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, maxConeSizeNew, maxSupportSizeNew, 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 = DMPlexGetMaxSizes(dmNew, &maxConeSizeNew, &maxSupportSizeNew);CHKERRQ(ierr); 153 ierr = PetscMalloc2(depth+1,PetscInt,&depthEnd,PetscMax(PetscMax(maxConeSize, maxSupportSize), PetscMax(maxConeSizeNew, maxSupportSizeNew)),PetscInt,&newpoints);CHKERRQ(ierr); 154 for (d = 0; d <= depth; ++d) { 155 ierr = DMPlexGetDepthStratum(dm, d, NULL, &depthEnd[d]);CHKERRQ(ierr); 156 } 157 /* Step 5: Set cones and supports */ 158 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 159 for (p = pStart; p < pEnd; ++p) { 160 const PetscInt *points = NULL, *orientations = NULL; 161 PetscInt size,sizeNew, i, newp = DMPlexShiftPoint_Internal(p, depth, depthEnd, depthShift); 162 163 ierr = DMPlexGetConeSize(dm, p, &size);CHKERRQ(ierr); 164 ierr = DMPlexGetCone(dm, p, &points);CHKERRQ(ierr); 165 ierr = DMPlexGetConeOrientation(dm, p, &orientations);CHKERRQ(ierr); 166 for (i = 0; i < size; ++i) { 167 newpoints[i] = DMPlexShiftPoint_Internal(points[i], depth, depthEnd, depthShift); 168 } 169 ierr = DMPlexSetCone(dmNew, newp, newpoints);CHKERRQ(ierr); 170 ierr = DMPlexSetConeOrientation(dmNew, newp, orientations);CHKERRQ(ierr); 171 ierr = DMPlexGetSupportSize(dm, p, &size);CHKERRQ(ierr); 172 ierr = DMPlexGetSupportSize(dmNew, newp, &sizeNew);CHKERRQ(ierr); 173 ierr = DMPlexGetSupport(dm, p, &points);CHKERRQ(ierr); 174 for (i = 0; i < size; ++i) { 175 newpoints[i] = DMPlexShiftPoint_Internal(points[i], depth, depthEnd, depthShift); 176 } 177 for (i = size; i < sizeNew; ++i) newpoints[i] = 0; 178 ierr = DMPlexSetSupport(dmNew, newp, newpoints);CHKERRQ(ierr); 179 } 180 ierr = PetscFree2(depthEnd,newpoints);CHKERRQ(ierr); 181 PetscFunctionReturn(0); 182 } 183 184 #undef __FUNCT__ 185 #define __FUNCT__ "DMPlexShiftCoordinates_Internal" 186 static PetscErrorCode DMPlexShiftCoordinates_Internal(DM dm, PetscInt depthShift[], DM dmNew) 187 { 188 PetscSection coordSection, newCoordSection; 189 Vec coordinates, newCoordinates; 190 PetscScalar *coords, *newCoords; 191 PetscInt *depthEnd, coordSize; 192 PetscInt dim, depth = 0, d, vStart, vEnd, vStartNew, vEndNew, v; 193 PetscErrorCode ierr; 194 195 PetscFunctionBegin; 196 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 197 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 198 ierr = PetscMalloc((depth+1) * sizeof(PetscInt), &depthEnd);CHKERRQ(ierr); 199 for (d = 0; d <= depth; ++d) { 200 ierr = DMPlexGetDepthStratum(dm, d, NULL, &depthEnd[d]);CHKERRQ(ierr); 201 } 202 /* Step 8: Convert coordinates */ 203 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 204 ierr = DMPlexGetDepthStratum(dmNew, 0, &vStartNew, &vEndNew);CHKERRQ(ierr); 205 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 206 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &newCoordSection);CHKERRQ(ierr); 207 ierr = PetscSectionSetNumFields(newCoordSection, 1);CHKERRQ(ierr); 208 ierr = PetscSectionSetFieldComponents(newCoordSection, 0, dim);CHKERRQ(ierr); 209 ierr = PetscSectionSetChart(newCoordSection, vStartNew, vEndNew);CHKERRQ(ierr); 210 for (v = vStartNew; v < vEndNew; ++v) { 211 ierr = PetscSectionSetDof(newCoordSection, v, dim);CHKERRQ(ierr); 212 ierr = PetscSectionSetFieldDof(newCoordSection, v, 0, dim);CHKERRQ(ierr); 213 } 214 ierr = PetscSectionSetUp(newCoordSection);CHKERRQ(ierr); 215 ierr = DMPlexSetCoordinateSection(dmNew, newCoordSection);CHKERRQ(ierr); 216 ierr = PetscSectionGetStorageSize(newCoordSection, &coordSize);CHKERRQ(ierr); 217 ierr = VecCreate(PetscObjectComm((PetscObject)dm), &newCoordinates);CHKERRQ(ierr); 218 ierr = PetscObjectSetName((PetscObject) newCoordinates, "coordinates");CHKERRQ(ierr); 219 ierr = VecSetSizes(newCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 220 ierr = VecSetType(newCoordinates,VECSTANDARD);CHKERRQ(ierr); 221 ierr = DMSetCoordinatesLocal(dmNew, newCoordinates);CHKERRQ(ierr); 222 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 223 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 224 ierr = VecGetArray(newCoordinates, &newCoords);CHKERRQ(ierr); 225 for (v = vStart; v < vEnd; ++v) { 226 PetscInt dof, off, noff, d; 227 228 ierr = PetscSectionGetDof(coordSection, v, &dof);CHKERRQ(ierr); 229 ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr); 230 ierr = PetscSectionGetOffset(newCoordSection, DMPlexShiftPoint_Internal(v, depth, depthEnd, depthShift), &noff);CHKERRQ(ierr); 231 for (d = 0; d < dof; ++d) { 232 newCoords[noff+d] = coords[off+d]; 233 } 234 } 235 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 236 ierr = VecRestoreArray(newCoordinates, &newCoords);CHKERRQ(ierr); 237 ierr = VecDestroy(&newCoordinates);CHKERRQ(ierr); 238 ierr = PetscSectionDestroy(&newCoordSection);CHKERRQ(ierr); 239 ierr = PetscFree(depthEnd);CHKERRQ(ierr); 240 PetscFunctionReturn(0); 241 } 242 243 #undef __FUNCT__ 244 #define __FUNCT__ "DMPlexShiftSF_Internal" 245 static PetscErrorCode DMPlexShiftSF_Internal(DM dm, PetscInt depthShift[], DM dmNew) 246 { 247 PetscInt *depthEnd; 248 PetscInt depth = 0, d; 249 PetscSF sfPoint, sfPointNew; 250 const PetscSFNode *remotePoints; 251 PetscSFNode *gremotePoints; 252 const PetscInt *localPoints; 253 PetscInt *glocalPoints, *newLocation, *newRemoteLocation; 254 PetscInt numRoots, numLeaves, l, pStart, pEnd, totShift = 0; 255 PetscErrorCode ierr; 256 257 PetscFunctionBegin; 258 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 259 ierr = PetscMalloc((depth+1) * sizeof(PetscInt), &depthEnd);CHKERRQ(ierr); 260 for (d = 0; d <= depth; ++d) { 261 totShift += depthShift[d]; 262 ierr = DMPlexGetDepthStratum(dm, d, NULL, &depthEnd[d]);CHKERRQ(ierr); 263 } 264 /* Step 9: Convert pointSF */ 265 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 266 ierr = DMGetPointSF(dmNew, &sfPointNew);CHKERRQ(ierr); 267 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 268 ierr = PetscSFGetGraph(sfPoint, &numRoots, &numLeaves, &localPoints, &remotePoints);CHKERRQ(ierr); 269 if (numRoots >= 0) { 270 ierr = PetscMalloc2(numRoots,PetscInt,&newLocation,pEnd-pStart,PetscInt,&newRemoteLocation);CHKERRQ(ierr); 271 for (l=0; l<numRoots; l++) newLocation[l] = DMPlexShiftPoint_Internal(l, depth, depthEnd, depthShift); 272 ierr = PetscSFBcastBegin(sfPoint, MPIU_INT, newLocation, newRemoteLocation);CHKERRQ(ierr); 273 ierr = PetscSFBcastEnd(sfPoint, MPIU_INT, newLocation, newRemoteLocation);CHKERRQ(ierr); 274 ierr = PetscMalloc(numLeaves * sizeof(PetscInt), &glocalPoints);CHKERRQ(ierr); 275 ierr = PetscMalloc(numLeaves * sizeof(PetscSFNode), &gremotePoints);CHKERRQ(ierr); 276 for (l = 0; l < numLeaves; ++l) { 277 glocalPoints[l] = DMPlexShiftPoint_Internal(localPoints[l], depth, depthEnd, depthShift); 278 gremotePoints[l].rank = remotePoints[l].rank; 279 gremotePoints[l].index = newRemoteLocation[localPoints[l]]; 280 } 281 ierr = PetscFree2(newLocation,newRemoteLocation);CHKERRQ(ierr); 282 ierr = PetscSFSetGraph(sfPointNew, numRoots + totShift, numLeaves, glocalPoints, PETSC_OWN_POINTER, gremotePoints, PETSC_OWN_POINTER);CHKERRQ(ierr); 283 } 284 ierr = PetscFree(depthEnd);CHKERRQ(ierr); 285 PetscFunctionReturn(0); 286 } 287 288 #undef __FUNCT__ 289 #define __FUNCT__ "DMPlexShiftLabels_Internal" 290 static PetscErrorCode DMPlexShiftLabels_Internal(DM dm, PetscInt depthShift[], DM dmNew) 291 { 292 PetscSF sfPoint; 293 DMLabel vtkLabel, ghostLabel; 294 PetscInt *depthEnd; 295 const PetscSFNode *leafRemote; 296 const PetscInt *leafLocal; 297 PetscInt depth = 0, d, numLeaves, numLabels, l, cStart, cEnd, c, fStart, fEnd, f; 298 PetscMPIInt rank; 299 PetscErrorCode ierr; 300 301 PetscFunctionBegin; 302 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 303 ierr = PetscMalloc((depth+1) * sizeof(PetscInt), &depthEnd);CHKERRQ(ierr); 304 for (d = 0; d <= depth; ++d) { 305 ierr = DMPlexGetDepthStratum(dm, d, NULL, &depthEnd[d]);CHKERRQ(ierr); 306 } 307 /* Step 10: Convert labels */ 308 ierr = DMPlexGetNumLabels(dm, &numLabels);CHKERRQ(ierr); 309 for (l = 0; l < numLabels; ++l) { 310 DMLabel label, newlabel; 311 const char *lname; 312 PetscBool isDepth; 313 IS valueIS; 314 const PetscInt *values; 315 PetscInt numValues, val; 316 317 ierr = DMPlexGetLabelName(dm, l, &lname);CHKERRQ(ierr); 318 ierr = PetscStrcmp(lname, "depth", &isDepth);CHKERRQ(ierr); 319 if (isDepth) continue; 320 ierr = DMPlexCreateLabel(dmNew, lname);CHKERRQ(ierr); 321 ierr = DMPlexGetLabel(dm, lname, &label);CHKERRQ(ierr); 322 ierr = DMPlexGetLabel(dmNew, lname, &newlabel);CHKERRQ(ierr); 323 ierr = DMLabelGetValueIS(label, &valueIS);CHKERRQ(ierr); 324 ierr = ISGetLocalSize(valueIS, &numValues);CHKERRQ(ierr); 325 ierr = ISGetIndices(valueIS, &values);CHKERRQ(ierr); 326 for (val = 0; val < numValues; ++val) { 327 IS pointIS; 328 const PetscInt *points; 329 PetscInt numPoints, p; 330 331 ierr = DMLabelGetStratumIS(label, values[val], &pointIS);CHKERRQ(ierr); 332 ierr = ISGetLocalSize(pointIS, &numPoints);CHKERRQ(ierr); 333 ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); 334 for (p = 0; p < numPoints; ++p) { 335 const PetscInt newpoint = DMPlexShiftPoint_Internal(points[p], depth, depthEnd, depthShift); 336 337 ierr = DMLabelSetValue(newlabel, newpoint, values[val]);CHKERRQ(ierr); 338 } 339 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 340 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 341 } 342 ierr = ISRestoreIndices(valueIS, &values);CHKERRQ(ierr); 343 ierr = ISDestroy(&valueIS);CHKERRQ(ierr); 344 } 345 ierr = PetscFree(depthEnd);CHKERRQ(ierr); 346 /* Step 11: Make label for output (vtk) and to mark ghost points (ghost) */ 347 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr); 348 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 349 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 350 ierr = PetscSFGetGraph(sfPoint, NULL, &numLeaves, &leafLocal, &leafRemote);CHKERRQ(ierr); 351 ierr = DMPlexCreateLabel(dmNew, "vtk");CHKERRQ(ierr); 352 ierr = DMPlexCreateLabel(dmNew, "ghost");CHKERRQ(ierr); 353 ierr = DMPlexGetLabel(dmNew, "vtk", &vtkLabel);CHKERRQ(ierr); 354 ierr = DMPlexGetLabel(dmNew, "ghost", &ghostLabel);CHKERRQ(ierr); 355 for (l = 0, c = cStart; l < numLeaves && c < cEnd; ++l, ++c) { 356 for (; c < leafLocal[l] && c < cEnd; ++c) { 357 ierr = DMLabelSetValue(vtkLabel, c, 1);CHKERRQ(ierr); 358 } 359 if (leafLocal[l] >= cEnd) break; 360 if (leafRemote[l].rank == rank) { 361 ierr = DMLabelSetValue(vtkLabel, c, 1);CHKERRQ(ierr); 362 } else { 363 ierr = DMLabelSetValue(ghostLabel, c, 2);CHKERRQ(ierr); 364 } 365 } 366 for (; c < cEnd; ++c) { 367 ierr = DMLabelSetValue(vtkLabel, c, 1);CHKERRQ(ierr); 368 } 369 if (0) { 370 ierr = PetscViewerASCIISynchronizedAllow(PETSC_VIEWER_STDOUT_WORLD, PETSC_TRUE);CHKERRQ(ierr); 371 ierr = DMLabelView(vtkLabel, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 372 ierr = PetscViewerFlush(PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 373 } 374 ierr = DMPlexGetHeightStratum(dmNew, 1, &fStart, &fEnd);CHKERRQ(ierr); 375 for (f = fStart; f < fEnd; ++f) { 376 PetscInt numCells; 377 378 ierr = DMPlexGetSupportSize(dmNew, f, &numCells);CHKERRQ(ierr); 379 if (numCells < 2) { 380 ierr = DMLabelSetValue(ghostLabel, f, 1);CHKERRQ(ierr); 381 } else { 382 const PetscInt *cells = NULL; 383 PetscInt vA, vB; 384 385 ierr = DMPlexGetSupport(dmNew, f, &cells);CHKERRQ(ierr); 386 ierr = DMLabelGetValue(vtkLabel, cells[0], &vA);CHKERRQ(ierr); 387 ierr = DMLabelGetValue(vtkLabel, cells[1], &vB);CHKERRQ(ierr); 388 if (!vA && !vB) {ierr = DMLabelSetValue(ghostLabel, f, 1);CHKERRQ(ierr);} 389 } 390 } 391 if (0) { 392 ierr = PetscViewerASCIISynchronizedAllow(PETSC_VIEWER_STDOUT_WORLD, PETSC_TRUE);CHKERRQ(ierr); 393 ierr = DMLabelView(ghostLabel, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 394 ierr = PetscViewerFlush(PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 395 } 396 PetscFunctionReturn(0); 397 } 398 399 #undef __FUNCT__ 400 #define __FUNCT__ "DMPlexConstructGhostCells_Internal" 401 static PetscErrorCode DMPlexConstructGhostCells_Internal(DM dm, DMLabel label, PetscInt *numGhostCells, DM gdm) 402 { 403 IS valueIS; 404 const PetscInt *values; 405 PetscInt *depthShift; 406 PetscInt depth = 0, numFS, fs, ghostCell, cEnd, c; 407 PetscErrorCode ierr; 408 409 PetscFunctionBegin; 410 /* Count ghost cells */ 411 ierr = DMLabelGetValueIS(label, &valueIS);CHKERRQ(ierr); 412 ierr = ISGetLocalSize(valueIS, &numFS);CHKERRQ(ierr); 413 ierr = ISGetIndices(valueIS, &values);CHKERRQ(ierr); 414 415 *numGhostCells = 0; 416 for (fs = 0; fs < numFS; ++fs) { 417 PetscInt numBdFaces; 418 419 ierr = DMLabelGetStratumSize(label, values[fs], &numBdFaces);CHKERRQ(ierr); 420 421 *numGhostCells += numBdFaces; 422 } 423 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 424 ierr = PetscMalloc((depth+1) * sizeof(PetscInt), &depthShift);CHKERRQ(ierr); 425 ierr = PetscMemzero(depthShift, (depth+1) * sizeof(PetscInt));CHKERRQ(ierr); 426 if (depth >= 0) depthShift[depth] = *numGhostCells; 427 ierr = DMPlexShiftSizes_Internal(dm, depthShift, gdm);CHKERRQ(ierr); 428 /* Step 3: Set cone/support sizes for new points */ 429 ierr = DMPlexGetHeightStratum(dm, 0, NULL, &cEnd);CHKERRQ(ierr); 430 for (c = cEnd; c < cEnd + *numGhostCells; ++c) { 431 ierr = DMPlexSetConeSize(gdm, c, 1);CHKERRQ(ierr); 432 } 433 for (fs = 0; fs < numFS; ++fs) { 434 IS faceIS; 435 const PetscInt *faces; 436 PetscInt numFaces, f; 437 438 ierr = DMLabelGetStratumIS(label, values[fs], &faceIS);CHKERRQ(ierr); 439 ierr = ISGetLocalSize(faceIS, &numFaces);CHKERRQ(ierr); 440 ierr = ISGetIndices(faceIS, &faces);CHKERRQ(ierr); 441 for (f = 0; f < numFaces; ++f) { 442 PetscInt size; 443 444 ierr = DMPlexGetSupportSize(dm, faces[f], &size);CHKERRQ(ierr); 445 if (size != 1) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "DM has boundary face %d with %d support cells", faces[f], size); 446 ierr = DMPlexSetSupportSize(gdm, faces[f] + *numGhostCells, 2);CHKERRQ(ierr); 447 } 448 ierr = ISRestoreIndices(faceIS, &faces);CHKERRQ(ierr); 449 ierr = ISDestroy(&faceIS);CHKERRQ(ierr); 450 } 451 /* Step 4: Setup ghosted DM */ 452 ierr = DMSetUp(gdm);CHKERRQ(ierr); 453 ierr = DMPlexShiftPoints_Internal(dm, depthShift, gdm);CHKERRQ(ierr); 454 /* Step 6: Set cones and supports for new points */ 455 ghostCell = cEnd; 456 for (fs = 0; fs < numFS; ++fs) { 457 IS faceIS; 458 const PetscInt *faces; 459 PetscInt numFaces, f; 460 461 ierr = DMLabelGetStratumIS(label, values[fs], &faceIS);CHKERRQ(ierr); 462 ierr = ISGetLocalSize(faceIS, &numFaces);CHKERRQ(ierr); 463 ierr = ISGetIndices(faceIS, &faces);CHKERRQ(ierr); 464 for (f = 0; f < numFaces; ++f, ++ghostCell) { 465 PetscInt newFace = faces[f] + *numGhostCells; 466 467 ierr = DMPlexSetCone(gdm, ghostCell, &newFace);CHKERRQ(ierr); 468 ierr = DMPlexInsertSupport(gdm, newFace, 1, ghostCell);CHKERRQ(ierr); 469 } 470 ierr = ISRestoreIndices(faceIS, &faces);CHKERRQ(ierr); 471 ierr = ISDestroy(&faceIS);CHKERRQ(ierr); 472 } 473 ierr = ISRestoreIndices(valueIS, &values);CHKERRQ(ierr); 474 ierr = ISDestroy(&valueIS);CHKERRQ(ierr); 475 /* Step 7: Stratify */ 476 ierr = DMPlexStratify(gdm);CHKERRQ(ierr); 477 ierr = DMPlexShiftCoordinates_Internal(dm, depthShift, gdm);CHKERRQ(ierr); 478 ierr = DMPlexShiftSF_Internal(dm, depthShift, gdm);CHKERRQ(ierr); 479 ierr = DMPlexShiftLabels_Internal(dm, depthShift, gdm);CHKERRQ(ierr); 480 ierr = PetscFree(depthShift);CHKERRQ(ierr); 481 PetscFunctionReturn(0); 482 } 483 484 #undef __FUNCT__ 485 #define __FUNCT__ "DMPlexConstructGhostCells" 486 /*@C 487 DMPlexConstructGhostCells - Construct ghost cells which connect to every boundary