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 /* 534 We are adding two kinds of points here: 535 Replicated: Copies of points which exist in the mesh, such as vertices identified across a fault 536 Hybrid: Entirely new points, such as cohesive cells 537 */ 538 static PetscErrorCode DMPlexConstructCohesiveCells_Internal(DM dm, DMLabel label, DM sdm) 539 { 540 MPI_Comm comm; 541 IS valueIS; 542 PetscInt numSP = 0; /* The number of depths for which we have replicated points */ 543 const PetscInt *values; /* List of depths for which we have replicated points */ 544 IS *pointIS; 545 PetscInt *numSplitPoints; /* The number of replicated points at each depth */ 546 PetscInt *numHybridPoints; /* The number of hybrid points at each depth */ 547 const PetscInt **splitPoints; /* Replicated points for each depth */ 548 PetscSection coordSection; 549 Vec coordinates; 550 PetscScalar *coords; 551 PetscInt depths[4]; /* Depths in the order that plex points are numbered */ 552 PetscInt *depthShift; /* Number of replicated+hybrid points at each depth */ 553 PetscInt *depthOffset; /* Prefix sums of depthShift */ 554 PetscInt *pMaxNew; /* The first replicated point at each depth in the new mesh, hybrids come after this */ 555 PetscInt *coneNew, *coneONew, *supportNew; 556 PetscInt shift = 100, depth = 0, dep, dim, d, sp, maxConeSize, maxSupportSize, numLabels, vStart, vEnd, pEnd, p, v; 557 PetscErrorCode ierr; 558 559 PetscFunctionBegin; 560 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 561 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 562 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 563 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 564 depths[0] = depth; 565 depths[1] = 0; 566 depths[2] = depth-1; 567 depths[3] = 1; 568 /* Count split points and add cohesive cells */ 569 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize);CHKERRQ(ierr); 570 ierr = PetscMalloc6(depth+1,PetscInt,&depthShift,depth+1,PetscInt,&depthOffset,depth+1,PetscInt,&pMaxNew,maxConeSize*3,PetscInt,&coneNew,maxConeSize*3,PetscInt,&coneONew,maxSupportSize,PetscInt,&supportNew);CHKERRQ(ierr); 571 ierr = PetscMalloc4(depth+1,IS,&pointIS,depth+1,PetscInt,&numSplitPoints,depth+1,PetscInt,&numHybridPoints,depth+1,const PetscInt*,&splitPoints);CHKERRQ(ierr); 572 ierr = PetscMemzero(depthShift, (depth+1) * sizeof(PetscInt));CHKERRQ(ierr); 573 ierr = PetscMemzero(depthOffset, (depth+1) * sizeof(PetscInt));CHKERRQ(ierr); 574 for (d = 0; d <= depth; ++d) { 575 ierr = DMPlexGetDepthStratum(dm, d, NULL, &pMaxNew[d]);CHKERRQ(ierr); 576 numSplitPoints[d] = 0; 577 numHybridPoints[d] = 0; 578 splitPoints[d] = NULL; 579 pointIS[d] = NULL; 580 } 581 if (label) { 582 ierr = DMLabelGetValueIS(label, &valueIS);CHKERRQ(ierr); 583 ierr = ISGetLocalSize(valueIS, &numSP);CHKERRQ(ierr); 584 ierr = ISGetIndices(valueIS, &values);CHKERRQ(ierr); 585 } 586 for (sp = 0; sp < numSP; ++sp) { 587 const PetscInt dep = values[sp]; 588 589 if ((dep < 0) || (dep > depth)) continue; 590 /* TAKE OUT*/ ierr = DMLabelGetStratumSize(label, dep, &depthShift[dep]);CHKERRQ(ierr); 591 ierr = DMLabelGetStratumIS(label, dep, &pointIS[dep]);CHKERRQ(ierr); 592 if (pointIS[dep]) { 593 ierr = ISGetLocalSize(pointIS[dep], &numSplitPoints[dep]);CHKERRQ(ierr); 594 ierr = ISGetIndices(pointIS[dep], &splitPoints[dep]);CHKERRQ(ierr); 595 } 596 } 597 /* Calculate number of hybrid points */ 598 for (d = 1; d <= depth; ++d) numHybridPoints[d] = numSplitPoints[d-1]; /* There is a hybrid cell/face/edge for every split face/edge/vertex */ 599 for (d = 0; d <= depth; ++d) depthShift[d] = numSplitPoints[d] + numHybridPoints[d]; 600 /* TAKE THIS OUT */ if (depth > 2) depthShift[2] = numSplitPoints[2]; 601 for (d = 1; d <= depth; ++d) depthOffset[depths[d]] = depthOffset[depths[d-1]] + depthShift[depths[d-1]]; 602 for (d = 0; d <= depth; ++d) pMaxNew[d] += depthOffset[d]; 603 ierr = DMPlexShiftSizes_Internal(dm, depthShift, sdm);CHKERRQ(ierr); 604 /* Step 3: Set cone/support sizes for new points */ 605 for (dep = 0; dep <= depth; ++dep) { 606 for (p = 0; p < numSplitPoints[dep]; ++p) { 607 const PetscInt oldp = splitPoints[dep][p]; 608 const PetscInt newp = depthOffset[dep] + oldp; 609 const PetscInt splitp = pMaxNew[dep] + p; 610 const PetscInt *support; 611 PetscInt coneSize, supportSize, q, e; 612 613 ierr = DMPlexGetConeSize(dm, oldp, &coneSize);CHKERRQ(ierr); 614 ierr = DMPlexSetConeSize(sdm, splitp, coneSize);CHKERRQ(ierr); 615 ierr = DMPlexGetSupportSize(dm, oldp, &supportSize);CHKERRQ(ierr); 616 ierr = DMPlexSetSupportSize(sdm, splitp, supportSize);CHKERRQ(ierr); 617 if (dep == depth-1) { 618 const PetscInt ccell = pMaxNew[depth] + p; 619 /* Add cohesive cells, they are prisms */ 620 ierr = DMPlexSetConeSize(sdm, ccell, 2 + coneSize);CHKERRQ(ierr); 621 } else if (dep == 0) { 622 const PetscInt cedge = pMaxNew[1] + (depthShift[1] - depthShift[0]) + p; 623 624 ierr = DMPlexGetSupport(dm, oldp, &support);CHKERRQ(ierr); 625 /* Split old vertex: Edges in old split faces and new cohesive edge */ 626 for (e = 0, q = 0; e < supportSize; ++e) { 627 PetscInt val; 628 629 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 630 if ((val == 1) || (val == (shift + 1))) ++q; 631 } 632 ierr = DMPlexSetSupportSize(sdm, newp, q+1);CHKERRQ(ierr); 633 /* Split new vertex: Edges in new split faces and new cohesive edge */ 634 for (e = 0, q = 0; e < supportSize; ++e) { 635 PetscInt val; 636 637 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 638 if ((val == 1) || (val == -(shift + 1))) ++q; 639 } 640 ierr = DMPlexSetSupportSize(sdm, splitp, q+1);CHKERRQ(ierr); 641 /* Add cohesive edges */ 642 ierr = DMPlexSetConeSize(sdm, cedge, 2);CHKERRQ(ierr); 643 /* Punt for now on support, you loop over closure, extract faces, check which ones are in the label */ 644 } else if (dep == dim-2) { 645 ierr = DMPlexGetSupport(dm, oldp, &support);CHKERRQ(ierr); 646 /* Split old edge: Faces in positive side cells and old split faces */ 647 for (e = 0, q = 0; e < supportSize; ++e) { 648 PetscInt val; 649 650 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 651 if ((val == dim-1) || (val == (shift + dim-1))) ++q; 652 } 653 ierr = DMPlexSetSupportSize(sdm, newp, q);CHKERRQ(ierr); 654 /* Split new edge: Faces in negative side cells and new split faces */ 655 for (e = 0, q = 0; e < supportSize; ++e) { 656 PetscInt val; 657 658 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 659 if ((val == dim-1) || (val == -(shift + dim-1))) ++q; 660 } 661 ierr = DMPlexSetSupportSize(sdm, splitp, q);CHKERRQ(ierr); 662 } 663 } 664 } 665 /* Step 4: Setup split DM */ 666 ierr = DMSetUp(sdm);CHKERRQ(ierr); 667 ierr = DMPlexShiftPoints_Internal(dm, depthShift, sdm);CHKERRQ(ierr); 668 /* Step 6: Set cones and supports for new points */ 669 for (dep = 0; dep <= depth; ++dep) { 670 for (p = 0; p < numSplitPoints[dep]; ++p) { 671 const PetscInt oldp = splitPoints[dep][p]; 672 const PetscInt newp = depthOffset[dep] + oldp; 673 const PetscInt splitp = pMaxNew[dep] + p; 674 const PetscInt *cone, *support, *ornt; 675 PetscInt coneSize, supportSize, q, v, e, s; 676 677 ierr = DMPlexGetConeSize(dm, oldp, &coneSize);CHKERRQ(ierr); 678 ierr = DMPlexGetCone(dm, oldp, &cone);CHKERRQ(ierr); 679 ierr = DMPlexGetConeOrientation(dm, oldp, &ornt);CHKERRQ(ierr); 680 ierr = DMPlexGetSupportSize(dm, oldp, &supportSize);CHKERRQ(ierr); 681 ierr = DMPlexGetSupport(dm, oldp, &support);CHKERRQ(ierr); 682 if (dep == depth-1) { 683 const PetscInt ccell = pMaxNew[depth] + p; 684 const PetscInt *supportF; 685 686 /* Split face: copy in old face to new face to start */ 687 ierr = DMPlexGetSupport(sdm, newp, &supportF);CHKERRQ(ierr); 688 ierr = DMPlexSetSupport(sdm, splitp, supportF);CHKERRQ(ierr); 689 /* Split old face: old vertices/edges in cone so no change */ 690 /* Split new face: new vertices/edges in cone */ 691 for (q = 0; q < coneSize; ++q) { 692 ierr = PetscFindInt(cone[q], numSplitPoints[dim-2], splitPoints[dim-2], &v);CHKERRQ(ierr); 693 694 coneNew[2+q] = pMaxNew[dim-2] + v; 695 } 696 ierr = DMPlexSetCone(sdm, splitp, &coneNew[2]);CHKERRQ(ierr); 697 ierr = DMPlexSetConeOrientation(sdm, splitp, ornt);CHKERRQ(ierr); 698 /* Face support */ 699 for (s = 0; s < supportSize; ++s) { 700 PetscInt val; 701 702 ierr = DMLabelGetValue(label, support[s], &val);CHKERRQ(ierr); 703 if (val < 0) { 704 /* Split old face: Replace negative side cell with cohesive cell */ 705 ierr = DMPlexInsertSupport(sdm, newp, s, ccell);CHKERRQ(ierr); 706 } else { 707 /* Split new face: Replace positive side cell with cohesive cell */ 708 ierr = DMPlexInsertSupport(sdm, splitp, s, ccell);CHKERRQ(ierr); 709 /* Get orientation for cohesive face */ 710 { 711 const PetscInt *ncone, *nconeO; 712 PetscInt nconeSize, nc; 713 714 ierr = DMPlexGetConeSize(dm, support[s], &nconeSize);CHKERRQ(ierr); 715 ierr = DMPlexGetCone(dm, support[s], &ncone);CHKERRQ(ierr); 716 ierr = DMPlexGetConeOrientation(dm, support[s], &nconeO);CHKERRQ(ierr); 717 for (nc = 0; nc < nconeSize; ++nc) { 718 if (ncone[nc] == oldp) { 719 coneONew[0] = nconeO[nc]; 720 break; 721 } 722 } 723 if (nc >= nconeSize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not locate face %d in neighboring cell %d", oldp, support[s]); 724 } 725 } 726 } 727 /* Cohesive cell: Old and new split face, then new cohesive edges */ 728 coneNew[0] = newp; /* Extracted negative side orientation above */ 729 coneNew[1] = splitp; coneONew[1] = coneONew[0]; 730 if (dim > 2) { 731 PetscInt *closure = NULL, closureSize, cl; 732 733 ierr = DMPlexGetTransitiveClosure(dm, oldp, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 734 for (cl = 0, q = 0; cl < closureSize*2; cl += 2) { 735 const PetscInt clp = closure[cl]; 736 737 if ((clp >= vStart) && (clp < vEnd)) { 738 ierr = PetscFindInt(clp, numSplitPoints[0], splitPoints[0], &v);CHKERRQ(ierr); 739 coneNew[2+q] = pMaxNew[1] + (depthShift[1] - depthShift[0]) + v; 740 coneONew[2+q] = 0; 741 ++q; 742 } 743 } 744 ierr = DMPlexRestoreTransitiveClosure(dm, oldp, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 745 if (q != coneSize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid number of split face vertices %d should be %d", q, coneSize); 746 } else { 747 for (q = 0; q < coneSize; ++q) { 748 coneNew[2+q] = (pMaxNew[1] - pMaxNew[dim-2]) + (depthShift[1] - depthShift[0]) + coneNew[2+q]; 749 coneONew[2+q] = 0; 750 } 751 } 752 ierr = DMPlexSetCone(sdm, ccell, coneNew);CHKERRQ(ierr); 753 ierr = DMPlexSetConeOrientation(sdm, ccell, coneONew);CHKERRQ(ierr); 754 } else if (dep == 0) { 755 const PetscInt cedge = pMaxNew[1] + (depthShift[1] - depthShift[0]) + p; 756 757 /* Split old vertex: Edges in old split faces and new cohesive edge */ 758 for (e = 0, q = 0; e < supportSize; ++e) { 759 PetscInt val; 760 761 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 762 if ((val == 1) || (val == (shift + 1))) { 763 supportNew[q++] = depthOffset[1] + support[e]; 764 } 765 } 766 supportNew[q] = cedge; 767 768 ierr = DMPlexSetSupport(sdm, newp, supportNew);CHKERRQ(ierr); 769 /* Split new vertex: Edges in new split faces and new cohesive edge */ 770 for (e = 0, q = 0; e < supportSize; ++e) { 771 PetscInt val, edge; 772 773 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 774 if (val == 1) { 775 ierr = PetscFindInt(support[e], numSplitPoints[1], splitPoints[1], &edge);CHKERRQ(ierr); 776 if (edge < 0) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Edge %d is not a split edge", support[e]); 777 supportNew[q++] = pMaxNew[1] + edge; 778 } else if (val == -(shift + 1)) { 779 supportNew[q++] = depthOffset[1] + support[e]; 780 } 781 } 782 supportNew[q] = cedge; 783 ierr = DMPlexSetSupport(sdm, splitp, supportNew);CHKERRQ(ierr); 784 /* Cohesive edge: Old and new split vertex, punting on support */ 785 coneNew[0] = newp; 786 coneNew[1] = splitp; 787 ierr = DMPlexSetCone(sdm, cedge, coneNew);CHKERRQ(ierr); 788 } else if (dep == dim-2) { 789 /* Split old edge: old vertices in cone so no change */ 790 /* Split new edge: new vertices in cone */ 791 for (q = 0; q < coneSize; ++q) { 792 ierr = PetscFindInt(cone[q], numSplitPoints[dim-3], splitPoints[dim-3], &v);CHKERRQ(ierr); 793 794 coneNew[q] = pMaxNew[dim-3] + v; 795 } 796 ierr = DMPlexSetCone(sdm, splitp, coneNew);CHKERRQ(ierr); 797 /* Split old edge: Faces in positive side cells and old split faces */ 798 for (e = 0, q = 0; e < supportSize; ++e) { 799 PetscInt val; 800 801 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 802 if ((val == dim-1) || (val == (shift + dim-1))) { 803 supportNew[q++] = depthOffset[dim-1] + support[e]; 804 } 805 } 806 ierr = DMPlexSetSupport(sdm, newp, supportNew);CHKERRQ(ierr); 807 /* Split new edge: Faces in negative side cells and new split faces */ 808 for (e = 0, q = 0; e < supportSize; ++e) { 809 PetscInt val, face; 810 811 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 812 if (val == dim-1) { 813 ierr = PetscFindInt(support[e], numSplitPoints[dim-1], splitPoints[dim-1], &face);CHKERRQ(ierr); 814 if (face < 0) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Face %d is not a split face", support[e]); 815 supportNew[q++] = pMaxNew[dim-1] + face; 816 } else if (val == -(shift + dim-1)) { 817 supportNew[q++] = depthOffset[dim-1] + support[e]; 818 } 819 } 820 ierr = DMPlexSetSupport(sdm, splitp, supportNew);CHKERRQ(ierr); 821 } 822 } 823 } 824 /* Step 6b: Replace split points in negative side cones */ 825 for (sp = 0; sp < numSP; ++sp) { 826 PetscInt dep = values[sp]; 827 IS pIS; 828 PetscInt numPoints; 829 const PetscInt *points; 830 831 if (dep >= 0) continue; 832 ierr = DMLabelGetStratumIS(label, dep, &pIS);CHKERRQ(ierr); 833 if (!pIS) continue; 834 dep = -dep - shift; 835 ierr = ISGetLocalSize(pIS, &numPoints);CHKERRQ(ierr); 836 ierr = ISGetIndices(pIS, &points);CHKERRQ(ierr); 837 for (p = 0; p < numPoints; ++p) { 838 const PetscInt oldp = points[p]; 839 const PetscInt newp = depthOffset[dep] + oldp; 840 const PetscInt *cone; 841 PetscInt coneSize, c; 842 PetscBool replaced = PETSC_FALSE; 843 844 /* Negative edge: replace split vertex */ 845 /* Negative cell: replace split face */ 846 ierr = DMPlexGetConeSize(sdm, newp, &coneSize);CHKERRQ(ierr); 847 ierr = DMPlexGetCone(sdm, newp, &cone);CHKERRQ(ierr); 848 for (c = 0; c < coneSize; ++c) { 849 const PetscInt coldp = cone[c] - depthOffset[dep-1]; 850 PetscInt csplitp, cp, val; 851 852 ierr = DMLabelGetValue(label, coldp, &val);CHKERRQ(ierr); 853 if (val == dep-1) { 854 ierr = PetscFindInt(coldp, numSplitPoints[dep-1], splitPoints[dep-1], &cp);CHKERRQ(ierr); 855 if (cp < 0) SETERRQ2(comm, PETSC_ERR_ARG_WRONG, "Point %d is not a split point of dimension %d", oldp, dep-1); 856 csplitp = pMaxNew[dep-1] + cp; 857 ierr = DMPlexInsertCone(sdm, newp, c, csplitp);CHKERRQ(ierr); 858 replaced = PETSC_TRUE; 859 } 860 } 861 /* Cells with only a vertex or edge on the submesh have no replacement */ 862 /* if (!replaced) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "The cone of point %d does not contain split points", oldp); */ 863 } 864 ierr = ISRestoreIndices(pIS, &points);CHKERRQ(ierr); 865 ierr = ISDestroy(&pIS);CHKERRQ(ierr); 866 } 867 /* Step 7: Stratify */ 868 ierr = DMPlexStratify(sdm);CHKERRQ(ierr); 869 /* Step 8: Coordinates */ 870 ierr = DMPlexShiftCoordinates_Internal(dm, depthShift, sdm);CHKERRQ(ierr); 871 ierr = DMPlexGetCoordinateSection(sdm, &coordSection);CHKERRQ(ierr); 872 ierr = DMGetCoordinatesLocal(sdm, &coordinates);CHKERRQ(ierr); 873 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 874 for (v = 0; v < (numSplitPoints ? numSplitPoints[0] : 0); ++v) { 875 const PetscInt newp = depthOffset[0] + splitPoints[0][v]; 876 const PetscInt splitp = pMaxNew[0] + v; 877 PetscInt dof, off, soff, d; 878 879 ierr = PetscSectionGetDof(coordSection, newp, &dof);CHKERRQ(ierr); 880 ierr = PetscSectionGetOffset(coordSection, newp, &off);CHKERRQ(ierr); 881 ierr = PetscSectionGetOffset(coordSection, splitp, &soff);CHKERRQ(ierr); 882 for (d = 0; d < dof; ++d) coords[soff+d] = coords[off+d]; 883 } 884 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 885 /* Step 9: SF, if I can figure this out we can split the mesh in parallel */ 886 ierr = DMPlexShiftSF_Internal(dm, depthShift, sdm);CHKERRQ(ierr); 887 /* Step 10: Labels */ 888 ierr = DMPlexShiftLabels_Internal(dm, depthShift, sdm);CHKERRQ(ierr); 889 ierr = DMPlexGetNumLabels(sdm, &numLabels);CHKERRQ(ierr); 890 for (dep = 0; dep <= depth; ++dep) { 891 for (p = 0; p < numSplitPoints[dep]; ++p) { 892 const PetscInt newp = depthOffset[dep] + splitPoints[dep][p]; 893 const PetscInt splitp = pMaxNew[dep] + p; 894 PetscInt l; 895 896 for (l = 0; l < numLabels; ++l) { 897 DMLabel mlabel; 898 const char *lname; 899 PetscInt val; 900 PetscBool isDepth; 901 902 ierr = DMPlexGetLabelName(sdm, l, &lname);CHKERRQ(ierr); 903 ierr = PetscStrcmp(lname, "depth", &isDepth);CHKERRQ(ierr); 904 if (isDepth) continue; 905 ierr = DMPlexGetLabel(sdm, lname, &mlabel);CHKERRQ(ierr); 906 ierr = DMLabelGetValue(mlabel, newp, &val);CHKERRQ(ierr); 907 if (val >= 0) { 908 ierr = DMLabelSetValue(mlabel, splitp, val);CHKERRQ(ierr); 909 #if 0 910 /* Do not put cohesive edges into the label */ 911 if (dep == 0) { 912 const PetscInt cedge = pMaxNew[1] + (depthShift[1] - depthShift[0]) + p; 913 ierr = DMLabelSetValue(mlabel, cedge, val);CHKERRQ(ierr); 914 } 915 #endif 916 } 917 } 918 } 919 } 920 for (sp = 0; sp < numSP; ++sp) { 921 const PetscInt dep = values[sp]; 922 923 if ((dep < 0) || (dep > depth)) continue; 924 if (pointIS[dep]) {ierr = ISRestoreIndices(pointIS[dep], &splitPoints[dep]);CHKERRQ(ierr);} 925 ierr = ISDestroy(&pointIS[dep]);CHKERRQ(ierr); 926 } 927 if (label) { 928 ierr = ISRestoreIndices(valueIS, &values);CHKERRQ(ierr); 929 ierr = ISDestroy(&valueIS);CHKERRQ(ierr); 930 } 931 ierr = DMPlexGetChart(sdm, NULL, &pEnd);CHKERRQ(ierr); 932 if (depth > 0) pMaxNew[0] += depthShift[0]; /* Account for shadow vertices */ 933 if (depth > 1) pMaxNew[1] = pEnd - depthShift[0]; /* There is a hybrid edge for every shadow vertex */ 934 if (depth > 2) pMaxNew[2] = -1; /* There are no hybrid faces */ 935 ierr = DMPlexSetHybridBounds(sdm, depth >= 0 ? pMaxNew[depth] : PETSC_DETERMINE, depth>1 ? pMaxNew[depth-1] : PETSC_DETERMINE, depth>2 ? pMaxNew[1] : PETSC_DETERMINE, depth >= 0 ? pMaxNew[0] : PETSC_DETERMINE);CHKERRQ(ierr); 936 ierr = PetscFree6(depthShift, depthOffset, pMaxNew, coneNew, coneONew, supportNew);CHKERRQ(ierr); 937 ierr = PetscFree4(pointIS, numSplitPoints, numHybridPoints, splitPoints);CHKERRQ(ierr); 938 PetscFunctionReturn(0); 939 } 940 941 #undef __FUNCT__ 942 #define __FUNCT__ "DMPlexConstructCohesiveCells" 943 /*@C 944 DMPlexConstructCohesiveCells - Construct cohesive cells which split the face along an internal interface 945 946 Collective on dm 947 948 Input Parameters: 949 + dm - The original DM 950 - labelName - The label specifying the boundary faces (this could be auto-generated) 951 952 Output Parameters: 953 - dmSplit - The new DM 954 955 Level: developer 956 957 .seealso: DMCreate(), DMPlexLabelCohesiveComplete() 958 @*/ 959 PetscErrorCode DMPlexConstructCohesiveCells(DM dm, DMLabel label, DM *dmSplit) 960 { 961 DM sdm; 962 PetscInt dim; 963 PetscErrorCode ierr; 964 965 PetscFunctionBegin; 966 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 967 PetscValidPointer(dmSplit, 4); 968 ierr = DMCreate(PetscObjectComm((PetscObject)dm), &sdm);CHKERRQ(ierr); 969 ierr = DMSetType(sdm, DMPLEX);CHKERRQ(ierr); 970 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 971 ierr = DMPlexSetDimension(sdm, dim);CHKERRQ(ierr); 972 switch (dim) { 973 case 2: 974 case 3: 975 ierr = DMPlexConstructCohesiveCells_Internal(dm, label, sdm);CHKERRQ(ierr); 976 break; 977 default: 978 SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Cannot construct cohesive cells for dimension %d", dim); 979 } 980 *dmSplit = sdm; 981 PetscFunctionReturn(0); 982 } 983 984 #undef __FUNCT__ 985 #define __FUNCT__ "DMPlexLabelCohesiveComplete" 986 /*@ 987 DMPlexLabelCohesiveComplete - Starting with a label marking vertices on an internal surface, we add all other mesh pieces 988 to complete the surface 989 990 Input Parameters: 991 + dm - The DM 992 . label - A DMLabel marking the surface vertices 993 . flip - Flag to flip the submesh normal and replace points on the other side 994 - subdm - The subDM associated with the label, or NULL 995 996 Output Parameter: 997 . label - A DMLabel marking all surface points 998 999 Level: developer 1000 1001 .seealso: DMPlexConstructCohesiveCells(), DMPlexLabelComplete() 1002 @*/ 1003 PetscErrorCode DMPlexLabelCohesiveComplete(DM dm, DMLabel label, PetscBool flip, DM subdm) 1004 { 1005 DMLabel depthLabel; 1006 IS dimIS, subpointIS; 1007 const PetscInt *points, *subpoints; 1008 const PetscInt rev = flip ? -1 : 1; 1009 PetscInt shift = 100, dim, dep, cStart, cEnd, numPoints, numSubpoints, p, val; 1010 PetscErrorCode ierr; 1011 1012 PetscFunctionBegin; 1013 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 1014 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1015 if (subdm) { 1016 ierr = DMPlexCreateSubpointIS(subdm, &subpointIS);CHKERRQ(ierr); 1017 if (subpointIS) { 1018 ierr = ISGetLocalSize(subpointIS, &numSubpoints);CHKERRQ(ierr); 1019 ierr = ISGetIndices(subpointIS, &subpoints);CHKERRQ(ierr); 1020 } 1021 } 1022 /* Cell orientation for face gives the side of the fault */ 1023 ierr = DMLabelGetStratumIS(label, dim-1, &dimIS);CHKERRQ(ierr); 1024 if (!dimIS) PetscFunctionReturn(0); 1025 ierr = ISGetLocalSize(dimIS, &numPoints);CHKERRQ(ierr); 1026 ierr = ISGetIndices(dimIS, &points);CHKERRQ(ierr); 1027 for (p = 0; p < numPoints; ++p) { 1028 const PetscInt *support; 1029 PetscInt supportSize, s; 1030 1031 ierr = DMPlexGetSupportSize(dm, points[p], &supportSize);CHKERRQ(ierr); 1032 if (supportSize != 2) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Split face %d has %d != 2 supports", points[p], supportSize); 1033 ierr = DMPlexGetSupport(dm, points[p], &support);CHKERRQ(ierr); 1034 for (s = 0; s < supportSize; ++s) { 1035 const PetscInt *cone, *ornt; 1036 PetscInt coneSize, c; 1037 PetscBool pos = PETSC_TRUE; 1038 1039 ierr = DMPlexGetConeSize(dm, support[s], &coneSize);CHKERRQ(ierr); 1040 ierr = DMPlexGetCone(dm, support[s], &cone);CHKERRQ(ierr); 1041 ierr = DMPlexGetConeOrientation(dm, support[s], &ornt);CHKERRQ(ierr); 1042 for (c = 0; c < coneSize; ++c) { 1043 if (cone[c] == points[p]) { 1044 PetscInt o = ornt[c]; 1045 1046 if (subdm) { 1047 const PetscInt *subcone, *subornt; 1048 PetscInt subpoint, subface, subconeSize, sc; 1049 1050 ierr = PetscFindInt(support[s], numSubpoints, subpoints, &subpoint);CHKERRQ(ierr); 1051 ierr = PetscFindInt(points[p], numSubpoints, subpoints, &subface);CHKERRQ(ierr); 1052 ierr = DMPlexGetConeSize(subdm, subpoint, &subconeSize);CHKERRQ(ierr); 1053 ierr = DMPlexGetCone(subdm, subpoint, &subcone);CHKERRQ(ierr); 1054 ierr = DMPlexGetConeOrientation(subdm, subpoint, &subornt);CHKERRQ(ierr); 1055 for (sc = 0; sc < subconeSize; ++sc) { 1056 if (subcone[sc] == subface) { 1057 o = subornt[0]; 1058 break; 1059 } 1060 } 1061 if (sc >= subconeSize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not find point %d in cone for subpoint %d", points[p], subpoint); 1062 } 1063 if (o >= 0) { 1064 ierr = DMLabelSetValue(label, support[s], rev*(shift+dim));CHKERRQ(ierr); 1065 pos = rev > 0 ? PETSC_TRUE : PETSC_FALSE; 1066 } else { 1067 ierr = DMLabelSetValue(label, support[s], -rev*(shift+dim));CHKERRQ(ierr); 1068 pos = rev > 0 ? PETSC_FALSE : PETSC_TRUE; 1069 } 1070 break; 1071 } 1072 } 1073 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]); 1074 /* Put faces touching the fault in the label */ 1075 for (c = 0; c < coneSize; ++c) { 1076 const PetscInt point = cone[c]; 1077 1078 ierr = DMLabelGetValue(label, point, &val);CHKERRQ(ierr); 1079 if (val == -1) { 1080 PetscInt *closure = NULL; 1081 PetscInt closureSize, cl; 1082 1083 ierr = DMPlexGetTransitiveClosure(dm, point, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1084 for (cl = 0; cl < closureSize*2; cl += 2) { 1085 const PetscInt clp = closure[cl]; 1086 1087 ierr = DMLabelGetValue(label, clp, &val);CHKERRQ(ierr); 1088 