1 #include <petsc-private/dmpleximpl.h> /*I "petscdmplex.h" I*/ 2 3 #include <petscfe.h> 4 5 #undef __FUNCT__ 6 #define __FUNCT__ "DMPlexGetScale" 7 PetscErrorCode DMPlexGetScale(DM dm, PetscUnit unit, PetscReal *scale) 8 { 9 DM_Plex *mesh = (DM_Plex*) dm->data; 10 11 PetscFunctionBegin; 12 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 13 PetscValidPointer(scale, 3); 14 *scale = mesh->scale[unit]; 15 PetscFunctionReturn(0); 16 } 17 18 #undef __FUNCT__ 19 #define __FUNCT__ "DMPlexSetScale" 20 PetscErrorCode DMPlexSetScale(DM dm, PetscUnit unit, PetscReal scale) 21 { 22 DM_Plex *mesh = (DM_Plex*) dm->data; 23 24 PetscFunctionBegin; 25 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 26 mesh->scale[unit] = scale; 27 PetscFunctionReturn(0); 28 } 29 30 PETSC_STATIC_INLINE PetscInt epsilon(PetscInt i, PetscInt j, PetscInt k) 31 { 32 switch (i) { 33 case 0: 34 switch (j) { 35 case 0: return 0; 36 case 1: 37 switch (k) { 38 case 0: return 0; 39 case 1: return 0; 40 case 2: return 1; 41 } 42 case 2: 43 switch (k) { 44 case 0: return 0; 45 case 1: return -1; 46 case 2: return 0; 47 } 48 } 49 case 1: 50 switch (j) { 51 case 0: 52 switch (k) { 53 case 0: return 0; 54 case 1: return 0; 55 case 2: return -1; 56 } 57 case 1: return 0; 58 case 2: 59 switch (k) { 60 case 0: return 1; 61 case 1: return 0; 62 case 2: return 0; 63 } 64 } 65 case 2: 66 switch (j) { 67 case 0: 68 switch (k) { 69 case 0: return 0; 70 case 1: return 1; 71 case 2: return 0; 72 } 73 case 1: 74 switch (k) { 75 case 0: return -1; 76 case 1: return 0; 77 case 2: return 0; 78 } 79 case 2: return 0; 80 } 81 } 82 return 0; 83 } 84 85 #undef __FUNCT__ 86 #define __FUNCT__ "DMPlexCreateRigidBody" 87 /*@C 88 DMPlexCreateRigidBody - create rigid body modes from coordinates 89 90 Collective on DM 91 92 Input Arguments: 93 + dm - the DM 94 . section - the local section associated with the rigid field, or NULL for the default section 95 - globalSection - the global section associated with the rigid field, or NULL for the default section 96 97 Output Argument: 98 . sp - the null space 99 100 Note: This is necessary to take account of Dirichlet conditions on the displacements 101 102 Level: advanced 103 104 .seealso: MatNullSpaceCreate() 105 @*/ 106 PetscErrorCode DMPlexCreateRigidBody(DM dm, PetscSection section, PetscSection globalSection, MatNullSpace *sp) 107 { 108 MPI_Comm comm; 109 Vec coordinates, localMode, mode[6]; 110 PetscSection coordSection; 111 PetscScalar *coords; 112 PetscInt dim, vStart, vEnd, v, n, m, d, i, j; 113 PetscErrorCode ierr; 114 115 PetscFunctionBegin; 116 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 117 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 118 if (dim == 1) { 119 ierr = MatNullSpaceCreate(comm, PETSC_TRUE, 0, NULL, sp);CHKERRQ(ierr); 120 PetscFunctionReturn(0); 121 } 122 if (!section) {ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr);} 123 if (!globalSection) {ierr = DMGetDefaultGlobalSection(dm, &globalSection);CHKERRQ(ierr);} 124 ierr = PetscSectionGetConstrainedStorageSize(globalSection, &n);CHKERRQ(ierr); 125 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 126 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 127 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 128 m = (dim*(dim+1))/2; 129 ierr = VecCreate(comm, &mode[0]);CHKERRQ(ierr); 130 ierr = VecSetSizes(mode[0], n, PETSC_DETERMINE);CHKERRQ(ierr); 131 ierr = VecSetUp(mode[0]);CHKERRQ(ierr); 132 for (i = 1; i < m; ++i) {ierr = VecDuplicate(mode[0], &mode[i]);CHKERRQ(ierr);} 133 /* Assume P1 */ 134 ierr = DMGetLocalVector(dm, &localMode);CHKERRQ(ierr); 135 for (d = 0; d < dim; ++d) { 136 PetscScalar values[3] = {0.0, 0.0, 0.0}; 137 138 values[d] = 1.0; 139 ierr = VecSet(localMode, 0.0);CHKERRQ(ierr); 140 for (v = vStart; v < vEnd; ++v) { 141 ierr = DMPlexVecSetClosure(dm, section, localMode, v, values, INSERT_VALUES);CHKERRQ(ierr); 142 } 143 ierr = DMLocalToGlobalBegin(dm, localMode, INSERT_VALUES, mode[d]);CHKERRQ(ierr); 144 ierr = DMLocalToGlobalEnd(dm, localMode, INSERT_VALUES, mode[d]);CHKERRQ(ierr); 145 } 146 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 147 for (d = dim; d < dim*(dim+1)/2; ++d) { 148 PetscInt i, j, k = dim > 2 ? d - dim : d; 149 150 ierr = VecSet(localMode, 0.0);CHKERRQ(ierr); 151 for (v = vStart; v < vEnd; ++v) { 152 PetscScalar values[3] = {0.0, 0.0, 0.0}; 153 PetscInt off; 154 155 ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr); 156 for (i = 0; i < dim; ++i) { 157 for (j = 0; j < dim; ++j) { 158 values[j] += epsilon(i, j, k)*PetscRealPart(coords[off+i]); 159 } 160 } 161 ierr = DMPlexVecSetClosure(dm, section, localMode, v, values, INSERT_VALUES);CHKERRQ(ierr); 162 } 163 ierr = DMLocalToGlobalBegin(dm, localMode, INSERT_VALUES, mode[d]);CHKERRQ(ierr); 164 ierr = DMLocalToGlobalEnd(dm, localMode, INSERT_VALUES, mode[d]);CHKERRQ(ierr); 165 } 166 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 167 ierr = DMRestoreLocalVector(dm, &localMode);CHKERRQ(ierr); 168 for (i = 0; i < dim; ++i) {ierr = VecNormalize(mode[i], NULL);CHKERRQ(ierr);} 169 /* Orthonormalize system */ 170 for (i = dim; i < m; ++i) { 171 PetscScalar dots[6]; 172 173 ierr = VecMDot(mode[i], i, mode, dots);CHKERRQ(ierr); 174 for (j = 0; j < i; ++j) dots[j] *= -1.0; 175 ierr = VecMAXPY(mode[i], i, dots, mode);CHKERRQ(ierr); 176 ierr = VecNormalize(mode[i], NULL);CHKERRQ(ierr); 177 } 178 ierr = MatNullSpaceCreate(comm, PETSC_FALSE, m, mode, sp);CHKERRQ(ierr); 179 for (i = 0; i< m; ++i) {ierr = VecDestroy(&mode[i]);CHKERRQ(ierr);} 180 PetscFunctionReturn(0); 181 } 182 183 #undef __FUNCT__ 184 #define __FUNCT__ "DMPlexProjectFunctionLabelLocal" 185 PetscErrorCode DMPlexProjectFunctionLabelLocal(DM dm, DMLabel label, PetscInt numIds, const PetscInt ids[], PetscFE fe[], void (**funcs)(const PetscReal [], PetscScalar *, void *), void **ctxs, InsertMode mode, Vec localX) 186 { 187 PetscDualSpace *sp; 188 PetscSection section; 189 PetscScalar *values; 190 PetscReal *v0, *J, detJ; 191 PetscInt numFields, numComp, dim, spDim, totDim = 0, numValues, cStart, cEnd, f, d, v, i, comp; 192 PetscErrorCode ierr; 193 194 PetscFunctionBegin; 195 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 196 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 197 ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); 198 ierr = PetscMalloc3(numFields,&sp,dim,&v0,dim*dim,&J);CHKERRQ(ierr); 199 for (f = 0; f < numFields; ++f) { 200 ierr = PetscFEGetDualSpace(fe[f], &sp[f]);CHKERRQ(ierr); 201 ierr = PetscFEGetNumComponents(fe[f], &numComp);CHKERRQ(ierr); 202 ierr = PetscDualSpaceGetDimension(sp[f], &spDim);CHKERRQ(ierr); 203 totDim += spDim*numComp; 204 } 205 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 206 ierr = DMPlexVecGetClosure(dm, section, localX, cStart, &numValues, NULL);CHKERRQ(ierr); 207 if (numValues != totDim) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "The section cell closure size %d != dual space dimension %d", numValues, totDim); 208 ierr = DMGetWorkArray(dm, numValues, PETSC_SCALAR, &values);CHKERRQ(ierr); 209 for (i = 0; i < numIds; ++i) { 210 IS pointIS; 211 const PetscInt *points; 212 PetscInt n, p; 213 214 ierr = DMLabelGetStratumIS(label, ids[i], &pointIS);CHKERRQ(ierr); 215 ierr = ISGetLocalSize(pointIS, &n);CHKERRQ(ierr); 216 ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); 217 for (p = 0; p < n; ++p) { 218 const PetscInt point = points[p]; 219 PetscCellGeometry geom; 220 221 if ((point < cStart) || (point >= cEnd)) continue; 222 ierr = DMPlexComputeCellGeometry(dm, point, v0, J, NULL, &detJ);CHKERRQ(ierr); 223 geom.v0 = v0; 224 geom.J = J; 225 geom.detJ = &detJ; 226 for (f = 0, v = 0; f < numFields; ++f) { 227 void * const ctx = ctxs ? ctxs[f] : NULL; 228 ierr = PetscFEGetNumComponents(fe[f], &numComp);CHKERRQ(ierr); 229 ierr = PetscDualSpaceGetDimension(sp[f], &spDim);CHKERRQ(ierr); 230 for (d = 0; d < spDim; ++d) { 231 if (funcs[f]) { 232 ierr = PetscDualSpaceApply(sp[f], d, geom, numComp, funcs[f], ctx, &values[v]);CHKERRQ(ierr); 233 } else { 234 for (comp = 0; comp < numComp; ++comp) values[v+comp] = 0.0; 235 } 236 v += numComp; 237 } 238 } 239 ierr = DMPlexVecSetClosure(dm, section, localX, point, values, mode);CHKERRQ(ierr); 240 } 241 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 242 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 243 } 244 ierr = DMRestoreWorkArray(dm, numValues, PETSC_SCALAR, &values);CHKERRQ(ierr); 245 ierr = PetscFree3(sp,v0,J);CHKERRQ(ierr); 246 PetscFunctionReturn(0); 247 } 248 249 #undef __FUNCT__ 250 #define __FUNCT__ "DMPlexProjectFunctionLocal" 251 PetscErrorCode DMPlexProjectFunctionLocal(DM dm, PetscFE fe[], void (**funcs)(const PetscReal [], PetscScalar *, void *), void **ctxs, InsertMode mode, Vec localX) 252 { 253 PetscDualSpace *sp; 254 PetscSection section; 255 PetscScalar *values; 256 PetscReal *v0, *J, detJ; 257 PetscInt numFields, numComp, dim, spDim, totDim = 0, numValues, cStart, cEnd, c, f, d, v, comp; 258 PetscErrorCode ierr; 259 260 PetscFunctionBegin; 261 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 262 ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); 263 ierr = PetscMalloc1(numFields, &sp);CHKERRQ(ierr); 