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 for (r = 0; r < cDof; r++) { 1571 rows[r] = cOff + r; 1572 } 1573 numCols = 0; 1574 for (i = 0; i < closureSize; i++) { 1575 PetscInt q = closure[2*i]; 1576 PetscInt o = closure[2*i+1]; 1577 PetscInt aDof, aOff, j; 1578 1579 if (numFields > 1) { 1580 ierr = PetscSectionGetFieldDof(refSection,q,f,&aDof);CHKERRQ(ierr); 1581 ierr = PetscSectionGetFieldOffset(refSection,q,f,&aOff);CHKERRQ(ierr); 1582 } 1583 else { 1584 ierr = PetscSectionGetDof(refSection,q,&aDof);CHKERRQ(ierr); 1585 ierr = PetscSectionGetOffset(refSection,q,&aOff);CHKERRQ(ierr); 1586 } 1587 1588 for (j = 0; j < aDof; j++) { 1589 PetscInt node = (o >= 0) ? (j / fComp) : ((aDof - 1 - j) / fComp); 1590 PetscInt comp = (j % fComp); 1591 1592 cols[numCols++] = aOff + node * fComp + comp; 1593 } 1594 } 1595 refPointFieldN[p-pRefStart][f] = numCols; 1596 ierr = PetscMalloc1(cDof*numCols,&refPointFieldMats[p-pRefStart][f]);CHKERRQ(ierr); 1597 ierr = MatGetValues(refCmat,cDof,rows,numCols,cols,refPointFieldMats[p-pRefStart][f]);CHKERRQ(ierr); 1598 } 1599 ierr = DMPlexRestoreTransitiveClosure(refTree,parent,PETSC_TRUE,&closureSize,&closure);CHKERRQ(ierr); 1600 } 1601 *childrenMats = refPointFieldMats; 1602 *childrenN = refPointFieldN; 1603 ierr = ISRestoreIndices(refAnIS,&refAnchors);CHKERRQ(ierr); 1604 ierr = PetscFree(rows);CHKERRQ(ierr); 1605 ierr = PetscFree(cols);CHKERRQ(ierr); 1606 PetscFunctionReturn(0); 1607 } 1608 1609 #undef __FUNCT__ 1610 #define __FUNCT__ "DMPlexReferenceTreeRestoreChildrenMatrices" 1611 static PetscErrorCode DMPlexReferenceTreeRestoreChildrenMatrices(DM refTree, PetscScalar ****childrenMats, PetscInt ***childrenN) 1612 { 1613 PetscDS ds; 1614 PetscInt **refPointFieldN; 1615 PetscScalar ***refPointFieldMats; 1616 PetscInt numFields, pRefStart, pRefEnd, p, f; 1617 PetscSection refConSec; 1618 PetscErrorCode ierr; 1619 1620 PetscFunctionBegin; 1621 refPointFieldN = *childrenN; 1622 *childrenN = NULL; 1623 refPointFieldMats = *childrenMats; 1624 *childrenMats = NULL; 1625 ierr = DMGetDS(refTree,&ds);CHKERRQ(ierr); 1626 ierr = PetscDSGetNumFields(ds,&numFields);CHKERRQ(ierr); 1627 ierr = DMGetDefaultConstraints(refTree,&refConSec,NULL);CHKERRQ(ierr); 1628 ierr = PetscSectionGetChart(refConSec,&pRefStart,&pRefEnd);CHKERRQ(ierr); 1629 for (p = pRefStart; p < pRefEnd; p++) { 1630 PetscInt parent, pDof; 1631 1632 ierr = DMPlexGetTreeParent(refTree,p,&parent,NULL);CHKERRQ(ierr); 1633 ierr = PetscSectionGetDof(refConSec,p,&pDof);CHKERRQ(ierr); 1634 if (!pDof || parent == p) continue; 1635 1636 for (f = 0; f < numFields; f++) { 1637 PetscInt cDof; 1638 1639 if (numFields > 1) { 1640 ierr = PetscSectionGetFieldDof(refConSec,p,f,&cDof);CHKERRQ(ierr); 1641 } 1642 else { 1643 ierr = PetscSectionGetDof(refConSec,p,&cDof);CHKERRQ(ierr); 1644 } 1645 1646 ierr = PetscFree(refPointFieldMats[p - pRefStart][f]);CHKERRQ(ierr); 1647 } 1648 ierr = PetscFree(refPointFieldMats[p - pRefStart]);CHKERRQ(ierr); 1649 ierr = PetscFree(refPointFieldN[p - pRefStart]);CHKERRQ(ierr); 1650 } 1651 ierr = PetscFree(refPointFieldMats);CHKERRQ(ierr); 1652 ierr = PetscFree(refPointFieldN);CHKERRQ(ierr); 1653 PetscFunctionReturn(0); 1654 } 1655 1656 #undef __FUNCT__ 1657 #define __FUNCT__ "DMPlexComputeAnchorMatrix_Tree_FromReference" 1658 static PetscErrorCode DMPlexComputeAnchorMatrix_Tree_FromReference(DM dm, PetscSection section, PetscSection conSec, Mat cMat) 1659 { 1660 DM refTree; 1661 PetscDS ds; 1662 Mat refCmat; 1663 PetscInt numFields, f, pRefStart, pRefEnd, p, maxDof, maxAnDof, *perm, *iperm, pStart, pEnd, conStart, conEnd, **refPointFieldN; 1664 PetscScalar ***refPointFieldMats, *pointWork; 1665 PetscSection refConSec, refAnSec, anSec; 1666 IS refAnIS, anIS; 1667 const PetscInt *anchors; 1668 PetscErrorCode ierr; 1669 1670 PetscFunctionBegin; 1671 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1672 ierr = DMGetDS(dm,&ds);CHKERRQ(ierr); 1673 ierr = PetscDSGetNumFields(ds,&numFields);CHKERRQ(ierr); 1674 ierr = DMPlexGetReferenceTree(dm,&refTree);CHKERRQ(ierr); 1675 ierr = DMSetDS(refTree,ds);CHKERRQ(ierr); 1676 ierr = DMGetDefaultConstraints(refTree,&refConSec,&refCmat);CHKERRQ(ierr); 1677 ierr = DMPlexGetAnchors(refTree,&refAnSec,&refAnIS);CHKERRQ(ierr); 1678 ierr = DMPlexGetAnchors(dm,&anSec,&anIS);CHKERRQ(ierr); 1679 ierr = ISGetIndices(anIS,&anchors);CHKERRQ(ierr); 1680 ierr = PetscSectionGetChart(refConSec,&pRefStart,&pRefEnd);CHKERRQ(ierr); 1681 ierr = PetscSectionGetChart(conSec,&conStart,&conEnd);CHKERRQ(ierr); 1682 ierr = PetscSectionGetMaxDof(refConSec,&maxDof);CHKERRQ(ierr); 1683 ierr = PetscSectionGetMaxDof(refAnSec,&maxAnDof);CHKERRQ(ierr); 1684 ierr = PetscMalloc1(maxDof*maxDof*maxAnDof,&pointWork);CHKERRQ(ierr); 1685 1686 /* step 1: get submats for every constrained point in the reference tree */ 1687 ierr = DMPlexReferenceTreeGetChildrenMatrices(refTree,&refPointFieldMats,&refPointFieldN);CHKERRQ(ierr); 1688 1689 /* step 2: compute the preorder */ 1690 ierr = DMPlexGetChart(dm,&pStart,&pEnd);CHKERRQ(ierr); 1691 ierr = PetscMalloc2(pEnd-pStart,&perm,pEnd-pStart,&iperm);CHKERRQ(ierr); 1692 for (p = pStart; p < pEnd; p++) { 1693 perm[p - pStart] = p; 1694 iperm[p - pStart] = p-pStart; 1695 } 1696 for (p = 0; p < pEnd - pStart;) { 1697 PetscInt point = perm[p]; 1698 PetscInt parent; 1699 1700 ierr = DMPlexGetTreeParent(dm,point,&parent,NULL);CHKERRQ(ierr); 1701 if (parent == point) { 1702 p++; 1703 } 1704 else { 1705 PetscInt size, closureSize, *closure = NULL, i; 1706 1707 ierr = DMPlexGetTransitiveClosure(dm,parent,PETSC_TRUE,&closureSize,&closure);CHKERRQ(ierr); 1708 for (i = 0; i < closureSize; i++) { 1709 PetscInt q = closure[2*i]; 1710 if (iperm[q-pStart] > iperm[point-pStart]) { 1711 /* swap */ 1712 perm[p] = q; 1713 perm[iperm[q-pStart]] = point; 1714 iperm[point-pStart] = iperm[q-pStart]; 1715 iperm[q-pStart] = p; 1716 break; 1717 } 1718 } 1719 size = closureSize; 1720 ierr = DMPlexRestoreTransitiveClosure(dm,parent,PETSC_TRUE,&closureSize,&closure);CHKERRQ(ierr); 1721 if (i == size) { 1722 p++; 1723 } 1724 } 1725 } 1726 1727 /* step 3: fill the constraint matrix */ 1728 /* we are going to use a preorder progressive fill strategy. Mat doesn't 1729 * allow progressive fill without assembly, so we are going to set up the 1730 * values outside of the Mat first. 1731 */ 1732 { 1733 PetscInt nRows, row, nnz; 1734 PetscBool done; 1735 const PetscInt *ia, *ja; 1736 PetscScalar *vals; 1737 1738 ierr = MatGetRowIJ(cMat,0,PETSC_FALSE,PETSC_FALSE,&nRows,&ia,&ja,&done);CHKERRQ(ierr); 1739 if (!done) SETERRQ(PetscObjectComm((PetscObject)cMat),PETSC_ERR_PLIB,"Could not get RowIJ of constraint matrix"); 1740 nnz = ia[nRows]; 1741 /* malloc and then zero rows right before we fill them: this way valgrind 1742 * can tell if we are doing progressive fill in the wrong order */ 1743 ierr = PetscMalloc1(nnz,&vals);CHKERRQ(ierr); 1744 for (p = 0; p < pEnd - pStart; p++) { 1745 PetscInt parent, childid, closureSize, *closure = NULL; 1746 PetscInt point = perm[p], pointDof; 1747 1748 ierr = DMPlexGetTreeParent(dm,point,&parent,&childid);CHKERRQ(ierr); 1749 if ((point < conStart) || (point >= conEnd) || (parent == point)) continue; 1750 ierr = PetscSectionGetDof(conSec,point,&pointDof);CHKERRQ(ierr); 1751 if (!pointDof) continue; 1752 ierr = DMPlexGetTransitiveClosure(dm,parent,PETSC_TRUE,&closureSize,&closure);CHKERRQ(ierr); 1753 for (f = 0; f < numFields; f++) { 1754 PetscInt cDof, cOff, numCols, numFillCols, i, r, fComp = -1, matOffset, offset; 1755 PetscScalar *pointMat; 1756 PetscObject disc; 1757 PetscClassId id; 1758 PetscFE fe = NULL; 1759 PetscFV fv = NULL; 1760 1761 ierr = PetscDSGetDiscretization(ds,f,&disc);CHKERRQ(ierr); 1762 ierr = PetscObjectGetClassId(disc,&id);CHKERRQ(ierr); 1763 if (id == PETSCFE_CLASSID) { 1764 fe = (PetscFE) disc; 1765 ierr = PetscFEGetNumComponents(fe,&fComp);CHKERRQ(ierr); 1766 } 1767 else if (id == PETSCFV_CLASSID) { 1768 fv = (PetscFV) disc; 1769 ierr = PetscFVGetNumComponents(fv,&fComp);CHKERRQ(ierr); 1770 } 1771 else { 1772 SETERRQ(PetscObjectComm((PetscObject)disc),PETSC_ERR_SUP,"Unsupported discretization"); 1773 } 1774 1775 if (numFields > 1) { 1776 ierr = PetscSectionGetFieldDof(conSec,point,f,&cDof);CHKERRQ(ierr); 1777 ierr = PetscSectionGetFieldOffset(conSec,point,f,&cOff);CHKERRQ(ierr); 1778 } 1779 else { 1780 ierr = PetscSectionGetDof(conSec,point,&cDof);CHKERRQ(ierr); 1781 ierr = PetscSectionGetOffset(conSec,point,&cOff);CHKERRQ(ierr); 1782 } 1783 if (!cDof) continue; 1784 1785 /* make sure that every row for this point is the same size */ 1786 #if defined(PETSC_USE_DEBUG) 1787 for (r = 0; r < cDof; r++) { 1788 if (cDof > 1 && r) { 1789 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])); 1790 } 1791 } 1792 #endif 1793 /* zero rows */ 1794 for (i = ia[cOff] ; i< ia[cOff+cDof];i++) { 1795 vals[i] = 0.; 1796 } 1797 matOffset = ia[cOff]; 1798 numFillCols = ia[cOff+1] - matOffset; 1799 pointMat = refPointFieldMats[childid-pRefStart][f]; 1800 numCols = refPointFieldN[childid-pRefStart][f]; 1801 offset = 0; 1802 for (i = 0; i < closureSize; i++) { 1803 PetscInt q = closure[2*i]; 1804 PetscInt o = closure[2*i+1]; 1805 PetscInt aDof, aOff, j, k, qConDof, qConOff; 1806 1807 qConDof = qConOff = 0; 1808 if (numFields > 1) { 1809 ierr = PetscSectionGetFieldDof(section,q,f,&aDof);CHKERRQ(ierr); 1810 ierr = PetscSectionGetFieldOffset(section,q,f,&aOff);CHKERRQ(ierr); 1811 if (q >= conStart && q < conEnd) { 1812 ierr = PetscSectionGetFieldDof(conSec,q,f,&qConDof);CHKERRQ(ierr); 1813 ierr = PetscSectionGetFieldOffset(conSec,q,f,&qConOff);CHKERRQ(ierr); 1814 } 1815 } 1816 else { 1817 ierr = PetscSectionGetDof(section,q,&aDof);CHKERRQ(ierr); 1818 ierr = PetscSectionGetOffset(section,q,&aOff);CHKERRQ(ierr); 1819 if (q >= conStart && q < conEnd) { 1820 ierr = PetscSectionGetDof(conSec,q,&qConDof);CHKERRQ(ierr); 1821 ierr = PetscSectionGetOffset(conSec,q,&qConOff);CHKERRQ(ierr); 1822 } 1823 } 1824 if (!aDof) continue; 1825 if (qConDof) { 1826 /* this point has anchors: its rows of the matrix should already 1827 * be filled, thanks to preordering */ 1828 /* first multiply into pointWork, then set in matrix */ 1829 PetscInt aMatOffset = ia[qConOff]; 1830 PetscInt aNumFillCols = ia[qConOff + 1] - aMatOffset; 1831 for (r = 0; r < cDof; r++) { 1832 for (j = 0; j < aNumFillCols; j++) { 1833 PetscScalar inVal = 0; 1834 for (k = 0; k < aDof; k++) { 1835 PetscInt node = (o >= 0) ? (k / fComp) : ((aDof - 1 - k) / fComp); 1836 PetscInt comp = (k % fComp); 1837 PetscInt col = node * fComp + comp; 1838 1839 inVal += pointMat[r * numCols + offset + col] * vals[aMatOffset + aNumFillCols * k + j]; 1840 } 1841 pointWork[r * aNumFillCols + j] = inVal; 1842 } 1843 } 1844 /* assume that the columns are sorted, spend less time searching */ 1845 for (j = 0, k = 0; j < aNumFillCols; j++) { 1846 PetscInt col = ja[aMatOffset + j]; 1847 for (;k < numFillCols; k++) { 1848 if (ja[matOffset + k] == col) { 1849 break; 1850 } 1851 } 1852 if (k == numFillCols) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"No nonzero space for (%d, %d)", cOff, col); 1853 for (r = 0; r < cDof; r++) { 1854 vals[matOffset + numFillCols * r + k] = pointWork[r * aNumFillCols + j]; 1855 } 1856 } 1857 } 1858 else { 1859 /* find where to put this portion of pointMat into the matrix */ 1860 for (k = 0; k < numFillCols; k++) { 1861 if (ja[matOffset + k] == aOff) { 1862 break; 1863 } 1864 } 1865 if (k == numFillCols) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"No nonzero space for (%d, %d)", cOff, aOff); 1866 for (j = 0; j < aDof; j++) { 1867 PetscInt node = (o >= 0) ? (j / fComp) : ((aDof - 1 - j) / fComp); 1868 PetscInt comp = (j % fComp); 1869 PetscInt col = node * fComp + comp; 1870 for (r = 0; r < cDof; r++) { 1871 vals[matOffset + numFillCols * r + k + col] += pointMat[r * numCols + offset + col]; 1872 } 1873 } 1874 } 1875 offset += aDof; 1876 } 1877 } 1878 ierr = DMPlexRestoreTransitiveClosure(dm,parent,PETSC_TRUE,&closureSize,&closure);CHKERRQ(ierr); 1879 } 1880 for (row = 0; row < nRows; row++) { 1881 ierr = MatSetValues(cMat,1,&row,ia[row+1]-ia[row],&ja[ia[row]],&vals[ia[row]],INSERT_VALUES);CHKERRQ(ierr); 1882 } 1883 ierr = MatRestoreRowIJ(cMat,0,PETSC_FALSE,PETSC_FALSE,&nRows,&ia,&ja,&done);CHKERRQ(ierr); 1884 if (!done) SETERRQ(PetscObjectComm((PetscObject)cMat),PETSC_ERR_PLIB,"Could not restore RowIJ of constraint matrix"); 1885 ierr = MatAssemblyBegin(cMat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1886 ierr = MatAssemblyEnd(cMat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1887 ierr = PetscFree(vals);CHKERRQ(ierr); 1888 } 1889 1890 /* clean up */ 1891 ierr = ISRestoreIndices(anIS,&anchors);CHKERRQ(ierr); 1892 ierr = PetscFree2(perm,iperm);CHKERRQ(ierr); 1893 ierr = PetscFree(pointWork);CHKERRQ(ierr); 1894 ierr = DMPlexReferenceTreeRestoreChildrenMatrices(refTree,&refPointFieldMats,&refPointFieldN);CHKERRQ(ierr); 1895 PetscFunctionReturn(0); 1896 } 1897 1898 #undef __FUNCT__ 1899 #define __FUNCT__ "DMPlexTreeRefineCell" 1900 /* refine a single cell on rank 0: this is not intended to provide good local refinement, only to create an example of 1901 * a non-conforming mesh. Local refinement comes later */ 1902 PetscErrorCode DMPlexTreeRefineCell (DM dm, PetscInt cell, DM *ncdm) 1903 { 1904 DM K; 1905 PetscMPIInt rank; 1906 PetscInt dim, *pNewStart, *pNewEnd, *pNewCount, *pOldStart, *pOldEnd, offset, d, pStart, pEnd; 1907 PetscInt numNewCones, *newConeSizes, *newCones, *newOrientations; 1908 PetscInt *Kembedding; 1909 PetscInt *cellClosure=NULL, nc; 1910 PetscScalar *newVertexCoords; 1911 PetscInt numPointsWithParents, *parents, *childIDs, *perm, *iperm, *preOrient, pOffset; 1912 PetscSection parentSection; 1913 PetscErrorCode ierr; 1914 1915 PetscFunctionBegin; 1916 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm),&rank);CHKERRQ(ierr); 1917 ierr = DMGetDimension(dm,&dim);CHKERRQ(ierr); 1918 ierr = DMPlexCreate(PetscObjectComm((PetscObject)dm), ncdm);CHKERRQ(ierr); 1919 ierr = DMSetDimension(*ncdm,dim);CHKERRQ(ierr); 1920 1921 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 1922 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm),&parentSection);CHKERRQ(ierr); 