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; 2238 2239 for (p = pStartF, numPointsWithDofs = 0; p < pEndF; p++) { 2240 ierr = PetscSectionGetDof(globalFine,p,&dof);CHKERRQ(ierr); 2241 ierr = PetscSectionGetConstraintDof(globalFine,p,&cdof);CHKERRQ(ierr); 2242 if ((dof - cdof) > 0) { 2243 numPointsWithDofs++; 2244 } 2245 } 2246 ierr = PetscMalloc1(numPointsWithDofs,&pointsWithDofs);CHKERRQ(ierr); 2247 for (p = pStartF, offset = 0; p < pEndF; p++) { 2248 ierr = PetscSectionGetDof(globalFine,p,&dof);CHKERRQ(ierr); 2249 ierr = PetscSectionGetConstraintDof(globalFine,p,&cdof);CHKERRQ(ierr); 2250 if ((dof - cdof) > 0) { 2251 pointsWithDofs[offset++] = p - pStartF; 2252 } 2253 } 2254 ierr = PetscSFCreateEmbeddedLeafSF(coarseToFine, numPointsWithDofs, pointsWithDofs, &coarseToFineEmbedded);CHKERRQ(ierr); 2255 ierr = PetscFree(pointsWithDofs);CHKERRQ(ierr); 2256 } 2257 /* communicate back to the coarse mesh which coarse points have children (that may require interpolation) */ 2258 ierr = PetscMalloc1(pEndC-pStartC,&maxChildIds);CHKERRQ(ierr); 2259 for (p = pStartC; p < pEndC; p++) { 2260 maxChildIds[p - pStartC] = -2; 2261 } 2262 ierr = PetscSFReduceBegin(coarseToFineEmbedded,MPIU_INT,childIds,maxChildIds,MPIU_MAX);CHKERRQ(ierr); 2263 ierr = PetscSFReduceEnd(coarseToFineEmbedded,MPIU_INT,childIds,maxChildIds,MPIU_MAX);CHKERRQ(ierr); 2264 2265 ierr = DMGetDefaultSection(coarse,&localCoarse);CHKERRQ(ierr); 2266 ierr = DMGetDefaultGlobalSection(coarse,&globalCoarse);CHKERRQ(ierr); 2267 2268 ierr = DMPlexGetAnchors(coarse,&aSec,&aIS);CHKERRQ(ierr); 2269 ierr = ISGetIndices(aIS,&anchors);CHKERRQ(ierr); 2270 ierr = PetscSectionGetChart(aSec,&aStart,&aEnd);CHKERRQ(ierr); 2271 2272 ierr = DMGetDefaultConstraints(coarse,&cSec,&cMat);CHKERRQ(ierr); 2273 ierr = PetscSectionGetChart(cSec,&cStart,&cEnd);CHKERRQ(ierr); 2274 2275 /* create sections that will send to children the indices and matrices they will need to construct the interpolator */ 2276 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)coarse),&rootIndicesSec);CHKERRQ(ierr); 2277 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)coarse),&rootMatricesSec);CHKERRQ(ierr); 2278 ierr = PetscSectionSetChart(rootIndicesSec,pStartC,pEndC);CHKERRQ(ierr); 2279 ierr = PetscSectionSetChart(rootMatricesSec,pStartC,pEndC);CHKERRQ(ierr); 2280 ierr = PetscSectionGetNumFields(localCoarse,&numFields);CHKERRQ(ierr); 2281 { 2282 PetscInt maxFields = PetscMax(1,numFields) + 1; 2283 ierr = PetscMalloc7(maxFields,&offsets,maxFields,&offsetsCopy,maxFields,&newOffsets,maxFields,&newOffsetsCopy,maxFields,&rowOffsets,maxFields,&numD,maxFields,&numO);CHKERRQ(ierr); 2284 } 2285 2286 for (p = pStartC; p < pEndC; p++) { /* count the sizes of the indices and matrices */ 2287 PetscInt dof, matSize = 0; 2288 PetscInt aDof = 0; 2289 PetscInt cDof = 0; 2290 PetscInt maxChildId = maxChildIds[p - pStartC]; 2291 PetscInt numRowIndices = 0; 2292 PetscInt numColIndices = 0; 2293 PetscInt f; 2294 2295 ierr = PetscSectionGetDof(globalCoarse,p,&dof);CHKERRQ(ierr); 2296 if (dof < 0) { 2297 dof = -(dof + 1); 2298 } 2299 if (p >= aStart && p < aEnd) { 2300 ierr = PetscSectionGetDof(aSec,p,&aDof);CHKERRQ(ierr); 2301 } 2302 if (p >= cStart && p < cEnd) { 2303 ierr = PetscSectionGetDof(cSec,p,&cDof);CHKERRQ(ierr); 2304 } 2305 for (f = 0; f <= numFields; f++) offsets[f] = 0; 2306 for (f = 0; f <= numFields; f++) newOffsets[f] = 0; 2307 if (maxChildId >= 0) { /* this point has children (with dofs) that will need to be interpolated from the closure of p */ 2308 PetscInt *closure = NULL, closureSize, cl; 2309 2310 ierr = DMPlexGetTransitiveClosure(coarse,p,PETSC_TRUE,&closureSize,&closure);CHKERRQ(ierr); 2311 for (cl = 0; cl < closureSize; cl++) { /* get the closure */ 2312 PetscInt c = closure[2 * cl], clDof; 2313 2314 ierr = PetscSectionGetDof(localCoarse,c,&clDof);CHKERRQ(ierr); 2315 numRowIndices += clDof; 2316 for (f = 0; f < numFields; f++) { 2317 ierr = PetscSectionGetFieldDof(localCoarse,c,f,&clDof);CHKERRQ(ierr); 2318 offsets[f + 1] += clDof; 2319 } 2320 } 2321 for (f = 0; f < numFields; f++) { 2322 offsets[f + 1] += offsets[f]; 2323 newOffsets[f + 1] = offsets[f + 1]; 2324 } 2325 /* get the number of indices needed and their field offsets */ 2326 ierr = DMPlexAnchorsModifyMat(coarse,localCoarse,closureSize,numRowIndices,closure,NULL,NULL,&numColIndices,NULL,NULL,newOffsets,PETSC_FALSE);CHKERRQ(ierr); 2327 ierr = DMPlexRestoreTransitiveClosure(coarse,p,PETSC_TRUE,&closureSize,&closure);CHKERRQ(ierr); 2328 if (!numColIndices) { /* there are no hanging constraint modifications, so the matrix is just the identity: do not send it */ 2329 numColIndices = numRowIndices; 2330 matSize = 0; 2331 } 2332 else if (numFields) { /* we send one submat for each field: sum their sizes */ 2333 matSize = 0; 2334 for (f = 0; f < numFields; f++) { 2335 PetscInt numRow, numCol; 2336 2337 numRow = offsets[f + 1] - offsets[f]; 2338 numCol = newOffsets[f + 1] - newOffsets[f]; 2339 matSize += numRow * numCol; 2340 } 2341 } 2342 else { 2343 matSize = numRowIndices * numColIndices; 2344 } 2345 } else if (maxChildId == -1) { 2346 if (cDof > 0) { /* this point's dofs are interpolated via cMat: get the submatrix of cMat */ 2347 PetscInt aOff, a; 2348 2349 ierr = PetscSectionGetOffset(aSec,p,&aOff);CHKERRQ(ierr); 2350 for (f = 0; f < numFields; f++) { 2351 PetscInt fDof; 2352 2353 ierr = PetscSectionGetFieldDof(localCoarse,p,f,&fDof);CHKERRQ(ierr); 2354 offsets[f+1] = fDof; 2355 } 2356 for (a = 0; a < aDof; a++) { 2357 PetscInt anchor = anchors[a + aOff], aLocalDof; 2358 2359 ierr = PetscSectionGetDof(localCoarse,anchor,&aLocalDof);CHKERRQ(ierr); 2360 numColIndices += aLocalDof; 2361 for (f = 0; f < numFields; f++) { 2362 PetscInt fDof; 2363 2364 ierr = PetscSectionGetFieldDof(localCoarse,anchor,f,&fDof);CHKERRQ(ierr); 2365 newOffsets[f+1] += fDof; 2366 } 2367 } 2368 if (numFields) { 2369 matSize = 0; 2370 for (f = 0; f < numFields; f++) { 2371 matSize += offsets[f+1] * newOffsets[f+1]; 2372 } 2373 } 2374 else { 2375 matSize = numColIndices * dof; 2376 } 2377 } 2378 else { /* no children, and no constraints on dofs: just get the global indices */ 2379 numColIndices = dof; 2380 matSize = 0; 2381 } 2382 } 2383 /* we will pack the column indices with the field offsets */ 2384 ierr = PetscSectionSetDof(rootIndicesSec,p,numColIndices ? numColIndices+2*numFields : 0);CHKERRQ(ierr); 2385 ierr = PetscSectionSetDof(rootMatricesSec,p,matSize);CHKERRQ(ierr); 2386 } 2387 ierr = PetscSectionSetUp(rootIndicesSec);CHKERRQ(ierr); 2388 ierr = PetscSectionSetUp(rootMatricesSec);CHKERRQ(ierr); 2389 { 2390 PetscInt numRootIndices, numRootMatrices; 2391 2392 ierr = PetscSectionGetStorageSize(rootIndicesSec,&numRootIndices);CHKERRQ(ierr); 2393 ierr = PetscSectionGetStorageSize(rootMatricesSec,&numRootMatrices);CHKERRQ(ierr); 2394 ierr = PetscMalloc2(numRootIndices,&rootIndices,numRootMatrices,&rootMatrices);CHKERRQ(ierr); 2395 for (p = pStartC; p < pEndC; p++) { 2396 PetscInt numRowIndices, numColIndices, matSize, dof; 2397 PetscInt pIndOff, pMatOff, f; 2398 PetscInt *pInd; 2399 PetscInt maxChildId = maxChildIds[p - pStartC]; 2400 PetscScalar *pMat = NULL; 2401 2402 ierr = PetscSectionGetDof(rootIndicesSec,p,&numColIndices);CHKERRQ(ierr); 2403 if (!numColIndices) { 2404 continue; 2405 } 2406 for (f = 0; f <= numFields; f++) { 2407 offsets[f] = 0; 2408 newOffsets[f] = 0; 2409 offsetsCopy[f] = 0; 2410 newOffsetsCopy[f] = 0; 2411 } 2412 numColIndices -= 2 * numFields; 2413 ierr = PetscSectionGetOffset(rootIndicesSec,p,&pIndOff);CHKERRQ(ierr); 2414 pInd = &(rootIndices[pIndOff]); 2415 ierr = PetscSectionGetDof(rootMatricesSec,p,&matSize);CHKERRQ(ierr); 2416 if (matSize) { 2417 ierr = PetscSectionGetOffset(rootMatricesSec,p,&pMatOff);CHKERRQ(ierr); 2418 pMat = &rootMatrices[pMatOff]; 2419 } 2420 ierr = PetscSectionGetDof(globalCoarse,p,&dof);CHKERRQ(ierr); 2421 if (dof < 0) { 2422 dof = -(dof + 1); 2423 } 2424 if (maxChildId >= 0) { /* build an identity matrix, apply matrix constraints on the right */ 2425 PetscInt i, j; 2426 PetscInt numRowIndices = matSize / numColIndices; 2427 2428 if (!numRowIndices) { /* don't need to calculate the mat, just the indices */ 2429 PetscInt numIndices, *indices; 2430 ierr = DMPlexGetClosureIndices(coarse,localCoarse,globalCoarse,p,&numIndices,&indices,offsets);CHKERRQ(ierr); 2431 if (numIndices != numColIndices) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"mismatching constraint indices calculations"); 2432 for (i = 0; i < numColIndices; i++) { 2433 pInd[i] = indices[i]; 2434 } 2435 for (i = 0; i < numFields; i++) { 2436 pInd[numColIndices + i] = offsets[i+1]; 2437 pInd[numColIndices + numFields + i] = offsets[i+1]; 2438 } 2439 ierr = DMPlexRestoreClosureIndices(coarse,localCoarse,globalCoarse,p,&numIndices,&indices,offsets);CHKERRQ(ierr); 2440 } 2441 else { 2442 PetscInt closureSize, *closure = NULL, cl; 2443 PetscScalar *pMatIn, *pMatModified; 2444 PetscInt numPoints,*points; 2445 2446 ierr = DMGetWorkArray(coarse,numRowIndices * numRowIndices,PETSC_SCALAR,&pMatIn);CHKERRQ(ierr); 2447 for (i = 0; i < numRowIndices; i++) { /* initialize to the identity */ 2448 for (j = 0; j < numRowIndices; j++) { 2449 pMatIn[i * numRowIndices + j] = (i == j) ? 1. : 0.; 2450 } 2451 } 2452 ierr = DMPlexGetTransitiveClosure(coarse, p, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 2453 if (numFields) { 2454 for (cl = 0; cl < closureSize; cl++) { 2455 PetscInt c = closure[2 * cl]; 2456 2457 for (f = 0; f < numFields; f++) { 2458 PetscInt fDof; 2459 2460 ierr = PetscSectionGetFieldDof(localCoarse,c,f,&fDof);CHKERRQ(ierr); 2461 offsets[f + 1] += fDof; 2462 } 2463 } 2464 for (f = 0; f < numFields; f++) { 2465 offsets[f + 1] += offsets[f]; 2466 newOffsets[f + 1] = offsets[f + 1]; 2467 } 2468 } 2469 /* apply hanging node constraints on the right, get the new points and the new offsets */ 2470 ierr = DMPlexAnchorsModifyMat(coarse,localCoarse,closureSize,numRowIndices,closure,pMatIn,&numPoints,NULL,&points,&pMatModified,newOffsets,PETSC_FALSE);CHKERRQ(ierr); 2471 if (!numFields) { 2472 for (i = 0; i < numRowIndices * numColIndices; i++) { 2473 pMat[i] = pMatModified[i]; 2474 } 2475 } 2476 else { 2477 PetscInt i, j, count; 2478 for (f = 0, count = 0; f < numFields; f++) { 2479 for (i = offsets[f]; i < offsets[f+1]; i++) { 2480 for (j = newOffsets[f]; j < newOffsets[f+1]; j++, count++) { 2481 pMat[count] = pMatModified[i * numColIndices + j]; 2482 } 2483 } 2484 } 2485 } 2486 ierr = DMRestoreWorkArray(coarse,numRowIndices * numColIndices,PETSC_SCALAR,&pMatModified);CHKERRQ(ierr); 2487 ierr = DMPlexRestoreTransitiveClosure(coarse, p, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 2488 ierr = DMRestoreWorkArray(coarse,numRowIndices * numColIndices,PETSC_SCALAR,&pMatIn);CHKERRQ(ierr); 2489 if (numFields) { 2490 for (f = 0; f < numFields; f++) { 2491 pInd[numColIndices + f] = offsets[f+1]; 2492 pInd[numColIndices + numFields + f] = newOffsets[f+1]; 2493 } 2494 for (cl = 0; cl < numPoints*2; cl += 2) { 2495 PetscInt o = points[cl+1], globalOff, c = points[cl]; 2496 ierr = PetscSectionGetOffset(globalCoarse, c, &globalOff);CHKERRQ(ierr); 2497 DMPlexGetIndicesPointFields_Internal(localCoarse, c, globalOff < 0 ? -(globalOff+1) : globalOff, newOffsets, PETSC_FALSE, o, pInd); 2498 } 2499 } else { 2500 for (cl = 0; cl < numPoints*2; cl += 2) { 2501 PetscInt o = points[cl+1], c = points[cl], globalOff; 2502 ierr = PetscSectionGetOffset(globalCoarse, c, &globalOff);CHKERRQ(ierr); 2503 DMPlexGetIndicesPoint_Internal(localCoarse, c, globalOff < 0 ? -(globalOff+1) : globalOff, newOffsets, PETSC_FALSE, o, pInd); 2504 } 2505 } 2506 ierr = DMRestoreWorkArray(coarse,numPoints,PETSC_SCALAR,&points);CHKERRQ(ierr); 2507 } 2508 } 2509 else if (matSize) { 2510 PetscInt cOff; 2511 PetscInt *rowIndices, *colIndices, a, aDof, aOff; 2512 2513 numRowIndices = matSize / numColIndices; 2514 if (numRowIndices != dof) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Miscounted dofs"); 2515 ierr = DMGetWorkArray(coarse,numRowIndices,PETSC_INT,&rowIndices);CHKERRQ(ierr); 