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 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 = PetscArraycpy(ctx->points, points, n*ctx->dim);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 PetscTabulation T; 548 const PetscScalar *coords; 549 PetscScalar *a; 550 PetscReal xir[2]; 551 PetscInt Nf, p; 552 const PetscInt dof = ctx->dof; 553 PetscErrorCode ierr; 554 555 PetscFunctionBegin; 556 ierr = DMGetNumFields(dm, &Nf);CHKERRQ(ierr); 557 if (Nf) {ierr = DMGetField(dm, 0, NULL, (PetscObject *) &fem);CHKERRQ(ierr);} 558 ierr = DMGetCoordinatesLocal(dm, &coordsLocal);CHKERRQ(ierr); 559 ierr = DMGetCoordinateDM(dm, &dmCoord);CHKERRQ(ierr); 560 ierr = SNESCreate(PETSC_COMM_SELF, &snes);CHKERRQ(ierr); 561 ierr = SNESSetOptionsPrefix(snes, "quad_interp_");CHKERRQ(ierr); 562 ierr = VecCreate(PETSC_COMM_SELF, &r);CHKERRQ(ierr); 563 ierr = VecSetSizes(r, 2, 2);CHKERRQ(ierr); 564 ierr = VecSetType(r,dm->vectype);CHKERRQ(ierr); 565 ierr = VecDuplicate(r, &ref);CHKERRQ(ierr); 566 ierr = VecDuplicate(r, &real);CHKERRQ(ierr); 567 ierr = MatCreate(PETSC_COMM_SELF, &J);CHKERRQ(ierr); 568 ierr = MatSetSizes(J, 2, 2, 2, 2);CHKERRQ(ierr); 569 ierr = MatSetType(J, MATSEQDENSE);CHKERRQ(ierr); 570 ierr = MatSetUp(J);CHKERRQ(ierr); 571 ierr = SNESSetFunction(snes, r, QuadMap_Private, NULL);CHKERRQ(ierr); 572 ierr = SNESSetJacobian(snes, J, J, QuadJacobian_Private, NULL);CHKERRQ(ierr); 573 ierr = SNESGetKSP(snes, &ksp);CHKERRQ(ierr); 574 ierr = KSPGetPC(ksp, &pc);CHKERRQ(ierr); 575 ierr = PCSetType(pc, PCLU);CHKERRQ(ierr); 576 ierr = SNESSetFromOptions(snes);CHKERRQ(ierr); 577 578 ierr = VecGetArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 579 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 580 ierr = PetscFECreateTabulation(fem, 1, 1, xir, 0, &T);CHKERRQ(ierr); 581 for (p = 0; p < ctx->n; ++p) { 582 PetscScalar *x = NULL, *vertices = NULL; 583 PetscScalar *xi; 584 PetscInt c = ctx->cells[p], comp, coordSize, xSize; 585 586 /* Can make this do all points at once */ 587 ierr = DMPlexVecGetClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);CHKERRQ(ierr); 588 if (4*2 != coordSize) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid closure size %D should be %d", coordSize, 4*2); 589 ierr = DMPlexVecGetClosure(dm, NULL, xLocal, c, &xSize, &x);CHKERRQ(ierr); 590 ierr = SNESSetFunction(snes, NULL, NULL, (void*) vertices);CHKERRQ(ierr); 591 ierr = SNESSetJacobian(snes, NULL, NULL, NULL, (void*) vertices);CHKERRQ(ierr); 592 ierr = VecGetArray(real, &xi);CHKERRQ(ierr); 593 xi[0] = coords[p*ctx->dim+0]; 594 xi[1] = coords[p*ctx->dim+1]; 595 ierr = VecRestoreArray(real, &xi);CHKERRQ(ierr); 596 ierr = SNESSolve(snes, real, ref);CHKERRQ(ierr); 597 ierr = VecGetArray(ref, &xi);CHKERRQ(ierr); 598 xir[0] = PetscRealPart(xi[0]); 599 xir[1] = PetscRealPart(xi[1]); 600 if (4*dof != xSize) { 601 PetscInt d; 602 603 xir[0] = 2.0*xir[0] - 1.0; xir[1] = 2.0*xir[1] - 1.0; 604 ierr = PetscFEComputeTabulation(fem, 1, xir, 0, T);CHKERRQ(ierr); 605 for (comp = 0; comp < dof; ++comp) { 606 a[p*dof+comp] = 0.0; 607 for (d = 0; d < xSize/dof; ++d) { 608 a[p*dof+comp] += x[d*dof+comp]*T->T[0][d*dof+comp]; 609 } 610 } 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 = PetscTabulationDestroy(&T);CHKERRQ(ierr); 620 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 621 ierr = VecRestoreArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 622 623 ierr = SNESDestroy(&snes);CHKERRQ(ierr); 624 ierr = VecDestroy(&r);CHKERRQ(ierr); 625 ierr = VecDestroy(&ref);CHKERRQ(ierr); 626 ierr = VecDestroy(&real);CHKERRQ(ierr); 627 ierr = MatDestroy(&J);CHKERRQ(ierr); 628 PetscFunctionReturn(0); 629 } 630 631 PETSC_STATIC_INLINE PetscErrorCode HexMap_Private(SNES snes, Vec Xref, Vec Xreal, void *ctx) 632 { 633 const PetscScalar *vertices = (const PetscScalar*) ctx; 634 const PetscScalar x0 = vertices[0]; 635 const PetscScalar y0 = vertices[1]; 636 const PetscScalar z0 = vertices[2]; 637 const PetscScalar x1 = vertices[9]; 638 const PetscScalar y1 = vertices[10]; 639 const PetscScalar z1 = vertices[11]; 640 const PetscScalar x2 = vertices[6]; 641 const PetscScalar y2 = vertices[7]; 642 const PetscScalar z2 = vertices[8]; 643 const PetscScalar x3 = vertices[3]; 644 const PetscScalar y3 = vertices[4]; 645 const PetscScalar z3 = vertices[5]; 646 const PetscScalar x4 = vertices[12]; 647 const PetscScalar y4 = vertices[13]; 648 const PetscScalar z4 = vertices[14]; 649 const PetscScalar x5 = vertices[15]; 650 const PetscScalar y5 = vertices[16]; 651 const PetscScalar z5 = vertices[17]; 652 const PetscScalar x6 = vertices[18]; 653 const PetscScalar y6 = vertices[19]; 654 const PetscScalar z6 = vertices[20]; 655 const PetscScalar x7 = vertices[21]; 656 const PetscScalar y7 = vertices[22]; 657 const PetscScalar z7 = vertices[23]; 658 const PetscScalar f_1 = x1 - x0; 659 const PetscScalar g_1 = y1 - y0; 660 const PetscScalar h_1 = z1 - z0; 661 const PetscScalar f_3 = x3 - x0; 662 const PetscScalar g_3 = y3 - y0; 663 const PetscScalar h_3 = z3 - z0; 664 const PetscScalar f_4 = x4 - x0; 665 const PetscScalar g_4 = y4 - y0; 666 const PetscScalar h_4 = z4 - z0; 667 const PetscScalar f_01 = x2 - x1 - x3 + x0; 668 const PetscScalar g_01 = y2 - y1 - y3 + y0; 669 const PetscScalar h_01 = z2 - z1 - z3 + z0; 670 const PetscScalar f_12 = x7 - x3 - x4 + x0; 671 const PetscScalar g_12 = y7 - y3 - y4 + y0; 672 const PetscScalar h_12 = z7 - z3 - z4 + z0; 673 const PetscScalar f_02 = x5 - x1 - x4 + x0; 674 const PetscScalar g_02 = y5 - y1 - y4 + y0; 675 const PetscScalar h_02 = z5 - z1 - z4 + z0; 676 const PetscScalar f_012 = x6 - x0 + x1 - x2 + x3 + x4 - x5 - x7; 677 const PetscScalar g_012 = y6 - y0 + y1 - y2 + y3 + y4 - y5 - y7; 678 const PetscScalar h_012 = z6 - z0 + z1 - z2 + z3 + z4 - z5 - z7; 679 const PetscScalar *ref; 680 PetscScalar *real; 681 PetscErrorCode ierr; 682 683 PetscFunctionBegin; 684 ierr = VecGetArrayRead(Xref, &ref);CHKERRQ(ierr); 685 ierr = VecGetArray(Xreal, &real);CHKERRQ(ierr); 686 { 687 const PetscScalar p0 = ref[0]; 688 const PetscScalar p1 = ref[1]; 689 const PetscScalar p2 = ref[2]; 690 691 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; 692 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; 693 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; 694 } 695 ierr = PetscLogFlops(114);CHKERRQ(ierr); 696 ierr = VecRestoreArrayRead(Xref, &ref);CHKERRQ(ierr); 697 ierr = VecRestoreArray(Xreal, &real);CHKERRQ(ierr); 698 PetscFunctionReturn(0); 699 } 700 701 PETSC_STATIC_INLINE PetscErrorCode HexJacobian_Private(SNES snes, Vec Xref, Mat J, Mat M, void *ctx) 702 { 703 const PetscScalar *vertices = (const PetscScalar*) ctx; 704 const PetscScalar x0 = vertices[0]; 705 const PetscScalar y0 = vertices[1]; 706 const PetscScalar z0 = vertices[2]; 707 const PetscScalar x1 = vertices[9]; 708 const PetscScalar y1 = vertices[10]; 709 const PetscScalar z1 = vertices[11]; 710 const PetscScalar x2 = vertices[6]; 711 const PetscScalar y2 = vertices[7]; 712 const PetscScalar z2 = vertices[8]; 713 const PetscScalar x3 = vertices[3]; 714 const PetscScalar y3 = vertices[4]; 715 const PetscScalar z3 = vertices[5]; 716 const PetscScalar x4 = vertices[12]; 717 const PetscScalar y4 = vertices[13]; 718 const PetscScalar z4 = vertices[14]; 719 const PetscScalar x5 = vertices[15]; 720 const PetscScalar y5 = vertices[16]; 721 const PetscScalar z5 = vertices[17]; 722 const PetscScalar x6 = vertices[18]; 723 const PetscScalar y6 = vertices[19]; 724 const PetscScalar z6 = vertices[20]; 725 const PetscScalar x7 = vertices[21]; 726 const PetscScalar y7 = vertices[22]; 727 const PetscScalar z7 = vertices[23]; 728 const PetscScalar f_xy = x2 - x1 - x3 + x0; 729 const PetscScalar g_xy = y2 - y1 - y3 + y0; 730 const PetscScalar h_xy = z2 - z1 - z3 + z0; 731 const PetscScalar f_yz = x7 - x3 - x4 + x0; 732 const PetscScalar g_yz = y7 - y3 - y4 + y0; 733 const PetscScalar h_yz = z7 - z3 - z4 + z0; 734 const PetscScalar f_xz = x5 - x1 - x4 + x0; 735 const PetscScalar g_xz = y5 - y1 - y4 + y0; 736 const PetscScalar h_xz = z5 - z1 - z4 + z0; 737 const PetscScalar f_xyz = x6 - x0 + x1 - x2 + x3 + x4 - x5 - x7; 738 const PetscScalar g_xyz = y6 - y0 + y1 - y2 + y3 + y4 - y5 - y7; 739 const PetscScalar h_xyz = z6 - z0 + z1 - z2 + z3 + z4 - z5 - z7; 740 const PetscScalar *ref; 741 PetscErrorCode ierr; 742 743 PetscFunctionBegin; 744 ierr = VecGetArrayRead(Xref, &ref);CHKERRQ(ierr); 745 { 746 const PetscScalar x = ref[0]; 747 const PetscScalar y = ref[1]; 748 const PetscScalar z = ref[2]; 749 const PetscInt rows[3] = {0, 1, 2}; 750 PetscScalar values[9]; 751 752 values[0] = (x1 - x0 + f_xy*y + f_xz*z + f_xyz*y*z) / 2.0; 753 values[1] = (x3 - x0 + f_xy*x + f_yz*z + f_xyz*x*z) / 2.0; 754 values[2] = (x4 - x0 + f_yz*y + f_xz*x + f_xyz*x*y) / 2.0; 755 values[3] = (y1 - y0 + g_xy*y + g_xz*z + g_xyz*y*z) / 2.0; 756 values[4] = (y3 - y0 + g_xy*x + g_yz*z + g_xyz*x*z) / 2.0; 757 values[5] = (y4 - y0 + g_yz*y + g_xz*x + g_xyz*x*y) / 2.0; 758 values[6] = (z1 - z0 + h_xy*y + h_xz*z + h_xyz*y*z) / 2.0; 759 values[7] = (z3 - z0 + h_xy*x + h_yz*z + h_xyz*x*z) / 2.0; 760 values[8] = (z4 - z0 + h_yz*y + h_xz*x + h_xyz*x*y) / 2.0; 761 762 ierr = MatSetValues(J, 3, rows, 3, rows, values, INSERT_VALUES);CHKERRQ(ierr); 763 } 764 ierr = PetscLogFlops(152);CHKERRQ(ierr); 765 ierr = VecRestoreArrayRead(Xref, &ref);CHKERRQ(ierr); 766 ierr = MatAssemblyBegin(J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 767 ierr = MatAssemblyEnd(J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 768 PetscFunctionReturn(0); 769 } 770 771 PETSC_STATIC_INLINE PetscErrorCode DMInterpolate_Hex_Private(DMInterpolationInfo ctx, DM dm, Vec xLocal, Vec v) 772 { 773 DM dmCoord; 774 SNES snes; 775 KSP ksp; 776 PC pc; 777 Vec coordsLocal, r, ref, real; 778 Mat J; 779 const PetscScalar *coords; 780 PetscScalar *a; 781 PetscInt p; 782 PetscErrorCode ierr; 783 784 PetscFunctionBegin; 785 ierr = DMGetCoordinatesLocal(dm, &coordsLocal);CHKERRQ(ierr); 786 ierr = DMGetCoordinateDM(dm, &dmCoord);CHKERRQ(ierr); 787 ierr = SNESCreate(PETSC_COMM_SELF, &snes);CHKERRQ(ierr); 788 ierr = SNESSetOptionsPrefix(snes, "hex_interp_");CHKERRQ(ierr); 789 ierr = VecCreate(PETSC_COMM_SELF, &r);CHKERRQ(ierr); 790 ierr = VecSetSizes(r, 3, 3);CHKERRQ(ierr); 791 ierr = VecSetType(r,dm->vectype);CHKERRQ(ierr); 792 ierr = VecDuplicate(r, &ref);CHKERRQ(ierr); 793 ierr = VecDuplicate(r, &real);CHKERRQ(ierr); 794 ierr = MatCreate(PETSC_COMM_SELF, &J);CHKERRQ(ierr); 795 ierr = MatSetSizes(J, 3, 3, 3, 3);CHKERRQ(ierr); 796 ierr = MatSetType(J, MATSEQDENSE);CHKERRQ(ierr); 797 ierr = MatSetUp(J);CHKERRQ(ierr); 798 ierr = SNESSetFunction(snes, r, HexMap_Private, NULL);CHKERRQ(ierr); 799 ierr = SNESSetJacobian(snes, J, J, HexJacobian_Private, NULL);CHKERRQ(ierr); 800 ierr = SNESGetKSP(snes, &ksp);CHKERRQ(ierr); 801 ierr = KSPGetPC(ksp, &pc);CHKERRQ(ierr); 802 ierr = PCSetType(pc, PCLU);CHKERRQ(ierr); 803 ierr = SNESSetFromOptions(snes);CHKERRQ(ierr); 804 805 ierr = VecGetArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 806 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 807 for (p = 0; p < ctx->n; ++p) { 808 PetscScalar *x = NULL, *vertices = NULL; 809 PetscScalar *xi; 810 PetscReal xir[3]; 811 PetscInt c = ctx->cells[p], comp, coordSize, xSize; 812 813 /* Can make this do all points at once */ 814 ierr = DMPlexVecGetClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);CHKERRQ(ierr); 815 if (8*3 != coordSize) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid closure size %D should be %d", coordSize, 8*3); 816 ierr = DMPlexVecGetClosure(dm, NULL, xLocal, c, &xSize, &x);CHKERRQ(ierr); 817 if (8*ctx->dof != xSize) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid closure size %D should be %D", xSize, 8*ctx->dof); 818 ierr = SNESSetFunction(snes, NULL, NULL, (void*) vertices);CHKERRQ(ierr); 819 ierr = SNESSetJacobian(snes, NULL, NULL, NULL, (void*) vertices);CHKERRQ(ierr); 820 ierr = VecGetArray(real, &xi);CHKERRQ(ierr); 821 xi[0] = coords[p*ctx->dim+0]; 822 xi[1] = coords[p*ctx->dim+1]; 823 xi[2] = coords[p*ctx->dim+2]; 824 ierr = VecRestoreArray(real, &xi);CHKERRQ(ierr); 825 ierr = SNESSolve(snes, real, ref);CHKERRQ(ierr); 826 ierr = VecGetArray(ref, &xi);CHKERRQ(ierr); 827 xir[0] = PetscRealPart(xi[0]); 828 xir[1] = PetscRealPart(xi[1]); 829 xir[2] = PetscRealPart(xi[2]); 830 for (comp = 0; comp < ctx->dof; ++comp) { 831 a[p*ctx->dof+comp] = 832 x[0*ctx->dof+comp]*(1-xir[0])*(1-xir[1])*(1-xir[2]) + 833 x[3*ctx->dof+comp]* xir[0]*(1-xir[1])*(1-xir[2]) + 834 x[2*ctx->dof+comp]* xir[0]* xir[1]*(1-xir[2]) + 835 x[1*ctx->dof+comp]*(1-xir[0])* xir[1]*(1-xir[2]) + 836 x[4*ctx->dof+comp]*(1-xir[0])*(1-xir[1])* xir[2] + 837 x[5*ctx->dof+comp]* xir[0]*(1-xir[1])* xir[2] + 838 x[6*ctx->dof+comp]* xir[0]* xir[1]* xir[2] + 839 x[7*ctx->dof+comp]*(1-xir[0])* xir[1]* xir[2]; 840 } 841 ierr = VecRestoreArray(ref, &xi);CHKERRQ(ierr); 842 ierr = DMPlexVecRestoreClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);CHKERRQ(ierr); 843 ierr = DMPlexVecRestoreClosure(dm, NULL, xLocal, c, &xSize, &x);CHKERRQ(ierr); 844 } 845 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 846 ierr = VecRestoreArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 847 848 ierr = SNESDestroy(&snes);CHKERRQ(ierr); 849 ierr = VecDestroy(&r);CHKERRQ(ierr); 850 ierr = VecDestroy(&ref);CHKERRQ(ierr); 851 ierr = VecDestroy(&real);CHKERRQ(ierr); 852 ierr = MatDestroy(&J);CHKERRQ(ierr); 853 PetscFunctionReturn(0); 854 } 855 856 /*@C 857 DMInterpolationEvaluate - Using the input from dm and x, calculates interpolated field values at the interpolation points. 858 859 Input Parameters: 860 + ctx - The DMInterpolationInfo context 861 . dm - The DM 862 - x - The local vector containing the field to be interpolated 863 864 Output Parameters: 865 . v - The vector containing the interpolated values 866 867 Note: A suitable v can be obtained using DMInterpolationGetVector(). 