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