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 PetscErrorCode ierr; 253 254 PetscFunctionBegin; 255 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 256 ierr = PetscMalloc((depth+1) * sizeof(PetscInt), &depthEnd);CHKERRQ(ierr); 257 for (d = 0; d <= depth; ++d) { 258 totShift += depthShift[d]; 259 ierr = DMPlexGetDepthStratum(dm, d, NULL, &depthEnd[d]);CHKERRQ(ierr); 260 } 261 /* Step 9: Convert pointSF */ 262 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 263 ierr = DMGetPointSF(dmNew, &sfPointNew);CHKERRQ(ierr); 264 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 265 ierr = PetscSFGetGraph(sfPoint, &numRoots, &numLeaves, &localPoints, &remotePoints);CHKERRQ(ierr); 266 if (numRoots >= 0) { 267 ierr = PetscMalloc2(numRoots,PetscInt,&newLocation,pEnd-pStart,PetscInt,&newRemoteLocation);CHKERRQ(ierr); 268 for (l=0; l<numRoots; l++) newLocation[l] = DMPlexShiftPoint_Internal(l, depth, depthEnd, depthShift); 269 ierr = PetscSFBcastBegin(sfPoint, MPIU_INT, newLocation, newRemoteLocation);CHKERRQ(ierr); 270 ierr = PetscSFBcastEnd(sfPoint, MPIU_INT, newLocation, newRemoteLocation);CHKERRQ(ierr); 271 ierr = PetscMalloc(numLeaves * sizeof(PetscInt), &glocalPoints);CHKERRQ(ierr); 272 ierr = PetscMalloc(numLeaves * sizeof(PetscSFNode), &gremotePoints);CHKERRQ(ierr); 273 for (l = 0; l < numLeaves; ++l) { 274 glocalPoints[l] = DMPlexShiftPoint_Internal(localPoints[l], depth, depthEnd, depthShift); 275 gremotePoints[l].rank = remotePoints[l].rank; 276 gremotePoints[l].index = newRemoteLocation[localPoints[l]]; 277 } 278 ierr = PetscFree2(newLocation,newRemoteLocation);CHKERRQ(ierr); 279 ierr = PetscSFSetGraph(sfPointNew, numRoots + totShift, numLeaves, glocalPoints, PETSC_OWN_POINTER, gremotePoints, PETSC_OWN_POINTER);CHKERRQ(ierr); 280 } 281 ierr = PetscFree(depthEnd);CHKERRQ(ierr); 282 PetscFunctionReturn(0); 283 } 284 285 #undef __FUNCT__ 286 #define __FUNCT__ "DMPlexShiftLabels_Internal" 287 static PetscErrorCode DMPlexShiftLabels_Internal(DM dm, PetscInt depthShift[], DM dmNew) 288 { 289 PetscSF sfPoint; 290 DMLabel vtkLabel, ghostLabel; 291 PetscInt *depthEnd; 292 const PetscSFNode *leafRemote; 293 const PetscInt *leafLocal; 294 PetscInt depth = 0, d, numLeaves, numLabels, l, cStart, cEnd, c, fStart, fEnd, f; 295 PetscMPIInt rank; 296 PetscErrorCode ierr; 297 298 PetscFunctionBegin; 299 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 300 ierr = PetscMalloc((depth+1) * sizeof(PetscInt), &depthEnd);CHKERRQ(ierr); 301 for (d = 0; d <= depth; ++d) { 302 ierr = DMPlexGetDepthStratum(dm, d, NULL, &depthEnd[d]);CHKERRQ(ierr); 303 } 304 /* Step 10: Convert labels */ 305 ierr = DMPlexGetNumLabels(dm, &numLabels);CHKERRQ(ierr); 306 for (l = 0; l < numLabels; ++l) { 307 DMLabel label, newlabel; 308 const char *lname; 309 PetscBool isDepth; 310 IS valueIS; 311 const PetscInt *values; 312 PetscInt numValues, val; 313 314 ierr = DMPlexGetLabelName(dm, l, &lname);CHKERRQ(ierr); 315 ierr = PetscStrcmp(lname, "depth", &isDepth);CHKERRQ(ierr); 316 if (isDepth) continue; 317 ierr = DMPlexCreateLabel(dmNew, lname);CHKERRQ(ierr); 318 ierr = DMPlexGetLabel(dm, lname, &label);CHKERRQ(ierr); 319 ierr = DMPlexGetLabel(dmNew, lname, &newlabel);CHKERRQ(ierr); 320 ierr = DMLabelGetValueIS(label, &valueIS);CHKERRQ(ierr); 321 ierr = ISGetLocalSize(valueIS, &numValues);CHKERRQ(ierr); 322 ierr = ISGetIndices(valueIS, &values);CHKERRQ(ierr); 323 for (val = 0; val < numValues; ++val) { 324 IS pointIS; 325 const PetscInt *points; 326 PetscInt numPoints, p; 327 328 ierr = DMLabelGetStratumIS(label, values[val], &pointIS);CHKERRQ(ierr); 329 ierr = ISGetLocalSize(pointIS, &numPoints);CHKERRQ(ierr); 330 ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); 331 for (p = 0; p < numPoints; ++p) { 332 const PetscInt newpoint = DMPlexShiftPoint_Internal(points[p], depth, depthEnd, depthShift); 333 334 ierr = DMLabelSetValue(newlabel, newpoint, values[val]);CHKERRQ(ierr); 335 } 336 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 337 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 338 } 339 ierr = ISRestoreIndices(valueIS, &values);CHKERRQ(ierr); 340 ierr = ISDestroy(&valueIS);CHKERRQ(ierr); 341 } 342 ierr = PetscFree(depthEnd);CHKERRQ(ierr); 343 /* Step 11: Make label for output (vtk) and to mark ghost points (ghost) */ 344 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr); 345 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 346 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 347 ierr = PetscSFGetGraph(sfPoint, NULL, &numLeaves, &leafLocal, &leafRemote);CHKERRQ(ierr); 348 ierr = DMPlexCreateLabel(dmNew, "vtk");CHKERRQ(ierr); 349 ierr = DMPlexCreateLabel(dmNew, "ghost");CHKERRQ(ierr); 350 ierr = DMPlexGetLabel(dmNew, "vtk", &vtkLabel);CHKERRQ(ierr); 351 ierr = DMPlexGetLabel(dmNew, "ghost", &ghostLabel);CHKERRQ(ierr); 352 for (l = 0, c = cStart; l < numLeaves && c < cEnd; ++l, ++c) { 353 for (; c < leafLocal[l] && c < cEnd; ++c) { 354 ierr = DMLabelSetValue(vtkLabel, c, 1);CHKERRQ(ierr); 355 } 356 if (leafLocal[l] >= cEnd) break; 357 if (leafRemote[l].rank == rank) { 358 ierr = DMLabelSetValue(vtkLabel, c, 1);CHKERRQ(ierr); 359 } else { 360 ierr = DMLabelSetValue(ghostLabel, c, 2);CHKERRQ(ierr); 361 } 362 } 363 for (; c < cEnd; ++c) { 364 ierr = DMLabelSetValue(vtkLabel, c, 1);CHKERRQ(ierr); 365 } 366 if (0) { 367 ierr = PetscViewerASCIISynchronizedAllow(PETSC_VIEWER_STDOUT_WORLD, PETSC_TRUE);CHKERRQ(ierr); 368 ierr = DMLabelView(vtkLabel, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 369 ierr = PetscViewerFlush(PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 370 } 371 ierr = DMPlexGetHeightStratum(dmNew, 1, &fStart, &fEnd);CHKERRQ(ierr); 372 for (f = fStart; f < fEnd; ++f) { 373 PetscInt numCells; 374 375 ierr = DMPlexGetSupportSize(dmNew, f, &numCells);CHKERRQ(ierr); 376 if (numCells < 2) { 377 ierr = DMLabelSetValue(ghostLabel, f, 1);CHKERRQ(ierr); 378 } else { 379 const PetscInt *cells = NULL; 380 PetscInt vA, vB; 381 382 ierr = DMPlexGetSupport(dmNew, f, &cells);CHKERRQ(ierr); 383 ierr = DMLabelGetValue(vtkLabel, cells[0], &vA);CHKERRQ(ierr); 384 ierr = DMLabelGetValue(vtkLabel, cells[1], &vB);CHKERRQ(ierr); 385 if (!vA && !vB) {ierr = DMLabelSetValue(ghostLabel, f, 1);CHKERRQ(ierr);} 386 } 387 } 388 if (0) { 389 ierr = PetscViewerASCIISynchronizedAllow(PETSC_VIEWER_STDOUT_WORLD, PETSC_TRUE);CHKERRQ(ierr); 390 ierr = DMLabelView(ghostLabel, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 391 ierr = PetscViewerFlush(PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 392 } 393 PetscFunctionReturn(0); 394 } 395 396 #undef __FUNCT__ 397 #define __FUNCT__ "DMPlexConstructGhostCells_Internal" 398 static PetscErrorCode DMPlexConstructGhostCells_Internal(DM dm, DMLabel label, PetscInt *numGhostCells, DM gdm) 399 { 400 IS valueIS; 401 const PetscInt *values; 402 PetscInt *depthShift; 403 PetscInt depth = 0, numFS, fs, ghostCell, cEnd, c; 404 PetscErrorCode ierr; 405 406 PetscFunctionBegin; 407 /* Count ghost cells */ 408 ierr = DMLabelGetValueIS(label, &valueIS);CHKERRQ(ierr); 409 ierr = ISGetLocalSize(valueIS, &numFS);CHKERRQ(ierr); 410 ierr = ISGetIndices(valueIS, &values);CHKERRQ(ierr); 411 412 *numGhostCells = 0; 413 for (fs = 0; fs < numFS; ++fs) { 414 PetscInt numBdFaces; 415 416 ierr = DMLabelGetStratumSize(label, values[fs], &numBdFaces);CHKERRQ(ierr); 417 418 *numGhostCells += numBdFaces; 419 } 420 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 421 ierr = PetscMalloc((depth+1) * sizeof(PetscInt), &depthShift);CHKERRQ(ierr); 422 ierr = PetscMemzero(depthShift, (depth+1) * sizeof(PetscInt));CHKERRQ(ierr); 423 if (depth >= 0) depthShift[depth] = *numGhostCells; 424 ierr = DMPlexShiftSizes_Internal(dm, depthShift, gdm);CHKERRQ(ierr); 425 /* Step 3: Set cone/support sizes for new points */ 426 ierr = DMPlexGetHeightStratum(dm, 0, NULL, &cEnd);CHKERRQ(ierr); 427 for (c = cEnd; c < cEnd + *numGhostCells; ++c) { 428 ierr = DMPlexSetConeSize(gdm, c, 1);CHKERRQ(ierr); 429 } 430 for (fs = 0; fs < numFS; ++fs) { 431 IS faceIS; 432 const PetscInt *faces; 433 PetscInt numFaces, f; 434 435 ierr = DMLabelGetStratumIS(label, values[fs], &faceIS);CHKERRQ(ierr); 436 ierr = ISGetLocalSize(faceIS, &numFaces);CHKERRQ(ierr); 437 ierr = ISGetIndices(faceIS, &faces);CHKERRQ(ierr); 438 for (f = 0; f < numFaces; ++f) { 439 PetscInt size; 440 441 ierr = DMPlexGetSupportSize(dm, faces[f], &size);CHKERRQ(ierr); 442 if (size != 1) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "DM has boundary face %d with %d support cells", faces[f], size); 443 ierr = DMPlexSetSupportSize(gdm, faces[f] + *numGhostCells, 2);CHKERRQ(ierr); 444 } 445 ierr = ISRestoreIndices(faceIS, &faces);CHKERRQ(ierr); 446 ierr = ISDestroy(&faceIS);CHKERRQ(ierr); 447 } 448 /* Step 4: Setup ghosted DM */ 449 ierr = DMSetUp(gdm);CHKERRQ(ierr); 450 ierr = DMPlexShiftPoints_Internal(dm, depthShift, gdm);CHKERRQ(ierr); 451 /* Step 6: Set cones and supports for new points */ 452 ghostCell = cEnd; 453 for (fs = 0; fs < numFS; ++fs) { 454 IS faceIS; 455 const PetscInt *faces; 456 PetscInt numFaces, f; 457 458 ierr = DMLabelGetStratumIS(label, values[fs], &faceIS);CHKERRQ(ierr); 459 ierr = ISGetLocalSize(faceIS, &numFaces);CHKERRQ(ierr); 460 ierr = ISGetIndices(faceIS, &faces);CHKERRQ(ierr); 461 for (f = 0; f < numFaces; ++f, ++ghostCell) { 462 PetscInt newFace = faces[f] + *numGhostCells; 463 464 ierr = DMPlexSetCone(gdm, ghostCell, &newFace);CHKERRQ(ierr); 465 ierr = DMPlexInsertSupport(gdm, newFace, 1, ghostCell);CHKERRQ(ierr); 466 } 467 ierr = ISRestoreIndices(faceIS, &faces);CHKERRQ(ierr); 468 ierr = ISDestroy(&faceIS);CHKERRQ(ierr); 469 } 470 ierr = ISRestoreIndices(valueIS, &values);CHKERRQ(ierr); 471 ierr = ISDestroy(&valueIS);CHKERRQ(ierr); 472 /* Step 7: Stratify */ 473 ierr = DMPlexStratify(gdm);CHKERRQ(ierr); 474 ierr = DMPlexShiftCoordinates_Internal(dm, depthShift, gdm);CHKERRQ(ierr); 475 ierr = DMPlexShiftSF_Internal(dm, depthShift, gdm);CHKERRQ(ierr); 476 ierr = DMPlexShiftLabels_Internal(dm, depthShift, gdm);CHKERRQ(ierr); 477 ierr = PetscFree(depthShift);CHKERRQ(ierr); 478 PetscFunctionReturn(0); 479 } 480 481 #undef __FUNCT__ 482 #define __FUNCT__ "DMPlexConstructGhostCells" 483 /*@C 484 DMPlexConstructGhostCells - Construct ghost cells which connect to every boundary face 485 486 Collective on dm 487 488 Input Parameters: 489 + dm - The original DM 490 - labelName - The label