1 #include <../src/mat/impls/aij/seq/aij.h> 2 #include <petsc/private/dmpleximpl.h> /*I "petscdmplex.h" I*/ 3 #include <petsclandau.h> /*I "petsclandau.h" I*/ 4 #include <petscts.h> 5 #include <petscdmforest.h> 6 #include <petscdmcomposite.h> 7 8 /* Landau collision operator */ 9 10 /* relativistic terms */ 11 #if defined(PETSC_USE_REAL_SINGLE) 12 #define SPEED_OF_LIGHT 2.99792458e8F 13 #define C_0(v0) (SPEED_OF_LIGHT / v0) /* needed for relativistic tensor on all architectures */ 14 #else 15 #define SPEED_OF_LIGHT 2.99792458e8 16 #define C_0(v0) (SPEED_OF_LIGHT / v0) /* needed for relativistic tensor on all architectures */ 17 #endif 18 19 #define PETSC_THREAD_SYNC 20 #include "land_tensors.h" 21 22 #if defined(PETSC_HAVE_OPENMP) 23 #include <omp.h> 24 #endif 25 26 static PetscErrorCode LandauGPUMapsDestroy(void *ptr) 27 { 28 P4estVertexMaps *maps = (P4estVertexMaps *)ptr; 29 PetscFunctionBegin; 30 // free device data 31 if (maps[0].deviceType != LANDAU_CPU) { 32 #if defined(PETSC_HAVE_KOKKOS_KERNELS) 33 if (maps[0].deviceType == LANDAU_KOKKOS) { 34 PetscCall(LandauKokkosDestroyMatMaps(maps, maps[0].numgrids)); // implies Kokkos does 35 } // else could be CUDA 36 #elif defined(PETSC_HAVE_CUDA) 37 if (maps[0].deviceType == LANDAU_CUDA) { 38 PetscCall(LandauCUDADestroyMatMaps(maps, maps[0].numgrids)); 39 } else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "maps->deviceType %d ?????", maps->deviceType); 40 #endif 41 } 42 // free host data 43 for (PetscInt grid = 0; grid < maps[0].numgrids; grid++) { 44 PetscCall(PetscFree(maps[grid].c_maps)); 45 PetscCall(PetscFree(maps[grid].gIdx)); 46 } 47 PetscCall(PetscFree(maps)); 48 49 PetscFunctionReturn(PETSC_SUCCESS); 50 } 51 static PetscErrorCode energy_f(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf_dummy, PetscScalar *u, void *actx) 52 { 53 PetscReal v2 = 0; 54 PetscFunctionBegin; 55 /* compute v^2 / 2 */ 56 for (int i = 0; i < dim; ++i) v2 += x[i] * x[i]; 57 /* evaluate the Maxwellian */ 58 u[0] = v2 / 2; 59 PetscFunctionReturn(PETSC_SUCCESS); 60 } 61 62 /* needs double */ 63 static PetscErrorCode gamma_m1_f(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf_dummy, PetscScalar *u, void *actx) 64 { 65 PetscReal *c2_0_arr = ((PetscReal *)actx); 66 double u2 = 0, c02 = (double)*c2_0_arr, xx; 67 68 PetscFunctionBegin; 69 /* compute u^2 / 2 */ 70 for (int i = 0; i < dim; ++i) u2 += x[i] * x[i]; 71 /* gamma - 1 = g_eps, for conditioning and we only take derivatives */ 72 xx = u2 / c02; 73 #if defined(PETSC_USE_DEBUG) 74 u[0] = PetscSqrtReal(1. + xx); 75 #else 76 u[0] = xx / (PetscSqrtReal(1. + xx) + 1.) - 1.; // better conditioned. -1 might help condition and only used for derivative 77 #endif 78 PetscFunctionReturn(PETSC_SUCCESS); 79 } 80 81 /* 82 LandauFormJacobian_Internal - Evaluates Jacobian matrix. 83 84 Input Parameters: 85 . globX - input vector 86 . actx - optional user-defined context 87 . dim - dimension 88 89 Output Parameters: 90 . J0acP - Jacobian matrix filled, not created 91 */ 92 static PetscErrorCode LandauFormJacobian_Internal(Vec a_X, Mat JacP, const PetscInt dim, PetscReal shift, void *a_ctx) 93 { 94 LandauCtx *ctx = (LandauCtx *)a_ctx; 95 PetscInt numCells[LANDAU_MAX_GRIDS], Nq, Nb; 96 PetscQuadrature quad; 97 PetscReal Eq_m[LANDAU_MAX_SPECIES]; // could be static data w/o quench (ex2) 98 PetscScalar *cellClosure = NULL; 99 const PetscScalar *xdata = NULL; 100 PetscDS prob; 101 PetscContainer container; 102 P4estVertexMaps *maps; 103 Mat subJ[LANDAU_MAX_GRIDS * LANDAU_MAX_BATCH_SZ]; 104 105 PetscFunctionBegin; 106 PetscValidHeaderSpecific(a_X, VEC_CLASSID, 1); 107 PetscValidHeaderSpecific(JacP, MAT_CLASSID, 2); 108 PetscValidPointer(ctx, 5); 109 /* check for matrix container for GPU assembly. Support CPU assembly for debugging */ 110 PetscCheck(ctx->plex[0] != NULL, ctx->comm, PETSC_ERR_ARG_WRONG, "Plex not created"); 111 PetscCall(PetscLogEventBegin(ctx->events[10], 0, 0, 0, 0)); 112 PetscCall(DMGetDS(ctx->plex[0], &prob)); // same DS for all grids 113 PetscCall(PetscObjectQuery((PetscObject)JacP, "assembly_maps", (PetscObject *)&container)); 114 if (container) { 115 PetscCheck(ctx->gpu_assembly, ctx->comm, PETSC_ERR_ARG_WRONG, "maps but no GPU assembly"); 116 PetscCall(PetscContainerGetPointer(container, (void **)&maps)); 117 PetscCheck(maps, ctx->comm, PETSC_ERR_ARG_WRONG, "empty GPU matrix container"); 118 for (PetscInt i = 0; i < ctx->num_grids * ctx->batch_sz; i++) subJ[i] = NULL; 119 } else { 120 PetscCheck(!ctx->gpu_assembly, ctx->comm, PETSC_ERR_ARG_WRONG, "No maps but GPU assembly"); 121 for (PetscInt tid = 0; tid < ctx->batch_sz; tid++) { 122 for (PetscInt grid = 0; grid < ctx->num_grids; grid++) PetscCall(DMCreateMatrix(ctx->plex[grid], &subJ[LAND_PACK_IDX(tid, grid)])); 123 } 124 maps = NULL; 125 } 126 // get dynamic data (Eq is odd, for quench and Spitzer test) for CPU assembly and raw data for Jacobian GPU assembly. Get host numCells[], Nq (yuck) 127 PetscCall(PetscFEGetQuadrature(ctx->fe[0], &quad)); 128 PetscCall(PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, NULL)); 129 Nb = Nq; 130 PetscCheck(Nq <= LANDAU_MAX_NQ, ctx->comm, PETSC_ERR_ARG_WRONG, "Order too high. Nq = %" PetscInt_FMT " > LANDAU_MAX_NQ (%d)", Nq, LANDAU_MAX_NQ); 131 // get metadata for collecting dynamic data 132 for (PetscInt grid = 0; grid < ctx->num_grids; grid++) { 133 PetscInt cStart, cEnd; 134 PetscCheck(ctx->plex[grid] != NULL, ctx->comm, PETSC_ERR_ARG_WRONG, "Plex not created"); 135 PetscCall(DMPlexGetHeightStratum(ctx->plex[grid], 0, &cStart, &cEnd)); 136 numCells[grid] = cEnd - cStart; // grids can have different topology 137 } 138 PetscCall(PetscLogEventEnd(ctx->events[10], 0, 0, 0, 0)); 139 if (shift == 0) { /* create dynamic point data: f_alpha for closure of each cell (cellClosure[nbatch,ngrids,ncells[g],f[Nb,ns[g]]]) or xdata */ 140 DM pack; 141 PetscCall(VecGetDM(a_X, &pack)); 142 PetscCheck(pack, PETSC_COMM_SELF, PETSC_ERR_PLIB, "pack has no DM"); 143 PetscCall(PetscLogEventBegin(ctx->events[1], 0, 0, 0, 0)); 144 for (PetscInt fieldA = 0; fieldA < ctx->num_species; fieldA++) { 145 Eq_m[fieldA] = ctx->Ez * ctx->t_0 * ctx->charges[fieldA] / (ctx->v_0 * ctx->masses[fieldA]); /* normalize dimensionless */ 146 if (dim == 2) Eq_m[fieldA] *= 2 * PETSC_PI; /* add the 2pi term that is not in Landau */ 147 } 148 if (!ctx->gpu_assembly) { 149 Vec *locXArray, *globXArray; 150 PetscScalar *cellClosure_it; 151 PetscInt cellClosure_sz = 0, nDMs, Nf[LANDAU_MAX_GRIDS]; 152 PetscSection section[LANDAU_MAX_GRIDS], globsection[LANDAU_MAX_GRIDS]; 153 for (PetscInt grid = 0; grid < ctx->num_grids; grid++) { 154 PetscCall(DMGetLocalSection(ctx->plex[grid], §ion[grid])); 155 PetscCall(DMGetGlobalSection(ctx->plex[grid], &globsection[grid])); 156 PetscCall(PetscSectionGetNumFields(section[grid], &Nf[grid])); 157 } 158 /* count cellClosure size */ 159 PetscCall(DMCompositeGetNumberDM(pack, &nDMs)); 160 for (PetscInt grid = 0; grid < ctx->num_grids; grid++) cellClosure_sz += Nb * Nf[grid] * numCells[grid]; 161 PetscCall(PetscMalloc1(cellClosure_sz * ctx->batch_sz, &cellClosure)); 162 cellClosure_it = cellClosure; 163 PetscCall(PetscMalloc(sizeof(*locXArray) * nDMs, &locXArray)); 164 PetscCall(PetscMalloc(sizeof(*globXArray) * nDMs, &globXArray)); 165 PetscCall(DMCompositeGetLocalAccessArray(pack, a_X, nDMs, NULL, locXArray)); 166 PetscCall(DMCompositeGetAccessArray(pack, a_X, nDMs, NULL, globXArray)); 167 for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) { // OpenMP (once) 168 for (PetscInt grid = 0; grid < ctx->num_grids; grid++) { 169 Vec locX = locXArray[LAND_PACK_IDX(b_id, grid)], globX = globXArray[LAND_PACK_IDX(b_id, grid)], locX2; 170 PetscInt cStart, cEnd, ei; 171 PetscCall(VecDuplicate(locX, &locX2)); 172 PetscCall(DMGlobalToLocalBegin(ctx->plex[grid], globX, INSERT_VALUES, locX2)); 173 PetscCall(DMGlobalToLocalEnd(ctx->plex[grid], globX, INSERT_VALUES, locX2)); 174 PetscCall(DMPlexGetHeightStratum(ctx->plex[grid], 0, &cStart, &cEnd)); 175 for (ei = cStart; ei < cEnd; ++ei) { 176 PetscScalar *coef = NULL; 177 PetscCall(DMPlexVecGetClosure(ctx->plex[grid], section[grid], locX2, ei, NULL, &coef)); 178 PetscCall(PetscMemcpy(cellClosure_it, coef, Nb * Nf[grid] * sizeof(*cellClosure_it))); /* change if LandauIPReal != PetscScalar */ 179 PetscCall(DMPlexVecRestoreClosure(ctx->plex[grid], section[grid], locX2, ei, NULL, &coef)); 180 cellClosure_it += Nb * Nf[grid]; 181 } 182 PetscCall(VecDestroy(&locX2)); 183 } 184 } 185 PetscCheck(cellClosure_it - cellClosure == cellClosure_sz * ctx->batch_sz, PETSC_COMM_SELF, PETSC_ERR_PLIB, "iteration wrong %" PetscCount_FMT " != cellClosure_sz = %" PetscInt_FMT, (PetscCount)(cellClosure_it - cellClosure), 186 cellClosure_sz * ctx->batch_sz); 187 PetscCall(DMCompositeRestoreLocalAccessArray(pack, a_X, nDMs, NULL, locXArray)); 188 PetscCall(DMCompositeRestoreAccessArray(pack, a_X, nDMs, NULL, globXArray)); 189 PetscCall(PetscFree(locXArray)); 190 PetscCall(PetscFree(globXArray)); 191 xdata = NULL; 192 } else { 193 PetscMemType mtype; 194 if (ctx->jacobian_field_major_order) { // get data in batch ordering 195 PetscCall(VecScatterBegin(ctx->plex_batch, a_X, ctx->work_vec, INSERT_VALUES, SCATTER_FORWARD)); 196 PetscCall(VecScatterEnd(ctx->plex_batch, a_X, ctx->work_vec, INSERT_VALUES, SCATTER_FORWARD)); 197 PetscCall(VecGetArrayReadAndMemType(ctx->work_vec, &xdata, &mtype)); 198 } else { 199 PetscCall(VecGetArrayReadAndMemType(a_X, &xdata, &mtype)); 200 } 201 PetscCheck(mtype == PETSC_MEMTYPE_HOST || ctx->deviceType != LANDAU_CPU, ctx->comm, PETSC_ERR_ARG_WRONG, "CPU run with device data: use -mat_type aij"); 202 cellClosure = NULL; 203 } 204 PetscCall(PetscLogEventEnd(ctx->events[1], 0, 0, 0, 0)); 205 } else xdata = cellClosure = NULL; 206 207 /* do it */ 208 if (ctx->deviceType == LANDAU_CUDA || ctx->deviceType == LANDAU_KOKKOS) { 209 if (ctx->deviceType == LANDAU_CUDA) { 210 #if defined(PETSC_HAVE_CUDA) 211 PetscCall(LandauCUDAJacobian(ctx->plex, Nq, ctx->batch_sz, ctx->num_grids, numCells, Eq_m, cellClosure, xdata, &ctx->SData_d, shift, ctx->events, ctx->mat_offset, ctx->species_offset, subJ, JacP)); 212 #else 213 SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONG, "-landau_device_type %s not built", "cuda"); 214 #endif 215 } else if (ctx->deviceType == LANDAU_KOKKOS) { 216 #if defined(PETSC_HAVE_KOKKOS_KERNELS) 217 PetscCall(LandauKokkosJacobian(ctx->plex, Nq, ctx->batch_sz, ctx->num_grids, numCells, Eq_m, cellClosure, xdata, &ctx->SData_d, shift, ctx->events, ctx->mat_offset, ctx->species_offset, subJ, JacP)); 218 #else 219 SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONG, "-landau_device_type %s not built", "kokkos"); 220 #endif 221 } 222 } else { /* CPU version */ 223 PetscTabulation *Tf; // used for CPU and print info. Same on all grids and all species 224 PetscInt ip_offset[LANDAU_MAX_GRIDS + 1], ipf_offset[LANDAU_MAX_GRIDS + 1], elem_offset[LANDAU_MAX_GRIDS + 1], IPf_sz_glb, IPf_sz_tot, num_grids = ctx->num_grids, Nf[LANDAU_MAX_GRIDS]; 225 PetscReal *ff, *dudx, *dudy, *dudz, *invJ_a = (PetscReal *)ctx->SData_d.invJ, *xx = (PetscReal *)ctx->SData_d.x, *yy = (PetscReal *)ctx->SData_d.y, *zz = (PetscReal *)ctx->SData_d.z, *ww = (PetscReal *)ctx->SData_d.w; 226 PetscReal *nu_alpha = (PetscReal *)ctx->SData_d.alpha, *nu_beta = (PetscReal *)ctx->SData_d.beta, *invMass = (PetscReal *)ctx->SData_d.invMass; 227 PetscReal(*lambdas)[LANDAU_MAX_GRIDS][LANDAU_MAX_GRIDS] = (PetscReal(*)[LANDAU_MAX_GRIDS][LANDAU_MAX_GRIDS])ctx->SData_d.lambdas; 228 PetscSection section[LANDAU_MAX_GRIDS], globsection[LANDAU_MAX_GRIDS]; 229 PetscScalar *coo_vals = NULL; 230 for (PetscInt grid = 0; grid < ctx->num_grids; grid++) { 231 PetscCall(DMGetLocalSection(ctx->plex[grid], §ion[grid])); 232 PetscCall(DMGetGlobalSection(ctx->plex[grid], &globsection[grid])); 233 PetscCall(PetscSectionGetNumFields(section[grid], &Nf[grid])); 234 } 235 /* count IPf size, etc */ 236 PetscCall(PetscDSGetTabulation(prob, &Tf)); // Bf, &Df same for all grids 237 const PetscReal *const BB = Tf[0]->T[0], *const DD = Tf[0]->T[1]; 238 ip_offset[0] = ipf_offset[0] = elem_offset[0] = 0; 239 for (PetscInt grid = 0; grid < num_grids; grid++) { 240 PetscInt nfloc = ctx->species_offset[grid + 1] - ctx->species_offset[grid]; 241 elem_offset[grid + 1] = elem_offset[grid] + numCells[grid]; 242 ip_offset[grid + 1] = ip_offset[grid] + numCells[grid] * Nq; 243 ipf_offset[grid + 1] = ipf_offset[grid] + Nq * nfloc * numCells[grid]; 244 } 245 IPf_sz_glb = ipf_offset[num_grids]; 246 IPf_sz_tot = IPf_sz_glb * ctx->batch_sz; 247 // prep COO 248 if (ctx->coo_assembly) { 249 PetscCall(PetscMalloc1(ctx->SData_d.coo_size, &coo_vals)); // allocate every time? 250 PetscCall(PetscInfo(ctx->plex[0], "COO Allocate %" PetscInt_FMT " values\n", (PetscInt)ctx->SData_d.coo_size)); 251 } 252 if (shift == 0.0) { /* compute dynamic data f and df and init data for Jacobian */ 253 #if defined(PETSC_HAVE_THREADSAFETY) 254 double starttime, endtime; 255 starttime = MPI_Wtime(); 256 #endif 257 PetscCall(PetscLogEventBegin(ctx->events[8], 0, 0, 0, 0)); 258 PetscCall(PetscMalloc4(IPf_sz_tot, &ff, IPf_sz_tot, &dudx, IPf_sz_tot, &dudy, dim == 3 ? IPf_sz_tot : 0, &dudz)); 259 // F df/dx 260 for (PetscInt tid = 0; tid < ctx->batch_sz * elem_offset[num_grids]; tid++) { // for each element 261 const PetscInt b_Nelem = elem_offset[num_grids], b_elem_idx = tid % b_Nelem, b_id = tid / b_Nelem; // b_id == OMP thd_id in batch 262 // find my grid: 263 PetscInt grid = 0; 264 while (b_elem_idx >= elem_offset[grid + 1]) grid++; // yuck search for grid 265 { 266 const PetscInt loc_nip = numCells[grid] * Nq, loc_Nf = ctx->species_offset[grid + 1] - ctx->species_offset[grid], loc_elem = b_elem_idx - elem_offset[grid]; 267 const PetscInt moffset = LAND_MOFFSET(b_id, grid, ctx->batch_sz, ctx->num_grids, ctx->mat_offset); //b_id*b_N + ctx->mat_offset[grid]; 268 PetscScalar *coef, coef_buff[LANDAU_MAX_SPECIES * LANDAU_MAX_NQ]; 269 PetscReal *invJe = &invJ_a[(ip_offset[grid] + loc_elem * Nq) * dim * dim]; // ingJ is static data on batch 0 270 PetscInt b, f, q; 271 if (cellClosure) { 272 coef = &cellClosure[b_id * IPf_sz_glb + ipf_offset[grid] + loc_elem * Nb * loc_Nf]; // this is const 273 } else { 274 coef = coef_buff; 275 for (f = 0; f < loc_Nf; ++f) { 276 LandauIdx *const Idxs = &maps[grid].gIdx[loc_elem][f][0]; 277 for (b = 0; b < Nb; ++b) { 278 PetscInt idx = Idxs[b]; 279 if (idx >= 0) { 280 coef[f * Nb + b] = xdata[idx + moffset]; 281 } else { 282 idx = -idx - 1; 283 coef[f * Nb + b] = 0; 284 for (q = 0; q < maps[grid].num_face; q++) { 285 PetscInt id = maps[grid].c_maps[idx][q].gid; 286 PetscScalar scale = maps[grid].c_maps[idx][q].scale; 287 coef[f * Nb + b] += scale * xdata[id + moffset]; 288 } 289 } 290 } 291 } 292 } 293 /* get f and df */ 294 for (PetscInt qi = 0; qi < Nq; qi++) { 295 const PetscReal *invJ = &invJe[qi * dim * dim]; 296 const PetscReal *Bq = &BB[qi * Nb]; 297 const PetscReal *Dq = &DD[qi * Nb * dim]; 298 PetscReal u_x[LANDAU_DIM]; 299 /* get f & df */ 300 for (f = 0; f < loc_Nf; ++f) { 301 const PetscInt idx = b_id * IPf_sz_glb + ipf_offset[grid] + f * loc_nip + loc_elem * Nq + qi; 302 PetscInt b, e; 303 PetscReal refSpaceDer[LANDAU_DIM]; 304 ff[idx] = 0.0; 305 for (int d = 0; d < LANDAU_DIM; ++d) refSpaceDer[d] = 0.0; 306 for (b = 0; b < Nb; ++b) { 307 const PetscInt cidx = b; 308 ff[idx] += Bq[cidx] * PetscRealPart(coef[f * Nb + cidx]); 309 for (int d = 0; d < dim; ++d) refSpaceDer[d] += Dq[cidx * dim + d] * PetscRealPart(coef[f * Nb + cidx]); 310 } 311 for (int d = 0; d < LANDAU_DIM; ++d) { 312 for (e = 0, u_x[d] = 0.0; e < LANDAU_DIM; ++e) u_x[d] += invJ[e * dim + d] * refSpaceDer[e]; 313 } 314 dudx[idx] = u_x[0]; 315 dudy[idx] = u_x[1]; 316 #if LANDAU_DIM == 3 317 dudz[idx] = u_x[2]; 318 #endif 319 } 320 } // q 321 } // grid 322 } // grid*batch 323 PetscCall(PetscLogEventEnd(ctx->events[8], 0, 0, 0, 0)); 324 #if defined(PETSC_HAVE_THREADSAFETY) 325 endtime = MPI_Wtime(); 326 if (ctx->stage) ctx->times[LANDAU_F_DF] += (endtime - starttime); 327 #endif 328 } // Jacobian setup 329 // assemble Jacobian (or mass) 330 for (PetscInt tid = 0; tid < ctx->batch_sz * elem_offset[num_grids]; tid++) { // for each element 331 const PetscInt b_Nelem = elem_offset[num_grids]; 332 const PetscInt glb_elem_idx = tid % b_Nelem, b_id = tid / b_Nelem; 333 PetscInt grid = 0; 334 #if defined(PETSC_HAVE_THREADSAFETY) 335 double starttime, endtime; 336 starttime = MPI_Wtime(); 337 #endif 338 while (glb_elem_idx >= elem_offset[grid + 1]) grid++; 339 { 340 const PetscInt loc_Nf = ctx->species_offset[grid + 1] - ctx->species_offset[grid], loc_elem = glb_elem_idx - elem_offset[grid]; 341 const PetscInt moffset = LAND_MOFFSET(b_id, grid, ctx->batch_sz, ctx->num_grids, ctx->mat_offset), totDim = loc_Nf * Nq, elemMatSize = totDim * totDim; 342 PetscScalar *elemMat; 343 const PetscReal *invJe = &invJ_a[(ip_offset[grid] + loc_elem * Nq) * dim * dim]; 344 PetscCall(PetscMalloc1(elemMatSize, &elemMat)); 345 PetscCall(PetscMemzero(elemMat, elemMatSize * sizeof(*elemMat))); 346 if (shift == 0.0) { // Jacobian 347 PetscCall(PetscLogEventBegin(ctx->events[4], 0, 0, 0, 0)); 348 } else { // mass 349 PetscCall(PetscLogEventBegin(ctx->events[16], 0, 0, 0, 0)); 350 } 351 for (PetscInt qj = 0; qj < Nq; ++qj) { 352 const PetscInt jpidx_glb = ip_offset[grid] + qj + loc_elem * Nq; 353 PetscReal g0[LANDAU_MAX_SPECIES], g2[LANDAU_MAX_SPECIES][LANDAU_DIM], g3[LANDAU_MAX_SPECIES][LANDAU_DIM][LANDAU_DIM]; // could make a LANDAU_MAX_SPECIES_GRID ~ number of ions - 1 354 PetscInt d, d2, dp, d3, IPf_idx; 355 if (shift == 0.0) { // Jacobian 356 const PetscReal *const invJj = &invJe[qj * dim * dim]; 357 PetscReal gg2[LANDAU_MAX_SPECIES][LANDAU_DIM], gg3[LANDAU_MAX_SPECIES][LANDAU_DIM][LANDAU_DIM], gg2_temp[LANDAU_DIM], gg3_temp[LANDAU_DIM][LANDAU_DIM]; 358 const PetscReal vj[3] = {xx[jpidx_glb], yy[jpidx_glb], zz ? zz[jpidx_glb] : 0}, wj = ww[jpidx_glb]; 359 // create g2 & g3 360 for (d = 0; d < LANDAU_DIM; d++) { // clear accumulation data D & K 361 gg2_temp[d] = 0; 362 for (d2 = 0; d2 < LANDAU_DIM; d2++) gg3_temp[d][d2] = 0; 363 } 364 /* inner beta reduction */ 365 IPf_idx = 0; 366 for (PetscInt grid_r = 0, f_off = 0, ipidx = 0; grid_r < ctx->num_grids; grid_r++, f_off = ctx->species_offset[grid_r]) { // IPf_idx += nip_loc_r*Nfloc_r 367 PetscInt nip_loc_r = numCells[grid_r] * Nq, Nfloc_r = Nf[grid_r]; 368 for (PetscInt ei_r = 0, loc_fdf_idx = 0; ei_r < numCells[grid_r]; ++ei_r) { 369 for (PetscInt qi = 0; qi < Nq; qi++, ipidx++, loc_fdf_idx++) { 370 const PetscReal wi = ww[ipidx], x = xx[ipidx], y = yy[ipidx]; 371 PetscReal temp1[3] = {0, 0, 0}, temp2 = 0; 372 #if LANDAU_DIM == 2 373 PetscReal Ud[2][2], Uk[2][2], mask = (PetscAbs(vj[0] - x) < 100 * PETSC_SQRT_MACHINE_EPSILON && PetscAbs(vj[1] - y) < 100 * PETSC_SQRT_MACHINE_EPSILON) ? 