1 #include <petsc/private/dmpleximpl.h> /*I "petscdmplex.h" I*/ 2 #include <../src/sys/utils/hash.h> 3 #include <petsc/private/isimpl.h> 4 #include <petsc/private/petscfeimpl.h> 5 #include <petscsf.h> 6 #include <petscds.h> 7 8 /** hierarchy routines */ 9 10 #undef __FUNCT__ 11 #define __FUNCT__ "DMPlexSetReferenceTree" 12 /*@ 13 DMPlexSetReferenceTree - set the reference tree for hierarchically non-conforming meshes. 14 15 Not collective 16 17 Input Parameters: 18 + dm - The DMPlex object 19 - ref - The reference tree DMPlex object 20 21 Level: intermediate 22 23 .seealso: DMPlexGetReferenceTree(), DMPlexCreateDefaultReferenceTree() 24 @*/ 25 PetscErrorCode DMPlexSetReferenceTree(DM dm, DM ref) 26 { 27 DM_Plex *mesh = (DM_Plex *)dm->data; 28 PetscErrorCode ierr; 29 30 PetscFunctionBegin; 31 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 32 if (ref) {PetscValidHeaderSpecific(ref, DM_CLASSID, 2);} 33 ierr = PetscObjectReference((PetscObject)ref);CHKERRQ(ierr); 34 ierr = DMDestroy(&mesh->referenceTree);CHKERRQ(ierr); 35 mesh->referenceTree = ref; 36 PetscFunctionReturn(0); 37 } 38 39 #undef __FUNCT__ 40 #define __FUNCT__ "DMPlexGetReferenceTree" 41 /*@ 42 DMPlexGetReferenceTree - get the reference tree for hierarchically non-conforming meshes. 43 44 Not collective 45 46 Input Parameters: 47 . dm - The DMPlex object 48 49 Output Parameters 50 . ref - The reference tree DMPlex object 51 52 Level: intermediate 53 54 .seealso: DMPlexSetReferenceTree(), DMPlexCreateDefaultReferenceTree() 55 @*/ 56 PetscErrorCode DMPlexGetReferenceTree(DM dm, DM *ref) 57 { 58 DM_Plex *mesh = (DM_Plex *)dm->data; 59 60 PetscFunctionBegin; 61 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 62 PetscValidPointer(ref,2); 63 *ref = mesh->referenceTree; 64 PetscFunctionReturn(0); 65 } 66 67 #undef __FUNCT__ 68 #define __FUNCT__ "DMPlexReferenceTreeGetChildSymmetry_Default" 69 static PetscErrorCode DMPlexReferenceTreeGetChildSymmetry_Default(DM dm, PetscInt parent, PetscInt parentOrientA, PetscInt childOrientA, PetscInt childA, PetscInt parentOrientB, PetscInt *childOrientB, PetscInt *childB) 70 { 71 PetscInt coneSize, dStart, dEnd, dim, ABswap, oAvert, oBvert, ABswapVert; 72 PetscErrorCode ierr; 73 74 PetscFunctionBegin; 75 if (parentOrientA == parentOrientB) { 76 if (childOrientB) *childOrientB = childOrientA; 77 if (childB) *childB = childA; 78 PetscFunctionReturn(0); 79 } 80 for (dim = 0; dim < 3; dim++) { 81 ierr = DMPlexGetDepthStratum(dm,dim,&dStart,&dEnd);CHKERRQ(ierr); 82 if (parent >= dStart && parent <= dEnd) { 83 break; 84 } 85 } 86 if (dim > 2) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Cannot perform child symmetry for %d-cells",dim); 87 if (!dim) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"A vertex has no children"); 88 if (childA < dStart || childA >= dEnd) { 89 /* this is a lower-dimensional child: bootstrap */ 90 PetscInt size, i, sA = -1, sB, sOrientB, sConeSize; 91 const PetscInt *supp, *coneA, *coneB, *oA, *oB; 92 93 ierr = DMPlexGetSupportSize(dm,childA,&size);CHKERRQ(ierr); 94 ierr = DMPlexGetSupport(dm,childA,&supp);CHKERRQ(ierr); 95 96 /* find a point sA in supp(childA) that has the same parent */ 97 for (i = 0; i < size; i++) { 98 PetscInt sParent; 99 100 sA = supp[i]; 101 if (sA == parent) continue; 102 ierr = DMPlexGetTreeParent(dm,sA,&sParent,NULL);CHKERRQ(ierr); 103 if (sParent == parent) { 104 break; 105 } 106 } 107 if (i == size) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"could not find support in children"); 108 /* find out which point sB is in an equivalent position to sA under 109 * parentOrientB */ 110 ierr = DMPlexReferenceTreeGetChildSymmetry_Default(dm,parent,parentOrientA,0,sA,parentOrientB,&sOrientB,&sB);CHKERRQ(ierr); 111 ierr = DMPlexGetConeSize(dm,sA,&sConeSize);CHKERRQ(ierr); 112 ierr = DMPlexGetCone(dm,sA,&coneA);CHKERRQ(ierr); 113 ierr = DMPlexGetCone(dm,sB,&coneB);CHKERRQ(ierr); 114 ierr = DMPlexGetConeOrientation(dm,sA,&oA);CHKERRQ(ierr); 115 ierr = DMPlexGetConeOrientation(dm,sB,&oB);CHKERRQ(ierr); 116 /* step through the cone of sA in natural order */ 117 for (i = 0; i < sConeSize; i++) { 118 if (coneA[i] == childA) { 119 /* if childA is at position i in coneA, 120 * then we want the point that is at sOrientB*i in coneB */ 121 PetscInt j = (sOrientB >= 0) ? ((sOrientB + i) % sConeSize) : ((sConeSize -(sOrientB+1) - i) % sConeSize); 122 if (childB) *childB = coneB[j]; 123 if (childOrientB) { 124 PetscInt oBtrue; 125 126 ierr = DMPlexGetConeSize(dm,childA,&coneSize);CHKERRQ(ierr); 127 /* compose sOrientB and oB[j] */ 128 if (coneSize != 0 && coneSize != 2) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Expected a vertex or an edge"); 129 /* we may have to flip an edge */ 130 oBtrue = coneSize ? ((sOrientB >= 0) ? oB[j] : -(oB[j] + 2)) : 0; 131 ABswap = DihedralSwap(coneSize,oA[i],oBtrue);CHKERRQ(ierr); 132 *childOrientB = DihedralCompose(coneSize,childOrientA,ABswap); 133 } 134 break; 135 } 136 } 137 if (i == sConeSize) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"support cone mismatch"); 138 PetscFunctionReturn(0); 139 } 140 /* get the cone size and symmetry swap */ 141 ierr = DMPlexGetConeSize(dm,parent,&coneSize);CHKERRQ(ierr); 142 ABswap = DihedralSwap(coneSize, parentOrientA, parentOrientB); 143 if (dim == 2) { 144 /* orientations refer to cones: we want them to refer to vertices: 145 * if it's a rotation, they are the same, but if the order is reversed, a 146 * permutation that puts side i first does *not* put vertex i first */ 147 oAvert = (parentOrientA >= 0) ? parentOrientA : -((-parentOrientA % coneSize) + 1); 148 oBvert = (parentOrientB >= 0) ? parentOrientB : -((-parentOrientB % coneSize) + 1); 149 ABswapVert = DihedralSwap(coneSize, oAvert, oBvert); 150 } 151 else { 152 oAvert = parentOrientA; 153 oBvert = parentOrientB; 154 ABswapVert = ABswap; 155 } 156 if (childB) { 157 /* assume that each child corresponds to a vertex, in the same order */ 158 PetscInt p, posA = -1, numChildren, i; 159 const PetscInt *children; 160 161 /* count which position the child is in */ 162 ierr = DMPlexGetTreeChildren(dm,parent,&numChildren,&children);CHKERRQ(ierr); 163 for (i = 0; i < numChildren; i++) { 164 p = children[i]; 165 if (p == childA) { 166 posA = i; 167 break; 168 } 169 } 170 if (posA >= coneSize) { 171 /* this is the triangle in the middle of a uniformly refined triangle: it 172 * is invariant */ 173 if (dim != 2 || posA != 3) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Expected a middle triangle, got something else"); 174 *childB = childA; 175 } 176 else { 177 /* figure out position B by applying ABswapVert */ 178 PetscInt posB; 179 180 posB = (ABswapVert >= 0) ? ((ABswapVert + posA) % coneSize) : ((coneSize -(ABswapVert + 1) - posA) % coneSize); 181 if (childB) *childB = children[posB]; 182 } 183 } 184 if (childOrientB) *childOrientB = DihedralCompose(coneSize,childOrientA,ABswap); 185 PetscFunctionReturn(0); 186 } 187 188 #undef __FUNCT__ 189 #define __FUNCT__ "DMPlexReferenceTreeGetChildSymmetry" 190 /*@ 191 DMPlexReferenceTreeGetChildSymmetry - Given a reference tree, transform a childid and orientation from one parent frame to another 192 193 Input Parameters: 194 + dm - the reference tree DMPlex object 195 . parent - the parent point 196 . parentOrientA - the reference orientation for describing the parent 197 . childOrientA - the reference orientation for describing the child 198 . childA - the reference childID for describing the child 199 - parentOrientB - the new orientation for describing the parent 200 201 Output Parameters: 202 + childOrientB - if not NULL, set to the new oreintation for describing the child 203 . childB - if not NULL, the new childID for describing the child 204 205 Level: developer 206 207 .seealso: DMPlexGetReferenceTree(), DMPlexSetReferenceTree(), DMPlexSetTree() 208 @*/ 209 PetscErrorCode DMPlexReferenceTreeGetChildSymmetry(DM dm, PetscInt parent, PetscInt parentOrientA, PetscInt childOrientA, PetscInt childA, PetscInt parentOrientB, PetscInt *childOrientB, PetscInt *childB) 210 { 211 DM_Plex *mesh = (DM_Plex *)dm->data; 212 PetscErrorCode ierr; 213 214 PetscFunctionBegin; 215 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 216 if (!mesh->getchildsymmetry) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"DMPlexReferenceTreeGetChildSymmetry not implemented"); 217 ierr = mesh->getchildsymmetry(dm,parent,parentOrientA,childOrientA,childA,parentOrientB,childOrientB,childB);CHKERRQ(ierr); 218 PetscFunctionReturn(0); 219 } 220 221 static PetscErrorCode DMPlexSetTree_Internal(DM,PetscSection,PetscInt*,PetscInt*,PetscBool,PetscBool); 222 223 #undef __FUNCT__ 224 #define __FUNCT__ "DMPlexCreateDefaultReferenceTree" 225 /*@ 226 DMPlexCreateDefaultReferenceTree - create a reference tree for isotropic hierarchical mesh refinement. 