2516 ierr = DMGetWorkArray(coarse,numColIndices,PETSC_INT,&colIndices);CHKERRQ(ierr); 2517 ierr = PetscSectionGetOffset(cSec,p,&cOff);CHKERRQ(ierr); 2518 ierr = PetscSectionGetDof(aSec,p,&aDof);CHKERRQ(ierr); 2519 ierr = PetscSectionGetOffset(aSec,p,&aOff);CHKERRQ(ierr); 2520 if (numFields) { 2521 for (f = 0; f < numFields; f++) { 2522 PetscInt fDof; 2523 2524 ierr = PetscSectionGetFieldDof(cSec,p,f,&fDof);CHKERRQ(ierr); 2525 offsets[f + 1] = fDof; 2526 for (a = 0; a < aDof; a++) { 2527 PetscInt anchor = anchors[a + aOff]; 2528 ierr = PetscSectionGetFieldDof(localCoarse,anchor,f,&fDof);CHKERRQ(ierr); 2529 newOffsets[f + 1] += fDof; 2530 } 2531 } 2532 for (f = 0; f < numFields; f++) { 2533 offsets[f + 1] += offsets[f]; 2534 offsetsCopy[f + 1] = offsets[f + 1]; 2535 newOffsets[f + 1] += newOffsets[f]; 2536 newOffsetsCopy[f + 1] = newOffsets[f + 1]; 2537 } 2538 DMPlexGetIndicesPointFields_Internal(cSec,p,cOff,offsetsCopy,PETSC_TRUE,0,rowIndices);CHKERRQ(ierr); 2539 for (a = 0; a < aDof; a++) { 2540 PetscInt anchor = anchors[a + aOff], lOff; 2541 ierr = PetscSectionGetOffset(localCoarse,anchor,&lOff);CHKERRQ(ierr); 2542 DMPlexGetIndicesPointFields_Internal(localCoarse,anchor,lOff,newOffsetsCopy,PETSC_TRUE,0,colIndices);CHKERRQ(ierr); 2543 } 2544 } 2545 else { 2546 DMPlexGetIndicesPoint_Internal(cSec,p,cOff,offsetsCopy,PETSC_TRUE,0,rowIndices);CHKERRQ(ierr); 2547 for (a = 0; a < aDof; a++) { 2548 PetscInt anchor = anchors[a + aOff], lOff; 2549 ierr = PetscSectionGetOffset(localCoarse,anchor,&lOff);CHKERRQ(ierr); 2550 DMPlexGetIndicesPoint_Internal(localCoarse,anchor,lOff,newOffsetsCopy,PETSC_TRUE,0,colIndices);CHKERRQ(ierr); 2551 } 2552 } 2553 if (numFields) { 2554 PetscInt count, a; 2555 2556 for (f = 0, count = 0; f < numFields; f++) { 2557 PetscInt iSize = offsets[f + 1] - offsets[f]; 2558 PetscInt jSize = newOffsets[f + 1] - newOffsets[f]; 2559 ierr = MatGetValues(cMat,iSize,&rowIndices[offsets[f]],jSize,&colIndices[newOffsets[f]],&pMat[count]);CHKERRQ(ierr); 2560 count += iSize * jSize; 2561 pInd[numColIndices + f] = offsets[f+1]; 2562 pInd[numColIndices + numFields + f] = newOffsets[f+1]; 2563 } 2564 for (a = 0; a < aDof; a++) { 2565 PetscInt anchor = anchors[a + aOff]; 2566 PetscInt gOff; 2567 ierr = PetscSectionGetOffset(globalCoarse,anchor,&gOff);CHKERRQ(ierr); 2568 DMPlexGetIndicesPointFields_Internal(localCoarse,anchor,gOff < 0 ? -(gOff + 1) : gOff,newOffsets,PETSC_FALSE,0,pInd);CHKERRQ(ierr); 2569 } 2570 } 2571 else { 2572 PetscInt a; 2573 ierr = MatGetValues(cMat,numRowIndices,rowIndices,numColIndices,colIndices,pMat);CHKERRQ(ierr); 2574 for (a = 0; a < aDof; a++) { 2575 PetscInt anchor = anchors[a + aOff]; 2576 PetscInt gOff; 2577 ierr = PetscSectionGetOffset(globalCoarse,anchor,&gOff);CHKERRQ(ierr); 2578 DMPlexGetIndicesPoint_Internal(localCoarse,anchor,gOff < 0 ? -(gOff + 1) : gOff,newOffsets,PETSC_FALSE,0,pInd);CHKERRQ(ierr); 2579 } 2580 } 2581 ierr = DMRestoreWorkArray(coarse,numColIndices,PETSC_INT,&colIndices);CHKERRQ(ierr); 2582 ierr = DMRestoreWorkArray(coarse,numRowIndices,PETSC_INT,&rowIndices);CHKERRQ(ierr); 2583 } 2584 else { 2585 PetscInt gOff; 2586 2587 ierr = PetscSectionGetOffset(globalCoarse,p,&gOff);CHKERRQ(ierr); 2588 if (numFields) { 2589 for (f = 0; f < numFields; f++) { 2590 PetscInt fDof; 2591 ierr = PetscSectionGetFieldDof(localCoarse,p,f,&fDof);CHKERRQ(ierr); 2592 offsets[f + 1] = fDof + offsets[f]; 2593 } 2594 for (f = 0; f < numFields; f++) { 2595 pInd[numColIndices + f] = offsets[f+1]; 2596 pInd[numColIndices + numFields + f] = offsets[f+1]; 2597 } 2598 DMPlexGetIndicesPointFields_Internal(localCoarse,p,gOff < 0 ? -(gOff + 1) : gOff,offsets,PETSC_FALSE,0,pInd);CHKERRQ(ierr); 2599 } 2600 else { 2601 DMPlexGetIndicesPoint_Internal(localCoarse,p,gOff < 0 ? -(gOff + 1) : gOff,offsets,PETSC_FALSE,0,pInd);CHKERRQ(ierr); 2602 } 2603 } 2604 } 2605 ierr = PetscFree(maxChildIds);CHKERRQ(ierr); 2606 } 2607 { 2608 PetscSF indicesSF, matricesSF; 2609 PetscInt *remoteOffsetsIndices, *remoteOffsetsMatrices, numLeafIndices, numLeafMatrices; 2610 2611 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)fine),&leafIndicesSec);CHKERRQ(ierr); 2612 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)fine),&leafMatricesSec);CHKERRQ(ierr); 2613 ierr = PetscSFDistributeSection(coarseToFineEmbedded,rootIndicesSec,&remoteOffsetsIndices,leafIndicesSec);CHKERRQ(ierr); 2614 ierr = PetscSFDistributeSection(coarseToFineEmbedded,rootMatricesSec,&remoteOffsetsMatrices,leafMatricesSec);CHKERRQ(ierr); 2615 ierr = PetscSFCreateSectionSF(coarseToFineEmbedded,rootIndicesSec,remoteOffsetsIndices,leafIndicesSec,&indicesSF);CHKERRQ(ierr); 2616 ierr = PetscSFCreateSectionSF(coarseToFineEmbedded,rootMatricesSec,remoteOffsetsMatrices,leafMatricesSec,&matricesSF);CHKERRQ(ierr); 2617 ierr = PetscSFDestroy(&coarseToFineEmbedded);CHKERRQ(ierr); 2618 ierr = PetscFree(remoteOffsetsIndices);CHKERRQ(ierr); 2619 ierr = PetscFree(remoteOffsetsMatrices);CHKERRQ(ierr); 2620 ierr = PetscSectionGetStorageSize(leafIndicesSec,&numLeafIndices);CHKERRQ(ierr); 2621 ierr = PetscSectionGetStorageSize(leafMatricesSec,&numLeafMatrices);CHKERRQ(ierr); 2622 ierr = PetscMalloc2(numLeafIndices,&leafIndices,numLeafMatrices,&leafMatrices);CHKERRQ(ierr); 2623 ierr = PetscSFBcastBegin(indicesSF,MPIU_INT,rootIndices,leafIndices);CHKERRQ(ierr); 2624 ierr = PetscSFBcastBegin(matricesSF,MPIU_SCALAR,rootMatrices,leafMatrices);CHKERRQ(ierr); 2625 ierr = PetscSFBcastEnd(indicesSF,MPIU_INT,rootIndices,leafIndices);CHKERRQ(ierr); 2626 ierr = PetscSFBcastEnd(matricesSF,MPIU_SCALAR,rootMatrices,leafMatrices);CHKERRQ(ierr); 2627 ierr = PetscSFDestroy(&matricesSF);CHKERRQ(ierr); 2628 ierr = PetscSFDestroy(&indicesSF);CHKERRQ(ierr); 2629 ierr = PetscFree2(rootIndices,rootMatrices);CHKERRQ(ierr); 2630 ierr = PetscSectionDestroy(&rootIndicesSec);CHKERRQ(ierr); 2631 ierr = PetscSectionDestroy(&rootMatricesSec);CHKERRQ(ierr); 2632 } 2633 /* count to preallocate */ 2634 ierr = DMGetDefaultSection(fine,&localFine);CHKERRQ(ierr); 2635 { 2636 PetscInt nGlobal; 2637 PetscInt *dnnz, *onnz; 2638 PetscLayout rowMap, colMap; 2639 PetscInt rowStart, rowEnd, colStart, colEnd; 2640 PetscInt maxDof; 2641 PetscInt *rowIndices; 2642 DM refTree; 2643 PetscInt **refPointFieldN; 2644 PetscScalar ***refPointFieldMats; 2645 PetscSection refConSec, refAnSec; 2646 PetscInt pRefStart,pRefEnd,maxConDof,maxColumns,leafStart,leafEnd; 2647 PetscScalar *pointWork; 2648 2649 ierr = PetscSectionGetConstrainedStorageSize(globalFine,&nGlobal);CHKERRQ(ierr); 2650 ierr = PetscCalloc2(nGlobal,&dnnz,nGlobal,&onnz);CHKERRQ(ierr); 2651 ierr = MatGetLayouts(mat,&rowMap,&colMap);CHKERRQ(ierr); 2652 ierr = PetscLayoutSetUp(rowMap);CHKERRQ(ierr); 2653 ierr = PetscLayoutSetUp(colMap);CHKERRQ(ierr); 2654 ierr = PetscLayoutGetRange(rowMap,&rowStart,&rowEnd);CHKERRQ(ierr); 2655 ierr = PetscLayoutGetRange(colMap,&colStart,&colEnd);CHKERRQ(ierr); 2656 ierr = PetscSectionGetMaxDof(globalFine,&maxDof);CHKERRQ(ierr); 2657 ierr = PetscSectionGetChart(leafIndicesSec,&leafStart,&leafEnd);CHKERRQ(ierr); 2658 ierr = DMGetWorkArray(fine,maxDof,PETSC_INT,&rowIndices);CHKERRQ(ierr); 2659 for (p = leafStart; p < leafEnd; p++) { 2660 PetscInt gDof, gcDof, gOff; 2661 PetscInt numColIndices, pIndOff, *pInd; 2662 PetscInt matSize; 2663 PetscInt i; 2664 2665 ierr = PetscSectionGetDof(globalFine,p,&gDof);CHKERRQ(ierr); 2666 ierr = PetscSectionGetConstraintDof(globalFine,p,&gcDof);CHKERRQ(ierr); 2667 if ((gDof - gcDof) <= 0) { 2668 continue; 2669 } 2670 ierr = PetscSectionGetOffset(globalFine,p,&gOff);CHKERRQ(ierr); 2671 if (gOff < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"I though having global dofs meant a non-negative offset"); 2672 if ((gOff < rowStart) || ((gOff + gDof - gcDof) > rowEnd)) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"I thought the row map would constrain the global dofs"); 2673 ierr = PetscSectionGetDof(leafIndicesSec,p,&numColIndices);CHKERRQ(ierr); 2674 ierr = PetscSectionGetOffset(leafIndicesSec,p,&pIndOff);CHKERRQ(ierr); 2675 numColIndices -= 2 * numFields; 2676 if (numColIndices <= 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"global fine dof with no dofs to interpolate from"); 2677 pInd = &leafIndices[pIndOff]; 2678 offsets[0] = 0; 2679 offsetsCopy[0] = 0; 2680 newOffsets[0] = 0; 2681 newOffsetsCopy[0] = 0; 2682 if (numFields) { 2683 PetscInt f; 2684 for (f = 0; f < numFields; f++) { 2685 PetscInt rowDof; 2686 2687 ierr = PetscSectionGetFieldDof(localFine,p,f,&rowDof);CHKERRQ(ierr); 2688 offsets[f + 1] = offsets[f] + rowDof; 2689 offsetsCopy[f + 1] = offsets[f + 1]; 2690 newOffsets[f + 1] = pInd[numColIndices + numFields + f]; 2691 numD[f] = 0; 2692 numO[f] = 0; 2693 } 2694 ierr = DMPlexGetIndicesPointFields_Internal(localFine,p,gOff,offsetsCopy,PETSC_FALSE,0,rowIndices);CHKERRQ(ierr); 2695 for (f = 0; f < numFields; f++) { 2696 PetscInt colOffset = newOffsets[f]; 2697 PetscInt numFieldCols = newOffsets[f + 1] - newOffsets[f]; 2698 2699 for (i = 0; i < numFieldCols; i++) { 2700 PetscInt gInd = pInd[i + colOffset]; 2701 2702 if (gInd >= colStart && gInd < colEnd) { 2703 numD[f]++; 2704 } 2705 else if (gInd >= 0) { /* negative means non-entry */ 2706 numO[f]++; 2707 } 2708 } 2709 } 2710 } 2711 else { 2712 ierr = DMPlexGetIndicesPoint_Internal(localFine,p,gOff,offsetsCopy,PETSC_FALSE,0,rowIndices);CHKERRQ(ierr); 2713 numD[0] = 0; 2714 numO[0] = 0; 2715 for (i = 0; i < numColIndices; i++) { 2716 PetscInt gInd = pInd[i]; 2717 2718 if (gInd >= colStart && gInd < colEnd) { 2719 numD[0]++; 2720 } 2721 else if (gInd >= 0) { /* negative means non-entry */ 2722 numO[0]++; 2723 } 2724 } 2725 } 2726 ierr = PetscSectionGetDof(leafMatricesSec,p,&matSize);CHKERRQ(ierr); 2727 if (!matSize) { /* incoming matrix is identity */ 2728 PetscInt childId; 2729 2730 childId = childIds[p-pStartF]; 2731 if (childId < 0) { /* no child interpolation: one nnz per */ 2732 if (numFields) { 2733 PetscInt f; 2734 for (f = 0; f < numFields; f++) { 2735 PetscInt numRows = offsets[f+1] - offsets[f], row; 2736 for (row = 0; row < numRows; row++) { 2737 PetscInt gIndCoarse = pInd[newOffsets[f] + row]; 2738 PetscInt gIndFine = rowIndices[offsets[f] + row]; 2739 if (gIndCoarse >= colStart && gIndCoarse < colEnd) { /* local */ 2740 if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs"); 2741 dnnz[gIndFine - rowStart] = 1; 2742 } 2743 else if (gIndCoarse >= 0) { /* remote */ 2744 if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs"); 2745 onnz[gIndFine - rowStart] = 1; 2746 } 2747 else { /* constrained */ 2748 if (gIndFine >= 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs"); 2749 } 2750 } 2751 } 2752 } 2753 else { 2754 PetscInt i; 2755 for (i = 0; i < gDof; i++) { 2756 PetscInt gIndCoarse = pInd[i]; 2757 PetscInt gIndFine = rowIndices[i]; 2758 if (gIndCoarse >= colStart && gIndCoarse < colEnd) { /* local */ 2759 if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs"); 2760 dnnz[gIndFine - rowStart] = 1; 2761 } 2762 else if (gIndCoarse >= 0) { /* remote */ 2763 if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs"); 2764 onnz[gIndFine - rowStart] = 1; 2765 } 2766 else { /* constrained */ 2767 if (gIndFine >= 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs"); 2768 } 2769 } 2770 } 2771 } 2772 else { /* interpolate from all */ 2773 if (numFields) { 2774 PetscInt f; 2775 for (f = 0; f < numFields; f++) { 2776 PetscInt numRows = offsets[f+1] - offsets[f], row; 2777 for (row = 0; row < numRows; row++) { 2778 PetscInt gIndFine = rowIndices[offsets[f] + row]; 2779 if (gIndFine >= 0) { 2780 if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs"); 2781 dnnz[gIndFine - rowStart] = numD[f]; 2782 onnz[gIndFine - rowStart] = numO[f]; 2783 } 2784 } 2785 } 2786 } 2787 else { 2788 PetscInt i; 2789 for (i = 0; i < gDof; i++) { 2790 PetscInt gIndFine = rowIndices[i]; 2791 if (gIndFine >= 0) { 2792 if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs"); 2793 dnnz[gIndFine - rowStart] = numD[0]; 2794 onnz[gIndFine - rowStart] = numO[0]; 2795 } 2796 } 2797 } 2798 } 2799 } 2800 