComplete() 943 @*/ 944 PetscErrorCode DMPlexLabelCohesiveComplete(DM dm, DMLabel label) 945 { 946 IS dimIS; 947 const PetscInt *points; 948 PetscInt shift = 100, dim, dep, cStart, cEnd, numPoints, p, val; 949 PetscErrorCode ierr; 950 951 PetscFunctionBegin; 952 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 953 /* Cell orientation for face gives the side of the fault */ 954 ierr = DMLabelGetStratumIS(label, dim-1, &dimIS);CHKERRQ(ierr); 955 if (!dimIS) PetscFunctionReturn(0); 956 ierr = ISGetLocalSize(dimIS, &numPoints);CHKERRQ(ierr); 957 ierr = ISGetIndices(dimIS, &points);CHKERRQ(ierr); 958 for (p = 0; p < numPoints; ++p) { 959 const PetscInt *support; 960 PetscInt supportSize, s; 961 962 ierr = DMPlexGetSupportSize(dm, points[p], &supportSize);CHKERRQ(ierr); 963 if (supportSize != 2) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Split face %d has %d != 2 supports", points[p], supportSize); 964 ierr = DMPlexGetSupport(dm, points[p], &support);CHKERRQ(ierr); 965 for (s = 0; s < supportSize; ++s) { 966 const PetscInt *cone, *ornt; 967 PetscInt coneSize, c; 968 PetscBool pos = PETSC_TRUE; 969 970 ierr = DMPlexGetConeSize(dm, support[s], &coneSize);CHKERRQ(ierr); 971 ierr = DMPlexGetCone(dm, support[s], &cone);CHKERRQ(ierr); 972 ierr = DMPlexGetConeOrientation(dm, support[s], &ornt);CHKERRQ(ierr); 973 for (c = 0; c < coneSize; ++c) { 974 if (cone[c] == points[p]) { 975 if (ornt[c] >= 0) { 976 ierr = DMLabelSetValue(label, support[s], shift+dim);CHKERRQ(ierr); 977 } else { 978 ierr = DMLabelSetValue(label, support[s], -(shift+dim));CHKERRQ(ierr); 979 pos = PETSC_FALSE; 980 } 981 break; 982 } 983 } 984 if (c == coneSize) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Cell split face %d support does not have it in the cone", points[p]); 985 /* Put faces touching the fault in the label */ 986 for (c = 0; c < coneSize; ++c) { 987 const PetscInt point = cone[c]; 988 989 ierr = DMLabelGetValue(label, point, &val);CHKERRQ(ierr); 990 if (val == -1) { 991 PetscInt *closure = NULL; 992 PetscInt closureSize, cl; 993 994 ierr = DMPlexGetTransitiveClosure(dm, point, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 995 for (cl = 0; cl < closureSize*2; cl += 2) { 996 const PetscInt clp = closure[cl]; 997 998 ierr = DMLabelGetValue(label, clp, &val);CHKERRQ(ierr); 999 if ((val >= 0) && (val < dim-1)) { 1000 ierr = DMLabelSetValue(label, point, pos == PETSC_TRUE ? shift+dim-1 : -(shift+dim-1));CHKERRQ(ierr); 1001 break; 1002 } 1003 } 1004 ierr = DMPlexRestoreTransitiveClosure(dm, point, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1005 } 1006 } 1007 } 1008 } 1009 ierr = ISRestoreIndices(dimIS, &points);CHKERRQ(ierr); 1010 ierr = ISDestroy(&dimIS);CHKERRQ(ierr); 1011 /* Search for other cells/faces/edges connected to the fault by a vertex */ 1012 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1013 ierr = DMLabelGetStratumIS(label, 0, &dimIS);CHKERRQ(ierr); 1014 if (!dimIS) PetscFunctionReturn(0); 1015 ierr = ISGetLocalSize(dimIS, &numPoints);CHKERRQ(ierr); 1016 ierr = ISGetIndices(dimIS, &points);CHKERRQ(ierr); 1017 for (p = 0; p < numPoints; ++p) { 1018 PetscInt *star = NULL; 1019 PetscInt starSize, s; 1020 PetscInt again = 1; /* 0: Finished 1: Keep iterating after a change 2: No change */ 1021 1022 /* First mark cells connected to the fault */ 1023 ierr = DMPlexGetTransitiveClosure(dm, points[p], PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1024 while (again) { 1025 if (again > 1) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Could not classify all cells connected to the fault"); 1026 again = 0; 1027 for (s = 0; s < starSize*2; s += 2) { 1028 const PetscInt point = star[s]; 1029 const PetscInt *cone; 1030 PetscInt coneSize, c; 1031 1032 if ((point < cStart) || (point >= cEnd)) continue; 1033 ierr = DMLabelGetValue(label, point, &val);CHKERRQ(ierr); 1034 if (val != -1) continue; 1035 again = 2; 1036 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 1037 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 1038 for (c = 0; c < coneSize; ++c) { 1039 ierr = DMLabelGetValue(label, cone[c], &val);CHKERRQ(ierr); 1040 if (val != -1) { 1041 if (abs(val) < shift) SETERRQ3(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Face %d on cell %d has an invalid label %d", cone[c], point, val); 1042 if (val > 0) { 1043 ierr = DMLabelSetValue(label, point, shift+dim);CHKERRQ(ierr); 1044 } else { 1045 ierr = DMLabelSetValue(label, point, -(shift+dim));CHKERRQ(ierr); 1046 } 1047 again = 1; 1048 break; 1049 } 1050 } 1051 } 1052 } 1053 /* Classify the rest by cell membership */ 1054 for (s = 0; s < starSize*2; s += 2) { 1055 const PetscInt point = star[s]; 1056 1057 ierr = DMLabelGetValue(label, point, &val);CHKERRQ(ierr); 1058 if (val == -1) { 1059 PetscInt *sstar = NULL; 1060 PetscInt sstarSize, ss; 1061 PetscBool marked = PETSC_FALSE; 1062 1063 ierr = DMPlexGetTransitiveClosure(dm, point, PETSC_FALSE, &sstarSize, &sstar);CHKERRQ(ierr); 1064 for (ss = 0; ss < sstarSize*2; ss += 2) { 1065 const PetscInt spoint = sstar[ss]; 1066 1067 if ((spoint < cStart) || (spoint >= cEnd)) continue; 1068 ierr = DMLabelGetValue(label, spoint, &val);CHKERRQ(ierr); 1069 if (val == -1) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Cell %d in star of %d does not have a valid label", spoint, point); 1070 ierr = DMPlexGetLabelValue(dm, "depth", point, &dep);CHKERRQ(ierr); 1071 if (val > 0) { 1072 ierr = DMLabelSetValue(label, point, shift+dep);CHKERRQ(ierr); 1073 } else { 1074 ierr = DMLabelSetValue(label, point, -(shift+dep));CHKERRQ(ierr); 1075 } 1076 marked = PETSC_TRUE; 1077 break; 1078 } 1079 ierr = DMPlexRestoreTransitiveClosure(dm, point, PETSC_FALSE, &sstarSize, &sstar);CHKERRQ(ierr); 1080 if (!marked) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Point %d could not be classified", point); 1081 } 1082 } 1083 ierr = DMPlexRestoreTransitiveClosure(dm, points[p], PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1084 } 1085 ierr = ISRestoreIndices(dimIS, &points);CHKERRQ(ierr); 1086 ierr = ISDestroy(&dimIS);CHKERRQ(ierr); 1087 PetscFunctionReturn(0); 1088 } 1089 1090 #undef __FUNCT__ 1091 #define __FUNCT__ "DMPlexMarkSubmesh_Uninterpolated" 1092 /* Here we need the explicit assumption that: 1093 1094 For any marked cell, the marked vertices constitute a single face 1095 */ 1096 static PetscErrorCode DMPlexMarkSubmesh_Uninterpolated(DM dm, DMLabel vertexLabel, PetscInt value, DMLabel subpointMap, PetscInt *numFaces, PetscInt *nFV, DM subdm) 1097 { 1098 IS subvertexIS; 1099 const PetscInt *subvertices; 1100 PetscInt *pStart, *pEnd, *pMax, pSize; 1101 PetscInt depth, dim, d, numSubVerticesInitial = 0, v; 1102 PetscErrorCode ierr; 1103 1104 PetscFunctionBegin; 1105 *numFaces = 0; 1106 *nFV = 0; 1107 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 1108 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1109 pSize = PetscMax(depth, dim) + 1; 1110 ierr = PetscMalloc3(pSize,PetscInt,&pStart,pSize,PetscInt,&pEnd,pSize,PetscInt,&pMax);CHKERRQ(ierr); 1111 ierr = DMPlexGetHybridBounds(dm, &pMax[depth], depth>1 ? &pMax[depth-1] : NULL, depth > 2 ? &pMax[1] : NULL, &pMax[0]);CHKERRQ(ierr); 1112 for (d = 0; d <= depth; ++d) { 1113 ierr = DMPlexGetDepthStratum(dm, d, &pStart[d], &pEnd[d]);CHKERRQ(ierr); 1114 if (pMax[d] >= 0) pEnd[d] = PetscMin(pEnd[d], pMax[d]); 1115 } 1116 /* Loop over initial vertices and mark all faces in the collective star() */ 1117 ierr = DMLabelGetStratumIS(vertexLabel, value, &subvertexIS);CHKERRQ(ierr); 1118 if (subvertexIS) { 1119 ierr = ISGetSize(subvertexIS, &numSubVerticesInitial);CHKERRQ(ierr); 1120 ierr = ISGetIndices(subvertexIS, &subvertices);CHKERRQ(ierr); 1121 } 1122 for (v = 0; v < numSubVerticesInitial; ++v) { 1123 const PetscInt vertex = subvertices[v]; 1124 PetscInt *star = NULL; 1125 PetscInt starSize, s, numCells = 0, c; 1126 1127 ierr = DMPlexGetTransitiveClosure(dm, vertex, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1128 for (s = 0; s < starSize*2; s += 2) { 1129 const PetscInt point = star[s]; 1130 if ((point >= pStart[depth]) && (point < pEnd[depth])) star[numCells++] = point; 1131 } 1132 for (c = 0; c < numCells; ++c) { 1133 const PetscInt cell = star[c]; 1134 PetscInt *closure = NULL; 1135 PetscInt closureSize, cl; 1136 PetscInt cellLoc, numCorners = 0, faceSize = 0; 1137 1138 ierr = DMLabelGetValue(subpointMap, cell, &cellLoc);CHKERRQ(ierr); 1139 if (cellLoc == 2) continue; 1140 if (cellLoc >= 0) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Cell %d has dimension %d in the surface label", cell, cellLoc); 1141 ierr = DMPlexGetTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1142 for (cl = 0; cl < closureSize*2; cl += 2) { 1143 const PetscInt point = closure[cl]; 1144 PetscInt vertexLoc; 1145 1146 if ((point >= pStart[0]) && (point < pEnd[0])) { 1147 ++numCorners; 1148 ierr = DMLabelGetValue(vertexLabel, point, &vertexLoc);CHKERRQ(ierr); 1149 if (vertexLoc == value) closure[faceSize++] = point; 1150 } 1151 } 1152 if (!