1923 ierr = DMPlexGetReferenceTree(dm,&K);CHKERRQ(ierr); 1924 if (!rank) { 1925 /* compute the new charts */ 1926 ierr = PetscMalloc5(dim+1,&pNewCount,dim+1,&pNewStart,dim+1,&pNewEnd,dim+1,&pOldStart,dim+1,&pOldEnd);CHKERRQ(ierr); 1927 offset = 0; 1928 for (d = 0; d <= dim; d++) { 1929 PetscInt pOldCount, kStart, kEnd, k; 1930 1931 pNewStart[d] = offset; 1932 ierr = DMPlexGetHeightStratum(dm,d,&pOldStart[d],&pOldEnd[d]);CHKERRQ(ierr); 1933 ierr = DMPlexGetHeightStratum(K,d,&kStart,&kEnd);CHKERRQ(ierr); 1934 pOldCount = pOldEnd[d] - pOldStart[d]; 1935 /* adding the new points */ 1936 pNewCount[d] = pOldCount + kEnd - kStart; 1937 if (!d) { 1938 /* removing the cell */ 1939 pNewCount[d]--; 1940 } 1941 for (k = kStart; k < kEnd; k++) { 1942 PetscInt parent; 1943 ierr = DMPlexGetTreeParent(K,k,&parent,NULL);CHKERRQ(ierr); 1944 if (parent == k) { 1945 /* avoid double counting points that won't actually be new */ 1946 pNewCount[d]--; 1947 } 1948 } 1949 pNewEnd[d] = pNewStart[d] + pNewCount[d]; 1950 offset = pNewEnd[d]; 1951 1952 } 1953 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]); 1954 /* get the current closure of the cell that we are removing */ 1955 ierr = DMPlexGetTransitiveClosure(dm,cell,PETSC_TRUE,&nc,&cellClosure);CHKERRQ(ierr); 1956 1957 ierr = PetscMalloc1(pNewEnd[dim],&newConeSizes);CHKERRQ(ierr); 1958 { 1959 PetscInt kStart, kEnd, k, closureSizeK, *closureK = NULL, j; 1960 1961 ierr = DMPlexGetChart(K,&kStart,&kEnd);CHKERRQ(ierr); 1962 ierr = PetscMalloc4(kEnd-kStart,&Kembedding,kEnd-kStart,&perm,kEnd-kStart,&iperm,kEnd-kStart,&preOrient);CHKERRQ(ierr); 1963 1964 for (k = kStart; k < kEnd; k++) { 1965 perm[k - kStart] = k; 1966 iperm [k - kStart] = k - kStart; 1967 preOrient[k - kStart] = 0; 1968 } 1969 1970 ierr = DMPlexGetTransitiveClosure(K,0,PETSC_TRUE,&closureSizeK,&closureK);CHKERRQ(ierr); 1971 for (j = 1; j < closureSizeK; j++) { 1972 PetscInt parentOrientA = closureK[2*j+1]; 1973 PetscInt parentOrientB = cellClosure[2*j+1]; 1974 PetscInt p, q; 1975 1976 p = closureK[2*j]; 1977 q = cellClosure[2*j]; 1978 for (d = 0; d <= dim; d++) { 1979 if (q >= pOldStart[d] && q < pOldEnd[d]) { 1980 Kembedding[p] = (q - pOldStart[d]) + pNewStart[d]; 1981 } 1982 } 1983 if (parentOrientA != parentOrientB) { 1984 PetscInt numChildren, i; 1985 const PetscInt *children; 1986 1987 ierr = DMPlexGetTreeChildren(K,p,&numChildren,&children);CHKERRQ(ierr); 1988 for (i = 0; i < numChildren; i++) { 1989 PetscInt kPerm, oPerm; 1990 1991 k = children[i]; 1992 ierr = DMPlexReferenceTreeGetChildSymmetry(K,p,parentOrientA,0,k,parentOrientB,&oPerm,&kPerm);CHKERRQ(ierr); 1993 /* perm = what refTree position I'm in */ 1994 perm[kPerm-kStart] = k; 1995 /* iperm = who is at this position */ 1996 iperm[k-kStart] = kPerm-kStart; 1997 preOrient[kPerm-kStart] = oPerm; 1998 } 1999 } 2000 } 2001 ierr = DMPlexRestoreTransitiveClosure(K,0,PETSC_TRUE,&closureSizeK,&closureK);CHKERRQ(ierr); 2002 } 2003 ierr = PetscSectionSetChart(parentSection,0,pNewEnd[dim]);CHKERRQ(ierr); 2004 offset = 0; 2005 numNewCones = 0; 2006 for (d = 0; d <= dim; d++) { 2007 PetscInt kStart, kEnd, k; 2008 PetscInt p; 2009 PetscInt size; 2010 2011 for (p = pOldStart[d]; p < pOldEnd[d]; p++) { 2012 /* skip cell 0 */ 2013 if (p == cell) continue; 2014 /* old cones to new cones */ 2015 ierr = DMPlexGetConeSize(dm,p,&size);CHKERRQ(ierr); 2016 newConeSizes[offset++] = size; 2017 numNewCones += size; 2018 } 2019 2020 ierr = DMPlexGetHeightStratum(K,d,&kStart,&kEnd);CHKERRQ(ierr); 2021 for (k = kStart; k < kEnd; k++) { 2022 PetscInt kParent; 2023 2024 ierr = DMPlexGetTreeParent(K,k,&kParent,NULL);CHKERRQ(ierr); 2025 if (kParent != k) { 2026 Kembedding[k] = offset; 2027 ierr = DMPlexGetConeSize(K,k,&size);CHKERRQ(ierr); 2028 newConeSizes[offset++] = size; 2029 numNewCones += size; 2030 if (kParent != 0) { 2031 ierr = PetscSectionSetDof(parentSection,Kembedding[k],1);CHKERRQ(ierr); 2032 } 2033 } 2034 } 2035 } 2036 2037 ierr = PetscSectionSetUp(parentSection);CHKERRQ(ierr); 2038 ierr = PetscSectionGetStorageSize(parentSection,&numPointsWithParents);CHKERRQ(ierr); 2039 ierr = PetscMalloc2(numNewCones,&newCones,numNewCones,&newOrientations);CHKERRQ(ierr); 2040 ierr = PetscMalloc2(numPointsWithParents,&parents,numPointsWithParents,&childIDs);CHKERRQ(ierr); 2041 2042 /* fill new cones */ 2043 offset = 0; 2044 for (d = 0; d <= dim; d++) { 2045 PetscInt kStart, kEnd, k, l; 2046 PetscInt p; 2047 PetscInt size; 2048 const PetscInt *cone, *orientation; 2049 2050 for (p = pOldStart[d]; p < pOldEnd[d]; p++) { 2051 /* skip cell 0 */ 2052 if (p == cell) continue; 2053 /* old cones to new cones */ 2054 ierr = DMPlexGetConeSize(dm,p,&size);CHKERRQ(ierr); 2055 ierr = DMPlexGetCone(dm,p,&cone);CHKERRQ(ierr); 2056 ierr = DMPlexGetConeOrientation(dm,p,&orientation);CHKERRQ(ierr); 2057 for (l = 0; l < size; l++) { 2058 newCones[offset] = (cone[l] - pOldStart[d + 1]) + pNewStart[d + 1]; 2059 newOrientations[offset++] = orientation[l]; 2060 } 2061 } 2062 2063 ierr = DMPlexGetHeightStratum(K,d,&kStart,&kEnd);CHKERRQ(ierr); 2064 for (k = kStart; k < kEnd; k++) { 2065 PetscInt kPerm = perm[k], kParent; 2066 PetscInt preO = preOrient[k]; 2067 2068 ierr = DMPlexGetTreeParent(K,k,&kParent,NULL);CHKERRQ(ierr); 2069 if (kParent != k) { 2070 /* embed new cones */ 2071 ierr = DMPlexGetConeSize(K,k,&size);CHKERRQ(ierr); 2072 ierr = DMPlexGetCone(K,kPerm,&cone);CHKERRQ(ierr); 2073 ierr = DMPlexGetConeOrientation(K,kPerm,&orientation);CHKERRQ(ierr); 2074 for (l = 0; l < size; l++) { 2075 PetscInt q, m = (preO >= 0) ? ((preO + l) % size) : ((size -(preO + 1) - l) % size); 2076 PetscInt newO, lSize, oTrue; 2077 2078 q = iperm[cone[m]]; 2079 newCones[offset] = Kembedding[q]; 2080 ierr = DMPlexGetConeSize(K,q,&lSize);CHKERRQ(ierr); 2081 oTrue = orientation[m]; 2082 oTrue = ((!lSize) || (preOrient[k] >= 0)) ? oTrue : -(oTrue + 2); 2083 newO = DihedralCompose(lSize,oTrue,preOrient[q]); 2084 newOrientations[offset++] = newO; 2085 } 2086 if (kParent != 0) { 2087 PetscInt newPoint = Kembedding[kParent]; 2088 ierr = PetscSectionGetOffset(parentSection,Kembedding[k],&pOffset);CHKERRQ(ierr); 2089 parents[pOffset] = newPoint; 2090 childIDs[pOffset] = k; 2091 } 2092 } 2093 } 2094 } 2095 2096 ierr = PetscMalloc1(dim*(pNewEnd[dim]-pNewStart[dim]),&newVertexCoords);CHKERRQ(ierr); 2097 2098 /* fill coordinates */ 2099 offset = 0; 2100 { 2101 PetscInt kStart, kEnd, l; 2102 PetscSection vSection; 2103 PetscInt v; 2104 Vec coords; 2105 PetscScalar *coordvals; 2106 PetscInt dof, off; 2107 PetscReal v0[3], J[9], detJ; 2108 2109 #if defined(PETSC_USE_DEBUG) 2110 { 2111 PetscInt k; 2112 ierr = DMPlexGetHeightStratum(K,0,&kStart,&kEnd);CHKERRQ(ierr); 2113 for (k = kStart; k < kEnd; k++) { 2114 ierr = DMPlexComputeCellGeometryFEM(K, k, NULL, v0, J, NULL, &detJ);CHKERRQ(ierr); 2115 if (detJ <= 0.) SETERRQ1 (PETSC_COMM_SELF,PETSC_ERR_PLIB,"reference tree cell %d has bad determinant",k); 2116 } 2117 } 2118 #endif 2119 ierr = DMPlexComputeCellGeometryFEM(dm, cell, NULL, v0, J, NULL, &detJ);CHKERRQ(ierr); 2120 ierr = DMGetCoordinateSection(dm,&vSection);CHKERRQ(ierr); 2121 ierr = DMGetCoordinatesLocal(dm,&coords);CHKERRQ(ierr); 2122 ierr = VecGetArray(coords,&coordvals);CHKERRQ(ierr); 2123 for (v = pOldStart[dim]; v < pOldEnd[dim]; v++) { 2124 2125 ierr = PetscSectionGetDof(vSection,v,&dof);CHKERRQ(ierr); 2126 ierr = PetscSectionGetOffset(vSection,v,&off);CHKERRQ(ierr); 2127 for (l = 0; l < dof; l++) { 2128 newVertexCoords[offset++] = coordvals[off + l]; 2129 } 2130 } 2131 ierr = VecRestoreArray(coords,&coordvals);CHKERRQ(ierr); 2132 2133 ierr = DMGetCoordinateSection(K,&vSection);CHKERRQ(ierr); 2134 ierr = DMGetCoordinatesLocal(K,&coords);CHKERRQ(ierr); 2135 ierr = VecGetArray(coords,&coordvals);CHKERRQ(ierr); 2136 ierr = DMPlexGetDepthStratum(K,0,&kStart,&kEnd);CHKERRQ(ierr); 2137 for (v = kStart; v < kEnd; v++) { 2138 PetscReal coord[3], newCoord[3]; 2139 PetscInt vPerm = perm[v]; 2140 PetscInt kParent; 2141 2142 ierr = DMPlexGetTreeParent(K,v,&kParent,NULL);CHKERRQ(ierr); 2143 if (kParent != v) { 2144 /* this is a new vertex */ 2145 ierr = PetscSectionGetOffset(vSection,vPerm,&off);CHKERRQ(ierr); 2146 for (l = 0; l < dim; ++l) coord[l] = PetscRealPart(coordvals[off+l]); 2147 CoordinatesRefToReal(dim, dim, v0, J, coord, newCoord);CHKERRQ(ierr); 2148 for (l = 0; l < dim; ++l) newVertexCoords[offset+l] = newCoord[l]; 2149 offset += dim; 2150 } 2151 } 2152 ierr = VecRestoreArray(coords,&coordvals);CHKERRQ(ierr); 2153 } 2154 2155 /* need to reverse the order of pNewCount: vertices first, cells last */ 2156 for (d = 0; d < (dim + 1) / 2; d++) { 2157 PetscInt tmp; 2158 2159 tmp = pNewCount[d]; 2160 pNewCount[d] = pNewCount[dim - d]; 2161 pNewCount[dim - d] = tmp; 2162 } 2163 2164 ierr = DMPlexCreateFromDAG(*ncdm,dim,pNewCount,newConeSizes,newCones,newOrientations,newVertexCoords);CHKERRQ(ierr); 2165 ierr = DMPlexSetReferenceTree(*ncdm,K);CHKERRQ(ierr); 2166 ierr = DMPlexSetTree(*ncdm,parentSection,parents,childIDs);CHKERRQ(ierr); 2167 2168 /* clean up */ 2169 ierr = DMPlexRestoreTransitiveClosure(dm,cell,PETSC_TRUE,&nc,&cellClosure);CHKERRQ(ierr); 2170 ierr = PetscFree5(pNewCount,pNewStart,pNewEnd,pOldStart,pOldEnd);CHKERRQ(ierr); 2171 ierr = PetscFree(newConeSizes);CHKERRQ(ierr); 2172 ierr = PetscFree2(newCones,newOrientations);CHKERRQ(ierr); 2173 ierr = PetscFree(newVertexCoords);CHKERRQ(ierr); 2174 ierr = PetscFree2(parents,childIDs);CHKERRQ(ierr); 2175 ierr = PetscFree4(Kembedding,perm,iperm,preOrient);CHKERRQ(ierr); 2176 } 2177 else { 2178 PetscInt p, counts[4]; 2179 PetscInt *coneSizes, *cones, *orientations; 2180 Vec coordVec; 2181 PetscScalar *coords; 2182 2183 for (d = 0; d <= dim; d++) { 2184 PetscInt dStart, dEnd; 2185 2186 ierr = DMPlexGetDepthStratum(dm,d,&dStart,&dEnd);CHKERRQ(ierr); 2187 counts[d] = dEnd - dStart; 2188 } 2189 ierr = PetscMalloc1(pEnd-pStart,&coneSizes);CHKERRQ(ierr); 2190 for (p = pStart; p < pEnd; p++) { 2191 ierr = DMPlexGetConeSize(dm,p,&coneSizes[p-pStart]);CHKERRQ(ierr); 2192 } 2193 ierr = DMPlexGetCones(dm, &cones);CHKERRQ(ierr); 2194 ierr = DMPlexGetConeOrientations(dm, &orientations);CHKERRQ(ierr); 2195 ierr = DMGetCoordinatesLocal(dm,&coordVec);CHKERRQ(ierr); 2196 ierr = VecGetArray(coordVec,&coords);CHKERRQ(ierr); 2197 2198 ierr = PetscSectionSetChart(parentSection,pStart,pEnd);CHKERRQ(ierr); 2199 ierr = PetscSectionSetUp(parentSection);CHKERRQ(ierr); 2200 ierr = DMPlexCreateFromDAG(*ncdm,dim,counts,coneSizes,cones,orientations,NULL);CHKERRQ(ierr); 2201 ierr = DMPlexSetReferenceTree(*ncdm,K);CHKERRQ(ierr); 2202 ierr = DMPlexSetTree(*ncdm,parentSection,NULL,NULL);CHKERRQ(ierr); 2203 ierr = VecRestoreArray(coordVec,&coords);CHKERRQ(ierr); 2204 } 2205 ierr = PetscSectionDestroy(&parentSection);CHKERRQ(ierr); 2206 2207 PetscFunctionReturn(0); 2208 } 2209 2210 #undef __FUNCT__ 2211 #define __FUNCT__ "DMPlexComputeInterpolatorTree" 2212 PetscErrorCode DMPlexComputeInterpolatorTree(DM coarse, DM fine, PetscSF coarseToFine, PetscInt *childIds, Mat mat) 2213 { 2214 PetscSF coarseToFineEmbedded; 2215 PetscSection globalCoarse, globalFine; 2216 PetscSection localCoarse, localFine; 2217 PetscSection aSec, cSec; 2218 PetscSection rootIndicesSec, rootMatricesSec; 2219 PetscSection leafIndicesSec, leafMatricesSec; 2220 PetscInt *rootIndices, *leafIndices; 2221 PetscScalar *rootMatrices, *leafMatrices; 2222 IS aIS; 2223 const PetscInt *anchors; 2224 Mat cMat; 2225 PetscInt numFields; 2226 PetscInt pStartC, pEndC, pStartF, pEndF, p; 2227 PetscInt aStart, aEnd, cStart, cEnd; 2228 PetscInt *maxChildIds; 2229 PetscInt *offsets, *newOffsets, *offsetsCopy, *newOffsetsCopy, *rowOffsets, *numD, *numO; 2230 PetscErrorCode ierr; 2231 2232 PetscFunctionBegin; 2233 ierr = DMPlexGetChart(coarse,&pStartC,&pEndC);CHKERRQ(ierr); 2234 ierr = DMPlexGetChart(fine,&pStartF,&pEndF);CHKERRQ(ierr); 2235 ierr = DMGetDefaultGlobalSection(fine,&globalFine);CHKERRQ(ierr); 2236 { /* winnow fine points that don't have global dofs out of the sf */ 2237 PetscInt dof, cdof, numPointsWithDofs, offset, *pointsWithDofs, nleaves, l; 2238 const PetscInt *leaves; 2239 2240 ierr = PetscSFGetGraph(coarseToFine,NULL,&nleaves,&leaves,NULL);CHKERRQ(ierr); 2241 for (l = 0, numPointsWithDofs = 0; l < nleaves; l++) { 2242 p = leaves ? leaves[l] : l; 2243 ierr = PetscSectionGetDof(globalFine,p,&dof);CHKERRQ(ierr); 2244 ierr = PetscSectionGetConstraintDof(globalFine,p,&cdof);CHKERRQ(ierr); 2245 if ((dof - cdof) > 0) { 2246 numPointsWithDofs++; 2247 } 2248 } 2249 ierr = PetscMalloc1(numPointsWithDofs,&pointsWithDofs);CHKERRQ(ierr); 2250 for (l = 0, offset = 0; l < nleaves; l++) { 2251 p = leaves ? leaves[l] : l; 2252 ierr = PetscSectionGetDof(globalFine,p,&dof);CHKERRQ(ierr); 2253 ierr = PetscSectionGetConstraintDof(globalFine,p,&cdof);CHKERRQ(ierr); 2254 if ((dof - cdof) > 0) { 2255 pointsWithDofs[offset++] = l; 2256 } 2257 } 2258 ierr = PetscSFCreateEmbeddedLeafSF(coarseToFine, numPointsWithDofs, pointsWithDofs, &coarseToFineEmbedded);CHKERRQ(ierr); 2259 ierr = PetscFree(pointsWithDofs);CHKERRQ(ierr); 2260 } 2261 /* communicate back to the coarse mesh which coarse points have children (that may require interpolation) */ 2262 ierr = PetscMalloc1(pEndC-pStartC,&maxChildIds);CHKERRQ(ierr); 2263 for (p = pStartC; p < pEndC; p++) { 2264 maxChildIds[p - pStartC] = -2; 2265 } 2266 ierr = PetscSFReduceBegin(coarseToFineEmbedded,MPIU_INT,childIds,maxChildIds,MPIU_MAX);CHKERRQ(ierr); 2267 ierr = PetscSFReduceEnd(coarseToFineEmbedded,MPIU_INT,childIds,maxChildIds,MPIU_MAX);CHKERRQ(ierr); 2268 2269 ierr = DMGetDefaultSection(coarse,&localCoarse);CHKERRQ(ierr); 2270 ierr = DMGetDefaultGlobalSection(coarse,&globalCoarse);CHKERRQ(ierr); 2271 2272 ierr = DMPlexGetAnchors(coarse,&aSec,&aIS);CHKERRQ(ierr); 2273 ierr = ISGetIndices(aIS,&anchors);CHKERRQ(ierr); 2274 ierr = PetscSectionGetChart(aSec,&aStart,&aEnd);CHKERRQ(ierr); 2275 2276 ierr = DMGetDefaultConstraints(coarse,&cSec,&cMat);CHKERRQ(ierr); 2277 ierr = PetscSectionGetChart(cSec,&cStart,&cEnd);CHKERRQ(ierr); 2278 2279 /* create sections that will send to children the indices and matrices they will need to construct the interpolator */ 2280 