227 228 Collective on comm 229 230 Input Parameters: 231 + comm - the MPI communicator 232 . dim - the spatial dimension 233 - simplex - Flag for simplex, otherwise use a tensor-product cell 234 235 Output Parameters: 236 . ref - the reference tree DMPlex object 237 238 Level: intermediate 239 240 .keywords: reference cell 241 .seealso: DMPlexSetReferenceTree(), DMPlexGetReferenceTree() 242 @*/ 243 PetscErrorCode DMPlexCreateDefaultReferenceTree(MPI_Comm comm, PetscInt dim, PetscBool simplex, DM *ref) 244 { 245 DM_Plex *mesh; 246 DM K, Kref; 247 PetscInt p, pStart, pEnd, pRefStart, pRefEnd, d, offset, parentSize, *parents, *childIDs; 248 PetscInt *permvals, *unionCones, *coneSizes, *unionOrientations, numUnionPoints, *numDimPoints, numCones, numVerts; 249 DMLabel identity, identityRef; 250 PetscSection unionSection, unionConeSection, parentSection; 251 PetscScalar *unionCoords; 252 IS perm; 253 PetscErrorCode ierr; 254 255 PetscFunctionBegin; 256 #if 1 257 comm = PETSC_COMM_SELF; 258 #endif 259 /* create a reference element */ 260 ierr = DMPlexCreateReferenceCell(comm, dim, simplex, &K);CHKERRQ(ierr); 261 ierr = DMPlexCreateLabel(K, "identity");CHKERRQ(ierr); 262 ierr = DMPlexGetLabel(K, "identity", &identity);CHKERRQ(ierr); 263 ierr = DMPlexGetChart(K, &pStart, &pEnd);CHKERRQ(ierr); 264 for (p = pStart; p < pEnd; p++) { 265 ierr = DMLabelSetValue(identity, p, p);CHKERRQ(ierr); 266 } 267 /* refine it */ 268 ierr = DMRefine(K,comm,&Kref);CHKERRQ(ierr); 269 270 /* the reference tree is the union of these two, without duplicating 271 * points that appear in both */ 272 ierr = DMPlexGetLabel(Kref, "identity", &identityRef);CHKERRQ(ierr); 273 ierr = DMPlexGetChart(Kref, &pRefStart, &pRefEnd);CHKERRQ(ierr); 274 ierr = PetscSectionCreate(comm, &unionSection);CHKERRQ(ierr); 275 ierr = PetscSectionSetChart(unionSection, 0, (pEnd - pStart) + (pRefEnd - pRefStart));CHKERRQ(ierr); 276 /* count points that will go in the union */ 277 for (p = pStart; p < pEnd; p++) { 278 ierr = PetscSectionSetDof(unionSection, p - pStart, 1);CHKERRQ(ierr); 279 } 280 for (p = pRefStart; p < pRefEnd; p++) { 281 PetscInt q, qSize; 282 ierr = DMLabelGetValue(identityRef, p, &q);CHKERRQ(ierr); 283 ierr = DMLabelGetStratumSize(identityRef, q, &qSize);CHKERRQ(ierr); 284 if (qSize > 1) { 285 ierr = PetscSectionSetDof(unionSection, p - pRefStart + (pEnd - pStart), 1);CHKERRQ(ierr); 286 } 287 } 288 ierr = PetscMalloc1(pEnd - pStart + pRefEnd - pRefStart,&permvals);CHKERRQ(ierr); 289 offset = 0; 290 /* stratify points in the union by topological dimension */ 291 for (d = 0; d <= dim; d++) { 292 PetscInt cStart, cEnd, c; 293 294 ierr = DMPlexGetHeightStratum(K, d, &cStart, &cEnd);CHKERRQ(ierr); 295 for (c = cStart; c < cEnd; c++) { 296 permvals[offset++] = c; 297 } 298 299 ierr = DMPlexGetHeightStratum(Kref, d, &cStart, &cEnd);CHKERRQ(ierr); 300 for (c = cStart; c < cEnd; c++) { 301 permvals[offset++] = c + (pEnd - pStart); 302 } 303 } 304 ierr = ISCreateGeneral(comm, (pEnd - pStart) + (pRefEnd - pRefStart), permvals, PETSC_OWN_POINTER, &perm);CHKERRQ(ierr); 305 ierr = PetscSectionSetPermutation(unionSection,perm);CHKERRQ(ierr); 306 ierr = PetscSectionSetUp(unionSection);CHKERRQ(ierr); 307 ierr = PetscSectionGetStorageSize(unionSection,&numUnionPoints);CHKERRQ(ierr); 308 ierr = PetscMalloc2(numUnionPoints,&coneSizes,dim+1,&numDimPoints);CHKERRQ(ierr); 309 /* count dimension points */ 310 for (d = 0; d <= dim; d++) { 311 PetscInt cStart, cOff, cOff2; 312 ierr = DMPlexGetHeightStratum(K,d,&cStart,NULL);CHKERRQ(ierr); 313 ierr = PetscSectionGetOffset(unionSection,cStart-pStart,&cOff);CHKERRQ(ierr); 314 if (d < dim) { 315 ierr = DMPlexGetHeightStratum(K,d+1,&cStart,NULL);CHKERRQ(ierr); 316 ierr = PetscSectionGetOffset(unionSection,cStart-pStart,&cOff2);CHKERRQ(ierr); 317 } 318 else { 319 cOff2 = numUnionPoints; 320 } 321 numDimPoints[dim - d] = cOff2 - cOff; 322 } 323 ierr = PetscSectionCreate(comm, &unionConeSection);CHKERRQ(ierr); 324 ierr = PetscSectionSetChart(unionConeSection, 0, numUnionPoints);CHKERRQ(ierr); 325 /* count the cones in the union */ 326 for (p = pStart; p < pEnd; p++) { 327 PetscInt dof, uOff; 328 329 ierr = DMPlexGetConeSize(K, p, &dof);CHKERRQ(ierr); 330 ierr = PetscSectionGetOffset(unionSection, p - pStart,&uOff);CHKERRQ(ierr); 331 ierr = PetscSectionSetDof(unionConeSection, uOff, dof);CHKERRQ(ierr); 332 coneSizes[uOff] = dof; 333 } 334 for (p = pRefStart; p < pRefEnd; p++) { 335 PetscInt dof, uDof, uOff; 336 337 ierr = DMPlexGetConeSize(Kref, p, &dof);CHKERRQ(ierr); 338 ierr = PetscSectionGetDof(unionSection, p - pRefStart + (pEnd - pStart),&uDof);CHKERRQ(ierr); 339 ierr = PetscSectionGetOffset(unionSection, p - pRefStart + (pEnd - pStart),&uOff);CHKERRQ(ierr); 340 if (uDof) { 341 ierr = PetscSectionSetDof(unionConeSection, uOff, dof);CHKERRQ(ierr); 342 coneSizes[uOff] = dof; 343 } 344 } 345 ierr = PetscSectionSetUp(unionConeSection);CHKERRQ(ierr); 346 ierr = PetscSectionGetStorageSize(unionConeSection,&numCones);CHKERRQ(ierr); 347 ierr = PetscMalloc2(numCones,&unionCones,numCones,&unionOrientations);CHKERRQ(ierr); 348 /* write the cones in the union */ 349 for (p = pStart; p < pEnd; p++) { 350 PetscInt dof, uOff, c, cOff; 351 const PetscInt *cone, *orientation; 352 353 ierr = DMPlexGetConeSize(K, p, &dof);CHKERRQ(ierr); 354 ierr = DMPlexGetCone(K, p, &cone);CHKERRQ(ierr); 355 ierr = DMPlexGetConeOrientation(K, p, &orientation);CHKERRQ(ierr); 356 ierr = PetscSectionGetOffset(unionSection, p - pStart,&uOff);CHKERRQ(ierr); 357 ierr = PetscSectionGetOffset(unionConeSection,uOff,&cOff);CHKERRQ(ierr); 358 for (c = 0; c < dof; c++) { 359 PetscInt e, eOff; 360 e = cone[c]; 361 ierr = PetscSectionGetOffset(unionSection, e - pStart, &eOff);CHKERRQ(ierr); 362 unionCones[cOff + c] = eOff; 363 unionOrientations[cOff + c] = orientation[c]; 364 } 365 } 366 for (p = pRefStart; p < pRefEnd; p++) { 367 PetscInt dof, uDof, uOff, c, cOff; 368 const PetscInt *cone, *orientation; 369 370 ierr = DMPlexGetConeSize(Kref, p, &dof);CHKERRQ(ierr); 371 ierr = DMPlexGetCone(Kref, p, &cone);CHKERRQ(ierr); 372 ierr = DMPlexGetConeOrientation(Kref, p, &orientation);CHKERRQ(ierr); 373 ierr = PetscSectionGetDof(unionSection, p - pRefStart + (pEnd - pStart),&uDof);CHKERRQ(ierr); 374 ierr = PetscSectionGetOffset(unionSection, p - pRefStart + (pEnd - pStart),&uOff);CHKERRQ(ierr); 375 if (uDof) { 376 ierr = PetscSectionGetOffset(unionConeSection,uOff,&cOff);CHKERRQ(ierr); 377 for (c = 0; c < dof; c++) { 378 PetscInt e, eOff, eDof; 379 380 e = cone[c]; 381 ierr = PetscSectionGetDof(unionSection, e - pRefStart + (pEnd - pStart),&eDof);CHKERRQ(ierr); 382 if (eDof) { 383 ierr = PetscSectionGetOffset(unionSection, e - pRefStart + (pEnd - pStart), &eOff);CHKERRQ(ierr); 384 } 385 else { 386 ierr = DMLabelGetValue(identityRef, e, &e);CHKERRQ(ierr); 387 ierr = PetscSectionGetOffset(unionSection, e - pStart, &eOff);CHKERRQ(ierr); 388 } 389 unionCones[cOff + c] = eOff; 390 unionOrientations[cOff + c] = orientation[c]; 391 } 392 } 393 } 394 /* get the coordinates */ 395 { 396 PetscInt vStart, vEnd, vRefStart, vRefEnd, v, vDof, vOff; 397 PetscSection KcoordsSec, KrefCoordsSec; 398 Vec KcoordsVec, KrefCoordsVec; 399 PetscScalar *Kcoords; 400 401 DMGetCoordinateSection(K, &KcoordsSec);CHKERRQ(ierr); 402 DMGetCoordinatesLocal(K, &KcoordsVec);CHKERRQ(ierr); 403 DMGetCoordinateSection(Kref, &KrefCoordsSec);CHKERRQ(ierr); 404 DMGetCoordinatesLocal(Kref, &KrefCoordsVec);CHKERRQ(ierr); 405 406 numVerts = numDimPoints[0]; 407 ierr = PetscMalloc1(numVerts * dim,&unionCoords);CHKERRQ(ierr); 408 ierr = DMPlexGetDepthStratum(K,0,&vStart,&vEnd);CHKERRQ(ierr); 409 410 offset = 0; 411 for (v = vStart; v < vEnd; v++) { 412 ierr = PetscSectionGetOffset(unionSection,v - pStart,&vOff);CHKERRQ(ierr); 413 ierr = VecGetValuesSection(KcoordsVec, KcoordsSec, v, &Kcoords);CHKERRQ(ierr); 414 for (d = 0; d < dim; d++) { 415 unionCoords[offset * dim + d] = Kcoords[d]; 416 } 417 offset++; 418 } 419 ierr = DMPlexGetDepthStratum(Kref,0,&vRefStart,&vRefEnd);CHKERRQ(ierr); 420 for (v = vRefStart; v < vRefEnd; v++) { 421 ierr = PetscSectionGetDof(unionSection,v - pRefStart + (pEnd - pStart),&vDof);CHKERRQ(ierr); 422 ierr = PetscSectionGetOffset(unionSection,v - pRefStart + (pEnd - pStart),&vOff);CHKERRQ(ierr); 423 ierr = VecGetValuesSection(KrefCoordsVec, KrefCoordsSec, v, &Kcoords);CHKERRQ(ierr); 424 if (vDof) { 425 for (d = 0; d < dim; d++) { 426 unionCoords[offset * dim + d] = Kcoords[d]; 427 } 428 offset++; 429 } 430 } 431 } 432 ierr = DMCreate(comm,ref);CHKERRQ(ierr); 433 ierr = DMSetType(*ref,DMPLEX);CHKERRQ(ierr); 434 ierr = DMSetDimension(*ref,dim);CHKERRQ(ierr); 435 ierr = DMPlexCreateFromDAG(*ref,dim,numDimPoints,coneSizes,unionCones,unionOrientations,unionCoords);CHKERRQ(ierr); 436 /* set the tree */ 437 ierr = PetscSectionCreate(comm,&parentSection);CHKERRQ(ierr); 438 ierr = PetscSectionSetChart(parentSection,0,numUnionPoints);CHKERRQ(ierr); 439 for (p = pRefStart; p < pRefEnd; p++) { 440 PetscInt uDof, uOff; 441 442 ierr = PetscSectionGetDof(unionSection, p - pRefStart + (pEnd - pStart),&uDof);CHKERRQ(ierr); 443 ierr = PetscSectionGetOffset(unionSection, p - pRefStart + (pEnd - pStart),&uOff);CHKERRQ(ierr); 444 if (uDof) { 445 PetscSectionSetDof(parentSection,uOff,1);CHKERRQ(ierr); 446 } 447 } 448 ierr = PetscSectionSetUp(parentSection);CHKERRQ(ierr); 449 ierr = PetscSectionGetStorageSize(parentSection,&parentSize);CHKERRQ(ierr); 450 ierr = PetscMalloc2(parentSize,&parents,parentSize,&childIDs);CHKERRQ(ierr); 451 for (p = pRefStart; p < pRefEnd; p++) { 452 PetscInt uDof, uOff; 453 454 ierr = PetscSectionGetDof(unionSection, p - pRefStart + (pEnd - pStart),&uDof);CHKERRQ(ierr); 455 ierr = PetscSectionGetOffset(unionSection, p - pRefStart + (pEnd - pStart),&uOff);CHKERRQ(ierr); 456 if (uDof) { 457 PetscInt pOff, parent, parentU; 458 PetscSectionGetOffset(parentSection,uOff,&pOff);CHKERRQ(ierr); 459 DMLabelGetValue(identityRef,p,&parent);CHKERRQ(ierr); 460 ierr = PetscSectionGetOffset(unionSection, parent - pStart,&parentU);CHKERRQ(ierr); 461 parents[pOff] = parentU; 462 childIDs[pOff] = uOff; 463 } 464 } 465 ierr = DMPlexSetTree_Internal(*ref,parentSection,parents,childIDs,PETSC_TRUE,PETSC_FALSE);CHKERRQ(ierr); 466 mesh = (DM_Plex *) (*ref)->data; 467 mesh->getchildsymmetry = DMPlexReferenceTreeGetChildSymmetry_Default; 468 ierr = PetscSectionDestroy(&parentSection);CHKERRQ(ierr); 469 ierr = PetscFree2(parents,childIDs);CHKERRQ(ierr); 470 471 /* clean up */ 472 ierr = PetscSectionDestroy(&unionSection);CHKERRQ(ierr); 473 ierr = PetscSectionDestroy(&unionConeSection);CHKERRQ(ierr); 474 ierr = ISDestroy(&perm);CHKERRQ(ierr); 475 ierr = PetscFree(unionCoords);CHKERRQ(ierr); 476 ierr = PetscFree2(unionCones,unionOrientations);CHKERRQ(ierr); 477 ierr = PetscFree2(coneSizes,numDimPoints);CHKERRQ(ierr); 478 ierr = DMDestroy(&K);CHKERRQ(ierr); 479 ierr = DMDestroy(&Kref);CHKERRQ(ierr); 480 PetscFunctionReturn(0); 481 } 482 483 #undef __FUNCT__ 484 #define __FUNCT__ "DMPlexTreeSymmetrize" 485 static PetscErrorCode DMPlexTreeSymmetrize(DM dm) 486 { 487 DM_Plex *mesh = (DM_Plex *)dm->data; 488 PetscSection childSec, pSec; 489 PetscInt p, pSize, cSize, parMax = PETSC_MIN_INT, parMin = PETSC_MAX_INT; 490 PetscInt *offsets, *children, pStart, pEnd; 491 PetscErrorCode ierr; 492 493 PetscFunctionBegin; 494 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 495 