if ((val >= 0) && (val < dim-1)) { 1089 ierr = DMLabelSetValue(label, point, pos == PETSC_TRUE ? shift+dim-1 : -(shift+dim-1));CHKERRQ(ierr); 1090 break; 1091 } 1092 } 1093 ierr = DMPlexRestoreTransitiveClosure(dm, point, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1094 } 1095 } 1096 } 1097 } 1098 if (subdm) { 1099 if (subpointIS) {ierr = ISRestoreIndices(subpointIS, &subpoints);CHKERRQ(ierr);} 1100 ierr = ISDestroy(&subpointIS);CHKERRQ(ierr); 1101 } 1102 ierr = ISRestoreIndices(dimIS, &points);CHKERRQ(ierr); 1103 ierr = ISDestroy(&dimIS);CHKERRQ(ierr); 1104 /* Search for other cells/faces/edges connected to the fault by a vertex */ 1105 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1106 ierr = DMLabelGetStratumIS(label, 0, &dimIS);CHKERRQ(ierr); 1107 if (!dimIS) PetscFunctionReturn(0); 1108 ierr = ISGetLocalSize(dimIS, &numPoints);CHKERRQ(ierr); 1109 ierr = ISGetIndices(dimIS, &points);CHKERRQ(ierr); 1110 for (p = 0; p < numPoints; ++p) { 1111 PetscInt *star = NULL; 1112 PetscInt starSize, s; 1113 PetscInt again = 1; /* 0: Finished 1: Keep iterating after a change 2: No change */ 1114 1115 /* First mark cells connected to the fault */ 1116 ierr = DMPlexGetTransitiveClosure(dm, points[p], PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1117 while (again) { 1118 if (again > 1) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Could not classify all cells connected to the fault"); 1119 again = 0; 1120 for (s = 0; s < starSize*2; s += 2) { 1121 const PetscInt point = star[s]; 1122 const PetscInt *cone; 1123 PetscInt coneSize, c; 1124 1125 if ((point < cStart) || (point >= cEnd)) continue; 1126 ierr = DMLabelGetValue(label, point, &val);CHKERRQ(ierr); 1127 if (val != -1) continue; 1128 again = 2; 1129 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 1130 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 1131 for (c = 0; c < coneSize; ++c) { 1132 ierr = DMLabelGetValue(label, cone[c], &val);CHKERRQ(ierr); 1133 if (val != -1) { 1134 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); 1135 if (val > 0) { 1136 ierr = DMLabelSetValue(label, point, shift+dim);CHKERRQ(ierr); 1137 } else { 1138 ierr = DMLabelSetValue(label, point, -(shift+dim));CHKERRQ(ierr); 1139 } 1140 again = 1; 1141 break; 1142 } 1143 } 1144 } 1145 } 1146 /* Classify the rest by cell membership */ 1147 for (s = 0; s < starSize*2; s += 2) { 1148 const PetscInt point = star[s]; 1149 1150 ierr = DMLabelGetValue(label, point, &val);CHKERRQ(ierr); 1151 if (val == -1) { 1152 PetscInt *sstar = NULL; 1153 PetscInt sstarSize, ss; 1154 PetscBool marked = PETSC_FALSE; 1155 1156 ierr = DMPlexGetTransitiveClosure(dm, point, PETSC_FALSE, &sstarSize, &sstar);CHKERRQ(ierr); 1157 for (ss = 0; ss < sstarSize*2; ss += 2) { 1158 const PetscInt spoint = sstar[ss]; 1159 1160 if ((spoint < cStart) || (spoint >= cEnd)) continue; 1161 ierr = DMLabelGetValue(label, spoint, &val);CHKERRQ(ierr); 1162 if (val == -1) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Cell %d in star of %d does not have a valid label", spoint, point); 1163 ierr = DMLabelGetValue(depthLabel, point, &dep);CHKERRQ(ierr); 1164 if (val > 0) { 1165 ierr = DMLabelSetValue(label, point, shift+dep);CHKERRQ(ierr); 1166 } else { 1167 ierr = DMLabelSetValue(label, point, -(shift+dep));CHKERRQ(ierr); 1168 } 1169 marked = PETSC_TRUE; 1170 break; 1171 } 1172 ierr = DMPlexRestoreTransitiveClosure(dm, point, PETSC_FALSE, &sstarSize, &sstar);CHKERRQ(ierr); 1173 if (!marked) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Point %d could not be classified", point); 1174 } 1175 } 1176 ierr = DMPlexRestoreTransitiveClosure(dm, points[p], PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1177 } 1178 ierr = ISRestoreIndices(dimIS, &points);CHKERRQ(ierr); 1179 ierr = ISDestroy(&dimIS);CHKERRQ(ierr); 1180 PetscFunctionReturn(0); 1181 } 1182 1183 #undef __FUNCT__ 1184 #define __FUNCT__ "DMPlexMarkSubmesh_Uninterpolated" 1185 /* Here we need the explicit assumption that: 1186 1187 For any marked cell, the marked vertices constitute a single face 1188 */ 1189 static PetscErrorCode DMPlexMarkSubmesh_Uninterpolated(DM dm, DMLabel vertexLabel, PetscInt value, DMLabel subpointMap, PetscInt *numFaces, PetscInt *nFV, DM subdm) 1190 { 1191 IS subvertexIS = NULL; 1192 const PetscInt *subvertices; 1193 PetscInt *pStart, *pEnd, *pMax, pSize; 1194 PetscInt depth, dim, d, numSubVerticesInitial = 0, v; 1195 PetscErrorCode ierr; 1196 1197 PetscFunctionBegin; 1198 *numFaces = 0; 1199 *nFV = 0; 1200 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 1201 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1202 pSize = PetscMax(depth, dim) + 1; 1203 ierr = PetscMalloc3(pSize,PetscInt,&pStart,pSize,PetscInt,&pEnd,pSize,PetscInt,&pMax);CHKERRQ(ierr); 1204 ierr = DMPlexGetHybridBounds(dm, depth >= 0 ? &pMax[depth] : NULL, depth>1 ? &pMax[depth-1] : NULL, depth>2 ? &pMax[1] : NULL, &pMax[0]);CHKERRQ(ierr); 1205 for (d = 0; d <= depth; ++d) { 1206 ierr = DMPlexGetDepthStratum(dm, d, &pStart[d], &pEnd[d]);CHKERRQ(ierr); 1207 if (pMax[d] >= 0) pEnd[d] = PetscMin(pEnd[d], pMax[d]); 1208 } 1209 /* Loop over initial vertices and mark all faces in the collective star() */ 1210 if (vertexLabel) {ierr = DMLabelGetStratumIS(vertexLabel, value, &subvertexIS);CHKERRQ(ierr);} 1211 if (subvertexIS) { 1212 ierr = ISGetSize(subvertexIS, &numSubVerticesInitial);CHKERRQ(ierr); 1213 ierr = ISGetIndices(subvertexIS, &subvertices);CHKERRQ(ierr); 1214 } 1215 for (v = 0; v < numSubVerticesInitial; ++v) { 1216 const PetscInt vertex = subvertices[v]; 1217 PetscInt *star = NULL; 1218 PetscInt starSize, s, numCells = 0, c; 1219 1220 ierr = DMPlexGetTransitiveClosure(dm, vertex, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1221 for (s = 0; s < starSize*2; s += 2) { 1222 const PetscInt point = star[s]; 1223 if ((point >= pStart[depth]) && (point < pEnd[depth])) star[numCells++] = point; 1224 } 1225 for (c = 0; c < numCells; ++c) { 1226 const PetscInt cell = star[c]; 1227 PetscInt *closure = NULL; 1228 PetscInt closureSize, cl; 1229 PetscInt cellLoc, numCorners = 0, faceSize = 0; 1230 1231 ierr = DMLabelGetValue(subpointMap, cell, &cellLoc);CHKERRQ(ierr); 1232 if (cellLoc == 2) continue; 1233 if (cellLoc >= 0) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Cell %d has dimension %d in the surface label", cell, cellLoc); 1234 ierr = DMPlexGetTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1235 for (cl = 0; cl < closureSize*2; cl += 2) { 1236 const PetscInt point = closure[cl]; 1237 PetscInt vertexLoc; 1238 1239 if ((point >= pStart[0]) && (point < pEnd[0])) { 1240 ++numCorners; 1241 ierr = DMLabelGetValue(vertexLabel, point, &vertexLoc);CHKERRQ(ierr); 1242 if (vertexLoc == value) closure[faceSize++] = point; 1243 } 1244 } 1245 if (!(*nFV)) {ierr = DMPlexGetNumFaceVertices(dm, dim, numCorners, nFV);CHKERRQ(ierr);} 1246 if (faceSize > *nFV) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Invalid submesh: Too many vertices %d of an element on the surface", faceSize); 1247 if (faceSize == *nFV) { 1248 const PetscInt *cells = NULL; 1249 PetscInt numCells, nc; 1250 1251 ++(*numFaces); 1252 for (cl = 0; cl < faceSize; ++cl) { 1253 ierr = DMLabelSetValue(subpointMap, closure[cl], 0);CHKERRQ(ierr); 1254 } 1255 ierr = DMPlexGetJoin(dm, faceSize, closure, &numCells, &cells);CHKERRQ(ierr); 1256 for (nc = 0; nc < numCells; ++nc) { 1257 ierr = DMLabelSetValue(subpointMap, cells[nc], 2);CHKERRQ(ierr); 1258 } 1259 ierr = DMPlexRestoreJoin(dm, faceSize, closure, &numCells, &cells);CHKERRQ(ierr); 1260 } 1261 ierr = DMPlexRestoreTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1262 } 1263 ierr = DMPlexRestoreTransitiveClosure(dm, vertex, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1264 } 1265 if (subvertexIS) { 1266 ierr = ISRestoreIndices(subvertexIS, &subvertices);CHKERRQ(ierr); 1267 } 1268 ierr = ISDestroy(&subvertexIS);CHKERRQ(ierr); 1269 ierr = PetscFree3(pStart,pEnd,pMax);CHKERRQ(ierr); 1270 PetscFunctionReturn(0); 1271 } 1272 1273 #undef __FUNCT__ 1274 #define __FUNCT__ "DMPlexMarkSubmesh_Interpolated" 1275 static PetscErrorCode DMPlexMarkSubmesh_Interpolated(DM dm, DMLabel vertexLabel, PetscInt value, DMLabel subpointMap, DM subdm) 1276 { 1277 IS subvertexIS; 1278 const PetscInt *subvertices; 1279 PetscInt *pStart, *pEnd, *pMax; 1280 PetscInt dim, d, numSubVerticesInitial = 0, v; 1281 PetscErrorCode ierr; 1282 1283 PetscFunctionBegin; 1284 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1285 ierr = PetscMalloc3(dim+1,PetscInt,&pStart,dim+1,PetscInt,&pEnd,dim+1,PetscInt,&pMax);CHKERRQ(ierr); 1286 ierr = DMPlexGetHybridBounds(dm, &pMax[dim], dim>1 ? &pMax[dim-1] : NULL, dim > 2 ? &pMax[1] : NULL, &pMax[0]);CHKERRQ(ierr); 1287 for (d = 0; d <= dim; ++d) { 1288 ierr = DMPlexGetDepthStratum(dm, d, &pStart[d], &pEnd[d]);CHKERRQ(ierr); 1289 if (pMax[d] >= 0) pEnd[d] = PetscMin(pEnd[d], pMax[d]); 1290 } 1291 /* Loop over initial vertices and mark all faces in the collective star() */ 1292 ierr = DMLabelGetStratumIS(vertexLabel, value, &subvertexIS);CHKERRQ(ierr); 1293 if (subvertexIS) { 1294 ierr = ISGetSize(subvertexIS, &numSubVerticesInitial);CHKERRQ(ierr); 1295 ierr = ISGetIndices(subvertexIS, &subvertices);CHKERRQ(ierr); 1296 } 1297 for (v = 0; v < numSubVerticesInitial; ++v) { 1298 const PetscInt vertex = subvertices[v]; 1299 PetscInt *star = NULL; 1300 PetscInt starSize, s, numFaces = 0, f; 1301 1302 ierr = DMPlexGetTransitiveClosure(dm, vertex, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1303 for (s = 0; s < starSize*2; s += 2) { 1304 const PetscInt point = star[s]; 1305 if ((point >= pStart[dim-1]) && (point < pEnd[dim-1])) star[numFaces++] = point; 1306 } 1307 for (f = 0; f < numFaces; ++f) { 1308 const PetscInt face = star[f]; 1309 PetscInt *closure = NULL; 1310 PetscInt closureSize, c; 1311 PetscInt faceLoc; 1312 1313 ierr = DMLabelGetValue(subpointMap, face, &faceLoc);CHKERRQ(ierr); 1314 if (faceLoc == dim-1) continue; 1315 if (faceLoc >= 0) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Face %d has dimension %d in the surface label", face, faceLoc); 1316 ierr = DMPlexGetTransitiveClosure(dm, face, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1317 for (c = 0; c < closureSize*2; c += 2) { 1318 const PetscInt point = closure[c]; 1319 PetscInt vertexLoc; 1320 1321 if ((point >= pStart[0]) && (point < pEnd[0])) { 1322 ierr = DMLabelGetValue(vertexLabel, point, &vertexLoc);CHKERRQ(ierr); 1323 if (vertexLoc != value) break; 1324 } 1325 } 1326 if (c == closureSize*2) { 1327 const PetscInt *support; 1328 PetscInt supportSize, s; 1329 1330 for (c = 0; c < closureSize*2; c += 2) { 1331 const PetscInt point = closure[c]; 1332 1333 for (d = 0; d < dim; ++d) { 1334 if ((point >= pStart[d]) && (point < pEnd[d])) { 1335 ierr = DMLabelSetValue(subpointMap, point, d);CHKERRQ(ierr); 1336 break; 1337 } 1338 } 1339 } 1340 ierr = DMPlexGetSupportSize(dm, face, &supportSize);CHKERRQ(ierr); 1341 ierr = DMPlexGetSupport(dm, face, &support);CHKERRQ(ierr); 1342 for (s = 0; s < supportSize; ++s) { 1343 ierr = DMLabelSetValue(subpointMap, support[s], dim);CHKERRQ(ierr); 1344 } 1345 } 1346 ierr = DMPlexRestoreTransitiveClosure(dm, face, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1347 } 1348 ierr = DMPlexRestoreTransitiveClosure(dm, vertex, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1349 } 1350 if (subvertexIS) { 1351 ierr = ISRestoreIndices(subvertexIS, &subvertices);CHKERRQ(ierr); 1352 } 1353 ierr = ISDestroy(&subvertexIS);CHKERRQ(ierr); 1354 ierr = PetscFree3(pStart,pEnd,pMax);CHKERRQ(ierr); 1355 PetscFunctionReturn(0); 1356 } 1357 1358 #undef __FUNCT__ 1359 #define __FUNCT__ "DMPlexMarkCohesiveSubmesh_Uninterpolated" 1360 static PetscErrorCode DMPlexMarkCohesiveSubmesh_Uninterpolated(DM dm, PetscBool hasLagrange, const char labelname[], PetscInt value, DMLabel subpointMap, PetscInt *numFaces, PetscInt *nFV, PetscInt *subCells[], DM subdm) 1361 { 1362 DMLabel label = NULL; 1363 const PetscInt *cone; 1364 PetscInt dim, cMax, cEnd, c, subc = 0, p, coneSize; 1365 PetscErrorCode ierr; 