else { /* interpolate from all */ 2801 if (numFields) { 2802 PetscInt f; 2803 for (f = 0; f < numFields; f++) { 2804 PetscInt numRows = offsets[f+1] - offsets[f], row; 2805 for (row = 0; row < numRows; row++) { 2806 PetscInt gIndFine = rowIndices[offsets[f] + row]; 2807 if (gIndFine >= 0) { 2808 if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs"); 2809 dnnz[gIndFine - rowStart] = numD[f]; 2810 onnz[gIndFine - rowStart] = numO[f]; 2811 } 2812 } 2813 } 2814 } 2815 else { /* every dof get a full row */ 2816 PetscInt i; 2817 for (i = 0; i < gDof; i++) { 2818 PetscInt gIndFine = rowIndices[i]; 2819 if (gIndFine >= 0) { 2820 if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs"); 2821 dnnz[gIndFine - rowStart] = numD[0]; 2822 onnz[gIndFine - rowStart] = numO[0]; 2823 } 2824 } 2825 } 2826 } 2827 } 2828 ierr = MatXAIJSetPreallocation(mat,1,dnnz,onnz,NULL,NULL);CHKERRQ(ierr); 2829 ierr = PetscFree2(dnnz,onnz);CHKERRQ(ierr); 2830 2831 ierr = DMPlexGetReferenceTree(fine,&refTree);CHKERRQ(ierr); 2832 ierr = DMPlexReferenceTreeGetChildrenMatrices(refTree,&refPointFieldMats,&refPointFieldN);CHKERRQ(ierr); 2833 ierr = DMGetDefaultConstraints(refTree,&refConSec,NULL);CHKERRQ(ierr); 2834 ierr = DMPlexGetAnchors(refTree,&refAnSec,NULL);CHKERRQ(ierr); 2835 ierr = PetscSectionGetChart(refConSec,&pRefStart,&pRefEnd);CHKERRQ(ierr); 2836 ierr = PetscSectionGetMaxDof(refConSec,&maxConDof);CHKERRQ(ierr); 2837 ierr = PetscSectionGetMaxDof(leafIndicesSec,&maxColumns);CHKERRQ(ierr); 2838 ierr = PetscMalloc1(maxConDof*maxColumns,&pointWork);CHKERRQ(ierr); 2839 for (p = leafStart; p < leafEnd; p++) { 2840 PetscInt gDof, gcDof, gOff; 2841 PetscInt numColIndices, pIndOff, *pInd; 2842 PetscInt matSize; 2843 PetscInt childId; 2844 2845 2846 ierr = PetscSectionGetDof(globalFine,p,&gDof);CHKERRQ(ierr); 2847 ierr = PetscSectionGetConstraintDof(globalFine,p,&gcDof);CHKERRQ(ierr); 2848 if ((gDof - gcDof) <= 0) { 2849 continue; 2850 } 2851 childId = childIds[p-pStartF]; 2852 ierr = PetscSectionGetOffset(globalFine,p,&gOff);CHKERRQ(ierr); 2853 ierr = PetscSectionGetDof(leafIndicesSec,p,&numColIndices);CHKERRQ(ierr); 2854 ierr = PetscSectionGetOffset(leafIndicesSec,p,&pIndOff);CHKERRQ(ierr); 2855 numColIndices -= 2 * numFields; 2856 pInd = &leafIndices[pIndOff]; 2857 offsets[0] = 0; 2858 offsetsCopy[0] = 0; 2859 newOffsets[0] = 0; 2860 newOffsetsCopy[0] = 0; 2861 rowOffsets[0] = 0; 2862 if (numFields) { 2863 PetscInt f; 2864 for (f = 0; f < numFields; f++) { 2865 PetscInt rowDof; 2866 2867 ierr = PetscSectionGetFieldDof(localFine,p,f,&rowDof);CHKERRQ(ierr); 2868 offsets[f + 1] = offsets[f] + rowDof; 2869 offsetsCopy[f + 1] = offsets[f + 1]; 2870 rowOffsets[f + 1] = pInd[numColIndices + f]; 2871 newOffsets[f + 1] = pInd[numColIndices + numFields + f]; 2872 } 2873 ierr = DMPlexGetIndicesPointFields_Internal(localFine,p,gOff,offsetsCopy,PETSC_FALSE,0,rowIndices);CHKERRQ(ierr); 2874 } 2875 else { 2876 ierr = DMPlexGetIndicesPoint_Internal(localFine,p,gOff,offsetsCopy,PETSC_FALSE,0,rowIndices);CHKERRQ(ierr); 2877 } 2878 ierr = PetscSectionGetDof(leafMatricesSec,p,&matSize);CHKERRQ(ierr); 2879 if (!matSize) { /* incoming matrix is identity */ 2880 if (childId < 0) { /* no child interpolation: scatter */ 2881 if (numFields) { 2882 PetscInt f; 2883 for (f = 0; f < numFields; f++) { 2884 PetscInt numRows = offsets[f+1] - offsets[f], row; 2885 for (row = 0; row < numRows; row++) { 2886 ierr = MatSetValue(mat,rowIndices[offsets[f]+row],pInd[newOffsets[f]+row],1.,INSERT_VALUES);CHKERRQ(ierr); 2887 } 2888 } 2889 } 2890 else { 2891 PetscInt numRows = gDof, row; 2892 for (row = 0; row < numRows; row++) { 2893 ierr = MatSetValue(mat,rowIndices[row],pInd[row],1.,INSERT_VALUES);CHKERRQ(ierr); 2894 } 2895 } 2896 } 2897 else { /* interpolate from all */ 2898 if (numFields) { 2899 PetscInt f; 2900 for (f = 0; f < numFields; f++) { 2901 PetscInt numRows = offsets[f+1] - offsets[f]; 2902 PetscInt numCols = newOffsets[f + 1] - newOffsets[f]; 2903 ierr = MatSetValues(mat,numRows,&rowIndices[offsets[f]],numCols,&pInd[newOffsets[f]],refPointFieldMats[childId - pRefStart][f],INSERT_VALUES);CHKERRQ(ierr); 2904 } 2905 } 2906 else { 2907 ierr = MatSetValues(mat,gDof,rowIndices,numColIndices,pInd,refPointFieldMats[childId - pRefStart][0],INSERT_VALUES);CHKERRQ(ierr); 2908 } 2909 } 2910 } 2911 else { /* interpolate from all */ 2912 PetscInt pMatOff; 2913 PetscScalar *pMat; 2914 2915 ierr = PetscSectionGetOffset(leafMatricesSec,p,&pMatOff);CHKERRQ(ierr); 2916 pMat = &leafMatrices[pMatOff]; 2917 if (childId < 0) { /* copy the incoming matrix */ 2918 if (numFields) { 2919 PetscInt f, count; 2920 for (f = 0, count = 0; f < numFields; f++) { 2921 PetscInt numRows = offsets[f+1]-offsets[f]; 2922 PetscInt numCols = newOffsets[f+1]-newOffsets[f]; 2923 PetscInt numInRows = rowOffsets[f+1]-rowOffsets[f]; 2924 PetscScalar *inMat = &pMat[count]; 2925 2926 ierr = MatSetValues(mat,numRows,&rowIndices[offsets[f]],numCols,&pInd[newOffsets[f]],inMat,INSERT_VALUES);CHKERRQ(ierr); 2927 count += numCols * numInRows; 2928 } 2929 } 2930 else { 2931 ierr = MatSetValues(mat,gDof,rowIndices,numColIndices,pInd,pMat,INSERT_VALUES);CHKERRQ(ierr); 2932 } 2933 } 2934 else { /* multiply the incoming matrix by the child interpolation */ 2935 if (numFields) { 2936 PetscInt f, count; 2937 for (f = 0, count = 0; f < numFields; f++) { 2938 PetscInt numRows = offsets[f+1]-offsets[f]; 2939 PetscInt numCols = newOffsets[f+1]-newOffsets[f]; 2940 PetscInt numInRows = rowOffsets[f+1]-rowOffsets[f]; 2941 PetscScalar *inMat = &pMat[count]; 2942 PetscInt i, j, k; 2943 if (refPointFieldN[childId - pRefStart][f] != numInRows) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Point constraint matrix multiply dimension mismatch"); 2944 for (i = 0; i < numRows; i++) { 2945 for (j = 0; j < numCols; j++) { 2946 PetscScalar val = 0.; 2947 for (k = 0; k < numInRows; k++) { 2948 val += refPointFieldMats[childId - pRefStart][f][i * numInRows + k] * inMat[k * numCols + j]; 2949 } 2950 pointWork[i * numCols + j] = val; 2951 } 2952 } 2953 ierr = MatSetValues(mat,numRows,&rowIndices[offsets[f]],numCols,&pInd[newOffsets[f]],pointWork,INSERT_VALUES);CHKERRQ(ierr); 2954 count += numCols * numInRows; 2955 } 2956 } 2957 else { /* every dof gets a full row */ 2958 PetscInt numRows = gDof; 2959 PetscInt numCols = numColIndices; 2960 PetscInt numInRows = matSize / numColIndices; 2961 PetscInt i, j, k; 2962 if (refPointFieldN[childId - pRefStart][0] != numInRows) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Point constraint matrix multiply dimension mismatch"); 2963 for (i = 0; i < numRows; i++) { 2964 for (j = 0; j < numCols; j++) { 2965 PetscScalar val = 0.; 2966 for (k = 0; k < numInRows; k++) { 2967 val += refPointFieldMats[childId - pRefStart][0][i * numInRows + k] * pMat[k * numCols + j]; 2968 } 2969 pointWork[i * numCols + j] = val; 2970 } 2971 } 2972 ierr = MatSetValues(mat,numRows,rowIndices,numCols,pInd,pointWork,INSERT_VALUES);CHKERRQ(ierr); 2973 } 2974 } 2975 } 2976 } 2977 ierr = DMPlexReferenceTreeRestoreChildrenMatrices(refTree,&refPointFieldMats,&refPointFieldN);CHKERRQ(ierr); 2978 ierr = DMRestoreWorkArray(fine,maxDof,PETSC_INT,&rowIndices);CHKERRQ(ierr); 2979 ierr = PetscFree(pointWork);CHKERRQ(ierr); 2980 } 2981 ierr = MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2982 ierr = MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2983 ierr = PetscSectionDestroy(&leafIndicesSec);CHKERRQ(ierr); 2984 ierr = PetscSectionDestroy(&leafMatricesSec);CHKERRQ(ierr); 2985 ierr = PetscFree2(leafIndices,leafMatrices);CHKERRQ(ierr); 2986 ierr = PetscFree7(offsets,offsetsCopy,newOffsets,newOffsetsCopy,rowOffsets,numD,numO);CHKERRQ(ierr); 2987 ierr = ISRestoreIndices(aIS,&anchors);CHKERRQ(ierr); 2988 PetscFunctionReturn(0); 2989 } 2990 2991 #undef __FUNCT__ 2992 #define __FUNCT__ "DMPlexComputeInjectorReferenceTree" 2993 /* 2994 * Assuming a nodal basis (w.r.t. the dual basis) basis: 2995 * 2996 * for each coarse dof \phi^c_i: 2997 * for each quadrature point (w_l,x_l) in the dual basis definition of \phi^c_i: 2998 * for each fine dof \phi^f_j; 2999 * a_{i,j} = 0; 3000 * for each fine dof \phi^f_k: 3001 * a_{i,j} += interp_{i,k} * \phi^f_k(x_l) * \phi^f_j(x_l) * w_l 3002 * [^^^ this is = \phi^c_i ^^^] 3003 */ 3004 PetscErrorCode DMPlexComputeInjectorReferenceTree(DM refTree, Mat *inj) 3005 { 3006 PetscDS ds; 3007 PetscSection section, cSection; 3008 DMLabel canonical, depth; 3009 Mat cMat, mat; 3010 PetscInt *nnz; 3011 PetscInt f, dim, numFields, numSecFields, p, pStart, pEnd, cStart, cEnd; 3012 PetscInt m, n; 3013 PetscScalar *pointScalar; 3014 PetscReal *v0, *v0parent, *vtmp, *J, *Jparent, *invJ, *pointRef, detJ, detJparent; 3015 PetscErrorCode ierr; 3016 3017 PetscFunctionBegin; 3018 ierr = DMGetDefaultSection(refTree,§ion);CHKERRQ(ierr); 3019 ierr = DMGetDimension(refTree, &dim);CHKERRQ(ierr); 3020 ierr = PetscMalloc6(dim,&v0,dim,&v0parent,dim,&vtmp,dim*dim,&J,dim*dim,&Jparent,dim*dim,&invJ);CHKERRQ(ierr); 3021 ierr = PetscMalloc2(dim,&pointScalar,dim,&pointRef);CHKERRQ(ierr); 3022 ierr = DMGetDS(refTree,&ds);CHKERRQ(ierr); 3023 ierr = PetscDSGetNumFields(ds,&numFields);CHKERRQ(ierr); 3024 ierr = PetscSectionGetNumFields(section,&numSecFields);CHKERRQ(ierr); 3025 ierr = DMGetLabel(refTree,"canonical",&canonical);CHKERRQ(ierr); 3026 ierr = DMGetLabel(refTree,"depth",&depth);CHKERRQ(ierr); 3027 ierr = DMGetDefaultConstraints(refTree,&cSection,&cMat);CHKERRQ(ierr); 3028 ierr = DMPlexGetChart(refTree, &pStart, &pEnd);CHKERRQ(ierr); 3029 ierr = DMPlexGetHeightStratum(refTree, 0, &cStart, &cEnd);CHKERRQ(ierr); 3030 ierr = MatGetSize(cMat,&n,&m);CHKERRQ(ierr); /* the injector has transpose sizes from the constraint matrix */ 3031 /* Step 1: compute non-zero pattern. A proper subset of constraint matrix non-zero */ 3032 ierr = PetscCalloc1(m,&nnz);CHKERRQ(ierr); 3033 for (p = pStart; p < pEnd; p++) { /* a point will have non-zeros if it is canonical, it has dofs, and its children have dofs */ 3034 const PetscInt *children; 3035 PetscInt numChildren; 3036 PetscInt i, numChildDof, numSelfDof; 3037 3038 if (canonical) { 3039 PetscInt pCanonical; 3040 ierr = DMLabelGetValue(canonical,p,&pCanonical);CHKERRQ(ierr); 3041 if (p != pCanonical) continue; 3042 } 3043 ierr = DMPlexGetTreeChildren(refTree,p,&numChildren,&children);CHKERRQ(ierr); 3044 if (!numChildren) continue; 3045 for (i = 0, numChildDof = 0; i < numChildren; i++) { 3046 PetscInt child = children[i]; 3047 PetscInt dof; 3048 3049 ierr = PetscSectionGetDof(section,child,&dof);CHKERRQ(ierr); 3050 numChildDof += dof; 3051 } 3052 ierr = PetscSectionGetDof(section,p,&numSelfDof);CHKERRQ(ierr); 3053 if (!numChildDof || !numSelfDof) continue; 3054 for (f = 0; f < numFields; f++) { 3055 PetscInt selfOff; 3056 3057 if (numSecFields) { /* count the dofs for just this field */ 3058 for (i = 0, numChildDof = 0; i < numChildren; i++) { 3059 PetscInt child = children[i]; 3060 PetscInt dof; 3061 3062 ierr = PetscSectionGetFieldDof(section,child,f,&dof);CHKERRQ(ierr); 3063 numChildDof += dof; 3064 } 3065 ierr = PetscSectionGetFieldDof(section,p,f,&numSelfDof);CHKERRQ(ierr); 3066 ierr = PetscSectionGetFieldOffset(section,p,f,&selfOff);CHKERRQ(ierr); 3067 } 3068 else { 3069 ierr = PetscSectionGetOffset(section,p,&selfOff);CHKERRQ(ierr); 3070 } 3071 for (i = 0; i < numSelfDof; i++) { 3072 nnz[selfOff + i] = numChildDof; 3073 } 3074 } 3075 } 3076 ierr = MatCreateAIJ(PETSC_COMM_SELF,m,n,m,n,-1,nnz,-1,NULL,&mat);CHKERRQ(ierr); 3077 ierr = PetscFree(nnz);CHKERRQ(ierr); 3078 /* Setp 2: compute entries */ 3079 for (p = pStart; p < pEnd; p++) { 3080 const PetscInt *children; 3081 PetscInt numChildren; 3082 PetscInt i, numChildDof, numSelfDof; 3083 3084 /* same conditions about when entries occur */ 3085 if (canonical) { 3086 PetscInt pCanonical; 3087 ierr = DMLabelGetValue(canonical,p,&pCanonical);CHKERRQ(ierr); 3088 if (p != pCanonical) continue; 3089 } 3090 ierr = DMPlexGetTreeChildren(refTree,p,&numChildren,&children);CHKERRQ(ierr); 3091 if (!numChildren) continue; 3092 for (i = 