1 #include "../include/petscutils.h" 2 3 // ----------------------------------------------------------------------------- 4 // Convert PETSc MemType to libCEED MemType 5 // ----------------------------------------------------------------------------- 6 CeedMemType MemTypeP2C(PetscMemType mem_type) { 7 return PetscMemTypeDevice(mem_type) ? CEED_MEM_DEVICE : CEED_MEM_HOST; 8 } 9 10 // ----------------------------------------------------------------------------- 11 // Apply 3D Kershaw mesh transformation 12 // ----------------------------------------------------------------------------- 13 // Transition from a value of "a" for x=0, to a value of "b" for x=1. Optionally 14 // smooth -- see the commented versions at the end. 15 static double step(const double a, const double b, double x) { 16 if (x <= 0) return a; 17 if (x >= 1) return b; 18 return a + (b-a) * (x); 19 } 20 21 // 1D transformation at the right boundary 22 static double right(const double eps, const double x) { 23 return (x <= 0.5) ? (2-eps) * x : 1 + eps*(x-1); 24 } 25 26 // 1D transformation at the left boundary 27 static double left(const double eps, const double x) { 28 return 1-right(eps,1-x); 29 } 30 31 // Apply 3D Kershaw mesh transformation 32 // The eps parameters are in (0, 1] 33 // Uniform mesh is recovered for eps=1 34 PetscErrorCode Kershaw(DM dm_orig, PetscScalar eps) { 35 PetscErrorCode ierr; 36 Vec coord; 37 PetscInt ncoord; 38 PetscScalar *c; 39 40 PetscFunctionBeginUser; 41 ierr = DMGetCoordinatesLocal(dm_orig, &coord); CHKERRQ(ierr); 42 ierr = VecGetLocalSize(coord, &ncoord); CHKERRQ(ierr); 43 ierr = VecGetArray(coord, &c); CHKERRQ(ierr); 44 45 for (PetscInt i = 0; i < ncoord; i += 3) { 46 PetscScalar x = c[i], y = c[i+1], z = c[i+2]; 47 PetscInt layer = x*6; 48 PetscScalar lambda = (x-layer/6.0)*6; 49 c[i] = x; 50 51 switch (layer) { 52 case 0: 53 c[i+1] = left(eps, y); 54 c[i+2] = left(eps, z); 55 break; 56 case 1: 57 case 4: 58 c[i+1] = step(left(eps, y), right(eps, y), lambda); 59 c[i+2] = step(left(eps, z), right(eps, z), lambda); 60 break; 61 case 2: 62 c[i+1] = step(right(eps, y), left(eps, y), lambda/2); 63 c[i+2] = step(right(eps, z), left(eps, z), lambda/2); 64 break; 65 case 3: 66 c[i+1] = step(right(eps, y), left(eps, y), (1+lambda)/2); 67 c[i+2] = step(right(eps, z), left(eps, z), (1+lambda)/2); 68 break; 69 default: 70 c[i+1] = right(eps, y); 71 c[i+2] = right(eps, z); 72 } 73 } 74 ierr = VecRestoreArray(coord, &c); CHKERRQ(ierr); 75 PetscFunctionReturn(0); 76 } 77 78 // ----------------------------------------------------------------------------- 79 // Create BC label 80 // ----------------------------------------------------------------------------- 81 static PetscErrorCode CreateBCLabel(DM dm, const char name[]) { 82 83 DMLabel label; 84 85 PetscFunctionBeginUser; 86 87 PetscCall(DMCreateLabel(dm, name)); 88 PetscCall(DMGetLabel(dm, name, &label)); 89 PetscCall(DMPlexMarkBoundaryFaces(dm, PETSC_DETERMINE, label)); 90 PetscCall(DMPlexLabelComplete(dm, label)); 91 92 PetscFunctionReturn(0); 93 }; 94 95 // ----------------------------------------------------------------------------- 96 // This function sets up a DM for a given degree 97 // ----------------------------------------------------------------------------- 98 PetscErrorCode SetupDMByDegree(DM dm, PetscInt p_degree, PetscInt q_extra, 99 PetscInt num_comp_u, 100 PetscInt dim, bool enforce_bc, BCFunction bc_func) { 101 PetscInt ierr, marker_ids[1] = {1}; 102 PetscInt q_degree = p_degree + q_extra; 103 PetscFE fe; 104 MPI_Comm comm; 105 PetscBool is_simplex = PETSC_TRUE; 106 107 PetscFunctionBeginUser; 108 109 // Check if simplex or tensor-product mesh 110 ierr = DMPlexIsSimplex(dm, &is_simplex); CHKERRQ(ierr); 111 // Setup FE 112 ierr = PetscObjectGetComm((PetscObject)dm, &comm); CHKERRQ(ierr); 113 ierr = PetscFECreateLagrange(comm, dim, num_comp_u, is_simplex, p_degree, 114 q_degree, &fe); CHKERRQ(ierr); 115 ierr = DMAddField(dm, NULL, (PetscObject)fe); CHKERRQ(ierr); 116 ierr = DMCreateDS(dm); CHKERRQ(ierr); 117 118 { 119 // create FE field for coordinates 120 PetscFE fe_coords; 121 PetscInt num_comp_coord; 122 ierr = DMGetCoordinateDim(dm, &num_comp_coord); CHKERRQ(ierr); 123 ierr = PetscFECreateLagrange(comm, dim, num_comp_coord, is_simplex, 1, q_degree, 124 &fe_coords); CHKERRQ(ierr); 125 ierr = DMProjectCoordinates(dm, fe_coords); CHKERRQ(ierr); 126 ierr = PetscFEDestroy(&fe_coords); CHKERRQ(ierr); 127 } 128 129 // Setup DM 130 if (enforce_bc) { 131 PetscBool has_label; 132 DMHasLabel(dm, "marker", &has_label); 133 if (!has_label) {CreateBCLabel(dm, "marker");} 134 DMLabel label; 135 ierr = DMGetLabel(dm, "marker", &label); CHKERRQ(ierr); 136 ierr = DMAddBoundary(dm, DM_BC_ESSENTIAL, "wall", label, 1, 137 marker_ids, 0, 0, NULL, (void(*)(void))bc_func, 138 NULL, NULL, NULL); CHKERRQ(ierr); 139 PetscCall(DMSetOptionsPrefix(dm, "final_")); 140 PetscCall(DMViewFromOptions(dm, NULL, "-dm_view")); 141 } 142 143 if (!is_simplex) { 144 DM dm_coord; 145 ierr = DMGetCoordinateDM(dm, &dm_coord); CHKERRQ(ierr); 146 ierr = DMPlexSetClosurePermutationTensor(dm, PETSC_DETERMINE, NULL); 147 CHKERRQ(ierr); 148 ierr = DMPlexSetClosurePermutationTensor(dm_coord, PETSC_DETERMINE, NULL); 149 CHKERRQ(ierr); 150 } 151 ierr = PetscFEDestroy(&fe); CHKERRQ(ierr); 152 153 PetscFunctionReturn(0); 154 }; 155 156 // ----------------------------------------------------------------------------- 157 // Get CEED restriction data from DMPlex 158 // ----------------------------------------------------------------------------- 159 PetscErrorCode CreateRestrictionFromPlex(Ceed ceed, DM dm, CeedInt height, 160 DMLabel domain_label, CeedInt value, CeedElemRestriction *elem_restr) { 161 PetscInt num_elem, elem_size, num_dof, num_comp, *elem_restr_offsets; 162 PetscErrorCode ierr; 163 164 PetscFunctionBeginUser; 165 166 ierr = DMPlexGetLocalOffsets(dm, domain_label, value, height, 0, &num_elem, 167 &elem_size, &num_comp, &num_dof, &elem_restr_offsets); 168 CHKERRQ(ierr); 169 170 CeedElemRestrictionCreate(ceed, num_elem, elem_size, num_comp, 171 1, num_dof, CEED_MEM_HOST, CEED_COPY_VALUES, 172 elem_restr_offsets, elem_restr); 173 ierr = PetscFree(elem_restr_offsets); CHKERRQ(ierr); 174 175 PetscFunctionReturn(0); 176 }; 177 178 // ----------------------------------------------------------------------------- 179 // Utility function - convert from