face 488 489 Collective on dm 490 491 Input Parameters: 492 + dm - The original DM 493 - labelName - The label specifying the boundary faces, or "Face Sets" if this is NULL 494 495 Output Parameters: 496 + numGhostCells - The number of ghost cells added to the DM 497 - dmGhosted - The new DM 498 499 Note: If no label exists of that name, one will be created marking all boundary faces 500 501 Level: developer 502 503 .seealso: DMCreate() 504 */ 505 PetscErrorCode DMPlexConstructGhostCells(DM dm, const char labelName[], PetscInt *numGhostCells, DM *dmGhosted) 506 { 507 DM gdm; 508 DMLabel label; 509 const char *name = labelName ? labelName : "Face Sets"; 510 PetscInt dim; 511 PetscErrorCode ierr; 512 513 PetscFunctionBegin; 514 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 515 PetscValidPointer(numGhostCells, 3); 516 PetscValidPointer(dmGhosted, 4); 517 ierr = DMCreate(PetscObjectComm((PetscObject)dm), &gdm);CHKERRQ(ierr); 518 ierr = DMSetType(gdm, DMPLEX);CHKERRQ(ierr); 519 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 520 ierr = DMPlexSetDimension(gdm, dim);CHKERRQ(ierr); 521 ierr = DMPlexGetLabel(dm, name, &label);CHKERRQ(ierr); 522 if (!label) { 523 /* Get label for boundary faces */ 524 ierr = DMPlexCreateLabel(dm, name);CHKERRQ(ierr); 525 ierr = DMPlexGetLabel(dm, name, &label);CHKERRQ(ierr); 526 ierr = DMPlexMarkBoundaryFaces(dm, label);CHKERRQ(ierr); 527 } 528 ierr = DMPlexConstructGhostCells_Internal(dm, label, numGhostCells, gdm);CHKERRQ(ierr); 529 ierr = DMSetFromOptions(gdm);CHKERRQ(ierr); 530 *dmGhosted = gdm; 531 PetscFunctionReturn(0); 532 } 533 534 #undef __FUNCT__ 535 #define __FUNCT__ "DMPlexConstructCohesiveCells_Internal" 536 /* 537 We are adding two kinds of points here: 538 Replicated: Copies of points which exist in the mesh, such as vertices identified across a fault 539 Hybrid: Entirely new points, such as cohesive cells 540 */ 541 static PetscErrorCode DMPlexConstructCohesiveCells_Internal(DM dm, DMLabel label, DM sdm) 542 { 543 MPI_Comm comm; 544 IS valueIS; 545 PetscInt numSP = 0; /* The number of depths for which we have replicated points */ 546 const PetscInt *values; /* List of depths for which we have replicated points */ 547 IS *splitIS; 548 IS *unsplitIS; 549 PetscInt *numSplitPoints; /* The number of replicated points at each depth */ 550 PetscInt *numUnsplitPoints; /* The number of non-replicated points at each depth which still give rise to hybrid points */ 551 PetscInt *numHybridPoints; /* The number of hybrid points at each depth */ 552 const PetscInt **splitPoints; /* Replicated points for each depth */ 553 const PetscInt **unsplitPoints; /* Non-replicated points for each depth */ 554 PetscSection coordSection; 555 Vec coordinates; 556 PetscScalar *coords; 557 PetscInt depths[4]; /* Depths in the order that plex points are numbered */ 558 PetscInt *depthShift; /* Number of replicated+hybrid points at each depth */ 559 PetscInt *depthOffset; /* Prefix sums of depthShift */ 560 PetscInt *pMaxNew; /* The first replicated point at each depth in the new mesh, hybrids come after this */ 561 PetscInt *coneNew, *coneONew, *supportNew; 562 PetscInt shift = 100, shift2 = 200, depth = 0, dep, dim, d, sp, maxConeSize, maxSupportSize, maxConeSizeNew, maxSupportSizeNew, numLabels, vStart, vEnd, pEnd, p, v; 563 PetscErrorCode ierr; 564 565 PetscFunctionBegin; 566 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 567 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 568 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 569 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 570 depths[0] = depth; 571 depths[1] = 0; 572 depths[2] = depth-1; 573 depths[3] = 1; 574 /* Count split points and add cohesive cells */ 575 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize);CHKERRQ(ierr); 576 ierr = PetscMalloc3(depth+1,PetscInt,&depthShift,depth+1,PetscInt,&depthOffset,depth+1,PetscInt,&pMaxNew);CHKERRQ(ierr); 577 ierr = PetscMalloc7(depth+1,IS,&splitIS,depth+1,IS,&unsplitIS,depth+1,PetscInt,&numSplitPoints,depth+1,PetscInt,&numUnsplitPoints,depth+1,PetscInt,&numHybridPoints,depth+1,const PetscInt*,&splitPoints,depth+1,const PetscInt*,&unsplitPoints);CHKERRQ(ierr); 578 ierr = PetscMemzero(depthShift, (depth+1) * sizeof(PetscInt));CHKERRQ(ierr); 579 ierr = PetscMemzero(depthOffset, (depth+1) * sizeof(PetscInt));CHKERRQ(ierr); 580 for (d = 0; d <= depth; ++d) { 581 ierr = DMPlexGetDepthStratum(dm, d, NULL, &pMaxNew[d]);CHKERRQ(ierr); 582 numSplitPoints[d] = 0; 583 numUnsplitPoints[d] = 0; 584 numHybridPoints[d] = 0; 585 splitPoints[d] = NULL; 586 unsplitPoints[d] = NULL; 587 splitIS[d] = NULL; 588 unsplitIS[d] = NULL; 589 } 590 if (label) { 591 ierr = DMLabelGetValueIS(label, &valueIS);CHKERRQ(ierr); 592 ierr = ISGetLocalSize(valueIS, &numSP);CHKERRQ(ierr); 593 ierr = ISGetIndices(valueIS, &values);CHKERRQ(ierr); 594 } 595 for (sp = 0; sp < numSP; ++sp) { 596 const PetscInt dep = values[sp]; 597 598 if ((dep < 0) || (dep > depth)) continue; 599 ierr = DMLabelGetStratumIS(label, dep, &splitIS[dep]);CHKERRQ(ierr); 600 if (splitIS[dep]) { 601 ierr = ISGetLocalSize(splitIS[dep], &numSplitPoints[dep]);CHKERRQ(ierr); 602 ierr = ISGetIndices(splitIS[dep], &splitPoints[dep]);CHKERRQ(ierr); 603 } 604 ierr = DMLabelGetStratumIS(label, shift2+dep, &unsplitIS[dep]);CHKERRQ(ierr); 605 if (unsplitIS[dep]) { 606 ierr = ISGetLocalSize(unsplitIS[dep], &numUnsplitPoints[dep]);CHKERRQ(ierr); 607 ierr = ISGetIndices(unsplitIS[dep], &unsplitPoints[dep]);CHKERRQ(ierr); 608 } 609 } 610 /* Calculate number of hybrid points */ 611 for (d = 1; d <= depth; ++d) numHybridPoints[d] = numSplitPoints[d-1] + numUnsplitPoints[d-1]; /* There is a hybrid cell/face/edge for every split face/edge/vertex */ 612 for (d = 0; d <= depth; ++d) depthShift[d] = numSplitPoints[d] + numHybridPoints[d]; 613 for (d = 1; d <= depth; ++d) depthOffset[depths[d]] = depthOffset[depths[d-1]] + depthShift[depths[d-1]]; 614 for (d = 0; d <= depth; ++d) pMaxNew[d] += depthOffset[d]; 615 ierr = DMPlexShiftSizes_Internal(dm, depthShift, sdm);CHKERRQ(ierr); 616 /* Step 3: Set cone/support sizes for new points */ 617 for (dep = 0; dep <= depth; ++dep) { 618 for (p = 0; p < numSplitPoints[dep]; ++p) { 619 const PetscInt oldp = splitPoints[dep][p]; 620 const PetscInt newp = oldp + depthOffset[dep]; 621 const PetscInt splitp = p + pMaxNew[dep]; 622 const PetscInt *support; 623 PetscInt coneSize, supportSize, qf, qn, qp, e; 624 625 ierr = DMPlexGetConeSize(dm, oldp, &coneSize);CHKERRQ(ierr); 626 ierr = DMPlexSetConeSize(sdm, splitp, coneSize);CHKERRQ(ierr); 627 ierr = DMPlexGetSupportSize(dm, oldp, &supportSize);CHKERRQ(ierr); 628 ierr = DMPlexSetSupportSize(sdm, splitp, supportSize);CHKERRQ(ierr); 629 if (dep == depth-1) { 630 const PetscInt hybcell = p + pMaxNew[dep+1] + numSplitPoints[dep+1]; 631 632 /* Add cohesive cells, they are prisms */ 633 ierr = DMPlexSetConeSize(sdm, hybcell, 2 + coneSize);CHKERRQ(ierr); 634 } else if (dep == 0) { 635 const PetscInt hybedge = p + pMaxNew[dep+1] + numSplitPoints[dep+1]; 636 637 ierr = DMPlexGetSupport(dm, oldp, &support);CHKERRQ(ierr); 638 for (e = 0, qn = 0, qp = 0, qf = 0; e < supportSize; ++e) { 639 PetscInt val; 640 641 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 642 if (val == 1) ++qf; 643 if ((val == 1) || (val == (shift + 1))) ++qn; 644 if ((val == 1) || (val == -(shift + 1))) ++qp; 645 } 646 /* Split old vertex: Edges into original vertex and new cohesive edge */ 647 ierr = DMPlexSetSupportSize(sdm, newp, qn+1);CHKERRQ(ierr); 648 /* Split new vertex: Edges into split vertex and new cohesive edge */ 649 ierr = DMPlexSetSupportSize(sdm, splitp, qp+1);CHKERRQ(ierr); 650 /* Add hybrid edge */ 651 ierr = DMPlexSetConeSize(sdm, hybedge, 2);CHKERRQ(ierr); 652 ierr = DMPlexSetSupportSize(sdm, hybedge, qf);CHKERRQ(ierr); 653 } else if (dep == dim-2) { 654 const PetscInt hybface = p + pMaxNew[dep+1] + numSplitPoints[dep+1]; 655 656 ierr = DMPlexGetSupport(dm, oldp, &support);CHKERRQ(ierr); 657 for (e = 0, qn = 0, qp = 0, qf = 0; e < supportSize; ++e) { 658 PetscInt val; 659 660 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 661 if (val == dim-1) ++qf; 662 if ((val == dim-1) || (val == (shift + dim-1))) ++qn; 663 if ((val == dim-1) || (val == -(shift + dim-1))) ++qp; 664 } 665 /* Split old edge: Faces into original edge and cohesive face (positive side?) */ 666 ierr = DMPlexSetSupportSize(sdm, newp, qn+1);CHKERRQ(ierr); 667 /* Split new edge: Faces into split edge and cohesive face (negative side?) */ 668 ierr = DMPlexSetSupportSize(sdm, splitp, qp+1);CHKERRQ(ierr); 669 /* Add hybrid face */ 670 ierr = DMPlexSetConeSize(sdm, hybface, 4);CHKERRQ(ierr); 671 ierr = DMPlexSetSupportSize(sdm, hybface, qf);CHKERRQ(ierr); 672 } 673 } 674 } 675 for (dep = 0; dep <= depth; ++dep) { 676 for (p = 0; p < numUnsplitPoints[dep]; ++p) { 677 const PetscInt oldp = unsplitPoints[dep][p]; 678 const PetscInt newp = oldp + depthOffset[dep]; 679 const PetscInt *support; 680 PetscInt coneSize, supportSize, qf, qn, qp, e; 681 682 ierr = DMPlexGetConeSize(dm, oldp, &coneSize);CHKERRQ(ierr); 683 ierr = DMPlexGetSupportSize(dm, oldp, &supportSize);CHKERRQ(ierr); 684 if (dep == 0) { 685 const PetscInt hybedge = p + pMaxNew[dep+1] + numSplitPoints[dep+1] + numSplitPoints[dep]; 686 687 /* Unsplit vertex: Edges into original vertex, split edge, and new cohesive edge twice */ 688 ierr = DMPlexSetSupportSize(sdm, newp, supportSize+3);CHKERRQ(ierr); 689 /* Add hybrid edge */ 690 ierr = DMPlexSetConeSize(sdm, hybedge, 2);CHKERRQ(ierr); 691 ierr = DMPlexSetSupportSize(sdm, hybedge, 1);CHKERRQ(ierr); 692 } else if (dep == dim-2) { 693 const PetscInt hybface = p + pMaxNew[dep+1] + numSplitPoints[dep+1] + numSplitPoints[dep]; 694 695 ierr = DMPlexGetSupport(dm, oldp, &support);CHKERRQ(ierr); 696 for (e = 0, qn = 0, qp = 0, qf = 0; e < supportSize; ++e) { 697 PetscInt val; 698 699 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 700 if (val == dim-1) ++qf; 701 if ((val == dim-1) || (val == (shift + dim-1))) ++qn; 702 if ((val == dim-1) || (val == -(shift + dim-1))) ++qp; 703 } 704 /* Unsplit edge: Faces into original edge, split face, and cohesive face twice */ 705 ierr = DMPlexSetSupportSize(sdm, newp, supportSize+3);CHKERRQ(ierr); 706 /* Add hybrid face */ 707 ierr = DMPlexSetConeSize(sdm, hybface, 4);CHKERRQ(ierr); 708 ierr = DMPlexSetSupportSize(sdm, hybface, 1);CHKERRQ(ierr); 709 } 710 } 711 } 712 /* Step 4: Setup split DM */ 713 ierr = DMSetUp(sdm);CHKERRQ(ierr); 714 ierr = DMPlexShiftPoints_Internal(dm, depthShift, sdm);CHKERRQ(ierr); 715 ierr = DMPlexGetMaxSizes(sdm, &maxConeSizeNew, &maxSupportSizeNew);CHKERRQ(ierr); 716 ierr = PetscMalloc3(PetscMax(maxConeSize, maxConeSizeNew)*3,PetscInt,&coneNew,PetscMax(maxConeSize, maxConeSizeNew)*3,PetscInt,&coneONew,PetscMax(maxSupportSize, maxSupportSizeNew),PetscInt,&supportNew);CHKERRQ(ierr); 717 /* Step 6: Set cones and supports for new points */ 718 for (dep = 0; dep <= depth; ++dep) { 719 for (p = 0; p < numSplitPoints[dep]; ++p) { 720 const PetscInt oldp = splitPoints[dep][p]; 721 const PetscInt newp = oldp + depthOffset[dep]; 722 const PetscInt splitp = p + pMaxNew[dep]; 723 const PetscInt *cone, *support, *ornt; 724 PetscInt coneSize, supportSize, q, qf, qn, qp, v, e, s; 725 726 ierr = DMPlexGetConeSize(dm, oldp, &coneSize);CHKERRQ(ierr); 727 ierr = DMPlexGetCone(dm, oldp, &cone);CHKERRQ(ierr); 728 ierr = DMPlexGetConeOrientation(dm, oldp, &ornt);CHKERRQ(ierr); 729 ierr = DMPlexGetSupportSize(dm, oldp, &supportSize);CHKERRQ(ierr); 730 ierr = DMPlexGetSupport(dm, oldp, &support);CHKERRQ(ierr); 731 if (dep == depth-1) { 732 const PetscInt hybcell = p + pMaxNew[dep+1] + numSplitPoints[dep+1]; 733 const PetscInt *supportF; 734 735 /* Split face: copy in old face to new face to start */ 736 ierr = DMPlexGetSupport(sdm, newp, &supportF);CHKERRQ(ierr); 737 ierr = DMPlexSetSupport(sdm, splitp, supportF);CHKERRQ(ierr); 738 /* Split old face: old vertices/edges in cone so no change */ 739 /* Split new face: new vertices/edges in cone */ 740 for (q = 0; q < coneSize; ++q) { 741 ierr = PetscFindInt(cone[q], numSplitPoints[dep-1], splitPoints[dep-1], &v);CHKERRQ(ierr); 742 if (v < 0) { 743 ierr = PetscFindInt(cone[q], numUnsplitPoints[dep-1], unsplitPoints[dep-1], &v);CHKERRQ(ierr); 744 if (v < 0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not locate point %d in split or unsplit points of depth %d", cone[q], dep-1); 745 coneNew[2+q] = cone[q] + depthOffset[dep-1]; 746 } else { 747 coneNew[2+q] = v + pMaxNew[dep-1]; 748 } 749 } 750 ierr = DMPlexSetCone(sdm, splitp, &coneNew[2]);CHKERRQ(ierr); 751 ierr = DMPlexSetConeOrientation(sdm, splitp, ornt);CHKERRQ(ierr); 752 /* Face support */ 753 for (s = 0; s < supportSize; ++s) { 754 PetscInt val; 755 756 ierr = DMLabelGetValue(label, support[s], &val);CHKERRQ(ierr); 757 if (val < 0) { 758 /* Split old face: Replace negative side cell with cohesive cell */ 759 ierr = DMPlexInsertSupport(sdm, newp, s, hybcell);CHKERRQ(ierr); 760 } else { 761 /* Split new face: Replace positive side cell with cohesive cell */ 762 ierr = DMPlexInsertSupport(sdm, splitp, s, hybcell);CHKERRQ(ierr); 763 /* Get orientation for cohesive face */ 764 { 765 const PetscInt *ncone, *nconeO; 766 PetscInt nconeSize, nc; 767 768 ierr = DMPlexGetConeSize(dm, support[s], &nconeSize);CHKERRQ(ierr); 769 ierr = DMPlexGetCone(dm, support[s], &ncone);CHKERRQ(ierr); 770 ierr = DMPlexGetConeOrientation(dm, support[s], &nconeO);CHKERRQ(ierr); 771 for (nc = 0; nc < nconeSize; ++nc) { 772 if (ncone[nc] == oldp) { 773 coneONew[0] = nconeO[nc]; 774 break; 775 } 776 } 777 if (nc >= nconeSize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not locate face %d in neighboring cell %d", oldp, support[s]); 778 } 779 } 780 } 781 /* Cohesive cell: Old and new split face, then new cohesive faces */ 782 coneNew[0] = newp; /* Extracted negative side orientation above */ 783 coneNew[1] = splitp; 784 coneONew[1] = coneONew[0]; 785 for (q = 0; q < coneSize; ++q) { 786 ierr = PetscFindInt(cone[q], numSplitPoints[dep-1], splitPoints[dep-1], &v);CHKERRQ(ierr); 787 if (v < 0) { 788 ierr = PetscFindInt(cone[q], numUnsplitPoints[dep-1], unsplitPoints[dep-1], &v);CHKERRQ(ierr); 789 coneNew[2+q] = v + pMaxNew[dep] + numSplitPoints[dep] + numSplitPoints[dep-1]; 790 coneONew[2+q] = 0; 791 } else { 792 coneNew[2+q] = v + pMaxNew[dep] + numSplitPoints[dep]; 793 } 794 coneONew[2+q] = 0; 795 } 796 ierr = DMPlexSetCone(sdm, hybcell, coneNew);CHKERRQ(ierr); 797 ierr = DMPlexSetConeOrientation(sdm, hybcell, coneONew);CHKERRQ(ierr); 798 } else if (dep == 0) { 799 const PetscInt hybedge = p + pMaxNew[dep+1] + numSplitPoints[dep+1]; 800 801 /* Split old vertex: Edges in old split faces and new cohesive edge */ 802 for (e = 0, qn = 0; e < supportSize; ++e) { 803 PetscInt val; 804 805 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 806 if ((val == 1) || (val == (shift + 1))) { 807 supportNew[qn++] = support[e] + depthOffset[dep+1]; 808 } 809 } 810 supportNew[qn] = hybedge; 811 ierr = DMPlexSetSupport(sdm, newp, supportNew);CHKERRQ(ierr); 812 /* Split new vertex: Edges in new split faces and new cohesive edge */ 813 for (e = 0, qp = 0; e < supportSize; ++e) { 814 PetscInt val, edge; 815 816 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 817 if (val == 1) { 818 ierr = PetscFindInt(support[e], numSplitPoints[dep+1], splitPoints[dep+1], &edge);CHKERRQ(ierr); 819 if (edge < 0) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Edge %d is not a split edge", support[e]); 820 supportNew[qp++] = edge + pMaxNew[dep+1]; 821 } else