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author | 2019-09-27 13:58:28 -0700 | |
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committer | 2019-09-27 13:58:28 -0700 | |
commit | 66885c39fd0f58d7e4ad7398ea6a595391ca60c5 (patch) | |
tree | 554173d4bf99cc0a46a0f1029882d3700a6a19a9 /Source/Particles/PhysicalParticleContainer.cpp | |
parent | 3052787173ae746445fba2575c7835959f184b63 (diff) | |
parent | 46e29ba5d4ac5d745e3d6c3dc2b9408a2a3753de (diff) | |
download | WarpX-66885c39fd0f58d7e4ad7398ea6a595391ca60c5.tar.gz WarpX-66885c39fd0f58d7e4ad7398ea6a595391ca60c5.tar.zst WarpX-66885c39fd0f58d7e4ad7398ea6a595391ca60c5.zip |
Merge branch 'dev' into generalize_nodal_deposition
Diffstat (limited to 'Source/Particles/PhysicalParticleContainer.cpp')
-rw-r--r-- | Source/Particles/PhysicalParticleContainer.cpp | 610 |
1 files changed, 267 insertions, 343 deletions
diff --git a/Source/Particles/PhysicalParticleContainer.cpp b/Source/Particles/PhysicalParticleContainer.cpp index 2dc25e6fa..02dee1967 100644 --- a/Source/Particles/PhysicalParticleContainer.cpp +++ b/Source/Particles/PhysicalParticleContainer.cpp @@ -31,10 +31,13 @@ PhysicalParticleContainer::PhysicalParticleContainer (AmrCore* amr_core, int isp pp.query("boost_adjust_transverse_positions", boost_adjust_transverse_positions); pp.query("do_backward_propagation", do_backward_propagation); + + // Initialize splitting pp.query("do_splitting", do_splitting); pp.query("split_type", split_type); + pp.query("do_continuous_injection", do_continuous_injection); - // Whether to plot back-transformed (lab-frame) diagnostics + // Whether to plot back-transformed (lab-frame) diagnostics // for this species. pp.query("do_boosted_frame_diags", do_boosted_frame_diags); @@ -51,7 +54,7 @@ PhysicalParticleContainer::PhysicalParticleContainer (AmrCore* amr_core, int isp do_user_plot_vars = pp.queryarr("plot_vars", plot_vars); if (not do_user_plot_vars){ // By default, all particle variables are dumped to plotfiles, - // including {x,y,z,ux,uy,uz}old variables when running in a + // including {x,y,z,ux,uy,uz}old variables when running in a // boosted frame if (WarpX::do_boosted_frame_diagnostic && do_boosted_frame_diags){ plot_flags.resize(PIdx::nattribs + 6, 1); @@ -68,9 +71,9 @@ PhysicalParticleContainer::PhysicalParticleContainer (AmrCore* amr_core, int isp // If not none, set plot_flags values to 1 for elements in plot_vars. if (plot_vars[0] != "none"){ for (const auto& var : plot_vars){ - // Return error if var not in PIdx. - AMREX_ALWAYS_ASSERT_WITH_MESSAGE( - ParticleStringNames::to_index.count(var), + // Return error if var not in PIdx. + AMREX_ALWAYS_ASSERT_WITH_MESSAGE( + ParticleStringNames::to_index.count(var), "plot_vars argument not in ParticleStringNames"); plot_flags[ParticleStringNames::to_index.at(var)] = 1; } @@ -142,7 +145,7 @@ void PhysicalParticleContainer::MapParticletoBoostedFrame(Real& x, Real& y, Real void PhysicalParticleContainer::AddGaussianBeam(Real x_m, Real y_m, Real z_m, Real x_rms, Real y_rms, Real z_rms, - Real q_tot, long npart, + Real q_tot, long npart, int do_symmetrize) { const Geometry& geom = m_gdb->Geom(0); @@ -154,7 +157,7 @@ PhysicalParticleContainer::AddGaussianBeam(Real x_m, Real y_m, Real z_m, std::normal_distribution<double> distz(z_m, z_rms); if (ParallelDescriptor::IOProcessor()) { - // If do_symmetrize, create 4x fewer particles, and + // If do_symmetrize, create 4x fewer particles, and // Replicate each particle 4 times (x,y) (-x,y) (x,-y) (-x,-y) if (do_symmetrize){ npart /= 4; @@ -196,7 +199,7 @@ PhysicalParticleContainer::CheckAndAddParticle(Real x, Real y, Real z, std::array<Real, 3> u, Real weight) { - std::array<Real,PIdx::nattribs> attribs; + std::array<ParticleReal,PIdx::nattribs> attribs; attribs.fill(0.0); // update attribs with input arguments @@ -361,13 +364,13 @@ PhysicalParticleContainer::AddPlasma (int lev, RealBox part_realbox) for (int dir=0; dir<AMREX_SPACEDIM; dir++) { if ( tile_realbox.lo(dir) <= part_realbox.hi(dir) ) { Real ncells_adjust = std::floor( (tile_realbox.lo(dir) - part_realbox.lo(dir))/dx[dir] ); - overlap_realbox.setLo( dir, part_realbox.lo(dir) + std::max(ncells_adjust, 0.) * dx[dir]); + overlap_realbox.setLo( dir, part_realbox.lo(dir) + std::max(ncells_adjust, Real(0.)) * dx[dir]); } else { no_overlap = true; break; } if ( tile_realbox.hi(dir) >= part_realbox.lo(dir) ) { Real ncells_adjust = std::floor( (part_realbox.hi(dir) - tile_realbox.hi(dir))/dx[dir] ); - overlap_realbox.setHi( dir, part_realbox.hi(dir) - std::max(ncells_adjust, 