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, fStart, fEnd, ghostCell, cEnd, c; 407 PetscErrorCode ierr; 408 409 PetscFunctionBegin; 410 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 411 /* Count ghost cells */ 412 ierr = DMLabelGetValueIS(label, &valueIS);CHKERRQ(ierr); 413 ierr = ISGetLocalSize(valueIS, &numFS);CHKERRQ(ierr); 414 ierr = ISGetIndices(valueIS, &values);CHKERRQ(ierr); 415 *numGhostCells = 0; 416 for (fs = 0; fs < numFS; ++fs) { 417 IS faceIS; 418 const PetscInt *faces; 419 PetscInt numFaces, f, numBdFaces = 0; 420 421 ierr = DMLabelGetStratumIS(label, values[fs], &faceIS);CHKERRQ(ierr); 422 ierr = ISGetLocalSize(faceIS, &numFaces);CHKERRQ(ierr); 423 ierr = ISGetIndices(faceIS, &faces);CHKERRQ(ierr); 424 for (f = 0; f < numFaces; ++f) { 425 if ((faces[f] >= fStart) && (faces[f] < fEnd)) ++numBdFaces; 426 } 427 *numGhostCells += numBdFaces; 428 ierr = ISDestroy(&faceIS);CHKERRQ(ierr); 429 } 430 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 431 ierr = PetscMalloc((depth+1) * sizeof(PetscInt), &depthShift);CHKERRQ(ierr); 432 ierr = PetscMemzero(depthShift, (depth+1) * sizeof(PetscInt));CHKERRQ(ierr); 433 if (depth >= 0) depthShift[depth] = *numGhostCells; 434 ierr = DMPlexShiftSizes_Internal(dm, depthShift, gdm);CHKERRQ(ierr); 435 /* Step 3: Set cone/support sizes for new points */ 436 ierr = DMPlexGetHeightStratum(dm, 0, NULL, &cEnd);CHKERRQ(ierr); 437 for (c = cEnd; c < cEnd + *numGhostCells; ++c) { 438 ierr = DMPlexSetConeSize(gdm, c, 1);CHKERRQ(ierr); 439 } 440 for (fs = 0; fs < numFS; ++fs) { 441 IS faceIS; 442 const PetscInt *faces; 443 PetscInt numFaces, f; 444 445 ierr = DMLabelGetStratumIS(label, values[fs], &faceIS);CHKERRQ(ierr); 446 ierr = ISGetLocalSize(faceIS, &numFaces);CHKERRQ(ierr); 447 ierr = ISGetIndices(faceIS, &faces);CHKERRQ(ierr); 448 for (f = 0; f < numFaces; ++f) { 449 PetscInt size; 450 451 if ((faces[f] < fStart) || (faces[f] >= fEnd)) continue; 452 ierr = DMPlexGetSupportSize(dm, faces[f], &size);CHKERRQ(ierr); 453 if (size != 1) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "DM has boundary face %d with %d support cells", faces[f], size); 454 ierr = DMPlexSetSupportSize(gdm, faces[f] + *numGhostCells, 2);CHKERRQ(ierr); 455 } 456 ierr = ISRestoreIndices(faceIS, &faces);CHKERRQ(ierr); 457 ierr = ISDestroy(&faceIS);CHKERRQ(ierr); 458 } 459 /* Step 4: Setup ghosted DM */ 460 ierr = DMSetUp(gdm);CHKERRQ(ierr); 461 ierr = DMPlexShiftPoints_Internal(dm, depthShift, gdm);CHKERRQ(ierr); 462 /* Step 6: Set cones and supports for new points */ 463 ghostCell = cEnd; 464 for (fs = 0; fs < numFS; ++fs) { 465 IS faceIS; 466 const PetscInt *faces; 467 PetscInt numFaces, f; 468 469 ierr = DMLabelGetStratumIS(label, values[fs], &faceIS);CHKERRQ(ierr); 470 ierr = ISGetLocalSize(faceIS, &numFaces);CHKERRQ(ierr); 471 ierr = ISGetIndices(faceIS, &faces);CHKERRQ(ierr); 472 for (f = 0; f < numFaces; ++f) { 473 PetscInt newFace = faces[f] + *numGhostCells; 474 475 if ((faces[f] < fStart) || (faces[f] >= fEnd)) continue; 476 ierr = DMPlexSetCone(gdm, ghostCell, &newFace);CHKERRQ(ierr); 477 ierr = DMPlexInsertSupport(gdm, newFace, 1, ghostCell);CHKERRQ(ierr); 478 ++ghostCell; 479 } 480 ierr = ISRestoreIndices(faceIS, &faces);CHKERRQ(ierr); 481 ierr = ISDestroy(&faceIS);CHKERRQ(ierr); 482 } 483 ierr = ISRestoreIndices(valueIS, &values);CHKERRQ(ierr); 484 ierr = ISDestroy(&valueIS);CHKERRQ(ierr); 485 /* Step 7: Stratify */ 486 ierr = DMPlexStratify(gdm);CHKERRQ(ierr); 487 ierr = DMPlexShiftCoordinates_Internal(dm, depthShift, gdm);CHKERRQ(ierr); 488 ierr = DMPlexShiftSF_Internal(dm, depthShift, gdm);CHKERRQ(ierr); 489 ierr = DMPlexShiftLabels_Internal(dm, depthShift, gdm);CHKERRQ(ierr); 490 ierr = PetscFree(depthShift);CHKERRQ(ierr); 491 PetscFunctionReturn(0); 492 } 493 494 #undef __FUNCT__ 495 #define __FUNCT__ "DMPlexConstructGhostCells" 496 /*@C 497 DMPlexConstructGhostCells - Construct ghost cells which connect to every boundary face 498 499 Collective on dm 500 501 Input Parameters: 502 + dm - The original DM 503 - labelName - The label specifying the boundary faces, or "Face Sets" if this is NULL 504 505 Output Parameters: 506 + numGhostCells - The number of ghost cells added to the DM 507 - dmGhosted - The new DM 508 509 Note: If no label exists of that name, one will be created marking all boundary faces 510 511 Level: developer 512 513 .seealso: DMCreate() 514 @*/ 515 PetscErrorCode DMPlexConstructGhostCells(DM dm, const char labelName[], PetscInt *numGhostCells, DM *dmGhosted) 516 { 517 DM gdm; 518 DMLabel label; 519 const char *name = labelName ? labelName : "Face Sets"; 520 PetscInt dim; 521 PetscErrorCode ierr; 522 523 PetscFunctionBegin; 524 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 525 PetscValidPointer(numGhostCells, 3); 526 PetscValidPointer(dmGhosted, 4); 527 ierr = DMCreate(PetscObjectComm((PetscObject)dm), &gdm);CHKERRQ(ierr); 528 ierr = DMSetType(gdm, DMPLEX);CHKERRQ(ierr); 529 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 530 ierr = DMPlexSetDimension(gdm, dim);CHKERRQ(ierr); 531 ierr = DMPlexGetLabel(dm, name, &label);CHKERRQ(ierr); 532 if (!label) { 533 /* Get label for boundary faces */ 534 ierr = DMPlexCreateLabel(dm, name);CHKERRQ(ierr); 535 ierr = DMPlexGetLabel(dm, name, &label);CHKERRQ(ierr); 536 ierr = DMPlexMarkBoundaryFaces(dm, label);CHKERRQ(ierr); 537 } 538 ierr = DMPlexConstructGhostCells_Internal(dm, label, numGhostCells, gdm);CHKERRQ(ierr); 539 ierr = DMSetFromOptions(gdm);CHKERRQ(ierr); 540 *dmGhosted = gdm; 541 PetscFunctionReturn(0); 542 } 543 544 #undef __FUNCT__ 545 #define __FUNCT__ "DMPlexConstructCohesiveCells_Internal" 546 /* 547 We are adding two kinds of points here: 548 Replicated: Copies of points which exist in the mesh, such as vertices identified across a fault 549 Hybrid: Entirely new points, such as cohesive cells 550 */ 551 static PetscErrorCode DMPlexConstructCohesiveCells_Internal(DM dm, DMLabel label, DM sdm) 552 { 553 MPI_Comm comm; 554 IS valueIS; 555 PetscInt numSP = 0; /* The number of depths for which we have replicated points */ 556 const PetscInt *values; /* List of depths for which we have replicated points */ 557 IS *splitIS; 558 IS *unsplitIS; 559 PetscInt *numSplitPoints; /* The number of replicated points at each depth */ 560 PetscInt *numUnsplitPoints; /* The number of non-replicated points at each depth which still give rise to hybrid points */ 561 PetscInt *numHybridPoints; /* The number of hybrid points at each depth */ 562 const PetscInt **splitPoints; /* Replicated points for each depth */ 563 const PetscInt **unsplitPoints; /* Non-replicated points for each depth */ 564 PetscSection coordSection; 565 Vec coordinates; 566 PetscScalar *coords; 567 PetscInt depths[4]; /* Depths in the order that plex points are numbered */ 568 PetscInt *depthShift; /* Number of replicated+hybrid points at each depth */ 569 PetscInt *depthOffset; /* Prefix sums of depthShift */ 570 PetscInt *pMaxNew; /* The first replicated point at each depth in the new mesh, hybrids come after this */ 571 PetscInt *coneNew, *coneONew, *supportNew; 572 PetscInt shift = 100, shift2 = 200, depth = 0, dep, dim, d, sp, maxConeSize, maxSupportSize, maxConeSizeNew, maxSupportSizeNew, numLabels, vStart, vEnd, pEnd, p, v; 573 PetscErrorCode ierr; 574 575 PetscFunctionBegin; 576 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 577 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 578 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 579 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 580 depths[0] = depth; 581 depths[1] = 0; 582 depths[2] = depth-1; 583 depths[3] = 1; 584 /* Count split points and add cohesive cells */ 585 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize);CHKERRQ(ierr); 586 ierr = PetscMalloc3(depth+1,PetscInt,&depthShift,depth+1,PetscInt,&depthOffset,depth+1,PetscInt,&pMaxNew);CHKERRQ(ierr); 587 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); 588 ierr = PetscMemzero(depthShift, (depth+1) * sizeof(PetscInt));CHKERRQ(ierr); 589 ierr = PetscMemzero(depthOffset, (depth+1) * sizeof(PetscInt));CHKERRQ(ierr); 590 for (d = 0; d <= depth; ++d) { 591 ierr = DMPlexGetDepthStratum(dm, d, NULL, &pMaxNew[d]);CHKERRQ(ierr); 592 numSplitPoints[d] = 0; 593 numUnsplitPoints[d] = 0; 594 numHybridPoints[d] = 0; 595 splitPoints[d] = NULL; 596 unsplitPoints[d] = NULL; 597 splitIS[d] = NULL; 598 unsplitIS[d] = NULL; 599 } 600 if (label) { 601 ierr = DMLabelGetValueIS(label, &valueIS);CHKERRQ(ierr); 602 ierr = ISGetLocalSize(valueIS, &numSP);CHKERRQ(ierr); 603 ierr = ISGetIndices(valueIS, &values);CHKERRQ(ierr); 604 } 605 for (sp = 0; sp < numSP; ++sp) { 606 const PetscInt dep = values[sp]; 607 608 if ((dep < 0) || (dep > depth)) continue; 609 ierr = DMLabelGetStratumIS(label, dep, &splitIS[dep]);CHKERRQ(ierr); 610 if (splitIS[dep]) { 611 ierr = ISGetLocalSize(splitIS[dep], &numSplitPoints[dep]);CHKERRQ(ierr); 612 ierr = ISGetIndices(splitIS[dep], &splitPoints[dep]);CHKERRQ(ierr); 613 } 614 ierr = DMLabelGetStratumIS(label, shift2+dep, &unsplitIS[dep]);CHKERRQ(ierr); 615 if (unsplitIS[dep]) { 616 ierr = ISGetLocalSize(unsplitIS[dep], &numUnsplitPoints[dep]);CHKERRQ(ierr); 617 ierr = ISGetIndices(unsplitIS[dep], &unsplitPoints[dep]);CHKERRQ(ierr); 618 } 619 } 620 /* Calculate number of hybrid points */ 621 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 */ 622 for (d = 0; d <= depth; ++d) depthShift[d] = numSplitPoints[d] + numHybridPoints[d]; 623 for (d = 1; d <= depth; ++d) depthOffset[depths[d]] = depthOffset[depths[d-1]] + depthShift[depths[d-1]]; 624 for (d = 0; d <= depth; ++d) pMaxNew[d] += depthOffset[d]; 625 ierr = DMPlexShiftSizes_Internal(dm, depthShift, sdm);CHKERRQ(ierr); 626 /* Step 3: Set cone/support sizes for new points */ 627 for (dep = 0; dep <= depth; ++dep) { 628 for (p = 0; p < numSplitPoints[dep]; ++p) { 629 const PetscInt oldp = splitPoints[dep][p]; 630 const PetscInt newp = oldp + depthOffset[dep]; 631 const PetscInt splitp = p + pMaxNew[dep]; 632 const PetscInt *support; 633 PetscInt coneSize, supportSize, qf, qn, qp, e; 634 635 ierr = DMPlexGetConeSize(dm, oldp, &coneSize);CHKERRQ(ierr); 636 ierr = DMPlexSetConeSize(sdm, splitp, coneSize);CHKERRQ(ierr); 637 ierr = DMPlexGetSupportSize(dm, oldp, &supportSize);CHKERRQ(ierr); 638 ierr = DMPlexSetSupportSize(sdm, splitp, supportSize);CHKERRQ(ierr); 639 if (dep == depth-1) { 640 const PetscInt hybcell = p + pMaxNew[dep+1] + numSplitPoints[dep+1]; 641 642 /* Add cohesive cells, they are prisms */ 643 ierr = DMPlexSetConeSize(sdm, hybcell, 2 + coneSize);CHKERRQ(ierr); 644 } else if (dep == 0) { 645 const PetscInt hybedge = p + pMaxNew[dep+1] + numSplitPoints[dep+1]; 646 647 ierr = DMPlexGetSupport(dm, oldp, &support);CHKERRQ(ierr); 648 for (e = 0, qn = 0, qp = 0, qf = 0; e < supportSize; ++e) { 649 PetscInt val; 650 651 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 652 if (val == 1) ++qf; 653 if ((val == 1) || (val == (shift + 1))) ++qn; 654 if ((val == 1) || (val == -(shift + 1))) ++qp; 655 } 656 /* Split old vertex: Edges into original vertex and new cohesive edge */ 657 ierr = DMPlexSetSupportSize(sdm, newp, qn+1);CHKERRQ(ierr); 658 /* Split new vertex: Edges into split vertex and new cohesive edge */ 659 ierr = DMPlexSetSupportSize(sdm, splitp, qp+1);CHKERRQ(ierr); 660 /* Add hybrid edge */ 661 ierr = DMPlexSetConeSize(sdm, hybedge, 2);CHKERRQ(ierr); 662 ierr = DMPlexSetSupportSize(sdm, hybedge, qf);CHKERRQ(ierr); 663 } else if (dep == dim-2) { 664 const PetscInt hybface = p + pMaxNew[dep+1] + numSplitPoints[dep+1]; 665 666 ierr = DMPlexGetSupport(dm, oldp, &support);CHKERRQ(ierr); 667 for (e = 0, qn = 0, qp = 0, qf = 0; e < supportSize; ++e) { 668 PetscInt val; 669 670 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 671 if (val == dim-1) ++qf; 672 if ((val == dim-1) || (val == (shift + dim-1))) ++qn; 673 if ((val == dim-1) || (val == -(shift + dim-1))) ++qp; 674 } 675 /* Split old edge: Faces into original edge and cohesive face (positive side?) */ 676 ierr = DMPlexSetSupportSize(sdm, newp, qn+1);CHKERRQ(ierr); 677 /* Split new edge: Faces into split edge and cohesive face (negative side?) */ 678 ierr = DMPlexSetSupportSize(sdm, splitp, qp+1);CHKERRQ(ierr); 679 /* Add hybrid face */ 680 ierr = DMPlexSetConeSize(sdm, hybface, 4);CHKERRQ(ierr); 681 ierr = DMPlexSetSupportSize(sdm, hybface, qf);CHKERRQ(ierr); 682 } 683 } 684 } 685 for (dep = 0; dep <= depth; ++dep) { 686 for (p = 0; p < numUnsplitPoints[dep]; ++p) { 687 const PetscInt oldp = unsplitPoints[dep][p]; 688 const PetscInt newp = oldp + depthOffset[dep]; 689 const PetscInt *support; 690 PetscInt coneSize, supportSize, qf, qn, qp, e; 691 692 ierr = DMPlexGetConeSize(dm, oldp, &coneSize);CHKERRQ(ierr); 693 ierr = DMPlexGetSupportSize(dm, oldp, &supportSize);CHKERRQ(ierr); 694 if (dep == 0) { 695 const PetscInt hybedge = p + pMaxNew[dep+1] + numSplitPoints[dep+1] + numSplitPoints[dep]; 696 697 /* Unsplit vertex: Edges into original vertex, split edge, and new cohesive edge twice */ 698 ierr = DMPlexSetSupportSize(sdm, newp, supportSize+3);CHKERRQ(ierr); 699 /* Add hybrid edge */ 700 ierr = DMPlexSetConeSize(sdm, hybedge, 2);CHKERRQ(ierr); 701 ierr = DMPlexGetSupport(dm, oldp, &support);CHKERRQ(ierr); 702 for (e = 0, qf = 0; e < supportSize; ++e) { 703 PetscInt val; 704 705 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 706 /* Split and unsplit edges produce hybrid faces */ 707 if ((val == 1) || (val == (shift2 + 1))) ++qf; 708 } 709 ierr = DMPlexSetSupportSize(sdm, hybedge, qf);CHKERRQ(ierr); 710 } else if (dep == dim-2) { 711 const PetscInt hybface = p + pMaxNew[dep+1] + numSplitPoints[dep+1] + numSplitPoints[dep]; 712 713 ierr = DMPlexGetSupport(dm, oldp, &support);CHKERRQ(ierr); 714 for (e = 0, qn = 0, qp = 0, qf = 0; e < supportSize; ++e) { 715 PetscInt val; 716 717 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 718 if (val == dim-1) ++qf; 719 if ((val == dim-1) || (val == (shift + dim-1))) ++qn; 720 if ((val == dim-1) || (val == -(shift + dim-1))) ++qp; 721 } 722 /* Unsplit edge: Faces into original edge, split face, and cohesive face twice */ 723 ierr = DMPlexSetSupportSize(sdm, newp, supportSize+3);CHKERRQ(ierr); 724 /* Add hybrid face */ 725 ierr = DMPlexSetConeSize(sdm, hybface, 4);CHKERRQ(ierr); 726 /* TODO: Here we should check for neighboring faults for which this is unsplit */ 727 ierr = DMPlexSetSupportSize(sdm, hybface, 1);CHKERRQ(ierr); 728 } 729 } 730 } 731 /* Step 4: