1 #include <petsc/private/dmpleximpl.h> /*I "petscdmplex.h" I*/ 2 #include <petsc/private/snesimpl.h> /*I "petscsnes.h" I*/ 3 #include <petscds.h> 4 #include <petscblaslapack.h> 5 #include <petsc/private/petscimpl.h> 6 #include <petsc/private/petscfeimpl.h> 7 8 /************************** Interpolation *******************************/ 9 10 static PetscErrorCode DMSNESConvertPlex(DM dm, DM *plex, PetscBool copy) 11 { 12 PetscBool isPlex; 13 PetscErrorCode ierr; 14 15 PetscFunctionBegin; 16 ierr = PetscObjectTypeCompare((PetscObject) dm, DMPLEX, &isPlex);CHKERRQ(ierr); 17 if (isPlex) { 18 *plex = dm; 19 ierr = PetscObjectReference((PetscObject) dm);CHKERRQ(ierr); 20 } else { 21 ierr = PetscObjectQuery((PetscObject) dm, "dm_plex", (PetscObject *) plex);CHKERRQ(ierr); 22 if (!*plex) { 23 ierr = DMConvert(dm,DMPLEX,plex);CHKERRQ(ierr); 24 ierr = PetscObjectCompose((PetscObject) dm, "dm_plex", (PetscObject) *plex);CHKERRQ(ierr); 25 if (copy) { 26 PetscInt i; 27 PetscObject obj; 28 const char *comps[3] = {"A","dmAux","dmCh"}; 29 30 ierr = DMCopyDMSNES(dm, *plex);CHKERRQ(ierr); 31 for (i = 0; i < 3; i++) { 32 ierr = PetscObjectQuery((PetscObject) dm, comps[i], &obj);CHKERRQ(ierr); 33 ierr = PetscObjectCompose((PetscObject) *plex, comps[i], obj);CHKERRQ(ierr); 34 } 35 } 36 } else { 37 ierr = PetscObjectReference((PetscObject) *plex);CHKERRQ(ierr); 38 } 39 } 40 PetscFunctionReturn(0); 41 } 42 43 /*@C 44 DMInterpolationCreate - Creates a DMInterpolationInfo context 45 46 Collective on comm 47 48 Input Parameter: 49 . comm - the communicator 50 51 Output Parameter: 52 . ctx - the context 53 54 Level: beginner 55 56 .seealso: DMInterpolationEvaluate(), DMInterpolationAddPoints(), DMInterpolationDestroy() 57 @*/ 58 PetscErrorCode DMInterpolationCreate(MPI_Comm comm, DMInterpolationInfo *ctx) 59 { 60 PetscErrorCode ierr; 61 62 PetscFunctionBegin; 63 PetscValidPointer(ctx, 2); 64 ierr = PetscNew(ctx);CHKERRQ(ierr); 65 66 (*ctx)->comm = comm; 67 (*ctx)->dim = -1; 68 (*ctx)->nInput = 0; 69 (*ctx)->points = NULL; 70 (*ctx)->cells = NULL; 71 (*ctx)->n = -1; 72 (*ctx)->coords = NULL; 73 PetscFunctionReturn(0); 74 } 75 76 /*@C 77 DMInterpolationSetDim - Sets the spatial dimension for the interpolation context 78 79 Not collective 80 81 Input Parameters: 82 + ctx - the context 83 - dim - the spatial dimension 84 85 Level: intermediate 86 87 .seealso: DMInterpolationGetDim(), DMInterpolationEvaluate(), DMInterpolationAddPoints() 88 @*/ 89 PetscErrorCode DMInterpolationSetDim(DMInterpolationInfo ctx, PetscInt dim) 90 { 91 PetscFunctionBegin; 92 if ((dim < 1) || (dim > 3)) SETERRQ1(ctx->comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid dimension for points: %d", dim); 93 ctx->dim = dim; 94 PetscFunctionReturn(0); 95 } 96 97 /*@C 98 DMInterpolationGetDim - Gets the spatial dimension for the interpolation context 99 100 Not collective 101 102 Input Parameter: 103 . ctx - the context 104 105 Output Parameter: 106 . dim - the spatial dimension 107 108 Level: intermediate 109 110 .seealso: DMInterpolationSetDim(), DMInterpolationEvaluate(), DMInterpolationAddPoints() 111 @*/ 112 PetscErrorCode DMInterpolationGetDim(DMInterpolationInfo ctx, PetscInt *dim) 113 { 114 PetscFunctionBegin; 115 PetscValidIntPointer(dim, 2); 116 *dim = ctx->dim; 117 PetscFunctionReturn(0); 118 } 119 120 /*@C 121 DMInterpolationSetDof - Sets the number of fields interpolated at a point for the interpolation context 122 123 Not collective 124 125 Input Parameters: 126 + ctx - the context 127 - dof - the number of fields 128 129 Level: intermediate 130 131 .seealso: DMInterpolationGetDof(), DMInterpolationEvaluate(), DMInterpolationAddPoints() 132 @*/ 133 PetscErrorCode DMInterpolationSetDof(DMInterpolationInfo ctx, PetscInt dof) 134 { 135 PetscFunctionBegin; 136 if (dof < 1) SETERRQ1(ctx->comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid number of components: %d", dof); 137 ctx->dof = dof; 138 PetscFunctionReturn(0); 139 } 140 141 /*@C 142 DMInterpolationGetDof - Gets the number of fields interpolated at a point for the interpolation context 143 144 Not collective 145 146 Input Parameter: 147 . ctx - the context 148 149 Output Parameter: 150 . dof - the number of fields 151 152 Level: intermediate 153 154 .seealso: DMInterpolationSetDof(), DMInterpolationEvaluate(), DMInterpolationAddPoints() 155 @*/ 156 PetscErrorCode DMInterpolationGetDof(DMInterpolationInfo ctx, PetscInt *dof) 157 { 158 PetscFunctionBegin; 159 PetscValidIntPointer(dof, 2); 160 *dof = ctx->dof; 161 PetscFunctionReturn(0); 162 } 163 164 /*@C 165 DMInterpolationAddPoints - Add points at which we will interpolate the fields 166 167 Not collective 168 169 Input Parameters: 170 + ctx - the context 171 . n - the number of points 172 - points - the coordinates for each point, an array of size n * dim 173 174 Note: The coordinate information is copied. 175 176 Level: intermediate 177 178 .seealso: DMInterpolationSetDim(), DMInterpolationEvaluate(), DMInterpolationCreate() 179 @*/ 180 PetscErrorCode DMInterpolationAddPoints(DMInterpolationInfo ctx, PetscInt n, PetscReal points[]) 181 { 182 PetscErrorCode ierr; 183 184 PetscFunctionBegin; 185 if (ctx->dim < 0) SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONGSTATE, "The spatial dimension has not been set"); 186 if (ctx->points) SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONGSTATE, "Cannot add points multiple times yet"); 187 ctx->nInput = n; 188 189 ierr = PetscMalloc1(n*ctx->dim, &ctx->points);CHKERRQ(ierr); 190 ierr = PetscMemcpy(ctx->points, points, n*ctx->dim * sizeof(PetscReal));CHKERRQ(ierr); 191 PetscFunctionReturn(0); 192 } 193 194 /*@C 195 DMInterpolationSetUp - Computea spatial indices that add in point location during interpolation 196 197 Collective on ctx 198 199 Input Parameters: 200 + ctx - the context 201 . dm - the DM for the function space used for interpolation 202 - redundantPoints - If PETSC_TRUE, all processes are passing in the same array of points. Otherwise, points need to be communicated among processes. 203 204 Level: intermediate 205 206 .seealso: DMInterpolationEvaluate(), DMInterpolationAddPoints(), DMInterpolationCreate() 207 @*/ 208 PetscErrorCode DMInterpolationSetUp(DMInterpolationInfo ctx, DM dm, PetscBool redundantPoints) 209 { 210 MPI_Comm comm = ctx->comm; 211 PetscScalar *a; 212 PetscInt p, q, i; 213 PetscMPIInt rank, size; 214 PetscErrorCode ierr; 215 Vec pointVec; 216 PetscSF cellSF; 217 PetscLayout layout; 218 PetscReal *globalPoints; 219 PetscScalar *globalPointsScalar; 220 const PetscInt *ranges; 221 PetscMPIInt *counts, *displs; 222 const PetscSFNode *foundCells; 223 const PetscInt *foundPoints; 224 PetscMPIInt *foundProcs, *globalProcs; 225 PetscInt n, N, numFound; 226 227 PetscFunctionBegin; 228 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 229 ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr); 230 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 231 if (ctx->dim < 0) SETERRQ(comm, PETSC_ERR_ARG_WRONGSTATE, "The spatial dimension has not been set"); 232 /* Locate points */ 233 n = ctx->nInput; 234 if (!redundantPoints) { 235 ierr = PetscLayoutCreate(comm, &layout);CHKERRQ(ierr); 236 ierr = PetscLayoutSetBlockSize(layout, 1);CHKERRQ(ierr); 237 ierr = PetscLayoutSetLocalSize(layout, n);CHKERRQ(ierr); 238 ierr = PetscLayoutSetUp(layout);CHKERRQ(ierr); 239 ierr = PetscLayoutGetSize(layout, &N);CHKERRQ(ierr); 240 /* Communicate all points to all processes */ 241 ierr = PetscMalloc3(N*ctx->dim,&globalPoints,size,&counts,size,&displs);CHKERRQ(ierr); 242 ierr = PetscLayoutGetRanges(layout, &ranges);CHKERRQ(ierr); 243 for (p = 0; p < size; ++p) { 244 counts[p] = (ranges[p+1] - ranges[p])*ctx->dim; 245 displs[p] = ranges[p]*ctx->dim; 246 } 247 ierr = MPI_Allgatherv(ctx->points, n*ctx->dim, MPIU_REAL, globalPoints, counts, displs, MPIU_REAL, comm);CHKERRQ(ierr); 248 } else { 249 N = n; 250 globalPoints = ctx->points; 251 counts = displs = NULL; 252 layout = NULL; 253 } 254 #if 0 255 ierr = PetscMalloc3(N,&foundCells,N,&foundProcs,N,&globalProcs);CHKERRQ(ierr); 256 /* foundCells[p] = m->locatePoint(&globalPoints[p*ctx->dim]); */ 257 #else 258 #if defined(PETSC_USE_COMPLEX) 259 ierr = PetscMalloc1(N*ctx->dim,&globalPointsScalar);CHKERRQ(ierr); 260 for (i=0; i<N*ctx->dim; i++) globalPointsScalar[i] = globalPoints[i]; 261 #else 262 globalPointsScalar = globalPoints; 263 #endif 264 ierr = VecCreateSeqWithArray(PETSC_COMM_SELF, ctx->dim, N*ctx->dim, globalPointsScalar, &pointVec);CHKERRQ(ierr); 265 ierr = PetscMalloc2(N,&foundProcs,N,&globalProcs);CHKERRQ(ierr); 266 for (p = 0; p < N; ++p) {foundProcs[p] = size;} 267 cellSF = NULL; 268 ierr = DMLocatePoints(dm, pointVec, DM_POINTLOCATION_REMOVE, &cellSF);CHKERRQ(ierr); 269 ierr = PetscSFGetGraph(cellSF,NULL,&numFound,&foundPoints,&foundCells);CHKERRQ(ierr); 270 #endif 271 for (p = 0; p < numFound; ++p) { 272 if (foundCells[p].index >= 0) foundProcs[foundPoints ? foundPoints[p] : p] = rank; 273 } 274 /* Let the lowest rank process own each point */ 275 ierr = MPIU_Allreduce(foundProcs, globalProcs, N, MPI_INT, MPI_MIN, comm);CHKERRQ(ierr); 276 ctx->n = 0; 277 for (p = 0; p < N; ++p) { 278 if (globalProcs[p] == size) SETERRQ4(comm, PETSC_ERR_PLIB, "Point %d: %g %g %g not located in mesh", p, (double)globalPoints[p*ctx->dim+0], (double)(ctx->dim > 1 ? globalPoints[p*ctx->dim+1] : 0.0), (double)(ctx->dim > 2 ? globalPoints[p*ctx->dim+2] : 0.0)); 279 else if (globalProcs[p] == rank) ctx->n++; 280 } 281 /* Create coordinates vector and array of owned cells */ 282 ierr = PetscMalloc1(ctx->n, &ctx->cells);CHKERRQ(ierr); 283 ierr = VecCreate(comm, &ctx->coords);CHKERRQ(ierr); 284 ierr = VecSetSizes(ctx->coords, ctx->n*ctx->dim, PETSC_DECIDE);CHKERRQ(ierr); 285 ierr = VecSetBlockSize(ctx->coords, ctx->dim);CHKERRQ(ierr); 286 ierr = VecSetType(ctx->coords,VECSTANDARD);CHKERRQ(ierr); 287 ierr = VecGetArray(ctx->coords, &a);CHKERRQ(ierr); 288 for (p = 0, q = 0, i = 0; p < N; ++p) { 289 if (globalProcs[p] == rank) { 290 PetscInt d; 291 292 for (d = 0; d < ctx->dim; ++d, ++i) a[i] = globalPoints[p*ctx->dim+d]; 293 ctx->cells[q] = foundCells[q].index; 294 ++q; 295 } 296 } 297 ierr = VecRestoreArray(ctx->coords, &a);CHKERRQ(ierr); 298 #if 0 299 ierr = PetscFree3(foundCells,foundProcs,globalProcs);CHKERRQ(ierr); 300 #else 301 ierr = PetscFree2(foundProcs,globalProcs);CHKERRQ(ierr); 302 ierr = PetscSFDestroy(&cellSF);CHKERRQ(ierr); 303 ierr = VecDestroy(&pointVec);CHKERRQ(ierr); 304 #endif 305 if ((void*)globalPointsScalar != (void*)globalPoints) {ierr = PetscFree(globalPointsScalar);CHKERRQ(ierr);} 306 if (!redundantPoints) {ierr = PetscFree3(globalPoints,counts,displs);CHKERRQ(ierr);} 307 ierr = PetscLayoutDestroy(&layout);CHKERRQ(ierr); 308 PetscFunctionReturn(0); 309 } 310 311 /*@C 312 DMInterpolationGetCoordinates - Gets a Vec with the coordinates of each interpolation point 313 314 Collective on ctx 315 316 Input Parameter: 317 . ctx - the context 318 319 Output Parameter: 320 . coordinates - the coordinates of interpolation points 321 322 Note: The local vector entries correspond to interpolation points lying on this process, according to the associated DM. This is a borrowed vector that the user should not destroy. 323 324 Level: intermediate 325 326 .seealso: DMInterpolationEvaluate(), DMInterpolationAddPoints(), DMInterpolationCreate() 327 @*/ 328 PetscErrorCode DMInterpolationGetCoordinates(DMInterpolationInfo ctx, Vec *coordinates) 329 { 330 PetscFunctionBegin; 331 PetscValidPointer(coordinates, 2); 332 if (!ctx->coords) SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONGSTATE, "The interpolation context has not been setup."); 333 *coordinates = ctx->coords; 334 PetscFunctionReturn(0); 335 } 336 337 /*@C 338 DMInterpolationGetVector - Gets a Vec which can hold all the interpolated field values 339 340 Collective on ctx 341 342 Input Parameter: 343 . ctx - the context 344 345 Output Parameter: 346 . v - a vector capable of holding the interpolated field values 347 348 Note: This vector should be returned using DMInterpolationRestoreVector(). 349 350 Level: intermediate 351 352 .seealso: DMInterpolationRestoreVector(), DMInterpolationEvaluate(), DMInterpolationAddPoints(), DMInterpolationCreate() 353 @*/ 354 PetscErrorCode DMInterpolationGetVector(DMInterpolationInfo ctx, Vec *v) 355 { 356 PetscErrorCode ierr; 357 358 PetscFunctionBegin; 359 PetscValidPointer(v, 2); 360 if (!ctx->coords) SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONGSTATE, "The interpolation context has not been setup."); 361 ierr = VecCreate(ctx->comm, v);CHKERRQ(ierr); 362 ierr = VecSetSizes(*v, ctx->n*ctx->dof, PETSC_DECIDE);CHKERRQ(ierr); 363 ierr = VecSetBlockSize(*v, ctx->dof);CHKERRQ(ierr); 364 ierr = VecSetType(*v,VECSTANDARD);CHKERRQ(ierr); 365 PetscFunctionReturn(0); 366 } 367 368 /*@C 369 DMInterpolationRestoreVector - Returns a Vec which can hold all the interpolated field values 370 371 Collective on ctx 372 373 Input Parameters: 374 + ctx - the context 375 - v - a vector capable of holding the interpolated field values 376 377 Level: intermediate 378 379 .seealso: DMInterpolationGetVector(), DMInterpolationEvaluate(), DMInterpolationAddPoints(), DMInterpolationCreate() 380 @*/ 381 PetscErrorCode DMInterpolationRestoreVector(DMInterpolationInfo ctx, Vec *v) 382 { 383 PetscErrorCode ierr; 384 385 PetscFunctionBegin; 386 PetscValidPointer(v, 2); 387 if (!ctx->coords) SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONGSTATE, "The interpolation context has not been setup."); 388 ierr = VecDestroy(v);CHKERRQ(ierr); 389 PetscFunctionReturn(0); 390 } 391 392 PETSC_STATIC_INLINE PetscErrorCode DMInterpolate_Triangle_Private(DMInterpolationInfo ctx, DM dm, Vec xLocal, Vec v) 393 { 394 PetscReal *v0, *J, *invJ, detJ; 395 const PetscScalar *coords; 396 PetscScalar *a; 397 PetscInt p; 398 PetscErrorCode ierr; 399 400 PetscFunctionBegin; 401 ierr = PetscMalloc3(ctx->dim,&v0,ctx->dim*ctx->dim,&J,ctx->dim*ctx->dim,&invJ);CHKERRQ(ierr); 402 ierr = VecGetArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 403 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 404 for (p = 0; p < ctx->n; ++p) { 405 PetscInt c = ctx->cells[p]; 406 PetscScalar *x = NULL; 407 PetscReal xi[4]; 408 PetscInt d, f, comp; 409 410 ierr = DMPlexComputeCellGeometryFEM(dm, c, NULL, v0, J, invJ, &detJ);CHKERRQ(ierr); 411 if (detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", (double)detJ, c); 412 ierr = DMPlexVecGetClosure(dm, NULL, xLocal, c, NULL, &x);CHKERRQ(ierr); 413 for (comp = 0; comp < ctx->dof; ++comp) a[p*ctx->dof+comp] = x[0*ctx->dof+comp]; 414 415 for (d = 0; d < ctx->dim; ++d) { 416 xi[d] = 0.0; 417 for (f = 0; f < ctx->dim; ++f) xi[d] += invJ[d*ctx->dim+f]*0.5*PetscRealPart(coords[p*ctx->dim+f] - v0[f]); 418 for (comp = 0; comp < ctx->dof; ++comp) a[p*ctx->dof+comp] += PetscRealPart(x[(d+1)*ctx->dof+comp] - x[0*ctx->dof+comp])*xi[d]; 419 } 420 ierr = DMPlexVecRestoreClosure(dm, NULL, xLocal, c, NULL, &x);CHKERRQ(ierr); 421 } 422 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 423 ierr = VecRestoreArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 424 ierr = PetscFree3(v0, J, invJ);CHKERRQ(ierr); 425 PetscFunctionReturn(0); 426 } 427 428 PETSC_STATIC_INLINE PetscErrorCode DMInterpolate_Tetrahedron_Private(DMInterpolationInfo ctx, DM dm, Vec xLocal, Vec v) 429 { 430 PetscReal *v0, *J, *invJ, detJ; 431 const PetscScalar *coords; 432 PetscScalar *a; 433 PetscInt p; 434 PetscErrorCode ierr; 435 436 PetscFunctionBegin; 437 ierr = PetscMalloc3(ctx->dim,&v0,ctx->dim*ctx->dim,&J,ctx->dim*ctx->dim,&invJ);CHKERRQ(ierr); 438 ierr = VecGetArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 439 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 440 for (p = 0; p < ctx->n; ++p) { 441 PetscInt c = ctx->cells[p]; 442 const PetscInt order[3] = {2, 1, 3}; 443 PetscScalar *x = NULL; 444 PetscReal xi[4]; 445 PetscInt d, f, comp; 446 447 ierr = DMPlexComputeCellGeometryFEM(dm, c, NULL, v0, J, invJ, &detJ);CHKERRQ(ierr); 448 if (detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", (double)detJ, c); 449 ierr = DMPlexVecGetClosure(dm, NULL, xLocal, c, NULL, &x);CHKERRQ(ierr); 450 for (comp = 0; comp < ctx->dof; ++comp) a[p*ctx->dof+comp] = x[0*ctx->dof+comp]; 451 452 for (d = 0; d < ctx->dim; ++d) { 453 xi[d] = 0.0; 454 for (f = 0; f < ctx->dim; ++f) xi[d] += invJ[d*ctx->dim+f]*0.5*PetscRealPart(coords[p*ctx->dim+f] - v0[f]); 455 for (comp = 0; comp < ctx->dof; ++comp) a[p*ctx->dof+comp] += PetscRealPart(x[order[d]*ctx->dof+comp] - x[0*ctx->dof+comp])*xi[d]; 456 } 457 ierr = DMPlexVecRestoreClosure(dm, NULL, xLocal, c, NULL, &x);CHKERRQ(ierr); 458 } 459 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 460 ierr = VecRestoreArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 461 ierr = PetscFree3(v0, J, invJ);CHKERRQ(ierr); 462 PetscFunctionReturn(0); 463 } 464 465 PETSC_STATIC_INLINE PetscErrorCode QuadMap_Private(SNES snes, Vec Xref, Vec Xreal, void *ctx) 466 { 467 const PetscScalar *vertices = (const PetscScalar*) ctx; 468 const PetscScalar x0 = vertices[0]; 469 const PetscScalar y0 = vertices[1]; 470 const PetscScalar x1 = vertices[2]; 471 const PetscScalar y1 = vertices[3]; 472 const PetscScalar x2 = vertices[4]; 473 const PetscScalar y2 = vertices[5]; 474 const PetscScalar x3 = vertices[6]; 475 const PetscScalar y3 = vertices[7]; 476 const PetscScalar f_1 = x1 - x0; 477 const PetscScalar g_1 = y1 - y0; 478 const PetscScalar f_3 = x3 - x0; 479 const PetscScalar g_3 = y3 - y0; 480 const PetscScalar f_01 = x2 - x1 - x3 + x0; 481 const PetscScalar g_01 = y2 - y1 - y3 + y0; 482 const PetscScalar *ref; 483 PetscScalar *real; 484 PetscErrorCode ierr; 485 486 PetscFunctionBegin; 487 ierr = VecGetArrayRead(Xref, &ref);CHKERRQ(ierr); 488 ierr = VecGetArray(Xreal, &real);CHKERRQ(ierr); 489 { 490 const PetscScalar p0 = ref[0]; 491 const PetscScalar p1 = ref[1]; 492 493 real[0] = x0 + f_1 * p0 + f_3 * p1 + f_01 * p0 * p1; 494 real[1] = y0 + g_1 * p0 + g_3 * p1 + g_01 * p0 * p1; 495 } 496 ierr = PetscLogFlops(28);CHKERRQ(ierr); 497 ierr = VecRestoreArrayRead(Xref, &ref);CHKERRQ(ierr); 498 ierr = VecRestoreArray(Xreal, &real);CHKERRQ(ierr); 499 PetscFunctionReturn(0); 500 } 501 502 #include <petsc/private/dmimpl.h> 503 PETSC_STATIC_INLINE PetscErrorCode QuadJacobian_Private(SNES snes, Vec Xref, Mat J, Mat M, void *ctx) 504 { 505 const PetscScalar *vertices = (const PetscScalar*) ctx; 506 const PetscScalar x0 = vertices[0]; 507 const PetscScalar y0 = vertices[1]; 508 const PetscScalar x1 = vertices[2]; 509 const PetscScalar y1 = vertices[3]; 510 const PetscScalar x2 = vertices[4]; 511 const PetscScalar y2 = vertices[5]; 512 const PetscScalar x3 = vertices[6]; 513 const PetscScalar y3 = vertices[7]; 514 const PetscScalar f_01 = x2 - x1 - x3 + x0; 515 const PetscScalar g_01 = y2 - y1 - y3 + y0; 516 const PetscScalar *ref; 517 PetscErrorCode ierr; 518 519 PetscFunctionBegin; 520 ierr = VecGetArrayRead(Xref, &ref);CHKERRQ(ierr); 521 { 522 const PetscScalar x = ref[0]; 523 const PetscScalar y = ref[1]; 524 const PetscInt rows[2] = {0, 1}; 525 PetscScalar values[4]; 526 527 values[0] = (x1 - x0 + f_01*y) * 0.5; values[1] = (x3 - x0 + f_01*x) * 0.5; 528 values[2] = (y1 - y0 + g_01*y) * 0.5; values[3] = (y3 - y0 + g_01*x) * 0.5; 529 ierr = MatSetValues(J, 2, rows, 2, rows, values, INSERT_VALUES);CHKERRQ(ierr); 530 } 531 ierr = PetscLogFlops(30);CHKERRQ(ierr); 532 ierr = VecRestoreArrayRead(Xref, &ref);CHKERRQ(ierr); 533 ierr = MatAssemblyBegin(J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 534 ierr = MatAssemblyEnd(J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 535 PetscFunctionReturn(0); 536 } 537 538 PETSC_STATIC_INLINE PetscErrorCode DMInterpolate_Quad_Private(DMInterpolationInfo ctx, DM dm, Vec xLocal, Vec v) 539 { 540 DM dmCoord; 541 PetscFE fem = NULL; 542 SNES snes; 543 KSP ksp; 544 PC pc; 545 Vec coordsLocal, r, ref, real; 546 Mat J; 547 const PetscScalar *coords; 548 PetscScalar *a; 549 PetscInt Nf, p; 550 const PetscInt dof = ctx->dof; 551 PetscErrorCode ierr; 552 553 PetscFunctionBegin; 554 ierr = DMGetNumFields(dm, &Nf);CHKERRQ(ierr); 555 if (Nf) {ierr = DMGetField(dm, 0, NULL, (PetscObject *) &fem);CHKERRQ(ierr);} 556 ierr = DMGetCoordinatesLocal(dm, &coordsLocal);CHKERRQ(ierr); 557 ierr = DMGetCoordinateDM(dm, &dmCoord);CHKERRQ(ierr); 558 ierr = SNESCreate(PETSC_COMM_SELF, &snes);CHKERRQ(ierr); 559 ierr = SNESSetOptionsPrefix(snes, "quad_interp_");CHKERRQ(ierr); 560 ierr = VecCreate(PETSC_COMM_SELF, &r);CHKERRQ(ierr); 561 ierr = VecSetSizes(r, 2, 2);CHKERRQ(ierr); 562 ierr = VecSetType(r,dm->vectype);CHKERRQ(ierr); 563 ierr = VecDuplicate(r, &ref);CHKERRQ(ierr); 564 ierr = VecDuplicate(r, &real);CHKERRQ(ierr); 565 ierr = MatCreate(PETSC_COMM_SELF, &J);CHKERRQ(ierr); 566 ierr = MatSetSizes(J, 2, 2, 2, 2);CHKERRQ(ierr); 567 ierr = MatSetType(J, MATSEQDENSE);CHKERRQ(ierr); 568 ierr = MatSetUp(J);CHKERRQ(ierr); 569 ierr = SNESSetFunction(snes, r, QuadMap_Private, NULL);CHKERRQ(ierr); 570 ierr = SNESSetJacobian(snes, J, J, QuadJacobian_Private, NULL);CHKERRQ(ierr); 571 ierr = SNESGetKSP(snes, &ksp);CHKERRQ(ierr); 572 ierr = KSPGetPC(ksp, &pc);CHKERRQ(ierr); 573 ierr = PCSetType(pc, PCLU);CHKERRQ(ierr); 574 ierr = SNESSetFromOptions(snes);CHKERRQ(ierr); 575 576 ierr = VecGetArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 577 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 578 for (p = 0; p < ctx->n; ++p) { 579 PetscScalar *x = NULL, *vertices = NULL; 580 PetscScalar *xi; 581 PetscReal xir[2]; 582 PetscInt c = ctx->cells[p], comp, coordSize, xSize; 583 584 /* Can make this do all points at once */ 585 ierr = DMPlexVecGetClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);CHKERRQ(ierr); 586 if (4*2 != coordSize) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid closure size %d should be %d", coordSize, 4*2); 587 ierr = DMPlexVecGetClosure(dm, NULL, xLocal, c, &xSize, &x);CHKERRQ(ierr); 588 ierr = SNESSetFunction(snes, NULL, NULL, (void*) vertices);CHKERRQ(ierr); 589 ierr = SNESSetJacobian(snes, NULL, NULL, NULL, (void*) vertices);CHKERRQ(ierr); 590 ierr = VecGetArray(real, &xi);CHKERRQ(ierr); 591 xi[0] = coords[p*ctx->dim+0]; 592 xi[1] = coords[p*ctx->dim+1]; 593 ierr = VecRestoreArray(real, &xi);CHKERRQ(ierr); 594 ierr = SNESSolve(snes, real, ref);CHKERRQ(ierr); 595 ierr = VecGetArray(ref, &xi);CHKERRQ(ierr); 596 xir[0] = PetscRealPart(xi[0]); 597 xir[1] = PetscRealPart(xi[1]); 598 if (4*dof != xSize) { 599 PetscReal *B; 600 PetscInt d; 601 602 xir[0] = 2.0*xir[0] - 1.0; xir[1] = 2.0*xir[1] - 1.0; 603 ierr = PetscFEGetTabulation(fem, 1, xir, &B, NULL, NULL);CHKERRQ(ierr); 604 for (comp = 0; comp < dof; ++comp) { 605 a[p*dof+comp] = 0.0; 606 for (d = 0; d < xSize/dof; ++d) { 607 a[p*dof+comp] += x[d*dof+comp]*B[d*dof+comp]; 608 } 609 } 610 ierr = PetscFERestoreTabulation(fem, 1, xir, &B, NULL, NULL);CHKERRQ(ierr); 611 } else { 612 for (comp = 0; comp < dof; ++comp) 613 a[p*dof+comp] = x[0*dof+comp]*(1 - xir[0])*(1 - xir[1]) + x[1*dof+comp]*xir[0]*(1 - xir[1]) + x[2*dof+comp]*xir[0]*xir[1] + x[3*dof+comp]*(1 - xir[0])*xir[1]; 614 } 615 ierr = VecRestoreArray(ref, &xi);CHKERRQ(ierr); 616 ierr = DMPlexVecRestoreClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);CHKERRQ(ierr); 617 ierr = DMPlexVecRestoreClosure(dm, NULL, xLocal, c, &xSize, &x);CHKERRQ(ierr); 618 } 619 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 620 ierr = VecRestoreArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 621 622 ierr = SNESDestroy(&snes);CHKERRQ(ierr); 623 ierr = VecDestroy(&r);CHKERRQ(ierr); 624 ierr = VecDestroy(&ref);CHKERRQ(ierr); 625 ierr = VecDestroy(&real);CHKERRQ(ierr); 626 ierr = MatDestroy(&J);CHKERRQ(ierr); 627 PetscFunctionReturn(0); 628 } 629 630 PETSC_STATIC_INLINE PetscErrorCode HexMap_Private(SNES snes, Vec Xref, Vec Xreal, void *ctx) 631 { 632 const PetscScalar *vertices = (const PetscScalar*) ctx; 633 const PetscScalar x0 = vertices[0]; 634 const PetscScalar y0 = vertices[1]; 635 const PetscScalar z0 = vertices[2]; 636 const PetscScalar x1 = vertices[9]; 637 const PetscScalar y1 = vertices[10]; 638 const PetscScalar z1 = vertices[11]; 639 const PetscScalar x2 = vertices[6]; 640 const PetscScalar y2 = vertices[7]; 641 const PetscScalar z2 = vertices[8]; 642 const PetscScalar x3 = vertices[3]; 643 const PetscScalar y3 = vertices[4]; 644 const PetscScalar z3 = vertices[5]; 645 const PetscScalar x4 = vertices[12]; 646 const PetscScalar y4 = vertices[13]; 647 const PetscScalar z4 = vertices[14]; 648 const PetscScalar x5 = vertices[15]; 649 const PetscScalar y5 = vertices[16]; 650 const PetscScalar z5 = vertices[17]; 651 const PetscScalar x6 = vertices[18]; 652 const PetscScalar y6 = vertices[19]; 653 const PetscScalar z6 = vertices[20]; 654 const PetscScalar x7 = vertices[21]; 655 const PetscScalar y7 = vertices[22]; 656 const PetscScalar z7 = vertices[23]; 657 const PetscScalar f_1 = x1 - x0; 658 const PetscScalar g_1 = y1 - y0; 659 const PetscScalar h_1 = z1 - z0; 660 const PetscScalar f_3 = x3 - x0; 661 const PetscScalar g_3 = y3 - y0; 662 const PetscScalar h_3 = z3 - z0; 663 const PetscScalar f_4 = x4 - x0; 664 const PetscScalar g_4 = y4 - y0; 665 const PetscScalar h_4 = z4 - z0; 666 const PetscScalar f_01 = x2 - x1 - x3 + x0; 667 const PetscScalar g_01 = y2 - y1 - y3 + y0; 668 const PetscScalar h_01 = z2 - z1 - z3 + z0; 669 const PetscScalar f_12 = x7 - x3 - x4 + x0; 670 const PetscScalar g_12 = y7 - y3 - y4 + y0; 671 const PetscScalar h_12 = z7 - z3 - z4 + z0; 672 const PetscScalar f_02 = x5 - x1 - x4 + x0; 673 const PetscScalar g_02 = y5 - y1 - y4 + y0; 674 const PetscScalar h_02 = z5 - z1 - z4 + z0; 675 const PetscScalar f_012 = x6 - x0 + x1 - x2 + x3 + x4 - x5 - x7; 676 const PetscScalar g_012 = y6 - y0 + y1 - y2 + y3 + y4 - y5 - y7; 677 const PetscScalar h_012 = z6 - z0 + z1 - z2 + z3 + z4 - z5 - z7; 678 const PetscScalar *ref; 679 PetscScalar *real; 680 PetscErrorCode ierr; 681 682 PetscFunctionBegin; 683 ierr = VecGetArrayRead(Xref, &ref);CHKERRQ(ierr); 684 ierr = VecGetArray(Xreal, &real);CHKERRQ(ierr); 685 { 686 const PetscScalar p0 = ref[0]; 687 const PetscScalar p1 = ref[1]; 688 const PetscScalar p2 = ref[2]; 689 690 real[0] = x0 + f_1*p0 + f_3*p1 + f_4*p2 + f_01*p0*p1 + f_12*p1*p2 + f_02*p0*p2 + f_012*p0*p1*p2; 691 real[1] = y0 + g_1*p0 + g_3*p1 + g_4*p2 + g_01*p0*p1 + g_01*p0*p1 + g_12*p1*p2 + g_02*p0*p2 + g_012*p0*p1*p2; 692 real[2] = z0 + h_1*p0 + h_3*p1 + h_4*p2 + h_01*p0*p1 + h_01*p0*p1 + h_12*p1*p2 + h_02*p0*p2 + h_012*p0*p1*p2; 693 } 694 ierr = PetscLogFlops(114);CHKERRQ(ierr); 695 ierr = VecRestoreArrayRead(Xref, &ref);CHKERRQ(ierr); 696 ierr = VecRestoreArray(Xreal, &real);CHKERRQ(ierr); 697 PetscFunctionReturn(0); 698 } 699 700 PETSC_STATIC_INLINE PetscErrorCode HexJacobian_Private(SNES snes, Vec Xref, Mat J, Mat M, void *ctx) 701 { 702 const PetscScalar *vertices = (const PetscScalar*) ctx; 703 const PetscScalar x0 = vertices[0]; 704 const PetscScalar y0 = vertices[1]; 705 const PetscScalar z0 = vertices[2]; 706 const PetscScalar x1 = vertices[9]; 707 const PetscScalar y1 = vertices[10]; 708 const PetscScalar z1 = vertices[11]; 709 const PetscScalar x2 = vertices[6]; 710 const PetscScalar y2 = vertices[7]; 711 const PetscScalar z2 = vertices[8]; 712 const PetscScalar x3 = vertices[3]; 713 const PetscScalar y3 = vertices[4]; 714 const PetscScalar z3 = vertices[5]; 715 const PetscScalar x4 = vertices[12]; 716 const PetscScalar y4 = vertices[13]; 717 const PetscScalar z4 = vertices[14]; 718 const PetscScalar x5 = vertices[15]; 719 const PetscScalar y5 = vertices[16]; 720 const PetscScalar z5 = vertices[17]; 721 const PetscScalar x6 = vertices[18]; 722 const PetscScalar y6 = vertices[19]; 723 const PetscScalar z6 = vertices[20]; 724 const PetscScalar x7 = vertices[21]; 725 const PetscScalar y7 = vertices[22]; 726 const PetscScalar z7 = vertices[23]; 727 const PetscScalar f_xy = x2 - x1 - x3 + x0; 728 const PetscScalar g_xy = y2 - y1 - y3 + y0; 729 const PetscScalar h_xy = z2 - z1 - z3 + z0; 730 const PetscScalar f_yz = x7 - x3 - x4 + x0; 731 const PetscScalar g_yz = y7 - y3 - y4 + y0; 732 const PetscScalar h_yz = z7 - z3 - z4 + z0; 733 const PetscScalar f_xz = x5 - x1 - x4 + x0; 734 const PetscScalar g_xz = y5 - y1 - y4 + y0; 735 const PetscScalar h_xz = z5 - z1 - z4 + z0; 736 const PetscScalar f_xyz = x6 - x0 + x1 - x2 + x3 + x4 - x5 - x7; 737 const PetscScalar g_xyz = y6 - y0 + y1 - y2 + y3 + y4 - y5 - y7; 738 const PetscScalar h_xyz = z6 - z0 + z1 - z2 + z3 + z4 - z5 - z7; 739 const PetscScalar *ref; 740 PetscErrorCode ierr; 741 742 PetscFunctionBegin; 743 ierr = VecGetArrayRead(Xref, &ref);CHKERRQ(ierr); 744 { 745 const PetscScalar x = ref[0]; 746 const PetscScalar y = ref[1]; 747 const PetscScalar z = ref[2]; 748 const PetscInt rows[3] = {0, 1, 2}; 749 PetscScalar values[9]; 750 751 values[0] = (x1 - x0 + f_xy*y + f_xz*z + f_xyz*y*z) / 2.0; 752 values[1] = (x3 - x0 + f_xy*x + f_yz*z + f_xyz*x*z) / 2.0; 753 values[2] = (x4 - x0 + f_yz*y + f_xz*x + f_xyz*x*y) / 2.0; 754 values[3] = (y1 - y0 + g_xy*y + g_xz*z + g_xyz*y*z) / 2.0; 755 values[4] = (y3 - y0 + g_xy*x + g_yz*z + g_xyz*x*z) / 2.0; 756 values[5] = (y4 - y0 + g_yz*y + g_xz*x + g_xyz*x*y) / 2.0; 757 values[6] = (z1 - z0 + h_xy*y + h_xz*z + h_xyz*y*z) / 2.0; 758 values[7] = (z3 - z0 + h_xy*x + h_yz*z + h_xyz*x*z) / 2.0; 759 values[8] = (z4 - z0 + h_yz*y + h_xz*x + h_xyz*x*y) / 2.0; 760 761 ierr = MatSetValues(J, 3, rows, 3, rows, values, INSERT_VALUES);CHKERRQ(ierr); 762 } 763 ierr = PetscLogFlops(152);CHKERRQ(ierr); 764 ierr = VecRestoreArrayRead(Xref, &ref);CHKERRQ(ierr); 765 ierr = MatAssemblyBegin(J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 766 ierr = MatAssemblyEnd(J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 767 PetscFunctionReturn(0); 768 } 769 770 PETSC_STATIC_INLINE PetscErrorCode DMInterpolate_Hex_Private(DMInterpolationInfo ctx, DM dm, Vec xLocal, Vec v) 771 { 772 DM dmCoord; 773 SNES snes; 774 KSP ksp; 775 PC pc; 776 Vec coordsLocal, r, ref, real; 777 Mat J; 778 const PetscScalar *coords; 779 PetscScalar *a; 780 PetscInt p; 781 PetscErrorCode ierr; 782 783 PetscFunctionBegin; 784 ierr = DMGetCoordinatesLocal(dm, &coordsLocal);CHKERRQ(ierr); 785 ierr = DMGetCoordinateDM(dm, &dmCoord);CHKERRQ(ierr); 786 ierr = SNESCreate(PETSC_COMM_SELF, &snes);CHKERRQ(ierr); 787 ierr = SNESSetOptionsPrefix(snes, "hex_interp_");CHKERRQ(ierr); 788 ierr = VecCreate(PETSC_COMM_SELF, &r);CHKERRQ(ierr); 789 ierr = VecSetSizes(r, 3, 3);CHKERRQ(ierr); 790 ierr = VecSetType(r,dm->vectype);CHKERRQ(ierr); 791 ierr = VecDuplicate(r, &ref);CHKERRQ(ierr); 792 ierr = VecDuplicate(r, &real);CHKERRQ(ierr); 793 ierr = MatCreate(PETSC_COMM_SELF, &J);CHKERRQ(ierr); 794 ierr = MatSetSizes(J, 3, 3, 3, 3);CHKERRQ(ierr); 795 ierr = MatSetType(J, MATSEQDENSE);CHKERRQ(ierr); 796 ierr = MatSetUp(J);CHKERRQ(ierr); 797 ierr = SNESSetFunction(snes, r, HexMap_Private, NULL);CHKERRQ(ierr); 798 ierr = SNESSetJacobian(snes, J, J, HexJacobian_Private, NULL);CHKERRQ(ierr); 799 ierr = SNESGetKSP(snes, &ksp);CHKERRQ(ierr); 800 ierr = KSPGetPC(ksp, &pc);CHKERRQ(ierr); 801 ierr = PCSetType(pc, PCLU);CHKERRQ(ierr); 802 ierr = SNESSetFromOptions(snes);CHKERRQ(ierr); 803 804 ierr = VecGetArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 805 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 806 for (p = 0; p < ctx->n; ++p) { 807 PetscScalar *x = NULL, *vertices = NULL; 808 PetscScalar *xi; 809 PetscReal xir[3]; 810 PetscInt c = ctx->cells[p], comp, coordSize, xSize; 811 812 /* Can make this do all points at once */ 813 ierr = DMPlexVecGetClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);CHKERRQ(ierr); 814 if (8*3 != coordSize) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid closure size %d should be %d", coordSize, 8*3); 815 ierr = DMPlexVecGetClosure(dm, NULL, xLocal, c, &xSize, &x);CHKERRQ(ierr); 816 if (8*ctx->dof != xSize) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid closure size %d should be %d", xSize, 8*ctx->dof); 817 ierr = SNESSetFunction(snes, NULL, NULL, (void*) vertices);CHKERRQ(ierr); 818 ierr = SNESSetJacobian(snes, NULL, NULL, NULL, (void*) vertices);CHKERRQ(ierr); 819 ierr = VecGetArray(real, &xi);CHKERRQ(ierr); 820 xi[0] = coords[p*ctx->dim+0]; 821 xi[1] = coords[p*ctx->dim+1]; 822 xi[2] = coords[p*ctx->dim+2]; 823 ierr = VecRestoreArray(real, &xi);CHKERRQ(ierr); 824 ierr = SNESSolve(snes, real, ref);CHKERRQ(ierr); 825 ierr = VecGetArray(ref, &xi);CHKERRQ(ierr); 826 xir[0] = PetscRealPart(xi[0]); 827 xir[1] = PetscRealPart(xi[1]); 828 xir[2] = PetscRealPart(xi[2]); 829 for (comp = 0; comp < ctx->dof; ++comp) { 830 a[p*ctx->dof+comp] = 831 x[0*ctx->dof+comp]*(1-xir[0])*(1-xir[1])*(1-xir[2]) + 832 x[3*ctx->dof+comp]* xir[0]*(1-xir[1])*(1-xir[2]) + 833 x[2*ctx->dof+comp]* xir[0]* xir[1]*(1-xir[2]) + 834 x[1*ctx->dof+comp]*(1-xir[0])* xir[1]*(1-xir[2]) + 835 x[4*ctx->dof+comp]*(1-xir[0])*(1-xir[1])* xir[2] + 836 x[5*ctx->dof+comp]* xir[0]*(1-xir[1])* xir[2] + 837 x[6*ctx->dof+comp]* xir[0]* xir[1]* xir[2] + 838 x[7*ctx->dof+comp]*(1-xir[0])* xir[1]* xir[2]; 839 } 840 ierr = VecRestoreArray(ref, &xi);CHKERRQ(ierr); 841 ierr = DMPlexVecRestoreClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);CHKERRQ(ierr); 842 ierr = DMPlexVecRestoreClosure(dm, NULL, xLocal, c, &xSize, &x);CHKERRQ(ierr); 843 } 844 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 845 ierr = VecRestoreArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 846 847 ierr = SNESDestroy(&snes);CHKERRQ(ierr); 848 ierr = VecDestroy(&r);CHKERRQ(ierr); 849 ierr = VecDestroy(&ref);CHKERRQ(ierr); 850 ierr = VecDestroy(&real);CHKERRQ(ierr); 851 ierr = MatDestroy(&J);CHKERRQ(ierr); 852 PetscFunctionReturn(0); 853 } 854 855 /*@C 856 DMInterpolationEvaluate - Using the input from dm and x, calculates interpolated field values at the interpolation points. 857 858 Input Parameters: 859 + ctx - The DMInterpolationInfo context 860 . dm - The DM 861 - x - The local vector containing the field to be interpolated 862 863 Output Parameters: 864 . v - The vector containing the interpolated values 865 866 Note: A suitable v can be obtained using DMInterpolationGetVector(). 867 868 Level: beginner 869 870 .seealso: DMInterpolationGetVector(), DMInterpolationAddPoints(), DMInterpolationCreate() 871 @*/ 872 PetscErrorCode DMInterpolationEvaluate(DMInterpolationInfo ctx, DM dm, Vec x, Vec v) 873 { 874 PetscInt dim, coneSize, n; 875 PetscErrorCode ierr; 876 877 PetscFunctionBegin; 878 PetscValidHeaderSpecific(dm, DM_CLASSID, 2); 879 PetscValidHeaderSpecific(x, VEC_CLASSID, 3); 880 PetscValidHeaderSpecific(v, VEC_CLASSID, 4); 881 ierr = VecGetLocalSize(v, &n);CHKERRQ(ierr); 882 if (n != ctx->n*ctx->dof) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid input vector size %d should be %d", n, ctx->n*ctx->dof); 883 if (n) { 884 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 885 ierr = DMPlexGetConeSize(dm, ctx->cells[0], &coneSize);CHKERRQ(ierr); 886 if (dim == 2) { 887 if (coneSize == 3) { 888 ierr = DMInterpolate_Triangle_Private(ctx, dm, x, v);CHKERRQ(ierr); 889 } else if (coneSize == 4) { 890 ierr = DMInterpolate_Quad_Private(ctx, dm, x, v);CHKERRQ(ierr); 891 } else SETERRQ1(ctx->comm, PETSC_ERR_ARG_OUTOFRANGE, "Unsupported dimension %d for point interpolation", dim); 892 } else if (dim == 3) { 893 if (coneSize == 4) { 894 ierr = DMInterpolate_Tetrahedron_Private(ctx, dm, x, v);CHKERRQ(ierr); 895 } else { 896 ierr = DMInterpolate_Hex_Private(ctx, dm, x, v);CHKERRQ(ierr); 897 } 898 } else SETERRQ1(ctx->comm, PETSC_ERR_ARG_OUTOFRANGE, "Unsupported dimension %d for point interpolation", dim); 899 } 900 PetscFunctionReturn(0); 901 } 902 903 /*@C 904 DMInterpolationDestroy - Destroys a DMInterpolationInfo context 905 906 Collective on ctx 907 908 Input Parameter: 909 . ctx - the context 910 911 Level: beginner 912 913 .seealso: DMInterpolationEvaluate(), DMInterpolationAddPoints(), DMInterpolationCreate() 914 @*/ 915 PetscErrorCode DMInterpolationDestroy(DMInterpolationInfo *ctx) 916 { 917 PetscErrorCode ierr; 918 919 PetscFunctionBegin; 920 PetscValidPointer(ctx, 2); 921 ierr = VecDestroy(&(*ctx)->coords);CHKERRQ(ierr); 922 ierr = PetscFree((*ctx)->points);CHKERRQ(ierr); 923 ierr = PetscFree((*ctx)->cells);CHKERRQ(ierr); 924 ierr = PetscFree(*ctx);CHKERRQ(ierr); 925 *ctx = NULL; 926 PetscFunctionReturn(0); 927 } 928 929 /*@C 930 SNESMonitorFields - Monitors the residual for each field separately 931 932 Collective on SNES 933 934 Input Parameters: 935 + snes - the SNES context 936 . its - iteration number 937 . fgnorm - 2-norm of residual 938 - vf - PetscViewerAndFormat of type ASCII 939 940 Notes: 941 This routine prints the residual norm at each iteration. 942 943 Level: intermediate 944 945 .keywords: SNES, nonlinear, default, monitor, norm 946 .seealso: SNESMonitorSet(), SNESMonitorDefault() 947 @*/ 948 PetscErrorCode SNESMonitorFields(SNES snes, PetscInt its, PetscReal fgnorm, PetscViewerAndFormat *vf) 949 { 950 PetscViewer viewer = vf->viewer; 951 Vec res; 952 DM dm; 953 PetscSection s; 954 const PetscScalar *r; 955 PetscReal *lnorms, *norms; 956 PetscInt numFields, f, pStart, pEnd, p; 957 PetscErrorCode ierr; 958 959 PetscFunctionBegin; 960 PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,4); 961 ierr = SNESGetFunction(snes, &res, 0, 0);CHKERRQ(ierr); 962 ierr = SNESGetDM(snes, &dm);CHKERRQ(ierr); 963 ierr = DMGetSection(dm, &s);CHKERRQ(ierr); 964 ierr = PetscSectionGetNumFields(s, &numFields);CHKERRQ(ierr); 965 ierr = PetscSectionGetChart(s, &pStart, &pEnd);CHKERRQ(ierr); 966 ierr = PetscCalloc2(numFields, &lnorms, numFields, &norms);CHKERRQ(ierr); 967 ierr = VecGetArrayRead(res, &r);CHKERRQ(ierr); 968 for (p = pStart; p < pEnd; ++p) { 969 for (f = 0; f < numFields; ++f) { 970 PetscInt fdof, foff, d; 971 972 ierr = PetscSectionGetFieldDof(s, p, f, &fdof);CHKERRQ(ierr); 973 ierr = PetscSectionGetFieldOffset(s, p, f, &foff);CHKERRQ(ierr); 974 for (d = 0; d < fdof; ++d) lnorms[f] += PetscRealPart(PetscSqr(r[foff+d])); 975 } 976 } 977 ierr = VecRestoreArrayRead(res, &r);CHKERRQ(ierr); 978 ierr = MPIU_Allreduce(lnorms, norms, numFields, MPIU_REAL, MPIU_SUM, PetscObjectComm((PetscObject) dm));CHKERRQ(ierr); 979 ierr = PetscViewerPushFormat(viewer,vf->format);CHKERRQ(ierr); 980 ierr = PetscViewerASCIIAddTab(viewer, ((PetscObject) snes)->tablevel);CHKERRQ(ierr); 981 ierr = PetscViewerASCIIPrintf(viewer, "%3D SNES Function norm %14.12e [", its, (double) fgnorm);CHKERRQ(ierr); 982 for (f = 0; f < numFields; ++f) { 983 if (f > 0) {ierr = PetscViewerASCIIPrintf(viewer, ", ");CHKERRQ(ierr);} 984 ierr = PetscViewerASCIIPrintf(viewer, "%14.12e", (double) PetscSqrtReal(norms[f]));CHKERRQ(ierr); 985 } 986 ierr = PetscViewerASCIIPrintf(viewer, "]\n");CHKERRQ(ierr); 987 ierr = PetscViewerASCIISubtractTab(viewer, ((PetscObject) snes)->tablevel);CHKERRQ(ierr); 988 ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr); 989 ierr = PetscFree2(lnorms, norms);CHKERRQ(ierr); 990 PetscFunctionReturn(0); 991 } 992 993 /********************* Residual Computation **************************/ 994 995 996 /*@ 997 DMPlexSNESGetGeometryFVM - Return precomputed geometric data 998 999 Input Parameter: 1000 . dm - The DM 1001 1002 Output Parameters: 1003 + facegeom - The values precomputed from face geometry 1004 . cellgeom - The values precomputed from cell geometry 1005 - minRadius - The minimum radius over the mesh of an inscribed sphere in a cell 1006 1007 Level: developer 1008 1009 .seealso: DMPlexTSSetRHSFunctionLocal() 1010 @*/ 1011 PetscErrorCode DMPlexSNESGetGeometryFVM(DM dm, Vec *facegeom, Vec *cellgeom, PetscReal *minRadius) 1012 { 1013 DM plex; 1014 PetscErrorCode ierr; 1015 1016 PetscFunctionBegin; 1017 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 1018 ierr = DMSNESConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr); 1019 ierr = DMPlexGetDataFVM(plex, NULL, cellgeom, facegeom, NULL);CHKERRQ(ierr); 1020 if (minRadius) {ierr = DMPlexGetMinRadius(plex, minRadius);CHKERRQ(ierr);} 1021 ierr = DMDestroy(&plex);CHKERRQ(ierr); 1022 PetscFunctionReturn(0); 1023 } 1024 1025 /*@ 1026 DMPlexSNESGetGradientDM - Return gradient data layout 1027 1028 Input Parameters: 1029 + dm - The DM 1030 - fv - The PetscFV 1031 1032 Output Parameter: 1033 . dmGrad - The layout for gradient values 1034 1035 Level: developer 1036 1037 .seealso: DMPlexSNESGetGeometryFVM() 1038 @*/ 1039 PetscErrorCode DMPlexSNESGetGradientDM(DM dm, PetscFV fv, DM *dmGrad) 1040 { 1041 DM plex; 1042 PetscBool computeGradients; 1043 PetscErrorCode ierr; 1044 1045 PetscFunctionBegin; 1046 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 1047 PetscValidHeaderSpecific(fv,PETSCFV_CLASSID,2); 1048 PetscValidPointer(dmGrad,3); 1049 ierr = PetscFVGetComputeGradients(fv, &computeGradients);CHKERRQ(ierr); 1050 if (!computeGradients) {*dmGrad = NULL; PetscFunctionReturn(0);} 1051 ierr = DMSNESConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr); 1052 ierr = DMPlexGetDataFVM(plex, fv, NULL, NULL, dmGrad);CHKERRQ(ierr); 1053 ierr = DMDestroy(&plex);CHKERRQ(ierr); 1054 PetscFunctionReturn(0); 1055 } 1056 1057 static PetscErrorCode DMPlexComputeBdResidual_Single_Internal(DM dm, PetscReal t, DMLabel label, PetscInt numValues, const PetscInt values[], PetscInt field, Vec locX, Vec locX_t, Vec locF, DMField coordField, IS facetIS) 1058 { 1059 DM_Plex *mesh = (DM_Plex *) dm->data; 1060 DM plex = NULL, plexA = NULL; 1061 PetscDS prob, probAux = NULL; 1062 PetscSection section, sectionAux = NULL; 1063 Vec locA = NULL; 1064 PetscScalar *u = NULL, *u_t = NULL, *a = NULL, *elemVec = NULL; 1065 PetscInt v; 1066 PetscInt totDim, totDimAux = 0; 1067 PetscErrorCode ierr; 1068 1069 PetscFunctionBegin; 1070 ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); 1071 ierr = DMGetSection(dm, §ion);CHKERRQ(ierr); 1072 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1073 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1074 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);CHKERRQ(ierr); 1075 if (locA) { 1076 DM dmAux; 1077 1078 ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); 1079 ierr = DMConvert(dmAux, DMPLEX, &plexA);CHKERRQ(ierr); 1080 ierr = DMGetDS(plexA, &probAux);CHKERRQ(ierr); 1081 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 1082 ierr = DMGetSection(plexA, §ionAux);CHKERRQ(ierr); 1083 } 1084 for (v = 0; v < numValues; ++v) { 1085 PetscFEGeom *fgeom; 1086 PetscInt maxDegree; 1087 PetscQuadrature qGeom = NULL; 1088 IS pointIS; 1089 const PetscInt *points; 1090 PetscInt numFaces, face, Nq; 1091 1092 ierr = DMLabelGetStratumIS(label, values[v], &pointIS);CHKERRQ(ierr); 1093 if (!pointIS) continue; /* No