1366 1367 PetscFunctionBegin; 1368 *numFaces = 0; 1369 *nFV = 0; 1370 if (labelname) {ierr = DMPlexGetLabel(dm, labelname, &label);CHKERRQ(ierr);} 1371 *subCells = NULL; 1372 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1373 ierr = DMPlexGetHeightStratum(dm, 0, NULL, &cEnd);CHKERRQ(ierr); 1374 ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); 1375 if (cMax < 0) PetscFunctionReturn(0); 1376 if (label) { 1377 for (c = cMax; c < cEnd; ++c) { 1378 PetscInt val; 1379 1380 ierr = DMLabelGetValue(label, c, &val);CHKERRQ(ierr); 1381 if (val == value) { 1382 ++(*numFaces); 1383 ierr = DMPlexGetConeSize(dm, c, &coneSize);CHKERRQ(ierr); 1384 } 1385 } 1386 } else { 1387 *numFaces = cEnd - cMax; 1388 ierr = DMPlexGetConeSize(dm, cMax, &coneSize);CHKERRQ(ierr); 1389 } 1390 *nFV = hasLagrange ? coneSize/3 : coneSize/2; 1391 ierr = PetscMalloc(*numFaces *2 * sizeof(PetscInt), subCells);CHKERRQ(ierr); 1392 for (c = cMax; c < cEnd; ++c) { 1393 const PetscInt *cells; 1394 PetscInt numCells; 1395 1396 if (label) { 1397 PetscInt val; 1398 1399 ierr = DMLabelGetValue(label, c, &val);CHKERRQ(ierr); 1400 if (val != value) continue; 1401 } 1402 ierr = DMPlexGetCone(dm, c, &cone);CHKERRQ(ierr); 1403 for (p = 0; p < *nFV; ++p) { 1404 ierr = DMLabelSetValue(subpointMap, cone[p], 0);CHKERRQ(ierr); 1405 } 1406 /* Negative face */ 1407 ierr = DMPlexGetJoin(dm, *nFV, cone, &numCells, &cells);CHKERRQ(ierr); 1408 /* Not true in parallel 1409 if (numCells != 2) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive cells should separate two cells"); */ 1410 for (p = 0; p < numCells; ++p) { 1411 ierr = DMLabelSetValue(subpointMap, cells[p], 2);CHKERRQ(ierr); 1412 (*subCells)[subc++] = cells[p]; 1413 } 1414 ierr = DMPlexRestoreJoin(dm, *nFV, cone, &numCells, &cells);CHKERRQ(ierr); 1415 /* Positive face is not included */ 1416 } 1417 PetscFunctionReturn(0); 1418 } 1419 1420 #undef __FUNCT__ 1421 #define __FUNCT__ "DMPlexMarkCohesiveSubmesh_Interpolated" 1422 static PetscErrorCode DMPlexMarkCohesiveSubmesh_Interpolated(DM dm, PetscBool hasLagrange, const char labelname[], PetscInt value, DMLabel subpointMap, DM subdm) 1423 { 1424 DMLabel label = NULL; 1425 PetscInt *pStart, *pEnd; 1426 PetscInt dim, cMax, cEnd, c, d; 1427 PetscErrorCode ierr; 1428 1429 PetscFunctionBegin; 1430 if (labelname) {ierr = DMPlexGetLabel(dm, labelname, &label);CHKERRQ(ierr);} 1431 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1432 ierr = DMPlexGetHeightStratum(dm, 0, NULL, &cEnd);CHKERRQ(ierr); 1433 ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); 1434 if (cMax < 0) PetscFunctionReturn(0); 1435 ierr = PetscMalloc2(dim+1,PetscInt,&pStart,dim+1,PetscInt,&pEnd);CHKERRQ(ierr); 1436 for (d = 0; d <= dim; ++d) { 1437 ierr = DMPlexGetDepthStratum(dm, d, &pStart[d], &pEnd[d]);CHKERRQ(ierr); 1438 } 1439 for (c = cMax; c < cEnd; ++c) { 1440 const PetscInt *cone; 1441 PetscInt *closure = NULL; 1442 PetscInt coneSize, closureSize, cl; 1443 1444 if (label) { 1445 PetscInt val; 1446 1447 ierr = DMLabelGetValue(label, c, &val);CHKERRQ(ierr); 1448 if (val != value) continue; 1449 } 1450 ierr = DMPlexGetConeSize(dm, c, &coneSize);CHKERRQ(ierr); 1451 if (hasLagrange) { 1452 if (coneSize != 3) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive cells should separate two cells"); 1453 } else { 1454 if (coneSize != 2) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive cells should separate two cells"); 1455 } 1456 /* Negative face */ 1457 ierr = DMPlexGetCone(dm, c, &cone);CHKERRQ(ierr); 1458 ierr = DMPlexGetTransitiveClosure(dm, cone[0], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1459 for (cl = 0; cl < closureSize*2; cl += 2) { 1460 const PetscInt point = closure[cl]; 1461 1462 for (d = 0; d <= dim; ++d) { 1463 if ((point >= pStart[d]) && (point < pEnd[d])) { 1464 ierr = DMLabelSetValue(subpointMap, point, d);CHKERRQ(ierr); 1465 break; 1466 } 1467 } 1468 } 1469 ierr = DMPlexRestoreTransitiveClosure(dm, cone[0], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1470 /* Cells -- positive face is not included */ 1471 for (cl = 0; cl < 1; ++cl) { 1472 const PetscInt *support; 1473 PetscInt supportSize, s; 1474 1475 ierr = DMPlexGetSupportSize(dm, cone[cl], &supportSize);CHKERRQ(ierr); 1476 if (supportSize != 2) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive faces should separate two cells"); 1477 ierr = DMPlexGetSupport(dm, cone[cl], &support);CHKERRQ(ierr); 1478 for (s = 0; s < supportSize; ++s) { 1479 ierr = DMLabelSetValue(subpointMap, support[s], dim);CHKERRQ(ierr); 1480 } 1481 } 1482 } 1483 ierr = PetscFree2(pStart, pEnd);CHKERRQ(ierr); 1484 PetscFunctionReturn(0); 1485 } 1486 1487 #undef __FUNCT__ 1488 #define __FUNCT__ "DMPlexGetFaceOrientation" 1489 PetscErrorCode DMPlexGetFaceOrientation(DM dm, PetscInt cell, PetscInt numCorners, PetscInt indices[], PetscInt oppositeVertex, PetscInt origVertices[], PetscInt faceVertices[], PetscBool *posOriented) 1490 { 1491 MPI_Comm comm; 1492 PetscBool posOrient = PETSC_FALSE; 1493 const PetscInt debug = 0; 1494 PetscInt cellDim, faceSize, f; 1495 PetscErrorCode ierr; 1496 1497 PetscFunctionBegin; 1498 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 1499 ierr = DMPlexGetDimension(dm, &cellDim);CHKERRQ(ierr); 1500 if (debug) {PetscPrintf(comm, "cellDim: %d numCorners: %d\n", cellDim, numCorners);CHKERRQ(ierr);} 1501 1502 if (cellDim == 1 && numCorners == 2) { 1503 /* Triangle */ 1504 faceSize = numCorners-1; 1505 posOrient = !(oppositeVertex%2) ? PETSC_TRUE : PETSC_FALSE; 1506 } else if (cellDim == 2 && numCorners == 3) { 1507 /* Triangle */ 1508 faceSize = numCorners-1; 1509 posOrient = !(oppositeVertex%2) ? PETSC_TRUE : PETSC_FALSE; 1510 } else if (cellDim == 3 && numCorners == 4) { 1511 /* Tetrahedron */ 1512 faceSize = numCorners-1; 1513 posOrient = (oppositeVertex%2) ? PETSC_TRUE : PETSC_FALSE; 1514 } else if (cellDim == 1 && numCorners == 3) { 1515 /* Quadratic line */ 1516 faceSize = 1; 1517 posOrient = PETSC_TRUE; 1518 } else if (cellDim == 2 && numCorners == 4) { 1519 /* Quads */ 1520 faceSize = 2; 1521 if ((indices[1] > indices[0]) && (indices[1] - indices[0] == 1)) { 1522 posOrient = PETSC_TRUE; 1523 } else if ((indices[0] == 3) && (indices[1] == 0)) { 1524 posOrient = PETSC_TRUE; 1525 } else { 1526 if (((indices[0] > indices[1]) && (indices[0] - indices[1] == 1)) || ((indices[0] == 0) && (indices[1] == 3))) { 1527 posOrient = PETSC_FALSE; 1528 } else SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid quad crossedge"); 1529 } 1530 } else if (cellDim == 2 && numCorners == 6) { 1531 /* Quadratic triangle (I hate this) */ 1532 /* Edges are determined by the first 2 vertices (corners of edges) */ 1533 const PetscInt faceSizeTri = 3; 1534 PetscInt sortedIndices[3], i, iFace; 1535 PetscBool found = PETSC_FALSE; 1536 PetscInt faceVerticesTriSorted[9] = { 1537 0, 3, 4, /* bottom */ 1538 1, 4, 5, /* right */ 1539 2, 3, 5, /* left */ 1540 }; 1541 PetscInt faceVerticesTri[9] = { 1542 0, 3, 4, /* bottom */ 1543 1, 4, 5, /* right */ 1544 2, 5, 3, /* left */ 1545 }; 1546 1547 faceSize = faceSizeTri; 1548 for (i = 0; i < faceSizeTri; ++i) sortedIndices[i] = indices[i]; 1549 ierr = PetscSortInt(faceSizeTri, sortedIndices);CHKERRQ(ierr); 1550 for (iFace = 0; iFace < 3; ++iFace) { 1551 const PetscInt ii = iFace*faceSizeTri; 1552 PetscInt fVertex, cVertex; 1553 1554 if ((sortedIndices[0] == faceVerticesTriSorted[ii+0]) && 1555 (sortedIndices[1] == faceVerticesTriSorted[ii+1])) { 1556 for (fVertex = 0; fVertex < faceSizeTri; ++fVertex) { 1557 for (cVertex = 0; cVertex < faceSizeTri; ++cVertex) { 1558 if (indices[cVertex] == faceVerticesTri[ii+fVertex]) { 1559 faceVertices[fVertex] = origVertices[cVertex]; 1560 break; 1561 } 1562 } 1563 } 1564 found = PETSC_TRUE; 1565 break; 1566 } 1567 } 1568 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid tri crossface"); 1569 if (posOriented) *posOriented = PETSC_TRUE; 1570 PetscFunctionReturn(0); 1571 } else if (cellDim == 2 && numCorners == 9) { 1572 /* Quadratic quad (I hate this) */ 1573 /* Edges are determined by the first 2 vertices (corners of edges) */ 1574 const PetscInt faceSizeQuad = 3; 1575 PetscInt sortedIndices[3], i, iFace; 1576 PetscBool found = PETSC_FALSE; 1577 PetscInt faceVerticesQuadSorted[12] = { 1578 0, 1, 4, /* bottom */ 1579 1, 2, 5, /* right */ 1580 2, 3, 6, /* top */ 1581 0, 3, 7, /* left */ 1582 }; 1583 PetscInt faceVerticesQuad[12] = { 1584 0, 1, 4, /* bottom */ 1585 1, 2, 5, /* right */ 1586 2, 3, 6, /* top */ 1587 3, 0, 7, /* left */ 1588 }; 1589 1590 faceSize = faceSizeQuad; 1591 for (i = 0; i < faceSizeQuad; ++i) sortedIndices[i] = indices[i]; 1592 ierr = PetscSortInt(faceSizeQuad, sortedIndices);CHKERRQ(ierr); 1593 for (iFace = 0; iFace < 4; ++iFace) { 1594 const PetscInt ii = iFace*faceSizeQuad; 1595 PetscInt fVertex, cVertex; 1596 1597 if ((sortedIndices[0] == faceVerticesQuadSorted[ii+0]) && 1598 (sortedIndices[1] == faceVerticesQuadSorted[ii+1])) { 1599 for (fVertex = 0; fVertex < faceSizeQuad; ++fVertex) { 1600 for (cVertex = 0; cVertex < faceSizeQuad; ++cVertex) { 1601 if (indices[cVertex] == faceVerticesQuad[ii+fVertex]) { 1602 faceVertices[fVertex] = origVertices[cVertex]; 1603 break; 1604 } 1605 } 1606 } 1607 found = PETSC_TRUE; 1608 break; 1609 } 1610 } 1611 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid quad crossface"); 1612 if (posOriented) *posOriented = PETSC_TRUE; 1613 PetscFunctionReturn(0); 1614 } else if (cellDim == 3 && numCorners == 8) { 1615 /* Hexes 1616 A hex is two oriented quads with the normal of the first 1617 pointing up at the second. 1618 1619 7---6 1620 /| /| 1621 4---5 | 1622 | 1-|-2 1623 |/ |/ 1624 0---3 1625 1626 Faces are determined by the first 4 vertices (corners of faces) */ 1627 const PetscInt faceSizeHex = 4; 1628 PetscInt sortedIndices[4], i, iFace; 1629 PetscBool found = PETSC_FALSE; 1630 PetscInt faceVerticesHexSorted[24] = { 1631 0, 1, 2, 3, /* bottom */ 1632 4, 5, 6, 7, /* top */ 1633 0, 3, 4, 5, /* front */ 1634 2, 3, 5, 6, /* right */ 1635 1, 2, 6, 7, /* back */ 1636 0, 1, 4, 7, /* left */ 1637 }; 1638 PetscInt faceVerticesHex[24] = { 1639 1, 2, 3, 0, /* bottom */ 1640 4, 5, 6, 7, /* top */ 1641 0, 3, 5, 4, /* front */ 1642 3, 2, 6, 5, /* right */ 1643 2, 1, 7, 6, /* back */ 1644 1, 0, 4, 7, /* left */ 1645 }; 1646 1647 faceSize = faceSizeHex; 1648 for (i = 0; i < faceSizeHex; ++i) sortedIndices[i] = indices[i]; 1649 ierr = PetscSortInt(faceSizeHex, sortedIndices);CHKERRQ(ierr); 1650 for (iFace = 0; iFace < 6; ++iFace) { 1651 const PetscInt ii = iFace*faceSizeHex; 1652 PetscInt fVertex, cVertex; 1653 1654 if ((sortedIndices[0] == faceVerticesHexSorted[ii+0]) && 1655 (sortedIndices[1] == faceVerticesHexSorted[ii+1]) && 1656 (sortedIndices[2] == faceVerticesHexSorted[ii+2]) && 1657 (sortedIndices[3] == faceVerticesHexSorted[ii+3])) { 1658 for (fVertex = 0; fVertex < faceSizeHex; ++fVertex) { 1659 for (cVertex = 0; cVertex < faceSizeHex; ++cVertex) { 1660 if (indices[cVertex] == faceVerticesHex[ii+fVertex]) { 1661 faceVertices[fVertex] = origVertices[cVertex]; 1662 break; 1663 } 1664 } 1665 } 1666 found = PETSC_TRUE; 1667 break; 1668 } 1669 } 1670 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid hex crossface"); 1671 if (posOriented) *posOriented = PETSC_TRUE; 1672 PetscFunctionReturn(0); 1673 } else if (cellDim == 3 && numCorners == 10) { 1674 /* Quadratic tet */ 1675 /* Faces are determined by the first 3 vertices (corners of faces) */ 1676 const PetscInt faceSizeTet = 6; 1677 PetscInt sortedIndices[6], i, iFace; 1678 PetscBool found = PETSC_FALSE; 1679 PetscInt faceVerticesTetSorted[24] = { 1680 0, 1, 2, 6, 7, 8, /* bottom */ 1681 0, 3, 4, 6, 7, 9, /* front */ 1682 1, 4, 5, 7, 8, 9, /* right */ 1683 2, 3, 5, 6, 8, 9, /* left */ 1684 }; 1685 PetscInt faceVerticesTet[24] = { 1686 0, 1, 2, 6, 7, 8, /* bottom */ 1687 0, 4, 3, 6, 7, 9, /* front */ 1688 1, 5, 4, 7, 8, 9, /* right */ 1689 2, 3, 5, 8, 6, 9, /* left */ 1690 }; 1691 1692 faceSize = faceSizeTet; 1693 for (i = 0; i < faceSizeTet; ++i) sortedIndices[i] = indices[i]; 1694 ierr = PetscSortInt(faceSizeTet, sortedIndices);CHKERRQ(ierr); 1695 for (iFace=0; iFace < 4; ++iFace) { 1696 const PetscInt ii = iFace*faceSizeTet; 1697 PetscInt fVertex, cVertex; 1698 1699 if ((sortedIndices[0] == faceVerticesTetSorted[ii+0]) && 1700 (sortedIndices[1] == faceVerticesTetSorted[ii+1]) && 1701 (sortedIndices[2] == faceVerticesTetSorted[ii+2]) && 1702 (sortedIndices[3] == faceVerticesTetSorted[ii+3])) { 1703 for (fVertex = 0; fVertex < faceSizeTet; ++fVertex) { 1704 for (cVertex = 0; cVertex < faceSizeTet; ++cVertex) { 1705 if (indices[cVertex] == faceVerticesTet[ii+fVertex]) { 1706 faceVertices[fVertex] = origVertices[cVertex]; 1707 break; 1708 } 1709 } 1710 } 1711 found = PETSC_TRUE; 1712 break; 1713 } 1714 } 1715 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid tet crossface"); 1716 if (posOriented) *posOriented = PETSC_TRUE; 1717 PetscFunctionReturn(0); 1718 } else if (cellDim == 3 && numCorners == 27) { 1719 /* Quadratic hexes (I hate this) 1720 A hex is two oriented quads with the normal of the first 1721 pointing up at the second. 