Setup split DM */ 732 ierr = DMSetUp(sdm);CHKERRQ(ierr); 733 ierr = DMPlexShiftPoints_Internal(dm, depthShift, sdm);CHKERRQ(ierr); 734 ierr = DMPlexGetMaxSizes(sdm, &maxConeSizeNew, &maxSupportSizeNew);CHKERRQ(ierr); 735 ierr = PetscMalloc3(PetscMax(maxConeSize, maxConeSizeNew)*3,PetscInt,&coneNew,PetscMax(maxConeSize, maxConeSizeNew)*3,PetscInt,&coneONew,PetscMax(maxSupportSize, maxSupportSizeNew),PetscInt,&supportNew);CHKERRQ(ierr); 736 /* Step 6: Set cones and supports for new points */ 737 for (dep = 0; dep <= depth; ++dep) { 738 for (p = 0; p < numSplitPoints[dep]; ++p) { 739 const PetscInt oldp = splitPoints[dep][p]; 740 const PetscInt newp = oldp + depthOffset[dep]; 741 const PetscInt splitp = p + pMaxNew[dep]; 742 const PetscInt *cone, *support, *ornt; 743 PetscInt coneSize, supportSize, q, qf, qn, qp, v, e, s; 744 745 ierr = DMPlexGetConeSize(dm, oldp, &coneSize);CHKERRQ(ierr); 746 ierr = DMPlexGetCone(dm, oldp, &cone);CHKERRQ(ierr); 747 ierr = DMPlexGetConeOrientation(dm, oldp, &ornt);CHKERRQ(ierr); 748 ierr = DMPlexGetSupportSize(dm, oldp, &supportSize);CHKERRQ(ierr); 749 ierr = DMPlexGetSupport(dm, oldp, &support);CHKERRQ(ierr); 750 if (dep == depth-1) { 751 const PetscInt hybcell = p + pMaxNew[dep+1] + numSplitPoints[dep+1]; 752 const PetscInt *supportF; 753 754 /* Split face: copy in old face to new face to start */ 755 ierr = DMPlexGetSupport(sdm, newp, &supportF);CHKERRQ(ierr); 756 ierr = DMPlexSetSupport(sdm, splitp, supportF);CHKERRQ(ierr); 757 /* Split old face: old vertices/edges in cone so no change */ 758 /* Split new face: new vertices/edges in cone */ 759 for (q = 0; q < coneSize; ++q) { 760 ierr = PetscFindInt(cone[q], numSplitPoints[dep-1], splitPoints[dep-1], &v);CHKERRQ(ierr); 761 if (v < 0) { 762 ierr = PetscFindInt(cone[q], numUnsplitPoints[dep-1], unsplitPoints[dep-1], &v);CHKERRQ(ierr); 763 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); 764 coneNew[2+q] = cone[q] + depthOffset[dep-1]; 765 } else { 766 coneNew[2+q] = v + pMaxNew[dep-1]; 767 } 768 } 769 ierr = DMPlexSetCone(sdm, splitp, &coneNew[2]);CHKERRQ(ierr); 770 ierr = DMPlexSetConeOrientation(sdm, splitp, ornt);CHKERRQ(ierr); 771 /* Face support */ 772 for (s = 0; s < supportSize; ++s) { 773 PetscInt val; 774 775 ierr = DMLabelGetValue(label, support[s], &val);CHKERRQ(ierr); 776 if (val < 0) { 777 /* Split old face: Replace negative side cell with cohesive cell */ 778 ierr = DMPlexInsertSupport(sdm, newp, s, hybcell);CHKERRQ(ierr); 779 } else { 780 /* Split new face: Replace positive side cell with cohesive cell */ 781 ierr = DMPlexInsertSupport(sdm, splitp, s, hybcell);CHKERRQ(ierr); 782 /* Get orientation for cohesive face */ 783 { 784 const PetscInt *ncone, *nconeO; 785 PetscInt nconeSize, nc; 786 787 ierr = DMPlexGetConeSize(dm, support[s], &nconeSize);CHKERRQ(ierr); 788 ierr = DMPlexGetCone(dm, support[s], &ncone);CHKERRQ(ierr); 789 ierr = DMPlexGetConeOrientation(dm, support[s], &nconeO);CHKERRQ(ierr); 790 for (nc = 0; nc < nconeSize; ++nc) { 791 if (ncone[nc] == oldp) { 792 coneONew[0] = nconeO[nc]; 793 break; 794 } 795 } 796 if (nc >= nconeSize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not locate face %d in neighboring cell %d", oldp, support[s]); 797 } 798 } 799 } 800 /* Cohesive cell: Old and new split face, then new cohesive faces */ 801 coneNew[0] = newp; /* Extracted negative side orientation above */ 802 coneNew[1] = splitp; 803 coneONew[1] = coneONew[0]; 804 for (q = 0; q < coneSize; ++q) { 805 ierr = PetscFindInt(cone[q], numSplitPoints[dep-1], splitPoints[dep-1], &v);CHKERRQ(ierr); 806 if (v < 0) { 807 ierr = PetscFindInt(cone[q], numUnsplitPoints[dep-1], unsplitPoints[dep-1], &v);CHKERRQ(ierr); 808 coneNew[2+q] = v + pMaxNew[dep] + numSplitPoints[dep] + numSplitPoints[dep-1]; 809 coneONew[2+q] = 0; 810 } else { 811 coneNew[2+q] = v + pMaxNew[dep] + numSplitPoints[dep]; 812 } 813 coneONew[2+q] = 0; 814 } 815 ierr = DMPlexSetCone(sdm, hybcell, coneNew);CHKERRQ(ierr); 816 ierr = DMPlexSetConeOrientation(sdm, hybcell, coneONew);CHKERRQ(ierr); 817 } else if (dep == 0) { 818 const PetscInt hybedge = p + pMaxNew[dep+1] + numSplitPoints[dep+1]; 819 820 /* Split old vertex: Edges in old split faces and new cohesive edge */ 821 for (e = 0, qn = 0; e < supportSize; ++e) { 822 PetscInt val; 823 824 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 825 if ((val == 1) || (val == (shift + 1))) { 826 supportNew[qn++] = support[e] + depthOffset[dep+1]; 827 } 828 } 829 supportNew[qn] = hybedge; 830 ierr = DMPlexSetSupport(sdm, newp, supportNew);CHKERRQ(ierr); 831 /* Split new vertex: Edges in new split faces and new cohesive edge */ 832 for (e = 0, qp = 0; e < supportSize; ++e) { 833 PetscInt val, edge; 834 835 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 836 if (val == 1) { 837 ierr = PetscFindInt(support[e], numSplitPoints[dep+1], splitPoints[dep+1], &edge);CHKERRQ(ierr); 838 if (edge < 0) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Edge %d is not a split edge", support[e]); 839 supportNew[qp++] = edge + pMaxNew[dep+1]; 840 } else if (val == -(shift + 1)) { 841 supportNew[qp++] = support[e] + depthOffset[dep+1]; 842 } 843 } 844 supportNew[qp] = hybedge; 845 ierr = DMPlexSetSupport(sdm, splitp, supportNew);CHKERRQ(ierr); 846 /* Hybrid edge: Old and new split vertex */ 847 coneNew[0] = newp; 848 coneNew[1] = splitp; 849 ierr = DMPlexSetCone(sdm, hybedge, coneNew);CHKERRQ(ierr); 850 for (e = 0, qf = 0; e < supportSize; ++e) { 851 PetscInt val, edge; 852 853 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 854 if (val == 1) { 855 ierr = PetscFindInt(support[e], numSplitPoints[dep+1], splitPoints[dep+1], &edge);CHKERRQ(ierr); 856 if (edge < 0) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Edge %d is not a split edge", support[e]); 857 supportNew[qf++] = edge + pMaxNew[dep+2] + numSplitPoints[dep+2]; 858 } 859 } 860 ierr = DMPlexSetSupport(sdm, hybedge, supportNew);CHKERRQ(ierr); 861 } else if (dep == dim-2) { 862 const PetscInt hybface = p + pMaxNew[dep+1] + numSplitPoints[dep+1]; 863 864 /* Split old edge: old vertices in cone so no change */ 865 /* Split new edge: new vertices in cone */ 866 for (q = 0; q < coneSize; ++q) { 867 ierr = PetscFindInt(cone[q], numSplitPoints[dep-1], splitPoints[dep-1], &v);CHKERRQ(ierr); 868 if (v < 0) { 869 ierr = PetscFindInt(cone[q], numUnsplitPoints[dep-1], unsplitPoints[dep-1], &v);CHKERRQ(ierr); 870 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); 871 coneNew[q] = cone[q] + depthOffset[dep-1]; 872 } else { 873 coneNew[q] = v + pMaxNew[dep-1]; 874 } 875 } 876 ierr = DMPlexSetCone(sdm, splitp, coneNew);CHKERRQ(ierr); 877 /* Split old edge: Faces in positive side cells and old split faces */ 878 for (e = 0, q = 0; e < supportSize; ++e) { 879 PetscInt val; 880 881 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 882 if (val == dim-1) { 883 supportNew[q++] = support[e] + depthOffset[dep+1]; 884 } else if (val == (shift + dim-1)) { 885 supportNew[q++] = support[e] + depthOffset[dep+1]; 886 } 887 } 888 supportNew[q++] = p + pMaxNew[dep+1] + numSplitPoints[dep+1]; 889 ierr = DMPlexSetSupport(sdm, newp, supportNew);CHKERRQ(ierr); 890 /* Split new edge: Faces in negative side cells and new split faces */ 891 for (e = 0, q = 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[q++] = face + pMaxNew[dep+1]; 899 } else if (val == -(shift + dim-1)) { 900 supportNew[q++] = support[e] + depthOffset[dep+1]; 901 } 902 } 903 supportNew[q++] = p + pMaxNew[dep+1] + numSplitPoints[dep+1]; 904 ierr = DMPlexSetSupport(sdm, splitp, supportNew);CHKERRQ(ierr); 905 /* Hybrid face */ 906 coneNew[0] = newp; 907 coneNew[1] = splitp; 908 for (v = 0; v < coneSize; ++v) { 909 PetscInt vertex; 910 ierr = PetscFindInt(cone[v], numSplitPoints[dep-1], splitPoints[dep-1], &vertex);CHKERRQ(ierr); 911 if (vertex < 0) { 912 ierr = PetscFindInt(cone[v], numUnsplitPoints[dep-1], unsplitPoints[dep-1], &vertex);CHKERRQ(ierr); 913 if (vertex < 0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not locate point %d in split or unsplit points of depth %d", cone[v], dep-1); 914 coneNew[2+v] = vertex + pMaxNew[dep] + numSplitPoints[dep] + numSplitPoints[dep-1]; 915 } else { 916 coneNew[2+v] = vertex + pMaxNew[dep] + numSplitPoints[dep]; 917 } 918 } 919 ierr = DMPlexSetCone(sdm, hybface, coneNew);CHKERRQ(ierr); 920 for (e = 0, qf = 0; e < supportSize; ++e) { 921 PetscInt val, face; 922 923 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 924 if (val == dim-1) { 925 ierr = PetscFindInt(support[e], numSplitPoints[dep+1], splitPoints[dep+1], &face);CHKERRQ(ierr); 926 if (face < 0) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Face %d is not a split face", support[e]); 927 supportNew[qf++] = face + pMaxNew[dep+2] + numSplitPoints[dep+2]; 928 } 929 } 930 ierr = DMPlexSetSupport(sdm, hybface, supportNew);CHKERRQ(ierr); 931 } 932 } 933 } 934 for (dep = 0; dep <= depth; ++dep) { 935 for (p = 0; p < numUnsplitPoints[dep]; ++p) { 936 const PetscInt oldp = unsplitPoints[dep][p]; 937 const PetscInt newp = oldp + depthOffset[dep]; 938 const PetscInt *cone, *support, *ornt; 939 PetscInt coneSize, supportSize, supportSizeNew, q, qf, e, f, s; 940 941 ierr = DMPlexGetConeSize(dm, oldp, &coneSize);CHKERRQ(ierr); 942 ierr = DMPlexGetCone(dm, oldp, &cone);CHKERRQ(ierr); 943 ierr = DMPlexGetConeOrientation(dm, oldp, &ornt);CHKERRQ(ierr); 944 ierr = DMPlexGetSupportSize(dm, oldp, &supportSize);CHKERRQ(ierr); 945 ierr = DMPlexGetSupport(dm, oldp, &support);CHKERRQ(ierr); 946 if (dep == 0) { 947 const PetscInt hybedge = p + pMaxNew[dep+1] + numSplitPoints[dep+1] + numSplitPoints[dep]; 948 949 /* Unsplit vertex */ 950 ierr = DMPlexGetSupportSize(sdm, newp, &supportSizeNew);CHKERRQ(ierr); 951 for (s = 0, q = 0; s < supportSize; ++s) { 952 supportNew[q++] = support[s] + depthOffset[dep+1]; 953 ierr = PetscFindInt(support[s], numSplitPoints[dep+1], splitPoints[dep+1], &e);CHKERRQ(ierr); 954 if (e >= 0) { 955 supportNew[q++] = e + pMaxNew[dep+1]; 956 } 957 } 958 supportNew[q++] = hybedge; 959 supportNew[q++] = hybedge; 960 if (q != supportSizeNew) SETERRQ3(comm, PETSC_ERR_ARG_WRONG, "Support size %d != %d for vertex %d", q, supportSizeNew, newp); 961 ierr = DMPlexSetSupport(sdm, newp, supportNew);CHKERRQ(ierr); 962 /* Hybrid edge */ 963 coneNew[0] = newp; 964 coneNew[1] = newp; 965 ierr = DMPlexSetCone(sdm, hybedge, coneNew);CHKERRQ(ierr); 966 for (e = 0, qf = 0; e < supportSize; ++e) { 967 PetscInt val, edge; 968 969 ierr = DMLabelGetValue(label, support[e], &val);CHKERRQ(ierr); 970 if (val == 1) { 971 ierr = PetscFindInt(support[e], numSplitPoints[dep+1], splitPoints[dep+1], &edge);CHKERRQ(ierr); 972 if (edge < 0) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Edge %d is not a split edge", support[e]); 973 supportNew[qf++] = edge + pMaxNew[dep+2] + numSplitPoints[dep+2]; 974 } else if (val == (shift2 + 1)) { 975 ierr = PetscFindInt(support[e], numUnsplitPoints[dep+1], unsplitPoints[dep+1], &edge);CHKERRQ(ierr); 976 if (edge < 0) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Edge %d is not a unsplit edge", support[e]); 977 supportNew[qf++] = edge + pMaxNew[dep+2] + numSplitPoints[dep+2] + numSplitPoints[dep+1]; 978 } 979 } 980 ierr = DMPlexSetSupport(sdm, hybedge, supportNew);CHKERRQ(ierr); 981 } else if (dep == dim-2) { 982 const PetscInt hybface = p + pMaxNew[dep+1] + numSplitPoints[dep+1] + numSplitPoints[dep]; 983 PetscInt hybcell; 984 985 /* Unsplit edge: Faces into original edge, split face, and cohesive face twice */ 986 for (f = 0, qf = 0; f < supportSize; ++f) { 987 PetscInt val, face; 988 989 ierr = DMLabelGetValue(label, support[f], &val);CHKERRQ(ierr); 990 if (val == dim-1) { 991 ierr = PetscFindInt(support[f], numSplitPoints[dep+1], splitPoints[dep+1], &face);CHKERRQ(ierr); 992 if (face < 0) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Face %d is not a split face", support[f]); 993 supportNew[qf++] = support[f] + depthOffset[dep+1]; 994 supportNew[qf++] = face + pMaxNew[dep+1]; 995 hybcell = face + pMaxNew[dep+2] + numSplitPoints[dep+2]; 996 } else { 997 supportNew[qf++] = support[f] + depthOffset[dep+1]; 998 } 999 } 1000 supportNew[qf++] = hybface; 1001 supportNew[qf++] = hybface; 1002 ierr = DMPlexSetSupport(sdm, newp, supportNew);CHKERRQ(ierr); 1003 /* Add hybrid face */ 1004 coneNew[0] = newp; 1005 ierr = PetscFindInt(cone[0], numUnsplitPoints[dep-1], unsplitPoints[dep-1], &v);CHKERRQ(ierr); 1006 if (v < 0) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Vertex %d is not an unsplit vertex", cone[0]); 1007 coneNew[1] = v + pMaxNew[dep] + numSplitPoints[dep] + numSplitPoints[dep-1]; 1008 coneNew[2] = newp; 1009 ierr = PetscFindInt(cone[1], numUnsplitPoints[dep-1], unsplitPoints[dep-1], &v);CHKERRQ(ierr); 1010 if (v < 0) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Vertex %d is not an unsplit vertex", cone[1]); 1011 coneNew[3] = v + pMaxNew[dep] + numSplitPoints[dep] + numSplitPoints[dep-1]; 1012 ierr = DMPlexSetCone(sdm, hybface, coneNew);CHKERRQ(ierr); 1013 supportNew[0] = hybcell; 1014 ierr = DMPlexSetSupport(sdm, hybface, supportNew);CHKERRQ(ierr); 1015 } 1016 } 1017 } 1018 /* Step 6b: Replace split points in negative side cones */ 1019 for (sp = 0; sp < numSP; ++sp) { 1020 PetscInt dep = values[sp]; 1021 IS pIS; 1022 PetscInt numPoints; 1023 const PetscInt *points; 1024 1025 if (dep >= 0) continue; 1026 ierr = DMLabelGetStratumIS(label, dep, &pIS);CHKERRQ(ierr); 1027 if (!pIS) continue; 1028 dep = -dep - shift; 1029 ierr = ISGetLocalSize(pIS, &numPoints);CHKERRQ(ierr); 1030 ierr = ISGetIndices(pIS, &points);CHKERRQ(ierr); 1031 for (p = 0; p < numPoints; ++p) { 1032 const PetscInt oldp = points[p]; 1033 const PetscInt newp = depthOffset[dep] + oldp; 1034 const PetscInt *cone; 1035 PetscInt coneSize, c; 1036 /* PetscBool replaced = PETSC_FALSE; */ 1037 1038 /* Negative edge: replace split vertex */ 1039 /* Negative cell: replace split face */ 1040 ierr = DMPlexGetConeSize(sdm, newp, &coneSize);CHKERRQ(ierr); 1041 ierr = DMPlexGetCone(sdm, newp, &cone);CHKERRQ(ierr); 1042 for (c = 0; c < coneSize; ++c) { 1043 const PetscInt coldp = cone[c] - depthOffset[dep-1]; 1044 PetscInt csplitp, cp, val; 1045 1046 ierr = DMLabelGetValue(label, coldp, &val);CHKERRQ(ierr); 1047 if (val == dep-1) { 1048 ierr = PetscFindInt(coldp, numSplitPoints[dep-1], splitPoints[dep-1], &cp);CHKERRQ(ierr); 1049 if (cp < 0) SETERRQ2(comm, PETSC_ERR_ARG_WRONG, "Point %d is not a split point of dimension %d", oldp, dep-1); 1050 csplitp = pMaxNew[dep-1] + cp; 1051 ierr = DMPlexInsertCone(sdm, newp, c, csplitp);CHKERRQ(ierr); 1052 /* replaced = PETSC_TRUE; */ 1053 } 1054 } 1055 /* Cells with only a vertex or edge on the submesh have no replacement */ 1056 /* if (!replaced) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "The cone of point %d does not contain split points", oldp); */ 1057 } 1058 ierr = ISRestoreIndices(pIS, &points);CHKERRQ(ierr); 1059 ierr = ISDestroy(&pIS);CHKERRQ(ierr); 1060 } 1061 /* Step 7: Stratify */ 1062 ierr = DMPlexStratify(sdm);CHKERRQ(ierr); 1063 /* Step 8: Coordinates */ 1064 ierr = DMPlexShiftCoordinates_Internal(dm, depthShift, sdm);CHKERRQ(ierr); 1065 ierr = DMPlexGetCoordinateSection(sdm, &coordSection);CHKERRQ(ierr); 1066 ierr = DMGetCoordinatesLocal(sdm, &coordinates);CHKERRQ(ierr); 1067 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1068 for (v = 0; v < (numSplitPoints ? numSplitPoints[0] : 0); ++v) { 1069 const PetscInt newp = depthOffset[0] + splitPoints[0][v]; 1070 const PetscInt splitp = pMaxNew[0] + v; 1071 PetscInt dof, off, soff, d; 1072 1073 ierr = PetscSectionGetDof(coordSection, newp, &dof);CHKERRQ(ierr); 1074 ierr = PetscSectionGetOffset(coordSection, newp, &off);CHKERRQ(ierr); 1075 ierr = PetscSectionGetOffset(coordSection, splitp, &soff);CHKERRQ(ierr); 1076 for (d = 0; d < dof; ++d) coords[soff+d] = coords[off+d]; 1077 } 1078 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1079 /* Step 9: SF, if I can figure this out we can split the mesh in parallel */ 1080 ierr = DMPlexShiftSF_Internal(dm, depthShift, sdm);CHKERRQ(ierr); 1081 /* Step 10: Labels */ 1082 ierr = DMPlexShiftLabels_Internal(dm, depthShift, sdm);CHKERRQ(ierr); 1083 ierr = DMPlexGetNumLabels(sdm, &numLabels);CHKERRQ(ierr); 1084 for (dep = 0; dep <= depth; ++dep) { 1085 for (p = 0; p < numSplitPoints[dep]; ++p) { 1086 const PetscInt newp = depthOffset[dep] + splitPoints[dep][p]; 1087 const PetscInt splitp = pMaxNew[dep] + p; 1088 PetscInt l; 1089 1090 for (l = 0; l < numLabels; ++l) { 1091 DMLabel mlabel; 1092 const char *lname; 1093 PetscInt val; 1094 PetscBool isDepth; 1095 1096 ierr = DMPlexGetLabelName(sdm, l, &lname);CHKERRQ(ierr); 1097 ierr = PetscStrcmp(lname, "depth", &isDepth);CHKERRQ(ierr); 1098 if (isDepth) continue; 1099 ierr = DMPlexGetLabel(sdm, lname, &mlabel);CHKERRQ(ierr); 1100 ierr = DMLabelGetValue(mlabel, newp, &val);CHKERRQ(ierr); 1101 if (val >= 0) { 1102 ierr = DMLabelSetValue(mlabel, splitp, val);CHKERRQ(ierr); 1103 #if 0 1104 /* Do not put cohesive edges into the label */ 1105 if (dep == 0) { 1106 const PetscInt cedge = p + pMaxNew[dep+1] + numSplitPoints[dep+1]; 1107 ierr = DMLabelSetValue(mlabel, cedge, val);CHKERRQ(ierr); 1108 } else if (dep == dim-2) { 1109 const PetscInt cface = p + pMaxNew[dep+1] + numSplitPoints[dep+1]; 1110 ierr = DMLabelSetValue(mlabel, cface, val);CHKERRQ(ierr); 1111 } 1112 /* Do not put cohesive faces into the label */ 1113 #endif 1114 } 1115 } 1116 } 1117 } 1118 for (sp = 0; sp < numSP; ++sp) { 1119 const PetscInt dep = values[sp]; 1120 1121 if ((dep < 0) || (dep > depth)) continue; 1122 if (splitIS[dep]) {ierr = ISRestoreIndices(splitIS[dep], &splitPoints[dep]);CHKERRQ(ierr);} 1123 ierr = ISDestroy(&splitIS[dep]);CHKERRQ(ierr); 1124 if (unsplitIS[dep]) {ierr = ISRestoreIndices(unsplitIS[dep], &unsplitPoints[dep]);CHKERRQ(ierr);} 1125 ierr = ISDestroy(&unsplitIS[dep]);CHKERRQ(ierr); 1126 } 1127 if (label) { 1128 ierr = ISRestoreIndices(valueIS, &values);CHKERRQ(ierr); 1129 ierr = ISDestroy(&valueIS);CHKERRQ(ierr); 1130 } 1131 for (d = 0; d <= depth; ++d) { 1132 ierr = DMPlexGetDepthStratum(sdm, d, NULL, &pEnd);CHKERRQ(ierr); 1133 pMaxNew[d] = pEnd - numHybridPoints[d]; 1134 } 1135 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); 1136 ierr = PetscFree3(depthShift, depthOffset, pMaxNew);CHKERRQ(ierr); 1137 ierr = PetscFree3(coneNew, coneONew, supportNew);CHKERRQ(ierr); 1138 ierr = PetscFree7(splitIS, unsplitIS, numSplitPoints, numUnsplitPoints, numHybridPoints, splitPoints, unsplitPoints);CHKERRQ(ierr); 1139 PetscFunctionReturn(0); 1140 } 1141 1142 #undef __FUNCT__ 1143 #define __FUNCT__ "DMPlexConstructCohesiveCells" 1144 /*@C 1145 DMPlexConstructCohesiveCells - Construct cohesive cells which split the face along an internal interface 1146 1147 Collective on dm 1148 1149 Input Parameters: 1150 + dm - The original DM 1151 - label - The label specifying the boundary faces (this could be auto-generated) 1152 1153 Output Parameters: 1154 - dmSplit - The new DM 1155 1156 Level: developer 1157 1158 .seealso: DMCreate(), DMPlexLabelCohesiveComplete() 1159 @*/ 1160 PetscErrorCode DMPlexConstructCohesiveCells(DM dm, DMLabel label, DM *dmSplit) 1161 { 1162 DM sdm; 1163 PetscInt dim; 1164 PetscErrorCode ierr; 1165 1166 PetscFunctionBegin; 1167 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1168 PetscValidPointer(dmSplit, 3); 1169 ierr = DMCreate(PetscObjectComm((PetscObject)dm), &sdm);CHKERRQ(ierr); 1170 ierr = DMSetType(sdm, DMPLEX);CHKERRQ(ierr); 1171 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1172 ierr = DMPlexSetDimension(sdm, dim);CHKERRQ(ierr); 1173 switch (dim) { 1174 case 2: 1175 case 3: 1176 ierr = DMPlexConstructCohesiveCells_Internal(dm, label, sdm);CHKERRQ(ierr); 1177 break; 1178 default: 1179 SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Cannot construct cohesive cells for dimension %d", dim); 1180 } 1181 *dmSplit = sdm; 1182 PetscFunctionReturn(0); 1183 } 1184 1185 #undef __FUNCT__ 1186 #define __FUNCT__ "DMPlexLabelCohesiveComplete" 1187 /*@ 1188 DMPlexLabelCohesiveComplete - Starting with a label marking vertices on an internal surface, we add all other mesh pieces 1189 to complete the surface 1190 1191 Input Parameters: 1192 + dm - The DM 1193 . label - A DMLabel marking the surface vertices 1194 . flip - Flag to flip the submesh normal and replace points on the other side 1195 - subdm - The subDM associated with the label, or NULL 1196 1197 Output Parameter: 1198 . label - A DMLabel marking all surface points 1199 1200 Level: developer 1201 1202 .seealso: DMPlexConstructCohesiveCells(), DMPlexLabelComplete() 1203 @*/ 1204 PetscErrorCode DMPlexLabelCohesiveComplete(DM dm, DMLabel label, PetscBool flip, DM subdm) 1205 { 1206 DMLabel depthLabel; 1207 IS dimIS, subpointIS, facePosIS, faceNegIS; 1208 const PetscInt *points, *subpoints; 1209 const PetscInt rev = flip ? -1 : 1; 1210 PetscInt shift = 100, shift2 = 200, dim, dep, cStart, cEnd, numPoints, numSubpoints, p, val; 1211 PetscErrorCode ierr; 1212 1213 PetscFunctionBegin; 1214 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 1215 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1216 if (subdm) { 1217 ierr = DMPlexCreateSubpointIS(subdm, &subpointIS);CHKERRQ(ierr); 1218 if (subpointIS) { 1219 ierr = ISGetLocalSize(subpointIS, &numSubpoints);CHKERRQ(ierr); 1220 ierr = ISGetIndices(subpointIS, &subpoints);CHKERRQ(ierr); 1221 } 1222 } 1223 /* Mark cell on the fault, and its faces which touch the fault: cell orientation for face gives the side of the fault */ 1224 ierr = DMLabelGetStratumIS(label, dim-1, &dimIS);CHKERRQ(ierr); 1225 if (!dimIS) PetscFunctionReturn(0); 1226 ierr = ISGetLocalSize(dimIS, &numPoints);CHKERRQ(ierr); 1227 ierr = ISGetIndices(dimIS, &points);CHKERRQ(ierr); 1228 for (p = 0; p < numPoints; ++p) { /* Loop over fault faces */ 1229 const PetscInt *support; 1230 PetscInt supportSize, s; 1231 1232 ierr = DMPlexGetSupportSize(dm, points[p], &supportSize);CHKERRQ(ierr); 1233 if (supportSize != 2) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Split face %d has %d != 2 supports", points[p], supportSize); 1234 ierr = DMPlexGetSupport(dm, points[p], &support);CHKERRQ(ierr); 1235 for (s = 0; s < supportSize; ++s) { 1236 const PetscInt *cone, *ornt; 1237 PetscInt coneSize, c; 1238 PetscBool pos = PETSC_TRUE; 1239 1240 ierr = DMPlexGetConeSize(dm, support[s], &coneSize);CHKERRQ(ierr); 1241 ierr = DMPlexGetCone(dm, support[s], &cone);CHKERRQ(ierr); 1242 ierr = DMPlexGetConeOrientation(dm, support[s], &ornt);CHKERRQ(ierr); 1243 for (c = 0; c < coneSize; ++c) { 1244 if (cone[c] == points[p]) { 1245 PetscInt o = ornt[c]; 1246 1247 if (subdm) { 1248 const PetscInt *subcone, *subornt; 1249 PetscInt subpoint, subface, subconeSize, sc; 1250 1251 ierr = PetscFindInt(support[s], numSubpoints, subpoints, &subpoint);CHKERRQ(ierr); 1252 ierr = PetscFindInt(points[p], numSubpoints, subpoints, &subface);CHKERRQ(ierr); 1253 ierr = DMPlexGetConeSize(subdm, subpoint, &subconeSize);CHKERRQ(ierr); 1254 ierr = DMPlexGetCone(subdm, subpoint, &subcone);CHKERRQ(ierr); 1255 ierr = DMPlexGetConeOrientation(subdm, subpoint, &subornt);CHKERRQ(ierr); 1256 for (sc = 0; sc < subconeSize; ++sc) { 1257 if (subcone[sc] == subface) { 1258 o = subornt[0]; 1259 break; 1260 } 1261 } 1262 if (sc >= subconeSize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not find point %d in cone for subpoint %d", points[p], subpoint); 1263 } 1264 if (o >= 0) { 1265 ierr = DMLabelSetValue(label, support[s], rev*(shift+dim));CHKERRQ(ierr); 1266 pos = rev > 0 ? PETSC_TRUE : PETSC_FALSE; 1267 } else { 1268 ierr = DMLabelSetValue(label, support[s], -rev*(shift+dim));CHKERRQ(ierr); 1269 pos = rev > 0 ? PETSC_FALSE : PETSC_TRUE; 1270 } 1271 break; 1272 } 1273 } 1274 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]); 1275 /* Put faces touching the fault in the label */ 1276 for (c = 0; c < coneSize; ++c) { 1277 const PetscInt point = cone[c]; 1278 1279 ierr = DMLabelGetValue(label, point, &val);CHKERRQ(ierr); 1280 if (val == -1) { 1281 PetscInt *closure = NULL; 1282 PetscInt closureSize, cl; 1283 1284 ierr = DMPlexGetTransitiveClosure(dm, point, 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 >= 0) && (val < dim-1)) { 1290 ierr = DMLabelSetValue(label, point, pos == PETSC_TRUE ? shift+dim-1 : -(shift+dim-1));CHKERRQ(ierr); 1291 break; 1292 } 1293 } 1294 ierr = DMPlexRestoreTransitiveClosure(dm, point, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1295 } 1296 } 1297 } 1298 } 1299 if (subdm) { 1300 if (subpointIS) {ierr = ISRestoreIndices(subpointIS, &subpoints);CHKERRQ(ierr);} 1301 ierr = ISDestroy(&subpointIS);CHKERRQ(ierr); 1302 } 1303 ierr = ISRestoreIndices(dimIS, &points);CHKERRQ(ierr); 1304 ierr = ISDestroy(&dimIS);CHKERRQ(ierr); 1305 /* Search for other cells/faces/edges connected to the fault by a vertex */ 1306 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1307 ierr = DMLabelGetStratumIS(label, 0, &dimIS);CHKERRQ(ierr); 1308 if (!dimIS) PetscFunctionReturn(0); 1309 ierr = ISGetLocalSize(dimIS, &numPoints);CHKERRQ(ierr); 1310 ierr = ISGetIndices(dimIS, &points);CHKERRQ(ierr); 1311 for (p = 0; p < numPoints; ++p) { /* Loop over fault vertices */ 1312 PetscInt *star = NULL; 1313 PetscInt starSize, s; 1314 PetscInt again = 1; /* 0: Finished 1: Keep iterating after a change 2: No change */ 1315 1316 /* All points connected to the fault are inside a cell, so at the top level we will only check cells */ 1317 ierr = DMPlexGetTransitiveClosure(dm, points[p], PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1318 while (again) { 1319 if (again > 1) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Could not classify all cells connected to the fault"); 1320 again = 0; 1321 for (s = 0; s < starSize*2; s += 2) { 1322 const PetscInt point = star[s]; 1323 const PetscInt *cone; 1324 PetscInt coneSize, c; 1325 1326 if ((point < cStart) || (point >= cEnd)) continue; 1327 ierr = DMLabelGetValue(label, point, &val);CHKERRQ(ierr); 1328 if (val != -1) continue; 1329 again = again == 1 ? 1 : 2; 1330 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 1331 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 1332 for (c = 0; c < coneSize; ++c) { 1333 ierr = DMLabelGetValue(label, cone[c], &val);CHKERRQ(ierr); 1334 if (val != -1) { 1335 const PetscInt *ccone; 1336 PetscInt cconeSize, cc, side; 1337 1338 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); 1339 if (val > 0) side = 1; 1340 else side = -1; 1341 ierr = DMLabelSetValue(label, point, side*(shift+dim));CHKERRQ(ierr); 1342 /* Mark cell faces which touch the fault */ 1343 ierr = DMPlexGetConeSize(dm, point, &cconeSize);CHKERRQ(ierr); 1344 ierr = DMPlexGetCone(dm, point, &ccone);CHKERRQ(ierr); 1345 for (cc = 0; cc < cconeSize; ++cc) { 1346 PetscInt *closure = NULL; 1347 PetscInt closureSize, cl; 1348 1349 ierr = DMLabelGetValue(label, ccone[cc], &val);CHKERRQ(ierr); 1350 if (val != -1) continue; 1351 ierr = DMPlexGetTransitiveClosure(dm, ccone[cc], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1352 for (cl = 0; cl < closureSize*2; cl += 2) { 1353 const PetscInt clp = closure[cl]; 1354 1355 ierr = DMLabelGetValue(label, clp, &val);CHKERRQ(ierr); 1356 if (val == -1) continue; 1357 ierr = DMLabelSetValue(label, ccone[cc], side*(shift+dim-1));CHKERRQ(ierr); 1358 break; 1359 } 1360 ierr = DMPlexRestoreTransitiveClosure(dm, ccone[cc], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1361 } 1362 again = 1; 1363 break; 1364 } 1365 } 1366 } 1367 } 1368 /* Classify the rest by cell membership */ 1369 for (s = 0; s < starSize*2; s += 2) { 1370 const PetscInt point = star[s]; 1371 1372 ierr = DMLabelGetValue(label, point, &val);CHKERRQ(ierr); 1373 if (val == -1) { 1374 PetscInt *sstar = NULL; 1375 PetscInt sstarSize, ss; 1376 PetscBool marked = PETSC_FALSE; 1377 1378 ierr = DMPlexGetTransitiveClosure(dm, point, PETSC_FALSE, &sstarSize, &sstar);CHKERRQ(ierr); 1379 for (ss = 0; ss < sstarSize*2; ss += 2) { 1380 const PetscInt spoint = sstar[ss]; 1381 1382 if ((spoint < cStart) || (spoint >= cEnd)) continue; 1383 ierr = DMLabelGetValue(label, spoint, &val);CHKERRQ(ierr); 1384 if (val == -1) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Cell %d in star of %d does not have a valid label", spoint, point); 1385 ierr = DMLabelGetValue(depthLabel, point, &dep);CHKERRQ(ierr); 1386 if (val > 0) { 1387 ierr = DMLabelSetValue(label, point, shift+dep);CHKERRQ(ierr); 1388 } else { 1389 ierr = DMLabelSetValue(label, point, -(shift+dep));CHKERRQ(ierr); 1390 } 1391 marked = PETSC_TRUE; 1392 break; 1393 } 1394 ierr = DMPlexRestoreTransitiveClosure(dm, point, PETSC_FALSE, &sstarSize, &sstar);CHKERRQ(ierr); 1395 if (!marked) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Point %d could not be classified", point); 1396 } 1397 } 1398 ierr = DMPlexRestoreTransitiveClosure(dm, points[p], PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1399 } 1400 ierr = ISRestoreIndices(dimIS, &points);CHKERRQ(ierr); 1401 ierr = ISDestroy(&dimIS);CHKERRQ(ierr); 1402 /* If any faces touching the fault divide cells on either side, split them */ 1403 ierr = DMLabelGetStratumIS(label, shift+dim-1, &facePosIS);CHKERRQ(ierr); 1404 ierr = DMLabelGetStratumIS(label, -(shift+dim-1), &faceNegIS);CHKERRQ(ierr); 1405 ierr = ISExpand(facePosIS, faceNegIS, &dimIS);CHKERRQ(ierr); 1406 ierr = ISDestroy(&facePosIS);CHKERRQ(ierr); 1407 ierr = ISDestroy(&faceNegIS);CHKERRQ(ierr); 1408 ierr = ISGetLocalSize(dimIS, &numPoints);CHKERRQ(ierr); 1409 ierr = ISGetIndices(dimIS, &points);CHKERRQ(ierr); 1410 for (p = 0; p < numPoints; ++p) { 1411 const PetscInt point = points[p]; 1412 const PetscInt *support; 1413 PetscInt supportSize, valA, valB; 1414 1415 ierr = DMPlexGetSupportSize(dm, point, &supportSize);CHKERRQ(ierr); 1416 if (supportSize != 2) continue; 1417 ierr = DMPlexGetSupport(dm, point, &support);CHKERRQ(ierr); 1418 ierr = DMLabelGetValue(label, support[0], &valA);CHKERRQ(ierr); 1419 ierr = DMLabelGetValue(label, support[1], &valB);CHKERRQ(ierr); 1420 if ((valA == -1) || (valB == -1)) continue; 1421 if (valA*valB > 0) continue; 1422 /* Split the face */ 1423 ierr = DMLabelGetValue(label, point, &valA);CHKERRQ(ierr); 1424 ierr = DMLabelClearValue(label, point, valA);CHKERRQ(ierr); 1425 ierr = DMLabelSetValue(label, point, dim-1);CHKERRQ(ierr); 1426 /* Label its closure: 1427 unmarked: label as unsplit 1428 incident: relabel as split 1429 split: do nothing 1430 */ 1431 { 1432 PetscInt *closure = NULL; 1433 PetscInt closureSize, cl; 1434 1435 ierr = DMPlexGetTransitiveClosure(dm, point, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1436 for (cl = 0; cl < closureSize*2; cl += 2) { 1437 ierr = DMLabelGetValue(label, closure[cl], &valA);CHKERRQ(ierr); 1438 if (valA < 0) { /* Mark as unsplit */ 1439 ierr = DMLabelGetValue(depthLabel, closure[cl], &dep);CHKERRQ(ierr); 1440 ierr = DMLabelSetValue(label, closure[cl], shift2+dep);CHKERRQ(ierr); 1441 } else if (valA >= shift) { 1442 ierr = DMLabelGetValue(depthLabel, closure[cl], &dep);CHKERRQ(ierr); 1443 ierr = DMLabelClearValue(label, closure[cl], valA);CHKERRQ(ierr); 1444 ierr = DMLabelSetValue(label, closure[cl], dep);CHKERRQ(ierr); 1445 } 1446 } 1447 ierr = DMPlexRestoreTransitiveClosure(dm, point, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1448 } 1449 } 1450 ierr = ISRestoreIndices(dimIS, &points);CHKERRQ(ierr); 1451 ierr = ISDestroy(&dimIS);CHKERRQ(ierr); 1452 PetscFunctionReturn(0); 1453 } 1454 1455 #undef __FUNCT__ 1456 #define __FUNCT__ "DMPlexCreateHybridMesh" 1457 /*@C 1458 DMPlexCreateHybridMesh - Create a mesh with hybrid cells along an internal interface 1459 1460 Collective on dm 1461 1462 Input Parameters: 1463 + dm - The original DM 1464 - labelName - The label specifying the interface vertices 1465 1466 Output Parameters: 1467 + hybridLabel - The label fully marking the interface 1468 - dmHybrid - The new DM 1469 1470 Level: developer 1471 1472 .seealso: DMPlexConstructCohesiveCells(), DMPlexLabelCohesiveComplete(), DMCreate() 1473 @*/ 1474 PetscErrorCode DMPlexCreateHybridMesh(DM dm, DMLabel label, DMLabel *hybridLabel, DM *dmHybrid) 1475 { 1476 DM idm; 1477 DMLabel subpointMap, hlabel; 1478 PetscInt dim; 1479 PetscErrorCode ierr; 1480 1481 PetscFunctionBegin; 1482 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1483 if (hybridLabel) PetscValidPointer(hybridLabel, 3); 1484 PetscValidPointer(dmHybrid, 4); 1485 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1486 ierr = DMPlexCreateSubmesh(dm, label, 1, &idm);CHKERRQ(ierr); 1487 ierr = DMPlexOrient(idm);CHKERRQ(ierr); 1488 ierr = DMPlexGetSubpointMap(idm, &subpointMap);CHKERRQ(ierr); 1489 ierr = DMLabelDuplicate(subpointMap, &hlabel);CHKERRQ(ierr); 1490 ierr = DMLabelClearStratum(hlabel, dim);CHKERRQ(ierr); 1491 ierr = DMPlexLabelCohesiveComplete(dm, hlabel, PETSC_FALSE, idm);CHKERRQ(ierr); 1492 ierr = DMDestroy(&idm);CHKERRQ(ierr); 1493 ierr = DMPlexConstructCohesiveCells(dm, hlabel, dmHybrid);CHKERRQ(ierr); 1494 if (hybridLabel) *hybridLabel = hlabel; 1495 else {ierr = DMLabelDestroy(&hlabel);CHKERRQ(ierr);} 1496 PetscFunctionReturn(0); 1497 } 1498 1499 #undef __FUNCT__ 1500 #define __FUNCT__ "DMPlexMarkSubmesh_Uninterpolated" 1501 /* Here we need the explicit assumption that: 1502 1503 For any marked cell, the marked vertices constitute a single face 1504 */ 1505 static PetscErrorCode DMPlexMarkSubmesh_Uninterpolated(DM dm, DMLabel vertexLabel, PetscInt value, DMLabel subpointMap, PetscInt *numFaces, PetscInt *nFV, DM subdm) 1506 { 1507 IS subvertexIS = NULL; 1508 const PetscInt *subvertices; 1509 PetscInt *pStart, *pEnd, *pMax, pSize; 1510 PetscInt depth, dim, d, numSubVerticesInitial = 0, v; 1511 PetscErrorCode ierr; 1512 1513 PetscFunctionBegin; 1514 *numFaces = 0; 1515 *nFV = 0; 1516 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 1517 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1518 pSize = PetscMax(depth, dim) + 1; 1519 ierr = PetscMalloc3(pSize,PetscInt,&pStart,pSize,PetscInt,&pEnd,pSize,PetscInt,&pMax);CHKERRQ(ierr); 1520 ierr = DMPlexGetHybridBounds(dm, depth >= 0 ? &pMax[depth] : NULL, depth>1 ? &pMax[depth-1] : NULL, depth>2 ? &pMax[1] : NULL, &pMax[0]);CHKERRQ(ierr); 1521 for (d = 0; d <= depth; ++d) { 1522 ierr = DMPlexGetDepthStratum(dm, d, &pStart[d], &pEnd[d]);CHKERRQ(ierr); 1523 if (pMax[d] >= 0) pEnd[d] = PetscMin(pEnd[d], pMax[d]); 1524 } 1525 /* Loop over initial vertices and mark all faces in the collective star() */ 1526 if (vertexLabel) {ierr = DMLabelGetStratumIS(vertexLabel, value, &subvertexIS);CHKERRQ(ierr);} 1527 if (subvertexIS) { 1528 ierr = ISGetSize(subvertexIS, &numSubVerticesInitial);CHKERRQ(ierr); 1529 ierr = ISGetIndices(subvertexIS, &subvertices);CHKERRQ(ierr); 1530 } 1531 for (v = 0; v < numSubVerticesInitial; ++v) { 1532 const PetscInt vertex = subvertices[v]; 1533 PetscInt *star = NULL; 1534 PetscInt starSize, s, numCells = 0, c; 1535 1536 ierr = DMPlexGetTransitiveClosure(dm, vertex, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1537 for (s = 0; s < starSize*2; s += 2) { 1538 const PetscInt point = star[s]; 1539 if ((point >= pStart[depth]) && (point < pEnd[depth])) star[numCells++] = point; 1540 } 1541 for (c = 0; c < numCells; ++c) { 1542 const PetscInt cell = star[c]; 1543 PetscInt *closure = NULL; 1544 PetscInt closureSize, cl; 1545 PetscInt cellLoc, numCorners = 0, faceSize = 0; 1546 1547 ierr = DMLabelGetValue(subpointMap, cell, &cellLoc);CHKERRQ(ierr); 1548 if (cellLoc == 2) continue; 1549 if (cellLoc >= 0) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Cell %d has dimension %d in the surface label", cell, cellLoc); 1550 ierr = DMPlexGetTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1551 for (cl = 0; cl < closureSize*2; cl += 2) { 1552 const PetscInt point = closure[cl]; 1553 PetscInt vertexLoc; 1554 1555 if ((point >= pStart[0]) && (point < pEnd[0])) { 1556 ++numCorners; 1557 ierr = DMLabelGetValue(vertexLabel, point, &vertexLoc);CHKERRQ(ierr); 1558 if (vertexLoc == value) closure[faceSize++] = point; 1559 } 1560 } 1561 if (!(*nFV)) {ierr = DMPlexGetNumFaceVertices(dm, dim, numCorners, nFV);CHKERRQ(ierr);} 1562 if (faceSize > *nFV) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Invalid submesh: Too many vertices %d of an element on the surface", faceSize); 1563 if (faceSize == *nFV) { 1564 const PetscInt *cells = NULL; 1565 PetscInt numCells, nc; 1566 1567 ++(*numFaces); 1568 for (cl = 0; cl < faceSize; ++cl) { 1569 ierr = DMLabelSetValue(subpointMap, closure[cl], 0);CHKERRQ(ierr); 1570 } 1571 ierr = DMPlexGetJoin(dm, faceSize, closure, &numCells, &cells);CHKERRQ(ierr); 1572 for (nc = 0; nc < numCells; ++nc) { 1573 ierr = DMLabelSetValue(subpointMap, cells[nc], 2);CHKERRQ(ierr); 1574 } 1575 ierr = DMPlexRestoreJoin(dm, faceSize, closure, &numCells, &cells);CHKERRQ(ierr); 1576 } 1577 ierr = DMPlexRestoreTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1578 } 1579 ierr = DMPlexRestoreTransitiveClosure(dm, vertex, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1580 } 1581 if (subvertexIS) { 1582 ierr = ISRestoreIndices(subvertexIS, &subvertices);CHKERRQ(ierr); 1583 } 1584 ierr = ISDestroy(&subvertexIS);CHKERRQ(ierr); 1585 ierr = PetscFree3(pStart,pEnd,pMax);CHKERRQ(ierr); 1586 PetscFunctionReturn(0); 1587 } 1588 1589 #undef __FUNCT__ 1590 #define __FUNCT__ "DMPlexMarkSubmesh_Interpolated" 1591 static PetscErrorCode DMPlexMarkSubmesh_Interpolated(DM dm, DMLabel vertexLabel, PetscInt value, DMLabel subpointMap, DM subdm) 1592 { 1593 IS subvertexIS; 1594 const PetscInt *subvertices; 1595 PetscInt *pStart, *pEnd, *pMax; 1596 PetscInt dim, d, numSubVerticesInitial = 0, v; 1597 PetscErrorCode ierr; 1598 1599 PetscFunctionBegin; 1600 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1601 ierr = PetscMalloc3(dim+1,PetscInt,&pStart,dim+1,PetscInt,&pEnd,dim+1,PetscInt,&pMax);CHKERRQ(ierr); 1602 ierr = DMPlexGetHybridBounds(dm, &pMax[dim], dim>1 ? &pMax[dim-1] : NULL, dim > 2 ? &pMax[1] : NULL, &pMax[0]);CHKERRQ(ierr); 1603 for (d = 0; d <= dim; ++d) { 1604 ierr = DMPlexGetDepthStratum(dm, d, &pStart[d], &pEnd[d]);CHKERRQ(ierr); 1605 if (pMax[d] >= 0) pEnd[d] = PetscMin(pEnd[d], pMax[d]); 1606 } 1607 /* Loop over initial vertices and mark all faces in the collective star() */ 1608 ierr = DMLabelGetStratumIS(vertexLabel, value, &subvertexIS);CHKERRQ(ierr); 1609 if (subvertexIS) { 1610 ierr = ISGetSize(subvertexIS, &numSubVerticesInitial);CHKERRQ(ierr); 1611 ierr = ISGetIndices(subvertexIS, &subvertices);CHKERRQ(ierr); 1612 } 1613 for (v = 0; v < numSubVerticesInitial; ++v) { 1614 const PetscInt vertex = subvertices[v]; 1615 PetscInt *star = NULL; 1616 PetscInt starSize, s, numFaces = 0, f; 1617 1618 ierr = DMPlexGetTransitiveClosure(dm, vertex, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1619 for (s = 0; s < starSize*2; s += 2) { 1620 const PetscInt point = star[s]; 1621 if ((point >= pStart[dim-1]) && (point < pEnd[dim-1])) star[numFaces++] = point; 1622 } 1623 for (f = 0; f < numFaces; ++f) { 1624 const PetscInt face = star[f]; 1625 PetscInt *closure = NULL; 1626 PetscInt closureSize, c; 1627 PetscInt faceLoc; 1628 1629 ierr = DMLabelGetValue(subpointMap, face, &faceLoc);CHKERRQ(ierr); 1630 if (faceLoc == dim-1) continue; 1631 if (faceLoc >= 0) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Face %d has dimension %d in the surface label", face, faceLoc); 1632 ierr = DMPlexGetTransitiveClosure(dm, face, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1633 for (c = 0; c < closureSize*2; c += 2) { 1634 const PetscInt point = closure[c]; 1635 PetscInt vertexLoc; 1636 1637 if ((point >= pStart[0]) && (point < pEnd[0])) { 1638 ierr = DMLabelGetValue(vertexLabel, point, &vertexLoc);CHKERRQ(ierr); 1639 if (vertexLoc != value) break; 1640 } 1641 } 1642 if (c == closureSize*2) { 1643 const PetscInt *support; 1644 PetscInt supportSize, s; 1645 1646 for (c = 0; c < closureSize*2; c += 2) { 1647 const PetscInt point = closure[c]; 1648 1649 for (d = 0; d < dim; ++d) { 1650 if ((point >= pStart[d]) && (point < pEnd[d])) { 1651 ierr = DMLabelSetValue(subpointMap, point, d);CHKERRQ(ierr); 1652 break; 1653 } 1654 } 1655 } 1656 ierr = DMPlexGetSupportSize(dm, face, &supportSize);CHKERRQ(ierr); 1657 ierr = DMPlexGetSupport(dm, face, &support);CHKERRQ(ierr); 1658 for (s = 0; s < supportSize; ++s) { 1659 ierr = DMLabelSetValue(subpointMap, support[s], dim);CHKERRQ(ierr); 1660 } 1661 } 1662 ierr = DMPlexRestoreTransitiveClosure(dm, face, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1663 } 1664 ierr = DMPlexRestoreTransitiveClosure(dm, vertex, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1665 } 1666 if (subvertexIS) { 1667 ierr = ISRestoreIndices(subvertexIS, &subvertices);CHKERRQ(ierr); 1668 } 1669 ierr = ISDestroy(&subvertexIS);CHKERRQ(ierr); 1670 ierr = PetscFree3(pStart,pEnd,pMax);CHKERRQ(ierr); 1671 PetscFunctionReturn(0); 1672 } 1673 1674 #undef __FUNCT__ 1675 #define __FUNCT__ "DMPlexMarkCohesiveSubmesh_Uninterpolated" 1676 static PetscErrorCode DMPlexMarkCohesiveSubmesh_Uninterpolated(DM dm, PetscBool hasLagrange, const char labelname[], PetscInt value, DMLabel subpointMap, PetscInt *numFaces, PetscInt *nFV, PetscInt *subCells[], DM subdm) 1677 { 1678 DMLabel label = NULL; 1679 const PetscInt *cone; 1680 PetscInt dim, cMax, cEnd, c, subc = 0, p, coneSize; 1681 PetscErrorCode ierr; 1682 1683 PetscFunctionBegin; 1684 *numFaces = 0; 1685 *nFV = 0; 1686 if (labelname) {ierr = DMPlexGetLabel(dm, labelname, &label);CHKERRQ(ierr);} 1687 *subCells = NULL; 1688 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1689 ierr = DMPlexGetHeightStratum(dm, 0, NULL, &cEnd);CHKERRQ(ierr); 1690 ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); 1691 if (cMax < 0) PetscFunctionReturn(0); 1692 if (label) { 1693 for (c = cMax; c < cEnd; ++c) { 1694 PetscInt val; 1695 1696 ierr = DMLabelGetValue(label, c, &val);CHKERRQ(ierr); 1697 if (val == value) { 1698 ++(*numFaces); 1699 ierr = DMPlexGetConeSize(dm, c, &coneSize);CHKERRQ(ierr); 1700 } 1701 } 1702 } else { 1703 *numFaces = cEnd - cMax; 1704 ierr = DMPlexGetConeSize(dm, cMax, &coneSize);CHKERRQ(ierr); 1705 } 1706 *nFV = hasLagrange ? coneSize/3 : coneSize/2; 1707 ierr = PetscMalloc(*numFaces *2 * sizeof(PetscInt), subCells);CHKERRQ(ierr); 1708 for (c = cMax; c < cEnd; ++c) { 1709 const PetscInt *cells; 1710 PetscInt numCells; 1711 1712 if (label) { 1713 PetscInt val; 1714 1715 ierr = DMLabelGetValue(label, c, &val);CHKERRQ(ierr); 1716 if (val != value) continue; 1717 } 1718 ierr = DMPlexGetCone(dm, c, &cone);CHKERRQ(ierr); 1719 for (p = 0; p < *nFV; ++p) { 1720 ierr = DMLabelSetValue(subpointMap, cone[p], 0);CHKERRQ(ierr); 1721 } 1722 /* Negative face */ 1723 ierr = DMPlexGetJoin(dm, *nFV, cone, &numCells, &cells);CHKERRQ(ierr); 1724 /* Not true in parallel 1725 if (numCells != 2) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive cells should separate two cells"); */ 1726 for (p = 0; p < numCells; ++p) { 1727 ierr = DMLabelSetValue(subpointMap, cells[p], 2);CHKERRQ(ierr); 1728 (*subCells)[subc++] = cells[p]; 1729 } 1730 ierr = DMPlexRestoreJoin(dm, *nFV, cone, &numCells, &cells);CHKERRQ(ierr); 1731 /* Positive face is not included */ 1732 } 1733 PetscFunctionReturn(0); 1734 } 1735 1736 #undef __FUNCT__ 1737 #define __FUNCT__ "DMPlexMarkCohesiveSubmesh_Interpolated" 1738 static PetscErrorCode DMPlexMarkCohesiveSubmesh_Interpolated(DM dm, const char labelname[], PetscInt value, DMLabel subpointMap, DM subdm) 1739 { 1740 DMLabel label = NULL; 1741 