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, DMLabel subpointMap, PetscInt *numFaces, PetscInt *nFV, PetscInt *subCells[], DM subdm) 1268 { 1269 const PetscInt *cone; 1270 PetscInt dim, cMax, cEnd, c, p, coneSize; 1271 PetscErrorCode ierr; 1272 1273 PetscFunctionBegin; 1274 *numFaces = 0; 1275 *nFV = 0; 1276 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1277 ierr = DMPlexGetHeightStratum(dm, 0, NULL, &cEnd);CHKERRQ(ierr); 1278 ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); 1279 if (cMax < 0) PetscFunctionReturn(0); 1280 ierr = DMPlexGetConeSize(dm, cMax, &coneSize);CHKERRQ(ierr); 1281 *numFaces = cEnd - cMax; 1282 *nFV = hasLagrange ? coneSize/3 : coneSize/2; 1283 ierr = PetscMalloc(*numFaces *2 * sizeof(PetscInt), subCells);CHKERRQ(ierr); 1284 for (c = cMax; c < cEnd; ++c) { 1285 const PetscInt *cells; 1286 PetscInt numCells; 1287 1288 ierr = DMPlexGetCone(dm, c, &cone);CHKERRQ(ierr); 1289 for (p = 0; p < *nFV; ++p) { 1290 ierr = DMLabelSetValue(subpointMap, cone[p], 0);CHKERRQ(ierr); 1291 } 1292 /* Negative face */ 1293 ierr = DMPlexGetJoin(dm, *nFV, cone, &numCells, &cells);CHKERRQ(ierr); 1294 if (numCells != 2) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive cells should separate two cells"); 1295 for (p = 0; p < numCells; ++p) { 1296 ierr = DMLabelSetValue(subpointMap, cells[p], 2);CHKERRQ(ierr); 1297 (*subCells)[(c-cMax)*2+p] = cells[p]; 1298 } 1299 ierr = DMPlexRestoreJoin(dm, *nFV, cone, &numCells, &cells);CHKERRQ(ierr); 1300 /* Positive face is not included */ 1301 } 1302 PetscFunctionReturn(0); 1303 } 1304 1305 #undef __FUNCT__ 1306 #define __FUNCT__ "DMPlexMarkCohesiveSubmesh_Interpolated" 1307 static PetscErrorCode DMPlexMarkCohesiveSubmesh_Interpolated(DM dm, PetscBool hasLagrange, DMLabel subpointMap, DM subdm) 1308 { 1309 PetscInt *pStart, *pEnd; 1310 PetscInt dim, cMax, cEnd, c, d; 1311 PetscErrorCode ierr; 1312 1313 PetscFunctionBegin; 1314 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1315 ierr = DMPlexGetHeightStratum(dm, 0, NULL, &cEnd);CHKERRQ(ierr); 1316 ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); 1317 if (cMax < 0) PetscFunctionReturn(0); 1318 ierr = PetscMalloc2(dim+1,PetscInt,&pStart,dim+1,PetscInt,&pEnd);CHKERRQ(ierr); 1319 for (d = 0; d <= dim; ++d) { 1320 ierr = DMPlexGetDepthStratum(dm, d, &pStart[d], &pEnd[d]);CHKERRQ(ierr); 1321 } 1322 for (c = cMax; c < cEnd; ++c) { 1323 const PetscInt *cone; 1324 PetscInt *closure = NULL; 1325 PetscInt coneSize, closureSize, cl; 1326 1327 ierr = DMPlexGetConeSize(dm, c, &coneSize);CHKERRQ(ierr); 1328 if (hasLagrange) { 1329 if (coneSize != 3) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive cells should separate two cells"); 1330 } else { 1331 if (coneSize != 2) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive cells should separate two cells"); 1332 } 1333 /* Negative face */ 1334 ierr = DMPlexGetCone(dm, c, &cone);CHKERRQ(ierr); 1335 ierr = DMPlexGetTransitiveClosure(dm, cone[0], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1336 for (cl = 0; cl < closureSize*2; cl += 2) { 1337 const PetscInt point = closure[cl]; 1338 1339 for (d = 0; d <= dim; ++d) { 1340 if ((point >= pStart[d]) && (point < pEnd[d])) { 1341 ierr = DMLabelSetValue(subpointMap, point, d);CHKERRQ(ierr); 1342 break; 1343 } 1344 } 1345 } 1346 ierr = DMPlexRestoreTransitiveClosure(dm, cone[0], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1347 /* Cells -- positive face is not included */ 1348 for (cl = 0; cl < 1; ++cl) { 1349 const PetscInt *support; 1350 PetscInt supportSize, s; 1351 1352 ierr = DMPlexGetSupportSize(dm, cone[cl], &supportSize);CHKERRQ(ierr); 1353 if (supportSize != 2) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive faces should separate two cells"); 1354 ierr = DMPlexGetSupport(dm, cone[cl], &support);CHKERRQ(ierr); 1355 for (s = 0; s < supportSize; ++s) { 1356 ierr = DMLabelSetValue(subpointMap, support[s], dim);CHKERRQ(ierr); 1357 } 1358 } 1359 } 1360 ierr = PetscFree2(pStart, pEnd);CHKERRQ(ierr); 1361 PetscFunctionReturn(0); 1362 } 1363 1364 #undef __FUNCT__ 1365 #define __FUNCT__ "DMPlexGetFaceOrientation" 1366 PetscErrorCode DMPlexGetFaceOrientation(DM dm, PetscInt cell, PetscInt numCorners, PetscInt indices[], PetscInt oppositeVertex, PetscInt origVertices[], PetscInt faceVertices[], PetscBool *posOriented) 1367 { 1368 MPI_Comm comm; 1369 PetscBool posOrient = PETSC_FALSE; 1370 const PetscInt debug = 0; 1371 PetscInt cellDim, faceSize, f; 1372 PetscErrorCode ierr; 1373 1374 PetscFunctionBegin; 1375 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 1376 ierr = DMPlexGetDimension(dm, &cellDim);CHKERRQ(ierr); 1377 if (debug) {PetscPrintf(comm, "cellDim: %d numCorners: %d\n", cellDim, numCorners);CHKERRQ(ierr);} 1378 1379 if (cellDim == 1 && numCorners == 2) { 1380 /* Triangle */ 1381 faceSize = numCorners-1; 1382 posOrient = !(oppositeVertex%2) ? PETSC_TRUE : PETSC_FALSE; 1383 } else if (cellDim == 2 && numCorners == 3) { 1384 /* Triangle */ 1385 faceSize = numCorners-1; 1386 posOrient = !(oppositeVertex%2) ? PETSC_TRUE : PETSC_FALSE; 1387 } else if (cellDim == 3 && numCorners == 4) { 1388 /* Tetrahedron */ 1389 faceSize = numCorners-1; 1390 posOrient = (oppositeVertex%2) ? PETSC_TRUE : PETSC_FALSE; 1391 } else if (cellDim == 1 && numCorners == 3) { 1392 /* Quadratic line */ 1393 faceSize = 1; 1394 posOrient = PETSC_TRUE; 1395 } else if (cellDim == 2 && numCorners == 4) { 1396 /* Quads */ 1397 faceSize = 2; 1398 if ((indices[1] > indices[0]) && (indices[1] - indices[0] == 1)) { 1399 posOrient = PETSC_TRUE; 1400 } else if ((indices[0] == 3) && (indices[1] == 0)) { 1401 posOrient = PETSC_TRUE; 1402 } else { 1403 if (((indices[0] > indices[1]) && (indices[0] - indices[1] == 1)) || ((indices[0] == 0) && (indices[1] == 3))) { 1404 posOrient = PETSC_FALSE; 1405 } else SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid quad crossedge"); 1406 } 1407 } else if (cellDim == 2 && numCorners == 6) { 1408 /* Quadratic triangle (I hate this) */ 1409 /* Edges are determined by the first 2 vertices (corners of edges) */ 1410 const PetscInt faceSizeTri = 3; 1411 PetscInt sortedIndices[3], i, iFace; 1412 PetscBool found = PETSC_FALSE; 1413 PetscInt faceVerticesTriSorted[9] = { 1414 0, 3, 4, /* bottom */ 1415 1, 4, 5, /* right */ 1416 2, 3, 5, /* left */ 1417 }; 1418 PetscInt faceVerticesTri[9] = { 1419 0, 3, 4, /* bottom */ 1420 1, 4, 5, /* right */ 1421 2, 5, 3, /* left */ 1422 }; 1423 1424 faceSize = faceSizeTri; 1425 for (i = 0; i < faceSizeTri; ++i) sortedIndices[i] = indices[i]; 1426 ierr = PetscSortInt(faceSizeTri, sortedIndices);CHKERRQ(ierr); 1427 for (iFace = 0; iFace < 3; ++iFace) { 1428 const PetscInt ii = iFace*faceSizeTri; 1429 PetscInt fVertex, cVertex; 1430 1431 if ((sortedIndices[0] == faceVerticesTriSorted[ii+0]) && 1432 (sortedIndices[1] == faceVerticesTriSorted[ii+1])) { 1433 for (fVertex = 0; fVertex < faceSizeTri; ++fVertex) { 1434 for (cVertex = 0; cVertex < faceSizeTri; ++cVertex) { 1435 if (indices[cVertex] == faceVerticesTri[ii+fVertex]) { 1436 faceVertices[fVertex] = origVertices[cVertex]; 1437 break; 1438 } 1439 } 1440 } 1441 found = PETSC_TRUE; 1442 break; 1443 } 1444 } 1445 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid tri crossface"); 1446 if (posOriented) *posOriented = PETSC_TRUE; 1447 PetscFunctionReturn(0); 1448 } else if (cellDim == 2 && numCorners == 9) { 1449 /* Quadratic quad (I hate this) */ 1450 /* Edges are determined by the first 2 vertices (corners of edges) */ 1451 const PetscInt faceSizeQuad = 3; 1452 PetscInt sortedIndices[3], i, iFace; 1453 PetscBool found = PETSC_FALSE; 1454 PetscInt faceVerticesQuadSorted[12] = { 1455 0, 1, 4, /* bottom */ 1456 1, 2, 5, /* right */ 1457 2, 3, 6, /* top */ 1458 0, 3, 7, /* left */ 1459 }; 1460 PetscInt faceVerticesQuad[12] = { 1461 0, 1, 4, /* bottom */ 1462 1, 2, 5, /* right */ 1463 2, 3, 6, /* top */ 1464 3, 0, 7, /* left */ 1465 }; 1466 1467 faceSize = faceSizeQuad; 1468 for (i = 0; i < faceSizeQuad; ++i) sortedIndices[i] = indices[i]; 1469 ierr = PetscSortInt(faceSizeQuad, sortedIndices);CHKERRQ(ierr); 1470 for (iFace = 0; iFace < 4; ++iFace) { 1471 const PetscInt ii = iFace*faceSizeQuad; 1472 PetscInt fVertex, cVertex; 1473 1474 if ((sortedIndices[0] == faceVerticesQuadSorted[ii+0]) && 1475 (sortedIndices[1] == faceVerticesQuadSorted[ii+1])) { 1476 for (fVertex = 0; fVertex < faceSizeQuad; ++fVertex) { 1477 for (cVertex = 0; cVertex < faceSizeQuad; ++cVertex) { 1478 if (indices[cVertex] == faceVerticesQuad[ii+fVertex]) { 1479 faceVertices[fVertex] = origVertices[cVertex]; 1480 break; 1481 } 1482 } 1483 } 1484 found = PETSC_TRUE; 1485 break; 1486 } 1487 } 1488 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid quad crossface"); 1489 if (posOriented) *posOriented = PETSC_TRUE; 1490 PetscFunctionReturn(0); 1491 } else if (cellDim == 3 && numCorners == 8) { 1492 /* Hexes 1493 A hex is two oriented quads with the normal of the first 1494 pointing up at the second. 1495 1496 7---6 1497 /| /| 1498 4---5 | 1499 | 1-|-2 1500 |/ |/ 1501 0---3 1502 1503 Faces are determined by the first 4 vertices (corners of faces) */ 1504 const PetscInt faceSizeHex = 4; 1505 PetscInt sortedIndices[4], i, iFace; 1506 PetscBool found = PETSC_FALSE; 1507 PetscInt faceVerticesHexSorted[24] = { 1508 0, 1, 2, 3, /* bottom */ 1509 4, 5, 6, 7, /* top */ 1510 0, 3, 4, 5, /* front */ 1511 2, 3, 5, 6, /* right */ 1512 1, 2, 6, 7, /* back */ 1513 0, 1, 4, 7, /* left */ 1514 }; 1515 PetscInt faceVerticesHex[24] = { 1516 1, 2, 3, 0, /* bottom */ 1517 4, 5, 6, 7, /* top */ 1518 0, 3, 5, 4, /* front */ 1519 3, 2, 6, 5, /* right */ 1520 2, 1, 7, 6, /* back */ 1521 1, 0, 4, 7, /* left */ 1522 }; 1523 1524 faceSize = faceSizeHex; 1525 for (i = 0; i < faceSizeHex; ++i) sortedIndices[i] = indices[i]; 1526 ierr = PetscSortInt(faceSizeHex, sortedIndices);CHKERRQ(ierr); 1527 for (iFace = 0; iFace < 6; ++iFace) { 1528 const PetscInt ii = iFace*faceSizeHex; 1529 PetscInt fVertex, cVertex; 1530 1531 if ((sortedIndices[0] == faceVerticesHexSorted[ii+0]) && 1532 (sortedIndices[1] == faceVerticesHexSorted[ii+1]) && 1533 (sortedIndices[2] == faceVerticesHexSorted[ii+2]) && 1534 (sortedIndices[3] == faceVerticesHexSorted[ii+3])) { 1535 for (fVertex = 0; fVertex < faceSizeHex; ++fVertex) { 1536 for (cVertex = 0; cVertex < faceSizeHex; ++cVertex) { 1537 if (indices[cVertex] == faceVerticesHex[ii+fVertex]) { 1538 faceVertices[fVertex] = origVertices[cVertex]; 1539 break; 1540 } 1541 } 1542 } 1543 found = PETSC_TRUE; 1544 break; 1545 } 1546 } 1547 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid hex crossface"); 1548 if (posOriented) *posOriented = PETSC_TRUE; 1549 PetscFunctionReturn(0); 1550 } else if (cellDim == 3 && numCorners == 10) { 1551 /* Quadratic tet */ 1552 /* Faces are determined by the first 3 vertices (corners of faces) */ 1553 const PetscInt faceSizeTet = 6; 1554 PetscInt sortedIndices[6], i, iFace; 1555 PetscBool found = PETSC_FALSE; 1556 PetscInt faceVerticesTetSorted[24] = { 1557 0, 1, 2, 6, 7, 8, /* bottom */ 1558 0, 3, 4, 6, 7, 9, /* front */ 1559 1, 4, 5, 7, 8, 9, /* right */ 1560 2, 3, 5, 6, 8, 9, /* left */ 1561 }; 1562 PetscInt faceVerticesTet[24] = { 1563 0, 1, 2, 6, 7, 8, /* bottom */ 1564 0, 4, 3, 6, 7, 9, /* front */ 1565 1, 5, 4, 7, 8, 9, /* right */ 1566 2, 3, 5, 8, 6, 9, /* left */ 1567 }; 1568 1569 faceSize = faceSizeTet; 1570 for (i = 0; i < faceSizeTet; ++i) sortedIndices[i] = indices[i]; 1571 ierr = PetscSortInt(faceSizeTet, sortedIndices);CHKERRQ(ierr); 1572 for (iFace=0; iFace < 4; ++iFace) { 1573 const PetscInt ii = iFace*faceSizeTet; 1574 PetscInt fVertex, cVertex; 1575 1576 if ((sortedIndices[0] == faceVerticesTetSorted[ii+0]) && 1577 (sortedIndices[1] == faceVerticesTetSorted[ii+1]) && 1578 (sortedIndices[2] == faceVerticesTetSorted[ii+2]) && 1579 (sortedIndices[3] == faceVerticesTetSorted[ii+3])) { 1580 for (fVertex = 0; fVertex < faceSizeTet; ++fVertex) { 1581 for (cVertex = 0; cVertex < faceSizeTet; ++cVertex) { 1582 if (indices[cVertex] == faceVerticesTet[ii+fVertex]) { 1583 faceVertices[fVertex] = origVertices[cVertex]; 1584 break; 1585 } 1586 } 1587 } 1588 found = PETSC_TRUE; 1589 break; 1590 } 1591 } 1592 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid tet crossface"); 1593 if (posOriented) *posOriented = PETSC_TRUE; 1594 PetscFunctionReturn(0); 1595 } else if (cellDim == 3 && numCorners == 27) { 1596 /* Quadratic hexes (I hate this) 1597 A hex is two oriented quads with the normal of the first 1598 pointing up at the second. 1599 1600 7---6 1601 /| /| 1602 4---5 | 1603 | 3-|-2 1604 |/ |/ 1605 0---1 1606 1607 Faces are determined by the first 4 vertices (corners of faces) */ 1608 const PetscInt faceSizeQuadHex = 9; 1609 PetscInt sortedIndices[9], i, iFace; 1610 PetscBool found = PETSC_FALSE; 1611 PetscInt faceVerticesQuadHexSorted[54] = { 1612 0, 1, 2, 3, 8, 9, 10, 11, 24, /* bottom */ 1613 4, 5, 6, 7, 12, 13, 14, 15, 25, /* top */ 1614 0, 1, 4, 5, 8, 12, 16, 17, 22, /* front */ 1615 1, 2, 5, 6, 9, 13, 17, 18, 21, /* right */ 1616 2, 3, 6, 7, 10, 14, 18, 19, 23, /* back */ 1617 0, 3, 4, 7, 11, 15, 16, 19, 20, /* left */ 1618 }; 1619 PetscInt faceVerticesQuadHex[54] = { 1620 3, 2, 1, 0, 10, 9, 8, 11, 24, /* bottom */ 1621 4, 5, 6, 7, 12, 13, 14, 15, 25, /* top */ 1622 0, 1, 5, 4, 8, 17, 12, 16, 22, /* front */ 1623 1, 2, 6, 5, 9, 18, 13, 17, 21, /* right */ 1624 2, 3, 7, 6, 10, 19, 14, 18, 23, /* back */ 1625 3, 0, 4, 7, 11, 16, 15, 19, 20 /* left */ 1626 }; 1627 1628 faceSize = faceSizeQuadHex; 1629 for (i = 0; i < faceSizeQuadHex; ++i) sortedIndices[i] = indices[i]; 1630 ierr = PetscSortInt(faceSizeQuadHex, sortedIndices);CHKERRQ(ierr); 1631 for (iFace = 0; iFace < 6; ++iFace) { 1632 const PetscInt ii = iFace*faceSizeQuadHex; 