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 = MPI_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 PetscScalar *a, *coords; 234 PetscInt p; 235 PetscErrorCode ierr; 236 237 PetscFunctionBegin; 238 ierr = PetscMalloc3(ctx->dim,&v0,ctx->dim*ctx->dim,&J,ctx->dim*ctx->dim,&invJ);CHKERRQ(ierr); 239 ierr = VecGetArray(ctx->coords, &coords);CHKERRQ(ierr); 240 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 241 for (p = 0; p < ctx->n; ++p) { 242 PetscInt c = ctx->cells[p]; 243 PetscScalar *x = NULL; 244 PetscReal xi[4]; 245 PetscInt d, f, comp; 246 247 ierr = DMPlexComputeCellGeometryFEM(dm, c, NULL, v0, J, invJ, &detJ);CHKERRQ(ierr); 248 if (detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", detJ, c); 249 ierr = DMPlexVecGetClosure(dm, NULL, xLocal, c, NULL, &x);CHKERRQ(ierr); 250 for (comp = 0; comp < ctx->dof; ++comp) a[p*ctx->dof+comp] = x[0*ctx->dof+comp]; 251 252 for (d = 0; d < ctx->dim; ++d) { 253 xi[d] = 0.0; 254 for (f = 0; f < ctx->dim; ++f) xi[d] += invJ[d*ctx->dim+f]*0.5*PetscRealPart(coords[p*ctx->dim+f] - v0[f]); 255 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]; 256 } 257 ierr = DMPlexVecRestoreClosure(dm, NULL, xLocal, c, NULL, &x);CHKERRQ(ierr); 258 } 259 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 260 ierr = VecRestoreArray(ctx->coords, &coords);CHKERRQ(ierr); 261 ierr = PetscFree3(v0, J, invJ);CHKERRQ(ierr); 262 PetscFunctionReturn(0); 263 } 264 265 #undef __FUNCT__ 266 #define __FUNCT__ "DMInterpolate_Tetrahedron_Private" 267 PETSC_STATIC_INLINE PetscErrorCode DMInterpolate_Tetrahedron_Private(DMInterpolationInfo ctx, DM dm, Vec xLocal, Vec v) 268 { 269 PetscReal *v0, *J, *invJ, detJ; 270 PetscScalar *a, *coords; 271 PetscInt p; 272 PetscErrorCode ierr; 273 274 PetscFunctionBegin; 275 ierr = PetscMalloc3(ctx->dim,&v0,ctx->dim*ctx->dim,&J,ctx->dim*ctx->dim,&invJ);CHKERRQ(ierr); 276 ierr = VecGetArray(ctx->coords, &coords);CHKERRQ(ierr); 277 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 278 for (p = 0; p < ctx->n; ++p) { 279 PetscInt c = ctx->cells[p]; 280 const PetscInt order[3] = {2, 1, 3}; 281 PetscScalar *x = NULL; 282 PetscReal xi[4]; 283 PetscInt d, f, comp; 284 285 ierr = DMPlexComputeCellGeometryFEM(dm, c, NULL, v0, J, invJ, &detJ);CHKERRQ(ierr); 286 if (detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", detJ, c); 287 ierr = DMPlexVecGetClosure(dm, NULL, xLocal, c, NULL, &x);CHKERRQ(ierr); 288 for (comp = 0; comp < ctx->dof; ++comp) a[p*ctx->dof+comp] = x[0*ctx->dof+comp]; 289 290 for (d = 0; d < ctx->dim; ++d) { 291 xi[d] = 0.0; 292 for (f = 0; f < ctx->dim; ++f) xi[d] += invJ[d*ctx->dim+f]*0.5*PetscRealPart(coords[p*ctx->dim+f] - v0[f]); 293 for (comp = 0; comp < ctx->dof; ++comp) a[p*ctx->dof+comp] += PetscRealPart(x[order[d]*ctx->dof+comp] - x[0*ctx->dof+comp])*xi[d]; 294 } 295 ierr = DMPlexVecRestoreClosure(dm, NULL, xLocal, c, NULL, &x);CHKERRQ(ierr); 296 } 297 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 298 ierr = VecRestoreArray(ctx->coords, &coords);CHKERRQ(ierr); 299 ierr = PetscFree3(v0, J, invJ);CHKERRQ(ierr); 300 PetscFunctionReturn(0); 301 } 302 303 #undef __FUNCT__ 304 #define __FUNCT__ "QuadMap_Private" 305 PETSC_STATIC_INLINE PetscErrorCode QuadMap_Private(SNES snes, Vec Xref, Vec Xreal, void *ctx) 306 { 307 const PetscScalar *vertices = (const PetscScalar*) ctx; 308 const PetscScalar x0 = vertices[0]; 309 const PetscScalar y0 = vertices[1]; 310 const PetscScalar x1 = vertices[2]; 311 const PetscScalar y1 = vertices[3]; 312 const PetscScalar x2 = vertices[4]; 313 const PetscScalar y2 = vertices[5]; 314 const PetscScalar x3 = vertices[6]; 315 const PetscScalar y3 = vertices[7]; 316 const PetscScalar f_1 = x1 - x0; 317 const PetscScalar g_1 = y1 - y0; 318 const PetscScalar f_3 = x3 - x0; 319 const PetscScalar g_3 = y3 - y0; 320 const PetscScalar f_01 = x2 - x1 - x3 + x0; 321 const PetscScalar g_01 = y2 - y1 - y3 + y0; 322 PetscScalar *ref, *real; 323 PetscErrorCode ierr; 324 325 PetscFunctionBegin; 326 ierr = VecGetArray(Xref, &ref);CHKERRQ(ierr); 327 ierr = VecGetArray(Xreal, &real);CHKERRQ(ierr); 328 { 329 const PetscScalar p0 = ref[0]; 330 const PetscScalar p1 = ref[1]; 331 332 real[0] = x0 + f_1 * p0 + f_3 * p1 + f_01 * p0 * p1; 333 real[1] = y0 + g_1 * p0 + g_3 * p1 + g_01 * p0 * p1; 334 } 335 ierr = PetscLogFlops(28);CHKERRQ(ierr); 336 ierr = VecRestoreArray(Xref, &ref);CHKERRQ(ierr); 337 ierr = VecRestoreArray(Xreal, &real);CHKERRQ(ierr); 338 PetscFunctionReturn(0); 339 } 340 341 #include <petsc-private/dmimpl.h> 342 #undef __FUNCT__ 343 #define __FUNCT__ "QuadJacobian_Private" 344 PETSC_STATIC_INLINE PetscErrorCode QuadJacobian_Private(SNES snes, Vec Xref, Mat J, Mat M, void *ctx) 345 { 346 const PetscScalar *vertices = (const PetscScalar*) ctx; 347 const PetscScalar x0 = vertices[0]; 348 const PetscScalar y0 = vertices[1]; 349 const PetscScalar x1 = vertices[2]; 350 const PetscScalar y1 = vertices[3]; 351 const PetscScalar x2 = vertices[4]; 352 const PetscScalar y2 = vertices[5]; 353 const PetscScalar x3 = vertices[6]; 354 const PetscScalar y3 = vertices[7]; 355 const PetscScalar f_01 = x2 - x1 - x3 + x0; 356 const PetscScalar g_01 = y2 - y1 - y3 + y0; 357 PetscScalar *ref; 358 PetscErrorCode ierr; 359 360 PetscFunctionBegin; 361 ierr = VecGetArray(Xref, &ref);CHKERRQ(ierr); 362 { 363 const PetscScalar x = ref[0]; 364 const PetscScalar y = ref[1]; 365 const PetscInt rows[2] = {0, 1}; 366 PetscScalar values[4]; 367 368 values[0] = (x1 - x0 + f_01*y) * 0.5; values[1] = (x3 - x0 + f_01*x) * 0.5; 369 values[2] = (y1 - y0 + g_01*y) * 0.5; values[3] = (y3 - y0 + g_01*x) * 0.5; 370 ierr = MatSetValues(J, 2, rows, 2, rows, values, INSERT_VALUES);CHKERRQ(ierr); 371 } 372 ierr = PetscLogFlops(30);CHKERRQ(ierr); 373 ierr = VecRestoreArray(Xref, &ref);CHKERRQ(ierr); 374 ierr = MatAssemblyBegin(J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 375 ierr = MatAssemblyEnd(J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 376 PetscFunctionReturn(0); 377 } 378 379 #undef __FUNCT__ 380 #define __FUNCT__ "DMInterpolate_Quad_Private" 381 PETSC_STATIC_INLINE PetscErrorCode DMInterpolate_Quad_Private(DMInterpolationInfo ctx, DM dm, Vec xLocal, Vec v) 382 { 383 DM dmCoord; 384 SNES snes; 385 KSP ksp; 386 PC pc; 387 Vec coordsLocal, r, ref, real; 388 Mat J; 389 PetscScalar *a, *coords; 390 PetscInt p; 391 PetscErrorCode ierr; 392 393 PetscFunctionBegin; 394 ierr = DMGetCoordinatesLocal(dm, &coordsLocal);CHKERRQ(ierr); 395 ierr = DMGetCoordinateDM(dm, &dmCoord);CHKERRQ(ierr); 396 ierr = SNESCreate(PETSC_COMM_SELF, &snes);CHKERRQ(ierr); 397 ierr = SNESSetOptionsPrefix(snes, "quad_interp_");CHKERRQ(ierr); 398 ierr = VecCreate(PETSC_COMM_SELF, &r);CHKERRQ(ierr); 399 ierr = VecSetSizes(r, 2, 2);CHKERRQ(ierr); 400 ierr = VecSetType(r,dm->vectype);CHKERRQ(ierr); 401 ierr = VecDuplicate(r, &ref);CHKERRQ(ierr); 402 ierr = VecDuplicate(r, &real);CHKERRQ(ierr); 403 ierr = MatCreate(PETSC_COMM_SELF, &J);CHKERRQ(ierr); 404 ierr = MatSetSizes(J, 2, 2, 2, 2);CHKERRQ(ierr); 405 ierr = MatSetType(J, MATSEQDENSE);CHKERRQ(ierr); 406 ierr = MatSetUp(J);CHKERRQ(ierr); 407 ierr = SNESSetFunction(snes, r, QuadMap_Private, NULL);CHKERRQ(ierr); 408 ierr = SNESSetJacobian(snes, J, J, QuadJacobian_Private, NULL);CHKERRQ(ierr); 409 ierr = SNESGetKSP(snes, &ksp);CHKERRQ(ierr); 410 ierr = KSPGetPC(ksp, &pc);CHKERRQ(ierr); 411 ierr = PCSetType(pc, PCLU);CHKERRQ(ierr); 412 ierr = SNESSetFromOptions(snes);CHKERRQ(ierr); 413 414 ierr = VecGetArray(ctx->coords, &coords);CHKERRQ(ierr); 415 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 416 for (p = 0; p < ctx->n; ++p) { 417 PetscScalar *x = NULL, *vertices = NULL; 418 PetscScalar *xi; 419 PetscReal xir[2]; 420 PetscInt c = ctx->cells[p], comp, coordSize, xSize; 421 422 /* Can make this do all points at once */ 423 ierr = DMPlexVecGetClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);CHKERRQ(ierr); 424 if (4*2 != coordSize) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid closure size %d should be %d", coordSize, 4*2); 425 ierr = DMPlexVecGetClosure(dm, NULL, xLocal, c, &xSize, &x);CHKERRQ(ierr); 426 if (4*ctx->dof != xSize) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid closure size %d should be %d", xSize, 4*ctx->dof); 427 ierr = SNESSetFunction(snes, NULL, NULL, (void*) vertices);CHKERRQ(ierr); 428 ierr = SNESSetJacobian(snes, NULL, NULL, NULL, (void*) vertices);CHKERRQ(ierr); 429 ierr = VecGetArray(real, &xi);CHKERRQ(ierr); 430 xi[0] = coords[p*ctx->dim+0]; 431 xi[1] = coords[p*ctx->dim+1]; 432 ierr = VecRestoreArray(real, &xi);CHKERRQ(ierr); 433 ierr = SNESSolve(snes, real, ref);CHKERRQ(ierr); 434 ierr = VecGetArray(ref, &xi);CHKERRQ(ierr); 435 xir[0] = PetscRealPart(xi[0]); 436 xir[1] = PetscRealPart(xi[1]); 437 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]; 438 439 ierr = VecRestoreArray(ref, &xi);CHKERRQ(ierr); 440 ierr = DMPlexVecRestoreClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);CHKERRQ(ierr); 441 ierr = DMPlexVecRestoreClosure(dm, NULL, xLocal, c, &xSize, &x);CHKERRQ(ierr); 442 } 443 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 444 ierr = VecRestoreArray(ctx->coords, &coords);CHKERRQ(ierr); 445 446 ierr = SNESDestroy(&snes);CHKERRQ(ierr); 447 ierr = VecDestroy(&r);CHKERRQ(ierr); 448 ierr = VecDestroy(&ref);CHKERRQ(ierr); 449 ierr = VecDestroy(&real);CHKERRQ(ierr); 450 ierr = MatDestroy(&J);CHKERRQ(ierr); 451 PetscFunctionReturn(0); 452 } 453 454 #undef __FUNCT__ 455 #define __FUNCT__ "HexMap_Private" 456 PETSC_STATIC_INLINE PetscErrorCode HexMap_Private(SNES snes, Vec Xref, Vec Xreal, void *ctx) 457 { 458 const PetscScalar *vertices = (const PetscScalar*) ctx; 459 const PetscScalar x0 = vertices[0]; 460 const PetscScalar y0 = vertices[1]; 461 const PetscScalar z0 = vertices[2]; 462 const PetscScalar x1 = vertices[9]; 463 const PetscScalar y1 = vertices[10]; 464 const PetscScalar z1 = vertices[11]; 465 const PetscScalar x2 = vertices[6]; 466 const PetscScalar y2 = vertices[7]; 467 const PetscScalar z2 = vertices[8]; 468 const PetscScalar x3 = vertices[3]; 469 const PetscScalar y3 = vertices[4]; 470 const PetscScalar z3 = vertices[5]; 471 const PetscScalar x4 = vertices[12]; 472 const PetscScalar y4 = vertices[13]; 473 const PetscScalar z4 = vertices[14]; 474 const PetscScalar x5 = vertices[15]; 475 const PetscScalar