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 <petsc/private/petscimpl.h> 5 #include <petsc/private/petscfeimpl.h> 6 7 /************************** Interpolation *******************************/ 8 9 #undef __FUNCT__ 10 #define __FUNCT__ "DMInterpolationCreate" 11 PetscErrorCode DMInterpolationCreate(MPI_Comm comm, DMInterpolationInfo *ctx) 12 { 13 PetscErrorCode ierr; 14 15 PetscFunctionBegin; 16 PetscValidPointer(ctx, 2); 17 ierr = PetscMalloc(sizeof(struct _DMInterpolationInfo), ctx);CHKERRQ(ierr); 18 19 (*ctx)->comm = comm; 20 (*ctx)->dim = -1; 21 (*ctx)->nInput = 0; 22 (*ctx)->points = NULL; 23 (*ctx)->cells = NULL; 24 (*ctx)->n = -1; 25 (*ctx)->coords = NULL; 26 PetscFunctionReturn(0); 27 } 28 29 #undef __FUNCT__ 30 #define __FUNCT__ "DMInterpolationSetDim" 31 PetscErrorCode DMInterpolationSetDim(DMInterpolationInfo ctx, PetscInt dim) 32 { 33 PetscFunctionBegin; 34 if ((dim < 1) || (dim > 3)) SETERRQ1(ctx->comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid dimension for points: %d", dim); 35 ctx->dim = dim; 36 PetscFunctionReturn(0); 37 } 38 39 #undef __FUNCT__ 40 #define __FUNCT__ "DMInterpolationGetDim" 41 PetscErrorCode DMInterpolationGetDim(DMInterpolationInfo ctx, PetscInt *dim) 42 { 43 PetscFunctionBegin; 44 PetscValidIntPointer(dim, 2); 45 *dim = ctx->dim; 46 PetscFunctionReturn(0); 47 } 48 49 #undef __FUNCT__ 50 #define __FUNCT__ "DMInterpolationSetDof" 51 PetscErrorCode DMInterpolationSetDof(DMInterpolationInfo ctx, PetscInt dof) 52 { 53 PetscFunctionBegin; 54 if (dof < 1) SETERRQ1(ctx->comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid number of components: %d", dof); 55 ctx->dof = dof; 56 PetscFunctionReturn(0); 57 } 58 59 #undef __FUNCT__ 60 #define __FUNCT__ "DMInterpolationGetDof" 61 PetscErrorCode DMInterpolationGetDof(DMInterpolationInfo ctx, PetscInt *dof) 62 { 63 PetscFunctionBegin; 64 PetscValidIntPointer(dof, 2); 65 *dof = ctx->dof; 66 PetscFunctionReturn(0); 67 } 68 69 #undef __FUNCT__ 70 #define __FUNCT__ "DMInterpolationAddPoints" 71 PetscErrorCode DMInterpolationAddPoints(DMInterpolationInfo ctx, PetscInt n, PetscReal points[]) 72 { 73 PetscErrorCode ierr; 74 75 PetscFunctionBegin; 76 if (ctx->dim < 0) SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONGSTATE, "The spatial dimension has not been set"); 77 if (ctx->points) SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONGSTATE, "Cannot add points multiple times yet"); 78 ctx->nInput = n; 79 80 ierr = PetscMalloc1(n*ctx->dim, &ctx->points);CHKERRQ(ierr); 81 ierr = PetscMemcpy(ctx->points, points, n*ctx->dim * sizeof(PetscReal));CHKERRQ(ierr); 82 PetscFunctionReturn(0); 83 } 84 85 #undef __FUNCT__ 86 #define __FUNCT__ "DMInterpolationSetUp" 87 PetscErrorCode DMInterpolationSetUp(DMInterpolationInfo ctx, DM dm, PetscBool redundantPoints) 88 { 89 MPI_Comm comm = ctx->comm; 90 PetscScalar *a; 91 PetscInt p, q, i; 92 PetscMPIInt rank, size; 93 PetscErrorCode ierr; 94 Vec pointVec; 95 IS cellIS; 96 PetscLayout layout; 97 PetscReal *globalPoints; 98 PetscScalar *globalPointsScalar; 99 const PetscInt *ranges; 100 PetscMPIInt *counts, *displs; 101 const PetscInt *foundCells; 102 PetscMPIInt *foundProcs, *globalProcs; 103 PetscInt n, N; 104 105 PetscFunctionBegin; 106 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 107 ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr); 108 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 109 if (ctx->dim < 0) SETERRQ(comm, PETSC_ERR_ARG_WRONGSTATE, "The spatial dimension has not been set"); 110 /* Locate points */ 111 n = ctx->nInput; 112 if (!redundantPoints) { 113 ierr = PetscLayoutCreate(comm, &layout);CHKERRQ(ierr); 114 ierr = PetscLayoutSetBlockSize(layout, 1);CHKERRQ(ierr); 115 ierr = PetscLayoutSetLocalSize(layout, n);CHKERRQ(ierr); 116 ierr = PetscLayoutSetUp(layout);CHKERRQ(ierr); 117 ierr = PetscLayoutGetSize(layout, &N);CHKERRQ(ierr); 118 /* Communicate all points to all processes */ 119 ierr = PetscMalloc3(N*ctx->dim,&globalPoints,size,&counts,size,&displs);CHKERRQ(ierr); 120 ierr = PetscLayoutGetRanges(layout, &ranges);CHKERRQ(ierr); 121 for (p = 0; p < size; ++p) { 122 counts[p] = (ranges[p+1] - ranges[p])*ctx->dim; 123 displs[p] = ranges[p]*ctx->dim; 124 } 125 ierr = MPI_Allgatherv(ctx->points, n*ctx->dim, MPIU_REAL, globalPoints, counts, displs, MPIU_REAL, comm);CHKERRQ(ierr); 126 } else { 127 N = n; 128 globalPoints = ctx->points; 129 counts = displs = NULL; 130 layout = NULL; 131 } 132 #if 0 133 ierr = PetscMalloc3(N,&foundCells,N,&foundProcs,N,&globalProcs);CHKERRQ(ierr); 134 /* foundCells[p] = m->locatePoint(&globalPoints[p*ctx->dim]); */ 135 #else 136 #if defined(PETSC_USE_COMPLEX) 137 ierr = PetscMalloc1(N,&globalPointsScalar);CHKERRQ(ierr); 138 for (i=0; i<N; i++) globalPointsScalar[i] = globalPoints[i]; 139 #else 140 globalPointsScalar = globalPoints; 141 #endif 142 ierr = VecCreateSeqWithArray(PETSC_COMM_SELF, ctx->dim, N*ctx->dim, globalPointsScalar, &pointVec);CHKERRQ(ierr); 143 ierr = PetscMalloc2(N,&foundProcs,N,&globalProcs);CHKERRQ(ierr); 144 ierr = DMLocatePoints(dm, pointVec, &cellIS);CHKERRQ(ierr); 145 ierr = ISGetIndices(cellIS, &foundCells);CHKERRQ(ierr); 146 #endif 147 for (p = 0; p < N; ++p) { 148 if (foundCells[p] >= 0) foundProcs[p] = rank; 149 else foundProcs[p] = size; 150 } 151 /* Let the lowest rank process own each point */ 152 ierr = MPIU_Allreduce(foundProcs, globalProcs, N, MPI_INT, MPI_MIN, comm);CHKERRQ(ierr); 153 ctx->n = 0; 154 for (p = 0; p < N; ++p) { 155 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); 156 else if (globalProcs[p] == rank) ctx->n++; 157 } 158 /* Create coordinates vector and array of owned cells */ 159 ierr = PetscMalloc1(ctx->n, &ctx->cells);CHKERRQ(ierr); 160 ierr = VecCreate(comm, &ctx->coords);CHKERRQ(ierr); 161 ierr = VecSetSizes(ctx->coords, ctx->n*ctx->dim, PETSC_DECIDE);CHKERRQ(ierr); 162 ierr = VecSetBlockSize(ctx->coords, ctx->dim);CHKERRQ(ierr); 163 ierr = VecSetType(ctx->coords,VECSTANDARD);CHKERRQ(ierr); 164 ierr = VecGetArray(ctx->coords, &a);CHKERRQ(ierr); 165 for (p = 0, q = 0, i = 0; p < N; ++p) { 166 if (globalProcs[p] == rank) { 167 PetscInt d; 168 169 for (d = 0; d < ctx->dim; ++d, ++i) a[i] = globalPoints[p*ctx->dim+d]; 170 ctx->cells[q++] = foundCells[p]; 171 } 172 } 173 ierr = VecRestoreArray(ctx->coords, &a);CHKERRQ(ierr); 174 #if 0 175 ierr = PetscFree3(foundCells,foundProcs,globalProcs);CHKERRQ(ierr); 176 #else 177 ierr = PetscFree2(foundProcs,globalProcs);CHKERRQ(ierr); 178 ierr = ISRestoreIndices(cellIS, &foundCells);CHKERRQ(ierr); 179 ierr = ISDestroy(&cellIS);CHKERRQ(ierr); 180 ierr = VecDestroy(&pointVec);CHKERRQ(ierr); 181 #endif 182 if ((void*)globalPointsScalar != (void*)globalPoints) {ierr = PetscFree(globalPointsScalar);CHKERRQ(ierr);} 183 if (!redundantPoints) {ierr = PetscFree3(globalPoints,counts,displs);CHKERRQ(ierr);} 184 ierr = PetscLayoutDestroy(&layout);CHKERRQ(ierr); 185 PetscFunctionReturn(0); 186 } 187 188 #undef __FUNCT__ 189 #define __FUNCT__ "DMInterpolationGetCoordinates" 190 PetscErrorCode DMInterpolationGetCoordinates(DMInterpolationInfo ctx, Vec *coordinates) 191 { 192 PetscFunctionBegin; 193 PetscValidPointer(coordinates, 2); 194 if (!ctx->coords) SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONGSTATE, "The interpolation context has not been setup."); 195 *coordinates = ctx->coords; 196 PetscFunctionReturn(0); 197 } 198 199 #undef __FUNCT__ 200 #define __FUNCT__ "DMInterpolationGetVector" 201 PetscErrorCode DMInterpolationGetVector(DMInterpolationInfo ctx, Vec *v) 202 { 203 PetscErrorCode ierr; 204 205 PetscFunctionBegin; 206 PetscValidPointer(v, 2); 207 if (!ctx->coords) SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONGSTATE, "The interpolation context has not been setup."); 208 ierr = VecCreate(ctx->comm, v);CHKERRQ(ierr); 209 ierr = VecSetSizes(*v, ctx->n*ctx->dof, PETSC_DECIDE);CHKERRQ(ierr); 210 ierr = VecSetBlockSize(*v, ctx->dof);CHKERRQ(ierr); 211 ierr = VecSetType(*v,VECSTANDARD);CHKERRQ(ierr); 212 PetscFunctionReturn(0); 213 } 214 215 #undef __FUNCT__ 216 #define __FUNCT__ "DMInterpolationRestoreVector" 217 PetscErrorCode DMInterpolationRestoreVector(DMInterpolationInfo ctx, Vec *v) 218 { 219 PetscErrorCode ierr; 220 221 PetscFunctionBegin; 222 PetscValidPointer(v, 2); 223 if (!ctx->coords) SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONGSTATE, "The interpolation context has not been setup."); 224 ierr = VecDestroy(v);CHKERRQ(ierr); 225 PetscFunctionReturn(0); 226 } 227 228 #undef __FUNCT__ 229 #define __FUNCT__ "DMInterpolate_Triangle_Private" 230 PETSC_STATIC_INLINE PetscErrorCode DMInterpolate_Triangle_Private(DMInterpolationInfo ctx, DM dm, Vec xLocal, Vec v) 231 { 232 PetscReal *v0, *J, *invJ, detJ; 233 const PetscScalar *coords; 234 PetscScalar *a; 235 PetscInt p; 236 PetscErrorCode ierr; 237 238 PetscFunctionBegin; 239 ierr = PetscMalloc3(ctx->dim,&v0,ctx->dim*ctx->dim,&J,ctx->dim*ctx->dim,&invJ);CHKERRQ(ierr); 240 ierr = VecGetArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 241 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 242 for (p = 0; p < ctx->n; ++p) { 243 PetscInt c = ctx->cells[p]; 244 PetscScalar *x = NULL; 245 PetscReal xi[4]; 246 PetscInt d, f, comp; 247 248 ierr = DMPlexComputeCellGeometryFEM(dm, c, NULL, v0, J, invJ, &detJ);CHKERRQ(ierr); 249 if (detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", detJ, c); 250 ierr = DMPlexVecGetClosure(dm, NULL, xLocal, c, NULL, &x);CHKERRQ(ierr); 251 for (comp = 0; comp < ctx->dof; ++comp) a[p*ctx->dof+comp] = x[0*ctx->dof+comp]; 252 253 for (d = 0; d < ctx->dim; ++d) { 254 xi[d] = 0.0; 255 for (f = 0; f < ctx->dim; ++f) xi[d] += invJ[d*ctx->dim+f]*0.5*PetscRealPart(coords[p*ctx->dim+f] - v0[f]); 256 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]; 257 } 258 ierr = DMPlexVecRestoreClosure(dm, NULL, xLocal, c, NULL, &x);CHKERRQ(ierr); 259 } 260 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 261 ierr = VecRestoreArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 262 ierr = PetscFree3(v0, J, invJ);CHKERRQ(ierr); 263 PetscFunctionReturn(0); 264 } 265 266 #undef __FUNCT__ 267 #define __FUNCT__ "DMInterpolate_Tetrahedron_Private" 268 PETSC_STATIC_INLINE PetscErrorCode DMInterpolate_Tetrahedron_Private(DMInterpolationInfo ctx, DM dm, Vec xLocal, Vec v) 269 { 270 PetscReal *v0, *J, *invJ, detJ; 271 const PetscScalar *coords; 272 PetscScalar *a; 273 PetscInt p; 274 PetscErrorCode ierr; 275 276 PetscFunctionBegin; 277 ierr = PetscMalloc3(ctx->dim,&v0,ctx->dim*ctx->dim,&J,ctx->dim*ctx->dim,&invJ);CHKERRQ(ierr); 278 ierr = VecGetArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 279 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 280 for (p = 0; p < ctx->n; ++p) { 281 PetscInt c = ctx->cells[p]; 282 const PetscInt order[3] = {2, 1, 3}; 283 PetscScalar *x = NULL; 284 PetscReal xi[4]; 285 PetscInt d, f, comp; 286 287 ierr = DMPlexComputeCellGeometryFEM(dm, c, NULL, v0, J, invJ, &detJ);CHKERRQ(ierr); 288 if (detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", detJ, c); 289 ierr = DMPlexVecGetClosure(dm, NULL, xLocal, c, NULL, &x);CHKERRQ(ierr); 290 for (comp = 0; comp < ctx->dof; ++comp) a[p*ctx->dof+comp] = x[0*ctx->dof+comp]; 291 292 for (d = 0; d < ctx->dim; ++d) { 293 xi[d] = 0.0; 294 for (f = 0; f < ctx->dim; ++f) xi[d] += invJ[d*ctx->dim+f]*0.5*PetscRealPart(coords[p*ctx->dim+f] - v0[f]); 295 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]; 296 } 297 ierr = DMPlexVecRestoreClosure(dm, NULL, xLocal, c, NULL, &x);CHKERRQ(ierr); 298 } 299 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 300 ierr = VecRestoreArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 301 ierr = PetscFree3(v0, J, invJ);CHKERRQ(ierr); 302 PetscFunctionReturn(0); 303 } 304 305 #undef __FUNCT__ 306 #define __FUNCT__ "QuadMap_Private" 307 PETSC_STATIC_INLINE PetscErrorCode QuadMap_Private(SNES snes, Vec Xref, Vec Xreal, void *ctx) 308 { 309 const PetscScalar *vertices = (const PetscScalar*) ctx; 310 const PetscScalar x0 = vertices[0]; 311 const PetscScalar y0 = vertices[1]; 312 const PetscScalar x1 = vertices[2]; 313 const PetscScalar y1 = vertices[3]; 314 const PetscScalar x2 = vertices[4]; 315 const PetscScalar y2 = vertices[5]; 316 const PetscScalar x3 = vertices[6]; 317 const PetscScalar y3 = vertices[7]; 318 const PetscScalar f_1 = x1 - x0; 319 const PetscScalar g_1 = y1 - y0; 320 const PetscScalar f_3 = x3 - x0; 321 const PetscScalar g_3 = y3 - y0; 322 const PetscScalar f_01 = x2 - x1 - x3 + x0; 323 const PetscScalar g_01 = y2 - y1 - y3 + y0; 324 const PetscScalar *ref; 325 PetscScalar *real; 326 PetscErrorCode ierr; 327 328 PetscFunctionBegin; 329 ierr = VecGetArrayRead(Xref, &ref);CHKERRQ(ierr); 330 ierr = VecGetArray(Xreal, &real);CHKERRQ(ierr); 331 { 332 const PetscScalar p0 = ref[0]; 333 const PetscScalar p1 = ref[1]; 334 335 real[0] = x0 + f_1 * p0 + f_3 * p1 + f_01 * p0 * p1; 336 real[1] = y0 + g_1 * p0 + g_3 * p1 + g_01 * p0 * p1; 337 } 338 ierr = PetscLogFlops(28);CHKERRQ(ierr); 339 ierr = VecRestoreArrayRead(Xref, &ref);CHKERRQ(ierr); 340 ierr = VecRestoreArray(Xreal, &real);CHKERRQ(ierr); 341 PetscFunctionReturn(0); 342 } 343 344 #include <petsc/private/dmimpl.h> 345 #undef __FUNCT__ 346 #define __FUNCT__ "QuadJacobian_Private" 347 PETSC_STATIC_INLINE PetscErrorCode QuadJacobian_Private(SNES snes, Vec Xref, Mat J, Mat M, void *ctx) 348 { 349 const PetscScalar *vertices = (const PetscScalar*) ctx; 350 const PetscScalar x0 = vertices[0]; 351 const PetscScalar y0 = vertices[1]; 352 const PetscScalar x1 = vertices[2]; 353 const PetscScalar y1 = vertices[3]; 354 const PetscScalar x2 = vertices[4]; 355 const PetscScalar y2 = vertices[5]; 356 const PetscScalar x3 = vertices[6]; 357 const PetscScalar y3 = vertices[7]; 358 const PetscScalar f_01 = x2 - x1 - x3 + x0; 359 const PetscScalar g_01 = y2 - y1 - y3 + y0; 360 const PetscScalar *ref; 361 PetscErrorCode ierr; 362 363 PetscFunctionBegin; 364 ierr = VecGetArrayRead(Xref, &ref);CHKERRQ(ierr); 365 { 366 const PetscScalar x = ref[0]; 367 const PetscScalar y = ref[1]; 368 const PetscInt rows[2] = {0, 1}; 369 PetscScalar values[4]; 370 371 values[0] = (x1 - x0 + f_01*y) * 0.5; values[1] = (x3 - x0 + f_01*x) * 0.5; 372 values[2] = (y1 - y0 + g_01*y) * 0.5; values[3] = (y3 - y0 + g_01*x) * 0.5; 373 ierr = MatSetValues(J, 2, rows, 2, rows, values, INSERT_VALUES);CHKERRQ(ierr); 374 } 375 ierr = PetscLogFlops(30);CHKERRQ(ierr); 376 ierr = VecRestoreArrayRead(Xref, &ref);CHKERRQ(ierr); 377 ierr = MatAssemblyBegin(J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 378 ierr = MatAssemblyEnd(J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 379 PetscFunctionReturn(0); 380 } 381 382 #undef __FUNCT__ 383 #define __FUNCT__ "DMInterpolate_Quad_Private" 384 PETSC_STATIC_INLINE PetscErrorCode DMInterpolate_Quad_Private(DMInterpolationInfo ctx, DM dm, Vec xLocal, Vec v) 385 { 386 DM dmCoord; 387 SNES snes; 388 KSP ksp; 389 PC pc; 390 Vec coordsLocal, r, ref, real; 391 Mat J; 392 const PetscScalar *coords; 393 PetscScalar *a; 394 PetscInt p; 395 PetscErrorCode ierr; 396 397 PetscFunctionBegin; 398 ierr = DMGetCoordinatesLocal(dm, &coordsLocal);CHKERRQ(ierr); 399 ierr = DMGetCoordinateDM(dm, &dmCoord);CHKERRQ(ierr); 400 ierr = SNESCreate(PETSC_COMM_SELF, &snes);CHKERRQ(ierr); 401 ierr = SNESSetOptionsPrefix(snes, "quad_interp_");CHKERRQ(ierr); 402 ierr = VecCreate(PETSC_COMM_SELF, &r);CHKERRQ(ierr); 403 ierr = VecSetSizes(r, 2, 2);CHKERRQ(ierr); 404 ierr = VecSetType(r,dm->vectype);CHKERRQ(ierr); 405 ierr = VecDuplicate(r, &ref);CHKERRQ(ierr); 406 ierr = VecDuplicate(r, &real);CHKERRQ(ierr); 407 ierr = MatCreate(PETSC_COMM_SELF, &J);CHKERRQ(ierr); 408 ierr = MatSetSizes(J, 2, 2, 2, 2);CHKERRQ(ierr); 409 ierr = MatSetType(J, MATSEQDENSE);CHKERRQ(ierr); 410 ierr = MatSetUp(J);CHKERRQ(ierr); 411 ierr = SNESSetFunction(snes, r, QuadMap_Private, NULL);CHKERRQ(ierr); 412 ierr = SNESSetJacobian(snes, J, J, QuadJacobian_Private, NULL);CHKERRQ(ierr); 413 ierr = SNESGetKSP(snes, &ksp);CHKERRQ(ierr); 414 ierr = KSPGetPC(ksp, &pc);CHKERRQ(ierr); 415 ierr = PCSetType(pc, PCLU);CHKERRQ(ierr); 416 ierr = SNESSetFromOptions(snes);CHKERRQ(ierr); 417 418 ierr = VecGetArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 419 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 420 for (p = 0; p < ctx->n; ++p) { 421 PetscScalar *x = NULL, *vertices = NULL; 422 PetscScalar *xi; 423 PetscReal xir[2]; 424 PetscInt c = ctx->cells[p], comp, coordSize, xSize; 425 426 /* Can make this do all points at once */ 427 ierr = DMPlexVecGetClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);CHKERRQ(ierr); 428 if (4*2 != coordSize) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid closure size %d should be %d", coordSize, 4*2); 429 ierr = DMPlexVecGetClosure(dm, NULL, xLocal, c, &xSize, &x);CHKERRQ(ierr); 430 if (4*ctx->dof != xSize) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid closure size %d should be %d", xSize, 4*ctx->dof); 431 ierr = SNESSetFunction(snes, NULL, NULL, (void*) vertices);CHKERRQ(ierr); 432 ierr = SNESSetJacobian(snes, NULL, NULL, NULL, (void*) vertices);CHKERRQ(ierr); 433 ierr = VecGetArray(real, &xi);CHKERRQ(ierr); 434 xi[0] = coords[p*ctx->dim+0]; 435 xi[1] = coords[p*ctx->dim+1]; 436 ierr = VecRestoreArray(real, &xi);CHKERRQ(ierr); 437 ierr = SNESSolve(snes, real, ref);CHKERRQ(ierr); 438 ierr = VecGetArray(ref, &xi);CHKERRQ(ierr); 439 xir[0] = PetscRealPart(xi[0]); 440 xir[1] = PetscRealPart(xi[1]); 441 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]; 442 443 ierr = VecRestoreArray(ref, &xi);CHKERRQ(ierr); 444 ierr = DMPlexVecRestoreClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);CHKERRQ(ierr); 445 ierr = DMPlexVecRestoreClosure(dm, NULL, xLocal, c, &xSize, &x);CHKERRQ(ierr); 446 } 447 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 448 ierr = VecRestoreArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 449 450 ierr = SNESDestroy(&snes);CHKERRQ(ierr); 451 ierr = VecDestroy(&r);CHKERRQ(ierr); 452 ierr = VecDestroy(&ref);CHKERRQ(ierr); 453 ierr = VecDestroy(&real);CHKERRQ(ierr); 454 ierr = MatDestroy(&J);CHKERRQ(ierr); 455 PetscFunctionReturn(0); 456 } 457 458 #undef __FUNCT__ 459 #define __FUNCT__ "HexMap_Private" 460 PETSC_STATIC_INLINE PetscErrorCode HexMap_Private(SNES snes, Vec Xref, Vec Xreal, void *ctx) 461 { 462 const PetscScalar *vertices = (const PetscScalar*) ctx; 463 const PetscScalar x0 = vertices[0]; 464 const PetscScalar y0 = vertices[1]; 465 const PetscScalar z0 = vertices[2]; 466 const PetscScalar x1 = vertices[9]; 467 const PetscScalar y1 = vertices[10]; 468 const PetscScalar z1 = vertices[11]; 469 const PetscScalar x2 = vertices[6]; 470 const PetscScalar y2 = vertices[7]; 471 const PetscScalar z2 = vertices[8]; 472 const PetscScalar x3 = vertices[3]; 473 const PetscScalar y3 = vertices[4]; 474 const PetscScalar z3 = vertices[5]; 475 const PetscScalar x4 = vertices[12]; 476 const PetscScalar y4 = vertices[13]; 477 const PetscScalar z4 = vertices[14]; 478 const PetscScalar x5 = vertices[15]; 479 const PetscScalar y5 = vertices[16]; 480 const PetscScalar z5 = vertices[17]; 481 const PetscScalar x6 = vertices[18]; 482 const PetscScalar y6 = vertices[19]; 483 const PetscScalar z6 = vertices[20]; 484 const PetscScalar x7 = vertices[21]; 485 const PetscScalar y7 = vertices[22]; 486 const PetscScalar z7 = vertices[23]; 487 const PetscScalar f_1 = x1 - x0; 488 const PetscScalar g_1 = y1 - y0; 489 const PetscScalar h_1 = z1 - z0; 490 const PetscScalar f_3 = x3 - x0; 491 const PetscScalar g_3 = y3 - y0; 492 const PetscScalar h_3 = z3 - z0; 493 const PetscScalar f_4 = x4 - x0; 494 const PetscScalar g_4 = y4 - y0; 495 const PetscScalar h_4 = z4 - z0; 496 const PetscScalar f_01 = x2 - x1 - x3 + x0; 497 const PetscScalar g_01 = y2 - y1 - y3 + y0; 498 const PetscScalar h_01 = z2 - z1 - z3 + z0; 499 const PetscScalar f_12 = x7 - x3 - x4 + x0; 500 const PetscScalar g_12 = y7 - y3 - y4 + y0; 501 const PetscScalar h_12 = z7 - z3 - z4 + z0; 502 const PetscScalar f_02 = x5 - x1 - x4 + x0; 503 const PetscScalar g_02 = y5 - y1 - y4 + y0; 504 const PetscScalar h_02 = z5 - z1 - z4 + z0; 505 const PetscScalar f_012 = x6 - x0 + x1 - x2 + x3 + x4 - x5 - x7; 506 const PetscScalar g_012 = y6 - y0 + y1 - y2 + y3 + y4 - y5 - y7; 507 const PetscScalar h_012 = z6 - z0 + z1 - z2 + z3 + z4 - z5 - z7; 508 const PetscScalar *ref; 509 PetscScalar *real; 510 PetscErrorCode ierr; 511 512 PetscFunctionBegin; 513 ierr = VecGetArrayRead(Xref, &ref);CHKERRQ(ierr); 514 ierr = VecGetArray(Xreal, &real);CHKERRQ(ierr); 515 { 516 const PetscScalar p0 = ref[0]; 517 const PetscScalar p1 = ref[1]; 518 const PetscScalar p2 = ref[2]; 519 520 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; 521 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; 522 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; 523 } 524 ierr = PetscLogFlops(114);CHKERRQ(ierr); 525 ierr = VecRestoreArrayRead(Xref, &ref);CHKERRQ(ierr); 526 ierr = VecRestoreArray(Xreal, &real);CHKERRQ(ierr); 527 PetscFunctionReturn(0); 528 } 529 530 #undef __FUNCT__ 531 #define __FUNCT__ "HexJacobian_Private" 532 PETSC_STATIC_INLINE PetscErrorCode HexJacobian_Private(SNES snes, Vec Xref, Mat J, Mat M, void *ctx) 533 { 534 const PetscScalar *vertices = (const PetscScalar*) ctx; 535 const PetscScalar x0 = vertices[0]; 536 const PetscScalar y0 = vertices[1]; 537 const PetscScalar z0 = vertices[2]; 538 const PetscScalar x1 = vertices[9]; 539 const PetscScalar y1 = vertices[10]; 540 const PetscScalar z1 = vertices[11]; 541 const PetscScalar x2 = vertices[6]; 542 const PetscScalar y2 = vertices[7]; 543 const PetscScalar z2 = vertices[8]; 544 const PetscScalar x3 = vertices[3]; 545 const PetscScalar y3 = vertices[4]; 546 const PetscScalar z3 = vertices[5]; 547 const PetscScalar x4 = vertices[12]; 548 const PetscScalar y4 = vertices[13]; 549 const PetscScalar z4 = vertices[14]; 550 const PetscScalar x5 = vertices[15]; 551 const PetscScalar y5 = vertices[16]; 552 const PetscScalar z5 = vertices[17]; 553 const PetscScalar x6 = vertices[18]; 554 const PetscScalar y6 = vertices[19]; 555 const PetscScalar z6 = vertices[20]; 556 const PetscScalar x7 = vertices[21]; 557 const PetscScalar y7 = vertices[22]; 558 const PetscScalar z7 = vertices[23]; 559 const PetscScalar f_xy = x2 - x1 - x3 + x0; 560 const PetscScalar g_xy = y2 - y1 - y3 + y0; 561 const PetscScalar h_xy = z2 - z1 - z3 + z0; 562 const PetscScalar f_yz = x7 - x3 - x4 + x0; 563 const PetscScalar g_yz = y7 - y3 - y4 + y0; 564 const PetscScalar h_yz = z7 - z3 - z4 + z0; 565 const PetscScalar f_xz = x5 - x1 - x4 + x0; 566 const PetscScalar g_xz = y5 - y1 - y4 + y0; 567 const PetscScalar h_xz = z5 - z1 - z4 + z0; 568 const PetscScalar f_xyz = x6 - x0 + x1 - x2 + x3 + x4 - x5 - x7; 569 const PetscScalar g_xyz = y6 - y0 + y1 - y2 + y3 + y4 - y5 - y7; 570 const PetscScalar h_xyz = z6 - z0 + z1 - z2 + z3 + z4 - z5 - z7; 571 const PetscScalar *ref; 572 PetscErrorCode ierr; 573 574 PetscFunctionBegin; 575 ierr = VecGetArrayRead(Xref, &ref);CHKERRQ(ierr); 576 { 577 const PetscScalar x = ref[0]; 578 const PetscScalar y = ref[1]; 579 const PetscScalar z = ref[2]; 580 const PetscInt rows[3] = {0, 1, 2}; 581 PetscScalar values[9]; 582 583 values[0] = (x1 - x0 + f_xy*y + f_xz*z + f_xyz*y*z) / 2.0; 584 values[1] = (x3 - x0 + f_xy*x + f_yz*z + f_xyz*x*z) / 2.0; 585 values[2] = (x4 - x0 + f_yz*y + f_xz*x + f_xyz*x*y) / 2.0; 586 values[3] = (y1 - y0 + g_xy*y + g_xz*z + g_xyz*y*z) / 2.0; 587 values[4] = (y3 - y0 + g_xy*x + g_yz*z + g_xyz*x*z) / 2.0; 588 values[5] = (y4 - y0 + g_yz*y + g_xz*x + g_xyz*x*y) / 2.0; 589 values[6] = (z1 - z0 + h_xy*y + h_xz*z + h_xyz*y*z) / 2.0; 590 values[7] = (z3 - z0 + h_xy*x + h_yz*z + h_xyz*x*z) / 2.0; 591 values[8] = (z4 - z0 + h_yz*y + h_xz*x + h_xyz*x*y) / 2.0; 592 593 ierr = MatSetValues(J, 3, rows, 3, rows, values, INSERT_VALUES);CHKERRQ(ierr); 594 } 595 ierr = PetscLogFlops(152);CHKERRQ(ierr); 596 ierr = VecRestoreArrayRead(Xref, &ref);CHKERRQ(ierr); 597 ierr = MatAssemblyBegin(J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 598 ierr = MatAssemblyEnd(J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 599 PetscFunctionReturn(0); 600 } 601 602 #undef __FUNCT__ 603 #define __FUNCT__ "DMInterpolate_Hex_Private" 604 PETSC_STATIC_INLINE PetscErrorCode DMInterpolate_Hex_Private(DMInterpolationInfo ctx, DM dm, Vec xLocal, Vec v) 605 { 606 DM dmCoord; 607 SNES snes; 608 KSP ksp; 609 PC pc; 610 Vec coordsLocal, r, ref, real; 611 Mat J; 612 const PetscScalar *coords; 613 PetscScalar *a; 614 PetscInt p; 615 PetscErrorCode ierr; 616 617 PetscFunctionBegin; 618 ierr = DMGetCoordinatesLocal(dm, &coordsLocal);CHKERRQ(ierr); 619 ierr = DMGetCoordinateDM(dm, &dmCoord);CHKERRQ(ierr); 620 ierr = SNESCreate(PETSC_COMM_SELF, &snes);CHKERRQ(ierr); 621 ierr = SNESSetOptionsPrefix(snes, "hex_interp_");CHKERRQ(ierr); 622 ierr = VecCreate(PETSC_COMM_SELF, &r);CHKERRQ(ierr); 623 ierr = VecSetSizes(r, 3, 3);CHKERRQ(ierr); 624 ierr = VecSetType(r,dm->vectype);CHKERRQ(ierr); 625 ierr = VecDuplicate(r, &ref);CHKERRQ(ierr); 626 ierr = VecDuplicate(r, &real);CHKERRQ(ierr); 627 ierr = MatCreate(PETSC_COMM_SELF, &J);CHKERRQ(ierr); 628 ierr = MatSetSizes(J, 3, 3, 3, 3);CHKERRQ(ierr); 629 ierr = MatSetType(J, MATSEQDENSE);CHKERRQ(ierr); 630 ierr = MatSetUp(J);CHKERRQ(ierr); 631 ierr = SNESSetFunction(snes, r, HexMap_Private, NULL);CHKERRQ(ierr); 632 ierr = SNESSetJacobian(snes, J, J, HexJacobian_Private, NULL);CHKERRQ(ierr); 633 ierr = SNESGetKSP(snes, &ksp);CHKERRQ(ierr); 634 ierr = KSPGetPC(ksp, &pc);CHKERRQ(ierr); 635 ierr = PCSetType(pc, PCLU);CHKERRQ(ierr); 636 ierr = SNESSetFromOptions(snes);CHKERRQ(ierr); 637 638 ierr = VecGetArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 639 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 640 for (p = 0; p < ctx->n; ++p) { 641 PetscScalar *x = NULL, *vertices = NULL; 642 PetscScalar *xi; 643 PetscReal xir[3]; 644 PetscInt c = ctx->cells[p], comp, coordSize, xSize; 645 646 /* Can make this do all points at once */ 647 ierr = DMPlexVecGetClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);CHKERRQ(ierr); 648 if (8*3 != coordSize) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid closure size %d should be %d", coordSize, 8*3); 649 ierr = DMPlexVecGetClosure(dm, NULL, xLocal, c, &xSize, &x);CHKERRQ(ierr); 650 if (8*ctx->dof != xSize) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid closure size %d should be %d", xSize, 8*ctx->dof); 651 ierr = SNESSetFunction(snes, NULL, NULL, (void*) vertices);CHKERRQ(ierr); 652 ierr = SNESSetJacobian(snes, NULL, NULL, NULL, (void*) vertices);CHKERRQ(ierr); 653 ierr = VecGetArray(real, &xi);CHKERRQ(ierr); 