(*nFV)) {ierr = DMPlexGetNumFaceVertices(dm, dim, numCorners, nFV);CHKERRQ(ierr);} 1153 if (faceSize > *nFV) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Invalid submesh: Too many vertices %d of an element on the surface", faceSize); 1154 if (faceSize == *nFV) { 1155 const PetscInt *cells = NULL; 1156 PetscInt numCells, nc; 1157 1158 ++(*numFaces); 1159 for (cl = 0; cl < faceSize; ++cl) { 1160 ierr = DMLabelSetValue(subpointMap, closure[cl], 0);CHKERRQ(ierr); 1161 } 1162 ierr = DMPlexGetJoin(dm, faceSize, closure, &numCells, &cells);CHKERRQ(ierr); 1163 for (nc = 0; nc < numCells; ++nc) { 1164 ierr = DMLabelSetValue(subpointMap, cells[nc], 2);CHKERRQ(ierr); 1165 } 1166 ierr = DMPlexRestoreJoin(dm, faceSize, closure, &numCells, &cells);CHKERRQ(ierr); 1167 } 1168 ierr = DMPlexRestoreTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1169 } 1170 ierr = DMPlexRestoreTransitiveClosure(dm, vertex, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1171 } 1172 if (subvertexIS) { 1173 ierr = ISRestoreIndices(subvertexIS, &subvertices);CHKERRQ(ierr); 1174 } 1175 ierr = ISDestroy(&subvertexIS);CHKERRQ(ierr); 1176 ierr = PetscFree3(pStart,pEnd,pMax);CHKERRQ(ierr); 1177 PetscFunctionReturn(0); 1178 } 1179 1180 #undef __FUNCT__ 1181 #define __FUNCT__ "DMPlexMarkSubmesh_Interpolated" 1182 static PetscErrorCode DMPlexMarkSubmesh_Interpolated(DM dm, DMLabel vertexLabel, PetscInt value, DMLabel subpointMap, DM subdm) 1183 { 1184 IS subvertexIS; 1185 const PetscInt *subvertices; 1186 PetscInt *pStart, *pEnd, *pMax; 1187 PetscInt dim, d, numSubVerticesInitial = 0, v; 1188 PetscErrorCode ierr; 1189 1190 PetscFunctionBegin; 1191 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1192 ierr = PetscMalloc3(dim+1,PetscInt,&pStart,dim+1,PetscInt,&pEnd,dim+1,PetscInt,&pMax);CHKERRQ(ierr); 1193 ierr = DMPlexGetHybridBounds(dm, &pMax[dim], dim>1 ? &pMax[dim-1] : NULL, dim > 2 ? &pMax[1] : NULL, &pMax[0]);CHKERRQ(ierr); 1194 for (d = 0; d <= dim; ++d) { 1195 ierr = DMPlexGetDepthStratum(dm, d, &pStart[d], &pEnd[d]);CHKERRQ(ierr); 1196 if (pMax[d] >= 0) pEnd[d] = PetscMin(pEnd[d], pMax[d]); 1197 } 1198 /* Loop over initial vertices and mark all faces in the collective star() */ 1199 ierr = DMLabelGetStratumIS(vertexLabel, value, &subvertexIS);CHKERRQ(ierr); 1200 if (subvertexIS) { 1201 ierr = ISGetSize(subvertexIS, &numSubVerticesInitial);CHKERRQ(ierr); 1202 ierr = ISGetIndices(subvertexIS, &subvertices);CHKERRQ(ierr); 1203 } 1204 for (v = 0; v < numSubVerticesInitial; ++v) { 1205 const PetscInt vertex = subvertices[v]; 1206 PetscInt *star = NULL; 1207 PetscInt starSize, s, numFaces = 0, f; 1208 1209 ierr = DMPlexGetTransitiveClosure(dm, vertex, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1210 for (s = 0; s < starSize*2; s += 2) { 1211 const PetscInt point = star[s]; 1212 if ((point >= pStart[dim-1]) && (point < pEnd[dim-1])) star[numFaces++] = point; 1213 } 1214 for (f = 0; f < numFaces; ++f) { 1215 const PetscInt face = star[f]; 1216 PetscInt *closure = NULL; 1217 PetscInt closureSize, c; 1218 PetscInt faceLoc; 1219 1220 ierr = DMLabelGetValue(subpointMap, face, &faceLoc);CHKERRQ(ierr); 1221 if (faceLoc == dim-1) continue; 1222 if (faceLoc >= 0) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Face %d has dimension %d in the surface label", face, faceLoc); 1223 ierr = DMPlexGetTransitiveClosure(dm, face, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1224 for (c = 0; c < closureSize*2; c += 2) { 1225 const PetscInt point = closure[c]; 1226 PetscInt vertexLoc; 1227 1228 if ((point >= pStart[0]) && (point < pEnd[0])) { 1229 ierr = DMLabelGetValue(vertexLabel, point, &vertexLoc);CHKERRQ(ierr); 1230 if (vertexLoc != value) break; 1231 } 1232 } 1233 if (c == closureSize*2) { 1234 const PetscInt *support; 1235 PetscInt supportSize, s; 1236 1237 for (c = 0; c < closureSize*2; c += 2) { 1238 const PetscInt point = closure[c]; 1239 1240 for (d = 0; d < dim; ++d) { 1241 if ((point >= pStart[d]) && (point < pEnd[d])) { 1242 ierr = DMLabelSetValue(subpointMap, point, d);CHKERRQ(ierr); 1243 break; 1244 } 1245 } 1246 } 1247 ierr = DMPlexGetSupportSize(dm, face, &supportSize);CHKERRQ(ierr); 1248 ierr = DMPlexGetSupport(dm, face, &support);CHKERRQ(ierr); 1249 for (s = 0; s < supportSize; ++s) { 1250 ierr = DMLabelSetValue(subpointMap, support[s], dim);CHKERRQ(ierr); 1251 } 1252 } 1253 ierr = DMPlexRestoreTransitiveClosure(dm, face, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1254 } 1255 ierr = DMPlexRestoreTransitiveClosure(dm, vertex, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1256 } 1257 if (subvertexIS) { 1258 ierr = ISRestoreIndices(subvertexIS, &subvertices);CHKERRQ(ierr); 1259 } 1260 ierr = ISDestroy(&subvertexIS);CHKERRQ(ierr); 1261 ierr = PetscFree3(pStart,pEnd,pMax);CHKERRQ(ierr); 1262 PetscFunctionReturn(0); 1263 } 1264 1265 #undef __FUNCT__ 1266 #define __FUNCT__ "DMPlexMarkCohesiveSubmesh_Uninterpolated" 1267 static PetscErrorCode DMPlexMarkCohesiveSubmesh_Uninterpolated(DM dm, PetscBool hasLagrange, const char labelname[], PetscInt value, DMLabel subpointMap, PetscInt *numFaces, PetscInt *nFV, PetscInt *subCells[], DM subdm) 1268 { 1269 DMLabel label = NULL; 1270 const PetscInt *cone; 1271 PetscInt dim, cMax, cEnd, c, p, coneSize; 1272 PetscErrorCode ierr; 1273 1274 PetscFunctionBegin; 1275 if (labelname) {ierr = DMPlexGetLabel(dm, labelname, &label);CHKERRQ(ierr);} 1276 *numFaces = 0; 1277 *nFV = 0; 1278 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1279 ierr = DMPlexGetHeightStratum(dm, 0, NULL, &cEnd);CHKERRQ(ierr); 1280 ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); 1281 if (cMax < 0) PetscFunctionReturn(0); 1282 if (label) { 1283 for (c = cMax; c < cEnd; ++c) { 1284 PetscInt val; 1285 1286 ierr = DMLabelGetValue(label, c, &val);CHKERRQ(ierr); 1287 if (val == value) { 1288 ++(*numFaces); 1289 ierr = DMPlexGetConeSize(dm, c, &coneSize);CHKERRQ(ierr); 1290 } 1291 } 1292 } else { 1293 *numFaces = cEnd - cMax; 1294 ierr = DMPlexGetConeSize(dm, cMax, &coneSize);CHKERRQ(ierr); 1295 } 1296 *nFV = hasLagrange ? coneSize/3 : coneSize/2; 1297 ierr = PetscMalloc(*numFaces *2 * sizeof(PetscInt), subCells);CHKERRQ(ierr); 1298 for (c = cMax; c < cEnd; ++c) { 1299 const PetscInt *cells; 1300 PetscInt numCells; 1301 1302 if (label) { 1303 PetscInt val; 1304 1305 ierr = DMLabelGetValue(label, c, &val);CHKERRQ(ierr); 1306 if (val != value) continue; 1307 } 1308 ierr = DMPlexGetCone(dm, c, &cone);CHKERRQ(ierr); 1309 for (p = 0; p < *nFV; ++p) { 1310 ierr = DMLabelSetValue(subpointMap, cone[p], 0);CHKERRQ(ierr); 1311 } 1312 /* Negative face */ 1313 ierr = DMPlexGetJoin(dm, *nFV, cone, &numCells, &cells);CHKERRQ(ierr); 1314 if (numCells != 2) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive cells should separate two cells"); 1315 for (p = 0; p < numCells; ++p) { 1316 ierr = DMLabelSetValue(subpointMap, cells[p], 2);CHKERRQ(ierr); 1317 (*subCells)[(c-cMax)*2+p] = cells[p]; 1318 } 1319 ierr = DMPlexRestoreJoin(dm, *nFV, cone, &numCells, &cells);CHKERRQ(ierr); 1320 /* Positive face is not included */ 1321 } 1322 PetscFunctionReturn(0); 1323 } 1324 1325 #undef __FUNCT__ 1326 #define __FUNCT__ "DMPlexMarkCohesiveSubmesh_Interpolated" 1327 static PetscErrorCode DMPlexMarkCohesiveSubmesh_Interpolated(DM dm, PetscBool hasLagrange, const char labelname[], PetscInt value, DMLabel subpointMap, DM subdm) 1328 { 1329 DMLabel label = NULL; 1330 PetscInt *pStart, *pEnd; 1331 PetscInt dim, cMax, cEnd, c, d; 1332 PetscErrorCode ierr; 1333 1334 PetscFunctionBegin; 1335 if (labelname) {ierr = DMPlexGetLabel(dm, labelname, &label);CHKERRQ(ierr);} 1336 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1337 ierr = DMPlexGetHeightStratum(dm, 0, NULL, &cEnd);CHKERRQ(ierr); 1338 ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); 1339 if (cMax < 0) PetscFunctionReturn(0); 1340 ierr = PetscMalloc2(dim+1,PetscInt,&pStart,dim+1,PetscInt,&pEnd);CHKERRQ(ierr); 1341 for (d = 0; d <= dim; ++d) { 1342 ierr = DMPlexGetDepthStratum(dm, d, &pStart[d], &pEnd[d]);CHKERRQ(ierr); 1343 } 1344 for (c = cMax; c < cEnd; ++c) { 1345 const PetscInt *cone; 1346 PetscInt *closure = NULL; 1347 PetscInt coneSize, closureSize, cl; 1348 1349 if (label) { 1350 PetscInt val; 1351 1352 ierr = DMLabelGetValue(label, c, &val);CHKERRQ(ierr); 1353 if (val != value) continue; 1354 } 1355 ierr = DMPlexGetConeSize(dm, c, &coneSize);CHKERRQ(ierr); 1356 if (hasLagrange) { 1357 