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 DMSNES dmsnes; 908 PetscObject obj; 909 PetscErrorCode ierr; 910 911 PetscFunctionBegin; 912 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 913 ierr = DMGetDMSNES(dm, &dmsnes);CHKERRQ(ierr); 914 ierr = PetscObjectQuery((PetscObject) dmsnes, "DMPlexSNES_facegeom_fvm", &obj);CHKERRQ(ierr); 915 if (!obj) { 916 Vec cellgeom, facegeom; 917 918 ierr = DMPlexGetDataFVM(dm, NULL, &cellgeom, &facegeom, NULL);CHKERRQ(ierr); 919 ierr = PetscObjectCompose((PetscObject) dmsnes, "DMPlexSNES_facegeom_fvm", (PetscObject) facegeom);CHKERRQ(ierr); 920 ierr = PetscObjectCompose((PetscObject) dmsnes, "DMPlexSNES_cellgeom_fvm", (PetscObject) cellgeom);CHKERRQ(ierr); 921 } 922 if (facegeom) {PetscValidPointer(facegeom, 2); ierr = PetscObjectQuery((PetscObject) dmsnes, "DMPlexSNES_facegeom_fvm", (PetscObject *) facegeom);CHKERRQ(ierr);} 923 if (cellgeom) {PetscValidPointer(cellgeom, 3); ierr = PetscObjectQuery((PetscObject) dmsnes, "DMPlexSNES_cellgeom_fvm", (PetscObject *) cellgeom);CHKERRQ(ierr);} 924 if (minRadius) {ierr = DMPlexGetMinRadius(dm, minRadius);CHKERRQ(ierr);} 925 PetscFunctionReturn(0); 926 } 927 928 #undef __FUNCT__ 929 #define __FUNCT__ "DMPlexSNESGetGradientDM" 930 /*@ 931 DMPlexSNESGetGradientDM - Return gradient data layout 932 933 Input Parameters: 934 + dm - The DM 935 - fv - The PetscFV 936 937 Output Parameter: 938 . dmGrad - The layout for gradient values 939 940 Level: developer 941 942 .seealso: DMPlexSNESGetGeometryFVM() 943 @*/ 944 PetscErrorCode DMPlexSNESGetGradientDM(DM dm, PetscFV fv, DM *dmGrad) 945 { 946 DMSNES dmsnes; 947 PetscObject obj; 948 PetscBool computeGradients; 949 PetscErrorCode ierr; 950 951 PetscFunctionBegin; 952 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 953 PetscValidHeaderSpecific(fv,PETSCFV_CLASSID,2); 954 PetscValidPointer(dmGrad,3); 955 ierr = PetscFVGetComputeGradients(fv, &computeGradients);CHKERRQ(ierr); 956 if (!computeGradients) {*dmGrad = NULL; PetscFunctionReturn(0);} 957 ierr = DMGetDMSNES(dm, &dmsnes);CHKERRQ(ierr); 958 ierr = PetscObjectQuery((PetscObject) dmsnes, "DMPlexSNES_dmgrad_fvm", &obj);CHKERRQ(ierr); 959 if (!obj) { 960 DM dmGrad; 961 Vec faceGeometry, cellGeometry; 962 963 ierr = DMPlexGetDataFVM(dm, fv, &cellGeometry, &faceGeometry, &dmGrad);CHKERRQ(ierr); 964 ierr = PetscObjectCompose((PetscObject) dmsnes, "DMPlexSNES_dmgrad_fvm", (PetscObject) dmGrad);CHKERRQ(ierr); 965 } 966 ierr = PetscObjectQuery((PetscObject) dmsnes, "DMPlexSNES_dmgrad_fvm", (PetscObject *) dmGrad);CHKERRQ(ierr); 967 PetscFunctionReturn(0); 968 } 969 970 #undef __FUNCT__ 971 #define __FUNCT__ "DMPlexGetCellFields" 972 /*@C 973 DMPlexGetCellFields - Retrieve the field values values for a chunk of cells 974 975 Input Parameters: 976 + dm - The DM 977 . cStart - The first cell to include 978 . cEnd - The first cell to exclude 979 . locX - A local vector with the solution fields 980 . locX_t - A local vector with solution field time derivatives, or NULL 981 - locA - A local vector with auxiliary fields, or NULL 982 983 Output Parameters: 984 + u - The field coefficients 985 . u_t - The fields derivative coefficients 986 - a - The auxiliary field coefficients 987 988 Level: developer 989 990 .seealso: DMPlexGetFaceFields() 991 @*/ 992 PetscErrorCode DMPlexGetCellFields(DM dm, PetscInt cStart, PetscInt cEnd, Vec locX, Vec locX_t, Vec locA, PetscScalar **u, PetscScalar **u_t, PetscScalar **a) 993 { 994 DM dmAux; 995 PetscSection section, sectionAux; 996 PetscDS prob; 997 PetscInt numCells = cEnd - cStart, totDim, totDimAux, c; 998 PetscErrorCode ierr; 999 1000 PetscFunctionBegin; 1001 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1002 PetscValidHeaderSpecific(locX, VEC_CLASSID, 4); 1003 if (locX_t) {PetscValidHeaderSpecific(locX_t, VEC_CLASSID, 5);} 1004 if (locA) {PetscValidHeaderSpecific(locA, VEC_CLASSID, 6);} 1005 PetscValidPointer(u, 7); 1006 PetscValidPointer(u_t, 8); 1007 PetscValidPointer(a, 9); 1008 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 1009 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1010 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1011 if (locA) { 1012 PetscDS probAux; 1013 1014 ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); 1015 ierr = DMGetDefaultSection(dmAux, §ionAux);CHKERRQ(ierr); 1016 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 1017 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 1018 } 1019 ierr = DMGetWorkArray(dm, numCells*totDim, PETSC_SCALAR, u);CHKERRQ(ierr); 1020 if (locX_t) {ierr = DMGetWorkArray(dm, numCells*totDim, PETSC_SCALAR, u_t);CHKERRQ(ierr);} else {*u_t = NULL;} 1021 if (locA) {ierr = DMGetWorkArray(dm, numCells*totDimAux, PETSC_SCALAR, a);CHKERRQ(ierr);} else {*a = NULL;} 1022 for (c = cStart; c < cEnd; ++c) { 1023 PetscScalar *x = NULL, *x_t = NULL, *ul = *u, *ul_t = *u_t, *al = *a; 1024 PetscInt i; 1025 1026 ierr = DMPlexVecGetClosure(dm, section, locX, c, NULL, &x);CHKERRQ(ierr); 1027 for (i = 0; i < totDim; ++i) ul[(c-cStart)*totDim+i] = x[i]; 1028 ierr = DMPlexVecRestoreClosure(dm, section, locX, c, NULL, &x);CHKERRQ(ierr); 1029 if (locX_t) { 1030 ierr = DMPlexVecGetClosure(dm, section, locX_t, c, NULL, &x_t);CHKERRQ(ierr); 1031 for (i = 0; i < totDim; ++i) ul_t[(c-cStart)*totDim+i] = x_t[i]; 1032 ierr = DMPlexVecRestoreClosure(dm, section, locX_t, c, NULL, &x_t);CHKERRQ(ierr); 1033 } 1034 if (locA) { 1035 DM dmAuxPlex; 1036 1037 ierr = DMSNESConvertPlex(dmAux, &dmAuxPlex, PETSC_FALSE);CHKERRQ(ierr); 1038 ierr = DMPlexVecGetClosure(dmAuxPlex, sectionAux, locA, c, NULL, &x);CHKERRQ(ierr); 1039 for (i = 0; i < totDimAux; ++i) al[(c-cStart)*totDimAux+i] = x[i]; 1040 ierr = DMPlexVecRestoreClosure(dmAuxPlex, sectionAux, locA, c, NULL, &x);CHKERRQ(ierr); 1041 ierr = DMDestroy(&dmAuxPlex);CHKERRQ(ierr); 1042 } 1043 } 1044 PetscFunctionReturn(0); 1045 } 1046 1047 #undef __FUNCT__ 1048 #define __FUNCT__ "DMPlexRestoreCellFields" 1049 /*@C 1050 DMPlexRestoreCellFields - Restore the field values values for a chunk of cells 1051 1052 Input Parameters: 1053 + dm - The DM 1054 . cStart - The first cell to include 1055 . cEnd - The first cell to exclude 1056 . locX - A local vector with the solution fields 1057 . locX_t - A local vector with solution field time derivatives, or NULL 1058 - locA - A local vector with auxiliary fields, or NULL 1059 1060 Output Parameters: 1061 + u - The field coefficients 1062 . u_t - The fields derivative coefficients 1063 - a - The auxiliary field coefficients 1064 1065 Level: developer 1066 1067 .seealso: DMPlexGetFaceFields() 1068 @*/ 1069 PetscErrorCode DMPlexRestoreCellFields(DM dm, PetscInt cStart, PetscInt cEnd, Vec locX, Vec locX_t, Vec locA, PetscScalar **u, PetscScalar **u_t, PetscScalar **a) 1070 { 1071 PetscErrorCode ierr; 1072 1073 PetscFunctionBegin; 1074 ierr = DMRestoreWorkArray(dm, 0, PETSC_SCALAR, u);CHKERRQ(ierr); 1075 if (*u_t) {ierr = DMRestoreWorkArray(dm, 0, PETSC_SCALAR, u_t);CHKERRQ(ierr);} 1076 if (*a) {ierr = DMRestoreWorkArray(dm, 0, PETSC_SCALAR, a);CHKERRQ(ierr);} 1077 PetscFunctionReturn(0); 1078 } 1079 1080 #undef __FUNCT__ 1081 #define __FUNCT__ "DMPlexGetFaceFields" 1082 /*@C 1083 DMPlexGetFaceFields - Retrieve the field values values for a chunk of faces 1084 1085 Input Parameters: 1086 + dm - The DM 1087 . fStart - The first face to include 1088 . fEnd - The first face to exclude 1089 . locX - A local vector with the solution fields 1090 . locX_t - A local vector with solution field time derivatives, or NULL 1091 . faceGeometry - A local vector with face geometry 1092 . cellGeometry - A local vector with cell geometry 1093 - locaGrad - A local vector with field gradients, or NULL 1094 1095 Output Parameters: 1096 + uL - The field values at the left side of the face 1097 - uR - The field values at the right side of the face 1098 1099 Level: developer 1100 1101 .seealso: DMPlexGetCellFields() 1102 @*/ 1103 PetscErrorCode DMPlexGetFaceFields(DM dm, PetscInt fStart, PetscInt fEnd, Vec locX, Vec locX_t, Vec faceGeometry, Vec cellGeometry, Vec locGrad, PetscScalar **uL, PetscScalar **uR) 1104 { 1105 DM dmFace, dmCell, dmGrad = NULL; 1106 PetscSection section; 1107 PetscDS prob; 1108 DMLabel ghostLabel; 1109 const PetscScalar *facegeom, *cellgeom, *x, *lgrad; 1110 PetscBool *isFE; 1111 PetscInt dim, Nf, f, Nc, numFaces = fEnd - fStart, iface, face; 1112 PetscErrorCode ierr; 1113 1114 PetscFunctionBegin; 1115 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1116 PetscValidHeaderSpecific(locX, VEC_CLASSID, 4); 1117 if (locX_t) {PetscValidHeaderSpecific(locX_t, VEC_CLASSID, 5);} 1118 PetscValidHeaderSpecific(faceGeometry, VEC_CLASSID, 6); 1119 PetscValidHeaderSpecific(cellGeometry, VEC_CLASSID, 7); 1120 if (locGrad) {PetscValidHeaderSpecific(locGrad, VEC_CLASSID, 8);} 1121 PetscValidPointer(uL, 9); 1122 PetscValidPointer(uR, 10); 1123 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1124 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1125 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 1126 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 1127 ierr = PetscDSGetTotalComponents(prob, &Nc);CHKERRQ(ierr); 1128 ierr = PetscMalloc1(Nf, &isFE);CHKERRQ(ierr); 1129 for (f = 0; f < Nf; ++f) { 1130 PetscObject obj; 1131 PetscClassId id; 1132 1133 ierr = DMGetField(dm, f, &obj);CHKERRQ(ierr); 1134 