1 #include <petsc/private/dmpleximpl.h> /*I "petscdmplex.h" I*/ 2 #include <petscsf.h> 3 4 #include <petscblaslapack.h> 5 #include <petsc/private/hashsetij.h> 6 #include <petsc/private/petscfeimpl.h> 7 #include <petsc/private/petscfvimpl.h> 8 9 static PetscErrorCode DMPlexConvertPlex(DM dm, DM *plex, PetscBool copy) 10 { 11 PetscBool isPlex; 12 PetscErrorCode ierr; 13 14 PetscFunctionBegin; 15 ierr = PetscObjectTypeCompare((PetscObject) dm, DMPLEX, &isPlex);CHKERRQ(ierr); 16 if (isPlex) { 17 *plex = dm; 18 ierr = PetscObjectReference((PetscObject) dm);CHKERRQ(ierr); 19 } else { 20 ierr = PetscObjectQuery((PetscObject) dm, "dm_plex", (PetscObject *) plex);CHKERRQ(ierr); 21 if (!*plex) { 22 ierr = DMConvert(dm, DMPLEX, plex);CHKERRQ(ierr); 23 ierr = PetscObjectCompose((PetscObject) dm, "dm_plex", (PetscObject) *plex);CHKERRQ(ierr); 24 if (copy) { 25 DMSubDomainHookLink link; 26 27 ierr = DMCopyAuxiliaryVec(dm, *plex);CHKERRQ(ierr); 28 /* Run the subdomain hook (this will copy the DMSNES/DMTS) */ 29 for (link = dm->subdomainhook; link; link = link->next) { 30 if (link->ddhook) {ierr = (*link->ddhook)(dm, *plex, link->ctx);CHKERRQ(ierr);} 31 } 32 } 33 } else { 34 ierr = PetscObjectReference((PetscObject) *plex);CHKERRQ(ierr); 35 } 36 } 37 PetscFunctionReturn(0); 38 } 39 40 static PetscErrorCode PetscContainerUserDestroy_PetscFEGeom (void *ctx) 41 { 42 PetscFEGeom *geom = (PetscFEGeom *) ctx; 43 PetscErrorCode ierr; 44 45 PetscFunctionBegin; 46 ierr = PetscFEGeomDestroy(&geom);CHKERRQ(ierr); 47 PetscFunctionReturn(0); 48 } 49 50 static PetscErrorCode DMPlexGetFEGeom(DMField coordField, IS pointIS, PetscQuadrature quad, PetscBool faceData, PetscFEGeom **geom) 51 { 52 char composeStr[33] = {0}; 53 PetscObjectId id; 54 PetscContainer container; 55 PetscErrorCode ierr; 56 57 PetscFunctionBegin; 58 ierr = PetscObjectGetId((PetscObject)quad,&id);CHKERRQ(ierr); 59 ierr = PetscSNPrintf(composeStr, 32, "DMPlexGetFEGeom_%x\n", id);CHKERRQ(ierr); 60 ierr = PetscObjectQuery((PetscObject) pointIS, composeStr, (PetscObject *) &container);CHKERRQ(ierr); 61 if (container) { 62 ierr = PetscContainerGetPointer(container, (void **) geom);CHKERRQ(ierr); 63 } else { 64 ierr = DMFieldCreateFEGeom(coordField, pointIS, quad, faceData, geom);CHKERRQ(ierr); 65 ierr = PetscContainerCreate(PETSC_COMM_SELF,&container);CHKERRQ(ierr); 66 ierr = PetscContainerSetPointer(container, (void *) *geom);CHKERRQ(ierr); 67 ierr = PetscContainerSetUserDestroy(container, PetscContainerUserDestroy_PetscFEGeom);CHKERRQ(ierr); 68 ierr = PetscObjectCompose((PetscObject) pointIS, composeStr, (PetscObject) container);CHKERRQ(ierr); 69 ierr = PetscContainerDestroy(&container);CHKERRQ(ierr); 70 } 71 PetscFunctionReturn(0); 72 } 73 74 static PetscErrorCode DMPlexRestoreFEGeom(DMField coordField, IS pointIS, PetscQuadrature quad, PetscBool faceData, PetscFEGeom **geom) 75 { 76 PetscFunctionBegin; 77 *geom = NULL; 78 PetscFunctionReturn(0); 79 } 80 81 /*@ 82 DMPlexGetScale - Get the scale for the specified fundamental unit 83 84 Not collective 85 86 Input Arguments: 87 + dm - the DM 88 - unit - The SI unit 89 90 Output Argument: 91 . scale - The value used to scale all quantities with this unit 92 93 Level: advanced 94 95 .seealso: DMPlexSetScale(), PetscUnit 96 @*/ 97 PetscErrorCode DMPlexGetScale(DM dm, PetscUnit unit, PetscReal *scale) 98 { 99 DM_Plex *mesh = (DM_Plex*) dm->data; 100 101 PetscFunctionBegin; 102 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 103 PetscValidPointer(scale, 3); 104 *scale = mesh->scale[unit]; 105 PetscFunctionReturn(0); 106 } 107 108 /*@ 109 DMPlexSetScale - Set the scale for the specified fundamental unit 110 111 Not collective 112 113 Input Arguments: 114 + dm - the DM 115 . unit - The SI unit 116 - scale - The value used to scale all quantities with this unit 117 118 Level: advanced 119 120 .seealso: DMPlexGetScale(), PetscUnit 121 @*/ 122 PetscErrorCode DMPlexSetScale(DM dm, PetscUnit unit, PetscReal scale) 123 { 124 DM_Plex *mesh = (DM_Plex*) dm->data; 125 126 PetscFunctionBegin; 127 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 128 mesh->scale[unit] = scale; 129 PetscFunctionReturn(0); 130 } 131 132 static PetscErrorCode DMPlexProjectRigidBody_Private(PetscInt dim, PetscReal t, const PetscReal X[], PetscInt Nc, PetscScalar *mode, void *ctx) 133 { 134 const PetscInt eps[3][3][3] = {{{0, 0, 0}, {0, 0, 1}, {0, -1, 0}}, {{0, 0, -1}, {0, 0, 0}, {1, 0, 0}}, {{0, 1, 0}, {-1, 0, 0}, {0, 0, 0}}}; 135 PetscInt *ctxInt = (PetscInt *) ctx; 136 PetscInt dim2 = ctxInt[0]; 137 PetscInt d = ctxInt[1]; 138 PetscInt i, j, k = dim > 2 ? d - dim : d; 139 140 PetscFunctionBegin; 141 if (dim != dim2) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Input dimension %D does not match context dimension %D", dim, dim2); 142 for (i = 0; i < dim; i++) mode[i] = 0.; 143 if (d < dim) { 144 mode[d] = 1.; /* Translation along axis d */ 145 } else { 146 for (i = 0; i < dim; i++) { 147 for (j = 0; j < dim; j++) { 148 mode[j] += eps[i][j][k]*X[i]; /* Rotation about axis d */ 149 } 150 } 151 } 152 PetscFunctionReturn(0); 153 } 154 155 /*@ 156 DMPlexCreateRigidBody - For the default global section, create rigid body modes by function space interpolation 157 158 Collective on dm 159 160 Input Arguments: 161 + dm - the DM 162 - field - The field number for the rigid body space, or 0 for the default 163 164 Output Argument: 165 . sp - the null space 166 167 Note: This is necessary to provide a suitable coarse space for algebraic multigrid 168 169 Level: advanced 170 171 .seealso: MatNullSpaceCreate(), PCGAMG 172 @*/ 173 PetscErrorCode DMPlexCreateRigidBody(DM dm, PetscInt field, MatNullSpace *sp) 174 { 175 PetscErrorCode (**func)(PetscInt, PetscReal, const PetscReal *, PetscInt, PetscScalar *, void *); 176 MPI_Comm comm; 177 Vec mode[6]; 178 PetscSection section, globalSection; 179 PetscInt dim, dimEmbed, Nf, n, m, mmin, d, i, j; 180 PetscErrorCode ierr; 181 182 PetscFunctionBegin; 183 ierr = PetscObjectGetComm((PetscObject) dm, &comm);CHKERRQ(ierr); 184 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 185 ierr = DMGetCoordinateDim(dm, &dimEmbed);CHKERRQ(ierr); 186 ierr = DMGetNumFields(dm, &Nf);CHKERRQ(ierr); 187 if (Nf && (field < 0 || field >= Nf)) SETERRQ2(comm, PETSC_ERR_ARG_OUTOFRANGE, "Field %D is not in [0, Nf)", field, Nf); 188 if (dim == 1 && Nf < 2) { 189 ierr = MatNullSpaceCreate(comm, PETSC_TRUE, 0, NULL, sp);CHKERRQ(ierr); 190 PetscFunctionReturn(0); 191 } 192 ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); 193 ierr = DMGetGlobalSection(dm, &globalSection);CHKERRQ(ierr); 194 ierr = PetscSectionGetConstrainedStorageSize(globalSection, &n);CHKERRQ(ierr); 195 ierr = PetscCalloc1(Nf, &func);CHKERRQ(ierr); 196 m = (dim*(dim+1))/2; 197 ierr = VecCreate(comm, &mode[0]);CHKERRQ(ierr); 198 ierr = VecSetSizes(mode[0], n, PETSC_DETERMINE);CHKERRQ(ierr); 199 ierr = VecSetUp(mode[0]);CHKERRQ(ierr); 200 ierr = VecGetSize(mode[0], &n);CHKERRQ(ierr); 201 mmin = PetscMin(m, n); 202 func[field] = DMPlexProjectRigidBody_Private; 203 for (i = 1; i < m; ++i) {ierr = VecDuplicate(mode[0], &mode[i]);CHKERRQ(ierr);} 204 for (d = 0; d < m; d++) { 205 PetscInt ctx[2]; 206 void *voidctx = (void *) (&ctx[0]); 207 208 ctx[0] = dimEmbed; 209 ctx[1] = d; 210 ierr = DMProjectFunction(dm, 0.0, func, &voidctx, INSERT_VALUES, mode[d]);CHKERRQ(ierr); 211 } 212 /* Orthonormalize system */ 213 for (i = 0; i < mmin; ++i) { 214 PetscScalar dots[6]; 215 216 ierr = VecNormalize(mode[i], NULL);CHKERRQ(ierr); 217 ierr = VecMDot(mode[i], mmin-i-1, mode+i+1, dots+i+1);CHKERRQ(ierr); 218 for (j = i+1; j < mmin; ++j) { 219 dots[j] *= -1.0; 220 ierr = VecAXPY(mode[j], dots[j], mode[i]);CHKERRQ(ierr); 221 } 222 } 223 ierr = MatNullSpaceCreate(comm, PETSC_FALSE, mmin, mode, sp);CHKERRQ(ierr); 224 for (i = 0; i < m; ++i) {ierr = VecDestroy(&mode[i]);CHKERRQ(ierr);} 225 ierr = PetscFree(func);CHKERRQ(ierr); 226 PetscFunctionReturn(0); 227 } 228 229 /*@ 230 DMPlexCreateRigidBodies - For the default global section, create rigid body modes by function space interpolation 231 232 Collective on dm 233 234 Input Arguments: 235 + dm - the DM 236 . nb - The number of bodies 237 . label - The DMLabel marking each domain 238 . nids - The number of ids per body 239 - ids - An array of the label ids in sequence for each domain 240 241 Output Argument: 242 . sp - the null space 243 244 Note: This is necessary to provide a suitable coarse space for algebraic multigrid 245 246 Level: advanced 247 248 .seealso: MatNullSpaceCreate() 249 @*/ 250 PetscErrorCode DMPlexCreateRigidBodies(DM dm, PetscInt nb, DMLabel label, const PetscInt nids[], const PetscInt ids[], MatNullSpace *sp) 251 { 252 MPI_Comm comm; 253 PetscSection section, globalSection; 254 Vec *mode; 255 PetscScalar *dots; 256 PetscInt dim, dimEmbed, n, m, b, d, i, j, off; 257 PetscErrorCode ierr; 258 259 PetscFunctionBegin; 260 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 261 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 262 ierr = DMGetCoordinateDim(dm, &dimEmbed);CHKERRQ(ierr); 263 ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); 264 ierr = DMGetGlobalSection(dm, &globalSection);CHKERRQ(ierr); 265 ierr = PetscSectionGetConstrainedStorageSize(globalSection, &n);CHKERRQ(ierr); 266 m = nb * (dim*(dim+1))/2; 267 ierr = PetscMalloc2(m, &mode, m, &dots);CHKERRQ(ierr); 268 ierr = VecCreate(comm, &mode[0]);CHKERRQ(ierr); 269 ierr = VecSetSizes(mode[0], n, PETSC_DETERMINE);CHKERRQ(ierr); 270 ierr = VecSetUp(mode[0]);CHKERRQ(ierr); 271 for (i = 1; i < m; ++i) {ierr = VecDuplicate(mode[0], &mode[i]);CHKERRQ(ierr);} 272 for (b = 0, off = 0; b < nb; ++b) { 273 for (d = 0; d < m/nb; ++d) { 274 PetscInt ctx[2]; 275 PetscErrorCode (*func)(PetscInt, PetscReal, const PetscReal *, PetscInt, PetscScalar *, void *) = DMPlexProjectRigidBody_Private; 276 void *voidctx = (void *) (&ctx[0]); 277 278 ctx[0] = dimEmbed; 279 ctx[1] = d; 280 ierr = DMProjectFunctionLabel(dm, 0.0, label, nids[b], &ids[off], 0, NULL, &func, &voidctx, INSERT_VALUES, mode[d]);CHKERRQ(ierr); 281 off += nids[b]; 282 } 283 } 284 /* Orthonormalize system */ 285 for (i = 0; i < m; ++i) { 286 PetscScalar dots[6]; 287 288 ierr = VecNormalize(mode[i], NULL);CHKERRQ(ierr); 289 ierr = VecMDot(mode[i], m-i-1, mode+i+1, dots+i+1);CHKERRQ(ierr); 290 for (j = i+1; j < m; ++j) { 291 dots[j] *= -1.0; 292 ierr = VecAXPY(mode[j], dots[j], mode[i]);CHKERRQ(ierr); 293 } 294 } 295 ierr = MatNullSpaceCreate(comm, PETSC_FALSE, m, mode, sp);CHKERRQ(ierr); 296 for (i = 0; i< m; ++i) {ierr = VecDestroy(&mode[i]);CHKERRQ(ierr);} 297 ierr = PetscFree2(mode, dots);CHKERRQ(ierr); 298 PetscFunctionReturn(0); 299 } 300 301 /*@ 302 DMPlexSetMaxProjectionHeight - In DMPlexProjectXXXLocal() functions, the projected values of a basis function's dofs 303 are computed by associating the basis function with one of the mesh points in its transitively-closed support, and 304 evaluating the dual space basis of that point. A basis function is associated with the point in its 305 transitively-closed support whose mesh height is highest (w.r.t. DAG height), but not greater than the maximum 306 projection height, which is set with this function. By default, the maximum projection height is zero, which means 307 that only mesh cells are used to project basis functions. A height of one, for example, evaluates a cell-interior 308 basis functions using its cells dual space basis, but all other basis functions with the dual space basis of a face. 309 310 Input Parameters: 311 + dm - the DMPlex object 312 - height - the maximum projection height >= 0 313 314 Level: advanced 315 316 .seealso: DMPlexGetMaxProjectionHeight(), DMProjectFunctionLocal(), DMProjectFunctionLabelLocal() 317 @*/ 318 PetscErrorCode DMPlexSetMaxProjectionHeight(DM dm, PetscInt height) 319 { 320 DM_Plex *plex = (DM_Plex *) dm->data; 321 322 PetscFunctionBegin; 323 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 324 plex->maxProjectionHeight = height; 325 PetscFunctionReturn(0); 326 } 327 328 /*@ 329 DMPlexGetMaxProjectionHeight - Get the maximum height (w.r.t. DAG) of mesh points used to evaluate dual bases in 330 DMPlexProjectXXXLocal() functions. 331 332 Input Parameters: 333 . dm - the DMPlex object 334 335 Output Parameters: 336 . height - the maximum projection height 337 338 Level: intermediate 339 340 .seealso: DMPlexSetMaxProjectionHeight(), DMProjectFunctionLocal(), DMProjectFunctionLabelLocal() 341 @*/ 342 PetscErrorCode DMPlexGetMaxProjectionHeight(DM dm, PetscInt *height) 343 { 344 DM_Plex *plex = (DM_Plex *) dm->data; 345 346 PetscFunctionBegin; 347 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 348 *height = plex->maxProjectionHeight; 349 PetscFunctionReturn(0); 350 } 351 352 typedef struct { 353 PetscReal alpha; /* The first Euler angle, and in 2D the only one */ 354 PetscReal beta; /* The second Euler angle */ 355 PetscReal gamma; /* The third Euler angle */ 356 PetscInt dim; /* The dimension of R */ 357 PetscScalar *R; /* The rotation matrix, transforming a vector in the local basis to the global basis */ 358 PetscScalar *RT; /* The transposed rotation matrix, transforming a vector in the global basis to the local basis */ 359 } RotCtx; 360 361 /* 362 Note: Following https://en.wikipedia.org/wiki/Euler_angles, we will specify Euler angles by extrinsic rotations, meaning that 363 we rotate with respect to a fixed initial coordinate system, the local basis (x-y-z). The global basis (X-Y-Z) is reached as follows: 364 $ The XYZ system rotates about the z axis by alpha. The X axis is now at angle alpha with respect to the x axis. 365 $ The XYZ system rotates again about the x axis by beta. The Z axis is now at angle beta with respect to the z axis. 366 $ The XYZ system rotates a third time about the z axis by gamma. 367 */ 368 static PetscErrorCode DMPlexBasisTransformSetUp_Rotation_Internal(DM dm, void *ctx) 369 { 370 RotCtx *rc = (RotCtx *) ctx; 371 PetscInt dim = rc->dim; 372 PetscReal c1, s1, c2, s2, c3, s3; 373 PetscErrorCode ierr; 374 375 PetscFunctionBegin; 376 ierr = PetscMalloc2(PetscSqr(dim), &rc->R, PetscSqr(dim), &rc->RT);CHKERRQ(ierr); 377 switch (dim) { 378 case 2: 379 c1 = PetscCosReal(rc->alpha);s1 = PetscSinReal(rc->alpha); 380 rc->R[0] = c1;rc->R[1] = s1; 381 rc->R[2] = -s1;rc->R[3] = c1; 382 ierr = PetscArraycpy(rc->RT, rc->R, PetscSqr(dim));CHKERRQ(ierr); 383 DMPlex_Transpose2D_Internal(rc->RT); 384 break; 385 case 3: 386 c1 = PetscCosReal(rc->alpha);s1 = PetscSinReal(rc->alpha); 387 c2 = PetscCosReal(rc->beta); s2 = PetscSinReal(rc->beta); 388 c3 = PetscCosReal(rc->gamma);s3 = PetscSinReal(rc->gamma); 389 rc->R[0] = c1*c3 - c2*s1*s3;rc->R[1] = c3*s1 + c1*c2*s3;rc->R[2] = s2*s3; 390 rc->R[3] = -c1*s3 - c2*c3*s1;rc->R[4] = c1*c2*c3 - s1*s3; rc->R[5] = c3*s2; 391 rc->R[6] = s1*s2; rc->R[7] = -c1*s2; rc->R[8] = c2; 392 ierr = PetscArraycpy(rc->RT, rc->R, PetscSqr(dim));CHKERRQ(ierr); 393 DMPlex_Transpose3D_Internal(rc->RT); 394 break; 395 default: SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_OUTOFRANGE, "Dimension %D not supported", dim); 396 } 397 PetscFunctionReturn(0); 398 } 399 400 static PetscErrorCode DMPlexBasisTransformDestroy_Rotation_Internal(DM dm, void *ctx) 401 { 402 RotCtx *rc = (RotCtx *) ctx; 403 PetscErrorCode ierr; 404 405 PetscFunctionBegin; 406 ierr = PetscFree2(rc->R, rc->RT);CHKERRQ(ierr); 407 ierr = PetscFree(rc);CHKERRQ(ierr); 408 PetscFunctionReturn(0); 409 } 410 411 static PetscErrorCode DMPlexBasisTransformGetMatrix_Rotation_Internal(DM dm, const PetscReal x[], PetscBool l2g, const PetscScalar **A, void *ctx) 412 { 413 RotCtx *rc = (RotCtx *) ctx; 414 415 PetscFunctionBeginHot; 416 PetscValidPointer(ctx, 5); 417 if (l2g) {*A = rc->R;} 418 else {*A = rc->RT;} 419 PetscFunctionReturn(0); 420 } 421 422 PetscErrorCode DMPlexBasisTransformApplyReal_Internal(DM dm, const PetscReal x[], PetscBool l2g, PetscInt dim, const PetscReal *y, PetscReal *z, void *ctx) 423 { 424 PetscErrorCode ierr; 425 426 PetscFunctionBegin; 427 #if defined(PETSC_USE_COMPLEX) 428 switch (dim) { 429 case 2: 430 { 431 PetscScalar yt[2], zt[2] = {0.0,0.0}; 432 433 yt[0] = y[0]; yt[1] = y[1]; 434 ierr = DMPlexBasisTransformApply_Internal(dm, x, l2g, dim, yt, zt, ctx);CHKERRQ(ierr); 435 z[0] = PetscRealPart(zt[0]); z[1] = PetscRealPart(zt[1]); 436 } 437 break; 438 case 3: 439 { 440 PetscScalar yt[3], zt[3] = {0.0,0.0,0.0}; 441 442 yt[0] = y[0]; yt[1] = y[1]; yt[2] = y[2]; 443 ierr = DMPlexBasisTransformApply_Internal(dm, x, l2g, dim, yt, zt, ctx);CHKERRQ(ierr); 444 z[0] = PetscRealPart(zt[0]); z[1] = PetscRealPart(zt[1]); z[2] = PetscRealPart(zt[2]); 445 } 446 break; 447 } 448 #else 449 ierr = DMPlexBasisTransformApply_Internal(dm, x, l2g, dim, y, z, ctx);CHKERRQ(ierr); 450 #endif 451 PetscFunctionReturn(0); 452 } 453 454 PetscErrorCode DMPlexBasisTransformApply_Internal(DM dm, const PetscReal x[], PetscBool l2g, PetscInt dim, const PetscScalar *y, PetscScalar *z, void *ctx) 455 { 456 const PetscScalar *A; 457 PetscErrorCode ierr; 458 459 PetscFunctionBeginHot; 460 ierr = (*dm->transformGetMatrix)(dm, x, l2g, &A, ctx);CHKERRQ(ierr); 461 switch (dim) { 462 case 2: DMPlex_Mult2D_Internal(A, 1, y, z);break; 463 case 3: DMPlex_Mult3D_Internal(A, 1, y, z);break; 464 } 465 PetscFunctionReturn(0); 466 } 467 468 static PetscErrorCode DMPlexBasisTransformField_Internal(DM dm, DM tdm, Vec tv, PetscInt p, PetscInt f, PetscBool l2g, PetscScalar *a) 469 { 470 PetscSection ts; 471 const PetscScalar *ta, *tva; 472 PetscInt dof; 473 PetscErrorCode ierr; 474 475 PetscFunctionBeginHot; 476 ierr = DMGetLocalSection(tdm, &ts);CHKERRQ(ierr); 477 ierr = PetscSectionGetFieldDof(ts, p, f, &dof);CHKERRQ(ierr); 478 ierr = VecGetArrayRead(tv, &ta);CHKERRQ(ierr); 479 ierr = DMPlexPointLocalFieldRead(tdm, p, f, ta, (void *) &tva);CHKERRQ(ierr); 480 if (l2g) { 481 switch (dof) { 482 case 4: DMPlex_Mult2D_Internal(tva, 1, a, a);break; 483 case 9: DMPlex_Mult3D_Internal(tva, 1, a, a);break; 484 } 485 } else { 486 switch (dof) { 487 case 4: DMPlex_MultTranspose2D_Internal(tva, 1, a, a);break; 488 case 9: DMPlex_MultTranspose3D_Internal(tva, 1, a, a);break; 489 } 490 } 491 ierr = VecRestoreArrayRead(tv, &ta);CHKERRQ(ierr); 492 PetscFunctionReturn(0); 493 } 494 495 static PetscErrorCode DMPlexBasisTransformFieldTensor_Internal(DM dm, DM tdm, Vec tv, PetscInt pf, PetscInt f, PetscInt pg, PetscInt g, PetscBool l2g, PetscInt lda, PetscScalar *a) 496 { 497 PetscSection s, ts; 498 const PetscScalar *ta, *tvaf, *tvag; 499 PetscInt fdof, gdof, fpdof, gpdof; 500 PetscErrorCode ierr; 501 502 PetscFunctionBeginHot; 503 ierr = DMGetLocalSection(dm, &s);CHKERRQ(ierr); 504 ierr = DMGetLocalSection(tdm, &ts);CHKERRQ(ierr); 505 ierr = PetscSectionGetFieldDof(s, pf, f, &fpdof);CHKERRQ(ierr); 506 ierr = PetscSectionGetFieldDof(s, pg, g, &gpdof);CHKERRQ(ierr); 507 ierr = PetscSectionGetFieldDof(ts, pf, f, &fdof);CHKERRQ(ierr); 508 ierr = PetscSectionGetFieldDof(ts, pg, g, &gdof);CHKERRQ(ierr); 509 ierr = VecGetArrayRead(tv, &ta);CHKERRQ(ierr); 510 ierr = DMPlexPointLocalFieldRead(tdm, pf, f, ta, (void *) &tvaf);CHKERRQ(ierr); 511 ierr = DMPlexPointLocalFieldRead(tdm, pg, g, ta, (void *) &tvag);CHKERRQ(ierr); 512 if (l2g) { 513 switch (fdof) { 514 case 4: DMPlex_MatMult2D_Internal(tvaf, gpdof, lda, a, a);break; 515 case 9: DMPlex_MatMult3D_Internal(tvaf, gpdof, lda, a, a);break; 516 } 517 switch (gdof) { 518 case 4: DMPlex_MatMultTransposeLeft2D_Internal(tvag, fpdof, lda, a, a);break; 519 case 9: DMPlex_MatMultTransposeLeft3D_Internal(tvag, fpdof, lda, a, a);break; 520 } 521 } else { 522 switch (fdof) { 523 case 4: DMPlex_MatMultTranspose2D_Internal(tvaf, gpdof, lda, a, a);break; 524 case 9: DMPlex_MatMultTranspose3D_Internal(tvaf, gpdof, lda, a, a);break; 525 } 526 switch (gdof) { 527 case 4: DMPlex_MatMultLeft2D_Internal(tvag, fpdof, lda, a, a);break; 528 case 9: DMPlex_MatMultLeft3D_Internal(tvag, fpdof, lda, a, a);break; 529 } 530 } 531 ierr = VecRestoreArrayRead(tv, &ta);CHKERRQ(ierr); 532 PetscFunctionReturn(0); 533 } 534 535 PetscErrorCode DMPlexBasisTransformPoint_Internal(DM dm, DM tdm, Vec tv, PetscInt p, PetscBool fieldActive[], PetscBool l2g, PetscScalar *a) 536 { 537 PetscSection s; 538 PetscSection clSection; 539 IS clPoints; 540 const PetscInt *clp; 541 PetscInt *points = NULL; 542 PetscInt Nf, f, Np, cp, dof, d = 0; 543 PetscErrorCode ierr; 544 545 PetscFunctionBegin; 546 ierr = DMGetLocalSection(dm, &s);CHKERRQ(ierr); 547 ierr = PetscSectionGetNumFields(s, &Nf);CHKERRQ(ierr); 548 ierr = DMPlexGetCompressedClosure(dm, s, p, &Np, &points, &clSection, &clPoints, &clp);CHKERRQ(ierr); 549 for (f = 0; f < Nf; ++f) { 550 for (cp = 0; cp < Np*2; cp += 2) { 551 ierr = PetscSectionGetFieldDof(s, points[cp], f, &dof);CHKERRQ(ierr); 552 if (!dof) continue; 553 if (fieldActive[f]) {ierr = DMPlexBasisTransformField_Internal(dm, tdm, tv, points[cp], f, l2g, &a[d]);CHKERRQ(ierr);} 554 d += dof; 555 } 556 } 557 ierr = DMPlexRestoreCompressedClosure(dm, s, p, &Np, &points, &clSection, &clPoints, &clp);CHKERRQ(ierr); 558 PetscFunctionReturn(0); 559 } 560 561 PetscErrorCode DMPlexBasisTransformPointTensor_Internal(DM dm, DM tdm, Vec tv, PetscInt p, PetscBool l2g, PetscInt lda, PetscScalar *a) 562 { 563 PetscSection s; 564 PetscSection clSection; 565 IS clPoints; 566 const PetscInt *clp; 567 PetscInt *points = NULL; 568 PetscInt Nf, f, g, Np, cpf, cpg, fdof, gdof, r, c = 0; 569 PetscErrorCode ierr; 570 571 PetscFunctionBegin; 572 ierr = DMGetLocalSection(dm, &s);CHKERRQ(ierr); 573 ierr = PetscSectionGetNumFields(s, &Nf);CHKERRQ(ierr); 574 ierr = DMPlexGetCompressedClosure(dm, s, p, &Np, &points, &clSection, &clPoints, &clp);CHKERRQ(ierr); 575 for (f = 0, r = 0; f < Nf; ++f) { 576 for (cpf = 0; cpf < Np*2; cpf += 2) { 577 ierr = PetscSectionGetFieldDof(s, points[cpf], f, &fdof);CHKERRQ(ierr); 578 for (g = 0, c = 0; g < Nf; ++g) { 579 for (cpg = 0; cpg < Np*2; cpg += 2) { 580 ierr = PetscSectionGetFieldDof(s, points[cpg], g, &gdof);CHKERRQ(ierr); 581 ierr = DMPlexBasisTransformFieldTensor_Internal(dm, tdm, tv, points[cpf], f, points[cpg], g, l2g, lda, &a[r*lda+c]);CHKERRQ(ierr); 582 c += gdof; 583 } 584 } 585 if (c != lda) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid number of columns %D should be %D", c, lda); 586 r += fdof; 587 } 588 } 589 if (r != lda) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid number of rows %D should be %D", c, lda); 590 ierr = DMPlexRestoreCompressedClosure(dm, s, p, &Np, &points, &clSection, &clPoints, &clp);CHKERRQ(ierr); 591 PetscFunctionReturn(0); 592 } 593 594 static PetscErrorCode DMPlexBasisTransform_Internal(DM dm, Vec lv, PetscBool l2g) 595 { 596 DM tdm; 597 Vec tv; 598 PetscSection ts, s; 599 const PetscScalar *ta; 600 PetscScalar *a, *va; 601 PetscInt pStart, pEnd, p, Nf, f; 602 PetscErrorCode ierr; 603 604 PetscFunctionBegin; 605 ierr = DMGetBasisTransformDM_Internal(dm, &tdm);CHKERRQ(ierr); 606 ierr = DMGetBasisTransformVec_Internal(dm, &tv);CHKERRQ(ierr); 607 ierr = DMGetLocalSection(tdm, &ts);CHKERRQ(ierr); 608 ierr = DMGetLocalSection(dm, &s);CHKERRQ(ierr); 609 ierr = PetscSectionGetChart(s, &pStart, &pEnd);CHKERRQ(ierr); 610 ierr = PetscSectionGetNumFields(s, &Nf);CHKERRQ(ierr); 611 ierr = VecGetArray(lv, &a);CHKERRQ(ierr); 612 ierr = VecGetArrayRead(tv, &ta);CHKERRQ(ierr); 613 for (p = pStart; p < pEnd; ++p) { 614 for (f = 0; f < Nf; ++f) { 615 ierr = DMPlexPointLocalFieldRef(dm, p, f, a, (void *) &va);CHKERRQ(ierr); 616 ierr = DMPlexBasisTransformField_Internal(dm, tdm, tv, p, f, l2g, va);CHKERRQ(ierr); 617 } 618 } 619 ierr = VecRestoreArray(lv, &a);CHKERRQ(ierr); 620 ierr = VecRestoreArrayRead(tv, &ta);CHKERRQ(ierr); 621 PetscFunctionReturn(0); 622 } 623 624 /*@ 625 DMPlexGlobalToLocalBasis - Transform the values in the given local vector from the global basis to the local basis 626 627 Input Parameters: 628 + dm - The DM 629 - lv - A local vector with values in the global basis 630 631 Output Parameters: 632 . lv - A local vector with values in the local basis 633 634 Note: This method is only intended to be called inside DMGlobalToLocal(). It is unlikely that a user will have a local vector full of coefficients for the global basis unless they are reimplementing GlobalToLocal. 635 636 Level: developer 637 638 .seealso: DMPlexLocalToGlobalBasis(), DMGetLocalSection(), DMPlexCreateBasisRotation() 639 @*/ 640 PetscErrorCode DMPlexGlobalToLocalBasis(DM dm, Vec lv) 641 { 642 PetscErrorCode ierr; 643 644 PetscFunctionBegin; 645 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 646 PetscValidHeaderSpecific(lv, VEC_CLASSID, 2); 647 ierr = DMPlexBasisTransform_Internal(dm, lv, PETSC_FALSE);CHKERRQ(ierr); 648 PetscFunctionReturn(0); 649 } 650 651 /*@ 652 DMPlexLocalToGlobalBasis - Transform the values in the given local vector from the local basis to the global basis 653 654 Input Parameters: 655 + dm - The DM 656 - lv - A local vector with values in the local basis 657 658 Output Parameters: 659 . lv - A local vector with values in the global basis 660 661 Note: This method is only intended to be called inside DMGlobalToLocal(). It is unlikely that a user would want a local vector full of coefficients for the global basis unless they are reimplementing GlobalToLocal. 662 663 Level: developer 664 665 .seealso: DMPlexGlobalToLocalBasis(), DMGetLocalSection(), DMPlexCreateBasisRotation() 666 @*/ 667 PetscErrorCode DMPlexLocalToGlobalBasis(DM dm, Vec lv) 668 { 669 PetscErrorCode ierr; 670 671 PetscFunctionBegin; 672 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 673 PetscValidHeaderSpecific(lv, VEC_CLASSID, 2); 674 ierr = DMPlexBasisTransform_Internal(dm, lv, PETSC_TRUE);CHKERRQ(ierr); 675 PetscFunctionReturn(0); 676 } 677 678 /*@ 679 DMPlexCreateBasisRotation - Create an internal transformation from the global basis, used to specify boundary conditions 680 and global solutions, to a local basis, appropriate for discretization integrals and assembly. 681 682 Input Parameters: 683 + dm - The DM 684 . alpha - The first Euler angle, and in 2D the only one 685 . beta - The second Euler angle 686 - gamma - The third Euler angle 687 688 Note: Following https://en.wikipedia.org/wiki/Euler_angles, we will specify Euler angles by extrinsic rotations, meaning that 689 we rotate with respect to a fixed initial coordinate system, the local basis (x-y-z). The global basis (X-Y-Z) is reached as follows: 690 $ The XYZ system rotates about the z axis by alpha. The X axis is now at angle alpha with respect to the x axis. 691 $ The XYZ system rotates again about the x axis by beta. The Z axis is now at angle beta with respect to the z axis. 692 $ The XYZ system rotates a third time about the z axis by gamma. 693 694 Level: developer 695 696 .seealso: DMPlexGlobalToLocalBasis(), DMPlexLocalToGlobalBasis() 697 @*/ 698 PetscErrorCode DMPlexCreateBasisRotation(DM dm, PetscReal alpha, PetscReal beta, PetscReal gamma) 699 { 700 RotCtx *rc; 701 PetscInt cdim; 702 PetscErrorCode ierr; 703 704 PetscFunctionBegin; 705 ierr = DMGetCoordinateDim(dm, &cdim);CHKERRQ(ierr); 706 ierr = PetscMalloc1(1, &rc);CHKERRQ(ierr); 707 dm->transformCtx = rc; 708 dm->transformSetUp = DMPlexBasisTransformSetUp_Rotation_Internal; 709 dm->transformDestroy = DMPlexBasisTransformDestroy_Rotation_Internal; 710 dm->transformGetMatrix = DMPlexBasisTransformGetMatrix_Rotation_Internal; 711 rc->dim = cdim; 712 rc->alpha = alpha; 713 rc->beta = beta; 714 rc->gamma = gamma; 715 ierr = (*dm->transformSetUp)(dm, dm->transformCtx);CHKERRQ(ierr); 716 ierr = DMConstructBasisTransform_Internal(dm);CHKERRQ(ierr); 717 PetscFunctionReturn(0); 718 } 719 720 /*@C 721 DMPlexInsertBoundaryValuesEssential - Insert boundary values into a local vector using a function of the coordinates 722 723 Input Parameters: 724 + dm - The DM, with a PetscDS that matches the problem being constrained 725 . time - The time 726 . field - The field to constrain 727 . Nc - The number of constrained field components, or 0 for all components 728 . comps - An array of constrained component numbers, or NULL for all components 729 . label - The DMLabel defining constrained points 730 . numids - The number of DMLabel ids for constrained points 731 . ids - An array of ids for constrained points 732 . func - A pointwise function giving boundary values 733 - ctx - An optional user context for bcFunc 734 735 Output Parameter: 736 . locX - A local vector to receives the boundary values 737 738 Level: developer 739 740 .seealso: DMPlexInsertBoundaryValuesEssentialField(), DMPlexInsertBoundaryValuesEssentialBdField(), DMAddBoundary() 741 @*/ 742 PetscErrorCode DMPlexInsertBoundaryValuesEssential(DM dm, PetscReal time, PetscInt field, PetscInt Nc, const PetscInt comps[], DMLabel label, PetscInt numids, const PetscInt ids[], PetscErrorCode (*func)(PetscInt, PetscReal, const PetscReal[], PetscInt, PetscScalar *, void *), void *ctx, Vec locX) 743 { 744 PetscErrorCode (**funcs)(PetscInt, PetscReal, const PetscReal x[], PetscInt, PetscScalar *u, void *ctx); 745 void **ctxs; 746 PetscInt numFields; 747 PetscErrorCode ierr; 748 749 PetscFunctionBegin; 750 ierr = DMGetNumFields(dm, &numFields);CHKERRQ(ierr); 751 ierr = PetscCalloc2(numFields,&funcs,numFields,&ctxs);CHKERRQ(ierr); 752 funcs[field] = func; 753 ctxs[field] = ctx; 754 ierr = DMProjectFunctionLabelLocal(dm, time, label, numids, ids, Nc, comps, funcs, ctxs, INSERT_BC_VALUES, locX);CHKERRQ(ierr); 755 ierr = PetscFree2(funcs,ctxs);CHKERRQ(ierr); 756 PetscFunctionReturn(0); 757 } 758 759 /*@C 760 DMPlexInsertBoundaryValuesEssentialField - Insert boundary values into a local vector using a function of the coordinates and field data 761 762 Input Parameters: 763 + dm - The DM, with a PetscDS that matches the problem being constrained 764 . time - The time 765 . locU - A local vector with the input solution values 766 . field - The field to constrain 767 . Nc - The number of constrained field components, or 0 for all components 768 . comps - An array of constrained component numbers, or NULL for all components 769 . label - The DMLabel defining constrained points 770 . numids - The number of DMLabel ids for constrained points 771 . ids - An array of ids for constrained points 772 . func - A pointwise function giving boundary values 773 - ctx - An optional user context for bcFunc 774 775 Output Parameter: 776 . locX - A local vector to receives the boundary values 777 778 Level: developer 779 780 .seealso: DMPlexInsertBoundaryValuesEssential(), DMPlexInsertBoundaryValuesEssentialBdField(), DMAddBoundary() 781 @*/ 782 PetscErrorCode DMPlexInsertBoundaryValuesEssentialField(DM dm, PetscReal time, Vec locU, PetscInt field, PetscInt Nc, const PetscInt comps[], DMLabel label, PetscInt numids, const PetscInt ids[], 783 void (*func)(PetscInt, PetscInt, PetscInt, 784 const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[], 785 const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[], 786 PetscReal, const PetscReal[], PetscInt, const PetscScalar[], 787 PetscScalar[]), 788 void *ctx, Vec locX) 789 { 790 void (**funcs)(PetscInt, PetscInt, PetscInt, 791 const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[], 792 const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[], 793 PetscReal, const PetscReal[], PetscInt, const PetscScalar[], PetscScalar[]); 794 void **ctxs; 795 PetscInt numFields; 796 PetscErrorCode ierr; 797 798 PetscFunctionBegin; 799 ierr = DMGetNumFields(dm, &numFields);CHKERRQ(ierr); 800 ierr = PetscCalloc2(numFields,&funcs,numFields,&ctxs);CHKERRQ(ierr); 801 funcs[field] = func; 802 ctxs[field] = ctx; 803 ierr = DMProjectFieldLabelLocal(dm, time, label, numids, ids, Nc, comps, locU, funcs, INSERT_BC_VALUES, locX);CHKERRQ(ierr); 804 ierr = PetscFree2(funcs,ctxs);CHKERRQ(ierr); 805 PetscFunctionReturn(0); 806 } 807 808 /*@C 809 DMPlexInsertBoundaryValuesEssentialBdField - Insert boundary values into a local vector using a function of the coodinates and boundary field data 810 811 Collective on dm 812 813 Input Parameters: 814 + dm - The DM, with a PetscDS that matches the problem being constrained 815 . time - The time 816 . locU - A local vector with the input solution values 817 . field - The field to constrain 818 . Nc - The number of constrained field components, or 0 for all components 819 . comps - An array of constrained component numbers, or NULL for all components 820 . label - The DMLabel defining constrained points 821 . numids - The number of DMLabel ids for constrained points 822 . ids - An array of ids for constrained points 823 . func - A pointwise function giving boundary values, the calling sequence is given in DMProjectBdFieldLabelLocal() 824 - ctx - An optional user context for bcFunc 825 826 Output Parameter: 827 . locX - A local vector to receive the boundary values 828 829 Level: developer 830 831 .seealso: DMProjectBdFieldLabelLocal(), DMPlexInsertBoundaryValuesEssential(), DMPlexInsertBoundaryValuesEssentialField(), DMAddBoundary() 832 @*/ 833 PetscErrorCode DMPlexInsertBoundaryValuesEssentialBdField(DM dm, PetscReal time, Vec locU, PetscInt field, PetscInt Nc, const PetscInt comps[], DMLabel label, PetscInt numids, const PetscInt ids[], 834 void (*func)(PetscInt, PetscInt, PetscInt, 835 const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[], 836 const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[], 837 PetscReal, const PetscReal[], const PetscReal[], PetscInt, const PetscScalar[], 838 PetscScalar[]), 839 void *ctx, Vec locX) 840 { 841 void (**funcs)(PetscInt, PetscInt, PetscInt, 842 const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[], 843 const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[], 844 PetscReal, const PetscReal[], const PetscReal[], PetscInt, const PetscScalar[], PetscScalar[]); 845 void **ctxs; 846 PetscInt numFields; 847 PetscErrorCode ierr; 848 849 PetscFunctionBegin; 850 ierr = DMGetNumFields(dm, &numFields);CHKERRQ(ierr); 851 ierr = PetscCalloc2(numFields,&funcs,numFields,&ctxs);CHKERRQ(ierr); 852 funcs[field] = func; 853 ctxs[field] = ctx; 854 ierr = DMProjectBdFieldLabelLocal(dm, time, label, numids, ids, Nc, comps, locU, funcs, INSERT_BC_VALUES, locX);CHKERRQ(ierr); 855 ierr = PetscFree2(funcs,ctxs);CHKERRQ(ierr); 856 PetscFunctionReturn(0); 857 } 858 859 /*@C 860 DMPlexInsertBoundaryValuesRiemann - Insert boundary values into a local vector 861 862 Input Parameters: 863 + dm - The DM, with a PetscDS that matches the problem being constrained 864 . time - The time 865 . faceGeometry - A vector with the FVM face geometry information 866 . cellGeometry - A