if (coneSize != 3) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive cells should separate two cells"); 1358 } else { 1359 if (coneSize != 2) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive cells should separate two cells"); 1360 } 1361 /* Negative face */ 1362 ierr = DMPlexGetCone(dm, c, &cone);CHKERRQ(ierr); 1363 ierr = DMPlexGetTransitiveClosure(dm, cone[0], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1364 for (cl = 0; cl < closureSize*2; cl += 2) { 1365 const PetscInt point = closure[cl]; 1366 1367 for (d = 0; d <= dim; ++d) { 1368 if ((point >= pStart[d]) && (point < pEnd[d])) { 1369 ierr = DMLabelSetValue(subpointMap, point, d);CHKERRQ(ierr); 1370 break; 1371 } 1372 } 1373 } 1374 ierr = DMPlexRestoreTransitiveClosure(dm, cone[0], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1375 /* Cells -- positive face is not included */ 1376 for (cl = 0; cl < 1; ++cl) { 1377 const PetscInt *support; 1378 PetscInt supportSize, s; 1379 1380 ierr = DMPlexGetSupportSize(dm, cone[cl], &supportSize);CHKERRQ(ierr); 1381 if (supportSize != 2) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive faces should separate two cells"); 1382 ierr = DMPlexGetSupport(dm, cone[cl], &support);CHKERRQ(ierr); 1383 for (s = 0; s < supportSize; ++s) { 1384 ierr = DMLabelSetValue(subpointMap, support[s], dim);CHKERRQ(ierr); 1385 } 1386 } 1387 } 1388 ierr = PetscFree2(pStart, pEnd);CHKERRQ(ierr); 1389 PetscFunctionReturn(0); 1390 } 1391 1392 #undef __FUNCT__ 1393 #define __FUNCT__ "DMPlexGetFaceOrientation" 1394 PetscErrorCode DMPlexGetFaceOrientation(DM dm, PetscInt cell, PetscInt numCorners, PetscInt indices[], PetscInt oppositeVertex, PetscInt origVertices[], PetscInt faceVertices[], PetscBool *posOriented) 1395 { 1396 MPI_Comm comm; 1397 PetscBool posOrient = PETSC_FALSE; 1398 const PetscInt debug = 0; 1399 PetscInt cellDim, faceSize, f; 1400 PetscErrorCode ierr; 1401 1402 PetscFunctionBegin; 1403 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 1404 ierr = DMPlexGetDimension(dm, &cellDim);CHKERRQ(ierr); 1405 if (debug) {PetscPrintf(comm, "cellDim: %d numCorners: %d\n", cellDim, numCorners);CHKERRQ(ierr);} 1406 1407 if (cellDim == numCorners-1) { 1408 /* Simplices */ 1409 faceSize = numCorners-1; 1410 posOrient = !(oppositeVertex%2) ? PETSC_TRUE : PETSC_FALSE; 1411 } else if (cellDim == 1 && numCorners == 3) { 1412 /* Quadratic line */ 1413 faceSize = 1; 1414 posOrient = PETSC_TRUE; 1415 } else if (cellDim == 2 && numCorners == 4) { 1416 /* Quads */ 1417 faceSize = 2; 1418 if ((indices[1] > indices[0]) && (indices[1] - indices[0] == 1)) { 1419 posOrient = PETSC_TRUE; 1420 } else if ((indices[0] == 3) && (indices[1] == 0)) { 1421 posOrient = PETSC_TRUE; 1422 } else { 1423 if (((indices[0] > indices[1]) && (indices[0] - indices[1] == 1)) || ((indices[0] == 0) && (indices[1] == 3))) { 1424 posOrient = PETSC_FALSE; 1425 } else SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid quad crossedge"); 1426 } 1427 } else if (cellDim == 2 && numCorners == 6) { 1428 /* Quadratic triangle (I hate this) */ 1429 /* Edges are determined by the first 2 vertices (corners of edges) */ 1430 const PetscInt faceSizeTri = 3; 1431 PetscInt sortedIndices[3], i, iFace; 1432 PetscBool found = PETSC_FALSE; 1433 PetscInt faceVerticesTriSorted[9] = { 1434 0, 3, 4, /* bottom */ 1435 1, 4, 5, /* right */ 1436 2, 3, 5, /* left */ 1437 }; 1438 PetscInt faceVerticesTri[9] = { 1439 0, 3, 4, /* bottom */ 1440 1, 4, 5, /* right */ 1441 2, 5, 3, /* left */ 1442 }; 1443 1444 faceSize = faceSizeTri; 1445 for (i = 0; i < faceSizeTri; ++i) sortedIndices[i] = indices[i]; 1446 ierr = PetscSortInt(faceSizeTri, sortedIndices);CHKERRQ(ierr); 1447 for (iFace = 0; iFace < 3; ++iFace) { 1448 const PetscInt ii = iFace*faceSizeTri; 1449 PetscInt fVertex, cVertex; 1450 1451 if ((sortedIndices[0] == faceVerticesTriSorted[ii+0]) && 1452 (sortedIndices[1] == faceVerticesTriSorted[ii+1])) { 1453 for (fVertex = 0; fVertex < faceSizeTri; ++fVertex) { 1454 for (cVertex = 0; cVertex < faceSizeTri; ++cVertex) { 1455 if (indices[cVertex] == faceVerticesTri[ii+fVertex]) { 1456 faceVertices[fVertex] = origVertices[cVertex]; 1457 break; 1458 } 1459 } 1460 } 1461 found = PETSC_TRUE; 1462 break; 1463 } 1464 } 1465 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid tri crossface"); 1466 if (posOriented) *posOriented = PETSC_TRUE; 1467 PetscFunctionReturn(0); 1468 } else if (cellDim == 2 && numCorners == 9) { 1469 /* Quadratic quad (I hate this) */ 1470 /* Edges are determined by the first 2 vertices (corners of edges) */ 1471 const PetscInt faceSizeQuad = 3; 1472 PetscInt sortedIndices[3], i, iFace; 1473 PetscBool found = PETSC_FALSE; 1474 PetscInt faceVerticesQuadSorted[12] = { 1475 0, 1, 4, /* bottom */ 1476 1, 2, 5, /* right */ 1477 2, 3, 6, /* top */ 1478 0, 3, 7, /* left */ 1479 }; 1480 PetscInt faceVerticesQuad[12] = { 1481 0, 1, 4, /* bottom */ 1482 1, 2, 5, /* right */ 1483 2, 3, 6, /* top */ 1484 3, 0, 7, /* left */ 1485 }; 1486 1487 faceSize = faceSizeQuad; 1488 for (i = 0; i < faceSizeQuad; ++i) sortedIndices[i] = indices[i]; 1489 ierr = PetscSortInt(faceSizeQuad, sortedIndices);CHKERRQ(ierr); 1490 for (iFace = 0; iFace < 4; ++iFace) { 1491 const PetscInt ii = iFace*faceSizeQuad; 1492 PetscInt fVertex, cVertex; 1493 1494 if ((sortedIndices[0] == faceVerticesQuadSorted[ii+0]) && 1495 (sortedIndices[1] == faceVerticesQuadSorted[ii+1])) { 1496 for (fVertex = 0; fVertex < faceSizeQuad; ++fVertex) { 1497 for (cVertex = 0; cVertex < faceSizeQuad; ++cVertex) { 1498 if (indices[cVertex] == faceVerticesQuad[ii+fVertex]) { 1499 faceVertices[fVertex] = origVertices[cVertex]; 1500 break; 1501 } 1502 } 1503 } 1504 found = PETSC_TRUE; 1505 break; 1506 } 1507 } 1508 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid quad crossface"); 1509 if (posOriented) *posOriented = PETSC_TRUE; 1510 PetscFunctionReturn(0); 1511 } else if (cellDim == 3 && numCorners == 8) { 1512 /* Hexes 1513 A hex is two oriented quads with the normal of the first 1514 pointing up at the second. 1515 1516 7---6 1517 /| /| 1518 4---5 | 1519 | 3-|-2 1520 |/ |/ 1521 0---1 1522 1523 Faces are determined by the first 4 vertices (corners of faces) */ 1524 const PetscInt faceSizeHex = 4; 1525 PetscInt sortedIndices[4], i, iFace; 1526 PetscBool found = PETSC_FALSE; 1527 PetscInt faceVerticesHexSorted[24] = { 1528 0, 1, 2, 3, /* bottom */ 1529 4, 5, 6, 7, /* top */ 1530 0, 1, 4, 5, /* front */ 1531 1, 2, 5, 6, /* right */ 1532 2, 3, 6, 7, /* back */ 1533 0, 3, 4, 7, /* left */ 1534 }; 1535 PetscInt faceVerticesHex[24] = { 1536 3, 2, 1, 0, /* bottom */ 1537 4, 5, 6, 7, /* top */ 1538 0, 1, 5, 4, /* front */ 1539 1, 2, 6, 5, /* right */ 1540 2, 3, 7, 6, /* back */ 1541 3, 0, 4, 7, /* left */ 1542 }; 1543 1544 faceSize = faceSizeHex; 1545 for (i = 0; i < faceSizeHex; ++i) sortedIndices[i] = indices[i]; 1546 ierr = PetscSortInt(faceSizeHex, sortedIndices);CHKERRQ(ierr); 1547 for (iFace = 0; iFace < 6; ++iFace) { 1548 const PetscInt ii = iFace*faceSizeHex; 1549 PetscInt fVertex, cVertex; 1550 1551 if ((sortedIndices[0] == faceVerticesHexSorted[ii+0]) && 1552 (sortedIndices[1] == faceVerticesHexSorted[ii+1]) && 1553 (sortedIndices[2] == faceVerticesHexSorted[ii+2]) && 1554 (sortedIndices[3] == faceVerticesHexSorted[ii+3])) { 1555 for (fVertex = 0; fVertex < faceSizeHex; ++fVertex) { 1556 for (cVertex = 0; cVertex < faceSizeHex; ++cVertex) { 1557 if (indices[cVertex] == faceVerticesHex[ii+fVertex]) { 1558 faceVertices[fVertex] = origVertices[cVertex]; 1559 break; 1560 } 1561 } 1562 } 1563 found = PETSC_TRUE; 1564 break; 1565 } 1566 } 1567 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid hex crossface"); 1568 if (posOriented) *posOriented = PETSC_TRUE; 1569 PetscFunctionReturn(0); 1570 } else if (cellDim == 3 && numCorners == 10) { 1571 /* Quadratic tet */ 1572 /* Faces are determined by the first 3 vertices (corners of faces) */ 1573 const PetscInt faceSizeTet = 6; 1574 PetscInt sortedIndices[6], i, iFace; 1575 PetscBool found = PETSC_FALSE; 1576 PetscInt faceVerticesTetSorted[24] = { 1577 0, 1, 2, 6, 7, 8, /* bottom */ 1578 0, 3, 4, 6, 7, 9, /* front */ 1579 1, 4, 5, 7, 8, 9, /* right */ 1580 2, 3, 5, 6, 8, 9, /* left */ 1581 }; 1582 PetscInt faceVerticesTet[24] = { 1583 0, 1, 2, 6, 7, 8, /* bottom */ 1584 0, 4, 3, 6, 7, 9, /* front */ 1585 1, 5, 4, 7, 8, 9, /* right */ 1586 2, 3, 5, 8, 6, 9, /* left */ 1587 }; 1588 1589 faceSize = faceSizeTet; 1590 for (i = 0; i < faceSizeTet; ++i) sortedIndices[i] = indices[i]; 1591 ierr = PetscSortInt(faceSizeTet, sortedIndices);CHKERRQ(ierr); 1592 for (iFace=0; iFace < 4; ++iFace) { 1593 const PetscInt ii = iFace*faceSizeTet; 1594 PetscInt fVertex, cVertex; 1595 1596 if ((sortedIndices[0] == faceVerticesTetSorted[ii+0]) && 1597 (sortedIndices[1] == faceVerticesTetSorted[ii+1]) && 1598 (sortedIndices[2] == faceVerticesTetSorted[ii+2]) && 1599 (sortedIndices[3] == faceVerticesTetSorted[ii+3])) { 1600 for (fVertex = 0; fVertex < faceSizeTet; ++fVertex) { 1601 for (cVertex = 0; cVertex < faceSizeTet; ++cVertex) { 1602 if (indices[cVertex] == faceVerticesTet[ii+fVertex]) { 1603 faceVertices[fVertex] = origVertices[cVertex]; 1604 break; 1605 } 1606 } 1607 } 1608 found = PETSC_TRUE; 1609 break; 1610 } 1611 } 1612 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid tet crossface"); 1613 if (posOriented) *posOriented = PETSC_TRUE; 1614 PetscFunctionReturn(0); 1615 } else if (cellDim == 3 && numCorners == 27) { 1616 /* Quadratic hexes (I hate this) 1617 A hex is two oriented quads with the normal of the first 1618 pointing up at the second. 