1 // Copyright (c) 2017, Lawrence Livermore National Security, LLC. Produced at 2 // the Lawrence Livermore National Laboratory. LLNL-CODE-734707. All Rights 3 // reserved. See files LICENSE and NOTICE for details. 4 // 5 // This file is part of CEED, a collection of benchmarks, miniapps, software 6 // libraries and APIs for efficient high-order finite element and spectral 7 // element discretizations for exascale applications. For more information and 8 // source code availability see http://github.com/ceed. 9 // 10 // The CEED research is supported by the Exascale Computing Project 17-SC-20-SC, 11 // a collaborative effort of two U.S. Department of Energy organizations (Office 12 // of Science and the National Nuclear Security Administration) responsible for 13 // the planning and preparation of a capable exascale ecosystem, including 14 // software, applications, hardware, advanced system engineering and early 15 // testbed platforms, in support of the nation's exascale computing imperative. 16 17 // libCEED + PETSc Example: Navier-Stokes 18 // 19 // This example demonstrates a simple usage of libCEED with PETSc to solve a 20 // Navier-Stokes problem. 21 // 22 // The code is intentionally "raw", using only low-level communication 23 // primitives. 24 // 25 // Build with: 26 // 27 // make [PETSC_DIR=</path/to/petsc>] [CEED_DIR=</path/to/libceed>] navierstokes 28 // 29 // Sample runs: 30 // 31 // ./navierstokes -ceed /cpu/self -problem density_current -degree 1 32 // ./navierstokes -ceed /gpu/occa -problem advection -degree 1 33 // 34 //TESTARGS -ceed {ceed_resource} -test -degree 1 35 36 /// @file 37 /// Navier-Stokes example using PETSc 38 39 const char help[] = "Solve Navier-Stokes using PETSc and libCEED\n"; 40 41 #include <petscts.h> 42 #include <petscdmplex.h> 43 #include <ceed.h> 44 #include <stdbool.h> 45 #include <petscsys.h> 46 #include "common.h" 47 #include "advection.h" 48 #include "advection2d.h" 49 #include "densitycurrent.h" 50 51 // Problem Options 52 typedef enum { 53 NS_DENSITY_CURRENT = 0, 54 NS_ADVECTION = 1, 55 NS_ADVECTION2D = 2, 56 } problemType; 57 static const char *const problemTypes[] = { 58 "density_current", 59 "advection", 60 "advection2d", 61 "problemType","NS_",0 62 }; 63 64 typedef enum { 65 STAB_NONE = 0, 66 STAB_SU = 1, // Streamline Upwind 67 STAB_SUPG = 2, // Streamline Upwind Petrov-Galerkin 68 } StabilizationType; 69 static const char *const StabilizationTypes[] = { 70 "NONE", 71 "SU", 72 "SUPG", 73 "StabilizationType", "STAB_", NULL 74 }; 75 76 // Problem specific data 77 typedef struct { 78 CeedInt dim, qdatasize; 79 CeedQFunctionUser setup, ics, apply_rhs, apply_ifunction; 80 PetscErrorCode (*bc)(PetscInt, PetscReal, const PetscReal[], PetscInt, 81 PetscScalar[], void *); 82 const char *setup_loc, *ics_loc, *apply_rhs_loc, *apply_ifunction_loc; 83 const bool non_zero_time; 84 } problemData; 85 86 problemData problemOptions[] = { 87 [NS_DENSITY_CURRENT] = { 88 .dim = 3, 89 .qdatasize = 10, 90 .setup = Setup, 91 .setup_loc = Setup_loc, 92 .ics = ICsDC, 93 .ics_loc = ICsDC_loc, 94 .apply_rhs = DC, 95 .apply_rhs_loc = DC_loc, 96 .apply_ifunction = IFunction_DC, 97 .apply_ifunction_loc = IFunction_DC_loc, 98 .bc = Exact_DC, 99 .non_zero_time = false, 100 }, 101 [NS_ADVECTION] = { 102 .dim = 3, 103 .qdatasize = 10, 104 .setup = Setup, 105 .setup_loc = Setup_loc, 106 .ics = ICsAdvection, 107 .ics_loc = ICsAdvection_loc, 108 .apply_rhs = Advection, 109 .apply_rhs_loc = Advection_loc, 110 .apply_ifunction = IFunction_Advection, 111 .apply_ifunction_loc = IFunction_Advection_loc, 112 .bc = Exact_Advection, 113 .non_zero_time = false, 114 }, 115 [NS_ADVECTION2D] = { 116 .dim = 2, 117 .qdatasize = 5, 118 .setup = Setup2d, 119 .setup_loc = Setup2d_loc, 120 .ics = ICsAdvection2d, 121 .ics_loc = ICsAdvection2d_loc, 122 .apply_rhs = Advection2d, 123 .apply_rhs_loc = Advection2d_loc, 124 .apply_ifunction = IFunction_Advection2d, 125 .apply_ifunction_loc = IFunction_Advection2d_loc, 126 .bc = Exact_Advection2d, 127 .non_zero_time = true, 128 }, 129 }; 130 131 // PETSc user data 132 typedef struct User_ *User; 133 typedef struct Units_ *Units; 134 135 struct User_ { 136 MPI_Comm comm; 137 PetscInt outputfreq; 138 DM dm; 139 DM dmviz; 140 Mat interpviz; 141 Ceed ceed; 142 Units units; 143 CeedVector qceed, qdotceed, gceed; 144 CeedOperator op_rhs, op_ifunction; 145 Vec M; 146 char outputfolder[PETSC_MAX_PATH_LEN]; 147 PetscInt contsteps; 148 }; 149 150 struct Units_ { 151 // fundamental units 152 PetscScalar meter; 153 PetscScalar kilogram; 154 PetscScalar second; 155 PetscScalar Kelvin; 156 // derived units 157 PetscScalar Pascal; 158 PetscScalar JperkgK; 159 PetscScalar mpersquareds; 160 PetscScalar WpermK; 161 PetscScalar kgpercubicm; 162 PetscScalar kgpersquaredms; 163 PetscScalar Joulepercubicm; 164 }; 165 166 typedef struct SimpleBC_ *SimpleBC; 167 struct SimpleBC_ { 168 PetscInt nwall, nslip[3]; 169 PetscInt walls[10], slips[3][10]; 170 }; 171 172 // Essential BC dofs are encoded in closure indices as -(i+1). 173 static PetscInt Involute(PetscInt i) { 174 return i >= 0 ? i : -(i+1); 175 } 176 177 // Utility function to create local CEED restriction 178 static PetscErrorCode CreateRestrictionFromPlex(Ceed ceed, DM dm, CeedInt P, 179 CeedElemRestriction *Erestrict) { 180 181 PetscSection section; 182 PetscInt c, cStart, cEnd, Nelem, Ndof, *erestrict, eoffset, nfields, dim; 183 PetscErrorCode ierr; 184 Vec Uloc; 185 186 PetscFunctionBeginUser; 187 ierr = DMGetDimension(dm, &dim); CHKERRQ(ierr); 188 ierr = DMGetLocalSection(dm,§ion); CHKERRQ(ierr); 189 ierr = PetscSectionGetNumFields(section, &nfields); CHKERRQ(ierr); 190 PetscInt ncomp[nfields], fieldoff[nfields+1]; 191 fieldoff[0] = 0; 192 for (PetscInt f=0; f<nfields; f++) { 193 ierr = PetscSectionGetFieldComponents(section, f, &ncomp[f]); CHKERRQ(ierr); 194 fieldoff[f+1] = fieldoff[f] + ncomp[f]; 195 } 196 197 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd); CHKERRQ(ierr); 198 Nelem = cEnd - cStart; 199 ierr = PetscMalloc1(Nelem*PetscPowInt(P, dim), &erestrict); CHKERRQ(ierr); 200 for (c=cStart,eoffset=0; c<cEnd; c++) { 201 PetscInt numindices, *indices, nnodes; 202 ierr = DMPlexGetClosureIndices(dm, section, section, c, &numindices, 203 &indices, NULL); CHKERRQ(ierr); 204 if (numindices % fieldoff[nfields]) SETERRQ1(PETSC_COMM_SELF, 205 PETSC_ERR_ARG_INCOMP, "Number of closure indices not compatible with Cell %D", 206 c); 207 nnodes = numindices / fieldoff[nfields]; 208 for (PetscInt i=0; i<nnodes; i++) { 209 // Check that indices are blocked by node and thus can be coalesced as a single field with 210 // fieldoff[nfields] = sum(ncomp) components. 