0, numChildDof = 0; i < numChildren; i++) { 3093 PetscInt child = children[i]; 3094 PetscInt dof; 3095 3096 ierr = PetscSectionGetDof(section,child,&dof);CHKERRQ(ierr); 3097 numChildDof += dof; 3098 } 3099 ierr = PetscSectionGetDof(section,p,&numSelfDof);CHKERRQ(ierr); 3100 if (!numChildDof || !numSelfDof) continue; 3101 3102 for (f = 0; f < numFields; f++) { 3103 PetscInt selfOff, fComp, numSelfShapes, numChildShapes, parentCell; 3104 PetscInt cellShapeOff; 3105 PetscObject disc; 3106 PetscDualSpace dsp; 3107 PetscClassId classId; 3108 PetscScalar *pointMat; 3109 PetscInt *matRows, *matCols; 3110 PetscInt pO = PETSC_MIN_INT; 3111 const PetscInt *depthNumDof; 3112 3113 if (numSecFields) { 3114 for (i = 0, numChildDof = 0; i < numChildren; i++) { 3115 PetscInt child = children[i]; 3116 PetscInt dof; 3117 3118 ierr = PetscSectionGetFieldDof(section,child,f,&dof);CHKERRQ(ierr); 3119 numChildDof += dof; 3120 } 3121 ierr = PetscSectionGetFieldDof(section,p,f,&numSelfDof);CHKERRQ(ierr); 3122 ierr = PetscSectionGetFieldOffset(section,p,f,&selfOff);CHKERRQ(ierr); 3123 ierr = PetscSectionGetFieldComponents(section,f,&fComp);CHKERRQ(ierr); 3124 } 3125 else { 3126 ierr = PetscSectionGetOffset(section,p,&selfOff);CHKERRQ(ierr); 3127 fComp = 1; 3128 } 3129 numSelfShapes = numSelfDof / fComp; 3130 numChildShapes = numChildDof / fComp; 3131 3132 /* find a cell whose closure contains p */ 3133 if (p >= cStart && p < cEnd) { 3134 parentCell = p; 3135 } 3136 else { 3137 PetscInt *star = NULL; 3138 PetscInt numStar; 3139 3140 parentCell = -1; 3141 ierr = DMPlexGetTransitiveClosure(refTree,p,PETSC_FALSE,&numStar,&star);CHKERRQ(ierr); 3142 for (i = numStar - 1; i >= 0; i--) { 3143 PetscInt c = star[2 * i]; 3144 3145 if (c >= cStart && c < cEnd) { 3146 parentCell = c; 3147 break; 3148 } 3149 } 3150 ierr = DMPlexRestoreTransitiveClosure(refTree,p,PETSC_FALSE,&numStar,&star);CHKERRQ(ierr); 3151 } 3152 /* determine the offset of p's shape functions withing parentCell's shape functions */ 3153 ierr = PetscDSGetDiscretization(ds,f,&disc);CHKERRQ(ierr); 3154 ierr = PetscObjectGetClassId(disc,&classId);CHKERRQ(ierr); 3155 if (classId == PETSCFE_CLASSID) { 3156 ierr = PetscFEGetDualSpace((PetscFE)disc,&dsp);CHKERRQ(ierr); 3157 } 3158 else if (classId == PETSCFV_CLASSID) { 3159 ierr = PetscFVGetDualSpace((PetscFV)disc,&dsp);CHKERRQ(ierr); 3160 } 3161 else { 3162 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Unsupported discretization object");CHKERRQ(ierr); 3163 } 3164 ierr = PetscDualSpaceGetNumDof(dsp,&depthNumDof);CHKERRQ(ierr); 3165 { 3166 PetscInt *closure = NULL; 3167 PetscInt numClosure; 3168 3169 ierr = DMPlexGetTransitiveClosure(refTree,parentCell,PETSC_TRUE,&numClosure,&closure);CHKERRQ(ierr); 3170 for (i = 0, cellShapeOff = 0; i < numClosure; i++) { 3171 PetscInt point = closure[2 * i], pointDepth; 3172 3173 pO = closure[2 * i + 1]; 3174 if (point == p) break; 3175 ierr = DMLabelGetValue(depth,point,&pointDepth);CHKERRQ(ierr); 3176 cellShapeOff += depthNumDof[pointDepth]; 3177 } 3178 ierr = DMPlexRestoreTransitiveClosure(refTree,parentCell,PETSC_TRUE,&numClosure,&closure);CHKERRQ(ierr); 3179 } 3180 3181 ierr = DMGetWorkArray(refTree, numSelfShapes * numChildShapes, PETSC_SCALAR,&pointMat);CHKERRQ(ierr); 3182 ierr = DMGetWorkArray(refTree, numSelfShapes + numChildShapes, PETSC_INT,&matRows);CHKERRQ(ierr); 3183 matCols = matRows + numSelfShapes; 3184 for (i = 0; i < numSelfShapes; i++) { 3185 matRows[i] = selfOff + i * fComp; 3186 } 3187 { 3188 PetscInt colOff = 0; 3189 3190 for (i = 0; i < numChildren; i++) { 3191 PetscInt child = children[i]; 3192 PetscInt dof, off, j; 3193 3194 if (numSecFields) { 3195 ierr = PetscSectionGetFieldDof(cSection,child,f,&dof);CHKERRQ(ierr); 3196 ierr = PetscSectionGetFieldOffset(cSection,child,f,&off);CHKERRQ(ierr); 3197 } 3198 else { 3199 ierr = PetscSectionGetDof(cSection,child,&dof);CHKERRQ(ierr); 3200 ierr = PetscSectionGetOffset(cSection,child,&off);CHKERRQ(ierr); 3201 } 3202 3203 for (j = 0; j < dof / fComp; j++) { 3204 matCols[colOff++] = off + j * fComp; 3205 } 3206 } 3207 } 3208 if (classId == PETSCFE_CLASSID) { 3209 PetscFE fe = (PetscFE) disc; 3210 PetscInt fSize; 3211 3212 ierr = PetscFEGetDualSpace(fe,&dsp);CHKERRQ(ierr); 3213 ierr = PetscDualSpaceGetDimension(dsp,&fSize);CHKERRQ(ierr); 3214 for (i = 0; i < numSelfShapes; i++) { /* for every shape function */ 3215 PetscQuadrature q; 3216 PetscInt dim, numPoints, j, k; 3217 const PetscReal *points; 3218 const PetscReal *weights; 3219 PetscInt *closure = NULL; 3220 PetscInt numClosure; 3221 PetscInt parentCellShapeDof = cellShapeOff + (pO < 0 ? (numSelfShapes - 1 - i) : i); 3222 PetscReal *Bparent; 3223 3224 ierr = PetscDualSpaceGetFunctional(dsp,parentCellShapeDof,&q);CHKERRQ(ierr); 3225 ierr = PetscQuadratureGetData(q,&dim,&numPoints,&points,&weights);CHKERRQ(ierr); 3226 ierr = PetscFEGetTabulation(fe,numPoints,points,&Bparent,NULL,NULL);CHKERRQ(ierr); /* I'm expecting a nodal basis: weights[:]' * Bparent[:,cellShapeDof] = 1. */ 3227 for (k = 0; k < numChildShapes; k++) { 3228 pointMat[numChildShapes * i + k] = 0.; 3229 } 3230 for (j = 0; j < numPoints; j++) { 3231 PetscInt childCell = -1; 3232 PetscReal parentValAtPoint; 3233 const PetscReal *pointReal = &points[dim * j]; 3234 const PetscScalar *point; 3235 PetscReal *Bchild; 3236 PetscInt childCellShapeOff, pointMatOff; 3237 #if defined(PETSC_USE_COMPLEX) 3238 PetscInt d; 3239 3240 for (d = 0; d < dim; d++) { 3241 pointScalar[d] = points[dim * j + d]; 3242 } 3243 point = pointScalar; 3244 #else 3245 point = pointReal; 3246 #endif 3247 3248 parentValAtPoint = Bparent[(fSize * j + parentCellShapeDof) * fComp]; 3249 3250 for (k = 0; k < numChildren; k++) { /* locate the point in a child's star cell*/ 3251 PetscInt child = children[k]; 3252 PetscInt *star = NULL; 3253 PetscInt numStar, s; 3254 3255 ierr = DMPlexGetTransitiveClosure(refTree,child,PETSC_FALSE,&numStar,&star);CHKERRQ(ierr); 3256 for (s = numStar - 1; s >= 0; s--) { 3257 PetscInt c = star[2 * s]; 3258 3259 if (c < cStart || c >= cEnd) continue; 3260 ierr = DMPlexLocatePoint_Internal(refTree,dim,point,c,&childCell);CHKERRQ(ierr); 3261 if (childCell >= 0) break; 3262 } 3263 ierr = DMPlexRestoreTransitiveClosure(refTree,child,PETSC_FALSE,&numStar,&star);CHKERRQ(ierr); 3264 if (childCell >= 0) break; 3265 } 3266 if (childCell < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Could not locate quadrature point");CHKERRQ(ierr); 3267 ierr = DMPlexComputeCellGeometryFEM(refTree, childCell, NULL, v0, J, invJ, &detJ);CHKERRQ(ierr); 3268 ierr = DMPlexComputeCellGeometryFEM(refTree, parentCell, NULL, v0parent, Jparent, NULL, &detJparent);CHKERRQ(ierr); 3269 CoordinatesRefToReal(dim, dim, v0parent, Jparent, pointReal, vtmp); 3270 CoordinatesRealToRef(dim, dim, v0, invJ, vtmp, pointRef); 3271 3272 ierr = PetscFEGetTabulation(fe,1,pointRef,&Bchild,NULL,NULL);CHKERRQ(ierr); 3273 ierr = DMPlexGetTransitiveClosure(refTree,childCell,PETSC_TRUE,&numClosure,&closure);CHKERRQ(ierr); 3274 for (k = 0, pointMatOff = 0; k < numChildren; k++) { /* point is located in cell => child dofs support at point are in closure of cell */ 3275 PetscInt child = children[k], childDepth, childDof, childO = PETSC_MIN_INT; 3276 PetscInt l; 3277 3278 ierr = DMLabelGetValue(depth,child,&childDepth);CHKERRQ(ierr); 3279 childDof = depthNumDof[childDepth]; 3280 for (l = 0, childCellShapeOff = 0; l < numClosure; l++) { 3281 PetscInt point = closure[2 * l]; 3282 PetscInt pointDepth; 3283 3284 childO = closure[2 * l + 1]; 3285 if (point == child) break; 3286 ierr = DMLabelGetValue(depth,point,&pointDepth);CHKERRQ(ierr); 3287 childCellShapeOff += depthNumDof[pointDepth]; 3288 } 3289 if (l == numClosure) { 3290 pointMatOff += childDof; 3291 continue; /* child is not in the closure of the cell: has nothing to contribute to this point */ 3292 } 3293 for (l = 0; l < childDof; l++) { 3294 PetscInt childCellDof = childCellShapeOff + (childO ? (childDof - 1 - l) : l); 3295 PetscReal childValAtPoint = Bchild[childCellDof * fComp]; 3296 3297 pointMat[i * numChildShapes + pointMatOff + l] += weights[j] * parentValAtPoint * childValAtPoint; 3298 } 3299 pointMatOff += childDof; 3300 } 3301 ierr = DMPlexRestoreTransitiveClosure(refTree,childCell,PETSC_TRUE,&numClosure,&closure);CHKERRQ(ierr); 3302 ierr = PetscFERestoreTabulation(fe,1,pointRef,&Bchild,NULL,NULL);CHKERRQ(ierr); 3303 } 3304 ierr = PetscFERestoreTabulation(fe,numPoints,points,&Bparent,NULL,NULL);CHKERRQ(ierr); 3305 } 3306 } 3307 else { /* just the volume-weighted averages of the children */ 3308 PetscInt childShapeOff; 3309 PetscReal parentVol; 3310 3311 ierr = DMPlexComputeCellGeometryFVM(refTree, p, &parentVol, NULL, NULL);CHKERRQ(ierr); 3312 for (i = 0, childShapeOff = 0; i < numChildren; i++) { 3313 PetscInt child = children[i]; 3314 PetscReal childVol; 3315 3316 if (child < cStart || child >= cEnd) continue; 3317 ierr = DMPlexComputeCellGeometryFVM(refTree, child, &childVol, NULL, NULL);CHKERRQ(ierr); 3318 pointMat[childShapeOff] = childVol / parentVol; 3319 childShapeOff++; 3320 } 3321 } 3322 /* Insert pointMat into mat */ 3323 for (i = 0; i < fComp; i++) { 3324 PetscInt j; 3325 ierr = MatSetValues(mat,numSelfShapes,matRows,numChildShapes,matCols,pointMat,INSERT_VALUES);CHKERRQ(ierr); 3326 3327 for (j = 0; j < numSelfShapes; j++) { 3328 matRows[j]++; 3329 } 3330 for (j = 0; j < numChildShapes; j++) { 3331 matCols[j]++; 3332 } 3333 } 3334 ierr = DMRestoreWorkArray(refTree, numSelfShapes + numChildShapes, PETSC_INT,&matRows);CHKERRQ(ierr); 3335 ierr = DMRestoreWorkArray(refTree, numSelfShapes * numChildShapes, PETSC_SCALAR,&pointMat);CHKERRQ(ierr); 3336 } 3337 } 3338 ierr = PetscFree6(v0,v0parent,vtmp,J,Jparent,invJ);CHKERRQ(ierr); 3339 ierr = PetscFree2(pointScalar,pointRef);CHKERRQ(ierr); 3340 ierr = MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3341 ierr = MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3342 *inj = mat; 3343 PetscFunctionReturn(0); 3344 } 3345 3346 #undef __FUNCT__ 3347 #define __FUNCT__ "DMPlexReferenceTreeGetChildrenMatrices_Injection" 3348 static PetscErrorCode DMPlexReferenceTreeGetChildrenMatrices_Injection(DM refTree, Mat inj, PetscScalar ****childrenMats) 3349 { 3350 PetscDS ds; 3351 PetscInt numFields, f, pRefStart, pRefEnd, p, *rows, *cols, maxDof; 3352 PetscScalar ***refPointFieldMats; 3353 PetscSection refConSec, refSection; 3354 PetscErrorCode ierr; 3355 3356 PetscFunctionBegin; 3357 ierr = DMGetDS(refTree,&ds);CHKERRQ(ierr); 3358 ierr = PetscDSGetNumFields(ds,&numFields);CHKERRQ(ierr); 3359 ierr = DMGetDefaultConstraints(refTree,&refConSec,NULL);CHKERRQ(ierr); 3360 ierr = DMGetDefaultSection(refTree,&refSection);CHKERRQ(ierr); 3361 ierr = PetscSectionGetChart(refConSec,&pRefStart,&pRefEnd);CHKERRQ(ierr); 3362 ierr = PetscMalloc1(pRefEnd-pRefStart,&refPointFieldMats);CHKERRQ(ierr); 3363 ierr = PetscSectionGetMaxDof(refConSec,&maxDof);CHKERRQ(ierr); 3364 ierr = PetscMalloc1(maxDof,&rows);CHKERRQ(ierr); 3365 ierr = PetscMalloc1(maxDof*maxDof,&cols);CHKERRQ(ierr); 3366 for (p = pRefStart; p < pRefEnd; p++) { 3367 PetscInt parent, pDof, parentDof; 3368 3369 ierr = DMPlexGetTreeParent(refTree,p,&parent,NULL);CHKERRQ(ierr); 3370 ierr = PetscSectionGetDof(refConSec,p,&pDof);CHKERRQ(ierr); 3371 ierr = PetscSectionGetDof(refSection,parent,&parentDof);CHKERRQ(ierr); 3372 if (!pDof || !parentDof || parent == p) continue; 3373 3374 ierr = PetscMalloc1(numFields,&refPointFieldMats[p-pRefStart]);CHKERRQ(ierr); 3375 for (f = 0; f < numFields; f++) { 3376 PetscInt cDof, cOff, numCols, r, fComp; 3377 PetscObject disc; 3378 PetscClassId id; 3379 PetscFE fe = NULL; 3380 PetscFV fv = NULL; 3381 3382 ierr = PetscDSGetDiscretization(ds,f,&disc);CHKERRQ(ierr); 3383 ierr = PetscObjectGetClassId(disc,&id);CHKERRQ(ierr); 3384 if (id == PETSCFE_CLASSID) { 3385 fe = (PetscFE) disc; 3386 ierr = PetscFEGetNumComponents(fe,&fComp);CHKERRQ(ierr); 3387 } 3388 else if (id == PETSCFV_CLASSID) { 3389 fv = (PetscFV) disc; 3390 ierr = PetscFVGetNumComponents(fv,&fComp);CHKERRQ(ierr); 3391 } 3392 else