vector with the FVM cell geometry information 867 . Grad - A vector with the FVM cell gradient information 868 . field - The field to constrain 869 . Nc - The number of constrained field components, or 0 for all components 870 . comps - An array of constrained component numbers, or NULL for all components 871 . label - The DMLabel defining constrained points 872 . numids - The number of DMLabel ids for constrained points 873 . ids - An array of ids for constrained points 874 . func - A pointwise function giving boundary values 875 - ctx - An optional user context for bcFunc 876 877 Output Parameter: 878 . locX - A local vector to receives the boundary values 879 880 Note: This implementation currently ignores the numcomps/comps argument from DMAddBoundary() 881 882 Level: developer 883 884 .seealso: DMPlexInsertBoundaryValuesEssential(), DMPlexInsertBoundaryValuesEssentialField(), DMAddBoundary() 885 @*/ 886 PetscErrorCode DMPlexInsertBoundaryValuesRiemann(DM dm, PetscReal time, Vec faceGeometry, Vec cellGeometry, Vec Grad, PetscInt field, PetscInt Nc, const PetscInt comps[], DMLabel label, PetscInt numids, const PetscInt ids[], 887 PetscErrorCode (*func)(PetscReal,const PetscReal*,const PetscReal*,const PetscScalar*,PetscScalar*,void*), void *ctx, Vec locX) 888 { 889 PetscDS prob; 890 PetscSF sf; 891 DM dmFace, dmCell, dmGrad; 892 const PetscScalar *facegeom, *cellgeom = NULL, *grad; 893 const PetscInt *leaves; 894 PetscScalar *x, *fx; 895 PetscInt dim, nleaves, loc, fStart, fEnd, pdim, i; 896 PetscErrorCode ierr, ierru = 0; 897 898 PetscFunctionBegin; 899 ierr = DMGetPointSF(dm, &sf);CHKERRQ(ierr); 900 ierr = PetscSFGetGraph(sf, NULL, &nleaves, &leaves, NULL);CHKERRQ(ierr); 901 nleaves = PetscMax(0, nleaves); 902 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 903 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 904 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 905 ierr = VecGetDM(faceGeometry, &dmFace);CHKERRQ(ierr); 906 ierr = VecGetArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); 907 if (cellGeometry) { 908 ierr = VecGetDM(cellGeometry, &dmCell);CHKERRQ(ierr); 909 ierr = VecGetArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr); 910 } 911 if (Grad) { 912 PetscFV fv; 913 914 ierr = PetscDSGetDiscretization(prob, field, (PetscObject *) &fv);CHKERRQ(ierr); 915 ierr = VecGetDM(Grad, &dmGrad);CHKERRQ(ierr); 916 ierr = VecGetArrayRead(Grad, &grad);CHKERRQ(ierr); 917 ierr = PetscFVGetNumComponents(fv, &pdim);CHKERRQ(ierr); 918 ierr = DMGetWorkArray(dm, pdim, MPIU_SCALAR, &fx);CHKERRQ(ierr); 919 } 920 ierr = VecGetArray(locX, &x);CHKERRQ(ierr); 921 for (i = 0; i < numids; ++i) { 922 IS faceIS; 923 const PetscInt *faces; 924 PetscInt numFaces, f; 925 926 ierr = DMLabelGetStratumIS(label, ids[i], &faceIS);CHKERRQ(ierr); 927 if (!faceIS) continue; /* No points with that id on this process */ 928 ierr = ISGetLocalSize(faceIS, &numFaces);CHKERRQ(ierr); 929 ierr = ISGetIndices(faceIS, &faces);CHKERRQ(ierr); 930 for (f = 0; f < numFaces; ++f) { 931 const PetscInt face = faces[f], *cells; 932 PetscFVFaceGeom *fg; 933 934 if ((face < fStart) || (face >= fEnd)) continue; /* Refinement adds non-faces to labels */ 935 ierr = PetscFindInt(face, nleaves, (PetscInt *) leaves, &loc);CHKERRQ(ierr); 936 if (loc >= 0) continue; 937 ierr = DMPlexPointLocalRead(dmFace, face, facegeom, &fg);CHKERRQ(ierr); 938 ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr); 939 if (Grad) { 940 PetscFVCellGeom *cg; 941 PetscScalar *cx, *cgrad; 942 PetscScalar *xG; 943 PetscReal dx[3]; 944 PetscInt d; 945 946 ierr = DMPlexPointLocalRead(dmCell, cells[0], cellgeom, &cg);CHKERRQ(ierr); 947 ierr = DMPlexPointLocalRead(dm, cells[0], x, &cx);CHKERRQ(ierr); 948 ierr = DMPlexPointLocalRead(dmGrad, cells[0], grad, &cgrad);CHKERRQ(ierr); 949 ierr = DMPlexPointLocalFieldRef(dm, cells[1], field, x, &xG);CHKERRQ(ierr); 950 DMPlex_WaxpyD_Internal(dim, -1, cg->centroid, fg->centroid, dx); 951 for (d = 0; d < pdim; ++d) fx[d] = cx[d] + DMPlex_DotD_Internal(dim, &cgrad[d*dim], dx); 952 ierru = (*func)(time, fg->centroid, fg->normal, fx, xG, ctx); 953 if (ierru) { 954 ierr = ISRestoreIndices(faceIS, &faces);CHKERRQ(ierr); 955 ierr = ISDestroy(&faceIS);CHKERRQ(ierr); 956 goto cleanup; 957 } 958 } else { 959 PetscScalar *xI; 960 PetscScalar *xG; 961 962 ierr = DMPlexPointLocalRead(dm, cells[0], x, &xI);CHKERRQ(ierr); 963 ierr = DMPlexPointLocalFieldRef(dm, cells[1], field, x, &xG);CHKERRQ(ierr); 964 ierru = (*func)(time, fg->centroid, fg->normal, xI, xG, ctx); 965 if (ierru) { 966 ierr = ISRestoreIndices(faceIS, &faces);CHKERRQ(ierr); 967 ierr = ISDestroy(&faceIS);CHKERRQ(ierr); 968 goto cleanup; 969 } 970 } 971 } 972 ierr = ISRestoreIndices(faceIS, &faces);CHKERRQ(ierr); 973 ierr = ISDestroy(&faceIS);CHKERRQ(ierr); 974 } 975 cleanup: 976 ierr = VecRestoreArray(locX, &x);CHKERRQ(ierr); 977 if (Grad) { 978 ierr = DMRestoreWorkArray(dm, pdim, MPIU_SCALAR, &fx);CHKERRQ(ierr); 979 ierr = VecRestoreArrayRead(Grad, &grad);CHKERRQ(ierr); 980 } 981 if (cellGeometry) {ierr = VecRestoreArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr);} 982 ierr = VecRestoreArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); 983 CHKERRQ(ierru); 984 PetscFunctionReturn(0); 985 } 986 987 static PetscErrorCode zero(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nc, PetscScalar *u, void *ctx) 988 { 989 PetscInt c; 990 for (c = 0; c < Nc; ++c) u[c] = 0.0; 991 return 0; 992 } 993 994 PetscErrorCode DMPlexInsertBoundaryValues_Plex(DM dm, PetscBool insertEssential, Vec locX, PetscReal time, Vec faceGeomFVM, Vec cellGeomFVM, Vec gradFVM) 995 { 996 PetscObject isZero; 997 PetscDS prob; 998 PetscInt numBd, b; 999 PetscErrorCode ierr; 1000 1001 PetscFunctionBegin; 1002 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1003 ierr = PetscDSGetNumBoundary(prob, &numBd);CHKERRQ(ierr); 1004 ierr = PetscObjectQuery((PetscObject) locX, "__Vec_bc_zero__", &isZero);CHKERRQ(ierr); 1005 for (b = 0; b < numBd; ++b) { 1006 PetscWeakForm wf; 1007 DMBoundaryConditionType type; 1008 const char *name; 1009 DMLabel label; 1010 PetscInt field, Nc; 1011 const PetscInt *comps; 1012 PetscObject obj; 1013 PetscClassId id; 1014 void (*bvfunc)(void); 1015 PetscInt numids; 1016 const PetscInt *ids; 1017 void *ctx; 1018 1019 ierr = PetscDSGetBoundary(prob, b, &wf, &type, &name, &label, &numids, &ids, &field, &Nc, &comps, &bvfunc, NULL, &ctx);CHKERRQ(ierr); 1020 if (insertEssential != (type & DM_BC_ESSENTIAL)) continue; 1021 ierr = DMGetField(dm, field, NULL, &obj);CHKERRQ(ierr); 1022 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1023 if (id == PETSCFE_CLASSID) { 1024 switch (type) { 1025 /* for FEM, there is no insertion to be done for non-essential boundary conditions */ 1026 case DM_BC_ESSENTIAL: 1027 { 1028 PetscSimplePointFunc func = (PetscSimplePointFunc) bvfunc; 1029 1030 if (isZero) func = zero; 1031 ierr = DMPlexLabelAddCells(dm,label);CHKERRQ(ierr); 1032 ierr = DMPlexInsertBoundaryValuesEssential(dm, time, field, Nc, comps, label, numids, ids, func, ctx, locX);CHKERRQ(ierr); 1033 ierr = DMPlexLabelClearCells(dm,label);CHKERRQ(ierr); 1034 } 1035 break; 1036 case DM_BC_ESSENTIAL_FIELD: 1037 { 1038 PetscPointFunc func = (PetscPointFunc) bvfunc; 1039 1040 ierr = DMPlexLabelAddCells(dm,label);CHKERRQ(ierr); 1041 ierr = DMPlexInsertBoundaryValuesEssentialField(dm, time, locX, field, Nc, comps, label, numids, ids, func, ctx, locX);CHKERRQ(ierr); 1042 ierr = DMPlexLabelClearCells(dm,label);CHKERRQ(ierr); 1043 } 1044 break; 1045 default: break; 1046 } 1047 } else if (id == PETSCFV_CLASSID) { 1048 { 1049 PetscErrorCode (*func)(PetscReal,const PetscReal*,const PetscReal*,const PetscScalar*,PetscScalar*,void*) = (PetscErrorCode (*)(PetscReal,const PetscReal*,const PetscReal*,const PetscScalar*,PetscScalar*,void*)) bvfunc; 1050 1051 if (!faceGeomFVM) continue; 1052 ierr = DMPlexInsertBoundaryValuesRiemann(dm, time, faceGeomFVM, cellGeomFVM, gradFVM, field, Nc, comps, label, numids, ids, func, ctx, locX);CHKERRQ(ierr); 1053 } 1054 } else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field); 1055 } 1056 PetscFunctionReturn(0); 1057 } 1058 1059 PetscErrorCode DMPlexInsertTimeDerivativeBoundaryValues_Plex(DM dm, PetscBool insertEssential, Vec locX, PetscReal time, Vec faceGeomFVM, Vec cellGeomFVM, Vec gradFVM) 1060 { 1061 PetscObject isZero; 1062 PetscDS prob; 1063 PetscInt numBd, b; 1064 PetscErrorCode ierr; 1065 1066 PetscFunctionBegin; 1067 if (!locX) PetscFunctionReturn(0); 1068 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1069 ierr = PetscDSGetNumBoundary(prob, &numBd);CHKERRQ(ierr); 1070 ierr = PetscObjectQuery((PetscObject) locX, "__Vec_bc_zero__", &isZero);CHKERRQ(ierr); 1071 for (b = 0; b < numBd; ++b) { 1072 PetscWeakForm wf; 1073 DMBoundaryConditionType type; 1074 const char *name; 1075 DMLabel label; 1076 PetscInt field, Nc; 1077 const PetscInt *comps; 1078 PetscObject obj; 1079 PetscClassId id; 1080 PetscInt numids; 1081 const PetscInt *ids; 1082 void (*bvfunc)(void); 1083 void *ctx; 1084 1085 ierr = PetscDSGetBoundary(prob, b, &wf, &type, &name, &label, &numids, &ids, &field, &Nc, &comps, NULL, &bvfunc, &ctx);CHKERRQ(ierr); 1086 if (insertEssential != (type & DM_BC_ESSENTIAL)) continue; 1087 ierr = DMGetField(dm, field, NULL, &obj);CHKERRQ(ierr); 1088 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1089 if (id == PETSCFE_CLASSID) { 1090 switch (type) { 1091 /* for FEM, there is no insertion to be done for non-essential boundary conditions */ 1092 case DM_BC_ESSENTIAL: 1093 { 1094 PetscSimplePointFunc func_t = (PetscSimplePointFunc) bvfunc; 1095 1096 if (isZero) func_t = zero; 1097 ierr = DMPlexLabelAddCells(dm,label);CHKERRQ(ierr); 1098 ierr = DMPlexInsertBoundaryValuesEssential(dm, time, field, Nc, comps, label, numids, ids, func_t, ctx, locX);CHKERRQ(ierr); 1099 ierr = DMPlexLabelClearCells(dm,label);CHKERRQ(ierr); 1100 } 1101 break; 1102 case DM_BC_ESSENTIAL_FIELD: 1103 { 1104 PetscPointFunc func_t = (PetscPointFunc) bvfunc; 1105 1106 ierr = DMPlexLabelAddCells(dm,label);CHKERRQ(ierr); 1107 ierr = DMPlexInsertBoundaryValuesEssentialField(dm, time, locX, field, Nc, comps, label, numids, ids, func_t, ctx, locX);CHKERRQ(ierr); 1108 ierr = DMPlexLabelClearCells(dm,label);CHKERRQ(ierr); 1109 } 1110 break; 1111 default: break; 1112 } 1113 } else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field); 1114 } 1115 PetscFunctionReturn(0); 1116 } 1117 1118 /*@ 1119 DMPlexInsertBoundaryValues - Puts coefficients which represent boundary values into the local solution vector 1120 1121 Input Parameters: 1122 + dm - The DM 1123 . insertEssential - Should I insert essential (e.g. Dirichlet) or inessential (e.g. Neumann) boundary conditions 1124 . time - The time 1125 . faceGeomFVM - Face geometry data for FV discretizations 1126 . cellGeomFVM - Cell geometry data for FV discretizations 1127 - gradFVM - Gradient reconstruction data for FV discretizations 1128 1129 Output Parameters: 1130 . locX - Solution updated with boundary values 1131 1132 Level: developer 1133 1134 .seealso: DMProjectFunctionLabelLocal() 1135 @*/ 1136 PetscErrorCode DMPlexInsertBoundaryValues(DM dm, PetscBool insertEssential, Vec locX, PetscReal time, Vec faceGeomFVM, Vec cellGeomFVM, Vec gradFVM) 1137 { 1138 PetscErrorCode ierr; 1139 1140 PetscFunctionBegin; 1141 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1142 PetscValidHeaderSpecific(locX, VEC_CLASSID, 3); 1143 if (faceGeomFVM) {PetscValidHeaderSpecific(faceGeomFVM, VEC_CLASSID, 5);} 1144 if (cellGeomFVM) {PetscValidHeaderSpecific(cellGeomFVM, VEC_CLASSID, 6);} 1145 if (gradFVM) {PetscValidHeaderSpecific(gradFVM, VEC_CLASSID, 7);} 1146 ierr = PetscTryMethod(dm,"DMPlexInsertBoundaryValues_C",(DM,PetscBool,Vec,PetscReal,Vec,Vec,Vec),(dm,insertEssential,locX,time,faceGeomFVM,cellGeomFVM,gradFVM));CHKERRQ(ierr); 1147 PetscFunctionReturn(0); 1148 } 1149 1150 /*@ 1151 DMPlexInsertTimeDerivativeBoundaryValues - Puts coefficients which represent boundary values of the time derviative into the local solution vector 1152 1153 Input Parameters: 1154 + dm - The DM 1155 . insertEssential - Should I insert essential (e.g. Dirichlet) or inessential (e.g. Neumann) boundary conditions 1156 . time - The time 1157 . faceGeomFVM - Face geometry data for FV discretizations 1158 . cellGeomFVM - Cell geometry data for FV discretizations 1159 - gradFVM - Gradient reconstruction data for FV discretizations 1160 1161 Output Parameters: 1162 . locX_t - Solution updated with boundary values 1163 1164 Level: developer 1165 1166 .seealso: DMProjectFunctionLabelLocal() 1167 @*/ 1168 PetscErrorCode DMPlexInsertTimeDerivativeBoundaryValues(DM dm, PetscBool insertEssential, Vec locX_t, PetscReal time, Vec faceGeomFVM, Vec cellGeomFVM, Vec gradFVM) 1169 { 1170 PetscErrorCode ierr; 1171 1172 PetscFunctionBegin; 1173 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1174 if (locX_t) {PetscValidHeaderSpecific(locX_t, VEC_CLASSID, 3);} 1175 if (faceGeomFVM) {PetscValidHeaderSpecific(faceGeomFVM, VEC_CLASSID, 5);} 1176 if (cellGeomFVM) {PetscValidHeaderSpecific(cellGeomFVM, VEC_CLASSID, 6);} 1177 if (gradFVM) {PetscValidHeaderSpecific(gradFVM, VEC_CLASSID, 7);} 1178 ierr = PetscTryMethod(dm,"DMPlexInsertTimeDerviativeBoundaryValues_C",(DM,PetscBool,Vec,PetscReal,Vec,Vec,Vec),(dm,insertEssential,locX_t,time,faceGeomFVM,cellGeomFVM,gradFVM));CHKERRQ(ierr); 1179 PetscFunctionReturn(0); 1180 } 1181 1182 PetscErrorCode DMComputeL2Diff_Plex(DM dm, PetscReal time, PetscErrorCode (**funcs)(PetscInt, PetscReal, const PetscReal [], PetscInt, PetscScalar *, void *), void **ctxs, Vec X, PetscReal *diff) 1183 { 1184 Vec localX; 1185 PetscErrorCode ierr; 1186 1187 PetscFunctionBegin; 1188 ierr = DMGetLocalVector(dm, &localX);CHKERRQ(ierr); 1189 ierr = DMPlexInsertBoundaryValues(dm, PETSC_TRUE, localX, time, NULL, NULL, NULL);CHKERRQ(ierr); 1190 ierr = DMGlobalToLocalBegin(dm, X, INSERT_VALUES, localX);CHKERRQ(ierr); 1191 ierr = DMGlobalToLocalEnd(dm, X, INSERT_VALUES, localX);CHKERRQ(ierr); 1192 ierr = DMPlexComputeL2DiffLocal(dm, time, funcs, ctxs, localX, diff);CHKERRQ(ierr); 1193 ierr = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr); 1194 PetscFunctionReturn(0); 1195 } 1196 1197 /*@C 1198 DMComputeL2DiffLocal - This function computes the L_2 difference between a function u and an FEM interpolant solution u_h. 1199 1200 Collective on dm 1201 1202 Input Parameters: 1203 + dm - The DM 1204 . time - The time 1205 . funcs - The functions to evaluate for each field component 1206 . ctxs - Optional array of contexts to pass to each function, or NULL. 1207 - localX - The coefficient vector u_h, a local vector 1208 1209 Output Parameter: 1210 . diff - The diff ||u - u_h||_2 1211 1212 Level: developer 1213 1214 .seealso: DMProjectFunction(), DMComputeL2FieldDiff(), DMComputeL2GradientDiff() 1215 @*/ 1216 PetscErrorCode DMPlexComputeL2DiffLocal(DM dm, PetscReal time, PetscErrorCode (**funcs)(PetscInt, PetscReal, const PetscReal [], PetscInt, PetscScalar *, void *), void **ctxs, Vec localX, PetscReal *diff) 1217 { 1218 const PetscInt debug = ((DM_Plex*)dm->data)->printL2; 1219 DM tdm; 1220 Vec tv; 1221 PetscSection section; 1222 PetscQuadrature quad; 1223 PetscFEGeom fegeom; 1224 PetscScalar *funcVal, *interpolant; 1225 PetscReal *coords, *gcoords; 1226 PetscReal localDiff = 0.0; 1227 const PetscReal *quadWeights; 1228 PetscInt dim, coordDim, numFields, numComponents = 0, qNc, Nq, cellHeight, cStart, cEnd, c, field, fieldOffset; 1229 PetscBool transform; 1230 PetscErrorCode ierr; 1231 1232 PetscFunctionBegin; 1233 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1234 ierr = DMGetCoordinateDim(dm, &coordDim);CHKERRQ(ierr); 1235 fegeom.dimEmbed = coordDim; 1236 ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); 1237 ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); 1238 ierr = DMGetBasisTransformDM_Internal(dm, &tdm);CHKERRQ(ierr); 1239 ierr = DMGetBasisTransformVec_Internal(dm, &tv);CHKERRQ(ierr); 1240 ierr = DMHasBasisTransform(dm, &transform);CHKERRQ(ierr); 1241 for (field = 0; field < numFields; ++field) { 1242 PetscObject obj; 1243 PetscClassId id; 1244 PetscInt Nc; 1245 1246 ierr = DMGetField(dm, field, NULL, &obj);CHKERRQ(ierr); 1247 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1248 if (id == PETSCFE_CLASSID) { 1249 PetscFE fe = (PetscFE) obj; 1250 1251 ierr = PetscFEGetQuadrature(fe, &quad);CHKERRQ(ierr); 1252 ierr = PetscFEGetNumComponents(fe, &Nc);CHKERRQ(ierr); 1253 } else if (id == PETSCFV_CLASSID) { 1254 PetscFV fv = (PetscFV) obj; 1255 1256 ierr = PetscFVGetQuadrature(fv, &quad);CHKERRQ(ierr); 1257 ierr = PetscFVGetNumComponents(fv, &Nc);CHKERRQ(ierr); 1258 } else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field); 1259 numComponents += Nc; 1260 } 1261 ierr = PetscQuadratureGetData(quad, NULL, &qNc, &Nq, NULL, &quadWeights);CHKERRQ(ierr); 1262 if ((qNc != 1) && (qNc != numComponents)) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_SIZ, "Quadrature components %D != %D field components", qNc, numComponents); 1263 ierr = PetscMalloc6(numComponents,&funcVal,numComponents,&interpolant,coordDim*Nq,&coords,Nq,&fegeom.detJ,coordDim*coordDim*Nq,&fegeom.J,coordDim*coordDim*Nq,&fegeom.invJ);CHKERRQ(ierr); 1264 ierr = DMPlexGetVTKCellHeight(dm, &cellHeight);CHKERRQ(ierr); 1265 ierr = DMPlexGetSimplexOrBoxCells(dm, cellHeight, &cStart, &cEnd);CHKERRQ(ierr); 1266 for (c = cStart; c < cEnd; ++c) { 1267 PetscScalar *x = NULL; 1268 PetscReal elemDiff = 0.0; 1269 PetscInt qc = 0; 1270 1271 ierr = DMPlexComputeCellGeometryFEM(dm, c, quad, coords, fegeom.J, fegeom.invJ, fegeom.detJ);CHKERRQ(ierr); 1272 ierr = DMPlexVecGetClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr); 1273 1274 for (field = 0, fieldOffset = 0; field < numFields; ++field) { 1275 PetscObject obj; 1276 PetscClassId id; 1277 void * const ctx = ctxs ? ctxs[field] : NULL; 1278 PetscInt Nb, Nc, q, fc; 1279 1280 ierr = DMGetField(dm, field, NULL, &obj);CHKERRQ(ierr); 1281 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1282 if (id == PETSCFE_CLASSID) {ierr = PetscFEGetNumComponents((PetscFE) obj, &Nc);CHKERRQ(ierr);ierr = PetscFEGetDimension((PetscFE) obj, &Nb);CHKERRQ(ierr);} 1283 else if (id == PETSCFV_CLASSID) {ierr = PetscFVGetNumComponents((PetscFV) obj, &Nc);CHKERRQ(ierr);Nb = 1;} 1284 else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field); 1285 if (debug) { 1286 char title[1024]; 1287 ierr = PetscSNPrintf(title, 1023, "Solution for Field %D", field);CHKERRQ(ierr); 1288 ierr = DMPrintCellVector(c, title, Nb, &x[fieldOffset]);CHKERRQ(ierr); 1289 } 1290 for (q = 0; q < Nq; ++q) { 1291 PetscFEGeom qgeom; 1292 1293 qgeom.dimEmbed = fegeom.dimEmbed; 1294 qgeom.J = &fegeom.J[q*coordDim*coordDim]; 1295 qgeom.invJ = &fegeom.invJ[q*coordDim*coordDim]; 1296 qgeom.detJ = &fegeom.detJ[q]; 1297 if (fegeom.detJ[q] <= 0.0) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %D, point %D", (double)fegeom.detJ[q], c, q); 1298 if (transform) { 1299 gcoords = &coords[coordDim*Nq]; 1300 ierr = DMPlexBasisTransformApplyReal_Internal(dm, &coords[coordDim*q], PETSC_TRUE, coordDim, &coords[coordDim*q], gcoords, dm->transformCtx);CHKERRQ(ierr); 1301 } else { 1302 gcoords = &coords[coordDim*q]; 1303 } 1304 ierr = (*funcs[field])(coordDim, time, gcoords, Nc, funcVal, ctx); 1305 if (ierr) { 1306 PetscErrorCode ierr2; 1307 ierr2 = DMPlexVecRestoreClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr2); 1308 ierr2 = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr2); 1309 ierr2 = PetscFree6(funcVal,interpolant,coords,fegeom.detJ,fegeom.J,fegeom.invJ);CHKERRQ(ierr2); 1310 CHKERRQ(ierr); 1311 } 1312 if (transform) {ierr = DMPlexBasisTransformApply_Internal(dm, &coords[coordDim*q], PETSC_FALSE, Nc, funcVal, funcVal, dm->transformCtx);CHKERRQ(ierr);} 1313 if (id == PETSCFE_CLASSID) {ierr = PetscFEInterpolate_Static((PetscFE) obj, &x[fieldOffset], &qgeom, q, interpolant);CHKERRQ(ierr);} 1314 else if (id == PETSCFV_CLASSID) {ierr = PetscFVInterpolate_Static((PetscFV) obj, &x[fieldOffset], q, interpolant);CHKERRQ(ierr);} 1315 else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field); 1316 for (fc = 0; fc < Nc; ++fc) { 1317 const PetscReal wt = quadWeights[q*qNc+(qNc == 1 ? 0 : qc+fc)]; 1318 if (debug) {ierr = PetscPrintf(PETSC_COMM_SELF, " elem %D field %D,%D point %g %g %g diff %g\n", c, field, fc, (double)(coordDim > 0 ? coords[coordDim*q] : 0.), (double)(coordDim > 1 ? coords[coordDim*q+1] : 0.),(double)(coordDim > 2 ? coords[coordDim*q+2] : 0.), (double)(PetscSqr(PetscRealPart(interpolant[fc] - funcVal[fc]))*wt*fegeom.detJ[q]));CHKERRQ(ierr);} 1319 elemDiff += PetscSqr(PetscRealPart(interpolant[fc] - funcVal[fc]))*wt*fegeom.detJ[q]; 1320 } 1321 } 1322 fieldOffset += Nb; 1323 qc += Nc; 1324 } 1325 ierr = DMPlexVecRestoreClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr); 1326 if (debug) {ierr = PetscPrintf(PETSC_COMM_SELF, " elem %D diff %g\n", c, (double)elemDiff);CHKERRQ(ierr);} 1327 localDiff += elemDiff; 1328 } 1329 ierr = PetscFree6(funcVal,interpolant,coords,fegeom.detJ,fegeom.J,fegeom.invJ);CHKERRQ(ierr); 1330 ierr = MPIU_Allreduce(&localDiff, diff, 1, MPIU_REAL, MPIU_SUM, PetscObjectComm((PetscObject)dm));CHKERRMPI(ierr); 1331 *diff = PetscSqrtReal(*diff); 1332 PetscFunctionReturn(0); 1333 } 1334 1335 PetscErrorCode DMComputeL2GradientDiff_Plex(DM dm, PetscReal time, PetscErrorCode (**funcs)(PetscInt, PetscReal, const PetscReal [], const PetscReal [], PetscInt, PetscScalar *, void *), void **ctxs, Vec X, const PetscReal n[], PetscReal *diff) 1336 { 1337 const PetscInt debug = ((DM_Plex*)dm->data)->printL2; 1338 DM tdm; 1339 PetscSection section; 1340 PetscQuadrature quad; 1341 Vec localX, tv; 1342 PetscScalar *funcVal, *interpolant; 1343 const PetscReal *quadWeights; 1344 PetscFEGeom fegeom; 1345 PetscReal *coords, *gcoords; 1346 PetscReal localDiff = 0.0; 1347 PetscInt dim, coordDim, qNc = 0, Nq = 0, numFields, numComponents = 0, cStart, cEnd, c, field, fieldOffset; 1348 PetscBool transform; 1349 PetscErrorCode ierr; 1350 1351 PetscFunctionBegin; 1352 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1353 ierr = DMGetCoordinateDim(dm, &coordDim);CHKERRQ(ierr); 1354 fegeom.dimEmbed = coordDim; 1355 ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); 1356 ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); 1357 ierr = DMGetLocalVector(dm, &localX);CHKERRQ(ierr); 1358 ierr = DMGlobalToLocalBegin(dm, X, INSERT_VALUES, localX);CHKERRQ(ierr); 1359 ierr = DMGlobalToLocalEnd(dm, X, INSERT_VALUES, localX);CHKERRQ(ierr); 1360 ierr = DMGetBasisTransformDM_Internal(dm, &tdm);CHKERRQ(ierr); 1361 ierr = DMGetBasisTransformVec_Internal(dm, &tv);CHKERRQ(ierr); 1362 ierr = DMHasBasisTransform(dm, &transform);CHKERRQ(ierr); 1363 for (field = 0; field < numFields; ++field) { 1364 PetscFE fe; 1365 PetscInt Nc; 1366 1367 ierr = DMGetField(dm, field, NULL, (PetscObject *) &fe);CHKERRQ(ierr); 1368 ierr = PetscFEGetQuadrature(fe, &quad);CHKERRQ(ierr); 1369 ierr = PetscFEGetNumComponents(fe, &Nc);CHKERRQ(ierr); 1370 numComponents += Nc; 1371 } 1372 ierr = PetscQuadratureGetData(quad, NULL, &qNc, &Nq, NULL, &quadWeights);CHKERRQ(ierr); 1373 if ((qNc != 1) && (qNc != numComponents)) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_SIZ, "Quadrature components %D != %D field components", qNc, numComponents); 1374 /* ierr = DMProjectFunctionLocal(dm, fe, funcs, INSERT_BC_VALUES, localX);CHKERRQ(ierr); */ 1375 ierr = PetscMalloc6(numComponents,&funcVal,coordDim*Nq,&coords,coordDim*coordDim*Nq,&fegeom.J,coordDim*coordDim*Nq,&fegeom.invJ,numComponents*coordDim,&interpolant,Nq,&fegeom.detJ);CHKERRQ(ierr); 1376 ierr = DMPlexGetSimplexOrBoxCells(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1377 for (c = cStart; c < cEnd; ++c) { 1378 PetscScalar *x = NULL; 1379 PetscReal elemDiff = 0.0; 1380 PetscInt qc = 0; 1381 1382 ierr = DMPlexComputeCellGeometryFEM(dm, c, quad, coords, fegeom.J, fegeom.invJ, fegeom.detJ);CHKERRQ(ierr); 1383 ierr = DMPlexVecGetClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr); 1384 1385 for (field = 0, fieldOffset = 0; field < numFields; ++field) { 1386 PetscFE fe; 1387 void * const ctx = ctxs ? ctxs[field] : NULL; 1388 PetscInt Nb, Nc, q, fc; 1389 1390 ierr = DMGetField(dm, field, NULL, (PetscObject *) &fe);CHKERRQ(ierr); 1391 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 1392 ierr = PetscFEGetNumComponents(fe, &Nc);CHKERRQ(ierr); 1393 if (debug) { 1394 char title[1024]; 1395 ierr = PetscSNPrintf(title, 1023, "Solution for Field %D", field);CHKERRQ(ierr); 1396 ierr = DMPrintCellVector(c, title, Nb, &x[fieldOffset]);CHKERRQ(ierr); 1397 } 1398 for (q = 0; q < Nq; ++q) { 1399 PetscFEGeom qgeom; 1400 1401 qgeom.dimEmbed = fegeom.dimEmbed; 1402 qgeom.J = &fegeom.J[q*coordDim*coordDim]; 1403 qgeom.invJ = &fegeom.invJ[q*coordDim*coordDim]; 1404 qgeom.detJ = &fegeom.detJ[q]; 1405 if (fegeom.detJ[q] <= 0.0) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %D, quadrature points %D", (double)fegeom.detJ[q], c, q); 1406 if (transform) { 1407 gcoords = &coords[coordDim*Nq]; 1408 ierr = DMPlexBasisTransformApplyReal_Internal(dm, &coords[coordDim*q], PETSC_TRUE, coordDim, &coords[coordDim*q], gcoords, dm->transformCtx);CHKERRQ(ierr); 1409 } else { 1410 gcoords = &coords[coordDim*q]; 1411 } 1412 ierr = (*funcs[field])(coordDim, time, gcoords, n, Nc, funcVal, ctx); 1413 if (ierr) { 1414 PetscErrorCode ierr2; 1415 ierr2 = DMPlexVecRestoreClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr2); 1416 ierr2 = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr2); 1417 ierr2 = PetscFree6(funcVal,coords,fegeom.J,fegeom.invJ,interpolant,fegeom.detJ);CHKERRQ(ierr2); 1418 CHKERRQ(ierr); 1419 } 1420 if (transform) {ierr = DMPlexBasisTransformApply_Internal(dm, &coords[coordDim*q], PETSC_FALSE, Nc, funcVal, funcVal, dm->transformCtx);CHKERRQ(ierr);} 1421 ierr = PetscFEInterpolateGradient_Static(fe, 1, &x[fieldOffset], &qgeom, q, interpolant);CHKERRQ(ierr); 1422 /* Overwrite with the dot product if the normal is given */ 1423 if (n) { 1424 for (fc = 0; fc < Nc; ++fc) { 1425 PetscScalar sum = 0.0; 1426 PetscInt d; 1427 for (d = 0; d < dim; ++d) sum += interpolant[fc*dim+d]*n[d]; 1428 interpolant[fc] = sum; 1429 } 1430 } 1431 for (fc = 0; fc < Nc; ++fc) { 1432 const PetscReal wt = quadWeights[q*qNc+(qNc == 1 ? 0 : qc+fc)]; 1433 if (debug) {ierr = PetscPrintf(PETSC_COMM_SELF, " elem %D fieldDer %D,%D diff %g\n", c, field, fc, (double)(PetscSqr(PetscRealPart(interpolant[fc] - funcVal[fc]))*wt*fegeom.detJ[q]));CHKERRQ(ierr);} 1434 elemDiff += PetscSqr(PetscRealPart(interpolant[fc] - funcVal[fc]))*wt*fegeom.detJ[q]; 1435 } 1436 } 1437 fieldOffset += Nb; 1438 qc += Nc; 1439 } 1440 ierr = DMPlexVecRestoreClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr); 1441 if (debug) {ierr = PetscPrintf(PETSC_COMM_SELF, " elem %D diff %g\n", c, (double)elemDiff);CHKERRQ(ierr);} 1442 localDiff += elemDiff; 1443 } 1444 ierr = PetscFree6(funcVal,coords,fegeom.J,fegeom.invJ,interpolant,fegeom.detJ);CHKERRQ(ierr); 1445 ierr = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr); 1446 ierr = MPIU_Allreduce(&localDiff, diff, 1, MPIU_REAL, MPIU_SUM, PetscObjectComm((PetscObject)dm));CHKERRMPI(ierr); 1447 *diff = PetscSqrtReal(*diff); 1448 PetscFunctionReturn(0); 1449 } 1450 1451 PetscErrorCode DMComputeL2FieldDiff_Plex(DM dm, PetscReal time, PetscErrorCode (**funcs)(PetscInt, PetscReal, const PetscReal [], PetscInt, PetscScalar *, void *), void **ctxs, Vec X, PetscReal *diff) 1452 { 1453 const PetscInt debug = ((DM_Plex*)dm->data)->printL2; 1454 DM tdm; 1455 DMLabel depthLabel; 1456 PetscSection section; 1457 Vec localX, tv; 1458 PetscReal *localDiff; 1459 PetscInt dim, depth, dE, Nf, f, Nds, s; 1460 PetscBool transform; 1461 PetscErrorCode ierr; 1462 1463 PetscFunctionBegin; 1464 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1465 ierr = DMGetCoordinateDim(dm, &dE);CHKERRQ(ierr); 1466 ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); 1467 ierr = DMGetLocalVector(dm, &localX);CHKERRQ(ierr); 1468 ierr = DMGetBasisTransformDM_Internal(dm, &tdm);CHKERRQ(ierr); 1469 ierr = DMGetBasisTransformVec_Internal(dm, &tv);CHKERRQ(ierr); 1470 ierr = DMHasBasisTransform(dm, &transform);CHKERRQ(ierr); 1471 ierr = DMGetNumFields(dm, &Nf);CHKERRQ(ierr); 1472 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 1473 ierr = DMLabelGetNumValues(depthLabel, &depth);CHKERRQ(ierr); 1474 1475 ierr = VecSet(localX, 0.0);CHKERRQ(ierr); 1476 ierr = DMGlobalToLocalBegin(dm, X, INSERT_VALUES, localX);CHKERRQ(ierr); 1477 ierr = DMGlobalToLocalEnd(dm, X, INSERT_VALUES, localX);CHKERRQ(ierr); 1478 ierr = DMProjectFunctionLocal(dm, time, funcs, ctxs, INSERT_BC_VALUES, localX);CHKERRQ(ierr); 1479 ierr = DMGetNumDS(dm, &Nds);CHKERRQ(ierr); 1480 ierr = PetscCalloc1(Nf, &localDiff);CHKERRQ(ierr); 1481 for (s = 0; s < Nds; ++s) { 1482 PetscDS ds; 1483 DMLabel label; 1484 IS fieldIS, pointIS; 1485 const PetscInt *fields, *points = NULL; 1486 PetscQuadrature quad; 1487 const PetscReal *quadPoints, *quadWeights; 1488 PetscFEGeom fegeom; 1489 PetscReal *coords, *gcoords; 1490 PetscScalar *funcVal, *interpolant; 1491 PetscBool isHybrid; 1492 PetscInt qNc, Nq, totNc, cStart = 0, cEnd, c, dsNf; 1493 1494 ierr = DMGetRegionNumDS(dm, s, &label, &fieldIS, &ds);CHKERRQ(ierr); 1495 ierr = ISGetIndices(fieldIS, &fields);CHKERRQ(ierr); 1496 ierr = PetscDSGetHybrid(ds, &isHybrid);CHKERRQ(ierr); 1497 ierr = PetscDSGetNumFields(ds, &dsNf);CHKERRQ(ierr); 1498 ierr = PetscDSGetTotalComponents(ds, &totNc);CHKERRQ(ierr); 1499 ierr = PetscDSGetQuadrature(ds, &quad);CHKERRQ(ierr); 1500 ierr = PetscQuadratureGetData(quad, NULL, &qNc, &Nq, &quadPoints, &quadWeights);CHKERRQ(ierr); 1501 if ((qNc != 1) && (qNc != totNc)) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Quadrature components %D != %D field components", qNc, totNc); 1502 ierr = PetscCalloc6(totNc, &funcVal, totNc, &interpolant, dE*(Nq+1), &coords,Nq, &fegeom.detJ, dE*dE*Nq, &fegeom.J, dE*dE*Nq, &fegeom.invJ);CHKERRQ(ierr); 1503 if (!label) { 1504 ierr = DMPlexGetSimplexOrBoxCells(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1505 } else { 1506 ierr = DMLabelGetStratumIS(label, 1, &pointIS);CHKERRQ(ierr); 1507 ierr = ISGetLocalSize(pointIS, &cEnd);CHKERRQ(ierr); 1508 ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); 1509 } 1510 for (c = cStart; c < cEnd; ++c) { 1511 const PetscInt cell = points ? points[c] : c; 1512 PetscScalar *x = NULL; 1513 PetscInt qc = 0, fOff = 0, dep, fStart = isHybrid ? dsNf-1 : 0; 1514 1515 ierr = DMLabelGetValue(depthLabel, cell, &dep);CHKERRQ(ierr); 1516 if (dep != depth-1) continue; 1517 if (isHybrid) { 1518 const PetscInt *cone; 1519 1520 ierr = DMPlexGetCone(dm, cell, &cone);CHKERRQ(ierr); 1521 ierr = DMPlexComputeCellGeometryFEM(dm, cone[0], quad, coords, fegeom.J, fegeom.invJ, fegeom.detJ);CHKERRQ(ierr); 1522 } else { 1523 ierr = DMPlexComputeCellGeometryFEM(dm, cell, quad, coords, fegeom.J, fegeom.invJ, fegeom.detJ);CHKERRQ(ierr); 1524 } 1525 ierr = DMPlexVecGetClosure(dm, NULL, localX, cell, NULL, &x);CHKERRQ(ierr); 1526 for (f = fStart; f < dsNf; ++f) { 1527 PetscObject obj; 1528 PetscClassId id; 1529 void * const ctx = ctxs ? ctxs[fields[f]] : NULL; 1530 PetscInt Nb, Nc, q, fc; 1531 PetscReal elemDiff = 0.0; 1532 1533 ierr = PetscDSGetDiscretization(ds, f, &obj);CHKERRQ(ierr); 1534 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1535 if (id == PETSCFE_CLASSID) {ierr = PetscFEGetNumComponents((PetscFE) obj, &Nc);CHKERRQ(ierr);ierr = PetscFEGetDimension((PetscFE) obj, &Nb);CHKERRQ(ierr);} 1536 else if (id == PETSCFV_CLASSID) {ierr = PetscFVGetNumComponents((PetscFV) obj, &Nc);CHKERRQ(ierr);Nb = 1;} 1537 else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", fields[f]); 1538 if (debug) { 1539 char title[1024]; 1540 ierr = PetscSNPrintf(title, 1023, "Solution for Field %D", fields[f]);CHKERRQ(ierr); 1541 ierr = DMPrintCellVector(cell, title, Nb, &x[fOff]);CHKERRQ(ierr); 1542 } 1543 for (q = 0; q < Nq; ++q) { 1544 PetscFEGeom qgeom; 1545 1546 qgeom.dimEmbed = fegeom.dimEmbed; 1547 qgeom.J = &fegeom.J[q*dE*dE]; 1548 qgeom.invJ = &fegeom.invJ[q*dE*dE]; 1549 qgeom.detJ = &fegeom.detJ[q]; 1550 if (fegeom.detJ[q] <= 0.0) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for cell %D, quadrature point %D", (double)fegeom.detJ[q], cell, q); 1551 if (transform) { 1552 gcoords = &coords[dE*Nq]; 1553 ierr = DMPlexBasisTransformApplyReal_Internal(dm, &coords[dE*q], PETSC_TRUE, dE, &coords[dE*q], gcoords, dm->transformCtx);CHKERRQ(ierr); 1554 } else { 1555 gcoords = &coords[dE*q]; 1556 } 1557 ierr = (*funcs[fields[f]])(dE, time, gcoords, Nc, funcVal, ctx); 1558 if (ierr) { 1559 PetscErrorCode ierr2; 1560 ierr2 = DMPlexVecRestoreClosure(dm, NULL, localX, cell, NULL, &x);CHKERRQ(ierr2); 1561 ierr2 = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr2); 1562 ierr2 = PetscFree6(funcVal,interpolant,coords,fegeom.detJ,fegeom.J,fegeom.invJ);CHKERRQ(ierr2); 1563 CHKERRQ(ierr); 1564 } 1565 if (transform) {ierr = DMPlexBasisTransformApply_Internal(dm, &coords[dE*q], PETSC_FALSE, Nc, funcVal, funcVal, dm->transformCtx);CHKERRQ(ierr);} 1566 /* Call once for each face, except for lagrange field */ 1567 if (id == PETSCFE_CLASSID) {ierr = PetscFEInterpolate_Static((PetscFE) obj, &x[fOff], &qgeom, q, interpolant);CHKERRQ(ierr);} 1568 else if (id == PETSCFV_CLASSID) {ierr = PetscFVInterpolate_Static((PetscFV) obj, &x[fOff], q, interpolant);CHKERRQ(ierr);} 1569 else SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", fields[f]); 1570 for (fc = 0; fc < Nc; ++fc) { 1571 const PetscReal wt = quadWeights[q*qNc+(qNc == 1 ? 