264 for (f = 0; f < numFields; ++f) { 265 ierr = PetscFEGetDualSpace(fe[f], &sp[f]);CHKERRQ(ierr); 266 ierr = PetscFEGetNumComponents(fe[f], &numComp);CHKERRQ(ierr); 267 ierr = PetscDualSpaceGetDimension(sp[f], &spDim);CHKERRQ(ierr); 268 totDim += spDim*numComp; 269 } 270 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 271 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 272 ierr = DMPlexVecGetClosure(dm, section, localX, cStart, &numValues, NULL);CHKERRQ(ierr); 273 if (numValues != totDim) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "The section cell closure size %d != dual space dimension %d", numValues, totDim); 274 ierr = DMGetWorkArray(dm, numValues, PETSC_SCALAR, &values);CHKERRQ(ierr); 275 ierr = PetscMalloc2(dim,&v0,dim*dim,&J);CHKERRQ(ierr); 276 for (c = cStart; c < cEnd; ++c) { 277 PetscCellGeometry geom; 278 279 ierr = DMPlexComputeCellGeometry(dm, c, v0, J, NULL, &detJ);CHKERRQ(ierr); 280 geom.v0 = v0; 281 geom.J = J; 282 geom.detJ = &detJ; 283 for (f = 0, v = 0; f < numFields; ++f) { 284 void * const ctx = ctxs ? ctxs[f] : NULL; 285 ierr = PetscFEGetNumComponents(fe[f], &numComp);CHKERRQ(ierr); 286 ierr = PetscDualSpaceGetDimension(sp[f], &spDim);CHKERRQ(ierr); 287 for (d = 0; d < spDim; ++d) { 288 if (funcs[f]) { 289 ierr = PetscDualSpaceApply(sp[f], d, geom, numComp, funcs[f], ctx, &values[v]);CHKERRQ(ierr); 290 } else { 291 for (comp = 0; comp < numComp; ++comp) values[v+comp] = 0.0; 292 } 293 v += numComp; 294 } 295 } 296 ierr = DMPlexVecSetClosure(dm, section, localX, c, values, mode);CHKERRQ(ierr); 297 } 298 ierr = DMRestoreWorkArray(dm, numValues, PETSC_SCALAR, &values);CHKERRQ(ierr); 299 ierr = PetscFree2(v0,J);CHKERRQ(ierr); 300 ierr = PetscFree(sp);CHKERRQ(ierr); 301 PetscFunctionReturn(0); 302 } 303 304 #undef __FUNCT__ 305 #define __FUNCT__ "DMPlexProjectFunction" 306 /*@C 307 DMPlexProjectFunction - This projects the given function into the function space provided. 308 309 Input Parameters: 310 + dm - The DM 311 . fe - The PetscFE associated with the field 312 . funcs - The coordinate functions to evaluate, one per field 313 . ctxs - Optional array of contexts to pass to each coordinate function. ctxs itself may be null. 314 - mode - The insertion mode for values 315 316 Output Parameter: 317 . X - vector 318 319 Level: developer 320 321 .seealso: DMPlexComputeL2Diff() 322 @*/ 323 PetscErrorCode DMPlexProjectFunction(DM dm, PetscFE fe[], void (**funcs)(const PetscReal [], PetscScalar *, void *), void **ctxs, InsertMode mode, Vec X) 324 { 325 Vec localX; 326 PetscErrorCode ierr; 327 328 PetscFunctionBegin; 329 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 330 ierr = DMGetLocalVector(dm, &localX);CHKERRQ(ierr); 331 ierr = DMPlexProjectFunctionLocal(dm, fe, funcs, ctxs, mode, localX);CHKERRQ(ierr); 332 ierr = DMLocalToGlobalBegin(dm, localX, mode, X);CHKERRQ(ierr); 333 ierr = DMLocalToGlobalEnd(dm, localX, mode, X);CHKERRQ(ierr); 334 ierr = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr); 335 PetscFunctionReturn(0); 336 } 337 338 #undef __FUNCT__ 339 #define __FUNCT__ "DMPlexInsertBoundaryValuesFEM" 340 PetscErrorCode DMPlexInsertBoundaryValuesFEM(DM dm, Vec localX) 341 { 342 void (**funcs)(const PetscReal x[], PetscScalar *u, void *ctx); 343 void **ctxs; 344 PetscFE *fe; 345 PetscInt numFields, f, numBd, b; 346 PetscErrorCode ierr; 347 348 PetscFunctionBegin; 349 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 350 PetscValidHeaderSpecific(localX, VEC_CLASSID, 2); 351 ierr = DMGetNumFields(dm, &numFields);CHKERRQ(ierr); 352 ierr = PetscMalloc3(numFields,&fe,numFields,&funcs,numFields,&ctxs);CHKERRQ(ierr); 353 for (f = 0; f < numFields; ++f) {ierr = DMGetField(dm, f, (PetscObject *) &fe[f]);CHKERRQ(ierr);} 354 /* OPT: Could attempt to do multiple BCs at once */ 355 ierr = DMPlexGetNumBoundary(dm, &numBd);CHKERRQ(ierr); 356 for (b = 0; b < numBd; ++b) { 357 DMLabel label; 358 const PetscInt *ids; 359 const char *name; 360 PetscInt numids, field; 361 PetscBool isEssential; 362 void (*func)(); 363 void *ctx; 364 365 /* TODO: We need to set only the part indicated by the ids */ 366 ierr = DMPlexGetBoundary(dm, b, &isEssential, &name, &field, &func, &numids, &ids, &ctx);CHKERRQ(ierr); 367 ierr = DMPlexGetLabel(dm, name, &label);CHKERRQ(ierr); 368 for (f = 0; f < numFields; ++f) { 369 funcs[f] = field == f ? (void (*)(const PetscReal[], PetscScalar *, void *)) func : NULL; 370 ctxs[f] = field == f ? ctx : NULL; 371 } 372 ierr = DMPlexProjectFunctionLabelLocal(dm, label, numids, ids, fe, funcs, ctxs, INSERT_BC_VALUES, localX);CHKERRQ(ierr); 373 } 374 ierr = PetscFree3(fe,funcs,ctxs);CHKERRQ(ierr); 375 PetscFunctionReturn(0); 376 } 377 378 /* Assuming dim == 3 */ 379 typedef struct { 380 PetscScalar normal[3]; /* Area-scaled normals */ 381 PetscScalar centroid[3]; /* Location of centroid (quadrature point) */ 382 PetscScalar grad[2][3]; /* Face contribution to gradient in left and right cell */ 383 } FaceGeom; 384 385 #undef __FUNCT__ 386 #define __FUNCT__ "DMPlexInsertBoundaryValuesFVM" 387 PetscErrorCode DMPlexInsertBoundaryValuesFVM(DM dm, PetscReal time, Vec locX) 388 { 389 DM dmFace; 390 Vec faceGeometry; 391 DMLabel label; 392 const PetscScalar *facegeom; 393 PetscScalar *x; 394 PetscInt numBd, b; 395 PetscErrorCode ierr; 396 397 PetscFunctionBegin; 398 /* TODO Pull this geometry calculation into the library */ 399 ierr = PetscObjectQuery((PetscObject) dm, "FaceGeometry", (PetscObject *) &faceGeometry);CHKERRQ(ierr); 400 ierr = DMPlexGetLabel(dm, "Face Sets", &label);CHKERRQ(ierr); 401 ierr = DMPlexGetNumBoundary(dm, &numBd);CHKERRQ(ierr); 402 ierr = VecGetDM(faceGeometry, &dmFace);CHKERRQ(ierr); 403 ierr = VecGetArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); 404 ierr = VecGetArray(locX, &x);CHKERRQ(ierr); 405 for (b = 0; b < numBd; ++b) { 406 PetscErrorCode (*func)(PetscReal,const PetscScalar*,const PetscScalar*,const PetscScalar*,PetscScalar*,void*); 407 const PetscInt *ids; 408 PetscInt numids, i; 409 void *ctx; 410 411 ierr = DMPlexGetBoundary(dm, b, NULL, NULL, NULL, (void (**)()) &func, &numids, &ids, &ctx);CHKERRQ(ierr); 412 for (i = 0; i < numids; ++i) { 413 IS faceIS; 414 const PetscInt *faces; 415 PetscInt numFaces, f; 416 417 ierr = DMLabelGetStratumIS(label, ids[i], &faceIS);CHKERRQ(ierr); 418 if (!faceIS) continue; /* No points with that id on this process */ 419 ierr = ISGetLocalSize(faceIS, &numFaces);CHKERRQ(ierr); 420 ierr = ISGetIndices(faceIS, &faces);CHKERRQ(ierr); 421 for (f = 0; f < numFaces; ++f) { 422 const PetscInt face = faces[f], *cells; 423 const PetscScalar *xI; 424 PetscScalar *xG; 425 const FaceGeom *fg; 426 427 ierr = DMPlexPointLocalRead(dmFace, face, facegeom, &fg);CHKERRQ(ierr); 428 ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr); 429 ierr = DMPlexPointLocalRead(dm, cells[0], x, &xI);CHKERRQ(ierr); 430 ierr = DMPlexPointLocalRef(dm, cells[1], x, &xG);CHKERRQ(ierr); 431 ierr = (*func)(time, fg->centroid, fg->normal, xI, xG, ctx);CHKERRQ(ierr); 432 } 433 ierr = ISRestoreIndices(faceIS, &faces);CHKERRQ(ierr); 434 ierr = ISDestroy(&faceIS);CHKERRQ(ierr); 435 } 436 } 437 ierr = VecRestoreArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); 438 ierr = VecRestoreArray(locX, &x);CHKERRQ(ierr); 439 PetscFunctionReturn(0); 440 } 441 442 #undef __FUNCT__ 443 #define __FUNCT__ "DMPlexComputeL2Diff" 444 /*@C 445 DMPlexComputeL2Diff - This function computes the L_2 difference between a function u and an FEM interpolant solution u_h. 446 447 Input Parameters: 448 + dm - The DM 449 . fe - The PetscFE object for each field 450 . funcs - The functions to evaluate for each field component 451 . ctxs - Optional array of contexts to pass to each function, or NULL. 452 - X - The coefficient vector u_h 453 454 Output Parameter: 455 . diff - The diff ||u - u_h||_2 456 457 Level: developer 458 459 .seealso: DMPlexProjectFunction(), DMPlexComputeL2GradientDiff() 460 @*/ 461 PetscErrorCode DMPlexComputeL2Diff(DM dm, PetscFE fe[], void (**funcs)(const PetscReal [], PetscScalar *, void *), void **ctxs, Vec X, PetscReal *diff) 462 { 463 const PetscInt debug = 0; 464 PetscSection section; 465 PetscQuadrature quad; 466 Vec localX; 467 PetscScalar *funcVal; 468 PetscReal *coords, *v0, *J, *invJ, detJ; 469 PetscReal localDiff = 0.0; 470 PetscInt dim, numFields, numComponents = 0, cStart, cEnd, c, field, fieldOffset, comp; 471 PetscErrorCode ierr; 472 473 PetscFunctionBegin; 474 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 475 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 476 ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); 477 ierr = DMGetLocalVector(dm, &localX);CHKERRQ(ierr); 478 ierr = DMGlobalToLocalBegin(dm, X, INSERT_VALUES, localX);CHKERRQ(ierr); 479 ierr = DMGlobalToLocalEnd(dm, X, INSERT_VALUES, localX);CHKERRQ(ierr); 480 for (field = 0; field < numFields; ++field) { 481 PetscInt Nc; 482 483 ierr = PetscFEGetNumComponents(fe[field], &Nc);CHKERRQ(ierr); 484 numComponents += Nc; 485 } 486 ierr = DMPlexProjectFunctionLocal(dm, fe, funcs, ctxs, INSERT_BC_VALUES, localX);CHKERRQ(ierr); 487 ierr = PetscMalloc5(numComponents,&funcVal,dim,&coords,dim,&v0,dim*dim,&J,dim*dim,&invJ);CHKERRQ(ierr); 