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1135 if (id == PETSCFE_CLASSID) {isFE[f] = PETSC_TRUE;} 1136 else if (id == PETSCFV_CLASSID) {isFE[f] = PETSC_FALSE;} 1137 else {isFE[f] = PETSC_FALSE;} 1138 } 1139 ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 1140 ierr = VecGetArrayRead(locX, &x);CHKERRQ(ierr); 1141 ierr = VecGetDM(faceGeometry, &dmFace);CHKERRQ(ierr); 1142 ierr = VecGetArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); 1143 ierr = VecGetDM(cellGeometry, &dmCell);CHKERRQ(ierr); 1144 ierr = VecGetArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr); 1145 if (locGrad) { 1146 ierr = VecGetDM(locGrad, &dmGrad);CHKERRQ(ierr); 1147 ierr = VecGetArrayRead(locGrad, &lgrad);CHKERRQ(ierr); 1148 } 1149 ierr = DMGetWorkArray(dm, numFaces*Nc, PETSC_SCALAR, uL);CHKERRQ(ierr); 1150 ierr = DMGetWorkArray(dm, numFaces*Nc, PETSC_SCALAR, uR);CHKERRQ(ierr); 1151 /* Right now just eat the extra work for FE (could make a cell loop) */ 1152 for (face = fStart, iface = 0; face < fEnd; ++face) { 1153 const PetscInt *cells; 1154 PetscFVFaceGeom *fg; 1155 PetscFVCellGeom *cgL, *cgR; 1156 PetscScalar *xL, *xR, *gL, *gR; 1157 PetscScalar *uLl = *uL, *uRl = *uR; 1158 PetscInt ghost, nsupp; 1159 1160 ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr); 1161 ierr = DMPlexGetSupportSize(dm, face, &nsupp);CHKERRQ(ierr); 1162 if (ghost >= 0) continue; 1163 ierr = DMPlexPointLocalRead(dmFace, face, facegeom, &fg);CHKERRQ(ierr); 1164 ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr); 1165 ierr = DMPlexPointLocalRead(dmCell, cells[0], cellgeom, &cgL);CHKERRQ(ierr); 1166 ierr = DMPlexPointLocalRead(dmCell, cells[1], cellgeom, &cgR);CHKERRQ(ierr); 1167 for (f = 0; f < Nf; ++f) { 1168 PetscInt off; 1169 1170 ierr = PetscDSGetComponentOffset(prob, f, &off);CHKERRQ(ierr); 1171 if (isFE[f]) { 1172 const PetscInt *cone; 1173 PetscInt comp, coneSize, faceLocL, faceLocR, ldof, rdof, d; 1174 1175 xL = xR = NULL; 1176 ierr = DMPlexVecGetClosure(dm, section, locX, cells[0], &ldof, (PetscScalar **) &xL);CHKERRQ(ierr); 1177 ierr = DMPlexVecGetClosure(dm, section, locX, cells[1], &rdof, (PetscScalar **) &xR);CHKERRQ(ierr); 1178 ierr = DMPlexGetCone(dm, cells[0], &cone);CHKERRQ(ierr); 1179 ierr = DMPlexGetConeSize(dm, cells[0], &coneSize);CHKERRQ(ierr); 1180 for (faceLocL = 0; faceLocL < coneSize; ++faceLocL) if (cone[faceLocL] == face) break; 1181 if (faceLocL == coneSize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Could not find face %d in cone of cell %d", face, cells[0]); 1182 ierr = DMPlexGetCone(dm, cells[1], &cone);CHKERRQ(ierr); 1183 ierr = DMPlexGetConeSize(dm, cells[1], &coneSize);CHKERRQ(ierr); 1184 for (faceLocR = 0; faceLocR < coneSize; ++faceLocR) if (cone[faceLocR] == face) break; 1185 if (faceLocR == coneSize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Could not find face %d in cone of cell %d", face, cells[1]); 1186 /* Check that FEM field has values in the right cell (sometimes its an FV ghost cell) */ 1187 ierr = EvaluateFaceFields(prob, f, faceLocL, xL, &uLl[iface*Nc+off]);CHKERRQ(ierr); 1188 if (rdof == ldof) {ierr = EvaluateFaceFields(prob, f, faceLocR, xR, &uRl[iface*Nc+off]);CHKERRQ(ierr);} 1189 else {ierr = PetscSectionGetFieldComponents(section, f, &comp);CHKERRQ(ierr); for(d = 0; d < comp; ++d) uRl[iface*Nc+off+d] = uLl[iface*Nc+off+d];} 1190 ierr = DMPlexVecRestoreClosure(dm, section, locX, cells[0], &ldof, (PetscScalar **) &xL);CHKERRQ(ierr); 1191 ierr = DMPlexVecRestoreClosure(dm, section, locX, cells[1], &rdof, (PetscScalar **) &xR);CHKERRQ(ierr); 1192 } else { 1193 PetscFV fv; 1194 PetscInt numComp, c; 1195 1196 ierr = PetscDSGetDiscretization(prob, f, (PetscObject *) &fv);CHKERRQ(ierr); 1197 ierr = PetscFVGetNumComponents(fv, &numComp);CHKERRQ(ierr); 1198 if (nsupp > 2) { 1199 for (f = 0; f < Nf; ++f) { 1200 PetscInt off; 1201 1202 ierr = PetscDSGetComponentOffset(prob, f, &off);CHKERRQ(ierr); 1203 ierr = PetscFVGetNumComponents(fv, &numComp);CHKERRQ(ierr); 1204 for (c = 0; c < numComp; ++c) { 1205 uLl[iface*Nc+off+c] = 0.; 1206 uRl[iface*Nc+off+c] = 0.; 1207 } 1208 } 1209 continue; 1210 } 1211 ierr = DMPlexPointLocalFieldRead(dm, cells[0], f, x, &xL);CHKERRQ(ierr); 1212 ierr = DMPlexPointLocalFieldRead(dm, cells[1], f, x, &xR);CHKERRQ(ierr); 1213 if (dmGrad) { 1214 PetscReal dxL[3], dxR[3]; 1215 1216 ierr = DMPlexPointLocalRead(dmGrad, cells[0], lgrad, &gL);CHKERRQ(ierr); 1217 ierr = DMPlexPointLocalRead(dmGrad, cells[1], lgrad, &gR);CHKERRQ(ierr); 1218 DMPlex_WaxpyD_Internal(dim, -1, cgL->centroid, fg->centroid, dxL); 1219 DMPlex_WaxpyD_Internal(dim, -1, cgR->centroid, fg->centroid, dxR); 1220 for (c = 0; c < numComp; ++c) { 1221 uLl[iface*Nc+off+c] = xL[c] + DMPlex_DotD_Internal(dim, &gL[c*dim], dxL); 1222 uRl[iface*Nc+off+c] = xR[c] + DMPlex_DotD_Internal(dim, &gR[c*dim], dxR); 1223 } 1224 } else { 1225 for (c = 0; c < numComp; ++c) { 1226 uLl[iface*Nc+off+c] = xL[c]; 1227 uRl[iface*Nc+off+c] = xR[c]; 1228 } 1229 } 1230 } 1231 } 1232 ++iface; 1233 } 1234 ierr = VecRestoreArrayRead(locX, &x);CHKERRQ(ierr); 1235 ierr = VecRestoreArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); 1236 ierr = VecRestoreArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr); 1237 if (locGrad) { 1238 ierr = VecRestoreArrayRead(locGrad, &lgrad);CHKERRQ(ierr); 1239 } 1240 ierr = PetscFree(isFE);CHKERRQ(ierr); 1241 PetscFunctionReturn(0); 1242 } 1243 1244 #undef __FUNCT__ 1245 #define __FUNCT__ "DMPlexRestoreFaceFields" 1246 /*@C 1247 DMPlexRestoreFaceFields - Restore the field values values for a chunk of faces 1248 1249 Input Parameters: 1250 + dm - The DM 1251 . fStart - The first face to include 1252 . fEnd - The first face to exclude 1253 . locX - A local vector with the solution fields 1254 . locX_t - A local vector with solution field time derivatives, or NULL 1255 . faceGeometry - A local vector with face geometry 1256 . cellGeometry - A local vector with cell geometry 1257 - locaGrad - A local vector with field gradients, or NULL 1258 1259 Output Parameters: 1260 + uL - The field values at the left side of the face 1261 - uR - The field values at the right side of the face 1262 1263 Level: developer 1264 1265 .seealso: DMPlexGetFaceFields() 1266 @*/ 1267 PetscErrorCode DMPlexRestoreFaceFields(DM dm, PetscInt fStart, PetscInt fEnd, Vec locX, Vec locX_t, Vec faceGeometry, Vec cellGeometry, Vec locGrad, PetscScalar **uL, PetscScalar **uR) 1268 { 1269 PetscErrorCode ierr; 1270 1271 PetscFunctionBegin; 1272 ierr = DMRestoreWorkArray(dm, 0, PETSC_SCALAR, uL);CHKERRQ(ierr); 1273 ierr = DMRestoreWorkArray(dm, 0, PETSC_SCALAR, uR);CHKERRQ(ierr); 1274 PetscFunctionReturn(0); 1275 } 1276 1277 #undef __FUNCT__ 1278 #define __FUNCT__ "DMPlexGetFaceGeometry" 1279 /*@C 1280 DMPlexGetFaceGeometry - Retrieve the geometric values for a chunk of faces 1281 1282 Input Parameters: 1283 + dm - The DM 1284 . fStart - The first face to include 1285 . fEnd - The first face to exclude 1286 . faceGeometry - A local vector with face geometry 1287 - cellGeometry - A local vector with cell geometry 1288 1289 Output Parameters: 1290 + fgeom - The extract the face centroid and normal 1291 - vol - The cell volume 1292 1293 Level: developer 1294 1295 .seealso: DMPlexGetCellFields() 1296 @*/ 1297 PetscErrorCode DMPlexGetFaceGeometry(DM dm, PetscInt fStart, PetscInt fEnd, Vec faceGeometry, Vec cellGeometry, PetscFVFaceGeom **fgeom, PetscReal **vol) 1298 { 1299 DM dmFace, dmCell; 1300 DMLabel ghostLabel; 1301 const PetscScalar *facegeom, *cellgeom; 1302 PetscInt dim, numFaces = fEnd - fStart, iface, face; 1303 PetscErrorCode ierr; 1304 1305 PetscFunctionBegin; 1306 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1307 PetscValidHeaderSpecific(faceGeometry, VEC_CLASSID, 4); 1308 PetscValidHeaderSpecific(cellGeometry, VEC_CLASSID, 5); 1309 PetscValidPointer(fgeom, 6); 1310 PetscValidPointer(vol, 7); 1311 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1312 ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 1313 ierr = VecGetDM(faceGeometry, &dmFace);CHKERRQ(ierr); 1314 ierr = VecGetArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); 1315 ierr = VecGetDM(cellGeometry, &dmCell);CHKERRQ(ierr); 1316 ierr = VecGetArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr); 1317 ierr = PetscMalloc1(numFaces, fgeom);CHKERRQ(ierr); 1318 ierr = DMGetWorkArray(dm, numFaces*2, PETSC_SCALAR, vol);CHKERRQ(ierr); 1319 for (face = fStart, iface = 0; face < fEnd; ++face) { 1320 const PetscInt *cells; 1321 PetscFVFaceGeom *fg; 1322 PetscFVCellGeom *cgL, *cgR; 1323 PetscFVFaceGeom *fgeoml = *fgeom; 1324 PetscReal *voll = *vol; 1325 PetscInt ghost, d; 1326 1327 ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr); 1328 if (ghost >= 0) continue; 1329 ierr = DMPlexPointLocalRead(dmFace, face, facegeom, &fg);CHKERRQ(ierr); 1330 ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr); 1331 ierr = DMPlexPointLocalRead(dmCell, cells[0], cellgeom, &cgL);CHKERRQ(ierr); 1332 ierr = DMPlexPointLocalRead(dmCell, cells[1], cellgeom, &cgR);CHKERRQ(ierr); 1333 for (d = 0; d < dim; ++d) { 1334 fgeoml[iface].centroid[d] = fg->centroid[d]; 1335 fgeoml[iface].normal[d] = fg->normal[d]; 1336 } 1337 voll[iface*2+0] = cgL->volume; 1338 voll[iface*2+1] = cgR->volume; 1339 ++iface; 1340 } 1341 ierr = VecRestoreArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); 1342 ierr = VecRestoreArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr); 