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 } else { 151 ABswapVert = ABswap; 152 } 153 if (childB) { 154 /* assume that each child corresponds to a vertex, in the same order */ 155 PetscInt p, posA = -1, numChildren, i; 156 const PetscInt *children; 157 158 /* count which position the child is in */ 159 ierr = DMPlexGetTreeChildren(dm,parent,&numChildren,&children);CHKERRQ(ierr); 160 for (i = 0; i < numChildren; i++) { 161 p = children[i]; 162 if (p == childA) { 163 posA = i; 164 break; 165 } 166 } 167 if (posA >= coneSize) { 168 /* this is the triangle in the middle of a uniformly refined triangle: it 169 * is invariant */ 170 if (dim != 2 || posA != 3) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Expected a middle triangle, got something else"); 171 *childB = childA; 172 } 173 else { 174 /* figure out position B by applying ABswapVert */ 175 PetscInt posB; 176 177 posB = (ABswapVert >= 0) ? ((ABswapVert + posA) % coneSize) : ((coneSize -(ABswapVert + 1) - posA) % coneSize); 178 if (childB) *childB = children[posB]; 179 } 180 } 181 if (childOrientB) *childOrientB = DihedralCompose(coneSize,childOrientA,ABswap); 182 PetscFunctionReturn(0); 183 } 184 185 #undef __FUNCT__ 186 #define __FUNCT__ "DMPlexReferenceTreeGetChildSymmetry" 187 /*@ 188 DMPlexReferenceTreeGetChildSymmetry - Given a reference tree, transform a childid and orientation from one parent frame to another 189 190 Input Parameters: 191 + dm - the reference tree DMPlex object 192 . parent - the parent point 193 . parentOrientA - the reference orientation for describing the parent 194 . childOrientA - the reference orientation for describing the child 195 . childA - the reference childID for describing the child 196 - parentOrientB - the new orientation for describing the parent 197 198 Output Parameters: 199 + childOrientB - if not NULL, set to the new oreintation for describing the child 200 . childB - if not NULL, the new childID for describing the child 201 202 Level: developer 203 204 .seealso: DMPlexGetReferenceTree(), DMPlexSetReferenceTree(), DMPlexSetTree() 205 @*/ 206 PetscErrorCode DMPlexReferenceTreeGetChildSymmetry(DM dm, PetscInt parent, PetscInt parentOrientA, PetscInt childOrientA, PetscInt childA, PetscInt parentOrientB, PetscInt *childOrientB, PetscInt *childB) 207 { 208 DM_Plex *mesh = (DM_Plex *)dm->data; 209 PetscErrorCode ierr; 210 211 PetscFunctionBegin; 212 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 213 if (!mesh->getchildsymmetry) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"DMPlexReferenceTreeGetChildSymmetry not implemented"); 214 ierr = mesh->getchildsymmetry(dm,parent,parentOrientA,childOrientA,childA,parentOrientB,childOrientB,childB);CHKERRQ(ierr); 215 PetscFunctionReturn(0); 216 } 217 218 static PetscErrorCode DMPlexSetTree_Internal(DM,PetscSection,PetscInt*,PetscInt*,PetscBool,PetscBool); 219 220 #undef __FUNCT__ 221 #define __FUNCT__ "DMPlexCreateReferenceTree_Union" 222 PetscErrorCode DMPlexCreateReferenceTree_Union(DM K, DM Kref, const char *labelName, DM *ref) 223 { 224 MPI_Comm comm; 225 PetscInt dim, p, pStart, pEnd, pRefStart, pRefEnd, d, offset, parentSize, *parents, *childIDs; 226 PetscInt *permvals, *unionCones, *coneSizes, *unionOrientations, numUnionPoints, *numDimPoints, numCones, numVerts; 227 DMLabel identity, identityRef; 228 PetscSection unionSection, unionConeSection, parentSection; 229 PetscScalar *unionCoords; 230 IS perm; 231 PetscErrorCode ierr; 232 233 PetscFunctionBegin; 234 comm = PetscObjectComm((PetscObject)K); 235 ierr = DMGetDimension(K, &dim);CHKERRQ(ierr); 236 ierr = DMPlexGetChart(K, &pStart, &pEnd);CHKERRQ(ierr); 237 ierr = DMGetLabel(K, labelName, &identity);CHKERRQ(ierr); 238 ierr = DMGetLabel(Kref, labelName, &identityRef);CHKERRQ(ierr); 239 ierr = DMPlexGetChart(Kref, &pRefStart, &pRefEnd);CHKERRQ(ierr); 240 ierr = PetscSectionCreate(comm, &unionSection);CHKERRQ(ierr); 241 ierr = PetscSectionSetChart(unionSection, 0, (pEnd - pStart) + (pRefEnd - pRefStart));CHKERRQ(ierr); 242 /* count points that will go in the union */ 243 for (p = pStart; p < pEnd; p++) { 244 ierr = PetscSectionSetDof(unionSection, p - pStart, 1);CHKERRQ(ierr); 245 } 246 for (p = pRefStart; p < pRefEnd; p++) { 247 PetscInt q, qSize; 248 ierr = DMLabelGetValue(identityRef, p, &q);CHKERRQ(ierr); 249 ierr = DMLabelGetStratumSize(identityRef, q, &qSize);CHKERRQ(ierr); 250 if (qSize > 1) { 251 ierr = PetscSectionSetDof(unionSection, p - pRefStart + (pEnd - pStart), 1);CHKERRQ(ierr); 252 } 253 } 254 ierr = PetscMalloc1(pEnd - pStart + pRefEnd - pRefStart,&permvals);CHKERRQ(ierr); 255 offset = 0; 256 /* stratify points in the union by topological dimension */ 257 for (d = 0; d <= dim; d++) { 258 PetscInt cStart, cEnd, c; 259 260 ierr = DMPlexGetHeightStratum(K, d, &cStart, &cEnd);CHKERRQ(ierr); 261 for (c = cStart; c < cEnd; c++) { 262 permvals[offset++] = c; 263 } 264 265 ierr = DMPlexGetHeightStratum(Kref, d, &cStart, &cEnd);CHKERRQ(ierr); 266 for (c = cStart; c < cEnd; c++) { 267 permvals[offset++] = c + (pEnd - pStart); 268 } 269 } 270 ierr = ISCreateGeneral(comm, (pEnd - pStart) + (pRefEnd - pRefStart), permvals, PETSC_OWN_POINTER, &perm);CHKERRQ(ierr); 271 ierr = PetscSectionSetPermutation(unionSection,perm);CHKERRQ(ierr); 272 ierr = PetscSectionSetUp(unionSection);CHKERRQ(ierr); 273 ierr = PetscSectionGetStorageSize(unionSection,&numUnionPoints);CHKERRQ(ierr); 274 ierr = PetscMalloc2(numUnionPoints,&coneSizes,dim+1,&numDimPoints);CHKERRQ(ierr); 275 /* count dimension points */ 276 for (d = 0; d <= dim; d++) { 277 PetscInt cStart, cOff, cOff2; 278 ierr = DMPlexGetHeightStratum(K,d,&cStart,NULL);CHKERRQ(ierr); 279 ierr = PetscSectionGetOffset(unionSection,cStart-pStart,&cOff);CHKERRQ(ierr); 280 if (d < dim) { 281 ierr = DMPlexGetHeightStratum(K,d+1,&cStart,NULL);CHKERRQ(ierr); 282 ierr = PetscSectionGetOffset(unionSection,cStart-pStart,&cOff2);CHKERRQ(ierr); 283 } 284 else { 285 cOff2 = numUnionPoints; 286 } 287 numDimPoints[dim - d] = cOff2 - cOff; 288 } 289 ierr = PetscSectionCreate(comm, &unionConeSection);CHKERRQ(ierr); 290 ierr = PetscSectionSetChart(unionConeSection, 0, numUnionPoints);CHKERRQ(ierr); 291 /* count the cones in the union */ 292 for (p = pStart; p < pEnd; p++) { 293 PetscInt dof, uOff; 294 295 ierr = DMPlexGetConeSize(K, p, &dof);CHKERRQ(ierr); 296 ierr = PetscSectionGetOffset(unionSection, p - pStart,&uOff);CHKERRQ(ierr); 297 ierr = PetscSectionSetDof(unionConeSection, uOff, dof);CHKERRQ(ierr); 298 coneSizes[uOff] = dof; 299 } 300 for (p = pRefStart; p < pRefEnd; p++) { 301 PetscInt dof, uDof, uOff; 302 303 ierr = DMPlexGetConeSize(Kref, p, &dof);CHKERRQ(ierr); 304 ierr = PetscSectionGetDof(unionSection, p - pRefStart + (pEnd - pStart),&uDof);CHKERRQ(ierr); 305 ierr = PetscSectionGetOffset(unionSection, p - pRefStart + (pEnd - pStart),&uOff);CHKERRQ(ierr); 306 if (uDof) { 307 ierr = PetscSectionSetDof(unionConeSection, uOff, dof);CHKERRQ(ierr); 308 coneSizes[uOff] = dof; 309 } 310 } 311 ierr = PetscSectionSetUp(unionConeSection);CHKERRQ(ierr); 312 ierr = PetscSectionGetStorageSize(unionConeSection,&numCones);CHKERRQ(ierr); 313 ierr = PetscMalloc2(numCones,&unionCones,numCones,&unionOrientations);CHKERRQ(ierr); 314 /* write the cones in the union */ 315 for (p = pStart; p < pEnd; p++) { 316 PetscInt dof, uOff, c, cOff; 317 const PetscInt *cone, *orientation; 318 319 ierr = DMPlexGetConeSize(K, p, &dof);CHKERRQ(ierr); 320 ierr = DMPlexGetCone(K, p, &cone);CHKERRQ(ierr); 321 ierr = DMPlexGetConeOrientation(K, p, &orientation);CHKERRQ(ierr); 322 ierr = PetscSectionGetOffset(unionSection, p - pStart,&uOff);CHKERRQ(ierr); 323 ierr = PetscSectionGetOffset(unionConeSection,uOff,&cOff);CHKERRQ(ierr); 324 for (c = 0; c < dof; c++) { 325 PetscInt e, eOff; 326 e = cone[c]; 327 ierr = PetscSectionGetOffset(unionSection, e - pStart, &eOff);CHKERRQ(ierr); 328 unionCones[cOff + c] = eOff; 329 unionOrientations[cOff + c] = orientation[c]; 330 } 331 } 332 for (p = pRefStart; p < pRefEnd; p++) { 333 PetscInt dof, uDof, uOff, c, cOff; 334 const PetscInt *cone, *orientation; 335 336 ierr = DMPlexGetConeSize(Kref, p, &dof);CHKERRQ(ierr); 337 ierr = DMPlexGetCone(Kref, p, &cone);CHKERRQ(ierr); 338 ierr = DMPlexGetConeOrientation(Kref, p, &orientation);CHKERRQ(ierr); 339 ierr = PetscSectionGetDof(unionSection, p - pRefStart + (pEnd - pStart),&uDof);CHKERRQ(ierr); 340 ierr = PetscSectionGetOffset(unionSection, p - pRefStart + (pEnd - pStart),&uOff);CHKERRQ(ierr); 341 if (uDof) { 342 ierr = PetscSectionGetOffset(unionConeSection,uOff,&cOff);CHKERRQ(ierr); 343 for (c = 0; c < dof; c++) { 344 PetscInt e, eOff, eDof; 345 346 e = cone[c]; 347 ierr = PetscSectionGetDof(unionSection, e - pRefStart + (pEnd - pStart),&eDof);CHKERRQ(ierr); 348 if (eDof) { 349 ierr = PetscSectionGetOffset(unionSection, e - pRefStart + (pEnd - pStart), &eOff);CHKERRQ(ierr); 350 } 351 else { 352 ierr = DMLabelGetValue(identityRef, e, &e);CHKERRQ(ierr); 353 ierr = PetscSectionGetOffset(unionSection, e - pStart, &eOff);CHKERRQ(ierr); 354 } 355 unionCones[cOff + c] = eOff; 356 unionOrientations[cOff + c] = orientation[c]; 357 } 358 } 359 } 360 /* get the coordinates */ 361 { 362 PetscInt vStart, vEnd, vRefStart, vRefEnd, v, vDof, vOff; 363 PetscSection KcoordsSec, KrefCoordsSec; 364 Vec KcoordsVec, KrefCoordsVec; 365 PetscScalar *Kcoords; 366 367 DMGetCoordinateSection(K, &KcoordsSec);CHKERRQ(ierr); 368 DMGetCoordinatesLocal(K, &KcoordsVec);CHKERRQ(ierr); 369 DMGetCoordinateSection(Kref, &KrefCoordsSec);CHKERRQ(ierr); 370 DMGetCoordinatesLocal(Kref, &KrefCoordsVec);CHKERRQ(ierr); 371 372 numVerts = numDimPoints[0]; 373 ierr = PetscMalloc1(numVerts * dim,&unionCoords);CHKERRQ(ierr); 374 ierr = DMPlexGetDepthStratum(K,0,&vStart,&vEnd);CHKERRQ(ierr); 375 376 offset = 0; 377 for (v = vStart; v < vEnd; v++) { 378 ierr = PetscSectionGetOffset(unionSection,v - pStart,&vOff);CHKERRQ(ierr); 379 ierr = VecGetValuesSection(KcoordsVec, KcoordsSec, v, &Kcoords);CHKERRQ(ierr); 380 for (d = 0; d < dim; d++) { 381 unionCoords[offset * dim + d] = Kcoords[d]; 382 } 383 offset++; 384 } 385 ierr = DMPlexGetDepthStratum(Kref,0,&vRefStart,&vRefEnd);CHKERRQ(ierr); 386 for (v = vRefStart; v < vRefEnd; v++) { 387 ierr = PetscSectionGetDof(unionSection,v - pRefStart + (pEnd - pStart),&vDof);CHKERRQ(ierr); 388 ierr = PetscSectionGetOffset(unionSection,v - pRefStart + (pEnd - pStart),&vOff);CHKERRQ(ierr); 389 ierr = VecGetValuesSection(KrefCoordsVec, KrefCoordsSec, v, &Kcoords);CHKERRQ(ierr); 390 if (vDof) { 391 for (d = 0; d < dim; d++) { 392 unionCoords[offset * dim + d] = Kcoords[d]; 393 } 394 offset++; 395 } 396 } 397 } 398 ierr = DMCreate(comm,ref);CHKERRQ(ierr); 399 ierr = DMSetType(*ref,DMPLEX);CHKERRQ(ierr); 400 ierr = DMSetDimension(*ref,dim);CHKERRQ(ierr); 401 ierr = DMPlexCreateFromDAG(*ref,dim,numDimPoints,coneSizes,unionCones,unionOrientations,unionCoords);CHKERRQ(ierr); 402 /* set the tree */ 403 ierr = PetscSectionCreate(comm,&parentSection);CHKERRQ(ierr); 404 ierr = PetscSectionSetChart(parentSection,0,numUnionPoints);CHKERRQ(ierr); 405 for (p = pRefStart; p < pRefEnd; p++) { 406 PetscInt uDof, uOff; 407 408 ierr = PetscSectionGetDof(unionSection, p - pRefStart + (pEnd - pStart),&uDof);CHKERRQ(ierr); 409 ierr = PetscSectionGetOffset(unionSection, p - pRefStart + (pEnd - pStart),&uOff);CHKERRQ(ierr); 410 if (uDof) { 411 PetscSectionSetDof(parentSection,uOff,1);CHKERRQ(ierr); 412 } 413 } 414 ierr = PetscSectionSetUp(parentSection);CHKERRQ(ierr); 415 ierr = PetscSectionGetStorageSize(parentSection,&parentSize);CHKERRQ(ierr); 416 ierr = PetscMalloc2(parentSize,&parents,parentSize,&childIDs);CHKERRQ(ierr); 417 for (p = pRefStart; p < pRefEnd; p++) { 418 PetscInt uDof, uOff; 419 420 ierr = PetscSectionGetDof(unionSection, p - pRefStart + (pEnd - pStart),&uDof);CHKERRQ(ierr); 421 ierr = PetscSectionGetOffset(unionSection, p - pRefStart + (pEnd - pStart),&uOff);CHKERRQ(ierr); 422 if (uDof) { 423 PetscInt pOff, parent, parentU; 424 PetscSectionGetOffset(parentSection,uOff,&pOff);CHKERRQ(ierr); 425 DMLabelGetValue(identityRef,p,&parent);CHKERRQ(ierr); 426 ierr = PetscSectionGetOffset(unionSection, parent - pStart,&parentU);CHKERRQ(ierr); 427 parents[pOff] = parentU; 428 childIDs[pOff] = uOff; 429 } 430 } 431 ierr = DMPlexSetTree_Internal(*ref,parentSection,parents,childIDs,PETSC_TRUE,PETSC_FALSE);CHKERRQ(ierr); 432 ierr = PetscSectionDestroy(&parentSection);CHKERRQ(ierr); 433 ierr = PetscFree2(parents,childIDs);CHKERRQ(ierr); 434 435 /* clean up */ 436 ierr = PetscSectionDestroy(&unionSection);CHKERRQ(ierr); 437 ierr = PetscSectionDestroy(&unionConeSection);CHKERRQ(ierr); 438 ierr = ISDestroy(&perm);CHKERRQ(ierr); 439 ierr = PetscFree(unionCoords);CHKERRQ(ierr); 440 ierr = PetscFree2(unionCones,unionOrientations);CHKERRQ(ierr); 441 ierr = PetscFree2(coneSizes,numDimPoints);CHKERRQ(ierr); 442 PetscFunctionReturn(0); 443 } 444 445 #undef __FUNCT__ 446 #define __FUNCT__ "DMPlexCreateDefaultReferenceTree" 447 /*@ 448 DMPlexCreateDefaultReferenceTree - create a reference tree for isotropic hierarchical mesh refinement. 449 450 Collective on comm 451 452 Input Parameters: 453 + comm - the MPI communicator 454 . dim - the spatial dimension 455 - simplex - Flag for simplex, otherwise use a tensor-product cell 456 457 Output Parameters: 458 . ref - the reference tree DMPlex object 459 460 Level: intermediate 461 462 .keywords: reference cell 463 .seealso: DMPlexSetReferenceTree(), DMPlexGetReferenceTree() 464 @*/ 465 PetscErrorCode DMPlexCreateDefaultReferenceTree(MPI_Comm comm, PetscInt dim, PetscBool simplex, DM *ref) 466 { 467 DM_Plex *mesh; 468 DM K, Kref; 469 PetscInt p, pStart, pEnd; 470 DMLabel identity; 471 PetscErrorCode ierr; 472 473 PetscFunctionBegin; 474 #if 1 475 comm = PETSC_COMM_SELF; 476 #endif 477 /* create a reference element */ 478 ierr = DMPlexCreateReferenceCell(comm, dim, simplex, &K);CHKERRQ(ierr); 479 ierr = DMCreateLabel(K, "identity");CHKERRQ(ierr); 480 ierr = DMGetLabel(K, "identity", &identity);CHKERRQ(ierr); 481 ierr = DMPlexGetChart(K, &pStart, &pEnd);CHKERRQ(ierr); 482 for (p = pStart; p < pEnd; p++) { 483 ierr = DMLabelSetValue(identity, p, p);CHKERRQ(ierr); 484 } 485 /* refine it */ 486 ierr = DMRefine(K,comm,&Kref);CHKERRQ(ierr); 487 488 /* the reference tree is the union of these two, without duplicating 489 * points that appear in both */ 490 ierr = DMPlexCreateReferenceTree_Union(K, Kref, "identity", ref);CHKERRQ(ierr); 491 mesh = (DM_Plex *) (*ref)->data; 492 mesh->getchildsymmetry = DMPlexReferenceTreeGetChildSymmetry_Default; 493 ierr = DMDestroy(&K);CHKERRQ(ierr); 494 ierr = DMDestroy(&Kref);CHKERRQ(ierr); 495 PetscFunctionReturn(0); 496 } 497 498 #undef __FUNCT__ 499 #define __FUNCT__ "DMPlexTreeSymmetrize" 500 static PetscErrorCode DMPlexTreeSymmetrize(DM dm) 501 { 502 DM_Plex *mesh = (DM_Plex *)dm->data; 503 PetscSection childSec, pSec; 504 PetscInt p, pSize, cSize, parMax = PETSC_MIN_INT, parMin = PETSC_MAX_INT; 505 PetscInt *offsets, *children, pStart, pEnd; 506 PetscErrorCode ierr; 507 508 PetscFunctionBegin; 509 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 510 ierr = PetscSectionDestroy(&mesh->childSection);CHKERRQ(ierr); 511 ierr = PetscFree(mesh->children);CHKERRQ(ierr); 512 pSec = mesh->parentSection; 513 if (!pSec) PetscFunctionReturn(0); 514 ierr = PetscSectionGetStorageSize(pSec,&pSize);CHKERRQ(ierr); 515 for (p = 0; p < pSize; p++) { 516 PetscInt par = mesh->parents[p]; 517 518 parMax = PetscMax(parMax,par+1); 519 parMin = PetscMin(parMin,par); 520 } 521 if (parMin > parMax) { 522 parMin = -1; 523 parMax = -1; 524 } 525 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)pSec),&childSec);CHKERRQ(ierr); 526 ierr = PetscSectionSetChart(childSec,parMin,parMax);CHKERRQ(ierr); 527 for (p = 0; p < pSize; p++) { 528 PetscInt par = mesh->parents[p]; 529 530 ierr = PetscSectionAddDof(childSec,par,1);CHKERRQ(ierr); 531 } 532 ierr = PetscSectionSetUp(childSec);CHKERRQ(ierr); 533 ierr = PetscSectionGetStorageSize(childSec,&cSize);CHKERRQ(ierr); 534 ierr = PetscMalloc1(cSize,&children);CHKERRQ(ierr); 535 ierr = PetscCalloc1(parMax-parMin,&offsets);CHKERRQ(ierr); 536 ierr = PetscSectionGetChart(pSec,&pStart,&pEnd);CHKERRQ(ierr); 537 for (p = pStart; p < pEnd; p++) { 538 PetscInt dof, off, i; 539 540 ierr = PetscSectionGetDof(pSec,p,&dof);CHKERRQ(ierr); 541 ierr = PetscSectionGetOffset(pSec,p,&off);CHKERRQ(ierr); 542 for (i = 0; i < dof; i++) { 543 PetscInt par = mesh->parents[off + i], cOff; 544 545 ierr = PetscSectionGetOffset(childSec,par,&cOff);CHKERRQ(ierr); 546 children[cOff + offsets[par-parMin]++] = p; 547 } 548 } 549 mesh->childSection = childSec; 550 mesh->children = children; 551 ierr = PetscFree(offsets);CHKERRQ(ierr); 552 PetscFunctionReturn(0); 553 } 554 555 #undef __FUNCT__ 556 #define __FUNCT__ "AnchorsFlatten" 557 static PetscErrorCode AnchorsFlatten (PetscSection section, IS is, PetscSection *sectionNew, IS *isNew) 558 { 559 PetscInt pStart, pEnd, size, sizeNew, i, p, *valsNew = NULL; 560 const PetscInt *vals; 561 PetscSection secNew; 562 PetscBool anyNew, globalAnyNew; 563 PetscBool compress; 564 PetscErrorCode ierr; 565 566 PetscFunctionBegin; 567 ierr = PetscSectionGetChart(section,&pStart,&pEnd);CHKERRQ(ierr); 568 ierr = ISGetLocalSize(is,&size);CHKERRQ(ierr); 569 ierr = ISGetIndices(is,&vals);CHKERRQ(ierr); 570 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)section),&secNew);CHKERRQ(ierr); 571 ierr = PetscSectionSetChart(secNew,pStart,pEnd);CHKERRQ(ierr); 572 for (i = 0; i < size; i++) { 573 PetscInt dof; 574 575 p = vals[i]; 576 if (p < pStart || p >= pEnd) continue; 577 ierr = PetscSectionGetDof(section, p, &dof);CHKERRQ(ierr); 578 if (dof) break; 579 } 580 if (i == size) { 581 ierr = PetscSectionSetUp(secNew);CHKERRQ(ierr); 582 anyNew = PETSC_FALSE; 583 compress = PETSC_FALSE; 584 sizeNew = 0; 585 } 586 else { 587 anyNew = PETSC_TRUE; 588 for (p = pStart; p < pEnd; p++) { 589 PetscInt dof, off; 590 591 ierr = PetscSectionGetDof(section, p, &dof);CHKERRQ(ierr); 592 ierr = PetscSectionGetOffset(section, p, &off);CHKERRQ(ierr); 593 for (i = 0; i < dof; i++) { 594 PetscInt q = vals[off + i], qDof = 0; 595 596 if (q >= pStart && q < pEnd) { 597 ierr = PetscSectionGetDof(section, q, &qDof);CHKERRQ(ierr); 598 } 599 if (qDof) { 600 ierr = PetscSectionAddDof(secNew, p, qDof);CHKERRQ(ierr); 601 } 602 else { 603 ierr = PetscSectionAddDof(secNew, p, 1);CHKERRQ(ierr); 604 } 605 } 606 } 607 ierr = PetscSectionSetUp(secNew);CHKERRQ(ierr); 608 ierr = PetscSectionGetStorageSize(secNew,&sizeNew);CHKERRQ(ierr); 609 ierr = PetscMalloc1(sizeNew,&valsNew);CHKERRQ(ierr); 610 compress = PETSC_FALSE; 611 for (p = pStart; p < pEnd; p++) { 612 PetscInt dof, off, count, offNew, dofNew; 613 614 ierr = PetscSectionGetDof(section, p, &dof);CHKERRQ(ierr); 615 ierr = PetscSectionGetOffset(section, p, &off);CHKERRQ(ierr); 616 ierr = PetscSectionGetDof(secNew, p, &dofNew);CHKERRQ(ierr); 617 ierr = PetscSectionGetOffset(secNew, p, &offNew);CHKERRQ(ierr); 618 count = 0; 619 for (i = 0; i < dof; i++) { 620 PetscInt q = vals[off + i], qDof = 0, qOff = 0, j; 621 622 if (q >= pStart && q < pEnd) { 623 ierr = PetscSectionGetDof(section, q, &qDof);CHKERRQ(ierr); 624 ierr = PetscSectionGetOffset(section, q, &qOff);CHKERRQ(ierr); 625 } 626 if (qDof) { 627 PetscInt oldCount = count; 628 629 for (j = 0; j < qDof; j++) { 630 PetscInt k, r = vals[qOff + j]; 631 632 for (k = 0; k < oldCount; k++) { 633 if (valsNew[offNew + k] == r) { 634 break; 635 } 636 } 637 if (k == oldCount) { 638 valsNew[offNew + count++] = r; 639 } 640 } 641 } 642 else { 643 PetscInt k, oldCount = count; 644 645 for (k = 0; k < oldCount; k++) { 646 if (valsNew[offNew + k] == q) { 647 break; 648 } 649 } 650 if (k == oldCount) { 651 valsNew[offNew + count++] = q; 652 } 653 } 654 } 655 if (count < dofNew) { 656 ierr = PetscSectionSetDof(secNew, p, count);CHKERRQ(ierr); 657 compress = PETSC_TRUE; 658 } 659 } 660 } 661 ierr = ISRestoreIndices(is,&vals);CHKERRQ(ierr); 662 ierr = MPIU_Allreduce(&anyNew,&globalAnyNew,1,MPIU_BOOL,MPI_LOR,PetscObjectComm((PetscObject)secNew));CHKERRQ(ierr); 663 if (!globalAnyNew) { 664 ierr = PetscSectionDestroy(&secNew);CHKERRQ(ierr); 665 *sectionNew = NULL; 666 *isNew = NULL; 667 } 668 else { 669 PetscBool globalCompress; 670 671 ierr = MPIU_Allreduce(&compress,&globalCompress,1,MPIU_BOOL,MPI_LOR,PetscObjectComm((PetscObject)secNew));CHKERRQ(ierr); 672 if (compress) { 673 PetscSection secComp; 674 PetscInt *valsComp = NULL; 675 676 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)section),&secComp);CHKERRQ(ierr); 677 ierr = PetscSectionSetChart(secComp,pStart,pEnd);CHKERRQ(ierr); 678 for (p = pStart; p < pEnd; p++) { 679 PetscInt dof; 680 681 ierr = PetscSectionGetDof(secNew, p, &dof);CHKERRQ(ierr); 682 ierr = PetscSectionSetDof(secComp, p, dof);CHKERRQ(ierr); 683 } 684 ierr = PetscSectionSetUp(secComp);CHKERRQ(ierr); 685 ierr = PetscSectionGetStorageSize(secComp,&sizeNew);CHKERRQ(ierr); 686 ierr = PetscMalloc1(sizeNew,&valsComp);CHKERRQ(ierr); 687 for (p = pStart; p < pEnd; p++) { 688 PetscInt dof, off, offNew, j; 689 690 ierr = PetscSectionGetDof(secNew, p, &dof);CHKERRQ(ierr); 691 ierr = PetscSectionGetOffset(secNew, p, &off);CHKERRQ(ierr); 692 ierr = PetscSectionGetOffset(secComp, p, &offNew);CHKERRQ(ierr); 693 for (j = 0; j < dof; j++) { 694 valsComp[offNew + j] = valsNew[off + j]; 695 } 696 } 697 ierr = PetscSectionDestroy(&secNew);CHKERRQ(ierr); 698 secNew = secComp; 699 ierr = PetscFree(valsNew);CHKERRQ(ierr); 700 valsNew = valsComp; 701 } 702 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)is),sizeNew,valsNew,PETSC_OWN_POINTER,isNew);CHKERRQ(ierr); 703 } 704 PetscFunctionReturn(0); 705 } 706 707 #undef __FUNCT__ 708 #define __FUNCT__ "DMPlexCreateAnchors_Tree" 709 static PetscErrorCode DMPlexCreateAnchors_Tree(DM dm) 710 { 711 PetscInt p, pStart, pEnd, *anchors, size; 712 PetscInt aMin = PETSC_MAX_INT, aMax = PETSC_MIN_INT; 713 PetscSection aSec; 714 DMLabel canonLabel; 715 IS aIS; 716 PetscErrorCode ierr; 717 718 PetscFunctionBegin; 719 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 720 ierr = DMPlexGetChart(dm,&pStart,&pEnd);CHKERRQ(ierr); 721 ierr = DMGetLabel(dm,"canonical",&canonLabel);CHKERRQ(ierr); 722 for (p = pStart; p < pEnd; p++) { 723 PetscInt parent; 724 725 if (canonLabel) { 726 PetscInt canon; 727 728 ierr = DMLabelGetValue(canonLabel,p,&canon);CHKERRQ(ierr); 729 if (p != canon) continue; 730 } 731 ierr = DMPlexGetTreeParent(dm,p,&parent,NULL);CHKERRQ(ierr); 732 if (parent != p) { 733 aMin = PetscMin(aMin,p); 734 aMax = PetscMax(aMax,p+1); 735 } 736 } 737 if (aMin > aMax) { 738 aMin = -1; 739 aMax = -1; 740 } 741 ierr = PetscSectionCreate(PETSC_COMM_SELF,&aSec);CHKERRQ(ierr); 742 ierr = PetscSectionSetChart(aSec,aMin,aMax);CHKERRQ(ierr); 743 for (p = aMin; p < aMax; p++) { 744 PetscInt parent, ancestor = p; 745 746 if (canonLabel) { 747 PetscInt canon; 748 749 ierr = DMLabelGetValue(canonLabel,p,&canon);CHKERRQ(ierr); 750 if (p != canon) continue; 751 } 752 ierr = DMPlexGetTreeParent(dm,p,&parent,NULL);CHKERRQ(ierr); 753 while (parent != ancestor) { 754 ancestor = parent; 755 ierr = DMPlexGetTreeParent(dm,ancestor,&parent,NULL);CHKERRQ(ierr); 756 } 757 if (ancestor != p) { 758 PetscInt closureSize, *closure = NULL; 759 760 ierr = DMPlexGetTransitiveClosure(dm,ancestor,PETSC_TRUE,&closureSize,&closure);CHKERRQ(ierr); 761 ierr = PetscSectionSetDof(aSec,p,closureSize);CHKERRQ(ierr); 762 ierr = DMPlexRestoreTransitiveClosure(dm,ancestor,PETSC_TRUE,&closureSize,&closure);CHKERRQ(ierr); 763 } 764 } 765 ierr = PetscSectionSetUp(aSec);CHKERRQ(ierr); 766 ierr = PetscSectionGetStorageSize(aSec,&size);CHKERRQ(ierr); 767 ierr = PetscMalloc1(size,&anchors);CHKERRQ(ierr); 768 for (p = aMin; p < aMax; p++) { 769 PetscInt parent, ancestor = p; 770 771 if (canonLabel) { 772 PetscInt canon; 773 774 ierr = DMLabelGetValue(canonLabel,p,&canon);CHKERRQ(ierr); 775 if (p != canon) continue; 776 } 777 ierr = DMPlexGetTreeParent(dm,p,&parent,NULL);CHKERRQ(ierr); 778 while (parent != ancestor) { 779 ancestor = parent; 780 ierr = DMPlexGetTreeParent(dm,ancestor,&parent,NULL);CHKERRQ(ierr); 781 } 782 if (ancestor != p) { 783 PetscInt j, closureSize, *closure = NULL, aOff; 784 785 ierr = PetscSectionGetOffset(aSec,p,&aOff);CHKERRQ(ierr); 786 787 ierr = DMPlexGetTransitiveClosure(dm,ancestor,PETSC_TRUE,&closureSize,&closure);CHKERRQ(ierr); 788 for (j = 0; j < closureSize; j++) { 789 anchors[aOff + j] = closure[2*j]; 790 } 791 ierr = DMPlexRestoreTransitiveClosure(dm,ancestor,PETSC_TRUE,&closureSize,&closure);CHKERRQ(ierr); 792 } 793 } 794 ierr = ISCreateGeneral(PETSC_COMM_SELF,size,anchors,PETSC_OWN_POINTER,&aIS);CHKERRQ(ierr); 795 { 796 PetscSection aSecNew = aSec; 797 IS aISNew = aIS; 798 799 ierr = PetscObjectReference((PetscObject)aSec);CHKERRQ(ierr); 800 ierr = PetscObjectReference((PetscObject)aIS);CHKERRQ(ierr); 801 while (aSecNew) { 802 ierr = PetscSectionDestroy(&aSec);CHKERRQ(ierr); 803 ierr = ISDestroy(&aIS);CHKERRQ(ierr); 804 aSec = aSecNew; 805 aIS = aISNew; 806 aSecNew = NULL; 807 aISNew = NULL; 808 ierr = AnchorsFlatten(aSec,aIS,&aSecNew,&aISNew);CHKERRQ(ierr); 809 } 810 } 811 ierr = DMPlexSetAnchors(dm,aSec,aIS);CHKERRQ(ierr); 812 ierr = PetscSectionDestroy(&aSec);CHKERRQ(ierr); 813 ierr = ISDestroy(&aIS);CHKERRQ(ierr); 814 PetscFunctionReturn(0); 815 } 816 817 #undef __FUNCT__ 818 #define __FUNCT__ "DMPlexGetTrueSupportSize" 819 static PetscErrorCode DMPlexGetTrueSupportSize(DM dm,PetscInt p,PetscInt *dof,PetscInt *numTrueSupp) 820 { 821 PetscErrorCode ierr; 822 823 PetscFunctionBegin; 824 if (numTrueSupp[p] == -1) { 825 PetscInt i, alldof; 826 const PetscInt *supp; 827 PetscInt count = 0; 828 829 ierr = DMPlexGetSupportSize(dm,p,&alldof);CHKERRQ(ierr); 830 ierr = DMPlexGetSupport(dm,p,&supp);CHKERRQ(ierr); 831 for (i = 0; i < alldof; i++) { 832 PetscInt q = supp[i], numCones, j; 833 const PetscInt *cone; 834 835 ierr = DMPlexGetConeSize(dm,q,&numCones);CHKERRQ(ierr); 836 ierr = DMPlexGetCone(dm,q,&cone);CHKERRQ(ierr); 837 for (j = 0; j < numCones; j++) { 838 if (cone[j] == p) break; 839 } 840 if (j < numCones) count++; 841 } 842 numTrueSupp[p] = count; 843 } 844 *dof = numTrueSupp[p]; 845 PetscFunctionReturn(0); 846 } 847 848 #undef __FUNCT__ 849 #define __FUNCT__ "DMPlexTreeExchangeSupports" 850 static PetscErrorCode DMPlexTreeExchangeSupports(DM dm) 851 { 852 DM_Plex *mesh = (DM_Plex *)dm->data; 853 PetscSection newSupportSection; 854 PetscInt newSize, *newSupports, pStart, pEnd, p, d, depth; 855 PetscInt *numTrueSupp; 856 PetscInt *offsets; 857 PetscErrorCode ierr; 858 859 PetscFunctionBegin; 860 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 861 /* symmetrize the hierarchy */ 862 ierr = DMPlexGetDepth(dm,&depth);CHKERRQ(ierr); 863 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)(mesh->supportSection)),&newSupportSection);CHKERRQ(ierr); 864 ierr = DMPlexGetChart(dm,&pStart,&pEnd);CHKERRQ(ierr); 865 ierr = PetscSectionSetChart(newSupportSection,pStart,pEnd);CHKERRQ(ierr); 866 ierr = PetscCalloc1(pEnd,&offsets);CHKERRQ(ierr); 867 ierr = PetscMalloc1(pEnd,&numTrueSupp);CHKERRQ(ierr); 868 for (p = 0; p < pEnd; p++) numTrueSupp[p] = -1; 869 /* if a point is in the (true) support of q, it should be in the support of 870 * parent(q) */ 871 for (d = 0; d <= depth; d++) { 872 ierr = DMPlexGetHeightStratum(dm,d,&pStart,&pEnd);CHKERRQ(ierr); 873 for (p = pStart; p < pEnd; ++p) { 874 PetscInt dof, q, qdof, parent; 875 876 ierr = DMPlexGetTrueSupportSize(dm,p,&dof,numTrueSupp);CHKERRQ(ierr); 877 ierr = PetscSectionAddDof(newSupportSection, p, dof);CHKERRQ(ierr); 878 q = p; 879 ierr = DMPlexGetTreeParent(dm,q,&parent,NULL);CHKERRQ(ierr); 880 while (parent != q && parent >= pStart && parent < pEnd) { 881 q = parent; 882 883 ierr = DMPlexGetTrueSupportSize(dm,q,&qdof,numTrueSupp);CHKERRQ(ierr); 884 ierr = PetscSectionAddDof(newSupportSection,p,qdof);CHKERRQ(ierr); 885 ierr = PetscSectionAddDof(newSupportSection,q,dof);CHKERRQ(ierr); 886 ierr = DMPlexGetTreeParent(dm,q,&parent,NULL);CHKERRQ(ierr); 887 } 888 } 889 } 890 ierr = PetscSectionSetUp(newSupportSection);CHKERRQ(ierr); 891 ierr = PetscSectionGetStorageSize(newSupportSection,&newSize);CHKERRQ(ierr); 892 ierr = PetscMalloc1(newSize,&newSupports);CHKERRQ(ierr); 893 for (d = 0; d <= depth; d++) { 894 ierr = DMPlexGetHeightStratum(dm,d,&pStart,&pEnd);CHKERRQ(ierr); 895 for (p = pStart; p < pEnd; p++) { 896 PetscInt dof, off, q, qdof, qoff, newDof, newOff, newqOff, i, parent; 897 898 ierr = PetscSectionGetDof(mesh->supportSection, p, &dof);CHKERRQ(ierr); 899 ierr = PetscSectionGetOffset(mesh->supportSection, p, &off);CHKERRQ(ierr); 900 ierr = PetscSectionGetDof(newSupportSection, p, &newDof);CHKERRQ(ierr); 901 ierr = PetscSectionGetOffset(newSupportSection, p, &newOff);CHKERRQ(ierr); 902 for (i = 0; i < dof; i++) { 903 PetscInt numCones, j; 904 const PetscInt *cone; 905 PetscInt q = mesh->supports[off + i]; 906 907 ierr = DMPlexGetConeSize(dm,q,&numCones);CHKERRQ(ierr); 908 ierr = DMPlexGetCone(dm,q,&cone);CHKERRQ(ierr); 909 for (j = 0; j < numCones; j++) { 910 if (cone[j] == p) break; 911 } 912 if (j < numCones) newSupports[newOff+offsets[p]++] = q; 913 } 914 mesh->maxSupportSize = PetscMax(mesh->maxSupportSize,newDof); 915 916 q = p; 917 ierr = DMPlexGetTreeParent(dm,q,&parent,NULL);CHKERRQ(ierr); 918 while (parent != q && parent >= pStart && parent < pEnd) { 919 q = parent; 920 ierr = PetscSectionGetDof(mesh->supportSection, q, &qdof);CHKERRQ(ierr); 921 ierr = PetscSectionGetOffset(mesh->supportSection, q, &qoff);CHKERRQ(ierr); 922 ierr = PetscSectionGetOffset(newSupportSection, q, &newqOff);CHKERRQ(ierr); 923 for (i = 0; i < qdof; i++) { 924 PetscInt numCones, j; 925 const PetscInt *cone; 926 PetscInt r = mesh->supports[qoff + i]; 927 928 ierr = DMPlexGetConeSize(dm,r,&numCones);CHKERRQ(ierr); 929 ierr = DMPlexGetCone(dm,r,&cone);CHKERRQ(ierr); 930 for (j = 0; j < numCones; j++) { 931 if (cone[j] == q) break; 932 } 933 if (j < numCones) newSupports[newOff+offsets[p]++] = r; 934 } 935 for (i = 0; i < dof; i++) { 936 PetscInt numCones, j; 937 const PetscInt *cone; 938 PetscInt r = mesh->supports[off + i]; 939 940 ierr = DMPlexGetConeSize(dm,r,&numCones);CHKERRQ(ierr); 941 ierr = DMPlexGetCone(dm,r,&cone);CHKERRQ(ierr); 942 for (j = 0; j < numCones; j++) { 943 if (cone[j] == p) break; 944 } 945 if (j < numCones) newSupports[newqOff+offsets[q]++] = r; 946 } 947 ierr = DMPlexGetTreeParent(dm,q,&parent,NULL);CHKERRQ(ierr); 948 } 949 } 950 } 951 ierr = PetscSectionDestroy(&mesh->supportSection);CHKERRQ(ierr); 952 mesh->supportSection = newSupportSection; 953 ierr = PetscFree(mesh->supports);CHKERRQ(ierr); 954 mesh->supports = newSupports; 955 ierr = PetscFree(offsets);CHKERRQ(ierr); 956 ierr = PetscFree(numTrueSupp);CHKERRQ(ierr); 957 958 PetscFunctionReturn(0); 959 } 960 961 static PetscErrorCode DMPlexComputeAnchorMatrix_Tree_Direct(DM,PetscSection,PetscSection,Mat); 962 static PetscErrorCode DMPlexComputeAnchorMatrix_Tree_FromReference(DM,PetscSection,PetscSection,Mat); 963 964 #undef __FUNCT__ 965 #define __FUNCT__ "DMPlexSetTree_Internal" 966 static PetscErrorCode DMPlexSetTree_Internal(DM dm, PetscSection parentSection, PetscInt *parents, PetscInt *childIDs, PetscBool computeCanonical, PetscBool exchangeSupports) 967 { 968 DM_Plex *mesh = (DM_Plex *)dm->data; 969 DM refTree; 970 PetscInt size; 971 PetscErrorCode ierr; 972 973 PetscFunctionBegin; 974 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 975 PetscValidHeaderSpecific(parentSection, PETSC_SECTION_CLASSID, 2); 976 ierr = PetscObjectReference((PetscObject)parentSection);CHKERRQ(ierr); 977 ierr = PetscSectionDestroy(&mesh->parentSection);CHKERRQ(ierr); 978 mesh->parentSection = parentSection; 979 ierr = PetscSectionGetStorageSize(parentSection,&size);CHKERRQ(ierr); 980 if (parents != mesh->parents) { 981 ierr = PetscFree(mesh->parents);CHKERRQ(ierr); 982 ierr = PetscMalloc1(size,&mesh->parents);CHKERRQ(ierr); 983 ierr = PetscMemcpy(mesh->parents, parents, size * sizeof(*parents));CHKERRQ(ierr); 984 } 985 if (childIDs != mesh->childIDs) { 986 ierr = PetscFree(mesh->childIDs);CHKERRQ(ierr); 987 ierr = PetscMalloc1(size,&mesh->childIDs);CHKERRQ(ierr); 988 ierr = PetscMemcpy(mesh->childIDs, childIDs, size * sizeof(*childIDs));CHKERRQ(ierr); 989 } 990 ierr = DMPlexGetReferenceTree(dm,&refTree);CHKERRQ(ierr); 991 if (refTree) { 992 DMLabel canonLabel; 993 994 ierr = DMGetLabel(refTree,"canonical",&canonLabel);CHKERRQ(ierr); 995 if (canonLabel) { 996 PetscInt i; 997 998 for (i = 0; i < size; i++) { 999 PetscInt canon; 1000 ierr = DMLabelGetValue(canonLabel, mesh->childIDs[i], &canon);CHKERRQ(ierr); 1001 if (canon >= 0) { 1002 mesh->childIDs[i] = canon; 1003 } 1004 } 1005 } 1006 mesh->computeanchormatrix = DMPlexComputeAnchorMatrix_Tree_FromReference; 1007 } 1008 else { 1009 mesh->computeanchormatrix = DMPlexComputeAnchorMatrix_Tree_Direct; 1010 } 1011 ierr = DMPlexTreeSymmetrize(dm);CHKERRQ(ierr); 1012 if (computeCanonical) { 1013 PetscInt d, dim; 1014 1015 /* add the canonical label */ 1016 ierr = DMGetDimension(dm,&dim);CHKERRQ(ierr); 1017 ierr = DMCreateLabel(dm,"canonical");CHKERRQ(ierr); 1018 for (d = 0; d <= dim; d++) { 1019 PetscInt p, dStart, dEnd, canon = -1, cNumChildren; 1020 const PetscInt *cChildren; 1021 1022 ierr = DMPlexGetDepthStratum(dm,d,&dStart,&dEnd);CHKERRQ(ierr); 1023 for (p = dStart; p < dEnd; p++) { 1024 ierr = DMPlexGetTreeChildren(dm,p,&cNumChildren,&cChildren);CHKERRQ(ierr); 1025 if (cNumChildren) { 1026 canon = p; 1027 break; 1028 } 1029 } 1030 if (canon == -1) continue; 1031 for (p = dStart; p < dEnd; p++) { 1032 PetscInt numChildren, i; 1033 const PetscInt *children; 1034 1035 ierr = DMPlexGetTreeChildren(dm,p,&numChildren,&children);CHKERRQ(ierr); 1036 if (numChildren) { 1037 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); 1038 ierr = DMSetLabelValue(dm,"canonical",p,canon);CHKERRQ(ierr); 1039 for (i = 0; i < numChildren; i++) { 1040 ierr = DMSetLabelValue(dm,"canonical",children[i],cChildren[i]);CHKERRQ(ierr); 1041 } 1042 } 1043 } 1044 } 1045 } 1046 if (exchangeSupports) { 1047 ierr = DMPlexTreeExchangeSupports(dm);CHKERRQ(ierr); 1048 } 1049 mesh->createanchors = DMPlexCreateAnchors_Tree; 1050 /* reset anchors */ 1051 ierr = DMPlexSetAnchors(dm,NULL,NULL);CHKERRQ(ierr); 1052 PetscFunctionReturn(0); 1053 } 1054 1055 #undef __FUNCT__ 1056 #define __FUNCT__ "DMPlexSetTree" 1057 /*@ 1058 DMPlexSetTree - set the tree that describes the hierarchy of non-conforming mesh points. This routine also creates 1059 the point-to-point constraints determined by the tree: a point is constained to the points in the closure of its 1060 tree root. 1061 1062 Collective on dm 1063 1064 Input Parameters: 1065 + dm - the DMPlex object 1066 . parentSection - a section describing the tree: a point has a parent if it has 1 dof in the section; the section 1067 offset indexes the parent and childID list; the reference count of parentSection is incremented 1068 . parents - a list of the point parents; copied, can be destroyed 1069 - childIDs - identifies the relationship of the child point to the parent point; if there is a reference tree, then 1070 the child corresponds to the point in the reference tree with index childIDs; copied, can be destroyed 1071 1072 Level: intermediate 1073 1074 .seealso: DMPlexGetTree(), DMPlexSetReferenceTree(), DMPlexSetAnchors(), DMPlexGetTreeParent(), DMPlexGetTreeChildren() 1075 @*/ 1076 PetscErrorCode DMPlexSetTree(DM dm, PetscSection parentSection, PetscInt parents[], PetscInt childIDs[]) 1077 { 1078 PetscErrorCode ierr; 1079 1080 PetscFunctionBegin; 1081 ierr = DMPlexSetTree_Internal(dm,parentSection,parents,childIDs,PETSC_FALSE,PETSC_TRUE);CHKERRQ(ierr); 1082 PetscFunctionReturn(0); 1083 } 1084 1085 #undef __FUNCT__ 1086 #define __FUNCT__ "DMPlexGetTree" 1087 /*@ 1088 DMPlexGetTree - get the tree that describes the hierarchy of non-conforming mesh points. 1089 Collective on dm 1090 1091 Input Parameters: 1092 . dm - the DMPlex object 1093 1094 Output Parameters: 1095 + parentSection - a section describing the tree: a point has a parent if it has 1 dof in the section; the section 1096 offset indexes the parent and childID list 1097 . parents - a list of the point parents 1098 . childIDs - identifies the relationship of the child point to the parent point; if there is a reference tree, then 1099 the child corresponds to the point in the reference tree with index childID 1100 . childSection - the inverse of the parent section 1101 - children - a list of the point children 1102 1103 Level: intermediate 1104 1105 .seealso: DMPlexSetTree(), DMPlexSetReferenceTree(), DMPlexSetAnchors(), DMPlexGetTreeParent(), DMPlexGetTreeChildren() 1106 @*/ 1107 PetscErrorCode DMPlexGetTree(DM dm, PetscSection *parentSection, PetscInt *parents[], PetscInt *childIDs[], PetscSection *childSection, PetscInt *children[]) 1108 { 1109 DM_Plex *mesh = (DM_Plex *)dm->data; 1110 1111 PetscFunctionBegin; 1112 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1113 if (parentSection) *parentSection = mesh->parentSection; 1114 if (parents) *parents = mesh->parents; 1115 if (childIDs) *childIDs = mesh->childIDs; 1116 if (childSection) *childSection = mesh->childSection; 1117 if (children) *children = mesh->children; 1118 PetscFunctionReturn(0); 1119 } 1120 1121 #undef __FUNCT__ 1122 #define __FUNCT__ "DMPlexGetTreeParent" 1123 /*@ 1124 DMPlexGetTreeParent - get the parent of a point in the tree describing the point hierarchy (not the Sieve DAG) 1125 1126 Input Parameters: 1127 + dm - the DMPlex object 1128 - point - the query point 1129 1130 Output Parameters: 1131 + parent - if not NULL, set to the parent of the point, or the point itself if the point does not have a parent 1132 - childID - if not NULL, set to the child ID of the point with respect to its parent, or 0 if the point 1133 does not have a parent 1134 1135 Level: intermediate 1136 1137 .seealso: DMPlexSetTree(), DMPlexGetTree(), DMPlexGetTreeChildren() 1138 @*/ 1139 PetscErrorCode DMPlexGetTreeParent(DM dm, PetscInt point, PetscInt *parent, PetscInt *childID) 1140 { 1141 DM_Plex *mesh = (DM_Plex *)dm->data; 1142 PetscSection pSec; 1143 PetscErrorCode ierr; 1144 1145 PetscFunctionBegin; 1146 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1147 pSec = mesh->parentSection; 1148 if (pSec && point >= pSec->pStart && point < pSec->pEnd) { 1149 PetscInt dof; 1150 1151 ierr = PetscSectionGetDof (pSec, point, &dof);CHKERRQ(ierr); 1152 if (dof) { 1153 PetscInt off; 1154 1155 ierr = PetscSectionGetOffset (pSec, point, &off);CHKERRQ(ierr); 1156 if (parent) *parent = mesh->parents[off]; 1157 if (childID) *childID = mesh->childIDs[off]; 1158 PetscFunctionReturn(0); 1159 } 1160 } 1161 if (parent) { 1162 *parent = point; 1163 } 1164 if (childID) { 1165 *childID = 0; 1166 } 1167 PetscFunctionReturn(0); 1168 } 1169 1170 #undef __FUNCT__ 1171 #define __FUNCT__ "DMPlexGetTreeChildren" 1172 /*@C 1173 DMPlexGetTreeChildren - get the children of a point in the tree describing the point hierarchy (not the Sieve DAG) 1174 1175 Input Parameters: 1176 + dm - the DMPlex object 1177 - point - the query point 1178 1179 Output Parameters: 1180 + numChildren - if not NULL, set to the number of children 1181 - children - if not NULL, set to a list children, or set to NULL if the point has no children 1182 1183 Level: intermediate 1184 1185 Fortran Notes: 1186 Since it returns an array, this routine is only available in Fortran 90, and you must 1187 include petsc.h90 in your code. 1188 1189 .seealso: DMPlexSetTree(), DMPlexGetTree(), DMPlexGetTreeParent() 1190 @*/ 1191 PetscErrorCode DMPlexGetTreeChildren(DM dm, PetscInt point, PetscInt *numChildren, const PetscInt *children[]) 1192 { 1193 DM_Plex *mesh = (DM_Plex *)dm->data; 1194 PetscSection childSec; 1195 PetscInt dof = 0; 1196 PetscErrorCode ierr; 1197 1198 PetscFunctionBegin; 1199 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1200 childSec = mesh->childSection; 1201 if (childSec && point >= childSec->pStart && point < childSec->pEnd) { 1202 ierr = PetscSectionGetDof (childSec, point, &dof);CHKERRQ(ierr); 1203 } 1204 if (numChildren) *numChildren = dof; 1205 if (children) { 1206 if (dof) { 1207 PetscInt off; 1208 1209 ierr = PetscSectionGetOffset (childSec, point, &off);CHKERRQ(ierr); 1210 *children = &mesh->children[off]; 1211 } 1212 else { 1213 *children = NULL; 1214 } 1215 } 1216 PetscFunctionReturn(0); 1217 } 1218 1219 #undef __FUNCT__ 1220 #define __FUNCT__ "DMPlexComputeAnchorMatrix_Tree_Direct" 1221 static PetscErrorCode DMPlexComputeAnchorMatrix_Tree_Direct(DM dm, PetscSection section, PetscSection cSec, Mat cMat) 1222 { 1223 PetscDS ds; 1224 PetscInt spdim; 1225 PetscInt numFields, f, c, cStart, cEnd, pStart, pEnd, conStart, conEnd; 1226 const PetscInt *anchors; 1227 PetscSection aSec; 1228 PetscReal *v0, *v0parent, *vtmp, *J, *Jparent, *invJparent, detJ, detJparent; 1229 IS aIS; 1230 PetscErrorCode ierr; 1231 1232 PetscFunctionBegin; 1233 ierr = DMPlexGetChart(dm,&pStart,&pEnd);CHKERRQ(ierr); 1234 ierr = DMGetDS(dm,&ds);CHKERRQ(ierr); 1235 ierr = PetscDSGetNumFields(ds,&numFields);CHKERRQ(ierr); 1236 ierr = DMPlexGetHeightStratum(dm,0,&cStart,&cEnd);CHKERRQ(ierr); 1237 ierr = DMPlexGetAnchors(dm,&aSec,&aIS);CHKERRQ(ierr); 1238 ierr = ISGetIndices(aIS,&anchors);CHKERRQ(ierr); 1239 ierr = PetscSectionGetChart(cSec,&conStart,&conEnd);CHKERRQ(ierr); 1240 ierr = DMGetDimension(dm,&spdim);CHKERRQ(ierr); 1241 ierr = PetscMalloc6(spdim,&v0,spdim,&v0parent,spdim,&vtmp,spdim*spdim,&J,spdim*spdim,&Jparent,spdim*spdim,&invJparent);CHKERRQ(ierr); 1242 1243 for (f = 0; f < numFields; f++) { 1244 PetscObject disc; 1245 PetscFE fe = NULL; 1246 PetscFV fv = NULL; 1247 PetscClassId id; 1248 PetscDualSpace space; 1249 PetscInt i, j, k, nPoints, offset; 1250 PetscInt fSize, fComp; 1251 PetscReal *B = NULL; 1252 PetscReal *weights, *pointsRef, *pointsReal; 1253 Mat Amat, Bmat, Xmat; 1254 1255 ierr = PetscDSGetDiscretization(ds,f,&disc);CHKERRQ(ierr); 1256 ierr = PetscObjectGetClassId(disc,&id);CHKERRQ(ierr); 1257 if (id == PETSCFE_CLASSID) { 1258 fe = (PetscFE) disc; 1259 ierr = PetscFEGetDualSpace(fe,&space);CHKERRQ(ierr); 1260 ierr = PetscDualSpaceGetDimension(space,&fSize);CHKERRQ(ierr); 1261 ierr = PetscFEGetNumComponents(fe,&fComp);CHKERRQ(ierr); 1262 } 1263 else if (id == PETSCFV_CLASSID) { 1264 fv = (PetscFV) disc; 1265 ierr = PetscFVGetDualSpace(fv,&space);CHKERRQ(ierr); 1266 ierr = PetscDualSpaceGetDimension(space,&fSize);CHKERRQ(ierr); 1267 ierr = PetscFVGetNumComponents(fv,&fComp);CHKERRQ(ierr); 1268 } 1269 else SETERRQ1(PetscObjectComm(disc),PETSC_ERR_ARG_UNKNOWN_TYPE, "PetscDS discretization id %d not recognized.", id); 1270 1271 ierr = MatCreate(PETSC_COMM_SELF,&Amat);CHKERRQ(ierr); 1272 ierr = MatSetSizes(Amat,fSize,fSize,fSize,fSize);CHKERRQ(ierr); 1273 ierr = MatSetType(Amat,MATSEQDENSE);CHKERRQ(ierr); 1274 ierr = MatSetUp(Amat);CHKERRQ(ierr); 1275 ierr = MatDuplicate(Amat,MAT_DO_NOT_COPY_VALUES,&Bmat);CHKERRQ(ierr); 1276 ierr = MatDuplicate(Amat,MAT_DO_NOT_COPY_VALUES,&Xmat);CHKERRQ(ierr); 1277 nPoints = 0; 1278 for (i = 0; i < fSize; i++) { 1279 PetscInt qPoints; 1280 PetscQuadrature quad; 1281 1282 ierr = PetscDualSpaceGetFunctional(space,i,&quad);CHKERRQ(ierr); 1283 ierr = PetscQuadratureGetData(quad,NULL,&qPoints,NULL,NULL);CHKERRQ(ierr); 1284 nPoints += qPoints; 1285 } 1286 ierr = PetscMalloc3(nPoints,&weights,spdim*nPoints,&pointsRef,spdim*nPoints,&pointsReal);CHKERRQ(ierr); 1287 offset = 0; 1288 for (i = 0; i < fSize; i++) { 1289 PetscInt qPoints; 1290 const PetscReal *p, *w; 1291 PetscQuadrature quad; 1292 1293 ierr = PetscDualSpaceGetFunctional(space,i,&quad);CHKERRQ(ierr); 1294 ierr = PetscQuadratureGetData(quad,NULL,&qPoints,&p,&w);CHKERRQ(ierr); 1295 ierr = PetscMemcpy(weights+offset,w,qPoints*sizeof(*w));CHKERRQ(ierr); 1296 ierr = PetscMemcpy(pointsRef+spdim*offset,p,spdim*qPoints*sizeof(*p));CHKERRQ(ierr); 1297 offset += qPoints; 1298 } 1299 if (id == PETSCFE_CLASSID) { 1300 ierr = PetscFEGetTabulation(fe,nPoints,pointsRef,&B,NULL,NULL);CHKERRQ(ierr); 1301 } 1302 else { 1303 ierr = PetscFVGetTabulation(fv,nPoints,pointsRef,&B,NULL,NULL);CHKERRQ(ierr); 1304 } 1305 offset = 0; 1306 for (i = 0; i < fSize; i++) { 1307 PetscInt qPoints; 1308 PetscQuadrature quad; 1309 1310 ierr = PetscDualSpaceGetFunctional(space,i,&quad);CHKERRQ(ierr); 