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[6], slips[3][6]; 170 PetscBool userbc; 171 }; 172 173 // Essential BC dofs are encoded in closure indices as -(i+1). 174 static PetscInt Involute(PetscInt i) { 175 return i >= 0 ? i : -(i+1); 176 } 177 178 // Utility function to create local CEED restriction 179 static PetscErrorCode CreateRestrictionFromPlex(Ceed ceed, DM dm, CeedInt P, 180 CeedElemRestriction *Erestrict) { 181 182 PetscSection section; 183 PetscInt c, cStart, cEnd, Nelem, Ndof, *erestrict, eoffset, nfields, dim; 184 PetscErrorCode ierr; 185 Vec Uloc; 186 187 PetscFunctionBeginUser; 188 ierr = DMGetDimension(dm, &dim); CHKERRQ(ierr); 189 ierr = DMGetLocalSection(dm,§ion); CHKERRQ(ierr); 190 ierr = PetscSectionGetNumFields(section, &nfields); CHKERRQ(ierr); 191 PetscInt ncomp[nfields], fieldoff[nfields+1]; 192 fieldoff[0] = 0; 193 for (PetscInt f=0; f<nfields; f++) { 194 ierr = PetscSectionGetFieldComponents(section, f, &ncomp[f]); CHKERRQ(ierr); 195 fieldoff[f+1] = fieldoff[f] + ncomp[f]; 196 } 197 198 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd); CHKERRQ(ierr); 199 Nelem = cEnd - cStart; 200 ierr = PetscMalloc1(Nelem*PetscPowInt(P, dim), &erestrict); CHKERRQ(ierr); 201 for (c=cStart,eoffset=0; c<cEnd; c++) { 202 PetscInt numindices, *indices, nnodes; 203 ierr = DMPlexGetClosureIndices(dm, section, section, c, &numindices, 204 &indices, NULL); CHKERRQ(ierr); 205 if (numindices % fieldoff[nfields]) SETERRQ1(PETSC_COMM_SELF, 206 PETSC_ERR_ARG_INCOMP, "Number of closure indices not compatible with Cell %D", 207 c); 208 nnodes = numindices / fieldoff[nfields]; 209 for (PetscInt i=0; i<nnodes; i++) { 210 // Check that indices are blocked by node and thus can be coalesced as a single field with 211 // fieldoff[nfields] = sum(ncomp) components. 212 for (PetscInt f=0; f<nfields; f++) { 213 for (PetscInt j=0; j<ncomp[f]; j++) { 214 if (Involute(indices[fieldoff[f]*nnodes + i*ncomp[f] + j]) 215 != Involute(indices[i*ncomp[0]]) + fieldoff[f] + j) 216 SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP, 217 "Cell %D closure indices not interlaced for node %D field %D component %D", 218 c, i, f, j); 219 } 220 } 221 // Essential boundary conditions are encoded as -(loc+1), but we don't care so we decode. 222 PetscInt loc = Involute(indices[i*ncomp[0]]); 223 erestrict[eoffset++] = loc / fieldoff[nfields]; 224 } 225 ierr = DMPlexRestoreClosureIndices(dm, section, section, c, &numindices, 226 &indices, NULL); CHKERRQ(ierr); 227 } 228 if (eoffset != Nelem*PetscPowInt(P, dim)) SETERRQ3(PETSC_COMM_SELF, 229 PETSC_ERR_LIB, "ElemRestriction of size (%D,%D) initialized %D nodes", Nelem, 230 PetscPowInt(P, dim),eoffset); 231 ierr = DMGetLocalVector(dm, &Uloc); CHKERRQ(ierr); 232 ierr = VecGetLocalSize(Uloc, &Ndof); CHKERRQ(ierr); 233 ierr = DMRestoreLocalVector(dm, &Uloc); CHKERRQ(ierr); 234 CeedElemRestrictionCreate(ceed, CEED_INTERLACED, Nelem, PetscPowInt(P, dim), 235 Ndof/fieldoff[nfields], fieldoff[nfields], 236 CEED_MEM_HOST, CEED_COPY_VALUES, erestrict, Erestrict); 237 ierr = PetscFree(erestrict); CHKERRQ(ierr); 238 PetscFunctionReturn(0); 239 } 240 241 static int CreateVectorFromPetscVec(Ceed ceed, Vec p, CeedVector *v) { 242 PetscErrorCode ierr; 243 PetscInt m; 244 245 PetscFunctionBeginUser; 246 ierr = VecGetLocalSize(p, &m); CHKERRQ(ierr); 247 ierr = CeedVectorCreate(ceed, m, v); CHKERRQ(ierr); 248 PetscFunctionReturn(0); 249 } 250 251 static int VectorPlacePetscVec(CeedVector c, Vec p) { 252 PetscErrorCode ierr; 253 PetscInt mceed,mpetsc; 254 PetscScalar *a; 255 256 PetscFunctionBeginUser; 257 ierr = CeedVectorGetLength(c, &mceed); CHKERRQ(ierr); 258 ierr = VecGetLocalSize(p, &mpetsc); CHKERRQ(ierr); 259 if (mceed != mpetsc) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP, 260 "Cannot place PETSc Vec of length %D in CeedVector of length %D", 261 mpetsc, mceed); 262 ierr = VecGetArray(p, &a); CHKERRQ(ierr); 263 CeedVectorSetArray(c, CEED_MEM_HOST, CEED_USE_POINTER, a); 264 PetscFunctionReturn(0); 265 } 266 267 static PetscErrorCode DMPlexInsertBoundaryValues_NS(DM dm, 268 PetscBool insertEssential, Vec Qloc, PetscReal time, Vec faceGeomFVM, 269 Vec cellGeomFVM, Vec gradFVM) { 270 PetscErrorCode ierr; 271 Vec Qbc; 272 273 PetscFunctionBegin; 274 ierr = DMGetNamedLocalVector(dm, "Qbc", &Qbc); CHKERRQ(ierr); 275 ierr = VecAXPY(Qloc, 1., Qbc); CHKERRQ(ierr); 276 ierr = DMRestoreNamedLocalVector(dm, "Qbc", &Qbc); CHKERRQ(ierr); 277 PetscFunctionReturn(0); 278 } 279 280 // This is the RHS of the ODE, given as u_t = G(t,u) 281 // This function takes in a state vector Q and writes into G 282 static PetscErrorCode RHS_NS(TS ts, PetscReal t, Vec Q, Vec G, void *userData) { 283 PetscErrorCode ierr; 284 User user = *(User *)userData; 285 PetscScalar *q, *g; 286 Vec Qloc, Gloc; 287 288 // Global-to-local 289 PetscFunctionBeginUser; 290 ierr = DMGetLocalVector(user->dm, &Qloc); CHKERRQ(ierr); 291 ierr = DMGetLocalVector(user->dm, &Gloc); CHKERRQ(ierr); 292 ierr = VecZeroEntries(Qloc); CHKERRQ(ierr); 293 ierr = DMGlobalToLocal(user->dm, Q, INSERT_VALUES, Qloc); CHKERRQ(ierr); 294 ierr = DMPlexInsertBoundaryValues(user->dm, PETSC_TRUE, Qloc, 0.0, 295 NULL, NULL, NULL); CHKERRQ(ierr); 296 ierr = VecZeroEntries(Gloc); CHKERRQ(ierr); 297 298 // Ceed Vectors 299 ierr = VecGetArrayRead(Qloc, (const PetscScalar **)&q); CHKERRQ(ierr); 300 ierr = VecGetArray(Gloc, &g); CHKERRQ(ierr); 301 CeedVectorSetArray(user->qceed, CEED_MEM_HOST, CEED_USE_POINTER, q); 302 CeedVectorSetArray(user->gceed, CEED_MEM_HOST, CEED_USE_POINTER, g); 303 304 // Apply CEED operator 305 CeedOperatorApply(user->op_rhs, user->qceed, user->gceed, 306 CEED_REQUEST_IMMEDIATE); 307 308 // Restore vectors 309 ierr = VecRestoreArrayRead(Qloc, (const PetscScalar **)&q); CHKERRQ(ierr); 310 ierr = VecRestoreArray(Gloc, &g); CHKERRQ(ierr); 311 312 