1343 PetscFunctionReturn(0); 1344 } 1345 1346 #undef __FUNCT__ 1347 #define __FUNCT__ "DMPlexRestoreFaceGeometry" 1348 /*@C 1349 DMPlexRestoreFaceGeometry - Restore the field values values for a chunk of faces 1350 1351 Input Parameters: 1352 + dm - The DM 1353 . fStart - The first face to include 1354 . fEnd - The first face to exclude 1355 . faceGeometry - A local vector with face geometry 1356 - cellGeometry - A local vector with cell geometry 1357 1358 Output Parameters: 1359 + fgeom - The extract the face centroid and normal 1360 - vol - The cell volume 1361 1362 Level: developer 1363 1364 .seealso: DMPlexGetFaceFields() 1365 @*/ 1366 PetscErrorCode DMPlexRestoreFaceGeometry(DM dm, PetscInt fStart, PetscInt fEnd, Vec faceGeometry, Vec cellGeometry, PetscFVFaceGeom **fgeom, PetscReal **vol) 1367 { 1368 PetscErrorCode ierr; 1369 1370 PetscFunctionBegin; 1371 ierr = PetscFree(*fgeom);CHKERRQ(ierr); 1372 ierr = DMRestoreWorkArray(dm, 0, PETSC_REAL, vol);CHKERRQ(ierr); 1373 PetscFunctionReturn(0); 1374 } 1375 1376 #undef __FUNCT__ 1377 #define __FUNCT__ "DMPlexComputeBdResidual_Internal" 1378 PetscErrorCode DMPlexComputeBdResidual_Internal(DM dm, Vec locX, Vec locX_t, PetscReal t, Vec locF, void *user) 1379 { 1380 DM_Plex *mesh = (DM_Plex *) dm->data; 1381 PetscSection section; 1382 PetscDS prob; 1383 DMLabel depth; 1384 PetscFECellGeom *cgeom; 1385 PetscScalar *u = NULL, *u_t = NULL, *elemVec = NULL; 1386 PetscInt dim, Nf, f, totDimBd, numBd, bd; 1387 PetscErrorCode ierr; 1388 1389 PetscFunctionBegin; 1390 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1391 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 1392 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1393 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 1394 ierr = PetscDSGetTotalBdDimension(prob, &totDimBd);CHKERRQ(ierr); 1395 ierr = DMPlexGetDepthLabel(dm, &depth);CHKERRQ(ierr); 1396 ierr = DMGetNumBoundary(dm, &numBd);CHKERRQ(ierr); 1397 for (bd = 0; bd < numBd; ++bd) { 1398 const char *bdLabel; 1399 DMLabel label; 1400 IS pointIS; 1401 const PetscInt *points; 1402 const PetscInt *values; 1403 PetscInt field, numValues, v, numPoints, p, dep, numFaces; 1404 PetscBool isEssential; 1405 PetscObject obj; 1406 PetscClassId id; 1407 1408 ierr = DMGetBoundary(dm, bd, &isEssential, NULL, &bdLabel, &field, NULL, NULL, NULL, &numValues, &values, NULL);CHKERRQ(ierr); 1409 ierr = DMGetField(dm, field, &obj);CHKERRQ(ierr); 1410 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1411 if ((id != PETSCFE_CLASSID) || isEssential) continue; 1412 ierr = DMGetLabel(dm, bdLabel, &label);CHKERRQ(ierr); 1413 for (v = 0; v < numValues; ++v) { 1414 ierr = DMLabelGetStratumSize(label, values[v], &numPoints);CHKERRQ(ierr); 1415 ierr = DMLabelGetStratumIS(label, values[v], &pointIS);CHKERRQ(ierr); 1416 if (!pointIS) continue; /* No points with that id on this process */ 1417 ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); 1418 for (p = 0, numFaces = 0; p < numPoints; ++p) { 1419 ierr = DMLabelGetValue(depth, points[p], &dep);CHKERRQ(ierr); 1420 if (dep == dim-1) ++numFaces; 1421 } 1422 ierr = PetscMalloc3(numFaces*totDimBd,&u,numFaces,&cgeom,numFaces*totDimBd,&elemVec);CHKERRQ(ierr); 1423 if (locX_t) {ierr = PetscMalloc1(numFaces*totDimBd,&u_t);CHKERRQ(ierr);} 1424 for (p = 0, f = 0; p < numPoints; ++p) { 1425 const PetscInt point = points[p]; 1426 PetscScalar *x = NULL; 1427 PetscInt i; 1428 1429 ierr = DMLabelGetValue(depth, points[p], &dep);CHKERRQ(ierr); 1430 if (dep != dim-1) continue; 1431 ierr = DMPlexComputeCellGeometryFEM(dm, point, NULL, cgeom[f].v0, cgeom[f].J, cgeom[f].invJ, &cgeom[f].detJ);CHKERRQ(ierr); 1432 ierr = DMPlexComputeCellGeometryFVM(dm, point, NULL, NULL, cgeom[f].n);CHKERRQ(ierr); 1433 if (cgeom[f].detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for face %d", cgeom[f].detJ, point); 1434 /* TODO: Matt, this is wrong if feBd does not match fe: i.e., if the order differs. */ 1435 ierr = DMPlexVecGetClosure(dm, section, locX, point, NULL, &x);CHKERRQ(ierr); 1436 for (i = 0; i < totDimBd; ++i) u[f*totDimBd+i] = x[i]; 1437 ierr = DMPlexVecRestoreClosure(dm, section, locX, point, NULL, &x);CHKERRQ(ierr); 1438 if (locX_t) { 1439 ierr = DMPlexVecGetClosure(dm, section, locX_t, point, NULL, &x);CHKERRQ(ierr); 1440 for (i = 0; i < totDimBd; ++i) u_t[f*totDimBd+i] = x[i]; 1441 ierr = DMPlexVecRestoreClosure(dm, section, locX_t, point, NULL, &x);CHKERRQ(ierr); 1442 } 1443 ++f; 1444 } 1445 for (f = 0; f < Nf; ++f) { 1446 PetscFE fe; 1447 PetscQuadrature q; 1448 PetscInt numQuadPoints, Nb; 1449 /* Conforming batches */ 1450 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 1451 /* Remainder */ 1452 PetscInt Nr, offset; 1453 1454 ierr = PetscDSGetBdDiscretization(prob, f, (PetscObject *) &fe);CHKERRQ(ierr); 1455 ierr = PetscFEGetQuadrature(fe, &q);CHKERRQ(ierr); 1456 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 1457 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1458 ierr = PetscQuadratureGetData(q, NULL, &numQuadPoints, NULL, NULL);CHKERRQ(ierr); 1459 blockSize = Nb*numQuadPoints; 1460 batchSize = numBlocks * blockSize; 1461 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1462 numChunks = numFaces / (numBatches*batchSize); 1463 Ne = numChunks*numBatches*batchSize; 1464 Nr = numFaces % (numBatches*batchSize); 1465 offset = numFaces - Nr; 1466 ierr = PetscFEIntegrateBdResidual(fe, prob, f, Ne, cgeom, u, u_t, NULL, NULL, t, elemVec);CHKERRQ(ierr); 1467 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); 1468 } 1469 for (p = 0, f = 0; p < numPoints; ++p) { 1470 const PetscInt point = points[p]; 1471 1472 ierr = DMLabelGetValue(depth, point, &dep);CHKERRQ(ierr); 1473 if (dep != dim-1) continue; 1474 if (mesh->printFEM > 1) {ierr = DMPrintCellVector(point, "BdResidual", totDimBd, &elemVec[f*totDimBd]);CHKERRQ(ierr);} 1475 ierr = DMPlexVecSetClosure(dm, NULL, locF, point, &elemVec[f*totDimBd], ADD_ALL_VALUES);CHKERRQ(ierr); 1476 ++f; 1477 } 1478 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 1479 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 1480 ierr = PetscFree3(u,cgeom,elemVec);CHKERRQ(ierr); 1481 if (locX_t) {ierr = PetscFree(u_t);CHKERRQ(ierr);} 1482 } 1483 } 1484 PetscFunctionReturn(0); 1485 } 1486 1487 #undef __FUNCT__ 1488 #define __FUNCT__ "DMPlexComputeResidual_Internal" 1489 PetscErrorCode DMPlexComputeResidual_Internal(DM dm, PetscInt cStart, PetscInt cEnd, PetscReal time, Vec locX, Vec locX_t, PetscReal t, Vec locF, void *user) 1490 { 1491 DM_Plex *mesh = (DM_Plex *) dm->data; 1492 const char *name = "Residual"; 1493 DM dmAux = NULL; 1494 DM dmGrad = NULL; 1495 DMLabel ghostLabel = NULL; 1496 PetscDS prob = NULL; 1497 PetscDS probAux = NULL; 1498 PetscSection section = NULL; 1499 PetscBool useFEM = PETSC_FALSE; 1500 PetscBool useFVM = PETSC_FALSE; 1501 PetscBool isImplicit = (locX_t || time == PETSC_MIN_REAL) ? PETSC_TRUE : PETSC_FALSE; 1502 PetscFV fvm = NULL; 1503 PetscFECellGeom *cgeomFEM = NULL; 1504 PetscScalar *cgeomScal; 1505 PetscFVCellGeom *cgeomFVM = NULL; 1506 PetscFVFaceGeom *fgeomFVM = NULL; 1507 Vec locA, cellGeometryFEM = NULL, cellGeometryFVM = NULL, faceGeometryFVM = NULL, grad, locGrad = NULL; 1508 PetscScalar *u, *u_t, *a, *uL, *uR; 1509 PetscInt Nf, f, totDim, totDimAux, numChunks, cellChunkSize, faceChunkSize, chunk, fStart, fEnd; 1510 PetscErrorCode ierr; 1511 1512 PetscFunctionBegin; 1513 ierr = PetscLogEventBegin(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr); 1514 /* TODO The places where we have to use isFE are probably the member functions for the PetscDisc class */ 1515 /* TODO The FVM geometry is over-manipulated. Make the precalc functions return exactly what we need */ 1516 /* FEM+FVM */ 1517 /* 1: Get sizes from dm and dmAux */ 1518 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 1519 ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 1520 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1521 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 1522 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1523 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);CHKERRQ(ierr); 1524 if (locA) { 1525 ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); 1526 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 1527 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 1528 } 1529 /* 2: Get geometric data */ 1530 for (f = 0; f < Nf; ++f) { 1531 PetscObject obj; 1532 PetscClassId id; 1533 PetscBool fimp; 1534 1535 ierr = PetscDSGetImplicit(prob, f, &fimp);CHKERRQ(ierr); 1536 if (isImplicit != fimp) continue; 1537 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1538 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1539 if (id == PETSCFE_CLASSID) {useFEM = PETSC_TRUE;} 1540 if (id == PETSCFV_CLASSID) {useFVM = PETSC_TRUE; fvm = (PetscFV) obj;} 1541 } 1542 if (useFEM) { 1543 ierr = DMPlexSNESGetGeometryFEM(dm, &cellGeometryFEM);CHKERRQ(ierr); 1544 ierr = VecGetArray(cellGeometryFEM, &cgeomScal);CHKERRQ(ierr); 1545 if (sizeof(PetscFECellGeom) % sizeof(PetscScalar)) { 1546 DM dmCell; 1547 PetscInt c; 1548 1549 ierr = VecGetDM(cellGeometryFEM,&dmCell);CHKERRQ(ierr); 1550 ierr = PetscMalloc1(cEnd-cStart,&cgeomFEM);CHKERRQ(ierr); 1551 for (c = 0; c < cEnd - cStart; c++) { 1552 PetscScalar *thisgeom; 1553 1554 ierr = DMPlexPointLocalRef(dmCell, c + cStart, cgeomScal, &thisgeom);CHKERRQ(ierr); 1555 cgeomFEM[c] = *((PetscFECellGeom *) thisgeom); 1556 } 1557 } 1558 else { 1559 cgeomFEM = (PetscFECellGeom *) cgeomScal; 1560 } 1561 } 1562 if (useFVM) { 1563 ierr = DMPlexSNESGetGeometryFVM(dm, &faceGeometryFVM, &cellGeometryFVM, NULL);CHKERRQ(ierr); 1564 ierr = VecGetArrayRead(faceGeometryFVM, (const PetscScalar **) &fgeomFVM);CHKERRQ(ierr); 1565 ierr = VecGetArrayRead(cellGeometryFVM, (const PetscScalar **) &cgeomFVM);CHKERRQ(ierr); 1566 /* Reconstruct and limit cell gradients */ 1567 ierr = DMPlexSNESGetGradientDM(dm, fvm, &dmGrad);CHKERRQ(ierr); 1568 if (dmGrad) { 1569 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 1570 ierr = DMGetGlobalVector(dmGrad, &grad);CHKERRQ(ierr); 1571 ierr = DMPlexReconstructGradients_Internal(dm, fStart, fEnd, faceGeometryFVM, cellGeometryFVM, locX, grad);CHKERRQ(ierr); 1572 /* Communicate gradient values */ 1573 ierr = DMGetLocalVector(dmGrad, &locGrad);CHKERRQ(ierr); 1574 ierr = DMGlobalToLocalBegin(dmGrad, grad, INSERT_VALUES, locGrad);CHKERRQ(ierr); 1575 ierr = DMGlobalToLocalEnd(dmGrad, grad, INSERT_VALUES, locGrad);CHKERRQ(ierr); 1576 ierr = DMRestoreGlobalVector(dmGrad, &grad);CHKERRQ(ierr); 1577 } 1578 /* Handle non-essential (e.g. outflow) boundary values */ 1579 ierr = DMPlexInsertBoundaryValues(dm, PETSC_FALSE, locX, time, faceGeometryFVM, cellGeometryFVM, locGrad);CHKERRQ(ierr); 1580 } 1581 /* Loop over chunks */ 1582 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 1583 numChunks = 1; 1584 cellChunkSize = (cEnd - cStart)/numChunks; 1585 faceChunkSize = (fEnd - fStart)/numChunks; 1586 for (chunk = 0; chunk < numChunks; ++chunk) { 1587 PetscScalar *elemVec, *fluxL, *fluxR; 1588 PetscReal *vol; 1589 PetscFVFaceGeom *fgeom; 1590 PetscInt cS = cStart+chunk*cellChunkSize, cE = PetscMin(cS+cellChunkSize, cEnd), numCells = cE - cS, cell; 1591 PetscInt fS = fStart+chunk*faceChunkSize, fE = PetscMin(fS+faceChunkSize, fEnd), numFaces = fE - fS, face; 1592 1593 /* Extract field coefficients */ 1594 if (useFEM) { 1595 ierr = DMPlexGetCellFields(dm, cS, cE, locX, locX_t, locA, &u, &u_t, &a);CHKERRQ(ierr); 1596 ierr = DMGetWorkArray(dm, numCells*totDim, PETSC_SCALAR, &elemVec);CHKERRQ(ierr); 1597 ierr = PetscMemzero(elemVec, numCells*totDim * sizeof(PetscScalar));CHKERRQ(ierr); 1598 } 1599 if (useFVM) { 1600 ierr = DMPlexGetFaceFields(dm, fS, fE, locX, locX_t, faceGeometryFVM, cellGeometryFVM, locGrad, &uL, &uR);CHKERRQ(ierr); 1601 ierr = DMPlexGetFaceGeometry(dm, fS, fE, faceGeometryFVM, cellGeometryFVM, &fgeom, &vol);CHKERRQ(ierr); 1602 ierr = DMGetWorkArray(dm, numFaces*totDim, PETSC_SCALAR, &fluxL);CHKERRQ(ierr); 1603 ierr = DMGetWorkArray(dm, numFaces*totDim, PETSC_SCALAR, &fluxR);CHKERRQ(ierr); 1604 ierr = PetscMemzero(fluxL, numFaces*totDim * sizeof(PetscScalar));CHKERRQ(ierr); 1605 ierr = PetscMemzero(fluxR, numFaces*totDim * sizeof(PetscScalar));CHKERRQ(ierr); 1606 } 1607 /* TODO We will interlace both our field coefficients (u, u_t, uL, uR, etc.) and our output (elemVec, fL, fR). I think this works */ 1608 /* Loop over fields */ 1609 for (f = 0; f < Nf; ++f) { 1610 PetscObject obj; 1611 PetscClassId id; 1612 PetscBool fimp; 1613 PetscInt numChunks, numBatches, batchSize, numBlocks, blockSize, Ne, Nr, offset; 1614 1615 ierr = PetscDSGetImplicit(prob, f, &fimp);CHKERRQ(ierr); 1616 if (isImplicit != fimp) continue; 1617 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1618 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1619 if (id == PETSCFE_CLASSID) { 1620 PetscFE fe = (PetscFE) obj; 1621 PetscQuadrature q; 1622 PetscInt Nq, Nb; 1623 1624 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1625 1626 ierr = PetscFEGetQuadrature(fe, &q);CHKERRQ(ierr); 1627 ierr = PetscQuadratureGetData(q, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 1628 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 1629 blockSize = Nb*Nq; 1630 batchSize = numBlocks * blockSize; 1631 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1632 numChunks = numCells / (numBatches*batchSize); 1633 Ne = numChunks*numBatches*batchSize; 1634 Nr = numCells % (numBatches*batchSize); 1635 offset = numCells - Nr; 1636 /* Integrate FE residual to get elemVec (need fields at quadrature points) */ 1637 /* 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) */ 1638 ierr = PetscFEIntegrateResidual(fe, prob, f, Ne, cgeomFEM, u, u_t, probAux, a, t, elemVec);CHKERRQ(ierr); 1639 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); 1640 } else if (id == PETSCFV_CLASSID) { 1641 PetscFV fv = (PetscFV) obj; 1642 1643 Ne = numFaces; 1644 /* Riemann solve over faces (need fields at face centroids) */ 1645 /* We need to evaluate FE fields at those coordinates */ 1646 ierr = PetscFVIntegrateRHSFunction(fv, prob, f, Ne, fgeom, vol, uL, uR, fluxL, fluxR);CHKERRQ(ierr); 1647 } else SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %d", f); 1648 } 1649 if (sizeof(PetscFECellGeom) % sizeof(PetscScalar)) { 1650 ierr = PetscFree(cgeomFEM);CHKERRQ(ierr); 1651 } 1652 else { 1653 cgeomFEM = NULL; 1654 } 1655 if (cellGeometryFEM) {ierr = VecRestoreArray(cellGeometryFEM, &cgeomScal);CHKERRQ(ierr);} 1656 /* Loop over domain */ 1657 if (useFEM) { 1658 /* Add elemVec to locX */ 1659 for (cell = cS; cell < cE; ++cell) { 1660 if (mesh->printFEM > 1) {ierr = DMPrintCellVector(cell, name, totDim, &elemVec[cell*totDim]);CHKERRQ(ierr);} 1661 ierr = DMPlexVecSetClosure(dm, section, locF, cell, &elemVec[cell*totDim], ADD_ALL_VALUES);CHKERRQ(ierr); 1662 } 1663 } 1664 if (useFVM) { 1665 PetscScalar *fa; 1666 PetscInt iface; 1667 1668 ierr = VecGetArray(locF, &fa);CHKERRQ(ierr); 1669 for (f = 0; f < Nf; ++f) { 1670 PetscFV fv; 1671 PetscObject obj; 1672 PetscClassId id; 1673 PetscInt foff, pdim; 1674 1675 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1676 ierr = PetscDSGetFieldOffset(prob, f, &foff);CHKERRQ(ierr); 1677 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1678 if (id != PETSCFV_CLASSID) continue; 1679 fv = (PetscFV) obj; 1680 ierr = PetscFVGetNumComponents(fv, &pdim);CHKERRQ(ierr); 1681 /* Accumulate fluxes to cells */ 1682 for (face = fS, iface = 0; face < fE; ++face) { 1683 const PetscInt *cells; 1684 PetscScalar *fL, *fR; 1685 PetscInt ghost, d, nsupp; 1686 1687 ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr); 1688 ierr = DMPlexGetSupportSize(dm, face, &nsupp);CHKERRQ(ierr); 1689 if (ghost >= 0) continue; 1690 if (nsupp > 2) { /* noop */ 1691 ++iface; 1692 continue; 1693 } 1694 ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr); 1695 ierr = DMPlexPointGlobalFieldRef(dm, cells[0], f, fa, &fL);CHKERRQ(ierr); 1696 ierr = DMPlexPointGlobalFieldRef(dm, cells[1], f, fa, &fR);CHKERRQ(ierr); 1697 for (d = 0; d < pdim; ++d) { 1698 if (fL) fL[d] -= fluxL[iface*totDim+foff+d]; 1699 if (fR) fR[d] += fluxR[iface*totDim+foff+d]; 1700 } 1701 ++iface; 1702 } 1703 } 1704 ierr = VecRestoreArray(locF, &fa);CHKERRQ(ierr); 1705 } 1706 /* Handle time derivative */ 1707 if (locX_t) { 1708 PetscScalar *x_t, *fa; 1709 1710 ierr = VecGetArray(locF, &fa);CHKERRQ(ierr); 1711 ierr = VecGetArray(locX_t, &x_t);CHKERRQ(ierr); 1712 for (f = 0; f < Nf; ++f) { 1713 PetscFV fv; 1714 PetscObject obj; 1715 PetscClassId id; 1716 PetscInt pdim, d; 1717 1718 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1719 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1720 if (id != PETSCFV_CLASSID) continue; 1721 fv = (PetscFV) obj; 1722 ierr = PetscFVGetNumComponents(fv, &pdim);CHKERRQ(ierr); 1723 for (cell = cS; cell < cE; ++cell) { 1724 PetscScalar *u_t, *r; 1725 1726 ierr = DMPlexPointLocalFieldRead(dm, cell, f, x_t, &u_t);CHKERRQ(ierr); 1727 ierr = DMPlexPointLocalFieldRef(dm, cell, f, fa, &r);CHKERRQ(ierr); 1728 for (d = 0; d < pdim; ++d) r[d] += u_t[d]; 1729 } 1730 } 1731 ierr = VecRestoreArray(locX_t, &x_t);CHKERRQ(ierr); 1732 ierr = VecRestoreArray(locF, &fa);CHKERRQ(ierr); 1733 } 1734 if (useFEM) { 1735 ierr = DMPlexRestoreCellFields(dm, cS, cE, locX, locX_t, locA, &u, &u_t, &a);CHKERRQ(ierr); 1736 ierr = DMRestoreWorkArray(dm, numCells*totDim, PETSC_SCALAR, &elemVec);CHKERRQ(ierr); 1737 } 1738 if (useFVM) { 1739 ierr = DMPlexRestoreFaceFields(dm, fS, fE, locX, locX_t, faceGeometryFVM, cellGeometryFVM, locGrad, &uL, &uR);CHKERRQ(ierr); 1740 ierr = DMPlexRestoreFaceGeometry(dm, fS, fE, faceGeometryFVM, cellGeometryFVM, &fgeom, &vol);CHKERRQ(ierr); 1741 ierr = DMRestoreWorkArray(dm, numFaces*totDim, PETSC_SCALAR, &fluxL);CHKERRQ(ierr); 1742 ierr = DMRestoreWorkArray(dm, numFaces*totDim, PETSC_SCALAR, &fluxR);CHKERRQ(ierr); 1743 if (dmGrad) {ierr = DMRestoreLocalVector(dmGrad, &locGrad);CHKERRQ(ierr);} 1744 } 1745 } 1746 1747 if (useFEM) {ierr = DMPlexComputeBdResidual_Internal(dm, locX, locX_t, t, locF, user);CHKERRQ(ierr);} 1748 1749 /* FEM */ 1750 /* 1: Get sizes from dm and dmAux */ 1751 /* 2: Get geometric data */ 1752 /* 3: Handle boundary values */ 1753 /* 4: Loop over domain */ 1754 /* Extract coefficients */ 1755 /* Loop over fields */ 1756 /* Set tiling for FE*/ 1757 /* Integrate FE residual to get elemVec */ 1758 /* Loop over subdomain */ 1759 /* Loop over quad points */ 1760 /* Transform coords to real space */ 1761 /* Evaluate field and aux fields at point */ 1762 /* Evaluate residual at point */ 1763 /* Transform residual to real space */ 1764 /* Add residual to elemVec */ 1765 /* Loop over domain */ 1766 /* Add elemVec