0 : qc+fc)]; 1572 if (debug) {ierr = PetscPrintf(PETSC_COMM_SELF, " cell %D field %D,%D point %g %g %g diff %g\n", cell, fields[f], fc, (double)(dE > 0 ? coords[dE*q] : 0.), (double)(dE > 1 ? coords[dE*q+1] : 0.),(double)(dE > 2 ? coords[dE*q+2] : 0.), (double)(PetscSqr(PetscRealPart(interpolant[fc] - funcVal[fc]))*wt*fegeom.detJ[q]));CHKERRQ(ierr);} 1573 elemDiff += PetscSqr(PetscRealPart(interpolant[fc] - funcVal[fc]))*wt*fegeom.detJ[q]; 1574 } 1575 } 1576 fOff += Nb; 1577 qc += Nc; 1578 localDiff[fields[f]] += elemDiff; 1579 if (debug) {ierr = PetscPrintf(PETSC_COMM_SELF, " cell %D field %D cum diff %g\n", cell, fields[f], (double)localDiff[fields[f]]);CHKERRQ(ierr);} 1580 } 1581 ierr = DMPlexVecRestoreClosure(dm, NULL, localX, cell, NULL, &x);CHKERRQ(ierr); 1582 } 1583 if (label) { 1584 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 1585 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 1586 } 1587 ierr = ISRestoreIndices(fieldIS, &fields);CHKERRQ(ierr); 1588 ierr = PetscFree6(funcVal, interpolant, coords, fegeom.detJ, fegeom.J, fegeom.invJ);CHKERRQ(ierr); 1589 } 1590 ierr = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr); 1591 ierr = MPIU_Allreduce(localDiff, diff, Nf, MPIU_REAL, MPIU_SUM, PetscObjectComm((PetscObject)dm));CHKERRMPI(ierr); 1592 ierr = PetscFree(localDiff);CHKERRQ(ierr); 1593 for (f = 0; f < Nf; ++f) diff[f] = PetscSqrtReal(diff[f]); 1594 PetscFunctionReturn(0); 1595 } 1596 1597 /*@C 1598 DMPlexComputeL2DiffVec - This function computes the cellwise L_2 difference between a function u and an FEM interpolant solution u_h, and stores it in a Vec. 1599 1600 Collective on dm 1601 1602 Input Parameters: 1603 + dm - The DM 1604 . time - The time 1605 . funcs - The functions to evaluate for each field component: NULL means that component does not contribute to error calculation 1606 . ctxs - Optional array of contexts to pass to each function, or NULL. 1607 - X - The coefficient vector u_h 1608 1609 Output Parameter: 1610 . D - A Vec which holds the difference ||u - u_h||_2 for each cell 1611 1612 Level: developer 1613 1614 .seealso: DMProjectFunction(), DMComputeL2Diff(), DMPlexComputeL2FieldDiff(), DMComputeL2GradientDiff() 1615 @*/ 1616 PetscErrorCode DMPlexComputeL2DiffVec(DM dm, PetscReal time, PetscErrorCode (**funcs)(PetscInt, PetscReal, const PetscReal [], PetscInt, PetscScalar *, void *), void **ctxs, Vec X, Vec D) 1617 { 1618 PetscSection section; 1619 PetscQuadrature quad; 1620 Vec localX; 1621 PetscFEGeom fegeom; 1622 PetscScalar *funcVal, *interpolant; 1623 PetscReal *coords; 1624 const PetscReal *quadPoints, *quadWeights; 1625 PetscInt dim, coordDim, numFields, numComponents = 0, qNc, Nq, cStart, cEnd, c, field, fieldOffset; 1626 PetscErrorCode ierr; 1627 1628 PetscFunctionBegin; 1629 ierr = VecSet(D, 0.0);CHKERRQ(ierr); 1630 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1631 ierr = DMGetCoordinateDim(dm, &coordDim);CHKERRQ(ierr); 1632 ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); 1633 ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); 1634 ierr = DMGetLocalVector(dm, &localX);CHKERRQ(ierr); 1635 ierr = DMProjectFunctionLocal(dm, time, funcs, ctxs, INSERT_BC_VALUES, localX);CHKERRQ(ierr); 1636 ierr = DMGlobalToLocalBegin(dm, X, INSERT_VALUES, localX);CHKERRQ(ierr); 1637 ierr = DMGlobalToLocalEnd(dm, X, INSERT_VALUES, localX);CHKERRQ(ierr); 1638 for (field = 0; field < numFields; ++field) { 1639 PetscObject obj; 1640 PetscClassId id; 1641 PetscInt Nc; 1642 1643 ierr = DMGetField(dm, field, NULL, &obj);CHKERRQ(ierr); 1644 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1645 if (id == PETSCFE_CLASSID) { 1646 PetscFE fe = (PetscFE) obj; 1647 1648 ierr = PetscFEGetQuadrature(fe, &quad);CHKERRQ(ierr); 1649 ierr = PetscFEGetNumComponents(fe, &Nc);CHKERRQ(ierr); 1650 } else if (id == PETSCFV_CLASSID) { 1651 PetscFV fv = (PetscFV) obj; 1652 1653 ierr = PetscFVGetQuadrature(fv, &quad);CHKERRQ(ierr); 1654 ierr = PetscFVGetNumComponents(fv, &Nc);CHKERRQ(ierr); 1655 } else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field); 1656 numComponents += Nc; 1657 } 1658 ierr = PetscQuadratureGetData(quad, NULL, &qNc, &Nq, &quadPoints, &quadWeights);CHKERRQ(ierr); 1659 if ((qNc != 1) && (qNc != numComponents)) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_SIZ, "Quadrature components %D != %D field components", qNc, numComponents); 1660 ierr = PetscMalloc6(numComponents,&funcVal,numComponents,&interpolant,coordDim*Nq,&coords,Nq,&fegeom.detJ,coordDim*coordDim*Nq,&fegeom.J,coordDim*coordDim*Nq,&fegeom.invJ);CHKERRQ(ierr); 1661 ierr = DMPlexGetSimplexOrBoxCells(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1662 for (c = cStart; c < cEnd; ++c) { 1663 PetscScalar *x = NULL; 1664 PetscScalar elemDiff = 0.0; 1665 PetscInt qc = 0; 1666 1667 ierr = DMPlexComputeCellGeometryFEM(dm, c, quad, coords, fegeom.J, fegeom.invJ, fegeom.detJ);CHKERRQ(ierr); 1668 ierr = DMPlexVecGetClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr); 1669 1670 for (field = 0, fieldOffset = 0; field < numFields; ++field) { 1671 PetscObject obj; 1672 PetscClassId id; 1673 void * const ctx = ctxs ? ctxs[field] : NULL; 1674 PetscInt Nb, Nc, q, fc; 1675 1676 ierr = DMGetField(dm, field, NULL, &obj);CHKERRQ(ierr); 1677 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1678 if (id == PETSCFE_CLASSID) {ierr = PetscFEGetNumComponents((PetscFE) obj, &Nc);CHKERRQ(ierr);ierr = PetscFEGetDimension((PetscFE) obj, &Nb);CHKERRQ(ierr);} 1679 else if (id == PETSCFV_CLASSID) {ierr = PetscFVGetNumComponents((PetscFV) obj, &Nc);CHKERRQ(ierr);Nb = 1;} 1680 else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field); 1681 if (funcs[field]) { 1682 for (q = 0; q < Nq; ++q) { 1683 PetscFEGeom qgeom; 1684 1685 qgeom.dimEmbed = fegeom.dimEmbed; 1686 qgeom.J = &fegeom.J[q*coordDim*coordDim]; 1687 qgeom.invJ = &fegeom.invJ[q*coordDim*coordDim]; 1688 qgeom.detJ = &fegeom.detJ[q]; 1689 if (fegeom.detJ[q] <= 0.0) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %D, quadrature points %D", (double)fegeom.detJ[q], c, q); 1690 ierr = (*funcs[field])(coordDim, time, &coords[q*coordDim], Nc, funcVal, ctx); 1691 if (ierr) { 1692 PetscErrorCode ierr2; 1693 ierr2 = DMPlexVecRestoreClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr2); 1694 ierr2 = PetscFree6(funcVal,interpolant,coords,fegeom.detJ,fegeom.J,fegeom.invJ);CHKERRQ(ierr2); 1695 ierr2 = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr2); 1696 CHKERRQ(ierr); 1697 } 1698 if (id == PETSCFE_CLASSID) {ierr = PetscFEInterpolate_Static((PetscFE) obj, &x[fieldOffset], &qgeom, q, interpolant);CHKERRQ(ierr);} 1699 else if (id == PETSCFV_CLASSID) {ierr = PetscFVInterpolate_Static((PetscFV) obj, &x[fieldOffset], q, interpolant);CHKERRQ(ierr);} 1700 else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field); 1701 for (fc = 0; fc < Nc; ++fc) { 1702 const PetscReal wt = quadWeights[q*qNc+(qNc == 1 ? 0 : qc+fc)]; 1703 elemDiff += PetscSqr(PetscRealPart(interpolant[fc] - funcVal[fc]))*wt*fegeom.detJ[q]; 1704 } 1705 } 1706 } 1707 fieldOffset += Nb; 1708 qc += Nc; 1709 } 1710 ierr = DMPlexVecRestoreClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr); 1711 ierr = VecSetValue(D, c - cStart, elemDiff, INSERT_VALUES);CHKERRQ(ierr); 1712 } 1713 ierr = PetscFree6(funcVal,interpolant,coords,fegeom.detJ,fegeom.J,fegeom.invJ);CHKERRQ(ierr); 1714 ierr = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr); 1715 ierr = VecSqrtAbs(D);CHKERRQ(ierr); 1716 PetscFunctionReturn(0); 1717 } 1718 1719 /*@C 1720 DMPlexComputeGradientClementInterpolant - This function computes the L2 projection of the cellwise gradient of a function u onto P1, and stores it in a Vec. 1721 1722 Collective on dm 1723 1724 Input Parameters: 1725 + dm - The DM 1726 - LocX - The coefficient vector u_h 1727 1728 Output Parameter: 1729 . locC - A Vec which holds the Clement interpolant of the gradient 1730 1731 Notes: 1732 Add citation to (Clement, 1975) and definition of the interpolant 1733 \nabla u_h(v_i) = \sum_{T_i \in support(v_i)} |T_i| \nabla u_h(T_i) / \sum_{T_i \in support(v_i)} |T_i| where |T_i| is the cell volume 1734 1735 Level: developer 1736 1737 .seealso: DMProjectFunction(), DMComputeL2Diff(), DMPlexComputeL2FieldDiff(), DMComputeL2GradientDiff() 1738 @*/ 1739 PetscErrorCode DMPlexComputeGradientClementInterpolant(DM dm, Vec locX, Vec locC) 1740 { 1741 DM_Plex *mesh = (DM_Plex *) dm->data; 1742 PetscInt debug = mesh->printFEM; 1743 DM dmC; 1744 PetscSection section; 1745 PetscQuadrature quad; 1746 PetscScalar *interpolant, *gradsum; 1747 PetscFEGeom fegeom; 1748 PetscReal *coords; 1749 const PetscReal *quadPoints, *quadWeights; 1750 PetscInt dim, coordDim, numFields, numComponents = 0, qNc, Nq, cStart, cEnd, vStart, vEnd, v, field, fieldOffset; 1751 PetscErrorCode ierr; 1752 1753 PetscFunctionBegin; 1754 ierr = VecGetDM(locC, &dmC);CHKERRQ(ierr); 1755 ierr = VecSet(locC, 0.0);CHKERRQ(ierr); 1756 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1757 ierr = DMGetCoordinateDim(dm, &coordDim);CHKERRQ(ierr); 1758 fegeom.dimEmbed = coordDim; 1759 ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); 1760 ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); 1761 for (field = 0; field < numFields; ++field) { 1762 PetscObject obj; 1763 PetscClassId id; 1764 PetscInt Nc; 1765 1766 ierr = DMGetField(dm, field, NULL, &obj);CHKERRQ(ierr); 1767 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1768 if (id == PETSCFE_CLASSID) { 1769 PetscFE fe = (PetscFE) obj; 1770 1771 ierr = PetscFEGetQuadrature(fe, &quad);CHKERRQ(ierr); 1772 ierr = PetscFEGetNumComponents(fe, &Nc);CHKERRQ(ierr); 1773 } else if (id == PETSCFV_CLASSID) { 1774 PetscFV fv = (PetscFV) obj; 1775 1776 ierr = PetscFVGetQuadrature(fv, &quad);CHKERRQ(ierr); 1777 ierr = PetscFVGetNumComponents(fv, &Nc);CHKERRQ(ierr); 1778 } else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field); 1779 numComponents += Nc; 1780 } 1781 ierr = PetscQuadratureGetData(quad, NULL, &qNc, &Nq, &quadPoints, &quadWeights);CHKERRQ(ierr); 1782 if ((qNc != 1) && (qNc != numComponents)) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_SIZ, "Quadrature components %D != %D field components", qNc, numComponents); 1783 ierr = PetscMalloc6(coordDim*numComponents*2,&gradsum,coordDim*numComponents,&interpolant,coordDim*Nq,&coords,Nq,&fegeom.detJ,coordDim*coordDim*Nq,&fegeom.J,coordDim*coordDim*Nq,&fegeom.invJ);CHKERRQ(ierr); 1784 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 1785 ierr = DMPlexGetSimplexOrBoxCells(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1786 for (v = vStart; v < vEnd; ++v) { 1787 PetscScalar volsum = 0.0; 1788 PetscInt *star = NULL; 1789 PetscInt starSize, st, d, fc; 1790 1791 ierr = PetscArrayzero(gradsum, coordDim*numComponents);CHKERRQ(ierr); 1792 ierr = DMPlexGetTransitiveClosure(dm, v, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1793 for (st = 0; st < starSize*2; st += 2) { 1794 const PetscInt cell = star[st]; 1795 PetscScalar *grad = &gradsum[coordDim*numComponents]; 1796 PetscScalar *x = NULL; 1797 PetscReal vol = 0.0; 1798 1799 if ((cell < cStart) || (cell >= cEnd)) continue; 1800 ierr = DMPlexComputeCellGeometryFEM(dm, cell, quad, coords, fegeom.J, fegeom.invJ, fegeom.detJ);CHKERRQ(ierr); 1801 ierr = DMPlexVecGetClosure(dm, NULL, locX, cell, NULL, &x);CHKERRQ(ierr); 1802 for (field = 0, fieldOffset = 0; field < numFields; ++field) { 1803 PetscObject obj; 1804 PetscClassId id; 1805 PetscInt Nb, Nc, q, qc = 0; 1806 1807 ierr = PetscArrayzero(grad, coordDim*numComponents);CHKERRQ(ierr); 1808 ierr = DMGetField(dm, field, NULL, &obj);CHKERRQ(ierr); 1809 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1810 if (id == PETSCFE_CLASSID) {ierr = PetscFEGetNumComponents((PetscFE) obj, &Nc);CHKERRQ(ierr);ierr = PetscFEGetDimension((PetscFE) obj, &Nb);CHKERRQ(ierr);} 1811 else if (id == PETSCFV_CLASSID) {ierr = PetscFVGetNumComponents((PetscFV) obj, &Nc);CHKERRQ(ierr);Nb = 1;} 1812 else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field); 1813 for (q = 0; q < Nq; ++q) { 1814 PetscFEGeom qgeom; 1815 1816 qgeom.dimEmbed = fegeom.dimEmbed; 1817 qgeom.J = &fegeom.J[q*coordDim*coordDim]; 1818 qgeom.invJ = &fegeom.invJ[q*coordDim*coordDim]; 1819 qgeom.detJ = &fegeom.detJ[q]; 1820 if (fegeom.detJ[q] <= 0.0) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %D, quadrature points %D", (double)fegeom.detJ[q], cell, q); 1821 if (ierr) { 1822 PetscErrorCode ierr2; 1823 ierr2 = DMPlexVecRestoreClosure(dm, NULL, locX, cell, NULL, &x);CHKERRQ(ierr2); 1824 ierr2 = DMPlexRestoreTransitiveClosure(dm, v, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr2); 1825 ierr2 = PetscFree6(gradsum,interpolant,coords,fegeom.detJ,fegeom.J,fegeom.invJ);CHKERRQ(ierr2); 1826 CHKERRQ(ierr); 1827 } 1828 if (id == PETSCFE_CLASSID) {ierr = PetscFEInterpolateGradient_Static((PetscFE) obj, 1, &x[fieldOffset], &qgeom, q, interpolant);CHKERRQ(ierr);} 1829 else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field); 1830 for (fc = 0; fc < Nc; ++fc) { 1831 const PetscReal wt = quadWeights[q*qNc+qc+fc]; 1832 1833 for (d = 0; d < coordDim; ++d) grad[fc*coordDim+d] += interpolant[fc*dim+d]*wt*fegeom.detJ[q]; 1834 } 1835 vol += quadWeights[q*qNc]*fegeom.detJ[q]; 1836 } 1837 fieldOffset += Nb; 1838 qc += Nc; 1839 } 1840 ierr = DMPlexVecRestoreClosure(dm, NULL, locX, cell, NULL, &x);CHKERRQ(ierr); 1841 for (fc = 0; fc < numComponents; ++fc) { 1842 for (d = 0; d < coordDim; ++d) { 1843 gradsum[fc*coordDim+d] += grad[fc*coordDim+d]; 1844 } 1845 } 1846 volsum += vol; 1847 if (debug) { 1848 ierr = PetscPrintf(PETSC_COMM_SELF, "Cell %D gradient: [", cell);CHKERRQ(ierr); 1849 for (fc = 0; fc < numComponents; ++fc) { 1850 for (d = 0; d < coordDim; ++d) { 1851 if (fc || d > 0) {ierr = PetscPrintf(PETSC_COMM_SELF, ", ");CHKERRQ(ierr);} 1852 ierr = PetscPrintf(PETSC_COMM_SELF, "%g", (double)PetscRealPart(grad[fc*coordDim+d]));CHKERRQ(ierr); 1853 } 1854 } 1855 ierr = PetscPrintf(PETSC_COMM_SELF, "]\n");CHKERRQ(ierr); 1856 } 1857 } 1858 for (fc = 0; fc < numComponents; ++fc) { 1859 for (d = 0; d < coordDim; ++d) gradsum[fc*coordDim+d] /= volsum; 1860 } 1861 ierr = DMPlexRestoreTransitiveClosure(dm, v, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 1862 ierr = DMPlexVecSetClosure(dmC, NULL, locC, v, gradsum, INSERT_VALUES);CHKERRQ(ierr); 1863 } 1864 ierr = PetscFree6(gradsum,interpolant,coords,fegeom.detJ,fegeom.J,fegeom.invJ);CHKERRQ(ierr); 1865 PetscFunctionReturn(0); 1866 } 1867 1868 static PetscErrorCode DMPlexComputeIntegral_Internal(DM dm, Vec X, PetscInt cStart, PetscInt cEnd, PetscScalar *cintegral, void *user) 1869 { 1870 DM dmAux = NULL; 1871 PetscDS prob, probAux = NULL; 1872 PetscSection section, sectionAux; 1873 Vec locX, locA; 1874 PetscInt dim, numCells = cEnd - cStart, c, f; 1875 PetscBool useFVM = PETSC_FALSE; 1876 /* DS */ 1877 PetscInt Nf, totDim, *uOff, *uOff_x, numConstants; 1878 PetscInt NfAux, totDimAux, *aOff; 1879 PetscScalar *u, *a; 1880 const PetscScalar *constants; 1881 /* Geometry */ 1882 PetscFEGeom *cgeomFEM; 1883 DM dmGrad; 1884 PetscQuadrature affineQuad = NULL; 1885 Vec cellGeometryFVM = NULL, faceGeometryFVM = NULL, locGrad = NULL; 1886 PetscFVCellGeom *cgeomFVM; 1887 const PetscScalar *lgrad; 1888 PetscInt maxDegree; 1889 DMField coordField; 1890 IS cellIS; 1891 PetscErrorCode ierr; 1892 1893 PetscFunctionBegin; 1894 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1895 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1896 ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); 1897 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); 1898 /* Determine which discretizations we have */ 1899 for (f = 0; f < Nf; ++f) { 1900 PetscObject obj; 1901 PetscClassId id; 1902 1903 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1904 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1905 if (id == PETSCFV_CLASSID) useFVM = PETSC_TRUE; 1906 } 1907 /* Get local solution with boundary values */ 1908 ierr = DMGetLocalVector(dm, &locX);CHKERRQ(ierr); 1909 ierr = DMPlexInsertBoundaryValues(dm, PETSC_TRUE, locX, 0.0, NULL, NULL, NULL);CHKERRQ(ierr); 1910 ierr = DMGlobalToLocalBegin(dm, X, INSERT_VALUES, locX);CHKERRQ(ierr); 1911 ierr = DMGlobalToLocalEnd(dm, X, INSERT_VALUES, locX);CHKERRQ(ierr); 1912 /* Read DS information */ 1913 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1914 ierr = PetscDSGetComponentOffsets(prob, &uOff);CHKERRQ(ierr); 1915 ierr = PetscDSGetComponentDerivativeOffsets(prob, &uOff_x);CHKERRQ(ierr); 1916 ierr = ISCreateStride(PETSC_COMM_SELF,numCells,cStart,1,&cellIS);CHKERRQ(ierr); 1917 ierr = PetscDSGetConstants(prob, &numConstants, &constants);CHKERRQ(ierr); 1918 /* Read Auxiliary DS information */ 1919 ierr = DMGetAuxiliaryVec(dm, NULL, 0, &locA);CHKERRQ(ierr); 1920 if (locA) { 1921 ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); 1922 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 1923 ierr = PetscDSGetNumFields(probAux, &NfAux);CHKERRQ(ierr); 1924 ierr = DMGetLocalSection(dmAux, §ionAux);CHKERRQ(ierr); 1925 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 1926 ierr = PetscDSGetComponentOffsets(probAux, &aOff);CHKERRQ(ierr); 1927 } 1928 /* Allocate data arrays */ 1929 ierr = PetscCalloc1(numCells*totDim, &u);CHKERRQ(ierr); 1930 if (dmAux) {ierr = PetscMalloc1(numCells*totDimAux, &a);CHKERRQ(ierr);} 1931 /* Read out geometry */ 1932 ierr = DMGetCoordinateField(dm,&coordField);CHKERRQ(ierr); 1933 ierr = DMFieldGetDegree(coordField,cellIS,NULL,&maxDegree);CHKERRQ(ierr); 1934 if (maxDegree <= 1) { 1935 ierr = DMFieldCreateDefaultQuadrature(coordField,cellIS,&affineQuad);CHKERRQ(ierr); 1936 if (affineQuad) { 1937 ierr = DMFieldCreateFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&cgeomFEM);CHKERRQ(ierr); 1938 } 1939 } 1940 if (useFVM) { 1941 PetscFV fv = NULL; 1942 Vec grad; 1943 PetscInt fStart, fEnd; 1944 PetscBool compGrad; 1945 1946 for (f = 0; f < Nf; ++f) { 1947 PetscObject obj; 1948 PetscClassId id; 1949 1950 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1951 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1952 if (id == PETSCFV_CLASSID) {fv = (PetscFV) obj; break;} 1953 } 1954 ierr = PetscFVGetComputeGradients(fv, &compGrad);CHKERRQ(ierr); 1955 ierr = PetscFVSetComputeGradients(fv, PETSC_TRUE);CHKERRQ(ierr); 1956 ierr = DMPlexComputeGeometryFVM(dm, &cellGeometryFVM, &faceGeometryFVM);CHKERRQ(ierr); 1957 ierr = DMPlexComputeGradientFVM(dm, fv, faceGeometryFVM, cellGeometryFVM, &dmGrad);CHKERRQ(ierr); 1958 ierr = PetscFVSetComputeGradients(fv, compGrad);CHKERRQ(ierr); 1959 ierr = VecGetArrayRead(cellGeometryFVM, (const PetscScalar **) &cgeomFVM);CHKERRQ(ierr); 1960 /* Reconstruct and limit cell gradients */ 1961 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 1962 ierr = DMGetGlobalVector(dmGrad, &grad);CHKERRQ(ierr); 1963 ierr = DMPlexReconstructGradients_Internal(dm, fv, fStart, fEnd, faceGeometryFVM, cellGeometryFVM, locX, grad);CHKERRQ(ierr); 1964 /* Communicate gradient values */ 1965 ierr = DMGetLocalVector(dmGrad, &locGrad);CHKERRQ(ierr); 1966 ierr = DMGlobalToLocalBegin(dmGrad, grad, INSERT_VALUES, locGrad);CHKERRQ(ierr); 1967 ierr = DMGlobalToLocalEnd(dmGrad, grad, INSERT_VALUES, locGrad);CHKERRQ(ierr); 1968 ierr = DMRestoreGlobalVector(dmGrad, &grad);CHKERRQ(ierr); 1969 /* Handle non-essential (e.g. outflow) boundary values */ 1970 ierr = DMPlexInsertBoundaryValues(dm, PETSC_FALSE, locX, 0.0, faceGeometryFVM, cellGeometryFVM, locGrad);CHKERRQ(ierr); 1971 ierr = VecGetArrayRead(locGrad, &lgrad);CHKERRQ(ierr); 1972 } 1973 /* Read out data from inputs */ 1974 for (c = cStart; c < cEnd; ++c) { 1975 PetscScalar *x = NULL; 1976 PetscInt i; 1977 1978 ierr = DMPlexVecGetClosure(dm, section, locX, c, NULL, &x);CHKERRQ(ierr); 1979 for (i = 0; i < totDim; ++i) u[c*totDim+i] = x[i]; 1980 ierr = DMPlexVecRestoreClosure(dm, section, locX, c, NULL, &x);CHKERRQ(ierr); 1981 if (dmAux) { 1982 ierr = DMPlexVecGetClosure(dmAux, sectionAux, locA, c, NULL, &x);CHKERRQ(ierr); 1983 for (i = 0; i < totDimAux; ++i) a[c*totDimAux+i] = x[i]; 1984 ierr = DMPlexVecRestoreClosure(dmAux, sectionAux, locA, c, NULL, &x);CHKERRQ(ierr); 1985 } 1986 } 1987 /* Do integration for each field */ 1988 for (f = 0; f < Nf; ++f) { 1989 PetscObject obj; 1990 PetscClassId id; 1991 PetscInt numChunks, numBatches, batchSize, numBlocks, blockSize, Ne, Nr, offset; 1992 1993 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1994 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1995 if (id == PETSCFE_CLASSID) { 1996 PetscFE fe = (PetscFE) obj; 1997 PetscQuadrature q; 1998 PetscFEGeom *chunkGeom = NULL; 1999 PetscInt Nq, Nb; 2000 2001 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 2002 ierr = PetscFEGetQuadrature(fe, &q);CHKERRQ(ierr); 2003 ierr = PetscQuadratureGetData(q, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 2004 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 2005 blockSize = Nb*Nq; 2006 batchSize = numBlocks * blockSize; 2007 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 2008 numChunks = numCells / (numBatches*batchSize); 2009 Ne = numChunks*numBatches*batchSize; 2010 Nr = numCells % (numBatches*batchSize); 2011 offset = numCells - Nr; 2012 if (!affineQuad) { 2013 ierr = DMFieldCreateFEGeom(coordField,cellIS,q,PETSC_FALSE,&cgeomFEM);CHKERRQ(ierr); 2014 } 2015 ierr = PetscFEGeomGetChunk(cgeomFEM,0,offset,&chunkGeom);CHKERRQ(ierr); 2016 ierr = PetscFEIntegrate(prob, f, Ne, chunkGeom, u, probAux, a, cintegral);CHKERRQ(ierr); 2017 ierr = PetscFEGeomGetChunk(cgeomFEM,offset,numCells,&chunkGeom);CHKERRQ(ierr); 2018 ierr = PetscFEIntegrate(prob, f, Nr, chunkGeom, &u[offset*totDim], probAux, &a[offset*totDimAux], &cintegral[offset*Nf]);CHKERRQ(ierr); 2019 ierr = PetscFEGeomRestoreChunk(cgeomFEM,offset,numCells,&chunkGeom);CHKERRQ(ierr); 2020 if (!affineQuad) { 2021 ierr = PetscFEGeomDestroy(&cgeomFEM);CHKERRQ(ierr); 2022 } 2023 } else if (id == PETSCFV_CLASSID) { 2024 PetscInt foff; 2025 PetscPointFunc obj_func; 2026 PetscScalar lint; 2027 2028 ierr = PetscDSGetObjective(prob, f, &obj_func);CHKERRQ(ierr); 2029 ierr = PetscDSGetFieldOffset(prob, f, &foff);CHKERRQ(ierr); 2030 if (obj_func) { 2031 for (c = 0; c < numCells; ++c) { 2032 PetscScalar *u_x; 2033 2034 ierr = DMPlexPointLocalRead(dmGrad, c, lgrad, &u_x);CHKERRQ(ierr); 2035 obj_func(dim, Nf, NfAux, uOff, uOff_x, &u[totDim*c+foff], NULL, u_x, aOff, NULL, &a[totDimAux*c], NULL, NULL, 0.0, cgeomFVM[c].centroid, numConstants, constants, &lint); 2036 cintegral[c*Nf+f] += PetscRealPart(lint)*cgeomFVM[c].volume; 2037 } 2038 } 2039 } else SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", f); 2040 } 2041 /* Cleanup data arrays */ 2042 if (useFVM) { 2043 ierr = VecRestoreArrayRead(locGrad, &lgrad);CHKERRQ(ierr); 2044 ierr = VecRestoreArrayRead(cellGeometryFVM, (const PetscScalar **) &cgeomFVM);CHKERRQ(ierr); 2045 ierr = DMRestoreLocalVector(dmGrad, &locGrad);CHKERRQ(ierr); 2046 ierr = VecDestroy(&faceGeometryFVM);CHKERRQ(ierr); 2047 ierr = VecDestroy(&cellGeometryFVM);CHKERRQ(ierr); 2048 ierr = DMDestroy(&dmGrad);CHKERRQ(ierr); 2049 } 2050 if (dmAux) {ierr = PetscFree(a);CHKERRQ(ierr);} 2051 ierr = PetscFree(u);CHKERRQ(ierr); 2052 /* Cleanup */ 2053 if (affineQuad) { 2054 ierr = PetscFEGeomDestroy(&cgeomFEM);CHKERRQ(ierr); 2055 } 2056 ierr = PetscQuadratureDestroy(&affineQuad);CHKERRQ(ierr); 2057 ierr = ISDestroy(&cellIS);CHKERRQ(ierr); 2058 ierr = DMRestoreLocalVector(dm, &locX);CHKERRQ(ierr); 2059 PetscFunctionReturn(0); 2060 } 2061 2062 /*@ 2063 DMPlexComputeIntegralFEM - Form the integral over the domain from the global input X using pointwise functions specified by the user 2064 2065 Input Parameters: 2066 + dm - The mesh 2067 . X - Global input vector 2068 - user - The user context 2069 2070 Output Parameter: 2071 . integral - Integral for each field 2072 2073 Level: developer 2074 2075 .seealso: DMPlexSNESComputeResidualFEM() 2076 @*/ 2077 PetscErrorCode DMPlexComputeIntegralFEM(DM dm, Vec X, PetscScalar *integral, void *user) 2078 { 2079 DM_Plex *mesh = (DM_Plex *) dm->data; 2080 PetscScalar *cintegral, *lintegral; 2081 PetscInt Nf, f, cellHeight, cStart, cEnd, cell; 2082 PetscErrorCode ierr; 2083 2084 PetscFunctionBegin; 2085 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2086 PetscValidHeaderSpecific(X, VEC_CLASSID, 2); 2087 PetscValidPointer(integral, 3); 2088 ierr = PetscLogEventBegin(DMPLEX_IntegralFEM,dm,0,0,0);CHKERRQ(ierr); 2089 ierr = DMGetNumFields(dm, &Nf);CHKERRQ(ierr); 2090 ierr = DMPlexGetVTKCellHeight(dm, &cellHeight);CHKERRQ(ierr); 2091 ierr = DMPlexGetSimplexOrBoxCells(dm, cellHeight, &cStart, &cEnd);CHKERRQ(ierr); 2092 /* TODO Introduce a loop over large chunks (right now this is a single chunk) */ 2093 ierr = PetscCalloc2(Nf, &lintegral, (cEnd-cStart)*Nf, &cintegral);CHKERRQ(ierr); 2094 ierr = DMPlexComputeIntegral_Internal(dm, X, cStart, cEnd, cintegral, user);CHKERRQ(ierr); 2095 /* Sum up values */ 2096 for (cell = cStart; cell < cEnd; ++cell) { 2097 const PetscInt c = cell - cStart; 2098 2099 if (mesh->printFEM > 1) {ierr = DMPrintCellVector(cell, "Cell Integral", Nf, &cintegral[c*Nf]);CHKERRQ(ierr);} 2100 for (f = 0; f < Nf; ++f) lintegral[f] += cintegral[c*Nf+f]; 2101 } 2102 ierr = MPIU_Allreduce(lintegral, integral, Nf, MPIU_SCALAR, MPIU_SUM, PetscObjectComm((PetscObject) dm));CHKERRMPI(ierr); 2103 if (mesh->printFEM) { 2104 ierr = PetscPrintf(PetscObjectComm((PetscObject) dm), "Integral:");CHKERRQ(ierr); 2105 for (f = 0; f < Nf; ++f) {ierr = PetscPrintf(PetscObjectComm((PetscObject) dm), " %g", (double) PetscRealPart(integral[f]));CHKERRQ(ierr);} 2106 ierr = PetscPrintf(PetscObjectComm((PetscObject) dm), "\n");CHKERRQ(ierr); 2107 } 2108 ierr = PetscFree2(lintegral, cintegral);CHKERRQ(ierr); 2109 ierr = PetscLogEventEnd(DMPLEX_IntegralFEM,dm,0,0,0);CHKERRQ(ierr); 2110 PetscFunctionReturn(0); 2111 } 2112 2113 /*@ 2114 DMPlexComputeCellwiseIntegralFEM - Form the vector of cellwise integrals F from the global input X using pointwise functions specified by the user 2115 2116 Input Parameters: 2117 + dm - The mesh 2118 . X - Global input vector 2119 - user - The user context 2120 2121 Output Parameter: 2122 . integral - Cellwise integrals for each field 2123 2124 Level: developer 2125 2126 .seealso: DMPlexSNESComputeResidualFEM() 2127 @*/ 2128 PetscErrorCode DMPlexComputeCellwiseIntegralFEM(DM dm, Vec X, Vec F, void *user) 2129 { 2130 DM_Plex *mesh = (DM_Plex *) dm->data; 2131 DM dmF; 2132 PetscSection sectionF; 2133 PetscScalar *cintegral, *af; 2134 PetscInt Nf, f, cellHeight, cStart, cEnd, cell; 2135 PetscErrorCode ierr; 2136 2137 PetscFunctionBegin; 2138 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2139 PetscValidHeaderSpecific(X, VEC_CLASSID, 2); 2140 PetscValidHeaderSpecific(F, VEC_CLASSID, 3); 2141 ierr = PetscLogEventBegin(DMPLEX_IntegralFEM,dm,0,0,0);CHKERRQ(ierr); 2142 ierr = DMGetNumFields(dm, &Nf);CHKERRQ(ierr); 2143 ierr = DMPlexGetVTKCellHeight(dm, &cellHeight);CHKERRQ(ierr); 2144 ierr = DMPlexGetSimplexOrBoxCells(dm, cellHeight, &cStart, &cEnd);CHKERRQ(ierr); 2145 /* TODO Introduce a loop over large chunks (right now this is a single chunk) */ 2146 ierr = PetscCalloc1((cEnd-cStart)*Nf, &cintegral);CHKERRQ(ierr); 2147 ierr = DMPlexComputeIntegral_Internal(dm, X, cStart, cEnd, cintegral, user);CHKERRQ(ierr); 2148 /* Put values in F*/ 2149 ierr = VecGetDM(F, &dmF);CHKERRQ(ierr); 2150 ierr = DMGetLocalSection(dmF, §ionF);CHKERRQ(ierr); 2151 ierr = VecGetArray(F, &af);CHKERRQ(ierr); 2152 for (cell = cStart; cell < cEnd; ++cell) { 2153 const PetscInt c = cell - cStart; 2154 PetscInt dof, off; 2155 2156 if (mesh->printFEM > 1) {ierr = DMPrintCellVector(cell, "Cell Integral", Nf, &cintegral[c*Nf]);CHKERRQ(ierr);} 2157 ierr = PetscSectionGetDof(sectionF, cell, &dof);CHKERRQ(ierr); 2158 ierr = PetscSectionGetOffset(sectionF, cell, &off);CHKERRQ(ierr); 2159 if (dof != Nf) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "The number of cell dofs %D != %D", dof, Nf); 2160 for (f = 0; f < Nf; ++f) af[off+f] = cintegral[c*Nf+f]; 2161 } 2162 ierr = VecRestoreArray(F, &af);CHKERRQ(ierr); 2163 ierr = PetscFree(cintegral);CHKERRQ(ierr); 2164 ierr = PetscLogEventEnd(DMPLEX_IntegralFEM,dm,0,0,0);CHKERRQ(ierr); 2165 PetscFunctionReturn(0); 2166 } 2167 2168 static PetscErrorCode DMPlexComputeBdIntegral_Internal(DM dm, Vec locX, IS pointIS, 2169 void (*func)(PetscInt, PetscInt, PetscInt, 2170 const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[], 2171 const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[], 2172 PetscReal, const PetscReal[], const PetscReal[], PetscInt, const PetscScalar[], PetscScalar[]), 2173 PetscScalar *fintegral, void *user) 2174 { 2175 DM plex = NULL, plexA = NULL; 2176 DMEnclosureType encAux; 2177 PetscDS prob, probAux = NULL; 2178 PetscSection section, sectionAux = NULL; 2179 Vec locA = NULL; 2180 DMField coordField; 2181 PetscInt Nf, totDim, *uOff, *uOff_x; 2182 PetscInt NfAux = 0, totDimAux = 0, *aOff = NULL; 2183 PetscScalar *u, *a = NULL; 2184 const PetscScalar *constants; 2185 PetscInt numConstants, f; 2186 PetscErrorCode ierr; 2187 2188 PetscFunctionBegin; 2189 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 2190 ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); 2191 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 2192 ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); 2193 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); 2194 /* Determine which discretizations we have */ 2195 for (f = 0; f < Nf; ++f) { 2196 PetscObject obj; 2197 PetscClassId id; 2198 2199 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 2200 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 2201 if (id == PETSCFV_CLASSID) SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Not supported for FVM (field %D)", f); 2202 } 2203 /* Read DS information */ 2204 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 2205 ierr = PetscDSGetComponentOffsets(prob, &uOff);CHKERRQ(ierr); 2206 ierr = PetscDSGetComponentDerivativeOffsets(prob, &uOff_x);CHKERRQ(ierr); 2207 ierr = PetscDSGetConstants(prob, &numConstants, &constants);CHKERRQ(ierr); 2208 /* Read Auxiliary DS information */ 2209 ierr = DMGetAuxiliaryVec(dm, NULL, 0, &locA);CHKERRQ(ierr); 2210 if (locA) { 2211 DM dmAux; 2212 2213 ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); 2214 ierr = DMGetEnclosureRelation(dmAux, dm, &encAux);CHKERRQ(ierr); 2215 ierr = DMConvert(dmAux, DMPLEX, &plexA);CHKERRQ(ierr); 2216 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 2217 ierr = PetscDSGetNumFields(probAux, &NfAux);CHKERRQ(ierr); 2218 ierr = DMGetLocalSection(dmAux, §ionAux);CHKERRQ(ierr); 2219 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 2220 ierr = PetscDSGetComponentOffsets(probAux, &aOff);CHKERRQ(ierr); 2221 } 2222 /* Integrate over points */ 2223 { 2224 PetscFEGeom *fgeom, *chunkGeom = NULL; 2225 PetscInt maxDegree; 2226 PetscQuadrature qGeom = NULL; 2227 const PetscInt *points; 2228 PetscInt numFaces, face, Nq, field; 2229 PetscInt numChunks, chunkSize, chunk, Nr, offset; 2230 2231 ierr = ISGetLocalSize(pointIS, &numFaces);CHKERRQ(ierr); 2232 ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); 2233 ierr = PetscCalloc2(numFaces*totDim, &u, locA ? numFaces*totDimAux : 0, &a);CHKERRQ(ierr); 2234 ierr = DMFieldGetDegree(coordField, pointIS, NULL, &maxDegree);CHKERRQ(ierr); 2235 for (field = 0; field < Nf; ++field) { 2236 PetscFE fe; 2237 2238 ierr = PetscDSGetDiscretization(prob, field, (PetscObject *) &fe);CHKERRQ(ierr); 2239 if (maxDegree <= 1) {ierr = DMFieldCreateDefaultQuadrature(coordField, pointIS, &qGeom);CHKERRQ(ierr);} 2240 if (!qGeom) { 2241 ierr = PetscFEGetFaceQuadrature(fe, &qGeom);CHKERRQ(ierr); 2242 ierr = PetscObjectReference((PetscObject) qGeom);CHKERRQ(ierr); 2243 } 2244 ierr = PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 2245 ierr = DMPlexGetFEGeom(coordField, pointIS, qGeom, PETSC_TRUE, &fgeom);CHKERRQ(ierr); 2246 for (face = 0; face < numFaces; ++face) { 2247 const PetscInt point = points[face], *support; 2248 PetscScalar *x = NULL; 2249 PetscInt i; 2250 2251 ierr = DMPlexGetSupport(dm, point, &support);CHKERRQ(ierr); 2252 ierr = DMPlexVecGetClosure(plex, section, locX, support[0], NULL, &x);CHKERRQ(ierr); 2253 for (i = 0; i < totDim; ++i) u[face*totDim+i] = x[i]; 2254 ierr = DMPlexVecRestoreClosure(plex, section, locX, support[0], NULL, &x);CHKERRQ(ierr); 2255 if (locA) { 2256 PetscInt subp; 2257 ierr = DMGetEnclosurePoint(plexA, dm, encAux, support[0], &subp);CHKERRQ(ierr); 2258 ierr = DMPlexVecGetClosure(plexA, sectionAux, locA, subp, NULL, &x);CHKERRQ(ierr); 2259 for (i = 0; i < totDimAux; ++i) a[f*totDimAux+i] = x[i]; 2260 ierr = DMPlexVecRestoreClosure(plexA, sectionAux, locA, subp, NULL, &x);CHKERRQ(ierr); 2261 } 2262 } 2263 /* Get blocking */ 2264 { 2265 PetscQuadrature q; 2266 PetscInt numBatches, batchSize, numBlocks, blockSize; 2267 PetscInt Nq, Nb; 2268 2269 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 2270 ierr = PetscFEGetQuadrature(fe, &q);CHKERRQ(ierr); 2271 ierr = PetscQuadratureGetData(q, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 2272 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 2273 blockSize = Nb*Nq; 2274 batchSize = numBlocks * blockSize; 2275 chunkSize = numBatches*batchSize; 2276 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 2277 numChunks = numFaces / chunkSize; 2278 Nr = numFaces % chunkSize; 2279 offset = numFaces - Nr; 2280 } 2281 /* Do integration for each field */ 2282 for (chunk = 0; chunk < numChunks; ++chunk) { 2283 ierr = PetscFEGeomGetChunk(fgeom, chunk*chunkSize, (chunk+1)*chunkSize, &chunkGeom);CHKERRQ(ierr); 2284 ierr = PetscFEIntegrateBd(prob, field, func, chunkSize, chunkGeom, u, probAux, a, fintegral);CHKERRQ(ierr); 2285 ierr = PetscFEGeomRestoreChunk(fgeom, 0, offset, &chunkGeom);CHKERRQ(ierr); 2286 } 2287 ierr = PetscFEGeomGetChunk(fgeom, offset, numFaces, &chunkGeom);CHKERRQ(ierr); 2288 ierr = PetscFEIntegrateBd(prob, field, func, Nr, chunkGeom, &u[offset*totDim], probAux, a ? &a[offset*totDimAux] : NULL, &fintegral[offset*Nf]);CHKERRQ(ierr); 2289 ierr = PetscFEGeomRestoreChunk(fgeom, offset, numFaces, &chunkGeom);CHKERRQ(ierr); 2290 /* Cleanup data arrays */ 2291 ierr = DMPlexRestoreFEGeom(coordField, pointIS, qGeom, PETSC_TRUE, &fgeom);CHKERRQ(ierr); 2292 ierr = PetscQuadratureDestroy(&qGeom);CHKERRQ(ierr); 2293 ierr = PetscFree2(u, a);CHKERRQ(ierr); 2294 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 2295 } 2296 } 2297 if (plex) {ierr = DMDestroy(&plex);CHKERRQ(ierr);} 2298 if (plexA) {ierr = DMDestroy(&plexA);CHKERRQ(ierr);} 2299 PetscFunctionReturn(0); 2300 } 2301 2302 /*@ 2303 DMPlexComputeBdIntegral - Form the integral over the specified boundary from the global input X using pointwise functions specified by the user 2304 2305 Input Parameters: 2306 + dm - The mesh 2307 . X - Global input vector 2308 . label - The boundary DMLabel 2309 . numVals - The number of label values to use, or PETSC_DETERMINE for all values 2310 . vals - The label values to use, or PETSC_NULL for all values 2311 . func = The function to integrate along the boundary 2312 - user - The user context 2313 2314 Output Parameter: 2315 . integral - Integral for each field 2316 2317 Level: developer 2318 2319 .seealso: DMPlexComputeIntegralFEM(), DMPlexComputeBdResidualFEM() 2320 @*/ 2321 PetscErrorCode DMPlexComputeBdIntegral(DM dm, Vec X, DMLabel label, PetscInt numVals, const PetscInt vals[], 2322 void (*func)(PetscInt, PetscInt, PetscInt, 