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 const PetscScalar *coords; 548 PetscScalar *a; 549 PetscInt Nf, p; 550 const PetscInt dof = ctx->dof; 551 PetscErrorCode ierr; 552 553 PetscFunctionBegin; 554 ierr = DMGetNumFields(dm, &Nf);CHKERRQ(ierr); 555 if (Nf) {ierr = DMGetField(dm, 0, NULL, (PetscObject *) &fem);CHKERRQ(ierr);} 556 ierr = DMGetCoordinatesLocal(dm, &coordsLocal);CHKERRQ(ierr); 557 ierr = DMGetCoordinateDM(dm, &dmCoord);CHKERRQ(ierr); 558 ierr = SNESCreate(PETSC_COMM_SELF, &snes);CHKERRQ(ierr); 559 ierr = SNESSetOptionsPrefix(snes, "quad_interp_");CHKERRQ(ierr); 560 ierr = VecCreate(PETSC_COMM_SELF, &r);CHKERRQ(ierr); 561 ierr = VecSetSizes(r, 2, 2);CHKERRQ(ierr); 562 ierr = VecSetType(r,dm->vectype);CHKERRQ(ierr); 563 ierr = VecDuplicate(r, &ref);CHKERRQ(ierr); 564 ierr = VecDuplicate(r, &real);CHKERRQ(ierr); 565 ierr = MatCreate(PETSC_COMM_SELF, &J);CHKERRQ(ierr); 566 ierr = MatSetSizes(J, 2, 2, 2, 2);CHKERRQ(ierr); 567 ierr = MatSetType(J, MATSEQDENSE);CHKERRQ(ierr); 568 ierr = MatSetUp(J);CHKERRQ(ierr); 569 ierr = SNESSetFunction(snes, r, QuadMap_Private, NULL);CHKERRQ(ierr); 570 ierr = SNESSetJacobian(snes, J, J, QuadJacobian_Private, NULL);CHKERRQ(ierr); 571 ierr = SNESGetKSP(snes, &ksp);CHKERRQ(ierr); 572 ierr = KSPGetPC(ksp, &pc);CHKERRQ(ierr); 573 ierr = PCSetType(pc, PCLU);CHKERRQ(ierr); 574 ierr = SNESSetFromOptions(snes);CHKERRQ(ierr); 575 576 ierr = VecGetArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 577 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 578 for (p = 0; p < ctx->n; ++p) { 579 PetscScalar *x = NULL, *vertices = NULL; 580 PetscScalar *xi; 581 PetscReal xir[2]; 582 PetscInt c = ctx->cells[p], comp, coordSize, xSize; 583 584 /* Can make this do all points at once */ 585 ierr = DMPlexVecGetClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);CHKERRQ(ierr); 586 if (4*2 != coordSize) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid closure size %D should be %d", coordSize, 4*2); 587 ierr = DMPlexVecGetClosure(dm, NULL, xLocal, c, &xSize, &x);CHKERRQ(ierr); 588 ierr = SNESSetFunction(snes, NULL, NULL, (void*) vertices);CHKERRQ(ierr); 589 ierr = SNESSetJacobian(snes, NULL, NULL, NULL, (void*) vertices);CHKERRQ(ierr); 590 ierr = VecGetArray(real, &xi);CHKERRQ(ierr); 591 xi[0] = coords[p*ctx->dim+0]; 592 xi[1] = coords[p*ctx->dim+1]; 593 ierr = VecRestoreArray(real, &xi);CHKERRQ(ierr); 594 ierr = SNESSolve(snes, real, ref);CHKERRQ(ierr); 595 ierr = VecGetArray(ref, &xi);CHKERRQ(ierr); 596 xir[0] = PetscRealPart(xi[0]); 597 xir[1] = PetscRealPart(xi[1]); 598 if (4*dof != xSize) { 599 PetscReal *B; 600 PetscInt d; 601 602 xir[0] = 2.0*xir[0] - 1.0; xir[1] = 2.0*xir[1] - 1.0; 603 ierr = PetscFEGetTabulation(fem, 1, xir, &B, NULL, NULL);CHKERRQ(ierr); 604 for (comp = 0; comp < dof; ++comp) { 605 a[p*dof+comp] = 0.0; 606 for (d = 0; d < xSize/dof; ++d) { 607 a[p*dof+comp] += x[d*dof+comp]*B[d*dof+comp]; 608 } 609 } 610 ierr = PetscFERestoreTabulation(fem, 1, xir, &B, NULL, NULL);CHKERRQ(ierr); 611 } else { 612 for (comp = 0; comp < dof; ++comp) 613 a[p*dof+comp] = x[0*dof+comp]*(1 - xir[0])*(1 - xir[1]) + x[1*dof+comp]*xir[0]*(1 - xir[1]) + x[2*dof+comp]*xir[0]*xir[1] + x[3*dof+comp]*(1 - xir[0])*xir[1]; 614 } 615 ierr = VecRestoreArray(ref, &xi);CHKERRQ(ierr); 616 ierr = DMPlexVecRestoreClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);CHKERRQ(ierr); 617 ierr = DMPlexVecRestoreClosure(dm, NULL, xLocal, c, &xSize, &x);CHKERRQ(ierr); 618 } 619 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 620 ierr = VecRestoreArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 621 622 ierr = SNESDestroy(&snes);CHKERRQ(ierr); 623 ierr = VecDestroy(&r);CHKERRQ(ierr); 624 ierr = VecDestroy(&ref);CHKERRQ(ierr); 625 ierr = VecDestroy(&real);CHKERRQ(ierr); 626 ierr = MatDestroy(&J);CHKERRQ(ierr); 627 PetscFunctionReturn(0); 628 } 629 630 PETSC_STATIC_INLINE PetscErrorCode HexMap_Private(SNES snes, Vec Xref, Vec Xreal, void *ctx) 631 { 632 const PetscScalar *vertices = (const PetscScalar*) ctx; 633 const PetscScalar x0 = vertices[0]; 634 const PetscScalar y0 = vertices[1]; 635 const PetscScalar z0 = vertices[2]; 636 const PetscScalar x1 = vertices[9]; 637 const PetscScalar y1 = vertices[10]; 638 const PetscScalar z1 = vertices[11]; 639 const PetscScalar x2 = vertices[6]; 640 const PetscScalar y2 = vertices[7]; 641 const PetscScalar z2 = vertices[8]; 642 const PetscScalar x3 = vertices[3]; 643 const PetscScalar y3 = vertices[4]; 644 const PetscScalar z3 = vertices[5]; 645 const PetscScalar x4 = vertices[12]; 646 const PetscScalar y4 = vertices[13]; 647 const PetscScalar z4 = vertices[14]; 648 const PetscScalar x5 = vertices[15]; 649 const PetscScalar y5 = vertices[16]; 650 const PetscScalar z5 = vertices[17]; 651 const PetscScalar x6 = vertices[18]; 652 const PetscScalar y6 = vertices[19]; 653 const PetscScalar z6 = vertices[20]; 654 const PetscScalar x7 = vertices[21]; 655 const PetscScalar y7 = vertices[22]; 656 const PetscScalar z7 = vertices[23]; 657 const PetscScalar f_1 = x1 - x0; 658 const PetscScalar g_1 = y1 - y0; 659 const PetscScalar h_1 = z1 - z0; 660 const PetscScalar f_3 = x3 - x0; 661 const PetscScalar g_3 = y3 - y0; 662 const PetscScalar h_3 = z3 - z0; 663 const PetscScalar f_4 = x4 - x0; 664 const PetscScalar g_4 = y4 - y0; 665 const PetscScalar h_4 = z4 - z0; 666 const PetscScalar f_01 = x2 - x1 - x3 + x0; 667 const PetscScalar g_01 = y2 - y1 - y3 + y0; 668 const PetscScalar h_01 = z2 - z1 - z3 + z0; 669 const PetscScalar f_12 = x7 - x3 - x4 + x0; 670 const PetscScalar g_12 = y7 - y3 - y4 + y0; 671 const PetscScalar h_12 = z7 - z3 - z4 + z0; 672 const PetscScalar f_02 = x5 - x1 - x4 + x0; 673 const PetscScalar g_02 = y5 - y1 - y4 + y0; 674 const PetscScalar h_02 = z5 - z1 - z4 + z0; 675 const PetscScalar f_012 = x6 - x0 + x1 - x2 + x3 + x4 - x5 - x7; 676 const PetscScalar g_012 = y6 - y0 + y1 - y2 + y3 + y4 - y5 - y7; 677 const PetscScalar h_012 = z6 - z0 + z1 - z2 + z3 + z4 - z5 - z7; 678 const PetscScalar *ref; 679 PetscScalar *real; 680 PetscErrorCode ierr; 681 682 PetscFunctionBegin; 683 ierr = VecGetArrayRead(Xref, &ref);CHKERRQ(ierr); 684 ierr = VecGetArray(Xreal, &real);CHKERRQ(ierr); 685 { 686 const PetscScalar p0 = ref[0]; 687 const PetscScalar p1 = ref[1]; 688 const PetscScalar p2 = ref[2]; 689 690 real[0] = x0 + f_1*p0 + f_3*p1 + f_4*p2 + f_01*p0*p1 + f_12*p1*p2 + f_02*p0*p2 + f_012*p0*p1*p2; 691 real[1] = y0 + g_1*p0 + g_3*p1 + g_4*p2 + g_01*p0*p1 + g_01*p0*p1 + g_12*p1*p2 + g_02*p0*p2 + g_012*p0*p1*p2; 692 real[2] = z0 + h_1*p0 + h_3*p1 + h_4*p2 + h_01*p0*p1 + h_01*p0*p1 + h_12*p1*p2 + h_02*p0*p2 + h_012*p0*p1*p2; 693 } 694 ierr = PetscLogFlops(114);CHKERRQ(ierr); 695 ierr = VecRestoreArrayRead(Xref, &ref);CHKERRQ(ierr); 696 ierr = VecRestoreArray(Xreal, &real);CHKERRQ(ierr); 697 PetscFunctionReturn(0); 698 } 699 700 PETSC_STATIC_INLINE PetscErrorCode HexJacobian_Private(SNES snes, Vec Xref, Mat J, Mat M, void *ctx) 701 { 702 const PetscScalar *vertices = (const PetscScalar*) ctx; 703 const PetscScalar x0 = vertices[0]; 704 const PetscScalar y0 = vertices[1]; 705 const PetscScalar z0 = vertices[2]; 706 const PetscScalar x1 = vertices[9]; 707 const PetscScalar y1 = vertices[10]; 708 const PetscScalar z1 = vertices[11]; 709 const PetscScalar x2 = vertices[6]; 710 const PetscScalar y2 = vertices[7]; 711 const PetscScalar z2 = vertices[8]; 712 const PetscScalar x3 = vertices[3]; 713 const PetscScalar y3 = vertices[4]; 714 const PetscScalar z3 = vertices[5]; 715 const PetscScalar x4 = vertices[12]; 716 const PetscScalar y4 = vertices[13]; 717 const PetscScalar z4 = vertices[14]; 718 const PetscScalar x5 = vertices[15]; 719 const PetscScalar y5 = vertices[16]; 720 const PetscScalar z5 = vertices[17]; 721 const PetscScalar x6 = vertices[18]; 722 const PetscScalar y6 = vertices[19]; 723 const PetscScalar z6 = vertices[20]; 724 const PetscScalar x7 = vertices[21]; 725 const PetscScalar y7 = vertices[22]; 726 const PetscScalar z7 = vertices[23]; 727 const PetscScalar f_xy = x2 - x1 - x3 + x0; 728 const PetscScalar g_xy = y2 - y1 - y3 + y0; 729 const PetscScalar h_xy = z2 - z1 - z3 + z0; 730 const PetscScalar f_yz = x7 - x3 - x4 + x0; 731 const PetscScalar g_yz = y7 - y3 - y4 + y0; 732 const PetscScalar h_yz = z7 - z3 - z4 + z0; 733 const PetscScalar f_xz = x5 - x1 - x4 + x0; 734 const PetscScalar g_xz = y5 - y1 - y4 + y0; 735 const PetscScalar h_xz = z5 - z1 - z4 + z0; 736 const PetscScalar f_xyz = x6 - x0 + x1 - x2 + x3 + x4 - x5 - x7; 737 const PetscScalar g_xyz = y6 - y0 + y1 - y2 + y3 + y4 - y5 - y7; 738 const PetscScalar h_xyz = z6 - z0 + z1 - z2 + z3 + z4 - z5 - z7; 739 const PetscScalar *ref; 740 PetscErrorCode ierr; 741 742 PetscFunctionBegin; 743 ierr = VecGetArrayRead(Xref, &ref);CHKERRQ(ierr); 744 { 745 const PetscScalar x = ref[0]; 746 const PetscScalar y = ref[1]; 747 const PetscScalar z = ref[2]; 748 const PetscInt rows[3] = {0, 1, 2}; 749 PetscScalar values[9]; 750 751 values[0] = (x1 - x0 + f_xy*y + f_xz*z + f_xyz*y*z) / 2.0; 752 values[1] = (x3 - x0 + f_xy*x + f_yz*z + f_xyz*x*z) / 2.0; 753 values[2] = (x4 - x0 + f_yz*y + f_xz*x + f_xyz*x*y) / 2.0; 754 values[3] = (y1 - y0 + g_xy*y + g_xz*z + g_xyz*y*z) / 2.0; 755 values[4] = (y3 - y0 + g_xy*x + g_yz*z + g_xyz*x*z) / 2.0; 756 values[5] = (y4 - y0 + g_yz*y + g_xz*x + g_xyz*x*y) / 2.0; 757 values[6] = (z1 - z0 + h_xy*y + h_xz*z + h_xyz*y*z) / 2.0; 758 values[7] = (z3 - z0 + h_xy*x + h_yz*z + h_xyz*x*z) / 2.0; 759 values[8] = (z4 - z0 + h_yz*y + h_xz*x + h_xyz*x*y) / 2.0; 760 761 ierr = MatSetValues(J, 3, rows, 3, rows, values, INSERT_VALUES);CHKERRQ(ierr); 762 } 763 ierr = PetscLogFlops(152);CHKERRQ(ierr); 764 ierr = VecRestoreArrayRead(Xref, &ref);CHKERRQ(ierr); 765 ierr = MatAssemblyBegin(J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 766 ierr = MatAssemblyEnd(J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 767 PetscFunctionReturn(0); 768 } 769 770 PETSC_STATIC_INLINE PetscErrorCode DMInterpolate_Hex_Private(DMInterpolationInfo ctx, DM dm, Vec xLocal, Vec v) 771 { 772 DM dmCoord; 773 SNES snes; 774 KSP ksp; 775 PC pc; 776 Vec coordsLocal, r, ref, real; 777 Mat J; 778 const PetscScalar *coords; 779 PetscScalar *a; 780 PetscInt p; 781 PetscErrorCode ierr; 782 783 PetscFunctionBegin; 784 ierr = DMGetCoordinatesLocal(dm, &coordsLocal);CHKERRQ(ierr); 785 ierr = DMGetCoordinateDM(dm, &dmCoord);CHKERRQ(ierr); 786 ierr = SNESCreate(PETSC_COMM_SELF, &snes);CHKERRQ(ierr); 787 ierr = SNESSetOptionsPrefix(snes, "hex_interp_");CHKERRQ(ierr); 788 ierr = VecCreate(PETSC_COMM_SELF, &r);CHKERRQ(ierr); 789 ierr = VecSetSizes(r, 3, 3);CHKERRQ(ierr); 790 ierr = VecSetType(r,dm->vectype);CHKERRQ(ierr); 791 ierr = VecDuplicate(r, &ref);CHKERRQ(ierr); 792 ierr = VecDuplicate(r, &real);CHKERRQ(ierr); 793 ierr = MatCreate(PETSC_COMM_SELF, &J);CHKERRQ(ierr); 794 ierr = MatSetSizes(J, 3, 3, 3, 3);CHKERRQ(ierr); 795 ierr = MatSetType(J, MATSEQDENSE);CHKERRQ(ierr); 796 ierr = MatSetUp(J);CHKERRQ(ierr); 797 ierr = SNESSetFunction(snes, r, HexMap_Private, NULL);CHKERRQ(ierr); 798 ierr = SNESSetJacobian(snes, J, J, HexJacobian_Private, NULL);CHKERRQ(ierr); 799 ierr = SNESGetKSP(snes, &ksp);CHKERRQ(ierr); 800 ierr = KSPGetPC(ksp, &pc);CHKERRQ(ierr); 801 ierr = PCSetType(pc, PCLU);CHKERRQ(ierr); 802 ierr = SNESSetFromOptions(snes);CHKERRQ(ierr); 803 804 ierr = VecGetArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 805 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 806 for (p = 0; p < ctx->n; ++p) { 807 PetscScalar *x = NULL, *vertices = NULL; 808 PetscScalar *xi; 809 PetscReal xir[3]; 810 PetscInt c = ctx->cells[p], comp, coordSize, xSize; 811 812 /* Can make this do all points at once */ 813 ierr = DMPlexVecGetClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);CHKERRQ(ierr); 814 if (8*3 != coordSize) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid closure size %D should be %d", coordSize, 8*3); 815 ierr = DMPlexVecGetClosure(dm, NULL, xLocal, c, &xSize, &x);CHKERRQ(ierr); 816 if (8*ctx->dof != xSize) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid closure size %D should be %D", xSize, 8*ctx->dof); 817 ierr = SNESSetFunction(snes, NULL, NULL, (void*) vertices);CHKERRQ(ierr); 818 ierr = SNESSetJacobian(snes, NULL, NULL, NULL, (void*) vertices);CHKERRQ(ierr); 819 ierr = VecGetArray(real, &xi);CHKERRQ(ierr); 820 xi[0] = coords[p*ctx->dim+0]; 821 xi[1] = coords[p*ctx->dim+1]; 822 xi[2] = coords[p*ctx->dim+2]; 823 ierr = VecRestoreArray(real, &xi);CHKERRQ(ierr); 824 ierr = SNESSolve(snes, real, ref);CHKERRQ(ierr); 825 ierr = VecGetArray(ref, &xi);CHKERRQ(ierr); 826 xir[0] = PetscRealPart(xi[0]); 827 xir[1] = PetscRealPart(xi[1]); 828 xir[2] = PetscRealPart(xi[2]); 829 for (comp = 0; comp < ctx->dof; ++comp) { 830 a[p*ctx->dof+comp] = 831 x[0*ctx->dof+comp]*(1-xir[0])*(1-xir[1])*(1-xir[2]) + 832 x[3*ctx->dof+comp]* xir[0]*(1-xir[1])*(1-xir[2]) + 833 x[2*ctx->dof+comp]* xir[0]* xir[1]*(1-xir[2]) + 834 x[1*ctx->dof+comp]*(1-xir[0])* xir[1]*(1-xir[2]) + 835 x[4*ctx->dof+comp]*(1-xir[0])*(1-xir[1])* xir[2] + 836 x[5*ctx->dof+comp]* xir[0]*(1-xir[1])* xir[2] + 837 x[6*ctx->dof+comp]* xir[0]* xir[1]* xir[2] + 838 x[7*ctx->dof+comp]*(1-xir[0])* xir[1]* xir[2]; 839 } 840 ierr = VecRestoreArray(ref, &xi);CHKERRQ(ierr); 841 ierr = DMPlexVecRestoreClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);CHKERRQ(ierr); 842 ierr = DMPlexVecRestoreClosure(dm, NULL, xLocal, c, &xSize, &x);CHKERRQ(ierr); 843 } 844 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 845 ierr = VecRestoreArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 846 847 ierr = SNESDestroy(&snes);CHKERRQ(ierr); 848 ierr = VecDestroy(&r);CHKERRQ(ierr); 849 ierr = VecDestroy(&ref);CHKERRQ(ierr); 850 ierr = VecDestroy(&real);CHKERRQ(ierr); 851 ierr = MatDestroy(&J);CHKERRQ(ierr); 852 PetscFunctionReturn(0); 853 } 854 855 /*@C 856 DMInterpolationEvaluate - Using the input from dm and x, calculates interpolated field values at the interpolation points. 857 858 Input Parameters: 859 + ctx - The DMInterpolationInfo context 860 . dm - The DM 861 - x - The local vector containing the field to be interpolated 862 863 Output Parameters: 864 . v - The vector containing the interpolated values 865 866 Note: A suitable v can be obtained using DMInterpolationGetVector(). 867 868 Level: beginner 869 870 .seealso: DMInterpolationGetVector(), DMInterpolationAddPoints(), DMInterpolationCreate() 871 @*/ 872 PetscErrorCode DMInterpolationEvaluate(DMInterpolationInfo ctx, DM dm, Vec x, Vec v) 873 { 874 PetscInt dim, coneSize, n; 875 PetscErrorCode ierr; 876 877 PetscFunctionBegin; 878 PetscValidHeaderSpecific(dm, DM_CLASSID, 2); 879 PetscValidHeaderSpecific(x, VEC_CLASSID, 3); 880 PetscValidHeaderSpecific(v, VEC_CLASSID, 4); 881 ierr = VecGetLocalSize(v, &n);CHKERRQ(ierr); 882 if (n != ctx->n*ctx->dof) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid input vector size %D should be %D", n, ctx->n*ctx->dof); 883 if (n) { 884 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 885 ierr = DMPlexGetConeSize(dm, ctx->cells[0], &coneSize);CHKERRQ(ierr); 886 if (dim == 2) { 887 if (coneSize == 3) { 888 ierr = DMInterpolate_Triangle_Private(ctx, dm, x, v);CHKERRQ(ierr); 889 } else if (coneSize == 4) { 890 ierr = DMInterpolate_Quad_Private(ctx, dm, x, v);CHKERRQ(ierr); 891 } else SETERRQ1(ctx->comm, PETSC_ERR_ARG_OUTOFRANGE, "Unsupported dimension %D for point interpolation", dim); 892 } else if (dim == 3) { 893 if (coneSize == 4) { 894 ierr = DMInterpolate_Tetrahedron_Private(ctx, dm, x, v);CHKERRQ(ierr); 895 } else { 896 ierr = DMInterpolate_Hex_Private(ctx, dm, x, v);CHKERRQ(ierr); 897 } 898 } else SETERRQ1(ctx->comm, PETSC_ERR_ARG_OUTOFRANGE, "Unsupported dimension %D for point interpolation", dim); 899 } 900 PetscFunctionReturn(0); 901 } 902 903 /*@C 904 DMInterpolationDestroy - Destroys a DMInterpolationInfo context 905 906 Collective on ctx 907 908 Input Parameter: 909 . ctx - the context 910 911 Level: beginner 912 913 .seealso: DMInterpolationEvaluate(), DMInterpolationAddPoints(), DMInterpolationCreate() 914 @*/ 915 PetscErrorCode DMInterpolationDestroy(DMInterpolationInfo *ctx) 916 { 917 PetscErrorCode ierr; 918 919 PetscFunctionBegin; 920 PetscValidPointer(ctx, 2); 921 ierr = VecDestroy(&(*ctx)->coords);CHKERRQ(ierr); 922 ierr = PetscFree((*ctx)->points);CHKERRQ(ierr); 923 ierr = PetscFree((*ctx)->cells);CHKERRQ(ierr); 924 ierr = PetscFree(*ctx);CHKERRQ(ierr); 925 *ctx = NULL; 926 PetscFunctionReturn(0); 927 } 928 929 /*@C 930 SNESMonitorFields - Monitors the residual for each field separately 931 932 Collective on SNES 933 934 Input Parameters: 935 + snes - the SNES context 936 . its - iteration number 937 . fgnorm - 2-norm of residual 938 - vf - PetscViewerAndFormat of type ASCII 939 940 Notes: 941 This routine prints the residual norm at each iteration. 942 943 Level: intermediate 944 945 .seealso: SNESMonitorSet(), SNESMonitorDefault() 946 @*/ 947 PetscErrorCode SNESMonitorFields(SNES snes, PetscInt its, PetscReal fgnorm, PetscViewerAndFormat *vf) 948 { 949 PetscViewer viewer = vf->viewer; 950 Vec res; 951 DM dm; 952 PetscSection s; 953 const PetscScalar *r; 954 PetscReal *lnorms, *norms; 955 PetscInt numFields, f, pStart, pEnd, p; 956 PetscErrorCode ierr; 957 958 PetscFunctionBegin; 959 PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,4); 960 ierr = SNESGetFunction(snes, &res, 0, 0);CHKERRQ(ierr); 961 ierr = SNESGetDM(snes, &dm);CHKERRQ(ierr); 962 ierr = DMGetLocalSection(dm, &s);CHKERRQ(ierr); 963 ierr = PetscSectionGetNumFields(s, &numFields);CHKERRQ(ierr); 964 ierr = PetscSectionGetChart(s, &pStart, &pEnd);CHKERRQ(ierr); 965 ierr = PetscCalloc2(numFields, &lnorms, numFields, &norms);CHKERRQ(ierr); 966 ierr = VecGetArrayRead(res, &r);CHKERRQ(ierr); 967 for (p = pStart; p < pEnd; ++p) { 968 for (f = 0; f < numFields; ++f) { 969 PetscInt fdof, foff, d; 970 971 ierr = PetscSectionGetFieldDof(s, p, f, &fdof);CHKERRQ(ierr); 972 ierr = PetscSectionGetFieldOffset(s, p, f, &foff);CHKERRQ(ierr); 973 for (d = 0; d < fdof; ++d) lnorms[f] += PetscRealPart(PetscSqr(r[foff+d])); 974 } 975 } 976 ierr = VecRestoreArrayRead(res, &r);CHKERRQ(ierr); 977 ierr = MPIU_Allreduce(lnorms, norms, numFields, MPIU_REAL, MPIU_SUM, PetscObjectComm((PetscObject) dm));CHKERRQ(ierr); 978 ierr = PetscViewerPushFormat(viewer,vf->format);CHKERRQ(ierr); 979 ierr = PetscViewerASCIIAddTab(viewer, ((PetscObject) snes)->tablevel);CHKERRQ(ierr); 980 ierr = PetscViewerASCIIPrintf(viewer, "%3D SNES Function norm %14.12e [", its, (double) fgnorm);CHKERRQ(ierr); 981 for (f = 0; f < numFields; ++f) { 982 if (f > 0) {ierr = PetscViewerASCIIPrintf(viewer, ", ");CHKERRQ(ierr);} 983 ierr = PetscViewerASCIIPrintf(viewer, "%14.12e", (double) PetscSqrtReal(norms[f]));CHKERRQ(ierr); 984 } 985 ierr = PetscViewerASCIIPrintf(viewer, "]\n");CHKERRQ(ierr); 986 ierr = PetscViewerASCIISubtractTab(viewer, ((PetscObject) snes)->tablevel);CHKERRQ(ierr); 987 ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr); 988 ierr = PetscFree2(lnorms, norms);CHKERRQ(ierr); 989 PetscFunctionReturn(0); 990 } 991 992 /********************* Residual Computation **************************/ 993 994 995 /*@ 996 DMPlexSNESGetGeometryFVM - Return precomputed geometric data 997 998 Input Parameter: 999 . dm - The DM 1000 1001 Output Parameters: 1002 + facegeom - The values precomputed from face geometry 1003 . cellgeom - The values precomputed from cell geometry 1004 - minRadius - The minimum radius over the mesh of an inscribed sphere in a cell 1005 1006 Level: developer 1007 1008 .seealso: DMPlexTSSetRHSFunctionLocal() 1009 @*/ 1010 PetscErrorCode DMPlexSNESGetGeometryFVM(DM dm, Vec *facegeom, Vec *cellgeom, PetscReal *minRadius) 1011 { 1012 DM plex; 1013 PetscErrorCode ierr; 1014 1015 PetscFunctionBegin; 1016 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 1017 ierr = DMSNESConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr); 1018 ierr = DMPlexGetDataFVM(plex, NULL, cellgeom, facegeom, NULL);CHKERRQ(ierr); 1019 if (minRadius) {ierr = DMPlexGetMinRadius(plex, minRadius);CHKERRQ(ierr);} 1020 ierr = DMDestroy(&plex);CHKERRQ(ierr); 1021 PetscFunctionReturn(0); 1022 } 1023 1024 /*@ 1025 DMPlexSNESGetGradientDM - Return gradient data layout 1026 1027 Input Parameters: 1028 + dm - The DM 1029 - fv - The PetscFV 1030 1031 Output Parameter: 1032 . dmGrad - The layout for gradient values 1033 1034 Level: developer 1035 1036 .seealso: DMPlexSNESGetGeometryFVM() 1037 @*/ 1038 PetscErrorCode DMPlexSNESGetGradientDM(DM dm, PetscFV fv, DM *dmGrad) 1039 { 1040 DM plex; 1041 PetscBool computeGradients; 1042 PetscErrorCode ierr; 1043 1044 PetscFunctionBegin; 1045 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 1046 PetscValidHeaderSpecific(fv,PETSCFV_CLASSID,2); 1047 PetscValidPointer(dmGrad,3); 1048 ierr = PetscFVGetComputeGradients(fv, &computeGradients);CHKERRQ(ierr); 1049 if (!computeGradients) {*dmGrad = NULL; PetscFunctionReturn(0);} 1050 ierr = DMSNESConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr); 1051 ierr = DMPlexGetDataFVM(plex, fv, NULL, NULL, dmGrad);CHKERRQ(ierr); 1052 ierr = DMDestroy(&plex);CHKERRQ(ierr); 1053 PetscFunctionReturn(0); 1054 } 1055 1056 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) 1057 { 1058 DM_Plex *mesh = (DM_Plex *) dm->data; 1059 DM plex = NULL, plexA = NULL; 1060 DMEnclosureType encAux; 1061 PetscDS prob, probAux = NULL; 1062 PetscSection section, sectionAux = NULL; 1063 Vec locA = NULL; 1064 PetscScalar *u = NULL, *u_t = NULL, *a = NULL, *elemVec = NULL; 1065 PetscInt v; 1066 PetscInt totDim, totDimAux = 0; 1067 PetscErrorCode ierr; 1068 1069 PetscFunctionBegin; 1070 ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); 1071 ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); 1072 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1073 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1074 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);CHKERRQ(ierr); 1075 if (locA) { 1076 DM dmAux; 1077 1078 ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); 1079 ierr = DMGetEnclosureRelation(dmAux, dm, &encAux);CHKERRQ(ierr); 1080 ierr = DMConvert(dmAux, DMPLEX, &plexA);CHKERRQ(ierr); 1081 ierr = DMGetDS(plexA, &probAux);CHKERRQ(ierr); 1082 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 1083 ierr = DMGetLocalSection(plexA, §ionAux);CHKERRQ(ierr); 1084 } 1085 for (v = 0; v < numValues; ++v) { 1086 PetscFEGeom *fgeom; 1087 PetscInt maxDegree; 1088 PetscQuadrature qGeom = NULL; 1089 IS pointIS; 1090 const PetscInt *points; 1091 PetscInt numFaces, face, Nq; 1092 1093 ierr = DMLabelGetStratumIS(label, values[v], &pointIS);CHKERRQ(ierr); 1094 if (!pointIS) continue; /* No points with that id on this process */ 1095 { 1096 IS isectIS; 1097 1098 /* TODO: Special cases of ISIntersect where it is quick to check a priori if one is a superset of the other */ 1099 ierr = ISIntersect_Caching_Internal(facetIS,pointIS,&isectIS);CHKERRQ(ierr); 1100 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 1101 pointIS = isectIS; 1102 } 1103 ierr = ISGetLocalSize(pointIS,&numFaces);CHKERRQ(ierr); 1104 ierr = ISGetIndices(pointIS,&points);CHKERRQ(ierr); 1105 ierr = PetscMalloc4(numFaces*totDim, &u, locX_t ? numFaces*totDim : 0, &u_t, numFaces*totDim, &elemVec, locA ? numFaces*totDimAux : 0, &a);CHKERRQ(ierr); 1106 ierr = DMFieldGetDegree(coordField,pointIS,NULL,&maxDegree);CHKERRQ(ierr); 1107 if (maxDegree <= 1) { 1108 ierr = DMFieldCreateDefaultQuadrature(coordField,pointIS,&qGeom);CHKERRQ(ierr); 1109 } 1110 if (!qGeom) { 1111 PetscFE fe; 1112 1113 ierr = PetscDSGetDiscretization(prob, field, (PetscObject *) &fe);CHKERRQ(ierr); 1114 ierr = PetscFEGetFaceQuadrature(fe, &qGeom);CHKERRQ(ierr); 1115 ierr = PetscObjectReference((PetscObject)qGeom);CHKERRQ(ierr); 1116 } 1117 ierr = PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 1118 ierr = DMSNESGetFEGeom(coordField,pointIS,qGeom,PETSC_TRUE,&fgeom);CHKERRQ(ierr); 1119 for (face = 0; face < numFaces; ++face) { 1120 const PetscInt point = points[face], *support, *cone; 1121 PetscScalar *x = NULL; 1122 PetscInt i, coneSize, faceLoc; 1123 1124 ierr = DMPlexGetSupport(dm, point, &support);CHKERRQ(ierr); 1125 ierr = DMPlexGetConeSize(dm, support[0], &coneSize);CHKERRQ(ierr); 1126 ierr = DMPlexGetCone(dm, support[0], &cone);CHKERRQ(ierr); 1127 for (faceLoc = 0; faceLoc < coneSize; ++faceLoc) if (cone[faceLoc] == point) break; 1128 if (faceLoc == coneSize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Could not find face %D in cone of support[0] %D", point, support[0]); 1129 fgeom->face[face][0] = faceLoc; 1130 ierr = DMPlexVecGetClosure(plex, section, locX, support[0], NULL, &x);CHKERRQ(ierr); 1131 for (i = 0; i < totDim; ++i) u[face*totDim+i] = x[i]; 1132 ierr = DMPlexVecRestoreClosure(plex, section, locX, support[0], NULL, &x);CHKERRQ(ierr); 1133 if (locX_t) { 1134 ierr = DMPlexVecGetClosure(plex, section, locX_t, support[0], NULL, &x);CHKERRQ(ierr); 1135 for (i = 0; i < totDim; ++i) u_t[face*totDim+i] = x[i]; 1136 ierr = DMPlexVecRestoreClosure(plex, section, locX_t, support[0], NULL, &x);CHKERRQ(ierr); 1137 } 1138 if (locA) { 1139 PetscInt subp; 1140 1141 ierr = DMGetEnclosurePoint(plexA, dm, encAux, support[0], &subp);CHKERRQ(ierr); 1142 ierr = DMPlexVecGetClosure(plexA, sectionAux, locA, subp, NULL, &x);CHKERRQ(ierr); 1143 for (i = 0; i < totDimAux; ++i) a[face*totDimAux+i] = x[i]; 1144 ierr = DMPlexVecRestoreClosure(plexA, sectionAux, locA, subp, NULL, &x);CHKERRQ(ierr); 1145 } 1146 } 1147 ierr = PetscArrayzero(elemVec, numFaces*totDim);CHKERRQ(ierr); 1148 { 1149 PetscFE fe; 1150 PetscInt Nb; 1151 PetscFEGeom *chunkGeom = NULL; 1152 /* Conforming batches */ 1153 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 1154 /* Remainder */ 1155 PetscInt Nr, offset; 1156 1157 ierr = PetscDSGetDiscretization(prob, field, (PetscObject *) &fe);CHKERRQ(ierr); 1158 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 1159 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1160 /* TODO: documentation is unclear about what is going on with these numbers: how should Nb / Nq factor in ? */ 1161 blockSize = Nb; 1162 batchSize = numBlocks * blockSize; 1163 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1164 numChunks = numFaces / (numBatches*batchSize); 1165 Ne = numChunks*numBatches*batchSize; 1166 Nr = numFaces % (numBatches*batchSize); 1167 offset = numFaces - Nr; 1168 ierr = PetscFEGeomGetChunk(fgeom,0,offset,&chunkGeom);CHKERRQ(ierr); 1169 ierr = PetscFEIntegrateBdResidual(prob, field, Ne, chunkGeom, u, u_t, probAux, a, t, elemVec);CHKERRQ(ierr); 1170 ierr = PetscFEGeomRestoreChunk(fgeom, 0, offset, &chunkGeom);CHKERRQ(ierr); 1171 ierr = PetscFEGeomGetChunk(fgeom,offset,numFaces,&chunkGeom);CHKERRQ(ierr); 1172 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); 1173 ierr = PetscFEGeomRestoreChunk(fgeom,offset,numFaces,&chunkGeom);CHKERRQ(ierr); 1174 } 1175 for (face = 0; face < numFaces; ++face) { 1176 const PetscInt point = points[face], *support; 1177 1178 if (mesh->printFEM > 1) {ierr = DMPrintCellVector(point, "BdResidual", totDim, &elemVec[face*totDim]);CHKERRQ(ierr);} 1179 ierr = DMPlexGetSupport(plex, point, &support);CHKERRQ(ierr); 1180 ierr = DMPlexVecSetClosure(plex, NULL, locF, support[0], &elemVec[face*totDim], ADD_ALL_VALUES);CHKERRQ(ierr); 1181 } 1182 ierr = DMSNESRestoreFEGeom(coordField,pointIS,qGeom,PETSC_TRUE,&fgeom);CHKERRQ(ierr); 1183 ierr = PetscQuadratureDestroy(&qGeom);CHKERRQ(ierr); 1184 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 1185 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 1186 ierr = PetscFree4(u, u_t, elemVec, a);CHKERRQ(ierr); 1187 } 1188 if (plex) {ierr = DMDestroy(&plex);CHKERRQ(ierr);} 1189 if (plexA) {ierr = DMDestroy(&plexA);CHKERRQ(ierr);} 1190 PetscFunctionReturn(0); 1191 } 1192 1193 PetscErrorCode DMPlexComputeBdResidualSingle(DM dm, PetscReal t, DMLabel label, PetscInt numValues, const PetscInt values[], PetscInt field, Vec locX, Vec locX_t, Vec locF) 1194 { 1195 DMField coordField; 1196 DMLabel depthLabel; 1197 IS facetIS; 1198 PetscInt dim; 1199 PetscErrorCode ierr; 1200 1201 PetscFunctionBegin; 1202 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1203 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 1204 ierr = DMLabelGetStratumIS(depthLabel, dim-1, &facetIS);CHKERRQ(ierr); 1205 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 1206 ierr = DMPlexComputeBdResidual_Single_Internal(dm, t, label, numValues, values, field, locX, locX_t, locF, coordField, facetIS);CHKERRQ(ierr); 1207 ierr = ISDestroy(&facetIS);CHKERRQ(ierr); 1208 PetscFunctionReturn(0); 1209 } 1210 1211 PetscErrorCode DMPlexComputeBdResidual_Internal(DM dm, Vec locX, Vec locX_t, PetscReal t, Vec locF, void *user) 1212 { 1213 PetscDS prob; 1214 PetscInt numBd, bd; 1215 DMField coordField = NULL; 1216 IS facetIS = NULL; 1217 DMLabel depthLabel; 1218 PetscInt dim; 1219 PetscErrorCode ierr; 1220 1221 PetscFunctionBegin; 1222 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1223 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 1224 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1225 ierr = DMLabelGetStratumIS(depthLabel,dim - 1,&facetIS);CHKERRQ(ierr); 1226 ierr = PetscDSGetNumBoundary(prob, &numBd);CHKERRQ(ierr); 1227 for (bd = 0; bd < numBd; ++bd) { 1228 DMBoundaryConditionType type; 1229 const char *bdLabel; 1230 DMLabel label; 1231 const PetscInt *values; 1232 PetscInt field, numValues; 1233 PetscObject obj; 1234 PetscClassId id; 1235 1236 ierr = PetscDSGetBoundary(prob, bd, &type, NULL, &bdLabel, &field, NULL, NULL, NULL, &numValues, &values, NULL);CHKERRQ(ierr); 1237 ierr = PetscDSGetDiscretization(prob, field, &obj);CHKERRQ(ierr); 1238 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1239 if ((id != PETSCFE_CLASSID) || (type & DM_BC_ESSENTIAL)) continue; 1240 if (!facetIS) { 1241 DMLabel depthLabel; 1242 PetscInt dim; 1243 1244 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 1245 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1246 ierr = DMLabelGetStratumIS(depthLabel, dim - 1, &facetIS);CHKERRQ(ierr); 1247 } 1248 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 1249 ierr = DMGetLabel(dm, bdLabel, &label);CHKERRQ(ierr); 1250 ierr = DMPlexComputeBdResidual_Single_Internal(dm, t, label, numValues, values, field, locX, locX_t, locF, coordField, facetIS);CHKERRQ(ierr); 1251 } 1252 ierr = ISDestroy(&facetIS);CHKERRQ(ierr); 1253 PetscFunctionReturn(0); 1254 } 1255 1256 PetscErrorCode DMPlexComputeResidual_Internal(DM dm, IS cellIS, PetscReal time, Vec locX, Vec locX_t, PetscReal t, Vec locF, void *user) 1257 { 1258 DM_Plex *mesh = (DM_Plex *) dm->data; 1259 const char *name = "Residual"; 1260 DM dmAux = NULL; 1261 DM dmGrad = NULL; 1262 DMLabel ghostLabel = NULL; 1263 PetscDS prob = NULL; 1264 PetscDS probAux = NULL; 1265 PetscSection section = NULL; 1266 PetscBool useFEM = PETSC_FALSE; 1267 PetscBool useFVM = PETSC_FALSE; 1268 PetscBool isImplicit = (locX_t || time == PETSC_MIN_REAL) ? PETSC_TRUE : PETSC_FALSE; 1269 PetscFV fvm = NULL; 1270 PetscFVCellGeom *cgeomFVM = NULL; 1271 PetscFVFaceGeom *fgeomFVM = NULL; 1272 DMField coordField = NULL; 1273 Vec locA, cellGeometryFVM = NULL, faceGeometryFVM = NULL, grad, locGrad = NULL; 1274 PetscScalar *u = NULL, *u_t, *a, *uL, *uR; 1275 IS chunkIS; 1276 const PetscInt *cells; 1277 PetscInt cStart, cEnd, numCells; 1278 PetscInt Nf, f, totDim, totDimAux, numChunks, cellChunkSize, faceChunkSize, chunk, fStart, fEnd; 1279 PetscInt maxDegree = PETSC_MAX_INT; 1280 PetscQuadrature affineQuad = NULL, *quads = NULL; 1281 PetscFEGeom *affineGeom = NULL, **geoms = NULL; 1282 PetscErrorCode ierr; 1283 1284 PetscFunctionBegin; 1285 ierr = PetscLogEventBegin(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr); 1286 /* TODO The places where we have to use isFE are probably the member functions for the PetscDisc class */ 1287 /* TODO The FVM geometry is over-manipulated. Make the precalc functions return exactly what we need */ 1288 /* FEM+FVM */ 1289 ierr = ISGetPointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 1290 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 1291 /* 1: Get sizes from dm and dmAux */ 1292 ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); 1293 ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 1294 ierr = DMGetCellDS(dm, cStart, &prob);CHKERRQ(ierr); 1295 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 1296 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1297 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);CHKERRQ(ierr); 1298 if (locA) { 1299 PetscInt subcell; 1300 ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); 1301 ierr = DMGetEnclosurePoint(dmAux, dm, DM_ENC_UNKNOWN, cStart, &subcell);CHKERRQ(ierr); 1302 ierr = DMGetCellDS(dmAux, subcell, &probAux);CHKERRQ(ierr); 1303 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 1304 } 1305 /* 2: Get geometric data */ 1306 for (f = 0; f < Nf; ++f) { 1307 PetscObject obj; 1308 PetscClassId id; 1309 PetscBool fimp; 1310 1311 ierr = PetscDSGetImplicit(prob, f, &fimp);CHKERRQ(ierr); 1312 if (isImplicit != fimp) continue; 1313 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1314 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1315 if (id == PETSCFE_CLASSID) {useFEM = PETSC_TRUE;} 1316 if (id == PETSCFV_CLASSID) {useFVM = PETSC_TRUE; fvm = (PetscFV) obj;} 1317 } 1318 if (useFEM) { 1319 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 1320 ierr = DMFieldGetDegree(coordField,cellIS,NULL,&maxDegree);CHKERRQ(ierr); 1321 if (maxDegree <= 1) { 1322 ierr = DMFieldCreateDefaultQuadrature(coordField,cellIS,&affineQuad);CHKERRQ(ierr); 1323 if (affineQuad) { 1324 ierr = DMSNESGetFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&affineGeom);CHKERRQ(ierr); 1325 } 1326 } else { 1327 ierr = PetscCalloc2(Nf,&quads,Nf,&geoms);CHKERRQ(ierr); 1328 for (f = 0; f < Nf; ++f) { 1329 PetscObject obj; 1330 PetscClassId id; 1331 PetscBool fimp; 1332 1333 ierr = PetscDSGetImplicit(prob, f, &fimp);CHKERRQ(ierr); 1334 if (isImplicit != fimp) continue; 1335 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1336 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1337 if (id == PETSCFE_CLASSID) { 1338 PetscFE fe = (PetscFE) obj; 1339 1340 ierr = PetscFEGetQuadrature(fe, &quads[f]);CHKERRQ(ierr); 1341 ierr = PetscObjectReference((PetscObject)quads[f]);CHKERRQ(ierr); 1342 ierr = DMSNESGetFEGeom(coordField,cellIS,quads[f],PETSC_FALSE,&geoms[f]);CHKERRQ(ierr); 1343 } 1344 } 1345 } 1346 } 1347 if (useFVM) { 1348 ierr = DMPlexSNESGetGeometryFVM(dm, &faceGeometryFVM, &cellGeometryFVM, NULL);CHKERRQ(ierr); 1349 ierr = VecGetArrayRead(faceGeometryFVM, (const PetscScalar **) &fgeomFVM);CHKERRQ(ierr); 1350 ierr = VecGetArrayRead(cellGeometryFVM, (const PetscScalar **) &cgeomFVM);CHKERRQ(ierr); 1351 /* Reconstruct and limit cell gradients */ 1352 ierr = DMPlexSNESGetGradientDM(dm, fvm, &dmGrad);CHKERRQ(ierr); 1353 if (dmGrad) { 1354 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 1355 ierr = DMGetGlobalVector(dmGrad, &grad);CHKERRQ(ierr); 1356 ierr = DMPlexReconstructGradients_Internal(dm, fvm, fStart, fEnd, faceGeometryFVM, cellGeometryFVM, locX, grad);CHKERRQ(ierr); 1357 /* Communicate gradient values */ 1358 ierr = DMGetLocalVector(dmGrad, &locGrad);CHKERRQ(ierr); 1359 ierr = DMGlobalToLocalBegin(dmGrad, grad, INSERT_VALUES, locGrad);CHKERRQ(ierr); 1360 ierr = DMGlobalToLocalEnd(dmGrad, grad, INSERT_VALUES, locGrad);CHKERRQ(ierr); 1361 ierr = DMRestoreGlobalVector(dmGrad, &grad);CHKERRQ(ierr); 1362 } 1363 /* Handle non-essential (e.g. outflow) boundary values */ 1364 ierr = DMPlexInsertBoundaryValues(dm, PETSC_FALSE, locX, time, faceGeometryFVM, cellGeometryFVM, locGrad);CHKERRQ(ierr); 1365 } 1366 /* Loop over chunks */ 1367 if (useFEM) {ierr = ISCreate(PETSC_COMM_SELF, &chunkIS);CHKERRQ(ierr);} 1368 numCells = cEnd - cStart; 1369 numChunks = 1; 1370 cellChunkSize = numCells/numChunks; 1371 faceChunkSize = (fEnd - fStart)/numChunks; 1372 numChunks = PetscMin(1,numCells); 1373 for (chunk = 0; chunk < numChunks; ++chunk) { 1374 PetscScalar *elemVec, *fluxL, *fluxR; 1375 PetscReal *vol; 1376 PetscFVFaceGeom *fgeom; 1377 PetscInt cS = cStart+chunk*cellChunkSize, cE = PetscMin(cS+cellChunkSize, cEnd), numCells = cE - cS, c; 1378 PetscInt fS = fStart+chunk*faceChunkSize, fE = PetscMin(fS+faceChunkSize, fEnd), numFaces = 0, face; 1379 1380 /* Extract field coefficients */ 1381 if (useFEM) { 1382 ierr = ISGetPointSubrange(chunkIS, cS, cE, cells);CHKERRQ(ierr); 1383 ierr = DMPlexGetCellFields(dm, chunkIS, locX, locX_t, locA, &u, &u_t, &a);CHKERRQ(ierr); 1384 ierr = DMGetWorkArray(dm, numCells*totDim, MPIU_SCALAR, &elemVec);CHKERRQ(ierr); 1385 ierr = PetscArrayzero(elemVec, numCells*totDim);CHKERRQ(ierr); 1386 } 1387 if (useFVM) { 1388 ierr = DMPlexGetFaceFields(dm, fS, fE, locX, locX_t, faceGeometryFVM, cellGeometryFVM, locGrad, &numFaces, &uL, &uR);CHKERRQ(ierr); 1389 ierr = DMPlexGetFaceGeometry(dm, fS, fE, faceGeometryFVM, cellGeometryFVM, &numFaces, &fgeom, &vol);CHKERRQ(ierr); 1390 ierr = DMGetWorkArray(dm, numFaces*totDim, MPIU_SCALAR, &fluxL);CHKERRQ(ierr); 1391 ierr = DMGetWorkArray(dm, numFaces*totDim, MPIU_SCALAR, &fluxR);CHKERRQ(ierr); 1392 ierr = PetscArrayzero(fluxL, numFaces*totDim);CHKERRQ(ierr); 1393 ierr = PetscArrayzero(fluxR, numFaces*totDim);CHKERRQ(ierr); 1394 } 1395 /* TODO We will interlace both our field coefficients (u, u_t, uL, uR, etc.) and our output (elemVec, fL, fR). I think this works */ 1396 /* Loop over fields */ 1397 for (f = 0; f < Nf; ++f) { 1398 PetscObject obj; 1399 PetscClassId id; 1400 PetscBool fimp; 1401 PetscInt numChunks, numBatches, batchSize, numBlocks, blockSize, Ne, Nr, offset; 1402 1403 ierr = PetscDSGetImplicit(prob, f, &fimp);CHKERRQ(ierr); 1404 if (isImplicit != fimp) continue; 1405 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1406 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1407 if (id == PETSCFE_CLASSID) { 1408 PetscFE fe = (PetscFE) obj; 1409 PetscFEGeom *geom = affineGeom ? affineGeom : geoms[f]; 1410 PetscFEGeom *chunkGeom = NULL; 1411 PetscQuadrature quad = affineQuad ? affineQuad : quads[f]; 1412 PetscInt Nq, Nb; 1413 1414 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1415 ierr = PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 1416 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 1417 blockSize = Nb; 1418 batchSize = numBlocks * blockSize; 1419 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1420 numChunks = numCells / (numBatches*batchSize); 1421 Ne = numChunks*numBatches*batchSize; 1422 Nr = numCells % (numBatches*batchSize); 1423 offset = numCells - Nr; 1424 /* Integrate FE residual to get elemVec (need fields at quadrature points) */ 1425 /* 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) */ 1426 ierr = PetscFEGeomGetChunk(geom,0,offset,&chunkGeom);CHKERRQ(ierr); 1427 ierr = PetscFEIntegrateResidual(prob, f, Ne, chunkGeom, u, u_t, probAux, a, t, elemVec);CHKERRQ(ierr); 1428 ierr = PetscFEGeomGetChunk(geom,offset,numCells,&chunkGeom);CHKERRQ(ierr); 1429 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); 1430 ierr = PetscFEGeomRestoreChunk(geom,offset,numCells,&chunkGeom);CHKERRQ(ierr); 1431 } else if (id == PETSCFV_CLASSID) { 1432 PetscFV fv = (PetscFV) obj; 1433 1434 Ne = numFaces; 1435 /* Riemann solve over faces (need fields at face centroids) */ 1436 /* We need to evaluate FE fields at those coordinates */ 1437 ierr = PetscFVIntegrateRHSFunction(fv, prob, f, Ne, fgeom, vol, uL, uR, fluxL, fluxR);CHKERRQ(ierr); 1438 } else SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", f); 1439 } 1440 /* Loop over domain */ 1441 if (useFEM) { 1442 /* Add elemVec to locX */ 1443 for (c = cS; c < cE; ++c) { 1444 const PetscInt cell = cells ? cells[c] : c; 1445 const PetscInt cind = c - cStart; 1446 1447 if (mesh->printFEM > 1) {ierr = DMPrintCellVector(cell, name, totDim, &elemVec[cind*totDim]);CHKERRQ(ierr);} 1448 if (ghostLabel) { 1449 PetscInt ghostVal; 1450 1451 ierr = DMLabelGetValue(ghostLabel,cell,&ghostVal);CHKERRQ(ierr); 1452 if (ghostVal > 0) continue; 1453 } 1454 ierr = DMPlexVecSetClosure(dm, section, locF, cell, &elemVec[cind*totDim], ADD_ALL_VALUES);CHKERRQ(ierr); 1455 } 1456 } 1457 if (useFVM) { 1458 PetscScalar *fa; 1459 PetscInt iface; 1460 1461 ierr = VecGetArray(locF, &fa);CHKERRQ(ierr); 1462 for (f = 0; f < Nf; ++f) { 1463 PetscFV fv; 1464 PetscObject obj; 1465 PetscClassId id; 1466 PetscInt foff, pdim; 1467 1468 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1469 ierr = PetscDSGetFieldOffset(prob, f, &foff);CHKERRQ(ierr); 1470 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1471 if (id != PETSCFV_CLASSID) continue; 1472 fv = (PetscFV) obj; 1473 ierr = PetscFVGetNumComponents(fv, &pdim);CHKERRQ(ierr); 1474 /* Accumulate fluxes to cells */ 1475 for (face = fS, iface = 0; face < fE; ++face) { 1476 const PetscInt *scells; 1477 PetscScalar *fL = NULL, *fR = NULL; 1478 PetscInt ghost, d, nsupp, nchild; 1479 1480 ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr); 1481 ierr = DMPlexGetSupportSize(dm, face, &nsupp);CHKERRQ(ierr); 1482 ierr = DMPlexGetTreeChildren(dm, face, &nchild, NULL);CHKERRQ(ierr); 1483 if (ghost >= 0 || nsupp > 2 || nchild > 0) continue; 1484 ierr = DMPlexGetSupport(dm, face, &scells);CHKERRQ(ierr); 1485 ierr = DMLabelGetValue(ghostLabel,scells[0],&ghost);CHKERRQ(ierr); 1486 if (ghost <= 0) {ierr = DMPlexPointLocalFieldRef(dm, scells[0], f, fa, &fL);CHKERRQ(ierr);} 1487 ierr = DMLabelGetValue(ghostLabel,scells[1],&ghost);CHKERRQ(ierr); 1488 if (ghost <= 0) {ierr = DMPlexPointLocalFieldRef(dm, scells[1], f, fa, &fR);CHKERRQ(ierr);} 1489 for (d = 0; d < pdim; ++d) { 1490 if (fL) fL[d] -= fluxL[iface*totDim+foff+d]; 1491 if (fR) fR[d] += fluxR[iface*totDim+foff+d]; 1492 } 1493 ++iface; 1494 } 1495 } 1496 ierr = VecRestoreArray(locF, &fa);CHKERRQ(ierr); 1497 } 1498 /* Handle time derivative */ 1499 if (locX_t) { 1500 PetscScalar *x_t, *fa; 1501 1502 ierr = VecGetArray(locF, &fa);CHKERRQ(ierr); 1503 ierr = VecGetArray(locX_t, &x_t);CHKERRQ(ierr); 1504 for (f = 0; f < Nf; ++f) { 1505 PetscFV fv; 1506 PetscObject obj; 1507 PetscClassId id; 1508 PetscInt pdim, d; 1509 1510 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1511 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1512 if (id != PETSCFV_CLASSID) continue; 1513 fv = (PetscFV) obj; 1514 ierr = PetscFVGetNumComponents(fv, &pdim);CHKERRQ(ierr); 1515 for (c = cS; c < cE; ++c) { 1516 const PetscInt cell = cells ? cells[c] : c; 1517 PetscScalar *u_t, *r; 1518 1519 if (ghostLabel) { 1520 PetscInt ghostVal; 1521 1522 ierr = DMLabelGetValue(ghostLabel, cell, &ghostVal);CHKERRQ(ierr); 1523 if (ghostVal > 0) continue; 1524 } 1525 ierr = DMPlexPointLocalFieldRead(dm, cell, f, x_t, &u_t);CHKERRQ(ierr); 1526 ierr = DMPlexPointLocalFieldRef(dm, cell, f, fa, &r);CHKERRQ(ierr); 1527 for (d = 0; d < pdim; ++d) r[d] += u_t[d]; 1528 } 1529 } 1530 ierr = VecRestoreArray(locX_t, &x_t);CHKERRQ(ierr); 1531 ierr = VecRestoreArray(locF, &fa);CHKERRQ(ierr); 1532 } 1533 if (useFEM) { 1534 ierr = DMPlexRestoreCellFields(dm, chunkIS, locX, locX_t, locA, &u, &u_t, &a);CHKERRQ(ierr); 1535 ierr = DMRestoreWorkArray(dm, numCells*totDim, MPIU_SCALAR, &elemVec);CHKERRQ(ierr); 1536 } 1537 if (useFVM) { 1538 ierr = DMPlexRestoreFaceFields(dm, fS, fE, locX, locX_t, faceGeometryFVM, cellGeometryFVM, locGrad, &numFaces, &uL, &uR);CHKERRQ(ierr); 1539 ierr = DMPlexRestoreFaceGeometry(dm, fS, fE, faceGeometryFVM, cellGeometryFVM, &numFaces, &fgeom, &vol);CHKERRQ(ierr); 1540 ierr = DMRestoreWorkArray(dm, numFaces*totDim, MPIU_SCALAR, &fluxL);CHKERRQ(ierr); 1541 ierr = DMRestoreWorkArray(dm, numFaces*totDim, MPIU_SCALAR, &fluxR);CHKERRQ(ierr); 1542 if (dmGrad) {ierr = DMRestoreLocalVector(dmGrad, &locGrad);CHKERRQ(ierr);} 1543 } 1544 } 1545 if (useFEM) {ierr = ISDestroy(&chunkIS);CHKERRQ(ierr);} 1546 ierr = ISRestorePointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 1547 1548 if (useFEM) { 1549 ierr = DMPlexComputeBdResidual_Internal(dm, locX, locX_t, t, locF, user);CHKERRQ(ierr); 1550 1551 if (maxDegree <= 1) { 1552 ierr = DMSNESRestoreFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&affineGeom);CHKERRQ(ierr); 1553 ierr = PetscQuadratureDestroy(&affineQuad);CHKERRQ(ierr); 1554 } else { 1555 for (f = 0; f < Nf; ++f) { 1556 ierr = DMSNESRestoreFEGeom(coordField,cellIS,quads[f],PETSC_FALSE,&geoms[f]);CHKERRQ(ierr); 1557 ierr = PetscQuadratureDestroy(&quads[f]);CHKERRQ(ierr); 1558 } 1559 ierr = PetscFree2(quads,geoms);CHKERRQ(ierr); 1560 } 1561 } 1562 1563 /* FEM */ 1564 /* 1: Get sizes from dm and dmAux */ 1565 /* 2: Get geometric data */ 1566 /* 3: Handle boundary values */ 1567 /* 4: Loop over domain */ 1568 /* Extract coefficients */ 1569 /* Loop over fields */ 1570 /* Set tiling for FE*/ 1571 /* Integrate FE residual to get elemVec */ 1572 /* Loop over subdomain */ 1573 /* Loop over quad points */ 1574 /* Transform coords to real space */ 1575 /* Evaluate field and aux fields at point */ 1576 /* Evaluate residual at point */ 1577 /* Transform residual to real space */ 1578 /* Add residual to elemVec */ 1579 /* Loop over domain */ 1580 /* Add elemVec to locX */ 1581 1582 /* FVM */ 1583 /* Get geometric data */ 1584 /* If using gradients */ 1585 /* Compute gradient data */ 1586 /* Loop over domain faces */ 1587 /* Count computational faces */ 1588 /* Reconstruct cell gradient */ 1589 /* Loop over domain cells */ 1590 /* Limit cell gradients */ 1591 /* Handle boundary values */ 1592 /* Loop over domain faces */ 1593 /* Read out field, centroid, normal, volume for each side of face */ 1594 /* Riemann solve over faces */ 1595 /* Loop over domain faces */ 1596 /* Accumulate fluxes to cells */ 1597 /* TODO Change printFEM to printDisc here */ 1598 if (mesh->printFEM) { 1599 Vec locFbc; 1600 PetscInt pStart, pEnd, p, maxDof; 1601 PetscScalar *zeroes; 1602 1603 ierr = VecDuplicate(locF,&locFbc);CHKERRQ(ierr); 1604 ierr = VecCopy(locF,locFbc);CHKERRQ(ierr); 1605 ierr = PetscSectionGetChart(section,&pStart,&pEnd);CHKERRQ(ierr); 1606 ierr = PetscSectionGetMaxDof(section,&maxDof);CHKERRQ(ierr); 1607 ierr = PetscCalloc1(maxDof,&zeroes);CHKERRQ(ierr); 1608 for (p = pStart; p < pEnd; p++) { 1609 ierr = VecSetValuesSection(locFbc,section,p,zeroes,INSERT_BC_VALUES);CHKERRQ(ierr); 1610 } 1611 ierr = PetscFree(zeroes);CHKERRQ(ierr); 1612 ierr = DMPrintLocalVec(dm, name, mesh->printTol, locFbc);CHKERRQ(ierr); 1613 ierr = VecDestroy(&locFbc);CHKERRQ(ierr); 1614 } 1615 ierr = PetscLogEventEnd(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr); 1616 PetscFunctionReturn(0); 1617 } 1618 1619 /*@ 1620 DMPlexSNESComputeResidualFEM - Form the local residual F from the local input X using pointwise functions specified by the user 1621 1622 Input Parameters: 1623 + dm - The mesh 1624 . X - Local solution 1625 - user - The user context 1626 1627 Output Parameter: 1628 . F - Local output vector 1629 1630 Level: developer 1631 1632 .seealso: DMPlexComputeJacobianAction() 1633 @*/ 1634 PetscErrorCode DMPlexSNESComputeResidualFEM(DM dm, Vec X, Vec F, void *user) 1635 { 1636 DM plex; 1637 IS cellIS; 1638 PetscInt depth; 1639 PetscErrorCode ierr; 1640 1641 PetscFunctionBegin; 1642 ierr = DMSNESConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr); 1643 ierr = DMPlexGetDepth(plex, &depth);CHKERRQ(ierr); 1644 ierr = DMGetStratumIS(plex, "dim", depth, &cellIS);CHKERRQ(ierr); 1645 if (!cellIS) { 1646 ierr = DMGetStratumIS(plex, "depth", depth, &cellIS);CHKERRQ(ierr); 1647 } 1648 ierr = DMPlexComputeResidual_Internal(plex, cellIS, PETSC_MIN_REAL, X, NULL, 0.0, F, user);CHKERRQ(ierr); 1649 ierr = ISDestroy(&cellIS);CHKERRQ(ierr); 1650 ierr = DMDestroy(&plex);CHKERRQ(ierr); 1651 PetscFunctionReturn(0); 1652 } 1653 1654 /*@ 1655 DMPlexSNESComputeBoundaryFEM - Form the boundary values for the local input X 1656 1657 Input Parameters: 1658 + dm - The mesh 1659 - user - The user context 1660 1661 Output Parameter: 1662 . X - Local solution 1663 1664 Level: developer 1665 1666 .seealso: DMPlexComputeJacobianAction() 1667 @*/ 1668 PetscErrorCode DMPlexSNESComputeBoundaryFEM(DM dm, Vec X, void *user) 1669 { 1670 DM plex; 1671 PetscErrorCode ierr; 1672 1673 PetscFunctionBegin; 1674 ierr = DMSNESConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr); 1675 ierr = DMPlexInsertBoundaryValues(plex, PETSC_TRUE, X, PETSC_MIN_REAL, NULL, NULL, NULL);CHKERRQ(ierr); 1676 ierr = DMDestroy(&plex);CHKERRQ(ierr); 1677 PetscFunctionReturn(0); 1678 } 1679 1680 