1 #include <petsc-private/dmpleximpl.h> /*I "petscdmplex.h" I*/ 2 #include <petscsf.h> 3 4 #undef __FUNCT__ 5 #define __FUNCT__ "DMPlexMarkBoundaryFaces" 6 /*@ 7 DMPlexMarkBoundaryFaces - Mark all faces on the boundary 8 9 Not Collective 10 11 Input Parameter: 12 . dm - The original DM 13 14 Output Parameter: 15 . label - The DMLabel marking boundary faces with value 1 16 17 Level: developer 18 19 .seealso: DMLabelCreate(), DMPlexCreateLabel() 20 @*/ 21 PetscErrorCode DMPlexMarkBoundaryFaces(DM dm, DMLabel label) 22 { 23 PetscInt fStart, fEnd, f; 24 PetscErrorCode ierr; 25 26 PetscFunctionBegin; 27 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 28 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 29 for (f = fStart; f < fEnd; ++f) { 30 PetscInt supportSize; 31 32 ierr = DMPlexGetSupportSize(dm, f, &supportSize);CHKERRQ(ierr); 33 if (supportSize == 1) { 34 ierr = DMLabelSetValue(label, f, 1);CHKERRQ(ierr); 35 } 36 } 37 PetscFunctionReturn(0); 38 } 39 40 #undef __FUNCT__ 41 #define __FUNCT__ "DMPlexLabelComplete" 42 /*@ 43 DMPlexLabelComplete - Starting with a label marking points on a surface, we add the transitive closure to the surface 44 45 Input Parameters: 46 + dm - The DM 47 - label - A DMLabel marking the surface points 48 49 Output Parameter: 50 . label - A DMLabel marking all surface points in the transitive closure 51 52 Level: developer 53 54 .seealso: DMPlexLabelCohesiveComplete() 55 @*/ 56 PetscErrorCode DMPlexLabelComplete(DM dm, DMLabel label) 57 { 58 IS valueIS; 59 const PetscInt *values; 60 PetscInt numValues, v; 61 PetscErrorCode ierr; 62 63 PetscFunctionBegin; 64 ierr = DMLabelGetNumValues(label, &numValues);CHKERRQ(ierr); 65 ierr = DMLabelGetValueIS(label, &valueIS);CHKERRQ(ierr); 66 ierr = ISGetIndices(valueIS, &values);CHKERRQ(ierr); 67 for (v = 0; v < numValues; ++v) { 68 IS pointIS; 69 const PetscInt *points; 70 PetscInt numPoints, p; 71 72 ierr = DMLabelGetStratumSize(label, values[v], &numPoints);CHKERRQ(ierr); 73 ierr = DMLabelGetStratumIS(label, values[v], &pointIS);CHKERRQ(ierr); 74 ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); 75 for (p = 0; p < numPoints; ++p) { 76 PetscInt *closure = NULL; 77 PetscInt closureSize, c; 78 79 ierr = DMPlexGetTransitiveClosure(dm, points[p], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 80 for (c = 0; c < closureSize*2; c += 2) { 81 ierr = DMLabelSetValue(label, closure[c], values[v]);CHKERRQ(ierr); 82 } 83 ierr = DMPlexRestoreTransitiveClosure(dm, points[p], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 84 } 85 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 86 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 87 } 88 ierr = ISRestoreIndices(valueIS, &values);CHKERRQ(ierr); 89 ierr = ISDestroy(&valueIS);CHKERRQ(ierr); 90 PetscFunctionReturn(0); 91 } 92 93 #undef __FUNCT__ 94 #define __FUNCT__ "DMPlexShiftPoint_Internal" 95 PETSC_STATIC_INLINE PetscInt DMPlexShiftPoint_Internal(PetscInt p, PetscInt depth, PetscInt depthEnd[], PetscInt depthShift[]) 96 { 97 if (depth < 0) return p; 98 /* Cells */ if (p < depthEnd[depth]) return p; 99 /* Vertices */ if (p < depthEnd[0]) return p + depthShift[depth]; 100 /* Faces */ if (p < depthEnd[depth-1]) return p + depthShift[depth] + depthShift[0]; 101 /* Edges */ return p + depthShift[depth] + depthShift[0] + depthShift[depth-1]; 102 } 103 104 #undef __FUNCT__ 105 #define __FUNCT__ "DMPlexShiftSizes_Internal" 106 static PetscErrorCode DMPlexShiftSizes_Internal(DM dm, PetscInt depthShift[], DM dmNew) 107 { 108 PetscInt *depthEnd; 109 PetscInt depth = 0, d, pStart, pEnd, p; 110 PetscErrorCode ierr; 111 112 PetscFunctionBegin; 113 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 114 if (depth < 0) PetscFunctionReturn(0); 115 ierr = PetscMalloc((depth+1) * sizeof(PetscInt), &depthEnd);CHKERRQ(ierr); 116 /* Step 1: Expand chart */ 117 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 118 for (d = 0; d <= depth; ++d) { 119 pEnd += depthShift[d]; 120 ierr = DMPlexGetDepthStratum(dm, d, NULL, &depthEnd[d]);CHKERRQ(ierr); 121 } 122 ierr = DMPlexSetChart(dmNew, pStart, pEnd);CHKERRQ(ierr); 123 /* Step 2: Set cone and support sizes */ 124 for (d = 0; d <= depth; ++d) { 125 ierr = DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);CHKERRQ(ierr); 126 for (p = pStart; p < pEnd; ++p) { 127 PetscInt newp = DMPlexShiftPoint_Internal(p, depth, depthEnd, depthShift); 128 PetscInt size; 129 130 ierr = DMPlexGetConeSize(dm, p, &size);CHKERRQ(ierr); 131 ierr = DMPlexSetConeSize(dmNew, newp, size);CHKERRQ(ierr); 132 ierr = DMPlexGetSupportSize(dm, p, &size);CHKERRQ(ierr); 133 ierr = DMPlexSetSupportSize(dmNew, newp, size);CHKERRQ(ierr); 134 } 135 } 136 ierr = PetscFree(depthEnd);CHKERRQ(ierr); 137 PetscFunctionReturn(0); 138 } 139 140 #undef __FUNCT__ 141 #define __FUNCT__ "DMPlexShiftPoints_Internal" 142 static PetscErrorCode DMPlexShiftPoints_Internal(DM dm, PetscInt depthShift[], DM dmNew) 143 { 144 PetscInt *depthEnd, *newpoints; 145 PetscInt depth = 0, d, maxConeSize, maxSupportSize, pStart, pEnd, p; 146 PetscErrorCode ierr; 147 148 PetscFunctionBegin; 149 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 150 if (depth < 0) PetscFunctionReturn(0); 151 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize);CHKERRQ(ierr); 152 ierr = PetscMalloc2(depth+1,PetscInt,&depthEnd,PetscMax(maxConeSize, maxSupportSize),PetscInt,&newpoints);CHKERRQ(ierr); 153 for (d = 0; d <= depth; ++d) { 154 ierr = DMPlexGetDepthStratum(dm, d, NULL, &depthEnd[d]);CHKERRQ(ierr); 155 } 156 /* Step 5: Set cones and supports */ 157 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 158 for (p = pStart; p < pEnd; ++p) { 159 const PetscInt *points = NULL, *orientations = NULL; 160 PetscInt size, i, newp = DMPlexShiftPoint_Internal(p, depth, depthEnd, depthShift); 161 162 ierr = DMPlexGetConeSize(dm, p, &size);CHKERRQ(ierr); 163 ierr = DMPlexGetCone(dm, p, &points);CHKERRQ(ierr); 164 ierr = DMPlexGetConeOrientation(dm, p, &orientations);CHKERRQ(ierr); 165 for (i = 0; i < size; ++i) { 166 newpoints[i] = DMPlexShiftPoint_Internal(points[i], depth, depthEnd, depthShift); 167 } 168 ierr = DMPlexSetCone(dmNew, newp, newpoints);CHKERRQ(ierr); 169 ierr = DMPlexSetConeOrientation(dmNew, newp, orientations);CHKERRQ(ierr); 170 ierr = DMPlexGetSupportSize(dm, p, &size);CHKERRQ(ierr); 171 ierr = DMPlexGetSupport(dm, p, &points);CHKERRQ(ierr); 172 for (i = 0; i < size; ++i) { 173 newpoints[i] = DMPlexShiftPoint_Internal(points[i], depth, depthEnd, depthShift); 174 } 175 ierr = DMPlexSetSupport(dmNew, newp, newpoints);CHKERRQ(ierr); 176 } 177 ierr = PetscFree2(depthEnd,newpoints);CHKERRQ(ierr); 178 PetscFunctionReturn(0); 179 } 180 181 #undef __FUNCT__ 182 #define __FUNCT__ "DMPlexShiftCoordinates_Internal" 183 static PetscErrorCode DMPlexShiftCoordinates_Internal(DM dm, PetscInt depthShift[], DM dmNew) 184 { 185 PetscSection coordSection, newCoordSection; 186 Vec coordinates, newCoordinates; 187 PetscScalar *coords, *newCoords; 188 PetscInt *depthEnd, coordSize; 189 PetscInt dim, depth = 0, d, vStart, vEnd, vStartNew, vEndNew, v; 190 PetscErrorCode ierr; 191 192 PetscFunctionBegin; 193 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 194 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 195 ierr = PetscMalloc((depth+1) * sizeof(PetscInt), &depthEnd);CHKERRQ(ierr); 196 for (d = 0; d <= depth; ++d) { 197 ierr = DMPlexGetDepthStratum(dm, d, NULL, &depthEnd[d]);CHKERRQ(ierr); 198 } 199 /* Step 8: Convert coordinates */ 200 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 201 ierr = DMPlexGetDepthStratum(dmNew, 0, &vStartNew, &vEndNew);CHKERRQ(ierr); 202 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 203 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &newCoordSection);CHKERRQ(ierr); 204 ierr = PetscSectionSetNumFields(newCoordSection, 1);CHKERRQ(ierr); 205 ierr = PetscSectionSetFieldComponents(newCoordSection, 0, dim);CHKERRQ(ierr); 206 ierr = PetscSectionSetChart(newCoordSection, vStartNew, vEndNew);CHKERRQ(ierr); 207 for (v = vStartNew; v < vEndNew; ++v) { 208 ierr = PetscSectionSetDof(newCoordSection, v, dim);CHKERRQ(ierr); 209 ierr = PetscSectionSetFieldDof(newCoordSection, v, 0, dim);CHKERRQ(ierr); 210 } 211 ierr = PetscSectionSetUp(newCoordSection);CHKERRQ(ierr); 212 ierr = DMPlexSetCoordinateSection(dmNew, newCoordSection);CHKERRQ(ierr); 213 ierr = PetscSectionGetStorageSize(newCoordSection, &coordSize);CHKERRQ(ierr); 214 ierr = VecCreate(PetscObjectComm((PetscObject)dm), &newCoordinates);CHKERRQ(ierr); 215 ierr = PetscObjectSetName((PetscObject) newCoordinates, "coordinates");CHKERRQ(ierr); 216 ierr = VecSetSizes(newCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 217 ierr = VecSetFromOptions(newCoordinates);CHKERRQ(ierr); 218 ierr = DMSetCoordinatesLocal(dmNew, newCoordinates);CHKERRQ(ierr); 219 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 220 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 221 ierr = VecGetArray(newCoordinates, &newCoords);CHKERRQ(ierr); 222 for (v = vStart; v < vEnd; ++v) { 223 PetscInt dof, off, noff, d; 224 225 ierr = PetscSectionGetDof(coordSection, v, &dof);CHKERRQ(ierr); 226 ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr); 227 ierr = PetscSectionGetOffset(newCoordSection, DMPlexShiftPoint_Internal(v, depth, depthEnd, depthShift), &noff);CHKERRQ(ierr); 228 for (d = 0; d < dof; ++d) { 229 newCoords[noff+d] = coords[off+d]; 230 } 231 } 232 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 233 ierr = VecRestoreArray(newCoordinates, &newCoords);CHKERRQ(ierr); 234 ierr = VecDestroy(&newCoordinates);CHKERRQ(ierr); 235 ierr = PetscSectionDestroy(&newCoordSection);CHKERRQ(ierr); 236 ierr = PetscFree(depthEnd);CHKERRQ(ierr); 237 PetscFunctionReturn(0); 238 } 239 240 #undef __FUNCT__ 241 #define __FUNCT__ "DMPlexShiftSF_Internal" 242 static PetscErrorCode DMPlexShiftSF_Internal(DM dm, PetscInt depthShift[], DM dmNew) 243 { 244 PetscInt *depthEnd; 245 PetscInt depth = 0, d; 246 PetscSF sfPoint, sfPointNew; 247 const PetscSFNode *remotePoints; 248 PetscSFNode *gremotePoints; 249 const PetscInt *localPoints; 250 PetscInt *glocalPoints, *newLocation, *newRemoteLocation; 251 PetscInt numRoots, numLeaves, l, pStart, pEnd, totShift = 0; 252 PetscMPIInt numProcs; 253 PetscErrorCode ierr; 254 255 PetscFunctionBegin; 256 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 257 ierr = PetscMalloc((depth+1) * sizeof(PetscInt), &depthEnd);CHKERRQ(ierr); 258 for (d = 0; d <= depth; ++d) { 259 totShift += depthShift[d]; 260 ierr = DMPlexGetDepthStratum(dm, d, NULL, &depthEnd[d]);CHKERRQ(ierr); 261 } 262 /* Step 9: Convert pointSF */ 263 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)dm), &numProcs);CHKERRQ(ierr); 264 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 265 ierr = DMGetPointSF(dmNew, &sfPointNew);CHKERRQ(ierr); 266 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 267 ierr = PetscSFGetGraph(sfPoint, &numRoots, &numLeaves, &localPoints, &remotePoints);CHKERRQ(ierr); 268 if (numRoots >= 0) { 269 ierr = PetscMalloc2(numRoots,PetscInt,&newLocation,pEnd-pStart,PetscInt,&newRemoteLocation);CHKERRQ(ierr); 270 for (l=0; l<numRoots; l++) newLocation[l] = DMPlexShiftPoint_Internal(l, depth, depthEnd, depthShift); 271 ierr = PetscSFBcastBegin(sfPoint, MPIU_INT, newLocation, newRemoteLocation);CHKERRQ(ierr); 272 ierr = PetscSFBcastEnd(sfPoint, MPIU_INT, newLocation, newRemoteLocation);CHKERRQ(ierr); 273 ierr = PetscMalloc(numLeaves * sizeof(PetscInt), &glocalPoints);CHKERRQ(ierr); 274 ierr = PetscMalloc(numLeaves * sizeof(PetscSFNode), &gremotePoints);CHKERRQ(ierr); 275 for (l = 0; l < numLeaves; ++l) { 276 glocalPoints[l] = DMPlexShiftPoint_Internal(localPoints[l], depth, depthEnd, depthShift); 277 gremotePoints[l].rank = remotePoints[l].rank; 278 gremotePoints[l].index = newRemoteLocation[localPoints[l]]; 279 } 280 ierr = PetscFree2(newLocation,newRemoteLocation);CHKERRQ(ierr); 281 ierr = PetscSFSetGraph(sfPointNew, numRoots + totShift, numLeaves, glocalPoints, PETSC_OWN_POINTER, gremotePoints, PETSC_OWN_POINTER);CHKERRQ(ierr); 282 } 283 ierr = PetscFree(depthEnd);CHKERRQ(ierr); 284 PetscFunctionReturn(0); 285 } 286 287 #undef __FUNCT__ 288 #define __FUNCT__ "DMPlexShiftLabels_Internal" 289 static PetscErrorCode DMPlexShiftLabels_Internal(DM dm, PetscInt depthShift[], DM dmNew) 290 { 291 PetscSF sfPoint; 292 DMLabel vtkLabel, ghostLabel; 293 PetscInt *depthEnd; 294 const PetscSFNode *leafRemote; 295 const PetscInt *leafLocal; 296 PetscInt depth = 0, d, numLeaves, numLabels, l, cStart, cEnd, c, fStart, fEnd, f; 297 PetscMPIInt rank; 298 PetscErrorCode ierr; 299 300 PetscFunctionBegin; 301 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 302 ierr = PetscMalloc((depth+1) * sizeof(PetscInt), &depthEnd);CHKERRQ(ierr); 303 for (d = 0; d <= depth; ++d) { 304 ierr = DMPlexGetDepthStratum(dm, d, NULL, &depthEnd[d]);CHKERRQ(ierr); 305 } 306 /* Step 10: Convert labels */ 307 ierr = DMPlexGetNumLabels(dm, &numLabels);CHKERRQ(ierr); 308 for (l = 0; l < numLabels; ++l) { 309 DMLabel label, newlabel; 310 const char *lname; 311 PetscBool isDepth; 312 IS valueIS; 313 const PetscInt *values; 314 PetscInt numValues, val; 315 316 ierr = DMPlexGetLabelName(dm, l, &lname);CHKERRQ(ierr); 317 ierr = PetscStrcmp(lname, "depth", &isDepth);CHKERRQ(ierr); 318 if (isDepth) continue; 319 ierr = DMPlexCreateLabel(dmNew, lname);CHKERRQ(ierr); 320 ierr = DMPlexGetLabel(dm, lname, &label);CHKERRQ(ierr); 321 ierr = DMPlexGetLabel(dmNew, lname, &newlabel);CHKERRQ(ierr); 322 ierr = DMLabelGetValueIS(label, &valueIS);CHKERRQ(ierr); 323 ierr = ISGetLocalSize(valueIS, &numValues);CHKERRQ(ierr); 324 ierr = ISGetIndices(valueIS, &values);CHKERRQ(ierr); 325 for (val = 0; val < numValues; ++val) { 326 IS pointIS; 327 const PetscInt *points; 328 PetscInt numPoints, p; 329 330 ierr = DMLabelGetStratumIS(label, values[val], &pointIS);CHKERRQ(ierr); 331 ierr = ISGetLocalSize(pointIS, &numPoints);CHKERRQ(ierr); 332 ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); 333 for (p = 0; p < numPoints; ++p) { 334 const PetscInt newpoint = DMPlexShiftPoint_Internal(points[p], depth, depthEnd, depthShift); 335 336 ierr = DMLabelSetValue(newlabel, newpoint, values[val]);CHKERRQ(ierr); 337 } 338 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 339 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 340 } 341 ierr = ISRestoreIndices(valueIS, &values);CHKERRQ(ierr); 342 ierr = ISDestroy(&valueIS);CHKERRQ(ierr); 343 } 344 ierr = PetscFree(depthEnd);CHKERRQ(ierr); 345 /* Step 11: Make label for output (vtk) and to mark ghost points (ghost) */ 346 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr); 347 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 348 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 349 ierr = PetscSFGetGraph(sfPoint, NULL, &numLeaves, &leafLocal, &leafRemote);CHKERRQ(ierr); 350 ierr = DMPlexCreateLabel(dmNew, "vtk");CHKERRQ(ierr); 351 ierr = DMPlexCreateLabel(dmNew, "ghost");CHKERRQ(ierr); 352 ierr = DMPlexGetLabel(dmNew, "vtk", &vtkLabel);CHKERRQ(ierr); 353 ierr = DMPlexGetLabel(dmNew, "ghost", &ghostLabel);CHKERRQ(ierr); 354 for (l = 0, c = cStart; l < numLeaves && c < cEnd; ++l, ++c) { 355 for (; c < leafLocal[l] && c < cEnd; ++c) { 356 ierr = DMLabelSetValue(vtkLabel, c, 1);CHKERRQ(ierr); 357 } 358 if (leafLocal[l] >= cEnd) break; 359 if (leafRemote[l].rank == rank) { 360 ierr = DMLabelSetValue(vtkLabel, c, 1);CHKERRQ(ierr); 361 } else { 362 ierr = DMLabelSetValue(ghostLabel, c, 2);CHKERRQ(ierr); 363 } 364 } 365 for (; c < cEnd; ++c) { 366 ierr = DMLabelSetValue(vtkLabel, c, 1);CHKERRQ(ierr); 367 } 368 if (0) { 369 ierr = PetscViewerASCIISynchronizedAllow(PETSC_VIEWER_STDOUT_WORLD, PETSC_TRUE);CHKERRQ(ierr); 370 ierr = DMLabelView(vtkLabel, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 371 ierr = PetscViewerFlush(PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 372 } 373 ierr = DMPlexGetHeightStratum(dmNew, 1, &fStart, &fEnd);CHKERRQ(ierr); 374 for (f = fStart; f < fEnd; ++f) { 375 PetscInt numCells; 376 377 ierr = DMPlexGetSupportSize(dmNew, f, &numCells);CHKERRQ(ierr); 378 if (numCells < 2) { 379 ierr = DMLabelSetValue(ghostLabel, f, 1);CHKERRQ(ierr); 380 } else { 381 const PetscInt *cells = NULL; 382 PetscInt vA, vB; 383 384 ierr = DMPlexGetSupport(dmNew, f, &cells);CHKERRQ(ierr); 385 ierr = DMLabelGetValue(vtkLabel, cells[0], &vA);CHKERRQ(ierr); 386 ierr = DMLabelGetValue(vtkLabel, cells[1], &vB);CHKERRQ(ierr); 387 if (!vA && !vB) {ierr = DMLabelSetValue(ghostLabel, f, 1);CHKERRQ(ierr);} 388 } 389 } 390 if (0) { 391 ierr = PetscViewerASCIISynchronizedAllow(PETSC_VIEWER_STDOUT_WORLD, PETSC_TRUE);CHKERRQ(ierr); 392 ierr = DMLabelView(ghostLabel, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 393 ierr = PetscViewerFlush(PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 394 } 395 PetscFunctionReturn(0); 396 } 397 398 #undef __FUNCT__ 399 #define __FUNCT__ "DMPlexConstructGhostCells_Internal" 400 static PetscErrorCode DMPlexConstructGhostCells_Internal(DM dm, DMLabel label, PetscInt *numGhostCells, DM gdm) 401 { 402 IS valueIS; 403 const PetscInt *values; 404 PetscInt *depthShift; 405 PetscInt depth = 0, numFS, fs, ghostCell, cEnd, c; 406 PetscErrorCode ierr; 407 408 PetscFunctionBegin; 409 /* Count ghost cells */ 410 ierr = DMLabelGetValueIS(label, &valueIS);CHKERRQ(ierr); 411 ierr = ISGetLocalSize(valueIS, &numFS);CHKERRQ(ierr); 412 ierr = ISGetIndices(valueIS, &values);CHKERRQ(ierr); 413 414 *numGhostCells = 0; 415 for (fs = 0; fs < numFS; ++fs) { 416 PetscInt numBdFaces; 417 418 ierr = DMLabelGetStratumSize(label, values[fs], &numBdFaces);CHKERRQ(ierr); 419 420 *numGhostCells += numBdFaces; 421 } 422 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 423 ierr = PetscMalloc((depth+1) * sizeof(PetscInt), &depthShift);CHKERRQ(ierr); 424 ierr = PetscMemzero(depthShift, (depth+1) * sizeof(PetscInt));CHKERRQ(ierr); 425 if (depth >= 0) depthShift[depth] = *numGhostCells; 426 ierr = DMPlexShiftSizes_Internal(dm, depthShift, gdm);CHKERRQ(ierr); 427 /* Step 3: Set cone/support sizes for new points */ 428 ierr = DMPlexGetHeightStratum(dm, 0, NULL, &cEnd);CHKERRQ(ierr); 429 for (c = cEnd; c < cEnd + *numGhostCells; ++c) { 430 ierr = DMPlexSetConeSize(gdm, c, 1);CHKERRQ(ierr); 431 } 432 for (fs = 0; fs < numFS; ++fs) { 433 IS faceIS; 434 const PetscInt *faces; 435 PetscInt numFaces, f; 436 437 ierr = DMLabelGetStratumIS(label, values[fs], &faceIS);CHKERRQ(ierr); 438 ierr = ISGetLocalSize(faceIS, &numFaces);CHKERRQ(ierr); 439 ierr = ISGetIndices(faceIS, &faces);CHKERRQ(ierr); 440 for (f = 0; f < numFaces; ++f) { 441 PetscInt size; 442 443 ierr = DMPlexGetSupportSize(dm, faces[f], &size);CHKERRQ(ierr); 444 if (size != 1) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "DM has boundary face %d with %d support cells", faces[f], size); 445 ierr = DMPlexSetSupportSize(gdm, faces[f] + *numGhostCells, 2);CHKERRQ(ierr); 446 } 447 ierr = ISRestoreIndices(faceIS, &faces);CHKERRQ(ierr); 448 ierr = ISDestroy(&faceIS);CHKERRQ(ierr); 449 } 450 /* Step 4: Setup ghosted DM */ 451 ierr = DMSetUp(gdm);CHKERRQ(ierr); 452 ierr = DMPlexShiftPoints_Internal(dm, depthShift, gdm);CHKERRQ(ierr); 453 /* Step 6: Set cones and supports for new points */ 454 ghostCell = cEnd; 455 for (fs = 0; fs < numFS; ++fs) { 456 IS faceIS; 457 const PetscInt *faces; 458 PetscInt numFaces, f; 459 460 ierr = DMLabelGetStratumIS(label, values[fs], &faceIS);CHKERRQ(ierr); 461 ierr = ISGetLocalSize(faceIS, &numFaces);CHKERRQ(ierr); 462 ierr = ISGetIndices(faceIS, &faces);CHKERRQ(ierr); 463 for (f = 0; f < numFaces; ++f, ++ghostCell) { 464 PetscInt newFace = faces[f] + *numGhostCells; 465 466 ierr = DMPlexSetCone(gdm, ghostCell, &newFace);CHKERRQ(ierr); 467 ierr = DMPlexInsertSupport(gdm, newFace, 1, ghostCell);CHKERRQ(ierr); 468 } 469 ierr = ISRestoreIndices(faceIS, &faces);CHKERRQ(ierr); 470 ierr = ISDestroy(&faceIS);CHKERRQ(ierr); 471 } 472 ierr = ISRestoreIndices(valueIS, &values);CHKERRQ(ierr); 473 ierr = ISDestroy(&valueIS);CHKERRQ(ierr); 474 /* Step 7: Stratify */ 475 ierr = DMPlexStratify(gdm);CHKERRQ(ierr); 476 ierr = DMPlexShiftCoordinates_Internal(dm, depthShift, gdm);CHKERRQ(ierr); 477 ierr = DMPlexShiftSF_Internal(dm, depthShift, gdm);CHKERRQ(ierr); 478 ierr = DMPlexShiftLabels_Internal(dm, depthShift, gdm);CHKERRQ(ierr); 479 ierr = PetscFree(depthShift);CHKERRQ(ierr); 480 PetscFunctionReturn(0); 481 } 482 483 #undef __FUNCT__ 484 #define __FUNCT__ "DMPlexConstructGhostCells" 485 /*@C 486 DMPlexConstructGhostCells - Construct ghost cells which connect to every boundary face 487 488 Collective on dm 489 490 Input Parameters: 491 + dm - The original DM 492 - labelName - The label specifying the boundary faces, or "Face Sets" if this is NULL 493 494 Output Parameters: 495 + numGhostCells - The number of ghost cells added to the DM 496 - dmGhosted - The new DM 497 498 Note: If no label exists of that name, one will be created marking all boundary faces 499 500 Level: developer 501 502 .seealso: DMCreate() 503 */ 504 PetscErrorCode DMPlexConstructGhostCells(DM dm, const char labelName[], PetscInt *numGhostCells, DM *dmGhosted) 505 { 506 DM gdm; 507 DMLabel label; 508 const char *name = labelName ? labelName : "Face Sets"; 509 PetscInt dim; 510 PetscErrorCode ierr; 511 512 PetscFunctionBegin; 513 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 514 PetscValidPointer(numGhostCells, 3); 515 PetscValidPointer(dmGhosted, 4); 516 ierr = DMCreate(PetscObjectComm((PetscObject)dm), &gdm);CHKERRQ(ierr); 517 ierr = DMSetType(gdm, DMPLEX);CHKERRQ(ierr); 518 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 519 ierr = DMPlexSetDimension(gdm, dim);CHKERRQ(ierr); 520 ierr = DMPlexGetLabel(dm, name, &label);CHKERRQ(ierr); 521 if (!label) { 522 /* Get label for boundary faces */ 523 ierr = DMPlexCreateLabel(dm, name);CHKERRQ(ierr); 524 ierr = DMPlexGetLabel(dm, name, &label);CHKERRQ(ierr); 525 ierr = DMPlexMarkBoundaryFaces(dm, label);CHKERRQ(ierr); 526 } 527 ierr = DMPlexConstructGhostCells_Internal(dm, label, numGhostCells, gdm);CHKERRQ(ierr); 528 ierr = DMSetFromOptions(gdm);CHKERRQ(ierr); 529 *dmGhosted = gdm; 530 PetscFunctionReturn(0); 531 } 532 533 #undef __FUNCT__ 534 #define __FUNCT__ "DMPlexConstructCohesiveCells_Internal" 535 static PetscErrorCode DMPlexConstructCohesiveCells_Internal(DM dm, DMLabel label, DM sdm) 536 { 537 MPI_Comm comm; 538 IS valueIS, *pointIS; 539 const PetscInt *values, **splitPoints; 540 PetscSection coordSection; 541 Vec coordinates; 542 PetscScalar *coords; 543 PetscInt *depthShift, *depthOffset, *pMaxNew, *numSplitPoints, *coneNew, *supportNew; 544 PetscInt shift = 100, depth = 0, dep, dim, d, numSP = 0, sp, maxConeSize, maxSupportSize, numLabels, 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 /* Count split points and add cohesive cells */ 551 if (label) { 552 ierr = DMLabelGetValueIS(label, &valueIS);CHKERRQ(ierr); 553 ierr = ISGetLocalSize(valueIS, &numSP);CHKERRQ(ierr); 554 ierr = ISGetIndices(valueIS, &values);CHKERRQ(ierr); 555 } 556 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 557 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize);CHKERRQ(ierr); 558 ierr = PetscMalloc5(depth+1,PetscInt,&depthShift,depth+1,PetscInt,&depthOffset,depth+1,PetscInt,&pMaxNew,maxConeSize*3,PetscInt,&coneNew,maxSupportSize,PetscInt,&supportNew);CHKERRQ(ierr); 559 ierr = PetscMalloc3(depth+1,IS,&pointIS,depth+1,PetscInt,&numSplitPoints,depth+1,const PetscInt*,&splitPoints);CHKERRQ(ierr); 560 ierr = PetscMemzero(depthShift, (depth+1) * sizeof(PetscInt));CHKERRQ(ierr); 561 for (d = 0; d <= depth; ++d) { 562 ierr = DMPlexGetDepthStratum(dm, d, NULL, &pMaxNew[d]);CHKERRQ(ierr); 563 numSplitPoints[d] = 0; 564 splitPoints[d] = NULL; 565 pointIS[d] = NULL; 566 } 567 for (sp = 0; sp < numSP; ++sp) { 568 const PetscInt dep = values[sp]; 569 570 if ((dep < 0) || (dep > depth)) continue; 571 ierr = DMLabelGetStratumSize(label, dep, &depthShift[dep]);CHKERRQ(ierr); 572 ierr = DMLabelGetStratumIS(label, dep, &pointIS[dep]);CHKERRQ(ierr); 573 if (pointIS[dep]) { 574 ierr = ISGetLocalSize(pointIS[dep], &numSplitPoints[dep]);CHKERRQ(ierr); 575 ierr = ISGetIndices(pointIS[dep], &splitPoints[dep]);CHKERRQ(ierr); 576 } 577 } 578 if (depth >= 0) { 579 /* Calculate number of additional points */ 580 depthShift[depth] = depthShift[depth-1]; /* There is a cohesive cell for every split face */ 581 depthShift[1] += depthShift[0]; /* There is a cohesive edge for every split vertex */ 582 /* Calculate hybrid bound for each dimension */ 583 pMaxNew[0] += depthShift[depth]; 584 if (depth > 1) pMaxNew[dim-1] += depthShift[depth] + depthShift[0]; 585 if (depth > 2) pMaxNew[1] += depthShift[depth] + depthShift[0] + depthShift[dim-1]; 586 587 /* Calculate point offset for each dimension */ 588 depthOffset[depth] = 0; 589 depthOffset[0] = depthOffset[depth] + depthShift[depth]; 590 if (depth > 1) depthOffset[dim-1] = depthOffset[0] + depthShift[0]; 591 if (depth > 2) depthOffset[1] = depthOffset[dim-1] + depthShift[dim-1]; 592 } 593 ierr = DMPlexShiftSizes_Internal(dm, depthShift, sdm);CHKERRQ(ierr); 594 /* Step 3: Set cone/support sizes for new points */ 595 for (dep = 0; dep <= depth; ++dep) { 596 for (p = 0; p < numSplitPoints[dep]; ++p) { 597 const PetscInt oldp = splitPoints[dep][p]; 598 const PetscInt newp = depthOffset[dep] + oldp; 599 const PetscInt splitp = pMaxNew[dep] + p; 600 const PetscInt *support; 601 PetscInt coneSize, supportSize, q, e; 602 603 ierr = DMPlexGetConeSize(dm, oldp, &coneSize);CHKERRQ(ierr); 604 ierr = DMPlexSetConeSize(sdm, splitp, coneSize);CHKERRQ(ierr); 605 ierr = DMPlexGetSupportSize(dm, oldp, &supportSize);CHKERRQ(ierr); 606 ierr = DMPlexSetSupportSize(sdm, splitp, supportSize);CHKERRQ(ierr); 607 if (dep == depth-1) { 608 const PetscInt ccell = pMaxNew[depth] + p; 609 /* Add cohesive cells, they are prisms */ 610 ierr = DMPlexSetConeSize(sdm, ccell, 2 + coneSize);CHKERRQ(ierr); 611 } else if (dep == 0) { 612 const PetscInt cedge = pMaxNew[1] + (depthShift[1] - depthShift[0]) + p; 613 614 ierr = DMPlexGetSupport(dm, oldp, &support);CHKERRQ(ierr); 615 /* Split old vertex: Edges in old split faces and new cohesive edge */ 616 for (e = 0, q = 0; e < supportSize; ++e) { 617 PetscInt val; 618 619 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 620 if ((val == 1) || (val == (shift + 1))) ++q; 621 } 622 ierr = DMPlexSetSupportSize(sdm, newp, q+1);CHKERRQ(ierr); 623 /* Split new vertex: Edges in new split faces and new cohesive edge */ 624 for (e = 0, q = 0; e < supportSize; ++e) { 625 PetscInt val; 626 627 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 628 if ((val == 1) || (val == -(shift + 1))) ++q; 629 } 630 ierr = DMPlexSetSupportSize(sdm, splitp, q+1);CHKERRQ(ierr); 631 /* Add cohesive edges */ 632 ierr = DMPlexSetConeSize(sdm, cedge, 2);CHKERRQ(ierr); 633 /* Punt for now on support, you loop over closure, extract faces, check which ones are in the label */ 634 } else if (dep == dim-2) { 635 ierr = DMPlexGetSupport(dm, oldp, &support);CHKERRQ(ierr); 636 /* Split old edge: Faces in positive side cells and old split faces */ 637 for (e = 0, q = 0; e < supportSize; ++e) { 638 PetscInt val; 639 640 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 641 if ((val == dim-1) || (val == (shift + dim-1))) ++q; 642 } 643 ierr = DMPlexSetSupportSize(sdm, newp, q);CHKERRQ(ierr); 644 /* Split new edge: Faces in negative side cells and new