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