1619 1620 7---6 1621 /| /| 1622 4---5 | 1623 | 3-|-2 1624 |/ |/ 1625 0---1 1626 1627 Faces are determined by the first 4 vertices (corners of faces) */ 1628 const PetscInt faceSizeQuadHex = 9; 1629 PetscInt sortedIndices[9], i, iFace; 1630 PetscBool found = PETSC_FALSE; 1631 PetscInt faceVerticesQuadHexSorted[54] = { 1632 0, 1, 2, 3, 8, 9, 10, 11, 24, /* bottom */ 1633 4, 5, 6, 7, 12, 13, 14, 15, 25, /* top */ 1634 0, 1, 4, 5, 8, 12, 16, 17, 22, /* front */ 1635 1, 2, 5, 6, 9, 13, 17, 18, 21, /* right */ 1636 2, 3, 6, 7, 10, 14, 18, 19, 23, /* back */ 1637 0, 3, 4, 7, 11, 15, 16, 19, 20, /* left */ 1638 }; 1639 PetscInt faceVerticesQuadHex[54] = { 1640 3, 2, 1, 0, 10, 9, 8, 11, 24, /* bottom */ 1641 4, 5, 6, 7, 12, 13, 14, 15, 25, /* top */ 1642 0, 1, 5, 4, 8, 17, 12, 16, 22, /* front */ 1643 1, 2, 6, 5, 9, 18, 13, 17, 21, /* right */ 1644 2, 3, 7, 6, 10, 19, 14, 18, 23, /* back */ 1645 3, 0, 4, 7, 11, 16, 15, 19, 20 /* left */ 1646 }; 1647 1648 faceSize = faceSizeQuadHex; 1649 for (i = 0; i < faceSizeQuadHex; ++i) sortedIndices[i] = indices[i]; 1650 ierr = PetscSortInt(faceSizeQuadHex, sortedIndices);CHKERRQ(ierr); 1651 for (iFace = 0; iFace < 6; ++iFace) { 1652 const PetscInt ii = iFace*faceSizeQuadHex; 1653 PetscInt fVertex, cVertex; 1654 1655 if ((sortedIndices[0] == faceVerticesQuadHexSorted[ii+0]) && 1656 (sortedIndices[1] == faceVerticesQuadHexSorted[ii+1]) && 1657 (sortedIndices[2] == faceVerticesQuadHexSorted[ii+2]) && 1658 (sortedIndices[3] == faceVerticesQuadHexSorted[ii+3])) { 1659 for (fVertex = 0; fVertex < faceSizeQuadHex; ++fVertex) { 1660 for (cVertex = 0; cVertex < faceSizeQuadHex; ++cVertex) { 1661 if (indices[cVertex] == faceVerticesQuadHex[ii+fVertex]) { 1662 faceVertices[fVertex] = origVertices[cVertex]; 1663 break; 1664 } 1665 } 1666 } 1667 found = PETSC_TRUE; 1668 break; 1669 } 1670 } 1671 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid hex crossface"); 1672 if (posOriented) *posOriented = PETSC_TRUE; 1673 PetscFunctionReturn(0); 1674 } else SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Unknown cell type for faceOrientation()."); 1675 if (!posOrient) { 1676 if (debug) {ierr = PetscPrintf(comm, " Reversing initial face orientation\n");CHKERRQ(ierr);} 1677 for (f = 0; f < faceSize; ++f) faceVertices[f] = origVertices[faceSize-1 - f]; 1678 } else { 1679 if (debug) {ierr = PetscPrintf(comm, " Keeping initial face orientation\n");CHKERRQ(ierr);} 1680 for (f = 0; f < faceSize; ++f) faceVertices[f] = origVertices[f]; 1681 } 1682 if (posOriented) *posOriented = posOrient; 1683 PetscFunctionReturn(0); 1684 } 1685 1686 #undef __FUNCT__ 1687 #define __FUNCT__ "DMPlexGetOrientedFace" 1688 /* 1689 Given a cell and a face, as a set of vertices, 1690 return the oriented face, as a set of vertices, in faceVertices 1691 The orientation is such that the face normal points out of the cell 1692 */ 1693 PetscErrorCode DMPlexGetOrientedFace(DM dm, PetscInt cell, PetscInt faceSize, const PetscInt face[], PetscInt numCorners, PetscInt indices[], PetscInt origVertices[], PetscInt faceVertices[], PetscBool *posOriented) 1694 { 1695 const PetscInt *cone = NULL; 1696 PetscInt coneSize, v, f, v2; 1697 PetscInt oppositeVertex = -1; 1698 PetscErrorCode ierr; 1699 1700 PetscFunctionBegin; 1701 ierr = DMPlexGetConeSize(dm, cell, &coneSize);CHKERRQ(ierr); 1702 ierr = DMPlexGetCone(dm, cell, &cone);CHKERRQ(ierr); 1703 for (v = 0, v2 = 0; v < coneSize; ++v) { 1704 PetscBool found = PETSC_FALSE; 1705 1706 for (f = 0; f < faceSize; ++f) { 1707 if (face[f] == cone[v]) { 1708 found = PETSC_TRUE; break; 1709 } 1710 } 1711 if (found) { 1712 indices[v2] = v; 1713 origVertices[v2] = cone[v]; 1714 ++v2; 1715 } else { 1716 oppositeVertex = v; 1717 } 1718 } 1719 ierr = DMPlexGetFaceOrientation(dm, cell, numCorners, indices, oppositeVertex, origVertices, faceVertices, posOriented);CHKERRQ(ierr); 1720 PetscFunctionReturn(0); 1721 } 1722 1723 #undef __FUNCT__ 1724 #define __FUNCT__ "DMPlexInsertFace_Internal" 1725 /* 1726 DMPlexInsertFace_Internal - Puts a face into the mesh 1727 1728 Not collective 1729 1730 Input Parameters: 1731 + dm - The DMPlex 1732 . numFaceVertex - The number of vertices in the face 1733 . faceVertices - The vertices in the face for dm 1734 . subfaceVertices - The vertices in the face for subdm 1735 . numCorners - The number of vertices in the cell 1736 . cell - A cell in dm containing the face 1737 . subcell - A cell in subdm containing the face 1738 . firstFace - First face in the mesh 1739 - newFacePoint - Next face in the mesh 1740 1741 Output Parameters: 1742 . newFacePoint - Contains next face point number on input, updated on output 1743 1744 Level: developer 1745 */ 1746 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) 1747 { 1748 MPI_Comm comm; 1749 DM_Plex *submesh = (DM_Plex*) subdm->data; 1750 const PetscInt *faces; 1751 PetscInt numFaces, coneSize; 1752 PetscErrorCode ierr; 1753 1754 PetscFunctionBegin; 1755 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 1756 ierr = DMPlexGetConeSize(subdm, subcell, &coneSize);CHKERRQ(ierr); 1757 if (coneSize != 1) SETERRQ2(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cone size of cell %d is %d != 1", cell, coneSize); 1758 #if 0 1759 /* Cannot use this because support() has not been constructed yet */ 1760 ierr = DMPlexGetJoin(subdm, numFaceVertices, subfaceVertices, &numFaces, &faces);CHKERRQ(ierr); 1761 #else 1762 { 1763 PetscInt f; 1764 1765 numFaces = 0; 1766 ierr = DMGetWorkArray(subdm, 1, PETSC_INT, (void **) &faces);CHKERRQ(ierr); 1767 for (f = firstFace; f < *newFacePoint; ++f) { 1768 PetscInt dof, off, d; 1769 1770 ierr = PetscSectionGetDof(submesh->coneSection, f, &dof);CHKERRQ(ierr); 1771 ierr = PetscSectionGetOffset(submesh->coneSection, f, &off);CHKERRQ(ierr); 1772 /* Yes, I know this is quadratic, but I expect the sizes to be <5 */ 1773 for (d = 0; d < dof; ++d) { 1774 const PetscInt p = submesh->cones[off+d]; 1775 PetscInt v; 1776 1777 for (v = 0; v < numFaceVertices; ++v) { 1778 if (subfaceVertices[v] == p) break; 1779 } 1780 if (v == numFaceVertices) break; 1781 } 1782 if (d == dof) { 1783 numFaces = 1; 1784 ((PetscInt*) faces)[0] = f; 1785 } 1786 } 1787 } 1788 #endif 1789 if (numFaces > 1) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Vertex set had %d faces, not one", numFaces); 1790 else if (numFaces == 1) { 1791 /* Add the other cell neighbor for this face */ 1792 ierr = DMPlexSetCone(subdm, subcell, faces);CHKERRQ(ierr); 1793 } else { 1794 PetscInt *indices, *origVertices, *orientedVertices, *orientedSubVertices, v, ov; 1795 PetscBool posOriented; 1796 1797 ierr = DMGetWorkArray(subdm, 4*numFaceVertices * sizeof(PetscInt), PETSC_INT, &orientedVertices);CHKERRQ(ierr); 1798 origVertices = &orientedVertices[numFaceVertices]; 1799 indices = &orientedVertices[numFaceVertices*2]; 1800 orientedSubVertices = &orientedVertices[numFaceVertices*3]; 1801 ierr = DMPlexGetOrientedFace(dm, cell, numFaceVertices, faceVertices, numCorners, indices, origVertices, orientedVertices, &posOriented);CHKERRQ(ierr); 1802 /* TODO: I know that routine should return a permutation, not the indices */ 1803 for (v = 0; v < numFaceVertices; ++v) { 1804 const PetscInt vertex = faceVertices[v], subvertex = subfaceVertices[v]; 1805 for (ov = 0; ov < numFaceVertices; ++ov) { 1806 if (orientedVertices[ov] == vertex) { 1807 orientedSubVertices[ov] = subvertex; 1808 break; 1809 } 1810 } 1811 if (ov == numFaceVertices) SETERRQ1(comm, PETSC_ERR_PLIB, "Could not find face vertex %d in orientated set", vertex); 1812 } 1813 ierr = DMPlexSetCone(subdm, *newFacePoint, orientedSubVertices);CHKERRQ(ierr); 1814 ierr = DMPlexSetCone(subdm, subcell, newFacePoint);CHKERRQ(ierr); 1815 ierr = DMRestoreWorkArray(subdm, 4*numFaceVertices * sizeof(PetscInt), PETSC_INT, &orientedVertices);CHKERRQ(ierr); 