1633 PetscInt fVertex, cVertex; 1634 1635 if ((sortedIndices[0] == faceVerticesQuadHexSorted[ii+0]) && 1636 (sortedIndices[1] == faceVerticesQuadHexSorted[ii+1]) && 1637 (sortedIndices[2] == faceVerticesQuadHexSorted[ii+2]) && 1638 (sortedIndices[3] == faceVerticesQuadHexSorted[ii+3])) { 1639 for (fVertex = 0; fVertex < faceSizeQuadHex; ++fVertex) { 1640 for (cVertex = 0; cVertex < faceSizeQuadHex; ++cVertex) { 1641 if (indices[cVertex] == faceVerticesQuadHex[ii+fVertex]) { 1642 faceVertices[fVertex] = origVertices[cVertex]; 1643 break; 1644 } 1645 } 1646 } 1647 found = PETSC_TRUE; 1648 break; 1649 } 1650 } 1651 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid hex crossface"); 1652 if (posOriented) *posOriented = PETSC_TRUE; 1653 PetscFunctionReturn(0); 1654 } else SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Unknown cell type for faceOrientation()."); 1655 if (!posOrient) { 1656 if (debug) {ierr = PetscPrintf(comm, " Reversing initial face orientation\n");CHKERRQ(ierr);} 1657 for (f = 0; f < faceSize; ++f) faceVertices[f] = origVertices[faceSize-1 - f]; 1658 } else { 1659 if (debug) {ierr = PetscPrintf(comm, " Keeping initial face orientation\n");CHKERRQ(ierr);} 1660 for (f = 0; f < faceSize; ++f) faceVertices[f] = origVertices[f]; 1661 } 1662 if (posOriented) *posOriented = posOrient; 1663 PetscFunctionReturn(0); 1664 } 1665 1666 #undef __FUNCT__ 1667 #define __FUNCT__ "DMPlexGetOrientedFace" 1668 /* 1669 Given a cell and a face, as a set of vertices, 1670 return the oriented face, as a set of vertices, in faceVertices 1671 The orientation is such that the face normal points out of the cell 1672 */ 1673 PetscErrorCode DMPlexGetOrientedFace(DM dm, PetscInt cell, PetscInt faceSize, const PetscInt face[], PetscInt numCorners, PetscInt indices[], PetscInt origVertices[], PetscInt faceVertices[], PetscBool *posOriented) 1674 { 1675 const PetscInt *cone = NULL; 1676 PetscInt coneSize, v, f, v2; 1677 PetscInt oppositeVertex = -1; 1678 PetscErrorCode ierr; 1679 1680 PetscFunctionBegin; 1681 ierr = DMPlexGetConeSize(dm, cell, &coneSize);CHKERRQ(ierr); 1682 ierr = DMPlexGetCone(dm, cell, &cone);CHKERRQ(ierr); 1683 for (v = 0, v2 = 0; v < coneSize; ++v) { 1684 PetscBool found = PETSC_FALSE; 1685 1686 for (f = 0; f < faceSize; ++f) { 1687 if (face[f] == cone[v]) { 1688 found = PETSC_TRUE; break; 1689 } 1690 } 1691 if (found) { 1692 indices[v2] = v; 1693 origVertices[v2] = cone[v]; 1694 ++v2; 1695 } else { 1696 oppositeVertex = v; 1697 } 1698 } 1699 ierr = DMPlexGetFaceOrientation(dm, cell, numCorners, indices, oppositeVertex, origVertices, faceVertices, posOriented);CHKERRQ(ierr); 1700 PetscFunctionReturn(0); 1701 } 1702 1703 #undef __FUNCT__ 1704 #define __FUNCT__ "DMPlexInsertFace_Internal" 1705 /* 1706 DMPlexInsertFace_Internal - Puts a face into the mesh 1707 1708 Not collective 1709 1710 Input Parameters: 1711 + dm - The DMPlex 1712 . numFaceVertex - The number of vertices in the face 1713 . faceVertices - The vertices in the face for dm 1714 . subfaceVertices - The vertices in the face for subdm 1715 . numCorners - The number of vertices in the cell 1716 . cell - A cell in dm containing the face 1717 . subcell - A cell in subdm containing the face 1718 . firstFace - First face in the mesh 1719 - newFacePoint - Next face in the mesh 1720 1721 Output Parameters: 1722 . newFacePoint - Contains next face point number on input, updated on output 1723 1724 Level: developer 1725 */ 1726 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) 1727 { 1728 MPI_Comm comm; 1729 DM_Plex *submesh = (DM_Plex*) subdm->data; 1730 const PetscInt *faces; 1731 PetscInt numFaces, coneSize; 1732 PetscErrorCode ierr; 1733 1734 PetscFunctionBegin; 1735 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 1736 ierr = DMPlexGetConeSize(subdm, subcell, &coneSize);CHKERRQ(ierr); 1737 if (coneSize != 1) SETERRQ2(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cone size of cell %d is %d != 1", cell, coneSize); 1738 #if 0 1739 /* Cannot use this because support() has not been constructed yet */ 1740 ierr = DMPlexGetJoin(subdm, numFaceVertices, subfaceVertices, &numFaces, &faces);CHKERRQ(ierr); 1741 #else 1742 { 1743 PetscInt f; 1744 1745 numFaces = 0; 1746 ierr = DMGetWorkArray(subdm, 1, PETSC_INT, (void **) &faces);CHKERRQ(ierr); 1747 for (f = firstFace; f < *newFacePoint; ++f) { 1748 PetscInt dof, off, d; 1749 1750 ierr = PetscSectionGetDof(submesh->coneSection, f, &dof);CHKERRQ(ierr); 1751 ierr = PetscSectionGetOffset(submesh->coneSection, f, &off);CHKERRQ(ierr); 1752 /* Yes, I know this is quadratic, but I expect the sizes to be <5 */ 1753 for (d = 0; d < dof; ++d) { 1754 const PetscInt p = submesh->cones[off+d]; 1755 PetscInt v; 1756 1757 for (v = 0; v < numFaceVertices; ++v) { 1758 if (subfaceVertices[v] == p) break; 1759 } 1760 if (v == numFaceVertices) break; 1761 } 1762 if (d == dof) { 1763 numFaces = 1; 1764 ((PetscInt*) faces)[0] = f; 1765 } 1766 } 1767 } 1768 #endif 1769 if (numFaces > 1) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Vertex set had %d faces, not one", numFaces); 1770 else if (numFaces == 1) { 1771 /* Add the other cell neighbor for this face */ 1772 ierr = DMPlexSetCone(subdm, subcell, faces);CHKERRQ(ierr); 1773 } else { 1774 PetscInt *indices, *origVertices, *orientedVertices, *orientedSubVertices, v, ov; 1775 PetscBool posOriented; 1776 1777 ierr = DMGetWorkArray(subdm, 4*numFaceVertices * sizeof(PetscInt), PETSC_INT, &orientedVertices);CHKERRQ(ierr); 1778 origVertices = &orientedVertices[numFaceVertices]; 1779 indices = &orientedVertices[numFaceVertices*2]; 1780 orientedSubVertices = &orientedVertices[numFaceVertices*3]; 1781 ierr = DMPlexGetOrientedFace(dm, cell, numFaceVertices, faceVertices, numCorners, indices, origVertices, orientedVertices, &posOriented);CHKERRQ(ierr); 1782 /* TODO: I know that routine should return a permutation, not the indices */ 1783 for (v = 0; v < numFaceVertices; ++v) { 1784 const PetscInt vertex = faceVertices[v], subvertex = subfaceVertices[v]; 1785 for (ov = 0; ov < numFaceVertices; ++ov) { 1786 if (orientedVertices[ov] == vertex) { 1787 orientedSubVertices[ov] = subvertex; 1788 break; 1789 } 1790 } 1791 if (ov == numFaceVertices) SETERRQ1(comm, PETSC_ERR_PLIB, "Could not find face vertex %d in orientated set", vertex); 1792 } 1793 ierr = DMPlexSetCone(subdm, *newFacePoint, orientedSubVertices);CHKERRQ(ierr); 1794 ierr = DMPlexSetCone(subdm, subcell, newFacePoint);CHKERRQ(ierr); 1795 ierr = DMRestoreWorkArray(subdm, 4*numFaceVertices * sizeof(PetscInt), PETSC_INT, &orientedVertices);CHKERRQ(ierr); 1796 ++(*newFacePoint); 1797 } 1798 #if 0 1799 ierr = DMPlexRestoreJoin(subdm, numFaceVertices, subfaceVertices, &numFaces, &faces);CHKERRQ(ierr); 1800 #else 1801 ierr = DMRestoreWorkArray(subdm, 1, PETSC_INT, (void **) &faces);CHKERRQ(ierr); 1802 #endif 1803 