points with that id on this process */ 1094 { 1095 IS isectIS; 1096 1097 /* TODO: Special cases of ISIntersect where it is quick to check a priori if one is a superset of the other */ 1098 ierr = ISIntersect_Caching_Internal(facetIS,pointIS,&isectIS);CHKERRQ(ierr); 1099 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 1100 pointIS = isectIS; 1101 } 1102 ierr = ISGetLocalSize(pointIS,&numFaces);CHKERRQ(ierr); 1103 ierr = ISGetIndices(pointIS,&points);CHKERRQ(ierr); 1104 ierr = PetscMalloc4(numFaces*totDim, &u, locX_t ? numFaces*totDim : 0, &u_t, numFaces*totDim, &elemVec, locA ? numFaces*totDimAux : 0, &a);CHKERRQ(ierr); 1105 ierr = DMFieldGetDegree(coordField,pointIS,NULL,&maxDegree);CHKERRQ(ierr); 1106 if (maxDegree <= 1) { 1107 ierr = DMFieldCreateDefaultQuadrature(coordField,pointIS,&qGeom);CHKERRQ(ierr); 1108 } 1109 if (!qGeom) { 1110 PetscFE fe; 1111 1112 ierr = PetscDSGetDiscretization(prob, field, (PetscObject *) &fe);CHKERRQ(ierr); 1113 ierr = PetscFEGetFaceQuadrature(fe, &qGeom);CHKERRQ(ierr); 1114 ierr = PetscObjectReference((PetscObject)qGeom);CHKERRQ(ierr); 1115 } 1116 ierr = PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 1117 ierr = DMSNESGetFEGeom(coordField,pointIS,qGeom,PETSC_TRUE,&fgeom);CHKERRQ(ierr); 1118 for (face = 0; face < numFaces; ++face) { 1119 const PetscInt point = points[face], *support, *cone; 1120 PetscScalar *x = NULL; 1121 PetscInt i, coneSize, faceLoc; 1122 1123 ierr = DMPlexGetSupport(dm, point, &support);CHKERRQ(ierr); 1124 ierr = DMPlexGetConeSize(dm, support[0], &coneSize);CHKERRQ(ierr); 1125 ierr = DMPlexGetCone(dm, support[0], &cone);CHKERRQ(ierr); 1126 for (faceLoc = 0; faceLoc < coneSize; ++faceLoc) if (cone[faceLoc] == point) break; 1127 if (faceLoc == coneSize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Could not find face %D in cone of support[0] %D", point, support[0]); 1128 fgeom->face[face][0] = faceLoc; 1129 ierr = DMPlexVecGetClosure(plex, section, locX, support[0], NULL, &x);CHKERRQ(ierr); 1130 for (i = 0; i < totDim; ++i) u[face*totDim+i] = x[i]; 1131 ierr = DMPlexVecRestoreClosure(plex, section, locX, support[0], NULL, &x);CHKERRQ(ierr); 1132 if (locX_t) { 1133 ierr = DMPlexVecGetClosure(plex, section, locX_t, support[0], NULL, &x);CHKERRQ(ierr); 1134 for (i = 0; i < totDim; ++i) u_t[face*totDim+i] = x[i]; 1135 ierr = DMPlexVecRestoreClosure(plex, section, locX_t, support[0], NULL, &x);CHKERRQ(ierr); 1136 } 1137 if (locA) { 1138 PetscInt subp; 1139 1140 ierr = DMPlexGetAuxiliaryPoint(plex, plexA, support[0], &subp);CHKERRQ(ierr); 1141 ierr = DMPlexVecGetClosure(plexA, sectionAux, locA, subp, NULL, &x);CHKERRQ(ierr); 1142 for (i = 0; i < totDimAux; ++i) a[face*totDimAux+i] = x[i]; 1143 ierr = DMPlexVecRestoreClosure(plexA, sectionAux, locA, subp, NULL, &x);CHKERRQ(ierr); 1144 } 1145 } 1146 ierr = PetscMemzero(elemVec, numFaces*totDim * sizeof(PetscScalar));CHKERRQ(ierr); 1147 { 1148 PetscFE fe; 1149 PetscInt Nb; 1150 PetscFEGeom *chunkGeom = NULL; 1151 /* Conforming batches */ 1152 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 1153 /* Remainder */ 1154 PetscInt Nr, offset; 1155 1156 ierr = PetscDSGetDiscretization(prob, field, (PetscObject *) &fe);CHKERRQ(ierr); 1157 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 1158 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1159 /* TODO: documentation is unclear about what is going on with these numbers: how should Nb / Nq factor in ? */ 1160 blockSize = Nb; 1161 batchSize = numBlocks * blockSize; 1162 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1163 numChunks = numFaces / (numBatches*batchSize); 1164 Ne = numChunks*numBatches*batchSize; 1165 Nr = numFaces % (numBatches*batchSize); 1166 offset = numFaces - Nr; 1167 ierr = PetscFEGeomGetChunk(fgeom,0,offset,&chunkGeom);CHKERRQ(ierr); 1168 ierr = PetscFEIntegrateBdResidual(fe, prob, field, Ne, chunkGeom, u, u_t, probAux, a, t, elemVec);CHKERRQ(ierr); 1169 ierr = PetscFEGeomRestoreChunk(fgeom, 0, offset, &chunkGeom);CHKERRQ(ierr); 1170 ierr = PetscFEGeomGetChunk(fgeom,offset,numFaces,&chunkGeom);CHKERRQ(ierr); 1171 ierr = PetscFEIntegrateBdResidual(fe, prob, field, Nr, chunkGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, a ? &a[offset*totDimAux] : NULL, t, &elemVec[offset*totDim]);CHKERRQ(ierr); 1172 ierr = PetscFEGeomRestoreChunk(fgeom,offset,numFaces,&chunkGeom);CHKERRQ(ierr); 1173 } 1174 for (face = 0; face < numFaces; ++face) { 1175 const PetscInt point = points[face], *support; 1176 1177 if (mesh->printFEM > 1) {ierr = DMPrintCellVector(point, "BdResidual", totDim, &elemVec[face*totDim]);CHKERRQ(ierr);} 1178 ierr = DMPlexGetSupport(plex, point, &support);CHKERRQ(ierr); 1179 ierr = DMPlexVecSetClosure(plex, NULL, locF, support[0], &elemVec[face*totDim], ADD_ALL_VALUES);CHKERRQ(ierr); 1180 } 1181 ierr = DMSNESRestoreFEGeom(coordField,pointIS,qGeom,PETSC_TRUE,&fgeom);CHKERRQ(ierr); 1182 ierr = PetscQuadratureDestroy(&qGeom);CHKERRQ(ierr); 1183 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 1184 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 1185 ierr = PetscFree4(u, u_t, elemVec, a);CHKERRQ(ierr); 1186 } 1187 if (plex) {ierr = DMDestroy(&plex);CHKERRQ(ierr);} 1188 if (plexA) {ierr = DMDestroy(&plexA);CHKERRQ(ierr);} 1189 PetscFunctionReturn(0); 1190 } 1191 1192 PetscErrorCode DMPlexComputeBdResidualSingle(DM dm, PetscReal t, DMLabel label, PetscInt numValues, const PetscInt values[], PetscInt field, Vec locX, Vec locX_t, Vec locF) 1193 { 1194 DMField coordField; 1195 DMLabel depthLabel; 1196 IS facetIS; 1197 PetscInt dim; 1198 PetscErrorCode ierr; 1199 1200 PetscFunctionBegin; 1201 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1202 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 1203 ierr = DMLabelGetStratumIS(depthLabel, dim-1, &facetIS);CHKERRQ(ierr); 1204 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 1205 ierr = DMPlexComputeBdResidual_Single_Internal(dm, t, label, numValues, values, field, locX, locX_t, locF, coordField, facetIS);CHKERRQ(ierr); 1206 PetscFunctionReturn(0); 1207 } 1208 1209 PetscErrorCode DMPlexComputeBdResidual_Internal(DM dm, Vec locX, Vec locX_t, PetscReal t, Vec locF, void *user) 1210 { 1211 PetscDS prob; 1212 PetscInt numBd, bd; 1213 DMField coordField = NULL; 1214 IS facetIS = NULL; 1215 DMLabel depthLabel; 1216 PetscInt dim; 1217 PetscErrorCode ierr; 1218 1219 PetscFunctionBegin; 1220 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1221 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 1222 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1223 ierr = DMLabelGetStratumIS(depthLabel,dim - 1,&facetIS);CHKERRQ(ierr); 1224 ierr = PetscDSGetNumBoundary(prob, &numBd);CHKERRQ(ierr); 1225 for (bd = 0; bd < numBd; ++bd) { 1226 DMBoundaryConditionType type; 1227 const char *bdLabel; 1228 DMLabel label; 1229 const PetscInt *values; 1230 PetscInt field, numValues; 1231 PetscObject obj; 1232 PetscClassId id; 1233 1234 ierr = PetscDSGetBoundary(prob, bd, &type, NULL, &bdLabel, &field, NULL, NULL, NULL, &numValues, &values, NULL);CHKERRQ(ierr); 1235 ierr = PetscDSGetDiscretization(prob, field, &obj);CHKERRQ(ierr); 1236 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1237 if ((id != PETSCFE_CLASSID) || (type & DM_BC_ESSENTIAL)) continue; 1238 if (!facetIS) { 1239 DMLabel depthLabel; 1240 PetscInt dim; 1241 1242 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 1243 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1244 ierr = DMLabelGetStratumIS(depthLabel, dim - 1, &facetIS);CHKERRQ(ierr); 1245 } 1246 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 1247 ierr = DMGetLabel(dm, bdLabel, &label);CHKERRQ(ierr); 1248 ierr = DMPlexComputeBdResidual_Single_Internal(dm, t, label, numValues, values, field, locX, locX_t, locF, coordField, facetIS);CHKERRQ(ierr); 1249 } 1250 ierr = ISDestroy(&facetIS);CHKERRQ(ierr); 1251 PetscFunctionReturn(0); 1252 } 1253 1254 PetscErrorCode DMPlexComputeResidual_Internal(DM dm, IS cellIS, PetscReal time, Vec locX, Vec locX_t, PetscReal t, Vec locF, void *user) 1255 { 1256 DM_Plex *mesh = (DM_Plex *) dm->data; 1257 const char *name = "Residual"; 1258 DM dmAux = NULL; 1259 DM dmGrad = NULL; 1260 DMLabel ghostLabel = NULL; 1261 PetscDS prob = NULL; 1262 PetscDS probAux = NULL; 1263 PetscSection section = NULL; 1264 PetscBool useFEM = PETSC_FALSE; 1265 PetscBool useFVM = PETSC_FALSE; 1266 PetscBool isImplicit = (locX_t || time == PETSC_MIN_REAL) ? PETSC_TRUE : PETSC_FALSE; 1267 PetscFV fvm = NULL; 1268 PetscFVCellGeom *cgeomFVM = NULL; 1269 PetscFVFaceGeom *fgeomFVM = NULL; 1270 DMField coordField = NULL; 1271 Vec locA, cellGeometryFVM = NULL, faceGeometryFVM = NULL, grad, locGrad = NULL; 1272 PetscScalar *u = NULL, *u_t, *a, *uL, *uR; 1273 IS chunkIS; 1274 const PetscInt *cells; 1275 PetscInt cStart, cEnd, numCells; 1276 PetscInt Nf, f, totDim, totDimAux, numChunks, cellChunkSize, faceChunkSize, chunk, fStart, fEnd; 1277 PetscInt maxDegree = PETSC_MAX_INT; 1278 PetscQuadrature affineQuad = NULL, *quads = NULL; 1279 PetscFEGeom *affineGeom = NULL, **geoms = NULL; 1280 PetscErrorCode ierr; 1281 1282 PetscFunctionBegin; 1283 ierr = PetscLogEventBegin(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr); 1284 /* TODO The places where we have to use isFE are probably the member functions for the PetscDisc class */ 1285 /* TODO The FVM geometry is over-manipulated. Make the precalc functions return exactly what we need */ 1286 /* FEM+FVM */ 1287 ierr = ISGetPointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 1288 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 1289 /* 1: Get sizes from dm and dmAux */ 1290 ierr = DMGetSection(dm, §ion);CHKERRQ(ierr); 1291 ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 1292 ierr = DMGetCellDS(dm, cStart, &prob);CHKERRQ(ierr); 1293 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 1294 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1295 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);CHKERRQ(ierr); 1296 if (locA) { 1297 PetscInt subcell; 1298 ierr = DMPlexGetAuxiliaryPoint(dm, dmAux, cStart, &subcell);CHKERRQ(ierr); 1299 ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); 1300 ierr = DMGetCellDS(dmAux, subcell, &probAux);CHKERRQ(ierr); 1301 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 1302 } 1303 /* 2: Get geometric data */ 1304 for (f = 0; f < Nf; ++f) { 1305 PetscObject obj; 1306 PetscClassId id; 1307 PetscBool fimp; 1308 1309 ierr = PetscDSGetImplicit(prob, f, &fimp);CHKERRQ(ierr); 1310 if (isImplicit != fimp) continue; 1311 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1312 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1313 if (id == PETSCFE_CLASSID) {useFEM = PETSC_TRUE;} 1314 if (id == PETSCFV_CLASSID) {useFVM = PETSC_TRUE; fvm = (PetscFV) obj;} 1315 } 1316 if (useFEM) { 1317 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 1318 ierr = DMFieldGetDegree(coordField,cellIS,NULL,&maxDegree);CHKERRQ(ierr); 1319 if (maxDegree <= 1) { 1320 ierr = DMFieldCreateDefaultQuadrature(coordField,cellIS,&affineQuad);CHKERRQ(ierr); 1321 if (affineQuad) { 1322 ierr = DMSNESGetFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&affineGeom);CHKERRQ(ierr); 1323 } 1324 } else { 1325 ierr = PetscCalloc2(Nf,&quads,Nf,&geoms);CHKERRQ(ierr); 1326 for (f = 0; f < Nf; ++f) { 1327 PetscObject obj; 1328 PetscClassId id; 1329 PetscBool fimp; 1330 1331 ierr = PetscDSGetImplicit(prob, f, &fimp);CHKERRQ(ierr); 1332 if (isImplicit != fimp) continue; 1333 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1334 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1335 if (id == PETSCFE_CLASSID) { 1336 PetscFE fe = (PetscFE) obj; 1337 1338 ierr = PetscFEGetQuadrature(fe, &quads[f]);CHKERRQ(ierr); 1339 ierr = PetscObjectReference((PetscObject)quads[f]);CHKERRQ(ierr); 1340 ierr = DMSNESGetFEGeom(coordField,cellIS,quads[f],PETSC_FALSE,&geoms[f]);CHKERRQ(ierr); 1341 } 1342 } 1343 } 1344 } 1345 if (useFVM) { 1346 ierr = DMPlexSNESGetGeometryFVM(dm, &faceGeometryFVM, &cellGeometryFVM, NULL);CHKERRQ(ierr); 1347 ierr = VecGetArrayRead(faceGeometryFVM, (const PetscScalar **) &fgeomFVM);CHKERRQ(ierr); 1348 ierr = VecGetArrayRead(cellGeometryFVM, (const PetscScalar **) &cgeomFVM);CHKERRQ(ierr); 1349 /* Reconstruct and limit cell gradients */ 1350 ierr = DMPlexSNESGetGradientDM(dm, fvm, &dmGrad);CHKERRQ(ierr); 1351 if (dmGrad) { 1352 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 1353 ierr = DMGetGlobalVector(dmGrad, &grad);CHKERRQ(ierr); 1354 ierr = DMPlexReconstructGradients_Internal(dm, fvm, fStart, fEnd, faceGeometryFVM, cellGeometryFVM, locX, grad);CHKERRQ(ierr); 1355 /* Communicate gradient values */ 1356 ierr = DMGetLocalVector(dmGrad, &locGrad);CHKERRQ(ierr); 1357 ierr = DMGlobalToLocalBegin(dmGrad, grad, INSERT_VALUES, locGrad);CHKERRQ(ierr); 1358 ierr = DMGlobalToLocalEnd(dmGrad, grad, INSERT_VALUES, locGrad);CHKERRQ(ierr); 1359 ierr = DMRestoreGlobalVector(dmGrad, &grad);CHKERRQ(ierr); 1360 } 1361 /* Handle non-essential (e.g. outflow) boundary values */ 1362 ierr = DMPlexInsertBoundaryValues(dm, PETSC_FALSE, locX, time, faceGeometryFVM, cellGeometryFVM, locGrad);CHKERRQ(ierr); 1363 } 1364 /* Loop over chunks */ 1365 if (useFEM) {ierr = ISCreate(PETSC_COMM_SELF, &chunkIS);CHKERRQ(ierr);} 1366 numCells = cEnd - cStart; 1367 numChunks = 1; 1368 cellChunkSize = numCells/numChunks; 1369 faceChunkSize = (fEnd - fStart)/numChunks; 1370 numChunks = PetscMin(1,numCells); 1371 for (chunk = 0; chunk < numChunks; ++chunk) { 1372 PetscScalar *elemVec, *fluxL, *fluxR; 1373 PetscReal *vol; 1374 PetscFVFaceGeom *fgeom; 1375 PetscInt cS = cStart+chunk*cellChunkSize, cE = PetscMin(cS+cellChunkSize, cEnd), numCells = cE - cS, c; 1376 PetscInt fS = fStart+chunk*faceChunkSize, fE = PetscMin(fS+faceChunkSize, fEnd), numFaces = 0, face; 1377 1378 /* Extract field coefficients */ 1379 if (useFEM) { 1380 ierr = ISGetPointSubrange(chunkIS, cS, cE, cells);CHKERRQ(ierr); 1381 ierr = DMPlexGetCellFields(dm, chunkIS, locX, locX_t, locA, &u, &u_t, &a);CHKERRQ(ierr); 1382 ierr = DMGetWorkArray(dm, numCells*totDim, MPIU_SCALAR, &elemVec);CHKERRQ(ierr); 1383 ierr = PetscMemzero(elemVec, numCells*totDim * sizeof(PetscScalar));CHKERRQ(ierr); 1384 } 1385 if (useFVM) { 1386 ierr = DMPlexGetFaceFields(dm, fS, fE, locX, locX_t, faceGeometryFVM, cellGeometryFVM, locGrad, &numFaces, &uL, &uR);CHKERRQ(ierr); 1387 ierr = DMPlexGetFaceGeometry(dm, fS, fE, faceGeometryFVM, cellGeometryFVM, &numFaces, &fgeom, &vol);CHKERRQ(ierr); 1388 ierr = DMGetWorkArray(dm, numFaces*totDim, MPIU_SCALAR, &fluxL);CHKERRQ(ierr); 1389 ierr = DMGetWorkArray(dm, numFaces*totDim, MPIU_SCALAR, &fluxR);CHKERRQ(ierr); 1390 ierr = PetscMemzero(fluxL, numFaces*totDim * sizeof(PetscScalar));CHKERRQ(ierr); 1391 ierr = PetscMemzero(fluxR, numFaces*totDim * sizeof(PetscScalar));CHKERRQ(ierr); 1392 } 1393 /* TODO We will interlace both our field coefficients (u, u_t, uL, uR, etc.) and our output (elemVec, fL, fR). I think this works */ 1394 /* Loop over fields */ 1395 for (f = 0; f < Nf; ++f) { 1396 PetscObject obj; 1397 PetscClassId id; 1398 PetscBool fimp; 1399 PetscInt numChunks, numBatches, batchSize, numBlocks, blockSize, Ne, Nr, offset; 1400 1401 ierr = PetscDSGetImplicit(prob, f, &fimp);CHKERRQ(ierr); 1402 if (isImplicit != fimp) continue; 1403 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1404 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1405 if (id == PETSCFE_CLASSID) { 1406 PetscFE fe = (PetscFE) obj; 1407 PetscFEGeom *geom = affineGeom ? affineGeom : geoms[f]; 1408 PetscFEGeom *chunkGeom = NULL; 1409 PetscQuadrature quad = affineQuad ? affineQuad : quads[f]; 1410 PetscInt Nq, Nb; 1411 1412 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1413 ierr = PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 1414 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 1415 blockSize = Nb; 1416 batchSize = numBlocks * blockSize; 1417 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1418 numChunks = numCells / (numBatches*batchSize); 1419 Ne = numChunks*numBatches*batchSize; 1420 Nr = numCells % (numBatches*batchSize); 1421 offset = numCells - Nr; 1422 /* Integrate FE residual to get elemVec (need fields at quadrature points) */ 1423 /* 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) */ 1424 ierr = PetscFEGeomGetChunk(geom,0,offset,&chunkGeom);CHKERRQ(ierr); 1425 ierr = PetscFEIntegrateResidual(fe, prob, f, Ne, chunkGeom, u, u_t, probAux, a, t, elemVec);CHKERRQ(ierr); 1426 ierr = PetscFEGeomGetChunk(geom,offset,numCells,&chunkGeom);CHKERRQ(ierr); 1427 ierr = PetscFEIntegrateResidual(fe, prob, f, Nr, chunkGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, &elemVec[offset*totDim]);CHKERRQ(ierr); 1428 ierr = PetscFEGeomRestoreChunk(geom,offset,numCells,&chunkGeom);CHKERRQ(ierr); 1429 } else if (id == PETSCFV_CLASSID) { 1430 PetscFV fv = (PetscFV) obj; 1431 1432 Ne = numFaces; 1433 /* Riemann solve over faces (need fields at face centroids) */ 1434 /* We need to evaluate FE fields at those coordinates */ 1435 ierr = PetscFVIntegrateRHSFunction(fv, prob, f, Ne, fgeom, vol, uL, uR, fluxL, fluxR);CHKERRQ(ierr); 1436 } else SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %d", f); 1437 } 1438 /* Loop over domain */ 1439 if (useFEM) { 1440 /* Add elemVec to locX */ 1441 for (c = cS; c < cE; ++c) { 1442 const PetscInt cell = cells ? cells[c] : c; 1443 const PetscInt cind = c - cStart; 1444 1445 if (mesh->printFEM > 1) {ierr = DMPrintCellVector(cell, name, totDim, &elemVec[cind*totDim]);CHKERRQ(ierr);} 1446 if (ghostLabel) { 1447 PetscInt ghostVal; 1448 1449 ierr = DMLabelGetValue(ghostLabel,cell,&ghostVal);CHKERRQ(ierr); 1450 if (ghostVal > 0) continue; 1451 } 1452 ierr = DMPlexVecSetClosure(dm, section, locF, cell, &elemVec[cind*totDim], ADD_ALL_VALUES);CHKERRQ(ierr); 1453 } 1454 } 1455 if (useFVM) { 1456 PetscScalar *fa; 1457 PetscInt iface; 1458 1459 ierr = VecGetArray(locF, &fa);CHKERRQ(ierr); 1460 for (f = 0; f < Nf; ++f) { 1461 PetscFV fv; 1462 PetscObject obj; 1463 PetscClassId id; 1464 PetscInt foff, pdim; 1465 1466 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1467 ierr = PetscDSGetFieldOffset(prob, f, &foff);CHKERRQ(ierr); 1468 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1469 if (id != PETSCFV_CLASSID) continue; 1470 fv = (PetscFV) obj; 1471 ierr = PetscFVGetNumComponents(fv, &pdim);CHKERRQ(ierr); 1472 /* Accumulate fluxes to cells */ 1473 for (face = fS, iface = 0; face < fE; ++face) { 1474 const PetscInt *scells; 1475 PetscScalar *fL = NULL, *fR = NULL; 1476 PetscInt ghost, d, nsupp, nchild; 1477 1478 ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr); 1479 ierr = DMPlexGetSupportSize(dm, face, &nsupp);CHKERRQ(ierr); 1480 ierr = DMPlexGetTreeChildren(dm, face, &nchild, NULL);CHKERRQ(ierr); 1481 if (ghost >= 0 || nsupp > 2 || nchild > 0) continue; 1482 ierr = DMPlexGetSupport(dm, face, &scells);CHKERRQ(ierr); 1483 ierr = DMLabelGetValue(ghostLabel,scells[0],&ghost);CHKERRQ(ierr); 1484 if (ghost <= 0) {ierr = DMPlexPointLocalFieldRef(dm, scells[0], f, fa, &fL);CHKERRQ(ierr);} 1485 ierr = DMLabelGetValue(ghostLabel,scells[1],&ghost);CHKERRQ(ierr); 1486 if (ghost <= 0) {ierr = DMPlexPointLocalFieldRef(dm, scells[1], f, fa, &fR);CHKERRQ(ierr);} 1487 for (d = 0; d < pdim; ++d) { 1488 if (fL) fL[d] -= fluxL[iface*totDim+foff+d]; 1489 if (fR) fR[d] += fluxR[iface*totDim+foff+d]; 1490 } 1491 ++iface; 1492 } 1493 } 1494 ierr = VecRestoreArray(locF, &fa);CHKERRQ(ierr); 1495 } 1496 /* Handle time derivative */ 1497 if (locX_t) { 1498 PetscScalar *x_t, *fa; 1499 1500 ierr = VecGetArray(locF, &fa);CHKERRQ(ierr); 1501 ierr = VecGetArray(locX_t, &x_t);CHKERRQ(ierr); 1502 for (f = 0; f < Nf; ++f) { 1503 PetscFV fv; 1504 PetscObject obj; 1505 PetscClassId id; 1506 PetscInt pdim, d; 1507 1508 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1509 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1510 if (id != PETSCFV_CLASSID) continue; 1511 fv = (PetscFV) obj; 1512 ierr = PetscFVGetNumComponents(fv, &pdim);CHKERRQ(ierr); 1513 for (c = cS; c < cE; ++c) { 1514 const PetscInt cell = cells ? cells[c] : c; 1515 PetscScalar *u_t, *r; 1516 1517 if (ghostLabel) { 1518 PetscInt ghostVal; 1519 1520 ierr = DMLabelGetValue(ghostLabel, cell, &ghostVal);CHKERRQ(ierr); 1521 if (ghostVal > 0) continue; 1522 } 1523 ierr = DMPlexPointLocalFieldRead(dm, cell, f, x_t, &u_t);CHKERRQ(ierr); 1524 ierr = DMPlexPointLocalFieldRef(dm, cell, f, fa, &r);CHKERRQ(ierr); 1525 for (d = 0; d < pdim; ++d) r[d] += u_t[d]; 1526 } 1527 } 1528 ierr = VecRestoreArray(locX_t, &x_t);CHKERRQ(ierr); 1529 ierr = VecRestoreArray(locF, &fa);CHKERRQ(ierr); 1530 } 1531 if (useFEM) { 1532 ierr = DMPlexRestoreCellFields(dm, chunkIS, locX, locX_t, locA, &u, &u_t, &a);CHKERRQ(ierr); 1533 ierr = DMRestoreWorkArray(dm, numCells*totDim, MPIU_SCALAR, &elemVec);CHKERRQ(ierr); 1534 } 1535 if (useFVM) { 1536 ierr = DMPlexRestoreFaceFields(dm, fS, fE, locX, locX_t, faceGeometryFVM, cellGeometryFVM, locGrad, &numFaces, &uL, &uR);CHKERRQ(ierr); 1537 ierr = DMPlexRestoreFaceGeometry(dm, fS, fE, faceGeometryFVM, cellGeometryFVM, &numFaces, &fgeom, &vol);CHKERRQ(ierr); 1538 ierr = DMRestoreWorkArray(dm, numFaces*totDim, MPIU_SCALAR, &fluxL);CHKERRQ(ierr); 1539 ierr = DMRestoreWorkArray(dm, numFaces*totDim, MPIU_SCALAR, &fluxR);CHKERRQ(ierr); 1540 if (dmGrad) {ierr = DMRestoreLocalVector(dmGrad, &locGrad);CHKERRQ(ierr);} 1541 } 1542 } 1543 if (useFEM) {ierr = ISDestroy(&chunkIS);CHKERRQ(ierr);} 1544 ierr = ISRestorePointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 1545 1546 if (useFEM) { 1547 ierr = DMPlexComputeBdResidual_Internal(dm, locX, locX_t, t, locF, user);CHKERRQ(ierr); 1548 1549 if (maxDegree <= 1) { 1550 ierr = DMSNESRestoreFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&affineGeom);CHKERRQ(ierr); 1551 ierr = PetscQuadratureDestroy(&affineQuad);CHKERRQ(ierr); 1552 } else { 1553 for (f = 0; f < Nf; ++f) { 1554 ierr = DMSNESRestoreFEGeom(coordField,cellIS,quads[f],PETSC_FALSE,&geoms[f]);CHKERRQ(ierr); 1555 ierr = PetscQuadratureDestroy(&quads[f]);CHKERRQ(ierr); 1556 } 1557 ierr = PetscFree2(quads,geoms);CHKERRQ(ierr); 1558 } 1559 } 1560 1561 /* FEM */ 1562 /* 1: Get sizes from dm and dmAux */ 1563 /* 2: Get geometric data */ 1564 /* 3: Handle boundary values */ 1565 /* 4: Loop over domain */ 1566 /* Extract coefficients */ 1567 /* Loop over fields */ 1568 /* Set tiling for FE*/ 1569 /* Integrate FE residual to get elemVec */ 1570 /* Loop over subdomain */ 1571 /* Loop over quad points */ 1572 /* Transform coords to real space */ 1573 /* Evaluate field and aux fields at point */ 1574 /* Evaluate residual at point */ 1575 /* Transform residual to real space */ 1576 /* Add residual to elemVec */ 1577 /* Loop over domain */ 1578 /* Add elemVec to locX */ 1579 1580 /* FVM */ 1581 /* Get geometric data */ 1582 /* If using gradients */ 1583 /* Compute gradient data */ 1584 /* Loop over domain faces */ 1585 /* Count computational faces */ 1586 /* Reconstruct cell gradient */ 1587 /* Loop over domain cells */ 1588 /* Limit cell gradients */ 1589 /* Handle boundary values */ 1590 /* Loop over domain faces */ 1591 /* Read out field, centroid, normal, volume for each side of face */ 1592 /* Riemann solve over faces */ 1593 /* Loop over domain faces */ 1594 /* Accumulate fluxes to cells */ 1595 /* TODO Change printFEM to printDisc here */ 1596 if (mesh->printFEM) { 1597 Vec locFbc; 1598 PetscInt pStart, pEnd, p, maxDof; 1599 PetscScalar *zeroes; 1600 1601 ierr = VecDuplicate(locF,&locFbc);CHKERRQ(ierr); 1602 ierr = VecCopy(locF,locFbc);CHKERRQ(ierr); 1603 ierr = PetscSectionGetChart(section,&pStart,&pEnd);CHKERRQ(ierr); 1604 ierr = PetscSectionGetMaxDof(section,&maxDof);CHKERRQ(ierr); 1605 ierr = PetscCalloc1(maxDof,&zeroes);CHKERRQ(ierr); 1606 for (p = pStart; p < pEnd; p++) { 1607 ierr = VecSetValuesSection(locFbc,section,p,zeroes,INSERT_BC_VALUES);CHKERRQ(ierr); 1608 } 1609 ierr = PetscFree(zeroes);CHKERRQ(ierr); 1610 ierr = DMPrintLocalVec(dm, name, mesh->printTol, locFbc);CHKERRQ(ierr); 1611 ierr = VecDestroy(&locFbc);CHKERRQ(ierr); 1612 } 1613 ierr = PetscLogEventEnd(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr); 1614 PetscFunctionReturn(0); 1615 } 1616 1617 static PetscErrorCode DMPlexComputeResidualFEM_Check_Internal(DM dm, Vec X, Vec X_t, PetscReal t, Vec F, void *user) 1618 { 1619 DM dmCh, dmAux; 1620 Vec A; 1621 DMField coordField = NULL; 1622 PetscDS prob, probCh, probAux = NULL; 1623 PetscSection section, sectionAux; 1624 PetscScalar *elemVec, *elemVecCh, *u, *u_t, *a = NULL; 1625 PetscInt Nf, f, numCells, cStart, cEnd, c; 1626 PetscInt totDim, totDimAux = 0, diffCell = 0; 1627 PetscInt depth; 1628 PetscInt maxDegree; 1629 IS cellIS; 1630 DMLabel depthLabel; 1631 PetscErrorCode ierr; 1632 1633 PetscFunctionBegin; 1634 ierr = DMGetSection(dm, §ion);CHKERRQ(ierr); 1635 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1636 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1637 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); 1638 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1639 numCells = cEnd - cStart; 1640 ierr = PetscObjectQuery((PetscObject) dm, "dmCh", (PetscObject *) &dmCh);CHKERRQ(ierr); 1641 ierr = DMGetDS(dmCh, &probCh);CHKERRQ(ierr); 1642 ierr = PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);CHKERRQ(ierr); 1643 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);CHKERRQ(ierr); 1644 if (dmAux) { 1645 ierr = DMGetSection(dmAux, §ionAux);CHKERRQ(ierr); 1646 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 1647 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 1648 } 1649 ierr = VecSet(F, 0.0);CHKERRQ(ierr); 1650 ierr = PetscMalloc3(numCells*totDim,&u,X_t ? numCells*totDim : 0,&u_t,numCells*totDim,&elemVec);CHKERRQ(ierr); 1651 ierr = PetscMalloc1(numCells*totDim,&elemVecCh);CHKERRQ(ierr); 1652 if (dmAux) {ierr = PetscMalloc1(numCells*totDimAux, &a);CHKERRQ(ierr);} 1653 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 1654 ierr = DMPlexGetDepth(dm,&depth);CHKERRQ(ierr); 1655 ierr = DMLabelGetStratumIS(depthLabel,depth,&cellIS);CHKERRQ(ierr); 1656 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 1657 for (c = cStart; c < cEnd; ++c) { 1658 PetscScalar *x = NULL, *x_t = NULL; 1659 PetscInt i; 1660 1661 ierr = DMPlexVecGetClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr); 1662 for (i = 0; i < totDim; ++i) u[c*totDim+i] = x[i]; 1663 ierr = DMPlexVecRestoreClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr); 1664 if (X_t) { 1665 ierr = DMPlexVecGetClosure(dm, section, X_t, c, NULL, &x_t);CHKERRQ(ierr); 1666 for (i = 0; i < totDim; ++i) u_t[c*totDim+i] = x_t[i]; 1667 ierr = DMPlexVecRestoreClosure(dm, section, X_t, c, NULL, &x_t);CHKERRQ(ierr); 1668 } 1669 if (dmAux) { 1670 DM dmAuxPlex; 1671 1672 ierr = DMSNESConvertPlex(dmAux,&dmAuxPlex, PETSC_FALSE);CHKERRQ(ierr); 1673 ierr = DMPlexVecGetClosure(dmAuxPlex, sectionAux, A, c, NULL, &x);CHKERRQ(ierr); 1674 for (i = 0; i < totDimAux; ++i) a[c*totDimAux+i] = x[i]; 1675 ierr = DMPlexVecRestoreClosure(dmAuxPlex, sectionAux, A, c, NULL, &x);CHKERRQ(ierr); 1676 ierr = DMDestroy(&dmAuxPlex);CHKERRQ(ierr); 1677 } 1678 } 1679 for (f = 0; f < Nf; ++f) { 1680 PetscFE fe, feCh; 1681 PetscInt Nq, Nb; 1682 /* Conforming batches */ 1683 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 1684 /* Remainder */ 1685 PetscInt Nr, offset; 1686 PetscQuadrature qGeom = NULL; 1687 PetscFEGeom *cgeomFEM, *chunkGeom = NULL; 1688 1689 ierr = PetscDSGetDiscretization(prob, f, (PetscObject *) &fe);CHKERRQ(ierr); 1690 ierr = PetscDSGetDiscretization(probCh, f, (PetscObject *) &feCh);CHKERRQ(ierr); 1691 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 1692 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1693 ierr = DMFieldGetDegree(coordField,cellIS,NULL,&maxDegree);CHKERRQ(ierr); 1694 if (maxDegree <= 1) { 1695 ierr = DMFieldCreateDefaultQuadrature(coordField,cellIS,&qGeom);CHKERRQ(ierr); 1696 } 1697 if (!qGeom) { 1698 ierr = PetscFEGetQuadrature(fe, &qGeom);CHKERRQ(ierr); 1699 ierr = PetscObjectReference((PetscObject)qGeom);CHKERRQ(ierr); 1700 } 1701 ierr = PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 1702 ierr = DMSNESGetFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);CHKERRQ(ierr); 1703 blockSize = Nb; 1704 batchSize = numBlocks * blockSize; 1705 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1706 numChunks = numCells / (numBatches*batchSize); 1707 Ne = numChunks*numBatches*batchSize; 