1 #include <petsc/private/dmpleximpl.h> /*I "petscdmplex.h" I*/ 2 #include <petsc/private/snesimpl.h> /*I "petscsnes.h" I*/ 3 #include <petscds.h> 4 #include <petscblaslapack.h> 5 #include <petsc/private/petscimpl.h> 6 #include <petsc/private/petscfeimpl.h> 7 8 /************************** Interpolation *******************************/ 9 10 static PetscErrorCode DMSNESConvertPlex(DM dm, DM *plex, PetscBool copy) 11 { 12 PetscBool isPlex; 13 PetscErrorCode ierr; 14 15 PetscFunctionBegin; 16 ierr = PetscObjectTypeCompare((PetscObject) dm, DMPLEX, &isPlex);CHKERRQ(ierr); 17 if (isPlex) { 18 *plex = dm; 19 ierr = PetscObjectReference((PetscObject) dm);CHKERRQ(ierr); 20 } else { 21 ierr = PetscObjectQuery((PetscObject) dm, "dm_plex", (PetscObject *) plex);CHKERRQ(ierr); 22 if (!*plex) { 23 ierr = DMConvert(dm,DMPLEX,plex);CHKERRQ(ierr); 24 ierr = PetscObjectCompose((PetscObject) dm, "dm_plex", (PetscObject) *plex);CHKERRQ(ierr); 25 if (copy) { 26 PetscInt i; 27 PetscObject obj; 28 const char *comps[3] = {"A","dmAux","dmCh"}; 29 30 ierr = DMCopyDMSNES(dm, *plex);CHKERRQ(ierr); 31 for (i = 0; i < 3; i++) { 32 ierr = PetscObjectQuery((PetscObject) dm, comps[i], &obj);CHKERRQ(ierr); 33 ierr = PetscObjectCompose((PetscObject) *plex, comps[i], obj);CHKERRQ(ierr); 34 } 35 } 36 } else { 37 ierr = PetscObjectReference((PetscObject) *plex);CHKERRQ(ierr); 38 } 39 } 40 PetscFunctionReturn(0); 41 } 42 43 /*@C 44 DMInterpolationCreate - Creates a DMInterpolationInfo context 45 46 Collective 47 48 Input Parameter: 49 . comm - the communicator 50 51 Output Parameter: 52 . ctx - the context 53 54 Level: beginner 55 56 .seealso: DMInterpolationEvaluate(), DMInterpolationAddPoints(), DMInterpolationDestroy() 57 @*/ 58 PetscErrorCode DMInterpolationCreate(MPI_Comm comm, DMInterpolationInfo *ctx) 59 { 60 PetscErrorCode ierr; 61 62 PetscFunctionBegin; 63 PetscValidPointer(ctx, 2); 64 ierr = PetscNew(ctx);CHKERRQ(ierr); 65 66 (*ctx)->comm = comm; 67 (*ctx)->dim = -1; 68 (*ctx)->nInput = 0; 69 (*ctx)->points = NULL; 70 (*ctx)->cells = NULL; 71 (*ctx)->n = -1; 72 (*ctx)->coords = NULL; 73 PetscFunctionReturn(0); 74 } 75 76 /*@C 77 DMInterpolationSetDim - Sets the spatial dimension for the interpolation context 78 79 Not collective 80 81 Input Parameters: 82 + ctx - the context 83 - dim - the spatial dimension 84 85 Level: intermediate 86 87 .seealso: DMInterpolationGetDim(), DMInterpolationEvaluate(), DMInterpolationAddPoints() 88 @*/ 89 PetscErrorCode DMInterpolationSetDim(DMInterpolationInfo ctx, PetscInt dim) 90 { 91 PetscFunctionBegin; 92 if ((dim < 1) || (dim > 3)) SETERRQ1(ctx->comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid dimension for points: %D", dim); 93 ctx->dim = dim; 94 PetscFunctionReturn(0); 95 } 96 97 /*@C 98 DMInterpolationGetDim - Gets the spatial dimension for the interpolation context 99 100 Not collective 101 102 Input Parameter: 103 . ctx - the context 104 105 Output Parameter: 106 . dim - the spatial dimension 107 108 Level: intermediate 109 110 .seealso: DMInterpolationSetDim(), DMInterpolationEvaluate(), DMInterpolationAddPoints() 111 @*/ 112 PetscErrorCode DMInterpolationGetDim(DMInterpolationInfo ctx, PetscInt *dim) 113 { 114 PetscFunctionBegin; 115 PetscValidIntPointer(dim, 2); 116 *dim = ctx->dim; 117 PetscFunctionReturn(0); 118 } 119 120 /*@C 121 DMInterpolationSetDof - Sets the number of fields interpolated at a point for the interpolation context 122 123 Not collective 124 125 Input Parameters: 126 + ctx - the context 127 - dof - the number of fields 128 129 Level: intermediate 130 131 .seealso: DMInterpolationGetDof(), DMInterpolationEvaluate(), DMInterpolationAddPoints() 132 @*/ 133 PetscErrorCode DMInterpolationSetDof(DMInterpolationInfo ctx, PetscInt dof) 134 { 135 PetscFunctionBegin; 136 if (dof < 1) SETERRQ1(ctx->comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid number of components: %D", dof); 137 ctx->dof = dof; 138 PetscFunctionReturn(0); 139 } 140 141 /*@C 142 DMInterpolationGetDof - Gets the number of fields interpolated at a point for the interpolation context 143 144 Not collective 145 146 Input Parameter: 147 . ctx - the context 148 149 Output Parameter: 150 . dof - the number of fields 151 152 Level: intermediate 153 154 .seealso: DMInterpolationSetDof(), DMInterpolationEvaluate(), DMInterpolationAddPoints() 155 @*/ 156 PetscErrorCode DMInterpolationGetDof(DMInterpolationInfo ctx, PetscInt *dof) 157 { 158 PetscFunctionBegin; 159 PetscValidIntPointer(dof, 2); 160 *dof = ctx->dof; 161 PetscFunctionReturn(0); 162 } 163 164 /*@C 165 DMInterpolationAddPoints - Add points at which we will interpolate the fields 166 167 Not collective 168 169 Input Parameters: 170 + ctx - the context 171 . n - the number of points 172 - points - the coordinates for each point, an array of size n * dim 173 174 Note: The coordinate information is copied. 175 176 Level: intermediate 177 178 .seealso: DMInterpolationSetDim(), DMInterpolationEvaluate(), DMInterpolationCreate() 179 @*/ 180 PetscErrorCode DMInterpolationAddPoints(DMInterpolationInfo ctx, PetscInt n, PetscReal points[]) 181 { 182 PetscErrorCode ierr; 183 184 PetscFunctionBegin; 185 if (ctx->dim < 0) SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONGSTATE, "The spatial dimension has not been set"); 186 if (ctx->points) SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONGSTATE, "Cannot add points multiple times yet"); 187 ctx->nInput = n; 188 189 ierr = PetscMalloc1(n*ctx->dim, &ctx->points);CHKERRQ(ierr); 190 ierr = PetscArraycpy(ctx->points, points, n*ctx->dim);CHKERRQ(ierr); 191 PetscFunctionReturn(0); 192 } 193 194 /*@C 195 DMInterpolationSetUp - Computea spatial indices that add in point location during interpolation 196 197 Collective on ctx 198 199 Input Parameters: 200 + ctx - the context 201 . dm - the DM for the function space used for interpolation 202 - redundantPoints - If PETSC_TRUE, all processes are passing in the same array of points. Otherwise, points need to be communicated among processes. 203 204 Level: intermediate 205 206 .seealso: DMInterpolationEvaluate(), DMInterpolationAddPoints(), DMInterpolationCreate() 207 @*/ 208 PetscErrorCode DMInterpolationSetUp(DMInterpolationInfo ctx, DM dm, PetscBool redundantPoints) 209 { 210 MPI_Comm comm = ctx->comm; 211 PetscScalar *a; 212 PetscInt p, q, i; 213 PetscMPIInt rank, size; 214 PetscErrorCode ierr; 215 Vec pointVec; 216 PetscSF cellSF; 217 PetscLayout layout; 218 PetscReal *globalPoints; 219 PetscScalar *globalPointsScalar; 220 const PetscInt *ranges; 221 PetscMPIInt *counts, *displs; 222 const PetscSFNode *foundCells; 223 const PetscInt *foundPoints; 224 PetscMPIInt *foundProcs, *globalProcs; 225 PetscInt n, N, numFound; 226 227 PetscFunctionBegin; 228 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 229 ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr); 230 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 231 if (ctx->dim < 0) SETERRQ(comm, PETSC_ERR_ARG_WRONGSTATE, "The spatial dimension has not been set"); 232 /* Locate points */ 233 n = ctx->nInput; 234 if (!redundantPoints) { 235 ierr = PetscLayoutCreate(comm, &layout);CHKERRQ(ierr); 236 ierr = PetscLayoutSetBlockSize(layout, 1);CHKERRQ(ierr); 237 ierr = PetscLayoutSetLocalSize(layout, n);CHKERRQ(ierr); 238 ierr = PetscLayoutSetUp(layout);CHKERRQ(ierr); 239 ierr = PetscLayoutGetSize(layout, &N);CHKERRQ(ierr); 240 /* Communicate all points to all processes */ 241 ierr = PetscMalloc3(N*ctx->dim,&globalPoints,size,&counts,size,&displs);CHKERRQ(ierr); 242 ierr = PetscLayoutGetRanges(layout, &ranges);CHKERRQ(ierr); 243 for (p = 0; p < size; ++p) { 244 counts[p] = (ranges[p+1] - ranges[p])*ctx->dim; 245 displs[p] = ranges[p]*ctx->dim; 246 } 247 ierr = MPI_Allgatherv(ctx->points, n*ctx->dim, MPIU_REAL, globalPoints, counts, displs, MPIU_REAL, comm);CHKERRQ(ierr); 248 } else { 249 N = n; 250 globalPoints = ctx->points; 251 counts = displs = NULL; 252 layout = NULL; 253 } 254 #if 0 255 ierr = PetscMalloc3(N,&foundCells,N,&foundProcs,N,&globalProcs);CHKERRQ(ierr); 256 /* foundCells[p] = m->locatePoint(&globalPoints[p*ctx->dim]); */ 257 #else 258 #if defined(PETSC_USE_COMPLEX) 259 ierr = PetscMalloc1(N*ctx->dim,&globalPointsScalar);CHKERRQ(ierr); 260 for (i=0; i<N*ctx->dim; i++) globalPointsScalar[i] = globalPoints[i]; 261 #else 262 globalPointsScalar = globalPoints; 263 #endif 264 ierr = VecCreateSeqWithArray(PETSC_COMM_SELF, ctx->dim, N*ctx->dim, globalPointsScalar, &pointVec);CHKERRQ(ierr); 265 ierr = PetscMalloc2(N,&foundProcs,N,&globalProcs);CHKERRQ(ierr); 266 for (p = 0; p < N; ++p) {foundProcs[p] = size;} 267 cellSF = NULL; 268 ierr = DMLocatePoints(dm, pointVec, DM_POINTLOCATION_REMOVE, &cellSF);CHKERRQ(ierr); 269 ierr = PetscSFGetGraph(cellSF,NULL,&numFound,&foundPoints,&foundCells);CHKERRQ(ierr); 270 #endif 271 for (p = 0; p < numFound; ++p) { 272 if (foundCells[p].index >= 0) foundProcs[foundPoints ? foundPoints[p] : p] = rank; 273 } 274 /* Let the lowest rank process own each point */ 275 ierr = MPIU_Allreduce(foundProcs, globalProcs, N, MPI_INT, MPI_MIN, comm);CHKERRQ(ierr); 276 ctx->n = 0; 277 for (p = 0; p < N; ++p) { 278 if (globalProcs[p] == size) SETERRQ4(comm, PETSC_ERR_PLIB, "Point %d: %g %g %g not located in mesh", p, (double)globalPoints[p*ctx->dim+0], (double)(ctx->dim > 1 ? globalPoints[p*ctx->dim+1] : 0.0), (double)(ctx->dim > 2 ? globalPoints[p*ctx->dim+2] : 0.0)); 279 else if (globalProcs[p] == rank) ctx->n++; 280 } 281 /* Create coordinates vector and array of owned cells */ 282 ierr = PetscMalloc1(ctx->n, &ctx->cells);CHKERRQ(ierr); 283 ierr = VecCreate(comm, &ctx->coords);CHKERRQ(ierr); 284 ierr = VecSetSizes(ctx->coords, ctx->n*ctx->dim, PETSC_DECIDE);CHKERRQ(ierr); 285 ierr = VecSetBlockSize(ctx->coords, ctx->dim);CHKERRQ(ierr); 286 ierr = VecSetType(ctx->coords,VECSTANDARD);CHKERRQ(ierr); 287 ierr = VecGetArray(ctx->coords, &a);CHKERRQ(ierr); 288 for (p = 0, q = 0, i = 0; p < N; ++p) { 289 if (globalProcs[p] == rank) { 290 PetscInt d; 291 292 for (d = 0; d < ctx->dim; ++d, ++i) a[i] = globalPoints[p*ctx->dim+d]; 293 ctx->cells[q] = foundCells[q].index; 294 ++q; 295 } 296 } 297 ierr = VecRestoreArray(ctx->coords, &a);CHKERRQ(ierr); 298 #if 0 299 ierr = PetscFree3(foundCells,foundProcs,globalProcs);CHKERRQ(ierr); 300 #else 301 ierr = PetscFree2(foundProcs,globalProcs);CHKERRQ(ierr); 302 ierr = PetscSFDestroy(&cellSF);CHKERRQ(ierr); 303 ierr = VecDestroy(&pointVec);CHKERRQ(ierr); 304 #endif 305 if ((void*)globalPointsScalar != (void*)globalPoints) {ierr = PetscFree(globalPointsScalar);CHKERRQ(ierr);} 306 if (!redundantPoints) {ierr = PetscFree3(globalPoints,counts,displs);CHKERRQ(ierr);} 307 ierr = PetscLayoutDestroy(&layout);CHKERRQ(ierr); 308 PetscFunctionReturn(0); 309 } 310 311 /*@C 312 DMInterpolationGetCoordinates - Gets a Vec with the coordinates of each interpolation point 313 314 Collective on ctx 315 316 Input Parameter: 317 . ctx - the context 318 319 Output Parameter: 320 . coordinates - the coordinates of interpolation points 321 322 Note: The local vector entries correspond to interpolation points lying on this process, according to the associated DM. This is a borrowed vector that the user should not destroy. 323 324 Level: intermediate 325 326 .seealso: DMInterpolationEvaluate(), DMInterpolationAddPoints(), DMInterpolationCreate() 327 @*/ 328 PetscErrorCode DMInterpolationGetCoordinates(DMInterpolationInfo ctx, Vec *coordinates) 329 { 330 PetscFunctionBegin; 331 PetscValidPointer(coordinates, 2); 332 if (!ctx->coords) SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONGSTATE, "The interpolation context has not been setup."); 333 *coordinates = ctx->coords; 334 PetscFunctionReturn(0); 335 } 336 337 /*@C 338 DMInterpolationGetVector - Gets a Vec which can hold all the interpolated field values 339 340 Collective on ctx 341 342 Input Parameter: 343 . ctx - the context 344 345 Output Parameter: 346 . v - a vector capable of holding the interpolated field values 347 348 Note: This vector should be returned using DMInterpolationRestoreVector(). 349 350 Level: intermediate 351 352 .seealso: DMInterpolationRestoreVector(), DMInterpolationEvaluate(), DMInterpolationAddPoints(), DMInterpolationCreate() 353 @*/ 354 PetscErrorCode DMInterpolationGetVector(DMInterpolationInfo ctx, Vec *v) 355 { 356 PetscErrorCode ierr; 357 358 PetscFunctionBegin; 359 PetscValidPointer(v, 2); 360 if (!ctx->coords) SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONGSTATE, "The interpolation context has not been setup."); 361 ierr = VecCreate(ctx->comm, v);CHKERRQ(ierr); 362 ierr = VecSetSizes(*v, ctx->n*ctx->dof, PETSC_DECIDE);CHKERRQ(ierr); 363 ierr = VecSetBlockSize(*v, ctx->dof);CHKERRQ(ierr); 364 ierr = VecSetType(*v,VECSTANDARD);CHKERRQ(ierr); 365 PetscFunctionReturn(0); 366 } 367 368 /*@C 369 DMInterpolationRestoreVector - Returns a Vec which can hold all the interpolated field values 370 371 Collective on ctx 372 373 Input Parameters: 374 + ctx - the context 375 - v - a vector capable of holding the interpolated field values 376 377 Level: intermediate 378 379 .seealso: DMInterpolationGetVector(), DMInterpolationEvaluate(), DMInterpolationAddPoints(), DMInterpolationCreate() 380 @*/ 381 PetscErrorCode DMInterpolationRestoreVector(DMInterpolationInfo ctx, Vec *v) 382 { 383 PetscErrorCode ierr; 384 385 PetscFunctionBegin; 386 PetscValidPointer(v, 2); 387 if (!ctx->coords) SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONGSTATE, "The interpolation context has not been setup."); 388 ierr = VecDestroy(v);CHKERRQ(ierr); 389 PetscFunctionReturn(0); 390 } 391 392 PETSC_STATIC_INLINE PetscErrorCode DMInterpolate_Triangle_Private(DMInterpolationInfo ctx, DM dm, Vec xLocal, Vec v) 393 { 394 PetscReal *v0, *J, *invJ, detJ; 395 const PetscScalar *coords; 396 PetscScalar *a; 397 PetscInt p; 398 PetscErrorCode ierr; 399 400 PetscFunctionBegin; 401 ierr = PetscMalloc3(ctx->dim,&v0,ctx->dim*ctx->dim,&J,ctx->dim*ctx->dim,&invJ);CHKERRQ(ierr); 402 ierr = VecGetArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 403 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 404 for (p = 0; p < ctx->n; ++p) { 405 PetscInt c = ctx->cells[p]; 406 PetscScalar *x = NULL; 407 PetscReal xi[4]; 408 PetscInt d, f, comp; 409 410 ierr = DMPlexComputeCellGeometryFEM(dm, c, NULL, v0, J, invJ, &detJ);CHKERRQ(ierr); 411 if (detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %D", (double)detJ, c); 412 ierr = DMPlexVecGetClosure(dm, NULL, xLocal, c, NULL, &x);CHKERRQ(ierr); 413 for (comp = 0; comp < ctx->dof; ++comp) a[p*ctx->dof+comp] = x[0*ctx->dof+comp]; 414 415 for (d = 0; d < ctx->dim; ++d) { 416 xi[d] = 0.0; 417 for (f = 0; f < ctx->dim; ++f) xi[d] += invJ[d*ctx->dim+f]*0.5*PetscRealPart(coords[p*ctx->dim+f] - v0[f]); 418 for (comp = 0; comp < ctx->dof; ++comp) a[p*ctx->dof+comp] += PetscRealPart(x[(d+1)*ctx->dof+comp] - x[0*ctx->dof+comp])*xi[d]; 419 } 420 ierr = DMPlexVecRestoreClosure(dm, NULL, xLocal, c, NULL, &x);CHKERRQ(ierr); 421 } 422 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 423 ierr = VecRestoreArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 424 ierr = PetscFree3(v0, J, invJ);CHKERRQ(ierr); 425 PetscFunctionReturn(0); 426 } 427 428 PETSC_STATIC_INLINE PetscErrorCode DMInterpolate_Tetrahedron_Private(DMInterpolationInfo ctx, DM dm, Vec xLocal, Vec v) 429 { 430 PetscReal *v0, *J, *invJ, detJ; 431 const PetscScalar *coords; 432 PetscScalar *a; 433 PetscInt p; 434 PetscErrorCode ierr; 435 436 PetscFunctionBegin; 437 ierr = PetscMalloc3(ctx->dim,&v0,ctx->dim*ctx->dim,&J,ctx->dim*ctx->dim,&invJ);CHKERRQ(ierr); 438 ierr = VecGetArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 439 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 440 for (p = 0; p < ctx->n; ++p) { 441 PetscInt c = ctx->cells[p]; 442 const PetscInt order[3] = {2, 1, 3}; 443 PetscScalar *x = NULL; 444 PetscReal xi[4]; 445 PetscInt d, f, comp; 446 447 ierr = DMPlexComputeCellGeometryFEM(dm, c, NULL, v0, J, invJ, &detJ);CHKERRQ(ierr); 448 if (detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %D", (double)detJ, c); 449 ierr = DMPlexVecGetClosure(dm, NULL, xLocal, c, NULL, &x);CHKERRQ(ierr); 450 for (comp = 0; comp < ctx->dof; ++comp) a[p*ctx->dof+comp] = x[0*ctx->dof+comp]; 451 452 for (d = 0; d < ctx->dim; ++d) { 453 xi[d] = 0.0; 454 for (f = 0; f < ctx->dim; ++f) xi[d] += invJ[d*ctx->dim+f]*0.5*PetscRealPart(coords[p*ctx->dim+f] - v0[f]); 455 for (comp = 0; comp < ctx->dof; ++comp) a[p*ctx->dof+comp] += PetscRealPart(x[order[d]*ctx->dof+comp] - x[0*ctx->dof+comp])*xi[d]; 456 } 457 ierr = DMPlexVecRestoreClosure(dm, NULL, xLocal, c, NULL, &x);CHKERRQ(ierr); 458 } 459 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 460 ierr = VecRestoreArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 461 ierr = PetscFree3(v0, J, invJ);CHKERRQ(ierr); 462 PetscFunctionReturn(0); 463 } 464 465 PETSC_STATIC_INLINE PetscErrorCode QuadMap_Private(SNES snes, Vec Xref, Vec Xreal, void *ctx) 466 { 467 const PetscScalar *vertices = (const PetscScalar*) ctx; 468 const PetscScalar x0 = vertices[0]; 469 const PetscScalar y0 = vertices[1]; 470 const PetscScalar x1 = vertices[2]; 471 const PetscScalar y1 = vertices[3]; 472 const PetscScalar x2 = vertices[4]; 473 const PetscScalar y2 = vertices[5]; 474 const PetscScalar x3 = vertices[6]; 475 const PetscScalar y3 = vertices[7]; 476 const PetscScalar f_1 = x1 - x0; 477 const PetscScalar g_1 = y1 - y0; 478 const PetscScalar f_3 = x3 - x0; 479 const PetscScalar g_3 = y3 - y0; 480 const PetscScalar f_01 = x2 - x1 - x3 + x0; 481 const PetscScalar g_01 = y2 - y1 - y3 + y0; 482 const PetscScalar *ref; 483 PetscScalar *real; 484 PetscErrorCode ierr; 485 486 PetscFunctionBegin; 487 ierr = VecGetArrayRead(Xref, &ref);CHKERRQ(ierr); 488 ierr = VecGetArray(Xreal, &real);CHKERRQ(ierr); 489 { 490 const PetscScalar p0 = ref[0]; 491 const PetscScalar p1 = ref[1]; 492 493 real[0] = x0 + f_1 * p0 + f_3 * p1 + f_01 * p0 * p1; 494 real[1] = y0 + g_1 * p0 + g_3 * p1 + g_01 * p0 * p1; 495 } 496 ierr = PetscLogFlops(28);CHKERRQ(ierr); 497 ierr = VecRestoreArrayRead(Xref, &ref);CHKERRQ(ierr); 498 ierr = VecRestoreArray(Xreal, &real);CHKERRQ(ierr); 499 PetscFunctionReturn(0); 500 } 501 502 #include <petsc/private/dmimpl.h> 503 PETSC_STATIC_INLINE PetscErrorCode QuadJacobian_Private(SNES snes, Vec Xref, Mat J, Mat M, void *ctx) 504 { 505 const PetscScalar *vertices = (const PetscScalar*) ctx; 506 const PetscScalar x0 = vertices[0]; 507 const PetscScalar y0 = vertices[1]; 508 const PetscScalar x1 = vertices[2]; 509 const PetscScalar y1 = vertices[3]; 510 const PetscScalar x2 = vertices[4]; 511 const PetscScalar y2 = vertices[5]; 512 const PetscScalar x3 = vertices[6]; 513 const PetscScalar y3 = vertices[7]; 514 const PetscScalar f_01 = x2 - x1 - x3 + x0; 515 const PetscScalar g_01 = y2 - y1 - y3 + y0; 516 const PetscScalar *ref; 517 PetscErrorCode ierr; 518 519 PetscFunctionBegin; 520 ierr = VecGetArrayRead(Xref, &ref);CHKERRQ(ierr); 521 { 522 const PetscScalar x = ref[0]; 523 const PetscScalar y = ref[1]; 524 const PetscInt rows[2] = {0, 1}; 525 PetscScalar values[4]; 526 527 values[0] = (x1 - x0 + f_01*y) * 0.5; values[1] = (x3 - x0 + f_01*x) * 0.5; 528 values[2] = (y1 - y0 + g_01*y) * 0.5; values[3] = (y3 - y0 + g_01*x) * 0.5; 529 ierr = MatSetValues(J, 2, rows, 2, rows, values, INSERT_VALUES);CHKERRQ(ierr); 530 } 531 ierr = PetscLogFlops(30);CHKERRQ(ierr); 532 ierr = VecRestoreArrayRead(Xref, &ref);CHKERRQ(ierr); 533 ierr = MatAssemblyBegin(J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 534 ierr = MatAssemblyEnd(J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 535 PetscFunctionReturn(0); 536 } 537 538 PETSC_STATIC_INLINE PetscErrorCode DMInterpolate_Quad_Private(DMInterpolationInfo ctx, DM dm, Vec xLocal, Vec v) 539 { 540 DM dmCoord; 541 PetscFE fem = NULL; 542 SNES snes; 543 KSP ksp; 544 PC pc; 545 Vec coordsLocal, r, ref, real; 546 Mat J; 547 PetscTabulation T; 548 const PetscScalar *coords; 549 PetscScalar *a; 550 PetscReal xir[2]; 551 PetscInt Nf, p; 552 const PetscInt dof = ctx->dof; 553 PetscErrorCode ierr; 554 555 PetscFunctionBegin; 556 ierr = DMGetNumFields(dm, &Nf);CHKERRQ(ierr); 557 if (Nf) {ierr = DMGetField(dm, 0, NULL, (PetscObject *) &fem);CHKERRQ(ierr);} 558 ierr = DMGetCoordinatesLocal(dm, &coordsLocal);CHKERRQ(ierr); 559 ierr = DMGetCoordinateDM(dm, &dmCoord);CHKERRQ(ierr); 560 ierr = SNESCreate(PETSC_COMM_SELF, &snes);CHKERRQ(ierr); 561 ierr = SNESSetOptionsPrefix(snes, "quad_interp_");CHKERRQ(ierr); 562 ierr = VecCreate(PETSC_COMM_SELF, &r);CHKERRQ(ierr); 563 ierr = VecSetSizes(r, 2, 2);CHKERRQ(ierr); 564 ierr = VecSetType(r,dm->vectype);CHKERRQ(ierr); 565 ierr = VecDuplicate(r, &ref);CHKERRQ(ierr); 566 ierr = VecDuplicate(r, &real);CHKERRQ(ierr); 567 ierr = MatCreate(PETSC_COMM_SELF, &J);CHKERRQ(ierr); 568 ierr = MatSetSizes(J, 2, 2, 2, 2);CHKERRQ(ierr); 569 ierr = MatSetType(J, MATSEQDENSE);CHKERRQ(ierr); 570 ierr = MatSetUp(J);CHKERRQ(ierr); 571 ierr = SNESSetFunction(snes, r, QuadMap_Private, NULL);CHKERRQ(ierr); 572 ierr = SNESSetJacobian(snes, J, J, QuadJacobian_Private, NULL);CHKERRQ(ierr); 573 ierr = SNESGetKSP(snes, &ksp);CHKERRQ(ierr); 574 ierr = KSPGetPC(ksp, &pc);CHKERRQ(ierr); 575 ierr = PCSetType(pc, PCLU);CHKERRQ(ierr); 576 ierr = SNESSetFromOptions(snes);CHKERRQ(ierr); 577 578 ierr = VecGetArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 579 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 580 ierr = PetscFECreateTabulation(fem, 1, 1, xir, 0, &T);CHKERRQ(ierr); 581 for (p = 0; p < ctx->n; ++p) { 582 PetscScalar *x = NULL, *vertices = NULL; 583 PetscScalar *xi; 584 PetscInt c = ctx->cells[p], comp, coordSize, xSize; 585 586 /* Can make this do all points at once */ 587 ierr = DMPlexVecGetClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);CHKERRQ(ierr); 588 if (4*2 != coordSize) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid closure size %D should be %d", coordSize, 4*2); 589 ierr = DMPlexVecGetClosure(dm, NULL, xLocal, c, &xSize, &x);CHKERRQ(ierr); 590 ierr = SNESSetFunction(snes, NULL, NULL, (void*) vertices);CHKERRQ(ierr); 591 ierr = SNESSetJacobian(snes, NULL, NULL, NULL, (void*) vertices);CHKERRQ(ierr); 592 ierr = VecGetArray(real, &xi);CHKERRQ(ierr); 593 xi[0] = coords[p*ctx->dim+0]; 594 xi[1] = coords[p*ctx->dim+1]; 595 ierr = VecRestoreArray(real, &xi);CHKERRQ(ierr); 596 ierr = SNESSolve(snes, real, ref);CHKERRQ(ierr); 597 ierr = VecGetArray(ref, &xi);CHKERRQ(ierr); 598 xir[0] = PetscRealPart(xi[0]); 599 xir[1] = PetscRealPart(xi[1]); 600 if (4*dof != xSize) { 601 PetscInt d; 602 603 xir[0] = 2.0*xir[0] - 1.0; xir[1] = 2.0*xir[1] - 1.0; 604 ierr = PetscFEComputeTabulation(fem, 1, xir, 0, T);CHKERRQ(ierr); 605 for (comp = 0; comp < dof; ++comp) { 606 a[p*dof+comp] = 0.0; 607 for (d = 0; d < xSize/dof; ++d) { 608 a[p*dof+comp] += x[d*dof+comp]*T->T[0][d*dof+comp]; 609 } 610 } 611 } else { 612 for (comp = 0; comp < dof; ++comp) 613 a[p*dof+comp] = x[0*dof+comp]*(1 - xir[0])*(1 - xir[1]) + x[1*dof+comp]*xir[0]*(1 - xir[1]) + x[2*dof+comp]*xir[0]*xir[1] + x[3*dof+comp]*(1 - xir[0])*xir[1]; 614 } 615 ierr = VecRestoreArray(ref, &xi);CHKERRQ(ierr); 616 ierr = DMPlexVecRestoreClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);CHKERRQ(ierr); 617 ierr = DMPlexVecRestoreClosure(dm, NULL, xLocal, c, &xSize, &x);CHKERRQ(ierr); 618 } 619 ierr = PetscTabulationDestroy(&T);CHKERRQ(ierr); 620 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 621 ierr = VecRestoreArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 622 623 ierr = SNESDestroy(&snes);CHKERRQ(ierr); 624 ierr = VecDestroy(&r);CHKERRQ(ierr); 625 ierr = VecDestroy(&ref);CHKERRQ(ierr); 626 ierr = VecDestroy(&real);CHKERRQ(ierr); 627 ierr = MatDestroy(&J);CHKERRQ(ierr); 628 PetscFunctionReturn(0); 629 } 630 631 PETSC_STATIC_INLINE PetscErrorCode HexMap_Private(SNES snes, Vec Xref, Vec Xreal, void *ctx) 632 { 633 const PetscScalar *vertices = (const PetscScalar*) ctx; 634 const PetscScalar x0 = vertices[0]; 635 const PetscScalar y0 = vertices[1]; 636 const PetscScalar z0 = vertices[2]; 637 const PetscScalar x1 = vertices[9]; 638 const PetscScalar y1 = vertices[10]; 639 const PetscScalar z1 = vertices[11]; 640 const PetscScalar x2 = vertices[6]; 641 const PetscScalar y2 = vertices[7]; 642 const PetscScalar z2 = vertices[8]; 643 const PetscScalar x3 = vertices[3]; 644 const PetscScalar y3 = vertices[4]; 645 const PetscScalar z3 = vertices[5]; 646 const PetscScalar x4 = vertices[12]; 647 const PetscScalar y4 = vertices[13]; 648 const PetscScalar z4 = vertices[14]; 649 const PetscScalar x5 = vertices[15]; 650 const PetscScalar y5 = vertices[16]; 651 const PetscScalar z5 = vertices[17]; 652 const PetscScalar x6 = vertices[18]; 653 const PetscScalar y6 = vertices[19]; 654 const PetscScalar z6 = vertices[20]; 655 const PetscScalar x7 = vertices[21]; 656 const PetscScalar y7 = vertices[22]; 657 const PetscScalar z7 = vertices[23]; 658 const PetscScalar f_1 = x1 - x0; 659 const PetscScalar g_1 = y1 - y0; 660 const PetscScalar h_1 = z1 - z0; 661 const PetscScalar f_3 = x3 - x0; 662 const PetscScalar g_3 = y3 - y0; 663 const PetscScalar h_3 = z3 - z0; 664 const PetscScalar f_4 = x4 - x0; 665 const PetscScalar g_4 = y4 - y0; 666 const PetscScalar h_4 = z4 - z0; 667 const PetscScalar f_01 = x2 - x1 - x3 + x0; 668 const PetscScalar g_01 = y2 - y1 - y3 + y0; 669 const PetscScalar h_01 = z2 - z1 - z3 + z0; 670 const PetscScalar f_12 = x7 - x3 - x4 + x0; 671 const PetscScalar g_12 = y7 - y3 - y4 + y0; 672 const PetscScalar h_12 = z7 - z3 - z4 + z0; 673 const PetscScalar f_02 = x5 - x1 - x4 + x0; 674 const PetscScalar g_02 = y5 - y1 - y4 + y0; 675 const PetscScalar h_02 = z5 - z1 - z4 + z0; 676 const PetscScalar f_012 = x6 - x0 + x1 - x2 + x3 + x4 - x5 - x7; 677 const PetscScalar g_012 = y6 - y0 + y1 - y2 + y3 + y4 - y5 - y7; 678 const PetscScalar h_012 = z6 - z0 + z1 - z2 + z3 + z4 - z5 - z7; 679 const PetscScalar *ref; 680 PetscScalar *real; 681 PetscErrorCode ierr; 682 683 PetscFunctionBegin; 684 ierr = VecGetArrayRead(Xref, &ref);CHKERRQ(ierr); 685 ierr = VecGetArray(Xreal, &real);CHKERRQ(ierr); 686 { 687 const PetscScalar p0 = ref[0]; 688 const PetscScalar p1 = ref[1]; 689 const PetscScalar p2 = ref[2]; 690 691 real[0] = x0 + f_1*p0 + f_3*p1 + f_4*p2 + f_01*p0*p1 + f_12*p1*p2 + f_02*p0*p2 + f_012*p0*p1*p2; 692 real[1] = y0 + g_1*p0 + g_3*p1 + g_4*p2 + g_01*p0*p1 + g_01*p0*p1 + g_12*p1*p2 + g_02*p0*p2 + g_012*p0*p1*p2; 693 real[2] = z0 + h_1*p0 + h_3*p1 + h_4*p2 + h_01*p0*p1 + h_01*p0*p1 + h_12*p1*p2 + h_02*p0*p2 + h_012*p0*p1*p2; 694 } 695 ierr = PetscLogFlops(114);CHKERRQ(ierr); 696 ierr = VecRestoreArrayRead(Xref, &ref);CHKERRQ(ierr); 697 ierr = VecRestoreArray(Xreal, &real);CHKERRQ(ierr); 698 PetscFunctionReturn(0); 699 } 700 701 PETSC_STATIC_INLINE PetscErrorCode HexJacobian_Private(SNES snes, Vec Xref, Mat J, Mat M, void *ctx) 702 { 703 const PetscScalar *vertices = (const PetscScalar*) ctx; 704 const PetscScalar x0 = vertices[0]; 705 const PetscScalar y0 = vertices[1]; 706 const PetscScalar z0 = vertices[2]; 707 const PetscScalar x1 = vertices[9]; 708 const PetscScalar y1 = vertices[10]; 709 const PetscScalar z1 = vertices[11]; 710 const PetscScalar x2 = vertices[6]; 711 const PetscScalar y2 = vertices[7]; 712 const PetscScalar z2 = vertices[8]; 713 const PetscScalar x3 = vertices[3]; 714 const PetscScalar y3 = vertices[4]; 715 const PetscScalar z3 = vertices[5]; 716 const PetscScalar x4 = vertices[12]; 717 const PetscScalar y4 = vertices[13]; 718 const PetscScalar z4 = vertices[14]; 719 const PetscScalar x5 = vertices[15]; 720 const PetscScalar y5 = vertices[16]; 721 const PetscScalar z5 = vertices[17]; 722 const PetscScalar x6 = vertices[18]; 723 const PetscScalar y6 = vertices[19]; 724 const PetscScalar z6 = vertices[20]; 725 const PetscScalar x7 = vertices[21]; 726 const PetscScalar y7 = vertices[22]; 727 const PetscScalar z7 = vertices[23]; 728 const PetscScalar f_xy = x2 - x1 - x3 + x0; 729 const PetscScalar g_xy = y2 - y1 - y3 + y0; 730 const PetscScalar h_xy = z2 - z1 - z3 + z0; 731 const PetscScalar f_yz = x7 - x3 - x4 + x0; 732 const PetscScalar g_yz = y7 - y3 - y4 + y0; 733 const PetscScalar h_yz = z7 - z3 - z4 + z0; 734 const PetscScalar f_xz = x5 - x1 - x4 + x0; 735 const PetscScalar g_xz = y5 - y1 - y4 + y0; 736 const PetscScalar h_xz = z5 - z1 - z4 + z0; 737 const PetscScalar f_xyz = x6 - x0 + x1 - x2 + x3 + x4 - x5 - x7; 738 const PetscScalar g_xyz = y6 - y0 + y1 - y2 + y3 + y4 - y5 - y7; 739 const PetscScalar h_xyz = z6 - z0 + z1 - z2 + z3 + z4 - z5 - z7; 740 const PetscScalar *ref; 741 PetscErrorCode ierr; 742 743 PetscFunctionBegin; 744 ierr = VecGetArrayRead(Xref, &ref);CHKERRQ(ierr); 745 { 746 const PetscScalar x = ref[0]; 747 const PetscScalar y = ref[1]; 748 const PetscScalar z = ref[2]; 749 const PetscInt rows[3] = {0, 1, 2}; 750 PetscScalar values[9]; 751 752 values[0] = (x1 - x0 + f_xy*y + f_xz*z + f_xyz*y*z) / 2.0; 753 values[1] = (x3 - x0 + f_xy*x + f_yz*z + f_xyz*x*z) / 2.0; 754 values[2] = (x4 - x0 + f_yz*y + f_xz*x + f_xyz*x*y) / 2.0; 755 values[3] = (y1 - y0 + g_xy*y + g_xz*z + g_xyz*y*z) / 2.0; 756 values[4] = (y3 - y0 + g_xy*x + g_yz*z + g_xyz*x*z) / 2.0; 757 values[5] = (y4 - y0 + g_yz*y + g_xz*x + g_xyz*x*y) / 2.0; 758 values[6] = (z1 - z0 + h_xy*y + h_xz*z + h_xyz*y*z) / 2.0; 759 values[7] = (z3 - z0 + h_xy*x + h_yz*z + h_xyz*x*z) / 2.0; 760 values[8] = (z4 - z0 + h_yz*y + h_xz*x + h_xyz*x*y) / 2.0; 761 762 ierr = MatSetValues(J, 3, rows, 3, rows, values, INSERT_VALUES);CHKERRQ(ierr); 763 } 764 ierr = PetscLogFlops(152);CHKERRQ(ierr); 765 ierr = VecRestoreArrayRead(Xref, &ref);CHKERRQ(ierr); 766 ierr = MatAssemblyBegin(J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 767 ierr = MatAssemblyEnd(J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 768 PetscFunctionReturn(0); 769 } 770 771 PETSC_STATIC_INLINE PetscErrorCode DMInterpolate_Hex_Private(DMInterpolationInfo ctx, DM dm, Vec xLocal, Vec v) 772 { 773 DM dmCoord; 774 SNES snes; 775 KSP ksp; 776 PC pc; 777 Vec coordsLocal, r, ref, real; 778 Mat J; 779 const PetscScalar *coords; 780 PetscScalar *a; 781 PetscInt p; 782 PetscErrorCode ierr; 783 784 PetscFunctionBegin; 785 ierr = DMGetCoordinatesLocal(dm, &coordsLocal);CHKERRQ(ierr); 786 ierr = DMGetCoordinateDM(dm, &dmCoord);CHKERRQ(ierr); 787 ierr = SNESCreate(PETSC_COMM_SELF, &snes);CHKERRQ(ierr); 788 ierr = SNESSetOptionsPrefix(snes, "hex_interp_");CHKERRQ(ierr); 789 ierr = VecCreate(PETSC_COMM_SELF, &r);CHKERRQ(ierr); 790 ierr = VecSetSizes(r, 3, 3);CHKERRQ(ierr); 791 ierr = VecSetType(r,dm->vectype);CHKERRQ(ierr); 792 ierr = VecDuplicate(r, &ref);CHKERRQ(ierr); 793 ierr = VecDuplicate(r, &real);CHKERRQ(ierr); 794 ierr = MatCreate(PETSC_COMM_SELF, &J);CHKERRQ(ierr); 795 ierr = MatSetSizes(J, 3, 3, 3, 3);CHKERRQ(ierr); 796 ierr = MatSetType(J, MATSEQDENSE);CHKERRQ(ierr); 797 ierr = MatSetUp(J);CHKERRQ(ierr); 798 ierr = SNESSetFunction(snes, r, HexMap_Private, NULL);CHKERRQ(ierr); 799 ierr = SNESSetJacobian(snes, J, J, HexJacobian_Private, NULL);CHKERRQ(ierr); 800 ierr = SNESGetKSP(snes, &ksp);CHKERRQ(ierr); 801 ierr = KSPGetPC(ksp, &pc);CHKERRQ(ierr); 802 ierr = PCSetType(pc, PCLU);CHKERRQ(ierr); 803 ierr = SNESSetFromOptions(snes);CHKERRQ(ierr); 804 805 ierr = VecGetArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 806 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 807 for (p = 0; p < ctx->n; ++p) { 808 PetscScalar *x = NULL, *vertices = NULL; 809 PetscScalar *xi; 810 PetscReal xir[3]; 811 PetscInt c = ctx->cells[p], comp, coordSize, xSize; 812 813 /* Can make this do all points at once */ 814 ierr = DMPlexVecGetClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);CHKERRQ(ierr); 815 if (8*3 != coordSize) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid closure size %D should be %d", coordSize, 8*3); 816 ierr = DMPlexVecGetClosure(dm, NULL, xLocal, c, &xSize, &x);CHKERRQ(ierr); 817 if (8*ctx->dof != xSize) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid closure size %D should be %D", xSize, 8*ctx->dof); 818 ierr = SNESSetFunction(snes, NULL, NULL, (void*) vertices);CHKERRQ(ierr); 819 ierr = SNESSetJacobian(snes, NULL, NULL, NULL, (void*) vertices);CHKERRQ(ierr); 820 ierr = VecGetArray(real, &xi);CHKERRQ(ierr); 821 xi[0] = coords[p*ctx->dim+0]; 822 xi[1] = coords[p*ctx->dim+1]; 823 xi[2] = coords[p*ctx->dim+2]; 824 ierr = VecRestoreArray(real, &xi);CHKERRQ(ierr); 825 ierr = SNESSolve(snes, real, ref);CHKERRQ(ierr); 826 ierr = VecGetArray(ref, &xi);CHKERRQ(ierr); 827 xir[0] = PetscRealPart(xi[0]); 828 xir[1] = PetscRealPart(xi[1]); 829 xir[2] = PetscRealPart(xi[2]); 830 for (comp = 0; comp < ctx->dof; ++comp) { 831 a[p*ctx->dof+comp] = 832 x[0*ctx->dof+comp]*(1-xir[0])*(1-xir[1])*(1-xir[2]) + 833 x[3*ctx->dof+comp]* xir[0]*(1-xir[1])*(1-xir[2]) + 834 x[2*ctx->dof+comp]* xir[0]* xir[1]*(1-xir[2]) + 835 x[1*ctx->dof+comp]*(1-xir[0])* xir[1]*(1-xir[2]) + 836 x[4*ctx->dof+comp]*(1-xir[0])*(1-xir[1])* xir[2] + 837 x[5*ctx->dof+comp]* xir[0]*(1-xir[1])* xir[2] + 838 x[6*ctx->dof+comp]* xir[0]* xir[1]* xir[2] + 839 x[7*ctx->dof+comp]*(1-xir[0])* xir[1]* xir[2]; 840 } 841 ierr = VecRestoreArray(ref, &xi);CHKERRQ(ierr); 842 ierr = DMPlexVecRestoreClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);CHKERRQ(ierr); 843 ierr = DMPlexVecRestoreClosure(dm, NULL, xLocal, c, &xSize, &x);CHKERRQ(ierr); 844 } 845 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 846 ierr = VecRestoreArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 847 848 ierr = SNESDestroy(&snes);CHKERRQ(ierr); 849 ierr = VecDestroy(&r);CHKERRQ(ierr); 850 ierr = VecDestroy(&ref);CHKERRQ(ierr); 851 ierr = VecDestroy(&real);CHKERRQ(ierr); 852 ierr = MatDestroy(&J);CHKERRQ(ierr); 853 PetscFunctionReturn(0); 854 } 855 856 /*@C 857 DMInterpolationEvaluate - Using the input from dm and x, calculates interpolated field values at the interpolation points. 858 859 Input Parameters: 860 + ctx - The DMInterpolationInfo context 861 . dm - The DM 862 - x - The local vector containing the field to be interpolated 863 864 Output Parameters: 865 . v - The vector containing the interpolated values 866 867 Note: A suitable v can be obtained using DMInterpolationGetVector(). 868 869 Level: beginner 870 871 .seealso: DMInterpolationGetVector(), DMInterpolationAddPoints(), DMInterpolationCreate() 872 @*/ 873 PetscErrorCode DMInterpolationEvaluate(DMInterpolationInfo ctx, DM dm, Vec x, Vec v) 874 { 875 PetscInt dim, coneSize, n; 876 PetscErrorCode ierr; 877 878 PetscFunctionBegin; 879 PetscValidHeaderSpecific(dm, DM_CLASSID, 2); 880 PetscValidHeaderSpecific(x, VEC_CLASSID, 3); 881 PetscValidHeaderSpecific(v, VEC_CLASSID, 4); 882 ierr = VecGetLocalSize(v, &n);CHKERRQ(ierr); 883 if (n != ctx->n*ctx->dof) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid input vector size %D should be %D", n, ctx->n*ctx->dof); 884 if (n) { 885 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 886 ierr = DMPlexGetConeSize(dm, ctx->cells[0], &coneSize);CHKERRQ(ierr); 887 if (dim == 2) { 888 if (coneSize == 3) { 889 ierr = DMInterpolate_Triangle_Private(ctx, dm, x, v);CHKERRQ(ierr); 890 } else if (coneSize == 4) { 891 ierr = DMInterpolate_Quad_Private(ctx, dm, x, v);CHKERRQ(ierr); 892 } else SETERRQ1(ctx->comm, PETSC_ERR_ARG_OUTOFRANGE, "Unsupported dimension %D for point interpolation", dim); 893 } else if (dim == 3) { 894 if (coneSize == 4) { 895 ierr = DMInterpolate_Tetrahedron_Private(ctx, dm, x, v);CHKERRQ(ierr); 896 } else { 897 ierr = DMInterpolate_Hex_Private(ctx, dm, x, v);CHKERRQ(ierr); 898 } 899 } else SETERRQ1(ctx->comm, PETSC_ERR_ARG_OUTOFRANGE, "Unsupported dimension %D for point interpolation", dim); 900 } 901 PetscFunctionReturn(0); 902 } 903 904 /*@C 905 DMInterpolationDestroy - Destroys a DMInterpolationInfo context 906 907 Collective on ctx 908 909 Input Parameter: 910 . ctx - the context 911 912 Level: beginner 913 914 .seealso: DMInterpolationEvaluate(), DMInterpolationAddPoints(), DMInterpolationCreate() 915 @*/ 916 PetscErrorCode DMInterpolationDestroy(DMInterpolationInfo *ctx) 917 { 918 PetscErrorCode ierr; 919 920 PetscFunctionBegin; 921 PetscValidPointer(ctx, 2); 922 ierr = VecDestroy(&(*ctx)->coords);CHKERRQ(ierr); 923 ierr = PetscFree((*ctx)->points);CHKERRQ(ierr); 924 ierr = PetscFree((*ctx)->cells);CHKERRQ(ierr); 925 ierr = PetscFree(*ctx);CHKERRQ(ierr); 926 *ctx = NULL; 927 PetscFunctionReturn(0); 928 } 929 930 /*@C 931 SNESMonitorFields - Monitors the residual for each field separately 932 933 Collective on SNES 934 935 Input Parameters: 936 + snes - the SNES context 937 . its - iteration number 938 . fgnorm - 2-norm of residual 939 - vf - PetscViewerAndFormat of type ASCII 940 941 Notes: 942 This routine prints the residual norm at each iteration. 943 944 Level: intermediate 945 946 .seealso: SNESMonitorSet(), SNESMonitorDefault() 947 @*/ 948 PetscErrorCode SNESMonitorFields(SNES snes, PetscInt its, PetscReal fgnorm, PetscViewerAndFormat *vf) 949 { 950 PetscViewer viewer = vf->viewer; 951 Vec res; 952 DM dm; 953 PetscSection s; 954 const PetscScalar *r; 955 PetscReal *lnorms, *norms; 956 PetscInt numFields, f, pStart, pEnd, p; 957 PetscErrorCode ierr; 958 959 PetscFunctionBegin; 960 PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,4); 961 ierr = SNESGetFunction(snes, &res, 0, 0);CHKERRQ(ierr); 962 ierr = SNESGetDM(snes, &dm);CHKERRQ(ierr); 963 ierr = DMGetLocalSection(dm, &s);CHKERRQ(ierr); 964 ierr = PetscSectionGetNumFields(s, &numFields);CHKERRQ(ierr); 965 ierr = PetscSectionGetChart(s, &pStart, &pEnd);CHKERRQ(ierr); 966 ierr = PetscCalloc2(numFields, &lnorms, numFields, &norms);CHKERRQ(ierr); 967 ierr = VecGetArrayRead(res, &r);CHKERRQ(ierr); 968 for (p = pStart; p < pEnd; ++p) { 969 for (f = 0; f < numFields; ++f) { 970 PetscInt fdof, foff, d; 971 972 ierr = PetscSectionGetFieldDof(s, p, f, &fdof);CHKERRQ(ierr); 973 ierr = PetscSectionGetFieldOffset(s, p, f, &foff);CHKERRQ(ierr); 974 for (d = 0; d < fdof; ++d) lnorms[f] += PetscRealPart(PetscSqr(r[foff+d])); 975 } 976 } 977 ierr = VecRestoreArrayRead(res, &r);CHKERRQ(ierr); 978 ierr = MPIU_Allreduce(lnorms, norms, numFields, MPIU_REAL, MPIU_SUM, PetscObjectComm((PetscObject) dm));CHKERRQ(ierr); 979 ierr = PetscViewerPushFormat(viewer,vf->format);CHKERRQ(ierr); 980 ierr = PetscViewerASCIIAddTab(viewer, ((PetscObject) snes)->tablevel);CHKERRQ(ierr); 981 ierr = PetscViewerASCIIPrintf(viewer, "%3D SNES Function norm %14.12e [", its, (double) fgnorm);CHKERRQ(ierr); 982 for (f = 0; f < numFields; ++f) { 983 if (f > 0) {ierr = PetscViewerASCIIPrintf(viewer, ", ");CHKERRQ(ierr);} 984 ierr = PetscViewerASCIIPrintf(viewer, "%14.12e", (double) PetscSqrtReal(norms[f]));CHKERRQ(ierr); 985 } 986 ierr = PetscViewerASCIIPrintf(viewer, "]\n");CHKERRQ(ierr); 987 ierr = PetscViewerASCIISubtractTab(viewer, ((PetscObject) snes)->tablevel);CHKERRQ(ierr); 988 ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr); 989 ierr = PetscFree2(lnorms, norms);CHKERRQ(ierr); 990 PetscFunctionReturn(0); 991 } 992 993 /********************* Residual Computation **************************/ 994 995 996 /*@ 997 DMPlexSNESGetGeometryFVM - Return precomputed geometric data 998 999 Input Parameter: 1000 . dm - The DM 1001 1002 Output Parameters: 1003 + facegeom - The values precomputed from face geometry 1004 . cellgeom - The values precomputed from cell geometry 1005 - minRadius - The minimum radius over the mesh of an inscribed sphere in a cell 1006 1007 Level: developer 1008 1009 .seealso: DMPlexTSSetRHSFunctionLocal() 1010 @*/ 1011 PetscErrorCode DMPlexSNESGetGeometryFVM(DM dm, Vec *facegeom, Vec *cellgeom, PetscReal *minRadius) 1012 { 1013 DM plex; 1014 PetscErrorCode ierr; 1015 1016 PetscFunctionBegin; 1017 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 1018 ierr = DMSNESConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr); 1019 ierr = DMPlexGetDataFVM(plex, NULL, cellgeom, facegeom, NULL);CHKERRQ(ierr); 1020 if (minRadius) {ierr = DMPlexGetMinRadius(plex, minRadius);CHKERRQ(ierr);} 1021 ierr = DMDestroy(&plex);CHKERRQ(ierr); 1022 PetscFunctionReturn(0); 1023 } 1024 1025 /*@ 1026 DMPlexSNESGetGradientDM - Return gradient data layout 1027 1028 Input Parameters: 1029 + dm - The DM 1030 - fv - The PetscFV 1031 1032 Output Parameter: 1033 . dmGrad - The layout for gradient values 1034 1035 Level: developer 1036 1037 .seealso: DMPlexSNESGetGeometryFVM() 1038 @*/ 1039 PetscErrorCode DMPlexSNESGetGradientDM(DM dm, PetscFV fv, DM *dmGrad) 1040 { 1041 DM plex; 1042 PetscBool computeGradients; 1043 PetscErrorCode ierr; 1044 1045 PetscFunctionBegin; 1046 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 1047 PetscValidHeaderSpecific(fv,PETSCFV_CLASSID,2); 1048 PetscValidPointer(dmGrad,3); 1049 ierr = PetscFVGetComputeGradients(fv, &computeGradients);CHKERRQ(ierr); 1050 if (!computeGradients) {*dmGrad = NULL; PetscFunctionReturn(0);} 1051 ierr = DMSNESConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr); 1052 ierr = DMPlexGetDataFVM(plex, fv, NULL, NULL, dmGrad);CHKERRQ(ierr); 1053 ierr = DMDestroy(&plex);CHKERRQ(ierr); 1054 PetscFunctionReturn(0); 1055 } 1056 1057 static PetscErrorCode DMPlexComputeBdResidual_Single_Internal(DM dm, PetscReal t, DMLabel label, PetscInt numValues, const PetscInt values[], PetscInt field, Vec locX, Vec locX_t, Vec locF, DMField coordField, IS facetIS) 1058 { 1059 DM_Plex *mesh = (DM_Plex *) dm->data; 1060 DM plex = NULL, plexA = NULL; 1061 DMEnclosureType encAux; 1062 PetscDS prob, probAux = NULL; 1063 PetscSection section, sectionAux = NULL; 1064 Vec locA = NULL; 1065 PetscScalar *u = NULL, *u_t = NULL, *a = NULL, *elemVec = NULL; 1066 PetscInt v; 1067 PetscInt totDim, totDimAux = 0; 1068 PetscErrorCode ierr; 1069 1070 PetscFunctionBegin; 1071 ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); 1072 ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); 1073 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1074 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1075 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);CHKERRQ(ierr); 1076 if (locA) { 1077 DM dmAux; 1078 1079 ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); 1080 ierr = DMGetEnclosureRelation(dmAux, dm, &encAux);CHKERRQ(ierr); 1081 ierr = DMConvert(dmAux, DMPLEX, &plexA);CHKERRQ(ierr); 1082 ierr = DMGetDS(plexA, &probAux);CHKERRQ(ierr); 1083 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 1084 ierr = DMGetLocalSection(plexA, §ionAux);CHKERRQ(ierr); 1085 } 1086 for (v = 0; v < numValues; ++v) { 1087 PetscFEGeom *fgeom; 1088 PetscInt maxDegree; 1089 PetscQuadrature qGeom = NULL; 1090 IS pointIS; 1091 const PetscInt *points; 1092 PetscInt numFaces, face, Nq; 1093 1094 ierr = DMLabelGetStratumIS(label, values[v], &pointIS);CHKERRQ(ierr); 1095 if (!pointIS) continue; /* No points with that id on this process */ 1096 { 1097 IS isectIS; 1098 1099 /* TODO: Special cases of ISIntersect where it is quick to check a priori if one is a superset of the other */ 1100 ierr = ISIntersect_Caching_Internal(facetIS,pointIS,&isectIS);CHKERRQ(ierr); 1101 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 1102 pointIS = isectIS; 1103 } 1104 ierr = ISGetLocalSize(pointIS,&numFaces);CHKERRQ(ierr); 1105 ierr = ISGetIndices(pointIS,&points);CHKERRQ(ierr); 1106 ierr = PetscMalloc4(numFaces*totDim, &u, locX_t ? numFaces*totDim : 0, &u_t, numFaces*totDim, &elemVec, locA ? numFaces*totDimAux : 0, &a);CHKERRQ(ierr); 1107 ierr = DMFieldGetDegree(coordField,pointIS,NULL,&maxDegree);CHKERRQ(ierr); 1108 if (maxDegree <= 1) { 1109 ierr = DMFieldCreateDefaultQuadrature(coordField,pointIS,&qGeom);CHKERRQ(ierr); 1110 } 1111 if (!qGeom) { 1112 PetscFE fe; 1113 1114 ierr = PetscDSGetDiscretization(prob, field, (PetscObject *) &fe);CHKERRQ(ierr); 1115 ierr = PetscFEGetFaceQuadrature(fe, &qGeom);CHKERRQ(ierr); 1116 ierr = PetscObjectReference((PetscObject)qGeom);CHKERRQ(ierr); 1117 } 1118 ierr = PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 1119 ierr = DMSNESGetFEGeom(coordField,pointIS,qGeom,PETSC_TRUE,&fgeom);CHKERRQ(ierr); 1120 for (face = 0; face < numFaces; ++face) { 1121 const PetscInt point = points[face], *support, *cone; 1122 PetscScalar *x = NULL; 1123 PetscInt i, coneSize, faceLoc; 1124 1125 ierr = DMPlexGetSupport(dm, point, &support);CHKERRQ(ierr); 1126 ierr = DMPlexGetConeSize(dm, support[0], &coneSize);CHKERRQ(ierr); 1127 ierr = DMPlexGetCone(dm, support[0], &cone);CHKERRQ(ierr); 1128 for (faceLoc = 0; faceLoc < coneSize; ++faceLoc) if (cone[faceLoc] == point) break; 1129 if (faceLoc == coneSize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Could not find face %D in cone of support[0] %D", point, support[0]); 1130 fgeom->face[face][0] = faceLoc; 1131 ierr = DMPlexVecGetClosure(plex, section, locX, support[0], NULL, &x);CHKERRQ(ierr); 1132 for (i = 0; i < totDim; ++i) u[face*totDim+i] = x[i]; 1133 ierr = DMPlexVecRestoreClosure(plex, section, locX, support[0], NULL, &x);CHKERRQ(ierr); 1134 if (locX_t) { 1135 ierr = DMPlexVecGetClosure(plex, section, locX_t, support[0], NULL, &x);CHKERRQ(ierr); 1136 for (i = 0; i < totDim; ++i) u_t[face*totDim+i] = x[i]; 1137 ierr = DMPlexVecRestoreClosure(plex, section, locX_t, support[0], NULL, &x);CHKERRQ(ierr); 1138 } 1139 if (locA) { 1140 PetscInt subp; 1141 1142 ierr = DMGetEnclosurePoint(plexA, dm, encAux, support[0], &subp);CHKERRQ(ierr); 1143 ierr = DMPlexVecGetClosure(plexA, sectionAux, locA, subp, NULL, &x);CHKERRQ(ierr); 1144 for (i = 0; i < totDimAux; ++i) a[face*totDimAux+i] = x[i]; 1145 ierr = DMPlexVecRestoreClosure(plexA, sectionAux, locA, subp, NULL, &x);CHKERRQ(ierr); 1146 } 1147 } 1148 ierr = PetscArrayzero(elemVec, numFaces*totDim);CHKERRQ(ierr); 1149 { 1150 PetscFE fe; 1151 PetscInt Nb; 1152 PetscFEGeom *chunkGeom = NULL; 1153 /* Conforming batches */ 1154 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 1155 /* Remainder */ 1156 PetscInt Nr, offset; 1157 1158 ierr = PetscDSGetDiscretization(prob, field, (PetscObject *) &fe);CHKERRQ(ierr); 1159 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 1160 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1161 /* TODO: documentation is unclear about what is going on with these numbers: how should Nb / Nq factor in ? */ 1162 blockSize = Nb; 1163 batchSize = numBlocks * blockSize; 1164 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1165 numChunks = numFaces / (numBatches*batchSize); 1166 Ne = numChunks*numBatches*batchSize; 1167 Nr = numFaces % (numBatches*batchSize); 1168 offset = numFaces - Nr; 1169 ierr = PetscFEGeomGetChunk(fgeom,0,offset,&chunkGeom);CHKERRQ(ierr); 1170 ierr = PetscFEIntegrateBdResidual(prob, field, Ne, chunkGeom, u, u_t, probAux, a, t, elemVec);CHKERRQ(ierr); 1171 ierr = PetscFEGeomRestoreChunk(fgeom, 0, offset, &chunkGeom);CHKERRQ(ierr); 1172 ierr = PetscFEGeomGetChunk(fgeom,offset,numFaces,&chunkGeom);CHKERRQ(ierr); 1173 ierr = PetscFEIntegrateBdResidual(prob, field, Nr, chunkGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, a ? &a[offset*totDimAux] : NULL, t, &elemVec[offset*totDim]);CHKERRQ(ierr); 1174 ierr = PetscFEGeomRestoreChunk(fgeom,offset,numFaces,&chunkGeom);CHKERRQ(ierr); 1175 } 1176 for (face = 0; face < numFaces; ++face) { 1177 const PetscInt point = points[face], *support; 1178 1179 if (mesh->printFEM > 1) {ierr = DMPrintCellVector(point, "BdResidual", totDim, &elemVec[face*totDim]);CHKERRQ(ierr);} 1180 ierr = DMPlexGetSupport(plex, point, &support);CHKERRQ(ierr); 1181 ierr = DMPlexVecSetClosure(plex, NULL, locF, support[0], &elemVec[face*totDim], ADD_ALL_VALUES);CHKERRQ(ierr); 1182 } 1183 ierr = DMSNESRestoreFEGeom(coordField,pointIS,qGeom,PETSC_TRUE,&fgeom);CHKERRQ(ierr); 1184 ierr = PetscQuadratureDestroy(&qGeom);CHKERRQ(ierr); 1185 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 1186 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 1187 ierr = PetscFree4(u, u_t, elemVec, a);CHKERRQ(ierr); 1188 } 1189 if (plex) {ierr = DMDestroy(&plex);CHKERRQ(ierr);} 1190 if (plexA) {ierr = DMDestroy(&plexA);CHKERRQ(ierr);} 1191 PetscFunctionReturn(0); 1192 } 1193 1194 PetscErrorCode DMPlexComputeBdResidualSingle(DM dm, PetscReal t, DMLabel label, PetscInt numValues, const PetscInt values[], PetscInt field, Vec locX, Vec locX_t, Vec locF) 1195 { 1196 DMField coordField; 1197 DMLabel depthLabel; 1198 IS facetIS; 1199 PetscInt dim; 1200 PetscErrorCode ierr; 1201 1202 PetscFunctionBegin; 1203 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1204 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 1205 ierr = DMLabelGetStratumIS(depthLabel, dim-1, &facetIS);CHKERRQ(ierr); 1206 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 1207 ierr = DMPlexComputeBdResidual_Single_Internal(dm, t, label, numValues, values, field, locX, locX_t, locF, coordField, facetIS);CHKERRQ(ierr); 1208 ierr = ISDestroy(&facetIS);CHKERRQ(ierr); 1209 PetscFunctionReturn(0); 1210 } 1211 1212 PetscErrorCode DMPlexComputeBdResidual_Internal(DM dm, Vec locX, Vec locX_t, PetscReal t, Vec locF, void *user) 1213 { 1214 PetscDS prob; 1215 PetscInt numBd, bd; 1216 DMField coordField = NULL; 1217 IS facetIS = NULL; 1218 DMLabel depthLabel; 1219 PetscInt dim; 1220 PetscErrorCode ierr; 1221 1222 PetscFunctionBegin; 1223 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1224 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 1225 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1226 ierr = DMLabelGetStratumIS(depthLabel,dim - 1,&facetIS);CHKERRQ(ierr); 1227 ierr = PetscDSGetNumBoundary(prob, &numBd);CHKERRQ(ierr); 1228 for (bd = 0; bd < numBd; ++bd) { 1229 DMBoundaryConditionType type; 1230 const char *bdLabel; 1231 DMLabel label; 1232 const PetscInt *values; 1233 PetscInt field, numValues; 1234 PetscObject obj; 1235 PetscClassId id; 1236 1237 ierr = PetscDSGetBoundary(prob, bd, &type, NULL, &bdLabel, &field, NULL, NULL, NULL, &numValues, &values, NULL);CHKERRQ(ierr); 1238 ierr = PetscDSGetDiscretization(prob, field, &obj);CHKERRQ(ierr); 1239 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1240 if ((id != PETSCFE_CLASSID) || (type & DM_BC_ESSENTIAL)) continue; 1241 if (!facetIS) { 1242 DMLabel depthLabel; 1243 PetscInt dim; 1244 1245 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 1246 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1247 ierr = DMLabelGetStratumIS(depthLabel, dim - 1, &facetIS);CHKERRQ(ierr); 1248 } 1249 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 1250 ierr = DMGetLabel(dm, bdLabel, &label);CHKERRQ(ierr); 1251 ierr = DMPlexComputeBdResidual_Single_Internal(dm, t, label, numValues, values, field, locX, locX_t, locF, coordField, facetIS);CHKERRQ(ierr); 1252 } 1253 ierr = ISDestroy(&facetIS);CHKERRQ(ierr); 1254 PetscFunctionReturn(0); 1255 } 1256 1257 PetscErrorCode DMPlexComputeResidual_Internal(DM dm, IS cellIS, PetscReal time, Vec locX, Vec locX_t, PetscReal t, Vec locF, void *user) 1258 { 1259 DM_Plex *mesh = (DM_Plex *) dm->data; 1260 const char *name = "Residual"; 1261 DM dmAux = NULL; 1262 DM dmGrad = NULL; 1263 DMLabel ghostLabel = NULL; 1264 PetscDS prob = NULL; 1265 PetscDS probAux = NULL; 1266 PetscSection section = NULL; 1267 PetscBool useFEM = PETSC_FALSE; 1268 PetscBool useFVM = PETSC_FALSE; 1269 PetscBool isImplicit = (locX_t || time == PETSC_MIN_REAL) ? PETSC_TRUE : PETSC_FALSE; 1270 PetscFV fvm = NULL; 1271 PetscFVCellGeom *cgeomFVM = NULL; 1272 PetscFVFaceGeom *fgeomFVM = NULL; 1273 DMField coordField = NULL; 1274 Vec locA, cellGeometryFVM = NULL, faceGeometryFVM = NULL, grad, locGrad = NULL; 1275 PetscScalar *u = NULL, *u_t, *a, *uL, *uR; 1276 IS chunkIS; 1277 const PetscInt *cells; 1278 PetscInt cStart, cEnd, numCells; 1279 PetscInt Nf, f, totDim, totDimAux, numChunks, cellChunkSize, faceChunkSize, chunk, fStart, fEnd; 1280 PetscInt maxDegree = PETSC_MAX_INT; 1281 PetscQuadrature affineQuad = NULL, *quads = NULL; 1282 PetscFEGeom *affineGeom = NULL, **geoms = NULL; 1283 PetscErrorCode ierr; 1284 1285 PetscFunctionBegin; 1286 ierr = PetscLogEventBegin(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr); 1287 /* TODO The places where we have to use isFE are probably the member functions for the PetscDisc class */ 1288 /* TODO The FVM geometry is over-manipulated. Make the precalc functions return exactly what we need */ 1289 /* FEM+FVM */ 1290 ierr = ISGetPointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 1291 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 1292 /* 1: Get sizes from dm and dmAux */ 1293 ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); 1294 ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 1295 ierr = DMGetCellDS(dm, cStart, &prob);CHKERRQ(ierr); 1296 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 1297 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1298 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);CHKERRQ(ierr); 1299 if (locA) { 1300 PetscInt subcell; 1301 ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); 1302 ierr = DMGetEnclosurePoint(dmAux, dm, DM_ENC_UNKNOWN, cStart, &subcell);CHKERRQ(ierr); 1303 ierr = DMGetCellDS(dmAux, subcell, &probAux);CHKERRQ(ierr); 1304 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 1305 } 1306 /* 2: Get geometric data */ 1307 for (f = 0; f < Nf; ++f) { 1308 PetscObject obj; 1309 PetscClassId id; 1310 PetscBool fimp; 1311 1312 ierr = PetscDSGetImplicit(prob, f, &fimp);CHKERRQ(ierr); 1313 if (isImplicit != fimp) continue; 1314 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1315 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1316 if (id == PETSCFE_CLASSID) {useFEM = PETSC_TRUE;} 1317 if (id == PETSCFV_CLASSID) {useFVM = PETSC_TRUE; fvm = (PetscFV) obj;} 1318 } 1319 if (useFEM) { 1320 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 1321 ierr = DMFieldGetDegree(coordField,cellIS,NULL,&maxDegree);CHKERRQ(ierr); 1322 if (maxDegree <= 1) { 1323 ierr = DMFieldCreateDefaultQuadrature(coordField,cellIS,&affineQuad);CHKERRQ(ierr); 1324 if (affineQuad) { 1325 ierr = DMSNESGetFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&affineGeom);CHKERRQ(ierr); 1326 } 1327 } else { 1328 ierr = PetscCalloc2(Nf,&quads,Nf,&geoms);CHKERRQ(ierr); 1329 for (f = 0; f < Nf; ++f) { 1330 PetscObject obj; 1331 PetscClassId id; 1332 PetscBool fimp; 1333 1334 ierr = PetscDSGetImplicit(prob, f, &fimp);CHKERRQ(ierr); 1335 if (isImplicit != fimp) continue; 1336 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1337 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1338 if (id == PETSCFE_CLASSID) { 1339 PetscFE fe = (PetscFE) obj; 1340 1341 ierr = PetscFEGetQuadrature(fe, &quads[f]);CHKERRQ(ierr); 1342 ierr = PetscObjectReference((PetscObject)quads[f]);CHKERRQ(ierr); 1343 ierr = DMSNESGetFEGeom(coordField,cellIS,quads[f],PETSC_FALSE,&geoms[f]);CHKERRQ(ierr); 1344 } 1345 } 1346 } 1347 } 1348 if (useFVM) { 1349 ierr = DMPlexSNESGetGeometryFVM(dm, &faceGeometryFVM, &cellGeometryFVM, NULL);CHKERRQ(ierr); 1350 ierr = VecGetArrayRead(faceGeometryFVM, (const PetscScalar **) &fgeomFVM);CHKERRQ(ierr); 1351 ierr = VecGetArrayRead(cellGeometryFVM, (const PetscScalar **) &cgeomFVM);CHKERRQ(ierr); 1352 /* Reconstruct and limit cell gradients */ 1353 ierr = DMPlexSNESGetGradientDM(dm, fvm, &dmGrad);CHKERRQ(ierr); 1354 if (dmGrad) { 1355 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 1356 ierr = DMGetGlobalVector(dmGrad, &grad);CHKERRQ(ierr); 1357 ierr = DMPlexReconstructGradients_Internal(dm, fvm, fStart, fEnd, faceGeometryFVM, cellGeometryFVM, locX, grad);CHKERRQ(ierr); 1358 /* Communicate gradient values */ 1359 ierr = DMGetLocalVector(dmGrad, &locGrad);CHKERRQ(ierr); 1360 ierr = DMGlobalToLocalBegin(dmGrad, grad, INSERT_VALUES, locGrad);CHKERRQ(ierr); 1361 ierr = DMGlobalToLocalEnd(dmGrad, grad, INSERT_VALUES, locGrad);CHKERRQ(ierr); 1362 ierr = DMRestoreGlobalVector(dmGrad, &grad);CHKERRQ(ierr); 1363 } 1364 /* Handle non-essential (e.g. outflow) boundary values */ 1365 ierr = DMPlexInsertBoundaryValues(dm, PETSC_FALSE, locX, time, faceGeometryFVM, cellGeometryFVM, locGrad);CHKERRQ(ierr); 1366 } 1367 /* Loop over chunks */ 1368 if (useFEM) {ierr = ISCreate(PETSC_COMM_SELF, &chunkIS);CHKERRQ(ierr);} 1369 numCells = cEnd - cStart; 1370 numChunks = 1; 1371 cellChunkSize = numCells/numChunks; 1372 faceChunkSize = (fEnd - fStart)/numChunks; 1373 numChunks = PetscMin(1,numCells); 1374 for (chunk = 0; chunk < numChunks; ++chunk) { 1375 PetscScalar *elemVec, *fluxL, *fluxR; 1376 PetscReal *vol; 1377 PetscFVFaceGeom *fgeom; 1378 PetscInt cS = cStart+chunk*cellChunkSize, cE = PetscMin(cS+cellChunkSize, cEnd), numCells = cE - cS, c; 1379 PetscInt fS = fStart+chunk*faceChunkSize, fE = PetscMin(fS+faceChunkSize, fEnd), numFaces = 0, face; 1380 1381 /* Extract field coefficients */ 1382 if (useFEM) { 1383 ierr = ISGetPointSubrange(chunkIS, cS, cE, cells);CHKERRQ(ierr); 1384 ierr = DMPlexGetCellFields(dm, chunkIS, locX, locX_t, locA, &u, &u_t, &a);CHKERRQ(ierr); 1385 ierr = DMGetWorkArray(dm, numCells*totDim, MPIU_SCALAR, &elemVec);CHKERRQ(ierr); 1386 ierr = PetscArrayzero(elemVec, numCells*totDim);CHKERRQ(ierr); 1387 } 1388 if (useFVM) { 1389 ierr = DMPlexGetFaceFields(dm, fS, fE, locX, locX_t, faceGeometryFVM, cellGeometryFVM, locGrad, &numFaces, &uL, &uR);CHKERRQ(ierr); 1390 ierr = DMPlexGetFaceGeometry(dm, fS, fE, faceGeometryFVM, cellGeometryFVM, &numFaces, &fgeom, &vol);CHKERRQ(ierr); 1391 ierr = DMGetWorkArray(dm, numFaces*totDim, MPIU_SCALAR, &fluxL);CHKERRQ(ierr); 1392 ierr = DMGetWorkArray(dm, numFaces*totDim, MPIU_SCALAR, &fluxR);CHKERRQ(ierr); 1393 ierr = PetscArrayzero(fluxL, numFaces*totDim);CHKERRQ(ierr); 1394 ierr = PetscArrayzero(fluxR, numFaces*totDim);CHKERRQ(ierr); 1395 } 1396 /* TODO We will interlace both our field coefficients (u, u_t, uL, uR, etc.) and our output (elemVec, fL, fR). I think this works */ 1397 /* Loop over fields */ 1398 for (f = 0; f < Nf; ++f) { 1399 PetscObject obj; 1400 PetscClassId id; 1401 PetscBool fimp; 1402 PetscInt numChunks, numBatches, batchSize, numBlocks, blockSize, Ne, Nr, offset; 1403 1404 ierr = PetscDSGetImplicit(prob, f, &fimp);CHKERRQ(ierr); 1405 if (isImplicit != fimp) continue; 1406 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1407 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1408 if (id == PETSCFE_CLASSID) { 1409 PetscFE fe = (PetscFE) obj; 1410 PetscFEGeom *geom = affineGeom ? affineGeom : geoms[f]; 1411 PetscFEGeom *chunkGeom = NULL; 1412 PetscQuadrature quad = affineQuad ? affineQuad : quads[f]; 1413 PetscInt Nq, Nb; 1414 1415 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1416 ierr = PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 1417 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 1418 blockSize = Nb; 1419 batchSize = numBlocks * blockSize; 1420 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1421 numChunks = numCells / (numBatches*batchSize); 1422 Ne = numChunks*numBatches*batchSize; 1423 Nr = numCells % (numBatches*batchSize); 1424 offset = numCells - Nr; 1425 /* Integrate FE residual to get elemVec (need fields at quadrature points) */ 1426 /* For FV, I think we use a P0 basis and the cell coefficients (for subdivided cells, we can tweak the basis tabulation to be the indicator function) */ 1427 ierr = PetscFEGeomGetChunk(geom,0,offset,&chunkGeom);CHKERRQ(ierr); 1428 ierr = PetscFEIntegrateResidual(prob, f, Ne, chunkGeom, u, u_t, probAux, a, t, elemVec);CHKERRQ(ierr); 1429 ierr = PetscFEGeomGetChunk(geom,offset,numCells,&chunkGeom);CHKERRQ(ierr); 1430 ierr = PetscFEIntegrateResidual(prob, f, Nr, chunkGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, &elemVec[offset*totDim]);CHKERRQ(ierr); 1431 ierr = PetscFEGeomRestoreChunk(geom,offset,numCells,&chunkGeom);CHKERRQ(ierr); 1432 } else if (id == PETSCFV_CLASSID) { 1433 PetscFV fv = (PetscFV) obj; 1434 1435 Ne = numFaces; 1436 /* Riemann solve over faces (need fields at face centroids) */ 1437 /* We need to evaluate FE fields at those coordinates */ 1438 ierr = PetscFVIntegrateRHSFunction(fv, prob, f, Ne, fgeom, vol, uL, uR, fluxL, fluxR);CHKERRQ(ierr); 1439 } else SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", f); 1440 } 1441 /* Loop over domain */ 1442 if (useFEM) { 1443 /* Add elemVec to locX */ 1444 for (c = cS; c < cE; ++c) { 1445 const PetscInt cell = cells ? cells[c] : c; 1446 const PetscInt cind = c - cStart; 1447 1448 if (mesh->printFEM > 1) {ierr = DMPrintCellVector(cell, name, totDim, &elemVec[cind*totDim]);CHKERRQ(ierr);} 1449 if (ghostLabel) { 1450 PetscInt ghostVal; 1451 1452 ierr = DMLabelGetValue(ghostLabel,cell,&ghostVal);CHKERRQ(ierr); 1453 if (ghostVal > 0) continue; 1454 } 1455 ierr = DMPlexVecSetClosure(dm, section, locF, cell, &elemVec[cind*totDim], ADD_ALL_VALUES);CHKERRQ(ierr); 1456 } 1457 } 1458 if (useFVM) { 1459 PetscScalar *fa; 1460 PetscInt iface; 1461 1462 ierr = VecGetArray(locF, &fa);CHKERRQ(ierr); 1463 for (f = 0; f < Nf; ++f) { 1464 PetscFV fv; 1465 PetscObject obj; 1466 PetscClassId id; 1467 PetscInt foff, pdim; 1468 1469 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1470 ierr = PetscDSGetFieldOffset(prob, f, &foff);CHKERRQ(ierr); 1471 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1472 if (id != PETSCFV_CLASSID) continue; 1473 fv = (PetscFV) obj; 1474 ierr = PetscFVGetNumComponents(fv, &pdim);CHKERRQ(ierr); 1475 /* Accumulate fluxes to cells */ 1476 for (face = fS, iface = 0; face < fE; ++face) { 1477 const PetscInt *scells; 1478 PetscScalar *fL = NULL, *fR = NULL; 1479 PetscInt ghost, d, nsupp, nchild; 1480 1481 ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr); 1482 ierr = DMPlexGetSupportSize(dm, face, &nsupp);CHKERRQ(ierr); 1483 ierr = DMPlexGetTreeChildren(dm, face, &nchild, NULL);CHKERRQ(ierr); 1484 if (ghost >= 0 || nsupp > 2 || nchild > 0) continue; 1485 ierr = DMPlexGetSupport(dm, face, &scells);CHKERRQ(ierr); 1486 ierr = DMLabelGetValue(ghostLabel,scells[0],&ghost);CHKERRQ(ierr); 1487 if (ghost <= 0) {ierr = DMPlexPointLocalFieldRef(dm, scells[0], f, fa, &fL);CHKERRQ(ierr);} 1488 ierr = DMLabelGetValue(ghostLabel,scells[1],&ghost);CHKERRQ(ierr); 1489 if (ghost <= 0) {ierr = DMPlexPointLocalFieldRef(dm, scells[1], f, fa, &fR);CHKERRQ(ierr);} 1490 for (d = 0; d < pdim; ++d) { 1491 if (fL) fL[d] -= fluxL[iface*totDim+foff+d]; 1492 if (fR) fR[d] += fluxR[iface*totDim+foff+d]; 1493 } 1494 ++iface; 1495 } 1496 } 1497 ierr = VecRestoreArray(locF, &fa);CHKERRQ(ierr); 1498 } 1499 /* Handle time derivative */ 1500 if (locX_t) { 1501 PetscScalar *x_t, *fa; 1502 1503 ierr = VecGetArray(locF, &fa);CHKERRQ(ierr); 1504 ierr = VecGetArray(locX_t, &x_t);CHKERRQ(ierr); 1505 for (f = 0; f < Nf; ++f) { 1506 PetscFV fv; 1507 PetscObject obj; 1508 PetscClassId id; 1509 PetscInt pdim, d; 1510 1511 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1512 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1513 if (id != PETSCFV_CLASSID) continue; 1514 fv = (PetscFV) obj; 1515 ierr = PetscFVGetNumComponents(fv, &pdim);CHKERRQ(ierr); 1516 for (c = cS; c < cE; ++c) { 1517 const PetscInt cell = cells ? cells[c] : c; 1518 PetscScalar *u_t, *r; 1519 1520 if (ghostLabel) { 1521 PetscInt ghostVal; 1522 1523 ierr = DMLabelGetValue(ghostLabel, cell, &ghostVal);CHKERRQ(ierr); 1524 if (ghostVal > 0) continue; 1525 } 1526 ierr = DMPlexPointLocalFieldRead(dm, cell, f, x_t, &u_t);CHKERRQ(ierr); 1527 ierr = DMPlexPointLocalFieldRef(dm, cell, f, fa, &r);CHKERRQ(ierr); 1528 for (d = 0; d < pdim; ++d) r[d] += u_t[d]; 1529 } 1530 } 1531 ierr = VecRestoreArray(locX_t, &x_t);CHKERRQ(ierr); 1532 ierr = VecRestoreArray(locF, &fa);CHKERRQ(ierr); 1533 } 1534 if (useFEM) { 1535 ierr = DMPlexRestoreCellFields(dm, chunkIS, locX, locX_t, locA, &u, &u_t, &a);CHKERRQ(ierr); 1536 ierr = DMRestoreWorkArray(dm, numCells*totDim, MPIU_SCALAR, &elemVec);CHKERRQ(ierr); 1537 } 1538 if (useFVM) { 1539 ierr = DMPlexRestoreFaceFields(dm, fS, fE, locX, locX_t, faceGeometryFVM, cellGeometryFVM, locGrad, &numFaces, &uL, &uR);CHKERRQ(ierr); 1540 ierr = DMPlexRestoreFaceGeometry(dm, fS, fE, faceGeometryFVM, cellGeometryFVM, &numFaces, &fgeom, &vol);CHKERRQ(ierr); 1541 ierr = DMRestoreWorkArray(dm, numFaces*totDim, MPIU_SCALAR, &fluxL);CHKERRQ(ierr); 1542 ierr = DMRestoreWorkArray(dm, numFaces*totDim, MPIU_SCALAR, &fluxR);CHKERRQ(ierr); 1543 if (dmGrad) {ierr = DMRestoreLocalVector(dmGrad, &locGrad);CHKERRQ(ierr);} 1544 } 1545 } 1546 if (useFEM) {ierr = ISDestroy(&chunkIS);CHKERRQ(ierr);} 1547 ierr = ISRestorePointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 1548 1549 if (useFEM) { 1550 ierr = DMPlexComputeBdResidual_Internal(dm, locX, locX_t, t, locF, user);CHKERRQ(ierr); 1551 1552 if (maxDegree <= 1) { 1553 ierr = DMSNESRestoreFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&affineGeom);CHKERRQ(ierr); 1554 ierr = PetscQuadratureDestroy(&affineQuad);CHKERRQ(ierr); 1555 } else { 1556 for (f = 0; f < Nf; ++f) { 1557 ierr = DMSNESRestoreFEGeom(coordField,cellIS,quads[f],PETSC_FALSE,&geoms[f]);CHKERRQ(ierr); 1558 ierr = PetscQuadratureDestroy(&quads[f]);CHKERRQ(ierr); 1559 } 1560 ierr = PetscFree2(quads,geoms);CHKERRQ(ierr); 1561 } 1562 } 1563 1564 /* FEM */ 1565 /* 1: Get sizes from dm and dmAux */ 1566 /* 2: Get geometric data */ 1567 /* 3: Handle boundary values */ 1568 /* 4: Loop over domain */ 1569 /* Extract coefficients */ 1570 /* Loop over fields */ 1571 /* Set tiling for FE*/ 1572 /* Integrate FE residual to get elemVec */ 1573 /* Loop over subdomain */ 1574 /* Loop over quad points */ 1575 /* Transform coords to real space */ 1576 /* Evaluate field and aux fields at point */ 1577 /* Evaluate residual at point */ 1578 /* Transform residual to real space */ 1579 /* Add residual to elemVec */ 1580 /* Loop over domain */ 1581 /* Add elemVec to locX */ 1582 1583 /* FVM */ 1584 /* Get geometric data */ 1585 /* If using gradients */ 1586 /* Compute gradient data */ 1587 /* Loop over domain faces */ 1588 /* Count computational faces */ 1589 /* Reconstruct cell gradient */ 1590 /* Loop over domain cells */ 1591 /* Limit cell gradients */ 1592 /* Handle boundary values */ 1593 /* Loop over domain faces */ 1594 /* Read out field, centroid, normal, volume for each side of face */ 1595 /* Riemann solve over faces */ 1596 /* Loop over domain faces */ 1597 /* Accumulate fluxes to cells */ 1598 /* TODO Change printFEM to printDisc here */ 1599 if (mesh->printFEM) { 1600 Vec locFbc; 1601 PetscInt pStart, pEnd, p, maxDof; 1602 PetscScalar *zeroes; 1603 1604 ierr = VecDuplicate(locF,&locFbc);CHKERRQ(ierr); 1605 ierr = VecCopy(locF,locFbc);CHKERRQ(ierr); 1606 ierr = PetscSectionGetChart(section,&pStart,&pEnd);CHKERRQ(ierr); 1607 ierr = PetscSectionGetMaxDof(section,&maxDof);CHKERRQ(ierr); 1608 ierr = PetscCalloc1(maxDof,&zeroes);CHKERRQ(ierr); 1609 for (p = pStart; p < pEnd; p++) { 1610 ierr = VecSetValuesSection(locFbc,section,p,zeroes,INSERT_BC_VALUES);CHKERRQ(ierr); 1611 } 1612 ierr = PetscFree(zeroes);CHKERRQ(ierr); 1613 ierr = DMPrintLocalVec(dm, name, mesh->printTol, locFbc);CHKERRQ(ierr); 1614 ierr = VecDestroy(&locFbc);CHKERRQ(ierr); 1615 } 1616 ierr = PetscLogEventEnd(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr); 1617 PetscFunctionReturn(0); 1618 } 1619 1620 /*@ 1621 DMPlexSNESComputeResidualFEM - Form the local residual F from the local input X using pointwise functions specified by the user 1622 1623 Input Parameters: 1624 + dm - The mesh 1625 . X - Local solution 1626 - user - The user context 1627 1628 Output Parameter: 1629 . F - Local output vector 1630 1631 Level: developer 1632 1633 .seealso: DMPlexComputeJacobianAction() 1634 @*/ 1635 PetscErrorCode DMPlexSNESComputeResidualFEM(DM dm, Vec X, Vec F, void *user) 1636 { 1637 DM plex; 1638 IS cellIS; 1639 PetscInt depth; 1640 PetscErrorCode ierr; 1641 1642 PetscFunctionBegin; 1643 ierr = DMSNESConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr); 1644 ierr = DMPlexGetDepth(plex, &depth);CHKERRQ(ierr); 1645 ierr = DMGetStratumIS(plex, "dim", depth, &cellIS);CHKERRQ(ierr); 1646 if (!cellIS) { 1647 ierr = DMGetStratumIS(plex, "depth", depth, &cellIS);CHKERRQ(ierr); 1648 } 1649 ierr = DMPlexComputeResidual_Internal(plex, cellIS, PETSC_MIN_REAL, X, NULL, 0.0, F, user);CHKERRQ(ierr); 1650 ierr = ISDestroy(&cellIS);CHKERRQ(ierr); 1651 ierr = DMDestroy(&plex);CHKERRQ(ierr); 1652 PetscFunctionReturn(0); 1653 } 1654 1655 /*@ 1656 DMPlexSNESComputeBoundaryFEM - Form the boundary values for the local input X 1657 1658 Input Parameters: 1659 + dm - The mesh 1660 - user - The user context 1661 1662 Output Parameter: 1663 . X - Local solution 1664 1665 Level: developer 1666 1667 .seealso: DMPlexComputeJacobianAction() 1668 @*/ 1669 PetscErrorCode DMPlexSNESComputeBoundaryFEM(DM dm, Vec X, void *user) 1670 { 1671 DM plex; 1672 PetscErrorCode ierr; 1673 1674 PetscFunctionBegin; 1675 ierr = DMSNESConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr); 1676 ierr = DMPlexInsertBoundaryValues(plex, PETSC_TRUE, X, PETSC_MIN_REAL, NULL, NULL, NULL);CHKERRQ(ierr); 1677 ierr = DMDestroy(&plex);CHKERRQ(ierr); 1678 PetscFunctionReturn(0); 1679 } 1680 1681 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) 1682 { 1683 DM_Plex *mesh = (DM_Plex *) dm->data; 1684 DM plex = NULL, plexA = NULL, tdm; 1685 DMEnclosureType encAux; 1686 PetscDS prob, probAux = NULL; 1687 PetscSection section, sectionAux = NULL; 1688 PetscSection globalSection, subSection = NULL; 1689 Vec locA = NULL, tv; 1690 PetscScalar *u = NULL, *u_t = NULL, *a = NULL, *elemMat = NULL; 1691 PetscInt v; 1692 PetscInt Nf, totDim, totDimAux = 0; 1693 PetscBool isMatISP, transform; 1694 PetscErrorCode ierr; 1695 1696 PetscFunctionBegin; 1697 ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); 1698 ierr = DMHasBasisTransform(dm, &transform);CHKERRQ(ierr); 1699 ierr = DMGetBasisTransformDM_Internal(dm, &tdm);CHKERRQ(ierr); 1700 ierr = DMGetBasisTransformVec_Internal(dm, &tv);CHKERRQ(ierr); 1701 ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); 1702 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1703 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 1704 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1705 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);CHKERRQ(ierr); 1706 if (locA) { 1707 DM dmAux; 1708 1709 ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); 1710 ierr = DMGetEnclosureRelation(dmAux, dm, &encAux);CHKERRQ(ierr); 1711 ierr = DMConvert(dmAux, DMPLEX, &plexA);CHKERRQ(ierr); 1712 ierr = DMGetDS(plexA, &probAux);CHKERRQ(ierr); 1713 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 1714 ierr = DMGetLocalSection(plexA, §ionAux);CHKERRQ(ierr); 1715 } 1716 1717 ierr = PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatISP);CHKERRQ(ierr); 1718 ierr = DMGetGlobalSection(dm, &globalSection);CHKERRQ(ierr); 1719 if (isMatISP) {ierr = DMPlexGetSubdomainSection(dm, &subSection);CHKERRQ(ierr);} 1720 for (v = 0; v < numValues; ++v) { 1721 PetscFEGeom *fgeom; 1722 PetscInt maxDegree; 1723 PetscQuadrature qGeom = NULL; 1724 IS pointIS; 1725 const PetscInt *points; 1726 PetscInt numFaces, face, Nq; 1727 1728 ierr = DMLabelGetStratumIS(label, values[v], &pointIS);CHKERRQ(ierr); 1729 if (!pointIS) continue; /* No points with that id on this process */ 1730 { 1731 IS isectIS; 1732 1733 /* TODO: Special cases of ISIntersect where it is quick to check a prior if one is a superset of the other */ 1734 ierr = ISIntersect_Caching_Internal(facetIS,pointIS,&isectIS);CHKERRQ(ierr); 1735 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 1736 pointIS = isectIS; 1737 } 1738 ierr = ISGetLocalSize(pointIS, &numFaces);CHKERRQ(ierr); 1739 ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); 1740 ierr = PetscMalloc4(numFaces*totDim, &u, locX_t ? numFaces*totDim : 0, &u_t, numFaces*totDim*totDim, &elemMat, locA ? numFaces*totDimAux : 0, &a);CHKERRQ(ierr); 1741 ierr = DMFieldGetDegree(coordField,pointIS,NULL,&maxDegree);CHKERRQ(ierr); 1742 if (maxDegree <= 1) { 1743 ierr = DMFieldCreateDefaultQuadrature(coordField,pointIS,&qGeom);CHKERRQ(ierr); 1744 } 1745 if (!qGeom) { 1746 PetscFE fe; 1747 1748 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); 1749 ierr = PetscFEGetFaceQuadrature(fe, &qGeom);CHKERRQ(ierr); 1750 ierr = PetscObjectReference((PetscObject)qGeom);CHKERRQ(ierr); 1751 } 1752 ierr = PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 1753 ierr = DMSNESGetFEGeom(coordField,pointIS,qGeom,PETSC_TRUE,&fgeom);CHKERRQ(ierr); 1754 for (face = 0; face < numFaces; ++face) { 1755 const PetscInt point = points[face], *support, *cone; 1756 PetscScalar *x = NULL; 1757 PetscInt i, coneSize, faceLoc; 1758 1759 ierr = DMPlexGetSupport(dm, point, &support);CHKERRQ(ierr); 1760 ierr = DMPlexGetConeSize(dm, support[0], &coneSize);CHKERRQ(ierr); 1761 ierr = DMPlexGetCone(dm, support[0], &cone);CHKERRQ(ierr); 1762 for (faceLoc = 0; faceLoc < coneSize; ++faceLoc) if (cone[faceLoc] == point) break; 1763 if (faceLoc == coneSize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Could not find face %D in cone of support[0] %D", point, support[0]); 1764 fgeom->face[face][0] = faceLoc; 1765 ierr = DMPlexVecGetClosure(plex, section, locX, support[0], NULL, &x);CHKERRQ(ierr); 1766 for (i = 0; i < totDim; ++i) u[face*totDim+i] = x[i]; 1767 ierr = DMPlexVecRestoreClosure(plex, section, locX, support[0], NULL, &x);CHKERRQ(ierr); 1768 if (locX_t) { 1769 ierr = DMPlexVecGetClosure(plex, section, locX_t, support[0], NULL, &x);CHKERRQ(ierr); 1770 for (i = 0; i < totDim; ++i) u_t[face*totDim+i] = x[i]; 1771 ierr = DMPlexVecRestoreClosure(plex, section, locX_t, support[0], NULL, &x);CHKERRQ(ierr); 