654 xi[0] = coords[p*ctx->dim+0]; 655 xi[1] = coords[p*ctx->dim+1]; 656 xi[2] = coords[p*ctx->dim+2]; 657 ierr = VecRestoreArray(real, &xi);CHKERRQ(ierr); 658 ierr = SNESSolve(snes, real, ref);CHKERRQ(ierr); 659 ierr = VecGetArray(ref, &xi);CHKERRQ(ierr); 660 xir[0] = PetscRealPart(xi[0]); 661 xir[1] = PetscRealPart(xi[1]); 662 xir[2] = PetscRealPart(xi[2]); 663 for (comp = 0; comp < ctx->dof; ++comp) { 664 a[p*ctx->dof+comp] = 665 x[0*ctx->dof+comp]*(1-xir[0])*(1-xir[1])*(1-xir[2]) + 666 x[3*ctx->dof+comp]* xir[0]*(1-xir[1])*(1-xir[2]) + 667 x[2*ctx->dof+comp]* xir[0]* xir[1]*(1-xir[2]) + 668 x[1*ctx->dof+comp]*(1-xir[0])* xir[1]*(1-xir[2]) + 669 x[4*ctx->dof+comp]*(1-xir[0])*(1-xir[1])* xir[2] + 670 x[5*ctx->dof+comp]* xir[0]*(1-xir[1])* xir[2] + 671 x[6*ctx->dof+comp]* xir[0]* xir[1]* xir[2] + 672 x[7*ctx->dof+comp]*(1-xir[0])* xir[1]* xir[2]; 673 } 674 ierr = VecRestoreArray(ref, &xi);CHKERRQ(ierr); 675 ierr = DMPlexVecRestoreClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);CHKERRQ(ierr); 676 ierr = DMPlexVecRestoreClosure(dm, NULL, xLocal, c, &xSize, &x);CHKERRQ(ierr); 677 } 678 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 679 ierr = VecRestoreArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 680 681 ierr = SNESDestroy(&snes);CHKERRQ(ierr); 682 ierr = VecDestroy(&r);CHKERRQ(ierr); 683 ierr = VecDestroy(&ref);CHKERRQ(ierr); 684 ierr = VecDestroy(&real);CHKERRQ(ierr); 685 ierr = MatDestroy(&J);CHKERRQ(ierr); 686 PetscFunctionReturn(0); 687 } 688 689 #undef __FUNCT__ 690 #define __FUNCT__ "DMInterpolationEvaluate" 691 /* 692 Input Parameters: 693 + ctx - The DMInterpolationInfo context 694 . dm - The DM 695 - x - The local vector containing the field to be interpolated 696 697 Output Parameters: 698 . v - The vector containing the interpolated values 699 */ 700 PetscErrorCode DMInterpolationEvaluate(DMInterpolationInfo ctx, DM dm, Vec x, Vec v) 701 { 702 PetscInt dim, coneSize, n; 703 PetscErrorCode ierr; 704 705 PetscFunctionBegin; 706 PetscValidHeaderSpecific(dm, DM_CLASSID, 2); 707 PetscValidHeaderSpecific(x, VEC_CLASSID, 3); 708 PetscValidHeaderSpecific(v, VEC_CLASSID, 4); 709 ierr = VecGetLocalSize(v, &n);CHKERRQ(ierr); 710 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); 711 if (n) { 712 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 713 ierr = DMPlexGetConeSize(dm, ctx->cells[0], &coneSize);CHKERRQ(ierr); 714 if (dim == 2) { 715 if (coneSize == 3) { 716 ierr = DMInterpolate_Triangle_Private(ctx, dm, x, v);CHKERRQ(ierr); 717 } else if (coneSize == 4) { 718 ierr = DMInterpolate_Quad_Private(ctx, dm, x, v);CHKERRQ(ierr); 719 } else SETERRQ1(ctx->comm, PETSC_ERR_ARG_OUTOFRANGE, "Unsupported dimension %d for point interpolation", dim); 720 } else if (dim == 3) { 721 if (coneSize == 4) { 722 ierr = DMInterpolate_Tetrahedron_Private(ctx, dm, x, v);CHKERRQ(ierr); 723 } else { 724 ierr = DMInterpolate_Hex_Private(ctx, dm, x, v);CHKERRQ(ierr); 725 } 726 } else SETERRQ1(ctx->comm, PETSC_ERR_ARG_OUTOFRANGE, "Unsupported dimension %d for point interpolation", dim); 727 } 728 PetscFunctionReturn(0); 729 } 730 731 #undef __FUNCT__ 732 #define __FUNCT__ "DMInterpolationDestroy" 733 PetscErrorCode DMInterpolationDestroy(DMInterpolationInfo *ctx) 734 { 735 PetscErrorCode ierr; 736 737 PetscFunctionBegin; 738 PetscValidPointer(ctx, 2); 739 ierr = VecDestroy(&(*ctx)->coords);CHKERRQ(ierr); 740 ierr = PetscFree((*ctx)->points);CHKERRQ(ierr); 741 ierr = PetscFree((*ctx)->cells);CHKERRQ(ierr); 742 ierr = PetscFree(*ctx);CHKERRQ(ierr); 743 *ctx = NULL; 744 PetscFunctionReturn(0); 745 } 746 747 #undef __FUNCT__ 748 #define __FUNCT__ "SNESMonitorFields" 749 /*@C 750 SNESMonitorFields - Monitors the residual for each field separately 751 752 Collective on SNES 753 754 Input Parameters: 755 + snes - the SNES context 756 . its - iteration number 757 . fgnorm - 2-norm of residual 758 - dummy - PetscViewer of type ASCII 759 760 Notes: 761 This routine prints the residual norm at each iteration. 762 763 Level: intermediate 764 765 .keywords: SNES, nonlinear, default, monitor, norm 766 .seealso: SNESMonitorSet(), SNESMonitorDefault() 767 @*/ 768 PetscErrorCode SNESMonitorFields(SNES snes, PetscInt its, PetscReal fgnorm, void *dummy) 769 { 770 PetscViewer viewer = (PetscViewer) dummy; 771 Vec res; 772 DM dm; 773 PetscSection s; 774 const PetscScalar *r; 775 PetscReal *lnorms, *norms; 776 PetscInt numFields, f, pStart, pEnd, p; 777 PetscErrorCode ierr; 778 779 PetscFunctionBegin; 780 PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,4); 781 ierr = SNESGetFunction(snes, &res, 0, 0);CHKERRQ(ierr); 782 ierr = SNESGetDM(snes, &dm);CHKERRQ(ierr); 783 ierr = DMGetDefaultSection(dm, &s);CHKERRQ(ierr); 784 ierr = PetscSectionGetNumFields(s, &numFields);CHKERRQ(ierr); 785 ierr = PetscSectionGetChart(s, &pStart, &pEnd);CHKERRQ(ierr); 786 ierr = PetscCalloc2(numFields, &lnorms, numFields, &norms);CHKERRQ(ierr); 787 ierr = VecGetArrayRead(res, &r);CHKERRQ(ierr); 788 for (p = pStart; p < pEnd; ++p) { 789 for (f = 0; f < numFields; ++f) { 790 PetscInt fdof, foff, d; 791 792 ierr = PetscSectionGetFieldDof(s, p, f, &fdof);CHKERRQ(ierr); 793 ierr = PetscSectionGetFieldOffset(s, p, f, &foff);CHKERRQ(ierr); 794 for (d = 0; d < fdof; ++d) lnorms[f] += PetscRealPart(PetscSqr(r[foff+d])); 795 } 796 } 797 ierr = VecRestoreArrayRead(res, &r);CHKERRQ(ierr); 798 ierr = MPIU_Allreduce(lnorms, norms, numFields, MPIU_REAL, MPIU_SUM, PetscObjectComm((PetscObject) dm));CHKERRQ(ierr); 799 ierr = PetscViewerASCIIAddTab(viewer, ((PetscObject) snes)->tablevel);CHKERRQ(ierr); 800 ierr = PetscViewerASCIIPrintf(viewer, "%3D SNES Function norm %14.12e [", its, (double) fgnorm);CHKERRQ(ierr); 801 for (f = 0; f < numFields; ++f) { 802 if (f > 0) {ierr = PetscViewerASCIIPrintf(viewer, ", ");CHKERRQ(ierr);} 803 ierr = PetscViewerASCIIPrintf(viewer, "%14.12e", (double) PetscSqrtReal(norms[f]));CHKERRQ(ierr); 804 } 805 ierr = PetscViewerASCIIPrintf(viewer, "]\n");CHKERRQ(ierr); 806 ierr = PetscViewerASCIISubtractTab(viewer, ((PetscObject) snes)->tablevel);CHKERRQ(ierr); 807 ierr = PetscFree2(lnorms, norms);CHKERRQ(ierr); 808 PetscFunctionReturn(0); 809 } 810 811 /********************* Residual Computation **************************/ 812 813 #undef __FUNCT__ 814 #define __FUNCT__ "DMPlexSNESGetGeometryFEM" 815 /*@ 816 DMPlexSNESGetGeometryFEM - Return precomputed geometric data 817 818 Input Parameter: 819 . dm - The DM 820 821 Output Parameters: 822 . cellgeom - The values precomputed from cell geometry 823 824 Level: developer 825 826 .seealso: DMPlexSNESSetFunctionLocal() 827 @*/ 828 PetscErrorCode DMPlexSNESGetGeometryFEM(DM dm, Vec *cellgeom) 829 { 830 DMSNES dmsnes; 831 PetscObject obj; 832 PetscErrorCode ierr; 833 834 PetscFunctionBegin; 835 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 836 ierr = DMGetDMSNES(dm, &dmsnes);CHKERRQ(ierr); 837 ierr = PetscObjectQuery((PetscObject) dmsnes, "DMPlexSNES_cellgeom_fem", &obj);CHKERRQ(ierr); 838 if (!obj) { 839 Vec cellgeom; 840 841 ierr = DMPlexComputeGeometryFEM(dm, &cellgeom);CHKERRQ(ierr); 842 ierr = PetscObjectCompose((PetscObject) dmsnes, "DMPlexSNES_cellgeom_fem", (PetscObject) cellgeom);CHKERRQ(ierr); 843 ierr = VecDestroy(&cellgeom);CHKERRQ(ierr); 844 } 845 if (cellgeom) {PetscValidPointer(cellgeom, 3); ierr = PetscObjectQuery((PetscObject) dmsnes, "DMPlexSNES_cellgeom_fem", (PetscObject *) cellgeom);CHKERRQ(ierr);} 846 PetscFunctionReturn(0); 847 } 848 849 #undef __FUNCT__ 850 #define __FUNCT__ "DMPlexSNESGetGeometryFVM" 851 /*@ 852 DMPlexSNESGetGeometryFVM - Return precomputed geometric data 853 854 Input Parameter: 855 . dm - The DM 856 857 Output Parameters: 858 + facegeom - The values precomputed from face geometry 859 . cellgeom - The values precomputed from cell geometry 860 - minRadius - The minimum radius over the mesh of an inscribed sphere in a cell 861 862 Level: developer 863 864 .seealso: DMPlexTSSetRHSFunctionLocal() 865 @*/ 866 PetscErrorCode DMPlexSNESGetGeometryFVM(DM dm, Vec *facegeom, Vec *cellgeom, PetscReal *minRadius) 867 { 868 DMSNES dmsnes; 869 PetscObject obj; 870 PetscErrorCode ierr; 871 872 PetscFunctionBegin; 873 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 874 ierr = DMGetDMSNES(dm, &dmsnes);CHKERRQ(ierr); 875 ierr = PetscObjectQuery((PetscObject) dmsnes, "DMPlexSNES_facegeom_fvm", &obj);CHKERRQ(ierr); 876 if (!obj) { 877 Vec cellgeom, facegeom; 878 879 ierr = DMPlexComputeGeometryFVM(dm, &cellgeom, &facegeom);CHKERRQ(ierr); 880 ierr = PetscObjectCompose((PetscObject) dmsnes, "DMPlexSNES_facegeom_fvm", (PetscObject) facegeom);CHKERRQ(ierr); 881 ierr = PetscObjectCompose((PetscObject) dmsnes, "DMPlexSNES_cellgeom_fvm", (PetscObject) cellgeom);CHKERRQ(ierr); 882 ierr = VecDestroy(&facegeom);CHKERRQ(ierr); 883 ierr = VecDestroy(&cellgeom);CHKERRQ(ierr); 884 } 885 if (facegeom) {PetscValidPointer(facegeom, 2); ierr = PetscObjectQuery((PetscObject) dmsnes, "DMPlexSNES_facegeom_fvm", (PetscObject *) facegeom);CHKERRQ(ierr);} 886 if (cellgeom) {PetscValidPointer(cellgeom, 3); ierr = PetscObjectQuery((PetscObject) dmsnes, "DMPlexSNES_cellgeom_fvm", (PetscObject *) cellgeom);CHKERRQ(ierr);} 887 if (minRadius) {ierr = DMPlexGetMinRadius(dm, minRadius);CHKERRQ(ierr);} 888 PetscFunctionReturn(0); 889 } 890 891 #undef __FUNCT__ 892 #define __FUNCT__ "DMPlexSNESGetGradientDM" 893 /*@ 894 DMPlexSNESGetGradientDM - Return gradient data layout 895 896 Input Parameters: 897 + dm - The DM 898 - fv - The PetscFV 899 900 Output Parameter: 901 . dmGrad - The layout for gradient values 902 903 Level: developer 904 905 .seealso: DMPlexSNESGetGeometryFVM() 906 @*/ 907 PetscErrorCode DMPlexSNESGetGradientDM(DM dm, PetscFV fv, DM *dmGrad) 908 { 909 DMSNES dmsnes; 910 PetscObject obj; 911 PetscBool computeGradients; 912 PetscErrorCode ierr; 913 914 PetscFunctionBegin; 915 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 916 PetscValidHeaderSpecific(fv,PETSCFV_CLASSID,2); 917 PetscValidPointer(dmGrad,3); 918 ierr = PetscFVGetComputeGradients(fv, &computeGradients);CHKERRQ(ierr); 919 if (!computeGradients) {*dmGrad = NULL; PetscFunctionReturn(0);} 920 ierr = DMGetDMSNES(dm, &dmsnes);CHKERRQ(ierr); 921 ierr = PetscObjectQuery((PetscObject) dmsnes, "DMPlexSNES_dmgrad_fvm", &obj);CHKERRQ(ierr); 922 if (!obj) { 923 DM dmGrad; 924 Vec faceGeometry, cellGeometry; 925 926 ierr = DMPlexSNESGetGeometryFVM(dm, &faceGeometry, &cellGeometry, NULL);CHKERRQ(ierr); 927 ierr = DMPlexComputeGradientFVM(dm, fv, faceGeometry, cellGeometry, &dmGrad);CHKERRQ(ierr); 928 ierr = PetscObjectCompose((PetscObject) dmsnes, "DMPlexSNES_dmgrad_fvm", (PetscObject) dmGrad);CHKERRQ(ierr); 929 ierr = DMDestroy(&dmGrad);CHKERRQ(ierr); 930 } 931 ierr = PetscObjectQuery((PetscObject) dmsnes, "DMPlexSNES_dmgrad_fvm", (PetscObject *) dmGrad);CHKERRQ(ierr); 932 PetscFunctionReturn(0); 933 } 934 935 #undef __FUNCT__ 936 #define __FUNCT__ "DMPlexGetCellFields" 937 /*@C 938 DMPlexGetCellFields - Retrieve the field values values for a chunk of cells 939 940 Input Parameters: 941 + dm - The DM 942 . cStart - The first cell to include 943 . cEnd - The first cell to exclude 944 . locX - A local vector with the solution fields 945 . locX_t - A local vector with solution field time derivatives, or NULL 946 - locA - A local vector with auxiliary fields, or NULL 947 948 Output Parameters: 949 + u - The field coefficients 950 . u_t - The fields derivative coefficients 951 - a - The auxiliary field coefficients 952 953 Level: developer 954 955 .seealso: DMPlexGetFaceFields() 956 @*/ 957 PetscErrorCode DMPlexGetCellFields(DM dm, PetscInt cStart, PetscInt cEnd, Vec locX, Vec locX_t, Vec locA, PetscScalar **u, PetscScalar **u_t, PetscScalar **a) 958 { 959 DM dmAux; 960 PetscSection section, sectionAux; 961 PetscDS prob; 962 PetscInt numCells = cEnd - cStart, totDim, totDimAux, c; 963 PetscErrorCode ierr; 964 965 PetscFunctionBegin; 966 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 967 PetscValidHeaderSpecific(locX, VEC_CLASSID, 4); 968 if (locX_t) {PetscValidHeaderSpecific(locX_t, VEC_CLASSID, 5);} 969 if (locA) {PetscValidHeaderSpecific(locA, VEC_CLASSID, 6);} 970 PetscValidPointer(u, 7); 971 PetscValidPointer(u_t, 8); 972 PetscValidPointer(a, 9); 973 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 974 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 975 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 976 if (locA) { 977 PetscDS probAux; 978 979 ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); 980 ierr = DMGetDefaultSection(dmAux, §ionAux);CHKERRQ(ierr); 981 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 982 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 983 } 984 ierr = DMGetWorkArray(dm, numCells*totDim, PETSC_SCALAR, u);CHKERRQ(ierr); 985 if (locX_t) {ierr = DMGetWorkArray(dm, numCells*totDim, PETSC_SCALAR, u_t);CHKERRQ(ierr);} else {*u_t = NULL;} 986 if (locA) {ierr = DMGetWorkArray(dm, numCells*totDimAux, PETSC_SCALAR, a);CHKERRQ(ierr);} else {*a = NULL;} 987 for (c = cStart; c < cEnd; ++c) { 988 PetscScalar *x = NULL, *x_t = NULL, *ul = *u, *ul_t = *u_t, *al = *a; 989 PetscInt i; 990 991 ierr = DMPlexVecGetClosure(dm, section, locX, c, NULL, &x);CHKERRQ(ierr); 992 for (i = 0; i < totDim; ++i) ul[(c-cStart)*totDim+i] = x[i]; 993 ierr = DMPlexVecRestoreClosure(dm, section, locX, c, NULL, &x);CHKERRQ(ierr); 