0.) * dx[dir]); + overlap_realbox.setHi( dir, part_realbox.hi(dir) - std::max(ncells_adjust, Real(0.)) * dx[dir]); } else { no_overlap = true; break; } @@ -387,11 +390,11 @@ PhysicalParticleContainer::AddPlasma (int lev, RealBox part_realbox) const int tile_id = mfi.LocalTileIndex(); // Max number of new particles, if particles are created in the whole - // overlap_box. All of them are created, and invalid ones are then + // overlap_box. All of them are created, and invalid ones are then // discaded int max_new_particles = overlap_box.numPts() * num_ppc; - // If refine injection, build pointer dp_cellid that holds pointer to + // If refine injection, build pointer dp_cellid that holds pointer to // array of refined cell IDs. Vector<int> cellid_v; if (refine_injection and lev == 0) @@ -437,7 +440,7 @@ PhysicalParticleContainer::AddPlasma (int lev, RealBox part_realbox) ParticleType* pp = particle_tile.GetArrayOfStructs()().data() + old_size; auto& soa = particle_tile.GetStructOfArrays(); - GpuArray<Real*,PIdx::nattribs> pa; + GpuArray<ParticleReal*,PIdx::nattribs> pa; for (int ia = 0; ia < PIdx::nattribs; ++ia) { pa[ia] = soa.GetRealData(ia).data() + old_size; } @@ -446,7 +449,7 @@ PhysicalParticleContainer::AddPlasma (int lev, RealBox part_realbox) if (do_field_ionization) { pi = soa.GetIntData(particle_icomps["ionization_level"]).data() + old_size; } - + const GpuArray<Real,AMREX_SPACEDIM> overlap_corner {AMREX_D_DECL(overlap_realbox.lo(0), overlap_realbox.lo(1), @@ -455,12 +458,12 @@ PhysicalParticleContainer::AddPlasma (int lev, RealBox part_realbox) std::size_t shared_mem_bytes = plasma_injector->sharedMemoryNeeded(); int lrrfac = rrfac; - bool loc_do_field_ionization = do_field_ionization; - int loc_ionization_initial_level = ionization_initial_level; + bool loc_do_field_ionization = do_field_ionization; + int loc_ionization_initial_level = ionization_initial_level; - // Loop over all new particles and inject them (creates too many + // Loop over all new particles and inject them (creates too many // particles, in particular does not consider xmin, xmax etc.). - // The invalid ones are given negative ID and are deleted during the + // The invalid ones are given negative ID and are deleted during the // next redistribute. amrex::For(max_new_particles, [=] AMREX_GPU_DEVICE (int ip) noexcept { @@ -627,7 +630,7 @@ PhysicalParticleContainer::AddPlasma (int lev, RealBox part_realbox) p.pos(1) = z; #endif }, shared_mem_bytes); - + if (cost) { wt = (amrex::second() - wt) / tile_box.d_numPts(); Array4<Real> const& costarr = cost->array(mfi); @@ -865,7 +868,7 @@ PhysicalParticleContainer::FieldGather (int lev, MultiFab* cost = WarpX::getCosts(lev); #ifdef _OPENMP -#pragma omp parallel +#pragma omp parallel #endif { #ifdef _OPENMP @@ -915,7 +918,7 @@ PhysicalParticleContainer::FieldGather (int lev, // int e_is_nodal = Ex.is_nodal() and Ey.is_nodal() and Ez.is_nodal(); FieldGather(pti, Exp, Eyp, Ezp, Bxp, Byp, Bzp, - &exfab, &eyfab, &ezfab, &bxfab, &byfab, &bzfab, + &exfab, &eyfab, &ezfab, &bxfab, &byfab, &bzfab, Ex.nGrow(), e_is_nodal, 0, np, thread_num, lev, lev); @@ -942,25 +945,23 @@ PhysicalParticleContainer::Evolve (int lev, MultiFab* rho, MultiFab* crho, const MultiFab* cEx, const MultiFab* cEy, const MultiFab* cEz, const MultiFab* cBx, const MultiFab* cBy, const MultiFab* cBz, - Real t, Real dt) + Real t, Real dt, DtType a_dt_type) { BL_PROFILE("PPC::Evolve()"); BL_PROFILE_VAR_NS("PPC::Evolve::Copy", blp_copy); BL_PROFILE_VAR_NS("PPC::FieldGather", blp_fg); BL_PROFILE_VAR_NS("PPC::ParticlePush", blp_ppc_pp); - BL_PROFILE_VAR_NS("PPC::Evolve::partition", blp_partition); - + const std::array<Real,3>& dx = WarpX::CellSize(lev); const std::array<Real,3>& cdx = WarpX::CellSize(std::max(lev-1,0)); - // Get instances of NCI Godfrey filters + // Get instances of NCI Godfrey filters const auto& nci_godfrey_filter_exeybz = WarpX::GetInstance().nci_godfrey_filter_exeybz; const auto& nci_godfrey_filter_bxbyez = WarpX::GetInstance().nci_godfrey_filter_bxbyez; BL_ASSERT(OnSameGrids(lev,jx)); MultiFab* cost = WarpX::getCosts(lev); - const iMultiFab* current_masks = WarpX::CurrentBufferMasks(lev); const iMultiFab* gather_masks = WarpX::GatherBufferMasks(lev); @@ -978,9 +979,9 @@ PhysicalParticleContainer::Evolve (int lev, tmp_particle_data[lev][index][i].resize(np); } } - + #ifdef _OPENMP -#pragma omp parallel +#pragma omp parallel #endif { #ifdef _OPENMP @@ -991,10 +992,6 @@ PhysicalParticleContainer::Evolve (int