0. : 1.; 374 LandauTensor2D(vj, x, y, Ud, Uk, mask); 375 #else 376 PetscReal U[3][3], z = zz[ipidx], mask = (PetscAbs(vj[0] - x) < 100 * PETSC_SQRT_MACHINE_EPSILON && PetscAbs(vj[1] - y) < 100 * PETSC_SQRT_MACHINE_EPSILON && PetscAbs(vj[2] - z) < 100 * PETSC_SQRT_MACHINE_EPSILON) ? 0. : 1.; 377 if (ctx->use_relativistic_corrections) { 378 LandauTensor3DRelativistic(vj, x, y, z, U, mask, C_0(ctx->v_0)); 379 } else { 380 LandauTensor3D(vj, x, y, z, U, mask); 381 } 382 #endif 383 for (int f = 0; f < Nfloc_r; ++f) { 384 const PetscInt idx = b_id * IPf_sz_glb + ipf_offset[grid_r] + f * nip_loc_r + ei_r * Nq + qi; // IPf_idx + f*nip_loc_r + loc_fdf_idx; 385 temp1[0] += dudx[idx] * nu_beta[f + f_off] * invMass[f + f_off] * (*lambdas)[grid][grid_r]; 386 temp1[1] += dudy[idx] * nu_beta[f + f_off] * invMass[f + f_off] * (*lambdas)[grid][grid_r]; 387 #if LANDAU_DIM == 3 388 temp1[2] += dudz[idx] * nu_beta[f + f_off] * invMass[f + f_off] * (*lambdas)[grid][grid_r]; 389 #endif 390 temp2 += ff[idx] * nu_beta[f + f_off] * (*lambdas)[grid][grid_r]; 391 } 392 temp1[0] *= wi; 393 temp1[1] *= wi; 394 #if LANDAU_DIM == 3 395 temp1[2] *= wi; 396 #endif 397 temp2 *= wi; 398 #if LANDAU_DIM == 2 399 for (d2 = 0; d2 < 2; d2++) { 400 for (d3 = 0; d3 < 2; ++d3) { 401 /* K = U * grad(f): g2=e: i,A */ 402 gg2_temp[d2] += Uk[d2][d3] * temp1[d3]; 403 /* D = -U * (I \kron (fx)): g3=f: i,j,A */ 404 gg3_temp[d2][d3] += Ud[d2][d3] * temp2; 405 } 406 } 407 #else 408 for (d2 = 0; d2 < 3; ++d2) { 409 for (d3 = 0; d3 < 3; ++d3) { 410 /* K = U * grad(f): g2 = e: i,A */ 411 gg2_temp[d2] += U[d2][d3] * temp1[d3]; 412 /* D = -U * (I \kron (fx)): g3 = f: i,j,A */ 413 gg3_temp[d2][d3] += U[d2][d3] * temp2; 414 } 415 } 416 #endif 417 } // qi 418 } // ei_r 419 IPf_idx += nip_loc_r * Nfloc_r; 420 } /* grid_r - IPs */ 421 PetscCheck(IPf_idx == IPf_sz_glb, PETSC_COMM_SELF, PETSC_ERR_PLIB, "IPf_idx != IPf_sz %" PetscInt_FMT " %" PetscInt_FMT, IPf_idx, IPf_sz_glb); 422 // add alpha and put in gg2/3 423 for (PetscInt fieldA = 0, f_off = ctx->species_offset[grid]; fieldA < loc_Nf; ++fieldA) { 424 for (d2 = 0; d2 < LANDAU_DIM; d2++) { 425 gg2[fieldA][d2] = gg2_temp[d2] * nu_alpha[fieldA + f_off]; 426 for (d3 = 0; d3 < LANDAU_DIM; d3++) gg3[fieldA][d2][d3] = -gg3_temp[d2][d3] * nu_alpha[fieldA + f_off] * invMass[fieldA + f_off]; 427 } 428 } 429 /* add electric field term once per IP */ 430 for (PetscInt fieldA = 0, f_off = ctx->species_offset[grid]; fieldA < loc_Nf; ++fieldA) gg2[fieldA][LANDAU_DIM - 1] += Eq_m[fieldA + f_off]; 431 /* Jacobian transform - g2, g3 */ 432 for (PetscInt fieldA = 0; fieldA < loc_Nf; ++fieldA) { 433 for (d = 0; d < dim; ++d) { 434 g2[fieldA][d] = 0.0; 435 for (d2 = 0; d2 < dim; ++d2) { 436 g2[fieldA][d] += invJj[d * dim + d2] * gg2[fieldA][d2]; 437 g3[fieldA][d][d2] = 0.0; 438 for (d3 = 0; d3 < dim; ++d3) { 439 for (dp = 0; dp < dim; ++dp) g3[fieldA][d][d2] += invJj[d * dim + d3] * gg3[fieldA][d3][dp] * invJj[d2 * dim + dp]; 440 } 441 g3[fieldA][d][d2] *= wj; 442 } 443 g2[fieldA][d] *= wj; 444 } 445 } 446 } else { // mass 447 PetscReal wj = ww[jpidx_glb]; 448 /* Jacobian transform - g0 */ 449 for (PetscInt fieldA = 0; fieldA < loc_Nf; ++fieldA) { 450 if (dim == 2) { 451 g0[fieldA] = wj * shift * 2. * PETSC_PI; // move this to below and remove g0 452 } else { 453 g0[fieldA] = wj * shift; // move this to below and remove g0 454 } 455 } 456 } 457 /* FE matrix construction */ 458 { 459 PetscInt fieldA, d, f, d2, g; 460 const PetscReal *BJq = &BB[qj * Nb], *DIq = &DD[qj * Nb * dim]; 461 /* assemble - on the diagonal (I,I) */ 462 for (fieldA = 0; fieldA < loc_Nf; fieldA++) { 463 for (f = 0; f < Nb; f++) { 464 const PetscInt i = fieldA * Nb + f; /* Element matrix row */ 465 for (g = 0; g < Nb; ++g) { 466 const PetscInt j = fieldA * Nb + g; /* Element matrix column */ 467 const PetscInt fOff = i * totDim + j; 468 if (shift == 0.0) { 469 for (d = 0; d < dim; ++d) { 470 elemMat[fOff] += DIq[f * dim + d] * g2[fieldA][d] * BJq[g]; 471 for (d2 = 0; d2 < dim; ++d2) elemMat[fOff] += DIq[f * dim + d] * g3[fieldA][d][d2] * DIq[g * dim + d2]; 472 } 473 } else { // mass 474 elemMat[fOff] += BJq[f] * g0[fieldA] * BJq[g]; 475 } 476 } 477 } 478 } 479 } 480 } /* qj loop */ 481 if (shift == 0.0) { // Jacobian 482 PetscCall(PetscLogEventEnd(ctx->events[4], 0, 0, 0, 0)); 483 } else { 484 PetscCall(PetscLogEventEnd(ctx->events[16], 0, 0, 0, 0)); 485 } 486 #if defined(PETSC_HAVE_THREADSAFETY) 487 endtime = MPI_Wtime(); 488 if (ctx->stage) ctx->times[LANDAU_KERNEL] += (endtime - starttime); 489 #endif 490 /* assemble matrix */ 491 if (!container) { 492 PetscInt cStart; 493 PetscCall(PetscLogEventBegin(ctx->events[6], 0, 0, 0, 0)); 494 PetscCall(DMPlexGetHeightStratum(ctx->plex[grid], 0, &cStart, NULL)); 495 PetscCall(DMPlexMatSetClosure(ctx->plex[grid], section[grid], globsection[grid], subJ[LAND_PACK_IDX(b_id, grid)], loc_elem + cStart, elemMat, ADD_VALUES)); 496 PetscCall(PetscLogEventEnd(ctx->events[6], 0, 0, 0, 0)); 497 } else { // GPU like assembly for debugging 498 PetscInt fieldA, q, f, g, d, nr, nc, rows0[LANDAU_MAX_Q_FACE] = {0}, cols0[LANDAU_MAX_Q_FACE] = {0}, rows[LANDAU_MAX_Q_FACE], cols[LANDAU_MAX_Q_FACE]; 499 PetscScalar vals[LANDAU_MAX_Q_FACE * LANDAU_MAX_Q_FACE] = {0}, row_scale[LANDAU_MAX_Q_FACE] = {0}, col_scale[LANDAU_MAX_Q_FACE] = {0}; 500 LandauIdx *coo_elem_offsets = (LandauIdx *)ctx->SData_d.coo_elem_offsets, *coo_elem_fullNb = (LandauIdx *)ctx->SData_d.coo_elem_fullNb, (*coo_elem_point_offsets)[LANDAU_MAX_NQ + 1] = (LandauIdx(*)[LANDAU_MAX_NQ + 1]) ctx->SData_d.coo_elem_point_offsets; 501 /* assemble - from the diagonal (I,I) in this format for DMPlexMatSetClosure */ 502 for (fieldA = 0; fieldA < loc_Nf; fieldA++) { 503 LandauIdx *const Idxs = &maps[grid].gIdx[loc_elem][fieldA][0]; 504 for (f = 0; f < Nb; f++) { 505 PetscInt idx = Idxs[f]; 506 if (idx >= 0) { 507 nr = 1; 508 rows0[0] = idx; 509 row_scale[0] = 1.; 510 } else { 511 idx = -idx - 1; 512 for (q = 0, nr = 0; q < maps[grid].num_face; q++, nr++) { 513 if (maps[grid].c_maps[idx][q].gid < 0) break; 514 rows0[q] = maps[grid].c_maps[idx][q].gid; 515 row_scale[q] = maps[grid].c_maps[idx][q].scale; 516 } 517 } 518 for (g = 0; g < Nb; ++g) { 519 idx = Idxs[g]; 520 if (idx >= 0) { 521 nc = 1; 522 cols0[0] = idx; 523 col_scale[0] = 1.; 524 } else { 525 idx = -idx - 1; 526 nc = maps[grid].num_face; 527 for (q = 0, nc = 0; q < maps[grid].num_face; q++, nc++) { 528 if (maps[grid].c_maps[idx][q].gid < 0) break; 529 cols0[q] = maps[grid].c_maps[idx][q].gid; 530 col_scale[q] = maps[grid].c_maps[idx][q].scale; 531 } 532 } 533 const PetscInt i = fieldA * Nb + f; /* Element matrix row */ 534 const PetscInt j = fieldA * Nb + g; /* Element matrix column */ 535 const PetscScalar Aij = elemMat[i * totDim + j]; 536 if (coo_vals) { // mirror (i,j) in CreateStaticGPUData 537 const int fullNb = coo_elem_fullNb[glb_elem_idx], fullNb2 = fullNb * fullNb; 538 const int idx0 = b_id * coo_elem_offsets[elem_offset[num_grids]] + coo_elem_offsets[glb_elem_idx] + fieldA * fullNb2 + fullNb * coo_elem_point_offsets[glb_elem_idx][f] + nr * coo_elem_point_offsets[glb_elem_idx][g]; 539 for (int q = 0, idx2 = idx0; q < nr; q++) { 540 for (int d = 0; d < nc; d++, idx2++) coo_vals[idx2] = row_scale[q] * col_scale[d] * Aij; 541 } 542 } else { 543 for (q = 0; q < nr; q++) rows[q] = rows0[q] + moffset; 544 for (d = 0; d < nc; d++) cols[d] = cols0[d] + moffset; 545 for (q = 0; q < nr; q++) { 546 for (d = 0; d < nc; d++) vals[q * nc + d] = row_scale[q] * col_scale[d] * Aij; 547 } 548 PetscCall(MatSetValues(JacP, nr, rows, nc, cols, vals, ADD_VALUES)); 549 } 550 } 551 } 552 } 553 } 554 if (loc_elem == -1) { 555 PetscCall(PetscPrintf(ctx->comm, "CPU Element matrix\n")); 556 for (int d = 0; d < totDim; ++d) { 557 for (int f = 0; f < totDim; ++f) PetscCall(PetscPrintf(ctx->comm, " %12.5e", (double)PetscRealPart(elemMat[d * totDim + f]))); 558 PetscCall(PetscPrintf(ctx->comm, "\n")); 559 } 560 exit(12); 561 } 562 PetscCall(PetscFree(elemMat)); 563 } /* grid */ 564 } /* outer element & batch loop */ 565 if (shift == 0.0) { // mass 566 PetscCall(PetscFree4(ff, dudx, dudy, dudz)); 567 } 568 if (!container) { // 'CPU' assembly move nest matrix to global JacP 569 for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) { // OpenMP 570 for (PetscInt grid = 0; grid < ctx->num_grids; grid++) { 571 const PetscInt moffset = LAND_MOFFSET(b_id, grid, ctx->batch_sz, ctx->num_grids, ctx->mat_offset); // b_id*b_N + ctx->mat_offset[grid]; 572 PetscInt nloc, nzl, colbuf[1024], row; 573 const PetscInt *cols; 574 const PetscScalar *vals; 575 Mat B = subJ[LAND_PACK_IDX(b_id, grid)]; 576 PetscCall(MatAssemblyBegin(B, MAT_FINAL_ASSEMBLY)); 577 PetscCall(MatAssemblyEnd(B, MAT_FINAL_ASSEMBLY)); 578 PetscCall(MatGetSize(B, &nloc, NULL)); 579 for (int i = 0; i < nloc; i++) { 580 PetscCall(MatGetRow(B, i, &nzl, &cols, &vals)); 581 PetscCheck(nzl <= 1024, PetscObjectComm((PetscObject)B), PETSC_ERR_PLIB, "Row too big: %" PetscInt_FMT, nzl); 582 for (int j = 0; j < nzl; j++) colbuf[j] = moffset + cols[j]; 583 row = moffset + i; 584 PetscCall(MatSetValues(JacP, 1, &row, nzl, colbuf, vals, ADD_VALUES)); 585 PetscCall(MatRestoreRow(B, i, &nzl, &cols, &vals)); 586 } 587 PetscCall(MatDestroy(&B)); 588 } 589 } 590 } 591 if (coo_vals) { 592 PetscCall(MatSetValuesCOO(JacP, coo_vals, ADD_VALUES)); 593 PetscCall(PetscFree(coo_vals)); 594 } 595 } /* CPU version */ 596 PetscCall(MatAssemblyBegin(JacP, MAT_FINAL_ASSEMBLY)); 597 PetscCall(MatAssemblyEnd(JacP, MAT_FINAL_ASSEMBLY)); 598 /* clean up */ 599 if (cellClosure) PetscCall(PetscFree(cellClosure)); 600 if (xdata) PetscCall(VecRestoreArrayReadAndMemType(a_X, &xdata)); 601 PetscFunctionReturn(PETSC_SUCCESS); 602 } 603 604 static PetscErrorCode GeometryDMLandau(DM base, PetscInt point, PetscInt dim, const PetscReal abc[], PetscReal xyz[], void *a_ctx) 605 { 606 PetscReal r = abc[0], z = abc[1]; 607 608 PetscFunctionBegin; 609 xyz[0] = r; 610 xyz[1] = z; 611 if (dim == 3) xyz[2] = abc[2]; 612 613 PetscFunctionReturn(PETSC_SUCCESS); 614 } 615 616 /* create DMComposite of meshes for each species group */ 617 static PetscErrorCode LandauDMCreateVMeshes(MPI_Comm comm_self, const PetscInt dim, const char prefix[], LandauCtx *ctx, DM pack) 618 { 619 PetscFunctionBegin; 620 { /* p4est, quads */ 621 /* Create plex mesh of Landau domain */ 622 for (PetscInt grid = 0; grid < ctx->num_grids; grid++) { 623 PetscReal par_radius = ctx->radius_par[grid], perp_radius = ctx->radius_perp[grid]; 624 if (!ctx->sphere) { 625 PetscReal lo[] = {-perp_radius, -par_radius, -par_radius}, hi[] = {perp_radius, par_radius, par_radius}; 626 DMBoundaryType periodicity[3] = {DM_BOUNDARY_NONE, dim == 2 ? DM_BOUNDARY_NONE : DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 627 if (dim == 2) lo[0] = 0; 628 else { 629 lo[1] = -perp_radius; 630 hi[1] = perp_radius; // 3D y is a perp 631 } 632 PetscCall(DMPlexCreateBoxMesh(comm_self, dim, PETSC_FALSE, ctx->cells0, lo, hi, periodicity, PETSC_TRUE, &ctx->plex[grid])); // todo: make composite and create dm[grid] here 633 PetscCall(DMLocalizeCoordinates(ctx->plex[grid])); /* needed for periodic */ 634 if (dim == 3) PetscCall(PetscObjectSetName((PetscObject)ctx->plex[grid], "cube")); 635 else PetscCall(PetscObjectSetName((PetscObject)ctx->plex[grid], "half-plane")); 636 } else if (dim == 2) { 637 PetscInt numCells, cells[16][4], i, j; 638 PetscInt numVerts; 639 PetscReal *flatCoords = NULL; 640 PetscInt *flatCells = NULL, *pcell; 641 numCells = 10; 642 numVerts = 16; 643 int cells2[][4] = { 644 {0, 1, 6, 5 }, 645 {1, 2, 7, 6 }, 646 {2, 3, 8, 7 }, 647 {3, 4, 9, 8 }, 648 {5, 6, 11, 10}, 649 {6, 7, 12, 11}, 650 {7, 8, 13, 12}, 651 {8, 9, 14, 13}, 652 {10, 11, 12, 15}, 653 {12, 13, 14, 15} 654 }; 655 for (i = 0; i < numCells; i++) 656 for (j = 0; j < 4; j++) cells[i][j] = cells2[i][j]; 657 PetscCall(PetscMalloc2(numVerts * 2, &flatCoords, numCells * 4, &flatCells)); 658 { 659 PetscReal(*coords)[2] = (PetscReal(*)[2])flatCoords; 660 for (j = 0; j < numVerts - 1; j++) { 661 PetscReal z, r, theta = -PETSC_PI / 2 + (j % 5) * PETSC_PI / 4; 662 PetscReal rad = ctx->radius[grid]; 663 z = rad * PetscSinReal(theta); 664 coords[j][1] = z; 665 r = rad * PetscCosReal(theta); 666 coords[j][0] = r; 667 } 668 coords[numVerts - 1][0] = coords[numVerts - 1][1] = 0; 669 } 670 for (j = 0, pcell = flatCells; j < numCells; j++, pcell += 4) { 671 pcell[0] = cells[j][0]; 672 pcell[1] = cells[j][1]; 673 pcell[2] = cells[j][2]; 674 pcell[3] = cells[j][3]; 675 } 676 PetscCall(DMPlexCreateFromCellListPetsc(comm_self, 2, numCells, numVerts, 4, ctx->interpolate, flatCells, 2, flatCoords, &ctx->plex[grid])); 677 PetscCall(PetscFree2(flatCoords, flatCells)); 678 PetscCall(PetscObjectSetName((PetscObject)ctx->plex[grid], "semi-circle")); 679 } else SETERRQ(ctx->comm, PETSC_ERR_PLIB, "Velocity space meshes does not support cubed sphere"); 680 681 PetscCall(DMSetFromOptions(ctx->plex[grid])); 682 } // grid loop 683 PetscCall(PetscObjectSetOptionsPrefix((PetscObject)pack, prefix)); 684 685 { /* convert to p4est (or whatever), wait for discretization to create pack */ 686 char convType[256]; 687 PetscBool flg; 688 689 PetscOptionsBegin(ctx->comm, prefix, "Mesh conversion options", "DMPLEX"); 690 PetscCall(PetscOptionsFList("-dm_landau_type", "Convert DMPlex to another format (p4est)", "plexland.c", DMList, DMPLEX, convType, 256, &flg)); 691 PetscOptionsEnd(); 692 if (flg) { 693 ctx->use_p4est = PETSC_TRUE; /* flag for Forest */ 694 for (PetscInt grid = 0; grid < ctx->num_grids; grid++) { 695 DM dmforest; 696 PetscCall(DMConvert(ctx->plex[grid], convType, &dmforest)); 697 if (dmforest) { 698 PetscBool isForest; 699 PetscCall(PetscObjectSetOptionsPrefix((PetscObject)dmforest, prefix)); 700 PetscCall(DMIsForest(dmforest, &isForest)); 701 if (isForest) { 702 if (ctx->sphere) PetscCall(DMForestSetBaseCoordinateMapping(dmforest, GeometryDMLandau, ctx)); 703 PetscCall(DMDestroy(&ctx->plex[grid])); 704 ctx->plex[grid] = dmforest; // Forest for adaptivity 705 } else SETERRQ(ctx->comm, PETSC_ERR_PLIB, "Converted to non Forest?"); 706 } else SETERRQ(ctx->comm, PETSC_ERR_PLIB, "Convert failed?"); 707 } 708 } else ctx->use_p4est = PETSC_FALSE; /* flag for Forest */ 709 } 710 } /* non-file */ 711 PetscCall(DMSetDimension(pack, dim)); 712 PetscCall(PetscObjectSetName((PetscObject)pack, "Mesh")); 713 PetscCall(DMSetApplicationContext(pack, ctx)); 714 715 PetscFunctionReturn(PETSC_SUCCESS); 716 } 717 718 static PetscErrorCode SetupDS(DM pack, PetscInt dim, PetscInt grid, LandauCtx *ctx) 719 { 720 PetscInt ii, i0; 721 char buf[256]; 722 PetscSection section; 723 724 PetscFunctionBegin; 725 for (ii = ctx->species_offset[grid], i0 = 0; ii < ctx->species_offset[grid + 1]; ii++, i0++) { 726 if (ii == 0) PetscCall(PetscSNPrintf(buf, sizeof(buf), "e")); 727 else PetscCall(PetscSNPrintf(buf, sizeof(buf), "i%" PetscInt_FMT, ii)); 728 /* Setup Discretization - FEM */ 729 PetscCall(PetscFECreateDefault(PETSC_COMM_SELF, dim, 1, PETSC_FALSE, NULL, PETSC_DECIDE, &ctx->fe[ii])); 730 PetscCall(PetscObjectSetName((PetscObject)ctx->fe[ii], buf)); 731 PetscCall(DMSetField(ctx->plex[grid], i0, NULL, (PetscObject)ctx->fe[ii])); 732 } 733 PetscCall(DMCreateDS(ctx->plex[grid])); 734 PetscCall(DMGetSection(ctx->plex[grid], §ion)); 735 for (PetscInt ii = ctx->species_offset[grid], i0 = 0; ii < ctx->species_offset[grid + 1]; ii++, i0++) { 736 if (ii == 0) PetscCall(PetscSNPrintf(buf, sizeof(buf), "se")); 737 else PetscCall(PetscSNPrintf(buf, sizeof(buf), "si%" PetscInt_FMT, ii)); 738 PetscCall(PetscSectionSetComponentName(section, i0, 0, buf)); 739 } 740 PetscFunctionReturn(PETSC_SUCCESS); 741 } 742 743 /* Define a Maxwellian function for testing out the operator. */ 744 745 /* Using cartesian velocity space coordinates, the particle */ 746 /* density, [1/m^3], is defined according to */ 747 748 /* $$ n=\int_{R^3} dv^3 \left(\frac{m}{2\pi T}\right)^{3/2}\exp [- mv^2/(2T)] $$ */ 749 750 /* Using some constant, c, we normalize the velocity vector into a */ 751 /* dimensionless variable according to v=c*x. Thus the density, $n$, becomes */ 752 753 /* $$ n=\int_{R^3} dx^3 \left(\frac{mc^2}{2\pi T}\right)^{3/2}\exp [- mc^2/(2T)*x^2] $$ */ 754 755 /* Defining $\theta=2T/mc^2$, we thus find that the probability density */ 756 /* for finding the particle within the interval in a box dx^3 around x is */ 757 758 /* f(x;\theta)=\left(\frac{1}{\pi\theta}\right)^{3/2} \exp [ -x^2/\theta ] */ 759 760 typedef struct { 761 PetscReal v_0; 762 PetscReal kT_m; 763 PetscReal n; 764 PetscReal shift; 765 } MaxwellianCtx; 766 767 static PetscErrorCode maxwellian(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf_dummy, PetscScalar *u, void *actx) 768 { 769 MaxwellianCtx *mctx = (MaxwellianCtx *)actx; 770 PetscInt i; 771 PetscReal v2 = 0, theta = 2 * mctx->kT_m / (mctx->v_0 * mctx->v_0), shift; /* theta = 2kT/mc^2 */ 772 PetscFunctionBegin; 773 /* compute the exponents, v^2 */ 774 for (i = 0; i < dim; ++i) v2 += x[i] * x[i]; 775 /* evaluate the Maxwellian */ 776 if (mctx->shift < 0) shift = -mctx->shift; 777 else { 778 u[0] = mctx->n * PetscPowReal(PETSC_PI * theta, -1.5) * (PetscExpReal(-v2 / theta)); 779 shift = mctx->shift; 780 } 781 if (shift != 0.) { 782 v2 = 0; 783 for (i = 0; i < dim - 1; ++i) v2 += x[i] * x[i]; 784 v2 += (x[dim - 1] - shift) * (x[dim - 1] - shift); 785 /* evaluate the shifted Maxwellian */ 786 u[0] += mctx->n * PetscPowReal(PETSC_PI * theta, -1.5) * (PetscExpReal(-v2 / theta)); 787 } 788 PetscFunctionReturn(PETSC_SUCCESS); 789 } 790 791 /*@ 792 DMPlexLandauAddMaxwellians - Add a Maxwellian distribution to a state 793 794 Collective 795 796 Input Parameters: 797 . dm - The mesh (local) 798 + time - Current time 799 - temps - Temperatures of each species (global) 800 . ns - Number density of each species (global) 801 - grid - index into current grid - just used for offset into temp and ns 802 . b_id - batch index 803 - n_batch - number of batches 804 + actx - Landau context 805 806 Output Parameter: 807 . X - The state (local to this grid) 808 809 Level: beginner 810 811 .keywords: mesh 812 .seealso: `DMPlexLandauCreateVelocitySpace()` 813 @*/ 814 PetscErrorCode DMPlexLandauAddMaxwellians(DM dm, Vec X, PetscReal time, PetscReal temps[], PetscReal ns[], PetscInt grid, PetscInt b_id, PetscInt n_batch, void *actx) 815 { 816 LandauCtx *ctx = (LandauCtx *)actx; 817 PetscErrorCode (*initu[LANDAU_MAX_SPECIES])(PetscInt, PetscReal, const PetscReal[], PetscInt, PetscScalar[], void *); 818 PetscInt dim; 819 MaxwellianCtx *mctxs[LANDAU_MAX_SPECIES], data[LANDAU_MAX_SPECIES]; 820 821 PetscFunctionBegin; 822 PetscCall(DMGetDimension(dm, &dim)); 823 if (!ctx) PetscCall(DMGetApplicationContext(dm, &ctx)); 824 for (PetscInt ii = ctx->species_offset[grid], i0 = 0; ii < ctx->species_offset[grid + 1]; ii++, i0++) { 825 mctxs[i0] = &data[i0]; 826 data[i0].v_0 = ctx->v_0; // v_0 same for all grids 827 data[i0].kT_m = ctx->k * temps[ii] / ctx->masses[ii]; /* kT/m */ 828 data[i0].n = ns[ii]; 829 initu[i0] = maxwellian; 830 data[i0].shift = 0; 831 } 832 data[0].shift = ctx->electronShift; 833 /* need to make ADD_ALL_VALUES work - TODO */ 834 PetscCall(DMProjectFunction(dm, time, initu, (void **)mctxs, INSERT_ALL_VALUES, X)); 835 PetscFunctionReturn(PETSC_SUCCESS); 836 } 837 838 /* 839 LandauSetInitialCondition - Addes Maxwellians with context 840 841 Collective 842 843 Input Parameters: 844 . dm - The mesh 845 - grid - index into current grid - just used for offset into temp and ns 846 . b_id - batch index 847 - n_batch - number of batches 848 + actx - Landau context with T and n 849 850 Output Parameter: 851 . X - The state 852 853 Level: beginner 854 855 .keywords: mesh 856 .seealso: `DMPlexLandauCreateVelocitySpace()`, `DMPlexLandauAddMaxwellians()` 857 */ 858 static PetscErrorCode LandauSetInitialCondition(DM dm, Vec X, PetscInt grid, PetscInt b_id, PetscInt n_batch, void *actx) 859 { 860 LandauCtx *ctx = (LandauCtx *)actx; 861 PetscFunctionBegin; 862 if (!ctx) PetscCall(DMGetApplicationContext(dm, &ctx)); 863 PetscCall(VecZeroEntries(X)); 864 PetscCall(DMPlexLandauAddMaxwellians(dm, X, 0.0, ctx->thermal_temps, ctx->n, grid, b_id, n_batch, ctx)); 865 PetscFunctionReturn(PETSC_SUCCESS); 866 } 867 868 // adapt a level once. Forest in/out 869 static const char *s_refine_names[] = {"RE", "Z1", "Origin", "Z2", "Uniform"}; 870 static PetscErrorCode adaptToleranceFEM(PetscFE fem, Vec sol, PetscInt type, PetscInt grid, LandauCtx *ctx, DM *newForest) 871 { 872 DM forest, plex, adaptedDM = NULL; 873 PetscDS prob; 874 PetscBool isForest; 875 PetscQuadrature quad; 876 PetscInt Nq, *Nb, cStart, cEnd, c, dim, qj, k; 877 DMLabel adaptLabel = NULL; 878 879 PetscFunctionBegin; 880 forest = ctx->plex[grid]; 881 PetscCall(DMCreateDS(forest)); 882 PetscCall(DMGetDS(forest, &prob)); 883 PetscCall(DMGetDimension(forest, &dim)); 884 PetscCall(DMIsForest(forest, &isForest)); 885 PetscCheck(isForest, ctx->comm, PETSC_ERR_ARG_WRONG, "! Forest"); 886 PetscCall(DMConvert(forest, DMPLEX, &plex)); 887 PetscCall(DMPlexGetHeightStratum(plex, 0, &cStart, &cEnd)); 888 PetscCall(DMLabelCreate(PETSC_COMM_SELF, "adapt", &adaptLabel)); 889 PetscCall(PetscFEGetQuadrature(fem, &quad)); 890 PetscCall(PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, NULL)); 891 PetscCheck(Nq <= LANDAU_MAX_NQ, ctx->comm, PETSC_ERR_ARG_WRONG, "Order too high. Nq = %" PetscInt_FMT " > LANDAU_MAX_NQ (%d)", Nq, LANDAU_MAX_NQ); 892 PetscCall(PetscDSGetDimensions(prob, &Nb)); 893 PetscCall(PetscInfo(sol, "%" PetscInt_FMT ") Refine phase: %s\n", grid, s_refine_names[type])); 894 if (type == 4) { 895 for (c = cStart; c < cEnd; c++) PetscCall(DMLabelSetValue(adaptLabel, c, DM_ADAPT_REFINE)); 896 } else if (type == 2) { 897 PetscInt rCellIdx[8], nr = 0, nrmax = (dim == 3) ? 8 : 2; 898 PetscReal minRad = PETSC_INFINITY, r; 899 for (c = cStart; c < cEnd; c++) { 900 PetscReal tt, v0[LANDAU_MAX_NQ * 3], detJ[LANDAU_MAX_NQ]; 901 PetscCall(DMPlexComputeCellGeometryFEM(plex, c, quad, v0, NULL, NULL, detJ)); 902 for (qj = 0; qj < Nq; ++qj) { 903 tt = PetscSqr(v0[dim * qj + 0]) + PetscSqr(v0[dim * qj + 1]) + PetscSqr(((dim == 3) ? v0[dim * qj + 2] : 0)); 904 r = PetscSqrtReal(tt); 905 if (r < minRad - PETSC_SQRT_MACHINE_EPSILON * 10.) { 906 minRad = r; 907 nr = 0; 908 rCellIdx[nr++] = c; 909 PetscCall(PetscInfo(sol, "\t\t%" PetscInt_FMT ") Found first inner r=%e, cell %" PetscInt_FMT ", qp %" PetscInt_FMT "/%" PetscInt_FMT "\n", grid, (double)r, c, qj + 1, Nq)); 910 } else if ((r - minRad) < PETSC_SQRT_MACHINE_EPSILON * 100. && nr < nrmax) { 911 for (k = 0; k < nr; k++) 912 if (c == rCellIdx[k]) break; 913 if (k == nr) { 914 rCellIdx[nr++] = c; 915 PetscCall(PetscInfo(sol, "\t\t\t%" PetscInt_FMT ") Found another inner r=%e, cell %" PetscInt_FMT ", qp %" PetscInt_FMT "/%" PetscInt_FMT ", d=%e\n", grid, (double)r, c, qj + 1, Nq, (double)(r - minRad))); 916 } 917 } 918 } 919 } 920 for (k = 0; k < nr; k++) PetscCall(DMLabelSetValue(adaptLabel, rCellIdx[k], DM_ADAPT_REFINE)); 921 PetscCall(PetscInfo(sol, "\t\t\t%" PetscInt_FMT ") Refined %" PetscInt_FMT " origin cells %" PetscInt_FMT ",%" PetscInt_FMT " r=%g\n", grid, nr, rCellIdx[0], rCellIdx[1], (double)minRad)); 922 } else if (type == 0 || type == 1 || type == 3) { /* refine along r=0 axis */ 923 PetscScalar *coef = NULL; 924 Vec coords; 925 PetscInt csize, Nv, d, nz, nrefined = 0; 926 DM cdm; 927 PetscSection cs; 928 PetscCall(DMGetCoordinatesLocal(forest, &coords)); 929 PetscCall(DMGetCoordinateDM(forest, &cdm)); 930 PetscCall(DMGetLocalSection(cdm, &cs)); 931 for (c = cStart; c < cEnd; c++) { 932 PetscInt doit = 0, outside = 0; 933 PetscCall(DMPlexVecGetClosure(cdm, cs, coords, c, &csize, &coef)); 934 Nv = csize / dim; 935 for (nz = d = 0; d < Nv; d++) { 936 PetscReal z = PetscRealPart(coef[d * dim + (dim - 1)]), x = PetscSqr(PetscRealPart(coef[d * dim + 0])) + ((dim == 3) ? PetscSqr(PetscRealPart(coef[d * dim + 1])) : 0); 937 x = PetscSqrtReal(x); 938 if (type == 0) { 939 if (ctx->re_radius > PETSC_SQRT_MACHINE_EPSILON && (z < -PETSC_MACHINE_EPSILON * 10. || z > ctx->re_radius + PETSC_MACHINE_EPSILON * 10.)) outside++; /* first pass don't refine bottom */ 940 } else if (type == 1 && (z > ctx->vperp0_radius1 || z < -ctx->vperp0_radius1)) { 941 outside++; /* don't refine outside electron refine radius */ 942 PetscCall(PetscInfo(sol, "\t%" PetscInt_FMT ") (debug) found %s cells\n", grid, s_refine_names[type])); 943 } else if (type == 3 && (z > ctx->vperp0_radius2 || z < -ctx->vperp0_radius2)) { 944 outside++; /* refine r=0 cells on refinement front */ 945 PetscCall(PetscInfo(sol, "\t%" PetscInt_FMT ") (debug) found %s cells\n", grid, s_refine_names[type])); 946 } 947 if (x < PETSC_MACHINE_EPSILON * 10. && (type != 0 || ctx->re_radius > PETSC_SQRT_MACHINE_EPSILON)) nz++; 948 } 949 PetscCall(DMPlexVecRestoreClosure(cdm, cs, coords, c, &csize, &coef)); 950 if (doit || (outside < Nv && nz)) { 951 PetscCall(DMLabelSetValue(adaptLabel, c, DM_ADAPT_REFINE)); 952 nrefined++; 953 } 954 } 955 PetscCall(PetscInfo(sol, "\t%" PetscInt_FMT ") Refined %" PetscInt_FMT " cells\n", grid, nrefined)); 956 } 957 PetscCall(DMDestroy(&plex)); 958 PetscCall(DMAdaptLabel(forest, adaptLabel, &adaptedDM)); 959 PetscCall(DMLabelDestroy(&adaptLabel)); 960 *newForest = adaptedDM; 961 if (adaptedDM) { 962 if (isForest) { 963 PetscCall(DMForestSetAdaptivityForest(adaptedDM, NULL)); // ???? 964 } 965 PetscCall(DMConvert(adaptedDM, DMPLEX, &plex)); 966 PetscCall(DMPlexGetHeightStratum(plex, 0, &cStart, &cEnd)); 967 PetscCall(PetscInfo(sol, "\t\t\t\t%" PetscInt_FMT ") %" PetscInt_FMT " cells, %" PetscInt_FMT " total quadrature points\n", grid, cEnd - cStart, Nq * (cEnd - cStart))); 968 PetscCall(DMDestroy(&plex)); 969 } else *newForest = NULL; 970 PetscFunctionReturn(PETSC_SUCCESS); 971 } 972 973 // forest goes in (ctx->plex[grid]), plex comes out 974 static PetscErrorCode adapt(PetscInt grid, LandauCtx *ctx, Vec *uu) 975 { 976 PetscInt adaptIter; 977 978 PetscFunctionBegin; 979 PetscInt type, limits[5] = {(grid == 0) ? ctx->numRERefine : 0, (grid == 0) ? ctx->nZRefine1 : 0, ctx->numAMRRefine[grid], (grid == 0) ? ctx->nZRefine2 : 0, ctx->postAMRRefine[grid]}; 980 for (type = 0; type < 5; type++) { 981 for (adaptIter = 0; adaptIter < limits[type]; adaptIter++) { 982 DM newForest = NULL; 983 PetscCall(adaptToleranceFEM(ctx->fe[0], *uu, type, grid, ctx, &newForest)); 984 if (newForest) { 985 PetscCall(DMDestroy(&ctx->plex[grid])); 986 PetscCall(VecDestroy(uu)); 987 PetscCall(DMCreateGlobalVector(newForest, uu)); 988 PetscCall(PetscObjectSetName((PetscObject)*uu, "uAMR")); 989 PetscCall(LandauSetInitialCondition(newForest, *uu, grid, 0, 1, ctx)); 990 ctx->plex[grid] = newForest; 991 } else { 992 PetscCall(PetscInfo(*uu, "No refinement\n")); 993 } 994 } 995 } 996 PetscFunctionReturn(PETSC_SUCCESS); 997 } 998 999 // make log(Lambdas) from NRL Plasma formulary 1000 static PetscErrorCode makeLambdas(LandauCtx *ctx) 1001 { 1002 PetscFunctionBegin; 1003 for (PetscInt gridi = 0; gridi < ctx->num_grids; gridi++) { 1004 int iii = ctx->species_offset[gridi]; 1005 PetscReal Ti_ev = (ctx->thermal_temps[iii] / 1.1604525e7) * 1000; // convert (back) to eV 1006 PetscReal ni = ctx->n[iii] * ctx->n_0; 1007 for (PetscInt gridj = gridi; gridj < ctx->num_grids; gridj++) { 1008 PetscInt jjj = ctx->species_offset[gridj]; 1009 PetscReal Zj = ctx->charges[jjj] / 1.6022e-19; 1010 if (gridi == 0) { 1011 if (gridj == 0) { // lam_ee 1012 ctx->lambdas[gridi][gridj] = 23.5 - PetscLogReal(PetscSqrtReal(ni) * PetscPowReal(Ti_ev, -1.25)) - PetscSqrtReal(1e-5 + PetscSqr(PetscLogReal(Ti_ev) - 2) / 16); 1013 } else { // lam_ei == lam_ie 1014 if (10 * Zj * Zj > Ti_ev) { 1015 ctx->lambdas[gridi][gridj] = ctx->lambdas[gridj][gridi] = 23 - PetscLogReal(PetscSqrtReal(ni) * Zj * PetscPowReal(Ti_ev, -1.5)); 1016 } else { 1017 ctx->lambdas[gridi][gridj] = ctx->lambdas[gridj][gridi] = 24 - PetscLogReal(PetscSqrtReal(ni) / Ti_ev); 1018 } 1019 } 1020 } else { // lam_ii' 1021 PetscReal mui = ctx->masses[iii] / 1.6720e-27, Zi = ctx->charges[iii] / 1.6022e-19; 1022 PetscReal Tj_ev = (ctx->thermal_temps[jjj] / 1.1604525e7) * 1000; // convert (back) to eV 1023 PetscReal muj = ctx->masses[jjj] / 1.6720e-27; 1024 PetscReal nj = ctx->n[jjj] * ctx->n_0; 1025 ctx->lambdas[gridi][gridj] = ctx->lambdas[gridj][gridi] = 23 - PetscLogReal(Zi * Zj * (mui + muj) / (mui * Tj_ev + muj * Ti_ev) * PetscSqrtReal(ni * Zi * Zi / Ti_ev + nj * Zj * Zj / Tj_ev)); 1026 } 1027 } 1028 } 1029 //PetscReal v0 = PetscSqrtReal(ctx->k * ctx->thermal_temps[iii] / ctx->masses[iii]); /* arbitrary units for non-dimensionalization: plasma formulary def */ 1030 PetscFunctionReturn(PETSC_SUCCESS); 1031 } 1032 1033 static PetscErrorCode ProcessOptions(LandauCtx *ctx, const char prefix[]) 1034 { 1035 PetscBool flg, sph_flg; 1036 PetscInt ii, nt, nm, nc, num_species_grid[LANDAU_MAX_GRIDS], non_dim_grid; 1037 PetscReal v0_grid[LANDAU_MAX_GRIDS], lnLam = 10; 1038 DM dummy; 1039 1040 PetscFunctionBegin; 1041 PetscCall(DMCreate(ctx->comm, &dummy)); 1042 /* get options - initialize context */ 1043 ctx->verbose = 1; // should be 0 for silent compliance 1044 #if defined(PETSC_HAVE_THREADSAFETY) && defined(PETSC_HAVE_OPENMP) 1045 ctx->batch_sz = PetscNumOMPThreads; 1046 #else 1047 ctx->batch_sz = 1; 1048 #endif 1049 ctx->batch_view_idx = 0; 1050 ctx->interpolate = PETSC_TRUE; 1051 ctx->gpu_assembly = PETSC_TRUE; 1052 ctx->norm_state = 0; 1053 ctx->electronShift = 0; 1054 ctx->M = NULL; 1055 ctx->J = NULL; 1056 /* geometry and grids */ 1057 ctx->sphere = PETSC_FALSE; 1058 ctx->use_p4est = PETSC_FALSE; 1059 for (PetscInt grid = 0; grid < LANDAU_MAX_GRIDS; grid++) { 1060 ctx->radius[grid] = 5.; /* thermal radius (velocity) */ 1061 ctx->radius_perp[grid] = 5.; /* thermal radius (velocity) */ 1062 ctx->radius_par[grid] = 5.; /* thermal radius (velocity) */ 1063 ctx->numAMRRefine[grid] = 0; 1064 ctx->postAMRRefine[grid] = 0; 1065 ctx->species_offset[grid + 1] = 1; // one species default 1066 num_species_grid[grid] = 0; 1067 ctx->plex[grid] = NULL; /* cache as expensive to Convert */ 1068 } 1069 ctx->species_offset[0] = 0; 1070 ctx->re_radius = 0.; 1071 ctx->vperp0_radius1 = 0; 1072 ctx->vperp0_radius2 = 0; 1073 ctx->nZRefine1 = 0; 1074 ctx->nZRefine2 = 0; 1075 ctx->numRERefine = 0; 1076 num_species_grid[0] = 1; // one species default 1077 /* species - [0] electrons, [1] one ion species eg, duetarium, [2] heavy impurity ion, ... */ 1078 ctx->charges[0] = -1; /* electron charge (MKS) */ 1079 ctx->masses[0] = 1 / 1835.469965278441013; /* temporary value in proton mass */ 1080 ctx->n[0] = 1; 1081 ctx->v_0 = 1; /* thermal velocity, we could start with a scale != 1 */ 1082 ctx->thermal_temps[0] = 1; 1083 /* constants, etc. */ 1084 ctx->epsilon0 = 8.8542e-12; /* permittivity of free space (MKS) F/m */ 1085 ctx->k = 1.38064852e-23; /* Boltzmann constant (MKS) J/K */ 1086 ctx->n_0 = 1.e20; /* typical plasma n, but could set it to 1 */ 1087 ctx->Ez = 0; 1088 for (PetscInt grid = 0; grid < LANDAU_NUM_TIMERS; grid++) ctx->times[grid] = 0; 1089 for (PetscInt ii = 0; ii < LANDAU_DIM; ii++) ctx->cells0[ii] = 2; 1090 if (LANDAU_DIM == 2) ctx->cells0[0] = 1; 1091 ctx->use_matrix_mass = PETSC_FALSE; 1092 ctx->use_relativistic_corrections = PETSC_FALSE; 1093 ctx->use_energy_tensor_trick = PETSC_FALSE; /* Use Eero's trick for energy conservation v --> grad(v^2/2) */ 1094 ctx->SData_d.w = NULL; 1095 ctx->SData_d.x = NULL; 1096 ctx->SData_d.y = NULL; 1097 ctx->SData_d.z = NULL; 1098 ctx->SData_d.invJ = NULL; 1099 ctx->jacobian_field_major_order = PETSC_FALSE; 1100 ctx->SData_d.coo_elem_offsets = NULL; 1101 ctx->SData_d.coo_elem_point_offsets = NULL; 1102 ctx->coo_assembly = PETSC_FALSE; 1103 ctx->SData_d.coo_elem_fullNb = NULL; 1104 ctx->SData_d.coo_size = 0; 1105 PetscOptionsBegin(ctx->comm, prefix, "Options for Fokker-Plank-Landau collision operator", "none"); 1106 { 1107 char opstring[256]; 1108 #if defined(PETSC_HAVE_KOKKOS_KERNELS) 1109 ctx->deviceType = LANDAU_KOKKOS; 1110 PetscCall(PetscStrncpy(opstring, "kokkos", sizeof(opstring))); 1111 #elif defined(PETSC_HAVE_CUDA) 1112 ctx->deviceType = LANDAU_CUDA; 1113 PetscCall(PetscStrncpy(opstring, "cuda", sizeof(opstring))); 1114 #else 1115 ctx->deviceType = LANDAU_CPU; 1116 PetscCall(PetscStrncpy(opstring, "cpu", sizeof(opstring))); 1117 #endif 1118 PetscCall(PetscOptionsString("-dm_landau_device_type", "Use kernels on 'cpu', 'cuda', or 'kokkos'", "plexland.c", opstring, opstring, sizeof(opstring), NULL)); 1119 PetscCall(PetscStrcmp("cpu", opstring, &flg)); 1120 if (flg) { 1121 ctx->deviceType = LANDAU_CPU; 1122 } else { 1123 PetscCall(PetscStrcmp("cuda", opstring, &flg)); 1124 if (flg) { 1125 ctx->deviceType = LANDAU_CUDA; 1126 } else { 1127 PetscCall(PetscStrcmp("kokkos", opstring, &flg)); 1128 if (flg) ctx->deviceType = LANDAU_KOKKOS; 1129 else SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONG, "-dm_landau_device_type %s", opstring); 1130 } 1131 } 1132 } 1133 PetscCall(PetscOptionsReal("-dm_landau_electron_shift", "Shift in thermal velocity of electrons", "none", ctx->electronShift, &ctx->electronShift, NULL)); 1134 