to locX */ 1767 1768 /* FVM */ 1769 /* Get geometric data */ 1770 /* If using gradients */ 1771 /* Compute gradient data */ 1772 /* Loop over domain faces */ 1773 /* Count computational faces */ 1774 /* Reconstruct cell gradient */ 1775 /* Loop over domain cells */ 1776 /* Limit cell gradients */ 1777 /* Handle boundary values */ 1778 /* Loop over domain faces */ 1779 /* Read out field, centroid, normal, volume for each side of face */ 1780 /* Riemann solve over faces */ 1781 /* Loop over domain faces */ 1782 /* Accumulate fluxes to cells */ 1783 /* TODO Change printFEM to printDisc here */ 1784 if (mesh->printFEM) { 1785 Vec locFbc; 1786 PetscInt pStart, pEnd, p, maxDof; 1787 PetscScalar *zeroes; 1788 1789 ierr = VecDuplicate(locF,&locFbc);CHKERRQ(ierr); 1790 ierr = VecCopy(locF,locFbc);CHKERRQ(ierr); 1791 ierr = PetscSectionGetChart(section,&pStart,&pEnd);CHKERRQ(ierr); 1792 ierr = PetscSectionGetMaxDof(section,&maxDof);CHKERRQ(ierr); 1793 ierr = PetscCalloc1(maxDof,&zeroes);CHKERRQ(ierr); 1794 for (p = pStart; p < pEnd; p++) { 1795 ierr = VecSetValuesSection(locFbc,section,p,zeroes,INSERT_BC_VALUES);CHKERRQ(ierr); 1796 } 1797 ierr = PetscFree(zeroes);CHKERRQ(ierr); 1798 ierr = DMPrintLocalVec(dm, name, mesh->printTol, locFbc);CHKERRQ(ierr); 1799 ierr = VecDestroy(&locFbc);CHKERRQ(ierr); 1800 } 1801 ierr = PetscLogEventEnd(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr); 1802 PetscFunctionReturn(0); 1803 } 1804 1805 #undef __FUNCT__ 1806 #define __FUNCT__ "DMPlexComputeResidualFEM_Check_Internal" 1807 static PetscErrorCode DMPlexComputeResidualFEM_Check_Internal(DM dm, Vec X, Vec X_t, PetscReal t, Vec F, void *user) 1808 { 1809 DM dmCh, dmAux; 1810 Vec A, cellgeom; 1811 PetscDS prob, probCh, probAux = NULL; 1812 PetscQuadrature q; 1813 PetscSection section, sectionAux; 1814 PetscFECellGeom *cgeom = NULL; 1815 PetscScalar *cgeomScal; 1816 PetscScalar *elemVec, *elemVecCh, *u, *u_t, *a = NULL; 1817 PetscInt dim, Nf, f, numCells, cStart, cEnd, c; 1818 PetscInt totDim, totDimAux, diffCell = 0; 1819 PetscErrorCode ierr; 1820 1821 PetscFunctionBegin; 1822 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1823 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 1824 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1825 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1826 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); 1827 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1828 numCells = cEnd - cStart; 1829 ierr = PetscObjectQuery((PetscObject) dm, "dmCh", (PetscObject *) &dmCh);CHKERRQ(ierr); 1830 ierr = DMGetDS(dmCh, &probCh);CHKERRQ(ierr); 1831 ierr = PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);CHKERRQ(ierr); 1832 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);CHKERRQ(ierr); 1833 if (dmAux) { 1834 ierr = DMGetDefaultSection(dmAux, §ionAux);CHKERRQ(ierr); 1835 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 1836 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 1837 } 1838 ierr = VecSet(F, 0.0);CHKERRQ(ierr); 1839 ierr = PetscMalloc3(numCells*totDim,&u,X_t ? numCells*totDim : 0,&u_t,numCells*totDim,&elemVec);CHKERRQ(ierr); 1840 ierr = PetscMalloc1(numCells*totDim,&elemVecCh);CHKERRQ(ierr); 1841 if (dmAux) {ierr = PetscMalloc1(numCells*totDimAux, &a);CHKERRQ(ierr);} 1842 ierr = DMPlexSNESGetGeometryFEM(dm, &cellgeom);CHKERRQ(ierr); 1843 ierr = VecGetArray(cellgeom, &cgeomScal);CHKERRQ(ierr); 1844 if (sizeof(PetscFECellGeom) % sizeof(PetscScalar)) { 1845 DM dmCell; 1846 1847 ierr = VecGetDM(cellgeom,&dmCell);CHKERRQ(ierr); 1848 ierr = PetscMalloc1(cEnd-cStart,&cgeom);CHKERRQ(ierr); 1849 for (c = 0; c < cEnd - cStart; c++) { 1850 PetscScalar *thisgeom; 1851 1852 ierr = DMPlexPointLocalRef(dmCell, c + cStart, cgeomScal, &thisgeom);CHKERRQ(ierr); 1853 cgeom[c] = *((PetscFECellGeom *) thisgeom); 1854 } 1855 } 1856 else { 1857 cgeom = (PetscFECellGeom *) cgeomScal; 1858 } 1859 for (c = cStart; c < cEnd; ++c) { 1860 PetscScalar *x = NULL, *x_t = NULL; 1861 PetscInt i; 1862 1863 ierr = DMPlexVecGetClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr); 1864 for (i = 0; i < totDim; ++i) u[c*totDim+i] = x[i]; 1865 ierr = DMPlexVecRestoreClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr); 1866 if (X_t) { 1867 ierr = DMPlexVecGetClosure(dm, section, X_t, c, NULL, &x_t);CHKERRQ(ierr); 1868 for (i = 0; i < totDim; ++i) u_t[c*totDim+i] = x_t[i]; 1869 ierr = DMPlexVecRestoreClosure(dm, section, X_t, c, NULL, &x_t);CHKERRQ(ierr); 1870 } 1871 if (dmAux) { 1872 DM dmAuxPlex; 1873 1874 ierr = DMSNESConvertPlex(dmAux,&dmAuxPlex, PETSC_FALSE);CHKERRQ(ierr); 1875 ierr = DMPlexVecGetClosure(dmAuxPlex, sectionAux, A, c, NULL, &x);CHKERRQ(ierr); 1876 for (i = 0; i < totDimAux; ++i) a[c*totDimAux+i] = x[i]; 1877 ierr = DMPlexVecRestoreClosure(dmAuxPlex, sectionAux, A, c, NULL, &x);CHKERRQ(ierr); 1878 ierr = DMDestroy(&dmAuxPlex);CHKERRQ(ierr); 1879 } 1880 } 1881 for (f = 0; f < Nf; ++f) { 1882 PetscFE fe, feCh; 1883 PetscInt numQuadPoints, Nb; 1884 /* Conforming batches */ 1885 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 1886 /* Remainder */ 1887 PetscInt Nr, offset; 1888 1889 ierr = PetscDSGetDiscretization(prob, f, (PetscObject *) &fe);CHKERRQ(ierr); 1890 ierr = PetscDSGetDiscretization(probCh, f, (PetscObject *) &feCh);CHKERRQ(ierr); 1891 ierr = PetscFEGetQuadrature(fe, &q);CHKERRQ(ierr); 1892 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 1893 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1894 ierr = PetscQuadratureGetData(q, NULL, &numQuadPoints, NULL, NULL);CHKERRQ(ierr); 1895 blockSize = Nb*numQuadPoints; 1896 batchSize = numBlocks * blockSize; 1897 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1898 numChunks = numCells / (numBatches*batchSize); 1899 Ne = numChunks*numBatches*batchSize; 1900 Nr = numCells % (numBatches*batchSize); 1901 offset = numCells - Nr; 1902 ierr = PetscFEIntegrateResidual(fe, prob, f, Ne, cgeom, u, u_t, probAux, a, t, elemVec);CHKERRQ(ierr); 1903 ierr = PetscFEIntegrateResidual(feCh, prob, f, Ne, cgeom, u, u_t, probAux, a, t, elemVecCh);CHKERRQ(ierr); 1904 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); 1905 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); 1906 } 1907 for (c = cStart; c < cEnd; ++c) { 1908 PetscBool diff = PETSC_FALSE; 1909 PetscInt d; 1910 1911 for (d = 0; d < totDim; ++d) if (PetscAbsScalar(elemVec[c*totDim+d] - elemVecCh[c*totDim+d]) > 1.0e-7) {diff = PETSC_TRUE;break;} 1912 if (diff) { 1913 ierr = PetscPrintf(PetscObjectComm((PetscObject) dm), "Different cell %d\n", c);CHKERRQ(ierr); 1914 ierr = DMPrintCellVector(c, "Residual", totDim, &elemVec[c*totDim]);CHKERRQ(ierr); 1915 ierr = DMPrintCellVector(c, "Check Residual", totDim, &elemVecCh[c*totDim]);CHKERRQ(ierr); 1916 ++diffCell; 1917 } 1918 if (diffCell > 9) break; 1919 ierr = DMPlexVecSetClosure(dm, section, F, c, &elemVec[c*totDim], ADD_ALL_VALUES);CHKERRQ(ierr); 1920 } 1921 if (sizeof(PetscFECellGeom) % sizeof(PetscScalar)) { 1922 ierr = PetscFree(cgeom);CHKERRQ(ierr); 1923 } 1924 else { 1925 cgeom = NULL; 1926 } 1927 ierr = VecRestoreArray(cellgeom, &cgeomScal);CHKERRQ(ierr); 1928 ierr = PetscFree3(u,u_t,elemVec);CHKERRQ(ierr); 1929 ierr = PetscFree(elemVecCh);CHKERRQ(ierr); 1930 if (dmAux) {ierr = PetscFree(a);CHKERRQ(ierr);} 1931 PetscFunctionReturn(0); 1932 } 1933 1934 #undef __FUNCT__ 1935 #define __FUNCT__ "DMPlexSNESComputeResidualFEM" 1936 /*@ 1937 DMPlexSNESComputeResidualFEM - Form the local residual F from the local input X using pointwise functions specified by the user 1938 1939 Input Parameters: 1940 + dm - The mesh 1941 . X - Local solution 1942 - user - The user context 1943 1944 Output Parameter: 1945 . F - Local output vector 1946 1947 Level: developer 1948 1949 .seealso: DMPlexComputeJacobianActionFEM() 1950 @*/ 1951 PetscErrorCode DMPlexSNESComputeResidualFEM(DM dm, Vec X, Vec F, void *user) 1952 { 1953 PetscObject check; 1954 PetscInt cStart, cEnd, cEndInterior; 1955 DM plex; 1956 PetscErrorCode ierr; 1957 1958 PetscFunctionBegin; 1959 ierr = DMSNESConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr); 1960 ierr = DMPlexGetHeightStratum(plex, 0, &cStart, &cEnd);CHKERRQ(ierr); 1961 ierr = DMPlexGetHybridBounds(plex, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr); 1962 cEnd = cEndInterior < 0 ? cEnd : cEndInterior; 1963 /* The dmCh is used to check two mathematically equivalent discretizations for computational equivalence */ 1964 ierr = PetscObjectQuery((PetscObject) plex, "dmCh", &check);CHKERRQ(ierr); 1965 if (check) {ierr = DMPlexComputeResidualFEM_Check_Internal(plex, X, NULL, 0.0, F, user);CHKERRQ(ierr);} 1966 else {ierr = DMPlexComputeResidual_Internal(plex, cStart, cEnd, PETSC_MIN_REAL, X, NULL, 0.0, F, user);CHKERRQ(ierr);} 1967 ierr = DMDestroy(&plex);CHKERRQ(ierr); 1968 PetscFunctionReturn(0); 1969 } 1970 1971 #undef __FUNCT__ 1972 #define __FUNCT__ "DMPlexSNESComputeBoundaryFEM" 1973 /*@ 1974 DMPlexSNESComputeBoundaryFEM - Form the boundary values for the local input X 1975 1976 Input Parameters: 1977 + dm - The mesh 1978 - user - The user context 1979 1980 Output Parameter: 1981 . X - Local solution 1982 1983 Level: developer 1984 1985 .seealso: DMPlexComputeJacobianActionFEM() 1986 @*/ 1987 PetscErrorCode DMPlexSNESComputeBoundaryFEM(DM dm, Vec X, void *user) 1988 { 1989 DM plex; 1990 PetscErrorCode ierr; 1991 1992 PetscFunctionBegin; 