ierr = VecZeroEntries(G); CHKERRQ(ierr); 313 ierr = DMLocalToGlobal(user->dm, Gloc, ADD_VALUES, G); CHKERRQ(ierr); 314 315 // Inverse of the lumped mass matrix 316 ierr = VecPointwiseMult(G, G, user->M); // M is Minv 317 CHKERRQ(ierr); 318 319 ierr = DMRestoreLocalVector(user->dm, &Qloc); CHKERRQ(ierr); 320 ierr = DMRestoreLocalVector(user->dm, &Gloc); CHKERRQ(ierr); 321 PetscFunctionReturn(0); 322 } 323 324 static PetscErrorCode IFunction_NS(TS ts, PetscReal t, Vec Q, Vec Qdot, Vec G, 325 void *userData) { 326 PetscErrorCode ierr; 327 User user = *(User *)userData; 328 const PetscScalar *q, *qdot; 329 PetscScalar *g; 330 Vec Qloc, Qdotloc, Gloc; 331 332 // Global-to-local 333 PetscFunctionBeginUser; 334 ierr = DMGetLocalVector(user->dm, &Qloc); CHKERRQ(ierr); 335 ierr = DMGetLocalVector(user->dm, &Qdotloc); CHKERRQ(ierr); 336 ierr = DMGetLocalVector(user->dm, &Gloc); CHKERRQ(ierr); 337 ierr = VecZeroEntries(Qloc); CHKERRQ(ierr); 338 ierr = DMGlobalToLocal(user->dm, Q, INSERT_VALUES, Qloc); CHKERRQ(ierr); 339 ierr = DMPlexInsertBoundaryValues(user->dm, PETSC_TRUE, Qloc, 0.0, 340 NULL, NULL, NULL); CHKERRQ(ierr); 341 ierr = VecZeroEntries(Qdotloc); CHKERRQ(ierr); 342 ierr = DMGlobalToLocal(user->dm, Qdot, INSERT_VALUES, Qdotloc); CHKERRQ(ierr); 343 ierr = VecZeroEntries(Gloc); CHKERRQ(ierr); 344 345 // Ceed Vectors 346 ierr = VecGetArrayRead(Qloc, &q); CHKERRQ(ierr); 347 ierr = VecGetArrayRead(Qdotloc, &qdot); CHKERRQ(ierr); 348 ierr = VecGetArray(Gloc, &g); CHKERRQ(ierr); 349 CeedVectorSetArray(user->qceed, CEED_MEM_HOST, CEED_USE_POINTER, 350 (PetscScalar *)q); 351 CeedVectorSetArray(user->qdotceed, CEED_MEM_HOST, CEED_USE_POINTER, 352 (PetscScalar *)qdot); 353 CeedVectorSetArray(user->gceed, CEED_MEM_HOST, CEED_USE_POINTER, g); 354 355 // Apply CEED operator 356 CeedOperatorApply(user->op_ifunction, user->qceed, user->gceed, 357 CEED_REQUEST_IMMEDIATE); 358 359 // Restore vectors 360 ierr = VecRestoreArrayRead(Qloc, &q); CHKERRQ(ierr); 361 ierr = VecRestoreArrayRead(Qdotloc, &qdot); CHKERRQ(ierr); 362 ierr = VecRestoreArray(Gloc, &g); CHKERRQ(ierr); 363 364 ierr = VecZeroEntries(G); CHKERRQ(ierr); 365 ierr = DMLocalToGlobal(user->dm, Gloc, ADD_VALUES, G); CHKERRQ(ierr); 366 367 ierr = DMRestoreLocalVector(user->dm, &Qloc); CHKERRQ(ierr); 368 ierr = DMRestoreLocalVector(user->dm, &Qdotloc); CHKERRQ(ierr); 369 ierr = DMRestoreLocalVector(user->dm, &Gloc); CHKERRQ(ierr); 370 PetscFunctionReturn(0); 371 } 372 373 // User provided TS Monitor 374 static PetscErrorCode TSMonitor_NS(TS ts, PetscInt stepno, PetscReal time, 375 Vec Q, void *ctx) { 376 User user = ctx; 377 Vec Qloc; 378 char filepath[PETSC_MAX_PATH_LEN]; 379 PetscViewer viewer; 380 PetscErrorCode ierr; 381 382 // Set up output 383 PetscFunctionBeginUser; 384 // Print every 'outputfreq' steps 385 if (stepno % user->outputfreq != 0) 386 PetscFunctionReturn(0); 387 ierr = DMGetLocalVector(user->dm, &Qloc); CHKERRQ(ierr); 388 ierr = PetscObjectSetName((PetscObject)Qloc, "StateVec"); CHKERRQ(ierr); 389 ierr = VecZeroEntries(Qloc); CHKERRQ(ierr); 390 ierr = DMGlobalToLocal(user->dm, Q, INSERT_VALUES, Qloc); CHKERRQ(ierr); 391 392 // Output 393 ierr = PetscSNPrintf(filepath, sizeof filepath, "%s/ns-%03D.vtu", 394 user->outputfolder, stepno + user->contsteps); 395 CHKERRQ(ierr); 396 ierr = PetscViewerVTKOpen(PetscObjectComm((PetscObject)Q), filepath, 397 FILE_MODE_WRITE, &viewer); CHKERRQ(ierr); 398 ierr = VecView(Qloc, viewer); CHKERRQ(ierr); 399 if (user->dmviz) { 400 Vec Qrefined, Qrefined_loc; 401 char filepath_refined[PETSC_MAX_PATH_LEN]; 402 PetscViewer viewer_refined; 403 404 ierr = DMGetGlobalVector(user->dmviz, &Qrefined); CHKERRQ(ierr); 405 ierr = DMGetLocalVector(user->dmviz, &Qrefined_loc); CHKERRQ(ierr); 406 ierr = PetscObjectSetName((PetscObject)Qrefined_loc, "Refined"); 407 CHKERRQ(ierr); 408 ierr = MatInterpolate(user->interpviz, Q, Qrefined); CHKERRQ(ierr); 409 ierr = VecZeroEntries(Qrefined_loc); CHKERRQ(ierr); 410 ierr = DMGlobalToLocal(user->dmviz, Qrefined, INSERT_VALUES, Qrefined_loc); 411 CHKERRQ(ierr); 412 ierr = PetscSNPrintf(filepath_refined, sizeof filepath_refined, 413 "%s/nsrefined-%03D.vtu", 414 user->outputfolder, stepno + user->contsteps); 415 CHKERRQ(ierr); 416 ierr = PetscViewerVTKOpen(PetscObjectComm((PetscObject)Qrefined), 417 filepath_refined, 418 FILE_MODE_WRITE, &viewer_refined); CHKERRQ(ierr); 419 ierr = VecView(Qrefined_loc, viewer_refined); CHKERRQ(ierr); 420 ierr = DMRestoreLocalVector(user->dmviz, &Qrefined_loc); CHKERRQ(ierr); 421 ierr = DMRestoreGlobalVector(user->dmviz, &Qrefined); CHKERRQ(ierr); 422 ierr = PetscViewerDestroy(&viewer_refined); CHKERRQ(ierr); 423 } 424 ierr = PetscViewerDestroy(&viewer); CHKERRQ(ierr); 425 ierr = DMRestoreLocalVector(user->dm, &Qloc); CHKERRQ(ierr); 426 427 // Save data in a binary file for continuation of simulations 428 ierr = PetscSNPrintf(filepath, sizeof filepath, "%s/ns-solution.bin", 429 user->outputfolder); CHKERRQ(ierr); 430 ierr = PetscViewerBinaryOpen(user->comm, filepath, FILE_MODE_WRITE, &viewer); 431 CHKERRQ(ierr); 432 ierr = VecView(Q, viewer); CHKERRQ(ierr); 433 ierr = PetscViewerDestroy(&viewer); CHKERRQ(ierr); 434 435 // Save time stamp 436 // Dimensionalize time back 437 time /= user->units->second; 438 ierr = PetscSNPrintf(filepath, sizeof filepath, "%s/ns-time.bin", 439 user->outputfolder); CHKERRQ(ierr); 440 ierr = PetscViewerBinaryOpen(user->comm, filepath, FILE_MODE_WRITE, &viewer); 441 CHKERRQ(ierr); 442 #if PETSC_VERSION_GE(3,13,0) 443 ierr = PetscViewerBinaryWrite(viewer, &time, 1, PETSC_REAL); 444 #else 445 ierr = PetscViewerBinaryWrite(viewer, &time, 1, PETSC_REAL, true); 446 #endif 447 CHKERRQ(ierr); 448 ierr = PetscViewerDestroy(&viewer); CHKERRQ(ierr); 449 450 PetscFunctionReturn(0); 451 } 452 453 static PetscErrorCode ICs_FixMultiplicity(CeedOperator op_ics, 