2323 const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[], 2324 const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[], 2325 PetscReal, const PetscReal[], const PetscReal[], PetscInt, const PetscScalar[], PetscScalar[]), 2326 PetscScalar *integral, void *user) 2327 { 2328 Vec locX; 2329 PetscSection section; 2330 DMLabel depthLabel; 2331 IS facetIS; 2332 PetscInt dim, Nf, f, v; 2333 PetscErrorCode ierr; 2334 2335 PetscFunctionBegin; 2336 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2337 PetscValidHeaderSpecific(X, VEC_CLASSID, 2); 2338 PetscValidPointer(label, 3); 2339 if (vals) PetscValidPointer(vals, 5); 2340 PetscValidPointer(integral, 7); 2341 ierr = PetscLogEventBegin(DMPLEX_IntegralFEM,dm,0,0,0);CHKERRQ(ierr); 2342 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 2343 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 2344 ierr = DMLabelGetStratumIS(depthLabel, dim-1, &facetIS);CHKERRQ(ierr); 2345 ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); 2346 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); 2347 /* Get local solution with boundary values */ 2348 ierr = DMGetLocalVector(dm, &locX);CHKERRQ(ierr); 2349 ierr = DMPlexInsertBoundaryValues(dm, PETSC_TRUE, locX, 0.0, NULL, NULL, NULL);CHKERRQ(ierr); 2350 ierr = DMGlobalToLocalBegin(dm, X, INSERT_VALUES, locX);CHKERRQ(ierr); 2351 ierr = DMGlobalToLocalEnd(dm, X, INSERT_VALUES, locX);CHKERRQ(ierr); 2352 /* Loop over label values */ 2353 ierr = PetscArrayzero(integral, Nf);CHKERRQ(ierr); 2354 for (v = 0; v < numVals; ++v) { 2355 IS pointIS; 2356 PetscInt numFaces, face; 2357 PetscScalar *fintegral; 2358 2359 ierr = DMLabelGetStratumIS(label, vals[v], &pointIS);CHKERRQ(ierr); 2360 if (!pointIS) continue; /* No points with that id on this process */ 2361 { 2362 IS isectIS; 2363 2364 /* TODO: Special cases of ISIntersect where it is quick to check a priori if one is a superset of the other */ 2365 ierr = ISIntersect_Caching_Internal(facetIS, pointIS, &isectIS);CHKERRQ(ierr); 2366 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 2367 pointIS = isectIS; 2368 } 2369 ierr = ISGetLocalSize(pointIS, &numFaces);CHKERRQ(ierr); 2370 ierr = PetscCalloc1(numFaces*Nf, &fintegral);CHKERRQ(ierr); 2371 ierr = DMPlexComputeBdIntegral_Internal(dm, locX, pointIS, func, fintegral, user);CHKERRQ(ierr); 2372 /* Sum point contributions into integral */ 2373 for (f = 0; f < Nf; ++f) for (face = 0; face < numFaces; ++face) integral[f] += fintegral[face*Nf+f]; 2374 ierr = PetscFree(fintegral);CHKERRQ(ierr); 2375 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 2376 } 2377 ierr = DMRestoreLocalVector(dm, &locX);CHKERRQ(ierr); 2378 ierr = ISDestroy(&facetIS);CHKERRQ(ierr); 2379 ierr = PetscLogEventEnd(DMPLEX_IntegralFEM,dm,0,0,0);CHKERRQ(ierr); 2380 PetscFunctionReturn(0); 2381 } 2382 2383 /*@ 2384 DMPlexComputeInterpolatorNested - Form the local portion of the interpolation matrix I from the coarse DM to a uniformly refined DM. 2385 2386 Input Parameters: 2387 + dmc - The coarse mesh 2388 . dmf - The fine mesh 2389 . isRefined - Flag indicating regular refinement, rather than the same topology 2390 - user - The user context 2391 2392 Output Parameter: 2393 . In - The interpolation matrix 2394 2395 Level: developer 2396 2397 .seealso: DMPlexComputeInterpolatorGeneral(), DMPlexComputeJacobianFEM() 2398 @*/ 2399 PetscErrorCode DMPlexComputeInterpolatorNested(DM dmc, DM dmf, PetscBool isRefined, Mat In, void *user) 2400 { 2401 DM_Plex *mesh = (DM_Plex *) dmc->data; 2402 const char *name = "Interpolator"; 2403 PetscFE *feRef; 2404 PetscFV *fvRef; 2405 PetscSection fsection, fglobalSection; 2406 PetscSection csection, cglobalSection; 2407 PetscScalar *elemMat; 2408 PetscInt dim, Nf, f, fieldI, fieldJ, offsetI, offsetJ, cStart, cEnd, c; 2409 PetscInt cTotDim=0, rTotDim = 0; 2410 PetscErrorCode ierr; 2411 2412 PetscFunctionBegin; 2413 ierr = PetscLogEventBegin(DMPLEX_InterpolatorFEM,dmc,dmf,0,0);CHKERRQ(ierr); 2414 ierr = DMGetDimension(dmf, &dim);CHKERRQ(ierr); 2415 ierr = DMGetLocalSection(dmf, &fsection);CHKERRQ(ierr); 2416 ierr = DMGetGlobalSection(dmf, &fglobalSection);CHKERRQ(ierr); 2417 ierr = DMGetLocalSection(dmc, &csection);CHKERRQ(ierr); 2418 ierr = DMGetGlobalSection(dmc, &cglobalSection);CHKERRQ(ierr); 2419 ierr = PetscSectionGetNumFields(fsection, &Nf);CHKERRQ(ierr); 2420 ierr = DMPlexGetSimplexOrBoxCells(dmc, 0, &cStart, &cEnd);CHKERRQ(ierr); 2421 ierr = PetscCalloc2(Nf, &feRef, Nf, &fvRef);CHKERRQ(ierr); 2422 for (f = 0; f < Nf; ++f) { 2423 PetscObject obj, objc; 2424 PetscClassId id, idc; 2425 PetscInt rNb = 0, Nc = 0, cNb = 0; 2426 2427 ierr = DMGetField(dmf, f, NULL, &obj);CHKERRQ(ierr); 2428 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 2429 if (id == PETSCFE_CLASSID) { 2430 PetscFE fe = (PetscFE) obj; 2431 2432 if (isRefined) { 2433 ierr = PetscFERefine(fe, &feRef[f]);CHKERRQ(ierr); 2434 } else { 2435 ierr = PetscObjectReference((PetscObject) fe);CHKERRQ(ierr); 2436 feRef[f] = fe; 2437 } 2438 ierr = PetscFEGetDimension(feRef[f], &rNb);CHKERRQ(ierr); 2439 ierr = PetscFEGetNumComponents(fe, &Nc);CHKERRQ(ierr); 2440 } else if (id == PETSCFV_CLASSID) { 2441 PetscFV fv = (PetscFV) obj; 2442 PetscDualSpace Q; 2443 2444 if (isRefined) { 2445 ierr = PetscFVRefine(fv, &fvRef[f]);CHKERRQ(ierr); 2446 } else { 2447 ierr = PetscObjectReference((PetscObject) fv);CHKERRQ(ierr); 2448 fvRef[f] = fv; 2449 } 2450 ierr = PetscFVGetDualSpace(fvRef[f], &Q);CHKERRQ(ierr); 2451 ierr = PetscDualSpaceGetDimension(Q, &rNb);CHKERRQ(ierr); 2452 ierr = PetscFVGetDualSpace(fv, &Q);CHKERRQ(ierr); 2453 ierr = PetscFVGetNumComponents(fv, &Nc);CHKERRQ(ierr); 2454 } 2455 ierr = DMGetField(dmc, f, NULL, &objc);CHKERRQ(ierr); 2456 ierr = PetscObjectGetClassId(objc, &idc);CHKERRQ(ierr); 2457 if (idc == PETSCFE_CLASSID) { 2458 PetscFE fe = (PetscFE) objc; 2459 2460 ierr = PetscFEGetDimension(fe, &cNb);CHKERRQ(ierr); 2461 } else if (id == PETSCFV_CLASSID) { 2462 PetscFV fv = (PetscFV) obj; 2463 PetscDualSpace Q; 2464 2465 ierr = PetscFVGetDualSpace(fv, &Q);CHKERRQ(ierr); 2466 ierr = PetscDualSpaceGetDimension(Q, &cNb);CHKERRQ(ierr); 2467 } 2468 rTotDim += rNb; 2469 cTotDim += cNb; 2470 } 2471 ierr = PetscMalloc1(rTotDim*cTotDim,&elemMat);CHKERRQ(ierr); 2472 ierr = PetscArrayzero(elemMat, rTotDim*cTotDim);CHKERRQ(ierr); 2473 for (fieldI = 0, offsetI = 0; fieldI < Nf; ++fieldI) { 2474 PetscDualSpace Qref; 2475 PetscQuadrature f; 2476 const PetscReal *qpoints, *qweights; 2477 PetscReal *points; 2478 PetscInt npoints = 0, Nc, Np, fpdim, i, k, p, d; 2479 2480 /* Compose points from all dual basis functionals */ 2481 if (feRef[fieldI]) { 2482 ierr = PetscFEGetDualSpace(feRef[fieldI], &Qref);CHKERRQ(ierr); 2483 ierr = PetscFEGetNumComponents(feRef[fieldI], &Nc);CHKERRQ(ierr); 2484 } else { 2485 ierr = PetscFVGetDualSpace(fvRef[fieldI], &Qref);CHKERRQ(ierr); 2486 ierr = PetscFVGetNumComponents(fvRef[fieldI], &Nc);CHKERRQ(ierr); 2487 } 2488 ierr = PetscDualSpaceGetDimension(Qref, &fpdim);CHKERRQ(ierr); 2489 for (i = 0; i < fpdim; ++i) { 2490 ierr = PetscDualSpaceGetFunctional(Qref, i, &f);CHKERRQ(ierr); 2491 ierr = PetscQuadratureGetData(f, NULL, NULL, &Np, NULL, NULL);CHKERRQ(ierr); 2492 npoints += Np; 2493 } 2494 ierr = PetscMalloc1(npoints*dim,&points);CHKERRQ(ierr); 2495 for (i = 0, k = 0; i < fpdim; ++i) { 2496 ierr = PetscDualSpaceGetFunctional(Qref, i, &f);CHKERRQ(ierr); 2497 ierr = PetscQuadratureGetData(f, NULL, NULL, &Np, &qpoints, NULL);CHKERRQ(ierr); 2498 for (p = 0; p < Np; ++p, ++k) for (d = 0; d < dim; ++d) points[k*dim+d] = qpoints[p*dim+d]; 2499 } 2500 2501 for (fieldJ = 0, offsetJ = 0; fieldJ < Nf; ++fieldJ) { 2502 PetscObject obj; 2503 PetscClassId id; 2504 PetscInt NcJ = 0, cpdim = 0, j, qNc; 2505 2506 ierr = DMGetField(dmc, fieldJ, NULL, &obj);CHKERRQ(ierr); 2507 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 2508 if (id == PETSCFE_CLASSID) { 2509 PetscFE fe = (PetscFE) obj; 2510 PetscTabulation T = NULL; 2511 2512 /* Evaluate basis at points */ 2513 ierr = PetscFEGetNumComponents(fe, &NcJ);CHKERRQ(ierr); 2514 ierr = PetscFEGetDimension(fe, &cpdim);CHKERRQ(ierr); 2515 /* For now, fields only interpolate themselves */ 2516 if (fieldI == fieldJ) { 2517 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); 2518 ierr = PetscFECreateTabulation(fe, 1, npoints, points, 0, &T);CHKERRQ(ierr); 2519 for (i = 0, k = 0; i < fpdim; ++i) { 2520 ierr = PetscDualSpaceGetFunctional(Qref, i, &f);CHKERRQ(ierr); 2521 ierr = PetscQuadratureGetData(f, NULL, &qNc, &Np, NULL, &qweights);CHKERRQ(ierr); 2522 if (qNc != NcJ) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Number of components in quadrature %D does not match coarse field %D", qNc, NcJ); 2523 for (p = 0; p < Np; ++p, ++k) { 2524 for (j = 0; j < cpdim; ++j) { 2525 /* 2526 cTotDim: Total columns in element interpolation matrix, sum of number of dual basis functionals in each field 2527 offsetI, offsetJ: Offsets into the larger element interpolation matrix for different fields 2528 fpdim, i, cpdim, j: Dofs for fine and coarse grids, correspond to dual space basis functionals 2529 qNC, Nc, Ncj, c: Number of components in this field 2530 Np, p: Number of quad points in the fine grid functional i 2531 k: i*Np + p, overall point number for the interpolation 2532 */ 2533 for (c = 0; c < Nc; ++c) elemMat[(offsetI + i)*cTotDim + offsetJ + j] += T->T[0][k*cpdim*NcJ+j*Nc+c]*qweights[p*qNc+c]; 2534 } 2535 } 2536 } 2537 ierr = PetscTabulationDestroy(&T);CHKERRQ(ierr);CHKERRQ(ierr); 2538 } 2539 } else if (id == PETSCFV_CLASSID) { 2540 PetscFV fv = (PetscFV) obj; 2541 2542 /* Evaluate constant function at points */ 2543 ierr = PetscFVGetNumComponents(fv, &NcJ);CHKERRQ(ierr); 2544 cpdim = 1; 2545 /* For now, fields only interpolate themselves */ 2546 if (fieldI == fieldJ) { 2547 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); 2548 for (i = 0, k = 0; i < fpdim; ++i) { 2549 ierr = PetscDualSpaceGetFunctional(Qref, i, &f);CHKERRQ(ierr); 2550 ierr = PetscQuadratureGetData(f, NULL, &qNc, &Np, NULL, &qweights);CHKERRQ(ierr); 2551 if (qNc != NcJ) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Number of components in quadrature %D does not match coarse field %D", qNc, NcJ); 2552 for (p = 0; p < Np; ++p, ++k) { 2553 for (j = 0; j < cpdim; ++j) { 2554 for (c = 0; c < Nc; ++c) elemMat[(offsetI + i)*cTotDim + offsetJ + j] += 1.0*qweights[p*qNc+c]; 2555 } 2556 } 2557 } 2558 } 2559 } 2560 offsetJ += cpdim; 2561 } 2562 offsetI += fpdim; 2563 ierr = PetscFree(points);CHKERRQ(ierr); 2564 } 2565 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(0, name, rTotDim, cTotDim, elemMat);CHKERRQ(ierr);} 2566 /* Preallocate matrix */ 2567 { 2568 Mat preallocator; 2569 PetscScalar *vals; 2570 PetscInt *cellCIndices, *cellFIndices; 2571 PetscInt locRows, locCols, cell; 2572 2573 ierr = MatGetLocalSize(In, &locRows, &locCols);CHKERRQ(ierr); 2574 ierr = MatCreate(PetscObjectComm((PetscObject) In), &preallocator);CHKERRQ(ierr); 2575 ierr = MatSetType(preallocator, MATPREALLOCATOR);CHKERRQ(ierr); 2576 ierr = MatSetSizes(preallocator, locRows, locCols, PETSC_DETERMINE, PETSC_DETERMINE);CHKERRQ(ierr); 2577 ierr = MatSetUp(preallocator);CHKERRQ(ierr); 2578 ierr = PetscCalloc3(rTotDim*cTotDim, &vals,cTotDim,&cellCIndices,rTotDim,&cellFIndices);CHKERRQ(ierr); 2579 for (cell = cStart; cell < cEnd; ++cell) { 2580 if (isRefined) { 2581 ierr = DMPlexMatGetClosureIndicesRefined(dmf, fsection, fglobalSection, dmc, csection, cglobalSection, cell, cellCIndices, cellFIndices);CHKERRQ(ierr); 2582 ierr = MatSetValues(preallocator, rTotDim, cellFIndices, cTotDim, cellCIndices, vals, INSERT_VALUES);CHKERRQ(ierr); 2583 } else { 2584 ierr = DMPlexMatSetClosureGeneral(dmf, fsection, fglobalSection, dmc, csection, cglobalSection, preallocator, cell, vals, INSERT_VALUES);CHKERRQ(ierr); 2585 } 2586 } 2587 ierr = PetscFree3(vals,cellCIndices,cellFIndices);CHKERRQ(ierr); 2588 ierr = MatAssemblyBegin(preallocator, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2589 ierr = MatAssemblyEnd(preallocator, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2590 ierr = MatPreallocatorPreallocate(preallocator, PETSC_TRUE, In);CHKERRQ(ierr); 2591 ierr = MatDestroy(&preallocator);CHKERRQ(ierr); 2592 } 2593 /* Fill matrix */ 2594 ierr = MatZeroEntries(In);CHKERRQ(ierr); 2595 for (c = cStart; c < cEnd; ++c) { 2596 if (isRefined) { 2597 ierr = DMPlexMatSetClosureRefined(dmf, fsection, fglobalSection, dmc, csection, cglobalSection, In, c, elemMat, INSERT_VALUES);CHKERRQ(ierr); 2598 } else { 2599 ierr = DMPlexMatSetClosureGeneral(dmf, fsection, fglobalSection, dmc, csection, cglobalSection, In, c, elemMat, INSERT_VALUES);CHKERRQ(ierr); 2600 } 2601 } 2602 for (f = 0; f < Nf; ++f) {ierr = PetscFEDestroy(&feRef[f]);CHKERRQ(ierr);} 2603 ierr = PetscFree2(feRef,fvRef);CHKERRQ(ierr); 2604 ierr = PetscFree(elemMat);CHKERRQ(ierr); 2605 ierr = MatAssemblyBegin(In, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2606 ierr = MatAssemblyEnd(In, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2607 if (mesh->printFEM > 1) { 2608 ierr = PetscPrintf(PetscObjectComm((PetscObject)In), "%s:\n", name);CHKERRQ(ierr); 2609 ierr = MatChop(In, 1.0e-10);CHKERRQ(ierr); 2610 ierr = MatView(In, NULL);CHKERRQ(ierr); 2611 } 2612 ierr = PetscLogEventEnd(DMPLEX_InterpolatorFEM,dmc,dmf,0,0);CHKERRQ(ierr); 2613 PetscFunctionReturn(0); 2614 } 2615 2616 PetscErrorCode DMPlexComputeMassMatrixNested(DM dmc, DM dmf, Mat mass, void *user) 2617 { 2618 SETERRQ(PetscObjectComm((PetscObject) dmc), PETSC_ERR_SUP, "Laziness"); 2619 } 2620 2621 /*@ 2622 DMPlexComputeInterpolatorGeneral - Form the local portion of the interpolation matrix I from the coarse DM to a non-nested fine DM. 2623 2624 Input Parameters: 2625 + dmf - The fine mesh 2626 . dmc - The coarse mesh 2627 - user - The user context 2628 2629 Output Parameter: 2630 . In - The interpolation matrix 2631 2632 Level: developer 2633 2634 .seealso: DMPlexComputeInterpolatorNested(), DMPlexComputeJacobianFEM() 2635 @*/ 2636 PetscErrorCode DMPlexComputeInterpolatorGeneral(DM dmc, DM dmf, Mat In, void *user) 2637 { 2638 DM_Plex *mesh = (DM_Plex *) dmf->data; 2639 const char *name = "Interpolator"; 2640 PetscDS prob; 2641 PetscSection fsection, csection, globalFSection, globalCSection; 2642 PetscHSetIJ ht; 2643 PetscLayout rLayout; 2644 PetscInt *dnz, *onz; 2645 PetscInt locRows, rStart, rEnd; 2646 PetscReal *x, *v0, *J, *invJ, detJ; 2647 PetscReal *v0c, *Jc, *invJc, detJc; 2648 PetscScalar *elemMat; 2649 PetscInt dim, Nf, field, totDim, cStart, cEnd, cell, ccell; 2650 PetscErrorCode ierr; 2651 2652 PetscFunctionBegin; 2653 ierr = PetscLogEventBegin(DMPLEX_InterpolatorFEM,dmc,dmf,0,0);CHKERRQ(ierr); 2654 ierr = DMGetCoordinateDim(dmc, &dim);CHKERRQ(ierr); 2655 ierr = DMGetDS(dmc, &prob);CHKERRQ(ierr); 2656 ierr = PetscDSGetWorkspace(prob, &x, NULL, NULL, NULL, NULL);CHKERRQ(ierr); 2657 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 2658 ierr = PetscMalloc3(dim,&v0,dim*dim,&J,dim*dim,&invJ);CHKERRQ(ierr); 2659 ierr = PetscMalloc3(dim,&v0c,dim*dim,&Jc,dim*dim,&invJc);CHKERRQ(ierr); 2660 ierr = DMGetLocalSection(dmf, &fsection);CHKERRQ(ierr); 2661 ierr = DMGetGlobalSection(dmf, &globalFSection);CHKERRQ(ierr); 2662 ierr = DMGetLocalSection(dmc, &csection);CHKERRQ(ierr); 2663 ierr = DMGetGlobalSection(dmc, &globalCSection);CHKERRQ(ierr); 2664 ierr = DMPlexGetHeightStratum(dmf, 0, &cStart, &cEnd);CHKERRQ(ierr); 2665 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 2666 ierr = PetscMalloc1(totDim, &elemMat);CHKERRQ(ierr); 2667 2668 ierr = MatGetLocalSize(In, &locRows, NULL);CHKERRQ(ierr); 2669 ierr = PetscLayoutCreate(PetscObjectComm((PetscObject) In), &rLayout);CHKERRQ(ierr); 2670 ierr = PetscLayoutSetLocalSize(rLayout, locRows);CHKERRQ(ierr); 2671 ierr = PetscLayoutSetBlockSize(rLayout, 1);CHKERRQ(ierr); 2672 ierr = PetscLayoutSetUp(rLayout);CHKERRQ(ierr); 2673 ierr = PetscLayoutGetRange(rLayout, &rStart, &rEnd);CHKERRQ(ierr); 2674 ierr = PetscLayoutDestroy(&rLayout);CHKERRQ(ierr); 2675 ierr = PetscCalloc2(locRows,&dnz,locRows,&onz);CHKERRQ(ierr); 2676 ierr = PetscHSetIJCreate(&ht);CHKERRQ(ierr); 2677 for (field = 0; field < Nf; ++field) { 2678 PetscObject obj; 2679 PetscClassId id; 2680 PetscDualSpace Q = NULL; 2681 PetscQuadrature f; 2682 const PetscReal *qpoints; 2683 PetscInt Nc, Np, fpdim, i, d; 2684 2685 ierr = PetscDSGetDiscretization(prob, field, &obj);CHKERRQ(ierr); 2686 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 2687 if (id == PETSCFE_CLASSID) { 2688 PetscFE fe = (PetscFE) obj; 2689 2690 ierr = PetscFEGetDualSpace(fe, &Q);CHKERRQ(ierr); 2691 ierr = PetscFEGetNumComponents(fe, &Nc);CHKERRQ(ierr); 2692 } else if (id == PETSCFV_CLASSID) { 2693 PetscFV fv = (PetscFV) obj; 2694 2695 ierr = PetscFVGetDualSpace(fv, &Q);CHKERRQ(ierr); 2696 Nc = 1; 2697 } 2698 ierr = PetscDualSpaceGetDimension(Q, &fpdim);CHKERRQ(ierr); 2699 /* For each fine grid cell */ 2700 for (cell = cStart; cell < cEnd; ++cell) { 2701 PetscInt *findices, *cindices; 2702 PetscInt numFIndices, numCIndices; 2703 2704 ierr = DMPlexGetClosureIndices(dmf, fsection, globalFSection, cell, PETSC_FALSE, &numFIndices, &findices, NULL, NULL);CHKERRQ(ierr); 2705 ierr = DMPlexComputeCellGeometryFEM(dmf, cell, NULL, v0, J, invJ, &detJ);CHKERRQ(ierr); 2706 if (numFIndices != fpdim) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Number of fine indices %D != %D dual basis vecs", numFIndices, fpdim); 2707 for (i = 0; i < fpdim; ++i) { 2708 Vec pointVec; 2709 PetscScalar *pV; 2710 PetscSF coarseCellSF = NULL; 2711 const PetscSFNode *coarseCells; 2712 PetscInt numCoarseCells, q, c; 2713 2714 /* Get points from the dual basis functional quadrature */ 2715 ierr = PetscDualSpaceGetFunctional(Q, i, &f);CHKERRQ(ierr); 2716 ierr = PetscQuadratureGetData(f, NULL, NULL, &Np, &qpoints, NULL);CHKERRQ(ierr); 2717 ierr = VecCreateSeq(PETSC_COMM_SELF, Np*dim, &pointVec);CHKERRQ(ierr); 2718 ierr = VecSetBlockSize(pointVec, dim);CHKERRQ(ierr); 2719 ierr = VecGetArray(pointVec, &pV);CHKERRQ(ierr); 2720 for (q = 0; q < Np; ++q) { 2721 const PetscReal xi0[3] = {-1., -1., -1.}; 2722 2723 /* Transform point to real space */ 2724 CoordinatesRefToReal(dim, dim, xi0, v0, J, &qpoints[q*dim], x); 2725 for (d = 0; d < dim; ++d) pV[q*dim+d] = x[d]; 2726 } 2727 ierr = VecRestoreArray(pointVec, &pV);CHKERRQ(ierr); 2728 /* Get set of coarse cells that overlap points (would like to group points by coarse cell) */ 2729 /* OPT: Pack all quad points from fine cell */ 2730 ierr = DMLocatePoints(dmc, pointVec, DM_POINTLOCATION_NEAREST, &coarseCellSF);CHKERRQ(ierr); 2731 ierr = PetscSFViewFromOptions(coarseCellSF, NULL, "-interp_sf_view");CHKERRQ(ierr); 2732 /* Update preallocation info */ 2733 ierr = PetscSFGetGraph(coarseCellSF, NULL, &numCoarseCells, NULL, &coarseCells);CHKERRQ(ierr); 2734 if (numCoarseCells != Np) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Not all closure points located"); 2735 { 2736 PetscHashIJKey key; 2737 PetscBool missing; 2738 2739 key.i = findices[i]; 2740 if (key.i >= 0) { 2741 /* Get indices for coarse elements */ 2742 for (ccell = 0; ccell < numCoarseCells; ++ccell) { 2743 ierr = DMPlexGetClosureIndices(dmc, csection, globalCSection, coarseCells[ccell].index, PETSC_FALSE, &numCIndices, &cindices, NULL, NULL);CHKERRQ(ierr); 2744 for (c = 0; c < numCIndices; ++c) { 2745 key.j = cindices[c]; 2746 if (key.j < 0) continue; 2747 ierr = PetscHSetIJQueryAdd(ht, key, &missing);CHKERRQ(ierr); 2748 if (missing) { 2749 if ((key.j >= rStart) && (key.j < rEnd)) ++dnz[key.i-rStart]; 2750 else ++onz[key.i-rStart]; 2751 } 2752 } 2753 ierr = DMPlexRestoreClosureIndices(dmc, csection, globalCSection, coarseCells[ccell].index, PETSC_FALSE, &numCIndices, &cindices, NULL, NULL);CHKERRQ(ierr); 2754 } 2755 } 2756 } 2757 ierr = PetscSFDestroy(&coarseCellSF);CHKERRQ(ierr); 2758 ierr = VecDestroy(&pointVec);CHKERRQ(ierr); 2759 } 2760 ierr = DMPlexRestoreClosureIndices(dmf, fsection, globalFSection, cell, PETSC_FALSE, &numFIndices, &findices, NULL, NULL);CHKERRQ(ierr); 2761 } 2762 } 2763 ierr = PetscHSetIJDestroy(&ht);CHKERRQ(ierr); 2764 ierr = MatXAIJSetPreallocation(In, 1, dnz, onz, NULL, NULL);CHKERRQ(ierr); 2765 ierr = MatSetOption(In, MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 2766 ierr = PetscFree2(dnz,onz);CHKERRQ(ierr); 2767 for (field = 0; field < Nf; ++field) { 2768 PetscObject obj; 2769 PetscClassId id; 2770 PetscDualSpace Q = NULL; 2771 PetscTabulation T = NULL; 2772 PetscQuadrature f; 2773 const PetscReal *qpoints, *qweights; 2774 PetscInt Nc, qNc, Np, fpdim, i, d; 2775 2776 ierr = PetscDSGetDiscretization(prob, field, &obj);CHKERRQ(ierr); 2777 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 2778 if (id == PETSCFE_CLASSID) { 2779 PetscFE fe = (PetscFE) obj; 2780 2781 ierr = PetscFEGetDualSpace(fe, &Q);CHKERRQ(ierr); 2782 ierr = PetscFEGetNumComponents(fe, &Nc);CHKERRQ(ierr); 2783 ierr = PetscFECreateTabulation(fe, 1, 1, x, 0, &T);CHKERRQ(ierr); 2784 } else if (id == PETSCFV_CLASSID) { 2785 PetscFV fv = (PetscFV) obj; 2786 2787 ierr = PetscFVGetDualSpace(fv, &Q);CHKERRQ(ierr); 2788 Nc = 1; 2789 } else SETERRQ1(PetscObjectComm((PetscObject)dmc),PETSC_ERR_ARG_WRONG,"Unknown discretization type for field %D",field); 2790 ierr = PetscDualSpaceGetDimension(Q, &fpdim);CHKERRQ(ierr); 2791 /* For each fine grid cell */ 2792 for (cell = cStart; cell < cEnd; ++cell) { 2793 PetscInt *findices, *cindices; 2794 PetscInt numFIndices, numCIndices; 2795 2796 ierr = DMPlexGetClosureIndices(dmf, fsection, globalFSection, cell, PETSC_FALSE, &numFIndices, &findices, NULL, NULL);CHKERRQ(ierr); 2797 ierr = DMPlexComputeCellGeometryFEM(dmf, cell, NULL, v0, J, invJ, &detJ);CHKERRQ(ierr); 2798 if (numFIndices != fpdim) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Number of fine indices %D != %D dual basis vecs", numFIndices, fpdim); 2799 for (i = 0; i < fpdim; ++i) { 2800 Vec pointVec; 2801 PetscScalar *pV; 2802 PetscSF coarseCellSF = NULL; 2803 const PetscSFNode *coarseCells; 2804 PetscInt numCoarseCells, cpdim, q, c, j; 2805 2806 /* Get points from the dual basis functional quadrature */ 2807 ierr = PetscDualSpaceGetFunctional(Q, i, &f);CHKERRQ(ierr); 2808 ierr = PetscQuadratureGetData(f, NULL, &qNc, &Np, &qpoints, &qweights);CHKERRQ(ierr); 2809 if (qNc != Nc) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Number of components in quadrature %D does not match coarse field %D", qNc, Nc); 2810 ierr = VecCreateSeq(PETSC_COMM_SELF, Np*dim, &pointVec);CHKERRQ(ierr); 2811 ierr = VecSetBlockSize(pointVec, dim);CHKERRQ(ierr); 2812 ierr = VecGetArray(pointVec, &pV);CHKERRQ(ierr); 2813 for (q = 0; q < Np; ++q) { 2814 const PetscReal xi0[3] = {-1., -1., -1.}; 2815 2816 /* Transform point to real space */ 2817 CoordinatesRefToReal(dim, dim, xi0, v0, J, &qpoints[q*dim], x); 2818 for (d = 0; d < dim; ++d) pV[q*dim+d] = x[d]; 2819 } 2820 ierr = VecRestoreArray(pointVec, &pV);CHKERRQ(ierr); 2821 /* Get set of coarse cells that overlap points (would like to group points by coarse cell) */ 2822 /* OPT: Read this out from preallocation information */ 2823 ierr = DMLocatePoints(dmc, pointVec, DM_POINTLOCATION_NEAREST, &coarseCellSF);CHKERRQ(ierr); 2824 /* Update preallocation info */ 2825 ierr = PetscSFGetGraph(coarseCellSF, NULL, &numCoarseCells, NULL, &coarseCells);CHKERRQ(ierr); 2826 if (numCoarseCells != Np) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Not all closure points located"); 2827 ierr = VecGetArray(pointVec, &pV);CHKERRQ(ierr); 2828 for (ccell = 0; ccell < numCoarseCells; ++ccell) { 2829 PetscReal pVReal[3]; 2830 const PetscReal xi0[3] = {-1., -1., -1.}; 2831 2832 ierr = DMPlexGetClosureIndices(dmc, csection, globalCSection, coarseCells[ccell].index, PETSC_FALSE, &numCIndices, &cindices, NULL, NULL);CHKERRQ(ierr); 2833 /* Transform points from real space to coarse reference space */ 2834 ierr = DMPlexComputeCellGeometryFEM(dmc, coarseCells[ccell].index, NULL, v0c, Jc, invJc, &detJc);CHKERRQ(ierr); 2835 for (d = 0; d < dim; ++d) pVReal[d] = PetscRealPart(pV[ccell*dim+d]); 2836 CoordinatesRealToRef(dim, dim, xi0, v0c, invJc, pVReal, x); 2837 2838 if (id == PETSCFE_CLASSID) { 2839 PetscFE fe = (PetscFE) obj; 2840 2841 /* Evaluate coarse basis on contained point */ 2842 ierr = PetscFEGetDimension(fe, &cpdim);CHKERRQ(ierr); 2843 ierr = PetscFEComputeTabulation(fe, 1, x, 0, T);CHKERRQ(ierr); 2844 ierr = PetscArrayzero(elemMat, cpdim);CHKERRQ(ierr); 2845 /* Get elemMat entries by multiplying by weight */ 2846 for (j = 0; j < cpdim; ++j) { 2847 for (c = 0; c < Nc; ++c) elemMat[j] += T->T[0][j*Nc + c]*qweights[ccell*qNc + c]; 2848 } 2849 } else { 2850 cpdim = 1; 2851 for (j = 0; j < cpdim; ++j) { 2852 for (c = 0; c < Nc; ++c) elemMat[j] += 1.0*qweights[ccell*qNc + c]; 2853 } 2854 } 2855 /* Update interpolator */ 2856 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(cell, name, 1, numCIndices, elemMat);CHKERRQ(ierr);} 2857 if (numCIndices != cpdim) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Number of element matrix columns %D != %D", numCIndices, cpdim); 2858 ierr = MatSetValues(In, 1, &findices[i], numCIndices, cindices, elemMat, INSERT_VALUES);CHKERRQ(ierr); 2859 ierr = DMPlexRestoreClosureIndices(dmc, csection, globalCSection, coarseCells[ccell].index, PETSC_FALSE, &numCIndices, &cindices, NULL, NULL);CHKERRQ(ierr); 2860 } 2861 ierr = VecRestoreArray(pointVec, &pV);CHKERRQ(ierr); 2862 ierr = PetscSFDestroy(&coarseCellSF);CHKERRQ(ierr); 2863 ierr = VecDestroy(&pointVec);CHKERRQ(ierr); 2864 } 2865 ierr = DMPlexRestoreClosureIndices(dmf, fsection, globalFSection, cell, PETSC_FALSE, &numFIndices, &findices, NULL, NULL);CHKERRQ(ierr); 2866 } 2867 if (id == PETSCFE_CLASSID) {ierr = PetscTabulationDestroy(&T);CHKERRQ(ierr);} 2868 } 2869 ierr = PetscFree3(v0,J,invJ);CHKERRQ(ierr); 2870 ierr = PetscFree3(v0c,Jc,invJc);CHKERRQ(ierr); 2871 ierr = PetscFree(elemMat);CHKERRQ(ierr); 2872 ierr = MatAssemblyBegin(In, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2873 ierr = MatAssemblyEnd(In, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2874 ierr = PetscLogEventEnd(DMPLEX_InterpolatorFEM,dmc,dmf,0,0);CHKERRQ(ierr); 2875 PetscFunctionReturn(0); 2876 } 2877 2878 /*@ 2879 DMPlexComputeMassMatrixGeneral - Form the local portion of the mass matrix M from the coarse DM to a non-nested fine DM. 2880 2881 Input Parameters: 2882 + dmf - The fine mesh 2883 . dmc - The coarse mesh 2884 - user - The user context 2885 2886 Output Parameter: 2887 . mass - The mass matrix 2888 2889 Level: developer 2890 2891 .seealso: DMPlexComputeMassMatrixNested(), DMPlexComputeInterpolatorNested(), DMPlexComputeInterpolatorGeneral(), DMPlexComputeJacobianFEM() 2892 @*/ 2893 PetscErrorCode DMPlexComputeMassMatrixGeneral(DM dmc, DM dmf, Mat mass, void *user) 2894 { 2895 DM_Plex *mesh = (DM_Plex *) dmf->data; 2896 const char *name = "Mass Matrix"; 2897 PetscDS prob; 2898 PetscSection fsection, csection, globalFSection, globalCSection; 2899 PetscHSetIJ ht; 2900 PetscLayout rLayout; 2901 PetscInt *dnz, *onz; 2902 PetscInt locRows, rStart, rEnd; 2903 PetscReal *x, *v0, *J, *invJ, detJ; 2904 PetscReal *v0c, *Jc, *invJc, detJc; 2905 PetscScalar *elemMat; 2906 PetscInt dim, Nf, field, totDim, cStart, cEnd, cell, ccell; 2907 PetscErrorCode ierr; 2908 2909 PetscFunctionBegin; 2910 ierr = DMGetCoordinateDim(dmc, &dim);CHKERRQ(ierr); 2911 ierr = DMGetDS(dmc, &prob);CHKERRQ(ierr); 2912 ierr = PetscDSGetWorkspace(prob, &x, NULL, NULL, NULL, NULL);CHKERRQ(ierr); 2913 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 2914 ierr = PetscMalloc3(dim,&v0,dim*dim,&J,dim*dim,&invJ);CHKERRQ(ierr); 2915 ierr = PetscMalloc3(dim,&v0c,dim*dim,&Jc,dim*dim,&invJc);CHKERRQ(ierr); 2916 ierr = DMGetLocalSection(dmf, &fsection);CHKERRQ(ierr); 2917 ierr = DMGetGlobalSection(dmf, &globalFSection);CHKERRQ(ierr); 2918 ierr = DMGetLocalSection(dmc, &csection);CHKERRQ(ierr); 2919 ierr = DMGetGlobalSection(dmc, &globalCSection);CHKERRQ(ierr); 2920 ierr = DMPlexGetHeightStratum(dmf, 0, &cStart, &cEnd);CHKERRQ(ierr); 2921 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 2922 ierr = PetscMalloc1(totDim, &elemMat);CHKERRQ(ierr); 2923 2924 ierr = MatGetLocalSize(mass, &locRows, NULL);CHKERRQ(ierr); 2925 ierr = PetscLayoutCreate(PetscObjectComm((PetscObject) mass), &rLayout);CHKERRQ(ierr); 2926 ierr = PetscLayoutSetLocalSize(rLayout, locRows);CHKERRQ(ierr); 2927 ierr = PetscLayoutSetBlockSize(rLayout, 1);CHKERRQ(ierr); 2928 ierr = PetscLayoutSetUp(rLayout);CHKERRQ(ierr); 2929 ierr = PetscLayoutGetRange(rLayout, &rStart, &rEnd);CHKERRQ(ierr); 2930 ierr = PetscLayoutDestroy(&rLayout);CHKERRQ(ierr); 2931 ierr = PetscCalloc2(locRows,&dnz,locRows,&onz);CHKERRQ(ierr); 2932 ierr = PetscHSetIJCreate(&ht);CHKERRQ(ierr); 2933 for (field = 0; field < Nf; ++field) { 2934 PetscObject obj; 2935 PetscClassId id; 2936 PetscQuadrature quad; 2937 const PetscReal *qpoints; 2938 PetscInt Nq, Nc, i, d; 2939 2940 ierr = PetscDSGetDiscretization(prob, field, &obj);CHKERRQ(ierr); 2941 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 2942 if (id == PETSCFE_CLASSID) {ierr = PetscFEGetQuadrature((PetscFE) obj, &quad);CHKERRQ(ierr);} 2943 else {ierr = PetscFVGetQuadrature((PetscFV) obj, &quad);CHKERRQ(ierr);} 2944 ierr = PetscQuadratureGetData(quad, NULL, &Nc, &Nq, &qpoints, NULL);CHKERRQ(ierr); 2945 /* For each fine grid cell */ 2946 for (cell = cStart; cell < cEnd; ++cell) { 2947 Vec pointVec; 2948 PetscScalar *pV; 2949 PetscSF coarseCellSF = NULL; 2950 const PetscSFNode *coarseCells; 2951 PetscInt numCoarseCells, q, c; 2952 PetscInt *findices, *cindices; 2953 PetscInt numFIndices, numCIndices; 2954 2955 ierr = DMPlexGetClosureIndices(dmf, fsection, globalFSection, cell, PETSC_FALSE, &numFIndices, &findices, NULL, NULL);CHKERRQ(ierr); 2956 ierr = DMPlexComputeCellGeometryFEM(dmf, cell, NULL, v0, J, invJ, &detJ);CHKERRQ(ierr); 2957 /* Get points from the quadrature */ 2958 ierr = VecCreateSeq(PETSC_COMM_SELF, Nq*dim, &pointVec);CHKERRQ(ierr); 2959 ierr = VecSetBlockSize(pointVec, dim);CHKERRQ(ierr); 2960 ierr = VecGetArray(pointVec, &pV);CHKERRQ(ierr); 2961 for (q = 0; q < Nq; ++q) { 2962 const PetscReal xi0[3] = {-1., -1., -1.}; 2963 2964 /* Transform point to real space */ 2965 CoordinatesRefToReal(dim, dim, xi0, v0, J, &qpoints[q*dim], x); 2966 for (d = 0; d < dim; ++d) pV[q*dim+d] = x[d]; 2967 } 2968 ierr = VecRestoreArray(pointVec, &pV);CHKERRQ(ierr); 2969 /* Get set of coarse cells that overlap points (would like to group points by coarse cell) */ 2970 ierr = DMLocatePoints(dmc, pointVec, DM_POINTLOCATION_NEAREST, &coarseCellSF);CHKERRQ(ierr); 2971 ierr = PetscSFViewFromOptions(coarseCellSF, NULL, "-interp_sf_view");CHKERRQ(ierr); 2972 /* Update preallocation info */ 2973 ierr = PetscSFGetGraph(coarseCellSF, NULL, &numCoarseCells, NULL, &coarseCells);CHKERRQ(ierr); 2974 if (numCoarseCells != Nq) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Not all closure points located"); 2975 { 2976 PetscHashIJKey key; 2977 PetscBool missing; 2978 2979 for (i = 0; i < numFIndices; ++i) { 2980 key.i = findices[i]; 2981 if (key.i >= 0) { 2982 /* Get indices for coarse elements */ 2983 for (ccell = 0; ccell < numCoarseCells; ++ccell) { 2984 ierr = DMPlexGetClosureIndices(dmc, csection, globalCSection, coarseCells[ccell].index, PETSC_FALSE, &numCIndices, &cindices, NULL, NULL);CHKERRQ(ierr); 2985 for (c = 0; c < numCIndices; ++c) { 2986 key.j = cindices[c]; 2987 if (key.j < 0) continue; 2988 ierr = PetscHSetIJQueryAdd(ht, key, &missing);CHKERRQ(ierr); 2989 if (missing) { 2990 if ((key.j >= rStart) && (key.j < rEnd)) ++dnz[key.i-rStart]; 2991 else ++onz[key.i-rStart]; 2992 } 2993 } 2994 ierr = DMPlexRestoreClosureIndices(dmc, csection, globalCSection, coarseCells[ccell].index, PETSC_FALSE, &numCIndices, &cindices, NULL, NULL);CHKERRQ(ierr); 2995 } 2996 } 2997 } 2998 } 2999 ierr = PetscSFDestroy(&coarseCellSF);CHKERRQ(ierr); 3000 ierr = VecDestroy(&pointVec);CHKERRQ(ierr); 3001 ierr = DMPlexRestoreClosureIndices(dmf, fsection, globalFSection, cell, PETSC_FALSE, &numFIndices, &findices, NULL, NULL);CHKERRQ(ierr); 3002 } 3003 } 3004 ierr = PetscHSetIJDestroy(&ht);CHKERRQ(ierr); 3005 ierr = MatXAIJSetPreallocation(mass, 1, dnz, onz, NULL, NULL);CHKERRQ(ierr); 3006 ierr = MatSetOption(mass, MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 3007 ierr = PetscFree2(dnz,onz);CHKERRQ(ierr); 3008 for (field = 0; field < Nf; ++field) { 3009 PetscObject obj; 3010 PetscClassId id; 3011 PetscTabulation T, Tfine; 3012 PetscQuadrature quad; 3013 const PetscReal *qpoints, *qweights; 3014 PetscInt Nq, Nc, i, d; 3015 3016 ierr = PetscDSGetDiscretization(prob, field, &obj);CHKERRQ(ierr); 3017 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 3018 if (id == PETSCFE_CLASSID) { 3019 ierr = PetscFEGetQuadrature((PetscFE) obj, &quad);CHKERRQ(ierr); 3020 ierr = PetscFEGetCellTabulation((PetscFE) obj, 1, &Tfine);CHKERRQ(ierr); 3021 ierr = PetscFECreateTabulation((PetscFE) obj, 1, 1, x, 0, &T);CHKERRQ(ierr); 3022 } else { 3023 ierr = PetscFVGetQuadrature((PetscFV) obj, &quad);CHKERRQ(ierr); 3024 } 3025 ierr = PetscQuadratureGetData(quad, NULL, &Nc, &Nq, &qpoints, &qweights);CHKERRQ(ierr); 3026 /* For each fine grid cell */ 3027 for (cell = cStart; cell < cEnd; ++cell) { 3028 Vec pointVec; 3029 PetscScalar *pV; 3030 PetscSF coarseCellSF = NULL; 3031 const PetscSFNode *coarseCells; 3032 PetscInt numCoarseCells, cpdim, q, c, j; 3033 PetscInt *findices, *cindices; 3034 PetscInt numFIndices, numCIndices; 3035 3036 ierr = DMPlexGetClosureIndices(dmf, fsection, globalFSection, cell, PETSC_FALSE, &numFIndices, &findices, NULL, NULL);CHKERRQ(ierr); 3037 ierr = DMPlexComputeCellGeometryFEM(dmf, cell, NULL, v0, J, invJ, &detJ);CHKERRQ(ierr); 3038 /* Get points from the quadrature */ 3039 ierr = VecCreateSeq(PETSC_COMM_SELF, Nq*dim, &pointVec);CHKERRQ(ierr); 3040 ierr = VecSetBlockSize(pointVec, dim);CHKERRQ(ierr); 3041 ierr = VecGetArray(pointVec, &pV);CHKERRQ(ierr); 3042 for (q = 0; q < Nq; ++q) { 3043 const PetscReal xi0[3] = {-1., -1., -1.}; 3044 3045 /* Transform point to real space */ 3046 CoordinatesRefToReal(dim, dim, xi0, v0, J, &qpoints[q*dim], x); 3047 for (d = 0; d < dim; ++d) pV[q*dim+d] = x[d]; 3048 } 3049 ierr = VecRestoreArray(pointVec, &pV);CHKERRQ(ierr); 3050 /* Get set of coarse cells that overlap points (would like to group points by coarse cell) */ 3051 ierr = DMLocatePoints(dmc, pointVec, DM_POINTLOCATION_NEAREST, &coarseCellSF);CHKERRQ(ierr); 3052 /* Update matrix */ 3053 ierr = PetscSFGetGraph(coarseCellSF, NULL, &numCoarseCells, NULL, &coarseCells);CHKERRQ(ierr); 3054 if (numCoarseCells != Nq) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Not all closure points located"); 3055 ierr = VecGetArray(pointVec, &pV);CHKERRQ(ierr); 3056 for (ccell = 0; ccell < numCoarseCells; ++ccell) { 3057 PetscReal pVReal[3]; 3058 const PetscReal xi0[3] = {-1., -1., -1.