split faces */ 645 for (e = 0, q = 0; e < supportSize; ++e) { 646 PetscInt val; 647 648 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 649 if ((val == dim-1) || (val == -(shift + dim-1))) ++q; 650 } 651 ierr = DMPlexSetSupportSize(sdm, splitp, q);CHKERRQ(ierr); 652 } 653 } 654 } 655 /* Step 4: Setup split DM */ 656 ierr = DMSetUp(sdm);CHKERRQ(ierr); 657 ierr = DMPlexShiftPoints_Internal(dm, depthShift, sdm);CHKERRQ(ierr); 658 /* Step 6: Set cones and supports for new points */ 659 for (dep = 0; dep <= depth; ++dep) { 660 for (p = 0; p < numSplitPoints[dep]; ++p) { 661 const PetscInt oldp = splitPoints[dep][p]; 662 const PetscInt newp = depthOffset[dep] + oldp; 663 const PetscInt splitp = pMaxNew[dep] + p; 664 const PetscInt *cone, *support, *ornt; 665 PetscInt coneSize, supportSize, q, v, e, s; 666 667 ierr = DMPlexGetConeSize(dm, oldp, &coneSize);CHKERRQ(ierr); 668 ierr = DMPlexGetCone(dm, oldp, &cone);CHKERRQ(ierr); 669 ierr = DMPlexGetConeOrientation(dm, oldp, &ornt);CHKERRQ(ierr); 670 ierr = DMPlexGetSupportSize(dm, oldp, &supportSize);CHKERRQ(ierr); 671 ierr = DMPlexGetSupport(dm, oldp, &support);CHKERRQ(ierr); 672 if (dep == depth-1) { 673 const PetscInt ccell = pMaxNew[depth] + p; 674 const PetscInt *supportF; 675 676 /* Split face: copy in old face to new face to start */ 677 ierr = DMPlexGetSupport(sdm, newp, &supportF);CHKERRQ(ierr); 678 ierr = DMPlexSetSupport(sdm, splitp, supportF);CHKERRQ(ierr); 679 /* Split old face: old vertices/edges in cone so no change */ 680 /* Split new face: new vertices/edges in cone */ 681 for (q = 0; q < coneSize; ++q) { 682 ierr = PetscFindInt(cone[q], numSplitPoints[dim-2], splitPoints[dim-2], &v);CHKERRQ(ierr); 683 684 coneNew[2+q] = pMaxNew[dim-2] + v; 685 } 686 ierr = DMPlexSetCone(sdm, splitp, &coneNew[2]);CHKERRQ(ierr); 687 ierr = DMPlexSetConeOrientation(sdm, splitp, ornt);CHKERRQ(ierr); 688 /* Cohesive cell: Old and new split face, then new cohesive edges */ 689 coneNew[0] = newp; 690 coneNew[1] = splitp; 691 for (q = 0; q < coneSize; ++q) { 692 coneNew[2+q] = (pMaxNew[1] - pMaxNew[dim-2]) + (depthShift[1] - depthShift[0]) + coneNew[2+q]; 693 } 694 ierr = DMPlexSetCone(sdm, ccell, coneNew);CHKERRQ(ierr); 695 696 697 for (s = 0; s < supportSize; ++s) { 698 PetscInt val; 699 700 ierr = DMLabelGetValue(label, support[s], &val);CHKERRQ(ierr); 701 if (val < 0) { 702 /* Split old face: Replace negative side cell with cohesive cell */ 703 ierr = DMPlexInsertSupport(sdm, newp, s, ccell);CHKERRQ(ierr); 704 } else { 705 /* Split new face: Replace positive side cell with cohesive cell */ 706 ierr = DMPlexInsertSupport(sdm, splitp, s, ccell);CHKERRQ(ierr); 707 } 708 } 709 } else if (dep == 0) { 710 const PetscInt cedge = pMaxNew[1] + (depthShift[1] - depthShift[0]) + p; 711 712 /* Split old vertex: Edges in old split faces and new cohesive edge */ 713 for (e = 0, q = 0; e < supportSize; ++e) { 714 PetscInt val; 715 716 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 717 if ((val == 1) || (val == (shift + 1))) { 718 supportNew[q++] = depthOffset[1] + support[e]; 719 } 720 } 721 supportNew[q] = cedge; 722 723 ierr = DMPlexSetSupport(sdm, newp, supportNew);CHKERRQ(ierr); 724 /* Split new vertex: Edges in new split faces and new cohesive edge */ 725 for (e = 0, q = 0; e < supportSize; ++e) { 726 PetscInt val, edge; 727 728 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 729 if (val == 1) { 730 ierr = PetscFindInt(support[e], numSplitPoints[1], splitPoints[1], &edge);CHKERRQ(ierr); 731 if (edge < 0) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Edge %d is not a split edge", support[e]); 732 supportNew[q++] = pMaxNew[1] + edge; 733 } else if (val == -(shift + 1)) { 734 supportNew[q++] = depthOffset[1] + support[e]; 735 } 736 } 737 supportNew[q] = cedge; 738 ierr = DMPlexSetSupport(sdm, splitp, supportNew);CHKERRQ(ierr); 739 /* Cohesive edge: Old and new split vertex, punting on support */ 740 coneNew[0] = newp; 741 coneNew[1] = splitp; 742 ierr = DMPlexSetCone(sdm, cedge, coneNew);CHKERRQ(ierr); 743 } else if (dep == dim-2) { 744 /* Split old edge: old vertices in cone so no change */ 745 /* Split new edge: new vertices in cone */ 746 for (q = 0; q < coneSize; ++q) { 747 ierr = PetscFindInt(cone[q], numSplitPoints[dim-3], splitPoints[dim-3], &v);CHKERRQ(ierr); 748 749 coneNew[q] = pMaxNew[dim-3] + v; 750 } 751 ierr = DMPlexSetCone(sdm, splitp, coneNew);CHKERRQ(ierr); 752 /* Split old edge: Faces in positive side cells and old split faces */ 753 for (e = 0, q = 0; e < supportSize; ++e) { 754 PetscInt val; 755 756 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 757 if ((val == dim-1) || (val == (shift + dim-1))) { 758 supportNew[q++] = depthOffset[dim-1] + support[e]; 759 } 760 } 761 ierr = DMPlexSetSupport(sdm, newp, supportNew);CHKERRQ(ierr); 762 /* Split new edge: Faces in negative side cells and new split faces */ 763 for (e = 0, q = 0; e < supportSize; ++e) { 764 PetscInt val, face; 765 766 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 767 if (val == dim-1) { 768 ierr = PetscFindInt(support[e], numSplitPoints[dim-1], splitPoints[dim-1], &face);CHKERRQ(ierr); 769 if (face < 0) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Face %d is not a split face", support[e]); 770 supportNew[q++] = pMaxNew[dim-1] + face; 771 } else if (val == -(shift + dim-1)) { 772 supportNew[q++] = depthOffset[dim-1] + support[e]; 773 } 774 } 775 ierr = DMPlexSetSupport(sdm, splitp, supportNew);CHKERRQ(ierr); 776 } 777 } 778 } 779 /* Step 6b: Replace split points in negative side cones */ 780 for (sp = 0; sp < numSP; ++sp) { 781 PetscInt dep = values[sp]; 782 IS pIS; 783 PetscInt numPoints; 784 const PetscInt *points; 785 786 if (dep >= 0) continue; 787 ierr = DMLabelGetStratumIS(label, dep, &pIS);CHKERRQ(ierr); 788 if (!pIS) continue; 789 dep = -dep - shift; 790 ierr = ISGetLocalSize(pIS, &numPoints);CHKERRQ(ierr); 791 ierr = ISGetIndices(pIS, &points);CHKERRQ(ierr); 792 for (p = 0; p < numPoints; ++p) { 793 const PetscInt oldp = points[p]; 794 const PetscInt newp = depthOffset[dep] + oldp; 795 const PetscInt *cone; 796 PetscInt coneSize, c; 797 PetscBool replaced = PETSC_FALSE; 798 799 /* Negative edge: replace split vertex */ 800 /* Negative cell: replace split face */ 801 ierr = DMPlexGetConeSize(sdm, newp, &coneSize);CHKERRQ(ierr); 802 ierr = DMPlexGetCone(sdm, newp, &cone);CHKERRQ(ierr); 803 for (c = 0; c < coneSize; ++c) { 804 const PetscInt coldp = cone[c] - depthOffset[dep-1]; 805 PetscInt csplitp, cp, val; 806 807 ierr = DMLabelGetValue(label, coldp, &val);CHKERRQ(ierr); 808 if (val == dep-1) { 809 ierr = PetscFindInt(coldp, numSplitPoints[dep-1], splitPoints[dep-1], &cp);CHKERRQ(ierr); 810 if (cp < 0) SETERRQ2(comm, PETSC_ERR_ARG_WRONG, "Point %d is not a split point of dimension %d", oldp, dep-1); 811 csplitp = pMaxNew[dep-1] + cp; 812 ierr = DMPlexInsertCone(sdm, newp, c, csplitp);CHKERRQ(ierr); 813 replaced = PETSC_TRUE; 814 } 815 } 816 if (!replaced) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "The cone of point %d does not contain split points", oldp); 817 } 818 ierr = ISRestoreIndices(pIS, &points);CHKERRQ(ierr); 819 ierr = ISDestroy(&pIS);CHKERRQ(ierr); 820 } 821 /* Step 7: Stratify */ 822 ierr = DMPlexStratify(sdm);CHKERRQ(ierr); 823 /* Step 8: Coordinates */ 824 ierr = DMPlexShiftCoordinates_Internal(dm, depthShift, sdm);CHKERRQ(ierr); 825 ierr = DMPlexGetCoordinateSection(sdm, &coordSection);CHKERRQ(ierr); 826 ierr = DMGetCoordinatesLocal(sdm, &coordinates);CHKERRQ(ierr); 827 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 828 for (v = 0; v < (numSplitPoints ? numSplitPoints[0] : 0); ++v) { 829 const PetscInt newp = depthOffset[0] + splitPoints[0][v]; 830 const PetscInt splitp = pMaxNew[0] + v; 831 PetscInt dof, off, soff, d; 832 833 ierr = PetscSectionGetDof(coordSection, newp, &dof);CHKERRQ(ierr); 834 ierr = PetscSectionGetOffset(coordSection, newp, &off);CHKERRQ(ierr); 835 ierr = PetscSectionGetOffset(coordSection, splitp, &soff);CHKERRQ(ierr); 836 for (d = 0; d < dof; ++d) coords[soff+d] = coords[off+d]; 837 } 838 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 839 /* Step 9: SF, if I can figure this out we can split the mesh in parallel */ 840 ierr = DMPlexShiftSF_Internal(dm, depthShift, sdm);CHKERRQ(ierr); 841 /* Step 10: Labels */ 842 ierr = DMPlexShiftLabels_Internal(dm, depthShift, sdm);CHKERRQ(ierr); 843 ierr = DMPlexGetNumLabels(sdm, &numLabels);CHKERRQ(ierr); 844 for (dep = 0; dep <= depth; ++dep) { 845 for (p = 0; p < numSplitPoints[dep]; ++p) { 846 const PetscInt newp = depthOffset[dep] + splitPoints[dep][p]; 847 const PetscInt splitp = pMaxNew[dep] + p; 848 PetscInt l; 849 850 for (l = 0; l < numLabels; ++l) { 851 DMLabel mlabel; 852 const char *lname; 853 PetscInt val; 854 PetscBool isDepth; 855 856 ierr = DMPlexGetLabelName(sdm, l, &lname);CHKERRQ(ierr); 857 ierr = PetscStrcmp(lname, "depth", &isDepth);CHKERRQ(ierr); 858 if (isDepth) continue; 859 ierr = DMPlexGetLabel(sdm, lname, &mlabel);CHKERRQ(ierr); 860 ierr = DMLabelGetValue(mlabel, newp, &val);CHKERRQ(ierr); 861 if (val >= 0) { 862 ierr = DMLabelSetValue(mlabel, splitp, val);CHKERRQ(ierr); 863 #if 0 864 /* Do not put cohesive edges into the label */ 865 if (dep == 0) { 866 const PetscInt cedge = pMaxNew[1] + (depthShift[1] - depthShift[0]) + p; 867 ierr = DMLabelSetValue(mlabel, cedge, val);CHKERRQ(ierr); 868 } 869 #endif 870 } 871 } 872 } 873 } 874 for (sp = 0; sp < numSP; ++sp) { 875 const PetscInt dep = values[sp]; 876 877 if ((dep < 0) || (dep > depth)) continue; 878 if (pointIS[dep]) {ierr = ISRestoreIndices(pointIS[dep], &splitPoints[dep]);CHKERRQ(ierr);} 879 ierr = ISDestroy(&pointIS[dep]);CHKERRQ(ierr); 880 } 881 if (label) { 882 ierr = ISRestoreIndices(valueIS, &values);CHKERRQ(ierr); 883 ierr = ISDestroy(&valueIS);CHKERRQ(ierr); 884 } 885 ierr = DMPlexGetChart(sdm, NULL, &pEnd);CHKERRQ(ierr); 886 pMaxNew[0] += depthShift[0]; /* Account for shadow vertices */ 887 if (depth > 1) pMaxNew[1] = pEnd - depthShift[0]; /* There is a hybrid edge for every shadow vertex */ 888 if (depth > 2) pMaxNew[2] = -1; /* There are no hybrid faces */ 889 ierr = DMPlexSetHybridBounds(sdm, depth >= 0 ? pMaxNew[depth] : PETSC_DETERMINE, depth>1 ? pMaxNew[depth-1] : PETSC_DETERMINE, depth>2 ? pMaxNew[1] : PETSC_DETERMINE, pMaxNew[0]);CHKERRQ(ierr); 890 ierr = PetscFree5(depthShift, depthOffset, pMaxNew, coneNew, supportNew);CHKERRQ(ierr); 891 ierr = PetscFree3(pointIS, numSplitPoints, splitPoints);CHKERRQ(ierr); 892 PetscFunctionReturn(0); 893 } 894 895 #undef __FUNCT__ 896 #define __FUNCT__ "DMPlexConstructCohesiveCells" 897 /*@C 898 DMPlexConstructCohesiveCells - Construct cohesive cells which split the face along an internal interface 899 900 Collective on dm 901 902 Input Parameters: 903 + dm - The original DM 904 - labelName - The label specifying the boundary faces (this could be auto-generated) 905 906 Output Parameters: 907 - dmSplit - The new DM 908 909 Level: developer 910 911 .seealso: DMCreate(), DMPlexLabelCohesiveComplete() 912 @*/ 913 PetscErrorCode DMPlexConstructCohesiveCells(DM dm, DMLabel label, DM *dmSplit) 914 { 915 DM sdm; 916 PetscInt dim; 917 PetscErrorCode ierr; 918 919 PetscFunctionBegin; 920 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 921 PetscValidPointer(dmSplit, 4); 922 ierr = DMCreate(PetscObjectComm((PetscObject)dm), &sdm);CHKERRQ(ierr); 923 ierr = DMSetType(sdm, DMPLEX);CHKERRQ(ierr); 924 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 925 ierr = DMPlexSetDimension(sdm, dim);CHKERRQ(ierr); 926 switch (dim) { 927 case 2: 928 case 3: 929 ierr = DMPlexConstructCohesiveCells_Internal(dm, label, sdm);CHKERRQ(ierr); 930 break; 931 default: 932 SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Cannot construct cohesive cells for dimension %d", dim); 933 } 934 *dmSplit = sdm; 935 PetscFunctionReturn(0); 936 } 937 938 #undef __FUNCT__ 939 #define __FUNCT__ "DMPlexLabelCohesiveComplete" 940 /*@ 941 DMPlexLabelCohesiveComplete - Starting with a label marking vertices on an internal surface, we add all other mesh pieces 942 to complete the surface 943 944 Input Parameters: 945 + dm - The DM 946 - label - A DMLabel marking the surface vertices 947 948 Output Parameter: 949 . label - A DMLabel marking all surface points 950 951 Level: developer 952 953 .seealso: DMPlexConstructCohesiveCells(), DMPlexLabelComplete() 954 @*/ 955 PetscErrorCode DMPlexLabelCohesiveComplete(DM dm, DMLabel label) 956 { 957 IS dimIS; 958 const PetscInt *points; 959 PetscInt shift = 100, dim, dep, cStart, cEnd, numPoints, p, val; 960 PetscErrorCode ierr; 961 962 PetscFunctionBegin; 963 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 964 /* Cell orientation for face gives the side of the fault */ 965 ierr = DMLabelGetStratumIS(label, dim-1, &dimIS);CHKERRQ(ierr); 966 if (!dimIS) PetscFunctionReturn(0); 967 ierr = ISGetLocalSize(dimIS, &numPoints);CHKERRQ(ierr); 968 ierr = ISGetIndices(dimIS, &points);CHKERRQ(ierr); 969 for (p = 0; p < numPoints; ++p) { 970 const PetscInt *support; 971 PetscInt supportSize, s; 972 973 ierr = DMPlexGetSupportSize(dm, points[p], &supportSize);CHKERRQ(ierr); 974 if (supportSize != 2) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Split face %d has %d != 2 supports", points[p], supportSize); 975 ierr = DMPlexGetSupport(dm, points[p], &support);CHKERRQ(ierr); 976 for (s = 0; s < supportSize; ++s) { 977 const PetscInt *cone, *ornt; 978 PetscInt coneSize, c; 979 PetscBool pos = PETSC_TRUE; 980 981 ierr = DMPlexGetConeSize(dm, support[s], &coneSize);CHKERRQ(ierr); 982 ierr = DMPlexGetCone(dm, support[s], &cone);CHKERRQ(ierr); 983 ierr = DMPlexGetConeOrientation(dm, support[s], &ornt);CHKERRQ(ierr); 984 for (c = 0; c < coneSize; ++c) { 985 if (cone[c] == points[p]) { 986 if (ornt[c] >= 0) { 987 ierr = DMLabelSetValue(label, support[s], shift+dim);CHKERRQ(ierr); 988 } else { 989 ierr = DMLabelSetValue(label, support[s], -(shift+dim));CHKERRQ(ierr); 990 pos = PETSC_FALSE; 991 } 992 break; 993 } 994 } 995 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]); 996 /* Put faces touching the fault in the label */ 997 for (c = 0; c < coneSize; ++c) { 998 const PetscInt point = cone[c]; 999 1000 ierr = DMLabelGetValue(label, point, &val);CHKERRQ(ierr); 1001 if (val == -1) { 1002 PetscInt *closure = NULL; 1003 PetscInt closureSize, cl; 1004 1005 ierr = DMPlexGetTransitiveClosure(dm, point, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1006 for (cl = 0; cl < closureSize*2; cl += 2) { 1007 const PetscInt clp = closure[cl]; 1008 1009 ierr = DMLabelGetValue(label, clp, &val);CHKERRQ(ierr); 1010 if ((val >= 0) && (val < dim-1)) { 1011 ierr = DMLabelSetValue(label, point, pos == PETSC_TRUE ? shift+dim-1 : -(shift+dim-1));CHKERRQ(ierr); 1012 break; 1013 } 1014 } 1015 ierr = DMPlexRestoreTransitiveClosure(dm, point, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1016 } 1017 } 1018 } 1019 } 1020 ierr = ISRestoreIndices(dimIS, &points);CHKERRQ(ierr); 1021 ierr = ISDestroy(&dimIS);CHKERRQ(ierr); 1022 /* Search for other cells/faces/edges connected to the fault by a vertex */ 1023 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1024 ierr = DMLabelGetStratumIS(label, 0, &dimIS);CHKERRQ(ierr); 1025 if (!dimIS) PetscFunctionReturn(0); 1026 ierr = ISGetLocalSize(dimIS, &numPoints);CHKERRQ(ierr); 1027 ierr = ISGetIndices(dimIS, &points);CHKERRQ(ierr); 1028 for (p = 0; p < numPoints; ++p) { 1029 PetscInt *star = NULL; 1030 PetscInt starSize, s; 1031 PetscInt again = 1; /* 0: Finished 1: Keep iterating after a change 2: No change */ 1032 1033 /* First mark cells connected to the fault */ 1034 ierr = DMPlexGetTransitiveClosure(dm, points[p], PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1035 while (again) { 1036 if (again > 1) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Could not classify all cells connected to the fault"); 1037 again = 0; 1038 for (s = 0; s < starSize*2; s += 2) { 1039 const PetscInt point = star[s]; 1040 const PetscInt *cone; 1041 PetscInt coneSize, c; 1042 1043 if ((point < cStart) || (point >= cEnd)) continue; 1044 ierr = DMLabelGetValue(label, point, &val);CHKERRQ(ierr); 1045 if (val != -1) continue; 1046 again = 2; 1047 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 1048 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 1049 for (c = 0; c < coneSize; ++c) { 1050 ierr = DMLabelGetValue(label, cone[c], &val);CHKERRQ(ierr); 1051 if (val != -1) { 1052 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); 1053 if (val > 0) { 1054 ierr = DMLabelSetValue(label, point, shift+dim);CHKERRQ(ierr); 1055 } else { 1056 ierr = DMLabelSetValue(label, point, -(shift+dim));CHKERRQ(ierr); 1057 } 1058 again = 1; 1059 break; 1060 } 1061 } 1062 } 1063 } 1064 /* Classify the rest by cell membership */ 1065 for (s = 0; s < starSize*2; s += 2) { 1066 const PetscInt point = star[s]; 1067 1068 ierr = DMLabelGetValue(label, point, &val);CHKERRQ(ierr); 1069 if (val == -1) { 1070 PetscInt *sstar = NULL; 1071 PetscInt sstarSize, ss; 1072 PetscBool marked = PETSC_FALSE; 1073 1074 ierr = DMPlexGetTransitiveClosure(dm, point, PETSC_FALSE, &sstarSize, &sstar);CHKERRQ(ierr); 1075 for (ss = 0; ss < sstarSize*2; ss += 2) { 1076 const PetscInt spoint = sstar[ss]; 1077 1078 if ((spoint < cStart) || (spoint >= cEnd)) continue; 1079 ierr = DMLabelGetValue(label, spoint, &val);CHKERRQ(ierr); 1080 if (val == -1) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Cell %d in star of %d does not have a valid label", spoint, point); 1081 ierr = DMPlexGetLabelValue(dm, "depth", point, &dep);CHKERRQ(ierr); 1082 if (val > 0) { 1083 ierr = DMLabelSetValue(label, point, shift+dep);CHKERRQ(ierr); 1084 } else { 1085 ierr = DMLabelSetValue(label, point, -(shift+dep));CHKERRQ(ierr); 1086 } 1087 marked = PETSC_TRUE; 1088 break; 1089 } 1090 ierr = DMPlexRestoreTransitiveClosure(dm, point, PETSC_FALSE, &sstarSize, &sstar);CHKERRQ(ierr); 1091 if (!marked) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Point %d could not be classified", point); 1092 } 1093 } 1094 ierr = DMPlexRestoreTransitiveClosure(dm, points[p], PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1095 } 1096 ierr = ISRestoreIndices(dimIS, &points);CHKERRQ(ierr); 1097 ierr = ISDestroy(&dimIS);CHKERRQ(ierr); 1098 PetscFunctionReturn(0); 1099 } 1100 1101 #undef __FUNCT__ 1102 #define __FUNCT__ "DMPlexMarkSubmesh_Uninterpolated" 1103 /* Here we need the explicit assumption that: 1104 1105 For any marked cell, the marked vertices constitute a single face 1106 */ 1107 static PetscErrorCode DMPlexMarkSubmesh_Uninterpolated(DM dm, DMLabel vertexLabel, PetscInt value, DMLabel subpointMap, PetscInt *numFaces, PetscInt *nFV, DM subdm) 1108 { 1109 IS subvertexIS; 1110 const PetscInt *subvertices; 1111 PetscInt *pStart, *pEnd, *pMax, pSize; 1112 PetscInt depth, dim, d, numSubVerticesInitial = 0, v; 1113 PetscErrorCode ierr; 1114 1115 PetscFunctionBegin; 1116 *numFaces = 0; 1117 *nFV = 0; 1118 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 1119 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1120 pSize = PetscMax(depth, dim) + 1; 1121 ierr = PetscMalloc3(pSize,PetscInt,&pStart,pSize,PetscInt,&pEnd,pSize,PetscInt,&pMax);CHKERRQ(ierr); 1122 ierr = DMPlexGetHybridBounds(dm, &pMax[depth], depth>1 ? &pMax[depth-1] : NULL, depth > 2 ? &pMax[1] : NULL, &pMax[0]);CHKERRQ(ierr); 1123 for (d = 0; d <= depth; ++d) { 1124 ierr = DMPlexGetDepthStratum(dm, d, &pStart[d], &pEnd[d]);CHKERRQ(ierr); 1125 if (pMax[d] >= 0) pEnd[d] = PetscMin(pEnd[d], pMax[d]); 1126 } 1127 /* Loop over initial vertices and mark all faces in the collective star() */ 1128 ierr = DMLabelGetStratumIS(vertexLabel, value, &subvertexIS);CHKERRQ(ierr); 1129 if (subvertexIS) { 1130 ierr = ISGetSize(subvertexIS, &numSubVerticesInitial);CHKERRQ(ierr); 1131 ierr = ISGetIndices(subvertexIS, &subvertices);CHKERRQ(ierr); 1132 } 1133 for (v = 0; v < numSubVerticesInitial; ++v) { 1134 const PetscInt vertex = subvertices[v]; 1135 PetscInt *star = NULL; 1136 PetscInt starSize, s, numCells = 0, c; 1137 1138 ierr = DMPlexGetTransitiveClosure(dm, vertex, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1139 for (s = 0; s < starSize*2; s += 2) { 1140 const PetscInt point = star[s]; 1141 if ((point >= pStart[depth]) && (point < pEnd[depth])) star[numCells++] = point; 1142 } 1143 for (c = 0; c < numCells; ++c) { 1144 const PetscInt cell = star[c]; 1145 PetscInt *closure = NULL; 1146 PetscInt closureSize, cl; 1147 PetscInt cellLoc, numCorners = 0, faceSize = 0; 1148 1149 ierr = DMLabelGetValue(subpointMap, cell, &cellLoc);CHKERRQ(ierr); 1150 if (cellLoc == 2) continue; 1151 if (cellLoc >= 0) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Cell %d has dimension %d in the surface label", cell, cellLoc); 1152 ierr = DMPlexGetTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1153 for (cl = 0; cl < closureSize*2; cl += 2) { 1154 const PetscInt point = closure[cl]; 1155 PetscInt vertexLoc; 1156 1157 if ((point >= pStart[0]) && (point < pEnd[0])) { 1158 ++numCorners; 1159 ierr = DMLabelGetValue(vertexLabel, point, &vertexLoc);CHKERRQ(ierr); 1160 if (vertexLoc == value) closure[faceSize++] = point; 1161 } 1162 } 1163 if (!(*nFV)) {ierr = DMPlexGetNumFaceVertices(dm, dim, numCorners, nFV);CHKERRQ(ierr);} 1164 if (faceSize > *nFV) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Invalid submesh: Too many vertices %d of an element on the surface", faceSize); 1165 if (faceSize == *nFV) { 1166 const PetscInt *cells = NULL; 1167 PetscInt numCells, nc; 1168 1169 ++(*numFaces); 1170 for (cl = 0; cl < faceSize; ++cl) { 1171 ierr = DMLabelSetValue(subpointMap, closure[cl], 0);CHKERRQ(ierr); 1172 } 1173 ierr = DMPlexGetJoin(dm, faceSize, closure, &numCells, &cells);CHKERRQ(ierr); 1174 for (nc = 0; nc < numCells; ++nc) { 1175 ierr = DMLabelSetValue(subpointMap, cells[nc], 2);CHKERRQ(ierr); 1176 } 1177 ierr = DMPlexRestoreJoin(dm, faceSize, closure, &numCells, &cells);CHKERRQ(ierr); 1178 } 1179 ierr = DMPlexRestoreTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1180 } 1181 ierr = DMPlexRestoreTransitiveClosure(dm, vertex, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1182 } 1183 if (subvertexIS) { 1184 ierr = ISRestoreIndices(subvertexIS, &subvertices);CHKERRQ(ierr); 1185 } 1186 ierr = ISDestroy(&subvertexIS);CHKERRQ(ierr); 1187 ierr = PetscFree3(pStart,pEnd,pMax);CHKERRQ(ierr); 1188 PetscFunctionReturn(0); 1189 } 1190 1191 #undef __FUNCT__ 1192 #define __FUNCT__ "DMPlexMarkSubmesh_Interpolated" 1193 static PetscErrorCode DMPlexMarkSubmesh_Interpolated(DM dm, DMLabel vertexLabel, PetscInt value, DMLabel subpointMap, DM subdm) 1194 { 1195 IS subvertexIS; 1196 const PetscInt *subvertices; 1197 PetscInt *pStart, *pEnd, *pMax; 1198 PetscInt dim, d, numSubVerticesInitial = 0, v; 1199 PetscErrorCode ierr; 1200 1201 PetscFunctionBegin; 1202 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1203 ierr = PetscMalloc3(dim+1,PetscInt,&pStart,dim+1,PetscInt,&pEnd,dim+1,PetscInt,&pMax);CHKERRQ(ierr); 1204 ierr = DMPlexGetHybridBounds(dm, &pMax[dim], dim>1 ? &pMax[dim-1] : NULL, dim > 2 ? &pMax[1] : NULL, &pMax[0]);CHKERRQ(ierr); 1205 for (d = 0; d <= dim; ++d) { 1206 ierr = DMPlexGetDepthStratum(dm, d, &pStart[d], &pEnd[d]);CHKERRQ(ierr); 1207 if (pMax[d] >= 0) pEnd[d] = PetscMin(pEnd[d], pMax[d]); 1208 } 1209 /* Loop over initial vertices and mark all faces in the collective star() */ 1210 ierr = DMLabelGetStratumIS(vertexLabel, value, &subvertexIS);CHKERRQ(ierr); 1211 if (subvertexIS) { 1212 ierr = ISGetSize(subvertexIS, &numSubVerticesInitial);CHKERRQ(ierr); 1213 ierr = ISGetIndices(subvertexIS, &subvertices);CHKERRQ(ierr); 1214 } 1215 for (v = 0; v < numSubVerticesInitial; ++v) { 1216 const PetscInt vertex = subvertices[v]; 1217 PetscInt *star = NULL; 1218 PetscInt starSize, s, numFaces = 0, f; 1219 1220 ierr = DMPlexGetTransitiveClosure(dm, vertex, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1221 for (s = 0; s < starSize*2; s += 2) { 1222 const PetscInt point = star[s]; 1223 if ((point >= pStart[dim-1]) && (point < pEnd[dim-1])) star[numFaces++] = point; 1224 } 1225 for (f = 0; f < numFaces; ++f) { 1226 const PetscInt face = star[f]; 1227 PetscInt *closure = NULL; 1228 PetscInt closureSize, c; 1229 PetscInt faceLoc; 1230 1231 ierr = DMLabelGetValue(subpointMap, face, &faceLoc);CHKERRQ(ierr); 1232 if (faceLoc == dim-1) continue; 1233 if (faceLoc >= 0) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Face %d has dimension %d in the surface label", face, faceLoc); 1234 ierr = DMPlexGetTransitiveClosure(dm, face, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1235 for (c = 0; c < closureSize*2; c += 2) { 1236 const PetscInt point = closure[c]; 1237 PetscInt vertexLoc; 1238 1239 if ((point >= pStart[0]) && (point < pEnd[0])) { 1240 ierr = DMLabelGetValue(vertexLabel, point, &vertexLoc);CHKERRQ(ierr); 1241 if (vertexLoc != value) break; 1242 } 1243 } 1244 if (c == closureSize*2) { 1245 const PetscInt *support; 1246 PetscInt supportSize, s; 1247 1248 for (c = 0; c < closureSize*2; c += 2) { 1249 const PetscInt point = closure[c]; 1250 1251 for (d = 0; d < dim; ++d) { 1252 if ((point >= pStart[d]) && (point < pEnd[d])) { 1253 ierr = DMLabelSetValue(subpointMap, point, d);CHKERRQ(ierr); 1254 break; 1255 } 1256 } 1257 } 1258 ierr = DMPlexGetSupportSize(dm, face, &supportSize);CHKERRQ(ierr); 1259 ierr = DMPlexGetSupport(dm, face, &support);CHKERRQ(ierr); 1260 for (s = 0; s < supportSize; ++s) { 1261 ierr = DMLabelSetValue(subpointMap, support[s], dim);CHKERRQ(ierr); 1262 } 1263 } 1264 ierr = DMPlexRestoreTransitiveClosure(dm, face, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1265 } 1266 ierr = DMPlexRestoreTransitiveClosure(dm, vertex, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1267 } 1268 if (subvertexIS) { 1269 ierr = ISRestoreIndices(subvertexIS, &subvertices);CHKERRQ(ierr); 1270 } 1271 ierr = ISDestroy(&subvertexIS);CHKERRQ(ierr); 1272 ierr = PetscFree3(pStart,pEnd,pMax);CHKERRQ(ierr); 1273 PetscFunctionReturn(0); 1274 } 1275 1276 #undef __FUNCT__ 1277 #define __FUNCT__ "DMPlexMarkCohesiveSubmesh_Uninterpolated" 1278 static PetscErrorCode DMPlexMarkCohesiveSubmesh_Uninterpolated(DM dm, PetscBool hasLagrange, const char labelname[], PetscInt value, DMLabel subpointMap, PetscInt *numFaces, PetscInt *nFV, PetscInt *subCells[], DM subdm) 1279 { 1280 DMLabel label = NULL; 1281 const PetscInt *cone; 1282 PetscInt dim, cMax, cEnd, c, p, coneSize; 1283 PetscErrorCode ierr; 1284 1285 PetscFunctionBegin; 1286 *numFaces = 0; 1287 *nFV = 0; 1288 if (labelname) {ierr = DMPlexGetLabel(dm, labelname, &label);CHKERRQ(ierr);} 1289 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1290 ierr = DMPlexGetHeightStratum(dm, 0, NULL, &cEnd);CHKERRQ(ierr); 1291 ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); 1292 if (cMax < 0) PetscFunctionReturn(0); 1293 if (label) { 1294 for (c = cMax; c < cEnd; ++c) { 1295 PetscInt val; 1296 1297 ierr = DMLabelGetValue(label, c, &val);CHKERRQ(ierr); 1298 if (val == value) { 1299 ++(*numFaces); 1300 ierr = DMPlexGetConeSize(dm, c, &coneSize);CHKERRQ(ierr); 1301 } 1302 } 1303 } else { 1304 *numFaces = cEnd - cMax; 1305 ierr = DMPlexGetConeSize(dm, cMax, &coneSize);CHKERRQ(ierr); 1306 } 1307 *nFV = hasLagrange ? coneSize/3 : coneSize/2; 1308 ierr = PetscMalloc(*numFaces *2 * sizeof(PetscInt), subCells);CHKERRQ(ierr); 1309 for (c = cMax; c < cEnd; ++c) { 1310 const PetscInt *cells; 1311 PetscInt