ierr = PetscSectionDestroy(&mesh->childSection);CHKERRQ(ierr); 496 ierr = PetscFree(mesh->children);CHKERRQ(ierr); 497 pSec = mesh->parentSection; 498 if (!pSec) PetscFunctionReturn(0); 499 ierr = PetscSectionGetStorageSize(pSec,&pSize);CHKERRQ(ierr); 500 for (p = 0; p < pSize; p++) { 501 PetscInt par = mesh->parents[p]; 502 503 parMax = PetscMax(parMax,par+1); 504 parMin = PetscMin(parMin,par); 505 } 506 if (parMin > parMax) { 507 parMin = -1; 508 parMax = -1; 509 } 510 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)pSec),&childSec);CHKERRQ(ierr); 511 ierr = PetscSectionSetChart(childSec,parMin,parMax);CHKERRQ(ierr); 512 for (p = 0; p < pSize; p++) { 513 PetscInt par = mesh->parents[p]; 514 515 ierr = PetscSectionAddDof(childSec,par,1);CHKERRQ(ierr); 516 } 517 ierr = PetscSectionSetUp(childSec);CHKERRQ(ierr); 518 ierr = PetscSectionGetStorageSize(childSec,&cSize);CHKERRQ(ierr); 519 ierr = PetscMalloc1(cSize,&children);CHKERRQ(ierr); 520 ierr = PetscCalloc1(parMax-parMin,&offsets);CHKERRQ(ierr); 521 ierr = PetscSectionGetChart(pSec,&pStart,&pEnd);CHKERRQ(ierr); 522 for (p = pStart; p < pEnd; p++) { 523 PetscInt dof, off, i; 524 525 ierr = PetscSectionGetDof(pSec,p,&dof);CHKERRQ(ierr); 526 ierr = PetscSectionGetOffset(pSec,p,&off);CHKERRQ(ierr); 527 for (i = 0; i < dof; i++) { 528 PetscInt par = mesh->parents[off + i], cOff; 529 530 ierr = PetscSectionGetOffset(childSec,par,&cOff);CHKERRQ(ierr); 531 children[cOff + offsets[par-parMin]++] = p; 532 } 533 } 534 mesh->childSection = childSec; 535 mesh->children = children; 536 ierr = PetscFree(offsets);CHKERRQ(ierr); 537 PetscFunctionReturn(0); 538 } 539 540 #undef __FUNCT__ 541 #define __FUNCT__ "AnchorsFlatten" 542 static PetscErrorCode AnchorsFlatten (PetscSection section, IS is, PetscSection *sectionNew, IS *isNew) 543 { 544 PetscInt pStart, pEnd, size, sizeNew, i, p, *valsNew = NULL; 545 const PetscInt *vals; 546 PetscSection secNew; 547 PetscBool anyNew, globalAnyNew; 548 PetscBool compress; 549 PetscErrorCode ierr; 550 551 PetscFunctionBegin; 552 ierr = PetscSectionGetChart(section,&pStart,&pEnd);CHKERRQ(ierr); 553 ierr = ISGetLocalSize(is,&size);CHKERRQ(ierr); 554 ierr = ISGetIndices(is,&vals);CHKERRQ(ierr); 555 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)section),&secNew);CHKERRQ(ierr); 556 ierr = PetscSectionSetChart(secNew,pStart,pEnd);CHKERRQ(ierr); 557 for (i = 0; i < size; i++) { 558 PetscInt dof; 559 560 p = vals[i]; 561 if (p < pStart || p >= pEnd) continue; 562 ierr = PetscSectionGetDof(section, p, &dof);CHKERRQ(ierr); 563 if (dof) break; 564 } 565 if (i == size) { 566 ierr = PetscSectionSetUp(secNew);CHKERRQ(ierr); 567 anyNew = PETSC_FALSE; 568 compress = PETSC_FALSE; 569 sizeNew = 0; 570 } 571 else { 572 anyNew = PETSC_TRUE; 573 for (p = pStart; p < pEnd; p++) { 574 PetscInt dof, off; 575 576 ierr = PetscSectionGetDof(section, p, &dof);CHKERRQ(ierr); 577 ierr = PetscSectionGetOffset(section, p, &off);CHKERRQ(ierr); 578 for (i = 0; i < dof; i++) { 579 PetscInt q = vals[off + i], qDof = 0; 580 581 if (q >= pStart && q < pEnd) { 582 ierr = PetscSectionGetDof(section, q, &qDof);CHKERRQ(ierr); 583 } 584 if (qDof) { 585 ierr = PetscSectionAddDof(secNew, p, qDof);CHKERRQ(ierr); 586 } 587 else { 588 ierr = PetscSectionAddDof(secNew, p, 1);CHKERRQ(ierr); 589 } 590 } 591 } 592 ierr = PetscSectionSetUp(secNew);CHKERRQ(ierr); 593 ierr = PetscSectionGetStorageSize(secNew,&sizeNew);CHKERRQ(ierr); 594 ierr = PetscMalloc1(sizeNew,&valsNew);CHKERRQ(ierr); 595 compress = PETSC_FALSE; 596 for (p = pStart; p < pEnd; p++) { 597 PetscInt dof, off, count, offNew, dofNew; 598 599 ierr = PetscSectionGetDof(section, p, &dof);CHKERRQ(ierr); 600 ierr = PetscSectionGetOffset(section, p, &off);CHKERRQ(ierr); 601 ierr = PetscSectionGetDof(secNew, p, &dofNew);CHKERRQ(ierr); 602 ierr = PetscSectionGetOffset(secNew, p, &offNew);CHKERRQ(ierr); 603 count = 0; 604 for (i = 0; i < dof; i++) { 605 PetscInt q = vals[off + i], qDof = 0, qOff = 0, j; 606 607 if (q >= pStart && q < pEnd) { 608 ierr = PetscSectionGetDof(section, q, &qDof);CHKERRQ(ierr); 609 ierr = PetscSectionGetOffset(section, q, &qOff);CHKERRQ(ierr); 610 } 611 if (qDof) { 612 PetscInt oldCount = count; 613 614 for (j = 0; j < qDof; j++) { 615 PetscInt k, r = vals[qOff + j]; 616 617 for (k = 0; k < oldCount; k++) { 618 if (valsNew[offNew + k] == r) { 619 break; 620 } 621 } 622 if (k == oldCount) { 623 valsNew[offNew + count++] = r; 624 } 625 } 626 } 627 else { 628 PetscInt k, oldCount = count; 629 630 for (k = 0; k < oldCount; k++) { 631 if (valsNew[offNew + k] == q) { 632 break; 633 } 634 } 635 if (k == oldCount) { 636 valsNew[offNew + count++] = q; 637 } 638 } 639 } 640 if (count < dofNew) { 641 ierr = PetscSectionSetDof(secNew, p, count);CHKERRQ(ierr); 642 compress = PETSC_TRUE; 643 } 644 } 645 } 646 ierr = ISRestoreIndices(is,&vals);CHKERRQ(ierr); 647 ierr = MPI_Allreduce(&anyNew,&globalAnyNew,1,MPIU_BOOL,MPI_LOR,PetscObjectComm((PetscObject)secNew));CHKERRQ(ierr); 648 if (!globalAnyNew) { 649 ierr = PetscSectionDestroy(&secNew);CHKERRQ(ierr); 650 *sectionNew = NULL; 651 *isNew = NULL; 652 } 653 else { 654 PetscBool globalCompress; 655 656 ierr = MPI_Allreduce(&compress,&globalCompress,1,MPIU_BOOL,MPI_LOR,PetscObjectComm((PetscObject)secNew));CHKERRQ(ierr); 657 if (compress) { 658 PetscSection secComp; 659 PetscInt *valsComp = NULL; 660 661 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)section),&secComp);CHKERRQ(ierr); 662 ierr = PetscSectionSetChart(secComp,pStart,pEnd);CHKERRQ(ierr); 663 for (p = pStart; p < pEnd; p++) { 664 PetscInt dof; 665 666 ierr = PetscSectionGetDof(secNew, p, &dof);CHKERRQ(ierr); 667 ierr = PetscSectionSetDof(secComp, p, dof);CHKERRQ(ierr); 668 } 669 ierr = PetscSectionSetUp(secComp);CHKERRQ(ierr); 670 ierr = PetscSectionGetStorageSize(secComp,&sizeNew);CHKERRQ(ierr); 671 ierr = PetscMalloc1(sizeNew,&valsComp);CHKERRQ(ierr); 672 for (p = pStart; p < pEnd; p++) { 673 PetscInt dof, off, offNew, j; 674 675 ierr = PetscSectionGetDof(secNew, p, &dof);CHKERRQ(ierr); 676 ierr = PetscSectionGetOffset(secNew, p, &off);CHKERRQ(ierr); 677 ierr = PetscSectionGetOffset(secComp, p, &offNew);CHKERRQ(ierr); 678 for (j = 0; j < dof; j++) { 679 valsComp[offNew + j] = valsNew[off + j]; 680 } 681 } 682 ierr = PetscSectionDestroy(&secNew);CHKERRQ(ierr); 683 secNew = secComp; 684 ierr = PetscFree(valsNew);CHKERRQ(ierr); 685 valsNew = valsComp; 686 } 687 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)is),sizeNew,valsNew,PETSC_OWN_POINTER,isNew);CHKERRQ(ierr); 688 } 689 PetscFunctionReturn(0); 690 } 691 692 #undef __FUNCT__ 693 #define __FUNCT__ "DMPlexCreateAnchors_Tree" 694 static PetscErrorCode DMPlexCreateAnchors_Tree(DM dm) 695 { 696 PetscInt p, pStart, pEnd, *anchors, size; 697 PetscInt aMin = PETSC_MAX_INT, aMax = PETSC_MIN_INT; 698 PetscSection aSec; 699 DMLabel canonLabel; 700 IS aIS; 701 PetscErrorCode ierr; 702 703 PetscFunctionBegin; 704 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 705 ierr = DMPlexGetChart(dm,&pStart,&pEnd);CHKERRQ(ierr); 706 ierr = DMPlexGetLabel(dm,"canonical",&canonLabel);CHKERRQ(ierr); 707 for (p = pStart; p < pEnd; p++) { 708 PetscInt parent; 709 710 if (canonLabel) { 711 PetscInt canon; 712 713 ierr = DMLabelGetValue(canonLabel,p,&canon);CHKERRQ(ierr); 714 if (p != canon) continue; 715 } 716 ierr = DMPlexGetTreeParent(dm,p,&parent,NULL);CHKERRQ(ierr); 717 if (parent != p) { 718 aMin = PetscMin(aMin,p); 719 aMax = PetscMax(aMax,p+1); 720 } 721 } 722 if (aMin > aMax) { 723 aMin = -1; 724 aMax = -1; 725 } 726 ierr = PetscSectionCreate(PETSC_COMM_SELF,&aSec);CHKERRQ(ierr); 727 ierr = PetscSectionSetChart(aSec,aMin,aMax);CHKERRQ(ierr); 728 for (p = aMin; p < aMax; p++) { 729 PetscInt parent, ancestor = p; 730 731 if (canonLabel) { 732 PetscInt canon; 733 734 ierr = DMLabelGetValue(canonLabel,p,&canon);CHKERRQ(ierr); 735 if (p != canon) continue; 736 } 737 ierr = DMPlexGetTreeParent(dm,p,&parent,NULL);CHKERRQ(ierr); 738 while (parent != ancestor) { 739 ancestor = parent; 740 ierr = DMPlexGetTreeParent(dm,ancestor,&parent,NULL);CHKERRQ(ierr); 741 } 742 if (ancestor != p) { 743 PetscInt closureSize, *closure = NULL; 744 745 ierr = DMPlexGetTransitiveClosure(dm,ancestor,PETSC_TRUE,&closureSize,&closure);CHKERRQ(ierr); 746 ierr = PetscSectionSetDof(aSec,p,closureSize);CHKERRQ(ierr); 747 ierr = DMPlexRestoreTransitiveClosure(dm,ancestor,PETSC_TRUE,&closureSize,&closure);CHKERRQ(ierr); 748 } 749 } 750 ierr = PetscSectionSetUp(aSec);CHKERRQ(ierr); 751 ierr = PetscSectionGetStorageSize(aSec,&size);CHKERRQ(ierr); 752 ierr = PetscMalloc1(size,&anchors);CHKERRQ(ierr); 753 for (p = aMin; p < aMax; p++) { 754 PetscInt parent, ancestor = p; 755 756 if (canonLabel) { 757 PetscInt canon; 758 759 ierr = DMLabelGetValue(canonLabel,p,&canon);CHKERRQ(ierr); 760 if (p != canon) continue; 761 } 762 ierr = DMPlexGetTreeParent(dm,p,&parent,NULL);CHKERRQ(ierr); 763 while (parent != ancestor) { 764 ancestor = parent; 765 ierr = DMPlexGetTreeParent(dm,ancestor,&parent,NULL);CHKERRQ(ierr); 766 } 767 if (ancestor != p) { 768 PetscInt j, closureSize, *closure = NULL, aOff; 769 770 ierr = PetscSectionGetOffset(aSec,p,&aOff);CHKERRQ(ierr); 771 772 ierr = DMPlexGetTransitiveClosure(dm,ancestor,PETSC_TRUE,&closureSize,&closure);CHKERRQ(ierr); 773 for (j = 0; j < closureSize; j++) { 774 anchors[aOff + j] = closure[2*j]; 775 } 776 ierr = DMPlexRestoreTransitiveClosure(dm,ancestor,PETSC_TRUE,&closureSize,&closure);CHKERRQ(ierr); 777 } 778 } 779 ierr = ISCreateGeneral(PETSC_COMM_SELF,size,anchors,PETSC_OWN_POINTER,&aIS);CHKERRQ(ierr); 780 { 781 PetscSection aSecNew = aSec; 782 IS aISNew = aIS; 783 784 ierr = PetscObjectReference((PetscObject)aSec);CHKERRQ(ierr); 785 ierr = PetscObjectReference((PetscObject)aIS);CHKERRQ(ierr); 786 while (aSecNew) { 787 ierr = PetscSectionDestroy(&aSec);CHKERRQ(ierr); 788 ierr = ISDestroy(&aIS);CHKERRQ(ierr); 789 aSec = aSecNew; 790 aIS = aISNew; 791 aSecNew = NULL; 792 aISNew = NULL; 793 ierr = AnchorsFlatten(aSec,aIS,&aSecNew,&aISNew);CHKERRQ(ierr); 794 } 795 } 796 ierr = DMPlexSetAnchors(dm,aSec,aIS);CHKERRQ(ierr); 797 ierr = PetscSectionDestroy(&aSec);CHKERRQ(ierr); 798 ierr = ISDestroy(&aIS);CHKERRQ(ierr); 799 PetscFunctionReturn(0); 800 } 801 802 #undef __FUNCT__ 803 #define __FUNCT__ "DMPlexTreeExchangeSupports" 804 static PetscErrorCode DMPlexTreeExchangeSupports(DM dm) 805 { 806 DM_Plex *mesh = (DM_Plex *)dm->data; 807 PetscSection newSupportSection; 808 PetscInt newSize, *newSupports, pStart, pEnd, p, d, depth; 809 PetscInt *offsets; 810 PetscErrorCode ierr; 811 812 PetscFunctionBegin; 813 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 814 /* symmetrize the hierarchy */ 815 ierr = DMPlexGetDepth(dm,&depth);CHKERRQ(ierr); 816 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)(mesh->supportSection)),&newSupportSection);CHKERRQ(ierr); 817 ierr = DMPlexGetChart(dm,&pStart,&pEnd);CHKERRQ(ierr); 818 ierr = PetscSectionSetChart(newSupportSection,pStart,pEnd);CHKERRQ(ierr); 819 ierr = PetscCalloc1(pEnd,&offsets);CHKERRQ(ierr); 820 /* if a point is in the support of q, it should be in the support of 821 * parent(q) */ 822 for (d = 0; d <= depth; d++) { 823 ierr = DMPlexGetHeightStratum(dm,d,&pStart,&pEnd);CHKERRQ(ierr); 824 for (p = pStart; p < pEnd; ++p) { 825 PetscInt dof, q, qdof, parent; 826 827 ierr = PetscSectionGetDof(mesh->supportSection, p, &dof);CHKERRQ(ierr); 828 ierr = PetscSectionAddDof(newSupportSection, p, dof);CHKERRQ(ierr); 829 q = p; 830 ierr = DMPlexGetTreeParent(dm,q,&parent,NULL);CHKERRQ(ierr); 831 while (parent != q && parent >= pStart && parent < pEnd) { 832 q = parent; 833 834 ierr = PetscSectionGetDof(mesh->supportSection, q, &qdof);CHKERRQ(ierr); 835 ierr = PetscSectionAddDof(newSupportSection,p,qdof);CHKERRQ(ierr); 836 ierr = PetscSectionAddDof(newSupportSection,q,dof);CHKERRQ(ierr); 837 ierr = DMPlexGetTreeParent(dm,q,&parent,NULL);CHKERRQ(ierr); 838 } 839 } 840 } 841 ierr = PetscSectionSetUp(newSupportSection);CHKERRQ(ierr); 842 ierr = PetscSectionGetStorageSize(newSupportSection,&newSize);CHKERRQ(ierr); 843 ierr = PetscMalloc1(newSize,&newSupports);CHKERRQ(ierr); 844 for (d = 0; d <= depth; d++) { 845 ierr = DMPlexGetHeightStratum(dm,d,&pStart,&pEnd);CHKERRQ(ierr); 846 for (p = pStart; p < pEnd; p++) { 847 PetscInt dof, off, q, qdof, qoff, newDof, newOff, newqOff, i, parent; 848 849 ierr = PetscSectionGetDof(mesh->supportSection, p, &dof);CHKERRQ(ierr); 850 ierr = PetscSectionGetOffset(mesh->supportSection, p, &off);CHKERRQ(ierr); 851 ierr = PetscSectionGetDof(newSupportSection, p, &newDof);CHKERRQ(ierr); 852 ierr = PetscSectionGetOffset(newSupportSection, p, &newOff);CHKERRQ(ierr); 853 for (i = 0; i < dof; i++) { 854 newSupports[newOff+offsets[p]++] = mesh->supports[off + i]; 855 } 856 mesh->maxSupportSize = PetscMax(mesh->maxSupportSize,newDof); 857 858 q = p; 859 ierr = DMPlexGetTreeParent(dm,q,&parent,NULL);CHKERRQ(ierr); 860 while (parent != q && parent >= pStart && parent < pEnd) { 861 q = parent; 862 ierr = PetscSectionGetDof(mesh->supportSection, q, &qdof);CHKERRQ(ierr); 863 ierr = PetscSectionGetOffset(mesh->supportSection, q, &qoff);CHKERRQ(ierr); 864 ierr = PetscSectionGetOffset(newSupportSection, q, &newqOff);CHKERRQ(ierr); 865 for (i = 0; i < qdof; i++) { 866 newSupports[newOff+offsets[p]++] = mesh->supports[qoff + i]; 867 } 868 for (i = 0; i < dof; i++) { 869 newSupports[newqOff+offsets[q]++] = mesh->supports[off + i]; 870 } 871 ierr = DMPlexGetTreeParent(dm,q,&parent,NULL);CHKERRQ(ierr); 872 } 873 } 874 } 875 ierr = PetscSectionDestroy(&mesh->supportSection);CHKERRQ(ierr); 876 mesh->supportSection = newSupportSection; 877 ierr = PetscFree(mesh->supports);CHKERRQ(ierr); 878 mesh->supports = newSupports; 879 ierr = PetscFree(offsets);CHKERRQ(ierr); 880 881 PetscFunctionReturn(0); 882 } 883 884 static PetscErrorCode DMPlexComputeAnchorMatrix_Tree_Direct(DM,PetscSection,PetscSection,Mat); 885 static PetscErrorCode DMPlexComputeAnchorMatrix_Tree_FromReference(DM,PetscSection,PetscSection,Mat); 886 887 #undef __FUNCT__ 888 #define __FUNCT__ "DMPlexSetTree_Internal" 889 static PetscErrorCode DMPlexSetTree_Internal(DM dm, PetscSection parentSection, PetscInt *parents, PetscInt *childIDs, PetscBool computeCanonical, PetscBool exchangeSupports) 890 { 891 DM_Plex *mesh = (DM_Plex *)dm->data; 892 DM refTree; 893 PetscInt size; 894 PetscErrorCode ierr; 895 896 PetscFunctionBegin; 897 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 898 PetscValidHeaderSpecific(parentSection, PETSC_SECTION_CLASSID, 2); 899 ierr = PetscObjectReference((PetscObject)parentSection);CHKERRQ(ierr); 900 ierr = PetscSectionDestroy(&mesh->parentSection);CHKERRQ(ierr); 901 mesh->parentSection = parentSection; 902 ierr = PetscSectionGetStorageSize(parentSection,&size);CHKERRQ(ierr); 903 if (parents != mesh->parents) { 904 ierr = PetscFree(mesh->parents);CHKERRQ(ierr); 905 ierr = PetscMalloc1(size,&mesh->parents);CHKERRQ(ierr); 906 ierr = PetscMemcpy(mesh->parents, parents, size * sizeof(*parents));CHKERRQ(ierr); 907 } 908 if (childIDs != mesh->childIDs) { 909 ierr = PetscFree(mesh->childIDs);CHKERRQ(ierr); 910 ierr = PetscMalloc1(size,&mesh->childIDs);CHKERRQ(ierr); 911 ierr = PetscMemcpy(mesh->childIDs, childIDs, size * sizeof(*childIDs));CHKERRQ(ierr); 912 } 913 ierr = DMPlexGetReferenceTree(dm,&refTree);CHKERRQ(ierr); 914 if (refTree) { 915 DMLabel canonLabel; 916 917 ierr = DMPlexGetLabel(refTree,"canonical",&canonLabel);CHKERRQ(ierr); 918 if (canonLabel) { 919 PetscInt i; 920 921 for (i = 0; i < size; i++) { 922 PetscInt canon; 923 ierr = DMLabelGetValue(canonLabel, mesh->childIDs[i], &canon);CHKERRQ(ierr); 924 if (canon >= 0) { 925 mesh->childIDs[i] = canon; 926 } 927 } 928 } 929 mesh->computeanchormatrix = DMPlexComputeAnchorMatrix_Tree_FromReference; 930 } 931 else { 932 mesh->computeanchormatrix = DMPlexComputeAnchorMatrix_Tree_Direct; 933 } 934 ierr = DMPlexTreeSymmetrize(dm);CHKERRQ(ierr); 935 if (computeCanonical) { 936 PetscInt d, dim; 937 938 /* add the canonical label */ 939 ierr = DMGetDimension(dm,&dim);CHKERRQ(ierr); 940 ierr = DMPlexCreateLabel(dm,"canonical");CHKERRQ(ierr); 941 for (d = 0; d <= dim; d++) { 942 PetscInt p, dStart, dEnd, canon = -1, cNumChildren; 943 const PetscInt *cChildren; 944 945 ierr = DMPlexGetDepthStratum(dm,d,&dStart,&dEnd);CHKERRQ(ierr); 946 for (p = dStart; p < dEnd; p++) { 947 ierr = DMPlexGetTreeChildren(dm,p,&cNumChildren,&cChildren);CHKERRQ(ierr); 948 if (cNumChildren) { 949 canon = p; 950 break; 951 } 952 } 953 if (canon == -1) continue; 954 for (p = dStart; p < dEnd; p++) { 955 PetscInt numChildren, i; 956 const PetscInt *children; 957 958 ierr = DMPlexGetTreeChildren(dm,p,&numChildren,&children);CHKERRQ(ierr); 959 if (numChildren) { 960 if (numChildren != cNumChildren) SETERRQ2(PetscObjectComm((PetscObject)dm),PETSC_ERR_PLIB,"All parent points in a stratum should have the same number of children: %d != %d", numChildren, cNumChildren); 961 ierr = DMPlexSetLabelValue(dm,"canonical",p,canon);CHKERRQ(ierr); 962 for (i = 0; i < numChildren; i++) { 963 ierr = DMPlexSetLabelValue(dm,"canonical",children[i],cChildren[i]);CHKERRQ(ierr); 964 } 965 } 966 } 967 } 968 } 969 if (exchangeSupports) { 970 ierr = DMPlexTreeExchangeSupports(dm);CHKERRQ(ierr); 971 } 972 mesh->createanchors = DMPlexCreateAnchors_Tree; 973 /* reset anchors */ 974 ierr = DMPlexSetAnchors(dm,NULL,NULL);CHKERRQ(ierr); 975 PetscFunctionReturn(0); 976 } 977 978 #undef __FUNCT__ 979 #define __FUNCT__ "DMPlexSetTree" 980 /*@ 981 DMPlexSetTree - set the tree that describes the hierarchy of non-conforming mesh points. This routine also creates 982 the point-to-point constraints determined by the tree: a point is constained to the points in the closure of its 983 tree root. 984 985 Collective on dm 986 987 Input Parameters: 988 + dm - the DMPlex object 989 . parentSection - a section describing the tree: a point has a parent if it has 1 dof in the section; the section 990 offset indexes the parent and childID list; the reference count of parentSection is incremented 991 . parents - a list of the point parents; copied, can be destroyed 992 - childIDs - identifies the relationship of the child point to the parent point; if there is a reference tree, then 993 the child corresponds to the point in the reference tree with index childIDs; copied, can be destroyed 994 995 Level: intermediate 996 997 .seealso: DMPlexGetTree(), DMPlexSetReferenceTree(), DMPlexSetAnchors(), DMPlexGetTreeParent(), DMPlexGetTreeChildren() 998 @*/ 999 PetscErrorCode DMPlexSetTree(DM dm, PetscSection parentSection, PetscInt parents[], PetscInt childIDs[]) 1000 { 1001 PetscErrorCode ierr; 1002 1003 PetscFunctionBegin; 1004 ierr = DMPlexSetTree_Internal(dm,parentSection,parents,childIDs,PETSC_FALSE,PETSC_TRUE);CHKERRQ(ierr); 1005 PetscFunctionReturn(0); 1006 } 1007 1008 #undef __FUNCT__ 1009 #define __FUNCT__ "DMPlexGetTree" 1010 /*@ 1011 DMPlexGetTree - get the tree that describes the hierarchy of non-conforming mesh points. 