1816 ++(*newFacePoint); 1817 } 1818 #if 0 1819 ierr = DMPlexRestoreJoin(subdm, numFaceVertices, subfaceVertices, &numFaces, &faces);CHKERRQ(ierr); 1820 #else 1821 ierr = DMRestoreWorkArray(subdm, 1, PETSC_INT, (void **) &faces);CHKERRQ(ierr); 1822 #endif 1823 PetscFunctionReturn(0); 1824 } 1825 1826 #undef __FUNCT__ 1827 #define __FUNCT__ "DMPlexCreateSubmesh_Uninterpolated" 1828 static PetscErrorCode DMPlexCreateSubmesh_Uninterpolated(DM dm, const char vertexLabelName[], PetscInt value, DM subdm) 1829 { 1830 MPI_Comm comm; 1831 DMLabel vertexLabel, subpointMap; 1832 IS subvertexIS, subcellIS; 1833 const PetscInt *subVertices, *subCells; 1834 PetscInt numSubVertices, firstSubVertex, numSubCells; 1835 PetscInt *subface, maxConeSize, numSubFaces, firstSubFace, newFacePoint, nFV; 1836 PetscInt vStart, vEnd, c, f; 1837 PetscErrorCode ierr; 1838 1839 PetscFunctionBegin; 1840 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 1841 /* Create subpointMap which marks the submesh */ 1842 ierr = DMLabelCreate("subpoint_map", &subpointMap);CHKERRQ(ierr); 1843 ierr = DMPlexSetSubpointMap(subdm, subpointMap);CHKERRQ(ierr); 1844 ierr = DMLabelDestroy(&subpointMap);CHKERRQ(ierr); 1845 ierr = DMPlexGetLabel(dm, vertexLabelName, &vertexLabel);CHKERRQ(ierr); 1846 ierr = DMPlexMarkSubmesh_Uninterpolated(dm, vertexLabel, value, subpointMap, &numSubFaces, &nFV, subdm);CHKERRQ(ierr); 1847 /* Setup chart */ 1848 ierr = DMLabelGetStratumSize(subpointMap, 0, &numSubVertices);CHKERRQ(ierr); 1849 ierr = DMLabelGetStratumSize(subpointMap, 2, &numSubCells);CHKERRQ(ierr); 1850 ierr = DMPlexSetChart(subdm, 0, numSubCells+numSubFaces+numSubVertices);CHKERRQ(ierr); 1851 ierr = DMPlexSetVTKCellHeight(subdm, 1);CHKERRQ(ierr); 1852 /* Set cone sizes */ 1853 firstSubVertex = numSubCells; 1854 firstSubFace = numSubCells+numSubVertices; 1855 newFacePoint = firstSubFace; 1856 ierr = DMLabelGetStratumIS(subpointMap, 0, &subvertexIS);CHKERRQ(ierr); 1857 if (subvertexIS) {ierr = ISGetIndices(subvertexIS, &subVertices);CHKERRQ(ierr);} 1858 ierr = DMLabelGetStratumIS(subpointMap, 2, &subcellIS);CHKERRQ(ierr); 1859 if (subcellIS) {ierr = ISGetIndices(subcellIS, &subCells);CHKERRQ(ierr);} 1860 for (c = 0; c < numSubCells; ++c) { 1861 ierr = DMPlexSetConeSize(subdm, c, 1);CHKERRQ(ierr); 1862 } 1863 for (f = firstSubFace; f < firstSubFace+numSubFaces; ++f) { 1864 ierr = DMPlexSetConeSize(subdm, f, nFV);CHKERRQ(ierr); 1865 } 1866 ierr = DMSetUp(subdm);CHKERRQ(ierr); 1867 /* Create face cones */ 1868 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 1869 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, NULL);CHKERRQ(ierr); 1870 ierr = DMGetWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);CHKERRQ(ierr); 1871 for (c = 0; c < numSubCells; ++c) { 1872 const PetscInt cell = subCells[c]; 1873 const PetscInt subcell = c; 1874 PetscInt *closure = NULL; 1875 PetscInt closureSize, cl, numCorners = 0, faceSize = 0; 1876 1877 ierr = DMPlexGetTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1878 for (cl = 0; cl < closureSize*2; cl += 2) { 1879 const PetscInt point = closure[cl]; 1880 PetscInt subVertex; 1881 1882 if ((point >= vStart) && (point < vEnd)) { 1883 ++numCorners; 1884 ierr = PetscFindInt(point, numSubVertices, subVertices, &subVertex);CHKERRQ(ierr); 1885 if (subVertex >= 0) { 1886 closure[faceSize] = point; 1887 subface[faceSize] = firstSubVertex+subVertex; 1888 ++faceSize; 1889 } 1890 } 1891 } 1892 if (faceSize > nFV) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Invalid submesh: Too many vertices %d of an element on the surface", faceSize); 1893 if (faceSize == nFV) { 1894 ierr = DMPlexInsertFace_Internal(dm, subdm, faceSize, closure, subface, numCorners, cell, subcell, firstSubFace, &newFacePoint);CHKERRQ(ierr); 1895 } 1896 ierr = DMPlexRestoreTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1897 } 1898 ierr = DMRestoreWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);CHKERRQ(ierr); 1899 ierr = DMPlexSymmetrize(subdm);CHKERRQ(ierr); 1900 ierr = DMPlexStratify(subdm);CHKERRQ(ierr); 1901 /* Build coordinates */ 1902 { 1903 PetscSection coordSection, subCoordSection; 1904 Vec coordinates, subCoordinates; 1905 PetscScalar *coords, *subCoords; 1906 PetscInt numComp, coordSize, v; 1907 1908 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1909 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 1910 ierr = DMPlexGetCoordinateSection(subdm, &subCoordSection);CHKERRQ(ierr); 1911 ierr = PetscSectionSetNumFields(subCoordSection, 1);CHKERRQ(ierr); 1912 ierr = PetscSectionGetFieldComponents(coordSection, 0, &numComp);CHKERRQ(ierr); 1913 ierr = PetscSectionSetFieldComponents(subCoordSection, 0, numComp);CHKERRQ(ierr); 1914 ierr = PetscSectionSetChart(subCoordSection, firstSubVertex, firstSubVertex+numSubVertices);CHKERRQ(ierr); 1915 for (v = 0; v < numSubVertices; ++v) { 1916 const PetscInt vertex = subVertices[v]; 1917 const PetscInt subvertex = firstSubVertex+v; 1918 PetscInt dof; 1919 1920 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 1921 ierr = PetscSectionSetDof(subCoordSection, subvertex, dof);CHKERRQ(ierr); 1922 ierr = PetscSectionSetFieldDof(subCoordSection, subvertex, 0, dof);CHKERRQ(ierr); 1923 } 1924 ierr = PetscSectionSetUp(subCoordSection);CHKERRQ(ierr); 1925 ierr = PetscSectionGetStorageSize(subCoordSection, &coordSize);CHKERRQ(ierr); 1926 ierr = VecCreate(comm, &subCoordinates);CHKERRQ(ierr); 1927 ierr = VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1928 ierr = VecSetFromOptions(subCoordinates);CHKERRQ(ierr); 1929 if (coordSize) { 1930 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1931 ierr = VecGetArray(subCoordinates, &subCoords);CHKERRQ(ierr); 1932 for (v = 0; v < numSubVertices; ++v) { 1933 const PetscInt vertex = subVertices[v]; 1934 const PetscInt subvertex = firstSubVertex+v; 1935 PetscInt dof, off, sdof, soff, d; 1936 1937 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 1938 ierr = PetscSectionGetOffset(coordSection, vertex, &off);CHKERRQ(ierr); 1939 ierr = PetscSectionGetDof(subCoordSection, subvertex, &sdof);CHKERRQ(ierr); 1940 ierr = PetscSectionGetOffset(subCoordSection, subvertex, &soff);CHKERRQ(ierr); 1941 if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof); 1942 for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d]; 1943 } 1944 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1945 ierr = VecRestoreArray(subCoordinates, &subCoords);CHKERRQ(ierr); 1946 } 1947 ierr = DMSetCoordinatesLocal(subdm, subCoordinates);CHKERRQ(ierr); 1948 ierr = VecDestroy(&subCoordinates);CHKERRQ(ierr); 1949 } 1950 /* Cleanup */ 1951 if (subvertexIS) {ierr = ISRestoreIndices(subvertexIS, &subVertices);CHKERRQ(ierr);} 1952 ierr = ISDestroy(&subvertexIS);CHKERRQ(ierr); 1953 if (subcellIS) {ierr = ISRestoreIndices(subcellIS, &subCells);CHKERRQ(ierr);} 1954 ierr = ISDestroy(&subcellIS);CHKERRQ(ierr); 1955 PetscFunctionReturn(0); 1956 } 1957 1958 #undef __FUNCT__ 1959 #define __FUNCT__ "DMPlexCreateSubmesh_Interpolated" 1960 static PetscErrorCode DMPlexCreateSubmesh_Interpolated(DM dm, const char vertexLabelName[], PetscInt value, DM subdm) 1961 { 1962 MPI_Comm comm; 1963 DMLabel subpointMap, vertexLabel; 1964 IS *subpointIS; 1965 const PetscInt **subpoints; 1966 PetscInt *numSubPoints, *firstSubPoint, *coneNew; 1967 PetscInt totSubPoints = 0, maxConeSize, dim, p, d, v; 1968 PetscErrorCode ierr; 1969 1970 PetscFunctionBegin; 1971 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 1972 /* Create subpointMap which marks the submesh */ 1973 ierr = DMLabelCreate("subpoint_map", &subpointMap);CHKERRQ(ierr); 1974 ierr = DMPlexSetSubpointMap(subdm, subpointMap);CHKERRQ(ierr); 1975 ierr = DMLabelDestroy(&subpointMap);CHKERRQ(ierr); 1976 ierr = DMPlexGetLabel(dm, vertexLabelName, &vertexLabel);CHKERRQ(ierr); 1977 ierr = DMPlexMarkSubmesh_Interpolated(dm, vertexLabel, value, subpointMap, subdm);CHKERRQ(ierr); 1978 /* Setup chart */ 1979 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1980 ierr = PetscMalloc4(dim+1,PetscInt,&numSubPoints,dim+1,PetscInt,&firstSubPoint,dim+1,IS,&subpointIS,dim+1,const PetscInt *,&subpoints);CHKERRQ(ierr); 1981 for (d = 0; d <= dim; ++d) { 1982 ierr = DMLabelGetStratumSize(subpointMap, d, &numSubPoints[d]);CHKERRQ(ierr); 1983 totSubPoints += numSubPoints[d]; 1984 } 1985 ierr = DMPlexSetChart(subdm, 0, totSubPoints);CHKERRQ(ierr); 1986 ierr = DMPlexSetVTKCellHeight(subdm, 1);CHKERRQ(ierr); 1987 /* Set cone sizes */ 1988 firstSubPoint[dim] = 0; 1989 firstSubPoint[0] = firstSubPoint[dim] + numSubPoints[dim]; 1990 if (dim > 1) {firstSubPoint[dim-1] = firstSubPoint[0] + numSubPoints[0];} 1991 if (dim > 2) {firstSubPoint[dim-2] = firstSubPoint[dim-1] + numSubPoints[dim-1];} 