994 if (locX_t) { 995 ierr = DMPlexVecGetClosure(dm, section, locX_t, c, NULL, &x_t);CHKERRQ(ierr); 996 for (i = 0; i < totDim; ++i) ul_t[(c-cStart)*totDim+i] = x_t[i]; 997 ierr = DMPlexVecRestoreClosure(dm, section, locX_t, c, NULL, &x_t);CHKERRQ(ierr); 998 } 999 if (locA) { 1000 ierr = DMPlexVecGetClosure(dmAux, sectionAux, locA, c, NULL, &x);CHKERRQ(ierr); 1001 for (i = 0; i < totDimAux; ++i) al[(c-cStart)*totDimAux+i] = x[i]; 1002 ierr = DMPlexVecRestoreClosure(dmAux, sectionAux, locA, c, NULL, &x);CHKERRQ(ierr); 1003 } 1004 } 1005 PetscFunctionReturn(0); 1006 } 1007 1008 #undef __FUNCT__ 1009 #define __FUNCT__ "DMPlexRestoreCellFields" 1010 /*@C 1011 DMPlexRestoreCellFields - Restore the field values values for a chunk of cells 1012 1013 Input Parameters: 1014 + dm - The DM 1015 . cStart - The first cell to include 1016 . cEnd - The first cell to exclude 1017 . locX - A local vector with the solution fields 1018 . locX_t - A local vector with solution field time derivatives, or NULL 1019 - locA - A local vector with auxiliary fields, or NULL 1020 1021 Output Parameters: 1022 + u - The field coefficients 1023 . u_t - The fields derivative coefficients 1024 - a - The auxiliary field coefficients 1025 1026 Level: developer 1027 1028 .seealso: DMPlexGetFaceFields() 1029 @*/ 1030 PetscErrorCode DMPlexRestoreCellFields(DM dm, PetscInt cStart, PetscInt cEnd, Vec locX, Vec locX_t, Vec locA, PetscScalar **u, PetscScalar **u_t, PetscScalar **a) 1031 { 1032 PetscErrorCode ierr; 1033 1034 PetscFunctionBegin; 1035 ierr = DMRestoreWorkArray(dm, 0, PETSC_SCALAR, u);CHKERRQ(ierr); 1036 if (*u_t) {ierr = DMRestoreWorkArray(dm, 0, PETSC_SCALAR, u_t);CHKERRQ(ierr);} 1037 if (*a) {ierr = DMRestoreWorkArray(dm, 0, PETSC_SCALAR, a);CHKERRQ(ierr);} 1038 PetscFunctionReturn(0); 1039 } 1040 1041 #undef __FUNCT__ 1042 #define __FUNCT__ "DMPlexGetFaceFields" 1043 /*@C 1044 DMPlexGetFaceFields - Retrieve the field values values for a chunk of faces 1045 1046 Input Parameters: 1047 + dm - The DM 1048 . fStart - The first face to include 1049 . fEnd - The first face to exclude 1050 . locX - A local vector with the solution fields 1051 . locX_t - A local vector with solution field time derivatives, or NULL 1052 . faceGeometry - A local vector with face geometry 1053 . cellGeometry - A local vector with cell geometry 1054 - locaGrad - A local vector with field gradients, or NULL 1055 1056 Output Parameters: 1057 + uL - The field values at the left side of the face 1058 - uR - The field values at the right side of the face 1059 1060 Level: developer 1061 1062 .seealso: DMPlexGetCellFields() 1063 @*/ 1064 PetscErrorCode DMPlexGetFaceFields(DM dm, PetscInt fStart, PetscInt fEnd, Vec locX, Vec locX_t, Vec faceGeometry, Vec cellGeometry, Vec locGrad, PetscScalar **uL, PetscScalar **uR) 1065 { 1066 DM dmFace, dmCell, dmGrad = NULL; 1067 PetscSection section; 1068 PetscDS prob; 1069 DMLabel ghostLabel; 1070 const PetscScalar *facegeom, *cellgeom, *x, *lgrad; 1071 PetscBool *isFE; 1072 PetscInt dim, Nf, f, Nc, numFaces = fEnd - fStart, iface, face; 1073 PetscErrorCode ierr; 1074 1075 PetscFunctionBegin; 1076 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1077 PetscValidHeaderSpecific(locX, VEC_CLASSID, 4); 1078 if (locX_t) {PetscValidHeaderSpecific(locX_t, VEC_CLASSID, 5);} 1079 PetscValidHeaderSpecific(faceGeometry, VEC_CLASSID, 6); 1080 PetscValidHeaderSpecific(cellGeometry, VEC_CLASSID, 7); 1081 if (locGrad) {PetscValidHeaderSpecific(locGrad, VEC_CLASSID, 8);} 1082 PetscValidPointer(uL, 9); 1083 PetscValidPointer(uR, 10); 1084 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1085 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1086 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 1087 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 1088 ierr = PetscDSGetTotalComponents(prob, &Nc);CHKERRQ(ierr); 1089 ierr = PetscMalloc1(Nf, &isFE);CHKERRQ(ierr); 1090 for (f = 0; f < Nf; ++f) { 1091 PetscObject obj; 1092 PetscClassId id; 1093 1094 ierr = DMGetField(dm, f, &obj);CHKERRQ(ierr); 1095 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1096 if (id == PETSCFE_CLASSID) {isFE[f] = PETSC_TRUE;} 1097 else if (id == PETSCFV_CLASSID) {isFE[f] = PETSC_FALSE;} 1098 else {isFE[f] = PETSC_FALSE;} 1099 } 1100 ierr = DMPlexGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 1101 ierr = VecGetArrayRead(locX, &x);CHKERRQ(ierr); 1102 ierr = VecGetDM(faceGeometry, &dmFace);CHKERRQ(ierr); 1103 ierr = VecGetArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); 1104 ierr = VecGetDM(cellGeometry, &dmCell);CHKERRQ(ierr); 1105 ierr = VecGetArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr); 1106 if (locGrad) { 1107 ierr = VecGetDM(locGrad, &dmGrad);CHKERRQ(ierr); 1108 ierr = VecGetArrayRead(locGrad, &lgrad);CHKERRQ(ierr); 1109 } 1110 ierr = DMGetWorkArray(dm, numFaces*Nc, PETSC_SCALAR, uL);CHKERRQ(ierr); 1111 ierr = DMGetWorkArray(dm, numFaces*Nc, PETSC_SCALAR, uR);CHKERRQ(ierr); 1112 /* Right now just eat the extra work for FE (could make a cell loop) */ 1113 for (face = fStart, iface = 0; face < fEnd; ++face) { 1114 const PetscInt *cells; 1115 const PetscFVFaceGeom *fg; 1116 const PetscFVCellGeom *cgL, *cgR; 1117 const PetscScalar *xL, *xR, *gL, *gR; 1118 PetscScalar *uLl = *uL, *uRl = *uR; 1119 PetscInt ghost, nsupp; 1120 1121 ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr); 1122 ierr = DMPlexGetSupportSize(dm, face, &nsupp);CHKERRQ(ierr); 1123 if (ghost >= 0) continue; 1124 ierr = DMPlexPointLocalRead(dmFace, face, facegeom, &fg);CHKERRQ(ierr); 1125 ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr); 1126 ierr = DMPlexPointLocalRead(dmCell, cells[0], cellgeom, &cgL);CHKERRQ(ierr); 1127 ierr = DMPlexPointLocalRead(dmCell, cells[1], cellgeom, &cgR);CHKERRQ(ierr); 1128 for (f = 0; f < Nf; ++f) { 1129 PetscInt off; 1130 1131 ierr = PetscDSGetComponentOffset(prob, f, &off);CHKERRQ(ierr); 1132 if (isFE[f]) { 1133 const PetscInt *cone; 1134 PetscInt comp, coneSize, faceLocL, faceLocR, ldof, rdof, d; 1135 1136 xL = xR = NULL; 1137 ierr = DMPlexVecGetClosure(dm, section, locX, cells[0], &ldof, (PetscScalar **) &xL);CHKERRQ(ierr); 1138 ierr = DMPlexVecGetClosure(dm, section, locX, cells[1], &rdof, (PetscScalar **) &xR);CHKERRQ(ierr); 1139 ierr = DMPlexGetCone(dm, cells[0], &cone);CHKERRQ(ierr); 1140 ierr = DMPlexGetConeSize(dm, cells[0], &coneSize);CHKERRQ(ierr); 1141 for (faceLocL = 0; faceLocL < coneSize; ++faceLocL) if (cone[faceLocL] == face) break; 1142 if (faceLocL == coneSize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Could not find face %d in cone of cell %d", face, cells[0]); 1143 ierr = DMPlexGetCone(dm, cells[1], &cone);CHKERRQ(ierr); 1144 ierr = DMPlexGetConeSize(dm, cells[1], &coneSize);CHKERRQ(ierr); 1145 for (faceLocR = 0; faceLocR < coneSize; ++faceLocR) if (cone[faceLocR] == face) break; 1146 if (faceLocR == coneSize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Could not find face %d in cone of cell %d", face, cells[1]); 1147 /* Check that FEM field has values in the right cell (sometimes its an FV ghost cell) */ 1148 ierr = EvaluateFaceFields(prob, f, faceLocL, xL, &uLl[iface*Nc+off]);CHKERRQ(ierr); 1149 if (rdof == ldof) {ierr = EvaluateFaceFields(prob, f, faceLocR, xR, &uRl[iface*Nc+off]);CHKERRQ(ierr);} 1150 else {ierr = PetscSectionGetFieldComponents(section, f, &comp);CHKERRQ(ierr); for(d = 0; d < comp; ++d) uRl[iface*Nc+off+d] = uLl[iface*Nc+off+d];} 1151 ierr = DMPlexVecRestoreClosure(dm, section, locX, cells[0], &ldof, (PetscScalar **) &xL);CHKERRQ(ierr); 1152 ierr = DMPlexVecRestoreClosure(dm, section, locX, cells[1], &rdof, (PetscScalar **) &xR);CHKERRQ(ierr); 1153 } else { 1154 PetscFV fv; 1155 PetscInt numComp, c; 1156 1157 ierr = PetscDSGetDiscretization(prob, f, (PetscObject *) &fv);CHKERRQ(ierr); 1158 ierr = PetscFVGetNumComponents(fv, &numComp);CHKERRQ(ierr); 1159 if (nsupp > 2) { 1160 for (f = 0; f < Nf; ++f) { 1161 PetscInt off; 1162 1163 ierr = PetscDSGetComponentOffset(prob, f, &off);CHKERRQ(ierr); 1164 ierr = PetscFVGetNumComponents(fv, &numComp);CHKERRQ(ierr); 1165 for (c = 0; c < numComp; ++c) { 1166 uLl[iface*Nc+off+c] = 0.; 1167 uRl[iface*Nc+off+c] = 0.; 1168 } 1169 } 1170 continue; 1171 } 1172 ierr = DMPlexPointLocalFieldRead(dm, cells[0], f, x, &xL);CHKERRQ(ierr); 1173 ierr = DMPlexPointLocalFieldRead(dm, cells[1], f, x, &xR);CHKERRQ(ierr); 1174 if (dmGrad) { 1175 PetscReal dxL[3], dxR[3]; 1176 1177 ierr = DMPlexPointLocalRead(dmGrad, cells[0], lgrad, &gL);CHKERRQ(ierr); 1178 ierr = DMPlexPointLocalRead(dmGrad, cells[1], lgrad, &gR);CHKERRQ(ierr); 1179 DMPlex_WaxpyD_Internal(dim, -1, cgL->centroid, fg->centroid, dxL); 1180 DMPlex_WaxpyD_Internal(dim, -1, cgR->centroid, fg->centroid, dxR); 1181 for (c = 0; c < numComp; ++c) { 1182 uLl[iface*Nc+off+c] = xL[c] + DMPlex_DotD_Internal(dim, &gL[c*dim], dxL); 1183 uRl[iface*Nc+off+c] = xR[c] + DMPlex_DotD_Internal(dim, &gR[c*dim], dxR); 1184 } 1185 } else { 1186 for (c = 0; c < numComp; ++c) { 1187 uLl[iface*Nc+off+c] = xL[c]; 1188 uRl[iface*Nc+off+c] = xR[c]; 1189 } 1190 } 1191 } 1192 } 1193 ++iface; 1194 } 1195 ierr = VecRestoreArrayRead(locX, &x);CHKERRQ(ierr); 1196 ierr = VecRestoreArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); 1197 ierr = VecRestoreArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr); 1198 if (locGrad) { 1199 ierr = VecRestoreArrayRead(locGrad, &lgrad);CHKERRQ(ierr); 1200 } 1201 ierr = PetscFree(isFE);CHKERRQ(ierr); 1202 PetscFunctionReturn(0); 1203 } 1204 1205 #undef __FUNCT__ 1206 #define __FUNCT__ "DMPlexRestoreFaceFields" 1207 /*@C 1208 DMPlexRestoreFaceFields - Restore the field values values for a chunk of faces 1209 1210 Input Parameters: 1211 + dm - The DM 1212 . fStart - The first face to include 1213 . fEnd - The first face to exclude 1214 . locX - A local vector with the solution fields 1215 . locX_t - A local vector with solution field time derivatives, or NULL 1216 . faceGeometry - A local vector with face geometry 1217 . cellGeometry - A local vector with cell geometry 1218 - locaGrad - A local vector with field gradients, or NULL 1219 1220 Output Parameters: 1221 + uL - The field values at the left side of the face 1222 - uR - The field values at the right side of the face 1223 1224 Level: developer 1225 1226 .seealso: DMPlexGetFaceFields() 1227 @*/ 1228 PetscErrorCode DMPlexRestoreFaceFields(DM dm, PetscInt fStart, PetscInt fEnd, Vec locX, Vec locX_t, Vec faceGeometry, Vec cellGeometry, Vec locGrad, PetscScalar **uL, PetscScalar **uR) 1229 { 1230 PetscErrorCode ierr; 1231 1232 PetscFunctionBegin; 1233 ierr = DMRestoreWorkArray(dm, 0, PETSC_SCALAR, uL);CHKERRQ(ierr); 1234 ierr = DMRestoreWorkArray(dm, 0, PETSC_SCALAR, uR);CHKERRQ(ierr); 1235 PetscFunctionReturn(0); 1236 } 1237 1238 #undef __FUNCT__ 1239 #define __FUNCT__ "DMPlexGetFaceGeometry" 1240 /*@C 1241 DMPlexGetFaceGeometry - Retrieve the geometric values for a chunk of faces 1242 1243 Input Parameters: 1244 + dm - The DM 1245 . fStart - The first face to include 1246 . fEnd - The first face to exclude 1247 . faceGeometry - A local vector with face geometry 1248 - cellGeometry - A local vector with cell geometry 1249 1250 Output Parameters: 1251 + fgeom - The extract the face centroid and normal 1252 - vol - The cell volume 1253 1254 Level: developer 1255 1256 .seealso: DMPlexGetCellFields() 1257 @*/ 1258 PetscErrorCode DMPlexGetFaceGeometry(DM dm, PetscInt fStart, PetscInt fEnd, Vec faceGeometry, Vec cellGeometry, PetscFVFaceGeom **fgeom, PetscReal **vol) 1259 { 1260 DM dmFace, dmCell; 1261 DMLabel ghostLabel; 1262 const PetscScalar *facegeom, *cellgeom; 1263 PetscInt dim, numFaces = fEnd - fStart, iface, face; 1264 PetscErrorCode ierr; 1265 1266 PetscFunctionBegin; 1267 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1268 PetscValidHeaderSpecific(faceGeometry, VEC_CLASSID, 4); 1269 PetscValidHeaderSpecific(cellGeometry, VEC_CLASSID, 5); 1270 PetscValidPointer(fgeom, 6); 1271 PetscValidPointer(vol, 7); 1272 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1273 ierr = DMPlexGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 1274 ierr = VecGetDM(faceGeometry, &dmFace);CHKERRQ(ierr); 1275 ierr = VecGetArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); 1276 ierr = VecGetDM(cellGeometry, &dmCell);CHKERRQ(ierr); 1277 ierr = VecGetArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr); 1278 ierr = PetscMalloc1(numFaces, fgeom);CHKERRQ(ierr); 1279 ierr = DMGetWorkArray(dm, numFaces*2, PETSC_SCALAR, vol);CHKERRQ(ierr); 1280 for (face = fStart, iface = 0; face < fEnd; ++face) { 1281 const PetscInt *cells; 1282 const PetscFVFaceGeom *fg; 1283 const PetscFVCellGeom *cgL, *cgR; 1284 PetscFVFaceGeom *fgeoml = *fgeom; 1285 PetscReal *voll = *vol; 1286 PetscInt ghost, d; 1287 1288 ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr); 1289 if (ghost >= 0) continue; 1290 ierr = DMPlexPointLocalRead(dmFace, face, facegeom, &fg);CHKERRQ(ierr); 1291 ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr); 1292 ierr = DMPlexPointLocalRead(dmCell, cells[0], cellgeom, &cgL);CHKERRQ(ierr); 1293 ierr = DMPlexPointLocalRead(dmCell, cells[1], cellgeom, &cgR);CHKERRQ(ierr); 1294 for (d = 0; d < dim; ++d) { 1295 fgeoml[iface].centroid[d] = fg->centroid[d]; 1296 fgeoml[iface].normal[d] = fg->normal[d]; 