if (val == -(shift + 1)) { 822 supportNew[qp++] = support[e] + depthOffset[dep+1]; 823 } 824 } 825 supportNew[qp] = hybedge; 826 ierr = DMPlexSetSupport(sdm, splitp, supportNew);CHKERRQ(ierr); 827 /* Hybrid edge: Old and new split vertex */ 828 coneNew[0] = newp; 829 coneNew[1] = splitp; 830 ierr = DMPlexSetCone(sdm, hybedge, coneNew);CHKERRQ(ierr); 831 for (e = 0, qf = 0; e < supportSize; ++e) { 832 PetscInt val, edge; 833 834 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 835 if (val == 1) { 836 ierr = PetscFindInt(support[e], numSplitPoints[dep+1], splitPoints[dep+1], &edge);CHKERRQ(ierr); 837 if (edge < 0) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Edge %d is not a split edge", support[e]); 838 supportNew[qf++] = edge + pMaxNew[dep+2] + numSplitPoints[dep+2]; 839 } 840 } 841 ierr = DMPlexSetSupport(sdm, hybedge, supportNew);CHKERRQ(ierr); 842 } else if (dep == dim-2) { 843 const PetscInt hybface = p + pMaxNew[dep+1] + numSplitPoints[dep+1]; 844 845 /* Split old edge: old vertices in cone so no change */ 846 /* Split new edge: new vertices in cone */ 847 for (q = 0; q < coneSize; ++q) { 848 ierr = PetscFindInt(cone[q], numSplitPoints[dep-1], splitPoints[dep-1], &v);CHKERRQ(ierr); 849 850 coneNew[q] = v + pMaxNew[dep-1]; 851 } 852 ierr = DMPlexSetCone(sdm, splitp, coneNew);CHKERRQ(ierr); 853 /* Split old edge: Faces in positive side cells and old split faces */ 854 for (e = 0, q = 0; e < supportSize; ++e) { 855 PetscInt val; 856 857 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 858 if (val == dim-1) { 859 supportNew[q++] = support[e] + depthOffset[dep+1]; 860 } else if (val == (shift + dim-1)) { 861 supportNew[q++] = support[e] + depthOffset[dep+1]; 862 } 863 } 864 supportNew[q++] = p + pMaxNew[dep+1] + numSplitPoints[dep+1]; 865 ierr = DMPlexSetSupport(sdm, newp, supportNew);CHKERRQ(ierr); 866 /* Split new edge: Faces in negative side cells and new split faces */ 867 for (e = 0, q = 0; e < supportSize; ++e) { 868 PetscInt val, face; 869 870 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 871 if (val == dim-1) { 872 ierr = PetscFindInt(support[e], numSplitPoints[dep+1], splitPoints[dep+1], &face);CHKERRQ(ierr); 873 if (face < 0) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Face %d is not a split face", support[e]); 874 supportNew[q++] = face + pMaxNew[dep+1]; 875 } else if (val == -(shift + dim-1)) { 876 supportNew[q++] = support[e] + depthOffset[dep+1]; 877 } 878 } 879 supportNew[q++] = p + pMaxNew[dep+1] + numSplitPoints[dep+1]; 880 ierr = DMPlexSetSupport(sdm, splitp, supportNew);CHKERRQ(ierr); 881 /* Hybrid face */ 882 coneNew[0] = newp; 883 coneNew[1] = splitp; 884 for (v = 0; v < coneSize; ++v) { 885 PetscInt vertex; 886 ierr = PetscFindInt(cone[v], numSplitPoints[dep-1], splitPoints[dep-1], &vertex);CHKERRQ(ierr); 887 if (vertex < 0) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Vertex %d is not a split vertex", support[e]); 888 coneNew[2+v] = vertex + pMaxNew[dep] + numSplitPoints[dep]; 889 } 890 ierr = DMPlexSetCone(sdm, hybface, coneNew);CHKERRQ(ierr); 891 for (e = 0, qf = 0; e < supportSize; ++e) { 892 PetscInt val, face; 893 894 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 895 if (val == dim-1) { 896 ierr = PetscFindInt(support[e], numSplitPoints[dep+1], splitPoints[dep+1], &face);CHKERRQ(ierr); 897 if (face < 0) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Face %d is not a split face", support[e]); 898 supportNew[qf++] = face + pMaxNew[dep+2] + numSplitPoints[dep+2]; 899 } 900 } 901 ierr = DMPlexSetSupport(sdm, hybface, supportNew);CHKERRQ(ierr); 902 } 903 } 904 } 905 for (dep = 0; dep <= depth; ++dep) { 906 for (p = 0; p < numUnsplitPoints[dep]; ++p) { 907 const PetscInt oldp = unsplitPoints[dep][p]; 908 const PetscInt newp = oldp + depthOffset[dep]; 909 const PetscInt *cone, *support, *ornt; 910 PetscInt coneSize, supportSize, supportSizeNew, q, qf, e, s; 911 912 ierr = DMPlexGetConeSize(dm, oldp, &coneSize);CHKERRQ(ierr); 913 ierr = DMPlexGetCone(dm, oldp, &cone);CHKERRQ(ierr); 914 ierr = DMPlexGetConeOrientation(dm, oldp, &ornt);CHKERRQ(ierr); 915 ierr = DMPlexGetSupportSize(dm, oldp, &supportSize);CHKERRQ(ierr); 916 ierr = DMPlexGetSupport(dm, oldp, &support);CHKERRQ(ierr); 917 if (dep == 0) { 918 const PetscInt hybedge = p + pMaxNew[dep+1] + numSplitPoints[dep+1] + numSplitPoints[dep]; 919 920 /* Unsplit vertex */ 921 ierr = DMPlexGetSupportSize(sdm, newp, &supportSizeNew);CHKERRQ(ierr); 922 for (s = 0, q = 0; s < supportSize; ++s) { 923 supportNew[q++] = support[s] + depthOffset[dep+1]; 924 ierr = PetscFindInt(support[s], numSplitPoints[dep+1], splitPoints[dep+1], &e);CHKERRQ(ierr); 925 if (e >= 0) { 926 supportNew[q++] = e + pMaxNew[dep+1]; 927 } 928 } 929 supportNew[q++] = hybedge; 930 supportNew[q++] = hybedge; 931 if (q != supportSizeNew) SETERRQ3(comm, PETSC_ERR_ARG_WRONG, "Support size %d != %d for vertex %d", q, supportSizeNew, newp); 932 ierr = DMPlexSetSupport(sdm, newp, supportNew);CHKERRQ(ierr); 933 /* Hybrid edge */ 934 coneNew[0] = newp; 935 coneNew[1] = newp; 936 ierr = DMPlexSetCone(sdm, hybedge, coneNew);CHKERRQ(ierr); 937 for (e = 0, qf = 0; e < supportSize; ++e) { 938 PetscInt val, edge; 939 940 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 941 if (val == 1) { 942 ierr = PetscFindInt(support[e], numSplitPoints[dep+1], splitPoints[dep+1], &edge);CHKERRQ(ierr); 943 if (edge < 0) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Edge %d is not a split edge", support[e]); 944 supportNew[qf++] = edge + pMaxNew[dep+2] + numSplitPoints[dep+2]; 945 } 946 } 947 ierr = DMPlexSetSupport(sdm, hybedge, supportNew);CHKERRQ(ierr); 948 } 949 } 950 } 951 /* Step 6b: Replace split points in negative side cones */ 952 for (sp = 0; sp < numSP; ++sp) { 953 PetscInt dep = values[sp]; 954 IS pIS; 955 PetscInt numPoints; 956 const PetscInt *points; 957 958 if (dep >= 0) continue; 959 ierr = DMLabelGetStratumIS(label, dep, &pIS);CHKERRQ(ierr); 960 if (!pIS) continue; 961 dep = -dep - shift; 962 ierr = ISGetLocalSize(pIS, &numPoints);CHKERRQ(ierr); 963 ierr = ISGetIndices(pIS, &points);CHKERRQ(ierr); 964 for (p = 0; p < numPoints; ++p) { 965 const PetscInt oldp = points[p]; 966 const PetscInt newp = depthOffset[dep] + oldp; 967 const PetscInt *cone; 968 PetscInt coneSize, c; 969 /* PetscBool replaced = PETSC_FALSE; */ 970 971 /* Negative edge: replace split vertex */ 972 /* Negative cell: replace split face */ 973 ierr = DMPlexGetConeSize(sdm, newp, &coneSize);CHKERRQ(ierr); 974 ierr = DMPlexGetCone(sdm, newp, &cone);CHKERRQ(ierr); 975 for (c = 0; c < coneSize; ++c) { 976 const PetscInt coldp = cone[c] - depthOffset[dep-1]; 977 PetscInt csplitp, cp, val; 978 979 ierr = DMLabelGetValue(label, coldp, &val);CHKERRQ(ierr); 980 if (val == dep-1) { 981 ierr = PetscFindInt(coldp, numSplitPoints[dep-1], splitPoints[dep-1], &cp);CHKERRQ(ierr); 982 if (cp < 0) SETERRQ2(comm, PETSC_ERR_ARG_WRONG, "Point %d is not a split point of dimension %d", oldp, dep-1); 983 csplitp = pMaxNew[dep-1] + cp; 984 ierr = DMPlexInsertCone(sdm, newp, c, csplitp);CHKERRQ(ierr); 985 /* replaced = PETSC_TRUE; */ 986 } 987 } 988 /* Cells with only a vertex or edge on the submesh have no replacement */ 989 /* if (!replaced) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "The cone of point %d does not contain split points", oldp); */ 990 } 991 ierr = ISRestoreIndices(pIS, &points);CHKERRQ(ierr); 992 ierr = ISDestroy(&pIS);CHKERRQ(ierr); 993 } 994 /* Step 7: Stratify */ 995 ierr = DMPlexStratify(sdm);CHKERRQ(ierr); 996 /* Step 8: Coordinates */ 997 ierr = DMPlexShiftCoordinates_Internal(dm, depthShift, sdm);CHKERRQ(ierr); 998 ierr = DMPlexGetCoordinateSection(sdm, &coordSection);CHKERRQ(ierr); 999 ierr = DMGetCoordinatesLocal(sdm, &coordinates);CHKERRQ(ierr); 1000 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1001 for (v = 0; v < (numSplitPoints ? numSplitPoints[0] : 0); ++v) { 1002 const PetscInt newp = depthOffset[0] + splitPoints[0][v]; 1003 const PetscInt splitp = pMaxNew[0] + v; 1004 PetscInt dof, off, soff, d; 1005 1006 ierr = PetscSectionGetDof(coordSection, newp, &dof);CHKERRQ(ierr); 1007 ierr = PetscSectionGetOffset(coordSection, newp, &off);CHKERRQ(ierr); 1008 ierr = PetscSectionGetOffset(coordSection, splitp, &soff);CHKERRQ(ierr); 1009 for (d = 0; d < dof; ++d) coords[soff+d] = coords[off+d]; 1010 } 1011 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1012 /* Step 9: SF, if I can figure this out we can split the mesh in parallel */ 1013 ierr = DMPlexShiftSF_Internal(dm, depthShift, sdm);CHKERRQ(ierr); 1014 /* Step 10: Labels */ 1015 ierr = DMPlexShiftLabels_Internal(dm, depthShift, sdm);CHKERRQ(ierr); 1016 ierr = DMPlexGetNumLabels(sdm, &numLabels);CHKERRQ(ierr); 1017 for (dep = 0; dep <= depth; ++dep) { 1018 for (p = 0; p < numSplitPoints[dep]; ++p) { 1019 const PetscInt newp = depthOffset[dep] + splitPoints[dep][p]; 1020 const PetscInt splitp = pMaxNew[dep] + p; 1021 PetscInt l; 1022 1023 for (l = 0; l < numLabels; ++l) { 1024 DMLabel mlabel; 1025 const char *lname; 1026 PetscInt val; 1027 PetscBool isDepth; 1028 1029 ierr = DMPlexGetLabelName(sdm, l, &lname);CHKERRQ(ierr); 1030 ierr = PetscStrcmp(lname, "depth", &isDepth);CHKERRQ(ierr); 1031 if (isDepth) continue; 1032 ierr = DMPlexGetLabel(sdm, lname, &mlabel);CHKERRQ(ierr); 1033 ierr = DMLabelGetValue(mlabel, newp, &val);CHKERRQ(ierr); 1034 if (val >= 0) { 1035 ierr = DMLabelSetValue(mlabel, splitp, val);CHKERRQ(ierr); 1036 #if 0 1037 /* Do not put cohesive edges into the label */ 1038 if (dep == 0) { 1039 const PetscInt cedge = p + pMaxNew[dep+1] + numSplitPoints[dep+1]; 1040 ierr = DMLabelSetValue(mlabel, cedge, val);CHKERRQ(ierr); 1041 } else if (dep == dim-2) { 1042 const PetscInt cface = p + pMaxNew[dep+1] + numSplitPoints[dep+1]; 1043 ierr = DMLabelSetValue(mlabel, cface, val);CHKERRQ(ierr); 1044 } 1045 /* Do not put cohesive faces into the label */ 1046 #endif 1047 } 1048 } 1049 } 1050 } 1051 for (sp = 0; sp < numSP; ++sp) { 1052 const PetscInt dep = values[sp]; 1053 1054 if ((dep < 0) || (dep > depth)) continue; 1055 if (splitIS[dep]) {ierr = ISRestoreIndices(splitIS[dep], &splitPoints[dep]);CHKERRQ(ierr);} 1056 ierr = ISDestroy(&splitIS[dep]);CHKERRQ(ierr); 1057 if (unsplitIS[dep]) {ierr = ISRestoreIndices(unsplitIS[dep], &unsplitPoints[dep]);CHKERRQ(ierr);} 1058 ierr = ISDestroy(&unsplitIS[dep]);CHKERRQ(ierr); 1059 } 1060 if (label) { 1061 ierr = ISRestoreIndices(valueIS, &values);CHKERRQ(ierr); 1062 ierr = ISDestroy(&valueIS);CHKERRQ(ierr); 1063 } 1064 for (d = 0; d <= depth; ++d) { 1065 ierr = DMPlexGetDepthStratum(sdm, d, NULL, &pEnd);CHKERRQ(ierr); 1066 pMaxNew[d] = pEnd - numHybridPoints[d]; 1067 } 1068 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); 1069 ierr = PetscFree3(depthShift, depthOffset, pMaxNew);CHKERRQ(ierr); 1070 ierr = PetscFree3(coneNew, coneONew, supportNew);CHKERRQ(ierr); 1071 ierr = PetscFree7(splitIS, unsplitIS, numSplitPoints, numUnsplitPoints, numHybridPoints, splitPoints, unsplitPoints);CHKERRQ(ierr); 1072 PetscFunctionReturn(0); 1073 } 1074 1075 #undef __FUNCT__ 1076 #define __FUNCT__ "DMPlexConstructCohesiveCells" 1077 /*@C 1078 DMPlexConstructCohesiveCells - Construct cohesive cells which split the face along an internal interface 1079 1080 Collective on dm 1081 1082 Input Parameters: 1083 + dm - The original DM 1084 - label - The label specifying the boundary faces (this could be auto-generated) 1085 1086 Output Parameters: 1087 - dmSplit - The new DM 1088 1089 Level: developer 1090 1091 .seealso: DMCreate(), DMPlexLabelCohesiveComplete() 1092 @*/ 1093 PetscErrorCode DMPlexConstructCohesiveCells(DM dm, DMLabel label, DM *dmSplit) 1094 { 1095 DM sdm; 1096 PetscInt dim; 1097 PetscErrorCode ierr; 1098 1099 PetscFunctionBegin; 1100 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1101 PetscValidPointer(dmSplit, 3); 1102 ierr = DMCreate(PetscObjectComm((PetscObject)dm), &sdm);CHKERRQ(ierr); 1103 ierr = DMSetType(sdm, DMPLEX);CHKERRQ(ierr); 1104 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1105 ierr = DMPlexSetDimension(sdm, dim);CHKERRQ(ierr); 1106 switch (dim) { 1107 case 2: 1108 case 3: 1109 ierr = DMPlexConstructCohesiveCells_Internal(dm, label, sdm);CHKERRQ(ierr); 1110 break; 1111 default: 1112 SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Cannot construct cohesive cells for dimension %d", dim); 1113 } 1114 *dmSplit = sdm; 1115 PetscFunctionReturn(0); 1116 } 1117 1118 #undef __FUNCT__ 1119 #define __FUNCT__ "DMPlexLabelCohesiveComplete" 1120 /*@ 1121 DMPlexLabelCohesiveComplete - Starting with a label marking vertices on an internal surface, we add all other mesh pieces 1122 to complete the surface 1123 1124 Input Parameters: 1125 + dm - The DM 1126 . label - A DMLabel marking the surface vertices 1127 . flip - Flag to flip the submesh normal and replace points on the other side 1128 - subdm - The subDM associated with the label, or NULL 1129 1130 Output Parameter: 1131 . label - A DMLabel marking all surface points 1132 1133 Level: developer 1134 1135 .seealso: DMPlexConstructCohesiveCells(), DMPlexLabelComplete() 1136 @*/ 1137 PetscErrorCode DMPlexLabelCohesiveComplete(DM dm, DMLabel label, PetscBool flip, DM subdm) 1138 { 1139 DMLabel depthLabel; 1140 IS dimIS, subpointIS, facePosIS, faceNegIS; 1141 const PetscInt *points, *subpoints; 1142 const PetscInt rev = flip ? -1 : 1; 1143 PetscInt shift = 100, shift2 = 200, dim, dep, cStart, cEnd, numPoints, numSubpoints, p, val; 1144 PetscErrorCode ierr; 1145 1146 PetscFunctionBegin; 1147 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 1148 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1149 if (subdm) { 1150 ierr = DMPlexCreateSubpointIS(subdm, &subpointIS);CHKERRQ(ierr); 1151 if (subpointIS) { 1152 ierr = ISGetLocalSize(subpointIS, &numSubpoints);CHKERRQ(ierr); 1153 ierr = ISGetIndices(subpointIS, &subpoints);CHKERRQ(ierr); 1154 } 1155 } 1156 /* Mark cell on the fault, and its faces which touch the fault: cell orientation for face gives the side of the fault */ 1157 ierr = DMLabelGetStratumIS(label, dim-1, &dimIS);CHKERRQ(ierr); 1158 if (!dimIS) PetscFunctionReturn(0); 1159 ierr = ISGetLocalSize(dimIS, &numPoints);CHKERRQ(ierr); 1160 ierr = ISGetIndices(dimIS, &points);CHKERRQ(ierr); 1161 for (p = 0; p < numPoints; ++p) { /* Loop over fault faces */ 1162 const PetscInt *support; 1163 PetscInt supportSize, s; 1164 1165 ierr = DMPlexGetSupportSize(dm, points[p], &supportSize);CHKERRQ(ierr); 1166 if (supportSize != 2) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Split face %d has %d != 2 supports", points[p], supportSize); 1167 ierr = DMPlexGetSupport(dm, points[p], &support);CHKERRQ(ierr); 1168 for (s = 0; s < supportSize; ++s) { 1169 const PetscInt *cone, *ornt; 1170 PetscInt coneSize, c; 1171 PetscBool pos = PETSC_TRUE; 1172 1173 ierr = DMPlexGetConeSize(dm, support[s], &coneSize);CHKERRQ(ierr); 1174 ierr = DMPlexGetCone(dm, support[s], &cone);CHKERRQ(ierr); 1175 ierr = DMPlexGetConeOrientation(dm, support[s], &ornt);CHKERRQ(ierr); 1176 for (c = 0; c < coneSize; ++c) { 1177 if (cone[c] == points[p]) { 1178 PetscInt o = ornt[c]; 1179 1180 if (subdm) { 1181 const PetscInt *subcone, *subornt; 1182 PetscInt subpoint, subface, subconeSize, sc; 1183 1184 ierr = PetscFindInt(support[s], numSubpoints, subpoints, &subpoint);CHKERRQ(ierr); 1185 ierr = PetscFindInt(points[p], numSubpoints, subpoints, &subface);CHKERRQ(ierr); 1186 ierr = DMPlexGetConeSize(subdm, subpoint, &subconeSize);CHKERRQ(ierr); 1187 ierr = DMPlexGetCone(subdm, subpoint, &subcone);CHKERRQ(ierr); 1188 ierr = DMPlexGetConeOrientation(subdm, subpoint, &subornt);CHKERRQ(ierr); 