PetscInt *pStart, *pEnd; 1742 PetscInt dim, cMax, cEnd, c, d; 1743 PetscErrorCode ierr; 1744 1745 PetscFunctionBegin; 1746 if (labelname) {ierr = DMPlexGetLabel(dm, labelname, &label);CHKERRQ(ierr);} 1747 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1748 ierr = DMPlexGetHeightStratum(dm, 0, NULL, &cEnd);CHKERRQ(ierr); 1749 ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); 1750 if (cMax < 0) PetscFunctionReturn(0); 1751 ierr = PetscMalloc2(dim+1,PetscInt,&pStart,dim+1,PetscInt,&pEnd);CHKERRQ(ierr); 1752 for (d = 0; d <= dim; ++d) {ierr = DMPlexGetDepthStratum(dm, d, &pStart[d], &pEnd[d]);CHKERRQ(ierr);} 1753 for (c = cMax; c < cEnd; ++c) { 1754 const PetscInt *cone; 1755 PetscInt *closure = NULL; 1756 PetscInt fconeSize, coneSize, closureSize, cl, val; 1757 1758 if (label) { 1759 ierr = DMLabelGetValue(label, c, &val);CHKERRQ(ierr); 1760 if (val != value) continue; 1761 } 1762 ierr = DMPlexGetConeSize(dm, c, &coneSize);CHKERRQ(ierr); 1763 ierr = DMPlexGetCone(dm, c, &cone);CHKERRQ(ierr); 1764 ierr = DMPlexGetConeSize(dm, cone[0], &fconeSize);CHKERRQ(ierr); 1765 if (coneSize != (fconeSize ? fconeSize : 1) + 2) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive cells should separate two cells"); 1766 /* Negative face */ 1767 ierr = DMPlexGetTransitiveClosure(dm, cone[0], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1768 for (cl = 0; cl < closureSize*2; cl += 2) { 1769 const PetscInt point = closure[cl]; 1770 1771 for (d = 0; d <= dim; ++d) { 1772 if ((point >= pStart[d]) && (point < pEnd[d])) { 1773 ierr = DMLabelSetValue(subpointMap, point, d);CHKERRQ(ierr); 1774 break; 1775 } 1776 } 1777 } 1778 ierr = DMPlexRestoreTransitiveClosure(dm, cone[0], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1779 /* Cells -- positive face is not included */ 1780 for (cl = 0; cl < 1; ++cl) { 1781 const PetscInt *support; 1782 PetscInt supportSize, s; 1783 1784 ierr = DMPlexGetSupportSize(dm, cone[cl], &supportSize);CHKERRQ(ierr); 1785 if (supportSize != 2) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive faces should separate two cells"); 1786 ierr = DMPlexGetSupport(dm, cone[cl], &support);CHKERRQ(ierr); 1787 for (s = 0; s < supportSize; ++s) { 1788 ierr = DMLabelSetValue(subpointMap, support[s], dim);CHKERRQ(ierr); 1789 } 1790 } 1791 } 1792 ierr = PetscFree2(pStart, pEnd);CHKERRQ(ierr); 1793 PetscFunctionReturn(0); 1794 } 1795 1796 #undef __FUNCT__ 1797 #define __FUNCT__ "DMPlexGetFaceOrientation" 1798 PetscErrorCode DMPlexGetFaceOrientation(DM dm, PetscInt cell, PetscInt numCorners, PetscInt indices[], PetscInt oppositeVertex, PetscInt origVertices[], PetscInt faceVertices[], PetscBool *posOriented) 1799 { 1800 MPI_Comm comm; 1801 PetscBool posOrient = PETSC_FALSE; 1802 const PetscInt debug = 0; 1803 PetscInt cellDim, faceSize, f; 1804 PetscErrorCode ierr; 1805 1806 PetscFunctionBegin; 1807 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 1808 ierr = DMPlexGetDimension(dm, &cellDim);CHKERRQ(ierr); 1809 if (debug) {PetscPrintf(comm, "cellDim: %d numCorners: %d\n", cellDim, numCorners);CHKERRQ(ierr);} 1810 1811 if (cellDim == 1 && numCorners == 2) { 1812 /* Triangle */ 1813 faceSize = numCorners-1; 1814 posOrient = !(oppositeVertex%2) ? PETSC_TRUE : PETSC_FALSE; 1815 } else if (cellDim == 2 && numCorners == 3) { 1816 /* Triangle */ 1817 faceSize = numCorners-1; 1818 posOrient = !(oppositeVertex%2) ? PETSC_TRUE : PETSC_FALSE; 1819 } else if (cellDim == 3 && numCorners == 4) { 1820 /* Tetrahedron */ 1821 faceSize = numCorners-1; 1822 posOrient = (oppositeVertex%2) ? PETSC_TRUE : PETSC_FALSE; 1823 } else if (cellDim == 1 && numCorners == 3) { 1824 /* Quadratic line */ 1825 faceSize = 1; 1826 posOrient = PETSC_TRUE; 1827 } else if (cellDim == 2 && numCorners == 4) { 1828 /* Quads */ 1829 faceSize = 2; 1830 if ((indices[1] > indices[0]) && (indices[1] - indices[0] == 1)) { 1831 posOrient = PETSC_TRUE; 1832 } else if ((indices[0] == 3) && (indices[1] == 0)) { 1833 posOrient = PETSC_TRUE; 1834 } else { 1835 if (((indices[0] > indices[1]) && (indices[0] - indices[1] == 1)) || ((indices[0] == 0) && (indices[1] == 3))) { 1836 posOrient = PETSC_FALSE; 1837 } else SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid quad crossedge"); 1838 } 1839 } else if (cellDim == 2 && numCorners == 6) { 1840 /* Quadratic triangle (I hate this) */ 1841 /* Edges are determined by the first 2 vertices (corners of edges) */ 1842 const PetscInt faceSizeTri = 3; 1843 PetscInt sortedIndices[3], i, iFace; 1844 PetscBool found = PETSC_FALSE; 1845 PetscInt faceVerticesTriSorted[9] = { 1846 0, 3, 4, /* bottom */ 1847 1, 4, 5, /* right */ 1848 2, 3, 5, /* left */ 1849 }; 1850 PetscInt faceVerticesTri[9] = { 1851 0, 3, 4, /* bottom */ 1852 1, 4, 5, /* right */ 1853 2, 5, 3, /* left */ 1854 }; 1855 1856 faceSize = faceSizeTri; 1857 for (i = 0; i < faceSizeTri; ++i) sortedIndices[i] = indices[i]; 1858 ierr = PetscSortInt(faceSizeTri, sortedIndices);CHKERRQ(ierr); 1859 for (iFace = 0; iFace < 3; ++iFace) { 1860 const PetscInt ii = iFace*faceSizeTri; 1861 PetscInt fVertex, cVertex; 1862 1863 if ((sortedIndices[0] == faceVerticesTriSorted[ii+0]) && 1864 (sortedIndices[1] == faceVerticesTriSorted[ii+1])) { 1865 for (fVertex = 0; fVertex < faceSizeTri; ++fVertex) { 1866 for (cVertex = 0; cVertex < faceSizeTri; ++cVertex) { 1867 if (indices[cVertex] == faceVerticesTri[ii+fVertex]) { 1868 faceVertices[fVertex] = origVertices[cVertex]; 1869 break; 1870 } 1871 } 1872 } 1873 found = PETSC_TRUE; 1874 break; 1875 } 1876 } 1877 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid tri crossface"); 1878 if (posOriented) *posOriented = PETSC_TRUE; 1879 PetscFunctionReturn(0); 1880 } else if (cellDim == 2 && numCorners == 9) { 1881 /* Quadratic quad (I hate this) */ 1882 /* Edges are determined by the first 2 vertices (corners of edges) */ 1883 const PetscInt faceSizeQuad = 3; 1884 PetscInt sortedIndices[3], i, iFace; 1885 PetscBool found = PETSC_FALSE; 1886 PetscInt faceVerticesQuadSorted[12] = { 1887 0, 1, 4, /* bottom */ 1888 1, 2, 5, /* right */ 1889 2, 3, 6, /* top */ 1890 0, 3, 7, /* left */ 1891 }; 1892 PetscInt faceVerticesQuad[12] = { 1893 0, 1, 4, /* bottom */ 1894 1, 2, 5, /* right */ 1895 2, 3, 6, /* top */ 1896 3, 0, 7, /* left */ 1897 }; 1898 1899 faceSize = faceSizeQuad; 1900 for (i = 0; i < faceSizeQuad; ++i) sortedIndices[i] = indices[i]; 1901 ierr = PetscSortInt(faceSizeQuad, sortedIndices);CHKERRQ(ierr); 1902 for (iFace = 0; iFace < 4; ++iFace) { 1903 const PetscInt ii = iFace*faceSizeQuad; 1904 PetscInt fVertex, cVertex; 1905 1906 if ((sortedIndices[0] == faceVerticesQuadSorted[ii+0]) && 1907 (sortedIndices[1] == faceVerticesQuadSorted[ii+1])) { 1908 for (fVertex = 0; fVertex < faceSizeQuad; ++fVertex) { 1909 for (cVertex = 0; cVertex < faceSizeQuad; ++cVertex) { 1910 if (indices[cVertex] == faceVerticesQuad[ii+fVertex]) { 1911 faceVertices[fVertex] = origVertices[cVertex]; 1912 break; 1913 } 1914 } 1915 } 1916 found = PETSC_TRUE; 1917 break; 1918 } 1919 } 1920 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid quad crossface"); 1921 if (posOriented) *posOriented = PETSC_TRUE; 1922 PetscFunctionReturn(0); 1923 } else if (cellDim == 3 && numCorners == 8) { 1924 /* Hexes 1925 A hex is two oriented quads with the normal of the first 1926 pointing up at the second. 1927 1928 7---6 1929 /| /| 1930 4---5 | 1931 | 1-|-2 1932 |/ |/ 1933 0---3 1934 1935 Faces are determined by the first 4 vertices (corners of faces) */ 1936 const PetscInt faceSizeHex = 4; 1937 PetscInt sortedIndices[4], i, iFace; 1938 PetscBool found = PETSC_FALSE; 1939 PetscInt faceVerticesHexSorted[24] = { 1940 0, 1, 2, 3, /* bottom */ 1941 4, 5, 6, 7, /* top */ 1942 0, 3, 4, 5, /* front */ 1943 2, 3, 5, 6, /* right */ 1944 1, 2, 6, 7, /* back */ 1945 0, 1, 4, 7, /* left */ 1946 }; 1947 PetscInt faceVerticesHex[24] = { 1948 1, 2, 3, 0, /* bottom */ 1949 4, 5, 6, 7, /* top */ 1950 0, 3, 5, 4, /* front */ 1951 3, 2, 6, 5, /* right */ 1952 2, 1, 7, 6, /* back */ 1953 1, 0, 4, 7, /* left */ 1954 }; 1955 1956 faceSize = faceSizeHex; 1957 for (i = 0; i < faceSizeHex; ++i) sortedIndices[i] = indices[i]; 1958 ierr = PetscSortInt(faceSizeHex, sortedIndices);CHKERRQ(ierr); 1959 for (iFace = 0; iFace < 6; ++iFace) { 1960 const PetscInt ii = iFace*faceSizeHex; 1961 PetscInt fVertex, cVertex; 1962 1963 if ((sortedIndices[0] == faceVerticesHexSorted[ii+0]) && 1964 (sortedIndices[1] == faceVerticesHexSorted[ii+1]) && 1965 (sortedIndices[2] == faceVerticesHexSorted[ii+2]) && 1966 (sortedIndices[3] == faceVerticesHexSorted[ii+3])) { 1967 for (fVertex = 0; fVertex < faceSizeHex; ++fVertex) { 1968 for (cVertex = 0; cVertex < faceSizeHex; ++cVertex) { 1969 if (indices[cVertex] == faceVerticesHex[ii+fVertex]) { 1970 faceVertices[fVertex] = origVertices[cVertex]; 1971 break; 1972 } 1973 } 1974 } 1975 found = PETSC_TRUE; 1976 break; 1977 } 1978 } 1979 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid hex crossface"); 1980 if (posOriented) *posOriented = PETSC_TRUE; 1981 PetscFunctionReturn(0); 1982 } else if (cellDim == 3 && numCorners == 10) { 1983 /* Quadratic tet */ 1984 /* Faces are determined by the first 3 vertices (corners of faces) */ 1985 const PetscInt faceSizeTet = 6; 1986 PetscInt sortedIndices[6], i, iFace; 1987 PetscBool found = PETSC_FALSE; 1988 PetscInt faceVerticesTetSorted[24] = { 1989 0, 1, 2, 6, 7, 8, /* bottom */ 1990 0, 3, 4, 6, 7, 9, /* front */ 1991 1, 4, 5, 7, 8, 9, /* right */ 1992 2, 3, 5, 6, 8, 9, /* left */ 1993 }; 1994 PetscInt faceVerticesTet[24] = { 1995 0, 1, 2, 6, 7, 8, /* bottom */ 1996 0, 4, 3, 6, 7, 9, /* front */ 1997 1, 5, 4, 7, 8, 9, /* right */ 1998 2, 3, 5, 8, 6, 9, /* left */ 1999 }; 2000 2001 faceSize = faceSizeTet; 2002 for (i = 0; i < faceSizeTet; ++i) sortedIndices[i] = indices[i]; 2003 ierr = PetscSortInt(faceSizeTet, sortedIndices);CHKERRQ(ierr); 2004 for (iFace=0; iFace < 4; ++iFace) { 2005 const PetscInt ii = iFace*faceSizeTet; 2006 PetscInt fVertex, cVertex; 2007 2008 if ((sortedIndices[0] == faceVerticesTetSorted[ii+0]) && 2009 (sortedIndices[1] == faceVerticesTetSorted[ii+1]) && 2010 (sortedIndices[2] == faceVerticesTetSorted[ii+2]) && 2011 (sortedIndices[3] == faceVerticesTetSorted[ii+3])) { 2012 for (fVertex = 0; fVertex < faceSizeTet; ++fVertex) { 2013 for (cVertex = 0; cVertex < faceSizeTet; ++cVertex) { 2014 if (indices[cVertex] == faceVerticesTet[ii+fVertex]) { 2015 faceVertices[fVertex] = origVertices[cVertex]; 2016 break; 2017 } 2018 } 2019 } 2020 found = PETSC_TRUE; 2021 break; 2022 } 2023 } 2024 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid tet crossface"); 2025 if (posOriented) *posOriented = PETSC_TRUE; 2026 PetscFunctionReturn(0); 2027 } else if (cellDim == 3 && numCorners == 27) { 2028 /* Quadratic hexes (I hate this) 2029 A hex is two oriented quads with the normal of the first 2030 pointing up at the second. 2031 2032 7---6 2033 /| /| 2034 4---5 | 2035 | 3-|-2 2036 |/ |/ 2037 0---1 2038 2039 Faces are determined by the first 4 vertices (corners of faces) */ 2040 const PetscInt faceSizeQuadHex = 9; 2041 PetscInt sortedIndices[9], i, iFace; 2042 PetscBool found = PETSC_FALSE; 2043 PetscInt faceVerticesQuadHexSorted[54] = { 2044 0, 1, 2, 3, 8, 9, 10, 11, 24, /* bottom */ 2045 4, 5, 6, 7, 12, 13, 14, 15, 25, /* top */ 2046 0, 1, 4, 5, 8, 12, 16, 17, 22, /* front */ 2047 1, 2, 5, 6, 9, 13, 17, 18, 21, /* right */ 2048 2, 3, 6, 7, 10, 14, 18, 19, 23, /* back */ 2049 0, 3, 4, 7, 11, 15, 16, 19, 20, /* left */ 2050 }; 2051 PetscInt faceVerticesQuadHex[54] = { 2052 3, 2, 1, 0, 10, 9, 8, 11, 24, /* bottom */ 2053 4, 5, 6, 7, 12, 13, 14, 15, 25, /* top */ 2054 0, 1, 5, 4, 8, 17, 12, 16, 22, /* front */ 2055 1, 2, 6, 5, 9, 18, 13, 17, 21, /* right */ 2056 2, 3, 7, 6, 10, 19, 14, 18, 23, /* back */ 2057 3, 0, 4, 7, 11, 16, 15, 19, 20 /* left */ 2058 }; 2059 2060 faceSize = faceSizeQuadHex; 2061 for (i = 0; i < faceSizeQuadHex; ++i) sortedIndices[i] = indices[i]; 2062 ierr = PetscSortInt(faceSizeQuadHex, sortedIndices);CHKERRQ(ierr); 2063 for (iFace = 0; iFace < 6; ++iFace) { 2064 const PetscInt ii = iFace*faceSizeQuadHex; 2065 PetscInt fVertex, cVertex; 2066 2067 if ((sortedIndices[0] == faceVerticesQuadHexSorted[ii+0]) && 2068 (sortedIndices[1] == faceVerticesQuadHexSorted[ii+1]) && 2069 (sortedIndices[2] == faceVerticesQuadHexSorted[ii+2]) && 2070 (sortedIndices[3] == faceVerticesQuadHexSorted[ii+3])) { 2071 for (fVertex = 0; fVertex < faceSizeQuadHex; ++fVertex) { 2072 for (cVertex = 0; cVertex < faceSizeQuadHex; ++cVertex) { 2073 if (indices[cVertex] == faceVerticesQuadHex[ii+fVertex]) { 2074 faceVertices[fVertex] = origVertices[cVertex]; 2075 break; 2076 } 2077 } 2078 } 2079 found = PETSC_TRUE; 2080 break; 2081 } 2082 } 2083 if (!found) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Invalid hex crossface"); 2084 if (posOriented) *posOriented = PETSC_TRUE; 2085 PetscFunctionReturn(0); 2086 } else SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Unknown cell type for faceOrientation()."); 2087 if (!posOrient) { 2088 if (debug) {ierr = PetscPrintf(comm, " Reversing initial face orientation\n");CHKERRQ(ierr);} 2089 for (f = 0; f < faceSize; ++f) faceVertices[f] = origVertices[faceSize-1 - f]; 2090 } else { 2091 if (debug) {ierr = PetscPrintf(comm, " Keeping initial face orientation\n");CHKERRQ(ierr);} 2092 for (f = 0; f < faceSize; ++f) faceVertices[f] = origVertices[f]; 2093 } 2094 if (posOriented) *posOriented = posOrient; 2095 PetscFunctionReturn(0); 2096 } 2097 2098 #undef __FUNCT__ 2099 #define __FUNCT__ "DMPlexGetOrientedFace" 2100 /* 2101 Given a cell and a face, as a set of vertices, 2102 return the oriented face, as a set of vertices, in faceVertices 2103 The orientation is such that the face normal points out of the cell 2104 */ 2105 PetscErrorCode DMPlexGetOrientedFace(DM dm, PetscInt cell, PetscInt faceSize, const PetscInt face[], PetscInt numCorners, PetscInt indices[], PetscInt origVertices[], PetscInt faceVertices[], PetscBool *posOriented) 2106 { 2107 const PetscInt *cone = NULL; 2108 PetscInt coneSize, v, f, v2; 2109 PetscInt oppositeVertex = -1; 2110 PetscErrorCode ierr; 2111 2112 PetscFunctionBegin; 2113 ierr = DMPlexGetConeSize(dm, cell, &coneSize);CHKERRQ(ierr); 2114 ierr = DMPlexGetCone(dm, cell, &cone);CHKERRQ(ierr); 2115 for (v = 0, v2 = 0; v < coneSize; ++v) { 2116 PetscBool found = PETSC_FALSE; 2117 2118 for (f = 0; f < faceSize; ++f) { 2119 if (face[f] == cone[v]) { 2120 found = PETSC_TRUE; break; 2121 } 2122 } 2123 if (found) { 