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, *coneONew, *supportNew; 544 PetscInt shift = 100, depth = 0, dep, dim, d, numSP = 0, sp, maxConeSize, maxSupportSize, numLabels, vStart, vEnd, pEnd, p, v; 545 PetscErrorCode ierr; 546 547 PetscFunctionBegin; 548 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 549 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 550 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 551 /* Count split points and add cohesive cells */ 552 if (label) { 553 ierr = DMLabelGetValueIS(label, &valueIS);CHKERRQ(ierr); 554 ierr = ISGetLocalSize(valueIS, &numSP);CHKERRQ(ierr); 555 ierr = ISGetIndices(valueIS, &values);CHKERRQ(ierr); 556 } 557 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 558 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize);CHKERRQ(ierr); 559 ierr = PetscMalloc6(depth+1,PetscInt,&depthShift,depth+1,PetscInt,&depthOffset,depth+1,PetscInt,&pMaxNew,maxConeSize*3,PetscInt,&coneNew,maxConeSize*3,PetscInt,&coneONew,maxSupportSize,PetscInt,&supportNew);CHKERRQ(ierr); 560 ierr = PetscMalloc3(depth+1,IS,&pointIS,depth+1,PetscInt,&numSplitPoints,depth+1,const PetscInt*,&splitPoints);CHKERRQ(ierr); 561 ierr = PetscMemzero(depthShift, (depth+1) * sizeof(PetscInt));CHKERRQ(ierr); 562 for (d = 0; d <= depth; ++d) { 563 ierr = DMPlexGetDepthStratum(dm, d, NULL, &pMaxNew[d]);CHKERRQ(ierr); 564 numSplitPoints[d] = 0; 565 splitPoints[d] = NULL; 566 pointIS[d] = NULL; 567 } 568 for (sp = 0; sp < numSP; ++sp) { 569 const PetscInt dep = values[sp]; 570 571 if ((dep < 0) || (dep > depth)) continue; 572 ierr = DMLabelGetStratumSize(label, dep, &depthShift[dep]);CHKERRQ(ierr); 573 ierr = DMLabelGetStratumIS(label, dep, &pointIS[dep]);CHKERRQ(ierr); 574 if (pointIS[dep]) { 575 ierr = ISGetLocalSize(pointIS[dep], &numSplitPoints[dep]);CHKERRQ(ierr); 576 ierr = ISGetIndices(pointIS[dep], &splitPoints[dep]);CHKERRQ(ierr); 577 } 578 } 579 if (depth >= 0) { 580 /* Calculate number of additional points */ 581 depthShift[depth] = depthShift[depth-1]; /* There is a cohesive cell for every split face */ 582 depthShift[1] += depthShift[0]; /* There is a cohesive edge for every split vertex */ 583 /* Calculate hybrid bound for each dimension */ 584 pMaxNew[0] += depthShift[depth]; 585 if (depth > 1) pMaxNew[dim-1] += depthShift[depth] + depthShift[0]; 586 if (depth > 2) pMaxNew[1] += depthShift[depth] + depthShift[0] + depthShift[dim-1]; 587 588 /* Calculate point offset for each dimension */ 589 depthOffset[depth] = 0; 590 depthOffset[0] = depthOffset[depth] + depthShift[depth]; 591 if (depth > 1) depthOffset[dim-1] = depthOffset[0] + depthShift[0]; 592 if (depth > 2) depthOffset[1] = depthOffset[dim-1] + depthShift[dim-1]; 593 } 594 ierr = DMPlexShiftSizes_Internal(dm, depthShift, sdm);CHKERRQ(ierr); 595 /* Step 3: Set cone/support sizes for new points */ 596 for (dep = 0; dep <= depth; ++dep) { 597 for (p = 0; p < numSplitPoints[dep]; ++p) { 598 const PetscInt oldp = splitPoints[dep][p]; 599 const PetscInt newp = depthOffset[dep] + oldp; 600 const PetscInt splitp = pMaxNew[dep] + p; 601 const PetscInt *support; 602 PetscInt coneSize, supportSize, q, e; 603 604 ierr = DMPlexGetConeSize(dm, oldp, &coneSize);CHKERRQ(ierr); 605 ierr = DMPlexSetConeSize(sdm, splitp, coneSize);CHKERRQ(ierr); 606 ierr = DMPlexGetSupportSize(dm, oldp, &supportSize);CHKERRQ(ierr); 607 ierr = DMPlexSetSupportSize(sdm, splitp, supportSize);CHKERRQ(ierr); 608 if (dep == depth-1) { 609 const PetscInt ccell = pMaxNew[depth] + p; 610 /* Add cohesive cells, they are prisms */ 611 ierr = DMPlexSetConeSize(sdm, ccell, 2 + coneSize);CHKERRQ(ierr); 612 } else if (dep == 0) { 613 const PetscInt cedge = pMaxNew[1] + (depthShift[1] - depthShift[0]) + p; 614 615 ierr = DMPlexGetSupport(dm, oldp, &support);CHKERRQ(ierr); 616 /* Split old vertex: Edges in old split faces and new cohesive edge */ 617 for (e = 0, q = 0; e < supportSize; ++e) { 618 PetscInt val; 619 620 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 621 if ((val == 1) || (val == (shift + 1))) ++q; 622 } 623 ierr = DMPlexSetSupportSize(sdm, newp, q+1);CHKERRQ(ierr); 624 /* Split new vertex: Edges in new split faces and new cohesive edge */ 625 for (e = 0, q = 0; e < supportSize; ++e) { 626 PetscInt val; 627 628 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 629 if ((val == 1) || (val == -(shift + 1))) ++q; 630 } 631 ierr = DMPlexSetSupportSize(sdm, splitp, q+1);CHKERRQ(ierr); 632 /* Add cohesive edges */ 633 ierr = DMPlexSetConeSize(sdm, cedge, 2);CHKERRQ(ierr); 634 /* Punt for now on support, you loop over closure, extract faces, check which ones are in the label */ 635 } else if (dep == dim-2) { 636 ierr = DMPlexGetSupport(dm, oldp, &support);CHKERRQ(ierr); 637 /* Split old edge: Faces in positive side cells and old split faces */ 638 for (e = 0, q = 0; e < supportSize; ++e) { 639 PetscInt val; 640 641 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 642 if ((val == dim-1) || (val == (shift + dim-1))) ++q; 643 } 644 ierr = DMPlexSetSupportSize(sdm, newp, q);CHKERRQ(ierr); 645 /* Split new edge: Faces in negative side cells and new split faces */ 646 for (e = 0, q = 0; e < supportSize; ++e) { 647 PetscInt val; 648 649 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 650 if ((val == dim-1) || (val == -(shift + dim-1))) ++q; 651 } 652 ierr = DMPlexSetSupportSize(sdm, splitp, q);CHKERRQ(ierr); 653 } 654 } 655 } 656 /* Step 4: Setup split DM */ 657 ierr = DMSetUp(sdm);CHKERRQ(ierr); 658 ierr = DMPlexShiftPoints_Internal(dm, depthShift, sdm);CHKERRQ(ierr); 659 /* Step 6: Set cones and supports for new points */ 660 for (dep = 0; dep <= depth; ++dep) { 661 for (p = 0; p < numSplitPoints[dep]; ++p) { 662 const PetscInt oldp = splitPoints[dep][p]; 663 const PetscInt newp = depthOffset[dep] + oldp; 664 const PetscInt splitp = pMaxNew[dep] + p; 665 const PetscInt *cone, *support, *ornt; 666 PetscInt coneSize, supportSize, q, v, e, s; 667 668 ierr = DMPlexGetConeSize(dm, oldp, &coneSize);CHKERRQ(ierr); 669 ierr = DMPlexGetCone(dm, oldp, &cone);CHKERRQ(ierr); 670 ierr = DMPlexGetConeOrientation(dm, oldp, &ornt);CHKERRQ(ierr); 671 ierr = DMPlexGetSupportSize(dm, oldp, &supportSize);CHKERRQ(ierr); 672 ierr = DMPlexGetSupport(dm, oldp, &support);CHKERRQ(ierr); 673 if (dep == depth-1) { 674 const PetscInt ccell = pMaxNew[depth] + p; 675 const PetscInt *supportF; 676 677 /* Split face: copy in old face to new face to start */ 678 ierr = DMPlexGetSupport(sdm, newp, &supportF);CHKERRQ(ierr); 679 ierr = DMPlexSetSupport(sdm, splitp, supportF);CHKERRQ(ierr); 680 /* Split old face: old vertices/edges in cone so no change */ 681 /* Split new face: new vertices/edges in cone */ 682 for (q = 0; q < coneSize; ++q) { 683 ierr = PetscFindInt(cone[q], numSplitPoints[dim-2], splitPoints[dim-2], &v);CHKERRQ(ierr); 684 685 coneNew[2+q] = pMaxNew[dim-2] + v; 686 } 687 ierr = DMPlexSetCone(sdm, splitp, &coneNew[2]);CHKERRQ(ierr); 688 ierr = DMPlexSetConeOrientation(sdm, splitp, ornt);CHKERRQ(ierr); 689 /* Face support */ 690 for (s = 0; s < supportSize; ++s) { 691 PetscInt val; 692 693 ierr = DMLabelGetValue(label, support[s], &val);CHKERRQ(ierr); 694 if (val < 0) { 695 /* Split old face: Replace negative side cell with cohesive cell */ 696 ierr = DMPlexInsertSupport(sdm, newp, s, ccell);CHKERRQ(ierr); 697 } else { 698 /* Split new face: Replace positive side cell with cohesive cell */ 699 ierr = DMPlexInsertSupport(sdm, splitp, s, ccell);CHKERRQ(ierr); 700 /* Get orientation for cohesive face */ 701 { 702 const PetscInt *ncone, *nconeO; 703 PetscInt nconeSize, nc; 704 705 ierr = DMPlexGetConeSize(dm, support[s], &nconeSize);CHKERRQ(ierr); 706 ierr = DMPlexGetCone(dm, support[s], &ncone);CHKERRQ(ierr); 707 ierr = DMPlexGetConeOrientation(dm, support[s], &nconeO);CHKERRQ(ierr); 708 for (nc = 0; nc < nconeSize; ++nc) { 709 if (ncone[nc] == oldp) { 710 coneONew[0] = nconeO[nc]; 711 break; 712 } 713 } 714 if (nc >= nconeSize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not locate face %d in neighboring cell %d", oldp, support[s]); 715 } 716 } 717 } 718 /* Cohesive cell: Old and new split face, then new cohesive edges */ 719 coneNew[0] = newp; /* Extracted negative side orientation above */ 720 coneNew[1] = splitp; coneONew[1] = coneONew[0]; 721 if (dim > 2) { 722 PetscInt *closure = NULL, closureSize, cl; 723 724 ierr = DMPlexGetTransitiveClosure(dm, oldp, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 725 for (cl = 0, q = 0; cl < closureSize*2; cl += 2) { 726 const PetscInt clp = closure[cl]; 727 728 if ((clp >= vStart) && (clp < vEnd)) { 729 ierr = PetscFindInt(clp, numSplitPoints[0], splitPoints[0], &v);CHKERRQ(ierr); 730 coneNew[2+q] = pMaxNew[1] + (depthShift[1] - depthShift[0]) + v; 731 coneONew[2+q] = 0; 732 ++q; 733 } 734 } 735 ierr = DMPlexRestoreTransitiveClosure(dm, oldp, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 736 if (q != coneSize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid number of split face vertices %d should be %d", q, coneSize); 737 } else { 738 for (q = 0; q < coneSize; ++q) { 739 coneNew[2+q] = (pMaxNew[1] - pMaxNew[dim-2]) + (depthShift[1] - depthShift[0]) + coneNew[2+q]; 740 coneONew[2+q] = 0; 741 } 742 } 743 ierr = DMPlexSetCone(sdm, ccell, coneNew);CHKERRQ(ierr); 744 ierr = DMPlexSetConeOrientation(sdm, ccell, coneONew);CHKERRQ(ierr); 745 } else if (dep == 0) { 746 const PetscInt cedge = pMaxNew[1] + (depthShift[1] - depthShift[0]) + p; 747 748 /* Split old vertex: Edges in old split faces and new cohesive edge */ 749 for (e = 0, q = 0; e < supportSize; ++e) { 750 PetscInt val; 751 752 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 753 if ((val == 1) || (val == (shift + 1))) { 754 supportNew[q++] = depthOffset[1] + support[e]; 755 } 756 } 757 supportNew[q] = cedge; 758 759 ierr = DMPlexSetSupport(sdm, newp, supportNew);CHKERRQ(ierr); 760 /* Split new vertex: Edges in new split faces and new cohesive edge */ 761 for (e = 0, q = 0; e < supportSize; ++e) { 762 PetscInt val, edge; 763 764 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 765 if (val == 1) { 766 ierr = PetscFindInt(support[e], numSplitPoints[1], splitPoints[1], &edge);CHKERRQ(ierr); 767 if (edge < 0) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Edge %d is not a split edge", support[e]); 768 supportNew[q++] = pMaxNew[1] + edge; 769 } else if (val == -(shift + 1)) { 770 supportNew[q++] = depthOffset[1] + support[e]; 771 } 772 } 773 supportNew[q] = cedge; 774 ierr = DMPlexSetSupport(sdm, splitp, supportNew);CHKERRQ(ierr); 775 /* Cohesive edge: Old and new split vertex, punting on support */ 776 coneNew[0] = newp; 777 coneNew[1] = splitp; 778 ierr = DMPlexSetCone(sdm, cedge, coneNew);CHKERRQ(ierr); 779 } else if (dep == dim-2) { 780 /* Split old edge: old vertices in cone so no change */ 781 /* Split new edge: new vertices in cone */ 782 for (q = 0; q < coneSize; ++q) { 783 ierr = PetscFindInt(cone[q], numSplitPoints[dim-3], splitPoints[dim-3], &v);CHKERRQ(ierr); 784 785 coneNew[q] = pMaxNew[dim-3] + v; 786 } 787 ierr = DMPlexSetCone(sdm, splitp, coneNew);CHKERRQ(ierr); 788 /* Split old edge: Faces in positive side