1189 for (sc = 0; sc < subconeSize; ++sc) { 1190 if (subcone[sc] == subface) { 1191 o = subornt[0]; 1192 break; 1193 } 1194 } 1195 if (sc >= subconeSize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not find point %d in cone for subpoint %d", points[p], subpoint); 1196 } 1197 if (o >= 0) { 1198 ierr = DMLabelSetValue(label, support[s], rev*(shift+dim));CHKERRQ(ierr); 1199 pos = rev > 0 ? PETSC_TRUE : PETSC_FALSE; 1200 } else { 1201 ierr = DMLabelSetValue(label, support[s], -rev*(shift+dim));CHKERRQ(ierr); 1202 pos = rev > 0 ? PETSC_FALSE : PETSC_TRUE; 1203 } 1204 break; 1205 } 1206 } 1207 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]); 1208 /* Put faces touching the fault in the label */ 1209 for (c = 0; c < coneSize; ++c) { 1210 const PetscInt point = cone[c]; 1211 1212 ierr = DMLabelGetValue(label, point, &val);CHKERRQ(ierr); 1213 if (val == -1) { 1214 PetscInt *closure = NULL; 1215 PetscInt closureSize, cl; 1216 1217 ierr = DMPlexGetTransitiveClosure(dm, point, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1218 for (cl = 0; cl < closureSize*2; cl += 2) { 1219 const PetscInt clp = closure[cl]; 1220 1221 ierr = DMLabelGetValue(label, clp, &val);CHKERRQ(ierr); 1222 if ((val >= 0) && (val < dim-1)) { 1223 ierr = DMLabelSetValue(label, point, pos == PETSC_TRUE ? shift+dim-1 : -(shift+dim-1));CHKERRQ(ierr); 1224 break; 1225 } 1226 } 1227 ierr = DMPlexRestoreTransitiveClosure(dm, point, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1228 } 1229 } 1230 } 1231 } 1232 if (subdm) { 1233 if (subpointIS) {ierr = ISRestoreIndices(subpointIS, &subpoints);CHKERRQ(ierr);} 1234 ierr = ISDestroy(&subpointIS);CHKERRQ(ierr); 1235 } 1236 ierr = ISRestoreIndices(dimIS, &points);CHKERRQ(ierr); 1237 ierr = ISDestroy(&dimIS);CHKERRQ(ierr); 1238 /* Search for other cells/faces/edges connected to the fault by a vertex */ 1239 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1240 ierr = DMLabelGetStratumIS(label, 0, &dimIS);CHKERRQ(ierr); 1241 if (!dimIS) PetscFunctionReturn(0); 1242 ierr = ISGetLocalSize(dimIS, &numPoints);CHKERRQ(ierr); 1243 ierr = ISGetIndices(dimIS, &points);CHKERRQ(ierr); 1244 for (p = 0; p < numPoints; ++p) { /* Loop over fault vertices */ 1245 PetscInt *star = NULL; 1246 PetscInt starSize, s; 1247 PetscInt again = 1; /* 0: Finished 1: Keep iterating after a change 2: No change */ 1248 1249 /* All points connected to the fault are inside a cell, so at the top level we will only check cells */ 1250 ierr = DMPlexGetTransitiveClosure(dm, points[p], PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1251 while (again) { 1252 if (again > 1) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Could not classify all cells connected to the fault"); 1253 again = 0; 1254 for (s = 0; s < starSize*2; s += 2) { 1255 const PetscInt point = star[s]; 1256 const PetscInt *cone; 1257 PetscInt coneSize, c; 1258 1259 if ((point < cStart) || (point >= cEnd)) continue; 1260 ierr = DMLabelGetValue(label, point, &val);CHKERRQ(ierr); 1261 if (val != -1) continue; 1262 again = again == 1 ? 1 : 2; 1263 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 1264 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 1265 for (c = 0; c < coneSize; ++c) { 1266 ierr = DMLabelGetValue(label, cone[c], &val);CHKERRQ(ierr); 1267 if (val != -1) { 1268 const PetscInt *ccone; 1269 PetscInt cconeSize, cc, side; 1270 1271 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); 1272 if (val > 0) side = 1; 1273 else side = -1; 1274 ierr = DMLabelSetValue(label, point, side*(shift+dim));CHKERRQ(ierr); 1275 /* Mark cell faces which touch the fault */ 1276 ierr = DMPlexGetConeSize(dm, point, &cconeSize);CHKERRQ(ierr); 1277 ierr = DMPlexGetCone(dm, point, &ccone);CHKERRQ(ierr); 1278 for (cc = 0; cc < cconeSize; ++cc) { 1279 PetscInt *closure = NULL; 1280 PetscInt closureSize, cl; 1281 1282 ierr = DMLabelGetValue(label, ccone[cc], &val);CHKERRQ(ierr); 1283 if (val != -1) continue; 1284 ierr = DMPlexGetTransitiveClosure(dm, ccone[cc], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1285 for (cl = 0; cl < closureSize*2; cl += 2) { 1286 const PetscInt clp = closure[cl]; 1287 1288 ierr = DMLabelGetValue(label, clp, &val);CHKERRQ(ierr); 1289 if (val == -1) continue; 1290 ierr = DMLabelSetValue(label, ccone[cc], side*(shift+dim-1));CHKERRQ(ierr); 1291 break; 1292 } 1293 ierr = DMPlexRestoreTransitiveClosure(dm, ccone[cc], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1294 } 1295 again = 1; 1296 break; 1297 } 1298 } 1299 } 1300 } 1301 /* Classify the rest by cell membership */ 1302 for (s = 0; s < starSize*2; s += 2) { 1303 const PetscInt point = star[s]; 1304 1305 ierr = DMLabelGetValue(label, point, &val);CHKERRQ(ierr); 1306 if (val == -1) { 1307 PetscInt *sstar = NULL; 1308 PetscInt sstarSize, ss; 1309 PetscBool marked = PETSC_FALSE; 1310 1311 ierr = DMPlexGetTransitiveClosure(dm, point, PETSC_FALSE, &sstarSize, &sstar);CHKERRQ(ierr); 1312 for (ss = 0; ss < sstarSize*2; ss += 2) { 1313 const PetscInt spoint = sstar[ss]; 1314 1315 if ((spoint < cStart) || (spoint >= cEnd)) continue; 1316 ierr = DMLabelGetValue(label, spoint, &val);CHKERRQ(ierr); 1317 if (val == -1) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Cell %d in star of %d does not have a valid label", spoint, point); 1318 ierr = DMLabelGetValue(depthLabel, point, &dep);CHKERRQ(ierr); 1319 if (val > 0) { 1320 ierr = DMLabelSetValue(label, point, shift+dep);CHKERRQ(ierr); 1321 } else { 1322 ierr = DMLabelSetValue(label, point, -(shift+dep));CHKERRQ(ierr); 1323 } 1324 marked = PETSC_TRUE; 1325 break; 1326 } 1327 ierr = DMPlexRestoreTransitiveClosure(dm, point, PETSC_FALSE, &sstarSize, &sstar);CHKERRQ(ierr); 1328 if (!marked) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Point %d could not be classified", point); 1329 } 1330 } 1331 ierr = DMPlexRestoreTransitiveClosure(dm, points[p], PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1332 } 1333 ierr = ISRestoreIndices(dimIS, &points);CHKERRQ(ierr); 1334 ierr = ISDestroy(&dimIS);CHKERRQ(ierr); 1335 /* If any faces touching the fault divide cells on either side, split them */ 1336 ierr = DMLabelGetStratumIS(label, shift+dim-1, &facePosIS);CHKERRQ(ierr); 1337 ierr = DMLabelGetStratumIS(label, -(shift+dim-1), &faceNegIS);CHKERRQ(ierr); 1338 ierr = ISExpand(facePosIS, faceNegIS, &dimIS);CHKERRQ(ierr); 1339 ierr = ISDestroy(&facePosIS);CHKERRQ(ierr); 1340 ierr = ISDestroy(&faceNegIS);CHKERRQ(ierr); 1341 ierr = ISGetLocalSize(dimIS, &numPoints);CHKERRQ(ierr); 1342 ierr = ISGetIndices(dimIS, &points);CHKERRQ(ierr); 1343 for (p = 0; p < numPoints; ++p) { 1344 const PetscInt point = points[p]; 1345 const PetscInt *support; 1346 PetscInt supportSize, valA, valB; 1347 1348 ierr = DMPlexGetSupportSize(dm, point, &supportSize);CHKERRQ(ierr); 1349 if (supportSize != 2) continue; 1350 ierr = DMPlexGetSupport(dm, point, &support);CHKERRQ(ierr); 1351 ierr = DMLabelGetValue(label, support[0], &valA);CHKERRQ(ierr); 1352 ierr = DMLabelGetValue(label, support[1], &valB);CHKERRQ(ierr); 1353 if ((valA == -1) || (valB == -1)) continue; 1354 if (valA*valB > 0) continue; 1355 /* Split the face */ 1356 ierr = DMLabelGetValue(label, point, &valA);CHKERRQ(ierr); 1357 ierr = DMLabelClearValue(label, point, valA);CHKERRQ(ierr); 1358 ierr = DMLabelSetValue(label, point, dim-1);CHKERRQ(ierr); 1359 /* Label its closure as unsplit */ 1360 { 1361 PetscInt *closure = NULL; 1362 PetscInt closureSize, cl; 1363 1364 ierr = DMPlexGetTransitiveClosure(dm, point, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1365 for (cl = 0; cl < closureSize*2; cl += 2) { 1366 ierr = DMLabelGetValue(label, closure[cl], &valA);CHKERRQ(ierr); 1367 if (valA != -1) continue; 1368 ierr = DMLabelGetValue(depthLabel, closure[cl], &dep);CHKERRQ(ierr); 1369 ierr = DMLabelSetValue(label, closure[cl], shift2+dep);CHKERRQ(ierr); 1370 } 1371 ierr = DMPlexRestoreTransitiveClosure(dm, point, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1372 } 1373 } 1374 ierr = ISRestoreIndices(dimIS, &points);CHKERRQ(ierr); 1375 ierr = ISDestroy(&dimIS);CHKERRQ(ierr); 1376 PetscFunctionReturn(0); 1377 } 1378 1379 #undef __FUNCT__ 1380 #define __FUNCT__ "DMPlexCreateHybridMesh" 1381 /*@C 1382 DMPlexCreateHybridMesh - Create a mesh with hybrid cells along an internal interface 1383 1384 Collective on dm 1385 1386 Input Parameters: 1387 + dm - The original DM 1388 - labelName - The label specifying the interface vertices 1389 1390 Output Parameters: 1391 + hybridLabel - The label fully marking the interface 1392 - dmHybrid - The new DM 1393 1394 Level: developer 1395 1396 .seealso: DMPlexConstructCohesiveCells(), DMPlexLabelCohesiveComplete(), DMCreate() 1397 @*/ 1398 PetscErrorCode DMPlexCreateHybridMesh(DM dm, DMLabel label, DMLabel *hybridLabel, DM *dmHybrid) 1399 { 1400 DM idm; 1401 DMLabel subpointMap, hlabel; 1402 PetscInt dim; 1403 PetscErrorCode ierr; 1404 1405 PetscFunctionBegin; 1406 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1407 if (hybridLabel) PetscValidPointer(hybridLabel, 3); 1408 PetscValidPointer(dmHybrid, 4); 1409 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1410 ierr = DMPlexCreateSubmesh(dm, label, 1, &idm);CHKERRQ(ierr); 1411 ierr = DMPlexOrient(idm);CHKERRQ(ierr); 1412 ierr = DMPlexGetSubpointMap(idm, &subpointMap);CHKERRQ(ierr); 1413 ierr = DMLabelDuplicate(subpointMap, &hlabel);CHKERRQ(ierr); 1414 ierr = DMLabelClearStratum(hlabel, dim);CHKERRQ(ierr); 1415 ierr = DMPlexLabelCohesiveComplete(dm, hlabel, PETSC_FALSE, idm);CHKERRQ(ierr); 1416 ierr = DMDestroy(&idm);CHKERRQ(ierr); 1417 ierr = DMPlexConstructCohesiveCells(dm, hlabel, dmHybrid);CHKERRQ(ierr); 1418 if (hybridLabel) *hybridLabel = hlabel; 1419 else {ierr = DMLabelDestroy(&hlabel);CHKERRQ(ierr);} 1420 PetscFunctionReturn(0); 1421 } 1422 1423 #undef __FUNCT__ 1424 #define __FUNCT__ "DMPlexMarkSubmesh_Uninterpolated" 1425 /* Here we need the explicit assumption that: 1426 1427 For any marked cell, the marked vertices constitute a single face 1428 */ 1429 static PetscErrorCode DMPlexMarkSubmesh_Uninterpolated(DM dm, DMLabel vertexLabel, PetscInt value, DMLabel subpointMap, PetscInt *numFaces, PetscInt *nFV, DM subdm) 1430 { 1431 IS subvertexIS = NULL; 1432 const PetscInt *subvertices; 1433 PetscInt *pStart, *pEnd, *pMax, pSize; 1434 PetscInt depth, dim, d, numSubVerticesInitial = 0, v; 1435 PetscErrorCode ierr; 1436 1437 PetscFunctionBegin; 1438 *numFaces = 0; 1439 *nFV = 0; 1440 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 1441 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1442 pSize = PetscMax(depth, dim) + 1; 1443 ierr = PetscMalloc3(pSize,PetscInt,&pStart,pSize,PetscInt,&pEnd,pSize,PetscInt,&pMax);CHKERRQ(ierr); 1444 ierr = DMPlexGetHybridBounds(dm, depth >= 0 ? &pMax[depth] : NULL, depth>1 ? &pMax[depth-1] : NULL, depth>2 ? &pMax[1] : NULL, &pMax[0]);CHKERRQ(ierr); 1445 for (d = 0; d <= depth; ++d) { 1446 ierr = DMPlexGetDepthStratum(dm, d, &pStart[d], &pEnd[d]);CHKERRQ(ierr); 1447 if (pMax[d] >= 0) pEnd[d] = PetscMin(pEnd[d], pMax[d]); 1448 } 1449 /* Loop over initial vertices and mark all faces in the collective star() */ 1450 if (vertexLabel) {ierr = DMLabelGetStratumIS(vertexLabel, value, &subvertexIS);CHKERRQ(ierr);} 1451 if (subvertexIS) { 1452 ierr = ISGetSize(subvertexIS, &numSubVerticesInitial);CHKERRQ(ierr); 1453 ierr = ISGetIndices(subvertexIS, &subvertices);CHKERRQ(ierr); 1454 } 1455 for (v = 0; v < numSubVerticesInitial; ++v) { 1456 const PetscInt vertex = subvertices[v]; 1457 PetscInt *star = NULL; 1458 PetscInt starSize, s, numCells = 0, c; 1459 1460 ierr = DMPlexGetTransitiveClosure(dm, vertex, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1461 for (s = 0; s < starSize*2; s += 2) { 1462 const PetscInt point = star[s]; 1463 if ((point >= pStart[depth]) && (point < pEnd[depth])) star[numCells++] = point; 1464 } 1465 for (c = 0; c < numCells; ++c) { 1466 const PetscInt cell = star[c]; 1467 PetscInt *closure = NULL; 1468 PetscInt closureSize, cl; 1469 PetscInt cellLoc, numCorners = 0, faceSize = 0; 1470 1471 ierr = DMLabelGetValue(subpointMap, cell, &cellLoc);CHKERRQ(ierr); 1472 if (cellLoc == 2) continue; 1473 if (cellLoc >= 0) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Cell %d has dimension %d in the surface label", cell, cellLoc); 1474 ierr = DMPlexGetTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1475 for (cl = 0; cl < closureSize*2; cl += 2) { 1476 const PetscInt point = closure[cl]; 1477 PetscInt vertexLoc; 1478 1479 if ((point >= pStart[0]) && (point < pEnd[0])) { 1480 ++numCorners; 1481 ierr = DMLabelGetValue(vertexLabel, point, &vertexLoc);CHKERRQ(ierr); 1482 if (vertexLoc == value) closure[faceSize++] = point; 1483 } 1484 } 1485 if (!(*nFV)) {ierr = DMPlexGetNumFaceVertices(dm, dim, numCorners, nFV);CHKERRQ(ierr);} 1486 if (faceSize > *nFV) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Invalid submesh: Too many vertices %d of an element on the surface", faceSize); 1487 if (faceSize == *nFV) { 1488 const PetscInt *cells = NULL; 1489 PetscInt numCells, nc; 1490 1491 ++(*numFaces); 1492 for (cl = 0; cl < faceSize; ++cl) { 1493 ierr = DMLabelSetValue(subpointMap, closure[cl], 0);CHKERRQ(ierr); 1494 } 1495 ierr = DMPlexGetJoin(dm, faceSize, closure, &numCells, &cells);CHKERRQ(ierr); 1496 for (nc = 0; nc < numCells; ++nc) { 1497 ierr = DMLabelSetValue(subpointMap, cells[nc], 2);CHKERRQ(ierr); 1498 } 1499 ierr = DMPlexRestoreJoin(dm, faceSize, closure, &numCells, &cells);CHKERRQ(ierr); 1500 } 1501 ierr = DMPlexRestoreTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1502 } 1503 ierr = DMPlexRestoreTransitiveClosure(dm, vertex, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1504 } 1505 if (subvertexIS) { 1506 ierr = ISRestoreIndices(subvertexIS, &subvertices);CHKERRQ(ierr); 1507 } 1508 ierr = ISDestroy(&subvertexIS);CHKERRQ(ierr); 1509 ierr = PetscFree3(pStart,pEnd,pMax);CHKERRQ(ierr); 1510 PetscFunctionReturn(0); 1511 } 1512 1513 #undef __FUNCT__ 1514 #define __FUNCT__ "DMPlexMarkSubmesh_Interpolated" 1515 static PetscErrorCode DMPlexMarkSubmesh_Interpolated(DM dm, DMLabel vertexLabel, PetscInt value, DMLabel subpointMap, DM subdm) 1516 { 1517 IS subvertexIS; 1518 const PetscInt *subvertices; 1519 PetscInt *pStart, *pEnd, *pMax; 1520 PetscInt dim, d, numSubVerticesInitial = 0, v; 1521 PetscErrorCode ierr; 1522 1523 PetscFunctionBegin; 1524 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1525 ierr = PetscMalloc3(dim+1,PetscInt,&pStart,dim+1,PetscInt,&pEnd,dim+1,PetscInt,&pMax);CHKERRQ(ierr); 1526 ierr = DMPlexGetHybridBounds(dm, &pMax[dim], dim>1 ? &pMax[dim-1] : NULL, dim > 2 ? &pMax[1] : NULL, &pMax[0]);CHKERRQ(ierr); 1527 for (d = 0; d <= dim; ++d) { 1528 ierr = DMPlexGetDepthStratum(dm, d, &pStart[d], &pEnd[d]);CHKERRQ(ierr); 1529 if (pMax[d] >= 0) pEnd[d] = PetscMin(pEnd[d], pMax[d]); 1530 } 1531 /* Loop over initial vertices and mark all faces in the collective star() */ 1532 ierr = DMLabelGetStratumIS(vertexLabel, value, &subvertexIS);CHKERRQ(ierr); 1533 if (subvertexIS) { 1534 ierr = ISGetSize(subvertexIS, &numSubVerticesInitial);CHKERRQ(ierr); 1535 ierr = ISGetIndices(subvertexIS, &subvertices);CHKERRQ(ierr); 1536 } 1537 for (v = 0; v < numSubVerticesInitial; ++v) { 1538 const PetscInt vertex = subvertices[v]; 1539 PetscInt *star = NULL; 1540 PetscInt starSize, s, numFaces = 0, f; 1541 1542 ierr = DMPlexGetTransitiveClosure(dm, vertex, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1543 for (s = 0; s < starSize*2; s += 2) { 1544 const PetscInt point = star[s]; 1545 if ((point >= pStart[dim-1]) && (point < pEnd[dim-1])) star[numFaces++] = point; 1546 } 1547 for (f = 0; f < numFaces; ++f) { 1548 const PetscInt face = star[f]; 1549 PetscInt *closure = NULL; 1550 PetscInt closureSize, c; 1551 PetscInt faceLoc; 1552 1553 ierr = DMLabelGetValue(subpointMap, face, &faceLoc);CHKERRQ(ierr); 1554 if (faceLoc == dim-1) continue; 1555 if (faceLoc >= 0) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Face %d has dimension %d in the surface label", face, faceLoc); 1556 ierr = DMPlexGetTransitiveClosure(dm, face, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1557 for (c = 0; c < closureSize*2; c += 2) { 1558 const PetscInt point = closure[c]; 1559 PetscInt vertexLoc; 1560 1561 if ((point >= pStart[0]) && (point < pEnd[0])) { 1562 ierr = DMLabelGetValue(vertexLabel, point, &vertexLoc);CHKERRQ(ierr); 1563 if (vertexLoc != value) break; 1564 } 1565 } 1566 if (c == closureSize*2) { 1567 const PetscInt *support; 1568 PetscInt supportSize, s; 1569 1570 for (c = 0; c < closureSize*2; c += 2) { 1571 const PetscInt point = closure[c]; 1572 1573 for (d = 0; d < dim; ++d) { 1574 if ((point >= pStart[d]) && (point < pEnd[d])) { 1575 ierr = DMLabelSetValue(subpointMap, point, d);CHKERRQ(ierr); 1576 break; 1577 } 1578 } 1579 } 1580 ierr = DMPlexGetSupportSize(dm, face, &supportSize);CHKERRQ(ierr); 1581 ierr = DMPlexGetSupport(dm, face, &support);CHKERRQ(ierr); 1582 for (s = 0; s < supportSize; ++s) { 1583 ierr = DMLabelSetValue(subpointMap, support[s], dim);CHKERRQ(ierr); 1584 } 1585 } 1586 ierr = DMPlexRestoreTransitiveClosure(dm, face, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1587 } 1588 ierr = DMPlexRestoreTransitiveClosure(dm, vertex, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1589 } 1590 if (subvertexIS) { 1591 ierr = ISRestoreIndices(subvertexIS, &subvertices);CHKERRQ(ierr); 1592 } 1593 ierr = ISDestroy(&subvertexIS);CHKERRQ(ierr); 1594 ierr = PetscFree3(pStart,pEnd,pMax);CHKERRQ(ierr); 1595 PetscFunctionReturn(0); 1596 } 1597 1598 #undef __FUNCT__ 1599 #define __FUNCT__ "DMPlexMarkCohesiveSubmesh_Uninterpolated" 1600 static PetscErrorCode DMPlexMarkCohesiveSubmesh_Uninterpolated(DM dm, PetscBool hasLagrange, const char labelname[], PetscInt value, DMLabel subpointMap, PetscInt *numFaces, PetscInt *nFV, PetscInt *subCells[], DM subdm) 1601 { 1602 DMLabel label = NULL; 1603 const PetscInt *cone; 1604 PetscInt dim, cMax, cEnd, c, subc = 0, p, coneSize; 1605 PetscErrorCode ierr; 1606 1607 PetscFunctionBegin; 1608 *numFaces = 0; 1609 *nFV = 0; 1610 if (labelname) {ierr = DMPlexGetLabel(dm, labelname, &label);CHKERRQ(ierr);} 1611 *subCells = NULL; 1612 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1613 ierr = DMPlexGetHeightStratum(dm, 0, NULL, &cEnd);CHKERRQ(ierr); 1614 ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); 1615 if (cMax < 0) PetscFunctionReturn(0); 1616 if (label) { 1617 for (c = cMax; c < cEnd; ++c) { 1618 PetscInt val; 1619 1620 ierr = DMLabelGetValue(label, c, &val);CHKERRQ(ierr); 1621 if (val == value) { 1622 ++(*numFaces); 1623 ierr = DMPlexGetConeSize(dm, c, &coneSize);CHKERRQ(ierr); 1624 } 1625 } 1626 } else { 1627 *numFaces = cEnd - cMax; 1628 ierr = DMPlexGetConeSize(dm, cMax, &coneSize);CHKERRQ(ierr); 1629 } 1630 *nFV = hasLagrange ? coneSize/3 : coneSize/2; 1631 ierr = PetscMalloc(*numFaces *2 * sizeof(PetscInt), subCells);CHKERRQ(ierr); 1632 for (c = cMax; c < cEnd; ++c) { 1633 const PetscInt *cells; 1634 PetscInt numCells; 1635 1636 if (label) { 1637 PetscInt val; 1638 1639 ierr = DMLabelGetValue(label, c, &val);CHKERRQ(ierr); 1640 if (val != value) continue; 1641 } 1642 ierr = DMPlexGetCone(dm, c, &cone);CHKERRQ(ierr); 1643 for (p = 0; p < *nFV; ++p) { 1644 ierr = DMLabelSetValue(subpointMap, cone[p], 0);CHKERRQ(ierr); 1645 } 1646 /* Negative face */ 1647 ierr = DMPlexGetJoin(dm, *nFV, cone, &numCells, &cells);CHKERRQ(ierr); 1648 /* Not true in parallel 1649 if (numCells != 2) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive cells should separate two cells"); */ 1650 for (p = 0; p < numCells; ++p) { 1651 ierr = DMLabelSetValue(subpointMap, cells[p], 2);CHKERRQ(ierr); 1652 (*subCells)[subc++] = cells[p]; 1653 } 1654 ierr = DMPlexRestoreJoin(dm, *nFV, cone, &numCells, &cells);CHKERRQ(ierr); 1655 /* Positive face is not included */ 1656 } 1657 PetscFunctionReturn(0); 1658 } 1659 1660 #undef __FUNCT__ 1661 #define __FUNCT__ "DMPlexMarkCohesiveSubmesh_Interpolated" 1662 static PetscErrorCode DMPlexMarkCohesiveSubmesh_Interpolated(DM dm, const char labelname[], PetscInt value, DMLabel subpointMap, DM subdm) 1663 { 1664 DMLabel label = NULL; 1665 PetscInt *pStart, *pEnd; 1666 PetscInt dim, cMax, cEnd, c, d; 1667 PetscErrorCode ierr; 1668 1669 PetscFunctionBegin; 1670 if (labelname) {ierr = DMPlexGetLabel(dm, labelname, &label);CHKERRQ(ierr);} 1671 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1672 ierr = DMPlexGetHeightStratum(dm, 0, NULL, &cEnd);CHKERRQ(ierr); 1673 ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); 1674 if (cMax < 0) PetscFunctionReturn(0); 1675 ierr = PetscMalloc2(dim+1,PetscInt,&pStart,dim+1,PetscInt,&pEnd);CHKERRQ(ierr); 1676 for (d = 0; d <= dim; ++d) {ierr = DMPlexGetDepthStratum(dm, d, &pStart[d], &pEnd[d]);CHKERRQ(ierr);} 1677 for (c = cMax; c < cEnd; ++c) { 1678 const PetscInt *cone; 1679 PetscInt *closure = NULL; 1680 PetscInt fconeSize, coneSize, closureSize, cl, val; 1681 1682 if (label) { 1683 ierr = DMLabelGetValue(label, c, &val);CHKERRQ(ierr); 1684 if (val != value) continue; 1685 } 1686 ierr = DMPlexGetConeSize(dm, c, &coneSize);CHKERRQ(ierr); 1687 ierr = DMPlexGetCone(dm, c, &cone);CHKERRQ(ierr); 1688 ierr = DMPlexGetConeSize(dm, cone[0], &fconeSize);CHKERRQ(ierr); 1689 if (coneSize != (fconeSize ? fconeSize : 1) + 2) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive cells should separate two cells"); 1690 /* Negative face */ 1691 ierr = DMPlexGetTransitiveClosure(dm, cone[0], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1692 for (cl = 0; cl < closureSize*2; cl += 2) { 1693 const PetscInt point = closure[cl]; 1694 1695 for (d = 0; d <= dim; ++d) { 1696 if ((point >= pStart[d]) && (point < pEnd[d])) { 1697 ierr = DMLabelSetValue(subpointMap, point, d);CHKERRQ(ierr); 1698 break; 1699 } 1700 } 1701 } 1702 ierr = DMPlexRestoreTransitiveClosure(dm, cone[0], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1703 /* Cells -- positive face is not included */ 1704 for (cl = 0; cl < 1; ++cl) { 1705 const PetscInt *support; 1706 PetscInt supportSize, s; 1707 1708 ierr = DMPlexGetSupportSize(dm, cone[cl], &supportSize);CHKERRQ(ierr); 1709 if (supportSize != 2) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive faces should separate two cells"); 1710 ierr = DMPlexGetSupport(dm, cone[cl], &support);CHKERRQ(ierr); 1711 for (s = 0; s < supportSize; ++s) { 1712 ierr = DMLabelSetValue(subpointMap, support[s], dim);CHKERRQ(ierr); 1713 } 1714 } 1715 } 1716 ierr = PetscFree2(pStart, pEnd);CHKERRQ(ierr); 1717 PetscFunctionReturn(0); 1718 } 1719 1720 #undef __FUNCT__ 1721 #define __FUNCT__ "DMPlexGetFaceOrientation" 1722 PetscErrorCode DMPlexGetFaceOrientation(DM dm, PetscInt cell, PetscInt numCorners, PetscInt indices[], PetscInt oppositeVertex, PetscInt origVertices[], PetscInt faceVertices[], PetscBool *posOriented) 1723 { 1724 MPI_Comm comm; 1725 PetscBool posOrient = PETSC_FALSE; 1726 const PetscInt debug = 0; 1727 PetscInt cellDim, faceSize, f; 1728 PetscErrorCode ierr; 1729 1730 PetscFunctionBegin; 1731 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 1732 ierr = DMPlexGetDimension(dm, &cellDim);CHKERRQ(ierr); 1733 if (debug) {PetscPrintf(comm, "cellDim: %d numCorners: %d\n", cellDim, numCorners);CHKERRQ(ierr);} 1734 1735 if (cellDim == 1 && numCorners == 2) { 1736 /* Triangle */ 1737 faceSize = numCorners-1; 1738 posOrient = !(oppositeVertex%2) ? PETSC_TRUE : PETSC_FALSE; 1739 } else if (cellDim == 2 && numCorners == 3) { 1740 /* Triangle */ 1741 faceSize = numCorners-1; 1742 posOrient = !(oppositeVertex%2) ? PETSC_TRUE : PETSC_FALSE; 1743 } else if (cellDim == 3 && numCorners == 4) { 1744 /* Tetrahedron */ 1745 faceSize = numCorners-1; 1746 posOrient = (oppositeVertex%2) ? PETSC_TRUE : PETSC_FALSE; 1747 } else if (cellDim == 1 && numCorners == 3) { 1748 /* Quadratic line */ 1749 faceSize = 1; 1750 posOrient = PETSC_TRUE; 1751 } else if (cellDim == 2 && numCorners == 4) { 1752 /* Quads */ 1753 faceSize = 2; 1754 if ((indices[1] > indices[0]) && (indices[1] - indices[0] == 1)) { 1755 posOrient = PETSC_TRUE; 1756 } else if ((indices[0] == 3) && (indices[1] == 0)) { 1757 posOrient = PETSC_TRUE; 1758 } else { 1759 if (((indices[0] > indices[1]) && (indices[0] - indices[1] == 1)) || ((indices[0] == 0) && (indices[1] == 3))) { 1760 posOrient = PETSC_FALSE; 1761 } else SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid quad crossedge"); 1762 } 1763 } else if (cellDim == 2 && numCorners == 6) { 1764 /* Quadratic triangle (I hate this) */ 1765 /* Edges are determined by the first 2 vertices (corners of edges) */ 1766 const PetscInt faceSizeTri = 3; 1767 PetscInt sortedIndices[3], i, iFace; 1768 PetscBool found = PETSC_FALSE; 1769 PetscInt faceVerticesTriSorted[9] = { 1770 0, 3, 4, /* bottom */ 1771 1, 4, 5, /* right */ 1772 2, 3, 5, /* left */ 1773 }; 1774 PetscInt faceVerticesTri[9] = { 1775 0, 3, 4, /* bottom */ 1776 1, 4, 5, /* right */ 1777 2, 5, 3, /* left */ 1778 }; 1779 1780 faceSize = faceSizeTri; 1781 for (i = 0; i < faceSizeTri; ++i) sortedIndices[i] = indices[i]; 1782 ierr = PetscSortInt(faceSizeTri, sortedIndices);CHKERRQ(ierr); 1783 for (iFace = 0; iFace < 3; ++iFace) { 1784 const PetscInt ii = iFace*faceSizeTri; 1785 PetscInt fVertex, cVertex; 1786 1787 if ((sortedIndices[0] == faceVerticesTriSorted[ii+0]) && 1788 (sortedIndices[1] == faceVerticesTriSorted[ii+1])) { 1789 for (fVertex = 0; fVertex < faceSizeTri; ++fVertex) { 1790 for (cVertex = 0; cVertex < faceSizeTri; ++cVertex) { 1791 if (indices[cVertex] == faceVerticesTri[ii+fVertex]) { 1792 faceVertices[fVertex] = origVertices[cVertex]; 1793 break; 1794 } 1795 } 1796 } 1797 found = PETSC_TRUE; 1798 break; 1799 } 1800 } 1801 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid tri crossface"); 1802 if (posOriented) *posOriented = PETSC_TRUE; 1803 PetscFunctionReturn(0); 1804 } else if (cellDim == 2 && numCorners == 9) { 1805 /* Quadratic quad (I hate this) */ 1806 /* Edges are determined by the first 2 vertices (corners of edges) */ 1807 const PetscInt faceSizeQuad = 3; 1808 PetscInt sortedIndices[3], i, iFace; 1809 PetscBool found = PETSC_FALSE; 1810 PetscInt faceVerticesQuadSorted[12] = { 1811 0, 1, 4, /* bottom */ 1812 1, 2, 5, /* right */ 1813 2, 3, 6, /* top */ 1814 0, 3, 7, /* left */ 1815 }; 1816 PetscInt faceVerticesQuad[12] = { 1817 0, 1, 4, /* bottom */ 1818 1, 2, 5, /* right */ 1819 2, 3, 6, /* top */ 1820 3, 0, 7, /* left */ 1821 }; 1822 1823 faceSize = faceSizeQuad; 1824 for (i = 0; i < faceSizeQuad; ++i) sortedIndices[i] = indices[i]; 1825 ierr = PetscSortInt(faceSizeQuad, sortedIndices);CHKERRQ(ierr); 1826 for (iFace = 0; iFace < 4; ++iFace) { 1827 const PetscInt ii = iFace*faceSizeQuad; 1828 PetscInt fVertex, cVertex; 1829 1830 if ((sortedIndices[0] == faceVerticesQuadSorted[ii+0]) && 1831 (sortedIndices[1] == faceVerticesQuadSorted[ii+1])) { 1832 for (fVertex = 0; fVertex < faceSizeQuad; ++fVertex) { 1833 for (cVertex = 0; cVertex < faceSizeQuad; ++cVertex) { 1834 if (indices[cVertex] == faceVerticesQuad[ii+fVertex]) { 1835 faceVertices[fVertex] = origVertices[cVertex]; 1836 break; 1837 } 1838 } 1839 } 1840 found = PETSC_TRUE; 1841 break; 1842 } 1843 } 1844 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid quad crossface"); 1845 if (posOriented) *posOriented = PETSC_TRUE; 1846 PetscFunctionReturn(0); 1847 } else if (cellDim == 3 && numCorners == 8) { 1848 /* Hexes 1849 A hex is two oriented quads with the normal of the first 1850 pointing up at the second. 1851 1852 7---6 1853 /| /| 1854 4---5 | 1855 | 1-|-2 1856 |/ |/ 1857 0---3 1858 1859 Faces are determined by the first 4 vertices (corners of faces) */ 1860 const PetscInt faceSizeHex = 4; 1861 PetscInt sortedIndices[4], i, iFace; 1862 PetscBool found = PETSC_FALSE; 1863 PetscInt faceVerticesHexSorted[24] = { 1864 0, 1, 2, 3, /* bottom */ 1865 4, 5, 6, 7, /* top */ 1866 0, 3, 4, 5, /* front */ 1867 2, 3, 5, 6, /* right */ 1868 1, 2, 6, 7, /* back */ 1869 0, 1, 4, 7, /* left */ 1870 }; 1871 PetscInt faceVerticesHex[24] = { 1872 1, 2, 3, 0, /* bottom */ 1873 4, 5, 6, 7, /* top */ 1874 0, 3, 5, 4, /* front */ 1875 3, 2, 6, 5, /* right */ 1876 2, 1, 7, 6, /* back */ 1877 1, 0, 4, 7, /* left */ 1878 }; 1879 1880 faceSize = faceSizeHex; 1881 for (i = 0; i < faceSizeHex; ++i) sortedIndices[i] = indices[i]; 1882 ierr = PetscSortInt(faceSizeHex, sortedIndices);CHKERRQ(ierr); 1883 for (iFace = 0; iFace < 6; ++iFace) { 1884 const PetscInt ii = iFace*faceSizeHex; 1885 PetscInt fVertex, cVertex; 1886 1887 if ((sortedIndices[0] == faceVerticesHexSorted[ii+0]) && 1888 (sortedIndices[1] == faceVerticesHexSorted[ii+1]) && 1889 (sortedIndices[2] == faceVerticesHexSorted[ii+2]) && 1890 (sortedIndices[3] == faceVerticesHexSorted[ii+3])) { 1891 for (fVertex = 0; fVertex < faceSizeHex; ++fVertex) { 1892 for (cVertex = 0; cVertex < faceSizeHex; ++cVertex) { 1893 if (indices[cVertex] == faceVerticesHex[ii+fVertex]) { 1894 faceVertices[fVertex] = origVertices[cVertex]; 1895 break; 1896 } 1897 } 1898 } 1899 found = PETSC_TRUE; 1900 break; 1901 } 1902 } 1903 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid hex crossface"); 1904 if (posOriented) *posOriented = PETSC_TRUE; 1905 PetscFunctionReturn(0); 1906 } else if (cellDim == 3 && numCorners == 10) { 1907 /* Quadratic tet */ 1908 /* Faces are determined by the first 3 vertices (corners of faces) */ 1909 const PetscInt faceSizeTet = 6; 1910 PetscInt sortedIndices[6], i, iFace; 1911 PetscBool found = PETSC_FALSE; 1912 PetscInt faceVerticesTetSorted[24] = { 1913 0, 1, 2, 6, 7, 8, /* bottom */ 1914 0, 3, 4, 6, 7, 9, /* front */ 1915 1, 4, 5, 7, 8, 9, /* right */ 1916 2, 3, 5, 6, 8, 9, /* left */ 1917 }; 1918 PetscInt faceVerticesTet[24] = { 1919 0, 1, 2, 6, 7, 8, /* bottom */ 1920 0, 4, 3, 6, 7, 9, /* front */ 1921 1, 5, 4, 7, 8, 9, /* right */ 1922 2, 3, 5, 8, 6, 9, /* left */ 1923 }; 1924 1925 faceSize = faceSizeTet; 1926 for (i = 0; i < faceSizeTet; ++i) sortedIndices[i] = indices[i]; 1927 ierr = PetscSortInt(faceSizeTet, sortedIndices);CHKERRQ(ierr); 1928 for (iFace=0; iFace < 4; ++iFace) { 1929 const PetscInt ii = iFace*faceSizeTet; 1930 PetscInt fVertex, cVertex; 1931 1932 if ((sortedIndices[0] == faceVerticesTetSorted[ii+0]) && 1933 (sortedIndices[1] == faceVerticesTetSorted[ii+1]) && 1934 (sortedIndices[2] == faceVerticesTetSorted[ii+2]) && 1935 (sortedIndices[3] == faceVerticesTetSorted[ii+3])) { 1936 for (fVertex = 0; fVertex < faceSizeTet; ++fVertex) { 1937 for (cVertex = 0; cVertex < faceSizeTet; ++cVertex) { 1938 if (indices[cVertex] == faceVerticesTet[ii+fVertex]) { 1939 faceVertices[fVertex] = origVertices[cVertex]; 1940 break; 1941 } 1942 } 1943 } 1944 found = PETSC_TRUE; 1945 break; 1946 } 1947 } 1948 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid tet crossface"); 1949 if (posOriented) *posOriented = PETSC_TRUE; 1950 PetscFunctionReturn(0); 1951 } else if (cellDim == 3 && numCorners == 27) { 1952 /* Quadratic hexes (I hate this) 1953 A hex is two oriented quads with the normal of the first 1954 pointing up at the second. 