1708 Nr = numCells % (numBatches*batchSize); 1709 offset = numCells - Nr; 1710 ierr = PetscFEGeomGetChunk(cgeomFEM,0,offset,&chunkGeom);CHKERRQ(ierr); 1711 ierr = PetscFEIntegrateResidual(fe, prob, f, Ne, chunkGeom, u, u_t, probAux, a, t, elemVec);CHKERRQ(ierr); 1712 ierr = PetscFEIntegrateResidual(feCh, prob, f, Ne, chunkGeom, u, u_t, probAux, a, t, elemVecCh);CHKERRQ(ierr); 1713 ierr = PetscFEGeomGetChunk(cgeomFEM,offset,numCells,&chunkGeom);CHKERRQ(ierr); 1714 ierr = PetscFEIntegrateResidual(fe, prob, f, Nr, chunkGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, &elemVec[offset*totDim]);CHKERRQ(ierr); 1715 ierr = PetscFEIntegrateResidual(feCh, prob, f, Nr, chunkGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, &elemVecCh[offset*totDim]);CHKERRQ(ierr); 1716 ierr = PetscFEGeomRestoreChunk(cgeomFEM,offset,numCells,&chunkGeom);CHKERRQ(ierr); 1717 ierr = DMSNESRestoreFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);CHKERRQ(ierr); 1718 ierr = PetscQuadratureDestroy(&qGeom);CHKERRQ(ierr); 1719 } 1720 ierr = ISDestroy(&cellIS);CHKERRQ(ierr); 1721 for (c = cStart; c < cEnd; ++c) { 1722 PetscBool diff = PETSC_FALSE; 1723 PetscInt d; 1724 1725 for (d = 0; d < totDim; ++d) if (PetscAbsScalar(elemVec[c*totDim+d] - elemVecCh[c*totDim+d]) > 1.0e-7) {diff = PETSC_TRUE;break;} 1726 if (diff) { 1727 ierr = PetscPrintf(PetscObjectComm((PetscObject) dm), "Different cell %d\n", c);CHKERRQ(ierr); 1728 ierr = DMPrintCellVector(c, "Residual", totDim, &elemVec[c*totDim]);CHKERRQ(ierr); 1729 ierr = DMPrintCellVector(c, "Check Residual", totDim, &elemVecCh[c*totDim]);CHKERRQ(ierr); 1730 ++diffCell; 1731 } 1732 if (diffCell > 9) break; 1733 ierr = DMPlexVecSetClosure(dm, section, F, c, &elemVec[c*totDim], ADD_ALL_VALUES);CHKERRQ(ierr); 1734 } 1735 ierr = PetscFree3(u,u_t,elemVec);CHKERRQ(ierr); 1736 ierr = PetscFree(elemVecCh);CHKERRQ(ierr); 1737 if (dmAux) {ierr = PetscFree(a);CHKERRQ(ierr);} 1738 PetscFunctionReturn(0); 1739 } 1740 1741 /*@ 1742 DMPlexSNESComputeResidualFEM - Form the local residual F from the local input X using pointwise functions specified by the user 1743 1744 Input Parameters: 1745 + dm - The mesh 1746 . X - Local solution 1747 - user - The user context 1748 1749 Output Parameter: 1750 . F - Local output vector 1751 1752 Level: developer 1753 1754 .seealso: DMPlexComputeJacobianAction() 1755 @*/ 1756 PetscErrorCode DMPlexSNESComputeResidualFEM(DM dm, Vec X, Vec F, void *user) 1757 { 1758 PetscObject check; 1759 DM plex; 1760 IS cellIS; 1761 PetscInt depth; 1762 PetscErrorCode ierr; 1763 1764 PetscFunctionBegin; 1765 ierr = DMSNESConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr); 1766 ierr = DMPlexGetDepth(plex, &depth);CHKERRQ(ierr); 1767 ierr = DMGetStratumIS(plex, "dim", depth, &cellIS);CHKERRQ(ierr); 1768 if (!cellIS) { 1769 ierr = DMGetStratumIS(plex, "depth", depth, &cellIS);CHKERRQ(ierr); 1770 } 1771 /* The dmCh is used to check two mathematically equivalent discretizations for computational equivalence */ 1772 ierr = PetscObjectQuery((PetscObject) plex, "dmCh", &check);CHKERRQ(ierr); 1773 if (check) {ierr = DMPlexComputeResidualFEM_Check_Internal(plex, X, NULL, 0.0, F, user);CHKERRQ(ierr);} 1774 else {ierr = DMPlexComputeResidual_Internal(plex, cellIS, PETSC_MIN_REAL, X, NULL, 0.0, F, user);CHKERRQ(ierr);} 1775 ierr = ISDestroy(&cellIS);CHKERRQ(ierr); 1776 ierr = DMDestroy(&plex);CHKERRQ(ierr); 1777 PetscFunctionReturn(0); 1778 } 1779 1780 /*@ 1781 DMPlexSNESComputeBoundaryFEM - Form the boundary values for the local input X 1782 1783 Input Parameters: 1784 + dm - The mesh 1785 - user - The user context 1786 1787 Output Parameter: 1788 . X - Local solution 1789 1790 Level: developer 1791 1792 .seealso: DMPlexComputeJacobianAction() 1793 @*/ 1794 PetscErrorCode DMPlexSNESComputeBoundaryFEM(DM dm, Vec X, void *user) 1795 { 1796 DM plex; 1797 PetscErrorCode ierr; 1798 1799 PetscFunctionBegin; 1800 ierr = DMSNESConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr); 1801 ierr = DMPlexInsertBoundaryValues(plex, PETSC_TRUE, X, PETSC_MIN_REAL, NULL, NULL, NULL);CHKERRQ(ierr); 1802 ierr = DMDestroy(&plex);CHKERRQ(ierr); 1803 PetscFunctionReturn(0); 1804 } 1805 1806 PetscErrorCode DMPlexComputeBdJacobian_Single_Internal(DM dm, PetscReal t, 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) 1807 { 1808 DM_Plex *mesh = (DM_Plex *) dm->data; 1809 DM plex = NULL, plexA = NULL; 1810 PetscDS prob, probAux = NULL; 1811 PetscSection section, sectionAux = NULL; 1812 PetscSection globalSection, subSection = NULL; 1813 Vec locA = NULL; 1814 PetscScalar *u = NULL, *u_t = NULL, *a = NULL, *elemMat = NULL; 1815 PetscInt v; 1816 PetscInt Nf, totDim, totDimAux = 0; 1817 PetscBool isMatISP; 1818 PetscErrorCode ierr; 1819 1820 PetscFunctionBegin; 1821 ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); 1822 ierr = DMGetSection(dm, §ion);CHKERRQ(ierr); 1823 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1824 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 1825 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1826 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);CHKERRQ(ierr); 1827 if (locA) { 1828 DM dmAux; 1829 1830 ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); 1831 ierr = DMConvert(dmAux, DMPLEX, &plexA);CHKERRQ(ierr); 1832 ierr = DMGetDS(plexA, &probAux);CHKERRQ(ierr); 1833 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 1834 ierr = DMGetSection(plexA, §ionAux);CHKERRQ(ierr); 1835 } 1836 1837 ierr = PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatISP);CHKERRQ(ierr); 1838 ierr = DMGetGlobalSection(dm, &globalSection);CHKERRQ(ierr); 1839 if (isMatISP) {ierr = DMPlexGetSubdomainSection(dm, &subSection);CHKERRQ(ierr);} 1840 for (v = 0; v < numValues; ++v) { 1841 PetscFEGeom *fgeom; 1842 PetscInt maxDegree; 1843 PetscQuadrature qGeom = NULL; 1844 IS pointIS; 1845 const PetscInt *points; 1846 PetscInt numFaces, face, Nq; 1847 1848 ierr = DMLabelGetStratumIS(label, values[v], &pointIS);CHKERRQ(ierr); 1849 if (!pointIS) continue; /* No points with that id on this process */ 1850 { 1851 IS isectIS; 1852 1853 /* TODO: Special cases of ISIntersect where it is quick to check a prior if one is a superset of the other */ 1854 ierr = ISIntersect_Caching_Internal(facetIS,pointIS,&isectIS);CHKERRQ(ierr); 1855 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 1856 pointIS = isectIS; 1857 } 1858 ierr = ISGetLocalSize(pointIS, &numFaces);CHKERRQ(ierr); 1859 ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); 1860 ierr = PetscMalloc4(numFaces*totDim, &u, locX_t ? numFaces*totDim : 0, &u_t, numFaces*totDim*totDim, &elemMat, locA ? numFaces*totDimAux : 0, &a);CHKERRQ(ierr); 1861 ierr = DMFieldGetDegree(coordField,pointIS,NULL,&maxDegree);CHKERRQ(ierr); 1862 if (maxDegree <= 1) { 1863 ierr = DMFieldCreateDefaultQuadrature(coordField,pointIS,&qGeom);CHKERRQ(ierr); 1864 } 1865 if (!qGeom) { 1866 PetscFE fe; 1867 1868 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); 1869 ierr = PetscFEGetFaceQuadrature(fe, &qGeom);CHKERRQ(ierr); 1870 ierr = PetscObjectReference((PetscObject)qGeom);CHKERRQ(ierr); 1871 } 1872 ierr = PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 1873 ierr = DMSNESGetFEGeom(coordField,pointIS,qGeom,PETSC_TRUE,&fgeom);CHKERRQ(ierr); 1874 for (face = 0; face < numFaces; ++face) { 1875 const PetscInt point = points[face], *support, *cone; 1876 PetscScalar *x = NULL; 1877 PetscInt i, coneSize, faceLoc; 1878 1879 ierr = DMPlexGetSupport(dm, point, &support);CHKERRQ(ierr); 1880 ierr = DMPlexGetConeSize(dm, support[0], &coneSize);CHKERRQ(ierr); 1881 ierr = DMPlexGetCone(dm, support[0], &cone);CHKERRQ(ierr); 1882 for (faceLoc = 0; faceLoc < coneSize; ++faceLoc) if (cone[faceLoc] == point) break; 1883 if (faceLoc == coneSize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Could not find face %d in cone of support[0] %d", point, support[0]); 1884 fgeom->face[face][0] = faceLoc; 1885 ierr = DMPlexVecGetClosure(plex, section, locX, support[0], NULL, &x);CHKERRQ(ierr); 1886 for (i = 0; i < totDim; ++i) u[face*totDim+i] = x[i]; 1887 ierr = DMPlexVecRestoreClosure(plex, section, locX, support[0], NULL, &x);CHKERRQ(ierr); 1888 if (locX_t) { 1889 ierr = DMPlexVecGetClosure(plex, section, locX_t, support[0], NULL, &x);CHKERRQ(ierr); 1890 for (i = 0; i < totDim; ++i) u_t[face*totDim+i] = x[i]; 1891 ierr = DMPlexVecRestoreClosure(plex, section, locX_t, support[0], NULL, &x);CHKERRQ(ierr); 1892 } 1893 if (locA) { 1894 PetscInt subp; 1895 ierr = DMPlexGetSubpoint(plexA, support[0], &subp);CHKERRQ(ierr); 1896 ierr = DMPlexVecGetClosure(plexA, sectionAux, locA, subp, NULL, &x);CHKERRQ(ierr); 1897 for (i = 0; i < totDimAux; ++i) a[face*totDimAux+i] = x[i]; 1898 ierr = DMPlexVecRestoreClosure(plexA, sectionAux, locA, subp, NULL, &x);CHKERRQ(ierr); 1899 } 1900 } 1901 ierr = PetscMemzero(elemMat, numFaces*totDim*totDim * sizeof(PetscScalar));CHKERRQ(ierr); 1902 { 1903 PetscFE fe; 1904 PetscInt Nb; 1905 /* Conforming batches */ 1906 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 1907 /* Remainder */ 1908 PetscFEGeom *chunkGeom = NULL; 1909 PetscInt fieldJ, Nr, offset; 1910 1911 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); 1912 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 1913 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1914 blockSize = Nb; 1915 batchSize = numBlocks * blockSize; 1916 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1917 numChunks = numFaces / (numBatches*batchSize); 1918 Ne = numChunks*numBatches*batchSize; 1919 Nr = numFaces % (numBatches*batchSize); 1920 offset = numFaces - Nr; 1921 ierr = PetscFEGeomGetChunk(fgeom,0,offset,&chunkGeom);CHKERRQ(ierr); 1922 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 1923 ierr = PetscFEIntegrateBdJacobian(fe, prob, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMat);CHKERRQ(ierr); 1924 } 1925 ierr = PetscFEGeomGetChunk(fgeom,offset,numFaces,&chunkGeom);CHKERRQ(ierr); 1926 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 1927 ierr = PetscFEIntegrateBdJacobian(fe, prob, fieldI, fieldJ, 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); 1928 } 1929 ierr = PetscFEGeomRestoreChunk(fgeom,offset,numFaces,&chunkGeom);CHKERRQ(ierr); 1930 } 1931 for (face = 0; face < numFaces; ++face) { 1932 const PetscInt point = points[face], *support; 1933 1934 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(point, "BdJacobian", totDim, totDim, &elemMat[face*totDim*totDim]);CHKERRQ(ierr);} 1935 ierr = DMPlexGetSupport(plex, point, &support);CHKERRQ(ierr); 1936 if (!isMatISP) { 1937 ierr = DMPlexMatSetClosure(plex, section, globalSection, JacP, support[0], &elemMat[face*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 1938 } else { 1939 Mat lJ; 1940 1941 ierr = MatISGetLocalMat(JacP, &lJ);CHKERRQ(ierr); 1942 ierr = DMPlexMatSetClosure(plex, section, subSection, lJ, support[0], &elemMat[face*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 1943 } 1944 } 1945 ierr = DMSNESRestoreFEGeom(coordField,pointIS,qGeom,PETSC_TRUE,&fgeom);CHKERRQ(ierr); 1946 ierr = PetscQuadratureDestroy(&qGeom);CHKERRQ(ierr); 1947 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 1948 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 1949 ierr = PetscFree4(u, u_t, elemMat, a);CHKERRQ(ierr); 1950 } 1951 if (plex) {ierr = DMDestroy(&plex);CHKERRQ(ierr);} 1952 if (plexA) {ierr = DMDestroy(&plexA);CHKERRQ(ierr);} 1953 PetscFunctionReturn(0); 1954 } 1955 1956 PetscErrorCode DMPlexComputeBdJacobianSingle(DM dm, PetscReal t, DMLabel label, PetscInt numValues, const PetscInt values[], PetscInt field, Vec locX, Vec locX_t, PetscReal X_tShift, Mat Jac, Mat JacP) 1957 { 1958 DMField coordField; 1959 DMLabel depthLabel; 1960 IS facetIS; 1961 PetscInt dim; 1962 PetscErrorCode ierr; 1963 1964 PetscFunctionBegin; 1965 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1966 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 1967 ierr = DMLabelGetStratumIS(depthLabel, dim-1, &facetIS);CHKERRQ(ierr); 1968 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 1969 ierr = DMPlexComputeBdJacobian_Single_Internal(dm, t, label, numValues, values, field, locX, locX_t, X_tShift, Jac, JacP, coordField, facetIS);CHKERRQ(ierr); 1970 PetscFunctionReturn(0); 1971 } 1972 1973 PetscErrorCode DMPlexComputeBdJacobian_Internal(DM dm, Vec locX, Vec locX_t, PetscReal t, PetscReal X_tShift, Mat Jac, Mat JacP, void *user) 1974 { 1975 PetscDS prob; 1976 PetscInt dim, numBd, bd; 1977 DMLabel depthLabel; 1978 DMField coordField = NULL; 1979 IS facetIS; 1980 PetscErrorCode ierr; 1981 1982 PetscFunctionBegin; 1983 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1984 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 1985 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1986 ierr = DMLabelGetStratumIS(depthLabel, dim-1, &facetIS);CHKERRQ(ierr); 1987 ierr = PetscDSGetNumBoundary(prob, &numBd);CHKERRQ(ierr); 1988 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 1989 for (bd = 0; bd < numBd; ++bd) { 1990 DMBoundaryConditionType type; 1991 const char *bdLabel; 1992 DMLabel label; 1993 const PetscInt *values; 1994 PetscInt fieldI, numValues; 1995 PetscObject obj; 1996 PetscClassId id; 1997 1998 ierr = PetscDSGetBoundary(prob, bd, &type, NULL, &bdLabel, &fieldI, NULL, NULL, NULL, &numValues, &values, NULL);CHKERRQ(ierr); 1999 ierr = PetscDSGetDiscretization(prob, fieldI, &obj);CHKERRQ(ierr); 2000 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 2001 if ((id != PETSCFE_CLASSID) || (type & DM_BC_ESSENTIAL)) continue; 2002 ierr = DMGetLabel(dm, bdLabel, &label);CHKERRQ(ierr); 2003 ierr = DMPlexComputeBdJacobian_Single_Internal(dm, t, label, numValues, values, fieldI, locX, locX_t, X_tShift, Jac, JacP, coordField, facetIS);CHKERRQ(ierr); 2004 } 2005 ierr = ISDestroy(&facetIS);CHKERRQ(ierr); 2006 PetscFunctionReturn(0); 2007 } 2008 2009 PetscErrorCode DMPlexComputeJacobian_Internal(DM dm, IS cellIS, PetscReal t, PetscReal X_tShift, Vec X, Vec X_t, Mat Jac, Mat JacP,void *user) 2010 { 2011 DM_Plex *mesh = (DM_Plex *) dm->data; 2012 const char *name = "Jacobian"; 2013 DM dmAux, plex; 2014 Vec A; 2015 DMField coordField; 2016 PetscDS prob, probAux = NULL; 2017 PetscSection section, globalSection, subSection, sectionAux; 