2124 indices[v2] = v; 2125 origVertices[v2] = cone[v]; 2126 ++v2; 2127 } else { 2128 oppositeVertex = v; 2129 } 2130 } 2131 ierr = DMPlexGetFaceOrientation(dm, cell, numCorners, indices, oppositeVertex, origVertices, faceVertices, posOriented);CHKERRQ(ierr); 2132 PetscFunctionReturn(0); 2133 } 2134 2135 #undef __FUNCT__ 2136 #define __FUNCT__ "DMPlexInsertFace_Internal" 2137 /* 2138 DMPlexInsertFace_Internal - Puts a face into the mesh 2139 2140 Not collective 2141 2142 Input Parameters: 2143 + dm - The DMPlex 2144 . numFaceVertex - The number of vertices in the face 2145 . faceVertices - The vertices in the face for dm 2146 . subfaceVertices - The vertices in the face for subdm 2147 . numCorners - The number of vertices in the cell 2148 . cell - A cell in dm containing the face 2149 . subcell - A cell in subdm containing the face 2150 . firstFace - First face in the mesh 2151 - newFacePoint - Next face in the mesh 2152 2153 Output Parameters: 2154 . newFacePoint - Contains next face point number on input, updated on output 2155 2156 Level: developer 2157 */ 2158 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) 2159 { 2160 MPI_Comm comm; 2161 DM_Plex *submesh = (DM_Plex*) subdm->data; 2162 const PetscInt *faces; 2163 PetscInt numFaces, coneSize; 2164 PetscErrorCode ierr; 2165 2166 PetscFunctionBegin; 2167 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 2168 ierr = DMPlexGetConeSize(subdm, subcell, &coneSize);CHKERRQ(ierr); 2169 if (coneSize != 1) SETERRQ2(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cone size of cell %d is %d != 1", cell, coneSize); 2170 #if 0 2171 /* Cannot use this because support() has not been constructed yet */ 2172 ierr = DMPlexGetJoin(subdm, numFaceVertices, subfaceVertices, &numFaces, &faces);CHKERRQ(ierr); 2173 #else 2174 { 2175 PetscInt f; 2176 2177 numFaces = 0; 2178 ierr = DMGetWorkArray(subdm, 1, PETSC_INT, (void **) &faces);CHKERRQ(ierr); 2179 for (f = firstFace; f < *newFacePoint; ++f) { 2180 PetscInt dof, off, d; 2181 2182 ierr = PetscSectionGetDof(submesh->coneSection, f, &dof);CHKERRQ(ierr); 2183 ierr = PetscSectionGetOffset(submesh->coneSection, f, &off);CHKERRQ(ierr); 2184 /* Yes, I know this is quadratic, but I expect the sizes to be <5 */ 2185 for (d = 0; d < dof; ++d) { 2186 const PetscInt p = submesh->cones[off+d]; 2187 PetscInt v; 2188 2189 for (v = 0; v < numFaceVertices; ++v) { 2190 if (subfaceVertices[v] == p) break; 2191 } 2192 if (v == numFaceVertices) break; 2193 } 2194 if (d == dof) { 2195 numFaces = 1; 2196 ((PetscInt*) faces)[0] = f; 2197 } 2198 } 2199 } 2200 #endif 2201 if (numFaces > 1) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Vertex set had %d faces, not one", numFaces); 2202 else if (numFaces == 1) { 2203 /* Add the other cell neighbor for this face */ 2204 ierr = DMPlexSetCone(subdm, subcell, faces);CHKERRQ(ierr); 2205 } else { 2206 PetscInt *indices, *origVertices, *orientedVertices, *orientedSubVertices, v, ov; 2207 PetscBool posOriented; 2208 2209 ierr = DMGetWorkArray(subdm, 4*numFaceVertices * sizeof(PetscInt), PETSC_INT, &orientedVertices);CHKERRQ(ierr); 2210 origVertices = &orientedVertices[numFaceVertices]; 2211 indices = &orientedVertices[numFaceVertices*2]; 2212 orientedSubVertices = &orientedVertices[numFaceVertices*3]; 2213 ierr = DMPlexGetOrientedFace(dm, cell, numFaceVertices, faceVertices, numCorners, indices, origVertices, orientedVertices, &posOriented);CHKERRQ(ierr); 2214 /* TODO: I know that routine should return a permutation, not the indices */ 2215 for (v = 0; v < numFaceVertices; ++v) { 2216 const PetscInt vertex = faceVertices[v], subvertex = subfaceVertices[v]; 2217 for (ov = 0; ov < numFaceVertices; ++ov) { 2218 if (orientedVertices[ov] == vertex) { 2219 orientedSubVertices[ov] = subvertex; 2220 break; 2221 } 2222 } 2223 if (ov == numFaceVertices) SETERRQ1(comm, PETSC_ERR_PLIB, "Could not find face vertex %d in orientated set", vertex); 2224 } 2225 ierr = DMPlexSetCone(subdm, *newFacePoint, orientedSubVertices);CHKERRQ(ierr); 2226 ierr = DMPlexSetCone(subdm, subcell, newFacePoint);CHKERRQ(ierr); 2227 ierr = DMRestoreWorkArray(subdm, 4*numFaceVertices * sizeof(PetscInt), PETSC_INT, &orientedVertices);CHKERRQ(ierr); 2228 ++(*newFacePoint); 2229 } 2230 #if 0 2231 ierr = DMPlexRestoreJoin(subdm, numFaceVertices, subfaceVertices, &numFaces, &faces);CHKERRQ(ierr); 2232 #else 2233 ierr = DMRestoreWorkArray(subdm, 1, PETSC_INT, (void **) &faces);CHKERRQ(ierr); 2234 #endif 2235 PetscFunctionReturn(0); 2236 } 2237 2238 #undef __FUNCT__ 2239 #define __FUNCT__ "DMPlexCreateSubmesh_Uninterpolated" 2240 static PetscErrorCode DMPlexCreateSubmesh_Uninterpolated(DM dm, DMLabel vertexLabel, PetscInt value, DM subdm) 2241 { 2242 MPI_Comm comm; 2243 DMLabel subpointMap; 2244 IS subvertexIS, subcellIS; 2245 const PetscInt *subVertices, *subCells; 2246 PetscInt numSubVertices, firstSubVertex, numSubCells; 2247 PetscInt *subface, maxConeSize, numSubFaces = 0, firstSubFace, newFacePoint, nFV = 0; 2248 PetscInt vStart, vEnd, c, f; 2249 PetscErrorCode ierr; 2250 2251 PetscFunctionBegin; 2252 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 2253 /* Create subpointMap which marks the submesh */ 2254 ierr = DMLabelCreate("subpoint_map", &subpointMap);CHKERRQ(ierr); 2255 ierr = DMPlexSetSubpointMap(subdm, subpointMap);CHKERRQ(ierr); 2256 ierr = DMLabelDestroy(&subpointMap);CHKERRQ(ierr); 2257 if (vertexLabel) {ierr = DMPlexMarkSubmesh_Uninterpolated(dm, vertexLabel, value, subpointMap, &numSubFaces, &nFV, subdm);CHKERRQ(ierr);} 2258 /* Setup chart */ 2259 ierr = DMLabelGetStratumSize(subpointMap, 0, &numSubVertices);CHKERRQ(ierr); 2260 ierr = DMLabelGetStratumSize(subpointMap, 2, &numSubCells);CHKERRQ(ierr); 2261 ierr = DMPlexSetChart(subdm, 0, numSubCells+numSubFaces+numSubVertices);CHKERRQ(ierr); 2262 ierr = DMPlexSetVTKCellHeight(subdm, 1);CHKERRQ(ierr); 2263 /* Set cone sizes */ 2264 firstSubVertex = numSubCells; 2265 firstSubFace = numSubCells+numSubVertices; 2266 newFacePoint = firstSubFace; 2267 ierr = DMLabelGetStratumIS(subpointMap, 0, &subvertexIS);CHKERRQ(ierr); 2268 if (subvertexIS) {ierr = ISGetIndices(subvertexIS, &subVertices);CHKERRQ(ierr);} 2269 ierr = DMLabelGetStratumIS(subpointMap, 2, &subcellIS);CHKERRQ(ierr); 2270 if (subcellIS) {ierr = ISGetIndices(subcellIS, &subCells);CHKERRQ(ierr);} 2271 for (c = 0; c < numSubCells; ++c) { 2272 ierr = DMPlexSetConeSize(subdm, c, 1);CHKERRQ(ierr); 2273 } 2274 for (f = firstSubFace; f < firstSubFace+numSubFaces; ++f) { 2275 ierr = DMPlexSetConeSize(subdm, f, nFV);CHKERRQ(ierr); 2276 } 2277 ierr = DMSetUp(subdm);CHKERRQ(ierr); 2278 /* Create face cones */ 2279 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 2280 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, NULL);CHKERRQ(ierr); 2281 ierr = DMGetWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);CHKERRQ(ierr); 2282 for (c = 0; c < numSubCells; ++c) { 2283 const PetscInt cell = subCells[c]; 2284 const PetscInt subcell = c; 2285 PetscInt *closure = NULL; 2286 PetscInt closureSize, cl, numCorners = 0, faceSize = 0; 2287 2288 ierr = DMPlexGetTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 2289 for (cl = 0; cl < closureSize*2; cl += 2) { 2290 const PetscInt point = closure[cl]; 2291 PetscInt subVertex; 2292 2293 if ((point >= vStart) && (point < vEnd)) { 2294 ++numCorners; 2295 ierr = PetscFindInt(point, numSubVertices, subVertices, &subVertex);CHKERRQ(ierr); 2296 if (subVertex >= 0) { 2297 closure[faceSize] = point; 2298 subface[faceSize] = firstSubVertex+subVertex; 2299 ++faceSize; 2300 } 2301 } 2302 } 2303 if (faceSize > nFV) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Invalid submesh: Too many vertices %d of an element on the surface", faceSize); 2304 if (faceSize == nFV) { 2305 ierr = DMPlexInsertFace_Internal(dm, subdm, faceSize, closure, subface, numCorners, cell, subcell, firstSubFace, &newFacePoint);CHKERRQ(ierr); 2306 } 2307 ierr = DMPlexRestoreTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 2308 } 2309 ierr = DMRestoreWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);CHKERRQ(ierr); 2310 ierr = DMPlexSymmetrize(subdm);CHKERRQ(ierr); 2311 ierr = DMPlexStratify(subdm);CHKERRQ(ierr); 2312 /* Build coordinates */ 2313 { 2314 PetscSection coordSection, subCoordSection; 2315 Vec coordinates, subCoordinates; 2316 PetscScalar *coords, *subCoords; 2317 PetscInt numComp, coordSize, v; 2318 2319 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2320 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 2321 ierr = DMPlexGetCoordinateSection(subdm, &subCoordSection);CHKERRQ(ierr); 2322 ierr = PetscSectionSetNumFields(subCoordSection, 1);CHKERRQ(ierr); 2323 ierr = PetscSectionGetFieldComponents(coordSection, 0, &numComp);CHKERRQ(ierr); 2324 ierr = PetscSectionSetFieldComponents(subCoordSection, 0, numComp);CHKERRQ(ierr); 2325 ierr = PetscSectionSetChart(subCoordSection, firstSubVertex, firstSubVertex+numSubVertices);CHKERRQ(ierr); 2326 for (v = 0; v < numSubVertices; ++v) { 2327 const PetscInt vertex = subVertices[v]; 2328 const PetscInt subvertex = firstSubVertex+v; 2329 PetscInt dof; 2330 2331 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2332 ierr = PetscSectionSetDof(subCoordSection, subvertex, dof);CHKERRQ(ierr); 2333 ierr = PetscSectionSetFieldDof(subCoordSection, subvertex, 0, dof);CHKERRQ(ierr); 2334 } 2335 ierr = PetscSectionSetUp(subCoordSection);CHKERRQ(ierr); 2336 ierr = PetscSectionGetStorageSize(subCoordSection, &coordSize);CHKERRQ(ierr); 2337 ierr = VecCreate(comm, &subCoordinates);CHKERRQ(ierr); 2338 ierr = VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2339 ierr = VecSetType(subCoordinates,VECSTANDARD);CHKERRQ(ierr); 2340 if (coordSize) { 2341 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2342 ierr = VecGetArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2343 for (v = 0; v < numSubVertices; ++v) { 2344 const PetscInt vertex = subVertices[v]; 2345 const PetscInt subvertex = firstSubVertex+v; 2346 PetscInt dof, off, sdof, soff, d; 2347 2348 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2349 ierr = PetscSectionGetOffset(coordSection, vertex, &off);CHKERRQ(ierr); 2350 ierr = PetscSectionGetDof(subCoordSection, subvertex, &sdof);CHKERRQ(ierr); 2351 ierr = PetscSectionGetOffset(subCoordSection, subvertex, &soff);CHKERRQ(ierr); 2352 if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof); 2353 for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d]; 2354 } 2355 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2356 ierr = VecRestoreArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2357 } 2358 ierr = DMSetCoordinatesLocal(subdm, subCoordinates);CHKERRQ(ierr); 2359 ierr = VecDestroy(&subCoordinates);CHKERRQ(ierr); 2360 } 2361 /* Cleanup */ 2362 if (subvertexIS) {ierr = ISRestoreIndices(subvertexIS, &subVertices);CHKERRQ(ierr);} 2363 ierr = ISDestroy(&subvertexIS);CHKERRQ(ierr); 2364 if (subcellIS) {ierr = ISRestoreIndices(subcellIS, &subCells);CHKERRQ(ierr);} 2365 ierr = ISDestroy(&subcellIS);CHKERRQ(ierr); 2366 PetscFunctionReturn(0); 2367 } 2368 2369 #undef __FUNCT__ 2370 #define __FUNCT__ "DMPlexCreateSubmesh_Interpolated" 2371 static PetscErrorCode DMPlexCreateSubmesh_Interpolated(DM dm, DMLabel vertexLabel, PetscInt value, DM subdm) 2372 { 2373 MPI_Comm comm; 2374 DMLabel subpointMap; 2375 IS *subpointIS; 2376 const PetscInt **subpoints; 2377 PetscInt *numSubPoints, *firstSubPoint, *coneNew, *coneONew; 2378 PetscInt totSubPoints = 0, maxConeSize, dim, p, d, v; 2379 PetscErrorCode ierr; 2380 2381 PetscFunctionBegin; 2382 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 2383 /* Create subpointMap which marks the submesh */ 2384 ierr = DMLabelCreate("subpoint_map", &subpointMap);CHKERRQ(ierr); 2385 ierr = DMPlexSetSubpointMap(subdm, subpointMap);CHKERRQ(ierr); 2386 ierr = DMLabelDestroy(&subpointMap);CHKERRQ(ierr); 2387 if (vertexLabel) {ierr = DMPlexMarkSubmesh_Interpolated(dm, vertexLabel, value, subpointMap, subdm);CHKERRQ(ierr);} 2388 /* Setup chart */ 2389 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 2390 ierr = PetscMalloc4(dim+1,PetscInt,&numSubPoints,dim+1,PetscInt,&firstSubPoint,dim+1,IS,&subpointIS,dim+1,const PetscInt *,&subpoints);CHKERRQ(ierr); 2391 for (d = 0; d <= dim; ++d) { 2392 ierr = DMLabelGetStratumSize(subpointMap, d, &numSubPoints[d]);CHKERRQ(ierr); 2393 totSubPoints += numSubPoints[d]; 2394 } 2395 ierr = DMPlexSetChart(subdm, 0, totSubPoints);CHKERRQ(ierr); 2396 ierr = DMPlexSetVTKCellHeight(subdm, 1);CHKERRQ(ierr); 2397 /* Set cone sizes */ 2398 firstSubPoint[dim] = 0; 2399 firstSubPoint[0] = firstSubPoint[dim] + numSubPoints[dim]; 2400 if (dim > 1) {firstSubPoint[dim-1] = firstSubPoint[0] + numSubPoints[0];} 2401 if (dim > 2) {firstSubPoint[dim-2] = firstSubPoint[dim-1] + numSubPoints[dim-1];} 2402 for (d = 0; d <= dim; ++d) { 2403 ierr = DMLabelGetStratumIS(subpointMap, d, &subpointIS[d]);CHKERRQ(ierr); 2404 ierr = ISGetIndices(subpointIS[d], &subpoints[d]);CHKERRQ(ierr); 2405 } 2406 for (d = 0; d <= dim; ++d) { 2407 for (p = 0; p < numSubPoints[d]; ++p) { 2408 const PetscInt point = subpoints[d][p]; 2409 const PetscInt subpoint = firstSubPoint[d] + p; 2410 const PetscInt *cone; 2411 PetscInt coneSize, coneSizeNew, c, val; 2412 2413 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 2414 ierr = DMPlexSetConeSize(subdm, subpoint, coneSize);CHKERRQ(ierr); 2415 if (d == dim) { 2416 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 2417 for (c = 0, coneSizeNew = 0; c < coneSize; ++c) { 2418 ierr = DMLabelGetValue(subpointMap, cone[c], &val);CHKERRQ(ierr); 2419 if (val >= 0) coneSizeNew++; 2420 } 2421 ierr = DMPlexSetConeSize(subdm, subpoint, coneSizeNew);CHKERRQ(ierr); 2422 } 2423 } 2424 } 2425 ierr = DMSetUp(subdm);CHKERRQ(ierr); 2426 /* Set cones */ 2427 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, NULL);CHKERRQ(ierr); 2428 ierr = PetscMalloc2(maxConeSize,PetscInt,&coneNew,maxConeSize,PetscInt,&coneONew);CHKERRQ(ierr); 2429 for (d = 0; d <= dim; ++d) { 2430 for (p = 0; p < numSubPoints[d]; ++p) { 2431 const PetscInt point = subpoints[d][p]; 2432 const PetscInt subpoint = firstSubPoint[d] + p; 2433 const PetscInt *cone, *ornt; 2434 PetscInt coneSize, subconeSize, coneSizeNew, c, subc; 2435 2436 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 2437 ierr = DMPlexGetConeSize(subdm, subpoint, &subconeSize);CHKERRQ(ierr); 2438 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 2439 ierr = DMPlexGetConeOrientation(dm, point, &ornt);CHKERRQ(ierr); 