1 #include <petsc/private/dmpleximpl.h> /*I "petscdmplex.h" I*/ 2 #include <petsc/private/snesimpl.h> /*I "petscsnes.h" I*/ 3 #include <petscds.h> 4 #include <petscblaslapack.h> 5 #include <petsc/private/petscimpl.h> 6 #include <petsc/private/petscfeimpl.h> 7 8 /************************** Interpolation *******************************/ 9 10 static PetscErrorCode DMSNESConvertPlex(DM dm, DM *plex, PetscBool copy) 11 { 12 PetscBool isPlex; 13 PetscErrorCode ierr; 14 15 PetscFunctionBegin; 16 ierr = PetscObjectTypeCompare((PetscObject) dm, DMPLEX, &isPlex);CHKERRQ(ierr); 17 if (isPlex) { 18 *plex = dm; 19 ierr = PetscObjectReference((PetscObject) dm);CHKERRQ(ierr); 20 } else { 21 ierr = PetscObjectQuery((PetscObject) dm, "dm_plex", (PetscObject *) plex);CHKERRQ(ierr); 22 if (!*plex) { 23 ierr = DMConvert(dm,DMPLEX,plex);CHKERRQ(ierr); 24 ierr = PetscObjectCompose((PetscObject) dm, "dm_plex", (PetscObject) *plex);CHKERRQ(ierr); 25 if (copy) { 26 PetscInt i; 27 PetscObject obj; 28 const char *comps[3] = {"A","dmAux","dmCh"}; 29 30 ierr = DMCopyDMSNES(dm, *plex);CHKERRQ(ierr); 31 for (i = 0; i < 3; i++) { 32 ierr = PetscObjectQuery((PetscObject) dm, comps[i], &obj);CHKERRQ(ierr); 33 ierr = PetscObjectCompose((PetscObject) *plex, comps[i], obj);CHKERRQ(ierr); 34 } 35 } 36 } else { 37 ierr = PetscObjectReference((PetscObject) *plex);CHKERRQ(ierr); 38 } 39 } 40 PetscFunctionReturn(0); 41 } 42 43 /*@C 44 DMInterpolationCreate - Creates a DMInterpolationInfo context 45 46 Collective 47 48 Input Parameter: 49 . comm - the communicator 50 51 Output Parameter: 52 . ctx - the context 53 54 Level: beginner 55 56 .seealso: DMInterpolationEvaluate(), DMInterpolationAddPoints(), DMInterpolationDestroy() 57 @*/ 58 PetscErrorCode DMInterpolationCreate(MPI_Comm comm, DMInterpolationInfo *ctx) 59 { 60 PetscErrorCode ierr; 61 62 PetscFunctionBegin; 63 PetscValidPointer(ctx, 2); 64 ierr = PetscNew(ctx);CHKERRQ(ierr); 65 66 (*ctx)->comm = comm; 67 (*ctx)->dim = -1; 68 (*ctx)->nInput = 0; 69 (*ctx)->points = NULL; 70 (*ctx)->cells = NULL; 71 (*ctx)->n = -1; 72 (*ctx)->coords = NULL; 73 PetscFunctionReturn(0); 74 } 75 76 /*@C 77 DMInterpolationSetDim - Sets the spatial dimension for the interpolation context 78 79 Not collective 80 81 Input Parameters: 82 + ctx - the context 83 - dim - the spatial dimension 84 85 Level: intermediate 86 87 .seealso: DMInterpolationGetDim(), DMInterpolationEvaluate(), DMInterpolationAddPoints() 88 @*/ 89 PetscErrorCode DMInterpolationSetDim(DMInterpolationInfo ctx, PetscInt dim) 90 { 91 PetscFunctionBegin; 92 if ((dim < 1) || (dim > 3)) SETERRQ1(ctx->comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid dimension for points: %D", dim); 93 ctx->dim = dim; 94 PetscFunctionReturn(0); 95 } 96 97 /*@C 98 DMInterpolationGetDim - Gets the spatial dimension for the interpolation context 99 100 Not collective 101 102 Input Parameter: 103 . ctx - the context 104 105 Output Parameter: 106 . dim - the spatial dimension 107 108 Level: intermediate 109 110 .seealso: DMInterpolationSetDim(), DMInterpolationEvaluate(), DMInterpolationAddPoints() 111 @*/ 112 PetscErrorCode DMInterpolationGetDim(DMInterpolationInfo ctx, PetscInt *dim) 113 { 114 PetscFunctionBegin; 115 PetscValidIntPointer(dim, 2); 116 *dim = ctx->dim; 117 PetscFunctionReturn(0); 118 } 119 120 /*@C 121 DMInterpolationSetDof - Sets the number of fields interpolated at a point for the interpolation context 122 123 Not collective 124 125 Input Parameters: 126 + ctx - the context 127 - dof - the number of fields 128 129 Level: intermediate 130 131 .seealso: DMInterpolationGetDof(), DMInterpolationEvaluate(), DMInterpolationAddPoints() 132 @*/ 133 PetscErrorCode DMInterpolationSetDof(DMInterpolationInfo ctx, PetscInt dof) 134 { 135 PetscFunctionBegin; 136 if (dof < 1) SETERRQ1(ctx->comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid number of components: %D", dof); 137 ctx->dof = dof; 138 PetscFunctionReturn(0); 139 } 140 141 /*@C 142 DMInterpolationGetDof - Gets the number of fields interpolated at a point for the interpolation context 143 144 Not collective 145 146 Input Parameter: 147 . ctx - the context 148 149 Output Parameter: 150 . dof - the number of fields 151 152 Level: intermediate 153 154 .seealso: DMInterpolationSetDof(), DMInterpolationEvaluate(), DMInterpolationAddPoints() 155 @*/ 156 PetscErrorCode DMInterpolationGetDof(DMInterpolationInfo ctx, PetscInt *dof) 157 { 158 PetscFunctionBegin; 159 PetscValidIntPointer(dof, 2); 160 *dof = ctx->dof; 161 PetscFunctionReturn(0); 162 } 163 164 /*@C 165 DMInterpolationAddPoints - Add points at which we will interpolate the fields 166 167 Not collective 168 169 Input Parameters: 170 + ctx - the context 171 . n - the number of points 172 - points - the coordinates for each point, an array of size n * dim 173 174 Note: The coordinate information is copied. 175 176 Level: intermediate 177 178 .seealso: DMInterpolationSetDim(), DMInterpolationEvaluate(), DMInterpolationCreate() 179 @*/ 180 PetscErrorCode DMInterpolationAddPoints(DMInterpolationInfo ctx, PetscInt n, PetscReal points[]) 181 { 182 PetscErrorCode ierr; 183 184 PetscFunctionBegin; 185 if (ctx->dim < 0) SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONGSTATE, "The spatial dimension has not been set"); 186 if (ctx->points) SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONGSTATE, "Cannot add points multiple times yet"); 187 ctx->nInput = n; 188 189 ierr = PetscMalloc1(n*ctx->dim, &ctx->points);CHKERRQ(ierr); 190 ierr = PetscArraycpy(ctx->points, points, n*ctx->dim);CHKERRQ(ierr); 191 PetscFunctionReturn(0); 192 } 193 194 /*@C 195 DMInterpolationSetUp - Computea spatial indices that add in point location during interpolation 196 197 Collective on ctx 198 199 Input Parameters: 200 + ctx - the context 201 . dm - the DM for the function space used for interpolation 202 - redundantPoints - If PETSC_TRUE, all processes are passing in the same array of points. Otherwise, points need to be communicated among processes. 203 204 Level: intermediate 205 206 .seealso: DMInterpolationEvaluate(), DMInterpolationAddPoints(), DMInterpolationCreate() 207 @*/ 208 PetscErrorCode DMInterpolationSetUp(DMInterpolationInfo ctx, DM dm, PetscBool redundantPoints) 209 { 210 MPI_Comm comm = ctx->comm; 211 PetscScalar *a; 212 PetscInt p, q, i; 213 PetscMPIInt rank, size; 214 PetscErrorCode ierr; 215 Vec pointVec; 216 PetscSF cellSF; 217 PetscLayout layout; 218 PetscReal *globalPoints; 219 PetscScalar *globalPointsScalar; 220 const PetscInt *ranges; 221 PetscMPIInt *counts, *displs; 222 const PetscSFNode *foundCells; 223 const PetscInt *foundPoints; 224 PetscMPIInt *foundProcs, *globalProcs; 225 PetscInt n, N, numFound; 226 227 PetscFunctionBegin; 228 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 229 ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr); 230 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 231 if (ctx->dim < 0) SETERRQ(comm, PETSC_ERR_ARG_WRONGSTATE, "The spatial dimension has not been set"); 232 /* Locate points */ 233 n = ctx->nInput; 234 if (!redundantPoints) { 235 ierr = PetscLayoutCreate(comm, &layout);CHKERRQ(ierr); 236 ierr = PetscLayoutSetBlockSize(layout, 1);CHKERRQ(ierr); 237 ierr = PetscLayoutSetLocalSize(layout, n);CHKERRQ(ierr); 238 ierr = PetscLayoutSetUp(layout);CHKERRQ(ierr); 239 ierr = PetscLayoutGetSize(layout, &N);CHKERRQ(ierr); 240 /* Communicate all points to all processes */ 241 ierr = PetscMalloc3(N*ctx->dim,&globalPoints,size,&counts,size,&displs);CHKERRQ(ierr); 242 ierr = PetscLayoutGetRanges(layout, &ranges);CHKERRQ(ierr); 243 for (p = 0; p < size; ++p) { 244 counts[p] = (ranges[p+1] - ranges[p])*ctx->dim; 245 displs[p] = ranges[p]*ctx->dim; 246 } 247 ierr = MPI_Allgatherv(ctx->points, n*ctx->dim, MPIU_REAL, globalPoints, counts, displs, MPIU_REAL, comm);CHKERRQ(ierr); 248 } else { 249 N = n; 250 globalPoints = ctx->points; 251 counts = displs = NULL; 252 layout = NULL; 253 } 254 #if 0 255 ierr = PetscMalloc3(N,&foundCells,N,&foundProcs,N,&globalProcs);CHKERRQ(ierr); 256 /* foundCells[p] = m->locatePoint(&globalPoints[p*ctx->dim]); */ 257 #else 258 #if defined(PETSC_USE_COMPLEX) 259 ierr = PetscMalloc1(N*ctx->dim,&globalPointsScalar);CHKERRQ(ierr); 260 for (i=0; i<N*ctx->dim; i++) globalPointsScalar[i] = globalPoints[i]; 261 #else 262 globalPointsScalar = globalPoints; 263 #endif 264 ierr = VecCreateSeqWithArray(PETSC_COMM_SELF, ctx->dim, N*ctx->dim, globalPointsScalar, &pointVec);CHKERRQ(ierr); 265 ierr = PetscMalloc2(N,&foundProcs,N,&globalProcs);CHKERRQ(ierr); 266 for (p = 0; p < N; ++p) {foundProcs[p] = size;} 267 cellSF = NULL; 268 ierr = DMLocatePoints(dm, pointVec, DM_POINTLOCATION_REMOVE, &cellSF);CHKERRQ(ierr); 269 ierr = PetscSFGetGraph(cellSF,NULL,&numFound,&foundPoints,&foundCells);CHKERRQ(ierr); 270 #endif 271 for (p = 0; p < numFound; ++p) { 272 if (foundCells[p].index >= 0) foundProcs[foundPoints ? foundPoints[p] : p] = rank; 273 } 274 /* Let the lowest rank process own each point */ 275 ierr = MPIU_Allreduce(foundProcs, globalProcs, N, MPI_INT, MPI_MIN, comm);CHKERRQ(ierr); 276 ctx->n = 0; 277 for (p = 0; p < N; ++p) { 278 if (globalProcs[p] == size) SETERRQ4(comm, PETSC_ERR_PLIB, "Point %d: %g %g %g not located in mesh", p, (double)globalPoints[p*ctx->dim+0], (double)(ctx->dim > 1 ? globalPoints[p*ctx->dim+1] : 0.0), (double)(ctx->dim > 2 ? globalPoints[p*ctx->dim+2] : 0.0)); 279 else if (globalProcs[p] == rank) ctx->n++; 280 } 281 /* Create coordinates vector and array of owned cells */ 282 ierr = PetscMalloc1(ctx->n, &ctx->cells);CHKERRQ(ierr); 283 ierr = VecCreate(comm, &ctx->coords);CHKERRQ(ierr); 284 ierr = VecSetSizes(ctx->coords, ctx->n*ctx->dim, PETSC_DECIDE);CHKERRQ(ierr); 285 ierr = VecSetBlockSize(ctx->coords, ctx->dim);CHKERRQ(ierr); 286 ierr = VecSetType(ctx->coords,VECSTANDARD);CHKERRQ(ierr); 287 ierr = VecGetArray(ctx->coords, &a);CHKERRQ(ierr); 288 for (p = 0, q = 0, i = 0; p < N; ++p) { 289 if (globalProcs[p] == rank) { 290 PetscInt d; 291 292 for (d = 0; d < ctx->dim; ++d, ++i) a[i] = globalPoints[p*ctx->dim+d]; 293 ctx->cells[q] = foundCells[q].index; 294 ++q; 295 } 296 } 297 ierr = VecRestoreArray(ctx->coords, &a);CHKERRQ(ierr); 298 #if 0 299 ierr = PetscFree3(foundCells,foundProcs,globalProcs);CHKERRQ(ierr); 300 #else 301 ierr = PetscFree2(foundProcs,globalProcs);CHKERRQ(ierr); 302 ierr = PetscSFDestroy(&cellSF);CHKERRQ(ierr); 303 ierr = VecDestroy(&pointVec);CHKERRQ(ierr); 304 #endif 305 if ((void*)globalPointsScalar != (void*)globalPoints) {ierr = PetscFree(globalPointsScalar);CHKERRQ(ierr);} 306 if (!redundantPoints) {ierr = PetscFree3(globalPoints,counts,displs);CHKERRQ(ierr);} 307 ierr = PetscLayoutDestroy(&layout);CHKERRQ(ierr); 308 PetscFunctionReturn(0); 309 } 310 311 /*@C 312 DMInterpolationGetCoordinates - Gets a Vec with the coordinates of each interpolation point 313 314 Collective on ctx 315 316 Input Parameter: 317 . ctx - the context 318 319 Output Parameter: 320 . coordinates - the coordinates of interpolation points 321 322 Note: The local vector entries correspond to interpolation points lying on this process, according to the associated DM. This is a borrowed vector that the user should not destroy. 323 324 Level: intermediate 325 326 .seealso: DMInterpolationEvaluate(), DMInterpolationAddPoints(), DMInterpolationCreate() 327 @*/ 328 PetscErrorCode DMInterpolationGetCoordinates(DMInterpolationInfo ctx, Vec *coordinates) 329 { 330 PetscFunctionBegin; 331 PetscValidPointer(coordinates, 2); 332 if (!ctx->coords) SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONGSTATE, "The interpolation context has not been setup."); 333 *coordinates = ctx->coords; 334 PetscFunctionReturn(0); 335 } 336 337 /*@C 338 DMInterpolationGetVector - Gets a Vec which can hold all the interpolated field values 339 340 Collective on ctx 341 342 Input Parameter: 343 . ctx - the context 344 345 Output Parameter: 346 . v - a vector capable of holding the interpolated field values 347 348 Note: This vector should be returned using DMInterpolationRestoreVector(). 349 350 Level: intermediate 351 352 .seealso: DMInterpolationRestoreVector(), DMInterpolationEvaluate(), DMInterpolationAddPoints(), DMInterpolationCreate() 353 @*/ 354 PetscErrorCode DMInterpolationGetVector(DMInterpolationInfo ctx, Vec *v) 355 { 356 PetscErrorCode ierr; 357 358 PetscFunctionBegin; 359 PetscValidPointer(v, 2); 360 if (!ctx->coords) SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONGSTATE, "The interpolation context has not been setup."); 361 ierr = VecCreate(ctx->comm, v);CHKERRQ(ierr); 362 ierr = VecSetSizes(*v, ctx->n*ctx->dof, PETSC_DECIDE);CHKERRQ(ierr); 363 ierr = VecSetBlockSize(*v, ctx->dof);CHKERRQ(ierr); 364 ierr = VecSetType(*v,VECSTANDARD);CHKERRQ(ierr); 365 PetscFunctionReturn(0); 366 } 367 368 /*@C 369 DMInterpolationRestoreVector - Returns a Vec which can hold all the interpolated field values 370 371 Collective on ctx 372 373 Input Parameters: 374 + ctx - the context 375 - v - a vector capable of holding the interpolated field values 376 377 Level: intermediate 378 379 .seealso: DMInterpolationGetVector(), DMInterpolationEvaluate(), DMInterpolationAddPoints(), DMInterpolationCreate() 380 @*/ 381 PetscErrorCode DMInterpolationRestoreVector(DMInterpolationInfo ctx, Vec *v) 382 { 383 PetscErrorCode ierr; 384 385 PetscFunctionBegin; 386 PetscValidPointer(v, 2); 387 if (!ctx->coords) SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONGSTATE, "The interpolation context has not been setup."); 388 ierr = VecDestroy(v);CHKERRQ(ierr); 389 PetscFunctionReturn(0); 390 } 391 392 PETSC_STATIC_INLINE PetscErrorCode DMInterpolate_Triangle_Private(DMInterpolationInfo ctx, DM dm, Vec xLocal, Vec v) 393 { 394 PetscReal *v0, *J, *invJ, detJ; 395 const PetscScalar *coords; 396 PetscScalar *a; 397 PetscInt p; 398 PetscErrorCode ierr; 399 400 PetscFunctionBegin; 401 ierr = PetscMalloc3(ctx->dim,&v0,ctx->dim*ctx->dim,&J,ctx->dim*ctx->dim,&invJ);CHKERRQ(ierr); 402 ierr = VecGetArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 403 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 404 for (p = 0; p < ctx->n; ++p) { 405 PetscInt c = ctx->cells[p]; 406 PetscScalar *x = NULL; 407 PetscReal xi[4]; 408 PetscInt d, f, comp; 409 410 ierr = DMPlexComputeCellGeometryFEM(dm, c, NULL, v0, J, invJ, &detJ);CHKERRQ(ierr); 411 if (detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %D", (double)detJ, c); 412 ierr = DMPlexVecGetClosure(dm, NULL, xLocal, c, NULL, &x);CHKERRQ(ierr); 413 for (comp = 0; comp < ctx->dof; ++comp) a[p*ctx->dof+comp] = x[0*ctx->dof+comp]; 414 415 for (d = 0; d < ctx->dim; ++d) { 416 xi[d] = 0.0; 417 for (f = 0; f < ctx->dim; ++f) xi[d] += invJ[d*ctx->dim+f]*0.5*PetscRealPart(coords[p*ctx->dim+f] - v0[f]); 418 for (comp = 0; comp < ctx->dof; ++comp) a[p*ctx->dof+comp] += PetscRealPart(x[(d+1)*ctx->dof+comp] - x[0*ctx->dof+comp])*xi[d]; 419 } 420 ierr = DMPlexVecRestoreClosure(dm, NULL, xLocal, c, NULL, &x);CHKERRQ(ierr); 421 } 422 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 423 ierr = VecRestoreArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 424 ierr = PetscFree3(v0, J, invJ);CHKERRQ(ierr); 425 PetscFunctionReturn(0); 426 } 427 428 PETSC_STATIC_INLINE PetscErrorCode DMInterpolate_Tetrahedron_Private(DMInterpolationInfo ctx, DM dm, Vec xLocal, Vec v) 429 { 430 PetscReal *v0, *J, *invJ, detJ; 431 const PetscScalar *coords; 432 PetscScalar *a; 433 PetscInt p; 434 PetscErrorCode ierr; 435 436 PetscFunctionBegin; 437 ierr = PetscMalloc3(ctx->dim,&v0,ctx->dim*ctx->dim,&J,ctx->dim*ctx->dim,&invJ);CHKERRQ(ierr); 438 ierr = VecGetArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 439 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 440 for (p = 0; p < ctx->n; ++p) { 441 PetscInt c = ctx->cells[p]; 442 const PetscInt order[3] = {2, 1, 3}; 443 PetscScalar *x = NULL; 444 PetscReal xi[4]; 445 PetscInt d, f, comp; 446 447 ierr = DMPlexComputeCellGeometryFEM(dm, c, NULL, v0, J, invJ, &detJ);CHKERRQ(ierr); 448 if (detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %D", (double)detJ, c); 449 ierr = DMPlexVecGetClosure(dm, NULL, xLocal, c, NULL, &x);CHKERRQ(ierr); 450 for (comp = 0; comp < ctx->dof; ++comp) a[p*ctx->dof+comp] = x[0*ctx->dof+comp]; 451 452 for (d = 0; d < ctx->dim; ++d) { 453 xi[d] = 0.0; 454 for (f = 0; f < ctx->dim; ++f) xi[d] += invJ[d*ctx->dim+f]*0.5*PetscRealPart(coords[p*ctx->dim+f] - v0[f]); 455 for (comp = 0; comp < ctx->dof; ++comp) a[p*ctx->dof+comp] += PetscRealPart(x[order[d]*ctx->dof+comp] - x[0*ctx->dof+comp])*xi[d]; 456 } 457 ierr = DMPlexVecRestoreClosure(dm, NULL, xLocal, c, NULL, &x);CHKERRQ(ierr); 458 } 459 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 460 ierr = VecRestoreArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 461 ierr = PetscFree3(v0, J, invJ);CHKERRQ(ierr); 462 PetscFunctionReturn(0); 463 } 464 465 PETSC_STATIC_INLINE PetscErrorCode