1772 } 1773 if (locA) { 1774 PetscInt subp; 1775 ierr = DMGetEnclosurePoint(plexA, dm, encAux, support[0], &subp);CHKERRQ(ierr); 1776 ierr = DMPlexVecGetClosure(plexA, sectionAux, locA, subp, NULL, &x);CHKERRQ(ierr); 1777 for (i = 0; i < totDimAux; ++i) a[face*totDimAux+i] = x[i]; 1778 ierr = DMPlexVecRestoreClosure(plexA, sectionAux, locA, subp, NULL, &x);CHKERRQ(ierr); 1779 } 1780 } 1781 ierr = PetscArrayzero(elemMat, numFaces*totDim*totDim);CHKERRQ(ierr); 1782 { 1783 PetscFE fe; 1784 PetscInt Nb; 1785 /* Conforming batches */ 1786 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 1787 /* Remainder */ 1788 PetscFEGeom *chunkGeom = NULL; 1789 PetscInt fieldJ, Nr, offset; 1790 1791 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); 1792 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 1793 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1794 blockSize = Nb; 1795 batchSize = numBlocks * blockSize; 1796 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1797 numChunks = numFaces / (numBatches*batchSize); 1798 Ne = numChunks*numBatches*batchSize; 1799 Nr = numFaces % (numBatches*batchSize); 1800 offset = numFaces - Nr; 1801 ierr = PetscFEGeomGetChunk(fgeom,0,offset,&chunkGeom);CHKERRQ(ierr); 1802 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 1803 ierr = PetscFEIntegrateBdJacobian(prob, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMat);CHKERRQ(ierr); 1804 } 1805 ierr = PetscFEGeomGetChunk(fgeom,offset,numFaces,&chunkGeom);CHKERRQ(ierr); 1806 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 1807 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); 1808 } 1809 ierr = PetscFEGeomRestoreChunk(fgeom,offset,numFaces,&chunkGeom);CHKERRQ(ierr); 1810 } 1811 for (face = 0; face < numFaces; ++face) { 1812 const PetscInt point = points[face], *support; 1813 1814 /* Transform to global basis before insertion in Jacobian */ 1815 ierr = DMPlexGetSupport(plex, point, &support);CHKERRQ(ierr); 1816 if (transform) {ierr = DMPlexBasisTransformPointTensor_Internal(dm, tdm, tv, support[0], PETSC_TRUE, totDim, &elemMat[face*totDim*totDim]);CHKERRQ(ierr);} 1817 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(point, "BdJacobian", totDim, totDim, &elemMat[face*totDim*totDim]);CHKERRQ(ierr);} 1818 if (!isMatISP) { 1819 ierr = DMPlexMatSetClosure(plex, section, globalSection, JacP, support[0], &elemMat[face*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 1820 } else { 1821 Mat lJ; 1822 1823 ierr = MatISGetLocalMat(JacP, &lJ);CHKERRQ(ierr); 1824 ierr = DMPlexMatSetClosure(plex, section, subSection, lJ, support[0], &elemMat[face*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 1825 } 1826 } 1827 ierr = DMSNESRestoreFEGeom(coordField,pointIS,qGeom,PETSC_TRUE,&fgeom);CHKERRQ(ierr); 1828 ierr = PetscQuadratureDestroy(&qGeom);CHKERRQ(ierr); 1829 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 1830 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 1831 ierr = PetscFree4(u, u_t, elemMat, a);CHKERRQ(ierr); 1832 } 1833 if (plex) {ierr = DMDestroy(&plex);CHKERRQ(ierr);} 1834 if (plexA) {ierr = DMDestroy(&plexA);CHKERRQ(ierr);} 1835 PetscFunctionReturn(0); 1836 } 1837 1838 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) 1839 { 1840 DMField coordField; 1841 DMLabel depthLabel; 1842 IS facetIS; 1843 PetscInt dim; 1844 PetscErrorCode ierr; 1845 1846 PetscFunctionBegin; 1847 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1848 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 1849 ierr = DMLabelGetStratumIS(depthLabel, dim-1, &facetIS);CHKERRQ(ierr); 1850 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 1851 ierr = DMPlexComputeBdJacobian_Single_Internal(dm, t, label, numValues, values, field, locX, locX_t, X_tShift, Jac, JacP, coordField, facetIS);CHKERRQ(ierr); 1852 ierr = ISDestroy(&facetIS);CHKERRQ(ierr); 1853 PetscFunctionReturn(0); 1854 } 1855 1856 PetscErrorCode DMPlexComputeBdJacobian_Internal(DM dm, Vec locX, Vec locX_t, PetscReal t, PetscReal X_tShift, Mat Jac, Mat JacP, void *user) 1857 { 1858 PetscDS prob; 1859 PetscInt dim, numBd, bd; 1860 DMLabel depthLabel; 1861 DMField coordField = NULL; 1862 IS facetIS; 1863 PetscErrorCode ierr; 1864 1865 PetscFunctionBegin; 1866 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1867 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 1868 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1869 ierr = DMLabelGetStratumIS(depthLabel, dim-1, &facetIS);CHKERRQ(ierr); 1870 ierr = PetscDSGetNumBoundary(prob, &numBd);CHKERRQ(ierr); 1871 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 1872 for (bd = 0; bd < numBd; ++bd) { 1873 DMBoundaryConditionType type; 1874 const char *bdLabel; 1875 DMLabel label; 1876 const PetscInt *values; 1877 PetscInt fieldI, numValues; 1878 PetscObject obj; 1879 PetscClassId id; 1880 1881 ierr = PetscDSGetBoundary(prob, bd, &type, NULL, &bdLabel, &fieldI, NULL, NULL, NULL, &numValues, &values, NULL);CHKERRQ(ierr); 1882 ierr = PetscDSGetDiscretization(prob, fieldI, &obj);CHKERRQ(ierr); 1883 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1884 if ((id != PETSCFE_CLASSID) || (type & DM_BC_ESSENTIAL)) continue; 1885 ierr = DMGetLabel(dm, bdLabel, &label);CHKERRQ(ierr); 1886 ierr = DMPlexComputeBdJacobian_Single_Internal(dm, t, label, numValues, values, fieldI, locX, locX_t, X_tShift, Jac, JacP, coordField, facetIS);CHKERRQ(ierr); 1887 } 1888 ierr = ISDestroy(&facetIS);CHKERRQ(ierr); 1889 PetscFunctionReturn(0); 1890 } 1891 1892 PetscErrorCode DMPlexComputeJacobian_Internal(DM dm, IS cellIS, PetscReal t, PetscReal X_tShift, Vec X, Vec X_t, Mat Jac, Mat JacP,void *user) 1893 { 1894 DM_Plex *mesh = (DM_Plex *) dm->data; 1895 const char *name = "Jacobian"; 1896 DM dmAux, plex, tdm; 1897 DMEnclosureType encAux; 1898 Vec A, tv; 1899 DMField coordField; 1900 PetscDS prob, probAux = NULL; 1901 PetscSection section, globalSection, subSection, sectionAux; 1902 PetscScalar *elemMat, *elemMatP, *elemMatD, *u, *u_t, *a = NULL; 1903 const PetscInt *cells; 1904 PetscInt Nf, fieldI, fieldJ; 1905 PetscInt totDim, totDimAux, cStart, cEnd, numCells, c; 1906 PetscBool isMatIS, isMatISP, hasJac, hasPrec, hasDyn, hasFV = PETSC_FALSE, transform; 1907 PetscErrorCode ierr; 1908 1909 PetscFunctionBegin; 1910 ierr = PetscLogEventBegin(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 1911 ierr = DMHasBasisTransform(dm, &transform);CHKERRQ(ierr); 1912 ierr = DMGetBasisTransformDM_Internal(dm, &tdm);CHKERRQ(ierr); 1913 ierr = DMGetBasisTransformVec_Internal(dm, &tv);CHKERRQ(ierr); 1914 ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); 1915 ierr = PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatISP);CHKERRQ(ierr); 1916 ierr = DMGetGlobalSection(dm, &globalSection);CHKERRQ(ierr); 1917 if (isMatISP) {ierr = DMPlexGetSubdomainSection(dm, &subSection);CHKERRQ(ierr);} 1918 ierr = ISGetLocalSize(cellIS, &numCells);CHKERRQ(ierr); 1919 ierr = ISGetPointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 1920 ierr = DMGetCellDS(dm, cStart, &prob);CHKERRQ(ierr); 1921 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 1922 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1923 ierr = PetscDSHasJacobian(prob, &hasJac);CHKERRQ(ierr); 1924 ierr = PetscDSHasJacobianPreconditioner(prob, &hasPrec);CHKERRQ(ierr); 1925 /* user passed in the same matrix, avoid double contributions and 1926 only assemble the Jacobian */ 1927 if (hasJac && Jac == JacP) hasPrec = PETSC_FALSE; 1928 ierr = PetscDSHasDynamicJacobian(prob, &hasDyn);CHKERRQ(ierr); 1929 hasDyn = hasDyn && (X_tShift != 0.0) ? PETSC_TRUE : PETSC_FALSE; 1930 ierr = PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);CHKERRQ(ierr); 1931 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);CHKERRQ(ierr); 1932 if (dmAux) { 1933 ierr = DMGetEnclosureRelation(dmAux, dm, &encAux);CHKERRQ(ierr); 1934 ierr = DMConvert(dmAux, DMPLEX, &plex);CHKERRQ(ierr); 1935 ierr = DMGetLocalSection(plex, §ionAux);CHKERRQ(ierr); 1936 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 1937 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 1938 } 1939 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); 1940 if (dmAux) {ierr = PetscMalloc1(numCells*totDimAux, &a);CHKERRQ(ierr);} 1941 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 1942 for (c = cStart; c < cEnd; ++c) { 1943 const PetscInt cell = cells ? cells[c] : c; 1944 const PetscInt cind = c - cStart; 1945 PetscScalar *x = NULL, *x_t = NULL; 1946 PetscInt i; 1947 1948 ierr = DMPlexVecGetClosure(dm, section, X, cell, NULL, &x);CHKERRQ(ierr); 1949 for (i = 0; i < totDim; ++i) u[cind*totDim+i] = x[i]; 1950 ierr = DMPlexVecRestoreClosure(dm, section, X, cell, NULL, &x);CHKERRQ(ierr); 1951 if (X_t) { 1952 ierr = DMPlexVecGetClosure(dm, section, X_t, cell, NULL, &x_t);CHKERRQ(ierr); 1953 for (i = 0; i < totDim; ++i) u_t[cind*totDim+i] = x_t[i]; 1954 ierr = DMPlexVecRestoreClosure(dm, section, X_t, cell, NULL, &x_t);CHKERRQ(ierr); 1955 } 1956 if (dmAux) { 1957 PetscInt subcell; 1958 ierr = DMGetEnclosurePoint(dmAux, dm, encAux, cell, &subcell);CHKERRQ(ierr); 1959 ierr = DMPlexVecGetClosure(plex, sectionAux, A, subcell, NULL, &x);CHKERRQ(ierr); 1960 for (i = 0; i < totDimAux; ++i) a[cind*totDimAux+i] = x[i]; 1961 ierr = DMPlexVecRestoreClosure(plex, sectionAux, A, subcell, NULL, &x);CHKERRQ(ierr); 1962 } 1963 } 1964 if (hasJac) {ierr = PetscArrayzero(elemMat, numCells*totDim*totDim);CHKERRQ(ierr);} 1965 if (hasPrec) {ierr = PetscArrayzero(elemMatP, numCells*totDim*totDim);CHKERRQ(ierr);} 1966 if (hasDyn) {ierr = PetscArrayzero(elemMatD, numCells*totDim*totDim);CHKERRQ(ierr);} 1967 for (fieldI = 0; fieldI < Nf; ++fieldI) { 1968 PetscClassId id; 1969 PetscFE fe; 1970 PetscQuadrature qGeom = NULL; 1971 PetscInt Nb; 1972 /* Conforming batches */ 1973 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 1974 /* Remainder */ 1975 PetscInt Nr, offset, Nq; 1976 PetscInt maxDegree; 1977 PetscFEGeom *cgeomFEM, *chunkGeom = NULL, *remGeom = NULL; 1978 1979 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); 1980 ierr = PetscObjectGetClassId((PetscObject) fe, &id);CHKERRQ(ierr); 1981 if (id == PETSCFV_CLASSID) {hasFV = PETSC_TRUE; continue;} 1982 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 1983 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1984 ierr = DMFieldGetDegree(coordField,cellIS,NULL,&maxDegree);CHKERRQ(ierr); 1985 if (maxDegree <= 1) { 1986 ierr = DMFieldCreateDefaultQuadrature(coordField,cellIS,&qGeom);CHKERRQ(ierr); 1987 } 1988 if (!qGeom) { 1989 ierr = PetscFEGetQuadrature(fe,&qGeom);CHKERRQ(ierr); 1990 ierr = PetscObjectReference((PetscObject)qGeom);CHKERRQ(ierr); 1991 } 1992 ierr = PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 1993 ierr = DMSNESGetFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);CHKERRQ(ierr); 1994 blockSize = Nb; 1995 batchSize = numBlocks * blockSize; 1996 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1997 numChunks = numCells / (numBatches*batchSize); 1998 Ne = numChunks*numBatches*batchSize; 1999 Nr = numCells % (numBatches*batchSize); 2000 offset = numCells - Nr; 2001 ierr = PetscFEGeomGetChunk(cgeomFEM,0,offset,&chunkGeom);CHKERRQ(ierr); 2002 ierr = PetscFEGeomGetChunk(cgeomFEM,offset,numCells,&remGeom);CHKERRQ(ierr); 2003 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 2004 if (hasJac) { 2005 ierr = PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMat);CHKERRQ(ierr); 2006 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); 2007 } 2008 if (hasPrec) { 2009 ierr = PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN_PRE, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMatP);CHKERRQ(ierr); 2010 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); 2011 } 2012 if (hasDyn) { 2013 ierr = PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN_DYN, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMatD);CHKERRQ(ierr); 2014 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); 2015 } 2016 } 2017 ierr = PetscFEGeomRestoreChunk(cgeomFEM,offset,numCells,&remGeom);CHKERRQ(ierr); 2018 ierr = PetscFEGeomRestoreChunk(cgeomFEM,0,offset,&chunkGeom);CHKERRQ(ierr); 2019 ierr = DMSNESRestoreFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);CHKERRQ(ierr); 2020 ierr = PetscQuadratureDestroy(&qGeom);CHKERRQ(ierr); 2021 } 2022 /* Add contribution from X_t */ 2023 if (hasDyn) {for (c = 0; c < numCells*totDim*totDim; ++c) elemMat[c] += X_tShift*elemMatD[c];} 2024 if (hasFV) { 2025 PetscClassId id; 2026 PetscFV fv; 2027 PetscInt offsetI, NcI, NbI = 1, fc, f; 2028 2029 for (fieldI = 0; fieldI < Nf; ++fieldI) { 2030 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fv);CHKERRQ(ierr); 2031 ierr = PetscDSGetFieldOffset(prob, fieldI, &offsetI);CHKERRQ(ierr); 2032 ierr = PetscObjectGetClassId((PetscObject) fv, &id);CHKERRQ(ierr); 2033 if (id != PETSCFV_CLASSID) continue; 2034 /* Put in the identity */ 2035 ierr = PetscFVGetNumComponents(fv, &NcI);CHKERRQ(ierr); 2036 for (c = cStart; c < cEnd; ++c) { 2037 const PetscInt cind = c - cStart; 2038 const PetscInt eOffset = cind*totDim*totDim; 2039 for (fc = 0; fc < NcI; ++fc) { 2040 for (f = 0; f < NbI; ++f) { 2041 const PetscInt i = offsetI + f*NcI+fc; 2042 if (hasPrec) { 2043 if (hasJac) {elemMat[eOffset+i*totDim+i] = 1.0;} 2044 elemMatP[eOffset+i*totDim+i] = 1.0; 2045 } else {elemMat[eOffset+i*totDim+i] = 1.0;} 2046 } 2047 } 2048 } 2049 } 2050 /* No allocated space for FV stuff, so ignore the zero entries */ 2051 ierr = MatSetOption(JacP, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE);CHKERRQ(ierr); 2052 } 2053 /* Insert values into matrix */ 2054 isMatIS = PETSC_FALSE; 2055 if (hasPrec && hasJac) { 2056 ierr = PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatIS);CHKERRQ(ierr); 2057 } 2058 if (isMatIS && !subSection) { 2059 ierr = DMPlexGetSubdomainSection(dm, &subSection);CHKERRQ(ierr); 2060 } 2061 for (c = cStart; c < cEnd; ++c) { 2062 const PetscInt cell = cells ? cells[c] : c; 2063 const PetscInt cind = c - cStart; 2064 2065 /* Transform to global basis before insertion in Jacobian */ 2066 if (transform) {ierr = DMPlexBasisTransformPointTensor_Internal(dm, tdm, tv, cell, PETSC_TRUE, totDim, &elemMat[cind*totDim*totDim]);CHKERRQ(ierr);} 2067 if (hasPrec) { 2068 if (hasJac) { 2069 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(cell, name, totDim, totDim, &elemMat[cind*totDim*totDim]);CHKERRQ(ierr);} 2070 if (!isMatIS) { 2071 ierr = DMPlexMatSetClosure(dm, section, globalSection, Jac, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2072 } else { 2073 Mat lJ; 2074 2075 ierr = MatISGetLocalMat(Jac,&lJ);CHKERRQ(ierr); 2076 ierr = DMPlexMatSetClosure(dm, section, subSection, lJ, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2077 } 2078 } 2079 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(cell, name, totDim, totDim, &elemMatP[cind*totDim*totDim]);CHKERRQ(ierr);} 2080 if (!isMatISP) { 2081 ierr = DMPlexMatSetClosure(dm, section, globalSection, JacP, cell, &elemMatP[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2082 } else { 2083 Mat lJ; 2084 2085 ierr = MatISGetLocalMat(JacP,&lJ);CHKERRQ(ierr); 2086 ierr = DMPlexMatSetClosure(dm, section, subSection, lJ, cell, &elemMatP[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2087 } 2088 } else { 2089 if (hasJac) { 2090 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(cell, name, totDim, totDim, &elemMat[cind*totDim*totDim]);CHKERRQ(ierr);} 2091 if (!isMatISP) { 2092 ierr = DMPlexMatSetClosure(dm, section, globalSection, JacP, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2093 } else { 2094 Mat lJ; 2095 2096 ierr = MatISGetLocalMat(JacP,&lJ);CHKERRQ(ierr); 2097 ierr = DMPlexMatSetClosure(dm, section, subSection, lJ, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2098 } 2099 } 2100 } 2101 } 2102 ierr = ISRestorePointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 2103 if (hasFV) {ierr = MatSetOption(JacP, MAT_IGNORE_ZERO_ENTRIES, PETSC_FALSE);CHKERRQ(ierr);} 2104 ierr = PetscFree5(u,u_t,elemMat,elemMatP,elemMatD);CHKERRQ(ierr); 2105 if (dmAux) { 2106 ierr = PetscFree(a);CHKERRQ(ierr); 2107 ierr = DMDestroy(&plex);CHKERRQ(ierr); 2108 } 2109 /* Compute boundary integrals */ 2110 ierr = DMPlexComputeBdJacobian_Internal(dm, X, X_t, t, X_tShift, Jac, JacP, user);CHKERRQ(ierr); 2111 /* Assemble matrix */ 2112 if (hasJac && hasPrec) { 2113 ierr = MatAssemblyBegin(Jac, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2114 ierr = MatAssemblyEnd(Jac, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2115 } 2116 ierr = MatAssemblyBegin(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2117 ierr = MatAssemblyEnd(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2118 ierr = PetscLogEventEnd(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 2119 PetscFunctionReturn(0); 2120 } 2121 2122 /*@ 2123 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. 