868 869 Level: beginner 870 871 .seealso: DMInterpolationGetVector(), DMInterpolationAddPoints(), DMInterpolationCreate() 872 @*/ 873 PetscErrorCode DMInterpolationEvaluate(DMInterpolationInfo ctx, DM dm, Vec x, Vec v) 874 { 875 PetscInt dim, coneSize, n; 876 PetscErrorCode ierr; 877 878 PetscFunctionBegin; 879 PetscValidHeaderSpecific(dm, DM_CLASSID, 2); 880 PetscValidHeaderSpecific(x, VEC_CLASSID, 3); 881 PetscValidHeaderSpecific(v, VEC_CLASSID, 4); 882 ierr = VecGetLocalSize(v, &n);CHKERRQ(ierr); 883 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); 884 if (n) { 885 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 886 ierr = DMPlexGetConeSize(dm, ctx->cells[0], &coneSize);CHKERRQ(ierr); 887 if (dim == 2) { 888 if (coneSize == 3) { 889 ierr = DMInterpolate_Triangle_Private(ctx, dm, x, v);CHKERRQ(ierr); 890 } else if (coneSize == 4) { 891 ierr = DMInterpolate_Quad_Private(ctx, dm, x, v);CHKERRQ(ierr); 892 } else SETERRQ1(ctx->comm, PETSC_ERR_ARG_OUTOFRANGE, "Unsupported dimension %D for point interpolation", dim); 893 } else if (dim == 3) { 894 if (coneSize == 4) { 895 ierr = DMInterpolate_Tetrahedron_Private(ctx, dm, x, v);CHKERRQ(ierr); 896 } else { 897 ierr = DMInterpolate_Hex_Private(ctx, dm, x, v);CHKERRQ(ierr); 898 } 899 } else SETERRQ1(ctx->comm, PETSC_ERR_ARG_OUTOFRANGE, "Unsupported dimension %D for point interpolation", dim); 900 } 901 PetscFunctionReturn(0); 902 } 903 904 /*@C 905 DMInterpolationDestroy - Destroys a DMInterpolationInfo context 906 907 Collective on ctx 908 909 Input Parameter: 910 . ctx - the context 911 912 Level: beginner 913 914 .seealso: DMInterpolationEvaluate(), DMInterpolationAddPoints(), DMInterpolationCreate() 915 @*/ 916 PetscErrorCode DMInterpolationDestroy(DMInterpolationInfo *ctx) 917 { 918 PetscErrorCode ierr; 919 920 PetscFunctionBegin; 921 PetscValidPointer(ctx, 2); 922 ierr = VecDestroy(&(*ctx)->coords);CHKERRQ(ierr); 923 ierr = PetscFree((*ctx)->points);CHKERRQ(ierr); 924 ierr = PetscFree((*ctx)->cells);CHKERRQ(ierr); 925 ierr = PetscFree(*ctx);CHKERRQ(ierr); 926 *ctx = NULL; 927 PetscFunctionReturn(0); 928 } 929 930 /*@C 931 SNESMonitorFields - Monitors the residual for each field separately 932 933 Collective on SNES 934 935 Input Parameters: 936 + snes - the SNES context 937 . its - iteration number 938 . fgnorm - 2-norm of residual 939 - vf - PetscViewerAndFormat of type ASCII 940 941 Notes: 942 This routine prints the residual norm at each iteration. 943 944 Level: intermediate 945 946 .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, NULL, NULL);CHKERRQ(ierr); 962 ierr = SNESGetDM(snes, &dm);CHKERRQ(ierr); 963 ierr = DMGetLocalSection(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 DMEnclosureType encAux; 1062 PetscDS prob, probAux = NULL; 1063 PetscSection section, sectionAux = NULL; 1064 Vec locA = NULL; 1065 PetscScalar *u = NULL, *u_t = NULL, *a = NULL, *elemVec = NULL; 1066 PetscInt v; 1067 PetscInt totDim, totDimAux = 0; 1068 PetscErrorCode ierr; 1069 1070 PetscFunctionBegin; 1071 ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); 1072 ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); 1073 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1074 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1075 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);CHKERRQ(ierr); 1076 if (locA) { 1077 DM dmAux; 1078 1079 ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); 1080 ierr = DMGetEnclosureRelation(dmAux, dm, &encAux);CHKERRQ(ierr); 1081 ierr = DMConvert(dmAux, DMPLEX, &plexA);CHKERRQ(ierr); 1082 ierr = DMGetDS(plexA, &probAux);CHKERRQ(ierr); 1083 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 1084 ierr = DMGetLocalSection(plexA, §ionAux);CHKERRQ(ierr); 1085 } 1086 for (v = 0; v < numValues; ++v) { 1087 PetscFEGeom *fgeom; 1088 PetscInt maxDegree; 1089 PetscQuadrature qGeom = NULL; 1090 IS pointIS; 1091 const PetscInt *points; 1092 PetscInt numFaces, face, Nq; 1093 1094 ierr = DMLabelGetStratumIS(label, values[v], &pointIS);CHKERRQ(ierr); 1095 if (!pointIS) continue; /* No points with that id on this process */ 1096 { 1097 IS isectIS; 1098 1099 /* TODO: Special cases of ISIntersect where it is quick to check a priori if one is a superset of the other */ 1100 ierr = ISIntersect_Caching_Internal(facetIS,pointIS,&isectIS);CHKERRQ(ierr); 1101 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 1102 pointIS = isectIS; 1103 } 1104 ierr = ISGetLocalSize(pointIS,&numFaces);CHKERRQ(ierr); 1105 ierr = ISGetIndices(pointIS,&points);CHKERRQ(ierr); 1106 ierr = PetscMalloc4(numFaces*totDim, &u, locX_t ? numFaces*totDim : 0, &u_t, numFaces*totDim, &elemVec, locA ? numFaces*totDimAux : 0, &a);CHKERRQ(ierr); 1107 ierr = DMFieldGetDegree(coordField,pointIS,NULL,&maxDegree);CHKERRQ(ierr); 1108 if (maxDegree <= 1) { 1109 ierr = DMFieldCreateDefaultQuadrature(coordField,pointIS,&qGeom);CHKERRQ(ierr); 1110 } 1111 if (!qGeom) { 1112 PetscFE fe; 1113 1114 ierr = PetscDSGetDiscretization(prob, field, (PetscObject *) &fe);CHKERRQ(ierr); 1115 ierr = PetscFEGetFaceQuadrature(fe, &qGeom);CHKERRQ(ierr); 1116 ierr = PetscObjectReference((PetscObject)qGeom);CHKERRQ(ierr); 1117 } 1118 ierr = PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 1119 ierr = DMSNESGetFEGeom(coordField,pointIS,qGeom,PETSC_TRUE,&fgeom);CHKERRQ(ierr); 1120 for (face = 0; face < numFaces; ++face) { 1121 const PetscInt point = points[face], *support, *cone; 1122 PetscScalar *x = NULL; 1123 PetscInt i, coneSize, faceLoc; 1124 1125 ierr = DMPlexGetSupport(dm, point, &support);CHKERRQ(ierr); 1126 ierr = DMPlexGetConeSize(dm, support[0], &coneSize);CHKERRQ(ierr); 1127 ierr = DMPlexGetCone(dm, support[0], &cone);CHKERRQ(ierr); 1128 for (faceLoc = 0; faceLoc < coneSize; ++faceLoc) if (cone[faceLoc] == point) break; 1129 if (faceLoc == coneSize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Could not find face %D in cone of support[0] %D", point, support[0]); 1130 fgeom->face[face][0] = faceLoc; 1131 ierr = DMPlexVecGetClosure(plex, section, locX, support[0], NULL, &x);CHKERRQ(ierr); 1132 for (i = 0; i < totDim; ++i) u[face*totDim+i] = x[i]; 1133 ierr = DMPlexVecRestoreClosure(plex, section, locX, support[0], NULL, &x);CHKERRQ(ierr); 1134 if (locX_t) { 1135 ierr = DMPlexVecGetClosure(plex, section, locX_t, support[0], NULL, &x);CHKERRQ(ierr); 1136 for (i = 0; i < totDim; ++i) u_t[face*totDim+i] = x[i]; 1137 ierr = DMPlexVecRestoreClosure(plex, section, locX_t, support[0], NULL, &x);CHKERRQ(ierr); 1138 } 1139 if (locA) { 1140 PetscInt subp; 1141 1142 ierr = DMGetEnclosurePoint(plexA, dm, encAux, support[0], &subp);CHKERRQ(ierr); 1143 ierr = DMPlexVecGetClosure(plexA, sectionAux, locA, subp, NULL, &x);CHKERRQ(ierr); 1144 for (i = 0; i < totDimAux; ++i) a[face*totDimAux+i] = x[i]; 1145 ierr = DMPlexVecRestoreClosure(plexA, sectionAux, locA, subp, NULL, &x);CHKERRQ(ierr); 1146 } 1147 } 1148 ierr = PetscArrayzero(elemVec, numFaces*totDim);CHKERRQ(ierr); 1149 { 1150 PetscFE fe; 1151 PetscInt Nb; 1152 PetscFEGeom *chunkGeom = NULL; 1153 /* Conforming batches */ 1154 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 1155 /* Remainder */ 1156 PetscInt Nr, offset; 1157 1158 ierr = PetscDSGetDiscretization(prob, field, (PetscObject *) &fe);CHKERRQ(ierr); 1159 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 1160 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1161 /* TODO: documentation is unclear about what is going on with these numbers: how should Nb / Nq factor in ? */ 1162 blockSize = Nb; 1163 batchSize = numBlocks * blockSize; 1164 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1165 numChunks = numFaces / (numBatches*batchSize); 1166 Ne = numChunks*numBatches*batchSize; 1167 Nr = numFaces % (numBatches*batchSize); 1168 offset = numFaces - Nr; 1169 ierr = PetscFEGeomGetChunk(fgeom,0,offset,&chunkGeom);CHKERRQ(ierr); 1170 ierr = PetscFEIntegrateBdResidual(prob, field, Ne, chunkGeom, u, u_t, probAux, a, t, elemVec);CHKERRQ(ierr); 1171 ierr = PetscFEGeomRestoreChunk(fgeom, 0, offset, &chunkGeom);CHKERRQ(ierr); 1172 ierr = PetscFEGeomGetChunk(fgeom,offset,numFaces,&chunkGeom);CHKERRQ(ierr); 1173 ierr = PetscFEIntegrateBdResidual(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); 1174 ierr = PetscFEGeomRestoreChunk(fgeom,offset,numFaces,&chunkGeom);CHKERRQ(ierr); 1175 } 1176 for (face = 0; face < numFaces; ++face) { 1177 const PetscInt point = points[face], *support; 1178 1179 if (mesh->printFEM > 1) {ierr = DMPrintCellVector(point, "BdResidual", totDim, &elemVec[face*totDim]);CHKERRQ(ierr);} 1180 ierr = DMPlexGetSupport(plex, point, &support);CHKERRQ(ierr); 1181 ierr = DMPlexVecSetClosure(plex, NULL, locF, support[0], &elemVec[face*totDim], ADD_ALL_VALUES);CHKERRQ(ierr); 1182 } 1183 ierr = DMSNESRestoreFEGeom(coordField,pointIS,qGeom,PETSC_TRUE,&fgeom);CHKERRQ(ierr); 1184 ierr = PetscQuadratureDestroy(&qGeom);CHKERRQ(ierr); 1185 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 1186 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 1187 ierr = PetscFree4(u, u_t, elemVec, a);CHKERRQ(ierr); 1188 } 1189 if (plex) {ierr = DMDestroy(&plex);CHKERRQ(ierr);} 1190 if (plexA) {ierr = DMDestroy(&plexA);CHKERRQ(ierr);} 1191 PetscFunctionReturn(0); 1192 } 1193 1194 PetscErrorCode DMPlexComputeBdResidualSingle(DM dm, PetscReal t, DMLabel label, PetscInt numValues, const PetscInt values[], PetscInt field, Vec locX, Vec locX_t, Vec locF) 1195 { 1196 DMField coordField; 1197 DMLabel depthLabel; 1198 IS facetIS; 1199 PetscInt dim; 1200 PetscErrorCode ierr; 1201 1202 PetscFunctionBegin; 1203 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1204 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 1205 ierr = DMLabelGetStratumIS(depthLabel, dim-1, &facetIS);CHKERRQ(ierr); 1206 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 1207 ierr = DMPlexComputeBdResidual_Single_Internal(dm, t, label, numValues, values, field, locX, locX_t, locF, coordField, facetIS);CHKERRQ(ierr); 1208 ierr = ISDestroy(&facetIS);CHKERRQ(ierr); 1209 PetscFunctionReturn(0); 1210 } 1211 1212 PetscErrorCode DMPlexComputeBdResidual_Internal(DM dm, Vec locX, Vec locX_t, PetscReal t, Vec locF, void *user) 1213 { 1214 PetscDS prob; 1215 PetscInt numBd, bd; 1216 DMField coordField = NULL; 1217 IS facetIS = NULL; 1218 DMLabel depthLabel; 1219 PetscInt dim; 1220 PetscErrorCode ierr; 1221 1222 PetscFunctionBegin; 1223 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1224 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 1225 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1226 ierr = DMLabelGetStratumIS(depthLabel,dim - 1,&facetIS);CHKERRQ(ierr); 1227 ierr = PetscDSGetNumBoundary(prob, &numBd);CHKERRQ(ierr); 1228 for (bd = 0; bd < numBd; ++bd) { 1229 DMBoundaryConditionType type; 1230 const char *bdLabel; 1231 DMLabel label; 1232 const PetscInt *values; 1233 PetscInt field, numValues; 1234 PetscObject obj; 1235 PetscClassId id; 1236 1237 ierr = PetscDSGetBoundary(prob, bd, &type, NULL, &bdLabel, &field, NULL, NULL, NULL, &numValues, &values, NULL);CHKERRQ(ierr); 1238 ierr = PetscDSGetDiscretization(prob, field, &obj);CHKERRQ(ierr); 1239 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1240 if ((id != PETSCFE_CLASSID) || (type & DM_BC_ESSENTIAL)) continue; 1241 if (!facetIS) { 1242 DMLabel depthLabel; 1243 PetscInt dim; 1244 1245 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 1246 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1247 ierr = DMLabelGetStratumIS(depthLabel, dim - 1, &facetIS);CHKERRQ(ierr); 1248 } 1249 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 1250 ierr = DMGetLabel(dm, bdLabel, &label);CHKERRQ(ierr); 1251 ierr = DMPlexComputeBdResidual_Single_Internal(dm, t, label, numValues, values, field, locX, locX_t, locF, coordField, facetIS);CHKERRQ(ierr); 1252 } 1253 ierr = ISDestroy(&facetIS);CHKERRQ(ierr); 1254 PetscFunctionReturn(0); 1255 } 1256 1257 PetscErrorCode DMPlexComputeResidual_Internal(DM dm, IS cellIS, PetscReal time, Vec locX, Vec locX_t, PetscReal t, Vec locF, void *user) 1258 { 1259 DM_Plex *mesh = (DM_Plex *) dm->data; 1260 const char *name = "Residual"; 1261 DM dmAux = NULL; 1262 DM dmGrad = NULL; 1263 DMLabel ghostLabel = NULL; 1264 PetscDS prob = NULL; 1265 PetscDS probAux = NULL; 1266 PetscSection section = NULL; 1267 PetscBool useFEM = PETSC_FALSE; 1268 PetscBool useFVM = PETSC_FALSE; 1269 PetscBool isImplicit = (locX_t || time == PETSC_MIN_REAL) ? PETSC_TRUE : PETSC_FALSE; 1270 PetscFV fvm = NULL; 1271 PetscFVCellGeom *cgeomFVM = NULL; 1272 PetscFVFaceGeom *fgeomFVM = NULL; 1273 DMField coordField = NULL; 1274 Vec locA, cellGeometryFVM = NULL, faceGeometryFVM = NULL, grad, locGrad = NULL; 1275 PetscScalar *u = NULL, *u_t, *a, *uL, *uR; 1276 IS chunkIS; 1277 const PetscInt *cells; 1278 PetscInt cStart, cEnd, numCells; 1279 PetscInt Nf, f, totDim, totDimAux, numChunks, cellChunkSize, faceChunkSize, chunk, fStart, fEnd; 1280 PetscInt maxDegree = PETSC_MAX_INT; 1281 PetscQuadrature affineQuad = NULL, *quads = NULL; 1282 PetscFEGeom *affineGeom = NULL, **geoms = NULL; 1283 PetscErrorCode ierr; 1284 1285 PetscFunctionBegin; 1286 ierr = PetscLogEventBegin(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr); 1287 /* TODO The places where we have to use isFE are probably the member functions for the PetscDisc class */ 1288 /* TODO The FVM geometry is over-manipulated. Make the precalc functions return exactly what we need */ 1289 /* FEM+FVM */ 1290 ierr = ISGetPointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 1291 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 1292 /* 1: Get sizes from dm and dmAux */ 1293 ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); 1294 ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 1295 ierr = DMGetCellDS(dm, cells ? cells[cStart] : cStart, &prob);CHKERRQ(ierr); 1296 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 1297 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1298 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);CHKERRQ(ierr); 1299 if (locA) { 1300 PetscInt subcell; 1301 ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); 1302 ierr = DMGetEnclosurePoint(dmAux, dm, DM_ENC_UNKNOWN, cStart, &subcell);CHKERRQ(ierr); 1303 ierr = DMGetCellDS(dmAux, subcell, &probAux);CHKERRQ(ierr); 1304 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 1305 } 1306 /* 2: Get geometric data */ 1307 for (f = 0; f < Nf; ++f) { 1308 PetscObject obj; 1309 PetscClassId id; 1310 PetscBool fimp; 1311 1312 ierr = PetscDSGetImplicit(prob, f, &fimp);CHKERRQ(ierr); 1313 if (isImplicit != fimp) continue; 