DMPolytopeType to CeedElemTopology 180 // ----------------------------------------------------------------------------- 181 CeedElemTopology ElemTopologyP2C(DMPolytopeType cell_type) { 182 switch (cell_type) { 183 case DM_POLYTOPE_TRIANGLE: return CEED_TOPOLOGY_TRIANGLE; 184 case DM_POLYTOPE_QUADRILATERAL: return CEED_TOPOLOGY_QUAD; 185 case DM_POLYTOPE_TETRAHEDRON: return CEED_TOPOLOGY_TET; 186 case DM_POLYTOPE_HEXAHEDRON: return CEED_TOPOLOGY_HEX; 187 default: return 0; 188 } 189 } 190 191 // ----------------------------------------------------------------------------- 192 // Convert DM field to DS field 193 // ----------------------------------------------------------------------------- 194 PetscErrorCode DMFieldToDSField(DM dm, DMLabel domain_label, PetscInt dm_field, 195 PetscInt *ds_field) { 196 PetscDS ds; 197 IS field_is; 198 const PetscInt *fields; 199 PetscInt num_fields; 200 201 PetscFunctionBeginUser; 202 203 // Translate dm_field to ds_field 204 PetscCall(DMGetRegionDS(dm, domain_label, &field_is, &ds)); 205 PetscCall(ISGetIndices(field_is, &fields)); 206 PetscCall(ISGetSize(field_is, &num_fields)); 207 for (PetscInt i = 0; i < num_fields; i++) { 208 if (dm_field == fields[i]) { 209 *ds_field = i; 210 break; 211 } 212 } 213 PetscCall(ISRestoreIndices(field_is, &fields)); 214 215 if (*ds_field == -1) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, 216 "Could not find dm_field %" PetscInt_FMT " in DS", dm_field); 217 218 PetscFunctionReturn(0); 219 } 220 221 // ----------------------------------------------------------------------------- 222 // Create libCEED Basis from PetscTabulation 223 // ----------------------------------------------------------------------------- 224 PetscErrorCode BasisCreateFromTabulation(Ceed ceed, DM dm, DMLabel domain_label, 225 PetscInt label_value, PetscInt height, PetscInt face, 226 PetscFE fe, PetscTabulation basis_tabulation, PetscQuadrature quadrature, 227 CeedBasis *basis) { 228 229 PetscInt first_point; 230 PetscInt ids[1] = {label_value}; 231 DMLabel depth_label; 232 DMPolytopeType cell_type; 233 CeedElemTopology elem_topo; 234 PetscScalar *q_points, *interp, *grad; 235 const PetscScalar *q_weights; 236 PetscDualSpace dual_space; 237 PetscInt num_dual_basis_vectors; 238 PetscInt dim, num_comp, P, Q; 239 240 PetscFunctionBeginUser; 241 242 // General basis information 243 PetscCall(PetscFEGetSpatialDimension(fe, &dim)); 244 PetscCall(PetscFEGetNumComponents(fe, &num_comp)); 245 PetscCall(PetscFEGetDualSpace(fe, &dual_space)); 246 PetscCall(PetscDualSpaceGetDimension(dual_space, &num_dual_basis_vectors)); 247 P = num_dual_basis_vectors / num_comp; 248 249 // Use depth label if no domain label present 250 if (!domain_label) { 251 PetscInt depth; 252 253 PetscCall(DMPlexGetDepth(dm, &depth)); 254 PetscCall(DMPlexGetDepthLabel(dm, &depth_label)); 255 ids[0] = depth - height; 256 } 257 258 // Get cell interp, grad, and quadrature data 259 PetscCall(DMGetFirstLabeledPoint(dm, dm, 260 domain_label ? domain_label : depth_label, 1, ids, height, &first_point, NULL)); 261 PetscCall(DMPlexGetCellType(dm, first_point, &cell_type)); 262 elem_topo = ElemTopologyP2C(cell_type); 263 if (!elem_topo) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, 264 "DMPlex topology not supported"); 265 { 266 size_t q_points_size; 267 const PetscScalar *q_points_petsc; 268 PetscInt q_dim; 269 270 PetscCall(PetscQuadratureGetData(quadrature, &q_dim, NULL, &Q, &q_points_petsc, 271 &q_weights)); 272 q_points_size = Q * dim * sizeof(CeedScalar); 273 PetscCall(PetscCalloc(q_points_size, &q_points)); 274 for (PetscInt q = 0; q < Q; q++) { 275 for (PetscInt d = 0; d < q_dim; 276 d++) q_points[q * dim + d] = q_points_petsc[q * q_dim + d]; 277 } 278 } 279 280 // Convert to libCEED orientation 281 { 282 PetscBool is_simplex = PETSC_FALSE; 283 IS permutation = NULL; 284 const PetscInt *permutation_indices; 285 286 PetscCall(DMPlexIsSimplex(dm, &is_simplex)); 287 if (!is_simplex) { 288 PetscSection section; 289 290 // -- Get permutation 291 PetscCall(DMGetLocalSection(dm, §ion)); 292 PetscCall(PetscSectionGetClosurePermutation(section, (PetscObject)dm, dim, 293 num_comp * P, &permutation)); 294 PetscCall(ISGetIndices(permutation, &permutation_indices)); 295 } 296 297 // -- Copy interp, grad matrices 298 PetscCall(PetscCalloc(P * Q * sizeof(CeedScalar), &interp)); 299 PetscCall(PetscCalloc(P * Q * dim * sizeof(CeedScalar), &grad)); 300 const CeedInt c = 0; 301 for (CeedInt q = 0; q < Q; q++) { 302 for (CeedInt p_ceed = 0; p_ceed < P; p_ceed++) { 303 CeedInt p_petsc = is_simplex ? (p_ceed * num_comp) : permutation_indices[p_ceed 304 * num_comp]; 305 306 interp[q * P + p_ceed] = basis_tabulation->T[0][((face * Q + q) * P * num_comp + 307 p_petsc) * num_comp + c]; 308 for (CeedInt d = 0; d < dim; d++) { 309 grad[(d * Q + q) * P + p_ceed] = basis_tabulation->T[1][((( 310 face * Q + q) * P * num_comp + p_petsc) * num_comp + c) * dim + d]; 311 } 312 } 313 } 314 315 // -- Cleanup 316 if (permutation) PetscCall(ISRestoreIndices(permutation, &permutation_indices)); 317 PetscCall(ISDestroy(&permutation)); 318 } 319 320 // Finally, create libCEED basis 321 CeedBasisCreateH1(ceed, elem_topo, num_comp, P, Q, interp, grad, q_points, 322 q_weights, basis); 323 PetscCall(PetscFree(q_points)); 324 PetscCall(PetscFree(interp)); 325 PetscCall(PetscFree(grad)); 326 327 PetscFunctionReturn(0); 328 } 329 330 // ----------------------------------------------------------------------------- 331 // Get CEED Basis from DMPlex 332 // ----------------------------------------------------------------------------- 333 PetscErrorCode CreateBasisFromPlex(Ceed ceed, DM dm, DMLabel domain_label, 334 CeedInt label_value, CeedInt height, 335 CeedInt dm_field, CeedBasis *basis) { 336 PetscDS ds; 337 PetscFE fe; 338 PetscQuadrature quadrature; 339 PetscBool is_simplex = PETSC_TRUE; 340 PetscInt ds_field = -1; 341 342 PetscFunctionBeginUser; 343 344 // Get element information 345 PetscCall(DMGetRegionDS(dm, domain_label, NULL, &ds)); 346 PetscCall(DMFieldToDSField(dm, domain_label, dm_field, &ds_field)); 347 PetscCall(PetscDSGetDiscretization(ds, ds_field, (PetscObject *)&fe)); 348 PetscCall(PetscFEGetHeightSubspace(fe, height, &fe)); 349 PetscCall(PetscFEGetQuadrature(fe, &quadrature)); 350 351 // Check if simplex or tensor-product mesh 352 PetscCall(DMPlexIsSimplex(dm, &is_simplex)); 