1992 for (d = 0; d <= dim; ++d) { 1993 ierr = DMLabelGetStratumIS(subpointMap, d, &subpointIS[d]);CHKERRQ(ierr); 1994 ierr = ISGetIndices(subpointIS[d], &subpoints[d]);CHKERRQ(ierr); 1995 } 1996 for (d = 0; d <= dim; ++d) { 1997 for (p = 0; p < numSubPoints[d]; ++p) { 1998 const PetscInt point = subpoints[d][p]; 1999 const PetscInt subpoint = firstSubPoint[d] + p; 2000 const PetscInt *cone; 2001 PetscInt coneSize, coneSizeNew, c, val; 2002 2003 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 2004 ierr = DMPlexSetConeSize(subdm, subpoint, coneSize);CHKERRQ(ierr); 2005 if (d == dim) { 2006 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 2007 for (c = 0, coneSizeNew = 0; c < coneSize; ++c) { 2008 ierr = DMLabelGetValue(subpointMap, cone[c], &val);CHKERRQ(ierr); 2009 if (val >= 0) coneSizeNew++; 2010 } 2011 ierr = DMPlexSetConeSize(subdm, subpoint, coneSizeNew);CHKERRQ(ierr); 2012 } 2013 } 2014 } 2015 ierr = DMSetUp(subdm);CHKERRQ(ierr); 2016 /* Set cones */ 2017 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, NULL);CHKERRQ(ierr); 2018 ierr = PetscMalloc(maxConeSize * sizeof(PetscInt), &coneNew);CHKERRQ(ierr); 2019 for (d = 0; d <= dim; ++d) { 2020 for (p = 0; p < numSubPoints[d]; ++p) { 2021 const PetscInt point = subpoints[d][p]; 2022 const PetscInt subpoint = firstSubPoint[d] + p; 2023 const PetscInt *cone; 2024 PetscInt coneSize, subconeSize, coneSizeNew, c, subc; 2025 2026 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 2027 ierr = DMPlexGetConeSize(subdm, subpoint, &subconeSize);CHKERRQ(ierr); 2028 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 2029 for (c = 0, coneSizeNew = 0; c < coneSize; ++c) { 2030 ierr = PetscFindInt(cone[c], numSubPoints[d-1], subpoints[d-1], &subc);CHKERRQ(ierr); 2031 if (subc >= 0) coneNew[coneSizeNew++] = firstSubPoint[d-1] + subc; 2032 } 2033 if (coneSizeNew != subconeSize) SETERRQ2(comm, PETSC_ERR_PLIB, "Number of cone points located %d does not match subcone size %d", coneSizeNew, subconeSize); 2034 ierr = DMPlexSetCone(subdm, subpoint, coneNew);CHKERRQ(ierr); 2035 } 2036 } 2037 ierr = PetscFree(coneNew);CHKERRQ(ierr); 2038 ierr = DMPlexSymmetrize(subdm);CHKERRQ(ierr); 2039 ierr = DMPlexStratify(subdm);CHKERRQ(ierr); 2040 /* Build coordinates */ 2041 { 2042 PetscSection coordSection, subCoordSection; 2043 Vec coordinates, subCoordinates; 2044 PetscScalar *coords, *subCoords; 2045 PetscInt numComp, coordSize; 2046 2047 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2048 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 2049 ierr = DMPlexGetCoordinateSection(subdm, &subCoordSection);CHKERRQ(ierr); 2050 ierr = PetscSectionSetNumFields(subCoordSection, 1);CHKERRQ(ierr); 2051 ierr = PetscSectionGetFieldComponents(coordSection, 0, &numComp);CHKERRQ(ierr); 2052 ierr = PetscSectionSetFieldComponents(subCoordSection, 0, numComp);CHKERRQ(ierr); 2053 ierr = PetscSectionSetChart(subCoordSection, firstSubPoint[0], firstSubPoint[0]+numSubPoints[0]);CHKERRQ(ierr); 2054 for (v = 0; v < numSubPoints[0]; ++v) { 2055 const PetscInt vertex = subpoints[0][v]; 2056 const PetscInt subvertex = firstSubPoint[0]+v; 2057 PetscInt dof; 2058 2059 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2060 ierr = PetscSectionSetDof(subCoordSection, subvertex, dof);CHKERRQ(ierr); 2061 ierr = PetscSectionSetFieldDof(subCoordSection, subvertex, 0, dof);CHKERRQ(ierr); 2062 } 2063 ierr = PetscSectionSetUp(subCoordSection);CHKERRQ(ierr); 2064 ierr = PetscSectionGetStorageSize(subCoordSection, &coordSize);CHKERRQ(ierr); 2065 ierr = VecCreate(comm, &subCoordinates);CHKERRQ(ierr); 2066 ierr = VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2067 ierr = VecSetFromOptions(subCoordinates);CHKERRQ(ierr); 2068 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2069 ierr = VecGetArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2070 for (v = 0; v < numSubPoints[0]; ++v) { 2071 const PetscInt vertex = subpoints[0][v]; 2072 const PetscInt subvertex = firstSubPoint[0]+v; 2073 PetscInt dof, off, sdof, soff, d; 2074 2075 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2076 ierr = PetscSectionGetOffset(coordSection, vertex, &off);CHKERRQ(ierr); 2077 ierr = PetscSectionGetDof(subCoordSection, subvertex, &sdof);CHKERRQ(ierr); 2078 ierr = PetscSectionGetOffset(subCoordSection, subvertex, &soff);CHKERRQ(ierr); 2079 if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof); 2080 for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d]; 2081 } 2082 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2083 ierr = VecRestoreArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2084 ierr = DMSetCoordinatesLocal(subdm, subCoordinates);CHKERRQ(ierr); 2085 ierr = VecDestroy(&subCoordinates);CHKERRQ(ierr); 2086 } 2087 /* Cleanup */ 2088 for (d = 0; d <= dim; ++d) { 2089 ierr = ISRestoreIndices(subpointIS[d], &subpoints[d]);CHKERRQ(ierr); 2090 ierr = ISDestroy(&subpointIS[d]);CHKERRQ(ierr); 2091 } 2092 ierr = PetscFree4(numSubPoints,firstSubPoint,subpointIS,subpoints);CHKERRQ(ierr); 2093 PetscFunctionReturn(0); 2094 } 2095 2096 #undef __FUNCT__ 2097 #define __FUNCT__ "DMPlexCreateSubmesh" 2098 /*@C 2099 DMPlexCreateSubmesh - Extract a hypersurface from the mesh using vertices defined by a label 2100 2101 Input Parameters: 2102 + dm - The original mesh 2103 . vertexLabel - The DMLabel marking vertices contained in the surface 2104 - value - The label value to use 2105 2106 Output Parameter: 2107 . subdm - The surface mesh 2108 2109 Note: This function produces a DMLabel mapping original points in the submesh to their depth. This can be obtained using DMPlexGetSubpointMap(). 2110 2111 Level: developer 2112 2113 .seealso: DMPlexGetSubpointMap(), DMPlexGetLabel(), DMLabelSetValue() 2114 @*/ 2115 PetscErrorCode DMPlexCreateSubmesh(DM dm, const char vertexLabel[], PetscInt value, DM *subdm) 2116 { 2117 PetscInt dim, depth; 2118 PetscErrorCode ierr; 2119 2120 PetscFunctionBegin; 2121 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2122 PetscValidCharPointer(vertexLabel, 2); 2123 PetscValidPointer(subdm, 3); 2124 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 2125 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 2126 ierr = DMCreate(PetscObjectComm((PetscObject)dm), subdm);CHKERRQ(ierr); 2127 ierr = DMSetType(*subdm, DMPLEX);CHKERRQ(ierr); 2128 ierr = DMPlexSetDimension(*subdm, dim-1);CHKERRQ(ierr); 2129 if (depth == dim) { 2130 ierr = DMPlexCreateSubmesh_Interpolated(dm, vertexLabel, value, *subdm);CHKERRQ(ierr); 2131 } else { 2132 ierr = DMPlexCreateSubmesh_Uninterpolated(dm, vertexLabel, value, *subdm);CHKERRQ(ierr); 2133 } 2134 PetscFunctionReturn(0); 2135 } 2136 2137 #undef __FUNCT__ 2138 #define __FUNCT__ "DMPlexCreateCohesiveSubmesh_Uninterpolated" 2139 static PetscErrorCode DMPlexCreateCohesiveSubmesh_Uninterpolated(DM dm, PetscBool hasLagrange, const char label[], PetscInt value, DM subdm) 2140 { 2141 MPI_Comm comm; 2142 DMLabel subpointMap; 2143 IS subvertexIS; 2144 const PetscInt *subVertices; 2145 PetscInt numSubVertices, firstSubVertex, numSubCells, *subCells; 2146 PetscInt *subface, maxConeSize, numSubFaces, firstSubFace, newFacePoint, nFV; 2147 PetscInt cMax, c, f; 2148 PetscErrorCode ierr; 2149 2150 PetscFunctionBegin; 2151 ierr = PetscObjectGetComm((PetscObject)dm, &comm);CHKERRQ(ierr); 2152 /* Create subpointMap which marks the submesh */ 2153 ierr = DMLabelCreate("subpoint_map", &subpointMap);CHKERRQ(ierr); 2154 ierr = DMPlexSetSubpointMap(subdm, subpointMap);CHKERRQ(ierr); 2155 ierr = DMLabelDestroy(&subpointMap);CHKERRQ(ierr); 2156 ierr = DMPlexMarkCohesiveSubmesh_Uninterpolated(dm, hasLagrange, label, value, subpointMap, &numSubFaces, &nFV, &subCells, subdm);CHKERRQ(ierr); 2157 /* Setup chart */ 2158 ierr = DMLabelGetStratumSize(subpointMap, 0, &numSubVertices);CHKERRQ(ierr); 2159 ierr = DMLabelGetStratumSize(subpointMap, 2, &numSubCells);CHKERRQ(ierr); 2160 ierr = DMPlexSetChart(subdm, 0, numSubCells+numSubFaces+numSubVertices);CHKERRQ(ierr); 2161 ierr = DMPlexSetVTKCellHeight(subdm, 1);CHKERRQ(ierr); 2162 /* Set cone sizes */ 2163 firstSubVertex = numSubCells; 2164 firstSubFace = numSubCells+numSubVertices; 2165 newFacePoint = firstSubFace; 2166 ierr = DMLabelGetStratumIS(subpointMap, 0, &subvertexIS);CHKERRQ(ierr); 2167 if (subvertexIS) {ierr = ISGetIndices(subvertexIS, &subVertices);CHKERRQ(ierr);} 2168 for (c = 0; c < numSubCells; ++c) { 2169 ierr = DMPlexSetConeSize(subdm, c, 1);CHKERRQ(ierr); 2170 } 2171 for (f = firstSubFace; f < firstSubFace+numSubFaces; ++f) { 2172 ierr = DMPlexSetConeSize(subdm, f, nFV);CHKERRQ(ierr); 2173 } 2174 ierr = DMSetUp(subdm);CHKERRQ(ierr); 2175 /* Create face cones */ 2176 