1314 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1315 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1316 if (id == PETSCFE_CLASSID) {useFEM = PETSC_TRUE;} 1317 if (id == PETSCFV_CLASSID) {useFVM = PETSC_TRUE; fvm = (PetscFV) obj;} 1318 } 1319 if (useFEM) { 1320 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 1321 ierr = DMFieldGetDegree(coordField,cellIS,NULL,&maxDegree);CHKERRQ(ierr); 1322 if (maxDegree <= 1) { 1323 ierr = DMFieldCreateDefaultQuadrature(coordField,cellIS,&affineQuad);CHKERRQ(ierr); 1324 if (affineQuad) { 1325 ierr = DMSNESGetFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&affineGeom);CHKERRQ(ierr); 1326 } 1327 } else { 1328 ierr = PetscCalloc2(Nf,&quads,Nf,&geoms);CHKERRQ(ierr); 1329 for (f = 0; f < Nf; ++f) { 1330 PetscObject obj; 1331 PetscClassId id; 1332 PetscBool fimp; 1333 1334 ierr = PetscDSGetImplicit(prob, f, &fimp);CHKERRQ(ierr); 1335 if (isImplicit != fimp) continue; 1336 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1337 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1338 if (id == PETSCFE_CLASSID) { 1339 PetscFE fe = (PetscFE) obj; 1340 1341 ierr = PetscFEGetQuadrature(fe, &quads[f]);CHKERRQ(ierr); 1342 ierr = PetscObjectReference((PetscObject)quads[f]);CHKERRQ(ierr); 1343 ierr = DMSNESGetFEGeom(coordField,cellIS,quads[f],PETSC_FALSE,&geoms[f]);CHKERRQ(ierr); 1344 } 1345 } 1346 } 1347 } 1348 if (useFVM) { 1349 ierr = DMPlexSNESGetGeometryFVM(dm, &faceGeometryFVM, &cellGeometryFVM, NULL);CHKERRQ(ierr); 1350 ierr = VecGetArrayRead(faceGeometryFVM, (const PetscScalar **) &fgeomFVM);CHKERRQ(ierr); 1351 ierr = VecGetArrayRead(cellGeometryFVM, (const PetscScalar **) &cgeomFVM);CHKERRQ(ierr); 1352 /* Reconstruct and limit cell gradients */ 1353 ierr = DMPlexSNESGetGradientDM(dm, fvm, &dmGrad);CHKERRQ(ierr); 1354 if (dmGrad) { 1355 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 1356 ierr = DMGetGlobalVector(dmGrad, &grad);CHKERRQ(ierr); 1357 ierr = DMPlexReconstructGradients_Internal(dm, fvm, fStart, fEnd, faceGeometryFVM, cellGeometryFVM, locX, grad);CHKERRQ(ierr); 1358 /* Communicate gradient values */ 1359 ierr = DMGetLocalVector(dmGrad, &locGrad);CHKERRQ(ierr); 1360 ierr = DMGlobalToLocalBegin(dmGrad, grad, INSERT_VALUES, locGrad);CHKERRQ(ierr); 1361 ierr = DMGlobalToLocalEnd(dmGrad, grad, INSERT_VALUES, locGrad);CHKERRQ(ierr); 1362 ierr = DMRestoreGlobalVector(dmGrad, &grad);CHKERRQ(ierr); 1363 } 1364 /* Handle non-essential (e.g. outflow) boundary values */ 1365 ierr = DMPlexInsertBoundaryValues(dm, PETSC_FALSE, locX, time, faceGeometryFVM, cellGeometryFVM, locGrad);CHKERRQ(ierr); 1366 } 1367 /* Loop over chunks */ 1368 if (useFEM) {ierr = ISCreate(PETSC_COMM_SELF, &chunkIS);CHKERRQ(ierr);} 1369 numCells = cEnd - cStart; 1370 numChunks = 1; 1371 cellChunkSize = numCells/numChunks; 1372 faceChunkSize = (fEnd - fStart)/numChunks; 1373 numChunks = PetscMin(1,numCells); 1374 for (chunk = 0; chunk < numChunks; ++chunk) { 1375 PetscScalar *elemVec, *fluxL, *fluxR; 1376 PetscReal *vol; 1377 PetscFVFaceGeom *fgeom; 1378 PetscInt cS = cStart+chunk*cellChunkSize, cE = PetscMin(cS+cellChunkSize, cEnd), numCells = cE - cS, c; 1379 PetscInt fS = fStart+chunk*faceChunkSize, fE = PetscMin(fS+faceChunkSize, fEnd), numFaces = 0, face; 1380 1381 /* Extract field coefficients */ 1382 if (useFEM) { 1383 ierr = ISGetPointSubrange(chunkIS, cS, cE, cells);CHKERRQ(ierr); 1384 ierr = DMPlexGetCellFields(dm, chunkIS, locX, locX_t, locA, &u, &u_t, &a);CHKERRQ(ierr); 1385 ierr = DMGetWorkArray(dm, numCells*totDim, MPIU_SCALAR, &elemVec);CHKERRQ(ierr); 1386 ierr = PetscArrayzero(elemVec, numCells*totDim);CHKERRQ(ierr); 1387 } 1388 if (useFVM) { 1389 ierr = DMPlexGetFaceFields(dm, fS, fE, locX, locX_t, faceGeometryFVM, cellGeometryFVM, locGrad, &numFaces, &uL, &uR);CHKERRQ(ierr); 1390 ierr = DMPlexGetFaceGeometry(dm, fS, fE, faceGeometryFVM, cellGeometryFVM, &numFaces, &fgeom, &vol);CHKERRQ(ierr); 1391 ierr = DMGetWorkArray(dm, numFaces*totDim, MPIU_SCALAR, &fluxL);CHKERRQ(ierr); 1392 ierr = DMGetWorkArray(dm, numFaces*totDim, MPIU_SCALAR, &fluxR);CHKERRQ(ierr); 1393 ierr = PetscArrayzero(fluxL, numFaces*totDim);CHKERRQ(ierr); 1394 ierr = PetscArrayzero(fluxR, numFaces*totDim);CHKERRQ(ierr); 1395 } 1396 /* TODO We will interlace both our field coefficients (u, u_t, uL, uR, etc.) and our output (elemVec, fL, fR). I think this works */ 1397 /* Loop over fields */ 1398 for (f = 0; f < Nf; ++f) { 1399 PetscObject obj; 1400 PetscClassId id; 1401 PetscBool fimp; 1402 PetscInt numChunks, numBatches, batchSize, numBlocks, blockSize, Ne, Nr, offset; 1403 1404 ierr = PetscDSGetImplicit(prob, f, &fimp);CHKERRQ(ierr); 1405 if (isImplicit != fimp) continue; 1406 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1407 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1408 if (id == PETSCFE_CLASSID) { 1409 PetscFE fe = (PetscFE) obj; 1410 PetscFEGeom *geom = affineGeom ? affineGeom : geoms[f]; 1411 PetscFEGeom *chunkGeom = NULL; 1412 PetscQuadrature quad = affineQuad ? affineQuad : quads[f]; 1413 PetscInt Nq, Nb; 1414 1415 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1416 ierr = PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 1417 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 1418 blockSize = Nb; 1419 batchSize = numBlocks * blockSize; 1420 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1421 numChunks = numCells / (numBatches*batchSize); 1422 Ne = numChunks*numBatches*batchSize; 1423 Nr = numCells % (numBatches*batchSize); 1424 offset = numCells - Nr; 1425 /* Integrate FE residual to get elemVec (need fields at quadrature points) */ 1426 /* 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) */ 1427 ierr = PetscFEGeomGetChunk(geom,0,offset,&chunkGeom);CHKERRQ(ierr); 1428 ierr = PetscFEIntegrateResidual(prob, f, Ne, chunkGeom, u, u_t, probAux, a, t, elemVec);CHKERRQ(ierr); 1429 ierr = PetscFEGeomGetChunk(geom,offset,numCells,&chunkGeom);CHKERRQ(ierr); 1430 ierr = PetscFEIntegrateResidual(prob, f, Nr, chunkGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, &elemVec[offset*totDim]);CHKERRQ(ierr); 1431 ierr = PetscFEGeomRestoreChunk(geom,offset,numCells,&chunkGeom);CHKERRQ(ierr); 1432 } else if (id == PETSCFV_CLASSID) { 1433 PetscFV fv = (PetscFV) obj; 1434 1435 Ne = numFaces; 1436 /* Riemann solve over faces (need fields at face centroids) */ 1437 /* We need to evaluate FE fields at those coordinates */ 1438 ierr = PetscFVIntegrateRHSFunction(fv, prob, f, Ne, fgeom, vol, uL, uR, fluxL, fluxR);CHKERRQ(ierr); 1439 } else SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", f); 1440 } 1441 /* Loop over domain */ 1442 if (useFEM) { 1443 /* Add elemVec to locX */ 1444 for (c = cS; c < cE; ++c) { 1445 const PetscInt cell = cells ? cells[c] : c; 1446 const PetscInt cind = c - cStart; 1447 1448 if (mesh->printFEM > 1) {ierr = DMPrintCellVector(cell, name, totDim, &elemVec[cind*totDim]);CHKERRQ(ierr);} 1449 if (ghostLabel) { 1450 PetscInt ghostVal; 1451 1452 ierr = DMLabelGetValue(ghostLabel,cell,&ghostVal);CHKERRQ(ierr); 1453 if (ghostVal > 0) continue; 1454 } 1455 ierr = DMPlexVecSetClosure(dm, section, locF, cell, &elemVec[cind*totDim], ADD_ALL_VALUES);CHKERRQ(ierr); 1456 } 1457 } 1458 if (useFVM) { 1459 PetscScalar *fa; 1460 PetscInt iface; 1461 1462 ierr = VecGetArray(locF, &fa);CHKERRQ(ierr); 1463 for (f = 0; f < Nf; ++f) { 1464 PetscFV fv; 1465 PetscObject obj; 1466 PetscClassId id; 1467 PetscInt foff, pdim; 1468 1469 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1470 ierr = PetscDSGetFieldOffset(prob, f, &foff);CHKERRQ(ierr); 1471 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1472 if (id != PETSCFV_CLASSID) continue; 1473 fv = (PetscFV) obj; 1474 ierr = PetscFVGetNumComponents(fv, &pdim);CHKERRQ(ierr); 1475 /* Accumulate fluxes to cells */ 1476 for (face = fS, iface = 0; face < fE; ++face) { 1477 const PetscInt *scells; 1478 PetscScalar *fL = NULL, *fR = NULL; 1479 PetscInt ghost, d, nsupp, nchild; 1480 1481 ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr); 1482 ierr = DMPlexGetSupportSize(dm, face, &nsupp);CHKERRQ(ierr); 1483 ierr = DMPlexGetTreeChildren(dm, face, &nchild, NULL);CHKERRQ(ierr); 1484 if (ghost >= 0 || nsupp > 2 || nchild > 0) continue; 1485 ierr = DMPlexGetSupport(dm, face, &scells);CHKERRQ(ierr); 1486 ierr = DMLabelGetValue(ghostLabel,scells[0],&ghost);CHKERRQ(ierr); 1487 if (ghost <= 0) {ierr = DMPlexPointLocalFieldRef(dm, scells[0], f, fa, &fL);CHKERRQ(ierr);} 1488 ierr = DMLabelGetValue(ghostLabel,scells[1],&ghost);CHKERRQ(ierr); 1489 if (ghost <= 0) {ierr = DMPlexPointLocalFieldRef(dm, scells[1], f, fa, &fR);CHKERRQ(ierr);} 1490 for (d = 0; d < pdim; ++d) { 1491 if (fL) fL[d] -= fluxL[iface*totDim+foff+d]; 1492 if (fR) fR[d] += fluxR[iface*totDim+foff+d]; 1493 } 1494 ++iface; 1495 } 1496 } 1497 ierr = VecRestoreArray(locF, &fa);CHKERRQ(ierr); 1498 } 1499 /* Handle time derivative */ 1500 if (locX_t) { 1501 PetscScalar *x_t, *fa; 1502 1503 ierr = VecGetArray(locF, &fa);CHKERRQ(ierr); 1504 ierr = VecGetArray(locX_t, &x_t);CHKERRQ(ierr); 1505 for (f = 0; f < Nf; ++f) { 1506 PetscFV fv; 1507 PetscObject obj; 1508 PetscClassId id; 1509 PetscInt pdim, d; 1510 1511 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1512 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1513 if (id != PETSCFV_CLASSID) continue; 1514 fv = (PetscFV) obj; 1515 ierr = PetscFVGetNumComponents(fv, &pdim);CHKERRQ(ierr); 1516 for (c = cS; c < cE; ++c) { 1517 const PetscInt cell = cells ? cells[c] : c; 1518 PetscScalar *u_t, *r; 1519 1520 if (ghostLabel) { 1521 PetscInt ghostVal; 1522 1523 ierr = DMLabelGetValue(ghostLabel, cell, &ghostVal);CHKERRQ(ierr); 1524 if (ghostVal > 0) continue; 1525 } 1526 ierr = DMPlexPointLocalFieldRead(dm, cell, f, x_t, &u_t);CHKERRQ(ierr); 1527 ierr = DMPlexPointLocalFieldRef(dm, cell, f, fa, &r);CHKERRQ(ierr); 1528 for (d = 0; d < pdim; ++d) r[d] += u_t[d]; 1529 } 1530 } 1531 ierr = VecRestoreArray(locX_t, &x_t);CHKERRQ(ierr); 1532 ierr = VecRestoreArray(locF, &fa);CHKERRQ(ierr); 1533 } 1534 if (useFEM) { 1535 ierr = DMPlexRestoreCellFields(dm, chunkIS, locX, locX_t, locA, &u, &u_t, &a);CHKERRQ(ierr); 1536 ierr = DMRestoreWorkArray(dm, numCells*totDim, MPIU_SCALAR, &elemVec);CHKERRQ(ierr); 1537 } 1538 if (useFVM) { 1539 ierr = DMPlexRestoreFaceFields(dm, fS, fE, locX, locX_t, faceGeometryFVM, cellGeometryFVM, locGrad, &numFaces, &uL, &uR);CHKERRQ(ierr); 1540 ierr = DMPlexRestoreFaceGeometry(dm, fS, fE, faceGeometryFVM, cellGeometryFVM, &numFaces, &fgeom, &vol);CHKERRQ(ierr); 1541 ierr = DMRestoreWorkArray(dm, numFaces*totDim, MPIU_SCALAR, &fluxL);CHKERRQ(ierr); 1542 ierr = DMRestoreWorkArray(dm, numFaces*totDim, MPIU_SCALAR, &fluxR);CHKERRQ(ierr); 1543 if (dmGrad) {ierr = DMRestoreLocalVector(dmGrad, &locGrad);CHKERRQ(ierr);} 1544 } 1545 } 1546 if (useFEM) {ierr = ISDestroy(&chunkIS);CHKERRQ(ierr);} 1547 ierr = ISRestorePointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 1548 1549 if (useFEM) { 1550 ierr = DMPlexComputeBdResidual_Internal(dm, locX, locX_t, t, locF, user);CHKERRQ(ierr); 1551 1552 if (maxDegree <= 1) { 1553 ierr = DMSNESRestoreFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&affineGeom);CHKERRQ(ierr); 1554 ierr = PetscQuadratureDestroy(&affineQuad);CHKERRQ(ierr); 1555 } else { 1556 for (f = 0; f < Nf; ++f) { 1557 ierr = DMSNESRestoreFEGeom(coordField,cellIS,quads[f],PETSC_FALSE,&geoms[f]);CHKERRQ(ierr); 1558 ierr = PetscQuadratureDestroy(&quads[f]);CHKERRQ(ierr); 1559 } 1560 ierr = PetscFree2(quads,geoms);CHKERRQ(ierr); 1561 } 1562 } 1563 1564 /* FEM */ 1565 /* 1: Get sizes from dm and dmAux */ 1566 /* 2: Get geometric data */ 1567 /* 3: Handle boundary values */ 1568 /* 4: Loop over domain */ 1569 /* Extract coefficients */ 1570 /* Loop over fields */ 1571 /* Set tiling for FE*/ 1572 /* Integrate FE residual to get elemVec */ 1573 /* Loop over subdomain */ 1574 /* Loop over quad points */ 1575 /* Transform coords to real space */ 1576 /* Evaluate field and aux fields at point */ 1577 /* Evaluate residual at point */ 1578 /* Transform residual to real space */ 1579 /* Add residual to elemVec */ 1580 /* Loop over domain */ 1581 /* Add elemVec to locX */ 1582 1583 /* FVM */ 1584 /* Get geometric data */ 1585 /* If using gradients */ 1586 /* Compute gradient data */ 1587 /* Loop over domain faces */ 1588 /* Count computational faces */ 1589 /* Reconstruct cell gradient */ 1590 /* Loop over domain cells */ 1591 /* Limit cell gradients */ 1592 /* Handle boundary values */ 1593 /* Loop over domain faces */ 1594 /* Read out field, centroid, normal, volume for each side of face */ 1595 /* Riemann solve over faces */ 1596 /* Loop over domain faces */ 1597 /* Accumulate fluxes to cells */ 1598 /* TODO Change printFEM to printDisc here */ 1599 if (mesh->printFEM) { 1600 Vec locFbc; 1601 PetscInt pStart, pEnd, p, maxDof; 1602 PetscScalar *zeroes; 1603 1604 ierr = VecDuplicate(locF,&locFbc);CHKERRQ(ierr); 1605 ierr = VecCopy(locF,locFbc);CHKERRQ(ierr); 1606 ierr = PetscSectionGetChart(section,&pStart,&pEnd);CHKERRQ(ierr); 1607 ierr = PetscSectionGetMaxDof(section,&maxDof);CHKERRQ(ierr); 1608 ierr = PetscCalloc1(maxDof,&zeroes);CHKERRQ(ierr); 1609 for (p = pStart; p < pEnd; p++) { 1610 ierr = VecSetValuesSection(locFbc,section,p,zeroes,INSERT_BC_VALUES);CHKERRQ(ierr); 1611 } 1612 ierr = PetscFree(zeroes);CHKERRQ(ierr); 1613 ierr = DMPrintLocalVec(dm, name, mesh->printTol, locFbc);CHKERRQ(ierr); 1614 ierr = VecDestroy(&locFbc);CHKERRQ(ierr); 1615 } 1616 ierr = PetscLogEventEnd(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr); 1617 PetscFunctionReturn(0); 1618 } 1619 1620 PetscErrorCode DMPlexComputeResidual_Hybrid_Internal(DM dm, IS cellIS, PetscReal time, Vec locX, Vec locX_t, PetscReal t, Vec locF, void *user) 1621 { 1622 DM_Plex *mesh = (DM_Plex *) dm->data; 1623 const char *name = "Hybrid Residual"; 1624 DM dmAux = NULL; 1625 DMLabel ghostLabel = NULL; 1626 PetscDS prob = NULL; 1627 PetscDS probAux = NULL; 1628 PetscSection section = NULL; 1629 DMField coordField = NULL; 1630 Vec locA; 1631 PetscScalar *u = NULL, *u_t, *a; 1632 PetscScalar *elemVec; 1633 IS chunkIS; 1634 const PetscInt *cells; 1635 PetscInt *faces; 1636 PetscInt cStart, cEnd, numCells; 1637 PetscInt Nf, f, totDim, totDimAux, numChunks, cellChunkSize, chunk; 1638 PetscInt maxDegree = PETSC_MAX_INT; 1639 PetscQuadrature affineQuad = NULL, *quads = NULL; 1640 PetscFEGeom *affineGeom = NULL, **geoms = NULL; 1641 PetscErrorCode ierr; 1642 1643 PetscFunctionBegin; 1644 ierr = PetscLogEventBegin(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr); 1645 /* TODO The places where we have to use isFE are probably the member functions for the PetscDisc class */ 1646 /* FEM */ 1647 ierr = ISGetPointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 1648 /* 1: Get sizes from dm and dmAux */ 1649 ierr = DMGetSection(dm, §ion);CHKERRQ(ierr); 1650 ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 1651 ierr = DMGetCellDS(dm, cStart, &prob);CHKERRQ(ierr); 1652 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 1653 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1654 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);CHKERRQ(ierr); 1655 if (locA) { 1656 ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); 1657 ierr = DMGetCellDS(dmAux, cStart, &probAux);CHKERRQ(ierr); 1658 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 1659 } 1660 /* 2: Setup geometric data */ 1661 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 1662 ierr = DMFieldGetDegree(coordField, cellIS, NULL, &maxDegree);CHKERRQ(ierr); 1663 if (maxDegree > 1) { 1664 ierr = PetscCalloc2(Nf,&quads,Nf,&geoms);CHKERRQ(ierr); 1665 for (f = 0; f < Nf; ++f) { 1666 PetscFE fe; 1667 1668 ierr = PetscDSGetDiscretization(prob, f, (PetscObject *) &fe);CHKERRQ(ierr); 1669 if (fe) { 1670 ierr = PetscFEGetQuadrature(fe, &quads[f]);CHKERRQ(ierr); 1671 ierr = PetscObjectReference((PetscObject) quads[f]);CHKERRQ(ierr); 1672 } 1673 } 1674 } 1675 /* Loop over chunks */ 1676 numCells = cEnd - cStart; 1677 cellChunkSize = numCells; 1678 numChunks = !numCells ? 