488 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 489 ierr = PetscFEGetQuadrature(fe[0], &quad);CHKERRQ(ierr); 490 for (c = cStart; c < cEnd; ++c) { 491 PetscScalar *x = NULL; 492 PetscReal elemDiff = 0.0; 493 494 ierr = DMPlexComputeCellGeometry(dm, c, v0, J, invJ, &detJ);CHKERRQ(ierr); 495 if (detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", detJ, c); 496 ierr = DMPlexVecGetClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr); 497 498 for (field = 0, comp = 0, fieldOffset = 0; field < numFields; ++field) { 499 void * const ctx = ctxs ? ctxs[field] : NULL; 500 const PetscReal *quadPoints, *quadWeights; 501 PetscReal *basis; 502 PetscInt numQuadPoints, numBasisFuncs, numBasisComps, q, d, e, fc, f; 503 504 ierr = PetscQuadratureGetData(quad, NULL, &numQuadPoints, &quadPoints, &quadWeights);CHKERRQ(ierr); 505 ierr = PetscFEGetDimension(fe[field], &numBasisFuncs);CHKERRQ(ierr); 506 ierr = PetscFEGetNumComponents(fe[field], &numBasisComps);CHKERRQ(ierr); 507 ierr = PetscFEGetDefaultTabulation(fe[field], &basis, NULL, NULL);CHKERRQ(ierr); 508 if (debug) { 509 char title[1024]; 510 ierr = PetscSNPrintf(title, 1023, "Solution for Field %d", field);CHKERRQ(ierr); 511 ierr = DMPrintCellVector(c, title, numBasisFuncs*numBasisComps, &x[fieldOffset]);CHKERRQ(ierr); 512 } 513 for (q = 0; q < numQuadPoints; ++q) { 514 for (d = 0; d < dim; d++) { 515 coords[d] = v0[d]; 516 for (e = 0; e < dim; e++) { 517 coords[d] += J[d*dim+e]*(quadPoints[q*dim+e] + 1.0); 518 } 519 } 520 (*funcs[field])(coords, funcVal, ctx); 521 for (fc = 0; fc < numBasisComps; ++fc) { 522 PetscScalar interpolant = 0.0; 523 524 for (f = 0; f < numBasisFuncs; ++f) { 525 const PetscInt fidx = f*numBasisComps+fc; 526 interpolant += x[fieldOffset+fidx]*basis[q*numBasisFuncs*numBasisComps+fidx]; 527 } 528 if (debug) {ierr = PetscPrintf(PETSC_COMM_SELF, " elem %d field %d diff %g\n", c, field, PetscSqr(PetscRealPart(interpolant - funcVal[fc]))*quadWeights[q]*detJ);CHKERRQ(ierr);} 529 elemDiff += PetscSqr(PetscRealPart(interpolant - funcVal[fc]))*quadWeights[q]*detJ; 530 } 531 } 532 comp += numBasisComps; 533 fieldOffset += numBasisFuncs*numBasisComps; 534 } 535 ierr = DMPlexVecRestoreClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr); 536 if (debug) {ierr = PetscPrintf(PETSC_COMM_SELF, " elem %d diff %g\n", c, elemDiff);CHKERRQ(ierr);} 537 localDiff += elemDiff; 538 } 539 ierr = PetscFree5(funcVal,coords,v0,J,invJ);CHKERRQ(ierr); 540 ierr = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr); 541 ierr = MPI_Allreduce(&localDiff, diff, 1, MPIU_REAL, MPI_SUM, PetscObjectComm((PetscObject)dm));CHKERRQ(ierr); 542 *diff = PetscSqrtReal(*diff); 543 PetscFunctionReturn(0); 544 } 545 546 #undef __FUNCT__ 547 #define __FUNCT__ "DMPlexComputeL2GradientDiff" 548 /*@C 549 DMPlexComputeL2GradientDiff - This function computes the L_2 difference between the gradient of a function u and an FEM interpolant solution grad u_h. 550 551 Input Parameters: 552 + dm - The DM 553 . fe - The PetscFE object for each field 554 . funcs - The gradient functions to evaluate for each field component 555 . ctxs - Optional array of contexts to pass to each function, or NULL. 556 . X - The coefficient vector u_h 557 - n - The vector to project along 558 559 Output Parameter: 560 . diff - The diff ||(grad u - grad u_h) . n||_2 561 562 Level: developer 563 564 .seealso: DMPlexProjectFunction(), DMPlexComputeL2Diff() 565 @*/ 566 PetscErrorCode DMPlexComputeL2GradientDiff(DM dm, PetscFE fe[], void (**funcs)(const PetscReal [], const PetscReal [], PetscScalar *, void *), void **ctxs, Vec X, const PetscReal n[], PetscReal *diff) 567 { 568 const PetscInt debug = 0; 569 PetscSection section; 570 PetscQuadrature quad; 571 Vec localX; 572 PetscScalar *funcVal, *interpolantVec; 573 PetscReal *coords, *realSpaceDer, *v0, *J, *invJ, detJ; 574 PetscReal localDiff = 0.0; 575 PetscInt dim, numFields, numComponents = 0, cStart, cEnd, c, field, fieldOffset, comp; 576 PetscErrorCode ierr; 577 578 PetscFunctionBegin; 579 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 580 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 581 ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); 582 ierr = DMGetLocalVector(dm, &localX);CHKERRQ(ierr); 583 ierr = DMGlobalToLocalBegin(dm, X, INSERT_VALUES, localX);CHKERRQ(ierr); 584 ierr = DMGlobalToLocalEnd(dm, X, INSERT_VALUES, localX);CHKERRQ(ierr); 585 for (field = 0; field < numFields; ++field) { 586 PetscInt Nc; 587 588 ierr = PetscFEGetNumComponents(fe[field], &Nc);CHKERRQ(ierr); 589 numComponents += Nc; 590 } 591 /* ierr = DMPlexProjectFunctionLocal(dm, fe, funcs, INSERT_BC_VALUES, localX);CHKERRQ(ierr); */ 592 ierr = PetscMalloc7(numComponents,&funcVal,dim,&coords,dim,&realSpaceDer,dim,&v0,dim*dim,&J,dim*dim,&invJ,dim,&interpolantVec);CHKERRQ(ierr); 593 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 594 ierr = PetscFEGetQuadrature(fe[0], &quad);CHKERRQ(ierr); 595 for (c = cStart; c < cEnd; ++c) { 596 PetscScalar *x = NULL; 597 PetscReal elemDiff = 0.0; 598 599 ierr = DMPlexComputeCellGeometry(dm, c, v0, J, invJ, &detJ);CHKERRQ(ierr); 600 if (detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", detJ, c); 601 ierr = DMPlexVecGetClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr); 602 603 for (field = 0, comp = 0, fieldOffset = 0; field < numFields; ++field) { 604 void * const ctx = ctxs ? ctxs[field] : NULL; 605 const PetscReal *quadPoints, *quadWeights; 606 PetscReal *basisDer; 607 PetscInt numQuadPoints, Nb, Ncomp, q, d, e, fc, f, g; 608 609 ierr = PetscQuadratureGetData(quad, NULL, &numQuadPoints, &quadPoints, &quadWeights);CHKERRQ(ierr); 610 ierr = PetscFEGetDimension(fe[field], &Nb);CHKERRQ(ierr); 611 ierr = PetscFEGetNumComponents(fe[field], &Ncomp);CHKERRQ(ierr); 612 ierr = PetscFEGetDefaultTabulation(fe[field], NULL, &basisDer, NULL);CHKERRQ(ierr); 613 if (debug) { 614 char title[1024]; 615 ierr = PetscSNPrintf(title, 1023, "Solution for Field %d", field);CHKERRQ(ierr); 616 ierr = DMPrintCellVector(c, title, Nb*Ncomp, &x[fieldOffset]);CHKERRQ(ierr); 617 } 618 for (q = 0; q < numQuadPoints; ++q) { 619 for (d = 0; d < dim; d++) { 620 coords[d] = v0[d]; 621 for (e = 0; e < dim; e++) { 622 coords[d] += J[d*dim+e]*(quadPoints[q*dim+e] + 1.0); 623 } 624 } 625 (*funcs[field])(coords, n, funcVal, ctx); 626 for (fc = 0; fc < Ncomp; ++fc) { 627 PetscScalar interpolant = 0.0; 628 629 for (d = 0; d < dim; ++d) interpolantVec[d] = 0.0; 630 for (f = 0; f < Nb; ++f) { 631 const PetscInt fidx = f*Ncomp+fc; 632 633 for (d = 0; d < dim; ++d) { 634 realSpaceDer[d] = 0.0; 635 for (g = 0; g < dim; ++g) { 636 realSpaceDer[d] += invJ[g*dim+d]*basisDer[(q*Nb*Ncomp+fidx)*dim+g]; 637 } 638 interpolantVec[d] += x[fieldOffset+fidx]*realSpaceDer[d]; 639 } 640 } 641 for (d = 0; d < dim; ++d) interpolant += interpolantVec[d]*n[d]; 642 if (debug) {ierr = PetscPrintf(PETSC_COMM_SELF, " elem %d fieldDer %d diff %g\n", c, field, PetscSqr(PetscRealPart(interpolant - funcVal[fc]))*quadWeights[q]*detJ);CHKERRQ(ierr);} 643 elemDiff += PetscSqr(PetscRealPart(interpolant - funcVal[fc]))*quadWeights[q]*detJ; 644 } 645 } 646 comp += Ncomp; 647 fieldOffset += Nb*Ncomp; 648 } 649 ierr = DMPlexVecRestoreClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr); 650 if (debug) {ierr = PetscPrintf(PETSC_COMM_SELF, " elem %d diff %g\n", c, elemDiff);CHKERRQ(ierr);} 651 localDiff += elemDiff; 652 } 653 ierr = PetscFree7(funcVal,coords,realSpaceDer,v0,J,invJ,interpolantVec);CHKERRQ(ierr); 654 ierr = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr); 655 ierr = MPI_Allreduce(&localDiff, diff, 1, MPIU_REAL, MPI_SUM, PetscObjectComm((PetscObject)dm));CHKERRQ(ierr); 656 *diff = PetscSqrtReal(*diff); 657 PetscFunctionReturn(0); 658 } 659 660 #undef __FUNCT__ 661 #define __FUNCT__ "DMPlexComputeResidualFEM" 662 /*@ 663 DMPlexComputeResidualFEM - Form the local residual F from the local input X using pointwise functions specified by the user 664 665 Input Parameters: 666 + dm - The mesh 667 . X - Local input vector 668 - user - The user context 669 670 Output Parameter: 671 . F - Local output vector 672 673 Note: 674 The first member of the user context must be an FEMContext. 675 676 We form the residual one batch of elements at a time. This allows us to offload work onto an accelerator, 677 like a GPU, or vectorize on a multicore machine. 