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, NULL);CHKERRQ(ierr); 2177 ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); 2178 ierr = DMGetWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);CHKERRQ(ierr); 2179 for (c = 0; c < numSubCells; ++c) { 2180 const PetscInt cell = subCells[c]; 2181 const PetscInt subcell = c; 2182 const PetscInt *cone, *cells; 2183 PetscInt numCells, subVertex, p, v; 2184 2185 if (cell < cMax) continue; 2186 ierr = DMPlexGetCone(dm, cell, &cone);CHKERRQ(ierr); 2187 for (v = 0; v < nFV; ++v) { 2188 ierr = PetscFindInt(cone[v], numSubVertices, subVertices, &subVertex);CHKERRQ(ierr); 2189 subface[v] = firstSubVertex+subVertex; 2190 } 2191 ierr = DMPlexSetCone(subdm, newFacePoint, subface);CHKERRQ(ierr); 2192 ierr = DMPlexSetCone(subdm, subcell, &newFacePoint);CHKERRQ(ierr); 2193 ierr = DMPlexGetJoin(dm, nFV, cone, &numCells, &cells);CHKERRQ(ierr); 2194 if (numCells != 2) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive cells should separate two cells"); 2195 for (p = 0; p < numCells; ++p) { 2196 PetscInt negsubcell; 2197 2198 if (cells[p] >= cMax) continue; 2199 /* I know this is a crap search */ 2200 for (negsubcell = 0; negsubcell < numSubCells; ++negsubcell) { 2201 if (subCells[negsubcell] == cells[p]) break; 2202 } 2203 if (negsubcell == numSubCells) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not find negative face neighbor for cohesive cell %d", cell); 2204 ierr = DMPlexSetCone(subdm, negsubcell, &newFacePoint);CHKERRQ(ierr); 2205 } 2206 ierr = DMPlexRestoreJoin(dm, nFV, cone, &numCells, &cells);CHKERRQ(ierr); 2207 ++newFacePoint; 2208 } 2209 ierr = DMRestoreWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);CHKERRQ(ierr); 2210 ierr = DMPlexSymmetrize(subdm);CHKERRQ(ierr); 2211 ierr = DMPlexStratify(subdm);CHKERRQ(ierr); 2212 /* Build coordinates */ 2213 { 2214 PetscSection coordSection, subCoordSection; 2215 Vec coordinates, subCoordinates; 2216 PetscScalar *coords, *subCoords; 2217 PetscInt numComp, coordSize, v; 2218 2219 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2220 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 2221 ierr = DMPlexGetCoordinateSection(subdm, &subCoordSection);CHKERRQ(ierr); 2222 ierr = PetscSectionSetNumFields(subCoordSection, 1);CHKERRQ(ierr); 2223 ierr = PetscSectionGetFieldComponents(coordSection, 0, &numComp);CHKERRQ(ierr); 2224 ierr = PetscSectionSetFieldComponents(subCoordSection, 0, numComp);CHKERRQ(ierr); 2225 ierr = PetscSectionSetChart(subCoordSection, firstSubVertex, firstSubVertex+numSubVertices);CHKERRQ(ierr); 2226 for (v = 0; v < numSubVertices; ++v) { 2227 const PetscInt vertex = subVertices[v]; 2228 const PetscInt subvertex = firstSubVertex+v; 2229 PetscInt dof; 2230 2231 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2232 ierr = PetscSectionSetDof(subCoordSection, subvertex, dof);CHKERRQ(ierr); 2233 ierr = PetscSectionSetFieldDof(subCoordSection, subvertex, 0, dof);CHKERRQ(ierr); 2234 } 2235 ierr = PetscSectionSetUp(subCoordSection);CHKERRQ(ierr); 2236 ierr = PetscSectionGetStorageSize(subCoordSection, &coordSize);CHKERRQ(ierr); 2237 ierr = VecCreate(comm, &subCoordinates);CHKERRQ(ierr); 2238 if (coordSize) { 2239 ierr = VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2240 ierr = VecSetFromOptions(subCoordinates);CHKERRQ(ierr); 2241 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2242 ierr = VecGetArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2243 for (v = 0; v < numSubVertices; ++v) { 2244 const PetscInt vertex = subVertices[v]; 2245 const PetscInt subvertex = firstSubVertex+v; 2246 PetscInt dof, off, sdof, soff, d; 2247 2248 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2249 ierr = PetscSectionGetOffset(coordSection, vertex, &off);CHKERRQ(ierr); 2250 ierr = PetscSectionGetDof(subCoordSection, subvertex, &sdof);CHKERRQ(ierr); 2251 ierr = PetscSectionGetOffset(subCoordSection, subvertex, &soff);CHKERRQ(ierr); 2252 if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof); 2253 for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d]; 2254 } 2255 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2256 ierr = VecRestoreArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2257 } 2258 ierr = DMSetCoordinatesLocal(subdm, subCoordinates);CHKERRQ(ierr); 2259 ierr = VecDestroy(&subCoordinates);CHKERRQ(ierr); 2260 } 2261 /* Cleanup */ 2262 if (subvertexIS) {ierr = ISRestoreIndices(subvertexIS, &subVertices);CHKERRQ(ierr);} 2263 ierr = ISDestroy(&subvertexIS);CHKERRQ(ierr); 2264 ierr = PetscFree(subCells);CHKERRQ(ierr); 2265 PetscFunctionReturn(0); 2266 } 2267 2268 #undef __FUNCT__ 2269 #define __FUNCT__ "DMPlexCreateCohesiveSubmesh_Interpolated" 2270 static PetscErrorCode DMPlexCreateCohesiveSubmesh_Interpolated(DM dm, PetscBool hasLagrange, const char label[], PetscInt value, DM subdm) 2271 { 2272 MPI_Comm comm; 2273 DMLabel subpointMap; 2274 IS *subpointIS; 2275 const PetscInt **subpoints; 2276 PetscInt *numSubPoints, *firstSubPoint, *coneNew; 2277 PetscInt totSubPoints = 0, maxConeSize, dim, p, d, v; 2278 PetscErrorCode ierr; 2279 2280 PetscFunctionBegin; 2281 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 2282 /* Create subpointMap which marks the submesh */ 2283 ierr = DMLabelCreate("subpoint_map", &subpointMap);CHKERRQ(ierr); 2284 ierr = DMPlexSetSubpointMap(subdm, subpointMap);CHKERRQ(ierr); 2285 ierr = DMLabelDestroy(&subpointMap);CHKERRQ(ierr); 2286 ierr = DMPlexMarkCohesiveSubmesh_Interpolated(dm, hasLagrange, label, value, subpointMap, subdm);CHKERRQ(ierr); 2287 /* Setup chart */ 2288 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 2289 ierr = PetscMalloc4(dim+1,PetscInt,&numSubPoints,dim+1,PetscInt,&firstSubPoint,dim+1,IS,&subpointIS,dim+1,const PetscInt *,&subpoints);CHKERRQ(ierr); 2290 for (d = 0; d <= dim; ++d) { 2291 ierr = DMLabelGetStratumSize(subpointMap, d, &numSubPoints[d]);CHKERRQ(ierr); 2292 totSubPoints += numSubPoints[d]; 2293 } 2294 ierr = DMPlexSetChart(subdm, 0, totSubPoints);CHKERRQ(ierr); 2295 ierr = DMPlexSetVTKCellHeight(subdm, 1);CHKERRQ(ierr); 2296 /* Set cone sizes */ 2297 firstSubPoint[dim] = 0; 2298 firstSubPoint[0] = firstSubPoint[dim] + numSubPoints[dim]; 2299 if (dim > 1) {firstSubPoint[dim-1] = firstSubPoint[0] + numSubPoints[0];} 2300 if (dim > 2) {firstSubPoint[dim-2] = firstSubPoint[dim-1] + numSubPoints[dim-1];} 2301 for (d = 0; d <= dim; ++d) { 2302 ierr = DMLabelGetStratumIS(subpointMap, d, &subpointIS[d]);CHKERRQ(ierr); 2303 ierr = ISGetIndices(subpointIS[d], &subpoints[d]);CHKERRQ(ierr); 2304 } 2305 for (d = 0; d <= dim; ++d) { 2306 for (p = 0; p < numSubPoints[d]; ++p) { 2307 const PetscInt point = subpoints[d][p]; 2308 const PetscInt subpoint = firstSubPoint[d] + p; 2309 const PetscInt *cone; 2310 PetscInt coneSize, coneSizeNew, c, val; 2311 2312 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 2313 ierr = DMPlexSetConeSize(subdm, subpoint, coneSize);CHKERRQ(ierr); 2314 if (d == dim) { 2315 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 2316 for (c = 0, coneSizeNew = 0; c < coneSize; ++c) { 2317 ierr = DMLabelGetValue(subpointMap, cone[c], &val);CHKERRQ(ierr); 2318 if (val >= 0) coneSizeNew++; 2319 } 2320 ierr = DMPlexSetConeSize(subdm, subpoint, coneSizeNew);CHKERRQ(ierr); 2321 } 2322 } 2323 } 2324 ierr = DMSetUp(subdm);CHKERRQ(ierr); 2325 /* Set cones */ 2326 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, NULL);CHKERRQ(ierr); 2327 ierr = PetscMalloc(maxConeSize * sizeof(PetscInt), &coneNew);CHKERRQ(ierr); 2328 for (d = 0; d <= dim; ++d) { 2329 for (p = 0; p < numSubPoints[d]; ++p) { 2330 const PetscInt point = subpoints[d][p]; 2331 const PetscInt subpoint = firstSubPoint[d] + p; 2332 const PetscInt *cone; 2333 PetscInt coneSize, subconeSize, coneSizeNew, c, subc; 2334 2335 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 2336 ierr = DMPlexGetConeSize(subdm, subpoint, &subconeSize);CHKERRQ(ierr); 2337 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 2338 for (c = 0, coneSizeNew = 0; c < coneSize; ++c) { 2339 ierr = PetscFindInt(cone[c], numSubPoints[d-1], subpoints[d-1], &subc);CHKERRQ(ierr); 2340 if (subc >= 0) coneNew[coneSizeNew++] = firstSubPoint[d-1] + subc; 2341 } 2342 if (coneSizeNew != subconeSize) SETERRQ2(comm, PETSC_ERR_PLIB, "Number of cone points located %d does not match subcone size %d", coneSizeNew, subconeSize); 2343 ierr = DMPlexSetCone(subdm, subpoint, coneNew);CHKERRQ(ierr); 2344 } 2345 } 2346 ierr = PetscFree(coneNew);CHKERRQ(ierr); 2347 ierr = DMPlexSymmetrize(subdm);CHKERRQ(ierr); 2348 ierr = DMPlexStratify(subdm);CHKERRQ(ierr); 2349 /* Build coordinates */ 2350 { 2351 PetscSection coordSection, subCoordSection; 2352 Vec coordinates, subCoordinates; 2353 PetscScalar *coords, *subCoords; 