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) 1681 { 1682 DM_Plex *mesh = (DM_Plex *) dm->data; 1683 DM plex = NULL, plexA = NULL, tdm; 1684 DMEnclosureType encAux; 1685 PetscDS prob, probAux = NULL; 1686 PetscSection section, sectionAux = NULL; 1687 PetscSection globalSection, subSection = NULL; 1688 Vec locA = NULL, tv; 1689 PetscScalar *u = NULL, *u_t = NULL, *a = NULL, *elemMat = NULL; 1690 PetscInt v; 1691 PetscInt Nf, totDim, totDimAux = 0; 1692 PetscBool isMatISP, transform; 1693 PetscErrorCode ierr; 1694 1695 PetscFunctionBegin; 1696 ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); 1697 ierr = DMHasBasisTransform(dm, &transform);CHKERRQ(ierr); 1698 ierr = DMGetBasisTransformDM_Internal(dm, &tdm);CHKERRQ(ierr); 1699 ierr = DMGetBasisTransformVec_Internal(dm, &tv);CHKERRQ(ierr); 1700 ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); 1701 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1702 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 1703 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1704 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);CHKERRQ(ierr); 1705 if (locA) { 1706 DM dmAux; 1707 1708 ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); 1709 ierr = DMGetEnclosureRelation(dmAux, dm, &encAux);CHKERRQ(ierr); 1710 ierr = DMConvert(dmAux, DMPLEX, &plexA);CHKERRQ(ierr); 1711 ierr = DMGetDS(plexA, &probAux);CHKERRQ(ierr); 1712 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 1713 ierr = DMGetLocalSection(plexA, §ionAux);CHKERRQ(ierr); 1714 } 1715 1716 ierr = PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatISP);CHKERRQ(ierr); 1717 ierr = DMGetGlobalSection(dm, &globalSection);CHKERRQ(ierr); 1718 if (isMatISP) {ierr = DMPlexGetSubdomainSection(dm, &subSection);CHKERRQ(ierr);} 1719 for (v = 0; v < numValues; ++v) { 1720 PetscFEGeom *fgeom; 1721 PetscInt maxDegree; 1722 PetscQuadrature qGeom = NULL; 1723 IS pointIS; 1724 const PetscInt *points; 1725 PetscInt numFaces, face, Nq; 1726 1727 ierr = DMLabelGetStratumIS(label, values[v], &pointIS);CHKERRQ(ierr); 1728 if (!pointIS) continue; /* No points with that id on this process */ 1729 { 1730 IS isectIS; 1731 1732 /* TODO: Special cases of ISIntersect where it is quick to check a prior if one is a superset of the other */ 1733 ierr = ISIntersect_Caching_Internal(facetIS,pointIS,&isectIS);CHKERRQ(ierr); 1734 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 1735 pointIS = isectIS; 1736 } 1737 ierr = ISGetLocalSize(pointIS, &numFaces);CHKERRQ(ierr); 1738 ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); 1739 ierr = PetscMalloc4(numFaces*totDim, &u, locX_t ? numFaces*totDim : 0, &u_t, numFaces*totDim*totDim, &elemMat, locA ? numFaces*totDimAux : 0, &a);CHKERRQ(ierr); 1740 ierr = DMFieldGetDegree(coordField,pointIS,NULL,&maxDegree);CHKERRQ(ierr); 1741 if (maxDegree <= 1) { 1742 ierr = DMFieldCreateDefaultQuadrature(coordField,pointIS,&qGeom);CHKERRQ(ierr); 1743 } 1744 if (!qGeom) { 1745 PetscFE fe; 1746 1747 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); 1748 ierr = PetscFEGetFaceQuadrature(fe, &qGeom);CHKERRQ(ierr); 1749 ierr = PetscObjectReference((PetscObject)qGeom);CHKERRQ(ierr); 1750 } 1751 ierr = PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 1752 ierr = DMSNESGetFEGeom(coordField,pointIS,qGeom,PETSC_TRUE,&fgeom);CHKERRQ(ierr); 1753 for (face = 0; face < numFaces; ++face) { 1754 const PetscInt point = points[face], *support, *cone; 1755 PetscScalar *x = NULL; 1756 PetscInt i, coneSize, faceLoc; 1757 1758 ierr = DMPlexGetSupport(dm, point, &support);CHKERRQ(ierr); 1759 ierr = DMPlexGetConeSize(dm, support[0], &coneSize);CHKERRQ(ierr); 1760 ierr = DMPlexGetCone(dm, support[0], &cone);CHKERRQ(ierr); 1761 for (faceLoc = 0; faceLoc < coneSize; ++faceLoc) if (cone[faceLoc] == point) break; 1762 if (faceLoc == coneSize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Could not find face %D in cone of support[0] %D", point, support[0]); 1763 fgeom->face[face][0] = faceLoc; 1764 ierr = DMPlexVecGetClosure(plex, section, locX, support[0], NULL, &x);CHKERRQ(ierr); 1765 for (i = 0; i < totDim; ++i) u[face*totDim+i] = x[i]; 1766 ierr = DMPlexVecRestoreClosure(plex, section, locX, support[0], NULL, &x);CHKERRQ(ierr); 1767 if (locX_t) { 1768 ierr = DMPlexVecGetClosure(plex, section, locX_t, support[0], NULL, &x);CHKERRQ(ierr); 1769 for (i = 0; i < totDim; ++i) u_t[face*totDim+i] = x[i]; 1770 ierr = DMPlexVecRestoreClosure(plex, section, locX_t, support[0], NULL, &x);CHKERRQ(ierr); 1771 } 1772 if (locA) { 1773 PetscInt subp; 1774 ierr = DMGetEnclosurePoint(plexA, dm, encAux, support[0], &subp);CHKERRQ(ierr); 1775 ierr = DMPlexVecGetClosure(plexA, sectionAux, locA, subp, NULL, &x);CHKERRQ(ierr); 1776 for (i = 0; i < totDimAux; ++i) a[face*totDimAux+i] = x[i]; 1777 ierr = DMPlexVecRestoreClosure(plexA, sectionAux, locA, subp, NULL, &x);CHKERRQ(ierr); 1778 } 1779 } 1780 ierr = PetscArrayzero(elemMat, numFaces*totDim*totDim);CHKERRQ(ierr); 1781 { 1782 PetscFE fe; 1783 PetscInt Nb; 1784 /* Conforming batches */ 1785 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 1786 /* Remainder */ 1787 PetscFEGeom *chunkGeom = NULL; 1788 PetscInt fieldJ, Nr, offset; 1789 1790 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); 1791 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 1792 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1793 blockSize = Nb; 1794 batchSize = numBlocks * blockSize; 1795 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1796 numChunks = numFaces / (numBatches*batchSize); 1797 Ne = numChunks*numBatches*batchSize; 1798 Nr = numFaces % (numBatches*batchSize); 1799 offset = numFaces - Nr; 1800 ierr = PetscFEGeomGetChunk(fgeom,0,offset,&chunkGeom);CHKERRQ(ierr); 1801 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 1802 ierr = PetscFEIntegrateBdJacobian(prob, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMat);CHKERRQ(ierr); 1803 } 1804 ierr = PetscFEGeomGetChunk(fgeom,offset,numFaces,&chunkGeom);CHKERRQ(ierr); 1805 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 1806 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); 1807 } 1808 ierr = PetscFEGeomRestoreChunk(fgeom,offset,numFaces,&chunkGeom);CHKERRQ(ierr); 1809 } 1810 for (face = 0; face < numFaces; ++face) { 1811 const PetscInt point = points[face], *support; 1812 1813 /* Transform to global basis before insertion in Jacobian */ 1814 ierr = DMPlexGetSupport(plex, point, &support);CHKERRQ(ierr); 1815 if (transform) {ierr = DMPlexBasisTransformPointTensor_Internal(dm, tdm, tv, support[0], PETSC_TRUE, totDim, &elemMat[face*totDim*totDim]);CHKERRQ(ierr);} 1816 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(point, "BdJacobian", totDim, totDim, &elemMat[face*totDim*totDim]);CHKERRQ(ierr);} 1817 if (!isMatISP) { 1818 ierr = DMPlexMatSetClosure(plex, section, globalSection, JacP, support[0], &elemMat[face*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 1819 } else { 1820 Mat lJ; 1821 1822 ierr = MatISGetLocalMat(JacP, &lJ);CHKERRQ(ierr); 1823 ierr = DMPlexMatSetClosure(plex, section, subSection, lJ, support[0], &elemMat[face*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 1824 } 1825 } 1826 ierr = DMSNESRestoreFEGeom(coordField,pointIS,qGeom,PETSC_TRUE,&fgeom);CHKERRQ(ierr); 1827 ierr = PetscQuadratureDestroy(&qGeom);CHKERRQ(ierr); 1828 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 1829 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 1830 ierr = PetscFree4(u, u_t, elemMat, a);CHKERRQ(ierr); 1831 } 1832 if (plex) {ierr = DMDestroy(&plex);CHKERRQ(ierr);} 1833 if (plexA) {ierr = DMDestroy(&plexA);CHKERRQ(ierr);} 1834 PetscFunctionReturn(0); 1835 } 1836 1837 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) 1838 { 1839 DMField coordField; 1840 DMLabel depthLabel; 1841 IS facetIS; 1842 PetscInt dim; 1843 PetscErrorCode ierr; 1844 1845 PetscFunctionBegin; 1846 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1847 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 1848 ierr = DMLabelGetStratumIS(depthLabel, dim-1, &facetIS);CHKERRQ(ierr); 1849 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 1850 ierr = DMPlexComputeBdJacobian_Single_Internal(dm, t, label, numValues, values, field, locX, locX_t, X_tShift, Jac, JacP, coordField, facetIS);CHKERRQ(ierr); 1851 ierr = ISDestroy(&facetIS);CHKERRQ(ierr); 1852 PetscFunctionReturn(0); 1853 } 1854 1855 PetscErrorCode DMPlexComputeBdJacobian_Internal(DM dm, Vec locX, Vec locX_t, PetscReal t, PetscReal X_tShift, Mat Jac, Mat JacP, void *user) 1856 { 1857 PetscDS prob; 1858 PetscInt dim, numBd, bd; 1859 DMLabel depthLabel; 1860 DMField coordField = NULL; 1861 IS facetIS; 1862 PetscErrorCode ierr; 1863 1864 PetscFunctionBegin; 1865 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1866 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 1867 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1868 ierr = DMLabelGetStratumIS(depthLabel, dim-1, &facetIS);CHKERRQ(ierr); 1869 ierr = PetscDSGetNumBoundary(prob, &numBd);CHKERRQ(ierr); 1870 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 1871 for (bd = 0; bd < numBd; ++bd) { 1872 DMBoundaryConditionType type; 1873 const char *bdLabel; 1874 DMLabel label; 1875 const PetscInt *values; 1876 PetscInt fieldI, numValues; 1877 PetscObject obj; 1878 PetscClassId id; 1879 1880 ierr = PetscDSGetBoundary(prob, bd, &type, NULL, &bdLabel, &fieldI, NULL, NULL, NULL, &numValues, &values, NULL);CHKERRQ(ierr); 1881 ierr = PetscDSGetDiscretization(prob, fieldI, &obj);CHKERRQ(ierr); 1882 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1883 if ((id != PETSCFE_CLASSID) || (type & DM_BC_ESSENTIAL)) continue; 1884 ierr = DMGetLabel(dm, bdLabel, &label);CHKERRQ(ierr); 1885 ierr = DMPlexComputeBdJacobian_Single_Internal(dm, t, label, numValues, values, fieldI, locX, locX_t, X_tShift, Jac, JacP, coordField, facetIS);CHKERRQ(ierr); 1886 } 1887 ierr = ISDestroy(&facetIS);CHKERRQ(ierr); 1888 PetscFunctionReturn(0); 1889 } 1890 1891 PetscErrorCode DMPlexComputeJacobian_Internal(DM dm, IS cellIS, PetscReal t, PetscReal X_tShift, Vec X, Vec X_t, Mat Jac, Mat JacP,void *user) 1892 { 1893 DM_Plex *mesh = (DM_Plex *) dm->data; 1894 const char *name = "Jacobian"; 1895 DM dmAux, plex, tdm; 1896 DMEnclosureType encAux; 1897 Vec A, tv; 1898 DMField coordField; 1899 PetscDS prob, probAux = NULL; 1900 PetscSection section, globalSection, subSection, sectionAux; 1901 PetscScalar *elemMat, *elemMatP, *elemMatD, *u, *u_t, *a = NULL; 1902 const PetscInt *cells; 1903 PetscInt Nf, fieldI, fieldJ; 1904 PetscInt totDim, totDimAux, cStart, cEnd, numCells, c; 1905 PetscBool isMatIS, isMatISP, hasJac, hasPrec, hasDyn, hasFV = PETSC_FALSE, transform; 1906 PetscErrorCode ierr; 1907 1908 PetscFunctionBegin; 1909 ierr = PetscLogEventBegin(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 1910 ierr = DMHasBasisTransform(dm, &transform);CHKERRQ(ierr); 1911 ierr = DMGetBasisTransformDM_Internal(dm, &tdm);CHKERRQ(ierr); 1912 ierr = DMGetBasisTransformVec_Internal(dm, &tv);CHKERRQ(ierr); 1913 ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); 1914 ierr = PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatISP);CHKERRQ(ierr); 1915 ierr = DMGetGlobalSection(dm, &globalSection);CHKERRQ(ierr); 1916 if (isMatISP) {ierr = DMPlexGetSubdomainSection(dm, &subSection);CHKERRQ(ierr);} 1917 ierr = ISGetLocalSize(cellIS, &numCells);CHKERRQ(ierr); 1918 ierr = ISGetPointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 1919 ierr = DMGetCellDS(dm, cStart, &prob);CHKERRQ(ierr); 1920 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 1921 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1922 ierr = PetscDSHasJacobian(prob, &hasJac);CHKERRQ(ierr); 1923 ierr = PetscDSHasJacobianPreconditioner(prob, &hasPrec);CHKERRQ(ierr); 1924 /* user passed in the same matrix, avoid double contributions and 1925 only assemble the Jacobian */ 1926 if (hasJac && Jac == JacP) hasPrec = PETSC_FALSE; 1927 ierr = PetscDSHasDynamicJacobian(prob, &hasDyn);CHKERRQ(ierr); 1928 hasDyn = hasDyn && (X_tShift != 0.0) ? PETSC_TRUE : PETSC_FALSE; 1929 ierr = PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);CHKERRQ(ierr); 