2018 PetscScalar *elemMat, *elemMatP, *elemMatD, *u, *u_t, *a = NULL; 2019 const PetscInt *cells; 2020 PetscInt Nf, fieldI, fieldJ; 2021 PetscInt totDim, totDimAux, cStart, cEnd, numCells, c; 2022 PetscBool isMatIS, isMatISP, hasJac, hasPrec, hasDyn, hasFV = PETSC_FALSE; 2023 PetscErrorCode ierr; 2024 2025 PetscFunctionBegin; 2026 ierr = PetscLogEventBegin(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 2027 ierr = DMGetSection(dm, §ion);CHKERRQ(ierr); 2028 ierr = PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatISP);CHKERRQ(ierr); 2029 ierr = DMGetGlobalSection(dm, &globalSection);CHKERRQ(ierr); 2030 if (isMatISP) {ierr = DMPlexGetSubdomainSection(dm, &subSection);CHKERRQ(ierr);} 2031 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 2032 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 2033 ierr = PetscDSHasJacobian(prob, &hasJac);CHKERRQ(ierr); 2034 ierr = PetscDSHasJacobianPreconditioner(prob, &hasPrec);CHKERRQ(ierr); 2035 ierr = PetscDSHasDynamicJacobian(prob, &hasDyn);CHKERRQ(ierr); 2036 hasDyn = hasDyn && (X_tShift != 0.0) ? PETSC_TRUE : PETSC_FALSE; 2037 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); 2038 ierr = ISGetLocalSize(cellIS, &numCells);CHKERRQ(ierr); 2039 ierr = ISGetPointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 2040 ierr = PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);CHKERRQ(ierr); 2041 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);CHKERRQ(ierr); 2042 if (dmAux) { 2043 ierr = DMConvert(dmAux, DMPLEX, &plex);CHKERRQ(ierr); 2044 ierr = DMGetSection(plex, §ionAux);CHKERRQ(ierr); 2045 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 2046 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 2047 } 2048 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); 2049 if (dmAux) {ierr = PetscMalloc1(numCells*totDimAux, &a);CHKERRQ(ierr);} 2050 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 2051 for (c = cStart; c < cEnd; ++c) { 2052 const PetscInt cell = cells ? cells[c] : c; 2053 const PetscInt cind = c - cStart; 2054 PetscScalar *x = NULL, *x_t = NULL; 2055 PetscInt i; 2056 2057 ierr = DMPlexVecGetClosure(dm, section, X, cell, NULL, &x);CHKERRQ(ierr); 2058 for (i = 0; i < totDim; ++i) u[cind*totDim+i] = x[i]; 2059 ierr = DMPlexVecRestoreClosure(dm, section, X, cell, NULL, &x);CHKERRQ(ierr); 2060 if (X_t) { 2061 ierr = DMPlexVecGetClosure(dm, section, X_t, cell, NULL, &x_t);CHKERRQ(ierr); 2062 for (i = 0; i < totDim; ++i) u_t[cind*totDim+i] = x_t[i]; 2063 ierr = DMPlexVecRestoreClosure(dm, section, X_t, cell, NULL, &x_t);CHKERRQ(ierr); 2064 } 2065 if (dmAux) { 2066 PetscInt subcell; 2067 ierr = DMPlexGetAuxiliaryPoint(dm, dmAux, cell, &subcell);CHKERRQ(ierr); 2068 ierr = DMPlexVecGetClosure(plex, sectionAux, A, subcell, NULL, &x);CHKERRQ(ierr); 2069 for (i = 0; i < totDimAux; ++i) a[cind*totDimAux+i] = x[i]; 2070 ierr = DMPlexVecRestoreClosure(plex, sectionAux, A, subcell, NULL, &x);CHKERRQ(ierr); 2071 } 2072 } 2073 if (hasJac) {ierr = PetscMemzero(elemMat, numCells*totDim*totDim * sizeof(PetscScalar));CHKERRQ(ierr);} 2074 if (hasPrec) {ierr = PetscMemzero(elemMatP, numCells*totDim*totDim * sizeof(PetscScalar));CHKERRQ(ierr);} 2075 if (hasDyn) {ierr = PetscMemzero(elemMatD, numCells*totDim*totDim * sizeof(PetscScalar));CHKERRQ(ierr);} 2076 for (fieldI = 0; fieldI < Nf; ++fieldI) { 2077 PetscClassId id; 2078 PetscFE fe; 2079 PetscQuadrature qGeom = NULL; 2080 PetscInt Nb; 2081 /* Conforming batches */ 2082 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 2083 /* Remainder */ 2084 PetscInt Nr, offset, Nq; 2085 PetscInt maxDegree; 2086 PetscFEGeom *cgeomFEM, *chunkGeom = NULL, *remGeom = NULL; 2087 2088 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); 2089 ierr = PetscObjectGetClassId((PetscObject) fe, &id);CHKERRQ(ierr); 2090 if (id == PETSCFV_CLASSID) {hasFV = PETSC_TRUE; continue;} 2091 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 2092 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 2093 ierr = DMFieldGetDegree(coordField,cellIS,NULL,&maxDegree);CHKERRQ(ierr); 2094 if (maxDegree <= 1) { 2095 ierr = DMFieldCreateDefaultQuadrature(coordField,cellIS,&qGeom);CHKERRQ(ierr); 2096 } 2097 if (!qGeom) { 2098 ierr = PetscFEGetQuadrature(fe,&qGeom);CHKERRQ(ierr); 2099 ierr = PetscObjectReference((PetscObject)qGeom);CHKERRQ(ierr); 2100 } 2101 ierr = PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 2102 ierr = DMSNESGetFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);CHKERRQ(ierr); 2103 blockSize = Nb; 2104 batchSize = numBlocks * blockSize; 2105 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 2106 numChunks = numCells / (numBatches*batchSize); 2107 Ne = numChunks*numBatches*batchSize; 2108 Nr = numCells % (numBatches*batchSize); 2109 offset = numCells - Nr; 2110 ierr = PetscFEGeomGetChunk(cgeomFEM,0,offset,&chunkGeom);CHKERRQ(ierr); 2111 ierr = PetscFEGeomGetChunk(cgeomFEM,offset,numCells,&remGeom);CHKERRQ(ierr); 2112 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 2113 if (hasJac) { 2114 ierr = PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMat);CHKERRQ(ierr); 2115 ierr = PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN, fieldI, fieldJ, 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); 2116 } 2117 if (hasPrec) { 2118 ierr = PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN_PRE, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMatP);CHKERRQ(ierr); 2119 ierr = PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN_PRE, fieldI, fieldJ, 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); 2120 } 2121 if (hasDyn) { 2122 ierr = PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN_DYN, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMatD);CHKERRQ(ierr); 2123 ierr = PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN_DYN, fieldI, fieldJ, 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); 2124 } 2125 } 2126 ierr = PetscFEGeomRestoreChunk(cgeomFEM,offset,numCells,&remGeom);CHKERRQ(ierr); 2127 ierr = PetscFEGeomRestoreChunk(cgeomFEM,0,offset,&chunkGeom);CHKERRQ(ierr); 2128 ierr = DMSNESRestoreFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);CHKERRQ(ierr); 2129 ierr = PetscQuadratureDestroy(&qGeom);CHKERRQ(ierr); 2130 } 2131 /* Add contribution from X_t */ 2132 if (hasDyn) {for (c = 0; c < numCells*totDim*totDim; ++c) elemMat[c] += X_tShift*elemMatD[c];} 2133 if (hasFV) { 2134 PetscClassId id; 2135 PetscFV fv; 2136 PetscInt offsetI, NcI, NbI = 1, fc, f; 2137 2138 for (fieldI = 0; fieldI < Nf; ++fieldI) { 2139 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fv);CHKERRQ(ierr); 2140 ierr = PetscDSGetFieldOffset(prob, fieldI, &offsetI);CHKERRQ(ierr); 2141 ierr = PetscObjectGetClassId((PetscObject) fv, &id);CHKERRQ(ierr); 2142 if (id != PETSCFV_CLASSID) continue; 2143 /* Put in the identity */ 2144 ierr = PetscFVGetNumComponents(fv, &NcI);CHKERRQ(ierr); 2145 for (c = cStart; c < cEnd; ++c) { 2146 const PetscInt cind = c - cStart; 2147 const PetscInt eOffset = cind*totDim*totDim; 2148 for (fc = 0; fc < NcI; ++fc) { 2149 for (f = 0; f < NbI; ++f) { 2150 const PetscInt i = offsetI + f*NcI+fc; 2151 if (hasPrec) { 2152 if (hasJac) {elemMat[eOffset+i*totDim+i] = 1.0;} 2153 elemMatP[eOffset+i*totDim+i] = 1.0; 2154 } else {elemMat[eOffset+i*totDim+i] = 1.0;} 2155 } 2156 } 2157 } 2158 } 2159 /* No allocated space for FV stuff, so ignore the zero entries */ 2160 ierr = MatSetOption(JacP, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE);CHKERRQ(ierr); 2161 } 2162 /* Insert values into matrix */ 2163 isMatIS = PETSC_FALSE; 2164 if (hasPrec && hasJac) { 2165 ierr = PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatIS);CHKERRQ(ierr); 2166 } 2167 if (isMatIS && !subSection) { 2168 ierr = DMPlexGetSubdomainSection(dm, &subSection);CHKERRQ(ierr); 2169 } 2170 for (c = cStart; c < cEnd; ++c) { 2171 const PetscInt cell = cells ? cells[c] : c; 2172 const PetscInt cind = c - cStart; 2173 2174 if (hasPrec) { 2175 if (hasJac) { 2176 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(cell, name, totDim, totDim, &elemMat[cind*totDim*totDim]);CHKERRQ(ierr);} 2177 if (!isMatIS) { 2178 ierr = DMPlexMatSetClosure(dm, section, globalSection, Jac, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2179 } else { 2180 Mat lJ; 2181 2182 ierr = MatISGetLocalMat(Jac,&lJ);CHKERRQ(ierr); 2183 ierr = DMPlexMatSetClosure(dm, section, subSection, lJ, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2184 } 2185 } 2186 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(cell, name, totDim, totDim, &elemMatP[cind*totDim*totDim]);CHKERRQ(ierr);} 2187 if (!isMatISP) { 2188 ierr = DMPlexMatSetClosure(dm, section, globalSection, JacP, cell, &elemMatP[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2189 } else { 2190 Mat lJ; 2191 2192 ierr = MatISGetLocalMat(JacP,&lJ);CHKERRQ(ierr); 2193 ierr = DMPlexMatSetClosure(dm, section, subSection, lJ, cell, &elemMatP[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2194 } 2195 } else { 2196 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(cell, name, totDim, totDim, &elemMat[cind*totDim*totDim]);CHKERRQ(ierr);} 2197 if (!isMatISP) { 2198 ierr = DMPlexMatSetClosure(dm, section, globalSection, JacP, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2199 } else { 2200 Mat lJ; 2201 2202 ierr = MatISGetLocalMat(JacP,&lJ);CHKERRQ(ierr); 2203 ierr = DMPlexMatSetClosure(dm, section, subSection, lJ, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2204 } 2205 } 2206 } 2207 ierr = ISRestorePointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 2208 if (hasFV) {ierr = MatSetOption(JacP, MAT_IGNORE_ZERO_ENTRIES, PETSC_FALSE);CHKERRQ(ierr);} 2209 ierr = PetscFree5(u,u_t,elemMat,elemMatP,elemMatD);CHKERRQ(ierr); 2210 if (dmAux) { 2211 ierr = PetscFree(a);CHKERRQ(ierr); 2212 ierr = DMDestroy(&plex);CHKERRQ(ierr); 2213 } 2214 /* Compute boundary integrals */ 2215 ierr = DMPlexComputeBdJacobian_Internal(dm, X, X_t, t, X_tShift, Jac, JacP, user);CHKERRQ(ierr); 2216 /* Assemble matrix */ 2217 if (hasJac && hasPrec) { 2218 ierr = MatAssemblyBegin(Jac, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2219 ierr = MatAssemblyEnd(Jac, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2220 } 2221 ierr = MatAssemblyBegin(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2222 ierr = MatAssemblyEnd(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2223 ierr = PetscLogEventEnd(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 2224 PetscFunctionReturn(0); 2225 } 2226 2227 /*@ 2228 DMPlexComputeJacobianAction - Form the local portion of the Jacobian action Z = J(X) Y at the local solution X using pointwise functions specified by the user. 2229 2230 Input Parameters: 2231 + dm - The mesh 2232 . cellIS - 2233 . t - The time 2234 . X_tShift - The multiplier for the Jacobian with repsect to X_t 2235 . X - Local solution vector 2236 . X_t - Time-derivative of the local solution vector 2237 . Y - Local input vector 2238 - user - The user context 2239 2240 Output Parameter: 2241 . Z - Local output vector 2242 2243 Note: 2244 We form the residual one batch of elements at a time. This allows us to offload work onto an accelerator, 2245 like a GPU, or vectorize on a multicore machine. 2246 2247 Level: developer 2248 2249 .seealso: FormFunctionLocal() 2250 @*/ 2251 PetscErrorCode DMPlexComputeJacobianAction(DM dm, IS cellIS, PetscReal t, PetscReal X_tShift, Vec X, Vec X_t, Vec Y, Vec Z, void *user) 2252 { 2253 DM_Plex *mesh = (DM_Plex *) dm->data; 2254 const char *name = "Jacobian"; 2255 DM dmAux, plex, plexAux = NULL; 2256 Vec A; 2257 PetscDS prob, probAux = NULL; 2258 PetscQuadrature quad; 2259 PetscSection section, globalSection, sectionAux; 2260 PetscScalar *elemMat, *elemMatD, *u, *u_t, *a = NULL, *y, *z; 2261 PetscInt Nf, fieldI, fieldJ; 2262 PetscInt totDim, totDimAux = 0; 2263 const PetscInt *cells; 2264 PetscInt cStart, cEnd, numCells, c; 2265 PetscBool hasDyn; 2266 DMField coordField; 2267 PetscErrorCode ierr; 2268 2269 PetscFunctionBegin; 2270 ierr = PetscLogEventBegin(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 2271 ierr = DMSNESConvertPlex(dm, &plex, PETSC_TRUE);CHKERRQ(ierr); 2272 if (!cellIS) { 2273 PetscInt depth; 2274 2275 ierr = DMPlexGetDepth(plex, &depth);CHKERRQ(ierr); 2276 ierr = DMGetStratumIS(plex, "dim", depth, &cellIS);CHKERRQ(ierr); 2277 if (!cellIS) {ierr = DMGetStratumIS(plex, "depth", depth, &cellIS);CHKERRQ(ierr);} 2278 } else { 2279 ierr = PetscObjectReference((PetscObject) cellIS);CHKERRQ(ierr); 2280 } 2281 ierr = DMGetSection(dm, §ion);CHKERRQ(ierr); 2282 ierr = DMGetGlobalSection(dm, &globalSection);CHKERRQ(ierr); 2283 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 2284 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 2285 ierr = PetscDSHasDynamicJacobian(prob, &hasDyn);CHKERRQ(ierr); 2286 hasDyn = hasDyn && (X_tShift != 0.0) ? PETSC_TRUE : PETSC_FALSE; 2287 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); 2288 ierr = ISGetLocalSize(cellIS, &numCells);CHKERRQ(ierr); 2289 ierr = ISGetPointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 2290 ierr = PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);CHKERRQ(ierr); 2291 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);CHKERRQ(ierr); 2292 if (dmAux) { 2293 ierr = DMConvert(dmAux, DMPLEX, &plexAux);CHKERRQ(ierr); 2294 ierr = DMGetSection(plexAux, §ionAux);CHKERRQ(ierr); 2295 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 2296 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 2297 } 2298 ierr = VecSet(Z, 0.0);CHKERRQ(ierr); 2299 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); 2300 if (dmAux) {ierr = PetscMalloc1(numCells*totDimAux, &a);CHKERRQ(ierr);} 2301 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 2302 for (c = cStart; c < cEnd; ++c) { 2303 const PetscInt cell = cells ? cells[c] : c; 2304 const PetscInt cind = c - cStart; 2305 PetscScalar *x = NULL, *x_t = NULL; 2306 PetscInt i; 2307 2308 ierr = DMPlexVecGetClosure(dm, section, X, cell, NULL, &x);CHKERRQ(ierr); 2309 for (i = 0; i < totDim; ++i) u[cind*totDim+i] = x[i]; 2310 ierr = DMPlexVecRestoreClosure(dm, section, X, cell, NULL, &x);CHKERRQ(ierr); 2311 if (X_t) { 2312 ierr = DMPlexVecGetClosure(dm, section, X_t, cell, NULL, &x_t);CHKERRQ(ierr); 