211 for (PetscInt f=0; f<nfields; f++) { 212 for (PetscInt j=0; j<ncomp[f]; j++) { 213 if (Involute(indices[fieldoff[f]*nnodes + i*ncomp[f] + j]) 214 != Involute(indices[i*ncomp[0]]) + fieldoff[f] + j) 215 SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP, 216 "Cell %D closure indices not interlaced for node %D field %D component %D", 217 c, i, f, j); 218 } 219 } 220 // Essential boundary conditions are encoded as -(loc+1), but we don't care so we decode. 221 PetscInt loc = Involute(indices[i*ncomp[0]]); 222 erestrict[eoffset++] = loc / fieldoff[nfields]; 223 } 224 ierr = DMPlexRestoreClosureIndices(dm, section, section, c, &numindices, 225 &indices, NULL); CHKERRQ(ierr); 226 } 227 if (eoffset != Nelem*PetscPowInt(P, dim)) SETERRQ3(PETSC_COMM_SELF, 228 PETSC_ERR_LIB, "ElemRestriction of size (%D,%D) initialized %D nodes", Nelem, 229 PetscPowInt(P, dim),eoffset); 230 ierr = DMGetLocalVector(dm, &Uloc); CHKERRQ(ierr); 231 ierr = VecGetLocalSize(Uloc, &Ndof); CHKERRQ(ierr); 232 ierr = DMRestoreLocalVector(dm, &Uloc); CHKERRQ(ierr); 233 CeedElemRestrictionCreate(ceed, CEED_INTERLACED, Nelem, PetscPowInt(P, dim), 234 Ndof/fieldoff[nfields], fieldoff[nfields], 235 CEED_MEM_HOST, CEED_COPY_VALUES, erestrict, Erestrict); 236 ierr = PetscFree(erestrict); CHKERRQ(ierr); 237 PetscFunctionReturn(0); 238 } 239 240 static int CreateVectorFromPetscVec(Ceed ceed, Vec p, CeedVector *v) { 241 PetscErrorCode ierr; 242 PetscInt m; 243 244 PetscFunctionBeginUser; 245 ierr = VecGetLocalSize(p, &m); CHKERRQ(ierr); 246 ierr = CeedVectorCreate(ceed, m, v); CHKERRQ(ierr); 247 PetscFunctionReturn(0); 248 } 249 250 static int VectorPlacePetscVec(CeedVector c, Vec p) { 251 PetscErrorCode ierr; 252 PetscInt mceed,mpetsc; 253 PetscScalar *a; 254 255 PetscFunctionBeginUser; 256 ierr = CeedVectorGetLength(c, &mceed); CHKERRQ(ierr); 257 ierr = VecGetLocalSize(p, &mpetsc); CHKERRQ(ierr); 258 if (mceed != mpetsc) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP, 259 "Cannot place PETSc Vec of length %D in CeedVector of length %D", 260 mpetsc, mceed); 261 ierr = VecGetArray(p, &a); CHKERRQ(ierr); 262 CeedVectorSetArray(c, CEED_MEM_HOST, CEED_USE_POINTER, a); 263 PetscFunctionReturn(0); 264 } 265 266 static PetscErrorCode DMPlexInsertBoundaryValues_NS(DM dm, 267 PetscBool insertEssential, Vec Qloc, PetscReal time, Vec faceGeomFVM, 268 Vec cellGeomFVM, Vec gradFVM) { 269 PetscErrorCode ierr; 270 Vec Qbc; 271 272 PetscFunctionBegin; 273 ierr = DMGetNamedLocalVector(dm, "Qbc", &Qbc); CHKERRQ(ierr); 274 ierr = VecAXPY(Qloc, 1., Qbc); CHKERRQ(ierr); 275 ierr = DMRestoreNamedLocalVector(dm, "Qbc", &Qbc); CHKERRQ(ierr); 276 PetscFunctionReturn(0); 277 } 278 279 // This is the RHS of the ODE, given as u_t = G(t,u) 280 // This function takes in a state vector Q and writes into G 281 static PetscErrorCode RHS_NS(TS ts, PetscReal t, Vec Q, Vec G, void *userData) { 282 PetscErrorCode ierr; 283 User user = *(User *)userData; 284 PetscScalar *q, *g; 285 Vec Qloc, Gloc; 286 287 // Global-to-local 288 PetscFunctionBeginUser; 289 ierr = DMGetLocalVector(user->dm, &Qloc); CHKERRQ(ierr); 290 ierr = DMGetLocalVector(user->dm, &Gloc); CHKERRQ(ierr); 291 ierr = VecZeroEntries(Qloc); CHKERRQ(ierr); 292 ierr = DMGlobalToLocal(user->dm, Q, INSERT_VALUES, Qloc); CHKERRQ(ierr); 293 ierr = DMPlexInsertBoundaryValues(user->dm, PETSC_TRUE, Qloc, 0.0, 294 NULL, NULL, NULL); CHKERRQ(ierr); 295 ierr = VecZeroEntries(Gloc); CHKERRQ(ierr); 296 297 // Ceed Vectors 298 ierr = VecGetArrayRead(Qloc, (const PetscScalar **)&q); CHKERRQ(ierr); 299 ierr = VecGetArray(Gloc, &g); CHKERRQ(ierr); 300 CeedVectorSetArray(user->qceed, CEED_MEM_HOST, CEED_USE_POINTER, q); 301 CeedVectorSetArray(user->gceed, CEED_MEM_HOST, CEED_USE_POINTER, g); 302 303 // Apply CEED operator 304 CeedOperatorApply(user->op_rhs, user->qceed, user->gceed, 305 CEED_REQUEST_IMMEDIATE); 306 307 // Restore vectors 308 ierr = VecRestoreArrayRead(Qloc, (const PetscScalar **)&q); CHKERRQ(ierr); 309 ierr = VecRestoreArray(Gloc, &g); CHKERRQ(ierr); 310 311 ierr = VecZeroEntries(G); CHKERRQ(ierr); 312 ierr = DMLocalToGlobal(user->dm, Gloc, ADD_VALUES, G); CHKERRQ(ierr); 313 314 // Inverse of the lumped mass matrix 315 ierr = VecPointwiseMult(G, G, user->M); // M is Minv 316 CHKERRQ(ierr); 317 318 ierr = DMRestoreLocalVector(user->dm, &Qloc); CHKERRQ(ierr); 319 ierr = DMRestoreLocalVector(user->dm, &Gloc); CHKERRQ(ierr); 320 PetscFunctionReturn(0); 321 } 322 323 static PetscErrorCode IFunction_NS(TS ts, PetscReal t, Vec Q, Vec Qdot, Vec G, 324 void *userData) { 325 PetscErrorCode ierr; 326 User user = *(User *)userData; 327 const PetscScalar *q, *qdot; 328 PetscScalar *g; 329 Vec Qloc, Qdotloc, Gloc; 330 331 // Global-to-local 332 PetscFunctionBeginUser; 333 ierr = DMGetLocalVector(user->dm, &Qloc); CHKERRQ(ierr); 334 ierr = DMGetLocalVector(user->dm, &Qdotloc); CHKERRQ(ierr); 335 ierr = DMGetLocalVector(user->dm, &Gloc); CHKERRQ(ierr); 336 ierr = VecZeroEntries(Qloc); CHKERRQ(ierr); 337 ierr = DMGlobalToLocal(user->dm, Q, INSERT_VALUES, Qloc); CHKERRQ(ierr); 338 ierr = DMPlexInsertBoundaryValues(user->dm, PETSC_TRUE, Qloc, 0.0, 339 NULL, NULL, NULL); CHKERRQ(ierr); 340 ierr = VecZeroEntries(Qdotloc); CHKERRQ(ierr); 341 ierr = DMGlobalToLocal(user->dm, Qdot, INSERT_VALUES, Qdotloc); CHKERRQ(ierr); 342 ierr = VecZeroEntries(Gloc); CHKERRQ(ierr); 343 344 // Ceed Vectors 345 ierr = VecGetArrayRead(Qloc, &q); CHKERRQ(ierr); 346 ierr = VecGetArrayRead(Qdotloc, &qdot); CHKERRQ(ierr); 347 ierr = VecGetArray(Gloc, &g); CHKERRQ(ierr); 348 CeedVectorSetArray(user->qceed, CEED_MEM_HOST, CEED_USE_POINTER, 349 (PetscScalar *)q); 350 CeedVectorSetArray(user->qdotceed, CEED_MEM_HOST, CEED_USE_POINTER, 351 (PetscScalar *)qdot); 352 CeedVectorSetArray(user->gceed, CEED_MEM_HOST, CEED_USE_POINTER, g); 353 354 // Apply CEED operator 355 CeedOperatorApply(user->op_ifunction, user->qceed, user->gceed, 356 CEED_REQUEST_IMMEDIATE); 357 358 // Restore vectors 359 ierr = VecRestoreArrayRead(Qloc, &q); CHKERRQ(ierr); 360 ierr = VecRestoreArrayRead(Qdotloc, &qdot); CHKERRQ(ierr); 361 ierr = VecRestoreArray(Gloc, &g); CHKERRQ(ierr); 362 363 ierr = VecZeroEntries(G); CHKERRQ(ierr); 364 ierr = DMLocalToGlobal(user->dm, Gloc, ADD_VALUES, G); CHKERRQ(ierr); 365 366 ierr = DMRestoreLocalVector(user->dm, &Qloc); CHKERRQ(ierr); 367 ierr = DMRestoreLocalVector(user->dm, &Qdotloc); CHKERRQ(ierr); 368 ierr = DMRestoreLocalVector(user->dm, &Gloc); CHKERRQ(ierr); 369 PetscFunctionReturn(0); 370 } 371 372 // User provided TS Monitor 373 static PetscErrorCode TSMonitor_NS(TS ts, PetscInt stepno, PetscReal time, 374 Vec Q, void *ctx) { 375 User user = ctx; 376 Vec Qloc; 377 char filepath[PETSC_MAX_PATH_LEN]; 378 PetscViewer viewer; 379 PetscErrorCode ierr; 380 381 // Set up output 382 PetscFunctionBeginUser; 383 // Print every 'outputfreq' steps 384 if (stepno % user->outputfreq != 0) 385 PetscFunctionReturn(0); 386 ierr = DMGetLocalVector(user->dm, &Qloc); CHKERRQ(ierr); 387 ierr = PetscObjectSetName((PetscObject)Qloc, "StateVec"); CHKERRQ(ierr); 388 ierr = VecZeroEntries(Qloc); CHKERRQ(ierr); 389 ierr = DMGlobalToLocal(user->dm, Q, INSERT_VALUES, Qloc); CHKERRQ(ierr); 390 391 // Output 392 ierr = PetscSNPrintf(filepath, sizeof filepath, "%s/ns-%03D.vtu", 393 user->outputfolder, stepno + user->contsteps); 394 CHKERRQ(ierr); 395 ierr = PetscViewerVTKOpen(PetscObjectComm((PetscObject)Q), filepath, 396 FILE_MODE_WRITE, &viewer); CHKERRQ(ierr); 397 ierr = VecView(Qloc, viewer); CHKERRQ(ierr); 398 if (user->dmviz) { 399 Vec Qrefined, Qrefined_loc; 400 char filepath_refined[PETSC_MAX_PATH_LEN]; 401 PetscViewer viewer_refined; 402 403 ierr = DMGetGlobalVector(user->dmviz, &Qrefined); CHKERRQ(ierr); 404 ierr = DMGetLocalVector(user->dmviz, &Qrefined_loc); CHKERRQ(ierr); 405 ierr = PetscObjectSetName((PetscObject)Qrefined_loc, "Refined"); 406 CHKERRQ(ierr); 407 ierr = MatInterpolate(user->interpviz, Q, Qrefined); CHKERRQ(ierr); 408 ierr = VecZeroEntries(Qrefined_loc); CHKERRQ(ierr); 409 ierr = DMGlobalToLocal(user->dmviz, Qrefined, INSERT_VALUES, Qrefined_loc); 410 CHKERRQ(ierr); 411 ierr = PetscSNPrintf(filepath_refined, sizeof filepath_refined, 412 "%s/nsrefined-%03D.vtu", 413 user->outputfolder, stepno + user->contsteps); 414 CHKERRQ(ierr); 415 ierr = PetscViewerVTKOpen(PetscObjectComm((PetscObject)Qrefined), 416 filepath_refined, 417 FILE_MODE_WRITE, &viewer_refined); CHKERRQ(ierr); 418 ierr = VecView(Qrefined_loc, viewer_refined); CHKERRQ(ierr); 419 ierr = DMRestoreLocalVector(user->dmviz, &Qrefined_loc); CHKERRQ(ierr); 420 ierr = DMRestoreGlobalVector(user->dmviz, &Qrefined); CHKERRQ(ierr); 421 ierr = PetscViewerDestroy(&viewer_refined); CHKERRQ(ierr); 422 } 423 ierr = PetscViewerDestroy(&viewer); CHKERRQ(ierr); 424 ierr = DMRestoreLocalVector(user->dm, &Qloc); CHKERRQ(ierr); 425 426 // Save data in a binary file for continuation of simulations 427 ierr = PetscSNPrintf(filepath, sizeof filepath, "%s/ns-solution.bin", 428 user->outputfolder); CHKERRQ(ierr); 429 ierr = PetscViewerBinaryOpen(user->comm, filepath, FILE_MODE_WRITE, &viewer); 430 CHKERRQ(ierr); 431 ierr = VecView(Q, viewer); CHKERRQ(ierr); 432 ierr = PetscViewerDestroy(&viewer); CHKERRQ(ierr); 433 434 // Save time stamp 435 // Dimensionalize time back 436 time /= user->units->second; 437 ierr = PetscSNPrintf(filepath, sizeof filepath, "%s/ns-time.bin", 438 user->outputfolder); CHKERRQ(ierr); 439 ierr = PetscViewerBinaryOpen(user->comm, filepath, FILE_MODE_WRITE, &viewer); 440 CHKERRQ(ierr); 441 #if PETSC_VERSION_GE(3,13,0) 442 ierr = PetscViewerBinaryWrite(viewer, &time, 1, PETSC_REAL); 443 #else 444 ierr = PetscViewerBinaryWrite(viewer, &time, 1, PETSC_REAL, true); 445 #endif 446 CHKERRQ(ierr); 447 ierr = PetscViewerDestroy(&viewer); CHKERRQ(ierr); 448 449 PetscFunctionReturn(0); 450 } 451 452 static PetscErrorCode ICs_FixMultiplicity(CeedOperator op_ics, 453 CeedVector xcorners, CeedVector q0ceed, DM dm, Vec Qloc, Vec Q, 454 CeedElemRestriction restrictq, SetupContext ctxSetup, CeedScalar time) { 455 PetscErrorCode ierr; 456 CeedVector multlvec; 457 Vec Multiplicity, MultiplicityLoc; 458 459 ctxSetup->time = time; 460 ierr = VecZeroEntries(Qloc); CHKERRQ(ierr); 461 ierr = VectorPlacePetscVec(q0ceed, Qloc); CHKERRQ(ierr); 462 CeedOperatorApply(op_ics, xcorners, q0ceed, CEED_REQUEST_IMMEDIATE); 463 ierr = VecZeroEntries(Q); CHKERRQ(ierr); 464 ierr = DMLocalToGlobal(dm, Qloc, ADD_VALUES, Q); CHKERRQ(ierr); 465 466 // Fix multiplicity for output of ICs 467 ierr = DMGetLocalVector(dm, &MultiplicityLoc); CHKERRQ(ierr); 468 CeedElemRestrictionCreateVector(restrictq, &multlvec, NULL); 469 ierr = VectorPlacePetscVec(multlvec, MultiplicityLoc); CHKERRQ(ierr); 470 CeedElemRestrictionGetMultiplicity(restrictq, multlvec); 471 CeedVectorDestroy(&multlvec); 472 ierr = DMGetGlobalVector(dm, &Multiplicity); CHKERRQ(ierr); 473 ierr = VecZeroEntries(Multiplicity); CHKERRQ(ierr); 474 ierr = DMLocalToGlobal(dm, MultiplicityLoc, ADD_VALUES, Multiplicity); 475 CHKERRQ(ierr); 476 ierr = VecPointwiseDivide(Q, Q, Multiplicity); CHKERRQ(ierr); 477 ierr = VecPointwiseDivide(Qloc, Qloc, MultiplicityLoc); CHKERRQ(ierr); 478 ierr = DMRestoreLocalVector(dm, &MultiplicityLoc); CHKERRQ(ierr); 479 ierr = DMRestoreGlobalVector(dm, &Multiplicity); CHKERRQ(ierr); 480 481 PetscFunctionReturn(0); 482 } 483 484 static PetscErrorCode ComputeLumpedMassMatrix(Ceed ceed, DM dm, 485 CeedElemRestriction restrictq, CeedBasis basisq, 486 CeedElemRestriction restrictqdi, CeedVector qdata, Vec M) { 487 PetscErrorCode ierr; 488 CeedQFunction qf_mass; 489 CeedOperator op_mass; 490 CeedVector mceed; 491 Vec Mloc; 492 CeedInt ncompq, qdatasize; 493 494 PetscFunctionBeginUser; 495 CeedElemRestrictionGetNumComponents(restrictq, &ncompq); 496 CeedElemRestrictionGetNumComponents(restrictqdi, &qdatasize); 497 // Create the Q-function that defines the action of the mass operator 498 CeedQFunctionCreateInterior(ceed, 1, Mass, Mass_loc, &qf_mass); 499 CeedQFunctionAddInput(qf_mass, "q", ncompq, CEED_EVAL_INTERP); 500 CeedQFunctionAddInput(qf_mass, "qdata", qdatasize, CEED_EVAL_NONE); 501 CeedQFunctionAddOutput(qf_mass, "v", ncompq, CEED_EVAL_INTERP); 502 503 // Create the mass operator 504 CeedOperatorCreate(ceed, qf_mass, NULL, NULL, &op_mass); 505 CeedOperatorSetField(op_mass, "q", restrictq, basisq, CEED_VECTOR_ACTIVE); 506 CeedOperatorSetField(op_mass, "qdata", restrictqdi, 507 CEED_BASIS_COLLOCATED, qdata); 508 CeedOperatorSetField(op_mass, "v", restrictq, basisq, CEED_VECTOR_ACTIVE); 509 510 ierr = DMGetLocalVector(dm, &Mloc); CHKERRQ(ierr); 511 ierr = VecZeroEntries(Mloc); CHKERRQ(ierr); 512 CeedElemRestrictionCreateVector(restrictq, &mceed, NULL); 513 ierr = VectorPlacePetscVec(mceed, Mloc); CHKERRQ(ierr); 514 