1311 ierr = PetscQuadratureGetData(quad,NULL,&qPoints,NULL,NULL);CHKERRQ(ierr); 1312 for (j = 0; j < fSize; j++) { 1313 PetscScalar val = 0.; 1314 1315 for (k = 0; k < qPoints; k++) { 1316 val += B[((offset + k) * fSize + j) * fComp] * weights[k]; 1317 } 1318 ierr = MatSetValue(Amat,i,j,val,INSERT_VALUES);CHKERRQ(ierr); 1319 } 1320 offset += qPoints; 1321 } 1322 if (id == PETSCFE_CLASSID) { 1323 ierr = PetscFERestoreTabulation(fe,nPoints,pointsRef,&B,NULL,NULL);CHKERRQ(ierr); 1324 } 1325 else { 1326 ierr = PetscFVRestoreTabulation(fv,nPoints,pointsRef,&B,NULL,NULL);CHKERRQ(ierr); 1327 } 1328 ierr = MatAssemblyBegin(Amat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1329 ierr = MatAssemblyEnd(Amat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1330 ierr = MatLUFactor(Amat,NULL,NULL,NULL);CHKERRQ(ierr); 1331 for (c = cStart; c < cEnd; c++) { 1332 PetscInt parent; 1333 PetscInt closureSize, closureSizeP, *closure = NULL, *closureP = NULL; 1334 PetscInt *childOffsets, *parentOffsets; 1335 1336 ierr = DMPlexGetTreeParent(dm,c,&parent,NULL);CHKERRQ(ierr); 1337 if (parent == c) continue; 1338 ierr = DMPlexGetTransitiveClosure(dm,c,PETSC_TRUE,&closureSize,&closure);CHKERRQ(ierr); 1339 for (i = 0; i < closureSize; i++) { 1340 PetscInt p = closure[2*i]; 1341 PetscInt conDof; 1342 1343 if (p < conStart || p >= conEnd) continue; 1344 if (numFields > 1) { 1345 ierr = PetscSectionGetFieldDof(cSec,p,f,&conDof);CHKERRQ(ierr); 1346 } 1347 else { 1348 ierr = PetscSectionGetDof(cSec,p,&conDof);CHKERRQ(ierr); 1349 } 1350 if (conDof) break; 1351 } 1352 if (i == closureSize) { 1353 ierr = DMPlexRestoreTransitiveClosure(dm,c,PETSC_TRUE,&closureSize,&closure);CHKERRQ(ierr); 1354 continue; 1355 } 1356 1357 ierr = DMPlexComputeCellGeometryFEM(dm, c, NULL, v0, J, NULL, &detJ);CHKERRQ(ierr); 1358 ierr = DMPlexComputeCellGeometryFEM(dm, parent, NULL, v0parent, Jparent, invJparent, &detJparent);CHKERRQ(ierr); 1359 for (i = 0; i < nPoints; i++) { 1360 CoordinatesRefToReal(spdim, spdim, v0, J, &pointsRef[i*spdim],vtmp);CHKERRQ(ierr); 1361 CoordinatesRealToRef(spdim, spdim, v0parent, invJparent, vtmp, &pointsReal[i*spdim]);CHKERRQ(ierr); 1362 } 1363 if (id == PETSCFE_CLASSID) { 1364 ierr = PetscFEGetTabulation(fe,nPoints,pointsReal,&B,NULL,NULL);CHKERRQ(ierr); 1365 } 1366 else { 1367 ierr = PetscFVGetTabulation(fv,nPoints,pointsReal,&B,NULL,NULL);CHKERRQ(ierr); 1368 } 1369 offset = 0; 1370 for (i = 0; i < fSize; i++) { 1371 PetscInt qPoints; 1372 PetscQuadrature quad; 1373 1374 ierr = PetscDualSpaceGetFunctional(space,i,&quad);CHKERRQ(ierr); 1375 ierr = PetscQuadratureGetData(quad,NULL,&qPoints,NULL,NULL);CHKERRQ(ierr); 1376 for (j = 0; j < fSize; j++) { 1377 PetscScalar val = 0.; 1378 1379 for (k = 0; k < qPoints; k++) { 1380 val += B[((offset + k) * fSize + j) * fComp] * weights[k]; 1381 } 1382 MatSetValue(Bmat,i,j,val,INSERT_VALUES);CHKERRQ(ierr); 1383 } 1384 offset += qPoints; 1385 } 1386 if (id == PETSCFE_CLASSID) { 1387 ierr = PetscFERestoreTabulation(fe,nPoints,pointsReal,&B,NULL,NULL);CHKERRQ(ierr); 1388 } 1389 else { 1390 ierr = PetscFVRestoreTabulation(fv,nPoints,pointsReal,&B,NULL,NULL);CHKERRQ(ierr); 1391 } 1392 ierr = MatAssemblyBegin(Bmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1393 ierr = MatAssemblyEnd(Bmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1394 ierr = MatMatSolve(Amat,Bmat,Xmat);CHKERRQ(ierr); 1395 ierr = DMPlexGetTransitiveClosure(dm,parent,PETSC_TRUE,&closureSizeP,&closureP);CHKERRQ(ierr); 1396 ierr = PetscMalloc2(closureSize+1,&childOffsets,closureSizeP+1,&parentOffsets);CHKERRQ(ierr); 1397 childOffsets[0] = 0; 1398 for (i = 0; i < closureSize; i++) { 1399 PetscInt p = closure[2*i]; 1400 PetscInt dof; 1401 1402 if (numFields > 1) { 1403 ierr = PetscSectionGetFieldDof(section,p,f,&dof);CHKERRQ(ierr); 1404 } 1405 else { 1406 ierr = PetscSectionGetDof(section,p,&dof);CHKERRQ(ierr); 1407 } 1408 childOffsets[i+1]=childOffsets[i]+dof / fComp; 1409 } 1410 parentOffsets[0] = 0; 1411 for (i = 0; i < closureSizeP; i++) { 1412 PetscInt p = closureP[2*i]; 1413 PetscInt dof; 1414 1415 if (numFields > 1) { 1416 ierr = PetscSectionGetFieldDof(section,p,f,&dof);CHKERRQ(ierr); 1417 } 1418 else { 1419 ierr = PetscSectionGetDof(section,p,&dof);CHKERRQ(ierr); 1420 } 1421 parentOffsets[i+1]=parentOffsets[i]+dof / fComp; 1422 } 1423 for (i = 0; i < closureSize; i++) { 1424 PetscInt conDof, conOff, aDof, aOff; 1425 PetscInt p = closure[2*i]; 1426 PetscInt o = closure[2*i+1]; 1427 1428 if (p < conStart || p >= conEnd) continue; 1429 if (numFields > 1) { 1430 ierr = PetscSectionGetFieldDof(cSec,p,f,&conDof);CHKERRQ(ierr); 1431 ierr = PetscSectionGetFieldOffset(cSec,p,f,&conOff);CHKERRQ(ierr); 1432 } 1433 else { 1434 ierr = PetscSectionGetDof(cSec,p,&conDof);CHKERRQ(ierr); 1435 ierr = PetscSectionGetOffset(cSec,p,&conOff);CHKERRQ(ierr); 1436 } 1437 if (!conDof) continue; 1438 ierr = PetscSectionGetDof(aSec,p,&aDof);CHKERRQ(ierr); 1439 ierr = PetscSectionGetOffset(aSec,p,&aOff);CHKERRQ(ierr); 1440 for (k = 0; k < aDof; k++) { 1441 PetscInt a = anchors[aOff + k]; 1442 PetscInt aSecDof, aSecOff; 1443 1444 if (numFields > 1) { 1445 ierr = PetscSectionGetFieldDof(section,a,f,&aSecDof);CHKERRQ(ierr); 1446 ierr = PetscSectionGetFieldOffset(section,a,f,&aSecOff);CHKERRQ(ierr); 1447 } 1448 else { 1449 ierr = PetscSectionGetDof(section,a,&aSecDof);CHKERRQ(ierr); 1450 ierr = PetscSectionGetOffset(section,a,&aSecOff);CHKERRQ(ierr); 1451 } 1452 if (!aSecDof) continue; 1453 1454 for (j = 0; j < closureSizeP; j++) { 1455 PetscInt q = closureP[2*j]; 1456 PetscInt oq = closureP[2*j+1]; 1457 1458 if (q == a) { 1459 PetscInt r, s, t; 1460 1461 for (r = childOffsets[i]; r < childOffsets[i+1]; r++) { 1462 for (s = parentOffsets[j]; s < parentOffsets[j+1]; s++) { 1463 PetscScalar val; 1464 PetscInt insertCol, insertRow; 1465 1466 ierr = MatGetValue(Xmat,r,s,&val);CHKERRQ(ierr); 1467 if (o >= 0) { 1468 insertRow = conOff + fComp * (r - childOffsets[i]); 1469 } 1470 else { 1471 insertRow = conOff + fComp * (childOffsets[i + 1] - 1 - r); 1472 } 1473 if (oq >= 0) { 1474 insertCol = aSecOff + fComp * (s - parentOffsets[j]); 1475 } 1476 else { 1477 insertCol = aSecOff + fComp * (parentOffsets[j + 1] - 1 - s); 1478 } 1479 for (t = 0; t < fComp; t++) { 1480 ierr = MatSetValue(cMat,insertRow + t,insertCol + t,val,INSERT_VALUES);CHKERRQ(ierr); 1481 } 1482 } 1483 } 1484 } 1485 } 1486 } 1487 } 1488 ierr = PetscFree2(childOffsets,parentOffsets);CHKERRQ(ierr); 1489 ierr = DMPlexRestoreTransitiveClosure(dm,c,PETSC_TRUE,&closureSize,&closure);CHKERRQ(ierr); 1490 ierr = DMPlexRestoreTransitiveClosure(dm,parent,PETSC_TRUE,&closureSizeP,&closureP);CHKERRQ(ierr); 1491 } 1492 ierr = MatDestroy(&Amat);CHKERRQ(ierr); 1493 ierr = MatDestroy(&Bmat);CHKERRQ(ierr); 1494 ierr = MatDestroy(&Xmat);CHKERRQ(ierr); 1495 ierr = PetscFree3(weights,pointsRef,pointsReal);CHKERRQ(ierr); 1496 } 1497 ierr = MatAssemblyBegin(cMat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1498 ierr = MatAssemblyEnd(cMat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1499 ierr = PetscFree6(v0,v0parent,vtmp,J,Jparent,invJparent);CHKERRQ(ierr); 1500 ierr = ISRestoreIndices(aIS,&anchors);CHKERRQ(ierr); 1501 1502 PetscFunctionReturn(0); 1503 } 1504 1505 #undef __FUNCT__ 1506 #define __FUNCT__ "DMPlexReferenceTreeGetChildrenMatrices" 1507 static PetscErrorCode DMPlexReferenceTreeGetChildrenMatrices(DM refTree, PetscScalar ****childrenMats, PetscInt ***childrenN) 1508 { 1509 Mat refCmat; 1510 PetscDS ds; 1511 PetscInt numFields, f, pRefStart, pRefEnd, p, *rows, *cols, maxDof, maxAnDof, **refPointFieldN; 1512 PetscScalar ***refPointFieldMats; 1513 PetscSection refConSec, refAnSec, refSection; 1514 IS refAnIS; 1515 const PetscInt *refAnchors; 1516 PetscErrorCode ierr; 1517 1518 PetscFunctionBegin; 1519 ierr = DMGetDS(refTree,&ds);CHKERRQ(ierr); 1520 ierr = PetscDSGetNumFields(ds,&numFields);CHKERRQ(ierr); 1521 ierr = DMGetDefaultConstraints(refTree,&refConSec,&refCmat);CHKERRQ(ierr); 1522 ierr = DMPlexGetAnchors(refTree,&refAnSec,&refAnIS);CHKERRQ(ierr); 1523 ierr = ISGetIndices(refAnIS,&refAnchors);CHKERRQ(ierr); 1524 ierr = DMGetDefaultSection(refTree,&refSection);CHKERRQ(ierr); 1525 ierr = PetscSectionGetChart(refConSec,&pRefStart,&pRefEnd);CHKERRQ(ierr); 1526 ierr = PetscMalloc1(pRefEnd-pRefStart,&refPointFieldMats);CHKERRQ(ierr); 1527 ierr = PetscMalloc1(pRefEnd-pRefStart,&refPointFieldN);CHKERRQ(ierr); 1528 ierr = PetscSectionGetMaxDof(refConSec,&maxDof);CHKERRQ(ierr); 1529 ierr = PetscSectionGetMaxDof(refAnSec,&maxAnDof);CHKERRQ(ierr); 1530 ierr = PetscMalloc1(maxDof,&rows);CHKERRQ(ierr); 1531 ierr = PetscMalloc1(maxDof*maxAnDof,&cols);CHKERRQ(ierr); 1532 for (p = pRefStart; p < pRefEnd; p++) { 1533 PetscInt parent, closureSize, *closure = NULL, pDof; 1534 1535 ierr = DMPlexGetTreeParent(refTree,p,&parent,NULL);CHKERRQ(ierr); 1536 ierr = PetscSectionGetDof(refConSec,p,&pDof);CHKERRQ(ierr); 1537 if (!pDof || parent == p) continue; 1538 1539 ierr = PetscMalloc1(numFields,&refPointFieldMats[p-pRefStart]);CHKERRQ(ierr); 1540 ierr = PetscCalloc1(numFields,&refPointFieldN[p-pRefStart]);CHKERRQ(ierr); 1541 ierr = DMPlexGetTransitiveClosure(refTree,parent,PETSC_TRUE,&closureSize,&closure);CHKERRQ(ierr); 1542 for (f = 0; f < numFields; f++) { 1543 PetscInt cDof, cOff, numCols, r, i, fComp; 1544 PetscObject disc; 1545 PetscClassId id; 1546 PetscFE fe = NULL; 1547 PetscFV fv = NULL; 1548 1549 ierr = PetscDSGetDiscretization(ds,f,&disc);CHKERRQ(ierr); 1550 ierr = PetscObjectGetClassId(disc,&id);CHKERRQ(ierr); 1551 if (id == PETSCFE_CLASSID) { 1552 fe = (PetscFE) disc; 1553 ierr = PetscFEGetNumComponents(fe,&fComp);CHKERRQ(ierr); 1554 } 1555 else if (id == PETSCFV_CLASSID) { 1556 fv = (PetscFV) disc; 1557 ierr = PetscFVGetNumComponents(fv,&fComp);CHKERRQ(ierr); 1558 } 1559 else SETERRQ1(PetscObjectComm(disc),PETSC_ERR_ARG_UNKNOWN_TYPE, "PetscDS discretization id %d not recognized.", id); 1560 1561 if (numFields > 1) { 1562 ierr = PetscSectionGetFieldDof(refConSec,p,f,&cDof);CHKERRQ(ierr); 1563 ierr = PetscSectionGetFieldOffset(refConSec,p,f,&cOff);CHKERRQ(ierr); 1564 } 1565 else { 1566 ierr = PetscSectionGetDof(refConSec,p,&cDof);CHKERRQ(ierr); 1567 ierr = PetscSectionGetOffset(refConSec,p,&cOff);CHKERRQ(ierr); 1568 } 1569 1570 if (!cDof) continue; 1571 for (r = 0; r < cDof; r++) { 1572 rows[r] = cOff + r; 1573 } 1574 numCols = 0; 1575 for (i = 0; i < closureSize; i++) { 1576 PetscInt q = closure[2*i]; 1577 PetscInt o = closure[2*i+1]; 1578 PetscInt aDof, aOff, j; 1579 1580 if (numFields > 1) { 1581 ierr = PetscSectionGetFieldDof(refSection,q,f,&aDof);CHKERRQ(ierr); 1582 ierr = PetscSectionGetFieldOffset(refSection,q,f,&aOff);CHKERRQ(ierr); 1583 } 1584 else { 1585 ierr = PetscSectionGetDof(refSection,q,&aDof);CHKERRQ(ierr); 1586 ierr = PetscSectionGetOffset(refSection,q,&aOff);CHKERRQ(ierr); 1587 } 1588 1589 for (j = 0; j < aDof; j++) { 1590 PetscInt node = (o >= 0) ? (j / fComp) : ((aDof - 1 - j) / fComp); 1591 PetscInt comp = (j % fComp); 1592 1593 cols[numCols++] = aOff + node * fComp + comp; 1594 } 1595 } 1596 refPointFieldN[p-pRefStart][f] = numCols; 1597 ierr = PetscMalloc1(cDof*numCols,&refPointFieldMats[p-pRefStart][f]);CHKERRQ(ierr); 1598 ierr = MatGetValues(refCmat,cDof,rows,numCols,cols,refPointFieldMats[p-pRefStart][f]);CHKERRQ(ierr); 1599 } 1600 ierr = DMPlexRestoreTransitiveClosure(refTree,parent,PETSC_TRUE,&closureSize,&closure);CHKERRQ(ierr); 1601 } 1602 *childrenMats = refPointFieldMats; 1603 *childrenN = refPointFieldN; 1604 ierr = ISRestoreIndices(refAnIS,&refAnchors);CHKERRQ(ierr); 1605 ierr = PetscFree(rows);CHKERRQ(ierr); 1606 ierr = PetscFree(cols);CHKERRQ(ierr); 1607 PetscFunctionReturn(0); 1608 } 1609 1610 #undef __FUNCT__ 1611 #define __FUNCT__ "DMPlexReferenceTreeRestoreChildrenMatrices" 1612 static PetscErrorCode DMPlexReferenceTreeRestoreChildrenMatrices(DM refTree, PetscScalar ****childrenMats, PetscInt ***childrenN) 1613 { 1614 PetscDS ds; 1615 PetscInt **refPointFieldN; 1616 PetscScalar ***refPointFieldMats; 1617 PetscInt numFields, pRefStart, pRefEnd, p, f; 1618 PetscSection refConSec; 1619 PetscErrorCode ierr; 1620 1621 PetscFunctionBegin; 1622 refPointFieldN = *childrenN; 1623 *childrenN = NULL; 1624 refPointFieldMats = *childrenMats; 1625 *childrenMats = NULL; 1626 ierr = DMGetDS(refTree,&ds);CHKERRQ(ierr); 1627 ierr = PetscDSGetNumFields(ds,&numFields);CHKERRQ(ierr); 1628 ierr = DMGetDefaultConstraints(refTree,&refConSec,NULL);CHKERRQ(ierr); 1629 ierr = PetscSectionGetChart(refConSec,&pRefStart,&pRefEnd);CHKERRQ(ierr); 1630 for (p = pRefStart; p < pRefEnd; p++) { 1631 PetscInt parent, pDof; 1632 1633 ierr = DMPlexGetTreeParent(refTree,p,&parent,NULL);CHKERRQ(ierr); 1634 ierr = PetscSectionGetDof(refConSec,p,&pDof);CHKERRQ(ierr); 1635 if (!pDof || parent == p) continue; 1636 1637 for (f = 0; f < numFields; f++) { 1638 PetscInt cDof; 1639 1640 if (numFields > 1) { 1641 ierr = PetscSectionGetFieldDof(refConSec,p,f,&cDof);CHKERRQ(ierr); 1642 } 1643 else { 1644 ierr = PetscSectionGetDof(refConSec,p,&cDof);CHKERRQ(ierr); 1645 } 1646 1647 if (!cDof) continue; 1648 ierr = PetscFree(refPointFieldMats[p - pRefStart][f]);CHKERRQ(ierr); 1649 } 1650 ierr = PetscFree(refPointFieldMats[p - pRefStart]);CHKERRQ(ierr); 1651 ierr = PetscFree(refPointFieldN[p - pRefStart]);CHKERRQ(ierr); 1652 } 1653 ierr = PetscFree(refPointFieldMats);CHKERRQ(ierr); 1654 ierr = PetscFree(refPointFieldN);CHKERRQ(ierr); 1655 PetscFunctionReturn(0); 1656 } 1657 1658 #undef __FUNCT__ 1659 #define __FUNCT__ "DMPlexComputeAnchorMatrix_Tree_FromReference" 1660 static PetscErrorCode DMPlexComputeAnchorMatrix_Tree_FromReference(DM dm, PetscSection section, PetscSection conSec, Mat cMat) 1661 { 1662 DM refTree; 1663 PetscDS ds; 1664 Mat refCmat; 1665 PetscInt numFields, f, pRefStart, pRefEnd, p, maxDof, maxAnDof, *perm, *iperm, pStart, pEnd, conStart, conEnd, **refPointFieldN; 1666 PetscScalar ***refPointFieldMats, *pointWork; 1667 PetscSection refConSec, refAnSec, anSec; 1668 IS refAnIS, anIS; 1669 const PetscInt *anchors; 1670 PetscErrorCode ierr; 1671 1672 PetscFunctionBegin; 1673 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1674 ierr = DMGetDS(dm,&ds);CHKERRQ(ierr); 1675 ierr = PetscDSGetNumFields(ds,&numFields);CHKERRQ(ierr); 1676 ierr = DMPlexGetReferenceTree(dm,&refTree);CHKERRQ(ierr); 1677 ierr = DMSetDS(refTree,ds);CHKERRQ(ierr); 1678 ierr = DMGetDefaultConstraints(refTree,&refConSec,&refCmat);CHKERRQ(ierr); 1679 ierr = DMPlexGetAnchors(refTree,&refAnSec,&refAnIS);CHKERRQ(ierr); 1680 ierr = DMPlexGetAnchors(dm,&anSec,&anIS);CHKERRQ(ierr); 1681 ierr = ISGetIndices(anIS,&anchors);CHKERRQ(ierr); 1682 ierr = PetscSectionGetChart(refConSec,&pRefStart,&pRefEnd);CHKERRQ(ierr); 1683 ierr = PetscSectionGetChart(conSec,&conStart,&conEnd);CHKERRQ(ierr); 1684 ierr = PetscSectionGetMaxDof(refConSec,&maxDof);CHKERRQ(ierr); 1685 ierr = PetscSectionGetMaxDof(refAnSec,&maxAnDof);CHKERRQ(ierr); 1686 ierr = PetscMalloc1(maxDof*maxDof*maxAnDof,&pointWork);CHKERRQ(ierr); 1687 1688 /* step 1: get submats for every constrained point in the reference tree */ 1689 ierr = DMPlexReferenceTreeGetChildrenMatrices(refTree,&refPointFieldMats,&refPointFieldN);CHKERRQ(ierr); 1690 1691 /* step 2: compute the preorder */ 1692 ierr = DMPlexGetChart(dm,&pStart,&pEnd);CHKERRQ(ierr); 1693 ierr = PetscMalloc2(pEnd-pStart,&perm,pEnd-pStart,&iperm);CHKERRQ(ierr); 1694 for (p = pStart; p < pEnd; p++) { 1695 perm[p - pStart] = p; 1696 iperm[p - pStart] = p-pStart; 1697 } 1698 for (p = 0; p < pEnd - pStart;) { 1699 PetscInt point = perm[p]; 1700 PetscInt parent; 1701 1702 ierr = DMPlexGetTreeParent(dm,point,&parent,NULL);CHKERRQ(ierr); 1703 if (parent == point) { 1704 p++; 1705 } 1706 else { 1707 PetscInt size, closureSize, *closure = NULL, i; 1708 1709 ierr = DMPlexGetTransitiveClosure(dm,parent,PETSC_TRUE,&closureSize,&closure);CHKERRQ(ierr); 1710 for (i = 0; i < closureSize; i++) { 1711 PetscInt q = closure[2*i]; 1712 if (iperm[q-pStart] > iperm[point-pStart]) { 1713 /* swap */ 1714 perm[p] = q; 1715 perm[iperm[q-pStart]] = point; 1716 iperm[point-pStart] = iperm[q-pStart]; 1717 iperm[q-pStart] = p; 1718 break; 1719 } 1720 } 1721 size = closureSize; 1722 ierr = DMPlexRestoreTransitiveClosure(dm,parent,PETSC_TRUE,&closureSize,&closure);CHKERRQ(ierr); 1723 if (i == size) { 1724 p++; 1725 } 1726 } 1727 } 1728 1729 /* step 3: fill the constraint matrix */ 1730 /* we are going to use a preorder progressive fill strategy. Mat doesn't 1731 * allow progressive fill without assembly, so we are going to set up the 1732 * values outside of the Mat first. 1733 */ 1734 { 1735 PetscInt nRows, row, nnz; 1736 PetscBool done; 1737 const PetscInt *ia, *ja; 1738 PetscScalar *vals; 1739 1740 ierr = MatGetRowIJ(cMat,0,PETSC_FALSE,PETSC_FALSE,&nRows,&ia,&ja,&done);CHKERRQ(ierr); 1741 if (!done) SETERRQ(PetscObjectComm((PetscObject)cMat),PETSC_ERR_PLIB,"Could not get RowIJ of constraint matrix"); 1742 nnz = ia[nRows]; 1743 /* malloc and then zero rows right before we fill them: this way valgrind 1744 * can tell if we are doing progressive fill in the wrong order */ 1745 ierr = PetscMalloc1(nnz,&vals);CHKERRQ(ierr); 1746 for (p = 0; p < pEnd - pStart; p++) { 1747 PetscInt parent, childid, closureSize, *closure = NULL; 1748 PetscInt point = perm[p], pointDof; 1749 1750 ierr = DMPlexGetTreeParent(dm,point,&parent,&childid);CHKERRQ(ierr); 1751 if ((point < conStart) || (point >= conEnd) || (parent == point)) continue; 1752 ierr = PetscSectionGetDof(conSec,point,&pointDof);CHKERRQ(ierr); 1753 if (!pointDof) continue; 1754 ierr = DMPlexGetTransitiveClosure(dm,parent,PETSC_TRUE,&closureSize,&closure);CHKERRQ(ierr); 1755 for (f = 0; f < numFields; f++) { 1756 PetscInt cDof, cOff, numCols, numFillCols, i, r, fComp = -1, matOffset, offset; 1757 PetscScalar *pointMat; 1758 PetscObject disc; 1759 PetscClassId id; 1760 PetscFE fe = NULL; 1761 PetscFV fv = NULL; 1762 1763 ierr = PetscDSGetDiscretization(ds,f,&disc);CHKERRQ(ierr); 1764 ierr = PetscObjectGetClassId(disc,&id);CHKERRQ(ierr); 1765 if (id == PETSCFE_CLASSID) { 1766 fe = (PetscFE) disc; 1767 ierr = PetscFEGetNumComponents(fe,&fComp);CHKERRQ(ierr); 1768 } 1769 else if (id == PETSCFV_CLASSID) { 1770 fv = (PetscFV) disc; 1771 ierr = PetscFVGetNumComponents(fv,&fComp);CHKERRQ(ierr); 1772 } 1773 else { 1774 SETERRQ(PetscObjectComm((PetscObject)disc),PETSC_ERR_SUP,"Unsupported discretization"); 1775 } 1776 1777 if (numFields > 1) { 1778 ierr = PetscSectionGetFieldDof(conSec,point,f,&cDof);CHKERRQ(ierr); 1779 ierr = PetscSectionGetFieldOffset(conSec,point,f,&cOff);CHKERRQ(ierr); 1780 } 1781 else { 1782 ierr = PetscSectionGetDof(conSec,point,&cDof);CHKERRQ(ierr); 1783 ierr = PetscSectionGetOffset(conSec,point,&cOff);CHKERRQ(ierr); 1784 } 1785 if (!cDof) continue; 1786 1787 /* make sure that every row for this point is the same size */ 1788 #if defined(PETSC_USE_DEBUG) 1789 for (r = 0; r < cDof; r++) { 1790 if (cDof > 1 && r) { 1791 if ((ia[cOff+r+1]-ia[cOff+r]) != (ia[cOff+r]-ia[cOff+r-1])) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Two point rows have different nnz: %D vs. %D", (ia[cOff+r+1]-ia[cOff+r]), (ia[cOff+r]-ia[cOff+r-1])); 1792 } 1793 } 1794 #endif 1795 /* zero rows */ 1796 for (i = ia[cOff] ; i< ia[cOff+cDof];i++) { 1797 vals[i] = 0.; 1798 } 1799 matOffset = ia[cOff]; 1800 numFillCols = ia[cOff+1] - matOffset; 1801 pointMat = refPointFieldMats[childid-pRefStart][f]; 1802 numCols = refPointFieldN[childid-pRefStart][f]; 1803 offset = 0; 1804 for (i = 0; i < closureSize; i++) { 1805 PetscInt q = closure[2*i]; 1806 PetscInt o = closure[2*i+1]; 1807 PetscInt aDof, aOff, j, k, qConDof, qConOff; 1808 1809 qConDof = qConOff = 0; 1810 if (numFields > 1) { 1811 ierr = PetscSectionGetFieldDof(section,q,f,&aDof);CHKERRQ(ierr); 1812 ierr = PetscSectionGetFieldOffset(section,q,f,&aOff);CHKERRQ(ierr); 1813 if (q >= conStart && q < conEnd) { 1814 ierr = PetscSectionGetFieldDof(conSec,q,f,&qConDof);CHKERRQ(ierr); 1815 ierr = PetscSectionGetFieldOffset(conSec,q,f,&qConOff);CHKERRQ(ierr); 1816 } 1817 } 1818 else { 1819 ierr = PetscSectionGetDof(section,q,&aDof);CHKERRQ(ierr); 1820 ierr = PetscSectionGetOffset(section,q,&aOff);CHKERRQ(ierr); 1821 if (q >= conStart && q < conEnd) { 1822 ierr = PetscSectionGetDof(conSec,q,&qConDof);CHKERRQ(ierr); 1823 ierr = PetscSectionGetOffset(conSec,q,&qConOff);CHKERRQ(ierr); 1824 } 1825 } 1826 if (!aDof) continue; 1827 if (qConDof) { 1828 /* this point has anchors: its rows of the matrix should already 1829 * be filled, thanks to preordering */ 1830 /* first multiply into pointWork, then set in matrix */ 1831 PetscInt aMatOffset = ia[qConOff]; 1832 PetscInt aNumFillCols = ia[qConOff + 1] - aMatOffset; 1833 for (r = 0; r < cDof; r++) { 1834 for (j = 0; j < aNumFillCols; j++) { 1835 PetscScalar inVal = 0; 1836 for (k = 0; k < aDof; k++) { 1837 PetscInt node = (o >= 0) ? (k / fComp) : ((aDof - 1 - k) / fComp); 1838 PetscInt comp = (k % fComp); 1839 PetscInt col = node * fComp + comp; 1840 1841 inVal += pointMat[r * numCols + offset + col] * vals[aMatOffset + aNumFillCols * k + j]; 1842 } 1843 pointWork[r * aNumFillCols + j] = inVal; 1844 } 1845 } 1846 /* assume that the columns are sorted, spend less time searching */ 1847 for (j = 0, k = 0; j < aNumFillCols; j++) { 1848 PetscInt col = ja[aMatOffset + j]; 1849 for (;k < numFillCols; k++) { 1850 if (ja[matOffset + k] == col) { 1851 break; 1852 } 1853 } 1854 if (k == numFillCols) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"No nonzero space for (%d, %d)", cOff, col); 1855 for (r = 0; r < cDof; r++) { 1856 vals[matOffset + numFillCols * r + k] = pointWork[r * aNumFillCols + j]; 1857 } 1858 } 1859 } 1860 else { 1861 /* find where to put this portion of pointMat into the matrix */ 1862 for (k = 0; k < numFillCols; k++) { 1863 if (ja[matOffset + k] == aOff) { 1864 break; 1865 } 1866 } 1867 if (k == numFillCols) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"No nonzero space for (%d, %d)", cOff, aOff); 1868 for (j = 0; j < aDof; j++) { 1869 PetscInt node = (o >= 0) ? (j / fComp) : ((aDof - 1 - j) / fComp); 1870 PetscInt comp = (j % fComp); 1871 PetscInt col = node * fComp + comp; 1872 for (r = 0; r < cDof; r++) { 1873 vals[matOffset + numFillCols * r + k + col] += pointMat[r * numCols + offset + col]; 1874 } 1875 } 1876 } 1877 offset += aDof; 1878 } 1879 } 1880 ierr = DMPlexRestoreTransitiveClosure(dm,parent,PETSC_TRUE,&closureSize,&closure);CHKERRQ(ierr); 1881 } 1882 for (row = 0; row < nRows; row++) { 1883 ierr = MatSetValues(cMat,1,&row,ia[row+1]-ia[row],&ja[ia[row]],&vals[ia[row]],INSERT_VALUES);CHKERRQ(ierr); 1884 } 1885 ierr = MatRestoreRowIJ(cMat,0,PETSC_FALSE,PETSC_FALSE,&nRows,&ia,&ja,&done);CHKERRQ(ierr); 1886 if (!done) SETERRQ(PetscObjectComm((PetscObject)cMat),PETSC_ERR_PLIB,"Could not restore RowIJ of constraint matrix"); 1887 ierr = MatAssemblyBegin(cMat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1888 ierr = MatAssemblyEnd(cMat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1889 ierr = PetscFree(vals);CHKERRQ(ierr); 1890 } 1891 1892 /* clean up */ 1893 ierr = ISRestoreIndices(anIS,&anchors);CHKERRQ(ierr); 1894 ierr = PetscFree2(perm,iperm);CHKERRQ(ierr); 1895 ierr = PetscFree(pointWork);CHKERRQ(ierr); 1896 ierr = DMPlexReferenceTreeRestoreChildrenMatrices(refTree,&refPointFieldMats,&refPointFieldN);CHKERRQ(ierr); 1897 PetscFunctionReturn(0); 1898 } 1899 1900 #undef __FUNCT__ 1901 #define __FUNCT__ "DMPlexTreeRefineCell" 1902 /* refine a single cell on rank 0: this is not intended to provide good local refinement, only to create an example of 1903 * a non-conforming mesh. Local refinement comes later */ 1904 PetscErrorCode DMPlexTreeRefineCell (DM dm, PetscInt cell, DM *ncdm) 1905 { 1906 DM K; 1907 PetscMPIInt rank; 1908 PetscInt dim, *pNewStart, *pNewEnd, *pNewCount, *pOldStart, *pOldEnd, offset, d, pStart, pEnd; 1909 PetscInt numNewCones, *newConeSizes, *newCones, *newOrientations; 1910 PetscInt *Kembedding; 1911 PetscInt *cellClosure=NULL, nc; 1912 PetscScalar *newVertexCoords; 1913 PetscInt numPointsWithParents, *parents, *childIDs, *perm, *iperm, *preOrient, pOffset; 1914 PetscSection parentSection; 1915 PetscErrorCode ierr; 1916 1917 PetscFunctionBegin; 1918 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm),&rank);CHKERRQ(ierr); 1919 ierr = DMGetDimension(dm,&dim);CHKERRQ(ierr); 1920 ierr = DMPlexCreate(PetscObjectComm((PetscObject)dm), ncdm);CHKERRQ(ierr); 1921 ierr = DMSetDimension(*ncdm,dim);CHKERRQ(ierr); 1922 1923 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 1924 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm),&parentSection);CHKERRQ(ierr); 1925 ierr = DMPlexGetReferenceTree(dm,&K);CHKERRQ(ierr); 1926 if (!rank) { 1927 /* compute the new charts */ 1928 ierr = PetscMalloc5(dim+1,&pNewCount,dim+1,&pNewStart,dim+1,&pNewEnd,dim+1,&pOldStart,dim+1,&pOldEnd);CHKERRQ(ierr); 1929 offset = 0; 1930 for (d = 0; d <= dim; d++) { 1931 PetscInt pOldCount, kStart, kEnd, k; 1932 1933 pNewStart[d] = offset; 1934 ierr = DMPlexGetHeightStratum(dm,d,&pOldStart[d],&pOldEnd[d]);CHKERRQ(ierr); 1935 ierr = DMPlexGetHeightStratum(K,d,&kStart,&kEnd);CHKERRQ(ierr); 1936 pOldCount = pOldEnd[d] - pOldStart[d]; 1937 /* adding the new points */ 1938 pNewCount[d] = pOldCount + kEnd - kStart; 1939 if (!d) { 1940 /* removing the cell */ 1941 pNewCount[d]--; 1942 } 1943 for (k = kStart; k < kEnd; k++) { 1944 PetscInt parent; 1945 ierr = DMPlexGetTreeParent(K,k,&parent,NULL);CHKERRQ(ierr); 1946 if (parent == k) { 1947 /* avoid double counting points that won't actually be new */ 1948 pNewCount[d]--; 1949 } 1950 } 1951 pNewEnd[d] = pNewStart[d] + pNewCount[d]; 1952 offset = pNewEnd[d]; 1953 1954 } 1955 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]); 1956 /* get the current closure of the cell that we are removing */ 1957 ierr = DMPlexGetTransitiveClosure(dm,cell,PETSC_TRUE,&nc,&cellClosure);CHKERRQ(ierr); 1958 1959 ierr = PetscMalloc1(pNewEnd[dim],&newConeSizes);CHKERRQ(ierr); 1960 { 1961 PetscInt kStart, kEnd, k, closureSizeK, *closureK = NULL, j; 1962 1963 ierr = DMPlexGetChart(K,&kStart,&kEnd);CHKERRQ(ierr); 1964 ierr = PetscMalloc4(kEnd-kStart,&Kembedding,kEnd-kStart,&perm,kEnd-kStart,&iperm,kEnd-kStart,&preOrient);CHKERRQ(ierr); 1965 1966 for (k = kStart; k < kEnd; k++) { 1967 perm[k - kStart] = k; 1968 iperm [k - kStart] = k - kStart; 1969 preOrient[k - kStart] = 0; 1970 } 1971 1972 ierr = DMPlexGetTransitiveClosure(K,0,PETSC_TRUE,&closureSizeK,&closureK);CHKERRQ(ierr); 1973 for (j = 1; j < closureSizeK; j++) { 1974 PetscInt parentOrientA = closureK[2*j+1]; 1975 PetscInt parentOrientB = cellClosure[2*j+1]; 1976 PetscInt p, q; 1977 1978 p = closureK[2*j]; 1979 q = cellClosure[2*j]; 1980 for (d = 0; d <= dim; d++) { 1981 if (q >= pOldStart[d] && q < pOldEnd[d]) { 1982 Kembedding[p] = (q - pOldStart[d]) + pNewStart[d]; 1983 } 1984 } 1985 if (parentOrientA != parentOrientB) { 1986 PetscInt numChildren, i; 1987 const PetscInt *children; 1988 1989 ierr = DMPlexGetTreeChildren(K,p,&numChildren,&children);CHKERRQ(ierr); 1990 for (i = 0; i < numChildren; i++) { 1991 PetscInt kPerm, oPerm; 1992 1993 k = children[i]; 1994 ierr = DMPlexReferenceTreeGetChildSymmetry(K,p,parentOrientA,0,k,parentOrientB,&oPerm,&kPerm);CHKERRQ(ierr); 1995 /* perm = what refTree position I'm in */ 1996 perm[kPerm-kStart] = k; 1997 /* iperm = who is at this position */ 1998 iperm[k-kStart] = kPerm-kStart; 1999 preOrient[kPerm-kStart] = oPerm; 2000 } 2001 } 2002 } 2003 ierr = DMPlexRestoreTransitiveClosure(K,0,PETSC_TRUE,&closureSizeK,&closureK);CHKERRQ(ierr); 2004 } 2005 ierr = PetscSectionSetChart(parentSection,0,pNewEnd[dim]);CHKERRQ(ierr); 2006 offset = 0; 2007 numNewCones = 0; 2008 for (d = 0; d <= dim; d++) { 2009 PetscInt kStart, kEnd, k; 2010 PetscInt p; 2011 PetscInt size; 2012 2013 for (p = pOldStart[d]; p < pOldEnd[d]; p++) { 2014 /* skip cell 0 */ 2015 if (p == cell) continue; 2016 /* old cones to new cones */ 2017 ierr = DMPlexGetConeSize(dm,p,&size);CHKERRQ(ierr); 2018 newConeSizes[offset++] = size; 2019 numNewCones += size; 2020 } 2021 2022 ierr = DMPlexGetHeightStratum(K,d,&kStart,&kEnd);CHKERRQ(ierr); 2023 for (k = kStart; k < kEnd; k++) { 2024 PetscInt kParent; 2025 2026 ierr = DMPlexGetTreeParent(K,k,&kParent,NULL);CHKERRQ(ierr); 2027 if (kParent != k) { 2028 Kembedding[k] = offset; 2029 ierr = DMPlexGetConeSize(K,k,&size);CHKERRQ(ierr); 2030 newConeSizes[offset++] = size; 2031 numNewCones += size; 2032 if (kParent != 0) { 2033 ierr = PetscSectionSetDof(parentSection,Kembedding[k],1);CHKERRQ(ierr); 2034 } 2035 } 2036 } 2037 } 2038 2039 ierr = PetscSectionSetUp(parentSection);CHKERRQ(ierr); 2040 ierr = PetscSectionGetStorageSize(parentSection,&numPointsWithParents);CHKERRQ(ierr); 2041 ierr = PetscMalloc2(numNewCones,&newCones,numNewCones,&newOrientations);CHKERRQ(ierr); 2042 ierr = PetscMalloc2(numPointsWithParents,&parents,numPointsWithParents,&childIDs);CHKERRQ(ierr); 2043 2044 /* fill new cones */ 2045 offset = 0; 2046 for (d = 0; d <= dim; d++) { 2047 PetscInt kStart, kEnd, k, l; 2048 PetscInt p; 2049 PetscInt size; 2050 const PetscInt *cone, *orientation; 2051 2052 for (p = pOldStart[d]; p < pOldEnd[d]; p++) { 2053 /* skip cell 0 */ 2054 if (p == cell) continue; 2055 /* old cones to new cones */ 2056 ierr = DMPlexGetConeSize(dm,p,&size);CHKERRQ(ierr); 2057 ierr = DMPlexGetCone(dm,p,&cone);CHKERRQ(ierr); 2058 ierr = DMPlexGetConeOrientation(dm,p,&orientation);CHKERRQ(ierr); 2059 for (l = 0; l < size; l++) { 2060 newCones[offset] = (cone[l] - pOldStart[d + 1]) + pNewStart[d + 1]; 2061 newOrientations[offset++] = orientation[l]; 2062 } 2063 } 2064 2065 ierr = DMPlexGetHeightStratum(K,d,&kStart,&kEnd);CHKERRQ(ierr); 2066 for (k = kStart; k < kEnd; k++) { 2067 PetscInt kPerm = perm[k], kParent; 2068 PetscInt preO = preOrient[k]; 2069 2070 ierr = DMPlexGetTreeParent(K,k,&kParent,NULL);CHKERRQ(ierr); 2071 if (kParent != k) { 2072 /* embed new cones */ 2073 ierr = DMPlexGetConeSize(K,k,&size);CHKERRQ(ierr); 2074 ierr = DMPlexGetCone(K,kPerm,&cone);CHKERRQ(ierr); 2075 ierr = DMPlexGetConeOrientation(K,kPerm,&orientation);CHKERRQ(ierr); 2076 for (l = 0; l < size; l++) { 2077 PetscInt q, m = (preO >= 0) ? ((preO + l) % size) : ((size -(preO + 1) - l) % size); 2078 PetscInt newO, lSize, oTrue; 2079 2080 q = iperm[cone[m]]; 2081 newCones[offset] = Kembedding[q]; 2082 ierr = DMPlexGetConeSize(K,q,&lSize);CHKERRQ(ierr); 2083 oTrue = orientation[m]; 2084 oTrue = ((!lSize) || (preOrient[k] >= 0)) ? oTrue : -(oTrue + 2); 2085 newO = DihedralCompose(lSize,oTrue,preOrient[q]); 2086 newOrientations[offset++] = newO; 2087 } 2088 if (kParent != 0) { 2089 PetscInt newPoint = Kembedding[kParent]; 2090 ierr = PetscSectionGetOffset(parentSection,Kembedding[k],&pOffset);CHKERRQ(ierr); 2091 parents[pOffset] = newPoint; 2092 childIDs[pOffset] = k; 2093 } 2094 } 2095 } 2096 } 2097 2098 ierr = PetscMalloc1(dim*(pNewEnd[dim]-pNewStart[dim]),&newVertexCoords);CHKERRQ(ierr); 2099 2100 /* fill coordinates */ 2101 offset = 0; 2102 { 2103 PetscInt kStart, kEnd, l; 2104 PetscSection vSection; 2105 PetscInt v; 2106 Vec coords; 2107 PetscScalar *coordvals; 2108 PetscInt dof, off; 2109 PetscReal v0[3], J[9], detJ; 2110 2111 #if defined(PETSC_USE_DEBUG) 2112 { 2113 PetscInt k; 2114 ierr = DMPlexGetHeightStratum(K,0,&kStart,&kEnd);CHKERRQ(ierr); 2115 for (k = kStart; k < kEnd; k++) { 2116 ierr = DMPlexComputeCellGeometryFEM(K, k, NULL, v0, J, NULL, &detJ);CHKERRQ(ierr); 2117 if (detJ <= 0.) SETERRQ1 (PETSC_COMM_SELF,PETSC_ERR_PLIB,"reference tree cell %d has bad determinant",k); 2118 } 2119 } 2120 #endif 2121 ierr = DMPlexComputeCellGeometryFEM(dm, cell, NULL, v0, J, NULL, &detJ);CHKERRQ(ierr); 2122 ierr = DMGetCoordinateSection(dm,&vSection);CHKERRQ(ierr); 2123 ierr = DMGetCoordinatesLocal(dm,&coords);CHKERRQ(ierr); 2124 ierr = VecGetArray(coords,&coordvals);CHKERRQ(ierr); 2125 for (v = pOldStart[dim]; v < pOldEnd[dim]; v++) { 2126 2127 ierr = PetscSectionGetDof(vSection,v,&dof);CHKERRQ(ierr); 2128 ierr = PetscSectionGetOffset(vSection,v,&off);CHKERRQ(ierr); 2129 for (l = 0; l < dof; l++) { 2130 newVertexCoords[offset++] = coordvals[off + l]; 2131 } 2132 } 2133 ierr = VecRestoreArray(coords,&coordvals);CHKERRQ(ierr); 2134 2135 ierr = DMGetCoordinateSection(K,&vSection);CHKERRQ(ierr); 2136 ierr = DMGetCoordinatesLocal(K,&coords);CHKERRQ(ierr); 2137 ierr = VecGetArray(coords,&coordvals);CHKERRQ(ierr); 2138 ierr = DMPlexGetDepthStratum(K,0,&kStart,&kEnd);CHKERRQ(ierr); 2139 for (v = kStart; v < kEnd; v++) { 2140 PetscReal coord[3], newCoord[3]; 2141 PetscInt vPerm = perm[v]; 2142 PetscInt kParent; 2143 2144 ierr = DMPlexGetTreeParent(K,v,&kParent,NULL);CHKERRQ(ierr); 2145 if (kParent != v) { 2146 /* this is a new vertex */ 2147 ierr = PetscSectionGetOffset(vSection,vPerm,&off);CHKERRQ(ierr); 2148 for (l = 0; l < dim; ++l) coord[l] = PetscRealPart(coordvals[off+l]); 2149 CoordinatesRefToReal(dim, dim, v0, J, coord, newCoord);CHKERRQ(ierr); 2150 for (l = 0; l < dim; ++l) newVertexCoords[offset+l] = newCoord[l]; 2151 offset += dim; 2152 } 2153 } 2154 ierr = VecRestoreArray(coords,&coordvals);CHKERRQ(ierr); 2155 } 2156 2157 /* need to reverse the order of pNewCount: vertices first, cells last */ 2158 for (d = 0; d < (dim + 1) / 2; d++) { 2159 PetscInt tmp; 2160 2161 tmp = pNewCount[d]; 2162 pNewCount[d] = pNewCount[dim - d]; 2163 pNewCount[dim - d] = tmp; 2164 } 2165 2166 ierr = DMPlexCreateFromDAG(*ncdm,dim,pNewCount,newConeSizes,newCones,newOrientations,newVertexCoords);CHKERRQ(ierr); 2167 ierr = DMPlexSetReferenceTree(*ncdm,K);CHKERRQ(ierr); 2168 ierr = DMPlexSetTree(*ncdm,parentSection,parents,childIDs);CHKERRQ(ierr); 2169 2170 /* clean up */ 2171 ierr = DMPlexRestoreTransitiveClosure(dm,cell,PETSC_TRUE,&nc,&cellClosure);CHKERRQ(ierr); 2172 ierr = PetscFree5(pNewCount,pNewStart,pNewEnd,pOldStart,pOldEnd);CHKERRQ(ierr); 2173 ierr = PetscFree(newConeSizes);CHKERRQ(ierr); 2174 ierr = PetscFree2(newCones,newOrientations);CHKERRQ(ierr); 2175 ierr = PetscFree(newVertexCoords);CHKERRQ(ierr); 2176 ierr = PetscFree2(parents,childIDs);CHKERRQ(ierr); 2177 ierr = PetscFree4(Kembedding,perm,iperm,preOrient);CHKERRQ(ierr); 2178 } 2179 else { 2180 PetscInt p, counts[4]; 2181 PetscInt *coneSizes, *cones, *orientations; 2182 Vec coordVec; 2183 PetscScalar *coords; 2184 2185 for (d = 0; d <= dim; d++) { 2186 PetscInt dStart, dEnd; 2187 2188 ierr = DMPlexGetDepthStratum(dm,d,&dStart,&dEnd);CHKERRQ(ierr); 2189 counts[d] = dEnd - dStart; 2190 } 2191 ierr = PetscMalloc1(pEnd-pStart,&coneSizes);CHKERRQ(ierr); 2192 for (p = pStart; p < pEnd; p++) { 2193 ierr = DMPlexGetConeSize(dm,p,&coneSizes[p-pStart]);CHKERRQ(ierr); 2194 } 2195 ierr = DMPlexGetCones(dm, &cones);CHKERRQ(ierr); 2196 ierr = DMPlexGetConeOrientations(dm, &orientations);CHKERRQ(ierr); 2197 ierr = DMGetCoordinatesLocal(dm,&coordVec);CHKERRQ(ierr); 2198 ierr = VecGetArray(coordVec,&coords);CHKERRQ(ierr); 2199 2200 ierr = PetscSectionSetChart(parentSection,pStart,pEnd);CHKERRQ(ierr); 2201 ierr = PetscSectionSetUp(parentSection);CHKERRQ(ierr); 2202 ierr = DMPlexCreateFromDAG(*ncdm,dim,counts,coneSizes,cones,orientations,NULL);CHKERRQ(ierr); 2203 ierr = DMPlexSetReferenceTree(*ncdm,K);CHKERRQ(ierr); 2204 ierr = DMPlexSetTree(*ncdm,parentSection,NULL,NULL);CHKERRQ(ierr); 2205 ierr = VecRestoreArray(coordVec,&coords);CHKERRQ(ierr); 2206 } 2207 ierr = PetscSectionDestroy(&parentSection);CHKERRQ(ierr); 2208 2209 PetscFunctionReturn(0); 2210 } 2211 2212 #undef __FUNCT__ 2213 #define __FUNCT__ "DMPlexComputeInterpolatorTree" 2214 PetscErrorCode DMPlexComputeInterpolatorTree(DM coarse, DM fine, PetscSF coarseToFine, PetscInt *childIds, Mat mat) 2215 { 2216 PetscSF coarseToFineEmbedded; 2217 PetscSection globalCoarse, globalFine; 2218 PetscSection localCoarse, localFine; 2219 PetscSection aSec, cSec; 2220 PetscSection rootIndicesSec, rootMatricesSec; 2221 PetscSection leafIndicesSec, leafMatricesSec; 2222 PetscInt *rootIndices, *leafIndices; 2223 PetscScalar *rootMatrices, *leafMatrices; 2224 IS aIS; 2225 const PetscInt *anchors; 2226 Mat cMat; 2227 PetscInt numFields; 2228 PetscInt pStartC, pEndC, pStartF, pEndF, p; 2229 PetscInt aStart, aEnd, cStart, cEnd; 2230 PetscInt *maxChildIds; 2231 PetscInt *offsets, *newOffsets, *offsetsCopy, *newOffsetsCopy, *rowOffsets, *numD, *numO; 2232 PetscErrorCode ierr; 2233 2234 PetscFunctionBegin; 2235 ierr = DMPlexGetChart(coarse,&pStartC,&pEndC);CHKERRQ(ierr); 2236 ierr = DMPlexGetChart(fine,&pStartF,&pEndF);CHKERRQ(ierr); 2237 ierr = DMGetDefaultGlobalSection(fine,&globalFine);CHKERRQ(ierr); 2238 { /* winnow fine points that don't have global dofs out of the sf */ 2239 PetscInt dof, cdof, numPointsWithDofs, offset, *pointsWithDofs; 2240 2241 for (p = pStartF, numPointsWithDofs = 0; p < pEndF; p++) { 2242 ierr = PetscSectionGetDof(globalFine,p,&dof);CHKERRQ(ierr); 2243 ierr = PetscSectionGetConstraintDof(globalFine,p,&cdof);CHKERRQ(ierr); 2244 if ((dof - cdof) > 0) { 2245 numPointsWithDofs++; 2246 } 2247 } 2248 ierr = PetscMalloc1(numPointsWithDofs,&pointsWithDofs);CHKERRQ(ierr); 2249 for (p = pStartF, offset = 0; p < pEndF; p++) { 2250 ierr = PetscSectionGetDof(globalFine,p,&dof);CHKERRQ(ierr); 2251 ierr = PetscSectionGetConstraintDof(globalFine,p,&cdof);CHKERRQ(ierr); 2252 if ((dof - cdof) > 0) { 2253 pointsWithDofs[offset++] = p - pStartF; 2254 } 2255 } 2256 ierr = PetscSFCreateEmbeddedLeafSF(coarseToFine, numPointsWithDofs, pointsWithDofs, &coarseToFineEmbedded);CHKERRQ(ierr); 2257 ierr = PetscFree(pointsWithDofs);CHKERRQ(ierr); 2258 } 2259 /* communicate back to the coarse mesh which coarse points have children (that may require interpolation) */ 2260 ierr = PetscMalloc1(pEndC-pStartC,&maxChildIds);CHKERRQ(ierr); 2261 for (p = pStartC; p < pEndC; p++) { 2262 maxChildIds[p - pStartC] = -2; 2263 } 2264 ierr = PetscSFReduceBegin(coarseToFineEmbedded,MPIU_INT,childIds,maxChildIds,MPIU_MAX);CHKERRQ(ierr); 2265 ierr = PetscSFReduceEnd(coarseToFineEmbedded,MPIU_INT,childIds,maxChildIds,MPIU_MAX);CHKERRQ(ierr); 2266 2267 ierr = DMGetDefaultSection(coarse,&localCoarse);CHKERRQ(ierr); 2268 ierr = DMGetDefaultGlobalSection(coarse,&globalCoarse);CHKERRQ(ierr); 2269 2270 ierr = DMPlexGetAnchors(coarse,&aSec,&aIS);CHKERRQ(ierr); 2271 ierr = ISGetIndices(aIS,&anchors);CHKERRQ(ierr); 2272 ierr = PetscSectionGetChart(aSec,&aStart,&aEnd);CHKERRQ(ierr); 2273 2274 ierr = DMGetDefaultConstraints(coarse,&cSec,&cMat);CHKERRQ(ierr); 2275 ierr = PetscSectionGetChart(cSec,&cStart,&cEnd);CHKERRQ(ierr); 2276 2277 /* create sections that will send to children the indices and matrices they will need to construct the interpolator */ 2278 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)coarse),&rootIndicesSec);CHKERRQ(ierr); 2279 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)coarse),&rootMatricesSec);CHKERRQ(ierr); 2280 ierr = PetscSectionSetChart(rootIndicesSec,pStartC,pEndC);CHKERRQ(ierr); 2281 ierr = PetscSectionSetChart(rootMatricesSec,pStartC,pEndC);CHKERRQ(ierr); 2282 ierr = PetscSectionGetNumFields(globalCoarse,&numFields);CHKERRQ(ierr); 2283 { 2284 PetscInt maxFields = PetscMax(1,numFields) + 1; 2285 ierr = PetscMalloc7(maxFields,&offsets,maxFields,&offsetsCopy,maxFields,&newOffsets,maxFields,&newOffsetsCopy,maxFields,&rowOffsets,maxFields,&numD,maxFields,&numO);CHKERRQ(ierr); 2286 } 2287 2288 for (p = pStartC; p < pEndC; p++) { /* count the sizes of the indices and matrices */ 2289 PetscInt dof, matSize = 0; 2290 PetscInt aDof = 0; 2291 PetscInt cDof = 0; 2292 PetscInt maxChildId = maxChildIds[p - pStartC]; 2293 PetscInt numRowIndices = 0; 2294 PetscInt numColIndices = 0; 2295 2296 ierr = PetscSectionGetDof(globalCoarse,p,&dof);CHKERRQ(ierr); 2297 if (dof < 0) { 2298 dof = -(dof + 1); 2299 } 2300 if (p >= aStart && p < aEnd) { 2301 ierr = PetscSectionGetDof(aSec,p,&aDof);CHKERRQ(ierr); 2302 } 2303 if (p >= cStart && p < cEnd) { 2304 ierr = PetscSectionGetDof(cSec,p,&cDof);CHKERRQ(ierr); 2305 } 2306 offsets[0] = 0; 2307 newOffsets[0] = 0; 2308 if (maxChildId >= 0) { /* this point has children (with dofs) that will need to be interpolated from the closure of p */ 2309 PetscInt *closure = NULL, closureSize, cl, f; 2310 2311 ierr = DMPlexGetTransitiveClosure(coarse,p,PETSC_TRUE,&closureSize,&closure);CHKERRQ(ierr); 2312 for (cl = 0; cl < closureSize; cl++) { /* get the closure */ 2313 PetscInt c = closure[2 * cl], clDof; 2314 2315 ierr = PetscSectionGetDof(localCoarse,c,&clDof);CHKERRQ(ierr); 2316 numRowIndices += clDof; 2317 for (f = 0; f < numFields; f++) { 2318 ierr = PetscSectionGetFieldDof(localCoarse,c,f,&clDof);CHKERRQ(ierr); 2319 offsets[f + 1] += clDof; 2320 } 2321 } 2322 for (f = 0; f < numFields; f++) { 2323 offsets[f + 1] += offsets[f]; 2324 newOffsets[f + 1] = offsets[f + 1]; 2325 } 2326 /* get the number of indices needed and their field offsets */ 2327 ierr = DMPlexAnchorsModifyMat(coarse,localCoarse,closureSize,numRowIndices,closure,NULL,NULL,&numColIndices,NULL,NULL,newOffsets,PETSC_FALSE);CHKERRQ(ierr); 2328 ierr = DMPlexRestoreTransitiveClosure(coarse,p,PETSC_TRUE,&closureSize,&closure);CHKERRQ(ierr); 2329 if (!numColIndices) { /* there are no hanging constraint modifications, so the matrix is just the identity: do not send it */ 2330 numColIndices = numRowIndices; 2331 matSize = 0; 2332 } 2333 else if (numFields) { /* we send one submat for each field: sum their sizes */ 2334 matSize = 0; 2335 for (f = 0; f < numFields; f++) { 2336 PetscInt numRow, numCol; 2337 2338 numRow = offsets[f + 1] - offsets[f]; 2339 numCol = newOffsets[f + 1] - newOffsets[f + 1]; 2340 matSize += numRow * numCol; 2341 } 2342 } 2343 else { 2344 matSize = numRowIndices * numColIndices; 2345 } 2346 } 2347 else if (maxChildId == -1) { 2348 if (cDof > 0) { /* this point's dofs are interpolated via cMat: get the submatrix of cMat */ 2349 PetscInt aOff, a, f; 2350 2351 ierr = PetscSectionGetOffset(aSec,p,&aOff);CHKERRQ(ierr); 2352 for (f = 0; f < numFields; f++) { 2353 PetscInt fDof; 2354 2355 ierr = PetscSectionGetFieldDof(localCoarse,p,f,&fDof);CHKERRQ(ierr); 2356 offsets[f+1] = fDof; 2357 } 2358 for (a = 0; a < aDof; a++) { 2359 PetscInt anchor = anchors[a + aOff], aLocalDof; 2360 2361 ierr = PetscSectionGetDof(localCoarse,anchor,&aLocalDof);CHKERRQ(ierr); 2362 numColIndices += aLocalDof; 2363 for (f = 0; f < numFields; f++) { 2364 PetscInt fDof; 2365 2366 ierr = PetscSectionGetFieldDof(localCoarse,anchor,f,&fDof);CHKERRQ(ierr); 2367 newOffsets[f+1] += fDof; 2368 } 2369 } 2370 if (numFields) { 2371 matSize = 0; 2372 for (f = 0; f < numFields; f++) { 2373 matSize += offsets[f+1] * newOffsets[f+1]; 2374 } 2375 } 2376 else { 2377 matSize = numColIndices * dof; 2378 } 2379 } 2380 else { /* no children, and no constraints on dofs: just get the global indices */ 2381 numColIndices = dof; 2382 matSize = 0; 2383 } 2384 } 2385 /* we will pack the column indices with the field offsets */ 2386 ierr = PetscSectionSetDof(rootIndicesSec,p,numColIndices ? numColIndices+2*numFields : 0);CHKERRQ(ierr); 2387 ierr = PetscSectionSetDof(rootMatricesSec,p,matSize);CHKERRQ(ierr); 2388 } 2389 ierr = PetscSectionSetUp(rootIndicesSec);CHKERRQ(ierr); 2390 ierr = PetscSectionSetUp(rootMatricesSec);CHKERRQ(ierr); 2391 { 2392 PetscInt numRootIndices, numRootMatrices; 2393 2394 ierr = PetscSectionGetStorageSize(rootIndicesSec,&numRootIndices);CHKERRQ(ierr); 2395 ierr = PetscSectionGetStorageSize(rootMatricesSec,&numRootMatrices);CHKERRQ(ierr); 2396 ierr = PetscMalloc2(numRootIndices,&rootIndices,numRootMatrices,&rootMatrices);CHKERRQ(ierr); 2397 for (p = pStartC; p < pEndC; p++) { 2398 PetscInt numRowIndices, numColIndices, matSize, dof; 2399 PetscInt pIndOff, pMatOff; 2400 PetscInt *pInd; 2401 PetscInt maxChildId = maxChildIds[p - pStartC]; 2402 PetscScalar *pMat = NULL; 2403 2404 ierr = PetscSectionGetDof(rootIndicesSec,p,&numColIndices);CHKERRQ(ierr); 2405 if (!numColIndices) { 2406 continue; 2407 } 2408 offsets[0] = 0; 2409 newOffsets[0] = 0; 2410 offsetsCopy[0] = 0; 2411 newOffsetsCopy[0] = 0; 2412 numColIndices -= 2 * numFields; 2413 ierr = PetscSectionGetOffset(rootIndicesSec,p,&pIndOff);CHKERRQ(ierr); 2414 pInd = &(rootIndices[pIndOff]); 2415 ierr = PetscSectionGetDof(rootMatricesSec,p,&matSize);CHKERRQ(ierr); 2416 if (matSize) { 2417 ierr = PetscSectionGetOffset(rootMatricesSec,p,&pMatOff);CHKERRQ(ierr); 2418 pMat = &rootMatrices[pMatOff]; 2419 } 2420 ierr = PetscSectionGetDof(globalCoarse,p,&dof);CHKERRQ(ierr); 2421 if (dof < 0) { 2422 dof = -(dof + 1); 2423 } 2424 if (maxChildId >= 0) { /* build an identity matrix, apply matrix constraints on the right */ 2425 PetscInt i, j; 2426 PetscInt numRowIndices = matSize / numColIndices; 2427 2428 if (!numRowIndices) { /* don't need to calculate the mat, just the indices */ 2429 PetscInt numIndices, *indices; 2430 ierr = DMPlexGetClosureIndices(coarse,localCoarse,globalCoarse,p,&numIndices,&indices,offsets);CHKERRQ(ierr); 2431 if (numIndices != numColIndices) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"mismatching constraint indices calculations"); 2432 for (i = 0; i < numColIndices; i++) { 2433 pInd[i] = indices[i]; 2434 } 2435 for (i = 0; i < numFields; i++) { 2436 pInd[numColIndices + i] = offsets[i+1]; 2437 pInd[numColIndices + numFields + i] = offsets[i+1]; 2438 } 2439 ierr = DMPlexRestoreClosureIndices(coarse,localCoarse,globalCoarse,p,&numIndices,&indices,offsets);CHKERRQ(ierr); 2440 } 2441 else { 2442 PetscInt closureSize, *closure = NULL, cl; 2443 PetscScalar *pMatIn, *pMatModified; 2444 PetscInt numPoints,*points; 2445 2446 ierr = DMGetWorkArray(coarse,numRowIndices * numRowIndices,PETSC_SCALAR,&pMatIn);CHKERRQ(ierr); 2447 for (i = 0; i < numRowIndices; i++) { /* initialize to the identity */ 2448 for (j = 0; j < numRowIndices; j++) { 2449 pMatIn[i * numRowIndices + j] = (i == j) ? 