cells and old split faces */ 789 for (e = 0, q = 0; e < supportSize; ++e) { 790 PetscInt val; 791 792 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 793 if ((val == dim-1) || (val == (shift + dim-1))) { 794 supportNew[q++] = depthOffset[dim-1] + support[e]; 795 } 796 } 797 ierr = DMPlexSetSupport(sdm, newp, supportNew);CHKERRQ(ierr); 798 /* Split new edge: Faces in negative side cells and new split faces */ 799 for (e = 0, q = 0; e < supportSize; ++e) { 800 PetscInt val, face; 801 802 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 803 if (val == dim-1) { 804 ierr = PetscFindInt(support[e], numSplitPoints[dim-1], splitPoints[dim-1], &face);CHKERRQ(ierr); 805 if (face < 0) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Face %d is not a split face", support[e]); 806 supportNew[q++] = pMaxNew[dim-1] + face; 807 } else if (val == -(shift + dim-1)) { 808 supportNew[q++] = depthOffset[dim-1] + support[e]; 809 } 810 } 811 ierr = DMPlexSetSupport(sdm, splitp, supportNew);CHKERRQ(ierr); 812 } 813 } 814 } 815 /* Step 6b: Replace split points in negative side cones */ 816 for (sp = 0; sp < numSP; ++sp) { 817 PetscInt dep = values[sp]; 818 IS pIS; 819 PetscInt numPoints; 820 const PetscInt *points; 821 822 if (dep >= 0) continue; 823 ierr = DMLabelGetStratumIS(label, dep, &pIS);CHKERRQ(ierr); 824 if (!pIS) continue; 825 dep = -dep - shift; 826 ierr = ISGetLocalSize(pIS, &numPoints);CHKERRQ(ierr); 827 ierr = ISGetIndices(pIS, &points);CHKERRQ(ierr); 828 for (p = 0; p < numPoints; ++p) { 829 const PetscInt oldp = points[p]; 830 const PetscInt newp = depthOffset[dep] + oldp; 831 const PetscInt *cone; 832 PetscInt coneSize, c; 833 PetscBool replaced = PETSC_FALSE; 834 835 /* Negative edge: replace split vertex */ 836 /* Negative cell: replace split face */ 837 ierr = DMPlexGetConeSize(sdm, newp, &coneSize);CHKERRQ(ierr); 838 ierr = DMPlexGetCone(sdm, newp, &cone);CHKERRQ(ierr); 839 for (c = 0; c < coneSize; ++c) { 840 const PetscInt coldp = cone[c] - depthOffset[dep-1]; 841 PetscInt csplitp, cp, val; 842 843 ierr = DMLabelGetValue(label, coldp, &val);CHKERRQ(ierr); 844 if (val == dep-1) { 845 ierr = PetscFindInt(coldp, numSplitPoints[dep-1], splitPoints[dep-1], &cp);CHKERRQ(ierr); 846 if (cp < 0) SETERRQ2(comm, PETSC_ERR_ARG_WRONG, "Point %d is not a split point of dimension %d", oldp, dep-1); 847 csplitp = pMaxNew[dep-1] + cp; 848 ierr = DMPlexInsertCone(sdm, newp, c, csplitp);CHKERRQ(ierr); 849 replaced = PETSC_TRUE; 850 } 851 } 852 if (!replaced) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "The cone of point %d does not contain split points", oldp); 853 } 854 ierr = ISRestoreIndices(pIS, &points);CHKERRQ(ierr); 855 ierr = ISDestroy(&pIS);CHKERRQ(ierr); 856 } 857 /* Step 7: Stratify */ 858 ierr = DMPlexStratify(sdm);CHKERRQ(ierr); 859 /* Step 8: Coordinates */ 860 ierr = DMPlexShiftCoordinates_Internal(dm, depthShift, sdm);CHKERRQ(ierr); 861 ierr = DMPlexGetCoordinateSection(sdm, &coordSection);CHKERRQ(ierr); 862 ierr = DMGetCoordinatesLocal(sdm, &coordinates);CHKERRQ(ierr); 863 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 864 for (v = 0; v < (numSplitPoints ? numSplitPoints[0] : 0); ++v) { 865 const PetscInt newp = depthOffset[0] + splitPoints[0][v]; 866 const PetscInt splitp = pMaxNew[0] + v; 867 PetscInt dof, off, soff, d; 868 869 ierr = PetscSectionGetDof(coordSection, newp, &dof);CHKERRQ(ierr); 870 ierr = PetscSectionGetOffset(coordSection, newp, &off);CHKERRQ(ierr); 871 ierr = PetscSectionGetOffset(coordSection, splitp, &soff);CHKERRQ(ierr); 872 for (d = 0; d < dof; ++d) coords[soff+d] = coords[off+d]; 873 } 874 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 875 /* Step 9: SF, if I can figure this out we can split the mesh in parallel */ 876 ierr = DMPlexShiftSF_Internal(dm, depthShift, sdm);CHKERRQ(ierr); 877 /* Step 10: Labels */ 878 ierr = DMPlexShiftLabels_Internal(dm, depthShift, sdm);CHKERRQ(ierr); 879 ierr = DMPlexGetNumLabels(sdm, &numLabels);CHKERRQ(ierr); 880 for (dep = 0; dep <= depth; ++dep) { 881 for (p = 0; p < numSplitPoints[dep]; ++p) { 882 const PetscInt newp = depthOffset[dep] + splitPoints[dep][p]; 883 const PetscInt splitp = pMaxNew[dep] + p; 884 PetscInt l; 885 886 for (l = 0; l < numLabels; ++l) { 887 DMLabel mlabel; 888 const char *lname; 889 PetscInt val; 890 891 ierr = DMPlexGetLabelName(sdm, l, &lname);CHKERRQ(ierr); 892 ierr = DMPlexGetLabel(sdm, lname, &mlabel);CHKERRQ(ierr); 893 ierr = DMLabelGetValue(mlabel, newp, &val);CHKERRQ(ierr); 894 if (val >= 0) { 895 ierr = DMLabelSetValue(mlabel, splitp, val);CHKERRQ(ierr); 896 if (dep == 0) { 897 const PetscInt cedge = pMaxNew[1] + (depthShift[1] - depthShift[0]) + p; 898 ierr = DMLabelSetValue(mlabel, cedge, val);CHKERRQ(ierr); 899 } 900 } 901 } 902 } 903 } 904 for (sp = 0; sp < numSP; ++sp) { 905 const PetscInt dep = values[sp]; 906 907 if ((dep < 0) || (dep > depth)) continue; 908 if (pointIS[dep]) {ierr = ISRestoreIndices(pointIS[dep], &splitPoints[dep]);CHKERRQ(ierr);} 909 ierr = ISDestroy(&pointIS[dep]);CHKERRQ(ierr); 910 } 911 if (label) { 912 ierr = ISRestoreIndices(valueIS, &values);CHKERRQ(ierr); 913 ierr = ISDestroy(&valueIS);CHKERRQ(ierr); 914 } 915 ierr = DMPlexGetChart(sdm, NULL, &pEnd);CHKERRQ(ierr); 916 if (depth > 0) pMaxNew[0] += depthShift[0]; /* Account for shadow vertices */ 917 if (depth > 1) pMaxNew[1] = pEnd - depthShift[0]; /* There is a hybrid edge for every shadow vertex */ 918 if (depth > 2) pMaxNew[2] = -1; /* There are no hybrid faces */ 919 ierr = DMPlexSetHybridBounds(sdm, depth >= 0 ? pMaxNew[depth] : PETSC_DETERMINE, depth>1 ? pMaxNew[depth-1] : PETSC_DETERMINE, depth>2 ? pMaxNew[1] : PETSC_DETERMINE, depth >= 0 ? pMaxNew[0] : PETSC_DETERMINE);CHKERRQ(ierr); 920 ierr = PetscFree6(depthShift, depthOffset, pMaxNew, coneNew, coneONew, supportNew);CHKERRQ(ierr); 921 ierr = PetscFree3(pointIS, numSplitPoints, splitPoints);CHKERRQ(ierr); 922 PetscFunctionReturn(0); 923 } 924 925 #undef __FUNCT__ 926 #define __FUNCT__ "DMPlexConstructCohesiveCells" 927 /*@C 928 DMPlexConstructCohesiveCells - Construct cohesive cells which split the face along an internal interface 929 930 Collective on dm 931 932 Input Parameters: 933 + dm - The original DM 934 - labelName - The label specifying the boundary faces (this could be auto-generated) 935 936 Output Parameters: 937 - dmSplit - The new DM 938 939 Level: developer 940 941 .seealso: DMCreate(), DMPlexLabelCohesiveComplete() 942 @*/ 943 PetscErrorCode DMPlexConstructCohesiveCells(DM dm, DMLabel label, DM *dmSplit) 944 { 945 DM sdm; 946 PetscInt dim; 947 PetscErrorCode ierr; 948 949 PetscFunctionBegin; 950 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 951 PetscValidPointer(dmSplit, 4); 952 ierr = DMCreate(PetscObjectComm((PetscObject)dm), &sdm);CHKERRQ(ierr); 953 ierr = DMSetType(sdm, DMPLEX);CHKERRQ(ierr); 954 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 955 ierr = DMPlexSetDimension(sdm, dim);CHKERRQ(ierr); 956 switch (dim) { 957 case 2: 958 case 3: 959 ierr = DMPlexConstructCohesiveCells_Internal(dm, label, sdm);CHKERRQ(ierr); 960 break; 961 default: 962 SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Cannot construct cohesive cells for dimension %d", dim); 963 } 964 *dmSplit = sdm; 965 PetscFunctionReturn(0); 966 } 967 968 #undef __FUNCT__ 969 #define __FUNCT__ "DMPlexLabelCohesiveComplete" 970 /*@ 971 DMPlexLabelCohesiveComplete - Starting with a label marking vertices on an internal surface, we add all other mesh pieces 972 to complete the surface 973 974 Input Parameters: 975 + dm - The DM 976 . label - A DMLabel marking the surface vertices 977 . flip - Flag to flip the submesh normal and replace points on the other side 978 - subdm - The subDM associated with the label, or NULL 979 980 Output Parameter: 981 . label - A DMLabel marking all surface points 982 983 Level: developer 984 985 .seealso: DMPlexConstructCohesiveCells(), DMPlexLabelComplete() 986 @*/ 987 PetscErrorCode DMPlexLabelCohesiveComplete(DM dm, DMLabel label, PetscBool flip, DM subdm) 988 { 989 IS dimIS, subpointIS; 990 const PetscInt *points, *subpoints; 991 const PetscInt rev = flip ? -1 : 1; 992 PetscInt shift = 100, dim, dep, cStart, cEnd, numPoints, numSubpoints, p, val; 993 PetscErrorCode ierr; 994 995 PetscFunctionBegin; 996 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 997 if (subdm) { 998 ierr = DMPlexCreateSubpointIS(subdm, &subpointIS);CHKERRQ(ierr); 999 if (subpointIS) { 1000 ierr = ISGetLocalSize(subpointIS, &numSubpoints);CHKERRQ(ierr); 1001 ierr = ISGetIndices(subpointIS, &subpoints);CHKERRQ(ierr); 1002 } 1003 } 1004 /* Cell orientation for face gives the side of the fault */ 1005 ierr = DMLabelGetStratumIS(label, dim-1, &dimIS);CHKERRQ(ierr); 1006 if (!dimIS) PetscFunctionReturn(0); 1007 ierr = ISGetLocalSize(dimIS, &numPoints);CHKERRQ(ierr); 1008 ierr = ISGetIndices(dimIS, &points);CHKERRQ(ierr); 1009 for (p = 0; p < numPoints; ++p) { 1010 const PetscInt *support; 1011 PetscInt supportSize, s; 1012 1013 ierr = DMPlexGetSupportSize(dm, points[p], &supportSize);CHKERRQ(ierr); 1014 if (supportSize != 2) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Split face %d has %d != 2 supports", points[p], supportSize); 1015 ierr = DMPlexGetSupport(dm, points[p], &support);CHKERRQ(ierr); 1016 for (s = 0; s < supportSize; ++s) { 1017 const PetscInt *cone, *ornt; 1018 PetscInt coneSize, c; 1019 PetscBool pos = PETSC_TRUE; 1020 1021 ierr = DMPlexGetConeSize(dm, support[s], &coneSize);CHKERRQ(ierr); 1022 ierr = DMPlexGetCone(dm, support[s], &cone);CHKERRQ(ierr); 1023 ierr = DMPlexGetConeOrientation(dm, support[s], &ornt);CHKERRQ(ierr); 1024 for (c = 0; c < coneSize; ++c) { 1025 if (cone[c] == points[p]) { 1026 PetscInt o = ornt[c]; 1027 1028 if (subdm) { 1029 const PetscInt *subcone, *subornt; 1030 PetscInt subpoint, subface, subconeSize, sc; 1031 1032 ierr = PetscFindInt(support[s], numSubpoints, subpoints, &subpoint);CHKERRQ(ierr); 1033 ierr = PetscFindInt(points[p], numSubpoints, subpoints, &subface);CHKERRQ(ierr); 1034 ierr = DMPlexGetConeSize(subdm, subpoint, &subconeSize);CHKERRQ(ierr); 1035 ierr = DMPlexGetCone(subdm, subpoint, &subcone);CHKERRQ(ierr); 1036 ierr = DMPlexGetConeOrientation(subdm, subpoint, &subornt);CHKERRQ(ierr); 1037 for (sc = 0; sc < subconeSize; ++sc) { 1038 if (subcone[sc] == subface) { 1039 o = subornt[0]; 1040 break; 1041 } 1042 } 1043 if (sc >= subconeSize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not find point %d in cone for subpoint %d", points[p], subpoint); 1044 } 1045 if (o >= 0) { 1046 ierr = DMLabelSetValue(label, support[s], rev*(shift+dim));CHKERRQ(ierr); 1047 } else { 1048 ierr = DMLabelSetValue(label, support[s], -rev*(shift+dim));CHKERRQ(ierr); 1049 pos = PETSC_FALSE; 1050 } 1051 break; 1052 } 1053 } 1054 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]); 1055 /* Put faces touching the fault in the label */ 1056 for (c = 0; c < coneSize; ++c) { 1057 const PetscInt point = cone[c]; 1058 1059 ierr = DMLabelGetValue(label, point, &val);CHKERRQ(ierr); 1060 if (val == -1) { 1061 PetscInt *closure = NULL; 1062 PetscInt closureSize, cl; 1063 1064 ierr = DMPlexGetTransitiveClosure(dm, point, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1065 for (cl = 0; cl < closureSize*2; cl += 2) { 1066 const PetscInt clp = closure[cl]; 1067 1068 ierr = DMLabelGetValue(label, clp, &val);CHKERRQ(ierr); 1069 if ((val >= 0) && (val < dim-1)) { 1070 ierr = DMLabelSetValue(label, point, pos == PETSC_TRUE ? shift+dim-1 : -(shift+dim-1));CHKERRQ(ierr); 1071 break; 1072 } 1073 } 1074 ierr = DMPlexRestoreTransitiveClosure(dm, point, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1075 } 1076 } 1077 } 1078 } 1079 if (subdm) { 1080 if (subpointIS) {ierr = ISRestoreIndices(subpointIS, &subpoints);CHKERRQ(ierr);} 1081 ierr = ISDestroy(&subpointIS);CHKERRQ(ierr); 1082 } 1083 ierr = ISRestoreIndices(dimIS, &points);CHKERRQ(ierr); 1084 ierr = ISDestroy(&dimIS);CHKERRQ(ierr); 1085 /* Search for other cells/faces/edges connected to the fault by a vertex */ 1086 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1087 ierr = DMLabelGetStratumIS(label, 0, &dimIS);CHKERRQ(ierr); 1088 if (!dimIS) PetscFunctionReturn(0); 1089 ierr = ISGetLocalSize(dimIS, &numPoints);CHKERRQ(ierr); 1090 ierr = ISGetIndices(dimIS, &points);CHKERRQ(ierr); 1091 for (p = 0; p < numPoints; ++p) { 1092 PetscInt *star = NULL; 1093 PetscInt starSize, s; 1094 PetscInt again = 1; /* 0: Finished 1: Keep iterating after a change 2: No change */ 1095 1096 /* First mark cells connected to the fault */ 1097 ierr = DMPlexGetTransitiveClosure(dm, points[p], PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1098 while (again) { 1099 if (again > 1) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Could not classify all cells connected to the fault"); 1100 again = 0; 1101 for (s = 0; s < starSize*2; s += 2) { 1102 const PetscInt point = star[s]; 1103 const PetscInt *cone; 1104 PetscInt coneSize, c; 1105 1106 if ((point < cStart) || (point >= cEnd)) continue; 1107 ierr = DMLabelGetValue(label, point, &val);CHKERRQ(ierr); 1108 if (val != -1) continue; 1109 again = 2; 1110 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 1111 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 1112 for (c = 0; c < coneSize; ++c) { 1113 ierr = DMLabelGetValue(label, cone[c], &val);CHKERRQ(ierr); 1114 if (val != -1) { 1115 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); 1116 if (val > 0) { 1117 ierr = DMLabelSetValue(label, point, shift+dim);CHKERRQ(ierr); 1118 } else { 1119 ierr = DMLabelSetValue(label, point, -(shift+dim));CHKERRQ(ierr); 1120 } 1121 again = 1; 1122 break; 1123 } 1124 } 1125 } 1126 } 1127 /* Classify the rest by cell membership */ 1128 for (s = 0; s < starSize*2; s += 2) { 1129 const PetscInt point = star[s]; 1130 1131 ierr = DMLabelGetValue(label, point, &val);CHKERRQ(ierr); 1132 if (val == -1) { 1133 PetscInt *sstar = NULL; 1134 PetscInt sstarSize, ss; 1135 PetscBool marked = PETSC_FALSE; 1136 1137 ierr = DMPlexGetTransitiveClosure(dm, point, PETSC_FALSE, &sstarSize, &sstar);CHKERRQ(ierr); 1138 for (ss = 0; ss < sstarSize*2; ss += 2) { 1139 const PetscInt spoint = sstar[ss]; 1140 1141 if ((spoint < cStart) || (spoint >= cEnd)) continue; 1142 ierr = DMLabelGetValue(label, spoint, &val);CHKERRQ(ierr); 1143 if (val == -1) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Cell %d in star of %d does not have a valid label", spoint, point); 1144 ierr = DMPlexGetLabelValue(dm, "depth", point, &dep);CHKERRQ(ierr); 1145 if (val > 0) { 1146 ierr = DMLabelSetValue(label, point, shift+dep);CHKERRQ(ierr); 1147 } else { 1148 ierr = DMLabelSetValue(label, point, -(shift+dep));CHKERRQ(ierr); 1149 } 1150 marked = PETSC_TRUE; 1151 break; 1152 } 1153 ierr = DMPlexRestoreTransitiveClosure(dm, point, PETSC_FALSE, &sstarSize, &sstar);CHKERRQ(ierr); 1154 if (!marked) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Point %d could not be classified", point); 1155 } 1156 } 1157 ierr = DMPlexRestoreTransitiveClosure(dm, points[p], PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1158 } 1159 ierr = ISRestoreIndices(dimIS, &points);CHKERRQ(ierr); 1160 ierr = ISDestroy(&dimIS);CHKERRQ(ierr); 1161 PetscFunctionReturn(0); 1162 } 1163 1164 #undef __FUNCT__ 1165 #define __FUNCT__ "DMPlexMarkSubmesh_Uninterpolated" 1166 /* Here we need the explicit assumption that: 1167 1168 For any marked cell, the marked vertices constitute a single face 1169 */ 1170 static PetscErrorCode DMPlexMarkSubmesh_Uninterpolated(DM dm, DMLabel vertexLabel, PetscInt value, DMLabel subpointMap, PetscInt *numFaces, PetscInt *nFV, DM subdm) 1171 { 1172 IS subvertexIS; 1173 const PetscInt *subvertices; 1174 PetscInt *pStart, *pEnd, *pMax, pSize; 1175 PetscInt depth, dim, d, numSubVerticesInitial = 0, v; 1176 PetscErrorCode ierr; 1177 1178 PetscFunctionBegin; 1179 *numFaces = 0; 1180 *nFV = 0; 1181 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 1182 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1183 pSize = PetscMax(depth, dim) + 1; 1184 ierr = PetscMalloc3(pSize,PetscInt,&pStart,pSize,PetscInt,&pEnd,pSize,PetscInt,&pMax);CHKERRQ(ierr); 1185 ierr = DMPlexGetHybridBounds(dm, &pMax[depth], depth>1 ? &pMax[depth-1] : NULL, depth > 2 ? &pMax[1] : NULL, &pMax[0]);CHKERRQ(ierr); 1186 for (d = 0; d <= depth; ++d) { 1187 ierr = DMPlexGetDepthStratum(dm, d, &pStart[d], &pEnd[d]);CHKERRQ(ierr); 1188 if (pMax[d] >= 0) pEnd[d] = PetscMin(pEnd[d], pMax[d]); 1189 } 1190 /* Loop over initial vertices and mark all faces in the collective star() */ 1191 ierr = DMLabelGetStratumIS(vertexLabel, value, &subvertexIS);CHKERRQ(ierr); 1192 if (subvertexIS) { 1193 ierr = ISGetSize(subvertexIS, &numSubVerticesInitial);CHKERRQ(ierr); 1194 ierr = ISGetIndices(subvertexIS, &subvertices);CHKERRQ(ierr); 1195 } 1196 for (v = 0; v < numSubVerticesInitial; ++v) { 1197 const PetscInt vertex = subvertices[v]; 1198 PetscInt *star = NULL; 1199 PetscInt starSize, s, numCells = 0, c; 1200 1201 ierr = DMPlexGetTransitiveClosure(dm, vertex, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1202 for (s = 0; s < starSize*2; s += 2) { 1203 const PetscInt point = star[s]; 1204 if ((point >= pStart[depth]) && (point < pEnd[depth])) star[numCells++] = point; 1205 } 1206 for (c = 0; c < numCells; ++c) { 1207 const PetscInt cell = star[c]; 1208 PetscInt *closure = NULL; 1209 PetscInt closureSize, cl; 1210 PetscInt cellLoc, numCorners = 0, faceSize = 0; 1211 1212 ierr = DMLabelGetValue(subpointMap, cell, &cellLoc);CHKERRQ(ierr); 1213 if (cellLoc == 2) continue; 1214 if (cellLoc >= 0) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Cell %d has dimension %d in the surface label", cell, cellLoc); 1215 ierr = DMPlexGetTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1216 for (cl = 0; cl < closureSize*2; cl += 2) { 1217 const PetscInt point = closure[cl]; 1218 PetscInt vertexLoc; 1219 1220 if ((point >= pStart[0]) && (point < pEnd[0])) { 1221 ++numCorners; 1222 ierr = DMLabelGetValue(vertexLabel, point, &vertexLoc);CHKERRQ(ierr); 1223 if (vertexLoc == value) closure[faceSize++] = point; 1224 } 1225 } 1226 if (!(*nFV)) {ierr = DMPlexGetNumFaceVertices(dm, dim, numCorners, nFV);CHKERRQ(ierr);} 1227 if (faceSize > *nFV) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Invalid submesh: Too many vertices %d of an element on the surface", faceSize); 1228 if (faceSize == *nFV) { 1229 const PetscInt *cells = NULL; 1230 PetscInt numCells, nc; 1231 1232 ++(*numFaces); 1233 for (cl = 0; cl < faceSize; ++cl) { 1234 ierr = DMLabelSetValue(subpointMap, closure[cl], 0);CHKERRQ(ierr); 1235 } 1236 ierr = DMPlexGetJoin(dm, faceSize, closure, &numCells, &cells);CHKERRQ(ierr); 1237 for (nc = 0; nc < numCells; ++nc) { 1238 ierr = DMLabelSetValue(subpointMap, cells[nc], 2);CHKERRQ(ierr); 1239 } 1240 ierr = DMPlexRestoreJoin(dm, faceSize, closure, &numCells, &cells);CHKERRQ(ierr); 1241 } 1242 ierr = DMPlexRestoreTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1243 } 1244 ierr = DMPlexRestoreTransitiveClosure(dm, vertex, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1245 } 1246 if (subvertexIS) { 1247 ierr = ISRestoreIndices(subvertexIS, &subvertices);CHKERRQ(ierr); 1248 } 1249 ierr = ISDestroy(&subvertexIS);CHKERRQ(ierr); 1250 ierr = PetscFree3(pStart,pEnd,pMax);CHKERRQ(ierr); 1251 PetscFunctionReturn(0); 1252 } 1253 1254 #undef __FUNCT__ 1255 #define __FUNCT__ "DMPlexMarkSubmesh_Interpolated" 1256 static PetscErrorCode DMPlexMarkSubmesh_Interpolated(DM dm, DMLabel vertexLabel, PetscInt value, DMLabel subpointMap, DM subdm) 1257 { 1258 IS subvertexIS; 1259 const PetscInt *subvertices; 1260 PetscInt *pStart, *pEnd, *pMax; 1261 PetscInt dim, d, numSubVerticesInitial = 0, v; 1262 PetscErrorCode ierr; 1263 1264 PetscFunctionBegin; 1265 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1266 ierr = PetscMalloc3(dim+1,PetscInt,&pStart,dim+1,PetscInt,&pEnd,dim+1,PetscInt,&pMax);CHKERRQ(ierr); 1267 ierr = DMPlexGetHybridBounds(dm, &pMax[dim], dim>1 ? &pMax[dim-1] : NULL, dim > 2 ? &pMax[1] : NULL, &pMax[0]);CHKERRQ(ierr); 1268 for (d = 0; d <= dim; ++d) { 1269 ierr = DMPlexGetDepthStratum(dm, d, &pStart[d], &pEnd[d]);CHKERRQ(ierr); 1270 if (pMax[d] >= 0) pEnd[d] = PetscMin(pEnd[d], pMax[d]); 1271 } 1272 /* Loop over initial vertices and mark all faces in the collective star() */ 1273 ierr = DMLabelGetStratumIS(vertexLabel, value, &subvertexIS);CHKERRQ(ierr); 1274 if (subvertexIS) { 1275 ierr = ISGetSize(subvertexIS, &numSubVerticesInitial);CHKERRQ(ierr); 1276 ierr = ISGetIndices(subvertexIS, &subvertices);CHKERRQ(ierr); 1277 } 1278 for (v = 0; v < numSubVerticesInitial; ++v) { 1279 const PetscInt vertex = subvertices[v]; 1280 PetscInt *star = NULL; 1281 PetscInt starSize, s, numFaces = 0, f; 1282 1283 ierr = DMPlexGetTransitiveClosure(dm, vertex, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1284 for (s = 0; s < starSize*2; s += 2) { 1285 const PetscInt point = star[s]; 1286 if ((point >= pStart[dim-1]) && (point < pEnd[dim-1])) star[numFaces++] = point; 1287 } 1288 for (f = 0; f < numFaces; ++f) { 1289 const PetscInt face = star[f]; 1290 PetscInt *closure = NULL; 1291 PetscInt closureSize, c; 1292 PetscInt faceLoc; 1293 1294 ierr = DMLabelGetValue(subpointMap, face, &faceLoc);CHKERRQ(ierr); 1295 if (faceLoc == dim-1) continue; 1296 if (faceLoc >= 0) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Face %d has dimension %d in the surface label", face, faceLoc); 1297 ierr = DMPlexGetTransitiveClosure(dm, face, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1298 for (c = 0; c < closureSize*2; c += 2) { 1299 const PetscInt point = closure[c]; 1300 PetscInt vertexLoc; 1301 1302 if ((point >= pStart[0]) && (point < pEnd[0])) { 1303 ierr = DMLabelGetValue(vertexLabel, point, &vertexLoc);CHKERRQ(ierr); 1304 if (vertexLoc != value) break; 1305 } 1306 } 1307 if (c == closureSize*2) { 1308 const PetscInt *support; 1309 PetscInt supportSize, s; 1310 1311 for (c = 0; c < closureSize*2; c += 2) { 1312 const PetscInt point = closure[c]; 1313 1314 for (d = 0; d < dim; ++d) { 1315 if ((point >= pStart[d]) && (point < pEnd[d])) { 1316 ierr = DMLabelSetValue(subpointMap, point, d);CHKERRQ(ierr); 1317 break; 1318 } 1319 } 1320 } 1321 ierr = DMPlexGetSupportSize(dm, face, &supportSize);CHKERRQ(ierr); 1322 ierr = DMPlexGetSupport(dm, face, &support);CHKERRQ(ierr); 1323 for (s = 0; s < supportSize; ++s) { 1324 ierr = DMLabelSetValue(subpointMap, support[s], dim);CHKERRQ(ierr); 1325 } 1326 } 1327 ierr = DMPlexRestoreTransitiveClosure(dm, face, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1328 } 1329 ierr = DMPlexRestoreTransitiveClosure(dm, vertex, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1330 } 1331 if (subvertexIS) { 1332 ierr = ISRestoreIndices(subvertexIS, &subvertices);CHKERRQ(ierr); 1333 } 1334 ierr = ISDestroy(&subvertexIS);CHKERRQ(ierr); 1335 ierr = PetscFree3(pStart,pEnd,pMax);CHKERRQ(ierr); 1336 PetscFunctionReturn(0); 1337 } 1338 1339 #undef __FUNCT__ 1340 #define __FUNCT__ "DMPlexMarkCohesiveSubmesh_Uninterpolated" 1341 static PetscErrorCode DMPlexMarkCohesiveSubmesh_Uninterpolated(DM dm, PetscBool hasLagrange, DMLabel subpointMap, PetscInt *numFaces, PetscInt *nFV, PetscInt *subCells[], DM subdm) 1342 { 1343 const PetscInt *cone; 1344 PetscInt dim, cMax, cEnd, c, p, coneSize; 1345 PetscErrorCode ierr; 1346 1347 PetscFunctionBegin; 1348 *numFaces = 0; 1349 *nFV = 0; 1350 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1351 ierr = DMPlexGetHeightStratum(dm, 0, NULL, &cEnd);CHKERRQ(ierr); 1352 ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); 1353 if (cMax < 0) PetscFunctionReturn(0); 1354 ierr = DMPlexGetConeSize(dm, cMax, &coneSize);CHKERRQ(ierr); 1355 *numFaces = cEnd - cMax; 1356 *nFV = hasLagrange ? coneSize/3 : coneSize/2; 1357 ierr = PetscMalloc(*numFaces *2 * sizeof(PetscInt), subCells);CHKERRQ(ierr); 1358 for (c = cMax; c < cEnd; ++c) { 1359 const PetscInt *cells; 1360 PetscInt numCells; 1361 1362 ierr = DMPlexGetCone(dm, c, &cone);CHKERRQ(ierr); 1363 for (p = 0; p < *nFV; ++p) { 1364 ierr = DMLabelSetValue(subpointMap, cone[p], 0);CHKERRQ(ierr); 1365 } 1366 /* Negative face */ 1367 ierr = DMPlexGetJoin(dm, *nFV, cone, &numCells, &cells);CHKERRQ(ierr); 1368 if (numCells != 2) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive cells should separate two cells"); 1369 for (p = 0; p < numCells; ++p) { 1370 ierr = DMLabelSetValue(subpointMap, cells[p], 2);CHKERRQ(ierr); 1371 (*subCells)[(c-cMax)*2+p] = cells[p]; 1372 } 1373 ierr = DMPlexRestoreJoin(dm, *nFV, cone, &numCells, &cells);CHKERRQ(ierr); 1374 /* Positive face is not included */ 1375 } 1376 PetscFunctionReturn(0); 1377 } 1378 1379 #undef __FUNCT__ 1380 #define __FUNCT__ "DMPlexMarkCohesiveSubmesh_Interpolated" 1381 static PetscErrorCode DMPlexMarkCohesiveSubmesh_Interpolated(DM dm, PetscBool hasLagrange, DMLabel subpointMap, DM subdm) 1382 { 1383 PetscInt *pStart, *pEnd; 1384 PetscInt dim, cMax, cEnd, c, d; 1385 PetscErrorCode ierr; 1386 1387 PetscFunctionBegin; 1388 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1389 ierr = DMPlexGetHeightStratum(dm, 0, NULL, &cEnd);CHKERRQ(ierr); 1390 ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); 1391 if (cMax < 0) PetscFunctionReturn(0); 1392 ierr = PetscMalloc2(dim+1,PetscInt,&pStart,dim+1,PetscInt,&pEnd);CHKERRQ(ierr); 1393 for (d = 0; d <= dim; ++d) { 1394 ierr = DMPlexGetDepthStratum(dm, d, &pStart[d], &pEnd[d]);CHKERRQ(ierr); 1395 } 1396 for (c = cMax; c < cEnd; ++c) { 1397 const PetscInt *cone; 1398 PetscInt *closure = NULL; 1399 PetscInt coneSize, closureSize, cl; 1400 1401 ierr = DMPlexGetConeSize(dm, c, &coneSize);CHKERRQ(ierr); 1402 if (hasLagrange) { 1403 if (coneSize != 3) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive cells should separate two cells"); 1404 } else { 1405 if (coneSize != 2) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive cells should separate two cells"); 1406 } 1407 /* Negative face */ 1408 ierr = DMPlexGetCone(dm, c, &cone);CHKERRQ(ierr); 1409 ierr = DMPlexGetTransitiveClosure(dm, cone[0], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1410 for (cl = 0; cl < closureSize*2; cl += 2) { 1411 const PetscInt point = closure[cl]; 1412 1413 for (d = 0; d <= dim; ++d) { 1414 if ((point >= pStart[d]) && (point < pEnd[d])) { 1415 ierr = DMLabelSetValue(subpointMap, point, d);CHKERRQ(ierr); 1416 break; 1417 } 1418 } 1419 } 1420 ierr = DMPlexRestoreTransitiveClosure(dm, cone[0], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1421 /* Cells -- positive face is not included */ 1422 for (cl = 0; cl < 1; ++cl) { 1423 const PetscInt *support; 1424 PetscInt supportSize, s; 1425 1426 ierr = DMPlexGetSupportSize(dm, cone[cl], &supportSize);CHKERRQ(ierr); 1427 if (supportSize != 2) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive faces should separate two cells"); 1428 ierr = DMPlexGetSupport(dm, cone[cl], &support);CHKERRQ(ierr); 1429 for (s = 0; s < supportSize; ++s) { 1430 ierr = DMLabelSetValue(subpointMap, support[s], dim);CHKERRQ(ierr); 1431 } 1432 } 1433 } 1434 ierr = PetscFree2(pStart, pEnd);CHKERRQ(ierr); 1435 PetscFunctionReturn(0); 1436 } 1437 1438 #undef __FUNCT__ 1439 #define __FUNCT__ "DMPlexGetFaceOrientation" 1440 PetscErrorCode DMPlexGetFaceOrientation(DM dm, PetscInt cell, PetscInt numCorners, PetscInt indices[], PetscInt oppositeVertex, PetscInt origVertices[], PetscInt faceVertices[], PetscBool *posOriented) 1441 { 1442 MPI_Comm comm; 1443 PetscBool posOrient = PETSC_FALSE; 1444 const PetscInt debug = 0; 1445 PetscInt cellDim, faceSize, f; 1446 PetscErrorCode ierr; 1447 1448 PetscFunctionBegin; 1449 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 1450 ierr = DMPlexGetDimension(dm, &cellDim);CHKERRQ(ierr); 1451 if (debug) {PetscPrintf(comm, "cellDim: %d numCorners: %d\n", cellDim, numCorners);CHKERRQ(ierr);} 1452 1453 if (cellDim == numCorners-1) { 1454 /* Simplices */ 1455 faceSize = numCorners-1; 1456 posOrient = !(oppositeVertex%2) ? PETSC_TRUE : PETSC_FALSE; 1457 } else if (cellDim == 1 && numCorners == 3) { 1458 /* Quadratic line */ 1459 faceSize = 1; 1460 posOrient = PETSC_TRUE; 1461 } else if (cellDim == 2 && numCorners == 4) { 1462 /* Quads */ 1463 faceSize = 2; 1464 if ((indices[1] > indices[0]) && (indices[1] - indices[0] == 1)) { 1465 posOrient = PETSC_TRUE; 1466 } else if ((indices[0] == 3) && (indices[1] == 0)) { 1467 posOrient = PETSC_TRUE; 1468 } else { 1469 if (((indices[0] > indices[1]) && (indices[0] - indices[1] == 1)) || ((indices[0] == 0) && (indices[1] == 3))) { 1470 posOrient = PETSC_FALSE; 1471 } else SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid quad crossedge"); 1472 } 1473 } else if (cellDim == 2 && numCorners == 6) { 1474 /* Quadratic triangle (I hate this) */ 1475 /* Edges are determined by the first 2 vertices (corners of edges) */ 1476 const PetscInt faceSizeTri = 3; 1477 PetscInt sortedIndices[3], i, iFace; 1478 PetscBool found = PETSC_FALSE; 1479 PetscInt faceVerticesTriSorted[9] = { 1480 0, 3, 4, /* bottom */ 1481 1, 4, 5, /* right */ 1482 2, 3, 5, /* left */ 1483 }; 1484 PetscInt faceVerticesTri[9] = { 1485 0, 3, 4, /* bottom */ 1486 1, 4, 5, /* right */ 1487 2, 5, 3, /* left */ 1488 }; 1489 1490 faceSize = faceSizeTri; 1491 for (i = 0; i < faceSizeTri; ++i) sortedIndices[i] = indices[i]; 1492 ierr = PetscSortInt(faceSizeTri, sortedIndices);CHKERRQ(ierr); 1493 for (iFace = 0; iFace < 3; ++iFace) { 1494 const PetscInt ii = iFace*faceSizeTri; 1495 PetscInt fVertex, cVertex; 1496 1497 if ((sortedIndices[0] == faceVerticesTriSorted[ii+0]) && 1498 (sortedIndices[1] == faceVerticesTriSorted[ii+1])) { 1499 for (fVertex = 0; fVertex < faceSizeTri; ++fVertex) { 1500 for (cVertex = 0; cVertex < faceSizeTri; ++cVertex) { 1501 if (indices[cVertex] == faceVerticesTri[ii+fVertex]) { 1502 faceVertices[fVertex] = origVertices[cVertex]; 1503 break; 1504 } 1505 } 1506 } 1507 found = PETSC_TRUE; 1508 break; 1509 } 1510 } 1511 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid tri crossface"); 1512 if (posOriented) *posOriented = PETSC_TRUE; 1513 PetscFunctionReturn(0); 1514 } else if (cellDim == 2 && numCorners == 9) { 1515 /* Quadratic quad (I hate this) */ 1516 /* Edges are determined by the first 2 vertices (corners of edges) */ 1517 const PetscInt faceSizeQuad = 3; 1518 PetscInt sortedIndices[3], i, iFace; 1519 PetscBool found = PETSC_FALSE; 1520 PetscInt faceVerticesQuadSorted[12] = { 1521 0, 1, 4, /* bottom */ 1522 1, 2, 5, /* right */ 1523 2, 3, 6, /* top */ 1524 0, 3, 7, /* left */ 1525 }; 1526 PetscInt faceVerticesQuad[12] = { 1527 0, 1, 4, /* bottom */ 1528 1, 2, 5, /* right */ 1529 2, 3, 6, /* top */ 1530 3, 0, 7, /* left */ 1531 }; 1532 1533 faceSize = faceSizeQuad; 1534 for (i = 0; i < faceSizeQuad; ++i) sortedIndices[i] = indices[i]; 1535 ierr = PetscSortInt(faceSizeQuad, sortedIndices);CHKERRQ(ierr); 1536 for (iFace = 0; iFace < 4; ++iFace) { 1537 const PetscInt ii = iFace*faceSizeQuad; 1538 PetscInt fVertex, cVertex; 1539 1540 if ((sortedIndices[0] == faceVerticesQuadSorted[ii+0]) && 1541 (sortedIndices[1] == faceVerticesQuadSorted[ii+1])) { 1542 for (fVertex = 0; fVertex < faceSizeQuad; ++fVertex) { 1543 for (cVertex = 0; cVertex < faceSizeQuad; ++cVertex) { 1544 if (indices[cVertex] == faceVerticesQuad[ii+fVertex]) { 1545 faceVertices[fVertex] = origVertices[cVertex]; 1546 break; 1547 } 1548 } 1549 } 1550 found = PETSC_TRUE; 1551 break; 1552 } 1553 } 1554 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid quad crossface"); 1555 if (posOriented) *posOriented = PETSC_TRUE; 1556 PetscFunctionReturn(0); 1557 } else if (cellDim == 3 && numCorners == 8) { 1558 /* Hexes 1559 A hex is two oriented quads with the normal of the first 1560 pointing up at the second. 1561 1562 7---6 1563 /| /| 1564 4---5 | 1565 | 3-|-2 1566 |/ |/ 1567 0---1 1568 1569 Faces are determined by the first 4 vertices (corners of faces) */ 1570 const PetscInt faceSizeHex = 4; 1571 PetscInt sortedIndices[4], i, iFace; 1572 PetscBool found = PETSC_FALSE; 1573 PetscInt faceVerticesHexSorted[24] = { 1574 0, 1, 2, 3, /* bottom */ 1575 4, 5, 6, 7, /* top */ 1576 0, 1, 4, 5, /* front */ 1577 1, 2, 5, 6, /* right */ 1578 2, 3, 6, 7, /* back */ 1579 0, 3, 4, 7, /* left */ 1580 }; 1581 PetscInt faceVerticesHex[24] = { 1582 3, 2, 1, 0, /* bottom */ 1583 4, 5, 6, 7, /* top */ 1584 0, 1, 5, 4, /* front */ 1585 1, 2, 6, 5, /* right */ 1586 2, 3, 7, 6, /* back */ 1587 3, 0, 4, 7, /* left */ 1588 }; 1589 1590 faceSize = faceSizeHex; 1591 for (i = 0; i < faceSizeHex; ++i) sortedIndices[i] = indices[i]; 1592 ierr = PetscSortInt(faceSizeHex, sortedIndices);CHKERRQ(ierr); 1593 for (iFace = 0; iFace < 6; ++iFace) { 1594 const PetscInt ii = iFace*faceSizeHex; 1595 PetscInt fVertex, cVertex; 1596 1597 if ((sortedIndices[0] == faceVerticesHexSorted[ii+0]) && 1598 (sortedIndices[1] == faceVerticesHexSorted[ii+1]) && 1599 (sortedIndices[2] == faceVerticesHexSorted[ii+2]) && 1600 (sortedIndices[3] == faceVerticesHexSorted[ii+3])) { 1601 for (fVertex = 0; fVertex < faceSizeHex; ++fVertex) { 1602 for (cVertex = 0; cVertex < faceSizeHex; ++cVertex) { 1603 if (indices[cVertex] == faceVerticesHex[ii+fVertex]) { 1604 faceVertices[fVertex] = origVertices[cVertex]; 1605 break; 1606 } 1607 } 1608 } 1609 found = PETSC_TRUE; 1610 break; 1611 } 1612 } 1613 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid hex crossface"); 1614 if (posOriented) *posOriented = PETSC_TRUE; 1615 PetscFunctionReturn(0); 