515 { 516 // Compute a lumped mass matrix 517 CeedVector onesvec; 518 CeedElemRestrictionCreateVector(restrictq, &onesvec, NULL); 519 CeedVectorSetValue(onesvec, 1.0); 520 CeedOperatorApply(op_mass, onesvec, mceed, CEED_REQUEST_IMMEDIATE); 521 CeedVectorDestroy(&onesvec); 522 CeedOperatorDestroy(&op_mass); 523 CeedVectorDestroy(&mceed); 524 } 525 CeedQFunctionDestroy(&qf_mass); 526 527 ierr = VecZeroEntries(M); CHKERRQ(ierr); 528 ierr = DMLocalToGlobal(dm, Mloc, ADD_VALUES, M); CHKERRQ(ierr); 529 ierr = DMRestoreLocalVector(dm, &Mloc); CHKERRQ(ierr); 530 531 // Invert diagonally lumped mass vector for RHS function 532 ierr = VecReciprocal(M); CHKERRQ(ierr); 533 PetscFunctionReturn(0); 534 } 535 536 PetscErrorCode SetUpDM(DM dm, problemData *problem, PetscInt degree, 537 SimpleBC bc, void *ctxSetup) { 538 PetscErrorCode ierr; 539 540 PetscFunctionBeginUser; 541 { 542 // Configure the finite element space and boundary conditions 543 PetscFE fe; 544 PetscSpace fespace; 545 PetscInt ncompq = 5; 546 ierr = PetscFECreateLagrange(PETSC_COMM_SELF, problem->dim, ncompq, 547 PETSC_FALSE, degree, PETSC_DECIDE, 548 &fe); 549 ierr = PetscObjectSetName((PetscObject)fe, "Q"); CHKERRQ(ierr); 550 ierr = DMAddField(dm,NULL,(PetscObject)fe); CHKERRQ(ierr); 551 ierr = DMCreateDS(dm); CHKERRQ(ierr); 552 // Wall boundary conditions are zero energy density and zero flux for 553 // velocity in advection/advection2d, and zero velocity and zero flux 554 // for mass density and energy density in density_current 555 { 556 if (problem->bc == Exact_Advection || problem->bc == Exact_Advection2d) { 557 PetscInt comps[1] = {4}; 558 ierr = DMAddBoundary(dm, DM_BC_ESSENTIAL, "wall", "Face Sets", 0, 559 1, comps, (void(*)(void))problem->bc, 560 bc->nwall, bc->walls, ctxSetup); CHKERRQ(ierr); 561 } else if (problem->bc == Exact_DC) { 562 PetscInt comps[3] = {1, 2, 3}; 563 ierr = DMAddBoundary(dm, DM_BC_ESSENTIAL, "wall", "Face Sets", 0, 564 3, comps, (void(*)(void))problem->bc, 565 bc->nwall, bc->walls, ctxSetup); CHKERRQ(ierr); 566 } 567 } 568 { 569 PetscInt comps[1] = {1}; 570 ierr = DMAddBoundary(dm, DM_BC_ESSENTIAL, "slipx", "Face Sets", 0, 571 1, comps, (void(*)(void))NULL, bc->nslip[0], 572 bc->slips[0], ctxSetup); CHKERRQ(ierr); 573 comps[0] = 2; 574 ierr = DMAddBoundary(dm, DM_BC_ESSENTIAL, "slipy", "Face Sets", 0, 575 1, comps, (void(*)(void))NULL, bc->nslip[1], 576 bc->slips[1], ctxSetup); CHKERRQ(ierr); 577 comps[0] = 3; 578 ierr = DMAddBoundary(dm, DM_BC_ESSENTIAL, "slipz", "Face Sets", 0, 579 1, comps, (void(*)(void))NULL, bc->nslip[2], 580 bc->slips[2], ctxSetup); CHKERRQ(ierr); 581 } 582 ierr = DMPlexSetClosurePermutationTensor(dm,PETSC_DETERMINE,NULL); 583 CHKERRQ(ierr); 584 ierr = PetscFEGetBasisSpace(fe, &fespace); CHKERRQ(ierr); 585 ierr = PetscFEDestroy(&fe); CHKERRQ(ierr); 586 } 587 { 588 // Empty name for conserved field (because there is only one field) 589 PetscSection section; 590 ierr = DMGetLocalSection(dm, §ion); CHKERRQ(ierr); 591 ierr = PetscSectionSetFieldName(section, 0, ""); CHKERRQ(ierr); 592 ierr = PetscSectionSetComponentName(section, 0, 0, "Density"); 593 CHKERRQ(ierr); 594 ierr = PetscSectionSetComponentName(section, 0, 1, "MomentumX"); 595 CHKERRQ(ierr); 596 ierr = PetscSectionSetComponentName(section, 0, 2, "MomentumY"); 597 CHKERRQ(ierr); 598 ierr = PetscSectionSetComponentName(section, 0, 3, "MomentumZ"); 599 CHKERRQ(ierr); 600 ierr = PetscSectionSetComponentName(section, 0, 4, "EnergyDensity"); 601 CHKERRQ(ierr); 602 } 603 PetscFunctionReturn(0); 604 } 605 606 int main(int argc, char **argv) { 607 PetscInt ierr; 608 MPI_Comm comm; 609 DM dm, dmcoord, dmviz; 610 Mat interpviz; 611 TS ts; 612 TSAdapt adapt; 613 User user; 614 Units units; 615 char ceedresource[4096] = "/cpu/self"; 616 PetscInt cStart, cEnd, localNelem, lnodes, steps; 617 const PetscInt ncompq = 5; 618 PetscMPIInt rank; 619 PetscScalar ftime; 620 Vec Q, Qloc, Xloc; 621 Ceed ceed; 622 CeedInt numP, numQ; 623 CeedVector xcorners, qdata, q0ceed; 624 CeedBasis basisx, basisxc, basisq; 625 CeedElemRestriction restrictx, restrictxcoord, restrictq, restrictqdi; 626 CeedQFunction qf_setup, qf_ics, qf_rhs, qf_ifunction; 627 CeedOperator op_setup, op_ics; 628 CeedScalar Rd; 629 PetscScalar WpermK, Pascal, JperkgK, mpersquareds, kgpercubicm, 630 kgpersquaredms, Joulepercubicm; 631 problemType problemChoice; 632 problemData *problem = NULL; 633 StabilizationType stab; 634 PetscBool test, implicit; 635 PetscInt viz_refine = 0; 636 struct SimpleBC_ bc = { 637 .nwall = 6, 638 .walls = {1,2,3,4,5,6}, 639 }; 640 double start, cpu_time_used; 641 642 // Create the libCEED contexts 643 PetscScalar meter = 1e-2; // 1 meter in scaled length units 644 PetscScalar second = 1e-2; // 1 second in scaled time units 645 PetscScalar kilogram = 1e-6; // 1 kilogram in scaled mass units 646 PetscScalar Kelvin = 1; // 1 Kelvin in scaled temperature units 647 CeedScalar theta0 = 300.; // K 648 CeedScalar thetaC = -15.; // K 649 CeedScalar P0 = 1.e5; // Pa 650 CeedScalar N = 0.01; // 1/s 651 CeedScalar cv = 717.; // J/(kg K) 652 CeedScalar cp = 1004.; // J/(kg K) 653 CeedScalar g = 9.81; // m/s^2 654 CeedScalar lambda = -2./3.; // - 655 CeedScalar mu = 75.; // Pa s, dynamic viscosity 656 // mu = 75 is not physical for air, but is good for numerical stability 657 CeedScalar k = 0.02638; // W/(m K) 658 CeedScalar CtauS = 0.; // dimensionless 659 CeedScalar strong_form = 0.; // [0,1] 660 PetscScalar lx = 8000.; // m 661 PetscScalar ly = 8000.; // m 662 PetscScalar lz = 4000.; // m 663 CeedScalar rc = 1000.; // m (Radius of bubble) 664 PetscScalar resx = 1000.; // m (resolution in x) 665 PetscScalar resy = 1000.; // m (resolution in y) 666 PetscScalar resz = 1000.; // m (resolution in z) 667 PetscInt outputfreq = 10; // - 668 PetscInt contsteps = 0; // - 669 PetscInt degree = 1; // - 670 PetscInt qextra = 2; // - 671 DMBoundaryType periodicity[] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, 672 DM_BOUNDARY_NONE 673 }; 674 PetscReal center[3], dc_axis[3] = {0, 0, 0}; 675 676 ierr = PetscInitialize(&argc, &argv, NULL, help); 677 if (ierr) return ierr; 678 679 // Allocate PETSc context 680 ierr = PetscCalloc1(1, &user); CHKERRQ(ierr); 681 ierr = PetscMalloc1(1, &units); CHKERRQ(ierr); 682 683 // Parse command line options 684 comm = PETSC_COMM_WORLD; 685 ierr = PetscOptionsBegin(comm, NULL, "Navier-Stokes in PETSc with libCEED", 686 NULL); CHKERRQ(ierr); 687 ierr = PetscOptionsString("-ceed", "CEED