y5 = vertices[16]; 476 const PetscScalar z5 = vertices[17]; 477 const PetscScalar x6 = vertices[18]; 478 const PetscScalar y6 = vertices[19]; 479 const PetscScalar z6 = vertices[20]; 480 const PetscScalar x7 = vertices[21]; 481 const PetscScalar y7 = vertices[22]; 482 const PetscScalar z7 = vertices[23]; 483 const PetscScalar f_1 = x1 - x0; 484 const PetscScalar g_1 = y1 - y0; 485 const PetscScalar h_1 = z1 - z0; 486 const PetscScalar f_3 = x3 - x0; 487 const PetscScalar g_3 = y3 - y0; 488 const PetscScalar h_3 = z3 - z0; 489 const PetscScalar f_4 = x4 - x0; 490 const PetscScalar g_4 = y4 - y0; 491 const PetscScalar h_4 = z4 - z0; 492 const PetscScalar f_01 = x2 - x1 - x3 + x0; 493 const PetscScalar g_01 = y2 - y1 - y3 + y0; 494 const PetscScalar h_01 = z2 - z1 - z3 + z0; 495 const PetscScalar f_12 = x7 - x3 - x4 + x0; 496 const PetscScalar g_12 = y7 - y3 - y4 + y0; 497 const PetscScalar h_12 = z7 - z3 - z4 + z0; 498 const PetscScalar f_02 = x5 - x1 - x4 + x0; 499 const PetscScalar g_02 = y5 - y1 - y4 + y0; 500 const PetscScalar h_02 = z5 - z1 - z4 + z0; 501 const PetscScalar f_012 = x6 - x0 + x1 - x2 + x3 + x4 - x5 - x7; 502 const PetscScalar g_012 = y6 - y0 + y1 - y2 + y3 + y4 - y5 - y7; 503 const PetscScalar h_012 = z6 - z0 + z1 - z2 + z3 + z4 - z5 - z7; 504 PetscScalar *ref, *real; 505 PetscErrorCode ierr; 506 507 PetscFunctionBegin; 508 ierr = VecGetArray(Xref, &ref);CHKERRQ(ierr); 509 ierr = VecGetArray(Xreal, &real);CHKERRQ(ierr); 510 { 511 const PetscScalar p0 = ref[0]; 512 const PetscScalar p1 = ref[1]; 513 const PetscScalar p2 = ref[2]; 514 515 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; 516 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; 517 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; 518 } 519 ierr = PetscLogFlops(114);CHKERRQ(ierr); 520 ierr = VecRestoreArray(Xref, &ref);CHKERRQ(ierr); 521 ierr = VecRestoreArray(Xreal, &real);CHKERRQ(ierr); 522 PetscFunctionReturn(0); 523 } 524 525 #undef __FUNCT__ 526 #define __FUNCT__ "HexJacobian_Private" 527 PETSC_STATIC_INLINE PetscErrorCode HexJacobian_Private(SNES snes, Vec Xref, Mat J, Mat M, void *ctx) 528 { 529 const PetscScalar *vertices = (const PetscScalar*) ctx; 530 const PetscScalar x0 = vertices[0]; 531 const PetscScalar y0 = vertices[1]; 532 const PetscScalar z0 = vertices[2]; 533 const PetscScalar x1 = vertices[9]; 534 const PetscScalar y1 = vertices[10]; 535 const PetscScalar z1 = vertices[11]; 536 const PetscScalar x2 = vertices[6]; 537 const PetscScalar y2 = vertices[7]; 538 const PetscScalar z2 = vertices[8]; 539 const PetscScalar x3 = vertices[3]; 540 const PetscScalar y3 = vertices[4]; 541 const PetscScalar z3 = vertices[5]; 542 const PetscScalar x4 = vertices[12]; 543 const PetscScalar y4 = vertices[13]; 544 const PetscScalar z4 = vertices[14]; 545 const PetscScalar x5 = vertices[15]; 546 const PetscScalar y5 = vertices[16]; 547 const PetscScalar z5 = vertices[17]; 548 const PetscScalar x6 = vertices[18]; 549 const PetscScalar y6 = vertices[19]; 550 const PetscScalar z6 = vertices[20]; 551 const PetscScalar x7 = vertices[21]; 552 const PetscScalar y7 = vertices[22]; 553 const PetscScalar z7 = vertices[23]; 554 const PetscScalar f_xy = x2 - x1 - x3 + x0; 555 const PetscScalar g_xy = y2 - y1 - y3 + y0; 556 const PetscScalar h_xy = z2 - z1 - z3 + z0; 557 const PetscScalar f_yz = x7 - x3 - x4 + x0; 558 const PetscScalar g_yz = y7 - y3 - y4 + y0; 559 const PetscScalar h_yz = z7 - z3 - z4 + z0; 560 const PetscScalar f_xz = x5 - x1 - x4 + x0; 561 const PetscScalar g_xz = y5 - y1 - y4 + y0; 562 const PetscScalar h_xz = z5 - z1 - z4 + z0; 563 const PetscScalar f_xyz = x6 - x0 + x1 - x2 + x3 + x4 - x5 - x7; 564 const PetscScalar g_xyz = y6 - y0 + y1 - y2 + y3 + y4 - y5 - y7; 565 const PetscScalar h_xyz = z6 - z0 + z1 - z2 + z3 + z4 - z5 - z7; 566 PetscScalar *ref; 567 PetscErrorCode ierr; 568 569 PetscFunctionBegin; 570 ierr = VecGetArray(Xref, &ref);CHKERRQ(ierr); 571 { 572 const PetscScalar x = ref[0]; 573 const PetscScalar y = ref[1]; 574 const PetscScalar z = ref[2]; 575 const PetscInt rows[3] = {0, 1, 2}; 576 PetscScalar values[9]; 577 578 values[0] = (x1 - x0 + f_xy*y + f_xz*z + f_xyz*y*z) / 2.0; 579 values[1] = (x3 - x0 + f_xy*x + f_yz*z + f_xyz*x*z) / 2.0; 580 values[2] = (x4 - x0 + f_yz*y + f_xz*x + f_xyz*x*y) / 2.0; 581 values[3] = (y1 - y0 + g_xy*y + g_xz*z + g_xyz*y*z) / 2.0; 582 values[4] = (y3 - y0 + g_xy*x + g_yz*z + g_xyz*x*z) / 2.0; 583 values[5] = (y4 - y0 + g_yz*y + g_xz*x + g_xyz*x*y) / 2.0; 584 values[6] = (z1 - z0 + h_xy*y + h_xz*z + h_xyz*y*z) / 2.0; 585 values[7] = (z3 - z0 + h_xy*x + h_yz*z + h_xyz*x*z) / 2.0; 586 values[8] = (z4 - z0 + h_yz*y + h_xz*x + h_xyz*x*y) / 2.0; 587 588 ierr = MatSetValues(J, 3, rows, 3, rows, values, INSERT_VALUES);CHKERRQ(ierr); 589 } 590 ierr = PetscLogFlops(152);CHKERRQ(ierr); 591 ierr = VecRestoreArray(Xref, &ref);CHKERRQ(ierr); 592 ierr = MatAssemblyBegin(J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 593 ierr = MatAssemblyEnd(J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 594 PetscFunctionReturn(0); 595 } 596 597 #undef __FUNCT__ 598 #define __FUNCT__ "DMInterpolate_Hex_Private" 599 PETSC_STATIC_INLINE PetscErrorCode DMInterpolate_Hex_Private(DMInterpolationInfo ctx, DM dm, Vec xLocal, Vec v) 600 { 601 DM dmCoord; 602 SNES snes; 603 KSP ksp; 604 PC pc; 605 Vec coordsLocal, r, ref, real; 606 Mat J; 607 PetscScalar *a, *coords; 608 PetscInt p; 609 PetscErrorCode ierr; 610 611 PetscFunctionBegin; 612 ierr = DMGetCoordinatesLocal(dm, &coordsLocal);CHKERRQ(ierr); 613 ierr = DMGetCoordinateDM(dm, &dmCoord);CHKERRQ(ierr); 614 ierr = SNESCreate(PETSC_COMM_SELF, &snes);CHKERRQ(ierr); 615 ierr = SNESSetOptionsPrefix(snes, "hex_interp_");CHKERRQ(ierr); 616 ierr = VecCreate(PETSC_COMM_SELF, &r);CHKERRQ(ierr); 617 ierr = VecSetSizes(r, 3, 3);CHKERRQ(ierr); 618 ierr = VecSetType(r,dm->vectype);CHKERRQ(ierr); 619 ierr = VecDuplicate(r, &ref);CHKERRQ(ierr); 620 ierr = VecDuplicate(r, &real);CHKERRQ(ierr); 621 ierr = MatCreate(PETSC_COMM_SELF, &J);CHKERRQ(ierr); 622 ierr = MatSetSizes(J, 3, 3, 3, 3);CHKERRQ(ierr); 623 ierr = MatSetType(J, MATSEQDENSE);CHKERRQ(ierr); 624 ierr = MatSetUp(J);CHKERRQ(ierr); 625 ierr = SNESSetFunction(snes, r, HexMap_Private, NULL);CHKERRQ(ierr); 626 ierr = SNESSetJacobian(snes, J, J, HexJacobian_Private, NULL);CHKERRQ(ierr); 627 ierr = SNESGetKSP(snes, &ksp);CHKERRQ(ierr); 628 ierr = KSPGetPC(ksp, &pc);CHKERRQ(ierr); 629 ierr = PCSetType(pc, PCLU);CHKERRQ(ierr); 630 ierr = SNESSetFromOptions(snes);CHKERRQ(ierr); 631 632 ierr = VecGetArray(ctx->coords, &coords);CHKERRQ(ierr); 633 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 634 for (p = 0; p < ctx->n; ++p) { 635 PetscScalar *x = NULL, *vertices = NULL; 636 PetscScalar *xi; 637 PetscReal xir[3]; 638 PetscInt c = ctx->cells[p], comp, coordSize, xSize; 639 640 /* Can make this do all points at once */ 641 ierr = DMPlexVecGetClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);CHKERRQ(ierr); 642 if (8*3 != coordSize) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid closure size %d should be %d", coordSize, 8*3); 643 ierr = DMPlexVecGetClosure(dm, NULL, xLocal, c, &xSize, &x);CHKERRQ(ierr); 644 if (8*ctx->dof != xSize) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid closure size %d should be %d", xSize, 8*ctx->dof); 645 ierr = SNESSetFunction(snes, NULL, NULL, (void*) vertices);CHKERRQ(ierr); 646 ierr = SNESSetJacobian(snes, NULL, NULL, NULL, (void*) vertices);CHKERRQ(ierr); 647 ierr = VecGetArray(real, &xi);CHKERRQ(ierr); 648 xi[0] = coords[p*ctx->dim+0]; 649 xi[1] = coords[p*ctx->dim+1]; 650 xi[2] = coords[p*ctx->dim+2]; 651 ierr = VecRestoreArray(real, &xi);CHKERRQ(ierr); 652 ierr = SNESSolve(snes, real, ref);CHKERRQ(ierr); 653 ierr = VecGetArray(ref, &xi);CHKERRQ(ierr); 654 xir[0] = PetscRealPart(xi[0]); 655 xir[1] = PetscRealPart(xi[1]); 656 xir[2] = PetscRealPart(xi[2]); 657 for (comp = 0; comp < ctx->dof; ++comp) { 658 a[p*ctx->dof+comp] = 659 x[0*ctx->dof+comp]*(1-xir[0])*(1-xir[1])*(1-xir[2]) + 660 x[3*ctx->dof+comp]* xir[0]*(1-xir[1])*(1-xir[2]) + 661 x[2*ctx->dof+comp]* xir[0]* xir[1]*(1-xir[2]) + 662 x[1*ctx->dof+comp]*(1-xir[0])* xir[1]*(1-xir[2]) + 663 x[4*ctx->dof+comp]*(1-xir[0])*(1-xir[1])* xir[2] + 664 x[5*ctx->dof+comp]* xir[0]*(1-xir[1])* xir[2] + 665 x[6*ctx->dof+comp]* xir[0]* xir[1]* xir[2] + 666 x[7*ctx->dof+comp]*(1-xir[0])* xir[1]* xir[2]; 667 } 668 ierr = VecRestoreArray(ref, &xi);CHKERRQ(ierr); 669 ierr = DMPlexVecRestoreClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);CHKERRQ(ierr); 670 ierr = DMPlexVecRestoreClosure(dm, NULL, xLocal, c, &xSize, &x);CHKERRQ(ierr); 671 } 672 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 673 ierr = VecRestoreArray(ctx->coords, &coords);CHKERRQ(ierr); 674 675 ierr = SNESDestroy(&snes);CHKERRQ(ierr); 676 ierr = VecDestroy(&r);CHKERRQ(ierr); 677 ierr = VecDestroy(&ref);CHKERRQ(ierr); 678 ierr = VecDestroy(&real);CHKERRQ(ierr); 679 ierr = MatDestroy(&J);CHKERRQ(ierr); 680 PetscFunctionReturn(0); 681 } 682 683 #undef __FUNCT__ 684 #define __FUNCT__ "DMInterpolationEvaluate" 685 /* 686 Input Parameters: 687 + ctx - The DMInterpolationInfo context 688 . dm - The DM 689 - x - The local vector containing the field to be interpolated 690 691 Output Parameters: 692 . v - The vector containing the interpolated values 693 */ 694 PetscErrorCode DMInterpolationEvaluate(DMInterpolationInfo ctx, DM dm, Vec x, Vec v) 695 { 696 PetscInt dim, coneSize, n; 697 PetscErrorCode ierr; 698 699 PetscFunctionBegin; 700 PetscValidHeaderSpecific(dm, DM_CLASSID, 2); 701 PetscValidHeaderSpecific(x, VEC_CLASSID, 3); 702 PetscValidHeaderSpecific(v, VEC_CLASSID, 4); 703 ierr = VecGetLocalSize(v, &n);CHKERRQ(ierr); 704 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); 705 if (n) { 706 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 707 ierr = DMPlexGetConeSize(dm, ctx->cells[0], &coneSize);CHKERRQ(ierr); 708 if (dim == 2) { 709 if (coneSize == 3) { 710 ierr = DMInterpolate_Triangle_Private(ctx, dm, x, v);CHKERRQ(ierr); 711 } else if (coneSize == 4) { 712 ierr = DMInterpolate_Quad_Private(ctx, dm, x, v);CHKERRQ(ierr); 713 } else SETERRQ1(ctx->comm, PETSC_ERR_ARG_OUTOFRANGE, "Unsupported dimension %d for point interpolation", dim); 714 } else if (dim == 3) { 715 if (coneSize == 4) { 716 ierr = DMInterpolate_Tetrahedron_Private(ctx, dm, x, v);CHKERRQ(ierr); 717 } else { 718 ierr = DMInterpolate_Hex_Private(ctx, dm, x, v);CHKERRQ(ierr); 719 } 720 } else SETERRQ1(ctx->comm, PETSC_ERR_ARG_OUTOFRANGE, "Unsupported dimension %d for point interpolation", dim); 721 } 722 PetscFunctionReturn(0); 723 } 724 725 #undef __FUNCT__ 726 #define __FUNCT__ "DMInterpolationDestroy" 727 PetscErrorCode DMInterpolationDestroy(DMInterpolationInfo *ctx) 728 { 729 PetscErrorCode ierr; 730 731 PetscFunctionBegin; 732 PetscValidPointer(ctx, 2); 733 ierr = VecDestroy(&(*ctx)->coords);CHKERRQ(ierr); 734 ierr = PetscFree((*ctx)->points);CHKERRQ(ierr); 735 ierr = PetscFree((*ctx)->cells);CHKERRQ(ierr); 736 ierr = PetscFree(*ctx);CHKERRQ(ierr); 737 *ctx = NULL; 738 PetscFunctionReturn(0); 739 } 740 741 #undef __FUNCT__ 742 #define __FUNCT__ "SNESMonitorFields" 743 /*@C 744 SNESMonitorFields - Monitors the residual for each field separately 745 746 Collective on SNES 747 748 Input Parameters: 749 + snes - the SNES context 750 . its - iteration number 751 . fgnorm - 2-norm of residual 752 - dummy - unused context 753 754 Notes: 755 This routine prints the residual norm at each iteration. 