454 CeedVector xcorners, CeedVector q0ceed, DM dm, Vec Qloc, Vec Q, 455 CeedElemRestriction restrictq, SetupContext ctxSetup, CeedScalar time) { 456 PetscErrorCode ierr; 457 CeedVector multlvec; 458 Vec Multiplicity, MultiplicityLoc; 459 460 ctxSetup->time = time; 461 ierr = VecZeroEntries(Qloc); CHKERRQ(ierr); 462 ierr = VectorPlacePetscVec(q0ceed, Qloc); CHKERRQ(ierr); 463 CeedOperatorApply(op_ics, xcorners, q0ceed, CEED_REQUEST_IMMEDIATE); 464 ierr = VecZeroEntries(Q); CHKERRQ(ierr); 465 ierr = DMLocalToGlobal(dm, Qloc, ADD_VALUES, Q); CHKERRQ(ierr); 466 467 // Fix multiplicity for output of ICs 468 ierr = DMGetLocalVector(dm, &MultiplicityLoc); CHKERRQ(ierr); 469 CeedElemRestrictionCreateVector(restrictq, &multlvec, NULL); 470 ierr = VectorPlacePetscVec(multlvec, MultiplicityLoc); CHKERRQ(ierr); 471 CeedElemRestrictionGetMultiplicity(restrictq, multlvec); 472 CeedVectorDestroy(&multlvec); 473 ierr = DMGetGlobalVector(dm, &Multiplicity); CHKERRQ(ierr); 474 ierr = VecZeroEntries(Multiplicity); CHKERRQ(ierr); 475 ierr = DMLocalToGlobal(dm, MultiplicityLoc, ADD_VALUES, Multiplicity); 476 CHKERRQ(ierr); 477 ierr = VecPointwiseDivide(Q, Q, Multiplicity); CHKERRQ(ierr); 478 ierr = VecPointwiseDivide(Qloc, Qloc, MultiplicityLoc); CHKERRQ(ierr); 479 ierr = DMRestoreLocalVector(dm, &MultiplicityLoc); CHKERRQ(ierr); 480 ierr = DMRestoreGlobalVector(dm, &Multiplicity); CHKERRQ(ierr); 481 482 PetscFunctionReturn(0); 483 } 484 485 static PetscErrorCode ComputeLumpedMassMatrix(Ceed ceed, DM dm, 486 CeedElemRestriction restrictq, CeedBasis basisq, 487 CeedElemRestriction restrictqdi, CeedVector qdata, Vec M) { 488 PetscErrorCode ierr; 489 CeedQFunction qf_mass; 490 CeedOperator op_mass; 491 CeedVector mceed; 492 Vec Mloc; 493 CeedInt ncompq, qdatasize; 494 495 PetscFunctionBeginUser; 496 CeedElemRestrictionGetNumComponents(restrictq, &ncompq); 497 CeedElemRestrictionGetNumComponents(restrictqdi, &qdatasize); 498 // Create the Q-function that defines the action of the mass operator 499 CeedQFunctionCreateInterior(ceed, 1, Mass, Mass_loc, &qf_mass); 500 CeedQFunctionAddInput(qf_mass, "q", ncompq, CEED_EVAL_INTERP); 501 CeedQFunctionAddInput(qf_mass, "qdata", qdatasize, CEED_EVAL_NONE); 502 CeedQFunctionAddOutput(qf_mass, "v", ncompq, CEED_EVAL_INTERP); 503 504 // Create the mass operator 505 CeedOperatorCreate(ceed, qf_mass, NULL, NULL, &op_mass); 506 CeedOperatorSetField(op_mass, "q", restrictq, basisq, CEED_VECTOR_ACTIVE); 507 CeedOperatorSetField(op_mass, "qdata", restrictqdi, 508 CEED_BASIS_COLLOCATED, qdata); 509 CeedOperatorSetField(op_mass, "v", restrictq, basisq, CEED_VECTOR_ACTIVE); 510 511 ierr = DMGetLocalVector(dm, &Mloc); CHKERRQ(ierr); 512 ierr = VecZeroEntries(Mloc); CHKERRQ(ierr); 513 CeedElemRestrictionCreateVector(restrictq, &mceed, NULL); 514 ierr = VectorPlacePetscVec(mceed, Mloc); CHKERRQ(ierr); 515 516 { 517 // Compute a lumped mass matrix 518 CeedVector onesvec; 519 CeedElemRestrictionCreateVector(restrictq, &onesvec, NULL); 520 CeedVectorSetValue(onesvec, 1.0); 521 CeedOperatorApply(op_mass, onesvec, mceed, CEED_REQUEST_IMMEDIATE); 522 CeedVectorDestroy(&onesvec); 523 CeedOperatorDestroy(&op_mass); 524 CeedVectorDestroy(&mceed); 525 } 526 CeedQFunctionDestroy(&qf_mass); 527 528 ierr = VecZeroEntries(M); CHKERRQ(ierr); 529 ierr = DMLocalToGlobal(dm, Mloc, ADD_VALUES, M); CHKERRQ(ierr); 530 ierr = DMRestoreLocalVector(dm, &Mloc); CHKERRQ(ierr); 531 532 // Invert diagonally lumped mass vector for RHS function 533 ierr = VecReciprocal(M); CHKERRQ(ierr); 534 PetscFunctionReturn(0); 535 } 536 537 static PetscErrorCode SetUpDM(DM dm, problemData *problem, PetscInt degree, 538 SimpleBC bc, void *ctxSetup) { 539 PetscErrorCode ierr; 540 541 PetscFunctionBeginUser; 542 { 543 // Configure the finite element space and boundary conditions 544 PetscFE fe; 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 { 553 PetscInt comps[1] = {1}; 554 ierr = DMAddBoundary(dm, DM_BC_ESSENTIAL, "slipx", "Face Sets", 0, 555 1, comps, (void(*)(void))NULL, bc->nslip[0], 556 bc->slips[0], ctxSetup); CHKERRQ(ierr); 557 comps[0] = 2; 558 ierr = DMAddBoundary(dm, DM_BC_ESSENTIAL, "slipy", "Face Sets", 0, 559 1, comps, (void(*)(void))NULL, bc->nslip[1], 560 bc->slips[1], ctxSetup); CHKERRQ(ierr); 561 comps[0] = 3; 562 ierr = DMAddBoundary(dm, DM_BC_ESSENTIAL, "slipz", "Face Sets", 0, 563 1, comps, (void(*)(void))NULL, bc->nslip[2], 564 bc->slips[2], ctxSetup); CHKERRQ(ierr); 565 } 566 if (bc->userbc == PETSC_TRUE) { 567 for (PetscInt c = 0; c < 3; c++) { 568 for (PetscInt s = 0; s < bc->nslip[c]; s++) { 569 for (PetscInt w = 0; w < bc->nwall; w++) { 570 if (bc->slips[c][s] == bc->walls[w]) 571 SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, 572 "Boundary condition already set on face %D!\n", bc->walls[w]); 573 574 } 575 } 576 } 577 } 578 // Wall boundary conditions are zero energy density and zero flux for 579 // velocity in advection/advection2d, and zero velocity and zero flux 580 // for mass density and energy density in density_current 581 { 582 if (problem->bc == Exact_Advection || problem->bc == Exact_Advection2d) { 583 PetscInt comps[1] = {4}; 584 ierr = DMAddBoundary(dm, DM_BC_ESSENTIAL, "wall", "Face Sets", 0, 585 1, comps, (void(*)(void))problem->bc, 586 bc->nwall, bc->walls, ctxSetup); CHKERRQ(ierr); 587 } else if (problem->bc == Exact_DC) { 588 PetscInt comps[3] = {1, 2, 3}; 589 ierr = DMAddBoundary(dm, DM_BC_ESSENTIAL, "wall", "Face Sets", 0, 590 3, comps, (void(*)(void))problem->bc, 591 bc->nwall, bc->walls, ctxSetup); CHKERRQ(ierr); 592 } else 593 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_NULL, 594 "Undefined boundary conditions for this problem"); 595 } 596 ierr = DMPlexSetClosurePermutationTensor(dm, PETSC_DETERMINE, NULL); 597 CHKERRQ(ierr); 598 ierr = PetscFEDestroy(&fe); CHKERRQ(ierr); 599 } 600 { 