1012 Collective on dm 1013 1014 Input Parameters: 1015 . dm - the DMPlex object 1016 1017 Output Parameters: 1018 + parentSection - a section describing the tree: a point has a parent if it has 1 dof in the section; the section 1019 offset indexes the parent and childID list 1020 . parents - a list of the point parents 1021 . childIDs - identifies the relationship of the child point to the parent point; if there is a reference tree, then 1022 the child corresponds to the point in the reference tree with index childID 1023 . childSection - the inverse of the parent section 1024 - children - a list of the point children 1025 1026 Level: intermediate 1027 1028 .seealso: DMPlexSetTree(), DMPlexSetReferenceTree(), DMPlexSetAnchors(), DMPlexGetTreeParent(), DMPlexGetTreeChildren() 1029 @*/ 1030 PetscErrorCode DMPlexGetTree(DM dm, PetscSection *parentSection, PetscInt *parents[], PetscInt *childIDs[], PetscSection *childSection, PetscInt *children[]) 1031 { 1032 DM_Plex *mesh = (DM_Plex *)dm->data; 1033 1034 PetscFunctionBegin; 1035 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1036 if (parentSection) *parentSection = mesh->parentSection; 1037 if (parents) *parents = mesh->parents; 1038 if (childIDs) *childIDs = mesh->childIDs; 1039 if (childSection) *childSection = mesh->childSection; 1040 if (children) *children = mesh->children; 1041 PetscFunctionReturn(0); 1042 } 1043 1044 #undef __FUNCT__ 1045 #define __FUNCT__ "DMPlexGetTreeParent" 1046 /*@ 1047 DMPlexGetTreeParent - get the parent of a point in the tree describing the point hierarchy (not the Sieve DAG) 1048 1049 Input Parameters: 1050 + dm - the DMPlex object 1051 - point - the query point 1052 1053 Output Parameters: 1054 + parent - if not NULL, set to the parent of the point, or the point itself if the point does not have a parent 1055 - childID - if not NULL, set to the child ID of the point with respect to its parent, or 0 if the point 1056 does not have a parent 1057 1058 Level: intermediate 1059 1060 .seealso: DMPlexSetTree(), DMPlexGetTree(), DMPlexGetTreeChildren() 1061 @*/ 1062 PetscErrorCode DMPlexGetTreeParent(DM dm, PetscInt point, PetscInt *parent, PetscInt *childID) 1063 { 1064 DM_Plex *mesh = (DM_Plex *)dm->data; 1065 PetscSection pSec; 1066 PetscErrorCode ierr; 1067 1068 PetscFunctionBegin; 1069 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1070 pSec = mesh->parentSection; 1071 if (pSec && point >= pSec->pStart && point < pSec->pEnd) { 1072 PetscInt dof; 1073 1074 ierr = PetscSectionGetDof (pSec, point, &dof);CHKERRQ(ierr); 1075 if (dof) { 1076 PetscInt off; 1077 1078 ierr = PetscSectionGetOffset (pSec, point, &off);CHKERRQ(ierr); 1079 if (parent) *parent = mesh->parents[off]; 1080 if (childID) *childID = mesh->childIDs[off]; 1081 PetscFunctionReturn(0); 1082 } 1083 } 1084 if (parent) { 1085 *parent = point; 1086 } 1087 if (childID) { 1088 *childID = 0; 1089 } 1090 PetscFunctionReturn(0); 1091 } 1092 1093 #undef __FUNCT__ 1094 #define __FUNCT__ "DMPlexGetTreeChildren" 1095 /*@C 1096 DMPlexGetTreeChildren - get the children of a point in the tree describing the point hierarchy (not the Sieve DAG) 1097 1098 Input Parameters: 1099 + dm - the DMPlex object 1100 - point - the query point 1101 1102 Output Parameters: 1103 + numChildren - if not NULL, set to the number of children 1104 - children - if not NULL, set to a list children, or set to NULL if the point has no children 1105 1106 Level: intermediate 1107 1108 Fortran Notes: 1109 Since it returns an array, this routine is only available in Fortran 90, and you must 1110 include petsc.h90 in your code. 1111 1112 .seealso: DMPlexSetTree(), DMPlexGetTree(), DMPlexGetTreeParent() 1113 @*/ 1114 PetscErrorCode DMPlexGetTreeChildren(DM dm, PetscInt point, PetscInt *numChildren, const PetscInt *children[]) 1115 { 1116 DM_Plex *mesh = (DM_Plex *)dm->data; 1117 PetscSection childSec; 1118 PetscInt dof = 0; 1119 PetscErrorCode ierr; 1120 1121 PetscFunctionBegin; 1122 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1123 childSec = mesh->childSection; 1124 if (childSec && point >= childSec->pStart && point < childSec->pEnd) { 1125 ierr = PetscSectionGetDof (childSec, point, &dof);CHKERRQ(ierr); 1126 } 1127 if (numChildren) *numChildren = dof; 1128 if (children) { 1129 if (dof) { 1130 PetscInt off; 1131 1132 ierr = PetscSectionGetOffset (childSec, point, &off);CHKERRQ(ierr); 1133 *children = &mesh->children[off]; 1134 } 1135 else { 1136 *children = NULL; 1137 } 1138 } 1139 PetscFunctionReturn(0); 1140 } 1141 1142 #undef __FUNCT__ 1143 #define __FUNCT__ "DMPlexComputeAnchorMatrix_Tree_Direct" 1144 static PetscErrorCode DMPlexComputeAnchorMatrix_Tree_Direct(DM dm, PetscSection section, PetscSection cSec, Mat cMat) 1145 { 1146 PetscDS ds; 1147 PetscInt spdim; 1148 PetscInt numFields, f, c, cStart, cEnd, pStart, pEnd, conStart, conEnd; 1149 const PetscInt *anchors; 1150 PetscSection aSec; 1151 PetscReal *v0, *v0parent, *vtmp, *J, *Jparent, *invJparent, detJ, detJparent; 1152 IS aIS; 1153 PetscErrorCode ierr; 1154 1155 PetscFunctionBegin; 1156 ierr = DMPlexGetChart(dm,&pStart,&pEnd);CHKERRQ(ierr); 1157 ierr = DMGetDS(dm,&ds);CHKERRQ(ierr); 1158 ierr = PetscDSGetNumFields(ds,&numFields);CHKERRQ(ierr); 1159 ierr = DMPlexGetHeightStratum(dm,0,&cStart,&cEnd);CHKERRQ(ierr); 1160 ierr = DMPlexGetAnchors(dm,&aSec,&aIS);CHKERRQ(ierr); 1161 ierr = ISGetIndices(aIS,&anchors);CHKERRQ(ierr); 1162 ierr = PetscSectionGetChart(cSec,&conStart,&conEnd);CHKERRQ(ierr); 1163 ierr = DMGetDimension(dm,&spdim);CHKERRQ(ierr); 1164 ierr = PetscMalloc6(spdim,&v0,spdim,&v0parent,spdim,&vtmp,spdim*spdim,&J,spdim*spdim,&Jparent,spdim*spdim,&invJparent);CHKERRQ(ierr); 1165 1166 for (f = 0; f < numFields; f++) { 1167 PetscObject disc; 1168 PetscFE fe = NULL; 1169 PetscFV fv = NULL; 1170 PetscClassId id; 1171 PetscDualSpace space; 1172 PetscInt i, j, k, nPoints, offset; 1173 PetscInt fSize, fComp; 1174 PetscReal *B = NULL; 1175 PetscReal *weights, *pointsRef, *pointsReal; 1176 Mat Amat, Bmat, Xmat; 1177 1178 ierr = PetscDSGetDiscretization(ds,f,&disc);CHKERRQ(ierr); 1179 ierr = PetscObjectGetClassId(disc,&id);CHKERRQ(ierr); 1180 if (id == PETSCFE_CLASSID) { 1181 fe = (PetscFE) disc; 1182 ierr = PetscFEGetDualSpace(fe,&space);CHKERRQ(ierr); 1183 ierr = PetscDualSpaceGetDimension(space,&fSize);CHKERRQ(ierr); 1184 ierr = PetscFEGetNumComponents(fe,&fComp);CHKERRQ(ierr); 1185 } 1186 else if (id == PETSCFV_CLASSID) { 1187 fv = (PetscFV) disc; 1188 ierr = PetscFVGetDualSpace(fv,&space);CHKERRQ(ierr); 1189 ierr = PetscDualSpaceGetDimension(space,&fSize);CHKERRQ(ierr); 1190 ierr = PetscFVGetNumComponents(fv,&fComp);CHKERRQ(ierr); 1191 } 1192 else SETERRQ1(PetscObjectComm(disc),PETSC_ERR_ARG_UNKNOWN_TYPE, "PetscDS discretization id %d not recognized.", id); 1193 1194 ierr = MatCreate(PETSC_COMM_SELF,&Amat);CHKERRQ(ierr); 1195 ierr = MatSetSizes(Amat,fSize,fSize,fSize,fSize);CHKERRQ(ierr); 1196 ierr = MatSetType(Amat,MATSEQDENSE);CHKERRQ(ierr); 1197 ierr = MatSetUp(Amat);CHKERRQ(ierr); 1198 ierr = MatDuplicate(Amat,MAT_DO_NOT_COPY_VALUES,&Bmat);CHKERRQ(ierr); 1199 ierr = MatDuplicate(Amat,MAT_DO_NOT_COPY_VALUES,&Xmat);CHKERRQ(ierr); 1200 nPoints = 0; 1201 for (i = 0; i < fSize; i++) { 1202 PetscInt qPoints; 1203 PetscQuadrature quad; 1204 1205 ierr = PetscDualSpaceGetFunctional(space,i,&quad);CHKERRQ(ierr); 1206 ierr = PetscQuadratureGetData(quad,NULL,&qPoints,NULL,NULL);CHKERRQ(ierr); 1207 nPoints += qPoints; 1208 } 1209 ierr = PetscMalloc3(nPoints,&weights,spdim*nPoints,&pointsRef,spdim*nPoints,&pointsReal);CHKERRQ(ierr); 1210 offset = 0; 1211 for (i = 0; i < fSize; i++) { 1212 PetscInt qPoints; 1213 const PetscReal *p, *w; 1214 PetscQuadrature quad; 1215 1216 ierr = PetscDualSpaceGetFunctional(space,i,&quad);CHKERRQ(ierr); 1217 ierr = PetscQuadratureGetData(quad,NULL,&qPoints,&p,&w);CHKERRQ(ierr); 1218 ierr = PetscMemcpy(weights+offset,w,qPoints*sizeof(*w));CHKERRQ(ierr); 1219 ierr = PetscMemcpy(pointsRef+spdim*offset,p,spdim*qPoints*sizeof(*p));CHKERRQ(ierr); 1220 offset += qPoints; 1221 } 1222 if (id == PETSCFE_CLASSID) { 1223 ierr = PetscFEGetTabulation(fe,nPoints,pointsRef,&B,NULL,NULL);CHKERRQ(ierr); 1224 } 1225 else { 1226 ierr = PetscFVGetTabulation(fv,nPoints,pointsRef,&B,NULL,NULL);CHKERRQ(ierr); 1227 } 1228 offset = 0; 1229 for (i = 0; i < fSize; i++) { 1230 PetscInt qPoints; 1231 PetscQuadrature quad; 1232 1233 ierr = PetscDualSpaceGetFunctional(space,i,&quad);CHKERRQ(ierr); 1234 ierr = PetscQuadratureGetData(quad,NULL,&qPoints,NULL,NULL);CHKERRQ(ierr); 1235 for (j = 0; j < fSize; j++) { 1236 PetscScalar val = 0.; 1237 1238 for (k = 0; k < qPoints; k++) { 1239 val += B[((offset + k) * fSize + j) * fComp] * weights[k]; 1240 } 1241 ierr = MatSetValue(Amat,i,j,val,INSERT_VALUES);CHKERRQ(ierr); 1242 } 1243 offset += qPoints; 1244 } 1245 if (id == PETSCFE_CLASSID) { 1246 ierr = PetscFERestoreTabulation(fe,nPoints,pointsRef,&B,NULL,NULL);CHKERRQ(ierr); 1247 } 1248 else { 1249 ierr = PetscFVRestoreTabulation(fv,nPoints,pointsRef,&B,NULL,NULL);CHKERRQ(ierr); 1250 } 1251 ierr = MatAssemblyBegin(Amat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1252 ierr = MatAssemblyEnd(Amat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1253 ierr = MatLUFactor(Amat,NULL,NULL,NULL);CHKERRQ(ierr); 1254 for (c = cStart; c < cEnd; c++) { 1255 PetscInt parent; 1256 PetscInt closureSize, closureSizeP, *closure = NULL, *closureP = NULL; 1257 PetscInt *childOffsets, *parentOffsets; 1258 1259 ierr = DMPlexGetTreeParent(dm,c,&parent,NULL);CHKERRQ(ierr); 1260 if (parent == c) continue; 1261 ierr = DMPlexGetTransitiveClosure(dm,c,PETSC_TRUE,&closureSize,&closure);CHKERRQ(ierr); 1262 for (i = 0; i < closureSize; i++) { 1263 PetscInt p = closure[2*i]; 1264 PetscInt conDof; 1265 1266 if (p < conStart || p >= conEnd) continue; 1267 if (numFields > 1) { 1268 ierr = PetscSectionGetFieldDof(cSec,p,f,&conDof);CHKERRQ(ierr); 1269 } 1270 else { 1271 ierr = PetscSectionGetDof(cSec,p,&conDof);CHKERRQ(ierr); 1272 } 1273 if (conDof) break; 1274 } 1275 if (i == closureSize) { 1276 ierr = DMPlexRestoreTransitiveClosure(dm,c,PETSC_TRUE,&closureSize,&closure);CHKERRQ(ierr); 1277 continue; 1278 } 1279 1280 ierr = DMPlexComputeCellGeometryFEM(dm, c, NULL, v0, J, NULL, &detJ);CHKERRQ(ierr); 1281 ierr = DMPlexComputeCellGeometryFEM(dm, parent, NULL, v0parent, Jparent, invJparent, &detJparent);CHKERRQ(ierr); 1282 for (i = 0; i < nPoints; i++) { 1283 CoordinatesRefToReal(spdim, spdim, v0, J, &pointsRef[i*spdim],vtmp);CHKERRQ(ierr); 1284 CoordinatesRealToRef(spdim, spdim, v0parent, invJparent, vtmp, &pointsReal[i*spdim]);CHKERRQ(ierr); 1285 } 1286 if (id == PETSCFE_CLASSID) { 1287 ierr = PetscFEGetTabulation(fe,nPoints,pointsReal,&B,NULL,NULL);CHKERRQ(ierr); 1288 } 1289 else { 1290 ierr = PetscFVGetTabulation(fv,nPoints,pointsReal,&B,NULL,NULL);CHKERRQ(ierr); 1291 } 1292 offset = 0; 1293 for (i = 0; i < fSize; i++) { 1294 PetscInt qPoints; 1295 PetscQuadrature quad; 1296 1297 ierr = PetscDualSpaceGetFunctional(space,i,&quad);CHKERRQ(ierr); 1298 ierr = PetscQuadratureGetData(quad,NULL,&qPoints,NULL,NULL);CHKERRQ(ierr); 1299 for (j = 0; j < fSize; j++) { 1300 PetscScalar val = 0.; 1301 1302 for (k = 0; k < qPoints; k++) { 1303 val += B[((offset + k) * fSize + j) * fComp] * weights[k]; 1304 } 1305 MatSetValue(Bmat,i,j,val,INSERT_VALUES);CHKERRQ(ierr); 1306 } 1307 offset += qPoints; 1308 } 1309 if (id == PETSCFE_CLASSID) { 1310 ierr = PetscFERestoreTabulation(fe,nPoints,pointsReal,&B,NULL,NULL);CHKERRQ(ierr); 1311 } 1312 else { 1313 ierr = PetscFVRestoreTabulation(fv,nPoints,pointsReal,&B,NULL,NULL);CHKERRQ(ierr); 1314 } 1315 ierr = MatAssemblyBegin(Bmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1316 ierr = MatAssemblyEnd(Bmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1317 ierr = MatMatSolve(Amat,Bmat,Xmat);CHKERRQ(ierr); 1318 ierr = DMPlexGetTransitiveClosure(dm,parent,PETSC_TRUE,&closureSizeP,&closureP);CHKERRQ(ierr); 1319 ierr = PetscMalloc2(closureSize+1,&childOffsets,closureSizeP+1,&parentOffsets);CHKERRQ(ierr); 1320 childOffsets[0] = 0; 1321 for (i = 0; i < closureSize; i++) { 1322 PetscInt p = closure[2*i]; 1323 PetscInt dof; 1324 1325 if (numFields > 1) { 1326 ierr = PetscSectionGetFieldDof(section,p,f,&dof);CHKERRQ(ierr); 1327 } 1328 else { 1329 ierr = PetscSectionGetDof(section,p,&dof);CHKERRQ(ierr); 1330 } 1331 childOffsets[i+1]=childOffsets[i]+dof / fComp; 1332 } 1333 parentOffsets[0] = 0; 1334 for (i = 0; i < closureSizeP; i++) { 1335 PetscInt p = closureP[2*i]; 1336 PetscInt dof; 1337 1338 if (numFields > 1) { 1339 ierr = PetscSectionGetFieldDof(section,p,f,&dof);CHKERRQ(ierr); 1340 } 1341 else { 1342 ierr = PetscSectionGetDof(section,p,&dof);CHKERRQ(ierr); 1343 } 1344 parentOffsets[i+1]=parentOffsets[i]+dof / fComp; 1345 } 1346 for (i = 0; i < closureSize; i++) { 1347 PetscInt conDof, conOff, aDof, aOff; 1348 PetscInt p = closure[2*i]; 1349 PetscInt o = closure[2*i+1]; 1350 1351 if (p < conStart || p >= conEnd) continue; 1352 if (numFields > 1) { 1353 ierr = PetscSectionGetFieldDof(cSec,p,f,&conDof);CHKERRQ(ierr); 1354 ierr = PetscSectionGetFieldOffset(cSec,p,f,&conOff);CHKERRQ(ierr); 1355 } 1356 else { 1357 ierr = PetscSectionGetDof(cSec,p,&conDof);CHKERRQ(ierr); 1358 ierr = PetscSectionGetOffset(cSec,p,&conOff);CHKERRQ(ierr); 1359 } 1360 if (!conDof) continue; 1361 ierr = PetscSectionGetDof(aSec,p,&aDof);CHKERRQ(ierr); 1362 ierr = PetscSectionGetOffset(aSec,p,&aOff);CHKERRQ(ierr); 1363 for (k = 0; k < aDof; k++) { 1364 PetscInt a = anchors[aOff + k]; 1365 PetscInt aSecDof, aSecOff; 1366 1367 if (numFields > 1) { 1368 ierr = PetscSectionGetFieldDof(section,a,f,&aSecDof);CHKERRQ(ierr); 1369 ierr = PetscSectionGetFieldOffset(section,a,f,&aSecOff);CHKERRQ(ierr); 1370 } 1371 else { 1372 ierr = PetscSectionGetDof(section,a,&aSecDof);CHKERRQ(ierr); 1373 ierr = PetscSectionGetOffset(section,a,&aSecOff);CHKERRQ(ierr); 1374 } 1375 if (!aSecDof) continue; 1376 1377 for (j = 0; j < closureSizeP; j++) { 1378 PetscInt q = closureP[2*j]; 1379 PetscInt oq = closureP[2*j+1]; 1380 1381 if (q == a) { 1382 PetscInt r, s, t; 1383 1384 for (r = childOffsets[i]; r < childOffsets[i+1]; r++) { 1385 for (s = parentOffsets[j]; s < parentOffsets[j+1]; s++) { 1386 PetscScalar val; 1387 PetscInt insertCol, insertRow; 1388 1389 ierr = MatGetValue(Xmat,r,s,&val);CHKERRQ(ierr); 1390 if (o >= 0) { 1391 insertRow = conOff + fComp * (r - childOffsets[i]); 1392 } 1393 else { 1394 insertRow = conOff + fComp * (childOffsets[i + 1] - 1 - r); 1395 } 1396 if (oq >= 0) { 1397 insertCol = aSecOff + fComp * (s - parentOffsets[j]); 1398 } 1399 else { 1400 insertCol = aSecOff + fComp * (parentOffsets[j + 1] - 1 - s); 1401 } 1402 for (t = 0; t < fComp; t++) { 1403 ierr = MatSetValue(cMat,insertRow + t,insertCol + t,val,INSERT_VALUES);CHKERRQ(ierr); 1404 } 1405 } 1406 } 1407 } 1408 } 1409 } 1410 } 1411 ierr = PetscFree2(childOffsets,parentOffsets);CHKERRQ(ierr); 1412 ierr = DMPlexRestoreTransitiveClosure(dm,c,PETSC_TRUE,&closureSize,&closure);CHKERRQ(ierr); 1413 ierr = DMPlexRestoreTransitiveClosure(dm,parent,PETSC_TRUE,&closureSizeP,&closureP);CHKERRQ(ierr); 1414 } 1415 ierr = MatDestroy(&Amat);CHKERRQ(ierr); 1416 ierr = MatDestroy(&Bmat);CHKERRQ(ierr); 1417 ierr = MatDestroy(&Xmat);CHKERRQ(ierr); 1418 ierr = PetscFree3(weights,pointsRef,pointsReal);CHKERRQ(ierr); 1419 } 1420 ierr = MatAssemblyBegin(cMat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1421 ierr = MatAssemblyEnd(cMat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1422 ierr = PetscFree6(v0,v0parent,vtmp,J,Jparent,invJparent);CHKERRQ(ierr); 1423 ierr = ISRestoreIndices(aIS,&anchors);CHKERRQ(ierr); 1424 1425 PetscFunctionReturn(0); 1426 } 1427 1428 #undef __FUNCT__ 1429 #define __FUNCT__ "DMPlexComputeAnchorMatrix_Tree_FromReference" 1430 static PetscErrorCode DMPlexComputeAnchorMatrix_Tree_FromReference(DM dm, PetscSection section, PetscSection conSec, Mat cMat) 1431 { 1432 DM refTree; 1433 PetscDS ds; 1434 Mat refCmat; 1435 PetscInt numFields, f, pRefStart, pRefEnd, p, *rows, *cols, maxDof, maxAnDof, *perm, *iperm, pStart, pEnd, conStart, conEnd, **refPointFieldN; 1436 PetscScalar ***refPointFieldMats, *pointWork; 1437 PetscSection refConSec, refAnSec, anSec, refSection; 1438 IS refAnIS, anIS; 1439 const PetscInt *refAnchors, *anchors; 1440 PetscErrorCode ierr; 1441 1442 PetscFunctionBegin; 1443 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1444 ierr = DMGetDS(dm,&ds);CHKERRQ(ierr); 1445 ierr = PetscDSGetNumFields(ds,&numFields);CHKERRQ(ierr); 1446 ierr = DMPlexGetReferenceTree(dm,&refTree);CHKERRQ(ierr); 1447 ierr = DMSetDS(refTree,ds);CHKERRQ(ierr); 1448 ierr = DMGetDefaultConstraints(refTree,&refConSec,&refCmat);CHKERRQ(ierr); 1449 ierr = DMPlexGetChart(refTree,&pRefStart,&pRefEnd);CHKERRQ(ierr); 1450 ierr = DMPlexGetAnchors(refTree,&refAnSec,&refAnIS);CHKERRQ(ierr); 1451 ierr = DMPlexGetAnchors(dm,&anSec,&anIS);CHKERRQ(ierr); 1452 ierr = ISGetIndices(refAnIS,&refAnchors);CHKERRQ(ierr); 1453 ierr = ISGetIndices(anIS,&anchors);CHKERRQ(ierr); 1454 ierr = DMGetDefaultSection(refTree,&refSection);CHKERRQ(ierr); 1455 ierr = PetscSectionGetChart(refConSec,&pRefStart,&pRefEnd);CHKERRQ(ierr); 1456 ierr = PetscSectionGetChart(conSec,&conStart,&conEnd);CHKERRQ(ierr); 1457 ierr = PetscMalloc1(pRefEnd-pRefStart,&refPointFieldMats);CHKERRQ(ierr); 1458 ierr = PetscMalloc1(pRefEnd-pRefStart,&refPointFieldN);CHKERRQ(ierr); 1459 ierr = PetscSectionGetMaxDof(refConSec,&maxDof);CHKERRQ(ierr); 1460 ierr = PetscSectionGetMaxDof(refAnSec,&maxAnDof);CHKERRQ(ierr); 1461 ierr = PetscMalloc1(maxDof,&rows);CHKERRQ(ierr); 1462 ierr = PetscMalloc1(maxDof*maxAnDof,&cols);CHKERRQ(ierr); 1463 ierr = PetscMalloc1(maxDof*maxDof*maxAnDof,&pointWork);CHKERRQ(ierr); 1464 1465 /* step 1: get submats for every constrained point in the reference tree */ 1466 for (p = pRefStart; p < pRefEnd; p++) { 1467 PetscInt parent, closureSize, *closure = NULL, pDof; 1468 1469 ierr = DMPlexGetTreeParent(refTree,p,&parent,NULL);CHKERRQ(ierr); 1470 ierr = PetscSectionGetDof(refConSec,p,&pDof);CHKERRQ(ierr); 1471 if (!pDof || parent == p) continue; 1472 1473 ierr = PetscMalloc1(numFields,&refPointFieldMats[p-pRefStart]);CHKERRQ(ierr); 1474 ierr = PetscCalloc1(numFields,&refPointFieldN[p-pRefStart]);CHKERRQ(ierr); 1475 ierr = DMPlexGetTransitiveClosure(refTree,parent,PETSC_TRUE,&closureSize,&closure);CHKERRQ(ierr); 1476 for (f = 0; f < numFields; f++) { 1477 PetscInt cDof, cOff, numCols, r, i, fComp; 1478 PetscObject disc; 1479 PetscClassId id; 1480 PetscFE fe = NULL; 1481 PetscFV fv = NULL; 1482 1483 ierr = PetscDSGetDiscretization(ds,f,&disc);CHKERRQ(ierr); 1484 ierr = PetscObjectGetClassId(disc,&id);CHKERRQ(ierr); 1485 if (id == PETSCFE_CLASSID) { 1486 fe = (PetscFE) disc; 1487 ierr = PetscFEGetNumComponents(fe,&fComp);CHKERRQ(ierr); 1488 } 1489 else if (id == PETSCFV_CLASSID) { 1490 fv = (PetscFV) disc; 1491 ierr = PetscFVGetNumComponents(fv,&fComp);CHKERRQ(ierr); 1492 } 1493 else SETERRQ1(PetscObjectComm(disc),PETSC_ERR_ARG_UNKNOWN_TYPE, "PetscDS discretization id %d not recognized.", id); 1494 1495 if (numFields > 1) { 1496 ierr = PetscSectionGetFieldDof(refConSec,p,f,&cDof);CHKERRQ(ierr); 1497 ierr = PetscSectionGetFieldOffset(refConSec,p,f,&cOff);CHKERRQ(ierr); 1498 } 1499 else { 1500 ierr = PetscSectionGetDof(refConSec,p,&cDof);CHKERRQ(ierr); 1501 ierr = PetscSectionGetOffset(refConSec,p,&cOff);CHKERRQ(ierr); 1502 } 1503 1504 if (!cDof) continue; 1505 for (r = 0; r < cDof; r++) { 1506 rows[r] = cOff + r; 1507 } 1508 numCols = 0; 1509 for (i = 0; i < closureSize; i++) { 1510 PetscInt q = closure[2*i]; 1511 PetscInt o = closure[2*i+1]; 1512 PetscInt aDof, aOff, j; 1513 1514 if (numFields > 1) { 1515 ierr = PetscSectionGetFieldDof(refSection,q,f,&aDof);CHKERRQ(ierr); 1516 ierr = PetscSectionGetFieldOffset(refSection,q,f,&aOff);CHKERRQ(ierr); 1517 } 1518 else { 1519 ierr = PetscSectionGetDof(refSection,q,&aDof);CHKERRQ(ierr); 1520 ierr = PetscSectionGetOffset(refSection,q,&aOff);CHKERRQ(ierr); 1521 } 1522 1523 for (j = 0; j < aDof; j++) { 1524 PetscInt node = (o >= 0) ? (j / fComp) : ((aDof - 1 - j) / fComp); 1525 PetscInt comp = (j % fComp); 1526 1527 cols[numCols++] = aOff + node * fComp + comp; 1528 } 1529 } 1530 refPointFieldN[p-pRefStart][f] = numCols; 1531 ierr = PetscMalloc1(cDof*numCols,&refPointFieldMats[p-pRefStart][f]);CHKERRQ(ierr); 1532 ierr = MatGetValues(refCmat,cDof,rows,numCols,cols,refPointFieldMats[p-pRefStart][f]);CHKERRQ(ierr); 1533 } 1534 ierr = DMPlexRestoreTransitiveClosure(refTree,parent,PETSC_TRUE,&closureSize,&closure);CHKERRQ(ierr); 1535 } 1536 1537 /* step 2: compute the preorder */ 1538 ierr = DMPlexGetChart(dm,&pStart,&pEnd);CHKERRQ(ierr); 1539 ierr = PetscMalloc2(pEnd-pStart,&perm,pEnd-pStart,&iperm);CHKERRQ(ierr); 1540 for (p = pStart; p < pEnd; p++) { 1541 perm[p - pStart] = p; 1542 iperm[p - pStart] = p-pStart; 1543 } 1544 for (p = 0; p < pEnd - pStart;) { 1545 PetscInt point = perm[p]; 1546 PetscInt parent; 1547 1548 ierr = DMPlexGetTreeParent(dm,point,&parent,NULL);CHKERRQ(ierr); 1549 if (parent == point) { 1550 p++; 1551 } 1552 else { 1553 PetscInt size, closureSize, *closure = NULL, i; 1554 1555 ierr = DMPlexGetTransitiveClosure(dm,parent,PETSC_TRUE,&closureSize,&closure);CHKERRQ(ierr); 1556 for (i = 0; i < closureSize; i++) { 1557 PetscInt q = closure[2*i]; 1558 if (iperm[q-pStart] > iperm[point-pStart]) { 1559 /* swap */ 1560 perm[p] = q; 1561 perm[iperm[q-pStart]] = point; 1562 iperm[point-pStart] = iperm[q-pStart]; 1563 iperm[q-pStart] = p; 1564 break; 1565 } 1566 } 1567 size = closureSize; 1568 ierr = DMPlexRestoreTransitiveClosure(dm,parent,PETSC_TRUE,&closureSize,&closure);CHKERRQ(ierr); 1569 if (i == size) { 1570 p++; 1571 } 1572 } 1573 } 1574 1575 /* step 3: fill the constraint matrix */ 1576 /* we are going to use a preorder progressive fill strategy. Mat doesn't 1577 * allow progressive fill without assembly, so we are going to set up the 1578 * values outside of the Mat first. 