1297 } 1298 voll[iface*2+0] = cgL->volume; 1299 voll[iface*2+1] = cgR->volume; 1300 ++iface; 1301 } 1302 ierr = VecRestoreArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); 1303 ierr = VecRestoreArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr); 1304 PetscFunctionReturn(0); 1305 } 1306 1307 #undef __FUNCT__ 1308 #define __FUNCT__ "DMPlexRestoreFaceGeometry" 1309 /*@C 1310 DMPlexRestoreFaceGeometry - Restore the field values values for a chunk of faces 1311 1312 Input Parameters: 1313 + dm - The DM 1314 . fStart - The first face to include 1315 . fEnd - The first face to exclude 1316 . faceGeometry - A local vector with face geometry 1317 - cellGeometry - A local vector with cell geometry 1318 1319 Output Parameters: 1320 + fgeom - The extract the face centroid and normal 1321 - vol - The cell volume 1322 1323 Level: developer 1324 1325 .seealso: DMPlexGetFaceFields() 1326 @*/ 1327 PetscErrorCode DMPlexRestoreFaceGeometry(DM dm, PetscInt fStart, PetscInt fEnd, Vec faceGeometry, Vec cellGeometry, PetscFVFaceGeom **fgeom, PetscReal **vol) 1328 { 1329 PetscErrorCode ierr; 1330 1331 PetscFunctionBegin; 1332 ierr = PetscFree(*fgeom);CHKERRQ(ierr); 1333 ierr = DMRestoreWorkArray(dm, 0, PETSC_REAL, vol);CHKERRQ(ierr); 1334 PetscFunctionReturn(0); 1335 } 1336 1337 #undef __FUNCT__ 1338 #define __FUNCT__ "DMPlexApplyLimiter_Internal" 1339 static PetscErrorCode DMPlexApplyLimiter_Internal (DM dm, DM dmCell, PetscLimiter lim, PetscInt dim, PetscInt totDim, PetscInt cell, PetscInt face, PetscInt fStart, PetscInt fEnd, PetscReal *cellPhi, const PetscScalar *x, 1340 const PetscScalar *cellgeom, const PetscFVCellGeom *cg, const PetscScalar *cx, const PetscScalar *cgrad) 1341 { 1342 const PetscInt *children; 1343 PetscInt numChildren; 1344 PetscErrorCode ierr; 1345 1346 PetscFunctionBegin; 1347 ierr = DMPlexGetTreeChildren(dm,face,&numChildren,&children);CHKERRQ(ierr); 1348 if (numChildren) { 1349 PetscInt c; 1350 1351 for (c = 0; c < numChildren; c++) { 1352 PetscInt childFace = children[c]; 1353 1354 if (childFace >= fStart && childFace < fEnd) { 1355 ierr = DMPlexApplyLimiter_Internal(dm,dmCell,lim,dim,totDim,cell,childFace,fStart,fEnd,cellPhi,x,cellgeom,cg,cx,cgrad);CHKERRQ(ierr); 1356 } 1357 } 1358 } 1359 else { 1360 const PetscScalar *ncx; 1361 const PetscFVCellGeom *ncg; 1362 const PetscInt *fcells; 1363 PetscInt ncell, d; 1364 PetscReal v[3]; 1365 1366 ierr = DMPlexGetSupport(dm, face, &fcells);CHKERRQ(ierr); 1367 ncell = cell == fcells[0] ? fcells[1] : fcells[0]; 1368 ierr = DMPlexPointLocalRead(dm, ncell, x, &ncx);CHKERRQ(ierr); 1369 ierr = DMPlexPointLocalRead(dmCell, ncell, cellgeom, &ncg);CHKERRQ(ierr); 1370 DMPlex_WaxpyD_Internal(dim, -1, cg->centroid, ncg->centroid, v); 1371 for (d = 0; d < totDim; ++d) { 1372 /* We use the symmetric slope limited form of Berger, Aftosmis, and Murman 2005 */ 1373 PetscReal phi, flim = 0.5 * PetscRealPart(ncx[d] - cx[d]) / DMPlex_DotD_Internal(dim, &cgrad[d*dim], v); 1374 1375 ierr = PetscLimiterLimit(lim, flim, &phi);CHKERRQ(ierr); 1376 cellPhi[d] = PetscMin(cellPhi[d], phi); 1377 } 1378 } 1379 PetscFunctionReturn(0); 1380 } 1381 1382 #undef __FUNCT__ 1383 #define __FUNCT__ "DMPlexReconstructGradients_Internal" 1384 PetscErrorCode DMPlexReconstructGradients_Internal(DM dm, PetscInt fStart, PetscInt fEnd, Vec faceGeometry, Vec cellGeometry, Vec locX, Vec grad) 1385 { 1386 DM dmFace, dmCell, dmGrad; 1387 DMLabel ghostLabel; 1388 PetscDS prob; 1389 PetscFV fvm; 1390 PetscLimiter lim; 1391 const PetscScalar *facegeom, *cellgeom, *x; 1392 PetscScalar *gr; 1393 PetscReal *cellPhi; 1394 PetscInt dim, face, cell, totDim, cStart, cEnd, cEndInterior; 1395 PetscErrorCode ierr; 1396 1397 PetscFunctionBegin; 1398 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1399 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1400 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1401 ierr = DMPlexGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 1402 ierr = PetscDSGetDiscretization(prob, 0, (PetscObject *) &fvm);CHKERRQ(ierr); 1403 ierr = PetscFVGetLimiter(fvm, &lim);CHKERRQ(ierr); 1404 ierr = VecGetDM(faceGeometry, &dmFace);CHKERRQ(ierr); 1405 ierr = VecGetArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); 1406 ierr = VecGetDM(cellGeometry, &dmCell);CHKERRQ(ierr); 1407 ierr = VecGetArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr); 1408 ierr = VecGetArrayRead(locX, &x);CHKERRQ(ierr); 1409 ierr = VecGetDM(grad, &dmGrad);CHKERRQ(ierr); 1410 ierr = VecZeroEntries(grad);CHKERRQ(ierr); 1411 ierr = VecGetArray(grad, &gr);CHKERRQ(ierr); 1412 /* Reconstruct gradients */ 1413 for (face = fStart; face < fEnd; ++face) { 1414 const PetscInt *cells; 1415 const PetscFVFaceGeom *fg; 1416 const PetscScalar *cx[2]; 1417 PetscScalar *cgrad[2]; 1418 PetscBool boundary; 1419 PetscInt ghost, c, pd, d, numChildren, numCells; 1420 1421 ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr); 1422 ierr = DMPlexIsBoundaryPoint(dm, face, &boundary);CHKERRQ(ierr); 1423 ierr = DMPlexGetTreeChildren(dm, face, &numChildren, NULL);CHKERRQ(ierr); 1424 if (ghost >= 0 || boundary || numChildren) continue; 1425 ierr = DMPlexGetSupportSize(dm, face, &numCells);CHKERRQ(ierr); 1426 if (numCells != 2) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "facet %d has %d support points: expected 2",face,numCells); 1427 ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr); 1428 ierr = DMPlexPointLocalRead(dmFace, face, facegeom, &fg);CHKERRQ(ierr); 1429 for (c = 0; c < 2; ++c) { 1430 ierr = DMPlexPointLocalRead(dm, cells[c], x, &cx[c]);CHKERRQ(ierr); 1431 ierr = DMPlexPointGlobalRef(dmGrad, cells[c], gr, &cgrad[c]);CHKERRQ(ierr); 1432 } 1433 for (pd = 0; pd < totDim; ++pd) { 1434 PetscScalar delta = cx[1][pd] - cx[0][pd]; 1435 1436 for (d = 0; d < dim; ++d) { 1437 if (cgrad[0]) cgrad[0][pd*dim+d] += fg->grad[0][d] * delta; 1438 if (cgrad[1]) cgrad[1][pd*dim+d] -= fg->grad[1][d] * delta; 1439 } 1440 } 1441 } 1442 /* Limit interior gradients (using cell-based loop because it generalizes better to vector limiters) */ 1443 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1444 ierr = DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr); 1445 cEndInterior = cEndInterior < 0 ? cEnd : cEndInterior; 1446 ierr = DMGetWorkArray(dm, totDim, PETSC_REAL, &cellPhi);CHKERRQ(ierr); 1447 for (cell = dmGrad && lim ? cStart : cEnd; cell < cEndInterior; ++cell) { 1448 const PetscInt *faces; 1449 const PetscScalar *cx; 1450 const PetscFVCellGeom *cg; 1451 PetscScalar *cgrad; 1452 PetscInt coneSize, f, pd, d; 1453 1454 ierr = DMPlexGetConeSize(dm, cell, &coneSize);CHKERRQ(ierr); 1455 ierr = DMPlexGetCone(dm, cell, &faces);CHKERRQ(ierr); 1456 ierr = DMPlexPointLocalRead(dm, cell, x, &cx);CHKERRQ(ierr); 1457 ierr = DMPlexPointLocalRead(dmCell, cell, cellgeom, &cg);CHKERRQ(ierr); 1458 ierr = DMPlexPointGlobalRef(dmGrad, cell, gr, &cgrad);CHKERRQ(ierr); 1459 if (!cgrad) continue; /* Unowned overlap cell, we do not compute */ 1460 /* Limiter will be minimum value over all neighbors */ 1461 for (d = 0; d < totDim; ++d) cellPhi[d] = PETSC_MAX_REAL; 1462 for (f = 0; f < coneSize; ++f) { 1463 ierr = DMPlexApplyLimiter_Internal(dm,dmCell,lim,dim,totDim,cell,faces[f],fStart,fEnd,cellPhi,x,cellgeom,cg,cx,cgrad);CHKERRQ(ierr); 1464 } 1465 /* Apply limiter to gradient */ 1466 for (pd = 0; pd < totDim; ++pd) 1467 /* Scalar limiter applied to each component separately */ 1468 for (d = 0; d < dim; ++d) cgrad[pd*dim+d] *= cellPhi[pd]; 1469 } 1470 ierr = DMRestoreWorkArray(dm, totDim, PETSC_REAL, &cellPhi);CHKERRQ(ierr); 1471 ierr = VecRestoreArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); 1472 ierr = VecRestoreArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr); 1473 ierr = VecRestoreArrayRead(locX, &x);CHKERRQ(ierr); 1474 ierr = VecRestoreArray(grad, &gr);CHKERRQ(ierr); 1475 PetscFunctionReturn(0); 1476 } 1477 1478 #undef __FUNCT__ 1479 #define __FUNCT__ "DMPlexComputeBdResidual_Internal" 1480 PetscErrorCode DMPlexComputeBdResidual_Internal(DM dm, Vec locX, Vec locX_t, Vec locF, void *user) 1481 { 1482 DM_Plex *mesh = (DM_Plex *) dm->data; 1483 PetscSection section; 1484 PetscDS prob; 1485 DMLabel depth; 1486 PetscFECellGeom *cgeom; 1487 PetscScalar *u = NULL, *u_t = NULL, *elemVec = NULL; 1488 PetscInt dim, Nf, f, totDimBd, numBd, bd; 1489 PetscErrorCode ierr; 1490 1491 PetscFunctionBegin; 1492 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1493 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 1494 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1495 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 1496 ierr = PetscDSGetTotalBdDimension(prob, &totDimBd);CHKERRQ(ierr); 1497 ierr = DMPlexGetDepthLabel(dm, &depth);CHKERRQ(ierr); 1498 ierr = DMPlexGetNumBoundary(dm, &numBd);CHKERRQ(ierr); 1499 for (bd = 0; bd < numBd; ++bd) { 1500 const char *bdLabel; 1501 DMLabel label; 1502 IS pointIS; 1503 const PetscInt *points; 1504 const PetscInt *values; 1505 PetscInt field, numValues, numPoints, p, dep, numFaces; 1506 PetscBool isEssential; 1507 1508 ierr = DMPlexGetBoundary(dm, bd, &isEssential, NULL, &bdLabel, &field, NULL, NULL, NULL, &numValues, &values, NULL);CHKERRQ(ierr); 1509 if (isEssential) continue; 1510 if (numValues != 1) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Bug me and I will fix this"); 1511 ierr = DMPlexGetLabel(dm, bdLabel, &label);CHKERRQ(ierr); 1512 ierr = DMLabelGetStratumSize(label, 1, &numPoints);CHKERRQ(ierr); 1513 ierr = DMLabelGetStratumIS(label, 1, &pointIS);CHKERRQ(ierr); 1514 ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); 1515 for (p = 0, numFaces = 0; p < numPoints; ++p) { 1516 ierr = DMLabelGetValue(depth, points[p], &dep);CHKERRQ(ierr); 1517 if (dep == dim-1) ++numFaces; 1518 } 1519 ierr = PetscMalloc3(numFaces*totDimBd,&u,numFaces,&cgeom,numFaces*totDimBd,&elemVec);CHKERRQ(ierr); 1520 if (locX_t) {ierr = PetscMalloc1(numFaces*totDimBd,&u_t);CHKERRQ(ierr);} 1521 for (p = 0, f = 0; p < numPoints; ++p) { 1522 const PetscInt point = points[p]; 1523 PetscScalar *x = NULL; 1524 PetscInt i; 1525 1526 ierr = DMLabelGetValue(depth, points[p], &dep);CHKERRQ(ierr); 1527 if (dep != dim-1) continue; 1528 ierr = DMPlexComputeCellGeometryFEM(dm, point, NULL, cgeom[f].v0, cgeom[f].J, cgeom[f].invJ, &cgeom[f].detJ);CHKERRQ(ierr); 1529 ierr = DMPlexComputeCellGeometryFVM(dm, point, NULL, NULL, cgeom[f].n);CHKERRQ(ierr); 1530 if (cgeom[f].detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for face %d", cgeom[f].detJ, point); 1531 ierr = DMPlexVecGetClosure(dm, section, locX, point, NULL, &x);CHKERRQ(ierr); 1532 for (i = 0; i < totDimBd; ++i) u[f*totDimBd+i] = x[i]; 1533 ierr = DMPlexVecRestoreClosure(dm, section, locX, point, NULL, &x);CHKERRQ(ierr); 1534 if (locX_t) { 1535 ierr = DMPlexVecGetClosure(dm, section, locX_t, point, NULL, &x);CHKERRQ(ierr); 1536 for (i = 0; i < totDimBd; ++i) u_t[f*totDimBd+i] = x[i]; 1537 ierr = DMPlexVecRestoreClosure(dm, section, locX_t, point, NULL, &x);CHKERRQ(ierr); 1538 } 1539 ++f; 1540 } 1541 for (f = 0; f < Nf; ++f) { 1542 PetscFE fe; 1543 PetscQuadrature q; 1544 PetscInt numQuadPoints, Nb; 1545 /* Conforming batches */ 1546 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 1547 /* Remainder */ 1548 PetscInt Nr, offset; 1549 1550 ierr = PetscDSGetBdDiscretization(prob, f, (PetscObject *) &fe);CHKERRQ(ierr); 1551 ierr = PetscFEGetQuadrature(fe, &q);CHKERRQ(ierr); 1552 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 1553 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1554 ierr = PetscQuadratureGetData(q, NULL, &numQuadPoints, NULL, NULL);CHKERRQ(ierr); 1555 blockSize = Nb*numQuadPoints; 1556 batchSize = numBlocks * blockSize; 1557 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1558 numChunks = numFaces / (numBatches*batchSize); 1559 Ne = numChunks*numBatches*batchSize; 1560 Nr = numFaces % (numBatches*batchSize); 1561 offset = numFaces - Nr; 1562 ierr = PetscFEIntegrateBdResidual(fe, prob, f, Ne, cgeom, u, u_t, NULL, NULL, elemVec);CHKERRQ(ierr); 1563 ierr = PetscFEIntegrateBdResidual(fe, prob, f, Nr, &cgeom[offset], &u[offset*totDimBd], u_t ? &u_t[offset*totDimBd] : NULL, NULL, NULL, &elemVec[offset*totDimBd]);CHKERRQ(ierr); 1564 } 1565 for (p = 0, f = 0; p < numPoints; ++p) { 1566 const PetscInt point = points[p]; 1567 1568 ierr = DMLabelGetValue(depth, point, &dep);CHKERRQ(ierr); 1569 if (dep != dim-1) continue; 1570 if (mesh->printFEM > 1) {ierr = DMPrintCellVector(point, "BdResidual", totDimBd, &elemVec[f*totDimBd]);CHKERRQ(ierr);} 1571 ierr = DMPlexVecSetClosure(dm, NULL, locF, point, &elemVec[f*totDimBd], ADD_VALUES);CHKERRQ(ierr); 1572 ++f; 1573 } 1574 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 1575 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 1576 ierr = PetscFree3(u,cgeom,elemVec);CHKERRQ(ierr); 1577 if (locX_t) {ierr = PetscFree(u_t);CHKERRQ(ierr);} 1578 } 1579 PetscFunctionReturn(0); 1580 } 1581 1582 #undef __FUNCT__ 1583 #define __FUNCT__ "DMPlexReconstructGradientsFVM" 1584 /*@ 1585 DMPlexReconstructGradientsFVM - reconstruct the gradient of a vector using a finite volume method. 