PetscFunctionReturn(0); 1804 } 1805 1806 #undef __FUNCT__ 1807 #define __FUNCT__ "DMPlexCreateSubmesh_Uninterpolated" 1808 static PetscErrorCode DMPlexCreateSubmesh_Uninterpolated(DM dm, const char vertexLabelName[], PetscInt value, DM subdm) 1809 { 1810 MPI_Comm comm; 1811 DMLabel vertexLabel, subpointMap; 1812 IS subvertexIS, subcellIS; 1813 const PetscInt *subVertices, *subCells; 1814 PetscInt numSubVertices, firstSubVertex, numSubCells; 1815 PetscInt *subface, maxConeSize, numSubFaces, firstSubFace, newFacePoint, nFV; 1816 PetscInt vStart, vEnd, c, f; 1817 PetscErrorCode ierr; 1818 1819 PetscFunctionBegin; 1820 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 1821 /* Create subpointMap which marks the submesh */ 1822 ierr = DMLabelCreate("subpoint_map", &subpointMap);CHKERRQ(ierr); 1823 ierr = DMPlexSetSubpointMap(subdm, subpointMap);CHKERRQ(ierr); 1824 ierr = DMLabelDestroy(&subpointMap);CHKERRQ(ierr); 1825 ierr = DMPlexGetLabel(dm, vertexLabelName, &vertexLabel);CHKERRQ(ierr); 1826 ierr = DMPlexMarkSubmesh_Uninterpolated(dm, vertexLabel, value, subpointMap, &numSubFaces, &nFV, subdm);CHKERRQ(ierr); 1827 /* Setup chart */ 1828 ierr = DMLabelGetStratumSize(subpointMap, 0, &numSubVertices);CHKERRQ(ierr); 1829 ierr = DMLabelGetStratumSize(subpointMap, 2, &numSubCells);CHKERRQ(ierr); 1830 ierr = DMPlexSetChart(subdm, 0, numSubCells+numSubFaces+numSubVertices);CHKERRQ(ierr); 1831 ierr = DMPlexSetVTKCellHeight(subdm, 1);CHKERRQ(ierr); 1832 /* Set cone sizes */ 1833 firstSubVertex = numSubCells; 1834 firstSubFace = numSubCells+numSubVertices; 1835 newFacePoint = firstSubFace; 1836 ierr = DMLabelGetStratumIS(subpointMap, 0, &subvertexIS);CHKERRQ(ierr); 1837 if (subvertexIS) {ierr = ISGetIndices(subvertexIS, &subVertices);CHKERRQ(ierr);} 1838 ierr = DMLabelGetStratumIS(subpointMap, 2, &subcellIS);CHKERRQ(ierr); 1839 if (subcellIS) {ierr = ISGetIndices(subcellIS, &subCells);CHKERRQ(ierr);} 1840 for (c = 0; c < numSubCells; ++c) { 1841 ierr = DMPlexSetConeSize(subdm, c, 1);CHKERRQ(ierr); 1842 } 1843 for (f = firstSubFace; f < firstSubFace+numSubFaces; ++f) { 1844 ierr = DMPlexSetConeSize(subdm, f, nFV);CHKERRQ(ierr); 1845 } 1846 ierr = DMSetUp(subdm);CHKERRQ(ierr); 1847 /* Create face cones */ 1848 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 1849 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, NULL);CHKERRQ(ierr); 1850 ierr = DMGetWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);CHKERRQ(ierr); 1851 for (c = 0; c < numSubCells; ++c) { 1852 const PetscInt cell = subCells[c]; 1853 const PetscInt subcell = c; 1854 PetscInt *closure = NULL; 1855 PetscInt closureSize, cl, numCorners = 0, faceSize = 0; 1856 1857 ierr = DMPlexGetTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1858 for (cl = 0; cl < closureSize*2; cl += 2) { 1859 const PetscInt point = closure[cl]; 1860 PetscInt subVertex; 1861 1862 if ((point >= vStart) && (point < vEnd)) { 1863 ++numCorners; 1864 ierr = PetscFindInt(point, numSubVertices, subVertices, &subVertex);CHKERRQ(ierr); 1865 if (subVertex >= 0) { 1866 closure[faceSize] = point; 1867 subface[faceSize] = firstSubVertex+subVertex; 1868 ++faceSize; 1869 } 1870 } 1871 } 1872 if (faceSize > nFV) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Invalid submesh: Too many vertices %d of an element on the surface", faceSize); 1873 if (faceSize == nFV) { 1874 ierr = DMPlexInsertFace_Internal(dm, subdm, faceSize, closure, subface, numCorners, cell, subcell, firstSubFace, &newFacePoint);CHKERRQ(ierr); 1875 } 1876 ierr = DMPlexRestoreTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1877 } 1878 ierr = DMRestoreWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);CHKERRQ(ierr); 1879 ierr = DMPlexSymmetrize(subdm);CHKERRQ(ierr); 1880 ierr = DMPlexStratify(subdm);CHKERRQ(ierr); 1881 /* Build coordinates */ 1882 { 1883 PetscSection coordSection, subCoordSection; 1884 Vec coordinates, subCoordinates; 1885 PetscScalar *coords, *subCoords; 1886 PetscInt numComp, coordSize, v; 1887 1888 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1889 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 1890 ierr = DMPlexGetCoordinateSection(subdm, &subCoordSection);CHKERRQ(ierr); 1891 ierr = PetscSectionSetNumFields(subCoordSection, 1);CHKERRQ(ierr); 1892 ierr = PetscSectionGetFieldComponents(coordSection, 0, &numComp);CHKERRQ(ierr); 1893 ierr = PetscSectionSetFieldComponents(subCoordSection, 0, numComp);CHKERRQ(ierr); 1894 ierr = PetscSectionSetChart(subCoordSection, firstSubVertex, firstSubVertex+numSubVertices);CHKERRQ(ierr); 1895 for (v = 0; v < numSubVertices; ++v) { 1896 const PetscInt vertex = subVertices[v]; 1897 const PetscInt subvertex = firstSubVertex+v; 1898 PetscInt dof; 1899 1900 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 1901 ierr = PetscSectionSetDof(subCoordSection, subvertex, dof);CHKERRQ(ierr); 1902 ierr = PetscSectionSetFieldDof(subCoordSection, subvertex, 0, dof);CHKERRQ(ierr); 1903 } 1904 ierr = PetscSectionSetUp(subCoordSection);CHKERRQ(ierr); 1905 ierr = PetscSectionGetStorageSize(subCoordSection, &coordSize);CHKERRQ(ierr); 1906 ierr = VecCreate(comm, &subCoordinates);CHKERRQ(ierr); 1907 ierr = VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1908 ierr = VecSetFromOptions(subCoordinates);CHKERRQ(ierr); 1909 if (coordSize) { 1910 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1911 ierr = VecGetArray(subCoordinates, &subCoords);CHKERRQ(ierr); 1912 for (v = 0; v < numSubVertices; ++v) { 1913 const PetscInt vertex = subVertices[v]; 1914 const PetscInt subvertex = firstSubVertex+v; 1915 PetscInt dof, off, sdof, soff, d; 1916 1917 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 1918 ierr = PetscSectionGetOffset(coordSection, vertex, &off);CHKERRQ(ierr); 1919 ierr = PetscSectionGetDof(subCoordSection, subvertex, &sdof);CHKERRQ(ierr); 1920 ierr = PetscSectionGetOffset(subCoordSection, subvertex, &soff);CHKERRQ(ierr); 1921 if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof); 1922 for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d]; 1923 } 1924 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1925 ierr = VecRestoreArray(subCoordinates, &subCoords);CHKERRQ(ierr); 1926 } 1927 ierr = DMSetCoordinatesLocal(subdm, subCoordinates);CHKERRQ(ierr); 1928 ierr = VecDestroy(&subCoordinates);CHKERRQ(ierr); 1929 } 1930 /* Cleanup */ 1931 if (subvertexIS) {ierr = ISRestoreIndices(subvertexIS, &subVertices);CHKERRQ(ierr);} 1932 ierr = ISDestroy(&subvertexIS);CHKERRQ(ierr); 1933 if (subcellIS) {ierr = ISRestoreIndices(subcellIS, &subCells);CHKERRQ(ierr);} 1934 ierr = ISDestroy(&subcellIS);CHKERRQ(ierr); 1935 PetscFunctionReturn(0); 1936 } 1937 1938 #undef __FUNCT__ 1939 #define __FUNCT__ "DMPlexCreateSubmesh_Interpolated" 1940 static PetscErrorCode DMPlexCreateSubmesh_Interpolated(DM dm, const char vertexLabelName[], PetscInt value, DM subdm) 1941 { 1942 MPI_Comm