QuadMap_Private(SNES snes, Vec Xref, Vec Xreal, void *ctx) 466 { 467 const PetscScalar *vertices = (const PetscScalar*) ctx; 468 const PetscScalar x0 = vertices[0]; 469 const PetscScalar y0 = vertices[1]; 470 const PetscScalar x1 = vertices[2]; 471 const PetscScalar y1 = vertices[3]; 472 const PetscScalar x2 = vertices[4]; 473 const PetscScalar y2 = vertices[5]; 474 const PetscScalar x3 = vertices[6]; 475 const PetscScalar y3 = vertices[7]; 476 const PetscScalar f_1 = x1 - x0; 477 const PetscScalar g_1 = y1 - y0; 478 const PetscScalar f_3 = x3 - x0; 479 const PetscScalar g_3 = y3 - y0; 480 const PetscScalar f_01 = x2 - x1 - x3 + x0; 481 const PetscScalar g_01 = y2 - y1 - y3 + y0; 482 const PetscScalar *ref; 483 PetscScalar *real; 484 PetscErrorCode ierr; 485 486 PetscFunctionBegin; 487 ierr = VecGetArrayRead(Xref, &ref);CHKERRQ(ierr); 488 ierr = VecGetArray(Xreal, &real);CHKERRQ(ierr); 489 { 490 const PetscScalar p0 = ref[0]; 491 const PetscScalar p1 = ref[1]; 492 493 real[0] = x0 + f_1 * p0 + f_3 * p1 + f_01 * p0 * p1; 494 real[1] = y0 + g_1 * p0 + g_3 * p1 + g_01 * p0 * p1; 495 } 496 ierr = PetscLogFlops(28);CHKERRQ(ierr); 497 ierr = VecRestoreArrayRead(Xref, &ref);CHKERRQ(ierr); 498 ierr = VecRestoreArray(Xreal, &real);CHKERRQ(ierr); 499 PetscFunctionReturn(0); 500 } 501 502 #include <petsc/private/dmimpl.h> 503 PETSC_STATIC_INLINE PetscErrorCode QuadJacobian_Private(SNES snes, Vec Xref, Mat J, Mat M, void *ctx) 504 { 505 const PetscScalar *vertices = (const PetscScalar*) ctx; 506 const PetscScalar x0 = vertices[0]; 507 const PetscScalar y0 = vertices[1]; 508 const PetscScalar x1 = vertices[2]; 509 const PetscScalar y1 = vertices[3]; 510 const PetscScalar x2 = vertices[4]; 511 const PetscScalar y2 = vertices[5]; 512 const PetscScalar x3 = vertices[6]; 513 const PetscScalar y3 = vertices[7]; 514 const PetscScalar f_01 = x2 - x1 - x3 + x0; 515 const PetscScalar g_01 = y2 - y1 - y3 + y0; 516 const PetscScalar *ref; 517 PetscErrorCode ierr; 518 519 PetscFunctionBegin; 520 ierr = VecGetArrayRead(Xref, &ref);CHKERRQ(ierr); 521 { 522 const PetscScalar x = ref[0]; 523 const PetscScalar y = ref[1]; 524 const PetscInt rows[2] = {0, 1}; 525 PetscScalar values[4]; 526 527 values[0] = (x1 - x0 + f_01*y) * 0.5; values[1] = (x3 - x0 + f_01*x) * 0.5; 528 values[2] = (y1 - y0 + g_01*y) * 0.5; values[3] = (y3 - y0 + g_01*x) * 0.5; 529 ierr = MatSetValues(J, 2, rows, 2, rows, values, INSERT_VALUES);CHKERRQ(ierr); 530 } 531 ierr = PetscLogFlops(30);CHKERRQ(ierr); 532 ierr = VecRestoreArrayRead(Xref, &ref);CHKERRQ(ierr); 533 ierr = MatAssemblyBegin(J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 534 ierr = MatAssemblyEnd(J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 535 PetscFunctionReturn(0); 536 } 537 538 PETSC_STATIC_INLINE PetscErrorCode DMInterpolate_Quad_Private(DMInterpolationInfo ctx, DM dm, Vec xLocal, Vec v) 539 { 540 DM dmCoord; 541 PetscFE fem = NULL; 542 SNES snes; 543 KSP ksp; 544 PC pc; 545 Vec coordsLocal, r, ref, real; 546 Mat J; 547 PetscTabulation T; 548 const PetscScalar *coords; 549 PetscScalar *a; 550 PetscReal xir[2]; 551 PetscInt Nf, p; 552 const PetscInt dof = ctx->dof; 553 PetscErrorCode ierr; 554 555 PetscFunctionBegin; 556 ierr = DMGetNumFields(dm, &Nf);CHKERRQ(ierr); 557 if (Nf) {ierr = DMGetField(dm, 0, NULL, (PetscObject *) &fem);CHKERRQ(ierr);} 558 ierr = DMGetCoordinatesLocal(dm, &coordsLocal);CHKERRQ(ierr); 559 ierr = DMGetCoordinateDM(dm, &dmCoord);CHKERRQ(ierr); 560 ierr = SNESCreate(PETSC_COMM_SELF, &snes);CHKERRQ(ierr); 561 ierr = SNESSetOptionsPrefix(snes, "quad_interp_");CHKERRQ(ierr); 562 ierr = VecCreate(PETSC_COMM_SELF, &r);CHKERRQ(ierr); 563 ierr = VecSetSizes(r, 2, 2);CHKERRQ(ierr); 564 ierr = VecSetType(r,dm->vectype);CHKERRQ(ierr); 565 ierr = VecDuplicate(r, &ref);CHKERRQ(ierr); 566 ierr = VecDuplicate(r, &real);CHKERRQ(ierr); 567 ierr = MatCreate(PETSC_COMM_SELF, &J);CHKERRQ(ierr); 568 ierr = MatSetSizes(J, 2, 2, 2, 2);CHKERRQ(ierr); 569 ierr = MatSetType(J, MATSEQDENSE);CHKERRQ(ierr); 570 ierr = MatSetUp(J);CHKERRQ(ierr); 571 ierr = SNESSetFunction(snes, r, QuadMap_Private, NULL);CHKERRQ(ierr); 572 ierr = SNESSetJacobian(snes, J, J, QuadJacobian_Private, NULL);CHKERRQ(ierr); 573 ierr = SNESGetKSP(snes, &ksp);CHKERRQ(ierr); 574 ierr = KSPGetPC(ksp, &pc);CHKERRQ(ierr); 575 ierr = PCSetType(pc, PCLU);CHKERRQ(ierr); 576 ierr = SNESSetFromOptions(snes);CHKERRQ(ierr); 577 578 ierr = VecGetArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 579 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 580 ierr = PetscFECreateTabulation(fem, 1, 1, xir, 0, &T);CHKERRQ(ierr); 581 for (p = 0; p < ctx->n; ++p) { 582 PetscScalar *x = NULL, *vertices = NULL; 583 PetscScalar *xi; 584 PetscInt c = ctx->cells[p], comp, coordSize, xSize; 585 586 /* Can make this do all points at once */ 587 ierr = DMPlexVecGetClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);CHKERRQ(ierr); 588 if (4*2 != coordSize) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid closure size %D should be %d", coordSize, 4*2); 589 ierr = DMPlexVecGetClosure(dm, NULL, xLocal, c, &xSize, &x);CHKERRQ(ierr); 590 ierr = SNESSetFunction(snes, NULL, NULL, (void*) vertices);CHKERRQ(ierr); 591 ierr = SNESSetJacobian(snes, NULL, NULL, NULL, (void*) vertices);CHKERRQ(ierr); 592 ierr = VecGetArray(real, &xi);CHKERRQ(ierr); 593 xi[0] = coords[p*ctx->dim+0]; 594 xi[1] = coords[p*ctx->dim+1]; 595 ierr = VecRestoreArray(real, &xi);CHKERRQ(ierr); 596 ierr = SNESSolve(snes, real, ref);CHKERRQ(ierr); 597 ierr = VecGetArray(ref, &xi);CHKERRQ(ierr); 598 xir[0] = PetscRealPart(xi[0]); 599 xir[1] = PetscRealPart(xi[1]); 600 if (4*dof != xSize) { 601 PetscInt d; 602 603 xir[0] = 2.0*xir[0] - 1.0; xir[1] = 2.0*xir[1] - 1.0; 604 ierr = PetscFEComputeTabulation(fem, 1, xir, 0, T);CHKERRQ(ierr); 605 for (comp = 0; comp < dof; ++comp) { 606 a[p*dof+comp] = 0.0; 607 for (d = 0; d < xSize/dof; ++d) { 608 a[p*dof+comp] += x[d*dof+comp]*T->T[0][d*dof+comp]; 609 } 610 } 611 } else { 612 for (comp = 0; comp < dof; ++comp) 613 a[p*dof+comp] = x[0*dof+comp]*(1 - xir[0])*(1 - xir[1]) + x[1*dof+comp]*xir[0]*(1 - xir[1]) + x[2*dof+comp]*xir[0]*xir[1] + x[3*dof+comp]*(1 - xir[0])*xir[1]; 614 } 615 ierr = VecRestoreArray(ref, &xi);CHKERRQ(ierr); 616 ierr = DMPlexVecRestoreClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);CHKERRQ(ierr); 617 ierr = DMPlexVecRestoreClosure(dm, NULL, xLocal, c, &xSize, &x);CHKERRQ(ierr); 618 } 619 ierr = PetscTabulationDestroy(&T);CHKERRQ(ierr); 620 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 621 ierr = VecRestoreArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 622 623 ierr = SNESDestroy(&snes);CHKERRQ(ierr); 624 ierr = VecDestroy(&r);CHKERRQ(ierr); 625 ierr = VecDestroy(&ref);CHKERRQ(ierr); 626 ierr = VecDestroy(&real);CHKERRQ(ierr); 627 ierr = MatDestroy(&J);CHKERRQ(ierr); 628 PetscFunctionReturn(0); 629 } 630 631 PETSC_STATIC_INLINE PetscErrorCode HexMap_Private(SNES snes, Vec Xref, Vec Xreal, void *ctx) 632 { 633 const PetscScalar *vertices = (const PetscScalar*) ctx; 634 const PetscScalar x0 = vertices[0]; 635 const PetscScalar y0 = vertices[1]; 636 const PetscScalar z0 = vertices[2]; 637 const PetscScalar x1 = vertices[9]; 638 const PetscScalar y1 = vertices[10]; 639 const PetscScalar z1 = vertices[11]; 640 const PetscScalar x2 = vertices[6]; 641 const PetscScalar y2 = vertices[7]; 642 const PetscScalar z2 = vertices[8]; 643 const PetscScalar x3 = vertices[3]; 644 const PetscScalar y3 = vertices[4]; 645 const PetscScalar z3 = vertices[5]; 646 const PetscScalar x4 = vertices[12]; 647 const PetscScalar y4 = vertices[13]; 648 const PetscScalar z4 = vertices[14]; 649 const PetscScalar x5 = vertices[15]; 650 const PetscScalar y5 = vertices[16]; 651 const PetscScalar z5 = vertices[17]; 652 const PetscScalar x6 = vertices[18]; 653 const PetscScalar y6 = vertices[19]; 654 const PetscScalar z6 = vertices[20]; 655 const PetscScalar x7 = vertices[21]; 656 const PetscScalar y7 = vertices[22]; 657 const PetscScalar z7 = vertices[23]; 658 const PetscScalar f_1 = x1 - x0; 659 const PetscScalar g_1 = y1 - y0; 660 const PetscScalar h_1 = z1 - z0; 661 const PetscScalar f_3 = x3 - x0; 662 const PetscScalar g_3 = y3 - y0; 663 const PetscScalar h_3 = z3 - z0; 664 const PetscScalar f_4 = x4 - x0; 665 const PetscScalar g_4 = y4 - y0; 666 const PetscScalar h_4 = z4 - z0; 667 const PetscScalar f_01 = x2 - x1 - x3 + x0; 668 const PetscScalar g_01 = y2 - y1 - y3 + y0; 669 const PetscScalar h_01 = z2 - z1 - z3 + z0; 670 const PetscScalar f_12 = x7 - x3 - x4 + x0; 671 const PetscScalar g_12 = y7 - y3 - y4 + y0; 672 const PetscScalar h_12 = z7 - z3 - z4 + z0; 673 const PetscScalar f_02 = x5 - x1 - x4 + x0; 674 const PetscScalar g_02 = y5 - y1 - y4 + y0; 675 const PetscScalar h_02 = z5 - z1 - z4 + z0; 676 const PetscScalar f_012 = x6 - x0 + x1 - x2 + x3 + x4 - x5 - x7; 677 const PetscScalar g_012 = y6 - y0 + y1 - y2 + y3 + y4 - y5 - y7; 678 const PetscScalar h_012 = z6 - z0 + z1 - z2 + z3 + z4 - z5 - z7; 679 const PetscScalar *ref; 680 PetscScalar *real; 681 PetscErrorCode ierr; 682 683 PetscFunctionBegin; 684 ierr = VecGetArrayRead(Xref, &ref);CHKERRQ(ierr); 685 ierr = VecGetArray(Xreal, &real);CHKERRQ(ierr); 686 { 687 const PetscScalar p0 = ref[0]; 688 const PetscScalar p1 = ref[1]; 689 const PetscScalar p2 = ref[2]; 690 691 real[0] = x0 + f_1*p0 + f_3*p1 + f_4*p2 + f_01*p0*p1 + f_12*p1*p2 + f_02*p0*p2 + f_012*p0*p1*p2; 692 real[1] = y0 + g_1*p0 + g_3*p1 + g_4*p2 + g_01*p0*p1 + g_01*p0*p1 + g_12*p1*p2 + g_02*p0*p2 + g_012*p0*p1*p2; 693 real[2] = z0 + h_1*p0 + h_3*p1 + h_4*p2 + h_01*p0*p1 + h_01*p0*p1 + h_12*p1*p2 + h_02*p0*p2 + h_012*p0*p1*p2; 694 } 695 ierr = PetscLogFlops(114);CHKERRQ(ierr); 696 ierr = VecRestoreArrayRead(Xref, &ref);CHKERRQ(ierr); 697 ierr = VecRestoreArray(Xreal, &real);CHKERRQ(ierr); 698 PetscFunctionReturn(0); 699 } 700 701 PETSC_STATIC_INLINE PetscErrorCode HexJacobian_Private(SNES snes, Vec Xref, Mat J, Mat M, void *ctx) 702 { 703 const PetscScalar *vertices = (const PetscScalar*) ctx; 704 const PetscScalar x0 = vertices[0]; 705 const PetscScalar y0 = vertices[1]; 706 const PetscScalar z0 = vertices[2]; 707 const PetscScalar x1 = vertices[9]; 708 const PetscScalar y1 = vertices[10]; 709 const PetscScalar z1 = vertices[11]; 710 const PetscScalar x2 = vertices[6]; 711 const PetscScalar y2 = vertices[7]; 712 const PetscScalar z2 = vertices[8]; 713 const PetscScalar x3 = vertices[3]; 714 const PetscScalar y3 = vertices[4]; 715 const PetscScalar z3 = vertices[5]; 716 const PetscScalar x4 = vertices[12]; 717 const PetscScalar y4 = vertices[13]; 718 const PetscScalar z4 = vertices[14]; 719 const PetscScalar x5 = vertices[15]; 720 const PetscScalar y5 = vertices[16]; 721 const PetscScalar z5 = vertices[17]; 722 const PetscScalar x6 = vertices[18]; 723 const PetscScalar y6 = vertices[19]; 724 const PetscScalar z6 = vertices[20]; 725 const PetscScalar x7 = vertices[21]; 726 const PetscScalar y7 = vertices[22]; 727 const PetscScalar z7 = vertices[23]; 728 const PetscScalar f_xy = x2 - x1 - x3 + x0; 729 const PetscScalar g_xy = y2 - y1 - y3 + y0; 730 const PetscScalar h_xy = z2 - z1 - z3 + z0; 731 const PetscScalar f_yz = x7 - x3 - x4 + x0; 732 const PetscScalar g_yz = y7 - y3 - y4 + y0; 733 const PetscScalar h_yz = z7 - z3 - z4 + z0; 734 const PetscScalar f_xz = x5 - x1 - x4 + x0; 735 const PetscScalar g_xz = y5 - y1 - y4 + y0; 736 const PetscScalar h_xz = z5 - z1 - z4 + z0; 737 const PetscScalar f_xyz = x6 - x0 + x1 - x2 + x3 + x4 - x5 - x7; 738 const PetscScalar g_xyz = y6 - y0 + y1 - y2 + y3 + y4 - y5 - y7; 739 const PetscScalar h_xyz = z6 - z0 + z1 - z2 + z3 + z4 - z5 - z7; 740 const PetscScalar *ref; 741 PetscErrorCode ierr; 742 743 PetscFunctionBegin; 744 ierr = VecGetArrayRead(Xref, &ref);CHKERRQ(ierr); 745 { 746 const PetscScalar x = ref[0]; 747 const PetscScalar y = ref[1]; 748 const PetscScalar z = ref[2]; 749 const PetscInt rows[3] = {0, 1, 2}; 750 PetscScalar values[9]; 751 752 values[0] = (x1 - x0 + f_xy*y + f_xz*z + f_xyz*y*z) / 2.0; 753 values[1] = (x3 - x0 + f_xy*x + f_yz*z + f_xyz*x*z) / 2.0; 754 values[2] = (x4 - x0 + f_yz*y + f_xz*x + f_xyz*x*y) / 2.0; 755 values[3] = (y1 - y0 + g_xy*y + g_xz*z + g_xyz*y*z) / 2.0; 756 values[4] = (y3 - y0 + g_xy*x + g_yz*z + g_xyz*x*z) / 2.0; 757 values[5] = (y4 - y0 + g_yz*y + g_xz*x + g_xyz*x*y) / 2.0; 758 values[6] = (z1 - z0 + h_xy*y + h_xz*z + h_xyz*y*z) / 2.0; 759 values[7] = (z3 - z0 + h_xy*x + h_yz*z + h_xyz*x*z) / 2.0; 760 values[8] = (z4 - z0 + h_yz*y + h_xz*x + h_xyz*x*y) / 2.0; 761 762 ierr = MatSetValues(J, 3, rows, 3, rows, values, INSERT_VALUES);CHKERRQ(ierr); 763 } 764 ierr = PetscLogFlops(152);CHKERRQ(ierr); 765 ierr = VecRestoreArrayRead(Xref, &ref);CHKERRQ(ierr); 766 ierr = MatAssemblyBegin(J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 767 ierr = MatAssemblyEnd(J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 768 PetscFunctionReturn(0); 769 } 770 771 PETSC_STATIC_INLINE PetscErrorCode DMInterpolate_Hex_Private(DMInterpolationInfo ctx, DM dm, Vec xLocal, Vec v) 772 { 773 DM dmCoord; 774 SNES snes; 775 KSP ksp; 776 PC pc; 777 Vec coordsLocal, r, ref, real; 778 Mat J; 779 const PetscScalar *coords; 780 PetscScalar *a; 781 PetscInt p; 782 PetscErrorCode ierr; 783 784 PetscFunctionBegin; 785 ierr = DMGetCoordinatesLocal(dm, &coordsLocal);CHKERRQ(ierr); 786 ierr = DMGetCoordinateDM(dm, &dmCoord);CHKERRQ(ierr); 787 ierr = SNESCreate(PETSC_COMM_SELF, &snes);CHKERRQ(ierr); 788 ierr = SNESSetOptionsPrefix(snes, "hex_interp_");CHKERRQ(ierr); 789 ierr = VecCreate(PETSC_COMM_SELF, &r);CHKERRQ(ierr); 790 ierr = VecSetSizes(r, 3, 3);CHKERRQ(ierr); 791 ierr = VecSetType(r,dm->vectype);CHKERRQ(ierr); 792 ierr = VecDuplicate(r, &ref);CHKERRQ(ierr); 793 ierr = VecDuplicate(r, &real);CHKERRQ(ierr); 794 ierr = MatCreate(PETSC_COMM_SELF, &J);CHKERRQ(ierr); 795 ierr = MatSetSizes(J, 3, 3, 3, 3);CHKERRQ(ierr); 796 ierr = MatSetType(J, MATSEQDENSE);CHKERRQ(ierr); 797 ierr = MatSetUp(J);CHKERRQ(ierr); 798 ierr = SNESSetFunction(snes, r, HexMap_Private, NULL);CHKERRQ(ierr); 799 ierr = SNESSetJacobian(snes, J, J, HexJacobian_Private, NULL);CHKERRQ(ierr); 800 ierr = SNESGetKSP(snes, &ksp);CHKERRQ(ierr); 801 ierr = KSPGetPC(ksp, &pc);CHKERRQ(ierr); 802 ierr = PCSetType(pc, PCLU);CHKERRQ(ierr); 803 ierr = SNESSetFromOptions(snes);CHKERRQ(ierr); 804 805 ierr = VecGetArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 806 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 807 for (p = 0; p < ctx->n; ++p) { 808 PetscScalar *x = NULL, *vertices = NULL; 809 PetscScalar *xi; 810 PetscReal xir[3]; 811 PetscInt c = ctx->cells[p], comp, coordSize, xSize; 812 813 /* Can make this do all points at once */ 814 ierr = DMPlexVecGetClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);CHKERRQ(ierr); 815 if (8*3 != coordSize) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid closure size %D should be %d", coordSize, 8*3); 816 ierr = DMPlexVecGetClosure(dm, NULL, xLocal, c, &xSize, &x);CHKERRQ(ierr); 817 if (8*ctx->dof != xSize) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid closure size %D should be %D", xSize, 8*ctx->dof); 818 ierr = SNESSetFunction(snes, NULL, NULL, (void*) vertices);CHKERRQ(ierr); 819 ierr = SNESSetJacobian(snes, NULL, NULL, NULL, (void*) vertices);CHKERRQ(ierr); 820 ierr = VecGetArray(real, &xi);CHKERRQ(ierr); 821 xi[0] = coords[p*ctx->dim+0]; 822 xi[1] = coords[p*ctx->dim+1]; 823 xi[2] = coords[p*ctx->dim+2]; 824 ierr = VecRestoreArray(real, &xi);CHKERRQ(ierr); 825 ierr = SNESSolve(snes, real, ref);CHKERRQ(ierr); 826 ierr = VecGetArray(ref, &xi);CHKERRQ(ierr); 827 xir[0] = PetscRealPart(xi[0]); 828 xir[1] = PetscRealPart(xi[1]); 829 xir[2] = PetscRealPart(xi[2]); 830 for (comp = 0; comp < ctx->dof; ++comp) { 831 a[p*ctx->dof+comp] = 832 x[0*ctx->dof+comp]*(1-xir[0])*(1-xir[1])*(1-xir[2]) + 833 x[3*ctx->dof+comp]* xir[0]*(1-xir[1])*(1-xir[2]) + 834 x[2*ctx->dof+comp]* xir[0]* xir[1]*(1-xir[2]) + 835 x[1*ctx->dof+comp]*(1-xir[0])* xir[1]*(1-xir[2]) + 836 x[4*ctx->dof+comp]*(1-xir[0])*(1-xir[1])* xir[2] + 837 x[5*ctx->dof+comp]* xir[0]*(1-xir[1])* xir[2] + 838 x[6*ctx->dof+comp]* xir[0]* xir[1]* xir[2] + 839 x[7*ctx->dof+comp]*(1-xir[0])* xir[1]* xir[2]; 840 } 841 ierr = VecRestoreArray(ref, &xi);CHKERRQ(ierr); 842 ierr = DMPlexVecRestoreClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);CHKERRQ(ierr); 843 ierr = DMPlexVecRestoreClosure(dm, NULL, xLocal, c, &xSize, &x);CHKERRQ(ierr); 844 } 845 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 846 ierr = VecRestoreArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 847 848 ierr = SNESDestroy(&snes);CHKERRQ(ierr); 849 ierr = VecDestroy(&r);CHKERRQ(ierr); 850 ierr = VecDestroy(&ref);CHKERRQ(ierr); 851 ierr = VecDestroy(&real);CHKERRQ(ierr); 852 ierr = MatDestroy(&J);CHKERRQ(ierr); 853 PetscFunctionReturn(0); 854 } 855 856 /*@C 857 DMInterpolationEvaluate - Using the input from dm and x, calculates interpolated field values at the interpolation points. 