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)coarse),&rootIndicesSec);CHKERRQ(ierr); 2281 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)coarse),&rootMatricesSec);CHKERRQ(ierr); 2282 ierr = PetscSectionSetChart(rootIndicesSec,pStartC,pEndC);CHKERRQ(ierr); 2283 ierr = PetscSectionSetChart(rootMatricesSec,pStartC,pEndC);CHKERRQ(ierr); 2284 ierr = PetscSectionGetNumFields(localCoarse,&numFields);CHKERRQ(ierr); 2285 { 2286 PetscInt maxFields = PetscMax(1,numFields) + 1; 2287 ierr = PetscMalloc7(maxFields,&offsets,maxFields,&offsetsCopy,maxFields,&newOffsets,maxFields,&newOffsetsCopy,maxFields,&rowOffsets,maxFields,&numD,maxFields,&numO);CHKERRQ(ierr); 2288 } 2289 2290 for (p = pStartC; p < pEndC; p++) { /* count the sizes of the indices and matrices */ 2291 PetscInt dof, matSize = 0; 2292 PetscInt aDof = 0; 2293 PetscInt cDof = 0; 2294 PetscInt maxChildId = maxChildIds[p - pStartC]; 2295 PetscInt numRowIndices = 0; 2296 PetscInt numColIndices = 0; 2297 PetscInt f; 2298 2299 ierr = PetscSectionGetDof(globalCoarse,p,&dof);CHKERRQ(ierr); 2300 if (dof < 0) { 2301 dof = -(dof + 1); 2302 } 2303 if (p >= aStart && p < aEnd) { 2304 ierr = PetscSectionGetDof(aSec,p,&aDof);CHKERRQ(ierr); 2305 } 2306 if (p >= cStart && p < cEnd) { 2307 ierr = PetscSectionGetDof(cSec,p,&cDof);CHKERRQ(ierr); 2308 } 2309 for (f = 0; f <= numFields; f++) offsets[f] = 0; 2310 for (f = 0; f <= numFields; f++) newOffsets[f] = 0; 2311 if (maxChildId >= 0) { /* this point has children (with dofs) that will need to be interpolated from the closure of p */ 2312 PetscInt *closure = NULL, closureSize, cl; 2313 2314 ierr = DMPlexGetTransitiveClosure(coarse,p,PETSC_TRUE,&closureSize,&closure);CHKERRQ(ierr); 2315 for (cl = 0; cl < closureSize; cl++) { /* get the closure */ 2316 PetscInt c = closure[2 * cl], clDof; 2317 2318 ierr = PetscSectionGetDof(localCoarse,c,&clDof);CHKERRQ(ierr); 2319 numRowIndices += clDof; 2320 for (f = 0; f < numFields; f++) { 2321 ierr = PetscSectionGetFieldDof(localCoarse,c,f,&clDof);CHKERRQ(ierr); 2322 offsets[f + 1] += clDof; 2323 } 2324 } 2325 for (f = 0; f < numFields; f++) { 2326 offsets[f + 1] += offsets[f]; 2327 newOffsets[f + 1] = offsets[f + 1]; 2328 } 2329 /* get the number of indices needed and their field offsets */ 2330 ierr = DMPlexAnchorsModifyMat(coarse,localCoarse,closureSize,numRowIndices,closure,NULL,NULL,&numColIndices,NULL,NULL,newOffsets,PETSC_FALSE);CHKERRQ(ierr); 2331 ierr = DMPlexRestoreTransitiveClosure(coarse,p,PETSC_TRUE,&closureSize,&closure);CHKERRQ(ierr); 2332 if (!numColIndices) { /* there are no hanging constraint modifications, so the matrix is just the identity: do not send it */ 2333 numColIndices = numRowIndices; 2334 matSize = 0; 2335 } 2336 else if (numFields) { /* we send one submat for each field: sum their sizes */ 2337 matSize = 0; 2338 for (f = 0; f < numFields; f++) { 2339 PetscInt numRow, numCol; 2340 2341 numRow = offsets[f + 1] - offsets[f]; 2342 numCol = newOffsets[f + 1] - newOffsets[f]; 2343 matSize += numRow * numCol; 2344 } 2345 } 2346 else { 2347 matSize = numRowIndices * numColIndices; 2348 } 2349 } else if (maxChildId == -1) { 2350 if (cDof > 0) { /* this point's dofs are interpolated via cMat: get the submatrix of cMat */ 2351 PetscInt aOff, a; 2352 2353 ierr = PetscSectionGetOffset(aSec,p,&aOff);CHKERRQ(ierr); 2354 for (f = 0; f < numFields; f++) { 2355 PetscInt fDof; 2356 2357 ierr = PetscSectionGetFieldDof(localCoarse,p,f,&fDof);CHKERRQ(ierr); 2358 offsets[f+1] = fDof; 2359 } 2360 for (a = 0; a < aDof; a++) { 2361 PetscInt anchor = anchors[a + aOff], aLocalDof; 2362 2363 ierr = PetscSectionGetDof(localCoarse,anchor,&aLocalDof);CHKERRQ(ierr); 2364 numColIndices += aLocalDof; 2365 for (f = 0; f < numFields; f++) { 2366 PetscInt fDof; 2367 2368 ierr = PetscSectionGetFieldDof(localCoarse,anchor,f,&fDof);CHKERRQ(ierr); 2369 newOffsets[f+1] += fDof; 2370 } 2371 } 2372 if (numFields) { 2373 matSize = 0; 2374 for (f = 0; f < numFields; f++) { 2375 matSize += offsets[f+1] * newOffsets[f+1]; 2376 } 2377 } 2378 else { 2379 matSize = numColIndices * dof; 2380 } 2381 } 2382 else { /* no children, and no constraints on dofs: just get the global indices */ 2383 numColIndices = dof; 2384 matSize = 0; 2385 } 2386 } 2387 /* we will pack the column indices with the field offsets */ 2388 ierr = PetscSectionSetDof(rootIndicesSec,p,numColIndices ? numColIndices+2*numFields : 0);CHKERRQ(ierr); 2389 ierr = PetscSectionSetDof(rootMatricesSec,p,matSize);CHKERRQ(ierr); 2390 } 2391 ierr = PetscSectionSetUp(rootIndicesSec);CHKERRQ(ierr); 2392 ierr = PetscSectionSetUp(rootMatricesSec);CHKERRQ(ierr); 2393 { 2394 PetscInt numRootIndices, numRootMatrices; 2395 2396 ierr = PetscSectionGetStorageSize(rootIndicesSec,&numRootIndices);CHKERRQ(ierr); 2397 ierr = PetscSectionGetStorageSize(rootMatricesSec,&numRootMatrices);CHKERRQ(ierr); 2398 ierr = PetscMalloc2(numRootIndices,&rootIndices,numRootMatrices,&rootMatrices);CHKERRQ(ierr); 2399 for (p = pStartC; p < pEndC; p++) { 2400 PetscInt numRowIndices, numColIndices, matSize, dof; 2401 PetscInt pIndOff, pMatOff, f; 2402 PetscInt *pInd; 2403 PetscInt maxChildId = maxChildIds[p - pStartC]; 2404 PetscScalar *pMat = NULL; 2405 2406 ierr = PetscSectionGetDof(rootIndicesSec,p,&numColIndices);CHKERRQ(ierr); 2407 if (!numColIndices) { 2408 continue; 2409 } 2410 for (f = 0; f <= numFields; f++) { 2411 offsets[f] = 0; 2412 newOffsets[f] = 0; 2413 offsetsCopy[f] = 0; 2414 newOffsetsCopy[f] = 0; 2415 } 2416 numColIndices -= 2 * numFields; 2417 ierr = PetscSectionGetOffset(rootIndicesSec,p,&pIndOff);CHKERRQ(ierr); 2418 pInd = &(rootIndices[pIndOff]); 2419 ierr = PetscSectionGetDof(rootMatricesSec,p,&matSize);CHKERRQ(ierr); 2420 if (matSize) { 2421 ierr = PetscSectionGetOffset(rootMatricesSec,p,&pMatOff);CHKERRQ(ierr); 2422 pMat = &rootMatrices[pMatOff]; 2423 } 2424 ierr = PetscSectionGetDof(globalCoarse,p,&dof);CHKERRQ(ierr); 2425 if (dof < 0) { 2426 dof = -(dof + 1); 2427 } 2428 if (maxChildId >= 0) { /* build an identity matrix, apply matrix constraints on the right */ 2429 PetscInt i, j; 2430 PetscInt numRowIndices = matSize / numColIndices; 2431 2432 if (!numRowIndices) { /* don't need to calculate the mat, just the indices */ 2433 PetscInt numIndices, *indices; 2434 ierr = DMPlexGetClosureIndices(coarse,localCoarse,globalCoarse,p,&numIndices,&indices,offsets);CHKERRQ(ierr); 2435 if (numIndices != numColIndices) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"mismatching constraint indices calculations"); 2436 for (i = 0; i < numColIndices; i++) { 2437 pInd[i] = indices[i]; 2438 } 2439 for (i = 0; i < numFields; i++) { 2440 pInd[numColIndices + i] = offsets[i+1]; 2441 pInd[numColIndices + numFields + i] = offsets[i+1]; 2442 } 2443 ierr = DMPlexRestoreClosureIndices(coarse,localCoarse,globalCoarse,p,&numIndices,&indices,offsets);CHKERRQ(ierr); 2444 } 2445 else { 2446 PetscInt closureSize, *closure = NULL, cl; 2447 PetscScalar *pMatIn, *pMatModified; 2448 PetscInt numPoints,*points; 2449 2450 ierr = DMGetWorkArray(coarse,numRowIndices * numRowIndices,PETSC_SCALAR,&pMatIn);CHKERRQ(ierr); 2451 for (i = 0; i < numRowIndices; i++) { /* initialize to the identity */ 2452 for (j = 0; j < numRowIndices; j++) { 2453 pMatIn[i * numRowIndices + j] = (i == j) ? 1. : 0.; 2454 } 2455 } 2456 ierr = DMPlexGetTransitiveClosure(coarse, p, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 2457 if (numFields) { 2458 for (cl = 0; cl < closureSize; cl++) { 2459 PetscInt c = closure[2 * cl]; 2460 2461 for (f = 0; f < numFields; f++) { 2462 PetscInt fDof; 2463 2464 ierr = PetscSectionGetFieldDof(localCoarse,c,f,&fDof);CHKERRQ(ierr); 2465 offsets[f + 1] += fDof; 2466 } 2467 } 2468 for (f = 0; f < numFields; f++) { 2469 offsets[f + 1] += offsets[f]; 2470 newOffsets[f + 1] = offsets[f + 1]; 2471 } 2472 } 2473 /* apply hanging node constraints on the right, get the new points and the new offsets */ 2474 ierr = DMPlexAnchorsModifyMat(coarse,localCoarse,closureSize,numRowIndices,closure,pMatIn,&numPoints,NULL,&points,&pMatModified,newOffsets,PETSC_FALSE);CHKERRQ(ierr); 2475 if (!numFields) { 2476 for (i = 0; i < numRowIndices * numColIndices; i++) { 2477 pMat[i] = pMatModified[i]; 2478 } 2479 } 2480 else { 2481 PetscInt i, j, count; 2482 for (f = 0, count = 0; f < numFields; f++) { 2483 for (i = offsets[f]; i < offsets[f+1]; i++) { 2484 for (j = newOffsets[f]; j < newOffsets[f+1]; j++, count++) { 2485 pMat[count] = pMatModified[i * numColIndices + j]; 2486 } 2487 } 2488 } 2489 } 2490 ierr = DMRestoreWorkArray(coarse,numRowIndices * numColIndices,PETSC_SCALAR,&pMatModified);CHKERRQ(ierr); 2491 ierr = DMPlexRestoreTransitiveClosure(coarse, p, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 2492 ierr = DMRestoreWorkArray(coarse,numRowIndices * numColIndices,PETSC_SCALAR,&pMatIn);CHKERRQ(ierr); 2493 if (numFields) { 2494 for (f = 0; f < numFields; f++) { 2495 pInd[numColIndices + f] = offsets[f+1]; 2496 pInd[numColIndices + numFields + f] = newOffsets[f+1]; 2497 } 2498 for (cl = 0; cl < numPoints*2; cl += 2) { 2499 PetscInt o = points[cl+1], globalOff, c = points[cl]; 2500 ierr = PetscSectionGetOffset(globalCoarse, c, &globalOff);CHKERRQ(ierr); 2501 DMPlexGetIndicesPointFields_Internal(localCoarse, c, globalOff < 0 ? -(globalOff+1) : globalOff, newOffsets, PETSC_FALSE, o, pInd); 2502 } 2503 } else { 2504 for (cl = 0; cl < numPoints*2; cl += 2) { 2505 PetscInt o = points[cl+1], c = points[cl], globalOff; 2506 ierr = PetscSectionGetOffset(globalCoarse, c, &globalOff);CHKERRQ(ierr); 2507 DMPlexGetIndicesPoint_Internal(localCoarse, c, globalOff < 0 ? -(globalOff+1) : globalOff, newOffsets, PETSC_FALSE, o, pInd); 2508 } 2509 } 2510 ierr = DMRestoreWorkArray(coarse,numPoints,PETSC_SCALAR,&points);CHKERRQ(ierr); 2511 } 2512 } 2513 else if (matSize) { 2514 PetscInt cOff; 2515 PetscInt *rowIndices, *colIndices, a, aDof, aOff; 2516 2517 numRowIndices = matSize / numColIndices; 2518 if (numRowIndices != dof) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Miscounted dofs"); 2519 ierr = DMGetWorkArray(coarse,numRowIndices,PETSC_INT,&rowIndices);CHKERRQ(ierr); 2520 ierr = DMGetWorkArray(coarse,numColIndices,PETSC_INT,&colIndices);CHKERRQ(ierr); 2521 ierr = PetscSectionGetOffset(cSec,p,&cOff);CHKERRQ(ierr); 2522 ierr = PetscSectionGetDof(aSec,p,&aDof);CHKERRQ(ierr); 2523 ierr = PetscSectionGetOffset(aSec,p,&aOff);CHKERRQ(ierr); 2524 if (numFields) { 2525 for (f = 0; f < numFields; f++) { 2526 PetscInt fDof; 2527 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, a; 2559 2560 for (f = 0, count = 0; f < numFields; f++) { 2561 PetscInt iSize = offsets[f + 1] - offsets[f]; 2562 PetscInt jSize = newOffsets[f + 1] - newOffsets[f]; 2563 ierr = MatGetValues(cMat,iSize,&rowIndices[offsets[f]],jSize,&colIndices[newOffsets[f]],&pMat[count]);CHKERRQ(ierr); 2564 count += iSize * jSize; 2565 pInd[numColIndices + f] = offsets[f+1]; 2566 pInd[numColIndices + numFields + f] = newOffsets[f+1]; 2567 } 2568 for (a = 0; a < aDof; a++) { 2569 PetscInt anchor = anchors[a + aOff]; 2570 PetscInt gOff; 2571 ierr = PetscSectionGetOffset(globalCoarse,anchor,&gOff);CHKERRQ(ierr); 2572 DMPlexGetIndicesPointFields_Internal(localCoarse,anchor,gOff < 0 ? -(gOff + 1) : gOff,newOffsets,PETSC_FALSE,0,pInd);CHKERRQ(ierr); 2573 } 2574 } 2575 else { 2576 PetscInt a; 2577 ierr = MatGetValues(cMat,numRowIndices,rowIndices,numColIndices,colIndices,pMat);CHKERRQ(ierr); 2578 for (a = 0; a < aDof; a++) { 2579 PetscInt anchor = anchors[a + aOff]; 2580 PetscInt gOff; 2581 ierr = PetscSectionGetOffset(globalCoarse,anchor,&gOff);CHKERRQ(ierr); 2582 DMPlexGetIndicesPoint_Internal(localCoarse,anchor,gOff < 0 ? -(gOff + 1) : gOff,newOffsets,PETSC_FALSE,0,pInd);CHKERRQ(ierr); 2583 } 2584 } 2585 ierr = DMRestoreWorkArray(coarse,numColIndices,PETSC_INT,&colIndices);CHKERRQ(ierr); 2586 ierr = DMRestoreWorkArray(coarse,numRowIndices,PETSC_INT,&rowIndices);CHKERRQ(ierr); 2587 } 2588 else { 2589 PetscInt gOff; 2590 2591 ierr = PetscSectionGetOffset(globalCoarse,p,&gOff);CHKERRQ(ierr); 2592 if (numFields) { 2593 for (f = 0; f < numFields; f++) { 2594 PetscInt fDof; 2595 ierr = PetscSectionGetFieldDof(localCoarse,p,f,&fDof);CHKERRQ(ierr); 2596 offsets[f + 1] = fDof + offsets[f]; 2597 } 2598 for (f = 0; f < numFields; f++) { 2599 pInd[numColIndices + f] = offsets[f+1]; 2600 pInd[numColIndices + numFields + f] = offsets[f+1]; 2601 } 2602 DMPlexGetIndicesPointFields_Internal(localCoarse,p,gOff < 0 ? -(gOff + 1) : gOff,offsets,PETSC_FALSE,0,pInd);CHKERRQ(ierr); 2603 } 2604 else { 2605 DMPlexGetIndicesPoint_Internal(localCoarse,p,gOff < 0 ? -(gOff + 1) : gOff,offsets,PETSC_FALSE,0,pInd);CHKERRQ(ierr); 2606 } 2607 } 2608 } 2609 ierr = PetscFree(maxChildIds);CHKERRQ(ierr); 2610 } 2611 { 2612 PetscSF indicesSF, matricesSF; 2613 PetscInt *remoteOffsetsIndices, *remoteOffsetsMatrices, numLeafIndices, numLeafMatrices; 2614 2615 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)fine),&leafIndicesSec);CHKERRQ(ierr); 2616 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)fine),&leafMatricesSec);CHKERRQ(ierr); 2617 ierr = PetscSFDistributeSection(coarseToFineEmbedded,rootIndicesSec,&remoteOffsetsIndices,leafIndicesSec);CHKERRQ(ierr); 2618 ierr = PetscSFDistributeSection(coarseToFineEmbedded,rootMatricesSec,&remoteOffsetsMatrices,leafMatricesSec);CHKERRQ(ierr); 2619 ierr = PetscSFCreateSectionSF(coarseToFineEmbedded,rootIndicesSec,remoteOffsetsIndices,leafIndicesSec,&indicesSF);CHKERRQ(ierr); 2620 ierr = PetscSFCreateSectionSF(coarseToFineEmbedded,rootMatricesSec,remoteOffsetsMatrices,leafMatricesSec,&matricesSF);CHKERRQ(ierr); 2621 ierr = PetscSFDestroy(&coarseToFineEmbedded);CHKERRQ(ierr); 2622 ierr = PetscFree(remoteOffsetsIndices);CHKERRQ(ierr); 2623 ierr = PetscFree(remoteOffsetsMatrices);CHKERRQ(ierr); 2624 ierr = PetscSectionGetStorageSize(leafIndicesSec,&numLeafIndices);CHKERRQ(ierr); 2625 ierr = PetscSectionGetStorageSize(leafMatricesSec,&numLeafMatrices);CHKERRQ(ierr); 2626 ierr = PetscMalloc2(numLeafIndices,&leafIndices,numLeafMatrices,&leafMatrices);CHKERRQ(ierr); 2627 ierr = PetscSFBcastBegin(indicesSF,MPIU_INT,rootIndices,leafIndices);CHKERRQ(ierr); 2628 ierr = PetscSFBcastBegin(matricesSF,MPIU_SCALAR,rootMatrices,leafMatrices);CHKERRQ(ierr); 2629 ierr = PetscSFBcastEnd(indicesSF,MPIU_INT,rootIndices,leafIndices);CHKERRQ(ierr); 2630 ierr = PetscSFBcastEnd(matricesSF,MPIU_SCALAR,rootMatrices,leafMatrices);CHKERRQ(ierr); 2631 ierr = PetscSFDestroy(&matricesSF);CHKERRQ(ierr); 2632 ierr = PetscSFDestroy(&indicesSF);CHKERRQ(ierr); 2633 ierr = PetscFree2(rootIndices,rootMatrices);CHKERRQ(ierr); 2634 ierr = PetscSectionDestroy(&rootIndicesSec);CHKERRQ(ierr); 2635 ierr = PetscSectionDestroy(&rootMatricesSec);CHKERRQ(ierr); 2636 } 2637 /* count to preallocate */ 2638 ierr = DMGetDefaultSection(fine,&localFine);CHKERRQ(ierr); 2639 { 2640 PetscInt nGlobal; 2641 PetscInt *dnnz, *onnz; 2642 PetscLayout rowMap, colMap; 2643 PetscInt rowStart, rowEnd, colStart, colEnd; 2644 PetscInt maxDof; 2645 PetscInt *rowIndices; 2646 DM refTree; 2647 PetscInt **refPointFieldN; 2648 PetscScalar ***refPointFieldMats; 2649 PetscSection refConSec, refAnSec; 2650 PetscInt pRefStart,pRefEnd,maxConDof,maxColumns,leafStart,leafEnd; 2651 PetscScalar *pointWork; 2652 2653 ierr = PetscSectionGetConstrainedStorageSize(globalFine,&nGlobal);CHKERRQ(ierr); 2654 ierr = PetscCalloc2(nGlobal,&dnnz,nGlobal,&onnz);CHKERRQ(ierr); 2655 ierr = MatGetLayouts(mat,&rowMap,&colMap);CHKERRQ(ierr); 2656 ierr = PetscLayoutSetUp(rowMap);CHKERRQ(ierr); 2657 ierr = PetscLayoutSetUp(colMap);CHKERRQ(ierr); 2658 ierr = PetscLayoutGetRange(rowMap,&rowStart,&rowEnd);CHKERRQ(ierr); 2659 ierr = PetscLayoutGetRange(colMap,&colStart,&colEnd);CHKERRQ(ierr); 2660 ierr = PetscSectionGetMaxDof(globalFine,&maxDof);CHKERRQ(ierr); 2661 ierr = PetscSectionGetChart(leafIndicesSec,&leafStart,&leafEnd);CHKERRQ(ierr); 2662 ierr = DMGetWorkArray(fine,maxDof,PETSC_INT,&rowIndices);CHKERRQ(ierr); 2663 for (p = leafStart; p < leafEnd; p++) { 2664 PetscInt gDof, gcDof, gOff; 2665 PetscInt numColIndices, pIndOff, *pInd; 2666 PetscInt matSize; 2667 PetscInt i; 2668 2669 ierr = PetscSectionGetDof(globalFine,p,&gDof);CHKERRQ(ierr); 2670 ierr = PetscSectionGetConstraintDof(globalFine,p,&gcDof);CHKERRQ(ierr); 2671 if ((gDof - gcDof) <= 0) { 2672 continue; 2673 } 2674 ierr = PetscSectionGetOffset(globalFine,p,&gOff);CHKERRQ(ierr); 2675 if (gOff < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"I though having global dofs meant a non-negative offset"); 2676 if ((gOff < rowStart) || ((gOff + gDof - gcDof) > rowEnd)) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"I thought the row map would constrain the global dofs"); 2677 ierr = PetscSectionGetDof(leafIndicesSec,p,&numColIndices);CHKERRQ(ierr); 2678 ierr = PetscSectionGetOffset(leafIndicesSec,p,&pIndOff);CHKERRQ(ierr); 2679 numColIndices -= 2 * numFields; 2680 if (numColIndices <= 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"global fine dof with no dofs to interpolate from"); 2681 pInd = &leafIndices[pIndOff]; 2682 offsets[0] = 0; 2683 offsetsCopy[0] = 0; 2684 newOffsets[0] = 0; 2685 newOffsetsCopy[0] = 0; 2686 if (numFields) { 2687 PetscInt f; 2688 for (f = 0; f < numFields; f++) { 2689 PetscInt rowDof; 2690 2691 ierr = PetscSectionGetFieldDof(localFine,p,f,&rowDof);CHKERRQ(ierr); 2692 offsets[f + 1] = offsets[f] + rowDof; 2693 offsetsCopy[f + 1] = offsets[f + 1]; 2694 newOffsets[f + 1] = pInd[numColIndices + numFields + f]; 2695 numD[f] = 0; 2696 numO[f] = 0; 2697 } 2698 ierr = DMPlexGetIndicesPointFields_Internal(localFine,p,gOff,offsetsCopy,PETSC_FALSE,0,rowIndices);CHKERRQ(ierr); 2699 for (f = 0; f < numFields; f++) { 2700 PetscInt colOffset = newOffsets[f]; 2701 PetscInt numFieldCols = newOffsets[f + 1] - newOffsets[f]; 2702 2703 for (i = 0; i < numFieldCols; i++) { 2704 PetscInt gInd = pInd[i + colOffset]; 2705 2706 if (gInd >= colStart && gInd < colEnd) { 2707 numD[f]++; 2708 } 2709 else if (gInd >= 0) { /* negative means non-entry */ 2710 numO[f]++; 2711 } 2712 } 2713 } 2714 } 2715 else { 2716 ierr = DMPlexGetIndicesPoint_Internal(localFine,p,gOff,offsetsCopy,PETSC_FALSE,0,rowIndices);CHKERRQ(ierr); 2717 numD[0] = 0; 2718 numO[0] = 0; 2719 for (i = 0; i < numColIndices; i++) { 2720 PetscInt gInd = pInd[i]; 2721 2722 if (gInd >= colStart && gInd < colEnd) { 2723 numD[0]++; 2724 } 2725 else if (gInd >= 0) { /* negative means non-entry */ 2726 numO[0]++; 2727 } 2728 } 2729 } 2730 ierr = PetscSectionGetDof(leafMatricesSec,p,&matSize);CHKERRQ(ierr); 2731 if (!matSize) { /* incoming matrix is identity */ 2732 PetscInt childId; 2733 2734 childId = childIds[p-pStartF]; 2735 if (childId < 0) { /* no child interpolation: one nnz per */ 2736 if (numFields) { 2737 PetscInt f; 2738 for (f = 0; f < numFields; f++) { 2739 PetscInt numRows = offsets[f+1] - offsets[f], row; 2740 for (row = 0; row < numRows; row++) { 2741 PetscInt gIndCoarse = pInd[newOffsets[f] + row]; 2742 PetscInt gIndFine = rowIndices[offsets[f] + row]; 2743 if (gIndCoarse >= colStart && gIndCoarse < colEnd) { /* local */ 2744 if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs"); 2745 dnnz[gIndFine - rowStart] = 1; 2746 } 2747 else if (gIndCoarse >= 0) { /* remote */ 2748 if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs"); 2749 onnz[gIndFine - rowStart] = 1; 2750 } 2751 else { /* constrained */ 2752 if (gIndFine >= 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs"); 2753 } 2754 } 2755 } 2756 } 2757 else { 2758 PetscInt i; 2759 for (i = 0; i < gDof; i++) { 2760 PetscInt gIndCoarse = pInd[i]; 2761 PetscInt gIndFine = rowIndices[i]; 2762 if (gIndCoarse >= colStart && gIndCoarse < colEnd) { /* local */ 2763 if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs"); 2764 dnnz[gIndFine - rowStart] = 1; 2765 } 2766 else if (gIndCoarse >= 0) { /* remote */ 2767 if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs"); 2768 onnz[gIndFine - rowStart] = 1; 2769 } 2770 else { /* constrained */ 2771 if (gIndFine >= 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs"); 2772 } 2773 } 2774 } 2775 } 2776 else { /* interpolate from all */ 2777 if (numFields) { 2778 PetscInt f; 2779 for (f = 0; f < numFields; f++) { 2780 PetscInt numRows = offsets[f+1] - offsets[f], row; 2781 for (row = 0; row < numRows; row++) { 2782 PetscInt gIndFine = rowIndices[offsets[f] + row]; 2783 if (gIndFine >= 0) { 2784 if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs"); 2785 dnnz[gIndFine - rowStart] = numD[f]; 2786 onnz[gIndFine - rowStart] = numO[f]; 2787 } 2788 } 2789 } 2790 } 2791 else { 2792 PetscInt i; 2793 for (i = 0; i < gDof; i++) { 2794 PetscInt gIndFine = rowIndices[i]; 2795 if (gIndFine >= 0) { 2796 if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs"); 2797 dnnz[gIndFine - rowStart] = numD[0]; 2798 onnz[gIndFine - rowStart] = numO[0]; 2799 } 2800 } 2801 } 2802 } 2803 } 2804 else { /* interpolate from all */ 2805 if (numFields) { 2806 PetscInt f; 2807 for (f = 0; f < numFields; f++) { 2808 PetscInt numRows = offsets[f+1] - offsets[f], row; 2809 for (row = 0; row < numRows; row++) { 2810 PetscInt gIndFine = rowIndices[offsets[f] + row]; 2811 if (gIndFine >= 0) { 2812 if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs"); 2813 dnnz[gIndFine - rowStart] = numD[f]; 2814 onnz[gIndFine - rowStart] = numO[f]; 2815 } 2816 } 2817 } 2818 } 2819 else { /* every dof get a full row */ 2820 PetscInt i; 2821 for (i = 0; i < gDof; i++) { 2822 PetscInt gIndFine = rowIndices[i]; 2823 if (gIndFine >= 0) { 2824 if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs"); 2825 dnnz[gIndFine - rowStart] = numD[0]; 2826 onnz[gIndFine - rowStart] = numO[0]; 2827 } 2828 } 2829 } 2830 } 2831 } 2832 ierr = MatXAIJSetPreallocation(mat,1,dnnz,onnz,NULL,NULL);CHKERRQ(ierr); 2833 ierr = PetscFree2(dnnz,onnz);CHKERRQ(ierr); 2834 2835 ierr = DMPlexGetReferenceTree(fine,&refTree);CHKERRQ(ierr); 2836 ierr = DMPlexReferenceTreeGetChildrenMatrices(refTree,&refPointFieldMats,&refPointFieldN);CHKERRQ(ierr); 2837 ierr = DMGetDefaultConstraints(refTree,&refConSec,NULL);CHKERRQ(ierr); 2838 ierr = DMPlexGetAnchors(refTree,&refAnSec,NULL);CHKERRQ(ierr); 2839 ierr = PetscSectionGetChart(refConSec,&pRefStart,&pRefEnd);CHKERRQ(ierr); 2840 ierr = PetscSectionGetMaxDof(refConSec,&maxConDof);CHKERRQ(ierr); 2841 ierr = PetscSectionGetMaxDof(leafIndicesSec,&maxColumns);CHKERRQ(ierr); 2842 ierr = PetscMalloc1(maxConDof*maxColumns,&pointWork);CHKERRQ(ierr); 2843 for (p = leafStart; p < leafEnd; p++) { 2844 PetscInt gDof, gcDof, gOff; 2845 PetscInt numColIndices, pIndOff, *pInd; 2846 PetscInt matSize; 2847 PetscInt childId; 2848 2849 2850 ierr = PetscSectionGetDof(globalFine,p,&gDof);CHKERRQ(ierr); 2851 ierr = PetscSectionGetConstraintDof(globalFine,p,&gcDof);CHKERRQ(ierr); 2852 if ((gDof - gcDof) <= 0) { 2853 continue; 2854 } 2855 childId = childIds[p-pStartF]; 2856 ierr = PetscSectionGetOffset(globalFine,p,&gOff);CHKERRQ(ierr); 2857 ierr = PetscSectionGetDof(leafIndicesSec,p,&numColIndices);CHKERRQ(ierr); 2858 ierr = PetscSectionGetOffset(leafIndicesSec,p,&pIndOff);CHKERRQ(ierr); 2859 numColIndices -= 2 * numFields; 2860 pInd = &leafIndices[pIndOff]; 2861 offsets[0] = 0; 2862 offsetsCopy[0] = 0; 2863 newOffsets[0] = 0; 2864 newOffsetsCopy[0] = 0; 2865 rowOffsets[0] = 0; 2866 if (numFields) { 2867 PetscInt f; 2868 for (f = 0; f < numFields; f++) { 2869 PetscInt rowDof; 2870 2871 ierr = PetscSectionGetFieldDof(localFine,p,f,&rowDof);CHKERRQ(ierr); 2872 offsets[f + 1] = offsets[f] + rowDof; 2873 offsetsCopy[f + 1] = offsets[f + 1]; 2874 rowOffsets[f + 1] = pInd[numColIndices + f]; 2875 newOffsets[f + 1] = pInd[numColIndices + numFields + f]; 2876 } 2877 ierr = DMPlexGetIndicesPointFields_Internal(localFine,p,gOff,offsetsCopy,PETSC_FALSE,0,rowIndices);CHKERRQ(ierr); 2878 } 2879 else { 2880 ierr = DMPlexGetIndicesPoint_Internal(localFine,p,gOff,offsetsCopy,PETSC_FALSE,0,rowIndices);CHKERRQ(ierr); 2881 } 2882 ierr = PetscSectionGetDof(leafMatricesSec,p,&matSize);CHKERRQ(ierr); 2883 if (!matSize) { /* incoming matrix is identity */ 2884 if (childId < 0) { /* no child interpolation: scatter */ 2885 if (numFields) { 2886 PetscInt f; 2887 for (f = 0; f < numFields; f++) { 2888 PetscInt numRows = offsets[f+1] - offsets[f], row; 2889 for (row = 0; row < numRows; row++) { 2890 ierr = MatSetValue(mat,rowIndices[offsets[f]+row],pInd[newOffsets[f]+row],1.,INSERT_VALUES);CHKERRQ(ierr); 2891 } 2892 } 2893 } 2894 else { 2895 PetscInt numRows = gDof, row; 2896 for (row = 0; row < numRows; row++) { 2897 ierr = MatSetValue(mat,rowIndices[row],pInd[row],1.,INSERT_VALUES);CHKERRQ(ierr); 2898 } 2899 } 2900 } 2901 else { /* interpolate from all */ 2902 if (numFields) { 2903 PetscInt f; 2904 for (f = 0; f < numFields; f++) { 2905 PetscInt numRows = offsets[f+1] - offsets[f]; 2906 PetscInt numCols = newOffsets[f + 1] - newOffsets[f]; 2907 ierr = MatSetValues(mat,numRows,&rowIndices[offsets[f]],numCols,&pInd[newOffsets[f]],refPointFieldMats[childId - pRefStart][f],INSERT_VALUES);CHKERRQ(ierr); 2908 } 2909 } 2910 else { 2911 ierr = MatSetValues(mat,gDof,rowIndices,numColIndices,pInd,refPointFieldMats[childId - pRefStart][0],INSERT_VALUES);CHKERRQ(ierr); 2912 } 2913 } 2914 } 2915 else { /* interpolate from all */ 2916 PetscInt pMatOff; 2917 PetscScalar *pMat; 2918 2919 ierr = PetscSectionGetOffset(leafMatricesSec,p,&pMatOff);CHKERRQ(ierr); 2920 pMat = &leafMatrices[pMatOff]; 2921 if (childId < 0) { /* copy the incoming matrix */ 2922 if (numFields) { 2923 PetscInt f, count; 2924 for (f = 0, count = 0; f < numFields; f++) { 2925 PetscInt numRows = offsets[f+1]-offsets[f]; 2926 PetscInt numCols = newOffsets[f+1]-newOffsets[f]; 2927 PetscInt numInRows = rowOffsets[f+1]-rowOffsets[f]; 2928 PetscScalar *inMat = &pMat[count]; 2929 2930 ierr = MatSetValues(mat,numRows,&rowIndices[offsets[f]],numCols,&pInd[newOffsets[f]],inMat,INSERT_VALUES);CHKERRQ(ierr); 2931 count += numCols * numInRows; 2932 } 2933 } 2934 else { 2935 ierr = MatSetValues(mat,gDof,rowIndices,numColIndices,pInd,pMat,INSERT_VALUES);CHKERRQ(ierr); 2936 } 2937 } 2938 else { /* multiply the incoming matrix by the child interpolation */ 2939 if (numFields) { 2940 PetscInt f, count; 2941 for (f = 0, count = 0; f < numFields; f++) { 2942 PetscInt numRows = offsets[f+1]-offsets[f]; 2943 PetscInt numCols = newOffsets[f+1]-newOffsets[f]; 2944 PetscInt numInRows = rowOffsets[f+1]-rowOffsets[f]; 2945 PetscScalar *inMat = &pMat[count]; 2946 PetscInt i, j, k; 2947 if (refPointFieldN[childId - pRefStart][f] != numInRows) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Point constraint matrix multiply dimension mismatch"); 2948 for (i = 0; i < numRows; i++) { 2949 for (j = 0; j < numCols; j++) { 2950 PetscScalar val = 0.; 2951 for (k = 0; k < numInRows; k++) { 2952 val += refPointFieldMats[childId - pRefStart][f][i * numInRows + k] * inMat[k * numCols + j]; 2953 } 2954 pointWork[i * numCols + j] = val; 2955 } 2956 } 2957 ierr = MatSetValues(mat,numRows,&rowIndices[offsets[f]],numCols,&pInd[newOffsets[f]],pointWork,INSERT_VALUES);CHKERRQ(ierr); 2958 count += numCols * numInRows; 2959 } 2960 } 2961 else { /* every dof gets a full row */ 2962 PetscInt numRows = gDof; 2963 PetscInt numCols = numColIndices; 2964 PetscInt numInRows = matSize / numColIndices; 2965 PetscInt i, j, k; 2966 if (refPointFieldN[childId - pRefStart][0] != numInRows) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Point constraint matrix multiply dimension mismatch"); 2967 for (i = 0; i < numRows; i++) { 2968 for (j = 0; j < numCols; j++) { 2969 PetscScalar val = 0.; 2970 for (k = 0; k < numInRows; k++) { 2971 val += refPointFieldMats[childId - pRefStart][0][i * numInRows + k] * pMat[k * numCols + j]; 2972 } 2973 pointWork[i * numCols + j] = val; 2974 } 2975 } 2976 ierr = MatSetValues(mat,numRows,rowIndices,numCols,pInd,pointWork,INSERT_VALUES);CHKERRQ(ierr); 2977 } 2978 } 2979 } 2980 } 2981 ierr = DMPlexReferenceTreeRestoreChildrenMatrices(refTree,&refPointFieldMats,&refPointFieldN);CHKERRQ(ierr); 2982 ierr = DMRestoreWorkArray(fine,maxDof,PETSC_INT,&rowIndices);CHKERRQ(ierr); 2983 ierr = PetscFree(pointWork);CHKERRQ(ierr); 2984 } 2985 ierr = MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2986 ierr = MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2987 ierr = PetscSectionDestroy(&leafIndicesSec);CHKERRQ(ierr); 2988 ierr = PetscSectionDestroy(&leafMatricesSec);CHKERRQ(ierr); 2989 ierr = PetscFree2(leafIndices,leafMatrices);CHKERRQ(ierr); 