lev, FArrayBox filtered_Ex, filtered_Ey, filtered_Ez; FArrayBox filtered_Bx, filtered_By, filtered_Bz; - std::vector<bool> inexflag; - Vector<long> pid; - RealVector tmp; - ParticleVector particle_tmp; for (WarpXParIter pti(*this, lev); pti.isValid(); ++pti) { @@ -1026,56 +1023,18 @@ PhysicalParticleContainer::Evolve (int lev, FArrayBox const* bzfab = &(Bz[pti]); Elixir exeli, eyeli, ezeli, bxeli, byeli, bzeli; + if (WarpX::use_fdtd_nci_corr) { -#if (AMREX_SPACEDIM == 2) - const Box& tbox = amrex::grow(pti.tilebox(),{static_cast<int>(WarpX::nox), - static_cast<int>(WarpX::noz)}); -#else - const Box& tbox = amrex::grow(pti.tilebox(),{static_cast<int>(WarpX::nox), - static_cast<int>(WarpX::noy), - static_cast<int>(WarpX::noz)}); -#endif - - // Filter Ex (Both 2D and 3D) - filtered_Ex.resize(amrex::convert(tbox,WarpX::Ex_nodal_flag)); - // Safeguard for GPU - exeli = filtered_Ex.elixir(); - // Apply filter on Ex, result stored in filtered_Ex - nci_godfrey_filter_exeybz[lev]->ApplyStencil(filtered_Ex, Ex[pti], filtered_Ex.box()); - // Update exfab reference - exfab = &filtered_Ex; - - // Filter Ez - filtered_Ez.resize(amrex::convert(tbox,WarpX::Ez_nodal_flag)); - ezeli = filtered_Ez.elixir(); - nci_godfrey_filter_bxbyez[lev]->ApplyStencil(filtered_Ez, Ez[pti], filtered_Ez.box()); - ezfab = &filtered_Ez; - - // Filter By - filtered_By.resize(amrex::convert(tbox,WarpX::By_nodal_flag)); - byeli = filtered_By.elixir(); - nci_godfrey_filter_bxbyez[lev]->ApplyStencil(filtered_By, By[pti], filtered_By.box()); - byfab = &filtered_By; -#if (AMREX_SPACEDIM == 3) - // Filter Ey - filtered_Ey.resize(amrex::convert(tbox,WarpX::Ey_nodal_flag)); - eyeli = filtered_Ey.elixir(); - nci_godfrey_filter_exeybz[lev]->ApplyStencil(filtered_Ey, Ey[pti], filtered_Ey.box()); - eyfab = &filtered_Ey; - - // Filter Bx - filtered_Bx.resize(amrex::convert(tbox,WarpX::Bx_nodal_flag)); - bxeli = filtered_Bx.elixir(); - nci_godfrey_filter_bxbyez[lev]->ApplyStencil(filtered_Bx, Bx[pti], filtered_Bx.box()); - bxfab = &filtered_Bx; - - // Filter Bz - filtered_Bz.resize(amrex::convert(tbox,WarpX::Bz_nodal_flag)); - bzeli = filtered_Bz.elixir(); - nci_godfrey_filter_exeybz[lev]->ApplyStencil(filtered_Bz, Bz[pti], filtered_Bz.box()); - bzfab = &filtered_Bz; -#endif + // Filter arrays Ex[pti], store the result in + // filtered_Ex and update pointer exfab so that it + // points to filtered_Ex (and do the same for all + // components of E and B). + applyNCIFilter(lev, pti.tilebox(), exeli, eyeli, ezeli, bxeli, byeli, bzeli, + filtered_Ex, filtered_Ey, filtered_Ez, + filtered_Bx, filtered_By, filtered_Bz, + Ex[pti], Ey[pti], Ez[pti], Bx[pti], By[pti], Bz[pti], + exfab, eyfab, ezfab, bxfab, byfab, bzfab); } Exp.assign(np,0.0); @@ -1085,101 +1044,25 @@ PhysicalParticleContainer::Evolve (int lev, Byp.assign(np,WarpX::B_external[1]); Bzp.assign(np,WarpX::B_external[2]); - m_giv[thread_num].resize(np); - + // Determine which particles deposit/gather in the buffer, and + // which particles deposit/gather in the fine patch long nfine_current = np; long nfine_gather = np; - if (has_buffer && !do_not_push) - { - BL_PROFILE_VAR_START(blp_partition); - inexflag.resize(np); - auto& aos = pti.GetArrayOfStructs(); - // We need to partition the large buffer first - iMultiFab const* bmasks = (WarpX::n_field_gather_buffer >= WarpX::n_current_deposition_buffer) ? - gather_masks : current_masks; - int i = 0; - const auto& msk = (*bmasks)[pti]; - for (const auto& p : aos) { - const IntVect& iv = Index(p, lev); - inexflag[i++] = msk(iv); - } - - pid.resize(np); - std::iota(pid.begin(), pid.end(), 0L); - - auto sep = std::stable_partition(pid.begin(), pid.end(), - [&inexflag](long id) { return inexflag[id]; }); - - if (WarpX::n_current_deposition_buffer == WarpX::n_field_gather_buffer) { - nfine_current = nfine_gather = std::distance(pid.begin(), sep); - } else if (sep != pid.end()) { - int n_buf; - if (bmasks == gather_masks) { - nfine_gather = std::distance(pid.begin(), sep); - bmasks = current_masks; - n_buf = WarpX::n_current_deposition_buffer; - } else { - nfine_current = std::distance(pid.begin(), sep); - bmasks = gather_masks; - n_buf = WarpX::n_field_gather_buffer; - } - if (n_buf > 0) - { - const auto& msk2 = (*bmasks)[pti]; - for (auto it = sep; it != pid.end(); ++it) { - const long id = *it; - const IntVect& iv = Index(aos[id], lev); - inexflag[id] = msk2(iv); - } - - auto sep2 = std::stable_partition(sep, pid.end(), - [&inexflag](long id) {return inexflag[id];}); - if (bmasks == gather_masks) { - nfine_gather = std::distance(pid.begin(), sep2); - } else { - nfine_current = std::distance(pid.begin(), sep2); - } - } - } - - if (deposit_on_main_grid && lev > 0) { - nfine_current = 0; - } - - if (nfine_current != np || nfine_gather != np) - { - particle_tmp.resize(np); - for (long ip = 0; ip < np; ++ip) { - particle_tmp[ip] = aos[pid[ip]]; - } - std::swap(aos(), particle_tmp); - - tmp.resize(np); - for (long ip = 0; ip < np; ++ip) { - tmp[ip] = wp[pid[ip]]; - } - std::swap(wp, tmp); - - for (long ip = 0; ip < np; ++ip) { - tmp[ip] = uxp[pid[ip]]; - } - std::swap(uxp, tmp); - - for (long ip = 0; ip < np; ++ip) { - tmp[ip] = uyp[pid[ip]]; - } - std::swap(uyp, tmp); - - for (long ip = 0; ip < np; ++ip) { - tmp[ip] = uzp[pid[ip]]; - } - std::swap(uzp, tmp); - } - BL_PROFILE_VAR_STOP(blp_partition); + if (has_buffer && !do_not_push) { + // - Modify `nfine_current` and `nfine_gather` (in place) + // so that they correspond to the number of particles + // that deposit/gather in the fine patch respectively. + // - Reorder the particle arrays, + // so that the `nfine_current`/`nfine_gather` first particles + // deposit/gather in the fine patch + // and (thus) the `np-nfine_current`/`np-nfine_gather` last particles + // deposit/gather in the buffer + PartitionParticlesInBuffers( nfine_current, nfine_gather, np, + pti, lev, current_masks, gather_masks, uxp, uyp, uzp, wp ); } const long np_current = (cjx) ? nfine_current : np; - + // // copy data from particle container to temp arrays // @@ -1195,14 +1078,14 @@ PhysicalParticleContainer::Evolve (int lev, } else { ion_lev = nullptr; } - DepositCharge(pti, wp, ion_lev, rho, 0, 0, + DepositCharge(pti, wp, ion_lev, rho, 0, 0, np_current, thread_num, lev, lev); if (has_buffer){ DepositCharge(pti, wp, ion_lev, crho, 0, np_current, np-np_current, thread_num, lev, lev-1); } } - + if (! do_not_push) { const long np_gather = (cEx) ? nfine_gather : np; @@ -1214,7 +1097,7 @@ PhysicalParticleContainer::Evolve (int lev, // BL_PROFILE_VAR_START(blp_fg); FieldGather(pti, Exp, Eyp, Ezp, Bxp, Byp, Bzp, - exfab, eyfab, ezfab, bxfab, byfab, bzfab, + exfab, eyfab, ezfab, bxfab, byfab, bzfab, Ex.nGrow(), e_is_nodal, 0, np_gather, thread_num, lev, lev); @@ -1230,66 +1113,28 @@ PhysicalParticleContainer::Evolve (int lev, FArrayBox const* cbxfab = &(*cBx)[pti]; FArrayBox const* cbyfab = &(*cBy)[pti]; FArrayBox const* cbzfab = &(*cBz)[pti]; - + if (WarpX::use_fdtd_nci_corr) { -#if (AMREX_SPACEDIM == 2) - const Box& tbox = amrex::grow(cbox,{static_cast<int>(WarpX::nox), - static_cast<int>(WarpX::noz)}); -#else - const Box& tbox = amrex::grow(cbox,{static_cast<int>(WarpX::nox), - static_cast<int>(WarpX::noy), - static_cast<int>(WarpX::noz)}); -#endif - - // Filter Ex (both 2D and 3D) - filtered_Ex.resize(amrex::convert(tbox,WarpX::Ex_nodal_flag)); - // Safeguard for GPU - exeli = filtered_Ex.elixir(); - // Apply filter on Ex, result stored in filtered_Ex - nci_godfrey_filter_exeybz[lev-1]->ApplyStencil(filtered_Ex, (*cEx)[pti], filtered_Ex.box()); - // Update exfab reference - cexfab = &filtered_Ex; - - // Filter Ez - filtered_Ez.resize(amrex::convert(tbox,WarpX::Ez_nodal_flag)); - ezeli = filtered_Ez.elixir(); - nci_godfrey_filter_bxbyez[lev-1]->ApplyStencil(filtered_Ez, (*cEz)[pti], filtered_Ez.box()); - cezfab = &filtered_Ez; - - // Filter By - filtered_By.resize(amrex::convert(tbox,WarpX::By_nodal_flag)); - byeli = filtered_By.elixir(); - nci_godfrey_filter_bxbyez[lev-1]->ApplyStencil(filtered_By, (*cBy)[pti], filtered_By.box()); - cbyfab = &filtered_By; -#if (AMREX_SPACEDIM == 3) - // Filter Ey - filtered_Ey.resize(amrex::convert(tbox,WarpX::Ey_nodal_flag)); - eyeli = filtered_Ey.elixir(); - nci_godfrey_filter_exeybz[lev-1]->ApplyStencil(filtered_Ey, (*cEy)[pti], filtered_Ey.box()); - ceyfab = &filtered_Ey; - - // Filter Bx - filtered_Bx.resize(amrex::convert(tbox,WarpX::Bx_nodal_flag)); - bxeli = filtered_Bx.elixir(); - nci_godfrey_filter_bxbyez[lev-1]->ApplyStencil(filtered_Bx, (*cBx)[pti], filtered_Bx.box()); - cbxfab = &filtered_Bx; - - // Filter Bz - filtered_Bz.resize(amrex::convert(tbox,WarpX::Bz_nodal_flag)); - bzeli = filtered_Bz.elixir(); - nci_godfrey_filter_exeybz[lev-1]->ApplyStencil(filtered_Bz, (*cBz)[pti], filtered_Bz.box()); - cbzfab = &filtered_Bz; -#endif + // Filter arrays (*cEx)[pti], store the result in + // filtered_Ex and update pointer cexfab so that it + // points to filtered_Ex (and do the same for all + // components of E and