1616 } else if (cellDim == 3 && numCorners == 10) { 1617 /* Quadratic tet */ 1618 /* Faces are determined by the first 3 vertices (corners of faces) */ 1619 const PetscInt faceSizeTet = 6; 1620 PetscInt sortedIndices[6], i, iFace; 1621 PetscBool found = PETSC_FALSE; 1622 PetscInt faceVerticesTetSorted[24] = { 1623 0, 1, 2, 6, 7, 8, /* bottom */ 1624 0, 3, 4, 6, 7, 9, /* front */ 1625 1, 4, 5, 7, 8, 9, /* right */ 1626 2, 3, 5, 6, 8, 9, /* left */ 1627 }; 1628 PetscInt faceVerticesTet[24] = { 1629 0, 1, 2, 6, 7, 8, /* bottom */ 1630 0, 4, 3, 6, 7, 9, /* front */ 1631 1, 5, 4, 7, 8, 9, /* right */ 1632 2, 3, 5, 8, 6, 9, /* left */ 1633 }; 1634 1635 faceSize = faceSizeTet; 1636 for (i = 0; i < faceSizeTet; ++i) sortedIndices[i] = indices[i]; 1637 ierr = PetscSortInt(faceSizeTet, sortedIndices);CHKERRQ(ierr); 1638 for (iFace=0; iFace < 4; ++iFace) { 1639 const PetscInt ii = iFace*faceSizeTet; 1640 PetscInt fVertex, cVertex; 1641 1642 if ((sortedIndices[0] == faceVerticesTetSorted[ii+0]) && 1643 (sortedIndices[1] == faceVerticesTetSorted[ii+1]) && 1644 (sortedIndices[2] == faceVerticesTetSorted[ii+2]) && 1645 (sortedIndices[3] == faceVerticesTetSorted[ii+3])) { 1646 for (fVertex = 0; fVertex < faceSizeTet; ++fVertex) { 1647 for (cVertex = 0; cVertex < faceSizeTet; ++cVertex) { 1648 if (indices[cVertex] == faceVerticesTet[ii+fVertex]) { 1649 faceVertices[fVertex] = origVertices[cVertex]; 1650 break; 1651 } 1652 } 1653 } 1654 found = PETSC_TRUE; 1655 break; 1656 } 1657 } 1658 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid tet crossface"); 1659 if (posOriented) *posOriented = PETSC_TRUE; 1660 PetscFunctionReturn(0); 1661 } else if (cellDim == 3 && numCorners == 27) { 1662 /* Quadratic hexes (I hate this) 1663 A hex is two oriented quads with the normal of the first 1664 pointing up at the second. 1665 1666 7---6 1667 /| /| 1668 4---5 | 1669 | 3-|-2 1670 |/ |/ 1671 0---1 1672 1673 Faces are determined by the first 4 vertices (corners of faces) */ 1674 const PetscInt faceSizeQuadHex = 9; 1675 PetscInt sortedIndices[9], i, iFace; 1676 PetscBool found = PETSC_FALSE; 1677 PetscInt faceVerticesQuadHexSorted[54] = { 1678 0, 1, 2, 3, 8, 9, 10, 11, 24, /* bottom */ 1679 4, 5, 6, 7, 12, 13, 14, 15, 25, /* top */ 1680 0, 1, 4, 5, 8, 12, 16, 17, 22, /* front */ 1681 1, 2, 5, 6, 9, 13, 17, 18, 21, /* right */ 1682 2, 3, 6, 7, 10, 14, 18, 19, 23, /* back */ 1683 0, 3, 4, 7, 11, 15, 16, 19, 20, /* left */ 1684 }; 1685 PetscInt faceVerticesQuadHex[54] = { 1686 3, 2, 1, 0, 10, 9, 8, 11, 24, /* bottom */ 1687 4, 5, 6, 7, 12, 13, 14, 15, 25, /* top */ 1688 0, 1, 5, 4, 8, 17, 12, 16, 22, /* front */ 1689 1, 2, 6, 5, 9, 18, 13, 17, 21, /* right */ 1690 2, 3, 7, 6, 10, 19, 14, 18, 23, /* back */ 1691 3, 0, 4, 7, 11, 16, 15, 19, 20 /* left */ 1692 }; 1693 1694 faceSize = faceSizeQuadHex; 1695 for (i = 0; i < faceSizeQuadHex; ++i) sortedIndices[i] = indices[i]; 1696 ierr = PetscSortInt(faceSizeQuadHex, sortedIndices);CHKERRQ(ierr); 1697 for (iFace = 0; iFace < 6; ++iFace) { 1698 const PetscInt ii = iFace*faceSizeQuadHex; 1699 PetscInt fVertex, cVertex; 1700 1701 if ((sortedIndices[0] == faceVerticesQuadHexSorted[ii+0]) && 1702 (sortedIndices[1] == faceVerticesQuadHexSorted[ii+1]) && 1703 (sortedIndices[2] == faceVerticesQuadHexSorted[ii+2]) && 1704 (sortedIndices[3] == faceVerticesQuadHexSorted[ii+3])) { 1705 for (fVertex = 0; fVertex < faceSizeQuadHex; ++fVertex) { 1706 for (cVertex = 0; cVertex < faceSizeQuadHex; ++cVertex) { 1707 if (indices[cVertex] == faceVerticesQuadHex[ii+fVertex]) { 1708 faceVertices[fVertex] = origVertices[cVertex]; 1709 break; 1710 } 1711 } 1712 } 1713 found = PETSC_TRUE; 1714 break; 1715 } 1716 } 1717 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid hex crossface"); 1718 if (posOriented) *posOriented = PETSC_TRUE; 1719 PetscFunctionReturn(0); 1720 } else SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Unknown cell type for faceOrientation()."); 1721 if (!posOrient) { 1722 if (debug) {ierr = PetscPrintf(comm, " Reversing initial face orientation\n");CHKERRQ(ierr);} 1723 for (f = 0; f < faceSize; ++f) faceVertices[f] = origVertices[faceSize-1 - f]; 1724 } else { 1725 if (debug) {ierr = PetscPrintf(comm, " Keeping initial face orientation\n");CHKERRQ(ierr);} 1726 for (f = 0; f < faceSize; ++f) faceVertices[f] = origVertices[f]; 1727 } 1728 if (posOriented) *posOriented = posOrient; 1729 PetscFunctionReturn(0); 1730 } 1731 1732 #undef __FUNCT__ 1733 #define __FUNCT__ "DMPlexGetOrientedFace" 1734 /* 1735 Given a cell and a face, as a set of vertices, 1736 return the oriented face, as a set of vertices, in faceVertices 1737 The orientation is such that the face normal points out of the cell 1738 */ 1739 PetscErrorCode DMPlexGetOrientedFace(DM dm, PetscInt cell, PetscInt faceSize, const PetscInt face[], PetscInt numCorners, PetscInt indices[], PetscInt origVertices[], PetscInt faceVertices[], PetscBool *posOriented) 1740 { 1741 const PetscInt *cone = NULL; 1742 PetscInt coneSize, v, f, v2; 1743 PetscInt oppositeVertex = -1; 1744 PetscErrorCode ierr; 1745 1746 PetscFunctionBegin; 1747 ierr = DMPlexGetConeSize(dm, cell, &coneSize);CHKERRQ(ierr); 1748 ierr = DMPlexGetCone(dm, cell, &cone);CHKERRQ(ierr); 1749 for (v = 0, v2 = 0; v < coneSize; ++v) { 1750 PetscBool found = PETSC_FALSE; 1751 1752 for (f = 0; f < faceSize; ++f) { 1753 if (face[f] == cone[v]) { 1754 found = PETSC_TRUE; break; 1755 } 1756 } 1757 if (found) { 1758 indices[v2] = v; 1759 origVertices[v2] = cone[v]; 1760 ++v2; 1761 } else { 1762 oppositeVertex = v; 1763 } 1764 } 1765 ierr = DMPlexGetFaceOrientation(dm, cell, numCorners, indices, oppositeVertex, origVertices, faceVertices, posOriented);CHKERRQ(ierr); 1766 PetscFunctionReturn(0); 1767 } 1768 1769 #undef __FUNCT__ 1770 #define __FUNCT__ "DMPlexInsertFace_Internal" 1771 /* 1772 DMPlexInsertFace_Internal - Puts a face into the mesh 1773 1774 Not collective 1775 1776 Input Parameters: 1777 + dm - The DMPlex 1778 . numFaceVertex - The number of vertices in the face 1779 . faceVertices - The vertices in the face for dm 1780 . subfaceVertices - The vertices in the face for subdm 1781 . numCorners - The number of vertices in the cell 1782 . cell - A cell in dm containing the face 1783 . subcell - A cell in subdm containing the face 1784 . firstFace - First face in the mesh 1785 - newFacePoint - Next face in the mesh 1786 1787 Output Parameters: 1788 . newFacePoint - Contains next face point number on input, updated on output 1789 1790 Level: developer 1791 */ 1792 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) 1793 { 1794 MPI_Comm comm; 1795 DM_Plex *submesh = (DM_Plex*) subdm->data; 1796 const PetscInt *faces; 1797 PetscInt numFaces, coneSize; 1798 PetscErrorCode ierr; 1799 1800 PetscFunctionBegin; 1801 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 1802 ierr = DMPlexGetConeSize(subdm, subcell, &coneSize);CHKERRQ(ierr); 1803 if (coneSize != 1) SETERRQ2(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cone size of cell %d is %d != 1", cell, coneSize); 1804 #if 0 1805 /* Cannot use this because support() has not been constructed yet */ 1806 ierr = DMPlexGetJoin(subdm, numFaceVertices, subfaceVertices, &numFaces, &faces);CHKERRQ(ierr); 1807 #else 1808 { 1809 PetscInt f; 1810 1811 numFaces = 0; 1812 ierr = DMGetWorkArray(subdm, 1, PETSC_INT, (void **) &faces);CHKERRQ(ierr); 1813 for (f = firstFace; f < *newFacePoint; ++f) { 1814 PetscInt dof, off, d; 1815 1816 ierr = PetscSectionGetDof(submesh->coneSection, f, &dof);CHKERRQ(ierr); 1817 ierr = PetscSectionGetOffset(submesh->coneSection, f, &off);CHKERRQ(ierr); 1818 /* Yes, I know this is quadratic, but I expect the sizes to be <5 */ 1819 for (d = 0; d < dof; ++d) { 1820 const PetscInt p = submesh->cones[off+d]; 1821 PetscInt v; 1822 1823 for (v = 0; v < numFaceVertices; ++v) { 1824 if (subfaceVertices[v] == p) break; 1825 } 1826 if (v == numFaceVertices) break; 1827 } 1828 if (d == dof) { 1829 numFaces = 1; 1830 ((PetscInt*) faces)[0] = f; 1831 } 1832 } 1833 } 1834 #endif 1835 if (numFaces > 1) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Vertex set had %d faces, not one", numFaces); 1836 else if (numFaces == 1) { 1837 /* Add the other cell neighbor for this face */ 1838 ierr = DMPlexSetCone(subdm, subcell, faces);CHKERRQ(ierr); 1839 } else { 1840 PetscInt *indices, *origVertices, *orientedVertices, *orientedSubVertices, v, ov; 1841 PetscBool posOriented; 1842 1843 ierr = DMGetWorkArray(subdm, 4*numFaceVertices * sizeof(PetscInt), PETSC_INT, &orientedVertices);CHKERRQ(ierr); 1844 origVertices = &orientedVertices[numFaceVertices]; 1845 indices = &orientedVertices[numFaceVertices*2]; 1846 orientedSubVertices = &orientedVertices[numFaceVertices*3]; 1847 ierr = DMPlexGetOrientedFace(dm, cell, numFaceVertices, faceVertices, numCorners, indices, origVertices, orientedVertices, &posOriented);CHKERRQ(ierr); 1848 /* TODO: I know that routine should return a permutation, not the indices */ 1849 for (v = 0; v < numFaceVertices; ++v) { 1850 const PetscInt vertex = faceVertices[v], subvertex = subfaceVertices[v]; 1851 for (ov = 0; ov < numFaceVertices; ++ov) { 1852 if (orientedVertices[ov] == vertex) { 1853 orientedSubVertices[ov] = subvertex; 1854 break; 1855 } 1856 } 1857 if (ov == numFaceVertices) SETERRQ1(comm, PETSC_ERR_PLIB, "Could not find face vertex %d in orientated set", vertex); 1858 } 1859 ierr = DMPlexSetCone(subdm, *newFacePoint, orientedSubVertices);CHKERRQ(ierr); 1860 ierr = DMPlexSetCone(subdm, subcell, newFacePoint);CHKERRQ(ierr); 1861 ierr = DMRestoreWorkArray(subdm, 4*numFaceVertices * sizeof(PetscInt), PETSC_INT, &orientedVertices);CHKERRQ(ierr); 1862 ++(*newFacePoint); 1863 } 1864 #if 0 1865 ierr = DMPlexRestoreJoin(subdm, numFaceVertices, subfaceVertices, &numFaces, &faces);CHKERRQ(ierr); 1866 #else 1867 ierr = DMRestoreWorkArray(subdm, 1, PETSC_INT, (void **) &faces);CHKERRQ(ierr); 1868 #endif 1869 PetscFunctionReturn(0); 1870 } 1871 1872 #undef __FUNCT__ 1873 #define __FUNCT__ "DMPlexCreateSubmesh_Uninterpolated" 1874 static PetscErrorCode DMPlexCreateSubmesh_Uninterpolated(DM dm, const char vertexLabelName[], PetscInt value, DM subdm) 1875 { 1876 MPI_Comm comm; 1877 DMLabel vertexLabel, subpointMap; 1878 IS subvertexIS, subcellIS; 1879 const PetscInt *subVertices, *subCells; 1880 PetscInt numSubVertices, firstSubVertex, numSubCells; 1881 PetscInt *subface, maxConeSize, numSubFaces, firstSubFace, newFacePoint, nFV; 1882 PetscInt vStart, vEnd, c, f; 1883 PetscErrorCode ierr; 1884 1885 PetscFunctionBegin; 1886 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 1887 /* Create subpointMap which marks the submesh */ 1888 ierr = DMLabelCreate("subpoint_map", &subpointMap);CHKERRQ(ierr); 1889 ierr = DMPlexSetSubpointMap(subdm, subpointMap);CHKERRQ(ierr); 1890 ierr = DMLabelDestroy(&subpointMap);CHKERRQ(ierr); 1891 ierr = DMPlexGetLabel(dm, vertexLabelName, &vertexLabel);CHKERRQ(ierr); 1892 ierr = DMPlexMarkSubmesh_Uninterpolated(dm, vertexLabel, value, subpointMap, &numSubFaces, &nFV, subdm);CHKERRQ(ierr); 1893 /* Setup chart */ 1894 ierr = DMLabelGetStratumSize(subpointMap, 0, &numSubVertices);CHKERRQ(ierr); 