756 757 Level: intermediate 758 759 .keywords: SNES, nonlinear, default, monitor, norm 760 .seealso: SNESMonitorSet(), SNESMonitorDefault() 761 @*/ 762 PetscErrorCode SNESMonitorFields(SNES snes, PetscInt its, PetscReal fgnorm, void *dummy) 763 { 764 PetscViewer viewer = dummy ? (PetscViewer) dummy : PETSC_VIEWER_STDOUT_(PetscObjectComm((PetscObject) snes)); 765 Vec res; 766 DM dm; 767 PetscSection s; 768 const PetscScalar *r; 769 PetscReal *lnorms, *norms; 770 PetscInt numFields, f, pStart, pEnd, p; 771 PetscErrorCode ierr; 772 773 PetscFunctionBegin; 774 ierr = SNESGetFunction(snes, &res, 0, 0);CHKERRQ(ierr); 775 ierr = SNESGetDM(snes, &dm);CHKERRQ(ierr); 776 ierr = DMGetDefaultSection(dm, &s);CHKERRQ(ierr); 777 ierr = PetscSectionGetNumFields(s, &numFields);CHKERRQ(ierr); 778 ierr = PetscSectionGetChart(s, &pStart, &pEnd);CHKERRQ(ierr); 779 ierr = PetscCalloc2(numFields, &lnorms, numFields, &norms);CHKERRQ(ierr); 780 ierr = VecGetArrayRead(res, &r);CHKERRQ(ierr); 781 for (p = pStart; p < pEnd; ++p) { 782 for (f = 0; f < numFields; ++f) { 783 PetscInt fdof, foff, d; 784 785 ierr = PetscSectionGetFieldDof(s, p, f, &fdof);CHKERRQ(ierr); 786 ierr = PetscSectionGetFieldOffset(s, p, f, &foff);CHKERRQ(ierr); 787 for (d = 0; d < fdof; ++d) lnorms[f] += PetscRealPart(PetscSqr(r[foff+d])); 788 } 789 } 790 ierr = VecRestoreArrayRead(res, &r);CHKERRQ(ierr); 791 ierr = MPI_Allreduce(lnorms, norms, numFields, MPIU_REAL, MPI_SUM, PetscObjectComm((PetscObject) dm));CHKERRQ(ierr); 792 ierr = PetscViewerASCIIAddTab(viewer, ((PetscObject) snes)->tablevel);CHKERRQ(ierr); 793 ierr = PetscViewerASCIIPrintf(viewer, "%3D SNES Function norm %14.12e [", its, (double) fgnorm);CHKERRQ(ierr); 794 for (f = 0; f < numFields; ++f) { 795 if (f > 0) {ierr = PetscViewerASCIIPrintf(viewer, ", ");CHKERRQ(ierr);} 796 ierr = PetscViewerASCIIPrintf(viewer, "%14.12e", (double) PetscSqrtReal(norms[f]));CHKERRQ(ierr); 797 } 798 ierr = PetscViewerASCIIPrintf(viewer, "]\n");CHKERRQ(ierr); 799 ierr = PetscViewerASCIISubtractTab(viewer, ((PetscObject) snes)->tablevel);CHKERRQ(ierr); 800 ierr = PetscFree2(lnorms, norms);CHKERRQ(ierr); 801 PetscFunctionReturn(0); 802 } 803 804 /********************* Residual Computation **************************/ 805 806 #undef __FUNCT__ 807 #define __FUNCT__ "DMPlexSNESGetGeometryFEM" 808 /*@ 809 DMPlexSNESGetGeometryFEM - Return precomputed geometric data 810 811 Input Parameter: 812 . dm - The DM 813 814 Output Parameters: 815 . cellgeom - The values precomputed from cell geometry 816 817 Level: developer 818 819 .seealso: DMPlexSNESSetFunctionLocal() 820 @*/ 821 PetscErrorCode DMPlexSNESGetGeometryFEM(DM dm, Vec *cellgeom) 822 { 823 DMSNES dmsnes; 824 PetscObject obj; 825 PetscErrorCode ierr; 826 827 PetscFunctionBegin; 828 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 829 ierr = DMGetDMSNES(dm, &dmsnes);CHKERRQ(ierr); 830 ierr = PetscObjectQuery((PetscObject) dmsnes, "DMPlexSNES_cellgeom_fem", &obj);CHKERRQ(ierr); 831 if (!obj) { 832 Vec cellgeom; 833 834 ierr = DMPlexComputeGeometryFEM(dm, &cellgeom);CHKERRQ(ierr); 835 ierr = PetscObjectCompose((PetscObject) dmsnes, "DMPlexSNES_cellgeom_fem", (PetscObject) cellgeom);CHKERRQ(ierr); 836 ierr = VecDestroy(&cellgeom);CHKERRQ(ierr); 837 } 838 if (cellgeom) {PetscValidPointer(cellgeom, 3); ierr = PetscObjectQuery((PetscObject) dmsnes, "DMPlexSNES_cellgeom_fem", (PetscObject *) cellgeom);CHKERRQ(ierr);} 839 PetscFunctionReturn(0); 840 } 841 842 #undef __FUNCT__ 843 #define __FUNCT__ "DMPlexSNESGetGeometryFVM" 844 /*@ 845 DMPlexSNESGetGeometryFVM - Return precomputed geometric data 846 847 Input Parameter: 848 . dm - The DM 849 850 Output Parameters: 851 + facegeom - The values precomputed from face geometry 852 . cellgeom - The values precomputed from cell geometry 853 - minRadius - The minimum radius over the mesh of an inscribed sphere in a cell 854 855 Level: developer 856 857 .seealso: DMPlexTSSetRHSFunctionLocal() 858 @*/ 859 PetscErrorCode DMPlexSNESGetGeometryFVM(DM dm, Vec *facegeom, Vec *cellgeom, PetscReal *minRadius) 860 { 861 DMSNES dmsnes; 862 PetscObject obj; 863 PetscErrorCode ierr; 864 865 PetscFunctionBegin; 866 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 867 ierr = DMGetDMSNES(dm, &dmsnes);CHKERRQ(ierr); 868 ierr = PetscObjectQuery((PetscObject) dmsnes, "DMPlexSNES_facegeom_fvm", &obj);CHKERRQ(ierr); 869 if (!obj) { 870 Vec cellgeom, facegeom; 871 872 ierr = DMPlexComputeGeometryFVM(dm, &cellgeom, &facegeom);CHKERRQ(ierr); 873 ierr = PetscObjectCompose((PetscObject) dmsnes, "DMPlexSNES_facegeom_fvm", (PetscObject) facegeom);CHKERRQ(ierr); 874 ierr = PetscObjectCompose((PetscObject) dmsnes, "DMPlexSNES_cellgeom_fvm", (PetscObject) cellgeom);CHKERRQ(ierr); 875 ierr = VecDestroy(&facegeom);CHKERRQ(ierr); 876 ierr = VecDestroy(&cellgeom);CHKERRQ(ierr); 877 } 878 if (facegeom) {PetscValidPointer(facegeom, 2); ierr = PetscObjectQuery((PetscObject) dmsnes, "DMPlexSNES_facegeom_fvm", (PetscObject *) facegeom);CHKERRQ(ierr);} 879 if (cellgeom) {PetscValidPointer(cellgeom, 3); ierr = PetscObjectQuery((PetscObject) dmsnes, "DMPlexSNES_cellgeom_fvm", (PetscObject *) cellgeom);CHKERRQ(ierr);} 880 if (minRadius) {ierr = DMPlexGetMinRadius(dm, minRadius);CHKERRQ(ierr);} 881 PetscFunctionReturn(0); 882 } 883 884 #undef __FUNCT__ 885 #define __FUNCT__ "DMPlexSNESGetGradientDM" 886 /*@ 887 DMPlexSNESGetGradientDM - Return gradient data layout 888 889 Input Parameters: 890 + dm - The DM 891 - fv - The PetscFV 892 893 Output Parameter: 894 . dmGrad - The layout for gradient values 895 896 Level: developer 897 898 .seealso: DMPlexSNESGetGeometryFVM() 899 @*/ 900 PetscErrorCode DMPlexSNESGetGradientDM(DM dm, PetscFV fv, DM *dmGrad) 901 { 902 DMSNES dmsnes; 903 PetscObject obj; 904 PetscBool computeGradients; 905 PetscErrorCode ierr; 906 907 PetscFunctionBegin; 908 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 909 PetscValidHeaderSpecific(fv,PETSCFV_CLASSID,2); 910 PetscValidPointer(dmGrad,3); 911 ierr = PetscFVGetComputeGradients(fv, &computeGradients);CHKERRQ(ierr); 912 if (!computeGradients) {*dmGrad = NULL; PetscFunctionReturn(0);} 913 ierr = DMGetDMSNES(dm, &dmsnes);CHKERRQ(ierr); 914 ierr = PetscObjectQuery((PetscObject) dmsnes, "DMPlexSNES_dmgrad_fvm", &obj);CHKERRQ(ierr); 915 if (!obj) { 916 DM dmGrad; 917 Vec faceGeometry, cellGeometry; 918 919 ierr = DMPlexSNESGetGeometryFVM(dm, &faceGeometry, &cellGeometry, NULL);CHKERRQ(ierr); 920 ierr = DMPlexComputeGradientFVM(dm, fv, faceGeometry, cellGeometry, &dmGrad);CHKERRQ(ierr); 921 ierr = PetscObjectCompose((PetscObject) dmsnes, "DMPlexSNES_dmgrad_fvm", (PetscObject) dmGrad);CHKERRQ(ierr); 922 ierr = DMDestroy(&dmGrad);CHKERRQ(ierr); 923 } 924 ierr = PetscObjectQuery((PetscObject) dmsnes, "DMPlexSNES_dmgrad_fvm", (PetscObject *) dmGrad);CHKERRQ(ierr); 925 PetscFunctionReturn(0); 926 } 927 928 #undef __FUNCT__ 929 #define __FUNCT__ "DMPlexGetCellFields" 930 /*@C 931 DMPlexGetCellFields - Retrieve the field values values for a chunk of cells 932 933 Input Parameters: 934 + dm - The DM 935 . cStart - The first cell to include 936 . cEnd - The first cell to exclude 937 . locX - A local vector with the solution fields 938 . locX_t - A local vector with solution field time derivatives, or NULL 939 - locA - A local vector with auxiliary fields, or NULL 940 941 Output Parameters: 942 + u - The field coefficients 943 . u_t - The fields derivative coefficients 944 - a - The auxiliary field coefficients 945 946 Level: developer 947 948 .seealso: DMPlexGetFaceFields() 949 @*/ 950 PetscErrorCode DMPlexGetCellFields(DM dm, PetscInt cStart, PetscInt cEnd, Vec locX, Vec locX_t, Vec locA, PetscScalar **u, PetscScalar **u_t, PetscScalar **a) 951 { 952 DM dmAux; 953 PetscSection section, sectionAux; 954 PetscDS prob; 955 PetscInt numCells = cEnd - cStart, totDim, totDimAux, c; 956 PetscErrorCode ierr; 957 958 PetscFunctionBegin; 959 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 960 PetscValidHeaderSpecific(locX, VEC_CLASSID, 4); 961 if (locX_t) {PetscValidHeaderSpecific(locX_t, VEC_CLASSID, 5);} 962 if (locA) {PetscValidHeaderSpecific(locA, VEC_CLASSID, 6);} 963 PetscValidPointer(u, 7); 964 PetscValidPointer(u_t, 8); 965 PetscValidPointer(a, 9); 966 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 967 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 968 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 969 if (locA) { 970 PetscDS probAux; 971 972 ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); 973 ierr = DMGetDefaultSection(dmAux, §ionAux);CHKERRQ(ierr); 974 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 975 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 976 } 977 ierr = DMGetWorkArray(dm, numCells*totDim, PETSC_SCALAR, u);CHKERRQ(ierr); 978 ierr = DMGetWorkArray(dm, locX_t ? numCells*totDim : 0, PETSC_SCALAR, u_t);CHKERRQ(ierr); 979 ierr = DMGetWorkArray(dm, locA ? numCells*totDimAux : 0, PETSC_SCALAR, a);CHKERRQ(ierr); 980 for (c = cStart; c < cEnd; ++c) { 981 PetscScalar *x = NULL, *x_t = NULL, *ul = *u, *ul_t = *u_t, *al = *a; 982 PetscInt i; 983 984 ierr = DMPlexVecGetClosure(dm, section, locX, c, NULL, &x);CHKERRQ(ierr); 