858 859 Input Parameters: 860 + ctx - The DMInterpolationInfo context 861 . dm - The DM 862 - x - The local vector containing the field to be interpolated 863 864 Output Parameters: 865 . v - The vector containing the interpolated values 866 867 Note: A suitable v can be obtained using DMInterpolationGetVector(). 868 869 Level: beginner 870 871 .seealso: DMInterpolationGetVector(), DMInterpolationAddPoints(), DMInterpolationCreate() 872 @*/ 873 PetscErrorCode DMInterpolationEvaluate(DMInterpolationInfo ctx, DM dm, Vec x, Vec v) 874 { 875 PetscInt dim, coneSize, n; 876 PetscErrorCode ierr; 877 878 PetscFunctionBegin; 879 PetscValidHeaderSpecific(dm, DM_CLASSID, 2); 880 PetscValidHeaderSpecific(x, VEC_CLASSID, 3); 881 PetscValidHeaderSpecific(v, VEC_CLASSID, 4); 882 ierr = VecGetLocalSize(v, &n);CHKERRQ(ierr); 883 if (n != ctx->n*ctx->dof) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid input vector size %D should be %D", n, ctx->n*ctx->dof); 884 if (n) { 885 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 886 ierr = DMPlexGetConeSize(dm, ctx->cells[0], &coneSize);CHKERRQ(ierr); 887 if (dim == 2) { 888 if (coneSize == 3) { 889 ierr = DMInterpolate_Triangle_Private(ctx, dm, x, v);CHKERRQ(ierr); 890 } else if (coneSize == 4) { 891 ierr = DMInterpolate_Quad_Private(ctx, dm, x, v);CHKERRQ(ierr); 892 } else SETERRQ1(ctx->comm, PETSC_ERR_ARG_OUTOFRANGE, "Unsupported dimension %D for point interpolation", dim); 893 } else if (dim == 3) { 894 if (coneSize == 4) { 895 ierr = DMInterpolate_Tetrahedron_Private(ctx, dm, x, v);CHKERRQ(ierr); 896 } else { 897 ierr = DMInterpolate_Hex_Private(ctx, dm, x, v);CHKERRQ(ierr); 898 } 899 } else SETERRQ1(ctx->comm, PETSC_ERR_ARG_OUTOFRANGE, "Unsupported dimension %D for point interpolation", dim); 900 } 901 PetscFunctionReturn(0); 902 } 903 904 /*@C 905 DMInterpolationDestroy - Destroys a DMInterpolationInfo context 906 907 Collective on ctx 908 909 Input Parameter: 910 . ctx - the context 911 912 Level: beginner 913 914 .seealso: DMInterpolationEvaluate(), DMInterpolationAddPoints(), DMInterpolationCreate() 915 @*/ 916 PetscErrorCode DMInterpolationDestroy(DMInterpolationInfo *ctx) 917 { 918 PetscErrorCode ierr; 919 920 PetscFunctionBegin; 921 PetscValidPointer(ctx, 2); 922 ierr = VecDestroy(&(*ctx)->coords);CHKERRQ(ierr); 923 ierr = PetscFree((*ctx)->points);CHKERRQ(ierr); 924 ierr = PetscFree((*ctx)->cells);CHKERRQ(ierr); 925 ierr = PetscFree(*ctx);CHKERRQ(ierr); 926 *ctx = NULL; 927 PetscFunctionReturn(0); 928 } 929 930 /*@C 931 SNESMonitorFields - Monitors the residual for each field separately 932 933 Collective on SNES 934 935 Input Parameters: 936 + snes - the SNES context 937 . its - iteration number 938 . fgnorm - 2-norm of residual 939 - vf - PetscViewerAndFormat of type ASCII 940 941 Notes: 942 This routine prints the residual norm at each iteration. 943 944 Level: intermediate 945 946 .seealso: SNESMonitorSet(), SNESMonitorDefault() 947 @*/ 948 PetscErrorCode SNESMonitorFields(SNES snes, PetscInt its, PetscReal fgnorm, PetscViewerAndFormat *vf) 949 { 950 PetscViewer viewer = vf->viewer; 951 Vec res; 952 DM dm; 953 PetscSection s; 954 const PetscScalar *r; 955 PetscReal *lnorms, *norms; 956 PetscInt numFields, f, pStart, pEnd, p; 957 PetscErrorCode ierr; 958 959 PetscFunctionBegin; 960 PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,4); 961 ierr = SNESGetFunction(snes, &res, NULL, NULL);CHKERRQ(ierr); 962 ierr = SNESGetDM(snes, &dm);CHKERRQ(ierr); 963 ierr = DMGetLocalSection(dm, &s);CHKERRQ(ierr); 964 ierr = PetscSectionGetNumFields(s, &numFields);CHKERRQ(ierr); 965 ierr = PetscSectionGetChart(s, &pStart, &pEnd);CHKERRQ(ierr); 966 ierr = PetscCalloc2(numFields, &lnorms, numFields, &norms);CHKERRQ(ierr); 967 ierr = VecGetArrayRead(res, &r);CHKERRQ(ierr); 968 for (p = pStart; p < pEnd; ++p) { 969 for (f = 0; f < numFields; ++f) { 970 PetscInt fdof, foff, d; 971 972 ierr = PetscSectionGetFieldDof(s, p, f, &fdof);CHKERRQ(ierr); 973 ierr = PetscSectionGetFieldOffset(s, p, f, &foff);CHKERRQ(ierr); 974 for (d = 0; d < fdof; ++d) lnorms[f] += PetscRealPart(PetscSqr(r[foff+d])); 975 } 976 } 977 ierr = VecRestoreArrayRead(res, &r);CHKERRQ(ierr); 978 ierr = MPIU_Allreduce(lnorms, norms, numFields, MPIU_REAL, MPIU_SUM, PetscObjectComm((PetscObject) dm));CHKERRQ(ierr); 979 ierr = PetscViewerPushFormat(viewer,vf->format);CHKERRQ(ierr); 980 ierr = PetscViewerASCIIAddTab(viewer, ((PetscObject) snes)->tablevel);CHKERRQ(ierr); 981 ierr = PetscViewerASCIIPrintf(viewer, "%3D SNES Function norm %14.12e [", its, (double) fgnorm);CHKERRQ(ierr); 982 for (f = 0; f < numFields; ++f) { 983 if (f > 0) {ierr = PetscViewerASCIIPrintf(viewer, ", ");CHKERRQ(ierr);} 984 ierr = PetscViewerASCIIPrintf(viewer, "%14.12e", (double) PetscSqrtReal(norms[f]));CHKERRQ(ierr); 985 } 986 ierr = PetscViewerASCIIPrintf(viewer, "]\n");CHKERRQ(ierr); 987 ierr = PetscViewerASCIISubtractTab(viewer, ((PetscObject) snes)->tablevel);CHKERRQ(ierr); 988 ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr); 989 ierr = PetscFree2(lnorms, norms);CHKERRQ(ierr); 990 PetscFunctionReturn(0); 991 } 992 993 /********************* Residual Computation **************************/ 994 995 996 /*@ 997 DMPlexSNESGetGeometryFVM - Return precomputed geometric data 998 999 Input Parameter: 1000 . dm - The DM 1001 1002 Output Parameters: 1003 + facegeom - The values precomputed from face geometry 1004 . cellgeom - The values precomputed from cell geometry 1005 - minRadius - The minimum radius over the mesh of an inscribed sphere in a cell 1006 1007 Level: developer 1008 1009 .seealso: DMPlexTSSetRHSFunctionLocal() 1010 @*/ 1011 PetscErrorCode DMPlexSNESGetGeometryFVM(DM dm, Vec *facegeom, Vec *cellgeom, PetscReal *minRadius) 1012 { 1013 DM plex; 1014 PetscErrorCode ierr; 1015 1016 PetscFunctionBegin; 1017 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 1018 ierr = DMSNESConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr); 1019 ierr = DMPlexGetDataFVM(plex, NULL, cellgeom, facegeom, NULL);CHKERRQ(ierr); 1020 if (minRadius) {ierr = DMPlexGetMinRadius(plex, minRadius);CHKERRQ(ierr);} 1021 ierr = DMDestroy(&plex);CHKERRQ(ierr); 1022 PetscFunctionReturn(0); 1023 } 1024 1025 /*@ 1026 DMPlexSNESGetGradientDM - Return gradient data layout 1027 1028 Input Parameters: 1029 + dm - The DM 1030 - fv - The PetscFV 1031 1032 Output Parameter: 1033 . dmGrad - The layout for gradient values 1034 1035 Level: developer 1036 1037 .seealso: DMPlexSNESGetGeometryFVM() 1038 @*/ 1039 PetscErrorCode DMPlexSNESGetGradientDM(DM dm, PetscFV fv, DM *dmGrad) 1040 { 1041 DM plex; 1042 PetscBool computeGradients; 1043 PetscErrorCode ierr; 1044 1045 PetscFunctionBegin; 1046 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 1047 PetscValidHeaderSpecific(fv,PETSCFV_CLASSID,2); 1048 PetscValidPointer(dmGrad,3); 1049 ierr = PetscFVGetComputeGradients(fv, &computeGradients);CHKERRQ(ierr); 1050 if (!computeGradients) {*dmGrad = NULL; PetscFunctionReturn(0);} 1051 ierr = DMSNESConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr); 1052 ierr = DMPlexGetDataFVM(plex, fv, NULL, NULL, dmGrad);CHKERRQ(ierr); 1053 ierr = DMDestroy(&plex);CHKERRQ(ierr); 1054 PetscFunctionReturn(0); 1055 } 1056 1057 static PetscErrorCode DMPlexComputeBdResidual_Single_Internal(DM dm, PetscReal t, DMLabel label, PetscInt numValues, const PetscInt values[], PetscInt field, Vec locX, Vec locX_t, Vec locF, DMField coordField, IS facetIS) 1058 { 1059 DM_Plex *mesh = (DM_Plex *) dm->data; 1060 DM plex = NULL, plexA = NULL; 1061 DMEnclosureType encAux; 1062 PetscDS prob, probAux = NULL; 1063 PetscSection section, sectionAux = NULL; 1064 Vec locA = NULL; 1065 PetscScalar *u = NULL, *u_t = NULL, *a = NULL, *elemVec = NULL; 1066 PetscInt v; 1067 PetscInt totDim, totDimAux = 0; 1068 PetscErrorCode ierr; 1069 1070 PetscFunctionBegin; 1071 ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); 1072 ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); 1073 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1074 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1075 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);CHKERRQ(ierr); 1076 if (locA) { 1077 DM dmAux; 1078 1079 ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); 1080 ierr = DMGetEnclosureRelation(dmAux, dm, &encAux);CHKERRQ(ierr); 1081 ierr = DMConvert(dmAux, DMPLEX, &plexA);CHKERRQ(ierr); 1082 ierr = DMGetDS(plexA, &probAux);CHKERRQ(ierr); 1083 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 1084 ierr = DMGetLocalSection(plexA, §ionAux);CHKERRQ(ierr); 1085 } 1086 for (v = 0; v < numValues; ++v) { 1087 PetscFEGeom *fgeom; 1088 PetscInt maxDegree; 1089 PetscQuadrature qGeom = NULL; 1090 IS pointIS; 1091 const PetscInt *points; 1092 PetscInt numFaces, face, Nq; 1093 1094 ierr = DMLabelGetStratumIS(label, values[v], &pointIS);CHKERRQ(ierr); 1095 if (!pointIS) continue; /* No points with that id on this process */ 1096 { 1097 IS isectIS; 1098 1099 /* TODO: Special cases of ISIntersect where it is quick to check a priori if one is a superset of the other */ 1100 ierr = ISIntersect_Caching_Internal(facetIS,pointIS,&isectIS);CHKERRQ(ierr); 1101 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 1102 pointIS = isectIS; 1103 } 1104 ierr = ISGetLocalSize(pointIS,&numFaces);CHKERRQ(ierr); 1105 ierr = ISGetIndices(pointIS,&points);CHKERRQ(ierr); 1106 ierr = PetscMalloc4(numFaces*totDim, &u, locX_t ? numFaces*totDim : 0, &u_t, numFaces*totDim, &elemVec, locA ? numFaces*totDimAux : 0, &a);CHKERRQ(ierr); 1107 ierr = DMFieldGetDegree(coordField,pointIS,NULL,&maxDegree);CHKERRQ(ierr); 1108 if (maxDegree <= 1) { 1109 ierr = DMFieldCreateDefaultQuadrature(coordField,pointIS,&qGeom);CHKERRQ(ierr); 1110 } 1111 if (!qGeom) { 1112 PetscFE fe; 1113 1114 ierr = PetscDSGetDiscretization(prob, field, (PetscObject *) &fe);CHKERRQ(ierr); 1115 ierr = PetscFEGetFaceQuadrature(fe, &qGeom);CHKERRQ(ierr); 1116 ierr = PetscObjectReference((PetscObject)qGeom);CHKERRQ(ierr); 1117 } 1118 ierr = PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 1119 ierr = DMSNESGetFEGeom(coordField,pointIS,qGeom,PETSC_TRUE,&fgeom);CHKERRQ(ierr); 1120 for (face = 0; face < numFaces; ++face) { 1121 const PetscInt point = points[face], *support, *cone; 1122 PetscScalar *x = NULL; 1123 PetscInt i, coneSize, faceLoc; 1124 1125 ierr = DMPlexGetSupport(dm, point, &support);CHKERRQ(ierr); 1126 ierr = DMPlexGetConeSize(dm, support[0], &coneSize);CHKERRQ(ierr); 1127 ierr = DMPlexGetCone(dm, support[0], &cone);CHKERRQ(ierr); 1128 for (faceLoc = 0; faceLoc < coneSize; ++faceLoc) if (cone[faceLoc] == point) break; 1129 if (faceLoc == coneSize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Could not find face %D in cone of support[0] %D", point, support[0]); 1130 fgeom->face[face][0] = faceLoc; 1131 ierr = DMPlexVecGetClosure(plex, section, locX, support[0], NULL, &x);CHKERRQ(ierr); 1132 for (i = 0; i < totDim; ++i) u[face*totDim+i] = x[i]; 1133 ierr = DMPlexVecRestoreClosure(plex, section, locX, support[0], NULL, &x);CHKERRQ(ierr); 1134 if (locX_t) { 1135 ierr = DMPlexVecGetClosure(plex, section, locX_t, support[0], NULL, &x);CHKERRQ(ierr); 1136 for (i = 0; i < totDim; ++i) u_t[face*totDim+i] = x[i]; 1137 ierr = DMPlexVecRestoreClosure(plex, section, locX_t, support[0], NULL, &x);CHKERRQ(ierr); 1138 } 1139 if (locA) { 1140 PetscInt subp; 1141 1142 ierr = DMGetEnclosurePoint(plexA, dm, encAux, support[0], &subp);CHKERRQ(ierr); 1143 ierr = DMPlexVecGetClosure(plexA, sectionAux, locA, subp, NULL, &x);CHKERRQ(ierr); 1144 for (i = 0; i < totDimAux; ++i) a[face*totDimAux+i] = x[i]; 1145 ierr = DMPlexVecRestoreClosure(plexA, sectionAux, locA, subp, NULL, &x);CHKERRQ(ierr); 1146 } 1147 } 1148 ierr = PetscArrayzero(elemVec, numFaces*totDim);CHKERRQ(ierr); 1149 { 1150 PetscFE fe; 1151 PetscInt Nb; 1152 PetscFEGeom *chunkGeom = NULL; 1153 /* Conforming batches */ 1154 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 1155 /* Remainder */ 1156 PetscInt Nr, offset; 1157 1158 ierr = PetscDSGetDiscretization(prob, field, (PetscObject *) &fe);CHKERRQ(ierr); 1159 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 1160 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1161 /* TODO: documentation is unclear about what is going on with these numbers: how should Nb / Nq factor in ? */ 1162 blockSize = Nb; 1163 batchSize = numBlocks * blockSize; 1164 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1165 numChunks = numFaces / (numBatches*batchSize); 1166 Ne = numChunks*numBatches*batchSize; 1167 Nr = numFaces % (numBatches*batchSize); 1168 offset = numFaces - Nr; 1169 ierr = PetscFEGeomGetChunk(fgeom,0,offset,&chunkGeom);CHKERRQ(ierr); 1170 ierr = PetscFEIntegrateBdResidual(prob, field, Ne, chunkGeom, u, u_t, probAux, a, t, elemVec);CHKERRQ(ierr); 1171 ierr = PetscFEGeomRestoreChunk(fgeom, 0, offset, &chunkGeom);CHKERRQ(ierr); 1172 ierr = PetscFEGeomGetChunk(fgeom,offset,numFaces,&chunkGeom);CHKERRQ(ierr); 1173 ierr = PetscFEIntegrateBdResidual(prob, field, Nr, chunkGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, a ? &a[offset*totDimAux] : NULL, t, &elemVec[offset*totDim]);CHKERRQ(ierr); 1174 ierr = PetscFEGeomRestoreChunk(fgeom,offset,numFaces,&chunkGeom);CHKERRQ(ierr); 1175 } 1176 for (face = 0; face < numFaces; ++face) { 1177 const PetscInt point = points[face], *support; 1178 1179 if (mesh->printFEM > 1) {ierr = DMPrintCellVector(point, "BdResidual", totDim, &elemVec[face*totDim]);CHKERRQ(ierr);} 1180 ierr = DMPlexGetSupport(plex, point, &support);CHKERRQ(ierr); 1181 ierr = DMPlexVecSetClosure(plex, NULL, locF, support[0], &elemVec[face*totDim], ADD_ALL_VALUES);CHKERRQ(ierr); 1182 } 1183 ierr = DMSNESRestoreFEGeom(coordField,pointIS,qGeom,PETSC_TRUE,&fgeom);CHKERRQ(ierr); 1184 ierr = PetscQuadratureDestroy(&qGeom);CHKERRQ(ierr); 1185 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 1186 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 1187 ierr = PetscFree4(u, u_t, elemVec, a);CHKERRQ(ierr); 1188 } 1189 if (plex) {ierr = DMDestroy(&plex);CHKERRQ(ierr);} 1190 if (plexA) {ierr = DMDestroy(&plexA);CHKERRQ(ierr);} 1191 PetscFunctionReturn(0); 1192 } 1193 1194 PetscErrorCode DMPlexComputeBdResidualSingle(DM dm, PetscReal t, DMLabel label, PetscInt numValues, const PetscInt values[], PetscInt field, Vec locX, Vec locX_t, Vec locF) 1195 { 1196 DMField coordField; 1197 DMLabel depthLabel; 1198 IS facetIS; 1199 PetscInt dim; 1200 PetscErrorCode ierr; 1201 1202 PetscFunctionBegin; 1203 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1204 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 1205 ierr = DMLabelGetStratumIS(depthLabel, dim-1, &facetIS);CHKERRQ(ierr); 1206 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 1207 ierr = DMPlexComputeBdResidual_Single_Internal(dm, t, label, numValues, values, field, locX, locX_t, locF, coordField, facetIS);CHKERRQ(ierr); 1208 ierr = ISDestroy(&facetIS);CHKERRQ(ierr); 1209 PetscFunctionReturn(0); 1210 } 1211 1212 PetscErrorCode DMPlexComputeBdResidual_Internal(DM dm, Vec locX, Vec locX_t, PetscReal t, Vec locF, void *user) 1213 { 1214 PetscDS prob; 1215 PetscInt numBd, bd; 1216 DMField coordField = NULL; 1217 IS facetIS = NULL; 1218 DMLabel depthLabel; 1219 PetscInt dim; 1220 PetscErrorCode ierr; 1221 1222 PetscFunctionBegin; 1223 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1224 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 1225 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1226 ierr = DMLabelGetStratumIS(depthLabel,dim - 1,&facetIS);CHKERRQ(ierr); 1227 ierr = PetscDSGetNumBoundary(prob, &numBd);CHKERRQ(ierr); 1228 for (bd = 0; bd < numBd; ++bd) { 1229 DMBoundaryConditionType type; 1230 const char *bdLabel; 1231 DMLabel label; 1232 const PetscInt *values; 1233 PetscInt field, numValues; 1234 PetscObject obj; 1235 PetscClassId id; 1236 1237 ierr = PetscDSGetBoundary(prob, bd, &type, NULL, &bdLabel, &field, NULL, NULL, NULL, &numValues, &values, NULL);CHKERRQ(ierr); 1238 ierr = PetscDSGetDiscretization(prob, field, &obj);CHKERRQ(ierr); 1239 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1240 if ((id != PETSCFE_CLASSID) || (type & DM_BC_ESSENTIAL)) continue; 1241 if (!facetIS) { 1242 DMLabel depthLabel; 1243 PetscInt dim; 1244 1245 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 1246 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1247 ierr = DMLabelGetStratumIS(depthLabel, dim - 1, &facetIS);CHKERRQ(ierr); 1248 } 1249 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 1250 ierr = DMGetLabel(dm, bdLabel, &label);CHKERRQ(ierr); 1251 ierr = DMPlexComputeBdResidual_Single_Internal(dm, t, label, numValues, values, field, locX, locX_t, locF, coordField, facetIS);CHKERRQ(ierr); 1252 } 1253 ierr = ISDestroy(&facetIS);CHKERRQ(ierr); 1254 PetscFunctionReturn(0); 1255 } 1256 1257 PetscErrorCode DMPlexComputeResidual_Internal(DM dm, IS cellIS, PetscReal time, Vec