1895 ierr = DMLabelGetStratumSize(subpointMap, 2, &numSubCells);CHKERRQ(ierr); 1896 ierr = DMPlexSetChart(subdm, 0, numSubCells+numSubFaces+numSubVertices);CHKERRQ(ierr); 1897 ierr = DMPlexSetVTKCellHeight(subdm, 1);CHKERRQ(ierr); 1898 /* Set cone sizes */ 1899 firstSubVertex = numSubCells; 1900 firstSubFace = numSubCells+numSubVertices; 1901 newFacePoint = firstSubFace; 1902 ierr = DMLabelGetStratumIS(subpointMap, 0, &subvertexIS);CHKERRQ(ierr); 1903 if (subvertexIS) {ierr = ISGetIndices(subvertexIS, &subVertices);CHKERRQ(ierr);} 1904 ierr = DMLabelGetStratumIS(subpointMap, 2, &subcellIS);CHKERRQ(ierr); 1905 if (subcellIS) {ierr = ISGetIndices(subcellIS, &subCells);CHKERRQ(ierr);} 1906 for (c = 0; c < numSubCells; ++c) { 1907 ierr = DMPlexSetConeSize(subdm, c, 1);CHKERRQ(ierr); 1908 } 1909 for (f = firstSubFace; f < firstSubFace+numSubFaces; ++f) { 1910 ierr = DMPlexSetConeSize(subdm, f, nFV);CHKERRQ(ierr); 1911 } 1912 ierr = DMSetUp(subdm);CHKERRQ(ierr); 1913 /* Create face cones */ 1914 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 1915 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, NULL);CHKERRQ(ierr); 1916 ierr = DMGetWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);CHKERRQ(ierr); 1917 for (c = 0; c < numSubCells; ++c) { 1918 const PetscInt cell = subCells[c]; 1919 const PetscInt subcell = c; 1920 PetscInt *closure = NULL; 1921 PetscInt closureSize, cl, numCorners = 0, faceSize = 0; 1922 1923 ierr = DMPlexGetTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1924 for (cl = 0; cl < closureSize*2; cl += 2) { 1925 const PetscInt point = closure[cl]; 1926 PetscInt subVertex; 1927 1928 if ((point >= vStart) && (point < vEnd)) { 1929 ++numCorners; 1930 ierr = PetscFindInt(point, numSubVertices, subVertices, &subVertex);CHKERRQ(ierr); 1931 if (subVertex >= 0) { 1932 closure[faceSize] = point; 1933 subface[faceSize] = firstSubVertex+subVertex; 1934 ++faceSize; 1935 } 1936 } 1937 } 1938 if (faceSize > nFV) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Invalid submesh: Too many vertices %d of an element on the surface", faceSize); 1939 if (faceSize == nFV) { 1940 ierr = DMPlexInsertFace_Internal(dm, subdm, faceSize, closure, subface, numCorners, cell, subcell, firstSubFace, &newFacePoint);CHKERRQ(ierr); 1941 } 1942 ierr = DMPlexRestoreTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1943 } 1944 ierr = DMRestoreWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);CHKERRQ(ierr); 1945 ierr = DMPlexSymmetrize(subdm);CHKERRQ(ierr); 1946 ierr = DMPlexStratify(subdm);CHKERRQ(ierr); 1947 /* Build coordinates */ 1948 { 1949 PetscSection coordSection, subCoordSection; 1950 Vec coordinates, subCoordinates; 1951 PetscScalar *coords, *subCoords; 1952 PetscInt numComp, coordSize, v; 1953 1954 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1955 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 1956 ierr = DMPlexGetCoordinateSection(subdm, &subCoordSection);CHKERRQ(ierr); 1957 ierr = PetscSectionSetNumFields(subCoordSection, 1);CHKERRQ(ierr); 1958 ierr = PetscSectionGetFieldComponents(coordSection, 0, &numComp);CHKERRQ(ierr); 1959 ierr = PetscSectionSetFieldComponents(subCoordSection, 0, numComp);CHKERRQ(ierr); 1960 ierr = PetscSectionSetChart(subCoordSection, firstSubVertex, firstSubVertex+numSubVertices);CHKERRQ(ierr); 1961 for (v = 0; v < numSubVertices; ++v) { 1962 const PetscInt vertex = subVertices[v]; 1963 const PetscInt subvertex = firstSubVertex+v; 1964 PetscInt dof; 1965 1966 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 1967 ierr = PetscSectionSetDof(subCoordSection, subvertex, dof);CHKERRQ(ierr); 1968 ierr = PetscSectionSetFieldDof(subCoordSection, subvertex, 0, dof);CHKERRQ(ierr); 1969 } 1970 ierr = PetscSectionSetUp(subCoordSection);CHKERRQ(ierr); 1971 ierr = PetscSectionGetStorageSize(subCoordSection, &coordSize);CHKERRQ(ierr); 1972 ierr = VecCreate(comm, &subCoordinates);CHKERRQ(ierr); 1973 ierr = VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1974 ierr = VecSetFromOptions(subCoordinates);CHKERRQ(ierr); 1975 if (coordSize) { 1976 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1977 ierr = VecGetArray(subCoordinates, &subCoords);CHKERRQ(ierr); 1978 for (v = 0; v < numSubVertices; ++v) { 1979 const PetscInt vertex = subVertices[v]; 1980 const PetscInt subvertex = firstSubVertex+v; 1981 PetscInt dof, off, sdof, soff, d; 1982 1983 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 1984 ierr = PetscSectionGetOffset(coordSection, vertex, &off);CHKERRQ(ierr); 1985 ierr = PetscSectionGetDof(subCoordSection, subvertex, &sdof);CHKERRQ(ierr); 1986 ierr = PetscSectionGetOffset(subCoordSection, subvertex, &soff);CHKERRQ(ierr); 1987 if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof); 1988 for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d]; 1989 } 1990 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1991 ierr = VecRestoreArray(subCoordinates, &subCoords);CHKERRQ(ierr); 1992 } 1993 ierr = DMSetCoordinatesLocal(subdm, subCoordinates);CHKERRQ(ierr); 1994 ierr = VecDestroy(&subCoordinates);CHKERRQ(ierr); 1995 } 1996 /* Cleanup */ 1997 if (subvertexIS) {ierr = ISRestoreIndices(subvertexIS, &subVertices);CHKERRQ(ierr);} 1998 ierr = ISDestroy(&subvertexIS);CHKERRQ(ierr); 1999 if (subcellIS) {ierr = ISRestoreIndices(subcellIS, &subCells);CHKERRQ(ierr);} 2000 ierr = ISDestroy(&subcellIS);CHKERRQ(ierr); 2001 PetscFunctionReturn(0); 2002 } 2003 2004 #undef __FUNCT__ 2005 #define __FUNCT__ "DMPlexCreateSubmesh_Interpolated" 2006 static PetscErrorCode DMPlexCreateSubmesh_Interpolated(DM dm, const char vertexLabelName[], PetscInt value, DM subdm) 2007 { 2008 MPI_Comm comm; 2009 DMLabel subpointMap, vertexLabel; 2010 IS *subpointIS; 2011 const PetscInt **subpoints; 2012 PetscInt *numSubPoints, *firstSubPoint, *coneNew, *coneONew; 2013 PetscInt totSubPoints = 0, maxConeSize, dim, p, d, v; 2014 PetscErrorCode ierr; 2015 2016 PetscFunctionBegin; 2017 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 2018 /* Create subpointMap which marks the submesh */ 2019 ierr = DMLabelCreate("subpoint_map", &subpointMap);CHKERRQ(ierr); 2020 ierr = DMPlexSetSubpointMap(subdm, subpointMap);CHKERRQ(ierr); 2021 ierr = DMLabelDestroy(&subpointMap);CHKERRQ(ierr); 2022 ierr = DMPlexGetLabel(dm, vertexLabelName, &vertexLabel);CHKERRQ(ierr); 2023 ierr = DMPlexMarkSubmesh_Interpolated(dm, vertexLabel, value, subpointMap, subdm);CHKERRQ(ierr); 2024 /* Setup chart */ 2025 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 2026 ierr = PetscMalloc4(dim+1,PetscInt,&numSubPoints,dim+1,PetscInt,&firstSubPoint,dim+1,IS,&subpointIS,dim+1,const PetscInt *,&subpoints);CHKERRQ(ierr); 2027 for (d = 0; d <= dim; ++d) { 2028 ierr = DMLabelGetStratumSize(subpointMap, d, &numSubPoints[d]);CHKERRQ(ierr); 2029 totSubPoints += numSubPoints[d]; 2030 } 2031 ierr = DMPlexSetChart(subdm, 0, totSubPoints);CHKERRQ(ierr); 2032 ierr = DMPlexSetVTKCellHeight(subdm, 1);CHKERRQ(ierr); 2033 /* Set cone sizes */ 2034 firstSubPoint[dim] = 0; 2035 firstSubPoint[0] = firstSubPoint[dim] + numSubPoints[dim]; 2036 if (dim > 1) {firstSubPoint[dim-1] = firstSubPoint[0] + numSubPoints[0];} 2037 if (dim > 2) {firstSubPoint[dim-2] = firstSubPoint[dim-1] + numSubPoints[dim-1];} 2038 for (d = 0; d <= dim; ++d) { 2039 ierr = DMLabelGetStratumIS(subpointMap, d, &subpointIS[d]);CHKERRQ(ierr); 2040 ierr = ISGetIndices(subpointIS[d], &subpoints[d]);CHKERRQ(ierr); 2041 } 2042 for (d = 0; d <= dim; ++d) { 2043 for (p = 0; p < numSubPoints[d]; ++p) { 2044 const PetscInt point = subpoints[d][p]; 2045 const PetscInt subpoint = firstSubPoint[d] + p; 2046 const PetscInt *cone; 2047 PetscInt coneSize, coneSizeNew, c, val; 2048 2049 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 2050 ierr = DMPlexSetConeSize(subdm, subpoint, coneSize);CHKERRQ(ierr); 2051 if (d == dim) { 2052 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 2053 for (c = 0, coneSizeNew = 0; c < coneSize; ++c) { 2054 ierr = DMLabelGetValue(subpointMap, cone[c], &val);CHKERRQ(ierr); 2055 if (val >= 0) coneSizeNew++; 2056 } 2057 ierr = DMPlexSetConeSize(subdm, subpoint, coneSizeNew);CHKERRQ(ierr); 2058 } 2059 } 2060 } 2061 ierr = DMSetUp(subdm);CHKERRQ(ierr); 2062 /* Set cones */ 2063 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, NULL);CHKERRQ(ierr); 2064 ierr = PetscMalloc2(maxConeSize,PetscInt,&coneNew,maxConeSize,PetscInt,&coneONew);CHKERRQ(ierr); 2065 for (d = 0; d <= dim; ++d) { 2066 for (p = 0; p < numSubPoints[d]; ++p) { 2067 const PetscInt point = subpoints[d][p]; 2068 const PetscInt subpoint = firstSubPoint[d] + p; 2069 const PetscInt *cone, *ornt; 2070 PetscInt coneSize, subconeSize, coneSizeNew, c, subc; 2071 2072 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 2073 ierr = DMPlexGetConeSize(subdm, subpoint, &subconeSize);CHKERRQ(ierr); 2074 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 2075 ierr = DMPlexGetConeOrientation(dm, point, &ornt);CHKERRQ(ierr); 2076 for (c = 0, coneSizeNew = 0; c < coneSize; ++c) { 2077 ierr = PetscFindInt(cone[c], numSubPoints[d-1], subpoints[d-1], &subc);CHKERRQ(ierr); 2078 if (subc >= 0) { 2079 coneNew[coneSizeNew] = firstSubPoint[d-1] + subc; 2080 coneONew[coneSizeNew] = ornt[c]; 2081 ++coneSizeNew; 2082 } 2083 } 2084 if (coneSizeNew != subconeSize) SETERRQ2(comm, PETSC_ERR_PLIB, "Number of cone points located %d does not match subcone size %d", coneSizeNew, subconeSize); 2085 ierr = DMPlexSetCone(subdm, subpoint, coneNew);CHKERRQ(ierr); 2086 ierr = DMPlexSetConeOrientation(subdm, subpoint, coneONew);CHKERRQ(ierr); 2087 } 2088 } 2089 ierr = PetscFree2(coneNew,coneONew);CHKERRQ(ierr); 2090 ierr = DMPlexSymmetrize(subdm);CHKERRQ(ierr); 2091 ierr = DMPlexStratify(subdm);CHKERRQ(ierr); 2092 /* Build coordinates */ 2093 { 2094 PetscSection coordSection, subCoordSection; 2095 Vec coordinates, subCoordinates; 2096 PetscScalar *coords, *subCoords; 2097 PetscInt numComp, coordSize; 2098 2099 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2100 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 2101 ierr = DMPlexGetCoordinateSection(subdm, &subCoordSection);CHKERRQ(ierr); 2102 ierr = PetscSectionSetNumFields(subCoordSection, 1);CHKERRQ(ierr); 2103 ierr = PetscSectionGetFieldComponents(coordSection, 0, &numComp);CHKERRQ(ierr); 2104 ierr = PetscSectionSetFieldComponents(subCoordSection, 0, numComp);CHKERRQ(ierr); 2105 ierr = PetscSectionSetChart(subCoordSection, firstSubPoint[0], firstSubPoint[0]+numSubPoints[0]);CHKERRQ(ierr); 2106 for (v = 0; v < numSubPoints[0]; ++v) { 2107 const PetscInt vertex = subpoints[0][v]; 2108 const PetscInt subvertex = firstSubPoint[0]+v; 2109 PetscInt dof; 2110 2111 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2112 ierr = PetscSectionSetDof(subCoordSection, subvertex, dof);CHKERRQ(ierr); 2113 ierr = PetscSectionSetFieldDof(subCoordSection, subvertex, 0, dof);CHKERRQ(ierr); 2114 } 2115 ierr = PetscSectionSetUp(subCoordSection);CHKERRQ(ierr); 2116 ierr = PetscSectionGetStorageSize(subCoordSection, &coordSize);CHKERRQ(ierr); 2117 ierr = VecCreate(comm, &subCoordinates);CHKERRQ(ierr); 2118 ierr = VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2119 