1586 1587 Input Parameters: 1588 + dm - the mesh 1589 - locX - the local representation of the vector 1590 1591 Output Parameter: 1592 . grad - the global representation of the gradient 1593 1594 Level: developer 1595 1596 .seealso: DMPlexSNESGetGradientDM() 1597 @*/ 1598 PetscErrorCode DMPlexReconstructGradientsFVM(DM dm, Vec locX, Vec grad) 1599 { 1600 PetscDS prob; 1601 PetscInt Nf, f, fStart, fEnd; 1602 PetscBool useFVM; 1603 PetscFV fvm = NULL; 1604 Vec faceGeometryFVM, cellGeometryFVM; 1605 PetscFVCellGeom *cgeomFVM = NULL; 1606 PetscFVFaceGeom *fgeomFVM = NULL; 1607 DM dmGrad = NULL; 1608 PetscErrorCode ierr; 1609 1610 PetscFunctionBegin; 1611 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1612 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 1613 for (f = 0; f < Nf; ++f) { 1614 PetscObject obj; 1615 PetscClassId id; 1616 1617 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1618 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1619 if (id == PETSCFV_CLASSID) {useFVM = PETSC_TRUE; fvm = (PetscFV) obj;} 1620 } 1621 if (!useFVM) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"This dm does not have a finite volume discretization"); 1622 ierr = DMPlexSNESGetGradientDM(dm, fvm, &dmGrad);CHKERRQ(ierr); 1623 if (!dmGrad) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"This dm's finite volume discretization does not reconstruct gradients"); 1624 ierr = DMPlexSNESGetGeometryFVM(dm, &faceGeometryFVM, &cellGeometryFVM, NULL);CHKERRQ(ierr); 1625 ierr = VecGetArrayRead(faceGeometryFVM, (const PetscScalar **) &fgeomFVM);CHKERRQ(ierr); 1626 ierr = VecGetArrayRead(cellGeometryFVM, (const PetscScalar **) &cgeomFVM);CHKERRQ(ierr); 1627 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 1628 ierr = DMPlexReconstructGradients_Internal(dm, fStart, fEnd, faceGeometryFVM, cellGeometryFVM, locX, grad);CHKERRQ(ierr); 1629 PetscFunctionReturn(0); 1630 } 1631 1632 #undef __FUNCT__ 1633 #define __FUNCT__ "DMPlexComputeResidual_Internal" 1634 PetscErrorCode DMPlexComputeResidual_Internal(DM dm, PetscInt cStart, PetscInt cEnd, PetscReal time, Vec locX, Vec locX_t, Vec locF, void *user) 1635 { 1636 DM_Plex *mesh = (DM_Plex *) dm->data; 1637 const char *name = "Residual"; 1638 DM dmAux = NULL; 1639 DM dmGrad = NULL; 1640 DMLabel ghostLabel = NULL; 1641 PetscDS prob = NULL; 1642 PetscDS probAux = NULL; 1643 PetscSection section = NULL; 1644 PetscBool useFEM = PETSC_FALSE; 1645 PetscBool useFVM = PETSC_FALSE; 1646 PetscBool isImplicit = (locX_t || time == PETSC_MIN_REAL) ? PETSC_TRUE : PETSC_FALSE; 1647 PetscFV fvm = NULL; 1648 PetscFECellGeom *cgeomFEM = NULL; 1649 PetscScalar *cgeomScal; 1650 PetscFVCellGeom *cgeomFVM = NULL; 1651 PetscFVFaceGeom *fgeomFVM = NULL; 1652 Vec locA, cellGeometryFEM = NULL, cellGeometryFVM = NULL, faceGeometryFVM = NULL, grad, locGrad = NULL; 1653 PetscScalar *u, *u_t, *a, *uL, *uR; 1654 PetscInt Nf, f, totDim, totDimAux, numChunks, cellChunkSize, faceChunkSize, chunk, fStart, fEnd; 1655 PetscErrorCode ierr; 1656 1657 PetscFunctionBegin; 1658 ierr = PetscLogEventBegin(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr); 1659 /* TODO The places where we have to use isFE are probably the member functions for the PetscDisc class */ 1660 /* TODO The FVM geometry is over-manipulated. Make the precalc functions return exactly what we need */ 1661 /* FEM+FVM */ 1662 /* 1: Get sizes from dm and dmAux */ 1663 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 1664 ierr = DMPlexGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 1665 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1666 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 1667 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1668 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);CHKERRQ(ierr); 1669 if (locA) { 1670 ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); 1671 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 1672 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 1673 } 1674 /* 2: Get geometric data */ 1675 for (f = 0; f < Nf; ++f) { 1676 PetscObject obj; 1677 PetscClassId id; 1678 PetscBool fimp; 1679 1680 ierr = PetscDSGetImplicit(prob, f, &fimp);CHKERRQ(ierr); 1681 if (isImplicit != fimp) continue; 1682 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1683 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1684 if (id == PETSCFE_CLASSID) {useFEM = PETSC_TRUE;} 1685 if (id == PETSCFV_CLASSID) {useFVM = PETSC_TRUE; fvm = (PetscFV) obj;} 1686 } 1687 if (useFEM) { 1688 ierr = DMPlexSNESGetGeometryFEM(dm, &cellGeometryFEM);CHKERRQ(ierr); 1689 ierr = VecGetArray(cellGeometryFEM, &cgeomScal);CHKERRQ(ierr); 1690 if (sizeof(PetscFECellGeom) % sizeof(PetscScalar)) { 1691 DM dmCell; 1692 PetscInt c; 1693 1694 ierr = VecGetDM(cellGeometryFEM,&dmCell);CHKERRQ(ierr); 1695 ierr = PetscMalloc1(cEnd-cStart,&cgeomFEM);CHKERRQ(ierr); 1696 for (c = 0; c < cEnd - cStart; c++) { 1697 PetscScalar *thisgeom; 1698 1699 ierr = DMPlexPointLocalRef(dmCell, c + cStart, cgeomScal, &thisgeom);CHKERRQ(ierr); 1700 cgeomFEM[c] = *((PetscFECellGeom *) thisgeom); 1701 } 1702 } 1703 else { 1704 cgeomFEM = (PetscFECellGeom *) cgeomScal; 1705 } 1706 } 1707 if (useFVM) { 1708 ierr = DMPlexSNESGetGeometryFVM(dm, &faceGeometryFVM, &cellGeometryFVM, NULL);CHKERRQ(ierr); 1709 ierr = VecGetArrayRead(faceGeometryFVM, (const PetscScalar **) &fgeomFVM);CHKERRQ(ierr); 1710 ierr = VecGetArrayRead(cellGeometryFVM, (const PetscScalar **) &cgeomFVM);CHKERRQ(ierr); 1711 /* Reconstruct and limit cell gradients */ 1712 ierr = DMPlexSNESGetGradientDM(dm, fvm, &dmGrad);CHKERRQ(ierr); 1713 if (dmGrad) { 1714 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 1715 ierr = DMGetGlobalVector(dmGrad, &grad);CHKERRQ(ierr); 1716 ierr = DMPlexReconstructGradients_Internal(dm, fStart, fEnd, faceGeometryFVM, cellGeometryFVM, locX, grad);CHKERRQ(ierr); 1717 /* Communicate gradient values */ 1718 ierr = DMGetLocalVector(dmGrad, &locGrad);CHKERRQ(ierr); 1719 ierr = DMGlobalToLocalBegin(dmGrad, grad, INSERT_VALUES, locGrad);CHKERRQ(ierr); 1720 ierr = DMGlobalToLocalEnd(dmGrad, grad, INSERT_VALUES, locGrad);CHKERRQ(ierr); 1721 ierr = DMRestoreGlobalVector(dmGrad, &grad);CHKERRQ(ierr); 1722 } 1723 } 1724 /* Handle boundary values */ 1725 ierr = DMPlexInsertBoundaryValues(dm, locX, time, faceGeometryFVM, cellGeometryFVM, locGrad);CHKERRQ(ierr); 1726 /* Loop over chunks */ 1727 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 1728 numChunks = 1; 1729 cellChunkSize = (cEnd - cStart)/numChunks; 1730 faceChunkSize = (fEnd - fStart)/numChunks; 1731 for (chunk = 0; chunk < numChunks; ++chunk) { 1732 PetscScalar *elemVec, *fluxL, *fluxR; 1733 PetscReal *vol; 1734 PetscFVFaceGeom *fgeom; 1735 PetscInt cS = cStart+chunk*cellChunkSize, cE = PetscMin(cS+cellChunkSize, cEnd), numCells = cE - cS, cell; 1736 PetscInt fS = fStart+chunk*faceChunkSize, fE = PetscMin(fS+faceChunkSize, fEnd), numFaces = fE - fS, face; 1737 1738 /* Extract field coefficients */ 1739 if (useFEM) { 1740 ierr = DMPlexGetCellFields(dm, cS, cE, locX, locX_t, locA, &u, &u_t, &a);CHKERRQ(ierr); 1741 ierr = DMGetWorkArray(dm, numCells*totDim, PETSC_SCALAR, &elemVec);CHKERRQ(ierr); 1742 ierr = PetscMemzero(elemVec, numCells*totDim * sizeof(PetscScalar));CHKERRQ(ierr); 1743 } 1744 if (useFVM) { 1745 ierr = DMPlexGetFaceFields(dm, fS, fE, locX, locX_t, faceGeometryFVM, cellGeometryFVM, locGrad, &uL, &uR);CHKERRQ(ierr); 1746 ierr = DMPlexGetFaceGeometry(dm, fS, fE, faceGeometryFVM, cellGeometryFVM, &fgeom, &vol);CHKERRQ(ierr); 1747 ierr = DMGetWorkArray(dm, numFaces*totDim, PETSC_SCALAR, &fluxL);CHKERRQ(ierr); 1748 ierr = DMGetWorkArray(dm, numFaces*totDim, PETSC_SCALAR, &fluxR);CHKERRQ(ierr); 1749 ierr = PetscMemzero(fluxL, numFaces*totDim * sizeof(PetscScalar));CHKERRQ(ierr); 1750 ierr = PetscMemzero(fluxR, numFaces*totDim * sizeof(PetscScalar));CHKERRQ(ierr); 1751 } 1752 /* TODO We will interlace both our field coefficients (u, u_t, uL, uR, etc.) and our output (elemVec, fL, fR). I think this works */ 1753 /* Loop over fields */ 1754 for (f = 0; f < Nf; ++f) { 1755 PetscObject obj; 1756 PetscClassId id; 1757 PetscBool fimp; 1758 PetscInt numChunks, numBatches, batchSize, numBlocks, blockSize, Ne, Nr, offset; 1759 1760 ierr = PetscDSGetImplicit(prob, f, &fimp);CHKERRQ(ierr); 1761 if (isImplicit != fimp) continue; 1762 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1763 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1764 if (id == PETSCFE_CLASSID) { 1765 PetscFE fe = (PetscFE) obj; 1766 PetscQuadrature q; 1767 PetscInt Nq, Nb; 1768 1769 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1770 1771 ierr = PetscFEGetQuadrature(fe, &q);CHKERRQ(ierr); 1772 ierr = PetscQuadratureGetData(q, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 1773 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 1774 blockSize = Nb*Nq; 1775 batchSize = numBlocks * blockSize; 1776 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1777 numChunks = numCells / (numBatches*batchSize); 1778 Ne = numChunks*numBatches*batchSize; 1779 Nr = numCells % (numBatches*batchSize); 1780 offset = numCells - Nr; 1781 /* Integrate FE residual to get elemVec (need fields at quadrature points) */ 1782 /* 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) */ 1783 ierr = PetscFEIntegrateResidual(fe, prob, f, Ne, cgeomFEM, u, u_t, probAux, a, elemVec);CHKERRQ(ierr); 1784 ierr = PetscFEIntegrateResidual(fe, prob, f, Nr, &cgeomFEM[offset], &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], &elemVec[offset*totDim]);CHKERRQ(ierr); 1785 } else if (id == PETSCFV_CLASSID) { 1786 PetscFV fv = (PetscFV) obj; 1787 1788 Ne = numFaces; 1789 Nr = 0; 1790 /* Riemann solve over faces (need fields at face centroids) */ 1791 /* We need to evaluate FE fields at those coordinates */ 1792 ierr = PetscFVIntegrateRHSFunction(fv, prob, f, Ne, fgeom, vol, uL, uR, fluxL, fluxR);CHKERRQ(ierr); 1793 } else SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %d", f); 1794 } 1795 if (sizeof(PetscFECellGeom) % sizeof(PetscScalar)) { 1796 ierr = PetscFree(cgeomFEM);CHKERRQ(ierr); 1797 } 1798 else { 1799 cgeomFEM = NULL; 1800 } 1801 if (cellGeometryFEM) {ierr = VecRestoreArray(cellGeometryFEM, &cgeomScal);CHKERRQ(ierr);} 1802 /* Loop over domain */ 1803 if (useFEM) { 1804 /* Add elemVec to locX */ 1805 for (cell = cS; cell < cE; ++cell) { 1806 if (mesh->printFEM > 1) {ierr = DMPrintCellVector(cell, name, totDim, &elemVec[cell*totDim]);CHKERRQ(ierr);} 1807 ierr = DMPlexVecSetClosure(dm, section, locF, cell, &elemVec[cell*totDim], ADD_VALUES);CHKERRQ(ierr); 1808 } 1809 } 1810 if (useFVM) { 1811 PetscScalar *fa; 1812 PetscInt iface; 1813 1814 ierr = VecGetArray(locF, &fa);CHKERRQ(ierr); 1815 for (f = 0; f < Nf; ++f) { 1816 PetscFV fv; 1817 PetscObject obj; 1818 PetscClassId id; 1819 PetscInt foff, pdim; 1820 1821 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1822 ierr = PetscDSGetFieldOffset(prob, f, &foff);CHKERRQ(ierr); 1823 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1824 if (id != PETSCFV_CLASSID) continue; 1825 fv = (PetscFV) obj; 1826 ierr = PetscFVGetNumComponents(fv, &pdim);CHKERRQ(ierr); 1827 /* Accumulate fluxes to cells */ 1828 for (face = fS, iface = 0; face < fE; ++face) { 1829 const PetscInt *cells; 1830 PetscScalar *fL, *fR; 1831 PetscInt ghost, d, nsupp; 1832 1833 ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr); 1834 ierr = DMPlexGetSupportSize(dm, face, &nsupp);CHKERRQ(ierr); 1835 if (ghost >= 0 || nsupp > 2) continue; 1836 ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr); 1837 ierr = DMPlexPointGlobalFieldRef(dm, cells[0], f, fa, &fL);CHKERRQ(ierr); 1838 ierr = DMPlexPointGlobalFieldRef(dm, cells[1], f, fa, &fR);CHKERRQ(ierr); 1839 for (d = 0; d < pdim; ++d) { 1840 if (fL) fL[d] -= fluxL[iface*totDim+foff+d]; 1841 if (fR) fR[d] += fluxR[iface*totDim+foff+d]; 1842 } 1843 ++iface; 1844 } 1845 } 1846 ierr = VecRestoreArray(locF, &fa);CHKERRQ(ierr); 1847 } 1848 /* Handle time derivative */ 1849 if (locX_t) { 1850 PetscScalar *x_t, *fa; 1851 1852 ierr = VecGetArray(locF, &fa);CHKERRQ(ierr); 1853 ierr = VecGetArray(locX_t, &x_t);CHKERRQ(ierr); 1854 for (f = 0; f < Nf; ++f) { 1855 PetscFV fv; 1856 PetscObject obj; 1857 PetscClassId id; 1858 PetscInt pdim, d; 1859 1860 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1861 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1862 if (id != PETSCFV_CLASSID) continue; 1863 fv = (PetscFV) obj; 1864 ierr = PetscFVGetNumComponents(fv, &pdim);CHKERRQ(ierr); 1865 for (cell = cS; cell < cE; ++cell) { 1866 PetscScalar *u_t, *r; 1867 1868 ierr = DMPlexPointLocalFieldRead(dm, cell, f, x_t, &u_t);CHKERRQ(ierr); 1869 ierr = DMPlexPointLocalFieldRef(dm, cell, f, fa, &r);CHKERRQ(ierr); 1870 for (d = 0; d < pdim; ++d) r[d] += u_t[d]; 1871 } 1872 } 1873 ierr = VecRestoreArray(locX_t, &x_t);CHKERRQ(ierr); 1874 ierr = VecRestoreArray(locF, &fa);CHKERRQ(ierr); 1875 } 1876 if (useFEM) { 1877 ierr = DMPlexRestoreCellFields(dm, cS, cE, locX, locX_t, locA, &u, &u_t, &a);CHKERRQ(ierr); 1878 ierr = DMRestoreWorkArray(dm, numCells*totDim, PETSC_SCALAR, &elemVec);CHKERRQ(ierr); 1879 } 1880 if (useFVM) { 1881 ierr = DMPlexRestoreFaceFields(dm, fS, fE, locX, locX_t, faceGeometryFVM, cellGeometryFVM, locGrad, &uL, &uR);CHKERRQ(ierr); 1882 ierr = DMPlexRestoreFaceGeometry(dm, fS, fE, faceGeometryFVM, cellGeometryFVM, &fgeom, &vol);CHKERRQ(ierr); 1883 ierr = DMRestoreWorkArray(dm, numFaces*totDim, PETSC_SCALAR, &fluxL);CHKERRQ(ierr); 1884 ierr = DMRestoreWorkArray(dm, numFaces*totDim, PETSC_SCALAR, &fluxR);CHKERRQ(ierr); 