1722 1723 7---6 1724 /| /| 1725 4---5 | 1726 | 3-|-2 1727 |/ |/ 1728 0---1 1729 1730 Faces are determined by the first 4 vertices (corners of faces) */ 1731 const PetscInt faceSizeQuadHex = 9; 1732 PetscInt sortedIndices[9], i, iFace; 1733 PetscBool found = PETSC_FALSE; 1734 PetscInt faceVerticesQuadHexSorted[54] = { 1735 0, 1, 2, 3, 8, 9, 10, 11, 24, /* bottom */ 1736 4, 5, 6, 7, 12, 13, 14, 15, 25, /* top */ 1737 0, 1, 4, 5, 8, 12, 16, 17, 22, /* front */ 1738 1, 2, 5, 6, 9, 13, 17, 18, 21, /* right */ 1739 2, 3, 6, 7, 10, 14, 18, 19, 23, /* back */ 1740 0, 3, 4, 7, 11, 15, 16, 19, 20, /* left */ 1741 }; 1742 PetscInt faceVerticesQuadHex[54] = { 1743 3, 2, 1, 0, 10, 9, 8, 11, 24, /* bottom */ 1744 4, 5, 6, 7, 12, 13, 14, 15, 25, /* top */ 1745 0, 1, 5, 4, 8, 17, 12, 16, 22, /* front */ 1746 1, 2, 6, 5, 9, 18, 13, 17, 21, /* right */ 1747 2, 3, 7, 6, 10, 19, 14, 18, 23, /* back */ 1748 3, 0, 4, 7, 11, 16, 15, 19, 20 /* left */ 1749 }; 1750 1751 faceSize = faceSizeQuadHex; 1752 for (i = 0; i < faceSizeQuadHex; ++i) sortedIndices[i] = indices[i]; 1753 ierr = PetscSortInt(faceSizeQuadHex, sortedIndices);CHKERRQ(ierr); 1754 for (iFace = 0; iFace < 6; ++iFace) { 1755 const PetscInt ii = iFace*faceSizeQuadHex; 1756 PetscInt fVertex, cVertex; 1757 1758 if ((sortedIndices[0] == faceVerticesQuadHexSorted[ii+0]) && 1759 (sortedIndices[1] == faceVerticesQuadHexSorted[ii+1]) && 1760 (sortedIndices[2] == faceVerticesQuadHexSorted[ii+2]) && 1761 (sortedIndices[3] == faceVerticesQuadHexSorted[ii+3])) { 1762 for (fVertex = 0; fVertex < faceSizeQuadHex; ++fVertex) { 1763 for (cVertex = 0; cVertex < faceSizeQuadHex; ++cVertex) { 1764 if (indices[cVertex] == faceVerticesQuadHex[ii+fVertex]) { 1765 faceVertices[fVertex] = origVertices[cVertex]; 1766 break; 1767 } 1768 } 1769 } 1770 found = PETSC_TRUE; 1771 break; 1772 } 1773 } 1774 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid hex crossface"); 1775 if (posOriented) *posOriented = PETSC_TRUE; 1776 PetscFunctionReturn(0); 1777 } else SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Unknown cell type for faceOrientation()."); 1778 if (!posOrient) { 1779 if (debug) {ierr = PetscPrintf(comm, " Reversing initial face orientation\n");CHKERRQ(ierr);} 1780 for (f = 0; f < faceSize; ++f) faceVertices[f] = origVertices[faceSize-1 - f]; 1781 } else { 1782 if (debug) {ierr = PetscPrintf(comm, " Keeping initial face orientation\n");CHKERRQ(ierr);} 1783 for (f = 0; f < faceSize; ++f) faceVertices[f] = origVertices[f]; 1784 } 1785 if (posOriented) *posOriented = posOrient; 1786 PetscFunctionReturn(0); 1787 } 1788 1789 #undef __FUNCT__ 1790 #define __FUNCT__ "DMPlexGetOrientedFace" 1791 /* 1792 Given a cell and a face, as a set of vertices, 1793 return the oriented face, as a set of vertices, in faceVertices 1794 The orientation is such that the face normal points out of the cell 1795 */ 1796 PetscErrorCode DMPlexGetOrientedFace(DM dm, PetscInt cell, PetscInt faceSize, const PetscInt face[], PetscInt numCorners, PetscInt indices[], PetscInt origVertices[], PetscInt faceVertices[], PetscBool *posOriented) 1797 { 1798 const PetscInt *cone = NULL; 1799 PetscInt coneSize, v, f, v2; 1800 PetscInt oppositeVertex = -1; 1801 PetscErrorCode ierr; 1802 1803 PetscFunctionBegin; 1804 ierr = DMPlexGetConeSize(dm, cell, &coneSize);CHKERRQ(ierr); 1805 ierr = DMPlexGetCone(dm, cell, &cone);CHKERRQ(ierr); 1806 for (v = 0, v2 = 0; v < coneSize; ++v) { 1807 PetscBool found = PETSC_FALSE; 1808 1809 for (f = 0; f < faceSize; ++f) { 1810 if (face[f] == cone[v]) { 1811 found = PETSC_TRUE; break; 1812 } 1813 } 1814 if (found) { 1815 indices[v2] = v; 1816 origVertices[v2] = cone[v]; 1817 ++v2; 1818 } else { 1819 oppositeVertex = v; 1820 } 1821 } 1822 ierr = DMPlexGetFaceOrientation(dm, cell, numCorners, indices, oppositeVertex, origVertices, faceVertices, posOriented);CHKERRQ(ierr); 1823 PetscFunctionReturn(0); 1824 } 1825 1826 #undef __FUNCT__ 1827 #define __FUNCT__ "DMPlexInsertFace_Internal" 1828 /* 1829 DMPlexInsertFace_Internal - Puts a face into the mesh 1830 1831 Not collective 1832 1833 Input Parameters: 1834 + dm - The DMPlex 1835 . numFaceVertex - The number of vertices in the face 1836 . faceVertices - The vertices in the face for dm 1837 . subfaceVertices - The vertices in the face for subdm 1838 . numCorners - The number of vertices in the cell 1839 . cell - A cell in dm containing the face 1840 . subcell - A cell in subdm containing the face 1841 . firstFace - First face in the mesh 1842 - newFacePoint - Next face in the mesh 1843 1844 Output Parameters: 1845 . newFacePoint - Contains next face point number on input, updated on output 1846 1847 Level: developer 1848 */ 1849 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) 1850 { 1851 MPI_Comm comm; 1852 DM_Plex *submesh = (DM_Plex*) subdm->data; 1853 const PetscInt *faces; 1854 PetscInt numFaces, coneSize; 1855 PetscErrorCode ierr; 1856 1857 PetscFunctionBegin; 1858 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 1859 ierr = DMPlexGetConeSize(subdm, subcell, &coneSize);CHKERRQ(ierr); 1860 if (coneSize != 1) SETERRQ2(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cone size of cell %d is %d != 1", cell, coneSize); 1861 #if 0 1862 /* Cannot use this because support() has not been constructed yet */ 1863 ierr = DMPlexGetJoin(subdm, numFaceVertices, subfaceVertices, &numFaces, &faces);CHKERRQ(ierr); 1864 #else 1865 { 1866 PetscInt f; 1867 1868 numFaces = 0; 1869 ierr = DMGetWorkArray(subdm, 1, PETSC_INT, (void **) &faces);CHKERRQ(ierr); 1870 for (f = firstFace; f < *newFacePoint; ++f) { 1871 PetscInt dof, off, d; 1872 1873 ierr = PetscSectionGetDof(submesh->coneSection, f, &dof);CHKERRQ(ierr); 1874 ierr = PetscSectionGetOffset(submesh->coneSection, f, &off);CHKERRQ(ierr); 1875 /* Yes, I know this is quadratic, but I expect the sizes to be <5 */ 1876 for (d = 0; d < dof; ++d) { 1877 const PetscInt p = submesh->cones[off+d]; 1878 PetscInt v; 1879 1880 for (v = 0; v < numFaceVertices; ++v) { 1881 if (subfaceVertices[v] == p) break; 1882 } 1883 if (v == numFaceVertices) break; 1884 } 1885 if (d == dof) { 1886 numFaces = 1; 1887 ((PetscInt*) faces)[0] = f; 1888 } 1889 } 1890 } 1891 #endif 1892 if (numFaces > 1) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Vertex set had %d faces, not one", numFaces); 1893 else if (numFaces == 1) { 1894 /* Add the other cell neighbor for this face */ 1895 ierr = DMPlexSetCone(subdm, subcell, faces);CHKERRQ(ierr); 1896 } else { 1897 PetscInt *indices, *origVertices, *orientedVertices, *orientedSubVertices, v, ov; 1898 PetscBool posOriented; 1899 1900 ierr = DMGetWorkArray(subdm, 4*numFaceVertices * sizeof(PetscInt), PETSC_INT, &orientedVertices);CHKERRQ(ierr); 1901 origVertices = &orientedVertices[numFaceVertices]; 1902 indices = &orientedVertices[numFaceVertices*2]; 1903 orientedSubVertices = &orientedVertices[numFaceVertices*3]; 1904 ierr = DMPlexGetOrientedFace(dm, cell, numFaceVertices, faceVertices, numCorners, indices, origVertices, orientedVertices, &posOriented);CHKERRQ(ierr); 1905 /* TODO: I know that routine should return a permutation, not the indices */ 1906 for (v = 0; v < numFaceVertices; ++v) { 1907 const PetscInt vertex = faceVertices[v], subvertex = subfaceVertices[v]; 1908 for (ov = 0; ov < numFaceVertices; ++ov) { 1909 if (orientedVertices[ov] == vertex) { 1910 orientedSubVertices[ov] = subvertex; 1911 break; 1912 } 1913 } 1914 if (ov == numFaceVertices) SETERRQ1(comm, PETSC_ERR_PLIB, "Could not find face vertex %d in orientated set", vertex); 1915 } 1916 ierr = DMPlexSetCone(subdm, *newFacePoint, orientedSubVertices);CHKERRQ(ierr); 1917 ierr = DMPlexSetCone(subdm, subcell, newFacePoint);CHKERRQ(ierr); 1918 ierr = DMRestoreWorkArray(subdm, 4*numFaceVertices * sizeof(PetscInt), PETSC_INT, &orientedVertices);CHKERRQ(ierr); 1919 ++(*newFacePoint); 1920 } 1921 #if 0 1922 ierr = DMPlexRestoreJoin(subdm, numFaceVertices, subfaceVertices, &numFaces, &faces);CHKERRQ(ierr); 1923 #else 1924 ierr = DMRestoreWorkArray(subdm, 1, PETSC_INT, (void **) &faces);CHKERRQ(ierr); 1925 #endif 1926 PetscFunctionReturn(0); 1927 } 1928 1929 #undef __FUNCT__ 1930 #define __FUNCT__ "DMPlexCreateSubmesh_Uninterpolated" 1931 static PetscErrorCode DMPlexCreateSubmesh_Uninterpolated(DM dm, const char vertexLabelName[], PetscInt value, DM subdm) 1932 { 1933 MPI_Comm comm; 1934 DMLabel vertexLabel, subpointMap; 1935 IS subvertexIS, subcellIS; 1936 const PetscInt *subVertices, *subCells; 1937 PetscInt numSubVertices, firstSubVertex, numSubCells; 1938 PetscInt *subface, maxConeSize, numSubFaces = 0, firstSubFace, newFacePoint, nFV = 0; 1939 PetscInt vStart, vEnd, c, f; 1940 PetscErrorCode ierr; 1941 1942 PetscFunctionBegin; 1943 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 1944 /* Create subpointMap which marks the submesh */ 1945 ierr = DMLabelCreate("subpoint_map", &subpointMap);CHKERRQ(ierr); 1946 ierr = DMPlexSetSubpointMap(subdm, subpointMap);CHKERRQ(ierr); 1947 ierr = DMLabelDestroy(&subpointMap);CHKERRQ(ierr); 1948 if (vertexLabelName) { 1949 ierr = DMPlexGetLabel(dm, vertexLabelName, &vertexLabel);CHKERRQ(ierr); 1950 ierr = DMPlexMarkSubmesh_Uninterpolated(dm, vertexLabel, value, subpointMap, &numSubFaces, &nFV, subdm);CHKERRQ(ierr); 1951 } 1952 /* Setup chart */ 1953 ierr = DMLabelGetStratumSize(subpointMap, 0, &numSubVertices);CHKERRQ(ierr); 1954 ierr = DMLabelGetStratumSize(subpointMap, 2, &numSubCells);CHKERRQ(ierr); 1955 ierr = DMPlexSetChart(subdm, 0, numSubCells+numSubFaces+numSubVertices);CHKERRQ(ierr); 1956 ierr = DMPlexSetVTKCellHeight(subdm, 1);CHKERRQ(ierr); 1957 /* Set cone sizes */ 1958 firstSubVertex = numSubCells; 1959 firstSubFace = numSubCells+numSubVertices; 1960 newFacePoint = firstSubFace; 1961 ierr = DMLabelGetStratumIS(subpointMap, 0, &subvertexIS);CHKERRQ(ierr); 1962 if (subvertexIS) {ierr = ISGetIndices(subvertexIS, &subVertices);CHKERRQ(ierr);} 1963 ierr = DMLabelGetStratumIS(subpointMap, 2, &subcellIS);CHKERRQ(ierr); 1964 if (subcellIS) {ierr = ISGetIndices(subcellIS, &subCells);CHKERRQ(ierr);} 1965 for (c = 0; c < numSubCells; ++c) { 1966 ierr = DMPlexSetConeSize(subdm, c, 1);CHKERRQ(ierr); 1967 } 1968 for (f = firstSubFace; f < firstSubFace+numSubFaces; ++f) { 1969 ierr = DMPlexSetConeSize(subdm, f, nFV);CHKERRQ(ierr); 1970 } 1971 ierr = DMSetUp(subdm);CHKERRQ(ierr); 1972 /* Create face cones */ 1973 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 1974 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, NULL);CHKERRQ(ierr); 1975 ierr = DMGetWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);CHKERRQ(ierr); 1976 for (c = 0; c < numSubCells; ++c) { 1977 const PetscInt cell = subCells[c]; 1978 const PetscInt subcell = c; 1979 PetscInt *closure = NULL; 1980 PetscInt closureSize, cl, numCorners = 0, faceSize = 0; 1981 1982 ierr = DMPlexGetTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1983 for (cl = 0; cl < closureSize*2; cl += 2) { 1984 const PetscInt point = closure[cl]; 1985 PetscInt subVertex; 1986 1987 if ((point >= vStart) && (point < vEnd)) { 1988 ++numCorners; 1989 ierr = PetscFindInt(point, numSubVertices, subVertices, &subVertex);CHKERRQ(ierr); 1990 if (subVertex >= 0) { 1991 closure[faceSize] = point; 1992 subface[faceSize] = firstSubVertex+subVertex; 1993 ++faceSize; 1994 } 1995 } 1996 } 1997 if (faceSize > nFV) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Invalid submesh: Too many vertices %d of an element on the surface", faceSize); 1998 if (faceSize == nFV) { 1999 ierr = DMPlexInsertFace_Internal(dm, subdm, faceSize, closure, subface, numCorners, cell, subcell, firstSubFace, &newFacePoint);CHKERRQ(ierr); 2000 } 2001 ierr = DMPlexRestoreTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 2002 } 2003 ierr = DMRestoreWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);CHKERRQ(ierr); 2004 ierr = DMPlexSymmetrize(subdm);CHKERRQ(ierr); 2005 ierr = DMPlexStratify(subdm);CHKERRQ(ierr); 2006 /* Build coordinates */ 2007 { 2008 PetscSection coordSection, subCoordSection; 2009 Vec coordinates, subCoordinates; 2010 PetscScalar *coords, *subCoords; 2011 PetscInt numComp, coordSize, v; 2012 2013 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2014 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 2015 ierr = DMPlexGetCoordinateSection(subdm, &subCoordSection);CHKERRQ(ierr); 2016 ierr = PetscSectionSetNumFields(subCoordSection, 1);CHKERRQ(ierr); 2017 ierr = PetscSectionGetFieldComponents(coordSection, 0, &numComp);CHKERRQ(ierr); 2018 ierr = PetscSectionSetFieldComponents(subCoordSection, 0, numComp);CHKERRQ(ierr); 2019 ierr = PetscSectionSetChart(subCoordSection, firstSubVertex, firstSubVertex+numSubVertices);CHKERRQ(ierr); 2020 for (v = 0; v < numSubVertices; ++v) { 2021 const PetscInt vertex = subVertices[v]; 2022 const PetscInt subvertex = firstSubVertex+v; 2023 PetscInt dof; 2024 2025 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2026 ierr = PetscSectionSetDof(subCoordSection, subvertex, dof);CHKERRQ(ierr); 2027 ierr = PetscSectionSetFieldDof(subCoordSection, subvertex, 0, dof);CHKERRQ(ierr); 2028 } 2029 ierr = PetscSectionSetUp(subCoordSection);CHKERRQ(ierr); 2030 ierr = PetscSectionGetStorageSize(subCoordSection, &coordSize);CHKERRQ(ierr); 2031 ierr = VecCreate(comm, &subCoordinates);CHKERRQ(ierr); 2032 ierr = VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2033 ierr = VecSetFromOptions(subCoordinates);CHKERRQ(ierr); 2034 if (coordSize) { 2035 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2036 ierr = VecGetArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2037 for (v = 0; v < numSubVertices; ++v) { 2038 const PetscInt vertex = subVertices[v]; 2039 const PetscInt subvertex = firstSubVertex+v; 2040 PetscInt dof, off, sdof, soff, d; 2041 2042 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2043 ierr = PetscSectionGetOffset(coordSection, vertex, &off);CHKERRQ(ierr); 2044 ierr = PetscSectionGetDof(subCoordSection, subvertex, &sdof);CHKERRQ(ierr); 2045 ierr = PetscSectionGetOffset(subCoordSection, subvertex, &soff);CHKERRQ(ierr); 2046 if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof); 2047 for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d]; 2048 } 2049 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2050 ierr = VecRestoreArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2051 } 2052 ierr = DMSetCoordinatesLocal(subdm, subCoordinates);CHKERRQ(ierr); 2053 ierr = VecDestroy(&subCoordinates);CHKERRQ(ierr); 2054 } 2055 /* Cleanup */ 2056 if (subvertexIS) {ierr = ISRestoreIndices(subvertexIS, &subVertices);CHKERRQ(ierr);} 2057 ierr = ISDestroy(&subvertexIS);CHKERRQ(ierr); 2058 if (subcellIS) {ierr = ISRestoreIndices(subcellIS, &subCells);CHKERRQ(ierr);} 2059 ierr = ISDestroy(&subcellIS);CHKERRQ(ierr); 2060 PetscFunctionReturn(0); 2061 } 2062 2063 #undef __FUNCT__ 2064 #define __FUNCT__ "DMPlexCreateSubmesh_Interpolated" 2065 static PetscErrorCode DMPlexCreateSubmesh_Interpolated(DM dm, const char vertexLabelName[], PetscInt value, DM subdm) 2066 { 2067 MPI_Comm comm; 2068 DMLabel subpointMap, vertexLabel; 2069 IS *subpointIS; 2070 const PetscInt **subpoints; 2071 PetscInt *numSubPoints, *firstSubPoint, *coneNew, *coneONew; 2072 PetscInt totSubPoints = 0, maxConeSize, dim, p, d, v; 2073 PetscErrorCode ierr; 2074 2075 PetscFunctionBegin; 2076 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 2077 /* Create subpointMap which marks the submesh */ 2078 ierr = DMLabelCreate("subpoint_map", &subpointMap);CHKERRQ(ierr); 2079 ierr = DMPlexSetSubpointMap(subdm, subpointMap);CHKERRQ(ierr); 2080 ierr = DMLabelDestroy(&subpointMap);CHKERRQ(ierr); 2081 if (vertexLabelName) { 2082 ierr = DMPlexGetLabel(dm, vertexLabelName, &vertexLabel);CHKERRQ(ierr); 2083 ierr = DMPlexMarkSubmesh_Interpolated(dm, vertexLabel, value, subpointMap, subdm);CHKERRQ(ierr); 2084 } 2085 /* Setup chart */ 2086 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 2087 ierr = PetscMalloc4(dim+1,PetscInt,&numSubPoints,dim+1,PetscInt,&firstSubPoint,dim+1,IS,&subpointIS,dim+1,const PetscInt *,&subpoints);CHKERRQ(ierr); 2088 for (d = 0; d <= dim; ++d) { 2089 ierr = DMLabelGetStratumSize(subpointMap, d, &numSubPoints[d]);CHKERRQ(ierr); 2090 totSubPoints += numSubPoints[d]; 2091 } 2092 ierr = DMPlexSetChart(subdm, 0, totSubPoints);CHKERRQ(ierr); 2093 ierr = DMPlexSetVTKCellHeight(subdm, 1);CHKERRQ(ierr); 2094 /* Set cone sizes */ 2095 firstSubPoint[dim] = 0; 2096 firstSubPoint[0] = firstSubPoint[dim] + numSubPoints[dim]; 2097 if (dim > 1) {firstSubPoint[dim-1] = firstSubPoint[0] + numSubPoints[0];} 2098 if (dim > 2) {firstSubPoint[dim-2] = firstSubPoint[dim-1] + numSubPoints[dim-1];} 2099 for (d = 0; d <= dim; ++d) { 2100 ierr = DMLabelGetStratumIS(subpointMap, d, &subpointIS[d]);CHKERRQ(ierr); 2101 ierr = ISGetIndices(subpointIS[d], &subpoints[d]);CHKERRQ(ierr); 2102 } 2103 for (d = 0; d <= dim; ++d) { 2104 for (p = 0; p < numSubPoints[d]; ++p) { 2105 const PetscInt point = subpoints[d][p]; 2106 const PetscInt subpoint = firstSubPoint[d] + p; 2107 const PetscInt *cone; 2108 PetscInt coneSize, coneSizeNew, c, val; 2109 2110 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 2111 ierr = DMPlexSetConeSize(subdm, subpoint, coneSize);CHKERRQ(ierr); 2112 if (d == dim) { 2113 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 2114 for (c = 0, coneSizeNew = 0; c < coneSize; ++c) { 2115 ierr = DMLabelGetValue(subpointMap, cone[c], &val);CHKERRQ(ierr); 2116 if (val >= 0) coneSizeNew++; 2117 } 2118 ierr = DMPlexSetConeSize(subdm, subpoint, coneSizeNew);CHKERRQ(ierr); 2119 } 2120 } 2121 } 2122 ierr = DMSetUp(subdm);CHKERRQ(ierr); 2123 /* Set cones */ 2124 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, NULL);CHKERRQ(ierr); 2125 ierr = PetscMalloc2(maxConeSize,PetscInt,&coneNew,maxConeSize,PetscInt,&coneONew);CHKERRQ(ierr); 2126 for (d = 0; d <= dim; ++d) { 2127 for (p = 0; p < numSubPoints[d]; ++p) { 2128 const PetscInt point = subpoints[d][p]; 2129 const PetscInt subpoint = firstSubPoint[d] + p; 2130 const PetscInt *cone, *ornt; 2131 PetscInt coneSize, subconeSize, coneSizeNew, c, subc; 2132 2133 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 2134 ierr = DMPlexGetConeSize(subdm, subpoint, &subconeSize);CHKERRQ(ierr); 2135 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 2136 ierr = DMPlexGetConeOrientation(dm, point, &ornt);CHKERRQ(ierr); 2137 for (c = 0, coneSizeNew = 0; c < coneSize; ++c) { 2138 ierr = PetscFindInt(cone[c], numSubPoints[d-1], subpoints[d-1], &subc);CHKERRQ(ierr); 2139 if (subc >= 0) { 2140 coneNew[coneSizeNew] = firstSubPoint[d-1] + subc; 2141 coneONew[coneSizeNew] = ornt[c]; 2142 ++coneSizeNew; 2143 } 2144 } 2145 if (coneSizeNew != subconeSize) SETERRQ2(comm, PETSC_ERR_PLIB, "Number of cone points located %d does not match subcone size %d", coneSizeNew, subconeSize); 2146 ierr = DMPlexSetCone(subdm, subpoint, coneNew);CHKERRQ(ierr); 2147 ierr = DMPlexSetConeOrientation(subdm, subpoint, coneONew);CHKERRQ(ierr); 2148 } 2149 } 2150 ierr = PetscFree2(coneNew,coneONew);CHKERRQ(ierr); 2151 ierr = DMPlexSymmetrize(subdm);CHKERRQ(ierr); 2152 ierr = DMPlexStratify(subdm);CHKERRQ(ierr); 2153 /* Build coordinates */ 2154 { 2155 PetscSection coordSection, subCoordSection; 2156 Vec coordinates, subCoordinates; 2157 PetscScalar *coords, *subCoords; 2158 PetscInt numComp, coordSize; 2159 2160 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2161 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 2162 ierr = DMPlexGetCoordinateSection(subdm, &subCoordSection);CHKERRQ(ierr); 2163 ierr = PetscSectionSetNumFields(subCoordSection, 1);CHKERRQ(ierr); 2164 ierr = PetscSectionGetFieldComponents(coordSection, 0, &numComp);CHKERRQ(ierr); 2165 ierr = PetscSectionSetFieldComponents(subCoordSection, 0, numComp);CHKERRQ(ierr); 2166 ierr = PetscSectionSetChart(subCoordSection, firstSubPoint[0], firstSubPoint[0]+numSubPoints[0]);CHKERRQ(ierr); 2167 for (v = 0; v < numSubPoints[0]; ++v) { 2168 const PetscInt vertex = subpoints[0][v]; 2169 const PetscInt subvertex = firstSubPoint[0]+v; 2170 PetscInt dof; 2171 2172 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2173 ierr = PetscSectionSetDof(subCoordSection, subvertex, dof);CHKERRQ(ierr); 2174 ierr = PetscSectionSetFieldDof(subCoordSection, subvertex, 0, dof);CHKERRQ(ierr); 2175 } 2176 ierr = PetscSectionSetUp(subCoordSection);CHKERRQ(ierr); 2177 ierr = PetscSectionGetStorageSize(subCoordSection, &coordSize);CHKERRQ(ierr); 2178 ierr = VecCreate(comm, &subCoordinates);CHKERRQ(ierr); 2179 ierr = VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2180 ierr = VecSetFromOptions(subCoordinates);CHKERRQ(ierr); 2181 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2182 ierr = VecGetArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2183 for (v = 0; v < numSubPoints[0]; ++v) { 2184 const PetscInt vertex = subpoints[0][v]; 2185 const PetscInt subvertex = firstSubPoint[0]+v; 2186 PetscInt dof, off, sdof, soff, d; 2187 2188 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2189 ierr = PetscSectionGetOffset(coordSection, vertex, &off);CHKERRQ(ierr); 2190 ierr = PetscSectionGetDof(subCoordSection, subvertex, &sdof);CHKERRQ(ierr); 2191 ierr = PetscSectionGetOffset(subCoordSection, subvertex, &soff);CHKERRQ(ierr); 2192 if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof); 2193 for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d]; 2194 } 2195 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2196 ierr = VecRestoreArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2197 ierr = DMSetCoordinatesLocal(subdm, subCoordinates);CHKERRQ(ierr); 2198 ierr = VecDestroy(&subCoordinates);CHKERRQ(ierr); 2199 } 2200 /* Cleanup */ 2201 for (d = 0; d <= dim; ++d) { 2202 ierr = ISRestoreIndices(subpointIS[d], &subpoints[d]);CHKERRQ(ierr); 2203 ierr = ISDestroy(&subpointIS[d]);CHKERRQ(ierr); 2204 } 2205 ierr = PetscFree4(numSubPoints,firstSubPoint,subpointIS,subpoints);CHKERRQ(ierr); 2206 PetscFunctionReturn(0); 2207 } 2208 2209 #undef __FUNCT__ 2210 #define __FUNCT__ "DMPlexCreateSubmesh" 2211 /*@C 2212 DMPlexCreateSubmesh - Extract a hypersurface from the mesh using vertices defined by a label 2213 2214 Input Parameters: 2215 + dm - The original mesh 2216 . vertexLabel - The DMLabel marking vertices contained in the surface 2217 - value - The label value to use 2218 2219 Output Parameter: 2220 . subdm - The surface mesh 2221 2222 Note: This function produces a DMLabel mapping original points in the submesh to their depth. This can be obtained using DMPlexGetSubpointMap(). 