985 for (i = 0; i < totDim; ++i) ul[c*totDim+i] = x[i]; 986 ierr = DMPlexVecRestoreClosure(dm, section, locX, c, NULL, &x);CHKERRQ(ierr); 987 if (locX_t) { 988 ierr = DMPlexVecGetClosure(dm, section, locX_t, c, NULL, &x_t);CHKERRQ(ierr); 989 for (i = 0; i < totDim; ++i) ul_t[c*totDim+i] = x_t[i]; 990 ierr = DMPlexVecRestoreClosure(dm, section, locX_t, c, NULL, &x_t);CHKERRQ(ierr); 991 } 992 if (locA) { 993 ierr = DMPlexVecGetClosure(dmAux, sectionAux, locA, c, NULL, &x);CHKERRQ(ierr); 994 for (i = 0; i < totDimAux; ++i) al[c*totDimAux+i] = x[i]; 995 ierr = DMPlexVecRestoreClosure(dmAux, sectionAux, locA, c, NULL, &x);CHKERRQ(ierr); 996 } 997 } 998 PetscFunctionReturn(0); 999 } 1000 1001 #undef __FUNCT__ 1002 #define __FUNCT__ "DMPlexRestoreCellFields" 1003 /*@C 1004 DMPlexRestoreCellFields - Restore the field values values for a chunk of cells 1005 1006 Input Parameters: 1007 + dm - The DM 1008 . cStart - The first cell to include 1009 . cEnd - The first cell to exclude 1010 . locX - A local vector with the solution fields 1011 . locX_t - A local vector with solution field time derivatives, or NULL 1012 - locA - A local vector with auxiliary fields, or NULL 1013 1014 Output Parameters: 1015 + u - The field coefficients 1016 . u_t - The fields derivative coefficients 1017 - a - The auxiliary field coefficients 1018 1019 Level: developer 1020 1021 .seealso: DMPlexGetFaceFields() 1022 @*/ 1023 PetscErrorCode DMPlexRestoreCellFields(DM dm, PetscInt cStart, PetscInt cEnd, Vec locX, Vec locX_t, Vec locA, PetscScalar **u, PetscScalar **u_t, PetscScalar **a) 1024 { 1025 PetscErrorCode ierr; 1026 1027 PetscFunctionBegin; 1028 ierr = DMRestoreWorkArray(dm, 0, PETSC_SCALAR, u);CHKERRQ(ierr); 1029 ierr = DMRestoreWorkArray(dm, 0, PETSC_SCALAR, u_t);CHKERRQ(ierr); 1030 ierr = DMRestoreWorkArray(dm, 0, PETSC_SCALAR, a);CHKERRQ(ierr); 1031 PetscFunctionReturn(0); 1032 } 1033 1034 #undef __FUNCT__ 1035 #define __FUNCT__ "DMPlexGetFaceFields" 1036 /*@C 1037 DMPlexGetFaceFields - Retrieve the field values values for a chunk of faces 1038 1039 Input Parameters: 1040 + dm - The DM 1041 . fStart - The first face to include 1042 . fEnd - The first face to exclude 1043 . locX - A local vector with the solution fields 1044 . locX_t - A local vector with solution field time derivatives, or NULL 1045 . faceGeometry - A local vector with face geometry 1046 . cellGeometry - A local vector with cell geometry 1047 - locaGrad - A local vector with field gradients, or NULL 1048 1049 Output Parameters: 1050 + uL - The field values at the left side of the face 1051 - uR - The field values at the right side of the face 1052 1053 Level: developer 1054 1055 .seealso: DMPlexGetCellFields() 1056 @*/ 1057 PetscErrorCode DMPlexGetFaceFields(DM dm, PetscInt fStart, PetscInt fEnd, Vec locX, Vec locX_t, Vec faceGeometry, Vec cellGeometry, Vec locGrad, PetscScalar **uL, PetscScalar **uR) 1058 { 1059 DM dmFace, dmCell, dmGrad = NULL; 1060 PetscDS prob; 1061 DMLabel ghostLabel; 1062 const PetscScalar *facegeom, *cellgeom, *x, *lgrad; 1063 PetscBool *isFE; 1064 PetscInt dim, Nf, f, Nc, numFaces = fEnd - fStart, iface, face; 1065 PetscErrorCode ierr; 1066 1067 PetscFunctionBegin; 1068 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1069 PetscValidHeaderSpecific(locX, VEC_CLASSID, 4); 1070 if (locX_t) {PetscValidHeaderSpecific(locX_t, VEC_CLASSID, 5);} 1071 PetscValidHeaderSpecific(faceGeometry, VEC_CLASSID, 6); 1072 PetscValidHeaderSpecific(cellGeometry, VEC_CLASSID, 7); 1073 if (locGrad) {PetscValidHeaderSpecific(locGrad, VEC_CLASSID, 8);} 1074 PetscValidPointer(uL, 9); 1075 PetscValidPointer(uR, 10); 1076 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1077 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1078 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 1079 ierr = PetscDSGetTotalComponents(prob, &Nc);CHKERRQ(ierr); 1080 ierr = PetscMalloc1(Nf, &isFE);CHKERRQ(ierr); 1081 for (f = 0; f < Nf; ++f) { 1082 PetscObject obj; 1083 PetscClassId id; 1084 1085 ierr = DMGetField(dm, f, &obj);CHKERRQ(ierr); 1086 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1087 if (id == PETSCFE_CLASSID) {isFE[f] = PETSC_TRUE;} 1088 else if (id == PETSCFV_CLASSID) {isFE[f] = PETSC_FALSE;} 1089 else {isFE[f] = PETSC_FALSE;} 1090 } 1091 ierr = DMPlexGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 1092 ierr = VecGetArrayRead(locX, &x);CHKERRQ(ierr); 1093 ierr = VecGetDM(faceGeometry, &dmFace);CHKERRQ(ierr); 1094 ierr = VecGetArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); 1095 ierr = VecGetDM(cellGeometry, &dmCell);CHKERRQ(ierr); 1096 ierr = VecGetArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr); 1097 if (locGrad) { 1098 ierr = VecGetDM(locGrad, &dmGrad);CHKERRQ(ierr); 1099 ierr = VecGetArrayRead(locGrad, &lgrad);CHKERRQ(ierr); 1100 } 1101 ierr = DMGetWorkArray(dm, numFaces*Nc, PETSC_SCALAR, uL);CHKERRQ(ierr); 1102 ierr = DMGetWorkArray(dm, numFaces*Nc, PETSC_SCALAR, uR);CHKERRQ(ierr); 1103 /* Right now just eat the extra work for FE (could make a cell loop) */ 1104 for (face = fStart, iface = 0; face < fEnd; ++face) { 1105 const PetscInt *cells; 1106 const PetscFVFaceGeom *fg; 1107 const PetscFVCellGeom *cgL, *cgR; 1108 const PetscScalar *xL, *xR, *gL, *gR; 1109 PetscScalar *uLl = *uL, *uRl = *uR; 1110 PetscInt ghost; 1111 1112 ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr); 1113 if (ghost >= 0) continue; 1114 ierr = DMPlexPointLocalRead(dmFace, face, facegeom, &fg);CHKERRQ(ierr); 1115 ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr); 1116 ierr = DMPlexPointLocalRead(dmCell, cells[0], cellgeom, &cgL);CHKERRQ(ierr); 1117 ierr = DMPlexPointLocalRead(dmCell, cells[1], cellgeom, &cgR);CHKERRQ(ierr); 1118 for (f = 0; f < Nf; ++f) { 1119 PetscInt off; 1120 1121 ierr = PetscDSGetFieldOffset(prob, f, &off);CHKERRQ(ierr); 1122 ierr = DMPlexPointLocalFieldRead(dm, cells[0], f, x, &xL);CHKERRQ(ierr); 1123 ierr = DMPlexPointLocalFieldRead(dm, cells[1], f, x, &xR);CHKERRQ(ierr); 1124 if (isFE[f]) { 1125 const PetscInt *cone; 1126 PetscInt coneSize, faceLocL, faceLocR; 1127 1128 ierr = DMPlexGetCone(dm, cells[0], &cone);CHKERRQ(ierr); 1129 ierr = DMPlexGetConeSize(dm, cells[0], &coneSize);CHKERRQ(ierr); 1130 for (faceLocL = 0; faceLocL < coneSize; ++faceLocL) if (cone[faceLocL] == face) break; 1131 if (faceLocL == coneSize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Could not find face %d in cone of cell %d", face, cells[0]); 1132 ierr = DMPlexGetCone(dm, cells[1], &cone);CHKERRQ(ierr); 1133 ierr = DMPlexGetConeSize(dm, cells[1], &coneSize);CHKERRQ(ierr); 1134 for (faceLocR = 0; faceLocR < coneSize; ++faceLocR) if (cone[faceLocR] == face) break; 1135 if (faceLocR == coneSize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Could not find face %d in cone of cell %d", face, cells[1]); 1136 ierr = EvaluateFaceFields(prob, f, faceLocL, xL, &uLl[iface*Nc+off]);CHKERRQ(ierr); 1137 ierr = EvaluateFaceFields(prob, f, faceLocR, xR, &uRl[iface*Nc+off]);CHKERRQ(ierr); 1138 } else { 1139 PetscFV fv; 1140 PetscInt numComp, c; 1141 1142 ierr = PetscDSGetDiscretization(prob, f, (PetscObject *) &fv);CHKERRQ(ierr); 1143 ierr = PetscFVGetNumComponents(fv, &numComp);CHKERRQ(ierr); 1144 if (dmGrad) { 1145 PetscReal dxL[3], dxR[3]; 1146 1147 ierr = DMPlexPointLocalRead(dmGrad, cells[0], lgrad, &gL);CHKERRQ(ierr); 1148 ierr = DMPlexPointLocalRead(dmGrad, cells[1], lgrad, &gR);CHKERRQ(ierr); 1149 DMPlex_WaxpyD_Internal(dim, -1, cgL->centroid, fg->centroid, dxL); 1150 DMPlex_WaxpyD_Internal(dim, -1, cgR->centroid, fg->centroid, dxR); 1151 for (c = 0; c < numComp; ++c) { 1152 uLl[iface*Nc+off+c] = xL[c] + DMPlex_DotD_Internal(dim, &gL[c*dim], dxL); 1153 uRl[iface*Nc+off+c] = xR[c] + DMPlex_DotD_Internal(dim, &gR[c*dim], dxR); 1154 } 1155 } else { 1156 for (c = 0; c < numComp; ++c) { 1157 uLl[iface*Nc+off+c] = xL[c]; 1158 uRl[iface*Nc+off+c] = xR[c]; 1159 } 1160 } 1161 } 1162 } 1163 ++iface; 1164 } 1165 ierr = VecRestoreArrayRead(locX, &x);CHKERRQ(ierr); 1166 ierr = VecRestoreArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); 1167 ierr = VecRestoreArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr); 1168 if (locGrad) { 1169 ierr = VecRestoreArrayRead(locGrad, &lgrad);CHKERRQ(ierr); 1170 } 1171 ierr = PetscFree(isFE);CHKERRQ(ierr); 1172 PetscFunctionReturn(0); 1173 } 1174 1175 #undef __FUNCT__ 1176 #define __FUNCT__ "DMPlexRestoreFaceFields" 1177 /*@C 1178 DMPlexRestoreFaceFields - Restore the field values values for a chunk of faces 1179 1180 Input Parameters: 1181 + dm - The DM 1182 . fStart - The first face to include 1183 . fEnd - The first face to exclude 1184 . locX - A local vector with the solution fields 1185 . locX_t - A local vector with solution field time derivatives, or NULL 1186 . faceGeometry - A local vector with face geometry 1187 . cellGeometry - A local vector with cell geometry 1188 - locaGrad - A local vector with field gradients, or NULL 1189 1190 Output Parameters: 1191 + uL - The field values at the left side of the face 1192 - uR - The field values at the right side of the face 1193 1194 Level: developer 1195 1196 .seealso: DMPlexGetFaceFields() 1197 @*/ 1198 PetscErrorCode DMPlexRestoreFaceFields(DM dm, PetscInt fStart, PetscInt fEnd, Vec locX, Vec locX_t, Vec faceGeometry, Vec cellGeometry, Vec locGrad, PetscScalar **uL, PetscScalar **uR) 1199 { 1200 PetscErrorCode ierr; 1201 1202 PetscFunctionBegin; 1203 ierr = DMRestoreWorkArray(dm, 0, PETSC_SCALAR, uL);CHKERRQ(ierr); 1204 ierr = DMRestoreWorkArray(dm, 0, PETSC_SCALAR, uR);CHKERRQ(ierr); 1205 PetscFunctionReturn(0); 1206 } 1207 1208 #undef __FUNCT__ 1209 #define __FUNCT__ "DMPlexGetFaceGeometry" 1210 /*@C 1211 DMPlexGetFaceGeometry - Retrieve the geometric values for a chunk of faces 1212 1213 Input Parameters: 1214 + dm - The DM 1215 . fStart - The first face to include 1216 . fEnd - The first face to exclude 1217 . faceGeometry - A local vector with face geometry 1218 - cellGeometry - A local vector with cell geometry 1219 1220 Output Parameters: 1221 + fgeom - The extract the face centroid and normal 1222 - vol - The cell volume 1223 1224 Level: developer 1225 1226 .seealso: DMPlexGetCellFields() 1227 @*/ 1228 PetscErrorCode DMPlexGetFaceGeometry(DM dm, PetscInt fStart, PetscInt fEnd, Vec faceGeometry, Vec