resource specifier", 688 NULL, ceedresource, ceedresource, 689 sizeof(ceedresource), NULL); CHKERRQ(ierr); 690 ierr = PetscOptionsBool("-test", "Run in test mode", 691 NULL, test=PETSC_FALSE, &test, NULL); CHKERRQ(ierr); 692 problemChoice = NS_DENSITY_CURRENT; 693 ierr = PetscOptionsEnum("-problem", "Problem to solve", NULL, 694 problemTypes, (PetscEnum)problemChoice, 695 (PetscEnum *)&problemChoice, NULL); CHKERRQ(ierr); 696 problem = &problemOptions[problemChoice]; 697 ierr = PetscOptionsEnum("-stab", "Stabilization method", NULL, 698 StabilizationTypes, (PetscEnum)(stab = STAB_NONE), 699 (PetscEnum *)&stab, NULL); CHKERRQ(ierr); 700 ierr = PetscOptionsBool("-implicit", "Use implicit (IFunction) formulation", 701 NULL, implicit=PETSC_FALSE, &implicit, NULL); 702 CHKERRQ(ierr); 703 if (!implicit && stab != STAB_NONE) { 704 ierr = PetscPrintf(comm, "Warning! Use -stab only with -implicit\n"); 705 CHKERRQ(ierr); 706 } 707 { 708 PetscInt len; 709 PetscBool flg; 710 ierr = PetscOptionsIntArray("-bc_wall", 711 "Use wall boundary conditions on this list of faces", 712 NULL, bc.walls, 713 (len = sizeof(bc.walls) / sizeof(bc.walls[0]), 714 &len), &flg); CHKERRQ(ierr); 715 if (flg) bc.nwall = len; 716 for (PetscInt j=0; j<3; j++) { 717 const char *flags[3] = {"-bc_slip_x", "-bc_slip_y", "-bc_slip_z"}; 718 ierr = PetscOptionsIntArray(flags[j], 719 "Use slip boundary conditions on this list of faces", 720 NULL, bc.slips[j], 721 (len = sizeof(bc.slips[j]) / sizeof(bc.slips[j][0]), 722 &len), &flg); 723 CHKERRQ(ierr); 724 if (flg) bc.nslip[j] = len; 725 } 726 } 727 ierr = PetscOptionsInt("-viz_refine", 728 "Regular refinement levels for visualization", 729 NULL, viz_refine, &viz_refine, NULL); 730 CHKERRQ(ierr); 731 ierr = PetscOptionsScalar("-units_meter", "1 meter in scaled length units", 732 NULL, meter, &meter, NULL); CHKERRQ(ierr); 733 meter = fabs(meter); 734 ierr = PetscOptionsScalar("-units_second","1 second in scaled time units", 735 NULL, second, &second, NULL); CHKERRQ(ierr); 736 second = fabs(second); 737 ierr = PetscOptionsScalar("-units_kilogram","1 kilogram in scaled mass units", 738 NULL, kilogram, &kilogram, NULL); CHKERRQ(ierr); 739 kilogram = fabs(kilogram); 740 ierr = PetscOptionsScalar("-units_Kelvin", 741 "1 Kelvin in scaled temperature units", 742 NULL, Kelvin, &Kelvin, NULL); CHKERRQ(ierr); 743 Kelvin = fabs(Kelvin); 744 ierr = PetscOptionsScalar("-theta0", "Reference potential temperature", 745 NULL, theta0, &theta0, NULL); CHKERRQ(ierr); 746 ierr = PetscOptionsScalar("-thetaC", "Perturbation of potential temperature", 747 NULL, thetaC, &thetaC, NULL); CHKERRQ(ierr); 748 ierr = PetscOptionsScalar("-P0", "Atmospheric pressure", 749 NULL, P0, &P0, NULL); CHKERRQ(ierr); 750 ierr = PetscOptionsScalar("-N", "Brunt-Vaisala frequency", 751 NULL, N, &N, NULL); CHKERRQ(ierr); 752 ierr = PetscOptionsScalar("-cv", "Heat capacity at constant volume", 753 NULL, cv, &cv, NULL); CHKERRQ(ierr); 754 ierr = PetscOptionsScalar("-cp", "Heat capacity at constant pressure", 755 NULL, cp, &cp, NULL); CHKERRQ(ierr); 756 ierr = PetscOptionsScalar("-g", "Gravitational acceleration", 757 NULL, g, &g, NULL); CHKERRQ(ierr); 758 ierr = PetscOptionsScalar("-lambda", 759 "Stokes hypothesis second viscosity coefficient", 760 NULL, lambda, &lambda, NULL); CHKERRQ(ierr); 761 ierr = PetscOptionsScalar("-mu", "Shear dynamic viscosity coefficient", 762 NULL, mu, &mu, NULL); CHKERRQ(ierr); 763 ierr = PetscOptionsScalar("-k", "Thermal conductivity", 764 NULL, k, &k, NULL); CHKERRQ(ierr); 765 ierr = PetscOptionsScalar("-CtauS", 766 "Scale coefficient for tau (nondimensional)", 767 NULL, CtauS, &CtauS, NULL); CHKERRQ(ierr); 768 if (stab == STAB_NONE && CtauS != 0) { 769 ierr = PetscPrintf(comm, "Warning! Use -CtauS only with -stab su or -stab supg\n"); 770 CHKERRQ(ierr); 771 } 772 ierr = PetscOptionsScalar("-strong_form", 773 "Strong (1) or weak/integrated by parts (0) advection residual", 774 NULL, strong_form, &strong_form, NULL); 775 CHKERRQ(ierr); 776 ierr = PetscOptionsScalar("-lx", "Length scale in x direction", 777 NULL, lx, &lx, NULL); CHKERRQ(ierr); 778 ierr = PetscOptionsScalar("-ly", "Length scale in y direction", 779 NULL, ly, &ly, NULL); CHKERRQ(ierr); 780 ierr = PetscOptionsScalar("-lz", "Length scale in z direction", 781 NULL, lz, &lz, NULL); CHKERRQ(ierr); 782 ierr = PetscOptionsScalar("-rc", "Characteristic radius of thermal bubble", 783 NULL, rc, &rc, NULL); CHKERRQ(ierr); 784 ierr = PetscOptionsScalar("-resx","Target resolution in x", 785 NULL, resx, &resx, NULL); CHKERRQ(ierr); 786 ierr = PetscOptionsScalar("-resy","Target resolution in y", 787 NULL, resy, &resy, NULL); CHKERRQ(ierr); 788 ierr = PetscOptionsScalar("-resz","Target resolution in z", 789 NULL, resz, &resz, NULL); CHKERRQ(ierr); 790 PetscInt n = problem->dim; 791 ierr = PetscOptionsEnumArray("-periodicity", "Periodicity per direction", 792 NULL, DMBoundaryTypes, (PetscEnum *)periodicity, 793 &n, NULL); CHKERRQ(ierr); 794 n = problem->dim; 795 center[0] = 0.5 * lx; 796 center[1] = 0.5 * ly; 797 center[2] = 0.5 * lz; 798 ierr = PetscOptionsRealArray("-center", "Location of bubble center", 799 NULL, center, &n, NULL); CHKERRQ(ierr); 800 n = problem->dim; 801 ierr = PetscOptionsRealArray("-dc_axis", 802 "Axis of density current cylindrical anomaly, or {0,0,0} for spherically symmetric", 803 NULL, dc_axis, &n, NULL); CHKERRQ(ierr); 804 { 805 PetscReal norm = PetscSqrtReal(PetscSqr(dc_axis[0]) + 806 PetscSqr(dc_axis[1]) + PetscSqr(dc_axis[2])); 807 if (norm > 0) { 808 for (int i=0; i<3; i++) dc_axis[i] /= norm; 809 } 810 } 811 ierr = PetscOptionsInt("-output_freq", 812 "Frequency of output, in number of steps", 813 NULL, outputfreq, &outputfreq, NULL); CHKERRQ(ierr); 814 ierr = PetscOptionsInt("-continue", "Continue from previous solution", 815 NULL, contsteps, &contsteps, NULL); CHKERRQ(ierr); 816 ierr = PetscOptionsInt("-degree", "Polynomial degree of finite elements", 817 NULL, degree, °ree, NULL); CHKERRQ(ierr); 818 ierr = PetscOptionsInt("-qextra", "Number of extra quadrature points", 819 NULL, qextra, &qextra, NULL); CHKERRQ(ierr); 820 PetscStrncpy(user->outputfolder, ".", 2); 821 ierr = PetscOptionsString("-of", "Output folder", 822 NULL, user->outputfolder, user->outputfolder, 823 sizeof(user->outputfolder), NULL); CHKERRQ(ierr); 824 ierr = PetscOptionsEnd(); CHKERRQ(ierr); 825 826 // Define derived units 827 Pascal = kilogram / (meter * PetscSqr(second)); 828 JperkgK = PetscSqr(meter) / (PetscSqr(second) * Kelvin); 829 mpersquareds = meter / PetscSqr(second); 830 WpermK = kilogram * meter / (pow(second,3) * Kelvin); 831 kgpercubicm = kilogram / pow(meter,3); 832 kgpersquaredms = kilogram / (PetscSqr(meter) * second); 833 Joulepercubicm = kilogram / (meter * PetscSqr(second)); 834 835 // Scale variables to desired units 836 theta0 *= Kelvin; 837 thetaC *= Kelvin; 838 P0 *= Pascal; 839 N *= (1./second); 840 cv *= JperkgK; 841 cp *= JperkgK; 842 Rd = cp - cv; 843 g *= mpersquareds; 844 mu *= Pascal * second; 845 k *= WpermK; 846 lx = fabs(lx) * meter; 847 ly = fabs(ly) * meter; 848 lz = fabs(lz) * meter; 849 rc = fabs(rc) * meter; 850 resx = fabs(resx) * meter; 851 resy = fabs(resy) * meter; 852 resz = fabs(resz) * meter; 853 for (int i=0; i<3; i++) center[i] *= meter; 854 855 const CeedInt dim = problem->dim, ncompx = problem->dim, 856 qdatasize = problem->qdatasize; 857 // Set up the libCEED context 858 struct SetupContext_ ctxSetup = { 859 .theta0 = theta0, 860 .thetaC = thetaC, 861 .P0 = P0, 862 .N = N, 863 .cv = cv, 864 .cp = cp, 865 .Rd = Rd, 866 .g = g, 867 .rc = rc, 868 .lx = lx, 869 .ly = ly, 870 .lz = lz, 871 .periodicity0 = periodicity[0], 872 .periodicity1 = periodicity[1], 873 .periodicity2 = periodicity[2], 874 .center[0] = center[0], 875 .center[1] = center[1], 876 .center[2] = center[2], 877 .dc_axis[0] = dc_axis[0], 878 .dc_axis[1] = dc_axis[1], 879 .dc_axis[2] = dc_axis[2], 880 .time = 0, 881 }; 882 883 // Create the mesh 884 { 885 const PetscReal scale[3] = {lx, ly, lz}; 886 ierr = DMPlexCreateBoxMesh(comm, dim, PETSC_FALSE, NULL, NULL, scale, 887 periodicity, PETSC_TRUE, &dm); 888 CHKERRQ(ierr); 889 } 890 891 // Distribute the mesh over processes 892 { 893 DM dmDist = NULL; 894 PetscPartitioner part; 895 896 ierr = DMPlexGetPartitioner(dm, &part); CHKERRQ(ierr); 897 ierr = PetscPartitionerSetFromOptions(part); CHKERRQ(ierr); 898 ierr = DMPlexDistribute(dm, 0, NULL, &dmDist); CHKERRQ(ierr); 899 if (dmDist) { 900 ierr = DMDestroy(&dm); CHKERRQ(ierr); 901 dm = dmDist; 902 } 903 } 904 ierr = DMViewFromOptions(dm, NULL, "-dm_view"); CHKERRQ(ierr); 905 906 // Setup DM 907 ierr = DMLocalizeCoordinates(dm); CHKERRQ(ierr); 908 ierr = DMSetFromOptions(dm); CHKERRQ(ierr); 909 ierr = SetUpDM(dm, problem, degree, &bc, &ctxSetup); CHKERRQ(ierr); 910 911 // Print FEM space information 912 if (!test) { 913 ierr = PetscPrintf(PETSC_COMM_WORLD, 914 "Degree of FEM space: %D\n", 915 degree); CHKERRQ(ierr); 916 } 917 918 // Refine DM for high-order viz 919 dmviz = NULL; 920 interpviz = NULL; 921 if (viz_refine) { 922 DM dmhierarchy[viz_refine+1]; 923 924 ierr = DMPlexSetRefinementUniform(dm, PETSC_TRUE); CHKERRQ(ierr); 925 dmhierarchy[0] = dm; 926 for (PetscInt i = 0, d = degree; i < viz_refine; i++) { 927 Mat interp_next; 928 929 ierr = DMRefine(dmhierarchy[i], MPI_COMM_NULL, &dmhierarchy[i+1]); 930 CHKERRQ(ierr); 931 ierr = DMSetCoarseDM(dmhierarchy[i+1], dmhierarchy[i]); CHKERRQ(ierr); 932 d = (d + 1) / 2; 933 if (i + 1 == viz_refine) d = 1; 934 ierr = SetUpDM(dmhierarchy[i+1], problem, d, &bc, &ctxSetup); CHKERRQ(ierr); 935 ierr = DMCreateInterpolation(dmhierarchy[i], dmhierarchy[i+1], 936 &interp_next, NULL); CHKERRQ(ierr); 937 if (!i) interpviz = interp_next; 938 else { 939 Mat C; 940 ierr = MatMatMult(interp_next, interpviz, MAT_INITIAL_MATRIX, 941 PETSC_DECIDE, &C); CHKERRQ(ierr); 942 ierr = MatDestroy(&interp_next); CHKERRQ(ierr); 943 ierr = MatDestroy(&interpviz); CHKERRQ(ierr); 944 interpviz = C; 945 } 946 } 947 for (PetscInt i=1; i<viz_refine; i++) { 948 ierr = DMDestroy(&dmhierarchy[i]); CHKERRQ(ierr); 949 } 950 dmviz = dmhierarchy[viz_refine]; 951 } 952 ierr = DMCreateGlobalVector(dm, &Q); CHKERRQ(ierr); 953 ierr = DMGetLocalVector(dm, &Qloc); CHKERRQ(ierr); 954 ierr = VecGetSize(Qloc, &lnodes); CHKERRQ(ierr); 955 lnodes /= ncompq; 956 957 { 958 // Print grid information 959 CeedInt gdofs, odofs; 960 int comm_size; 961 char box_faces_str[PETSC_MAX_PATH_LEN] = "NONE"; 962 ierr = VecGetSize(Q, &gdofs); CHKERRQ(ierr); 963 ierr = VecGetLocalSize(Q, &odofs); CHKERRQ(ierr); 964 ierr = MPI_Comm_size(comm, &comm_size); CHKERRQ(ierr); 965 ierr = PetscOptionsGetString(NULL, NULL, "-dm_plex_box_faces", box_faces_str, 966 sizeof(box_faces_str), NULL); CHKERRQ(ierr); 967 if (!test) { 968 ierr = PetscPrintf(comm, "Global FEM dofs: %D (%D owned) on %d rank(s)\n", 969 gdofs, odofs, comm_size); CHKERRQ(ierr); 970 ierr = PetscPrintf(comm, "Local FEM nodes: %D\n", lnodes); CHKERRQ(ierr); 971 ierr = PetscPrintf(comm, "dm_plex_box_faces: %s\n", box_faces_str); 972 CHKERRQ(ierr); 973 } 974 975 } 976 977 // Set up global mass vector 978 ierr = VecDuplicate(Q, &user->M); CHKERRQ(ierr); 979 980 // Set up CEED 981 // CEED Bases 982 CeedInit(ceedresource, &ceed); 983 numP = degree + 1; 984 numQ = numP + qextra; 985 CeedBasisCreateTensorH1Lagrange(ceed, dim, ncompq, numP, numQ, CEED_GAUSS, 986 &basisq); 987 CeedBasisCreateTensorH1Lagrange(ceed, dim, ncompx, 2, numQ, CEED_GAUSS, 988 &basisx); 989 CeedBasisCreateTensorH1Lagrange(ceed, dim, ncompx, 2, numP, 990 CEED_GAUSS_LOBATTO, &basisxc); 991 992 ierr = DMGetCoordinateDM(dm, &dmcoord); CHKERRQ(ierr); 993 ierr = DMPlexSetClosurePermutationTensor(dmcoord, PETSC_DETERMINE, NULL); 994 CHKERRQ(ierr); 995 996 // CEED Restrictions 997 ierr = CreateRestrictionFromPlex(ceed, dm, degree+1, &restrictq); 998 CHKERRQ(ierr); 999 ierr = CreateRestrictionFromPlex(ceed, dmcoord, 2, &restrictx); CHKERRQ(ierr); 1000 DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd); CHKERRQ(ierr); 1001 localNelem = cEnd - cStart; 1002 CeedInt numQdim = CeedIntPow(numQ, dim); 1003 CeedElemRestrictionCreateStrided(ceed, localNelem, numQdim, 1004 localNelem*numQdim, qdatasize, 1005 CEED_STRIDES_BACKEND, &restrictqdi); 1006 CeedElemRestrictionCreateStrided(ceed, localNelem, PetscPowInt(numP, dim), 1007 localNelem*PetscPowInt(numP, dim), ncompx, 1008 CEED_STRIDES_BACKEND, &restrictxcoord); 1009 1010 ierr = DMGetCoordinatesLocal(dm, &Xloc); CHKERRQ(ierr); 1011 ierr = CreateVectorFromPetscVec(ceed, Xloc, &xcorners); CHKERRQ(ierr); 1012 1013 // Create the CEED vectors that will be needed in setup 1014 CeedInt Nqpts; 1015 CeedBasisGetNumQuadraturePoints(basisq, &Nqpts); 1016 CeedVectorCreate(ceed, qdatasize*localNelem*Nqpts, &qdata); 1017 CeedElemRestrictionCreateVector(restrictq, &q0ceed, NULL); 1018 1019 // Create the Q-function that builds the quadrature data for the NS operator 1020 CeedQFunctionCreateInterior(ceed, 