0 : PetscCeilReal(((PetscReal) numCells)/cellChunkSize); 1679 ierr = PetscCalloc1(2*cellChunkSize, &faces);CHKERRQ(ierr); 1680 ierr = ISCreateGeneral(PETSC_COMM_SELF, cellChunkSize, faces, PETSC_USE_POINTER, &chunkIS);CHKERRQ(ierr); 1681 /* Extract field coefficients */ 1682 /* NOTE This needs the end cap faces to have identical orientations */ 1683 ierr = DMPlexGetCellFields(dm, cellIS, locX, locX_t, locA, &u, &u_t, &a);CHKERRQ(ierr); 1684 ierr = DMGetWorkArray(dm, cellChunkSize*totDim, MPIU_SCALAR, &elemVec);CHKERRQ(ierr); 1685 for (chunk = 0; chunk < numChunks; ++chunk) { 1686 PetscInt cS = cStart+chunk*cellChunkSize, cE = PetscMin(cS+cellChunkSize, cEnd), numCells = cE - cS, c; 1687 1688 ierr = PetscMemzero(elemVec, cellChunkSize*totDim * sizeof(PetscScalar));CHKERRQ(ierr); 1689 /* Get faces */ 1690 for (c = cS; c < cE; ++c) { 1691 const PetscInt cell = cells ? cells[c] : c; 1692 const PetscInt *cone; 1693 ierr = DMPlexGetCone(dm, cell, &cone);CHKERRQ(ierr); 1694 faces[(c-cS)*2+0] = cone[0]; 1695 faces[(c-cS)*2+1] = cone[1]; 1696 } 1697 ierr = ISGeneralSetIndices(chunkIS, cellChunkSize, faces, PETSC_USE_POINTER);CHKERRQ(ierr); 1698 /* Get geometric data */ 1699 if (maxDegree <= 1) { 1700 if (!affineQuad) {ierr = DMFieldCreateDefaultQuadrature(coordField, chunkIS, &affineQuad);CHKERRQ(ierr);} 1701 if (affineQuad) {ierr = DMSNESGetFEGeom(coordField, chunkIS, affineQuad, PETSC_TRUE, &affineGeom);CHKERRQ(ierr);} 1702 } else { 1703 for (f = 0; f < Nf; ++f) { 1704 if (quads[f]) {ierr = DMSNESGetFEGeom(coordField, chunkIS, quads[f], PETSC_TRUE, &geoms[f]);CHKERRQ(ierr);} 1705 } 1706 } 1707 /* Loop over fields */ 1708 for (f = 0; f < Nf; ++f) { 1709 PetscFE fe; 1710 PetscFEGeom *geom = affineGeom ? affineGeom : geoms[f]; 1711 PetscFEGeom *chunkGeom = NULL; 1712 PetscQuadrature quad = affineQuad ? affineQuad : quads[f]; 1713 PetscInt numChunks, numBatches, batchSize, numBlocks, blockSize, Ne, Nr, offset, Nq, Nb; 1714 1715 ierr = PetscDSGetDiscretization(prob, f, (PetscObject *) &fe);CHKERRQ(ierr); 1716 if (!fe) continue; 1717 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1718 ierr = PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 1719 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 1720 blockSize = Nb; 1721 batchSize = numBlocks * blockSize; 1722 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1723 numChunks = numCells / (numBatches*batchSize); 1724 Ne = numChunks*numBatches*batchSize; 1725 Nr = numCells % (numBatches*batchSize); 1726 offset = numCells - Nr; 1727 ierr = PetscFEGeomGetChunk(geom,0,offset,&chunkGeom);CHKERRQ(ierr); 1728 ierr = PetscFEIntegrateHybridResidual(prob, f, Ne, chunkGeom, u, u_t, probAux, a, t, elemVec);CHKERRQ(ierr); 1729 ierr = PetscFEGeomGetChunk(geom,offset,numCells,&chunkGeom);CHKERRQ(ierr); 1730 ierr = PetscFEIntegrateHybridResidual(prob, f, Nr, chunkGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, &elemVec[offset*totDim]);CHKERRQ(ierr); 1731 ierr = PetscFEGeomRestoreChunk(geom,offset,numCells,&chunkGeom);CHKERRQ(ierr); 1732 } 1733 /* Add elemVec to locX */ 1734 for (c = cS; c < cE; ++c) { 1735 const PetscInt cell = cells ? cells[c] : c; 1736 const PetscInt cind = c - cStart; 1737 1738 if (mesh->printFEM > 1) {ierr = DMPrintCellVector(cell, name, totDim, &elemVec[cind*totDim]);CHKERRQ(ierr);} 1739 if (ghostLabel) { 1740 PetscInt ghostVal; 1741 1742 ierr = DMLabelGetValue(ghostLabel,cell,&ghostVal);CHKERRQ(ierr); 1743 if (ghostVal > 0) continue; 1744 } 1745 ierr = DMPlexVecSetClosure(dm, section, locF, cell, &elemVec[cind*totDim], ADD_ALL_VALUES);CHKERRQ(ierr); 1746 } 1747 } 1748 ierr = DMPlexRestoreCellFields(dm, cellIS, locX, locX_t, locA, &u, &u_t, &a);CHKERRQ(ierr); 1749 ierr = DMRestoreWorkArray(dm, numCells*totDim, MPIU_SCALAR, &elemVec);CHKERRQ(ierr); 1750 ierr = PetscFree(faces);CHKERRQ(ierr); 1751 ierr = ISDestroy(&chunkIS);CHKERRQ(ierr); 1752 ierr = ISRestorePointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 1753 if (maxDegree <= 1) { 1754 ierr = DMSNESRestoreFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&affineGeom);CHKERRQ(ierr); 1755 ierr = PetscQuadratureDestroy(&affineQuad);CHKERRQ(ierr); 1756 } else { 1757 for (f = 0; f < Nf; ++f) { 1758 if (geoms) {ierr = DMSNESRestoreFEGeom(coordField,cellIS,quads[f],PETSC_FALSE,&geoms[f]);CHKERRQ(ierr);} 1759 if (quads) {ierr = PetscQuadratureDestroy(&quads[f]);CHKERRQ(ierr);} 1760 } 1761 ierr = PetscFree2(quads,geoms);CHKERRQ(ierr); 1762 } 1763 ierr = PetscLogEventEnd(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr); 1764 PetscFunctionReturn(0); 1765 } 1766 1767 /*@ 1768 DMPlexSNESComputeResidualFEM - Form the local residual F from the local input X using pointwise functions specified by the user 1769 1770 Input Parameters: 1771 + dm - The mesh 1772 . X - Local solution 1773 - user - The user context 1774 1775 Output Parameter: 1776 . F - Local output vector 1777 1778 Level: developer 1779 1780 .seealso: DMPlexComputeJacobianAction() 1781 @*/ 1782 PetscErrorCode DMPlexSNESComputeResidualFEM(DM dm, Vec X, Vec F, void *user) 1783 { 1784 DM plex; 1785 IS allcellIS; 1786 PetscInt Nds, s, depth; 1787 PetscErrorCode ierr; 1788 1789 PetscFunctionBegin; 1790 ierr = DMGetNumDS(dm, &Nds);CHKERRQ(ierr); 1791 ierr = DMSNESConvertPlex(dm, &plex, PETSC_TRUE);CHKERRQ(ierr); 1792 ierr = DMPlexGetDepth(plex, &depth);CHKERRQ(ierr); 1793 ierr = DMGetStratumIS(plex, "dim", depth, &allcellIS);CHKERRQ(ierr); 1794 if (!allcellIS) {ierr = DMGetStratumIS(plex, "depth", depth, &allcellIS);CHKERRQ(ierr);} 1795 for (s = 0; s < Nds; ++s) { 1796 PetscDS ds; 1797 DMLabel label; 1798 IS cellIS; 1799 1800 ierr = DMGetRegionNumDS(dm, s, &label, NULL, &ds);CHKERRQ(ierr); 1801 if (!label) { 1802 ierr = PetscObjectReference((PetscObject) allcellIS);CHKERRQ(ierr); 1803 cellIS = allcellIS; 1804 } else { 1805 IS pointIS; 1806 1807 ierr = DMLabelGetStratumIS(label, 1, &pointIS);CHKERRQ(ierr); 1808 ierr = ISIntersect_Caching_Internal(allcellIS, pointIS, &cellIS);CHKERRQ(ierr); 1809 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 1810 } 1811 ierr = DMPlexComputeResidual_Internal(plex, cellIS, PETSC_MIN_REAL, X, NULL, 0.0, F, user);CHKERRQ(ierr); 1812 ierr = ISDestroy(&cellIS);CHKERRQ(ierr); 1813 } 1814 ierr = ISDestroy(&allcellIS);CHKERRQ(ierr); 1815 ierr = DMDestroy(&plex);CHKERRQ(ierr); 1816 PetscFunctionReturn(0); 1817 } 1818 1819 /*@ 1820 DMPlexSNESComputeBoundaryFEM - Form the boundary values for the local input X 1821 1822 Input Parameters: 1823 + dm - The mesh 1824 - user - The user context 1825 1826 Output Parameter: 1827 . X - Local solution 1828 1829 Level: developer 1830 1831 .seealso: DMPlexComputeJacobianAction() 1832 @*/ 1833 PetscErrorCode DMPlexSNESComputeBoundaryFEM(DM dm, Vec X, void *user) 1834 { 1835 DM plex; 1836 PetscErrorCode ierr; 1837 1838 PetscFunctionBegin; 1839 ierr = DMSNESConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr); 1840 ierr = DMPlexInsertBoundaryValues(plex, PETSC_TRUE, X, PETSC_MIN_REAL, NULL, NULL, NULL);CHKERRQ(ierr); 1841 ierr = DMDestroy(&plex);CHKERRQ(ierr); 1842 PetscFunctionReturn(0); 1843 } 1844 1845 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) 1846 { 1847 DM_Plex *mesh = (DM_Plex *) dm->data; 1848 DM plex = NULL, plexA = NULL, tdm; 1849 DMEnclosureType encAux; 1850 PetscDS prob, probAux = NULL; 1851 PetscSection section, sectionAux = NULL; 1852 PetscSection globalSection, subSection = NULL; 1853 Vec locA = NULL, tv; 1854 PetscScalar *u = NULL, *u_t = NULL, *a = NULL, *elemMat = NULL; 1855 PetscInt v; 1856 PetscInt Nf, totDim, totDimAux = 0; 1857 PetscBool isMatISP, transform; 1858 PetscErrorCode ierr; 1859 1860 PetscFunctionBegin; 1861 ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); 1862 ierr = DMHasBasisTransform(dm, &transform);CHKERRQ(ierr); 1863 ierr = DMGetBasisTransformDM_Internal(dm, &tdm);CHKERRQ(ierr); 1864 ierr = DMGetBasisTransformVec_Internal(dm, &tv);CHKERRQ(ierr); 1865 ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); 1866 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1867 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 1868 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1869 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);CHKERRQ(ierr); 1870 if (locA) { 1871 DM dmAux; 1872 1873 ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); 1874 ierr = DMGetEnclosureRelation(dmAux, dm, &encAux);CHKERRQ(ierr); 1875 ierr = DMConvert(dmAux, DMPLEX, &plexA);CHKERRQ(ierr); 1876 ierr = DMGetDS(plexA, &probAux);CHKERRQ(ierr); 1877 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 1878 ierr = DMGetLocalSection(plexA, §ionAux);CHKERRQ(ierr); 1879 } 1880 1881 ierr = PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatISP);CHKERRQ(ierr); 1882 ierr = DMGetGlobalSection(dm, &globalSection);CHKERRQ(ierr); 1883 if (isMatISP) {ierr = DMPlexGetSubdomainSection(dm, &subSection);CHKERRQ(ierr);} 1884 for (v = 0; v < numValues; ++v) { 1885 PetscFEGeom *fgeom; 1886 PetscInt maxDegree; 1887 PetscQuadrature qGeom = NULL; 1888 IS pointIS; 1889 const PetscInt *points; 1890 PetscInt numFaces, face, Nq; 1891 1892 ierr = DMLabelGetStratumIS(label, values[v], &pointIS);CHKERRQ(ierr); 1893 if (!pointIS) continue; /* No points with that id on this process */ 1894 { 1895 IS isectIS; 1896 1897 /* TODO: Special cases of ISIntersect where it is quick to check a prior if one is a superset of the other */ 1898 ierr = ISIntersect_Caching_Internal(facetIS,pointIS,&isectIS);CHKERRQ(ierr); 1899 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 1900 pointIS = isectIS; 1901 } 1902 ierr = ISGetLocalSize(pointIS, &numFaces);CHKERRQ(ierr); 1903 ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); 1904 ierr = PetscMalloc4(numFaces*totDim, &u, locX_t ? numFaces*totDim : 0, &u_t, numFaces*totDim*totDim, &elemMat, locA ? numFaces*totDimAux : 0, &a);CHKERRQ(ierr); 1905 ierr = DMFieldGetDegree(coordField,pointIS,NULL,&maxDegree);CHKERRQ(ierr); 1906 if (maxDegree <= 1) { 1907 ierr = DMFieldCreateDefaultQuadrature(coordField,pointIS,&qGeom);CHKERRQ(ierr); 1908 } 1909 if (!qGeom) { 1910 PetscFE fe; 1911 1912 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); 1913 ierr = PetscFEGetFaceQuadrature(fe, &qGeom);CHKERRQ(ierr); 1914 ierr = PetscObjectReference((PetscObject)qGeom);CHKERRQ(ierr); 1915 } 1916 ierr = PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 1917 ierr = DMSNESGetFEGeom(coordField,pointIS,qGeom,PETSC_TRUE,&fgeom);CHKERRQ(ierr); 1918 for (face = 0; face < numFaces; ++face) { 1919 const PetscInt point = points[face], *support, *cone; 1920 PetscScalar *x = NULL; 1921 PetscInt i, coneSize, faceLoc; 1922 1923 ierr = DMPlexGetSupport(dm, point, &support);CHKERRQ(ierr); 1924 ierr = DMPlexGetConeSize(dm, support[0], &coneSize);CHKERRQ(ierr); 1925 ierr = DMPlexGetCone(dm, support[0], &cone);CHKERRQ(ierr); 1926 for (faceLoc = 0; faceLoc < coneSize; ++faceLoc) if (cone[faceLoc] == point) break; 1927 if (faceLoc == coneSize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Could not find face %D in cone of support[0] %D", point, support[0]); 1928 fgeom->face[face][0] = faceLoc; 1929 ierr = DMPlexVecGetClosure(plex, section, locX, support[0], NULL, &x);CHKERRQ(ierr); 1930 for (i = 0; i < totDim; ++i) u[face*totDim+i] = x[i]; 1931 ierr = DMPlexVecRestoreClosure(plex, section, locX, support[0], NULL, &x);CHKERRQ(ierr); 1932 if (locX_t) { 1933 ierr = DMPlexVecGetClosure(plex, section, locX_t, support[0], NULL, &x);CHKERRQ(ierr); 1934 for (i = 0; i < totDim; ++i) u_t[face*totDim+i] = x[i]; 1935 ierr = DMPlexVecRestoreClosure(plex, section, locX_t, support[0], NULL, &x);CHKERRQ(ierr); 1936 } 1937 if (locA) { 1938 PetscInt subp; 1939 ierr = DMGetEnclosurePoint(plexA, dm, encAux, support[0], &subp);CHKERRQ(ierr); 1940 ierr = DMPlexVecGetClosure(plexA, sectionAux, locA, subp, NULL, &x);CHKERRQ(ierr); 1941 for (i = 0; i < totDimAux; ++i) a[face*totDimAux+i] = x[i]; 1942 ierr = DMPlexVecRestoreClosure(plexA, sectionAux, locA, subp, NULL, &x);CHKERRQ(ierr); 1943 } 1944 } 1945 ierr = PetscArrayzero(elemMat, numFaces*totDim*totDim);CHKERRQ(ierr); 1946 { 1947 PetscFE fe; 1948 PetscInt Nb; 1949 /* Conforming batches */ 1950 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 1951 /* Remainder */ 1952 PetscFEGeom *chunkGeom = NULL; 1953 PetscInt fieldJ, Nr, offset; 1954 1955 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); 1956 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 