SETERRQ1(PetscObjectComm(disc),PETSC_ERR_ARG_UNKNOWN_TYPE, "PetscDS discretization id %d not recognized.", id); 3393 3394 if (numFields > 1) { 3395 ierr = PetscSectionGetFieldDof(refConSec,p,f,&cDof);CHKERRQ(ierr); 3396 ierr = PetscSectionGetFieldOffset(refConSec,p,f,&cOff);CHKERRQ(ierr); 3397 } 3398 else { 3399 ierr = PetscSectionGetDof(refConSec,p,&cDof);CHKERRQ(ierr); 3400 ierr = PetscSectionGetOffset(refConSec,p,&cOff);CHKERRQ(ierr); 3401 } 3402 3403 for (r = 0; r < cDof; r++) { 3404 rows[r] = cOff + r; 3405 } 3406 numCols = 0; 3407 { 3408 PetscInt aDof, aOff, j; 3409 3410 if (numFields > 1) { 3411 ierr = PetscSectionGetFieldDof(refSection,parent,f,&aDof);CHKERRQ(ierr); 3412 ierr = PetscSectionGetFieldOffset(refSection,parent,f,&aOff);CHKERRQ(ierr); 3413 } 3414 else { 3415 ierr = PetscSectionGetDof(refSection,parent,&aDof);CHKERRQ(ierr); 3416 ierr = PetscSectionGetOffset(refSection,parent,&aOff);CHKERRQ(ierr); 3417 } 3418 3419 for (j = 0; j < aDof; j++) { 3420 cols[numCols++] = aOff + j; 3421 } 3422 } 3423 ierr = PetscMalloc1(cDof*numCols,&refPointFieldMats[p-pRefStart][f]);CHKERRQ(ierr); 3424 /* transpose of constraint matrix */ 3425 ierr = MatGetValues(inj,numCols,cols,cDof,rows,refPointFieldMats[p-pRefStart][f]);CHKERRQ(ierr); 3426 } 3427 } 3428 *childrenMats = refPointFieldMats; 3429 ierr = PetscFree(rows);CHKERRQ(ierr); 3430 ierr = PetscFree(cols);CHKERRQ(ierr); 3431 PetscFunctionReturn(0); 3432 } 3433 3434 #undef __FUNCT__ 3435 #define __FUNCT__ "DMPlexReferenceTreeRestoreChildrenMatrices_Injection" 3436 static PetscErrorCode DMPlexReferenceTreeRestoreChildrenMatrices_Injection(DM refTree, Mat inj, PetscScalar ****childrenMats) 3437 { 3438 PetscDS ds; 3439 PetscScalar ***refPointFieldMats; 3440 PetscInt numFields, pRefStart, pRefEnd, p, f; 3441 PetscSection refConSec, refSection; 3442 PetscErrorCode ierr; 3443 3444 PetscFunctionBegin; 3445 refPointFieldMats = *childrenMats; 3446 *childrenMats = NULL; 3447 ierr = DMGetDS(refTree,&ds);CHKERRQ(ierr); 3448 ierr = DMGetDefaultSection(refTree,&refSection);CHKERRQ(ierr); 3449 ierr = PetscDSGetNumFields(ds,&numFields);CHKERRQ(ierr); 3450 ierr = DMGetDefaultConstraints(refTree,&refConSec,NULL);CHKERRQ(ierr); 3451 ierr = PetscSectionGetChart(refConSec,&pRefStart,&pRefEnd);CHKERRQ(ierr); 3452 for (p = pRefStart; p < pRefEnd; p++) { 3453 PetscInt parent, pDof, parentDof; 3454 3455 ierr = DMPlexGetTreeParent(refTree,p,&parent,NULL);CHKERRQ(ierr); 3456 ierr = PetscSectionGetDof(refConSec,p,&pDof);CHKERRQ(ierr); 3457 ierr = PetscSectionGetDof(refSection,parent,&parentDof);CHKERRQ(ierr); 3458 if (!pDof || !parentDof || parent == p) continue; 3459 3460 for (f = 0; f < numFields; f++) { 3461 PetscInt cDof; 3462 3463 if (numFields > 1) { 3464 ierr = PetscSectionGetFieldDof(refConSec,p,f,&cDof);CHKERRQ(ierr); 3465 } 3466 else { 3467 ierr = PetscSectionGetDof(refConSec,p,&cDof);CHKERRQ(ierr); 3468 } 3469 3470 ierr = PetscFree(refPointFieldMats[p - pRefStart][f]);CHKERRQ(ierr); 3471 } 3472 ierr = PetscFree(refPointFieldMats[p - pRefStart]);CHKERRQ(ierr); 3473 } 3474 ierr = PetscFree(refPointFieldMats);CHKERRQ(ierr); 3475 PetscFunctionReturn(0); 3476 } 3477 3478 #undef __FUNCT__ 3479 #define __FUNCT__ "DMPlexReferenceTreeGetInjector" 3480 static PetscErrorCode DMPlexReferenceTreeGetInjector(DM refTree,Mat *injRef) 3481 { 3482 Mat cMatRef; 3483 PetscObject injRefObj; 3484 PetscErrorCode ierr; 3485 3486 PetscFunctionBegin; 3487 ierr = DMGetDefaultConstraints(refTree,NULL,&cMatRef);CHKERRQ(ierr); 3488 ierr = PetscObjectQuery((PetscObject)cMatRef,"DMPlexComputeInjectorTree_refTree",&injRefObj);CHKERRQ(ierr); 3489 *injRef = (Mat) injRefObj; 3490 if (!*injRef) { 3491 ierr = DMPlexComputeInjectorReferenceTree(refTree,injRef);CHKERRQ(ierr); 3492 ierr = PetscObjectCompose((PetscObject)cMatRef,"DMPlexComputeInjectorTree_refTree",(PetscObject)*injRef);CHKERRQ(ierr); 3493 /* there is now a reference in cMatRef, which should be the only one for symmetry with the above case */ 3494 ierr = PetscObjectDereference((PetscObject)*injRef);CHKERRQ(ierr); 3495 } 3496 PetscFunctionReturn(0); 3497 } 3498 3499 #undef __FUNCT__ 3500 #define __FUNCT__ "DMPlexTransferInjectorTree" 3501 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) 3502 { 3503 PetscInt pStartF, pEndF, pStartC, pEndC, p, maxDof, numMulti; 3504 PetscSection globalCoarse, globalFine; 3505 PetscSection localCoarse, localFine, leafIndicesSec; 3506 PetscSection multiRootSec, rootIndicesSec; 3507 PetscInt *leafInds, *rootInds = NULL; 3508 const PetscInt *rootDegrees; 3509 PetscScalar *leafVals = NULL, *rootVals = NULL; 3510 PetscSF coarseToFineEmbedded; 3511 PetscErrorCode ierr; 3512 3513 PetscFunctionBegin; 3514 ierr = DMPlexGetChart(coarse,&pStartC,&pEndC);CHKERRQ(ierr); 3515 ierr = DMPlexGetChart(fine,&pStartF,&pEndF);CHKERRQ(ierr); 3516 ierr = DMGetDefaultSection(fine,&localFine);CHKERRQ(ierr); 3517 ierr = DMGetDefaultGlobalSection(fine,&globalFine);CHKERRQ(ierr); 3518 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)fine),&leafIndicesSec);CHKERRQ(ierr); 3519 ierr = PetscSectionSetChart(leafIndicesSec,pStartF, pEndF);CHKERRQ(ierr); 3520 ierr = PetscSectionGetMaxDof(localFine,&maxDof);CHKERRQ(ierr); 3521 { /* winnow fine points that don't have global dofs out of the sf */ 3522 PetscInt l, nleaves, dof, cdof, numPointsWithDofs, offset, *pointsWithDofs, numIndices; 3523 const PetscInt *leaves; 3524 3525 ierr = PetscSFGetGraph(coarseToFine,NULL,&nleaves,&leaves,NULL);CHKERRQ(ierr); 3526 for (l = 0, numPointsWithDofs = 0; l < nleaves; l++) { 3527 p = leaves ? leaves[l] : l; 3528 ierr = PetscSectionGetDof(globalFine,p,&dof);CHKERRQ(ierr); 3529 ierr = PetscSectionGetConstraintDof(globalFine,p,&cdof);CHKERRQ(ierr); 3530 if ((dof - cdof) > 0) { 3531 numPointsWithDofs++; 3532 3533 ierr = PetscSectionGetDof(localFine,p,&dof);CHKERRQ(ierr); 3534 ierr = PetscSectionSetDof(leafIndicesSec,p,dof + 1);CHKERRQ(ierr); 3535 } 3536 } 3537 ierr = PetscMalloc1(numPointsWithDofs,&pointsWithDofs);CHKERRQ(ierr); 3538 ierr = PetscSectionSetUp(leafIndicesSec);CHKERRQ(ierr); 3539 ierr = PetscSectionGetStorageSize(leafIndicesSec,&numIndices);CHKERRQ(ierr); 3540 ierr = PetscMalloc1(gatheredIndices ? numIndices : (maxDof + 1),&leafInds);CHKERRQ(ierr); 3541 if (gatheredValues) {ierr = PetscMalloc1(numIndices,&leafVals);CHKERRQ(ierr);} 3542 for (l = 0, offset = 0; l < nleaves; l++) { 3543 p = leaves ? leaves[l] : l; 3544 ierr = PetscSectionGetDof(globalFine,p,&dof);CHKERRQ(ierr); 3545 ierr = PetscSectionGetConstraintDof(globalFine,p,&cdof);CHKERRQ(ierr); 3546 if ((dof - cdof) > 0) { 3547 PetscInt off, gOff; 3548 PetscInt *pInd; 3549 PetscScalar *pVal = NULL; 3550 3551 pointsWithDofs[offset++] = l; 3552 3553 ierr = PetscSectionGetOffset(leafIndicesSec,p,&off);CHKERRQ(ierr); 3554 3555 pInd = gatheredIndices ? (&leafInds[off + 1]) : leafInds; 3556 if (gatheredValues) { 3557 PetscInt i; 3558 3559 pVal = &leafVals[off + 1]; 3560 for (i = 0; i < dof; i++) pVal[i] = 0.; 3561 } 3562 ierr = PetscSectionGetOffset(globalFine,p,&gOff);CHKERRQ(ierr); 3563 3564 offsets[0] = 0; 3565 if (numFields) { 3566 PetscInt f; 3567 3568 for (f = 0; f < numFields; f++) { 3569 PetscInt fDof; 3570 ierr = PetscSectionGetFieldDof(localFine,p,f,&fDof);CHKERRQ(ierr); 3571 offsets[f + 1] = fDof + offsets[f]; 3572 } 3573 DMPlexGetIndicesPointFields_Internal(localFine,p,gOff < 0 ? -(gOff + 1) : gOff,offsets,PETSC_FALSE,0,pInd);CHKERRQ(ierr); 3574 } 3575 else { 3576 DMPlexGetIndicesPoint_Internal(localFine,p,gOff < 0 ? -(gOff + 1) : gOff,offsets,PETSC_FALSE,0,pInd);CHKERRQ(ierr); 3577 } 3578 if (gatheredValues) {ierr = VecGetValues(fineVec,dof,pInd,pVal);CHKERRQ(ierr);} 3579 } 3580 } 3581 ierr = PetscSFCreateEmbeddedLeafSF(coarseToFine, numPointsWithDofs, pointsWithDofs, &coarseToFineEmbedded);CHKERRQ(ierr); 3582 ierr = PetscFree(pointsWithDofs);CHKERRQ(ierr); 3583 } 3584 3585 ierr = DMPlexGetChart(coarse,&pStartC,&pEndC);CHKERRQ(ierr); 3586 ierr = DMGetDefaultSection(coarse,&localCoarse);CHKERRQ(ierr); 3587 ierr = DMGetDefaultGlobalSection(coarse,&globalCoarse);CHKERRQ(ierr); 3588 3589 { /* there may be the case where an sf root has a parent: broadcast parents back to children */ 3590 MPI_Datatype threeInt; 3591 PetscMPIInt rank; 3592 PetscInt (*parentNodeAndIdCoarse)[3]; 3593 PetscInt (*parentNodeAndIdFine)[3]; 3594 PetscInt p, nleaves, nleavesToParents; 3595 PetscSF pointSF, sfToParents; 3596 const PetscInt *ilocal; 3597 const PetscSFNode *iremote; 3598 PetscSFNode *iremoteToParents; 3599 PetscInt *ilocalToParents; 3600 3601 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)coarse),&rank);CHKERRQ(ierr); 3602 ierr = MPI_Type_contiguous(3,MPIU_INT,&threeInt);CHKERRQ(ierr); 3603 ierr = MPI_Type_commit(&threeInt);CHKERRQ(ierr); 3604 ierr = PetscMalloc2(pEndC-pStartC,&parentNodeAndIdCoarse,pEndF-pStartF,&parentNodeAndIdFine);CHKERRQ(ierr); 3605 ierr = DMGetPointSF(coarse,&pointSF);CHKERRQ(ierr); 3606 ierr = PetscSFGetGraph(pointSF,NULL,&nleaves,&ilocal,&iremote);CHKERRQ(ierr); 3607 for (p = pStartC; p < pEndC; p++) { 3608 PetscInt parent, childId; 3609 ierr = DMPlexGetTreeParent(coarse,p,&parent,&childId);CHKERRQ(ierr); 3610 parentNodeAndIdCoarse[p - pStartC][0] = rank; 3611 parentNodeAndIdCoarse[p - pStartC][1] = parent - pStartC; 3612 parentNodeAndIdCoarse[p - pStartC][2] = (p == parent) ? -1 : childId; 3613 if (nleaves > 0) { 3614 PetscInt leaf = -1; 3615 3616 if (ilocal) { 3617 ierr = PetscFindInt(parent,nleaves,ilocal,&leaf);CHKERRQ(ierr); 3618 } 3619 else { 3620 leaf = p - pStartC; 3621 } 3622 if (leaf >= 0) { 3623 parentNodeAndIdCoarse[p - pStartC][0] = iremote[leaf].rank; 3624 parentNodeAndIdCoarse[p - pStartC][1] = iremote[leaf].index; 3625 } 3626 } 3627 } 3628 for (p = pStartF; p < pEndF; p++) { 3629 parentNodeAndIdFine[p - pStartF][0] = -1; 3630 parentNodeAndIdFine[p - pStartF][1] = -1; 3631 parentNodeAndIdFine[p - pStartF][2] = -1; 3632 } 3633 ierr = PetscSFBcastBegin(coarseToFineEmbedded,threeInt,parentNodeAndIdCoarse,parentNodeAndIdFine);CHKERRQ(ierr); 3634 ierr = PetscSFBcastEnd(coarseToFineEmbedded,threeInt,parentNodeAndIdCoarse,parentNodeAndIdFine);CHKERRQ(ierr); 3635 for (p = pStartF, nleavesToParents = 0; p < pEndF; p++) { 3636 PetscInt dof; 3637 3638 ierr = PetscSectionGetDof(leafIndicesSec,p,&dof);CHKERRQ(ierr); 3639 if (dof) { 3640 PetscInt off; 3641 3642 ierr = PetscSectionGetOffset(leafIndicesSec,p,&off);CHKERRQ(ierr); 3643 if (gatheredIndices) { 3644 leafInds[off] = PetscMax(childIds[p-pStartF],parentNodeAndIdFine[p-pStartF][2]); 3645 } else if (gatheredValues) { 3646 leafVals[off] = (PetscScalar) PetscMax(childIds[p-pStartF],parentNodeAndIdFine[p-pStartF][2]); 3647 } 3648 } 3649 if (parentNodeAndIdFine[p-pStartF][0] >= 0) { 3650 nleavesToParents++; 3651 } 3652 } 3653 ierr = PetscMalloc1(nleavesToParents,&ilocalToParents);CHKERRQ(ierr); 3654 ierr = PetscMalloc1(nleavesToParents,&iremoteToParents);CHKERRQ(ierr); 3655 for (p = pStartF, nleavesToParents = 0; p < pEndF; p++) { 3656 if (parentNodeAndIdFine[p-pStartF][0] >= 0) { 3657 ilocalToParents[nleavesToParents] = p - pStartF; 3658 iremoteToParents[nleavesToParents].rank = parentNodeAndIdFine[p-pStartF][0]; 3659 iremoteToParents[nleavesToParents].index = parentNodeAndIdFine[p-pStartF][1]; 3660 nleavesToParents++; 3661 } 3662 } 3663 ierr = PetscSFCreate(PetscObjectComm((PetscObject)coarse),&sfToParents);CHKERRQ(ierr); 3664 ierr = PetscSFSetGraph(sfToParents,pEndC-pStartC,nleavesToParents,ilocalToParents,PETSC_OWN_POINTER,iremoteToParents,PETSC_OWN_POINTER);CHKERRQ(ierr); 3665 ierr = PetscSFDestroy(&coarseToFineEmbedded);CHKERRQ(ierr); 3666 3667 coarseToFineEmbedded = sfToParents; 3668 3669 ierr = PetscFree2(parentNodeAndIdCoarse,parentNodeAndIdFine);CHKERRQ(ierr); 3670 ierr = MPI_Type_free(&threeInt);CHKERRQ(ierr); 3671 } 3672 3673 { /* winnow out coarse points that don't have dofs */ 3674 PetscInt dof, cdof, numPointsWithDofs, offset, *pointsWithDofs; 3675 PetscSF sfDofsOnly; 3676 3677 for (p = pStartC, numPointsWithDofs = 0; p < pEndC; p++) { 3678 ierr = PetscSectionGetDof(globalCoarse,p,&dof);CHKERRQ(ierr); 