1885 if (dmGrad) {ierr = DMRestoreLocalVector(dmGrad, &locGrad);CHKERRQ(ierr);} 1886 } 1887 } 1888 1889 if (useFEM) {ierr = DMPlexComputeBdResidual_Internal(dm, locX, locX_t, locF, user);CHKERRQ(ierr);} 1890 1891 /* FEM */ 1892 /* 1: Get sizes from dm and dmAux */ 1893 /* 2: Get geometric data */ 1894 /* 3: Handle boundary values */ 1895 /* 4: Loop over domain */ 1896 /* Extract coefficients */ 1897 /* Loop over fields */ 1898 /* Set tiling for FE*/ 1899 /* Integrate FE residual to get elemVec */ 1900 /* Loop over subdomain */ 1901 /* Loop over quad points */ 1902 /* Transform coords to real space */ 1903 /* Evaluate field and aux fields at point */ 1904 /* Evaluate residual at point */ 1905 /* Transform residual to real space */ 1906 /* Add residual to elemVec */ 1907 /* Loop over domain */ 1908 /* Add elemVec to locX */ 1909 1910 /* FVM */ 1911 /* Get geometric data */ 1912 /* If using gradients */ 1913 /* Compute gradient data */ 1914 /* Loop over domain faces */ 1915 /* Count computational faces */ 1916 /* Reconstruct cell gradient */ 1917 /* Loop over domain cells */ 1918 /* Limit cell gradients */ 1919 /* Handle boundary values */ 1920 /* Loop over domain faces */ 1921 /* Read out field, centroid, normal, volume for each side of face */ 1922 /* Riemann solve over faces */ 1923 /* Loop over domain faces */ 1924 /* Accumulate fluxes to cells */ 1925 /* TODO Change printFEM to printDisc here */ 1926 if (mesh->printFEM) {ierr = DMPrintLocalVec(dm, name, mesh->printTol, locF);CHKERRQ(ierr);} 1927 ierr = PetscLogEventEnd(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr); 1928 PetscFunctionReturn(0); 1929 } 1930 1931 #undef __FUNCT__ 1932 #define __FUNCT__ "DMPlexComputeResidualFEM_Check_Internal" 1933 static PetscErrorCode DMPlexComputeResidualFEM_Check_Internal(DM dm, Vec X, Vec X_t, Vec F, void *user) 1934 { 1935 DM dmCh, dmAux; 1936 Vec A, cellgeom; 1937 PetscDS prob, probCh, probAux = NULL; 1938 PetscQuadrature q; 1939 PetscSection section, sectionAux; 1940 PetscFECellGeom *cgeom = NULL; 1941 PetscScalar *cgeomScal; 1942 PetscScalar *elemVec, *elemVecCh, *u, *u_t, *a = NULL; 1943 PetscInt dim, Nf, f, numCells, cStart, cEnd, c; 1944 PetscInt totDim, totDimAux, diffCell = 0; 1945 PetscErrorCode ierr; 1946 1947 PetscFunctionBegin; 1948 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1949 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 1950 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1951 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1952 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); 1953 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1954 numCells = cEnd - cStart; 1955 ierr = PetscObjectQuery((PetscObject) dm, "dmCh", (PetscObject *) &dmCh);CHKERRQ(ierr); 1956 ierr = DMGetDS(dmCh, &probCh);CHKERRQ(ierr); 1957 ierr = PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);CHKERRQ(ierr); 1958 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);CHKERRQ(ierr); 1959 if (dmAux) { 1960 ierr = DMGetDefaultSection(dmAux, §ionAux);CHKERRQ(ierr); 1961 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 1962 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 1963 } 1964 ierr = DMPlexInsertBoundaryValues(dm, X, 0.0, NULL, NULL, NULL);CHKERRQ(ierr); 1965 ierr = VecSet(F, 0.0);CHKERRQ(ierr); 1966 ierr = PetscMalloc3(numCells*totDim,&u,X_t ? numCells*totDim : 0,&u_t,numCells*totDim,&elemVec);CHKERRQ(ierr); 1967 ierr = PetscMalloc1(numCells*totDim,&elemVecCh);CHKERRQ(ierr); 1968 if (dmAux) {ierr = PetscMalloc1(numCells*totDimAux, &a);CHKERRQ(ierr);} 1969 ierr = DMPlexSNESGetGeometryFEM(dm, &cellgeom);CHKERRQ(ierr); 1970 ierr = VecGetArray(cellgeom, &cgeomScal);CHKERRQ(ierr); 1971 if (sizeof(PetscFECellGeom) % sizeof(PetscScalar)) { 1972 DM dmCell; 1973 1974 ierr = VecGetDM(cellgeom,&dmCell);CHKERRQ(ierr); 1975 ierr = PetscMalloc1(cEnd-cStart,&cgeom);CHKERRQ(ierr); 1976 for (c = 0; c < cEnd - cStart; c++) { 1977 PetscScalar *thisgeom; 1978 1979 ierr = DMPlexPointLocalRef(dmCell, c + cStart, cgeomScal, &thisgeom);CHKERRQ(ierr); 1980 cgeom[c] = *((PetscFECellGeom *) thisgeom); 1981 } 1982 } 1983 else { 1984 cgeom = (PetscFECellGeom *) cgeomScal; 1985 } 1986 for (c = cStart; c < cEnd; ++c) { 1987 PetscScalar *x = NULL, *x_t = NULL; 1988 PetscInt i; 1989 1990 ierr = DMPlexVecGetClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr); 1991 for (i = 0; i < totDim; ++i) u[c*totDim+i] = x[i]; 1992 ierr = DMPlexVecRestoreClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr); 1993 if (X_t) { 1994 ierr = DMPlexVecGetClosure(dm, section, X_t, c, NULL, &x_t);CHKERRQ(ierr); 1995 for (i = 0; i < totDim; ++i) u_t[c*totDim+i] = x_t[i]; 1996 ierr = DMPlexVecRestoreClosure(dm, section, X_t, c, NULL, &x_t);CHKERRQ(ierr); 1997 } 1998 if (dmAux) { 1999 ierr = DMPlexVecGetClosure(dmAux, sectionAux, A, c, NULL, &x);CHKERRQ(ierr); 2000 for (i = 0; i < totDimAux; ++i) a[c*totDimAux+i] = x[i]; 2001 ierr = DMPlexVecRestoreClosure(dmAux, sectionAux, A, c, NULL, &x);CHKERRQ(ierr); 2002 } 2003 } 2004 for (f = 0; f < Nf; ++f) { 2005 PetscFE fe, feCh; 2006 PetscInt numQuadPoints, Nb; 2007 /* Conforming batches */ 2008 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 2009 /* Remainder */ 2010 PetscInt Nr, offset; 2011 2012 ierr = PetscDSGetDiscretization(prob, f, (PetscObject *) &fe);CHKERRQ(ierr); 2013 ierr = PetscDSGetDiscretization(probCh, f, (PetscObject *) &feCh);CHKERRQ(ierr); 2014 ierr = PetscFEGetQuadrature(fe, &q);CHKERRQ(ierr); 2015 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 2016 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 2017 ierr = PetscQuadratureGetData(q, NULL, &numQuadPoints, NULL, NULL);CHKERRQ(ierr); 2018 blockSize = Nb*numQuadPoints; 2019 batchSize = numBlocks * blockSize; 2020 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 2021 numChunks = numCells / (numBatches*batchSize); 2022 Ne = numChunks*numBatches*batchSize; 2023 Nr = numCells % (numBatches*batchSize); 2024 offset = numCells - Nr; 2025 ierr = PetscFEIntegrateResidual(fe, prob, f, Ne, cgeom, u, u_t, probAux, a, elemVec);CHKERRQ(ierr); 2026 ierr = PetscFEIntegrateResidual(feCh, prob, f, Ne, cgeom, u, u_t, probAux, a, elemVecCh);CHKERRQ(ierr); 2027 ierr = PetscFEIntegrateResidual(fe, prob, f, Nr, &cgeom[offset], &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], &elemVec[offset*totDim]);CHKERRQ(ierr); 2028 ierr = PetscFEIntegrateResidual(feCh, prob, f, Nr, &cgeom[offset], &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], &elemVecCh[offset*totDim]);CHKERRQ(ierr); 2029 } 2030 for (c = cStart; c < cEnd; ++c) { 2031 PetscBool diff = PETSC_FALSE; 2032 PetscInt d; 2033 2034 for (d = 0; d < totDim; ++d) if (PetscAbsScalar(elemVec[c*totDim+d] - elemVecCh[c*totDim+d]) > 1.0e-7) {diff = PETSC_TRUE;break;} 2035 if (diff) { 2036 ierr = PetscPrintf(PetscObjectComm((PetscObject) dm), "Different cell %d\n", c);CHKERRQ(ierr); 2037 ierr = DMPrintCellVector(c, "Residual", totDim, &elemVec[c*totDim]);CHKERRQ(ierr); 2038 ierr = DMPrintCellVector(c, "Check Residual", totDim, &elemVecCh[c*totDim]);CHKERRQ(ierr); 2039 ++diffCell; 2040 } 2041 if (diffCell > 9) break; 2042 ierr = DMPlexVecSetClosure(dm, section, F, c, &elemVec[c*totDim], ADD_VALUES);CHKERRQ(ierr); 2043 } 2044 if (sizeof(PetscFECellGeom) % sizeof(PetscScalar)) { 2045 ierr = PetscFree(cgeom);CHKERRQ(ierr); 2046 } 2047 else { 2048 cgeom = NULL; 2049 } 2050 ierr = VecRestoreArray(cellgeom, &cgeomScal);CHKERRQ(ierr); 2051 ierr = PetscFree3(u,u_t,elemVec);CHKERRQ(ierr); 2052 ierr = PetscFree(elemVecCh);CHKERRQ(ierr); 2053 if (dmAux) {ierr = PetscFree(a);CHKERRQ(ierr);} 2054 PetscFunctionReturn(0); 2055 } 2056 2057 #undef __FUNCT__ 2058 #define __FUNCT__ "DMPlexSNESComputeResidualFEM" 2059 /*@ 2060 DMPlexSNESComputeResidualFEM - Form the local residual F from the local input X using pointwise functions specified by the user 2061 2062 Input Parameters: 2063 + dm - The mesh 2064 . X - Local solution 2065 - user - The user context 2066 2067 Output Parameter: 2068 . F - Local output vector 2069 2070 Level: developer 2071 2072 .seealso: DMPlexComputeJacobianActionFEM() 2073 @*/ 2074 PetscErrorCode DMPlexSNESComputeResidualFEM(DM dm, Vec X, Vec F, void *user) 2075 { 2076 PetscObject check; 2077 PetscInt cStart, cEnd, cEndInterior; 2078 PetscErrorCode ierr; 2079 2080 PetscFunctionBegin; 2081 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 2082 ierr = DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr); 2083 cEnd = cEndInterior < 0 ? cEnd : cEndInterior; 2084 /* The dmCh is used to check two mathematically equivalent discretizations for computational equivalence */ 2085 ierr = PetscObjectQuery((PetscObject) dm, "dmCh", &check);CHKERRQ(ierr); 2086 if (check) {ierr = DMPlexComputeResidualFEM_Check_Internal(dm, X, NULL, F, user);CHKERRQ(ierr);} 2087 else {ierr = DMPlexComputeResidual_Internal(dm, cStart, cEnd, PETSC_MIN_REAL, X, NULL, F, user);CHKERRQ(ierr);} 2088 PetscFunctionReturn(0); 2089 } 2090 2091 #undef __FUNCT__ 2092 #define __FUNCT__ "DMPlexComputeJacobian_Internal" 2093 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) 2094 { 2095 DM_Plex *mesh = (DM_Plex *) dm->data; 2096 const char *name = "Jacobian"; 2097 DM dmAux; 2098 DMLabel depth; 2099 Vec A, cellgeom; 2100 PetscDS prob, probAux = NULL; 2101 PetscQuadrature quad; 2102 PetscSection section, globalSection, sectionAux; 2103 PetscFECellGeom *cgeom = NULL; 2104 PetscScalar *cgeomScal; 2105 PetscScalar *elemMat, *elemMatP, *u, *u_t, *a = NULL; 2106 PetscInt dim, Nf, f, fieldI, fieldJ, numCells, c; 2107 PetscInt totDim, totDimBd, totDimAux, numBd, bd; 2108 PetscBool isShell, hasPrec; 2109 PetscErrorCode ierr; 2110 2111 PetscFunctionBegin; 2112 ierr = PetscLogEventBegin(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 2113 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 2114 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 2115 ierr = DMGetDefaultGlobalSection(dm, &globalSection);CHKERRQ(ierr); 2116 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 2117 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 2118 ierr = PetscDSGetTotalBdDimension(prob, &totDimBd);CHKERRQ(ierr); 2119 ierr = PetscDSHasJacobianPreconditioner(prob, &hasPrec);CHKERRQ(ierr); 2120 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); 2121 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 2122 numCells = cEnd - cStart; 2123 ierr = PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);CHKERRQ(ierr); 2124 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);CHKERRQ(ierr); 2125 if (dmAux) { 2126 ierr = DMGetDefaultSection(dmAux, §ionAux);CHKERRQ(ierr); 2127 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 2128 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 2129 } 2130 ierr = DMPlexInsertBoundaryValues(dm, X, 0.0, NULL, NULL, NULL);CHKERRQ(ierr); 2131 ierr = MatZeroEntries(JacP);CHKERRQ(ierr); 2132 ierr = PetscMalloc4(numCells*totDim,&u,X_t ? numCells*totDim : 0,&u_t,numCells*totDim*totDim,&elemMat,hasPrec ? numCells*totDim*totDim : 0, &elemMatP);CHKERRQ(ierr); 2133 if (dmAux) {ierr = PetscMalloc1(numCells*totDimAux, &a);CHKERRQ(ierr);} 2134 ierr = DMPlexSNESGetGeometryFEM(dm, &cellgeom);CHKERRQ(ierr); 2135 ierr = VecGetArray(cellgeom, &cgeomScal);CHKERRQ(ierr); 2136 if (sizeof(PetscFECellGeom) % sizeof(PetscScalar)) { 2137 DM dmCell; 2138 2139 ierr = VecGetDM(cellgeom,&dmCell);CHKERRQ(ierr); 2140 ierr = PetscMalloc1(cEnd-cStart,&cgeom);CHKERRQ(ierr); 2141 for (c = 0; c < cEnd - cStart; c++) { 2142 PetscScalar *thisgeom; 2143 2144 ierr = DMPlexPointLocalRef(dmCell, c + cStart, cgeomScal, &thisgeom);CHKERRQ(ierr); 2145 cgeom[c] = *((PetscFECellGeom *) thisgeom); 2146 } 2147 } 2148 else { 2149 cgeom = (PetscFECellGeom *) cgeomScal; 2150 } 2151 for (c = cStart; c < cEnd; ++c) { 2152 PetscScalar *x = NULL, *x_t = NULL; 2153 PetscInt i; 2154 2155 ierr = DMPlexVecGetClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr); 2156 for (i = 0; i < totDim; ++i) u[(c-cStart)*totDim+i] = x[i]; 2157 ierr = DMPlexVecRestoreClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr); 2158 if (X_t) { 2159 ierr = DMPlexVecGetClosure(dm, section, X_t, c, NULL, &x_t);CHKERRQ(ierr); 2160 for (i = 0; i < totDim; ++i) u_t[(c-cStart)*totDim+i] = x_t[i]; 2161 ierr = DMPlexVecRestoreClosure(dm, section, X_t, c, NULL, &x_t);CHKERRQ(ierr); 2162 } 2163 if (dmAux) { 2164 ierr = DMPlexVecGetClosure(dmAux, sectionAux, A, c, NULL, &x);CHKERRQ(ierr); 2165 for (i = 0; i < totDimAux; ++i) a[(c-cStart)*totDimAux+i] = x[i]; 2166 ierr = DMPlexVecRestoreClosure(dmAux, sectionAux, A, c, NULL, &x);CHKERRQ(ierr); 2167 } 2168 } 2169 ierr = PetscMemzero(elemMat, numCells*totDim*totDim * sizeof(PetscScalar));CHKERRQ(ierr); 2170 if (hasPrec) {ierr = PetscMemzero(elemMatP, numCells*totDim*totDim * sizeof(PetscScalar));CHKERRQ(ierr);} 2171 for (fieldI = 0; fieldI < Nf; ++fieldI) { 2172 PetscFE fe; 2173 PetscInt numQuadPoints, Nb; 2174 /* Conforming batches */ 2175 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 2176 /* Remainder */ 2177 PetscInt Nr, offset; 2178 2179 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); 2180 ierr = PetscFEGetQuadrature(fe, &quad);CHKERRQ(ierr); 2181 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 2182 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 