1, problem->setup, problem->setup_loc, 1021 &qf_setup); 1022 CeedQFunctionAddInput(qf_setup, "dx", ncompx*dim, CEED_EVAL_GRAD); 1023 CeedQFunctionAddInput(qf_setup, "weight", 1, CEED_EVAL_WEIGHT); 1024 CeedQFunctionAddOutput(qf_setup, "qdata", qdatasize, CEED_EVAL_NONE); 1025 1026 // Create the Q-function that sets the ICs of the operator 1027 CeedQFunctionCreateInterior(ceed, 1, problem->ics, problem->ics_loc, &qf_ics); 1028 CeedQFunctionAddInput(qf_ics, "x", ncompx, CEED_EVAL_INTERP); 1029 CeedQFunctionAddOutput(qf_ics, "q0", ncompq, CEED_EVAL_NONE); 1030 1031 qf_rhs = NULL; 1032 if (problem->apply_rhs) { // Create the Q-function that defines the action of the RHS operator 1033 CeedQFunctionCreateInterior(ceed, 1, problem->apply_rhs, 1034 problem->apply_rhs_loc, &qf_rhs); 1035 CeedQFunctionAddInput(qf_rhs, "q", ncompq, CEED_EVAL_INTERP); 1036 CeedQFunctionAddInput(qf_rhs, "dq", ncompq*dim, CEED_EVAL_GRAD); 1037 CeedQFunctionAddInput(qf_rhs, "qdata", qdatasize, CEED_EVAL_NONE); 1038 CeedQFunctionAddInput(qf_rhs, "x", ncompx, CEED_EVAL_INTERP); 1039 CeedQFunctionAddOutput(qf_rhs, "v", ncompq, CEED_EVAL_INTERP); 1040 CeedQFunctionAddOutput(qf_rhs, "dv", ncompq*dim, CEED_EVAL_GRAD); 1041 } 1042 1043 qf_ifunction = NULL; 1044 if (problem->apply_ifunction) { // Create the Q-function that defines the action of the IFunction 1045 CeedQFunctionCreateInterior(ceed, 1, problem->apply_ifunction, 1046 problem->apply_ifunction_loc, &qf_ifunction); 1047 CeedQFunctionAddInput(qf_ifunction, "q", ncompq, CEED_EVAL_INTERP); 1048 CeedQFunctionAddInput(qf_ifunction, "dq", ncompq*dim, CEED_EVAL_GRAD); 1049 CeedQFunctionAddInput(qf_ifunction, "qdot", ncompq, CEED_EVAL_INTERP); 1050 CeedQFunctionAddInput(qf_ifunction, "qdata", qdatasize, CEED_EVAL_NONE); 1051 CeedQFunctionAddInput(qf_ifunction, "x", ncompx, CEED_EVAL_INTERP); 1052 CeedQFunctionAddOutput(qf_ifunction, "v", ncompq, CEED_EVAL_INTERP); 1053 CeedQFunctionAddOutput(qf_ifunction, "dv", ncompq*dim, CEED_EVAL_GRAD); 1054 } 1055 1056 // Create the operator that builds the quadrature data for the NS operator 1057 CeedOperatorCreate(ceed, qf_setup, NULL, NULL, &op_setup); 1058 CeedOperatorSetField(op_setup, "dx", restrictx, basisx, CEED_VECTOR_ACTIVE); 1059 CeedOperatorSetField(op_setup, "weight", CEED_ELEMRESTRICTION_NONE, 1060 basisx, CEED_VECTOR_NONE); 1061 CeedOperatorSetField(op_setup, "qdata", restrictqdi, 1062 CEED_BASIS_COLLOCATED, CEED_VECTOR_ACTIVE); 1063 1064 // Create the operator that sets the ICs 1065 CeedOperatorCreate(ceed, qf_ics, NULL, NULL, &op_ics); 1066 CeedOperatorSetField(op_ics, "x", restrictx, basisxc, CEED_VECTOR_ACTIVE); 1067 CeedOperatorSetField(op_ics, "q0", restrictq, 1068 CEED_BASIS_COLLOCATED, CEED_VECTOR_ACTIVE); 1069 1070 CeedElemRestrictionCreateVector(restrictq, &user->qceed, NULL); 1071 CeedElemRestrictionCreateVector(restrictq, &user->qdotceed, NULL); 1072 CeedElemRestrictionCreateVector(restrictq, &user->gceed, NULL); 1073 1074 if (qf_rhs) { // Create the RHS physics operator 1075 CeedOperator op; 1076 CeedOperatorCreate(ceed, qf_rhs, NULL, NULL, &op); 1077 CeedOperatorSetField(op, "q", restrictq, basisq, CEED_VECTOR_ACTIVE); 1078 CeedOperatorSetField(op, "dq", restrictq, basisq, CEED_VECTOR_ACTIVE); 1079 CeedOperatorSetField(op, "qdata", restrictqdi, 1080 CEED_BASIS_COLLOCATED, qdata); 1081 CeedOperatorSetField(op, "x", restrictx, basisx, xcorners); 1082 CeedOperatorSetField(op, "v", restrictq, basisq, CEED_VECTOR_ACTIVE); 1083 CeedOperatorSetField(op, "dv", restrictq, basisq, CEED_VECTOR_ACTIVE); 1084 user->op_rhs = op; 1085 } 1086 1087 if (qf_ifunction) { // Create the IFunction operator 1088 CeedOperator op; 1089 CeedOperatorCreate(ceed, qf_ifunction, NULL, NULL, &op); 1090 CeedOperatorSetField(op, "q", restrictq, basisq, CEED_VECTOR_ACTIVE); 1091 CeedOperatorSetField(op, "dq", restrictq, basisq, CEED_VECTOR_ACTIVE); 1092 CeedOperatorSetField(op, "qdot", restrictq, basisq, user->qdotceed); 1093 CeedOperatorSetField(op, "qdata", restrictqdi, 1094 CEED_BASIS_COLLOCATED, qdata); 1095 CeedOperatorSetField(op, "x", restrictx, basisx, xcorners); 1096 CeedOperatorSetField(op, "v", restrictq, basisq, CEED_VECTOR_ACTIVE); 1097 CeedOperatorSetField(op, "dv", restrictq, basisq, CEED_VECTOR_ACTIVE); 1098 user->op_ifunction = op; 1099 } 1100 1101 CeedQFunctionSetContext(qf_ics, &ctxSetup, sizeof ctxSetup); 1102 CeedScalar ctxNS[8] = {lambda, mu, k, cv, cp, g, Rd}; 1103 struct Advection2dContext_ ctxAdvection2d = { 1104 .CtauS = CtauS, 1105 .strong_form = strong_form, 1106 .stabilization = stab, 1107 }; 1108 switch (problemChoice) { 1109 case NS_DENSITY_CURRENT: 1110 if (qf_rhs) CeedQFunctionSetContext(qf_rhs, &ctxNS, sizeof ctxNS); 1111 if (qf_ifunction) CeedQFunctionSetContext(qf_ifunction, &ctxNS, 1112 sizeof ctxNS); 1113 break; 1114 case NS_ADVECTION: 1115 case NS_ADVECTION2D: 1116 if (qf_rhs) CeedQFunctionSetContext(qf_rhs, &ctxAdvection2d, 1117 sizeof ctxAdvection2d); 1118 if (qf_ifunction) CeedQFunctionSetContext(qf_ifunction, &ctxAdvection2d, 1119 sizeof ctxAdvection2d); 1120 } 1121 1122 // Set up PETSc context 1123 // Set up units structure 1124 units->meter = meter; 1125 units->kilogram = kilogram; 1126 units->second = second; 1127 units->Kelvin = Kelvin; 1128 units->Pascal = Pascal; 1129 units->JperkgK = JperkgK; 1130 units->mpersquareds = mpersquareds; 1131 units->WpermK = WpermK; 1132 units->kgpercubicm = kgpercubicm; 1133 units->kgpersquaredms = kgpersquaredms; 1134 units->Joulepercubicm = Joulepercubicm; 1135 1136 // Set up user structure 1137 user->comm = comm; 1138 user->outputfreq = outputfreq; 1139 user->contsteps = contsteps; 1140 user->units = units; 1141 user->dm = dm; 1142 user->dmviz = dmviz; 1143 user->interpviz = interpviz; 1144 user->ceed = ceed; 1145 1146 // Calculate qdata and ICs 1147 // Set up state global and local vectors 1148 ierr = VecZeroEntries(Q); CHKERRQ(ierr); 1149 1150 ierr = VectorPlacePetscVec(q0ceed, Qloc); CHKERRQ(ierr); 1151 1152 // Apply Setup Ceed Operators 1153 ierr = VectorPlacePetscVec(xcorners, Xloc); CHKERRQ(ierr); 1154 CeedOperatorApply(op_setup, xcorners, qdata, CEED_REQUEST_IMMEDIATE); 1155 ierr = ComputeLumpedMassMatrix(ceed, dm, restrictq, basisq, restrictqdi, qdata, 1156 user->M); CHKERRQ(ierr); 1157 1158 ierr = ICs_FixMultiplicity(op_ics, xcorners, q0ceed, dm, Qloc, Q, restrictq, 1159 &ctxSetup, 0.0); 1160 if (1) { // Record boundary values from initial condition and override DMPlexInsertBoundaryValues() 1161 // We use this for the main simulation DM because the reference DMPlexInsertBoundaryValues() is very slow. If we 1162 // disable this, we should still get the same results due to the problem->bc function, but with potentially much 1163 // slower execution. 