PetscCall(PetscOptionsInt("-dm_landau_verbose", "Level of verbosity output", "plexland.c", ctx->verbose, &ctx->verbose, NULL)); 1135 PetscCall(PetscOptionsInt("-dm_landau_batch_size", "Number of 'vertices' to batch", "ex2.c", ctx->batch_sz, &ctx->batch_sz, NULL)); 1136 PetscCheck(LANDAU_MAX_BATCH_SZ >= ctx->batch_sz, ctx->comm, PETSC_ERR_ARG_WRONG, "LANDAU_MAX_BATCH_SZ %" PetscInt_FMT " < ctx->batch_sz %" PetscInt_FMT, (PetscInt)LANDAU_MAX_BATCH_SZ, ctx->batch_sz); 1137 PetscCall(PetscOptionsInt("-dm_landau_batch_view_idx", "Index of batch for diagnostics like plotting", "ex2.c", ctx->batch_view_idx, &ctx->batch_view_idx, NULL)); 1138 PetscCheck(ctx->batch_view_idx < ctx->batch_sz, ctx->comm, PETSC_ERR_ARG_WRONG, "-ctx->batch_view_idx %" PetscInt_FMT " > ctx->batch_sz %" PetscInt_FMT, ctx->batch_view_idx, ctx->batch_sz); 1139 PetscCall(PetscOptionsReal("-dm_landau_Ez", "Initial parallel electric field in unites of Conner-Hastie critical field", "plexland.c", ctx->Ez, &ctx->Ez, NULL)); 1140 PetscCall(PetscOptionsReal("-dm_landau_n_0", "Normalization constant for number density", "plexland.c", ctx->n_0, &ctx->n_0, NULL)); 1141 PetscCall(PetscOptionsBool("-dm_landau_use_mataxpy_mass", "Use fast but slightly fragile MATAXPY to add mass term", "plexland.c", ctx->use_matrix_mass, &ctx->use_matrix_mass, NULL)); 1142 PetscCall(PetscOptionsBool("-dm_landau_use_relativistic_corrections", "Use relativistic corrections", "plexland.c", ctx->use_relativistic_corrections, &ctx->use_relativistic_corrections, NULL)); 1143 if (LANDAU_DIM == 2 && ctx->use_relativistic_corrections) ctx->use_relativistic_corrections = PETSC_FALSE; // should warn 1144 PetscCall(PetscOptionsBool("-dm_landau_use_energy_tensor_trick", "Use Eero's trick of using grad(v^2/2) instead of v as args to Landau tensor to conserve energy with relativistic corrections and Q1 elements", "plexland.c", ctx->use_energy_tensor_trick, 1145 &ctx->use_energy_tensor_trick, NULL)); 1146 1147 /* get num species with temperature, set defaults */ 1148 for (ii = 1; ii < LANDAU_MAX_SPECIES; ii++) { 1149 ctx->thermal_temps[ii] = 1; 1150 ctx->charges[ii] = 1; 1151 ctx->masses[ii] = 1; 1152 ctx->n[ii] = 1; 1153 } 1154 nt = LANDAU_MAX_SPECIES; 1155 PetscCall(PetscOptionsRealArray("-dm_landau_thermal_temps", "Temperature of each species [e,i_0,i_1,...] in keV (must be set to set number of species)", "plexland.c", ctx->thermal_temps, &nt, &flg)); 1156 if (flg) { 1157 PetscCall(PetscInfo(dummy, "num_species set to number of thermal temps provided (%" PetscInt_FMT ")\n", nt)); 1158 ctx->num_species = nt; 1159 } else SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONG, "-dm_landau_thermal_temps ,t1,t2,.. must be provided to set the number of species"); 1160 for (ii = 0; ii < ctx->num_species; ii++) ctx->thermal_temps[ii] *= 1.1604525e7; /* convert to Kelvin */ 1161 nm = LANDAU_MAX_SPECIES - 1; 1162 PetscCall(PetscOptionsRealArray("-dm_landau_ion_masses", "Mass of each species in units of proton mass [i_0=2,i_1=40...]", "plexland.c", &ctx->masses[1], &nm, &flg)); 1163 PetscCheck(!flg || nm == ctx->num_species - 1, ctx->comm, PETSC_ERR_ARG_WRONG, "num ion masses %" PetscInt_FMT " != num species %" PetscInt_FMT, nm, ctx->num_species - 1); 1164 nm = LANDAU_MAX_SPECIES; 1165 PetscCall(PetscOptionsRealArray("-dm_landau_n", "Number density of each species = n_s * n_0", "plexland.c", ctx->n, &nm, &flg)); 1166 PetscCheck(!flg || nm == ctx->num_species, ctx->comm, PETSC_ERR_ARG_WRONG, "wrong num n: %" PetscInt_FMT " != num species %" PetscInt_FMT, nm, ctx->num_species); 1167 for (ii = 0; ii < LANDAU_MAX_SPECIES; ii++) ctx->masses[ii] *= 1.6720e-27; /* scale by proton mass kg */ 1168 ctx->masses[0] = 9.10938356e-31; /* electron mass kg (should be about right already) */ 1169 nc = LANDAU_MAX_SPECIES - 1; 1170 PetscCall(PetscOptionsRealArray("-dm_landau_ion_charges", "Charge of each species in units of proton charge [i_0=2,i_1=18,...]", "plexland.c", &ctx->charges[1], &nc, &flg)); 1171 if (flg) PetscCheck(nc == ctx->num_species - 1, ctx->comm, PETSC_ERR_ARG_WRONG, "num charges %" PetscInt_FMT " != num species %" PetscInt_FMT, nc, ctx->num_species - 1); 1172 for (ii = 0; ii < LANDAU_MAX_SPECIES; ii++) ctx->charges[ii] *= 1.6022e-19; /* electron/proton charge (MKS) */ 1173 /* geometry and grids */ 1174 nt = LANDAU_MAX_GRIDS; 1175 PetscCall(PetscOptionsIntArray("-dm_landau_num_species_grid", "Number of species on each grid: [ 1, ....] or [S, 0 ....] for single grid", "plexland.c", num_species_grid, &nt, &flg)); 1176 if (flg) { 1177 ctx->num_grids = nt; 1178 for (ii = nt = 0; ii < ctx->num_grids; ii++) nt += num_species_grid[ii]; 1179 PetscCheck(ctx->num_species == nt, ctx->comm, PETSC_ERR_ARG_WRONG, "-dm_landau_num_species_grid: sum %" PetscInt_FMT " != num_species = %" PetscInt_FMT ". %" PetscInt_FMT " grids (check that number of grids <= LANDAU_MAX_GRIDS = %d)", nt, ctx->num_species, 1180 ctx->num_grids, LANDAU_MAX_GRIDS); 1181 } else { 1182 ctx->num_grids = 1; // go back to a single grid run 1183 num_species_grid[0] = ctx->num_species; 1184 } 1185 for (ctx->species_offset[0] = ii = 0; ii < ctx->num_grids; ii++) ctx->species_offset[ii + 1] = ctx->species_offset[ii] + num_species_grid[ii]; 1186 PetscCheck(ctx->species_offset[ctx->num_grids] == ctx->num_species, ctx->comm, PETSC_ERR_ARG_WRONG, "ctx->species_offset[ctx->num_grids] %" PetscInt_FMT " != ctx->num_species = %" PetscInt_FMT " ???????????", ctx->species_offset[ctx->num_grids], 1187 ctx->num_species); 1188 for (PetscInt grid = 0; grid < ctx->num_grids; grid++) { 1189 int iii = ctx->species_offset[grid]; // normalize with first (arbitrary) species on grid 1190 v0_grid[grid] = PetscSqrtReal(ctx->k * ctx->thermal_temps[iii] / ctx->masses[iii]); /* arbitrary units for non-dimensionalization: plasma formulary def */ 1191 } 1192 // get lambdas here because we need them for t_0 etc 1193 PetscCall(PetscOptionsReal("-dm_landau_ln_lambda", "Universal cross section parameter. Default uses NRL formulas", "plexland.c", lnLam, &lnLam, &flg)); 1194 if (flg) { 1195 for (PetscInt grid = 0; grid < LANDAU_MAX_GRIDS; grid++) { 1196 for (PetscInt gridj = 0; gridj < LANDAU_MAX_GRIDS; gridj++) ctx->lambdas[gridj][grid] = lnLam; /* cross section ratio large - small angle collisions */ 1197 } 1198 } else { 1199 PetscCall(makeLambdas(ctx)); 1200 } 1201 non_dim_grid = 0; 1202 PetscCall(PetscOptionsInt("-dm_landau_normalization_grid", "Index of grid to use for setting v_0, m_0, t_0. (Not recommended)", "plexland.c", non_dim_grid, &non_dim_grid, &flg)); 1203 if (non_dim_grid != 0) PetscCall(PetscInfo(dummy, "Normalization grid set to %" PetscInt_FMT ", but non-default not well verified\n", non_dim_grid)); 1204 PetscCheck(non_dim_grid >= 0 && non_dim_grid < ctx->num_species, ctx->comm, PETSC_ERR_ARG_WRONG, "Normalization grid wrong: %" PetscInt_FMT, non_dim_grid); 1205 ctx->v_0 = v0_grid[non_dim_grid]; /* arbitrary units for non dimensionalization: global mean velocity in 1D of electrons */ 1206 ctx->m_0 = ctx->masses[non_dim_grid]; /* arbitrary reference mass, electrons */ 1207 ctx->t_0 = 8 * PETSC_PI * PetscSqr(ctx->epsilon0 * ctx->m_0 / PetscSqr(ctx->charges[non_dim_grid])) / ctx->lambdas[non_dim_grid][non_dim_grid] / ctx->n_0 * PetscPowReal(ctx->v_0, 3); /* note, this t_0 makes nu[non_dim_grid,non_dim_grid]=1 */ 1208 /* domain */ 1209 nt = LANDAU_MAX_GRIDS; 1210 PetscCall(PetscOptionsRealArray("-dm_landau_domain_radius", "Phase space size in units of thermal velocity of grid", "plexland.c", ctx->radius, &nt, &flg)); 1211 if (flg) { 1212 PetscCheck(nt >= ctx->num_grids, ctx->comm, PETSC_ERR_ARG_WRONG, "-dm_landau_domain_radius: given %" PetscInt_FMT " radius != number grids %" PetscInt_FMT, nt, ctx->num_grids); 1213 while (nt--) ctx->radius_par[nt] = ctx->radius_perp[nt] = ctx->radius[nt]; 1214 } else { 1215 nt = LANDAU_MAX_GRIDS; 1216 PetscCall(PetscOptionsRealArray("-dm_landau_domain_max_par", "Parallel velocity domain size in units of thermal velocity of grid", "plexland.c", ctx->radius_par, &nt, &flg)); 1217 if (flg) PetscCheck(nt >= ctx->num_grids, ctx->comm, PETSC_ERR_ARG_WRONG, "-dm_landau_domain_max_par: given %" PetscInt_FMT " radius != number grids %" PetscInt_FMT, nt, ctx->num_grids); 1218 PetscCall(PetscOptionsRealArray("-dm_landau_domain_max_perp", "Perpendicular velocity domain size in units of thermal velocity of grid", "plexland.c", ctx->radius_perp, &nt, &flg)); 1219 if (flg) PetscCheck(nt >= ctx->num_grids, ctx->comm, PETSC_ERR_ARG_WRONG, "-dm_landau_domain_max_perp: given %" PetscInt_FMT " radius != number grids %" PetscInt_FMT, nt, ctx->num_grids); 1220 } 1221 for (PetscInt grid = 0; grid < ctx->num_grids; grid++) { 1222 if (flg && ctx->radius[grid] <= 0) { /* negative is ratio of c - need to set par and perp with this -- todo */ 1223 if (ctx->radius[grid] == 0) ctx->radius[grid] = 0.75; 1224 else ctx->radius[grid] = -ctx->radius[grid]; 1225 ctx->radius[grid] = ctx->radius[grid] * SPEED_OF_LIGHT / ctx->v_0; // use any species on grid to normalize (v_0 same for all on grid) 1226 PetscCall(PetscInfo(dummy, "Change domain radius to %g for grid %" PetscInt_FMT "\n", (double)ctx->radius[grid], grid)); 1227 } 1228 ctx->radius[grid] *= v0_grid[grid] / ctx->v_0; // scale domain by thermal radius relative to v_0 1229 ctx->radius_perp[grid] *= v0_grid[grid] / ctx->v_0; // scale domain by thermal radius relative to v_0 1230 ctx->radius_par[grid] *= v0_grid[grid] / ctx->v_0; // scale domain by thermal radius relative to v_0 1231 } 1232 /* amr parameters */ 1233 nt = LANDAU_DIM; 1234 PetscCall(PetscOptionsIntArray("-dm_landau_num_cells", "Number of cells in each dimension of base grid", "plexland.c", ctx->cells0, &nt, &flg)); 1235 nt = LANDAU_MAX_GRIDS; 1236 PetscCall(PetscOptionsIntArray("-dm_landau_amr_levels_max", "Number of AMR levels of refinement around origin, after (RE) refinements along z", "plexland.c", ctx->numAMRRefine, &nt, &flg)); 1237 PetscCheck(!flg || nt >= ctx->num_grids, ctx->comm, PETSC_ERR_ARG_WRONG, "-dm_landau_amr_levels_max: given %" PetscInt_FMT " != number grids %" PetscInt_FMT, nt, ctx->num_grids); 1238 nt = LANDAU_MAX_GRIDS; 1239 PetscCall(PetscOptionsIntArray("-dm_landau_amr_post_refine", "Number of levels to uniformly refine after AMR", "plexland.c", ctx->postAMRRefine, &nt, &flg)); 1240 for (ii = 1; ii < ctx->num_grids; ii++) ctx->postAMRRefine[ii] = ctx->postAMRRefine[0]; // all grids the same now 1241 PetscCall(PetscOptionsInt("-dm_landau_amr_re_levels", "Number of levels to refine along v_perp=0, z>0", "plexland.c", ctx->numRERefine, &ctx->numRERefine, &flg)); 1242 PetscCall(PetscOptionsInt("-dm_landau_amr_z_refine_pre", "Number of levels to refine along v_perp=0 before origin refine", "plexland.c", ctx->nZRefine1, &ctx->nZRefine1, &flg)); 1243 PetscCall(PetscOptionsInt("-dm_landau_amr_z_refine_post", "Number of levels to refine along v_perp=0 after origin refine", "plexland.c", ctx->nZRefine2, &ctx->nZRefine2, &flg)); 1244 PetscCall(PetscOptionsReal("-dm_landau_re_radius", "velocity range to refine on positive (z>0) r=0 axis for runaways", "plexland.c", ctx->re_radius, &ctx->re_radius, &flg)); 1245 PetscCall(PetscOptionsReal("-dm_landau_z_radius_pre", "velocity range to refine r=0 axis (for electrons)", "plexland.c", ctx->vperp0_radius1, &ctx->vperp0_radius1, &flg)); 1246 PetscCall(PetscOptionsReal("-dm_landau_z_radius_post", "velocity range to refine r=0 axis (for electrons) after origin AMR", "plexland.c", ctx->vperp0_radius2, &ctx->vperp0_radius2, &flg)); 1247 /* spherical domain (not used) */ 1248 PetscCall(PetscOptionsBool("-dm_landau_sphere", "use sphere/semi-circle domain instead of rectangle", "plexland.c", ctx->sphere, &ctx->sphere, &sph_flg)); 1249 /* processing options */ 1250 PetscCall(PetscOptionsBool("-dm_landau_gpu_assembly", "Assemble Jacobian on GPU", "plexland.c", ctx->gpu_assembly, &ctx->gpu_assembly, NULL)); 1251 if (ctx->deviceType == LANDAU_CPU || ctx->deviceType == LANDAU_KOKKOS) { // make Kokkos 1252 PetscCall(PetscOptionsBool("-dm_landau_coo_assembly", "Assemble Jacobian with Kokkos on 'device'", "plexland.c", ctx->coo_assembly, &ctx->coo_assembly, NULL)); 1253 if (ctx->coo_assembly) PetscCheck(ctx->gpu_assembly, ctx->comm, PETSC_ERR_ARG_WRONG, "COO assembly requires 'gpu assembly' even if Kokkos 'CPU' back-end %d", ctx->coo_assembly); 1254 } 1255 PetscCall(PetscOptionsBool("-dm_landau_jacobian_field_major_order", "Reorder Jacobian for GPU assembly with field major, or block diagonal, ordering (DEPRECATED)", "plexland.c", ctx->jacobian_field_major_order, &ctx->jacobian_field_major_order, NULL)); 1256 if (ctx->jacobian_field_major_order) PetscCheck(ctx->gpu_assembly, ctx->comm, PETSC_ERR_ARG_WRONG, "-dm_landau_jacobian_field_major_order requires -dm_landau_gpu_assembly"); 1257 PetscCheck(!ctx->jacobian_field_major_order, ctx->comm, PETSC_ERR_ARG_WRONG, "-dm_landau_jacobian_field_major_order DEPRECATED"); 1258 PetscOptionsEnd(); 1259 1260 for (ii = ctx->num_species; ii < LANDAU_MAX_SPECIES; ii++) ctx->masses[ii] = ctx->thermal_temps[ii] = ctx->charges[ii] = 0; 1261 if (ctx->verbose != 0) { 1262 PetscCall(PetscPrintf(PETSC_COMM_WORLD, "masses: e=%10.3e; ions in proton mass units: %10.3e %10.3e ...\n", (double)ctx->masses[0], (double)(ctx->masses[1] / 1.6720e-27), (double)(ctx->num_species > 2 ? ctx->masses[2] / 1.6720e-27 : 0))); 1263 PetscCall(PetscPrintf(PETSC_COMM_WORLD, "charges: e=%10.3e; charges in elementary units: %10.3e %10.3e\n", (double)ctx->charges[0], (double)(-ctx->charges[1] / ctx->charges[0]), (double)(ctx->num_species > 2 ? -ctx->charges[2] / ctx->charges[0] : 0))); 1264 PetscCall(PetscPrintf(PETSC_COMM_WORLD, "n: e: %10.3e i: %10.3e %10.3e\n", (double)ctx->n[0], (double)ctx->n[1], (double)(ctx->num_species > 2 ? ctx->n[2] : 0))); 1265 PetscCall(PetscPrintf(PETSC_COMM_WORLD, "thermal T (K): e=%10.3e i=%10.3e %10.3e. Normalization grid %d: v_0=%10.3e (%10.3ec) n_0=%10.3e t_0=%10.3e %" PetscInt_FMT " batched, view batch %" PetscInt_FMT "\n", (double)ctx->thermal_temps[0], 1266 (double)ctx->thermal_temps[1], (double)((ctx->num_species > 2) ? ctx->thermal_temps[2] : 0), (int)non_dim_grid, (double)ctx->v_0, (double)(ctx->v_0 / SPEED_OF_LIGHT), (double)ctx->n_0, (double)ctx->t_0, ctx->batch_sz, ctx->batch_view_idx)); 1267 PetscCall(PetscPrintf(PETSC_COMM_WORLD, "Domain radius (AMR levels) grid %d: par=%10.3e perp=%10.3e (%" PetscInt_FMT ") ", 0, (double)ctx->radius_par[0], (double)ctx->radius_perp[0], ctx->numAMRRefine[0])); 1268 for (ii = 1; ii < ctx->num_grids; ii++) PetscCall(PetscPrintf(PETSC_COMM_WORLD, ", %" PetscInt_FMT ": par=%10.3e perp=%10.3e (%" PetscInt_FMT ") ", ii, (double)ctx->radius_par[ii], (double)ctx->radius_perp[ii], ctx->numAMRRefine[ii])); 1269 if (ctx->use_relativistic_corrections) PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\nUse relativistic corrections\n")); 1270 else PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\n")); 1271 } 1272 PetscCall(DMDestroy(&dummy)); 1273 { 1274 PetscMPIInt rank; 1275 PetscCallMPI(MPI_Comm_rank(PETSC_COMM_WORLD, &rank)); 1276 ctx->stage = 0; 1277 PetscCall(PetscLogEventRegister("Landau Create", DM_CLASSID, &ctx->events[13])); /* 13 */ 1278 PetscCall(PetscLogEventRegister(" GPU ass. setup", DM_CLASSID, &ctx->events[2])); /* 2 */ 1279 PetscCall(PetscLogEventRegister(" Build matrix", DM_CLASSID, &ctx->events[12])); /* 12 */ 1280 PetscCall(PetscLogEventRegister(" Assembly maps", DM_CLASSID, &ctx->events[15])); /* 15 */ 1281 PetscCall(PetscLogEventRegister("Landau Mass mat", DM_CLASSID, &ctx->events[14])); /* 14 */ 1282 PetscCall(PetscLogEventRegister("Landau Operator", DM_CLASSID, &ctx->events[11])); /* 11 */ 1283 PetscCall(PetscLogEventRegister("Landau Jacobian", DM_CLASSID, &ctx->events[0])); /* 0 */ 1284 PetscCall(PetscLogEventRegister("Landau Mass", DM_CLASSID, &ctx->events[9])); /* 9 */ 1285 PetscCall(PetscLogEventRegister(" Preamble", DM_CLASSID, &ctx->events[10])); /* 10 */ 1286 PetscCall(PetscLogEventRegister(" static IP Data", DM_CLASSID, &ctx->events[7])); /* 7 */ 1287 PetscCall(PetscLogEventRegister(" dynamic IP-Jac", DM_CLASSID, &ctx->events[1])); /* 1 */ 1288 PetscCall(PetscLogEventRegister(" Kernel-init", DM_CLASSID, &ctx->events[3])); /* 3 */ 1289 PetscCall(PetscLogEventRegister(" Jac-f-df (GPU)", DM_CLASSID, &ctx->events[8])); /* 8 */ 1290 PetscCall(PetscLogEventRegister(" J Kernel (GPU)", DM_CLASSID, &ctx->events[4])); /* 4 */ 1291 PetscCall(PetscLogEventRegister(" M Kernel (GPU)", DM_CLASSID, &ctx->events[16])); /* 16 */ 1292 PetscCall(PetscLogEventRegister(" Copy to CPU", DM_CLASSID, &ctx->events[5])); /* 5 */ 1293 PetscCall(PetscLogEventRegister(" CPU assemble", DM_CLASSID, &ctx->events[6])); /* 6 */ 1294 1295 if (rank) { /* turn off output stuff for duplicate runs - do we need to add the prefix to all this? */ 1296 PetscCall(PetscOptionsClearValue(NULL, "-snes_converged_reason")); 1297 PetscCall(PetscOptionsClearValue(NULL, "-ksp_converged_reason")); 1298 PetscCall(PetscOptionsClearValue(NULL, "-snes_monitor")); 1299 PetscCall(PetscOptionsClearValue(NULL, "-ksp_monitor")); 1300 PetscCall(PetscOptionsClearValue(NULL, "-ts_monitor")); 1301 PetscCall(PetscOptionsClearValue(NULL, "-ts_view")); 1302 PetscCall(PetscOptionsClearValue(NULL, "-ts_adapt_monitor")); 1303 PetscCall(PetscOptionsClearValue(NULL, "-dm_landau_amr_dm_view")); 1304 