2440 for (c = 0, coneSizeNew = 0; c < coneSize; ++c) { 2441 ierr = PetscFindInt(cone[c], numSubPoints[d-1], subpoints[d-1], &subc);CHKERRQ(ierr); 2442 if (subc >= 0) { 2443 coneNew[coneSizeNew] = firstSubPoint[d-1] + subc; 2444 coneONew[coneSizeNew] = ornt[c]; 2445 ++coneSizeNew; 2446 } 2447 } 2448 if (coneSizeNew != subconeSize) SETERRQ2(comm, PETSC_ERR_PLIB, "Number of cone points located %d does not match subcone size %d", coneSizeNew, subconeSize); 2449 ierr = DMPlexSetCone(subdm, subpoint, coneNew);CHKERRQ(ierr); 2450 ierr = DMPlexSetConeOrientation(subdm, subpoint, coneONew);CHKERRQ(ierr); 2451 } 2452 } 2453 ierr = PetscFree2(coneNew,coneONew);CHKERRQ(ierr); 2454 ierr = DMPlexSymmetrize(subdm);CHKERRQ(ierr); 2455 ierr = DMPlexStratify(subdm);CHKERRQ(ierr); 2456 /* Build coordinates */ 2457 { 2458 PetscSection coordSection, subCoordSection; 2459 Vec coordinates, subCoordinates; 2460 PetscScalar *coords, *subCoords; 2461 PetscInt numComp, coordSize; 2462 2463 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2464 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 2465 ierr = DMPlexGetCoordinateSection(subdm, &subCoordSection);CHKERRQ(ierr); 2466 ierr = PetscSectionSetNumFields(subCoordSection, 1);CHKERRQ(ierr); 2467 ierr = PetscSectionGetFieldComponents(coordSection, 0, &numComp);CHKERRQ(ierr); 2468 ierr = PetscSectionSetFieldComponents(subCoordSection, 0, numComp);CHKERRQ(ierr); 2469 ierr = PetscSectionSetChart(subCoordSection, firstSubPoint[0], firstSubPoint[0]+numSubPoints[0]);CHKERRQ(ierr); 2470 for (v = 0; v < numSubPoints[0]; ++v) { 2471 const PetscInt vertex = subpoints[0][v]; 2472 const PetscInt subvertex = firstSubPoint[0]+v; 2473 PetscInt dof; 2474 2475 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2476 ierr = PetscSectionSetDof(subCoordSection, subvertex, dof);CHKERRQ(ierr); 2477 ierr = PetscSectionSetFieldDof(subCoordSection, subvertex, 0, dof);CHKERRQ(ierr); 2478 } 2479 ierr = PetscSectionSetUp(subCoordSection);CHKERRQ(ierr); 2480 ierr = PetscSectionGetStorageSize(subCoordSection, &coordSize);CHKERRQ(ierr); 2481 ierr = VecCreate(comm, &subCoordinates);CHKERRQ(ierr); 2482 ierr = VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2483 ierr = VecSetType(subCoordinates,VECSTANDARD);CHKERRQ(ierr); 2484 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2485 ierr = VecGetArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2486 for (v = 0; v < numSubPoints[0]; ++v) { 2487 const PetscInt vertex = subpoints[0][v]; 2488 const PetscInt subvertex = firstSubPoint[0]+v; 2489 PetscInt dof, off, sdof, soff, d; 2490 2491 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2492 ierr = PetscSectionGetOffset(coordSection, vertex, &off);CHKERRQ(ierr); 2493 ierr = PetscSectionGetDof(subCoordSection, subvertex, &sdof);CHKERRQ(ierr); 2494 ierr = PetscSectionGetOffset(subCoordSection, subvertex, &soff);CHKERRQ(ierr); 2495 if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof); 2496 for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d]; 2497 } 2498 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2499 ierr = VecRestoreArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2500 ierr = DMSetCoordinatesLocal(subdm, subCoordinates);CHKERRQ(ierr); 2501 ierr = VecDestroy(&subCoordinates);CHKERRQ(ierr); 2502 } 2503 /* Cleanup */ 2504 for (d = 0; d <= dim; ++d) { 2505 ierr = ISRestoreIndices(subpointIS[d], &subpoints[d]);CHKERRQ(ierr); 2506 ierr = ISDestroy(&subpointIS[d]);CHKERRQ(ierr); 2507 } 2508 ierr = PetscFree4(numSubPoints,firstSubPoint,subpointIS,subpoints);CHKERRQ(ierr); 2509 PetscFunctionReturn(0); 2510 } 2511 2512 #undef __FUNCT__ 2513 #define __FUNCT__ "DMPlexCreateSubmesh" 2514 /*@ 2515 DMPlexCreateSubmesh - Extract a hypersurface from the mesh using vertices defined by a label 2516 2517 Input Parameters: 2518 + dm - The original mesh 2519 . vertexLabel - The DMLabel marking vertices contained in the surface 2520 - value - The label value to use 2521 2522 Output Parameter: 2523 . subdm - The surface mesh 2524 2525 Note: This function produces a DMLabel mapping original points in the submesh to their depth. This can be obtained using DMPlexGetSubpointMap(). 2526 2527 Level: developer 2528 2529 .seealso: DMPlexGetSubpointMap(), DMPlexGetLabel(), DMLabelSetValue() 2530 @*/ 2531 PetscErrorCode DMPlexCreateSubmesh(DM dm, DMLabel vertexLabel, PetscInt value, DM *subdm) 2532 { 2533 PetscInt dim, depth; 2534 PetscErrorCode ierr; 2535 2536 PetscFunctionBegin; 2537 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2538 PetscValidPointer(subdm, 3); 2539 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 2540 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 2541 ierr = DMCreate(PetscObjectComm((PetscObject)dm), subdm);CHKERRQ(ierr); 2542 ierr = DMSetType(*subdm, DMPLEX);CHKERRQ(ierr); 2543 ierr = DMPlexSetDimension(*subdm, dim-1);CHKERRQ(ierr); 2544 if (depth == dim) { 2545 ierr = DMPlexCreateSubmesh_Interpolated(dm, vertexLabel, value, *subdm);CHKERRQ(ierr); 2546 } else { 2547 ierr = DMPlexCreateSubmesh_Uninterpolated(dm, vertexLabel, value, *subdm);CHKERRQ(ierr); 2548 } 2549 PetscFunctionReturn(0); 2550 } 2551 2552 #undef __FUNCT__ 2553 #define __FUNCT__ "DMPlexFilterPoint_Internal" 2554 PETSC_STATIC_INLINE PetscInt DMPlexFilterPoint_Internal(PetscInt point, PetscInt firstSubPoint, PetscInt numSubPoints, const PetscInt subPoints[]) 2555 { 2556 PetscInt subPoint; 2557 PetscErrorCode ierr; 2558 2559 ierr = PetscFindInt(point, numSubPoints, subPoints, &subPoint); if (ierr < 0) return ierr; 2560 return subPoint < 0 ? subPoint : firstSubPoint+subPoint; 2561 } 2562 2563 #undef __FUNCT__ 2564 #define __FUNCT__ "DMPlexCreateCohesiveSubmesh_Uninterpolated" 2565 static PetscErrorCode DMPlexCreateCohesiveSubmesh_Uninterpolated(DM dm, PetscBool hasLagrange, const char label[], PetscInt value, DM subdm) 2566 { 2567 MPI_Comm comm; 2568 DMLabel subpointMap; 2569 IS subvertexIS; 2570 const PetscInt *subVertices; 2571 PetscInt numSubVertices, firstSubVertex, numSubCells, *subCells = NULL; 2572 PetscInt *subface, maxConeSize, numSubFaces, firstSubFace, newFacePoint, nFV; 2573 PetscInt cMax, c, f; 2574 PetscErrorCode ierr; 2575 2576 PetscFunctionBegin; 2577 ierr = PetscObjectGetComm((PetscObject)dm, &comm);CHKERRQ(ierr); 2578 /* Create subpointMap which marks the submesh */ 2579 ierr = DMLabelCreate("subpoint_map", &subpointMap);CHKERRQ(ierr); 2580 ierr = DMPlexSetSubpointMap(subdm, subpointMap);CHKERRQ(ierr); 2581 ierr = DMLabelDestroy(&subpointMap);CHKERRQ(ierr); 2582 ierr = DMPlexMarkCohesiveSubmesh_Uninterpolated(dm, hasLagrange, label, value, subpointMap, &numSubFaces, &nFV, &subCells, subdm);CHKERRQ(ierr); 2583 /* Setup chart */ 2584 ierr = DMLabelGetStratumSize(subpointMap, 0, &numSubVertices);CHKERRQ(ierr); 2585 ierr = DMLabelGetStratumSize(subpointMap, 2, &numSubCells);CHKERRQ(ierr); 2586 ierr = DMPlexSetChart(subdm, 0, numSubCells+numSubFaces+numSubVertices);CHKERRQ(ierr); 2587 ierr = DMPlexSetVTKCellHeight(subdm, 1);CHKERRQ(ierr); 2588 /* Set cone sizes */ 2589 firstSubVertex = numSubCells; 2590 firstSubFace = numSubCells+numSubVertices; 2591 newFacePoint = firstSubFace; 2592 ierr = DMLabelGetStratumIS(subpointMap, 0, &subvertexIS);CHKERRQ(ierr); 2593 if (subvertexIS) {ierr = ISGetIndices(subvertexIS, &subVertices);CHKERRQ(ierr);} 2594 for (c = 0; c < numSubCells; ++c) { 2595 ierr = DMPlexSetConeSize(subdm, c, 1);CHKERRQ(ierr); 2596 } 2597 for (f = firstSubFace; f < firstSubFace+numSubFaces; ++f) { 2598 ierr = DMPlexSetConeSize(subdm, f, nFV);CHKERRQ(ierr); 2599 } 2600 ierr = DMSetUp(subdm);CHKERRQ(ierr); 2601 /* Create face cones */ 2602 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, NULL);CHKERRQ(ierr); 2603 ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); 2604 ierr = DMGetWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);CHKERRQ(ierr); 2605 for (c = 0; c < numSubCells; ++c) { 2606 const PetscInt cell = subCells[c]; 2607 const PetscInt subcell = c; 2608 const PetscInt *cone, *cells; 2609 PetscInt numCells, subVertex, p, v; 2610 2611 if (cell < cMax) continue; 2612 ierr = DMPlexGetCone(dm, cell, &cone);CHKERRQ(ierr); 2613 for (v = 0; v < nFV; ++v) { 2614 ierr = PetscFindInt(cone[v], numSubVertices, subVertices, &subVertex);CHKERRQ(ierr); 2615 subface[v] = firstSubVertex+subVertex; 2616 } 2617 ierr = DMPlexSetCone(subdm, newFacePoint, subface);CHKERRQ(ierr); 2618 ierr = DMPlexSetCone(subdm, subcell, &newFacePoint);CHKERRQ(ierr); 2619 ierr = DMPlexGetJoin(dm, nFV, cone, &numCells, &cells);CHKERRQ(ierr); 2620 /* Not true in parallel 2621 if (numCells != 2) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cohesive cells should separate two cells"); */ 2622 for (p = 0; p < numCells; ++p) { 2623 PetscInt negsubcell; 2624 2625 if (cells[p] >= cMax) continue; 2626 /* I know this is a crap search */ 2627 for (negsubcell = 0; negsubcell < numSubCells; ++negsubcell) { 2628 if (subCells[negsubcell] == cells[p]) break; 2629 } 2630 if (negsubcell == numSubCells) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not find negative face neighbor for cohesive cell %d", cell); 2631 ierr = DMPlexSetCone(subdm, negsubcell, &newFacePoint);CHKERRQ(ierr); 2632 } 2633 ierr = DMPlexRestoreJoin(dm, nFV, cone, &numCells, &cells);CHKERRQ(ierr); 2634 ++newFacePoint; 2635 } 2636 ierr = DMRestoreWorkArray(subdm, maxConeSize, PETSC_INT, (void**) &subface);CHKERRQ(ierr); 2637 ierr = DMPlexSymmetrize(subdm);CHKERRQ(ierr); 2638 ierr = DMPlexStratify(subdm);CHKERRQ(ierr); 2639 /* Build coordinates */ 2640 { 2641 PetscSection coordSection, subCoordSection; 2642 Vec coordinates, subCoordinates; 2643 PetscScalar *coords, *subCoords; 2644 PetscInt numComp, coordSize, v; 2645 2646 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2647 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 2648 ierr = DMPlexGetCoordinateSection(subdm, &subCoordSection);CHKERRQ(ierr); 2649 ierr = PetscSectionSetNumFields(subCoordSection, 1);CHKERRQ(ierr); 2650 ierr = PetscSectionGetFieldComponents(coordSection, 0, &numComp);CHKERRQ(ierr); 2651 ierr = PetscSectionSetFieldComponents(subCoordSection, 0, numComp);CHKERRQ(ierr); 2652 ierr = PetscSectionSetChart(subCoordSection, firstSubVertex, firstSubVertex+numSubVertices);CHKERRQ(ierr); 2653 for (v = 0; v < numSubVertices; ++v) { 2654 const PetscInt vertex = subVertices[v]; 2655 const PetscInt subvertex = firstSubVertex+v; 2656 PetscInt dof; 2657 2658 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2659 ierr = PetscSectionSetDof(subCoordSection, subvertex, dof);CHKERRQ(ierr); 2660 ierr = PetscSectionSetFieldDof(subCoordSection, subvertex, 0, dof);CHKERRQ(ierr); 2661 } 2662 ierr = PetscSectionSetUp(subCoordSection);CHKERRQ(ierr); 2663 ierr = PetscSectionGetStorageSize(subCoordSection, &coordSize);CHKERRQ(ierr); 2664 ierr = VecCreate(comm, &subCoordinates);CHKERRQ(ierr); 2665 ierr = VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2666 ierr = VecSetType(subCoordinates,VECSTANDARD);CHKERRQ(ierr); 2667 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2668 ierr = VecGetArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2669 for (v = 0; v < numSubVertices; ++v) { 2670 const PetscInt vertex = subVertices[v]; 2671 const PetscInt subvertex = firstSubVertex+v; 2672 PetscInt dof, off, sdof, soff, d; 2673 2674 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2675 ierr = PetscSectionGetOffset(coordSection, vertex, &off);CHKERRQ(ierr); 2676 ierr = PetscSectionGetDof(subCoordSection, subvertex, &sdof);CHKERRQ(ierr); 2677 ierr = PetscSectionGetOffset(subCoordSection, subvertex, &soff);CHKERRQ(ierr); 2678 if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof); 2679 for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d]; 2680 } 2681 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2682 ierr = VecRestoreArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2683 ierr = DMSetCoordinatesLocal(subdm, subCoordinates);CHKERRQ(ierr); 2684 ierr = VecDestroy(&subCoordinates);CHKERRQ(ierr); 2685 } 2686 /* Build SF */ 2687 CHKMEMQ; 2688 { 2689 PetscSF sfPoint, sfPointSub; 2690 const PetscSFNode *remotePoints; 2691 PetscSFNode *sremotePoints, *newLocalPoints, *newOwners; 2692 const PetscInt *localPoints; 2693 PetscInt *slocalPoints; 2694 PetscInt numRoots, numLeaves, numSubRoots = numSubCells+numSubFaces+numSubVertices, numSubLeaves = 0, l, sl, ll, pStart, pEnd, p, vStart, vEnd; 2695 PetscMPIInt rank; 2696 2697 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRQ(ierr); 2698 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 2699 ierr = DMGetPointSF(subdm, &sfPointSub);CHKERRQ(ierr); 2700 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 2701 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 2702 ierr = PetscSFGetGraph(sfPoint, &numRoots, &numLeaves, &localPoints, &remotePoints);CHKERRQ(ierr); 2703 if (numRoots >= 0) { 2704 /* Only vertices should be shared */ 2705 ierr = PetscMalloc2(pEnd-pStart,PetscSFNode,&newLocalPoints,numRoots,PetscSFNode,&newOwners);CHKERRQ(ierr); 2706 for (p = 0; p < pEnd-pStart; ++p) { 2707 newLocalPoints[p].rank = -2; 2708 newLocalPoints[p].index = -2; 2709 } 2710 /* Set subleaves */ 2711 for (l = 0; l < numLeaves; ++l) { 2712 const PetscInt point = localPoints[l]; 2713 const PetscInt subPoint = DMPlexFilterPoint_Internal(point, firstSubVertex, numSubVertices, subVertices); 2714 2715 if ((point < vStart) && (point >= vEnd)) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Should not be mapping anything but vertices, %d", point); 2716 if (subPoint < 0) continue; 2717 newLocalPoints[point-pStart].rank = rank; 2718 newLocalPoints[point-pStart].index = subPoint; 2719 ++numSubLeaves; 2720 } 2721 /* Must put in owned subpoints */ 2722 for (p = pStart; p < pEnd; ++p) { 2723 const PetscInt subPoint = DMPlexFilterPoint_Internal(p, firstSubVertex, numSubVertices, subVertices); 2724 2725 if (subPoint < 0) { 2726 newOwners[p-pStart].rank = -3; 2727 newOwners[p-pStart].index = -3; 2728 } else { 2729 newOwners[p-pStart].rank = rank; 2730 newOwners[p-pStart].index = subPoint; 2731 } 2732 } 2733 ierr = PetscSFReduceBegin(sfPoint, MPIU_2INT, newLocalPoints, newOwners, MPI_MAXLOC);CHKERRQ(ierr); 2734 ierr = PetscSFReduceEnd(sfPoint, MPIU_2INT, newLocalPoints, newOwners, MPI_MAXLOC);CHKERRQ(ierr); 2735 ierr = PetscSFBcastBegin(sfPoint, MPIU_2INT, newOwners, newLocalPoints);CHKERRQ(ierr); 2736 ierr = PetscSFBcastEnd(sfPoint, MPIU_2INT, newOwners, newLocalPoints);CHKERRQ(ierr); 2737 