B) + applyNCIFilter(lev-1, cbox, exeli, eyeli, ezeli, bxeli, byeli, bzeli, + filtered_Ex, filtered_Ey, filtered_Ez, + filtered_Bx, filtered_By, filtered_Bz, + (*cEx)[pti], (*cEy)[pti], (*cEz)[pti], + (*cBx)[pti], (*cBy)[pti], (*cBz)[pti], + cexfab, ceyfab, cezfab, cbxfab, cbyfab, cbzfab); } - + // Field gather for particles in gather buffers e_is_nodal = cEx->is_nodal() and cEy->is_nodal() and cEz->is_nodal(); - FieldGather(pti, Exp, Eyp, Ezp, Bxp, Byp, Bzp, + FieldGather(pti, Exp, Eyp, Ezp, Bxp, Byp, Bzp, cexfab, ceyfab, cezfab, cbxfab, cbyfab, cbzfab, - cEx->nGrow(), e_is_nodal, - nfine_gather, np-nfine_gather, + cEx->nGrow(), e_is_nodal, + nfine_gather, np-nfine_gather, thread_num, lev, lev-1); } @@ -1299,8 +1144,7 @@ PhysicalParticleContainer::Evolve (int lev, // Particle Push // BL_PROFILE_VAR_START(blp_ppc_pp); - PushPX(pti, m_xp[thread_num], m_yp[thread_num], m_zp[thread_num], - m_giv[thread_num], dt); + PushPX(pti, m_xp[thread_num], m_yp[thread_num], m_zp[thread_num], dt, a_dt_type); BL_PROFILE_VAR_STOP(blp_ppc_pp); // @@ -1313,7 +1157,7 @@ PhysicalParticleContainer::Evolve (int lev, } else { ion_lev = nullptr; } - + // Deposit inside domains DepositCurrent(pti, wp, uxp, uyp, uzp, ion_lev, &jx, &jy, &jz, 0, np_current, thread_num, @@ -1333,7 +1177,7 @@ PhysicalParticleContainer::Evolve (int lev, pti.SetPosition(m_xp[thread_num], m_yp[thread_num], m_zp[thread_num]); BL_PROFILE_VAR_STOP(blp_copy); } - + if (rho) { // Deposit charge after particle push, in component 1 of MultiFab rho. int* AMREX_RESTRICT ion_lev; @@ -1362,8 +1206,84 @@ PhysicalParticleContainer::Evolve (int lev, } } } - // Split particles - if (do_splitting){ SplitParticles(lev); } + // Split particles at the end of the timestep. + // When subcycling is ON, the splitting is done on the last call to + // PhysicalParticleContainer::Evolve on the finest level, i.e., at the + // end of the large timestep. Otherwise, the pushes on different levels + // are not consistent, and the call to Redistribute (inside + // SplitParticles) may result in split particles to deposit twice on the + // coarse level. + if (do_splitting && (a_dt_type == DtType::SecondHalf || a_dt_type == DtType::Full) ){ + SplitParticles(lev); + } +} + +void +PhysicalParticleContainer::applyNCIFilter ( + int lev, const Box& box, + Elixir& exeli, Elixir& eyeli, Elixir& ezeli, + Elixir& bxeli, Elixir& byeli, Elixir& bzeli, + FArrayBox& filtered_Ex, FArrayBox& filtered_Ey, FArrayBox& filtered_Ez, + FArrayBox& filtered_Bx, FArrayBox& filtered_By, FArrayBox& filtered_Bz, + const FArrayBox& Ex, const FArrayBox& Ey, const FArrayBox& Ez, + const FArrayBox& Bx, const FArrayBox& By, const FArrayBox& Bz, + FArrayBox const * & ex_ptr, FArrayBox const * & ey_ptr, + FArrayBox const * & ez_ptr, FArrayBox const * & bx_ptr, + FArrayBox const * & by_ptr, FArrayBox const * & bz_ptr) +{ + + // Get instances of NCI Godfrey filters + const auto& nci_godfrey_filter_exeybz = WarpX::GetInstance().nci_godfrey_filter_exeybz; + const auto& nci_godfrey_filter_bxbyez = WarpX::GetInstance().nci_godfrey_filter_bxbyez; + +#if (AMREX_SPACEDIM == 2) + const Box& tbox = amrex::grow(box,{static_cast<int>(WarpX::nox), + static_cast<int>(WarpX::noz)}); +#else + const Box& tbox = amrex::grow(box,{static_cast<int>(WarpX::nox), + static_cast<int>(WarpX::noy), + static_cast<int>(WarpX::noz)}); +#endif + + // Filter Ex (Both 2D and 3D) + filtered_Ex.resize(amrex::convert(tbox,WarpX::Ex_nodal_flag)); + // Safeguard for GPU + exeli = filtered_Ex.elixir(); + // Apply filter on Ex, result stored in filtered_Ex + nci_godfrey_filter_exeybz[lev]->ApplyStencil(filtered_Ex, Ex, filtered_Ex.box()); + // Update ex_ptr reference + ex_ptr = &filtered_Ex; + + // Filter Ez + filtered_Ez.resize(amrex::convert(tbox,WarpX::Ez_nodal_flag)); + ezeli = filtered_Ez.elixir(); + nci_godfrey_filter_bxbyez[lev]->ApplyStencil(filtered_Ez, Ez, filtered_Ez.box()); + ez_ptr = &filtered_Ez; + + // Filter By + filtered_By.resize(amrex::convert(tbox,WarpX::By_nodal_flag)); + byeli = filtered_By.elixir(); + nci_godfrey_filter_bxbyez[lev]->ApplyStencil(filtered_By, By, filtered_By.box()); + by_ptr = &filtered_By; +#if (AMREX_SPACEDIM == 3) + // Filter Ey + filtered_Ey.resize(amrex::convert(tbox,WarpX::Ey_nodal_flag)); + eyeli = filtered_Ey.elixir(); + nci_godfrey_filter_exeybz[lev]->ApplyStencil(filtered_Ey, Ey, filtered_Ey.box()); + ey_ptr = &filtered_Ey; + + // Filter Bx + filtered_Bx.resize(amrex::convert(tbox,WarpX::Bx_nodal_flag)); + bxeli = filtered_Bx.elixir(); + nci_godfrey_filter_bxbyez[lev]->ApplyStencil(filtered_Bx, Bx, filtered_Bx.box()); + bx_ptr = &filtered_Bx; + + // Filter Bz + filtered_Bz.resize(amrex::convert(tbox,WarpX::Bz_nodal_flag)); + bzeli = filtered_Bz.elixir(); + nci_godfrey_filter_exeybz[lev]->ApplyStencil(filtered_Bz, Bz, filtered_Bz.box()); + bz_ptr = &filtered_Bz; +#endif } // Loop over all particles in the particle container and @@ -1373,7 +1293,7 @@ PhysicalParticleContainer::SplitParticles(int lev) { auto& mypc = WarpX::GetInstance().GetPartContainer(); auto& pctmp_split = mypc.GetPCtmp(); - Cuda::ManagedDeviceVector<Real> xp, yp, zp; + Cuda::ManagedDeviceVector<ParticleReal> xp, yp, zp; RealVector psplit_x, psplit_y, psplit_z, psplit_w; RealVector psplit_ux, psplit_uy, psplit_uz; long np_split_to_add = 0; @@ -1389,7 +1309,16 @@ PhysicalParticleContainer::SplitParticles(int lev) for (WarpXParIter pti(*this, lev); pti.isValid(); ++pti) { pti.GetPosition(xp, yp, zp); + + // offset for split particles is computed as a function of cell size + // and number of particles per cell, so that a uniform distribution + // before splitting results in a uniform distribution after splitting + const amrex::Vector<int> ppc_nd = plasma_injector->num_particles_per_cell_each_dim; const std::array<Real,3>& dx = WarpX::CellSize(lev); + amrex::Vector<amrex::Real> split_offset = {dx[0]/2./ppc_nd[0], + dx[1]/2./ppc_nd[1], + dx[2]/2./ppc_nd[2]}; + // particle Array Of Structs data auto& particles = pti.GetArrayOfStructs(); // particle Struct Of Arrays data @@ -1402,19 +1331,19 @@ PhysicalParticleContainer::SplitParticles(int lev) for(int i=0; i<np; i++){ auto& p = particles[i]; if (p.id() == DoSplitParticleID){ - // If particle is tagged, split it and put the + // If particle is tagged, split it and put the // split particles in local arrays psplit_x etc. np_split_to_add += np_split; #if (AMREX_SPACEDIM==2) if (split_type==0){ - // Split particle in two along each axis + // Split particle in two along each diagonals // 4 particles in 2d for (int ishift = -1; ishift < 2; ishift +=2 ){ for (int kshift = -1; kshift < 2; kshift +=2 ){ // Add one particle with offset in x and z - psplit_x.push_back( xp[i] + ishift*dx[0]/2 ); + psplit_x.push_back( xp[i] + ishift*split_offset[0] ); psplit_y.push_back( yp[i] ); - psplit_z.push_back( zp[i] + kshift*dx[2]/2 ); + psplit_z.push_back( zp[i] + kshift*split_offset[2] ); psplit_ux.push_back( uxp[i] ); psplit_uy.push_back( uyp[i] ); psplit_uz.push_back( uzp[i] ); @@ -1422,11 +1351,11 @@ PhysicalParticleContainer::SplitParticles(int lev) } } } else { - // Split particle in two along each diagonal + // Split particle in two along each axis // 4 particles in 2d for (int ishift = -1; ishift < 2; ishift +=2 ){ // Add one particle with offset in x - psplit_x.push_back( xp[i] + ishift*dx[0]/2 ); + psplit_x.push_back( xp[i] + ishift*split_offset[0] ); psplit_y.push_back( yp[i] ); psplit_z.push_back( zp[i] ); psplit_ux.push_back( uxp[i] ); @@ -1436,7 +1365,7 @@ PhysicalParticleContainer::SplitParticles(int lev) // Add one particle with offset in z psplit_x.push_back( xp[i] ); psplit_y.push_back( yp[i] ); - psplit_z.push_back( zp[i] + ishift*dx[2]/2 ); + psplit_z.push_back( zp[i] + ishift*split_offset[2] ); psplit_ux.push_back( uxp[i] ); psplit_uy.push_back( uyp[i] ); psplit_uz.push_back( uzp[i] ); @@ -1445,15 +1374,15 @@ PhysicalParticleContainer::SplitParticles(int lev) } #elif (AMREX_SPACEDIM==3) if (split_type==0){ - // Split particle in two along each axis - // 6 particles in 2d + // Split particle in two along each diagonals + // 8 particles in 3d for (int ishift = -1; ishift < 2; ishift +=2 ){ for (int jshift = -1; jshift < 2; jshift +=2 ){ for (int kshift = -1; kshift < 2; kshift +=2 ){ // Add one particle with offset in x, y and z - psplit_x.push_back( xp[i] + ishift*dx[0]/2 ); - psplit_y.push_back( yp[i] + jshift*dx[1]/2 ); - psplit_z.push_back( zp[i] + jshift*dx[2]/2 ); + psplit_x.push_back( xp[i] + ishift*split_offset[0] ); + psplit_y.push_back( yp[i] + jshift*split_offset[1] ); + psplit_z.push_back( zp[i] + kshift*split_offset[2] ); psplit_ux.push_back( uxp[i] ); psplit_uy.push_back( uyp[i] ); psplit_uz.push_back( uzp[i] ); @@ -1462,11 +1391,11 @@ PhysicalParticleContainer::SplitParticles(int lev) } } } else { - // Split particle in two along each diagonal - // 8 particles in 3d + // Split particle in two along each axis + // 6 particles in 3d for (int ishift = -1; ishift < 2; ishift +=2 ){ // Add one particle with offset in x - psplit_x.push_back( xp[i] + ishift*dx[0]/2 ); + psplit_x.push_back( xp[i] + ishift*split_offset[0] ); psplit_y.push_back( yp[i] ); psplit_z.push_back( zp[i] ); psplit_ux.push_back( uxp[i] ); @@ -1475,7 +1404,7 @@ PhysicalParticleContainer::SplitParticles(int lev) psplit_w.push_back( wp[i]/np_split ); // Add one particle with offset in y psplit_x.push_back( xp[i] ); - psplit_y.push_back( yp[i] + ishift*dx[1]/2 ); + psplit_y.push_back( yp[i] + ishift*split_offset[1] ); psplit_z.push_back( zp[i] ); psplit_ux.push_back( uxp[i] ); psplit_uy.push_back( uyp[i] ); @@ -1484,7 +1413,7 @@ PhysicalParticleContainer::SplitParticles(int lev) // Add one particle with offset in z psplit_x.push_back( xp[i] ); psplit_y.push_back( yp[i] ); - psplit_z.push_back( zp[i] + ishift*dx[2]/2 ); + psplit_z.push_back( zp[i] + ishift*split_offset[2] ); psplit_ux.push_back( uxp[i] ); psplit_uy.push_back( uyp[i] ); psplit_uz.push_back( uzp[i] ); @@ -1497,13 +1426,13 @@ PhysicalParticleContainer::SplitParticles(int lev) } } } - // Add local arrays psplit_x etc. to the temporary - // particle container pctmp_split. Split particles - // are tagged with p.id()=NoSplitParticleID so that - // they are not re-split when entering a higher level - // AddNParticles calls Redistribute, so that particles - // in pctmp_split are in the proper grids and tiles - pctmp_split.AddNParticles(lev, + // Add local arrays psplit_x etc. to the temporary + // particle container pctmp_split. Split particles + // are tagged with p.id()=NoSplitParticleID so that + // they are not re-split when entering a higher level + // AddNParticles calls Redistribute, so that particles + // in pctmp_split are in the proper grids and tiles + pctmp_split.AddNParticles(lev, np_split_to_add, psplit_x.dataPtr(), psplit_y.dataPtr(), @@ -1514,39 +1443,37 @@ PhysicalParticleContainer::SplitParticles(int lev) 1, psplit_w.dataPtr(), 1, NoSplitParticleID); - // Copy particles from tmp to current particle container + // Copy particles from tmp to current particle container addParticles(pctmp_split,1); - // Clear tmp container + // Clear tmp container pctmp_split.clearParticles(); } void PhysicalParticleContainer::PushPX(WarpXParIter& pti, - Cuda::ManagedDeviceVector<Real>& xp, - Cuda::ManagedDeviceVector<Real>& yp, - Cuda::ManagedDeviceVector<Real>& zp, - Cuda::ManagedDeviceVector<Real>& giv, - Real dt) + Cuda::ManagedDeviceVector<ParticleReal>& xp, + Cuda::ManagedDeviceVector<ParticleReal>& yp, + Cuda::ManagedDeviceVector<ParticleReal>& zp, + Real dt, DtType a_dt_type) { // This wraps the momentum and position advance so that inheritors can modify the call. auto& attribs = pti.GetAttribs(); // Extract pointers to the different particle quantities - Real* const AMREX_RESTRICT x = xp.dataPtr(); - Real* const AMREX_RESTRICT y = yp.dataPtr(); - Real* const AMREX_RESTRICT z = zp.dataPtr(); - Real* const AMREX_RESTRICT gi = giv.dataPtr(); - Real* const AMREX_RESTRICT ux = attribs[PIdx::ux].dataPtr(); - Real* const AMREX_RESTRICT uy = attribs[PIdx::uy].dataPtr(); - Real* const AMREX_RESTRICT uz = attribs[PIdx::uz].dataPtr(); - const Real* const AMREX_RESTRICT Ex = attribs[PIdx::Ex].dataPtr(); - const Real* const AMREX_RESTRICT Ey = attribs[PIdx::Ey].dataPtr(); - const Real* const AMREX_RESTRICT Ez = attribs[PIdx::Ez].dataPtr(); - const Real* const AMREX_RESTRICT Bx = attribs[PIdx::Bx].dataPtr(); - const Real* const AMREX_RESTRICT By = attribs[PIdx::By].dataPtr(); - const Real* const AMREX_RESTRICT Bz = attribs[PIdx::Bz].dataPtr(); - - if (WarpX::do_boosted_frame_diagnostic && do_boosted_frame_diags) + ParticleReal* const AMREX_RESTRICT x = xp.dataPtr(); + ParticleReal* const AMREX_RESTRICT y = yp.dataPtr(); + ParticleReal* const AMREX_RESTRICT z = zp.dataPtr(); + ParticleReal* const AMREX_RESTRICT ux = attribs[PIdx::ux].dataPtr(); + ParticleReal* const AMREX_RESTRICT uy = attribs[PIdx::uy].dataPtr(); + ParticleReal* const AMREX_RESTRICT uz = attribs[PIdx::uz].dataPtr(); + const ParticleReal* const AMREX_RESTRICT Ex = attribs[PIdx::Ex].dataPtr(); + const ParticleReal* const AMREX_RESTRICT Ey = attribs[PIdx::Ey].dataPtr(); + const ParticleReal* const AMREX_RESTRICT Ez = attribs[PIdx::Ez].dataPtr(); + const ParticleReal* const AMREX_RESTRICT Bx = attribs[PIdx::Bx].dataPtr(); + const ParticleReal* const AMREX_RESTRICT By = attribs[PIdx::By].dataPtr(); + const ParticleReal* const AMREX_RESTRICT Bz = attribs[PIdx::Bz].dataPtr(); + + if (WarpX::do_boosted_frame_diagnostic && do_boosted_frame_diags && (a_dt_type!