locX, Vec locX_t, PetscReal t, Vec locF, void *user) 1258 { 1259 DM_Plex *mesh = (DM_Plex *) dm->data; 1260 const char *name = "Residual"; 1261 DM dmAux = NULL; 1262 DM dmGrad = NULL; 1263 DMLabel ghostLabel = NULL; 1264 PetscDS prob = NULL; 1265 PetscDS probAux = NULL; 1266 PetscSection section = NULL; 1267 PetscBool useFEM = PETSC_FALSE; 1268 PetscBool useFVM = PETSC_FALSE; 1269 PetscBool isImplicit = (locX_t || time == PETSC_MIN_REAL) ? PETSC_TRUE : PETSC_FALSE; 1270 PetscFV fvm = NULL; 1271 PetscFVCellGeom *cgeomFVM = NULL; 1272 PetscFVFaceGeom *fgeomFVM = NULL; 1273 DMField coordField = NULL; 1274 Vec locA, cellGeometryFVM = NULL, faceGeometryFVM = NULL, grad, locGrad = NULL; 1275 PetscScalar *u = NULL, *u_t, *a, *uL, *uR; 1276 IS chunkIS; 1277 const PetscInt *cells; 1278 PetscInt cStart, cEnd, numCells; 1279 PetscInt Nf, f, totDim, totDimAux, numChunks, cellChunkSize, faceChunkSize, chunk, fStart, fEnd; 1280 PetscInt maxDegree = PETSC_MAX_INT; 1281 PetscQuadrature affineQuad = NULL, *quads = NULL; 1282 PetscFEGeom *affineGeom = NULL, **geoms = NULL; 1283 PetscErrorCode ierr; 1284 1285 PetscFunctionBegin; 1286 ierr = PetscLogEventBegin(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr); 1287 /* TODO The places where we have to use isFE are probably the member functions for the PetscDisc class */ 1288 /* TODO The FVM geometry is over-manipulated. Make the precalc functions return exactly what we need */ 1289 /* FEM+FVM */ 1290 ierr = ISGetPointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 1291 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 1292 /* 1: Get sizes from dm and dmAux */ 1293 ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); 1294 ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 1295 ierr = DMGetCellDS(dm, cStart, &prob);CHKERRQ(ierr); 1296 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 1297 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1298 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);CHKERRQ(ierr); 1299 if (locA) { 1300 PetscInt subcell; 1301 ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); 1302 ierr = DMGetEnclosurePoint(dmAux, dm, DM_ENC_UNKNOWN, cStart, &subcell);CHKERRQ(ierr); 1303 ierr = DMGetCellDS(dmAux, subcell, &probAux);CHKERRQ(ierr); 1304 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 1305 } 1306 /* 2: Get geometric data */ 1307 for (f = 0; f < Nf; ++f) { 1308 PetscObject obj; 1309 PetscClassId id; 1310 PetscBool fimp; 1311 1312 ierr = PetscDSGetImplicit(prob, f, &fimp);CHKERRQ(ierr); 1313 if (isImplicit != fimp) continue; 1314 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1315 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1316 if (id == PETSCFE_CLASSID) {useFEM = PETSC_TRUE;} 1317 if (id == PETSCFV_CLASSID) {useFVM = PETSC_TRUE; fvm = (PetscFV) obj;} 1318 } 1319 if (useFEM) { 1320 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 1321 ierr = DMFieldGetDegree(coordField,cellIS,NULL,&maxDegree);CHKERRQ(ierr); 1322 if (maxDegree <= 1) { 1323 ierr = DMFieldCreateDefaultQuadrature(coordField,cellIS,&affineQuad);CHKERRQ(ierr); 1324 if (affineQuad) { 1325 ierr = DMSNESGetFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&affineGeom);CHKERRQ(ierr); 1326 } 1327 } else { 1328 ierr = PetscCalloc2(Nf,&quads,Nf,&geoms);CHKERRQ(ierr); 1329 for (f = 0; f < Nf; ++f) { 1330 PetscObject obj; 1331 PetscClassId id; 1332 PetscBool fimp; 1333 1334 ierr = PetscDSGetImplicit(prob, f, &fimp);CHKERRQ(ierr); 1335 if (isImplicit != fimp) continue; 1336 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1337 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1338 if (id == PETSCFE_CLASSID) { 1339 PetscFE fe = (PetscFE) obj; 1340 1341 ierr = PetscFEGetQuadrature(fe, &quads[f]);CHKERRQ(ierr); 1342 ierr = PetscObjectReference((PetscObject)quads[f]);CHKERRQ(ierr); 1343 ierr = DMSNESGetFEGeom(coordField,cellIS,quads[f],PETSC_FALSE,&geoms[f]);CHKERRQ(ierr); 1344 } 1345 } 1346 } 1347 } 1348 if (useFVM) { 1349 ierr = DMPlexSNESGetGeometryFVM(dm, &faceGeometryFVM, &cellGeometryFVM, NULL);CHKERRQ(ierr); 1350 ierr = VecGetArrayRead(faceGeometryFVM, (const PetscScalar **) &fgeomFVM);CHKERRQ(ierr); 1351 ierr = VecGetArrayRead(cellGeometryFVM, (const PetscScalar **) &cgeomFVM);CHKERRQ(ierr); 1352 /* Reconstruct and limit cell gradients */ 1353 ierr = DMPlexSNESGetGradientDM(dm, fvm, &dmGrad);CHKERRQ(ierr); 1354 if (dmGrad) { 1355 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 1356 ierr = DMGetGlobalVector(dmGrad, &grad);CHKERRQ(ierr); 1357 ierr = DMPlexReconstructGradients_Internal(dm, fvm, fStart, fEnd, faceGeometryFVM, cellGeometryFVM, locX, grad);CHKERRQ(ierr); 1358 /* Communicate gradient values */ 1359 ierr = DMGetLocalVector(dmGrad, &locGrad);CHKERRQ(ierr); 1360 ierr = DMGlobalToLocalBegin(dmGrad, grad, INSERT_VALUES, locGrad);CHKERRQ(ierr); 1361 ierr = DMGlobalToLocalEnd(dmGrad, grad, INSERT_VALUES, locGrad);CHKERRQ(ierr); 1362 ierr = DMRestoreGlobalVector(dmGrad, &grad);CHKERRQ(ierr); 1363 } 1364 /* Handle non-essential (e.g. outflow) boundary values */ 1365 ierr = DMPlexInsertBoundaryValues(dm, PETSC_FALSE, locX, time, faceGeometryFVM, cellGeometryFVM, locGrad);CHKERRQ(ierr); 1366 } 1367 /* Loop over chunks */ 1368 if (useFEM) {ierr = ISCreate(PETSC_COMM_SELF, &chunkIS);CHKERRQ(ierr);} 1369 numCells = cEnd - cStart; 1370 numChunks = 1; 1371 cellChunkSize = numCells/numChunks; 1372 faceChunkSize = (fEnd - fStart)/numChunks; 1373 numChunks = PetscMin(1,numCells); 1374 for (chunk = 0; chunk < numChunks; ++chunk) { 1375 PetscScalar *elemVec, *fluxL, *fluxR; 1376 PetscReal *vol; 1377 PetscFVFaceGeom *fgeom; 1378 PetscInt cS = cStart+chunk*cellChunkSize, cE = PetscMin(cS+cellChunkSize, cEnd), numCells = cE - cS, c; 1379 PetscInt fS = fStart+chunk*faceChunkSize, fE = PetscMin(fS+faceChunkSize, fEnd), numFaces = 0, face; 1380 1381 /* Extract field coefficients */ 1382 if (useFEM) { 1383 ierr = ISGetPointSubrange(chunkIS, cS, cE, cells);CHKERRQ(ierr); 1384 ierr = DMPlexGetCellFields(dm, chunkIS, locX, locX_t, locA, &u, &u_t, &a);CHKERRQ(ierr); 1385 ierr = DMGetWorkArray(dm, numCells*totDim, MPIU_SCALAR, &elemVec);CHKERRQ(ierr); 1386 ierr = PetscArrayzero(elemVec, numCells*totDim);CHKERRQ(ierr); 1387 } 1388 if (useFVM) { 1389 ierr = DMPlexGetFaceFields(dm, fS, fE, locX, locX_t, faceGeometryFVM, cellGeometryFVM, locGrad, &numFaces, &uL, &uR);CHKERRQ(ierr); 1390 ierr = DMPlexGetFaceGeometry(dm, fS, fE, faceGeometryFVM, cellGeometryFVM, &numFaces, &fgeom, &vol);CHKERRQ(ierr); 1391 ierr = DMGetWorkArray(dm, numFaces*totDim, MPIU_SCALAR, &fluxL);CHKERRQ(ierr); 1392 ierr = DMGetWorkArray(dm, numFaces*totDim, MPIU_SCALAR, &fluxR);CHKERRQ(ierr); 1393 ierr = PetscArrayzero(fluxL, numFaces*totDim);CHKERRQ(ierr); 1394 ierr = PetscArrayzero(fluxR, numFaces*totDim);CHKERRQ(ierr); 1395 } 1396 /* TODO We will interlace both our field coefficients (u, u_t, uL, uR, etc.) and our output (elemVec, fL, fR). I think this works */ 1397 /* Loop over fields */ 1398 for (f = 0; f < Nf; ++f) { 1399 PetscObject obj; 1400 PetscClassId id; 1401 PetscBool fimp; 1402 PetscInt numChunks, numBatches, batchSize, numBlocks, blockSize, Ne, Nr, offset; 1403 1404 ierr = PetscDSGetImplicit(prob, f, &fimp);CHKERRQ(ierr); 1405 if (isImplicit != fimp) continue; 1406 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1407 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1408 if (id == PETSCFE_CLASSID) { 1409 PetscFE fe = (PetscFE) obj; 1410 PetscFEGeom *geom = affineGeom ? affineGeom : geoms[f]; 1411 PetscFEGeom *chunkGeom = NULL; 1412 PetscQuadrature quad = affineQuad ? affineQuad : quads[f]; 1413 PetscInt Nq, Nb; 1414 1415 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1416 ierr = PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 1417 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 1418 blockSize = Nb; 1419 batchSize = numBlocks * blockSize; 1420 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1421 numChunks = numCells / (numBatches*batchSize); 1422 Ne = numChunks*numBatches*batchSize; 1423 Nr = numCells % (numBatches*batchSize); 1424 offset = numCells - Nr; 1425 /* Integrate FE residual to get elemVec (need fields at quadrature points) */ 1426 /* For FV, I think we use a P0 basis and the cell coefficients (for subdivided cells, we can tweak the basis tabulation to be the indicator function) */ 1427 ierr = PetscFEGeomGetChunk(geom,0,offset,&chunkGeom);CHKERRQ(ierr); 1428 ierr = PetscFEIntegrateResidual(prob, f, Ne, chunkGeom, u, u_t, probAux, a, t, elemVec);CHKERRQ(ierr); 1429 ierr = PetscFEGeomGetChunk(geom,offset,numCells,&chunkGeom);CHKERRQ(ierr); 1430 ierr = PetscFEIntegrateResidual(prob, f, Nr, chunkGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, &elemVec[offset*totDim]);CHKERRQ(ierr); 1431 ierr = PetscFEGeomRestoreChunk(geom,offset,numCells,&chunkGeom);CHKERRQ(ierr); 1432 } else if (id == PETSCFV_CLASSID) { 1433 PetscFV fv = (PetscFV) obj; 1434 1435 Ne = numFaces; 1436 /* Riemann solve over faces (need fields at face centroids) */ 1437 /* We need to evaluate FE fields at those coordinates */ 1438 ierr = PetscFVIntegrateRHSFunction(fv, prob, f, Ne, fgeom, vol, uL, uR, fluxL, fluxR);CHKERRQ(ierr); 1439 } else SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", f); 1440 } 1441 /* Loop over domain */ 1442 if (useFEM) { 1443 /* Add elemVec to locX */ 1444 for (c = cS; c < cE; ++c) { 1445 const PetscInt cell = cells ? cells[c] : c; 1446 const PetscInt cind = c - cStart; 1447 1448 if (mesh->printFEM > 1) {ierr = DMPrintCellVector(cell, name, totDim, &elemVec[cind*totDim]);CHKERRQ(ierr);} 1449 if (ghostLabel) { 1450 PetscInt ghostVal; 1451 1452 ierr = DMLabelGetValue(ghostLabel,cell,&ghostVal);CHKERRQ(ierr); 1453 if (ghostVal > 0) continue; 1454 } 1455 ierr = DMPlexVecSetClosure(dm, section, locF, cell, &elemVec[cind*totDim], ADD_ALL_VALUES);CHKERRQ(ierr); 1456 } 1457 } 1458 if (useFVM) { 1459 PetscScalar *fa; 1460 PetscInt iface; 1461 1462 ierr = VecGetArray(locF, &fa);CHKERRQ(ierr); 1463 for (f = 0; f < Nf; ++f) { 1464 PetscFV fv; 1465 PetscObject obj; 1466 PetscClassId id; 1467 PetscInt foff, pdim; 1468 1469 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1470 ierr = PetscDSGetFieldOffset(prob, f, &foff);CHKERRQ(ierr); 1471 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1472 if (id != PETSCFV_CLASSID) continue; 1473 fv = (PetscFV) obj; 1474 ierr = PetscFVGetNumComponents(fv, &pdim);CHKERRQ(ierr); 1475 /* Accumulate fluxes to cells */ 1476 for (face = fS, iface = 0; face < fE; ++face) { 1477 const PetscInt *scells; 1478 PetscScalar *fL = NULL, *fR = NULL; 1479 PetscInt ghost, d, nsupp, nchild; 1480 1481 ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr); 1482 ierr = DMPlexGetSupportSize(dm, face, &nsupp);CHKERRQ(ierr); 1483 ierr = DMPlexGetTreeChildren(dm, face, &nchild, NULL);CHKERRQ(ierr); 1484 if (ghost >= 0 || nsupp > 2 || nchild > 0) continue; 1485 ierr = DMPlexGetSupport(dm, face, &scells);CHKERRQ(ierr); 1486 ierr = DMLabelGetValue(ghostLabel,scells[0],&ghost);CHKERRQ(ierr); 1487 if (ghost <= 0) {ierr = DMPlexPointLocalFieldRef(dm, scells[0], f, fa, &fL);CHKERRQ(ierr);} 1488 ierr = DMLabelGetValue(ghostLabel,scells[1],&ghost);CHKERRQ(ierr); 1489 if (ghost <= 0) {ierr = DMPlexPointLocalFieldRef(dm, scells[1], f, fa, &fR);CHKERRQ(ierr);} 1490 for (d = 0; d < pdim; ++d) { 1491 if (fL) fL[d] -= fluxL[iface*totDim+foff+d]; 1492 if (fR) fR[d] += fluxR[iface*totDim+foff+d]; 1493 } 1494 ++iface; 1495 } 1496 } 1497 ierr = VecRestoreArray(locF, &fa);CHKERRQ(ierr); 1498 } 1499 /* Handle time derivative */ 1500 if (locX_t) { 1501 PetscScalar *x_t, *fa; 1502 1503 ierr = VecGetArray(locF, &fa);CHKERRQ(ierr); 1504 ierr = VecGetArray(locX_t, &x_t);CHKERRQ(ierr); 1505 for (f = 0; f < Nf; ++f) { 1506 PetscFV fv; 1507 PetscObject obj; 1508 PetscClassId id; 1509 PetscInt pdim, d; 1510 1511 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1512 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1513 if (id != PETSCFV_CLASSID) continue; 1514 fv = (PetscFV) obj; 1515 ierr = PetscFVGetNumComponents(fv, &pdim);CHKERRQ(ierr); 1516 for (c = cS; c < cE; ++c) { 1517 const PetscInt cell = cells ? cells[c] : c; 1518 PetscScalar *u_t, *r; 1519 1520 if (ghostLabel) { 1521 PetscInt ghostVal; 1522 1523 ierr = DMLabelGetValue(ghostLabel, cell, &ghostVal);CHKERRQ(ierr); 1524 if (ghostVal > 0) continue; 1525 } 1526 ierr = DMPlexPointLocalFieldRead(dm, cell, f, x_t, &u_t);CHKERRQ(ierr); 1527 ierr = DMPlexPointLocalFieldRef(dm, cell, f, fa, &r);CHKERRQ(ierr); 1528 for (d = 0; d < pdim; ++d) r[d] += u_t[d]; 1529 } 1530 } 1531 ierr = VecRestoreArray(locX_t, &x_t);CHKERRQ(ierr); 1532 ierr = VecRestoreArray(locF, &fa);CHKERRQ(ierr); 1533 } 1534 if (useFEM) { 1535 ierr = DMPlexRestoreCellFields(dm, chunkIS, locX, locX_t, locA, &u, &u_t, &a);CHKERRQ(ierr); 1536 ierr = DMRestoreWorkArray(dm, numCells*totDim, MPIU_SCALAR, &elemVec);CHKERRQ(ierr); 1537 } 1538 if (useFVM) { 1539 ierr = DMPlexRestoreFaceFields(dm, fS, fE, locX, locX_t, faceGeometryFVM, cellGeometryFVM, locGrad, &numFaces, &uL, &uR);CHKERRQ(ierr); 1540 ierr = DMPlexRestoreFaceGeometry(dm, fS, fE, faceGeometryFVM, cellGeometryFVM, &numFaces, &fgeom, &vol);CHKERRQ(ierr); 1541 ierr = DMRestoreWorkArray(dm, numFaces*totDim, MPIU_SCALAR, &fluxL);CHKERRQ(ierr); 1542 ierr = DMRestoreWorkArray(dm, numFaces*totDim, MPIU_SCALAR, &fluxR);CHKERRQ(ierr); 1543 if (dmGrad) {ierr = DMRestoreLocalVector(dmGrad, &locGrad);CHKERRQ(ierr);} 1544 } 1545 } 1546 if (useFEM) {ierr = ISDestroy(&chunkIS);CHKERRQ(ierr);} 1547 ierr = ISRestorePointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 1548 1549 if (useFEM) { 1550 ierr = DMPlexComputeBdResidual_Internal(dm, locX, locX_t, t, locF, user);CHKERRQ(ierr); 1551 1552 if (maxDegree <= 1) { 1553 ierr = DMSNESRestoreFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&affineGeom);CHKERRQ(ierr); 1554 ierr = PetscQuadratureDestroy(&affineQuad);CHKERRQ(ierr); 1555 } else { 1556 for (f = 0; f < Nf; ++f) { 1557 ierr = DMSNESRestoreFEGeom(coordField,cellIS,quads[f],PETSC_FALSE,&geoms[f]);CHKERRQ(ierr); 1558 ierr = PetscQuadratureDestroy(&quads[f]);CHKERRQ(ierr); 1559 } 1560 ierr = PetscFree2(quads,geoms);CHKERRQ(ierr); 1561 } 1562 } 1563 1564 /* FEM */ 1565 /* 1: Get sizes from dm and dmAux */ 1566 /* 2: Get geometric data */ 1567 /* 3: Handle boundary values */ 1568 /* 4: Loop over domain */ 1569 /* Extract coefficients */ 1570 /* Loop over fields */ 1571 /* Set tiling for FE*/ 1572 /* Integrate FE residual to get elemVec */ 1573 /* Loop over subdomain */ 1574 /* Loop over quad points */ 1575 /* Transform coords to real space */ 1576 /* Evaluate field and aux fields at point */ 1577 /* Evaluate residual at point */ 1578 /* Transform residual to real space */ 1579 /* Add residual to elemVec */ 1580 /* Loop over domain */ 1581 /* Add elemVec to locX */ 1582 1583 /* FVM */ 1584 /* Get geometric data */ 1585 /* If using gradients */ 1586 /* Compute gradient data */ 1587 /* Loop over domain faces */ 1588 /* Count computational faces */ 1589 /* Reconstruct cell gradient */ 1590 /* Loop over domain cells */ 1591 /* Limit cell gradients */ 1592 /* Handle boundary values */ 1593 /* Loop over domain faces */ 1594 /* Read out field, centroid, normal, volume for each side of face */ 1595 /* Riemann solve over faces */ 1596 /* Loop over domain faces */ 1597 /* Accumulate fluxes to cells */ 1598 /* TODO Change printFEM to printDisc here */ 1599 if (mesh->printFEM) { 1600 Vec locFbc; 1601 PetscInt pStart, pEnd, p, maxDof; 1602 PetscScalar *zeroes; 1603 1604 ierr = VecDuplicate(locF,&locFbc);CHKERRQ(ierr); 1605 ierr = VecCopy(locF,locFbc);CHKERRQ(ierr); 1606 ierr = PetscSectionGetChart(section,&pStart,&pEnd);CHKERRQ(ierr); 1607 ierr = PetscSectionGetMaxDof(section,&maxDof);CHKERRQ(ierr); 1608 ierr = PetscCalloc1(maxDof,&zeroes);CHKERRQ(ierr); 1609 for (p = pStart; p < pEnd; p++) { 1610 ierr = VecSetValuesSection(locFbc,section,p,zeroes,INSERT_BC_VALUES);CHKERRQ(ierr); 1611 } 1612 ierr = PetscFree(zeroes);CHKERRQ(ierr); 1613 ierr = DMPrintLocalVec(dm, name, mesh->printTol, locFbc);CHKERRQ(ierr); 1614 ierr = VecDestroy(&locFbc);CHKERRQ(ierr); 1615 } 1616 ierr = PetscLogEventEnd(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr); 1617 PetscFunctionReturn(0); 1618 } 1619 1620 PetscErrorCode DMPlexComputeResidual_Hybrid_Internal(DM dm, IS cellIS, PetscReal time, Vec locX, Vec locX_t, PetscReal t, Vec locF, void *user) 1621 { 1622 DM_Plex *mesh = (DM_Plex *) dm->data; 1623 const char *name = "Hybrid Residual"; 1624 DM dmAux = NULL; 1625 DMLabel ghostLabel = NULL; 1626 PetscDS prob = NULL; 1627 PetscDS probAux = NULL; 1628 PetscSection section = NULL; 1629 DMField coordField = NULL; 1630 Vec locA; 1631 PetscScalar *u = NULL, *u_t, *a; 1632 PetscScalar *elemVec; 1633 IS chunkIS; 1634 const PetscInt *cells; 1635 PetscInt *faces; 1636 PetscInt cStart, cEnd, numCells; 1637 PetscInt Nf, f, totDim, totDimAux, numChunks, cellChunkSize, chunk; 1638 PetscInt maxDegree = PETSC_MAX_INT; 1639 PetscQuadrature affineQuad = NULL, *quads = NULL; 1640 PetscFEGeom *affineGeom = NULL, **geoms = NULL; 1641 PetscErrorCode ierr; 1642 1643 PetscFunctionBegin; 1644 ierr = PetscLogEventBegin(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr); 1645 /* TODO The places where we have to use isFE are probably the member functions for the PetscDisc class */ 1646 /* FEM */ 1647 ierr = ISGetPointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 1648 /* 1: Get sizes from dm and dmAux */ 1649 ierr = DMGetSection(dm, §ion);CHKERRQ(ierr); 1650 ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 1651 ierr = DMGetCellDS(dm, cStart, &prob);CHKERRQ(ierr); 1652 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 1653 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1654 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);CHKERRQ(ierr); 1655 if (locA) { 1656 ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); 1657 ierr = DMGetCellDS(dmAux, cStart, &probAux);CHKERRQ(ierr); 1658 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 1659 } 1660 /* 2: Setup geometric data */ 1661 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 1662 ierr = DMFieldGetDegree(coordField, cellIS, NULL, &maxDegree);CHKERRQ(ierr); 1663 if (maxDegree > 1) { 1664 ierr = PetscCalloc2(Nf,&quads,Nf,&geoms);CHKERRQ(ierr); 1665 for (f = 0; f < Nf; ++f) { 1666 PetscFE fe; 1667 1668 ierr = PetscDSGetDiscretization(prob, f, (PetscObject *) &fe);CHKERRQ(ierr); 1669 if (fe) { 1670 ierr = PetscFEGetQuadrature(fe, &quads[f]);CHKERRQ(ierr); 1671 ierr = PetscObjectReference((PetscObject) quads[f]);CHKERRQ(ierr); 1672 } 1673 } 1674 } 1675 /* Loop over chunks */ 1676 numCells = cEnd - cStart; 1677 cellChunkSize = numCells; 1678 numChunks = !numCells ? 