1579 */ 1580 { 1581 PetscInt nRows, row, nnz; 1582 PetscBool done; 1583 const PetscInt *ia, *ja; 1584 PetscScalar *vals; 1585 1586 ierr = MatGetRowIJ(cMat,0,PETSC_FALSE,PETSC_FALSE,&nRows,&ia,&ja,&done);CHKERRQ(ierr); 1587 if (!done) SETERRQ(PetscObjectComm((PetscObject)cMat),PETSC_ERR_PLIB,"Could not get RowIJ of constraint matrix"); 1588 nnz = ia[nRows]; 1589 /* malloc and then zero rows right before we fill them: this way valgrind 1590 * can tell if we are doing progressive fill in the wrong order */ 1591 ierr = PetscMalloc1(nnz,&vals);CHKERRQ(ierr); 1592 for (p = 0; p < pEnd - pStart; p++) { 1593 PetscInt parent, childid, closureSize, *closure = NULL; 1594 PetscInt point = perm[p], pointDof; 1595 1596 ierr = DMPlexGetTreeParent(dm,point,&parent,&childid);CHKERRQ(ierr); 1597 if ((point < conStart) || (point >= conEnd) || (parent == point)) continue; 1598 ierr = PetscSectionGetDof(conSec,point,&pointDof);CHKERRQ(ierr); 1599 if (!pointDof) continue; 1600 ierr = DMPlexGetTransitiveClosure(dm,parent,PETSC_TRUE,&closureSize,&closure);CHKERRQ(ierr); 1601 for (f = 0; f < numFields; f++) { 1602 PetscInt cDof, cOff, numCols, numFillCols, i, r, fComp, matOffset, offset; 1603 PetscScalar *pointMat; 1604 PetscObject disc; 1605 PetscClassId id; 1606 PetscFE fe = NULL; 1607 PetscFV fv = NULL; 1608 1609 ierr = PetscDSGetDiscretization(ds,f,&disc);CHKERRQ(ierr); 1610 ierr = PetscObjectGetClassId(disc,&id);CHKERRQ(ierr); 1611 if (id == PETSCFE_CLASSID) { 1612 fe = (PetscFE) disc; 1613 ierr = PetscFEGetNumComponents(fe,&fComp);CHKERRQ(ierr); 1614 } 1615 else if (id == PETSCFV_CLASSID) { 1616 fv = (PetscFV) disc; 1617 ierr = PetscFVGetNumComponents(fv,&fComp);CHKERRQ(ierr); 1618 } 1619 1620 if (numFields > 1) { 1621 ierr = PetscSectionGetFieldDof(conSec,point,f,&cDof);CHKERRQ(ierr); 1622 ierr = PetscSectionGetFieldOffset(conSec,point,f,&cOff);CHKERRQ(ierr); 1623 } 1624 else { 1625 ierr = PetscSectionGetDof(conSec,point,&cDof);CHKERRQ(ierr); 1626 ierr = PetscSectionGetOffset(conSec,point,&cOff);CHKERRQ(ierr); 1627 } 1628 if (!cDof) continue; 1629 1630 /* make sure that every row for this point is the same size */ 1631 #if defined(PETSC_USE_DEBUG) 1632 for (r = 0; r < cDof; r++) { 1633 if (cDof > 1 && r) { 1634 if ((ia[cOff+r+1]-ia[cOff+r]) != (ia[cOff+r]-ia[cOff+r-1])) { 1635 SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Two point rows have different nnz: %d vs. %d", (ia[rows[r]+1]-ia[rows[r]]), (ia[rows[r]]-ia[rows[r]-1])); 1636 } 1637 } 1638 } 1639 #endif 1640 /* zero rows */ 1641 for (i = ia[cOff] ; i< ia[cOff+cDof];i++) { 1642 vals[i] = 0.; 1643 } 1644 matOffset = ia[cOff]; 1645 numFillCols = ia[cOff+1] - matOffset; 1646 pointMat = refPointFieldMats[childid-pRefStart][f]; 1647 numCols = refPointFieldN[childid-pRefStart][f]; 1648 offset = 0; 1649 for (i = 0; i < closureSize; i++) { 1650 PetscInt q = closure[2*i]; 1651 PetscInt o = closure[2*i+1]; 1652 PetscInt aDof, aOff, j, k, qConDof, qConOff; 1653 1654 qConDof = qConOff = 0; 1655 if (numFields > 1) { 1656 ierr = PetscSectionGetFieldDof(section,q,f,&aDof);CHKERRQ(ierr); 1657 ierr = PetscSectionGetFieldOffset(section,q,f,&aOff);CHKERRQ(ierr); 1658 if (q >= conStart && q < conEnd) { 1659 ierr = PetscSectionGetFieldDof(conSec,q,f,&qConDof);CHKERRQ(ierr); 1660 ierr = PetscSectionGetFieldOffset(conSec,q,f,&qConOff);CHKERRQ(ierr); 1661 } 1662 } 1663 else { 1664 ierr = PetscSectionGetDof(section,q,&aDof);CHKERRQ(ierr); 1665 ierr = PetscSectionGetOffset(section,q,&aOff);CHKERRQ(ierr); 1666 if (q >= conStart && q < conEnd) { 1667 ierr = PetscSectionGetDof(conSec,q,&qConDof);CHKERRQ(ierr); 1668 ierr = PetscSectionGetOffset(conSec,q,&qConOff);CHKERRQ(ierr); 1669 } 1670 } 1671 if (!aDof) continue; 1672 if (qConDof) { 1673 /* this point has anchors: its rows of the matrix should already 1674 * be filled, thanks to preordering */ 1675 /* first multiply into pointWork, then set in matrix */ 1676 PetscInt aMatOffset = ia[qConOff]; 1677 PetscInt aNumFillCols = ia[qConOff + 1] - aMatOffset; 1678 for (r = 0; r < cDof; r++) { 1679 for (j = 0; j < aNumFillCols; j++) { 1680 PetscScalar inVal = 0; 1681 for (k = 0; k < aDof; k++) { 1682 PetscInt node = (o >= 0) ? (k / fComp) : ((aDof - 1 - k) / fComp); 1683 PetscInt comp = (k % fComp); 1684 PetscInt col = node * fComp + comp; 1685 1686 inVal += pointMat[r * numCols + offset + col] * vals[aMatOffset + aNumFillCols * k + j]; 1687 } 1688 pointWork[r * aNumFillCols + j] = inVal; 1689 } 1690 } 1691 /* assume that the columns are sorted, spend less time searching */ 1692 for (j = 0, k = 0; j < aNumFillCols; j++) { 1693 PetscInt col = ja[aMatOffset + j]; 1694 for (;k < numFillCols; k++) { 1695 if (ja[matOffset + k] == col) { 1696 break; 1697 } 1698 } 1699 if (k == numFillCols) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"No nonzero space for (%d, %d)", cOff, col); 1700 for (r = 0; r < cDof; r++) { 1701 vals[matOffset + numFillCols * r + k] = pointWork[r * aNumFillCols + j]; 1702 } 1703 } 1704 } 1705 else { 1706 /* find where to put this portion of pointMat into the matrix */ 1707 for (k = 0; k < numFillCols; k++) { 1708 if (ja[matOffset + k] == aOff) { 1709 break; 1710 } 1711 } 1712 if (k == numFillCols) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"No nonzero space for (%d, %d)", cOff, aOff); 1713 for (j = 0; j < aDof; j++) { 1714 PetscInt node = (o >= 0) ? (j / fComp) : ((aDof - 1 - j) / fComp); 1715 PetscInt comp = (j % fComp); 1716 PetscInt col = node * fComp + comp; 1717 for (r = 0; r < cDof; r++) { 1718 vals[matOffset + numFillCols * r + k + col] += pointMat[r * numCols + offset + col]; 1719 } 1720 } 1721 } 1722 offset += aDof; 1723 } 1724 } 1725 ierr = DMPlexRestoreTransitiveClosure(dm,parent,PETSC_TRUE,&closureSize,&closure);CHKERRQ(ierr); 1726 } 1727 for (row = 0; row < nRows; row++) { 1728 ierr = MatSetValues(cMat,1,&row,ia[row+1]-ia[row],&ja[ia[row]],&vals[ia[row]],INSERT_VALUES);CHKERRQ(ierr); 1729 } 1730 ierr = MatRestoreRowIJ(cMat,0,PETSC_FALSE,PETSC_FALSE,&nRows,&ia,&ja,&done);CHKERRQ(ierr); 1731 if (!done) SETERRQ(PetscObjectComm((PetscObject)cMat),PETSC_ERR_PLIB,"Could not restore RowIJ of constraint matrix"); 1732 ierr = MatAssemblyBegin(cMat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1733 ierr = MatAssemblyEnd(cMat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1734 ierr = PetscFree(vals);CHKERRQ(ierr); 1735 } 1736 1737 /* clean up */ 1738 ierr = ISRestoreIndices(refAnIS,&refAnchors);CHKERRQ(ierr); 1739 ierr = ISRestoreIndices(anIS,&anchors);CHKERRQ(ierr); 1740 ierr = PetscFree2(perm,iperm);CHKERRQ(ierr); 1741 ierr = PetscFree(rows);CHKERRQ(ierr); 1742 ierr = PetscFree(cols);CHKERRQ(ierr); 1743 ierr = PetscFree(pointWork);CHKERRQ(ierr); 1744 for (p = pRefStart; p < pRefEnd; p++) { 1745 PetscInt parent, pDof; 1746 1747 ierr = DMPlexGetTreeParent(refTree,p,&parent,NULL);CHKERRQ(ierr); 1748 ierr = PetscSectionGetDof(refConSec,p,&pDof);CHKERRQ(ierr); 1749 if (!pDof || parent == p) continue; 1750 1751 for (f = 0; f < numFields; f++) { 1752 PetscInt cDof; 1753 1754 if (numFields > 1) { 1755 ierr = PetscSectionGetFieldDof(refConSec,p,f,&cDof);CHKERRQ(ierr); 1756 } 1757 else { 1758 ierr = PetscSectionGetDof(refConSec,p,&cDof);CHKERRQ(ierr); 1759 } 1760 1761 if (!cDof) continue; 1762 ierr = PetscFree(refPointFieldMats[p - pRefStart][f]);CHKERRQ(ierr); 1763 } 1764 ierr = PetscFree(refPointFieldMats[p - pRefStart]);CHKERRQ(ierr); 1765 ierr = PetscFree(refPointFieldN[p - pRefStart]);CHKERRQ(ierr); 1766 } 1767 ierr = PetscFree(refPointFieldMats);CHKERRQ(ierr); 1768 ierr = PetscFree(refPointFieldN);CHKERRQ(ierr); 1769 PetscFunctionReturn(0); 1770 } 1771 1772 #undef __FUNCT__ 1773 #define __FUNCT__ "DMPlexTreeRefineCell" 1774 /* refine a single cell on rank 0: this is not intended to provide good local refinement, only to create an example of 1775 * a non-conforming mesh. Local refinement comes later */ 1776 PetscErrorCode DMPlexTreeRefineCell (DM dm, PetscInt cell, DM *ncdm) 1777 { 1778 DM K; 1779 PetscMPIInt rank; 1780 PetscInt dim, *pNewStart, *pNewEnd, *pNewCount, *pOldStart, *pOldEnd, offset, d, pStart, pEnd; 1781 PetscInt numNewCones, *newConeSizes, *newCones, *newOrientations; 1782 PetscInt *Kembedding; 1783 PetscInt *cellClosure=NULL, nc; 1784 PetscScalar *newVertexCoords; 1785 PetscInt numPointsWithParents, *parents, *childIDs, *perm, *iperm, *preOrient, pOffset; 1786 PetscSection parentSection; 1787 PetscErrorCode ierr; 1788 1789 PetscFunctionBegin; 1790 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm),&rank);CHKERRQ(ierr); 1791 ierr = DMGetDimension(dm,&dim);CHKERRQ(ierr); 1792 ierr = DMPlexCreate(PetscObjectComm((PetscObject)dm), ncdm);CHKERRQ(ierr); 1793 ierr = DMSetDimension(*ncdm,dim);CHKERRQ(ierr); 1794 1795 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 1796 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm),&parentSection);CHKERRQ(ierr); 1797 ierr = DMPlexGetReferenceTree(dm,&K);CHKERRQ(ierr); 1798 if (!rank) { 1799 /* compute the new charts */ 1800 ierr = PetscMalloc5(dim+1,&pNewCount,dim+1,&pNewStart,dim+1,&pNewEnd,dim+1,&pOldStart,dim+1,&pOldEnd);CHKERRQ(ierr); 1801 offset = 0; 1802 for (d = 0; d <= dim; d++) { 1803 PetscInt pOldCount, kStart, kEnd, k; 1804 1805 pNewStart[d] = offset; 1806 ierr = DMPlexGetHeightStratum(dm,d,&pOldStart[d],&pOldEnd[d]);CHKERRQ(ierr); 1807 ierr = DMPlexGetHeightStratum(K,d,&kStart,&kEnd);CHKERRQ(ierr); 1808 pOldCount = pOldEnd[d] - pOldStart[d]; 1809 /* adding the new points */ 1810 pNewCount[d] = pOldCount + kEnd - kStart; 1811 if (!d) { 1812 /* removing the cell */ 1813 pNewCount[d]--; 1814 } 1815 for (k = kStart; k < kEnd; k++) { 1816 PetscInt parent; 1817 ierr = DMPlexGetTreeParent(K,k,&parent,NULL);CHKERRQ(ierr); 1818 if (parent == k) { 1819 /* avoid double counting points that won't actually be new */ 1820 pNewCount[d]--; 1821 } 1822 } 1823 pNewEnd[d] = pNewStart[d] + pNewCount[d]; 1824 offset = pNewEnd[d]; 1825 1826 } 1827 if (cell < pOldStart[0] || cell >= pOldEnd[0]) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"%d not in cell range [%d, %d)", cell, pOldStart[0], pOldEnd[0]); 1828 /* get the current closure of the cell that we are removing */ 1829 ierr = DMPlexGetTransitiveClosure(dm,cell,PETSC_TRUE,&nc,&cellClosure);CHKERRQ(ierr); 1830 1831 ierr = PetscMalloc1(pNewEnd[dim],&newConeSizes);CHKERRQ(ierr); 1832 { 1833 PetscInt kStart, kEnd, k, closureSizeK, *closureK = NULL, j; 1834 1835 ierr = DMPlexGetChart(K,&kStart,&kEnd);CHKERRQ(ierr); 1836 ierr = PetscMalloc4(kEnd-kStart,&Kembedding,kEnd-kStart,&perm,kEnd-kStart,&iperm,kEnd-kStart,&preOrient);CHKERRQ(ierr); 1837 1838 for (k = kStart; k < kEnd; k++) { 1839 perm[k - kStart] = k; 1840 iperm [k - kStart] = k - kStart; 1841 preOrient[k - kStart] = 0; 1842 } 1843 1844 ierr = DMPlexGetTransitiveClosure(K,0,PETSC_TRUE,&closureSizeK,&closureK);CHKERRQ(ierr); 1845 for (j = 1; j < closureSizeK; j++) { 1846 PetscInt parentOrientA = closureK[2*j+1]; 1847 PetscInt parentOrientB = cellClosure[2*j+1]; 1848 PetscInt p, q; 1849 1850 p = closureK[2*j]; 1851 q = cellClosure[2*j]; 1852 for (d = 0; d <= dim; d++) { 1853 if (q >= pOldStart[d] && q < pOldEnd[d]) { 1854 Kembedding[p] = (q - pOldStart[d]) + pNewStart[d]; 1855 } 1856 } 1857 if (parentOrientA != parentOrientB) { 1858 PetscInt numChildren, i; 1859 const PetscInt *children; 1860 1861 ierr = DMPlexGetTreeChildren(K,p,&numChildren,&children);CHKERRQ(ierr); 1862 for (i = 0; i < numChildren; i++) { 1863 PetscInt kPerm, oPerm; 1864 1865 k = children[i]; 1866 ierr = DMPlexReferenceTreeGetChildSymmetry(K,p,parentOrientA,0,k,parentOrientB,&oPerm,&kPerm);CHKERRQ(ierr); 1867 /* perm = what refTree position I'm in */ 1868 perm[kPerm-kStart] = k; 1869 /* iperm = who is at this position */ 1870 iperm[k-kStart] = kPerm-kStart; 1871 preOrient[kPerm-kStart] = oPerm; 1872 } 1873 } 1874 } 1875 ierr = DMPlexRestoreTransitiveClosure(K,0,PETSC_TRUE,&closureSizeK,&closureK);CHKERRQ(ierr); 1876 } 1877 ierr = PetscSectionSetChart(parentSection,0,pNewEnd[dim]);CHKERRQ(ierr); 1878 offset = 0; 1879 numNewCones = 0; 1880 for (d = 0; d <= dim; d++) { 1881 PetscInt kStart, kEnd, k; 1882 PetscInt p; 1883 PetscInt size; 1884 1885 for (p = pOldStart[d]; p < pOldEnd[d]; p++) { 1886 /* skip cell 0 */ 1887 if (p == cell) continue; 1888 /* old cones to new cones */ 1889 ierr = DMPlexGetConeSize(dm,p,&size);CHKERRQ(ierr); 1890 newConeSizes[offset++] = size; 1891 numNewCones += size; 1892 } 1893 1894 ierr = DMPlexGetHeightStratum(K,d,&kStart,&kEnd);CHKERRQ(ierr); 1895 for (k = kStart; k < kEnd; k++) { 1896 PetscInt kParent; 1897 1898 ierr = DMPlexGetTreeParent(K,k,&kParent,NULL);CHKERRQ(ierr); 1899 if (kParent != k) { 1900 Kembedding[k] = offset; 1901 ierr = DMPlexGetConeSize(K,k,&size);CHKERRQ(ierr); 1902 newConeSizes[offset++] = size; 1903 numNewCones += size; 1904 if (kParent != 0) { 1905 ierr = PetscSectionSetDof(parentSection,Kembedding[k],1);CHKERRQ(ierr); 1906 } 1907 } 1908 } 1909 } 1910 1911 ierr = PetscSectionSetUp(parentSection);CHKERRQ(ierr); 1912 ierr = PetscSectionGetStorageSize(parentSection,&numPointsWithParents);CHKERRQ(ierr); 1913 ierr = PetscMalloc2(numNewCones,&newCones,numNewCones,&newOrientations);CHKERRQ(ierr); 1914 ierr = PetscMalloc2(numPointsWithParents,&parents,numPointsWithParents,&childIDs);CHKERRQ(ierr); 1915 1916 /* fill new cones */ 1917 offset = 0; 1918 for (d = 0; d <= dim; d++) { 1919 PetscInt kStart, kEnd, k, l; 1920 PetscInt p; 1921 PetscInt size; 1922 const PetscInt *cone, *orientation; 1923 1924 for (p = pOldStart[d]; p < pOldEnd[d]; p++) { 1925 /* skip cell 0 */ 1926 if (p == cell) continue; 1927 /* old cones to new cones */ 1928 ierr = DMPlexGetConeSize(dm,p,&size);CHKERRQ(ierr); 1929 ierr = DMPlexGetCone(dm,p,&cone);CHKERRQ(ierr); 1930 ierr = DMPlexGetConeOrientation(dm,p,&orientation);CHKERRQ(ierr); 1931 for (l = 0; l < size; l++) { 1932 newCones[offset] = (cone[l] - pOldStart[d + 1]) + pNewStart[d + 1]; 1933 newOrientations[offset++] = orientation[l]; 1934 } 1935 } 1936 1937 ierr = DMPlexGetHeightStratum(K,d,&kStart,&kEnd);CHKERRQ(ierr); 1938 for (k = kStart; k < kEnd; k++) { 1939 PetscInt kPerm = perm[k], kParent; 1940 PetscInt preO = preOrient[k]; 1941 1942 ierr = DMPlexGetTreeParent(K,k,&kParent,NULL);CHKERRQ(ierr); 1943 if (kParent != k) { 1944 /* embed new cones */ 1945 ierr = DMPlexGetConeSize(K,k,&size);CHKERRQ(ierr); 1946 ierr = DMPlexGetCone(K,kPerm,&cone);CHKERRQ(ierr); 1947 ierr = DMPlexGetConeOrientation(K,kPerm,&orientation);CHKERRQ(ierr); 1948 for (l = 0; l < size; l++) { 1949 PetscInt q, m = (preO >= 0) ? ((preO + l) % size) : ((size -(preO + 1) - l) % size); 1950 PetscInt newO, lSize, oTrue; 1951 1952 q = iperm[cone[m]]; 1953 newCones[offset] = Kembedding[q]; 1954 ierr = DMPlexGetConeSize(K,q,&lSize);CHKERRQ(ierr); 1955 oTrue = orientation[m]; 1956 oTrue = ((!lSize) || (preOrient[k] >= 0)) ? oTrue : -(oTrue + 2); 1957 newO = DihedralCompose(lSize,oTrue,preOrient[q]); 1958 newOrientations[offset++] = newO; 1959 } 1960 if (kParent != 0) { 1961 PetscInt newPoint = Kembedding[kParent]; 1962 ierr = PetscSectionGetOffset(parentSection,Kembedding[k],&pOffset);CHKERRQ(ierr); 1963 parents[pOffset] = newPoint; 1964 childIDs[pOffset] = k; 1965 } 1966 } 1967 } 1968 } 1969 1970 ierr = PetscMalloc1(dim*(pNewEnd[dim]-pNewStart[dim]),&newVertexCoords);CHKERRQ(ierr); 1971 1972 /* fill coordinates */ 1973 offset = 0; 1974 { 1975 PetscInt kStart, kEnd, l; 1976 PetscSection vSection; 1977 PetscInt v; 1978 Vec coords; 1979 PetscScalar *coordvals; 1980 PetscInt dof, off; 1981 PetscReal v0[3], J[9], detJ; 1982 1983 #if defined(PETSC_USE_DEBUG) 1984 { 1985 PetscInt k; 1986 ierr = DMPlexGetHeightStratum(K,0,&kStart,&kEnd);CHKERRQ(ierr); 1987 for (k = kStart; k < kEnd; k++) { 1988 ierr = DMPlexComputeCellGeometryFEM(K, k, NULL, v0, J, NULL, &detJ);CHKERRQ(ierr); 1989 if (detJ <= 0.) SETERRQ1 (PETSC_COMM_SELF,PETSC_ERR_PLIB,"reference tree cell %d has bad determinant",k); 1990 } 1991 } 1992 #endif 1993 ierr = DMPlexComputeCellGeometryFEM(dm, cell, NULL, v0, J, NULL, &detJ);CHKERRQ(ierr); 1994 ierr = DMGetCoordinateSection(dm,&vSection);CHKERRQ(ierr); 1995 ierr = DMGetCoordinatesLocal(dm,&coords);CHKERRQ(ierr); 1996 ierr = VecGetArray(coords,&coordvals);CHKERRQ(ierr); 1997 for (v = pOldStart[dim]; v < pOldEnd[dim]; v++) { 1998 1999 ierr = PetscSectionGetDof(vSection,v,&dof);CHKERRQ(ierr); 2000 ierr = PetscSectionGetOffset(vSection,v,&off);CHKERRQ(ierr); 2001 for (l = 0; l < dof; l++) { 2002 newVertexCoords[offset++] = coordvals[off + l]; 2003 } 2004 } 2005 ierr = VecRestoreArray(coords,&coordvals);CHKERRQ(ierr); 2006 2007 ierr = DMGetCoordinateSection(K,&vSection);CHKERRQ(ierr); 2008 ierr = DMGetCoordinatesLocal(K,&coords);CHKERRQ(ierr); 2009 ierr = VecGetArray(coords,&coordvals);CHKERRQ(ierr); 2010 ierr = DMPlexGetDepthStratum(K,0,&kStart,&kEnd);CHKERRQ(ierr); 2011 for (v = kStart; v < kEnd; v++) { 2012 PetscReal coord[3], newCoord[3]; 2013 PetscInt vPerm = perm[v]; 2014 PetscInt kParent; 2015 2016 ierr = DMPlexGetTreeParent(K,v,&kParent,NULL);CHKERRQ(ierr); 2017 if (kParent != v) { 2018 /* this is a new vertex */ 2019 ierr = PetscSectionGetOffset(vSection,vPerm,&off);CHKERRQ(ierr); 2020 for (l = 0; l < dim; ++l) coord[l] = PetscRealPart(coordvals[off+l]); 2021 CoordinatesRefToReal(dim, dim, v0, J, coord, newCoord);CHKERRQ(ierr); 2022 for (l = 0; l < dim; ++l) newVertexCoords[offset+l] = newCoord[l]; 2023 offset += dim; 2024 } 2025 } 2026 ierr = VecRestoreArray(coords,&coordvals);CHKERRQ(ierr); 2027 } 2028 2029 /* need to reverse the order of pNewCount: vertices first, cells last */ 2030 for (d = 0; d < (dim + 1) / 2; d++) { 2031 PetscInt tmp; 2032 2033 tmp = pNewCount[d]; 2034 pNewCount[d] = pNewCount[dim - d]; 2035 pNewCount[dim - d] = tmp; 2036 } 2037 2038 ierr = DMPlexCreateFromDAG(*ncdm,dim,pNewCount,newConeSizes,newCones,newOrientations,newVertexCoords);CHKERRQ(ierr); 2039 ierr = DMPlexSetReferenceTree(*ncdm,K);CHKERRQ(ierr); 2040 ierr = DMPlexSetTree(*ncdm,parentSection,parents,childIDs);CHKERRQ(ierr); 2041 2042 /* clean up */ 2043 ierr = DMPlexRestoreTransitiveClosure(dm,cell,PETSC_TRUE,&nc,&cellClosure);CHKERRQ(ierr); 2044 ierr = PetscFree5(pNewCount,pNewStart,pNewEnd,pOldStart,pOldEnd);CHKERRQ(ierr); 2045 ierr = PetscFree(newConeSizes);CHKERRQ(ierr); 2046 ierr = PetscFree2(newCones,newOrientations);CHKERRQ(ierr); 2047 ierr = PetscFree(newVertexCoords);CHKERRQ(ierr); 2048 ierr = PetscFree2(parents,childIDs);CHKERRQ(ierr); 2049 ierr = PetscFree4(Kembedding,perm,iperm,preOrient);CHKERRQ(ierr); 2050 } 2051 else { 2052 PetscInt p, counts[4]; 2053 PetscInt *coneSizes, *cones, *orientations; 2054 Vec coordVec; 2055 PetscScalar *coords; 2056 2057 for (d = 0; d <= dim; d++) { 2058 PetscInt dStart, dEnd; 2059 2060 ierr = DMPlexGetDepthStratum(dm,d,&dStart,&dEnd);CHKERRQ(ierr); 2061 counts[d] = dEnd - dStart; 2062 } 2063 ierr = PetscMalloc1(pEnd-pStart,&coneSizes);CHKERRQ(ierr); 2064 for (p = pStart; p < pEnd; p++) { 2065 ierr = DMPlexGetConeSize(dm,p,&coneSizes[p-pStart]);CHKERRQ(ierr); 2066 } 2067 ierr = DMPlexGetCones(dm, &cones);CHKERRQ(ierr); 2068 ierr = DMPlexGetConeOrientations(dm, &orientations);CHKERRQ(ierr); 2069 ierr = DMGetCoordinatesLocal(dm,&coordVec);CHKERRQ(ierr); 2070 ierr = VecGetArray(coordVec,&coords);CHKERRQ(ierr); 2071 2072 ierr = PetscSectionSetChart(parentSection,pStart,pEnd);CHKERRQ(ierr); 2073 ierr = PetscSectionSetUp(parentSection);CHKERRQ(ierr); 2074 ierr = DMPlexCreateFromDAG(*ncdm,dim,counts,coneSizes,cones,orientations,NULL);CHKERRQ(ierr); 2075 ierr = DMPlexSetReferenceTree(*ncdm,K);CHKERRQ(ierr); 2076 ierr = DMPlexSetTree(*ncdm,parentSection,NULL,NULL);CHKERRQ(ierr); 2077 ierr = VecRestoreArray(coordVec,&coords);CHKERRQ(ierr); 2078 } 2079 ierr = PetscSectionDestroy(&parentSection);CHKERRQ(ierr); 2080 2081 PetscFunctionReturn(0); 2082 } 2083