601 // Empty name for conserved field (because there is only one field) 602 PetscSection section; 603 ierr = DMGetLocalSection(dm, §ion); CHKERRQ(ierr); 604 ierr = PetscSectionSetFieldName(section, 0, ""); CHKERRQ(ierr); 605 ierr = PetscSectionSetComponentName(section, 0, 0, "Density"); 606 CHKERRQ(ierr); 607 ierr = PetscSectionSetComponentName(section, 0, 1, "MomentumX"); 608 CHKERRQ(ierr); 609 ierr = PetscSectionSetComponentName(section, 0, 2, "MomentumY"); 610 CHKERRQ(ierr); 611 ierr = PetscSectionSetComponentName(section, 0, 3, "MomentumZ"); 612 CHKERRQ(ierr); 613 ierr = PetscSectionSetComponentName(section, 0, 4, "EnergyDensity"); 614 CHKERRQ(ierr); 615 } 616 PetscFunctionReturn(0); 617 } 618 619 int main(int argc, char **argv) { 620 PetscInt ierr; 621 MPI_Comm comm; 622 DM dm, dmcoord, dmviz; 623 Mat interpviz; 624 TS ts; 625 TSAdapt adapt; 626 User user; 627 Units units; 628 char ceedresource[4096] = "/cpu/self"; 629 PetscInt cStart, cEnd, localNelem, lnodes, steps; 630 const PetscInt ncompq = 5; 631 PetscMPIInt rank; 632 PetscScalar ftime; 633 Vec Q, Qloc, Xloc; 634 Ceed ceed; 635 CeedInt numP, numQ; 636 CeedVector xcorners, qdata, q0ceed; 637 CeedBasis basisx, basisxc, basisq; 638 CeedElemRestriction restrictx, restrictxcoord, restrictq, restrictqdi; 639 CeedQFunction qf_setup, qf_ics, qf_rhs, qf_ifunction; 640 CeedOperator op_setup, op_ics; 641 CeedScalar Rd; 642 PetscScalar WpermK, Pascal, JperkgK, mpersquareds, kgpercubicm, 643 kgpersquaredms, Joulepercubicm; 644 problemType problemChoice; 645 problemData *problem = NULL; 646 StabilizationType stab; 647 PetscBool test, implicit; 648 PetscInt viz_refine = 0; 649 struct SimpleBC_ bc = { 650 .nslip = {2, 2, 2}, 651 .slips = {{5, 6}, {3, 4}, {1, 2}} 652 }; 653 double start, cpu_time_used; 654 655 // Create the libCEED contexts 656 PetscScalar meter = 1e-2; // 1 meter in scaled length units 657 PetscScalar second = 1e-2; // 1 second in scaled time units 658 PetscScalar kilogram = 1e-6; // 1 kilogram in scaled mass units 659 PetscScalar Kelvin = 1; // 1 Kelvin in scaled temperature units 660 CeedScalar theta0 = 300.; // K 661 CeedScalar thetaC = -15.; // K 662 CeedScalar P0 = 1.e5; // Pa 663 CeedScalar N = 0.01; // 1/s 664 CeedScalar cv = 717.; // J/(kg K) 665 CeedScalar cp = 1004.; // J/(kg K) 666 CeedScalar g = 9.81; // m/s^2 667 CeedScalar lambda = -2./3.; // - 668 CeedScalar mu = 75.; // Pa s, dynamic viscosity 669 // mu = 75 is not physical for air, but is good for numerical stability 670 CeedScalar k = 0.02638; // W/(m K) 671 CeedScalar CtauS = 0.; // dimensionless 672 CeedScalar strong_form = 0.; // [0,1] 673 PetscScalar lx = 8000.; // m 674 PetscScalar ly = 8000.; // m 675 PetscScalar lz = 4000.; // m 676 CeedScalar rc = 1000.; // m (Radius of bubble) 677 PetscScalar resx = 1000.; // m (resolution in x) 678 PetscScalar resy = 1000.; // m (resolution in y) 679 PetscScalar resz = 1000.; // m (resolution in z) 680 PetscInt outputfreq = 10; // - 681 PetscInt contsteps = 0; // - 682 PetscInt degree = 1; // - 683 PetscInt qextra = 2; // - 684 PetscReal center[3], dc_axis[3] = {0, 0, 0}; 685 686 ierr = PetscInitialize(&argc, &argv, NULL, help); 687 if (ierr) return ierr; 688 689 // Allocate PETSc context 690 ierr = PetscCalloc1(1, &user); CHKERRQ(ierr); 691 ierr = PetscMalloc1(1, &units); CHKERRQ(ierr); 692 693 // Parse command line options 694 comm = PETSC_COMM_WORLD; 695 ierr = PetscOptionsBegin(comm, NULL, "Navier-Stokes in PETSc with libCEED", 696 NULL); CHKERRQ(ierr); 697 ierr = PetscOptionsString("-ceed", "CEED resource specifier", 698 NULL, ceedresource, ceedresource, 699 sizeof(ceedresource), NULL); CHKERRQ(ierr); 700 ierr = PetscOptionsBool("-test", "Run in test mode", 701 NULL, test=PETSC_FALSE, &test, NULL); CHKERRQ(ierr); 702 problemChoice = NS_DENSITY_CURRENT; 703 ierr = PetscOptionsEnum("-problem", "Problem to solve", NULL, 704 problemTypes, (PetscEnum)problemChoice, 705 (PetscEnum *)&problemChoice, NULL); CHKERRQ(ierr); 706 problem = &problemOptions[problemChoice]; 707 ierr = PetscOptionsEnum("-stab", "Stabilization method", NULL, 708 StabilizationTypes, (PetscEnum)(stab = STAB_NONE), 709 (PetscEnum *)&stab, NULL); CHKERRQ(ierr); 710 ierr = PetscOptionsBool("-implicit", "Use implicit (IFunction) formulation", 711 NULL, implicit=PETSC_FALSE, &implicit, NULL); 712 CHKERRQ(ierr); 713 if (!implicit && stab != STAB_NONE) { 714 ierr = PetscPrintf(comm, "Warning! Use -stab only with -implicit\n"); 715 CHKERRQ(ierr); 716 } 717 { 718 PetscInt len; 719 PetscBool flg; 720 ierr = PetscOptionsIntArray("-bc_wall", 721 "Use wall boundary conditions on this list of faces", 722 NULL, bc.walls, 723 (len = sizeof(bc.walls) / sizeof(bc.walls[0]), 724 &len), &flg); CHKERRQ(ierr); 725 if (flg) bc.nwall = len; 726 for (PetscInt j=0; j<3; j++) { 727 const char *flags[3] = {"-bc_slip_x", "-bc_slip_y", "-bc_slip_z"}; 728 ierr = PetscOptionsIntArray(flags[j], 729 "Use slip boundary conditions on this list of faces", 730 NULL, bc.slips[j], 731 (len = sizeof(bc.slips[j]) / sizeof(bc.slips[j][0]), 732 &len), &flg); 733 CHKERRQ(ierr); 734 if (flg) { 735 bc.nslip[j] = len; 736 bc.userbc = PETSC_TRUE; 737 } 738 } 739 } 740 ierr = PetscOptionsInt("-viz_refine", 741 "Regular refinement levels for visualization", 742 NULL, viz_refine, &viz_refine, NULL); 743 CHKERRQ(ierr); 744 ierr = PetscOptionsScalar("-units_meter", "1 meter in scaled length units", 745 NULL, meter, &meter, NULL); CHKERRQ(ierr); 746 meter = fabs(meter); 747 ierr = PetscOptionsScalar("-units_second","1 second in scaled time units", 748 NULL, second, &second, NULL); CHKERRQ(ierr); 749 second = fabs(second); 750 ierr = PetscOptionsScalar("-units_kilogram","1 kilogram in scaled mass units", 751 NULL, kilogram, &kilogram, NULL); CHKERRQ(ierr); 752 kilogram = fabs(kilogram); 753 ierr = PetscOptionsScalar("-units_Kelvin", 