}; 3059 3060 ierr = DMPlexGetClosureIndices(dmc, csection, globalCSection, coarseCells[ccell].index, PETSC_FALSE, &numCIndices, &cindices, NULL, NULL);CHKERRQ(ierr); 3061 /* Transform points from real space to coarse reference space */ 3062 ierr = DMPlexComputeCellGeometryFEM(dmc, coarseCells[ccell].index, NULL, v0c, Jc, invJc, &detJc);CHKERRQ(ierr); 3063 for (d = 0; d < dim; ++d) pVReal[d] = PetscRealPart(pV[ccell*dim+d]); 3064 CoordinatesRealToRef(dim, dim, xi0, v0c, invJc, pVReal, x); 3065 3066 if (id == PETSCFE_CLASSID) { 3067 PetscFE fe = (PetscFE) obj; 3068 3069 /* Evaluate coarse basis on contained point */ 3070 ierr = PetscFEGetDimension(fe, &cpdim);CHKERRQ(ierr); 3071 ierr = PetscFEComputeTabulation(fe, 1, x, 0, T);CHKERRQ(ierr); 3072 /* Get elemMat entries by multiplying by weight */ 3073 for (i = 0; i < numFIndices; ++i) { 3074 ierr = PetscArrayzero(elemMat, cpdim);CHKERRQ(ierr); 3075 for (j = 0; j < cpdim; ++j) { 3076 for (c = 0; c < Nc; ++c) elemMat[j] += T->T[0][j*Nc + c]*Tfine->T[0][(ccell*numFIndices + i)*Nc + c]*qweights[ccell*Nc + c]*detJ; 3077 } 3078 /* Update interpolator */ 3079 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(cell, name, 1, numCIndices, elemMat);CHKERRQ(ierr);} 3080 if (numCIndices != cpdim) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Number of element matrix columns %D != %D", numCIndices, cpdim); 3081 ierr = MatSetValues(mass, 1, &findices[i], numCIndices, cindices, elemMat, ADD_VALUES);CHKERRQ(ierr); 3082 } 3083 } else { 3084 cpdim = 1; 3085 for (i = 0; i < numFIndices; ++i) { 3086 ierr = PetscArrayzero(elemMat, cpdim);CHKERRQ(ierr); 3087 for (j = 0; j < cpdim; ++j) { 3088 for (c = 0; c < Nc; ++c) elemMat[j] += 1.0*1.0*qweights[ccell*Nc + c]*detJ; 3089 } 3090 /* Update interpolator */ 3091 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(cell, name, 1, numCIndices, elemMat);CHKERRQ(ierr);} 3092 ierr = PetscPrintf(PETSC_COMM_SELF, "Nq: %D %D Nf: %D %D Nc: %D %D\n", ccell, Nq, i, numFIndices, j, numCIndices);CHKERRQ(ierr); 3093 if (numCIndices != cpdim) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Number of element matrix columns %D != %D", numCIndices, cpdim); 3094 ierr = MatSetValues(mass, 1, &findices[i], numCIndices, cindices, elemMat, ADD_VALUES);CHKERRQ(ierr); 3095 } 3096 } 3097 ierr = DMPlexRestoreClosureIndices(dmc, csection, globalCSection, coarseCells[ccell].index, PETSC_FALSE, &numCIndices, &cindices, NULL, NULL);CHKERRQ(ierr); 3098 } 3099 ierr = VecRestoreArray(pointVec, &pV);CHKERRQ(ierr); 3100 ierr = PetscSFDestroy(&coarseCellSF);CHKERRQ(ierr); 3101 ierr = VecDestroy(&pointVec);CHKERRQ(ierr); 3102 ierr = DMPlexRestoreClosureIndices(dmf, fsection, globalFSection, cell, PETSC_FALSE, &numFIndices, &findices, NULL, NULL);CHKERRQ(ierr); 3103 } 3104 if (id == PETSCFE_CLASSID) {ierr = PetscTabulationDestroy(&T);CHKERRQ(ierr);} 3105 } 3106 ierr = PetscFree3(v0,J,invJ);CHKERRQ(ierr); 3107 ierr = PetscFree3(v0c,Jc,invJc);CHKERRQ(ierr); 3108 ierr = PetscFree(elemMat);CHKERRQ(ierr); 3109 ierr = MatAssemblyBegin(mass, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3110 ierr = MatAssemblyEnd(mass, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3111 PetscFunctionReturn(0); 3112 } 3113 3114 /*@ 3115 DMPlexComputeInjectorFEM - Compute a mapping from coarse unknowns to fine unknowns 3116 3117 Input Parameters: 3118 + dmc - The coarse mesh 3119 - dmf - The fine mesh 3120 - user - The user context 3121 3122 Output Parameter: 3123 . sc - The mapping 3124 3125 Level: developer 3126 3127 .seealso: DMPlexComputeInterpolatorNested(), DMPlexComputeJacobianFEM() 3128 @*/ 3129 PetscErrorCode DMPlexComputeInjectorFEM(DM dmc, DM dmf, VecScatter *sc, void *user) 3130 { 3131 PetscDS prob; 3132 PetscFE *feRef; 3133 PetscFV *fvRef; 3134 Vec fv, cv; 3135 IS fis, cis; 3136 PetscSection fsection, fglobalSection, csection, cglobalSection; 3137 PetscInt *cmap, *cellCIndices, *cellFIndices, *cindices, *findices; 3138 PetscInt cTotDim, fTotDim = 0, Nf, f, field, cStart, cEnd, c, dim, d, startC, endC, offsetC, offsetF, m; 3139 PetscBool *needAvg; 3140 PetscErrorCode ierr; 3141 3142 PetscFunctionBegin; 3143 ierr = PetscLogEventBegin(DMPLEX_InjectorFEM,dmc,dmf,0,0);CHKERRQ(ierr); 3144 ierr = DMGetDimension(dmf, &dim);CHKERRQ(ierr); 3145 ierr = DMGetLocalSection(dmf, &fsection);CHKERRQ(ierr); 3146 ierr = DMGetGlobalSection(dmf, &fglobalSection);CHKERRQ(ierr); 3147 ierr = DMGetLocalSection(dmc, &csection);CHKERRQ(ierr); 3148 ierr = DMGetGlobalSection(dmc, &cglobalSection);CHKERRQ(ierr); 3149 ierr = PetscSectionGetNumFields(fsection, &Nf);CHKERRQ(ierr); 3150 ierr = DMPlexGetSimplexOrBoxCells(dmc, 0, &cStart, &cEnd);CHKERRQ(ierr); 3151 ierr = DMGetDS(dmc, &prob);CHKERRQ(ierr); 3152 ierr = PetscCalloc3(Nf,&feRef,Nf,&fvRef,Nf,&needAvg);CHKERRQ(ierr); 3153 for (f = 0; f < Nf; ++f) { 3154 PetscObject obj; 3155 PetscClassId id; 3156 PetscInt fNb = 0, Nc = 0; 3157 3158 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 3159 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 3160 if (id == PETSCFE_CLASSID) { 3161 PetscFE fe = (PetscFE) obj; 3162 PetscSpace sp; 3163 PetscInt maxDegree; 3164 3165 ierr = PetscFERefine(fe, &feRef[f]);CHKERRQ(ierr); 3166 ierr = PetscFEGetDimension(feRef[f], &fNb);CHKERRQ(ierr); 3167 ierr = PetscFEGetNumComponents(fe, &Nc);CHKERRQ(ierr); 3168 ierr = PetscFEGetBasisSpace(fe, &sp);CHKERRQ(ierr); 3169 ierr = PetscSpaceGetDegree(sp, NULL, &maxDegree);CHKERRQ(ierr); 3170 if (!maxDegree) needAvg[f] = PETSC_TRUE; 3171 } else if (id == PETSCFV_CLASSID) { 3172 PetscFV fv = (PetscFV) obj; 3173 PetscDualSpace Q; 3174 3175 ierr = PetscFVRefine(fv, &fvRef[f]);CHKERRQ(ierr); 3176 ierr = PetscFVGetDualSpace(fvRef[f], &Q);CHKERRQ(ierr); 3177 ierr = PetscDualSpaceGetDimension(Q, &fNb);CHKERRQ(ierr); 3178 ierr = PetscFVGetNumComponents(fv, &Nc);CHKERRQ(ierr); 3179 needAvg[f] = PETSC_TRUE; 3180 } 3181 fTotDim += fNb; 3182 } 3183 ierr = PetscDSGetTotalDimension(prob, &cTotDim);CHKERRQ(ierr); 3184 ierr = PetscMalloc1(cTotDim,&cmap);CHKERRQ(ierr); 3185 for (field = 0, offsetC = 0, offsetF = 0; field < Nf; ++field) { 3186 PetscFE feC; 3187 PetscFV fvC; 3188 PetscDualSpace QF, QC; 3189 PetscInt order = -1, NcF, NcC, fpdim, cpdim; 3190 3191 if (feRef[field]) { 3192 ierr = PetscDSGetDiscretization(prob, field, (PetscObject *) &feC);CHKERRQ(ierr); 3193 ierr = PetscFEGetNumComponents(feC, &NcC);CHKERRQ(ierr); 3194 ierr = PetscFEGetNumComponents(feRef[field], &NcF);CHKERRQ(ierr); 3195 ierr = PetscFEGetDualSpace(feRef[field], &QF);CHKERRQ(ierr); 3196 ierr = PetscDualSpaceGetOrder(QF, &order);CHKERRQ(ierr); 3197 ierr = PetscDualSpaceGetDimension(QF, &fpdim);CHKERRQ(ierr); 3198 ierr = PetscFEGetDualSpace(feC, &QC);CHKERRQ(ierr); 3199 ierr = PetscDualSpaceGetDimension(QC, &cpdim);CHKERRQ(ierr); 3200 } else { 3201 ierr = PetscDSGetDiscretization(prob, field, (PetscObject *) &fvC);CHKERRQ(ierr); 3202 ierr = PetscFVGetNumComponents(fvC, &NcC);CHKERRQ(ierr); 3203 ierr = PetscFVGetNumComponents(fvRef[field], &NcF);CHKERRQ(ierr); 3204 ierr = PetscFVGetDualSpace(fvRef[field], &QF);CHKERRQ(ierr); 3205 ierr = PetscDualSpaceGetDimension(QF, &fpdim);CHKERRQ(ierr); 3206 ierr = PetscFVGetDualSpace(fvC, &QC);CHKERRQ(ierr); 3207 ierr = PetscDualSpaceGetDimension(QC, &cpdim);CHKERRQ(ierr); 3208 } 3209 if (NcF != NcC) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Number of components in fine space field %D does not match coarse field %D", NcF, NcC); 3210 for (c = 0; c < cpdim; ++c) { 3211 PetscQuadrature cfunc; 3212 const PetscReal *cqpoints, *cqweights; 3213 PetscInt NqcC, NpC; 3214 PetscBool found = PETSC_FALSE; 3215 3216 ierr = PetscDualSpaceGetFunctional(QC, c, &cfunc);CHKERRQ(ierr); 3217 ierr = PetscQuadratureGetData(cfunc, NULL, &NqcC, &NpC, &cqpoints, &cqweights);CHKERRQ(ierr); 3218 if (NqcC != NcC) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Number of quadrature components %D must match number of field components %D", NqcC, NcC); 3219 if (NpC != 1 && feRef[field]) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Do not know how to do injection for moments"); 3220 for (f = 0; f < fpdim; ++f) { 3221 PetscQuadrature ffunc; 3222 const PetscReal *fqpoints, *fqweights; 3223 PetscReal sum = 0.0; 3224 PetscInt NqcF, NpF; 3225 3226 ierr = PetscDualSpaceGetFunctional(QF, f, &ffunc);CHKERRQ(ierr); 3227 ierr = PetscQuadratureGetData(ffunc, NULL, &NqcF, &NpF, &fqpoints, &fqweights);CHKERRQ(ierr); 3228 if (NqcF != NcF) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Number of quadrature components %D must match number of field components %D", NqcF, NcF); 3229 if (NpC != NpF) continue; 3230 for (d = 0; d < dim; ++d) sum += PetscAbsReal(cqpoints[d] - fqpoints[d]); 3231 if (sum > 1.0e-9) continue; 3232 for (d = 0; d < NcC; ++d) sum += PetscAbsReal(cqweights[d]*fqweights[d]); 3233 if (sum < 1.0e-9) continue; 3234 cmap[offsetC+c] = offsetF+f; 3235 found = PETSC_TRUE; 3236 break; 3237 } 3238 if (!found) { 3239 /* TODO We really want the average here, but some asshole put VecScatter in the interface */ 3240 if (fvRef[field] || (feRef[field] && order == 0)) { 3241 cmap[offsetC+c] = offsetF+0; 3242 } else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not locate matching functional for injection"); 3243 } 3244 } 3245 offsetC += cpdim; 3246 offsetF += fpdim; 3247 } 3248 for (f = 0; f < Nf; ++f) {ierr = PetscFEDestroy(&feRef[f]);CHKERRQ(ierr);ierr = PetscFVDestroy(&fvRef[f]);CHKERRQ(ierr);} 3249 ierr = PetscFree3(feRef,fvRef,needAvg);CHKERRQ(ierr); 3250 3251 ierr = DMGetGlobalVector(dmf, &fv);CHKERRQ(ierr); 3252 ierr = DMGetGlobalVector(dmc, &cv);CHKERRQ(ierr); 3253 ierr = VecGetOwnershipRange(cv, &startC, &endC);CHKERRQ(ierr); 3254 ierr = PetscSectionGetConstrainedStorageSize(cglobalSection, &m);CHKERRQ(ierr); 3255 ierr = PetscMalloc2(cTotDim,&cellCIndices,fTotDim,&cellFIndices);CHKERRQ(ierr); 3256 ierr = PetscMalloc1(m,&cindices);CHKERRQ(ierr); 3257 ierr = PetscMalloc1(m,&findices);CHKERRQ(ierr); 3258 for (d = 0; d < m; ++d) cindices[d] = findices[d] = -1; 3259 for (c = cStart; c < cEnd; ++c) { 3260 ierr = DMPlexMatGetClosureIndicesRefined(dmf, fsection, fglobalSection, dmc, csection, cglobalSection, c, cellCIndices, cellFIndices);CHKERRQ(ierr); 3261 for (d = 0; d < cTotDim; ++d) { 3262 if ((cellCIndices[d] < startC) || (cellCIndices[d] >= endC)) continue; 3263 if ((findices[cellCIndices[d]-startC] >= 0) && (findices[cellCIndices[d]-startC] != cellFIndices[cmap[d]])) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Coarse dof %D maps to both %D and %D", cindices[cellCIndices[d]-startC], findices[cellCIndices[d]-startC], cellFIndices[cmap[d]]); 3264 cindices[cellCIndices[d]-startC] = cellCIndices[d]; 3265 findices[cellCIndices[d]-startC] = cellFIndices[cmap[d]]; 3266 } 3267 } 3268 ierr = PetscFree(cmap);CHKERRQ(ierr); 3269 ierr = PetscFree2(cellCIndices,cellFIndices);CHKERRQ(ierr); 3270 3271 ierr = ISCreateGeneral(PETSC_COMM_SELF, m, cindices, PETSC_OWN_POINTER, &cis);CHKERRQ(ierr); 3272 ierr = ISCreateGeneral(PETSC_COMM_SELF, m, findices, PETSC_OWN_POINTER, &fis);CHKERRQ(ierr); 3273 ierr = VecScatterCreate(cv, cis, fv, fis, sc);CHKERRQ(ierr); 3274 ierr = ISDestroy(&cis);CHKERRQ(ierr); 3275 ierr = ISDestroy(&fis);CHKERRQ(ierr); 3276 ierr = DMRestoreGlobalVector(dmf, &fv);CHKERRQ(ierr); 3277 ierr = DMRestoreGlobalVector(dmc, &cv);CHKERRQ(ierr); 3278 ierr = PetscLogEventEnd(DMPLEX_InjectorFEM,dmc,dmf,0,0);CHKERRQ(ierr); 3279 PetscFunctionReturn(0); 3280 } 3281 3282 /*@C 3283 DMPlexGetCellFields - Retrieve the field values values for a chunk of cells 3284 3285 Input Parameters: 3286 + dm - The DM 3287 . cellIS - The cells to include 3288 . locX - A local vector with the solution fields 3289 . locX_t - A local vector with solution field time derivatives, or NULL 3290 - locA - A local vector with auxiliary fields, or NULL 3291 3292 Output Parameters: 3293 + u - The field coefficients 3294 . u_t - The fields derivative coefficients 3295 - a - The auxiliary field coefficients 3296 3297 Level: developer 3298 3299 .seealso: DMPlexGetFaceFields() 3300 @*/ 3301 PetscErrorCode DMPlexGetCellFields(DM dm, IS cellIS, Vec locX, Vec locX_t, Vec locA, PetscScalar **u, PetscScalar **u_t, PetscScalar **a) 3302 { 3303 DM plex, plexA = NULL; 3304 DMEnclosureType encAux; 3305 PetscSection section, sectionAux; 3306 PetscDS prob; 3307 const PetscInt *cells; 3308 PetscInt cStart, cEnd, numCells, totDim, totDimAux, c; 3309 PetscErrorCode ierr; 3310 3311 PetscFunctionBegin; 3312 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3313 PetscValidHeaderSpecific(locX, VEC_CLASSID, 3); 3314 if (locX_t) {PetscValidHeaderSpecific(locX_t, VEC_CLASSID, 4);} 3315 if (locA) {PetscValidHeaderSpecific(locA, VEC_CLASSID, 5);} 3316 PetscValidPointer(u, 6); 3317 PetscValidPointer(u_t, 7); 3318 PetscValidPointer(a, 8); 3319 ierr = DMPlexConvertPlex(dm, &plex, PETSC_FALSE);CHKERRQ(ierr); 3320 ierr = ISGetPointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 3321 ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); 3322 ierr = DMGetCellDS(dm, cells ? cells[cStart] : cStart, &prob);CHKERRQ(ierr); 3323 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 3324 if (locA) { 3325 DM dmAux; 3326 PetscDS probAux; 3327 3328 ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); 3329 ierr = DMGetEnclosureRelation(dmAux, dm, &encAux);CHKERRQ(ierr); 3330 ierr = DMPlexConvertPlex(dmAux, &plexA, PETSC_FALSE);CHKERRQ(ierr); 3331 ierr = DMGetLocalSection(dmAux, §ionAux);CHKERRQ(ierr); 3332 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 3333 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 3334 } 3335 numCells = cEnd - cStart; 3336 ierr = DMGetWorkArray(dm, numCells*totDim, MPIU_SCALAR, u);CHKERRQ(ierr); 3337 if (locX_t) {ierr = DMGetWorkArray(dm, numCells*totDim, MPIU_SCALAR, u_t);CHKERRQ(ierr);} else {*u_t = NULL;} 3338 if (locA) {ierr = DMGetWorkArray(dm, numCells*totDimAux, MPIU_SCALAR, a);CHKERRQ(ierr);} else {*a = NULL;} 3339 for (c = cStart; c < cEnd; ++c) { 3340 const PetscInt cell = cells ? cells[c] : c; 3341 const PetscInt cind = c - cStart; 3342 PetscScalar *x = NULL, *x_t = NULL, *ul = *u, *ul_t = *u_t, *al = *a; 3343 PetscInt i; 3344 3345 ierr = DMPlexVecGetClosure(plex, section, locX, cell, NULL, &x);CHKERRQ(ierr); 3346 for (i = 0; i < totDim; ++i) ul[cind*totDim+i] = x[i]; 3347 ierr = DMPlexVecRestoreClosure(plex, section, locX, cell, NULL, &x);CHKERRQ(ierr); 3348 if (locX_t) { 3349 ierr = DMPlexVecGetClosure(plex, section, locX_t, cell, NULL, &x_t);CHKERRQ(ierr); 3350 for (i = 0; i < totDim; ++i) ul_t[cind*totDim+i] = x_t[i]; 3351 ierr = DMPlexVecRestoreClosure(plex, section, locX_t, cell, NULL, &x_t);CHKERRQ(ierr); 3352 } 3353 if (locA) { 3354 PetscInt subcell; 3355 ierr = DMGetEnclosurePoint(plexA, dm, encAux, cell, &subcell);CHKERRQ(ierr); 3356 ierr = DMPlexVecGetClosure(plexA, sectionAux, locA, subcell, NULL, &x);CHKERRQ(ierr); 3357 for (i = 0; i < totDimAux; ++i) al[cind*totDimAux+i] = x[i]; 3358 ierr = DMPlexVecRestoreClosure(plexA, sectionAux, locA, subcell, NULL, &x);CHKERRQ(ierr); 3359 } 3360 } 3361 ierr = DMDestroy(&plex);CHKERRQ(ierr); 3362 if (locA) {ierr = DMDestroy(&plexA);CHKERRQ(ierr);} 3363 ierr = ISRestorePointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 3364 PetscFunctionReturn(0); 3365 } 3366 3367 /*@C 3368 DMPlexRestoreCellFields - Restore the field values values for a chunk of cells 3369 3370 Input Parameters: 3371 + dm - The DM 3372 . cellIS - The cells to include 3373 . locX - A local vector with the solution fields 3374 . locX_t - A local vector with solution field time derivatives, or NULL 3375 - locA - A local vector with auxiliary fields, or NULL 3376 3377 Output Parameters: 3378 + u - The field coefficients 3379 . u_t - The fields derivative coefficients 3380 - a - The auxiliary field coefficients 3381 3382 Level: developer 3383 3384 .seealso: DMPlexGetFaceFields() 3385 @*/ 3386 PetscErrorCode DMPlexRestoreCellFields(DM dm, IS cellIS, Vec locX, Vec locX_t, Vec locA, PetscScalar **u, PetscScalar **u_t, PetscScalar **a) 3387 { 3388 PetscErrorCode ierr; 3389 3390 PetscFunctionBegin; 3391 ierr = DMRestoreWorkArray(dm, 0, MPIU_SCALAR, u);CHKERRQ(ierr); 3392 if (locX_t) {ierr = DMRestoreWorkArray(dm, 0, MPIU_SCALAR, u_t);CHKERRQ(ierr);} 3393 if (locA) {ierr = DMRestoreWorkArray(dm, 0, MPIU_SCALAR, a);CHKERRQ(ierr);} 3394 PetscFunctionReturn(0); 3395 } 3396 3397 static PetscErrorCode DMPlexGetHybridAuxFields(DM dm, DM dmAux[], PetscDS dsAux[], IS cellIS, Vec locA[], PetscScalar *a[]) 3398 { 3399 DM plexA[2]; 3400 DMEnclosureType encAux[2]; 3401 PetscSection sectionAux[2]; 3402 const PetscInt *cells; 3403 PetscInt cStart, cEnd, numCells, c, s, totDimAux[2]; 3404 PetscErrorCode ierr; 3405 3406 PetscFunctionBegin; 3407 PetscValidPointer(locA, 5); 3408 if (!locA[0] || !locA[1]) PetscFunctionReturn(0); 3409 PetscValidPointer(dmAux, 2); 3410 PetscValidPointer(dsAux, 3); 3411 PetscValidPointer(a, 6); 3412 ierr = ISGetPointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 3413 numCells = cEnd - cStart; 3414 for (s = 0; s < 2; ++s) { 3415 PetscValidHeaderSpecific(dmAux[s], DM_CLASSID, 2); 3416 PetscValidHeaderSpecific(dsAux[s], PETSCDS_CLASSID, 3); 3417 PetscValidHeaderSpecific(locA[s], VEC_CLASSID, 5); 3418 ierr = DMPlexConvertPlex(dmAux[s], &plexA[s], PETSC_FALSE);CHKERRQ(ierr); 3419 ierr = DMGetEnclosureRelation(dmAux[s], dm, &encAux[s]);CHKERRQ(ierr); 3420 ierr = DMGetLocalSection(dmAux[s], §ionAux[s]);CHKERRQ(ierr); 3421 ierr = PetscDSGetTotalDimension(dsAux[s], &totDimAux[s]);CHKERRQ(ierr); 3422 ierr = DMGetWorkArray(dmAux[s], numCells*totDimAux[s], MPIU_SCALAR, &a[s]);CHKERRQ(ierr); 3423 } 3424 for (c = cStart; c < cEnd; ++c) { 3425 const PetscInt cell = cells ? cells[c] : c; 3426 const PetscInt cind = c - cStart; 3427 const PetscInt *cone, *ornt; 3428 3429 ierr = DMPlexGetCone(dm, cell, &cone);CHKERRQ(ierr); 3430 ierr = DMPlexGetConeOrientation(dm, cell, &ornt);CHKERRQ(ierr); 3431 if (ornt[0]) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_SUP, "Face %D in hybrid cell %D has orientation %D != 0", cone[0], cell, ornt[0]); 3432 for (s = 0; s < 2; ++s) { 3433 PetscScalar *x = NULL, *al = a[s]; 3434 const PetscInt tdA = totDimAux[s]; 3435 PetscInt subface, Na, i; 3436 3437 ierr = DMGetEnclosurePoint(plexA[s], dm, encAux[s], cone[0], &subface);CHKERRQ(ierr); 3438 ierr = DMPlexVecGetClosure(plexA[s], sectionAux[s], locA[s], subface, &Na, &x);CHKERRQ(ierr); 3439 for (i = 0; i < Na; ++i) al[cind*tdA+i] = x[i]; 3440 ierr = DMPlexVecRestoreClosure(plexA[s], sectionAux[s], locA[s], subface, &Na, &x);CHKERRQ(ierr); 3441 } 3442 } 3443 for (s = 0; s < 2; ++s) {ierr = DMDestroy(&plexA[s]);CHKERRQ(ierr);} 3444 ierr = ISRestorePointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 3445 PetscFunctionReturn(0); 3446 } 3447 3448 static PetscErrorCode DMPlexRestoreHybridAuxFields(DM dmAux[], PetscDS dsAux[], IS cellIS, Vec locA[], PetscScalar *a[]) 3449 { 3450 PetscErrorCode ierr; 3451 3452 PetscFunctionBegin; 3453 if (!locA[0] || !locA[1]) PetscFunctionReturn(0); 3454 ierr = DMRestoreWorkArray(dmAux[0], 0, MPIU_SCALAR, &a[0]);CHKERRQ(ierr); 3455 ierr = DMRestoreWorkArray(dmAux[1], 0, MPIU_SCALAR, &a[1]);CHKERRQ(ierr); 3456 PetscFunctionReturn(0); 3457 } 3458 3459 /*@C 3460 DMPlexGetFaceFields - Retrieve the field values values for a chunk of faces 3461 3462 Input Parameters: 3463 + dm - The DM 3464 . fStart - The first face to include 3465 . fEnd - The first face to exclude 3466 . locX - A local vector with the solution fields 3467 . locX_t - A local vector with solution field time derivatives, or NULL 3468 . faceGeometry - A local vector with face geometry 3469 . cellGeometry - A local vector with cell geometry 3470 - locaGrad - A local vector with field gradients, or NULL 3471 3472 Output Parameters: 3473 + Nface - The number of faces with field values 3474 . uL - The field values at the left side of the face 3475 - uR - The field values at the right side of the face 3476 3477 Level: developer 3478 3479 .seealso: DMPlexGetCellFields() 3480 @*/ 3481 PetscErrorCode DMPlexGetFaceFields(DM dm, PetscInt fStart, PetscInt fEnd, Vec locX, Vec locX_t, Vec faceGeometry, Vec cellGeometry, Vec locGrad, PetscInt *Nface, PetscScalar **uL, PetscScalar **uR) 3482 { 3483 DM dmFace, dmCell, dmGrad = NULL; 3484 PetscSection section; 3485 PetscDS prob; 3486 DMLabel ghostLabel; 3487 const PetscScalar *facegeom, *cellgeom, *x, *lgrad; 3488 PetscBool *isFE; 3489 PetscInt dim, Nf, f, Nc, numFaces = fEnd - fStart, iface, face; 3490 PetscErrorCode ierr; 3491 3492 PetscFunctionBegin; 3493 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3494 PetscValidHeaderSpecific(locX, VEC_CLASSID, 4); 3495 if (locX_t) {PetscValidHeaderSpecific(locX_t, VEC_CLASSID, 5);} 3496 PetscValidHeaderSpecific(faceGeometry, VEC_CLASSID, 6); 3497 PetscValidHeaderSpecific(cellGeometry, VEC_CLASSID, 7); 3498 if (locGrad) {PetscValidHeaderSpecific(locGrad, VEC_CLASSID, 8);} 3499 PetscValidPointer(uL, 10); 3500 PetscValidPointer(uR, 11); 3501 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 3502 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 3503 ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); 3504 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 3505 ierr = PetscDSGetTotalComponents(prob, &Nc);CHKERRQ(ierr); 3506 ierr = PetscMalloc1(Nf, &isFE);CHKERRQ(ierr); 3507 for (f = 0; f < Nf; ++f) { 3508 PetscObject obj; 3509 PetscClassId id; 3510 3511 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 3512 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 3513 if (id == PETSCFE_CLASSID) {isFE[f] = PETSC_TRUE;} 3514 else if (id == PETSCFV_CLASSID) {isFE[f] = PETSC_FALSE;} 3515 else {isFE[f] = PETSC_FALSE;} 3516 } 3517 ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 3518 ierr = VecGetArrayRead(locX, &x);CHKERRQ(ierr); 3519 ierr = VecGetDM(faceGeometry, &dmFace);CHKERRQ(ierr); 3520 ierr = VecGetArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); 3521 ierr = VecGetDM(cellGeometry, &dmCell);CHKERRQ(ierr); 3522 ierr = VecGetArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr); 3523 if (locGrad) { 3524 ierr = VecGetDM(locGrad, &dmGrad);CHKERRQ(ierr); 3525 ierr = VecGetArrayRead(locGrad, &lgrad);CHKERRQ(ierr); 3526 } 3527 ierr = DMGetWorkArray(dm, numFaces*Nc, MPIU_SCALAR, uL);CHKERRQ(ierr); 3528 ierr = DMGetWorkArray(dm, numFaces*Nc, MPIU_SCALAR, uR);CHKERRQ(ierr); 3529 /* Right now just eat the extra work for FE (could make a cell loop) */ 3530 for (face = fStart, iface = 0; face < fEnd; ++face) { 3531 const PetscInt *cells; 3532 PetscFVFaceGeom *fg; 3533 PetscFVCellGeom *cgL, *cgR; 3534 PetscScalar *xL, *xR, *gL, *gR; 3535 PetscScalar *uLl = *uL, *uRl = *uR; 3536 PetscInt ghost, nsupp, nchild; 3537 3538 ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr); 3539 ierr = DMPlexGetSupportSize(dm, face, &nsupp);CHKERRQ(ierr); 3540 ierr = DMPlexGetTreeChildren(dm, face, &nchild, NULL);CHKERRQ(ierr); 3541 if (ghost >= 0 || nsupp > 2 || nchild > 0) continue; 3542 ierr = DMPlexPointLocalRead(dmFace, face, facegeom, &fg);CHKERRQ(ierr); 3543 ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr); 3544 ierr = DMPlexPointLocalRead(dmCell, cells[0], cellgeom, &cgL);CHKERRQ(ierr); 3545 ierr = DMPlexPointLocalRead(dmCell, cells[1], cellgeom, &cgR);CHKERRQ(ierr); 3546 for (f = 0; f < Nf; ++f) { 3547 PetscInt off; 3548 3549 ierr = PetscDSGetComponentOffset(prob, f, &off);CHKERRQ(ierr); 3550 if (isFE[f]) { 3551 const PetscInt *cone; 3552 PetscInt comp, coneSizeL, coneSizeR, faceLocL, faceLocR, ldof, rdof, d; 3553 3554 xL = xR = NULL; 3555 ierr = PetscSectionGetFieldComponents(section, f, &comp);CHKERRQ(ierr); 3556 ierr = DMPlexVecGetClosure(dm, section, locX, cells[0], &ldof, (PetscScalar **) &xL);CHKERRQ(ierr); 3557 ierr = DMPlexVecGetClosure(dm, section, locX, cells[1], &rdof, (PetscScalar **) &xR);CHKERRQ(ierr); 3558 ierr = DMPlexGetCone(dm, cells[0], &cone);CHKERRQ(ierr); 3559 ierr = DMPlexGetConeSize(dm, cells[0], &coneSizeL);CHKERRQ(ierr); 3560 for (faceLocL = 0; faceLocL < coneSizeL; ++faceLocL) if (cone[faceLocL] == face) break; 3561 ierr = DMPlexGetCone(dm, cells[1], &cone);CHKERRQ(ierr); 3562 ierr = DMPlexGetConeSize(dm, cells[1], &coneSizeR);CHKERRQ(ierr); 3563 for (faceLocR = 0; faceLocR < coneSizeR; ++faceLocR) if (cone[faceLocR] == face) break; 3564 if (faceLocL == coneSizeL && faceLocR == coneSizeR) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Could not find face %D in cone of cell %D or cell %D", face, cells[0], cells[1]); 3565 /* Check that FEM field has values in the right cell (sometimes its an FV ghost cell) */ 3566 /* TODO: this is a hack that might not be right for nonconforming */ 3567 if (faceLocL < coneSizeL) { 3568 ierr = PetscFEEvaluateFaceFields_Internal(prob, f, faceLocL, xL, &uLl[iface*Nc+off]);CHKERRQ(ierr); 3569 if (rdof == ldof && faceLocR < coneSizeR) {ierr = PetscFEEvaluateFaceFields_Internal(prob, f, faceLocR, xR, &uRl[iface*Nc+off]);CHKERRQ(ierr);} 3570 else {for (d = 0; d < comp; ++d) uRl[iface*Nc+off+d] = uLl[iface*Nc+off+d];} 3571 } 3572 else { 3573 ierr = PetscFEEvaluateFaceFields_Internal(prob, f, faceLocR, xR, &uRl[iface*Nc+off]);CHKERRQ(ierr); 3574 ierr = PetscSectionGetFieldComponents(section, f, &comp);CHKERRQ(ierr); 3575 for (d = 0; d < comp; ++d) uLl[iface*Nc+off+d] = uRl[iface*Nc+off+d]; 3576 } 3577 ierr = DMPlexVecRestoreClosure(dm, section, locX, cells[0], &ldof, (PetscScalar **) &xL);CHKERRQ(ierr); 3578 ierr = DMPlexVecRestoreClosure(dm, section, locX, cells[1], &rdof, (PetscScalar **) &xR);CHKERRQ(ierr); 3579 } else { 3580 PetscFV fv; 3581 PetscInt numComp, c; 3582 3583 ierr = PetscDSGetDiscretization(prob, f, (PetscObject *) &fv);CHKERRQ(ierr); 3584 ierr = PetscFVGetNumComponents(fv, &numComp);CHKERRQ(ierr); 3585 ierr = DMPlexPointLocalFieldRead(dm, cells[0], f, x, &xL);CHKERRQ(ierr); 3586 ierr = DMPlexPointLocalFieldRead(dm, cells[1], f, x, &xR);CHKERRQ(ierr); 3587 if (dmGrad) { 3588 PetscReal dxL[3], dxR[3]; 3589 3590 ierr = DMPlexPointLocalRead(dmGrad, cells[0], lgrad, &gL);CHKERRQ(ierr); 3591 ierr = DMPlexPointLocalRead(dmGrad, cells[1], lgrad, &gR);CHKERRQ(ierr); 3592 DMPlex_WaxpyD_Internal(dim, -1, cgL->centroid, fg->centroid, dxL); 3593 DMPlex_WaxpyD_Internal(dim, -1, cgR->centroid, fg->centroid, dxR); 3594 for (c = 0; c < numComp; ++c) { 3595 uLl[iface*Nc+off+c] = xL[c] + DMPlex_DotD_Internal(dim, &gL[c*dim], dxL); 3596 uRl[iface*Nc+off+c] = xR[c] + DMPlex_DotD_Internal(dim, &gR[c*dim], dxR); 3597 } 3598 } else { 3599 for (c = 0; c < numComp; ++c) { 3600 uLl[iface*Nc+off+c] = xL[c]; 3601 uRl[iface*Nc+off+c] = xR[c]; 3602 } 3603 } 3604 } 3605 } 3606 ++iface; 3607 } 3608 *Nface = iface; 3609 ierr = VecRestoreArrayRead(locX, &x);CHKERRQ(ierr); 3610 ierr = VecRestoreArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); 3611 ierr = VecRestoreArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr); 3612 if (locGrad) { 3613 ierr = VecRestoreArrayRead(locGrad, &lgrad);CHKERRQ(ierr); 3614 } 3615 ierr = PetscFree(isFE);CHKERRQ(ierr); 3616 PetscFunctionReturn(0); 3617 } 3618 3619 /*@C 3620 DMPlexRestoreFaceFields - Restore the field values values for a chunk of faces 3621 3622 Input Parameters: 3623 + dm - The DM 3624 . fStart - The first face to include 3625 . fEnd - The first face to exclude 3626 . locX - A local vector with the solution fields 3627 . locX_t - A local vector with solution field time derivatives, or NULL 3628 . faceGeometry - A local vector with face geometry 3629 . cellGeometry - A local vector with cell geometry 3630 - locaGrad - A local vector with field gradients, or NULL 3631 3632 Output Parameters: 3633 + Nface - The number of faces with field values 3634 . uL - The field values at the left side of the face 3635 - uR - The field values at the right side of the face 3636 3637 Level: developer 3638 3639 .seealso: DMPlexGetFaceFields() 3640 @*/ 3641 PetscErrorCode DMPlexRestoreFaceFields(DM dm, PetscInt fStart, PetscInt fEnd, Vec locX, Vec locX_t, Vec faceGeometry, Vec cellGeometry, Vec locGrad, PetscInt *Nface, PetscScalar **uL, PetscScalar **uR) 3642 { 3643 PetscErrorCode ierr; 3644 3645 PetscFunctionBegin; 3646 ierr = DMRestoreWorkArray(dm, 0, MPIU_SCALAR, uL);CHKERRQ(ierr); 3647 ierr = DMRestoreWorkArray(dm, 0, MPIU_SCALAR, uR);CHKERRQ(ierr); 3648 PetscFunctionReturn(0); 3649 } 3650 3651 /*@C 3652 DMPlexGetFaceGeometry - Retrieve the geometric values for a chunk of faces 3653 3654 Input Parameters: 3655 + dm - The DM 3656 . fStart - The first face to include 3657 . fEnd - The first face to exclude 3658 . faceGeometry - A local vector with face geometry 3659 - cellGeometry - A local vector with cell geometry 3660 3661 Output Parameters: 3662 + Nface - The number of faces with field values 3663 . fgeom - The extract the face centroid and normal 3664 - vol - The cell volume 3665 3666 Level: developer 3667 3668 .seealso: DMPlexGetCellFields() 3669 @*/ 3670 PetscErrorCode DMPlexGetFaceGeometry(DM dm, PetscInt fStart, PetscInt fEnd, Vec faceGeometry, Vec cellGeometry, PetscInt *Nface, PetscFVFaceGeom **fgeom, PetscReal **vol) 3671 { 3672 DM dmFace, dmCell; 3673 DMLabel ghostLabel; 3674 const PetscScalar *facegeom, *cellgeom; 3675 PetscInt dim, numFaces = fEnd - fStart, iface, face; 3676 PetscErrorCode ierr; 3677 3678 PetscFunctionBegin; 3679 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3680 PetscValidHeaderSpecific(faceGeometry, VEC_CLASSID, 4); 3681 PetscValidHeaderSpecific(cellGeometry, VEC_CLASSID, 5); 3682 PetscValidPointer(fgeom, 7); 3683 PetscValidPointer(vol, 8); 3684 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 3685 ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 3686 ierr = VecGetDM(faceGeometry, &dmFace);CHKERRQ(ierr); 3687 ierr = VecGetArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); 3688 ierr = VecGetDM(cellGeometry, &dmCell);CHKERRQ(ierr); 3689 ierr = VecGetArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr); 3690 ierr = PetscMalloc1(numFaces, fgeom);CHKERRQ(ierr); 3691 ierr = DMGetWorkArray(dm, numFaces*2, MPIU_SCALAR, vol);CHKERRQ(ierr); 3692 for (face = fStart, iface = 0; face < fEnd; ++face) { 3693 const PetscInt *cells; 3694 PetscFVFaceGeom *fg; 3695 PetscFVCellGeom *cgL, *cgR; 3696 PetscFVFaceGeom *fgeoml = *fgeom; 3697 PetscReal *voll = *vol; 3698 PetscInt ghost, d, nchild, nsupp; 3699 3700 ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr); 3701 ierr = DMPlexGetSupportSize(dm, face, &nsupp);CHKERRQ(ierr); 3702 ierr = DMPlexGetTreeChildren(dm, face, &nchild, NULL);CHKERRQ(ierr); 3703 if (ghost >= 0 || nsupp > 2 || nchild > 0) continue; 3704 ierr = DMPlexPointLocalRead(dmFace, face, facegeom, &fg);CHKERRQ(ierr); 3705 ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr); 3706 ierr = DMPlexPointLocalRead(dmCell, cells[0], cellgeom, &cgL);CHKERRQ(ierr); 3707 ierr = DMPlexPointLocalRead(dmCell, cells[1], cellgeom, &cgR);CHKERRQ(ierr); 3708 for (d = 0; d < dim; ++d) { 3709 fgeoml[iface].centroid[d] = fg->centroid[d]; 3710 fgeoml[iface].normal[d] = fg->normal[d]; 3711 } 3712 voll[iface*2+0] = cgL->volume; 3713 voll[iface*2+1] = cgR->volume; 3714 ++iface; 3715 } 3716 *Nface = iface; 3717 ierr = VecRestoreArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); 3718 ierr = VecRestoreArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr); 3719 PetscFunctionReturn(0); 3720 } 3721 3722 /*@C 3723 DMPlexRestoreFaceGeometry - Restore the field values values for a chunk of faces 3724 3725 Input Parameters: 3726 + dm - The DM 3727 . fStart - The first face to include 3728 . fEnd - The first face to exclude 3729 . faceGeometry - A local vector with face geometry 3730 - cellGeometry - A local vector with cell geometry 3731 3732 Output Parameters: 3733 + Nface - The number of faces with field values 3734 . fgeom - The extract the face centroid and normal 3735 - vol - The cell volume 3736 3737 Level: developer 3738 3739 .seealso: DMPlexGetFaceFields() 3740 @*/ 3741 PetscErrorCode DMPlexRestoreFaceGeometry(DM dm, PetscInt fStart, PetscInt fEnd, Vec faceGeometry, Vec cellGeometry, PetscInt *Nface, PetscFVFaceGeom **fgeom, PetscReal **vol) 3742 { 3743 PetscErrorCode ierr; 3744 3745 PetscFunctionBegin; 3746 ierr = PetscFree(*fgeom);CHKERRQ(ierr); 3747 ierr = DMRestoreWorkArray(dm, 0, MPIU_REAL, vol);CHKERRQ(ierr); 3748 PetscFunctionReturn(0); 3749 } 3750 3751 PetscErrorCode DMSNESGetFEGeom(DMField coordField, IS pointIS, PetscQuadrature quad, PetscBool faceData, PetscFEGeom **geom) 3752 { 3753 char composeStr[33] = {0}; 3754 PetscObjectId id; 3755 PetscContainer container; 3756 PetscErrorCode ierr; 3757 3758 PetscFunctionBegin; 3759 ierr = PetscObjectGetId((PetscObject)quad,&id);CHKERRQ(ierr); 3760 ierr = PetscSNPrintf(composeStr, 32, "DMSNESGetFEGeom_%x\n", id);CHKERRQ(ierr); 3761 ierr = PetscObjectQuery((PetscObject) pointIS, composeStr, (PetscObject *) &container);CHKERRQ(ierr); 3762 if (container) { 3763 ierr = PetscContainerGetPointer(container, (void **) geom);CHKERRQ(ierr); 3764 } else { 3765 ierr = DMFieldCreateFEGeom(coordField, pointIS, quad, faceData, geom);CHKERRQ(ierr); 3766 ierr = PetscContainerCreate(PETSC_COMM_SELF,&container);CHKERRQ(ierr); 3767 ierr = PetscContainerSetPointer(container, (void *) *geom);CHKERRQ(ierr); 3768 ierr = PetscContainerSetUserDestroy(container, PetscContainerUserDestroy_PetscFEGeom);CHKERRQ(ierr); 3769 ierr = PetscObjectCompose((PetscObject) pointIS, composeStr, (PetscObject) container);CHKERRQ(ierr); 3770 ierr = PetscContainerDestroy(&container);CHKERRQ(ierr); 3771 } 3772 PetscFunctionReturn(0); 3773 } 3774 3775 PetscErrorCode DMSNESRestoreFEGeom(DMField coordField, IS pointIS, PetscQuadrature quad, PetscBool faceData, PetscFEGeom **geom) 3776 { 3777 PetscFunctionBegin; 3778 *geom = NULL; 3779 PetscFunctionReturn(0); 3780 } 3781 3782 PetscErrorCode DMPlexComputeResidual_Patch_Internal(DM dm, PetscSection section, IS cellIS, PetscReal t, Vec locX, Vec locX_t, Vec locF, void *user) 3783 { 3784 DM_Plex *mesh = (DM_Plex *) dm->data; 3785 const char *name = "Residual"; 3786 DM dmAux = NULL; 3787 DMLabel ghostLabel = NULL; 3788 PetscDS prob = NULL; 3789 PetscDS probAux = NULL; 3790 PetscBool useFEM = PETSC_FALSE; 3791 PetscBool isImplicit = (locX_t || t == PETSC_MIN_REAL) ? PETSC_TRUE : PETSC_FALSE; 3792 DMField coordField = NULL; 3793 Vec locA; 