PetscCall(PetscOptionsClearValue(NULL, "-dm_landau_amr_vec_view")); 1305 PetscCall(PetscOptionsClearValue(NULL, "-dm_landau_mass_dm_view")); 1306 PetscCall(PetscOptionsClearValue(NULL, "-dm_landau_mass_view")); 1307 PetscCall(PetscOptionsClearValue(NULL, "-dm_landau_jacobian_view")); 1308 PetscCall(PetscOptionsClearValue(NULL, "-dm_landau_mat_view")); 1309 PetscCall(PetscOptionsClearValue(NULL, "-pc_bjkokkos_ksp_converged_reason")); 1310 PetscCall(PetscOptionsClearValue(NULL, "-pc_bjkokkos_ksp_monitor")); 1311 PetscCall(PetscOptionsClearValue(NULL, "-")); 1312 PetscCall(PetscOptionsClearValue(NULL, "-info")); 1313 } 1314 } 1315 PetscFunctionReturn(PETSC_SUCCESS); 1316 } 1317 1318 static PetscErrorCode CreateStaticData(PetscInt dim, IS grid_batch_is_inv[], LandauCtx *ctx) 1319 { 1320 PetscSection section[LANDAU_MAX_GRIDS], globsection[LANDAU_MAX_GRIDS]; 1321 PetscQuadrature quad; 1322 const PetscReal *quadWeights; 1323 PetscReal invMass[LANDAU_MAX_SPECIES], nu_alpha[LANDAU_MAX_SPECIES], nu_beta[LANDAU_MAX_SPECIES]; 1324 PetscInt numCells[LANDAU_MAX_GRIDS], Nq, Nf[LANDAU_MAX_GRIDS], ncellsTot = 0, MAP_BF_SIZE = 64 * LANDAU_DIM * LANDAU_DIM * LANDAU_MAX_Q_FACE * LANDAU_MAX_SPECIES; 1325 PetscTabulation *Tf; 1326 PetscDS prob; 1327 1328 PetscFunctionBegin; 1329 for (PetscInt grid = 0; grid < ctx->num_grids; grid++) { 1330 for (PetscInt ii = ctx->species_offset[grid]; ii < ctx->species_offset[grid + 1]; ii++) { 1331 invMass[ii] = ctx->m_0 / ctx->masses[ii]; 1332 nu_alpha[ii] = PetscSqr(ctx->charges[ii] / ctx->m_0) * ctx->m_0 / ctx->masses[ii]; 1333 nu_beta[ii] = PetscSqr(ctx->charges[ii] / ctx->epsilon0) / (8 * PETSC_PI) * ctx->t_0 * ctx->n_0 / PetscPowReal(ctx->v_0, 3); 1334 } 1335 } 1336 if (ctx->verbose == 4) { 1337 PetscCall(PetscPrintf(PETSC_COMM_WORLD, "nu_alpha: ")); 1338 for (PetscInt grid = 0; grid < ctx->num_grids; grid++) { 1339 int iii = ctx->species_offset[grid]; 1340 for (PetscInt ii = iii; ii < ctx->species_offset[grid + 1]; ii++) PetscCall(PetscPrintf(PETSC_COMM_WORLD, " %e", (double)nu_alpha[ii])); 1341 } 1342 PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\nnu_beta: ")); 1343 for (PetscInt grid = 0; grid < ctx->num_grids; grid++) { 1344 int iii = ctx->species_offset[grid]; 1345 for (PetscInt ii = iii; ii < ctx->species_offset[grid + 1]; ii++) PetscCall(PetscPrintf(PETSC_COMM_WORLD, " %e", (double)nu_beta[ii])); 1346 } 1347 PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\nnu_alpha[i]*nu_beta[j]*lambda[i][j]:\n")); 1348 for (PetscInt grid = 0; grid < ctx->num_grids; grid++) { 1349 int iii = ctx->species_offset[grid]; 1350 for (PetscInt ii = iii; ii < ctx->species_offset[grid + 1]; ii++) { 1351 for (PetscInt gridj = 0; gridj < ctx->num_grids; gridj++) { 1352 int jjj = ctx->species_offset[gridj]; 1353 for (PetscInt jj = jjj; jj < ctx->species_offset[gridj + 1]; jj++) PetscCall(PetscPrintf(PETSC_COMM_WORLD, " %14.9e", (double)(nu_alpha[ii] * nu_beta[jj] * ctx->lambdas[grid][gridj]))); 1354 } 1355 PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\n")); 1356 } 1357 } 1358 PetscCall(PetscPrintf(PETSC_COMM_WORLD, "lambda[i][j]:\n")); 1359 for (PetscInt grid = 0; grid < ctx->num_grids; grid++) { 1360 int iii = ctx->species_offset[grid]; 1361 for (PetscInt ii = iii; ii < ctx->species_offset[grid + 1]; ii++) { 1362 for (PetscInt gridj = 0; gridj < ctx->num_grids; gridj++) { 1363 int jjj = ctx->species_offset[gridj]; 1364 for (PetscInt jj = jjj; jj < ctx->species_offset[gridj + 1]; jj++) PetscCall(PetscPrintf(PETSC_COMM_WORLD, " %14.9e", (double)ctx->lambdas[grid][gridj])); 1365 } 1366 PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\n")); 1367 } 1368 } 1369 } 1370 PetscCall(DMGetDS(ctx->plex[0], &prob)); // same DS for all grids 1371 PetscCall(PetscDSGetTabulation(prob, &Tf)); // Bf, &Df same for all grids 1372 /* DS, Tab and quad is same on all grids */ 1373 PetscCheck(ctx->plex[0], ctx->comm, PETSC_ERR_ARG_WRONG, "Plex not created"); 1374 PetscCall(PetscFEGetQuadrature(ctx->fe[0], &quad)); 1375 PetscCall(PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, &quadWeights)); 1376 PetscCheck(Nq <= LANDAU_MAX_NQ, ctx->comm, PETSC_ERR_ARG_WRONG, "Order too high. Nq = %" PetscInt_FMT " > LANDAU_MAX_NQ (%d)", Nq, LANDAU_MAX_NQ); 1377 /* setup each grid */ 1378 for (PetscInt grid = 0; grid < ctx->num_grids; grid++) { 1379 PetscInt cStart, cEnd; 1380 PetscCheck(ctx->plex[grid] != NULL, ctx->comm, PETSC_ERR_ARG_WRONG, "Plex not created"); 1381 PetscCall(DMPlexGetHeightStratum(ctx->plex[grid], 0, &cStart, &cEnd)); 1382 numCells[grid] = cEnd - cStart; // grids can have different topology 1383 PetscCall(DMGetLocalSection(ctx->plex[grid], §ion[grid])); 1384 PetscCall(DMGetGlobalSection(ctx->plex[grid], &globsection[grid])); 1385 PetscCall(PetscSectionGetNumFields(section[grid], &Nf[grid])); 1386 ncellsTot += numCells[grid]; 1387 } 1388 /* create GPU assembly data */ 1389 if (ctx->gpu_assembly) { /* we need GPU object with GPU assembly */ 1390 PetscContainer container; 1391 PetscScalar *elemMatrix, *elMat; 1392 pointInterpolationP4est(*pointMaps)[LANDAU_MAX_Q_FACE]; 1393 P4estVertexMaps *maps; 1394 const PetscInt *plex_batch = NULL, Nb = Nq, elMatSz = Nq * Nq * ctx->num_species * ctx->num_species; // tensor elements; 1395 LandauIdx *coo_elem_offsets = NULL, *coo_elem_fullNb = NULL, (*coo_elem_point_offsets)[LANDAU_MAX_NQ + 1] = NULL; 1396 /* create GPU assembly data */ 1397 PetscCall(PetscInfo(ctx->plex[0], "Make GPU maps %d\n", 1)); 1398 PetscCall(PetscLogEventBegin(ctx->events[2], 0, 0, 0, 0)); 1399 PetscCall(PetscMalloc(sizeof(*maps) * ctx->num_grids, &maps)); 1400 PetscCall(PetscMalloc(sizeof(*pointMaps) * MAP_BF_SIZE, &pointMaps)); 1401 PetscCall(PetscMalloc(sizeof(*elemMatrix) * elMatSz, &elemMatrix)); 1402 1403 if (ctx->coo_assembly) { // setup COO assembly -- put COO metadata directly in ctx->SData_d 1404 PetscCall(PetscMalloc3(ncellsTot + 1, &coo_elem_offsets, ncellsTot, &coo_elem_fullNb, ncellsTot, &coo_elem_point_offsets)); // array of integer pointers 1405 coo_elem_offsets[0] = 0; // finish later 1406 PetscCall(PetscInfo(ctx->plex[0], "COO initialization, %" PetscInt_FMT " cells\n", ncellsTot)); 1407 ctx->SData_d.coo_n_cellsTot = ncellsTot; 1408 ctx->SData_d.coo_elem_offsets = (void *)coo_elem_offsets; 1409 ctx->SData_d.coo_elem_fullNb = (void *)coo_elem_fullNb; 1410 ctx->SData_d.coo_elem_point_offsets = (void *)coo_elem_point_offsets; 1411 } else { 1412 ctx->SData_d.coo_elem_offsets = ctx->SData_d.coo_elem_fullNb = NULL; 1413 ctx->SData_d.coo_elem_point_offsets = NULL; 1414 ctx->SData_d.coo_n_cellsTot = 0; 1415 } 1416 1417 ctx->SData_d.coo_max_fullnb = 0; 1418 for (PetscInt grid = 0, glb_elem_idx = 0; grid < ctx->num_grids; grid++) { 1419 PetscInt cStart, cEnd, Nfloc = Nf[grid], totDim = Nfloc * Nq; 1420 if (grid_batch_is_inv[grid]) PetscCall(ISGetIndices(grid_batch_is_inv[grid], &plex_batch)); 1421 PetscCall(DMPlexGetHeightStratum(ctx->plex[grid], 0, &cStart, &cEnd)); 1422 // make maps 1423 maps[grid].d_self = NULL; 1424 maps[grid].num_elements = numCells[grid]; 1425 maps[grid].num_face = (PetscInt)(pow(Nq, 1. / ((double)dim)) + .001); // Q 1426 maps[grid].num_face = (PetscInt)(pow(maps[grid].num_face, (double)(dim - 1)) + .001); // Q^2 1427 maps[grid].num_reduced = 0; 1428 maps[grid].deviceType = ctx->deviceType; 1429 maps[grid].numgrids = ctx->num_grids; 1430 // count reduced and get 1431 PetscCall(PetscMalloc(maps[grid].num_elements * sizeof(*maps[grid].gIdx), &maps[grid].gIdx)); 1432 for (int ej = cStart, eidx = 0; ej < cEnd; ++ej, ++eidx, glb_elem_idx++) { 1433 if (coo_elem_offsets) coo_elem_offsets[glb_elem_idx + 1] = coo_elem_offsets[glb_elem_idx]; // start with last one, then add 1434 for (int fieldA = 0; fieldA < Nf[grid]; fieldA++) { 1435 int fullNb = 0; 1436 for (int q = 0; q < Nb; ++q) { 1437 PetscInt numindices, *indices; 1438 PetscScalar *valuesOrig = elMat = elemMatrix; 1439 PetscCall(PetscArrayzero(elMat, totDim * totDim)); 1440 elMat[(fieldA * Nb + q) * totDim + fieldA * Nb + q] = 1; 1441 PetscCall(DMPlexGetClosureIndices(ctx->plex[grid], section[grid], globsection[grid], ej, PETSC_TRUE, &numindices, &indices, NULL, (PetscScalar **)&elMat)); 1442 for (PetscInt f = 0; f < numindices; ++f) { // look for a non-zero on the diagonal 1443 if (PetscAbs(PetscRealPart(elMat[f * numindices + f])) > PETSC_MACHINE_EPSILON) { 1444 // found it 1445 if (PetscAbs(PetscRealPart(elMat[f * numindices + f] - 1.)) < PETSC_MACHINE_EPSILON) { // normal vertex 1.0 1446 if (plex_batch) { 1447 maps[grid].gIdx[eidx][fieldA][q] = (LandauIdx)plex_batch[indices[f]]; 1448 } else { 1449 maps[grid].gIdx[eidx][fieldA][q] = (LandauIdx)indices[f]; 1450 } 1451 fullNb++; 1452 } else { //found a constraint 1453 int jj = 0; 1454 PetscReal sum = 0; 1455 const PetscInt ff = f; 1456 maps[grid].gIdx[eidx][fieldA][q] = -maps[grid].num_reduced - 1; // store (-)index: id = -(idx+1): idx = -id - 1 1457 1458 do { // constraints are continuous in Plex - exploit that here 1459 int ii; // get 'scale' 1460 for (ii = 0, pointMaps[maps[grid].num_reduced][jj].scale = 0; ii < maps[grid].num_face; ii++) { // sum row of outer product to recover vector value 1461 if (ff + ii < numindices) { // 3D has Q and Q^2 interps so might run off end. We could test that elMat[f*numindices + ff + ii] > 0, and break if not 1462 pointMaps[maps[grid].num_reduced][jj].scale += PetscRealPart(elMat[f * numindices + ff + ii]); 1463 } 1464 } 1465 sum += pointMaps[maps[grid].num_reduced][jj].scale; // diagnostic 1466 // get 'gid' 1467 if (pointMaps[maps[grid].num_reduced][jj].scale == 0) pointMaps[maps[grid].num_reduced][jj].gid = -1; // 3D has Q and Q^2 interps 1468 else { 1469 if (plex_batch) { 1470 pointMaps[maps[grid].num_reduced][jj].gid = plex_batch[indices[f]]; 1471 } else { 1472 pointMaps[maps[grid].num_reduced][jj].gid = indices[f]; 1473 } 1474 fullNb++; 1475 } 1476 } while (++jj < maps[grid].num_face && ++f < numindices); // jj is incremented if we hit the end 1477 while (jj < maps[grid].num_face) { 1478 pointMaps[maps[grid].num_reduced][jj].scale = 0; 1479 pointMaps[maps[grid].num_reduced][jj].gid = -1; 1480 jj++; 1481 } 1482 if (PetscAbs(sum - 1.0) > 10 * PETSC_MACHINE_EPSILON) { // debug 1483 int d, f; 1484 PetscReal tmp = 0; 1485 PetscCall(PetscPrintf(PETSC_COMM_SELF, "\t\t%d.%d.%d) ERROR total I = %22.16e (LANDAU_MAX_Q_FACE=%d, #face=%d)\n", eidx, q, fieldA, (double)sum, LANDAU_MAX_Q_FACE, maps[grid].num_face)); 1486 for (d = 0, tmp = 0; d < numindices; ++d) { 1487 if (tmp != 0 && PetscAbs(tmp - 1.0) > 10 * PETSC_MACHINE_EPSILON) PetscCall(PetscPrintf(PETSC_COMM_WORLD, "%3d) %3" PetscInt_FMT ": ", d, indices[d])); 1488 for (f = 0; f < numindices; ++f) tmp += PetscRealPart(elMat[d * numindices + f]); 1489 if (tmp != 0) PetscCall(PetscPrintf(ctx->comm, " | %22.16e\n", (double)tmp)); 1490 } 1491 } 1492 maps[grid].num_reduced++; 1493 PetscCheck(maps[grid].num_reduced < MAP_BF_SIZE, PETSC_COMM_SELF, PETSC_ERR_PLIB, "maps[grid].num_reduced %d > %" PetscInt_FMT, maps[grid].num_reduced, MAP_BF_SIZE); 1494 } 1495 break; 1496 } 1497 } 1498 // cleanup 1499 PetscCall(DMPlexRestoreClosureIndices(ctx->plex[grid], section[grid], globsection[grid], ej, PETSC_TRUE, &numindices, &indices, NULL, (PetscScalar **)&elMat)); 1500 if (elMat != valuesOrig) PetscCall(DMRestoreWorkArray(ctx->plex[grid], numindices * numindices, MPIU_SCALAR, &elMat)); 1501 } 1502 if (ctx->coo_assembly) { // setup COO assembly 1503 coo_elem_offsets[glb_elem_idx + 1] += fullNb * fullNb; // one species block, adds a block for each species, on this element in this grid 1504 if (fieldA == 0) { // cache full Nb for this element, on this grid per species 1505 coo_elem_fullNb[glb_elem_idx] = fullNb; 1506 if (fullNb > ctx->SData_d.coo_max_fullnb) ctx->SData_d.coo_max_fullnb = fullNb; 1507 } else PetscCheck(coo_elem_fullNb[glb_elem_idx] == fullNb, PETSC_COMM_SELF, PETSC_ERR_PLIB, "full element size change with species %d %d", coo_elem_fullNb[glb_elem_idx], fullNb); 1508 } 1509 } // field 1510 } // cell 1511 // allocate and copy point data maps[grid].gIdx[eidx][field][q] 1512 PetscCall(PetscMalloc(maps[grid].num_reduced * sizeof(*maps[grid].c_maps), &maps[grid].c_maps)); 1513 for (int ej = 0; ej < maps[grid].num_reduced; ++ej) { 1514 for (int q = 0; q < maps[grid].num_face; ++q) { 1515 maps[grid].c_maps[ej][q].scale = pointMaps[ej][q].scale; 1516 maps[grid].c_maps[ej][q].gid = pointMaps[ej][q].gid; 1517 } 1518 } 1519 #if defined(PETSC_HAVE_KOKKOS_KERNELS) 1520 if (ctx->deviceType == LANDAU_KOKKOS) { 1521 PetscCall(LandauKokkosCreateMatMaps(maps, pointMaps, Nf, Nq, grid)); // implies Kokkos does 1522 } // else could be CUDA 1523 #endif 1524 #if defined(PETSC_HAVE_CUDA) 1525 if (ctx->deviceType == LANDAU_CUDA) PetscCall(LandauCUDACreateMatMaps(maps, pointMaps, Nf, Nq, grid)); 1526 #endif 1527 if (plex_batch) { 1528 PetscCall(ISRestoreIndices(grid_batch_is_inv[grid], &plex_batch)); 1529 PetscCall(ISDestroy(&grid_batch_is_inv[grid])); // we are done with this 1530 } 1531 } /* grids */ 1532 // finish COO 1533 if (ctx->coo_assembly) { // setup COO assembly 1534 PetscInt *oor, *ooc; 1535 ctx->SData_d.coo_size = coo_elem_offsets[ncellsTot] * ctx->batch_sz; 1536 PetscCall(PetscMalloc2(ctx->SData_d.coo_size, &oor, ctx->SData_d.coo_size, &ooc)); 1537 for (int i = 0; i < ctx->SData_d.coo_size; i++) oor[i] = ooc[i] = -1; 1538 // get 1539 for (int grid = 0, glb_elem_idx = 0; grid < ctx->num_grids; grid++) { 1540 for (int ej = 0; ej < numCells[grid]; ++ej, glb_elem_idx++) { 1541 const int fullNb = coo_elem_fullNb[glb_elem_idx]; 1542 const LandauIdx *const Idxs = &maps[grid].gIdx[ej][0][0]; // just use field-0 maps, They should be the same but this is just for COO storage 1543 coo_elem_point_offsets[glb_elem_idx][0] = 0; 1544 for (int f = 0, cnt2 = 0; f < Nb; f++) { 1545 int idx = Idxs[f]; 1546 coo_elem_point_offsets[glb_elem_idx][f + 1] = coo_elem_point_offsets[glb_elem_idx][f]; // start at last 1547 if (idx >= 0) { 1548 cnt2++; 1549 coo_elem_point_offsets[glb_elem_idx][f + 1]++; // inc 1550 } else { 1551 idx = -idx - 1; 1552 for (int q = 0; q < maps[grid].num_face; q++) { 1553 if (maps[grid].c_maps[idx][q].gid < 0) break; 1554 cnt2++; 1555 coo_elem_point_offsets[glb_elem_idx][f + 1]++; // inc 1556 } 1557 } 1558 PetscCheck(cnt2 <= fullNb, PETSC_COMM_SELF, PETSC_ERR_PLIB, "wrong count %d < %d", fullNb, cnt2); 1559 } 1560 PetscCheck(coo_elem_point_offsets[glb_elem_idx][Nb] == fullNb, PETSC_COMM_SELF, PETSC_ERR_PLIB, "coo_elem_point_offsets size %d != fullNb=%d", coo_elem_point_offsets[glb_elem_idx][Nb], fullNb); 1561 } 1562 } 1563 // set 1564 for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) { 1565 for (int grid = 0, glb_elem_idx = 0; grid < ctx->num_grids; grid++) { 1566 const PetscInt moffset = LAND_MOFFSET(b_id, grid, ctx->batch_sz, ctx->num_grids, ctx->mat_offset); 1567 for (int ej = 0; ej < numCells[grid]; ++ej, glb_elem_idx++) { 1568 const int fullNb = coo_elem_fullNb[glb_elem_idx], fullNb2 = fullNb * fullNb; 1569 // set (i,j) 1570 for (int fieldA = 0; fieldA < Nf[grid]; fieldA++) { 1571 const LandauIdx *const Idxs = &maps[grid].gIdx[ej][fieldA][0]; 1572 int rows[LANDAU_MAX_Q_FACE], cols[LANDAU_MAX_Q_FACE]; 1573 for (int f = 0; f < Nb; ++f) { 1574 const int nr = coo_elem_point_offsets[glb_elem_idx][f + 1] - coo_elem_point_offsets[glb_elem_idx][f]; 1575 if (nr == 1) rows[0] = Idxs[f]; 1576 else { 1577 const int idx = -Idxs[f] - 1; 1578 for (int q = 0; q < nr; q++) rows[q] = maps[grid].c_maps[idx][q].gid; 1579 } 1580 for (int g = 0; g < Nb; ++g) { 1581 const int nc = coo_elem_point_offsets[glb_elem_idx][g + 1] - coo_elem_point_offsets[glb_elem_idx][g]; 1582 if (nc == 1) cols[0] = Idxs[g]; 1583 else { 1584 const int idx = -Idxs[g] - 1; 1585 for (int q = 0; q < nc; q++) cols[q] = maps[grid].c_maps[idx][q].gid; 1586 } 1587 const int idx0 = b_id * coo_elem_offsets[ncellsTot] + coo_elem_offsets[glb_elem_idx] + fieldA * fullNb2 + fullNb * coo_elem_point_offsets[glb_elem_idx][f] + nr * coo_elem_point_offsets[glb_elem_idx][g]; 1588 for (int q = 0, idx = idx0; q < nr; q++) { 1589 for (int d = 0; d < nc; d++, idx++) { 1590 oor[idx] = rows[q] + moffset; 1591 ooc[idx] = cols[d] + moffset; 1592 } 1593 } 1594 } 1595 } 1596 } 1597 } // cell 1598 } // grid 1599 } // batch 1600 PetscCall(MatSetPreallocationCOO(ctx->J, ctx->SData_d.coo_size, oor, ooc)); 1601 PetscCall(PetscFree2(oor, ooc)); 1602 } 1603 PetscCall(PetscFree(pointMaps)); 1604 PetscCall(PetscFree(elemMatrix)); 1605 PetscCall(PetscContainerCreate(PETSC_COMM_SELF, &container)); 1606 PetscCall(PetscContainerSetPointer(container, (void *)maps)); 1607 PetscCall(PetscContainerSetUserDestroy(container, LandauGPUMapsDestroy)); 1608 PetscCall(PetscObjectCompose((PetscObject)ctx->J, "assembly_maps", (PetscObject)container)); 1609 PetscCall(PetscContainerDestroy(&container)); 1610 PetscCall(PetscLogEventEnd(ctx->events[2], 0, 0, 0, 0)); 1611 } // end GPU assembly 1612 { /* create static point data, Jacobian called first, only one vertex copy */ 1613 PetscReal *invJe, *ww, *xx, *yy, *zz = NULL, *invJ_a; 1614 PetscInt outer_ipidx, outer_ej, grid, nip_glb = 0; 1615 PetscFE fe; 1616 const PetscInt Nb = Nq; 1617 PetscCall(PetscLogEventBegin(ctx->events[7], 0, 0, 0, 0)); 1618 PetscCall(PetscInfo(ctx->plex[0], "Initialize static data\n")); 1619 for (PetscInt grid = 0; grid < ctx->num_grids; grid++) nip_glb += Nq * numCells[grid]; 1620 /* collect f data, first time is for Jacobian, but make mass now */ 1621 if (ctx->verbose != 0) { 1622 PetscInt ncells = 0, N; 1623 PetscCall(MatGetSize(ctx->J, &N, NULL)); 1624 for (PetscInt grid = 0; grid < ctx->num_grids; grid++) ncells += numCells[grid]; 1625 PetscCall(PetscPrintf(PETSC_COMM_WORLD, "%d) %s %" PetscInt_FMT " IPs, %" PetscInt_FMT " cells total, Nb=%" PetscInt_FMT ", Nq=%" PetscInt_FMT ", dim=%" PetscInt_FMT ", Tab: Nb=%" PetscInt_FMT " Nf=%" PetscInt_FMT " Np=%" PetscInt_FMT " cdim=%" PetscInt_FMT " N=%" PetscInt_FMT "\n", 0, "FormLandau", nip_glb, ncells, Nb, Nq, dim, Nb, 1626 ctx->num_species, Nb, dim, N)); 1627 } 1628 PetscCall(PetscMalloc4(nip_glb, &ww, nip_glb, &xx, nip_glb, &yy, nip_glb * dim * dim, &invJ_a)); 1629 if (dim == 3) PetscCall(PetscMalloc1(nip_glb, &zz)); 1630 if (ctx->use_energy_tensor_trick) { 1631 PetscCall(PetscFECreateDefault(PETSC_COMM_SELF, dim, 1, PETSC_FALSE, NULL, PETSC_DECIDE, &fe)); 1632 PetscCall(PetscObjectSetName((PetscObject)fe, "energy")); 1633 } 1634 /* init each grids static data - no batch */ 1635 for (grid = 0, outer_ipidx = 0, outer_ej = 0; grid < ctx->num_grids; grid++) { // OpenMP (once) 1636 Vec v2_2 = NULL; // projected function: v^2/2 for non-relativistic, gamma... for relativistic 1637 PetscSection e_section; 1638 DM dmEnergy; 1639 PetscInt cStart, cEnd, ej; 1640 1641 PetscCall(DMPlexGetHeightStratum(ctx->plex[grid], 0, &cStart, &cEnd)); 1642 // prep energy trick, get v^2 / 2 vector 1643 if (ctx->use_energy_tensor_trick) { 1644 PetscErrorCode (*energyf[1])(PetscInt, PetscReal, const PetscReal[], PetscInt, PetscScalar[], void *) = {ctx->use_relativistic_corrections ? gamma_m1_f : energy_f}; 1645 Vec glob_v2; 1646 PetscReal *c2_0[1], data[1] = {PetscSqr(C_0(ctx->v_0))}; 1647 1648 PetscCall(DMClone(ctx->plex[grid], &dmEnergy)); 1649 PetscCall(PetscObjectSetName((PetscObject)dmEnergy, "energy")); 1650 PetscCall(DMSetField(dmEnergy, 0, NULL, (PetscObject)fe)); 1651 PetscCall(DMCreateDS(dmEnergy)); 1652 PetscCall(DMGetSection(dmEnergy, &e_section)); 1653 PetscCall(DMGetGlobalVector(dmEnergy, &glob_v2)); 1654 PetscCall(PetscObjectSetName((PetscObject)glob_v2, "trick")); 1655 c2_0[0] = &data[0]; 1656 PetscCall(DMProjectFunction(dmEnergy, 0., energyf, (void **)c2_0, INSERT_ALL_VALUES, glob_v2)); 1657 PetscCall(DMGetLocalVector(dmEnergy, &v2_2)); 1658 PetscCall(VecZeroEntries(v2_2)); /* zero BCs so don't set */ 1659 PetscCall(DMGlobalToLocalBegin(dmEnergy, glob_v2, INSERT_VALUES, v2_2)); 1660 PetscCall(DMGlobalToLocalEnd(dmEnergy, glob_v2, INSERT_VALUES, v2_2)); 1661 PetscCall(DMViewFromOptions(dmEnergy, NULL, "-energy_dm_view")); 1662 PetscCall(VecViewFromOptions(glob_v2, NULL, "-energy_vec_view")); 1663 PetscCall(DMRestoreGlobalVector(dmEnergy, &glob_v2)); 1664 } 1665 /* append part of the IP data for each grid */ 1666 for (ej = 0; ej < numCells[grid]; ++ej, ++outer_ej) { 1667 PetscScalar *coefs = NULL; 1668 PetscReal vj[LANDAU_MAX_NQ * LANDAU_DIM], detJj[LANDAU_MAX_NQ], Jdummy[LANDAU_MAX_NQ * LANDAU_DIM * LANDAU_DIM], c0 = C_0(ctx->v_0), c02 = PetscSqr(c0); 1669 invJe = invJ_a + outer_ej * Nq * dim * dim; 1670 PetscCall(DMPlexComputeCellGeometryFEM(ctx->plex[grid], ej + cStart, quad, vj, Jdummy, invJe, detJj)); 1671 if (ctx->use_energy_tensor_trick) PetscCall(DMPlexVecGetClosure(dmEnergy, e_section, v2_2, ej + cStart, NULL, &coefs)); 1672 /* create static point data */ 1673 for (PetscInt qj = 0; qj < Nq; qj++, outer_ipidx++) { 1674 const PetscInt gidx = outer_ipidx; 1675 const PetscReal *invJ = &invJe[qj * dim * dim]; 1676 ww[gidx] = detJj[qj] * quadWeights[qj]; 1677 if (dim == 2) ww[gidx] *= vj[qj * dim + 0]; /* cylindrical coordinate, w/o 2pi */ 1678 // get xx, yy, zz 1679 if (ctx->use_energy_tensor_trick) { 1680 double refSpaceDer[3], eGradPhi[3]; 1681 const PetscReal *const DD = Tf[0]->T[1]; 1682 const PetscReal *Dq = &DD[qj * Nb * dim]; 1683 for (int d = 0; d < 3; ++d) refSpaceDer[d] = eGradPhi[d] = 0.0; 1684 for (int b = 0; b < Nb; ++b) { 1685 for (int d = 0; d < dim; ++d) refSpaceDer[d] += Dq[b * dim + d] * PetscRealPart(coefs[b]); 1686 } 1687 xx[gidx] = 1e10; 1688 if (ctx->use_relativistic_corrections) { 1689 double dg2_c2 = 0; 1690 //for (int d = 0; d < dim; ++d) refSpaceDer[d] *= c02; 1691 for (int d = 0; d < dim; ++d) dg2_c2 += PetscSqr(refSpaceDer[d]); 1692 dg2_c2 *= (double)c02; 1693 if (dg2_c2 >= .999) { 1694 xx[gidx] = vj[qj * dim + 0]; /* coordinate */ 1695 yy[gidx] = vj[qj * dim + 1]; 1696 if (dim == 3) zz[gidx] = vj[qj * dim + 2]; 1697 PetscCall(PetscPrintf(ctx->comm, "Error: %12.5e %" PetscInt_FMT ".%" PetscInt_FMT ") dg2/c02 = %12.5e x= %12.5e %12.5e %12.5e\n", (double)PetscSqrtReal(xx[gidx] * xx[gidx] + yy[gidx] * yy[gidx] + zz[gidx] * zz[gidx]), ej, qj, dg2_c2, (double)xx[gidx], (double)yy[gidx], (double)zz[gidx])); 1698 } else { 1699 PetscReal fact = c02 / PetscSqrtReal(1. - dg2_c2); 1700 for (int d = 0; d < dim; ++d) refSpaceDer[d] *= fact; 1701 // could test with other point u' that (grad - grad') * U (refSpaceDer, refSpaceDer') == 0 1702 } 1703 } 1704 if (xx[gidx] == 1e10) { 1705 for (int d = 0; d < dim; ++d) { 1706 for (int e = 0; e < dim; ++e) eGradPhi[d] += invJ[e * dim + d] * refSpaceDer[e]; 1707 } 1708 xx[gidx] = eGradPhi[0]; 1709 yy[gidx] = eGradPhi[1]; 1710 if (dim == 3) zz[gidx] = eGradPhi[2]; 1711 } 1712 } else { 1713 xx[gidx] = vj[qj * dim + 0]; /* coordinate */ 1714 yy[gidx] = vj[qj * dim + 1]; 1715 if (dim == 3) zz[gidx] = vj[qj * dim + 2]; 1716 } 1717 } /* q */ 1718 if (ctx->use_energy_tensor_trick) PetscCall(DMPlexVecRestoreClosure(dmEnergy, e_section, v2_2, ej + cStart, NULL, &coefs)); 1719 } /* ej */ 1720 if (ctx->use_energy_tensor_trick) { 1721 PetscCall(DMRestoreLocalVector(dmEnergy, &v2_2)); 1722 PetscCall(DMDestroy(&dmEnergy)); 1723 } 1724 } /* grid */ 1725 if (ctx->use_energy_tensor_trick) PetscCall(PetscFEDestroy(&fe)); 1726 /* cache static data */ 1727 if (ctx->deviceType == LANDAU_CUDA || ctx->deviceType == LANDAU_KOKKOS) { 1728 #if defined(PETSC_HAVE_CUDA) || defined(PETSC_HAVE_KOKKOS_KERNELS) 1729 if (ctx->deviceType == LANDAU_CUDA) { 1730 #if defined(PETSC_HAVE_CUDA) 1731 PetscCall(LandauCUDAStaticDataSet(ctx->plex[0], Nq, ctx->batch_sz, ctx->num_grids, numCells, ctx->species_offset, ctx->mat_offset, nu_alpha, nu_beta, invMass, (PetscReal *)ctx->lambdas, invJ_a, xx, yy, zz, ww, &ctx->SData_d)); 1732 #else 1733 SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONG, "-landau_device_type cuda not built"); 1734 #endif 1735 } else if (ctx->deviceType == LANDAU_KOKKOS) { 1736 #if defined(PETSC_HAVE_KOKKOS_KERNELS) 1737 PetscCall(LandauKokkosStaticDataSet(ctx->plex[0], Nq, ctx->batch_sz, ctx->num_grids, numCells, ctx->species_offset, ctx->mat_offset, nu_alpha, nu_beta, invMass, (PetscReal *)ctx->lambdas, invJ_a, xx, yy, zz, ww, &ctx->SData_d)); 1738 #else 1739 SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONG, "-landau_device_type kokkos not built"); 1740 #endif 1741 } 1742 #endif 1743 /* free */ 1744 PetscCall(PetscFree4(ww, xx, yy, invJ_a)); 1745 if (dim == 3) PetscCall(PetscFree(zz)); 1746 } else { /* CPU version, just copy in, only use part */ 1747 PetscReal *nu_alpha_p = (PetscReal *)ctx->SData_d.alpha, *nu_beta_p = (PetscReal *)ctx->SData_d.beta, *invMass_p = (PetscReal *)ctx->SData_d.invMass, *lambdas_p = NULL; // why set these ? 1748 ctx->SData_d.w = (void *)ww; 1749 ctx->SData_d.x = (void *)xx; 1750 ctx->SData_d.y = (void *)yy; 1751 ctx->SData_d.z = (void *)zz; 1752 ctx->SData_d.invJ = (void *)invJ_a; 1753 PetscCall(PetscMalloc4(ctx->num_species, &nu_alpha_p, ctx->num_species, &nu_beta_p, ctx->num_species, &invMass_p, LANDAU_MAX_GRIDS * LANDAU_MAX_GRIDS, &lambdas_p)); 1754 for (PetscInt ii = 0; ii < ctx->num_species; ii++) { 1755 nu_alpha_p[ii] = nu_alpha[ii]; 1756 nu_beta_p[ii] = nu_beta[ii]; 1757 invMass_p[ii] = invMass[ii]; 1758 } 1759 ctx->SData_d.alpha = (void *)nu_alpha_p; 1760 ctx->SData_d.beta = (void *)nu_beta_p; 1761 ctx->SData_d.invMass = (void *)invMass_p; 1762 ctx->SData_d.lambdas = (void *)lambdas_p; 1763 for (PetscInt grid = 0; grid < LANDAU_MAX_GRIDS; grid++) { 1764 PetscReal(*lambdas)[LANDAU_MAX_GRIDS][LANDAU_MAX_GRIDS] = (PetscReal(*)[LANDAU_MAX_GRIDS][LANDAU_MAX_GRIDS])ctx->SData_d.lambdas; 1765 for (PetscInt gridj = 0; gridj < LANDAU_MAX_GRIDS; gridj++) { (*lambdas)[grid][gridj] = ctx->lambdas[grid][gridj]; } 1766 } 1767 } 1768 PetscCall(PetscLogEventEnd(ctx->events[7], 0, 0, 0, 0)); 1769 } // initialize 1770 PetscFunctionReturn(PETSC_SUCCESS); 1771 } 1772 1773 /* < v, u > */ 1774 static void g0_1(PetscInt dim, PetscInt Nf, PetscInt NfAux, const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], PetscReal t, PetscReal u_tShift, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar g0[]) 1775 { 1776 g0[0] = 1.; 1777 } 1778 1779 /* < v, u > */ 1780 static void g0_fake(PetscInt dim, PetscInt Nf, PetscInt NfAux, const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], PetscReal t, PetscReal u_tShift, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar g0[]) 1781 { 1782 static double ttt = 1e-12; 1783 g0[0] = ttt++; 1784 } 1785 1786 /* < v, u > */ 1787 static void g0_r(PetscInt dim, PetscInt Nf, PetscInt NfAux, const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], PetscReal t, PetscReal u_tShift, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar g0[]) 1788 { 1789 g0[0] = 2. * PETSC_PI * x[0]; 1790 } 1791 1792 static PetscErrorCode MatrixNfDestroy(void *ptr) 1793 { 1794 PetscInt *nf = (PetscInt *)ptr; 1795 PetscFunctionBegin; 1796 PetscCall(PetscFree(nf)); 1797 PetscFunctionReturn(PETSC_SUCCESS); 1798 } 1799 1800 /* 1801 LandauCreateJacobianMatrix - creates ctx->J with without real data. Hard to keep sparse. 1802 - Like DMPlexLandauCreateMassMatrix. Should remove one and combine 1803 - has old support for field major ordering 1804 */ 1805 static PetscErrorCode LandauCreateJacobianMatrix(MPI_Comm comm, Vec X, IS grid_batch_is_inv[LANDAU_MAX_GRIDS], LandauCtx *ctx) 1806 { 1807 PetscInt *idxs = NULL; 1808 Mat subM[LANDAU_MAX_GRIDS]; 1809 1810 PetscFunctionBegin; 1811 if (!ctx->gpu_assembly) { /* we need GPU object with GPU assembly */ 1812 PetscFunctionReturn(PETSC_SUCCESS); 1813 } 1814 // get the RCM for this grid to separate out species into blocks -- create 'idxs' & 'ctx->batch_is' -- not used 1815 if (ctx->gpu_assembly && ctx->jacobian_field_major_order) PetscCall(PetscMalloc1(ctx->mat_offset[ctx->num_grids] * ctx->batch_sz, &idxs)); 1816 for (PetscInt grid = 0; grid < ctx->num_grids; grid++) { 1817 const PetscInt *values, n = ctx->mat_offset[grid + 1] - ctx->mat_offset[grid]; 1818 Mat gMat; 1819 DM massDM; 1820 PetscDS prob; 1821 Vec tvec; 1822 // get "mass" matrix for reordering 1823 PetscCall(DMClone(ctx->plex[grid], &massDM)); 1824 PetscCall(DMCopyFields(ctx->plex[grid], massDM)); 1825 PetscCall(DMCreateDS(massDM)); 1826 PetscCall(DMGetDS(massDM, &prob)); 1827 for (int ix = 0, ii = ctx->species_offset[grid]; ii < ctx->species_offset[grid + 1]; ii++, ix++) PetscCall(PetscDSSetJacobian(prob, ix, ix, g0_fake, NULL, NULL, NULL)); 1828 PetscCall(PetscOptionsInsertString(NULL, "-dm_preallocate_only")); // this trick is need to both sparsify the matrix and avoid runtime error 1829 PetscCall(DMCreateMatrix(massDM, &gMat)); 1830 PetscCall(PetscOptionsInsertString(NULL, "-dm_preallocate_only false")); 1831 PetscCall(MatSetOption(gMat, MAT_STRUCTURALLY_SYMMETRIC, PETSC_TRUE)); 1832 PetscCall(MatSetOption(gMat, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE)); 1833 PetscCall(DMCreateLocalVector(ctx->plex[grid], &tvec)); 1834 PetscCall(DMPlexSNESComputeJacobianFEM(massDM, tvec, gMat, gMat, ctx)); 1835 PetscCall(MatViewFromOptions(gMat, NULL, "-dm_landau_reorder_mat_view")); 1836 PetscCall(DMDestroy(&massDM)); 1837 PetscCall(VecDestroy(&tvec)); 1838 subM[grid] = gMat; 1839 if (ctx->gpu_assembly && ctx->jacobian_field_major_order) { 1840 MatOrderingType rtype = MATORDERINGRCM; 1841 IS isrow, isicol; 1842 PetscCall(MatGetOrdering(gMat, rtype, &isrow, &isicol)); 1843 PetscCall(ISInvertPermutation(isrow, PETSC_DECIDE, &grid_batch_is_inv[grid])); 1844 PetscCall(ISGetIndices(isrow, &values)); 1845 for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) { // add batch size DMs for this species grid 1846 #if !defined(LANDAU_SPECIES_MAJOR) 1847 PetscInt N = ctx->mat_offset[ctx->num_grids], n0 = ctx->mat_offset[grid] + b_id * N; 1848 for (int ii = 0; ii < n; ++ii) idxs[n0 + ii] = values[ii] + n0; 1849 #else 1850 PetscInt n0 = ctx->mat_offset[grid] * ctx->batch_sz + b_id * n; 1851 for (int ii = 0; ii < n; ++ii) idxs[n0 + ii] = values[ii] + n0; 1852 #endif 1853 } 1854 PetscCall(ISRestoreIndices(isrow, &values)); 1855 PetscCall(ISDestroy(&isrow)); 1856 PetscCall(ISDestroy(&isicol)); 1857 } 1858 } 1859 if (ctx->gpu_assembly && ctx->jacobian_field_major_order) PetscCall(ISCreateGeneral(comm, ctx->mat_offset[ctx->num_grids] * ctx->batch_sz, idxs, PETSC_OWN_POINTER, &ctx->batch_is)); 1860 // get a block matrix 1861 for (PetscInt grid = 0; grid < ctx->num_grids; grid++) { 1862 Mat B = subM[grid]; 1863 PetscInt nloc, nzl, *colbuf, row, COL_BF_SIZE = 1024; 1864 PetscCall(PetscMalloc(sizeof(*colbuf) * COL_BF_SIZE, &colbuf)); 1865 PetscCall(MatGetSize(B, &nloc, NULL)); 1866 for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) { 1867 const PetscInt moffset = LAND_MOFFSET(b_id, grid, ctx->batch_sz, ctx->num_grids, ctx->mat_offset); 1868 const PetscInt *cols; 1869 const PetscScalar *vals; 1870 for (int i = 0; i < nloc; i++) { 1871 PetscCall(MatGetRow(B, i, &nzl, NULL, NULL)); 1872 if (nzl > COL_BF_SIZE) { 1873 PetscCall(PetscFree(colbuf)); 1874 PetscCall(PetscInfo(ctx->plex[grid], "Realloc buffer %" PetscInt_FMT " to %" PetscInt_FMT " (row size %" PetscInt_FMT ") \n", COL_BF_SIZE, 2 * COL_BF_SIZE, nzl)); 1875 COL_BF_SIZE = nzl; 1876 PetscCall(PetscMalloc(sizeof(*colbuf) * COL_BF_SIZE, &colbuf)); 1877 } 1878 PetscCall(MatGetRow(B, i, &nzl, &cols, &vals)); 1879 for (int j = 0; j < nzl; j++) colbuf[j] = cols[j] + moffset; 1880 row = i + moffset; 1881 PetscCall(MatSetValues(ctx->J, 1, &row, nzl, colbuf, vals, INSERT_VALUES)); 1882 PetscCall(MatRestoreRow(B, i, &nzl, &cols, &vals)); 1883 } 1884 } 1885 PetscCall(PetscFree(colbuf)); 1886 } 1887 for (PetscInt grid = 0; grid < ctx->num_grids; grid++) PetscCall(MatDestroy(&subM[grid])); 1888 PetscCall(MatAssemblyBegin(ctx->J, MAT_FINAL_ASSEMBLY)); 1889 PetscCall(MatAssemblyEnd(ctx->J, MAT_FINAL_ASSEMBLY)); 1890 1891 // debug 1892 PetscCall(MatViewFromOptions(ctx->J, NULL, "-dm_landau_mat_view")); 1893 if (ctx->gpu_assembly && ctx->jacobian_field_major_order) { 1894 Mat mat_block_order; 1895 PetscCall(MatCreateSubMatrix(ctx->J, ctx->batch_is, ctx->batch_is, MAT_INITIAL_MATRIX, &mat_block_order)); // use MatPermute 1896 PetscCall(MatViewFromOptions(mat_block_order, NULL, "-dm_landau_mat_view")); 1897 PetscCall(MatDestroy(&mat_block_order)); 1898 PetscCall(VecScatterCreate(X, ctx->batch_is, X, NULL, &ctx->plex_batch)); 1899 PetscCall(VecDuplicate(X, &ctx->work_vec)); 1900 } 1901 1902 PetscFunctionReturn(PETSC_SUCCESS); 1903 } 1904 1905 PetscErrorCode DMPlexLandauCreateMassMatrix(DM pack, Mat *Amat); 1906 /*@C 1907 DMPlexLandauCreateVelocitySpace - Create a DMPlex velocity space mesh 1908 1909 Collective 1910 1911 Input Parameters: 1912 + comm - The MPI communicator 1913 . dim - velocity space dimension (2 for axisymmetric, 3 for full 3X + 3V solver) 1914 - prefix - prefix for options (not tested) 1915 1916 Output Parameter: 1917 . pack - The DM object representing the mesh 1918 + X - A vector (user destroys) 1919 - J - Optional matrix (object destroys) 1920 1921 Level: beginner 1922 1923 .keywords: mesh 1924 .seealso: `DMPlexCreate()`, `DMPlexLandauDestroyVelocitySpace()` 1925 @*/ 1926 PetscErrorCode DMPlexLandauCreateVelocitySpace(MPI_Comm comm, PetscInt dim, const char prefix[], Vec *X, Mat *J, DM *pack) 1927 { 1928 LandauCtx *ctx; 1929 Vec Xsub[LANDAU_MAX_GRIDS]; 1930 IS grid_batch_is_inv[LANDAU_MAX_GRIDS]; 1931 1932 PetscFunctionBegin; 1933 PetscCheck(dim == 2 || dim == 3, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Only 2D and 3D supported"); 1934 PetscCheck(LANDAU_DIM == dim, PETSC_COMM_SELF, PETSC_ERR_PLIB, "dim %" PetscInt_FMT " != LANDAU_DIM %d", dim, LANDAU_DIM); 1935 PetscCall(PetscNew(&ctx)); 1936 ctx->comm = comm; /* used for diagnostics and global errors */ 1937 /* process options */ 1938 PetscCall(ProcessOptions(ctx, prefix)); 1939 if (dim == 2) ctx->use_relativistic_corrections = PETSC_FALSE; 1940 /* Create Mesh */ 1941 PetscCall(DMCompositeCreate(PETSC_COMM_SELF, pack)); 1942 PetscCall(PetscLogEventBegin(ctx->events[13], 0, 0, 0, 0)); 1943 PetscCall(PetscLogEventBegin(ctx->events[15], 0, 0, 0, 0)); 1944 PetscCall(LandauDMCreateVMeshes(PETSC_COMM_SELF, dim, prefix, ctx, *pack)); // creates grids (Forest of AMR) 1945 for (PetscInt grid = 0; grid < ctx->num_grids; grid++) { 1946 /* create FEM */ 1947 PetscCall(SetupDS(ctx->plex[grid], dim, grid, ctx)); 1948 /* set initial state */ 1949 PetscCall(DMCreateGlobalVector(ctx->plex[grid], &Xsub[grid])); 1950 PetscCall(PetscObjectSetName((PetscObject)Xsub[grid], "u_orig")); 1951 /* initial static refinement, no solve */ 1952 PetscCall(LandauSetInitialCondition(ctx->plex[grid], Xsub[grid], grid, 0, 1, ctx)); 1953 /* forest refinement - forest goes in (if forest), plex comes out */ 1954 if (ctx->use_p4est) { 1955 DM plex; 1956 PetscCall(adapt(grid, ctx, &Xsub[grid])); // forest goes in, plex comes out 1957 PetscCall(DMViewFromOptions(ctx->plex[grid], NULL, "-dm_landau_amr_dm_view")); // need to differentiate - todo 1958 PetscCall(VecViewFromOptions(Xsub[grid], NULL, "-dm_landau_amr_vec_view")); 1959 // convert to plex, all done with this level 1960 PetscCall(DMConvert(ctx->plex[grid], DMPLEX, &plex)); 1961 PetscCall(DMDestroy(&ctx->plex[grid])); 1962 ctx->plex[grid] = plex; 1963 } 1964 #if !defined(LANDAU_SPECIES_MAJOR) 1965 PetscCall(DMCompositeAddDM(*pack, ctx->plex[grid])); 1966 #else 1967 for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) { // add batch size DMs for this species grid 1968 PetscCall(DMCompositeAddDM(*pack, ctx->plex[grid])); 1969 } 1970 #endif 1971 PetscCall(DMSetApplicationContext(ctx->plex[grid], ctx)); 1972 } 1973 #if !defined(LANDAU_SPECIES_MAJOR) 1974 // stack the batched DMs, could do it all here!!! b_id=0 1975 for (PetscInt b_id = 1; b_id < ctx->batch_sz; b_id++) { 1976 for (PetscInt grid = 0; grid < ctx->num_grids; grid++) PetscCall(DMCompositeAddDM(*pack, ctx->plex[grid])); 1977 } 1978 #endif 1979 // create ctx->mat_offset 1980 ctx->mat_offset[0] = 0; 1981 for (PetscInt grid = 0; grid < ctx->num_grids; grid++) { 1982 PetscInt n; 1983 PetscCall(VecGetLocalSize(Xsub[grid], &n)); 1984 ctx->mat_offset[grid + 1] = ctx->mat_offset[grid] + n; 1985 } 1986 // creat DM & Jac 1987 PetscCall(DMSetApplicationContext(*pack, ctx)); 1988 PetscCall(PetscOptionsInsertString(NULL, "-dm_preallocate_only")); 1989 PetscCall(DMCreateMatrix(*pack, &ctx->J)); 1990 PetscCall(PetscOptionsInsertString(NULL, "-dm_preallocate_only false")); 1991 PetscCall(MatSetOption(ctx->J, MAT_STRUCTURALLY_SYMMETRIC, PETSC_TRUE)); 1992 PetscCall(MatSetOption(ctx->J, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE)); 1993 PetscCall(PetscObjectSetName((PetscObject)ctx->J, "Jac")); 1994 // construct initial conditions in X 1995 PetscCall(DMCreateGlobalVector(*pack, X)); 1996 for (PetscInt grid = 0; grid < ctx->num_grids; grid++) { 1997 PetscInt n; 1998 PetscCall(VecGetLocalSize(Xsub[grid], &n)); 1999 for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) { 2000 PetscScalar const *values; 2001 const PetscInt moffset = LAND_MOFFSET(b_id, grid, ctx->batch_sz, ctx->num_grids, ctx->mat_offset); 2002 PetscCall(LandauSetInitialCondition(ctx->plex[grid], Xsub[grid], grid, b_id, ctx->batch_sz, ctx)); 2003 PetscCall(VecGetArrayRead(Xsub[grid], &values)); // Drop whole grid in Plex ordering 2004 for (int i = 0, idx = moffset; i < n; i++, idx++) PetscCall(VecSetValue(*X, idx, values[i], INSERT_VALUES)); 2005 PetscCall(VecRestoreArrayRead(Xsub[grid], &values)); 2006 } 2007 } 2008 // cleanup 2009 for (PetscInt grid = 0; grid < ctx->num_grids; grid++) PetscCall(VecDestroy(&Xsub[grid])); 2010 /* check for correct matrix type */ 2011 if (ctx->gpu_assembly) { /* we need GPU object with GPU assembly */ 2012 PetscBool flg; 2013 if (ctx->deviceType == LANDAU_CUDA) { 2014 PetscCall(PetscObjectTypeCompareAny((PetscObject)ctx->J, &flg, MATSEQAIJCUSPARSE, MATMPIAIJCUSPARSE, MATAIJCUSPARSE, "")); 2015 PetscCheck(flg, ctx->comm, PETSC_ERR_ARG_WRONG, "must use '-dm_mat_type aijcusparse -dm_vec_type cuda' for GPU assembly and Cuda or use '-dm_landau_device_type cpu'"); 2016 } else if (ctx->deviceType == LANDAU_KOKKOS) { 2017 PetscCall(PetscObjectTypeCompareAny((PetscObject)ctx->J, &flg, MATSEQAIJKOKKOS, MATMPIAIJKOKKOS, MATAIJKOKKOS, "")); 2018 #if defined(PETSC_HAVE_KOKKOS_KERNELS) 2019 PetscCheck(flg, ctx->comm, PETSC_ERR_ARG_WRONG, "must use '-dm_mat_type aijkokkos -dm_vec_type kokkos' for GPU assembly and Kokkos or use '-dm_landau_device_type cpu'"); 2020 #else 2021 PetscCheck(flg, ctx->comm, PETSC_ERR_ARG_WRONG, "must configure with '--download-kokkos-kernels' for GPU assembly and Kokkos or use '-dm_landau_device_type cpu'"); 2022 #endif 2023 } 2024 } 2025 PetscCall(PetscLogEventEnd(ctx->events[15], 0, 0, 0, 0)); 2026 2027 // create field major ordering 2028 ctx->work_vec = NULL; 2029 ctx->plex_batch = NULL; 2030 ctx->batch_is = NULL; 2031 for (int i = 0; i < LANDAU_MAX_GRIDS; i++) grid_batch_is_inv[i] = NULL; 2032 PetscCall(PetscLogEventBegin(ctx->events[12], 0, 0, 0, 0)); 2033 PetscCall(LandauCreateJacobianMatrix(comm, *X, grid_batch_is_inv, ctx)); 2034 PetscCall(PetscLogEventEnd(ctx->events[12], 0, 0, 0, 0)); 2035 2036 // create AMR GPU assembly maps and static GPU data 2037 PetscCall(CreateStaticData(dim, grid_batch_is_inv, ctx)); 2038 2039 PetscCall(PetscLogEventEnd(ctx->events[13], 0, 0, 0, 0)); 2040 2041 // create mass matrix 2042 PetscCall(DMPlexLandauCreateMassMatrix(*pack, NULL)); 2043 2044 if (J) *J = ctx->J; 2045 2046 if (ctx->gpu_assembly && ctx->jacobian_field_major_order) { 2047 PetscContainer container; 2048 // cache ctx for KSP with batch/field major Jacobian ordering -ksp_type gmres/etc -dm_landau_jacobian_field_major_order 2049 PetscCall(PetscContainerCreate(PETSC_COMM_SELF, &container)); 2050 PetscCall(PetscContainerSetPointer(container, (void *)ctx)); 2051 PetscCall(PetscObjectCompose((PetscObject)ctx->J, "LandauCtx", (PetscObject)container)); 2052 PetscCall(PetscContainerDestroy(&container)); 2053 // batch solvers need to map -- can batch solvers work 2054 PetscCall(PetscContainerCreate(PETSC_COMM_SELF, &container)); 2055 PetscCall(PetscContainerSetPointer(container, (void *)ctx->plex_batch)); 2056 PetscCall(PetscObjectCompose((PetscObject)ctx->J, "plex_batch_is", (PetscObject)container)); 2057 PetscCall(PetscContainerDestroy(&container)); 2058 } 2059 // for batch solvers 2060 { 2061 PetscContainer container; 2062 PetscInt *pNf; 2063 PetscCall(PetscContainerCreate(PETSC_COMM_SELF, &container)); 2064 PetscCall(PetscMalloc1(sizeof(*pNf), &pNf)); 2065 *pNf = ctx->batch_sz; 2066 PetscCall(PetscContainerSetPointer(container, (void *)pNf)); 2067 PetscCall(PetscContainerSetUserDestroy(container, MatrixNfDestroy)); 2068 PetscCall(PetscObjectCompose((PetscObject)ctx->J, "batch size", (PetscObject)container)); 2069 PetscCall(PetscContainerDestroy(&container)); 2070 } 2071 2072 PetscFunctionReturn(PETSC_SUCCESS); 2073 } 2074 2075 /*@ 2076 DMPlexLandauAccess - Access to the distribution function with user callback 2077 2078 Collective 2079 2080 Input Parameters: 2081 . pack - the DMComposite 2082 + func - call back function 2083 . user_ctx - user context 2084 2085 Input/Output Parameters: 2086 + X - Vector to data to 2087 2088 Level: advanced 2089 2090 .keywords: mesh 2091 .seealso: `DMPlexLandauCreateVelocitySpace()` 2092 @*/ 2093 PetscErrorCode DMPlexLandauAccess(DM pack, Vec X, PetscErrorCode (*func)(DM, Vec, PetscInt, PetscInt, PetscInt, void *), void *user_ctx) 2094 { 2095 LandauCtx *ctx; 2096 PetscFunctionBegin; 2097 PetscCall(DMGetApplicationContext(pack, &ctx)); // uses ctx->num_grids; ctx->plex[grid]; ctx->batch_sz; ctx->mat_offset 2098 for (PetscInt grid = 0; grid < ctx->num_grids; grid++) { 2099 PetscInt dim, n; 2100 PetscCall(DMGetDimension(pack, &dim)); 2101 for (PetscInt sp = ctx->species_offset[grid], i0 = 0; sp < ctx->species_offset[grid + 1]; sp++, i0++) { 2102 Vec vec; 2103 PetscInt vf[1] = {i0}; 2104 IS vis; 2105 DM vdm; 2106 PetscCall(DMCreateSubDM(ctx->plex[grid], 1, vf, &vis, &vdm)); 2107 PetscCall(DMSetApplicationContext(vdm, ctx)); // the user might want this 2108 PetscCall(DMCreateGlobalVector(vdm, &vec)); 2109 PetscCall(VecGetSize(vec, &n)); 2110 for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) { 2111 const PetscInt moffset = LAND_MOFFSET(b_id, grid, ctx->batch_sz, ctx->num_grids, ctx->mat_offset); 2112 PetscCall(VecZeroEntries(vec)); 2113 /* Add your data with 'dm' for species 'sp' to 'vec' */ 2114 PetscCall(func(vdm, vec, i0, grid, b_id, user_ctx)); 2115 /* add to global */ 2116 PetscScalar const *values; 2117 const PetscInt *offsets; 2118 PetscCall(VecGetArrayRead(vec, &values)); 2119 PetscCall(ISGetIndices(vis, &offsets)); 2120 for (int i = 0; i < n; i++) PetscCall(VecSetValue(X, moffset + offsets[i], values[i], ADD_VALUES)); 2121 PetscCall(VecRestoreArrayRead(vec, &values)); 2122 PetscCall(ISRestoreIndices(vis, &offsets)); 2123 } // batch 2124 PetscCall(VecDestroy(&vec)); 2125 PetscCall(ISDestroy(&vis)); 2126 PetscCall(DMDestroy(&vdm)); 2127 } 2128 } // grid 2129 PetscFunctionReturn(PETSC_SUCCESS); 2130 } 2131 2132 /*@ 2133 DMPlexLandauDestroyVelocitySpace - Destroy a DMPlex velocity space mesh 2134 2135 Collective 2136 2137 Input/Output Parameters: 2138 . dm - the dm to destroy 2139 2140 Level: beginner 2141 2142 .keywords: mesh 2143 .seealso: `DMPlexLandauCreateVelocitySpace()` 2144 @*/ 2145 PetscErrorCode DMPlexLandauDestroyVelocitySpace(DM *dm) 2146 { 2147 LandauCtx *ctx; 2148 PetscFunctionBegin; 2149 PetscCall(DMGetApplicationContext(*dm, &ctx)); 2150 PetscCall(MatDestroy(&ctx->M)); 2151 PetscCall(MatDestroy(&ctx->J)); 2152 for (PetscInt ii = 0; ii < ctx->num_species; ii++) PetscCall(PetscFEDestroy(&ctx->fe[ii])); 2153 PetscCall(ISDestroy(&ctx->batch_is)); 2154 PetscCall(VecDestroy(&ctx->work_vec)); 2155 PetscCall(VecScatterDestroy(&ctx->plex_batch)); 2156 if (ctx->deviceType == LANDAU_CUDA) { 2157 #if defined(PETSC_HAVE_CUDA) 2158 PetscCall(LandauCUDAStaticDataClear(&ctx->SData_d)); 2159 #else 2160 SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONG, "-landau_device_type %s not built", "cuda"); 2161 #endif 2162 } else if (ctx->deviceType == LANDAU_KOKKOS) { 2163 #if defined(PETSC_HAVE_KOKKOS_KERNELS) 2164 PetscCall(LandauKokkosStaticDataClear(&ctx->SData_d)); 2165 #else 2166 SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONG, "-landau_device_type %s not built", "kokkos"); 2167 #endif 2168 } else { 2169 if (ctx->SData_d.x) { /* in a CPU run */ 2170 PetscReal *invJ = (PetscReal *)ctx->SData_d.invJ, *xx = (PetscReal *)ctx->SData_d.x, *yy = (PetscReal *)ctx->SData_d.y, *zz = (PetscReal *)ctx->SData_d.z, *ww = (PetscReal *)ctx->SData_d.w; 2171 LandauIdx *coo_elem_offsets = (LandauIdx *)ctx->SData_d.coo_elem_offsets, *coo_elem_fullNb = (LandauIdx *)ctx->SData_d.coo_elem_fullNb, (*coo_elem_point_offsets)[LANDAU_MAX_NQ + 1] = (LandauIdx(*)[LANDAU_MAX_NQ + 1]) ctx->SData_d.coo_elem_point_offsets; 2172 PetscCall(PetscFree4(ww, xx, yy, invJ)); 2173 if (zz) PetscCall(PetscFree(zz)); 2174 if (coo_elem_offsets) { 2175 PetscCall(PetscFree3(coo_elem_offsets, coo_elem_fullNb, coo_elem_point_offsets)); // could be NULL 2176 } 2177 PetscCall(PetscFree4(ctx->SData_d.alpha, ctx->SData_d.beta, ctx->SData_d.invMass, ctx->SData_d.lambdas)); 2178 } 2179 } 2180 2181 if (ctx->times[LANDAU_MATRIX_TOTAL] > 0) { // OMP timings 2182 PetscCall(PetscPrintf(ctx->comm, "TSStep N 1.0 %10.3e\n", ctx->times[LANDAU_EX2_TSSOLVE])); 2183 PetscCall(PetscPrintf(ctx->comm, "2: Solve: %10.3e with %" PetscInt_FMT " threads\n", ctx->times[LANDAU_EX2_TSSOLVE] - ctx->times[LANDAU_MATRIX_TOTAL], ctx->batch_sz)); 2184 PetscCall(PetscPrintf(ctx->comm, "3: Landau: %10.3e\n", ctx->times[LANDAU_MATRIX_TOTAL])); 2185 PetscCall(PetscPrintf(ctx->comm, "Landau Jacobian %" PetscInt_FMT " 1.0 %10.3e\n", (PetscInt)ctx->times[LANDAU_JACOBIAN_COUNT], ctx->times[LANDAU_JACOBIAN])); 2186 PetscCall(PetscPrintf(ctx->comm, "Landau Operator N 1.0 %10.3e\n", ctx->times[LANDAU_OPERATOR])); 2187 PetscCall(PetscPrintf(ctx->comm, "Landau Mass N 1.0 %10.3e\n", ctx->times[LANDAU_MASS])); 2188 PetscCall(PetscPrintf(ctx->comm, " Jac-f-df (GPU) N 1.0 %10.3e\n", ctx->times[LANDAU_F_DF])); 2189 PetscCall(PetscPrintf(ctx->comm, " Kernel (GPU) N 1.0 %10.3e\n", ctx->times[LANDAU_KERNEL])); 2190 PetscCall(PetscPrintf(ctx->comm, "MatLUFactorNum X 1.0 %10.3e\n", ctx->times[KSP_FACTOR])); 2191 PetscCall(PetscPrintf(ctx->comm, "MatSolve X 1.0 %10.3e\n", ctx->times[KSP_SOLVE])); 2192 } 2193 for (PetscInt grid = 0; grid < ctx->num_grids; grid++) PetscCall(DMDestroy(&ctx->plex[grid])); 2194 PetscCall(PetscFree(ctx)); 2195 PetscCall(DMDestroy(dm)); 2196 PetscFunctionReturn(PETSC_SUCCESS); 2197 } 2198 2199 /* < v, ru > */ 2200 static void f0_s_den(PetscInt dim, PetscInt Nf, PetscInt NfAux, const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0) 2201 { 2202 PetscInt ii = (PetscInt)PetscRealPart(constants[0]); 2203 f0[0] = u[ii]; 2204 } 2205 2206 /* < v, ru > */ 2207 static void f0_s_mom(PetscInt dim, PetscInt Nf, PetscInt NfAux, const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0) 2208 { 2209 PetscInt ii = (PetscInt)PetscRealPart(constants[0]), jj = (PetscInt)PetscRealPart(constants[1]); 2210 f0[0] = x[jj] * u[ii]; /* x momentum */ 2211 } 2212 2213 static void f0_s_v2(PetscInt dim, PetscInt Nf, PetscInt NfAux, const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0) 2214 { 2215 PetscInt i, ii = (PetscInt)PetscRealPart(constants[0]); 2216 double tmp1 = 0.; 2217 for (i = 0; i < dim; ++i) tmp1 += x[i] * x[i]; 2218 f0[0] = tmp1 * u[ii]; 2219 } 2220 2221 static PetscErrorCode gamma_n_f(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf, PetscScalar *u, void *actx) 2222 { 2223 const PetscReal *c2_0_arr = ((PetscReal *)actx); 2224 const PetscReal c02 = c2_0_arr[0]; 2225 2226 PetscFunctionBegin; 2227 for (int s = 0; s < Nf; s++) { 2228 PetscReal tmp1 = 0.; 2229 for (int i = 0; i < dim; ++i) tmp1 += x[i] * x[i]; 2230 #if defined(PETSC_USE_DEBUG) 2231 u[s] = PetscSqrtReal(1. + tmp1 / c02); // u[0] = PetscSqrtReal(1. + xx); 2232 #else 2233 { 2234 PetscReal xx = tmp1 / c02; 2235 u[s] = xx / (PetscSqrtReal(1. + xx) + 1.); // better conditioned = xx/(PetscSqrtReal(1. + xx) + 1.) 2236 } 2237 #endif 2238 } 2239 PetscFunctionReturn(PETSC_SUCCESS); 2240 } 2241 2242 /* < v, ru > */ 2243 static void f0_s_rden(PetscInt dim, PetscInt Nf, PetscInt NfAux, const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0) 2244 { 2245 PetscInt ii = (PetscInt)PetscRealPart(constants[0]); 2246 f0[0] = 2. * PETSC_PI * x[0] * u[ii]; 2247 } 2248 2249 /* < v, ru > */ 2250 static void f0_s_rmom(PetscInt dim, PetscInt Nf, PetscInt NfAux, const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0) 2251 { 2252 PetscInt ii = (PetscInt)PetscRealPart(constants[0]); 2253 f0[0] = 2. * PETSC_PI * x[0] * x[1] * u[ii]; 2254 } 2255 2256 static void f0_s_rv2(PetscInt dim, PetscInt Nf, PetscInt NfAux, const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0) 2257 { 2258 PetscInt ii = (PetscInt)PetscRealPart(constants[0]); 2259 f0[0] = 2. * PETSC_PI * x[0] * (x[0] * x[0] + x[1] * x[1]) * u[ii]; 2260 } 2261 2262 /*@ 2263 DMPlexLandauPrintNorms - collects moments and prints them 2264 2265 Collective 2266 2267 Input Parameters: 2268 + X - the state 2269 - stepi - current step to print 2270 2271 Level: beginner 2272 2273 .keywords: mesh 2274 .seealso: `DMPlexLandauCreateVelocitySpace()` 2275 @*/ 2276 PetscErrorCode DMPlexLandauPrintNorms(Vec X, PetscInt stepi) 2277 { 2278 LandauCtx *ctx; 2279 PetscDS prob; 2280 DM pack; 2281 PetscInt cStart, cEnd, dim, ii, i0, nDMs; 2282 PetscScalar xmomentumtot = 0, ymomentumtot = 0, zmomentumtot = 0, energytot = 0, densitytot = 0, tt[LANDAU_MAX_SPECIES]; 2283 PetscScalar xmomentum[LANDAU_MAX_SPECIES], ymomentum[LANDAU_MAX_SPECIES], zmomentum[LANDAU_MAX_SPECIES], energy[LANDAU_MAX_SPECIES], density[LANDAU_MAX_SPECIES]; 2284 Vec *globXArray; 2285 2286 PetscFunctionBegin; 2287 PetscCall(VecGetDM(X, &pack)); 2288 PetscCheck(pack, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Vector has no DM"); 2289 PetscCall(DMGetDimension(pack, &dim)); 2290 PetscCheck(dim == 2 || dim == 3, PETSC_COMM_SELF, PETSC_ERR_PLIB, "dim %" PetscInt_FMT " not in [2,3]", dim); 2291 PetscCall(DMGetApplicationContext(pack, &ctx)); 2292 PetscCheck(ctx, PETSC_COMM_SELF, PETSC_ERR_PLIB, "no context"); 2293 /* print momentum and energy */ 2294 PetscCall(DMCompositeGetNumberDM(pack, &nDMs)); 2295 PetscCheck(nDMs == ctx->num_grids * ctx->batch_sz, PETSC_COMM_WORLD, PETSC_ERR_PLIB, "#DM wrong %" PetscInt_FMT " %" PetscInt_FMT, nDMs, ctx->num_grids * ctx->batch_sz); 2296 PetscCall(PetscMalloc(sizeof(*globXArray) * nDMs, &globXArray)); 2297 PetscCall(DMCompositeGetAccessArray(pack, X, nDMs, NULL, globXArray)); 2298 for (PetscInt grid = 0; grid < ctx->num_grids; grid++) { 2299 Vec Xloc = globXArray[LAND_PACK_IDX(ctx->batch_view_idx, grid)]; 2300 PetscCall(DMGetDS(ctx->plex[grid], &prob)); 2301 for (ii = ctx->species_offset[grid], i0 = 0; ii < ctx->species_offset[grid + 1]; ii++, i0++) { 2302 PetscScalar user[2] = {(PetscScalar)i0, (PetscScalar)ctx->charges[ii]}; 2303 PetscCall(PetscDSSetConstants(prob, 2, user)); 2304 if (dim == 2) { /* 2/3X + 3V (cylindrical coordinates) */ 2305 PetscCall(PetscDSSetObjective(prob, 0, &f0_s_rden)); 2306 PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx)); 2307 density[ii] = tt[0] * ctx->n_0 * ctx->charges[ii]; 2308 PetscCall(PetscDSSetObjective(prob, 0, &f0_s_rmom)); 2309 PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx)); 2310 zmomentum[ii] = tt[0] * ctx->n_0 * ctx->v_0 * ctx->masses[ii]; 2311 PetscCall(PetscDSSetObjective(prob, 0, &f0_s_rv2)); 2312 PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx)); 2313 energy[ii] = tt[0] * 0.5 * ctx->n_0 * ctx->v_0 * ctx->v_0 * ctx->masses[ii]; 2314 zmomentumtot += zmomentum[ii]; 2315 energytot += energy[ii]; 2316 densitytot += density[ii]; 2317 PetscCall(PetscPrintf(PETSC_COMM_WORLD, "%3" PetscInt_FMT ") species-%" PetscInt_FMT ": charge density= %20.13e z-momentum= %20.13e