2223 2224 Level: developer 2225 2226 .seealso: DMPlexGetSubpointMap(), DMPlexGetLabel(), DMLabelSetValue() 2227 @*/ 2228 PetscErrorCode DMPlexCreateSubmesh(DM dm, const char vertexLabel[], PetscInt value, DM *subdm) 2229 { 2230 PetscInt dim, depth; 2231 PetscErrorCode ierr; 2232 2233 PetscFunctionBegin; 2234 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2235 PetscValidPointer(subdm, 3); 2236 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 2237 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 2238 ierr = DMCreate(PetscObjectComm((PetscObject)dm), subdm);CHKERRQ(ierr); 2239 ierr = DMSetType(*subdm, DMPLEX);CHKERRQ(ierr); 2240 ierr = DMPlexSetDimension(*subdm, dim-1);CHKERRQ(ierr); 2241 if (depth == dim) { 2242 ierr = DMPlexCreateSubmesh_Interpolated(dm, vertexLabel, value, *subdm);CHKERRQ(ierr); 2243 } else { 2244 ierr = DMPlexCreateSubmesh_Uninterpolated(dm, vertexLabel, value, *subdm);CHKERRQ(ierr); 2245 } 2246 PetscFunctionReturn(0); 2247 } 2248 2249 #undef __FUNCT__ 2250 #define __FUNCT__ "DMPlexFilterPoint_Internal" 2251 PETSC_STATIC_INLINE PetscInt DMPlexFilterPoint_Internal(PetscInt point, PetscInt firstSubPoint, PetscInt numSubPoints, const PetscInt subPoints[]) 2252 { 2253 PetscInt subPoint; 2254 PetscErrorCode ierr; 2255 2256 ierr = PetscFindInt(point, numSubPoints, subPoints, &subPoint); if (ierr < 0) return ierr; 2257 return subPoint < 0 ? subPoint : firstSubPoint+subPoint; 2258 } 2259 2260 #undef __FUNCT__ 2261 #define __FUNCT__ "DMPlexCreateCohesiveSubmesh_Uninterpolated" 2262 static PetscErrorCode DMPlexCreateCohesiveSubmesh_Uninterpolated(DM dm, PetscBool hasLagrange, const char label[], PetscInt value, DM subdm) 2263 { 2264 MPI_Comm comm; 2265 DMLabel subpointMap; 2266 IS subvertexIS; 2267 const PetscInt *subVertices; 2268 PetscInt numSubVertices, firstSubVertex, numSubCells, *subCells = NULL; 2269 PetscInt *subface, maxConeSize, numSubFaces, firstSubFace, newFacePoint, nFV; 2270 PetscInt cMax, c, f; 2271 PetscErrorCode ierr; 2272 2273 PetscFunctionBegin; 2274 ierr = PetscObjectGetComm((PetscObject)dm, &comm);CHKERRQ(ierr); 2275 /* Create subpointMap which marks the submesh */ 2276 ierr = DMLabelCreate("subpoint_map", &subpointMap);CHKERRQ(ierr); 2277 ierr = DMPlexSetSubpointMap(subdm, subpointMap);CHKERRQ(ierr); 2278 ierr = DMLabelDestroy(&subpointMap);CHKERRQ(ierr); 2279 ierr = DMPlexMarkCohesiveSubmesh_Uninterpolated(dm, hasLagrange, label, value, subpointMap, &numSubFaces, &nFV, &subCells, subdm);CHKERRQ(ierr); 2280 /* Setup chart */ 2281 ierr = DMLabelGetStratumSize(subpointMap, 0, &numSubVertices);CHKERRQ(ierr); 2282 ierr = DMLabelGetStratumSize(subpointMap, 2, &numSubCells);CHKERRQ(ierr); 2283 ierr = DMPlexSetChart(subdm, 0, numSubCells+numSubFaces+numSubVertices);CHKERRQ(ierr); 2284 ierr = DMPlexSetVTKCellHeight(subdm, 1);CHKERRQ(ierr); 2285 /* Set cone sizes */ 2286 firstSubVertex = numSubCells; 2287 firstSubFace = numSubCells+numSubVertices; 2288 newFacePoint = firstSubFace; 2289 ierr = DMLabelGetStratumIS(subpointMap, 0, &subvertexIS);CHKERRQ(ierr); 2290 if (subvertexIS) {ierr = ISGetIndices(subvertexIS, &subVertices);CHKERRQ(ierr);} 2291 for (c = 0; c < numSubCells; ++c) { 2292 ierr = DMPlexSetConeSize(subdm, c, 1);CHKERRQ(ierr); 2293 } 2294 for (f = firstSubFace; f < firstSubFace+numSubFaces; ++f) { 2295 ierr = DMPlexSetConeSize(subdm, f, nFV);CHKERRQ(ierr); 2296 } 2297 ierr = DMSetUp(subdm);CHKERRQ(ierr); 2298 /* Create face cones */ 2299 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, NULL);CHKERRQ(ierr); 2300 ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); 2301 ierr = DMGetWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);CHKERRQ(ierr); 2302 for (c = 0; c < numSubCells; ++c) { 2303 const PetscInt cell = subCells[c]; 2304 const PetscInt subcell = c; 2305 const PetscInt *cone, *cells; 2306 PetscInt numCells, subVertex, p, v; 2307 2308 if (cell < cMax) continue; 2309 ierr = DMPlexGetCone(dm, cell, &cone);CHKERRQ(ierr); 2310 for (v = 0; v < nFV; ++v) { 2311 ierr = PetscFindInt(cone[v], numSubVertices, subVertices, &subVertex);CHKERRQ(ierr); 2312 subface[v] = firstSubVertex+subVertex; 2313 } 2314 ierr = DMPlexSetCone(subdm, newFacePoint, subface);CHKERRQ(ierr); 2315 ierr = DMPlexSetCone(subdm, subcell, &newFacePoint);CHKERRQ(ierr); 2316 ierr = DMPlexGetJoin(dm, nFV, cone, &numCells, &cells);CHKERRQ(ierr); 2317 /* Not true in parallel 2318 if (numCells != 2) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive cells should separate two cells"); */ 2319 for (p = 0; p < numCells; ++p) { 2320 PetscInt negsubcell; 2321 2322 if (cells[p] >= cMax) continue; 2323 /* I know this is a crap search */ 2324 for (negsubcell = 0; negsubcell < numSubCells; ++negsubcell) { 2325 if (subCells[negsubcell] == cells[p]) break; 2326 } 2327 if (negsubcell == numSubCells) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not find negative face neighbor for cohesive cell %d", cell); 2328 ierr = DMPlexSetCone(subdm, negsubcell, &newFacePoint);CHKERRQ(ierr); 2329 } 2330 ierr = DMPlexRestoreJoin(dm, nFV, cone, &numCells, &cells);CHKERRQ(ierr); 2331 ++newFacePoint; 2332 } 2333 ierr = DMRestoreWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);CHKERRQ(ierr); 2334 ierr = DMPlexSymmetrize(subdm);CHKERRQ(ierr); 2335 ierr = DMPlexStratify(subdm);CHKERRQ(ierr); 2336 /* Build coordinates */ 2337 { 2338 PetscSection coordSection, subCoordSection; 2339 Vec coordinates, subCoordinates; 2340 PetscScalar *coords, *subCoords; 2341 PetscInt numComp, coordSize, v; 2342 2343 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2344 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 2345 ierr = DMPlexGetCoordinateSection(subdm, &subCoordSection);CHKERRQ(ierr); 2346 ierr = PetscSectionSetNumFields(subCoordSection, 1);CHKERRQ(ierr); 2347 ierr = PetscSectionGetFieldComponents(coordSection, 0, &numComp);CHKERRQ(ierr); 2348 ierr = PetscSectionSetFieldComponents(subCoordSection, 0, numComp);CHKERRQ(ierr); 2349 ierr = PetscSectionSetChart(subCoordSection, firstSubVertex, firstSubVertex+numSubVertices);CHKERRQ(ierr); 2350 for (v = 0; v < numSubVertices; ++v) { 2351 const PetscInt vertex = subVertices[v]; 2352 const PetscInt subvertex = firstSubVertex+v; 2353 PetscInt dof; 2354 2355 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2356 ierr = PetscSectionSetDof(subCoordSection, subvertex, dof);CHKERRQ(ierr); 2357 ierr = PetscSectionSetFieldDof(subCoordSection, subvertex, 0, dof);CHKERRQ(ierr); 2358 } 2359 ierr = PetscSectionSetUp(subCoordSection);CHKERRQ(ierr); 2360 ierr = PetscSectionGetStorageSize(subCoordSection, &coordSize);CHKERRQ(ierr); 2361 ierr = VecCreate(comm, &subCoordinates);CHKERRQ(ierr); 2362 ierr = VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2363 ierr = VecSetFromOptions(subCoordinates);CHKERRQ(ierr); 2364 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2365 ierr = VecGetArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2366 for (v = 0; v < numSubVertices; ++v) { 2367 const PetscInt vertex = subVertices[v]; 2368 const PetscInt subvertex = firstSubVertex+v; 2369 PetscInt dof, off, sdof, soff, d; 2370 2371 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2372 ierr = PetscSectionGetOffset(coordSection, vertex, &off);CHKERRQ(ierr); 2373 ierr = PetscSectionGetDof(subCoordSection, subvertex, &sdof);CHKERRQ(ierr); 2374 ierr = PetscSectionGetOffset(subCoordSection, subvertex, &soff);CHKERRQ(ierr); 2375 if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof); 2376 for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d]; 2377 } 2378 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2379 ierr = VecRestoreArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2380 ierr = DMSetCoordinatesLocal(subdm, subCoordinates);CHKERRQ(ierr); 2381 ierr = VecDestroy(&subCoordinates);CHKERRQ(ierr); 2382 } 2383 /* Build SF */ 2384 CHKMEMQ; 2385 { 2386 PetscSF sfPoint, sfPointSub; 2387 const PetscSFNode *remotePoints; 2388 PetscSFNode *sremotePoints, *newLocalPoints, *newOwners; 2389 const PetscInt *localPoints; 2390 PetscInt *slocalPoints; 2391 PetscInt numRoots, numLeaves, numSubRoots = numSubCells+numSubFaces+numSubVertices, numSubLeaves = 0, l, sl, ll, pStart, pEnd, p, vStart, vEnd; 2392 PetscMPIInt rank; 2393 2394 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRQ(ierr); 2395 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 2396 ierr = DMGetPointSF(subdm, &sfPointSub);CHKERRQ(ierr); 2397 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 2398 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 2399 ierr = PetscSFGetGraph(sfPoint, &numRoots, &numLeaves, &localPoints, &remotePoints);CHKERRQ(ierr); 2400 if (numRoots >= 0) { 2401 /* Only vertices should be shared */ 2402 ierr = PetscMalloc2(pEnd-pStart,PetscSFNode,&newLocalPoints,numRoots,PetscSFNode,&newOwners);CHKERRQ(ierr); 2403 for (p = 0; p < pEnd-pStart; ++p) { 2404 newLocalPoints[p].rank = -2; 2405 newLocalPoints[p].index = -2; 2406 } 2407 /* Set subleaves */ 2408 for (l = 0; l < numLeaves; ++l) { 2409 const PetscInt point = localPoints[l]; 2410 const PetscInt subPoint = DMPlexFilterPoint_Internal(point, firstSubVertex, numSubVertices, subVertices); 2411 2412 if ((point < vStart) && (point >= vEnd)) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Should not be mapping anything but vertices, %d", point); 2413 if (subPoint < 0) continue; 2414 newLocalPoints[point-pStart].rank = rank; 2415 newLocalPoints[point-pStart].index = subPoint; 2416 ++numSubLeaves; 2417 } 2418 /* Must put in owned subpoints */ 2419 for (p = pStart; p < pEnd; ++p) { 2420 const PetscInt subPoint = DMPlexFilterPoint_Internal(p, firstSubVertex, numSubVertices, subVertices); 2421 2422 if (subPoint < 0) { 2423 newOwners[p-pStart].rank = -3; 2424 newOwners[p-pStart].index = -3; 2425 } else { 2426 newOwners[p-pStart].rank = rank; 2427 newOwners[p-pStart].index = subPoint; 2428 } 2429 } 2430 ierr = PetscSFReduceBegin(sfPoint, MPIU_2INT, newLocalPoints, newOwners, MPI_MAXLOC);CHKERRQ(ierr); 2431 ierr = PetscSFReduceEnd(sfPoint, MPIU_2INT, newLocalPoints, newOwners, MPI_MAXLOC);CHKERRQ(ierr); 2432 ierr = PetscSFBcastBegin(sfPoint, MPIU_2INT, newOwners, newLocalPoints);CHKERRQ(ierr); 2433 ierr = PetscSFBcastEnd(sfPoint, MPIU_2INT, newOwners, newLocalPoints);CHKERRQ(ierr); 2434 ierr = PetscMalloc(numSubLeaves * sizeof(PetscInt), &slocalPoints);CHKERRQ(ierr); 2435 ierr = PetscMalloc(numSubLeaves * sizeof(PetscSFNode), &sremotePoints);CHKERRQ(ierr); 2436 for (l = 0, sl = 0, ll = 0; l < numLeaves; ++l) { 2437 const PetscInt point = localPoints[l]; 2438 const PetscInt subPoint = DMPlexFilterPoint_Internal(point, firstSubVertex, numSubVertices, subVertices); 2439 2440 if (subPoint < 0) continue; 2441 if (newLocalPoints[point].rank == rank) {++ll; continue;} 2442 slocalPoints[sl] = subPoint; 2443 sremotePoints[sl].rank = newLocalPoints[point].rank; 2444 sremotePoints[sl].index = newLocalPoints[point].index; 2445 if (sremotePoints[sl].rank < 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid remote rank for local point %d", point); 2446 if (sremotePoints[sl].index < 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid remote subpoint for local point %d", point); 2447 ++sl; 2448 } 2449 ierr = PetscFree2(newLocalPoints,newOwners);CHKERRQ(ierr); 2450 if (sl + ll != numSubLeaves) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Mismatch in number of subleaves %d + %d != %d", sl, ll, numSubLeaves); 2451 ierr = PetscSFSetGraph(sfPointSub, numSubRoots, sl, slocalPoints, PETSC_OWN_POINTER, sremotePoints, PETSC_OWN_POINTER);CHKERRQ(ierr); 2452 } 2453 } 2454 CHKMEMQ; 2455 /* Cleanup */ 2456 if (subvertexIS) {ierr = ISRestoreIndices(subvertexIS, &subVertices);CHKERRQ(ierr);} 2457 ierr = ISDestroy(&subvertexIS);CHKERRQ(ierr); 2458 ierr = PetscFree(subCells);CHKERRQ(ierr); 2459 PetscFunctionReturn(0); 2460 } 2461 2462 #undef __FUNCT__ 2463 #define __FUNCT__ "DMPlexCreateCohesiveSubmesh_Interpolated" 2464 static PetscErrorCode DMPlexCreateCohesiveSubmesh_Interpolated(DM dm, PetscBool hasLagrange, const char label[], PetscInt value, DM subdm) 2465 { 2466 MPI_Comm comm; 2467 DMLabel subpointMap; 2468 IS *subpointIS; 2469 const PetscInt **subpoints; 2470 PetscInt *numSubPoints, *firstSubPoint, *coneNew; 2471 PetscInt totSubPoints = 0, maxConeSize, dim, p, d, v; 2472 PetscErrorCode ierr; 2473 2474 PetscFunctionBegin; 2475 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 2476 /* Create subpointMap which marks the submesh */ 2477 ierr = DMLabelCreate("subpoint_map", &subpointMap);CHKERRQ(ierr); 2478 ierr = DMPlexSetSubpointMap(subdm, subpointMap);CHKERRQ(ierr); 2479 ierr = DMLabelDestroy(&subpointMap);CHKERRQ(ierr); 2480 ierr = DMPlexMarkCohesiveSubmesh_Interpolated(dm, hasLagrange, label, value, subpointMap, subdm);CHKERRQ(ierr); 2481 /* Setup chart */ 2482 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 2483 ierr = PetscMalloc4(dim+1,PetscInt,&numSubPoints,dim+1,PetscInt,&firstSubPoint,dim+1,IS,&subpointIS,dim+1,const PetscInt *,&subpoints);CHKERRQ(ierr); 2484 for (d = 0; d <= dim; ++d) { 2485 ierr = DMLabelGetStratumSize(subpointMap, d, &numSubPoints[d]);CHKERRQ(ierr); 2486 totSubPoints += numSubPoints[d]; 2487 } 2488 ierr = DMPlexSetChart(subdm, 0, totSubPoints);CHKERRQ(ierr); 2489 ierr = DMPlexSetVTKCellHeight(subdm, 1);CHKERRQ(ierr); 2490 /* Set cone sizes */ 2491 firstSubPoint[dim] = 0; 2492 firstSubPoint[0] = firstSubPoint[dim] + numSubPoints[dim]; 2493 if (dim > 1) {firstSubPoint[dim-1] = firstSubPoint[0] + numSubPoints[0];} 2494 if (dim > 2) {firstSubPoint[dim-2] = firstSubPoint[dim-1] + numSubPoints[dim-1];} 2495 for (d = 0; d <= dim; ++d) { 2496 ierr = DMLabelGetStratumIS(subpointMap, d, &subpointIS[d]);CHKERRQ(ierr); 2497 ierr = ISGetIndices(subpointIS[d], &subpoints[d]);CHKERRQ(ierr); 2498 } 2499 for (d = 0; d <= dim; ++d) { 2500 for (p = 0; p < numSubPoints[d]; ++p) { 2501 const PetscInt point = subpoints[d][p]; 2502 const PetscInt subpoint = firstSubPoint[d] + p; 2503 const PetscInt *cone; 2504 PetscInt coneSize, coneSizeNew, c, val; 2505 2506 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 2507 ierr = DMPlexSetConeSize(subdm, subpoint, coneSize);CHKERRQ(ierr); 2508 if (d == dim) { 2509 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 2510 for (c = 0, coneSizeNew = 0; c < coneSize; ++c) { 2511 ierr = DMLabelGetValue(subpointMap, cone[c], &val);CHKERRQ(ierr); 2512 if (val >= 0) coneSizeNew++; 2513 } 2514 ierr = DMPlexSetConeSize(subdm, subpoint, coneSizeNew);CHKERRQ(ierr); 2515 } 2516 } 2517 } 2518 ierr = DMSetUp(subdm);CHKERRQ(ierr); 2519 /* Set cones */ 2520 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, NULL);CHKERRQ(ierr); 2521 ierr = PetscMalloc(maxConeSize * sizeof(PetscInt), &coneNew);CHKERRQ(ierr); 2522 for (d = 0; d <= dim; ++d) { 2523 for (p = 0; p < numSubPoints[d]; ++p) { 2524 const PetscInt point = subpoints[d][p]; 2525 const PetscInt subpoint = firstSubPoint[d] + p; 2526 const PetscInt *cone; 2527 PetscInt coneSize, subconeSize, coneSizeNew, c, subc; 2528 2529 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 2530 ierr = DMPlexGetConeSize(subdm, subpoint, &subconeSize);CHKERRQ(ierr); 2531 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 2532 for (c = 0, coneSizeNew = 0; c < coneSize; ++c) { 2533 ierr = PetscFindInt(cone[c], numSubPoints[d-1], subpoints[d-1], &subc);CHKERRQ(ierr); 2534 if (subc >= 0) coneNew[coneSizeNew++] = firstSubPoint[d-1] + subc; 2535 } 2536 if (coneSizeNew != subconeSize) SETERRQ2(comm, PETSC_ERR_PLIB, "Number of cone points located %d does not match subcone size %d", coneSizeNew, subconeSize); 2537 ierr = DMPlexSetCone(subdm, subpoint, coneNew);CHKERRQ(ierr); 2538 } 2539 } 2540 ierr = PetscFree(coneNew);CHKERRQ(ierr); 2541 ierr = DMPlexSymmetrize(subdm);CHKERRQ(ierr); 2542 ierr = DMPlexStratify(subdm);CHKERRQ(ierr); 2543 /* Build coordinates */ 2544 { 2545 PetscSection coordSection, subCoordSection; 2546 Vec coordinates, subCoordinates; 2547 PetscScalar *coords, *subCoords; 2548 PetscInt numComp, coordSize; 2549 2550 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2551 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 2552 ierr = DMPlexGetCoordinateSection(subdm, &subCoordSection);CHKERRQ(ierr); 2553 ierr = PetscSectionSetNumFields(subCoordSection, 1);CHKERRQ(ierr); 2554 ierr = PetscSectionGetFieldComponents(coordSection, 0, &numComp);CHKERRQ(ierr); 2555 ierr = PetscSectionSetFieldComponents(subCoordSection, 0, numComp);CHKERRQ(ierr); 2556 ierr = PetscSectionSetChart(subCoordSection, firstSubPoint[0], firstSubPoint[0]+numSubPoints[0]);CHKERRQ(ierr); 2557 for (v = 0; v < numSubPoints[0]; ++v) { 2558 const PetscInt vertex = subpoints[0][v]; 2559 const PetscInt subvertex = firstSubPoint[0]+v; 2560 PetscInt dof; 2561 2562 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2563 ierr = PetscSectionSetDof(subCoordSection, subvertex, dof);CHKERRQ(ierr); 2564 ierr = PetscSectionSetFieldDof(subCoordSection, subvertex, 0, dof);CHKERRQ(ierr); 2565 } 2566 ierr = PetscSectionSetUp(subCoordSection);CHKERRQ(ierr); 2567 ierr = PetscSectionGetStorageSize(subCoordSection, &coordSize);CHKERRQ(ierr); 2568 ierr = VecCreate(comm, &subCoordinates);CHKERRQ(ierr); 2569 ierr = VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2570 ierr = VecSetFromOptions(subCoordinates);CHKERRQ(ierr); 2571 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2572 ierr = VecGetArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2573 for (v = 0; v < numSubPoints[0]; ++v) { 2574 const PetscInt vertex = subpoints[0][v]; 2575 const PetscInt subvertex = firstSubPoint[0]+v; 2576 PetscInt dof, off, sdof, soff, d; 2577 2578 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2579 ierr = PetscSectionGetOffset(coordSection, vertex, &off);CHKERRQ(ierr); 2580 ierr = PetscSectionGetDof(subCoordSection, subvertex, &sdof);CHKERRQ(ierr); 2581 ierr = PetscSectionGetOffset(subCoordSection, subvertex, &soff);CHKERRQ(ierr); 2582 if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof); 2583 for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d]; 2584 } 2585 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2586 ierr = VecRestoreArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2587 ierr = DMSetCoordinatesLocal(subdm, subCoordinates);CHKERRQ(ierr); 2588 ierr = VecDestroy(&subCoordinates);CHKERRQ(ierr); 2589 } 2590 /* Cleanup */ 2591 for (d = 0; d <= dim; ++d) { 2592 ierr = ISRestoreIndices(subpointIS[d], &subpoints[d]);CHKERRQ(ierr); 2593 ierr = ISDestroy(&subpointIS[d]);CHKERRQ(ierr); 2594 } 2595 ierr = PetscFree4(numSubPoints,firstSubPoint,subpointIS,subpoints);CHKERRQ(ierr); 2596 PetscFunctionReturn(0); 2597 } 2598 2599 #undef __FUNCT__ 2600 #define __FUNCT__ "DMPlexCreateCohesiveSubmesh" 2601 /* 2602 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. 2603 2604 Input Parameters: 2605 + dm - The original mesh 2606 . hasLagrange - The mesh has Lagrange unknowns in the cohesive cells 2607 . label - A label name, or PETSC_NULL 2608 - value - A label value 2609 2610 Output Parameter: 2611 . subdm - The surface mesh 2612 2613 Note: This function produces a DMLabel mapping original points in the submesh to their depth. This can be obtained using DMPlexGetSubpointMap(). 2614 2615 Level: developer 2616 2617 .seealso: DMPlexGetSubpointMap(), DMPlexCreateSubmesh() 2618 */ 2619 PetscErrorCode DMPlexCreateCohesiveSubmesh(DM dm, PetscBool hasLagrange, const char label[], PetscInt value, DM *subdm) 2620 { 2621 PetscInt dim, depth; 2622 PetscErrorCode ierr; 2623 2624 PetscFunctionBegin; 2625 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2626 PetscValidPointer(subdm, 5); 2627 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 2628 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 2629 ierr = DMCreate(PetscObjectComm((PetscObject)dm), subdm);CHKERRQ(ierr); 2630 ierr = DMSetType(*subdm, DMPLEX);CHKERRQ(ierr); 2631 ierr = DMPlexSetDimension(*subdm, dim-1);CHKERRQ(ierr); 2632 if (depth == dim) { 2633 ierr = DMPlexCreateCohesiveSubmesh_Interpolated(dm, hasLagrange, label, value, *subdm);CHKERRQ(ierr); 2634 } else { 2635 ierr = DMPlexCreateCohesiveSubmesh_Uninterpolated(dm, hasLagrange, label, value, *subdm);CHKERRQ(ierr); 2636 } 2637 PetscFunctionReturn(0); 2638 } 2639 2640 #undef __FUNCT__ 2641 #define __FUNCT__ "DMPlexGetSubpointMap" 2642 /*@ 2643 DMPlexGetSubpointMap - Returns a DMLabel with point dimension as values 2644 2645 Input Parameter: 2646 . dm - The submesh DM 2647 2648 Output Parameter: 2649 . subpointMap - The DMLabel of all the points from the original mesh in this submesh, or NULL if this is not a submesh 2650 2651 Level: developer 2652 2653 .seealso: DMPlexCreateSubmesh(), DMPlexCreateSubpointIS() 2654 @*/ 2655 PetscErrorCode DMPlexGetSubpointMap(DM dm, DMLabel *subpointMap) 2656 { 2657 DM_Plex *mesh = (DM_Plex*) dm->data; 2658 2659 PetscFunctionBegin; 2660 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2661 PetscValidPointer(subpointMap, 2); 2662 *subpointMap = mesh->subpointMap; 2663 PetscFunctionReturn(0); 2664 } 2665 2666 #undef __FUNCT__ 2667 #define __FUNCT__ "DMPlexSetSubpointMap" 2668 /* Note: Should normally not be called by the user, since it is set in DMPlexCreateSubmesh() */ 2669 PetscErrorCode DMPlexSetSubpointMap(DM dm, DMLabel subpointMap) 2670 { 2671 DM_Plex *mesh = (DM_Plex *) dm->data; 2672 DMLabel tmp; 2673 PetscErrorCode ierr; 2674 2675 PetscFunctionBegin; 2676 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2677 tmp = mesh->subpointMap; 2678 mesh->subpointMap = subpointMap; 2679 ++mesh->subpointMap->refct; 2680 ierr = DMLabelDestroy(&tmp);CHKERRQ(ierr); 2681 PetscFunctionReturn(0); 2682 } 2683 2684 #undef __FUNCT__ 2685 #define __FUNCT__ "DMPlexCreateSubpointIS" 2686 /*@ 2687 DMPlexCreateSubpointIS - Creates an IS covering the entire subdm chart with the original points as data 2688 2689 Input Parameter: 2690 . dm - The submesh DM 2691 2692 Output Parameter: 2693 . subpointIS - The IS of all the points from the original mesh in this submesh, or NULL if this is not a submesh 2694 2695 Note: This is IS is guaranteed to be sorted by the construction of the submesh 2696 2697 Level: developer 2698 2699 .seealso: DMPlexCreateSubmesh(), DMPlexGetSubpointMap() 2700 @*/ 2701 PetscErrorCode DMPlexCreateSubpointIS(DM dm, IS *subpointIS) 2702 { 2703 MPI_Comm comm; 2704 DMLabel subpointMap; 2705 IS is; 2706 const PetscInt *opoints; 2707 PetscInt *points, *depths; 2708 PetscInt depth, depStart, depEnd, d, pStart, pEnd, p, n, off; 2709 PetscErrorCode ierr; 2710 2711 PetscFunctionBegin; 2712 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2713 PetscValidPointer(subpointIS, 2); 2714 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 2715 *subpointIS = NULL; 2716 ierr = DMPlexGetSubpointMap(dm, &subpointMap);CHKERRQ(ierr); 2717 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 2718 if (subpointMap && depth >= 0) { 2719 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 2720 if (pStart) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Submeshes must start the point numbering at 0, not %d", pStart); 2721 ierr = DMGetWorkArray(dm, depth+1, PETSC_INT, &depths);CHKERRQ(ierr); 2722 depths[0] = depth; 2723 depths[1] = 0; 2724 for(d = 2; d <= depth; ++d) {depths[d] = depth+1 - d;} 2725 ierr = PetscMalloc(pEnd * sizeof(PetscInt), &points);CHKERRQ(ierr); 2726 for(d = 0, off = 0; d <= depth; ++d) { 2727 const PetscInt dep = depths[d]; 2728 2729 ierr = DMPlexGetDepthStratum(dm, dep, &depStart, &depEnd);CHKERRQ(ierr); 2730 ierr = DMLabelGetStratumSize(subpointMap, dep, &n);CHKERRQ(ierr); 2731 if (((d < 2) && (depth > 1)) || (d == 1)) { /* Only check vertices and cells for now since the map is broken for others */ 2732 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); 2733 } else { 2734 if (!n) { 2735 if (d == 0) { 2736 /* Missing cells */ 2737 for(p = 0; p < depEnd-depStart; ++p, ++off) points[off] = -1; 2738 } else { 2739 /* Missing faces */ 2740 for(p = 0; p < depEnd-depStart; ++p, ++off) points[off] = PETSC_MAX_INT; 2741 } 2742 } 2743 } 2744 if (n) { 2745 ierr = DMLabelGetStratumIS(subpointMap, dep, &is);CHKERRQ(ierr); 2746 ierr = ISGetIndices(is, &opoints);CHKERRQ(ierr); 2747 for(p = 0; p < n; ++p, ++off) points[off] = opoints[p]; 2748 ierr = ISRestoreIndices(is, &opoints);CHKERRQ(ierr); 2749 ierr = ISDestroy(&is);CHKERRQ(ierr); 2750 } 2751 } 2752 ierr = DMRestoreWorkArray(dm, depth+1, PETSC_INT, &depths);CHKERRQ(ierr); 2753 if (off != pEnd) SETERRQ2(comm, PETSC_ERR_ARG_WRONG, "The number of mapped submesh points %d should be %d", off, pEnd); 2754 ierr = ISCreateGeneral(PETSC_COMM_SELF, pEnd, points, PETSC_OWN_POINTER, subpointIS);CHKERRQ(ierr); 2755 } 2756 PetscFunctionReturn(0); 2757 } 2758