3794 PetscScalar *u = NULL, *u_t, *a, *uL = NULL, *uR = NULL; 3795 IS chunkIS; 3796 const PetscInt *cells; 3797 PetscInt cStart, cEnd, numCells; 3798 PetscInt Nf, f, totDim, totDimAux, numChunks, cellChunkSize, chunk, fStart, fEnd; 3799 PetscInt maxDegree = PETSC_MAX_INT; 3800 PetscFormKey key; 3801 PetscQuadrature affineQuad = NULL, *quads = NULL; 3802 PetscFEGeom *affineGeom = NULL, **geoms = NULL; 3803 PetscErrorCode ierr; 3804 3805 PetscFunctionBegin; 3806 ierr = PetscLogEventBegin(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr); 3807 /* FEM+FVM */ 3808 /* 1: Get sizes from dm and dmAux */ 3809 ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 3810 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 3811 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 3812 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 3813 ierr = DMGetAuxiliaryVec(dm, NULL, 0, &locA);CHKERRQ(ierr); 3814 if (locA) { 3815 ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); 3816 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 3817 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 3818 } 3819 /* 2: Get geometric data */ 3820 for (f = 0; f < Nf; ++f) { 3821 PetscObject obj; 3822 PetscClassId id; 3823 PetscBool fimp; 3824 3825 ierr = PetscDSGetImplicit(prob, f, &fimp);CHKERRQ(ierr); 3826 if (isImplicit != fimp) continue; 3827 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 3828 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 3829 if (id == PETSCFE_CLASSID) {useFEM = PETSC_TRUE;} 3830 if (id == PETSCFV_CLASSID) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Use of FVM with PCPATCH not yet implemented"); 3831 } 3832 if (useFEM) { 3833 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 3834 ierr = DMFieldGetDegree(coordField,cellIS,NULL,&maxDegree);CHKERRQ(ierr); 3835 if (maxDegree <= 1) { 3836 ierr = DMFieldCreateDefaultQuadrature(coordField,cellIS,&affineQuad);CHKERRQ(ierr); 3837 if (affineQuad) { 3838 ierr = DMSNESGetFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&affineGeom);CHKERRQ(ierr); 3839 } 3840 } else { 3841 ierr = PetscCalloc2(Nf,&quads,Nf,&geoms);CHKERRQ(ierr); 3842 for (f = 0; f < Nf; ++f) { 3843 PetscObject obj; 3844 PetscClassId id; 3845 PetscBool fimp; 3846 3847 ierr = PetscDSGetImplicit(prob, f, &fimp);CHKERRQ(ierr); 3848 if (isImplicit != fimp) continue; 3849 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 3850 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 3851 if (id == PETSCFE_CLASSID) { 3852 PetscFE fe = (PetscFE) obj; 3853 3854 ierr = PetscFEGetQuadrature(fe, &quads[f]);CHKERRQ(ierr); 3855 ierr = PetscObjectReference((PetscObject)quads[f]);CHKERRQ(ierr); 3856 ierr = DMSNESGetFEGeom(coordField,cellIS,quads[f],PETSC_FALSE,&geoms[f]);CHKERRQ(ierr); 3857 } 3858 } 3859 } 3860 } 3861 /* Loop over chunks */ 3862 ierr = ISGetPointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 3863 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 3864 if (useFEM) {ierr = ISCreate(PETSC_COMM_SELF, &chunkIS);CHKERRQ(ierr);} 3865 numCells = cEnd - cStart; 3866 numChunks = 1; 3867 cellChunkSize = numCells/numChunks; 3868 numChunks = PetscMin(1,numCells); 3869 key.label = NULL; 3870 key.value = 0; 3871 key.part = 0; 3872 for (chunk = 0; chunk < numChunks; ++chunk) { 3873 PetscScalar *elemVec, *fluxL = NULL, *fluxR = NULL; 3874 PetscReal *vol = NULL; 3875 PetscFVFaceGeom *fgeom = NULL; 3876 PetscInt cS = cStart+chunk*cellChunkSize, cE = PetscMin(cS+cellChunkSize, cEnd), numCells = cE - cS, c; 3877 PetscInt numFaces = 0; 3878 3879 /* Extract field coefficients */ 3880 if (useFEM) { 3881 ierr = ISGetPointSubrange(chunkIS, cS, cE, cells);CHKERRQ(ierr); 3882 ierr = DMPlexGetCellFields(dm, chunkIS, locX, locX_t, locA, &u, &u_t, &a);CHKERRQ(ierr); 3883 ierr = DMGetWorkArray(dm, numCells*totDim, MPIU_SCALAR, &elemVec);CHKERRQ(ierr); 3884 ierr = PetscArrayzero(elemVec, numCells*totDim);CHKERRQ(ierr); 3885 } 3886 /* TODO We will interlace both our field coefficients (u, u_t, uL, uR, etc.) and our output (elemVec, fL, fR). I think this works */ 3887 /* Loop over fields */ 3888 for (f = 0; f < Nf; ++f) { 3889 PetscObject obj; 3890 PetscClassId id; 3891 PetscBool fimp; 3892 PetscInt numChunks, numBatches, batchSize, numBlocks, blockSize, Ne, Nr, offset; 3893 3894 key.field = f; 3895 ierr = PetscDSGetImplicit(prob, f, &fimp);CHKERRQ(ierr); 3896 if (isImplicit != fimp) continue; 3897 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 3898 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 3899 if (id == PETSCFE_CLASSID) { 3900 PetscFE fe = (PetscFE) obj; 3901 PetscFEGeom *geom = affineGeom ? affineGeom : geoms[f]; 3902 PetscFEGeom *chunkGeom = NULL; 3903 PetscQuadrature quad = affineQuad ? affineQuad : quads[f]; 3904 PetscInt Nq, Nb; 3905 3906 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 3907 ierr = PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 3908 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 3909 blockSize = Nb; 3910 batchSize = numBlocks * blockSize; 3911 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 3912 numChunks = numCells / (numBatches*batchSize); 3913 Ne = numChunks*numBatches*batchSize; 3914 Nr = numCells % (numBatches*batchSize); 3915 offset = numCells - Nr; 3916 /* Integrate FE residual to get elemVec (need fields at quadrature points) */ 3917 /* For FV, I think we use a P0 basis and the cell coefficients (for subdivided cells, we can tweak the basis tabulation to be the indicator function) */ 3918 ierr = PetscFEGeomGetChunk(geom,0,offset,&chunkGeom);CHKERRQ(ierr); 3919 ierr = PetscFEIntegrateResidual(prob, key, Ne, chunkGeom, u, u_t, probAux, a, t, elemVec);CHKERRQ(ierr); 3920 ierr = PetscFEGeomGetChunk(geom,offset,numCells,&chunkGeom);CHKERRQ(ierr); 3921 ierr = PetscFEIntegrateResidual(prob, key, Nr, chunkGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, &elemVec[offset*totDim]);CHKERRQ(ierr); 3922 ierr = PetscFEGeomRestoreChunk(geom,offset,numCells,&chunkGeom);CHKERRQ(ierr); 3923 } else if (id == PETSCFV_CLASSID) { 3924 PetscFV fv = (PetscFV) obj; 3925 3926 Ne = numFaces; 3927 /* Riemann solve over faces (need fields at face centroids) */ 3928 /* We need to evaluate FE fields at those coordinates */ 3929 ierr = PetscFVIntegrateRHSFunction(fv, prob, f, Ne, fgeom, vol, uL, uR, fluxL, fluxR);CHKERRQ(ierr); 3930 } else SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", f); 3931 } 3932 /* Loop over domain */ 3933 if (useFEM) { 3934 /* Add elemVec to locX */ 3935 for (c = cS; c < cE; ++c) { 3936 const PetscInt cell = cells ? cells[c] : c; 3937 const PetscInt cind = c - cStart; 3938 3939 if (mesh->printFEM > 1) {ierr = DMPrintCellVector(cell, name, totDim, &elemVec[cind*totDim]);CHKERRQ(ierr);} 3940 if (ghostLabel) { 3941 PetscInt ghostVal; 3942 3943 ierr = DMLabelGetValue(ghostLabel,cell,&ghostVal);CHKERRQ(ierr); 3944 if (ghostVal > 0) continue; 3945 } 3946 ierr = DMPlexVecSetClosure(dm, section, locF, cell, &elemVec[cind*totDim], ADD_ALL_VALUES);CHKERRQ(ierr); 3947 } 3948 } 3949 /* Handle time derivative */ 3950 if (locX_t) { 3951 PetscScalar *x_t, *fa; 3952 3953 ierr = VecGetArray(locF, &fa);CHKERRQ(ierr); 3954 ierr = VecGetArray(locX_t, &x_t);CHKERRQ(ierr); 3955 for (f = 0; f < Nf; ++f) { 3956 PetscFV fv; 3957 PetscObject obj; 3958 PetscClassId id; 3959 PetscInt pdim, d; 3960 3961 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 3962 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 3963 if (id != PETSCFV_CLASSID) continue; 3964 fv = (PetscFV) obj; 3965 ierr = PetscFVGetNumComponents(fv, &pdim);CHKERRQ(ierr); 3966 for (c = cS; c < cE; ++c) { 3967 const PetscInt cell = cells ? cells[c] : c; 3968 PetscScalar *u_t, *r; 3969 3970 if (ghostLabel) { 3971 PetscInt ghostVal; 3972 3973 ierr = DMLabelGetValue(ghostLabel, cell, &ghostVal);CHKERRQ(ierr); 3974 if (ghostVal > 0) continue; 3975 } 3976 ierr = DMPlexPointLocalFieldRead(dm, cell, f, x_t, &u_t);CHKERRQ(ierr); 3977 ierr = DMPlexPointLocalFieldRef(dm, cell, f, fa, &r);CHKERRQ(ierr); 3978 for (d = 0; d < pdim; ++d) r[d] += u_t[d]; 3979 } 3980 } 3981 ierr = VecRestoreArray(locX_t, &x_t);CHKERRQ(ierr); 3982 ierr = VecRestoreArray(locF, &fa);CHKERRQ(ierr); 3983 } 3984 if (useFEM) { 3985 ierr = DMPlexRestoreCellFields(dm, chunkIS, locX, locX_t, locA, &u, &u_t, &a);CHKERRQ(ierr); 3986 ierr = DMRestoreWorkArray(dm, numCells*totDim, MPIU_SCALAR, &elemVec);CHKERRQ(ierr); 3987 } 3988 } 3989 if (useFEM) {ierr = ISDestroy(&chunkIS);CHKERRQ(ierr);} 3990 ierr = ISRestorePointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 3991 /* TODO Could include boundary residual here (see DMPlexComputeResidual_Internal) */ 3992 if (useFEM) { 3993 if (maxDegree <= 1) { 3994 ierr = DMSNESRestoreFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&affineGeom);CHKERRQ(ierr); 3995 ierr = PetscQuadratureDestroy(&affineQuad);CHKERRQ(ierr); 3996 } else { 3997 for (f = 0; f < Nf; ++f) { 3998 ierr = DMSNESRestoreFEGeom(coordField,cellIS,quads[f],PETSC_FALSE,&geoms[f]);CHKERRQ(ierr); 3999 ierr = PetscQuadratureDestroy(&quads[f]);CHKERRQ(ierr); 4000 } 4001 ierr = PetscFree2(quads,geoms);CHKERRQ(ierr); 4002 } 4003 } 4004 ierr = PetscLogEventEnd(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr); 4005 PetscFunctionReturn(0); 4006 } 4007 4008 /* 4009 We always assemble JacP, and if the matrix is different from Jac and two different sets of point functions are provided, we also assemble Jac 4010 4011 X - The local solution vector 4012 X_t - The local solution time derviative vector, or NULL 4013 */ 4014 PetscErrorCode DMPlexComputeJacobian_Patch_Internal(DM dm, PetscSection section, PetscSection globalSection, IS cellIS, 4015 PetscReal t, PetscReal X_tShift, Vec X, Vec X_t, Mat Jac, Mat JacP, void *ctx) 4016 { 4017 DM_Plex *mesh = (DM_Plex *) dm->data; 4018 const char *name = "Jacobian", *nameP = "JacobianPre"; 4019 DM dmAux = NULL; 4020 PetscDS prob, probAux = NULL; 4021 PetscSection sectionAux = NULL; 4022 Vec A; 4023 DMField coordField; 4024 PetscFEGeom *cgeomFEM; 4025 PetscQuadrature qGeom = NULL; 4026 Mat J = Jac, JP = JacP; 4027 PetscScalar *work, *u = NULL, *u_t = NULL, *a = NULL, *elemMat = NULL, *elemMatP = NULL, *elemMatD = NULL; 4028 PetscBool hasJac, hasPrec, hasDyn, assembleJac, isMatIS, isMatISP, *isFE, hasFV = PETSC_FALSE; 4029 const PetscInt *cells; 4030 PetscFormKey key; 4031 PetscInt Nf, fieldI, fieldJ, maxDegree, numCells, cStart, cEnd, numChunks, chunkSize, chunk, totDim, totDimAux = 0, sz, wsz, off = 0, offCell = 0; 4032 PetscErrorCode ierr; 4033 4034 PetscFunctionBegin; 4035 ierr = ISGetLocalSize(cellIS, &numCells);CHKERRQ(ierr); 4036 ierr = ISGetPointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 4037 ierr = PetscLogEventBegin(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 4038 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 4039 ierr = DMGetAuxiliaryVec(dm, NULL, 0, &A);CHKERRQ(ierr); 4040 if (A) { 4041 ierr = VecGetDM(A, &dmAux);CHKERRQ(ierr); 4042 ierr = DMGetLocalSection(dmAux, §ionAux);CHKERRQ(ierr); 4043 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 4044 } 4045 /* Get flags */ 4046 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 4047 ierr = DMGetWorkArray(dm, Nf, MPIU_BOOL, &isFE);CHKERRQ(ierr); 4048 for (fieldI = 0; fieldI < Nf; ++fieldI) { 4049 PetscObject disc; 4050 PetscClassId id; 4051 ierr = PetscDSGetDiscretization(prob, fieldI, &disc);CHKERRQ(ierr); 4052 ierr = PetscObjectGetClassId(disc, &id);CHKERRQ(ierr); 4053 if (id == PETSCFE_CLASSID) {isFE[fieldI] = PETSC_TRUE;} 4054 else if (id == PETSCFV_CLASSID) {hasFV = PETSC_TRUE; isFE[fieldI] = PETSC_FALSE;} 4055 } 4056 ierr = PetscDSHasJacobian(prob, &hasJac);CHKERRQ(ierr); 4057 ierr = PetscDSHasJacobianPreconditioner(prob, &hasPrec);CHKERRQ(ierr); 4058 ierr = PetscDSHasDynamicJacobian(prob, &hasDyn);CHKERRQ(ierr); 4059 assembleJac = hasJac && hasPrec && (Jac != JacP) ? PETSC_TRUE : PETSC_FALSE; 4060 hasDyn = hasDyn && (X_tShift != 0.0) ? PETSC_TRUE : PETSC_FALSE; 4061 ierr = PetscObjectTypeCompare((PetscObject) Jac, MATIS, &isMatIS);CHKERRQ(ierr); 4062 ierr = PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatISP);CHKERRQ(ierr); 4063 /* Setup input data and temp arrays (should be DMGetWorkArray) */ 4064 if (isMatISP || isMatISP) {ierr = DMPlexGetSubdomainSection(dm, &globalSection);CHKERRQ(ierr);} 4065 if (isMatIS) {ierr = MatISGetLocalMat(Jac, &J);CHKERRQ(ierr);} 4066 if (isMatISP) {ierr = MatISGetLocalMat(JacP, &JP);CHKERRQ(ierr);} 4067 if (hasFV) {ierr = MatSetOption(JP, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE);CHKERRQ(ierr);} /* No allocated space for FV stuff, so ignore the zero entries */ 4068 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 4069 if (probAux) {ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr);} 4070 /* Compute batch sizes */ 4071 if (isFE[0]) { 4072 PetscFE fe; 4073 PetscQuadrature q; 4074 PetscInt numQuadPoints, numBatches, batchSize, numBlocks, blockSize, Nb; 4075 4076 ierr = PetscDSGetDiscretization(prob, 0, (PetscObject *) &fe);CHKERRQ(ierr); 4077 ierr = PetscFEGetQuadrature(fe, &q);CHKERRQ(ierr); 4078 ierr = PetscQuadratureGetData(q, NULL, NULL, &numQuadPoints, NULL, NULL);CHKERRQ(ierr); 4079 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 4080 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 4081 blockSize = Nb*numQuadPoints; 4082 batchSize = numBlocks * blockSize; 4083 chunkSize = numBatches * batchSize; 4084 numChunks = numCells / chunkSize + numCells % chunkSize; 4085 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 4086 } else { 4087 chunkSize = numCells; 4088 numChunks = 1; 4089 } 4090 /* Get work space */ 4091 wsz = (((X?1:0) + (X_t?1:0) + (dmAux?1:0))*totDim + ((hasJac?1:0) + (hasPrec?1:0) + (hasDyn?1:0))*totDim*totDim)*chunkSize; 4092 ierr = DMGetWorkArray(dm, wsz, MPIU_SCALAR, &work);CHKERRQ(ierr); 4093 ierr = PetscArrayzero(work, wsz);CHKERRQ(ierr); 4094 off = 0; 4095 u = X ? (sz = chunkSize*totDim, off += sz, work+off-sz) : NULL; 4096 u_t = X_t ? (sz = chunkSize*totDim, off += sz, work+off-sz) : NULL; 4097 a = dmAux ? (sz = chunkSize*totDimAux, off += sz, work+off-sz) : NULL; 4098 elemMat = hasJac ? (sz = chunkSize*totDim*totDim, off += sz, work+off-sz) : NULL; 4099 elemMatP = hasPrec ? (sz = chunkSize*totDim*totDim, off += sz, work+off-sz) : NULL; 4100 elemMatD = hasDyn ? (sz = chunkSize*totDim*totDim, off += sz, work+off-sz) : NULL; 4101 if (off != wsz) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Error is workspace size %D should be %D", off, wsz); 4102 /* Setup geometry */ 4103 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 4104 ierr = DMFieldGetDegree(coordField, cellIS, NULL, &maxDegree);CHKERRQ(ierr); 4105 if (maxDegree <= 1) {ierr = DMFieldCreateDefaultQuadrature(coordField, cellIS, &qGeom);CHKERRQ(ierr);} 4106 if (!qGeom) { 4107 PetscFE fe; 4108 4109 ierr = PetscDSGetDiscretization(prob, 0, (PetscObject *) &fe);CHKERRQ(ierr); 4110 ierr = PetscFEGetQuadrature(fe, &qGeom);CHKERRQ(ierr); 4111 ierr = PetscObjectReference((PetscObject) qGeom);CHKERRQ(ierr); 4112 } 4113 ierr = DMSNESGetFEGeom(coordField, cellIS, qGeom, PETSC_FALSE, &cgeomFEM);CHKERRQ(ierr); 4114 /* Compute volume integrals */ 4115 if (assembleJac) {ierr = MatZeroEntries(J);CHKERRQ(ierr);} 4116 ierr = MatZeroEntries(JP);CHKERRQ(ierr); 4117 key.label = NULL; 4118 key.value = 0; 4119 key.part = 0; 4120 for (chunk = 0; chunk < numChunks; ++chunk, offCell += chunkSize) { 4121 const PetscInt Ncell = PetscMin(chunkSize, numCells - offCell); 4122 PetscInt c; 4123 4124 /* Extract values */ 4125 for (c = 0; c < Ncell; ++c) { 4126 const PetscInt cell = cells ? cells[c+offCell] : c+offCell; 4127 PetscScalar *x = NULL, *x_t = NULL; 4128 PetscInt i; 4129 4130 if (X) { 4131 ierr = DMPlexVecGetClosure(dm, section, X, cell, NULL, &x);CHKERRQ(ierr); 4132 for (i = 0; i < totDim; ++i) u[c*totDim+i] = x[i]; 4133 ierr = DMPlexVecRestoreClosure(dm, section, X, cell, NULL, &x);CHKERRQ(ierr); 4134 } 4135 if (X_t) { 4136 ierr = DMPlexVecGetClosure(dm, section, X_t, cell, NULL, &x_t);CHKERRQ(ierr); 4137 for (i = 0; i < totDim; ++i) u_t[c*totDim+i] = x_t[i]; 4138 ierr = DMPlexVecRestoreClosure(dm, section, X_t, cell, NULL, &x_t);CHKERRQ(ierr); 4139 } 4140 if (dmAux) { 4141 ierr = DMPlexVecGetClosure(dmAux, sectionAux, A, cell, NULL, &x);CHKERRQ(ierr); 4142 for (i = 0; i < totDimAux; ++i) a[c*totDimAux+i] = x[i]; 4143 ierr = DMPlexVecRestoreClosure(dmAux, sectionAux, A, cell, NULL, &x);CHKERRQ(ierr); 4144 } 4145 } 4146 for (fieldI = 0; fieldI < Nf; ++fieldI) { 4147 PetscFE fe; 4148 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); 4149 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 4150 key.field = fieldI*Nf + fieldJ; 4151 if (hasJac) {ierr = PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN, key, Ncell, cgeomFEM, u, u_t, probAux, a, t, X_tShift, elemMat);CHKERRQ(ierr);} 4152 if (hasPrec) {ierr = PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN_PRE, key, Ncell, cgeomFEM, u, u_t, probAux, a, t, X_tShift, elemMatP);CHKERRQ(ierr);} 4153 if (hasDyn) {ierr = PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN_DYN, key, Ncell, cgeomFEM, u, u_t, probAux, a, t, X_tShift, elemMatD);CHKERRQ(ierr);} 4154 } 4155 /* For finite volume, add the identity */ 4156 if (!isFE[fieldI]) { 4157 PetscFV fv; 4158 PetscInt eOffset = 0, Nc, fc, foff; 4159 4160 ierr = PetscDSGetFieldOffset(prob, fieldI, &foff);CHKERRQ(ierr); 4161 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fv);CHKERRQ(ierr); 4162 ierr = PetscFVGetNumComponents(fv, &Nc);CHKERRQ(ierr); 4163 for (c = 0; c < chunkSize; ++c, eOffset += totDim*totDim) { 4164 for (fc = 0; fc < Nc; ++fc) { 4165 const PetscInt i = foff + fc; 4166 if (hasJac) {elemMat [eOffset+i*totDim+i] = 1.0;} 4167 if (hasPrec) {elemMatP[eOffset+i*totDim+i] = 1.0;} 4168 } 4169 } 4170 } 4171 } 4172 /* Add contribution from X_t */ 4173 if (hasDyn) {for (c = 0; c < chunkSize*totDim*totDim; ++c) elemMat[c] += X_tShift*elemMatD[c];} 4174 /* Insert values into matrix */ 4175 for (c = 0; c < Ncell; ++c) { 4176 const PetscInt cell = cells ? cells[c+offCell] : c+offCell; 4177 if (mesh->printFEM > 1) { 4178 if (hasJac) {ierr = DMPrintCellMatrix(cell, name, totDim, totDim, &elemMat[(c-cStart)*totDim*totDim]);CHKERRQ(ierr);} 4179 if (hasPrec) {ierr = DMPrintCellMatrix(cell, nameP, totDim, totDim, &elemMatP[(c-cStart)*totDim*totDim]);CHKERRQ(ierr);} 4180 } 4181 if (assembleJac) {ierr = DMPlexMatSetClosure(dm, section, globalSection, Jac, cell, &elemMat[(c-cStart)*totDim*totDim], ADD_VALUES);CHKERRQ(ierr);} 4182 ierr = DMPlexMatSetClosure(dm, section, globalSection, JP, cell, &elemMat[(c-cStart)*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 4183 } 4184 } 4185 /* Cleanup */ 4186 ierr = DMSNESRestoreFEGeom(coordField, cellIS, qGeom, PETSC_FALSE, &cgeomFEM);CHKERRQ(ierr); 4187 ierr = PetscQuadratureDestroy(&qGeom);CHKERRQ(ierr); 4188 if (hasFV) {ierr = MatSetOption(JacP, MAT_IGNORE_ZERO_ENTRIES, PETSC_FALSE);CHKERRQ(ierr);} 4189 ierr = DMRestoreWorkArray(dm, Nf, MPIU_BOOL, &isFE);CHKERRQ(ierr); 4190 ierr = DMRestoreWorkArray(dm, ((1 + (X_t?1:0) + (dmAux?1:0))*totDim + ((hasJac?1:0) + (hasPrec?1:0) + (hasDyn?1:0))*totDim*totDim)*chunkSize, MPIU_SCALAR, &work);CHKERRQ(ierr); 4191 /* Compute boundary integrals */ 4192 /* ierr = DMPlexComputeBdJacobian_Internal(dm, X, X_t, t, X_tShift, Jac, JacP, ctx);CHKERRQ(ierr); */ 4193 /* Assemble matrix */ 4194 if (assembleJac) {ierr = MatAssemblyBegin(Jac, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);ierr = MatAssemblyEnd(Jac, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);} 4195 ierr = MatAssemblyBegin(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);ierr = MatAssemblyEnd(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4196 ierr = PetscLogEventEnd(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 4197 PetscFunctionReturn(0); 4198 } 4199 4200 /******** FEM Assembly Function ********/ 4201 4202 static PetscErrorCode DMConvertPlex_Internal(DM dm, DM *plex, PetscBool copy) 4203 { 4204 PetscBool isPlex; 4205 PetscErrorCode ierr; 4206 4207 PetscFunctionBegin; 4208 ierr = PetscObjectTypeCompare((PetscObject) dm, DMPLEX, &isPlex);CHKERRQ(ierr); 4209 if (isPlex) { 4210 *plex = dm; 4211 ierr = PetscObjectReference((PetscObject) dm);CHKERRQ(ierr); 4212 } else { 4213 ierr = PetscObjectQuery((PetscObject) dm, "dm_plex", (PetscObject *) plex);CHKERRQ(ierr); 4214 if (!*plex) { 4215 ierr = DMConvert(dm,DMPLEX,plex);CHKERRQ(ierr); 4216 ierr = PetscObjectCompose((PetscObject) dm, "dm_plex", (PetscObject) *plex);CHKERRQ(ierr); 4217 if (copy) { 4218 ierr = DMCopyAuxiliaryVec(dm, *plex);CHKERRQ(ierr); 4219 } 4220 } else { 4221 ierr = PetscObjectReference((PetscObject) *plex);CHKERRQ(ierr); 4222 } 4223 } 4224 PetscFunctionReturn(0); 4225 } 4226 4227 /*@ 4228 DMPlexGetGeometryFVM - Return precomputed geometric data 4229 4230 Collective on DM 4231 4232 Input Parameter: 4233 . dm - The DM 4234 4235 Output Parameters: 4236 + facegeom - The values precomputed from face geometry 4237 . cellgeom - The values precomputed from cell geometry 4238 - minRadius - The minimum radius over the mesh of an inscribed sphere in a cell 4239 4240 Level: developer 4241 4242 .seealso: DMTSSetRHSFunctionLocal() 4243 @*/ 4244 PetscErrorCode DMPlexGetGeometryFVM(DM dm, Vec *facegeom, Vec *cellgeom, PetscReal *minRadius) 4245 { 4246 DM plex; 4247 PetscErrorCode ierr; 4248 4249 PetscFunctionBegin; 4250 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 4251 ierr = DMConvertPlex_Internal(dm,&plex,PETSC_TRUE);CHKERRQ(ierr); 4252 ierr = DMPlexGetDataFVM(plex, NULL, cellgeom, facegeom, NULL);CHKERRQ(ierr); 4253 if (minRadius) {ierr = DMPlexGetMinRadius(plex, minRadius);CHKERRQ(ierr);} 4254 ierr = DMDestroy(&plex);CHKERRQ(ierr); 4255 PetscFunctionReturn(0); 4256 } 4257 4258 /*@ 4259 DMPlexGetGradientDM - Return gradient data layout 4260 4261 Collective on DM 4262 4263 Input Parameters: 4264 + dm - The DM 4265 - fv - The PetscFV 4266 4267 Output Parameter: 4268 . dmGrad - The layout for gradient values 4269 4270 Level: developer 4271 4272 .seealso: DMPlexGetGeometryFVM() 4273 @*/ 4274 PetscErrorCode DMPlexGetGradientDM(DM dm, PetscFV fv, DM *dmGrad) 4275 { 4276 DM plex; 4277 PetscBool computeGradients; 4278 PetscErrorCode ierr; 4279 4280 PetscFunctionBegin; 4281 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 4282 PetscValidHeaderSpecific(fv,PETSCFV_CLASSID,2); 4283 PetscValidPointer(dmGrad,3); 4284 ierr = PetscFVGetComputeGradients(fv, &computeGradients);CHKERRQ(ierr); 4285 if (!computeGradients) {*dmGrad = NULL; PetscFunctionReturn(0);} 4286 ierr = DMConvertPlex_Internal(dm,&plex,PETSC_TRUE);CHKERRQ(ierr); 4287 ierr = DMPlexGetDataFVM(plex, fv, NULL, NULL, dmGrad);CHKERRQ(ierr); 4288 ierr = DMDestroy(&plex);CHKERRQ(ierr); 4289 PetscFunctionReturn(0); 4290 } 4291 4292 static PetscErrorCode DMPlexComputeBdResidual_Single_Internal(DM dm, PetscReal t, PetscWeakForm wf, PetscFormKey key, Vec locX, Vec locX_t, Vec locF, DMField coordField, IS facetIS) 4293 { 4294 DM_Plex *mesh = (DM_Plex *) dm->data; 4295 DM plex = NULL, plexA = NULL; 4296 DMEnclosureType encAux; 4297 PetscDS prob, probAux = NULL; 4298 PetscSection section, sectionAux = NULL; 4299 Vec locA = NULL; 4300 PetscScalar *u = NULL, *u_t = NULL, *a = NULL, *elemVec = NULL; 4301 PetscInt totDim, totDimAux = 0; 4302 PetscErrorCode ierr; 4303 4304 PetscFunctionBegin; 4305 ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); 4306 ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); 4307 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 4308 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 4309 ierr = DMGetAuxiliaryVec(dm, key.label, key.value, &locA);CHKERRQ(ierr); 4310 if (locA) { 4311 DM dmAux; 4312 4313 ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); 4314 ierr = DMGetEnclosureRelation(dmAux, dm, &encAux);CHKERRQ(ierr); 4315 ierr = DMConvert(dmAux, DMPLEX, &plexA);CHKERRQ(ierr); 4316 ierr = DMGetDS(plexA, &probAux);CHKERRQ(ierr); 4317 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 4318 ierr = DMGetLocalSection(plexA, §ionAux);CHKERRQ(ierr); 4319 } 4320 { 4321 PetscFEGeom *fgeom; 4322 PetscInt maxDegree; 4323 PetscQuadrature qGeom = NULL; 4324 IS pointIS; 4325 const PetscInt *points; 4326 PetscInt numFaces, face, Nq; 4327 4328 ierr = DMLabelGetStratumIS(key.label, key.value, &pointIS);CHKERRQ(ierr); 4329 if (!pointIS) goto end; /* No points with that id on this process */ 4330 { 4331 IS isectIS; 4332 4333 /* TODO: Special cases of ISIntersect where it is quick to check a priori if one is a superset of the other */ 4334 ierr = ISIntersect_Caching_Internal(facetIS,pointIS,&isectIS);CHKERRQ(ierr); 4335 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 4336 pointIS = isectIS; 4337 } 4338 ierr = ISGetLocalSize(pointIS,&numFaces);CHKERRQ(ierr); 4339 ierr = ISGetIndices(pointIS,&points);CHKERRQ(ierr); 4340 ierr = PetscMalloc4(numFaces*totDim, &u, locX_t ? numFaces*totDim : 0, &u_t, numFaces*totDim, &elemVec, locA ? numFaces*totDimAux : 0, &a);CHKERRQ(ierr); 4341 ierr = DMFieldGetDegree(coordField,pointIS,NULL,&maxDegree);CHKERRQ(ierr); 4342 if (maxDegree <= 1) { 4343 ierr = DMFieldCreateDefaultQuadrature(coordField,pointIS,&qGeom);CHKERRQ(ierr); 4344 } 4345 if (!qGeom) { 4346 PetscFE fe; 4347 4348 ierr = PetscDSGetDiscretization(prob, key.field, (PetscObject *) &fe);CHKERRQ(ierr); 4349 ierr = PetscFEGetFaceQuadrature(fe, &qGeom);CHKERRQ(ierr); 4350 ierr = PetscObjectReference((PetscObject)qGeom);CHKERRQ(ierr); 4351 } 4352 ierr = PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 4353 ierr = DMSNESGetFEGeom(coordField,pointIS,qGeom,PETSC_TRUE,&fgeom);CHKERRQ(ierr); 4354 for (face = 0; face < numFaces; ++face) { 4355 const PetscInt point = points[face], *support; 4356 PetscScalar *x = NULL; 4357 PetscInt i; 4358 4359 ierr = DMPlexGetSupport(dm, point, &support);CHKERRQ(ierr); 4360 ierr = DMPlexVecGetClosure(plex, section, locX, support[0], NULL, &x);CHKERRQ(ierr); 4361 for (i = 0; i < totDim; ++i) u[face*totDim+i] = x[i]; 4362 ierr = DMPlexVecRestoreClosure(plex, section, locX, support[0], NULL, &x);CHKERRQ(ierr); 4363 if (locX_t) { 4364 ierr = DMPlexVecGetClosure(plex, section, locX_t, support[0], NULL, &x);CHKERRQ(ierr); 4365 for (i = 0; i < totDim; ++i) u_t[face*totDim+i] = x[i]; 4366 ierr = DMPlexVecRestoreClosure(plex, section, locX_t, support[0], NULL, &x);CHKERRQ(ierr); 4367 } 4368 if (locA) { 4369 PetscInt subp; 4370 4371 ierr = DMGetEnclosurePoint(plexA, dm, encAux, support[0], &subp);CHKERRQ(ierr); 4372 ierr = DMPlexVecGetClosure(plexA, sectionAux, locA, subp, NULL, &x);CHKERRQ(ierr); 4373 for (i = 0; i < totDimAux; ++i) a[face*totDimAux+i] = x[i]; 4374 ierr = DMPlexVecRestoreClosure(plexA, sectionAux, locA, subp, NULL, &x);CHKERRQ(ierr); 4375 } 4376 } 4377 ierr = PetscArrayzero(elemVec, numFaces*totDim);CHKERRQ(ierr); 4378 { 4379 PetscFE fe; 4380 PetscInt Nb; 4381 PetscFEGeom *chunkGeom = NULL; 4382 /* Conforming batches */ 4383 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 4384 /* Remainder */ 4385 PetscInt Nr, offset; 4386 4387 ierr = PetscDSGetDiscretization(prob, key.field, (PetscObject *) &fe);CHKERRQ(ierr); 4388 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 4389 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 4390 /* TODO: documentation is unclear about what is going on with these numbers: how should Nb / Nq factor in ? */ 4391 blockSize = Nb; 4392 batchSize = numBlocks * blockSize; 4393 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 4394 numChunks = numFaces / (numBatches*batchSize); 4395 Ne = numChunks*numBatches*batchSize; 4396 Nr = numFaces % (numBatches*batchSize); 4397 offset = numFaces - Nr; 4398 ierr = PetscFEGeomGetChunk(fgeom,0,offset,&chunkGeom);CHKERRQ(ierr); 4399 ierr = PetscFEIntegrateBdResidual(prob, wf, key, Ne, chunkGeom, u, u_t, probAux, a, t, elemVec);CHKERRQ(ierr); 4400 ierr = PetscFEGeomRestoreChunk(fgeom, 0, offset, &chunkGeom);CHKERRQ(ierr); 4401 ierr = PetscFEGeomGetChunk(fgeom,offset,numFaces,&chunkGeom);CHKERRQ(ierr); 4402 ierr = PetscFEIntegrateBdResidual(prob, wf, key, Nr, chunkGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, a ? &a[offset*totDimAux] : NULL, t, &elemVec[offset*totDim]);CHKERRQ(ierr); 4403 ierr = PetscFEGeomRestoreChunk(fgeom,offset,numFaces,&chunkGeom);CHKERRQ(ierr); 4404 } 4405 for (face = 0; face < numFaces; ++face) { 4406 const PetscInt point = points[face], *support; 4407 4408 if (mesh->printFEM > 1) {ierr = DMPrintCellVector(point, "BdResidual", totDim, &elemVec[face*totDim]);CHKERRQ(ierr);} 4409 ierr = DMPlexGetSupport(plex, point, &support);CHKERRQ(ierr); 4410 ierr = DMPlexVecSetClosure(plex, NULL, locF, support[0], &elemVec[face*totDim], ADD_ALL_VALUES);CHKERRQ(ierr); 4411 } 4412 ierr = DMSNESRestoreFEGeom(coordField,pointIS,qGeom,PETSC_TRUE,&fgeom);CHKERRQ(ierr); 4413 ierr = PetscQuadratureDestroy(&qGeom);CHKERRQ(ierr); 4414 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 4415 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 4416 ierr = PetscFree4(u, u_t, elemVec, a);CHKERRQ(ierr); 4417 } 4418 end: 4419 ierr = DMDestroy(&plex);CHKERRQ(ierr); 4420 ierr = DMDestroy(&plexA);CHKERRQ(ierr); 4421 PetscFunctionReturn(0); 4422 } 4423 4424 PetscErrorCode DMPlexComputeBdResidualSingle(DM dm, PetscReal t, PetscWeakForm wf, PetscFormKey key, Vec locX, Vec locX_t, Vec locF) 4425 { 4426 DMField coordField; 4427 DMLabel depthLabel; 4428 IS facetIS; 4429 PetscInt dim; 4430 PetscErrorCode ierr; 4431 4432 PetscFunctionBegin; 4433 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 4434 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 4435 ierr = DMLabelGetStratumIS(depthLabel, dim-1, &facetIS);CHKERRQ(ierr); 4436 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 4437 ierr = DMPlexComputeBdResidual_Single_Internal(dm, t, wf, key, locX, locX_t, locF, coordField, facetIS);CHKERRQ(ierr); 4438 ierr = ISDestroy(&facetIS);CHKERRQ(ierr); 4439 PetscFunctionReturn(0); 4440 } 4441 4442 PetscErrorCode DMPlexComputeBdResidual_Internal(DM dm, Vec locX, Vec locX_t, PetscReal t, Vec locF, void *user) 4443 { 4444 PetscDS prob; 4445 PetscInt numBd, bd; 4446 DMField coordField = NULL; 4447 IS facetIS = NULL; 4448 DMLabel depthLabel; 4449 PetscInt dim; 4450 PetscErrorCode ierr; 4451 4452 PetscFunctionBegin; 4453 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 4454 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 4455 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 4456 ierr = DMLabelGetStratumIS(depthLabel,dim - 1,&facetIS);CHKERRQ(ierr); 4457 ierr = PetscDSGetNumBoundary(prob, &numBd);CHKERRQ(ierr); 4458 for (bd = 0; bd < numBd; ++bd) { 4459 PetscWeakForm wf; 4460 DMBoundaryConditionType type; 4461 DMLabel label; 4462 const PetscInt *values; 4463 PetscInt field, numValues, v; 4464 PetscObject obj; 4465 PetscClassId id; 4466 PetscFormKey key; 4467 4468 ierr = PetscDSGetBoundary(prob, bd, &wf, &type, NULL, &label, &numValues, &values, &field, NULL, NULL, NULL, NULL, NULL);CHKERRQ(ierr); 4469 ierr = PetscDSGetDiscretization(prob, field, &obj);CHKERRQ(ierr); 4470 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 4471 if ((id != PETSCFE_CLASSID) || (type & DM_BC_ESSENTIAL)) continue; 4472 if (!facetIS) { 4473 DMLabel depthLabel; 4474 PetscInt dim; 4475 4476 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 4477 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 4478 ierr = DMLabelGetStratumIS(depthLabel, dim - 1, &facetIS);CHKERRQ(ierr); 4479 } 4480 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 4481 for (v = 0; v < numValues; ++v) { 4482 key.label = label; 4483 key.value = values[v]; 4484 key.field = field; 4485 key.part = 0; 4486 ierr = DMPlexComputeBdResidual_Single_Internal(dm, t, wf, key, locX, locX_t, locF, coordField, facetIS);CHKERRQ(ierr); 4487 } 4488 } 4489 ierr = ISDestroy(&facetIS);CHKERRQ(ierr); 4490 PetscFunctionReturn(0); 4491 } 4492 4493 PetscErrorCode DMPlexComputeResidual_Internal(DM dm, PetscFormKey key, IS cellIS, PetscReal time, Vec locX, Vec locX_t, PetscReal t, Vec locF, void *user) 4494 { 4495 DM_Plex *mesh = (DM_Plex *) dm->data; 4496 const char *name = "Residual"; 4497 DM dmAux = NULL; 4498 DM dmGrad = NULL; 4499 DMLabel ghostLabel = NULL; 4500 PetscDS ds = NULL; 4501 PetscDS dsAux = NULL; 4502 PetscSection section = NULL; 4503 PetscBool useFEM = PETSC_FALSE; 4504 PetscBool useFVM = PETSC_FALSE; 4505 PetscBool isImplicit = (locX_t || time == PETSC_MIN_REAL) ? PETSC_TRUE : PETSC_FALSE; 4506 PetscFV fvm = NULL; 4507 PetscFVCellGeom *cgeomFVM = NULL; 4508 PetscFVFaceGeom *fgeomFVM = NULL; 4509 DMField coordField = NULL; 4510 Vec locA, cellGeometryFVM = NULL, faceGeometryFVM = NULL, grad, locGrad = NULL; 4511 PetscScalar *u = NULL, *u_t, *a, *uL, *uR; 4512 IS chunkIS; 4513 const PetscInt *cells; 4514 PetscInt cStart, cEnd, numCells; 4515 PetscInt Nf, f, totDim, totDimAux, numChunks, cellChunkSize, faceChunkSize, chunk, fStart, fEnd; 4516 PetscInt maxDegree = PETSC_MAX_INT; 4517 PetscQuadrature affineQuad = NULL, *quads = NULL; 4518 PetscFEGeom *affineGeom = NULL, **geoms = NULL; 4519 PetscErrorCode ierr; 4520 4521 PetscFunctionBegin; 4522 ierr = PetscLogEventBegin(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr); 4523 /* TODO The places where we have to use isFE are probably the member functions for the PetscDisc class */ 4524 /* TODO The FVM geometry is over-manipulated. Make the precalc functions return exactly what we need */ 4525 /* FEM+FVM */ 4526 ierr = ISGetPointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 4527 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 4528 /* 1: Get sizes from dm and dmAux */ 4529 ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); 4530 ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 4531 ierr = DMGetCellDS(dm, cells ? cells[cStart] : cStart, &ds);CHKERRQ(ierr); 4532 ierr = PetscDSGetNumFields(ds, &Nf);CHKERRQ(ierr); 4533 ierr = PetscDSGetTotalDimension(ds, &totDim);CHKERRQ(ierr); 4534 ierr = DMGetAuxiliaryVec(dm, key.label, key.value, &locA);CHKERRQ(ierr); 4535 if (locA) { 4536 PetscInt subcell; 4537 ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); 4538 ierr = DMGetEnclosurePoint(dmAux, dm, DM_ENC_UNKNOWN, cStart, &subcell);CHKERRQ(ierr); 4539 ierr = DMGetCellDS(dmAux, subcell, &dsAux);CHKERRQ(ierr); 4540 ierr = PetscDSGetTotalDimension(dsAux, &totDimAux);CHKERRQ(ierr); 4541 } 4542 /* 2: Get geometric data */ 4543 for (f = 0; f < Nf; ++f) { 4544 PetscObject obj; 4545 PetscClassId id; 4546 PetscBool fimp; 4547 4548 ierr = PetscDSGetImplicit(ds, f, &fimp);CHKERRQ(ierr); 4549 if (isImplicit != fimp) continue; 4550 ierr = PetscDSGetDiscretization(ds, f, &obj);CHKERRQ(ierr); 4551 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 4552 if (id == PETSCFE_CLASSID) {useFEM = PETSC_TRUE;} 4553 if (id == PETSCFV_CLASSID) {useFVM = PETSC_TRUE; fvm = (PetscFV) obj;} 4554 } 4555 if (useFEM) { 4556 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 4557 ierr = DMFieldGetDegree(coordField,cellIS,NULL,&maxDegree);CHKERRQ(ierr); 4558 if (maxDegree <= 1) { 4559 ierr = DMFieldCreateDefaultQuadrature(coordField,cellIS,&affineQuad);CHKERRQ(ierr); 4560 if (affineQuad) { 4561 ierr = DMSNESGetFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&affineGeom);CHKERRQ(ierr); 4562 } 4563 } else { 4564 ierr = PetscCalloc2(Nf,&quads,Nf,&geoms);CHKERRQ(ierr); 4565 for (f = 0; f < Nf; ++f) { 4566 PetscObject obj; 4567 PetscClassId id; 4568 PetscBool fimp; 4569 4570 ierr = PetscDSGetImplicit(ds, f, &fimp);CHKERRQ(ierr); 4571 if (isImplicit != fimp) continue; 4572 ierr = PetscDSGetDiscretization(ds, f, &obj);CHKERRQ(ierr); 4573 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 4574 if (id == PETSCFE_CLASSID) { 4575 PetscFE fe = (PetscFE) obj; 4576 4577 ierr = PetscFEGetQuadrature(fe, &quads[f]);CHKERRQ(ierr); 4578 ierr = PetscObjectReference((PetscObject)quads[f]);CHKERRQ(ierr); 4579 ierr = DMSNESGetFEGeom(coordField,cellIS,quads[f],PETSC_FALSE,&geoms[f]);CHKERRQ(ierr); 4580 } 4581 } 4582 } 4583 } 4584 if (useFVM) { 4585 ierr = DMPlexGetGeometryFVM(dm, &faceGeometryFVM, &cellGeometryFVM, NULL);CHKERRQ(ierr); 4586 ierr = VecGetArrayRead(faceGeometryFVM, (const PetscScalar **) &fgeomFVM);CHKERRQ(ierr); 4587 ierr = VecGetArrayRead(cellGeometryFVM, (const PetscScalar **) &cgeomFVM);CHKERRQ(ierr); 4588 /* Reconstruct and limit cell gradients */ 4589 ierr = DMPlexGetGradientDM(dm, fvm, &dmGrad);CHKERRQ(ierr); 4590 if (dmGrad) { 4591 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 4592 ierr = DMGetGlobalVector(dmGrad, &grad);CHKERRQ(ierr); 4593 ierr = DMPlexReconstructGradients_Internal(dm, fvm, fStart, fEnd, faceGeometryFVM, cellGeometryFVM, locX, grad);CHKERRQ(ierr); 4594 /* Communicate gradient values */ 4595 ierr = DMGetLocalVector(dmGrad, &locGrad);CHKERRQ(ierr); 4596 ierr = DMGlobalToLocalBegin(dmGrad, grad, INSERT_VALUES, locGrad);CHKERRQ(ierr); 4597 ierr = DMGlobalToLocalEnd(dmGrad, grad, INSERT_VALUES, locGrad);CHKERRQ(ierr); 4598 ierr = DMRestoreGlobalVector(dmGrad, &grad);CHKERRQ(ierr); 4599 } 4600 /* Handle non-essential (e.g. outflow) boundary values */ 4601 ierr = DMPlexInsertBoundaryValues(dm, PETSC_FALSE, locX, time, faceGeometryFVM, cellGeometryFVM, locGrad);CHKERRQ(ierr); 4602 } 4603 /* Loop over chunks */ 4604 if (useFEM) {ierr = ISCreate(PETSC_COMM_SELF, &chunkIS);CHKERRQ(ierr);} 4605 numCells = cEnd - cStart; 4606 numChunks = 1; 4607 cellChunkSize = numCells/numChunks; 4608 faceChunkSize = (fEnd - fStart)/numChunks; 4609 numChunks = PetscMin(1,numCells); 4610 for (chunk = 0; chunk < numChunks; ++chunk) { 4611 PetscScalar *elemVec, *fluxL, *fluxR; 4612 PetscReal *vol; 4613 PetscFVFaceGeom *fgeom; 4614 PetscInt cS = cStart+chunk*cellChunkSize, cE = PetscMin(cS+cellChunkSize, cEnd), numCells = cE - cS, c; 4615 PetscInt fS = fStart+chunk*faceChunkSize, fE = PetscMin(fS+faceChunkSize, fEnd), numFaces = 0, face; 4616 4617 /* Extract field coefficients */ 4618 if (useFEM) { 4619 ierr = ISGetPointSubrange(chunkIS, cS, cE, cells);CHKERRQ(ierr); 4620 ierr = DMPlexGetCellFields(dm, chunkIS, locX, locX_t, locA, &u, &u_t, &a);CHKERRQ(ierr); 4621 ierr = DMGetWorkArray(dm, numCells*totDim, MPIU_SCALAR, &elemVec);CHKERRQ(ierr); 4622 ierr = PetscArrayzero(elemVec, numCells*totDim);CHKERRQ(ierr); 4623 } 4624 if (useFVM) { 4625 ierr = DMPlexGetFaceFields(dm, fS, fE, locX, locX_t, faceGeometryFVM, cellGeometryFVM, locGrad, &numFaces, &uL, &uR);CHKERRQ(ierr); 4626 ierr = DMPlexGetFaceGeometry(dm, fS, fE, faceGeometryFVM, cellGeometryFVM, &numFaces, &fgeom, &vol);CHKERRQ(ierr); 4627 ierr = DMGetWorkArray(dm, numFaces*totDim, MPIU_SCALAR, &fluxL);CHKERRQ(ierr); 4628 ierr = DMGetWorkArray(dm, numFaces*totDim, MPIU_SCALAR, &fluxR);CHKERRQ(ierr); 4629 ierr = PetscArrayzero(fluxL, numFaces*totDim);CHKERRQ(ierr); 4630 ierr = PetscArrayzero(fluxR, numFaces*totDim);CHKERRQ(ierr); 4631 } 4632 /* TODO We will interlace both our field coefficients (u, u_t, uL, uR, etc.) and our output (elemVec, fL, fR). I think this works */ 4633 /* Loop over fields */ 4634 for (f = 0; f < Nf; ++f) { 4635 PetscObject obj; 4636 PetscClassId id; 4637 PetscBool fimp; 4638 PetscInt numChunks, numBatches, batchSize, numBlocks, blockSize, Ne, Nr, offset; 4639 4640 key.field = f; 4641 ierr = PetscDSGetImplicit(ds, f, &fimp);CHKERRQ(ierr); 4642 if (isImplicit != fimp) continue; 4643 ierr = PetscDSGetDiscretization(ds, f, &obj);CHKERRQ(ierr); 4644 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 4645 if (id == PETSCFE_CLASSID) { 4646 PetscFE fe = (PetscFE) obj; 4647 PetscFEGeom *geom = affineGeom ? affineGeom : geoms[f]; 4648 PetscFEGeom *chunkGeom = NULL; 4649 PetscQuadrature quad = affineQuad ? affineQuad : quads[f]; 4650 PetscInt Nq, Nb; 4651 4652 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 4653 ierr = PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 4654 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 4655 blockSize = Nb; 4656 batchSize = numBlocks * blockSize; 4657 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 4658 numChunks = numCells / (numBatches*batchSize); 4659 Ne = numChunks*numBatches*batchSize; 4660 Nr = numCells % (numBatches*batchSize); 4661 offset = numCells - Nr; 4662 /* Integrate FE residual to get elemVec (need fields at quadrature points) */ 4663 /* For FV, I think we use a P0 basis and the cell coefficients (for subdivided cells, we can tweak the basis tabulation to be the indicator function) */ 4664 ierr = PetscFEGeomGetChunk(geom,0,offset,&chunkGeom);CHKERRQ(ierr); 4665 ierr = PetscFEIntegrateResidual(ds, key, Ne, chunkGeom, u, u_t, dsAux, a, t, elemVec);CHKERRQ(ierr); 4666 ierr = PetscFEGeomGetChunk(geom,offset,numCells,&chunkGeom);CHKERRQ(ierr); 4667 ierr = PetscFEIntegrateResidual(ds, key, Nr, chunkGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, dsAux, &a[offset*totDimAux], t, &elemVec[offset*totDim]);CHKERRQ(ierr); 4668 ierr = PetscFEGeomRestoreChunk(geom,offset,numCells,&chunkGeom);CHKERRQ(ierr); 4669 } else if (id == PETSCFV_CLASSID) { 4670 PetscFV fv = (PetscFV) obj; 4671 4672 Ne = numFaces; 4673 /* Riemann solve over faces (need fields at face centroids) */ 4674 /* We need to evaluate FE fields at those coordinates */ 4675 ierr = PetscFVIntegrateRHSFunction(fv, ds, f, Ne, fgeom, vol, uL, uR, fluxL, fluxR);CHKERRQ(ierr); 4676 } else SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", f); 4677 } 4678 /* Loop over domain */ 4679 if (useFEM) { 4680 /* Add elemVec to locX */ 4681 for (c = cS; c < cE; ++c) { 4682 const PetscInt cell = cells ? cells[c] : c; 4683 const PetscInt cind = c - cStart; 4684 4685 if (mesh->printFEM > 1) {ierr = DMPrintCellVector(cell, name, totDim, &elemVec[cind*totDim]);CHKERRQ(ierr);} 4686 if (ghostLabel) { 4687 PetscInt ghostVal; 4688 4689 ierr = DMLabelGetValue(ghostLabel,cell,&ghostVal);CHKERRQ(ierr); 4690 if (ghostVal > 0) continue; 4691 } 4692 ierr = DMPlexVecSetClosure(dm, section, locF, cell, &elemVec[cind*totDim], ADD_ALL_VALUES);CHKERRQ(ierr); 4693 } 4694 } 4695 if (useFVM) { 4696 PetscScalar *fa; 4697 PetscInt iface; 4698 4699 ierr = VecGetArray(locF, &fa);CHKERRQ(ierr); 4700 for (f = 0; f < Nf; ++f) { 4701 PetscFV fv; 4702 PetscObject obj; 4703 PetscClassId id; 4704 PetscInt foff, pdim; 4705 4706 ierr = PetscDSGetDiscretization(ds, f, &obj);CHKERRQ(ierr); 4707 ierr = PetscDSGetFieldOffset(ds, f, &foff);CHKERRQ(ierr); 4708 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 4709 if (id != PETSCFV_CLASSID) continue; 4710 fv = (PetscFV) obj; 4711 ierr = PetscFVGetNumComponents(fv, &pdim);CHKERRQ(ierr); 4712 /* Accumulate fluxes to cells */ 4713 for (face = fS, iface = 0; face < fE; ++face) { 4714 const PetscInt *scells; 4715 PetscScalar *fL = NULL, *fR = NULL; 4716 PetscInt ghost, d, nsupp, nchild; 4717 4718 ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr); 4719 ierr = DMPlexGetSupportSize(dm, face, &nsupp);CHKERRQ(ierr); 4720 ierr = DMPlexGetTreeChildren(dm, face, &nchild, NULL);CHKERRQ(ierr); 4721 if (ghost >= 0 || nsupp > 2 || nchild > 0) continue; 4722 ierr = DMPlexGetSupport(dm, face, &scells);CHKERRQ(ierr); 4723 ierr = DMLabelGetValue(ghostLabel,scells[0],&ghost);CHKERRQ(ierr); 4724 if (ghost <= 0) {ierr = DMPlexPointLocalFieldRef(dm, scells[0], f, fa, &fL);CHKERRQ(ierr);} 4725 ierr = DMLabelGetValue(ghostLabel,scells[1],&ghost);CHKERRQ(ierr); 4726 if (ghost <= 0) {ierr = DMPlexPointLocalFieldRef(dm, scells[1], f, fa, &fR);CHKERRQ(ierr);} 4727 for (d = 0; d < pdim; ++d) { 4728 if (fL) fL[d] -= fluxL[iface*totDim+foff+d]; 4729 if (fR) fR[d] += fluxR[iface*totDim+foff+d]; 4730 } 4731 ++iface; 4732 } 4733 } 4734 ierr = VecRestoreArray(locF, &fa);CHKERRQ(ierr); 4735 } 4736 /* Handle time derivative */ 4737 if (locX_t) { 4738 PetscScalar *x_t, *fa; 4739 4740 ierr = VecGetArray(locF, &fa);CHKERRQ(ierr); 4741 ierr = VecGetArray(locX_t, &x_t);CHKERRQ(ierr); 4742 for (f = 0; f < Nf; ++f) { 4743 PetscFV fv; 4744 PetscObject obj; 4745 PetscClassId id; 4746 PetscInt pdim, d; 4747 4748 ierr = PetscDSGetDiscretization(ds, f, &obj);CHKERRQ(ierr); 4749 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 4750 if (id != PETSCFV_CLASSID) continue; 4751 fv = (PetscFV) obj; 4752 ierr = PetscFVGetNumComponents(fv, &pdim);CHKERRQ(ierr); 4753 for (c = cS; c < cE; ++c) { 4754 const PetscInt cell = cells ? cells[c] : c; 4755 PetscScalar *u_t, *r; 4756 4757 if (ghostLabel) { 4758 PetscInt ghostVal; 4759 4760 ierr = DMLabelGetValue(ghostLabel, cell, &ghostVal);CHKERRQ(ierr); 4761 if (ghostVal > 0) continue; 4762 } 4763 ierr = DMPlexPointLocalFieldRead(dm, cell, f, x_t, &u_t);CHKERRQ(ierr); 4764 ierr = DMPlexPointLocalFieldRef(dm, cell, f, fa, &r);CHKERRQ(ierr); 4765 for (d = 0; d < pdim; ++d) r[d] += u_t[d]; 4766 } 4767 } 4768 ierr = VecRestoreArray(locX_t, &x_t);CHKERRQ(ierr); 4769 ierr = VecRestoreArray(locF, &fa);CHKERRQ(ierr); 4770 } 4771 if (useFEM) { 4772 ierr = DMPlexRestoreCellFields(dm, chunkIS, locX, locX_t, locA, &u, &u_t, &a);CHKERRQ(ierr); 4773 ierr = DMRestoreWorkArray(dm, numCells*totDim, MPIU_SCALAR, &elemVec);CHKERRQ(ierr); 4774 } 4775 if (useFVM) { 4776 ierr = DMPlexRestoreFaceFields(dm, fS, fE, locX, locX_t, faceGeometryFVM, cellGeometryFVM, locGrad, &numFaces, &uL, &uR);CHKERRQ(ierr); 4777 ierr = DMPlexRestoreFaceGeometry(dm, fS, fE, faceGeometryFVM, cellGeometryFVM, &numFaces, &fgeom, &vol);CHKERRQ(ierr); 4778 ierr = DMRestoreWorkArray(dm, numFaces*totDim, MPIU_SCALAR, &fluxL);CHKERRQ(ierr); 4779 ierr = DMRestoreWorkArray(dm, numFaces*totDim, MPIU_SCALAR, &fluxR);CHKERRQ(ierr); 4780 if (dmGrad) {ierr = DMRestoreLocalVector(dmGrad, &locGrad);CHKERRQ(ierr);} 4781 } 4782 } 4783 if (useFEM) {ierr = ISDestroy(&chunkIS);CHKERRQ(ierr);} 4784 ierr = ISRestorePointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 4785 4786 if (useFEM) { 4787 ierr = DMPlexComputeBdResidual_Internal(dm, locX, locX_t, t, locF, user);CHKERRQ(ierr); 4788 4789 if (maxDegree <= 1) { 4790 ierr = DMSNESRestoreFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&affineGeom);CHKERRQ(ierr); 4791 ierr = PetscQuadratureDestroy(&affineQuad);CHKERRQ(ierr); 4792 } else { 4793 for (f = 0; f < Nf; ++f) { 4794 ierr = DMSNESRestoreFEGeom(coordField,cellIS,quads[f],PETSC_FALSE,&geoms[f]);CHKERRQ(ierr); 4795 ierr = PetscQuadratureDestroy(&quads[f]);CHKERRQ(ierr); 4796 } 4797 ierr = PetscFree2(quads,geoms);CHKERRQ(ierr); 4798 } 4799 } 4800 4801 /* FEM */ 4802 /* 1: Get sizes from dm and dmAux */ 4803 /* 2: Get geometric data */ 4804 /* 3: Handle boundary values */ 4805 /* 4: Loop over domain */ 4806 /* Extract coefficients */ 4807 /* Loop over fields */ 4808 /* Set tiling for FE*/ 4809 /* Integrate FE residual to get elemVec */ 4810 /* Loop over subdomain */ 4811 /* Loop over quad points */ 4812 /* Transform coords to real space */ 4813 /* Evaluate field and aux fields at point */ 4814 /* Evaluate residual at point */ 4815 /* Transform residual to real space */ 4816 /* Add residual to elemVec */ 4817 /* Loop over domain */ 4818 /* Add elemVec to locX */ 4819 4820 /* FVM */ 4821 /* Get geometric data */ 4822 /* If using gradients */ 4823 /* Compute gradient data */ 4824 /* Loop over domain faces */ 4825 /* Count computational faces */ 4826 /* Reconstruct cell gradient */ 4827 /* Loop over domain cells */ 4828 /* Limit cell gradients */ 4829 /* Handle boundary values */ 4830 /* Loop over domain faces */ 4831 /* Read out field, centroid, normal, volume for each side of face */ 4832 /* Riemann solve over faces */ 4833 /* Loop over domain faces */ 4834 /* Accumulate fluxes to cells */ 4835 /* TODO Change printFEM to printDisc here */ 4836 if (mesh->printFEM) { 4837 Vec locFbc; 4838 PetscInt pStart, pEnd, p, maxDof; 4839 PetscScalar *zeroes; 4840 4841 ierr = VecDuplicate(locF,&locFbc);CHKERRQ(ierr); 4842 ierr = VecCopy(locF,locFbc);CHKERRQ(ierr); 4843 ierr = PetscSectionGetChart(section,&pStart,&pEnd);CHKERRQ(ierr); 4844 ierr = PetscSectionGetMaxDof(section,&maxDof);CHKERRQ(ierr); 4845 ierr = PetscCalloc1(maxDof,&zeroes);CHKERRQ(ierr); 4846 for (p = pStart; p < pEnd; p++) { 4847 ierr = VecSetValuesSection(locFbc,section,p,zeroes,INSERT_BC_VALUES);CHKERRQ(ierr); 4848 } 4849 ierr = PetscFree(zeroes);CHKERRQ(ierr); 4850 ierr = DMPrintLocalVec(dm, name, mesh->printTol, locFbc);CHKERRQ(ierr); 4851 ierr = VecDestroy(&locFbc);CHKERRQ(ierr); 4852 } 4853 ierr = PetscLogEventEnd(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr); 4854 PetscFunctionReturn(0); 4855 } 4856 4857 /* 4858 1) Allow multiple kernels for BdResidual for hybrid DS 4859 4860 DONE 2) Get out dsAux for either side at the same time as cohesive cell dsAux 4861 4862 DONE 3) Change DMGetCellFields() to get different aux data a[] for each side 4863 - I think I just need to replace a[] with the closure from each face 4864 4865 4) Run both kernels for each non-hybrid field with correct dsAux, and then hybrid field as before 4866 */ 4867 PetscErrorCode DMPlexComputeResidual_Hybrid_Internal(DM dm, PetscFormKey key[], IS cellIS, PetscReal time, Vec locX, Vec locX_t, PetscReal t, Vec locF, void *user) 4868 { 4869 DM_Plex *mesh = (DM_Plex *) dm->data; 4870 const char *name = "Hybrid Residual"; 4871 DM dmAux[3] = {NULL, NULL, NULL}; 4872 DMLabel ghostLabel = NULL; 4873 PetscDS ds = NULL; 4874 PetscDS dsAux[3] = {NULL, NULL, NULL}; 4875 Vec locA[3] = {NULL, NULL, NULL}; 4876 PetscSection section = NULL; 4877 DMField coordField = NULL; 4878 PetscScalar *u = NULL, *u_t, *a[3]; 4879 PetscScalar *elemVec; 4880 IS chunkIS; 4881 const PetscInt *cells; 4882 PetscInt *faces; 4883 PetscInt cStart, cEnd, numCells; 4884 PetscInt Nf, f, totDim, totDimAux[3], numChunks, cellChunkSize, chunk; 4885 PetscInt maxDegree = PETSC_MAX_INT; 4886 PetscQuadrature affineQuad = NULL, *quads = NULL; 4887 PetscFEGeom *affineGeom = NULL, **geoms = NULL; 4888 PetscErrorCode ierr; 4889 4890 PetscFunctionBegin; 4891 ierr = PetscLogEventBegin(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr); 4892 /* TODO The places where we have to use isFE are probably the member functions for the PetscDisc class */ 4893 /* FEM */ 4894 ierr = ISGetLocalSize(cellIS, &numCells);CHKERRQ(ierr); 4895 ierr = ISGetPointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 4896 /* 1: Get sizes from dm and dmAux */ 4897 ierr = DMGetSection(dm, §ion);CHKERRQ(ierr); 4898 ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 4899 ierr = DMGetCellDS(dm, cStart, &ds);CHKERRQ(ierr); 4900 ierr = PetscDSGetNumFields(ds, &Nf);CHKERRQ(ierr); 4901 ierr = PetscDSGetTotalDimension(ds, &totDim);CHKERRQ(ierr); 4902 ierr = DMGetAuxiliaryVec(dm, key[2].label, key[2].value, &locA[2]);CHKERRQ(ierr); 4903 if (locA[2]) { 4904 ierr = VecGetDM(locA[2], &dmAux[2]);CHKERRQ(ierr); 4905 ierr = DMGetCellDS(dmAux[2], cStart, &dsAux[2]);CHKERRQ(ierr); 4906 ierr = PetscDSGetTotalDimension(dsAux[2], &totDimAux[2]);CHKERRQ(ierr); 4907 { 4908 const PetscInt *cone; 4909 PetscInt c; 4910 4911 ierr = DMPlexGetCone(dm, cStart, &cone);CHKERRQ(ierr); 4912 for (c = 0; c < 2; ++c) { 4913 const PetscInt *support; 4914 PetscInt ssize, s; 4915 4916 ierr = DMPlexGetSupport(dm, cone[c], &support);CHKERRQ(ierr); 4917 ierr = DMPlexGetSupportSize(dm, cone[c], &ssize);CHKERRQ(ierr); 4918 if (ssize != 2) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Face %D from cell %D has support size %D != 2", cone[c], cStart, ssize); 4919 if (support[0] == cStart) s = 1; 4920 else if (support[1] == cStart) s = 0; 4921 else SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Face %D does not have cell %D in its support", cone[c], cStart); 4922 ierr = DMGetAuxiliaryVec(dm, key[c].label, key[c].value, &locA[c]);CHKERRQ(ierr); 4923 if (locA[c]) {ierr = VecGetDM(locA[c], &dmAux[c]);CHKERRQ(ierr);} 4924 else {dmAux[c] = dmAux[2];} 4925 ierr = DMGetCellDS(dmAux[c], support[s], &dsAux[c]);CHKERRQ(ierr); 4926 ierr = PetscDSGetTotalDimension(dsAux[c], &totDimAux[c]);CHKERRQ(ierr); 4927 } 4928 } 4929 } 4930 /* 2: Setup geometric data */ 4931 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 4932 ierr = DMFieldGetDegree(coordField, cellIS, NULL, &maxDegree);CHKERRQ(ierr); 4933 if (maxDegree > 1) { 4934 ierr = PetscCalloc2(Nf, &quads, Nf, &geoms);CHKERRQ(ierr); 4935 for (f = 0; f < Nf; ++f) { 4936 PetscFE fe; 4937 4938 ierr = PetscDSGetDiscretization(ds, f, (PetscObject *) &fe);CHKERRQ(ierr); 4939 if (fe) { 4940 ierr = PetscFEGetQuadrature(fe, &quads[f]);CHKERRQ(ierr); 4941 ierr = PetscObjectReference((PetscObject) quads[f]);CHKERRQ(ierr); 4942 } 4943 } 4944 } 4945 /* Loop over chunks */ 4946 cellChunkSize = numCells; 4947 numChunks = !numCells ? 0 : PetscCeilReal(((PetscReal) numCells)/cellChunkSize); 4948 ierr = PetscCalloc1(2*cellChunkSize, &faces);CHKERRQ(ierr); 4949 ierr = ISCreateGeneral(PETSC_COMM_SELF, cellChunkSize, faces, PETSC_USE_POINTER, &chunkIS);CHKERRQ(ierr); 4950 /* Extract field coefficients */ 4951 /* NOTE This needs the end cap faces to have identical orientations */ 4952 ierr = DMPlexGetCellFields(dm, cellIS, locX, locX_t, locA[2], &u, &u_t, &a[2]);CHKERRQ(ierr); 4953 ierr = DMPlexGetHybridAuxFields(dm, dmAux, dsAux, cellIS, locA, a);CHKERRQ(ierr); 4954 ierr = DMGetWorkArray(dm, cellChunkSize*totDim, MPIU_SCALAR, &elemVec);CHKERRQ(ierr); 4955 for (chunk = 0; chunk < numChunks; ++chunk) { 4956 PetscInt cS = cStart+chunk*cellChunkSize, cE = PetscMin(cS+cellChunkSize, cEnd), numCells = cE - cS, c; 4957 4958 ierr = PetscMemzero(elemVec, cellChunkSize*totDim * sizeof(PetscScalar));CHKERRQ(ierr); 4959 /* Get faces */ 4960 for (c = cS; c < cE; ++c) { 4961 const PetscInt cell = cells ? cells[c] : c; 4962 const PetscInt *cone; 4963 ierr = DMPlexGetCone(dm, cell, &cone);CHKERRQ(ierr); 4964 faces[(c-cS)*2+0] = cone[0]; 4965 faces[(c-cS)*2+1] = cone[1]; 4966 } 4967 ierr = ISGeneralSetIndices(chunkIS, cellChunkSize, faces, PETSC_USE_POINTER);CHKERRQ(ierr); 4968 /* Get geometric data */ 4969 if (maxDegree <= 1) { 4970 if (!affineQuad) {ierr = DMFieldCreateDefaultQuadrature(coordField, chunkIS, &affineQuad);CHKERRQ(ierr);} 4971 if (affineQuad) {ierr = DMSNESGetFEGeom(coordField, chunkIS, affineQuad, PETSC_TRUE, &affineGeom);CHKERRQ(ierr);} 4972 } else { 4973 for (f = 0; f < Nf; ++f) { 4974 if (quads[f]) {ierr = DMSNESGetFEGeom(coordField, chunkIS, quads[f], PETSC_TRUE, &geoms[f]);CHKERRQ(ierr);} 4975 } 4976 } 4977 /* Loop over fields */ 4978 for (f = 0; f < Nf; ++f) { 4979 PetscFE fe; 4980 PetscFEGeom *geom = affineGeom ? affineGeom : geoms[f]; 4981 PetscFEGeom *chunkGeom = NULL, *remGeom = NULL; 4982 PetscQuadrature quad = affineQuad ? affineQuad : quads[f]; 4983 PetscInt numChunks, numBatches, batchSize, numBlocks, blockSize, Ne, Nr, offset, Nq, Nb; 4984 4985 ierr = PetscDSGetDiscretization(ds, f, (PetscObject *) &fe);CHKERRQ(ierr); 4986 if (!fe) continue; 4987 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 4988 ierr = PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 4989 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 4990 blockSize = Nb; 4991 batchSize = numBlocks * blockSize; 4992 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 4993 numChunks = numCells / (numBatches*batchSize); 4994 Ne = numChunks*numBatches*batchSize; 4995 Nr = numCells % (numBatches*batchSize); 4996 offset = numCells - Nr; 4997 ierr = PetscFEGeomGetChunk(geom,0,offset,&chunkGeom);CHKERRQ(ierr); 4998 ierr = PetscFEGeomGetChunk(geom,offset,numCells,&remGeom);CHKERRQ(ierr); 4999 chunkGeom->isHybrid = remGeom->isHybrid = PETSC_TRUE; 5000 if (f == Nf-1) { 5001 key[2].field = f; 5002 ierr = PetscFEIntegrateHybridResidual(ds, key[2], Ne, chunkGeom, u, u_t, dsAux[2], a[2], t, elemVec);CHKERRQ(ierr); 5003 ierr = PetscFEIntegrateHybridResidual(ds, key[2], Nr, remGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, dsAux[2], &a[2][offset*totDimAux[2]], t, &elemVec[offset*totDim]);CHKERRQ(ierr); 5004 } else { 5005 key[0].field = f; 5006 key[1].field = f; 5007 ierr = PetscFEIntegrateHybridResidual(ds, key[0], Ne, chunkGeom, u, u_t, dsAux[0], a[0], t, elemVec);CHKERRQ(ierr); 5008 ierr = PetscFEIntegrateHybridResidual(ds, key[1], Ne, chunkGeom, u, u_t, dsAux[1], a[1], t, elemVec);CHKERRQ(ierr); 5009 ierr = PetscFEIntegrateHybridResidual(ds, key[0], Nr, remGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, dsAux[0], &a[0][offset*totDimAux[0]], t, &elemVec[offset*totDim]);CHKERRQ(ierr); 5010 ierr = PetscFEIntegrateHybridResidual(ds, key[1], Nr, remGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, dsAux[1], &a[1][offset*totDimAux[1]], t, &elemVec[offset*totDim]);CHKERRQ(ierr); 5011 } 5012 ierr = PetscFEGeomRestoreChunk(geom,offset,numCells,&remGeom);CHKERRQ(ierr); 5013 ierr = PetscFEGeomRestoreChunk(geom,0,offset,&chunkGeom);CHKERRQ(ierr); 5014 } 5015 /* Add elemVec to locX */ 5016 for (c = cS; c < cE; ++c) { 5017 const PetscInt cell = cells ? cells[c] : c; 5018 const PetscInt cind = c - cStart; 5019 5020 if (mesh->printFEM > 1) {ierr = DMPrintCellVector(cell, name, totDim, &elemVec[cind*totDim]);CHKERRQ(ierr);} 5021 if (ghostLabel) { 5022 PetscInt ghostVal; 5023 5024 ierr = DMLabelGetValue(ghostLabel,cell,&ghostVal);CHKERRQ(ierr); 5025 if (ghostVal > 0) continue; 5026 } 5027 ierr = DMPlexVecSetClosure(dm, section, locF, cell, &elemVec[cind*totDim], ADD_ALL_VALUES);CHKERRQ(ierr); 5028 } 5029 } 5030 ierr = DMPlexRestoreCellFields(dm, cellIS, locX, locX_t, locA[2], &u, &u_t, &a[2]);CHKERRQ(ierr); 5031 ierr = DMPlexRestoreHybridAuxFields(dmAux, dsAux, cellIS, locA, a);CHKERRQ(ierr); 5032 ierr = DMRestoreWorkArray(dm, numCells*totDim, MPIU_SCALAR, &elemVec);CHKERRQ(ierr); 5033 ierr = PetscFree(faces);CHKERRQ(ierr); 5034 ierr = ISDestroy(&chunkIS);CHKERRQ(ierr); 5035 ierr = ISRestorePointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 5036 if (maxDegree <= 1) { 5037 ierr = DMSNESRestoreFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&affineGeom);CHKERRQ(ierr); 5038 ierr = PetscQuadratureDestroy(&affineQuad);CHKERRQ(ierr); 5039 } else { 5040 for (f = 0; f < Nf; ++f) { 5041 if (geoms) {ierr = DMSNESRestoreFEGeom(coordField,cellIS,quads[f],PETSC_FALSE,&geoms[f]);CHKERRQ(ierr);} 5042 if (quads) {ierr = PetscQuadratureDestroy(&quads[f]);CHKERRQ(ierr);} 5043 } 5044 ierr = PetscFree2(quads,geoms);CHKERRQ(ierr); 5045 } 5046 ierr = PetscLogEventEnd(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr); 5047 PetscFunctionReturn(0); 5048 } 5049 5050 PetscErrorCode DMPlexComputeBdJacobian_Single_Internal(DM dm, PetscReal t, PetscWeakForm wf, DMLabel label, PetscInt numValues, const PetscInt values[], PetscInt fieldI, Vec locX, Vec locX_t, PetscReal X_tShift, Mat Jac, Mat JacP, DMField coordField, IS facetIS) 5051 { 5052 DM_Plex *mesh = (DM_Plex *) dm->data; 5053 DM plex = NULL, plexA = NULL, tdm; 5054 DMEnclosureType encAux; 5055 PetscDS prob, probAux = NULL; 5056 PetscSection section, sectionAux = NULL; 5057 PetscSection globalSection, subSection = NULL; 5058 Vec locA = NULL, tv; 5059 PetscScalar *u = NULL, *u_t = NULL, *a = NULL, *elemMat = NULL; 5060 PetscInt v; 5061 PetscInt Nf, totDim, totDimAux = 0; 5062 PetscBool isMatISP, transform; 5063 PetscErrorCode ierr; 5064 5065 PetscFunctionBegin; 5066 ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); 5067 ierr = DMHasBasisTransform(dm, &transform);CHKERRQ(ierr); 5068 ierr = DMGetBasisTransformDM_Internal(dm, &tdm);CHKERRQ(ierr); 5069 ierr = DMGetBasisTransformVec_Internal(dm, &tv);CHKERRQ(ierr); 5070 ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); 5071 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 5072 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 5073 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 5074 ierr = DMGetAuxiliaryVec(dm, label, values[0], &locA);CHKERRQ(ierr); 5075 if (locA) { 5076 DM dmAux; 5077 5078 ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); 5079 ierr = DMGetEnclosureRelation(dmAux, dm, &encAux);CHKERRQ(ierr); 5080 ierr = DMConvert(dmAux, DMPLEX, &plexA);CHKERRQ(ierr); 5081 ierr = DMGetDS(plexA, &probAux);CHKERRQ(ierr); 5082 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 5083 ierr = DMGetLocalSection(plexA, §ionAux);CHKERRQ(ierr); 5084 } 5085 5086 ierr = PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatISP);CHKERRQ(ierr); 5087 ierr = DMGetGlobalSection(dm, &globalSection);CHKERRQ(ierr); 5088 if (isMatISP) {ierr = DMPlexGetSubdomainSection(dm, &subSection);CHKERRQ(ierr);} 5089 for (v = 0; v < numValues; ++v) { 5090 PetscFEGeom *fgeom; 5091 PetscInt maxDegree; 5092 PetscQuadrature qGeom = NULL; 5093 IS pointIS; 5094 const PetscInt *points; 5095 PetscFormKey key; 5096 PetscInt numFaces, face, Nq; 5097 5098 key.label = label; 5099 key.value = values[v]; 5100 key.part = 0; 5101 ierr = DMLabelGetStratumIS(label, values[v], &pointIS);CHKERRQ(ierr); 5102 if (!pointIS) continue; /* No points with that id on this process */ 5103 { 5104 IS isectIS; 5105 5106 /* TODO: Special cases of ISIntersect where it is quick to check a prior if one is a superset of the other */ 5107 ierr = ISIntersect_Caching_Internal(facetIS,pointIS,&isectIS);CHKERRQ(ierr); 5108 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 5109 pointIS = isectIS; 5110 } 5111 ierr = ISGetLocalSize(pointIS, &numFaces);CHKERRQ(ierr); 5112 ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); 5113 ierr = PetscMalloc4(numFaces*totDim, &u, locX_t ? numFaces*totDim : 0, &u_t, numFaces*totDim*totDim, &elemMat, locA ? numFaces*totDimAux : 0, &a);CHKERRQ(ierr); 5114 ierr = DMFieldGetDegree(coordField,pointIS,NULL,&maxDegree);CHKERRQ(ierr); 5115 if (maxDegree <= 1) { 5116 ierr = DMFieldCreateDefaultQuadrature(coordField,pointIS,&qGeom);CHKERRQ(ierr); 5117 } 5118 if (!qGeom) { 5119 PetscFE fe; 5120 5121 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); 5122 ierr = PetscFEGetFaceQuadrature(fe, &qGeom);CHKERRQ(ierr); 5123 ierr = PetscObjectReference((PetscObject)qGeom);CHKERRQ(ierr); 5124 } 5125 ierr = PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 5126 ierr = DMSNESGetFEGeom(coordField,pointIS,qGeom,PETSC_TRUE,&fgeom);CHKERRQ(ierr); 5127 for (face = 0; face < numFaces; ++face) { 5128 const PetscInt point = points[face], *support; 5129 PetscScalar *x = NULL; 5130 PetscInt i; 5131 5132 ierr = DMPlexGetSupport(dm, point, &support);CHKERRQ(ierr); 5133 ierr = DMPlexVecGetClosure(plex, section, locX, support[0], NULL, &x);CHKERRQ(ierr); 5134 for (i = 0; i < totDim; ++i) u[face*totDim+i] = x[i]; 5135 ierr = DMPlexVecRestoreClosure(plex, section, locX, support[0], NULL, &x);CHKERRQ(ierr); 5136 if (locX_t) { 5137 ierr = DMPlexVecGetClosure(plex, section, locX_t, support[0], NULL, &x);CHKERRQ(ierr); 5138 for (i = 0; i < totDim; ++i) u_t[face*totDim+i] = x[i]; 5139 ierr = DMPlexVecRestoreClosure(plex, section, locX_t, support[0], NULL, &x);CHKERRQ(ierr); 5140 } 5141 if (locA) { 5142 PetscInt subp; 5143 ierr = DMGetEnclosurePoint(plexA, dm, encAux, support[0], &subp);CHKERRQ(ierr); 5144 ierr = DMPlexVecGetClosure(plexA, sectionAux, locA, subp, NULL, &x);CHKERRQ(ierr); 5145 for (i = 0; i < totDimAux; ++i) a[face*totDimAux+i] = x[i]; 5146 ierr = DMPlexVecRestoreClosure(plexA, sectionAux, locA, subp, NULL, &x);CHKERRQ(ierr); 5147 } 5148 } 5149 ierr = PetscArrayzero(elemMat, numFaces*totDim*totDim);CHKERRQ(ierr); 5150 { 5151 PetscFE fe; 5152 PetscInt Nb; 5153 /* Conforming batches */ 5154 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 5155 /* Remainder */ 5156 PetscFEGeom *chunkGeom = NULL; 5157 PetscInt fieldJ, Nr, offset; 5158 5159 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); 5160 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 5161 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 5162 blockSize = Nb; 5163 batchSize = numBlocks * blockSize; 5164 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 5165 numChunks = numFaces / (numBatches*batchSize); 5166 Ne = numChunks*numBatches*batchSize; 5167 Nr = numFaces % (numBatches*batchSize); 5168 offset = numFaces - Nr; 5169 ierr = PetscFEGeomGetChunk(fgeom,0,offset,&chunkGeom);CHKERRQ(ierr); 5170 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 5171 key.field = fieldI*Nf+fieldJ; 5172 ierr = PetscFEIntegrateBdJacobian(prob, wf, key, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMat);CHKERRQ(ierr); 5173 } 5174 ierr = PetscFEGeomGetChunk(fgeom,offset,numFaces,&chunkGeom);CHKERRQ(ierr); 5175 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 5176 key.field = fieldI*Nf+fieldJ; 5177 ierr = PetscFEIntegrateBdJacobian(prob, wf, key, Nr, chunkGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, a ? &a[offset*totDimAux] : NULL, t, X_tShift, &elemMat[offset*totDim*totDim]);CHKERRQ(ierr); 5178 } 5179 ierr = PetscFEGeomRestoreChunk(fgeom,offset,numFaces,&chunkGeom);CHKERRQ(ierr); 5180 } 5181 for (face = 0; face < numFaces; ++face) { 5182 const PetscInt point = points[face], *support; 5183 5184 /* Transform to global basis before insertion in Jacobian */ 5185 ierr = DMPlexGetSupport(plex, point, &support);CHKERRQ(ierr); 5186 if (transform) {ierr = DMPlexBasisTransformPointTensor_Internal(dm, tdm, tv, support[0], PETSC_TRUE, totDim, &elemMat[face*totDim*totDim]);CHKERRQ(ierr);} 5187 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(point, "BdJacobian", totDim, totDim, &elemMat[face*totDim*totDim]);CHKERRQ(ierr);} 5188 if (!isMatISP) { 5189 ierr = DMPlexMatSetClosure(plex, section, globalSection, JacP, support[0], &elemMat[face*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 5190 } else { 5191 Mat lJ; 5192 5193 ierr = MatISGetLocalMat(JacP, &lJ);CHKERRQ(ierr); 5194 ierr = DMPlexMatSetClosure(plex, section, subSection, lJ, support[0], &elemMat[face*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 5195 } 5196 } 5197 ierr = DMSNESRestoreFEGeom(coordField,pointIS,qGeom,PETSC_TRUE,&fgeom);CHKERRQ(ierr); 5198 ierr = PetscQuadratureDestroy(&qGeom);CHKERRQ(ierr); 5199 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 5200 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 5201 ierr = PetscFree4(u, u_t, elemMat, a);CHKERRQ(ierr); 5202 } 5203 if (plex) {ierr = DMDestroy(&plex);CHKERRQ(ierr);} 5204 if (plexA) {ierr = DMDestroy(&plexA);CHKERRQ(ierr);} 5205 PetscFunctionReturn(0); 5206 } 5207 5208 PetscErrorCode DMPlexComputeBdJacobianSingle(DM dm, PetscReal t, PetscWeakForm wf, DMLabel label, PetscInt numValues, const PetscInt values[], PetscInt field, Vec locX, Vec locX_t, PetscReal X_tShift, Mat Jac, Mat JacP) 5209 { 5210 DMField coordField; 5211 DMLabel depthLabel; 5212 IS facetIS; 5213 PetscInt dim; 5214 PetscErrorCode ierr; 5215 5216 PetscFunctionBegin; 5217 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 5218 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 5219 ierr = DMLabelGetStratumIS(depthLabel, dim-1, &facetIS);CHKERRQ(ierr); 5220 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 5221 ierr = DMPlexComputeBdJacobian_Single_Internal(dm, t, wf, label, numValues, values, field, locX, locX_t, X_tShift, Jac, JacP, coordField, facetIS);CHKERRQ(ierr); 5222 ierr = ISDestroy(&facetIS);CHKERRQ(ierr); 5223 PetscFunctionReturn(0); 5224 } 5225 5226 PetscErrorCode DMPlexComputeBdJacobian_Internal(DM dm, Vec locX, Vec locX_t, PetscReal t, PetscReal X_tShift, Mat Jac, Mat JacP, void *user) 5227 { 5228 PetscDS prob; 5229 PetscInt dim, numBd, bd; 5230 DMLabel depthLabel; 5231 DMField coordField = NULL; 5232 IS facetIS; 5233 PetscErrorCode ierr; 5234 5235 PetscFunctionBegin; 5236 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 5237 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 5238 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 5239 ierr = DMLabelGetStratumIS(depthLabel, dim-1, &facetIS);CHKERRQ(ierr); 5240 ierr = PetscDSGetNumBoundary(prob, &numBd);CHKERRQ(ierr); 5241 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 5242 for (bd = 0; bd < numBd; ++bd) { 5243 PetscWeakForm wf; 5244 DMBoundaryConditionType type; 5245 DMLabel label; 5246 const PetscInt *values; 5247 PetscInt fieldI, numValues; 5248 PetscObject obj; 5249 PetscClassId id; 5250 5251 ierr = PetscDSGetBoundary(prob, bd, &wf, &type, NULL, &label, &numValues, &values, &fieldI, NULL, NULL, NULL, NULL, NULL);CHKERRQ(ierr); 5252 ierr = PetscDSGetDiscretization(prob, fieldI, &obj);CHKERRQ(ierr); 5253 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 5254 if ((id != PETSCFE_CLASSID) || (type & DM_BC_ESSENTIAL)) continue; 5255 ierr = DMPlexComputeBdJacobian_Single_Internal(dm, t, wf, label, numValues, values, fieldI, locX, locX_t, X_tShift, Jac, JacP, coordField, facetIS);CHKERRQ(ierr); 5256 } 5257 ierr = ISDestroy(&facetIS);CHKERRQ(ierr); 5258 PetscFunctionReturn(0); 5259 } 5260 5261 PetscErrorCode DMPlexComputeJacobian_Internal(DM dm, PetscFormKey key, IS cellIS, PetscReal t, PetscReal X_tShift, Vec X, Vec X_t, Mat Jac, Mat JacP,void *user) 5262 { 5263 DM_Plex *mesh = (DM_Plex *) dm->data; 5264 const char *name = "Jacobian"; 5265 DM dmAux = NULL, plex, tdm; 5266 DMEnclosureType encAux; 5267 Vec A, tv; 5268 DMField coordField; 5269 PetscDS prob, probAux = NULL; 5270 PetscSection section, globalSection, subSection, sectionAux; 5271 PetscScalar *elemMat, *elemMatP, *elemMatD, *u, *u_t, *a = NULL; 5272 const PetscInt *cells; 5273 PetscInt Nf, fieldI, fieldJ; 5274 PetscInt totDim, totDimAux, cStart, cEnd, numCells, c; 5275 PetscBool isMatIS, isMatISP, hasJac, hasPrec, hasDyn, hasFV = PETSC_FALSE, transform; 5276 