specifying the boundary faces, or "Face Sets" if this is NULL 491 492 Output Parameters: 493 + numGhostCells - The number of ghost cells added to the DM 494 - dmGhosted - The new DM 495 496 Note: If no label exists of that name, one will be created marking all boundary faces 497 498 Level: developer 499 500 .seealso: DMCreate() 501 */ 502 PetscErrorCode DMPlexConstructGhostCells(DM dm, const char labelName[], PetscInt *numGhostCells, DM *dmGhosted) 503 { 504 DM gdm; 505 DMLabel label; 506 const char *name = labelName ? labelName : "Face Sets"; 507 PetscInt dim; 508 PetscErrorCode ierr; 509 510 PetscFunctionBegin; 511 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 512 PetscValidPointer(numGhostCells, 3); 513 PetscValidPointer(dmGhosted, 4); 514 ierr = DMCreate(PetscObjectComm((PetscObject)dm), &gdm);CHKERRQ(ierr); 515 ierr = DMSetType(gdm, DMPLEX);CHKERRQ(ierr); 516 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 517 ierr = DMPlexSetDimension(gdm, dim);CHKERRQ(ierr); 518 ierr = DMPlexGetLabel(dm, name, &label);CHKERRQ(ierr); 519 if (!label) { 520 /* Get label for boundary faces */ 521 ierr = DMPlexCreateLabel(dm, name);CHKERRQ(ierr); 522 ierr = DMPlexGetLabel(dm, name, &label);CHKERRQ(ierr); 523 ierr = DMPlexMarkBoundaryFaces(dm, label);CHKERRQ(ierr); 524 } 525 ierr = DMPlexConstructGhostCells_Internal(dm, label, numGhostCells, gdm);CHKERRQ(ierr); 526 ierr = DMSetFromOptions(gdm);CHKERRQ(ierr); 527 *dmGhosted = gdm; 528 PetscFunctionReturn(0); 529 } 530 531 #undef __FUNCT__ 532 #define __FUNCT__ "DMPlexConstructCohesiveCells_Internal" 533 static PetscErrorCode DMPlexConstructCohesiveCells_Internal(DM dm, DMLabel label, DM sdm) 534 { 535 MPI_Comm comm; 536 IS valueIS, *pointIS; 537 const PetscInt *values, **splitPoints; 538 PetscSection coordSection; 539 Vec coordinates; 540 PetscScalar *coords; 541 PetscInt *depthShift, *depthOffset, *pMaxNew, *numSplitPoints, *coneNew, *supportNew; 542 PetscInt shift = 100, depth = 0, dep, dim, d, numSP = 0, sp, maxConeSize, maxSupportSize, numLabels, pEnd, p, v; 543 PetscErrorCode ierr; 544 545 PetscFunctionBegin; 546 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 547 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 548 /* Count split points and add cohesive cells */ 549 if (label) { 550 ierr = DMLabelGetValueIS(label, &valueIS);CHKERRQ(ierr); 551 ierr = ISGetLocalSize(valueIS, &numSP);CHKERRQ(ierr); 552 ierr = ISGetIndices(valueIS, &values);CHKERRQ(ierr); 553 } 554 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 555 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize);CHKERRQ(ierr); 556 ierr = PetscMalloc5(depth+1,PetscInt,&depthShift,depth+1,PetscInt,&depthOffset,depth+1,PetscInt,&pMaxNew,maxConeSize*3,PetscInt,&coneNew,maxSupportSize,PetscInt,&supportNew);CHKERRQ(ierr); 557 ierr = PetscMalloc3(depth+1,IS,&pointIS,depth+1,PetscInt,&numSplitPoints,depth+1,const PetscInt*,&splitPoints);CHKERRQ(ierr); 558 ierr = PetscMemzero(depthShift, (depth+1) * sizeof(PetscInt));CHKERRQ(ierr); 559 for (d = 0; d <= depth; ++d) { 560 ierr = DMPlexGetDepthStratum(dm, d, NULL, &pMaxNew[d]);CHKERRQ(ierr); 561 numSplitPoints[d] = 0; 562 splitPoints[d] = NULL; 563 pointIS[d] = NULL; 564 } 565 for (sp = 0; sp < numSP; ++sp) { 566 const PetscInt dep = values[sp]; 567 568 if ((dep < 0) || (dep > depth)) continue; 569 ierr = DMLabelGetStratumSize(label, dep, &depthShift[dep]);CHKERRQ(ierr); 570 ierr = DMLabelGetStratumIS(label, dep, &pointIS[dep]);CHKERRQ(ierr); 571 if (pointIS[dep]) { 572 ierr = ISGetLocalSize(pointIS[dep], &numSplitPoints[dep]);CHKERRQ(ierr); 573 ierr = ISGetIndices(pointIS[dep], &splitPoints[dep]);CHKERRQ(ierr); 574 } 575 } 576 if (depth >= 0) { 577 /* Calculate number of additional points */ 578 depthShift[depth] = depthShift[depth-1]; /* There is a cohesive cell for every split face */ 579 depthShift[1] += depthShift[0]; /* There is a cohesive edge for every split vertex */ 580 /* Calculate hybrid bound for each dimension */ 581 pMaxNew[0] += depthShift[depth]; 582 if (depth > 1) pMaxNew[dim-1] += depthShift[depth] + depthShift[0]; 583 if (depth > 2) pMaxNew[1] += depthShift[depth] + depthShift[0] + depthShift[dim-1]; 584 585 /* Calculate point offset for each dimension */ 586 depthOffset[depth] = 0; 587 depthOffset[0] = depthOffset[depth] + depthShift[depth]; 588 if (depth > 1) depthOffset[dim-1] = depthOffset[0] + depthShift[0]; 589 if (depth > 2) depthOffset[1] = depthOffset[dim-1] + depthShift[dim-1]; 590 } 591 ierr = DMPlexShiftSizes_Internal(dm, depthShift, sdm);CHKERRQ(ierr); 592 /* Step 3: Set cone/support sizes for new points */ 593 for (dep = 0; dep <= depth; ++dep) { 594 for (p = 0; p < numSplitPoints[dep]; ++p) { 595 const PetscInt oldp = splitPoints[dep][p]; 596 const PetscInt newp = depthOffset[dep] + oldp; 597 const PetscInt splitp = pMaxNew[dep] + p; 598 const PetscInt *support; 599 PetscInt coneSize, supportSize, q, e; 600 601 ierr = DMPlexGetConeSize(dm, oldp, &coneSize);CHKERRQ(ierr); 602 ierr = DMPlexSetConeSize(sdm, splitp, coneSize);CHKERRQ(ierr); 603 ierr = DMPlexGetSupportSize(dm, oldp, &supportSize);CHKERRQ(ierr); 604 ierr = DMPlexSetSupportSize(sdm, splitp, supportSize);CHKERRQ(ierr); 605 if (dep == depth-1) { 606 const PetscInt ccell = pMaxNew[depth] + p; 607 /* Add cohesive cells, they are prisms */ 608 ierr = DMPlexSetConeSize(sdm, ccell, 2 + coneSize);CHKERRQ(ierr); 609 } else if (dep == 0) { 610 const PetscInt cedge = pMaxNew[1] + (depthShift[1] - depthShift[0]) + p; 611 612 ierr = DMPlexGetSupport(dm, oldp, &support);CHKERRQ(ierr); 613 /* Split old vertex: Edges in old split faces and new cohesive edge */ 614 for (e = 0, q = 0; e < supportSize; ++e) { 615 PetscInt val; 616 617 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 618 if ((val == 1) || (val == (shift + 1))) ++q; 619 } 620 ierr = DMPlexSetSupportSize(sdm, newp, q+1);CHKERRQ(ierr); 621 /* Split new vertex: Edges in new split faces and new cohesive edge */ 622 for (e = 0, q = 0; e < supportSize; ++e) { 623 PetscInt val; 624 625 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 626 if ((val == 1) || (val == -(shift + 1))) ++q; 627 } 628 ierr = DMPlexSetSupportSize(sdm, splitp, q+1);CHKERRQ(ierr); 629 /* Add cohesive edges */ 630 ierr = DMPlexSetConeSize(sdm, cedge, 2);CHKERRQ(ierr); 631 /* Punt for now on support, you loop over closure, extract faces, check which ones are in the label */ 632 } else if (dep == dim-2) { 633 ierr = DMPlexGetSupport(dm, oldp, &support);CHKERRQ(ierr); 634 /* Split old edge: Faces in positive side cells and old split faces */ 635 for (e = 0, q = 0; e < supportSize; ++e) { 636 PetscInt val; 637 638 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 639 if ((val == dim-1) || (val == (shift + dim-1))) ++q; 640 } 641 ierr = DMPlexSetSupportSize(sdm, newp, q);CHKERRQ(ierr); 642 /* Split new edge: Faces in negative side cells and new split faces */ 643 for (e = 0, q = 0; e < supportSize; ++e) { 644 PetscInt val; 645 646 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 647 if ((val == dim-1) || (val == -(shift + dim-1))) ++q; 648 } 649 ierr = DMPlexSetSupportSize(sdm, splitp, q);CHKERRQ(ierr); 650 } 651 } 652 } 653 /* Step 4: Setup split DM */ 654 ierr = DMSetUp(sdm);CHKERRQ(ierr); 655 ierr = DMPlexShiftPoints_Internal(dm, depthShift, sdm);CHKERRQ(ierr); 656 /* Step 6: Set cones and supports for new points */ 657 for (dep = 0; dep <= depth; ++dep) { 658 for (p = 0; p < numSplitPoints[dep]; ++p) { 659 const PetscInt oldp = splitPoints[dep][p]; 660 const PetscInt newp = depthOffset[dep] + oldp; 661 const PetscInt splitp = pMaxNew[dep] + p; 662 const PetscInt *cone, *support, *ornt; 663 PetscInt coneSize, supportSize, q, v, e, s; 664 665 ierr = DMPlexGetConeSize(dm, oldp, &coneSize);CHKERRQ(ierr); 666 ierr = DMPlexGetCone(dm, oldp, &cone);CHKERRQ(ierr); 667 ierr = DMPlexGetConeOrientation(dm, oldp, &ornt);CHKERRQ(ierr); 668 ierr = DMPlexGetSupportSize(dm, oldp, &supportSize);CHKERRQ(ierr); 669 ierr = DMPlexGetSupport(dm, oldp, &support);CHKERRQ(ierr); 670 if (dep == depth-1) { 671 const PetscInt ccell = pMaxNew[depth] + p; 672 const PetscInt *supportF; 673 674 /* Split face: copy in old face to new face to start */ 675 ierr = DMPlexGetSupport(sdm, newp, &supportF);CHKERRQ(ierr); 676 ierr = DMPlexSetSupport(sdm, splitp, supportF);CHKERRQ(ierr); 677 /* Split old face: old vertices/edges in cone so no change */ 678 /* Split new face: new vertices/edges in cone */ 679 for (q = 0; q < coneSize; ++q) { 680 ierr = PetscFindInt(cone[q], numSplitPoints[dim-2], splitPoints[dim-2], &v);CHKERRQ(ierr); 681 682 coneNew[2+q] = pMaxNew[dim-2] + v; 683 } 684 ierr = DMPlexSetCone(sdm, splitp, &coneNew[2]);CHKERRQ(ierr); 685 ierr = DMPlexSetConeOrientation(sdm, splitp, ornt);CHKERRQ(ierr); 686 /* Cohesive cell: Old and new split face, then new cohesive edges */ 687 coneNew[0] = newp; 688 coneNew[1] = splitp; 689 for (q = 0; q < coneSize; ++q) { 690 coneNew[2+q] = (pMaxNew[1] - pMaxNew[dim-2]) + (depthShift[1] - depthShift[0]) + coneNew[2+q]; 691 } 692 ierr = DMPlexSetCone(sdm, ccell, coneNew);CHKERRQ(ierr); 693 694 695 for (s = 0; s < supportSize; ++s) { 696 PetscInt val; 697 698 ierr = DMLabelGetValue(label, support[s], &val);CHKERRQ(ierr); 699 if (val < 0) { 700 /* Split old face: Replace negative side cell with cohesive cell */ 701 ierr = DMPlexInsertSupport(sdm, newp, s, ccell);CHKERRQ(ierr); 702 } else { 703 /* Split new face: Replace positive side cell with cohesive cell */ 704 ierr = DMPlexInsertSupport(sdm, splitp, s, ccell);CHKERRQ(ierr); 705 } 706 } 707 } else if (dep == 0) { 708 const PetscInt cedge = pMaxNew[1] + (depthShift[1] - depthShift[0]) + p; 709 710 /* Split old vertex: Edges in old split faces and new cohesive edge */ 711 for (e = 0, q = 0; e < supportSize; ++e) { 712 PetscInt val; 713 714 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 715 if ((val == 1) || (val == (shift + 1))) { 716 supportNew[q++] = depthOffset[1] + support[e]; 717 } 718 } 719 supportNew[q] = cedge; 720 721 ierr = DMPlexSetSupport(sdm, newp, supportNew);CHKERRQ(ierr); 722 /* Split new vertex: Edges in new split faces and new cohesive edge */ 723 for (e = 0, q = 0; e < supportSize; ++e) { 724 PetscInt val, edge; 725 726 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 727 if (val == 1) { 728 ierr = PetscFindInt(support[e], numSplitPoints[1], splitPoints[1], &edge);CHKERRQ(ierr); 729 if (edge < 0) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Edge %d is not a split edge", support[e]); 730 supportNew[q++] = pMaxNew[1] + edge; 731 } else if (val == -(shift + 1)) { 732 supportNew[q++] = depthOffset[1] + support[e]; 733 } 734 } 735 supportNew[q] = cedge; 736 ierr = DMPlexSetSupport(sdm, splitp, supportNew);CHKERRQ(ierr); 737 /* Cohesive edge: Old and new split vertex, punting on support */ 738 coneNew[0] = newp; 739 coneNew[1] = splitp; 740 ierr = DMPlexSetCone(sdm, cedge, coneNew);CHKERRQ(ierr); 741 } else if (dep == dim-2) { 742 /* Split old edge: old vertices in cone so no change */ 743 /* Split new edge: new vertices in cone */ 744 for (q = 0; q < coneSize; ++q) { 745 ierr = PetscFindInt(cone[q], numSplitPoints[dim-3], splitPoints[dim-3], &v);CHKERRQ(ierr); 746 747 coneNew[q] = pMaxNew[dim-3] + v; 748 } 749 ierr = DMPlexSetCone(sdm, splitp, coneNew);CHKERRQ(ierr); 750 /* Split old edge: Faces in positive side cells and old split faces */ 751 for (e = 0, q = 0; e < supportSize; ++e) { 752 PetscInt val; 753 754 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 755 if ((val == dim-1) || (val == (shift + dim-1))) { 756 supportNew[q++] = depthOffset[dim-1] + support[e]; 757 } 758 } 759 ierr = DMPlexSetSupport(sdm, newp, supportNew);CHKERRQ(ierr); 760 /* Split new edge: Faces in negative side cells and new split faces */ 761 for (e = 0, q = 0; e < supportSize; ++e) { 762 PetscInt val, face; 763 764 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 765 if (val == dim-1) { 766 ierr = PetscFindInt(support[e], numSplitPoints[dim-1], splitPoints[dim-1], &face);CHKERRQ(ierr); 767 if (face < 0) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Face %d is not a split face", support[e]); 768 supportNew[q++] = pMaxNew[dim-1] + face; 769 } else if (val == -(shift + dim-1)) { 770 supportNew[q++] = depthOffset[dim-1] + support[e]; 771 } 772 } 773 ierr = DMPlexSetSupport(sdm, splitp, supportNew);CHKERRQ(ierr); 774 } 775 } 776 } 777 /* Step 6b: Replace split points in negative side cones */ 778 for (sp = 0; sp < numSP; ++sp) { 779 PetscInt dep = values[sp]; 780 IS pIS; 781 PetscInt numPoints; 782 const PetscInt *points; 783 784 if (dep >= 0) continue; 785 ierr = DMLabelGetStratumIS(label, dep, &pIS);CHKERRQ(ierr); 786 if (!pIS) continue; 787 dep = -dep - shift; 788 ierr = ISGetLocalSize(pIS, &numPoints);CHKERRQ(ierr); 789 ierr = ISGetIndices(pIS, &points);CHKERRQ(ierr); 790 for (p = 0; p < numPoints; ++p) { 791 const PetscInt oldp = points[p]; 792 const PetscInt newp = depthOffset[dep] + oldp; 793 const PetscInt *cone; 794 PetscInt coneSize, c; 795 PetscBool replaced = PETSC_FALSE; 796 797 /* Negative edge: replace split vertex */ 798 /* Negative cell: replace split face */ 799 ierr = DMPlexGetConeSize(sdm, newp, &coneSize);CHKERRQ(ierr); 800 ierr = DMPlexGetCone(sdm, newp, &cone);CHKERRQ(ierr); 801 for (c = 0; c < coneSize; ++c) { 802 const PetscInt coldp = cone[c] - depthOffset[dep-1]; 803 PetscInt csplitp, cp, val; 804 805 ierr = DMLabelGetValue(label, coldp, &val);CHKERRQ(ierr); 806 if (val == dep-1) { 807 ierr = PetscFindInt(coldp, numSplitPoints[dep-1], splitPoints[dep-1], &cp);CHKERRQ(ierr); 808 if (cp < 0) SETERRQ2(comm, PETSC_ERR_ARG_WRONG, "Point %d is not a split point of dimension %d", oldp, dep-1); 809 csplitp = pMaxNew[dep-1] + cp; 810 ierr = DMPlexInsertCone(sdm, newp, c, csplitp);CHKERRQ(ierr); 811 replaced = PETSC_TRUE; 812 } 813 } 814 if (!replaced) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "The cone of point %d does not contain split points", oldp); 815 } 816 ierr = ISRestoreIndices(pIS, &points);CHKERRQ(ierr); 817 ierr = ISDestroy(&pIS);CHKERRQ(ierr); 818 } 819 /* Step 7: Stratify */ 820 ierr = DMPlexStratify(sdm);CHKERRQ(ierr); 821 /* Step 8: Coordinates */ 822 ierr = DMPlexShiftCoordinates_Internal(dm, depthShift, sdm);CHKERRQ(ierr); 823 ierr = DMPlexGetCoordinateSection(sdm, &coordSection);CHKERRQ(ierr); 824 ierr = DMGetCoordinatesLocal(sdm, &coordinates);CHKERRQ(ierr); 825 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 826 for (v = 0; v < (numSplitPoints ? numSplitPoints[0] : 0); ++v) { 827 const PetscInt newp = depthOffset[0] + splitPoints[0][v]; 828 const PetscInt splitp = pMaxNew[0] + v; 829 PetscInt dof, off, soff, d; 830 831 ierr = PetscSectionGetDof(coordSection, newp, &dof);CHKERRQ(ierr); 832 ierr = PetscSectionGetOffset(coordSection, newp, &off);CHKERRQ(ierr); 833 ierr = PetscSectionGetOffset(coordSection, splitp, &soff);CHKERRQ(ierr); 834 for (d = 0; d < dof; ++d) coords[soff+d] = coords[off+d]; 835 } 836 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 837 /* Step 9: SF, if I can figure this out we can split the mesh in parallel */ 838 ierr = DMPlexShiftSF_Internal(dm, depthShift, sdm);CHKERRQ(ierr); 839 /* Step 10: Labels */ 840 ierr = DMPlexShiftLabels_Internal(dm, depthShift, sdm);CHKERRQ(ierr); 841 ierr = DMPlexGetNumLabels(sdm, &numLabels);CHKERRQ(ierr); 842 for (dep = 0; dep <= depth; ++dep) { 843 for (p = 0; p < numSplitPoints[dep]; ++p) { 844 const PetscInt newp = depthOffset[dep] + splitPoints[dep][p]; 845 const PetscInt splitp = pMaxNew[dep] + p; 846 PetscInt l; 847 848 for (l = 0; l < numLabels; ++l) { 849 DMLabel mlabel; 850 const char *lname; 851 PetscInt val; 852 PetscBool isDepth; 853 854 ierr = DMPlexGetLabelName(sdm, l, &lname);CHKERRQ(ierr); 855 ierr = PetscStrcmp(lname, "depth", &isDepth);CHKERRQ(ierr); 856 if (isDepth) continue; 857 ierr = DMPlexGetLabel(sdm, lname, &mlabel);CHKERRQ(ierr); 858 ierr = DMLabelGetValue(mlabel, newp, &val);CHKERRQ(ierr); 859 if (val >= 0) { 860 ierr = DMLabelSetValue(mlabel, splitp, val);CHKERRQ(ierr); 861 #if 0 862 /* Do not put cohesive edges into the label */ 863 if (dep == 0) { 864 const PetscInt cedge = pMaxNew[1] + (depthShift[1] - depthShift[0]) + p; 865 ierr = DMLabelSetValue(mlabel, cedge, val);CHKERRQ(ierr); 866 } 867 #endif 868 } 869 } 870 } 871 } 872 for (sp = 0; sp < numSP; ++sp) { 873 const PetscInt dep = values[sp]; 874 875 if ((dep < 0) || (dep > depth)) continue; 876 if (pointIS[dep]) {ierr = ISRestoreIndices(pointIS[dep], &splitPoints[dep]);CHKERRQ(ierr);} 877 ierr = ISDestroy(&pointIS[dep]);CHKERRQ(ierr); 878 } 879 if (label) { 880 ierr = ISRestoreIndices(valueIS, &values);CHKERRQ(ierr); 881 ierr = ISDestroy(&valueIS);CHKERRQ(ierr); 882 } 883 ierr = DMPlexGetChart(sdm, NULL, &pEnd);CHKERRQ(ierr); 884 pMaxNew[0] += depthShift[0]; /* Account for shadow vertices */ 885 if (depth > 1) pMaxNew[1] = pEnd - depthShift[0]; /* There is a hybrid edge for every shadow vertex */ 886 if (depth > 2) pMaxNew[2] = -1; /* There are no hybrid faces */ 887 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); 888 ierr = PetscFree5(depthShift, depthOffset, pMaxNew, coneNew, supportNew);CHKERRQ(ierr); 889 ierr = PetscFree3(pointIS, numSplitPoints, splitPoints);CHKERRQ(ierr); 890 PetscFunctionReturn(0); 891 } 892 893 #undef __FUNCT__ 894 #define __FUNCT__ "DMPlexConstructCohesiveCells" 895 /*@C 896 DMPlexConstructCohesiveCells - Construct cohesive cells which split the face along an internal interface 897 898 Collective on dm 899 900 Input Parameters: 901 + dm - The original DM 902 - labelName - The label specifying the boundary faces (this could be auto-generated) 903 904 Output Parameters: 905 - dmSplit - The new DM 906 907 Level: developer 908 909 .seealso: DMCreate(), DMPlexLabelCohesiveComplete() 910 @*/ 911 PetscErrorCode DMPlexConstructCohesiveCells(DM dm, DMLabel label, DM *dmSplit) 912 { 913 DM sdm; 914 PetscInt dim; 915 PetscErrorCode ierr; 916 917 PetscFunctionBegin; 918 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 919 PetscValidPointer(dmSplit, 4); 920 ierr = DMCreate(PetscObjectComm((PetscObject)dm), &sdm);CHKERRQ(ierr); 921 ierr = DMSetType(sdm, DMPLEX);CHKERRQ(ierr); 922 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 923 ierr = DMPlexSetDimension(sdm, dim);CHKERRQ(ierr); 924 switch (dim) { 925 case 2: 926 case 3: 927 ierr = DMPlexConstructCohesiveCells_Internal(dm, label, sdm);CHKERRQ(ierr); 928 break; 929 default: 930 SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Cannot construct cohesive cells for dimension %d", dim); 931 } 932 *dmSplit = sdm; 933 PetscFunctionReturn(0); 934 } 935 936 #undef __FUNCT__ 937 #define __FUNCT__ "DMPlexLabelCohesiveComplete" 938 /*@ 939 DMPlexLabelCohesiveComplete - Starting with a label marking vertices on an internal surface, we add all other mesh pieces 940 to complete the surface 941 942 Input Parameters: 943 + dm - The DM 944 - label - A DMLabel marking the surface vertices 945 946 Output Parameter: 947 . label - A DMLabel marking all surface points 948 949 Level: developer 950 951 .seealso: DMPlexConstructCohesiveCells(), DMPlexLabelComplete() 952 @*/ 953 PetscErrorCode DMPlexLabelCohesiveComplete(DM dm, DMLabel label) 954 { 955 IS dimIS; 956 const PetscInt *points; 957 PetscInt shift = 100, dim, dep, cStart, cEnd, numPoints, p, val; 958 PetscErrorCode ierr; 959 960 PetscFunctionBegin; 961 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 962 /* Cell orientation for face gives the side of the fault */ 963 ierr = DMLabelGetStratumIS(label, dim-1, &dimIS);CHKERRQ(ierr); 964 if (!dimIS) PetscFunctionReturn(0); 965 ierr = ISGetLocalSize(dimIS, &numPoints);CHKERRQ(ierr); 966 ierr = ISGetIndices(dimIS, &points);CHKERRQ(ierr); 967 for (p = 0; p < numPoints; ++p) { 968 const PetscInt *support; 969 PetscInt supportSize, s; 970 971 ierr = DMPlexGetSupportSize(dm, points[p], &supportSize);CHKERRQ(ierr); 972 if (supportSize != 2) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Split face %d has %d != 2 supports", points[p], supportSize); 973 ierr = DMPlexGetSupport(dm, points[p], &support);CHKERRQ(ierr); 974 for (s = 0; s < supportSize; ++s) { 975 const PetscInt *cone, *ornt; 976 PetscInt coneSize, c; 977 PetscBool pos = PETSC_TRUE; 978 979 ierr = DMPlexGetConeSize(dm, support[s], &coneSize);CHKERRQ(ierr); 980 ierr = DMPlexGetCone(dm, support[s], &cone);CHKERRQ(ierr); 981 ierr = DMPlexGetConeOrientation(dm, support[s], &ornt);CHKERRQ(ierr); 982 for (c = 0; c < coneSize; ++c) { 983 if (cone[c] == points[p]) { 984 if (ornt[c] >= 0) { 985 ierr = DMLabelSetValue(label, support[s], shift+dim);CHKERRQ(ierr); 986 } else { 987 ierr = DMLabelSetValue(label, support[s], -(shift+dim));CHKERRQ(ierr); 988 pos = PETSC_FALSE; 989 } 990 break; 991 } 992 } 993 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]); 994 /* Put faces