2124 2125 Input Parameters: 2126 + dm - The mesh 2127 . cellIS - 2128 . t - The time 2129 . X_tShift - The multiplier for the Jacobian with repsect to X_t 2130 . X - Local solution vector 2131 . X_t - Time-derivative of the local solution vector 2132 . Y - Local input vector 2133 - user - The user context 2134 2135 Output Parameter: 2136 . Z - Local output vector 2137 2138 Note: 2139 We form the residual one batch of elements at a time. This allows us to offload work onto an accelerator, 2140 like a GPU, or vectorize on a multicore machine. 2141 2142 Level: developer 2143 2144 .seealso: FormFunctionLocal() 2145 @*/ 2146 PetscErrorCode DMPlexComputeJacobianAction(DM dm, IS cellIS, PetscReal t, PetscReal X_tShift, Vec X, Vec X_t, Vec Y, Vec Z, void *user) 2147 { 2148 DM_Plex *mesh = (DM_Plex *) dm->data; 2149 const char *name = "Jacobian"; 2150 DM dmAux, plex, plexAux = NULL; 2151 DMEnclosureType encAux; 2152 Vec A; 2153 PetscDS prob, probAux = NULL; 2154 PetscQuadrature quad; 2155 PetscSection section, globalSection, sectionAux; 2156 PetscScalar *elemMat, *elemMatD, *u, *u_t, *a = NULL, *y, *z; 2157 PetscInt Nf, fieldI, fieldJ; 2158 PetscInt totDim, totDimAux = 0; 2159 const PetscInt *cells; 2160 PetscInt cStart, cEnd, numCells, c; 2161 PetscBool hasDyn; 2162 DMField coordField; 2163 PetscErrorCode ierr; 2164 2165 PetscFunctionBegin; 2166 ierr = PetscLogEventBegin(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 2167 ierr = DMSNESConvertPlex(dm, &plex, PETSC_TRUE);CHKERRQ(ierr); 2168 if (!cellIS) { 2169 PetscInt depth; 2170 2171 ierr = DMPlexGetDepth(plex, &depth);CHKERRQ(ierr); 2172 ierr = DMGetStratumIS(plex, "dim", depth, &cellIS);CHKERRQ(ierr); 2173 if (!cellIS) {ierr = DMGetStratumIS(plex, "depth", depth, &cellIS);CHKERRQ(ierr);} 2174 } else { 2175 ierr = PetscObjectReference((PetscObject) cellIS);CHKERRQ(ierr); 2176 } 2177 ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); 2178 ierr = DMGetGlobalSection(dm, &globalSection);CHKERRQ(ierr); 2179 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 2180 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 2181 ierr = PetscDSHasDynamicJacobian(prob, &hasDyn);CHKERRQ(ierr); 2182 hasDyn = hasDyn && (X_tShift != 0.0) ? PETSC_TRUE : PETSC_FALSE; 2183 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); 2184 ierr = ISGetLocalSize(cellIS, &numCells);CHKERRQ(ierr); 2185 ierr = ISGetPointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 2186 ierr = PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);CHKERRQ(ierr); 2187 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);CHKERRQ(ierr); 2188 if (dmAux) { 2189 ierr = DMGetEnclosureRelation(dmAux, dm, &encAux);CHKERRQ(ierr); 2190 ierr = DMConvert(dmAux, DMPLEX, &plexAux);CHKERRQ(ierr); 2191 ierr = DMGetLocalSection(plexAux, §ionAux);CHKERRQ(ierr); 2192 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 2193 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 2194 } 2195 ierr = VecSet(Z, 0.0);CHKERRQ(ierr); 2196 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); 2197 if (dmAux) {ierr = PetscMalloc1(numCells*totDimAux, &a);CHKERRQ(ierr);} 2198 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 2199 for (c = cStart; c < cEnd; ++c) { 2200 const PetscInt cell = cells ? cells[c] : c; 2201 const PetscInt cind = c - cStart; 2202 PetscScalar *x = NULL, *x_t = NULL; 2203 PetscInt i; 2204 2205 ierr = DMPlexVecGetClosure(dm, section, X, cell, NULL, &x);CHKERRQ(ierr); 2206 for (i = 0; i < totDim; ++i) u[cind*totDim+i] = x[i]; 2207 ierr = DMPlexVecRestoreClosure(dm, section, X, cell, NULL, &x);CHKERRQ(ierr); 2208 if (X_t) { 2209 ierr = DMPlexVecGetClosure(dm, section, X_t, cell, NULL, &x_t);CHKERRQ(ierr); 2210 for (i = 0; i < totDim; ++i) u_t[cind*totDim+i] = x_t[i]; 2211 ierr = DMPlexVecRestoreClosure(dm, section, X_t, cell, NULL, &x_t);CHKERRQ(ierr); 2212 } 2213 if (dmAux) { 2214 PetscInt subcell; 2215 ierr = DMGetEnclosurePoint(dmAux, dm, encAux, cell, &subcell);CHKERRQ(ierr); 2216 ierr = DMPlexVecGetClosure(plexAux, sectionAux, A, subcell, NULL, &x);CHKERRQ(ierr); 2217 for (i = 0; i < totDimAux; ++i) a[cind*totDimAux+i] = x[i]; 2218 ierr = DMPlexVecRestoreClosure(plexAux, sectionAux, A, subcell, NULL, &x);CHKERRQ(ierr); 2219 } 2220 ierr = DMPlexVecGetClosure(dm, section, Y, cell, NULL, &x);CHKERRQ(ierr); 2221 for (i = 0; i < totDim; ++i) y[cind*totDim+i] = x[i]; 2222 ierr = DMPlexVecRestoreClosure(dm, section, Y, cell, NULL, &x);CHKERRQ(ierr); 2223 } 2224 ierr = PetscArrayzero(elemMat, numCells*totDim*totDim);CHKERRQ(ierr); 2225 if (hasDyn) {ierr = PetscArrayzero(elemMatD, numCells*totDim*totDim);CHKERRQ(ierr);} 2226 for (fieldI = 0; fieldI < Nf; ++fieldI) { 2227 PetscFE fe; 2228 PetscInt Nb; 2229 /* Conforming batches */ 2230 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 2231 /* Remainder */ 2232 PetscInt Nr, offset, Nq; 2233 PetscQuadrature qGeom = NULL; 2234 PetscInt maxDegree; 2235 PetscFEGeom *cgeomFEM, *chunkGeom = NULL, *remGeom = NULL; 2236 2237 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); 2238 ierr = PetscFEGetQuadrature(fe, &quad);CHKERRQ(ierr); 2239 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 2240 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 2241 ierr = DMFieldGetDegree(coordField,cellIS,NULL,&maxDegree);CHKERRQ(ierr); 2242 if (maxDegree <= 1) {ierr = DMFieldCreateDefaultQuadrature(coordField,cellIS,&qGeom);CHKERRQ(ierr);} 2243 if (!qGeom) { 2244 ierr = PetscFEGetQuadrature(fe,&qGeom);CHKERRQ(ierr); 2245 ierr = PetscObjectReference((PetscObject)qGeom);CHKERRQ(ierr); 2246 } 2247 ierr = PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 2248 ierr = DMSNESGetFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);CHKERRQ(ierr); 2249 blockSize = Nb; 2250 batchSize = numBlocks * blockSize; 2251 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 2252 numChunks = numCells / (numBatches*batchSize); 2253 Ne = numChunks*numBatches*batchSize; 2254 Nr = numCells % (numBatches*batchSize); 2255 offset = numCells - Nr; 2256 ierr = PetscFEGeomGetChunk(cgeomFEM,0,offset,&chunkGeom);CHKERRQ(ierr); 2257 ierr = PetscFEGeomGetChunk(cgeomFEM,offset,numCells,&remGeom);CHKERRQ(ierr); 2258 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 2259 ierr = PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMat);CHKERRQ(ierr); 2260 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); 2261 if (hasDyn) { 2262 ierr = PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN_DYN, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMatD);CHKERRQ(ierr); 2263 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); 2264 } 2265 } 2266 ierr = PetscFEGeomRestoreChunk(cgeomFEM,offset,numCells,&remGeom);CHKERRQ(ierr); 2267 ierr = PetscFEGeomRestoreChunk(cgeomFEM,0,offset,&chunkGeom);CHKERRQ(ierr); 2268 ierr = DMSNESRestoreFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);CHKERRQ(ierr); 2269 ierr = PetscQuadratureDestroy(&qGeom);CHKERRQ(ierr); 2270 } 2271 if (hasDyn) { 2272 for (c = 0; c < numCells*totDim*totDim; ++c) elemMat[c] += X_tShift*elemMatD[c]; 2273 } 2274 for (c = cStart; c < cEnd; ++c) { 2275 const PetscInt cell = cells ? cells[c] : c; 2276 const PetscInt cind = c - cStart; 2277 const PetscBLASInt M = totDim, one = 1; 2278 const PetscScalar a = 1.0, b = 0.0; 2279 2280 PetscStackCallBLAS("BLASgemv", BLASgemv_("N", &M, &M, &a, &elemMat[cind*totDim*totDim], &M, &y[cind*totDim], &one, &b, z, &one)); 2281 if (mesh->printFEM > 1) { 2282 ierr = DMPrintCellMatrix(c, name, totDim, totDim, &elemMat[cind*totDim*totDim]);CHKERRQ(ierr); 2283 ierr = DMPrintCellVector(c, "Y", totDim, &y[cind*totDim]);CHKERRQ(ierr); 2284 ierr = DMPrintCellVector(c, "Z", totDim, z);CHKERRQ(ierr); 2285 } 2286 ierr = DMPlexVecSetClosure(dm, section, Z, cell, z, ADD_VALUES);CHKERRQ(ierr); 2287 } 2288 ierr = PetscFree6(u,u_t,elemMat,elemMatD,y,z);CHKERRQ(ierr); 2289 if (mesh->printFEM) { 2290 ierr = PetscPrintf(PETSC_COMM_WORLD, "Z:\n");CHKERRQ(ierr); 2291 ierr = VecView(Z, NULL);CHKERRQ(ierr); 2292 } 2293 ierr = PetscFree(a);CHKERRQ(ierr); 2294 ierr = ISDestroy(&cellIS);CHKERRQ(ierr); 2295 ierr = DMDestroy(&plexAux);CHKERRQ(ierr); 2296 ierr = DMDestroy(&plex);CHKERRQ(ierr); 2297 ierr = PetscLogEventEnd(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 2298 PetscFunctionReturn(0); 2299 } 2300 2301 /*@ 2302 DMPlexSNESComputeJacobianFEM - Form the local portion of the Jacobian matrix J at the local solution X using pointwise functions specified by the user. 2303 2304 Input Parameters: 2305 + dm - The mesh 2306 . X - Local input vector 2307 - user - The user context 2308 2309 Output Parameter: 2310 . Jac - Jacobian matrix 2311 2312 Note: 2313 We form the residual one batch of elements at a time. This allows us to offload work onto an accelerator, 2314 like a GPU, or vectorize on a multicore machine. 2315 2316 Level: developer 2317 2318 .seealso: FormFunctionLocal() 2319 @*/ 2320 PetscErrorCode DMPlexSNESComputeJacobianFEM(DM dm, Vec X, Mat Jac, Mat JacP,void *user) 2321 { 2322 DM plex; 2323 PetscDS prob; 2324 IS cellIS; 2325 PetscBool hasJac, hasPrec; 2326 PetscInt depth; 2327 PetscErrorCode ierr; 2328 2329 PetscFunctionBegin; 2330 ierr = DMSNESConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr); 2331 ierr = DMPlexGetDepth(plex, &depth);CHKERRQ(ierr); 2332 ierr = DMGetStratumIS(plex, "dim", depth, &cellIS);CHKERRQ(ierr); 2333 if (!cellIS) {ierr = DMGetStratumIS(plex, "depth", depth, &cellIS);CHKERRQ(ierr);} 2334 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 2335 ierr = PetscDSHasJacobian(prob, &hasJac);CHKERRQ(ierr); 2336 ierr = PetscDSHasJacobianPreconditioner(prob, &hasPrec);CHKERRQ(ierr); 2337 if (hasJac && hasPrec) {ierr = MatZeroEntries(Jac);CHKERRQ(ierr);} 2338 ierr = MatZeroEntries(JacP);CHKERRQ(ierr); 2339 ierr = DMPlexComputeJacobian_Internal(plex, cellIS, 0.0, 0.0, X, NULL, Jac, JacP, user);CHKERRQ(ierr); 2340 ierr = ISDestroy(&cellIS);CHKERRQ(ierr); 2341 ierr = DMDestroy(&plex);CHKERRQ(ierr); 2342 PetscFunctionReturn(0); 2343 } 2344 2345 /* 2346 MatComputeNeumannOverlap - Computes an unassembled (Neumann) local overlapping Mat in nonlinear context. 2347 2348 Input Parameters: 2349 + X - SNES linearization point 2350 . ovl - index set of overlapping subdomains 2351 2352 Output Parameter: 2353 . J - unassembled (Neumann) local matrix 2354 2355 Level: intermediate 2356 2357 .seealso: DMCreateNeumannOverlap(), MATIS, PCHPDDMSetAuxiliaryMat() 2358 */ 2359 static PetscErrorCode MatComputeNeumannOverlap_Plex(Mat J, PetscReal t, Vec X, Vec X_t, PetscReal s, IS ovl, void *ctx) 2360 { 2361 SNES snes; 2362 Mat pJ; 2363 DM ovldm,origdm; 2364 DMSNES sdm; 2365 PetscErrorCode (*bfun)(DM,Vec,void*); 2366 PetscErrorCode (*jfun)(DM,Vec,Mat,Mat,void*); 2367 void *bctx,*jctx; 2368 PetscErrorCode ierr; 2369 2370 PetscFunctionBegin; 2371 ierr = PetscObjectQuery((PetscObject)ovl,"_DM_Overlap_HPDDM_MATIS",(PetscObject*)&pJ);CHKERRQ(ierr); 2372 if (!pJ) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Missing overlapping Mat");CHKERRQ(ierr); 2373 ierr = PetscObjectQuery((PetscObject)ovl,"_DM_Original_HPDDM",(PetscObject*)&origdm);CHKERRQ(ierr); 2374 if (!origdm) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Missing original DM");CHKERRQ(ierr); 2375 ierr = MatGetDM(pJ,&ovldm);CHKERRQ(ierr); 2376 ierr = DMSNESGetBoundaryLocal(origdm,&bfun,&bctx);CHKERRQ(ierr); 2377 ierr = DMSNESSetBoundaryLocal(ovldm,bfun,bctx);CHKERRQ(ierr); 2378 ierr = DMSNESGetJacobianLocal(origdm,&jfun,&jctx);CHKERRQ(ierr); 2379 ierr = DMSNESSetJacobianLocal(ovldm,jfun,jctx);CHKERRQ(ierr); 2380 ierr = PetscObjectQuery((PetscObject)ovl,"_DM_Overlap_HPDDM_SNES",(PetscObject*)&snes);CHKERRQ(ierr); 2381 if (!snes) { 2382 ierr = SNESCreate(PetscObjectComm((PetscObject)ovl),&snes);CHKERRQ(ierr); 2383 ierr = SNESSetDM(snes,ovldm);CHKERRQ(ierr); 2384 ierr = PetscObjectCompose((PetscObject)ovl,"_DM_Overlap_HPDDM_SNES",(PetscObject)snes);CHKERRQ(ierr); 2385 ierr = PetscObjectDereference((PetscObject)snes);CHKERRQ(ierr); 2386 } 2387 ierr = DMGetDMSNES(ovldm,&sdm);CHKERRQ(ierr); 2388 ierr = VecLockReadPush(X);CHKERRQ(ierr); 2389 PetscStackPush("SNES user Jacobian function"); 2390 ierr = (*sdm->ops->computejacobian)(snes,X,pJ,pJ,sdm->jacobianctx);CHKERRQ(ierr); 2391 PetscStackPop; 2392 ierr = VecLockReadPop(X);CHKERRQ(ierr); 2393 /* this is a no-hop, just in case we decide to change the placeholder for the local Neumann matrix */ 2394 { 2395 Mat locpJ; 2396 2397 ierr = MatISGetLocalMat(pJ,&locpJ);CHKERRQ(ierr); 2398 ierr = MatCopy(locpJ,J,SAME_NONZERO_PATTERN);CHKERRQ(ierr); 2399 } 2400 PetscFunctionReturn(0); 2401 } 2402 2403 /*@ 2404 DMPlexSetSNESLocalFEM - Use DMPlex's internal FEM routines to compute SNES boundary values, residual, and Jacobian. 