0 : PetscCeilReal(((PetscReal) numCells)/cellChunkSize); 1679 ierr = PetscCalloc1(2*cellChunkSize, &faces);CHKERRQ(ierr); 1680 ierr = ISCreateGeneral(PETSC_COMM_SELF, cellChunkSize, faces, PETSC_USE_POINTER, &chunkIS);CHKERRQ(ierr); 1681 /* Extract field coefficients */ 1682 /* NOTE This needs the end cap faces to have identical orientations */ 1683 ierr = DMPlexGetCellFields(dm, cellIS, locX, locX_t, locA, &u, &u_t, &a);CHKERRQ(ierr); 1684 ierr = DMGetWorkArray(dm, cellChunkSize*totDim, MPIU_SCALAR, &elemVec);CHKERRQ(ierr); 1685 for (chunk = 0; chunk < numChunks; ++chunk) { 1686 PetscInt cS = cStart+chunk*cellChunkSize, cE = PetscMin(cS+cellChunkSize, cEnd), numCells = cE - cS, c; 1687 1688 ierr = PetscMemzero(elemVec, cellChunkSize*totDim * sizeof(PetscScalar));CHKERRQ(ierr); 1689 /* Get faces */ 1690 for (c = cS; c < cE; ++c) { 1691 const PetscInt cell = cells ? cells[c] : c; 1692 const PetscInt *cone; 1693 ierr = DMPlexGetCone(dm, cell, &cone);CHKERRQ(ierr); 1694 faces[(c-cS)*2+0] = cone[0]; 1695 faces[(c-cS)*2+1] = cone[1]; 1696 } 1697 ierr = ISGeneralSetIndices(chunkIS, cellChunkSize, faces, PETSC_USE_POINTER);CHKERRQ(ierr); 1698 /* Get geometric data */ 1699 if (maxDegree <= 1) { 1700 if (!affineQuad) {ierr = DMFieldCreateDefaultQuadrature(coordField, chunkIS, &affineQuad);CHKERRQ(ierr);} 1701 if (affineQuad) {ierr = DMSNESGetFEGeom(coordField, chunkIS, affineQuad, PETSC_TRUE, &affineGeom);CHKERRQ(ierr);} 1702 } else { 1703 for (f = 0; f < Nf; ++f) { 1704 if (quads[f]) {ierr = DMSNESGetFEGeom(coordField, chunkIS, quads[f], PETSC_TRUE, &geoms[f]);CHKERRQ(ierr);} 1705 } 1706 } 1707 /* Loop over fields */ 1708 for (f = 0; f < Nf; ++f) { 1709 PetscFE fe; 1710 PetscFEGeom *geom = affineGeom ? affineGeom : geoms[f]; 1711 PetscFEGeom *chunkGeom = NULL; 1712 PetscQuadrature quad = affineQuad ? affineQuad : quads[f]; 1713 PetscInt numChunks, numBatches, batchSize, numBlocks, blockSize, Ne, Nr, offset, Nq, Nb; 1714 1715 ierr = PetscDSGetDiscretization(prob, f, (PetscObject *) &fe);CHKERRQ(ierr); 1716 if (!fe) continue; 1717 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1718 ierr = PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 1719 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 1720 blockSize = Nb; 1721 batchSize = numBlocks * blockSize; 1722 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1723 numChunks = numCells / (numBatches*batchSize); 1724 Ne = numChunks*numBatches*batchSize; 1725 Nr = numCells % (numBatches*batchSize); 1726 offset = numCells - Nr; 1727 ierr = PetscFEGeomGetChunk(geom,0,offset,&chunkGeom);CHKERRQ(ierr); 1728 ierr = PetscFEIntegrateHybridResidual(prob, f, Ne, chunkGeom, u, u_t, probAux, a, t, elemVec);CHKERRQ(ierr); 1729 ierr = PetscFEGeomGetChunk(geom,offset,numCells,&chunkGeom);CHKERRQ(ierr); 1730 ierr = PetscFEIntegrateHybridResidual(prob, f, Nr, chunkGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, &elemVec[offset*totDim]);CHKERRQ(ierr); 1731 ierr = PetscFEGeomRestoreChunk(geom,offset,numCells,&chunkGeom);CHKERRQ(ierr); 1732 } 1733 /* Add elemVec to locX */ 1734 for (c = cS; c < cE; ++c) { 1735 const PetscInt cell = cells ? cells[c] : c; 1736 const PetscInt cind = c - cStart; 1737 1738 if (mesh->printFEM > 1) {ierr = DMPrintCellVector(cell, name, totDim, &elemVec[cind*totDim]);CHKERRQ(ierr);} 1739 if (ghostLabel) { 1740 PetscInt ghostVal; 1741 1742 ierr = DMLabelGetValue(ghostLabel,cell,&ghostVal);CHKERRQ(ierr); 1743 if (ghostVal > 0) continue; 1744 } 1745 ierr = DMPlexVecSetClosure(dm, section, locF, cell, &elemVec[cind*totDim], ADD_ALL_VALUES);CHKERRQ(ierr); 1746 } 1747 } 1748 ierr = DMPlexRestoreCellFields(dm, cellIS, locX, locX_t, locA, &u, &u_t, &a);CHKERRQ(ierr); 1749 ierr = DMRestoreWorkArray(dm, numCells*totDim, MPIU_SCALAR, &elemVec);CHKERRQ(ierr); 1750 ierr = PetscFree(faces);CHKERRQ(ierr); 1751 ierr = ISDestroy(&chunkIS);CHKERRQ(ierr); 1752 ierr = ISRestorePointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 1753 if (maxDegree <= 1) { 1754 ierr = DMSNESRestoreFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&affineGeom);CHKERRQ(ierr); 1755 ierr = PetscQuadratureDestroy(&affineQuad);CHKERRQ(ierr); 1756 } else { 1757 for (f = 0; f < Nf; ++f) { 1758 if (geoms) {ierr = DMSNESRestoreFEGeom(coordField,cellIS,quads[f],PETSC_FALSE,&geoms[f]);CHKERRQ(ierr);} 1759 if (quads) {ierr = PetscQuadratureDestroy(&quads[f]);CHKERRQ(ierr);} 1760 } 1761 ierr = PetscFree2(quads,geoms);CHKERRQ(ierr); 1762 } 1763 ierr = PetscLogEventEnd(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr); 1764 PetscFunctionReturn(0); 1765 } 1766 1767 /*@ 1768 DMPlexSNESComputeResidualFEM - Form the local residual F from the local input X using pointwise functions specified by the user 1769 1770 Input Parameters: 1771 + dm - The mesh 1772 . X - Local solution 1773 - user - The user context 1774 1775 Output Parameter: 1776 . F - Local output vector 1777 1778 Level: developer 1779 1780 .seealso: DMPlexComputeJacobianAction() 1781 @*/ 1782 PetscErrorCode DMPlexSNESComputeResidualFEM(DM dm, Vec X, Vec F, void *user) 1783 { 1784 DM plex; 1785 IS cellIS; 1786 PetscInt depth; 1787 PetscErrorCode ierr; 1788 1789 PetscFunctionBegin; 1790 ierr = DMSNESConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr); 1791 ierr = DMPlexGetDepth(plex, &depth);CHKERRQ(ierr); 1792 ierr = DMGetStratumIS(plex, "dim", depth, &cellIS);CHKERRQ(ierr); 1793 if (!cellIS) { 1794 ierr = DMGetStratumIS(plex, "depth", depth, &cellIS);CHKERRQ(ierr); 1795 } 1796 ierr = DMPlexComputeResidual_Internal(plex, cellIS, PETSC_MIN_REAL, X, NULL, 0.0, F, user);CHKERRQ(ierr); 1797 ierr = ISDestroy(&cellIS);CHKERRQ(ierr); 1798 ierr = DMDestroy(&plex);CHKERRQ(ierr); 1799 PetscFunctionReturn(0); 1800 } 1801 1802 /*@ 1803 DMPlexSNESComputeBoundaryFEM - Form the boundary values for the local input X 1804 1805 Input Parameters: 1806 + dm - The mesh 1807 - user - The user context 1808 1809 Output Parameter: 1810 . X - Local solution 1811 1812 Level: developer 1813 1814 .seealso: DMPlexComputeJacobianAction() 1815 @*/ 1816 PetscErrorCode DMPlexSNESComputeBoundaryFEM(DM dm, Vec X, void *user) 1817 { 1818 DM plex; 1819 PetscErrorCode ierr; 1820 1821 PetscFunctionBegin; 1822 ierr = DMSNESConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr); 1823 ierr = DMPlexInsertBoundaryValues(plex, PETSC_TRUE, X, PETSC_MIN_REAL, NULL, NULL, NULL);CHKERRQ(ierr); 1824 ierr = DMDestroy(&plex);CHKERRQ(ierr); 1825 PetscFunctionReturn(0); 1826 } 1827 1828 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) 1829 { 1830 DM_Plex *mesh = (DM_Plex *) dm->data; 1831 DM plex = NULL, plexA = NULL, tdm; 1832 DMEnclosureType encAux; 1833 PetscDS prob, probAux = NULL; 1834 PetscSection section, sectionAux = NULL; 1835 PetscSection globalSection, subSection = NULL; 1836 Vec locA = NULL, tv; 1837 PetscScalar *u = NULL, *u_t = NULL, *a = NULL, *elemMat = NULL; 1838 PetscInt v; 1839 PetscInt Nf, totDim, totDimAux = 0; 1840 PetscBool isMatISP, transform; 1841 PetscErrorCode ierr; 1842 1843 PetscFunctionBegin; 1844 ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); 1845 ierr = DMHasBasisTransform(dm, &transform);CHKERRQ(ierr); 1846 ierr = DMGetBasisTransformDM_Internal(dm, &tdm);CHKERRQ(ierr); 1847 ierr = DMGetBasisTransformVec_Internal(dm, &tv);CHKERRQ(ierr); 1848 ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); 1849 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1850 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 1851 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1852 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);CHKERRQ(ierr); 1853 if (locA) { 1854 DM dmAux; 1855 1856 ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); 1857 ierr = DMGetEnclosureRelation(dmAux, dm, &encAux);CHKERRQ(ierr); 1858 ierr = DMConvert(dmAux, DMPLEX, &plexA);CHKERRQ(ierr); 1859 ierr = DMGetDS(plexA, &probAux);CHKERRQ(ierr); 1860 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 1861 ierr = DMGetLocalSection(plexA, §ionAux);CHKERRQ(ierr); 1862 } 1863 1864 ierr = PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatISP);CHKERRQ(ierr); 1865 ierr = DMGetGlobalSection(dm, &globalSection);CHKERRQ(ierr); 1866 if (isMatISP) {ierr = DMPlexGetSubdomainSection(dm, &subSection);CHKERRQ(ierr);} 1867 for (v = 0; v < numValues; ++v) { 1868 PetscFEGeom *fgeom; 1869 PetscInt maxDegree; 1870 PetscQuadrature qGeom = NULL; 1871 IS pointIS; 1872 const PetscInt *points; 1873 PetscInt numFaces, face, Nq; 1874 1875 ierr = DMLabelGetStratumIS(label, values[v], &pointIS);CHKERRQ(ierr); 1876 if (!pointIS) continue; /* No points with that id on this process */ 1877 { 1878 IS isectIS; 1879 1880 /* TODO: Special cases of ISIntersect where it is quick to check a prior if one is a superset of the other */ 1881 ierr = ISIntersect_Caching_Internal(facetIS,pointIS,&isectIS);CHKERRQ(ierr); 1882 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 1883 pointIS = isectIS; 1884 } 1885 ierr = ISGetLocalSize(pointIS, &numFaces);CHKERRQ(ierr); 1886 ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); 1887 ierr = PetscMalloc4(numFaces*totDim, &u, locX_t ? numFaces*totDim : 0, &u_t, numFaces*totDim*totDim, &elemMat, locA ? numFaces*totDimAux : 0, &a);CHKERRQ(ierr); 1888 ierr = DMFieldGetDegree(coordField,pointIS,NULL,&maxDegree);CHKERRQ(ierr); 1889 if (maxDegree <= 1) { 1890 ierr = DMFieldCreateDefaultQuadrature(coordField,pointIS,&qGeom);CHKERRQ(ierr); 1891 } 1892 if (!qGeom) { 1893 PetscFE fe; 1894 1895 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); 1896 ierr = PetscFEGetFaceQuadrature(fe, &qGeom);CHKERRQ(ierr); 1897 ierr = PetscObjectReference((PetscObject)qGeom);CHKERRQ(ierr); 1898 } 1899 ierr = PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 1900 ierr = DMSNESGetFEGeom(coordField,pointIS,qGeom,PETSC_TRUE,&fgeom);CHKERRQ(ierr); 1901 for (face = 0; face < numFaces; ++face) { 1902 const PetscInt point = points[face], *support, *cone; 1903 PetscScalar *x = NULL; 1904 PetscInt i, coneSize, faceLoc; 1905 1906 ierr = DMPlexGetSupport(dm, point, &support);CHKERRQ(ierr); 1907 ierr = DMPlexGetConeSize(dm, support[0], &coneSize);CHKERRQ(ierr); 1908 ierr = DMPlexGetCone(dm, support[0], &cone);CHKERRQ(ierr); 1909 for (faceLoc = 0; faceLoc < coneSize; ++faceLoc) if (cone[faceLoc] == point) break; 1910 if (faceLoc == coneSize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Could not find face %D in cone of support[0] %D", point, support[0]); 1911 fgeom->face[face][0] = faceLoc; 1912 ierr = DMPlexVecGetClosure(plex, section, locX, support[0], NULL, &x);CHKERRQ(ierr); 1913 for (i = 0; i < totDim; ++i) u[face*totDim+i] = x[i]; 1914 ierr = DMPlexVecRestoreClosure(plex, section, locX, support[0], NULL, &x);CHKERRQ(ierr); 1915 if (locX_t) { 1916 ierr = DMPlexVecGetClosure(plex, section, locX_t, support[0], NULL, &x);CHKERRQ(ierr); 1917 for (i = 0; i < totDim; ++i) u_t[face*totDim+i] = x[i]; 1918 ierr = DMPlexVecRestoreClosure(plex, section, locX_t, support[0], NULL, &x);CHKERRQ(ierr); 1919 } 1920 if (locA) { 1921 PetscInt subp; 1922 ierr = DMGetEnclosurePoint(plexA, dm, encAux, support[0], &subp);CHKERRQ(ierr); 1923 ierr = DMPlexVecGetClosure(plexA, sectionAux, locA, subp, NULL, &x);CHKERRQ(ierr); 1924 for (i = 0; i < totDimAux; ++i) a[face*totDimAux+i] = x[i]; 1925 ierr = DMPlexVecRestoreClosure(plexA, sectionAux, locA, subp, NULL, &x);CHKERRQ(ierr); 1926 } 1927 } 1928 ierr = PetscArrayzero(elemMat, numFaces*totDim*totDim);CHKERRQ(ierr); 1929 { 1930 PetscFE fe; 1931 PetscInt Nb; 1932 /* Conforming batches */ 1933 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 1934 /* Remainder */ 1935 PetscFEGeom *chunkGeom = NULL; 1936 PetscInt fieldJ, Nr, offset; 1937 1938 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); 1939 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 1940 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1941 blockSize = Nb; 1942 batchSize = numBlocks * blockSize; 1943 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1944 numChunks = numFaces / (numBatches*batchSize); 1945 Ne = numChunks*numBatches*batchSize; 1946 Nr = numFaces % (numBatches*batchSize); 1947 offset = numFaces - Nr; 1948 ierr = PetscFEGeomGetChunk(fgeom,0,offset,&chunkGeom);CHKERRQ(ierr); 1949 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 1950 ierr = PetscFEIntegrateBdJacobian(prob, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMat);CHKERRQ(ierr); 1951 } 1952 ierr = PetscFEGeomGetChunk(fgeom,offset,numFaces,&chunkGeom);CHKERRQ(ierr); 1953 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 1954 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); 1955 } 1956 ierr = PetscFEGeomRestoreChunk(fgeom,offset,numFaces,&chunkGeom);CHKERRQ(ierr); 1957 } 1958 for (face = 0; face < numFaces; ++face) { 1959 const PetscInt point = points[face], *support; 1960 1961 /* Transform to global basis before insertion in Jacobian */ 1962 ierr = DMPlexGetSupport(plex, point, &support);CHKERRQ(ierr); 1963 if (transform) {ierr = DMPlexBasisTransformPointTensor_Internal(dm, tdm, tv, support[0], PETSC_TRUE, totDim, &elemMat[face*totDim*totDim]);CHKERRQ(ierr);} 1964 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(point, "BdJacobian", totDim, totDim, &elemMat[face*totDim*totDim]);CHKERRQ(ierr);} 1965 if (!isMatISP) { 1966 ierr = DMPlexMatSetClosure(plex, section, globalSection, JacP, support[0], &elemMat[face*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 1967 } else { 1968 Mat lJ; 1969 1970 ierr = MatISGetLocalMat(JacP, &lJ);CHKERRQ(ierr); 1971 ierr = DMPlexMatSetClosure(plex, section, subSection, lJ, support[0], &elemMat[face*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 1972 } 1973 } 1974 ierr = DMSNESRestoreFEGeom(coordField,pointIS,qGeom,PETSC_TRUE,&fgeom);CHKERRQ(ierr); 1975 ierr = PetscQuadratureDestroy(&qGeom);CHKERRQ(ierr); 1976 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 1977 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 1978 ierr = PetscFree4(u, u_t, elemMat, a);CHKERRQ(ierr); 1979 } 1980 if (plex) {ierr = DMDestroy(&plex);CHKERRQ(ierr);} 1981 if (plexA) {ierr = DMDestroy(&plexA);CHKERRQ(ierr);} 1982 PetscFunctionReturn(0); 1983 } 1984 1985 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) 1986 { 1987 DMField coordField; 1988 DMLabel depthLabel; 1989 IS facetIS; 1990 PetscInt dim; 1991 PetscErrorCode ierr; 1992 1993 PetscFunctionBegin; 1994 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1995 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 1996 ierr = DMLabelGetStratumIS(depthLabel, dim-1, &facetIS);CHKERRQ(ierr); 1997 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 1998 ierr = DMPlexComputeBdJacobian_Single_Internal(dm, t, label, numValues, values, field, locX, locX_t, X_tShift, Jac, JacP, coordField, facetIS);CHKERRQ(ierr); 1999 ierr = ISDestroy(&facetIS);CHKERRQ(ierr); 2000 PetscFunctionReturn(0); 2001 } 2002 2003 PetscErrorCode DMPlexComputeBdJacobian_Internal(DM dm, Vec locX, Vec locX_t, PetscReal t, PetscReal X_tShift, Mat Jac, Mat JacP, void *user) 2004 { 2005 PetscDS prob; 2006 PetscInt dim, numBd, bd; 2007 DMLabel depthLabel; 2008 DMField coordField = NULL; 2009 