ierr = PetscMalloc(numSubLeaves * sizeof(PetscInt), &slocalPoints);CHKERRQ(ierr); 2738 ierr = PetscMalloc(numSubLeaves * sizeof(PetscSFNode), &sremotePoints);CHKERRQ(ierr); 2739 for (l = 0, sl = 0, ll = 0; l < numLeaves; ++l) { 2740 const PetscInt point = localPoints[l]; 2741 const PetscInt subPoint = DMPlexFilterPoint_Internal(point, firstSubVertex, numSubVertices, subVertices); 2742 2743 if (subPoint < 0) continue; 2744 if (newLocalPoints[point].rank == rank) {++ll; continue;} 2745 slocalPoints[sl] = subPoint; 2746 sremotePoints[sl].rank = newLocalPoints[point].rank; 2747 sremotePoints[sl].index = newLocalPoints[point].index; 2748 if (sremotePoints[sl].rank < 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid remote rank for local point %d", point); 2749 if (sremotePoints[sl].index < 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid remote subpoint for local point %d", point); 2750 ++sl; 2751 } 2752 ierr = PetscFree2(newLocalPoints,newOwners);CHKERRQ(ierr); 2753 if (sl + ll != numSubLeaves) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Mismatch in number of subleaves %d + %d != %d", sl, ll, numSubLeaves); 2754 ierr = PetscSFSetGraph(sfPointSub, numSubRoots, sl, slocalPoints, PETSC_OWN_POINTER, sremotePoints, PETSC_OWN_POINTER);CHKERRQ(ierr); 2755 } 2756 } 2757 CHKMEMQ; 2758 /* Cleanup */ 2759 if (subvertexIS) {ierr = ISRestoreIndices(subvertexIS, &subVertices);CHKERRQ(ierr);} 2760 ierr = ISDestroy(&subvertexIS);CHKERRQ(ierr); 2761 ierr = PetscFree(subCells);CHKERRQ(ierr); 2762 PetscFunctionReturn(0); 2763 } 2764 2765 #undef __FUNCT__ 2766 #define __FUNCT__ "DMPlexCreateCohesiveSubmesh_Interpolated" 2767 static PetscErrorCode DMPlexCreateCohesiveSubmesh_Interpolated(DM dm, const char label[], PetscInt value, DM subdm) 2768 { 2769 MPI_Comm comm; 2770 DMLabel subpointMap; 2771 IS *subpointIS; 2772 const PetscInt **subpoints; 2773 PetscInt *numSubPoints, *firstSubPoint, *coneNew; 2774 PetscInt totSubPoints = 0, maxConeSize, dim, p, d, v; 2775 PetscErrorCode ierr; 2776 2777 PetscFunctionBegin; 2778 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 2779 /* Create subpointMap which marks the submesh */ 2780 ierr = DMLabelCreate("subpoint_map", &subpointMap);CHKERRQ(ierr); 2781 ierr = DMPlexSetSubpointMap(subdm, subpointMap);CHKERRQ(ierr); 2782 ierr = DMLabelDestroy(&subpointMap);CHKERRQ(ierr); 2783 ierr = DMPlexMarkCohesiveSubmesh_Interpolated(dm, label, value, subpointMap, subdm);CHKERRQ(ierr); 2784 /* Setup chart */ 2785 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 2786 ierr = PetscMalloc4(dim+1,PetscInt,&numSubPoints,dim+1,PetscInt,&firstSubPoint,dim+1,IS,&subpointIS,dim+1,const PetscInt *,&subpoints);CHKERRQ(ierr); 2787 for (d = 0; d <= dim; ++d) { 2788 ierr = DMLabelGetStratumSize(subpointMap, d, &numSubPoints[d]);CHKERRQ(ierr); 2789 totSubPoints += numSubPoints[d]; 2790 } 2791 ierr = DMPlexSetChart(subdm, 0, totSubPoints);CHKERRQ(ierr); 2792 ierr = DMPlexSetVTKCellHeight(subdm, 1);CHKERRQ(ierr); 2793 /* Set cone sizes */ 2794 firstSubPoint[dim] = 0; 2795 firstSubPoint[0] = firstSubPoint[dim] + numSubPoints[dim]; 2796 if (dim > 1) {firstSubPoint[dim-1] = firstSubPoint[0] + numSubPoints[0];} 2797 if (dim > 2) {firstSubPoint[dim-2] = firstSubPoint[dim-1] + numSubPoints[dim-1];} 2798 for (d = 0; d <= dim; ++d) { 2799 ierr = DMLabelGetStratumIS(subpointMap, d, &subpointIS[d]);CHKERRQ(ierr); 2800 ierr = ISGetIndices(subpointIS[d], &subpoints[d]);CHKERRQ(ierr); 2801 } 2802 for (d = 0; d <= dim; ++d) { 2803 for (p = 0; p < numSubPoints[d]; ++p) { 2804 const PetscInt point = subpoints[d][p]; 2805 const PetscInt subpoint = firstSubPoint[d] + p; 2806 const PetscInt *cone; 2807 PetscInt coneSize, coneSizeNew, c, val; 2808 2809 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 2810 ierr = DMPlexSetConeSize(subdm, subpoint, coneSize);CHKERRQ(ierr); 2811 if (d == dim) { 2812 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 2813 for (c = 0, coneSizeNew = 0; c < coneSize; ++c) { 2814 ierr = DMLabelGetValue(subpointMap, cone[c], &val);CHKERRQ(ierr); 2815 if (val >= 0) coneSizeNew++; 2816 } 2817 ierr = DMPlexSetConeSize(subdm, subpoint, coneSizeNew);CHKERRQ(ierr); 2818 } 2819 } 2820 } 2821 ierr = DMSetUp(subdm);CHKERRQ(ierr); 2822 /* Set cones */ 2823 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, NULL);CHKERRQ(ierr); 2824 ierr = PetscMalloc(maxConeSize * sizeof(PetscInt), &coneNew);CHKERRQ(ierr); 2825 for (d = 0; d <= dim; ++d) { 2826 for (p = 0; p < numSubPoints[d]; ++p) { 2827 const PetscInt point = subpoints[d][p]; 2828 const PetscInt subpoint = firstSubPoint[d] + p; 2829 const PetscInt *cone; 2830 PetscInt coneSize, subconeSize, coneSizeNew, c, subc; 2831 2832 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 2833 ierr = DMPlexGetConeSize(subdm, subpoint, &subconeSize);CHKERRQ(ierr); 2834 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 2835 for (c = 0, coneSizeNew = 0; c < coneSize; ++c) { 2836 ierr = PetscFindInt(cone[c], numSubPoints[d-1], subpoints[d-1], &subc);CHKERRQ(ierr); 2837 if (subc >= 0) coneNew[coneSizeNew++] = firstSubPoint[d-1] + subc; 2838 } 2839 if (coneSizeNew != subconeSize) SETERRQ2(comm, PETSC_ERR_PLIB, "Number of cone points located %d does not match subcone size %d", coneSizeNew, subconeSize); 2840 ierr = DMPlexSetCone(subdm, subpoint, coneNew);CHKERRQ(ierr); 2841 } 2842 } 2843 ierr = PetscFree(coneNew);CHKERRQ(ierr); 2844 ierr = DMPlexSymmetrize(subdm);CHKERRQ(ierr); 2845 ierr = DMPlexStratify(subdm);CHKERRQ(ierr); 2846 /* Build coordinates */ 2847 { 2848 PetscSection coordSection, subCoordSection; 2849 Vec coordinates, subCoordinates; 2850 PetscScalar *coords, *subCoords; 2851 PetscInt numComp, coordSize; 2852 2853 ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2854 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 2855 ierr = DMPlexGetCoordinateSection(subdm, &subCoordSection);CHKERRQ(ierr); 2856 ierr = PetscSectionSetNumFields(subCoordSection, 1);CHKERRQ(ierr); 2857 ierr = PetscSectionGetFieldComponents(coordSection, 0, &numComp);CHKERRQ(ierr); 2858 ierr = PetscSectionSetFieldComponents(subCoordSection, 0, numComp);CHKERRQ(ierr); 2859 ierr = PetscSectionSetChart(subCoordSection, firstSubPoint[0], firstSubPoint[0]+numSubPoints[0]);CHKERRQ(ierr); 2860 for (v = 0; v < numSubPoints[0]; ++v) { 2861 const PetscInt vertex = subpoints[0][v]; 2862 const PetscInt subvertex = firstSubPoint[0]+v; 2863 PetscInt dof; 2864 2865 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2866 ierr = PetscSectionSetDof(subCoordSection, subvertex, dof);CHKERRQ(ierr); 2867 ierr = PetscSectionSetFieldDof(subCoordSection, subvertex, 0, dof);CHKERRQ(ierr); 2868 } 2869 ierr = PetscSectionSetUp(subCoordSection);CHKERRQ(ierr); 2870 ierr = PetscSectionGetStorageSize(subCoordSection, &coordSize);CHKERRQ(ierr); 2871 ierr = VecCreate(comm, &subCoordinates);CHKERRQ(ierr); 2872 ierr = VecSetSizes(subCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2873 ierr = VecSetType(subCoordinates,VECSTANDARD);CHKERRQ(ierr); 2874 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2875 ierr = VecGetArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2876 for (v = 0; v < numSubPoints[0]; ++v) { 2877 const PetscInt vertex = subpoints[0][v]; 2878 const PetscInt subvertex = firstSubPoint[0]+v; 2879 PetscInt dof, off, sdof, soff, d; 2880 2881 ierr = PetscSectionGetDof(coordSection, vertex, &dof);CHKERRQ(ierr); 2882 ierr = PetscSectionGetOffset(coordSection, vertex, &off);CHKERRQ(ierr); 2883 ierr = PetscSectionGetDof(subCoordSection, subvertex, &sdof);CHKERRQ(ierr); 2884 ierr = PetscSectionGetOffset(subCoordSection, subvertex, &soff);CHKERRQ(ierr); 2885 if (dof != sdof) SETERRQ4(comm, PETSC_ERR_PLIB, "Coordinate dimension %d on subvertex %d, vertex %d should be %d", sdof, subvertex, vertex, dof); 2886 for (d = 0; d < dof; ++d) subCoords[soff+d] = coords[off+d]; 2887 } 2888 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2889 ierr = VecRestoreArray(subCoordinates, &subCoords);CHKERRQ(ierr); 2890 ierr = DMSetCoordinatesLocal(subdm, subCoordinates);CHKERRQ(ierr); 2891 ierr = VecDestroy(&subCoordinates);CHKERRQ(ierr); 2892 } 2893 /* Cleanup */ 2894 for (d = 0; d <= dim; ++d) { 2895 ierr = ISRestoreIndices(subpointIS[d], &subpoints[d]);CHKERRQ(ierr); 2896 ierr = ISDestroy(&subpointIS[d]);CHKERRQ(ierr); 2897 } 2898 ierr = PetscFree4(numSubPoints,firstSubPoint,subpointIS,subpoints);CHKERRQ(ierr); 2899 PetscFunctionReturn(0); 2900 } 2901 2902 #undef __FUNCT__ 2903 #define __FUNCT__ "DMPlexCreateCohesiveSubmesh" 2904 /* 2905 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. 2906 2907 Input Parameters: 2908 + dm - The original mesh 2909 . hasLagrange - The mesh has Lagrange unknowns in the cohesive cells 2910 . label - A label name, or PETSC_NULL 2911 - value - A label value 2912 2913 Output Parameter: 2914 . subdm - The surface mesh 2915 2916 Note: This function produces a DMLabel mapping original points in the submesh to their depth. This can be obtained using DMPlexGetSubpointMap(). 2917 2918 Level: developer 2919 2920 .seealso: DMPlexGetSubpointMap(), DMPlexCreateSubmesh() 2921 */ 2922 PetscErrorCode DMPlexCreateCohesiveSubmesh(DM dm, PetscBool hasLagrange, const char label[], PetscInt value, DM *subdm) 2923 { 2924 PetscInt dim, depth; 2925 PetscErrorCode ierr; 2926 2927 PetscFunctionBegin; 2928 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2929 PetscValidPointer(subdm, 5); 2930 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 2931 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 2932 ierr = DMCreate(PetscObjectComm((PetscObject)dm), subdm);CHKERRQ(ierr); 2933 ierr = DMSetType(*subdm, DMPLEX);CHKERRQ(ierr); 2934 ierr = DMPlexSetDimension(*subdm, dim-1);CHKERRQ(ierr); 2935 if (depth == dim) { 2936 ierr = DMPlexCreateCohesiveSubmesh_Interpolated(dm, label, value, *subdm);CHKERRQ(ierr); 2937 } else { 2938 ierr = DMPlexCreateCohesiveSubmesh_Uninterpolated(dm, hasLagrange, label, value, *subdm);CHKERRQ(ierr); 2939 } 2940 PetscFunctionReturn(0); 2941 } 2942 2943 #undef __FUNCT__ 2944 #define __FUNCT__ "DMPlexGetSubpointMap" 2945 /*@ 2946 DMPlexGetSubpointMap - Returns a DMLabel with point dimension as values 2947 2948 Input Parameter: 2949 . dm - The submesh DM 2950 2951 Output Parameter: 2952 . subpointMap - The DMLabel of all the points from the original mesh in this submesh, or NULL if this is not a submesh 2953 2954 Level: developer 2955 2956 .seealso: DMPlexCreateSubmesh(), DMPlexCreateSubpointIS() 2957 @*/ 2958 PetscErrorCode DMPlexGetSubpointMap(DM dm, DMLabel *subpointMap) 2959 { 2960 DM_Plex *mesh = (DM_Plex*) dm->data; 2961 2962 PetscFunctionBegin; 2963 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2964 PetscValidPointer(subpointMap, 2); 2965 *subpointMap = mesh->subpointMap; 2966 PetscFunctionReturn(0); 2967 } 2968 2969 #undef __FUNCT__ 2970 #define __FUNCT__ "DMPlexSetSubpointMap" 2971 /* Note: Should normally not be called by the user, since it is set in DMPlexCreateSubmesh() */ 2972 PetscErrorCode DMPlexSetSubpointMap(DM dm, DMLabel subpointMap) 2973 { 2974 DM_Plex *mesh = (DM_Plex *) dm->data; 2975 DMLabel tmp; 2976 PetscErrorCode ierr; 2977 2978 PetscFunctionBegin; 2979 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2980 tmp = mesh->subpointMap; 2981 mesh->subpointMap = subpointMap; 2982 ++mesh->subpointMap->refct; 2983 ierr = DMLabelDestroy(&tmp);CHKERRQ(ierr); 2984 PetscFunctionReturn(0); 2985 } 2986 2987 #undef __FUNCT__ 2988 #define __FUNCT__ "DMPlexCreateSubpointIS" 2989 /*@ 2990 DMPlexCreateSubpointIS - Creates an IS covering the entire subdm chart with the original points as data 2991 2992 Input Parameter: 2993 . dm - The submesh DM 2994 2995 Output Parameter: 2996 . subpointIS - The IS of all the points from the original mesh in this submesh, or NULL if this is not a submesh 2997 2998 Note: This is IS is guaranteed to be sorted by the construction of the submesh 2999 3000 Level: developer 3001 3002 .seealso: DMPlexCreateSubmesh(), DMPlexGetSubpointMap() 3003 @*/ 3004 PetscErrorCode DMPlexCreateSubpointIS(DM dm, IS *subpointIS) 3005 { 3006 MPI_Comm comm; 3007 DMLabel subpointMap; 3008 IS is; 3009 const PetscInt *opoints; 3010 PetscInt *points, *depths; 3011 PetscInt depth, depStart, depEnd, d, pStart, pEnd, p, n, off; 3012 PetscErrorCode ierr; 3013 3014 PetscFunctionBegin; 3015 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3016 PetscValidPointer(subpointIS, 2); 3017 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 3018 *subpointIS = NULL; 3019 ierr = DMPlexGetSubpointMap(dm, &subpointMap);CHKERRQ(ierr); 3020 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 3021 if (subpointMap && depth >= 0) { 3022 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 3023 if (pStart) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Submeshes must start the point numbering at 0, not %d", pStart); 3024 ierr = DMGetWorkArray(dm, depth+1, PETSC_INT, &depths);CHKERRQ(ierr); 3025 depths[0] = depth; 3026 depths[1] = 0; 3027 for(d = 2; d <= depth; ++d) {depths[d] = depth+1 - d;} 3028 ierr = PetscMalloc(pEnd * sizeof(PetscInt), &points);CHKERRQ(ierr); 3029 for(d = 0, off = 0; d <= depth; ++d) { 3030 const PetscInt dep = depths[d]; 3031 3032 ierr = DMPlexGetDepthStratum(dm, dep, &depStart, &depEnd);CHKERRQ(ierr); 3033 ierr = DMLabelGetStratumSize(subpointMap, dep, &n);CHKERRQ(ierr); 3034 if (((d < 2) && (depth > 1)) || (d == 1)) { /* Only check vertices and cells for now since the map is broken for others */ 3035 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); 3036 } else { 3037 if (!n) { 3038 if (d == 0) { 3039 /* Missing cells */ 3040 for(p = 0; p < depEnd-depStart; ++p, ++off) points[off] = -1; 3041 } else { 3042 /* Missing faces */ 3043 for(p = 0; p < depEnd-depStart; ++p, ++off) points[off] = PETSC_MAX_INT; 3044 } 3045 } 3046 } 3047 if (n) { 3048 ierr = DMLabelGetStratumIS(subpointMap, dep, &is);CHKERRQ(ierr); 3049 ierr = ISGetIndices(is, &opoints);CHKERRQ(ierr); 3050 for(p = 0; p < n; ++p, ++off) points[off] = opoints[p]; 3051 ierr = ISRestoreIndices(is, &opoints);CHKERRQ(ierr); 3052 ierr = ISDestroy(&is);CHKERRQ(ierr); 3053 } 3054 } 3055 ierr = DMRestoreWorkArray(dm, depth+1, PETSC_INT, &depths);CHKERRQ(ierr); 3056 if (off != pEnd) SETERRQ2(comm, PETSC_ERR_ARG_WRONG, "The number of mapped submesh points %d should be %d", off, pEnd); 3057 ierr = ISCreateGeneral(PETSC_COMM_SELF, pEnd, points, PETSC_OWN_POINTER, subpointIS);CHKERRQ(ierr); 3058 } 3059 PetscFunctionReturn(0); 3060 } 3061