numCells; 1312 1313 if (label) { 1314 PetscInt val; 1315 1316 ierr = DMLabelGetValue(label, c, &val);CHKERRQ(ierr); 1317 if (val != value) continue; 1318 } 1319 ierr = DMPlexGetCone(dm, c, &cone);CHKERRQ(ierr); 1320 for (p = 0; p < *nFV; ++p) { 1321 ierr = DMLabelSetValue(subpointMap, cone[p], 0);CHKERRQ(ierr); 1322 } 1323 /* Negative face */ 1324 ierr = DMPlexGetJoin(dm, *nFV, cone, &numCells, &cells);CHKERRQ(ierr); 1325 if (numCells != 2) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive cells should separate two cells"); 1326 for (p = 0; p < numCells; ++p) { 1327 ierr = DMLabelSetValue(subpointMap, cells[p], 2);CHKERRQ(ierr); 1328 (*subCells)[(c-cMax)*2+p] = cells[p]; 1329 } 1330 ierr = DMPlexRestoreJoin(dm, *nFV, cone, &numCells, &cells);CHKERRQ(ierr); 1331 /* Positive face is not included */ 1332 } 1333 PetscFunctionReturn(0); 1334 } 1335 1336 #undef __FUNCT__ 1337 #define __FUNCT__ "DMPlexMarkCohesiveSubmesh_Interpolated" 1338 static PetscErrorCode DMPlexMarkCohesiveSubmesh_Interpolated(DM dm, PetscBool hasLagrange, const char labelname[], PetscInt value, DMLabel subpointMap, DM subdm) 1339 { 1340 DMLabel label = NULL; 1341 PetscInt *pStart, *pEnd; 1342 PetscInt dim, cMax, cEnd, c, d; 1343 PetscErrorCode ierr; 1344 1345 PetscFunctionBegin; 1346 if (labelname) {ierr = DMPlexGetLabel(dm, labelname, &label);CHKERRQ(ierr);} 1347 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1348 ierr = DMPlexGetHeightStratum(dm, 0, NULL, &cEnd);CHKERRQ(ierr); 1349 ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); 1350 if (cMax < 0) PetscFunctionReturn(0); 1351 ierr = PetscMalloc2(dim+1,PetscInt,&pStart,dim+1,PetscInt,&pEnd);CHKERRQ(ierr); 1352 for (d = 0; d <= dim; ++d) { 1353 ierr = DMPlexGetDepthStratum(dm, d, &pStart[d], &pEnd[d]);CHKERRQ(ierr); 1354 } 1355 for (c = cMax; c < cEnd; ++c) { 1356 const PetscInt *cone; 1357 PetscInt *closure = NULL; 1358 PetscInt coneSize, closureSize, cl; 1359 1360 if (label) { 1361 PetscInt val; 1362 1363 ierr = DMLabelGetValue(label, c, &val);CHKERRQ(ierr); 1364 if (val != value) continue; 1365 } 1366 ierr = DMPlexGetConeSize(dm, c, &coneSize);CHKERRQ(ierr); 1367 if (hasLagrange) { 1368 if (coneSize != 3) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive cells should separate two cells"); 1369 } else { 1370 if (coneSize != 2) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive cells should separate two cells"); 1371 } 1372 /* Negative face */ 1373 ierr = DMPlexGetCone(dm, c, &cone);CHKERRQ(ierr); 1374 ierr = DMPlexGetTransitiveClosure(dm, cone[0], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1375 for (cl = 0; cl < closureSize*2; cl += 2) { 1376 const PetscInt point = closure[cl]; 1377 1378 for (d = 0; d <= dim; ++d) { 1379 if ((point >= pStart[d]) && (point < pEnd[d])) { 1380 ierr = DMLabelSetValue(subpointMap, point, d);CHKERRQ(ierr); 1381 break; 1382 } 1383 } 1384 } 1385 ierr = DMPlexRestoreTransitiveClosure(dm, cone[0], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1386 /* Cells -- positive face is not included */ 1387 for (cl = 0; cl < 1; ++cl) { 1388 const PetscInt *support; 1389 PetscInt supportSize, s; 1390 1391 ierr = DMPlexGetSupportSize(dm, cone[cl], &supportSize);CHKERRQ(ierr); 1392 if (supportSize != 2) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive faces should separate two cells"); 1393 ierr = DMPlexGetSupport(dm, cone[cl], &support);CHKERRQ(ierr); 1394 for (s = 0; s < supportSize; ++s) { 1395 ierr = DMLabelSetValue(subpointMap, support[s], dim);CHKERRQ(ierr); 1396 } 1397 } 1398 } 1399 ierr = PetscFree2(pStart, pEnd);CHKERRQ(ierr); 1400 PetscFunctionReturn(0); 1401 } 1402 1403 #undef __FUNCT__ 1404 #define __FUNCT__ "DMPlexGetFaceOrientation" 1405 PetscErrorCode DMPlexGetFaceOrientation(DM dm, PetscInt cell, PetscInt numCorners, PetscInt indices[], PetscInt oppositeVertex, PetscInt origVertices[], PetscInt faceVertices[], PetscBool *posOriented) 1406 { 1407 MPI_Comm comm; 1408 PetscBool posOrient = PETSC_FALSE; 1409 const PetscInt debug = 0; 1410 PetscInt cellDim, faceSize, f; 1411 PetscErrorCode ierr; 1412 1413 PetscFunctionBegin; 1414 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 1415 ierr = DMPlexGetDimension(dm, &cellDim);CHKERRQ(ierr); 1416 if (debug) {PetscPrintf(comm, "cellDim: %d numCorners: %d\n", cellDim, numCorners);CHKERRQ(ierr);} 1417 1418 if (cellDim == 1 && numCorners == 2) { 1419 /* Triangle */ 1420 faceSize = numCorners-1; 1421 posOrient = !(oppositeVertex%2) ? PETSC_TRUE : PETSC_FALSE; 1422 } else if (cellDim == 2 && numCorners == 3) { 1423 /* Triangle */ 1424 faceSize = numCorners-1; 1425 posOrient = !(oppositeVertex%2) ? PETSC_TRUE : PETSC_FALSE; 1426 } else if (cellDim == 3 && numCorners == 4) { 1427 /* Tetrahedron */ 1428 faceSize = numCorners-1; 1429 posOrient = (oppositeVertex%2) ? PETSC_TRUE : PETSC_FALSE; 1430 } else if (cellDim == 1 && numCorners == 3) { 1431 /* Quadratic line */ 1432 faceSize = 1; 1433 posOrient = PETSC_TRUE; 1434 } else if (cellDim == 2 && numCorners == 4) { 1435 /* Quads */ 1436 faceSize = 2; 1437 if ((indices[1] > indices[0]) && (indices[1] - indices[0] == 1)) { 1438 posOrient = PETSC_TRUE; 1439 } else if ((indices[0] == 3) && (indices[1] == 0)) { 1440 posOrient = PETSC_TRUE; 1441 } else { 1442 if (((indices[0] > indices[1]) && (indices[0] - indices[1] == 1)) || ((indices[0] == 0) && (indices[1] == 3))) { 1443 posOrient = PETSC_FALSE; 1444 } else SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid quad crossedge"); 1445 } 1446 } else if (cellDim == 2 && numCorners == 6) { 1447 /* Quadratic triangle (I hate this) */ 1448 /* Edges are determined by the first 2 vertices (corners of edges) */ 1449 const PetscInt faceSizeTri = 3; 1450 PetscInt sortedIndices[3], i, iFace; 1451 PetscBool found = PETSC_FALSE; 1452 PetscInt faceVerticesTriSorted[9] = { 1453 0, 3, 4, /* bottom */ 1454 1, 4, 5, /* right */ 1455 2, 3, 5, /* left */ 1456 }; 1457 PetscInt faceVerticesTri[9] = { 1458 0, 3, 4, /* bottom */ 1459 1, 4, 5, /* right */ 1460 2, 5, 3, /* left */ 1461 }; 1462 1463 faceSize = faceSizeTri; 1464 for (i = 0; i < faceSizeTri; ++i) sortedIndices[i] = indices[i]; 1465 ierr = PetscSortInt(faceSizeTri, sortedIndices);CHKERRQ(ierr); 1466 for (iFace = 0; iFace < 3; ++iFace) { 1467 const PetscInt ii = iFace*faceSizeTri; 1468 PetscInt fVertex, cVertex; 1469 1470 if ((sortedIndices[0] == faceVerticesTriSorted[ii+0]) && 1471 (sortedIndices[1] == faceVerticesTriSorted[ii+1])) { 1472 for (fVertex = 0; fVertex < faceSizeTri; ++fVertex) { 1473 for (cVertex = 0; cVertex < faceSizeTri; ++cVertex) { 1474 if (indices[cVertex] == faceVerticesTri[ii+fVertex]) { 1475 faceVertices[fVertex] = origVertices[cVertex]; 1476 break; 1477 } 1478 } 1479 } 1480 found = PETSC_TRUE; 1481 break; 1482 } 1483 } 1484 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid tri crossface"); 1485 if (posOriented) *posOriented = PETSC_TRUE; 1486 PetscFunctionReturn(0); 1487 } else if (cellDim == 2 && numCorners == 9) { 1488 /* Quadratic quad (I hate this) */ 1489 /* Edges are determined by the first 2 vertices (corners of edges) */ 1490 const PetscInt faceSizeQuad = 3; 1491 PetscInt sortedIndices[3], i, iFace; 1492 PetscBool found = PETSC_FALSE; 1493 PetscInt faceVerticesQuadSorted[12] = { 1494 0, 1, 4, /* bottom */ 1495 1, 2, 5, /* right */ 1496 2, 3, 6, /* top */ 1497 0, 3, 7, /* left */ 1498 }; 1499 PetscInt faceVerticesQuad[12] = { 1500 0, 1, 4, /* bottom */ 1501 1, 2, 5, /* right */ 1502 2, 3, 6, /* top */ 1503 3, 0, 7, /* left */ 1504 }; 1505 1506 faceSize = faceSizeQuad; 1507 for (i = 0; i < faceSizeQuad; ++i) sortedIndices[i] = indices[i]; 1508 ierr = PetscSortInt(faceSizeQuad, sortedIndices);CHKERRQ(ierr); 1509 for (iFace = 0; iFace < 4; ++iFace) { 1510 const PetscInt ii = iFace*faceSizeQuad; 1511 PetscInt fVertex, cVertex; 1512 1513 if ((sortedIndices[0] == faceVerticesQuadSorted[ii+0]) && 1514 (sortedIndices[1] == faceVerticesQuadSorted[ii+1])) { 1515 for (fVertex = 0; fVertex < faceSizeQuad; ++fVertex) { 1516 for (cVertex = 0; cVertex < faceSizeQuad; ++cVertex) { 1517 if (indices[cVertex] == faceVerticesQuad[ii+fVertex]) { 1518 faceVertices[fVertex] = origVertices[cVertex]; 1519 break; 1520 } 1521 } 1522 } 1523 found = PETSC_TRUE; 1524 break; 1525 } 1526 } 1527 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid quad crossface"); 1528 if (posOriented) *posOriented = PETSC_TRUE; 1529 PetscFunctionReturn(0); 1530 } else if (cellDim == 3 && numCorners == 8) { 1531 /* Hexes 1532 A hex is two oriented quads with the normal of the first 1533 pointing up at the second. 1534 1535 7---6 1536 /| /| 1537 4---5 | 1538 | 1-|-2 1539 |/ |/ 1540 0---3 1541 1542 Faces are determined by the first 4 vertices (corners of faces) */ 1543 const PetscInt faceSizeHex = 4; 1544 PetscInt sortedIndices[4], i, iFace; 1545 PetscBool found = PETSC_FALSE; 1546 PetscInt faceVerticesHexSorted[24] = { 1547 0, 1, 2, 3, /* bottom */ 1548 4, 5, 6, 7, /* top */ 1549 0, 3, 4, 5, /* front */ 1550 2, 3, 5, 6, /* right */ 1551 1, 2, 6, 7, /* back */ 1552 0, 1, 4, 7, /* left */ 1553 }; 1554 PetscInt faceVerticesHex[24] = { 1555 1, 2, 3, 0, /* bottom */ 1556 4, 5, 6, 7, /* top */ 1557 0, 3, 5, 4, /* front */ 1558 3, 2, 6, 5, /* right */ 1559 2, 1, 7, 6, /* back */ 1560 1, 0, 4, 7, /* left */ 1561 }; 1562 1563 faceSize = faceSizeHex; 1564 for (i = 0; i < faceSizeHex; ++i) sortedIndices[i] = indices[i]; 1565 ierr = PetscSortInt(faceSizeHex, sortedIndices);CHKERRQ(ierr); 1566 for (iFace = 0; iFace < 6; ++iFace) { 1567 const PetscInt ii = iFace*faceSizeHex; 1568 PetscInt fVertex, cVertex; 1569 1570 if ((sortedIndices[0] == faceVerticesHexSorted[ii+0]) && 1571 (sortedIndices[1] == faceVerticesHexSorted[ii+1]) && 1572 (sortedIndices[2] == faceVerticesHexSorted[ii+2]) && 1573 (sortedIndices[3] == faceVerticesHexSorted[ii+3])) { 1574 for (fVertex = 0; fVertex < faceSizeHex; ++fVertex) { 1575 for (cVertex = 0; cVertex < faceSizeHex; ++cVertex) { 1576 if (indices[cVertex] == faceVerticesHex[ii+fVertex]) { 1577 faceVertices[fVertex] = origVertices[cVertex]; 1578 break; 1579 } 1580 } 1581 } 1582 found = PETSC_TRUE; 1583 break; 1584 } 1585 } 1586 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid hex crossface"); 1587 if (posOriented) *posOriented = PETSC_TRUE; 1588 PetscFunctionReturn(0); 1589 } else if (cellDim == 3 && numCorners == 10) { 1590 /* Quadratic tet */ 1591 /* Faces are determined by the first 3 vertices (corners of faces) */ 1592 const PetscInt faceSizeTet = 6; 1593 PetscInt sortedIndices[6], i, iFace; 1594 PetscBool found = PETSC_FALSE; 1595 PetscInt faceVerticesTetSorted[24] = { 1596 0, 1, 2, 6, 7, 8, /* bottom */ 1597 0, 3, 4, 6, 7, 9, /* front */ 1598 1, 4, 5, 7, 8, 9, /* right */ 1599 2, 3, 5, 6, 8, 9, /* left */ 1600 }; 1601 PetscInt faceVerticesTet[24] = { 1602 0, 1, 2, 6, 7, 8, /* bottom */ 1603 0, 4, 3, 6, 7, 9, /* front */ 1604 1, 5, 4, 7, 8, 9, /* right */ 1605 2, 3, 5, 8, 6, 9, /* left */ 1606 }; 1607 1608 faceSize = faceSizeTet; 1609 for (i = 0; i < faceSizeTet; ++i) sortedIndices[i] = indices[i]; 1610 ierr = PetscSortInt(faceSizeTet, sortedIndices);CHKERRQ(ierr); 1611 for (iFace=0; iFace < 4; ++iFace) { 1612 const PetscInt ii = iFace*faceSizeTet; 1613 PetscInt fVertex, cVertex; 1614 1615 if ((sortedIndices[0] == faceVerticesTetSorted[ii+0]) && 1616 (sortedIndices[1] == faceVerticesTetSorted[ii+1]) && 1617 (sortedIndices[2] == faceVerticesTetSorted[ii+2]) && 1618 (sortedIndices[3] == faceVerticesTetSorted[ii+3])) { 1619 for (fVertex = 0; fVertex < faceSizeTet; ++fVertex) { 1620 for (cVertex = 0; cVertex < faceSizeTet; ++cVertex) { 1621 if (indices[cVertex] == faceVerticesTet[ii+fVertex]) { 1622 faceVertices[fVertex] = origVertices[cVertex]; 1623 break; 1624 } 1625 } 1626 } 1627 found = PETSC_TRUE; 1628 break; 1629 } 1630 } 1631 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid tet crossface"); 1632 if (posOriented) *posOriented = PETSC_TRUE; 1633 PetscFunctionReturn(0); 1634 } else if (cellDim == 3 && numCorners == 27) { 1635 /* Quadratic hexes (I hate this) 1636 A hex is two oriented quads with the normal of the first 1637 pointing up at the second. 