touching the fault in the label */ 995 for (c = 0; c < coneSize; ++c) { 996 const PetscInt point = cone[c]; 997 998 ierr = DMLabelGetValue(label, point, &val);CHKERRQ(ierr); 999 if (val == -1) { 1000 PetscInt *closure = NULL; 1001 PetscInt closureSize, cl; 1002 1003 ierr = DMPlexGetTransitiveClosure(dm, point, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1004 for (cl = 0; cl < closureSize*2; cl += 2) { 1005 const PetscInt clp = closure[cl]; 1006 1007 ierr = DMLabelGetValue(label, clp, &val);CHKERRQ(ierr); 1008 if ((val >= 0) && (val < dim-1)) { 1009 ierr = DMLabelSetValue(label, point, pos == PETSC_TRUE ? shift+dim-1 : -(shift+dim-1));CHKERRQ(ierr); 1010 break; 1011 } 1012 } 1013 ierr = DMPlexRestoreTransitiveClosure(dm, point, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1014 } 1015 } 1016 } 1017 } 1018 ierr = ISRestoreIndices(dimIS, &points);CHKERRQ(ierr); 1019 ierr = ISDestroy(&dimIS);CHKERRQ(ierr); 1020 /* Search for other cells/faces/edges connected to the fault by a vertex */ 1021 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1022 ierr = DMLabelGetStratumIS(label, 0, &dimIS);CHKERRQ(ierr); 1023 if (!dimIS) PetscFunctionReturn(0); 1024 ierr = ISGetLocalSize(dimIS, &numPoints);CHKERRQ(ierr); 1025 ierr = ISGetIndices(dimIS, &points);CHKERRQ(ierr); 1026 for (p = 0; p < numPoints; ++p) { 1027 PetscInt *star = NULL; 1028 PetscInt starSize, s; 1029 PetscInt again = 1; /* 0: Finished 1: Keep iterating after a change 2: No change */ 1030 1031 /* First mark cells connected to the fault */ 1032 ierr = DMPlexGetTransitiveClosure(dm, points[p], PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1033 while (again) { 1034 if (again > 1) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Could not classify all cells connected to the fault"); 1035 again = 0; 1036 for (s = 0; s < starSize*2; s += 2) { 1037 const PetscInt point = star[s]; 1038 const PetscInt *cone; 1039 PetscInt coneSize, c; 1040 1041 if ((point < cStart) || (point >= cEnd)) continue; 1042 ierr = DMLabelGetValue(label, point, &val);CHKERRQ(ierr); 1043 if (val != -1) continue; 1044 again = 2; 1045 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 1046 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 1047 for (c = 0; c < coneSize; ++c) { 1048 ierr = DMLabelGetValue(label, cone[c], &val);CHKERRQ(ierr); 1049 if (val != -1) { 1050 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); 1051 if (val > 0) { 1052 ierr = DMLabelSetValue(label, point, shift+dim);CHKERRQ(ierr); 1053 } else { 1054 ierr = DMLabelSetValue(label, point, -(shift+dim));CHKERRQ(ierr); 1055 } 1056 again = 1; 1057 break; 1058 } 1059 } 1060 } 1061 } 1062 /* Classify the rest by cell membership */ 1063 for (s = 0; s < starSize*2; s += 2) { 1064 const PetscInt point = star[s]; 1065 1066 ierr = DMLabelGetValue(label, point, &val);CHKERRQ(ierr); 1067 if (val == -1) { 1068 PetscInt *sstar = NULL; 1069 PetscInt sstarSize, ss; 1070 PetscBool marked = PETSC_FALSE; 1071 1072 ierr = DMPlexGetTransitiveClosure(dm, point, PETSC_FALSE, &sstarSize, &sstar);CHKERRQ(ierr); 1073 for (ss = 0; ss < sstarSize*2; ss += 2) { 1074 const PetscInt spoint = sstar[ss]; 1075 1076 if ((spoint < cStart) || (spoint >= cEnd)) continue; 1077 ierr = DMLabelGetValue(label, spoint, &val);CHKERRQ(ierr); 1078 if (val == -1) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Cell %d in star of %d does not have a valid label", spoint, point); 1079 ierr = DMPlexGetLabelValue(dm, "depth", point, &dep);CHKERRQ(ierr); 1080 if (val > 0) { 1081 ierr = DMLabelSetValue(label, point, shift+dep);CHKERRQ(ierr); 1082 } else { 1083 ierr = DMLabelSetValue(label, point, -(shift+dep));CHKERRQ(ierr); 1084 } 1085 marked = PETSC_TRUE; 1086 break; 1087 } 1088 ierr = DMPlexRestoreTransitiveClosure(dm, point, PETSC_FALSE, &sstarSize, &sstar);CHKERRQ(ierr); 1089 if (!marked) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Point %d could not be classified", point); 1090 } 1091 } 1092 ierr = DMPlexRestoreTransitiveClosure(dm, points[p], PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1093 } 1094 ierr = ISRestoreIndices(dimIS, &points);CHKERRQ(ierr); 1095 ierr = ISDestroy(&dimIS);CHKERRQ(ierr); 1096 PetscFunctionReturn(0); 1097 } 1098 1099 #undef __FUNCT__ 1100 #define __FUNCT__ "DMPlexMarkSubmesh_Uninterpolated" 1101 /* Here we need the explicit assumption that: 1102 1103 For any marked cell, the marked vertices constitute a single face 1104 */ 1105 static PetscErrorCode DMPlexMarkSubmesh_Uninterpolated(DM dm, DMLabel vertexLabel, PetscInt value, DMLabel subpointMap, PetscInt *numFaces, PetscInt *nFV, DM subdm) 1106 { 1107 IS subvertexIS = NULL; 1108 const PetscInt *subvertices; 1109 PetscInt *pStart, *pEnd, *pMax, pSize; 1110 PetscInt depth, dim, d, numSubVerticesInitial = 0, v; 1111 PetscErrorCode ierr; 1112 1113 PetscFunctionBegin; 1114 *numFaces = 0; 1115 *nFV = 0; 1116 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 1117 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1118 pSize = PetscMax(depth, dim) + 1; 1119 ierr = PetscMalloc3(pSize,PetscInt,&pStart,pSize,PetscInt,&pEnd,pSize,PetscInt,&pMax);CHKERRQ(ierr); 1120 ierr = DMPlexGetHybridBounds(dm, depth >= 0 ? &pMax[depth] : NULL, depth>1 ? &pMax[depth-1] : NULL, depth>2 ? &pMax[1] : NULL, &pMax[0]);CHKERRQ(ierr); 1121 for (d = 0; d <= depth; ++d) { 1122 ierr = DMPlexGetDepthStratum(dm, d, &pStart[d], &pEnd[d]);CHKERRQ(ierr); 1123 if (pMax[d] >= 0) pEnd[d] = PetscMin(pEnd[d], pMax[d]); 1124 } 1125 /* Loop over initial vertices and mark all faces in the collective star() */ 1126 if (vertexLabel) {ierr = DMLabelGetStratumIS(vertexLabel, value, &subvertexIS);CHKERRQ(ierr);} 1127 if (subvertexIS) { 1128 ierr = ISGetSize(subvertexIS, &numSubVerticesInitial);CHKERRQ(ierr); 1129 ierr = ISGetIndices(subvertexIS, &subvertices);CHKERRQ(ierr); 1130 } 1131 for (v = 0; v < numSubVerticesInitial; ++v) { 1132 const PetscInt vertex = subvertices[v]; 1133 PetscInt *star = NULL; 1134 PetscInt starSize, s, numCells = 0, c; 1135 1136 ierr = DMPlexGetTransitiveClosure(dm, vertex, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1137 for (s = 0; s < starSize*2; s += 2) { 1138 const PetscInt point = star[s]; 1139 if ((point >= pStart[depth]) && (point < pEnd[depth])) star[numCells++] = point; 1140 } 1141 for (c = 0; c < numCells; ++c) { 1142 const PetscInt cell = star[c]; 1143 PetscInt *closure = NULL; 1144 PetscInt closureSize, cl; 1145 PetscInt cellLoc, numCorners = 0, faceSize = 0; 1146 1147 ierr = DMLabelGetValue(subpointMap, cell, &cellLoc);CHKERRQ(ierr); 1148 if (cellLoc == 2) continue; 1149 if (cellLoc >= 0) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Cell %d has dimension %d in the surface label", cell, cellLoc); 1150 ierr = DMPlexGetTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1151 for (cl = 0; cl < closureSize*2; cl += 2) { 1152 const PetscInt point = closure[cl]; 1153 PetscInt vertexLoc; 1154 1155 if ((point >= pStart[0]) && (point < pEnd[0])) { 1156 ++numCorners; 1157 ierr = DMLabelGetValue(vertexLabel, point, &vertexLoc);CHKERRQ(ierr); 1158 if (vertexLoc == value) closure[faceSize++] = point; 1159 } 1160 } 1161 if (!(*nFV)) {ierr = DMPlexGetNumFaceVertices(dm, dim, numCorners, nFV);CHKERRQ(ierr);} 1162 if (faceSize > *nFV) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Invalid submesh: Too many vertices %d of an element on the surface", faceSize); 1163 if (faceSize == *nFV) { 1164 const PetscInt *cells = NULL; 1165 PetscInt numCells, nc; 1166 1167 ++(*numFaces); 1168 for (cl = 0; cl < faceSize; ++cl) { 1169 ierr = DMLabelSetValue(subpointMap, closure[cl], 0);CHKERRQ(ierr); 1170 } 1171 ierr = DMPlexGetJoin(dm, faceSize, closure, &numCells, &cells);CHKERRQ(ierr); 1172 for (nc = 0; nc < numCells; ++nc) { 1173 ierr = DMLabelSetValue(subpointMap, cells[nc], 2);CHKERRQ(ierr); 1174 } 1175 ierr = DMPlexRestoreJoin(dm, faceSize, closure, &numCells, &cells);CHKERRQ(ierr); 1176 } 1177 ierr = DMPlexRestoreTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1178 } 1179 ierr = DMPlexRestoreTransitiveClosure(dm, vertex, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1180 } 1181 if (subvertexIS) { 1182 ierr = ISRestoreIndices(subvertexIS, &subvertices);CHKERRQ(ierr); 1183 } 1184 ierr = ISDestroy(&subvertexIS);CHKERRQ(ierr); 1185 ierr = PetscFree3(pStart,pEnd,pMax);CHKERRQ(ierr); 1186 PetscFunctionReturn(0); 1187 } 1188 1189 #undef __FUNCT__ 1190 #define __FUNCT__ "DMPlexMarkSubmesh_Interpolated" 1191 static PetscErrorCode DMPlexMarkSubmesh_Interpolated(DM dm, DMLabel vertexLabel, PetscInt value, DMLabel subpointMap, DM subdm) 1192 { 1193 IS subvertexIS; 1194 const PetscInt *subvertices; 1195 PetscInt *pStart, *pEnd, *pMax; 1196 PetscInt dim, d, numSubVerticesInitial = 0, v; 1197 PetscErrorCode ierr; 1198 1199 PetscFunctionBegin; 1200 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1201 ierr = PetscMalloc3(dim+1,PetscInt,&pStart,dim+1,PetscInt,&pEnd,dim+1,PetscInt,&pMax);CHKERRQ(ierr); 1202 ierr = DMPlexGetHybridBounds(dm, &pMax[dim], dim>1 ? &pMax[dim-1] : NULL, dim > 2 ? &pMax[1] : NULL, &pMax[0]);CHKERRQ(ierr); 1203 for (d = 0; d <= dim; ++d) { 1204 ierr = DMPlexGetDepthStratum(dm, d, &pStart[d], &pEnd[d]);CHKERRQ(ierr); 1205 if (pMax[d] >= 0) pEnd[d] = PetscMin(pEnd[d], pMax[d]); 1206 } 1207 /* Loop over initial vertices and mark all faces in the collective star() */ 1208 ierr = DMLabelGetStratumIS(vertexLabel, value, &subvertexIS);CHKERRQ(ierr); 1209 if (subvertexIS) { 1210 ierr = ISGetSize(subvertexIS, &numSubVerticesInitial);CHKERRQ(ierr); 1211 ierr = ISGetIndices(subvertexIS, &subvertices);CHKERRQ(ierr); 1212 } 1213 for (v = 0; v < numSubVerticesInitial; ++v) { 1214 const PetscInt vertex = subvertices[v]; 1215 PetscInt *star = NULL; 1216 PetscInt starSize, s, numFaces = 0, f; 1217 1218 ierr = DMPlexGetTransitiveClosure(dm, vertex, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1219 for (s = 0; s < starSize*2; s += 2) { 1220 const PetscInt point = star[s]; 1221 if ((point >= pStart[dim-1]) && (point < pEnd[dim-1])) star[numFaces++] = point; 1222 } 1223 for (f = 0; f < numFaces; ++f) { 1224 const PetscInt face = star[f]; 1225 PetscInt *closure = NULL; 1226 PetscInt closureSize, c; 1227 PetscInt faceLoc; 1228 1229 ierr = DMLabelGetValue(subpointMap, face, &faceLoc);CHKERRQ(ierr); 1230 if (faceLoc == dim-1) continue; 1231 if (faceLoc >= 0) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Face %d has dimension %d in the surface label", face, faceLoc); 1232 ierr = DMPlexGetTransitiveClosure(dm, face, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1233 for (c = 0; c < closureSize*2; c += 2) { 1234 const PetscInt point = closure[c]; 1235 PetscInt vertexLoc; 1236 1237 if ((point >= pStart[0]) && (point < pEnd[0])) { 1238 ierr = DMLabelGetValue(vertexLabel, point, &vertexLoc);CHKERRQ(ierr); 1239 if (vertexLoc != value) break; 1240 } 1241 } 1242 if (c == closureSize*2) { 1243 const PetscInt *support; 1244 PetscInt supportSize, s; 1245 1246 for (c = 0; c < closureSize*2; c += 2) { 1247 const PetscInt point = closure[c]; 1248 1249 for (d = 0; d < dim; ++d) { 1250 if ((point >= pStart[d]) && (point < pEnd[d])) { 1251 ierr = DMLabelSetValue(subpointMap, point, d);CHKERRQ(ierr); 1252 break; 1253 } 1254 } 1255 } 1256 ierr = DMPlexGetSupportSize(dm, face, &supportSize);CHKERRQ(ierr); 1257 ierr = DMPlexGetSupport(dm, face, &support);CHKERRQ(ierr); 1258 for (s = 0; s < supportSize; ++s) { 1259 ierr = DMLabelSetValue(subpointMap, support[s], dim);CHKERRQ(ierr); 1260 } 1261 } 1262 ierr = DMPlexRestoreTransitiveClosure(dm, face, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1263 } 1264 ierr = DMPlexRestoreTransitiveClosure(dm, vertex, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1265 } 1266 if (subvertexIS) { 1267 ierr = ISRestoreIndices(subvertexIS, &subvertices);CHKERRQ(ierr); 1268 } 1269 ierr = ISDestroy(&subvertexIS);CHKERRQ(ierr); 1270 ierr = PetscFree3(pStart,pEnd,pMax);CHKERRQ(ierr); 1271 PetscFunctionReturn(0); 1272 } 1273 1274 #undef __FUNCT__ 1275 #define __FUNCT__ "DMPlexMarkCohesiveSubmesh_Uninterpolated" 1276 static PetscErrorCode DMPlexMarkCohesiveSubmesh_Uninterpolated(DM dm, PetscBool hasLagrange, const char labelname[], PetscInt value, DMLabel subpointMap, PetscInt *numFaces, PetscInt *nFV, PetscInt *subCells[], DM subdm) 1277 { 1278 DMLabel label = NULL; 1279 const PetscInt *cone; 1280 PetscInt dim, cMax, cEnd, c, subc = 0, p, coneSize; 1281 PetscErrorCode ierr; 1282 1283 PetscFunctionBegin; 1284 *numFaces = 0; 1285 *nFV = 0; 1286 if (labelname) {ierr = DMPlexGetLabel(dm, labelname, &label);CHKERRQ(ierr);} 1287 *subCells = NULL; 1288 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1289 ierr = DMPlexGetHeightStratum(dm, 0, NULL, &cEnd);CHKERRQ(ierr); 1290 ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); 1291 if (cMax < 0) PetscFunctionReturn(0); 1292 if (label) { 1293 for (c = cMax; c < cEnd; ++c) { 1294 PetscInt val; 1295 1296 ierr = DMLabelGetValue(label, c, &val);CHKERRQ(ierr); 1297 if (val == value) { 1298 ++(*numFaces); 1299 ierr = DMPlexGetConeSize(dm, c, &coneSize);CHKERRQ(ierr); 1300 } 1301 } 1302 } else { 1303 *numFaces = cEnd - cMax; 1304 ierr = DMPlexGetConeSize(dm, cMax, &coneSize);CHKERRQ(ierr); 1305 } 1306 *nFV = hasLagrange ? coneSize/3 : coneSize/2; 1307 ierr = PetscMalloc(*numFaces *2 * sizeof(PetscInt), subCells);CHKERRQ(ierr); 1308 for (c = cMax; c < cEnd; ++c) { 1309 const PetscInt *cells; 1310 PetscInt numCells; 1311 1312 if (label) { 1313 PetscInt val; 1314 1315 ierr = DMLabelGetValue(label, c, &val);CHKERRQ(ierr); 1316 if (val != value) continue; 1317 } 1318 ierr = DMPlexGetCone(dm, c, &cone);CHKERRQ(ierr); 1319 for (p = 0; p < *nFV; ++p) { 1320 ierr = DMLabelSetValue(subpointMap, cone[p], 0);CHKERRQ(ierr); 1321 } 1322 /* Negative face */ 1323 ierr = DMPlexGetJoin(dm, *nFV, cone, &numCells, &cells);CHKERRQ(ierr); 1324 /* Not true in parallel 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)[subc++] = 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 = 0, firstSubFace, newFacePoint, nFV = 0; 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 if (vertexLabelName) { 1865 ierr = DMPlexGetLabel(dm, vertexLabelName, &vertexLabel);CHKERRQ(ierr); 1866 ierr = DMPlexMarkSubmesh_Uninterpolated(dm, vertexLabel, value, subpointMap, &numSubFaces, &nFV, subdm);CHKERRQ(ierr); 1867 } 1868 /* Setup chart */ 1869 ierr = DMLabelGetStratumSize(subpointMap, 0, &numSubVertices);CHKERRQ(ierr); 1870 ierr = DMLabelGetStratumSize(subpointMap, 2, &numSubCells);CHKERRQ(ierr); 1871 ierr = DMPlexSetChart(subdm, 0, numSubCells+numSubFaces+numSubVertices);CHKERRQ(ierr); 1872 ierr = DMPlexSetVTKCellHeight(subdm, 1);CHKERRQ(ierr); 1873 /* Set cone sizes */ 1874 firstSubVertex = numSubCells; 1875 firstSubFace = numSubCells+numSubVertices; 1876 newFacePoint = firstSubFace; 1877 ierr = DMLabelGetStratumIS(subpointMap, 0, &subvertexIS);CHKERRQ(ierr); 1878 if (subvertexIS) {ierr = ISGetIndices(subvertexIS, &subVertices);CHKERRQ(ierr);} 1879 ierr = DMLabelGetStratumIS(subpointMap, 2, &subcellIS);CHKERRQ(ierr); 1880 if (subcellIS) {ierr = ISGetIndices(subcellIS, &subCells);CHKERRQ(ierr);} 1881 for (c = 0; c < numSubCells; ++c) { 1882 ierr = DMPlexSetConeSize(subdm, c, 1);CHKERRQ(ierr); 1883 } 1884 for (f = firstSubFace; f < firstSubFace+numSubFaces; ++f) { 1885 ierr = DMPlexSetConeSize(subdm, f, nFV);CHKERRQ(ierr); 1886 } 1887 ierr = DMSetUp(subdm);CHKERRQ(ierr); 1888 /* Create face cones */ 1889 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 1890 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, NULL);CHKERRQ(ierr); 1891 ierr = DMGetWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);CHKERRQ(ierr); 1892 for (c = 0; c < numSubCells; ++c) { 1893 const PetscInt cell = subCells[c]; 1894 const PetscInt subcell = c; 1895 PetscInt *closure = NULL; 1896 PetscInt closureSize, cl, numCorners = 0, faceSize = 0; 1897 1898 ierr = DMPlexGetTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1899 for (cl = 0; cl < closureSize*2; cl += 2) { 1900 const PetscInt point = closure[cl]; 1901 PetscInt subVertex; 1902 1903 if ((point >= vStart) && (point < vEnd)) { 1904 ++numCorners; 1905 ierr = PetscFindInt(point, numSubVertices, subVertices, &subVertex);CHKERRQ(ierr); 1906 if (subVertex >= 0) { 1907 closure[faceSize] = point; 1908 subface[faceSize] = firstSubVertex+subVertex; 1909 ++faceSize; 1910 } 1911 } 1912 } 1913 if (faceSize > nFV) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Invalid submesh: Too many vertices %d of an element on the surface", faceSize); 1914 if (faceSize == nFV) { 1915 ierr = DMPlexInsertFace_Internal(dm, subdm, faceSize, closure, subface, numCorners, cell, subcell, firstSubFace, &newFacePoint);CHKERRQ(ierr); 1916 } 1917 ierr = DMPlexRestoreTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1918 } 1919 ierr = DMRestoreWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);CHKERRQ(ierr); 1920 ierr = DMPlexSymmetrize(subdm);CHKERRQ(ierr); 1921 ierr = DMPlexStratify(subdm);CHKERRQ(ierr); 1922 /* Build coordinates */ 1923 { 1924 PetscSection coordSection, subCoordSection; 1925 Vec coordinates, subCoordinates; 1926 PetscScalar *coords, *subCoords; 1927 PetscInt numComp, coordSize, v; 1928 1929 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1930 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 1931 ierr = DMPlexGetCoordinateSection(subdm, &subCoordSection);CHKERRQ(ierr); 1932 ierr = PetscSectionSetNumFields(subCoordSection, 1);CHKERRQ(ierr); 1933 ierr = PetscSectionGetFieldComponents(coordSection, 0, &numComp);CHKERRQ(ierr); 1934 ierr = PetscSectionSetFieldComponents(subCoordSection, 0, numComp);CHKERRQ(ierr); 1935 ierr = PetscSectionSetChart(subCoordSection, firstSubVertex, firstSubVertex+numSubVertices);CHKERRQ(ierr); 1936 for (v = 0; v < numSubVertices; ++v) { 1937 const PetscInt vertex = subVertices[v]; 1938 const PetscInt subvertex = firstSubVertex+v; 1939 PetscInt dof; 1940 1941 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 1942 ierr = PetscSectionSetDof(subCoordSection, subvertex, dof);CHKERRQ(ierr); 1943 ierr = PetscSectionSetFieldDof(subCoordSection, subvertex, 0, dof);CHKERRQ(ierr); 1944 } 1945 ierr = PetscSectionSetUp(subCoordSection);CHKERRQ(ierr); 1946 ierr = PetscSectionGetStorageSize(subCoordSection, &coordSize);CHKERRQ(ierr); 1947 ierr = VecCreate(comm, &subCoordinates);CHKERRQ(ierr); 1948 ierr = VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1949 ierr = VecSetFromOptions(subCoordinates);CHKERRQ(ierr); 1950 if (coordSize) { 1951 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1952 ierr = VecGetArray(subCoordinates, &subCoords);CHKERRQ(ierr); 1953 for (v = 0; v < numSubVertices; ++v) { 1954 const PetscInt vertex = subVertices[v]; 1955 const PetscInt subvertex = firstSubVertex+v; 1956 PetscInt dof, off, sdof, soff, d; 1957 1958 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 1959 ierr = PetscSectionGetOffset(coordSection, vertex, &off);CHKERRQ(ierr); 1960 ierr = PetscSectionGetDof(subCoordSection, subvertex, &sdof);CHKERRQ(ierr); 1961 ierr = PetscSectionGetOffset(subCoordSection, subvertex, &soff);CHKERRQ(ierr); 1962 if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof); 1963 for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d]; 1964 } 1965 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1966 ierr = VecRestoreArray(subCoordinates, &subCoords);CHKERRQ(ierr); 1967 } 1968 ierr = DMSetCoordinatesLocal(subdm, subCoordinates);CHKERRQ(ierr); 1969 ierr = VecDestroy(&subCoordinates);CHKERRQ(ierr); 1970 } 1971 /* Cleanup */ 1972 if (subvertexIS) {ierr = ISRestoreIndices(subvertexIS, &subVertices);CHKERRQ(ierr);} 1973 ierr = ISDestroy(&subvertexIS);CHKERRQ(ierr); 1974 if (subcellIS) {ierr = ISRestoreIndices(subcellIS, &subCells);CHKERRQ(ierr);} 1975 ierr = ISDestroy(&subcellIS);CHKERRQ(ierr); 1976 PetscFunctionReturn(0); 1977 } 1978 1979 #undef __FUNCT__ 1980 #define __FUNCT__ "DMPlexCreateSubmesh_Interpolated" 1981 static PetscErrorCode DMPlexCreateSubmesh_Interpolated(DM dm, const char vertexLabelName[], PetscInt value, DM subdm) 1982 { 1983 MPI_Comm comm; 1984 DMLabel subpointMap, vertexLabel; 1985 IS *subpointIS; 1986 const PetscInt **subpoints; 1987 PetscInt *numSubPoints, *firstSubPoint, *coneNew; 1988 PetscInt totSubPoints = 0, maxConeSize, dim, p, d, v; 1989 PetscErrorCode ierr; 1990 1991 PetscFunctionBegin; 1992 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 1993 /* Create subpointMap which marks the submesh */ 1994 ierr = DMLabelCreate("subpoint_map", &subpointMap);CHKERRQ(ierr); 1995 ierr = DMPlexSetSubpointMap(subdm, subpointMap);CHKERRQ(ierr); 1996 ierr = DMLabelDestroy(&subpointMap);CHKERRQ(ierr); 1997 if (vertexLabelName) { 1998 ierr = DMPlexGetLabel(dm, vertexLabelName, &vertexLabel);CHKERRQ(ierr); 1999 ierr = DMPlexMarkSubmesh_Interpolated(dm, vertexLabel, value, subpointMap, subdm);CHKERRQ(ierr); 2000 } 2001 /* Setup chart */ 2002 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 2003 ierr = PetscMalloc4(dim+1,PetscInt,&numSubPoints,dim+1,PetscInt,&firstSubPoint,dim+1,IS,&subpointIS,dim+1,const PetscInt *,&subpoints);CHKERRQ(ierr); 2004 for (d = 0; d <= dim; ++d) { 2005 ierr = DMLabelGetStratumSize(subpointMap, d, &numSubPoints[d]);CHKERRQ(ierr); 2006 totSubPoints += numSubPoints[d]; 2007 } 2008 ierr = DMPlexSetChart(subdm, 0, totSubPoints);CHKERRQ(ierr); 2009 ierr = DMPlexSetVTKCellHeight(subdm, 1);CHKERRQ(ierr); 2010 /* Set cone sizes */ 2011 firstSubPoint[dim] = 0; 2012 firstSubPoint[0] = firstSubPoint[dim] + numSubPoints[dim]; 2013 if (dim > 1) {firstSubPoint[dim-1] = firstSubPoint[0] + numSubPoints[0];} 2014 if (dim > 2) {firstSubPoint[dim-2] = firstSubPoint[dim-1] + numSubPoints[dim-1];} 2015 for (d = 0; d <= dim; ++d) { 2016 ierr = DMLabelGetStratumIS(subpointMap, d, &subpointIS[d]);CHKERRQ(ierr); 2017 ierr = ISGetIndices(subpointIS[d], &subpoints[d]);CHKERRQ(ierr); 2018 } 2019 for (d = 0; d <= dim; ++d) { 2020 for (p = 0; p < numSubPoints[d]; ++p) { 2021 const PetscInt point = subpoints[d][p]; 2022 const PetscInt subpoint = firstSubPoint[d] + p; 2023 const PetscInt *cone; 2024 PetscInt coneSize, coneSizeNew, c, val; 2025 2026 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 2027 ierr = DMPlexSetConeSize(subdm, subpoint, coneSize);CHKERRQ(ierr); 2028 if (d == dim) { 2029 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 2030 for (c = 0, coneSizeNew = 0; c < coneSize; ++c) { 2031 ierr = DMLabelGetValue(subpointMap, cone[c], &val);CHKERRQ(ierr); 2032 if (val >= 0) coneSizeNew++; 2033 } 2034 ierr = DMPlexSetConeSize(subdm, subpoint, coneSizeNew);CHKERRQ(ierr); 2035 } 2036 } 2037 } 2038 ierr = DMSetUp(subdm);CHKERRQ(ierr); 2039 /* Set cones */ 2040 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, NULL);CHKERRQ(ierr); 2041 ierr = PetscMalloc(maxConeSize * sizeof(PetscInt), &coneNew);CHKERRQ(ierr); 2042 for (d = 0; d <= dim; ++d) { 2043 for (p = 0; p < numSubPoints[d]; ++p) { 2044 const PetscInt point = subpoints[d][p]; 2045 const PetscInt subpoint = firstSubPoint[d] + p; 2046 const PetscInt *cone; 2047 PetscInt coneSize, subconeSize, coneSizeNew, c, subc; 2048 2049 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 2050 ierr = DMPlexGetConeSize(subdm, subpoint, &subconeSize);CHKERRQ(ierr); 2051 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 2052 for (c = 0, coneSizeNew = 0; c < coneSize; ++c) { 2053 ierr = PetscFindInt(cone[c], numSubPoints[d-1], subpoints[d-1], &subc);CHKERRQ(ierr); 2054 if (subc >= 0) coneNew[coneSizeNew++] = firstSubPoint[d-1] + subc; 2055 } 2056 if (coneSizeNew != subconeSize) SETERRQ2(comm, PETSC_ERR_PLIB, "Number of cone points located %d does not match subcone size %d", coneSizeNew, subconeSize); 2057 ierr = DMPlexSetCone(subdm, subpoint, coneNew);CHKERRQ(ierr); 2058 } 2059 } 2060 ierr = PetscFree(coneNew);CHKERRQ(ierr); 2061 ierr = DMPlexSymmetrize(subdm);CHKERRQ(ierr); 2062 ierr = DMPlexStratify(subdm);CHKERRQ(ierr); 2063 /* Build coordinates */ 2064 { 2065 PetscSection coordSection, subCoordSection; 2066 Vec coordinates, subCoordinates; 2067 PetscScalar *coords, *subCoords; 2068 PetscInt numComp, coordSize; 2069 2070 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2071 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 2072 ierr = DMPlexGetCoordinateSection(subdm, &subCoordSection);CHKERRQ(ierr); 2073 ierr = PetscSectionSetNumFields(subCoordSection, 1);CHKERRQ(ierr); 2074 ierr = PetscSectionGetFieldComponents(coordSection, 0, &numComp);CHKERRQ(ierr); 2075 ierr = PetscSectionSetFieldComponents(subCoordSection, 0, numComp);CHKERRQ(ierr); 2076 ierr = PetscSectionSetChart(subCoordSection, firstSubPoint[0], firstSubPoint[0]+numSubPoints[0]);CHKERRQ(ierr); 2077 for (v = 0; v < numSubPoints[0]; ++v) { 2078 const PetscInt vertex = subpoints[0][v]; 2079 const PetscInt subvertex = firstSubPoint[0]+v; 2080 PetscInt dof; 2081 2082 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2083 ierr = PetscSectionSetDof(subCoordSection, subvertex, dof);CHKERRQ(ierr); 2084 ierr = PetscSectionSetFieldDof(subCoordSection, subvertex, 0, dof);CHKERRQ(ierr); 2085 } 2086 ierr = PetscSectionSetUp(subCoordSection);CHKERRQ(ierr); 2087 ierr = PetscSectionGetStorageSize(subCoordSection, &coordSize);CHKERRQ(ierr); 2088 ierr = VecCreate(comm, &subCoordinates);CHKERRQ(ierr); 2089 ierr = VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2090 ierr = VecSetFromOptions(subCoordinates);CHKERRQ(ierr); 2091 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2092 ierr = VecGetArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2093 for (v = 0; v < numSubPoints[0]; ++v) { 2094 const PetscInt vertex = subpoints[0][v]; 2095 const PetscInt subvertex = firstSubPoint[0]+v; 2096 PetscInt dof, off, sdof, soff, d; 2097 2098 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2099 ierr = PetscSectionGetOffset(coordSection, vertex, &off);CHKERRQ(ierr); 2100 ierr = PetscSectionGetDof(subCoordSection, subvertex, &sdof);CHKERRQ(ierr); 2101 ierr = PetscSectionGetOffset(subCoordSection, subvertex, &soff);CHKERRQ(ierr); 2102 if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof); 2103 for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d]; 2104 } 2105 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2106 ierr = VecRestoreArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2107 ierr = DMSetCoordinatesLocal(subdm, subCoordinates);CHKERRQ(ierr); 2108 ierr = VecDestroy(&subCoordinates);CHKERRQ(ierr); 2109 } 2110 /* Cleanup */ 2111 for (d = 0; d <= dim; ++d) { 2112 ierr = ISRestoreIndices(subpointIS[d], &subpoints[d]);CHKERRQ(ierr); 2113 ierr = ISDestroy(&subpointIS[d]);CHKERRQ(ierr); 2114 } 2115 ierr = PetscFree4(numSubPoints,firstSubPoint,subpointIS,subpoints);CHKERRQ(ierr); 2116 PetscFunctionReturn(0); 2117 } 2118 2119 #undef __FUNCT__ 2120 #define __FUNCT__ "DMPlexCreateSubmesh" 2121 /*@C 2122 DMPlexCreateSubmesh - Extract a hypersurface from the mesh using vertices defined by a label 2123 2124 Input Parameters: 2125 + dm - The original mesh 2126 . vertexLabel - The DMLabel marking vertices contained in the surface 2127 - value - The label value to use 2128 2129 Output Parameter: 2130 . subdm - The surface mesh 2131 2132 Note: This function produces a DMLabel mapping original points in the submesh to their depth. This can be obtained using DMPlexGetSubpointMap(). 2133 2134 Level: developer 2135 2136 .seealso: DMPlexGetSubpointMap(), DMPlexGetLabel(), DMLabelSetValue() 2137 @*/ 2138 PetscErrorCode DMPlexCreateSubmesh(DM dm, const char vertexLabel[], PetscInt value, DM *subdm) 2139 { 2140 PetscInt dim, depth; 2141 PetscErrorCode ierr; 2142 2143 PetscFunctionBegin; 2144 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2145 PetscValidPointer(subdm, 3); 2146 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 2147 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 2148 ierr = DMCreate(PetscObjectComm((PetscObject)dm), subdm);CHKERRQ(ierr); 2149 ierr = DMSetType(*subdm, DMPLEX);CHKERRQ(ierr); 2150 ierr = DMPlexSetDimension(*subdm, dim-1);CHKERRQ(ierr); 2151 if (depth == dim) { 2152 ierr = DMPlexCreateSubmesh_Interpolated(dm, vertexLabel, value, *subdm);CHKERRQ(ierr); 2153 } else { 2154 ierr = DMPlexCreateSubmesh_Uninterpolated(dm, vertexLabel, value, *subdm);CHKERRQ(ierr); 2155 } 2156 PetscFunctionReturn(0); 2157 } 2158 2159 #undef __FUNCT__ 2160 #define __FUNCT__ "DMPlexFilterPoint_Internal" 2161 PETSC_STATIC_INLINE PetscInt DMPlexFilterPoint_Internal(PetscInt point, PetscInt firstSubPoint, PetscInt numSubPoints, const PetscInt subPoints[]) 2162 { 2163 PetscInt subPoint; 2164 PetscErrorCode ierr; 2165 2166 ierr = PetscFindInt(point, numSubPoints, subPoints, &subPoint); if (ierr < 0) return ierr; 2167 return subPoint < 0 ? subPoint : firstSubPoint+subPoint; 2168 } 2169 2170 #undef __FUNCT__ 2171 #define __FUNCT__ "DMPlexCreateCohesiveSubmesh_Uninterpolated" 2172 static PetscErrorCode DMPlexCreateCohesiveSubmesh_Uninterpolated(DM dm, PetscBool hasLagrange, const char label[], PetscInt value, DM subdm) 2173 { 2174 MPI_Comm comm; 2175 DMLabel subpointMap; 2176 IS subvertexIS; 2177 const PetscInt *subVertices; 2178 PetscInt numSubVertices, firstSubVertex, numSubCells, *subCells = NULL; 2179 PetscInt *subface, maxConeSize, numSubFaces, firstSubFace, newFacePoint, nFV; 2180 PetscInt cMax, c, f; 2181 PetscErrorCode ierr; 2182 2183 PetscFunctionBegin; 2184 ierr = PetscObjectGetComm((PetscObject)dm, &comm);CHKERRQ(ierr); 2185 /* Create subpointMap which marks the submesh */ 2186 ierr = DMLabelCreate("subpoint_map", &subpointMap);CHKERRQ(ierr); 2187 ierr = DMPlexSetSubpointMap(subdm, subpointMap);CHKERRQ(ierr); 2188 ierr = DMLabelDestroy(&subpointMap);CHKERRQ(ierr); 2189 ierr = DMPlexMarkCohesiveSubmesh_Uninterpolated(dm, hasLagrange, label, value, subpointMap, &numSubFaces, &nFV, &subCells, subdm);CHKERRQ(ierr); 2190 /* Setup chart */ 2191 ierr = DMLabelGetStratumSize(subpointMap, 0, &numSubVertices);CHKERRQ(ierr); 2192 ierr = DMLabelGetStratumSize(subpointMap, 2, &numSubCells);CHKERRQ(ierr); 2193 ierr = DMPlexSetChart(subdm, 0, numSubCells+numSubFaces+numSubVertices);CHKERRQ(ierr); 2194 ierr = DMPlexSetVTKCellHeight(subdm, 1);CHKERRQ(ierr); 2195 /* Set cone sizes */ 2196 firstSubVertex = numSubCells; 2197 firstSubFace = numSubCells+numSubVertices; 2198 newFacePoint = firstSubFace; 2199 ierr = DMLabelGetStratumIS(subpointMap, 0, &subvertexIS);CHKERRQ(ierr); 2200 if (subvertexIS) {ierr = ISGetIndices(subvertexIS, &subVertices);CHKERRQ(ierr);} 2201 for (c = 0; c < numSubCells; ++c) { 2202 ierr = DMPlexSetConeSize(subdm, c, 1);CHKERRQ(ierr); 2203 } 2204 for (f = firstSubFace; f < firstSubFace+numSubFaces; ++f) { 2205 ierr = DMPlexSetConeSize(subdm, f, nFV);CHKERRQ(ierr); 2206 } 2207 ierr = DMSetUp(subdm);CHKERRQ(ierr); 2208 /* Create face cones */ 2209 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, NULL);CHKERRQ(ierr); 2210 ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); 2211 ierr = DMGetWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);CHKERRQ(ierr); 2212 for (c = 0; c < numSubCells; ++c) { 2213 const PetscInt cell = subCells[c]; 2214 const PetscInt subcell = c; 2215 const PetscInt *cone, *cells; 2216 PetscInt numCells, subVertex, p, v; 2217 2218 if (cell < cMax) continue; 2219 ierr = DMPlexGetCone(dm, cell, &cone);CHKERRQ(ierr); 2220 for (v = 0; v < nFV; ++v) { 2221 ierr = PetscFindInt(cone[v], numSubVertices, subVertices, &subVertex);CHKERRQ(ierr); 2222 subface[v] = firstSubVertex+subVertex; 2223 } 2224 ierr = DMPlexSetCone(subdm, newFacePoint, subface);CHKERRQ(ierr); 2225 ierr = DMPlexSetCone(subdm, subcell, &newFacePoint);CHKERRQ(ierr); 2226 ierr = DMPlexGetJoin(dm, nFV, cone, &numCells, &cells);CHKERRQ(ierr); 2227 /* Not true in parallel 2228 if (numCells != 2) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive cells should separate two cells"); */ 2229 for (p = 0; p < numCells; ++p) { 2230 PetscInt negsubcell; 2231 2232 if (cells[p] >= cMax) continue; 2233 /* I know this is a crap search */ 2234 for (negsubcell = 0; negsubcell < numSubCells; ++negsubcell) { 2235 if (subCells[negsubcell] == cells[p]) break; 2236 } 2237 if (negsubcell == numSubCells) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not find negative face neighbor for cohesive cell %d", cell); 2238 ierr = DMPlexSetCone(subdm, negsubcell, &newFacePoint);CHKERRQ(ierr); 2239 } 2240 ierr = DMPlexRestoreJoin(dm, nFV, cone, &numCells, &cells);CHKERRQ(ierr); 2241 ++newFacePoint; 2242 } 2243 ierr = DMRestoreWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);CHKERRQ(ierr); 2244 ierr = DMPlexSymmetrize(subdm);CHKERRQ(ierr); 2245 ierr = DMPlexStratify(subdm);CHKERRQ(ierr); 2246 /* Build coordinates */ 2247 { 2248 PetscSection coordSection, subCoordSection; 2249 Vec coordinates, subCoordinates; 2250 PetscScalar *coords, *subCoords; 2251 PetscInt numComp, coordSize, v; 2252 2253 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2254 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 2255 ierr = DMPlexGetCoordinateSection(subdm, &subCoordSection);CHKERRQ(ierr); 2256 ierr = PetscSectionSetNumFields(subCoordSection, 1);CHKERRQ(ierr); 2257 ierr = PetscSectionGetFieldComponents(coordSection, 0, &numComp);CHKERRQ(ierr); 2258 ierr = PetscSectionSetFieldComponents(subCoordSection, 0, numComp);CHKERRQ(ierr); 2259 ierr = PetscSectionSetChart(subCoordSection, firstSubVertex, firstSubVertex+numSubVertices);CHKERRQ(ierr); 2260 for (v = 0; v < numSubVertices; ++v) { 2261 const PetscInt vertex = subVertices[v]; 2262 const PetscInt subvertex = firstSubVertex+v; 2263 PetscInt dof; 2264 2265 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2266 ierr = PetscSectionSetDof(subCoordSection, subvertex, dof);CHKERRQ(ierr); 2267 ierr = PetscSectionSetFieldDof(subCoordSection, subvertex, 0, dof);CHKERRQ(ierr); 2268 } 2269 ierr = PetscSectionSetUp(subCoordSection);CHKERRQ(ierr); 2270 ierr = PetscSectionGetStorageSize(subCoordSection, &coordSize);CHKERRQ(ierr); 2271 ierr = VecCreate(comm, &subCoordinates);CHKERRQ(ierr); 2272 ierr = VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2273 ierr = VecSetFromOptions(subCoordinates);CHKERRQ(ierr); 2274 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2275 ierr = VecGetArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2276 for (v = 0; v < numSubVertices; ++v) { 2277 const PetscInt vertex = subVertices[v]; 2278 const PetscInt subvertex = firstSubVertex+v; 2279 PetscInt dof, off, sdof, soff, d; 2280 2281 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2282 ierr = PetscSectionGetOffset(coordSection, vertex, &off);CHKERRQ(ierr); 2283 ierr = PetscSectionGetDof(subCoordSection, subvertex, &sdof);CHKERRQ(ierr); 2284 ierr = PetscSectionGetOffset(subCoordSection, subvertex, &soff);CHKERRQ(ierr); 2285 if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof); 2286 for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d]; 2287 } 2288 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2289 ierr = VecRestoreArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2290 ierr = DMSetCoordinatesLocal(subdm, subCoordinates);CHKERRQ(ierr); 2291 ierr = VecDestroy(&subCoordinates);CHKERRQ(ierr); 2292 } 2293 /* Build SF */ 2294 CHKMEMQ; 2295 { 2296 PetscSF sfPoint, sfPointSub; 2297 const PetscSFNode *remotePoints; 2298 PetscSFNode *sremotePoints, *newLocalPoints, *newOwners; 2299 const PetscInt *localPoints; 2300 PetscInt *slocalPoints; 2301 PetscInt numRoots, numLeaves, numSubRoots = numSubCells+numSubFaces+numSubVertices, numSubLeaves = 0, l, sl, ll, pStart, pEnd, p, vStart, vEnd; 2302 PetscMPIInt rank; 2303 2304 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRQ(ierr); 2305 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 2306 ierr = DMGetPointSF(subdm, &sfPointSub);CHKERRQ(ierr); 2307 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 2308 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 2309 ierr = PetscSFGetGraph(sfPoint, &numRoots, &numLeaves, &localPoints, &remotePoints);CHKERRQ(ierr); 2310 if (numRoots >= 0) { 2311 /* Only vertices should be shared */ 2312 ierr = PetscMalloc2(pEnd-pStart,PetscSFNode,&newLocalPoints,numRoots,PetscSFNode,&newOwners);CHKERRQ(ierr); 2313 for (p = 0; p < pEnd-pStart; ++p) { 2314 newLocalPoints[p].rank = -2; 2315 newLocalPoints[p].index = -2; 2316 } 2317 /* Set subleaves */ 2318 for (l = 0; l < numLeaves; ++l) { 2319 const PetscInt point = localPoints[l]; 2320 const PetscInt subPoint = DMPlexFilterPoint_Internal(point, firstSubVertex, numSubVertices, subVertices); 2321 2322 if ((point < vStart) && (point >= vEnd)) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Should not be mapping anything but vertices, %d", point); 2323 if (subPoint < 0) continue; 2324 newLocalPoints[point-pStart].rank = rank; 2325 newLocalPoints[point-pStart].index = subPoint; 2326 ++numSubLeaves; 2327 } 2328 /* Must put in owned subpoints */ 2329 for (p = pStart; p < pEnd; ++p) { 2330 const PetscInt subPoint = DMPlexFilterPoint_Internal(p, firstSubVertex, numSubVertices, subVertices); 2331 2332 if (subPoint < 0) { 2333 newOwners[p-pStart].rank = -3; 2334 newOwners[p-pStart].index = -3; 2335 } else { 2336 newOwners[p-pStart].rank = rank; 2337 newOwners[p-pStart].index = subPoint; 2338 } 2339 } 2340 ierr = PetscSFReduceBegin(sfPoint, MPIU_2INT, newLocalPoints, newOwners, MPI_MAXLOC);CHKERRQ(ierr); 2341 ierr = PetscSFReduceEnd(sfPoint, MPIU_2INT, newLocalPoints, newOwners, MPI_MAXLOC);CHKERRQ(ierr); 2342 ierr = PetscSFBcastBegin(sfPoint, MPIU_2INT, newOwners, newLocalPoints);CHKERRQ(ierr); 2343 ierr = PetscSFBcastEnd(sfPoint, MPIU_2INT, newOwners, newLocalPoints);CHKERRQ(ierr); 2344 ierr = PetscMalloc(numSubLeaves * sizeof(PetscInt), &slocalPoints);CHKERRQ(ierr); 2345 ierr = PetscMalloc(numSubLeaves * sizeof(PetscSFNode), &sremotePoints);CHKERRQ(ierr); 2346 for (l = 0, sl = 0, ll = 0; l < numLeaves; ++l) { 2347 const PetscInt point = localPoints[l]; 2348 const PetscInt subPoint = DMPlexFilterPoint_Internal(point, firstSubVertex, numSubVertices, subVertices); 2349 2350 if (subPoint < 0) continue; 2351 if (newLocalPoints[point].rank == rank) {++ll; continue;} 2352 slocalPoints[sl] = subPoint; 2353 sremotePoints[sl].rank = newLocalPoints[point].rank; 2354 sremotePoints[sl].index = newLocalPoints[point].index; 2355 if (sremotePoints[sl].rank < 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid remote rank for local point %d", point); 2356 if (sremotePoints[sl].index < 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid remote subpoint for local point %d", point); 2357 ++sl; 2358 } 2359 ierr = PetscFree2(newLocalPoints,newOwners);CHKERRQ(ierr); 2360 if (sl + ll != numSubLeaves) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Mismatch in number of subleaves %d + %d != %d", sl, ll, numSubLeaves); 2361 ierr = PetscSFSetGraph(sfPointSub, numSubRoots, sl, slocalPoints, PETSC_OWN_POINTER, sremotePoints, PETSC_OWN_POINTER);CHKERRQ(ierr); 2362 } 2363 } 2364 CHKMEMQ; 2365 /* Cleanup */ 2366 if (subvertexIS) {ierr = ISRestoreIndices(subvertexIS, &subVertices);CHKERRQ(ierr);} 2367 ierr = ISDestroy(&subvertexIS);CHKERRQ(ierr); 2368 ierr = PetscFree(subCells);CHKERRQ(ierr); 2369 PetscFunctionReturn(0); 2370 } 2371 2372 #undef __FUNCT__ 2373 #define __FUNCT__ "DMPlexCreateCohesiveSubmesh_Interpolated" 2374 static PetscErrorCode DMPlexCreateCohesiveSubmesh_Interpolated(DM dm, PetscBool hasLagrange, const char label[], PetscInt value, DM subdm) 2375 { 2376 MPI_Comm comm; 2377 DMLabel subpointMap; 2378 IS *subpointIS; 2379 const PetscInt **subpoints; 2380 PetscInt *numSubPoints, *firstSubPoint, *coneNew; 2381 PetscInt totSubPoints = 0, maxConeSize, dim, p, d, v; 2382 PetscErrorCode ierr; 2383 2384 PetscFunctionBegin; 2385 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 2386 /* Create subpointMap which marks the submesh */ 2387 ierr = DMLabelCreate("subpoint_map", &subpointMap);CHKERRQ(ierr); 2388 ierr = DMPlexSetSubpointMap(subdm, subpointMap);CHKERRQ(ierr); 2389 ierr = DMLabelDestroy(&subpointMap);CHKERRQ(ierr); 2390 ierr = DMPlexMarkCohesiveSubmesh_Interpolated(dm, hasLagrange, label, value, subpointMap, subdm);CHKERRQ(ierr); 2391 /* Setup chart */ 2392 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 2393 ierr = PetscMalloc4(dim+1,PetscInt,&numSubPoints,dim+1,PetscInt,&firstSubPoint,dim+1,IS,&subpointIS,dim+1,const PetscInt *,&subpoints);CHKERRQ(ierr); 2394 for (d = 0; d <= dim; ++d) { 2395 ierr = DMLabelGetStratumSize(subpointMap, d, &numSubPoints[d]);CHKERRQ(ierr); 2396 totSubPoints += numSubPoints[d]; 2397 } 2398 ierr = DMPlexSetChart(subdm, 0, totSubPoints);CHKERRQ(ierr); 2399 ierr = DMPlexSetVTKCellHeight(subdm, 1);CHKERRQ(ierr); 2400 /* Set cone sizes */ 2401 firstSubPoint[dim] = 0; 2402 firstSubPoint[0] = firstSubPoint[dim] + numSubPoints[dim]; 2403 if (dim > 1) {firstSubPoint[dim-1] = firstSubPoint[0] + numSubPoints[0];} 2404 if (dim > 2) {firstSubPoint[dim-2] = firstSubPoint[dim-1] + numSubPoints[dim-1];} 2405 for (d = 0; d <= dim; ++d) { 2406 ierr = DMLabelGetStratumIS(subpointMap, d, &subpointIS[d]);CHKERRQ(ierr); 2407 ierr = ISGetIndices(subpointIS[d], &subpoints[d]);CHKERRQ(ierr); 2408 } 2409 for (d = 0; d <= dim; ++d) { 2410 for (p = 0; p < numSubPoints[d]; ++p) { 2411 const PetscInt point = subpoints[d][p]; 2412 const PetscInt subpoint = firstSubPoint[d] + p; 2413 const PetscInt *cone; 2414 PetscInt coneSize, coneSizeNew, c, val; 2415 2416 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 2417 ierr = DMPlexSetConeSize(subdm, subpoint, coneSize);CHKERRQ(ierr); 2418 if (d == dim) { 2419 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 2420 for (c = 0, coneSizeNew = 0; c < coneSize; ++c) { 