2405 2406 Input Parameters: 2407 + dm - The DM object 2408 . boundaryctx - the user context that will be passed to pointwise evaluation of boundary values (see PetscDSAddBoundary()) 2409 . residualctx - the user context that will be passed to pointwise evaluation of finite element residual computations (see PetscDSSetResidual()) 2410 - jacobianctx - the user context that will be passed to pointwise evaluation of finite element Jacobian construction (see PetscDSSetJacobian()) 2411 2412 Level: developer 2413 @*/ 2414 PetscErrorCode DMPlexSetSNESLocalFEM(DM dm, void *boundaryctx, void *residualctx, void *jacobianctx) 2415 { 2416 PetscErrorCode ierr; 2417 2418 PetscFunctionBegin; 2419 ierr = DMSNESSetBoundaryLocal(dm,DMPlexSNESComputeBoundaryFEM,boundaryctx);CHKERRQ(ierr); 2420 ierr = DMSNESSetFunctionLocal(dm,DMPlexSNESComputeResidualFEM,residualctx);CHKERRQ(ierr); 2421 ierr = DMSNESSetJacobianLocal(dm,DMPlexSNESComputeJacobianFEM,jacobianctx);CHKERRQ(ierr); 2422 ierr = PetscObjectComposeFunction((PetscObject)dm,"MatComputeNeumannOverlap_C",MatComputeNeumannOverlap_Plex);CHKERRQ(ierr); 2423 PetscFunctionReturn(0); 2424 } 2425 2426 /*@C 2427 DMSNESCheckDiscretization - Check the discretization error of the exact solution 2428 2429 Input Parameters: 2430 + snes - the SNES object 2431 . dm - the DM 2432 . u - a DM vector 2433 . exactFuncs - pointwise functions of the exact solution for each field 2434 . ctxs - contexts for the functions 2435 - tol - A tolerance for the check, or -1 to print the results instead 2436 2437 Output Parameters: 2438 . error - An array which holds the discretization error in each field, or NULL 2439 2440 Level: developer 2441 2442 .seealso: DNSNESCheckFromOptions(), DMSNESCheckResidual(), DMSNESCheckJacobian() 2443 @*/ 2444 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[]) 2445 { 2446 PetscErrorCode (**exacts)(PetscInt, PetscReal, const PetscReal x[], PetscInt, PetscScalar *u, void *ctx); 2447 void **ectxs; 2448 MPI_Comm comm; 2449 PetscDS ds; 2450 PetscReal *err; 2451 PetscInt Nf, f; 2452 PetscErrorCode ierr; 2453 2454 PetscFunctionBegin; 2455 PetscValidHeaderSpecific(snes, SNES_CLASSID, 1); 2456 PetscValidHeaderSpecific(dm, DM_CLASSID, 2); 2457 PetscValidHeaderSpecific(u, VEC_CLASSID, 3); 2458 if (error) PetscValidRealPointer(error, 6); 2459 ierr = PetscObjectGetComm((PetscObject) snes, &comm);CHKERRQ(ierr); 2460 ierr = DMGetDS(dm, &ds);CHKERRQ(ierr); 2461 ierr = DMGetNumFields(dm, &Nf);CHKERRQ(ierr); 2462 ierr = PetscMalloc3(Nf, &exacts, Nf, &ectxs, PetscMax(1, Nf), &err);CHKERRQ(ierr); 2463 for (f = 0; f < Nf; ++f) {ierr = PetscDSGetExactSolution(ds, f, &exacts[f], &ectxs[f]);CHKERRQ(ierr);} 2464 ierr = DMProjectFunction(dm, 0.0, exactFuncs ? exactFuncs : exacts, ctxs ? ctxs : ectxs, INSERT_ALL_VALUES, u);CHKERRQ(ierr); 2465 ierr = PetscObjectSetName((PetscObject) u, "Exact Solution");CHKERRQ(ierr); 2466 ierr = PetscObjectSetOptionsPrefix((PetscObject) u, "exact_");CHKERRQ(ierr); 2467 ierr = VecViewFromOptions(u, NULL, "-vec_view");CHKERRQ(ierr); 2468 if (Nf > 1) { 2469 ierr = DMComputeL2FieldDiff(dm, 0.0, exactFuncs ? exactFuncs : exacts, ctxs ? ctxs : ectxs, u, err);CHKERRQ(ierr); 2470 if (tol >= 0.0) { 2471 for (f = 0; f < Nf; ++f) { 2472 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); 2473 } 2474 } else if (error) { 2475 for (f = 0; f < Nf; ++f) error[f] = err[f]; 2476 } else { 2477 ierr = PetscPrintf(comm, "L_2 Error: [");CHKERRQ(ierr); 2478 for (f = 0; f < Nf; ++f) { 2479 if (f) {ierr = PetscPrintf(comm, ", ");CHKERRQ(ierr);} 2480 ierr = PetscPrintf(comm, "%g", (double)err[f]);CHKERRQ(ierr); 2481 } 2482 ierr = PetscPrintf(comm, "]\n");CHKERRQ(ierr); 2483 } 2484 } else { 2485 ierr = DMComputeL2Diff(dm, 0.0, exactFuncs ? exactFuncs : exacts, ctxs ? ctxs : ectxs , u, &err[0]);CHKERRQ(ierr); 2486 if (tol >= 0.0) { 2487 if (err[0] > tol) SETERRQ2(comm, PETSC_ERR_ARG_WRONG, "L_2 Error %g exceeds tolerance %g", (double) err[0], (double) tol); 2488 } else if (error) { 2489 error[0] = err[0]; 2490 } else { 2491 ierr = PetscPrintf(comm, "L_2 Error: %g\n", (double)err[0]);CHKERRQ(ierr); 2492 } 2493 } 2494 ierr = PetscFree3(exacts, ectxs, err);CHKERRQ(ierr); 2495 PetscFunctionReturn(0); 2496 } 2497 2498 /*@C 2499 DMSNESCheckResidual - Check the residual of the exact solution 2500 2501 Input Parameters: 2502 + snes - the SNES object 2503 . dm - the DM 2504 . u - a DM vector 2505 - tol - A tolerance for the check, or -1 to print the results instead 2506 2507 Output Parameters: 2508 . residual - The residual norm of the exact solution, or NULL 2509 2510 Level: developer 2511 2512 .seealso: DNSNESCheckFromOptions(), DMSNESCheckDiscretization(), DMSNESCheckJacobian() 2513 @*/ 2514 PetscErrorCode DMSNESCheckResidual(SNES snes, DM dm, Vec u, PetscReal tol, PetscReal *residual) 2515 { 2516 PetscErrorCode (**exacts)(PetscInt, PetscReal, const PetscReal x[], PetscInt, PetscScalar *u, void *ctx); 2517 void **ectxs; 2518 MPI_Comm comm; 2519 PetscDS ds; 2520 Vec r; 2521 PetscReal res; 2522 PetscInt Nf, f; 2523 PetscBool computeSol = PETSC_FALSE; 2524 PetscErrorCode ierr; 2525 2526 PetscFunctionBegin; 2527 PetscValidHeaderSpecific(snes, SNES_CLASSID, 1); 2528 PetscValidHeaderSpecific(dm, DM_CLASSID, 2); 2529 PetscValidHeaderSpecific(u, VEC_CLASSID, 3); 2530 if (residual) PetscValidRealPointer(residual, 5); 2531 ierr = PetscObjectGetComm((PetscObject) snes, &comm);CHKERRQ(ierr); 2532 ierr = DMGetDS(dm, &ds);CHKERRQ(ierr); 2533 ierr = DMGetNumFields(dm, &Nf);CHKERRQ(ierr); 2534 ierr = PetscMalloc2(Nf, &exacts, Nf, &ectxs);CHKERRQ(ierr); 2535 for (f = 0; f < Nf; ++f) { 2536 ierr = PetscDSGetExactSolution(ds, f, &exacts[f], &ectxs[f]);CHKERRQ(ierr); 2537 if (exacts[f]) computeSol = PETSC_TRUE; 2538 } 2539 if (computeSol) {ierr = DMProjectFunction(dm, 0.0, exacts, ectxs, INSERT_ALL_VALUES, u);CHKERRQ(ierr);} 2540 ierr = PetscFree2(exacts, ectxs);CHKERRQ(ierr); 2541 2542 ierr = VecDuplicate(u, &r);CHKERRQ(ierr); 2543 ierr = SNESComputeFunction(snes, u, r);CHKERRQ(ierr); 2544 ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr); 2545 if (tol >= 0.0) { 2546 if (res > tol) SETERRQ2(comm, PETSC_ERR_ARG_WRONG, "L_2 Residual %g exceeds tolerance %g", (double) res, (double) tol); 2547 } else if (residual) { 2548 *residual = res; 2549 } else { 2550 ierr = PetscPrintf(comm, "L_2 Residual: %g\n", (double)res);CHKERRQ(ierr); 2551 ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr); 2552 ierr = PetscObjectSetName((PetscObject) r, "Initial Residual");CHKERRQ(ierr); 2553 ierr = PetscObjectSetOptionsPrefix((PetscObject)r,"res_");CHKERRQ(ierr); 2554 ierr = VecViewFromOptions(r, NULL, "-vec_view");CHKERRQ(ierr); 2555 } 2556 ierr = VecDestroy(&r);CHKERRQ(ierr); 2557 PetscFunctionReturn(0); 2558 } 2559 2560 /*@C 2561 DMSNESCheckJacobian - Check the Jacobian of the exact solution against the residual using the Taylor Test 2562 2563 Input Parameters: 2564 + snes - the SNES object 2565 . dm - the DM 2566 . u - a DM vector 2567 - tol - A tolerance for the check, or -1 to print the results instead 2568 2569 Output Parameters: 2570 + isLinear - Flag indicaing that the function looks linear, or NULL 2571 - convRate - The rate of convergence of the linear model, or NULL 2572 2573 Level: developer 2574 2575 .seealso: DNSNESCheckFromOptions(), DMSNESCheckDiscretization(), DMSNESCheckResidual() 2576 @*/ 2577 PetscErrorCode DMSNESCheckJacobian(SNES snes, DM dm, Vec u, PetscReal tol, PetscBool *isLinear, PetscReal *convRate) 2578 { 2579 PetscErrorCode (**exacts)(PetscInt, PetscReal, const PetscReal x[], PetscInt, PetscScalar *u, void *ctx); 2580 void **ectxs; 2581 MPI_Comm comm; 2582 PetscDS ds; 2583 Mat J, M; 2584 MatNullSpace nullspace; 2585 PetscReal slope, intercept; 2586 PetscInt Nf, f; 2587 PetscBool hasJac, hasPrec, isLin = PETSC_FALSE, computeSol = PETSC_FALSE; 2588 PetscErrorCode ierr; 2589 2590 PetscFunctionBegin; 2591 PetscValidHeaderSpecific(snes, SNES_CLASSID, 1); 2592 PetscValidHeaderSpecific(dm, DM_CLASSID, 2); 2593 PetscValidHeaderSpecific(u, VEC_CLASSID, 3); 2594 if (isLinear) PetscValidBoolPointer(isLinear, 5); 2595 if (convRate) PetscValidRealPointer(convRate, 5); 2596 ierr = PetscObjectGetComm((PetscObject) snes, &comm);CHKERRQ(ierr); 2597 ierr = DMGetDS(dm, &ds);CHKERRQ(ierr); 2598 ierr = DMGetNumFields(dm, &Nf);CHKERRQ(ierr); 2599 ierr = PetscMalloc2(Nf, &exacts, Nf, &ectxs);CHKERRQ(ierr); 2600 for (f = 0; f < Nf; ++f) { 2601 ierr = PetscDSGetExactSolution(ds, f, &exacts[f], &ectxs[f]);CHKERRQ(ierr); 2602 if (exacts[f]) computeSol = PETSC_TRUE; 2603 } 2604 if (computeSol) {ierr = DMProjectFunction(dm, 0.0, exacts, ectxs, INSERT_ALL_VALUES, u);CHKERRQ(ierr);} 2605 ierr = PetscFree2(exacts, ectxs);CHKERRQ(ierr); 2606 2607 /* Create and view matrices */ 2608 ierr = DMCreateMatrix(dm, &J);CHKERRQ(ierr); 2609 ierr = PetscDSHasJacobian(ds, &hasJac);CHKERRQ(ierr); 2610 ierr = PetscDSHasJacobianPreconditioner(ds, &hasPrec);CHKERRQ(ierr); 2611 if (hasJac && hasPrec) { 2612 ierr = DMCreateMatrix(dm, &M);CHKERRQ(ierr); 2613 ierr = SNESComputeJacobian(snes, u, J, M);CHKERRQ(ierr); 2614 ierr = PetscObjectSetName((PetscObject) M, "Preconditioning Matrix");CHKERRQ(ierr); 2615 ierr = PetscObjectSetOptionsPrefix((PetscObject) M, "jacpre_");CHKERRQ(ierr); 2616 ierr = MatViewFromOptions(M, NULL, "-mat_view");CHKERRQ(ierr); 2617 ierr = MatDestroy(&M);CHKERRQ(ierr); 2618 } else { 2619 ierr = SNESComputeJacobian(snes, u, J, J);CHKERRQ(ierr); 2620 } 2621 ierr = PetscObjectSetName((PetscObject) J, "Jacobian");CHKERRQ(ierr); 2622 ierr = PetscObjectSetOptionsPrefix((PetscObject) J, "jac_");CHKERRQ(ierr); 2623 ierr = MatViewFromOptions(J, NULL, "-mat_view");CHKERRQ(ierr); 2624 /* Check nullspace */ 2625 ierr = MatGetNullSpace(J, &nullspace);CHKERRQ(ierr); 2626 if (nullspace) { 2627 PetscBool isNull; 2628 ierr = MatNullSpaceTest(nullspace, J, &isNull);CHKERRQ(ierr); 2629 if (!isNull) SETERRQ(comm, PETSC_ERR_PLIB, "The null space calculated for the system operator is invalid."); 2630 } 2631 ierr = MatNullSpaceDestroy(&nullspace);CHKERRQ(ierr); 2632 /* Taylor test */ 2633 { 2634 PetscRandom rand; 2635 Vec du, uhat, r, rhat, df; 2636 PetscReal h; 2637 PetscReal *es, *hs, *errors; 2638 PetscReal hMax = 1.0, hMin = 1e-6, hMult = 0.1; 2639 PetscInt Nv, v; 2640 2641 /* Choose a perturbation direction */ 2642 ierr = PetscRandomCreate(comm, &rand);CHKERRQ(ierr); 2643 ierr = VecDuplicate(u, &du);CHKERRQ(ierr); 2644 ierr = VecSetRandom(du, rand); CHKERRQ(ierr); 2645 ierr = PetscRandomDestroy(&rand);CHKERRQ(ierr); 2646 ierr = VecDuplicate(u, &df);CHKERRQ(ierr); 2647 ierr = MatMult(J, du, df);CHKERRQ(ierr); 2648 /* Evaluate residual at u, F(u), save in vector r */ 2649 ierr = VecDuplicate(u, &r);CHKERRQ(ierr); 2650 ierr = SNESComputeFunction(snes, u, r);CHKERRQ(ierr); 2651 /* Look at the convergence of our Taylor approximation as we approach u */ 2652 for (h = hMax, Nv = 0; h >= hMin; h *= hMult, ++Nv); 2653 ierr = PetscCalloc3(Nv, &es, Nv, &hs, Nv, &errors);CHKERRQ(ierr); 2654 ierr = VecDuplicate(u, &uhat);CHKERRQ(ierr); 2655 ierr = VecDuplicate(u, &rhat);CHKERRQ(ierr); 2656 for (h = hMax, Nv = 0; h >= hMin; h *= hMult, ++Nv) { 2657 ierr = VecWAXPY(uhat, h, du, u);CHKERRQ(ierr); 2658 /* F(\hat u) \approx F(u) + J(u) (uhat - u) = F(u) + h * J(u) du */ 2659 ierr = SNESComputeFunction(snes, uhat, rhat);CHKERRQ(ierr); 2660 ierr = VecAXPBYPCZ(rhat, -1.0, -h, 1.0, r, df);CHKERRQ(ierr); 2661 ierr = VecNorm(rhat, NORM_2, &errors[Nv]);CHKERRQ(ierr); 2662 2663 es[Nv] = PetscLog10Real(errors[Nv]); 2664 hs[Nv] = PetscLog10Real(h); 2665 } 2666 ierr = VecDestroy(&uhat);CHKERRQ(ierr); 2667 ierr = VecDestroy(&rhat);CHKERRQ(ierr); 2668 ierr = VecDestroy(&df);CHKERRQ(ierr); 2669 ierr = VecDestroy(&r);CHKERRQ(ierr); 2670 ierr = VecDestroy(&du);CHKERRQ(ierr); 2671 for (v = 0; v < Nv; ++v) { 2672 if ((tol >= 0) && (errors[v] > tol)) break; 2673 else if (errors[v] > PETSC_SMALL) break; 2674 } 2675 if (v == Nv) isLin = PETSC_TRUE; 2676 ierr = PetscLinearRegression(Nv, hs, es, &slope, &intercept);CHKERRQ(ierr); 2677 ierr = PetscFree3(es, hs, errors);CHKERRQ(ierr); 2678 /* Slope should be about 2 */ 2679 if (tol >= 0) { 2680 if (!isLin && PetscAbsReal(2 - slope) > tol) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Taylor approximation convergence rate should be 2, not %0.2f", (double) slope); 2681 } else if (isLinear || convRate) { 2682 if (isLinear) *isLinear = isLin; 2683 if (convRate) *convRate = slope; 2684 } else { 2685 if (!isLin) {ierr = PetscPrintf(comm, "Taylor approximation converging at order %3.2f\n", (double) slope);CHKERRQ(ierr);} 2686 else {ierr = PetscPrintf(comm, "Function appears to be linear\n");CHKERRQ(ierr);} 2687 } 2688 } 2689 ierr = MatDestroy(&J);CHKERRQ(ierr); 2690 PetscFunctionReturn(0); 2691 } 2692 2693 PetscErrorCode DMSNESCheck_Internal(SNES snes, DM dm, Vec u, PetscErrorCode (**exactFuncs)(PetscInt, PetscReal, const PetscReal x[], PetscInt, PetscScalar *u, void *ctx), void **ctxs) 2694 { 2695 PetscErrorCode ierr; 2696 2697 PetscFunctionBegin; 2698 ierr = DMSNESCheckDiscretization(snes, dm, u, exactFuncs, ctxs, -1.0, NULL);CHKERRQ(ierr); 2699 ierr = DMSNESCheckResidual(snes, dm, u, -1.0, NULL);CHKERRQ(ierr); 2700 ierr = DMSNESCheckJacobian(snes, dm, u, -1.0, NULL, NULL);CHKERRQ(ierr); 2701 PetscFunctionReturn(0); 2702 } 2703 2704 /*@C 2705 DMSNESCheckFromOptions - Check the residual and Jacobian functions using the exact solution by outputting some diagnostic information 2706 2707 Input Parameters: 2708 + snes - the SNES object 2709 . u - representative SNES vector 2710 . exactFuncs - pointwise functions of the exact solution for each field 2711 - ctxs - contexts for the functions 2712 2713 Level: developer 2714 @*/ 2715 PetscErrorCode DMSNESCheckFromOptions(SNES snes, Vec u, PetscErrorCode (**exactFuncs)(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf, PetscScalar *u, void *ctx), void **ctxs) 2716 { 2717 DM dm; 2718 Vec sol; 2719 PetscBool check; 2720 PetscErrorCode ierr; 2721 2722 PetscFunctionBegin; 2723 ierr = PetscOptionsHasName(((PetscObject)snes)->options,((PetscObject)snes)->prefix, "-dmsnes_check", &check);CHKERRQ(ierr); 2724 if (!check) PetscFunctionReturn(0); 2725 ierr = SNESGetDM(snes, &dm);CHKERRQ(ierr); 2726 ierr = VecDuplicate(u, &sol);CHKERRQ(ierr); 2727 ierr = SNESSetSolution(snes, sol);CHKERRQ(ierr); 2728 ierr = DMSNESCheck_Internal(snes, dm, sol, exactFuncs, ctxs);CHKERRQ(ierr); 2729 ierr = VecDestroy(&sol);CHKERRQ(ierr); 2730 PetscFunctionReturn(0); 2731 } 2732