1. : 0.; 2450 } 2451 } 2452 ierr = DMPlexGetTransitiveClosure(coarse, p, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 2453 if (numFields) { 2454 PetscInt f; 2455 2456 for (cl = 0; cl < closureSize; cl++) { 2457 PetscInt c = closure[2 * cl]; 2458 2459 for (f = 0; f < numFields; f++) { 2460 PetscInt fDof; 2461 2462 ierr = PetscSectionGetFieldDof(localCoarse,c,f,&fDof);CHKERRQ(ierr); 2463 offsets[f + 1] += fDof; 2464 } 2465 } 2466 for (f = 0; f < numFields; f++) { 2467 offsets[f + 1] += offsets[f]; 2468 newOffsets[f + 1] = offsets[f + 1]; 2469 } 2470 } 2471 /* apply hanging node constraints on the right, get the new points and the new offsets */ 2472 ierr = DMPlexAnchorsModifyMat(coarse,localCoarse,closureSize,numRowIndices,closure,pMatIn,&numPoints,NULL,&points,&pMatModified,newOffsets,PETSC_FALSE);CHKERRQ(ierr); 2473 if (!numFields) { 2474 for (i = 0; i < numRowIndices * numColIndices; i++) { 2475 pMat[i] = pMatModified[i]; 2476 } 2477 } 2478 else { 2479 PetscInt f, i, j, count; 2480 for (f = 0, count = 0; f < numFields; f++) { 2481 for (i = offsets[f]; i < offsets[f+1]; i++) { 2482 for (j = newOffsets[f]; j < newOffsets[f+1]; j++, count++) { 2483 pMat[count] = pMatModified[i * numColIndices + j]; 2484 } 2485 } 2486 } 2487 } 2488 ierr = DMRestoreWorkArray(coarse,numRowIndices * numColIndices,PETSC_SCALAR,&pMatModified);CHKERRQ(ierr); 2489 ierr = DMPlexRestoreTransitiveClosure(coarse, p, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 2490 ierr = DMRestoreWorkArray(coarse,numRowIndices * numColIndices,PETSC_SCALAR,&pMatIn);CHKERRQ(ierr); 2491 if (numFields) { 2492 PetscInt f; 2493 for (f = 0; f < numFields; f++) { 2494 pInd[numColIndices + f] = offsets[f+1]; 2495 pInd[numColIndices + numFields + f] = newOffsets[f+1]; 2496 } 2497 for (cl = 0; cl < numPoints*2; cl += 2) { 2498 PetscInt o = points[cl+1], globalOff, c = points[cl]; 2499 ierr = PetscSectionGetOffset(globalCoarse, c, &globalOff);CHKERRQ(ierr); 2500 DMPlexGetIndicesPointFields_Internal(localCoarse, c, globalOff < 0 ? -(globalOff+1) : globalOff, newOffsets, PETSC_FALSE, o, pInd); 2501 } 2502 } else { 2503 for (cl = 0; cl < numPoints*2; cl += 2) { 2504 PetscInt o = points[cl+1], c = points[cl], globalOff; 2505 ierr = PetscSectionGetOffset(globalCoarse, c, &globalOff);CHKERRQ(ierr); 2506 DMPlexGetIndicesPoint_Internal(localCoarse, c, globalOff < 0 ? -(globalOff+1) : globalOff, newOffsets, PETSC_FALSE, o, pInd); 2507 } 2508 } 2509 ierr = DMRestoreWorkArray(coarse,numPoints,PETSC_SCALAR,&points);CHKERRQ(ierr); 2510 } 2511 } 2512 else if (matSize) { 2513 PetscInt cOff; 2514 PetscInt *rowIndices, *colIndices, a, aDof, aOff; 2515 2516 numRowIndices = matSize / numColIndices; 2517 if (numRowIndices != dof) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Miscounted dofs"); 2518 ierr = DMGetWorkArray(coarse,numRowIndices,PETSC_INT,&rowIndices);CHKERRQ(ierr); 2519 ierr = DMGetWorkArray(coarse,numColIndices,PETSC_INT,&colIndices);CHKERRQ(ierr); 2520 ierr = PetscSectionGetOffset(cSec,p,&cOff);CHKERRQ(ierr); 2521 ierr = PetscSectionGetDof(aSec,p,&aDof);CHKERRQ(ierr); 2522 ierr = PetscSectionGetOffset(aSec,p,&aOff);CHKERRQ(ierr); 2523 if (numFields) { 2524 PetscInt f; 2525 2526 for (f = 0; f < numFields; f++) { 2527 PetscInt fDof; 2528 ierr = PetscSectionGetFieldDof(cSec,p,f,&fDof);CHKERRQ(ierr); 2529 offsets[f + 1] = fDof; 2530 for (a = 0; a < aDof; a++) { 2531 PetscInt anchor = anchors[a + aOff]; 2532 ierr = PetscSectionGetFieldDof(localCoarse,anchor,f,&fDof);CHKERRQ(ierr); 2533 newOffsets[f + 1] += fDof; 2534 } 2535 } 2536 for (f = 0; f < numFields; f++) { 2537 offsets[f + 1] += offsets[f]; 2538 offsetsCopy[f + 1] = offsets[f + 1]; 2539 newOffsets[f + 1] += newOffsets[f]; 2540 newOffsetsCopy[f + 1] = newOffsets[f + 1]; 2541 } 2542 DMPlexGetIndicesPointFields_Internal(cSec,p,cOff,offsetsCopy,PETSC_TRUE,0,rowIndices);CHKERRQ(ierr); 2543 for (a = 0; a < aDof; a++) { 2544 PetscInt anchor = anchors[a + aOff], lOff; 2545 ierr = PetscSectionGetOffset(localCoarse,anchor,&lOff);CHKERRQ(ierr); 2546 DMPlexGetIndicesPointFields_Internal(localCoarse,anchor,lOff,newOffsetsCopy,PETSC_TRUE,0,colIndices);CHKERRQ(ierr); 2547 } 2548 } 2549 else { 2550 DMPlexGetIndicesPoint_Internal(cSec,p,cOff,offsetsCopy,PETSC_TRUE,0,rowIndices);CHKERRQ(ierr); 2551 for (a = 0; a < aDof; a++) { 2552 PetscInt anchor = anchors[a + aOff], lOff; 2553 ierr = PetscSectionGetOffset(localCoarse,anchor,&lOff);CHKERRQ(ierr); 2554 DMPlexGetIndicesPoint_Internal(localCoarse,anchor,lOff,newOffsetsCopy,PETSC_TRUE,0,colIndices);CHKERRQ(ierr); 2555 } 2556 } 2557 if (numFields) { 2558 PetscInt count, f, a; 2559 for (f = 0, count = 0; f < numFields; f++) { 2560 PetscInt iSize = offsets[f + 1] - offsets[f]; 2561 PetscInt jSize = newOffsets[f + 1] - newOffsets[f]; 2562 ierr = MatGetValues(cMat,iSize,&rowIndices[offsets[f]],jSize,&colIndices[newOffsets[f]],&pMat[count]);CHKERRQ(ierr); 2563 count += iSize * jSize; 2564 pInd[numColIndices + f] = offsets[f+1]; 2565 pInd[numColIndices + numFields + f] = newOffsets[f+1]; 2566 } 2567 for (a = 0; a < aDof; a++) { 2568 PetscInt anchor = anchors[a + aOff]; 2569 PetscInt gOff; 2570 ierr = PetscSectionGetOffset(globalCoarse,anchor,&gOff);CHKERRQ(ierr); 2571 DMPlexGetIndicesPointFields_Internal(localCoarse,anchor,gOff < 0 ? -(gOff + 1) : gOff,newOffsets,PETSC_FALSE,0,pInd);CHKERRQ(ierr); 2572 } 2573 } 2574 else { 2575 PetscInt a; 2576 ierr = MatGetValues(cMat,numRowIndices,rowIndices,numColIndices,colIndices,pMat);CHKERRQ(ierr); 2577 for (a = 0; a < aDof; a++) { 2578 PetscInt anchor = anchors[a + aOff]; 2579 PetscInt gOff; 2580 ierr = PetscSectionGetOffset(globalCoarse,anchor,&gOff);CHKERRQ(ierr); 2581 DMPlexGetIndicesPoint_Internal(localCoarse,anchor,gOff < 0 ? -(gOff + 1) : gOff,newOffsets,PETSC_FALSE,0,pInd);CHKERRQ(ierr); 2582 } 2583 } 2584 ierr = DMRestoreWorkArray(coarse,numColIndices,PETSC_INT,&colIndices);CHKERRQ(ierr); 2585 ierr = DMRestoreWorkArray(coarse,numRowIndices,PETSC_INT,&rowIndices);CHKERRQ(ierr); 2586 } 2587 else { 2588 PetscInt gOff; 2589 2590 ierr = PetscSectionGetOffset(globalCoarse,p,&gOff);CHKERRQ(ierr); 2591 if (numFields) { 2592 PetscInt f; 2593 2594 for (f = 0; f < numFields; f++) { 2595 PetscInt fDof; 2596 ierr = PetscSectionGetFieldDof(localCoarse,p,f,&fDof);CHKERRQ(ierr); 2597 offsets[f + 1] = fDof + offsets[f]; 2598 } 2599 for (f = 0; f < numFields; f++) { 2600 pInd[numColIndices + f] = offsets[f+1]; 2601 pInd[numColIndices + numFields + f] = offsets[f+1]; 2602 } 2603 DMPlexGetIndicesPointFields_Internal(localCoarse,p,gOff < 0 ? -(gOff + 1) : gOff,offsets,PETSC_FALSE,0,pInd);CHKERRQ(ierr); 2604 } 2605 else { 2606 DMPlexGetIndicesPoint_Internal(localCoarse,p,gOff < 0 ? -(gOff + 1) : gOff,offsets,PETSC_FALSE,0,pInd);CHKERRQ(ierr); 2607 } 2608 } 2609 } 2610 ierr = PetscFree(maxChildIds);CHKERRQ(ierr); 2611 } 2612 { 2613 PetscSF indicesSF, matricesSF; 2614 PetscInt *remoteOffsetsIndices, *remoteOffsetsMatrices, numLeafIndices, numLeafMatrices; 2615 2616 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)fine),&leafIndicesSec);CHKERRQ(ierr); 2617 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)fine),&leafMatricesSec);CHKERRQ(ierr); 2618 ierr = PetscSFDistributeSection(coarseToFineEmbedded,rootIndicesSec,&remoteOffsetsIndices,leafIndicesSec);CHKERRQ(ierr); 2619 ierr = PetscSFDistributeSection(coarseToFineEmbedded,rootMatricesSec,&remoteOffsetsMatrices,leafMatricesSec);CHKERRQ(ierr); 2620 ierr = PetscSFCreateSectionSF(coarseToFineEmbedded,rootIndicesSec,remoteOffsetsIndices,leafIndicesSec,&indicesSF);CHKERRQ(ierr); 2621 ierr = PetscSFCreateSectionSF(coarseToFineEmbedded,rootMatricesSec,remoteOffsetsMatrices,leafMatricesSec,&matricesSF);CHKERRQ(ierr); 2622 ierr = PetscSFDestroy(&coarseToFineEmbedded);CHKERRQ(ierr); 2623 ierr = PetscFree(remoteOffsetsIndices);CHKERRQ(ierr); 2624 ierr = PetscFree(remoteOffsetsMatrices);CHKERRQ(ierr); 2625 ierr = PetscSectionGetStorageSize(leafIndicesSec,&numLeafIndices);CHKERRQ(ierr); 2626 ierr = PetscSectionGetStorageSize(leafMatricesSec,&numLeafMatrices);CHKERRQ(ierr); 2627 ierr = PetscMalloc2(numLeafIndices,&leafIndices,numLeafMatrices,&leafMatrices);CHKERRQ(ierr); 2628 ierr = PetscSFBcastBegin(indicesSF,MPIU_INT,rootIndices,leafIndices);CHKERRQ(ierr); 2629 ierr = PetscSFBcastBegin(matricesSF,MPIU_SCALAR,rootMatrices,leafMatrices);CHKERRQ(ierr); 2630 ierr = PetscSFBcastEnd(indicesSF,MPIU_INT,rootIndices,leafIndices);CHKERRQ(ierr); 2631 ierr = PetscSFBcastEnd(matricesSF,MPIU_SCALAR,rootMatrices,leafMatrices);CHKERRQ(ierr); 2632 ierr = PetscSFDestroy(&matricesSF);CHKERRQ(ierr); 2633 ierr = PetscSFDestroy(&indicesSF);CHKERRQ(ierr); 2634 ierr = PetscFree2(rootIndices,rootMatrices);CHKERRQ(ierr); 2635 ierr = PetscSectionDestroy(&rootIndicesSec);CHKERRQ(ierr); 2636 ierr = PetscSectionDestroy(&rootMatricesSec);CHKERRQ(ierr); 2637 } 2638 /* count to preallocate */ 2639 ierr = DMGetDefaultSection(fine,&localFine);CHKERRQ(ierr); 2640 { 2641 PetscInt nGlobal; 2642 PetscInt *dnnz, *onnz; 2643 PetscLayout rowMap, colMap; 2644 PetscInt rowStart, rowEnd, colStart, colEnd; 2645 PetscInt maxDof; 2646 PetscInt *rowIndices; 2647 DM refTree; 2648 PetscInt **refPointFieldN; 2649 PetscScalar ***refPointFieldMats; 2650 PetscSection refConSec, refAnSec; 2651 PetscInt pRefStart,pRefEnd,maxConDof,maxColumns,leafStart,leafEnd; 2652 PetscScalar *pointWork; 2653 2654 ierr = PetscSectionGetConstrainedStorageSize(globalFine,&nGlobal);CHKERRQ(ierr); 2655 ierr = PetscCalloc2(nGlobal,&dnnz,nGlobal,&onnz);CHKERRQ(ierr); 2656 ierr = MatGetLayouts(mat,&rowMap,&colMap);CHKERRQ(ierr); 2657 ierr = PetscLayoutSetUp(rowMap);CHKERRQ(ierr); 2658 ierr = PetscLayoutSetUp(colMap);CHKERRQ(ierr); 2659 ierr = PetscLayoutGetRange(rowMap,&rowStart,&rowEnd);CHKERRQ(ierr); 2660 ierr = PetscLayoutGetRange(colMap,&colStart,&colEnd);CHKERRQ(ierr); 2661 ierr = PetscSectionGetMaxDof(globalFine,&maxDof);CHKERRQ(ierr); 2662 ierr = PetscSectionGetChart(leafIndicesSec,&leafStart,&leafEnd);CHKERRQ(ierr); 2663 ierr = DMGetWorkArray(fine,maxDof,PETSC_INT,&rowIndices);CHKERRQ(ierr); 2664 for (p = leafStart; p < leafEnd; p++) { 2665 PetscInt gDof, gcDof, gOff; 2666 PetscInt numColIndices, pIndOff, *pInd; 2667 PetscInt matSize; 2668 PetscInt i; 2669 2670 ierr = PetscSectionGetDof(globalFine,p,&gDof);CHKERRQ(ierr); 2671 ierr = PetscSectionGetConstraintDof(globalFine,p,&gcDof);CHKERRQ(ierr); 2672 if ((gDof - gcDof) <= 0) { 2673 continue; 2674 } 2675 ierr = PetscSectionGetOffset(globalFine,p,&gOff);CHKERRQ(ierr); 2676 if (gOff < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"I though having global dofs meant a non-negative offset"); 2677 if ((gOff < rowStart) || ((gOff + gDof - gcDof) > rowEnd)) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"I thought the row map would constrain the global dofs"); 2678 ierr = PetscSectionGetDof(leafIndicesSec,p,&numColIndices);CHKERRQ(ierr); 2679 ierr = PetscSectionGetOffset(leafIndicesSec,p,&pIndOff);CHKERRQ(ierr); 2680 numColIndices -= 2 * numFields; 2681 if (numColIndices <= 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"global fine dof with no dofs to interpolate from"); 2682 pInd = &leafIndices[pIndOff]; 2683 offsets[0] = 0; 2684 offsetsCopy[0] = 0; 2685 newOffsets[0] = 0; 2686 newOffsetsCopy[0] = 0; 2687 if (numFields) { 2688 PetscInt f; 2689 for (f = 0; f < numFields; f++) { 2690 PetscInt rowDof; 2691 2692 ierr = PetscSectionGetFieldDof(localFine,p,f,&rowDof);CHKERRQ(ierr); 2693 offsets[f + 1] = offsets[f] + rowDof; 2694 offsetsCopy[f + 1] = offsets[f + 1]; 2695 newOffsets[f + 1] = pInd[numColIndices + numFields + f]; 2696 numD[f] = 0; 2697 numO[f] = 0; 2698 } 2699 ierr = DMPlexGetIndicesPointFields_Internal(localFine,p,gOff,offsetsCopy,PETSC_FALSE,0,rowIndices);CHKERRQ(ierr); 2700 for (f = 0; f < numFields; f++) { 2701 PetscInt colOffset = newOffsets[f]; 2702 PetscInt numFieldCols = newOffsets[f + 1] - newOffsets[f]; 2703 2704 for (i = 0; i < numFieldCols; i++) { 2705 PetscInt gInd = pInd[i + colOffset]; 2706 2707 if (gInd >= colStart && gInd < colEnd) { 2708 numD[f]++; 2709 } 2710 else if (gInd >= 0) { /* negative means non-entry */ 2711 numO[f]++; 2712 } 2713 } 2714 } 2715 } 2716 else { 2717 ierr = DMPlexGetIndicesPoint_Internal(localFine,p,gOff,offsetsCopy,PETSC_FALSE,0,rowIndices);CHKERRQ(ierr); 2718 numD[0] = 0; 2719 numO[0] = 0; 2720 for (i = 0; i < numColIndices; i++) { 2721 PetscInt gInd = pInd[i]; 2722 2723 if (gInd >= colStart && gInd < colEnd) { 2724 numD[0]++; 2725 } 2726 else if (gInd >= 0) { /* negative means non-entry */ 2727 numO[0]++; 2728 } 2729 } 2730 } 2731 ierr = PetscSectionGetDof(leafMatricesSec,p,&matSize);CHKERRQ(ierr); 2732 if (!matSize) { /* incoming matrix is identity */ 2733 PetscInt childId; 2734 2735 childId = childIds[p-pStartF]; 2736 if (childId < 0) { /* no child interpolation: one nnz per */ 2737 if (numFields) { 2738 PetscInt f; 2739 for (f = 0; f < numFields; f++) { 2740 PetscInt numRows = offsets[f+1] - offsets[f], row; 2741 for (row = 0; row < numRows; row++) { 2742 PetscInt gIndCoarse = pInd[newOffsets[f] + row]; 2743 PetscInt gIndFine = rowIndices[offsets[f] + row]; 2744 if (gIndCoarse >= colStart && gIndCoarse < colEnd) { /* local */ 2745 if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs"); 2746 dnnz[gIndFine - rowStart] = 1; 2747 } 2748 else if (gIndCoarse >= 0) { /* remote */ 2749 if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs"); 2750 onnz[gIndFine - rowStart] = 1; 2751 } 2752 else { /* constrained */ 2753 if (gIndFine >= 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs"); 2754 } 2755 } 2756 } 2757 } 2758 else { 2759 PetscInt i; 2760 for (i = 0; i < gDof; i++) { 2761 PetscInt gIndCoarse = pInd[i]; 2762 PetscInt gIndFine = rowIndices[i]; 2763 if (gIndCoarse >= colStart && gIndCoarse < colEnd) { /* local */ 2764 if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs"); 2765 dnnz[gIndFine - rowStart] = 1; 2766 } 2767 else if (gIndCoarse >= 0) { /* remote */ 2768 if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs"); 2769 onnz[gIndFine - rowStart] = 1; 2770 } 2771 else { /* constrained */ 2772 if (gIndFine >= 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs"); 2773 } 2774 } 2775 } 2776 } 2777 else { /* interpolate from all */ 2778 if (numFields) { 2779 PetscInt f; 2780 for (f = 0; f < numFields; f++) { 2781 PetscInt numRows = offsets[f+1] - offsets[f], row; 2782 for (row = 0; row < numRows; row++) { 2783 PetscInt gIndFine = rowIndices[offsets[f] + row]; 2784 if (gIndFine >= 0) { 2785 if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs"); 2786 dnnz[gIndFine - rowStart] = numD[f]; 2787 onnz[gIndFine - rowStart] = numO[f]; 2788 } 2789 } 2790 } 2791 } 2792 else { 2793 PetscInt i; 2794 for (i = 0; i < gDof; i++) { 2795 PetscInt gIndFine = rowIndices[i]; 2796 if (gIndFine >= 0) { 2797 if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs"); 2798 dnnz[gIndFine - rowStart] = numD[0]; 2799 onnz[gIndFine - rowStart] = numO[0]; 2800 } 2801 } 2802 } 2803 } 2804 } 2805 else { /* interpolate from all */ 2806 if (numFields) { 2807 PetscInt f; 2808 for (f = 0; f < numFields; f++) { 2809 PetscInt numRows = offsets[f+1] - offsets[f], row; 2810 for (row = 0; row < numRows; row++) { 2811 PetscInt gIndFine = rowIndices[offsets[f] + row]; 2812 if (gIndFine >= 0) { 2813 if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs"); 2814 dnnz[gIndFine - rowStart] = numD[f]; 2815 onnz[gIndFine - rowStart] = numO[f]; 2816 } 2817 } 2818 } 2819 } 2820 else { /* every dof get a full row */ 2821 PetscInt i; 2822 for (i = 0; i < gDof; i++) { 2823 PetscInt gIndFine = rowIndices[i]; 2824 if (gIndFine >= 0) { 2825 if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs"); 2826 dnnz[gIndFine - rowStart] = numD[0]; 2827 onnz[gIndFine - rowStart] = numO[0]; 2828 } 2829 } 2830 } 2831 } 2832 } 2833 ierr = MatXAIJSetPreallocation(mat,1,dnnz,onnz,NULL,NULL);CHKERRQ(ierr); 2834 ierr = PetscFree2(dnnz,onnz);CHKERRQ(ierr); 2835 2836 ierr = DMPlexGetReferenceTree(fine,&refTree);CHKERRQ(ierr); 2837 ierr = DMPlexReferenceTreeGetChildrenMatrices(refTree,&refPointFieldMats,&refPointFieldN);CHKERRQ(ierr); 2838 ierr = DMGetDefaultConstraints(refTree,&refConSec,NULL);CHKERRQ(ierr); 2839 ierr = DMPlexGetAnchors(refTree,&refAnSec,NULL);CHKERRQ(ierr); 2840 ierr = PetscSectionGetChart(refConSec,&pRefStart,&pRefEnd);CHKERRQ(ierr); 2841 ierr = PetscSectionGetMaxDof(refConSec,&maxConDof);CHKERRQ(ierr); 2842 ierr = PetscSectionGetMaxDof(leafIndicesSec,&maxColumns);CHKERRQ(ierr); 2843 ierr = PetscMalloc1(maxConDof*maxColumns,&pointWork);CHKERRQ(ierr); 2844 for (p = leafStart; p < leafEnd; p++) { 2845 PetscInt gDof, gcDof, gOff; 2846 PetscInt numColIndices, pIndOff, *pInd; 2847 PetscInt matSize; 2848 PetscInt childId; 2849 2850 2851 ierr = PetscSectionGetDof(globalFine,p,&gDof);CHKERRQ(ierr); 2852 ierr = PetscSectionGetConstraintDof(globalFine,p,&gcDof);CHKERRQ(ierr); 2853 if ((gDof - gcDof) <= 0) { 2854 continue; 2855 } 2856 childId = childIds[p-pStartF]; 2857 ierr = PetscSectionGetOffset(globalFine,p,&gOff);CHKERRQ(ierr); 2858 ierr = PetscSectionGetDof(leafIndicesSec,p,&numColIndices);CHKERRQ(ierr); 2859 ierr = PetscSectionGetOffset(leafIndicesSec,p,&pIndOff);CHKERRQ(ierr); 2860 numColIndices -= 2 * numFields; 2861 pInd = &leafIndices[pIndOff]; 2862 offsets[0] = 0; 2863 offsetsCopy[0] = 0; 2864 newOffsets[0] = 0; 2865 newOffsetsCopy[0] = 0; 2866 rowOffsets[0] = 0; 2867 if (numFields) { 2868 PetscInt f; 2869 for (f = 0; f < numFields; f++) { 2870 PetscInt rowDof; 2871 2872 ierr = PetscSectionGetFieldDof(localFine,p,f,&rowDof);CHKERRQ(ierr); 2873 offsets[f + 1] = offsets[f] + rowDof; 2874 offsetsCopy[f + 1] = offsets[f + 1]; 2875 rowOffsets[f + 1] = pInd[numColIndices + f]; 2876 newOffsets[f + 1] = pInd[numColIndices + numFields + f]; 2877 } 2878 ierr = DMPlexGetIndicesPointFields_Internal(localFine,p,gOff,offsetsCopy,PETSC_FALSE,0,rowIndices);CHKERRQ(ierr); 2879 } 2880 else { 2881 ierr = DMPlexGetIndicesPoint_Internal(localFine,p,gOff,offsetsCopy,PETSC_FALSE,0,rowIndices);CHKERRQ(ierr); 2882 } 2883 ierr = PetscSectionGetDof(leafMatricesSec,p,&matSize);CHKERRQ(ierr); 2884 if (!matSize) { /* incoming matrix is identity */ 2885 if (childId < 0) { /* no child interpolation: scatter */ 2886 if (numFields) { 2887 PetscInt f; 2888 for (f = 0; f < numFields; f++) { 2889 PetscInt numRows = offsets[f+1] - offsets[f], row; 2890 for (row = 0; row < numRows; row++) { 2891 ierr = MatSetValue(mat,rowIndices[offsets[f]+row],pInd[newOffsets[f]+row],1.,INSERT_VALUES);CHKERRQ(ierr); 2892 } 2893 } 2894 } 2895 else { 2896 PetscInt numRows = gDof, row; 2897 for (row = 0; row < numRows; row++) { 2898 ierr = MatSetValue(mat,rowIndices[row],pInd[row],1.,INSERT_VALUES);CHKERRQ(ierr); 2899 } 2900 } 2901 } 2902 else { /* interpolate from all */ 2903 if (numFields) { 2904 PetscInt f; 2905 for (f = 0; f < numFields; f++) { 2906 PetscInt numRows = offsets[f+1] - offsets[f]; 2907 PetscInt numCols = newOffsets[f + 1] - newOffsets[f]; 2908 ierr = MatSetValues(mat,numRows,&rowIndices[offsets[f]],numCols,&pInd[newOffsets[f]],refPointFieldMats[childId - pRefStart][f],INSERT_VALUES);CHKERRQ(ierr); 2909 } 2910 } 2911 else { 2912 ierr = MatSetValues(mat,gDof,rowIndices,numColIndices,pInd,refPointFieldMats[childId - pRefStart][0],INSERT_VALUES);CHKERRQ(ierr); 2913 } 2914 } 2915 } 2916 else { /* interpolate from all */ 2917 PetscInt pMatOff; 2918 PetscScalar *pMat; 2919 2920 ierr = PetscSectionGetOffset(leafMatricesSec,p,&pMatOff);CHKERRQ(ierr); 2921 pMat = &leafMatrices[pMatOff]; 2922 if (childId < 0) { /* copy the incoming matrix */ 2923 if (numFields) { 2924 PetscInt f, count; 2925 for (f = 0, count = 0; f < numFields; f++) { 2926 PetscInt numRows = offsets[f+1]-offsets[f]; 2927 PetscInt numCols = newOffsets[f+1]-newOffsets[f]; 2928 PetscInt numInRows = rowOffsets[f+1]-rowOffsets[f]; 2929 PetscScalar *inMat = &pMat[count]; 2930 2931 ierr = MatSetValues(mat,numRows,&rowIndices[offsets[f]],numCols,&pInd[newOffsets[f]],inMat,INSERT_VALUES);CHKERRQ(ierr); 2932 count += numCols * numInRows; 2933 } 2934 } 2935 else { 2936 ierr = MatSetValues(mat,gDof,rowIndices,numColIndices,pInd,pMat,INSERT_VALUES);CHKERRQ(ierr); 2937 } 2938 } 2939 else { /* multiply the incoming matrix by the child interpolation */ 2940 if (numFields) { 2941 PetscInt f, count; 2942 for (f = 0, count = 0; f < numFields; f++) { 2943 PetscInt numRows = offsets[f+1]-offsets[f]; 2944 PetscInt numCols = newOffsets[f+1]-newOffsets[f]; 2945 PetscInt numInRows = rowOffsets[f+1]-rowOffsets[f]; 2946 PetscScalar *inMat = &pMat[count]; 2947 PetscInt i, j, k; 2948 if (refPointFieldN[childId - pRefStart][f] != numInRows) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Point constraint matrix multiply dimension mismatch"); 2949 for (i = 0; i < numRows; i++) { 