1993 ierr = DMSNESConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr); 1994 ierr = DMPlexInsertBoundaryValues(plex, PETSC_TRUE, X, PETSC_MIN_REAL, NULL, NULL, NULL);CHKERRQ(ierr); 1995 ierr = DMDestroy(&plex);CHKERRQ(ierr); 1996 PetscFunctionReturn(0); 1997 } 1998 1999 #undef __FUNCT__ 2000 #define __FUNCT__ "DMPlexComputeJacobian_Internal" 2001 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) 2002 { 2003 DM_Plex *mesh = (DM_Plex *) dm->data; 2004 const char *name = "Jacobian"; 2005 DM dmAux, plex; 2006 DMLabel depth; 2007 Vec A, cellgeom; 2008 PetscDS prob, probAux = NULL; 2009 PetscQuadrature quad; 2010 PetscSection section, globalSection, sectionAux; 2011 PetscFECellGeom *cgeom = NULL; 2012 PetscScalar *cgeomScal; 2013 PetscScalar *elemMat, *elemMatP, *elemMatD, *u, *u_t, *a = NULL; 2014 PetscInt dim, Nf, f, fieldI, fieldJ, numCells, c; 2015 PetscInt totDim, totDimBd, totDimAux, numBd, bd; 2016 PetscBool isShell, hasPrec, hasDyn; 2017 PetscErrorCode ierr; 2018 2019 PetscFunctionBegin; 2020 ierr = PetscLogEventBegin(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 2021 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 2022 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 2023 ierr = DMGetDefaultGlobalSection(dm, &globalSection);CHKERRQ(ierr); 2024 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 2025 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 2026 ierr = PetscDSGetTotalBdDimension(prob, &totDimBd);CHKERRQ(ierr); 2027 ierr = PetscDSHasJacobianPreconditioner(prob, &hasPrec);CHKERRQ(ierr); 2028 ierr = PetscDSHasDynamicJacobian(prob, &hasDyn);CHKERRQ(ierr); 2029 hasDyn = hasDyn && (X_tShift != 0.0) ? PETSC_TRUE : PETSC_FALSE; 2030 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); 2031 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 2032 numCells = cEnd - cStart; 2033 ierr = PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);CHKERRQ(ierr); 2034 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);CHKERRQ(ierr); 2035 if (dmAux) { 2036 ierr = DMConvert(dmAux, DMPLEX, &plex);CHKERRQ(ierr); 2037 ierr = DMGetDefaultSection(plex, §ionAux);CHKERRQ(ierr); 2038 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 2039 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 2040 } 2041 ierr = MatZeroEntries(JacP);CHKERRQ(ierr); 2042 ierr = PetscMalloc5(numCells*totDim,&u,X_t ? numCells*totDim : 0,&u_t,numCells*totDim*totDim,&elemMat,hasPrec ? numCells*totDim*totDim : 0, &elemMatP,hasDyn ? numCells*totDim*totDim : 0, &elemMatD);CHKERRQ(ierr); 2043 if (dmAux) {ierr = PetscMalloc1(numCells*totDimAux, &a);CHKERRQ(ierr);} 2044 ierr = DMPlexSNESGetGeometryFEM(dm, &cellgeom);CHKERRQ(ierr); 2045 ierr = VecGetArray(cellgeom, &cgeomScal);CHKERRQ(ierr); 2046 if (sizeof(PetscFECellGeom) % sizeof(PetscScalar)) { 2047 DM dmCell; 2048 2049 ierr = VecGetDM(cellgeom,&dmCell);CHKERRQ(ierr); 2050 ierr = PetscMalloc1(cEnd-cStart,&cgeom);CHKERRQ(ierr); 2051 for (c = 0; c < cEnd - cStart; c++) { 2052 PetscScalar *thisgeom; 2053 2054 ierr = DMPlexPointLocalRef(dmCell, c + cStart, cgeomScal, &thisgeom);CHKERRQ(ierr); 2055 cgeom[c] = *((PetscFECellGeom *) thisgeom); 2056 } 2057 } 2058 else { 2059 cgeom = (PetscFECellGeom *) cgeomScal; 2060 } 2061 for (c = cStart; c < cEnd; ++c) { 2062 PetscScalar *x = NULL, *x_t = NULL; 2063 PetscInt i; 2064 2065 ierr = DMPlexVecGetClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr); 2066 for (i = 0; i < totDim; ++i) u[(c-cStart)*totDim+i] = x[i]; 2067 ierr = DMPlexVecRestoreClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr); 2068 if (X_t) { 2069 ierr = DMPlexVecGetClosure(dm, section, X_t, c, NULL, &x_t);CHKERRQ(ierr); 2070 for (i = 0; i < totDim; ++i) u_t[(c-cStart)*totDim+i] = x_t[i]; 2071 ierr = DMPlexVecRestoreClosure(dm, section, X_t, c, NULL, &x_t);CHKERRQ(ierr); 2072 } 2073 if (dmAux) { 2074 ierr = DMPlexVecGetClosure(plex, sectionAux, A, c, NULL, &x);CHKERRQ(ierr); 2075 for (i = 0; i < totDimAux; ++i) a[(c-cStart)*totDimAux+i] = x[i]; 2076 ierr = DMPlexVecRestoreClosure(plex, sectionAux, A, c, NULL, &x);CHKERRQ(ierr); 2077 } 2078 } 2079 ierr = PetscMemzero(elemMat, numCells*totDim*totDim * sizeof(PetscScalar));CHKERRQ(ierr); 2080 if (hasPrec) {ierr = PetscMemzero(elemMatP, numCells*totDim*totDim * sizeof(PetscScalar));CHKERRQ(ierr);} 2081 if (hasDyn) {ierr = PetscMemzero(elemMatD, numCells*totDim*totDim * sizeof(PetscScalar));CHKERRQ(ierr);} 2082 for (fieldI = 0; fieldI < Nf; ++fieldI) { 2083 PetscFE fe; 2084 PetscInt numQuadPoints, Nb; 2085 /* Conforming batches */ 2086 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 2087 /* Remainder */ 2088 PetscInt Nr, offset; 2089 2090 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); 2091 ierr = PetscFEGetQuadrature(fe, &quad);CHKERRQ(ierr); 2092 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 2093 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 2094 ierr = PetscQuadratureGetData(quad, NULL, &numQuadPoints, NULL, NULL);CHKERRQ(ierr); 2095 blockSize = Nb*numQuadPoints; 2096 batchSize = numBlocks * blockSize; 2097 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 2098 numChunks = numCells / (numBatches*batchSize); 2099 Ne = numChunks*numBatches*batchSize; 2100 Nr = numCells % (numBatches*batchSize); 2101 offset = numCells - Nr; 2102 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 2103 ierr = PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN, fieldI, fieldJ, Ne, cgeom, u, u_t, probAux, a, t, X_tShift, elemMat);CHKERRQ(ierr); 2104 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); 2105 if (hasPrec) { 2106 ierr = PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN_PRE, fieldI, fieldJ, Ne, cgeom, u, u_t, probAux, a, t, X_tShift, elemMatP);CHKERRQ(ierr); 2107 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); 2108 } 2109 if (hasDyn) { 2110 ierr = PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN_DYN, fieldI, fieldJ, Ne, cgeom, u, u_t, probAux, a, t, X_tShift, elemMatD);CHKERRQ(ierr); 2111 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); 2112 } 2113 } 2114 } 2115 if (hasDyn) { 2116 for (c = 0; c < (cEnd - cStart)*totDim*totDim; ++c) elemMat[c] += X_tShift*elemMatD[c]; 2117 } 2118 for (c = cStart; c < cEnd; ++c) { 2119 if (hasPrec) { 2120 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(c, name, totDim, totDim, &elemMat[(c-cStart)*totDim*totDim]);CHKERRQ(ierr);} 2121 ierr = DMPlexMatSetClosure(dm, section, globalSection, Jac, c, &elemMat[(c-cStart)*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2122 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(c, name, totDim, totDim, &elemMatP[(c-cStart)*totDim*totDim]);CHKERRQ(ierr);} 2123 ierr = DMPlexMatSetClosure(dm, section, globalSection, JacP, c, &elemMatP[(c-cStart)*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2124 } else { 2125 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(c, name, totDim, totDim, &elemMat[(c-cStart)*totDim*totDim]);CHKERRQ(ierr);} 2126 ierr = DMPlexMatSetClosure(dm, section, globalSection, JacP, c, &elemMat[(c-cStart)*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2127 } 2128 } 2129 if (sizeof(PetscFECellGeom) % sizeof(PetscScalar)) { 2130 ierr = PetscFree(cgeom);CHKERRQ(ierr); 2131 } 2132 else { 2133 cgeom = NULL; 2134 } 2135 ierr = VecRestoreArray(cellgeom, &cgeomScal);CHKERRQ(ierr); 2136 ierr = PetscFree5(u,u_t,elemMat,elemMatP,elemMatD);CHKERRQ(ierr); 2137 if (dmAux) { 2138 ierr = PetscFree(a);CHKERRQ(ierr); 2139 ierr = DMDestroy(&plex);CHKERRQ(ierr); 2140 } 2141 ierr = DMPlexGetDepthLabel(dm, &depth);CHKERRQ(ierr); 2142 ierr = DMGetNumBoundary(dm, &numBd);CHKERRQ(ierr); 2143 ierr = DMPlexGetDepthLabel(dm, &depth);CHKERRQ(ierr); 2144 ierr = DMGetNumBoundary(dm, &numBd);CHKERRQ(ierr); 2145 for (bd = 0; bd < numBd; ++bd) { 2146 const char *bdLabel; 2147 DMLabel label; 2148 IS pointIS; 2149 const PetscInt *points; 2150 const PetscInt *values; 2151 PetscInt field, numValues, v, numPoints, p, dep, numFaces; 2152 PetscBool isEssential; 2153 PetscObject obj; 2154 PetscClassId id; 2155 2156 ierr = DMGetBoundary(dm, bd, &isEssential, NULL, &bdLabel, &field, NULL, NULL, NULL, &numValues, &values, NULL);CHKERRQ(ierr); 2157 ierr = DMGetField(dm, field, &obj);CHKERRQ(ierr); 2158 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 2159 if ((id != PETSCFE_CLASSID) || isEssential) continue; 2160 ierr = DMGetLabel(dm, bdLabel, &label);CHKERRQ(ierr); 2161 for (v = 0; v < numValues; ++v) { 2162 ierr = DMLabelGetStratumSize(label, values[v], &numPoints);CHKERRQ(ierr); 2163 ierr = DMLabelGetStratumIS(label, values[v], &pointIS);CHKERRQ(ierr); 2164 if (!pointIS) continue; /* No points with that id on this process */ 2165 ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); 2166 for (p = 0, numFaces = 0; p < numPoints; ++p) { 2167 ierr = DMLabelGetValue(depth, points[p], &dep);CHKERRQ(ierr); 2168 if (dep == dim-1) ++numFaces; 2169 } 2170 ierr = PetscMalloc3(numFaces*totDimBd,&u,numFaces,&cgeom,numFaces*totDimBd*totDimBd,&elemMat);CHKERRQ(ierr); 2171 if (X_t) {ierr = PetscMalloc1(numFaces*totDimBd,&u_t);CHKERRQ(ierr);} 2172 for (p = 0, f = 0; p < numPoints; ++p) { 2173 const PetscInt point = points[p]; 2174 PetscScalar *x = NULL; 2175 PetscInt i; 2176 2177 ierr = DMLabelGetValue(depth, points[p], &dep);CHKERRQ(ierr); 2178 if (dep != dim-1) continue; 2179 ierr = DMPlexComputeCellGeometryFEM(dm, point, NULL, cgeom[f].v0, cgeom[f].J, cgeom[f].invJ, &cgeom[f].detJ);CHKERRQ(ierr); 2180 ierr = DMPlexComputeCellGeometryFVM(dm, point, NULL, NULL, cgeom[f].n);CHKERRQ(ierr); 2181 if (cgeom[f].detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for face %d", cgeom[f].detJ, point); 2182 ierr = DMPlexVecGetClosure(dm, section, X, point, NULL, &x);CHKERRQ(ierr); 2183 for (i = 0; i < totDimBd; ++i) u[f*totDimBd+i] = x[i]; 2184 ierr = DMPlexVecRestoreClosure(dm, section, X, point, NULL, &x);CHKERRQ(ierr); 2185 if (X_t) { 2186 ierr = DMPlexVecGetClosure(dm, section, X_t, point, NULL, &x);CHKERRQ(ierr); 2187 for (i = 0; i < totDimBd; ++i) u_t[f*totDimBd+i] = x[i]; 2188 ierr = DMPlexVecRestoreClosure(dm, section, X_t, point, NULL, &x);CHKERRQ(ierr); 2189 } 2190 ++f; 2191 } 2192 ierr = PetscMemzero(elemMat, numFaces*totDimBd*totDimBd * sizeof(PetscScalar));CHKERRQ(ierr); 2193 for (fieldI = 0; fieldI < Nf; ++fieldI) { 2194 PetscFE fe; 2195 PetscInt numQuadPoints, Nb; 2196 /* Conforming batches */ 2197 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 2198 /* Remainder */ 2199 PetscInt Nr, offset; 2200 2201 ierr = PetscDSGetBdDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); 2202 ierr = PetscFEGetQuadrature(fe, &quad);CHKERRQ(ierr); 2203 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 2204 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 2205 ierr = PetscQuadratureGetData(quad, NULL, &numQuadPoints, NULL, NULL);CHKERRQ(ierr); 2206 blockSize = Nb*numQuadPoints; 2207 batchSize = numBlocks * blockSize; 2208 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 2209 numChunks = numFaces / (numBatches*batchSize); 2210 Ne = numChunks*numBatches*batchSize; 2211 Nr = numFaces % (numBatches*batchSize); 2212 offset = numFaces - Nr; 2213 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 2214 ierr = PetscFEIntegrateBdJacobian(fe, prob, fieldI, fieldJ, Ne, cgeom, u, u_t, NULL, NULL, t, X_tShift, elemMat);CHKERRQ(ierr); 2215 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); 2216 } 2217 } 2218 for (p = 0, f = 0; p < numPoints; ++p) { 2219 const PetscInt point = points[p]; 2220 2221 ierr = DMLabelGetValue(depth, point, &dep);CHKERRQ(ierr); 2222 if (dep != dim-1) continue; 2223 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(point, "BdJacobian", totDimBd, totDimBd, &elemMat[f*totDimBd*totDimBd]);CHKERRQ(ierr);} 2224 ierr = DMPlexMatSetClosure(dm, section, globalSection, JacP, point, &elemMat[f*totDimBd*totDimBd], ADD_VALUES);CHKERRQ(ierr); 2225 ++f; 2226 } 2227 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 2228 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 2229 ierr = PetscFree3(u,cgeom,elemMat);CHKERRQ(ierr); 2230 if (X_t) {ierr = PetscFree(u_t);CHKERRQ(ierr);} 2231 } 2232 } 2233 if (hasPrec) { 2234 ierr = MatAssemblyBegin(Jac, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2235 ierr = MatAssemblyEnd(Jac, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2236 } 2237 ierr = MatAssemblyBegin(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2238 ierr = MatAssemblyEnd(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2239 if (mesh->printFEM) { 2240 ierr = PetscPrintf(PETSC_COMM_WORLD, "%s:\n", name);CHKERRQ(ierr); 2241 ierr = MatChop(JacP, 1.0e-10);CHKERRQ(ierr); 2242 ierr = MatView(JacP, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 2243 } 2244 ierr = PetscLogEventEnd(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 2245 ierr = PetscObjectTypeCompare((PetscObject) Jac, MATSHELL, &isShell);CHKERRQ(ierr); 2246 if (isShell) { 2247 JacActionCtx *jctx; 2248 2249 ierr = MatShellGetContext(Jac, &jctx);CHKERRQ(ierr); 2250 ierr = VecCopy(X, jctx->u);CHKERRQ(ierr); 2251 } 2252 PetscFunctionReturn(0); 2253 } 2254 2255 2256 #undef __FUNCT__ 2257 #define __FUNCT__ "DMPlexComputeJacobianAction_Internal" 2258 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) 2259 { 2260 DM_Plex *mesh = (DM_Plex *) dm->data; 2261 const char *name = "Jacobian"; 2262 DM dmAux, plex; 2263 Vec A, cellgeom; 2264 PetscDS prob, probAux = NULL; 2265 PetscQuadrature quad; 2266 PetscSection section, globalSection, sectionAux; 2267 PetscFECellGeom *cgeom = NULL; 2268 PetscScalar *cgeomScal; 2269 PetscScalar *elemMat, *elemMatD, *u, *u_t, *a = NULL, *y, *z; 2270 PetscInt dim, Nf, fieldI, fieldJ, numCells, c; 2271 PetscInt totDim, totDimBd, totDimAux; 2272 PetscBool hasDyn; 2273 PetscErrorCode ierr; 2274 2275 PetscFunctionBegin; 2276 ierr = PetscLogEventBegin(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 2277 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 2278 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 2279 ierr = DMGetDefaultGlobalSection(dm, &globalSection);CHKERRQ(ierr); 2280 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 2281 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 2282 ierr = PetscDSGetTotalBdDimension(prob, &totDimBd);CHKERRQ(ierr); 2283 ierr = PetscDSHasDynamicJacobian(prob, &hasDyn);CHKERRQ(ierr); 2284 hasDyn = hasDyn && (X_tShift != 0.0) ? PETSC_TRUE : PETSC_FALSE; 2285 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); 2286 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 2287 numCells = cEnd - cStart; 2288 ierr = PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);CHKERRQ(ierr); 2289 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);CHKERRQ(ierr); 2290 if (dmAux) { 2291 ierr = DMConvert(dmAux, DMPLEX, &plex);CHKERRQ(ierr); 2292 ierr = DMGetDefaultSection(plex, §ionAux);CHKERRQ(ierr); 2293 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 2294 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 2295 } 2296 ierr = VecSet(Z, 0.0);CHKERRQ(ierr); 2297 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); 2298 if (dmAux) {ierr = PetscMalloc1(numCells*totDimAux, &a);CHKERRQ(ierr);} 2299 ierr = DMPlexSNESGetGeometryFEM(dm, &cellgeom);CHKERRQ(ierr); 2300 ierr = VecGetArray(cellgeom, &cgeomScal);CHKERRQ(ierr); 2301 if (sizeof(PetscFECellGeom) % sizeof(PetscScalar)) { 2302 DM dmCell; 2303 2304 ierr = VecGetDM(cellgeom,&dmCell);CHKERRQ(ierr); 2305 ierr = PetscMalloc1(cEnd-cStart,&cgeom);CHKERRQ(ierr); 2306 for (c = 0; c < cEnd - cStart; c++) { 2307 PetscScalar *thisgeom; 2308 2309 ierr = DMPlexPointLocalRef(dmCell, c + cStart, cgeomScal, &thisgeom);CHKERRQ(ierr); 2310 cgeom[c] = *((PetscFECellGeom *) thisgeom); 2311 } 2312 } else { 2313 cgeom = (PetscFECellGeom *) cgeomScal; 2314 } 2315 for (c = cStart; c < cEnd; ++c) { 2316 PetscScalar *x = NULL, *x_t = NULL; 2317 PetscInt i; 2318 2319 ierr = DMPlexVecGetClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr); 2320 for (i = 0; i < totDim; ++i) u[(c-cStart)*totDim+i] = x[i]; 2321 ierr = DMPlexVecRestoreClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr); 2322 if (X_t) { 2323 ierr = DMPlexVecGetClosure(dm, section, X_t, c, NULL, &x_t);CHKERRQ(ierr); 2324 for (i = 0; i < totDim; ++i) u_t[(c-cStart)*totDim+i] = x_t[i]; 2325 ierr = DMPlexVecRestoreClosure(dm, section, X_t, c, NULL, &x_t);CHKERRQ(ierr); 2326 } 2327 if (dmAux) { 2328 ierr = DMPlexVecGetClosure(plex, sectionAux, A, c, NULL, &x);CHKERRQ(ierr); 2329 for (i = 0; i < totDimAux; ++i) a[(c-cStart)*totDimAux+i] = x[i]; 2330 ierr = DMPlexVecRestoreClosure(plex, sectionAux, A, c, NULL, &x);CHKERRQ(ierr); 2331 } 2332 ierr = DMPlexVecGetClosure(dm, section, Y, c, NULL, &x);CHKERRQ(ierr); 2333 for (i = 0; i < totDim; ++i) y[(c-cStart)*totDim+i] = x[i]; 2334 ierr = DMPlexVecRestoreClosure(dm, section, Y, c, NULL, &x);CHKERRQ(ierr); 2335 } 2336 ierr = PetscMemzero(elemMat, numCells*totDim*totDim * sizeof(PetscScalar));CHKERRQ(ierr); 2337 if (hasDyn) {ierr = PetscMemzero(elemMatD, numCells*totDim*totDim * sizeof(PetscScalar));CHKERRQ(ierr);} 2338 for (fieldI = 0; fieldI < Nf; ++fieldI) { 2339 PetscFE fe; 2340 PetscInt numQuadPoints, Nb; 2341 /* Conforming batches */ 2342 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 2343 /* Remainder */ 2344 PetscInt Nr, offset; 2345 2346 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); 2347 ierr = PetscFEGetQuadrature(fe, &quad);CHKERRQ(ierr); 2348 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 2349 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 2350 ierr = PetscQuadratureGetData(quad, NULL, &numQuadPoints, NULL, NULL);CHKERRQ(ierr); 2351 blockSize = Nb*numQuadPoints; 2352 batchSize = numBlocks * blockSize; 2353 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 2354 numChunks = numCells / (numBatches*batchSize); 2355 Ne = numChunks*numBatches*batchSize; 2356 Nr = numCells % (numBatches*batchSize); 2357 offset = numCells - Nr; 2358 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 2359 ierr = PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN, fieldI, fieldJ, Ne, cgeom, u, u_t, probAux, a, t, X_tShift, elemMat);CHKERRQ(ierr); 2360 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); 2361 if (hasDyn) { 2362 ierr = PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN_DYN, fieldI, fieldJ, Ne, cgeom, u, u_t, probAux, a, t, X_tShift, elemMatD);CHKERRQ(ierr); 2363 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); 2364 } 2365 } 2366 } 2367 if (hasDyn) { 2368 for (c = 0; c < (cEnd - cStart)*totDim*totDim; ++c) elemMat[c] += X_tShift*elemMatD[c]; 2369 } 2370 for (c = cStart; c < cEnd; ++c) { 2371 const PetscBLASInt M = totDim, one = 1; 2372 const PetscScalar a = 1.0, b = 0.0; 2373 2374 