678 679 Level: developer 680 681 .seealso: DMPlexComputeJacobianActionFEM() 682 @*/ 683 PetscErrorCode DMPlexComputeResidualFEM(DM dm, Vec X, Vec F, void *user) 684 { 685 DM_Plex *mesh = (DM_Plex *) dm->data; 686 PetscFEM *fem = (PetscFEM *) user; 687 PetscFE *fe = fem->fe; 688 PetscFE *feAux = fem->feAux; 689 PetscFE *feBd = fem->feBd; 690 const char *name = "Residual"; 691 DM dmAux; 692 Vec A; 693 PetscQuadrature q; 694 PetscCellGeometry geom; 695 PetscSection section, sectionAux; 696 PetscReal *v0, *J, *invJ, *detJ; 697 PetscScalar *elemVec, *u, *a = NULL; 698 PetscInt dim, Nf, NfAux = 0, f, numCells, cStart, cEnd, c; 699 PetscInt cellDof = 0, numComponents = 0; 700 PetscInt cellDofAux = 0, numComponentsAux = 0; 701 PetscErrorCode ierr; 702 703 PetscFunctionBegin; 704 ierr = PetscLogEventBegin(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr); 705 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 706 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 707 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); 708 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 709 numCells = cEnd - cStart; 710 for (f = 0; f < Nf; ++f) { 711 PetscInt Nb, Nc; 712 713 ierr = PetscFEGetDimension(fe[f], &Nb);CHKERRQ(ierr); 714 ierr = PetscFEGetNumComponents(fe[f], &Nc);CHKERRQ(ierr); 715 cellDof += Nb*Nc; 716 numComponents += Nc; 717 } 718 ierr = PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);CHKERRQ(ierr); 719 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);CHKERRQ(ierr); 720 if (dmAux) { 721 ierr = DMGetDefaultSection(dmAux, §ionAux);CHKERRQ(ierr); 722 ierr = PetscSectionGetNumFields(sectionAux, &NfAux);CHKERRQ(ierr); 723 } 724 for (f = 0; f < NfAux; ++f) { 725 PetscInt Nb, Nc; 726 727 ierr = PetscFEGetDimension(feAux[f], &Nb);CHKERRQ(ierr); 728 ierr = PetscFEGetNumComponents(feAux[f], &Nc);CHKERRQ(ierr); 729 cellDofAux += Nb*Nc; 730 numComponentsAux += Nc; 731 } 732 ierr = DMPlexInsertBoundaryValuesFEM(dm, X);CHKERRQ(ierr); 733 ierr = VecSet(F, 0.0);CHKERRQ(ierr); 734 ierr = PetscMalloc6(numCells*cellDof,&u,numCells*dim,&v0,numCells*dim*dim,&J,numCells*dim*dim,&invJ,numCells,&detJ,numCells*cellDof,&elemVec);CHKERRQ(ierr); 735 if (dmAux) {ierr = PetscMalloc1(numCells*cellDofAux, &a);CHKERRQ(ierr);} 736 for (c = cStart; c < cEnd; ++c) { 737 PetscScalar *x = NULL; 738 PetscInt i; 739 740 ierr = DMPlexComputeCellGeometry(dm, c, &v0[c*dim], &J[c*dim*dim], &invJ[c*dim*dim], &detJ[c]);CHKERRQ(ierr); 741 if (detJ[c] <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", detJ[c], c); 742 ierr = DMPlexVecGetClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr); 743 for (i = 0; i < cellDof; ++i) u[c*cellDof+i] = x[i]; 744 ierr = DMPlexVecRestoreClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr); 745 if (dmAux) { 746 ierr = DMPlexVecGetClosure(dmAux, sectionAux, A, c, NULL, &x);CHKERRQ(ierr); 747 for (i = 0; i < cellDofAux; ++i) a[c*cellDofAux+i] = x[i]; 748 ierr = DMPlexVecRestoreClosure(dmAux, sectionAux, A, c, NULL, &x);CHKERRQ(ierr); 749 } 750 } 751 for (f = 0; f < Nf; ++f) { 752 void (*f0)(const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscReal[], PetscScalar[]) = fem->f0Funcs[f]; 753 void (*f1)(const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscReal[], PetscScalar[]) = fem->f1Funcs[f]; 754 PetscInt numQuadPoints, Nb; 755 /* Conforming batches */ 756 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 757 /* Remainder */ 758 PetscInt Nr, offset; 759 760 ierr = PetscFEGetQuadrature(fe[f], &q);CHKERRQ(ierr); 761 ierr = PetscFEGetDimension(fe[f], &Nb);CHKERRQ(ierr); 762 ierr = PetscFEGetTileSizes(fe[f], NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 763 ierr = PetscQuadratureGetData(q, NULL, &numQuadPoints, NULL, NULL);CHKERRQ(ierr); 764 blockSize = Nb*numQuadPoints; 765 batchSize = numBlocks * blockSize; 766 ierr = PetscFESetTileSizes(fe[f], blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 767 numChunks = numCells / (numBatches*batchSize); 768 Ne = numChunks*numBatches*batchSize; 769 Nr = numCells % (numBatches*batchSize); 770 offset = numCells - Nr; 771 geom.v0 = v0; 772 geom.J = J; 773 geom.invJ = invJ; 774 geom.detJ = detJ; 775 ierr = PetscFEIntegrateResidual(fe[f], Ne, Nf, fe, f, geom, u, NfAux, feAux, a, f0, f1, elemVec);CHKERRQ(ierr); 776 geom.v0 = &v0[offset*dim]; 777 geom.J = &J[offset*dim*dim]; 778 geom.invJ = &invJ[offset*dim*dim]; 779 geom.detJ = &detJ[offset]; 780 ierr = PetscFEIntegrateResidual(fe[f], Nr, Nf, fe, f, geom, &u[offset*cellDof], NfAux, feAux, &a[offset*cellDofAux], f0, f1, &elemVec[offset*cellDof]);CHKERRQ(ierr); 781 } 782 for (c = cStart; c < cEnd; ++c) { 783 if (mesh->printFEM > 1) {ierr = DMPrintCellVector(c, name, cellDof, &elemVec[c*cellDof]);CHKERRQ(ierr);} 784 ierr = DMPlexVecSetClosure(dm, section, F, c, &elemVec[c*cellDof], ADD_VALUES);CHKERRQ(ierr); 785 } 786 ierr = PetscFree6(u,v0,J,invJ,detJ,elemVec);CHKERRQ(ierr); 787 if (dmAux) {ierr = PetscFree(a);CHKERRQ(ierr);} 788 if (feBd) { 789 DMLabel depth; 790 PetscInt numBd, bd; 791 792 for (f = 0, cellDof = 0, numComponents = 0; f < Nf; ++f) { 793 PetscInt Nb, Nc; 794 795 ierr = PetscFEGetDimension(feBd[f], &Nb);CHKERRQ(ierr); 796 ierr = PetscFEGetNumComponents(feBd[f], &Nc);CHKERRQ(ierr); 797 cellDof += Nb*Nc; 798 numComponents += Nc; 799 } 800 ierr = DMPlexGetDepthLabel(dm, &depth);CHKERRQ(ierr); 801 ierr = DMPlexGetNumBoundary(dm, &numBd);CHKERRQ(ierr); 802 for (bd = 0; bd < numBd; ++bd) { 803 const char *bdLabel; 804 DMLabel label; 805 IS pointIS; 806 const PetscInt *points; 807 const PetscInt *values; 808 PetscReal *n; 809 PetscInt field, numValues, numPoints, p, dep, numFaces; 810 PetscBool isEssential; 811 812 ierr = DMPlexGetBoundary(dm, bd, &isEssential, &bdLabel, &field, NULL, &numValues, &values, NULL);CHKERRQ(ierr); 813 if (numValues != 1) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Bug me and I will fix this"); 814 ierr = DMPlexGetLabel(dm, bdLabel, &label);CHKERRQ(ierr); 815 ierr = DMLabelGetStratumSize(label, 1, &numPoints);CHKERRQ(ierr); 816 ierr = DMLabelGetStratumIS(label, 1, &pointIS);CHKERRQ(ierr); 817 ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); 818 for (p = 0, numFaces = 0; p < numPoints; ++p) { 819 ierr = DMLabelGetValue(depth, points[p], &dep);CHKERRQ(ierr); 820 if (dep == dim-1) ++numFaces; 821 } 822 ierr = PetscMalloc7(numFaces*cellDof,&u,numFaces*dim,&v0,numFaces*dim,&n,numFaces*dim*dim,&J,numFaces*dim*dim,&invJ,numFaces,&detJ,numFaces*cellDof,&elemVec);CHKERRQ(ierr); 823 for (p = 0, f = 0; p < numPoints; ++p) { 824 const PetscInt point = points[p]; 825 PetscScalar *x = NULL; 826 PetscInt i; 827 828 ierr = DMLabelGetValue(depth, points[p], &dep);CHKERRQ(ierr); 829 if (dep != dim-1) continue; 830 ierr = DMPlexComputeCellGeometry(dm, point, &v0[f*dim], &J[f*dim*dim], &invJ[f*dim*dim], &detJ[f]);CHKERRQ(ierr); 831 ierr = DMPlexComputeCellGeometryFVM(dm, point, NULL, NULL, &n[f*dim]); 832 if (detJ[f] <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for face %d", detJ[f], point); 833 ierr = DMPlexVecGetClosure(dm, section, X, point, NULL, &x);CHKERRQ(ierr); 834 for (i = 0; i < cellDof; ++i) u[f*cellDof+i] = x[i]; 835 ierr = DMPlexVecRestoreClosure(dm, section, X, point, NULL, &x);CHKERRQ(ierr); 836 ++f; 837 } 838 for (f = 0; f < Nf; ++f) { 839 void (*f0)(const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscReal[], const PetscReal[], PetscScalar[]) = fem->f0BdFuncs[f]; 840 void (*f1)(const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscReal[], const PetscReal[], PetscScalar[]) = fem->f1BdFuncs[f]; 841 PetscInt numQuadPoints, Nb; 842 /* Conforming batches */ 843 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 844 /* Remainder */ 845 PetscInt Nr, offset; 846 847 ierr = PetscFEGetQuadrature(feBd[f], &q);CHKERRQ(ierr); 848 ierr = PetscFEGetDimension(feBd[f], &Nb);CHKERRQ(ierr); 849 ierr = PetscFEGetTileSizes(feBd[f], NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 850 ierr = PetscQuadratureGetData(q, NULL, &numQuadPoints, NULL, NULL);CHKERRQ(ierr); 851 blockSize = Nb*numQuadPoints; 852 batchSize = numBlocks * blockSize; 853 ierr = PetscFESetTileSizes(feBd[f], blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 854 numChunks = numFaces / (numBatches*batchSize); 855 Ne = numChunks*numBatches*batchSize; 856 Nr = numFaces % (numBatches*batchSize); 857 offset = numFaces - Nr; 858 geom.v0 = v0; 859 geom.n = n; 860 geom.J = J; 861 geom.invJ = invJ; 862 geom.detJ = detJ; 863 ierr = PetscFEIntegrateBdResidual(feBd[f], Ne, Nf, feBd, f, geom, u, 0, NULL, NULL, f0, f1, elemVec);CHKERRQ(ierr); 864 geom.v0 = &v0[offset*dim]; 865 geom.n = &n[offset*dim]; 866 geom.J = &J[offset*dim*dim]; 867 geom.invJ = &invJ[offset*dim*dim]; 868 geom.detJ = &detJ[offset]; 869 ierr = PetscFEIntegrateBdResidual(feBd[f], Nr, Nf, feBd, f, geom, &u[offset*cellDof], 0, NULL, NULL, f0, f1, &elemVec[offset*cellDof]);CHKERRQ(ierr); 870 } 871 for (p = 0, f = 0; p < numPoints; ++p) { 872 const PetscInt point = points[p]; 873 874 ierr = DMLabelGetValue(depth, point, &dep);CHKERRQ(ierr); 875 if (dep != dim-1) continue; 876 if (mesh->printFEM > 1) {ierr = DMPrintCellVector(point, "BdResidual", cellDof, &elemVec[f*cellDof]);CHKERRQ(ierr);} 877 ierr = DMPlexVecSetClosure(dm, NULL, F, point, &elemVec[f*cellDof], ADD_VALUES);CHKERRQ(ierr); 878 ++f; 879 } 880 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 881 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 882 ierr = PetscFree7(u,v0,n,J,invJ,detJ,elemVec);CHKERRQ(ierr); 883 } 884 } 885 if (mesh->printFEM) {ierr = DMPrintLocalVec(dm, name, mesh->printTol, F);CHKERRQ(ierr);} 886 ierr = PetscLogEventEnd(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr); 887 PetscFunctionReturn(0); 888 } 889 890 #undef __FUNCT__ 891 #define __FUNCT__ "DMPlexComputeIFunctionFEM" 892 /*@ 893 DMPlexComputeIFunctionFEM - Form the local implicit function F from the local input X, X_t using pointwise functions specified by the user 894 895 Input Parameters: 896 + dm - The mesh 897 . time - The current time 898 . X - Local input vector 899 . X_t - Time derivative of the local input vector 900 - user - The user context 901 902 Output Parameter: 903 . F - Local output vector 904 905 Note: 906 The first member of the user context must be an FEMContext. 