2950 for (j = 0; j < numCols; j++) { 2951 PetscScalar val = 0.; 2952 for (k = 0; k < numInRows; k++) { 2953 val += refPointFieldMats[childId - pRefStart][f][i * numInRows + k] * inMat[k * numCols + j]; 2954 } 2955 pointWork[i * numCols + j] = val; 2956 } 2957 } 2958 ierr = MatSetValues(mat,numRows,&rowIndices[offsets[f]],numCols,&pInd[newOffsets[f]],pointWork,INSERT_VALUES);CHKERRQ(ierr); 2959 count += numCols * numInRows; 2960 } 2961 } 2962 else { /* every dof gets a full row */ 2963 PetscInt numRows = gDof; 2964 PetscInt numCols = numColIndices; 2965 PetscInt numInRows = matSize / numColIndices; 2966 PetscInt i, j, k; 2967 if (refPointFieldN[childId - pRefStart][0] != numInRows) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Point constraint matrix multiply dimension mismatch"); 2968 for (i = 0; i < numRows; i++) { 2969 for (j = 0; j < numCols; j++) { 2970 PetscScalar val = 0.; 2971 for (k = 0; k < numInRows; k++) { 2972 val += refPointFieldMats[childId - pRefStart][0][i * numInRows + k] * pMat[k * numCols + j]; 2973 } 2974 pointWork[i * numCols + j] = val; 2975 } 2976 } 2977 ierr = MatSetValues(mat,numRows,rowIndices,numCols,pInd,pointWork,INSERT_VALUES);CHKERRQ(ierr); 2978 } 2979 } 2980 } 2981 } 2982 ierr = DMPlexReferenceTreeRestoreChildrenMatrices(refTree,&refPointFieldMats,&refPointFieldN);CHKERRQ(ierr); 2983 ierr = DMRestoreWorkArray(fine,maxDof,PETSC_INT,&rowIndices);CHKERRQ(ierr); 2984 ierr = PetscFree(pointWork);CHKERRQ(ierr); 2985 } 2986 ierr = MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2987 ierr = MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2988 ierr = PetscSectionDestroy(&leafIndicesSec);CHKERRQ(ierr); 2989 ierr = PetscSectionDestroy(&leafMatricesSec);CHKERRQ(ierr); 2990 ierr = PetscFree2(leafIndices,leafMatrices);CHKERRQ(ierr); 2991 ierr = PetscFree7(offsets,offsetsCopy,newOffsets,newOffsetsCopy,rowOffsets,numD,numO);CHKERRQ(ierr); 2992 ierr = ISRestoreIndices(aIS,&anchors);CHKERRQ(ierr); 2993 PetscFunctionReturn(0); 2994 } 2995 2996 #undef __FUNCT__ 2997 #define __FUNCT__ "DMPlexComputeInjectorReferenceTree" 2998 /* 2999 * Assuming a nodal basis (w.r.t. the dual basis) basis: 3000 * 3001 * for each coarse dof \phi^c_i: 3002 * for each quadrature point (w_l,x_l) in the dual basis definition of \phi^c_i: 3003 * for each fine dof \phi^f_j; 3004 * a_{i,j} = 0; 3005 * for each fine dof \phi^f_k: 3006 * a_{i,j} += interp_{i,k} * \phi^f_k(x_l) * \phi^f_j(x_l) * w_l 3007 * [^^^ this is = \phi^c_i ^^^] 3008 */ 3009 PetscErrorCode DMPlexComputeInjectorReferenceTree(DM refTree, Mat *inj) 3010 { 3011 PetscDS ds; 3012 PetscSection section, cSection; 3013 DMLabel canonical, depth; 3014 Mat cMat, mat; 3015 PetscInt *nnz; 3016 PetscInt f, dim, numFields, numSecFields, p, pStart, pEnd, cStart, cEnd; 3017 PetscInt m, n; 3018 PetscScalar *pointScalar; 3019 PetscReal *v0, *v0parent, *vtmp, *J, *Jparent, *invJ, *pointRef, detJ, detJparent; 3020 PetscErrorCode ierr; 3021 3022 PetscFunctionBegin; 3023 ierr = DMGetDefaultSection(refTree,§ion);CHKERRQ(ierr); 3024 ierr = DMGetDimension(refTree, &dim);CHKERRQ(ierr); 3025 ierr = PetscMalloc6(dim,&v0,dim,&v0parent,dim,&vtmp,dim*dim,&J,dim*dim,&Jparent,dim*dim,&invJ);CHKERRQ(ierr); 3026 ierr = PetscMalloc2(dim,&pointScalar,dim,&pointRef);CHKERRQ(ierr); 3027 ierr = DMGetDS(refTree,&ds);CHKERRQ(ierr); 3028 ierr = PetscDSGetNumFields(ds,&numFields);CHKERRQ(ierr); 3029 ierr = PetscSectionGetNumFields(section,&numSecFields);CHKERRQ(ierr); 3030 ierr = DMGetLabel(refTree,"canonical",&canonical);CHKERRQ(ierr); 3031 ierr = DMGetLabel(refTree,"depth",&depth);CHKERRQ(ierr); 3032 ierr = DMGetDefaultConstraints(refTree,&cSection,&cMat);CHKERRQ(ierr); 3033 ierr = DMPlexGetChart(refTree, &pStart, &pEnd);CHKERRQ(ierr); 3034 ierr = DMPlexGetHeightStratum(refTree, 0, &cStart, &cEnd);CHKERRQ(ierr); 3035 ierr = MatGetSize(cMat,&n,&m);CHKERRQ(ierr); /* the injector has transpose sizes from the constraint matrix */ 3036 /* Step 1: compute non-zero pattern. A proper subset of constraint matrix non-zero */ 3037 ierr = PetscCalloc1(m,&nnz);CHKERRQ(ierr); 3038 for (p = pStart; p < pEnd; p++) { /* a point will have non-zeros if it is canonical, it has dofs, and its children have dofs */ 3039 const PetscInt *children; 3040 PetscInt numChildren; 3041 PetscInt i, numChildDof, numSelfDof; 3042 3043 if (canonical) { 3044 PetscInt pCanonical; 3045 ierr = DMLabelGetValue(canonical,p,&pCanonical);CHKERRQ(ierr); 3046 if (p != pCanonical) continue; 3047 } 3048 ierr = DMPlexGetTreeChildren(refTree,p,&numChildren,&children);CHKERRQ(ierr); 3049 if (!numChildren) continue; 3050 for (i = 0, numChildDof = 0; i < numChildren; i++) { 3051 PetscInt child = children[i]; 3052 PetscInt dof; 3053 3054 ierr = PetscSectionGetDof(section,child,&dof);CHKERRQ(ierr); 3055 numChildDof += dof; 3056 } 3057 ierr = PetscSectionGetDof(section,p,&numSelfDof);CHKERRQ(ierr); 3058 if (!numChildDof || !numSelfDof) continue; 3059 for (f = 0; f < numFields; f++) { 3060 PetscInt selfOff; 3061 3062 if (numSecFields) { /* count the dofs for just this field */ 3063 for (i = 0, numChildDof = 0; i < numChildren; i++) { 3064 PetscInt child = children[i]; 3065 PetscInt dof; 3066 3067 ierr = PetscSectionGetFieldDof(section,child,f,&dof);CHKERRQ(ierr); 3068 numChildDof += dof; 3069 } 3070 ierr = PetscSectionGetFieldDof(section,p,f,&numSelfDof);CHKERRQ(ierr); 3071 ierr = PetscSectionGetFieldOffset(section,p,f,&selfOff);CHKERRQ(ierr); 3072 } 3073 else { 3074 ierr = PetscSectionGetOffset(section,p,&selfOff);CHKERRQ(ierr); 3075 } 3076 for (i = 0; i < numSelfDof; i++) { 3077 nnz[selfOff + i] = numChildDof; 3078 } 3079 } 3080 } 3081 ierr = MatCreateAIJ(PETSC_COMM_SELF,m,n,m,n,-1,nnz,-1,NULL,&mat);CHKERRQ(ierr); 3082 ierr = PetscFree(nnz);CHKERRQ(ierr); 3083 /* Setp 2: compute entries */ 3084 for (p = pStart; p < pEnd; p++) { 3085 const PetscInt *children; 3086 PetscInt numChildren; 3087 PetscInt i, numChildDof, numSelfDof; 3088 3089 /* same conditions about when entries occur */ 3090 if (canonical) { 3091 PetscInt pCanonical; 3092 ierr = DMLabelGetValue(canonical,p,&pCanonical);CHKERRQ(ierr); 3093 if (p != pCanonical) continue; 3094 } 3095 ierr = DMPlexGetTreeChildren(refTree,p,&numChildren,&children);CHKERRQ(ierr); 3096 if (!numChildren) continue; 3097 for (i = 0, numChildDof = 0; i < numChildren; i++) { 3098 PetscInt child = children[i]; 3099 PetscInt dof; 3100 3101 ierr = PetscSectionGetDof(section,child,&dof);CHKERRQ(ierr); 3102 numChildDof += dof; 3103 } 3104 ierr = PetscSectionGetDof(section,p,&numSelfDof);CHKERRQ(ierr); 3105 if (!numChildDof || !numSelfDof) continue; 3106 3107 for (f = 0; f < numFields; f++) { 3108 PetscInt selfOff, fComp, numSelfShapes, numChildShapes, parentCell; 3109 PetscInt cellShapeOff; 3110 PetscObject disc; 3111 PetscDualSpace dsp; 3112 PetscClassId classId; 3113 PetscScalar *pointMat; 3114 PetscInt *matRows, *matCols; 3115 PetscInt pO = PETSC_MIN_INT; 3116 const PetscInt *depthNumDof; 3117 3118 if (numSecFields) { 3119 for (i = 0, numChildDof = 0; i < numChildren; i++) { 3120 PetscInt child = children[i]; 3121 PetscInt dof; 3122 3123 ierr = PetscSectionGetFieldDof(section,child,f,&dof);CHKERRQ(ierr); 3124 numChildDof += dof; 3125 } 3126 ierr = PetscSectionGetFieldDof(section,p,f,&numSelfDof);CHKERRQ(ierr); 3127 ierr = PetscSectionGetFieldOffset(section,p,f,&selfOff);CHKERRQ(ierr); 3128 ierr = PetscSectionGetFieldComponents(section,f,&fComp);CHKERRQ(ierr); 3129 } 3130 else { 3131 ierr = PetscSectionGetOffset(section,p,&selfOff);CHKERRQ(ierr); 3132 fComp = 1; 3133 } 3134 numSelfShapes = numSelfDof / fComp; 3135 numChildShapes = numChildDof / fComp; 3136 3137 /* find a cell whose closure contains p */ 3138 if (p >= cStart && p < cEnd) { 3139 parentCell = p; 3140 } 3141 else { 3142 PetscInt *star = NULL; 3143 PetscInt numStar; 3144 3145 parentCell = -1; 3146 ierr = DMPlexGetTransitiveClosure(refTree,p,PETSC_FALSE,&numStar,&star);CHKERRQ(ierr); 3147 for (i = numStar - 1; i >= 0; i--) { 3148 PetscInt c = star[2 * i]; 3149 3150 if (c >= cStart && c < cEnd) { 3151 parentCell = c; 3152 break; 3153 } 3154 } 3155 ierr = DMPlexRestoreTransitiveClosure(refTree,p,PETSC_FALSE,&numStar,&star);CHKERRQ(ierr); 3156 } 3157 /* determine the offset of p's shape functions withing parentCell's shape functions */ 3158 ierr = PetscDSGetDiscretization(ds,f,&disc);CHKERRQ(ierr); 3159 ierr = PetscObjectGetClassId(disc,&classId);CHKERRQ(ierr); 3160 if (classId == PETSCFE_CLASSID) { 3161 ierr = PetscFEGetDualSpace((PetscFE)disc,&dsp);CHKERRQ(ierr); 3162 } 3163 else if (classId == PETSCFV_CLASSID) { 3164 ierr = PetscFVGetDualSpace((PetscFV)disc,&dsp);CHKERRQ(ierr); 3165 } 3166 else { 3167 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Unsupported discretization object");CHKERRQ(ierr); 3168 } 3169 ierr = PetscDualSpaceGetNumDof(dsp,&depthNumDof);CHKERRQ(ierr); 3170 { 3171 PetscInt *closure = NULL; 3172 PetscInt numClosure; 3173 3174 ierr = DMPlexGetTransitiveClosure(refTree,parentCell,PETSC_TRUE,&numClosure,&closure);CHKERRQ(ierr); 3175 for (i = 0, cellShapeOff = 0; i < numClosure; i++) { 3176 PetscInt point = closure[2 * i], pointDepth; 3177 3178 pO = closure[2 * i + 1]; 3179 if (point == p) break; 3180 ierr = DMLabelGetValue(depth,point,&pointDepth);CHKERRQ(ierr); 3181 cellShapeOff += depthNumDof[pointDepth]; 3182 } 3183 ierr = DMPlexRestoreTransitiveClosure(refTree,parentCell,PETSC_TRUE,&numClosure,&closure);CHKERRQ(ierr); 3184 } 3185 3186 ierr = DMGetWorkArray(refTree, numSelfShapes * numChildShapes, PETSC_SCALAR,&pointMat);CHKERRQ(ierr); 3187 ierr = DMGetWorkArray(refTree, numSelfShapes + numChildShapes, PETSC_INT,&matRows);CHKERRQ(ierr); 3188 matCols = matRows + numSelfShapes; 3189 for (i = 0; i < numSelfShapes; i++) { 3190 matRows[i] = selfOff + i * fComp; 3191 } 3192 { 3193 PetscInt colOff = 0; 3194 3195 for (i = 0; i < numChildren; i++) { 3196 PetscInt child = children[i]; 3197 PetscInt dof, off, j; 3198 3199 if (numSecFields) { 3200 ierr = PetscSectionGetFieldDof(cSection,child,f,&dof);CHKERRQ(ierr); 3201 ierr = PetscSectionGetFieldOffset(cSection,child,f,&off);CHKERRQ(ierr); 3202 } 3203 else { 3204 ierr = PetscSectionGetDof(cSection,child,&dof);CHKERRQ(ierr); 3205 ierr = PetscSectionGetOffset(cSection,child,&off);CHKERRQ(ierr); 3206 } 3207 3208 for (j = 0; j < dof / fComp; j++) { 3209 matCols[colOff++] = off + j * fComp; 3210 } 3211 } 3212 } 3213 if (classId == PETSCFE_CLASSID) { 3214 PetscFE fe = (PetscFE) disc; 3215 PetscInt fSize; 3216 3217 ierr = PetscFEGetDualSpace(fe,&dsp);CHKERRQ(ierr); 3218 ierr = PetscDualSpaceGetDimension(dsp,&fSize);CHKERRQ(ierr); 3219 for (i = 0; i < numSelfShapes; i++) { /* for every shape function */ 3220 PetscQuadrature q; 3221 PetscInt dim, numPoints, j, k; 3222 const PetscReal *points; 3223 const PetscReal *weights; 3224 PetscInt *closure = NULL; 3225 PetscInt numClosure; 3226 PetscInt parentCellShapeDof = cellShapeOff + (pO < 0 ? (numSelfShapes - 1 - i) : i); 3227 PetscReal *Bparent; 3228 3229 ierr = PetscDualSpaceGetFunctional(dsp,parentCellShapeDof,&q);CHKERRQ(ierr); 3230 ierr = PetscQuadratureGetData(q,&dim,&numPoints,&points,&weights);CHKERRQ(ierr); 3231 ierr = PetscFEGetTabulation(fe,numPoints,points,&Bparent,NULL,NULL);CHKERRQ(ierr); /* I'm expecting a nodal basis: weights[:]' * Bparent[:,cellShapeDof] = 1. */ 3232 for (k = 0; k < numChildShapes; k++) { 3233 pointMat[numChildShapes * i + k] = 0.; 3234 } 3235 for (j = 0; j < numPoints; j++) { 3236 PetscInt childCell = -1; 3237 PetscReal parentValAtPoint; 3238 const PetscReal *pointReal = &points[dim * j]; 3239 const PetscScalar *point; 3240 PetscReal *Bchild; 3241 PetscInt childCellShapeOff, pointMatOff; 3242 #if defined(PETSC_USE_COMPLEX) 3243 PetscInt d; 3244 3245 for (d = 0; d < dim; d++) { 3246 pointScalar[d] = points[dim * j + d]; 3247 } 3248 point = pointScalar; 3249 #else 3250 point = pointReal; 3251 #endif 3252 3253 parentValAtPoint = Bparent[(fSize * j + parentCellShapeDof) * fComp]; 3254 3255 for (k = 0; k < numChildren; k++) { /* locate the point in a child's star cell*/ 3256 PetscInt child = children[k]; 3257 PetscInt *star = NULL; 3258 PetscInt numStar, s; 3259 3260 ierr = DMPlexGetTransitiveClosure(refTree,child,PETSC_FALSE,&numStar,&star);CHKERRQ(ierr); 3261 for (s = numStar - 1; s >= 0; s--) { 3262 PetscInt c = star[2 * s]; 3263 3264 if (c < cStart || c >= cEnd) continue; 3265 ierr = DMPlexLocatePoint_Internal(refTree,dim,point,c,&childCell);CHKERRQ(ierr); 3266 if (childCell >= 0) break; 3267 } 3268 ierr = DMPlexRestoreTransitiveClosure(refTree,child,PETSC_FALSE,&numStar,&star);CHKERRQ(ierr); 3269 if (childCell >= 0) break; 3270 } 3271 if (childCell < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Could not locate quadrature point");CHKERRQ(ierr); 3272 ierr = DMPlexComputeCellGeometryFEM(refTree, childCell, NULL, v0, J, invJ, &detJ);CHKERRQ(ierr); 3273 ierr = DMPlexComputeCellGeometryFEM(refTree, parentCell, NULL, v0parent, Jparent, NULL, &detJparent);CHKERRQ(ierr); 3274 CoordinatesRefToReal(dim, dim, v0parent, Jparent, pointReal, vtmp); 3275 CoordinatesRealToRef(dim, dim, v0, invJ, vtmp, pointRef); 3276 3277 ierr = PetscFEGetTabulation(fe,1,pointRef,&Bchild,NULL,NULL);CHKERRQ(ierr); 3278 ierr = DMPlexGetTransitiveClosure(refTree,childCell,PETSC_TRUE,&numClosure,&closure);CHKERRQ(ierr); 3279 for (k = 0, pointMatOff = 0; k < numChildren; k++) { /* point is located in cell => child dofs support at point are in closure of cell */ 3280 PetscInt child = children[k], childDepth, childDof, childO = PETSC_MIN_INT; 3281 PetscInt l; 3282 3283 ierr = DMLabelGetValue(depth,child,&childDepth);CHKERRQ(ierr); 3284 childDof = depthNumDof[childDepth]; 3285 for (l = 0, childCellShapeOff = 0; l < numClosure; l++) { 3286 PetscInt point = closure[2 * l]; 3287 PetscInt pointDepth; 3288 3289 childO = closure[2 * l + 1]; 3290 if (point == child) break; 3291 ierr = DMLabelGetValue(depth,point,&pointDepth);CHKERRQ(ierr); 3292 childCellShapeOff += depthNumDof[pointDepth]; 3293 } 3294 if (l == numClosure) { 3295 pointMatOff += childDof; 3296 continue; /* child is not in the closure of the cell: has nothing to contribute to this point */ 3297 } 3298 for (l = 0; l < childDof; l++) { 3299 PetscInt childCellDof = childCellShapeOff + (childO ? (childDof - 1 - l) : l); 3300 PetscReal childValAtPoint = Bchild[childCellDof * fComp]; 3301 3302 pointMat[i * numChildShapes + pointMatOff + l] += weights[j] * parentValAtPoint * childValAtPoint; 3303 } 3304 pointMatOff += childDof; 3305 } 3306 ierr = DMPlexRestoreTransitiveClosure(refTree,childCell,PETSC_TRUE,&numClosure,&closure);CHKERRQ(ierr); 3307 ierr = PetscFERestoreTabulation(fe,1,pointRef,&Bchild,NULL,NULL);CHKERRQ(ierr); 3308 } 3309 ierr = PetscFERestoreTabulation(fe,numPoints,points,&Bparent,NULL,NULL);CHKERRQ(ierr); 3310 } 3311 } 3312 else { /* just the volume-weighted averages of the children */ 3313 PetscInt childShapeOff; 3314 PetscReal parentVol; 3315 3316 ierr = DMPlexComputeCellGeometryFVM(refTree, p, &parentVol, NULL, NULL);CHKERRQ(ierr); 3317 for (i = 0, childShapeOff = 0; i < numChildren; i++) { 3318 PetscInt child = children[i]; 3319 PetscReal childVol; 3320 3321 if (child < cStart || child >= cEnd) continue; 3322 ierr = DMPlexComputeCellGeometryFVM(refTree, child, &childVol, NULL, NULL);CHKERRQ(ierr); 3323 pointMat[childShapeOff] = childVol / parentVol; 3324 childShapeOff++; 3325 } 3326 } 3327 /* Insert pointMat into mat */ 3328 for (i = 0; i < fComp; i++) { 3329 PetscInt j; 3330 ierr = MatSetValues(mat,numSelfShapes,matRows,numChildShapes,matCols,pointMat,INSERT_VALUES);CHKERRQ(ierr); 3331 3332 for (j = 0; j < numSelfShapes; j++) { 3333 matRows[j]++; 3334 } 3335 for (j = 0; j < numChildShapes; j++) { 3336 matCols[j]++; 3337 } 3338 } 3339 ierr = DMRestoreWorkArray(refTree, numSelfShapes + numChildShapes, PETSC_INT,&matRows);CHKERRQ(ierr); 3340 ierr = DMRestoreWorkArray(refTree, numSelfShapes * numChildShapes, PETSC_SCALAR,&pointMat);CHKERRQ(ierr); 3341 } 3342 } 3343 ierr = PetscFree6(v0,v0parent,vtmp,J,Jparent,invJ);CHKERRQ(ierr); 3344 ierr = PetscFree2(pointScalar,pointRef);CHKERRQ(ierr); 3345 ierr = MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3346 ierr = MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3347 *inj = mat; 3348 PetscFunctionReturn(0); 3349 } 3350 3351 #undef __FUNCT__ 3352 #define __FUNCT__ "DMPlexReferenceTreeGetChildrenMatrices_Injection" 3353 static PetscErrorCode DMPlexReferenceTreeGetChildrenMatrices_Injection(DM refTree, Mat inj, PetscScalar ****childrenMats) 3354 { 3355 PetscDS ds; 3356 PetscInt numFields, f, pRefStart, pRefEnd, p, *rows, *cols, maxDof; 3357 PetscScalar ***refPointFieldMats; 3358 PetscSection refConSec, refSection; 3359 PetscErrorCode ierr; 3360 3361 PetscFunctionBegin; 3362 ierr = DMGetDS(refTree,&ds);CHKERRQ(ierr); 3363 ierr = PetscDSGetNumFields(ds,&numFields);CHKERRQ(ierr); 3364 ierr = DMGetDefaultConstraints(refTree,&refConSec,NULL);CHKERRQ(ierr); 3365 ierr = DMGetDefaultSection(refTree,&refSection);CHKERRQ(ierr); 3366 ierr = PetscSectionGetChart(refConSec,&pRefStart,&pRefEnd);CHKERRQ(ierr); 3367 ierr = PetscMalloc1(pRefEnd-pRefStart,&refPointFieldMats);CHKERRQ(ierr); 3368 ierr = PetscSectionGetMaxDof(refConSec,&maxDof);CHKERRQ(ierr); 3369 ierr = PetscMalloc1(maxDof,&rows);CHKERRQ(ierr); 3370 ierr = PetscMalloc1(maxDof*maxDof,&cols);CHKERRQ(ierr); 3371 for (p = pRefStart; p < pRefEnd; p++) { 3372 PetscInt parent, pDof, parentDof; 3373 3374 ierr = DMPlexGetTreeParent(refTree,p,&parent,NULL);CHKERRQ(ierr); 3375 ierr = PetscSectionGetDof(refConSec,p,&pDof);CHKERRQ(ierr); 3376 ierr = PetscSectionGetDof(refSection,parent,&parentDof);CHKERRQ(ierr); 3377 if (!pDof || !parentDof || parent == p) continue; 3378 3379 ierr = PetscMalloc1(numFields,&refPointFieldMats[p-pRefStart]);CHKERRQ(ierr); 3380 for (f = 0; f < numFields; f++) { 3381 PetscInt cDof, cOff, numCols, r, fComp; 3382 PetscObject disc; 3383 PetscClassId id; 3384 PetscFE fe = NULL; 3385 PetscFV fv = NULL; 3386 3387 ierr = PetscDSGetDiscretization(ds,f,&disc);CHKERRQ(ierr); 3388 ierr = PetscObjectGetClassId(disc,&id);CHKERRQ(ierr); 3389 if (id == PETSCFE_CLASSID) { 3390 fe = (PetscFE) disc; 3391 ierr = PetscFEGetNumComponents(fe,&fComp);CHKERRQ(ierr); 3392 } 3393 else if (id == PETSCFV_CLASSID) { 3394 fv = (PetscFV) disc; 3395 ierr = PetscFVGetNumComponents(fv,&fComp);CHKERRQ(ierr); 3396 } 3397 else SETERRQ1(PetscObjectComm(disc),PETSC_ERR_ARG_UNKNOWN_TYPE, "PetscDS discretization id %d not recognized.", id); 3398 3399 if (numFields > 1) { 3400 ierr = PetscSectionGetFieldDof(refConSec,p,f,&cDof);CHKERRQ(ierr); 3401 ierr = PetscSectionGetFieldOffset(refConSec,p,f,&cOff);CHKERRQ(ierr); 3402 } 3403 else { 3404 ierr = PetscSectionGetDof(refConSec,p,&cDof);CHKERRQ(ierr); 3405 ierr = PetscSectionGetOffset(refConSec,p,&cOff);CHKERRQ(ierr); 3406 } 3407 3408 if (!cDof) continue; 3409 for (r = 0; r < cDof; r++) { 3410 rows[r] = cOff + r; 3411 } 3412 numCols = 0; 3413 { 3414 PetscInt aDof, aOff, j; 3415 3416 if (numFields > 1) { 3417 ierr = PetscSectionGetFieldDof(refSection,parent,f,&aDof);CHKERRQ(ierr); 3418 ierr = PetscSectionGetFieldOffset(refSection,parent,f,&aOff);CHKERRQ(ierr); 3419 } 3420 else { 3421 ierr = PetscSectionGetDof(refSection,parent,&aDof);CHKERRQ(ierr); 3422 ierr = PetscSectionGetOffset(refSection,parent,&aOff);CHKERRQ(ierr); 3423 } 3424 3425 for (j = 0; j < aDof; j++) { 3426 cols[numCols++] = aOff + j; 3427 } 3428 } 3429 ierr = PetscMalloc1(cDof*numCols,&refPointFieldMats[p-pRefStart][f]);CHKERRQ(ierr); 3430 /* transpose of constraint matrix */ 3431 ierr = MatGetValues(inj,numCols,cols,cDof,rows,refPointFieldMats[p-pRefStart][f]);CHKERRQ(ierr); 3432 } 3433 } 3434 *childrenMats = refPointFieldMats; 3435 ierr = PetscFree(rows);CHKERRQ(ierr); 3436 ierr = PetscFree(cols);CHKERRQ(ierr); 3437 PetscFunctionReturn(0); 3438 } 3439 3440 #undef __FUNCT__ 3441 #define __FUNCT__ "DMPlexReferenceTreeRestoreChildrenMatrices_Injection" 3442 static PetscErrorCode DMPlexReferenceTreeRestoreChildrenMatrices_Injection(DM refTree, Mat inj, PetscScalar ****childrenMats) 3443 { 3444 PetscDS ds; 3445 PetscScalar ***refPointFieldMats; 3446 PetscInt numFields, pRefStart, pRefEnd, p, f; 3447 PetscSection refConSec, refSection; 3448 PetscErrorCode ierr; 3449 3450 PetscFunctionBegin; 3451 refPointFieldMats = *childrenMats; 3452 *childrenMats = NULL; 3453 ierr = DMGetDS(refTree,&ds);CHKERRQ(ierr); 3454 ierr = DMGetDefaultSection(refTree,&refSection);CHKERRQ(ierr); 3455 ierr = PetscDSGetNumFields(ds,&numFields);CHKERRQ(ierr); 3456 ierr = DMGetDefaultConstraints(refTree,&refConSec,NULL);CHKERRQ(ierr); 3457 ierr = PetscSectionGetChart(refConSec,&pRefStart,&pRefEnd);CHKERRQ(ierr); 3458 for (p = pRefStart; p < pRefEnd; p++) { 3459 PetscInt parent, pDof, parentDof; 3460 3461 ierr = DMPlexGetTreeParent(refTree,p,&parent,NULL);CHKERRQ(ierr); 3462 ierr = PetscSectionGetDof(refConSec,p,&pDof);CHKERRQ(ierr); 3463 ierr = PetscSectionGetDof(refSection,parent,&parentDof);CHKERRQ(ierr); 3464 if (!pDof || !parentDof || parent == p) continue; 3465 3466 for (f = 0; f < numFields; f++) { 3467 PetscInt cDof; 3468 3469 if (numFields > 1) { 3470 ierr = PetscSectionGetFieldDof(refConSec,p,f,&cDof);CHKERRQ(ierr); 3471 } 3472 else { 3473 ierr = PetscSectionGetDof(refConSec,p,&cDof);CHKERRQ(ierr); 3474 } 3475 3476 if (!cDof) continue; 3477 ierr = PetscFree(refPointFieldMats[p - pRefStart][f]);CHKERRQ(ierr); 3478 } 3479 ierr = PetscFree(refPointFieldMats[p - pRefStart]);CHKERRQ(ierr); 3480 } 3481 ierr = PetscFree(refPointFieldMats);CHKERRQ(ierr); 3482 PetscFunctionReturn(0); 3483 } 3484 3485 #undef __FUNCT__ 3486 #define __FUNCT__ "DMPlexReferenceTreeGetInjector" 3487 static PetscErrorCode DMPlexReferenceTreeGetInjector(DM refTree,Mat *injRef) 3488 { 3489 Mat cMatRef; 3490 PetscObject injRefObj; 3491 PetscErrorCode ierr; 3492 3493 PetscFunctionBegin; 3494 ierr = DMGetDefaultConstraints(refTree,NULL,&cMatRef);CHKERRQ(ierr); 3495 ierr = PetscObjectQuery((PetscObject)cMatRef,"DMPlexComputeInjectorTree_refTree",&injRefObj);CHKERRQ(ierr); 3496 *injRef = (Mat) injRefObj; 3497 if (!