3679 ierr = PetscSectionGetConstraintDof(globalCoarse,p,&cdof);CHKERRQ(ierr); 3680 if ((dof - cdof) > 0) { 3681 numPointsWithDofs++; 3682 } 3683 } 3684 ierr = PetscMalloc1(numPointsWithDofs,&pointsWithDofs);CHKERRQ(ierr); 3685 for (p = pStartC, offset = 0; p < pEndC; p++) { 3686 ierr = PetscSectionGetDof(globalCoarse,p,&dof);CHKERRQ(ierr); 3687 ierr = PetscSectionGetConstraintDof(globalCoarse,p,&cdof);CHKERRQ(ierr); 3688 if ((dof - cdof) > 0) { 3689 pointsWithDofs[offset++] = p - pStartC; 3690 } 3691 } 3692 ierr = PetscSFCreateEmbeddedSF(coarseToFineEmbedded, numPointsWithDofs, pointsWithDofs, &sfDofsOnly);CHKERRQ(ierr); 3693 ierr = PetscSFDestroy(&coarseToFineEmbedded);CHKERRQ(ierr); 3694 ierr = PetscFree(pointsWithDofs);CHKERRQ(ierr); 3695 coarseToFineEmbedded = sfDofsOnly; 3696 } 3697 3698 /* communicate back to the coarse mesh which coarse points have children (that may require injection) */ 3699 ierr = PetscSFComputeDegreeBegin(coarseToFineEmbedded,&rootDegrees);CHKERRQ(ierr); 3700 ierr = PetscSFComputeDegreeEnd(coarseToFineEmbedded,&rootDegrees);CHKERRQ(ierr); 3701 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)coarse),&multiRootSec);CHKERRQ(ierr); 3702 ierr = PetscSectionSetChart(multiRootSec,pStartC,pEndC);CHKERRQ(ierr); 3703 for (p = pStartC; p < pEndC; p++) { 3704 ierr = PetscSectionSetDof(multiRootSec,p,rootDegrees[p-pStartC]);CHKERRQ(ierr); 3705 } 3706 ierr = PetscSectionSetUp(multiRootSec);CHKERRQ(ierr); 3707 ierr = PetscSectionGetStorageSize(multiRootSec,&numMulti);CHKERRQ(ierr); 3708 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)coarse),&rootIndicesSec);CHKERRQ(ierr); 3709 { /* distribute the leaf section */ 3710 PetscSF multi, multiInv, indicesSF; 3711 PetscInt *remoteOffsets, numRootIndices; 3712 3713 ierr = PetscSFGetMultiSF(coarseToFineEmbedded,&multi);CHKERRQ(ierr); 3714 ierr = PetscSFCreateInverseSF(multi,&multiInv);CHKERRQ(ierr); 3715 ierr = PetscSFDistributeSection(multiInv,leafIndicesSec,&remoteOffsets,rootIndicesSec);CHKERRQ(ierr); 3716 ierr = PetscSFCreateSectionSF(multiInv,leafIndicesSec,remoteOffsets,rootIndicesSec,&indicesSF);CHKERRQ(ierr); 3717 ierr = PetscFree(remoteOffsets);CHKERRQ(ierr); 3718 ierr = PetscSFDestroy(&multiInv);CHKERRQ(ierr); 3719 ierr = PetscSectionGetStorageSize(rootIndicesSec,&numRootIndices);CHKERRQ(ierr); 3720 if (gatheredIndices) { 3721 ierr = PetscMalloc1(numRootIndices,&rootInds);CHKERRQ(ierr); 3722 ierr = PetscSFBcastBegin(indicesSF,MPIU_INT,leafInds,rootInds);CHKERRQ(ierr); 3723 ierr = PetscSFBcastEnd(indicesSF,MPIU_INT,leafInds,rootInds);CHKERRQ(ierr); 3724 } 3725 if (gatheredValues) { 3726 ierr = PetscMalloc1(numRootIndices,&rootVals);CHKERRQ(ierr); 3727 ierr = PetscSFBcastBegin(indicesSF,MPIU_SCALAR,leafVals,rootVals);CHKERRQ(ierr); 3728 ierr = PetscSFBcastEnd(indicesSF,MPIU_SCALAR,leafVals,rootVals);CHKERRQ(ierr); 3729 } 3730 ierr = PetscSFDestroy(&indicesSF);CHKERRQ(ierr); 3731 } 3732 ierr = PetscSectionDestroy(&leafIndicesSec);CHKERRQ(ierr); 3733 ierr = PetscFree(leafInds);CHKERRQ(ierr); 3734 ierr = PetscFree(leafVals);CHKERRQ(ierr); 3735 ierr = PetscSFDestroy(&coarseToFineEmbedded);CHKERRQ(ierr); 3736 *rootMultiSec = multiRootSec; 3737 *multiLeafSec = rootIndicesSec; 3738 if (gatheredIndices) *gatheredIndices = rootInds; 3739 if (gatheredValues) *gatheredValues = rootVals; 3740 PetscFunctionReturn(0); 3741 } 3742 3743 #undef __FUNCT__ 3744 #define __FUNCT__ "DMPlexComputeInjectorTree" 3745 PetscErrorCode DMPlexComputeInjectorTree(DM coarse, DM fine, PetscSF coarseToFine, PetscInt *childIds, Mat mat) 3746 { 3747 DM refTree; 3748 PetscSection multiRootSec, rootIndicesSec; 3749 PetscSection globalCoarse, globalFine; 3750 PetscSection localCoarse, localFine; 3751 PetscSection cSecRef; 3752 PetscInt *rootIndices, *parentIndices, pRefStart, pRefEnd; 3753 Mat injRef; 3754 PetscInt numFields, maxDof; 3755 PetscInt pStartC, pEndC, pStartF, pEndF, p; 3756 PetscInt *offsets, *offsetsCopy, *rowOffsets; 3757 PetscLayout rowMap, colMap; 3758 PetscInt rowStart, rowEnd, colStart, colEnd, *nnzD, *nnzO; 3759 PetscScalar ***childrenMats=NULL ; /* gcc -O gives 'may be used uninitialized' warning'. Initializing to suppress this warning */ 3760 PetscErrorCode ierr; 3761 3762 PetscFunctionBegin; 3763 3764 /* get the templates for the fine-to-coarse injection from the reference tree */ 3765 ierr = DMPlexGetReferenceTree(coarse,&refTree);CHKERRQ(ierr); 3766 ierr = DMGetDefaultConstraints(refTree,&cSecRef,NULL);CHKERRQ(ierr); 3767 ierr = PetscSectionGetChart(cSecRef,&pRefStart,&pRefEnd);CHKERRQ(ierr); 3768 ierr = DMPlexReferenceTreeGetInjector(refTree,&injRef);CHKERRQ(ierr); 3769 3770 ierr = DMPlexGetChart(fine,&pStartF,&pEndF);CHKERRQ(ierr); 3771 ierr = DMGetDefaultSection(fine,&localFine);CHKERRQ(ierr); 3772 ierr = DMGetDefaultGlobalSection(fine,&globalFine);CHKERRQ(ierr); 3773 ierr = PetscSectionGetNumFields(localFine,&numFields);CHKERRQ(ierr); 3774 ierr = DMPlexGetChart(coarse,&pStartC,&pEndC);CHKERRQ(ierr); 3775 ierr = DMGetDefaultSection(coarse,&localCoarse);CHKERRQ(ierr); 3776 ierr = DMGetDefaultGlobalSection(coarse,&globalCoarse);CHKERRQ(ierr); 3777 ierr = PetscSectionGetMaxDof(localCoarse,&maxDof);CHKERRQ(ierr); 3778 { 3779 PetscInt maxFields = PetscMax(1,numFields) + 1; 3780 ierr = PetscMalloc3(maxFields,&offsets,maxFields,&offsetsCopy,maxFields,&rowOffsets);CHKERRQ(ierr); 3781 } 3782 3783 ierr = DMPlexTransferInjectorTree(coarse,fine,coarseToFine,childIds,NULL,numFields,offsets,&multiRootSec,&rootIndicesSec,&rootIndices,NULL);CHKERRQ(ierr); 3784 3785 ierr = PetscMalloc1(maxDof,&parentIndices);CHKERRQ(ierr); 3786 3787 /* count indices */ 3788 ierr = MatGetLayouts(mat,&rowMap,&colMap);CHKERRQ(ierr); 3789 ierr = PetscLayoutSetUp(rowMap);CHKERRQ(ierr); 3790 ierr = PetscLayoutSetUp(colMap);CHKERRQ(ierr); 3791 ierr = PetscLayoutGetRange(rowMap,&rowStart,&rowEnd);CHKERRQ(ierr); 3792 ierr = PetscLayoutGetRange(colMap,&colStart,&colEnd);CHKERRQ(ierr); 3793 ierr = PetscCalloc2(rowEnd-rowStart,&nnzD,rowEnd-rowStart,&nnzO);CHKERRQ(ierr); 3794 for (p = pStartC; p < pEndC; p++) { 3795 PetscInt numLeaves, leafStart, leafEnd, l, dof, cdof, gOff; 3796 3797 ierr = PetscSectionGetDof(globalCoarse,p,&dof);CHKERRQ(ierr); 3798 ierr = PetscSectionGetConstraintDof(globalCoarse,p,&cdof);CHKERRQ(ierr); 3799 if ((dof - cdof) <= 0) continue; 3800 ierr = PetscSectionGetOffset(globalCoarse,p,&gOff);CHKERRQ(ierr); 3801 3802 rowOffsets[0] = 0; 3803 offsetsCopy[0] = 0; 3804 if (numFields) { 3805 PetscInt f; 3806 3807 for (f = 0; f < numFields; f++) { 3808 PetscInt fDof; 3809 ierr = PetscSectionGetFieldDof(localCoarse,p,f,&fDof);CHKERRQ(ierr); 3810 rowOffsets[f + 1] = offsetsCopy[f + 1] = fDof + rowOffsets[f]; 3811 } 3812 DMPlexGetIndicesPointFields_Internal(localCoarse,p,gOff < 0 ? -(gOff + 1) : gOff,offsetsCopy,PETSC_FALSE,0,parentIndices);CHKERRQ(ierr); 3813 } 3814 else { 3815 DMPlexGetIndicesPoint_Internal(localCoarse,p,gOff < 0 ? -(gOff + 1) : gOff,offsetsCopy,PETSC_FALSE,0,parentIndices);CHKERRQ(ierr); 3816 rowOffsets[1] = offsetsCopy[0]; 3817 } 3818 3819 ierr = PetscSectionGetDof(multiRootSec,p,&numLeaves);CHKERRQ(ierr); 3820 ierr = PetscSectionGetOffset(multiRootSec,p,&leafStart);CHKERRQ(ierr); 3821 leafEnd = leafStart + numLeaves; 3822 for (l = leafStart; l < leafEnd; l++) { 3823 PetscInt numIndices, childId, offset; 3824 const PetscInt *childIndices; 3825 3826 ierr = PetscSectionGetDof(rootIndicesSec,l,&numIndices);CHKERRQ(ierr); 3827 ierr = PetscSectionGetOffset(rootIndicesSec,l,&offset);CHKERRQ(ierr); 3828 childId = rootIndices[offset++]; 3829 childIndices = &rootIndices[offset]; 3830 numIndices--; 3831 3832 if (childId == -1) { /* equivalent points: scatter */ 3833 PetscInt i; 3834 3835 for (i = 0; i < numIndices; i++) { 3836 PetscInt colIndex = childIndices[i]; 3837 PetscInt rowIndex = parentIndices[i]; 3838 if (rowIndex < 0) continue; 3839 if (colIndex < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Unconstrained fine and constrained coarse"); 3840 if (colIndex >= colStart && colIndex < colEnd) { 3841 nnzD[rowIndex - rowStart] = 1; 3842 } 3843 else { 3844 nnzO[rowIndex - rowStart] = 1; 3845 } 3846 } 3847 } 3848 else { 3849 PetscInt parentId, f, lim; 3850 3851 ierr = DMPlexGetTreeParent(refTree,childId,&parentId,NULL);CHKERRQ(ierr); 3852 3853 lim = PetscMax(1,numFields); 3854 offsets[0] = 0; 3855 if (numFields) { 3856 PetscInt f; 3857 3858 for (f = 0; f < numFields; f++) { 3859 PetscInt fDof; 3860 ierr = PetscSectionGetFieldDof(cSecRef,childId,f,&fDof);CHKERRQ(ierr); 3861 3862 offsets[f + 1] = fDof + offsets[f]; 3863 } 3864 } 3865 else { 3866 PetscInt cDof; 3867 3868 ierr = PetscSectionGetDof(cSecRef,childId,&cDof);CHKERRQ(ierr); 3869 offsets[1] = cDof; 3870 } 3871 for (f = 0; f < lim; f++) { 3872 PetscInt parentStart = rowOffsets[f], parentEnd = rowOffsets[f + 1]; 3873 PetscInt childStart = offsets[f], childEnd = offsets[f + 1]; 3874 PetscInt i, numD = 0, numO = 0; 3875 3876 for (i = childStart; i < childEnd; i++) { 3877 PetscInt colIndex = childIndices[i]; 3878 3879 if (colIndex < 0) continue; 3880 if (colIndex >= colStart && colIndex < colEnd) { 3881 numD++; 3882 } 3883 else { 3884 numO++; 3885 } 3886 } 3887 for (i = parentStart; i < parentEnd; i++) { 3888 PetscInt rowIndex = parentIndices[i]; 3889 3890 if (rowIndex < 0) continue; 3891 nnzD[rowIndex - rowStart] += numD; 3892 nnzO[rowIndex - rowStart] += numO; 3893 } 3894 } 3895 } 3896 } 3897 } 3898 /* preallocate */ 3899 ierr = MatXAIJSetPreallocation(mat,1,nnzD,nnzO,NULL,NULL);CHKERRQ(ierr); 3900 ierr = PetscFree2(nnzD,nnzO);CHKERRQ(ierr); 3901 /* insert values */ 3902 ierr = DMPlexReferenceTreeGetChildrenMatrices_Injection(refTree,injRef,&childrenMats);CHKERRQ(ierr); 3903 for (p = pStartC; p < pEndC; p++) { 3904 PetscInt numLeaves, leafStart, leafEnd, l, dof, cdof, gOff; 3905 3906 ierr = PetscSectionGetDof(globalCoarse,p,&dof);CHKERRQ(ierr); 3907 ierr = PetscSectionGetConstraintDof(globalCoarse,p,&cdof);CHKERRQ(ierr); 3908 if ((dof - cdof) <= 0) continue; 3909 ierr = PetscSectionGetOffset(globalCoarse,p,&gOff);CHKERRQ(ierr); 3910 3911 rowOffsets[0] = 0; 3912 offsetsCopy[0] = 0; 3913 if (numFields) { 3914 PetscInt f; 3915 3916 for (f = 0; f < numFields; f++) { 3917 PetscInt fDof; 3918 ierr = PetscSectionGetFieldDof(localCoarse,p,f,&fDof);CHKERRQ(ierr); 3919 rowOffsets[f + 1] = offsetsCopy[f + 1] = fDof + rowOffsets[f]; 3920 } 3921 DMPlexGetIndicesPointFields_Internal(localCoarse,p,gOff < 0 ? -(gOff + 1) : gOff,offsetsCopy,PETSC_FALSE,0,parentIndices);CHKERRQ(ierr); 3922 } 3923 else { 3924 DMPlexGetIndicesPoint_Internal(localCoarse,p,gOff < 0 ? -(gOff + 1) : gOff,offsetsCopy,PETSC_FALSE,0,parentIndices);CHKERRQ(ierr); 3925 rowOffsets[1] = offsetsCopy[0]; 3926 } 3927 3928 ierr = PetscSectionGetDof(multiRootSec,p,&numLeaves);CHKERRQ(ierr); 3929 ierr = PetscSectionGetOffset(multiRootSec,p,&leafStart);CHKERRQ(ierr); 3930 leafEnd = leafStart + numLeaves; 3931 for (l = leafStart; l < leafEnd; l++) { 3932 PetscInt numIndices, childId, offset; 3933 const PetscInt *childIndices; 3934 3935 ierr = PetscSectionGetDof(rootIndicesSec,l,&numIndices);CHKERRQ(ierr); 3936 ierr = PetscSectionGetOffset(rootIndicesSec,l,&offset);CHKERRQ(ierr); 3937 childId = rootIndices[offset++]; 3938 childIndices = &rootIndices[offset]; 3939 numIndices--; 3940 3941 if (childId == -1) { /* equivalent points: scatter */ 3942 PetscInt i; 3943 3944 for (i = 0; i < numIndices; i++) { 3945 ierr = MatSetValue(mat,parentIndices[i],childIndices[i],1.,INSERT_VALUES);CHKERRQ(ierr); 3946 } 3947 } 3948 else { 3949 PetscInt parentId, f, lim; 3950 3951 ierr = DMPlexGetTreeParent(refTree,childId,&parentId,NULL);CHKERRQ(ierr); 3952 3953 lim = PetscMax(1,numFields); 3954 offsets[0] = 0; 3955 if (numFields) { 3956 PetscInt f; 3957 3958 for (f = 0; f < numFields; f++) { 3959 PetscInt fDof; 3960 ierr = PetscSectionGetFieldDof(cSecRef,childId,f,&fDof);CHKERRQ(ierr); 3961 3962 offsets[f + 1] = fDof + offsets[f]; 3963 } 3964 } 3965 else { 3966 PetscInt cDof; 3967 3968 ierr = PetscSectionGetDof(cSecRef,childId,&cDof);CHKERRQ(ierr); 3969 offsets[1] = cDof; 3970 } 