1955 1956 7---6 1957 /| /| 1958 4---5 | 1959 | 3-|-2 1960 |/ |/ 1961 0---1 1962 1963 Faces are determined by the first 4 vertices (corners of faces) */ 1964 const PetscInt faceSizeQuadHex = 9; 1965 PetscInt sortedIndices[9], i, iFace; 1966 PetscBool found = PETSC_FALSE; 1967 PetscInt faceVerticesQuadHexSorted[54] = { 1968 0, 1, 2, 3, 8, 9, 10, 11, 24, /* bottom */ 1969 4, 5, 6, 7, 12, 13, 14, 15, 25, /* top */ 1970 0, 1, 4, 5, 8, 12, 16, 17, 22, /* front */ 1971 1, 2, 5, 6, 9, 13, 17, 18, 21, /* right */ 1972 2, 3, 6, 7, 10, 14, 18, 19, 23, /* back */ 1973 0, 3, 4, 7, 11, 15, 16, 19, 20, /* left */ 1974 }; 1975 PetscInt faceVerticesQuadHex[54] = { 1976 3, 2, 1, 0, 10, 9, 8, 11, 24, /* bottom */ 1977 4, 5, 6, 7, 12, 13, 14, 15, 25, /* top */ 1978 0, 1, 5, 4, 8, 17, 12, 16, 22, /* front */ 1979 1, 2, 6, 5, 9, 18, 13, 17, 21, /* right */ 1980 2, 3, 7, 6, 10, 19, 14, 18, 23, /* back */ 1981 3, 0, 4, 7, 11, 16, 15, 19, 20 /* left */ 1982 }; 1983 1984 faceSize = faceSizeQuadHex; 1985 for (i = 0; i < faceSizeQuadHex; ++i) sortedIndices[i] = indices[i]; 1986 ierr = PetscSortInt(faceSizeQuadHex, sortedIndices);CHKERRQ(ierr); 1987 for (iFace = 0; iFace < 6; ++iFace) { 1988 const PetscInt ii = iFace*faceSizeQuadHex; 1989 PetscInt fVertex, cVertex; 1990 1991 if ((sortedIndices[0] == faceVerticesQuadHexSorted[ii+0]) && 1992 (sortedIndices[1] == faceVerticesQuadHexSorted[ii+1]) && 1993 (sortedIndices[2] == faceVerticesQuadHexSorted[ii+2]) && 1994 (sortedIndices[3] == faceVerticesQuadHexSorted[ii+3])) { 1995 for (fVertex = 0; fVertex < faceSizeQuadHex; ++fVertex) { 1996 for (cVertex = 0; cVertex < faceSizeQuadHex; ++cVertex) { 1997 if (indices[cVertex] == faceVerticesQuadHex[ii+fVertex]) { 1998 faceVertices[fVertex] = origVertices[cVertex]; 1999 break; 2000 } 2001 } 2002 } 2003 found = PETSC_TRUE; 2004 break; 2005 } 2006 } 2007 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid hex crossface"); 2008 if (posOriented) *posOriented = PETSC_TRUE; 2009 PetscFunctionReturn(0); 2010 } else SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Unknown cell type for faceOrientation()."); 2011 if (!posOrient) { 2012 if (debug) {ierr = PetscPrintf(comm, " Reversing initial face orientation\n");CHKERRQ(ierr);} 2013 for (f = 0; f < faceSize; ++f) faceVertices[f] = origVertices[faceSize-1 - f]; 2014 } else { 2015 if (debug) {ierr = PetscPrintf(comm, " Keeping initial face orientation\n");CHKERRQ(ierr);} 2016 for (f = 0; f < faceSize; ++f) faceVertices[f] = origVertices[f]; 2017 } 2018 if (posOriented) *posOriented = posOrient; 2019 PetscFunctionReturn(0); 2020 } 2021 2022 #undef __FUNCT__ 2023 #define __FUNCT__ "DMPlexGetOrientedFace" 2024 /* 2025 Given a cell and a face, as a set of vertices, 2026 return the oriented face, as a set of vertices, in faceVertices 2027 The orientation is such that the face normal points out of the cell 2028 */ 2029 PetscErrorCode DMPlexGetOrientedFace(DM dm, PetscInt cell, PetscInt faceSize, const PetscInt face[], PetscInt numCorners, PetscInt indices[], PetscInt origVertices[], PetscInt faceVertices[], PetscBool *posOriented) 2030 { 2031 const PetscInt *cone = NULL; 2032 PetscInt coneSize, v, f, v2; 2033 PetscInt oppositeVertex = -1; 2034 PetscErrorCode ierr; 2035 2036 PetscFunctionBegin; 2037 ierr = DMPlexGetConeSize(dm, cell, &coneSize);CHKERRQ(ierr); 2038 ierr = DMPlexGetCone(dm, cell, &cone);CHKERRQ(ierr); 2039 for (v = 0, v2 = 0; v < coneSize; ++v) { 2040 PetscBool found = PETSC_FALSE; 2041 2042 for (f = 0; f < faceSize; ++f) { 2043 if (face[f] == cone[v]) { 2044 found = PETSC_TRUE; break; 2045 } 2046 } 2047 if (found) { 2048 indices[v2] = v; 2049 origVertices[v2] = cone[v]; 2050 ++v2; 2051 } else { 2052 oppositeVertex = v; 2053 } 2054 } 2055 ierr = DMPlexGetFaceOrientation(dm, cell, numCorners, indices, oppositeVertex, origVertices, faceVertices, posOriented);CHKERRQ(ierr); 2056 PetscFunctionReturn(0); 2057 } 2058 2059 #undef __FUNCT__ 2060 #define __FUNCT__ "DMPlexInsertFace_Internal" 2061 /* 2062 DMPlexInsertFace_Internal - Puts a face into the mesh 2063 2064 Not collective 2065 2066 Input Parameters: 2067 + dm - The DMPlex 2068 . numFaceVertex - The number of vertices in the face 2069 . faceVertices - The vertices in the face for dm 2070 . subfaceVertices - The vertices in the face for subdm 2071 . numCorners - The number of vertices in the cell 2072 . cell - A cell in dm containing the face 2073 . subcell - A cell in subdm containing the face 2074 . firstFace - First face in the mesh 2075 - newFacePoint - Next face in the mesh 2076 2077 Output Parameters: 2078 . newFacePoint - Contains next face point number on input, updated on output 2079 2080 Level: developer 2081 */ 2082 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) 2083 { 2084 MPI_Comm comm; 2085 DM_Plex *submesh = (DM_Plex*) subdm->data; 2086 const PetscInt *faces; 2087 PetscInt numFaces, coneSize; 2088 PetscErrorCode ierr; 2089 2090 PetscFunctionBegin; 2091 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 2092 ierr = DMPlexGetConeSize(subdm, subcell, &coneSize);CHKERRQ(ierr); 2093 if (coneSize != 1) SETERRQ2(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cone size of cell %d is %d != 1", cell, coneSize); 2094 #if 0 2095 /* Cannot use this because support() has not been constructed yet */ 2096 ierr = DMPlexGetJoin(subdm, numFaceVertices, subfaceVertices, &numFaces, &faces);CHKERRQ(ierr); 2097 #else 2098 { 2099 PetscInt f; 2100 2101 numFaces = 0; 2102 ierr = DMGetWorkArray(subdm, 1, PETSC_INT, (void **) &faces);CHKERRQ(ierr); 2103 for (f = firstFace; f < *newFacePoint; ++f) { 2104 PetscInt dof, off, d; 2105 2106 ierr = PetscSectionGetDof(submesh->coneSection, f, &dof);CHKERRQ(ierr); 2107 ierr = PetscSectionGetOffset(submesh->coneSection, f, &off);CHKERRQ(ierr); 2108 /* Yes, I know this is quadratic, but I expect the sizes to be <5 */ 2109 for (d = 0; d < dof; ++d) { 2110 const PetscInt p = submesh->cones[off+d]; 2111 PetscInt v; 2112 2113 for (v = 0; v < numFaceVertices; ++v) { 2114 if (subfaceVertices[v] == p) break; 2115 } 2116 if (v == numFaceVertices) break; 2117 } 2118 if (d == dof) { 2119 numFaces = 1; 2120 ((PetscInt*) faces)[0] = f; 2121 } 2122 } 2123 } 2124 #endif 2125 if (numFaces > 1) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Vertex set had %d faces, not one", numFaces); 2126 else if (numFaces == 1) { 2127 /* Add the other cell neighbor for this face */ 2128 ierr = DMPlexSetCone(subdm, subcell, faces);CHKERRQ(ierr); 2129 } else { 2130 PetscInt *indices, *origVertices, *orientedVertices, *orientedSubVertices, v, ov; 2131 PetscBool posOriented; 2132 2133 ierr = DMGetWorkArray(subdm, 4*numFaceVertices * sizeof(PetscInt), PETSC_INT, &orientedVertices);CHKERRQ(ierr); 2134 origVertices = &orientedVertices[numFaceVertices]; 2135 indices = &orientedVertices[numFaceVertices*2]; 2136 orientedSubVertices = &orientedVertices[numFaceVertices*3]; 2137 ierr = DMPlexGetOrientedFace(dm, cell, numFaceVertices, faceVertices, numCorners, indices, origVertices, orientedVertices, &posOriented);CHKERRQ(ierr); 2138 /* TODO: I know that routine should return a permutation, not the indices */ 2139 for (v = 0; v < numFaceVertices; ++v) { 2140 const PetscInt vertex = faceVertices[v], subvertex = subfaceVertices[v]; 2141 for (ov = 0; ov < numFaceVertices; ++ov) { 2142 if (orientedVertices[ov] == vertex) { 2143 orientedSubVertices[ov] = subvertex; 2144 break; 2145 } 2146 } 2147 if (ov == numFaceVertices) SETERRQ1(comm, PETSC_ERR_PLIB, "Could not find face vertex %d in orientated set", vertex); 2148 } 2149 ierr = DMPlexSetCone(subdm, *newFacePoint, orientedSubVertices);CHKERRQ(ierr); 2150 ierr = DMPlexSetCone(subdm, subcell, newFacePoint);CHKERRQ(ierr); 2151 ierr = DMRestoreWorkArray(subdm, 4*numFaceVertices * sizeof(PetscInt), PETSC_INT, &orientedVertices);CHKERRQ(ierr); 2152 ++(*newFacePoint); 2153 } 2154 #if 0 2155 ierr = DMPlexRestoreJoin(subdm, numFaceVertices, subfaceVertices, &numFaces, &faces);CHKERRQ(ierr); 2156 #else 2157 ierr = DMRestoreWorkArray(subdm, 1, PETSC_INT, (void **) &faces);CHKERRQ(ierr); 2158 #endif 2159 PetscFunctionReturn(0); 2160 } 2161 2162 #undef __FUNCT__ 2163 #define __FUNCT__ "DMPlexCreateSubmesh_Uninterpolated" 2164 static PetscErrorCode DMPlexCreateSubmesh_Uninterpolated(DM dm, DMLabel vertexLabel, PetscInt value, DM subdm) 2165 { 2166 MPI_Comm comm; 2167 DMLabel subpointMap; 2168 IS subvertexIS, subcellIS; 2169 const PetscInt *subVertices, *subCells; 2170 PetscInt numSubVertices, firstSubVertex, numSubCells; 2171 PetscInt *subface, maxConeSize, numSubFaces = 0, firstSubFace, newFacePoint, nFV = 0; 2172 PetscInt vStart, vEnd, c, f; 2173 PetscErrorCode ierr; 2174 2175 PetscFunctionBegin; 2176 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 2177 /* Create subpointMap which marks the submesh */ 2178 ierr = DMLabelCreate("subpoint_map", &subpointMap);CHKERRQ(ierr); 2179 ierr = DMPlexSetSubpointMap(subdm, subpointMap);CHKERRQ(ierr); 2180 ierr = DMLabelDestroy(&subpointMap);CHKERRQ(ierr); 2181 if (vertexLabel) {ierr = DMPlexMarkSubmesh_Uninterpolated(dm, vertexLabel, value, subpointMap, &numSubFaces, &nFV, subdm);CHKERRQ(ierr);} 2182 /* Setup chart */ 2183 ierr = DMLabelGetStratumSize(subpointMap, 0, &numSubVertices);CHKERRQ(ierr); 2184 ierr = DMLabelGetStratumSize(subpointMap, 2, &numSubCells);CHKERRQ(ierr); 2185 ierr = DMPlexSetChart(subdm, 0, numSubCells+numSubFaces+numSubVertices);CHKERRQ(ierr); 2186 ierr = DMPlexSetVTKCellHeight(subdm, 1);CHKERRQ(ierr); 2187 /* Set cone sizes */ 2188 firstSubVertex = numSubCells; 2189 firstSubFace = numSubCells+numSubVertices; 2190 newFacePoint = firstSubFace; 2191 ierr = DMLabelGetStratumIS(subpointMap, 0, &subvertexIS);CHKERRQ(ierr); 2192 if (subvertexIS) {ierr = ISGetIndices(subvertexIS, &subVertices);CHKERRQ(ierr);} 2193 ierr = DMLabelGetStratumIS(subpointMap, 2, &subcellIS);CHKERRQ(ierr); 2194 if (subcellIS) {ierr = ISGetIndices(subcellIS, &subCells);CHKERRQ(ierr);} 2195 for (c = 0; c < numSubCells; ++c) { 2196 ierr = DMPlexSetConeSize(subdm, c, 1);CHKERRQ(ierr); 2197 } 2198 for (f = firstSubFace; f < firstSubFace+numSubFaces; ++f) { 2199 ierr = DMPlexSetConeSize(subdm, f, nFV);CHKERRQ(ierr); 2200 } 2201 ierr = DMSetUp(subdm);CHKERRQ(ierr); 2202 /* Create face cones */ 2203 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 2204 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, NULL);CHKERRQ(ierr); 2205 ierr = DMGetWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);CHKERRQ(ierr); 2206 for (c = 0; c < numSubCells; ++c) { 2207 const PetscInt cell = subCells[c]; 2208 const PetscInt subcell = c; 2209 PetscInt *closure = NULL; 2210 PetscInt closureSize, cl, numCorners = 0, faceSize = 0; 2211 2212 ierr = DMPlexGetTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 2213 for (cl = 0; cl < closureSize*2; cl += 2) { 2214 const PetscInt point = closure[cl]; 2215 PetscInt subVertex; 2216 2217 if ((point >= vStart) && (point < vEnd)) { 2218 ++numCorners; 2219 ierr = PetscFindInt(point, numSubVertices, subVertices, &subVertex);CHKERRQ(ierr); 2220 if (subVertex >= 0) { 2221 closure[faceSize] = point; 2222 subface[faceSize] = firstSubVertex+subVertex; 2223 ++faceSize; 2224 } 2225 } 2226 } 2227 if (faceSize > nFV) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Invalid submesh: Too many vertices %d of an element on the surface", faceSize); 2228 if (faceSize == nFV) { 2229 ierr = DMPlexInsertFace_Internal(dm, subdm, faceSize, closure, subface, numCorners, cell, subcell, firstSubFace, &newFacePoint);CHKERRQ(ierr); 2230 } 2231 ierr = DMPlexRestoreTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 2232 } 2233 ierr = DMRestoreWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);CHKERRQ(ierr); 2234 ierr = DMPlexSymmetrize(subdm);CHKERRQ(ierr); 2235 ierr = DMPlexStratify(subdm);CHKERRQ(ierr); 2236 /* Build coordinates */ 2237 { 2238 PetscSection coordSection, subCoordSection; 2239 Vec coordinates, subCoordinates; 2240 PetscScalar *coords, *subCoords; 2241 PetscInt numComp, coordSize, v; 2242 2243 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2244 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 2245 ierr = DMPlexGetCoordinateSection(subdm, &subCoordSection);CHKERRQ(ierr); 2246 ierr = PetscSectionSetNumFields(subCoordSection, 1);CHKERRQ(ierr); 2247 ierr = PetscSectionGetFieldComponents(coordSection, 0, &numComp);CHKERRQ(ierr); 2248 ierr = PetscSectionSetFieldComponents(subCoordSection, 0, numComp);CHKERRQ(ierr); 2249 ierr = PetscSectionSetChart(subCoordSection, firstSubVertex, firstSubVertex+numSubVertices);CHKERRQ(ierr); 2250 for (v = 0; v < numSubVertices; ++v) { 2251 const PetscInt vertex = subVertices[v]; 2252 const PetscInt subvertex = firstSubVertex+v; 2253 PetscInt dof; 2254 2255 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2256 ierr = PetscSectionSetDof(subCoordSection, subvertex, dof);CHKERRQ(ierr); 2257 ierr = PetscSectionSetFieldDof(subCoordSection, subvertex, 0, dof);CHKERRQ(ierr); 2258 } 2259 ierr = PetscSectionSetUp(subCoordSection);CHKERRQ(ierr); 2260 ierr = PetscSectionGetStorageSize(subCoordSection, &coordSize);CHKERRQ(ierr); 2261 ierr = VecCreate(comm, &subCoordinates);CHKERRQ(ierr); 2262 ierr = VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2263 ierr = VecSetType(subCoordinates,VECSTANDARD);CHKERRQ(ierr); 2264 if (coordSize) { 2265 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2266 ierr = VecGetArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2267 for (v = 0; v < numSubVertices; ++v) { 2268 const PetscInt vertex = subVertices[v]; 2269 const PetscInt subvertex = firstSubVertex+v; 2270 PetscInt dof, off, sdof, soff, d; 2271 2272 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2273 ierr = PetscSectionGetOffset(coordSection, vertex, &off);CHKERRQ(ierr); 2274 ierr = PetscSectionGetDof(subCoordSection, subvertex, &sdof);CHKERRQ(ierr); 2275 ierr = PetscSectionGetOffset(subCoordSection, subvertex, &soff);CHKERRQ(ierr); 2276 if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof); 2277 for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d]; 2278 } 2279 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2280 ierr = VecRestoreArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2281 } 2282 ierr = DMSetCoordinatesLocal(subdm, subCoordinates);CHKERRQ(ierr); 2283 ierr = VecDestroy(&subCoordinates);CHKERRQ(ierr); 2284 } 2285 /* Cleanup */ 2286 if (subvertexIS) {ierr = ISRestoreIndices(subvertexIS, &subVertices);CHKERRQ(ierr);} 2287 ierr = ISDestroy(&subvertexIS);CHKERRQ(ierr); 2288 if (subcellIS) {ierr = ISRestoreIndices(subcellIS, &subCells);CHKERRQ(ierr);} 2289 ierr = ISDestroy(&subcellIS);CHKERRQ(ierr); 2290 PetscFunctionReturn(0); 2291 } 2292 2293 #undef __FUNCT__ 2294 #define __FUNCT__ "DMPlexCreateSubmesh_Interpolated" 2295 static PetscErrorCode DMPlexCreateSubmesh_Interpolated(DM dm, DMLabel vertexLabel, PetscInt value, DM subdm) 2296 { 2297 MPI_Comm comm; 2298 DMLabel subpointMap; 2299 IS *subpointIS; 2300 const PetscInt **subpoints; 2301 PetscInt *numSubPoints, *firstSubPoint, *coneNew, *coneONew; 2302 PetscInt totSubPoints = 0, maxConeSize, dim, p, d, v; 2303 PetscErrorCode ierr; 2304 2305 PetscFunctionBegin; 2306 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 2307 /* Create subpointMap which marks the submesh */ 2308 ierr = DMLabelCreate("subpoint_map", &subpointMap);CHKERRQ(ierr); 2309 ierr = DMPlexSetSubpointMap(subdm, subpointMap);CHKERRQ(ierr); 2310 ierr = DMLabelDestroy(&subpointMap);CHKERRQ(ierr); 2311 if (vertexLabel) {ierr = DMPlexMarkSubmesh_Interpolated(dm, vertexLabel, value, subpointMap, subdm);CHKERRQ(ierr);} 2312 /* Setup chart */ 2313 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 2314 ierr = PetscMalloc4(dim+1,PetscInt,&numSubPoints,dim+1,PetscInt,&firstSubPoint,dim+1,IS,&subpointIS,dim+1,const