PetscStackCallBLAS("BLASgemv", BLASgemv_("N", &M, &M, &a, &elemMat[(c-cStart)*totDim*totDim], &M, &y[(c-cStart)*totDim], &one, &b, z, &one)); 2375 if (mesh->printFEM > 1) { 2376 ierr = DMPrintCellMatrix(c, name, totDim, totDim, &elemMat[(c-cStart)*totDim*totDim]);CHKERRQ(ierr); 2377 ierr = DMPrintCellVector(c, "Y", totDim, &y[(c-cStart)*totDim]);CHKERRQ(ierr); 2378 ierr = DMPrintCellVector(c, "Z", totDim, z);CHKERRQ(ierr); 2379 } 2380 ierr = DMPlexVecSetClosure(dm, section, Z, c, z, ADD_VALUES);CHKERRQ(ierr); 2381 } 2382 if (sizeof(PetscFECellGeom) % sizeof(PetscScalar)) {ierr = PetscFree(cgeom);CHKERRQ(ierr);} 2383 else {cgeom = NULL;} 2384 ierr = VecRestoreArray(cellgeom, &cgeomScal);CHKERRQ(ierr); 2385 ierr = PetscFree6(u,u_t,elemMat,elemMatD,y,z);CHKERRQ(ierr); 2386 if (dmAux) { 2387 ierr = PetscFree(a);CHKERRQ(ierr); 2388 ierr = DMDestroy(&plex);CHKERRQ(ierr); 2389 } 2390 if (mesh->printFEM) { 2391 ierr = PetscPrintf(PETSC_COMM_WORLD, "Z:\n");CHKERRQ(ierr); 2392 ierr = VecView(Z, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 2393 } 2394 ierr = PetscLogEventEnd(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 2395 PetscFunctionReturn(0); 2396 } 2397 2398 #undef __FUNCT__ 2399 #define __FUNCT__ "DMPlexSNESComputeJacobianFEM" 2400 /*@ 2401 DMPlexSNESComputeJacobianFEM - Form the local portion of the Jacobian matrix J at the local solution X using pointwise functions specified by the user. 2402 2403 Input Parameters: 2404 + dm - The mesh 2405 . X - Local input vector 2406 - user - The user context 2407 2408 Output Parameter: 2409 . Jac - Jacobian matrix 2410 2411 Note: 2412 We form the residual one batch of elements at a time. This allows us to offload work onto an accelerator, 2413 like a GPU, or vectorize on a multicore machine. 2414 2415 Level: developer 2416 2417 .seealso: FormFunctionLocal() 2418 @*/ 2419 PetscErrorCode DMPlexSNESComputeJacobianFEM(DM dm, Vec X, Mat Jac, Mat JacP,void *user) 2420 { 2421 PetscInt cStart, cEnd, cEndInterior; 2422 DM plex; 2423 PetscErrorCode ierr; 2424 2425 PetscFunctionBegin; 2426 ierr = DMSNESConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr); 2427 ierr = DMPlexGetHeightStratum(plex, 0, &cStart, &cEnd);CHKERRQ(ierr); 2428 ierr = DMPlexGetHybridBounds(plex, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr); 2429 cEnd = cEndInterior < 0 ? cEnd : cEndInterior; 2430 ierr = DMPlexComputeJacobian_Internal(plex, cStart, cEnd, 0.0, 0.0, X, NULL, Jac, JacP, user);CHKERRQ(ierr); 2431 ierr = DMDestroy(&plex);CHKERRQ(ierr); 2432 PetscFunctionReturn(0); 2433 } 2434 2435 #undef __FUNCT__ 2436 #define __FUNCT__ "DMPlexSNESComputeJacobianActionFEM" 2437 /*@ 2438 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. 2439 2440 Input Parameters: 2441 + dm - The mesh 2442 . X - Local solution vector 2443 . Y - Local input vector 2444 - user - The user context 2445 2446 Output Parameter: 2447 . Z - Local output vector 2448 2449 Note: 2450 We form the residual one batch of elements at a time. This allows us to offload work onto an accelerator, 2451 like a GPU, or vectorize on a multicore machine. 2452 2453 Level: developer 2454 2455 .seealso: FormFunctionLocal() 2456 @*/ 2457 PetscErrorCode DMPlexSNESComputeJacobianActionFEM(DM dm, Vec X, Vec Y, Vec Z, void *user) 2458 { 2459 PetscInt cStart, cEnd, cEndInterior; 2460 DM plex; 2461 PetscErrorCode ierr; 2462 2463 PetscFunctionBegin; 2464 ierr = DMSNESConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr); 2465 ierr = DMPlexGetHeightStratum(plex, 0, &cStart, &cEnd);CHKERRQ(ierr); 2466 ierr = DMPlexGetHybridBounds(plex, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr); 2467 cEnd = cEndInterior < 0 ? cEnd : cEndInterior; 2468 ierr = DMPlexComputeJacobianAction_Internal(plex, cStart, cEnd, 0.0, 0.0, X, NULL, Y, Z, user);CHKERRQ(ierr); 2469 ierr = DMDestroy(&plex);CHKERRQ(ierr); 2470 PetscFunctionReturn(0); 2471 } 2472 2473 #undef __FUNCT__ 2474 #define __FUNCT__ "DMPlexSetSNESLocalFEM" 2475 /*@ 2476 DMPlexSetSNESLocalFEM - Use DMPlex's internal FEM routines to compute SNES boundary values, residual, and Jacobian. 2477 2478 Input Parameters: 2479 + dm - The DM object 2480 . boundaryctx - the user context that will be passed to pointwise evaluation of boundary values (see DMAddBoundary()) 2481 . residualctx - the user context that will be passed to pointwise evaluation of finite element residual computations (see PetscDSSetResidual()) 2482 - jacobianctx - the user context that will be passed to pointwise evaluation of finite element Jacobian construction (see PetscDSSetJacobian()) 2483 2484 Level: developer 2485 @*/ 2486 PetscErrorCode DMPlexSetSNESLocalFEM(DM dm, void *boundaryctx, void *residualctx, void *jacobianctx) 2487 { 2488 PetscErrorCode ierr; 2489 2490 PetscFunctionBegin; 2491 ierr = DMSNESSetBoundaryLocal(dm,DMPlexSNESComputeBoundaryFEM,boundaryctx);CHKERRQ(ierr); 2492 ierr = DMSNESSetFunctionLocal(dm,DMPlexSNESComputeResidualFEM,residualctx);CHKERRQ(ierr); 2493 ierr = DMSNESSetJacobianLocal(dm,DMPlexSNESComputeJacobianFEM,jacobianctx);CHKERRQ(ierr); 2494 PetscFunctionReturn(0); 2495 } 2496 2497 #undef __FUNCT__ 2498 #define __FUNCT__ "DMSNESCheckFromOptions_Internal" 2499 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) 2500 { 2501 Mat J, M; 2502 Vec r, b; 2503 MatNullSpace nullSpace; 2504 PetscReal *error, res = 0.0; 2505 PetscInt numFields; 2506 PetscErrorCode ierr; 2507 2508 PetscFunctionBegin; 2509 ierr = VecDuplicate(u, &r);CHKERRQ(ierr); 2510 ierr = DMCreateMatrix(dm, &J);CHKERRQ(ierr); 2511 M = J; 2512 /* TODO Null space for J */ 2513 /* Check discretization error */ 2514 ierr = DMGetNumFields(dm, &numFields);CHKERRQ(ierr); 2515 ierr = PetscMalloc1(PetscMax(1, numFields), &error);CHKERRQ(ierr); 2516 if (numFields > 1) { 2517 PetscInt f; 2518 2519 ierr = DMComputeL2FieldDiff(dm, 0.0, exactFuncs, ctxs, u, error);CHKERRQ(ierr); 2520 ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: [");CHKERRQ(ierr); 2521 for (f = 0; f < numFields; ++f) { 2522 if (f) {ierr = PetscPrintf(PETSC_COMM_WORLD, ", ");CHKERRQ(ierr);} 2523 if (error[f] >= 1.0e-11) {ierr = PetscPrintf(PETSC_COMM_WORLD, "%g", error[f]);CHKERRQ(ierr);} 2524 else {ierr = PetscPrintf(PETSC_COMM_WORLD, "< 1.0e-11");CHKERRQ(ierr);} 2525 } 2526 ierr = PetscPrintf(PETSC_COMM_WORLD, "]\n");CHKERRQ(ierr); 2527 } else { 2528 ierr = DMComputeL2Diff(dm, 0.0, exactFuncs, ctxs, u, &error[0]);CHKERRQ(ierr); 2529 if (error[0] >= 1.0e-11) {ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: %g\n", error[0]);CHKERRQ(ierr);} 2530 else {ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: < 1.0e-11\n");CHKERRQ(ierr);} 2531 } 2532 ierr = PetscFree(error);CHKERRQ(ierr); 2533 /* Check residual */ 2534 ierr = SNESComputeFunction(snes, u, r);CHKERRQ(ierr); 2535 ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr); 2536 ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Residual: %g\n", res);CHKERRQ(ierr); 2537 ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr); 2538 ierr = PetscObjectSetName((PetscObject) r, "Initial Residual");CHKERRQ(ierr); 2539 ierr = PetscObjectSetOptionsPrefix((PetscObject)r,"res_");CHKERRQ(ierr); 2540 ierr = VecViewFromOptions(r, NULL, "-vec_view");CHKERRQ(ierr); 2541 /* Check Jacobian */ 2542 ierr = SNESComputeJacobian(snes, u, M, M);CHKERRQ(ierr); 2543 ierr = MatGetNullSpace(J, &nullSpace);CHKERRQ(ierr); 2544 if (nullSpace) { 2545 PetscBool isNull; 2546 ierr = MatNullSpaceTest(nullSpace, J, &isNull);CHKERRQ(ierr); 2547 if (!isNull) SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_PLIB, "The null space calculated for the system operator is invalid."); 2548 } 2549 ierr = VecDuplicate(u, &b);CHKERRQ(ierr); 2550 ierr = VecSet(r, 0.0);CHKERRQ(ierr); 2551 ierr = SNESComputeFunction(snes, r, b);CHKERRQ(ierr); 2552 ierr = MatMult(M, u, r);CHKERRQ(ierr); 2553 ierr = VecAXPY(r, 1.0, b);CHKERRQ(ierr); 2554 ierr = VecDestroy(&b);CHKERRQ(ierr); 2555 ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr); 2556 ierr = PetscPrintf(PETSC_COMM_WORLD, "Linear L_2 Residual: %g\n", res);CHKERRQ(ierr); 2557 ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr); 2558 ierr = PetscObjectSetName((PetscObject) r, "Au - b = Au + F(0)");CHKERRQ(ierr); 2559 ierr = PetscObjectSetOptionsPrefix((PetscObject)r,"linear_res_");CHKERRQ(ierr); 2560 ierr = VecViewFromOptions(r, NULL, "-vec_view");CHKERRQ(ierr); 2561 ierr = VecDestroy(&r);CHKERRQ(ierr); 2562 ierr = MatNullSpaceDestroy(&nullSpace);CHKERRQ(ierr); 2563 ierr = MatDestroy(&J);CHKERRQ(ierr); 2564 PetscFunctionReturn(0); 2565 } 2566 2567 #undef __FUNCT__ 2568 #define __FUNCT__ "DMSNESCheckFromOptions" 2569 PetscErrorCode DMSNESCheckFromOptions(SNES snes, Vec u, PetscErrorCode (**exactFuncs)(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf, PetscScalar *u, void *ctx), void **ctxs) 2570 { 2571 DM dm; 2572 Vec sol; 2573 PetscBool check; 2574 PetscErrorCode ierr; 2575 2576 PetscFunctionBegin; 2577 ierr = PetscOptionsHasName(((PetscObject)snes)->options,((PetscObject)snes)->prefix, "-dmsnes_check", &check);CHKERRQ(ierr); 2578 if (!check) PetscFunctionReturn(0); 2579 ierr = SNESGetDM(snes, &dm);CHKERRQ(ierr); 2580 ierr = VecDuplicate(u, &sol);CHKERRQ(ierr); 2581 ierr = SNESSetSolution(snes, sol);CHKERRQ(ierr); 2582 ierr = DMSNESCheckFromOptions_Internal(snes, dm, u, sol, exactFuncs, ctxs);CHKERRQ(ierr); 2583 ierr = VecDestroy(&sol);CHKERRQ(ierr); 2584 PetscFunctionReturn(0); 2585 } 2586