IS facetIS; 2010 PetscErrorCode ierr; 2011 2012 PetscFunctionBegin; 2013 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 2014 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 2015 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 2016 ierr = DMLabelGetStratumIS(depthLabel, dim-1, &facetIS);CHKERRQ(ierr); 2017 ierr = PetscDSGetNumBoundary(prob, &numBd);CHKERRQ(ierr); 2018 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 2019 for (bd = 0; bd < numBd; ++bd) { 2020 DMBoundaryConditionType type; 2021 const char *bdLabel; 2022 DMLabel label; 2023 const PetscInt *values; 2024 PetscInt fieldI, numValues; 2025 PetscObject obj; 2026 PetscClassId id; 2027 2028 ierr = PetscDSGetBoundary(prob, bd, &type, NULL, &bdLabel, &fieldI, NULL, NULL, NULL, &numValues, &values, NULL);CHKERRQ(ierr); 2029 ierr = PetscDSGetDiscretization(prob, fieldI, &obj);CHKERRQ(ierr); 2030 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 2031 if ((id != PETSCFE_CLASSID) || (type & DM_BC_ESSENTIAL)) continue; 2032 ierr = DMGetLabel(dm, bdLabel, &label);CHKERRQ(ierr); 2033 ierr = DMPlexComputeBdJacobian_Single_Internal(dm, t, label, numValues, values, fieldI, locX, locX_t, X_tShift, Jac, JacP, coordField, facetIS);CHKERRQ(ierr); 2034 } 2035 ierr = ISDestroy(&facetIS);CHKERRQ(ierr); 2036 PetscFunctionReturn(0); 2037 } 2038 2039 PetscErrorCode DMPlexComputeJacobian_Internal(DM dm, IS cellIS, PetscReal t, PetscReal X_tShift, Vec X, Vec X_t, Mat Jac, Mat JacP,void *user) 2040 { 2041 DM_Plex *mesh = (DM_Plex *) dm->data; 2042 const char *name = "Jacobian"; 2043 DM dmAux, plex, tdm; 2044 DMEnclosureType encAux; 2045 Vec A, tv; 2046 DMField coordField; 2047 PetscDS prob, probAux = NULL; 2048 PetscSection section, globalSection, subSection, sectionAux; 2049 PetscScalar *elemMat, *elemMatP, *elemMatD, *u, *u_t, *a = NULL; 2050 const PetscInt *cells; 2051 PetscInt Nf, fieldI, fieldJ; 2052 PetscInt totDim, totDimAux, cStart, cEnd, numCells, c; 2053 PetscBool isMatIS, isMatISP, hasJac, hasPrec, hasDyn, hasFV = PETSC_FALSE, transform; 2054 PetscErrorCode ierr; 2055 2056 PetscFunctionBegin; 2057 ierr = PetscLogEventBegin(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 2058 ierr = ISGetLocalSize(cellIS, &numCells);CHKERRQ(ierr); 2059 ierr = ISGetPointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 2060 ierr = DMHasBasisTransform(dm, &transform);CHKERRQ(ierr); 2061 ierr = DMGetBasisTransformDM_Internal(dm, &tdm);CHKERRQ(ierr); 2062 ierr = DMGetBasisTransformVec_Internal(dm, &tv);CHKERRQ(ierr); 2063 ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); 2064 ierr = PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatISP);CHKERRQ(ierr); 2065 ierr = DMGetGlobalSection(dm, &globalSection);CHKERRQ(ierr); 2066 if (isMatISP) {ierr = DMPlexGetSubdomainSection(dm, &subSection);CHKERRQ(ierr);} 2067 ierr = ISGetLocalSize(cellIS, &numCells);CHKERRQ(ierr); 2068 ierr = ISGetPointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 2069 ierr = DMGetCellDS(dm, cStart, &prob);CHKERRQ(ierr); 2070 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 2071 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 2072 ierr = PetscDSHasJacobian(prob, &hasJac);CHKERRQ(ierr); 2073 ierr = PetscDSHasJacobianPreconditioner(prob, &hasPrec);CHKERRQ(ierr); 2074 /* user passed in the same matrix, avoid double contributions and 2075 only assemble the Jacobian */ 2076 if (hasJac && Jac == JacP) hasPrec = PETSC_FALSE; 2077 ierr = PetscDSHasDynamicJacobian(prob, &hasDyn);CHKERRQ(ierr); 2078 hasDyn = hasDyn && (X_tShift != 0.0) ? PETSC_TRUE : PETSC_FALSE; 2079 ierr = PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);CHKERRQ(ierr); 2080 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);CHKERRQ(ierr); 2081 if (dmAux) { 2082 ierr = DMGetEnclosureRelation(dmAux, dm, &encAux);CHKERRQ(ierr); 2083 ierr = DMConvert(dmAux, DMPLEX, &plex);CHKERRQ(ierr); 2084 ierr = DMGetLocalSection(plex, §ionAux);CHKERRQ(ierr); 2085 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 2086 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 2087 } 2088 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); 2089 if (dmAux) {ierr = PetscMalloc1(numCells*totDimAux, &a);CHKERRQ(ierr);} 2090 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 2091 for (c = cStart; c < cEnd; ++c) { 2092 const PetscInt cell = cells ? cells[c] : c; 2093 const PetscInt cind = c - cStart; 2094 PetscScalar *x = NULL, *x_t = NULL; 2095 PetscInt i; 2096 2097 ierr = DMPlexVecGetClosure(dm, section, X, cell, NULL, &x);CHKERRQ(ierr); 2098 for (i = 0; i < totDim; ++i) u[cind*totDim+i] = x[i]; 2099 ierr = DMPlexVecRestoreClosure(dm, section, X, cell, NULL, &x);CHKERRQ(ierr); 2100 if (X_t) { 2101 ierr = DMPlexVecGetClosure(dm, section, X_t, cell, NULL, &x_t);CHKERRQ(ierr); 2102 for (i = 0; i < totDim; ++i) u_t[cind*totDim+i] = x_t[i]; 2103 ierr = DMPlexVecRestoreClosure(dm, section, X_t, cell, NULL, &x_t);CHKERRQ(ierr); 2104 } 2105 if (dmAux) { 2106 PetscInt subcell; 2107 ierr = DMGetEnclosurePoint(dmAux, dm, encAux, cell, &subcell);CHKERRQ(ierr); 2108 ierr = DMPlexVecGetClosure(plex, sectionAux, A, subcell, NULL, &x);CHKERRQ(ierr); 2109 for (i = 0; i < totDimAux; ++i) a[cind*totDimAux+i] = x[i]; 2110 ierr = DMPlexVecRestoreClosure(plex, sectionAux, A, subcell, NULL, &x);CHKERRQ(ierr); 2111 } 2112 } 2113 if (hasJac) {ierr = PetscArrayzero(elemMat, numCells*totDim*totDim);CHKERRQ(ierr);} 2114 if (hasPrec) {ierr = PetscArrayzero(elemMatP, numCells*totDim*totDim);CHKERRQ(ierr);} 2115 if (hasDyn) {ierr = PetscArrayzero(elemMatD, numCells*totDim*totDim);CHKERRQ(ierr);} 2116 for (fieldI = 0; fieldI < Nf; ++fieldI) { 2117 PetscClassId id; 2118 PetscFE fe; 2119 PetscQuadrature qGeom = NULL; 2120 PetscInt Nb; 2121 /* Conforming batches */ 2122 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 2123 /* Remainder */ 2124 PetscInt Nr, offset, Nq; 2125 PetscInt maxDegree; 2126 PetscFEGeom *cgeomFEM, *chunkGeom = NULL, *remGeom = NULL; 2127 2128 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); 2129 ierr = PetscObjectGetClassId((PetscObject) fe, &id);CHKERRQ(ierr); 2130 if (id == PETSCFV_CLASSID) {hasFV = PETSC_TRUE; continue;} 2131 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 2132 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 2133 ierr = DMFieldGetDegree(coordField,cellIS,NULL,&maxDegree);CHKERRQ(ierr); 2134 if (maxDegree <= 1) { 2135 ierr = DMFieldCreateDefaultQuadrature(coordField,cellIS,&qGeom);CHKERRQ(ierr); 2136 } 2137 if (!qGeom) { 2138 ierr = PetscFEGetQuadrature(fe,&qGeom);CHKERRQ(ierr); 2139 ierr = PetscObjectReference((PetscObject)qGeom);CHKERRQ(ierr); 2140 } 2141 ierr = PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 2142 ierr = DMSNESGetFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);CHKERRQ(ierr); 2143 blockSize = Nb; 2144 batchSize = numBlocks * blockSize; 2145 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 2146 numChunks = numCells / (numBatches*batchSize); 2147 Ne = numChunks*numBatches*batchSize; 2148 Nr = numCells % (numBatches*batchSize); 2149 offset = numCells - Nr; 2150 ierr = PetscFEGeomGetChunk(cgeomFEM,0,offset,&chunkGeom);CHKERRQ(ierr); 2151 ierr = PetscFEGeomGetChunk(cgeomFEM,offset,numCells,&remGeom);CHKERRQ(ierr); 2152 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 2153 if (hasJac) { 2154 ierr = PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMat);CHKERRQ(ierr); 2155 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); 2156 } 2157 if (hasPrec) { 2158 ierr = PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN_PRE, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMatP);CHKERRQ(ierr); 2159 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); 2160 } 2161 if (hasDyn) { 2162 ierr = PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN_DYN, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMatD);CHKERRQ(ierr); 2163 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); 2164 } 2165 } 2166 ierr = PetscFEGeomRestoreChunk(cgeomFEM,offset,numCells,&remGeom);CHKERRQ(ierr); 2167 ierr = PetscFEGeomRestoreChunk(cgeomFEM,0,offset,&chunkGeom);CHKERRQ(ierr); 2168 ierr = DMSNESRestoreFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);CHKERRQ(ierr); 2169 ierr = PetscQuadratureDestroy(&qGeom);CHKERRQ(ierr); 2170 } 2171 /* Add contribution from X_t */ 2172 if (hasDyn) {for (c = 0; c < numCells*totDim*totDim; ++c) elemMat[c] += X_tShift*elemMatD[c];} 2173 if (hasFV) { 2174 PetscClassId id; 2175 PetscFV fv; 2176 PetscInt offsetI, NcI, NbI = 1, fc, f; 2177 2178 for (fieldI = 0; fieldI < Nf; ++fieldI) { 2179 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fv);CHKERRQ(ierr); 2180 ierr = PetscDSGetFieldOffset(prob, fieldI, &offsetI);CHKERRQ(ierr); 2181 ierr = PetscObjectGetClassId((PetscObject) fv, &id);CHKERRQ(ierr); 2182 if (id != PETSCFV_CLASSID) continue; 2183 /* Put in the identity */ 2184 ierr = PetscFVGetNumComponents(fv, &NcI);CHKERRQ(ierr); 2185 for (c = cStart; c < cEnd; ++c) { 2186 const PetscInt cind = c - cStart; 2187 const PetscInt eOffset = cind*totDim*totDim; 2188 for (fc = 0; fc < NcI; ++fc) { 2189 for (f = 0; f < NbI; ++f) { 2190 const PetscInt i = offsetI + f*NcI+fc; 2191 if (hasPrec) { 2192 if (hasJac) {elemMat[eOffset+i*totDim+i] = 1.0;} 2193 elemMatP[eOffset+i*totDim+i] = 1.0; 2194 } else {elemMat[eOffset+i*totDim+i] = 1.0;} 2195 } 2196 } 2197 } 2198 } 2199 /* No allocated space for FV stuff, so ignore the zero entries */ 2200 ierr = MatSetOption(JacP, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE);CHKERRQ(ierr); 2201 } 2202 /* Insert values into matrix */ 2203 isMatIS = PETSC_FALSE; 2204 if (hasPrec && hasJac) { 2205 ierr = PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatIS);CHKERRQ(ierr); 2206 } 2207 if (isMatIS && !subSection) { 2208 ierr = DMPlexGetSubdomainSection(dm, &subSection);CHKERRQ(ierr); 2209 } 2210 for (c = cStart; c < cEnd; ++c) { 2211 const PetscInt cell = cells ? cells[c] : c; 2212 const PetscInt cind = c - cStart; 2213 2214 /* Transform to global basis before insertion in Jacobian */ 2215 if (transform) {ierr = DMPlexBasisTransformPointTensor_Internal(dm, tdm, tv, cell, PETSC_TRUE, totDim, &elemMat[cind*totDim*totDim]);CHKERRQ(ierr);} 2216 if (hasPrec) { 2217 if (hasJac) { 2218 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(cell, name, totDim, totDim, &elemMat[cind*totDim*totDim]);CHKERRQ(ierr);} 2219 if (!isMatIS) { 2220 ierr = DMPlexMatSetClosure(dm, section, globalSection, Jac, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2221 } else { 2222 Mat lJ; 2223 2224 ierr = MatISGetLocalMat(Jac,&lJ);CHKERRQ(ierr); 2225 ierr = DMPlexMatSetClosure(dm, section, subSection, lJ, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2226 } 2227 } 2228 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(cell, name, totDim, totDim, &elemMatP[cind*totDim*totDim]);CHKERRQ(ierr);} 2229 if (!isMatISP) { 2230 ierr = DMPlexMatSetClosure(dm, section, globalSection, JacP, cell, &elemMatP[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2231 } else { 2232 Mat lJ; 2233 2234 ierr = MatISGetLocalMat(JacP,&lJ);CHKERRQ(ierr); 2235 ierr = DMPlexMatSetClosure(dm, section, subSection, lJ, cell, &elemMatP[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2236 } 2237 } else { 2238 if (hasJac) { 2239 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(cell, name, totDim, totDim, &elemMat[cind*totDim*totDim]);CHKERRQ(ierr);} 2240 if (!isMatISP) { 2241 ierr = DMPlexMatSetClosure(dm, section, globalSection, JacP, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2242 } else { 2243 Mat lJ; 2244 2245 ierr = MatISGetLocalMat(JacP,&lJ);CHKERRQ(ierr); 2246 ierr = DMPlexMatSetClosure(dm, section, subSection, lJ, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2247 } 2248 } 2249 } 2250 } 2251 ierr = ISRestorePointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 2252 if (hasFV) {ierr = MatSetOption(JacP, MAT_IGNORE_ZERO_ENTRIES, PETSC_FALSE);CHKERRQ(ierr);} 2253 ierr = PetscFree5(u,u_t,elemMat,elemMatP,elemMatD);CHKERRQ(ierr); 2254 if (dmAux) { 2255 ierr = PetscFree(a);CHKERRQ(ierr); 2256 ierr = DMDestroy(&plex);CHKERRQ(ierr); 2257 } 2258 /* Compute boundary integrals */ 2259 ierr = DMPlexComputeBdJacobian_Internal(dm, X, X_t, t, X_tShift, Jac, JacP, user);CHKERRQ(ierr); 2260 /* Assemble matrix */ 2261 if (hasJac && hasPrec) { 2262 ierr = MatAssemblyBegin(Jac, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2263 ierr = MatAssemblyEnd(Jac, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2264 } 2265 ierr = MatAssemblyBegin(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2266 ierr = MatAssemblyEnd(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2267 ierr = PetscLogEventEnd(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 2268 PetscFunctionReturn(0); 2269 } 2270 2271 PetscErrorCode DMPlexComputeJacobian_Hybrid_Internal(DM dm, IS cellIS, PetscReal t, PetscReal X_tShift, Vec locX, Vec locX_t, Mat Jac, Mat JacP, void *user) 2272 { 2273 DM_Plex *mesh = (DM_Plex *) dm->data; 2274 const char *name = "Hybrid Jacobian"; 2275 DM dmAux = NULL; 2276 DM plex = NULL; 2277 DM plexA = NULL; 2278 DMLabel ghostLabel = NULL; 2279 PetscDS prob = NULL; 2280 PetscDS probAux = NULL; 2281 PetscSection section = NULL; 2282 DMField coordField = NULL; 2283 Vec locA; 2284 PetscScalar *u = NULL, *u_t, *a = NULL; 2285 PetscScalar *elemMat, *elemMatP; 2286 PetscSection globalSection, subSection, sectionAux; 2287 IS chunkIS; 2288 const PetscInt *cells; 2289 PetscInt *faces; 2290 PetscInt cStart, cEnd, numCells; 2291 PetscInt Nf, fieldI, fieldJ, totDim, totDimAux, numChunks, cellChunkSize, chunk; 2292 PetscInt maxDegree = PETSC_MAX_INT; 2293 PetscQuadrature affineQuad = NULL, *quads = NULL; 2294 PetscFEGeom *affineGeom = NULL, **geoms = NULL; 2295 PetscBool isMatIS = PETSC_FALSE, isMatISP = PETSC_FALSE, hasBdJac, hasBdPrec; 2296 PetscErrorCode ierr; 2297 2298 PetscFunctionBegin; 2299 ierr = PetscLogEventBegin(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 2300 ierr = ISGetLocalSize(cellIS, &numCells);CHKERRQ(ierr); 2301 ierr = ISGetPointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 2302 ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); 2303 ierr = DMGetSection(dm, §ion);CHKERRQ(ierr); 2304 ierr = DMGetGlobalSection(dm, &globalSection);CHKERRQ(ierr); 2305 ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 2306 ierr = DMGetCellDS(dm, cStart, &prob);CHKERRQ(ierr); 2307 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 2308 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 2309 ierr = PetscDSHasBdJacobian(prob, &hasBdJac);CHKERRQ(ierr); 2310 ierr = PetscDSHasBdJacobianPreconditioner(prob, &hasBdPrec);CHKERRQ(ierr); 2311 ierr = PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatISP);CHKERRQ(ierr); 2312 if (isMatISP) {ierr = DMPlexGetSubdomainSection(plex, &subSection);CHKERRQ(ierr);} 2313 if (hasBdPrec && hasBdJac) {ierr = PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatIS);CHKERRQ(ierr);} 2314 if (isMatIS && !subSection) {ierr = DMPlexGetSubdomainSection(plex, &subSection);CHKERRQ(ierr);} 2315 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);CHKERRQ(ierr); 2316 if (locA) { 2317 ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); 2318 ierr = DMConvert(dmAux, DMPLEX, &plexA);CHKERRQ(ierr); 2319 ierr = DMGetSection(dmAux, §ionAux);CHKERRQ(ierr); 2320 ierr = DMGetCellDS(dmAux, cStart, &probAux);CHKERRQ(ierr); 2321 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 2322 } 2323 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 2324 ierr = DMFieldGetDegree(coordField, cellIS, NULL, &maxDegree);CHKERRQ(ierr); 2325 if (maxDegree > 1) { 2326 PetscInt f; 2327 ierr = PetscCalloc2(Nf,&quads,Nf,&geoms);CHKERRQ(ierr); 2328 for (f = 0; f < Nf; ++f) { 2329 PetscFE fe; 2330 2331 ierr = PetscDSGetDiscretization(prob, f, (PetscObject *) &fe);CHKERRQ(ierr); 2332 if (fe) { 2333 ierr = PetscFEGetQuadrature(fe, &quads[f]);CHKERRQ(ierr); 2334 ierr = PetscObjectReference((PetscObject) quads[f]);CHKERRQ(ierr); 2335 } 2336 } 2337 } 2338 cellChunkSize = numCells; 2339 numChunks = !numCells ? 