1638 1639 7---6 1640 /| /| 1641 4---5 | 1642 | 3-|-2 1643 |/ |/ 1644 0---1 1645 1646 Faces are determined by the first 4 vertices (corners of faces) */ 1647 const PetscInt faceSizeQuadHex = 9; 1648 PetscInt sortedIndices[9], i, iFace; 1649 PetscBool found = PETSC_FALSE; 1650 PetscInt faceVerticesQuadHexSorted[54] = { 1651 0, 1, 2, 3, 8, 9, 10, 11, 24, /* bottom */ 1652 4, 5, 6, 7, 12, 13, 14, 15, 25, /* top */ 1653 0, 1, 4, 5, 8, 12, 16, 17, 22, /* front */ 1654 1, 2, 5, 6, 9, 13, 17, 18, 21, /* right */ 1655 2, 3, 6, 7, 10, 14, 18, 19, 23, /* back */ 1656 0, 3, 4, 7, 11, 15, 16, 19, 20, /* left */ 1657 }; 1658 PetscInt faceVerticesQuadHex[54] = { 1659 3, 2, 1, 0, 10, 9, 8, 11, 24, /* bottom */ 1660 4, 5, 6, 7, 12, 13, 14, 15, 25, /* top */ 1661 0, 1, 5, 4, 8, 17, 12, 16, 22, /* front */ 1662 1, 2, 6, 5, 9, 18, 13, 17, 21, /* right */ 1663 2, 3, 7, 6, 10, 19, 14, 18, 23, /* back */ 1664 3, 0, 4, 7, 11, 16, 15, 19, 20 /* left */ 1665 }; 1666 1667 faceSize = faceSizeQuadHex; 1668 for (i = 0; i < faceSizeQuadHex; ++i) sortedIndices[i] = indices[i]; 1669 ierr = PetscSortInt(faceSizeQuadHex, sortedIndices);CHKERRQ(ierr); 1670 for (iFace = 0; iFace < 6; ++iFace) { 1671 const PetscInt ii = iFace*faceSizeQuadHex; 1672 PetscInt fVertex, cVertex; 1673 1674 if ((sortedIndices[0] == faceVerticesQuadHexSorted[ii+0]) && 1675 (sortedIndices[1] == faceVerticesQuadHexSorted[ii+1]) && 1676 (sortedIndices[2] == faceVerticesQuadHexSorted[ii+2]) && 1677 (sortedIndices[3] == faceVerticesQuadHexSorted[ii+3])) { 1678 for (fVertex = 0; fVertex < faceSizeQuadHex; ++fVertex) { 1679 for (cVertex = 0; cVertex < faceSizeQuadHex; ++cVertex) { 1680 if (indices[cVertex] == faceVerticesQuadHex[ii+fVertex]) { 1681 faceVertices[fVertex] = origVertices[cVertex]; 1682 break; 1683 } 1684 } 1685 } 1686 found = PETSC_TRUE; 1687 break; 1688 } 1689 } 1690 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid hex crossface"); 1691 if (posOriented) *posOriented = PETSC_TRUE; 1692 PetscFunctionReturn(0); 1693 } else SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Unknown cell type for faceOrientation()."); 1694 if (!posOrient) { 1695 if (debug) {ierr = PetscPrintf(comm, " Reversing initial face orientation\n");CHKERRQ(ierr);} 1696 for (f = 0; f < faceSize; ++f) faceVertices[f] = origVertices[faceSize-1 - f]; 1697 } else { 1698 if (debug) {ierr = PetscPrintf(comm, " Keeping initial face orientation\n");CHKERRQ(ierr);} 1699 for (f = 0; f < faceSize; ++f) faceVertices[f] = origVertices[f]; 1700 } 1701 if (posOriented) *posOriented = posOrient; 1702 PetscFunctionReturn(0); 1703 } 1704 1705 #undef __FUNCT__ 1706 #define __FUNCT__ "DMPlexGetOrientedFace" 1707 /* 1708 Given a cell and a face, as a set of vertices, 1709 return the oriented face, as a set of vertices, in faceVertices 1710 The orientation is such that the face normal points out of the cell 1711 */ 1712 PetscErrorCode DMPlexGetOrientedFace(DM dm, PetscInt cell, PetscInt faceSize, const PetscInt face[], PetscInt numCorners, PetscInt indices[], PetscInt origVertices[], PetscInt faceVertices[], PetscBool *posOriented) 1713 { 1714 const PetscInt *cone = NULL; 1715 PetscInt coneSize, v, f, v2; 1716 PetscInt oppositeVertex = -1; 1717 PetscErrorCode ierr; 1718 1719 PetscFunctionBegin; 1720 ierr = DMPlexGetConeSize(dm, cell, &coneSize);CHKERRQ(ierr); 1721 ierr = DMPlexGetCone(dm, cell, &cone);CHKERRQ(ierr); 1722 for (v = 0, v2 = 0; v < coneSize; ++v) { 1723 PetscBool found = PETSC_FALSE; 1724 1725 for (f = 0; f < faceSize; ++f) { 1726 if (face[f] == cone[v]) { 1727 found = PETSC_TRUE; break; 1728 } 1729 } 1730 if (found) { 1731 indices[v2] = v; 1732 origVertices[v2] = cone[v]; 1733 ++v2; 1734 } else { 1735 oppositeVertex = v; 1736 } 1737 } 1738 ierr = DMPlexGetFaceOrientation(dm, cell, numCorners, indices, oppositeVertex, origVertices, faceVertices, posOriented);CHKERRQ(ierr); 1739 PetscFunctionReturn(0); 1740 } 1741 1742 #undef __FUNCT__ 1743 #define __FUNCT__ "DMPlexInsertFace_Internal" 1744 /* 1745 DMPlexInsertFace_Internal - Puts a face into the mesh 1746 1747 Not collective 1748 1749 Input Parameters: 1750 + dm - The DMPlex 1751 . numFaceVertex - The number of vertices in the face 1752 . faceVertices - The vertices in the face for dm 1753 . subfaceVertices - The vertices in the face for subdm 1754 . numCorners - The number of vertices in the cell 1755 . cell - A cell in dm containing the face 1756 . subcell - A cell in subdm containing the face 1757 . firstFace - First face in the mesh 1758 - newFacePoint - Next face in the mesh 1759 1760 Output Parameters: 1761 . newFacePoint - Contains next face point number on input, updated on output 1762 1763 Level: developer 1764 */ 1765 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) 1766 { 1767 MPI_Comm comm; 1768 DM_Plex *submesh = (DM_Plex*) subdm->data; 1769 const PetscInt *faces; 1770 PetscInt numFaces, coneSize; 1771 PetscErrorCode ierr; 1772 1773 PetscFunctionBegin; 1774 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 1775 ierr = DMPlexGetConeSize(subdm, subcell, &coneSize);CHKERRQ(ierr); 1776 if (coneSize != 1) SETERRQ2(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cone size of cell %d is %d != 1", cell, coneSize); 1777 #if 0 1778 /* Cannot use this because support() has not been constructed yet */ 1779 ierr = DMPlexGetJoin(subdm, numFaceVertices, subfaceVertices, &numFaces, &faces);CHKERRQ(ierr); 1780 #else 1781 { 1782 PetscInt f; 1783 1784 numFaces = 0; 1785 ierr = DMGetWorkArray(subdm, 1, PETSC_INT, (void **) &faces);CHKERRQ(ierr); 1786 for (f = firstFace; f < *newFacePoint; ++f) { 1787 PetscInt dof, off, d; 1788 1789 ierr = PetscSectionGetDof(submesh->coneSection, f, &dof);CHKERRQ(ierr); 1790 ierr = PetscSectionGetOffset(submesh->coneSection, f, &off);CHKERRQ(ierr); 1791 /* Yes, I know this is quadratic, but I expect the sizes to be <5 */ 1792 for (d = 0; d < dof; ++d) { 1793 const PetscInt p = submesh->cones[off+d]; 1794 PetscInt v; 1795 1796 for (v = 0; v < numFaceVertices; ++v) { 1797 if (subfaceVertices[v] == p) break; 1798 } 1799 if (v == numFaceVertices) break; 1800 } 1801 if (d == dof) { 1802 numFaces = 1; 1803 ((PetscInt*) faces)[0] = f; 1804 } 1805 } 1806 } 1807 #endif 1808 if (numFaces > 1) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Vertex set had %d faces, not one", numFaces); 1809 else if (numFaces == 1) { 1810 /* Add the other cell neighbor for this face */ 1811 ierr = DMPlexSetCone(subdm, subcell, faces);CHKERRQ(ierr); 1812 } else { 1813 PetscInt *indices, *origVertices, *orientedVertices, *orientedSubVertices, v, ov; 1814 PetscBool posOriented; 1815 1816 ierr = DMGetWorkArray(subdm, 4*numFaceVertices * sizeof(PetscInt), PETSC_INT, &orientedVertices);CHKERRQ(ierr); 1817 origVertices = &orientedVertices[numFaceVertices]; 1818 indices = &orientedVertices[numFaceVertices*2]; 1819 orientedSubVertices = &orientedVertices[numFaceVertices*3]; 1820 ierr = DMPlexGetOrientedFace(dm, cell, numFaceVertices, faceVertices, numCorners, indices, origVertices, orientedVertices, &posOriented);CHKERRQ(ierr); 1821 /* TODO: I know that routine should return a permutation, not the indices */ 1822 for (v = 0; v < numFaceVertices; ++v) { 1823 const PetscInt vertex = faceVertices[v], subvertex = subfaceVertices[v]; 1824 for (ov = 0; ov < numFaceVertices; ++ov) { 1825 if (orientedVertices[ov] == vertex) { 1826 orientedSubVertices[ov] = subvertex; 1827 break; 1828 } 1829 } 1830 if (ov == numFaceVertices) SETERRQ1(comm, PETSC_ERR_PLIB, "Could not find face vertex %d in orientated set", vertex); 1831 } 1832 ierr = DMPlexSetCone(subdm, *newFacePoint, orientedSubVertices);CHKERRQ(ierr); 1833 ierr = DMPlexSetCone(subdm, subcell, newFacePoint);CHKERRQ(ierr); 1834 ierr = DMRestoreWorkArray(subdm, 4*numFaceVertices * sizeof(PetscInt), PETSC_INT, &orientedVertices);CHKERRQ(ierr); 1835 ++(*newFacePoint); 1836 } 1837 #if 0 1838 ierr = DMPlexRestoreJoin(subdm, numFaceVertices, subfaceVertices, &numFaces, &faces);CHKERRQ(ierr); 1839 #else 1840 ierr = DMRestoreWorkArray(subdm, 1, PETSC_INT, (void **) &faces);CHKERRQ(ierr); 1841 #endif 1842 PetscFunctionReturn(0); 1843 } 1844 1845 #undef __FUNCT__ 1846 #define __FUNCT__ "DMPlexCreateSubmesh_Uninterpolated" 1847 static PetscErrorCode DMPlexCreateSubmesh_Uninterpolated(DM dm, const char vertexLabelName[], PetscInt value, DM subdm) 1848 { 1849 MPI_Comm comm; 1850 DMLabel vertexLabel, subpointMap; 1851 IS subvertexIS, subcellIS; 1852 const PetscInt *subVertices, *subCells; 1853 PetscInt numSubVertices, firstSubVertex, numSubCells; 1854 PetscInt *subface, maxConeSize, numSubFaces, firstSubFace, newFacePoint, nFV; 1855 PetscInt vStart, vEnd, c, f; 1856 PetscErrorCode ierr; 1857 1858 PetscFunctionBegin; 1859 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 1860 /* Create subpointMap which marks the submesh */ 1861 ierr = DMLabelCreate("subpoint_map", &subpointMap);CHKERRQ(ierr); 1862 ierr = DMPlexSetSubpointMap(subdm, subpointMap);CHKERRQ(ierr); 1863 ierr = DMLabelDestroy(&subpointMap);CHKERRQ(ierr); 1864 ierr = DMPlexGetLabel(dm, vertexLabelName, &vertexLabel);CHKERRQ(ierr); 1865 ierr = DMPlexMarkSubmesh_Uninterpolated(dm, vertexLabel, value, subpointMap, &numSubFaces, &nFV, subdm);CHKERRQ(ierr); 1866 /* Setup chart */ 1867 ierr = DMLabelGetStratumSize(subpointMap, 0, &numSubVertices);CHKERRQ(ierr); 1868 ierr = DMLabelGetStratumSize(subpointMap, 2, &numSubCells);CHKERRQ(ierr); 1869 ierr = DMPlexSetChart(subdm, 0, numSubCells+numSubFaces+numSubVertices);CHKERRQ(ierr); 1870 ierr = DMPlexSetVTKCellHeight(subdm, 1);CHKERRQ(ierr); 1871 /* Set cone sizes */ 1872 firstSubVertex = numSubCells; 1873 firstSubFace = numSubCells+numSubVertices; 1874 newFacePoint = firstSubFace; 1875 ierr = DMLabelGetStratumIS(subpointMap, 0, &subvertexIS);CHKERRQ(ierr); 1876 if (subvertexIS) {ierr = ISGetIndices(subvertexIS, &subVertices);CHKERRQ(ierr);} 1877 ierr = DMLabelGetStratumIS(subpointMap, 2, &subcellIS);CHKERRQ(ierr); 1878 if (subcellIS) {ierr = ISGetIndices(subcellIS, &subCells);CHKERRQ(ierr);} 1879 for (c = 0; c < numSubCells; ++c) { 1880 ierr = DMPlexSetConeSize(subdm, c, 1);CHKERRQ(ierr); 1881 } 1882 for (f = firstSubFace; f < firstSubFace+numSubFaces; ++f) { 1883 ierr = DMPlexSetConeSize(subdm, f, nFV);CHKERRQ(ierr); 1884 } 1885 ierr = DMSetUp(subdm);CHKERRQ(ierr); 1886 /* Create face cones */ 1887 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 1888 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, NULL);CHKERRQ(ierr); 1889 ierr = DMGetWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);CHKERRQ(ierr); 1890 for (c = 0; c < numSubCells; ++c) { 1891 const PetscInt cell = subCells[c]; 1892 const PetscInt subcell = c; 1893 PetscInt *closure = NULL; 1894 PetscInt closureSize, cl, numCorners = 0, faceSize = 0; 1895 1896 ierr = DMPlexGetTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1897 for (cl = 0; cl < closureSize*2; cl += 2) { 1898 const PetscInt point = closure[cl]; 1899 PetscInt subVertex; 1900 1901 if ((point >= vStart) && (point < vEnd)) { 1902 ++numCorners; 1903 ierr = PetscFindInt(point, numSubVertices, subVertices, &subVertex);CHKERRQ(ierr); 1904 if (subVertex >= 0) { 1905 closure[faceSize] = point; 1906 subface[faceSize] = firstSubVertex+subVertex; 1907 ++faceSize; 1908 } 1909 } 1910 } 1911 if (faceSize > nFV) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Invalid submesh: Too many vertices %d of an element on the surface", faceSize); 1912 if (faceSize == nFV) { 1913 ierr = DMPlexInsertFace_Internal(dm, subdm, faceSize, closure, subface, numCorners, cell, subcell, firstSubFace, &newFacePoint);CHKERRQ(ierr); 1914 } 1915 ierr = DMPlexRestoreTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1916 } 1917 ierr = DMRestoreWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);CHKERRQ(ierr); 1918 ierr = DMPlexSymmetrize(subdm);CHKERRQ(ierr); 1919 ierr = DMPlexStratify(subdm);CHKERRQ(ierr); 1920 /* Build coordinates */ 1921 { 1922 PetscSection coordSection, subCoordSection; 1923 Vec coordinates, subCoordinates; 1924 PetscScalar *coords, *subCoords; 1925 PetscInt numComp, coordSize, v; 1926 1927 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1928 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 1929 ierr = DMPlexGetCoordinateSection(subdm, &subCoordSection);CHKERRQ(ierr); 1930 ierr = PetscSectionSetNumFields(subCoordSection, 1);CHKERRQ(ierr); 1931 ierr = PetscSectionGetFieldComponents(coordSection, 0, &numComp);CHKERRQ(ierr); 1932 ierr = PetscSectionSetFieldComponents(subCoordSection, 0, numComp);CHKERRQ(ierr); 1933 ierr = PetscSectionSetChart(subCoordSection, firstSubVertex, firstSubVertex+numSubVertices);CHKERRQ(ierr); 1934 for (v = 0; v < numSubVertices; ++v) { 1935 const PetscInt vertex = subVertices[v]; 1936 const PetscInt subvertex = firstSubVertex+v; 1937 PetscInt dof; 1938 1939 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 1940 ierr = PetscSectionSetDof(subCoordSection, subvertex, dof);CHKERRQ(ierr); 1941 ierr = PetscSectionSetFieldDof(subCoordSection, subvertex, 0, dof);CHKERRQ(ierr); 1942 } 1943 ierr = PetscSectionSetUp(subCoordSection);CHKERRQ(ierr); 1944 ierr = PetscSectionGetStorageSize(subCoordSection, &coordSize);CHKERRQ(ierr); 1945 ierr = VecCreate(comm, &subCoordinates);CHKERRQ(ierr); 1946 ierr = VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1947 ierr = VecSetFromOptions(subCoordinates);CHKERRQ(ierr); 1948 if (coordSize) { 1949 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1950 ierr = VecGetArray(subCoordinates, &subCoords);CHKERRQ(ierr); 1951 for (v = 0; v < numSubVertices; ++v) { 1952 const PetscInt vertex = subVertices[v]; 1953 const PetscInt subvertex = firstSubVertex+v; 1954 PetscInt dof, off, sdof, soff, d; 1955 1956 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 1957 ierr = PetscSectionGetOffset(coordSection, vertex, &off);CHKERRQ(ierr); 1958 ierr = PetscSectionGetDof(subCoordSection, subvertex, &sdof);CHKERRQ(ierr); 1959 ierr = PetscSectionGetOffset(subCoordSection, subvertex, &soff);CHKERRQ(ierr); 1960 if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof); 1961 for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d]; 1962 } 1963 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1964 ierr = VecRestoreArray(subCoordinates, &subCoords);CHKERRQ(ierr); 1965 } 1966 ierr = DMSetCoordinatesLocal(subdm, subCoordinates);CHKERRQ(ierr); 1967 ierr = VecDestroy(&subCoordinates);CHKERRQ(ierr); 1968 } 1969 /* Cleanup */ 1970 if (subvertexIS) {ierr = ISRestoreIndices(subvertexIS, &subVertices);CHKERRQ(ierr);} 1971 ierr = ISDestroy(&subvertexIS);CHKERRQ(ierr); 1972 if (subcellIS) {ierr = ISRestoreIndices(subcellIS, &subCells);CHKERRQ(ierr);} 1973 ierr = ISDestroy(&subcellIS);CHKERRQ(ierr); 1974 PetscFunctionReturn(0); 1975 } 1976 1977 #undef __FUNCT__ 1978 #define __FUNCT__ "DMPlexCreateSubmesh_Interpolated" 1979 static PetscErrorCode DMPlexCreateSubmesh_Interpolated(DM dm, const char vertexLabelName[], PetscInt value, DM subdm) 1980 { 1981 MPI_Comm comm; 1982 DMLabel subpointMap, vertexLabel; 1983 IS *subpointIS; 1984 const PetscInt **subpoints; 1985 PetscInt *numSubPoints, *firstSubPoint, *coneNew; 1986 PetscInt totSubPoints = 0, maxConeSize, dim, p, d, v; 1987 PetscErrorCode ierr; 1988 1989 PetscFunctionBegin; 1990 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 1991 /* Create subpointMap which