1930 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);CHKERRQ(ierr); 1931 if (dmAux) { 1932 ierr = DMGetEnclosureRelation(dmAux, dm, &encAux);CHKERRQ(ierr); 1933 ierr = DMConvert(dmAux, DMPLEX, &plex);CHKERRQ(ierr); 1934 ierr = DMGetLocalSection(plex, §ionAux);CHKERRQ(ierr); 1935 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 1936 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 1937 } 1938 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); 1939 if (dmAux) {ierr = PetscMalloc1(numCells*totDimAux, &a);CHKERRQ(ierr);} 1940 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 1941 for (c = cStart; c < cEnd; ++c) { 1942 const PetscInt cell = cells ? cells[c] : c; 1943 const PetscInt cind = c - cStart; 1944 PetscScalar *x = NULL, *x_t = NULL; 1945 PetscInt i; 1946 1947 ierr = DMPlexVecGetClosure(dm, section, X, cell, NULL, &x);CHKERRQ(ierr); 1948 for (i = 0; i < totDim; ++i) u[cind*totDim+i] = x[i]; 1949 ierr = DMPlexVecRestoreClosure(dm, section, X, cell, NULL, &x);CHKERRQ(ierr); 1950 if (X_t) { 1951 ierr = DMPlexVecGetClosure(dm, section, X_t, cell, NULL, &x_t);CHKERRQ(ierr); 1952 for (i = 0; i < totDim; ++i) u_t[cind*totDim+i] = x_t[i]; 1953 ierr = DMPlexVecRestoreClosure(dm, section, X_t, cell, NULL, &x_t);CHKERRQ(ierr); 1954 } 1955 if (dmAux) { 1956 PetscInt subcell; 1957 ierr = DMGetEnclosurePoint(dmAux, dm, encAux, cell, &subcell);CHKERRQ(ierr); 1958 ierr = DMPlexVecGetClosure(plex, sectionAux, A, subcell, NULL, &x);CHKERRQ(ierr); 1959 for (i = 0; i < totDimAux; ++i) a[cind*totDimAux+i] = x[i]; 1960 ierr = DMPlexVecRestoreClosure(plex, sectionAux, A, subcell, NULL, &x);CHKERRQ(ierr); 1961 } 1962 } 1963 if (hasJac) {ierr = PetscArrayzero(elemMat, numCells*totDim*totDim);CHKERRQ(ierr);} 1964 if (hasPrec) {ierr = PetscArrayzero(elemMatP, numCells*totDim*totDim);CHKERRQ(ierr);} 1965 if (hasDyn) {ierr = PetscArrayzero(elemMatD, numCells*totDim*totDim);CHKERRQ(ierr);} 1966 for (fieldI = 0; fieldI < Nf; ++fieldI) { 1967 PetscClassId id; 1968 PetscFE fe; 1969 PetscQuadrature qGeom = NULL; 1970 PetscInt Nb; 1971 /* Conforming batches */ 1972 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 1973 /* Remainder */ 1974 PetscInt Nr, offset, Nq; 1975 PetscInt maxDegree; 1976 PetscFEGeom *cgeomFEM, *chunkGeom = NULL, *remGeom = NULL; 1977 1978 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); 1979 ierr = PetscObjectGetClassId((PetscObject) fe, &id);CHKERRQ(ierr); 1980 if (id == PETSCFV_CLASSID) {hasFV = PETSC_TRUE; continue;} 1981 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 1982 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1983 ierr = DMFieldGetDegree(coordField,cellIS,NULL,&maxDegree);CHKERRQ(ierr); 1984 if (maxDegree <= 1) { 1985 ierr = DMFieldCreateDefaultQuadrature(coordField,cellIS,&qGeom);CHKERRQ(ierr); 1986 } 1987 if (!qGeom) { 1988 ierr = PetscFEGetQuadrature(fe,&qGeom);CHKERRQ(ierr); 1989 ierr = PetscObjectReference((PetscObject)qGeom);CHKERRQ(ierr); 1990 } 1991 ierr = PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 1992 ierr = DMSNESGetFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);CHKERRQ(ierr); 1993 blockSize = Nb; 1994 batchSize = numBlocks * blockSize; 1995 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1996 numChunks = numCells / (numBatches*batchSize); 1997 Ne = numChunks*numBatches*batchSize; 1998 Nr = numCells % (numBatches*batchSize); 1999 offset = numCells - Nr; 2000 ierr = PetscFEGeomGetChunk(cgeomFEM,0,offset,&chunkGeom);CHKERRQ(ierr); 2001 ierr = PetscFEGeomGetChunk(cgeomFEM,offset,numCells,&remGeom);CHKERRQ(ierr); 2002 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 2003 if (hasJac) { 2004 ierr = PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMat);CHKERRQ(ierr); 2005 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); 2006 } 2007 if (hasPrec) { 2008 ierr = PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN_PRE, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMatP);CHKERRQ(ierr); 2009 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); 2010 } 2011 if (hasDyn) { 2012 ierr = PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN_DYN, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMatD);CHKERRQ(ierr); 2013 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); 2014 } 2015 } 2016 ierr = PetscFEGeomRestoreChunk(cgeomFEM,offset,numCells,&remGeom);CHKERRQ(ierr); 2017 ierr = PetscFEGeomRestoreChunk(cgeomFEM,0,offset,&chunkGeom);CHKERRQ(ierr); 2018 ierr = DMSNESRestoreFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);CHKERRQ(ierr); 2019 ierr = PetscQuadratureDestroy(&qGeom);CHKERRQ(ierr); 2020 } 2021 /* Add contribution from X_t */ 2022 if (hasDyn) {for (c = 0; c < numCells*totDim*totDim; ++c) elemMat[c] += X_tShift*elemMatD[c];} 2023 if (hasFV) { 2024 PetscClassId id; 2025 PetscFV fv; 2026 PetscInt offsetI, NcI, NbI = 1, fc, f; 2027 2028 for (fieldI = 0; fieldI < Nf; ++fieldI) { 2029 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fv);CHKERRQ(ierr); 2030 ierr = PetscDSGetFieldOffset(prob, fieldI, &offsetI);CHKERRQ(ierr); 2031 ierr = PetscObjectGetClassId((PetscObject) fv, &id);CHKERRQ(ierr); 2032 if (id != PETSCFV_CLASSID) continue; 2033 /* Put in the identity */ 2034 ierr = PetscFVGetNumComponents(fv, &NcI);CHKERRQ(ierr); 2035 for (c = cStart; c < cEnd; ++c) { 2036 const PetscInt cind = c - cStart; 2037 const PetscInt eOffset = cind*totDim*totDim; 2038 for (fc = 0; fc < NcI; ++fc) { 2039 for (f = 0; f < NbI; ++f) { 2040 const PetscInt i = offsetI + f*NcI+fc; 2041 if (hasPrec) { 2042 if (hasJac) {elemMat[eOffset+i*totDim+i] = 1.0;} 2043 elemMatP[eOffset+i*totDim+i] = 1.0; 2044 } else {elemMat[eOffset+i*totDim+i] = 1.0;} 2045 } 2046 } 2047 } 2048 } 2049 /* No allocated space for FV stuff, so ignore the zero entries */ 2050 ierr = MatSetOption(JacP, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE);CHKERRQ(ierr); 2051 } 2052 /* Insert values into matrix */ 2053 isMatIS = PETSC_FALSE; 2054 if (hasPrec && hasJac) { 2055 ierr = PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatIS);CHKERRQ(ierr); 2056 } 2057 if (isMatIS && !subSection) { 2058 ierr = DMPlexGetSubdomainSection(dm, &subSection);CHKERRQ(ierr); 2059 } 2060 for (c = cStart; c < cEnd; ++c) { 2061 const PetscInt cell = cells ? cells[c] : c; 2062 const PetscInt cind = c - cStart; 2063 2064 /* Transform to global basis before insertion in Jacobian */ 2065 if (transform) {ierr = DMPlexBasisTransformPointTensor_Internal(dm, tdm, tv, cell, PETSC_TRUE, totDim, &elemMat[cind*totDim*totDim]);CHKERRQ(ierr);} 2066 if (hasPrec) { 2067 if (hasJac) { 2068 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(cell, name, totDim, totDim, &elemMat[cind*totDim*totDim]);CHKERRQ(ierr);} 2069 if (!isMatIS) { 2070 ierr = DMPlexMatSetClosure(dm, section, globalSection, Jac, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2071 } else { 2072 Mat lJ; 2073 2074 ierr = MatISGetLocalMat(Jac,&lJ);CHKERRQ(ierr); 2075 ierr = DMPlexMatSetClosure(dm, section, subSection, lJ, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2076 } 2077 } 2078 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(cell, name, totDim, totDim, &elemMatP[cind*totDim*totDim]);CHKERRQ(ierr);} 2079 if (!isMatISP) { 2080 ierr = DMPlexMatSetClosure(dm, section, globalSection, JacP, cell, &elemMatP[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2081 } else { 2082 Mat lJ; 2083 2084 ierr = MatISGetLocalMat(JacP,&lJ);CHKERRQ(ierr); 2085 ierr = DMPlexMatSetClosure(dm, section, subSection, lJ, cell, &elemMatP[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2086 } 2087 } else { 2088 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(cell, name, totDim, totDim, &elemMat[cind*totDim*totDim]);CHKERRQ(ierr);} 2089 if (!isMatISP) { 2090 ierr = DMPlexMatSetClosure(dm, section, globalSection, JacP, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2091 } else { 2092 Mat lJ; 2093 2094 ierr = MatISGetLocalMat(JacP,&lJ);CHKERRQ(ierr); 2095 ierr = DMPlexMatSetClosure(dm, section, subSection, lJ, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2096 } 2097 } 2098 } 2099 ierr = ISRestorePointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 2100 if (hasFV) {ierr = MatSetOption(JacP, MAT_IGNORE_ZERO_ENTRIES, PETSC_FALSE);CHKERRQ(ierr);} 2101 ierr = PetscFree5(u,u_t,elemMat,elemMatP,elemMatD);CHKERRQ(ierr); 2102 if (dmAux) { 2103 ierr = PetscFree(a);CHKERRQ(ierr); 2104 ierr = DMDestroy(&plex);CHKERRQ(ierr); 2105 } 2106 /* Compute boundary integrals */ 2107 ierr = DMPlexComputeBdJacobian_Internal(dm, X, X_t, t, X_tShift, Jac, JacP, user);CHKERRQ(ierr); 2108 /* Assemble matrix */ 2109 if (hasJac && hasPrec) { 2110 ierr = MatAssemblyBegin(Jac, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2111 ierr = MatAssemblyEnd(Jac, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2112 } 2113 ierr = MatAssemblyBegin(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2114 ierr = MatAssemblyEnd(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2115 ierr = PetscLogEventEnd(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 2116 PetscFunctionReturn(0); 2117 } 2118 2119 /*@ 2120 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. 2121 2122 Input Parameters: 2123 + dm - The mesh 2124 . cellIS - 2125 . t - The time 2126 . X_tShift - The multiplier for the Jacobian with repsect to X_t 2127 . X - Local solution vector 2128 . X_t - Time-derivative of the local solution vector 2129 . Y - Local input vector 2130 - user - The user context 2131 2132 Output Parameter: 2133 . Z - Local output vector 2134 2135 Note: 2136 We form the residual one batch of elements at a time. This allows us to offload work onto an accelerator, 2137 like a GPU, or vectorize on a multicore machine. 2138 2139 Level: developer 2140 2141 .seealso: FormFunctionLocal() 2142 @*/ 2143 PetscErrorCode DMPlexComputeJacobianAction(DM dm, IS cellIS, PetscReal t, PetscReal X_tShift, Vec X, Vec X_t, Vec Y, Vec Z, void *user) 2144 { 2145 DM_Plex *mesh = (DM_Plex *) dm->data; 2146 const char *name = "Jacobian"; 2147 DM dmAux, plex, plexAux = NULL; 2148 DMEnclosureType encAux; 2149 Vec A; 2150 PetscDS prob, probAux = NULL; 2151 PetscQuadrature quad; 2152 PetscSection section, globalSection, sectionAux; 2153 PetscScalar *elemMat, *elemMatD, *u, *u_t, *a = NULL, *y, *z; 2154 PetscInt Nf, fieldI, fieldJ; 2155 PetscInt totDim, totDimAux = 0; 2156 const PetscInt *cells; 2157 PetscInt cStart, cEnd, numCells, c; 2158 PetscBool hasDyn; 2159 DMField coordField; 2160 PetscErrorCode ierr; 2161 2162 PetscFunctionBegin; 2163 ierr = PetscLogEventBegin(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 2164 ierr = DMSNESConvertPlex(dm, &plex, PETSC_TRUE);CHKERRQ(ierr); 2165 if (!cellIS) { 2166 PetscInt depth; 2167 2168 ierr = DMPlexGetDepth(plex, &depth);CHKERRQ(ierr); 2169 ierr = DMGetStratumIS(plex, "dim", depth, &cellIS);CHKERRQ(ierr); 2170 if (!cellIS) {ierr = DMGetStratumIS(plex, "depth", depth, &cellIS);CHKERRQ(ierr);} 2171 } else { 2172 ierr = PetscObjectReference((PetscObject) cellIS);CHKERRQ(ierr); 2173 } 2174 ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); 2175 ierr = DMGetGlobalSection(dm, &globalSection);CHKERRQ(ierr); 2176 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 2177 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 2178 ierr = PetscDSHasDynamicJacobian(prob, &hasDyn);CHKERRQ(ierr); 2179 hasDyn = hasDyn && (X_tShift != 0.0) ? PETSC_TRUE : PETSC_FALSE; 2180 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); 2181 ierr = ISGetLocalSize(cellIS, &numCells);CHKERRQ(ierr); 2182 ierr = ISGetPointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 2183 ierr = PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);CHKERRQ(ierr); 2184 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);CHKERRQ(ierr); 2185 if (dmAux) { 2186 ierr = DMGetEnclosureRelation(dmAux, dm, &encAux);CHKERRQ(ierr); 2187 ierr = DMConvert(dmAux, DMPLEX, &plexAux);CHKERRQ(ierr); 2188 ierr = DMGetLocalSection(plexAux, §ionAux);CHKERRQ(ierr); 2189 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 2190 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 