754 "1 Kelvin in scaled temperature units", 755 NULL, Kelvin, &Kelvin, NULL); CHKERRQ(ierr); 756 Kelvin = fabs(Kelvin); 757 ierr = PetscOptionsScalar("-theta0", "Reference potential temperature", 758 NULL, theta0, &theta0, NULL); CHKERRQ(ierr); 759 ierr = PetscOptionsScalar("-thetaC", "Perturbation of potential temperature", 760 NULL, thetaC, &thetaC, NULL); CHKERRQ(ierr); 761 ierr = PetscOptionsScalar("-P0", "Atmospheric pressure", 762 NULL, P0, &P0, NULL); CHKERRQ(ierr); 763 ierr = PetscOptionsScalar("-N", "Brunt-Vaisala frequency", 764 NULL, N, &N, NULL); CHKERRQ(ierr); 765 ierr = PetscOptionsScalar("-cv", "Heat capacity at constant volume", 766 NULL, cv, &cv, NULL); CHKERRQ(ierr); 767 ierr = PetscOptionsScalar("-cp", "Heat capacity at constant pressure", 768 NULL, cp, &cp, NULL); CHKERRQ(ierr); 769 ierr = PetscOptionsScalar("-g", "Gravitational acceleration", 770 NULL, g, &g, NULL); CHKERRQ(ierr); 771 ierr = PetscOptionsScalar("-lambda", 772 "Stokes hypothesis second viscosity coefficient", 773 NULL, lambda, &lambda, NULL); CHKERRQ(ierr); 774 ierr = PetscOptionsScalar("-mu", "Shear dynamic viscosity coefficient", 775 NULL, mu, &mu, NULL); CHKERRQ(ierr); 776 ierr = PetscOptionsScalar("-k", "Thermal conductivity", 777 NULL, k, &k, NULL); CHKERRQ(ierr); 778 ierr = PetscOptionsScalar("-CtauS", 779 "Scale coefficient for tau (nondimensional)", 780 NULL, CtauS, &CtauS, NULL); CHKERRQ(ierr); 781 if (stab == STAB_NONE && CtauS != 0) { 782 ierr = PetscPrintf(comm, 783 "Warning! Use -CtauS only with -stab su or -stab supg\n"); 784 CHKERRQ(ierr); 785 } 786 ierr = PetscOptionsScalar("-strong_form", 787 "Strong (1) or weak/integrated by parts (0) advection residual", 788 NULL, strong_form, &strong_form, NULL); 789 CHKERRQ(ierr); 790 ierr = PetscOptionsScalar("-lx", "Length scale in x direction", 791 NULL, lx, &lx, NULL); CHKERRQ(ierr); 792 ierr = PetscOptionsScalar("-ly", "Length scale in y direction", 793 NULL, ly, &ly, NULL); CHKERRQ(ierr); 794 ierr = PetscOptionsScalar("-lz", "Length scale in z direction", 795 NULL, lz, &lz, NULL); CHKERRQ(ierr); 796 ierr = PetscOptionsScalar("-rc", "Characteristic radius of thermal bubble", 797 NULL, rc, &rc, NULL); CHKERRQ(ierr); 798 ierr = PetscOptionsScalar("-resx","Target resolution in x", 799 NULL, resx, &resx, NULL); CHKERRQ(ierr); 800 ierr = PetscOptionsScalar("-resy","Target resolution in y", 801 NULL, resy, &resy, NULL); CHKERRQ(ierr); 802 ierr = PetscOptionsScalar("-resz","Target resolution in z", 803 NULL, resz, &resz, NULL); CHKERRQ(ierr); 804 PetscInt n = problem->dim; 805 center[0] = 0.5 * lx; 806 center[1] = 0.5 * ly; 807 center[2] = 0.5 * lz; 808 ierr = PetscOptionsRealArray("-center", "Location of bubble center", 809 NULL, center, &n, NULL); CHKERRQ(ierr); 810 n = problem->dim; 811 ierr = PetscOptionsRealArray("-dc_axis", 812 "Axis of density current cylindrical anomaly, or {0,0,0} for spherically symmetric", 813 NULL, dc_axis, &n, NULL); CHKERRQ(ierr); 814 { 815 PetscReal norm = PetscSqrtReal(PetscSqr(dc_axis[0]) + 816 PetscSqr(dc_axis[1]) + PetscSqr(dc_axis[2])); 817 if (norm > 0) { 818 for (int i=0; i<3; i++) dc_axis[i] /= norm; 819 } 820 } 821 ierr = PetscOptionsInt("-output_freq", 822 "Frequency of output, in number of steps", 823 NULL, outputfreq, &outputfreq, NULL); CHKERRQ(ierr); 824 ierr = PetscOptionsInt("-continue", "Continue from previous solution", 825 NULL, contsteps, &contsteps, NULL); CHKERRQ(ierr); 826 ierr = PetscOptionsInt("-degree", "Polynomial degree of finite elements", 827 NULL, degree, °ree, NULL); CHKERRQ(ierr); 828 ierr = PetscOptionsInt("-qextra", "Number of extra quadrature points", 829 NULL, qextra, &qextra, NULL); CHKERRQ(ierr); 830 PetscStrncpy(user->outputfolder, ".", 2); 831 ierr = PetscOptionsString("-of", "Output folder", 832 NULL, user->outputfolder, user->outputfolder, 833 sizeof(user->outputfolder), NULL); CHKERRQ(ierr); 834 ierr = PetscOptionsEnd(); CHKERRQ(ierr); 835 836 // Define derived units 837 Pascal = kilogram / (meter * PetscSqr(second)); 838 JperkgK = PetscSqr(meter) / (PetscSqr(second) * Kelvin); 839 mpersquareds = meter / PetscSqr(second); 840 WpermK = kilogram * meter / (pow(second,3) * Kelvin); 841 kgpercubicm = kilogram / pow(meter,3); 842 kgpersquaredms = kilogram / (PetscSqr(meter) * second); 843 Joulepercubicm = kilogram / (meter * PetscSqr(second)); 844 845 // Scale variables to desired units 846 theta0 *= Kelvin; 847 thetaC *= Kelvin; 848 P0 *= Pascal; 849 N *= (1./second); 850 cv *= JperkgK; 851 cp *= JperkgK; 852 Rd = cp - cv; 853 g *= mpersquareds; 854 mu *= Pascal * second; 855 k *= WpermK; 856 lx = fabs(lx) * meter; 857 ly = fabs(ly) * meter; 858 lz = fabs(lz) * meter; 859 rc = fabs(rc) * meter; 860 resx = fabs(resx) * meter; 861 resy = fabs(resy) * meter; 862 resz = fabs(resz) * meter; 863 for (int i=0; i<3; i++) center[i] *= meter; 864 865 const CeedInt dim = problem->dim, ncompx = problem->dim, 866 qdatasize = problem->qdatasize; 867 // Set up the libCEED context 868 struct SetupContext_ ctxSetup = { 869 .theta0 = theta0, 870 .thetaC = thetaC, 871 .P0 = P0, 872 .N = N, 873 .cv = cv, 874 .cp = cp, 875 .Rd = Rd, 876 .g = g, 877 .rc = rc, 878 .lx = lx, 879 .ly = ly, 880 .lz = lz, 881 .center[0] = center[0], 882 .center[1] = center[1], 883 .center[2] = center[2], 884 .dc_axis[0] = dc_axis[0], 885 .dc_axis[1] = dc_axis[1], 886 .dc_axis[2] = dc_axis[2], 887 .time = 0, 888 }; 889 890 // Create the mesh 891 { 892 const PetscReal scale[3] = {lx, ly, lz}; 893 ierr = DMPlexCreateBoxMesh(comm, dim, PETSC_FALSE, NULL, NULL, scale, 894 NULL, PETSC_TRUE, &dm); 895 CHKERRQ(ierr); 896 } 897 898 // Distribute the mesh over processes 899 { 900 DM dmDist = NULL; 901 PetscPartitioner part; 902 903 ierr = DMPlexGetPartitioner(dm, &part); CHKERRQ(ierr); 904 ierr = PetscPartitionerSetFromOptions(part); CHKERRQ(ierr); 905 ierr = DMPlexDistribute(dm, 0, NULL, &dmDist); CHKERRQ(ierr); 906 if (dmDist) { 907 ierr = DMDestroy(&dm); CHKERRQ(ierr); 908 dm = dmDist; 909 } 910 } 911 ierr = DMViewFromOptions(dm, NULL, "-dm_view"); CHKERRQ(ierr); 912 913 // Setup DM 914 ierr = DMLocalizeCoordinates(dm); CHKERRQ(ierr); 915 ierr = DMSetFromOptions(dm); CHKERRQ(ierr); 916 ierr = SetUpDM(dm, problem, degree, &bc, &ctxSetup); CHKERRQ(ierr); 917 918 // Print FEM space information 919 if (!test) { 920 ierr = PetscPrintf(PETSC_COMM_WORLD, 921 "Degree of FEM space: %D\n", 922 degree); CHKERRQ(ierr); 923 } 924 925 // Refine DM for high-order viz 926 dmviz = NULL; 927 interpviz = NULL; 928 if (viz_refine) { 929 DM dmhierarchy[viz_refine+1]; 930 931 ierr = DMPlexSetRefinementUniform(dm, PETSC_TRUE); CHKERRQ(ierr); 932 dmhierarchy[0] = dm; 933 for (PetscInt i = 0, d = degree; i < viz_refine; i++) { 934 Mat interp_next; 935 936 ierr = DMRefine(dmhierarchy[i], MPI_COMM_NULL, &dmhierarchy[i+1]); 937 CHKERRQ(ierr); 938 ierr = DMSetCoarseDM(dmhierarchy[i+1], dmhierarchy[i]); CHKERRQ(ierr); 939 d = (d + 1) / 2; 940 if (i + 1 == viz_refine) d = 1; 941 ierr = SetUpDM(dmhierarchy[i+1], problem, d, &bc, &ctxSetup); CHKERRQ(ierr); 942 ierr = DMCreateInterpolation(dmhierarchy[i], dmhierarchy[i+1], 943 &interp_next, NULL); CHKERRQ(ierr); 944 if (!i) interpviz = interp_next; 945 else { 946 Mat C; 947 ierr = MatMatMult(interp_next, interpviz, MAT_INITIAL_MATRIX, 948 PETSC_DECIDE, &C); CHKERRQ(ierr); 949 ierr = MatDestroy(&interp_next); CHKERRQ(ierr); 950 ierr = MatDestroy(&interpviz); CHKERRQ(ierr); 951 interpviz = C; 952 } 953 } 954 for (PetscInt i=1; i<viz_refine; i++) { 955 ierr = DMDestroy(&dmhierarchy[i]); CHKERRQ(ierr); 956 } 957 dmviz = dmhierarchy[viz_refine]; 958 } 959 ierr = DMCreateGlobalVector(dm, &Q); CHKERRQ(ierr); 960 ierr = DMGetLocalVector(dm, &Qloc); CHKERRQ(ierr); 961 ierr = VecGetSize(Qloc, &lnodes); CHKERRQ(ierr); 962 lnodes /= ncompq; 963 964 { 965 // Print grid information 966 CeedInt gdofs, odofs; 967 int comm_size; 968 char box_faces_str[PETSC_MAX_PATH_LEN] = "NONE"; 969 ierr = VecGetSize(Q, &gdofs); CHKERRQ(ierr); 970 ierr = VecGetLocalSize(Q, &odofs); CHKERRQ(ierr); 971 ierr = MPI_Comm_size(comm, &comm_size); CHKERRQ(ierr); 972 ierr = PetscOptionsGetString(NULL, NULL, "-dm_plex_box_faces", box_faces_str, 973 sizeof(box_faces_str), NULL); CHKERRQ(ierr); 974 if (!test) { 975 ierr = PetscPrintf(comm, "Global FEM dofs: %D (%D owned) on %d rank(s)\n", 976 gdofs, odofs, comm_size); CHKERRQ(ierr); 977 ierr = PetscPrintf(comm, "Local FEM nodes: %D\n", lnodes); CHKERRQ(ierr); 978 ierr = PetscPrintf(comm, "dm_plex_box_faces: %s\n", box_faces_str); 979 CHKERRQ(ierr); 980 } 981 982 } 983 984 // Set up global mass vector 985 ierr = VecDuplicate(Q, &user->M); CHKERRQ(ierr); 986 987 // Set up CEED 988 // CEED Bases 989 CeedInit(ceedresource, &ceed); 990 numP = degree + 1; 991 numQ = numP + qextra; 992 CeedBasisCreateTensorH1Lagrange(ceed, dim, ncompq, numP, numQ, CEED_GAUSS, 993 &basisq); 994 CeedBasisCreateTensorH1Lagrange(ceed, dim, ncompx, 2, numQ, CEED_GAUSS, 995 &basisx); 996 CeedBasisCreateTensorH1Lagrange(ceed, dim, ncompx, 2, numP, 997 CEED_GAUSS_LOBATTO, &basisxc); 998 999 ierr = DMGetCoordinateDM(dm, &dmcoord); CHKERRQ(ierr); 1000 ierr = DMPlexSetClosurePermutationTensor(dmcoord, PETSC_DETERMINE, NULL); 1001 CHKERRQ(ierr); 1002 1003 // CEED Restrictions 1004 ierr = CreateRestrictionFromPlex(ceed, dm, degree+1, &restrictq); 1005 CHKERRQ(ierr); 1006 ierr = CreateRestrictionFromPlex(ceed, dmcoord, 2, &restrictx); CHKERRQ(ierr); 1007 DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd); CHKERRQ(ierr); 1008 localNelem = cEnd - cStart; 1009 CeedInt numQdim = CeedIntPow(numQ, dim); 1010 CeedElemRestrictionCreateStrided(ceed, localNelem, numQdim, 1011 localNelem*numQdim, qdatasize, 1012 CEED_STRIDES_BACKEND, &restrictqdi); 1013 CeedElemRestrictionCreateStrided(ceed, localNelem, PetscPowInt(numP, dim), 1014 localNelem*PetscPowInt(numP, dim), ncompx, 1015 CEED_STRIDES_BACKEND, &restrictxcoord); 1016 1017 ierr = DMGetCoordinatesLocal(dm, &Xloc); CHKERRQ(ierr); 1018 ierr = CreateVectorFromPetscVec(ceed, Xloc, &xcorners); CHKERRQ(ierr); 1019 1020 // Create the CEED vectors that will be needed in setup 1021 CeedInt Nqpts; 1022 CeedBasisGetNumQuadraturePoints(basisq, &Nqpts); 1023 CeedVectorCreate(ceed, qdatasize*localNelem*Nqpts, &qdata); 1024 CeedElemRestrictionCreateVector(restrictq, &q0ceed, NULL); 1025 1026 // Create the Q-function that builds the quadrature data for the NS operator 1027 CeedQFunctionCreateInterior(ceed, 1, problem->setup, problem->setup_loc, 1028 &qf_setup); 1029 CeedQFunctionAddInput(qf_setup, "dx", ncompx*dim, CEED_EVAL_GRAD); 1030 CeedQFunctionAddInput(qf_setup, "weight", 1, CEED_EVAL_WEIGHT); 1031 CeedQFunctionAddOutput(qf_setup, "qdata", qdatasize, CEED_EVAL_NONE); 1032 1033 // Create the Q-function that sets the ICs of the operator 1034 CeedQFunctionCreateInterior(ceed, 1, problem->ics, problem->ics_loc, &qf_ics); 1035 CeedQFunctionAddInput(qf_ics, "x", ncompx, CEED_EVAL_INTERP); 1036 CeedQFunctionAddOutput(qf_ics, "q0", ncompq, CEED_EVAL_NONE); 1037 1038 qf_rhs = NULL; 1039 if (problem->apply_rhs) { // Create the Q-function that defines the action of the RHS operator 1040 CeedQFunctionCreateInterior(ceed, 1, problem->apply_rhs, 1041 problem->apply_rhs_loc, &qf_rhs); 1042 CeedQFunctionAddInput(qf_rhs, "q", ncompq, CEED_EVAL_INTERP); 1043 CeedQFunctionAddInput(qf_rhs, "dq", ncompq*dim, CEED_EVAL_GRAD); 1044 CeedQFunctionAddInput(qf_rhs, "qdata", qdatasize, CEED_EVAL_NONE); 1045 CeedQFunctionAddInput(qf_rhs, "x", ncompx, CEED_EVAL_INTERP); 1046 CeedQFunctionAddOutput(qf_rhs, "v", ncompq, CEED_EVAL_INTERP); 1047 CeedQFunctionAddOutput(qf_rhs, "dv", ncompq*dim, CEED_EVAL_GRAD); 1048 } 1049 1050 qf_ifunction = NULL; 1051 if (problem->apply_ifunction) { // Create the Q-function that defines the action of the IFunction 1052 CeedQFunctionCreateInterior(ceed, 1, problem->apply_ifunction, 1053 problem->apply_ifunction_loc, &qf_ifunction); 1054 CeedQFunctionAddInput(qf_ifunction, "q", ncompq, CEED_EVAL_INTERP); 1055 CeedQFunctionAddInput(qf_ifunction, "dq", ncompq*dim, CEED_EVAL_GRAD); 1056 CeedQFunctionAddInput(qf_ifunction, "qdot", ncompq, CEED_EVAL_INTERP); 1057 CeedQFunctionAddInput(qf_ifunction, "qdata", qdatasize, CEED_EVAL_NONE); 1058 CeedQFunctionAddInput(qf_ifunction, "x", ncompx, CEED_EVAL_INTERP); 1059 CeedQFunctionAddOutput(qf_ifunction, "v", ncompq, CEED_EVAL_INTERP); 1060 CeedQFunctionAddOutput(qf_ifunction, "dv", ncompq*dim, CEED_EVAL_GRAD); 1061 } 1062 1063 // Create the operator that builds the quadrature data for the NS operator 1064 CeedOperatorCreate(ceed, qf_setup, NULL, NULL, &op_setup); 1065 CeedOperatorSetField(op_setup, "dx", restrictx, basisx, CEED_VECTOR_ACTIVE); 1066 CeedOperatorSetField(op_setup, "weight", CEED_ELEMRESTRICTION_NONE, 1067 basisx, CEED_VECTOR_NONE); 1068 CeedOperatorSetField(op_setup, "qdata", restrictqdi, 1069 CEED_BASIS_COLLOCATED, CEED_VECTOR_ACTIVE); 1070 1071 // Create the operator that sets the ICs 1072 CeedOperatorCreate(ceed, qf_ics, NULL, NULL, &op_ics); 1073 CeedOperatorSetField(op_ics, "x", restrictx, basisxc, CEED_VECTOR_ACTIVE); 1074 CeedOperatorSetField(op_ics, "q0", restrictq, 1075 CEED_BASIS_COLLOCATED, CEED_VECTOR_ACTIVE); 1076 1077 CeedElemRestrictionCreateVector(restrictq, &user->qceed, NULL); 1078 CeedElemRestrictionCreateVector(restrictq, &user->qdotceed, NULL); 1079 CeedElemRestrictionCreateVector(restrictq, &user->gceed, NULL); 1080 1081 if (qf_rhs) { // Create the RHS physics operator 1082 CeedOperator op; 1083 CeedOperatorCreate(ceed, qf_rhs, NULL, NULL, &op); 1084 CeedOperatorSetField(op, "q", restrictq, basisq, CEED_VECTOR_ACTIVE); 1085 CeedOperatorSetField(op, "dq", restrictq, basisq, CEED_VECTOR_ACTIVE); 1086 CeedOperatorSetField(op, "qdata", restrictqdi, 1087 CEED_BASIS_COLLOCATED, qdata); 1088 CeedOperatorSetField(op, "x", restrictx, basisx, xcorners); 1089 CeedOperatorSetField(op, "v", restrictq, basisq, CEED_VECTOR_ACTIVE); 1090 CeedOperatorSetField(op, "dv", restrictq, basisq, CEED_VECTOR_ACTIVE); 1091 user->op_rhs = op; 1092 } 1093 1094 if (qf_ifunction) { // Create the IFunction operator 1095 CeedOperator op; 1096 CeedOperatorCreate(ceed, qf_ifunction, NULL, NULL, &op); 1097 CeedOperatorSetField(op, "q", restrictq, basisq, CEED_VECTOR_ACTIVE); 1098 CeedOperatorSetField(op, "dq", restrictq, basisq, CEED_VECTOR_ACTIVE); 1099 CeedOperatorSetField(op, "qdot", restrictq, basisq, user->qdotceed); 1100 CeedOperatorSetField(op, "qdata", restrictqdi, 1101 CEED_BASIS_COLLOCATED, qdata); 1102 CeedOperatorSetField(op, "x", restrictx, basisx, xcorners); 1103 CeedOperatorSetField(op, "v", restrictq, basisq, CEED_VECTOR_ACTIVE); 1104 CeedOperatorSetField(op, "dv", restrictq, basisq, CEED_VECTOR_ACTIVE); 1105 user->op_ifunction = op; 1106 } 1107 1108 CeedQFunctionSetContext(qf_ics, &ctxSetup, sizeof ctxSetup); 1109 CeedScalar ctxNS[8] = {lambda, mu, k, cv, cp, g, Rd}; 1110 struct Advection2dContext_ ctxAdvection2d = { 1111 .CtauS = CtauS, 1112 .strong_form = strong_form, 1113 .stabilization = stab, 1114 }; 1115 switch (problemChoice) { 1116 case NS_DENSITY_CURRENT: 1117 if (qf_rhs) CeedQFunctionSetContext(qf_rhs, &ctxNS, sizeof ctxNS); 1118 if (qf_ifunction) CeedQFunctionSetContext(qf_ifunction, &ctxNS, 1119 sizeof ctxNS); 1120 break; 1121 case NS_ADVECTION: 1122 case NS_ADVECTION2D: 1123 if (qf_rhs) CeedQFunctionSetContext(qf_rhs, &ctxAdvection2d, 1124 sizeof ctxAdvection2d); 1125 if (qf_ifunction) CeedQFunctionSetContext(qf_ifunction, &ctxAdvection2d, 1126 sizeof ctxAdvection2d); 1127 } 1128 1129 // Set up PETSc context 1130 // Set up units structure 1131 units->meter = meter; 1132 units->kilogram = kilogram; 1133 units->second = second; 1134 units->Kelvin = Kelvin; 1135 units->Pascal = Pascal; 1136 units->JperkgK = JperkgK; 1137 units->mpersquareds = mpersquareds; 1138 units->WpermK = WpermK; 1139 units->kgpercubicm = kgpercubicm; 1140 units->kgpersquaredms = kgpersquaredms; 1141 units->Joulepercubicm = Joulepercubicm; 1142 1143 // Set up user structure 1144 user->comm = comm; 1145 user->outputfreq = outputfreq; 1146 user->contsteps = contsteps; 1147 user->units = units; 1148 user->dm = dm; 1149 user->dmviz = dmviz; 1150 user->interpviz = interpviz; 1151 user->ceed = ceed; 1152 1153 // Calculate qdata and ICs 1154 // Set up state global and local vectors 1155 ierr = VecZeroEntries(Q); CHKERRQ(ierr); 1156 1157 ierr = VectorPlacePetscVec(q0ceed, Qloc); CHKERRQ(ierr); 1158 1159 // Apply Setup Ceed Operators 1160 ierr = VectorPlacePetscVec(xcorners, Xloc); CHKERRQ(ierr); 1161 CeedOperatorApply(op_setup, xcorners, qdata, CEED_REQUEST_IMMEDIATE); 1162 ierr = ComputeLumpedMassMatrix(ceed, dm, restrictq, basisq, restrictqdi, qdata, 1163 user->M); CHKERRQ(ierr); 1164 1165 ierr = ICs_FixMultiplicity(op_ics, xcorners, q0ceed, dm, Qloc, Q, restrictq, 1166 &ctxSetup, 0.0); 1167 if (1) { // Record boundary values from initial condition and override DMPlexInsertBoundaryValues() 1168 // We use this for the main simulation DM because the reference DMPlexInsertBoundaryValues() is very slow. If we 1169 // disable this, we should still get the same results due to the problem->bc function, but with potentially much 1170 // slower execution. 