marks the submesh */ 1992 ierr = DMLabelCreate("subpoint_map", &subpointMap);CHKERRQ(ierr); 1993 ierr = DMPlexSetSubpointMap(subdm, subpointMap);CHKERRQ(ierr); 1994 ierr = DMLabelDestroy(&subpointMap);CHKERRQ(ierr); 1995 ierr = DMPlexGetLabel(dm, vertexLabelName, &vertexLabel);CHKERRQ(ierr); 1996 ierr = DMPlexMarkSubmesh_Interpolated(dm, vertexLabel, value, subpointMap, subdm);CHKERRQ(ierr); 1997 /* Setup chart */ 1998 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1999 ierr = PetscMalloc4(dim+1,PetscInt,&numSubPoints,dim+1,PetscInt,&firstSubPoint,dim+1,IS,&subpointIS,dim+1,const PetscInt *,&subpoints);CHKERRQ(ierr); 2000 for (d = 0; d <= dim; ++d) { 2001 ierr = DMLabelGetStratumSize(subpointMap, d, &numSubPoints[d]);CHKERRQ(ierr); 2002 totSubPoints += numSubPoints[d]; 2003 } 2004 ierr = DMPlexSetChart(subdm, 0, totSubPoints);CHKERRQ(ierr); 2005 ierr = DMPlexSetVTKCellHeight(subdm, 1);CHKERRQ(ierr); 2006 /* Set cone sizes */ 2007 firstSubPoint[dim] = 0; 2008 firstSubPoint[0] = firstSubPoint[dim] + numSubPoints[dim]; 2009 if (dim > 1) {firstSubPoint[dim-1] = firstSubPoint[0] + numSubPoints[0];} 2010 if (dim > 2) {firstSubPoint[dim-2] = firstSubPoint[dim-1] + numSubPoints[dim-1];} 2011 for (d = 0; d <= dim; ++d) { 2012 ierr = DMLabelGetStratumIS(subpointMap, d, &subpointIS[d]);CHKERRQ(ierr); 2013 ierr = ISGetIndices(subpointIS[d], &subpoints[d]);CHKERRQ(ierr); 2014 } 2015 for (d = 0; d <= dim; ++d) { 2016 for (p = 0; p < numSubPoints[d]; ++p) { 2017 const PetscInt point = subpoints[d][p]; 2018 const PetscInt subpoint = firstSubPoint[d] + p; 2019 const PetscInt *cone; 2020 PetscInt coneSize, coneSizeNew, c, val; 2021 2022 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 2023 ierr = DMPlexSetConeSize(subdm, subpoint, coneSize);CHKERRQ(ierr); 2024 if (d == dim) { 2025 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 2026 for (c = 0, coneSizeNew = 0; c < coneSize; ++c) { 2027 ierr = DMLabelGetValue(subpointMap, cone[c], &val);CHKERRQ(ierr); 2028 if (val >= 0) coneSizeNew++; 2029 } 2030 ierr = DMPlexSetConeSize(subdm, subpoint, coneSizeNew);CHKERRQ(ierr); 2031 } 2032 } 2033 } 2034 ierr = DMSetUp(subdm);CHKERRQ(ierr); 2035 /* Set cones */ 2036 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, NULL);CHKERRQ(ierr); 2037 ierr = PetscMalloc(maxConeSize * sizeof(PetscInt), &coneNew);CHKERRQ(ierr); 2038 for (d = 0; d <= dim; ++d) { 2039 for (p = 0; p < numSubPoints[d]; ++p) { 2040 const PetscInt point = subpoints[d][p]; 2041 const PetscInt subpoint = firstSubPoint[d] + p; 2042 const PetscInt *cone; 2043 PetscInt coneSize, subconeSize, coneSizeNew, c, subc; 2044 2045 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 2046 ierr = DMPlexGetConeSize(subdm, subpoint, &subconeSize);CHKERRQ(ierr); 2047 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 2048 for (c = 0, coneSizeNew = 0; c < coneSize; ++c) { 2049 ierr = PetscFindInt(cone[c], numSubPoints[d-1], subpoints[d-1], &subc);CHKERRQ(ierr); 2050 if (subc >= 0) coneNew[coneSizeNew++] = firstSubPoint[d-1] + subc; 2051 } 2052 if (coneSizeNew != subconeSize) SETERRQ2(comm, PETSC_ERR_PLIB, "Number of cone points located %d does not match subcone size %d", coneSizeNew, subconeSize); 2053 ierr = DMPlexSetCone(subdm, subpoint, coneNew);CHKERRQ(ierr); 2054 } 2055 } 2056 ierr = PetscFree(coneNew);CHKERRQ(ierr); 2057 ierr = DMPlexSymmetrize(subdm);CHKERRQ(ierr); 2058 ierr = DMPlexStratify(subdm);CHKERRQ(ierr); 2059 /* Build coordinates */ 2060 { 2061 PetscSection coordSection, subCoordSection; 2062 Vec coordinates, subCoordinates; 2063 PetscScalar *coords, *subCoords; 2064 PetscInt numComp, coordSize; 2065 2066 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2067 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 2068 ierr = DMPlexGetCoordinateSection(subdm, &subCoordSection);CHKERRQ(ierr); 2069 ierr = PetscSectionSetNumFields(subCoordSection, 1);CHKERRQ(ierr); 2070 ierr = PetscSectionGetFieldComponents(coordSection, 0, &numComp);CHKERRQ(ierr); 2071 ierr = PetscSectionSetFieldComponents(subCoordSection, 0, numComp);CHKERRQ(ierr); 2072 ierr = PetscSectionSetChart(subCoordSection, firstSubPoint[0], firstSubPoint[0]+numSubPoints[0]);CHKERRQ(ierr); 2073 for (v = 0; v < numSubPoints[0]; ++v) { 2074 const PetscInt vertex = subpoints[0][v]; 2075 const PetscInt subvertex = firstSubPoint[0]+v; 2076 PetscInt dof; 2077 2078 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2079 ierr = PetscSectionSetDof(subCoordSection, subvertex, dof);CHKERRQ(ierr); 2080 ierr = PetscSectionSetFieldDof(subCoordSection, subvertex, 0, dof);CHKERRQ(ierr); 2081 } 2082 ierr = PetscSectionSetUp(subCoordSection);CHKERRQ(ierr); 2083 ierr = PetscSectionGetStorageSize(subCoordSection, &coordSize);CHKERRQ(ierr); 2084 ierr = VecCreate(comm, &subCoordinates);CHKERRQ(ierr); 2085 ierr = VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2086 ierr = VecSetFromOptions(subCoordinates);CHKERRQ(ierr); 2087 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2088 ierr = VecGetArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2089 for (v = 0; v < numSubPoints[0]; ++v) { 2090 const PetscInt vertex = subpoints[0][v]; 2091 const PetscInt subvertex = firstSubPoint[0]+v; 2092 PetscInt dof, off, sdof, soff, d; 2093 2094 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2095 ierr = PetscSectionGetOffset(coordSection, vertex, &off);CHKERRQ(ierr); 2096 ierr = PetscSectionGetDof(subCoordSection, subvertex, &sdof);CHKERRQ(ierr); 2097 ierr = PetscSectionGetOffset(subCoordSection, subvertex, &soff);CHKERRQ(ierr); 2098 if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof); 2099 for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d]; 2100 } 2101 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2102 ierr = VecRestoreArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2103 ierr = DMSetCoordinatesLocal(subdm, subCoordinates);CHKERRQ(ierr); 2104 ierr = VecDestroy(&subCoordinates);CHKERRQ(ierr); 2105 } 2106 /* Cleanup */ 2107 for (d = 0; d <= dim; ++d) { 2108 ierr = ISRestoreIndices(subpointIS[d], &subpoints[d]);CHKERRQ(ierr); 2109 ierr = ISDestroy(&subpointIS[d]);CHKERRQ(ierr); 2110 } 2111 ierr = PetscFree4(numSubPoints,firstSubPoint,subpointIS,subpoints);CHKERRQ(ierr); 2112 PetscFunctionReturn(0); 2113 } 2114 2115 #undef __FUNCT__ 2116 #define __FUNCT__ "DMPlexCreateSubmesh" 2117 /*@C 2118 DMPlexCreateSubmesh - Extract a hypersurface from the mesh using vertices defined by a label 2119 2120 Input Parameters: 2121 + dm - The original mesh 2122 . vertexLabel - The DMLabel marking vertices contained in the surface 2123 - value - The label value to use 2124 2125 Output Parameter: 2126 . subdm - The surface mesh 2127 2128 Note: This function produces a DMLabel mapping original points in the submesh to their depth. This can be obtained using DMPlexGetSubpointMap(). 2129 2130 Level: developer 2131 2132 .seealso: DMPlexGetSubpointMap(), DMPlexGetLabel(), DMLabelSetValue() 2133 @*/ 2134 PetscErrorCode DMPlexCreateSubmesh(DM dm, const char vertexLabel[], PetscInt value, DM *subdm) 2135 { 2136 PetscInt dim, depth; 2137 PetscErrorCode ierr; 2138 2139 PetscFunctionBegin; 2140 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2141 PetscValidCharPointer(vertexLabel, 2); 2142 PetscValidPointer(subdm, 3); 2143 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 2144 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 2145 ierr = DMCreate(PetscObjectComm((PetscObject)dm), subdm);CHKERRQ(ierr); 2146 ierr = DMSetType(*subdm, DMPLEX);CHKERRQ(ierr); 2147 ierr = DMPlexSetDimension(*subdm, dim-1);CHKERRQ(ierr); 2148 if (depth == dim) { 2149 ierr = DMPlexCreateSubmesh_Interpolated(dm, vertexLabel, value, *subdm);CHKERRQ(ierr); 2150 } else { 2151 ierr = DMPlexCreateSubmesh_Uninterpolated(dm, vertexLabel, value, *subdm);CHKERRQ(ierr); 2152 } 2153 PetscFunctionReturn(0); 2154 } 2155 2156 #undef __FUNCT__ 2157 #define __FUNCT__ "DMPlexCreateCohesiveSubmesh_Uninterpolated" 2158 static PetscErrorCode DMPlexCreateCohesiveSubmesh_Uninterpolated(DM dm, PetscBool hasLagrange, const char label[], PetscInt value, DM subdm) 2159 { 2160 MPI_Comm comm; 2161 DMLabel subpointMap; 2162 IS subvertexIS; 2163 const PetscInt *subVertices; 2164 PetscInt numSubVertices, firstSubVertex, numSubCells, *subCells; 2165 PetscInt *subface, maxConeSize, numSubFaces, firstSubFace, newFacePoint, nFV; 2166 PetscInt cMax, c, f; 2167 PetscErrorCode ierr; 2168 2169 PetscFunctionBegin; 2170 ierr = PetscObjectGetComm((PetscObject)dm, &comm);CHKERRQ(ierr); 2171 /* Create subpointMap which marks the submesh */ 2172 ierr = DMLabelCreate("subpoint_map", &subpointMap);CHKERRQ(ierr); 2173 ierr = DMPlexSetSubpointMap(subdm, subpointMap);CHKERRQ(ierr); 2174 ierr = DMLabelDestroy(&subpointMap);CHKERRQ(ierr); 2175 ierr = DMPlexMarkCohesiveSubmesh_Uninterpolated(dm, hasLagrange, label, value, subpointMap, &numSubFaces, &nFV, &subCells, subdm);CHKERRQ(ierr); 2176 /* Setup chart */ 2177 ierr = DMLabelGetStratumSize(subpointMap, 0, &numSubVertices);CHKERRQ(ierr); 2178 ierr = DMLabelGetStratumSize(subpointMap, 2, &numSubCells);CHKERRQ(ierr); 2179 ierr = DMPlexSetChart(subdm, 0, numSubCells+numSubFaces+numSubVertices);CHKERRQ(ierr); 2180 ierr = DMPlexSetVTKCellHeight(subdm, 1);CHKERRQ(ierr); 2181 /* Set cone sizes */ 2182 firstSubVertex = numSubCells; 2183 firstSubFace = numSubCells+numSubVertices; 2184 newFacePoint = firstSubFace; 2185 ierr = DMLabelGetStratumIS(subpointMap, 0, &subvertexIS);CHKERRQ(ierr); 2186 if (subvertexIS) {ierr = ISGetIndices(subvertexIS, &subVertices);CHKERRQ(ierr);} 2187 for (c = 0; c < numSubCells; ++c) { 2188 ierr = DMPlexSetConeSize(subdm, c, 1);CHKERRQ(ierr); 2189 } 2190 for (f = firstSubFace; f < firstSubFace+numSubFaces; ++f) { 2191 ierr = DMPlexSetConeSize(subdm, f, nFV);CHKERRQ(ierr); 2192 } 2193 ierr = DMSetUp(subdm);CHKERRQ(ierr); 2194 /* Create face cones */ 2195 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, NULL);CHKERRQ(ierr); 2196 ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); 2197 ierr = DMGetWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);CHKERRQ(ierr); 2198 for (c = 0; c < numSubCells; ++c) { 2199 const PetscInt cell = subCells[c]; 2200 const PetscInt subcell = c; 2201 const PetscInt *cone, *cells; 2202 PetscInt numCells, subVertex, p, v; 2203 2204 if (cell < cMax) continue; 2205 ierr = DMPlexGetCone(dm, cell, &cone);CHKERRQ(ierr); 2206 for (v = 0; v < nFV; ++v) { 2207 ierr = PetscFindInt(cone[v], numSubVertices, subVertices, &subVertex);CHKERRQ(ierr); 2208 subface[v] = firstSubVertex+subVertex; 2209 } 2210 ierr = DMPlexSetCone(subdm, newFacePoint, subface);CHKERRQ(ierr); 2211 ierr = DMPlexSetCone(subdm, subcell, &newFacePoint);CHKERRQ(ierr); 2212 ierr = DMPlexGetJoin(dm, nFV, cone, &numCells, &cells);CHKERRQ(ierr); 2213 if (numCells != 2) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive cells should separate two cells"); 2214 for (p = 0; p < numCells; ++p) { 2215 PetscInt negsubcell; 2216 2217 if (cells[p] >= cMax) continue; 2218 /* I know this is a crap search */ 2219 for (negsubcell = 0; negsubcell < numSubCells; ++negsubcell) { 2220 if (subCells[negsubcell] == cells[p]) break; 2221 } 2222 if (negsubcell == numSubCells) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not find negative face neighbor for cohesive cell %d", cell); 2223 ierr = DMPlexSetCone(subdm, negsubcell, &newFacePoint);CHKERRQ(ierr); 2224 } 2225 ierr = DMPlexRestoreJoin(dm, nFV, cone, &numCells, &cells);CHKERRQ(ierr); 2226 ++newFacePoint; 2227 } 2228 ierr = DMRestoreWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);CHKERRQ(ierr); 2229 ierr = DMPlexSymmetrize(subdm);CHKERRQ(ierr); 2230 ierr = DMPlexStratify(subdm);CHKERRQ(ierr); 2231 /* Build coordinates */ 2232 { 2233 PetscSection coordSection, subCoordSection; 2234 Vec coordinates, subCoordinates; 2235 PetscScalar *coords, *subCoords; 2236 PetscInt numComp, coordSize, v; 2237 2238 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2239 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 2240 ierr = DMPlexGetCoordinateSection(subdm, &subCoordSection);CHKERRQ(ierr); 2241 ierr = PetscSectionSetNumFields(subCoordSection, 1);CHKERRQ(ierr); 2242 ierr = PetscSectionGetFieldComponents(coordSection, 0, &numComp);CHKERRQ(ierr); 2243 ierr = PetscSectionSetFieldComponents(subCoordSection, 0, numComp);CHKERRQ(ierr); 2244 ierr = PetscSectionSetChart(subCoordSection, firstSubVertex, firstSubVertex+numSubVertices);CHKERRQ(ierr); 2245 for (v = 0; v < numSubVertices; ++v) { 2246 const PetscInt vertex = subVertices[v]; 2247 const PetscInt subvertex = firstSubVertex+v; 2248 PetscInt dof; 2249 2250 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2251 ierr = PetscSectionSetDof(subCoordSection, subvertex, dof);CHKERRQ(ierr); 2252 ierr = PetscSectionSetFieldDof(subCoordSection, subvertex, 0, dof);CHKERRQ(ierr); 2253 } 2254 ierr = PetscSectionSetUp(subCoordSection);CHKERRQ(ierr); 2255 ierr = PetscSectionGetStorageSize(subCoordSection, &coordSize);CHKERRQ(ierr); 2256 ierr = VecCreate(comm, &subCoordinates);CHKERRQ(ierr); 2257 if (coordSize) { 2258 ierr = VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2259 ierr = VecSetFromOptions(subCoordinates);CHKERRQ(ierr); 2260 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2261 ierr = VecGetArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2262 for (v = 0; v < numSubVertices; ++v) { 2263 const PetscInt vertex = subVertices[v]; 2264 const PetscInt subvertex = firstSubVertex+v; 2265 PetscInt dof, off, sdof, soff, d; 2266 2267 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2268 ierr = PetscSectionGetOffset(coordSection, vertex, &off);CHKERRQ(ierr); 2269 ierr = PetscSectionGetDof(subCoordSection, subvertex, &sdof);CHKERRQ(ierr); 