comm; 1943 DMLabel subpointMap, vertexLabel; 1944 IS *subpointIS; 1945 const PetscInt **subpoints; 1946 PetscInt *numSubPoints, *firstSubPoint, *coneNew; 1947 PetscInt totSubPoints = 0, maxConeSize, dim, p, d, v; 1948 PetscErrorCode ierr; 1949 1950 PetscFunctionBegin; 1951 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 1952 /* Create subpointMap which marks the submesh */ 1953 ierr = DMLabelCreate("subpoint_map", &subpointMap);CHKERRQ(ierr); 1954 ierr = DMPlexSetSubpointMap(subdm, subpointMap);CHKERRQ(ierr); 1955 ierr = DMLabelDestroy(&subpointMap);CHKERRQ(ierr); 1956 ierr = DMPlexGetLabel(dm, vertexLabelName, &vertexLabel);CHKERRQ(ierr); 1957 ierr = DMPlexMarkSubmesh_Interpolated(dm, vertexLabel, value, subpointMap, subdm);CHKERRQ(ierr); 1958 /* Setup chart */ 1959 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1960 ierr = PetscMalloc4(dim+1,PetscInt,&numSubPoints,dim+1,PetscInt,&firstSubPoint,dim+1,IS,&subpointIS,dim+1,const PetscInt *,&subpoints);CHKERRQ(ierr); 1961 for (d = 0; d <= dim; ++d) { 1962 ierr = DMLabelGetStratumSize(subpointMap, d, &numSubPoints[d]);CHKERRQ(ierr); 1963 totSubPoints += numSubPoints[d]; 1964 } 1965 ierr = DMPlexSetChart(subdm, 0, totSubPoints);CHKERRQ(ierr); 1966 ierr = DMPlexSetVTKCellHeight(subdm, 1);CHKERRQ(ierr); 1967 /* Set cone sizes */ 1968 firstSubPoint[dim] = 0; 1969 firstSubPoint[0] = firstSubPoint[dim] + numSubPoints[dim]; 1970 if (dim > 1) {firstSubPoint[dim-1] = firstSubPoint[0] + numSubPoints[0];} 1971 if (dim > 2) {firstSubPoint[dim-2] = firstSubPoint[dim-1] + numSubPoints[dim-1];} 1972 for (d = 0; d <= dim; ++d) { 1973 ierr = DMLabelGetStratumIS(subpointMap, d, &subpointIS[d]);CHKERRQ(ierr); 1974 ierr = ISGetIndices(subpointIS[d], &subpoints[d]);CHKERRQ(ierr); 1975 } 1976 for (d = 0; d <= dim; ++d) { 1977 for (p = 0; p < numSubPoints[d]; ++p) { 1978 const PetscInt point = subpoints[d][p]; 1979 const PetscInt subpoint = firstSubPoint[d] + p; 1980 const PetscInt *cone; 1981 PetscInt coneSize, coneSizeNew, c, val; 1982 1983 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 1984 ierr = DMPlexSetConeSize(subdm, subpoint, coneSize);CHKERRQ(ierr); 1985 if (d == dim) { 1986 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 1987 for (c = 0, coneSizeNew = 0; c < coneSize; ++c) { 1988 ierr = DMLabelGetValue(subpointMap, cone[c], &val);CHKERRQ(ierr); 1989 if (val >= 0) coneSizeNew++; 1990 } 1991 ierr = DMPlexSetConeSize(subdm, subpoint, coneSizeNew);CHKERRQ(ierr); 1992 } 1993 } 1994 } 1995 ierr = DMSetUp(subdm);CHKERRQ(ierr); 1996 /* Set cones */ 1997 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, NULL);CHKERRQ(ierr); 1998 ierr = PetscMalloc(maxConeSize * sizeof(PetscInt), &coneNew);CHKERRQ(ierr); 1999 for (d = 0; d <= dim; ++d) { 2000 for (p = 0; p < numSubPoints[d]; ++p) { 2001 const PetscInt point = subpoints[d][p]; 2002 const PetscInt subpoint = firstSubPoint[d] + p; 2003 const PetscInt *cone; 2004 PetscInt coneSize, subconeSize, coneSizeNew, c, subc; 2005 2006 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 2007 ierr = DMPlexGetConeSize(subdm, subpoint, &subconeSize);CHKERRQ(ierr); 2008 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 2009 for (c = 0, coneSizeNew = 0; c < coneSize; ++c) { 2010 ierr = PetscFindInt(cone[c], numSubPoints[d-1], subpoints[d-1], &subc);CHKERRQ(ierr); 2011 if (subc >= 0) coneNew[coneSizeNew++] = firstSubPoint[d-1] + subc; 2012 } 2013 if (coneSizeNew != subconeSize) SETERRQ2(comm, PETSC_ERR_PLIB, "Number of cone points located %d does not match subcone size %d", coneSizeNew, subconeSize); 2014 ierr = DMPlexSetCone(subdm, subpoint, coneNew);CHKERRQ(ierr); 2015 } 2016 } 2017 ierr = PetscFree(coneNew);CHKERRQ(ierr); 2018 ierr = DMPlexSymmetrize(subdm);CHKERRQ(ierr); 2019 ierr = DMPlexStratify(subdm);CHKERRQ(ierr); 2020 /* Build coordinates */ 2021 { 2022 PetscSection coordSection, subCoordSection; 2023 Vec coordinates, subCoordinates; 2024 PetscScalar *coords, *subCoords; 2025 PetscInt numComp, coordSize; 2026 2027 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2028 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 2029 ierr = DMPlexGetCoordinateSection(subdm, &subCoordSection);CHKERRQ(ierr); 2030 ierr = PetscSectionSetNumFields(subCoordSection, 1);CHKERRQ(ierr); 2031 ierr = PetscSectionGetFieldComponents(coordSection, 0, &numComp);CHKERRQ(ierr); 2032 ierr = PetscSectionSetFieldComponents(subCoordSection, 0, numComp);CHKERRQ(ierr); 2033 ierr = PetscSectionSetChart(subCoordSection, firstSubPoint[0], firstSubPoint[0]+numSubPoints[0]);CHKERRQ(ierr); 2034 for (v = 0; v < numSubPoints[0]; ++v) { 2035 const PetscInt vertex = subpoints[0][v]; 2036 const PetscInt subvertex = firstSubPoint[0]+v; 2037 PetscInt dof; 2038 2039 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2040 ierr = PetscSectionSetDof(subCoordSection, subvertex, dof);CHKERRQ(ierr); 2041 ierr = PetscSectionSetFieldDof(subCoordSection, subvertex, 0, dof);CHKERRQ(ierr); 2042 } 2043 ierr = PetscSectionSetUp(subCoordSection);CHKERRQ(ierr); 2044 ierr = PetscSectionGetStorageSize(subCoordSection, &coordSize);CHKERRQ(ierr); 2045 ierr = VecCreate(comm, &subCoordinates);CHKERRQ(ierr); 2046 ierr = VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2047 ierr = VecSetFromOptions(subCoordinates);CHKERRQ(ierr); 2048 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2049 ierr = VecGetArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2050 for (v = 0; v < numSubPoints[0]; ++v) { 2051 const PetscInt vertex = subpoints[0][v]; 2052 const PetscInt subvertex = firstSubPoint[0]+v; 2053 PetscInt dof, off, sdof, soff, d; 2054 2055 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2056 ierr = PetscSectionGetOffset(coordSection, vertex, &off);CHKERRQ(ierr); 2057 ierr = PetscSectionGetDof(subCoordSection, subvertex, &sdof);CHKERRQ(ierr); 2058 ierr = PetscSectionGetOffset(subCoordSection, subvertex, &soff);CHKERRQ(ierr); 2059 if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof); 2060 for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d]; 2061 } 2062 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2063 ierr = VecRestoreArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2064 ierr = DMSetCoordinatesLocal(subdm, subCoordinates);CHKERRQ(ierr); 2065 ierr = VecDestroy(&subCoordinates);CHKERRQ(ierr); 2066 } 2067 /* Cleanup */ 2068 for (d = 0; d <= dim; ++d) { 2069 ierr = ISRestoreIndices(subpointIS[d], &subpoints[d]);CHKERRQ(ierr); 2070 ierr = ISDestroy(&subpointIS[d]);CHKERRQ(ierr); 2071 } 2072 ierr = PetscFree4(numSubPoints,firstSubPoint,subpointIS,subpoints);CHKERRQ(ierr); 2073 PetscFunctionReturn(0); 2074 } 2075 2076 #undef __FUNCT__ 2077 #define __FUNCT__ "DMPlexCreateSubmesh" 2078 /*@C 2079 DMPlexCreateSubmesh - Extract a hypersurface from the mesh using vertices defined by a label 2080 2081 Input Parameters: 2082 + dm - The original mesh 2083 . vertexLabel - The DMLabel marking vertices contained in the surface 2084 - value - The label value to use 2085 2086 Output Parameter: 2087 . subdm - The surface mesh 2088 2089 Note: This function produces a DMLabel mapping original points in the submesh to their depth. This can be obtained using DMPlexGetSubpointMap(). 