2990 ierr = PetscFree7(offsets,offsetsCopy,newOffsets,newOffsetsCopy,rowOffsets,numD,numO);CHKERRQ(ierr); 2991 ierr = ISRestoreIndices(aIS,&anchors);CHKERRQ(ierr); 2992 PetscFunctionReturn(0); 2993 } 2994 2995 #undef __FUNCT__ 2996 #define __FUNCT__ "DMPlexComputeInjectorReferenceTree" 2997 /* 2998 * Assuming a nodal basis (w.r.t. the dual basis) basis: 2999 * 3000 * for each coarse dof \phi^c_i: 3001 * for each quadrature point (w_l,x_l) in the dual basis definition of \phi^c_i: 3002 * for each fine dof \phi^f_j; 3003 * a_{i,j} = 0; 3004 * for each fine dof \phi^f_k: 3005 * a_{i,j} += interp_{i,k} * \phi^f_k(x_l) * \phi^f_j(x_l) * w_l 3006 * [^^^ this is = \phi^c_i ^^^] 3007 */ 3008 PetscErrorCode DMPlexComputeInjectorReferenceTree(DM refTree, Mat *inj) 3009 { 3010 PetscDS ds; 3011 PetscSection section, cSection; 3012 DMLabel canonical, depth; 3013 Mat cMat, mat; 3014 PetscInt *nnz; 3015 PetscInt f, dim, numFields, numSecFields, p, pStart, pEnd, cStart, cEnd; 3016 PetscInt m, n; 3017 PetscScalar *pointScalar; 3018 PetscReal *v0, *v0parent, *vtmp, *J, *Jparent, *invJ, *pointRef, detJ, detJparent; 3019 PetscErrorCode ierr; 3020 3021 PetscFunctionBegin; 3022 ierr = DMGetDefaultSection(refTree,§ion);CHKERRQ(ierr); 3023 ierr = DMGetDimension(refTree, &dim);CHKERRQ(ierr); 3024 ierr = PetscMalloc6(dim,&v0,dim,&v0parent,dim,&vtmp,dim*dim,&J,dim*dim,&Jparent,dim*dim,&invJ);CHKERRQ(ierr); 3025 ierr = PetscMalloc2(dim,&pointScalar,dim,&pointRef);CHKERRQ(ierr); 3026 ierr = DMGetDS(refTree,&ds);CHKERRQ(ierr); 3027 ierr = PetscDSGetNumFields(ds,&numFields);CHKERRQ(ierr); 3028 ierr = PetscSectionGetNumFields(section,&numSecFields);CHKERRQ(ierr); 3029 ierr = DMGetLabel(refTree,"canonical",&canonical);CHKERRQ(ierr); 3030 ierr = DMGetLabel(refTree,"depth",&depth);CHKERRQ(ierr); 3031 ierr = DMGetDefaultConstraints(refTree,&cSection,&cMat);CHKERRQ(ierr); 3032 ierr = DMPlexGetChart(refTree, &pStart, &pEnd);CHKERRQ(ierr); 3033 ierr = DMPlexGetHeightStratum(refTree, 0, &cStart, &cEnd);CHKERRQ(ierr); 3034 ierr = MatGetSize(cMat,&n,&m);CHKERRQ(ierr); /* the injector has transpose sizes from the constraint matrix */ 3035 /* Step 1: compute non-zero pattern. A proper subset of constraint matrix non-zero */ 3036 ierr = PetscCalloc1(m,&nnz);CHKERRQ(ierr); 3037 for (p = pStart; p < pEnd; p++) { /* a point will have non-zeros if it is canonical, it has dofs, and its children have dofs */ 3038 const PetscInt *children; 3039 PetscInt numChildren; 3040 PetscInt i, numChildDof, numSelfDof; 3041 3042 if (canonical) { 3043 PetscInt pCanonical; 3044 ierr = DMLabelGetValue(canonical,p,&pCanonical);CHKERRQ(ierr); 3045 if (p != pCanonical) continue; 3046 } 3047 ierr = DMPlexGetTreeChildren(refTree,p,&numChildren,&children);CHKERRQ(ierr); 3048 if (!numChildren) continue; 3049 for (i = 0, numChildDof = 0; i < numChildren; i++) { 3050 PetscInt child = children[i]; 3051 PetscInt dof; 3052 3053 ierr = PetscSectionGetDof(section,child,&dof);CHKERRQ(ierr); 3054 numChildDof += dof; 3055 } 3056 ierr = PetscSectionGetDof(section,p,&numSelfDof);CHKERRQ(ierr); 3057 if (!numChildDof || !numSelfDof) continue; 3058 for (f = 0; f < numFields; f++) { 3059 PetscInt selfOff; 3060 3061 if (numSecFields) { /* count the dofs for just this field */ 3062 for (i = 0, numChildDof = 0; i < numChildren; i++) { 3063 PetscInt child = children[i]; 3064 PetscInt dof; 3065 3066 ierr = PetscSectionGetFieldDof(section,child,f,&dof);CHKERRQ(ierr); 3067 numChildDof += dof; 3068 } 3069 ierr = PetscSectionGetFieldDof(section,p,f,&numSelfDof);CHKERRQ(ierr); 3070 ierr = PetscSectionGetFieldOffset(section,p,f,&selfOff);CHKERRQ(ierr); 3071 } 3072 else { 3073 ierr = PetscSectionGetOffset(section,p,&selfOff);CHKERRQ(ierr); 3074 } 3075 for (i = 0; i < numSelfDof; i++) { 3076 nnz[selfOff + i] = numChildDof; 3077 } 3078 } 3079 } 3080 ierr = MatCreateAIJ(PETSC_COMM_SELF,m,n,m,n,-1,nnz,-1,NULL,&mat);CHKERRQ(ierr); 3081 ierr = PetscFree(nnz);CHKERRQ(ierr); 3082 /* Setp 2: compute entries */ 3083 for (p = pStart; p < pEnd; p++) { 3084 const PetscInt *children; 3085 PetscInt numChildren; 3086 PetscInt i, numChildDof, numSelfDof; 3087 3088 /* same conditions about when entries occur */ 3089 if (canonical) { 3090 PetscInt pCanonical; 3091 ierr = DMLabelGetValue(canonical,p,&pCanonical);CHKERRQ(ierr); 3092 if (p != pCanonical) continue; 3093 } 3094 ierr = DMPlexGetTreeChildren(refTree,p,&numChildren,&children);CHKERRQ(ierr); 3095 if (!numChildren) continue; 3096 for (i = 0, numChildDof = 0; i < numChildren; i++) { 3097 PetscInt child = children[i]; 3098 PetscInt dof; 3099 3100 ierr = PetscSectionGetDof(section,child,&dof);CHKERRQ(ierr); 3101 numChildDof += dof; 3102 } 3103 ierr = PetscSectionGetDof(section,p,&numSelfDof);CHKERRQ(ierr); 3104 if (!numChildDof || !numSelfDof) continue; 3105 3106 for (f = 0; f < numFields; f++) { 3107 PetscInt selfOff, fComp, numSelfShapes, numChildShapes, parentCell; 3108 PetscInt cellShapeOff; 3109 PetscObject disc; 3110 PetscDualSpace dsp; 3111 PetscClassId classId; 3112 PetscScalar *pointMat; 3113 PetscInt *matRows, *matCols; 3114 PetscInt pO = PETSC_MIN_INT; 3115 const PetscInt *depthNumDof; 3116 3117 if (numSecFields) { 3118 for (i = 0, numChildDof = 0; i < numChildren; i++) { 3119 PetscInt child = children[i]; 3120 PetscInt dof; 3121 3122 ierr = PetscSectionGetFieldDof(section,child,f,&dof);CHKERRQ(ierr); 3123 numChildDof += dof; 3124 } 3125 ierr = PetscSectionGetFieldDof(section,p,f,&numSelfDof);CHKERRQ(ierr); 3126 ierr = PetscSectionGetFieldOffset(section,p,f,&selfOff);CHKERRQ(ierr); 3127 ierr = PetscSectionGetFieldComponents(section,f,&fComp);CHKERRQ(ierr); 3128 } 3129 else { 3130 ierr = PetscSectionGetOffset(section,p,&selfOff);CHKERRQ(ierr); 3131 fComp = 1; 3132 } 3133 numSelfShapes = numSelfDof / fComp; 3134 numChildShapes = numChildDof / fComp; 3135 3136 /* find a cell whose closure contains p */ 3137 if (p >= cStart && p < cEnd) { 3138 parentCell = p; 3139 } 3140 else { 3141 PetscInt *star = NULL; 3142 PetscInt numStar; 3143 3144 parentCell = -1; 3145 ierr = DMPlexGetTransitiveClosure(refTree,p,PETSC_FALSE,&numStar,&star);CHKERRQ(ierr); 3146 for (i = numStar - 1; i >= 0; i--) { 3147 PetscInt c = star[2 * i]; 3148 3149 if (c >= cStart && c < cEnd) { 3150 parentCell = c; 3151 break; 3152 } 3153 } 3154 ierr = DMPlexRestoreTransitiveClosure(refTree,p,PETSC_FALSE,&numStar,&star);CHKERRQ(ierr); 3155 } 3156 /* determine the offset of p's shape functions withing parentCell's shape functions */ 3157 ierr = PetscDSGetDiscretization(ds,f,&disc);CHKERRQ(ierr); 3158 ierr = PetscObjectGetClassId(disc,&classId);CHKERRQ(ierr); 3159 if (classId == PETSCFE_CLASSID) { 3160 ierr = PetscFEGetDualSpace((PetscFE)disc,&dsp);CHKERRQ(ierr); 3161 } 3162 else if (classId == PETSCFV_CLASSID) { 3163 ierr = PetscFVGetDualSpace((PetscFV)disc,&dsp);CHKERRQ(ierr); 3164 } 3165 else { 3166 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Unsupported discretization object");CHKERRQ(ierr); 3167 } 3168 ierr = PetscDualSpaceGetNumDof(dsp,&depthNumDof);CHKERRQ(ierr); 3169 { 3170 PetscInt *closure = NULL; 3171 PetscInt numClosure; 3172 3173 ierr = DMPlexGetTransitiveClosure(refTree,parentCell,PETSC_TRUE,&numClosure,&closure);CHKERRQ(ierr); 3174 for (i = 0, cellShapeOff = 0; i < numClosure; i++) { 3175 PetscInt point = closure[2 * i], pointDepth; 3176 3177 pO = closure[2 * i + 1]; 3178 if (point == p) break; 3179 ierr = DMLabelGetValue(depth,point,&pointDepth);CHKERRQ(ierr); 3180 cellShapeOff += depthNumDof[pointDepth]; 3181 } 3182 ierr = DMPlexRestoreTransitiveClosure(refTree,parentCell,PETSC_TRUE,&numClosure,&closure);CHKERRQ(ierr); 3183 } 3184 3185 ierr = DMGetWorkArray(refTree, numSelfShapes * numChildShapes, PETSC_SCALAR,&pointMat);CHKERRQ(ierr); 3186 ierr = DMGetWorkArray(refTree, numSelfShapes + numChildShapes, PETSC_INT,&matRows);CHKERRQ(ierr); 3187 matCols = matRows + numSelfShapes; 3188 for (i = 0; i < numSelfShapes; i++) { 3189 matRows[i] = selfOff + i * fComp; 3190 } 3191 { 3192 PetscInt colOff = 0; 3193 3194 for (i = 0; i < numChildren; i++) { 3195 PetscInt child = children[i]; 3196 PetscInt dof, off, j; 3197 3198 if (numSecFields) { 3199 ierr = PetscSectionGetFieldDof(cSection,child,f,&dof);CHKERRQ(ierr); 3200 ierr = PetscSectionGetFieldOffset(cSection,child,f,&off);CHKERRQ(ierr); 3201 } 3202 else { 3203 ierr = PetscSectionGetDof(cSection,child,&dof);CHKERRQ(ierr); 3204 ierr = PetscSectionGetOffset(cSection,child,&off);CHKERRQ(ierr); 3205 } 3206 3207 for (j = 0; j < dof / fComp; j++) { 3208 matCols[colOff++] = off + j * fComp; 3209 } 3210 } 3211 } 3212 if (classId == PETSCFE_CLASSID) { 3213 PetscFE fe = (PetscFE) disc; 3214 PetscInt fSize; 3215 3216 ierr = PetscFEGetDualSpace(fe,&dsp);CHKERRQ(ierr); 3217 ierr = PetscDualSpaceGetDimension(dsp,&fSize);CHKERRQ(ierr); 3218 for (i = 0; i < numSelfShapes; i++) { /* for every shape function */ 3219 PetscQuadrature q; 3220 PetscInt dim, numPoints, j, k; 3221 const PetscReal *points; 3222 const PetscReal *weights; 3223 PetscInt *closure = NULL; 3224 PetscInt numClosure; 3225 PetscInt parentCellShapeDof = cellShapeOff + (pO < 0 ? (numSelfShapes - 1 - i) : i); 3226 PetscReal *Bparent; 3227 3228 ierr = PetscDualSpaceGetFunctional(dsp,parentCellShapeDof,&q);CHKERRQ(ierr); 3229 ierr = PetscQuadratureGetData(q,&dim,&numPoints,&points,&weights);CHKERRQ(ierr); 3230 ierr = PetscFEGetTabulation(fe,numPoints,points,&Bparent,NULL,NULL);CHKERRQ(ierr); /* I'm expecting a nodal basis: weights[:]' * Bparent[:,cellShapeDof] = 1. */ 3231 for (k = 0; k < numChildShapes; k++) { 3232 pointMat[numChildShapes * i + k] = 0.; 3233 } 3234 for (j = 0; j < numPoints; j++) { 3235 PetscInt childCell = -1; 3236 PetscReal parentValAtPoint; 3237 const PetscReal *pointReal = &points[dim * j]; 3238 const PetscScalar *point; 3239 PetscReal *Bchild; 3240 PetscInt childCellShapeOff, pointMatOff; 3241 #if defined(PETSC_USE_COMPLEX) 3242 PetscInt d; 3243 3244 for (d = 0; d < dim; d++) { 3245 pointScalar[d] = points[dim * j + d]; 3246 } 3247 point = pointScalar; 3248 #else 3249 point = pointReal; 3250 #endif 3251 3252 parentValAtPoint = Bparent[(fSize * j + parentCellShapeDof) * fComp]; 3253 3254 for (k = 0; k < numChildren; k++) { /* locate the point in a child's star cell*/ 3255 PetscInt child = children[k]; 3256 PetscInt *star = NULL; 3257 PetscInt numStar, s; 3258 3259 ierr = DMPlexGetTransitiveClosure(refTree,child,PETSC_FALSE,&numStar,&star);CHKERRQ(ierr); 3260 for (s = numStar - 1; s >= 0; s--) { 3261 PetscInt c = star[2 * s]; 3262 3263 if (c < cStart || c >= cEnd) continue; 3264 ierr = DMPlexLocatePoint_Internal(refTree,dim,point,c,&childCell);CHKERRQ(ierr); 3265 if (childCell >= 0) break; 3266 } 3267 ierr = DMPlexRestoreTransitiveClosure(refTree,child,PETSC_FALSE,&numStar,&star);CHKERRQ(ierr); 3268 if (childCell >= 0) break; 3269 } 3270 if (childCell < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Could not locate quadrature point");CHKERRQ(ierr); 3271 ierr = DMPlexComputeCellGeometryFEM(refTree, childCell, NULL, v0, J, invJ, &detJ);CHKERRQ(ierr); 3272 ierr = DMPlexComputeCellGeometryFEM(refTree, parentCell, NULL, v0parent, Jparent, NULL, &detJparent);CHKERRQ(ierr); 3273 CoordinatesRefToReal(dim, dim, v0parent, Jparent, pointReal, vtmp); 3274 CoordinatesRealToRef(dim, dim, v0, invJ, vtmp, pointRef); 3275 3276 ierr = PetscFEGetTabulation(fe,1,pointRef,&Bchild,NULL,NULL);CHKERRQ(ierr); 3277 ierr = DMPlexGetTransitiveClosure(refTree,childCell,PETSC_TRUE,&numClosure,&closure);CHKERRQ(ierr); 3278 for (k = 0, pointMatOff = 0; k < numChildren; k++) { /* point is located in cell => child dofs support at point are in closure of cell */ 3279 PetscInt child = children[k], childDepth, childDof, childO = PETSC_MIN_INT; 3280 PetscInt l; 3281 3282 ierr = DMLabelGetValue(depth,child,&childDepth);CHKERRQ(ierr); 3283 childDof = depthNumDof[childDepth]; 3284 for (l = 0, childCellShapeOff = 0; l < numClosure; l++) { 3285 PetscInt point = closure[2 * l]; 3286 PetscInt pointDepth; 3287 3288 childO = closure[2 * l + 1]; 3289 if (point == child) break; 3290 ierr = DMLabelGetValue(depth,point,&pointDepth);CHKERRQ(ierr); 3291 childCellShapeOff += depthNumDof[pointDepth]; 3292 } 3293 if (l == numClosure) { 3294 pointMatOff += childDof; 3295 continue; /* child is not in the closure of the cell: has nothing to contribute to this point */ 3296 } 3297 for (l = 0; l < childDof; l++) { 3298 PetscInt childCellDof = childCellShapeOff + (childO ? (childDof - 1 - l) : l); 3299 PetscReal childValAtPoint = Bchild[childCellDof * fComp]; 3300 3301 pointMat[i * numChildShapes + pointMatOff + l] += weights[j] * parentValAtPoint * childValAtPoint; 3302 } 3303 pointMatOff += childDof; 3304 } 3305 ierr = DMPlexRestoreTransitiveClosure(refTree,childCell,PETSC_TRUE,&numClosure,&closure);CHKERRQ(ierr); 3306 ierr = PetscFERestoreTabulation(fe,1,pointRef,&Bchild,NULL,NULL);CHKERRQ(ierr); 3307 } 3308 ierr = PetscFERestoreTabulation(fe,numPoints,points,&Bparent,NULL,NULL);CHKERRQ(ierr); 3309 } 3310 } 3311 else { /* just the volume-weighted averages of the children */ 3312 PetscInt childShapeOff; 3313 PetscReal parentVol; 3314 3315 ierr = DMPlexComputeCellGeometryFVM(refTree, p, &parentVol, NULL, NULL);CHKERRQ(ierr); 3316 for (i = 0, childShapeOff = 0; i < numChildren; i++) { 3317 PetscInt child = children[i]; 3318 PetscReal childVol; 3319 3320 if (child < cStart || child >= cEnd) continue; 3321 ierr = DMPlexComputeCellGeometryFVM(refTree, child, &childVol, NULL, NULL);CHKERRQ(ierr); 3322 pointMat[childShapeOff] = childVol / parentVol; 3323 childShapeOff++; 3324 } 3325 } 3326 /* Insert pointMat into mat */ 3327 for (i = 0; i < fComp; i++) { 3328 PetscInt j; 3329 ierr = MatSetValues(mat,numSelfShapes,matRows,numChildShapes,matCols,pointMat,INSERT_VALUES);CHKERRQ(ierr); 3330 3331 for (j = 0; j < numSelfShapes; j++) { 3332 matRows[j]++; 3333 } 3334 for (j = 0; j < numChildShapes; j++) { 3335 matCols[j]++; 3336 } 3337 } 3338 ierr = DMRestoreWorkArray(refTree, numSelfShapes + numChildShapes, PETSC_INT,&matRows);CHKERRQ(ierr); 3339 ierr = DMRestoreWorkArray(refTree, numSelfShapes * numChildShapes, PETSC_SCALAR,&pointMat);CHKERRQ(ierr); 3340 } 3341 } 3342 ierr = PetscFree6(v0,v0parent,vtmp,J,Jparent,invJ);CHKERRQ(ierr); 