353 354 // Build libCEED basis 355 if (is_simplex) { 356 PetscTabulation basis_tabulation; 357 PetscInt num_derivatives = 1, face = 0; 358 359 PetscCall(PetscFEGetCellTabulation(fe, num_derivatives, &basis_tabulation)); 360 PetscCall(BasisCreateFromTabulation(ceed, dm, domain_label, label_value, height, 361 face, fe, basis_tabulation, quadrature, basis)); 362 } else { 363 PetscDualSpace dual_space; 364 PetscInt num_dual_basis_vectors; 365 PetscInt dim, num_comp, P, Q; 366 367 PetscCall(PetscFEGetSpatialDimension(fe, &dim)); 368 PetscCall(PetscFEGetNumComponents(fe, &num_comp)); 369 PetscCall(PetscFEGetDualSpace(fe, &dual_space)); 370 PetscCall(PetscDualSpaceGetDimension(dual_space, &num_dual_basis_vectors)); 371 P = num_dual_basis_vectors / num_comp; 372 PetscCall(PetscQuadratureGetData(quadrature, NULL, NULL, &Q, NULL, NULL)); 373 374 CeedInt P_1d = (CeedInt)round(pow(P, 1.0 / dim)); 375 CeedInt Q_1d = (CeedInt)round(pow(Q, 1.0 / dim)); 376 377 CeedBasisCreateTensorH1Lagrange(ceed, dim, num_comp, P_1d, Q_1d, CEED_GAUSS, 378 basis); 379 } 380 381 PetscFunctionReturn(0); 382 } 383 384 // ----------------------------------------------------------------------------- 385 // Utilities 386 // ----------------------------------------------------------------------------- 387 388 // Utility function, compute three factors of an integer 389 static void Split3(PetscInt size, PetscInt m[3], bool reverse) { 390 for (PetscInt d=0, size_left=size; d<3; d++) { 391 PetscInt try = (PetscInt)PetscCeilReal(PetscPowReal(size_left, 1./(3 - d))); 392 while (try * (size_left / try) != size_left) try++; 393 m[reverse ? 2-d : d] = try; 394 size_left /= try; 395 } 396 } 397 398 static int Max3(const PetscInt a[3]) { 399 return PetscMax(a[0], PetscMax(a[1], a[2])); 400 } 401 402 static int Min3(const PetscInt a[3]) { 403 return PetscMin(a[0], PetscMin(a[1], a[2])); 404 } 405 406 // ----------------------------------------------------------------------------- 407 // Create distribute dm 408 // ----------------------------------------------------------------------------- 409 PetscErrorCode CreateDistributedDM(RunParams rp, DM *dm) { 410 PetscErrorCode ierr; 411 412 PetscFunctionBeginUser; 413 // Setup DM 414 if (rp->read_mesh) { 415 ierr = DMPlexCreateFromFile(PETSC_COMM_WORLD, rp->filename, NULL, PETSC_TRUE, 416 dm); 417 CHKERRQ(ierr); 418 } else { 419 if (rp->user_l_nodes) { 420 // Find a nicely composite number of elements no less than global nodes 421 PetscMPIInt size; 422 ierr = MPI_Comm_size(rp->comm, &size); CHKERRQ(ierr); 423 for (PetscInt g_elem = 424 PetscMax(1, size * rp->local_nodes / PetscPowInt(rp->degree, rp->dim)); 425 ; 426 g_elem++) { 427 Split3(g_elem, rp->mesh_elem, true); 428 if (Max3(rp->mesh_elem) / Min3(rp->mesh_elem) <= 2) break; 429 } 430 } 431 ierr = DMPlexCreateBoxMesh(PETSC_COMM_WORLD, rp->dim, rp->simplex, 432 rp->mesh_elem, 433 NULL, NULL, NULL, PETSC_TRUE, dm); CHKERRQ(ierr); 434 } 435 436 ierr = DMSetFromOptions(*dm); CHKERRQ(ierr); 437 ierr = DMViewFromOptions(*dm, NULL, "-dm_view"); CHKERRQ(ierr); 438 439 PetscFunctionReturn(0); 440 } 441 442 // ----------------------------------------------------------------------------- 443