2090 2091 Level: developer 2092 2093 .seealso: DMPlexGetSubpointMap(), DMPlexGetLabel(), DMLabelSetValue() 2094 @*/ 2095 PetscErrorCode DMPlexCreateSubmesh(DM dm, const char vertexLabel[], PetscInt value, DM *subdm) 2096 { 2097 PetscInt dim, depth; 2098 PetscErrorCode ierr; 2099 2100 PetscFunctionBegin; 2101 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2102 PetscValidCharPointer(vertexLabel, 2); 2103 PetscValidPointer(subdm, 3); 2104 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 2105 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 2106 ierr = DMCreate(PetscObjectComm((PetscObject)dm), subdm);CHKERRQ(ierr); 2107 ierr = DMSetType(*subdm, DMPLEX);CHKERRQ(ierr); 2108 ierr = DMPlexSetDimension(*subdm, dim-1);CHKERRQ(ierr); 2109 if (depth == dim) { 2110 ierr = DMPlexCreateSubmesh_Interpolated(dm, vertexLabel, value, *subdm);CHKERRQ(ierr); 2111 } else { 2112 ierr = DMPlexCreateSubmesh_Uninterpolated(dm, vertexLabel, value, *subdm);CHKERRQ(ierr); 2113 } 2114 PetscFunctionReturn(0); 2115 } 2116 2117 #undef __FUNCT__ 2118 #define __FUNCT__ "DMPlexCreateCohesiveSubmesh_Uninterpolated" 2119 static PetscErrorCode DMPlexCreateCohesiveSubmesh_Uninterpolated(DM dm, PetscBool hasLagrange, DM subdm) 2120 { 2121 MPI_Comm comm; 2122 DMLabel subpointMap; 2123 IS subvertexIS; 2124 const PetscInt *subVertices; 2125 PetscInt numSubVertices, firstSubVertex, numSubCells, *subCells; 2126 PetscInt *subface, maxConeSize, numSubFaces, firstSubFace, newFacePoint, nFV; 2127 PetscInt cMax, c, f; 2128 PetscErrorCode ierr; 2129 2130 PetscFunctionBegin; 2131 ierr = PetscObjectGetComm((PetscObject)dm, &comm);CHKERRQ(ierr); 2132 /* Create subpointMap which marks the submesh */ 2133 ierr = DMLabelCreate("subpoint_map", &subpointMap);CHKERRQ(ierr); 2134 ierr = DMPlexSetSubpointMap(subdm, subpointMap);CHKERRQ(ierr); 2135 ierr = DMLabelDestroy(&subpointMap);CHKERRQ(ierr); 2136 ierr = DMPlexMarkCohesiveSubmesh_Uninterpolated(dm, hasLagrange, subpointMap, &numSubFaces, &nFV, &subCells, subdm);CHKERRQ(ierr); 2137 /* Setup chart */ 2138 ierr = DMLabelGetStratumSize(subpointMap, 0, &numSubVertices);CHKERRQ(ierr); 2139 ierr = DMLabelGetStratumSize(subpointMap, 2, &numSubCells);CHKERRQ(ierr); 2140 ierr = DMPlexSetChart(subdm, 0, numSubCells+numSubFaces+numSubVertices);CHKERRQ(ierr); 2141 ierr = DMPlexSetVTKCellHeight(subdm, 1);CHKERRQ(ierr); 2142 /* Set cone sizes */ 2143 firstSubVertex = numSubCells; 2144 firstSubFace = numSubCells+numSubVertices; 2145 newFacePoint = firstSubFace; 2146 ierr = DMLabelGetStratumIS(subpointMap, 0, &subvertexIS);CHKERRQ(ierr); 2147 if (subvertexIS) {ierr = ISGetIndices(subvertexIS, &subVertices);CHKERRQ(ierr);} 2148 for (c = 0; c < numSubCells; ++c) { 2149 ierr = DMPlexSetConeSize(subdm, c, 1);CHKERRQ(ierr); 2150 } 2151 for (f = firstSubFace; f < firstSubFace+numSubFaces; ++f) { 2152 ierr = DMPlexSetConeSize(subdm, f, nFV);CHKERRQ(ierr); 2153 } 2154 ierr = DMSetUp(subdm);CHKERRQ(ierr); 2155 /* Create face cones */ 2156 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, NULL);CHKERRQ(ierr); 2157 ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); 2158 ierr = DMGetWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);CHKERRQ(ierr); 2159 for (c = 0; c < numSubCells; ++c) { 2160 const PetscInt cell = subCells[c]; 2161 const PetscInt subcell = c; 2162 const PetscInt *cone, *cells; 2163 PetscInt numCells, subVertex, p, v; 2164 2165 if (cell < cMax) continue; 2166 ierr = DMPlexGetCone(dm, cell, &cone);CHKERRQ(ierr); 2167 for (v = 0; v < nFV; ++v) { 2168 ierr = PetscFindInt(cone[v], numSubVertices, subVertices, &subVertex);CHKERRQ(ierr); 2169 subface[v] = firstSubVertex+subVertex; 2170 } 2171 ierr = DMPlexSetCone(subdm, newFacePoint, subface);CHKERRQ(ierr); 2172 ierr = DMPlexSetCone(subdm, subcell, &newFacePoint);CHKERRQ(ierr); 2173 ierr = DMPlexGetJoin(dm, nFV, cone, &numCells, &cells);CHKERRQ(ierr); 2174 if (numCells != 2) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive cells should separate two cells"); 2175 for (p = 0; p < numCells; ++p) { 2176 PetscInt negsubcell; 2177 2178 if (cells[p] >= cMax) continue; 2179 /* I know this is a crap search */ 2180 for (negsubcell = 0; negsubcell < numSubCells; ++negsubcell) { 2181 if (subCells[negsubcell] == cells[p]) break; 2182 } 2183 if (negsubcell == numSubCells) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not find negative face neighbor for cohesive cell %d", cell); 2184 ierr = DMPlexSetCone(subdm, negsubcell, &newFacePoint);CHKERRQ(ierr); 2185 } 2186 ierr = DMPlexRestoreJoin(dm, nFV, cone, &numCells, &cells);CHKERRQ(ierr); 2187 ++newFacePoint; 2188 } 2189 ierr = DMRestoreWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);CHKERRQ(ierr); 2190 ierr = DMPlexSymmetrize(subdm);CHKERRQ(ierr); 2191 ierr = DMPlexStratify(subdm);CHKERRQ(ierr); 2192 /* Build coordinates */ 2193 { 2194 PetscSection coordSection, subCoordSection; 2195 Vec coordinates, subCoordinates; 2196 PetscScalar *coords, *subCoords; 2197 PetscInt numComp, coordSize, v; 2198 2199 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2200 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 2201 ierr = DMPlexGetCoordinateSection(subdm, &subCoordSection);CHKERRQ(ierr); 2202 ierr = PetscSectionSetNumFields(subCoordSection, 1);CHKERRQ(ierr); 2203 ierr = PetscSectionGetFieldComponents(coordSection, 0, &numComp);CHKERRQ(ierr); 2204 ierr = PetscSectionSetFieldComponents(subCoordSection, 0, numComp);CHKERRQ(ierr); 2205 ierr = PetscSectionSetChart(subCoordSection, firstSubVertex, firstSubVertex+numSubVertices);CHKERRQ(ierr); 2206 for (v = 0; v < numSubVertices; ++v) { 2207 const PetscInt vertex = subVertices[v]; 2208 const PetscInt subvertex = firstSubVertex+v; 2209 PetscInt dof; 2210 2211 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2212 ierr = PetscSectionSetDof(subCoordSection, subvertex, dof);CHKERRQ(ierr); 2213 ierr = PetscSectionSetFieldDof(subCoordSection, subvertex, 0, dof);CHKERRQ(ierr); 2214 } 2215 ierr = PetscSectionSetUp(subCoordSection);CHKERRQ(ierr); 2216 ierr = PetscSectionGetStorageSize(subCoordSection, &coordSize);CHKERRQ(ierr); 2217 ierr = VecCreate(comm, &subCoordinates);CHKERRQ(ierr); 2218 if (coordSize) { 2219 ierr = VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2220 ierr = VecSetFromOptions(subCoordinates);CHKERRQ(ierr); 2221 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2222 ierr = VecGetArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2223 for (v = 0; v < numSubVertices; ++v) { 2224 const PetscInt vertex = subVertices[v]; 2225 const PetscInt