3343 ierr = PetscFree2(pointScalar,pointRef);CHKERRQ(ierr); 3344 ierr = MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3345 ierr = MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3346 *inj = mat; 3347 PetscFunctionReturn(0); 3348 } 3349 3350 #undef __FUNCT__ 3351 #define __FUNCT__ "DMPlexReferenceTreeGetChildrenMatrices_Injection" 3352 static PetscErrorCode DMPlexReferenceTreeGetChildrenMatrices_Injection(DM refTree, Mat inj, PetscScalar ****childrenMats) 3353 { 3354 PetscDS ds; 3355 PetscInt numFields, f, pRefStart, pRefEnd, p, *rows, *cols, maxDof; 3356 PetscScalar ***refPointFieldMats; 3357 PetscSection refConSec, refSection; 3358 PetscErrorCode ierr; 3359 3360 PetscFunctionBegin; 3361 ierr = DMGetDS(refTree,&ds);CHKERRQ(ierr); 3362 ierr = PetscDSGetNumFields(ds,&numFields);CHKERRQ(ierr); 3363 ierr = DMGetDefaultConstraints(refTree,&refConSec,NULL);CHKERRQ(ierr); 3364 ierr = DMGetDefaultSection(refTree,&refSection);CHKERRQ(ierr); 3365 ierr = PetscSectionGetChart(refConSec,&pRefStart,&pRefEnd);CHKERRQ(ierr); 3366 ierr = PetscMalloc1(pRefEnd-pRefStart,&refPointFieldMats);CHKERRQ(ierr); 3367 ierr = PetscSectionGetMaxDof(refConSec,&maxDof);CHKERRQ(ierr); 3368 ierr = PetscMalloc1(maxDof,&rows);CHKERRQ(ierr); 3369 ierr = PetscMalloc1(maxDof*maxDof,&cols);CHKERRQ(ierr); 3370 for (p = pRefStart; p < pRefEnd; p++) { 3371 PetscInt parent, pDof, parentDof; 3372 3373 ierr = DMPlexGetTreeParent(refTree,p,&parent,NULL);CHKERRQ(ierr); 3374 ierr = PetscSectionGetDof(refConSec,p,&pDof);CHKERRQ(ierr); 3375 ierr = PetscSectionGetDof(refSection,parent,&parentDof);CHKERRQ(ierr); 3376 if (!pDof || !parentDof || parent == p) continue; 3377 3378 ierr = PetscMalloc1(numFields,&refPointFieldMats[p-pRefStart]);CHKERRQ(ierr); 3379 for (f = 0; f < numFields; f++) { 3380 PetscInt cDof, cOff, numCols, r, fComp; 3381 PetscObject disc; 3382 PetscClassId id; 3383 PetscFE fe = NULL; 3384 PetscFV fv = NULL; 3385 3386 ierr = PetscDSGetDiscretization(ds,f,&disc);CHKERRQ(ierr); 3387 ierr = PetscObjectGetClassId(disc,&id);CHKERRQ(ierr); 3388 if (id == PETSCFE_CLASSID) { 3389 fe = (PetscFE) disc; 3390 ierr = PetscFEGetNumComponents(fe,&fComp);CHKERRQ(ierr); 3391 } 3392 else if (id == PETSCFV_CLASSID) { 3393 fv = (PetscFV) disc; 3394 ierr = PetscFVGetNumComponents(fv,&fComp);CHKERRQ(ierr); 3395 } 3396 else SETERRQ1(PetscObjectComm(disc),PETSC_ERR_ARG_UNKNOWN_TYPE, "PetscDS discretization id %d not recognized.", id); 3397 3398 if (numFields > 1) { 3399 ierr = PetscSectionGetFieldDof(refConSec,p,f,&cDof);CHKERRQ(ierr); 3400 ierr = PetscSectionGetFieldOffset(refConSec,p,f,&cOff);CHKERRQ(ierr); 3401 } 3402 else { 3403 ierr = PetscSectionGetDof(refConSec,p,&cDof);CHKERRQ(ierr); 3404 ierr = PetscSectionGetOffset(refConSec,p,&cOff);CHKERRQ(ierr); 3405 } 3406 3407 for (r = 0; r < cDof; r++) { 3408 rows[r] = cOff + r; 3409 } 3410 numCols = 0; 3411 { 3412 PetscInt aDof, aOff, j; 3413 3414 if (numFields > 1) { 3415 ierr = PetscSectionGetFieldDof(refSection,parent,f,&aDof);CHKERRQ(ierr); 3416 ierr = PetscSectionGetFieldOffset(refSection,parent,f,&aOff);CHKERRQ(ierr); 3417 } 3418 else { 3419 ierr = PetscSectionGetDof(refSection,parent,&aDof);CHKERRQ(ierr); 3420 ierr = PetscSectionGetOffset(refSection,parent,&aOff);CHKERRQ(ierr); 3421 } 3422 3423 for (j = 0; j < aDof; j++) { 3424 cols[numCols++] = aOff + j; 3425 } 3426 } 3427 ierr = PetscMalloc1(cDof*numCols,&refPointFieldMats[p-pRefStart][f]);CHKERRQ(ierr); 3428 /* transpose of constraint matrix */ 3429 ierr = MatGetValues(inj,numCols,cols,cDof,rows,refPointFieldMats[p-pRefStart][f]);CHKERRQ(ierr); 3430 } 3431 } 3432 *childrenMats = refPointFieldMats; 3433 ierr = PetscFree(rows);CHKERRQ(ierr); 3434 ierr = PetscFree(cols);CHKERRQ(ierr); 3435 PetscFunctionReturn(0); 3436 } 3437 3438 #undef __FUNCT__ 3439 #define __FUNCT__ "DMPlexReferenceTreeRestoreChildrenMatrices_Injection" 3440 static PetscErrorCode DMPlexReferenceTreeRestoreChildrenMatrices_Injection(DM refTree, Mat inj, PetscScalar ****childrenMats) 3441 { 3442 PetscDS ds; 3443 PetscScalar ***refPointFieldMats; 3444 PetscInt numFields, pRefStart, pRefEnd, p, f; 3445 PetscSection refConSec, refSection; 3446 PetscErrorCode ierr; 3447 3448 PetscFunctionBegin; 3449 refPointFieldMats = *childrenMats; 3450 *childrenMats = NULL; 3451 ierr = DMGetDS(refTree,&ds);CHKERRQ(ierr); 3452 ierr = DMGetDefaultSection(refTree,&refSection);CHKERRQ(ierr); 3453 ierr = PetscDSGetNumFields(ds,&numFields);CHKERRQ(ierr); 3454 ierr = DMGetDefaultConstraints(refTree,&refConSec,NULL);CHKERRQ(ierr); 3455 ierr = PetscSectionGetChart(refConSec,&pRefStart,&pRefEnd);CHKERRQ(ierr); 3456 for (p = pRefStart; p < pRefEnd; p++) { 3457 PetscInt parent, pDof, parentDof; 3458 3459 ierr = DMPlexGetTreeParent(refTree,p,&parent,NULL);CHKERRQ(ierr); 3460 ierr = PetscSectionGetDof(refConSec,p,&pDof);CHKERRQ(ierr); 3461 ierr = PetscSectionGetDof(refSection,parent,&parentDof);CHKERRQ(ierr); 3462 if (!pDof || !parentDof || parent == p) continue; 3463 3464 for (f = 0; f < numFields; f++) { 3465 PetscInt cDof; 3466 3467 if (numFields > 1) { 3468 ierr = PetscSectionGetFieldDof(refConSec,p,f,&cDof);CHKERRQ(ierr); 3469 } 3470 else { 3471 ierr = PetscSectionGetDof(refConSec,p,&cDof);CHKERRQ(ierr); 3472 } 3473 3474 ierr = PetscFree(refPointFieldMats[p - pRefStart][f]);CHKERRQ(ierr); 3475 } 3476 ierr = PetscFree(refPointFieldMats[p - pRefStart]);CHKERRQ(ierr); 3477 } 3478 ierr = PetscFree(refPointFieldMats);CHKERRQ(ierr); 3479 PetscFunctionReturn(0); 3480 } 3481 3482 #undef __FUNCT__ 3483 #define __FUNCT__ "DMPlexReferenceTreeGetInjector" 3484 static PetscErrorCode DMPlexReferenceTreeGetInjector(DM refTree,Mat *injRef) 3485 { 3486 Mat cMatRef; 3487 PetscObject injRefObj; 3488 PetscErrorCode ierr; 3489 3490 PetscFunctionBegin; 3491 ierr = DMGetDefaultConstraints(refTree,NULL,&cMatRef);CHKERRQ(ierr); 3492 ierr = PetscObjectQuery((PetscObject)cMatRef,"DMPlexComputeInjectorTree_refTree",&injRefObj);CHKERRQ(ierr); 3493 *injRef = (Mat) injRefObj; 3494 if (!*injRef) { 3495 ierr = DMPlexComputeInjectorReferenceTree(refTree,injRef);CHKERRQ(ierr); 3496 ierr = PetscObjectCompose((PetscObject)cMatRef,"DMPlexComputeInjectorTree_refTree",(PetscObject)*injRef);CHKERRQ(ierr); 3497 /* there is now a reference in cMatRef, which should be the only one for symmetry with the above case */ 3498 ierr = PetscObjectDereference((PetscObject)*injRef);CHKERRQ(ierr); 3499 } 3500 PetscFunctionReturn(0); 3501 } 3502 3503 #undef __FUNCT__ 3504 #define __FUNCT__ "DMPlexTransferInjectorTree" 3505 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) 3506 { 3507 PetscInt pStartF, pEndF, pStartC, pEndC, p, maxDof, numMulti; 3508 PetscSection globalCoarse, globalFine; 3509 PetscSection localCoarse, localFine, leafIndicesSec; 3510 PetscSection multiRootSec, rootIndicesSec; 3511 PetscInt *leafInds, *rootInds = NULL; 3512 const PetscInt *rootDegrees; 3513 PetscScalar *leafVals = NULL, *rootVals = NULL; 3514 PetscSF coarseToFineEmbedded; 3515 PetscErrorCode ierr; 3516 3517 PetscFunctionBegin; 3518 ierr = DMPlexGetChart(coarse,&pStartC,&pEndC);CHKERRQ(ierr); 3519 ierr = DMPlexGetChart(fine,&pStartF,&pEndF);CHKERRQ(ierr); 3520 ierr = DMGetDefaultSection(fine,&localFine);CHKERRQ(ierr); 3521 ierr = DMGetDefaultGlobalSection(fine,&globalFine);CHKERRQ(ierr); 3522 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)fine),&leafIndicesSec);CHKERRQ(ierr); 3523 ierr = PetscSectionSetChart(leafIndicesSec,pStartF, pEndF);CHKERRQ(ierr); 3524 ierr = PetscSectionGetMaxDof(localFine,&maxDof);CHKERRQ(ierr); 3525 { /* winnow fine points that don't have global dofs out of the sf */ 3526 PetscInt l, nleaves, dof, cdof, numPointsWithDofs, offset, *pointsWithDofs, numIndices; 3527 const PetscInt *leaves; 3528 3529 ierr = PetscSFGetGraph(coarseToFine,NULL,&nleaves,&leaves,NULL);CHKERRQ(ierr); 3530 for (l = 0, numPointsWithDofs = 0; l < nleaves; l++) { 3531 p = leaves ? leaves[l] : l; 3532 ierr = PetscSectionGetDof(globalFine,p,&dof);CHKERRQ(ierr); 3533 ierr = PetscSectionGetConstraintDof(globalFine,p,&cdof);CHKERRQ(ierr); 3534 if ((dof - cdof) > 0) { 3535 numPointsWithDofs++; 3536 3537 ierr = PetscSectionGetDof(localFine,p,&dof);CHKERRQ(ierr); 3538 ierr = PetscSectionSetDof(leafIndicesSec,p,dof + 1);CHKERRQ(ierr); 3539 } 3540 } 3541 ierr = PetscMalloc1(numPointsWithDofs,&pointsWithDofs);CHKERRQ(ierr); 3542 ierr = PetscSectionSetUp(leafIndicesSec);CHKERRQ(ierr); 3543 ierr = PetscSectionGetStorageSize(leafIndicesSec,&numIndices);CHKERRQ(ierr); 3544 ierr = PetscMalloc1(gatheredIndices ? numIndices : (maxDof + 1),&leafInds);CHKERRQ(ierr); 3545 if (gatheredValues) {ierr = PetscMalloc1(numIndices,&leafVals);CHKERRQ(ierr);} 3546 for (l = 0, offset = 0; l < nleaves; l++) { 3547 p = leaves ? leaves[l] : l; 3548 ierr = PetscSectionGetDof(globalFine,p,&dof);CHKERRQ(ierr); 3549 ierr = PetscSectionGetConstraintDof(globalFine,p,&cdof);CHKERRQ(ierr); 3550 if ((dof - cdof) > 0) { 3551 PetscInt off, gOff; 3552 PetscInt *pInd; 3553 PetscScalar *pVal = NULL; 3554 3555 pointsWithDofs[offset++] = l; 3556 3557 ierr = PetscSectionGetOffset(leafIndicesSec,p,&off);CHKERRQ(ierr); 3558 3559 pInd = gatheredIndices ? (&leafInds[off + 1]) : leafInds; 3560 if (gatheredValues) { 3561 PetscInt i; 3562 3563 pVal = &leafVals[off + 1]; 3564 for (i = 0; i < dof; i++) pVal[i] = 0.; 3565 } 3566 ierr = PetscSectionGetOffset(globalFine,p,&gOff);CHKERRQ(ierr); 3567 3568 offsets[0] = 0; 3569 if (numFields) { 3570 PetscInt f; 3571 3572 for (f = 0; f < numFields; f++) { 3573 PetscInt fDof; 3574 ierr = PetscSectionGetFieldDof(localFine,p,f,&fDof);CHKERRQ(ierr); 3575 offsets[f + 1] = fDof + offsets[f]; 3576 } 3577 DMPlexGetIndicesPointFields_Internal(localFine,p,gOff < 0 ? -(gOff + 1) : gOff,offsets,PETSC_FALSE,0,pInd);CHKERRQ(ierr); 3578 } 3579 else { 3580 DMPlexGetIndicesPoint_Internal(localFine,p,gOff < 0 ? -(gOff + 1) : gOff,offsets,PETSC_FALSE,0,pInd);CHKERRQ(ierr); 3581 } 3582 if (gatheredValues) {ierr = VecGetValues(fineVec,dof,pInd,pVal);CHKERRQ(ierr);} 3583 } 3584 } 3585 ierr = PetscSFCreateEmbeddedLeafSF(coarseToFine, numPointsWithDofs, pointsWithDofs, &coarseToFineEmbedded);CHKERRQ(ierr); 3586 ierr = PetscFree(pointsWithDofs);CHKERRQ(ierr); 3587 } 3588 3589 ierr = DMPlexGetChart(coarse,&pStartC,&pEndC);CHKERRQ(ierr); 3590 ierr = DMGetDefaultSection(coarse,&localCoarse);CHKERRQ(ierr); 3591 ierr = DMGetDefaultGlobalSection(coarse,&globalCoarse);CHKERRQ(ierr); 3592 3593 { /* there may be the case where an sf root has a parent: broadcast parents back to children */ 3594 MPI_Datatype threeInt; 3595 PetscMPIInt rank; 3596 PetscInt (*parentNodeAndIdCoarse)[3]; 3597 PetscInt (*parentNodeAndIdFine)[3]; 3598 PetscInt p, nleaves, nleavesToParents; 3599 PetscSF pointSF, sfToParents; 3600 const PetscInt *ilocal; 3601 const PetscSFNode *iremote; 3602 PetscSFNode *iremoteToParents; 3603 PetscInt *ilocalToParents; 3604 3605 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)coarse),&rank);CHKERRQ(ierr); 3606 ierr = MPI_Type_contiguous(3,MPIU_INT,&threeInt);CHKERRQ(ierr); 3607 ierr = MPI_Type_commit(&threeInt);CHKERRQ(ierr); 3608 ierr = PetscMalloc2(pEndC-pStartC,&parentNodeAndIdCoarse,pEndF-pStartF,&parentNodeAndIdFine);CHKERRQ(ierr); 3609 ierr = DMGetPointSF(coarse,&pointSF);CHKERRQ(ierr); 3610 ierr = PetscSFGetGraph(pointSF,NULL,&nleaves,&ilocal,&iremote);CHKERRQ(ierr); 3611 for (p = pStartC; p < pEndC; p++) { 3612 PetscInt parent, childId; 3613 ierr = DMPlexGetTreeParent(coarse,p,&parent,&childId);CHKERRQ(ierr); 3614 parentNodeAndIdCoarse[p - pStartC][0] = rank; 3615 parentNodeAndIdCoarse[p - pStartC][1] = parent - pStartC; 3616 parentNodeAndIdCoarse[p - pStartC][2] = (p == parent) ? -1 : childId; 3617 if (nleaves > 0) { 3618 PetscInt leaf = -1; 3619 3620 if (ilocal) { 3621 ierr = PetscFindInt(parent,nleaves,ilocal,&leaf);CHKERRQ(ierr); 3622 } 3623 else { 3624 leaf = p - pStartC; 3625 } 3626 if (leaf >= 0) { 3627 parentNodeAndIdCoarse[p - pStartC][0] = iremote[leaf].rank; 3628 parentNodeAndIdCoarse[p - pStartC][1] = iremote[leaf].index; 3629 } 3630 } 3631 } 3632 for (p = pStartF; p < pEndF; p++) { 3633 parentNodeAndIdFine[p - pStartF][0] = -1; 3634 parentNodeAndIdFine[p - pStartF][1] = -1; 3635 parentNodeAndIdFine[p - pStartF][2] = -1; 3636 } 3637 ierr = PetscSFBcastBegin(coarseToFineEmbedded,threeInt,parentNodeAndIdCoarse,parentNodeAndIdFine);CHKERRQ(ierr); 3638 ierr = PetscSFBcastEnd(coarseToFineEmbedded,threeInt,parentNodeAndIdCoarse,parentNodeAndIdFine);CHKERRQ(ierr); 3639 for (p = pStartF, nleavesToParents = 0; p < pEndF; p++) { 3640 PetscInt dof; 3641 3642 ierr = PetscSectionGetDof(leafIndicesSec,p,&dof);CHKERRQ(ierr); 3643 if (dof) { 3644 PetscInt off; 3645 3646 ierr = PetscSectionGetOffset(leafIndicesSec,p,&off);CHKERRQ(ierr); 3647 if (gatheredIndices) { 3648 leafInds[off] = PetscMax(childIds[p-pStartF],parentNodeAndIdFine[p-pStartF][2]); 3649 } else if (gatheredValues) { 3650 leafVals[off] = (PetscScalar) PetscMax(childIds[p-pStartF],parentNodeAndIdFine[p-pStartF][2]); 3651 } 3652 } 3653 if (parentNodeAndIdFine[p-pStartF][0] >= 0) { 3654 nleavesToParents++; 3655 } 3656 } 3657 ierr = PetscMalloc1(nleavesToParents,&ilocalToParents);CHKERRQ(ierr); 3658 ierr = PetscMalloc1(nleavesToParents,&iremoteToParents);CHKERRQ(ierr); 3659 for (p = pStartF, nleavesToParents = 0; p < pEndF; p++) { 3660 if (parentNodeAndIdFine[p-pStartF][0] >= 0) { 3661 ilocalToParents[nleavesToParents] = p - pStartF; 3662 iremoteToParents[nleavesToParents].rank = parentNodeAndIdFine[p-pStartF][0]; 3663 iremoteToParents[nleavesToParents].index = parentNodeAndIdFine[p-pStartF][1]; 3664 nleavesToParents++; 3665 } 3666 } 3667 ierr = PetscSFCreate(PetscObjectComm((PetscObject)coarse),&sfToParents);CHKERRQ(ierr); 3668 ierr = PetscSFSetGraph(sfToParents,pEndC-pStartC,nleavesToParents,ilocalToParents,PETSC_OWN_POINTER,iremoteToParents,PETSC_OWN_POINTER);CHKERRQ(ierr); 3669 ierr = PetscSFDestroy(&coarseToFineEmbedded);CHKERRQ(ierr); 3670 3671 coarseToFineEmbedded = sfToParents; 3672 3673 ierr = PetscFree2(parentNodeAndIdCoarse,parentNodeAndIdFine);CHKERRQ(ierr); 3674 ierr = MPI_Type_free(&threeInt);CHKERRQ(ierr); 3675 } 3676 3677 { /* winnow out coarse points that don't have dofs */ 3678 PetscInt