2354 PetscInt numComp, coordSize; 2355 2356 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2357 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 2358 ierr = DMPlexGetCoordinateSection(subdm, &subCoordSection);CHKERRQ(ierr); 2359 ierr = PetscSectionSetNumFields(subCoordSection, 1);CHKERRQ(ierr); 2360 ierr = PetscSectionGetFieldComponents(coordSection, 0, &numComp);CHKERRQ(ierr); 2361 ierr = PetscSectionSetFieldComponents(subCoordSection, 0, numComp);CHKERRQ(ierr); 2362 ierr = PetscSectionSetChart(subCoordSection, firstSubPoint[0], firstSubPoint[0]+numSubPoints[0]);CHKERRQ(ierr); 2363 for (v = 0; v < numSubPoints[0]; ++v) { 2364 const PetscInt vertex = subpoints[0][v]; 2365 const PetscInt subvertex = firstSubPoint[0]+v; 2366 PetscInt dof; 2367 2368 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2369 ierr = PetscSectionSetDof(subCoordSection, subvertex, dof);CHKERRQ(ierr); 2370 ierr = PetscSectionSetFieldDof(subCoordSection, subvertex, 0, dof);CHKERRQ(ierr); 2371 } 2372 ierr = PetscSectionSetUp(subCoordSection);CHKERRQ(ierr); 2373 ierr = PetscSectionGetStorageSize(subCoordSection, &coordSize);CHKERRQ(ierr); 2374 ierr = VecCreate(comm, &subCoordinates);CHKERRQ(ierr); 2375 ierr = VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2376 ierr = VecSetFromOptions(subCoordinates);CHKERRQ(ierr); 2377 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2378 ierr = VecGetArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2379 for (v = 0; v < numSubPoints[0]; ++v) { 2380 const PetscInt vertex = subpoints[0][v]; 2381 const PetscInt subvertex = firstSubPoint[0]+v; 2382 PetscInt dof, off, sdof, soff, d; 2383 2384 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2385 ierr = PetscSectionGetOffset(coordSection, vertex, &off);CHKERRQ(ierr); 2386 ierr = PetscSectionGetDof(subCoordSection, subvertex, &sdof);CHKERRQ(ierr); 2387 ierr = PetscSectionGetOffset(subCoordSection, subvertex, &soff);CHKERRQ(ierr); 2388 if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof); 2389 for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d]; 2390 } 2391 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2392 ierr = VecRestoreArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2393 ierr = DMSetCoordinatesLocal(subdm, subCoordinates);CHKERRQ(ierr); 2394 ierr = VecDestroy(&subCoordinates);CHKERRQ(ierr); 2395 } 2396 /* Cleanup */ 2397 for (d = 0; d <= dim; ++d) { 2398 ierr = ISRestoreIndices(subpointIS[d], &subpoints[d]);CHKERRQ(ierr); 2399 ierr = ISDestroy(&subpointIS[d]);CHKERRQ(ierr); 2400 } 2401 ierr = PetscFree4(numSubPoints,firstSubPoint,subpointIS,subpoints);CHKERRQ(ierr); 2402 PetscFunctionReturn(0); 2403 } 2404 2405 #undef __FUNCT__ 2406 #define __FUNCT__ "DMPlexCreateCohesiveSubmesh" 2407 /* 2408 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. 2409 2410 Input Parameters: 2411 + dm - The original mesh 2412 . hasLagrange - The mesh has Lagrange unknowns in the cohesive cells 2413 . label - A label name, or PETSC_NULL 2414 - value - A label value 2415 2416 Output Parameter: 2417 . subdm - The surface mesh 2418 2419 Note: This function produces a DMLabel mapping original points in the submesh to their depth. This can be obtained using DMPlexGetSubpointMap(). 2420 2421 Level: developer 2422 2423 .seealso: DMPlexGetSubpointMap(), DMPlexCreateSubmesh() 2424 */ 2425 PetscErrorCode DMPlexCreateCohesiveSubmesh(DM dm, PetscBool hasLagrange, const char label[], PetscInt value, DM *subdm) 2426 { 2427 PetscInt dim, depth; 2428 PetscErrorCode ierr; 2429 2430 PetscFunctionBegin; 2431 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2432 PetscValidPointer(subdm, 5); 2433 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 2434 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 2435 ierr = DMCreate(PetscObjectComm((PetscObject)dm), subdm);CHKERRQ(ierr); 2436 ierr = DMSetType(*subdm, DMPLEX);CHKERRQ(ierr); 2437 ierr = DMPlexSetDimension(*subdm, dim-1);CHKERRQ(ierr); 2438 if (depth == dim) { 2439 ierr = DMPlexCreateCohesiveSubmesh_Interpolated(dm, hasLagrange, label, value, *subdm);CHKERRQ(ierr); 2440 } else { 2441 ierr = DMPlexCreateCohesiveSubmesh_Uninterpolated(dm, hasLagrange, label, value, *subdm);CHKERRQ(ierr); 2442 } 2443 PetscFunctionReturn(0); 2444 } 2445 2446 #undef __FUNCT__ 2447 #define __FUNCT__ "DMPlexGetSubpointMap" 2448 /*@ 2449 DMPlexGetSubpointMap - Returns a DMLabel with point dimension as values 2450 2451 Input Parameter: 2452 . dm - The submesh DM 2453 2454 Output Parameter: 2455 . subpointMap - The DMLabel of all the points from the original mesh in this submesh, or NULL if this is not a submesh 2456 2457 Level: developer 2458 2459 .seealso: DMPlexCreateSubmesh(), DMPlexCreateSubpointIS() 2460 @*/ 2461 PetscErrorCode DMPlexGetSubpointMap(DM dm, DMLabel *subpointMap) 2462 { 2463 DM_Plex *mesh = (DM_Plex*) dm->data; 2464 2465 PetscFunctionBegin; 2466 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2467 PetscValidPointer(subpointMap, 2); 2468 *subpointMap = mesh->subpointMap; 2469 PetscFunctionReturn(0); 2470 } 2471 2472 #undef __FUNCT__ 2473 #define __FUNCT__ "DMPlexSetSubpointMap" 2474 /* Note: Should normally not be called by the user, since it is set in DMPlexCreateSubmesh() */ 2475 PetscErrorCode DMPlexSetSubpointMap(DM dm, DMLabel subpointMap) 2476 { 2477 DM_Plex *mesh = (DM_Plex *) dm->data; 2478 DMLabel tmp; 2479 PetscErrorCode ierr; 2480 2481 PetscFunctionBegin; 2482 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2483 tmp = mesh->subpointMap; 2484 mesh->subpointMap = subpointMap; 2485 ++mesh->subpointMap->refct; 2486 ierr = DMLabelDestroy(&tmp);CHKERRQ(ierr); 2487 PetscFunctionReturn(0); 2488 } 2489 2490 #undef __FUNCT__ 2491 #define __FUNCT__ "DMPlexCreateSubpointIS" 2492 /*@ 2493 DMPlexCreateSubpointIS - Creates an IS covering the entire subdm chart with the original points as data 2494 2495 Input Parameter: 2496 . dm - The submesh DM 2497 2498 Output Parameter: 2499 . subpointIS - The IS of all the points from the original mesh in this submesh, or NULL if this is not a submesh 2500 2501 Note: This is IS is guaranteed to be sorted by the construction of the submesh 2502 2503 Level: developer 2504 2505 .seealso: DMPlexCreateSubmesh(), DMPlexGetSubpointMap() 2506 @*/ 2507 PetscErrorCode DMPlexCreateSubpointIS(DM dm, IS *subpointIS) 2508 { 2509 MPI_Comm comm; 2510 DMLabel subpointMap; 2511 IS is; 2512 const PetscInt *opoints; 2513 PetscInt *points, *depths; 2514 PetscInt depth, depStart, depEnd, d, pStart, pEnd, p, n, off; 2515 PetscErrorCode ierr; 2516 2517 PetscFunctionBegin; 2518 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2519 PetscValidPointer(subpointIS, 2); 2520 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 2521 *subpointIS = NULL; 2522 ierr = DMPlexGetSubpointMap(dm, &subpointMap);CHKERRQ(ierr); 2523 if (subpointMap) { 2524 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 2525 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 2526 if (pStart) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Submeshes must start the point numbering at 0, not %d", pStart); 2527 ierr = DMGetWorkArray(dm, depth+1, PETSC_INT, &depths);CHKERRQ(ierr); 2528 depths[0] = depth; 2529 depths[1] = 0; 2530 for(d = 2; d <= depth; ++d) {depths[d] = depth+1 - d;} 2531 ierr = PetscMalloc(pEnd * sizeof(PetscInt), &points);CHKERRQ(ierr); 2532 for(d = 0, off = 0; d <= depth; ++d) { 2533 const PetscInt dep = depths[d]; 2534 2535 ierr = DMPlexGetDepthStratum(dm, dep, &depStart, &depEnd);CHKERRQ(ierr); 2536 ierr = DMLabelGetStratumSize(subpointMap, dep, &n);CHKERRQ(ierr); 2537 if (((d < 2) && (depth > 1)) || (d == 1)) { /* Only check vertices and cells for now since the map is broken for others */ 2538 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); 2539 } else { 2540 if (!n) { 2541 if (d == 0) { 2542 /* Missing cells */ 2543 for(p = 0; p < depEnd-depStart; ++p, ++off) points[off] = -1; 2544 } else { 2545 /* Missing faces */ 2546 for(p = 0; p < depEnd-depStart; ++p, ++off) points[off] = PETSC_MAX_INT; 2547 } 2548 } 2549 } 2550 if (n) { 2551 ierr = DMLabelGetStratumIS(subpointMap, dep, &is);CHKERRQ(ierr); 2552 ierr = ISGetIndices(is, &opoints);CHKERRQ(ierr); 2553 for(p = 0; p < n; ++p, ++off) points[off] = opoints[p]; 2554 ierr = ISRestoreIndices(is, &opoints);CHKERRQ(ierr); 2555 ierr = ISDestroy(&is);CHKERRQ(ierr); 2556 } 2557 } 2558 ierr = DMRestoreWorkArray(dm, depth+1, PETSC_INT, &depths);CHKERRQ(ierr); 2559 if (off != pEnd) SETERRQ2(comm, PETSC_ERR_ARG_WRONG, "The number of mapped submesh points %d should be %d", off, pEnd); 2560 ierr = ISCreateGeneral(comm, pEnd, points, PETSC_OWN_POINTER, subpointIS);CHKERRQ(ierr); 2561 } 2562 PetscFunctionReturn(0); 2563 } 2564