subvertex = firstSubVertex+v; 2226 PetscInt dof, off, sdof, soff, d; 2227 2228 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2229 ierr = PetscSectionGetOffset(coordSection, vertex, &off);CHKERRQ(ierr); 2230 ierr = PetscSectionGetDof(subCoordSection, subvertex, &sdof);CHKERRQ(ierr); 2231 ierr = PetscSectionGetOffset(subCoordSection, subvertex, &soff);CHKERRQ(ierr); 2232 if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof); 2233 for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d]; 2234 } 2235 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2236 ierr = VecRestoreArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2237 } 2238 ierr = DMSetCoordinatesLocal(subdm, subCoordinates);CHKERRQ(ierr); 2239 ierr = VecDestroy(&subCoordinates);CHKERRQ(ierr); 2240 } 2241 /* Cleanup */ 2242 if (subvertexIS) {ierr = ISRestoreIndices(subvertexIS, &subVertices);CHKERRQ(ierr);} 2243 ierr = ISDestroy(&subvertexIS);CHKERRQ(ierr); 2244 ierr = PetscFree(subCells);CHKERRQ(ierr); 2245 PetscFunctionReturn(0); 2246 } 2247 2248 #undef __FUNCT__ 2249 #define __FUNCT__ "DMPlexCreateCohesiveSubmesh_Interpolated" 2250 static PetscErrorCode DMPlexCreateCohesiveSubmesh_Interpolated(DM dm, PetscBool hasLagrange, DM subdm) 2251 { 2252 MPI_Comm comm; 2253 DMLabel subpointMap; 2254 IS *subpointIS; 2255 const PetscInt **subpoints; 2256 PetscInt *numSubPoints, *firstSubPoint, *coneNew; 2257 PetscInt totSubPoints = 0, maxConeSize, dim, p, d, v; 2258 PetscErrorCode ierr; 2259 2260 PetscFunctionBegin; 2261 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 2262 /* Create subpointMap which marks the submesh */ 2263 ierr = DMLabelCreate("subpoint_map", &subpointMap);CHKERRQ(ierr); 2264 ierr = DMPlexSetSubpointMap(subdm, subpointMap);CHKERRQ(ierr); 2265 ierr = DMLabelDestroy(&subpointMap);CHKERRQ(ierr); 2266 ierr = DMPlexMarkCohesiveSubmesh_Interpolated(dm, hasLagrange, subpointMap, subdm);CHKERRQ(ierr); 2267 /* Setup chart */ 2268 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 2269 ierr = PetscMalloc4(dim+1,PetscInt,&numSubPoints,dim+1,PetscInt,&firstSubPoint,dim+1,IS,&subpointIS,dim+1,const PetscInt *,&subpoints);CHKERRQ(ierr); 2270 for (d = 0; d <= dim; ++d) { 2271 ierr = DMLabelGetStratumSize(subpointMap, d, &numSubPoints[d]);CHKERRQ(ierr); 2272 totSubPoints += numSubPoints[d]; 2273 } 2274 ierr = DMPlexSetChart(subdm, 0, totSubPoints);CHKERRQ(ierr); 2275 ierr = DMPlexSetVTKCellHeight(subdm, 1);CHKERRQ(ierr); 2276 /* Set cone sizes */ 2277 firstSubPoint[dim] = 0; 2278 firstSubPoint[0] = firstSubPoint[dim] + numSubPoints[dim]; 2279 if (dim > 1) {firstSubPoint[dim-1] = firstSubPoint[0] + numSubPoints[0];} 2280 if (dim > 2) {firstSubPoint[dim-2] = firstSubPoint[dim-1] + numSubPoints[dim-1];} 2281 for (d = 0; d <= dim; ++d) { 2282 ierr = DMLabelGetStratumIS(subpointMap, d, &subpointIS[d]);CHKERRQ(ierr); 2283 ierr = ISGetIndices(subpointIS[d], &subpoints[d]);CHKERRQ(ierr); 2284 } 2285 for (d = 0; d <= dim; ++d) { 2286 for (p = 0; p < numSubPoints[d]; ++p) { 2287 const PetscInt point = subpoints[d][p]; 2288 const PetscInt subpoint = firstSubPoint[d] + p; 2289 const PetscInt *cone; 2290 PetscInt coneSize, coneSizeNew, c, val; 2291 2292 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 2293 ierr = DMPlexSetConeSize(subdm, subpoint, coneSize);CHKERRQ(ierr); 2294 if (d == dim) { 2295 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 2296 for (c = 0, coneSizeNew = 0; c < coneSize; ++c) { 2297 ierr = DMLabelGetValue(subpointMap, cone[c], &val);CHKERRQ(ierr); 2298 if (val >= 0) coneSizeNew++; 2299 } 2300 ierr = DMPlexSetConeSize(subdm, subpoint, coneSizeNew);CHKERRQ(ierr); 2301 } 2302 } 2303 } 2304 ierr = DMSetUp(subdm);CHKERRQ(ierr); 2305 /* Set cones */ 2306 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, NULL);CHKERRQ(ierr); 2307 ierr = PetscMalloc(maxConeSize * sizeof(PetscInt), &coneNew);CHKERRQ(ierr); 2308 for (d = 0; d <= dim; ++d) { 2309 for (p = 0; p < numSubPoints[d]; ++p) { 2310 const PetscInt point = subpoints[d][p]; 2311 const PetscInt subpoint = firstSubPoint[d] + p; 2312 const PetscInt *cone; 2313 PetscInt coneSize, subconeSize, coneSizeNew, c, subc; 2314 2315 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 2316 ierr = DMPlexGetConeSize(subdm, subpoint, &subconeSize);CHKERRQ(ierr); 2317 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 2318 for (c = 0, coneSizeNew = 0; c < coneSize; ++c) { 2319 ierr = PetscFindInt(cone[c], numSubPoints[d-1], subpoints[d-1], &subc);CHKERRQ(ierr); 2320 if (subc >= 0) coneNew[coneSizeNew++] = firstSubPoint[d-1] + subc; 2321 } 2322 if (coneSizeNew != subconeSize) SETERRQ2(comm, PETSC_ERR_PLIB, "Number of cone points located %d does not match subcone size %d", coneSizeNew, subconeSize); 2323 ierr = DMPlexSetCone(subdm, subpoint, coneNew);CHKERRQ(ierr); 2324 } 2325 } 2326 ierr = PetscFree(coneNew);CHKERRQ(ierr); 2327 ierr = DMPlexSymmetrize(subdm);CHKERRQ(ierr); 2328 ierr = DMPlexStratify(subdm);CHKERRQ(ierr); 2329 /* Build coordinates */ 2330 { 2331 PetscSection coordSection, subCoordSection; 2332 Vec coordinates, subCoordinates; 2333 PetscScalar *coords, *subCoords; 2334 PetscInt numComp, coordSize; 2335 2336 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2337 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 2338 ierr = DMPlexGetCoordinateSection(subdm, &subCoordSection);CHKERRQ(ierr); 2339 ierr = PetscSectionSetNumFields(subCoordSection, 1);CHKERRQ(ierr); 2340 ierr = PetscSectionGetFieldComponents(coordSection, 0, &numComp);CHKERRQ(ierr); 2341 ierr = PetscSectionSetFieldComponents(subCoordSection, 0, numComp);CHKERRQ(ierr); 2342 ierr = PetscSectionSetChart(subCoordSection, firstSubPoint[0], firstSubPoint[0]+numSubPoints[0]);CHKERRQ(ierr); 2343 for (v = 0; v < numSubPoints[0]; ++v) { 2344 const PetscInt vertex = subpoints[0][v]; 2345 const PetscInt subvertex = firstSubPoint[0]+v; 2346 PetscInt dof; 2347 2348 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2349 ierr = PetscSectionSetDof(subCoordSection, subvertex, dof);CHKERRQ(ierr); 2350 ierr = PetscSectionSetFieldDof(subCoordSection, subvertex, 0, dof);CHKERRQ(ierr); 2351 } 2352 ierr = PetscSectionSetUp(subCoordSection);CHKERRQ(ierr); 2353 ierr = PetscSectionGetStorageSize(subCoordSection, &coordSize);CHKERRQ(ierr); 2354 ierr = VecCreate(comm, &subCoordinates);CHKERRQ(ierr); 2355 ierr = VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2356 ierr = VecSetFromOptions(subCoordinates);CHKERRQ(ierr); 2357 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2358 ierr = VecGetArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2359 for (v = 0; v < numSubPoints[0]; ++v) { 2360 const PetscInt vertex = subpoints[0][v]; 2361 const PetscInt subvertex = firstSubPoint[0]+v; 2362 PetscInt dof, off, sdof, soff, d; 2363 2364 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2365 ierr = PetscSectionGetOffset(coordSection, vertex, &off);CHKERRQ(ierr); 