cellGeometry, PetscFVFaceGeom **fgeom, PetscReal **vol) 1229 { 1230 DM dmFace, dmCell; 1231 DMLabel ghostLabel; 1232 const PetscScalar *facegeom, *cellgeom; 1233 PetscInt dim, numFaces = fEnd - fStart, iface, face; 1234 PetscErrorCode ierr; 1235 1236 PetscFunctionBegin; 1237 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1238 PetscValidHeaderSpecific(faceGeometry, VEC_CLASSID, 4); 1239 PetscValidHeaderSpecific(cellGeometry, VEC_CLASSID, 5); 1240 PetscValidPointer(fgeom, 6); 1241 PetscValidPointer(vol, 7); 1242 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1243 ierr = DMPlexGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 1244 ierr = VecGetDM(faceGeometry, &dmFace);CHKERRQ(ierr); 1245 ierr = VecGetArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); 1246 ierr = VecGetDM(cellGeometry, &dmCell);CHKERRQ(ierr); 1247 ierr = VecGetArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr); 1248 ierr = PetscMalloc1(numFaces, fgeom);CHKERRQ(ierr); 1249 ierr = DMGetWorkArray(dm, numFaces*2, PETSC_SCALAR, vol);CHKERRQ(ierr); 1250 for (face = fStart, iface = 0; face < fEnd; ++face) { 1251 const PetscInt *cells; 1252 const PetscFVFaceGeom *fg; 1253 const PetscFVCellGeom *cgL, *cgR; 1254 PetscFVFaceGeom *fgeoml = *fgeom; 1255 PetscReal *voll = *vol; 1256 PetscInt ghost, d; 1257 1258 ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr); 1259 if (ghost >= 0) continue; 1260 ierr = DMPlexPointLocalRead(dmFace, face, facegeom, &fg);CHKERRQ(ierr); 1261 ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr); 1262 ierr = DMPlexPointLocalRead(dmCell, cells[0], cellgeom, &cgL);CHKERRQ(ierr); 1263 ierr = DMPlexPointLocalRead(dmCell, cells[1], cellgeom, &cgR);CHKERRQ(ierr); 1264 for (d = 0; d < dim; ++d) { 1265 fgeoml[iface].centroid[d] = fg->centroid[d]; 1266 fgeoml[iface].normal[d] = fg->normal[d]; 1267 } 1268 voll[iface*2+0] = cgL->volume; 1269 voll[iface*2+1] = cgR->volume; 1270 ++iface; 1271 } 1272 ierr = VecRestoreArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); 1273 ierr = VecRestoreArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr); 1274 PetscFunctionReturn(0); 1275 } 1276 1277 #undef __FUNCT__ 1278 #define __FUNCT__ "DMPlexRestoreFaceGeometry" 1279 /*@C 1280 DMPlexRestoreFaceGeometry - Restore the field values values for a chunk of faces 1281 1282 Input Parameters: 1283 + dm - The DM 1284 . fStart - The first face to include 1285 . fEnd - The first face to exclude 1286 . faceGeometry - A local vector with face geometry 1287 - cellGeometry - A local vector with cell geometry 1288 1289 Output Parameters: 1290 + fgeom - The extract the face centroid and normal 1291 - vol - The cell volume 1292 1293 Level: developer 1294 1295 .seealso: DMPlexGetFaceFields() 1296 @*/ 1297 PetscErrorCode DMPlexRestoreFaceGeometry(DM dm, PetscInt fStart, PetscInt fEnd, Vec faceGeometry, Vec cellGeometry, PetscFVFaceGeom **fgeom, PetscReal **vol) 1298 { 1299 PetscErrorCode ierr; 1300 1301 PetscFunctionBegin; 1302 ierr = PetscFree(*fgeom);CHKERRQ(ierr); 1303 ierr = DMRestoreWorkArray(dm, 0, PETSC_REAL, vol);CHKERRQ(ierr); 1304 PetscFunctionReturn(0); 1305 } 1306 1307 #undef __FUNCT__ 1308 #define __FUNCT__ "DMPlexReconstructGradients_Internal" 1309 PetscErrorCode DMPlexReconstructGradients_Internal(DM dm, PetscInt fStart, PetscInt fEnd, Vec faceGeometry, Vec cellGeometry, Vec locX, Vec grad) 1310 { 1311 DM dmFace, dmCell, dmGrad; 1312 DMLabel ghostLabel; 1313 PetscDS prob; 1314 PetscFV fvm; 1315 PetscLimiter lim; 1316 const PetscScalar *facegeom, *cellgeom, *x; 1317 PetscScalar *gr; 1318 PetscReal *cellPhi; 1319 PetscInt dim, face, cell, totDim, cStart, cEnd, cEndInterior; 1320 PetscErrorCode ierr; 1321 1322 PetscFunctionBegin; 1323 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1324 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1325 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1326 ierr = DMPlexGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 1327 ierr = PetscDSGetDiscretization(prob, 0, (PetscObject *) &fvm);CHKERRQ(ierr); 1328 ierr = PetscFVGetLimiter(fvm, &lim);CHKERRQ(ierr); 1329 ierr = VecGetDM(faceGeometry, &dmFace);CHKERRQ(ierr); 1330 ierr = VecGetArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); 1331 ierr = VecGetDM(cellGeometry, &dmCell);CHKERRQ(ierr); 1332 ierr = VecGetArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr); 1333 ierr = VecGetArrayRead(locX, &x);CHKERRQ(ierr); 1334 ierr = VecGetDM(grad, &dmGrad);CHKERRQ(ierr); 1335 ierr = VecZeroEntries(grad);CHKERRQ(ierr); 1336 ierr = VecGetArray(grad, &gr);CHKERRQ(ierr); 1337 /* Reconstruct gradients */ 1338 for (face = fStart; face < fEnd; ++face) { 1339 const PetscInt *cells; 1340 const PetscFVFaceGeom *fg; 1341 const PetscScalar *cx[2]; 1342 PetscScalar *cgrad[2]; 1343 PetscBool boundary; 1344 PetscInt ghost, c, pd, d; 1345 1346 ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr); 1347 if (ghost >= 0) continue; 1348 ierr = DMPlexIsBoundaryPoint(dm, face, &boundary);CHKERRQ(ierr); 1349 if (boundary) continue; 1350 ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr); 1351 ierr = DMPlexPointLocalRead(dmFace, face, facegeom, &fg);CHKERRQ(ierr); 1352 for (c = 0; c < 2; ++c) { 1353 ierr = DMPlexPointLocalRead(dm, cells[c], x, &cx[c]);CHKERRQ(ierr); 1354 ierr = DMPlexPointGlobalRef(dmGrad, cells[c], gr, &cgrad[c]);CHKERRQ(ierr); 1355 } 1356 for (pd = 0; pd < totDim; ++pd) { 1357 PetscScalar delta = cx[1][pd] - cx[0][pd]; 1358 1359 for (d = 0; d < dim; ++d) { 1360 if (cgrad[0]) cgrad[0][pd*dim+d] += fg->grad[0][d] * delta; 1361 if (cgrad[1]) cgrad[1][pd*dim+d] -= fg->grad[1][d] * delta; 1362 } 1363 } 1364 } 1365 /* Limit interior gradients (using cell-based loop because it generalizes better to vector limiters) */ 1366 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1367 ierr = DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr); 1368 cEndInterior = cEndInterior < 0 ? cEnd : cEndInterior; 1369 ierr = DMGetWorkArray(dm, totDim, PETSC_REAL, &cellPhi);CHKERRQ(ierr); 1370 for (cell = dmGrad && lim ? cStart : cEnd; cell < cEndInterior; ++cell) { 1371 const PetscInt *faces; 1372 const PetscScalar *cx; 1373 const PetscFVCellGeom *cg; 1374 PetscScalar *cgrad; 1375 PetscInt coneSize, f, pd, d; 1376 1377 ierr = DMPlexGetConeSize(dm, cell, &coneSize);CHKERRQ(ierr); 1378 ierr = DMPlexGetCone(dm, cell, &faces);CHKERRQ(ierr); 1379 ierr = DMPlexPointLocalRead(dm, cell, x, &cx);CHKERRQ(ierr); 1380 ierr = DMPlexPointLocalRead(dmCell, cell, cellgeom, &cg);CHKERRQ(ierr); 1381 ierr = DMPlexPointGlobalRef(dmGrad, cell, gr, &cgrad);CHKERRQ(ierr); 1382 if (!cgrad) continue; /* Unowned overlap cell, we do not compute */ 1383 /* Limiter will be minimum value over all neighbors */ 1384 for (d = 0; d < totDim; ++d) cellPhi[d] = PETSC_MAX_REAL; 1385 for (f = 0; f < coneSize; ++f) { 1386 const PetscScalar *ncx; 1387 const PetscFVCellGeom *ncg; 1388 const PetscInt *fcells; 1389 PetscInt face = faces[f], ncell, ghost; 1390 PetscReal v[3]; 1391 PetscBool boundary; 1392 1393 ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr); 1394 ierr = DMPlexIsBoundaryPoint(dm, face, &boundary);CHKERRQ(ierr); 1395 if ((ghost >= 0) || boundary) continue; 1396 ierr = DMPlexGetSupport(dm, face, &fcells);CHKERRQ(ierr); 1397 ncell = cell == fcells[0] ? fcells[1] : fcells[0]; 1398 ierr = DMPlexPointLocalRead(dm, ncell, x, &ncx);CHKERRQ(ierr); 1399 ierr = DMPlexPointLocalRead(dmCell, ncell, cellgeom, &ncg);CHKERRQ(ierr); 1400 DMPlex_WaxpyD_Internal(dim, -1, cg->centroid, ncg->centroid, v); 1401 for (d = 0; d < totDim; ++d) { 1402 /* We use the symmetric slope limited form of Berger, Aftosmis, and Murman 2005 */ 1403 PetscReal phi, flim = 0.5 * PetscRealPart(ncx[d] - cx[d]) / DMPlex_DotD_Internal(dim, &cgrad[d*dim], v); 1404 1405 ierr = PetscLimiterLimit(lim, flim, &phi);CHKERRQ(ierr); 1406 cellPhi[d] = PetscMin(cellPhi[d], phi); 1407 } 1408 } 1409 /* Apply limiter to gradient */ 1410 for (pd = 0; pd < totDim; ++pd) 1411 /* Scalar limiter applied to each component separately */ 1412 for (d = 0; d < dim; ++d) cgrad[pd*dim+d] *= cellPhi[pd]; 1413 } 1414 ierr = DMRestoreWorkArray(dm, totDim, PETSC_REAL, &cellPhi);CHKERRQ(ierr); 1415 ierr = VecRestoreArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); 1416 ierr = VecRestoreArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr); 1417 ierr = VecRestoreArrayRead(locX, &x);CHKERRQ(ierr); 1418 ierr = VecRestoreArray(grad, &gr);CHKERRQ(ierr); 1419 PetscFunctionReturn(0); 1420 } 1421 1422 #undef __FUNCT__ 1423 #define __FUNCT__ "DMPlexComputeBdResidual_Internal" 1424 PetscErrorCode DMPlexComputeBdResidual_Internal(DM dm, Vec locX, Vec locX_t, Vec locF, void *user) 1425 { 1426 DM_Plex *mesh = (DM_Plex *) dm->data; 1427 PetscSection section; 1428 PetscDS prob; 1429 DMLabel depth; 1430 PetscFECellGeom *cgeom; 1431 PetscScalar *u = NULL, *u_t = NULL, *elemVec = NULL; 1432 PetscInt dim, Nf, f, totDimBd, numBd, bd; 1433 PetscErrorCode ierr; 1434 1435 PetscFunctionBegin; 1436 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1437 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 1438 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1439 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 1440 ierr = PetscDSGetTotalBdDimension(prob, &totDimBd);CHKERRQ(ierr); 1441 ierr = DMPlexGetDepthLabel(dm, &depth);CHKERRQ(ierr); 1442 ierr = DMPlexGetNumBoundary(dm, &numBd);CHKERRQ(ierr); 1443 for (bd = 0; bd < numBd; ++bd) { 1444 const char *bdLabel; 1445 DMLabel label; 1446 IS pointIS; 1447 const PetscInt *points; 1448 const PetscInt *values; 1449 PetscInt field, numValues, numPoints, p, dep, numFaces; 1450 PetscBool isEssential; 1451 1452 ierr = DMPlexGetBoundary(dm, bd, &isEssential, NULL, &bdLabel, &field, NULL, &numValues, &values, NULL);CHKERRQ(ierr); 1453 if (isEssential) continue; 1454 if (numValues != 1) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Bug me and I will fix this"); 1455 ierr = DMPlexGetLabel(dm, bdLabel, &label);CHKERRQ(ierr); 1456 ierr = DMLabelGetStratumSize(label, 1, &numPoints);CHKERRQ(ierr); 1457 ierr = DMLabelGetStratumIS(label, 1, &pointIS);CHKERRQ(ierr); 1458 ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); 1459 for (p = 0, numFaces = 0; p < numPoints; ++p) { 1460 ierr = DMLabelGetValue(depth, points[p], &dep);CHKERRQ(ierr); 1461 if (dep == dim-1) ++numFaces; 1462 } 1463 ierr = PetscMalloc3(numFaces*totDimBd,&u,numFaces,&cgeom,numFaces*totDimBd,&elemVec);CHKERRQ(ierr); 1464 if (locX_t) {ierr = PetscMalloc1(numFaces*totDimBd,&u_t);CHKERRQ(ierr);} 1465 for (p = 0, f = 0; p < numPoints; ++p) { 1466 const PetscInt point = points[p]; 1467 PetscScalar *x = NULL; 1468 PetscInt i; 1469 1470 ierr = DMLabelGetValue(depth, points[p], &dep);CHKERRQ(ierr); 1471 if (dep != dim-1) continue; 1472 ierr = DMPlexComputeCellGeometryFEM(dm, point, NULL, cgeom[f].v0, cgeom[f].J, cgeom[f].invJ, &cgeom[f].detJ);CHKERRQ(ierr); 1473 ierr = DMPlexComputeCellGeometryFVM(dm, point, NULL, NULL, cgeom[f].n); 1474 if (cgeom[f].detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for face %d", cgeom[f].detJ, point); 1475 ierr = DMPlexVecGetClosure(dm, section, locX, point, NULL, &x);CHKERRQ(ierr); 1476 for (i = 0; i < totDimBd; ++i) u[f*totDimBd+i] = x[i]; 1477 ierr = DMPlexVecRestoreClosure(dm, section, locX, point, NULL, &x);CHKERRQ(ierr); 1478 if (locX_t) { 1479 ierr = DMPlexVecGetClosure(dm, section, locX_t, point, NULL, &x);CHKERRQ(ierr); 1480 for (i = 0; i < totDimBd; ++i) u_t[f*totDimBd+i] = x[i]; 1481 ierr = DMPlexVecRestoreClosure(dm, section, locX_t, point, NULL, &x);CHKERRQ(ierr); 1482 } 1483 ++f; 1484 } 1485 for (f = 0; f < Nf; ++f) { 1486 PetscFE fe; 1487 PetscQuadrature q; 1488 PetscInt numQuadPoints, Nb; 1489 /* Conforming batches */ 1490 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 1491 /* Remainder */ 1492 PetscInt Nr, offset; 1493 1494 ierr = PetscDSGetBdDiscretization(prob, f, (PetscObject *) &fe);CHKERRQ(ierr); 1495 ierr = PetscFEGetQuadrature(fe, &q);CHKERRQ(ierr); 1496 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 1497 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1498 ierr = PetscQuadratureGetData(q, NULL, &numQuadPoints, NULL, NULL);CHKERRQ(ierr); 1499 blockSize = Nb*numQuadPoints; 1500 batchSize = numBlocks * blockSize; 1501 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1502 numChunks = numFaces / (numBatches*batchSize); 1503 Ne = numChunks*numBatches*batchSize; 1504 Nr = numFaces % (numBatches*batchSize); 1505 offset = numFaces - Nr; 1506 ierr = PetscFEIntegrateBdResidual(fe, prob, f, Ne, cgeom, u, u_t, NULL, NULL, elemVec);CHKERRQ(ierr); 1507 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); 1508 } 1509 for (p = 0, f = 0; p < numPoints; ++p) { 1510 const PetscInt point = points[p]; 1511 1512 ierr = DMLabelGetValue(depth, point, &dep);CHKERRQ(ierr); 1513 if (dep != dim-1) continue; 1514 if (mesh->printFEM > 1) {ierr = DMPrintCellVector(point, "BdResidual", totDimBd, &elemVec[f*totDimBd]);CHKERRQ(ierr);} 1515 ierr = DMPlexVecSetClosure(dm, NULL, locF, point, &elemVec[f*totDimBd], ADD_VALUES);CHKERRQ(ierr); 1516 ++f; 1517 } 1518 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 1519 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 1520 ierr = PetscFree3(u,cgeom,elemVec);CHKERRQ(ierr); 1521 if (locX_t) {ierr = PetscFree(u_t);CHKERRQ(ierr);} 1522 } 1523 PetscFunctionReturn(0); 1524 } 1525 1526 #undef __FUNCT__ 1527 #define __FUNCT__ "DMPlexComputeResidual_Internal" 1528 PetscErrorCode DMPlexComputeResidual_Internal(DM dm, PetscReal time, Vec locX, Vec locX_t, Vec locF, void *user) 1529 { 1530 DM_Plex *mesh = (DM_Plex *) dm->data; 1531 const char *name = "Residual"; 1532 DM dmAux = NULL; 1533 DM dmGrad = NULL; 1534 DMLabel ghostLabel = NULL; 1535 PetscDS prob = NULL; 1536 PetscDS probAux = NULL; 1537 PetscSection section = NULL; 1538 PetscBool useFEM = PETSC_FALSE; 1539 PetscBool useFVM = PETSC_FALSE; 1540 PetscFV fvm = NULL; 1541 PetscFECellGeom *cgeomFEM = NULL; 1542 PetscFVCellGeom *cgeomFVM = NULL; 1543 PetscFVFaceGeom *fgeomFVM = NULL; 1544 Vec locA, cellGeometryFEM = NULL, cellGeometryFVM = NULL, faceGeometryFVM = NULL, grad, locGrad = NULL; 1545 PetscScalar *u, *u_t, *a, *uL, *uR; 1546 PetscInt Nf, f, totDim, totDimAux, numChunks, cellChunkSize, faceChunkSize, chunk, cStart, cEnd, cEndInterior, fStart, fEnd; 1547 PetscErrorCode ierr; 1548 1549 PetscFunctionBegin; 1550 ierr = PetscLogEventBegin(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr); 1551 /* TODO The places where we have to use isFE are probably the member functions for the PetscDisc class */ 1552 /* TODO The FVM geometry is over-manipulated. Make the preclac functions return exactly what we need */ 1553 /* FEM+FVM */ 1554 /* 1: Get sizes from dm and dmAux */ 1555 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 1556 ierr = DMPlexGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 1557 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1558 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 1559 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1560 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);CHKERRQ(ierr); 1561 if (locA) { 1562 ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); 1563 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 1564 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 1565 } 1566 /* 2: Get geometric data */ 1567 for (f = 0; f < Nf; ++f) { 1568 PetscObject obj; 1569 PetscClassId id; 1570 1571 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1572 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1573 if (id == PETSCFE_CLASSID) {useFEM = PETSC_TRUE;} 1574 if (id == PETSCFV_CLASSID) {useFVM = PETSC_TRUE; fvm = (PetscFV) obj;} 1575 } 1576 if (useFEM) { 1577 ierr = DMPlexSNESGetGeometryFEM(dm, &cellGeometryFEM);CHKERRQ(ierr); 1578 ierr = VecGetArrayRead(cellGeometryFEM, (const PetscScalar **) &cgeomFEM);CHKERRQ(ierr); 1579 } 1580 if (useFVM) { 1581 ierr = DMPlexSNESGetGeometryFVM(dm, &faceGeometryFVM, &cellGeometryFVM, NULL);CHKERRQ(ierr); 1582 ierr = VecGetArrayRead(faceGeometryFVM, (const PetscScalar **) &fgeomFVM);CHKERRQ(ierr); 1583 ierr = VecGetArrayRead(cellGeometryFVM, (const PetscScalar **) &cgeomFVM);CHKERRQ(ierr); 1584 /* Reconstruct and limit cell gradients */ 1585 ierr = DMPlexSNESGetGradientDM(dm, fvm, &dmGrad);CHKERRQ(ierr); 1586 if (dmGrad) { 1587 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 1588 ierr = DMGetGlobalVector(dmGrad, &grad);CHKERRQ(ierr); 1589 ierr = DMPlexReconstructGradients_Internal(dm, fStart, fEnd, faceGeometryFVM, cellGeometryFVM, locX, grad);CHKERRQ(ierr); 1590 /* Communicate gradient values */ 1591 ierr = DMGetLocalVector(dmGrad, &locGrad);CHKERRQ(ierr); 1592 ierr = DMGlobalToLocalBegin(dmGrad, grad, INSERT_VALUES, locGrad);CHKERRQ(ierr); 1593 ierr = DMGlobalToLocalEnd(dmGrad, grad, INSERT_VALUES, locGrad);CHKERRQ(ierr); 1594 ierr = DMRestoreGlobalVector(dmGrad, &grad);CHKERRQ(ierr); 1595 } 1596 } 1597 /* Handle boundary values */ 1598 ierr = DMPlexInsertBoundaryValues(dm, locX, time, faceGeometryFVM, cellGeometryFVM, locGrad);CHKERRQ(ierr); 1599 /* Loop over chunks */ 1600 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1601 ierr = DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr); 1602 cEnd = cEndInterior < 0 ? cEnd : cEndInterior; 1603 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 1604 numChunks = 1; 1605 cellChunkSize = (cEnd - cStart)/numChunks; 1606 faceChunkSize = (fEnd - fStart)/numChunks; 1607 for (chunk = 0; chunk < numChunks; ++chunk) { 1608 PetscScalar *elemVec, *fluxL, *fluxR; 1609 PetscReal *vol; 1610 PetscFVFaceGeom *fgeom; 1611 PetscInt cS = cStart+chunk*cellChunkSize, cE = PetscMin(cS+cellChunkSize, cEnd), numCells = cE - cS, cell; 1612 PetscInt fS = fStart+chunk*faceChunkSize, fE = PetscMin(fS+faceChunkSize, fEnd), numFaces = fE - fS, face; 1613 1614 /* Extract field coefficients */ 1615 if (useFEM) { 1616 ierr = DMPlexGetCellFields(dm, cS, cE, locX, locX_t, locA, &u, &u_t, &a);CHKERRQ(ierr); 1617 ierr = DMGetWorkArray(dm, numCells*totDim, PETSC_SCALAR, &elemVec);CHKERRQ(ierr); 1618 ierr = PetscMemzero(elemVec, numCells*totDim * sizeof(PetscScalar));CHKERRQ(ierr); 1619 } 1620 if (useFVM) { 1621 ierr = DMPlexGetFaceFields(dm, fS, fE, locX, locX_t, faceGeometryFVM, cellGeometryFVM, locGrad, &uL, &uR);CHKERRQ(ierr); 1622 ierr = DMPlexGetFaceGeometry(dm, fS, fE, faceGeometryFVM, cellGeometryFVM, &fgeom, &vol);CHKERRQ(ierr); 1623 ierr = DMGetWorkArray(dm, numFaces*totDim, PETSC_SCALAR, &fluxL);CHKERRQ(ierr); 1624 ierr = DMGetWorkArray(dm, numFaces*totDim, PETSC_SCALAR, &fluxR);CHKERRQ(ierr); 1625 ierr = PetscMemzero(fluxL, numFaces*totDim * sizeof(PetscScalar));CHKERRQ(ierr); 1626 ierr = PetscMemzero(fluxR, numFaces*totDim * sizeof(PetscScalar));CHKERRQ(ierr); 1627 } 1628 /* TODO We will interlace both our field coefficients (u, u_t, uL, uR, etc.) and our output (elemVec, fL, fR). I think this works */ 1629 /* Loop over fields */ 1630 for (f = 0; f < Nf; ++f) { 1631 PetscObject obj; 1632 PetscClassId id; 1633 PetscInt numChunks, numBatches, batchSize, numBlocks, blockSize, Ne, Nr, offset; 1634 1635 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1636 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1637 if (id == PETSCFE_CLASSID) { 1638 PetscFE fe = (PetscFE) obj; 1639 PetscQuadrature q; 1640 PetscInt Nq, Nb; 1641 1642 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1643 1644 ierr = PetscFEGetQuadrature(fe, &q);CHKERRQ(ierr); 1645 ierr = PetscQuadratureGetData(q, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 1646 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 1647 blockSize = Nb*Nq; 1648 batchSize = numBlocks * blockSize; 1649 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1650 numChunks = numCells / (numBatches*batchSize); 1651 Ne = numChunks*numBatches*batchSize; 1652 Nr = numCells % (numBatches*batchSize); 1653 offset = numCells - Nr; 1654 /* Integrate FE residual to get elemVec (need fields at quadrature points) */ 1655 /* 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) */ 1656 ierr = PetscFEIntegrateResidual(fe, prob, f, Ne, cgeomFEM, u, u_t, probAux, a, elemVec);CHKERRQ(ierr); 1657 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); 1658 } else if (id == PETSCFV_CLASSID) { 1659 PetscFV fv = (PetscFV) obj; 1660 1661 Ne = numFaces; 1662 Nr = 0; 1663 /* Riemann solve over faces (need fields at face centroids) */ 1664 /* We need to evaluate FE fields at those coordinates */ 1665 ierr = PetscFVIntegrateRHSFunction(fv, prob, f, Ne, fgeom, vol, uL, uR, fluxL, fluxR);CHKERRQ(ierr); 1666 } else SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %d", f); 