2183 ierr = PetscQuadratureGetData(quad, NULL, &numQuadPoints, NULL, NULL);CHKERRQ(ierr); 2184 blockSize = Nb*numQuadPoints; 2185 batchSize = numBlocks * blockSize; 2186 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 2187 numChunks = numCells / (numBatches*batchSize); 2188 Ne = numChunks*numBatches*batchSize; 2189 Nr = numCells % (numBatches*batchSize); 2190 offset = numCells - Nr; 2191 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 2192 ierr = PetscFEIntegrateJacobian(fe, prob, PETSC_FALSE, fieldI, fieldJ, Ne, cgeom, u, u_t, probAux, a, elemMat);CHKERRQ(ierr); 2193 ierr = PetscFEIntegrateJacobian(fe, prob, PETSC_FALSE, fieldI, fieldJ, Nr, &cgeom[offset], &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], &elemMat[offset*totDim*totDim]);CHKERRQ(ierr); 2194 if (hasPrec) { 2195 ierr = PetscFEIntegrateJacobian(fe, prob, PETSC_TRUE, fieldI, fieldJ, Ne, cgeom, u, u_t, probAux, a, elemMatP);CHKERRQ(ierr); 2196 ierr = PetscFEIntegrateJacobian(fe, prob, PETSC_TRUE, fieldI, fieldJ, Nr, &cgeom[offset], &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], &elemMatP[offset*totDim*totDim]);CHKERRQ(ierr); 2197 } 2198 } 2199 } 2200 for (c = cStart; c < cEnd; ++c) { 2201 if (hasPrec) { 2202 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(c, name, totDim, totDim, &elemMat[(c-cStart)*totDim*totDim]);CHKERRQ(ierr);} 2203 ierr = DMPlexMatSetClosure(dm, section, globalSection, Jac, c, &elemMat[(c-cStart)*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2204 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(c, name, totDim, totDim, &elemMatP[(c-cStart)*totDim*totDim]);CHKERRQ(ierr);} 2205 ierr = DMPlexMatSetClosure(dm, section, globalSection, JacP, c, &elemMatP[(c-cStart)*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2206 } else { 2207 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(c, name, totDim, totDim, &elemMat[(c-cStart)*totDim*totDim]);CHKERRQ(ierr);} 2208 ierr = DMPlexMatSetClosure(dm, section, globalSection, JacP, c, &elemMat[(c-cStart)*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2209 } 2210 } 2211 if (sizeof(PetscFECellGeom) % sizeof(PetscScalar)) { 2212 ierr = PetscFree(cgeom);CHKERRQ(ierr); 2213 } 2214 else { 2215 cgeom = NULL; 2216 } 2217 ierr = VecRestoreArray(cellgeom, &cgeomScal);CHKERRQ(ierr); 2218 ierr = PetscFree4(u,u_t,elemMat,elemMatP);CHKERRQ(ierr); 2219 if (dmAux) {ierr = PetscFree(a);CHKERRQ(ierr);} 2220 ierr = DMPlexGetDepthLabel(dm, &depth);CHKERRQ(ierr); 2221 ierr = DMPlexGetNumBoundary(dm, &numBd);CHKERRQ(ierr); 2222 ierr = DMPlexGetDepthLabel(dm, &depth);CHKERRQ(ierr); 2223 ierr = DMPlexGetNumBoundary(dm, &numBd);CHKERRQ(ierr); 2224 for (bd = 0; bd < numBd; ++bd) { 2225 const char *bdLabel; 2226 DMLabel label; 2227 IS pointIS; 2228 const PetscInt *points; 2229 const PetscInt *values; 2230 PetscInt field, numValues, numPoints, p, dep, numFaces; 2231 PetscBool isEssential; 2232 2233 ierr = DMPlexGetBoundary(dm, bd, &isEssential, NULL, &bdLabel, &field, NULL, NULL, NULL, &numValues, &values, NULL);CHKERRQ(ierr); 2234 if (isEssential) continue; 2235 if (numValues != 1) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Bug me and I will fix this"); 2236 ierr = DMPlexGetLabel(dm, bdLabel, &label);CHKERRQ(ierr); 2237 ierr = DMLabelGetStratumSize(label, 1, &numPoints);CHKERRQ(ierr); 2238 ierr = DMLabelGetStratumIS(label, 1, &pointIS);CHKERRQ(ierr); 2239 ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); 2240 for (p = 0, numFaces = 0; p < numPoints; ++p) { 2241 ierr = DMLabelGetValue(depth, points[p], &dep);CHKERRQ(ierr); 2242 if (dep == dim-1) ++numFaces; 2243 } 2244 ierr = PetscMalloc3(numFaces*totDimBd,&u,numFaces,&cgeom,numFaces*totDimBd*totDimBd,&elemMat);CHKERRQ(ierr); 2245 if (X_t) {ierr = PetscMalloc1(numFaces*totDimBd,&u_t);CHKERRQ(ierr);} 2246 for (p = 0, f = 0; p < numPoints; ++p) { 2247 const PetscInt point = points[p]; 2248 PetscScalar *x = NULL; 2249 PetscInt i; 2250 2251 ierr = DMLabelGetValue(depth, points[p], &dep);CHKERRQ(ierr); 2252 if (dep != dim-1) continue; 2253 ierr = DMPlexComputeCellGeometryFEM(dm, point, NULL, cgeom[f].v0, cgeom[f].J, cgeom[f].invJ, &cgeom[f].detJ);CHKERRQ(ierr); 2254 ierr = DMPlexComputeCellGeometryFVM(dm, point, NULL, NULL, cgeom[f].n);CHKERRQ(ierr); 2255 if (cgeom[f].detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for face %d", cgeom[f].detJ, point); 2256 ierr = DMPlexVecGetClosure(dm, section, X, point, NULL, &x);CHKERRQ(ierr); 2257 for (i = 0; i < totDimBd; ++i) u[f*totDimBd+i] = x[i]; 2258 ierr = DMPlexVecRestoreClosure(dm, section, X, point, NULL, &x);CHKERRQ(ierr); 2259 if (X_t) { 2260 ierr = DMPlexVecGetClosure(dm, section, X_t, point, NULL, &x);CHKERRQ(ierr); 2261 for (i = 0; i < totDimBd; ++i) u_t[f*totDimBd+i] = x[i]; 2262 ierr = DMPlexVecRestoreClosure(dm, section, X_t, point, NULL, &x);CHKERRQ(ierr); 2263 } 2264 ++f; 2265 } 2266 ierr = PetscMemzero(elemMat, numFaces*totDimBd*totDimBd * sizeof(PetscScalar));CHKERRQ(ierr); 2267 for (fieldI = 0; fieldI < Nf; ++fieldI) { 2268 PetscFE fe; 2269 PetscInt numQuadPoints, Nb; 2270 /* Conforming batches */ 2271 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 2272 /* Remainder */ 2273 PetscInt Nr, offset; 2274 2275 ierr = PetscDSGetBdDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); 2276 ierr = PetscFEGetQuadrature(fe, &quad);CHKERRQ(ierr); 2277 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 2278 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 2279 ierr = PetscQuadratureGetData(quad, NULL, &numQuadPoints, NULL, NULL);CHKERRQ(ierr); 2280 blockSize = Nb*numQuadPoints; 2281 batchSize = numBlocks * blockSize; 2282 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 2283 numChunks = numFaces / (numBatches*batchSize); 2284 Ne = numChunks*numBatches*batchSize; 2285 Nr = numFaces % (numBatches*batchSize); 2286 offset = numFaces - Nr; 2287 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 2288 ierr = PetscFEIntegrateBdJacobian(fe, prob, fieldI, fieldJ, Ne, cgeom, u, u_t, NULL, NULL, elemMat);CHKERRQ(ierr); 2289 ierr = PetscFEIntegrateBdJacobian(fe, prob, fieldI, fieldJ, Nr, &cgeom[offset], &u[offset*totDimBd], u_t ? &u_t[offset*totDimBd] : NULL, NULL, NULL, &elemMat[offset*totDimBd*totDimBd]);CHKERRQ(ierr); 2290 } 2291 } 2292 for (p = 0, f = 0; p < numPoints; ++p) { 2293 const PetscInt point = points[p]; 2294 2295 ierr = DMLabelGetValue(depth, point, &dep);CHKERRQ(ierr); 2296 if (dep != dim-1) continue; 2297 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(point, "BdJacobian", totDimBd, totDimBd, &elemMat[f*totDimBd*totDimBd]);CHKERRQ(ierr);} 2298 ierr = DMPlexMatSetClosure(dm, section, globalSection, JacP, point, &elemMat[f*totDimBd*totDimBd], ADD_VALUES);CHKERRQ(ierr); 2299 ++f; 2300 } 2301 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 2302 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 2303 ierr = PetscFree3(u,cgeom,elemMat);CHKERRQ(ierr); 2304 if (X_t) {ierr = PetscFree(u_t);CHKERRQ(ierr);} 2305 } 2306 ierr = MatAssemblyBegin(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2307 ierr = MatAssemblyEnd(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2308 if (mesh->printFEM) { 2309 ierr = PetscPrintf(PETSC_COMM_WORLD, "%s:\n", name);CHKERRQ(ierr); 2310 ierr = MatChop(JacP, 1.0e-10);CHKERRQ(ierr); 2311 ierr = MatView(JacP, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 2312 } 2313 ierr = PetscLogEventEnd(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 2314 ierr = PetscObjectTypeCompare((PetscObject) Jac, MATSHELL, &isShell);CHKERRQ(ierr); 2315 if (isShell) { 2316 JacActionCtx *jctx; 2317 2318 ierr = MatShellGetContext(Jac, &jctx);CHKERRQ(ierr); 2319 ierr = VecCopy(X, jctx->u);CHKERRQ(ierr); 2320 } 2321 PetscFunctionReturn(0); 2322 } 2323 2324 #undef __FUNCT__ 2325 #define __FUNCT__ "DMPlexSNESComputeJacobianFEM" 2326 /*@ 2327 DMPlexSNESComputeJacobianFEM - Form the local portion of the Jacobian matrix J at the local solution X using pointwise functions specified by the user. 2328 2329 Input Parameters: 2330 + dm - The mesh 2331 . X - Local input vector 2332 - user - The user context 2333 2334 Output Parameter: 2335 . Jac - Jacobian matrix 2336 2337 Note: 2338 The first member of the user context must be an FEMContext. 2339 2340 We form the residual one batch of elements at a time. This allows us to offload work onto an accelerator, 2341 like a GPU, or vectorize on a multicore machine. 2342 2343 Level: developer 2344 2345 .seealso: FormFunctionLocal() 2346 @*/ 2347 PetscErrorCode DMPlexSNESComputeJacobianFEM(DM dm, Vec X, Mat Jac, Mat JacP,void *user) 2348 { 2349 PetscInt cStart, cEnd, cEndInterior; 2350 PetscErrorCode ierr; 2351 2352 PetscFunctionBegin; 2353 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 2354 ierr = DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr); 2355 cEnd = cEndInterior < 0 ? cEnd : cEndInterior; 2356 ierr = DMPlexComputeJacobian_Internal(dm, cStart, cEnd, 0.0, 0.0, X, NULL, Jac, JacP, user);CHKERRQ(ierr); 2357 PetscFunctionReturn(0); 2358 } 2359 2360 #undef __FUNCT__ 2361 #define __FUNCT__ "DMSNESCheckFromOptions_Internal" 2362 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) 2363 { 2364 Mat J, M; 2365 Vec r, b; 2366 MatNullSpace nullSpace; 2367 PetscReal *error, res = 0.0; 2368 PetscInt numFields; 2369 PetscErrorCode ierr; 2370 2371 PetscFunctionBegin; 2372 ierr = VecDuplicate(u, &r);CHKERRQ(ierr); 2373 ierr = DMCreateMatrix(dm, &J);CHKERRQ(ierr); 2374 M = J; 2375 /* TODO Null space for J */ 2376 /* Check discretization error */ 2377 ierr = DMGetNumFields(dm, &numFields);CHKERRQ(ierr); 2378 ierr = PetscMalloc1(PetscMax(1, numFields), &error);CHKERRQ(ierr); 2379 if (numFields > 1) { 2380 PetscInt f; 2381 2382 ierr = DMPlexComputeL2FieldDiff(dm, 0.0, exactFuncs, ctxs, u, error);CHKERRQ(ierr); 2383 ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: [");CHKERRQ(ierr); 2384 for (f = 0; f < numFields; ++f) { 2385 if (f) {ierr = PetscPrintf(PETSC_COMM_WORLD, ", ");CHKERRQ(ierr);} 2386 if (error[f] >= 1.0e-11) {ierr = PetscPrintf(PETSC_COMM_WORLD, "%g", error[f]);CHKERRQ(ierr);} 2387 else {ierr = PetscPrintf(PETSC_COMM_WORLD, "< 1.0e-11");CHKERRQ(ierr);} 2388 } 2389 ierr = PetscPrintf(PETSC_COMM_WORLD, "]\n");CHKERRQ(ierr); 2390 } else { 2391 ierr = DMPlexComputeL2Diff(dm, 0.0, exactFuncs, ctxs, u, &error[0]);CHKERRQ(ierr); 2392 if (error[0] >= 1.0e-11) {ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: %g\n", error[0]);CHKERRQ(ierr);} 2393 else {ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: < 1.0e-11\n");CHKERRQ(ierr);} 2394 } 2395 ierr = PetscFree(error);CHKERRQ(ierr); 2396 /* Check residual */ 2397 ierr = SNESComputeFunction(snes, u, r);CHKERRQ(ierr); 2398 ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr); 2399 ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Residual: %g\n", res);CHKERRQ(ierr); 2400 ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr); 2401 ierr = PetscObjectSetName((PetscObject) r, "Initial Residual");CHKERRQ(ierr); 2402 ierr = PetscObjectSetOptionsPrefix((PetscObject)r,"res_");CHKERRQ(ierr); 2403 ierr = VecViewFromOptions(r, NULL, "-vec_view");CHKERRQ(ierr); 2404 /* Check Jacobian */ 2405 ierr = SNESComputeJacobian(snes, u, M, M);CHKERRQ(ierr); 2406 ierr = MatGetNullSpace(J, &nullSpace);CHKERRQ(ierr); 2407 if (nullSpace) { 2408 PetscBool isNull; 2409 ierr = MatNullSpaceTest(nullSpace, J, &isNull);CHKERRQ(ierr); 2410 if (!isNull) SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_PLIB, "The null space calculated for the system operator is invalid."); 2411 } 2412 ierr = VecDuplicate(u, &b);CHKERRQ(ierr); 2413 ierr = VecSet(r, 0.0);CHKERRQ(ierr); 2414 ierr = SNESComputeFunction(snes, r, b);CHKERRQ(ierr); 2415 ierr = MatMult(M, u, r);CHKERRQ(ierr); 2416 ierr = VecAXPY(r, 1.0, b);CHKERRQ(ierr); 2417 ierr = VecDestroy(&b);CHKERRQ(ierr); 2418 ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr); 2419 ierr = PetscPrintf(PETSC_COMM_WORLD, "Linear L_2 Residual: %g\n", res);CHKERRQ(ierr); 2420 ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr); 2421 ierr = PetscObjectSetName((PetscObject) r, "Au - b = Au + F(0)");CHKERRQ(ierr); 2422 ierr = PetscObjectSetOptionsPrefix((PetscObject)r,"linear_res_");CHKERRQ(ierr); 2423 ierr = VecViewFromOptions(r, NULL, "-vec_view");CHKERRQ(ierr); 2424 ierr = VecDestroy(&r);CHKERRQ(ierr); 2425 ierr = MatNullSpaceDestroy(&nullSpace);CHKERRQ(ierr); 2426 ierr = MatDestroy(&J);CHKERRQ(ierr); 2427 PetscFunctionReturn(0); 2428 } 2429 2430 #undef __FUNCT__ 2431 #define __FUNCT__ "DMSNESCheckFromOptions" 2432 PetscErrorCode DMSNESCheckFromOptions(SNES snes, Vec u, PetscErrorCode (**exactFuncs)(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf, PetscScalar *u, void *ctx), void **ctxs) 2433 { 2434 DM dm; 2435 Vec sol; 2436 PetscBool check; 2437 PetscErrorCode ierr; 2438 2439 PetscFunctionBegin; 2440 ierr = PetscOptionsHasName(((PetscObject)snes)->options,((PetscObject)snes)->prefix, "-dmsnes_check", &check);CHKERRQ(ierr); 2441 if (!check) PetscFunctionReturn(0); 2442 ierr = SNESGetDM(snes, &dm);CHKERRQ(ierr); 2443 ierr = VecDuplicate(u, &sol);CHKERRQ(ierr); 2444 ierr = SNESSetSolution(snes, sol);CHKERRQ(ierr); 2445 ierr = DMSNESCheckFromOptions_Internal(snes, dm, u, sol, exactFuncs, ctxs);CHKERRQ(ierr); 2446 ierr = VecDestroy(&sol);CHKERRQ(ierr); 2447 PetscFunctionReturn(0); 2448 } 2449