2366 ierr = PetscSectionGetDof(subCoordSection, subvertex, &sdof);CHKERRQ(ierr); 2367 ierr = PetscSectionGetOffset(subCoordSection, subvertex, &soff);CHKERRQ(ierr); 2368 if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof); 2369 for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d]; 2370 } 2371 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2372 ierr = VecRestoreArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2373 ierr = DMSetCoordinatesLocal(subdm, subCoordinates);CHKERRQ(ierr); 2374 ierr = VecDestroy(&subCoordinates);CHKERRQ(ierr); 2375 } 2376 /* Cleanup */ 2377 for (d = 0; d <= dim; ++d) { 2378 ierr = ISRestoreIndices(subpointIS[d], &subpoints[d]);CHKERRQ(ierr); 2379 ierr = ISDestroy(&subpointIS[d]);CHKERRQ(ierr); 2380 } 2381 ierr = PetscFree4(numSubPoints,firstSubPoint,subpointIS,subpoints);CHKERRQ(ierr); 2382 PetscFunctionReturn(0); 2383 } 2384 2385 #undef __FUNCT__ 2386 #define __FUNCT__ "DMPlexCreateCohesiveSubmesh" 2387 /* 2388 DMPlexCreateCohesiveSubmesh - Extract from a mesh with cohesive cells the hypersurface defined by one face of the cells. 2389 2390 Input Parameters: 2391 + dm - The original mesh 2392 - hasLagrange - The mesh has Lagrange unknowns in the cohesive cells 2393 2394 Output Parameter: 2395 . subdm - The surface mesh 2396 2397 Note: This function produces a DMLabel mapping original points in the submesh to their depth. This can be obtained using DMPlexGetSubpointMap(). 2398 2399 Level: developer 2400 2401 .seealso: DMPlexGetSubpointMap(), DMPlexCreateSubmesh() 2402 */ 2403 PetscErrorCode DMPlexCreateCohesiveSubmesh(DM dm, PetscBool hasLagrange, DM *subdm) 2404 { 2405 PetscInt dim, depth; 2406 PetscErrorCode ierr; 2407 2408 PetscFunctionBegin; 2409 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2410 PetscValidPointer(subdm, 3); 2411 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 2412 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 2413 ierr = DMCreate(PetscObjectComm((PetscObject)dm), subdm);CHKERRQ(ierr); 2414 ierr = DMSetType(*subdm, DMPLEX);CHKERRQ(ierr); 2415 ierr = DMPlexSetDimension(*subdm, dim-1);CHKERRQ(ierr); 2416 if (depth == dim) { 2417 ierr = DMPlexCreateCohesiveSubmesh_Interpolated(dm, hasLagrange, *subdm);CHKERRQ(ierr); 2418 } else { 2419 ierr = DMPlexCreateCohesiveSubmesh_Uninterpolated(dm, hasLagrange, *subdm);CHKERRQ(ierr); 2420 } 2421 PetscFunctionReturn(0); 2422 } 2423 2424 #undef __FUNCT__ 2425 #define __FUNCT__ "DMPlexGetSubpointMap" 2426 /*@ 2427 DMPlexGetSubpointMap - Returns a DMLabel with point dimension as values 2428 2429 Input Parameter: 2430 . dm - The submesh DM 2431 2432 Output Parameter: 2433 . subpointMap - The DMLabel of all the points from the original mesh in this submesh, or NULL if this is not a submesh 2434 2435 Level: developer 2436 2437 .seealso: DMPlexCreateSubmesh(), DMPlexCreateSubpointIS() 2438 @*/ 2439 PetscErrorCode DMPlexGetSubpointMap(DM dm, DMLabel *subpointMap) 2440 { 2441 DM_Plex *mesh = (DM_Plex*) dm->data; 2442 2443 PetscFunctionBegin; 2444 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2445 PetscValidPointer(subpointMap, 2); 2446 *subpointMap = mesh->subpointMap; 2447 PetscFunctionReturn(0); 2448 } 2449 2450 #undef __FUNCT__ 2451 #define __FUNCT__ "DMPlexSetSubpointMap" 2452 /* Note: Should normally not be called by the user, since it is set in DMPlexCreateSubmesh() */ 2453 PetscErrorCode DMPlexSetSubpointMap(DM dm, DMLabel subpointMap) 2454 { 2455 DM_Plex *mesh = (DM_Plex *) dm->data; 2456 DMLabel tmp; 2457 PetscErrorCode ierr; 2458 2459 PetscFunctionBegin; 2460 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2461 tmp = mesh->subpointMap; 2462 mesh->subpointMap = subpointMap; 2463 ++mesh->subpointMap->refct; 2464 ierr = DMLabelDestroy(&tmp);CHKERRQ(ierr); 2465 PetscFunctionReturn(0); 2466 } 2467 2468 #undef __FUNCT__ 2469 #define __FUNCT__ "DMPlexCreateSubpointIS" 2470 /*@ 2471 DMPlexCreateSubpointIS - Creates an IS covering the entire subdm chart with the original points as data 2472 2473 Input Parameter: 2474 . dm - The submesh DM 2475 2476 Output Parameter: 2477 . subpointIS - The IS of all the points from the original mesh in this submesh, or NULL if this is not a submesh 2478 2479 Note: This is IS is guaranteed to be sorted by the construction of the submesh 2480 2481 Level: developer 2482 2483 .seealso: DMPlexCreateSubmesh(), DMPlexGetSubpointMap() 2484 @*/ 2485 PetscErrorCode DMPlexCreateSubpointIS(DM dm, IS *subpointIS) 2486 { 2487 MPI_Comm comm; 2488 DMLabel subpointMap; 2489 IS is; 2490 const PetscInt *opoints; 2491 PetscInt *points, *depths; 2492 PetscInt depth, depStart, depEnd, d, pStart, pEnd, p, n, off; 2493 PetscErrorCode ierr; 2494 2495 PetscFunctionBegin; 2496 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2497 PetscValidPointer(subpointIS, 2); 2498 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 2499 *subpointIS = NULL; 2500 ierr = DMPlexGetSubpointMap(dm, &subpointMap);CHKERRQ(ierr); 2501 if (subpointMap) { 2502 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 2503 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 2504 if (pStart) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Submeshes must start the point numbering at 0, not %d", pStart); 2505 ierr = DMGetWorkArray(dm, depth+1, PETSC_INT, &depths);CHKERRQ(ierr); 2506 depths[0] = depth; 2507 depths[1] = 0; 2508 for(d = 2; d <= depth; ++d) {depths[d] = depth+1 - d;} 2509 ierr = PetscMalloc(pEnd * sizeof(PetscInt), &points);CHKERRQ(ierr); 2510 for(d = 0, off = 0; d <= depth; ++d) { 2511 const PetscInt dep = depths[d]; 2512 2513 ierr = DMPlexGetDepthStratum(dm, dep, &depStart, &depEnd);CHKERRQ(ierr); 2514 ierr = DMLabelGetStratumSize(subpointMap, dep, &n);CHKERRQ(ierr); 2515 if (((d < 2) && (depth > 1)) || (d == 1)) { /* Only check vertices and cells for now since the map is broken for others */ 2516 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); 2517 } else { 2518 if (!n) { 2519 if (d == 0) { 2520 /* Missing cells */ 2521 for(p = 0; p < depEnd-depStart; ++p, ++off) points[off] = -1; 2522 } else { 2523 /* Missing faces */ 2524 for(p = 0; p < depEnd-depStart; ++p, ++off) points[off] = PETSC_MAX_INT; 2525 } 2526 } 2527 } 2528 if (n) { 2529 ierr = DMLabelGetStratumIS(subpointMap, dep, &is);CHKERRQ(ierr); 2530 ierr = ISGetIndices(is, &opoints);CHKERRQ(ierr); 2531 for(p = 0; p < n; ++p, ++off) points[off] = opoints[p]; 2532 ierr = ISRestoreIndices(is, &opoints);CHKERRQ(ierr); 2533 ierr = ISDestroy(&is);CHKERRQ(ierr); 2534 } 2535 } 2536 ierr = DMRestoreWorkArray(dm, depth+1, PETSC_INT, &depths);CHKERRQ(ierr); 2537 if (off != pEnd) SETERRQ2(comm, PETSC_ERR_ARG_WRONG, "The number of mapped submesh points %d should be %d", off, pEnd); 2538 ierr = ISCreateGeneral(comm, pEnd, points, PETSC_OWN_POINTER, subpointIS);CHKERRQ(ierr); 2539 } 2540 PetscFunctionReturn(0); 2541 } 2542