1164 Vec Qbc; 1165 ierr = DMGetNamedLocalVector(dm, "Qbc", &Qbc); CHKERRQ(ierr); 1166 ierr = VecCopy(Qloc, Qbc); CHKERRQ(ierr); 1167 ierr = VecZeroEntries(Qloc); CHKERRQ(ierr); 1168 ierr = DMGlobalToLocal(dm, Q, INSERT_VALUES, Qloc); CHKERRQ(ierr); 1169 ierr = VecAXPY(Qbc, -1., Qloc); CHKERRQ(ierr); 1170 ierr = DMRestoreNamedLocalVector(dm, "Qbc", &Qbc); CHKERRQ(ierr); 1171 ierr = PetscObjectComposeFunction((PetscObject)dm, 1172 "DMPlexInsertBoundaryValues_C", DMPlexInsertBoundaryValues_NS); 1173 CHKERRQ(ierr); 1174 } 1175 1176 MPI_Comm_rank(comm, &rank); 1177 if (!rank) {ierr = PetscMkdir(user->outputfolder); CHKERRQ(ierr);} 1178 // Gather initial Q values 1179 // In case of continuation of simulation, set up initial values from binary file 1180 if (contsteps) { // continue from existent solution 1181 PetscViewer viewer; 1182 char filepath[PETSC_MAX_PATH_LEN]; 1183 // Read input 1184 ierr = PetscSNPrintf(filepath, sizeof filepath, "%s/ns-solution.bin", 1185 user->outputfolder); 1186 CHKERRQ(ierr); 1187 ierr = PetscViewerBinaryOpen(comm, filepath, FILE_MODE_READ, &viewer); 1188 CHKERRQ(ierr); 1189 ierr = VecLoad(Q, viewer); CHKERRQ(ierr); 1190 ierr = PetscViewerDestroy(&viewer); CHKERRQ(ierr); 1191 } 1192 ierr = DMRestoreLocalVector(dm, &Qloc); CHKERRQ(ierr); 1193 1194 // Create and setup TS 1195 ierr = TSCreate(comm, &ts); CHKERRQ(ierr); 1196 ierr = TSSetDM(ts, dm); CHKERRQ(ierr); 1197 if (implicit) { 1198 ierr = TSSetType(ts, TSBDF); CHKERRQ(ierr); 1199 if (user->op_ifunction) { 1200 ierr = TSSetIFunction(ts, NULL, IFunction_NS, &user); CHKERRQ(ierr); 1201 } else { // Implicit integrators can fall back to using an RHSFunction 1202 ierr = TSSetRHSFunction(ts, NULL, RHS_NS, &user); CHKERRQ(ierr); 1203 } 1204 } else { 1205 if (!user->op_rhs) SETERRQ(comm,PETSC_ERR_ARG_NULL, 1206 "Problem does not provide RHSFunction"); 1207 ierr = TSSetType(ts, TSRK); CHKERRQ(ierr); 1208 ierr = TSRKSetType(ts, TSRK5F); CHKERRQ(ierr); 1209 ierr = TSSetRHSFunction(ts, NULL, RHS_NS, &user); CHKERRQ(ierr); 1210 } 1211 ierr = TSSetMaxTime(ts, 500. * units->second); CHKERRQ(ierr); 1212 ierr = TSSetExactFinalTime(ts, TS_EXACTFINALTIME_STEPOVER); CHKERRQ(ierr); 1213 ierr = TSSetTimeStep(ts, 1.e-2 * units->second); CHKERRQ(ierr); 1214 if (test) {ierr = TSSetMaxSteps(ts, 1); CHKERRQ(ierr);} 1215 ierr = TSGetAdapt(ts, &adapt); CHKERRQ(ierr); 1216 ierr = TSAdaptSetStepLimits(adapt, 1217 1.e-12 * units->second, 1218 1.e2 * units->second); CHKERRQ(ierr); 1219 ierr = TSSetFromOptions(ts); CHKERRQ(ierr); 1220 if (!contsteps) { // print initial condition 1221 if (!test) { 1222 ierr = TSMonitor_NS(ts, 0, 0., Q, user); CHKERRQ(ierr); 1223 } 1224 } else { // continue from time of last output 1225 PetscReal time; 1226 PetscInt count; 1227 PetscViewer viewer; 1228 char filepath[PETSC_MAX_PATH_LEN]; 1229 ierr = PetscSNPrintf(filepath, sizeof filepath, "%s/ns-time.bin", 1230 user->outputfolder); CHKERRQ(ierr); 1231 ierr = PetscViewerBinaryOpen(comm, filepath, FILE_MODE_READ, &viewer); 1232 CHKERRQ(ierr); 1233 ierr = PetscViewerBinaryRead(viewer, &time, 1, &count, PETSC_REAL); 1234 CHKERRQ(ierr); 1235 ierr = PetscViewerDestroy(&viewer); CHKERRQ(ierr); 1236 ierr = TSSetTime(ts, time * user->units->second); CHKERRQ(ierr); 1237 } 1238 if (!test) { 1239 ierr = TSMonitorSet(ts, TSMonitor_NS, user, NULL); CHKERRQ(ierr); 1240 } 1241 1242 // Solve 1243 start = MPI_Wtime(); 1244 ierr = PetscBarrier((PetscObject)ts); CHKERRQ(ierr); 1245 ierr = TSSolve(ts, Q); CHKERRQ(ierr); 1246 cpu_time_used = MPI_Wtime() - start; 1247 ierr = TSGetSolveTime(ts, &ftime); CHKERRQ(ierr); 1248 ierr = MPI_Allreduce(MPI_IN_PLACE, &cpu_time_used, 1, MPI_DOUBLE, MPI_MIN, 1249 comm); CHKERRQ(ierr); 1250 if (!test) { 1251 ierr = PetscPrintf(PETSC_COMM_WORLD, 1252 "Time taken for solution (sec): %g\n", 1253 (double)cpu_time_used); CHKERRQ(ierr); 1254 } 1255 1256 // Get error 1257 if (problem->non_zero_time && !test) { 1258 Vec Qexact, Qexactloc; 1259 PetscReal norm; 1260 ierr = DMCreateGlobalVector(dm, &Qexact); CHKERRQ(ierr); 1261 ierr = DMGetLocalVector(dm, &Qexactloc); CHKERRQ(ierr); 1262 ierr = VecGetSize(Qexactloc, &lnodes); CHKERRQ(ierr); 1263 1264 ierr = ICs_FixMultiplicity(op_ics, xcorners, q0ceed, dm, Qexactloc, Qexact, 1265 restrictq, &ctxSetup, ftime); CHKERRQ(ierr); 1266 1267 ierr = VecAXPY(Q, -1.0, Qexact); CHKERRQ(ierr); 1268 ierr = VecNorm(Q, NORM_MAX, &norm); CHKERRQ(ierr); 1269 CeedVectorDestroy(&q0ceed); 1270 ierr = PetscPrintf(PETSC_COMM_WORLD, 1271 "Max Error: %g\n", 1272 (double)norm); CHKERRQ(ierr); 1273 // Clean up vectors 1274 ierr = DMRestoreLocalVector(dm, &Qexactloc); CHKERRQ(ierr); 1275 ierr = VecDestroy(&Qexact); CHKERRQ(ierr); 1276 } 1277 1278 // Output Statistics 1279 ierr = TSGetStepNumber(ts,&steps); CHKERRQ(ierr); 1280 if (!test) { 1281 ierr = PetscPrintf(PETSC_COMM_WORLD, 1282 "Time integrator took %D time steps to reach final time %g\n", 1283 steps, (double)ftime); CHKERRQ(ierr); 1284 } 1285 1286 // Clean up libCEED 1287 CeedVectorDestroy(&qdata); 1288 CeedVectorDestroy(&user->qceed); 1289 CeedVectorDestroy(&user->qdotceed); 1290 CeedVectorDestroy(&user->gceed); 1291 CeedVectorDestroy(&xcorners); 1292 CeedBasisDestroy(&basisq); 1293 CeedBasisDestroy(&basisx); 1294 CeedBasisDestroy(&basisxc); 1295 CeedElemRestrictionDestroy(&restrictq); 1296 CeedElemRestrictionDestroy(&restrictx); 1297 CeedElemRestrictionDestroy(&restrictqdi); 1298 CeedElemRestrictionDestroy(&restrictxcoord); 1299 CeedQFunctionDestroy(&qf_setup); 1300 CeedQFunctionDestroy(&qf_ics); 1301 CeedQFunctionDestroy(&qf_rhs); 1302 CeedQFunctionDestroy(&qf_ifunction); 1303 CeedOperatorDestroy(&op_setup); 1304 CeedOperatorDestroy(&op_ics); 1305 CeedOperatorDestroy(&user->op_rhs); 1306 CeedOperatorDestroy(&user->op_ifunction); 1307 CeedDestroy(&ceed); 1308 1309 // Clean up PETSc 1310 ierr = VecDestroy(&Q); CHKERRQ(ierr); 1311 ierr = VecDestroy(&user->M); CHKERRQ(ierr); 1312 ierr = MatDestroy(&interpviz); CHKERRQ(ierr); 1313 ierr = DMDestroy(&dmviz); CHKERRQ(ierr); 1314 ierr = TSDestroy(&ts); CHKERRQ(ierr); 1315 ierr = DMDestroy(&dm); CHKERRQ(ierr); 1316 ierr = PetscFree(units); CHKERRQ(ierr); 1317 ierr = PetscFree(user); CHKERRQ(ierr); 1318 return PetscFinalize(); 1319 } 1320 1321