1957 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1958 blockSize = Nb; 1959 batchSize = numBlocks * blockSize; 1960 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1961 numChunks = numFaces / (numBatches*batchSize); 1962 Ne = numChunks*numBatches*batchSize; 1963 Nr = numFaces % (numBatches*batchSize); 1964 offset = numFaces - Nr; 1965 ierr = PetscFEGeomGetChunk(fgeom,0,offset,&chunkGeom);CHKERRQ(ierr); 1966 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 1967 ierr = PetscFEIntegrateBdJacobian(prob, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMat);CHKERRQ(ierr); 1968 } 1969 ierr = PetscFEGeomGetChunk(fgeom,offset,numFaces,&chunkGeom);CHKERRQ(ierr); 1970 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 1971 ierr = PetscFEIntegrateBdJacobian(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); 1972 } 1973 ierr = PetscFEGeomRestoreChunk(fgeom,offset,numFaces,&chunkGeom);CHKERRQ(ierr); 1974 } 1975 for (face = 0; face < numFaces; ++face) { 1976 const PetscInt point = points[face], *support; 1977 1978 /* Transform to global basis before insertion in Jacobian */ 1979 ierr = DMPlexGetSupport(plex, point, &support);CHKERRQ(ierr); 1980 if (transform) {ierr = DMPlexBasisTransformPointTensor_Internal(dm, tdm, tv, support[0], PETSC_TRUE, totDim, &elemMat[face*totDim*totDim]);CHKERRQ(ierr);} 1981 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(point, "BdJacobian", totDim, totDim, &elemMat[face*totDim*totDim]);CHKERRQ(ierr);} 1982 if (!isMatISP) { 1983 ierr = DMPlexMatSetClosure(plex, section, globalSection, JacP, support[0], &elemMat[face*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 1984 } else { 1985 Mat lJ; 1986 1987 ierr = MatISGetLocalMat(JacP, &lJ);CHKERRQ(ierr); 1988 ierr = DMPlexMatSetClosure(plex, section, subSection, lJ, support[0], &elemMat[face*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 1989 } 1990 } 1991 ierr = DMSNESRestoreFEGeom(coordField,pointIS,qGeom,PETSC_TRUE,&fgeom);CHKERRQ(ierr); 1992 ierr = PetscQuadratureDestroy(&qGeom);CHKERRQ(ierr); 1993 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 1994 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 1995 ierr = PetscFree4(u, u_t, elemMat, a);CHKERRQ(ierr); 1996 } 1997 if (plex) {ierr = DMDestroy(&plex);CHKERRQ(ierr);} 1998 if (plexA) {ierr = DMDestroy(&plexA);CHKERRQ(ierr);} 1999 PetscFunctionReturn(0); 2000 } 2001 2002 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) 2003 { 2004 DMField coordField; 2005 DMLabel depthLabel; 2006 IS facetIS; 2007 PetscInt dim; 2008 PetscErrorCode ierr; 2009 2010 PetscFunctionBegin; 2011 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 2012 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 2013 ierr = DMLabelGetStratumIS(depthLabel, dim-1, &facetIS);CHKERRQ(ierr); 2014 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 2015 ierr = DMPlexComputeBdJacobian_Single_Internal(dm, t, label, numValues, values, field, locX, locX_t, X_tShift, Jac, JacP, coordField, facetIS);CHKERRQ(ierr); 2016 ierr = ISDestroy(&facetIS);CHKERRQ(ierr); 2017 PetscFunctionReturn(0); 2018 } 2019 2020 PetscErrorCode DMPlexComputeBdJacobian_Internal(DM dm, Vec locX, Vec locX_t, PetscReal t, PetscReal X_tShift, Mat Jac, Mat JacP, void *user) 2021 { 2022 PetscDS prob; 2023 PetscInt dim, numBd, bd; 2024 DMLabel depthLabel; 2025 DMField coordField = NULL; 2026 IS facetIS; 2027 PetscErrorCode ierr; 2028 2029 PetscFunctionBegin; 2030 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 2031 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 2032 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 2033 ierr = DMLabelGetStratumIS(depthLabel, dim-1, &facetIS);CHKERRQ(ierr); 2034 ierr = PetscDSGetNumBoundary(prob, &numBd);CHKERRQ(ierr); 2035 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 2036 for (bd = 0; bd < numBd; ++bd) { 2037 DMBoundaryConditionType type; 2038 const char *bdLabel; 2039 DMLabel label; 2040 const PetscInt *values; 2041 PetscInt fieldI, numValues; 2042 PetscObject obj; 2043 PetscClassId id; 2044 2045 ierr = PetscDSGetBoundary(prob, bd, &type, NULL, &bdLabel, &fieldI, NULL, NULL, NULL, &numValues, &values, NULL);CHKERRQ(ierr); 2046 ierr = PetscDSGetDiscretization(prob, fieldI, &obj);CHKERRQ(ierr); 2047 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 2048 if ((id != PETSCFE_CLASSID) || (type & DM_BC_ESSENTIAL)) continue; 2049 ierr = DMGetLabel(dm, bdLabel, &label);CHKERRQ(ierr); 2050 ierr = DMPlexComputeBdJacobian_Single_Internal(dm, t, label, numValues, values, fieldI, locX, locX_t, X_tShift, Jac, JacP, coordField, facetIS);CHKERRQ(ierr); 2051 } 2052 ierr = ISDestroy(&facetIS);CHKERRQ(ierr); 2053 PetscFunctionReturn(0); 2054 } 2055 2056 PetscErrorCode DMPlexComputeJacobian_Internal(DM dm, IS cellIS, PetscReal t, PetscReal X_tShift, Vec X, Vec X_t, Mat Jac, Mat JacP,void *user) 2057 { 2058 DM_Plex *mesh = (DM_Plex *) dm->data; 2059 const char *name = "Jacobian"; 2060 DM dmAux, plex, tdm; 2061 DMEnclosureType encAux; 2062 Vec A, tv; 2063 DMField coordField; 2064 PetscDS prob, probAux = NULL; 2065 PetscSection section, globalSection, subSection, sectionAux; 2066 PetscScalar *elemMat, *elemMatP, *elemMatD, *u, *u_t, *a = NULL; 2067 const PetscInt *cells; 2068 PetscInt Nf, fieldI, fieldJ; 2069 PetscInt totDim, totDimAux, cStart, cEnd, numCells, c; 2070 PetscBool isMatIS, isMatISP, hasJac, hasPrec, hasDyn, hasFV = PETSC_FALSE, transform; 2071 PetscErrorCode ierr; 2072 2073 PetscFunctionBegin; 2074 ierr = PetscLogEventBegin(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 2075 ierr = ISGetLocalSize(cellIS, &numCells);CHKERRQ(ierr); 2076 ierr = ISGetPointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 2077 ierr = DMHasBasisTransform(dm, &transform);CHKERRQ(ierr); 2078 ierr = DMGetBasisTransformDM_Internal(dm, &tdm);CHKERRQ(ierr); 2079 ierr = DMGetBasisTransformVec_Internal(dm, &tv);CHKERRQ(ierr); 2080 ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); 2081 ierr = PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatISP);CHKERRQ(ierr); 2082 ierr = DMGetGlobalSection(dm, &globalSection);CHKERRQ(ierr); 2083 if (isMatISP) {ierr = DMPlexGetSubdomainSection(dm, &subSection);CHKERRQ(ierr);} 2084 ierr = ISGetLocalSize(cellIS, &numCells);CHKERRQ(ierr); 2085 ierr = ISGetPointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 2086 ierr = DMGetCellDS(dm, cells ? cells[cStart] : cStart, &prob);CHKERRQ(ierr); 2087 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 2088 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 2089 ierr = PetscDSHasJacobian(prob, &hasJac);CHKERRQ(ierr); 2090 ierr = PetscDSHasJacobianPreconditioner(prob, &hasPrec);CHKERRQ(ierr); 2091 /* user passed in the same matrix, avoid double contributions and 2092 only assemble the Jacobian */ 2093 if (hasJac && Jac == JacP) hasPrec = PETSC_FALSE; 2094 ierr = PetscDSHasDynamicJacobian(prob, &hasDyn);CHKERRQ(ierr); 2095 hasDyn = hasDyn && (X_tShift != 0.0) ? PETSC_TRUE : PETSC_FALSE; 2096 ierr = PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);CHKERRQ(ierr); 2097 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);CHKERRQ(ierr); 2098 if (dmAux) { 2099 ierr = DMGetEnclosureRelation(dmAux, dm, &encAux);CHKERRQ(ierr); 2100 ierr = DMConvert(dmAux, DMPLEX, &plex);CHKERRQ(ierr); 2101 ierr = DMGetLocalSection(plex, §ionAux);CHKERRQ(ierr); 2102 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 2103 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 2104 } 2105 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); 2106 if (dmAux) {ierr = PetscMalloc1(numCells*totDimAux, &a);CHKERRQ(ierr);} 2107 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 2108 for (c = cStart; c < cEnd; ++c) { 2109 const PetscInt cell = cells ? cells[c] : c; 2110 const PetscInt cind = c - cStart; 2111 PetscScalar *x = NULL, *x_t = NULL; 2112 PetscInt i; 2113 2114 ierr = DMPlexVecGetClosure(dm, section, X, cell, NULL, &x);CHKERRQ(ierr); 2115 for (i = 0; i < totDim; ++i) u[cind*totDim+i] = x[i]; 2116 ierr = DMPlexVecRestoreClosure(dm, section, X, cell, NULL, &x);CHKERRQ(ierr); 2117 if (X_t) { 2118 ierr = DMPlexVecGetClosure(dm, section, X_t, cell, NULL, &x_t);CHKERRQ(ierr); 2119 for (i = 0; i < totDim; ++i) u_t[cind*totDim+i] = x_t[i]; 2120 ierr = DMPlexVecRestoreClosure(dm, section, X_t, cell, NULL, &x_t);CHKERRQ(ierr); 2121 } 2122 if (dmAux) { 2123 PetscInt subcell; 2124 ierr = DMGetEnclosurePoint(dmAux, dm, encAux, cell, &subcell);CHKERRQ(ierr); 2125 ierr = DMPlexVecGetClosure(plex, sectionAux, A, subcell, NULL, &x);CHKERRQ(ierr); 2126 for (i = 0; i < totDimAux; ++i) a[cind*totDimAux+i] = x[i]; 2127 ierr = DMPlexVecRestoreClosure(plex, sectionAux, A, subcell, NULL, &x);CHKERRQ(ierr); 2128 } 2129 } 2130 if (hasJac) {ierr = PetscArrayzero(elemMat, numCells*totDim*totDim);CHKERRQ(ierr);} 2131 if (hasPrec) {ierr = PetscArrayzero(elemMatP, numCells*totDim*totDim);CHKERRQ(ierr);} 2132 if (hasDyn) {ierr = PetscArrayzero(elemMatD, numCells*totDim*totDim);CHKERRQ(ierr);} 2133 for (fieldI = 0; fieldI < Nf; ++fieldI) { 2134 PetscClassId id; 2135 PetscFE fe; 2136 PetscQuadrature qGeom = NULL; 2137 PetscInt Nb; 2138 /* Conforming batches */ 2139 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 2140 /* Remainder */ 2141 PetscInt Nr, offset, Nq; 2142 PetscInt maxDegree; 2143 PetscFEGeom *cgeomFEM, *chunkGeom = NULL, *remGeom = NULL; 2144 2145 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); 2146 ierr = PetscObjectGetClassId((PetscObject) fe, &id);CHKERRQ(ierr); 2147 if (id == PETSCFV_CLASSID) {hasFV = PETSC_TRUE; continue;} 2148 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 2149 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 2150 ierr = DMFieldGetDegree(coordField,cellIS,NULL,&maxDegree);CHKERRQ(ierr); 2151 if (maxDegree <= 1) { 2152 ierr = DMFieldCreateDefaultQuadrature(coordField,cellIS,&qGeom);CHKERRQ(ierr); 2153 } 2154 if (!qGeom) { 2155 ierr = PetscFEGetQuadrature(fe,&qGeom);CHKERRQ(ierr); 2156 ierr = PetscObjectReference((PetscObject)qGeom);CHKERRQ(ierr); 2157 } 2158 ierr = PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 2159 ierr = DMSNESGetFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);CHKERRQ(ierr); 2160 blockSize = Nb; 2161 batchSize = numBlocks * blockSize; 2162 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 2163 numChunks = numCells / (numBatches*batchSize); 2164 Ne = numChunks*numBatches*batchSize; 2165 Nr = numCells % (numBatches*batchSize); 2166 offset = numCells - Nr; 2167 ierr = PetscFEGeomGetChunk(cgeomFEM,0,offset,&chunkGeom);CHKERRQ(ierr); 2168 ierr = PetscFEGeomGetChunk(cgeomFEM,offset,numCells,&remGeom);CHKERRQ(ierr); 2169 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 2170 if (hasJac) { 2171 ierr = PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMat);CHKERRQ(ierr); 2172 ierr = PetscFEIntegrateJacobian(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); 2173 } 2174 if (hasPrec) { 2175 ierr = PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN_PRE, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMatP);CHKERRQ(ierr); 2176 ierr = PetscFEIntegrateJacobian(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); 2177 } 2178 if (hasDyn) { 2179 ierr = PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN_DYN, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMatD);CHKERRQ(ierr); 2180 ierr = PetscFEIntegrateJacobian(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); 2181 } 2182 } 2183 ierr = PetscFEGeomRestoreChunk(cgeomFEM,offset,numCells,&remGeom);CHKERRQ(ierr); 2184 ierr = PetscFEGeomRestoreChunk(cgeomFEM,0,offset,&chunkGeom);CHKERRQ(ierr); 2185 ierr = DMSNESRestoreFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);CHKERRQ(ierr); 2186 ierr = PetscQuadratureDestroy(&qGeom);CHKERRQ(ierr); 2187 } 2188 /* Add contribution from X_t */ 2189 if (hasDyn) {for (c = 0; c < numCells*totDim*totDim; ++c) elemMat[c] += X_tShift*elemMatD[c];} 2190 if (hasFV) { 2191 PetscClassId id; 2192 PetscFV fv; 2193 PetscInt offsetI, NcI, NbI = 1, fc, f; 2194 2195 for (fieldI = 0; fieldI < Nf; ++fieldI) { 2196 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fv);CHKERRQ(ierr); 2197 ierr = PetscDSGetFieldOffset(prob, fieldI, &offsetI);CHKERRQ(ierr); 2198 ierr = PetscObjectGetClassId((PetscObject) fv, &id);CHKERRQ(ierr); 2199 if (id != PETSCFV_CLASSID) continue; 2200 /* Put in the identity */ 2201 ierr = PetscFVGetNumComponents(fv, &NcI);CHKERRQ(ierr); 2202 for (c = cStart; c < cEnd; ++c) { 2203 const PetscInt cind = c - cStart; 2204 const PetscInt eOffset = cind*totDim*totDim; 2205 for (fc = 0; fc < NcI; ++fc) { 2206 for (f = 0; f < NbI; ++f) { 2207 const PetscInt i = offsetI + f*NcI+fc; 2208 if (hasPrec) { 2209 if (hasJac) {elemMat[eOffset+i*totDim+i] = 1.0;} 2210 elemMatP[eOffset+i*totDim+i] = 1.0; 2211 } else {elemMat[eOffset+i*totDim+i] = 1.0;} 2212 } 2213 } 2214 } 2215 } 2216 /* No allocated space for FV stuff, so ignore the zero entries */ 2217 ierr = MatSetOption(JacP, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE);CHKERRQ(ierr); 2218 } 2219 /* Insert values into matrix */ 2220 isMatIS = PETSC_FALSE; 2221 if (hasPrec && hasJac) { 2222 ierr = PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatIS);CHKERRQ(ierr); 2223 } 2224 if (isMatIS && !subSection) { 2225 ierr = DMPlexGetSubdomainSection(dm, &subSection);CHKERRQ(ierr); 2226 } 2227 for (c = cStart; c < cEnd; ++c) { 2228 const PetscInt cell = cells ? cells[c] : c; 2229 const PetscInt cind = c - cStart; 2230 2231 /* Transform to global basis before insertion in Jacobian */ 2232 if (transform) {ierr = DMPlexBasisTransformPointTensor_Internal(dm, tdm, tv, cell, PETSC_TRUE, totDim, &elemMat[cind*totDim*totDim]);CHKERRQ(ierr);} 2233 if (hasPrec) { 2234 if (hasJac) { 2235 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(cell, name, totDim, totDim, &elemMat[cind*totDim*totDim]);CHKERRQ(ierr);} 2236 if (!isMatIS) { 2237 ierr = DMPlexMatSetClosure(dm, section, globalSection, Jac, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2238 } else { 2239 Mat lJ; 2240 2241 ierr = MatISGetLocalMat(Jac,&lJ);CHKERRQ(ierr); 2242 ierr = DMPlexMatSetClosure(dm, section, subSection, lJ, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2243 } 2244 } 2245 