PetscInt *,&subpoints);CHKERRQ(ierr); 2315 for (d = 0; d <= dim; ++d) { 2316 ierr = DMLabelGetStratumSize(subpointMap, d, &numSubPoints[d]);CHKERRQ(ierr); 2317 totSubPoints += numSubPoints[d]; 2318 } 2319 ierr = DMPlexSetChart(subdm, 0, totSubPoints);CHKERRQ(ierr); 2320 ierr = DMPlexSetVTKCellHeight(subdm, 1);CHKERRQ(ierr); 2321 /* Set cone sizes */ 2322 firstSubPoint[dim] = 0; 2323 firstSubPoint[0] = firstSubPoint[dim] + numSubPoints[dim]; 2324 if (dim > 1) {firstSubPoint[dim-1] = firstSubPoint[0] + numSubPoints[0];} 2325 if (dim > 2) {firstSubPoint[dim-2] = firstSubPoint[dim-1] + numSubPoints[dim-1];} 2326 for (d = 0; d <= dim; ++d) { 2327 ierr = DMLabelGetStratumIS(subpointMap, d, &subpointIS[d]);CHKERRQ(ierr); 2328 ierr = ISGetIndices(subpointIS[d], &subpoints[d]);CHKERRQ(ierr); 2329 } 2330 for (d = 0; d <= dim; ++d) { 2331 for (p = 0; p < numSubPoints[d]; ++p) { 2332 const PetscInt point = subpoints[d][p]; 2333 const PetscInt subpoint = firstSubPoint[d] + p; 2334 const PetscInt *cone; 2335 PetscInt coneSize, coneSizeNew, c, val; 2336 2337 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 2338 ierr = DMPlexSetConeSize(subdm, subpoint, coneSize);CHKERRQ(ierr); 2339 if (d == dim) { 2340 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 2341 for (c = 0, coneSizeNew = 0; c < coneSize; ++c) { 2342 ierr = DMLabelGetValue(subpointMap, cone[c], &val);CHKERRQ(ierr); 2343 if (val >= 0) coneSizeNew++; 2344 } 2345 ierr = DMPlexSetConeSize(subdm, subpoint, coneSizeNew);CHKERRQ(ierr); 2346 } 2347 } 2348 } 2349 ierr = DMSetUp(subdm);CHKERRQ(ierr); 2350 /* Set cones */ 2351 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, NULL);CHKERRQ(ierr); 2352 ierr = PetscMalloc2(maxConeSize,PetscInt,&coneNew,maxConeSize,PetscInt,&coneONew);CHKERRQ(ierr); 2353 for (d = 0; d <= dim; ++d) { 2354 for (p = 0; p < numSubPoints[d]; ++p) { 2355 const PetscInt point = subpoints[d][p]; 2356 const PetscInt subpoint = firstSubPoint[d] + p; 2357 const PetscInt *cone, *ornt; 2358 PetscInt coneSize, subconeSize, coneSizeNew, c, subc; 2359 2360 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 2361 ierr = DMPlexGetConeSize(subdm, subpoint, &subconeSize);CHKERRQ(ierr); 2362 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 2363 ierr = DMPlexGetConeOrientation(dm, point, &ornt);CHKERRQ(ierr); 2364 for (c = 0, coneSizeNew = 0; c < coneSize; ++c) { 2365 ierr = PetscFindInt(cone[c], numSubPoints[d-1], subpoints[d-1], &subc);CHKERRQ(ierr); 2366 if (subc >= 0) { 2367 coneNew[coneSizeNew] = firstSubPoint[d-1] + subc; 2368 coneONew[coneSizeNew] = ornt[c]; 2369 ++coneSizeNew; 2370 } 2371 } 2372 if (coneSizeNew != subconeSize) SETERRQ2(comm, PETSC_ERR_PLIB, "Number of cone points located %d does not match subcone size %d", coneSizeNew, subconeSize); 2373 ierr = DMPlexSetCone(subdm, subpoint, coneNew);CHKERRQ(ierr); 2374 ierr = DMPlexSetConeOrientation(subdm, subpoint, coneONew);CHKERRQ(ierr); 2375 } 2376 } 2377 ierr = PetscFree2(coneNew,coneONew);CHKERRQ(ierr); 2378 ierr = DMPlexSymmetrize(subdm);CHKERRQ(ierr); 2379 ierr = DMPlexStratify(subdm);CHKERRQ(ierr); 2380 /* Build coordinates */ 2381 { 2382 PetscSection coordSection, subCoordSection; 2383 Vec coordinates, subCoordinates; 2384 PetscScalar *coords, *subCoords; 2385 PetscInt numComp, coordSize; 2386 2387 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2388 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 2389 ierr = DMPlexGetCoordinateSection(subdm, &subCoordSection);CHKERRQ(ierr); 2390 ierr = PetscSectionSetNumFields(subCoordSection, 1);CHKERRQ(ierr); 2391 ierr = PetscSectionGetFieldComponents(coordSection, 0, &numComp);CHKERRQ(ierr); 2392 ierr = PetscSectionSetFieldComponents(subCoordSection, 0, numComp);CHKERRQ(ierr); 2393 ierr = PetscSectionSetChart(subCoordSection, firstSubPoint[0], firstSubPoint[0]+numSubPoints[0]);CHKERRQ(ierr); 2394 for (v = 0; v < numSubPoints[0]; ++v) { 2395 const PetscInt vertex = subpoints[0][v]; 2396 const PetscInt subvertex = firstSubPoint[0]+v; 2397 PetscInt dof; 2398 2399 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2400 ierr = PetscSectionSetDof(subCoordSection, subvertex, dof);CHKERRQ(ierr); 2401 ierr = PetscSectionSetFieldDof(subCoordSection, subvertex, 0, dof);CHKERRQ(ierr); 2402 } 2403 ierr = PetscSectionSetUp(subCoordSection);CHKERRQ(ierr); 2404 ierr = PetscSectionGetStorageSize(subCoordSection, &coordSize);CHKERRQ(ierr); 2405 ierr = VecCreate(comm, &subCoordinates);CHKERRQ(ierr); 2406 ierr = VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2407 ierr = VecSetType(subCoordinates,VECSTANDARD);CHKERRQ(ierr); 2408 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2409 ierr = VecGetArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2410 for (v = 0; v < numSubPoints[0]; ++v) { 2411 const PetscInt vertex = subpoints[0][v]; 2412 const PetscInt subvertex = firstSubPoint[0]+v; 2413 PetscInt dof, off, sdof, soff, d; 2414 2415 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2416 ierr = PetscSectionGetOffset(coordSection, vertex, &off);CHKERRQ(ierr); 2417 ierr = PetscSectionGetDof(subCoordSection, subvertex, &sdof);CHKERRQ(ierr); 2418 ierr = PetscSectionGetOffset(subCoordSection, subvertex, &soff);CHKERRQ(ierr); 2419 if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof); 2420 for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d]; 2421 } 2422 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2423 ierr = VecRestoreArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2424 ierr = DMSetCoordinatesLocal(subdm, subCoordinates);CHKERRQ(ierr); 2425 ierr = VecDestroy(&subCoordinates);CHKERRQ(ierr); 2426 } 2427 /* Cleanup */ 2428 for (d = 0; d <= dim; ++d) { 2429 ierr = ISRestoreIndices(subpointIS[d], &subpoints[d]);CHKERRQ(ierr); 2430 ierr = ISDestroy(&subpointIS[d]);CHKERRQ(ierr); 2431 } 2432 ierr = PetscFree4(numSubPoints,firstSubPoint,subpointIS,subpoints);CHKERRQ(ierr); 2433 PetscFunctionReturn(0); 2434 } 2435 2436 #undef __FUNCT__ 2437 #define __FUNCT__ "DMPlexCreateSubmesh" 2438 /*@ 2439 DMPlexCreateSubmesh - Extract a hypersurface from the mesh using vertices defined by a label 2440 2441 Input Parameters: 2442 + dm - The original mesh 2443 . vertexLabel - The DMLabel marking vertices contained in the surface 2444 - value - The label value to use 2445 2446 Output Parameter: 2447 . subdm - The surface mesh 2448 2449 Note: This function produces a DMLabel mapping original points in the submesh to their depth. This can be obtained using DMPlexGetSubpointMap(). 2450 2451 Level: developer 2452 2453 .seealso: DMPlexGetSubpointMap(), DMPlexGetLabel(), DMLabelSetValue() 2454 @*/ 2455 PetscErrorCode DMPlexCreateSubmesh(DM dm, DMLabel vertexLabel, PetscInt value, DM *subdm) 2456 { 2457 PetscInt dim, depth; 2458 PetscErrorCode ierr; 2459 2460 PetscFunctionBegin; 2461 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2462 PetscValidPointer(subdm, 3); 2463 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 2464 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 2465 ierr = DMCreate(PetscObjectComm((PetscObject)dm), subdm);CHKERRQ(ierr); 2466 ierr = DMSetType(*subdm, DMPLEX);CHKERRQ(ierr); 2467 ierr = DMPlexSetDimension(*subdm, dim-1);CHKERRQ(ierr); 2468 if (depth == dim) { 2469 ierr = DMPlexCreateSubmesh_Interpolated(dm, vertexLabel, value, *subdm);CHKERRQ(ierr); 2470 } else { 2471 ierr = DMPlexCreateSubmesh_Uninterpolated(dm, vertexLabel, value, *subdm);CHKERRQ(ierr); 2472 } 2473 PetscFunctionReturn(0); 2474 } 2475 2476 #undef __FUNCT__ 2477 #define __FUNCT__ "DMPlexFilterPoint_Internal" 2478 PETSC_STATIC_INLINE PetscInt DMPlexFilterPoint_Internal(PetscInt point, PetscInt firstSubPoint, PetscInt numSubPoints, const PetscInt subPoints[]) 2479 { 2480 PetscInt subPoint; 2481 PetscErrorCode ierr; 2482 2483 ierr = PetscFindInt(point, numSubPoints, subPoints, &subPoint); if (ierr < 0) return ierr; 2484 return subPoint < 0 ? subPoint : firstSubPoint+subPoint; 2485 } 2486 2487 #undef __FUNCT__ 2488 #define __FUNCT__ "DMPlexCreateCohesiveSubmesh_Uninterpolated" 2489 static PetscErrorCode DMPlexCreateCohesiveSubmesh_Uninterpolated(DM dm, PetscBool hasLagrange, const char label[], PetscInt value, DM subdm) 2490 { 2491 MPI_Comm comm; 2492 DMLabel subpointMap; 2493 IS subvertexIS; 2494 const PetscInt *subVertices; 2495 PetscInt numSubVertices, firstSubVertex, numSubCells, *subCells = NULL; 2496 PetscInt *subface, maxConeSize, numSubFaces, firstSubFace, newFacePoint, nFV; 2497 PetscInt cMax, c, f; 2498 PetscErrorCode ierr; 2499 2500 PetscFunctionBegin; 2501 ierr = PetscObjectGetComm((PetscObject)dm, &comm);CHKERRQ(ierr); 2502 /* Create subpointMap which marks the submesh */ 2503 ierr = DMLabelCreate("subpoint_map", &subpointMap);CHKERRQ(ierr); 2504 ierr = DMPlexSetSubpointMap(subdm, subpointMap);CHKERRQ(ierr); 2505 ierr = DMLabelDestroy(&subpointMap);CHKERRQ(ierr); 2506 ierr = DMPlexMarkCohesiveSubmesh_Uninterpolated(dm, hasLagrange, label, value, subpointMap, &numSubFaces, &nFV, &subCells, subdm);CHKERRQ(ierr); 2507 /* Setup chart */ 2508 ierr = DMLabelGetStratumSize(subpointMap, 0, &numSubVertices);CHKERRQ(ierr); 2509 ierr = DMLabelGetStratumSize(subpointMap, 2, &numSubCells);CHKERRQ(ierr); 2510 ierr = DMPlexSetChart(subdm, 0, numSubCells+numSubFaces+numSubVertices);CHKERRQ(ierr); 2511 ierr = DMPlexSetVTKCellHeight(subdm, 1);CHKERRQ(ierr); 2512 /* Set cone sizes */ 2513 firstSubVertex = numSubCells; 2514 firstSubFace = numSubCells+numSubVertices; 2515 newFacePoint = firstSubFace; 2516 ierr = DMLabelGetStratumIS(subpointMap, 0, &subvertexIS);CHKERRQ(ierr); 2517 if (subvertexIS) {ierr = ISGetIndices(subvertexIS, &subVertices);CHKERRQ(ierr);} 2518 for (c = 0; c < numSubCells; ++c) { 2519 ierr = DMPlexSetConeSize(subdm, c, 1);CHKERRQ(ierr); 2520 } 2521 for (f = firstSubFace; f < firstSubFace+numSubFaces; ++f) { 2522 ierr = DMPlexSetConeSize(subdm, f, nFV);CHKERRQ(ierr); 2523 } 2524 ierr = DMSetUp(subdm);CHKERRQ(ierr); 2525 /* Create face cones */ 2526 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, NULL);CHKERRQ(ierr); 2527 ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); 2528 ierr = DMGetWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);CHKERRQ(ierr); 2529 for (c = 0; c < numSubCells; ++c) { 2530 const PetscInt cell = subCells[c]; 2531 const PetscInt subcell = c; 2532 const PetscInt *cone, *cells; 2533 PetscInt numCells, subVertex, p, v; 2534 2535 if (cell < cMax) continue; 2536 ierr = DMPlexGetCone(dm, cell, &cone);CHKERRQ(ierr); 2537 for (v = 0; v < nFV; ++v) { 2538 ierr = PetscFindInt(cone[v], numSubVertices, subVertices, &subVertex);CHKERRQ(ierr); 2539 subface[v] = firstSubVertex+subVertex; 2540 } 2541 ierr = DMPlexSetCone(subdm, newFacePoint, subface);CHKERRQ(ierr); 2542 ierr = DMPlexSetCone(subdm, subcell, &newFacePoint);CHKERRQ(ierr); 2543 ierr = DMPlexGetJoin(dm, nFV, cone, &numCells, &cells);CHKERRQ(ierr); 2544 /* Not true in parallel 2545 if (numCells != 2) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive cells should separate two cells"); */ 2546 for (p = 0; p < numCells; ++p) { 2547 PetscInt negsubcell; 2548 2549 if (cells[p] >= cMax) continue; 2550 /* I know this is a crap search */ 2551 for (negsubcell = 0; negsubcell < numSubCells; ++negsubcell) { 2552 if (subCells[negsubcell] == cells[p]) break; 2553 } 2554 if (negsubcell == numSubCells) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not find negative face neighbor for cohesive cell %d", cell); 2555 ierr = DMPlexSetCone(subdm, negsubcell, &newFacePoint);CHKERRQ(ierr); 2556 } 2557 ierr = DMPlexRestoreJoin(dm, nFV, cone, &numCells, &cells);CHKERRQ(ierr); 2558 ++newFacePoint; 2559 } 2560 ierr = DMRestoreWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);CHKERRQ(ierr); 2561 ierr = DMPlexSymmetrize(subdm);CHKERRQ(ierr); 2562 ierr = DMPlexStratify(subdm);CHKERRQ(ierr); 2563 /* Build coordinates */ 2564 { 2565 PetscSection coordSection, subCoordSection; 2566 Vec coordinates, subCoordinates; 2567 PetscScalar *coords, *subCoords; 2568 PetscInt numComp, coordSize, v; 2569 2570 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2571 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 2572 ierr = DMPlexGetCoordinateSection(subdm, &subCoordSection);CHKERRQ(ierr); 2573 ierr = PetscSectionSetNumFields(subCoordSection, 1);CHKERRQ(ierr); 2574 ierr = PetscSectionGetFieldComponents(coordSection, 0, &numComp);CHKERRQ(ierr); 2575 ierr = PetscSectionSetFieldComponents(subCoordSection, 0, numComp);CHKERRQ(ierr); 2576 ierr = PetscSectionSetChart(subCoordSection, firstSubVertex, firstSubVertex+numSubVertices);CHKERRQ(ierr); 2577 for (v = 0; v < numSubVertices; ++v) { 2578 const PetscInt vertex = subVertices[v]; 2579 const PetscInt subvertex = firstSubVertex+v; 2580 PetscInt dof; 2581 2582 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2583 ierr = PetscSectionSetDof(subCoordSection, subvertex, dof);CHKERRQ(ierr); 2584 ierr = PetscSectionSetFieldDof(subCoordSection, subvertex, 0, dof);CHKERRQ(ierr); 2585 } 2586 ierr = PetscSectionSetUp(subCoordSection);CHKERRQ(ierr); 2587 ierr = PetscSectionGetStorageSize(subCoordSection, &coordSize);CHKERRQ(ierr); 2588 ierr = VecCreate(comm, &subCoordinates);CHKERRQ(ierr); 2589 ierr = VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2590 ierr = VecSetType(subCoordinates,VECSTANDARD);CHKERRQ(ierr); 2591 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2592 ierr = VecGetArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2593 for (v = 0; v < numSubVertices; ++v) { 2594 const PetscInt vertex = subVertices[v]; 2595 const PetscInt subvertex = firstSubVertex+v; 2596 PetscInt dof, off, sdof, soff, d; 2597 2598 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2599 ierr = PetscSectionGetOffset(coordSection, vertex, &off);CHKERRQ(ierr); 2600 ierr = PetscSectionGetDof(subCoordSection, subvertex, &sdof);CHKERRQ(ierr); 2601 ierr = PetscSectionGetOffset(subCoordSection, subvertex, &soff);CHKERRQ(ierr); 2602 if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof); 2603 for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d]; 2604 } 2605 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2606 ierr = VecRestoreArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2607 ierr = DMSetCoordinatesLocal(subdm, subCoordinates);CHKERRQ(ierr); 2608 ierr = VecDestroy(&subCoordinates);CHKERRQ(ierr); 2609 } 2610 /* Build SF */ 2611 CHKMEMQ; 2612 { 2613 PetscSF sfPoint, sfPointSub; 2614 const PetscSFNode *remotePoints; 2615 PetscSFNode *sremotePoints, *newLocalPoints, *newOwners; 2616 const PetscInt *localPoints; 2617 PetscInt *slocalPoints; 2618 PetscInt numRoots, numLeaves, numSubRoots = numSubCells+numSubFaces+numSubVertices, numSubLeaves = 0, l, sl, ll, pStart, pEnd, p, vStart, vEnd; 2619 PetscMPIInt rank; 2620 2621 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRQ(ierr); 2622 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 2623 ierr = DMGetPointSF(subdm, &sfPointSub);CHKERRQ(ierr); 2624 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 2625 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 2626 ierr = PetscSFGetGraph(sfPoint, &numRoots, &numLeaves, &localPoints, &remotePoints);CHKERRQ(ierr); 2627 if (numRoots >= 0) { 2628 /* Only vertices should be shared */ 2629 ierr = PetscMalloc2(pEnd-pStart,PetscSFNode,&newLocalPoints,numRoots,PetscSFNode,&newOwners);CHKERRQ(ierr); 2630 for (p = 0; p < pEnd-pStart; ++p) { 2631 newLocalPoints[p].rank = -2; 2632 newLocalPoints[p].index = -2; 2633 } 2634 /* Set subleaves */ 2635 for (l = 0; l < numLeaves; ++l) { 2636 const PetscInt point = localPoints[l]; 2637 