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