2191 } 2192 ierr = VecSet(Z, 0.0);CHKERRQ(ierr); 2193 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); 2194 if (dmAux) {ierr = PetscMalloc1(numCells*totDimAux, &a);CHKERRQ(ierr);} 2195 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 2196 for (c = cStart; c < cEnd; ++c) { 2197 const PetscInt cell = cells ? cells[c] : c; 2198 const PetscInt cind = c - cStart; 2199 PetscScalar *x = NULL, *x_t = NULL; 2200 PetscInt i; 2201 2202 ierr = DMPlexVecGetClosure(dm, section, X, cell, NULL, &x);CHKERRQ(ierr); 2203 for (i = 0; i < totDim; ++i) u[cind*totDim+i] = x[i]; 2204 ierr = DMPlexVecRestoreClosure(dm, section, X, cell, NULL, &x);CHKERRQ(ierr); 2205 if (X_t) { 2206 ierr = DMPlexVecGetClosure(dm, section, X_t, cell, NULL, &x_t);CHKERRQ(ierr); 2207 for (i = 0; i < totDim; ++i) u_t[cind*totDim+i] = x_t[i]; 2208 ierr = DMPlexVecRestoreClosure(dm, section, X_t, cell, NULL, &x_t);CHKERRQ(ierr); 2209 } 2210 if (dmAux) { 2211 PetscInt subcell; 2212 ierr = DMGetEnclosurePoint(dmAux, dm, encAux, cell, &subcell);CHKERRQ(ierr); 2213 ierr = DMPlexVecGetClosure(plexAux, sectionAux, A, subcell, NULL, &x);CHKERRQ(ierr); 2214 for (i = 0; i < totDimAux; ++i) a[cind*totDimAux+i] = x[i]; 2215 ierr = DMPlexVecRestoreClosure(plexAux, sectionAux, A, subcell, NULL, &x);CHKERRQ(ierr); 2216 } 2217 ierr = DMPlexVecGetClosure(dm, section, Y, cell, NULL, &x);CHKERRQ(ierr); 2218 for (i = 0; i < totDim; ++i) y[cind*totDim+i] = x[i]; 2219 ierr = DMPlexVecRestoreClosure(dm, section, Y, cell, NULL, &x);CHKERRQ(ierr); 2220 } 2221 ierr = PetscArrayzero(elemMat, numCells*totDim*totDim);CHKERRQ(ierr); 2222 if (hasDyn) {ierr = PetscArrayzero(elemMatD, numCells*totDim*totDim);CHKERRQ(ierr);} 2223 for (fieldI = 0; fieldI < Nf; ++fieldI) { 2224 PetscFE fe; 2225 PetscInt Nb; 2226 /* Conforming batches */ 2227 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 2228 /* Remainder */ 2229 PetscInt Nr, offset, Nq; 2230 PetscQuadrature qGeom = NULL; 2231 PetscInt maxDegree; 2232 PetscFEGeom *cgeomFEM, *chunkGeom = NULL, *remGeom = NULL; 2233 2234 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); 2235 ierr = PetscFEGetQuadrature(fe, &quad);CHKERRQ(ierr); 2236 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 2237 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 2238 ierr = DMFieldGetDegree(coordField,cellIS,NULL,&maxDegree);CHKERRQ(ierr); 2239 if (maxDegree <= 1) {ierr = DMFieldCreateDefaultQuadrature(coordField,cellIS,&qGeom);CHKERRQ(ierr);} 2240 if (!qGeom) { 2241 ierr = PetscFEGetQuadrature(fe,&qGeom);CHKERRQ(ierr); 2242 ierr = PetscObjectReference((PetscObject)qGeom);CHKERRQ(ierr); 2243 } 2244 ierr = PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 2245 ierr = DMSNESGetFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);CHKERRQ(ierr); 2246 blockSize = Nb; 2247 batchSize = numBlocks * blockSize; 2248 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 2249 numChunks = numCells / (numBatches*batchSize); 2250 Ne = numChunks*numBatches*batchSize; 2251 Nr = numCells % (numBatches*batchSize); 2252 offset = numCells - Nr; 2253 ierr = PetscFEGeomGetChunk(cgeomFEM,0,offset,&chunkGeom);CHKERRQ(ierr); 2254 ierr = PetscFEGeomGetChunk(cgeomFEM,offset,numCells,&remGeom);CHKERRQ(ierr); 2255 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 2256 ierr = PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMat);CHKERRQ(ierr); 2257 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); 2258 if (hasDyn) { 2259 ierr = PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN_DYN, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMatD);CHKERRQ(ierr); 2260 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); 2261 } 2262 } 2263 ierr = PetscFEGeomRestoreChunk(cgeomFEM,offset,numCells,&remGeom);CHKERRQ(ierr); 2264 ierr = PetscFEGeomRestoreChunk(cgeomFEM,0,offset,&chunkGeom);CHKERRQ(ierr); 2265 ierr = DMSNESRestoreFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);CHKERRQ(ierr); 2266 ierr = PetscQuadratureDestroy(&qGeom);CHKERRQ(ierr); 2267 } 2268 if (hasDyn) { 2269 for (c = 0; c < numCells*totDim*totDim; ++c) elemMat[c] += X_tShift*elemMatD[c]; 2270 } 2271 for (c = cStart; c < cEnd; ++c) { 2272 const PetscInt cell = cells ? cells[c] : c; 2273 const PetscInt cind = c - cStart; 2274 const PetscBLASInt M = totDim, one = 1; 2275 const PetscScalar a = 1.0, b = 0.0; 2276 2277 PetscStackCallBLAS("BLASgemv", BLASgemv_("N", &M, &M, &a, &elemMat[cind*totDim*totDim], &M, &y[cind*totDim], &one, &b, z, &one)); 2278 if (mesh->printFEM > 1) { 2279 ierr = DMPrintCellMatrix(c, name, totDim, totDim, &elemMat[cind*totDim*totDim]);CHKERRQ(ierr); 2280 ierr = DMPrintCellVector(c, "Y", totDim, &y[cind*totDim]);CHKERRQ(ierr); 2281 ierr = DMPrintCellVector(c, "Z", totDim, z);CHKERRQ(ierr); 2282 } 2283 ierr = DMPlexVecSetClosure(dm, section, Z, cell, z, ADD_VALUES);CHKERRQ(ierr); 2284 } 2285 ierr = PetscFree6(u,u_t,elemMat,elemMatD,y,z);CHKERRQ(ierr); 2286 if (mesh->printFEM) { 2287 ierr = PetscPrintf(PETSC_COMM_WORLD, "Z:\n");CHKERRQ(ierr); 2288 ierr = VecView(Z, NULL);CHKERRQ(ierr); 2289 } 2290 ierr = PetscFree(a);CHKERRQ(ierr); 2291 ierr = ISDestroy(&cellIS);CHKERRQ(ierr); 2292 ierr = DMDestroy(&plexAux);CHKERRQ(ierr); 2293 ierr = DMDestroy(&plex);CHKERRQ(ierr); 2294 ierr = PetscLogEventEnd(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 2295 PetscFunctionReturn(0); 2296 } 2297 2298 /*@ 2299 DMPlexSNESComputeJacobianFEM - Form the local portion of the Jacobian matrix J at the local solution X using pointwise functions specified by the user. 2300 2301 Input Parameters: 2302 + dm - The mesh 2303 . X - Local input vector 2304 - user - The user context 2305 2306 Output Parameter: 2307 . Jac - Jacobian matrix 2308 2309 Note: 2310 We form the residual one batch of elements at a time. This allows us to offload work onto an accelerator, 2311 like a GPU, or vectorize on a multicore machine. 2312 2313 Level: developer 2314 2315 .seealso: FormFunctionLocal() 2316 @*/ 2317 PetscErrorCode DMPlexSNESComputeJacobianFEM(DM dm, Vec X, Mat Jac, Mat JacP,void *user) 2318 { 2319 DM plex; 2320 PetscDS prob; 2321 IS cellIS; 2322 PetscBool hasJac, hasPrec; 2323 PetscInt depth; 2324 PetscErrorCode ierr; 2325 2326 PetscFunctionBegin; 2327 ierr = DMSNESConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr); 2328 ierr = DMPlexGetDepth(plex, &depth);CHKERRQ(ierr); 2329 ierr = DMGetStratumIS(plex, "dim", depth, &cellIS);CHKERRQ(ierr); 2330 if (!cellIS) {ierr = DMGetStratumIS(plex, "depth", depth, &cellIS);CHKERRQ(ierr);} 2331 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 2332 ierr = PetscDSHasJacobian(prob, &hasJac);CHKERRQ(ierr); 2333 ierr = PetscDSHasJacobianPreconditioner(prob, &hasPrec);CHKERRQ(ierr); 2334 if (hasJac && hasPrec) {ierr = MatZeroEntries(Jac);CHKERRQ(ierr);} 2335 ierr = MatZeroEntries(JacP);CHKERRQ(ierr); 2336 ierr = DMPlexComputeJacobian_Internal(plex, cellIS, 0.0, 0.0, X, NULL, Jac, JacP, user);CHKERRQ(ierr); 2337 ierr = ISDestroy(&cellIS);CHKERRQ(ierr); 2338 ierr = DMDestroy(&plex);CHKERRQ(ierr); 2339 PetscFunctionReturn(0); 2340 } 2341 2342 /* 2343 MatComputeNeumannOverlap - Computes an unassembled (Neumann) local overlapping Mat in nonlinear context. 2344 2345 Input Parameters: 2346 + X - SNES linearization point 2347 . ovl - index set of overlapping subdomains 2348 2349 Output Parameter: 2350 . J - unassembled (Neumann) local matrix 2351 2352 Level: intermediate 2353 2354 .seealso: DMCreateNeumannOverlap(), MATIS, PCHPDDMSetAuxiliaryMat() 2355 */ 2356 static PetscErrorCode MatComputeNeumannOverlap_Plex(Mat J, PetscReal t, Vec X, Vec X_t, PetscReal s, IS ovl, void *ctx) 2357 { 2358 SNES snes; 2359 Mat pJ; 2360 DM ovldm,origdm; 2361 DMSNES sdm; 2362 PetscErrorCode (*bfun)(DM,Vec,void*); 2363 PetscErrorCode (*jfun)(DM,Vec,Mat,Mat,void*); 2364 void *bctx,*jctx; 2365 PetscErrorCode ierr; 2366 2367 PetscFunctionBegin; 2368 ierr = PetscObjectQuery((PetscObject)ovl,"_DM_Overlap_HPDDM_MATIS",(PetscObject*)&pJ);CHKERRQ(ierr); 2369 if (!pJ) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Missing overlapping Mat");CHKERRQ(ierr); 2370 ierr = PetscObjectQuery((PetscObject)ovl,"_DM_Original_HPDDM",(PetscObject*)&origdm);CHKERRQ(ierr); 2371 if (!origdm) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Missing original DM");CHKERRQ(ierr); 2372 ierr = MatGetDM(pJ,&ovldm);CHKERRQ(ierr); 2373 ierr = DMSNESGetBoundaryLocal(origdm,&bfun,&bctx);CHKERRQ(ierr); 2374 ierr = DMSNESSetBoundaryLocal(ovldm,bfun,bctx);CHKERRQ(ierr); 2375 ierr = DMSNESGetJacobianLocal(origdm,&jfun,&jctx);CHKERRQ(ierr); 2376 ierr = DMSNESSetJacobianLocal(ovldm,jfun,jctx);CHKERRQ(ierr); 2377 ierr = PetscObjectQuery((PetscObject)ovl,"_DM_Overlap_HPDDM_SNES",(PetscObject*)&snes);CHKERRQ(ierr); 2378 if (!snes) { 2379 ierr = SNESCreate(PetscObjectComm((PetscObject)ovl),&snes);CHKERRQ(ierr); 2380 ierr = SNESSetDM(snes,ovldm);CHKERRQ(ierr); 2381 ierr = PetscObjectCompose((PetscObject)ovl,"_DM_Overlap_HPDDM_SNES",(PetscObject)snes);CHKERRQ(ierr); 2382 ierr = PetscObjectDereference((PetscObject)snes);CHKERRQ(ierr); 2383 } 2384 ierr = DMGetDMSNES(ovldm,&sdm);CHKERRQ(ierr); 2385 ierr = VecLockReadPush(X);CHKERRQ(ierr); 2386 PetscStackPush("SNES user Jacobian function"); 2387 ierr = (*sdm->ops->computejacobian)(snes,X,pJ,pJ,sdm->jacobianctx);CHKERRQ(ierr); 2388 PetscStackPop; 2389 ierr = VecLockReadPop(X);CHKERRQ(ierr); 2390 /* this is a no-hop, just in case we decide to change the placeholder for the local Neumann matrix */ 2391 { 2392 Mat locpJ; 2393 2394 ierr = MatISGetLocalMat(pJ,&locpJ);CHKERRQ(ierr); 2395 ierr = MatCopy(locpJ,J,SAME_NONZERO_PATTERN);CHKERRQ(ierr); 2396 } 2397 PetscFunctionReturn(0); 2398 } 2399 2400 /*@ 2401 DMPlexSetSNESLocalFEM - Use DMPlex's internal FEM routines to compute SNES boundary values, residual, and Jacobian. 2402 2403 Input Parameters: 2404 + dm - The DM object 2405 . boundaryctx - the user context that will be passed to pointwise evaluation of boundary values (see PetscDSAddBoundary()) 2406 . residualctx - the user context that will be passed to pointwise evaluation of finite element residual computations (see PetscDSSetResidual()) 2407 - jacobianctx - the user context that will be passed to pointwise evaluation of finite element Jacobian construction (see PetscDSSetJacobian()) 2408 2409 Level: developer 2410 @*/ 2411 PetscErrorCode DMPlexSetSNESLocalFEM(DM dm, void *boundaryctx, void *residualctx, void *jacobianctx) 2412 { 2413 PetscErrorCode ierr; 2414 2415 PetscFunctionBegin; 2416 ierr = DMSNESSetBoundaryLocal(dm,DMPlexSNESComputeBoundaryFEM,boundaryctx);CHKERRQ(ierr); 2417 ierr = DMSNESSetFunctionLocal(dm,DMPlexSNESComputeResidualFEM,residualctx);CHKERRQ(ierr); 2418 ierr = DMSNESSetJacobianLocal(dm,DMPlexSNESComputeJacobianFEM,jacobianctx);CHKERRQ(ierr); 2419 ierr = PetscObjectComposeFunction((PetscObject)dm,"MatComputeNeumannOverlap_C",MatComputeNeumannOverlap_Plex);CHKERRQ(ierr); 2420 PetscFunctionReturn(0); 2421 } 2422 2423 /*@C 2424 DMSNESCheckDiscretization - Check the discretization error of the exact solution 2425 2426 Input Parameters: 2427 + snes - the SNES object 2428 . dm - the DM 2429 . u - a DM vector 2430 . exactFuncs - pointwise functions of the exact solution for each field 2431 . ctxs - contexts for the functions 2432 . tol - A tolerance for the check, or -1 to print the results instead 2433 2434 Output Parameters: 2435 . error - An array which holds the discretization error in each field, or NULL 2436 2437 Level: developer 2438 2439 .seealso: DNSNESCheckFromOptions(), DMSNESCheckResidual(), DMSNESCheckJacobian() 2440 @*/ 2441 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[]) 2442 { 2443 PetscErrorCode (**exacts)(PetscInt, PetscReal, const PetscReal x[], PetscInt, PetscScalar *u, void *ctx); 2444 void **ectxs; 2445 MPI_Comm comm; 2446 PetscDS ds; 2447 PetscReal *err; 2448 PetscInt Nf, f; 2449 PetscErrorCode ierr; 2450 2451 PetscFunctionBegin; 2452 PetscValidHeaderSpecific(snes, SNES_CLASSID, 1); 2453 PetscValidHeaderSpecific(dm, DM_CLASSID, 2); 2454 PetscValidHeaderSpecific(u, VEC_CLASSID, 3); 2455 if (error) PetscValidRealPointer(error, 6); 2456 ierr = PetscObjectGetComm((PetscObject) snes, &comm);CHKERRQ(ierr); 