0 : PetscCeilReal(((PetscReal) numCells)/cellChunkSize); 2340 ierr = PetscCalloc1(2*cellChunkSize, &faces);CHKERRQ(ierr); 2341 ierr = ISCreateGeneral(PETSC_COMM_SELF, cellChunkSize, faces, PETSC_USE_POINTER, &chunkIS);CHKERRQ(ierr); 2342 ierr = DMPlexGetCellFields(dm, cellIS, locX, locX_t, locA, &u, &u_t, &a);CHKERRQ(ierr); 2343 ierr = DMGetWorkArray(dm, hasBdJac ? cellChunkSize*totDim*totDim : 0, MPIU_SCALAR, &elemMat);CHKERRQ(ierr); 2344 ierr = DMGetWorkArray(dm, hasBdPrec ? cellChunkSize*totDim*totDim : 0, MPIU_SCALAR, &elemMatP);CHKERRQ(ierr); 2345 for (chunk = 0; chunk < numChunks; ++chunk) { 2346 PetscInt cS = cStart+chunk*cellChunkSize, cE = PetscMin(cS+cellChunkSize, cEnd), numCells = cE - cS, c; 2347 2348 if (hasBdJac) {ierr = PetscMemzero(elemMat, numCells*totDim*totDim * sizeof(PetscScalar));CHKERRQ(ierr);} 2349 if (hasBdPrec) {ierr = PetscMemzero(elemMatP, numCells*totDim*totDim * sizeof(PetscScalar));CHKERRQ(ierr);} 2350 /* Get faces */ 2351 for (c = cS; c < cE; ++c) { 2352 const PetscInt cell = cells ? cells[c] : c; 2353 const PetscInt *cone; 2354 ierr = DMPlexGetCone(plex, cell, &cone);CHKERRQ(ierr); 2355 faces[(c-cS)*2+0] = cone[0]; 2356 faces[(c-cS)*2+1] = cone[1]; 2357 } 2358 ierr = ISGeneralSetIndices(chunkIS, cellChunkSize, faces, PETSC_USE_POINTER);CHKERRQ(ierr); 2359 if (maxDegree <= 1) { 2360 if (!affineQuad) {ierr = DMFieldCreateDefaultQuadrature(coordField, chunkIS, &affineQuad);CHKERRQ(ierr);} 2361 if (affineQuad) {ierr = DMSNESGetFEGeom(coordField, chunkIS, affineQuad, PETSC_TRUE, &affineGeom);CHKERRQ(ierr);} 2362 } else { 2363 PetscInt f; 2364 for (f = 0; f < Nf; ++f) { 2365 if (quads[f]) {ierr = DMSNESGetFEGeom(coordField, chunkIS, quads[f], PETSC_TRUE, &geoms[f]);CHKERRQ(ierr);} 2366 } 2367 } 2368 2369 for (fieldI = 0; fieldI < Nf; ++fieldI) { 2370 PetscFE feI; 2371 PetscFEGeom *geom = affineGeom ? affineGeom : geoms[fieldI]; 2372 PetscFEGeom *chunkGeom = NULL, *remGeom = NULL; 2373 PetscQuadrature quad = affineQuad ? affineQuad : quads[fieldI]; 2374 PetscInt numChunks, numBatches, batchSize, numBlocks, blockSize, Ne, Nr, offset, Nq, Nb; 2375 2376 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &feI);CHKERRQ(ierr); 2377 if (!feI) continue; 2378 ierr = PetscFEGetTileSizes(feI, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 2379 ierr = PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 2380 ierr = PetscFEGetDimension(feI, &Nb);CHKERRQ(ierr); 2381 blockSize = Nb; 2382 batchSize = numBlocks * blockSize; 2383 ierr = PetscFESetTileSizes(feI, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 2384 numChunks = numCells / (numBatches*batchSize); 2385 Ne = numChunks*numBatches*batchSize; 2386 Nr = numCells % (numBatches*batchSize); 2387 offset = numCells - Nr; 2388 ierr = PetscFEGeomGetChunk(geom,0,offset,&chunkGeom);CHKERRQ(ierr); 2389 ierr = PetscFEGeomGetChunk(geom,offset,numCells,&remGeom);CHKERRQ(ierr); 2390 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 2391 PetscFE feJ; 2392 2393 ierr = PetscDSGetDiscretization(prob, fieldJ, (PetscObject *) &feJ);CHKERRQ(ierr); 2394 if (!feJ) continue; 2395 if (hasBdJac) { 2396 ierr = PetscFEIntegrateHybridJacobian(prob, PETSCFE_JACOBIAN, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMat);CHKERRQ(ierr); 2397 ierr = PetscFEIntegrateHybridJacobian(prob, PETSCFE_JACOBIAN, fieldI, fieldJ, Nr, remGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, X_tShift, &elemMat[offset*totDim*totDim]);CHKERRQ(ierr); 2398 } 2399 if (hasBdPrec) { 2400 ierr = PetscFEIntegrateHybridJacobian(prob, PETSCFE_JACOBIAN_PRE, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMatP);CHKERRQ(ierr); 2401 ierr = PetscFEIntegrateHybridJacobian(prob, PETSCFE_JACOBIAN_PRE, fieldI, fieldJ, Nr, remGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, X_tShift, &elemMatP[offset*totDim*totDim]);CHKERRQ(ierr); 2402 } 2403 } 2404 ierr = PetscFEGeomRestoreChunk(geom,offset,numCells,&remGeom);CHKERRQ(ierr); 2405 ierr = PetscFEGeomRestoreChunk(geom,0,offset,&chunkGeom);CHKERRQ(ierr); 2406 } 2407 /* Insert values into matrix */ 2408 for (c = cS; c < cE; ++c) { 2409 const PetscInt cell = cells ? cells[c] : c; 2410 const PetscInt cind = c - cS; 2411 2412 if (hasBdPrec) { 2413 if (hasBdJac) { 2414 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(cell, name, totDim, totDim, &elemMat[cind*totDim*totDim]);CHKERRQ(ierr);} 2415 if (!isMatIS) { 2416 ierr = DMPlexMatSetClosure(plex, section, globalSection, Jac, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2417 } else { 2418 Mat lJ; 2419 2420 ierr = MatISGetLocalMat(Jac,&lJ);CHKERRQ(ierr); 2421 ierr = DMPlexMatSetClosure(plex, section, subSection, lJ, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2422 } 2423 } 2424 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(cell, name, totDim, totDim, &elemMatP[cind*totDim*totDim]);CHKERRQ(ierr);} 2425 if (!isMatISP) { 2426 ierr = DMPlexMatSetClosure(plex, section, globalSection, JacP, cell, &elemMatP[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2427 } else { 2428 Mat lJ; 2429 2430 ierr = MatISGetLocalMat(JacP,&lJ);CHKERRQ(ierr); 2431 ierr = DMPlexMatSetClosure(plex, section, subSection, lJ, cell, &elemMatP[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2432 } 2433 } else if (hasBdJac) { 2434 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(cell, name, totDim, totDim, &elemMat[cind*totDim*totDim]);CHKERRQ(ierr);} 2435 if (!isMatISP) { 2436 ierr = DMPlexMatSetClosure(plex, section, globalSection, JacP, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2437 } else { 2438 Mat lJ; 2439 2440 ierr = MatISGetLocalMat(JacP,&lJ);CHKERRQ(ierr); 2441 ierr = DMPlexMatSetClosure(plex, section, subSection, lJ, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2442 } 2443 } 2444 } 2445 } 2446 ierr = DMPlexRestoreCellFields(dm, cellIS, locX, locX_t, locA, &u, &u_t, &a);CHKERRQ(ierr); 2447 ierr = DMRestoreWorkArray(dm, hasBdJac ? cellChunkSize*totDim*totDim : 0, MPIU_SCALAR, &elemMat);CHKERRQ(ierr); 2448 ierr = DMRestoreWorkArray(dm, hasBdPrec ? cellChunkSize*totDim*totDim : 0, MPIU_SCALAR, &elemMatP);CHKERRQ(ierr); 2449 ierr = PetscFree(faces);CHKERRQ(ierr); 2450 ierr = ISDestroy(&chunkIS);CHKERRQ(ierr); 2451 ierr = ISRestorePointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 2452 if (maxDegree <= 1) { 2453 ierr = DMSNESRestoreFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&affineGeom);CHKERRQ(ierr); 2454 ierr = PetscQuadratureDestroy(&affineQuad);CHKERRQ(ierr); 2455 } else { 2456 PetscInt f; 2457 for (f = 0; f < Nf; ++f) { 2458 if (geoms) {ierr = DMSNESRestoreFEGeom(coordField,cellIS,quads[f],PETSC_FALSE, &geoms[f]);CHKERRQ(ierr);} 2459 if (quads) {ierr = PetscQuadratureDestroy(&quads[f]);CHKERRQ(ierr);} 2460 } 2461 ierr = PetscFree2(quads,geoms);CHKERRQ(ierr); 2462 } 2463 if (dmAux) {ierr = DMDestroy(&plexA);CHKERRQ(ierr);} 2464 ierr = DMDestroy(&plex);CHKERRQ(ierr); 2465 /* Assemble matrix */ 2466 if (hasBdJac && hasBdPrec) { 2467 ierr = MatAssemblyBegin(Jac, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2468 ierr = MatAssemblyEnd(Jac, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2469 } 2470 ierr = MatAssemblyBegin(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2471 ierr = MatAssemblyEnd(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2472 ierr = PetscLogEventEnd(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 2473 PetscFunctionReturn(0); 2474 } 2475 2476 /*@ 2477 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. 2478 2479 Input Parameters: 2480 + dm - The mesh 2481 . cellIS - 2482 . t - The time 2483 . X_tShift - The multiplier for the Jacobian with repsect to X_t 2484 . X - Local solution vector 2485 . X_t - Time-derivative of the local solution vector 2486 . Y - Local input vector 2487 - user - The user context 2488 2489 Output Parameter: 2490 . Z - Local output vector 2491 2492 Note: 2493 We form the residual one batch of elements at a time. This allows us to offload work onto an accelerator, 2494 like a GPU, or vectorize on a multicore machine. 2495 2496 Level: developer 2497 2498 .seealso: FormFunctionLocal() 2499 @*/ 2500 PetscErrorCode DMPlexComputeJacobianAction(DM dm, IS cellIS, PetscReal t, PetscReal X_tShift, Vec X, Vec X_t, Vec Y, Vec Z, void *user) 2501 { 2502 DM_Plex *mesh = (DM_Plex *) dm->data; 2503 const char *name = "Jacobian"; 2504 DM dmAux, plex, plexAux = NULL; 2505 DMEnclosureType encAux; 2506 Vec A; 2507 PetscDS prob, probAux = NULL; 2508 PetscQuadrature quad; 2509 PetscSection section, globalSection, sectionAux; 2510 PetscScalar *elemMat, *elemMatD, *u, *u_t, *a = NULL, *y, *z; 2511 PetscInt Nf, fieldI, fieldJ; 2512 PetscInt totDim, totDimAux = 0; 2513 const PetscInt *cells; 2514 PetscInt cStart, cEnd, numCells, c; 2515 PetscBool hasDyn; 2516 DMField coordField; 2517 PetscErrorCode ierr; 2518 2519 PetscFunctionBegin; 2520 ierr = PetscLogEventBegin(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 2521 ierr = DMSNESConvertPlex(dm, &plex, PETSC_TRUE);CHKERRQ(ierr); 2522 if (!cellIS) { 2523 PetscInt depth; 2524 2525 ierr = DMPlexGetDepth(plex, &depth);CHKERRQ(ierr); 2526 ierr = DMGetStratumIS(plex, "dim", depth, &cellIS);CHKERRQ(ierr); 2527 if (!cellIS) {ierr = DMGetStratumIS(plex, "depth", depth, &cellIS);CHKERRQ(ierr);} 2528 } else { 2529 ierr = PetscObjectReference((PetscObject) cellIS);CHKERRQ(ierr); 2530 } 2531 ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); 2532 ierr = DMGetGlobalSection(dm, &globalSection);CHKERRQ(ierr); 2533 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 2534 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 2535 ierr = PetscDSHasDynamicJacobian(prob, &hasDyn);CHKERRQ(ierr); 2536 hasDyn = hasDyn && (X_tShift != 0.0) ? PETSC_TRUE : PETSC_FALSE; 2537 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); 2538 ierr = ISGetLocalSize(cellIS, &numCells);CHKERRQ(ierr); 2539 ierr = ISGetPointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 2540 ierr = PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);CHKERRQ(ierr); 2541 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);CHKERRQ(ierr); 2542 if (dmAux) { 2543 ierr = DMGetEnclosureRelation(dmAux, dm, &encAux);CHKERRQ(ierr); 2544 ierr = DMConvert(dmAux, DMPLEX, &plexAux);CHKERRQ(ierr); 2545 ierr = DMGetLocalSection(plexAux, §ionAux);CHKERRQ(ierr); 2546 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 2547 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 2548 } 2549 ierr = VecSet(Z, 0.0);CHKERRQ(ierr); 2550 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); 2551 if (dmAux) {ierr = PetscMalloc1(numCells*totDimAux, &a);CHKERRQ(ierr);} 2552 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 2553 for (c = cStart; c < cEnd; ++c) { 2554 const PetscInt cell = cells ? cells[c] : c; 2555 const PetscInt cind = c - cStart; 2556 PetscScalar *x = NULL, *x_t = NULL; 2557 PetscInt i; 2558 2559 ierr = DMPlexVecGetClosure(dm, section, X, cell, NULL, &x);CHKERRQ(ierr); 2560 for (i = 0; i < totDim; ++i) u[cind*totDim+i] = x[i]; 2561 ierr = DMPlexVecRestoreClosure(dm, section, X, cell, NULL, &x);CHKERRQ(ierr); 2562 if (X_t) { 2563 ierr = DMPlexVecGetClosure(dm, section, X_t, cell, NULL, &x_t);CHKERRQ(ierr); 2564 for (i = 0; i < totDim; ++i) u_t[cind*totDim+i] = x_t[i]; 2565 ierr = DMPlexVecRestoreClosure(dm, section, X_t, cell, NULL, &x_t);CHKERRQ(ierr); 2566 } 2567 if (dmAux) { 2568 PetscInt subcell; 2569 ierr = DMGetEnclosurePoint(dmAux, dm, encAux, cell, &subcell);CHKERRQ(ierr); 2570 ierr = DMPlexVecGetClosure(plexAux, sectionAux, A, subcell, NULL, &x);CHKERRQ(ierr); 2571 for (i = 0; i < totDimAux; ++i) a[cind*totDimAux+i] = x[i]; 2572 ierr = DMPlexVecRestoreClosure(plexAux, sectionAux, A, subcell, NULL, &x);CHKERRQ(ierr); 2573 } 2574 ierr = DMPlexVecGetClosure(dm, section, Y, cell, NULL, &x);CHKERRQ(ierr); 2575 for (i = 0; i < totDim; ++i) y[cind*totDim+i] = x[i]; 2576 ierr = DMPlexVecRestoreClosure(dm, section, Y, cell, NULL, &x);CHKERRQ(ierr); 2577 } 2578 ierr = PetscArrayzero(elemMat, numCells*totDim*totDim);CHKERRQ(ierr); 2579 if (hasDyn) {ierr = PetscArrayzero(elemMatD, numCells*totDim*totDim);CHKERRQ(ierr);} 2580 for (fieldI = 0; fieldI < Nf; ++fieldI) { 2581 PetscFE fe; 2582 PetscInt Nb; 2583 /* Conforming batches */ 2584 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 2585 /* Remainder */ 2586 PetscInt Nr, offset, Nq; 2587 PetscQuadrature qGeom = NULL; 2588 PetscInt maxDegree; 2589 PetscFEGeom *cgeomFEM, *chunkGeom = NULL, *remGeom = NULL; 2590 2591 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); 2592 ierr = PetscFEGetQuadrature(fe, &quad);CHKERRQ(ierr); 2593 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 2594 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 2595 ierr = DMFieldGetDegree(coordField,cellIS,NULL,&maxDegree);CHKERRQ(ierr); 2596 if (maxDegree <= 1) {ierr = DMFieldCreateDefaultQuadrature(coordField,cellIS,&qGeom);CHKERRQ(ierr);} 2597 if (!qGeom) { 2598 ierr = PetscFEGetQuadrature(fe,&qGeom);CHKERRQ(ierr); 2599 ierr = PetscObjectReference((PetscObject)qGeom);CHKERRQ(ierr); 2600 } 2601 ierr = PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 2602 ierr = DMSNESGetFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);CHKERRQ(ierr); 2603 blockSize = Nb; 2604 batchSize = numBlocks * blockSize; 2605 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 2606 numChunks = numCells / (numBatches*batchSize); 2607 Ne = numChunks*numBatches*batchSize; 2608 Nr = numCells % (numBatches*batchSize); 2609 offset = numCells - Nr; 2610 ierr = PetscFEGeomGetChunk(cgeomFEM,0,offset,&chunkGeom);CHKERRQ(ierr); 2611 ierr = PetscFEGeomGetChunk(cgeomFEM,offset,numCells,&remGeom);CHKERRQ(ierr); 2612 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 2613 ierr = PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMat);CHKERRQ(ierr); 2614 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); 2615 if (hasDyn) { 2616 ierr = PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN_DYN, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMatD);CHKERRQ(ierr); 2617 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); 2618 } 2619 } 2620 ierr = PetscFEGeomRestoreChunk(cgeomFEM,offset,numCells,&remGeom);CHKERRQ(ierr); 2621 ierr = PetscFEGeomRestoreChunk(cgeomFEM,0,offset,&chunkGeom);CHKERRQ(ierr); 2622 ierr = DMSNESRestoreFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);CHKERRQ(ierr); 2623 ierr = PetscQuadratureDestroy(&qGeom);CHKERRQ(ierr); 2624 } 2625 if (hasDyn) { 2626 for (c = 0; c < numCells*totDim*totDim; ++c) elemMat[c] += X_tShift*elemMatD[c]; 2627 } 2628 for (c = cStart; c < cEnd; ++c) { 2629 const PetscInt cell = cells ? cells[c] : c; 2630 const PetscInt cind = c - cStart; 2631 const PetscBLASInt M = totDim, one = 1; 2632 const PetscScalar a = 1.0, b = 0.0; 2633 2634 PetscStackCallBLAS("BLASgemv", BLASgemv_("N", &M, &M, &a, &elemMat[cind*totDim*totDim], &M, &y[cind*totDim], &one, &b, z, &one)); 2635 if (mesh->printFEM > 1) { 2636 ierr = DMPrintCellMatrix(c, name, totDim, totDim, &elemMat[cind*totDim*totDim]);CHKERRQ(ierr); 2637 ierr = DMPrintCellVector(c, "Y", totDim, &y[cind*totDim]);CHKERRQ(ierr); 2638 ierr = DMPrintCellVector(c, "Z", totDim, z);CHKERRQ(ierr); 2639 } 2640 ierr = DMPlexVecSetClosure(dm, section, Z, cell, z, ADD_VALUES);CHKERRQ(ierr); 2641 } 2642 ierr = PetscFree6(u,u_t,elemMat,elemMatD,y,z);CHKERRQ(ierr); 2643 if (mesh->printFEM) { 2644 ierr = PetscPrintf(PetscObjectComm((PetscObject)Z), "Z:\n");CHKERRQ(ierr); 2645 ierr = VecView(Z, NULL);CHKERRQ(ierr); 2646 } 2647 ierr = PetscFree(a);CHKERRQ(ierr); 2648 ierr = ISDestroy(&cellIS);CHKERRQ(ierr); 2649 ierr = DMDestroy(&plexAux);CHKERRQ(ierr); 2650 ierr = DMDestroy(&plex);CHKERRQ(ierr); 2651 ierr = PetscLogEventEnd(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 2652 PetscFunctionReturn(0); 2653 } 2654 2655 /*@ 2656 DMPlexSNESComputeJacobianFEM - Form the local portion of the Jacobian matrix J at the local solution X using pointwise functions specified by the user. 2657 2658 Input Parameters: 2659 + dm - The mesh 2660 . X - Local input vector 2661 - user - The user context 2662 2663 Output Parameter: 2664 . Jac - Jacobian matrix 2665 2666 Note: 2667 We form the residual one batch of elements at a time. This allows us to offload work onto an accelerator, 2668 like a GPU, or vectorize on a multicore machine. 2669 2670 Level: developer 2671 2672 .seealso: FormFunctionLocal() 2673 @*/ 2674 PetscErrorCode DMPlexSNESComputeJacobianFEM(DM dm, Vec X, Mat Jac, Mat JacP,void *user) 2675 { 2676 DM plex; 2677 PetscDS prob; 2678 IS cellIS; 2679 PetscBool hasJac, hasPrec; 2680 PetscInt depth; 2681 PetscErrorCode ierr; 2682 2683 PetscFunctionBegin; 2684 ierr = DMSNESConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr); 2685 ierr = DMPlexGetDepth(plex, &depth);CHKERRQ(ierr); 2686 ierr = DMGetStratumIS(plex, "dim", depth, &cellIS);CHKERRQ(ierr); 2687 if (!cellIS) {ierr = DMGetStratumIS(plex, "depth", depth, &cellIS);CHKERRQ(ierr);} 2688 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 2689 ierr = PetscDSHasJacobian(prob, &hasJac);CHKERRQ(ierr); 2690 ierr = PetscDSHasJacobianPreconditioner(prob, &hasPrec);CHKERRQ(ierr); 2691 if (hasJac && hasPrec) {ierr = MatZeroEntries(Jac);CHKERRQ(ierr);} 2692 ierr = MatZeroEntries(JacP);CHKERRQ(ierr); 2693 ierr = DMPlexComputeJacobian_Internal(plex, cellIS, 0.0, 0.0, X, NULL, Jac, JacP, user);CHKERRQ(ierr); 2694 ierr = ISDestroy(&cellIS);CHKERRQ(ierr); 2695 ierr = DMDestroy(&plex);CHKERRQ(ierr); 2696 PetscFunctionReturn(0); 2697 } 2698 2699 /* 2700 MatComputeNeumannOverlap - Computes an unassembled (Neumann) local overlapping Mat in nonlinear context. 