907 908 We form the residual one batch of elements at a time. This allows us to offload work onto an accelerator, 909 like a GPU, or vectorize on a multicore machine. 910 911 Level: developer 912 913 .seealso: DMPlexComputeResidualFEM() 914 @*/ 915 PetscErrorCode DMPlexComputeIFunctionFEM(DM dm, PetscReal time, Vec X, Vec X_t, Vec F, void *user) 916 { 917 DM_Plex *mesh = (DM_Plex *) dm->data; 918 PetscFEM *fem = (PetscFEM *) user; 919 PetscFE *fe = fem->fe; 920 PetscFE *feAux = fem->feAux; 921 PetscFE *feBd = fem->feBd; 922 const char *name = "Residual"; 923 DM dmAux; 924 Vec A; 925 PetscQuadrature q; 926 PetscCellGeometry geom; 927 PetscSection section, sectionAux; 928 PetscReal *v0, *J, *invJ, *detJ; 929 PetscScalar *elemVec, *u, *u_t, *a = NULL; 930 PetscInt dim, Nf, NfAux = 0, f, numCells, cStart, cEnd, c; 931 PetscInt cellDof = 0, numComponents = 0; 932 PetscInt cellDofAux = 0, numComponentsAux = 0; 933 PetscErrorCode ierr; 934 935 PetscFunctionBegin; 936 ierr = PetscLogEventBegin(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr); 937 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 938 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 939 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); 940 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 941 numCells = cEnd - cStart; 942 for (f = 0; f < Nf; ++f) { 943 PetscInt Nb, Nc; 944 945 ierr = PetscFEGetDimension(fe[f], &Nb);CHKERRQ(ierr); 946 ierr = PetscFEGetNumComponents(fe[f], &Nc);CHKERRQ(ierr); 947 cellDof += Nb*Nc; 948 numComponents += Nc; 949 } 950 ierr = PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);CHKERRQ(ierr); 951 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);CHKERRQ(ierr); 952 if (dmAux) { 953 ierr = DMGetDefaultSection(dmAux, §ionAux);CHKERRQ(ierr); 954 ierr = PetscSectionGetNumFields(sectionAux, &NfAux);CHKERRQ(ierr); 955 } 956 for (f = 0; f < NfAux; ++f) { 957 PetscInt Nb, Nc; 958 959 ierr = PetscFEGetDimension(feAux[f], &Nb);CHKERRQ(ierr); 960 ierr = PetscFEGetNumComponents(feAux[f], &Nc);CHKERRQ(ierr); 961 cellDofAux += Nb*Nc; 962 numComponentsAux += Nc; 963 } 964 ierr = DMPlexInsertBoundaryValuesFEM(dm, X);CHKERRQ(ierr); 965 ierr = VecSet(F, 0.0);CHKERRQ(ierr); 966 ierr = PetscMalloc7(numCells*cellDof,&u,numCells*cellDof,&u_t,numCells*dim,&v0,numCells*dim*dim,&J,numCells*dim*dim,&invJ,numCells,&detJ,numCells*cellDof,&elemVec);CHKERRQ(ierr); 967 if (dmAux) {ierr = PetscMalloc1(numCells*cellDofAux, &a);CHKERRQ(ierr);} 968 for (c = cStart; c < cEnd; ++c) { 969 PetscScalar *x = NULL, *x_t = NULL; 970 PetscInt i; 971 972 ierr = DMPlexComputeCellGeometry(dm, c, &v0[c*dim], &J[c*dim*dim], &invJ[c*dim*dim], &detJ[c]);CHKERRQ(ierr); 973 if (detJ[c] <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", detJ[c], c); 974 ierr = DMPlexVecGetClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr); 975 for (i = 0; i < cellDof; ++i) u[c*cellDof+i] = x[i]; 976 ierr = DMPlexVecRestoreClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr); 977 ierr = DMPlexVecGetClosure(dm, section, X_t, c, NULL, &x_t);CHKERRQ(ierr); 978 for (i = 0; i < cellDof; ++i) u_t[c*cellDof+i] = x_t[i]; 979 ierr = DMPlexVecRestoreClosure(dm, section, X_t, c, NULL, &x_t);CHKERRQ(ierr); 980 if (dmAux) { 981 PetscScalar *x_a = NULL; 982 ierr = DMPlexVecGetClosure(dmAux, sectionAux, A, c, NULL, &x_a);CHKERRQ(ierr); 983 for (i = 0; i < cellDofAux; ++i) a[c*cellDofAux+i] = x_a[i]; 984 ierr = DMPlexVecRestoreClosure(dmAux, sectionAux, A, c, NULL, &x_a);CHKERRQ(ierr); 985 } 986 } 987 for (f = 0; f < Nf; ++f) { 988 void (*f0)(const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscReal[], PetscScalar[]) = fem->f0IFuncs[f]; 989 void (*f1)(const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscReal[], PetscScalar[]) = fem->f1IFuncs[f]; 990 PetscInt numQuadPoints, Nb; 991 /* Conforming batches */ 992 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 993 /* Remainder */ 994 PetscInt Nr, offset; 995 996 ierr = PetscFEGetQuadrature(fe[f], &q);CHKERRQ(ierr); 997 ierr = PetscFEGetDimension(fe[f], &Nb);CHKERRQ(ierr); 998 ierr = PetscFEGetTileSizes(fe[f], NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 999 ierr = PetscQuadratureGetData(q, NULL, &numQuadPoints, NULL, NULL);CHKERRQ(ierr); 1000 blockSize = Nb*numQuadPoints; 1001 batchSize = numBlocks * blockSize; 1002 ierr = PetscFESetTileSizes(fe[f], blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1003 numChunks = numCells / (numBatches*batchSize); 1004 Ne = numChunks*numBatches*batchSize; 1005 Nr = numCells % (numBatches*batchSize); 1006 offset = numCells - Nr; 1007 geom.v0 = v0; 1008 geom.J = J; 1009 geom.invJ = invJ; 1010 geom.detJ = detJ; 1011 ierr = PetscFEIntegrateIFunction(fe[f], Ne, Nf, fe, f, geom, u, u_t, NfAux, feAux, a, f0, f1, elemVec);CHKERRQ(ierr); 1012 geom.v0 = &v0[offset*dim]; 1013 geom.J = &J[offset*dim*dim]; 1014 geom.invJ = &invJ[offset*dim*dim]; 1015 geom.detJ = &detJ[offset]; 1016 ierr = PetscFEIntegrateIFunction(fe[f], Nr, Nf, fe, f, geom, &u[offset*cellDof], &u_t[offset*cellDof], NfAux, feAux, &a[offset*cellDofAux], f0, f1, &elemVec[offset*cellDof]);CHKERRQ(ierr); 1017 } 1018 for (c = cStart; c < cEnd; ++c) { 1019 if (mesh->printFEM > 1) {ierr = DMPrintCellVector(c, name, cellDof, &elemVec[c*cellDof]);CHKERRQ(ierr);} 1020 ierr = DMPlexVecSetClosure(dm, section, F, c, &elemVec[c*cellDof], ADD_VALUES);CHKERRQ(ierr); 1021 } 1022 ierr = PetscFree7(u,u_t,v0,J,invJ,detJ,elemVec);CHKERRQ(ierr); 1023 if (dmAux) {ierr = PetscFree(a);CHKERRQ(ierr);} 1024 if (feBd) { 1025 DMLabel label, depth; 1026 IS pointIS; 1027 const PetscInt *points; 1028 PetscInt dep, numPoints, p, numFaces; 1029 PetscReal *n; 1030 1031 ierr = DMPlexGetLabel(dm, "boundary", &label);CHKERRQ(ierr); 1032 ierr = DMPlexGetDepthLabel(dm, &depth);CHKERRQ(ierr); 1033 ierr = DMLabelGetStratumSize(label, 1, &numPoints);CHKERRQ(ierr); 1034 ierr = DMLabelGetStratumIS(label, 1, &pointIS);CHKERRQ(ierr); 1035 ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); 1036 for (f = 0, cellDof = 0, numComponents = 0; f < Nf; ++f) { 1037 PetscInt Nb, Nc; 1038 1039 ierr = PetscFEGetDimension(feBd[f], &Nb);CHKERRQ(ierr); 1040 ierr = PetscFEGetNumComponents(feBd[f], &Nc);CHKERRQ(ierr); 1041 cellDof += Nb*Nc; 1042 numComponents += Nc; 1043 } 1044 for (p = 0, numFaces = 0; p < numPoints; ++p) { 1045 ierr = DMLabelGetValue(depth, points[p], &dep);CHKERRQ(ierr); 1046 if (dep == dim-1) ++numFaces; 1047 } 1048 ierr = PetscMalloc7(numFaces*cellDof,&u,numFaces*dim,&v0,numFaces*dim,&n,numFaces*dim*dim,&J,numFaces*dim*dim,&invJ,numFaces,&detJ,numFaces*cellDof,&elemVec);CHKERRQ(ierr); 1049 ierr = PetscMalloc1(numFaces*cellDof,&u_t);CHKERRQ(ierr); 1050 for (p = 0, f = 0; p < numPoints; ++p) { 1051 const PetscInt point = points[p]; 1052 PetscScalar *x = NULL; 1053 PetscInt i; 1054 1055 ierr = DMLabelGetValue(depth, points[p], &dep);CHKERRQ(ierr); 1056 if (dep != dim-1) continue; 1057 ierr = DMPlexComputeCellGeometry(dm, point, &v0[f*dim], &J[f*dim*dim], &invJ[f*dim*dim], &detJ[f]);CHKERRQ(ierr); 1058 ierr = DMPlexComputeCellGeometryFVM(dm, point, NULL, NULL, &n[f*dim]); 1059 if (detJ[f] <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for face %d", detJ[f], point); 1060 ierr = DMPlexVecGetClosure(dm, section, X, point, NULL, &x);CHKERRQ(ierr); 1061 for (i = 0; i < cellDof; ++i) u[f*cellDof+i] = x[i]; 1062 ierr = DMPlexVecRestoreClosure(dm, section, X, point, NULL, &x);CHKERRQ(ierr); 1063 ierr = DMPlexVecGetClosure(dm, section, X_t, point, NULL, &x);CHKERRQ(ierr); 1064 for (i = 0; i < cellDof; ++i) u_t[f*cellDof+i] = x[i]; 1065 ierr = DMPlexVecRestoreClosure(dm, section, X_t, point, NULL, &x);CHKERRQ(ierr); 1066 ++f; 1067 } 1068 for (f = 0; f < Nf; ++f) { 1069 void (*f0)(const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscReal[], const PetscReal[], PetscScalar[]) = fem->f0BdIFuncs[f]; 1070 void (*f1)(const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscReal[], const PetscReal[], PetscScalar[]) = fem->f1BdIFuncs[f]; 1071 PetscInt numQuadPoints, Nb; 1072 /* Conforming batches */ 1073 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 1074 /* Remainder */ 1075 PetscInt Nr, offset; 1076 1077 ierr = PetscFEGetQuadrature(feBd[f], &q);CHKERRQ(ierr); 1078 ierr = PetscFEGetDimension(feBd[f], &Nb);CHKERRQ(ierr); 1079 ierr = PetscFEGetTileSizes(feBd[f], NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1080 ierr = PetscQuadratureGetData(q, NULL, &numQuadPoints, NULL, NULL);CHKERRQ(ierr); 1081 blockSize = Nb*numQuadPoints; 1082 batchSize = numBlocks * blockSize; 1083 ierr = PetscFESetTileSizes(feBd[f], blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1084 numChunks = numFaces / (numBatches*batchSize); 1085 Ne = numChunks*numBatches*batchSize; 1086 Nr = numFaces % (numBatches*batchSize); 1087 offset = numFaces - Nr; 1088 geom.v0 = v0; 1089 geom.n = n; 1090 geom.J = J; 1091 geom.invJ = invJ; 1092 geom.detJ = detJ; 1093 ierr = PetscFEIntegrateBdIFunction(feBd[f], Ne, Nf, feBd, f, geom, u, u_t, 0, NULL, NULL, f0, f1, elemVec);CHKERRQ(ierr); 1094 geom.v0 = &v0[offset*dim]; 1095 geom.n = &n[offset*dim]; 1096 geom.J = &J[offset*dim*dim]; 1097 geom.invJ = &invJ[offset*dim*dim]; 1098 geom.detJ = &detJ[offset]; 1099 ierr = PetscFEIntegrateBdIFunction(feBd[f], Nr, Nf, feBd, f, geom, &u[offset*cellDof], &u_t[offset*cellDof], 0, NULL, NULL, f0, f1, &elemVec[offset*cellDof]);CHKERRQ(ierr); 1100 } 1101 for (p = 0, f = 0; p < numPoints; ++p) { 1102 const PetscInt point = points[p]; 1103 1104 ierr = DMLabelGetValue(depth, point, &dep);CHKERRQ(ierr); 1105 if (dep != dim-1) continue; 1106 if (mesh->printFEM > 1) {ierr = DMPrintCellVector(point, "BdResidual", cellDof, &elemVec[f*cellDof]);CHKERRQ(ierr);} 1107 ierr = DMPlexVecSetClosure(dm, NULL, F, point, &elemVec[f*cellDof], ADD_VALUES);CHKERRQ(ierr); 1108 ++f; 1109 } 1110 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 1111 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 1112 ierr = PetscFree7(u,v0,n,J,invJ,detJ,elemVec);CHKERRQ(ierr); 1113 ierr = PetscFree(u_t);CHKERRQ(ierr); 1114 } 1115 if (mesh->printFEM) {ierr = DMPrintLocalVec(dm, name, mesh->printTol, F);CHKERRQ(ierr);} 1116 ierr = PetscLogEventEnd(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr); 1117 PetscFunctionReturn(0); 1118 } 1119 1120 #undef __FUNCT__ 1121 #define __FUNCT__ "DMPlexComputeJacobianActionFEM" 1122 /*@C 1123 DMPlexComputeJacobianActionFEM - Form the local action of Jacobian J(u) on the local input X using pointwise functions specified by the user 1124 1125 Input Parameters: 1126 + dm - The mesh 1127 . J - The Jacobian shell matrix 1128 . X - Local input vector 1129 - user - The user context 1130 1131 Output Parameter: 1132 . F - Local output vector 1133 1134 Note: 1135 The first member of the user context must be an FEMContext. 1136 1137 We form the residual one batch of elements at a time. This allows us to offload work onto an accelerator, 1138 like a GPU, or vectorize on a multicore machine. 1139 1140 Level: developer 1141 1142 .seealso: DMPlexComputeResidualFEM() 1143 @*/ 1144 PetscErrorCode DMPlexComputeJacobianActionFEM(DM dm, Mat Jac, Vec X, Vec F, void *user) 1145 { 1146 DM_Plex *mesh = (DM_Plex *) dm->data; 1147 PetscFEM *fem = (PetscFEM *) user; 1148 PetscFE *fe = fem->fe; 1149 PetscQuadrature quad; 1150 PetscCellGeometry geom; 1151 PetscSection section; 1152 JacActionCtx *jctx; 1153 PetscReal *v0, *J, *invJ, *detJ; 1154 PetscScalar *elemVec, *u, *a; 1155 PetscInt dim, numFields, field, numCells, cStart, cEnd, c; 1156 PetscInt cellDof = 0; 1157 PetscErrorCode ierr; 1158 1159 PetscFunctionBegin; 1160 /* ierr = PetscLogEventBegin(DMPLEX_JacobianActionFEM,dm,0,0,0);CHKERRQ(ierr); */ 1161 ierr = MatShellGetContext(Jac, &jctx);CHKERRQ(ierr); 1162 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1163 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 1164 ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); 1165 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1166 numCells = cEnd - cStart; 1167 for (field = 0; field < numFields; ++field) { 1168 PetscInt Nb, Nc; 1169 1170 ierr = PetscFEGetDimension(fe[field], &Nb);CHKERRQ(ierr); 1171 ierr = PetscFEGetNumComponents(fe[field], &Nc);CHKERRQ(ierr); 1172 cellDof += Nb*Nc; 1173 } 1174 ierr = VecSet(F, 0.0);CHKERRQ(ierr); 1175 ierr = PetscMalloc7(numCells*cellDof,&u,numCells*cellDof,&a,numCells*dim,&v0,numCells*dim*dim,&J,numCells*dim*dim,&invJ,numCells,&detJ,numCells*cellDof,&elemVec);CHKERRQ(ierr); 1176 for (c = cStart; c < cEnd; ++c) { 1177 PetscScalar *x = NULL; 1178 PetscInt i; 1179 1180 ierr = DMPlexComputeCellGeometry(dm, c, &v0[c*dim], &J[c*dim*dim], &invJ[c*dim*dim], &detJ[c]);CHKERRQ(ierr); 1181 if (detJ[c] <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", detJ[c], c); 1182 ierr = DMPlexVecGetClosure(dm, NULL, jctx->u, c, NULL, &x);CHKERRQ(ierr); 1183 for (i = 0; i < cellDof; ++i) u[c*cellDof+i] = x[i]; 1184 ierr = DMPlexVecRestoreClosure(dm, NULL, jctx->u, c, NULL, &x);CHKERRQ(ierr); 1185 ierr = DMPlexVecGetClosure(dm, NULL, X, c, NULL, &x);CHKERRQ(ierr); 1186 for (i = 0; i < cellDof; ++i) a[c*cellDof+i] = x[i]; 1187 ierr = DMPlexVecRestoreClosure(dm, NULL, X, c, NULL, &x);CHKERRQ(ierr); 1188 } 1189 for (field = 0; field < numFields; ++field) { 1190 PetscInt numQuadPoints, Nb; 1191 /* Conforming batches */ 1192 PetscInt numBlocks = 1; 1193 PetscInt numBatches = 1; 1194 PetscInt numChunks, Ne, blockSize, batchSize; 1195 /* Remainder */ 1196 PetscInt Nr, offset; 1197 1198 ierr = PetscFEGetQuadrature(fe[field], &quad);CHKERRQ(ierr); 1199 ierr = PetscFEGetDimension(fe[field], &Nb);CHKERRQ(ierr); 1200 ierr = PetscQuadratureGetData(quad, NULL, &numQuadPoints, NULL, NULL);CHKERRQ(ierr); 1201 blockSize = Nb*numQuadPoints; 1202 batchSize = numBlocks * blockSize; 1203 numChunks = numCells / (numBatches*batchSize); 1204 Ne = numChunks*numBatches*batchSize; 1205 Nr = numCells % (numBatches*batchSize); 1206 offset = numCells - Nr; 1207 geom.v0 = v0; 1208 geom.J = J; 1209 geom.invJ = invJ; 1210 geom.detJ = detJ; 1211 ierr = PetscFEIntegrateJacobianAction(fe[field], Ne, numFields, fe, field, geom, u, a, fem->g0Funcs, fem->g1Funcs, fem->g2Funcs, fem->g3Funcs, elemVec);CHKERRQ(ierr); 1212 geom.v0 = &v0[offset*dim]; 1213 geom.J = &J[offset*dim*dim]; 1214 geom.invJ = &invJ[offset*dim*dim]; 1215 geom.detJ = &detJ[offset]; 1216 ierr = PetscFEIntegrateJacobianAction(fe[field], Nr, numFields, fe, field, geom, &u[offset*cellDof], &a[offset*cellDof], 1217 fem->g0Funcs, fem->g1Funcs, fem->g2Funcs, fem->g3Funcs, &elemVec[offset*cellDof]);CHKERRQ(ierr); 1218 } 1219 for (c = cStart; c < cEnd; ++c) { 1220 if (mesh->printFEM > 1) {ierr = DMPrintCellVector(c, "Jacobian Action", cellDof, &elemVec[c*cellDof]);CHKERRQ(ierr);} 1221 ierr = DMPlexVecSetClosure(dm, NULL, F, c, &elemVec[c*cellDof], ADD_VALUES);CHKERRQ(ierr); 1222 } 1223 ierr = PetscFree7(u,a,v0,J,invJ,detJ,elemVec);CHKERRQ(ierr); 1224 if (mesh->printFEM) { 1225 PetscMPIInt rank, numProcs; 1226 PetscInt p; 1227 1228 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr); 1229 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)dm), &numProcs);CHKERRQ(ierr); 1230 ierr = PetscPrintf(PetscObjectComm((PetscObject)dm), "Jacobian Action:\n");CHKERRQ(ierr); 1231 for (p = 0; p < numProcs; ++p) { 1232 if (p == rank) {ierr = VecView(F, PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);} 1233 ierr = PetscBarrier((PetscObject) dm);CHKERRQ(ierr); 1234 } 1235 } 1236 /* ierr = PetscLogEventEnd(DMPLEX_JacobianActionFEM,dm,0,0,0);CHKERRQ(ierr); */ 1237 PetscFunctionReturn(0); 1238 } 1239 1240 #undef __FUNCT__ 1241 #define __FUNCT__ "DMPlexComputeJacobianFEM" 1242 /*@ 1243 DMPlexComputeJacobianFEM - Form the local portion of the Jacobian matrix J at the local solution X using pointwise functions specified by the user. 1244 1245 Input Parameters: 1246 + dm - The mesh 1247 . X - Local input vector 1248 - user - The user context 1249 1250 Output Parameter: 1251 . Jac - Jacobian matrix 1252 1253 Note: 1254 The first member of the user context must be an FEMContext. 1255 1256 We form the residual one batch of elements at a time. This allows us to offload work onto an accelerator, 1257 like a GPU, or vectorize on a multicore machine. 1258 1259 Level: developer 1260 1261 .seealso: FormFunctionLocal() 1262 @*/ 1263 PetscErrorCode DMPlexComputeJacobianFEM(DM dm, Vec X, Mat Jac, Mat JacP,void *user) 1264 { 1265 DM_Plex *mesh = (DM_Plex *) dm->data; 1266 PetscFEM *fem = (PetscFEM *) user; 1267 PetscFE *fe = fem->fe; 1268 PetscFE *feAux = fem->feAux; 1269 PetscFE *feBd = fem->feBd; 1270 const char *name = "Jacobian"; 1271 DM dmAux; 1272 Vec A; 1273 PetscQuadrature quad; 1274 PetscCellGeometry geom; 1275 PetscSection section, globalSection, sectionAux; 1276 PetscReal *v0, *J, *invJ, *detJ; 1277 PetscScalar *elemMat, *u, *a; 1278 PetscInt dim, Nf, NfAux = 0, f, fieldI, fieldJ, numCells, cStart, cEnd, c; 1279 PetscInt cellDof = 0, numComponents = 0; 1280 PetscInt cellDofAux = 0, numComponentsAux = 0; 1281 PetscBool isShell; 1282 PetscErrorCode ierr; 1283 1284 PetscFunctionBegin; 1285 ierr = PetscLogEventBegin(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 1286 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1287 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 1288 ierr = DMGetDefaultGlobalSection(dm, &globalSection);CHKERRQ(ierr); 1289 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); 1290 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1291 numCells = cEnd - cStart; 1292 for (f = 0; f < Nf; ++f) { 1293 PetscInt Nb, Nc; 1294 1295 ierr = PetscFEGetDimension(fe[f], &Nb);CHKERRQ(ierr); 1296 ierr = PetscFEGetNumComponents(fe[f], &Nc);CHKERRQ(ierr); 1297 cellDof += Nb*Nc; 1298 numComponents += Nc; 1299 } 1300 ierr = PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);CHKERRQ(ierr); 1301 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);CHKERRQ(ierr); 1302 if (dmAux) { 1303 ierr = DMGetDefaultSection(dmAux, §ionAux);CHKERRQ(ierr); 1304 ierr = PetscSectionGetNumFields(sectionAux, &NfAux);CHKERRQ(ierr); 1305 } 1306 for (f = 0; f < NfAux; ++f) { 1307 PetscInt Nb, Nc; 1308 1309 ierr = PetscFEGetDimension(feAux[f], &Nb);CHKERRQ(ierr); 1310 ierr = PetscFEGetNumComponents(feAux[f], &Nc);CHKERRQ(ierr); 1311 cellDofAux += Nb*Nc; 1312 numComponentsAux += Nc; 1313 } 1314 ierr = DMPlexInsertBoundaryValuesFEM(dm, X);CHKERRQ(ierr); 1315 ierr = MatZeroEntries(JacP);CHKERRQ(ierr); 1316 ierr = PetscMalloc6(numCells*cellDof,&u,numCells*dim,&v0,numCells*dim*dim,&J,numCells*dim*dim,&invJ,numCells,&detJ,numCells*cellDof*cellDof,&elemMat);CHKERRQ(ierr); 1317 if (dmAux) {ierr = PetscMalloc1(numCells*cellDofAux, &a);CHKERRQ(ierr);} 1318 for (c = cStart; c < cEnd; ++c) { 1319 PetscScalar *x = NULL; 1320 PetscInt i; 1321 1322 ierr = DMPlexComputeCellGeometry(dm, c, &v0[c*dim], &J[c*dim*dim], &invJ[c*dim*dim], &detJ[c]);CHKERRQ(ierr); 1323 if (detJ[c] <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", detJ[c], c); 1324 ierr = DMPlexVecGetClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr); 1325 for (i = 0; i < cellDof; ++i) u[c*cellDof+i] = x[i]; 1326 ierr = DMPlexVecRestoreClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr); 1327 if (dmAux) { 1328 ierr = DMPlexVecGetClosure(dmAux, sectionAux, A, c, NULL, &x);CHKERRQ(ierr); 1329 for (i = 0; i < cellDofAux; ++i) a[c*cellDofAux+i] = x[i]; 1330 ierr = DMPlexVecRestoreClosure(dmAux, sectionAux, A, c, NULL, &x);CHKERRQ(ierr); 1331 } 1332 } 1333 ierr = PetscMemzero(elemMat, numCells*cellDof*cellDof * sizeof(PetscScalar));CHKERRQ(ierr); 1334 for (fieldI = 0; fieldI < Nf; ++fieldI) { 1335 PetscInt numQuadPoints, Nb; 1336 /* Conforming batches */ 1337 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 1338 /* Remainder */ 1339 PetscInt Nr, offset; 1340 1341 ierr = PetscFEGetQuadrature(fe[fieldI], &quad);CHKERRQ(ierr); 1342 ierr = PetscFEGetDimension(fe[fieldI], &Nb);CHKERRQ(ierr); 1343 ierr = PetscFEGetTileSizes(fe[fieldI], NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1344 ierr = PetscQuadratureGetData(quad, NULL, &numQuadPoints, NULL, NULL);CHKERRQ(ierr); 1345 blockSize = Nb*numQuadPoints; 1346 batchSize = numBlocks * blockSize; 1347 ierr = PetscFESetTileSizes(fe[fieldI], blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1348 numChunks = numCells / (numBatches*batchSize); 1349 Ne = numChunks*numBatches*batchSize; 1350 Nr = numCells % (numBatches*batchSize); 1351 offset = numCells - Nr; 1352 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 1353 void (*g0)(const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscReal[], PetscScalar[]) = fem->g0Funcs[fieldI*Nf+fieldJ]; 1354 void (*g1)(const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscReal[], PetscScalar[]) = fem->g1Funcs[fieldI*Nf+fieldJ]; 1355 void (*g2)(const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscReal[], PetscScalar[]) = fem->g2Funcs[fieldI*Nf+fieldJ]; 1356 void (*g3)(const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscReal[], PetscScalar[]) = fem->g3Funcs[fieldI*Nf+fieldJ]; 1357 1358 geom.v0 = v0; 1359 geom.J = J; 1360 geom.invJ = invJ; 1361 geom.detJ = detJ; 1362 ierr = PetscFEIntegrateJacobian(fe[fieldI], Ne, Nf, fe, fieldI, fieldJ, geom, u, NfAux, feAux, a, g0, g1, g2, g3, elemMat);CHKERRQ(ierr); 1363 geom.v0 = &v0[offset*dim]; 1364 geom.J = &J[offset*dim*dim]; 1365 geom.invJ = &invJ[offset*dim*dim]; 1366 geom.detJ = &detJ[offset]; 1367 ierr = PetscFEIntegrateJacobian(fe[fieldI], Nr, Nf, fe, fieldI, fieldJ, geom, &u[offset*cellDof], NfAux, feAux, &a[offset*cellDofAux], g0, g1, g2, g3, &elemMat[offset*cellDof*cellDof]);CHKERRQ(ierr); 1368 } 1369 } 1370 for (c = cStart; c < cEnd; ++c) { 1371 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(c, name, cellDof, cellDof, &elemMat[c*cellDof*cellDof]);CHKERRQ(ierr);} 1372 ierr = DMPlexMatSetClosure(dm, section, globalSection, JacP, c, &elemMat[c*cellDof*cellDof], ADD_VALUES);CHKERRQ(ierr); 1373 } 1374 ierr = PetscFree6(u,v0,J,invJ,detJ,elemMat);CHKERRQ(ierr); 1375 if (dmAux) {ierr = PetscFree(a);CHKERRQ(ierr);} 1376 if (feBd) { 1377 DMLabel depth; 1378 PetscInt numBd, bd; 1379 1380 for (f = 0, cellDof = 0, numComponents = 0; f < Nf; ++f) { 1381 PetscInt Nb, Nc; 1382 1383 ierr = PetscFEGetDimension(feBd[f], &Nb);CHKERRQ(ierr); 1384 ierr = PetscFEGetNumComponents(feBd[f], &Nc);CHKERRQ(ierr); 1385 cellDof += Nb*Nc; 1386 numComponents += Nc; 1387 } 1388 ierr = DMPlexGetDepthLabel(dm, &depth);CHKERRQ(ierr); 1389 ierr = DMPlexGetNumBoundary(dm, &numBd);CHKERRQ(ierr); 1390 for (bd = 0; bd < numBd; ++bd) { 1391 const char *bdLabel; 1392 DMLabel label; 1393 IS pointIS; 1394 const PetscInt *points; 1395 const PetscInt *values; 1396 PetscReal *n; 1397 PetscInt field, numValues, numPoints, p, dep, numFaces; 1398 PetscBool isEssential; 1399 1400 ierr = DMPlexGetBoundary(dm, bd, &isEssential, &bdLabel, &field, NULL, &numValues, &values, NULL);CHKERRQ(ierr); 1401 if (numValues != 1) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Bug me and I will fix this"); 1402 ierr = DMPlexGetLabel(dm, bdLabel, &label);CHKERRQ(ierr); 1403 ierr = DMLabelGetStratumSize(label, 1, &numPoints);CHKERRQ(ierr); 1404 ierr = DMLabelGetStratumIS(label, 1, &pointIS);CHKERRQ(ierr); 1405 ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); 1406 for (p = 0, numFaces = 0; p < numPoints; ++p) { 1407 ierr = DMLabelGetValue(depth, points[p], &dep);CHKERRQ(ierr); 1408 if (dep == dim-1) ++numFaces; 1409 } 1410 ierr = PetscMalloc7(numFaces*cellDof,&u,numFaces*dim,&v0,numFaces*dim,&n,numFaces*dim*dim,&J,numFaces*dim*dim,&invJ,numFaces,&detJ,numFaces*cellDof*cellDof,&elemMat);CHKERRQ(ierr); 1411 for (p = 0, f = 0; p < numPoints; ++p) { 1412 const PetscInt point = points[p]; 1413 PetscScalar *x = NULL; 1414 PetscInt i; 1415 1416 ierr = DMLabelGetValue(depth, points[p], &dep);CHKERRQ(ierr); 1417 if (dep != dim-1) continue; 1418 ierr = DMPlexComputeCellGeometry(dm, point, &v0[f*dim], &J[f*dim*dim], &invJ[f*dim*dim], &detJ[f]);CHKERRQ(ierr); 1419 ierr = DMPlexComputeCellGeometryFVM(dm, point, NULL, NULL, &n[f*dim]); 1420 if (detJ[f] <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for face %d", detJ[f], point); 1421 ierr = DMPlexVecGetClosure(dm, section, X, point, NULL, &x);CHKERRQ(ierr); 1422 for (i = 0; i < cellDof; ++i) u[f*cellDof+i] = x[i]; 1423 ierr = DMPlexVecRestoreClosure(dm, section, X, point, NULL, &x);CHKERRQ(ierr); 1424 ++f; 1425 } 1426 ierr = PetscMemzero(elemMat, numFaces*cellDof*cellDof * sizeof(PetscScalar));CHKERRQ(ierr); 1427 for (fieldI = 0; fieldI < Nf; ++fieldI) { 1428 PetscInt numQuadPoints, Nb; 1429 /* Conforming batches */ 1430 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 1431 /* Remainder */ 1432 PetscInt Nr, offset; 1433 1434 ierr = PetscFEGetQuadrature(feBd[fieldI], &quad);CHKERRQ(ierr); 1435 ierr = PetscFEGetDimension(feBd[fieldI], &Nb);CHKERRQ(ierr); 1436 ierr = PetscFEGetTileSizes(feBd[fieldI], NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1437 ierr = PetscQuadratureGetData(quad, NULL, &numQuadPoints, NULL, NULL);CHKERRQ(ierr); 1438 blockSize = Nb*numQuadPoints; 1439 batchSize = numBlocks * blockSize; 1440 ierr = PetscFESetTileSizes(feBd[fieldI], blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1441 numChunks = numFaces / (numBatches*batchSize); 1442 Ne = numChunks*numBatches*batchSize; 1443 Nr = numFaces % (numBatches*batchSize); 1444 offset = numFaces - Nr; 1445 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 1446 void (*g0)(const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscReal[], const PetscReal[], PetscScalar[]) = fem->g0BdFuncs[fieldI*Nf+fieldJ]; 1447 void (*g1)(const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscReal[], const PetscReal[], PetscScalar[]) = fem->g1BdFuncs[fieldI*Nf+fieldJ]; 1448 void (*g2)(const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscReal[], const PetscReal[], PetscScalar[]) = fem->g2BdFuncs[fieldI*Nf+fieldJ]; 1449 void (*g3)(const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscReal[], const PetscReal[], PetscScalar[]) = fem->g3BdFuncs[fieldI*Nf+fieldJ]; 1450 1451 geom.v0 = v0; 1452 geom.n = n; 1453 geom.J = J; 1454 geom.invJ = invJ; 1455 geom.detJ = detJ; 1456 ierr = PetscFEIntegrateBdJacobian(feBd[fieldI], Ne, Nf, feBd, fieldI, fieldJ, geom, u, 0, NULL, NULL, g0, g1, g2, g3, elemMat);CHKERRQ(ierr); 1457 geom.v0 = &v0[offset*dim]; 1458 geom.n = &n[offset*dim]; 1459 geom.J = &J[offset*dim*dim]; 1460 geom.invJ = &invJ[offset*dim*dim]; 1461 geom.detJ = &detJ[offset]; 1462 ierr = PetscFEIntegrateBdJacobian(feBd[fieldI], Nr, Nf, feBd, fieldI, fieldJ, geom, &u[offset*cellDof], 0, NULL, NULL, g0, g1, g2, g3, &elemMat[offset*cellDof*cellDof]);CHKERRQ(ierr); 1463 } 1464 } 1465 for (p = 0, f = 0; p < numPoints; ++p) { 1466 const PetscInt point = points[p]; 1467 1468 ierr = DMLabelGetValue(depth, point, &dep);CHKERRQ(ierr); 1469 if (dep != dim-1) continue; 1470 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(point, "BdJacobian", cellDof, cellDof, &elemMat[f*cellDof*cellDof]);CHKERRQ(ierr);} 1471 ierr = DMPlexMatSetClosure(dm, section, globalSection, JacP, point, &elemMat[f*cellDof*cellDof], ADD_VALUES);CHKERRQ(ierr); 1472 ++f; 1473 } 1474 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 1475 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 1476 ierr = PetscFree7(u,v0,n,J,invJ,detJ,elemMat);CHKERRQ(ierr); 1477 } 1478 } 1479 ierr = MatAssemblyBegin(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1480 ierr = MatAssemblyEnd(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1481 if (mesh->printFEM) { 1482 ierr = PetscPrintf(PETSC_COMM_WORLD, "%s:\n", name);CHKERRQ(ierr); 1483 ierr = MatChop(JacP, 1.0e-10);CHKERRQ(ierr); 1484 ierr = MatView(JacP, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 1485 } 1486 ierr = PetscLogEventEnd(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 1487 ierr = PetscObjectTypeCompare((PetscObject) Jac, MATSHELL, &isShell);CHKERRQ(ierr); 1488 if (isShell) { 1489 JacActionCtx *jctx; 1490 1491 ierr = MatShellGetContext(Jac, &jctx);CHKERRQ(ierr); 1492 ierr = VecCopy(X, jctx->u);CHKERRQ(ierr); 1493 } 1494 PetscFunctionReturn(0); 1495 } 1496 1497 #undef __FUNCT__ 1498 #define __FUNCT__ "DMPlexComputeInterpolatorFEM" 1499 /*@ 1500 DMPlexComputeInterpolatorFEM - Form the local portion of the interpolation matrix I from the coarse DM to the uniformly refined DM. 1501 1502 Input Parameters: 1503 + dmf - The fine mesh 1504 . dmc - The coarse mesh 1505 - user - The user context 1506 1507 Output Parameter: 1508 . In - The interpolation matrix 1509 1510 Note: 1511 The first member of the user context must be an FEMContext. 