2457 ierr = DMGetDS(dm, &ds);CHKERRQ(ierr); 2458 ierr = DMGetNumFields(dm, &Nf);CHKERRQ(ierr); 2459 ierr = PetscMalloc3(Nf, &exacts, Nf, &ectxs, PetscMax(1, Nf), &err);CHKERRQ(ierr); 2460 for (f = 0; f < Nf; ++f) {ierr = PetscDSGetExactSolution(ds, f, &exacts[f], &ectxs[f]);CHKERRQ(ierr);} 2461 ierr = DMProjectFunction(dm, 0.0, exactFuncs ? exactFuncs : exacts, ctxs ? ctxs : ectxs, INSERT_ALL_VALUES, u);CHKERRQ(ierr); 2462 ierr = PetscObjectSetName((PetscObject) u, "Exact Solution");CHKERRQ(ierr); 2463 ierr = PetscObjectSetOptionsPrefix((PetscObject) u, "exact_");CHKERRQ(ierr); 2464 ierr = VecViewFromOptions(u, NULL, "-vec_view");CHKERRQ(ierr); 2465 if (Nf > 1) { 2466 ierr = DMComputeL2FieldDiff(dm, 0.0, exactFuncs ? exactFuncs : exacts, ctxs ? ctxs : ectxs, u, err);CHKERRQ(ierr); 2467 if (tol >= 0.0) { 2468 for (f = 0; f < Nf; ++f) { 2469 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); 2470 } 2471 } else if (error) { 2472 for (f = 0; f < Nf; ++f) error[f] = err[f]; 2473 } else { 2474 ierr = PetscPrintf(comm, "L_2 Error: [");CHKERRQ(ierr); 2475 for (f = 0; f < Nf; ++f) { 2476 if (f) {ierr = PetscPrintf(comm, ", ");CHKERRQ(ierr);} 2477 ierr = PetscPrintf(comm, "%g", (double)err[f]);CHKERRQ(ierr); 2478 } 2479 ierr = PetscPrintf(comm, "]\n");CHKERRQ(ierr); 2480 } 2481 } else { 2482 ierr = DMComputeL2Diff(dm, 0.0, exactFuncs ? exactFuncs : exacts, ctxs ? ctxs : ectxs , u, &err[0]);CHKERRQ(ierr); 2483 if (tol >= 0.0) { 2484 if (err[0] > tol) SETERRQ2(comm, PETSC_ERR_ARG_WRONG, "L_2 Error %g exceeds tolerance %g", (double) err[0], (double) tol); 2485 } else if (error) { 2486 error[0] = err[0]; 2487 } else { 2488 ierr = PetscPrintf(comm, "L_2 Error: %g\n", (double)err[0]);CHKERRQ(ierr); 2489 } 2490 } 2491 ierr = PetscFree3(exacts, ectxs, err);CHKERRQ(ierr); 2492 PetscFunctionReturn(0); 2493 } 2494 2495 /*@C 2496 DMSNESCheckResidual - Check the residual of the exact solution 2497 2498 Input Parameters: 2499 + snes - the SNES object 2500 . dm - the DM 2501 . u - a DM vector 2502 . tol - A tolerance for the check, or -1 to print the results instead 2503 2504 Output Parameters: 2505 . residual - The residual norm of the exact solution, or NULL 2506 2507 Level: developer 2508 2509 .seealso: DNSNESCheckFromOptions(), DMSNESCheckDiscretization(), DMSNESCheckJacobian() 2510 @*/ 2511 PetscErrorCode DMSNESCheckResidual(SNES snes, DM dm, Vec u, PetscReal tol, PetscReal *residual) 2512 { 2513 PetscErrorCode (**exacts)(PetscInt, PetscReal, const PetscReal x[], PetscInt, PetscScalar *u, void *ctx); 2514 void **ectxs; 2515 MPI_Comm comm; 2516 PetscDS ds; 2517 Vec r; 2518 PetscReal res; 2519 PetscInt Nf, f; 2520 PetscBool computeSol = PETSC_FALSE; 2521 PetscErrorCode ierr; 2522 2523 PetscFunctionBegin; 2524 PetscValidHeaderSpecific(snes, SNES_CLASSID, 1); 2525 PetscValidHeaderSpecific(dm, DM_CLASSID, 2); 2526 PetscValidHeaderSpecific(u, VEC_CLASSID, 3); 2527 if (residual) PetscValidRealPointer(residual, 5); 2528 ierr = PetscObjectGetComm((PetscObject) snes, &comm);CHKERRQ(ierr); 2529 ierr = DMGetDS(dm, &ds);CHKERRQ(ierr); 2530 ierr = DMGetNumFields(dm, &Nf);CHKERRQ(ierr); 2531 ierr = PetscMalloc2(Nf, &exacts, Nf, &ectxs);CHKERRQ(ierr); 2532 for (f = 0; f < Nf; ++f) { 2533 ierr = PetscDSGetExactSolution(ds, f, &exacts[f], &ectxs[f]);CHKERRQ(ierr); 2534 if (exacts[f]) computeSol = PETSC_TRUE; 2535 } 2536 if (computeSol) {ierr = DMProjectFunction(dm, 0.0, exacts, ectxs, INSERT_ALL_VALUES, u);CHKERRQ(ierr);} 2537 ierr = PetscFree2(exacts, ectxs);CHKERRQ(ierr); 2538 2539 ierr = VecDuplicate(u, &r);CHKERRQ(ierr); 2540 ierr = SNESComputeFunction(snes, u, r);CHKERRQ(ierr); 2541 ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr); 2542 if (tol >= 0.0) { 2543 if (res > tol) SETERRQ2(comm, PETSC_ERR_ARG_WRONG, "L_2 Residual %g exceeds tolerance %g", (double) res, (double) tol); 2544 } else if (residual) { 2545 *residual = res; 2546 } else { 2547 ierr = PetscPrintf(comm, "L_2 Residual: %g\n", (double)res);CHKERRQ(ierr); 2548 ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr); 2549 ierr = PetscObjectSetName((PetscObject) r, "Initial Residual");CHKERRQ(ierr); 2550 ierr = PetscObjectSetOptionsPrefix((PetscObject)r,"res_");CHKERRQ(ierr); 2551 ierr = VecViewFromOptions(r, NULL, "-vec_view");CHKERRQ(ierr); 2552 } 2553 ierr = VecDestroy(&r);CHKERRQ(ierr); 2554 PetscFunctionReturn(0); 2555 } 2556 2557 /*@C 2558 DMSNESCheckJacobian - Check the Jacobian of the exact solution against the residual using the Taylor Test 2559 2560 Input Parameters: 2561 + snes - the SNES object 2562 . dm - the DM 2563 . u - a DM vector 2564 . tol - A tolerance for the check, or -1 to print the results instead 2565 2566 Output Parameters: 2567 + isLinear - Flag indicaing that the function looks linear, or NULL 2568 - convRate - The rate of convergence of the linear model, or NULL 2569 2570 Level: developer 2571 2572 .seealso: DNSNESCheckFromOptions(), DMSNESCheckDiscretization(), DMSNESCheckResidual() 2573 @*/ 2574 PetscErrorCode DMSNESCheckJacobian(SNES snes, DM dm, Vec u, PetscReal tol, PetscBool *isLinear, PetscReal *convRate) 2575 { 2576 PetscErrorCode (**exacts)(PetscInt, PetscReal, const PetscReal x[], PetscInt, PetscScalar *u, void *ctx); 2577 void **ectxs; 2578 MPI_Comm comm; 2579 PetscDS ds; 2580 Mat J, M; 2581 MatNullSpace nullspace; 2582 PetscReal slope, intercept; 2583 PetscInt Nf, f; 2584 PetscBool hasJac, hasPrec, isLin = PETSC_FALSE, computeSol = PETSC_FALSE; 2585 PetscErrorCode ierr; 2586 2587 PetscFunctionBegin; 2588 PetscValidHeaderSpecific(snes, SNES_CLASSID, 1); 2589 PetscValidHeaderSpecific(dm, DM_CLASSID, 2); 2590 PetscValidHeaderSpecific(u, VEC_CLASSID, 3); 2591 if (isLinear) PetscValidBoolPointer(isLinear, 5); 2592 if (convRate) PetscValidRealPointer(convRate, 5); 2593 ierr = PetscObjectGetComm((PetscObject) snes, &comm);CHKERRQ(ierr); 2594 ierr = DMGetDS(dm, &ds);CHKERRQ(ierr); 2595 ierr = DMGetNumFields(dm, &Nf);CHKERRQ(ierr); 2596 ierr = PetscMalloc2(Nf, &exacts, Nf, &ectxs);CHKERRQ(ierr); 2597 for (f = 0; f < Nf; ++f) { 2598 ierr = PetscDSGetExactSolution(ds, f, &exacts[f], &ectxs[f]);CHKERRQ(ierr); 2599 if (exacts[f]) computeSol = PETSC_TRUE; 2600 } 2601 if (computeSol) {ierr = DMProjectFunction(dm, 0.0, exacts, ectxs, INSERT_ALL_VALUES, u);CHKERRQ(ierr);} 2602 ierr = PetscFree2(exacts, ectxs);CHKERRQ(ierr); 2603 2604 /* Create and view matrices */ 2605 ierr = DMCreateMatrix(dm, &J);CHKERRQ(ierr); 2606 ierr = PetscDSHasJacobian(ds, &hasJac);CHKERRQ(ierr); 2607 ierr = PetscDSHasJacobianPreconditioner(ds, &hasPrec);CHKERRQ(ierr); 2608 if (hasJac && hasPrec) { 2609 ierr = DMCreateMatrix(dm, &M);CHKERRQ(ierr); 2610 ierr = SNESComputeJacobian(snes, u, J, M);CHKERRQ(ierr); 2611 ierr = PetscObjectSetName((PetscObject) M, "Preconditioning Matrix");CHKERRQ(ierr); 2612 ierr = PetscObjectSetOptionsPrefix((PetscObject) M, "jacpre_");CHKERRQ(ierr); 2613 ierr = MatViewFromOptions(M, NULL, "-mat_view");CHKERRQ(ierr); 2614 ierr = MatDestroy(&M);CHKERRQ(ierr); 2615 } else { 2616 ierr = SNESComputeJacobian(snes, u, J, J);CHKERRQ(ierr); 2617 } 2618 ierr = PetscObjectSetName((PetscObject) J, "Jacobian");CHKERRQ(ierr); 2619 ierr = PetscObjectSetOptionsPrefix((PetscObject) J, "jac_");CHKERRQ(ierr); 2620 ierr = MatViewFromOptions(J, NULL, "-mat_view");CHKERRQ(ierr); 2621 /* Check nullspace */ 2622 ierr = MatGetNullSpace(J, &nullspace);CHKERRQ(ierr); 2623 if (nullspace) { 2624 PetscBool isNull; 2625 ierr = MatNullSpaceTest(nullspace, J, &isNull);CHKERRQ(ierr); 2626 if (!isNull) SETERRQ(comm, PETSC_ERR_PLIB, "The null space calculated for the system operator is invalid."); 2627 } 2628 ierr = MatNullSpaceDestroy(&nullspace);CHKERRQ(ierr); 2629 /* Taylor test */ 2630 { 2631 PetscRandom rand; 2632 Vec du, uhat, r, rhat, df; 2633 PetscReal h; 2634 PetscReal *es, *hs, *errors; 2635 PetscReal hMax = 1.0, hMin = 1e-6, hMult = 0.1; 2636 PetscInt Nv, v; 2637 2638 /* Choose a perturbation direction */ 2639 ierr = PetscRandomCreate(comm, &rand);CHKERRQ(ierr); 2640 ierr = VecDuplicate(u, &du);CHKERRQ(ierr); 2641 ierr = VecSetRandom(du, rand); CHKERRQ(ierr); 2642 ierr = PetscRandomDestroy(&rand);CHKERRQ(ierr); 2643 ierr = VecDuplicate(u, &df);CHKERRQ(ierr); 2644 ierr = MatMult(J, du, df);CHKERRQ(ierr); 2645 /* Evaluate residual at u, F(u), save in vector r */ 2646 ierr = VecDuplicate(u, &r);CHKERRQ(ierr); 2647 ierr = SNESComputeFunction(snes, u, r);CHKERRQ(ierr); 2648 /* Look at the convergence of our Taylor approximation as we approach u */ 2649 for (h = hMax, Nv = 0; h >= hMin; h *= hMult, ++Nv); 2650 ierr = PetscCalloc3(Nv, &es, Nv, &hs, Nv, &errors);CHKERRQ(ierr); 2651 ierr = VecDuplicate(u, &uhat);CHKERRQ(ierr); 2652 ierr = VecDuplicate(u, &rhat);CHKERRQ(ierr); 2653 for (h = hMax, Nv = 0; h >= hMin; h *= hMult, ++Nv) { 2654 ierr = VecWAXPY(uhat, h, du, u);CHKERRQ(ierr); 2655 /* F(\hat u) \approx F(u) + J(u) (uhat - u) = F(u) + h * J(u) du */ 2656 ierr = SNESComputeFunction(snes, uhat, rhat);CHKERRQ(ierr); 2657 ierr = VecAXPBYPCZ(rhat, -1.0, -h, 1.0, r, df);CHKERRQ(ierr); 2658 ierr = VecNorm(rhat, NORM_2, &errors[Nv]);CHKERRQ(ierr); 2659 2660 es[Nv] = PetscLog10Real(errors[Nv]); 2661 hs[Nv] = PetscLog10Real(h); 2662 } 2663 ierr = VecDestroy(&uhat);CHKERRQ(ierr); 2664 ierr = VecDestroy(&rhat);CHKERRQ(ierr); 2665 ierr = VecDestroy(&df);CHKERRQ(ierr); 2666 ierr = VecDestroy(&r);CHKERRQ(ierr); 2667 ierr = VecDestroy(&du);CHKERRQ(ierr); 2668 for (v = 0; v < Nv; ++v) { 2669 if ((tol >= 0) && (errors[v] > tol)) break; 2670 else if (errors[v] > PETSC_SMALL) break; 2671 } 2672 if (v == Nv) isLin = PETSC_TRUE; 2673 ierr = PetscLinearRegression(Nv, hs, es, &slope, &intercept);CHKERRQ(ierr); 2674 ierr = PetscFree3(es, hs, errors);CHKERRQ(ierr); 2675 /* Slope should be about 2 */ 2676 if (tol >= 0) { 2677 if (!isLin && PetscAbsReal(2 - slope) > tol) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Taylor approximation convergence rate should be 2, not %0.2f", (double) slope); 2678 } else if (isLinear || convRate) { 2679 if (isLinear) *isLinear = isLin; 2680 if (convRate) *convRate = slope; 2681 } else { 2682 if (!isLin) {ierr = PetscPrintf(comm, "Taylor approximation converging at order %3.2f\n", (double) slope);CHKERRQ(ierr);} 2683 else {ierr = PetscPrintf(comm, "Function appears to be linear\n");CHKERRQ(ierr);} 2684 } 2685 } 2686 ierr = MatDestroy(&J);CHKERRQ(ierr); 2687 PetscFunctionReturn(0); 2688 } 2689 2690 PetscErrorCode DMSNESCheck_Internal(SNES snes, DM dm, Vec u, PetscErrorCode (**exactFuncs)(PetscInt, PetscReal, const PetscReal x[], PetscInt, PetscScalar *u, void *ctx), void **ctxs) 2691 { 2692 PetscErrorCode ierr; 2693 2694 PetscFunctionBegin; 2695 ierr = DMSNESCheckDiscretization(snes, dm, u, exactFuncs, ctxs, -1.0, NULL);CHKERRQ(ierr); 2696 ierr = DMSNESCheckResidual(snes, dm, u, -1.0, NULL);CHKERRQ(ierr); 2697 ierr = DMSNESCheckJacobian(snes, dm, u, -1.0, NULL, NULL);CHKERRQ(ierr); 2698 PetscFunctionReturn(0); 2699 } 2700 2701 /*@C 2702 DMSNESCheckFromOptions - Check the residual and Jacobian functions using the exact solution by outputting some diagnostic information 2703 2704 Input Parameters: 2705 + snes - the SNES object 2706 . u - representative SNES vector 2707 . exactFuncs - pointwise functions of the exact solution for each field 2708 - ctxs - contexts for the functions 2709 2710 Level: developer 2711 @*/ 2712 PetscErrorCode DMSNESCheckFromOptions(SNES snes, Vec u, PetscErrorCode (**exactFuncs)(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf, PetscScalar *u, void *ctx), void **ctxs) 2713 { 2714 DM dm; 2715 Vec sol; 2716 PetscBool check; 2717 PetscErrorCode ierr; 2718 2719 PetscFunctionBegin; 2720 ierr = PetscOptionsHasName(((PetscObject)snes)->options,((PetscObject)snes)->prefix, "-dmsnes_check", &check);CHKERRQ(ierr); 2721 if (!check) PetscFunctionReturn(0); 2722 ierr = SNESGetDM(snes, &dm);CHKERRQ(ierr); 2723 ierr = VecDuplicate(u, &sol);CHKERRQ(ierr); 2724 ierr = SNESSetSolution(snes, sol);CHKERRQ(ierr); 2725 ierr = DMSNESCheck_Internal(snes, dm, sol, exactFuncs, ctxs);CHKERRQ(ierr); 2726 ierr = VecDestroy(&sol);CHKERRQ(ierr); 2727 PetscFunctionReturn(0); 2728 } 2729