dof, cdof, numPointsWithDofs, offset, *pointsWithDofs; 3679 PetscSF sfDofsOnly; 3680 3681 for (p = pStartC, numPointsWithDofs = 0; p < pEndC; p++) { 3682 ierr = PetscSectionGetDof(globalCoarse,p,&dof);CHKERRQ(ierr); 3683 ierr = PetscSectionGetConstraintDof(globalCoarse,p,&cdof);CHKERRQ(ierr); 3684 if ((dof - cdof) > 0) { 3685 numPointsWithDofs++; 3686 } 3687 } 3688 ierr = PetscMalloc1(numPointsWithDofs,&pointsWithDofs);CHKERRQ(ierr); 3689 for (p = pStartC, offset = 0; p < pEndC; p++) { 3690 ierr = PetscSectionGetDof(globalCoarse,p,&dof);CHKERRQ(ierr); 3691 ierr = PetscSectionGetConstraintDof(globalCoarse,p,&cdof);CHKERRQ(ierr); 3692 if ((dof - cdof) > 0) { 3693 pointsWithDofs[offset++] = p - pStartC; 3694 } 3695 } 3696 ierr = PetscSFCreateEmbeddedSF(coarseToFineEmbedded, numPointsWithDofs, pointsWithDofs, &sfDofsOnly);CHKERRQ(ierr); 3697 ierr = PetscSFDestroy(&coarseToFineEmbedded);CHKERRQ(ierr); 3698 ierr = PetscFree(pointsWithDofs);CHKERRQ(ierr); 3699 coarseToFineEmbedded = sfDofsOnly; 3700 } 3701 3702 /* communicate back to the coarse mesh which coarse points have children (that may require injection) */ 3703 ierr = PetscSFComputeDegreeBegin(coarseToFineEmbedded,&rootDegrees);CHKERRQ(ierr); 3704 ierr = PetscSFComputeDegreeEnd(coarseToFineEmbedded,&rootDegrees);CHKERRQ(ierr); 3705 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)coarse),&multiRootSec);CHKERRQ(ierr); 3706 ierr = PetscSectionSetChart(multiRootSec,pStartC,pEndC);CHKERRQ(ierr); 3707 for (p = pStartC; p < pEndC; p++) { 3708 ierr = PetscSectionSetDof(multiRootSec,p,rootDegrees[p-pStartC]);CHKERRQ(ierr); 3709 } 3710 ierr = PetscSectionSetUp(multiRootSec);CHKERRQ(ierr); 3711 ierr = PetscSectionGetStorageSize(multiRootSec,&numMulti);CHKERRQ(ierr); 3712 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)coarse),&rootIndicesSec);CHKERRQ(ierr); 3713 { /* distribute the leaf section */ 3714 PetscSF multi, multiInv, indicesSF; 3715 PetscInt *remoteOffsets, numRootIndices; 3716 3717 ierr = PetscSFGetMultiSF(coarseToFineEmbedded,&multi);CHKERRQ(ierr); 3718 ierr = PetscSFCreateInverseSF(multi,&multiInv);CHKERRQ(ierr); 3719 ierr = PetscSFDistributeSection(multiInv,leafIndicesSec,&remoteOffsets,rootIndicesSec);CHKERRQ(ierr); 3720 ierr = PetscSFCreateSectionSF(multiInv,leafIndicesSec,remoteOffsets,rootIndicesSec,&indicesSF);CHKERRQ(ierr); 3721 ierr = PetscFree(remoteOffsets);CHKERRQ(ierr); 3722 ierr = PetscSFDestroy(&multiInv);CHKERRQ(ierr); 3723 ierr = PetscSectionGetStorageSize(rootIndicesSec,&numRootIndices);CHKERRQ(ierr); 3724 if (gatheredIndices) { 3725 ierr = PetscMalloc1(numRootIndices,&rootInds);CHKERRQ(ierr); 3726 ierr = PetscSFBcastBegin(indicesSF,MPIU_INT,leafInds,rootInds);CHKERRQ(ierr); 3727 ierr = PetscSFBcastEnd(indicesSF,MPIU_INT,leafInds,rootInds);CHKERRQ(ierr); 3728 } 3729 if (gatheredValues) { 3730 ierr = PetscMalloc1(numRootIndices,&rootVals);CHKERRQ(ierr); 3731 ierr = PetscSFBcastBegin(indicesSF,MPIU_SCALAR,leafVals,rootVals);CHKERRQ(ierr); 3732 ierr = PetscSFBcastEnd(indicesSF,MPIU_SCALAR,leafVals,rootVals);CHKERRQ(ierr); 3733 } 3734 ierr = PetscSFDestroy(&indicesSF);CHKERRQ(ierr); 3735 } 3736 ierr = PetscSectionDestroy(&leafIndicesSec);CHKERRQ(ierr); 3737 ierr = PetscFree(leafInds);CHKERRQ(ierr); 3738 ierr = PetscFree(leafVals);CHKERRQ(ierr); 3739 ierr = PetscSFDestroy(&coarseToFineEmbedded);CHKERRQ(ierr); 3740 *rootMultiSec = multiRootSec; 3741 *multiLeafSec = rootIndicesSec; 3742 if (gatheredIndices) *gatheredIndices = rootInds; 3743 if (gatheredValues) *gatheredValues = rootVals; 3744 PetscFunctionReturn(0); 3745 } 3746 3747 #undef __FUNCT__ 3748 #define __FUNCT__ "DMPlexComputeInjectorTree" 3749 PetscErrorCode DMPlexComputeInjectorTree(DM coarse, DM fine, PetscSF coarseToFine, PetscInt *childIds, Mat mat) 3750 { 3751 DM refTree; 3752 PetscSection multiRootSec, rootIndicesSec; 3753 PetscSection globalCoarse, globalFine; 3754 PetscSection localCoarse, localFine; 3755 PetscSection cSecRef; 3756 PetscInt *rootIndices, *parentIndices, pRefStart, pRefEnd; 3757 Mat injRef; 3758 PetscInt numFields, maxDof; 3759 PetscInt pStartC, pEndC, pStartF, pEndF, p; 3760 PetscInt *offsets, *offsetsCopy, *rowOffsets; 3761 PetscLayout rowMap, colMap; 3762 PetscInt rowStart, rowEnd, colStart, colEnd, *nnzD, *nnzO; 3763 PetscScalar ***childrenMats=NULL ; /* gcc -O gives 'may be used uninitialized' warning'. Initializing to suppress this warning */ 3764 PetscErrorCode ierr; 3765 3766 PetscFunctionBegin; 3767 3768 /* get the templates for the fine-to-coarse injection from the reference tree */ 3769 ierr = DMPlexGetReferenceTree(coarse,&refTree);CHKERRQ(ierr); 3770 ierr = DMGetDefaultConstraints(refTree,&cSecRef,NULL);CHKERRQ(ierr); 3771 ierr = PetscSectionGetChart(cSecRef,&pRefStart,&pRefEnd);CHKERRQ(ierr); 3772 ierr = DMPlexReferenceTreeGetInjector(refTree,&injRef);CHKERRQ(ierr); 3773 3774 ierr = DMPlexGetChart(fine,&pStartF,&pEndF);CHKERRQ(ierr); 3775 ierr = DMGetDefaultSection(fine,&localFine);CHKERRQ(ierr); 3776 ierr = DMGetDefaultGlobalSection(fine,&globalFine);CHKERRQ(ierr); 3777 ierr = PetscSectionGetNumFields(localFine,&numFields);CHKERRQ(ierr); 3778 ierr = DMPlexGetChart(coarse,&pStartC,&pEndC);CHKERRQ(ierr); 3779 ierr = DMGetDefaultSection(coarse,&localCoarse);CHKERRQ(ierr); 3780 ierr = DMGetDefaultGlobalSection(coarse,&globalCoarse);CHKERRQ(ierr); 3781 ierr = PetscSectionGetMaxDof(localCoarse,&maxDof);CHKERRQ(ierr); 3782 { 3783 PetscInt maxFields = PetscMax(1,numFields) + 1; 3784 ierr = PetscMalloc3(maxFields,&offsets,maxFields,&offsetsCopy,maxFields,&rowOffsets);CHKERRQ(ierr); 3785 } 3786 3787 ierr = DMPlexTransferInjectorTree(coarse,fine,coarseToFine,childIds,NULL,numFields,offsets,&multiRootSec,&rootIndicesSec,&rootIndices,NULL);CHKERRQ(ierr); 3788 3789 ierr = PetscMalloc1(maxDof,&parentIndices);CHKERRQ(ierr); 3790 3791 /* count indices */ 3792 ierr = MatGetLayouts(mat,&rowMap,&colMap);CHKERRQ(ierr); 3793 ierr = PetscLayoutSetUp(rowMap);CHKERRQ(ierr); 3794 ierr = PetscLayoutSetUp(colMap);CHKERRQ(ierr); 3795 ierr = PetscLayoutGetRange(rowMap,&rowStart,&rowEnd);CHKERRQ(ierr); 3796 ierr = PetscLayoutGetRange(colMap,&colStart,&colEnd);CHKERRQ(ierr); 3797 ierr = PetscCalloc2(rowEnd-rowStart,&nnzD,rowEnd-rowStart,&nnzO);CHKERRQ(ierr); 3798 for (p = pStartC; p < pEndC; p++) { 3799 PetscInt numLeaves, leafStart, leafEnd, l, dof, cdof, gOff; 3800 3801 ierr = PetscSectionGetDof(globalCoarse,p,&dof);CHKERRQ(ierr); 3802 ierr = PetscSectionGetConstraintDof(globalCoarse,p,&cdof);CHKERRQ(ierr); 3803 if ((dof - cdof) <= 0) continue; 3804 ierr = PetscSectionGetOffset(globalCoarse,p,&gOff);CHKERRQ(ierr); 3805 3806 rowOffsets[0] = 0; 3807 offsetsCopy[0] = 0; 3808 if (numFields) { 3809 PetscInt f; 3810 3811 for (f = 0; f < numFields; f++) { 3812 PetscInt fDof; 3813 ierr = PetscSectionGetFieldDof(localCoarse,p,f,&fDof);CHKERRQ(ierr); 3814 rowOffsets[f + 1] = offsetsCopy[f + 1] = fDof + rowOffsets[f]; 3815 } 3816 DMPlexGetIndicesPointFields_Internal(localCoarse,p,gOff < 0 ? -(gOff + 1) : gOff,offsetsCopy,PETSC_FALSE,0,parentIndices);CHKERRQ(ierr); 3817 } 3818 else { 3819 DMPlexGetIndicesPoint_Internal(localCoarse,p,gOff < 0 ? -(gOff + 1) : gOff,offsetsCopy,PETSC_FALSE,0,parentIndices);CHKERRQ(ierr); 3820 rowOffsets[1] = offsetsCopy[0]; 3821 } 3822 3823 ierr = PetscSectionGetDof(multiRootSec,p,&numLeaves);CHKERRQ(ierr); 3824 ierr = PetscSectionGetOffset(multiRootSec,p,&leafStart);CHKERRQ(ierr); 3825 leafEnd = leafStart + numLeaves; 3826 for (l = leafStart; l < leafEnd; l++) { 3827 PetscInt numIndices, childId, offset; 3828 const PetscInt *childIndices; 3829 3830 ierr = PetscSectionGetDof(rootIndicesSec,l,&numIndices);CHKERRQ(ierr); 3831 ierr = PetscSectionGetOffset(rootIndicesSec,l,&offset);CHKERRQ(ierr); 3832 childId = rootIndices[offset++]; 3833 childIndices = &rootIndices[offset]; 3834 numIndices--; 3835 3836 if (childId == -1) { /* equivalent points: scatter */ 3837 PetscInt i; 3838 3839 for (i = 0; i < numIndices; i++) { 3840 PetscInt colIndex = childIndices[i]; 3841 PetscInt rowIndex = parentIndices[i]; 3842 if (rowIndex < 0) continue; 3843 if (colIndex < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Unconstrained fine and constrained coarse"); 3844 if (colIndex >= colStart && colIndex < colEnd) { 3845 nnzD[rowIndex - rowStart] = 1; 3846 } 3847 else { 3848 nnzO[rowIndex - rowStart] = 1; 3849 } 3850 } 3851 } 3852 else { 3853 PetscInt parentId, f, lim; 3854 3855 ierr = DMPlexGetTreeParent(refTree,childId,&parentId,NULL);CHKERRQ(ierr); 3856 3857 lim = PetscMax(1,numFields); 3858 offsets[0] = 0; 3859 if (numFields) { 3860 PetscInt f; 3861 3862 for (f = 0; f < numFields; f++) { 3863 PetscInt fDof; 3864 ierr = PetscSectionGetFieldDof(cSecRef,childId,f,&fDof);CHKERRQ(ierr); 3865 3866 offsets[f + 1] = fDof + offsets[f]; 3867 } 3868 } 3869 else { 3870 PetscInt cDof; 3871 3872 ierr = PetscSectionGetDof(cSecRef,childId,&cDof);CHKERRQ(ierr); 3873 offsets[1] = cDof; 3874 } 3875 for (f = 0; f < lim; f++) { 3876 PetscInt parentStart = rowOffsets[f], parentEnd = rowOffsets[f + 1]; 3877 PetscInt childStart = offsets[f], childEnd = offsets[f + 1]; 3878 PetscInt i, numD = 0, numO = 0; 3879 3880 for (i = childStart; i < childEnd; i++) { 3881 PetscInt colIndex = childIndices[i]; 3882 3883 if (colIndex < 0) continue; 3884 if (colIndex >= colStart && colIndex < colEnd) { 3885 numD++; 3886 } 3887 else { 3888 numO++; 3889 } 3890 } 3891 for (i = parentStart; i < parentEnd; i++) { 3892 PetscInt rowIndex = parentIndices[i]; 3893 3894 if (rowIndex < 0) continue; 3895 nnzD[rowIndex - rowStart] += numD; 3896 nnzO[rowIndex - rowStart] += numO; 3897 } 3898 } 3899 } 3900 } 3901 } 3902 /* preallocate */ 3903 ierr = MatXAIJSetPreallocation(mat,1,nnzD,nnzO,NULL,NULL);CHKERRQ(ierr); 3904 ierr = PetscFree2(nnzD,nnzO);CHKERRQ(ierr); 3905 /* insert values */ 3906 ierr = DMPlexReferenceTreeGetChildrenMatrices_Injection(refTree,injRef,&childrenMats);CHKERRQ(ierr); 3907 for (p = pStartC; p < pEndC; p++) { 3908 PetscInt numLeaves, leafStart, leafEnd, l, dof, cdof, gOff; 3909 3910 ierr = PetscSectionGetDof(globalCoarse,p,&dof);CHKERRQ(ierr); 3911 ierr = PetscSectionGetConstraintDof(globalCoarse,p,&cdof);CHKERRQ(ierr); 3912 if ((dof - cdof) <= 0) continue; 3913 ierr = PetscSectionGetOffset(globalCoarse,p,&gOff);CHKERRQ(ierr); 3914 3915 rowOffsets[0] = 0; 3916 offsetsCopy[0] = 0; 3917 if (numFields) { 3918 PetscInt f; 3919 3920 for (f = 0; f < numFields; f++) { 3921 PetscInt fDof; 3922 ierr = PetscSectionGetFieldDof(localCoarse,p,f,&fDof);CHKERRQ(ierr); 3923 rowOffsets[f + 1] = offsetsCopy[f + 1] = fDof + rowOffsets[f]; 3924 } 3925 DMPlexGetIndicesPointFields_Internal(localCoarse,p,gOff < 0 ? -(gOff + 1) : gOff,offsetsCopy,PETSC_FALSE,0,parentIndices);CHKERRQ(ierr); 3926 } 3927 else { 3928 DMPlexGetIndicesPoint_Internal(localCoarse,p,gOff < 0 ? -(gOff + 1) : gOff,offsetsCopy,PETSC_FALSE,0,parentIndices);CHKERRQ(ierr); 3929 rowOffsets[1] = offsetsCopy[0]; 3930 } 3931 3932 ierr = PetscSectionGetDof(multiRootSec,p,&numLeaves);CHKERRQ(ierr); 3933 ierr = PetscSectionGetOffset(multiRootSec,p,&leafStart);CHKERRQ(ierr); 3934 leafEnd = leafStart + numLeaves; 3935 for (l = leafStart; l < leafEnd; l++) { 3936 PetscInt numIndices, childId, offset; 3937 const PetscInt *childIndices; 3938 3939 ierr = PetscSectionGetDof(rootIndicesSec,l,&numIndices);CHKERRQ(ierr); 3940 ierr = PetscSectionGetOffset(rootIndicesSec,l,&offset);CHKERRQ(ierr); 3941 childId = rootIndices[offset++]; 3942 childIndices = &rootIndices[offset]; 3943 numIndices--; 3944 3945 if (childId == -1) { /* equivalent points: scatter */ 3946 PetscInt i; 3947 3948 for (i = 0; i < numIndices; i++) { 3949 ierr = MatSetValue(mat,parentIndices[i],childIndices[i],1.,INSERT_VALUES);CHKERRQ(ierr); 3950 } 3951 } 3952 else { 3953 PetscInt parentId, f, lim; 3954 3955 ierr = DMPlexGetTreeParent(refTree,childId,&parentId,NULL);CHKERRQ(ierr); 3956 3957 lim = PetscMax(1,numFields); 3958 offsets[0] = 0; 3959 if (numFields) { 3960 PetscInt f; 3961 3962 for (f = 0; f < numFields; f++) { 3963 PetscInt fDof; 3964 ierr = PetscSectionGetFieldDof(cSecRef,childId,f,&fDof);CHKERRQ(ierr); 3965 3966 offsets[f + 1] = fDof + offsets[f]; 3967 } 3968 } 3969 else { 3970 PetscInt cDof; 3971 3972 ierr = PetscSectionGetDof(cSecRef,childId,&cDof);CHKERRQ(ierr); 3973 offsets[1] = cDof; 3974 } 3975 for (f = 0; f < lim; f++) { 3976 PetscScalar *childMat = &childrenMats[childId - pRefStart][f][0]; 3977 PetscInt *rowIndices = &parentIndices[rowOffsets[f]]; 3978 const PetscInt *colIndices = &childIndices[offsets[f]]; 3979 3980 ierr = MatSetValues(mat,rowOffsets[f+1]-rowOffsets[f],rowIndices,offsets[f+1]-offsets[f],colIndices,childMat,INSERT_VALUES);CHKERRQ(ierr); 3981 } 3982 } 3983 } 3984 } 3985 ierr = PetscSectionDestroy(&multiRootSec);CHKERRQ(ierr); 3986 ierr = PetscSectionDestroy(&rootIndicesSec);CHKERRQ(ierr); 3987 ierr = PetscFree(parentIndices);CHKERRQ(ierr); 3988 ierr = DMPlexReferenceTreeRestoreChildrenMatrices_Injection(refTree,injRef,&childrenMats);CHKERRQ(ierr); 3989 ierr = PetscFree(rootIndices);CHKERRQ(ierr); 3990 ierr = PetscFree3(offsets,offsetsCopy,rowOffsets);CHKERRQ(ierr); 3991 3992 ierr = MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3993 ierr = MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3994 PetscFunctionReturn(0); 3995 } 3996 3997 #undef __FUNCT__ 3998 #define __FUNCT__ "DMPlexTransferVecTree_Interpolate" 3999 static PetscErrorCode DMPlexTransferVecTree_Interpolate(DM coarse, Vec vecCoarseLocal, DM fine, Vec vecFine, PetscSF coarseToFine, PetscInt *cids, Vec grad, Vec cellGeom) 4000 { 4001 PetscDS ds; 4002 PetscSF coarseToFineEmbedded; 4003 PetscSection globalCoarse, globalFine; 4004 PetscSection localCoarse, localFine; 4005 PetscSection aSec, cSec; 4006 PetscSection rootValuesSec; 4007 PetscSection leafValuesSec; 4008 PetscScalar *rootValues, *leafValues; 4009 IS aIS; 4010 const PetscInt *anchors; 4011 Mat cMat; 4012 PetscInt numFields; 4013 PetscInt pStartC, pEndC, pStartF, pEndF, p, cellStart, cellEnd, cellEndInterior; 4014 PetscInt aStart, aEnd, cStart, cEnd; 4015 PetscInt *maxChildIds; 4016 PetscInt *offsets, *newOffsets, *offsetsCopy, *newOffsetsCopy, *rowOffsets, *numD, *numO; 4017 PetscFV fv = NULL; 4018 PetscInt dim, numFVcomps = -1, fvField = -1; 4019 DM cellDM = NULL, gradDM = NULL; 4020 const PetscScalar *cellGeomArray = NULL; 4021 const PetscScalar *gradArray = NULL; 4022 PetscErrorCode ierr; 4023 4024 PetscFunctionBegin; 4025 ierr = VecSetOption(vecFine,VEC_IGNORE_NEGATIVE_INDICES,PETSC_TRUE);CHKERRQ(ierr); 4026 ierr = DMPlexGetChart(coarse,&pStartC,&pEndC);CHKERRQ(ierr); 4027 ierr = DMPlexGetHeightStratum(coarse,0,&cellStart,&cellEnd);CHKERRQ(ierr); 4028 ierr = DMPlexGetHybridBounds(coarse,&cellEndInterior,NULL,NULL,NULL);CHKERRQ(ierr); 4029 cellEnd = (cellEndInterior < 0) ? cellEnd : cellEndInterior; 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(localCoarse,&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 PetscFVCellGeom *cg; 4176 PetscScalar *gradVals = NULL; 4177 PetscInt i; 4178 4179 pVal += (numValues - dim * (1 + numFVcomps)); 4180 4181 ierr = DMPlexPointLocalRead(cellDM,p,cellGeomArray,(void *) &cg);CHKERRQ(ierr); 4182 for (i = 0; i < dim; i++) pVal[i] = cg->centroid[i]; 4183 pVal += dim; 4184 ierr = DMPlexPointGlobalRead(gradDM,p,gradArray,(void *) &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 ierr = DMPlexGetHybridBounds(fine,&cellEndInterior,NULL,NULL,NULL);CHKERRQ(ierr); 4232 cellEnd = (cellEndInterior < 0) ? cellEnd : cellEndInterior; 4233 for (p = leafStart; p < leafEnd; p++) { 4234 PetscInt gDof, gcDof, gOff, lDof; 4235 PetscInt numValues, pValOff; 4236 PetscInt childId; 4237 const PetscScalar *pVal; 4238 const PetscScalar *fvGradData = NULL; 4239 4240 ierr = PetscSectionGetDof(globalFine,p,&gDof);CHKERRQ(ierr); 4241 ierr = PetscSectionGetDof(localFine,p,&lDof);CHKERRQ(ierr); 4242 ierr = PetscSectionGetConstraintDof(globalFine,p,&gcDof);CHKERRQ(ierr); 4243 if ((gDof - gcDof) <= 0) { 4244 continue; 4245 } 4246 ierr = PetscSectionGetOffset(globalFine,p,&gOff);CHKERRQ(ierr); 4247 ierr = PetscSectionGetDof(leafValuesSec,p,&numValues);CHKERRQ(ierr); 4248 if (!numValues) continue; 4249 ierr = PetscSectionGetOffset(leafValuesSec,p,&pValOff);CHKERRQ(ierr); 4250 pVal = &leafValues[pValOff]; 4251 offsets[0] = 0; 4252 offsetsCopy[0] = 0; 4253 newOffsets[0] = 0; 4254 newOffsetsCopy[0] = 0; 4255 childId = cids[p - pStartF]; 4256 if (grad && p >= cellStart && p < cellEnd) { 4257 numValues -= (dim * (1 + numFVcomps)); 4258 fvGradData = &pVal[numValues]; 4259 } 4260 if (numFields) { 4261 PetscInt f; 4262 for (f = 0; f < numFields; f++) { 4263 PetscInt rowDof; 4264 4265 ierr = PetscSectionGetFieldDof(localFine,p,f,&rowDof);CHKERRQ(ierr); 4266 offsets[f + 1] = offsets[f] + rowDof; 4267 offsetsCopy[f + 1] = offsets[f + 1]; 4268 /* TODO: closure indices */ 4269 newOffsets[f + 1] = newOffsets[f] + ((childId == -1) ? rowDof : refPointFieldN[childId - pRefStart][f]); 4270 } 4271 ierr = DMPlexGetIndicesPointFields_Internal(localFine,p,gOff,offsetsCopy,PETSC_FALSE,0,rowIndices);CHKERRQ(ierr); 4272 } 4273 else { 4274 offsets[0] = 0; 4275 offsets[1] = lDof; 4276 newOffsets[0] = 0; 4277 newOffsets[1] = (childId == -1) ? lDof : refPointFieldN[childId - pRefStart][0]; 4278 ierr = DMPlexGetIndicesPoint_Internal(localFine,p,gOff,offsetsCopy,PETSC_FALSE,0,rowIndices);CHKERRQ(ierr); 4279 } 4280 if (childId == -1) { /* no child interpolation: one nnz per */ 4281 ierr = VecSetValues(vecFine,numValues,rowIndices,pVal,INSERT_VALUES);CHKERRQ(ierr); 4282 } else { 4283 PetscInt f; 4284 4285 for (f = 0; f < PetscMax(1,numFields); f++) { 4286 const PetscScalar *childMat = refPointFieldMats[childId - pRefStart][f]; 4287 PetscInt numRows = offsets[f+1] - offsets[f]; 4288 PetscInt numCols = newOffsets[f + 1] - newOffsets[f]; 4289 const PetscScalar *cVal = &pVal[newOffsets[f]]; 4290 PetscScalar *rVal = &pointWork[offsets[f]]; 4291 PetscInt i, j; 4292 4293 #if 0 4294 ierr = PetscInfo6(coarse,"field %D, numFields %D, childId %D, numRows %D, numCols %D, refPointFieldN %D\n",f,numFields,childId,numRows,numCols,refPointFieldN[childId - pRefStart][f]);CHKERRQ(ierr); 4295 #endif 4296 for (i = 0; i < numRows; i++) { 4297 PetscScalar val = 0.; 4298 for (j = 0; j < numCols; j++) { 4299 val += childMat[i * numCols + j] * cVal[j]; 4300 } 4301 rVal[i] = val; 4302 } 4303 if (f == fvField && p >= cellStart && p < cellEnd) { 4304 PetscReal centroid[3]; 4305 PetscScalar diff[3]; 4306 const PetscScalar *parentCentroid = &fvGradData[0]; 4307 const PetscScalar *gradient = &fvGradData[dim]; 4308 4309 ierr = DMPlexComputeCellGeometryFVM(fine,p,NULL,centroid,NULL);CHKERRQ(ierr); 4310 for (i = 0; i < dim; i++) { 4311 diff[i] = centroid[i] - parentCentroid[i]; 4312 } 4313 for (i = 0; i < numFVcomps; i++) { 4314 PetscScalar val = 0.; 4315 4316 for (j = 0; j < dim; j++) { 4317 val += gradient[dim * i + j] * diff[j]; 4318 } 4319 rVal[i] += val; 4320 } 4321 } 4322 ierr = VecSetValues(vecFine,numRows,&rowIndices[offsets[f]],rVal,INSERT_VALUES);CHKERRQ(ierr); 4323 } 4324 } 4325 } 4326 ierr = DMPlexReferenceTreeRestoreChildrenMatrices(refTree,&refPointFieldMats,&refPointFieldN);CHKERRQ(ierr); 4327 ierr = DMRestoreWorkArray(fine,maxDof,PETSC_INT,&rowIndices);CHKERRQ(ierr); 4328 ierr = DMRestoreWorkArray(fine,maxDof,PETSC_SCALAR,&pointWork);CHKERRQ(ierr); 4329 } 4330 ierr = PetscFree(leafValues);CHKERRQ(ierr); 4331 ierr = PetscSectionDestroy(&leafValuesSec);CHKERRQ(ierr); 4332 ierr = PetscFree7(offsets,offsetsCopy,newOffsets,newOffsetsCopy,rowOffsets,numD,numO);CHKERRQ(ierr); 4333 ierr = ISRestoreIndices(aIS,&anchors);CHKERRQ(ierr); 4334 PetscFunctionReturn(0); 4335 } 4336 4337 #undef __FUNCT__ 4338 #define __FUNCT__ "DMPlexTransferVecTree_Inject" 4339 static PetscErrorCode DMPlexTransferVecTree_Inject(DM fine, Vec vecFine, DM coarse, Vec vecCoarse, PetscSF coarseToFine, PetscInt *cids) 4340 { 4341 PetscDS ds; 4342 DM refTree; 4343 PetscSection multiRootSec, rootIndicesSec; 4344 PetscSection globalCoarse, globalFine; 4345 PetscSection localCoarse, localFine; 4346 PetscSection cSecRef; 4347 PetscInt *parentIndices, pRefStart, pRefEnd; 4348 PetscScalar *rootValues, *parentValues; 4349 Mat injRef; 4350 PetscInt numFields, maxDof; 4351 PetscInt pStartC, pEndC, pStartF, pEndF, p; 4352 PetscInt *offsets, *offsetsCopy, *rowOffsets; 4353 PetscLayout rowMap, colMap; 4354 PetscInt rowStart, rowEnd, colStart, colEnd; 4355 PetscScalar ***childrenMats=NULL ; /* gcc -O gives 'may be used uninitialized' warning'. Initializing to suppress this warning */ 4356 PetscErrorCode ierr; 4357 4358 PetscFunctionBegin; 4359 4360 /* get the templates for the fine-to-coarse injection from the reference tree */ 4361 ierr = VecSetOption(vecFine,VEC_IGNORE_NEGATIVE_INDICES,PETSC_TRUE);CHKERRQ(ierr); 4362 ierr = VecSetOption(vecCoarse,VEC_IGNORE_NEGATIVE_INDICES,PETSC_TRUE);CHKERRQ(ierr); 4363 ierr = DMPlexGetReferenceTree(coarse,&refTree);CHKERRQ(ierr); 4364 ierr = DMGetDS(coarse,&ds);CHKERRQ(ierr); 4365 ierr = DMSetDS(refTree,ds);CHKERRQ(ierr); 4366 ierr = DMGetDefaultConstraints(refTree,&cSecRef,NULL);CHKERRQ(ierr); 4367 ierr = PetscSectionGetChart(cSecRef,&pRefStart,&pRefEnd);CHKERRQ(ierr); 4368 ierr = DMPlexReferenceTreeGetInjector(refTree,&injRef);CHKERRQ(ierr); 4369 4370 ierr = DMPlexGetChart(fine,&pStartF,&pEndF);CHKERRQ(ierr); 4371 ierr = DMGetDefaultSection(fine,&localFine);CHKERRQ(ierr); 4372 ierr = DMGetDefaultGlobalSection(fine,&globalFine);CHKERRQ(ierr); 4373 ierr = PetscSectionGetNumFields(localFine,&numFields);CHKERRQ(ierr); 4374 ierr = DMPlexGetChart(coarse,&pStartC,&pEndC);CHKERRQ(ierr); 4375 ierr = DMGetDefaultSection(coarse,&localCoarse);CHKERRQ(ierr); 4376 ierr = DMGetDefaultGlobalSection(coarse,&globalCoarse);CHKERRQ(ierr); 4377 ierr = PetscSectionGetMaxDof(localCoarse,&maxDof);CHKERRQ(ierr); 4378 { 4379 PetscInt maxFields = PetscMax(1,numFields) + 1; 4380 ierr = PetscMalloc3(maxFields,&offsets,maxFields,&offsetsCopy,maxFields,&rowOffsets);CHKERRQ(ierr); 4381 } 4382 4383 ierr = DMPlexTransferInjectorTree(coarse,fine,coarseToFine,cids,vecFine,numFields,offsets,&multiRootSec,&rootIndicesSec,NULL,&rootValues);CHKERRQ(ierr); 4384 4385 ierr = PetscMalloc2(maxDof,&parentIndices,maxDof,&parentValues);CHKERRQ(ierr); 4386 4387 /* count indices */ 4388 ierr = VecGetLayout(vecFine,&colMap);CHKERRQ(ierr); 4389 ierr = VecGetLayout(vecCoarse,&rowMap);CHKERRQ(ierr); 4390 ierr = PetscLayoutSetUp(rowMap);CHKERRQ(ierr); 4391 ierr = PetscLayoutSetUp(colMap);CHKERRQ(ierr); 4392 ierr = PetscLayoutGetRange(rowMap,&rowStart,&rowEnd);CHKERRQ(ierr); 4393 ierr = PetscLayoutGetRange(colMap,&colStart,&colEnd);CHKERRQ(ierr); 4394 /* insert values */ 4395 ierr = DMPlexReferenceTreeGetChildrenMatrices_Injection(refTree,injRef,&childrenMats);CHKERRQ(ierr); 4396 for (p = pStartC; p < pEndC; p++) { 4397 PetscInt numLeaves, leafStart, leafEnd, l, dof, cdof, gOff; 4398 4399 ierr = PetscSectionGetDof(globalCoarse,p,&dof);CHKERRQ(ierr); 4400 ierr = PetscSectionGetConstraintDof(globalCoarse,p,&cdof);CHKERRQ(ierr); 4401 if ((dof - cdof) <= 0) continue; 4402 ierr = PetscSectionGetDof(localCoarse,p,&dof);CHKERRQ(ierr); 4403 ierr = PetscSectionGetOffset(globalCoarse,p,&gOff);CHKERRQ(ierr); 4404 4405 rowOffsets[0] = 0; 4406 offsetsCopy[0] = 0; 4407 if (numFields) { 4408 PetscInt f; 4409 4410 for (f = 0; f < numFields; f++) { 4411 PetscInt fDof; 4412 ierr = PetscSectionGetFieldDof(localCoarse,p,f,&fDof);CHKERRQ(ierr); 4413 rowOffsets[f + 1] = offsetsCopy[f + 1] = fDof + rowOffsets[f]; 4414 } 4415 DMPlexGetIndicesPointFields_Internal(localCoarse,p,gOff < 0 ? -(gOff + 1) : gOff,offsetsCopy,PETSC_FALSE,0,parentIndices);CHKERRQ(ierr); 4416 } 4417 else { 4418 DMPlexGetIndicesPoint_Internal(localCoarse,p,gOff < 0 ? -(gOff + 1) : gOff,offsetsCopy,PETSC_FALSE,0,parentIndices);CHKERRQ(ierr); 4419 rowOffsets[1] = offsetsCopy[0]; 4420 } 4421 4422 ierr = PetscSectionGetDof(multiRootSec,p,&numLeaves);CHKERRQ(ierr); 4423 ierr = PetscSectionGetOffset(multiRootSec,p,&leafStart);CHKERRQ(ierr); 4424 leafEnd = leafStart + numLeaves; 4425 for (l = 0; l < dof; l++) parentValues[l] = 0.; 4426 for (l = leafStart; l < leafEnd; l++) { 4427 PetscInt numIndices, childId, offset; 4428 const PetscScalar *childValues; 4429 4430 ierr = PetscSectionGetDof(rootIndicesSec,l,&numIndices);CHKERRQ(ierr); 4431 ierr = PetscSectionGetOffset(rootIndicesSec,l,&offset);CHKERRQ(ierr); 4432 childId = (PetscInt) PetscRealPart(rootValues[offset++]); 4433 childValues = &rootValues[offset]; 4434 numIndices--; 4435 4436 if (childId == -2) { /* skip */ 4437 continue; 4438 } else if (childId == -1) { /* equivalent points: scatter */ 4439 PetscInt m; 4440 4441 for (m = 0; m < numIndices; m++) parentValues[m] = childValues[m]; 4442 } else { /* contributions from children: sum with injectors from reference tree */ 4443 PetscInt parentId, f, lim; 4444 4445 ierr = DMPlexGetTreeParent(refTree,childId,&parentId,NULL);CHKERRQ(ierr); 4446 4447 lim = PetscMax(1,numFields); 4448 offsets[0] = 0; 4449 if (numFields) { 4450 PetscInt f; 4451 4452 for (f = 0; f < numFields; f++) { 4453 PetscInt fDof; 4454 ierr = PetscSectionGetFieldDof(cSecRef,childId,f,&fDof);CHKERRQ(ierr); 4455 4456 offsets[f + 1] = fDof + offsets[f]; 4457 } 4458 } 4459 else { 4460 PetscInt cDof; 4461 4462 ierr = PetscSectionGetDof(cSecRef,childId,&cDof);CHKERRQ(ierr); 4463 offsets[1] = cDof; 4464 } 4465 for (f = 0; f < lim; f++) { 4466 PetscScalar *childMat = &childrenMats[childId - pRefStart][f][0]; 4467 PetscInt n = offsets[f+1]-offsets[f]; 4468 PetscInt i, j; 4469 const PetscScalar *colValues = &childValues[offsets[f]]; 4470 4471 for (i = rowOffsets[f]; i < rowOffsets[f + 1]; i++) { 4472 PetscScalar val = 0.; 4473 for (j = 0; j < n; j++) { 4474 val += childMat[n * i + j] * colValues[j]; 4475 } 4476 parentValues[i] += val; 4477 } 4478 } 4479 } 4480 ierr = VecSetValues(vecCoarse,dof,parentIndices,parentValues,INSERT_VALUES);CHKERRQ(ierr); 4481 } 4482 } 4483 ierr = PetscSectionDestroy(&multiRootSec);CHKERRQ(ierr); 4484 ierr = PetscSectionDestroy(&rootIndicesSec);CHKERRQ(ierr); 4485 ierr = PetscFree2(parentIndices,parentValues);CHKERRQ(ierr); 4486 ierr = DMPlexReferenceTreeRestoreChildrenMatrices_Injection(refTree,injRef,&childrenMats);CHKERRQ(ierr); 4487 ierr = PetscFree(rootValues);CHKERRQ(ierr); 4488 ierr = PetscFree3(offsets,offsetsCopy,rowOffsets);CHKERRQ(ierr); 4489 PetscFunctionReturn(0); 4490 } 4491 4492 #undef __FUNCT__ 4493 #define __FUNCT__ "DMPlexTransferVecTree" 4494 PetscErrorCode DMPlexTransferVecTree(DM dmIn, Vec vecIn, DM dmOut, Vec vecOut, PetscSF sfIn, PetscSF sfOut, PetscInt *cidsIn, PetscInt *cidsOut, PetscBool useBCs, PetscReal time) 4495 { 4496 PetscErrorCode ierr; 4497 4498 PetscFunctionBegin; 4499 if (sfIn) { 4500 Vec vecInLocal; 4501 DM dmGrad = NULL; 4502 Vec faceGeom = NULL, cellGeom = NULL, grad = NULL; 4503 4504 ierr = DMGetLocalVector(dmIn,&vecInLocal);CHKERRQ(ierr); 4505 ierr = VecSet(vecInLocal,0.0);CHKERRQ(ierr); 4506 { 4507 PetscInt numFields, i; 4508 4509 ierr = DMGetNumFields(dmIn, &numFields);CHKERRQ(ierr); 4510 for (i = 0; i < numFields; i++) { 4511 PetscObject obj; 4512 PetscClassId classid; 4513 4514 ierr = DMGetField(dmIn, i, &obj);CHKERRQ(ierr); 4515 ierr = PetscObjectGetClassId(obj, &classid);CHKERRQ(ierr); 4516 if (classid == PETSCFV_CLASSID) { 4517 ierr = DMPlexGetDataFVM(dmIn,(PetscFV)obj,&cellGeom,&faceGeom,&dmGrad);CHKERRQ(ierr); 4518 break; 4519 } 4520 } 4521 } 4522 if (useBCs) { 4523 ierr = DMPlexInsertBoundaryValues(dmIn,PETSC_TRUE,vecInLocal,time,faceGeom,cellGeom,NULL);CHKERRQ(ierr); 4524 } 4525 ierr = DMGlobalToLocalBegin(dmIn,vecIn,INSERT_VALUES,vecInLocal);CHKERRQ(ierr); 4526 ierr = DMGlobalToLocalEnd(dmIn,vecIn,INSERT_VALUES,vecInLocal);CHKERRQ(ierr); 4527 if (dmGrad) { 4528 ierr = DMGetGlobalVector(dmGrad,&grad);CHKERRQ(ierr); 4529 ierr = DMPlexReconstructGradientsFVM(dmIn,vecInLocal,grad);CHKERRQ(ierr); 4530 } 4531 ierr = DMPlexTransferVecTree_Interpolate(dmIn,vecInLocal,dmOut,vecOut,sfIn,cidsIn,grad,cellGeom);CHKERRQ(ierr); 4532 ierr = DMRestoreLocalVector(dmIn,&vecInLocal);CHKERRQ(ierr); 4533 if (dmGrad) { 4534 ierr = DMRestoreGlobalVector(dmGrad,&grad);CHKERRQ(ierr); 4535 } 4536 } 4537 if (sfOut) { 4538 ierr = DMPlexTransferVecTree_Inject(dmIn,vecIn,dmOut,vecOut,sfOut,cidsOut);CHKERRQ(ierr); 4539 } 4540 ierr = VecAssemblyBegin(vecOut);CHKERRQ(ierr); 4541 ierr = VecAssemblyEnd(vecOut);CHKERRQ(ierr); 4542 PetscFunctionReturn(0); 4543 } 4544