*injRef) { 3498 ierr = DMPlexComputeInjectorReferenceTree(refTree,injRef);CHKERRQ(ierr); 3499 ierr = PetscObjectCompose((PetscObject)cMatRef,"DMPlexComputeInjectorTree_refTree",(PetscObject)*injRef);CHKERRQ(ierr); 3500 /* there is now a reference in cMatRef, which should be the only one for symmetry with the above case */ 3501 ierr = PetscObjectDereference((PetscObject)*injRef);CHKERRQ(ierr); 3502 } 3503 PetscFunctionReturn(0); 3504 } 3505 3506 #undef __FUNCT__ 3507 #define __FUNCT__ "DMPlexTransferInjectorTree" 3508 static PetscErrorCode DMPlexTransferInjectorTree(DM coarse, DM fine, PetscSF coarseToFine, const PetscInt *childIds, Vec fineVec, PetscInt numFields, PetscInt *offsets, PetscSection *rootMultiSec, PetscSection *multiLeafSec, PetscInt **gatheredIndices, PetscScalar **gatheredValues) 3509 { 3510 PetscInt pStartF, pEndF, pStartC, pEndC, p, maxDof, numMulti; 3511 PetscSection globalCoarse, globalFine; 3512 PetscSection localCoarse, localFine, leafIndicesSec; 3513 PetscSection multiRootSec, rootIndicesSec; 3514 PetscInt *leafInds, *rootInds = NULL; 3515 const PetscInt *rootDegrees; 3516 PetscScalar *leafVals = NULL, *rootVals = NULL; 3517 PetscSF coarseToFineEmbedded; 3518 PetscErrorCode ierr; 3519 3520 PetscFunctionBegin; 3521 ierr = DMPlexGetChart(coarse,&pStartC,&pEndC);CHKERRQ(ierr); 3522 ierr = DMPlexGetChart(fine,&pStartF,&pEndF);CHKERRQ(ierr); 3523 ierr = DMGetDefaultSection(fine,&localFine);CHKERRQ(ierr); 3524 ierr = DMGetDefaultGlobalSection(fine,&globalFine);CHKERRQ(ierr); 3525 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)fine),&leafIndicesSec);CHKERRQ(ierr); 3526 ierr = PetscSectionSetChart(leafIndicesSec,pStartF, pEndF);CHKERRQ(ierr); 3527 ierr = PetscSectionGetMaxDof(localFine,&maxDof);CHKERRQ(ierr); 3528 { /* winnow fine points that don't have global dofs out of the sf */ 3529 PetscInt l, nleaves, dof, cdof, numPointsWithDofs, offset, *pointsWithDofs, numIndices; 3530 const PetscInt *leaves; 3531 3532 ierr = PetscSFGetGraph(coarseToFine,NULL,&nleaves,&leaves,NULL);CHKERRQ(ierr); 3533 for (l = 0, numPointsWithDofs = 0; l < nleaves; l++) { 3534 p = leaves ? leaves[l] : l; 3535 ierr = PetscSectionGetDof(globalFine,p,&dof);CHKERRQ(ierr); 3536 ierr = PetscSectionGetConstraintDof(globalFine,p,&cdof);CHKERRQ(ierr); 3537 if ((dof - cdof) > 0) { 3538 numPointsWithDofs++; 3539 3540 ierr = PetscSectionGetDof(localFine,p,&dof);CHKERRQ(ierr); 3541 ierr = PetscSectionSetDof(leafIndicesSec,p,dof + 1);CHKERRQ(ierr); 3542 } 3543 } 3544 ierr = PetscMalloc1(numPointsWithDofs,&pointsWithDofs);CHKERRQ(ierr); 3545 ierr = PetscSectionSetUp(leafIndicesSec);CHKERRQ(ierr); 3546 ierr = PetscSectionGetStorageSize(leafIndicesSec,&numIndices);CHKERRQ(ierr); 3547 ierr = PetscMalloc1(gatheredIndices ? numIndices : (maxDof + 1),&leafInds);CHKERRQ(ierr); 3548 if (gatheredValues) {ierr = PetscMalloc1(numIndices,&leafVals);CHKERRQ(ierr);} 3549 for (l = 0, offset = 0; l < nleaves; l++) { 3550 p = leaves ? leaves[l] : l; 3551 ierr = PetscSectionGetDof(globalFine,p,&dof);CHKERRQ(ierr); 3552 ierr = PetscSectionGetConstraintDof(globalFine,p,&cdof);CHKERRQ(ierr); 3553 if ((dof - cdof) > 0) { 3554 PetscInt off, gOff; 3555 PetscInt *pInd; 3556 PetscScalar *pVal = NULL; 3557 3558 pointsWithDofs[offset++] = l; 3559 3560 ierr = PetscSectionGetOffset(leafIndicesSec,p,&off);CHKERRQ(ierr); 3561 3562 pInd = gatheredIndices ? (&leafInds[off + 1]) : leafInds; 3563 if (gatheredValues) { 3564 PetscInt i; 3565 3566 pVal = &leafVals[off + 1]; 3567 for (i = 0; i < dof; i++) pVal[i] = 0.; 3568 } 3569 ierr = PetscSectionGetOffset(globalFine,p,&gOff);CHKERRQ(ierr); 3570 3571 offsets[0] = 0; 3572 if (numFields) { 3573 PetscInt f; 3574 3575 for (f = 0; f < numFields; f++) { 3576 PetscInt fDof; 3577 ierr = PetscSectionGetFieldDof(localFine,p,f,&fDof);CHKERRQ(ierr); 3578 offsets[f + 1] = fDof + offsets[f]; 3579 } 3580 DMPlexGetIndicesPointFields_Internal(localFine,p,gOff < 0 ? -(gOff + 1) : gOff,offsets,PETSC_FALSE,0,pInd);CHKERRQ(ierr); 3581 } 3582 else { 3583 DMPlexGetIndicesPoint_Internal(localFine,p,gOff < 0 ? -(gOff + 1) : gOff,offsets,PETSC_FALSE,0,pInd);CHKERRQ(ierr); 3584 } 3585 if (gatheredValues) {ierr = VecGetValues(fineVec,dof,pInd,pVal);CHKERRQ(ierr);} 3586 } 3587 } 3588 ierr = PetscSFCreateEmbeddedLeafSF(coarseToFine, numPointsWithDofs, pointsWithDofs, &coarseToFineEmbedded);CHKERRQ(ierr); 3589 ierr = PetscFree(pointsWithDofs);CHKERRQ(ierr); 3590 } 3591 3592 ierr = DMPlexGetChart(coarse,&pStartC,&pEndC);CHKERRQ(ierr); 3593 ierr = DMGetDefaultSection(coarse,&localCoarse);CHKERRQ(ierr); 3594 ierr = DMGetDefaultGlobalSection(coarse,&globalCoarse);CHKERRQ(ierr); 3595 3596 { /* there may be the case where an sf root has a parent: broadcast parents back to children */ 3597 MPI_Datatype threeInt; 3598 PetscMPIInt rank; 3599 PetscInt (*parentNodeAndIdCoarse)[3]; 3600 PetscInt (*parentNodeAndIdFine)[3]; 3601 PetscInt p, nleaves, nleavesToParents; 3602 PetscSF pointSF, sfToParents; 3603 const PetscInt *ilocal; 3604 const PetscSFNode *iremote; 3605 PetscSFNode *iremoteToParents; 3606 PetscInt *ilocalToParents; 3607 3608 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)coarse),&rank);CHKERRQ(ierr); 3609 ierr = MPI_Type_contiguous(3,MPIU_INT,&threeInt);CHKERRQ(ierr); 3610 ierr = MPI_Type_commit(&threeInt);CHKERRQ(ierr); 3611 ierr = PetscMalloc2(pEndC-pStartC,&parentNodeAndIdCoarse,pEndF-pStartF,&parentNodeAndIdFine);CHKERRQ(ierr); 3612 ierr = DMGetPointSF(coarse,&pointSF);CHKERRQ(ierr); 3613 ierr = PetscSFGetGraph(pointSF,NULL,&nleaves,&ilocal,&iremote);CHKERRQ(ierr); 3614 for (p = pStartC; p < pEndC; p++) { 3615 PetscInt parent, childId; 3616 ierr = DMPlexGetTreeParent(coarse,p,&parent,&childId);CHKERRQ(ierr); 3617 parentNodeAndIdCoarse[p - pStartC][0] = rank; 3618 parentNodeAndIdCoarse[p - pStartC][1] = parent - pStartC; 3619 parentNodeAndIdCoarse[p - pStartC][2] = (p == parent) ? -1 : childId; 3620 if (nleaves > 0) { 3621 PetscInt leaf = -1; 3622 3623 if (ilocal) { 3624 ierr = PetscFindInt(parent,nleaves,ilocal,&leaf);CHKERRQ(ierr); 3625 } 3626 else { 3627 leaf = p - pStartC; 3628 } 3629 if (leaf >= 0) { 3630 parentNodeAndIdCoarse[p - pStartC][0] = iremote[leaf].rank; 3631 parentNodeAndIdCoarse[p - pStartC][1] = iremote[leaf].index; 3632 } 3633 } 3634 } 3635 for (p = pStartF; p < pEndF; p++) { 3636 parentNodeAndIdFine[p - pStartF][0] = -1; 3637 parentNodeAndIdFine[p - pStartF][1] = -1; 3638 parentNodeAndIdFine[p - pStartF][2] = -1; 3639 } 3640 ierr = PetscSFBcastBegin(coarseToFineEmbedded,threeInt,parentNodeAndIdCoarse,parentNodeAndIdFine);CHKERRQ(ierr); 3641 ierr = PetscSFBcastEnd(coarseToFineEmbedded,threeInt,parentNodeAndIdCoarse,parentNodeAndIdFine);CHKERRQ(ierr); 3642 for (p = pStartF, nleavesToParents = 0; p < pEndF; p++) { 3643 PetscInt dof; 3644 3645 ierr = PetscSectionGetDof(leafIndicesSec,p,&dof);CHKERRQ(ierr); 3646 if (dof) { 3647 PetscInt off; 3648 3649 ierr = PetscSectionGetOffset(leafIndicesSec,p,&off);CHKERRQ(ierr); 3650 if (gatheredIndices) { 3651 leafInds[off] = PetscMax(childIds[p-pStartF],parentNodeAndIdFine[p-pStartF][2]); 3652 } else if (gatheredValues) { 3653 leafVals[off] = (PetscScalar) PetscMax(childIds[p-pStartF],parentNodeAndIdFine[p-pStartF][2]); 3654 } 3655 } 3656 if (parentNodeAndIdFine[p-pStartF][0] >= 0) { 3657 nleavesToParents++; 3658 } 3659 } 3660 ierr = PetscMalloc1(nleavesToParents,&ilocalToParents);CHKERRQ(ierr); 3661 ierr = PetscMalloc1(nleavesToParents,&iremoteToParents);CHKERRQ(ierr); 3662 for (p = pStartF, nleavesToParents = 0; p < pEndF; p++) { 3663 if (parentNodeAndIdFine[p-pStartF][0] >= 0) { 3664 ilocalToParents[nleavesToParents] = p - pStartF; 3665 iremoteToParents[nleavesToParents].rank = parentNodeAndIdFine[p-pStartF][0]; 3666 iremoteToParents[nleavesToParents].index = parentNodeAndIdFine[p-pStartF][1]; 3667 nleavesToParents++; 3668 } 3669 } 3670 ierr = PetscSFCreate(PetscObjectComm((PetscObject)coarse),&sfToParents);CHKERRQ(ierr); 3671 ierr = PetscSFSetGraph(sfToParents,pEndC-pStartC,nleavesToParents,ilocalToParents,PETSC_OWN_POINTER,iremoteToParents,PETSC_OWN_POINTER);CHKERRQ(ierr); 3672 ierr = PetscSFDestroy(&coarseToFineEmbedded);CHKERRQ(ierr); 3673 3674 coarseToFineEmbedded = sfToParents; 3675 3676 ierr = PetscFree2(parentNodeAndIdCoarse,parentNodeAndIdFine);CHKERRQ(ierr); 3677 ierr = MPI_Type_free(&threeInt);CHKERRQ(ierr); 3678 } 3679 3680 { /* winnow out coarse points that don't have dofs */ 3681 PetscInt dof, cdof, numPointsWithDofs, offset, *pointsWithDofs; 3682 PetscSF sfDofsOnly; 3683 3684 for (p = pStartC, numPointsWithDofs = 0; p < pEndC; p++) { 3685 ierr = PetscSectionGetDof(globalCoarse,p,&dof);CHKERRQ(ierr); 3686 ierr = PetscSectionGetConstraintDof(globalCoarse,p,&cdof);CHKERRQ(ierr); 3687 if ((dof - cdof) > 0) { 3688 numPointsWithDofs++; 3689 } 3690 } 3691 ierr = PetscMalloc1(numPointsWithDofs,&pointsWithDofs);CHKERRQ(ierr); 3692 for (p = pStartC, offset = 0; p < pEndC; p++) { 3693 ierr = PetscSectionGetDof(globalCoarse,p,&dof);CHKERRQ(ierr); 3694 ierr = PetscSectionGetConstraintDof(globalCoarse,p,&cdof);CHKERRQ(ierr); 3695 if ((dof - cdof) > 0) { 3696 pointsWithDofs[offset++] = p - pStartC; 3697 } 3698 } 3699 ierr = PetscSFCreateEmbeddedSF(coarseToFineEmbedded, numPointsWithDofs, pointsWithDofs, &sfDofsOnly);CHKERRQ(ierr); 3700 ierr = PetscSFDestroy(&coarseToFineEmbedded);CHKERRQ(ierr); 3701 ierr = PetscFree(pointsWithDofs);CHKERRQ(ierr); 3702 coarseToFineEmbedded = sfDofsOnly; 3703 } 3704 3705 /* communicate back to the coarse mesh which coarse points have children (that may require injection) */ 3706 ierr = PetscSFComputeDegreeBegin(coarseToFineEmbedded,&rootDegrees);CHKERRQ(ierr); 3707 ierr = PetscSFComputeDegreeEnd(coarseToFineEmbedded,&rootDegrees);CHKERRQ(ierr); 3708 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)coarse),&multiRootSec);CHKERRQ(ierr); 3709 ierr = PetscSectionSetChart(multiRootSec,pStartC,pEndC);CHKERRQ(ierr); 3710 for (p = pStartC; p < pEndC; p++) { 3711 ierr = PetscSectionSetDof(multiRootSec,p,rootDegrees[p-pStartC]);CHKERRQ(ierr); 3712 } 3713 ierr = PetscSectionSetUp(multiRootSec);CHKERRQ(ierr); 3714 ierr = PetscSectionGetStorageSize(multiRootSec,&numMulti);CHKERRQ(ierr); 3715 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)coarse),&rootIndicesSec);CHKERRQ(ierr); 3716 { /* distribute the leaf section */ 3717 PetscSF multi, multiInv, indicesSF; 3718 PetscInt *remoteOffsets, numRootIndices; 3719 3720 ierr = PetscSFGetMultiSF(coarseToFineEmbedded,&multi);CHKERRQ(ierr); 3721 ierr = PetscSFCreateInverseSF(multi,&multiInv);CHKERRQ(ierr); 3722 ierr = PetscSFDistributeSection(multiInv,leafIndicesSec,&remoteOffsets,rootIndicesSec);CHKERRQ(ierr); 3723 ierr = PetscSFCreateSectionSF(multiInv,leafIndicesSec,remoteOffsets,rootIndicesSec,&indicesSF);CHKERRQ(ierr); 3724 ierr = PetscFree(remoteOffsets);CHKERRQ(ierr); 3725 ierr = PetscSFDestroy(&multiInv);CHKERRQ(ierr); 3726 ierr = PetscSectionGetStorageSize(rootIndicesSec,&numRootIndices);CHKERRQ(ierr); 3727 if (gatheredIndices) { 3728 ierr = PetscMalloc1(numRootIndices,&rootInds);CHKERRQ(ierr); 3729 ierr = PetscSFBcastBegin(indicesSF,MPIU_INT,leafInds,rootInds);CHKERRQ(ierr); 3730 ierr = PetscSFBcastEnd(indicesSF,MPIU_INT,leafInds,rootInds);CHKERRQ(ierr); 3731 } 3732 if (gatheredValues) { 3733 ierr = PetscMalloc1(numRootIndices,&rootVals);CHKERRQ(ierr); 3734 ierr = PetscSFBcastBegin(indicesSF,MPIU_SCALAR,leafVals,rootVals);CHKERRQ(ierr); 3735 ierr = PetscSFBcastEnd(indicesSF,MPIU_SCALAR,leafVals,rootVals);CHKERRQ(ierr); 3736 } 3737 ierr = PetscSFDestroy(&indicesSF);CHKERRQ(ierr); 3738 } 3739 ierr = PetscSectionDestroy(&leafIndicesSec);CHKERRQ(ierr); 3740 ierr = PetscFree(leafInds);CHKERRQ(ierr); 3741 ierr = PetscFree(leafVals);CHKERRQ(ierr); 3742 ierr = PetscSFDestroy(&coarseToFineEmbedded);CHKERRQ(ierr); 3743 *rootMultiSec = multiRootSec; 3744 *multiLeafSec = rootIndicesSec; 3745 if (gatheredIndices) *gatheredIndices = rootInds; 3746 if (gatheredValues) *gatheredValues = rootVals; 3747 PetscFunctionReturn(0); 3748 } 3749 3750 #undef __FUNCT__ 3751 #define __FUNCT__ "DMPlexComputeInjectorTree" 3752 PetscErrorCode DMPlexComputeInjectorTree(DM coarse, DM fine, PetscSF coarseToFine, PetscInt *childIds, Mat mat) 3753 { 3754 DM refTree; 3755 PetscSection multiRootSec, rootIndicesSec; 3756 PetscSection globalCoarse, globalFine; 3757 PetscSection localCoarse, localFine; 3758 PetscSection cSecRef; 3759 PetscInt *rootIndices, *parentIndices, pRefStart, pRefEnd; 3760 Mat injRef; 3761 PetscInt numFields, maxDof; 3762 PetscInt pStartC, pEndC, pStartF, pEndF, p; 3763 PetscInt *offsets, *offsetsCopy, *rowOffsets; 3764 PetscLayout rowMap, colMap; 3765 PetscInt rowStart, rowEnd, colStart, colEnd, *nnzD, *nnzO; 3766 PetscScalar ***childrenMats=NULL ; /* gcc -O gives 'may be used uninitialized' warning'. Initializing to suppress this warning */ 3767 PetscErrorCode ierr; 3768 3769 PetscFunctionBegin; 3770 3771 /* get the templates for the fine-to-coarse injection from the reference tree */ 3772 ierr = DMPlexGetReferenceTree(coarse,&refTree);CHKERRQ(ierr); 3773 ierr = DMGetDefaultConstraints(refTree,&cSecRef,NULL);CHKERRQ(ierr); 3774 ierr = PetscSectionGetChart(cSecRef,&pRefStart,&pRefEnd);CHKERRQ(ierr); 3775 ierr = DMPlexReferenceTreeGetInjector(refTree,&injRef);CHKERRQ(ierr); 3776 3777 ierr = DMPlexGetChart(fine,&pStartF,&pEndF);CHKERRQ(ierr); 3778 ierr = DMGetDefaultSection(fine,&localFine);CHKERRQ(ierr); 3779 ierr = DMGetDefaultGlobalSection(fine,&globalFine);CHKERRQ(ierr); 3780 ierr = PetscSectionGetNumFields(localFine,&numFields);CHKERRQ(ierr); 3781 ierr = DMPlexGetChart(coarse,&pStartC,&pEndC);CHKERRQ(ierr); 3782 ierr = DMGetDefaultSection(coarse,&localCoarse);CHKERRQ(ierr); 3783 ierr = DMGetDefaultGlobalSection(coarse,&globalCoarse);CHKERRQ(ierr); 3784 ierr = PetscSectionGetMaxDof(localCoarse,&maxDof);CHKERRQ(ierr); 3785 { 3786 PetscInt maxFields = PetscMax(1,numFields) + 1; 3787 ierr = PetscMalloc3(maxFields,&offsets,maxFields,&offsetsCopy,maxFields,&rowOffsets);CHKERRQ(ierr); 3788 } 3789 3790 ierr = DMPlexTransferInjectorTree(coarse,fine,coarseToFine,childIds,NULL,numFields,offsets,&multiRootSec,&rootIndicesSec,&rootIndices,NULL);CHKERRQ(ierr); 3791 3792 ierr = PetscMalloc1(maxDof,&parentIndices);CHKERRQ(ierr); 3793 3794 /* count indices */ 3795 ierr = MatGetLayouts(mat,&rowMap,&colMap);CHKERRQ(ierr); 3796 ierr = PetscLayoutSetUp(rowMap);CHKERRQ(ierr); 3797 ierr = PetscLayoutSetUp(colMap);CHKERRQ(ierr); 3798 ierr = PetscLayoutGetRange(rowMap,&rowStart,&rowEnd);CHKERRQ(ierr); 3799 ierr = PetscLayoutGetRange(colMap,&colStart,&colEnd);CHKERRQ(ierr); 3800 ierr = PetscCalloc2(rowEnd-rowStart,&nnzD,rowEnd-rowStart,&nnzO);CHKERRQ(ierr); 3801 for (p = pStartC; p < pEndC; p++) { 3802 PetscInt numLeaves, leafStart, leafEnd, l, dof, cdof, gOff; 3803 3804 ierr = PetscSectionGetDof(globalCoarse,p,&dof);CHKERRQ(ierr); 3805 ierr = PetscSectionGetConstraintDof(globalCoarse,p,&cdof);CHKERRQ(ierr); 3806 if ((dof - cdof) <= 0) continue; 3807 ierr = PetscSectionGetOffset(globalCoarse,p,&gOff);CHKERRQ(ierr); 3808 3809 rowOffsets[0] = 0; 3810 offsetsCopy[0] = 0; 3811 if (numFields) { 3812 PetscInt f; 3813 3814 for (f = 0; f < numFields; f++) { 3815 PetscInt fDof; 3816 ierr = PetscSectionGetFieldDof(localCoarse,p,f,&fDof);CHKERRQ(ierr); 3817 rowOffsets[f + 1] = offsetsCopy[f + 1] = fDof + rowOffsets[f]; 3818 } 3819 DMPlexGetIndicesPointFields_Internal(localCoarse,p,gOff < 0 ? -(gOff + 1) : gOff,offsetsCopy,PETSC_FALSE,0,parentIndices);CHKERRQ(ierr); 3820 } 3821 else { 3822 DMPlexGetIndicesPoint_Internal(localCoarse,p,gOff < 0 ? -(gOff + 1) : gOff,offsetsCopy,PETSC_FALSE,0,parentIndices);CHKERRQ(ierr); 3823 rowOffsets[1] = offsetsCopy[0]; 3824 } 3825 3826 ierr = PetscSectionGetDof(multiRootSec,p,&numLeaves);CHKERRQ(ierr); 3827 ierr = PetscSectionGetOffset(multiRootSec,p,&leafStart);CHKERRQ(ierr); 3828 leafEnd = leafStart + numLeaves; 3829 for (l = leafStart; l < leafEnd; l++) { 3830 PetscInt numIndices, childId, offset; 3831 const PetscInt *childIndices; 3832 3833 ierr = PetscSectionGetDof(rootIndicesSec,l,&numIndices);CHKERRQ(ierr); 3834 ierr = PetscSectionGetOffset(rootIndicesSec,l,&offset);CHKERRQ(ierr); 3835 childId = rootIndices[offset++]; 3836 childIndices = &rootIndices[offset]; 3837 numIndices--; 3838 3839 if (childId == -1) { /* equivalent points: scatter */ 3840 PetscInt i; 3841 3842 for (i = 0; i < numIndices; i++) { 3843 PetscInt colIndex = childIndices[i]; 3844 PetscInt rowIndex = parentIndices[i]; 3845 if (rowIndex < 0) continue; 3846 if (colIndex < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Unconstrained fine and constrained coarse"); 3847 if (colIndex >= colStart && colIndex < colEnd) { 3848 nnzD[rowIndex - rowStart] = 1; 3849 } 3850 else { 3851 nnzO[rowIndex - rowStart] = 1; 3852 } 3853 } 3854 } 3855 else { 3856 PetscInt parentId, f, lim; 3857 3858 ierr = DMPlexGetTreeParent(refTree,childId,&parentId,NULL);CHKERRQ(ierr); 3859 3860 lim = PetscMax(1,numFields); 3861 offsets[0] = 0; 3862 if (numFields) { 3863 PetscInt f; 3864 3865 for (f = 0; f < numFields; f++) { 3866 PetscInt fDof; 3867 ierr = PetscSectionGetFieldDof(cSecRef,childId,f,&fDof);CHKERRQ(ierr); 3868 3869 offsets[f + 1] = fDof + offsets[f]; 3870 } 3871 } 3872 else { 3873 PetscInt cDof; 3874 3875 ierr = PetscSectionGetDof(cSecRef,childId,&cDof);CHKERRQ(ierr); 3876 offsets[1] = cDof; 3877 } 3878 for (f = 0; f < lim; f++) { 3879 PetscInt parentStart = rowOffsets[f], parentEnd = rowOffsets[f + 1]; 3880 PetscInt childStart = offsets[f], childEnd = offsets[f + 1]; 3881 PetscInt i, numD = 0, numO = 0; 3882 3883 for (i = childStart; i < childEnd; i++) { 3884 PetscInt colIndex = childIndices[i]; 3885 3886 if (colIndex < 0) continue; 3887 if (colIndex >= colStart && colIndex < colEnd) { 3888 numD++; 3889 } 3890 else { 3891 numO++; 3892 } 3893 } 3894 for (i = parentStart; i < parentEnd; i++) { 3895 PetscInt rowIndex = parentIndices[i]; 3896 3897 if (rowIndex < 0) continue; 3898 nnzD[rowIndex - rowStart] += numD; 3899 nnzO[rowIndex - rowStart] += numO; 3900 } 3901 } 3902 } 3903 } 3904 } 3905 /* preallocate */ 3906 ierr = MatXAIJSetPreallocation(mat,1,nnzD,nnzO,NULL,NULL);CHKERRQ(ierr); 3907 ierr = PetscFree2(nnzD,nnzO);CHKERRQ(ierr); 3908 /* insert values */ 3909 ierr = DMPlexReferenceTreeGetChildrenMatrices_Injection(refTree,injRef,&childrenMats);CHKERRQ(ierr); 3910 for (p = pStartC; p < pEndC; p++) { 3911 PetscInt numLeaves, leafStart, leafEnd, l, dof, cdof, gOff; 3912 3913 ierr = PetscSectionGetDof(globalCoarse,p,&dof);CHKERRQ(ierr); 3914 ierr = PetscSectionGetConstraintDof(globalCoarse,p,&cdof);CHKERRQ(ierr); 3915 if ((dof - cdof) <= 0) continue; 3916 ierr = PetscSectionGetOffset(globalCoarse,p,&gOff);CHKERRQ(ierr); 3917 3918 rowOffsets[0] = 0; 3919 offsetsCopy[0] = 0; 3920 if (numFields) { 3921 PetscInt f; 3922 3923 for (f = 0; f < numFields; f++) { 3924 PetscInt fDof; 3925 ierr = PetscSectionGetFieldDof(localCoarse,p,f,&fDof);CHKERRQ(ierr); 3926 rowOffsets[f + 1] = offsetsCopy[f + 1] = fDof + rowOffsets[f]; 3927 } 3928 DMPlexGetIndicesPointFields_Internal(localCoarse,p,gOff < 0 ? -(gOff + 1) : gOff,offsetsCopy,PETSC_FALSE,0,parentIndices);CHKERRQ(ierr); 3929 } 3930 else { 3931 DMPlexGetIndicesPoint_Internal(localCoarse,p,gOff < 0 ? -(gOff + 1) : gOff,offsetsCopy,PETSC_FALSE,0,parentIndices);CHKERRQ(ierr); 3932 rowOffsets[1] = offsetsCopy[0]; 3933 } 3934 3935 ierr = PetscSectionGetDof(multiRootSec,p,&numLeaves);CHKERRQ(ierr); 3936 ierr = PetscSectionGetOffset(multiRootSec,p,&leafStart);CHKERRQ(ierr); 3937 leafEnd = leafStart + numLeaves; 3938 for (l = leafStart; l < leafEnd; l++) { 3939 PetscInt numIndices, childId, offset; 3940 const PetscInt *childIndices; 3941 3942 ierr = PetscSectionGetDof(rootIndicesSec,l,&numIndices);CHKERRQ(ierr); 3943 ierr = PetscSectionGetOffset(rootIndicesSec,l,&offset);CHKERRQ(ierr); 3944 childId = rootIndices[offset++]; 3945 childIndices = &rootIndices[offset]; 3946 numIndices--; 3947 3948 if (childId == -1) { /* equivalent points: scatter */ 3949 PetscInt i; 3950 3951 for (i = 0; i < numIndices; i++) { 3952 ierr = MatSetValue(mat,parentIndices[i],childIndices[i],1.,INSERT_VALUES);CHKERRQ(ierr); 3953 } 3954 } 3955 else { 3956 PetscInt parentId, f, lim; 3957 3958 ierr = DMPlexGetTreeParent(refTree,childId,&parentId,NULL);CHKERRQ(ierr); 3959 3960 lim = PetscMax(1,numFields); 3961 offsets[0] = 0; 3962 if (numFields) { 3963 PetscInt f; 3964 3965 for (f = 0; f < numFields; f++) { 3966 PetscInt fDof; 3967 ierr = PetscSectionGetFieldDof(cSecRef,childId,f,&fDof);CHKERRQ(ierr); 3968 3969 offsets[f + 1] = fDof + offsets[f]; 3970 } 3971 } 3972 else { 3973 PetscInt cDof; 3974 3975 ierr = PetscSectionGetDof(cSecRef,childId,&cDof);CHKERRQ(ierr); 3976 offsets[1] = cDof; 3977 } 3978 for (f = 0; f < lim; f++) { 3979 PetscScalar *childMat = &childrenMats[childId - pRefStart][f][0]; 3980 PetscInt *rowIndices = &parentIndices[rowOffsets[f]]; 3981 const PetscInt *colIndices = &childIndices[offsets[f]]; 3982 3983 ierr = MatSetValues(mat,rowOffsets[f+1]-rowOffsets[f],rowIndices,offsets[f+1]-offsets[f],colIndices,childMat,INSERT_VALUES);CHKERRQ(ierr); 3984 } 3985 } 3986 } 3987 } 3988 ierr = PetscSectionDestroy(&multiRootSec);CHKERRQ(ierr); 3989 ierr = PetscSectionDestroy(&rootIndicesSec);CHKERRQ(ierr); 3990 ierr = PetscFree(parentIndices);CHKERRQ(ierr); 3991 ierr = DMPlexReferenceTreeRestoreChildrenMatrices_Injection(refTree,injRef,&childrenMats);CHKERRQ(ierr); 3992 ierr = PetscFree(rootIndices);CHKERRQ(ierr); 3993 ierr = PetscFree3(offsets,offsetsCopy,rowOffsets);CHKERRQ(ierr); 3994 3995 ierr = MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3996 ierr = MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3997 PetscFunctionReturn(0); 3998 } 3999 4000 #undef __FUNCT__ 4001 #define __FUNCT__ "DMPlexTransferVecTree_Interpolate" 4002 static PetscErrorCode DMPlexTransferVecTree_Interpolate(DM coarse, Vec vecCoarseLocal, DM fine, Vec vecFine, PetscSF coarseToFine, PetscInt *cids, Vec grad, Vec cellGeom) 4003 { 4004 PetscDS ds; 4005 PetscSF coarseToFineEmbedded; 4006 PetscSection globalCoarse, globalFine; 4007 PetscSection localCoarse, localFine; 4008 PetscSection aSec, cSec; 4009 PetscSection rootValuesSec; 4010 PetscSection leafValuesSec; 4011 PetscScalar *rootValues, *leafValues; 4012 IS aIS; 4013 const PetscInt *anchors; 4014 Mat