1667 } 1668 /* Loop over domain */ 1669 if (useFEM) { 1670 /* Add elemVec to locX */ 1671 for (cell = cS; cell < cE; ++cell) { 1672 if (mesh->printFEM > 1) {ierr = DMPrintCellVector(cell, name, totDim, &elemVec[cell*totDim]);CHKERRQ(ierr);} 1673 ierr = DMPlexVecSetClosure(dm, section, locF, cell, &elemVec[cell*totDim], ADD_VALUES);CHKERRQ(ierr); 1674 } 1675 } 1676 if (useFVM) { 1677 PetscScalar *fa; 1678 PetscInt iface; 1679 1680 /* Accumulate fluxes to cells */ 1681 ierr = VecGetArray(locF, &fa);CHKERRQ(ierr); 1682 for (face = fS, iface = 0; face < fE; ++face) { 1683 const PetscInt *cells; 1684 PetscScalar *fL, *fR; 1685 PetscInt ghost, d; 1686 1687 ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr); 1688 if (ghost >= 0) continue; 1689 ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr); 1690 ierr = DMPlexPointGlobalRef(dm, cells[0], fa, &fL);CHKERRQ(ierr); 1691 ierr = DMPlexPointGlobalRef(dm, cells[1], fa, &fR);CHKERRQ(ierr); 1692 for (d = 0; d < totDim; ++d) { 1693 if (fL) fL[d] -= fluxL[iface*totDim+d]; 1694 if (fR) fR[d] += fluxR[iface*totDim+d]; 1695 } 1696 ++iface; 1697 } 1698 ierr = VecRestoreArray(locF, &fa);CHKERRQ(ierr); 1699 } 1700 if (useFEM) { 1701 ierr = DMPlexRestoreCellFields(dm, cS, cE, locX, locX_t, locA, &u, &u_t, &a);CHKERRQ(ierr); 1702 ierr = DMRestoreWorkArray(dm, numCells*totDim, PETSC_SCALAR, &elemVec);CHKERRQ(ierr); 1703 } 1704 if (useFVM) { 1705 ierr = DMPlexRestoreFaceFields(dm, fS, fE, locX, locX_t, faceGeometryFVM, cellGeometryFVM, locGrad, &uL, &uR);CHKERRQ(ierr); 1706 ierr = DMPlexRestoreFaceGeometry(dm, fS, fE, faceGeometryFVM, cellGeometryFVM, &fgeom, &vol);CHKERRQ(ierr); 1707 ierr = DMRestoreWorkArray(dm, numFaces*totDim, PETSC_SCALAR, &fluxL);CHKERRQ(ierr); 1708 ierr = DMRestoreWorkArray(dm, numFaces*totDim, PETSC_SCALAR, &fluxR);CHKERRQ(ierr); 1709 if (dmGrad) {ierr = DMRestoreLocalVector(dmGrad, &locGrad);CHKERRQ(ierr);} 1710 } 1711 } 1712 1713 if (useFEM) {ierr = DMPlexComputeBdResidual_Internal(dm, locX, locX_t, locF, user);CHKERRQ(ierr);} 1714 1715 /* FEM */ 1716 /* 1: Get sizes from dm and dmAux */ 1717 /* 2: Get geometric data */ 1718 /* 3: Handle boundary values */ 1719 /* 4: Loop over domain */ 1720 /* Extract coefficients */ 1721 /* Loop over fields */ 1722 /* Set tiling for FE*/ 1723 /* Integrate FE residual to get elemVec */ 1724 /* Loop over subdomain */ 1725 /* Loop over quad points */ 1726 /* Transform coords to real space */ 1727 /* Evaluate field and aux fields at point */ 1728 /* Evaluate residual at point */ 1729 /* Transform residual to real space */ 1730 /* Add residual to elemVec */ 1731 /* Loop over domain */ 1732 /* Add elemVec to locX */ 1733 1734 /* FVM */ 1735 /* Get geometric data */ 1736 /* If using gradients */ 1737 /* Compute gradient data */ 1738 /* Loop over domain faces */ 1739 /* Count computational faces */ 1740 /* Reconstruct cell gradient */ 1741 /* Loop over domain cells */ 1742 /* Limit cell gradients */ 1743 /* Handle boundary values */ 1744 /* Loop over domain faces */ 1745 /* Read out field, centroid, normal, volume for each side of face */ 1746 /* Riemann solve over faces */ 1747 /* Loop over domain faces */ 1748 /* Accumulate fluxes to cells */ 1749 /* TODO Change printFEM to printDisc here */ 1750 if (mesh->printFEM) {ierr = DMPrintLocalVec(dm, name, mesh->printTol, locF);CHKERRQ(ierr);} 1751 ierr = PetscLogEventEnd(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr); 1752 PetscFunctionReturn(0); 1753 } 1754 1755 #undef __FUNCT__ 1756 #define __FUNCT__ "DMPlexComputeResidualFEM_Check_Internal" 1757 static PetscErrorCode DMPlexComputeResidualFEM_Check_Internal(DM dm, Vec X, Vec X_t, Vec F, void *user) 1758 { 1759 DM dmCh, dmAux; 1760 Vec A, cellgeom; 1761 PetscDS prob, probCh, probAux = NULL; 1762 PetscQuadrature q; 1763 PetscSection section, sectionAux; 1764 PetscFECellGeom *cgeom; 1765 PetscScalar *elemVec, *elemVecCh, *u, *u_t, *a = NULL; 1766 PetscInt dim, Nf, f, numCells, cStart, cEnd, c; 1767 PetscInt totDim, totDimAux, diffCell = 0; 1768 PetscErrorCode ierr; 1769 1770 PetscFunctionBegin; 1771 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1772 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 1773 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1774 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1775 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); 1776 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1777 numCells = cEnd - cStart; 1778 ierr = PetscObjectQuery((PetscObject) dm, "dmCh", (PetscObject *) &dmCh);CHKERRQ(ierr); 1779 ierr = DMGetDS(dmCh, &probCh);CHKERRQ(ierr); 1780 ierr = PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);CHKERRQ(ierr); 1781 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);CHKERRQ(ierr); 1782 if (dmAux) { 1783 ierr = DMGetDefaultSection(dmAux, §ionAux);CHKERRQ(ierr); 1784 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 1785 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 1786 } 1787 ierr = DMPlexInsertBoundaryValues(dm, X, 0.0, NULL, NULL, NULL);CHKERRQ(ierr); 1788 ierr = VecSet(F, 0.0);CHKERRQ(ierr); 1789 ierr = PetscMalloc3(numCells*totDim,&u,X_t ? numCells*totDim : 0,&u_t,numCells*totDim,&elemVec);CHKERRQ(ierr); 1790 ierr = PetscMalloc1(numCells*totDim,&elemVecCh);CHKERRQ(ierr); 1791 if (dmAux) {ierr = PetscMalloc1(numCells*totDimAux, &a);CHKERRQ(ierr);} 1792 ierr = DMPlexSNESGetGeometryFEM(dm, &cellgeom);CHKERRQ(ierr); 1793 ierr = VecGetArray(cellgeom, (PetscScalar **) &cgeom);CHKERRQ(ierr); 1794 for (c = cStart; c < cEnd; ++c) { 1795 PetscScalar *x = NULL, *x_t = NULL; 1796 PetscInt i; 1797 1798 ierr = DMPlexVecGetClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr); 1799 for (i = 0; i < totDim; ++i) u[c*totDim+i] = x[i]; 1800 ierr = DMPlexVecRestoreClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr); 1801 if (X_t) { 1802 ierr = DMPlexVecGetClosure(dm, section, X_t, c, NULL, &x_t);CHKERRQ(ierr); 1803 for (i = 0; i < totDim; ++i) u_t[c*totDim+i] = x_t[i]; 1804 ierr = DMPlexVecRestoreClosure(dm, section, X_t, c, NULL, &x_t);CHKERRQ(ierr); 1805 } 1806 if (dmAux) { 1807 ierr = DMPlexVecGetClosure(dmAux, sectionAux, A, c, NULL, &x);CHKERRQ(ierr); 1808 for (i = 0; i < totDimAux; ++i) a[c*totDimAux+i] = x[i]; 1809 ierr = DMPlexVecRestoreClosure(dmAux, sectionAux, A, c, NULL, &x);CHKERRQ(ierr); 1810 } 1811 } 1812 for (f = 0; f < Nf; ++f) { 1813 PetscFE fe, feCh; 1814 PetscInt numQuadPoints, Nb; 1815 /* Conforming batches */ 1816 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 1817 /* Remainder */ 1818 PetscInt Nr, offset; 1819 1820 ierr = PetscDSGetDiscretization(prob, f, (PetscObject *) &fe);CHKERRQ(ierr); 1821 ierr = PetscDSGetDiscretization(probCh, f, (PetscObject *) &feCh);CHKERRQ(ierr); 1822 ierr = PetscFEGetQuadrature(fe, &q);CHKERRQ(ierr); 1823 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 1824 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1825 ierr = PetscQuadratureGetData(q, NULL, &numQuadPoints, NULL, NULL);CHKERRQ(ierr); 1826 blockSize = Nb*numQuadPoints; 1827 batchSize = numBlocks * blockSize; 1828 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1829 numChunks = numCells / (numBatches*batchSize); 1830 Ne = numChunks*numBatches*batchSize; 1831 Nr = numCells % (numBatches*batchSize); 1832 offset = numCells - Nr; 1833 ierr = PetscFEIntegrateResidual(fe, prob, f, Ne, cgeom, u, u_t, probAux, a, elemVec);CHKERRQ(ierr); 1834 ierr = PetscFEIntegrateResidual(feCh, prob, f, Ne, cgeom, u, u_t, probAux, a, elemVecCh);CHKERRQ(ierr); 1835 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); 1836 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); 1837 } 1838 for (c = cStart; c < cEnd; ++c) { 1839 PetscBool diff = PETSC_FALSE; 1840 PetscInt d; 1841 1842 for (d = 0; d < totDim; ++d) if (PetscAbsScalar(elemVec[c*totDim+d] - elemVecCh[c*totDim+d]) > 1.0e-7) {diff = PETSC_TRUE;break;} 1843 if (diff) { 1844 ierr = PetscPrintf(PetscObjectComm((PetscObject) dm), "Different cell %d\n", c);CHKERRQ(ierr); 1845 ierr = DMPrintCellVector(c, "Residual", totDim, &elemVec[c*totDim]);CHKERRQ(ierr); 1846 ierr = DMPrintCellVector(c, "Check Residual", totDim, &elemVecCh[c*totDim]);CHKERRQ(ierr); 1847 ++diffCell; 1848 } 1849 if (diffCell > 9) break; 1850 ierr = DMPlexVecSetClosure(dm, section, F, c, &elemVec[c*totDim], ADD_VALUES);CHKERRQ(ierr); 1851 } 1852 ierr = VecRestoreArray(cellgeom, (PetscScalar **) &cgeom);CHKERRQ(ierr); 1853 ierr = PetscFree3(u,u_t,elemVec);CHKERRQ(ierr); 1854 ierr = PetscFree(elemVecCh);CHKERRQ(ierr); 1855 if (dmAux) {ierr = PetscFree(a);CHKERRQ(ierr);} 1856 PetscFunctionReturn(0); 1857 } 1858 1859 #undef __FUNCT__ 1860 #define __FUNCT__ "DMPlexSNESComputeResidualFEM" 1861 /*@ 1862 DMPlexSNESComputeResidualFEM - Form the local residual F from the local input X using pointwise functions specified by the user 1863 1864 Input Parameters: 1865 + dm - The mesh 1866 . X - Local solution 1867 - user - The user context 1868 1869 Output Parameter: 1870 . F - Local output vector 1871 1872 Level: developer 1873 1874 .seealso: DMPlexComputeJacobianActionFEM() 1875 @*/ 1876 PetscErrorCode DMPlexSNESComputeResidualFEM(DM dm, Vec X, Vec F, void *user) 1877 { 1878 PetscObject check; 1879 PetscErrorCode ierr; 1880 1881 PetscFunctionBegin; 1882 /* The dmCh is used to check two mathematically equivalent discretizations for computational equivalence */ 1883 ierr = PetscObjectQuery((PetscObject) dm, "dmCh", &check);CHKERRQ(ierr); 1884 if (check) {ierr = DMPlexComputeResidualFEM_Check_Internal(dm, X, NULL, F, user);CHKERRQ(ierr);} 1885 else {ierr = DMPlexComputeResidual_Internal(dm, 0.0, X, NULL, F, user);CHKERRQ(ierr);} 1886 PetscFunctionReturn(0); 1887 } 1888 1889 #undef __FUNCT__ 1890 #define __FUNCT__ "DMPlexComputeJacobianFEM_Internal" 1891 PetscErrorCode DMPlexComputeJacobianFEM_Internal(DM dm, Vec X, Vec X_t, Mat Jac, Mat JacP,void *user) 1892 { 1893 DM_Plex *mesh = (DM_Plex *) dm->data; 1894 const char *name = "Jacobian"; 1895 DM dmAux; 1896 DMLabel depth; 1897 Vec A, cellgeom; 1898 PetscDS prob, probAux = NULL; 1899 PetscQuadrature quad; 1900 PetscSection section, globalSection, sectionAux; 1901 PetscFECellGeom *cgeom; 1902 PetscScalar *elemMat, *u, *u_t, *a = NULL; 1903 PetscInt dim, Nf, f, fieldI, fieldJ, numCells, cStart, cEnd, c; 1904 PetscInt totDim, totDimBd, totDimAux, numBd, bd; 