energy= %20.13e", stepi, ii, (double)PetscRealPart(density[ii]), (double)PetscRealPart(zmomentum[ii]), (double)PetscRealPart(energy[ii]))); 2318 } else { /* 2/3Xloc + 3V */ 2319 PetscCall(PetscDSSetObjective(prob, 0, &f0_s_den)); 2320 PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx)); 2321 density[ii] = tt[0] * ctx->n_0 * ctx->charges[ii]; 2322 PetscCall(PetscDSSetObjective(prob, 0, &f0_s_mom)); 2323 user[1] = 0; 2324 PetscCall(PetscDSSetConstants(prob, 2, user)); 2325 PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx)); 2326 xmomentum[ii] = tt[0] * ctx->n_0 * ctx->v_0 * ctx->masses[ii]; 2327 user[1] = 1; 2328 PetscCall(PetscDSSetConstants(prob, 2, user)); 2329 PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx)); 2330 ymomentum[ii] = tt[0] * ctx->n_0 * ctx->v_0 * ctx->masses[ii]; 2331 user[1] = 2; 2332 PetscCall(PetscDSSetConstants(prob, 2, user)); 2333 PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx)); 2334 zmomentum[ii] = tt[0] * ctx->n_0 * ctx->v_0 * ctx->masses[ii]; 2335 if (ctx->use_relativistic_corrections) { 2336 /* gamma * M * f */ 2337 if (ii == 0 && grid == 0) { // do all at once 2338 Vec Mf, globGamma, *globMfArray, *globGammaArray; 2339 PetscErrorCode (*gammaf[1])(PetscInt, PetscReal, const PetscReal[], PetscInt, PetscScalar[], void *) = {gamma_n_f}; 2340 PetscReal *c2_0[1], data[1]; 2341 2342 PetscCall(VecDuplicate(X, &globGamma)); 2343 PetscCall(VecDuplicate(X, &Mf)); 2344 PetscCall(PetscMalloc(sizeof(*globMfArray) * nDMs, &globMfArray)); 2345 PetscCall(PetscMalloc(sizeof(*globMfArray) * nDMs, &globGammaArray)); 2346 /* M * f */ 2347 PetscCall(MatMult(ctx->M, X, Mf)); 2348 /* gamma */ 2349 PetscCall(DMCompositeGetAccessArray(pack, globGamma, nDMs, NULL, globGammaArray)); 2350 for (PetscInt grid = 0; grid < ctx->num_grids; grid++) { // yes a grid loop in a grid loop to print nice, need to fix for batching 2351 Vec v1 = globGammaArray[LAND_PACK_IDX(ctx->batch_view_idx, grid)]; 2352 data[0] = PetscSqr(C_0(ctx->v_0)); 2353 c2_0[0] = &data[0]; 2354 PetscCall(DMProjectFunction(ctx->plex[grid], 0., gammaf, (void **)c2_0, INSERT_ALL_VALUES, v1)); 2355 } 2356 PetscCall(DMCompositeRestoreAccessArray(pack, globGamma, nDMs, NULL, globGammaArray)); 2357 /* gamma * Mf */ 2358 PetscCall(DMCompositeGetAccessArray(pack, globGamma, nDMs, NULL, globGammaArray)); 2359 PetscCall(DMCompositeGetAccessArray(pack, Mf, nDMs, NULL, globMfArray)); 2360 for (PetscInt grid = 0; grid < ctx->num_grids; grid++) { // yes a grid loop in a grid loop to print nice 2361 PetscInt Nf = ctx->species_offset[grid + 1] - ctx->species_offset[grid], N, bs; 2362 Vec Mfsub = globMfArray[LAND_PACK_IDX(ctx->batch_view_idx, grid)], Gsub = globGammaArray[LAND_PACK_IDX(ctx->batch_view_idx, grid)], v1, v2; 2363 // get each component 2364 PetscCall(VecGetSize(Mfsub, &N)); 2365 PetscCall(VecCreate(ctx->comm, &v1)); 2366 PetscCall(VecSetSizes(v1, PETSC_DECIDE, N / Nf)); 2367 PetscCall(VecCreate(ctx->comm, &v2)); 2368 PetscCall(VecSetSizes(v2, PETSC_DECIDE, N / Nf)); 2369 PetscCall(VecSetFromOptions(v1)); // ??? 2370 PetscCall(VecSetFromOptions(v2)); 2371 // get each component 2372 PetscCall(VecGetBlockSize(Gsub, &bs)); 2373 PetscCheck(bs == Nf, PETSC_COMM_SELF, PETSC_ERR_PLIB, "bs %" PetscInt_FMT " != num_species %" PetscInt_FMT " in Gsub", bs, Nf); 2374 PetscCall(VecGetBlockSize(Mfsub, &bs)); 2375 PetscCheck(bs == Nf, PETSC_COMM_SELF, PETSC_ERR_PLIB, "bs %" PetscInt_FMT " != num_species %" PetscInt_FMT, bs, Nf); 2376 for (int i = 0, ix = ctx->species_offset[grid]; i < Nf; i++, ix++) { 2377 PetscScalar val; 2378 PetscCall(VecStrideGather(Gsub, i, v1, INSERT_VALUES)); // this is not right -- TODO 2379 PetscCall(VecStrideGather(Mfsub, i, v2, INSERT_VALUES)); 2380 PetscCall(VecDot(v1, v2, &val)); 2381 energy[ix] = PetscRealPart(val) * ctx->n_0 * ctx->v_0 * ctx->v_0 * ctx->masses[ix]; 2382 } 2383 PetscCall(VecDestroy(&v1)); 2384 PetscCall(VecDestroy(&v2)); 2385 } /* grids */ 2386 PetscCall(DMCompositeRestoreAccessArray(pack, globGamma, nDMs, NULL, globGammaArray)); 2387 PetscCall(DMCompositeRestoreAccessArray(pack, Mf, nDMs, NULL, globMfArray)); 2388 PetscCall(PetscFree(globGammaArray)); 2389 PetscCall(PetscFree(globMfArray)); 2390 PetscCall(VecDestroy(&globGamma)); 2391 PetscCall(VecDestroy(&Mf)); 2392 } 2393 } else { 2394 PetscCall(PetscDSSetObjective(prob, 0, &f0_s_v2)); 2395 PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx)); 2396 energy[ii] = 0.5 * tt[0] * ctx->n_0 * ctx->v_0 * ctx->v_0 * ctx->masses[ii]; 2397 } 2398 PetscCall(PetscPrintf(PETSC_COMM_WORLD, "%3" PetscInt_FMT ") species %" PetscInt_FMT ": density=%20.13e, x-momentum=%20.13e, y-momentum=%20.13e, z-momentum=%20.13e, energy=%21.13e", stepi, ii, (double)PetscRealPart(density[ii]), (double)PetscRealPart(xmomentum[ii]), (double)PetscRealPart(ymomentum[ii]), (double)PetscRealPart(zmomentum[ii]), (double)PetscRealPart(energy[ii]))); 2399 xmomentumtot += xmomentum[ii]; 2400 ymomentumtot += ymomentum[ii]; 2401 zmomentumtot += zmomentum[ii]; 2402 energytot += energy[ii]; 2403 densitytot += density[ii]; 2404 } 2405 if (ctx->num_species > 1) PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\n")); 2406 } 2407 } 2408 PetscCall(DMCompositeRestoreAccessArray(pack, X, nDMs, NULL, globXArray)); 2409 PetscCall(PetscFree(globXArray)); 2410 /* totals */ 2411 PetscCall(DMPlexGetHeightStratum(ctx->plex[0], 0, &cStart, &cEnd)); 2412 if (ctx->num_species > 1) { 2413 if (dim == 2) { 2414 PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\t%3" PetscInt_FMT ") Total: charge density=%21.13e, momentum=%21.13e, energy=%21.13e (m_i[0]/m_e = %g, %" PetscInt_FMT " cells on electron grid)", stepi, (double)PetscRealPart(densitytot), (double)PetscRealPart(zmomentumtot), (double)PetscRealPart(energytot), 2415 (double)(ctx->masses[1] / ctx->masses[0]), cEnd - cStart)); 2416 } else { 2417 PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\t%3" PetscInt_FMT ") Total: charge density=%21.13e, x-momentum=%21.13e, y-momentum=%21.13e, z-momentum=%21.13e, energy=%21.13e (m_i[0]/m_e = %g, %" PetscInt_FMT " cells)", stepi, (double)PetscRealPart(densitytot), (double)PetscRealPart(xmomentumtot), (double)PetscRealPart(ymomentumtot), (double)PetscRealPart(zmomentumtot), (double)PetscRealPart(energytot), 2418 (double)(ctx->masses[1] / ctx->masses[0]), cEnd - cStart)); 2419 } 2420 } else PetscCall(PetscPrintf(PETSC_COMM_WORLD, " -- %" PetscInt_FMT " cells", cEnd - cStart)); 2421 PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\n")); 2422 PetscFunctionReturn(PETSC_SUCCESS); 2423 } 2424 2425 /*@ 2426 DMPlexLandauCreateMassMatrix - Create mass matrix for Landau in Plex space (not field major order of Jacobian) 2427 - puts mass matrix into ctx->M 2428 2429 Collective 2430 2431 Input/Output Parameters: 2432 . pack - the DM object. Puts matrix in Landau context M field 2433 2434 Output Parameters: 2435 . Amat - The mass matrix (optional), mass matrix is added to the DM context 2436 2437 Level: beginner 2438 2439 .keywords: mesh 2440 .seealso: `DMPlexLandauCreateVelocitySpace()` 2441 @*/ 2442 PetscErrorCode DMPlexLandauCreateMassMatrix(DM pack, Mat *Amat) 2443 { 2444 DM mass_pack, massDM[LANDAU_MAX_GRIDS]; 2445 PetscDS prob; 2446 PetscInt ii, dim, N1 = 1, N2; 2447 LandauCtx *ctx; 2448 Mat packM, subM[LANDAU_MAX_GRIDS]; 2449 2450 PetscFunctionBegin; 2451 PetscValidHeaderSpecific(pack, DM_CLASSID, 1); 2452 if (Amat) PetscValidPointer(Amat, 2); 2453 PetscCall(DMGetApplicationContext(pack, &ctx)); 2454 PetscCheck(ctx, PETSC_COMM_SELF, PETSC_ERR_PLIB, "no context"); 2455 PetscCall(PetscLogEventBegin(ctx->events[14], 0, 0, 0, 0)); 2456 PetscCall(DMGetDimension(pack, &dim)); 2457 PetscCall(DMCompositeCreate(PetscObjectComm((PetscObject)pack), &mass_pack)); 2458 /* create pack mass matrix */ 2459 for (PetscInt grid = 0, ix = 0; grid < ctx->num_grids; grid++) { 2460 PetscCall(DMClone(ctx->plex[grid], &massDM[grid])); 2461 PetscCall(DMCopyFields(ctx->plex[grid], massDM[grid])); 2462 PetscCall(DMCreateDS(massDM[grid])); 2463 PetscCall(DMGetDS(massDM[grid], &prob)); 2464 for (ix = 0, ii = ctx->species_offset[grid]; ii < ctx->species_offset[grid + 1]; ii++, ix++) { 2465 if (dim == 3) PetscCall(PetscDSSetJacobian(prob, ix, ix, g0_1, NULL, NULL, NULL)); 2466 else PetscCall(PetscDSSetJacobian(prob, ix, ix, g0_r, NULL, NULL, NULL)); 2467 } 2468 #if !defined(LANDAU_SPECIES_MAJOR) 2469 PetscCall(DMCompositeAddDM(mass_pack, massDM[grid])); 2470 #else 2471 for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) { // add batch size DMs for this species grid 2472 PetscCall(DMCompositeAddDM(mass_pack, massDM[grid])); 2473 } 2474 #endif 2475 PetscCall(DMCreateMatrix(massDM[grid], &subM[grid])); 2476 } 2477 #if !defined(LANDAU_SPECIES_MAJOR) 2478 // stack the batched DMs 2479 for (PetscInt b_id = 1; b_id < ctx->batch_sz; b_id++) { 2480 for (PetscInt grid = 0; grid < ctx->num_grids; grid++) PetscCall(DMCompositeAddDM(mass_pack, massDM[grid])); 2481 } 2482 #endif 2483 PetscCall(PetscOptionsInsertString(NULL, "-dm_preallocate_only")); 2484 PetscCall(DMCreateMatrix(mass_pack, &packM)); 2485 PetscCall(PetscOptionsInsertString(NULL, "-dm_preallocate_only false")); 2486 PetscCall(MatSetOption(packM, MAT_STRUCTURALLY_SYMMETRIC, PETSC_TRUE)); 2487 PetscCall(MatSetOption(packM, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE)); 2488 PetscCall(DMDestroy(&mass_pack)); 2489 /* make mass matrix for each block */ 2490 for (PetscInt grid = 0; grid < ctx->num_grids; grid++) { 2491 Vec locX; 2492 DM plex = massDM[grid]; 2493 PetscCall(DMGetLocalVector(plex, &locX)); 2494 /* Mass matrix is independent of the input, so no need to fill locX */ 2495 PetscCall(DMPlexSNESComputeJacobianFEM(plex, locX, subM[grid], subM[grid], ctx)); 2496 PetscCall(DMRestoreLocalVector(plex, &locX)); 2497 PetscCall(DMDestroy(&massDM[grid])); 2498 } 2499 PetscCall(MatGetSize(ctx->J, &N1, NULL)); 2500 PetscCall(MatGetSize(packM, &N2, NULL)); 2501 PetscCheck(N1 == N2, PetscObjectComm((PetscObject)pack), PETSC_ERR_PLIB, "Incorrect matrix sizes: |Jacobian| = %" PetscInt_FMT ", |Mass|=%" PetscInt_FMT, N1, N2); 2502 /* assemble block diagonals */ 2503 for (PetscInt grid = 0; grid < ctx->num_grids; grid++) { 2504 Mat B = subM[grid]; 2505 PetscInt nloc, nzl, *colbuf, COL_BF_SIZE = 1024, row; 2506 PetscCall(PetscMalloc(sizeof(*colbuf) * COL_BF_SIZE, &colbuf)); 2507 PetscCall(MatGetSize(B, &nloc, NULL)); 2508 for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) { 2509 const PetscInt moffset = LAND_MOFFSET(b_id, grid, ctx->batch_sz, ctx->num_grids, ctx->mat_offset); 2510 const PetscInt *cols; 2511 const PetscScalar *vals; 2512 for (int i = 0; i < nloc; i++) { 2513 PetscCall(MatGetRow(B, i, &nzl, NULL, NULL)); 2514 if (nzl > COL_BF_SIZE) { 2515 PetscCall(PetscFree(colbuf)); 2516 PetscCall(PetscInfo(pack, "Realloc buffer %" PetscInt_FMT " to %" PetscInt_FMT " (row size %" PetscInt_FMT ") \n", COL_BF_SIZE, 2 * COL_BF_SIZE, nzl)); 2517 COL_BF_SIZE = nzl; 2518 PetscCall(PetscMalloc(sizeof(*colbuf) * COL_BF_SIZE, &colbuf)); 2519 } 2520 PetscCall(MatGetRow(B, i, &nzl, &cols, &vals)); 2521 for (int j = 0; j < nzl; j++) colbuf[j] = cols[j] + moffset; 2522 row = i + moffset; 2523 PetscCall(MatSetValues(packM, 1, &row, nzl, colbuf, vals, INSERT_VALUES)); 2524 PetscCall(MatRestoreRow(B, i, &nzl, &cols, &vals)); 2525 } 2526 } 2527 PetscCall(PetscFree(colbuf)); 2528 } 2529 // cleanup 2530 for (PetscInt grid = 0; grid < ctx->num_grids; grid++) PetscCall(MatDestroy(&subM[grid])); 2531 PetscCall(MatAssemblyBegin(packM, MAT_FINAL_ASSEMBLY)); 2532 PetscCall(MatAssemblyEnd(packM, MAT_FINAL_ASSEMBLY)); 2533 PetscCall(PetscObjectSetName((PetscObject)packM, "mass")); 2534 PetscCall(MatViewFromOptions(packM, NULL, "-dm_landau_mass_view")); 2535 ctx->M = packM; 2536 if (Amat) *Amat = packM; 2537 PetscCall(PetscLogEventEnd(ctx->events[14], 0, 0, 0, 0)); 2538 PetscFunctionReturn(PETSC_SUCCESS); 2539 } 2540 2541 /*@ 2542 DMPlexLandauIFunction - TS residual calculation, confusingly this computes the Jacobian w/o mass 2543 2544 Collective 2545 2546 Input Parameters: 2547 + TS - The time stepping context 2548 . time_dummy - current time (not used) 2549 . X - Current state 2550 . X_t - Time derivative of current state 2551 - actx - Landau context 2552 2553 Output Parameter: 2554 . F - The residual 2555 2556 Level: beginner 2557 2558 .keywords: mesh 2559 .seealso: `DMPlexLandauCreateVelocitySpace()`, `DMPlexLandauIJacobian()` 2560 @*/ 2561 PetscErrorCode DMPlexLandauIFunction(TS ts, PetscReal time_dummy, Vec X, Vec X_t, Vec F, void *actx) 2562 { 2563 LandauCtx *ctx = (LandauCtx *)actx; 2564 PetscInt dim; 2565 DM pack; 2566 #if defined(PETSC_HAVE_THREADSAFETY) 2567 double starttime, endtime; 2568 #endif 2569 PetscObjectState state; 2570 2571 PetscFunctionBegin; 2572 PetscCall(TSGetDM(ts, &pack)); 2573 PetscCall(DMGetApplicationContext(pack, &ctx)); 2574 PetscCheck(ctx, PETSC_COMM_SELF, PETSC_ERR_PLIB, "no context"); 2575 if (ctx->stage) PetscCall(PetscLogStagePush(ctx->stage)); 2576 PetscCall(PetscLogEventBegin(ctx->events[11], 0, 0, 0, 0)); 2577 PetscCall(PetscLogEventBegin(ctx->events[0], 0, 0, 0, 0)); 2578 #if defined(PETSC_HAVE_THREADSAFETY) 2579 starttime = MPI_Wtime(); 2580 #endif 2581 PetscCall(DMGetDimension(pack, &dim)); 2582 PetscCall(PetscObjectStateGet((PetscObject)ctx->J, &state)); 2583 if (state != ctx->norm_state) { 2584 PetscCall(PetscInfo(ts, "Create Landau Jacobian t=%g J.state %" PetscInt64_FMT " --> %" PetscInt64_FMT "\n", (double)time_dummy, ctx->norm_state, state)); 2585 PetscCall(MatZeroEntries(ctx->J)); 2586 PetscCall(LandauFormJacobian_Internal(X, ctx->J, dim, 0.0, (void *)ctx)); 2587 PetscCall(MatViewFromOptions(ctx->J, NULL, "-dm_landau_jacobian_view")); 2588 PetscCall(PetscObjectStateGet((PetscObject)ctx->J, &state)); 2589 ctx->norm_state = state; 2590 } else { 2591 PetscCall(PetscInfo(ts, "WARNING Skip forming Jacobian, has not changed %" PetscInt64_FMT "\n", state)); 2592 } 2593 /* mat vec for op */ 2594 PetscCall(MatMult(ctx->J, X, F)); /* C*f */ 2595 /* add time term */ 2596 if (X_t) PetscCall(MatMultAdd(ctx->M, X_t, F, F)); 2597 #if defined(PETSC_HAVE_THREADSAFETY) 2598 if (ctx->stage) { 2599 endtime = MPI_Wtime(); 2600 ctx->times[LANDAU_OPERATOR] += (endtime - starttime); 2601 ctx->times[LANDAU_JACOBIAN] += (endtime - starttime); 2602 ctx->times[LANDAU_MATRIX_TOTAL] += (endtime - starttime); 2603 ctx->times[LANDAU_JACOBIAN_COUNT] += 1; 2604 } 2605 #endif 2606 PetscCall(PetscLogEventEnd(ctx->events[0], 0, 0, 0, 0)); 2607 PetscCall(PetscLogEventEnd(ctx->events[11], 0, 0, 0, 0)); 2608 if (ctx->stage) PetscCall(PetscLogStagePop()); 2609 PetscFunctionReturn(PETSC_SUCCESS); 2610 } 2611 2612 /*@ 2613 DMPlexLandauIJacobian - TS Jacobian construction, confusingly this adds mass 2614 2615 Collective 2616 2617 Input Parameters: 2618 + TS - The time stepping context 2619 . time_dummy - current time (not used) 2620 . X - Current state 2621 . U_tdummy - Time derivative of current state (not used) 2622 . shift - shift for du/dt term 2623 - actx - Landau context 2624 2625 Output Parameters: 2626 + Amat - Jacobian 2627 - Pmat - same as Amat 2628 2629 Level: beginner 2630 2631 .keywords: mesh 2632 .seealso: `DMPlexLandauCreateVelocitySpace()`, `DMPlexLandauIFunction()` 2633 @*/ 2634 PetscErrorCode DMPlexLandauIJacobian(TS ts, PetscReal time_dummy, Vec X, Vec U_tdummy, PetscReal shift, Mat Amat, Mat Pmat, void *actx) 2635 { 2636 LandauCtx *ctx = NULL; 2637 PetscInt dim; 2638 DM pack; 2639 #if defined(PETSC_HAVE_THREADSAFETY) 2640 double starttime, endtime; 2641 #endif 2642 PetscObjectState state; 2643 2644 PetscFunctionBegin; 2645 PetscCall(TSGetDM(ts, &pack)); 2646 PetscCall(DMGetApplicationContext(pack, &ctx)); 2647 PetscCheck(ctx, PETSC_COMM_SELF, PETSC_ERR_PLIB, "no context"); 2648 PetscCheck(Amat == Pmat && Amat == ctx->J, ctx->comm, PETSC_ERR_PLIB, "Amat!=Pmat || Amat!=ctx->J"); 2649 PetscCall(DMGetDimension(pack, &dim)); 2650 /* get collision Jacobian into A */ 2651 if (ctx->stage) PetscCall(PetscLogStagePush(ctx->stage)); 2652 PetscCall(PetscLogEventBegin(ctx->events[11], 0, 0, 0, 0)); 2653 PetscCall(PetscLogEventBegin(ctx->events[9], 0, 0, 0, 0)); 2654 #if defined(PETSC_HAVE_THREADSAFETY) 2655 starttime = MPI_Wtime(); 2656 #endif 2657 PetscCall(PetscInfo(ts, "Adding mass to Jacobian t=%g, shift=%g\n", (double)time_dummy, (double)shift)); 2658 PetscCheck(shift != 0.0, ctx->comm, PETSC_ERR_PLIB, "zero shift"); 2659 PetscCall(PetscObjectStateGet((PetscObject)ctx->J, &state)); 2660 PetscCheck(state == ctx->norm_state, ctx->comm, PETSC_ERR_PLIB, "wrong state, %" PetscInt64_FMT " %" PetscInt64_FMT "", ctx->norm_state, state); 2661 if (!ctx->use_matrix_mass) { 2662 PetscCall(LandauFormJacobian_Internal(X, ctx->J, dim, shift, (void *)ctx)); 2663 } else { /* add mass */ 2664 PetscCall(MatAXPY(Pmat, shift, ctx->M, SAME_NONZERO_PATTERN)); 2665 } 2666 #if defined(PETSC_HAVE_THREADSAFETY) 2667 if (ctx->stage) { 2668 endtime = MPI_Wtime(); 2669 ctx->times[LANDAU_OPERATOR] += (endtime - starttime); 2670 ctx->times[LANDAU_MASS] += (endtime - starttime); 2671 ctx->times[LANDAU_MATRIX_TOTAL] += (endtime - starttime); 2672 } 2673 #endif 2674 PetscCall(PetscLogEventEnd(ctx->events[9], 0, 0, 0, 0)); 2675 PetscCall(PetscLogEventEnd(ctx->events[11], 0, 0, 0, 0)); 2676 if (ctx->stage) PetscCall(PetscLogStagePop()); 2677 PetscFunctionReturn(PETSC_SUCCESS); 2678 } 2679