cMat; 4015 PetscInt numFields; 4016 PetscInt pStartC, pEndC, pStartF, pEndF, p, cellStart, cellEnd; 4017 PetscInt aStart, aEnd, cStart, cEnd; 4018 PetscInt *maxChildIds; 4019 PetscInt *offsets, *newOffsets, *offsetsCopy, *newOffsetsCopy, *rowOffsets, *numD, *numO; 4020 PetscFV fv = NULL; 4021 PetscInt dim, numFVcomps = -1, fvField = -1; 4022 DM cellDM = NULL, gradDM = NULL; 4023 const PetscScalar *cellGeomArray = NULL; 4024 const PetscScalar *gradArray = NULL; 4025 PetscErrorCode ierr; 4026 4027 PetscFunctionBegin; 4028 ierr = DMPlexGetChart(coarse,&pStartC,&pEndC);CHKERRQ(ierr); 4029 ierr = DMPlexGetHeightStratum(coarse,0,&cellStart,&cellEnd);CHKERRQ(ierr); 4030 ierr = DMPlexGetChart(fine,&pStartF,&pEndF);CHKERRQ(ierr); 4031 ierr = DMGetDefaultGlobalSection(fine,&globalFine);CHKERRQ(ierr); 4032 ierr = DMGetCoordinateDim(coarse,&dim);CHKERRQ(ierr); 4033 { /* winnow fine points that don't have global dofs out of the sf */ 4034 PetscInt nleaves, l; 4035 const PetscInt *leaves; 4036 PetscInt dof, cdof, numPointsWithDofs, offset, *pointsWithDofs; 4037 4038 ierr = PetscSFGetGraph(coarseToFine,NULL,&nleaves,&leaves,NULL);CHKERRQ(ierr); 4039 4040 for (l = 0, numPointsWithDofs = 0; l < nleaves; l++) { 4041 PetscInt p = leaves ? leaves[l] : l; 4042 4043 ierr = PetscSectionGetDof(globalFine,p,&dof);CHKERRQ(ierr); 4044 ierr = PetscSectionGetConstraintDof(globalFine,p,&cdof);CHKERRQ(ierr); 4045 if ((dof - cdof) > 0) { 4046 numPointsWithDofs++; 4047 } 4048 } 4049 ierr = PetscMalloc1(numPointsWithDofs,&pointsWithDofs);CHKERRQ(ierr); 4050 for (l = 0, offset = 0; l < nleaves; l++) { 4051 PetscInt p = leaves ? leaves[l] : l; 4052 4053 ierr = PetscSectionGetDof(globalFine,p,&dof);CHKERRQ(ierr); 4054 ierr = PetscSectionGetConstraintDof(globalFine,p,&cdof);CHKERRQ(ierr); 4055 if ((dof - cdof) > 0) { 4056 pointsWithDofs[offset++] = l; 4057 } 4058 } 4059 ierr = PetscSFCreateEmbeddedLeafSF(coarseToFine, numPointsWithDofs, pointsWithDofs, &coarseToFineEmbedded);CHKERRQ(ierr); 4060 ierr = PetscFree(pointsWithDofs);CHKERRQ(ierr); 4061 } 4062 /* communicate back to the coarse mesh which coarse points have children (that may require interpolation) */ 4063 ierr = PetscMalloc1(pEndC-pStartC,&maxChildIds);CHKERRQ(ierr); 4064 for (p = pStartC; p < pEndC; p++) { 4065 maxChildIds[p - pStartC] = -2; 4066 } 4067 ierr = PetscSFReduceBegin(coarseToFineEmbedded,MPIU_INT,cids,maxChildIds,MPIU_MAX);CHKERRQ(ierr); 4068 ierr = PetscSFReduceEnd(coarseToFineEmbedded,MPIU_INT,cids,maxChildIds,MPIU_MAX);CHKERRQ(ierr); 4069 4070 ierr = DMGetDefaultSection(coarse,&localCoarse);CHKERRQ(ierr); 4071 ierr = DMGetDefaultGlobalSection(coarse,&globalCoarse);CHKERRQ(ierr); 4072 4073 ierr = DMPlexGetAnchors(coarse,&aSec,&aIS);CHKERRQ(ierr); 4074 ierr = ISGetIndices(aIS,&anchors);CHKERRQ(ierr); 4075 ierr = PetscSectionGetChart(aSec,&aStart,&aEnd);CHKERRQ(ierr); 4076 4077 ierr = DMGetDefaultConstraints(coarse,&cSec,&cMat);CHKERRQ(ierr); 4078 ierr = PetscSectionGetChart(cSec,&cStart,&cEnd);CHKERRQ(ierr); 4079 4080 /* create sections that will send to children the indices and matrices they will need to construct the interpolator */ 4081 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)coarse),&rootValuesSec);CHKERRQ(ierr); 4082 ierr = PetscSectionSetChart(rootValuesSec,pStartC,pEndC);CHKERRQ(ierr); 4083 ierr = PetscSectionGetNumFields(globalCoarse,&numFields);CHKERRQ(ierr); 4084 { 4085 PetscInt maxFields = PetscMax(1,numFields) + 1; 4086 ierr = PetscMalloc7(maxFields,&offsets,maxFields,&offsetsCopy,maxFields,&newOffsets,maxFields,&newOffsetsCopy,maxFields,&rowOffsets,maxFields,&numD,maxFields,&numO);CHKERRQ(ierr); 4087 } 4088 if (grad) { 4089 PetscInt i; 4090 4091 ierr = VecGetDM(cellGeom,&cellDM);CHKERRQ(ierr); 4092 ierr = VecGetArrayRead(cellGeom,&cellGeomArray);CHKERRQ(ierr); 4093 ierr = VecGetDM(grad,&gradDM);CHKERRQ(ierr); 4094 ierr = VecGetArrayRead(grad,&gradArray);CHKERRQ(ierr); 4095 for (i = 0; i < PetscMax(1,numFields); i++) { 4096 PetscObject obj; 4097 PetscClassId id; 4098 4099 ierr = DMGetField(coarse, i, &obj);CHKERRQ(ierr); 4100 ierr = PetscObjectGetClassId(obj,&id);CHKERRQ(ierr); 4101 if (id == PETSCFV_CLASSID) { 4102 fv = (PetscFV) obj; 4103 ierr = PetscFVGetNumComponents(fv,&numFVcomps);CHKERRQ(ierr); 4104 fvField = i; 4105 break; 4106 } 4107 } 4108 } 4109 4110 for (p = pStartC; p < pEndC; p++) { /* count the sizes of the indices and matrices */ 4111 PetscInt dof; 4112 PetscInt maxChildId = maxChildIds[p - pStartC]; 4113 PetscInt numValues = 0; 4114 4115 ierr = PetscSectionGetDof(globalCoarse,p,&dof);CHKERRQ(ierr); 4116 if (dof < 0) { 4117 dof = -(dof + 1); 4118 } 4119 offsets[0] = 0; 4120 newOffsets[0] = 0; 4121 if (maxChildId >= 0) { /* this point has children (with dofs) that will need to be interpolated from the closure of p */ 4122 PetscInt *closure = NULL, closureSize, cl; 4123 4124 ierr = DMPlexGetTransitiveClosure(coarse,p,PETSC_TRUE,&closureSize,&closure);CHKERRQ(ierr); 4125 for (cl = 0; cl < closureSize; cl++) { /* get the closure */ 4126 PetscInt c = closure[2 * cl], clDof; 4127 4128 ierr = PetscSectionGetDof(localCoarse,c,&clDof);CHKERRQ(ierr); 4129 numValues += clDof; 4130 } 4131 ierr = DMPlexRestoreTransitiveClosure(coarse,p,PETSC_TRUE,&closureSize,&closure);CHKERRQ(ierr); 4132 } 4133 else if (maxChildId == -1) { 4134 ierr = PetscSectionGetDof(localCoarse,p,&numValues);CHKERRQ(ierr); 4135 } 4136 /* we will pack the column indices with the field offsets */ 4137 if (maxChildId >= -1 && grad && p >= cellStart && p < cellEnd) { 4138 /* also send the centroid, and the gradient */ 4139 numValues += dim * (1 + numFVcomps); 4140 } 4141 ierr = PetscSectionSetDof(rootValuesSec,p,numValues);CHKERRQ(ierr); 4142 } 4143 ierr = PetscSectionSetUp(rootValuesSec);CHKERRQ(ierr); 4144 { 4145 PetscInt numRootValues; 4146 const PetscScalar *coarseArray; 4147 4148 ierr = PetscSectionGetStorageSize(rootValuesSec,&numRootValues);CHKERRQ(ierr); 4149 ierr = PetscMalloc1(numRootValues,&rootValues);CHKERRQ(ierr); 4150 ierr = VecGetArrayRead(vecCoarseLocal,&coarseArray);CHKERRQ(ierr); 4151 for (p = pStartC; p < pEndC; p++) { 4152 PetscInt numValues; 4153 PetscInt pValOff; 4154 PetscScalar *pVal; 4155 PetscInt maxChildId = maxChildIds[p - pStartC]; 4156 4157 ierr = PetscSectionGetDof(rootValuesSec,p,&numValues);CHKERRQ(ierr); 4158 if (!numValues) { 4159 continue; 4160 } 4161 ierr = PetscSectionGetOffset(rootValuesSec,p,&pValOff);CHKERRQ(ierr); 4162 pVal = &(rootValues[pValOff]); 4163 if (maxChildId >= 0) { /* build an identity matrix, apply matrix constraints on the right */ 4164 PetscInt closureSize = numValues; 4165 ierr = DMPlexVecGetClosure(coarse,NULL,vecCoarseLocal,p,&closureSize,&pVal);CHKERRQ(ierr); 4166 } 4167 else if (maxChildId == -1) { 4168 PetscInt lDof, lOff, i; 4169 4170 ierr = PetscSectionGetDof(localCoarse,p,&lDof);CHKERRQ(ierr); 4171 ierr = PetscSectionGetOffset(localCoarse,p,&lOff);CHKERRQ(ierr); 4172 for (i = 0; i < lDof; i++) pVal[i] = coarseArray[lOff + i]; 4173 } 4174 if (grad && p >= cellStart && p < cellEnd) { 4175 const PetscFVCellGeom *cg; 4176 PetscScalar *gradVals; 4177 PetscInt i; 4178 4179 pVal += (numValues - dim * (1 + numFVcomps)); 4180 4181 ierr = DMPlexPointLocalRead(cellDM,p,cellGeomArray,&cg);CHKERRQ(ierr); 4182 for (i = 0; i < dim; i++) pVal[i] = cg->centroid[i]; 4183 pVal += dim; 4184 ierr = DMPlexPointGlobalRead(gradDM,p,gradArray,&gradVals);CHKERRQ(ierr); 4185 for (i = 0; i < dim * numFVcomps; i++) pVal[i] = gradVals[i]; 4186 } 4187 } 4188 ierr = VecRestoreArrayRead(vecCoarseLocal,&coarseArray);CHKERRQ(ierr); 4189 ierr = PetscFree(maxChildIds);CHKERRQ(ierr); 4190 } 4191 { 4192 PetscSF valuesSF; 4193 PetscInt *remoteOffsetsValues, numLeafValues; 4194 4195 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)fine),&leafValuesSec);CHKERRQ(ierr); 4196 ierr = PetscSFDistributeSection(coarseToFineEmbedded,rootValuesSec,&remoteOffsetsValues,leafValuesSec);CHKERRQ(ierr); 4197 ierr = PetscSFCreateSectionSF(coarseToFineEmbedded,rootValuesSec,remoteOffsetsValues,leafValuesSec,&valuesSF);CHKERRQ(ierr); 4198 ierr = PetscSFDestroy(&coarseToFineEmbedded);CHKERRQ(ierr); 4199 ierr = PetscFree(remoteOffsetsValues);CHKERRQ(ierr); 4200 ierr = PetscSectionGetStorageSize(leafValuesSec,&numLeafValues);CHKERRQ(ierr); 4201 ierr = PetscMalloc1(numLeafValues,&leafValues);CHKERRQ(ierr); 4202 ierr = PetscSFBcastBegin(valuesSF,MPIU_SCALAR,rootValues,leafValues);CHKERRQ(ierr); 4203 ierr = PetscSFBcastEnd(valuesSF,MPIU_SCALAR,rootValues,leafValues);CHKERRQ(ierr); 4204 ierr = PetscSFDestroy(&valuesSF);CHKERRQ(ierr); 4205 ierr = PetscFree(rootValues);CHKERRQ(ierr); 4206 ierr = PetscSectionDestroy(&rootValuesSec);CHKERRQ(ierr); 4207 } 4208 ierr = DMGetDefaultSection(fine,&localFine);CHKERRQ(ierr); 4209 { 4210 PetscInt maxDof; 4211 PetscInt *rowIndices; 4212 DM refTree; 4213 PetscInt **refPointFieldN; 4214 PetscScalar ***refPointFieldMats; 4215 PetscSection refConSec, refAnSec; 4216 PetscInt pRefStart,pRefEnd,leafStart,leafEnd; 4217 PetscScalar *pointWork; 4218 4219 ierr = PetscSectionGetMaxDof(globalFine,&maxDof);CHKERRQ(ierr); 4220 ierr = DMGetWorkArray(fine,maxDof,PETSC_INT,&rowIndices);CHKERRQ(ierr); 4221 ierr = DMGetWorkArray(fine,maxDof,PETSC_SCALAR,&pointWork);CHKERRQ(ierr); 4222 ierr = DMPlexGetReferenceTree(fine,&refTree);CHKERRQ(ierr); 4223 ierr = DMGetDS(fine,&ds);CHKERRQ(ierr); 4224 ierr = DMSetDS(refTree,ds);CHKERRQ(ierr); 4225 ierr = DMPlexReferenceTreeGetChildrenMatrices(refTree,&refPointFieldMats,&refPointFieldN);CHKERRQ(ierr); 4226 ierr = DMGetDefaultConstraints(refTree,&refConSec,NULL);CHKERRQ(ierr); 4227 ierr = DMPlexGetAnchors(refTree,&refAnSec,NULL);CHKERRQ(ierr); 4228 ierr = PetscSectionGetChart(refConSec,&pRefStart,&pRefEnd);CHKERRQ(ierr); 4229 ierr = PetscSectionGetChart(leafValuesSec,&leafStart,&leafEnd);CHKERRQ(ierr); 4230 ierr = DMPlexGetHeightStratum(fine,0,&cellStart,&cellEnd);CHKERRQ(ierr); 4231 for (p = leafStart; p < leafEnd; p++) { 4232 PetscInt gDof, gcDof, gOff, lDof; 4233 PetscInt numValues, pValOff; 4234 PetscInt childId; 4235 const PetscScalar *pVal; 4236 const PetscScalar *fvGradData = NULL; 4237 4238 ierr = PetscSectionGetDof(globalFine,p,&gDof);CHKERRQ(ierr); 4239 ierr = PetscSectionGetDof(localFine,p,&lDof);CHKERRQ(ierr); 4240 ierr = PetscSectionGetConstraintDof(globalFine,p,&gcDof);CHKERRQ(ierr); 4241 if ((gDof - gcDof) <= 0) { 4242 continue; 4243 } 4244 ierr = PetscSectionGetOffset(globalFine,p,&gOff);CHKERRQ(ierr); 4245 ierr = PetscSectionGetDof(leafValuesSec,p,&numValues);CHKERRQ(ierr); 4246 if (!numValues) continue; 4247 ierr = PetscSectionGetOffset(leafValuesSec,p,&pValOff);CHKERRQ(ierr); 4248 pVal = &leafValues[pValOff]; 4249 offsets[0] = 0; 4250 offsetsCopy[0] = 0; 4251 newOffsets[0] = 0; 4252 newOffsetsCopy[0] = 0; 4253 childId = cids[p - pStartF]; 4254 if (grad && p >= cellStart && p < cellEnd) { 4255 numValues -= (dim * (1 + numFVcomps)); 4256 fvGradData = &pVal[numValues]; 4257 } 4258 if (numFields) { 4259 PetscInt f; 4260 for (f = 0; f < numFields; f++) { 4261 PetscInt rowDof; 4262 4263 ierr = PetscSectionGetFieldDof(localFine,p,f,&rowDof);CHKERRQ(ierr); 4264 offsets[f + 1] = offsets[f] + rowDof; 4265 offsetsCopy[f + 1] = offsets[f + 1]; 4266 /* TODO: closure indices */ 4267 newOffsets[f + 1] = newOffsets[f] + ((childId == -1) ? rowDof : refPointFieldN[childId - pRefStart][f]); 4268 } 4269 ierr = DMPlexGetIndicesPointFields_Internal(localFine,p,gOff,offsetsCopy,PETSC_FALSE,0,rowIndices);CHKERRQ(ierr); 4270 } 4271 else { 4272 offsets[0] = 0; 4273 offsets[1] = lDof; 4274 newOffsets[0] = 0; 4275 newOffsets[1] = (childId == -1) ? lDof : refPointFieldN[childId - pRefStart][0]; 4276 ierr = DMPlexGetIndicesPoint_Internal(localFine,p,gOff,offsetsCopy,PETSC_FALSE,0,rowIndices);CHKERRQ(ierr); 4277 } 4278 if (childId == -1) { /* no child interpolation: one nnz per */ 4279 ierr = VecSetValues(vecFine,numValues,rowIndices,pVal,ADD_VALUES);CHKERRQ(ierr); 4280 } else { 4281 PetscInt f; 4282 4283 for (f = 0; f < PetscMax(1,numFields); f++) { 4284 const PetscScalar *childMat = refPointFieldMats[childId - pRefStart][f]; 4285 PetscInt numRows = offsets[f+1] - offsets[f]; 4286 PetscInt numCols = newOffsets[f + 1] - newOffsets[f]; 4287 const PetscScalar *cVal = &pVal[newOffsets[f]]; 4288 PetscScalar *rVal = &pointWork[offsets[f]]; 4289 PetscInt i, j; 4290 4291 for (i = 0; i < numRows; i++) { 4292 PetscScalar val = 0.; 4293 for (j = 0; j < numCols; j++) { 4294 val += childMat[i * numCols + j] * cVal[j]; 4295 } 4296 rVal[i] = val; 4297 } 4298 if (f == fvField && p >= cellStart && p < cellEnd) { 4299 PetscReal centroid[3]; 4300 PetscScalar diff[3]; 4301 const PetscScalar *parentCentroid = &fvGradData[0]; 4302 const PetscScalar *gradient = &fvGradData[dim]; 4303 4304 ierr = DMPlexComputeCellGeometryFVM(fine,p,NULL,centroid,NULL);CHKERRQ(ierr); 4305 for (i = 0; i < dim; i++) { 4306 diff[i] = centroid[i] - parentCentroid[i]; 4307 } 4308 for (i = 0; i < numFVcomps; i++) { 4309 PetscScalar val = 0.; 4310 4311 for (j = 0; j < 3; j++) { 4312 val += gradient[dim * i + j] * diff[j]; 4313 } 4314 rVal[i] += val; 4315 } 4316 } 4317 ierr = VecSetValues(vecFine,numRows,&rowIndices[offsets[f]],rVal,ADD_VALUES);CHKERRQ(ierr); 4318 } 4319 } 4320 } 4321 ierr = DMPlexReferenceTreeRestoreChildrenMatrices(refTree,&refPointFieldMats,&refPointFieldN);CHKERRQ(ierr); 4322 ierr = DMRestoreWorkArray(fine,maxDof,PETSC_INT,&rowIndices);CHKERRQ(ierr); 4323 ierr = DMRestoreWorkArray(fine,maxDof,PETSC_SCALAR,&pointWork);CHKERRQ(ierr); 4324 } 4325 ierr = PetscFree(leafValues);CHKERRQ(ierr); 4326 ierr = PetscSectionDestroy(&leafValuesSec);CHKERRQ(ierr); 4327 ierr = PetscFree7(offsets,offsetsCopy,newOffsets,newOffsetsCopy,rowOffsets,numD,numO);CHKERRQ(ierr); 4328 ierr = ISRestoreIndices(aIS,&anchors);CHKERRQ(ierr); 4329 PetscFunctionReturn(0); 4330 } 4331 4332 #undef __FUNCT__ 4333 #define __FUNCT__ "DMPlexTransferVecTree_Inject" 4334 static PetscErrorCode DMPlexTransferVecTree_Inject(DM fine, Vec vecFine, DM coarse, Vec vecCoarse, PetscSF coarseToFine, PetscInt *cids) 4335 { 4336 PetscDS ds; 4337 DM refTree; 4338 PetscSection multiRootSec, rootIndicesSec; 4339 PetscSection globalCoarse, globalFine; 4340 PetscSection localCoarse, localFine; 4341 PetscSection cSecRef; 4342 PetscInt *parentIndices, pRefStart, pRefEnd; 4343 PetscScalar *rootValues, *parentValues; 4344 Mat injRef; 4345 PetscInt numFields, maxDof; 4346 PetscInt pStartC, pEndC, pStartF, pEndF, p; 4347 PetscInt *offsets, *offsetsCopy, *rowOffsets; 4348 PetscLayout rowMap, colMap; 4349 PetscInt rowStart, rowEnd, colStart, colEnd; 4350 PetscScalar ***childrenMats=NULL ; /* gcc -O gives 'may be used uninitialized' warning'. Initializing to suppress this warning */ 4351 PetscErrorCode ierr; 4352 4353 PetscFunctionBegin; 4354 4355 /* get the templates for the fine-to-coarse injection from the reference tree */ 4356 ierr = DMPlexGetReferenceTree(coarse,&refTree);CHKERRQ(ierr); 4357 ierr = DMGetDS(coarse,&ds);CHKERRQ(ierr); 4358 ierr = DMSetDS(refTree,ds);CHKERRQ(ierr); 4359 ierr = DMGetDefaultConstraints(refTree,&cSecRef,NULL);CHKERRQ(ierr); 4360 ierr = PetscSectionGetChart(cSecRef,&pRefStart,&pRefEnd);CHKERRQ(ierr); 4361 ierr = DMPlexReferenceTreeGetInjector(refTree,&injRef);CHKERRQ(ierr); 4362 4363 ierr = DMPlexGetChart(fine,&pStartF,&pEndF);CHKERRQ(ierr); 4364 ierr = DMGetDefaultSection(fine,&localFine);CHKERRQ(ierr); 4365 ierr = DMGetDefaultGlobalSection(fine,&globalFine);CHKERRQ(ierr); 4366 ierr = PetscSectionGetNumFields(localFine,&numFields);CHKERRQ(ierr); 4367 ierr = DMPlexGetChart(coarse,&pStartC,&pEndC);CHKERRQ(ierr); 4368 ierr = DMGetDefaultSection(coarse,&localCoarse);CHKERRQ(ierr); 4369 ierr = DMGetDefaultGlobalSection(coarse,&globalCoarse);CHKERRQ(ierr); 4370 ierr = PetscSectionGetMaxDof(localCoarse,&maxDof);CHKERRQ(ierr); 4371 { 4372 PetscInt maxFields = PetscMax(1,numFields) + 1; 4373 ierr = PetscMalloc3(maxFields,&offsets,maxFields,&offsetsCopy,maxFields,&rowOffsets);CHKERRQ(ierr); 4374 } 4375 4376 ierr = DMPlexTransferInjectorTree(coarse,fine,coarseToFine,cids,vecFine,numFields,offsets,&multiRootSec,&rootIndicesSec,NULL,&rootValues);CHKERRQ(ierr); 4377 4378 ierr = PetscMalloc2(maxDof,&parentIndices,maxDof,&parentValues);CHKERRQ(ierr); 4379 4380 /* count indices */ 4381 ierr = VecGetLayout(vecFine,&colMap);CHKERRQ(ierr); 4382 ierr = VecGetLayout(vecCoarse,&rowMap);CHKERRQ(ierr); 4383 ierr = PetscLayoutSetUp(rowMap);CHKERRQ(ierr); 4384 ierr = PetscLayoutSetUp(colMap);CHKERRQ(ierr); 4385 ierr = PetscLayoutGetRange(rowMap,&rowStart,&rowEnd);CHKERRQ(ierr); 4386 ierr = PetscLayoutGetRange(colMap,&colStart,&colEnd);CHKERRQ(ierr); 4387 /* insert values */ 4388 ierr = DMPlexReferenceTreeGetChildrenMatrices_Injection(refTree,injRef,&childrenMats);CHKERRQ(ierr); 4389 for (p = pStartC; p < pEndC; p++) { 4390 PetscInt numLeaves, leafStart, leafEnd, l, dof, cdof, gOff; 4391 4392 ierr = PetscSectionGetDof(globalCoarse,p,&dof);CHKERRQ(ierr); 4393 ierr = PetscSectionGetConstraintDof(globalCoarse,p,&cdof);CHKERRQ(ierr); 4394 if ((dof - cdof) <= 0) continue; 4395 ierr = PetscSectionGetOffset(globalCoarse,p,&gOff);CHKERRQ(ierr); 4396 4397 rowOffsets[0] = 0; 4398 offsetsCopy[0] = 0; 4399 if (numFields) { 4400 PetscInt f; 4401 4402 for (f = 0; f < numFields; f++) { 4403 PetscInt fDof; 4404 ierr = PetscSectionGetFieldDof(localCoarse,p,f,&fDof);CHKERRQ(ierr); 4405 rowOffsets[f + 1] = offsetsCopy[f + 1] = fDof + rowOffsets[f]; 4406 } 4407 DMPlexGetIndicesPointFields_Internal(localCoarse,p,gOff < 0 ? -(gOff + 1) : gOff,offsetsCopy,PETSC_FALSE,0,parentIndices);CHKERRQ(ierr); 4408 } 4409 else { 4410 DMPlexGetIndicesPoint_Internal(localCoarse,p,gOff < 0 ? -(gOff + 1) : gOff,offsetsCopy,PETSC_FALSE,0,parentIndices);CHKERRQ(ierr); 4411 rowOffsets[1] = offsetsCopy[0]; 4412 } 4413 4414 ierr = PetscSectionGetDof(multiRootSec,p,&numLeaves);CHKERRQ(ierr); 4415 ierr = PetscSectionGetOffset(multiRootSec,p,&leafStart);CHKERRQ(ierr); 4416 leafEnd = leafStart + numLeaves; 4417 for (l = leafStart; l < leafEnd; l++) { 4418 PetscInt numIndices, childId, offset; 4419 const PetscScalar *childValues; 4420 4421 ierr = PetscSectionGetDof(rootIndicesSec,l,&numIndices);CHKERRQ(ierr); 4422 ierr = PetscSectionGetOffset(rootIndicesSec,l,&offset);CHKERRQ(ierr); 4423 childId = (PetscInt) PetscRealPart(rootValues[offset++]); 4424 childValues = &rootValues[offset]; 4425 numIndices--; 4426 4427 if (childId == -2) { /* skip */ 4428 continue; 4429 } else if (childId == -1) { /* equivalent points: scatter */ 4430 ierr = VecSetValues(vecCoarse,numIndices,parentIndices,childValues,ADD_VALUES);CHKERRQ(ierr); 4431 } else { 4432 PetscInt parentId, f, lim; 4433 4434 ierr = DMPlexGetTreeParent(refTree,childId,&parentId,NULL);CHKERRQ(ierr); 4435 4436 lim = PetscMax(1,numFields); 4437 offsets[0] = 0; 4438 if (numFields) { 4439 PetscInt f; 4440 4441 for (f = 0; f < numFields; f++) { 4442 PetscInt fDof; 4443 ierr = PetscSectionGetFieldDof(cSecRef,childId,f,&fDof);CHKERRQ(ierr); 4444 4445 offsets[f + 1] = fDof + offsets[f]; 4446 } 4447 } 4448 else { 4449 PetscInt cDof; 4450 4451 ierr = PetscSectionGetDof(cSecRef,childId,&cDof);CHKERRQ(ierr); 4452 offsets[1] = cDof; 4453 } 4454 for (f = 0; f < lim; f++) { 4455 PetscScalar *childMat = &childrenMats[childId - pRefStart][f][0]; 4456 PetscInt *rowIndices = &parentIndices[rowOffsets[f]]; 4457 PetscInt m = rowOffsets[f+1]-rowOffsets[f]; 4458 PetscInt n = offsets[f+1]-offsets[f]; 4459 PetscInt i, j; 4460 const PetscScalar *colValues = &childValues[offsets[f]]; 4461 4462 for (i = 0; i < m; i++) { 4463 PetscScalar val = 0.; 4464 for (j = 0; j < n; j++) { 4465 val += childMat[n * i + j] * colValues[j]; 4466 } 4467 parentValues[i] = val; 4468 } 4469 ierr = VecSetValues(vecCoarse,m,rowIndices,parentValues,ADD_VALUES);CHKERRQ(ierr); 4470 } 4471 } 4472 } 4473 } 4474 ierr = PetscSectionDestroy(&multiRootSec);CHKERRQ(ierr); 4475 ierr = PetscSectionDestroy(&rootIndicesSec);CHKERRQ(ierr); 4476 ierr = PetscFree2(parentIndices,parentValues);CHKERRQ(ierr); 4477 ierr = DMPlexReferenceTreeRestoreChildrenMatrices_Injection(refTree,injRef,&childrenMats);CHKERRQ(ierr); 4478 ierr = PetscFree(rootValues);CHKERRQ(ierr); 4479 ierr = PetscFree3(offsets,offsetsCopy,rowOffsets);CHKERRQ(ierr); 4480 PetscFunctionReturn(0); 4481 } 4482 4483 #undef __FUNCT__ 4484 #define __FUNCT__ "DMPlexTransferVecTree" 4485 PetscErrorCode DMPlexTransferVecTree(DM dmIn, Vec vecIn, DM dmOut, Vec vecOut, PetscSF sfIn, PetscSF sfOut, PetscInt *cidsIn, PetscInt *cidsOut, PetscBool useBCs, PetscReal time) 4486 { 4487 PetscErrorCode ierr; 4488 4489 PetscFunctionBegin; 4490 if (sfIn) { 4491 Vec vecInLocal; 4492 DM dmGrad = NULL; 4493 Vec faceGeom = NULL, cellGeom = NULL, grad = NULL; 4494 4495 ierr = DMGetLocalVector(dmIn,&vecInLocal);CHKERRQ(ierr); 4496 ierr = VecSet(vecInLocal,0.0);CHKERRQ(ierr); 4497 { 4498 PetscInt numFields, i; 4499 4500 ierr = DMGetNumFields(dmIn, &numFields);CHKERRQ(ierr); 4501 for (i = 0; i < numFields; i++) { 4502 PetscObject obj; 4503 PetscClassId classid; 4504 4505 ierr = DMGetField(dmIn, i, &obj);CHKERRQ(ierr); 4506 ierr = PetscObjectGetClassId(obj, &classid);CHKERRQ(ierr); 4507 if (classid == PETSCFV_CLASSID) { 4508 ierr = DMPlexGetDataFVM(dmIn,(PetscFV)obj,&cellGeom,&faceGeom,&dmGrad);CHKERRQ(ierr); 4509 break; 4510 } 4511 } 4512 } 4513 if (useBCs) { 4514 ierr = DMPlexInsertBoundaryValues(dmIn,PETSC_TRUE,vecInLocal,time,faceGeom,cellGeom,NULL);CHKERRQ(ierr); 4515 } 4516 ierr = DMGlobalToLocalBegin(dmIn,vecIn,INSERT_VALUES,vecInLocal);CHKERRQ(ierr); 4517 ierr = DMGlobalToLocalEnd(dmIn,vecIn,INSERT_VALUES,vecInLocal);CHKERRQ(ierr); 4518 if (dmGrad) { 4519 ierr = DMGetGlobalVector(dmGrad,&grad);CHKERRQ(ierr); 4520 ierr = DMPlexReconstructGradientsFVM(dmIn,vecInLocal,grad);CHKERRQ(ierr); 4521 } 4522 ierr = DMPlexTransferVecTree_Interpolate(dmIn,vecInLocal,dmOut,vecOut,sfIn,cidsIn,grad,cellGeom);CHKERRQ(ierr); 4523 ierr = DMRestoreLocalVector(dmIn,&vecInLocal);CHKERRQ(ierr); 4524 if (dmGrad) { 4525 ierr = DMRestoreGlobalVector(dmGrad,&grad);CHKERRQ(ierr); 4526 } 4527 } 4528 if (sfOut) { 4529 ierr = DMPlexTransferVecTree_Inject(dmIn,vecIn,dmOut,vecOut,sfOut,cidsOut);CHKERRQ(ierr); 4530 } 4531 PetscFunctionReturn(0); 4532 } 4533