2421 ierr = DMLabelGetValue(subpointMap, cone[c], &val);CHKERRQ(ierr); 2422 if (val >= 0) coneSizeNew++; 2423 } 2424 ierr = DMPlexSetConeSize(subdm, subpoint, coneSizeNew);CHKERRQ(ierr); 2425 } 2426 } 2427 } 2428 ierr = DMSetUp(subdm);CHKERRQ(ierr); 2429 /* Set cones */ 2430 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, NULL);CHKERRQ(ierr); 2431 ierr = PetscMalloc(maxConeSize * sizeof(PetscInt), &coneNew);CHKERRQ(ierr); 2432 for (d = 0; d <= dim; ++d) { 2433 for (p = 0; p < numSubPoints[d]; ++p) { 2434 const PetscInt point = subpoints[d][p]; 2435 const PetscInt subpoint = firstSubPoint[d] + p; 2436 const PetscInt *cone; 2437 PetscInt coneSize, subconeSize, coneSizeNew, c, subc; 2438 2439 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 2440 ierr = DMPlexGetConeSize(subdm, subpoint, &subconeSize);CHKERRQ(ierr); 2441 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 2442 for (c = 0, coneSizeNew = 0; c < coneSize; ++c) { 2443 ierr = PetscFindInt(cone[c], numSubPoints[d-1], subpoints[d-1], &subc);CHKERRQ(ierr); 2444 if (subc >= 0) coneNew[coneSizeNew++] = firstSubPoint[d-1] + subc; 2445 } 2446 if (coneSizeNew != subconeSize) SETERRQ2(comm, PETSC_ERR_PLIB, "Number of cone points located %d does not match subcone size %d", coneSizeNew, subconeSize); 2447 ierr = DMPlexSetCone(subdm, subpoint, coneNew);CHKERRQ(ierr); 2448 } 2449 } 2450 ierr = PetscFree(coneNew);CHKERRQ(ierr); 2451 ierr = DMPlexSymmetrize(subdm);CHKERRQ(ierr); 2452 ierr = DMPlexStratify(subdm);CHKERRQ(ierr); 2453 /* Build coordinates */ 2454 { 2455 PetscSection coordSection, subCoordSection; 2456 Vec coordinates, subCoordinates; 2457 PetscScalar *coords, *subCoords; 2458 PetscInt numComp, coordSize; 2459 2460 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2461 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 2462 ierr = DMPlexGetCoordinateSection(subdm, &subCoordSection);CHKERRQ(ierr); 2463 ierr = PetscSectionSetNumFields(subCoordSection, 1);CHKERRQ(ierr); 2464 ierr = PetscSectionGetFieldComponents(coordSection, 0, &numComp);CHKERRQ(ierr); 2465 ierr = PetscSectionSetFieldComponents(subCoordSection, 0, numComp);CHKERRQ(ierr); 2466 ierr = PetscSectionSetChart(subCoordSection, firstSubPoint[0], firstSubPoint[0]+numSubPoints[0]);CHKERRQ(ierr); 2467 for (v = 0; v < numSubPoints[0]; ++v) { 2468 const PetscInt vertex = subpoints[0][v]; 2469 const PetscInt subvertex = firstSubPoint[0]+v; 2470 PetscInt dof; 2471 2472 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2473 ierr = PetscSectionSetDof(subCoordSection, subvertex, dof);CHKERRQ(ierr); 2474 ierr = PetscSectionSetFieldDof(subCoordSection, subvertex, 0, dof);CHKERRQ(ierr); 2475 } 2476 ierr = PetscSectionSetUp(subCoordSection);CHKERRQ(ierr); 2477 ierr = PetscSectionGetStorageSize(subCoordSection, &coordSize);CHKERRQ(ierr); 2478 ierr = VecCreate(comm, &subCoordinates);CHKERRQ(ierr); 2479 ierr = VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2480 ierr = VecSetFromOptions(subCoordinates);CHKERRQ(ierr); 2481 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2482 ierr = VecGetArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2483 for (v = 0; v < numSubPoints[0]; ++v) { 2484 const PetscInt vertex = subpoints[0][v]; 2485 const PetscInt subvertex = firstSubPoint[0]+v; 2486 PetscInt dof, off, sdof, soff, d; 2487 2488 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2489 ierr = PetscSectionGetOffset(coordSection, vertex, &off);CHKERRQ(ierr); 2490 ierr = PetscSectionGetDof(subCoordSection, subvertex, &sdof);CHKERRQ(ierr); 2491 ierr = PetscSectionGetOffset(subCoordSection, subvertex, &soff);CHKERRQ(ierr); 2492 if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof); 2493 for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d]; 2494 } 2495 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2496 ierr = VecRestoreArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2497 ierr = DMSetCoordinatesLocal(subdm, subCoordinates);CHKERRQ(ierr); 2498 ierr = VecDestroy(&subCoordinates);CHKERRQ(ierr); 2499 } 2500 /* Cleanup */ 2501 for (d = 0; d <= dim; ++d) { 2502 ierr = ISRestoreIndices(subpointIS[d], &subpoints[d]);CHKERRQ(ierr); 2503 ierr = ISDestroy(&subpointIS[d]);CHKERRQ(ierr); 2504 } 2505 ierr = PetscFree4(numSubPoints,firstSubPoint,subpointIS,subpoints);CHKERRQ(ierr); 2506 PetscFunctionReturn(0); 2507 } 2508 2509 #undef __FUNCT__ 2510 #define __FUNCT__ "DMPlexCreateCohesiveSubmesh" 2511 /* 2512 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. 2513 2514 Input Parameters: 2515 + dm - The original mesh 2516 . hasLagrange - The mesh has Lagrange unknowns in the cohesive cells 2517 . label - A label name, or PETSC_NULL 2518 - value - A label value 2519 2520 Output Parameter: 2521 . subdm - The surface mesh 2522 2523 Note: This function produces a DMLabel mapping original points in the submesh to their depth. This can be obtained using DMPlexGetSubpointMap(). 2524 2525 Level: developer 2526 2527 .seealso: DMPlexGetSubpointMap(), DMPlexCreateSubmesh() 2528 */ 2529 PetscErrorCode DMPlexCreateCohesiveSubmesh(DM dm, PetscBool hasLagrange, const char label[], PetscInt value, DM *subdm) 2530 { 2531 PetscInt dim, depth; 2532 PetscErrorCode ierr; 2533 2534 PetscFunctionBegin; 2535 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2536 PetscValidPointer(subdm, 5); 2537 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 2538 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 2539 ierr = DMCreate(PetscObjectComm((PetscObject)dm), subdm);CHKERRQ(ierr); 2540 ierr = DMSetType(*subdm, DMPLEX);CHKERRQ(ierr); 2541 ierr = DMPlexSetDimension(*subdm, dim-1);CHKERRQ(ierr); 2542 if (depth == dim) { 2543 ierr = DMPlexCreateCohesiveSubmesh_Interpolated(dm, hasLagrange, label, value, *subdm);CHKERRQ(ierr); 2544 } else { 2545 ierr = DMPlexCreateCohesiveSubmesh_Uninterpolated(dm, hasLagrange, label, value, *subdm);CHKERRQ(ierr); 2546 } 2547 PetscFunctionReturn(0); 2548 } 2549 2550 #undef __FUNCT__ 2551 #define __FUNCT__ "DMPlexGetSubpointMap" 2552 /*@ 2553 DMPlexGetSubpointMap - Returns a DMLabel with point dimension as values 2554 2555 Input Parameter: 2556 . dm - The submesh DM 2557 2558 Output Parameter: 2559 . subpointMap - The DMLabel of all the points from the original mesh in this submesh, or NULL if this is not a submesh 2560 2561 Level: developer 2562 2563 .seealso: DMPlexCreateSubmesh(), DMPlexCreateSubpointIS() 2564 @*/ 2565 PetscErrorCode DMPlexGetSubpointMap(DM dm, DMLabel *subpointMap) 2566 { 2567 DM_Plex *mesh = (DM_Plex*) dm->data; 2568 2569 PetscFunctionBegin; 2570 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2571 PetscValidPointer(subpointMap, 2); 2572 *subpointMap = mesh->subpointMap; 2573 PetscFunctionReturn(0); 2574 } 2575 2576 #undef __FUNCT__ 2577 #define __FUNCT__ "DMPlexSetSubpointMap" 2578 /* Note: Should normally not be called by the user, since it is set in DMPlexCreateSubmesh() */ 2579 PetscErrorCode DMPlexSetSubpointMap(DM dm, DMLabel subpointMap) 2580 { 2581 DM_Plex *mesh = (DM_Plex *) dm->data; 2582 DMLabel tmp; 2583 PetscErrorCode ierr; 2584 2585 PetscFunctionBegin; 2586 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2587 tmp = mesh->subpointMap; 2588 mesh->subpointMap = subpointMap; 2589 ++mesh->subpointMap->refct; 2590 ierr = DMLabelDestroy(&tmp);CHKERRQ(ierr); 2591 PetscFunctionReturn(0); 2592 } 2593 2594 #undef __FUNCT__ 2595 #define __FUNCT__ "DMPlexCreateSubpointIS" 2596 /*@ 2597 DMPlexCreateSubpointIS - Creates an IS covering the entire subdm chart with the original points as data 2598 2599 Input Parameter: 2600 . dm - The submesh DM 2601 2602 Output Parameter: 2603 . subpointIS - The IS of all the points from the original mesh in this submesh, or NULL if this is not a submesh 2604 2605 Note: This is IS is guaranteed to be sorted by the construction of the submesh 2606 2607 Level: developer 2608 2609 .seealso: DMPlexCreateSubmesh(), DMPlexGetSubpointMap() 2610 @*/ 2611 PetscErrorCode DMPlexCreateSubpointIS(DM dm, IS *subpointIS) 2612 { 2613 MPI_Comm comm; 2614 DMLabel subpointMap; 2615 IS is; 2616 const PetscInt *opoints; 2617 PetscInt *points, *depths; 2618 PetscInt depth, depStart, depEnd, d, pStart, pEnd, p, n, off; 2619 PetscErrorCode ierr; 2620 2621 PetscFunctionBegin; 2622 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2623 PetscValidPointer(subpointIS, 2); 2624 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 2625 *subpointIS = NULL; 2626 ierr = DMPlexGetSubpointMap(dm, &subpointMap);CHKERRQ(ierr); 2627 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 2628 if (subpointMap && depth >= 0) { 2629 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 2630 if (pStart) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Submeshes must start the point numbering at 0, not %d", pStart); 2631 ierr = DMGetWorkArray(dm, depth+1, PETSC_INT, &depths);CHKERRQ(ierr); 2632 depths[0] = depth; 2633 depths[1] = 0; 2634 for(d = 2; d <= depth; ++d) {depths[d] = depth+1 - d;} 2635 ierr = PetscMalloc(pEnd * sizeof(PetscInt), &points);CHKERRQ(ierr); 2636 for(d = 0, off = 0; d <= depth; ++d) { 2637 const PetscInt dep = depths[d]; 2638 2639 ierr = DMPlexGetDepthStratum(dm, dep, &depStart, &depEnd);CHKERRQ(ierr); 2640 ierr = DMLabelGetStratumSize(subpointMap, dep, &n);CHKERRQ(ierr); 2641 if (((d < 2) && (depth > 1)) || (d == 1)) { /* Only check vertices and cells for now since the map is broken for others */ 2642 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); 2643 } else { 2644 if (!n) { 2645 if (d == 0) { 2646 /* Missing cells */ 2647 for(p = 0; p < depEnd-depStart; ++p, ++off) points[off] = -1; 2648 } else { 2649 /* Missing faces */ 2650 for(p = 0; p < depEnd-depStart; ++p, ++off) points[off] = PETSC_MAX_INT; 2651 } 2652 } 2653 } 2654 if (n) { 2655 ierr = DMLabelGetStratumIS(subpointMap, dep, &is);CHKERRQ(ierr); 2656 ierr = ISGetIndices(is, &opoints);CHKERRQ(ierr); 2657 for(p = 0; p < n; ++p, ++off) points[off] = opoints[p]; 2658 ierr = ISRestoreIndices(is, &opoints);CHKERRQ(ierr); 2659 ierr = ISDestroy(&is);CHKERRQ(ierr); 2660 } 2661 } 2662 ierr = DMRestoreWorkArray(dm, depth+1, PETSC_INT, &depths);CHKERRQ(ierr); 2663 if (off != pEnd) SETERRQ2(comm, PETSC_ERR_ARG_WRONG, "The number of mapped submesh points %d should be %d", off, pEnd); 2664 ierr = ISCreateGeneral(PETSC_COMM_SELF, pEnd, points, PETSC_OWN_POINTER, subpointIS);CHKERRQ(ierr); 2665 } 2666 PetscFunctionReturn(0); 2667 } 2668