3971 for (f = 0; f < lim; f++) { 3972 PetscScalar *childMat = &childrenMats[childId - pRefStart][f][0]; 3973 PetscInt *rowIndices = &parentIndices[rowOffsets[f]]; 3974 const PetscInt *colIndices = &childIndices[offsets[f]]; 3975 3976 ierr = MatSetValues(mat,rowOffsets[f+1]-rowOffsets[f],rowIndices,offsets[f+1]-offsets[f],colIndices,childMat,INSERT_VALUES);CHKERRQ(ierr); 3977 } 3978 } 3979 } 3980 } 3981 ierr = PetscSectionDestroy(&multiRootSec);CHKERRQ(ierr); 3982 ierr = PetscSectionDestroy(&rootIndicesSec);CHKERRQ(ierr); 3983 ierr = PetscFree(parentIndices);CHKERRQ(ierr); 3984 ierr = DMPlexReferenceTreeRestoreChildrenMatrices_Injection(refTree,injRef,&childrenMats);CHKERRQ(ierr); 3985 ierr = PetscFree(rootIndices);CHKERRQ(ierr); 3986 ierr = PetscFree3(offsets,offsetsCopy,rowOffsets);CHKERRQ(ierr); 3987 3988 ierr = MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3989 ierr = MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3990 PetscFunctionReturn(0); 3991 } 3992 3993 #undef __FUNCT__ 3994 #define __FUNCT__ "DMPlexTransferVecTree_Interpolate" 3995 static PetscErrorCode DMPlexTransferVecTree_Interpolate(DM coarse, Vec vecCoarseLocal, DM fine, Vec vecFine, PetscSF coarseToFine, PetscInt *cids, Vec grad, Vec cellGeom) 3996 { 3997 PetscDS ds; 3998 PetscSF coarseToFineEmbedded; 3999 PetscSection globalCoarse, globalFine; 4000 PetscSection localCoarse, localFine; 4001 PetscSection aSec, cSec; 4002 PetscSection rootValuesSec; 4003 PetscSection leafValuesSec; 4004 PetscScalar *rootValues, *leafValues; 4005 IS aIS; 4006 const PetscInt *anchors; 4007 Mat cMat; 4008 PetscInt numFields; 4009 PetscInt pStartC, pEndC, pStartF, pEndF, p, cellStart, cellEnd; 4010 PetscInt aStart, aEnd, cStart, cEnd; 4011 PetscInt *maxChildIds; 4012 PetscInt *offsets, *newOffsets, *offsetsCopy, *newOffsetsCopy, *rowOffsets, *numD, *numO; 4013 PetscFV fv = NULL; 4014 PetscInt dim, numFVcomps = -1, fvField = -1; 4015 DM cellDM = NULL, gradDM = NULL; 4016 const PetscScalar *cellGeomArray = NULL; 4017 const PetscScalar *gradArray = NULL; 4018 PetscErrorCode ierr; 4019 4020 PetscFunctionBegin; 4021 ierr = VecSetOption(vecFine,VEC_IGNORE_NEGATIVE_INDICES,PETSC_TRUE);CHKERRQ(ierr); 4022 ierr = DMPlexGetChart(coarse,&pStartC,&pEndC);CHKERRQ(ierr); 4023 ierr = DMPlexGetHeightStratum(coarse,0,&cellStart,&cellEnd);CHKERRQ(ierr); 4024 ierr = DMPlexGetChart(fine,&pStartF,&pEndF);CHKERRQ(ierr); 4025 ierr = DMGetDefaultGlobalSection(fine,&globalFine);CHKERRQ(ierr); 4026 ierr = DMGetCoordinateDim(coarse,&dim);CHKERRQ(ierr); 4027 { /* winnow fine points that don't have global dofs out of the sf */ 4028 PetscInt nleaves, l; 4029 const PetscInt *leaves; 4030 PetscInt dof, cdof, numPointsWithDofs, offset, *pointsWithDofs; 4031 4032 ierr = PetscSFGetGraph(coarseToFine,NULL,&nleaves,&leaves,NULL);CHKERRQ(ierr); 4033 4034 for (l = 0, numPointsWithDofs = 0; l < nleaves; l++) { 4035 PetscInt p = leaves ? leaves[l] : l; 4036 4037 ierr = PetscSectionGetDof(globalFine,p,&dof);CHKERRQ(ierr); 4038 ierr = PetscSectionGetConstraintDof(globalFine,p,&cdof);CHKERRQ(ierr); 4039 if ((dof - cdof) > 0) { 4040 numPointsWithDofs++; 4041 } 4042 } 4043 ierr = PetscMalloc1(numPointsWithDofs,&pointsWithDofs);CHKERRQ(ierr); 4044 for (l = 0, offset = 0; l < nleaves; l++) { 4045 PetscInt p = leaves ? leaves[l] : l; 4046 4047 ierr = PetscSectionGetDof(globalFine,p,&dof);CHKERRQ(ierr); 4048 ierr = PetscSectionGetConstraintDof(globalFine,p,&cdof);CHKERRQ(ierr); 4049 if ((dof - cdof) > 0) { 4050 pointsWithDofs[offset++] = l; 4051 } 4052 } 4053 ierr = PetscSFCreateEmbeddedLeafSF(coarseToFine, numPointsWithDofs, pointsWithDofs, &coarseToFineEmbedded);CHKERRQ(ierr); 4054 ierr = PetscFree(pointsWithDofs);CHKERRQ(ierr); 4055 } 4056 /* communicate back to the coarse mesh which coarse points have children (that may require interpolation) */ 4057 ierr = PetscMalloc1(pEndC-pStartC,&maxChildIds);CHKERRQ(ierr); 4058 for (p = pStartC; p < pEndC; p++) { 4059 maxChildIds[p - pStartC] = -2; 4060 } 4061 ierr = PetscSFReduceBegin(coarseToFineEmbedded,MPIU_INT,cids,maxChildIds,MPIU_MAX);CHKERRQ(ierr); 4062 ierr = PetscSFReduceEnd(coarseToFineEmbedded,MPIU_INT,cids,maxChildIds,MPIU_MAX);CHKERRQ(ierr); 4063 4064 ierr = DMGetDefaultSection(coarse,&localCoarse);CHKERRQ(ierr); 4065 ierr = DMGetDefaultGlobalSection(coarse,&globalCoarse);CHKERRQ(ierr); 4066 4067 ierr = DMPlexGetAnchors(coarse,&aSec,&aIS);CHKERRQ(ierr); 4068 ierr = ISGetIndices(aIS,&anchors);CHKERRQ(ierr); 4069 ierr = PetscSectionGetChart(aSec,&aStart,&aEnd);CHKERRQ(ierr); 4070 4071 ierr = DMGetDefaultConstraints(coarse,&cSec,&cMat);CHKERRQ(ierr); 4072 ierr = PetscSectionGetChart(cSec,&cStart,&cEnd);CHKERRQ(ierr); 4073 4074 /* create sections that will send to children the indices and matrices they will need to construct the interpolator */ 4075 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)coarse),&rootValuesSec);CHKERRQ(ierr); 4076 ierr = PetscSectionSetChart(rootValuesSec,pStartC,pEndC);CHKERRQ(ierr); 4077 ierr = PetscSectionGetNumFields(localCoarse,&numFields);CHKERRQ(ierr); 4078 { 4079 PetscInt maxFields = PetscMax(1,numFields) + 1; 4080 ierr = PetscMalloc7(maxFields,&offsets,maxFields,&offsetsCopy,maxFields,&newOffsets,maxFields,&newOffsetsCopy,maxFields,&rowOffsets,maxFields,&numD,maxFields,&numO);CHKERRQ(ierr); 4081 } 4082 if (grad) { 4083 PetscInt i; 4084 4085 ierr = VecGetDM(cellGeom,&cellDM);CHKERRQ(ierr); 4086 ierr = VecGetArrayRead(cellGeom,&cellGeomArray);CHKERRQ(ierr); 4087 ierr = VecGetDM(grad,&gradDM);CHKERRQ(ierr); 4088 ierr = VecGetArrayRead(grad,&gradArray);CHKERRQ(ierr); 4089 for (i = 0; i < PetscMax(1,numFields); i++) { 4090 PetscObject obj; 4091 PetscClassId id; 4092 4093 ierr = DMGetField(coarse, i, &obj);CHKERRQ(ierr); 4094 ierr = PetscObjectGetClassId(obj,&id);CHKERRQ(ierr); 4095 if (id == PETSCFV_CLASSID) { 4096 fv = (PetscFV) obj; 4097 ierr = PetscFVGetNumComponents(fv,&numFVcomps);CHKERRQ(ierr); 4098 fvField = i; 4099 break; 4100 } 4101 } 4102 } 4103 4104 for (p = pStartC; p < pEndC; p++) { /* count the sizes of the indices and matrices */ 4105 PetscInt dof; 4106 PetscInt maxChildId = maxChildIds[p - pStartC]; 4107 PetscInt numValues = 0; 4108 4109 ierr = PetscSectionGetDof(globalCoarse,p,&dof);CHKERRQ(ierr); 4110 if (dof < 0) { 4111 dof = -(dof + 1); 4112 } 4113 offsets[0] = 0; 4114 newOffsets[0] = 0; 4115 if (maxChildId >= 0) { /* this point has children (with dofs) that will need to be interpolated from the closure of p */ 4116 PetscInt *closure = NULL, closureSize, cl; 4117 4118 ierr = DMPlexGetTransitiveClosure(coarse,p,PETSC_TRUE,&closureSize,&closure);CHKERRQ(ierr); 4119 for (cl = 0; cl < closureSize; cl++) { /* get the closure */ 4120 PetscInt c = closure[2 * cl], clDof; 4121 4122 ierr = PetscSectionGetDof(localCoarse,c,&clDof);CHKERRQ(ierr); 4123 numValues += clDof; 4124 } 4125 ierr = DMPlexRestoreTransitiveClosure(coarse,p,PETSC_TRUE,&closureSize,&closure);CHKERRQ(ierr); 4126 } 4127 else if (maxChildId == -1) { 4128 ierr = PetscSectionGetDof(localCoarse,p,&numValues);CHKERRQ(ierr); 4129 } 4130 /* we will pack the column indices with the field offsets */ 4131 if (maxChildId >= -1 && grad && p >= cellStart && p < cellEnd) { 4132 /* also send the centroid, and the gradient */ 4133 numValues += dim * (1 + numFVcomps); 4134 } 4135 ierr = PetscSectionSetDof(rootValuesSec,p,numValues);CHKERRQ(ierr); 4136 } 4137 ierr = PetscSectionSetUp(rootValuesSec);CHKERRQ(ierr); 4138 { 4139 PetscInt numRootValues; 4140 const PetscScalar *coarseArray; 4141 4142 ierr = PetscSectionGetStorageSize(rootValuesSec,&numRootValues);CHKERRQ(ierr); 4143 ierr = PetscMalloc1(numRootValues,&rootValues);CHKERRQ(ierr); 4144 ierr = VecGetArrayRead(vecCoarseLocal,&coarseArray);CHKERRQ(ierr); 4145 for (p = pStartC; p < pEndC; p++) { 4146 PetscInt numValues; 4147 PetscInt pValOff; 4148 PetscScalar *pVal; 4149 PetscInt maxChildId = maxChildIds[p - pStartC]; 4150 4151 ierr = PetscSectionGetDof(rootValuesSec,p,&numValues);CHKERRQ(ierr); 4152 if (!numValues) { 4153 continue; 4154 } 4155 ierr = PetscSectionGetOffset(rootValuesSec,p,&pValOff);CHKERRQ(ierr); 4156 pVal = &(rootValues[pValOff]); 4157 if (maxChildId >= 0) { /* build an identity matrix, apply matrix constraints on the right */ 4158 PetscInt closureSize = numValues; 4159 ierr = DMPlexVecGetClosure(coarse,NULL,vecCoarseLocal,p,&closureSize,&pVal);CHKERRQ(ierr); 4160 } 4161 else if (maxChildId == -1) { 4162 PetscInt lDof, lOff, i; 4163 4164 ierr = PetscSectionGetDof(localCoarse,p,&lDof);CHKERRQ(ierr); 4165 ierr = PetscSectionGetOffset(localCoarse,p,&lOff);CHKERRQ(ierr); 4166 for (i = 0; i < lDof; i++) pVal[i] = coarseArray[lOff + i]; 4167 } 4168 if (grad && p >= cellStart && p < cellEnd) { 4169 PetscFVCellGeom *cg; 4170 PetscScalar *gradVals = NULL; 4171 PetscInt i; 4172 4173 pVal += (numValues - dim * (1 + numFVcomps)); 4174 4175 ierr = DMPlexPointLocalRead(cellDM,p,cellGeomArray,(void *) &cg);CHKERRQ(ierr); 4176 for (i = 0; i < dim; i++) pVal[i] = cg->centroid[i]; 4177 pVal += dim; 4178 ierr = DMPlexPointGlobalRead(gradDM,p,gradArray,(void *) &gradVals);CHKERRQ(ierr); 4179 for (i = 0; i < dim * numFVcomps; i++) pVal[i] = gradVals[i]; 4180 } 4181 } 4182 ierr = VecRestoreArrayRead(vecCoarseLocal,&coarseArray);CHKERRQ(ierr); 4183 ierr = PetscFree(maxChildIds);CHKERRQ(ierr); 4184 } 4185 { 4186 PetscSF valuesSF; 4187 PetscInt *remoteOffsetsValues, numLeafValues; 4188 4189 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)fine),&leafValuesSec);CHKERRQ(ierr); 4190 ierr = PetscSFDistributeSection(coarseToFineEmbedded,rootValuesSec,&remoteOffsetsValues,leafValuesSec);CHKERRQ(ierr); 4191 ierr = PetscSFCreateSectionSF(coarseToFineEmbedded,rootValuesSec,remoteOffsetsValues,leafValuesSec,&valuesSF);CHKERRQ(ierr); 4192 ierr = PetscSFDestroy(&coarseToFineEmbedded);CHKERRQ(ierr); 4193 ierr = PetscFree(remoteOffsetsValues);CHKERRQ(ierr); 4194 ierr = PetscSectionGetStorageSize(leafValuesSec,&numLeafValues);CHKERRQ(ierr); 4195 ierr = PetscMalloc1(numLeafValues,&leafValues);CHKERRQ(ierr); 4196 ierr = PetscSFBcastBegin(valuesSF,MPIU_SCALAR,rootValues,leafValues);CHKERRQ(ierr); 4197 ierr = PetscSFBcastEnd(valuesSF,MPIU_SCALAR,rootValues,leafValues);CHKERRQ(ierr); 4198 ierr = PetscSFDestroy(&valuesSF);CHKERRQ(ierr); 4199 ierr = PetscFree(rootValues);CHKERRQ(ierr); 4200 ierr = PetscSectionDestroy(&rootValuesSec);CHKERRQ(ierr); 4201 } 4202 ierr = DMGetDefaultSection(fine,&localFine);CHKERRQ(ierr); 4203 { 4204 PetscInt maxDof; 4205 PetscInt *rowIndices; 4206 DM refTree; 4207 PetscInt **refPointFieldN; 4208 PetscScalar ***refPointFieldMats; 4209 PetscSection refConSec, refAnSec; 4210 PetscInt pRefStart,pRefEnd,leafStart,leafEnd; 4211 PetscScalar *pointWork; 4212 4213 ierr = PetscSectionGetMaxDof(globalFine,&maxDof);CHKERRQ(ierr); 4214 ierr = DMGetWorkArray(fine,maxDof,PETSC_INT,&rowIndices);CHKERRQ(ierr); 4215 ierr = DMGetWorkArray(fine,maxDof,PETSC_SCALAR,&pointWork);CHKERRQ(ierr); 4216 ierr = DMPlexGetReferenceTree(fine,&refTree);CHKERRQ(ierr); 4217 ierr = DMGetDS(fine,&ds);CHKERRQ(ierr); 4218 ierr = DMSetDS(refTree,ds);CHKERRQ(ierr); 4219 ierr = DMPlexReferenceTreeGetChildrenMatrices(refTree,&refPointFieldMats,&refPointFieldN);CHKERRQ(ierr); 4220 ierr = DMGetDefaultConstraints(refTree,&refConSec,NULL);CHKERRQ(ierr); 4221 ierr = DMPlexGetAnchors(refTree,&refAnSec,NULL);CHKERRQ(ierr); 4222 ierr = PetscSectionGetChart(refConSec,&pRefStart,&pRefEnd);CHKERRQ(ierr); 4223 ierr = PetscSectionGetChart(leafValuesSec,&leafStart,&leafEnd);CHKERRQ(ierr); 4224 ierr = DMPlexGetHeightStratum(fine,0,&cellStart,&cellEnd);CHKERRQ(ierr); 4225 for (p = leafStart; p < leafEnd; p++) { 4226 PetscInt gDof, gcDof, gOff, lDof; 4227 PetscInt numValues, pValOff; 4228 PetscInt childId; 4229 const PetscScalar *pVal; 4230 const PetscScalar *fvGradData = NULL; 4231 4232 ierr = PetscSectionGetDof(globalFine,p,&gDof);CHKERRQ(ierr); 4233 ierr = PetscSectionGetDof(localFine,p,&lDof);CHKERRQ(ierr); 4234 ierr = PetscSectionGetConstraintDof(globalFine,p,&gcDof);CHKERRQ(ierr); 4235 if ((gDof - gcDof) <= 0) { 4236 continue; 4237 } 4238 