const PetscInt subPoint = DMPlexFilterPoint_Internal(point, firstSubVertex, numSubVertices, subVertices); 2638 2639 if ((point < vStart) && (point >= vEnd)) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Should not be mapping anything but vertices, %d", point); 2640 if (subPoint < 0) continue; 2641 newLocalPoints[point-pStart].rank = rank; 2642 newLocalPoints[point-pStart].index = subPoint; 2643 ++numSubLeaves; 2644 } 2645 /* Must put in owned subpoints */ 2646 for (p = pStart; p < pEnd; ++p) { 2647 const PetscInt subPoint = DMPlexFilterPoint_Internal(p, firstSubVertex, numSubVertices, subVertices); 2648 2649 if (subPoint < 0) { 2650 newOwners[p-pStart].rank = -3; 2651 newOwners[p-pStart].index = -3; 2652 } else { 2653 newOwners[p-pStart].rank = rank; 2654 newOwners[p-pStart].index = subPoint; 2655 } 2656 } 2657 ierr = PetscSFReduceBegin(sfPoint, MPIU_2INT, newLocalPoints, newOwners, MPI_MAXLOC);CHKERRQ(ierr); 2658 ierr = PetscSFReduceEnd(sfPoint, MPIU_2INT, newLocalPoints, newOwners, MPI_MAXLOC);CHKERRQ(ierr); 2659 ierr = PetscSFBcastBegin(sfPoint, MPIU_2INT, newOwners, newLocalPoints);CHKERRQ(ierr); 2660 ierr = PetscSFBcastEnd(sfPoint, MPIU_2INT, newOwners, newLocalPoints);CHKERRQ(ierr); 2661 ierr = PetscMalloc(numSubLeaves * sizeof(PetscInt), &slocalPoints);CHKERRQ(ierr); 2662 ierr = PetscMalloc(numSubLeaves * sizeof(PetscSFNode), &sremotePoints);CHKERRQ(ierr); 2663 for (l = 0, sl = 0, ll = 0; l < numLeaves; ++l) { 2664 const PetscInt point = localPoints[l]; 2665 const PetscInt subPoint = DMPlexFilterPoint_Internal(point, firstSubVertex, numSubVertices, subVertices); 2666 2667 if (subPoint < 0) continue; 2668 if (newLocalPoints[point].rank == rank) {++ll; continue;} 2669 slocalPoints[sl] = subPoint; 2670 sremotePoints[sl].rank = newLocalPoints[point].rank; 2671 sremotePoints[sl].index = newLocalPoints[point].index; 2672 if (sremotePoints[sl].rank < 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid remote rank for local point %d", point); 2673 if (sremotePoints[sl].index < 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid remote subpoint for local point %d", point); 2674 ++sl; 2675 } 2676 ierr = PetscFree2(newLocalPoints,newOwners);CHKERRQ(ierr); 2677 if (sl + ll != numSubLeaves) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Mismatch in number of subleaves %d + %d != %d", sl, ll, numSubLeaves); 2678 ierr = PetscSFSetGraph(sfPointSub, numSubRoots, sl, slocalPoints, PETSC_OWN_POINTER, sremotePoints, PETSC_OWN_POINTER);CHKERRQ(ierr); 2679 } 2680 } 2681 CHKMEMQ; 2682 /* Cleanup */ 2683 if (subvertexIS) {ierr = ISRestoreIndices(subvertexIS, &subVertices);CHKERRQ(ierr);} 2684 ierr = ISDestroy(&subvertexIS);CHKERRQ(ierr); 2685 ierr = PetscFree(subCells);CHKERRQ(ierr); 2686 PetscFunctionReturn(0); 2687 } 2688 2689 #undef __FUNCT__ 2690 #define __FUNCT__ "DMPlexCreateCohesiveSubmesh_Interpolated" 2691 static PetscErrorCode DMPlexCreateCohesiveSubmesh_Interpolated(DM dm, const char label[], PetscInt value, DM subdm) 2692 { 2693 MPI_Comm comm; 2694 DMLabel subpointMap; 2695 IS *subpointIS; 2696 const PetscInt **subpoints; 2697 PetscInt *numSubPoints, *firstSubPoint, *coneNew; 2698 PetscInt totSubPoints = 0, maxConeSize, dim, p, d, v; 2699 PetscErrorCode ierr; 2700 2701 PetscFunctionBegin; 2702 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 2703 /* Create subpointMap which marks the submesh */ 2704 ierr = DMLabelCreate("subpoint_map", &subpointMap);CHKERRQ(ierr); 2705 ierr = DMPlexSetSubpointMap(subdm, subpointMap);CHKERRQ(ierr); 2706 ierr = DMLabelDestroy(&subpointMap);CHKERRQ(ierr); 2707 ierr = DMPlexMarkCohesiveSubmesh_Interpolated(dm, label, value, subpointMap, subdm);CHKERRQ(ierr); 2708 /* Setup chart */ 2709 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 2710 ierr = PetscMalloc4(dim+1,PetscInt,&numSubPoints,dim+1,PetscInt,&firstSubPoint,dim+1,IS,&subpointIS,dim+1,const PetscInt *,&subpoints);CHKERRQ(ierr); 2711 for (d = 0; d <= dim; ++d) { 2712 ierr = DMLabelGetStratumSize(subpointMap, d, &numSubPoints[d]);CHKERRQ(ierr); 2713 totSubPoints += numSubPoints[d]; 2714 } 2715 ierr = DMPlexSetChart(subdm, 0, totSubPoints);CHKERRQ(ierr); 2716 ierr = DMPlexSetVTKCellHeight(subdm, 1);CHKERRQ(ierr); 2717 /* Set cone sizes */ 2718 firstSubPoint[dim] = 0; 2719 firstSubPoint[0] = firstSubPoint[dim] + numSubPoints[dim]; 2720 if (dim > 1) {firstSubPoint[dim-1] = firstSubPoint[0] + numSubPoints[0];} 2721 if (dim > 2) {firstSubPoint[dim-2] = firstSubPoint[dim-1] + numSubPoints[dim-1];} 2722 for (d = 0; d <= dim; ++d) { 2723 ierr = DMLabelGetStratumIS(subpointMap, d, &subpointIS[d]);CHKERRQ(ierr); 2724 ierr = ISGetIndices(subpointIS[d], &subpoints[d]);CHKERRQ(ierr); 2725 } 2726 for (d = 0; d <= dim; ++d) { 2727 for (p = 0; p < numSubPoints[d]; ++p) { 2728 const PetscInt point = subpoints[d][p]; 2729 const PetscInt subpoint = firstSubPoint[d] + p; 2730 const PetscInt *cone; 2731 PetscInt coneSize, coneSizeNew, c, val; 2732 2733 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 2734 ierr = DMPlexSetConeSize(subdm, subpoint, coneSize);CHKERRQ(ierr); 2735 if (d == dim) { 2736 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 2737 for (c = 0, coneSizeNew = 0; c < coneSize; ++c) { 2738 ierr = DMLabelGetValue(subpointMap, cone[c], &val);CHKERRQ(ierr); 2739 if (val >= 0) coneSizeNew++; 2740 } 2741 ierr = DMPlexSetConeSize(subdm, subpoint, coneSizeNew);CHKERRQ(ierr); 2742 } 2743 } 2744 } 2745 ierr = DMSetUp(subdm);CHKERRQ(ierr); 2746 /* Set cones */ 2747 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, NULL);CHKERRQ(ierr); 2748 ierr = PetscMalloc(maxConeSize * sizeof(PetscInt), &coneNew);CHKERRQ(ierr); 2749 for (d = 0; d <= dim; ++d) { 2750 for (p = 0; p < numSubPoints[d]; ++p) { 2751 const PetscInt point = subpoints[d][p]; 2752 const PetscInt subpoint = firstSubPoint[d] + p; 2753 const PetscInt *cone; 2754 PetscInt coneSize, subconeSize, coneSizeNew, c, subc; 2755 2756 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 2757 ierr = DMPlexGetConeSize(subdm, subpoint, &subconeSize);CHKERRQ(ierr); 2758 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 2759 for (c = 0, coneSizeNew = 0; c < coneSize; ++c) { 2760 ierr = PetscFindInt(cone[c], numSubPoints[d-1], subpoints[d-1], &subc);CHKERRQ(ierr); 2761 if (subc >= 0) coneNew[coneSizeNew++] = firstSubPoint[d-1] + subc; 2762 } 2763 if (coneSizeNew != subconeSize) SETERRQ2(comm, PETSC_ERR_PLIB, "Number of cone points located %d does not match subcone size %d", coneSizeNew, subconeSize); 2764 ierr = DMPlexSetCone(subdm, subpoint, coneNew);CHKERRQ(ierr); 2765 } 2766 } 2767 ierr = PetscFree(coneNew);CHKERRQ(ierr); 2768 ierr = DMPlexSymmetrize(subdm);CHKERRQ(ierr); 2769 ierr = DMPlexStratify(subdm);CHKERRQ(ierr); 2770 /* Build coordinates */ 2771 { 2772 PetscSection coordSection, subCoordSection; 2773 Vec coordinates, subCoordinates; 2774 PetscScalar *coords, *subCoords; 2775 PetscInt numComp, coordSize; 2776 2777 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2778 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 2779 ierr = DMPlexGetCoordinateSection(subdm, &subCoordSection);CHKERRQ(ierr); 2780 ierr = PetscSectionSetNumFields(subCoordSection, 1);CHKERRQ(ierr); 2781 ierr = PetscSectionGetFieldComponents(coordSection, 0, &numComp);CHKERRQ(ierr); 2782 ierr = PetscSectionSetFieldComponents(subCoordSection, 0, numComp);CHKERRQ(ierr); 2783 ierr = PetscSectionSetChart(subCoordSection, firstSubPoint[0], firstSubPoint[0]+numSubPoints[0]);CHKERRQ(ierr); 2784 for (v = 0; v < numSubPoints[0]; ++v) { 2785 const PetscInt vertex = subpoints[0][v]; 2786 const PetscInt subvertex = firstSubPoint[0]+v; 2787 PetscInt dof; 2788 2789 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2790 ierr = PetscSectionSetDof(subCoordSection, subvertex, dof);CHKERRQ(ierr); 2791 ierr = PetscSectionSetFieldDof(subCoordSection, subvertex, 0, dof);CHKERRQ(ierr); 2792 } 2793 ierr = PetscSectionSetUp(subCoordSection);CHKERRQ(ierr); 2794 ierr = PetscSectionGetStorageSize(subCoordSection, &coordSize);CHKERRQ(ierr); 2795 ierr = VecCreate(comm, &subCoordinates);CHKERRQ(ierr); 2796 ierr = VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2797 ierr = VecSetType(subCoordinates,VECSTANDARD);CHKERRQ(ierr); 2798 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2799 ierr = VecGetArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2800 for (v = 0; v < numSubPoints[0]; ++v) { 2801 const PetscInt vertex = subpoints[0][v]; 2802 const PetscInt subvertex = firstSubPoint[0]+v; 2803 PetscInt dof, off, sdof, soff, d; 2804 2805 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2806 ierr = PetscSectionGetOffset(coordSection, vertex, &off);CHKERRQ(ierr); 2807 ierr = PetscSectionGetDof(subCoordSection, subvertex, &sdof);CHKERRQ(ierr); 2808 ierr = PetscSectionGetOffset(subCoordSection, subvertex, &soff);CHKERRQ(ierr); 2809 if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof); 2810 for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d]; 2811 } 2812 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2813 ierr = VecRestoreArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2814 ierr = DMSetCoordinatesLocal(subdm, subCoordinates);CHKERRQ(ierr); 2815 ierr = VecDestroy(&subCoordinates);CHKERRQ(ierr); 2816 } 2817 /* Cleanup */ 2818 for (d = 0; d <= dim; ++d) { 2819 ierr = ISRestoreIndices(subpointIS[d], &subpoints[d]);CHKERRQ(ierr); 2820 ierr = ISDestroy(&subpointIS[d]);CHKERRQ(ierr); 2821 } 2822 ierr = PetscFree4(numSubPoints,firstSubPoint,subpointIS,subpoints);CHKERRQ(ierr); 2823 PetscFunctionReturn(0); 2824 } 2825 2826 #undef __FUNCT__ 2827 #define __FUNCT__ "DMPlexCreateCohesiveSubmesh" 2828 /* 2829 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. 2830 2831 Input Parameters: 2832 + dm - The original mesh 2833 . hasLagrange - The mesh has Lagrange unknowns in the cohesive cells 2834 . label - A label name, or PETSC_NULL 2835 - value - A label value 2836 2837 Output Parameter: 2838 . subdm - The surface mesh 2839 2840 Note: This function produces a DMLabel mapping original points in the submesh to their depth. This can be obtained using DMPlexGetSubpointMap(). 2841 2842 Level: developer 2843 2844 .seealso: DMPlexGetSubpointMap(), DMPlexCreateSubmesh() 2845 */ 2846 PetscErrorCode DMPlexCreateCohesiveSubmesh(DM dm, PetscBool hasLagrange, const char label[], PetscInt value, DM *subdm) 2847 { 2848 PetscInt dim, depth; 2849 PetscErrorCode ierr; 2850 2851 PetscFunctionBegin; 2852 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2853 PetscValidPointer(subdm, 5); 2854 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 2855 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 2856 ierr = DMCreate(PetscObjectComm((PetscObject)dm), subdm);CHKERRQ(ierr); 2857 ierr = DMSetType(*subdm, DMPLEX);CHKERRQ(ierr); 2858 ierr = DMPlexSetDimension(*subdm, dim-1);CHKERRQ(ierr); 2859 if (depth == dim) { 2860 ierr = DMPlexCreateCohesiveSubmesh_Interpolated(dm, label, value, *subdm);CHKERRQ(ierr); 2861 } else { 2862 ierr = DMPlexCreateCohesiveSubmesh_Uninterpolated(dm, hasLagrange, label, value, *subdm);CHKERRQ(ierr); 2863 } 2864 PetscFunctionReturn(0); 2865 } 2866 2867 #undef __FUNCT__ 2868 #define __FUNCT__ "DMPlexGetSubpointMap" 2869 /*@ 2870 DMPlexGetSubpointMap - Returns a DMLabel with point dimension as values 2871 2872 Input Parameter: 2873 . dm - The submesh DM 2874 2875 Output Parameter: 2876 . subpointMap - The DMLabel of all the points from the original mesh in this submesh, or NULL if this is not a submesh 2877 2878 Level: developer 2879 2880 .seealso: DMPlexCreateSubmesh(), DMPlexCreateSubpointIS() 2881 @*/ 2882 PetscErrorCode DMPlexGetSubpointMap(DM dm, DMLabel *subpointMap) 2883 { 2884 DM_Plex *mesh = (DM_Plex*) dm->data; 2885 2886 PetscFunctionBegin; 2887 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2888 PetscValidPointer(subpointMap, 2); 2889 *subpointMap = mesh->subpointMap; 2890 PetscFunctionReturn(0); 2891 } 2892 2893 #undef __FUNCT__ 2894 #define __FUNCT__ "DMPlexSetSubpointMap" 2895 /* Note: Should normally not be called by the user, since it is set in DMPlexCreateSubmesh() */ 2896 PetscErrorCode DMPlexSetSubpointMap(DM dm, DMLabel subpointMap) 2897 { 2898 DM_Plex *mesh = (DM_Plex *) dm->data; 2899 DMLabel tmp; 2900 PetscErrorCode ierr; 2901 2902 PetscFunctionBegin; 2903 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2904 tmp = mesh->subpointMap; 2905 mesh->subpointMap = subpointMap; 2906 ++mesh->subpointMap->refct; 2907 ierr = DMLabelDestroy(&tmp);CHKERRQ(ierr); 2908 PetscFunctionReturn(0); 2909 } 2910 2911 #undef __FUNCT__ 2912 #define __FUNCT__ "DMPlexCreateSubpointIS" 2913 /*@ 2914 DMPlexCreateSubpointIS - Creates an IS covering the entire subdm chart with the original points as data 2915 2916 Input Parameter: 2917 . dm - The submesh DM 2918 2919 Output Parameter: 2920 . subpointIS - The IS of all the points from the original mesh in this submesh, or NULL if this is not a submesh 2921 2922 Note: This is IS is guaranteed to be sorted by the construction of the submesh 2923 2924 Level: developer 2925 2926 .seealso: DMPlexCreateSubmesh(), DMPlexGetSubpointMap() 2927 @*/ 2928 PetscErrorCode DMPlexCreateSubpointIS(DM dm, IS *subpointIS) 2929 { 2930 MPI_Comm comm; 2931 DMLabel subpointMap; 2932 IS is; 2933 const PetscInt *opoints; 2934 PetscInt *points, *depths; 2935 PetscInt depth, depStart, depEnd, d, pStart, pEnd, p, n, off; 2936 PetscErrorCode ierr; 2937 2938 PetscFunctionBegin; 2939 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2940 PetscValidPointer(subpointIS, 2); 2941 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 2942 *subpointIS = NULL; 2943 ierr = DMPlexGetSubpointMap(dm, &subpointMap);CHKERRQ(ierr); 2944 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 2945 if (subpointMap && depth >= 0) { 2946 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 2947 if (pStart) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Submeshes must start the point numbering at 0, not %d", pStart); 2948 ierr = DMGetWorkArray(dm, depth+1, PETSC_INT, &depths);CHKERRQ(ierr); 2949 depths[0] = depth; 2950 depths[1] = 0; 2951 for(d = 2; d <= depth; ++d) {depths[d] = depth+1 - d;} 2952 ierr = PetscMalloc(pEnd * sizeof(PetscInt), &points);CHKERRQ(ierr); 2953 for(d = 0, off = 0; d <= depth; ++d) { 2954 const PetscInt dep = depths[d]; 2955 2956 ierr = DMPlexGetDepthStratum(dm, dep, &depStart, &depEnd);CHKERRQ(ierr); 2957 ierr = DMLabelGetStratumSize(subpointMap, dep, &n);CHKERRQ(ierr); 2958 if (((d < 2) && (depth > 1)) || (d == 1)) { /* Only check vertices and cells for now since the map is broken for others */ 2959 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); 2960 } else { 2961 if (!n) { 2962 if (d == 0) { 2963 /* Missing cells */ 2964 for(p = 0; p < depEnd-depStart; ++p, ++off) points[off] = -1; 2965 } else { 2966 /* Missing faces */ 2967 for(p = 0; p < depEnd-depStart; ++p, ++off) points[off] = PETSC_MAX_INT; 2968 } 2969 } 2970 } 2971 if (n) { 2972 ierr = DMLabelGetStratumIS(subpointMap, dep, &is);CHKERRQ(ierr); 2973 ierr = ISGetIndices(is, &opoints);CHKERRQ(ierr); 2974 for(p = 0; p < n; ++p, ++off) points[off] = opoints[p]; 2975 ierr = ISRestoreIndices(is, &opoints);CHKERRQ(ierr); 2976 ierr = ISDestroy(&is);CHKERRQ(ierr); 2977 } 2978 } 2979 ierr = DMRestoreWorkArray(dm, depth+1, PETSC_INT, &depths);CHKERRQ(ierr); 2980 if (off != pEnd) SETERRQ2(comm, PETSC_ERR_ARG_WRONG, "The number of mapped submesh points %d should be %d", off, pEnd); 2981 ierr = ISCreateGeneral(PETSC_COMM_SELF, pEnd, points, PETSC_OWN_POINTER, subpointIS);CHKERRQ(ierr); 2982 } 2983 PetscFunctionReturn(0); 2984 } 2985