1905 PetscBool isShell; 1906 PetscErrorCode ierr; 1907 1908 PetscFunctionBegin; 1909 ierr = PetscLogEventBegin(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 1910 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1911 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 1912 ierr = DMGetDefaultGlobalSection(dm, &globalSection);CHKERRQ(ierr); 1913 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1914 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1915 ierr = PetscDSGetTotalBdDimension(prob, &totDimBd);CHKERRQ(ierr); 1916 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); 1917 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1918 numCells = cEnd - cStart; 1919 ierr = PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);CHKERRQ(ierr); 1920 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);CHKERRQ(ierr); 1921 if (dmAux) { 1922 ierr = DMGetDefaultSection(dmAux, §ionAux);CHKERRQ(ierr); 1923 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 1924 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 1925 } 1926 ierr = DMPlexInsertBoundaryValues(dm, X, 0.0, NULL, NULL, NULL);CHKERRQ(ierr); 1927 ierr = MatZeroEntries(JacP);CHKERRQ(ierr); 1928 ierr = PetscMalloc3(numCells*totDim,&u,X_t ? numCells*totDim : 0,&u_t,numCells*totDim*totDim,&elemMat);CHKERRQ(ierr); 1929 if (dmAux) {ierr = PetscMalloc1(numCells*totDimAux, &a);CHKERRQ(ierr);} 1930 ierr = DMPlexSNESGetGeometryFEM(dm, &cellgeom);CHKERRQ(ierr); 1931 ierr = VecGetArray(cellgeom, (PetscScalar **) &cgeom);CHKERRQ(ierr); 1932 for (c = cStart; c < cEnd; ++c) { 1933 PetscScalar *x = NULL, *x_t = NULL; 1934 PetscInt i; 1935 1936 ierr = DMPlexVecGetClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr); 1937 for (i = 0; i < totDim; ++i) u[c*totDim+i] = x[i]; 1938 ierr = DMPlexVecRestoreClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr); 1939 if (X_t) { 1940 ierr = DMPlexVecGetClosure(dm, section, X_t, c, NULL, &x_t);CHKERRQ(ierr); 1941 for (i = 0; i < totDim; ++i) u_t[c*totDim+i] = x_t[i]; 1942 ierr = DMPlexVecRestoreClosure(dm, section, X_t, c, NULL, &x_t);CHKERRQ(ierr); 1943 } 1944 if (dmAux) { 1945 ierr = DMPlexVecGetClosure(dmAux, sectionAux, A, c, NULL, &x);CHKERRQ(ierr); 1946 for (i = 0; i < totDimAux; ++i) a[c*totDimAux+i] = x[i]; 1947 ierr = DMPlexVecRestoreClosure(dmAux, sectionAux, A, c, NULL, &x);CHKERRQ(ierr); 1948 } 1949 } 1950 ierr = PetscMemzero(elemMat, numCells*totDim*totDim * sizeof(PetscScalar));CHKERRQ(ierr); 1951 for (fieldI = 0; fieldI < Nf; ++fieldI) { 1952 PetscFE fe; 1953 PetscInt numQuadPoints, Nb; 1954 /* Conforming batches */ 1955 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 1956 /* Remainder */ 1957 PetscInt Nr, offset; 1958 1959 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); 1960 ierr = PetscFEGetQuadrature(fe, &quad);CHKERRQ(ierr); 1961 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 1962 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1963 ierr = PetscQuadratureGetData(quad, NULL, &numQuadPoints, NULL, NULL);CHKERRQ(ierr); 1964 blockSize = Nb*numQuadPoints; 1965 batchSize = numBlocks * blockSize; 1966 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1967 numChunks = numCells / (numBatches*batchSize); 1968 Ne = numChunks*numBatches*batchSize; 1969 Nr = numCells % (numBatches*batchSize); 1970 offset = numCells - Nr; 1971 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 1972 ierr = PetscFEIntegrateJacobian(fe, prob, fieldI, fieldJ, Ne, cgeom, u, u_t, probAux, a, elemMat);CHKERRQ(ierr); 1973 ierr = PetscFEIntegrateJacobian(fe, prob, 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); 1974 } 1975 } 1976 for (c = cStart; c < cEnd; ++c) { 1977 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(c, name, totDim, totDim, &elemMat[c*totDim*totDim]);CHKERRQ(ierr);} 1978 ierr = DMPlexMatSetClosure(dm, section, globalSection, JacP, c, &elemMat[c*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 1979 } 1980 ierr = VecGetArray(cellgeom, (PetscScalar **) &cgeom);CHKERRQ(ierr); 1981 ierr = PetscFree3(u,u_t,elemMat);CHKERRQ(ierr); 1982 if (dmAux) {ierr = PetscFree(a);CHKERRQ(ierr);} 1983 ierr = DMPlexGetDepthLabel(dm, &depth);CHKERRQ(ierr); 1984 ierr = DMPlexGetNumBoundary(dm, &numBd);CHKERRQ(ierr); 1985 ierr = DMPlexGetDepthLabel(dm, &depth);CHKERRQ(ierr); 1986 ierr = DMPlexGetNumBoundary(dm, &numBd);CHKERRQ(ierr); 1987 for (bd = 0; bd < numBd; ++bd) { 1988 const char *bdLabel; 1989 DMLabel label; 1990 IS pointIS; 1991 const PetscInt *points; 1992 const PetscInt *values; 1993 PetscInt field, numValues, numPoints, p, dep, numFaces; 1994 PetscBool isEssential; 1995 1996 ierr = DMPlexGetBoundary(dm, bd, &isEssential, NULL, &bdLabel, &field, NULL, &numValues, &values, NULL);CHKERRQ(ierr); 1997 if (isEssential) continue; 1998 if (numValues != 1) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Bug me and I will fix this"); 1999 ierr = DMPlexGetLabel(dm, bdLabel, &label);CHKERRQ(ierr); 2000 ierr = DMLabelGetStratumSize(label, 1, &numPoints);CHKERRQ(ierr); 2001 ierr = DMLabelGetStratumIS(label, 1, &pointIS);CHKERRQ(ierr); 2002 ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); 2003 for (p = 0, numFaces = 0; p < numPoints; ++p) { 2004 ierr = DMLabelGetValue(depth, points[p], &dep);CHKERRQ(ierr); 2005 if (dep == dim-1) ++numFaces; 2006 } 2007 ierr = PetscMalloc3(numFaces*totDimBd,&u,numFaces,&cgeom,numFaces*totDimBd*totDimBd,&elemMat);CHKERRQ(ierr); 2008 if (X_t) {ierr = PetscMalloc1(numFaces*totDimBd,&u_t);CHKERRQ(ierr);} 2009 for (p = 0, f = 0; p < numPoints; ++p) { 2010 const PetscInt point = points[p]; 2011 PetscScalar *x = NULL; 2012 PetscInt i; 2013 2014 ierr = DMLabelGetValue(depth, points[p], &dep);CHKERRQ(ierr); 2015 if (dep != dim-1) continue; 2016 ierr = DMPlexComputeCellGeometryFEM(dm, point, NULL, cgeom[f].v0, cgeom[f].J, cgeom[f].invJ, &cgeom[f].detJ);CHKERRQ(ierr); 2017 ierr = DMPlexComputeCellGeometryFVM(dm, point, NULL, NULL, cgeom[f].n); 2018 if (cgeom[f].detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for face %d", cgeom[f].detJ, point); 2019 ierr = DMPlexVecGetClosure(dm, section, X, point, NULL, &x);CHKERRQ(ierr); 2020 for (i = 0; i < totDimBd; ++i) u[f*totDimBd+i] = x[i]; 2021 ierr = DMPlexVecRestoreClosure(dm, section, X, point, NULL, &x);CHKERRQ(ierr); 2022 if (X_t) { 2023 ierr = DMPlexVecGetClosure(dm, section, X_t, point, NULL, &x);CHKERRQ(ierr); 2024 for (i = 0; i < totDimBd; ++i) u_t[f*totDimBd+i] = x[i]; 2025 ierr = DMPlexVecRestoreClosure(dm, section, X_t, point, NULL, &x);CHKERRQ(ierr); 2026 } 2027 ++f; 2028 } 2029 ierr = PetscMemzero(elemMat, numFaces*totDimBd*totDimBd * sizeof(PetscScalar));CHKERRQ(ierr); 2030 for (fieldI = 0; fieldI < Nf; ++fieldI) { 2031 PetscFE fe; 2032 PetscInt numQuadPoints, Nb; 2033 /* Conforming batches */ 2034 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 2035 /* Remainder */ 2036 PetscInt Nr, offset; 2037 2038 ierr = PetscDSGetBdDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); 2039 ierr = PetscFEGetQuadrature(fe, &quad);CHKERRQ(ierr); 2040 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 2041 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 2042 ierr = PetscQuadratureGetData(quad, NULL, &numQuadPoints, NULL, NULL);CHKERRQ(ierr); 2043 blockSize = Nb*numQuadPoints; 2044 batchSize = numBlocks * blockSize; 2045 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 2046 numChunks = numFaces / (numBatches*batchSize); 2047 Ne = numChunks*numBatches*batchSize; 2048 Nr = numFaces % (numBatches*batchSize); 2049 offset = numFaces - Nr; 2050 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 2051 ierr = PetscFEIntegrateBdJacobian(fe, prob, fieldI, fieldJ, Ne, cgeom, u, u_t, NULL, NULL, elemMat);CHKERRQ(ierr); 2052 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); 2053 } 2054 } 2055 for (p = 0, f = 0; p < numPoints; ++p) { 2056 const PetscInt point = points[p]; 2057 2058 ierr = DMLabelGetValue(depth, point, &dep);CHKERRQ(ierr); 2059 if (dep != dim-1) continue; 2060 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(point, "BdJacobian", totDimBd, totDimBd, &elemMat[f*totDimBd*totDimBd]);CHKERRQ(ierr);} 2061 ierr = DMPlexMatSetClosure(dm, section, globalSection, JacP, point, &elemMat[f*totDimBd*totDimBd], ADD_VALUES);CHKERRQ(ierr); 2062 ++f; 2063 } 2064 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 2065 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 2066 ierr = PetscFree3(u,cgeom,elemMat);CHKERRQ(ierr); 2067 if (X_t) {ierr = PetscFree(u_t);CHKERRQ(ierr);} 2068 } 2069 ierr = MatAssemblyBegin(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2070 ierr = MatAssemblyEnd(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2071 if (mesh->printFEM) { 2072 ierr = PetscPrintf(PETSC_COMM_WORLD, "%s:\n", name);CHKERRQ(ierr); 2073 ierr = MatChop(JacP, 1.0e-10);CHKERRQ(ierr); 2074 ierr = MatView(JacP, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 2075 } 2076 ierr = PetscLogEventEnd(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 2077 ierr = PetscObjectTypeCompare((PetscObject) Jac, MATSHELL, &isShell);CHKERRQ(ierr); 2078 if (isShell) { 2079 JacActionCtx *jctx; 2080 2081 ierr = MatShellGetContext(Jac, &jctx);CHKERRQ(ierr); 2082 ierr = VecCopy(X, jctx->u);CHKERRQ(ierr); 2083 } 2084 PetscFunctionReturn(0); 2085 } 2086 2087 #undef __FUNCT__ 2088 #define __FUNCT__ "DMPlexSNESComputeJacobianFEM" 2089 /*@ 2090 DMPlexSNESComputeJacobianFEM - Form the local portion of the Jacobian matrix J at the local solution X using pointwise functions specified by the user. 2091 2092 Input Parameters: 2093 + dm - The mesh 2094 . X - Local input vector 2095 - user - The user context 2096 2097 Output Parameter: 2098 . Jac - Jacobian matrix 2099 2100 Note: 2101 The first member of the user context must be an FEMContext. 2102 2103 We form the residual one batch of elements at a time. This allows us to offload work onto an accelerator, 2104 like a GPU, or vectorize on a multicore machine. 2105 2106 Level: developer 2107 2108 .seealso: FormFunctionLocal() 2109 @*/ 2110 PetscErrorCode DMPlexSNESComputeJacobianFEM(DM dm, Vec X, Mat Jac, Mat JacP,void *user) 2111 { 2112 PetscErrorCode ierr; 2113 2114 PetscFunctionBegin; 2115 ierr = DMPlexComputeJacobianFEM_Internal(dm, X, NULL, Jac, JacP, user);CHKERRQ(ierr); 2116 PetscFunctionReturn(0); 2117 } 2118