2701 2702 Input Parameters: 2703 + X - SNES linearization point 2704 . ovl - index set of overlapping subdomains 2705 2706 Output Parameter: 2707 . J - unassembled (Neumann) local matrix 2708 2709 Level: intermediate 2710 2711 .seealso: DMCreateNeumannOverlap(), MATIS, PCHPDDMSetAuxiliaryMat() 2712 */ 2713 static PetscErrorCode MatComputeNeumannOverlap_Plex(Mat J, PetscReal t, Vec X, Vec X_t, PetscReal s, IS ovl, void *ctx) 2714 { 2715 SNES snes; 2716 Mat pJ; 2717 DM ovldm,origdm; 2718 DMSNES sdm; 2719 PetscErrorCode (*bfun)(DM,Vec,void*); 2720 PetscErrorCode (*jfun)(DM,Vec,Mat,Mat,void*); 2721 void *bctx,*jctx; 2722 PetscErrorCode ierr; 2723 2724 PetscFunctionBegin; 2725 ierr = PetscObjectQuery((PetscObject)ovl,"_DM_Overlap_HPDDM_MATIS",(PetscObject*)&pJ);CHKERRQ(ierr); 2726 if (!pJ) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Missing overlapping Mat");CHKERRQ(ierr); 2727 ierr = PetscObjectQuery((PetscObject)ovl,"_DM_Original_HPDDM",(PetscObject*)&origdm);CHKERRQ(ierr); 2728 if (!origdm) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Missing original DM");CHKERRQ(ierr); 2729 ierr = MatGetDM(pJ,&ovldm);CHKERRQ(ierr); 2730 ierr = DMSNESGetBoundaryLocal(origdm,&bfun,&bctx);CHKERRQ(ierr); 2731 ierr = DMSNESSetBoundaryLocal(ovldm,bfun,bctx);CHKERRQ(ierr); 2732 ierr = DMSNESGetJacobianLocal(origdm,&jfun,&jctx);CHKERRQ(ierr); 2733 ierr = DMSNESSetJacobianLocal(ovldm,jfun,jctx);CHKERRQ(ierr); 2734 ierr = PetscObjectQuery((PetscObject)ovl,"_DM_Overlap_HPDDM_SNES",(PetscObject*)&snes);CHKERRQ(ierr); 2735 if (!snes) { 2736 ierr = SNESCreate(PetscObjectComm((PetscObject)ovl),&snes);CHKERRQ(ierr); 2737 ierr = SNESSetDM(snes,ovldm);CHKERRQ(ierr); 2738 ierr = PetscObjectCompose((PetscObject)ovl,"_DM_Overlap_HPDDM_SNES",(PetscObject)snes);CHKERRQ(ierr); 2739 ierr = PetscObjectDereference((PetscObject)snes);CHKERRQ(ierr); 2740 } 2741 ierr = DMGetDMSNES(ovldm,&sdm);CHKERRQ(ierr); 2742 ierr = VecLockReadPush(X);CHKERRQ(ierr); 2743 PetscStackPush("SNES user Jacobian function"); 2744 ierr = (*sdm->ops->computejacobian)(snes,X,pJ,pJ,sdm->jacobianctx);CHKERRQ(ierr); 2745 PetscStackPop; 2746 ierr = VecLockReadPop(X);CHKERRQ(ierr); 2747 /* this is a no-hop, just in case we decide to change the placeholder for the local Neumann matrix */ 2748 { 2749 Mat locpJ; 2750 2751 ierr = MatISGetLocalMat(pJ,&locpJ);CHKERRQ(ierr); 2752 ierr = MatCopy(locpJ,J,SAME_NONZERO_PATTERN);CHKERRQ(ierr); 2753 } 2754 PetscFunctionReturn(0); 2755 } 2756 2757 /*@ 2758 DMPlexSetSNESLocalFEM - Use DMPlex's internal FEM routines to compute SNES boundary values, residual, and Jacobian. 2759 2760 Input Parameters: 2761 + dm - The DM object 2762 . boundaryctx - the user context that will be passed to pointwise evaluation of boundary values (see PetscDSAddBoundary()) 2763 . residualctx - the user context that will be passed to pointwise evaluation of finite element residual computations (see PetscDSSetResidual()) 2764 - jacobianctx - the user context that will be passed to pointwise evaluation of finite element Jacobian construction (see PetscDSSetJacobian()) 2765 2766 Level: developer 2767 @*/ 2768 PetscErrorCode DMPlexSetSNESLocalFEM(DM dm, void *boundaryctx, void *residualctx, void *jacobianctx) 2769 { 2770 PetscErrorCode ierr; 2771 2772 PetscFunctionBegin; 2773 ierr = DMSNESSetBoundaryLocal(dm,DMPlexSNESComputeBoundaryFEM,boundaryctx);CHKERRQ(ierr); 2774 ierr = DMSNESSetFunctionLocal(dm,DMPlexSNESComputeResidualFEM,residualctx);CHKERRQ(ierr); 2775 ierr = DMSNESSetJacobianLocal(dm,DMPlexSNESComputeJacobianFEM,jacobianctx);CHKERRQ(ierr); 2776 ierr = PetscObjectComposeFunction((PetscObject)dm,"MatComputeNeumannOverlap_C",MatComputeNeumannOverlap_Plex);CHKERRQ(ierr); 2777 PetscFunctionReturn(0); 2778 } 2779 2780 /*@C 2781 DMSNESCheckDiscretization - Check the discretization error of the exact solution 2782 2783 Input Parameters: 2784 + snes - the SNES object 2785 . dm - the DM 2786 . u - a DM vector 2787 . exactFuncs - pointwise functions of the exact solution for each field 2788 . ctxs - contexts for the functions 2789 - tol - A tolerance for the check, or -1 to print the results instead 2790 2791 Output Parameters: 2792 . error - An array which holds the discretization error in each field, or NULL 2793 2794 Level: developer 2795 2796 .seealso: DNSNESCheckFromOptions(), DMSNESCheckResidual(), DMSNESCheckJacobian() 2797 @*/ 2798 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[]) 2799 { 2800 PetscErrorCode (**exacts)(PetscInt, PetscReal, const PetscReal x[], PetscInt, PetscScalar *u, void *ctx); 2801 void **ectxs; 2802 MPI_Comm comm; 2803 PetscDS ds; 2804 PetscReal *err; 2805 PetscInt Nf, f; 2806 PetscErrorCode ierr; 2807 2808 PetscFunctionBegin; 2809 PetscValidHeaderSpecific(snes, SNES_CLASSID, 1); 2810 PetscValidHeaderSpecific(dm, DM_CLASSID, 2); 2811 PetscValidHeaderSpecific(u, VEC_CLASSID, 3); 2812 if (error) PetscValidRealPointer(error, 6); 2813 ierr = PetscObjectGetComm((PetscObject) snes, &comm);CHKERRQ(ierr); 2814 ierr = DMGetDS(dm, &ds);CHKERRQ(ierr); 2815 ierr = DMGetNumFields(dm, &Nf);CHKERRQ(ierr); 2816 ierr = PetscMalloc3(Nf, &exacts, Nf, &ectxs, PetscMax(1, Nf), &err);CHKERRQ(ierr); 2817 for (f = 0; f < Nf; ++f) {ierr = PetscDSGetExactSolution(ds, f, &exacts[f], &ectxs[f]);CHKERRQ(ierr);} 2818 ierr = DMProjectFunction(dm, 0.0, exactFuncs ? exactFuncs : exacts, ctxs ? ctxs : ectxs, INSERT_ALL_VALUES, u);CHKERRQ(ierr); 2819 ierr = PetscObjectSetName((PetscObject) u, "Exact Solution");CHKERRQ(ierr); 2820 ierr = PetscObjectSetOptionsPrefix((PetscObject) u, "exact_");CHKERRQ(ierr); 2821 ierr = VecViewFromOptions(u, NULL, "-vec_view");CHKERRQ(ierr); 2822 if (Nf > 1) { 2823 ierr = DMComputeL2FieldDiff(dm, 0.0, exactFuncs ? exactFuncs : exacts, ctxs ? ctxs : ectxs, u, err);CHKERRQ(ierr); 2824 if (tol >= 0.0) { 2825 for (f = 0; f < Nf; ++f) { 2826 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); 2827 } 2828 } else if (error) { 2829 for (f = 0; f < Nf; ++f) error[f] = err[f]; 2830 } else { 2831 ierr = PetscPrintf(comm, "L_2 Error: [");CHKERRQ(ierr); 2832 for (f = 0; f < Nf; ++f) { 2833 if (f) {ierr = PetscPrintf(comm, ", ");CHKERRQ(ierr);} 2834 ierr = PetscPrintf(comm, "%g", (double)err[f]);CHKERRQ(ierr); 2835 } 2836 ierr = PetscPrintf(comm, "]\n");CHKERRQ(ierr); 2837 } 2838 } else { 2839 ierr = DMComputeL2Diff(dm, 0.0, exactFuncs ? exactFuncs : exacts, ctxs ? ctxs : ectxs , u, &err[0]);CHKERRQ(ierr); 2840 if (tol >= 0.0) { 2841 if (err[0] > tol) SETERRQ2(comm, PETSC_ERR_ARG_WRONG, "L_2 Error %g exceeds tolerance %g", (double) err[0], (double) tol); 2842 } else if (error) { 2843 error[0] = err[0]; 2844 } else { 2845 ierr = PetscPrintf(comm, "L_2 Error: %g\n", (double)err[0]);CHKERRQ(ierr); 2846 } 2847 } 2848 ierr = PetscFree3(exacts, ectxs, err);CHKERRQ(ierr); 2849 PetscFunctionReturn(0); 2850 } 2851 2852 /*@C 2853 DMSNESCheckResidual - Check the residual of the exact solution 2854 2855 Input Parameters: 2856 + snes - the SNES object 2857 . dm - the DM 2858 . u - a DM vector 2859 - tol - A tolerance for the check, or -1 to print the results instead 2860 2861 Output Parameters: 2862 . residual - The residual norm of the exact solution, or NULL 2863 2864 Level: developer 2865 2866 .seealso: DNSNESCheckFromOptions(), DMSNESCheckDiscretization(), DMSNESCheckJacobian() 2867 @*/ 2868 PetscErrorCode DMSNESCheckResidual(SNES snes, DM dm, Vec u, PetscReal tol, PetscReal *residual) 2869 { 2870 PetscErrorCode (**exacts)(PetscInt, PetscReal, const PetscReal x[], PetscInt, PetscScalar *u, void *ctx); 2871 void **ectxs; 2872 MPI_Comm comm; 2873 PetscDS ds; 2874 Vec r; 2875 PetscReal res; 2876 PetscInt Nf, f; 2877 PetscBool computeSol = PETSC_FALSE; 2878 PetscErrorCode ierr; 2879 2880 PetscFunctionBegin; 2881 PetscValidHeaderSpecific(snes, SNES_CLASSID, 1); 2882 PetscValidHeaderSpecific(dm, DM_CLASSID, 2); 2883 PetscValidHeaderSpecific(u, VEC_CLASSID, 3); 2884 if (residual) PetscValidRealPointer(residual, 5); 2885 ierr = PetscObjectGetComm((PetscObject) snes, &comm);CHKERRQ(ierr); 2886 ierr = DMGetDS(dm, &ds);CHKERRQ(ierr); 2887 ierr = DMGetNumFields(dm, &Nf);CHKERRQ(ierr); 2888 ierr = PetscMalloc2(Nf, &exacts, Nf, &ectxs);CHKERRQ(ierr); 2889 for (f = 0; f < Nf; ++f) { 2890 ierr = PetscDSGetExactSolution(ds, f, &exacts[f], &ectxs[f]);CHKERRQ(ierr); 2891 if (exacts[f]) computeSol = PETSC_TRUE; 2892 } 2893 if (computeSol) {ierr = DMProjectFunction(dm, 0.0, exacts, ectxs, INSERT_ALL_VALUES, u);CHKERRQ(ierr);} 2894 ierr = PetscFree2(exacts, ectxs);CHKERRQ(ierr); 2895 2896 ierr = VecDuplicate(u, &r);CHKERRQ(ierr); 2897 ierr = SNESComputeFunction(snes, u, r);CHKERRQ(ierr); 2898 ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr); 2899 if (tol >= 0.0) { 2900 if (res > tol) SETERRQ2(comm, PETSC_ERR_ARG_WRONG, "L_2 Residual %g exceeds tolerance %g", (double) res, (double) tol); 2901 } else if (residual) { 2902 *residual = res; 2903 } else { 2904 ierr = PetscPrintf(comm, "L_2 Residual: %g\n", (double)res);CHKERRQ(ierr); 2905 ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr); 2906 ierr = PetscObjectSetName((PetscObject) r, "Initial Residual");CHKERRQ(ierr); 2907 ierr = PetscObjectSetOptionsPrefix((PetscObject)r,"res_");CHKERRQ(ierr); 2908 ierr = VecViewFromOptions(r, NULL, "-vec_view");CHKERRQ(ierr); 2909 } 2910 ierr = VecDestroy(&r);CHKERRQ(ierr); 2911 PetscFunctionReturn(0); 2912 } 2913 2914 /*@C 2915 DMSNESCheckJacobian - Check the Jacobian of the exact solution against the residual using the Taylor Test 2916 2917 Input Parameters: 2918 + snes - the SNES object 2919 . dm - the DM 2920 . u - a DM vector 2921 - tol - A tolerance for the check, or -1 to print the results instead 2922 2923 Output Parameters: 2924 + isLinear - Flag indicaing that the function looks linear, or NULL 2925 - convRate - The rate of convergence of the linear model, or NULL 2926 2927 Level: developer 2928 2929 .seealso: DNSNESCheckFromOptions(), DMSNESCheckDiscretization(), DMSNESCheckResidual() 2930 @*/ 2931 PetscErrorCode DMSNESCheckJacobian(SNES snes, DM dm, Vec u, PetscReal tol, PetscBool *isLinear, PetscReal *convRate) 2932 { 2933 PetscErrorCode (**exacts)(PetscInt, PetscReal, const PetscReal x[], PetscInt, PetscScalar *u, void *ctx); 2934 void **ectxs; 2935 MPI_Comm comm; 2936 PetscDS ds; 2937 Mat J, M; 2938 MatNullSpace nullspace; 2939 PetscReal slope, intercept; 2940 PetscInt Nf, f; 2941 PetscBool hasJac, hasPrec, isLin = PETSC_FALSE, computeSol = PETSC_FALSE; 2942 PetscErrorCode ierr; 2943 2944 PetscFunctionBegin; 2945 PetscValidHeaderSpecific(snes, SNES_CLASSID, 1); 2946 PetscValidHeaderSpecific(dm, DM_CLASSID, 2); 2947 PetscValidHeaderSpecific(u, VEC_CLASSID, 3); 2948 if (isLinear) PetscValidBoolPointer(isLinear, 5); 2949 if (convRate) PetscValidRealPointer(convRate, 5); 2950 ierr = PetscObjectGetComm((PetscObject) snes, &comm);CHKERRQ(ierr); 2951 ierr = DMGetDS(dm, &ds);CHKERRQ(ierr); 2952 ierr = DMGetNumFields(dm, &Nf);CHKERRQ(ierr); 2953 ierr = PetscMalloc2(Nf, &exacts, Nf, &ectxs);CHKERRQ(ierr); 2954 for (f = 0; f < Nf; ++f) { 2955 ierr = PetscDSGetExactSolution(ds, f, &exacts[f], &ectxs[f]);CHKERRQ(ierr); 2956 if (exacts[f]) computeSol = PETSC_TRUE; 2957 } 2958 if (computeSol) {ierr = DMProjectFunction(dm, 0.0, exacts, ectxs, INSERT_ALL_VALUES, u);CHKERRQ(ierr);} 2959 ierr = PetscFree2(exacts, ectxs);CHKERRQ(ierr); 2960 2961 /* Create and view matrices */ 2962 ierr = DMCreateMatrix(dm, &J);CHKERRQ(ierr); 2963 ierr = PetscDSHasJacobian(ds, &hasJac);CHKERRQ(ierr); 2964 ierr = PetscDSHasJacobianPreconditioner(ds, &hasPrec);CHKERRQ(ierr); 2965 if (hasJac && hasPrec) { 2966 ierr = DMCreateMatrix(dm, &M);CHKERRQ(ierr); 2967 ierr = SNESComputeJacobian(snes, u, J, M);CHKERRQ(ierr); 2968 ierr = PetscObjectSetName((PetscObject) M, "Preconditioning Matrix");CHKERRQ(ierr); 2969 ierr = PetscObjectSetOptionsPrefix((PetscObject) M, "jacpre_");CHKERRQ(ierr); 2970 ierr = MatViewFromOptions(M, NULL, "-mat_view");CHKERRQ(ierr); 2971 ierr = MatDestroy(&M);CHKERRQ(ierr); 2972 } else { 2973 ierr = SNESComputeJacobian(snes, u, J, J);CHKERRQ(ierr); 2974 } 2975 ierr = PetscObjectSetName((PetscObject) J, "Jacobian");CHKERRQ(ierr); 2976 ierr = PetscObjectSetOptionsPrefix((PetscObject) J, "jac_");CHKERRQ(ierr); 2977 ierr = MatViewFromOptions(J, NULL, "-mat_view");CHKERRQ(ierr); 2978 /* Check nullspace */ 2979 ierr = MatGetNullSpace(J, &nullspace);CHKERRQ(ierr); 2980 if (nullspace) { 2981 PetscBool isNull; 2982 ierr = MatNullSpaceTest(nullspace, J, &isNull);CHKERRQ(ierr); 2983 if (!isNull) SETERRQ(comm, PETSC_ERR_PLIB, "The null space calculated for the system operator is invalid."); 2984 } 2985 ierr = MatNullSpaceDestroy(&nullspace);CHKERRQ(ierr); 2986 /* Taylor test */ 2987 { 2988 PetscRandom rand; 2989 Vec du, uhat, r, rhat, df; 2990 PetscReal h; 2991 PetscReal *es, *hs, *errors; 2992 PetscReal hMax = 1.0, hMin = 1e-6, hMult = 0.1; 2993 PetscInt Nv, v; 2994 2995 /* Choose a perturbation direction */ 2996 ierr = PetscRandomCreate(comm, &rand);CHKERRQ(ierr); 2997 ierr = VecDuplicate(u, &du);CHKERRQ(ierr); 2998 ierr = VecSetRandom(du, rand); CHKERRQ(ierr); 2999 ierr = PetscRandomDestroy(&rand);CHKERRQ(ierr); 3000 ierr = VecDuplicate(u, &df);CHKERRQ(ierr); 3001 ierr = MatMult(J, du, df);CHKERRQ(ierr); 3002 /* Evaluate residual at u, F(u), save in vector r */ 3003 ierr = VecDuplicate(u, &r);CHKERRQ(ierr); 3004 ierr = SNESComputeFunction(snes, u, r);CHKERRQ(ierr); 3005 /* Look at the convergence of our Taylor approximation as we approach u */ 3006 for (h = hMax, Nv = 0; h >= hMin; h *= hMult, ++Nv); 3007 ierr = PetscCalloc3(Nv, &es, Nv, &hs, Nv, &errors);CHKERRQ(ierr); 3008 ierr = VecDuplicate(u, &uhat);CHKERRQ(ierr); 3009 ierr = VecDuplicate(u, &rhat);CHKERRQ(ierr); 3010 for (h = hMax, Nv = 0; h >= hMin; h *= hMult, ++Nv) { 3011 ierr = VecWAXPY(uhat, h, du, u);CHKERRQ(ierr); 3012 /* F(\hat u) \approx F(u) + J(u) (uhat - u) = F(u) + h * J(u) du */ 3013 ierr = SNESComputeFunction(snes, uhat, rhat);CHKERRQ(ierr); 3014 ierr = VecAXPBYPCZ(rhat, -1.0, -h, 1.0, r, df);CHKERRQ(ierr); 3015 ierr = VecNorm(rhat, NORM_2, &errors[Nv]);CHKERRQ(ierr); 3016 3017 es[Nv] = PetscLog10Real(errors[Nv]); 3018 hs[Nv] = PetscLog10Real(h); 3019 } 3020 ierr = VecDestroy(&uhat);CHKERRQ(ierr); 3021 ierr = VecDestroy(&rhat);CHKERRQ(ierr); 3022 ierr = VecDestroy(&df);CHKERRQ(ierr); 3023 ierr = VecDestroy(&r);CHKERRQ(ierr); 3024 ierr = VecDestroy(&du);CHKERRQ(ierr); 3025 for (v = 0; v < Nv; ++v) { 3026 if ((tol >= 0) && (errors[v] > tol)) break; 3027 else if (errors[v] > PETSC_SMALL) break; 3028 } 3029 if (v == Nv) isLin = PETSC_TRUE; 3030 ierr = PetscLinearRegression(Nv, hs, es, &slope, &intercept);CHKERRQ(ierr); 3031 ierr = PetscFree3(es, hs, errors);CHKERRQ(ierr); 3032 /* Slope should be about 2 */ 3033 if (tol >= 0) { 3034 if (!isLin && PetscAbsReal(2 - slope) > tol) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Taylor approximation convergence rate should be 2, not %0.2f", (double) slope); 3035 } else if (isLinear || convRate) { 3036 if (isLinear) *isLinear = isLin; 3037 if (convRate) *convRate = slope; 3038 } else { 3039 if (!isLin) {ierr = PetscPrintf(comm, "Taylor approximation converging at order %3.2f\n", (double) slope);CHKERRQ(ierr);} 3040 else {ierr = PetscPrintf(comm, "Function appears to be linear\n");CHKERRQ(ierr);} 3041 } 3042 } 3043 ierr = MatDestroy(&J);CHKERRQ(ierr); 3044 PetscFunctionReturn(0); 3045 } 3046 3047 PetscErrorCode DMSNESCheck_Internal(SNES snes, DM dm, Vec u, PetscErrorCode (**exactFuncs)(PetscInt, PetscReal, const PetscReal x[], PetscInt, PetscScalar *u, void *ctx), void **ctxs) 3048 { 3049 PetscErrorCode ierr; 3050 3051 PetscFunctionBegin; 3052 ierr = DMSNESCheckDiscretization(snes, dm, u, exactFuncs, ctxs, -1.0, NULL);CHKERRQ(ierr); 3053 ierr = DMSNESCheckResidual(snes, dm, u, -1.0, NULL);CHKERRQ(ierr); 3054 ierr = DMSNESCheckJacobian(snes, dm, u, -1.0, NULL, NULL);CHKERRQ(ierr); 3055 PetscFunctionReturn(0); 3056 } 3057 3058 /*@C 3059 DMSNESCheckFromOptions - Check the residual and Jacobian functions using the exact solution by outputting some diagnostic information 3060 3061 Input Parameters: 3062 + snes - the SNES object 3063 . u - representative SNES vector 3064 . exactFuncs - pointwise functions of the exact solution for each field 3065 - ctxs - contexts for the functions 3066 3067 Level: developer 3068 @*/ 3069 PetscErrorCode DMSNESCheckFromOptions(SNES snes, Vec u, PetscErrorCode (**exactFuncs)(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf, PetscScalar *u, void *ctx), void **ctxs) 3070 { 3071 DM dm; 3072 Vec sol; 3073 PetscBool check; 3074 PetscErrorCode ierr; 3075 3076 PetscFunctionBegin; 3077 ierr = PetscOptionsHasName(((PetscObject)snes)->options,((PetscObject)snes)->prefix, "-dmsnes_check", &check);CHKERRQ(ierr); 3078 if (!check) PetscFunctionReturn(0); 3079 ierr = SNESGetDM(snes, &dm);CHKERRQ(ierr); 3080 ierr = VecDuplicate(u, &sol);CHKERRQ(ierr); 3081 ierr = SNESSetSolution(snes, sol);CHKERRQ(ierr); 3082 ierr = DMSNESCheck_Internal(snes, dm, sol, exactFuncs, ctxs);CHKERRQ(ierr); 3083 ierr = VecDestroy(&sol);CHKERRQ(ierr); 3084 PetscFunctionReturn(0); 3085 } 3086