ierr = PetscSectionGetOffset(globalFine,p,&gOff);CHKERRQ(ierr); 4239 ierr = PetscSectionGetDof(leafValuesSec,p,&numValues);CHKERRQ(ierr); 4240 if (!numValues) continue; 4241 ierr = PetscSectionGetOffset(leafValuesSec,p,&pValOff);CHKERRQ(ierr); 4242 pVal = &leafValues[pValOff]; 4243 offsets[0] = 0; 4244 offsetsCopy[0] = 0; 4245 newOffsets[0] = 0; 4246 newOffsetsCopy[0] = 0; 4247 childId = cids[p - pStartF]; 4248 if (grad && p >= cellStart && p < cellEnd) { 4249 numValues -= (dim * (1 + numFVcomps)); 4250 fvGradData = &pVal[numValues]; 4251 } 4252 if (numFields) { 4253 PetscInt f; 4254 for (f = 0; f < numFields; f++) { 4255 PetscInt rowDof; 4256 4257 ierr = PetscSectionGetFieldDof(localFine,p,f,&rowDof);CHKERRQ(ierr); 4258 offsets[f + 1] = offsets[f] + rowDof; 4259 offsetsCopy[f + 1] = offsets[f + 1]; 4260 /* TODO: closure indices */ 4261 newOffsets[f + 1] = newOffsets[f] + ((childId == -1) ? rowDof : refPointFieldN[childId - pRefStart][f]); 4262 } 4263 ierr = DMPlexGetIndicesPointFields_Internal(localFine,p,gOff,offsetsCopy,PETSC_FALSE,0,rowIndices);CHKERRQ(ierr); 4264 } 4265 else { 4266 offsets[0] = 0; 4267 offsets[1] = lDof; 4268 newOffsets[0] = 0; 4269 newOffsets[1] = (childId == -1) ? lDof : refPointFieldN[childId - pRefStart][0]; 4270 ierr = DMPlexGetIndicesPoint_Internal(localFine,p,gOff,offsetsCopy,PETSC_FALSE,0,rowIndices);CHKERRQ(ierr); 4271 } 4272 if (childId == -1) { /* no child interpolation: one nnz per */ 4273 ierr = VecSetValues(vecFine,numValues,rowIndices,pVal,ADD_VALUES);CHKERRQ(ierr); 4274 } else { 4275 PetscInt f; 4276 4277 for (f = 0; f < PetscMax(1,numFields); f++) { 4278 const PetscScalar *childMat = refPointFieldMats[childId - pRefStart][f]; 4279 PetscInt numRows = offsets[f+1] - offsets[f]; 4280 PetscInt numCols = newOffsets[f + 1] - newOffsets[f]; 4281 const PetscScalar *cVal = &pVal[newOffsets[f]]; 4282 PetscScalar *rVal = &pointWork[offsets[f]]; 4283 PetscInt i, j; 4284 4285 #if 0 4286 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); 4287 #endif 4288 for (i = 0; i < numRows; i++) { 4289 PetscScalar val = 0.; 4290 for (j = 0; j < numCols; j++) { 4291 val += childMat[i * numCols + j] * cVal[j]; 4292 } 4293 rVal[i] = val; 4294 } 4295 if (f == fvField && p >= cellStart && p < cellEnd) { 4296 PetscReal centroid[3]; 4297 PetscScalar diff[3]; 4298 const PetscScalar *parentCentroid = &fvGradData[0]; 4299 const PetscScalar *gradient = &fvGradData[dim]; 4300 4301 ierr = DMPlexComputeCellGeometryFVM(fine,p,NULL,centroid,NULL);CHKERRQ(ierr); 4302 for (i = 0; i < dim; i++) { 4303 diff[i] = centroid[i] - parentCentroid[i]; 4304 } 4305 for (i = 0; i < numFVcomps; i++) { 4306 PetscScalar val = 0.; 4307 4308 for (j = 0; j < 3; j++) { 4309 val += gradient[dim * i + j] * diff[j]; 4310 } 4311 rVal[i] += val; 4312 } 4313 } 4314 ierr = VecSetValues(vecFine,numRows,&rowIndices[offsets[f]],rVal,ADD_VALUES);CHKERRQ(ierr); 4315 } 4316 } 4317 } 4318 ierr = DMPlexReferenceTreeRestoreChildrenMatrices(refTree,&refPointFieldMats,&refPointFieldN);CHKERRQ(ierr); 4319 ierr = DMRestoreWorkArray(fine,maxDof,PETSC_INT,&rowIndices);CHKERRQ(ierr); 4320 ierr = DMRestoreWorkArray(fine,maxDof,PETSC_SCALAR,&pointWork);CHKERRQ(ierr); 4321 } 4322 ierr = PetscFree(leafValues);CHKERRQ(ierr); 4323 ierr = PetscSectionDestroy(&leafValuesSec);CHKERRQ(ierr); 4324 ierr = PetscFree7(offsets,offsetsCopy,newOffsets,newOffsetsCopy,rowOffsets,numD,numO);CHKERRQ(ierr); 4325 ierr = ISRestoreIndices(aIS,&anchors);CHKERRQ(ierr); 4326 PetscFunctionReturn(0); 4327 } 4328 4329 #undef __FUNCT__ 4330 #define __FUNCT__ "DMPlexTransferVecTree_Inject" 4331 static PetscErrorCode DMPlexTransferVecTree_Inject(DM fine, Vec vecFine, DM coarse, Vec vecCoarse, PetscSF coarseToFine, PetscInt *cids) 4332 { 4333 PetscDS ds; 4334 DM refTree; 4335 PetscSection multiRootSec, rootIndicesSec; 4336 PetscSection globalCoarse, globalFine; 4337 PetscSection localCoarse, localFine; 4338 PetscSection cSecRef; 4339 PetscInt *parentIndices, pRefStart, pRefEnd; 4340 PetscScalar *rootValues, *parentValues; 4341 Mat injRef; 4342 PetscInt numFields, maxDof; 4343 PetscInt pStartC, pEndC, pStartF, pEndF, p; 4344 PetscInt *offsets, *offsetsCopy, *rowOffsets; 4345 PetscLayout rowMap, colMap; 4346 PetscInt rowStart, rowEnd, colStart, colEnd; 4347 PetscScalar ***childrenMats=NULL ; /* gcc -O gives 'may be used uninitialized' warning'. Initializing to suppress this warning */ 4348 PetscErrorCode ierr; 4349 4350 PetscFunctionBegin; 4351 4352 /* get the templates for the fine-to-coarse injection from the reference tree */ 4353 ierr = VecSetOption(vecFine,VEC_IGNORE_NEGATIVE_INDICES,PETSC_TRUE);CHKERRQ(ierr); 4354 ierr = VecSetOption(vecCoarse,VEC_IGNORE_NEGATIVE_INDICES,PETSC_TRUE);CHKERRQ(ierr); 4355 ierr = DMPlexGetReferenceTree(coarse,&refTree);CHKERRQ(ierr); 4356 ierr = DMGetDS(coarse,&ds);CHKERRQ(ierr); 4357 ierr = DMSetDS(refTree,ds);CHKERRQ(ierr); 4358 ierr = DMGetDefaultConstraints(refTree,&cSecRef,NULL);CHKERRQ(ierr); 4359 ierr = PetscSectionGetChart(cSecRef,&pRefStart,&pRefEnd);CHKERRQ(ierr); 4360 ierr = DMPlexReferenceTreeGetInjector(refTree,&injRef);CHKERRQ(ierr); 4361 4362 ierr = DMPlexGetChart(fine,&pStartF,&pEndF);CHKERRQ(ierr); 4363 ierr = DMGetDefaultSection(fine,&localFine);CHKERRQ(ierr); 4364 ierr = DMGetDefaultGlobalSection(fine,&globalFine);CHKERRQ(ierr); 4365 ierr = PetscSectionGetNumFields(localFine,&numFields);CHKERRQ(ierr); 4366 ierr = DMPlexGetChart(coarse,&pStartC,&pEndC);CHKERRQ(ierr); 4367 ierr = DMGetDefaultSection(coarse,&localCoarse);CHKERRQ(ierr); 4368 ierr = DMGetDefaultGlobalSection(coarse,&globalCoarse);CHKERRQ(ierr); 4369 ierr = PetscSectionGetMaxDof(localCoarse,&maxDof);CHKERRQ(ierr); 4370 { 4371 PetscInt maxFields = PetscMax(1,numFields) + 1; 4372 ierr = PetscMalloc3(maxFields,&offsets,maxFields,&offsetsCopy,maxFields,&rowOffsets);CHKERRQ(ierr); 4373 } 4374 4375 ierr = DMPlexTransferInjectorTree(coarse,fine,coarseToFine,cids,vecFine,numFields,offsets,&multiRootSec,&rootIndicesSec,NULL,&rootValues);CHKERRQ(ierr); 4376 4377 ierr = PetscMalloc2(maxDof,&parentIndices,maxDof,&parentValues);CHKERRQ(ierr); 4378 4379 /* count indices */ 4380 ierr = VecGetLayout(vecFine,&colMap);CHKERRQ(ierr); 4381 ierr = VecGetLayout(vecCoarse,&rowMap);CHKERRQ(ierr); 4382 ierr = PetscLayoutSetUp(rowMap);CHKERRQ(ierr); 4383 ierr = PetscLayoutSetUp(colMap);CHKERRQ(ierr); 4384 ierr = PetscLayoutGetRange(rowMap,&rowStart,&rowEnd);CHKERRQ(ierr); 4385 ierr = PetscLayoutGetRange(colMap,&colStart,&colEnd);CHKERRQ(ierr); 4386 /* insert values */ 4387 ierr = DMPlexReferenceTreeGetChildrenMatrices_Injection(refTree,injRef,&childrenMats);CHKERRQ(ierr); 4388 for (p = pStartC; p < pEndC; p++) { 4389 PetscInt numLeaves, leafStart, leafEnd, l, dof, cdof, gOff; 4390 4391 ierr = PetscSectionGetDof(globalCoarse,p,&dof);CHKERRQ(ierr); 4392 ierr = PetscSectionGetConstraintDof(globalCoarse,p,&cdof);CHKERRQ(ierr); 4393 if ((dof - cdof) <= 0) continue; 4394 ierr = PetscSectionGetOffset(globalCoarse,p,&gOff);CHKERRQ(ierr); 4395 4396 rowOffsets[0] = 0; 4397 offsetsCopy[0] = 0; 4398 if (numFields) { 4399 PetscInt f; 4400 4401 for (f = 0; f < numFields; f++) { 4402 PetscInt fDof; 4403 ierr = PetscSectionGetFieldDof(localCoarse,p,f,&fDof);CHKERRQ(ierr); 4404 rowOffsets[f + 1] = offsetsCopy[f + 1] = fDof + rowOffsets[f]; 4405 } 4406 DMPlexGetIndicesPointFields_Internal(localCoarse,p,gOff < 0 ? -(gOff + 1) : gOff,offsetsCopy,PETSC_FALSE,0,parentIndices);CHKERRQ(ierr); 4407 } 4408 else { 4409 DMPlexGetIndicesPoint_Internal(localCoarse,p,gOff < 0 ? -(gOff + 1) : gOff,offsetsCopy,PETSC_FALSE,0,parentIndices);CHKERRQ(ierr); 4410 rowOffsets[1] = offsetsCopy[0]; 4411 } 4412 4413 ierr = PetscSectionGetDof(multiRootSec,p,&numLeaves);CHKERRQ(ierr); 4414 ierr = PetscSectionGetOffset(multiRootSec,p,&leafStart);CHKERRQ(ierr); 4415 leafEnd = leafStart + numLeaves; 4416 for (l = leafStart; l < leafEnd; l++) { 4417 PetscInt numIndices, childId, offset; 4418 const PetscScalar *childValues; 4419 4420 ierr = PetscSectionGetDof(rootIndicesSec,l,&numIndices);CHKERRQ(ierr); 4421 ierr = PetscSectionGetOffset(rootIndicesSec,l,&offset);CHKERRQ(ierr); 4422 childId = (PetscInt) PetscRealPart(rootValues[offset++]); 4423 childValues = &rootValues[offset]; 4424 numIndices--; 4425 4426 if (childId == -2) { /* skip */ 4427 continue; 4428 } else if (childId == -1) { /* equivalent points: scatter */ 4429 ierr = VecSetValues(vecCoarse,numIndices,parentIndices,childValues,ADD_VALUES);CHKERRQ(ierr); 4430 } else { 4431 PetscInt parentId, f, lim; 4432 4433 ierr = DMPlexGetTreeParent(refTree,childId,&parentId,NULL);CHKERRQ(ierr); 4434 4435 lim = PetscMax(1,numFields); 4436 offsets[0] = 0; 4437 if (numFields) { 4438 PetscInt f; 4439 4440 for (f = 0; f < numFields; f++) { 4441 PetscInt fDof; 4442 ierr = PetscSectionGetFieldDof(cSecRef,childId,f,&fDof);CHKERRQ(ierr); 4443 4444 offsets[f + 1] = fDof + offsets[f]; 4445 } 4446 } 4447 else { 4448 PetscInt cDof; 4449 4450 ierr = PetscSectionGetDof(cSecRef,childId,&cDof);CHKERRQ(ierr); 4451 offsets[1] = cDof; 4452 } 4453 for (f = 0; f < lim; f++) { 4454 PetscScalar *childMat = &childrenMats[childId - pRefStart][f][0]; 4455 PetscInt *rowIndices = &parentIndices[rowOffsets[f]]; 4456 PetscInt m = rowOffsets[f+1]-rowOffsets[f]; 4457 PetscInt n = offsets[f+1]-offsets[f]; 4458 PetscInt i, j; 4459 const PetscScalar *colValues = &childValues[offsets[f]]; 4460 4461 for (i = 0; i < m; i++) { 4462 PetscScalar val = 0.; 4463 for (j = 0; j < n; j++) { 4464 val += childMat[n * i + j] * colValues[j]; 4465 } 4466 parentValues[i] = val; 4467 } 4468 ierr = VecSetValues(vecCoarse,m,rowIndices,parentValues,ADD_VALUES);CHKERRQ(ierr); 4469 } 4470 } 4471 } 4472 } 4473 ierr = PetscSectionDestroy(&multiRootSec);CHKERRQ(ierr); 4474 ierr = PetscSectionDestroy(&rootIndicesSec);CHKERRQ(ierr); 4475 ierr = PetscFree2(parentIndices,parentValues);CHKERRQ(ierr); 4476 ierr = DMPlexReferenceTreeRestoreChildrenMatrices_Injection(refTree,injRef,&childrenMats);CHKERRQ(ierr); 4477 ierr = PetscFree(rootValues);CHKERRQ(ierr); 4478 ierr = PetscFree3(offsets,offsetsCopy,rowOffsets);CHKERRQ(ierr); 4479 PetscFunctionReturn(0); 4480 } 4481 4482 #undef __FUNCT__ 4483 #define __FUNCT__ "DMPlexTransferVecTree" 4484 PetscErrorCode DMPlexTransferVecTree(DM dmIn, Vec vecIn, DM dmOut, Vec vecOut, PetscSF sfIn, PetscSF sfOut, PetscInt *cidsIn, PetscInt *cidsOut, PetscBool useBCs, PetscReal time) 4485 { 4486 PetscErrorCode ierr; 4487 4488 PetscFunctionBegin; 4489 if (sfIn) { 4490 Vec vecInLocal; 4491 DM dmGrad = NULL; 4492 Vec faceGeom = NULL, cellGeom = NULL, grad = NULL; 4493 4494 ierr = DMGetLocalVector(dmIn,&vecInLocal);CHKERRQ(ierr); 4495 ierr = VecSet(vecInLocal,0.0);CHKERRQ(ierr); 4496 { 4497 PetscInt numFields, i; 4498 4499 ierr = DMGetNumFields(dmIn, &numFields);CHKERRQ(ierr); 4500 for (i = 0; i < numFields; i++) { 4501 PetscObject obj; 4502 PetscClassId classid; 4503 4504 ierr = DMGetField(dmIn, i, &obj);CHKERRQ(ierr); 4505 ierr = PetscObjectGetClassId(obj, &classid);CHKERRQ(ierr); 4506 if (classid == PETSCFV_CLASSID) { 4507 ierr = DMPlexGetDataFVM(dmIn,(PetscFV)obj,&cellGeom,&faceGeom,&dmGrad);CHKERRQ(ierr); 4508 break; 4509 } 4510 } 4511 } 4512 if (useBCs) { 4513 ierr = DMPlexInsertBoundaryValues(dmIn,PETSC_TRUE,vecInLocal,time,faceGeom,cellGeom,NULL);CHKERRQ(ierr); 4514 } 4515 ierr = DMGlobalToLocalBegin(dmIn,vecIn,INSERT_VALUES,vecInLocal);CHKERRQ(ierr); 4516 ierr = DMGlobalToLocalEnd(dmIn,vecIn,INSERT_VALUES,vecInLocal);CHKERRQ(ierr); 4517 if (dmGrad) { 4518 ierr = DMGetGlobalVector(dmGrad,&grad);CHKERRQ(ierr); 4519 ierr = DMPlexReconstructGradientsFVM(dmIn,vecInLocal,grad);CHKERRQ(ierr); 4520 } 4521 ierr = DMPlexTransferVecTree_Interpolate(dmIn,vecInLocal,dmOut,vecOut,sfIn,cidsIn,grad,cellGeom);CHKERRQ(ierr); 4522 ierr = DMRestoreLocalVector(dmIn,&vecInLocal);CHKERRQ(ierr); 4523 if (dmGrad) { 4524 ierr = DMRestoreGlobalVector(dmGrad,&grad);CHKERRQ(ierr); 4525 } 4526 } 4527 if (sfOut) { 4528 ierr = DMPlexTransferVecTree_Inject(dmIn,vecIn,dmOut,vecOut,sfOut,cidsOut);CHKERRQ(ierr); 4529 } 4530 PetscFunctionReturn(0); 4531 } 4532