2270 ierr = PetscSectionGetOffset(subCoordSection, subvertex, &soff);CHKERRQ(ierr); 2271 if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof); 2272 for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d]; 2273 } 2274 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2275 ierr = VecRestoreArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2276 } 2277 ierr = DMSetCoordinatesLocal(subdm, subCoordinates);CHKERRQ(ierr); 2278 ierr = VecDestroy(&subCoordinates);CHKERRQ(ierr); 2279 } 2280 /* Cleanup */ 2281 if (subvertexIS) {ierr = ISRestoreIndices(subvertexIS, &subVertices);CHKERRQ(ierr);} 2282 ierr = ISDestroy(&subvertexIS);CHKERRQ(ierr); 2283 ierr = PetscFree(subCells);CHKERRQ(ierr); 2284 PetscFunctionReturn(0); 2285 } 2286 2287 #undef __FUNCT__ 2288 #define __FUNCT__ "DMPlexCreateCohesiveSubmesh_Interpolated" 2289 static PetscErrorCode DMPlexCreateCohesiveSubmesh_Interpolated(DM dm, PetscBool hasLagrange, const char label[], PetscInt value, DM subdm) 2290 { 2291 MPI_Comm comm; 2292 DMLabel subpointMap; 2293 IS *subpointIS; 2294 const PetscInt **subpoints; 2295 PetscInt *numSubPoints, *firstSubPoint, *coneNew; 2296 PetscInt totSubPoints = 0, maxConeSize, dim, p, d, v; 2297 PetscErrorCode ierr; 2298 2299 PetscFunctionBegin; 2300 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 2301 /* Create subpointMap which marks the submesh */ 2302 ierr = DMLabelCreate("subpoint_map", &subpointMap);CHKERRQ(ierr); 2303 ierr = DMPlexSetSubpointMap(subdm, subpointMap);CHKERRQ(ierr); 2304 ierr = DMLabelDestroy(&subpointMap);CHKERRQ(ierr); 2305 ierr = DMPlexMarkCohesiveSubmesh_Interpolated(dm, hasLagrange, label, value, subpointMap, subdm);CHKERRQ(ierr); 2306 /* Setup chart */ 2307 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 2308 ierr = PetscMalloc4(dim+1,PetscInt,&numSubPoints,dim+1,PetscInt,&firstSubPoint,dim+1,IS,&subpointIS,dim+1,const PetscInt *,&subpoints);CHKERRQ(ierr); 2309 for (d = 0; d <= dim; ++d) { 2310 ierr = DMLabelGetStratumSize(subpointMap, d, &numSubPoints[d]);CHKERRQ(ierr); 2311 totSubPoints += numSubPoints[d]; 2312 } 2313 ierr = DMPlexSetChart(subdm, 0, totSubPoints);CHKERRQ(ierr); 2314 ierr = DMPlexSetVTKCellHeight(subdm, 1);CHKERRQ(ierr); 2315 /* Set cone sizes */ 2316 firstSubPoint[dim] = 0; 2317 firstSubPoint[0] = firstSubPoint[dim] + numSubPoints[dim]; 2318 if (dim > 1) {firstSubPoint[dim-1] = firstSubPoint[0] + numSubPoints[0];} 2319 if (dim > 2) {firstSubPoint[dim-2] = firstSubPoint[dim-1] + numSubPoints[dim-1];} 2320 for (d = 0; d <= dim; ++d) { 2321 ierr = DMLabelGetStratumIS(subpointMap, d, &subpointIS[d]);CHKERRQ(ierr); 2322 ierr = ISGetIndices(subpointIS[d], &subpoints[d]);CHKERRQ(ierr); 2323 } 2324 for (d = 0; d <= dim; ++d) { 2325 for (p = 0; p < numSubPoints[d]; ++p) { 2326 const PetscInt point = subpoints[d][p]; 2327 const PetscInt subpoint = firstSubPoint[d] + p; 2328 const PetscInt *cone; 2329 PetscInt coneSize, coneSizeNew, c, val; 2330 2331 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 2332 ierr = DMPlexSetConeSize(subdm, subpoint, coneSize);CHKERRQ(ierr); 2333 if (d == dim) { 2334 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 2335 for (c = 0, coneSizeNew = 0; c < coneSize; ++c) { 2336 ierr = DMLabelGetValue(subpointMap, cone[c], &val);CHKERRQ(ierr); 2337 if (val >= 0) coneSizeNew++; 2338 } 2339 ierr = DMPlexSetConeSize(subdm, subpoint, coneSizeNew);CHKERRQ(ierr); 2340 } 2341 } 2342 } 2343 ierr = DMSetUp(subdm);CHKERRQ(ierr); 2344 /* Set cones */ 2345 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, NULL);CHKERRQ(ierr); 2346 ierr = PetscMalloc(maxConeSize * sizeof(PetscInt), &coneNew);CHKERRQ(ierr); 2347 for (d = 0; d <= dim; ++d) { 2348 for (p = 0; p < numSubPoints[d]; ++p) { 2349 const PetscInt point = subpoints[d][p]; 2350 const PetscInt subpoint = firstSubPoint[d] + p; 2351 const PetscInt *cone; 2352 PetscInt coneSize, subconeSize, coneSizeNew, c, subc; 2353 2354 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 2355 ierr = DMPlexGetConeSize(subdm, subpoint, &subconeSize);CHKERRQ(ierr); 2356 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 2357 for (c = 0, coneSizeNew = 0; c < coneSize; ++c) { 2358 ierr = PetscFindInt(cone[c], numSubPoints[d-1], subpoints[d-1], &subc);CHKERRQ(ierr); 2359 if (subc >= 0) coneNew[coneSizeNew++] = firstSubPoint[d-1] + subc; 2360 } 2361 if (coneSizeNew != subconeSize) SETERRQ2(comm, PETSC_ERR_PLIB, "Number of cone points located %d does not match subcone size %d", coneSizeNew, subconeSize); 2362 ierr = DMPlexSetCone(subdm, subpoint, coneNew);CHKERRQ(ierr); 2363 } 2364 } 2365 ierr = PetscFree(coneNew);CHKERRQ(ierr); 2366 ierr = DMPlexSymmetrize(subdm);CHKERRQ(ierr); 2367 ierr = DMPlexStratify(subdm);CHKERRQ(ierr); 2368 /* Build coordinates */ 2369 { 2370 PetscSection coordSection, subCoordSection; 2371 Vec coordinates, subCoordinates; 2372 PetscScalar *coords, *subCoords; 2373 PetscInt numComp, coordSize; 2374 2375 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2376 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 2377 ierr = DMPlexGetCoordinateSection(subdm, &subCoordSection);CHKERRQ(ierr); 2378 ierr = PetscSectionSetNumFields(subCoordSection, 1);CHKERRQ(ierr); 2379 ierr = PetscSectionGetFieldComponents(coordSection, 0, &numComp);CHKERRQ(ierr); 2380 ierr = PetscSectionSetFieldComponents(subCoordSection, 0, numComp);CHKERRQ(ierr); 2381 ierr = PetscSectionSetChart(subCoordSection, firstSubPoint[0], firstSubPoint[0]+numSubPoints[0]);CHKERRQ(ierr); 2382 for (v = 0; v < numSubPoints[0]; ++v) { 2383 const PetscInt vertex = subpoints[0][v]; 2384 const PetscInt subvertex = firstSubPoint[0]+v; 2385 PetscInt dof; 2386 2387 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2388 ierr = PetscSectionSetDof(subCoordSection, subvertex, dof);CHKERRQ(ierr); 2389 ierr = PetscSectionSetFieldDof(subCoordSection, subvertex, 0, dof);CHKERRQ(ierr); 2390 } 2391 ierr = PetscSectionSetUp(subCoordSection);CHKERRQ(ierr); 2392 ierr = PetscSectionGetStorageSize(subCoordSection, &coordSize);CHKERRQ(ierr); 2393 ierr = VecCreate(comm, &subCoordinates);CHKERRQ(ierr); 2394 ierr = VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2395 ierr = VecSetFromOptions(subCoordinates);CHKERRQ(ierr); 2396 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2397 ierr = VecGetArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2398 for (v = 0; v < numSubPoints[0]; ++v) { 2399 const PetscInt vertex = subpoints[0][v]; 2400 const PetscInt subvertex = firstSubPoint[0]+v; 2401 PetscInt dof, off, sdof, soff, d; 2402 2403 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2404 ierr = PetscSectionGetOffset(coordSection, vertex, &off);CHKERRQ(ierr); 2405 ierr = PetscSectionGetDof(subCoordSection, subvertex, &sdof);CHKERRQ(ierr); 2406 ierr = PetscSectionGetOffset(subCoordSection, subvertex, &soff);CHKERRQ(ierr); 2407 if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof); 2408 for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d]; 2409 } 2410 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2411 ierr = VecRestoreArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2412 ierr = DMSetCoordinatesLocal(subdm, subCoordinates);CHKERRQ(ierr); 2413 ierr = VecDestroy(&subCoordinates);CHKERRQ(ierr); 2414 } 2415 /* Cleanup */ 2416 for (d = 0; d <= dim; ++d) { 2417 ierr = ISRestoreIndices(subpointIS[d], &subpoints[d]);CHKERRQ(ierr); 2418 ierr = ISDestroy(&subpointIS[d]);CHKERRQ(ierr); 2419 } 2420 ierr = PetscFree4(numSubPoints,firstSubPoint,subpointIS,subpoints);CHKERRQ(ierr); 2421 PetscFunctionReturn(0); 2422 } 2423 2424 #undef __FUNCT__ 2425 #define __FUNCT__ "DMPlexCreateCohesiveSubmesh" 2426 /* 2427 DMPlexCreateCohesiveSubmesh - Extract from a mesh with cohesive cells the hypersurface defined by one face of the cells. Optionally, a Label an be given to restrict the cells. 2428 2429 Input Parameters: 2430 + dm - The original mesh 2431 . hasLagrange - The mesh has Lagrange unknowns in the cohesive cells 2432 . label - A label name, or PETSC_NULL 2433 - value - A label value 2434 2435 Output Parameter: 2436 . subdm - The surface mesh 2437 2438 Note: This function produces a DMLabel mapping original points in the submesh to their depth. This can be obtained using DMPlexGetSubpointMap(). 2439 2440 Level: developer 2441 2442 .seealso: DMPlexGetSubpointMap(), DMPlexCreateSubmesh() 2443 */ 2444 PetscErrorCode DMPlexCreateCohesiveSubmesh(DM dm, PetscBool hasLagrange, const char label[], PetscInt value, DM *subdm) 2445 { 2446 PetscInt dim, depth; 2447 PetscErrorCode ierr; 2448 2449 PetscFunctionBegin; 2450 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2451 PetscValidPointer(subdm, 5); 2452 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 2453 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 2454 ierr = DMCreate(PetscObjectComm((PetscObject)dm), subdm);CHKERRQ(ierr); 2455 ierr = DMSetType(*subdm, DMPLEX);CHKERRQ(ierr); 2456 ierr = DMPlexSetDimension(*subdm, dim-1);CHKERRQ(ierr); 2457 if (depth == dim) { 2458 ierr = DMPlexCreateCohesiveSubmesh_Interpolated(dm, hasLagrange, label, value, *subdm);CHKERRQ(ierr); 2459 } else { 2460 ierr = DMPlexCreateCohesiveSubmesh_Uninterpolated(dm, hasLagrange, label, value, *subdm);CHKERRQ(ierr); 2461 } 2462 PetscFunctionReturn(0); 2463 } 2464 2465 #undef __FUNCT__ 2466 #define __FUNCT__ "DMPlexGetSubpointMap" 2467 /*@ 2468 DMPlexGetSubpointMap - Returns a DMLabel with point dimension as values 2469 2470 Input Parameter: 2471 . dm - The submesh DM 2472 2473 Output Parameter: 2474 . subpointMap - The DMLabel of all the points from the original mesh in this submesh, or NULL if this is not a submesh 2475 2476 Level: developer 2477 2478 .seealso: DMPlexCreateSubmesh(), DMPlexCreateSubpointIS() 2479 @*/ 2480 PetscErrorCode DMPlexGetSubpointMap(DM dm, DMLabel *subpointMap) 2481 { 2482 DM_Plex *mesh = (DM_Plex*) dm->data; 2483 2484 PetscFunctionBegin; 2485 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2486 PetscValidPointer(subpointMap, 2); 2487 *subpointMap = mesh->subpointMap; 2488 PetscFunctionReturn(0); 2489 } 2490 2491 #undef __FUNCT__ 2492 #define __FUNCT__ "DMPlexSetSubpointMap" 2493 /* Note: Should normally not be called by the user, since it is set in DMPlexCreateSubmesh() */ 2494 PetscErrorCode DMPlexSetSubpointMap(DM dm, DMLabel subpointMap) 2495 { 2496 DM_Plex *mesh = (DM_Plex *) dm->data; 2497 DMLabel tmp; 2498 PetscErrorCode ierr; 2499 2500 PetscFunctionBegin; 2501 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2502 tmp = mesh->subpointMap; 2503 mesh->subpointMap = subpointMap; 2504 ++mesh->subpointMap->refct; 2505 ierr = DMLabelDestroy(&tmp);CHKERRQ(ierr); 2506 PetscFunctionReturn(0); 2507 } 2508 2509 #undef __FUNCT__ 2510 #define __FUNCT__ "DMPlexCreateSubpointIS" 2511 /*@ 2512 DMPlexCreateSubpointIS - Creates an IS covering the entire subdm chart with the original points as data 2513 2514 Input Parameter: 2515 . dm - The submesh DM 2516 2517 Output Parameter: 2518 . subpointIS - The IS of all the points from the original mesh in this submesh, or NULL if this is not a submesh 2519 2520 Note: This is IS is guaranteed to be sorted by the construction of the submesh 2521 2522 Level: developer 2523 2524 .seealso: DMPlexCreateSubmesh(), DMPlexGetSubpointMap() 2525 @*/ 2526 PetscErrorCode DMPlexCreateSubpointIS(DM dm, IS *subpointIS) 2527 { 2528 MPI_Comm comm; 2529 DMLabel subpointMap; 2530 IS is; 2531 const PetscInt *opoints; 2532 PetscInt *points, *depths; 2533 PetscInt depth, depStart, depEnd, d, pStart, pEnd, p, n, off; 2534 PetscErrorCode ierr; 2535 2536 PetscFunctionBegin; 2537 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2538 PetscValidPointer(subpointIS, 2); 2539 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 2540 *subpointIS = NULL; 2541 ierr = DMPlexGetSubpointMap(dm, &subpointMap);CHKERRQ(ierr); 2542 if (subpointMap) { 2543 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 2544 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 2545 if (pStart) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Submeshes must start the point numbering at 0, not %d", pStart); 2546 ierr = DMGetWorkArray(dm, depth+1, PETSC_INT, &depths);CHKERRQ(ierr); 2547 depths[0] = depth; 2548 depths[1] = 0; 2549 for(d = 2; d <= depth; ++d) {depths[d] = depth+1 - d;} 2550 ierr = PetscMalloc(pEnd * sizeof(PetscInt), &points);CHKERRQ(ierr); 2551 for(d = 0, off = 0; d <= depth; ++d) { 2552 const PetscInt dep = depths[d]; 2553 2554 ierr = DMPlexGetDepthStratum(dm, dep, &depStart, &depEnd);CHKERRQ(ierr); 2555 ierr = DMLabelGetStratumSize(subpointMap, dep, &n);CHKERRQ(ierr); 2556 if (((d < 2) && (depth > 1)) || (d == 1)) { /* Only check vertices and cells for now since the map is broken for others */ 2557 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); 2558 } else { 2559 if (!n) { 2560 if (d == 0) { 2561 /* Missing cells */ 2562 for(p = 0; p < depEnd-depStart; ++p, ++off) points[off] = -1; 2563 } else { 2564 /* Missing faces */ 2565 for(p = 0; p < depEnd-depStart; ++p, ++off) points[off] = PETSC_MAX_INT; 2566 } 2567 } 2568 } 2569 if (n) { 2570 ierr = DMLabelGetStratumIS(subpointMap, dep, &is);CHKERRQ(ierr); 2571 ierr = ISGetIndices(is, &opoints);CHKERRQ(ierr); 2572 for(p = 0; p < n; ++p, ++off) points[off] = opoints[p]; 2573 ierr = ISRestoreIndices(is, &opoints);CHKERRQ(ierr); 2574 ierr = ISDestroy(&is);CHKERRQ(ierr); 2575 } 2576 } 2577 ierr = DMRestoreWorkArray(dm, depth+1, PETSC_INT, &depths);CHKERRQ(ierr); 2578 if (off != pEnd) SETERRQ2(comm, PETSC_ERR_ARG_WRONG, "The number of mapped submesh points %d should be %d", off, pEnd); 2579 ierr = ISCreateGeneral(comm, pEnd, points, PETSC_OWN_POINTER, subpointIS);CHKERRQ(ierr); 2580 } 2581 PetscFunctionReturn(0); 2582 } 2583