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(cell, name, totDim, totDim, &elemMatP[cind*totDim*totDim]);CHKERRQ(ierr);} 2246 if (!isMatISP) { 2247 ierr = DMPlexMatSetClosure(dm, section, globalSection, JacP, cell, &elemMatP[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2248 } else { 2249 Mat lJ; 2250 2251 ierr = MatISGetLocalMat(JacP,&lJ);CHKERRQ(ierr); 2252 ierr = DMPlexMatSetClosure(dm, section, subSection, lJ, cell, &elemMatP[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2253 } 2254 } else { 2255 if (hasJac) { 2256 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(cell, name, totDim, totDim, &elemMat[cind*totDim*totDim]);CHKERRQ(ierr);} 2257 if (!isMatISP) { 2258 ierr = DMPlexMatSetClosure(dm, section, globalSection, JacP, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2259 } else { 2260 Mat lJ; 2261 2262 ierr = MatISGetLocalMat(JacP,&lJ);CHKERRQ(ierr); 2263 ierr = DMPlexMatSetClosure(dm, section, subSection, lJ, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2264 } 2265 } 2266 } 2267 } 2268 ierr = ISRestorePointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 2269 if (hasFV) {ierr = MatSetOption(JacP, MAT_IGNORE_ZERO_ENTRIES, PETSC_FALSE);CHKERRQ(ierr);} 2270 ierr = PetscFree5(u,u_t,elemMat,elemMatP,elemMatD);CHKERRQ(ierr); 2271 if (dmAux) { 2272 ierr = PetscFree(a);CHKERRQ(ierr); 2273 ierr = DMDestroy(&plex);CHKERRQ(ierr); 2274 } 2275 /* Compute boundary integrals */ 2276 ierr = DMPlexComputeBdJacobian_Internal(dm, X, X_t, t, X_tShift, Jac, JacP, user);CHKERRQ(ierr); 2277 /* Assemble matrix */ 2278 if (hasJac && hasPrec) { 2279 ierr = MatAssemblyBegin(Jac, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2280 ierr = MatAssemblyEnd(Jac, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2281 } 2282 ierr = MatAssemblyBegin(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2283 ierr = MatAssemblyEnd(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2284 ierr = PetscLogEventEnd(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 2285 PetscFunctionReturn(0); 2286 } 2287 2288 PetscErrorCode DMPlexComputeJacobian_Hybrid_Internal(DM dm, IS cellIS, PetscReal t, PetscReal X_tShift, Vec locX, Vec locX_t, Mat Jac, Mat JacP, void *user) 2289 { 2290 DM_Plex *mesh = (DM_Plex *) dm->data; 2291 const char *name = "Hybrid Jacobian"; 2292 DM dmAux = NULL; 2293 DM plex = NULL; 2294 DM plexA = NULL; 2295 DMLabel ghostLabel = NULL; 2296 PetscDS prob = NULL; 2297 PetscDS probAux = NULL; 2298 PetscSection section = NULL; 2299 DMField coordField = NULL; 2300 Vec locA; 2301 PetscScalar *u = NULL, *u_t, *a = NULL; 2302 PetscScalar *elemMat, *elemMatP; 2303 PetscSection globalSection, subSection, sectionAux; 2304 IS chunkIS; 2305 const PetscInt *cells; 2306 PetscInt *faces; 2307 PetscInt cStart, cEnd, numCells; 2308 PetscInt Nf, fieldI, fieldJ, totDim, totDimAux, numChunks, cellChunkSize, chunk; 2309 PetscInt maxDegree = PETSC_MAX_INT; 2310 PetscQuadrature affineQuad = NULL, *quads = NULL; 2311 PetscFEGeom *affineGeom = NULL, **geoms = NULL; 2312 PetscBool isMatIS = PETSC_FALSE, isMatISP = PETSC_FALSE, hasBdJac, hasBdPrec; 2313 PetscErrorCode ierr; 2314 2315 PetscFunctionBegin; 2316 ierr = PetscLogEventBegin(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 2317 ierr = ISGetLocalSize(cellIS, &numCells);CHKERRQ(ierr); 2318 ierr = ISGetPointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 2319 ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); 2320 ierr = DMGetSection(dm, §ion);CHKERRQ(ierr); 2321 ierr = DMGetGlobalSection(dm, &globalSection);CHKERRQ(ierr); 2322 ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 2323 ierr = DMGetCellDS(dm, cStart, &prob);CHKERRQ(ierr); 2324 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 2325 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 2326 ierr = PetscDSHasBdJacobian(prob, &hasBdJac);CHKERRQ(ierr); 2327 ierr = PetscDSHasBdJacobianPreconditioner(prob, &hasBdPrec);CHKERRQ(ierr); 2328 ierr = PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatISP);CHKERRQ(ierr); 2329 if (isMatISP) {ierr = DMPlexGetSubdomainSection(plex, &subSection);CHKERRQ(ierr);} 2330 if (hasBdPrec && hasBdJac) {ierr = PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatIS);CHKERRQ(ierr);} 2331 if (isMatIS && !subSection) {ierr = DMPlexGetSubdomainSection(plex, &subSection);CHKERRQ(ierr);} 2332 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);CHKERRQ(ierr); 2333 if (locA) { 2334 ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); 2335 ierr = DMConvert(dmAux, DMPLEX, &plexA);CHKERRQ(ierr); 2336 ierr = DMGetSection(dmAux, §ionAux);CHKERRQ(ierr); 2337 ierr = DMGetCellDS(dmAux, cStart, &probAux);CHKERRQ(ierr); 2338 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 2339 } 2340 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 2341 ierr = DMFieldGetDegree(coordField, cellIS, NULL, &maxDegree);CHKERRQ(ierr); 2342 if (maxDegree > 1) { 2343 PetscInt f; 2344 ierr = PetscCalloc2(Nf,&quads,Nf,&geoms);CHKERRQ(ierr); 2345 for (f = 0; f < Nf; ++f) { 2346 PetscFE fe; 2347 2348 ierr = PetscDSGetDiscretization(prob, f, (PetscObject *) &fe);CHKERRQ(ierr); 2349 if (fe) { 2350 ierr = PetscFEGetQuadrature(fe, &quads[f]);CHKERRQ(ierr); 2351 ierr = PetscObjectReference((PetscObject) quads[f]);CHKERRQ(ierr); 2352 } 2353 } 2354 } 2355 cellChunkSize = numCells; 2356 numChunks = !numCells ? 0 : PetscCeilReal(((PetscReal) numCells)/cellChunkSize); 2357 ierr = PetscCalloc1(2*cellChunkSize, &faces);CHKERRQ(ierr); 2358 ierr = ISCreateGeneral(PETSC_COMM_SELF, cellChunkSize, faces, PETSC_USE_POINTER, &chunkIS);CHKERRQ(ierr); 2359 ierr = DMPlexGetCellFields(dm, cellIS, locX, locX_t, locA, &u, &u_t, &a);CHKERRQ(ierr); 2360 ierr = DMGetWorkArray(dm, hasBdJac ? cellChunkSize*totDim*totDim : 0, MPIU_SCALAR, &elemMat);CHKERRQ(ierr); 2361 ierr = DMGetWorkArray(dm, hasBdPrec ? cellChunkSize*totDim*totDim : 0, MPIU_SCALAR, &elemMatP);CHKERRQ(ierr); 2362 for (chunk = 0; chunk < numChunks; ++chunk) { 2363 PetscInt cS = cStart+chunk*cellChunkSize, cE = PetscMin(cS+cellChunkSize, cEnd), numCells = cE - cS, c; 2364 2365 if (hasBdJac) {ierr = PetscMemzero(elemMat, numCells*totDim*totDim * sizeof(PetscScalar));CHKERRQ(ierr);} 2366 if (hasBdPrec) {ierr = PetscMemzero(elemMatP, numCells*totDim*totDim * sizeof(PetscScalar));CHKERRQ(ierr);} 2367 /* Get faces */ 2368 for (c = cS; c < cE; ++c) { 2369 const PetscInt cell = cells ? cells[c] : c; 2370 const PetscInt *cone; 2371 ierr = DMPlexGetCone(plex, cell, &cone);CHKERRQ(ierr); 2372 faces[(c-cS)*2+0] = cone[0]; 2373 faces[(c-cS)*2+1] = cone[1]; 2374 } 2375 ierr = ISGeneralSetIndices(chunkIS, cellChunkSize, faces, PETSC_USE_POINTER);CHKERRQ(ierr); 2376 if (maxDegree <= 1) { 2377 if (!affineQuad) {ierr = DMFieldCreateDefaultQuadrature(coordField, chunkIS, &affineQuad);CHKERRQ(ierr);} 2378 if (affineQuad) {ierr = DMSNESGetFEGeom(coordField, chunkIS, affineQuad, PETSC_TRUE, &affineGeom);CHKERRQ(ierr);} 2379 } else { 2380 PetscInt f; 2381 for (f = 0; f < Nf; ++f) { 2382 if (quads[f]) {ierr = DMSNESGetFEGeom(coordField, chunkIS, quads[f], PETSC_TRUE, &geoms[f]);CHKERRQ(ierr);} 2383 } 2384 } 2385 2386 for (fieldI = 0; fieldI < Nf; ++fieldI) { 2387 PetscFE feI; 2388 PetscFEGeom *geom = affineGeom ? affineGeom : geoms[fieldI]; 2389 PetscFEGeom *chunkGeom = NULL, *remGeom = NULL; 2390 PetscQuadrature quad = affineQuad ? affineQuad : quads[fieldI]; 2391 PetscInt numChunks, numBatches, batchSize, numBlocks, blockSize, Ne, Nr, offset, Nq, Nb; 2392 2393 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &feI);CHKERRQ(ierr); 2394 if (!feI) continue; 2395 ierr = PetscFEGetTileSizes(feI, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 2396 ierr = PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 2397 ierr = PetscFEGetDimension(feI, &Nb);CHKERRQ(ierr); 2398 blockSize = Nb; 2399 batchSize = numBlocks * blockSize; 2400 ierr = PetscFESetTileSizes(feI, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 2401 numChunks = numCells / (numBatches*batchSize); 2402 Ne = numChunks*numBatches*batchSize; 2403 Nr = numCells % (numBatches*batchSize); 2404 offset = numCells - Nr; 2405 ierr = PetscFEGeomGetChunk(geom,0,offset,&chunkGeom);CHKERRQ(ierr); 2406 ierr = PetscFEGeomGetChunk(geom,offset,numCells,&remGeom);CHKERRQ(ierr); 2407 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 2408 PetscFE feJ; 2409 2410 ierr = PetscDSGetDiscretization(prob, fieldJ, (PetscObject *) &feJ);CHKERRQ(ierr); 2411 if (!feJ) continue; 2412 if (hasBdJac) { 2413 ierr = PetscFEIntegrateHybridJacobian(prob, PETSCFE_JACOBIAN, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMat);CHKERRQ(ierr); 2414 ierr = PetscFEIntegrateHybridJacobian(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); 2415 } 2416 if (hasBdPrec) { 2417 ierr = PetscFEIntegrateHybridJacobian(prob, PETSCFE_JACOBIAN_PRE, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMatP);CHKERRQ(ierr); 2418 ierr = PetscFEIntegrateHybridJacobian(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); 2419 } 2420 } 2421 ierr = PetscFEGeomRestoreChunk(geom,offset,numCells,&remGeom);CHKERRQ(ierr); 2422 ierr = PetscFEGeomRestoreChunk(geom,0,offset,&chunkGeom);CHKERRQ(ierr); 2423 } 2424 /* Insert values into matrix */ 2425 for (c = cS; c < cE; ++c) { 2426 const PetscInt cell = cells ? cells[c] : c; 2427 const PetscInt cind = c - cS; 2428 2429 if (hasBdPrec) { 2430 if (hasBdJac) { 2431 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(cell, name, totDim, totDim, &elemMat[cind*totDim*totDim]);CHKERRQ(ierr);} 2432 if (!isMatIS) { 2433 ierr = DMPlexMatSetClosure(plex, section, globalSection, Jac, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2434 } else { 2435 Mat lJ; 2436 2437 ierr = MatISGetLocalMat(Jac,&lJ);CHKERRQ(ierr); 2438 ierr = DMPlexMatSetClosure(plex, section, subSection, lJ, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2439 } 2440 } 2441 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(cell, name, totDim, totDim, &elemMatP[cind*totDim*totDim]);CHKERRQ(ierr);} 2442 if (!isMatISP) { 2443 ierr = DMPlexMatSetClosure(plex, section, globalSection, JacP, cell, &elemMatP[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2444 } else { 2445 Mat lJ; 2446 2447 ierr = MatISGetLocalMat(JacP,&lJ);CHKERRQ(ierr); 2448 ierr = DMPlexMatSetClosure(plex, section, subSection, lJ, cell, &elemMatP[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2449 } 2450 } else if (hasBdJac) { 2451 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(cell, name, totDim, totDim, &elemMat[cind*totDim*totDim]);CHKERRQ(ierr);} 2452 if (!isMatISP) { 2453 ierr = DMPlexMatSetClosure(plex, section, globalSection, JacP, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2454 } else { 2455 Mat lJ; 2456 2457 ierr = MatISGetLocalMat(JacP,&lJ);CHKERRQ(ierr); 2458 ierr = DMPlexMatSetClosure(plex, section, subSection, lJ, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2459 } 2460 } 2461 } 2462 } 2463 ierr = DMPlexRestoreCellFields(dm, cellIS, locX, locX_t, locA, &u, &u_t, &a);CHKERRQ(ierr); 2464 ierr = DMRestoreWorkArray(dm, hasBdJac ? cellChunkSize*totDim*totDim : 0, MPIU_SCALAR, &elemMat);CHKERRQ(ierr); 2465 ierr = DMRestoreWorkArray(dm, hasBdPrec ? cellChunkSize*totDim*totDim : 0, MPIU_SCALAR, &elemMatP);CHKERRQ(ierr); 2466 ierr = PetscFree(faces);CHKERRQ(ierr); 2467 ierr = ISDestroy(&chunkIS);CHKERRQ(ierr); 2468 ierr = ISRestorePointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 2469 if (maxDegree <= 1) { 2470 ierr = DMSNESRestoreFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&affineGeom);CHKERRQ(ierr); 2471 ierr = PetscQuadratureDestroy(&affineQuad);CHKERRQ(ierr); 2472 } else { 2473 PetscInt f; 2474 for (f = 0; f < Nf; ++f) { 2475 if (geoms) {ierr = DMSNESRestoreFEGeom(coordField,cellIS,quads[f],PETSC_FALSE, &geoms[f]);CHKERRQ(ierr);} 2476 if (quads) {ierr = PetscQuadratureDestroy(&quads[f]);CHKERRQ(ierr);} 2477 } 2478 ierr = PetscFree2(quads,geoms);CHKERRQ(ierr); 2479 } 2480 if (dmAux) {ierr = DMDestroy(&plexA);CHKERRQ(ierr);} 2481 ierr = DMDestroy(&plex);CHKERRQ(ierr); 2482 /* Assemble matrix */ 2483 if (hasBdJac && hasBdPrec) { 2484 ierr = MatAssemblyBegin(Jac, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2485 ierr = MatAssemblyEnd(Jac, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2486 } 2487 ierr = MatAssemblyBegin(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2488 ierr = MatAssemblyEnd(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2489 ierr = PetscLogEventEnd(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 2490 PetscFunctionReturn(0); 2491 } 2492 2493 /*@ 2494 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. 2495 2496 Input Parameters: 2497 + dm - The mesh 2498 . cellIS - 2499 . t - The time 2500 . X_tShift - The multiplier for the Jacobian with repsect to X_t 2501 . X - Local solution vector 2502 . X_t - Time-derivative of the local solution vector 2503 . Y - Local input vector 2504 - user - The user context 2505 2506 Output Parameter: 2507 . Z - Local output vector 2508 2509 Note: 2510 We form the residual one batch of elements at a time. This allows us to offload work onto an accelerator, 2511 like a GPU, or vectorize on a multicore machine. 