1512 1513 We form the residual one batch of elements at a time. This allows us to offload work onto an accelerator, 1514 like a GPU, or vectorize on a multicore machine. 1515 1516 Level: developer 1517 1518 .seealso: DMPlexComputeJacobianFEM() 1519 @*/ 1520 PetscErrorCode DMPlexComputeInterpolatorFEM(DM dmc, DM dmf, Mat In, void *user) 1521 { 1522 DM_Plex *mesh = (DM_Plex *) dmc->data; 1523 PetscFEM *fem = (PetscFEM *) user; 1524 PetscFE *fe = fem->fe; 1525 const char *name = "Interpolator"; 1526 PetscFE *feRef; 1527 PetscSection fsection, fglobalSection; 1528 PetscSection csection, cglobalSection; 1529 PetscScalar *elemMat; 1530 PetscInt dim, Nf, f, fieldI, fieldJ, offsetI, offsetJ, cStart, cEnd, c; 1531 PetscInt rCellDof = 0, cCellDof = 0; 1532 PetscErrorCode ierr; 1533 1534 PetscFunctionBegin; 1535 #if 0 1536 ierr = PetscLogEventBegin(DMPLEX_InterpolatorFEM,dmc,dmf,0,0);CHKERRQ(ierr); 1537 #endif 1538 ierr = DMPlexGetDimension(dmf, &dim);CHKERRQ(ierr); 1539 ierr = DMGetDefaultSection(dmf, &fsection);CHKERRQ(ierr); 1540 ierr = DMGetDefaultGlobalSection(dmf, &fglobalSection);CHKERRQ(ierr); 1541 ierr = DMGetDefaultSection(dmc, &csection);CHKERRQ(ierr); 1542 ierr = DMGetDefaultGlobalSection(dmc, &cglobalSection);CHKERRQ(ierr); 1543 ierr = PetscSectionGetNumFields(fsection, &Nf);CHKERRQ(ierr); 1544 ierr = DMPlexGetHeightStratum(dmc, 0, &cStart, &cEnd);CHKERRQ(ierr); 1545 ierr = PetscMalloc1(Nf,&feRef);CHKERRQ(ierr); 1546 for (f = 0; f < Nf; ++f) { 1547 PetscInt rNb, cNb, Nc; 1548 1549 ierr = PetscFERefine(fe[f], &feRef[f]);CHKERRQ(ierr); 1550 ierr = PetscFEGetDimension(feRef[f], &rNb);CHKERRQ(ierr); 1551 ierr = PetscFEGetDimension(fe[f], &cNb);CHKERRQ(ierr); 1552 ierr = PetscFEGetNumComponents(fe[f], &Nc);CHKERRQ(ierr); 1553 rCellDof += rNb*Nc; 1554 cCellDof += cNb*Nc; 1555 } 1556 ierr = MatZeroEntries(In);CHKERRQ(ierr); 1557 ierr = PetscMalloc1(rCellDof*cCellDof,&elemMat);CHKERRQ(ierr); 1558 ierr = PetscMemzero(elemMat, rCellDof*cCellDof * sizeof(PetscScalar));CHKERRQ(ierr); 1559 for (fieldI = 0, offsetI = 0; fieldI < Nf; ++fieldI) { 1560 PetscDualSpace Qref; 1561 PetscQuadrature f; 1562 const PetscReal *qpoints, *qweights; 1563 PetscReal *points; 1564 PetscInt npoints = 0, Nc, Np, fpdim, i, k, p, d; 1565 1566 /* Compose points from all dual basis functionals */ 1567 ierr = PetscFEGetNumComponents(fe[fieldI], &Nc);CHKERRQ(ierr); 1568 ierr = PetscFEGetDualSpace(feRef[fieldI], &Qref);CHKERRQ(ierr); 1569 ierr = PetscDualSpaceGetDimension(Qref, &fpdim);CHKERRQ(ierr); 1570 for (i = 0; i < fpdim; ++i) { 1571 ierr = PetscDualSpaceGetFunctional(Qref, i, &f);CHKERRQ(ierr); 1572 ierr = PetscQuadratureGetData(f, NULL, &Np, NULL, NULL);CHKERRQ(ierr); 1573 npoints += Np; 1574 } 1575 ierr = PetscMalloc1(npoints*dim,&points);CHKERRQ(ierr); 1576 for (i = 0, k = 0; i < fpdim; ++i) { 1577 ierr = PetscDualSpaceGetFunctional(Qref, i, &f);CHKERRQ(ierr); 1578 ierr = PetscQuadratureGetData(f, NULL, &Np, &qpoints, NULL);CHKERRQ(ierr); 1579 for (p = 0; p < Np; ++p, ++k) for (d = 0; d < dim; ++d) points[k*dim+d] = qpoints[p*dim+d]; 1580 } 1581 1582 for (fieldJ = 0, offsetJ = 0; fieldJ < Nf; ++fieldJ) { 1583 PetscReal *B; 1584 PetscInt NcJ, cpdim, j; 1585 1586 /* Evaluate basis at points */ 1587 ierr = PetscFEGetNumComponents(fe[fieldJ], &NcJ);CHKERRQ(ierr); 1588 if (Nc != NcJ) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Number of components in fine space field %d does not match coarse field %d", Nc, NcJ); 1589 ierr = PetscFEGetDimension(fe[fieldJ], &cpdim);CHKERRQ(ierr); 1590 /* For now, fields only interpolate themselves */ 1591 if (fieldI == fieldJ) { 1592 ierr = PetscFEGetTabulation(fe[fieldJ], npoints, points, &B, NULL, NULL);CHKERRQ(ierr); 1593 for (i = 0, k = 0; i < fpdim; ++i) { 1594 ierr = PetscDualSpaceGetFunctional(Qref, i, &f);CHKERRQ(ierr); 1595 ierr = PetscQuadratureGetData(f, NULL, &Np, NULL, &qweights);CHKERRQ(ierr); 1596 for (p = 0; p < Np; ++p, ++k) { 1597 for (j = 0; j < cpdim; ++j) { 1598 for (c = 0; c < Nc; ++c) elemMat[(offsetI + i*Nc + c)*cCellDof + offsetJ + j*NcJ + c] += B[k*cpdim*NcJ+j*Nc+c]*qweights[p]; 1599 } 1600 } 1601 } 1602 ierr = PetscFERestoreTabulation(fe[fieldJ], npoints, points, &B, NULL, NULL);CHKERRQ(ierr);CHKERRQ(ierr); 1603 } 1604 offsetJ += cpdim*NcJ; 1605 } 1606 offsetI += fpdim*Nc; 1607 ierr = PetscFree(points);CHKERRQ(ierr); 1608 } 1609 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(0, name, rCellDof, cCellDof, elemMat);CHKERRQ(ierr);} 1610 for (c = cStart; c < cEnd; ++c) { 1611 ierr = DMPlexMatSetClosureRefined(dmf, fsection, fglobalSection, dmc, csection, cglobalSection, In, c, elemMat, INSERT_VALUES);CHKERRQ(ierr); 1612 } 1613 for (f = 0; f < Nf; ++f) {ierr = PetscFEDestroy(&feRef[f]);CHKERRQ(ierr);} 1614 ierr = PetscFree(feRef);CHKERRQ(ierr); 1615 ierr = PetscFree(elemMat);CHKERRQ(ierr); 1616 ierr = MatAssemblyBegin(In, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1617 ierr = MatAssemblyEnd(In, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1618 if (mesh->printFEM) { 1619 ierr = PetscPrintf(PETSC_COMM_WORLD, "%s:\n", name);CHKERRQ(ierr); 1620 ierr = MatChop(In, 1.0e-10);CHKERRQ(ierr); 1621 ierr = MatView(In, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 1622 } 1623 #if 0 1624 ierr = PetscLogEventEnd(DMPLEX_InterpolatorFEM,dmc,dmf,0,0);CHKERRQ(ierr); 1625 #endif 1626 PetscFunctionReturn(0); 1627 } 1628 1629 #undef __FUNCT__ 1630 #define __FUNCT__ "DMPlexAddBoundary" 1631 /* The ids can be overridden by the command line option -bc_<boundary name> */ 1632 PetscErrorCode DMPlexAddBoundary(DM dm, PetscBool isEssential, const char name[], PetscInt field, void (*bcFunc)(), PetscInt numids, const PetscInt *ids, void *ctx) 1633 { 1634 DM_Plex *mesh = (DM_Plex *) dm->data; 1635 DMBoundary b; 1636 PetscErrorCode ierr; 1637 1638 PetscFunctionBegin; 1639 ierr = PetscNew(&b);CHKERRQ(ierr); 1640 ierr = PetscStrallocpy(name, (char **) &b->name);CHKERRQ(ierr); 1641 ierr = PetscMalloc1(numids, &b->ids);CHKERRQ(ierr); 1642 ierr = PetscMemcpy(b->ids, ids, numids*sizeof(PetscInt));CHKERRQ(ierr); 1643 b->essential = isEssential; 1644 b->field = field; 1645 b->func = bcFunc; 1646 b->numids = numids; 1647 b->ctx = ctx; 1648 b->next = mesh->boundary; 1649 mesh->boundary = b; 1650 PetscFunctionReturn(0); 1651 } 1652 1653 #undef __FUNCT__ 1654 #define __FUNCT__ "DMPlexGetNumBoundary" 1655 PetscErrorCode DMPlexGetNumBoundary(DM dm, PetscInt *numBd) 1656 { 1657 DM_Plex *mesh = (DM_Plex *) dm->data; 1658 DMBoundary b = mesh->boundary; 1659 1660 PetscFunctionBegin; 1661 *numBd = 0; 1662 while (b) {++(*numBd); b = b->next;} 1663 PetscFunctionReturn(0); 1664 } 1665 1666 #undef __FUNCT__ 1667 #define __FUNCT__ "DMPlexGetBoundary" 1668 PetscErrorCode DMPlexGetBoundary(DM dm, PetscInt bd, PetscBool *isEssential, const char **name, PetscInt *field, void (**func)(), PetscInt *numids, const PetscInt **ids, void **ctx) 1669 { 1670 DM_Plex *mesh = (DM_Plex *) dm->data; 1671 DMBoundary b = mesh->boundary; 1672 PetscInt n = 0; 1673 1674 PetscFunctionBegin; 1675 while (b) { 1676 if (n == bd) break; 1677 b = b->next; 1678 ++n; 1679 } 1680 if (n != bd) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Boundary %d is not in [0, %d)", bd, n); 1681 if (isEssential) { 1682 PetscValidPointer(isEssential, 3); 1683 *isEssential = b->essential; 1684 } 1685 if (name) { 1686 PetscValidPointer(name, 4); 1687 *name = b->name; 1688 } 1689 if (field) { 1690 PetscValidPointer(field, 5); 1691 *field = b->field; 1692 } 1693 if (func) { 1694 PetscValidPointer(func, 6); 1695 *func = b->func; 1696 } 1697 if (numids) { 1698 PetscValidPointer(numids, 7); 1699 *numids = b->numids; 1700 } 1701 if (ids) { 1702 PetscValidPointer(ids, 8); 1703 *ids = b->ids; 1704 } 1705 if (ctx) { 1706 PetscValidPointer(ctx, 9); 1707 *ctx = b->ctx; 1708 } 1709 PetscFunctionReturn(0); 1710 } 1711