2313 for (i = 0; i < totDim; ++i) u_t[cind*totDim+i] = x_t[i]; 2314 ierr = DMPlexVecRestoreClosure(dm, section, X_t, cell, NULL, &x_t);CHKERRQ(ierr); 2315 } 2316 if (dmAux) { 2317 PetscInt subcell; 2318 ierr = DMPlexGetAuxiliaryPoint(dm, dmAux, cell, &subcell);CHKERRQ(ierr); 2319 ierr = DMPlexVecGetClosure(plexAux, sectionAux, A, subcell, NULL, &x);CHKERRQ(ierr); 2320 for (i = 0; i < totDimAux; ++i) a[cind*totDimAux+i] = x[i]; 2321 ierr = DMPlexVecRestoreClosure(plexAux, sectionAux, A, subcell, NULL, &x);CHKERRQ(ierr); 2322 } 2323 ierr = DMPlexVecGetClosure(dm, section, Y, cell, NULL, &x);CHKERRQ(ierr); 2324 for (i = 0; i < totDim; ++i) y[cind*totDim+i] = x[i]; 2325 ierr = DMPlexVecRestoreClosure(dm, section, Y, cell, NULL, &x);CHKERRQ(ierr); 2326 } 2327 ierr = PetscMemzero(elemMat, numCells*totDim*totDim * sizeof(PetscScalar));CHKERRQ(ierr); 2328 if (hasDyn) {ierr = PetscMemzero(elemMatD, numCells*totDim*totDim * sizeof(PetscScalar));CHKERRQ(ierr);} 2329 for (fieldI = 0; fieldI < Nf; ++fieldI) { 2330 PetscFE fe; 2331 PetscInt Nb; 2332 /* Conforming batches */ 2333 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 2334 /* Remainder */ 2335 PetscInt Nr, offset, Nq; 2336 PetscQuadrature qGeom = NULL; 2337 PetscInt maxDegree; 2338 PetscFEGeom *cgeomFEM, *chunkGeom = NULL, *remGeom = NULL; 2339 2340 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); 2341 ierr = PetscFEGetQuadrature(fe, &quad);CHKERRQ(ierr); 2342 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 2343 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 2344 ierr = DMFieldGetDegree(coordField,cellIS,NULL,&maxDegree);CHKERRQ(ierr); 2345 if (maxDegree <= 1) {ierr = DMFieldCreateDefaultQuadrature(coordField,cellIS,&qGeom);CHKERRQ(ierr);} 2346 if (!qGeom) { 2347 ierr = PetscFEGetQuadrature(fe,&qGeom);CHKERRQ(ierr); 2348 ierr = PetscObjectReference((PetscObject)qGeom);CHKERRQ(ierr); 2349 } 2350 ierr = PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 2351 ierr = DMSNESGetFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);CHKERRQ(ierr); 2352 blockSize = Nb; 2353 batchSize = numBlocks * blockSize; 2354 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 2355 numChunks = numCells / (numBatches*batchSize); 2356 Ne = numChunks*numBatches*batchSize; 2357 Nr = numCells % (numBatches*batchSize); 2358 offset = numCells - Nr; 2359 ierr = PetscFEGeomGetChunk(cgeomFEM,0,offset,&chunkGeom);CHKERRQ(ierr); 2360 ierr = PetscFEGeomGetChunk(cgeomFEM,offset,numCells,&remGeom);CHKERRQ(ierr); 2361 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 2362 ierr = PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMat);CHKERRQ(ierr); 2363 ierr = PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN, fieldI, fieldJ, 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); 2364 if (hasDyn) { 2365 ierr = PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN_DYN, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMatD);CHKERRQ(ierr); 2366 ierr = PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN_DYN, fieldI, fieldJ, 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); 2367 } 2368 } 2369 ierr = PetscFEGeomRestoreChunk(cgeomFEM,offset,numCells,&remGeom);CHKERRQ(ierr); 2370 ierr = PetscFEGeomRestoreChunk(cgeomFEM,0,offset,&chunkGeom);CHKERRQ(ierr); 2371 ierr = DMSNESRestoreFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);CHKERRQ(ierr); 2372 ierr = PetscQuadratureDestroy(&qGeom);CHKERRQ(ierr); 2373 } 2374 if (hasDyn) { 2375 for (c = 0; c < numCells*totDim*totDim; ++c) elemMat[c] += X_tShift*elemMatD[c]; 2376 } 2377 for (c = cStart; c < cEnd; ++c) { 2378 const PetscInt cell = cells ? cells[c] : c; 2379 const PetscInt cind = c - cStart; 2380 const PetscBLASInt M = totDim, one = 1; 2381 const PetscScalar a = 1.0, b = 0.0; 2382 2383 PetscStackCallBLAS("BLASgemv", BLASgemv_("N", &M, &M, &a, &elemMat[cind*totDim*totDim], &M, &y[cind*totDim], &one, &b, z, &one)); 2384 if (mesh->printFEM > 1) { 2385 ierr = DMPrintCellMatrix(c, name, totDim, totDim, &elemMat[cind*totDim*totDim]);CHKERRQ(ierr); 2386 ierr = DMPrintCellVector(c, "Y", totDim, &y[cind*totDim]);CHKERRQ(ierr); 2387 ierr = DMPrintCellVector(c, "Z", totDim, z);CHKERRQ(ierr); 2388 } 2389 ierr = DMPlexVecSetClosure(dm, section, Z, cell, z, ADD_VALUES);CHKERRQ(ierr); 2390 } 2391 ierr = PetscFree6(u,u_t,elemMat,elemMatD,y,z);CHKERRQ(ierr); 2392 if (mesh->printFEM) { 2393 ierr = PetscPrintf(PETSC_COMM_WORLD, "Z:\n");CHKERRQ(ierr); 2394 ierr = VecView(Z, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 2395 } 2396 ierr = PetscFree(a);CHKERRQ(ierr); 2397 ierr = ISDestroy(&cellIS);CHKERRQ(ierr); 2398 ierr = DMDestroy(&plexAux);CHKERRQ(ierr); 2399 ierr = DMDestroy(&plex);CHKERRQ(ierr); 2400 ierr = PetscLogEventEnd(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 2401 PetscFunctionReturn(0); 2402 } 2403 2404 /*@ 2405 DMPlexSNESComputeJacobianFEM - Form the local portion of the Jacobian matrix J at the local solution X using pointwise functions specified by the user. 2406 2407 Input Parameters: 2408 + dm - The mesh 2409 . X - Local input vector 2410 - user - The user context 2411 2412 Output Parameter: 2413 . Jac - Jacobian matrix 2414 2415 Note: 2416 We form the residual one batch of elements at a time. This allows us to offload work onto an accelerator, 2417 like a GPU, or vectorize on a multicore machine. 2418 2419 Level: developer 2420 2421 .seealso: FormFunctionLocal() 2422 @*/ 2423 PetscErrorCode DMPlexSNESComputeJacobianFEM(DM dm, Vec X, Mat Jac, Mat JacP,void *user) 2424 { 2425 DM plex; 2426 PetscDS prob; 2427 IS cellIS; 2428 PetscBool hasJac, hasPrec; 2429 PetscInt depth; 2430 PetscErrorCode ierr; 2431 2432 PetscFunctionBegin; 2433 ierr = DMSNESConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr); 2434 ierr = DMPlexGetDepth(plex, &depth);CHKERRQ(ierr); 2435 ierr = DMGetStratumIS(plex, "dim", depth, &cellIS);CHKERRQ(ierr); 2436 if (!cellIS) {ierr = DMGetStratumIS(plex, "depth", depth, &cellIS);CHKERRQ(ierr);} 2437 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 2438 ierr = PetscDSHasJacobian(prob, &hasJac);CHKERRQ(ierr); 2439 ierr = PetscDSHasJacobianPreconditioner(prob, &hasPrec);CHKERRQ(ierr); 2440 if (hasJac && hasPrec) {ierr = MatZeroEntries(Jac);CHKERRQ(ierr);} 2441 ierr = MatZeroEntries(JacP);CHKERRQ(ierr); 2442 ierr = DMPlexComputeJacobian_Internal(plex, cellIS, 0.0, 0.0, X, NULL, Jac, JacP, user);CHKERRQ(ierr); 2443 ierr = ISDestroy(&cellIS);CHKERRQ(ierr); 2444 ierr = DMDestroy(&plex);CHKERRQ(ierr); 2445 PetscFunctionReturn(0); 2446 } 2447 2448 /*@ 2449 DMPlexSetSNESLocalFEM - Use DMPlex's internal FEM routines to compute SNES boundary values, residual, and Jacobian. 2450 2451 Input Parameters: 2452 + dm - The DM object 2453 . boundaryctx - the user context that will be passed to pointwise evaluation of boundary values (see PetscDSAddBoundary()) 2454 . residualctx - the user context that will be passed to pointwise evaluation of finite element residual computations (see PetscDSSetResidual()) 2455 - jacobianctx - the user context that will be passed to pointwise evaluation of finite element Jacobian construction (see PetscDSSetJacobian()) 2456 2457 Level: developer 2458 @*/ 2459 PetscErrorCode DMPlexSetSNESLocalFEM(DM dm, void *boundaryctx, void *residualctx, void *jacobianctx) 2460 { 2461 PetscErrorCode ierr; 2462 2463 PetscFunctionBegin; 2464 ierr = DMSNESSetBoundaryLocal(dm,DMPlexSNESComputeBoundaryFEM,boundaryctx);CHKERRQ(ierr); 2465 ierr = DMSNESSetFunctionLocal(dm,DMPlexSNESComputeResidualFEM,residualctx);CHKERRQ(ierr); 2466 ierr = DMSNESSetJacobianLocal(dm,DMPlexSNESComputeJacobianFEM,jacobianctx);CHKERRQ(ierr); 2467 PetscFunctionReturn(0); 2468 } 2469 2470 PetscErrorCode DMSNESCheckFromOptions_Internal(SNES snes, DM dm, Vec u, PetscErrorCode (**exactFuncs)(PetscInt, PetscReal, const PetscReal x[], PetscInt, PetscScalar *u, void *ctx), void **ctxs) 2471 { 2472 PetscErrorCode (**exacts)(PetscInt, PetscReal, const PetscReal x[], PetscInt, PetscScalar *u, void *ctx); 2473 PetscDS prob; 2474 Mat J, M; 2475 Vec r, b; 2476 MatNullSpace nullSpace; 2477 PetscReal *error, res = 0.0; 2478 PetscInt numFields; 2479 PetscBool hasJac, hasPrec; 2480 PetscInt Nf, f; 2481 PetscErrorCode ierr; 2482 2483 PetscFunctionBegin; 2484 ierr = DMGetNumFields(dm, &Nf);CHKERRQ(ierr); 2485 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 2486 ierr = PetscMalloc1(Nf, &exacts);CHKERRQ(ierr); 2487 for (f = 0; f < Nf; ++f) {ierr = PetscDSGetExactSolution(prob, f, &exacts[f]);CHKERRQ(ierr);} 2488 ierr = VecDuplicate(u, &r);CHKERRQ(ierr); 2489 ierr = DMCreateMatrix(dm, &J);CHKERRQ(ierr); 2490 /* TODO Null space for J */ 2491 /* Check discretization error */ 2492 ierr = DMGetNumFields(dm, &numFields);CHKERRQ(ierr); 2493 ierr = PetscMalloc1(PetscMax(1, numFields), &error);CHKERRQ(ierr); 2494 ierr = DMProjectFunction(dm, 0.0, exactFuncs ? exactFuncs : exacts, ctxs, INSERT_ALL_VALUES, u);CHKERRQ(ierr); 2495 if (numFields > 1) { 2496 PetscInt f; 2497 2498 ierr = DMComputeL2FieldDiff(dm, 0.0, exactFuncs ? exactFuncs : exacts, ctxs, u, error);CHKERRQ(ierr); 2499 ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: [");CHKERRQ(ierr); 2500 for (f = 0; f < numFields; ++f) { 2501 if (f) {ierr = PetscPrintf(PETSC_COMM_WORLD, ", ");CHKERRQ(ierr);} 2502 if (error[f] >= 1.0e-11) {ierr = PetscPrintf(PETSC_COMM_WORLD, "%g", (double)error[f]);CHKERRQ(ierr);} 2503 else {ierr = PetscPrintf(PETSC_COMM_WORLD, "< 1.0e-11");CHKERRQ(ierr);} 2504 } 2505 ierr = PetscPrintf(PETSC_COMM_WORLD, "]\n");CHKERRQ(ierr); 2506 } else { 2507 ierr = DMComputeL2Diff(dm, 0.0, exactFuncs ? exactFuncs : exacts, ctxs, u, &error[0]);CHKERRQ(ierr); 2508 if (error[0] >= 1.0e-11) {ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: %g\n", (double)error[0]);CHKERRQ(ierr);} 2509 else {ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: < 1.0e-11\n");CHKERRQ(ierr);} 2510 } 2511 ierr = PetscFree(error);CHKERRQ(ierr); 2512 /* Check residual */ 2513 ierr = SNESComputeFunction(snes, u, r);CHKERRQ(ierr); 2514 ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr); 2515 ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Residual: %g\n", (double)res);CHKERRQ(ierr); 2516 ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr); 2517 ierr = PetscObjectSetName((PetscObject) r, "Initial Residual");CHKERRQ(ierr); 2518 ierr = PetscObjectSetOptionsPrefix((PetscObject)r,"res_");CHKERRQ(ierr); 2519 ierr = VecViewFromOptions(r, NULL, "-vec_view");CHKERRQ(ierr); 2520 /* Check Jacobian */ 2521 ierr = PetscDSHasJacobian(prob, &hasJac);CHKERRQ(ierr); 2522 ierr = PetscDSHasJacobianPreconditioner(prob, &hasPrec);CHKERRQ(ierr); 2523 if (hasJac && hasPrec) { 2524 ierr = DMCreateMatrix(dm, &M);CHKERRQ(ierr); 2525 ierr = SNESComputeJacobian(snes, u, J, M);CHKERRQ(ierr); 2526 ierr = PetscObjectSetOptionsPrefix((PetscObject) M, "jacpre_");CHKERRQ(ierr); 2527 ierr = MatViewFromOptions(M, NULL, "-mat_view");CHKERRQ(ierr); 2528 ierr = MatDestroy(&M);CHKERRQ(ierr); 2529 } else { 2530 ierr = SNESComputeJacobian(snes, u, J, J);CHKERRQ(ierr); 2531 } 2532 ierr = PetscObjectSetOptionsPrefix((PetscObject) J, "jac_");CHKERRQ(ierr); 2533 ierr = MatViewFromOptions(J, NULL, "-mat_view");CHKERRQ(ierr); 2534 ierr = MatGetNullSpace(J, &nullSpace);CHKERRQ(ierr); 2535 if (nullSpace) { 2536 PetscBool isNull; 2537 ierr = MatNullSpaceTest(nullSpace, J, &isNull);CHKERRQ(ierr); 2538 if (!isNull) SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_PLIB, "The null space calculated for the system operator is invalid."); 2539 } 2540 ierr = VecDuplicate(u, &b);CHKERRQ(ierr); 2541 ierr = VecSet(r, 0.0);CHKERRQ(ierr); 2542 ierr = SNESComputeFunction(snes, r, b);CHKERRQ(ierr); 2543 ierr = MatMult(J, u, r);CHKERRQ(ierr); 2544 ierr = VecAXPY(r, 1.0, b);CHKERRQ(ierr); 2545 ierr = VecDestroy(&b);CHKERRQ(ierr); 2546 ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr); 2547 ierr = PetscPrintf(PETSC_COMM_WORLD, "Linear L_2 Residual: %g\n", (double)res);CHKERRQ(ierr); 2548 ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr); 2549 ierr = PetscObjectSetName((PetscObject) r, "Au - b = Au + F(0)");CHKERRQ(ierr); 2550 ierr = PetscObjectSetOptionsPrefix((PetscObject)r,"linear_res_");CHKERRQ(ierr); 2551 ierr = VecViewFromOptions(r, NULL, "-vec_view");CHKERRQ(ierr); 2552 ierr = VecDestroy(&r);CHKERRQ(ierr); 2553 ierr = MatNullSpaceDestroy(&nullSpace);CHKERRQ(ierr); 2554 ierr = MatDestroy(&J);CHKERRQ(ierr); 2555 ierr = PetscFree(exacts);CHKERRQ(ierr); 2556 PetscFunctionReturn(0); 2557 } 2558 2559 /*@C 2560 DMSNESCheckFromOptions - Check the residual and Jacobian functions using the exact solution by outputting some diagnostic information 2561 2562 Input Parameters: 2563 + snes - the SNES object 2564 . u - representative SNES vector 2565 . exactFuncs - pointwise functions of the exact solution for each field 2566 - ctxs - contexts for the functions 2567 2568 Level: developer 2569 @*/ 2570 PetscErrorCode DMSNESCheckFromOptions(SNES snes, Vec u, PetscErrorCode (**exactFuncs)(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf, PetscScalar *u, void *ctx), void **ctxs) 2571 { 2572 PetscErrorCode (**exact)(PetscInt, PetscReal, const PetscReal[], PetscInt, PetscScalar *, void *) = NULL; 2573 DM dm; 2574 PetscDS prob; 2575 Vec sol; 2576 PetscBool check; 2577 PetscInt Nf, f; 2578 PetscErrorCode ierr; 2579 2580 PetscFunctionBegin; 2581 ierr = PetscOptionsHasName(((PetscObject)snes)->options,((PetscObject)snes)->prefix, "-dmsnes_check", &check);CHKERRQ(ierr); 2582 if (!check) PetscFunctionReturn(0); 2583 ierr = SNESGetDM(snes, &dm);CHKERRQ(ierr); 2584 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 2585 if (!exactFuncs) { 2586 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 2587 ierr = PetscMalloc1(Nf, &exact);CHKERRQ(ierr); 2588 for (f = 0; f < Nf; ++f) {ierr = PetscDSGetExactSolution(prob, f, &exact[f]);CHKERRQ(ierr);} 2589 } 2590 ierr = VecDuplicate(u, &sol);CHKERRQ(ierr); 2591 ierr = SNESSetSolution(snes, sol);CHKERRQ(ierr); 2592 ierr = DMSNESCheckFromOptions_Internal(snes, dm, sol, exactFuncs ? exactFuncs : exact, ctxs);CHKERRQ(ierr); 2593 ierr = VecDestroy(&sol);CHKERRQ(ierr); 2594 ierr = PetscFree(exact);CHKERRQ(ierr); 2595 PetscFunctionReturn(0); 2596 } 2597