ierr = VecSetFromOptions(subCoordinates);CHKERRQ(ierr); 2120 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2121 ierr = VecGetArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2122 for (v = 0; v < numSubPoints[0]; ++v) { 2123 const PetscInt vertex = subpoints[0][v]; 2124 const PetscInt subvertex = firstSubPoint[0]+v; 2125 PetscInt dof, off, sdof, soff, d; 2126 2127 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2128 ierr = PetscSectionGetOffset(coordSection, vertex, &off);CHKERRQ(ierr); 2129 ierr = PetscSectionGetDof(subCoordSection, subvertex, &sdof);CHKERRQ(ierr); 2130 ierr = PetscSectionGetOffset(subCoordSection, subvertex, &soff);CHKERRQ(ierr); 2131 if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof); 2132 for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d]; 2133 } 2134 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2135 ierr = VecRestoreArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2136 ierr = DMSetCoordinatesLocal(subdm, subCoordinates);CHKERRQ(ierr); 2137 ierr = VecDestroy(&subCoordinates);CHKERRQ(ierr); 2138 } 2139 /* Cleanup */ 2140 for (d = 0; d <= dim; ++d) { 2141 ierr = ISRestoreIndices(subpointIS[d], &subpoints[d]);CHKERRQ(ierr); 2142 ierr = ISDestroy(&subpointIS[d]);CHKERRQ(ierr); 2143 } 2144 ierr = PetscFree4(numSubPoints,firstSubPoint,subpointIS,subpoints);CHKERRQ(ierr); 2145 PetscFunctionReturn(0); 2146 } 2147 2148 #undef __FUNCT__ 2149 #define __FUNCT__ "DMPlexCreateSubmesh" 2150 /*@C 2151 DMPlexCreateSubmesh - Extract a hypersurface from the mesh using vertices defined by a label 2152 2153 Input Parameters: 2154 + dm - The original mesh 2155 . vertexLabel - The DMLabel marking vertices contained in the surface 2156 - value - The label value to use 2157 2158 Output Parameter: 2159 . subdm - The surface mesh 2160 2161 Note: This function produces a DMLabel mapping original points in the submesh to their depth. This can be obtained using DMPlexGetSubpointMap(). 2162 2163 Level: developer 2164 2165 .seealso: DMPlexGetSubpointMap(), DMPlexGetLabel(), DMLabelSetValue() 2166 @*/ 2167 PetscErrorCode DMPlexCreateSubmesh(DM dm, const char vertexLabel[], PetscInt value, DM *subdm) 2168 { 2169 PetscInt dim, depth; 2170 PetscErrorCode ierr; 2171 2172 PetscFunctionBegin; 2173 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2174 PetscValidCharPointer(vertexLabel, 2); 2175 PetscValidPointer(subdm, 3); 2176 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 2177 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 2178 ierr = DMCreate(PetscObjectComm((PetscObject)dm), subdm);CHKERRQ(ierr); 2179 ierr = DMSetType(*subdm, DMPLEX);CHKERRQ(ierr); 2180 ierr = DMPlexSetDimension(*subdm, dim-1);CHKERRQ(ierr); 2181 if (depth == dim) { 2182 ierr = DMPlexCreateSubmesh_Interpolated(dm, vertexLabel, value, *subdm);CHKERRQ(ierr); 2183 } else { 2184 ierr = DMPlexCreateSubmesh_Uninterpolated(dm, vertexLabel, value, *subdm);CHKERRQ(ierr); 2185 } 2186 PetscFunctionReturn(0); 2187 } 2188 2189 #undef __FUNCT__ 2190 #define __FUNCT__ "DMPlexCreateCohesiveSubmesh_Uninterpolated" 2191 static PetscErrorCode DMPlexCreateCohesiveSubmesh_Uninterpolated(DM dm, PetscBool hasLagrange, DM subdm) 2192 { 2193 MPI_Comm comm; 2194 DMLabel subpointMap; 2195 IS subvertexIS; 2196 const PetscInt *subVertices; 2197 PetscInt numSubVertices, firstSubVertex, numSubCells, *subCells; 2198 PetscInt *subface, maxConeSize, numSubFaces, firstSubFace, newFacePoint, nFV; 2199 PetscInt cMax, c, f; 2200 PetscErrorCode ierr; 2201 2202 PetscFunctionBegin; 2203 ierr = PetscObjectGetComm((PetscObject)dm, &comm);CHKERRQ(ierr); 2204 /* Create subpointMap which marks the submesh */ 2205 ierr = DMLabelCreate("subpoint_map", &subpointMap);CHKERRQ(ierr); 2206 ierr = DMPlexSetSubpointMap(subdm, subpointMap);CHKERRQ(ierr); 2207 ierr = DMLabelDestroy(&subpointMap);CHKERRQ(ierr); 2208 ierr = DMPlexMarkCohesiveSubmesh_Uninterpolated(dm, hasLagrange, subpointMap, &numSubFaces, &nFV, &subCells, subdm);CHKERRQ(ierr); 2209 /* Setup chart */ 2210 ierr = DMLabelGetStratumSize(subpointMap, 0, &numSubVertices);CHKERRQ(ierr); 2211 ierr = DMLabelGetStratumSize(subpointMap, 2, &numSubCells);CHKERRQ(ierr); 2212 ierr = DMPlexSetChart(subdm, 0, numSubCells+numSubFaces+numSubVertices);CHKERRQ(ierr); 2213 ierr = DMPlexSetVTKCellHeight(subdm, 1);CHKERRQ(ierr); 2214 /* Set cone sizes */ 2215 firstSubVertex = numSubCells; 2216 firstSubFace = numSubCells+numSubVertices; 2217 newFacePoint = firstSubFace; 2218 ierr = DMLabelGetStratumIS(subpointMap, 0, &subvertexIS);CHKERRQ(ierr); 2219 if (subvertexIS) {ierr = ISGetIndices(subvertexIS, &subVertices);CHKERRQ(ierr);} 2220 for (c = 0; c < numSubCells; ++c) { 2221 ierr = DMPlexSetConeSize(subdm, c, 1);CHKERRQ(ierr); 2222 } 2223 for (f = firstSubFace; f < firstSubFace+numSubFaces; ++f) { 2224 ierr = DMPlexSetConeSize(subdm, f, nFV);CHKERRQ(ierr); 2225 } 2226 ierr = DMSetUp(subdm);CHKERRQ(ierr); 2227 /* Create face cones */ 2228 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, NULL);CHKERRQ(ierr); 2229 ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); 2230 ierr = DMGetWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);CHKERRQ(ierr); 2231 for (c = 0; c < numSubCells; ++c) { 2232 const PetscInt cell = subCells[c]; 2233 const PetscInt subcell = c; 2234 const PetscInt *cone, *cells; 2235 PetscInt numCells, subVertex, p, v; 2236 2237 if (cell < cMax) continue; 2238 ierr = DMPlexGetCone(dm, cell, &cone);CHKERRQ(ierr); 2239 for (v = 0; v < nFV; ++v) { 2240 ierr = PetscFindInt(cone[v], numSubVertices, subVertices, &subVertex);CHKERRQ(ierr); 2241 subface[v] = firstSubVertex+subVertex; 2242 } 2243 ierr = DMPlexSetCone(subdm, newFacePoint, subface);CHKERRQ(ierr); 2244 ierr = DMPlexSetCone(subdm, subcell, &newFacePoint);CHKERRQ(ierr); 2245 ierr = DMPlexGetJoin(dm, nFV, cone, &numCells, &cells);CHKERRQ(ierr); 2246 if (numCells != 2) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive cells should separate two cells"); 2247 for (p = 0; p < numCells; ++p) { 2248 PetscInt negsubcell; 2249 2250 if (cells[p] >= cMax) continue; 2251 /* I know this is a crap search */ 2252 for (negsubcell = 0; negsubcell < numSubCells; ++negsubcell) { 2253 if (subCells[negsubcell] == cells[p]) break; 2254 } 2255 if (negsubcell == numSubCells) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not find negative face neighbor for cohesive cell %d", cell); 2256 ierr = DMPlexSetCone(subdm, negsubcell, &newFacePoint);CHKERRQ(ierr); 2257 } 2258 ierr = DMPlexRestoreJoin(dm, nFV, cone, &numCells, &cells);CHKERRQ(ierr); 2259 ++newFacePoint; 2260 } 2261 ierr = DMRestoreWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);CHKERRQ(ierr); 2262 ierr = DMPlexSymmetrize(subdm);CHKERRQ(ierr); 2263 ierr = DMPlexStratify(subdm);CHKERRQ(ierr); 2264 /* Build coordinates */ 2265 { 2266 PetscSection coordSection, subCoordSection; 2267 Vec coordinates, subCoordinates; 2268 PetscScalar *coords, *subCoords; 2269 PetscInt numComp, coordSize, v; 2270 2271 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2272 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 2273 ierr = DMPlexGetCoordinateSection(subdm, &subCoordSection);CHKERRQ(ierr); 2274 ierr = PetscSectionSetNumFields(subCoordSection, 1);CHKERRQ(ierr); 2275 ierr = PetscSectionGetFieldComponents(coordSection, 0, &numComp);CHKERRQ(ierr); 2276 ierr = PetscSectionSetFieldComponents(subCoordSection, 0, numComp);CHKERRQ(ierr); 2277 ierr = PetscSectionSetChart(subCoordSection, firstSubVertex, firstSubVertex+numSubVertices);CHKERRQ(ierr); 2278 for (v = 0; v < numSubVertices; ++v) { 2279 const PetscInt vertex = subVertices[v]; 2280 const PetscInt subvertex = firstSubVertex+v; 2281 PetscInt dof; 2282 2283 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2284 ierr = PetscSectionSetDof(subCoordSection, subvertex, dof);CHKERRQ(ierr); 2285 ierr = PetscSectionSetFieldDof(subCoordSection, subvertex, 0, dof);CHKERRQ(ierr); 2286 } 2287 ierr = PetscSectionSetUp(subCoordSection);CHKERRQ(ierr); 2288 ierr = PetscSectionGetStorageSize(subCoordSection, &coordSize);CHKERRQ(ierr); 2289 ierr = VecCreate(comm, &subCoordinates);CHKERRQ(ierr); 2290 if (coordSize) { 2291 ierr = VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2292 ierr = VecSetFromOptions(subCoordinates);CHKERRQ(ierr); 2293 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2294 ierr = VecGetArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2295 for (v = 0; v < numSubVertices; ++v) { 2296 const PetscInt vertex = subVertices[v]; 2297 const PetscInt subvertex = firstSubVertex+v; 2298 PetscInt dof, off, sdof, soff, d; 2299 2300 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2301 ierr = PetscSectionGetOffset(coordSection, vertex, &off);CHKERRQ(ierr); 2302 ierr = PetscSectionGetDof(subCoordSection, subvertex, &sdof);CHKERRQ(ierr); 2303 ierr = PetscSectionGetOffset(subCoordSection, subvertex, &soff);CHKERRQ(ierr); 2304 if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof); 2305 for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d]; 2306 } 2307 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2308 ierr = VecRestoreArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2309 } 2310 ierr = DMSetCoordinatesLocal(subdm, subCoordinates);CHKERRQ(ierr); 2311 ierr = VecDestroy(&subCoordinates);CHKERRQ(ierr); 2312 } 2313 /* Cleanup */ 2314 if (subvertexIS) {ierr = ISRestoreIndices(subvertexIS, &subVertices);CHKERRQ(ierr);} 2315 ierr = ISDestroy(&subvertexIS);CHKERRQ(ierr); 2316 ierr = PetscFree(subCells);CHKERRQ(ierr); 2317 PetscFunctionReturn(0); 2318 } 2319 2320 #undef __FUNCT__ 2321 #define __FUNCT__ "DMPlexCreateCohesiveSubmesh_Interpolated" 2322 static PetscErrorCode DMPlexCreateCohesiveSubmesh_Interpolated(DM dm, PetscBool hasLagrange, DM subdm) 2323 { 2324 MPI_Comm comm; 2325 DMLabel subpointMap; 2326 IS *subpointIS; 2327 const PetscInt **subpoints; 2328 PetscInt *numSubPoints, *firstSubPoint, *coneNew; 2329 PetscInt totSubPoints = 0, maxConeSize, dim, p, d, v; 2330 PetscErrorCode ierr; 2331 2332 PetscFunctionBegin; 2333 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 2334 /* Create subpointMap which marks the submesh */ 2335 ierr = DMLabelCreate("subpoint_map", &subpointMap);CHKERRQ(ierr); 2336 ierr = DMPlexSetSubpointMap(subdm, subpointMap);CHKERRQ(ierr); 2337 ierr = DMLabelDestroy(&subpointMap);CHKERRQ(ierr); 2338 ierr = DMPlexMarkCohesiveSubmesh_Interpolated(dm, hasLagrange, subpointMap, subdm);CHKERRQ(ierr); 2339 /* Setup chart */ 2340 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 2341 ierr = PetscMalloc4(dim+1,PetscInt,&numSubPoints,dim+1,PetscInt,&firstSubPoint,dim+1,IS,&subpointIS,dim+1,const PetscInt *,&subpoints);CHKERRQ(ierr); 2342 for (d = 0; d <= dim; ++d) { 2343 ierr = DMLabelGetStratumSize(subpointMap, d, &numSubPoints[d]);CHKERRQ(ierr); 2344 totSubPoints += numSubPoints[d]; 2345 } 2346 ierr = DMPlexSetChart(subdm, 0, totSubPoints);CHKERRQ(ierr); 2347 ierr = DMPlexSetVTKCellHeight(subdm, 1);CHKERRQ(ierr); 2348 /* Set cone sizes */ 2349 firstSubPoint[dim] = 0; 2350 firstSubPoint[0] = firstSubPoint[dim] + numSubPoints[dim]; 2351 if (dim > 