1171 Vec Qbc; 1172 ierr = DMGetNamedLocalVector(dm, "Qbc", &Qbc); CHKERRQ(ierr); 1173 ierr = VecCopy(Qloc, Qbc); CHKERRQ(ierr); 1174 ierr = VecZeroEntries(Qloc); CHKERRQ(ierr); 1175 ierr = DMGlobalToLocal(dm, Q, INSERT_VALUES, Qloc); CHKERRQ(ierr); 1176 ierr = VecAXPY(Qbc, -1., Qloc); CHKERRQ(ierr); 1177 ierr = DMRestoreNamedLocalVector(dm, "Qbc", &Qbc); CHKERRQ(ierr); 1178 ierr = PetscObjectComposeFunction((PetscObject)dm, 1179 "DMPlexInsertBoundaryValues_C", DMPlexInsertBoundaryValues_NS); 1180 CHKERRQ(ierr); 1181 } 1182 1183 MPI_Comm_rank(comm, &rank); 1184 if (!rank) {ierr = PetscMkdir(user->outputfolder); CHKERRQ(ierr);} 1185 // Gather initial Q values 1186 // In case of continuation of simulation, set up initial values from binary file 1187 if (contsteps) { // continue from existent solution 1188 PetscViewer viewer; 1189 char filepath[PETSC_MAX_PATH_LEN]; 1190 // Read input 1191 ierr = PetscSNPrintf(filepath, sizeof filepath, "%s/ns-solution.bin", 1192 user->outputfolder); 1193 CHKERRQ(ierr); 1194 ierr = PetscViewerBinaryOpen(comm, filepath, FILE_MODE_READ, &viewer); 1195 CHKERRQ(ierr); 1196 ierr = VecLoad(Q, viewer); CHKERRQ(ierr); 1197 ierr = PetscViewerDestroy(&viewer); CHKERRQ(ierr); 1198 } 1199 ierr = DMRestoreLocalVector(dm, &Qloc); CHKERRQ(ierr); 1200 1201 // Create and setup TS 1202 ierr = TSCreate(comm, &ts); CHKERRQ(ierr); 1203 ierr = TSSetDM(ts, dm); CHKERRQ(ierr); 1204 if (implicit) { 1205 ierr = TSSetType(ts, TSBDF); CHKERRQ(ierr); 1206 if (user->op_ifunction) { 1207 ierr = TSSetIFunction(ts, NULL, IFunction_NS, &user); CHKERRQ(ierr); 1208 } else { // Implicit integrators can fall back to using an RHSFunction 1209 ierr = TSSetRHSFunction(ts, NULL, RHS_NS, &user); CHKERRQ(ierr); 1210 } 1211 } else { 1212 if (!user->op_rhs) SETERRQ(comm,PETSC_ERR_ARG_NULL, 1213 "Problem does not provide RHSFunction"); 1214 ierr = TSSetType(ts, TSRK); CHKERRQ(ierr); 1215 ierr = TSRKSetType(ts, TSRK5F); CHKERRQ(ierr); 1216 ierr = TSSetRHSFunction(ts, NULL, RHS_NS, &user); CHKERRQ(ierr); 1217 } 1218 ierr = TSSetMaxTime(ts, 500. * units->second); CHKERRQ(ierr); 1219 ierr = TSSetExactFinalTime(ts, TS_EXACTFINALTIME_STEPOVER); CHKERRQ(ierr); 1220 ierr = TSSetTimeStep(ts, 1.e-2 * units->second); CHKERRQ(ierr); 1221 if (test) {ierr = TSSetMaxSteps(ts, 1); CHKERRQ(ierr);} 1222 ierr = TSGetAdapt(ts, &adapt); CHKERRQ(ierr); 1223 ierr = TSAdaptSetStepLimits(adapt, 1224 1.e-12 * units->second, 1225 1.e2 * units->second); CHKERRQ(ierr); 1226 ierr = TSSetFromOptions(ts); CHKERRQ(ierr); 1227 if (!contsteps) { // print initial condition 1228 if (!test) { 1229 ierr = TSMonitor_NS(ts, 0, 0., Q, user); CHKERRQ(ierr); 1230 } 1231 } else { // continue from time of last output 1232 PetscReal time; 1233 PetscInt count; 1234 PetscViewer viewer; 1235 char filepath[PETSC_MAX_PATH_LEN]; 1236 ierr = PetscSNPrintf(filepath, sizeof filepath, "%s/ns-time.bin", 1237 user->outputfolder); CHKERRQ(ierr); 1238 ierr = PetscViewerBinaryOpen(comm, filepath, FILE_MODE_READ, &viewer); 1239 CHKERRQ(ierr); 1240 ierr = PetscViewerBinaryRead(viewer, &time, 1, &count, PETSC_REAL); 1241 CHKERRQ(ierr); 1242 ierr = PetscViewerDestroy(&viewer); CHKERRQ(ierr); 1243 ierr = TSSetTime(ts, time * user->units->second); CHKERRQ(ierr); 1244 } 1245 if (!test) { 1246 ierr = TSMonitorSet(ts, TSMonitor_NS, user, NULL); CHKERRQ(ierr); 1247 } 1248 1249 // Solve 1250 start = MPI_Wtime(); 1251 ierr = PetscBarrier((PetscObject)ts); CHKERRQ(ierr); 1252 ierr = TSSolve(ts, Q); CHKERRQ(ierr); 1253 cpu_time_used = MPI_Wtime() - start; 1254 ierr = TSGetSolveTime(ts, &ftime); CHKERRQ(ierr); 1255 ierr = MPI_Allreduce(MPI_IN_PLACE, &cpu_time_used, 1, MPI_DOUBLE, MPI_MIN, 1256 comm); CHKERRQ(ierr); 1257 if (!test) { 1258 ierr = PetscPrintf(PETSC_COMM_WORLD, 1259 "Time taken for solution (sec): %g\n", 1260 (double)cpu_time_used); CHKERRQ(ierr); 1261 } 1262 1263 // Get error 1264 if (problem->non_zero_time && !test) { 1265 Vec Qexact, Qexactloc; 1266 PetscReal norm; 1267 ierr = DMCreateGlobalVector(dm, &Qexact); CHKERRQ(ierr); 1268 ierr = DMGetLocalVector(dm, &Qexactloc); CHKERRQ(ierr); 1269 ierr = VecGetSize(Qexactloc, &lnodes); CHKERRQ(ierr); 1270 1271 ierr = ICs_FixMultiplicity(op_ics, xcorners, q0ceed, dm, Qexactloc, Qexact, 1272 restrictq, &ctxSetup, ftime); CHKERRQ(ierr); 1273 1274 ierr = VecAXPY(Q, -1.0, Qexact); CHKERRQ(ierr); 1275 ierr = VecNorm(Q, NORM_MAX, &norm); CHKERRQ(ierr); 1276 CeedVectorDestroy(&q0ceed); 1277 ierr = PetscPrintf(PETSC_COMM_WORLD, 1278 "Max Error: %g\n", 1279 (double)norm); CHKERRQ(ierr); 1280 // Clean up vectors 1281 ierr = DMRestoreLocalVector(dm, &Qexactloc); CHKERRQ(ierr); 1282 ierr = VecDestroy(&Qexact); CHKERRQ(ierr); 1283 } 1284 1285 // Output Statistics 1286 ierr = TSGetStepNumber(ts,&steps); CHKERRQ(ierr); 1287 if (!test) { 1288 ierr = PetscPrintf(PETSC_COMM_WORLD, 1289 "Time integrator took %D time steps to reach final time %g\n", 1290 steps, (double)ftime); CHKERRQ(ierr); 1291 } 1292 1293 // Clean up libCEED 1294 CeedVectorDestroy(&qdata); 1295 CeedVectorDestroy(&user->qceed); 1296 CeedVectorDestroy(&user->qdotceed); 1297 CeedVectorDestroy(&user->gceed); 1298 CeedVectorDestroy(&xcorners); 1299 CeedBasisDestroy(&basisq); 1300 CeedBasisDestroy(&basisx); 1301 CeedBasisDestroy(&basisxc); 1302 CeedElemRestrictionDestroy(&restrictq); 1303 CeedElemRestrictionDestroy(&restrictx); 1304 CeedElemRestrictionDestroy(&restrictqdi); 1305 CeedElemRestrictionDestroy(&restrictxcoord); 1306 CeedQFunctionDestroy(&qf_setup); 1307 CeedQFunctionDestroy(&qf_ics); 1308 CeedQFunctionDestroy(&qf_rhs); 1309 CeedQFunctionDestroy(&qf_ifunction); 1310 CeedOperatorDestroy(&op_setup); 1311 CeedOperatorDestroy(&op_ics); 1312 CeedOperatorDestroy(&user->op_rhs); 1313 CeedOperatorDestroy(&user->op_ifunction); 1314 CeedDestroy(&ceed); 1315 1316 // Clean up PETSc 1317 ierr = VecDestroy(&Q); CHKERRQ(ierr); 1318 ierr = VecDestroy(&user->M); CHKERRQ(ierr); 1319 ierr = MatDestroy(&interpviz); CHKERRQ(ierr); 1320 ierr = DMDestroy(&dmviz); CHKERRQ(ierr); 1321 ierr = TSDestroy(&ts); CHKERRQ(ierr); 1322 ierr = DMDestroy(&dm); CHKERRQ(ierr); 1323 ierr = PetscFree(units); CHKERRQ(ierr); 1324 ierr = PetscFree(user); CHKERRQ(ierr); 1325 return PetscFinalize(); 1326 } 1327 1328