PetscErrorCode ierr; 5277 5278 PetscFunctionBegin; 5279 ierr = PetscLogEventBegin(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 5280 ierr = ISGetLocalSize(cellIS, &numCells);CHKERRQ(ierr); 5281 ierr = ISGetPointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 5282 ierr = DMHasBasisTransform(dm, &transform);CHKERRQ(ierr); 5283 ierr = DMGetBasisTransformDM_Internal(dm, &tdm);CHKERRQ(ierr); 5284 ierr = DMGetBasisTransformVec_Internal(dm, &tv);CHKERRQ(ierr); 5285 ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); 5286 ierr = PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatISP);CHKERRQ(ierr); 5287 ierr = DMGetGlobalSection(dm, &globalSection);CHKERRQ(ierr); 5288 if (isMatISP) {ierr = DMPlexGetSubdomainSection(dm, &subSection);CHKERRQ(ierr);} 5289 ierr = DMGetCellDS(dm, cells ? cells[cStart] : cStart, &prob);CHKERRQ(ierr); 5290 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 5291 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 5292 ierr = PetscDSHasJacobian(prob, &hasJac);CHKERRQ(ierr); 5293 ierr = PetscDSHasJacobianPreconditioner(prob, &hasPrec);CHKERRQ(ierr); 5294 /* user passed in the same matrix, avoid double contributions and 5295 only assemble the Jacobian */ 5296 if (hasJac && Jac == JacP) hasPrec = PETSC_FALSE; 5297 ierr = PetscDSHasDynamicJacobian(prob, &hasDyn);CHKERRQ(ierr); 5298 hasDyn = hasDyn && (X_tShift != 0.0) ? PETSC_TRUE : PETSC_FALSE; 5299 ierr = DMGetAuxiliaryVec(dm, key.label, key.value, &A);CHKERRQ(ierr); 5300 if (A) { 5301 ierr = VecGetDM(A, &dmAux);CHKERRQ(ierr); 5302 ierr = DMGetEnclosureRelation(dmAux, dm, &encAux);CHKERRQ(ierr); 5303 ierr = DMConvert(dmAux, DMPLEX, &plex);CHKERRQ(ierr); 5304 ierr = DMGetLocalSection(plex, §ionAux);CHKERRQ(ierr); 5305 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 5306 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 5307 } 5308 ierr = PetscMalloc5(numCells*totDim,&u,X_t ? numCells*totDim : 0,&u_t,hasJac ? numCells*totDim*totDim : 0,&elemMat,hasPrec ? numCells*totDim*totDim : 0, &elemMatP,hasDyn ? numCells*totDim*totDim : 0, &elemMatD);CHKERRQ(ierr); 5309 if (dmAux) {ierr = PetscMalloc1(numCells*totDimAux, &a);CHKERRQ(ierr);} 5310 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 5311 for (c = cStart; c < cEnd; ++c) { 5312 const PetscInt cell = cells ? cells[c] : c; 5313 const PetscInt cind = c - cStart; 5314 PetscScalar *x = NULL, *x_t = NULL; 5315 PetscInt i; 5316 5317 ierr = DMPlexVecGetClosure(dm, section, X, cell, NULL, &x);CHKERRQ(ierr); 5318 for (i = 0; i < totDim; ++i) u[cind*totDim+i] = x[i]; 5319 ierr = DMPlexVecRestoreClosure(dm, section, X, cell, NULL, &x);CHKERRQ(ierr); 5320 if (X_t) { 5321 ierr = DMPlexVecGetClosure(dm, section, X_t, cell, NULL, &x_t);CHKERRQ(ierr); 5322 for (i = 0; i < totDim; ++i) u_t[cind*totDim+i] = x_t[i]; 5323 ierr = DMPlexVecRestoreClosure(dm, section, X_t, cell, NULL, &x_t);CHKERRQ(ierr); 5324 } 5325 if (dmAux) { 5326 PetscInt subcell; 5327 ierr = DMGetEnclosurePoint(dmAux, dm, encAux, cell, &subcell);CHKERRQ(ierr); 5328 ierr = DMPlexVecGetClosure(plex, sectionAux, A, subcell, NULL, &x);CHKERRQ(ierr); 5329 for (i = 0; i < totDimAux; ++i) a[cind*totDimAux+i] = x[i]; 5330 ierr = DMPlexVecRestoreClosure(plex, sectionAux, A, subcell, NULL, &x);CHKERRQ(ierr); 5331 } 5332 } 5333 if (hasJac) {ierr = PetscArrayzero(elemMat, numCells*totDim*totDim);CHKERRQ(ierr);} 5334 if (hasPrec) {ierr = PetscArrayzero(elemMatP, numCells*totDim*totDim);CHKERRQ(ierr);} 5335 if (hasDyn) {ierr = PetscArrayzero(elemMatD, numCells*totDim*totDim);CHKERRQ(ierr);} 5336 for (fieldI = 0; fieldI < Nf; ++fieldI) { 5337 PetscClassId id; 5338 PetscFE fe; 5339 PetscQuadrature qGeom = NULL; 5340 PetscInt Nb; 5341 /* Conforming batches */ 5342 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 5343 /* Remainder */ 5344 PetscInt Nr, offset, Nq; 5345 PetscInt maxDegree; 5346 PetscFEGeom *cgeomFEM, *chunkGeom = NULL, *remGeom = NULL; 5347 5348 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); 5349 ierr = PetscObjectGetClassId((PetscObject) fe, &id);CHKERRQ(ierr); 5350 if (id == PETSCFV_CLASSID) {hasFV = PETSC_TRUE; continue;} 5351 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 5352 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 5353 ierr = DMFieldGetDegree(coordField,cellIS,NULL,&maxDegree);CHKERRQ(ierr); 5354 if (maxDegree <= 1) { 5355 ierr = DMFieldCreateDefaultQuadrature(coordField,cellIS,&qGeom);CHKERRQ(ierr); 5356 } 5357 if (!qGeom) { 5358 ierr = PetscFEGetQuadrature(fe,&qGeom);CHKERRQ(ierr); 5359 ierr = PetscObjectReference((PetscObject)qGeom);CHKERRQ(ierr); 5360 } 5361 ierr = PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 5362 ierr = DMSNESGetFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);CHKERRQ(ierr); 5363 blockSize = Nb; 5364 batchSize = numBlocks * blockSize; 5365 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 5366 numChunks = numCells / (numBatches*batchSize); 5367 Ne = numChunks*numBatches*batchSize; 5368 Nr = numCells % (numBatches*batchSize); 5369 offset = numCells - Nr; 5370 ierr = PetscFEGeomGetChunk(cgeomFEM,0,offset,&chunkGeom);CHKERRQ(ierr); 5371 ierr = PetscFEGeomGetChunk(cgeomFEM,offset,numCells,&remGeom);CHKERRQ(ierr); 5372 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 5373 key.field = fieldI*Nf+fieldJ; 5374 if (hasJac) { 5375 ierr = PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN, key, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMat);CHKERRQ(ierr); 5376 ierr = PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN, key, Nr, remGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, X_tShift, &elemMat[offset*totDim*totDim]);CHKERRQ(ierr); 5377 } 5378 if (hasPrec) { 5379 ierr = PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN_PRE, key, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMatP);CHKERRQ(ierr); 5380 ierr = PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN_PRE, key, Nr, remGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, X_tShift, &elemMatP[offset*totDim*totDim]);CHKERRQ(ierr); 5381 } 5382 if (hasDyn) { 5383 ierr = PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN_DYN, key, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMatD);CHKERRQ(ierr); 5384 ierr = PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN_DYN, key, Nr, remGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, X_tShift, &elemMatD[offset*totDim*totDim]);CHKERRQ(ierr); 5385 } 5386 } 5387 ierr = PetscFEGeomRestoreChunk(cgeomFEM,offset,numCells,&remGeom);CHKERRQ(ierr); 5388 ierr = PetscFEGeomRestoreChunk(cgeomFEM,0,offset,&chunkGeom);CHKERRQ(ierr); 5389 ierr = DMSNESRestoreFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);CHKERRQ(ierr); 5390 ierr = PetscQuadratureDestroy(&qGeom);CHKERRQ(ierr); 5391 } 5392 /* Add contribution from X_t */ 5393 if (hasDyn) {for (c = 0; c < numCells*totDim*totDim; ++c) elemMat[c] += X_tShift*elemMatD[c];} 5394 if (hasFV) { 5395 PetscClassId id; 5396 PetscFV fv; 5397 PetscInt offsetI, NcI, NbI = 1, fc, f; 5398 5399 for (fieldI = 0; fieldI < Nf; ++fieldI) { 5400 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fv);CHKERRQ(ierr); 5401 ierr = PetscDSGetFieldOffset(prob, fieldI, &offsetI);CHKERRQ(ierr); 5402 ierr = PetscObjectGetClassId((PetscObject) fv, &id);CHKERRQ(ierr); 5403 if (id != PETSCFV_CLASSID) continue; 5404 /* Put in the identity */ 5405 ierr = PetscFVGetNumComponents(fv, &NcI);CHKERRQ(ierr); 5406 for (c = cStart; c < cEnd; ++c) { 5407 const PetscInt cind = c - cStart; 5408 const PetscInt eOffset = cind*totDim*totDim; 5409 for (fc = 0; fc < NcI; ++fc) { 5410 for (f = 0; f < NbI; ++f) { 5411 const PetscInt i = offsetI + f*NcI+fc; 5412 if (hasPrec) { 5413 if (hasJac) {elemMat[eOffset+i*totDim+i] = 1.0;} 5414 elemMatP[eOffset+i*totDim+i] = 1.0; 5415 } else {elemMat[eOffset+i*totDim+i] = 1.0;} 5416 } 5417 } 5418 } 5419 } 5420 /* No allocated space for FV stuff, so ignore the zero entries */ 5421 ierr = MatSetOption(JacP, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE);CHKERRQ(ierr); 5422 } 5423 /* Insert values into matrix */ 5424 isMatIS = PETSC_FALSE; 5425 if (hasPrec && hasJac) { 5426 ierr = PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatIS);CHKERRQ(ierr); 5427 } 5428 if (isMatIS && !subSection) { 5429 ierr = DMPlexGetSubdomainSection(dm, &subSection);CHKERRQ(ierr); 5430 } 5431 for (c = cStart; c < cEnd; ++c) { 5432 const PetscInt cell = cells ? cells[c] : c; 5433 const PetscInt cind = c - cStart; 5434 5435 /* Transform to global basis before insertion in Jacobian */ 5436 if (transform) {ierr = DMPlexBasisTransformPointTensor_Internal(dm, tdm, tv, cell, PETSC_TRUE, totDim, &elemMat[cind*totDim*totDim]);CHKERRQ(ierr);} 5437 if (hasPrec) { 5438 if (hasJac) { 5439 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(cell, name, totDim, totDim, &elemMat[cind*totDim*totDim]);CHKERRQ(ierr);} 5440 if (!isMatIS) { 5441 ierr = DMPlexMatSetClosure(dm, section, globalSection, Jac, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 5442 } else { 5443 Mat lJ; 5444 5445 ierr = MatISGetLocalMat(Jac,&lJ);CHKERRQ(ierr); 5446 ierr = DMPlexMatSetClosure(dm, section, subSection, lJ, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 5447 } 5448 } 5449 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(cell, name, totDim, totDim, &elemMatP[cind*totDim*totDim]);CHKERRQ(ierr);} 5450 if (!isMatISP) { 5451 ierr = DMPlexMatSetClosure(dm, section, globalSection, JacP, cell, &elemMatP[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 5452 } else { 5453 Mat lJ; 5454 5455 ierr = MatISGetLocalMat(JacP,&lJ);CHKERRQ(ierr); 5456 ierr = DMPlexMatSetClosure(dm, section, subSection, lJ, cell, &elemMatP[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 5457 } 5458 } else { 5459 if (hasJac) { 5460 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(cell, name, totDim, totDim, &elemMat[cind*totDim*totDim]);CHKERRQ(ierr);} 5461 if (!isMatISP) { 5462 ierr = DMPlexMatSetClosure(dm, section, globalSection, JacP, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 5463 } else { 5464 Mat lJ; 5465 5466 ierr = MatISGetLocalMat(JacP,&lJ);CHKERRQ(ierr); 5467 ierr = DMPlexMatSetClosure(dm, section, subSection, lJ, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 5468 } 5469 } 5470 } 5471 } 5472 ierr = ISRestorePointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 5473 if (hasFV) {ierr = MatSetOption(JacP, MAT_IGNORE_ZERO_ENTRIES, PETSC_FALSE);CHKERRQ(ierr);} 5474 ierr = PetscFree5(u,u_t,elemMat,elemMatP,elemMatD);CHKERRQ(ierr); 5475 if (dmAux) { 5476 ierr = PetscFree(a);CHKERRQ(ierr); 5477 ierr = DMDestroy(&plex);CHKERRQ(ierr); 5478 } 5479 /* Compute boundary integrals */ 5480 ierr = DMPlexComputeBdJacobian_Internal(dm, X, X_t, t, X_tShift, Jac, JacP, user);CHKERRQ(ierr); 5481 /* Assemble matrix */ 5482 if (hasJac && hasPrec) { 5483 ierr = MatAssemblyBegin(Jac, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5484 ierr = MatAssemblyEnd(Jac, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5485 } 5486 ierr = MatAssemblyBegin(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5487 ierr = MatAssemblyEnd(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5488 ierr = PetscLogEventEnd(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 5489 PetscFunctionReturn(0); 5490 } 5491 5492 PetscErrorCode DMPlexComputeJacobian_Hybrid_Internal(DM dm, PetscFormKey key[], IS cellIS, PetscReal t, PetscReal X_tShift, Vec locX, Vec locX_t, Mat Jac, Mat JacP, void *user) 5493 { 5494 DM_Plex *mesh = (DM_Plex *) dm->data; 5495 const char *name = "Hybrid Jacobian"; 5496 DM dmAux[3] = {NULL, NULL, NULL}; 5497 DMLabel ghostLabel = NULL; 5498 DM plex = NULL; 5499 DM plexA = NULL; 5500 PetscDS ds = NULL; 5501 PetscDS dsAux[3] = {NULL, NULL, NULL}; 5502 Vec locA[3] = {NULL, NULL, NULL}; 5503 PetscSection section = NULL; 5504 PetscSection sectionAux[3] = {NULL, NULL, NULL}; 5505 DMField coordField = NULL; 5506 PetscScalar *u = NULL, *u_t, *a[3]; 5507 PetscScalar *elemMat, *elemMatP; 5508 PetscSection globalSection, subSection; 5509 IS chunkIS; 5510 const PetscInt *cells; 5511 PetscInt *faces; 5512 PetscInt cStart, cEnd, numCells; 5513 PetscInt Nf, fieldI, fieldJ, totDim, totDimAux[3], numChunks, cellChunkSize, chunk; 5514 PetscInt maxDegree = PETSC_MAX_INT; 5515 PetscQuadrature affineQuad = NULL, *quads = NULL; 5516 PetscFEGeom *affineGeom = NULL, **geoms = NULL; 5517 PetscBool repeatKey = PETSC_FALSE, isMatIS = PETSC_FALSE, isMatISP = PETSC_FALSE, hasBdJac, hasBdPrec; 5518 PetscErrorCode ierr; 5519 5520 PetscFunctionBegin; 5521 /* If keys are the same, both kernel will be run using the first key */ 5522 repeatKey = ((key[0].label == key[1].label) && (key[0].value == key[1].value)) ? PETSC_TRUE : PETSC_FALSE; 5523 ierr = PetscLogEventBegin(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 5524 ierr = ISGetLocalSize(cellIS, &numCells);CHKERRQ(ierr); 5525 ierr = ISGetPointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 5526 ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); 5527 ierr = DMGetSection(dm, §ion);CHKERRQ(ierr); 5528 ierr = DMGetGlobalSection(dm, &globalSection);CHKERRQ(ierr); 5529 ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 5530 ierr = DMGetCellDS(dm, cStart, &ds);CHKERRQ(ierr); 5531 ierr = PetscDSGetNumFields(ds, &Nf);CHKERRQ(ierr); 5532 ierr = PetscDSGetTotalDimension(ds, &totDim);CHKERRQ(ierr); 5533 ierr = PetscDSHasBdJacobian(ds, &hasBdJac);CHKERRQ(ierr); 5534 ierr = PetscDSHasBdJacobianPreconditioner(ds, &hasBdPrec);CHKERRQ(ierr); 5535 ierr = PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatISP);CHKERRQ(ierr); 5536 if (isMatISP) {ierr = DMPlexGetSubdomainSection(plex, &subSection);CHKERRQ(ierr);} 5537 if (hasBdPrec && hasBdJac) {ierr = PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatIS);CHKERRQ(ierr);} 5538 if (isMatIS && !subSection) {ierr = DMPlexGetSubdomainSection(plex, &subSection);CHKERRQ(ierr);} 5539 ierr = DMGetAuxiliaryVec(dm, key[2].label, key[2].value, &locA[2]);CHKERRQ(ierr); 5540 if (locA[2]) { 5541 ierr = VecGetDM(locA[2], &dmAux[2]);CHKERRQ(ierr); 5542 ierr = DMConvert(dmAux[2], DMPLEX, &plexA);CHKERRQ(ierr); 5543 ierr = DMGetSection(dmAux[2], §ionAux[2]);CHKERRQ(ierr); 5544 ierr = DMGetCellDS(dmAux[2], cStart, &dsAux[2]);CHKERRQ(ierr); 5545 ierr = PetscDSGetTotalDimension(dsAux[2], &totDimAux[2]);CHKERRQ(ierr); 5546 { 5547 const PetscInt *cone; 5548 PetscInt c; 5549 5550 ierr = DMPlexGetCone(dm, cStart, &cone);CHKERRQ(ierr); 5551 for (c = 0; c < 2; ++c) { 5552 const PetscInt *support; 5553 PetscInt ssize, s; 5554 5555 ierr = DMPlexGetSupport(dm, cone[c], &support);CHKERRQ(ierr); 5556 ierr = DMPlexGetSupportSize(dm, cone[c], &ssize);CHKERRQ(ierr); 5557 if (ssize != 2) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Face %D from cell %D has support size %D != 2", cone[c], cStart, ssize); 5558 if (support[0] == cStart) s = 1; 5559 else if (support[1] == cStart) s = 0; 5560 else SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Face %D does not have cell %D in its support", cone[c], cStart); 5561 ierr = DMGetAuxiliaryVec(dm, key[c].label, key[c].value, &locA[c]);CHKERRQ(ierr); 5562 if (locA[c]) {ierr = VecGetDM(locA[c], &dmAux[c]);CHKERRQ(ierr);} 5563 else {dmAux[c] = dmAux[2];} 5564 ierr = DMGetCellDS(dmAux[c], support[s], &dsAux[c]);CHKERRQ(ierr); 5565 ierr = PetscDSGetTotalDimension(dsAux[c], &totDimAux[c]);CHKERRQ(ierr); 5566 } 5567 } 5568 } 5569 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 5570 ierr = DMFieldGetDegree(coordField, cellIS, NULL, &maxDegree);CHKERRQ(ierr); 5571 if (maxDegree > 1) { 5572 PetscInt f; 5573 ierr = PetscCalloc2(Nf, &quads, Nf, &geoms);CHKERRQ(ierr); 5574 for (f = 0; f < Nf; ++f) { 5575 PetscFE fe; 5576 5577 ierr = PetscDSGetDiscretization(ds, f, (PetscObject *) &fe);CHKERRQ(ierr); 5578 if (fe) { 5579 ierr = PetscFEGetQuadrature(fe, &quads[f]);CHKERRQ(ierr); 5580 ierr = PetscObjectReference((PetscObject) quads[f]);CHKERRQ(ierr); 5581 } 5582 } 5583 } 5584 cellChunkSize = numCells; 5585 numChunks = !numCells ? 0 : PetscCeilReal(((PetscReal) numCells)/cellChunkSize); 5586 ierr = PetscCalloc1(2*cellChunkSize, &faces);CHKERRQ(ierr); 5587 ierr = ISCreateGeneral(PETSC_COMM_SELF, cellChunkSize, faces, PETSC_USE_POINTER, &chunkIS);CHKERRQ(ierr); 5588 ierr = DMPlexGetCellFields(dm, cellIS, locX, locX_t, locA[2], &u, &u_t, &a[2]);CHKERRQ(ierr); 5589 ierr = DMPlexGetHybridAuxFields(dm, dmAux, dsAux, cellIS, locA, a);CHKERRQ(ierr); 5590 ierr = DMGetWorkArray(dm, hasBdJac ? cellChunkSize*totDim*totDim : 0, MPIU_SCALAR, &elemMat);CHKERRQ(ierr); 5591 ierr = DMGetWorkArray(dm, hasBdPrec ? cellChunkSize*totDim*totDim : 0, MPIU_SCALAR, &elemMatP);CHKERRQ(ierr); 5592 for (chunk = 0; chunk < numChunks; ++chunk) { 5593 PetscInt cS = cStart+chunk*cellChunkSize, cE = PetscMin(cS+cellChunkSize, cEnd), numCells = cE - cS, c; 5594 5595 if (hasBdJac) {ierr = PetscMemzero(elemMat, numCells*totDim*totDim * sizeof(PetscScalar));CHKERRQ(ierr);} 5596 if (hasBdPrec) {ierr = PetscMemzero(elemMatP, numCells*totDim*totDim * sizeof(PetscScalar));CHKERRQ(ierr);} 5597 /* Get faces */ 5598 for (c = cS; c < cE; ++c) { 5599 const PetscInt cell = cells ? cells[c] : c; 5600 const PetscInt *cone; 5601 ierr = DMPlexGetCone(plex, cell, &cone);CHKERRQ(ierr); 5602 faces[(c-cS)*2+0] = cone[0]; 5603 faces[(c-cS)*2+1] = cone[1]; 5604 } 5605 ierr = ISGeneralSetIndices(chunkIS, cellChunkSize, faces, PETSC_USE_POINTER);CHKERRQ(ierr); 5606 if (maxDegree <= 1) { 5607 if (!affineQuad) {ierr = DMFieldCreateDefaultQuadrature(coordField, chunkIS, &affineQuad);CHKERRQ(ierr);} 5608 if (affineQuad) {ierr = DMSNESGetFEGeom(coordField, chunkIS, affineQuad, PETSC_TRUE, &affineGeom);CHKERRQ(ierr);} 5609 } else { 5610 PetscInt f; 5611 for (f = 0; f < Nf; ++f) { 5612 if (quads[f]) {ierr = DMSNESGetFEGeom(coordField, chunkIS, quads[f], PETSC_TRUE, &geoms[f]);CHKERRQ(ierr);} 5613 } 5614 } 5615 5616 for (fieldI = 0; fieldI < Nf; ++fieldI) { 5617 PetscFE feI; 5618 PetscFEGeom *geom = affineGeom ? affineGeom : geoms[fieldI]; 5619 PetscFEGeom *chunkGeom = NULL, *remGeom = NULL; 5620 PetscQuadrature quad = affineQuad ? affineQuad : quads[fieldI]; 5621 PetscInt numChunks, numBatches, batchSize, numBlocks, blockSize, Ne, Nr, offset, Nq, Nb; 5622 5623 ierr = PetscDSGetDiscretization(ds, fieldI, (PetscObject *) &feI);CHKERRQ(ierr); 5624 if (!feI) continue; 5625 ierr = PetscFEGetTileSizes(feI, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 5626 ierr = PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 5627 ierr = PetscFEGetDimension(feI, &Nb);CHKERRQ(ierr); 5628 blockSize = Nb; 5629 batchSize = numBlocks * blockSize; 5630 ierr = PetscFESetTileSizes(feI, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 5631 numChunks = numCells / (numBatches*batchSize); 5632 Ne = numChunks*numBatches*batchSize; 5633 Nr = numCells % (numBatches*batchSize); 5634 offset = numCells - Nr; 5635 ierr = PetscFEGeomGetChunk(geom,0,offset,&chunkGeom);CHKERRQ(ierr); 5636 ierr = PetscFEGeomGetChunk(geom,offset,numCells,&remGeom);CHKERRQ(ierr); 5637 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 5638 PetscFE feJ; 5639 5640 ierr = PetscDSGetDiscretization(ds, fieldJ, (PetscObject *) &feJ);CHKERRQ(ierr); 5641 if (!feJ) continue; 5642 if (fieldI == Nf-1) { 5643 key[2].field = fieldI*Nf+fieldJ; 5644 if (hasBdJac) { 5645 ierr = PetscFEIntegrateHybridJacobian(ds, PETSCFE_JACOBIAN, key[2], Ne, chunkGeom, u, u_t, dsAux[2], a[2], t, X_tShift, elemMat);CHKERRQ(ierr); 5646 ierr = PetscFEIntegrateHybridJacobian(ds, PETSCFE_JACOBIAN, key[2], Nr, remGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, dsAux[2], &a[2][offset*totDimAux[2]], t, X_tShift, &elemMat[offset*totDim*totDim]);CHKERRQ(ierr); 5647 } 5648 if (hasBdPrec) { 5649 ierr = PetscFEIntegrateHybridJacobian(ds, PETSCFE_JACOBIAN_PRE, key[2], Ne, chunkGeom, u, u_t, dsAux[2], a[2], t, X_tShift, elemMatP);CHKERRQ(ierr); 5650 ierr = PetscFEIntegrateHybridJacobian(ds, PETSCFE_JACOBIAN_PRE, key[2], Nr, remGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, dsAux[2], &a[2][offset*totDimAux[2]], t, X_tShift, &elemMatP[offset*totDim*totDim]);CHKERRQ(ierr); 5651 } 5652 } else { 5653 key[0].field = fieldI*Nf+fieldJ; 5654 key[1].field = fieldI*Nf+fieldJ; 5655 if (hasBdJac) { 5656 ierr = PetscFEIntegrateHybridJacobian(ds, PETSCFE_JACOBIAN, key[0], Ne, chunkGeom, u, u_t, dsAux[0], a[0], t, X_tShift, elemMat);CHKERRQ(ierr); 5657 ierr = PetscFEIntegrateHybridJacobian(ds, PETSCFE_JACOBIAN, key[0], Nr, remGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, dsAux[0], &a[0][offset*totDimAux[0]], t, X_tShift, &elemMat[offset*totDim*totDim]);CHKERRQ(ierr); 5658 if (!repeatKey) { 5659 ierr = PetscFEIntegrateHybridJacobian(ds, PETSCFE_JACOBIAN, key[1], Ne, chunkGeom, u, u_t, dsAux[1], a[1], t, X_tShift, elemMat);CHKERRQ(ierr); 5660 ierr = PetscFEIntegrateHybridJacobian(ds, PETSCFE_JACOBIAN, key[1], Nr, remGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, dsAux[1], &a[1][offset*totDimAux[1]], t, X_tShift, &elemMat[offset*totDim*totDim]);CHKERRQ(ierr); 5661 } 5662 } 5663 if (hasBdPrec) { 5664 ierr = PetscFEIntegrateHybridJacobian(ds, PETSCFE_JACOBIAN_PRE, key[0], Ne, chunkGeom, u, u_t, dsAux[0], a[0], t, X_tShift, elemMatP);CHKERRQ(ierr); 5665 ierr = PetscFEIntegrateHybridJacobian(ds, PETSCFE_JACOBIAN_PRE, key[0], Nr, remGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, dsAux[0], &a[0][offset*totDimAux[0]], t, X_tShift, &elemMatP[offset*totDim*totDim]);CHKERRQ(ierr); 5666 if (!repeatKey) { 5667 ierr = PetscFEIntegrateHybridJacobian(ds, PETSCFE_JACOBIAN_PRE, key[1], Ne, chunkGeom, u, u_t, dsAux[1], a[1], t, X_tShift, elemMatP);CHKERRQ(ierr); 5668 ierr = PetscFEIntegrateHybridJacobian(ds, PETSCFE_JACOBIAN_PRE, key[1], Nr, remGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, dsAux[1], &a[1][offset*totDimAux[1]], t, X_tShift, &elemMatP[offset*totDim*totDim]);CHKERRQ(ierr); 5669 } 5670 } 5671 } 5672 } 5673 ierr = PetscFEGeomRestoreChunk(geom,offset,numCells,&remGeom);CHKERRQ(ierr); 5674 ierr = PetscFEGeomRestoreChunk(geom,0,offset,&chunkGeom);CHKERRQ(ierr); 5675 } 5676 /* Insert values into matrix */ 5677 for (c = cS; c < cE; ++c) { 5678 const PetscInt cell = cells ? cells[c] : c; 5679 const PetscInt cind = c - cS; 5680 5681 if (hasBdPrec) { 5682 if (hasBdJac) { 5683 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(cell, name, totDim, totDim, &elemMat[cind*totDim*totDim]);CHKERRQ(ierr);} 5684 if (!isMatIS) { 5685 ierr = DMPlexMatSetClosure(plex, section, globalSection, Jac, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 5686 } else { 5687 Mat lJ; 5688 5689 ierr = MatISGetLocalMat(Jac,&lJ);CHKERRQ(ierr); 5690 ierr = DMPlexMatSetClosure(plex, section, subSection, lJ, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 5691 } 5692 } 5693 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(cell, name, totDim, totDim, &elemMatP[cind*totDim*totDim]);CHKERRQ(ierr);} 5694 if (!isMatISP) { 5695 ierr = DMPlexMatSetClosure(plex, section, globalSection, JacP, cell, &elemMatP[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 5696 } else { 5697 Mat lJ; 5698 5699 ierr = MatISGetLocalMat(JacP,&lJ);CHKERRQ(ierr); 5700 ierr = DMPlexMatSetClosure(plex, section, subSection, lJ, cell, &elemMatP[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 5701 } 5702 } else if (hasBdJac) { 5703 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(cell, name, totDim, totDim, &elemMat[cind*totDim*totDim]);CHKERRQ(ierr);} 5704 if (!isMatISP) { 5705 ierr = DMPlexMatSetClosure(plex, section, globalSection, JacP, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 5706 } else { 5707 Mat lJ; 5708 5709 ierr = MatISGetLocalMat(JacP,&lJ);CHKERRQ(ierr); 5710 ierr = DMPlexMatSetClosure(plex, section, subSection, lJ, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 5711 } 5712 } 5713 } 5714 } 5715 ierr = DMPlexRestoreCellFields(dm, cellIS, locX, locX_t, locA[2], &u, &u_t, &a[2]);CHKERRQ(ierr); 5716 ierr = DMPlexRestoreHybridAuxFields(dmAux, dsAux, cellIS, locA, a);CHKERRQ(ierr); 5717 ierr = DMRestoreWorkArray(dm, hasBdJac ? cellChunkSize*totDim*totDim : 0, MPIU_SCALAR, &elemMat);CHKERRQ(ierr); 5718 ierr = DMRestoreWorkArray(dm, hasBdPrec ? cellChunkSize*totDim*totDim : 0, MPIU_SCALAR, &elemMatP);CHKERRQ(ierr); 5719 ierr = PetscFree(faces);CHKERRQ(ierr); 5720 ierr = ISDestroy(&chunkIS);CHKERRQ(ierr); 5721 ierr = ISRestorePointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 5722 if (maxDegree <= 1) { 5723 ierr = DMSNESRestoreFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&affineGeom);CHKERRQ(ierr); 5724 ierr = PetscQuadratureDestroy(&affineQuad);CHKERRQ(ierr); 5725 } else { 5726 PetscInt f; 5727 for (f = 0; f < Nf; ++f) { 5728 if (geoms) {ierr = DMSNESRestoreFEGeom(coordField,cellIS,quads[f],PETSC_FALSE, &geoms[f]);CHKERRQ(ierr);} 5729 if (quads) {ierr = PetscQuadratureDestroy(&quads[f]);CHKERRQ(ierr);} 5730 } 5731 ierr = PetscFree2(quads,geoms);CHKERRQ(ierr); 5732 } 5733 if (dmAux[2]) {ierr = DMDestroy(&plexA);CHKERRQ(ierr);} 5734 ierr = DMDestroy(&plex);CHKERRQ(ierr); 5735 /* Assemble matrix */ 5736 if (hasBdJac && hasBdPrec) { 5737 ierr = MatAssemblyBegin(Jac, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5738 ierr = MatAssemblyEnd(Jac, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5739 } 5740 ierr = MatAssemblyBegin(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5741 ierr = MatAssemblyEnd(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5742 ierr = PetscLogEventEnd(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 5743 PetscFunctionReturn(0); 5744 } 5745 5746 /* 5747 DMPlexComputeJacobian_Action_Internal - Form the local portion of the Jacobian action Z = J(X) Y at the local solution X using pointwise functions specified by the user. 5748 5749 Input Parameters: 5750 + dm - The mesh 5751 . key - The PetscWeakFormKey indcating where integration should happen 5752 . cellIS - The cells to integrate over 5753 . t - The time 5754 . X_tShift - The multiplier for the Jacobian with repsect to X_t 5755 . X - Local solution vector 5756 . X_t - Time-derivative of the local solution vector 5757 . Y - Local input vector 5758 - user - the user context 5759 5760 Output Parameter: 5761 . Z - Local output vector 5762 5763 Note: 5764 We form the residual one batch of elements at a time. This allows us to offload work onto an accelerator, 5765 like a GPU, or vectorize on a multicore machine. 5766 */ 5767 PetscErrorCode DMPlexComputeJacobian_Action_Internal(DM dm, PetscFormKey key, IS cellIS, PetscReal t, PetscReal X_tShift, Vec X, Vec X_t, Vec Y, Vec Z, void *user) 5768 { 5769 DM_Plex *mesh = (DM_Plex *) dm->data; 5770 const char *name = "Jacobian"; 5771 DM dmAux = NULL, plex, plexAux = NULL; 5772 DMEnclosureType encAux; 5773 Vec A; 5774 DMField coordField; 5775 PetscDS prob, probAux = NULL; 5776 PetscQuadrature quad; 5777 PetscSection section, globalSection, sectionAux; 5778 PetscScalar *elemMat, *elemMatD, *u, *u_t, *a = NULL, *y, *z; 5779 const PetscInt *cells; 5780 PetscInt Nf, fieldI, fieldJ; 5781 PetscInt totDim, totDimAux = 0, cStart, cEnd, numCells, c; 5782 PetscBool hasDyn; 5783 PetscErrorCode ierr; 5784 5785 PetscFunctionBegin; 5786 ierr = PetscLogEventBegin(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 5787 ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); 5788 if (!cellIS) { 5789 PetscInt depth; 5790 5791 ierr = DMPlexGetDepth(plex, &depth);CHKERRQ(ierr); 5792 ierr = DMGetStratumIS(plex, "dim", depth, &cellIS);CHKERRQ(ierr); 5793 if (!cellIS) {ierr = DMGetStratumIS(plex, "depth", depth, &cellIS);CHKERRQ(ierr);} 5794 } else { 5795 ierr = PetscObjectReference((PetscObject) cellIS);CHKERRQ(ierr); 5796 } 5797 ierr = ISGetLocalSize(cellIS, &numCells);CHKERRQ(ierr); 5798 ierr = ISGetPointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 5799 ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); 5800 ierr = DMGetGlobalSection(dm, &globalSection);CHKERRQ(ierr); 5801 ierr = DMGetCellDS(dm, cells ? cells[cStart] : cStart, &prob);CHKERRQ(ierr); 5802 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 5803 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 5804 ierr = PetscDSHasDynamicJacobian(prob, &hasDyn);CHKERRQ(ierr); 5805 hasDyn = hasDyn && (X_tShift != 0.0) ? PETSC_TRUE : PETSC_FALSE; 5806 ierr = DMGetAuxiliaryVec(dm, key.label, key.value, &A);CHKERRQ(ierr); 5807 if (A) { 5808 ierr = VecGetDM(A, &dmAux);CHKERRQ(ierr); 5809 ierr = DMGetEnclosureRelation(dmAux, dm, &encAux);CHKERRQ(ierr); 5810 ierr = DMConvert(dmAux, DMPLEX, &plexAux);CHKERRQ(ierr); 5811 ierr = DMGetLocalSection(plexAux, §ionAux);CHKERRQ(ierr); 5812 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 5813 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 5814 } 5815 ierr = VecSet(Z, 0.0);CHKERRQ(ierr); 5816 ierr = PetscMalloc6(numCells*totDim,&u,X_t ? numCells*totDim : 0,&u_t,numCells*totDim*totDim,&elemMat,hasDyn ? numCells*totDim*totDim : 0, &elemMatD,numCells*totDim,&y,totDim,&z);CHKERRQ(ierr); 5817 if (dmAux) {ierr = PetscMalloc1(numCells*totDimAux, &a);CHKERRQ(ierr);} 5818 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 5819 for (c = cStart; c < cEnd; ++c) { 5820 const PetscInt cell = cells ? cells[c] : c; 5821 const PetscInt cind = c - cStart; 5822 PetscScalar *x = NULL, *x_t = NULL; 5823 PetscInt i; 5824 5825 ierr = DMPlexVecGetClosure(plex, section, X, cell, NULL, &x);CHKERRQ(ierr); 5826 for (i = 0; i < totDim; ++i) u[cind*totDim+i] = x[i]; 5827 ierr = DMPlexVecRestoreClosure(plex, section, X, cell, NULL, &x);CHKERRQ(ierr); 5828 if (X_t) { 5829 ierr = DMPlexVecGetClosure(plex, section, X_t, cell, NULL, &x_t);CHKERRQ(ierr); 5830 for (i = 0; i < totDim; ++i) u_t[cind*totDim+i] = x_t[i]; 5831 ierr = DMPlexVecRestoreClosure(plex, section, X_t, cell, NULL, &x_t);CHKERRQ(ierr); 5832 } 5833 if (dmAux) { 5834 PetscInt subcell; 5835 ierr = DMGetEnclosurePoint(dmAux, dm, encAux, cell, &subcell);CHKERRQ(ierr); 5836 ierr = DMPlexVecGetClosure(plexAux, sectionAux, A, subcell, NULL, &x);CHKERRQ(ierr); 5837 for (i = 0; i < totDimAux; ++i) a[cind*totDimAux+i] = x[i]; 5838 ierr = DMPlexVecRestoreClosure(plexAux, sectionAux, A, subcell, NULL, &x);CHKERRQ(ierr); 5839 } 5840 ierr = DMPlexVecGetClosure(plex, section, Y, cell, NULL, &x);CHKERRQ(ierr); 5841 for (i = 0; i < totDim; ++i) y[cind*totDim+i] = x[i]; 5842 ierr = DMPlexVecRestoreClosure(plex, section, Y, cell, NULL, &x);CHKERRQ(ierr); 5843 } 5844 ierr = PetscArrayzero(elemMat, numCells*totDim*totDim);CHKERRQ(ierr); 5845 if (hasDyn) {ierr = PetscArrayzero(elemMatD, numCells*totDim*totDim);CHKERRQ(ierr);} 5846 for (fieldI = 0; fieldI < Nf; ++fieldI) { 5847 PetscFE fe; 5848 PetscInt Nb; 5849 /* Conforming batches */ 5850 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 5851 /* Remainder */ 5852 PetscInt Nr, offset, Nq; 5853 PetscQuadrature qGeom = NULL; 5854 PetscInt maxDegree; 5855 PetscFEGeom *cgeomFEM, *chunkGeom = NULL, *remGeom = NULL; 5856 5857 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); 5858 ierr = PetscFEGetQuadrature(fe, &quad);CHKERRQ(ierr); 5859 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 5860 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 5861 ierr = DMFieldGetDegree(coordField,cellIS,NULL,&maxDegree);CHKERRQ(ierr); 5862 if (maxDegree <= 1) {ierr = DMFieldCreateDefaultQuadrature(coordField,cellIS,&qGeom);CHKERRQ(ierr);} 5863 if (!qGeom) { 5864 ierr = PetscFEGetQuadrature(fe,&qGeom);CHKERRQ(ierr); 5865 ierr = PetscObjectReference((PetscObject)qGeom);CHKERRQ(ierr); 5866 } 5867 ierr = PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 5868 ierr = DMSNESGetFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);CHKERRQ(ierr); 5869 blockSize = Nb; 5870 batchSize = numBlocks * blockSize; 5871 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 5872 numChunks = numCells / (numBatches*batchSize); 5873 Ne = numChunks*numBatches*batchSize; 5874 Nr = numCells % (numBatches*batchSize); 5875 offset = numCells - Nr; 5876 ierr = PetscFEGeomGetChunk(cgeomFEM,0,offset,&chunkGeom);CHKERRQ(ierr); 5877 ierr = PetscFEGeomGetChunk(cgeomFEM,offset,numCells,&remGeom);CHKERRQ(ierr); 5878 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 5879 key.field = fieldI*Nf + fieldJ; 5880 ierr = PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN, key, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMat);CHKERRQ(ierr); 5881 ierr = PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN, key, Nr, remGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, X_tShift, &elemMat[offset*totDim*totDim]);CHKERRQ(ierr); 5882 if (hasDyn) { 5883 ierr = PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN_DYN, key, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMatD);CHKERRQ(ierr); 5884 ierr = PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN_DYN, key, Nr, remGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, X_tShift, &elemMatD[offset*totDim*totDim]);CHKERRQ(ierr); 5885 } 5886 } 5887 ierr = PetscFEGeomRestoreChunk(cgeomFEM,offset,numCells,&remGeom);CHKERRQ(ierr); 5888 ierr = PetscFEGeomRestoreChunk(cgeomFEM,0,offset,&chunkGeom);CHKERRQ(ierr); 5889 ierr = DMSNESRestoreFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);CHKERRQ(ierr); 5890 ierr = PetscQuadratureDestroy(&qGeom);CHKERRQ(ierr); 5891 } 5892 if (hasDyn) { 5893 for (c = 0; c < numCells*totDim*totDim; ++c) elemMat[c] += X_tShift*elemMatD[c]; 5894 } 5895 for (c = cStart; c < cEnd; ++c) { 5896 const PetscInt cell = cells ? cells[c] : c; 5897 const PetscInt cind = c - cStart; 5898 const PetscBLASInt M = totDim, one = 1; 5899 const PetscScalar a = 1.0, b = 0.0; 5900 5901 PetscStackCallBLAS("BLASgemv", BLASgemv_("N", &M, &M, &a, &elemMat[cind*totDim*totDim], &M, &y[cind*totDim], &one, &b, z, &one)); 5902 if (mesh->printFEM > 1) { 5903 ierr = DMPrintCellMatrix(c, name, totDim, totDim, &elemMat[cind*totDim*totDim]);CHKERRQ(ierr); 5904 ierr = DMPrintCellVector(c, "Y", totDim, &y[cind*totDim]);CHKERRQ(ierr); 5905 ierr = DMPrintCellVector(c, "Z", totDim, z);CHKERRQ(ierr); 5906 } 5907 ierr = DMPlexVecSetClosure(dm, section, Z, cell, z, ADD_VALUES);CHKERRQ(ierr); 5908 } 5909 ierr = PetscFree6(u,u_t,elemMat,elemMatD,y,z);CHKERRQ(ierr); 5910 if (mesh->printFEM) { 5911 ierr = PetscPrintf(PetscObjectComm((PetscObject)Z), "Z:\n");CHKERRQ(ierr); 5912 ierr = VecView(Z, NULL);CHKERRQ(ierr); 5913 } 5914 ierr = PetscFree(a);CHKERRQ(ierr); 5915 ierr = ISDestroy(&cellIS);CHKERRQ(ierr); 5916 ierr = DMDestroy(&plexAux);CHKERRQ(ierr); 5917 ierr = DMDestroy(&plex);CHKERRQ(ierr); 5918 ierr = PetscLogEventEnd(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 5919 PetscFunctionReturn(0); 5920 } 5921