1) {firstSubPoint[dim-1] = firstSubPoint[0] + numSubPoints[0];} 2352 if (dim > 2) {firstSubPoint[dim-2] = firstSubPoint[dim-1] + numSubPoints[dim-1];} 2353 for (d = 0; d <= dim; ++d) { 2354 ierr = DMLabelGetStratumIS(subpointMap, d, &subpointIS[d]);CHKERRQ(ierr); 2355 ierr = ISGetIndices(subpointIS[d], &subpoints[d]);CHKERRQ(ierr); 2356 } 2357 for (d = 0; d <= dim; ++d) { 2358 for (p = 0; p < numSubPoints[d]; ++p) { 2359 const PetscInt point = subpoints[d][p]; 2360 const PetscInt subpoint = firstSubPoint[d] + p; 2361 const PetscInt *cone; 2362 PetscInt coneSize, coneSizeNew, c, val; 2363 2364 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 2365 ierr = DMPlexSetConeSize(subdm, subpoint, coneSize);CHKERRQ(ierr); 2366 if (d == dim) { 2367 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 2368 for (c = 0, coneSizeNew = 0; c < coneSize; ++c) { 2369 ierr = DMLabelGetValue(subpointMap, cone[c], &val);CHKERRQ(ierr); 2370 if (val >= 0) coneSizeNew++; 2371 } 2372 ierr = DMPlexSetConeSize(subdm, subpoint, coneSizeNew);CHKERRQ(ierr); 2373 } 2374 } 2375 } 2376 ierr = DMSetUp(subdm);CHKERRQ(ierr); 2377 /* Set cones */ 2378 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, NULL);CHKERRQ(ierr); 2379 ierr = PetscMalloc(maxConeSize * sizeof(PetscInt), &coneNew);CHKERRQ(ierr); 2380 for (d = 0; d <= dim; ++d) { 2381 for (p = 0; p < numSubPoints[d]; ++p) { 2382 const PetscInt point = subpoints[d][p]; 2383 const PetscInt subpoint = firstSubPoint[d] + p; 2384 const PetscInt *cone; 2385 PetscInt coneSize, subconeSize, coneSizeNew, c, subc; 2386 2387 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 2388 ierr = DMPlexGetConeSize(subdm, subpoint, &subconeSize);CHKERRQ(ierr); 2389 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 2390 for (c = 0, coneSizeNew = 0; c < coneSize; ++c) { 2391 ierr = PetscFindInt(cone[c], numSubPoints[d-1], subpoints[d-1], &subc);CHKERRQ(ierr); 2392 if (subc >= 0) coneNew[coneSizeNew++] = firstSubPoint[d-1] + subc; 2393 } 2394 if (coneSizeNew != subconeSize) SETERRQ2(comm, PETSC_ERR_PLIB, "Number of cone points located %d does not match subcone size %d", coneSizeNew, subconeSize); 2395 ierr = DMPlexSetCone(subdm, subpoint, coneNew);CHKERRQ(ierr); 2396 } 2397 } 2398 ierr = PetscFree(coneNew);CHKERRQ(ierr); 2399 ierr = DMPlexSymmetrize(subdm);CHKERRQ(ierr); 2400 ierr = DMPlexStratify(subdm);CHKERRQ(ierr); 2401 /* Build coordinates */ 2402 { 2403 PetscSection coordSection, subCoordSection; 2404 Vec coordinates, subCoordinates; 2405 PetscScalar *coords, *subCoords; 2406 PetscInt numComp, coordSize; 2407 2408 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2409 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 2410 ierr = DMPlexGetCoordinateSection(subdm, &subCoordSection);CHKERRQ(ierr); 2411 ierr = PetscSectionSetNumFields(subCoordSection, 1);CHKERRQ(ierr); 2412 ierr = PetscSectionGetFieldComponents(coordSection, 0, &numComp);CHKERRQ(ierr); 2413 ierr = PetscSectionSetFieldComponents(subCoordSection, 0, numComp);CHKERRQ(ierr); 2414 ierr = PetscSectionSetChart(subCoordSection, firstSubPoint[0], firstSubPoint[0]+numSubPoints[0]);CHKERRQ(ierr); 2415 for (v = 0; v < numSubPoints[0]; ++v) { 2416 const PetscInt vertex = subpoints[0][v]; 2417 const PetscInt subvertex = firstSubPoint[0]+v; 2418 PetscInt dof; 2419 2420 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2421 ierr = PetscSectionSetDof(subCoordSection, subvertex, dof);CHKERRQ(ierr); 2422 ierr = PetscSectionSetFieldDof(subCoordSection, subvertex, 0, dof);CHKERRQ(ierr); 2423 } 2424 ierr = PetscSectionSetUp(subCoordSection);CHKERRQ(ierr); 2425 ierr = PetscSectionGetStorageSize(subCoordSection, &coordSize);CHKERRQ(ierr); 2426 ierr = VecCreate(comm, &subCoordinates);CHKERRQ(ierr); 2427 ierr = VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2428 ierr = VecSetFromOptions(subCoordinates);CHKERRQ(ierr); 2429 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2430 ierr = VecGetArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2431 for (v = 0; v < numSubPoints[0]; ++v) { 2432 const PetscInt vertex = subpoints[0][v]; 2433 const PetscInt subvertex = firstSubPoint[0]+v; 2434 PetscInt dof, off, sdof, soff, d; 2435 2436 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2437 ierr = PetscSectionGetOffset(coordSection, vertex, &off);CHKERRQ(ierr); 2438 ierr = PetscSectionGetDof(subCoordSection, subvertex, &sdof);CHKERRQ(ierr); 2439 ierr = PetscSectionGetOffset(subCoordSection, subvertex, &soff);CHKERRQ(ierr); 2440 if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof); 2441 for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d]; 2442 } 2443 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2444 ierr = VecRestoreArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2445 ierr = DMSetCoordinatesLocal(subdm, subCoordinates);CHKERRQ(ierr); 2446 ierr = VecDestroy(&subCoordinates);CHKERRQ(ierr); 2447 } 2448 /* Cleanup */ 2449 for (d = 0; d <= dim; ++d) { 2450 ierr = ISRestoreIndices(subpointIS[d], &subpoints[d]);CHKERRQ(ierr); 2451 ierr = ISDestroy(&subpointIS[d]);CHKERRQ(ierr); 2452 } 2453 ierr = PetscFree4(numSubPoints,firstSubPoint,subpointIS,subpoints);CHKERRQ(ierr); 2454 PetscFunctionReturn(0); 2455 } 2456 2457 #undef __FUNCT__ 2458 #define __FUNCT__ "DMPlexCreateCohesiveSubmesh" 2459 /* 2460 DMPlexCreateCohesiveSubmesh - Extract from a mesh with cohesive cells the hypersurface defined by one face of the cells. 2461 2462 Input Parameters: 2463 + dm - The original mesh 2464 - hasLagrange - The mesh has Lagrange unknowns in the cohesive cells 2465 2466 Output Parameter: 2467 . subdm - The surface mesh 2468 2469 Note: This function produces a DMLabel mapping original points in the submesh to their depth. This can be obtained using DMPlexGetSubpointMap(). 2470 2471 Level: developer 2472 2473 .seealso: DMPlexGetSubpointMap(), DMPlexCreateSubmesh() 2474 */ 2475 PetscErrorCode DMPlexCreateCohesiveSubmesh(DM dm, PetscBool hasLagrange, DM *subdm) 2476 { 2477 PetscInt dim, depth; 2478 PetscErrorCode ierr; 2479 2480 PetscFunctionBegin; 2481 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2482 PetscValidPointer(subdm, 3); 2483 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 2484 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 2485 ierr = DMCreate(PetscObjectComm((PetscObject)dm), subdm);CHKERRQ(ierr); 2486 ierr = DMSetType(*subdm, DMPLEX);CHKERRQ(ierr); 2487 ierr = DMPlexSetDimension(*subdm, dim-1);CHKERRQ(ierr); 2488 if (depth == dim) { 2489 ierr = DMPlexCreateCohesiveSubmesh_Interpolated(dm, hasLagrange, *subdm);CHKERRQ(ierr); 2490 } else { 2491 ierr = DMPlexCreateCohesiveSubmesh_Uninterpolated(dm, hasLagrange, *subdm);CHKERRQ(ierr); 2492 } 2493 PetscFunctionReturn(0); 2494 } 2495 2496 #undef __FUNCT__ 2497 #define __FUNCT__ "DMPlexGetSubpointMap" 2498 /*@ 2499 DMPlexGetSubpointMap - Returns a DMLabel with point dimension as values 2500 2501 Input Parameter: 2502 . dm - The submesh DM 2503 2504 Output Parameter: 2505 . subpointMap - The DMLabel of all the points from the original mesh in this submesh, or NULL if this is not a submesh 2506 2507 Level: developer 2508 2509 .seealso: DMPlexCreateSubmesh(), DMPlexCreateSubpointIS() 2510 @*/ 2511 PetscErrorCode DMPlexGetSubpointMap(DM dm, DMLabel *subpointMap) 2512 { 2513 DM_Plex *mesh = (DM_Plex*) dm->data; 2514 2515 PetscFunctionBegin; 2516 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2517 PetscValidPointer(subpointMap, 2); 2518 *subpointMap = mesh->subpointMap; 2519 PetscFunctionReturn(0); 2520 } 2521 2522 #undef __FUNCT__ 2523 #define __FUNCT__ "DMPlexSetSubpointMap" 2524 /* Note: Should normally not be called by the user, since it is set in DMPlexCreateSubmesh() */ 2525 PetscErrorCode DMPlexSetSubpointMap(DM dm, DMLabel subpointMap) 2526 { 2527 DM_Plex *mesh = (DM_Plex *) dm->data; 2528 DMLabel tmp; 2529 PetscErrorCode ierr; 2530 2531 PetscFunctionBegin; 2532 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2533 tmp = mesh->subpointMap; 2534 mesh->subpointMap = subpointMap; 2535 ++mesh->subpointMap->refct; 2536 ierr = DMLabelDestroy(&tmp);CHKERRQ(ierr); 2537 PetscFunctionReturn(0); 2538 } 2539 2540 #undef __FUNCT__ 2541 #define __FUNCT__ "DMPlexCreateSubpointIS" 2542 /*@ 2543 DMPlexCreateSubpointIS - Creates an IS covering the entire subdm chart with the original points as data 2544 2545 Input Parameter: 2546 . dm - The submesh DM 2547 2548 Output Parameter: 2549 . subpointIS - The IS of all the points from the original mesh in this submesh, or NULL if this is not a submesh 2550 2551 Note: This is IS is guaranteed to be sorted by the construction of the submesh 2552 2553 Level: developer 2554 2555 .seealso: DMPlexCreateSubmesh(), DMPlexGetSubpointMap() 2556 @*/ 2557 PetscErrorCode DMPlexCreateSubpointIS(DM dm, IS *subpointIS) 2558 { 2559 MPI_Comm comm; 2560 DMLabel subpointMap; 2561 IS is; 2562 const PetscInt *opoints; 2563 PetscInt *points, *depths; 2564 PetscInt depth, depStart, depEnd, d, pStart, pEnd, p, n, off; 2565 PetscErrorCode ierr; 2566 2567 PetscFunctionBegin; 2568 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2569 PetscValidPointer(subpointIS, 2); 2570 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 2571 *subpointIS = NULL; 2572 ierr = DMPlexGetSubpointMap(dm, &subpointMap);CHKERRQ(ierr); 2573 if (subpointMap) { 2574 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 2575 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 2576 if (pStart) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Submeshes must start the point numbering at 0, not %d", pStart); 2577 ierr = DMGetWorkArray(dm, depth+1, PETSC_INT, &depths);CHKERRQ(ierr); 2578 depths[0] = depth; 2579 depths[1] = 0; 2580 for(d = 2; d <= depth; ++d) {depths[d] = depth+1 - d;} 2581 ierr = PetscMalloc(pEnd * sizeof(PetscInt), &points);CHKERRQ(ierr); 2582 for(d = 0, off = 0; d <= depth; ++d) { 2583 const PetscInt dep = depths[d]; 2584 2585 ierr = DMPlexGetDepthStratum(dm, dep, &depStart, &depEnd);CHKERRQ(ierr); 2586 ierr = DMLabelGetStratumSize(subpointMap, dep, &n);CHKERRQ(ierr); 2587 if (((d < 2) && (depth > 1)) || (d == 1)) { /* Only check vertices and cells for now since the map is broken for others */ 2588 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); 2589 } else { 2590 if (!n) { 2591 if (d == 0) { 2592 /* Missing cells */ 2593 for(p = 0; p < depEnd-depStart; ++p, ++off) points[off] = -1; 2594 } else { 2595 /* Missing faces */ 2596 for(p = 0; p < depEnd-depStart; ++p, ++off) points[off] = PETSC_MAX_INT; 2597 } 2598 } 2599 } 2600 if (n) { 2601 ierr = DMLabelGetStratumIS(subpointMap, dep, &is);CHKERRQ(ierr); 2602 ierr = ISGetIndices(is, &opoints);CHKERRQ(ierr); 2603 for(p = 0; p < n; ++p, ++off) points[off] = opoints[p]; 2604 ierr = ISRestoreIndices(is, &opoints);CHKERRQ(ierr); 2605 ierr = ISDestroy(&is);CHKERRQ(ierr); 2606 } 2607 } 2608 ierr = DMRestoreWorkArray(dm, depth+1, PETSC_INT, &depths);CHKERRQ(ierr); 2609 if (off != pEnd) SETERRQ2(comm, PETSC_ERR_ARG_WRONG, "The number of mapped submesh points %d should be %d", off, pEnd); 2610 ierr = ISCreateGeneral(comm, pEnd, points, PETSC_OWN_POINTER, subpointIS);CHKERRQ(ierr); 2611 } 2612 PetscFunctionReturn(0); 2613 } 2614