2512 2513 Level: developer 2514 2515 .seealso: FormFunctionLocal() 2516 @*/ 2517 PetscErrorCode DMPlexComputeJacobianAction(DM dm, IS cellIS, PetscReal t, PetscReal X_tShift, Vec X, Vec X_t, Vec Y, Vec Z, void *user) 2518 { 2519 DM_Plex *mesh = (DM_Plex *) dm->data; 2520 const char *name = "Jacobian"; 2521 DM dmAux, plex, plexAux = NULL; 2522 DMEnclosureType encAux; 2523 Vec A; 2524 PetscDS prob, probAux = NULL; 2525 PetscQuadrature quad; 2526 PetscSection section, globalSection, sectionAux; 2527 PetscScalar *elemMat, *elemMatD, *u, *u_t, *a = NULL, *y, *z; 2528 PetscInt Nf, fieldI, fieldJ; 2529 PetscInt totDim, totDimAux = 0; 2530 const PetscInt *cells; 2531 PetscInt cStart, cEnd, numCells, c; 2532 PetscBool hasDyn; 2533 DMField coordField; 2534 PetscErrorCode ierr; 2535 2536 PetscFunctionBegin; 2537 ierr = PetscLogEventBegin(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 2538 ierr = DMSNESConvertPlex(dm, &plex, PETSC_TRUE);CHKERRQ(ierr); 2539 if (!cellIS) { 2540 PetscInt depth; 2541 2542 ierr = DMPlexGetDepth(plex, &depth);CHKERRQ(ierr); 2543 ierr = DMGetStratumIS(plex, "dim", depth, &cellIS);CHKERRQ(ierr); 2544 if (!cellIS) {ierr = DMGetStratumIS(plex, "depth", depth, &cellIS);CHKERRQ(ierr);} 2545 } else { 2546 ierr = PetscObjectReference((PetscObject) cellIS);CHKERRQ(ierr); 2547 } 2548 ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); 2549 ierr = DMGetGlobalSection(dm, &globalSection);CHKERRQ(ierr); 2550 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 2551 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 2552 ierr = PetscDSHasDynamicJacobian(prob, &hasDyn);CHKERRQ(ierr); 2553 hasDyn = hasDyn && (X_tShift != 0.0) ? PETSC_TRUE : PETSC_FALSE; 2554 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); 2555 ierr = ISGetLocalSize(cellIS, &numCells);CHKERRQ(ierr); 2556 ierr = ISGetPointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 2557 ierr = PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);CHKERRQ(ierr); 2558 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);CHKERRQ(ierr); 2559 if (dmAux) { 2560 ierr = DMGetEnclosureRelation(dmAux, dm, &encAux);CHKERRQ(ierr); 2561 ierr = DMConvert(dmAux, DMPLEX, &plexAux);CHKERRQ(ierr); 2562 ierr = DMGetLocalSection(plexAux, §ionAux);CHKERRQ(ierr); 2563 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 2564 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 2565 } 2566 ierr = VecSet(Z, 0.0);CHKERRQ(ierr); 2567 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); 2568 if (dmAux) {ierr = PetscMalloc1(numCells*totDimAux, &a);CHKERRQ(ierr);} 2569 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 2570 for (c = cStart; c < cEnd; ++c) { 2571 const PetscInt cell = cells ? cells[c] : c; 2572 const PetscInt cind = c - cStart; 2573 PetscScalar *x = NULL, *x_t = NULL; 2574 PetscInt i; 2575 2576 ierr = DMPlexVecGetClosure(dm, section, X, cell, NULL, &x);CHKERRQ(ierr); 2577 for (i = 0; i < totDim; ++i) u[cind*totDim+i] = x[i]; 2578 ierr = DMPlexVecRestoreClosure(dm, section, X, cell, NULL, &x);CHKERRQ(ierr); 2579 if (X_t) { 2580 ierr = DMPlexVecGetClosure(dm, section, X_t, cell, NULL, &x_t);CHKERRQ(ierr); 2581 for (i = 0; i < totDim; ++i) u_t[cind*totDim+i] = x_t[i]; 2582 ierr = DMPlexVecRestoreClosure(dm, section, X_t, cell, NULL, &x_t);CHKERRQ(ierr); 2583 } 2584 if (dmAux) { 2585 PetscInt subcell; 2586 ierr = DMGetEnclosurePoint(dmAux, dm, encAux, cell, &subcell);CHKERRQ(ierr); 2587 ierr = DMPlexVecGetClosure(plexAux, sectionAux, A, subcell, NULL, &x);CHKERRQ(ierr); 2588 for (i = 0; i < totDimAux; ++i) a[cind*totDimAux+i] = x[i]; 2589 ierr = DMPlexVecRestoreClosure(plexAux, sectionAux, A, subcell, NULL, &x);CHKERRQ(ierr); 2590 } 2591 ierr = DMPlexVecGetClosure(dm, section, Y, cell, NULL, &x);CHKERRQ(ierr); 2592 for (i = 0; i < totDim; ++i) y[cind*totDim+i] = x[i]; 2593 ierr = DMPlexVecRestoreClosure(dm, section, Y, cell, NULL, &x);CHKERRQ(ierr); 2594 } 2595 ierr = PetscArrayzero(elemMat, numCells*totDim*totDim);CHKERRQ(ierr); 2596 if (hasDyn) {ierr = PetscArrayzero(elemMatD, numCells*totDim*totDim);CHKERRQ(ierr);} 2597 for (fieldI = 0; fieldI < Nf; ++fieldI) { 2598 PetscFE fe; 2599 PetscInt Nb; 2600 /* Conforming batches */ 2601 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 2602 /* Remainder */ 2603 PetscInt Nr, offset, Nq; 2604 PetscQuadrature qGeom = NULL; 2605 PetscInt maxDegree; 2606 PetscFEGeom *cgeomFEM, *chunkGeom = NULL, *remGeom = NULL; 2607 2608 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); 2609 ierr = PetscFEGetQuadrature(fe, &quad);CHKERRQ(ierr); 2610 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 2611 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 2612 ierr = DMFieldGetDegree(coordField,cellIS,NULL,&maxDegree);CHKERRQ(ierr); 2613 if (maxDegree <= 1) {ierr = DMFieldCreateDefaultQuadrature(coordField,cellIS,&qGeom);CHKERRQ(ierr);} 2614 if (!qGeom) { 2615 ierr = PetscFEGetQuadrature(fe,&qGeom);CHKERRQ(ierr); 2616 ierr = PetscObjectReference((PetscObject)qGeom);CHKERRQ(ierr); 2617 } 2618 ierr = PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 2619 ierr = DMSNESGetFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);CHKERRQ(ierr); 2620 blockSize = Nb; 2621 batchSize = numBlocks * blockSize; 2622 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 2623 numChunks = numCells / (numBatches*batchSize); 2624 Ne = numChunks*numBatches*batchSize; 2625 Nr = numCells % (numBatches*batchSize); 2626 offset = numCells - Nr; 2627 ierr = PetscFEGeomGetChunk(cgeomFEM,0,offset,&chunkGeom);CHKERRQ(ierr); 2628 ierr = PetscFEGeomGetChunk(cgeomFEM,offset,numCells,&remGeom);CHKERRQ(ierr); 2629 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 2630 ierr = PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMat);CHKERRQ(ierr); 2631 ierr = PetscFEIntegrateJacobian(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); 2632 if (hasDyn) { 2633 ierr = PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN_DYN, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMatD);CHKERRQ(ierr); 2634 ierr = PetscFEIntegrateJacobian(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); 2635 } 2636 } 2637 ierr = PetscFEGeomRestoreChunk(cgeomFEM,offset,numCells,&remGeom);CHKERRQ(ierr); 2638 ierr = PetscFEGeomRestoreChunk(cgeomFEM,0,offset,&chunkGeom);CHKERRQ(ierr); 2639 ierr = DMSNESRestoreFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);CHKERRQ(ierr); 2640 ierr = PetscQuadratureDestroy(&qGeom);CHKERRQ(ierr); 2641 } 2642 if (hasDyn) { 2643 for (c = 0; c < numCells*totDim*totDim; ++c) elemMat[c] += X_tShift*elemMatD[c]; 2644 } 2645 for (c = cStart; c < cEnd; ++c) { 2646 const PetscInt cell = cells ? cells[c] : c; 2647 const PetscInt cind = c - cStart; 2648 const PetscBLASInt M = totDim, one = 1; 2649 const PetscScalar a = 1.0, b = 0.0; 2650 2651 PetscStackCallBLAS("BLASgemv", BLASgemv_("N", &M, &M, &a, &elemMat[cind*totDim*totDim], &M, &y[cind*totDim], &one, &b, z, &one)); 2652 if (mesh->printFEM > 1) { 2653 ierr = DMPrintCellMatrix(c, name, totDim, totDim, &elemMat[cind*totDim*totDim]);CHKERRQ(ierr); 2654 ierr = DMPrintCellVector(c, "Y", totDim, &y[cind*totDim]);CHKERRQ(ierr); 2655 ierr = DMPrintCellVector(c, "Z", totDim, z);CHKERRQ(ierr); 2656 } 2657 ierr = DMPlexVecSetClosure(dm, section, Z, cell, z, ADD_VALUES);CHKERRQ(ierr); 2658 } 2659 ierr = PetscFree6(u,u_t,elemMat,elemMatD,y,z);CHKERRQ(ierr); 2660 if (mesh->printFEM) { 2661 ierr = PetscPrintf(PETSC_COMM_WORLD, "Z:\n");CHKERRQ(ierr); 2662 ierr = VecView(Z, NULL);CHKERRQ(ierr); 2663 } 2664 ierr = PetscFree(a);CHKERRQ(ierr); 2665 ierr = ISDestroy(&cellIS);CHKERRQ(ierr); 2666 ierr = DMDestroy(&plexAux);CHKERRQ(ierr); 2667 ierr = DMDestroy(&plex);CHKERRQ(ierr); 2668 ierr = PetscLogEventEnd(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 2669 PetscFunctionReturn(0); 2670 } 2671 2672 /*@ 2673 DMPlexSNESComputeJacobianFEM - Form the local portion of the Jacobian matrix J at the local solution X using pointwise functions specified by the user. 2674 2675 Input Parameters: 2676 + dm - The mesh 2677 . X - Local input vector 2678 - user - The user context 2679 2680 Output Parameter: 2681 . Jac - Jacobian matrix 2682 2683 Note: 2684 We form the residual one batch of elements at a time. This allows us to offload work onto an accelerator, 2685 like a GPU, or vectorize on a multicore machine. 2686 2687 Level: developer 2688 2689 .seealso: FormFunctionLocal() 2690 @*/ 2691 PetscErrorCode DMPlexSNESComputeJacobianFEM(DM dm, Vec X, Mat Jac, Mat JacP,void *user) 2692 { 2693 DM plex; 2694 IS allcellIS; 2695 PetscBool hasJac, hasPrec; 2696 PetscInt Nds, s, depth; 2697 PetscErrorCode ierr; 2698 2699 PetscFunctionBegin; 2700 ierr = DMGetNumDS(dm, &Nds);CHKERRQ(ierr); 2701 ierr = DMSNESConvertPlex(dm, &plex, PETSC_TRUE);CHKERRQ(ierr); 2702 ierr = DMPlexGetDepth(plex, &depth);CHKERRQ(ierr); 2703 ierr = DMGetStratumIS(plex, "dim", depth, &allcellIS);CHKERRQ(ierr); 2704 if (!allcellIS) {ierr = DMGetStratumIS(plex, "depth", depth, &allcellIS);CHKERRQ(ierr);} 2705 for (s = 0; s < Nds; ++s) { 2706 PetscDS ds; 2707 DMLabel label; 2708 IS cellIS; 2709 2710 ierr = DMGetRegionNumDS(dm, s, &label, NULL, &ds);CHKERRQ(ierr); 2711 if (!label) { 2712 ierr = PetscObjectReference((PetscObject) allcellIS);CHKERRQ(ierr); 2713 cellIS = allcellIS; 2714 } else { 2715 IS pointIS; 2716 2717 ierr = DMLabelGetStratumIS(label, 1, &pointIS);CHKERRQ(ierr); 2718 ierr = ISIntersect_Caching_Internal(allcellIS, pointIS, &cellIS);CHKERRQ(ierr); 2719 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 2720 } 2721 if (!s) { 2722 ierr = PetscDSHasJacobian(ds, &hasJac);CHKERRQ(ierr); 2723 ierr = PetscDSHasJacobianPreconditioner(ds, &hasPrec);CHKERRQ(ierr); 2724 if (hasJac && hasPrec) {ierr = MatZeroEntries(Jac);CHKERRQ(ierr);} 2725 ierr = MatZeroEntries(JacP);CHKERRQ(ierr); 2726 } 2727 ierr = DMPlexComputeJacobian_Internal(plex, cellIS, 0.0, 0.0, X, NULL, Jac, JacP, user);CHKERRQ(ierr); 2728 ierr = ISDestroy(&cellIS);CHKERRQ(ierr); 2729 } 2730 ierr = ISDestroy(&allcellIS);CHKERRQ(ierr); 2731 ierr = DMDestroy(&plex);CHKERRQ(ierr); 2732 PetscFunctionReturn(0); 2733 } 2734 2735 /* 2736 MatComputeNeumannOverlap - Computes an unassembled (Neumann) local overlapping Mat in nonlinear context. 2737 2738 Input Parameters: 2739 + X - SNES linearization point 2740 . ovl - index set of overlapping subdomains 2741 2742 Output Parameter: 2743 . J - unassembled (Neumann) local matrix 2744 2745 Level: intermediate 2746 2747 .seealso: DMCreateNeumannOverlap(), MATIS, PCHPDDMSetAuxiliaryMat() 2748 */ 2749 static PetscErrorCode MatComputeNeumannOverlap_Plex(Mat J, PetscReal t, Vec X, Vec X_t, PetscReal s, IS ovl, void *ctx) 2750 { 2751 SNES snes; 2752 Mat pJ; 2753 DM ovldm,origdm; 2754 DMSNES sdm; 2755 PetscErrorCode (*bfun)(DM,Vec,void*); 2756 PetscErrorCode (*jfun)(DM,Vec,Mat,Mat,void*); 2757 void *bctx,*jctx; 2758 PetscErrorCode ierr; 2759 2760 PetscFunctionBegin; 2761 ierr = PetscObjectQuery((PetscObject)ovl,"_DM_Overlap_HPDDM_MATIS",(PetscObject*)&pJ);CHKERRQ(ierr); 2762 if (!pJ) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Missing overlapping Mat");CHKERRQ(ierr); 2763 ierr = PetscObjectQuery((PetscObject)ovl,"_DM_Original_HPDDM",(PetscObject*)&origdm);CHKERRQ(ierr); 2764 if (!origdm) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Missing original DM");CHKERRQ(ierr); 2765 ierr = MatGetDM(pJ,&ovldm);CHKERRQ(ierr); 2766 ierr = DMSNESGetBoundaryLocal(origdm,&bfun,&bctx);CHKERRQ(ierr); 2767 ierr = DMSNESSetBoundaryLocal(ovldm,bfun,bctx);CHKERRQ(ierr); 2768 ierr = DMSNESGetJacobianLocal(origdm,&jfun,&jctx);CHKERRQ(ierr); 2769 ierr = DMSNESSetJacobianLocal(ovldm,jfun,jctx);CHKERRQ(ierr); 2770 ierr = PetscObjectQuery((PetscObject)ovl,"_DM_Overlap_HPDDM_SNES",(PetscObject*)&snes);CHKERRQ(ierr); 2771 if (!snes) { 2772 ierr = SNESCreate(PetscObjectComm((PetscObject)ovl),&snes);CHKERRQ(ierr); 2773 ierr = SNESSetDM(snes,ovldm);CHKERRQ(ierr); 2774 ierr = PetscObjectCompose((PetscObject)ovl,"_DM_Overlap_HPDDM_SNES",(PetscObject)snes);CHKERRQ(ierr); 2775 ierr = PetscObjectDereference((PetscObject)snes);CHKERRQ(ierr); 2776 } 2777 ierr = DMGetDMSNES(ovldm,&sdm);CHKERRQ(ierr); 2778 ierr = VecLockReadPush(X);CHKERRQ(ierr); 2779 PetscStackPush("SNES user Jacobian function"); 2780 ierr = (*sdm->ops->computejacobian)(snes,X,pJ,pJ,sdm->jacobianctx);CHKERRQ(ierr); 2781 PetscStackPop; 2782 ierr = VecLockReadPop(X);CHKERRQ(ierr); 2783 /* this is a no-hop, just in case we decide to change the placeholder for the local Neumann matrix */ 2784 { 2785 Mat locpJ; 2786 2787 ierr = MatISGetLocalMat(pJ,&locpJ);CHKERRQ(ierr); 2788 ierr = MatCopy(locpJ,J,SAME_NONZERO_PATTERN);CHKERRQ(ierr); 2789 } 2790 PetscFunctionReturn(0); 2791 } 2792 2793 /*@ 2794 DMPlexSetSNESLocalFEM - Use DMPlex's internal FEM routines to compute SNES boundary values, residual, and Jacobian. 2795 2796 Input Parameters: 2797 + dm - The DM object 2798 . boundaryctx - the user context that will be passed to pointwise evaluation of boundary values (see PetscDSAddBoundary()) 2799 . residualctx - the user context that will be passed to pointwise evaluation of finite element residual computations (see PetscDSSetResidual()) 2800 - jacobianctx - the user context that will be passed to pointwise evaluation of finite element Jacobian construction (see PetscDSSetJacobian()) 2801 2802 Level: developer 2803 @*/ 2804 PetscErrorCode DMPlexSetSNESLocalFEM(DM dm, void *boundaryctx, void *residualctx, void *jacobianctx) 2805 { 2806 PetscErrorCode ierr; 2807 2808 PetscFunctionBegin; 2809 ierr = DMSNESSetBoundaryLocal(dm,DMPlexSNESComputeBoundaryFEM,boundaryctx);CHKERRQ(ierr); 2810 ierr = DMSNESSetFunctionLocal(dm,DMPlexSNESComputeResidualFEM,residualctx);CHKERRQ(ierr); 2811 ierr = DMSNESSetJacobianLocal(dm,DMPlexSNESComputeJacobianFEM,jacobianctx);CHKERRQ(ierr); 2812 ierr = PetscObjectComposeFunction((PetscObject)dm,"MatComputeNeumannOverlap_C",MatComputeNeumannOverlap_Plex);CHKERRQ(ierr); 2813 PetscFunctionReturn(0); 2814 } 2815 2816 /*@C 2817 DMSNESCheckDiscretization - Check the discretization error of the exact solution 2818 2819 Input Parameters: 2820 + snes - the SNES object 2821 . dm - the DM 2822 . u - a DM vector 2823 . exactFuncs - pointwise functions of the exact solution for each field 2824 . ctxs - contexts for the functions 2825 - tol - A tolerance for the check, or -1 to print the results instead 2826 2827 Output Parameters: 2828 . error - An array which holds the discretization error in each field, or NULL 2829 2830 Level: developer 2831 2832 .seealso: DNSNESCheckFromOptions(), DMSNESCheckResidual(), DMSNESCheckJacobian() 2833 @*/ 2834 PetscErrorCode DMSNESCheckDiscretization(SNES snes, DM dm, Vec u, PetscErrorCode (**exactFuncs)(PetscInt, PetscReal, const PetscReal x[], PetscInt, PetscScalar *u, void *ctx), void **ctxs, PetscReal tol, PetscReal error[]) 2835 { 2836 PetscErrorCode (**exacts)(PetscInt, PetscReal, const PetscReal x[], PetscInt, PetscScalar *u, void *ctx); 2837 void **ectxs; 2838 MPI_Comm comm; 2839 PetscDS ds; 2840 PetscReal *err; 2841 PetscInt Nf, f, Nds, s; 2842 PetscErrorCode ierr; 2843 2844 PetscFunctionBegin; 2845 PetscValidHeaderSpecific(snes, SNES_CLASSID, 1); 2846 PetscValidHeaderSpecific(dm, DM_CLASSID, 2); 2847 PetscValidHeaderSpecific(u, VEC_CLASSID, 3); 2848 if (error) PetscValidRealPointer(error, 6); 2849 ierr = PetscObjectGetComm((PetscObject) snes, &comm);CHKERRQ(ierr); 2850 ierr = DMGetNumFields(dm, &Nf);CHKERRQ(ierr); 2851 ierr = PetscCalloc3(Nf, &exacts, Nf, &ectxs, PetscMax(1, Nf), &err);CHKERRQ(ierr); 2852 ierr = DMGetNumDS(dm, &Nds);CHKERRQ(ierr); 2853 for (s = 0; s < Nds; ++s) { 2854 DMLabel label; 2855 IS fieldIS; 2856 const PetscInt *fields, id = 1; 2857 PetscInt dsNf; 2858 2859 ierr = DMGetRegionNumDS(dm, s, &label, &fieldIS, &ds);CHKERRQ(ierr); 2860 ierr = PetscDSGetNumFields(ds, &dsNf);CHKERRQ(ierr); 2861 ierr = ISGetIndices(fieldIS, &fields);CHKERRQ(ierr); 2862 for (f = 0; f < dsNf; ++f) { 2863 const PetscInt field = fields[f]; 2864 ierr = PetscDSGetExactSolution(ds, field, &exacts[field], &ectxs[field]);CHKERRQ(ierr); 2865 } 2866 ierr = ISRestoreIndices(fieldIS, &fields);CHKERRQ(ierr); 2867 if (label) { 2868 ierr = DMProjectFunctionLabel(dm, 0.0, label, 1, &id, 0, NULL, exactFuncs ? exactFuncs : exacts, ctxs ? ctxs : ectxs, INSERT_ALL_VALUES, u);CHKERRQ(ierr); 2869 } else { 2870 ierr = DMProjectFunction(dm, 0.0, exactFuncs ? exactFuncs : exacts, ctxs ? ctxs : ectxs, INSERT_ALL_VALUES, u);CHKERRQ(ierr); 2871 } 2872 } 2873 ierr = PetscObjectSetName((PetscObject) u, "Exact Solution");CHKERRQ(ierr); 2874 ierr = PetscObjectSetOptionsPrefix((PetscObject) u, "exact_");CHKERRQ(ierr); 2875 ierr = VecViewFromOptions(u, NULL, "-vec_view");CHKERRQ(ierr); 2876 if (Nf > 1) { 2877 ierr = DMComputeL2FieldDiff(dm, 0.0, exactFuncs ? exactFuncs : exacts, ctxs ? ctxs : ectxs, u, err);CHKERRQ(ierr); 2878 if (tol >= 0.0) { 2879 for (f = 0; f < Nf; ++f) { 2880 if (err[f] > tol) SETERRQ3(comm, PETSC_ERR_ARG_WRONG, "L_2 Error %g for field %D exceeds tolerance %g", (double) err[f], f, (double) tol); 2881 } 2882 } else if (error) { 2883 for (f = 0; f < Nf; ++f) error[f] = err[f]; 2884 } else { 2885 ierr = PetscPrintf(comm, "L_2 Error: [");CHKERRQ(ierr); 2886 for (f = 0; f < Nf; ++f) { 2887 if (f) {ierr = PetscPrintf(comm, ", ");CHKERRQ(ierr);} 2888 ierr = PetscPrintf(comm, "%g", (double)err[f]);CHKERRQ(ierr); 2889 } 2890 ierr = PetscPrintf(comm, "]\n");CHKERRQ(ierr); 2891 } 2892 } else { 2893 ierr = DMComputeL2Diff(dm, 0.0, exactFuncs ? exactFuncs : exacts, ctxs ? ctxs : ectxs , u, &err[0]);CHKERRQ(ierr); 2894 if (tol >= 0.0) { 2895 if (err[0] > tol) SETERRQ2(comm, PETSC_ERR_ARG_WRONG, "L_2 Error %g exceeds tolerance %g", (double) err[0], (double) tol); 2896 } else if (error) { 2897 error[0] = err[0]; 2898 } else { 2899 ierr = PetscPrintf(comm, "L_2 Error: %g\n", (double)err[0]);CHKERRQ(ierr); 2900 } 2901 } 2902 ierr = PetscFree3(exacts, ectxs, err);CHKERRQ(ierr); 2903 PetscFunctionReturn(0); 2904 } 2905 2906 /*@C 2907 DMSNESCheckResidual - Check the residual of the exact solution 2908 2909 Input Parameters: 2910 + snes - the SNES object 2911 . dm - the DM 2912 . u - a DM vector 2913 - tol - A tolerance for the check, or -1 to print the results instead 2914 2915 Output Parameters: 2916 . residual - The residual norm of the exact solution, or NULL 2917 2918 Level: developer 2919 2920 .seealso: DNSNESCheckFromOptions(), DMSNESCheckDiscretization(), DMSNESCheckJacobian() 2921 @*/ 2922 PetscErrorCode DMSNESCheckResidual(SNES snes, DM dm, Vec u, PetscReal tol, PetscReal *residual) 2923 { 2924 PetscErrorCode (**exacts)(PetscInt, PetscReal, const PetscReal x[], PetscInt, PetscScalar *u, void *ctx); 2925 void **ectxs; 2926 MPI_Comm comm; 2927 PetscDS ds; 2928 Vec r; 2929 PetscReal res; 2930 PetscInt Nf, f, Nds, s; 2931 PetscBool computeSol = PETSC_FALSE; 2932 PetscErrorCode ierr; 2933 2934 PetscFunctionBegin; 2935 PetscValidHeaderSpecific(snes, SNES_CLASSID, 1); 2936 PetscValidHeaderSpecific(dm, DM_CLASSID, 2); 2937 PetscValidHeaderSpecific(u, VEC_CLASSID, 3); 2938 if (residual) PetscValidRealPointer(residual, 5); 2939 ierr = PetscObjectGetComm((PetscObject) snes, &comm);CHKERRQ(ierr); 2940 ierr = DMGetDS(dm, &ds);CHKERRQ(ierr); 2941 ierr = DMGetNumFields(dm, &Nf);CHKERRQ(ierr); 2942 ierr = PetscCalloc2(Nf, &exacts, Nf, &ectxs);CHKERRQ(ierr); 2943 ierr = DMGetNumDS(dm, &Nds);CHKERRQ(ierr); 2944 for (s = 0; s < Nds; ++s) { 2945 DMLabel label; 2946 IS fieldIS; 2947 const PetscInt *fields, id = 1; 2948 PetscInt dsNf; 2949 2950 ierr = DMGetRegionNumDS(dm, s, &label, &fieldIS, &ds);CHKERRQ(ierr); 2951 ierr = PetscDSGetNumFields(ds, &dsNf);CHKERRQ(ierr); 2952 ierr = ISGetIndices(fieldIS, &fields);CHKERRQ(ierr); 2953 for (f = 0; f < dsNf; ++f) { 2954 const PetscInt field = fields[f]; 2955 ierr = PetscDSGetExactSolution(ds, field, &exacts[field], &ectxs[field]);CHKERRQ(ierr); 2956 if (exacts[f]) computeSol = PETSC_TRUE; 2957 } 2958 ierr = ISRestoreIndices(fieldIS, &fields);CHKERRQ(ierr); 2959 if (computeSol) { 2960 if (label) { 2961 ierr = DMProjectFunctionLabel(dm, 0.0, label, 1, &id, 0, NULL, exacts, ectxs, INSERT_ALL_VALUES, u);CHKERRQ(ierr); 2962 } else { 2963 ierr = DMProjectFunction(dm, 0.0, exacts, ectxs, INSERT_ALL_VALUES, u);CHKERRQ(ierr); 2964 } 2965 } 2966 } 2967 ierr = PetscFree2(exacts, ectxs);CHKERRQ(ierr); 2968 ierr = VecDuplicate(u, &r);CHKERRQ(ierr); 2969 ierr = SNESComputeFunction(snes, u, r);CHKERRQ(ierr); 2970 ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr); 2971 if (tol >= 0.0) { 2972 if (res > tol) SETERRQ2(comm, PETSC_ERR_ARG_WRONG, "L_2 Residual %g exceeds tolerance %g", (double) res, (double) tol); 2973 } else if (residual) { 2974 *residual = res; 2975 } else { 2976 ierr = PetscPrintf(comm, "L_2 Residual: %g\n", (double)res);CHKERRQ(ierr); 2977 ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr); 2978 ierr = PetscObjectSetName((PetscObject) r, "Initial Residual");CHKERRQ(ierr); 2979 ierr = PetscObjectSetOptionsPrefix((PetscObject)r,"res_");CHKERRQ(ierr); 2980 ierr = VecViewFromOptions(r, NULL, "-vec_view");CHKERRQ(ierr); 2981 } 2982 ierr = VecDestroy(&r);CHKERRQ(ierr); 2983 PetscFunctionReturn(0); 2984 } 2985 2986 /*@C 2987 DMSNESCheckJacobian - Check the Jacobian of the exact solution against the residual using the Taylor Test 2988 2989 Input Parameters: 2990 + snes - the SNES object 2991 . dm - the DM 2992 . u - a DM vector 2993 - tol - A tolerance for the check, or -1 to print the results instead 2994 2995 Output Parameters: 2996 + isLinear - Flag indicaing that the function looks linear, or NULL 2997 - convRate - The rate of convergence of the linear model, or NULL 2998 2999 Level: developer 3000 3001 .seealso: DNSNESCheckFromOptions(), DMSNESCheckDiscretization(), DMSNESCheckResidual() 3002 @*/ 3003 PetscErrorCode DMSNESCheckJacobian(SNES snes, DM dm, Vec u, PetscReal tol, PetscBool *isLinear, PetscReal *convRate) 3004 { 3005 PetscErrorCode (**exacts)(PetscInt, PetscReal, const PetscReal x[], PetscInt, PetscScalar *u, void *ctx); 3006 void **ectxs; 3007 MPI_Comm comm; 3008 PetscDS ds; 3009 Mat J, M; 3010 MatNullSpace nullspace; 3011 PetscReal slope, intercept; 3012 PetscInt Nf, f, Nds, s; 3013 PetscBool hasJac, hasPrec, isLin = PETSC_FALSE, computeSol = PETSC_FALSE; 3014 PetscErrorCode ierr; 3015 3016 PetscFunctionBegin; 3017 PetscValidHeaderSpecific(snes, SNES_CLASSID, 1); 3018 PetscValidHeaderSpecific(dm, DM_CLASSID, 2); 3019 PetscValidHeaderSpecific(u, VEC_CLASSID, 3); 3020 if (isLinear) PetscValidBoolPointer(isLinear, 5); 3021 if (convRate) PetscValidRealPointer(convRate, 5); 3022 ierr = PetscObjectGetComm((PetscObject) snes, &comm);CHKERRQ(ierr); 3023 ierr = DMGetDS(dm, &ds);CHKERRQ(ierr); 3024 ierr = DMGetNumFields(dm, &Nf);CHKERRQ(ierr); 3025 ierr = PetscMalloc2(Nf, &exacts, Nf, &ectxs);CHKERRQ(ierr); 3026 ierr = DMGetNumDS(dm, &Nds);CHKERRQ(ierr); 3027 for (s = 0; s < Nds; ++s) { 3028 DMLabel label; 3029 IS fieldIS; 3030 const PetscInt *fields, id = 1; 3031 PetscInt dsNf; 3032 3033 ierr = DMGetRegionNumDS(dm, s, &label, &fieldIS, &ds);CHKERRQ(ierr); 3034 ierr = PetscDSGetNumFields(ds, &dsNf);CHKERRQ(ierr); 3035 ierr = ISGetIndices(fieldIS, &fields);CHKERRQ(ierr); 3036 for (f = 0; f < dsNf; ++f) { 3037 const PetscInt field = fields[f]; 3038 ierr = PetscDSGetExactSolution(ds, field, &exacts[field], &ectxs[field]);CHKERRQ(ierr); 3039 if (exacts[f]) computeSol = PETSC_TRUE; 3040 } 3041 ierr = ISRestoreIndices(fieldIS, &fields);CHKERRQ(ierr); 3042 if (computeSol) { 3043 if (label) { 3044 ierr = DMProjectFunctionLabel(dm, 0.0, label, 1, &id, 0, NULL, exacts, ectxs, INSERT_ALL_VALUES, u);CHKERRQ(ierr); 3045 } else { 3046 ierr = DMProjectFunction(dm, 0.0, exacts, ectxs, INSERT_ALL_VALUES, u);CHKERRQ(ierr); 3047 } 3048 } 3049 } 3050 ierr = PetscFree2(exacts, ectxs);CHKERRQ(ierr); 3051 3052 /* Create and view matrices */ 3053 ierr = DMCreateMatrix(dm, &J);CHKERRQ(ierr); 3054 ierr = PetscDSHasJacobian(ds, &hasJac);CHKERRQ(ierr); 3055 ierr = PetscDSHasJacobianPreconditioner(ds, &hasPrec);CHKERRQ(ierr); 3056 if (hasJac && hasPrec) { 3057 ierr = DMCreateMatrix(dm, &M);CHKERRQ(ierr); 3058 ierr = SNESComputeJacobian(snes, u, J, M);CHKERRQ(ierr); 3059 ierr = PetscObjectSetName((PetscObject) M, "Preconditioning Matrix");CHKERRQ(ierr); 3060 ierr = PetscObjectSetOptionsPrefix((PetscObject) M, "jacpre_");CHKERRQ(ierr); 3061 ierr = MatViewFromOptions(M, NULL, "-mat_view");CHKERRQ(ierr); 3062 ierr = MatDestroy(&M);CHKERRQ(ierr); 3063 } else { 3064 ierr = SNESComputeJacobian(snes, u, J, J);CHKERRQ(ierr); 3065 } 3066 ierr = PetscObjectSetName((PetscObject) J, "Jacobian");CHKERRQ(ierr); 3067 ierr = PetscObjectSetOptionsPrefix((PetscObject) J, "jac_");CHKERRQ(ierr); 3068 ierr = MatViewFromOptions(J, NULL, "-mat_view");CHKERRQ(ierr); 3069 /* Check nullspace */ 3070 ierr = MatGetNullSpace(J, &nullspace);CHKERRQ(ierr); 3071 if (nullspace) { 3072 PetscBool isNull; 3073 ierr = MatNullSpaceTest(nullspace, J, &isNull);CHKERRQ(ierr); 3074 if (!isNull) SETERRQ(comm, PETSC_ERR_PLIB, "The null space calculated for the system operator is invalid."); 3075 } 3076 ierr = MatNullSpaceDestroy(&nullspace);CHKERRQ(ierr); 3077 /* Taylor test */ 3078 { 3079 PetscRandom rand; 3080 Vec du, uhat, r, rhat, df; 3081 PetscReal h; 3082 PetscReal *es, *hs, *errors; 3083 PetscReal hMax = 1.0, hMin = 1e-6, hMult = 0.1; 3084 PetscInt Nv, v; 3085 3086 /* Choose a perturbation direction */ 3087 ierr = PetscRandomCreate(comm, &rand);CHKERRQ(ierr); 3088 ierr = VecDuplicate(u, &du);CHKERRQ(ierr); 3089 ierr = VecSetRandom(du, rand); CHKERRQ(ierr); 3090 ierr = PetscRandomDestroy(&rand);CHKERRQ(ierr); 3091 ierr = VecDuplicate(u, &df);CHKERRQ(ierr); 3092 ierr = MatMult(J, du, df);CHKERRQ(ierr); 3093 /* Evaluate residual at u, F(u), save in vector r */ 3094 ierr = VecDuplicate(u, &r);CHKERRQ(ierr); 3095 ierr = SNESComputeFunction(snes, u, r);CHKERRQ(ierr); 3096 /* Look at the convergence of our Taylor approximation as we approach u */ 3097 for (h = hMax, Nv = 0; h >= hMin; h *= hMult, ++Nv); 3098 ierr = PetscCalloc3(Nv, &es, Nv, &hs, Nv, &errors);CHKERRQ(ierr); 3099 ierr = VecDuplicate(u, &uhat);CHKERRQ(ierr); 3100 ierr = VecDuplicate(u, &rhat);CHKERRQ(ierr); 3101 for (h = hMax, Nv = 0; h >= hMin; h *= hMult, ++Nv) { 3102 ierr = VecWAXPY(uhat, h, du, u);CHKERRQ(ierr); 3103 /* F(\hat u) \approx F(u) + J(u) (uhat - u) = F(u) + h * J(u) du */ 3104 ierr = SNESComputeFunction(snes, uhat, rhat);CHKERRQ(ierr); 3105 ierr = VecAXPBYPCZ(rhat, -1.0, -h, 1.0, r, df);CHKERRQ(ierr); 3106 ierr = VecNorm(rhat, NORM_2, &errors[Nv]);CHKERRQ(ierr); 3107 3108 es[Nv] = PetscLog10Real(errors[Nv]); 3109 hs[Nv] = PetscLog10Real(h); 3110 } 3111 ierr = VecDestroy(&uhat);CHKERRQ(ierr); 3112 ierr = VecDestroy(&rhat);CHKERRQ(ierr); 3113 ierr = VecDestroy(&df);CHKERRQ(ierr); 3114 ierr = VecDestroy(&r);CHKERRQ(ierr); 3115 ierr = VecDestroy(&du);CHKERRQ(ierr); 3116 for (v = 0; v < Nv; ++v) { 3117 if ((tol >= 0) && (errors[v] > tol)) break; 3118 else if (errors[v] > PETSC_SMALL) break; 3119 } 3120 if (v == Nv) isLin = PETSC_TRUE; 3121 ierr = PetscLinearRegression(Nv, hs, es, &slope, &intercept);CHKERRQ(ierr); 3122 ierr = PetscFree3(es, hs, errors);CHKERRQ(ierr); 3123 /* Slope should be about 2 */ 3124 if (tol >= 0) { 3125 if (!isLin && PetscAbsReal(2 - slope) > tol) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Taylor approximation convergence rate should be 2, not %0.2f", (double) slope); 3126 } else if (isLinear || convRate) { 3127 if (isLinear) *isLinear = isLin; 3128 if (convRate) *convRate = slope; 3129 } else { 3130 if (!isLin) {ierr = PetscPrintf(comm, "Taylor approximation converging at order %3.2f\n", (double) slope);CHKERRQ(ierr);} 3131 else {ierr = PetscPrintf(comm, "Function appears to be linear\n");CHKERRQ(ierr);} 3132 } 3133 } 3134 ierr = MatDestroy(&J);CHKERRQ(ierr); 3135 PetscFunctionReturn(0); 3136 } 3137 3138 PetscErrorCode DMSNESCheck_Internal(SNES snes, DM dm, Vec u, PetscErrorCode (**exactFuncs)(PetscInt, PetscReal, const PetscReal x[], PetscInt, PetscScalar *u, void *ctx), void **ctxs) 3139 { 3140 PetscErrorCode ierr; 3141 3142 PetscFunctionBegin; 3143 ierr = DMSNESCheckDiscretization(snes, dm, u, exactFuncs, ctxs, -1.0, NULL);CHKERRQ(ierr); 3144 ierr = DMSNESCheckResidual(snes, dm, u, -1.0, NULL);CHKERRQ(ierr); 3145 ierr = DMSNESCheckJacobian(snes, dm, u, -1.0, NULL, NULL);CHKERRQ(ierr); 3146 PetscFunctionReturn(0); 3147 } 3148 3149 /*@C 3150 DMSNESCheckFromOptions - Check the residual and Jacobian functions using the exact solution by outputting some diagnostic information 3151 3152 Input Parameters: 3153 + snes - the SNES object 3154 . u - representative SNES vector 3155 . exactFuncs - pointwise functions of the exact solution for each field 3156 - ctxs - contexts for the functions 3157 3158 Level: developer 3159 @*/ 3160 PetscErrorCode DMSNESCheckFromOptions(SNES snes, Vec u, PetscErrorCode (**exactFuncs)(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf, PetscScalar *u, void *ctx), void **ctxs) 3161 { 3162 DM dm; 3163 Vec sol; 3164 PetscBool check; 3165 PetscErrorCode ierr; 3166 3167 PetscFunctionBegin; 3168 ierr = PetscOptionsHasName(((PetscObject)snes)->options,((PetscObject)snes)->prefix, "-dmsnes_check", &check);CHKERRQ(ierr); 3169 if (!check) PetscFunctionReturn(0); 3170 ierr = SNESGetDM(snes, &dm);CHKERRQ(ierr); 3171 ierr = VecDuplicate(u, &sol);CHKERRQ(ierr); 3172 ierr = SNESSetSolution(snes, sol);CHKERRQ(ierr); 3173 ierr = DMSNESCheck_Internal(snes, dm, sol, exactFuncs, ctxs);CHKERRQ(ierr); 3174 ierr = VecDestroy(&sol);CHKERRQ(ierr); 3175 PetscFunctionReturn(0); 3176 } 3177