=DtType::SecondHalf)) { copy_attribs(pti, x, y, z); } @@ -1555,17 +1482,17 @@ PhysicalParticleContainer::PushPX(WarpXParIter& pti, if (do_field_ionization){ ion_lev = pti.GetiAttribs(particle_icomps["ionization_level"]).dataPtr(); } - + // Loop over the particles and update their momentum const Real q = this->charge; const Real m = this-> mass; if (WarpX::particle_pusher_algo == ParticlePusherAlgo::Boris){ - amrex::ParallelFor( + amrex::ParallelFor( pti.numParticles(), [=] AMREX_GPU_DEVICE (long i) { Real qp = q; if (ion_lev){ qp *= ion_lev[i]; } - UpdateMomentumBoris( ux[i], uy[i], uz[i], gi[i], + UpdateMomentumBoris( ux[i], uy[i], uz[i], Ex[i], Ey[i], Ez[i], Bx[i], By[i], Bz[i], qp, m, dt); UpdatePosition( x[i], y[i], z[i], @@ -1578,7 +1505,7 @@ PhysicalParticleContainer::PushPX(WarpXParIter& pti, [=] AMREX_GPU_DEVICE (long i) { Real qp = q; if (ion_lev){ qp *= ion_lev[i]; } - UpdateMomentumVay( ux[i], uy[i], uz[i], gi[i], + UpdateMomentumVay( ux[i], uy[i], uz[i], Ex[i], Ey[i], Ez[i], Bx[i], By[i], Bz[i], qp, m, dt); UpdatePosition( x[i], y[i], z[i], @@ -1609,7 +1536,7 @@ PhysicalParticleContainer::PushP (int lev, Real dt, int thread_num = omp_get_thread_num(); #else int thread_num = 0; -#endif +#endif for (WarpXParIter pti(*this, lev); pti.isValid(); ++pti) { const Box& box = pti.validbox(); @@ -1640,8 +1567,6 @@ PhysicalParticleContainer::PushP (int lev, Real dt, Byp.assign(np,WarpX::B_external[1]); Bzp.assign(np,WarpX::B_external[2]); - m_giv[thread_num].resize(np); - // // copy data from particle container to temp arrays // @@ -1649,22 +1574,21 @@ PhysicalParticleContainer::PushP (int lev, Real dt, int e_is_nodal = Ex.is_nodal() and Ey.is_nodal() and Ez.is_nodal(); FieldGather(pti, Exp, Eyp, Ezp, Bxp, Byp, Bzp, - &exfab, &eyfab, &ezfab, &bxfab, &byfab, &bzfab, + &exfab, &eyfab, &ezfab, &bxfab, &byfab, &bzfab, Ex.nGrow(), e_is_nodal, 0, np, thread_num, lev, lev); // This wraps the momentum advance so that inheritors can modify the call. // Extract pointers to the different particle quantities - Real* const AMREX_RESTRICT gi = m_giv[thread_num].dataPtr(); - Real* const AMREX_RESTRICT ux = attribs[PIdx::ux].dataPtr(); - Real* const AMREX_RESTRICT uy = attribs[PIdx::uy].dataPtr(); - Real* const AMREX_RESTRICT uz = attribs[PIdx::uz].dataPtr(); - const Real* const AMREX_RESTRICT Expp = Exp.dataPtr(); - const Real* const AMREX_RESTRICT Eypp = Eyp.dataPtr(); - const Real* const AMREX_RESTRICT Ezpp = Ezp.dataPtr(); - const Real* const AMREX_RESTRICT Bxpp = Bxp.dataPtr(); - const Real* const AMREX_RESTRICT Bypp = Byp.dataPtr(); - const Real* const AMREX_RESTRICT Bzpp = Bzp.dataPtr(); + ParticleReal* const AMREX_RESTRICT ux = attribs[PIdx::ux].dataPtr(); + ParticleReal* const AMREX_RESTRICT uy = attribs[PIdx::uy].dataPtr(); + ParticleReal* const AMREX_RESTRICT uz = attribs[PIdx::uz].dataPtr(); + const ParticleReal* const AMREX_RESTRICT Expp = Exp.dataPtr(); + const ParticleReal* const AMREX_RESTRICT Eypp = Eyp.dataPtr(); + const ParticleReal* const AMREX_RESTRICT Ezpp = Ezp.dataPtr(); + const ParticleReal* const AMREX_RESTRICT Bxpp = Bxp.dataPtr(); + const ParticleReal* const AMREX_RESTRICT Bypp = Byp.dataPtr(); + const ParticleReal* const AMREX_RESTRICT Bzpp = Bzp.dataPtr(); // Loop over the particles and update their momentum const Real q = this->charge; @@ -1672,14 +1596,14 @@ PhysicalParticleContainer::PushP (int lev, Real dt, if (WarpX::particle_pusher_algo == ParticlePusherAlgo::Boris){ amrex::ParallelFor( pti.numParticles(), [=] AMREX_GPU_DEVICE (long i) { - UpdateMomentumBoris( ux[i], uy[i], uz[i], gi[i], + UpdateMomentumBoris( ux[i], uy[i], uz[i], Expp[i], Eypp[i], Ezpp[i], Bxpp[i], Bypp[i], Bzpp[i], q, m, dt); } ); } else if (WarpX::particle_pusher_algo == ParticlePusherAlgo::Vay) { amrex::ParallelFor( pti.numParticles(), [=] AMREX_GPU_DEVICE (long i) { - UpdateMomentumVay( ux[i], uy[i], uz[i], gi[i], + UpdateMomentumVay( ux[i], uy[i], uz[i], Expp[i], Eypp[i], Ezpp[i], Bxpp[i], Bypp[i], Bzpp[i], q, m, dt); } ); @@ -1690,30 +1614,30 @@ PhysicalParticleContainer::PushP (int lev, Real dt, } } -void PhysicalParticleContainer::copy_attribs(WarpXParIter& pti,const Real* xp, - const Real* yp, const Real* zp) +void PhysicalParticleContainer::copy_attribs(WarpXParIter& pti,const ParticleReal* xp, + const ParticleReal* yp, const ParticleReal* zp) { auto& attribs = pti.GetAttribs(); - Real* AMREX_RESTRICT uxp = attribs[PIdx::ux].dataPtr(); - Real* AMREX_RESTRICT uyp = attribs[PIdx::uy].dataPtr(); - Real* AMREX_RESTRICT uzp = attribs[PIdx::uz].dataPtr(); - + ParticleReal* AMREX_RESTRICT uxp = attribs[PIdx::ux].dataPtr(); + ParticleReal* AMREX_RESTRICT uyp = attribs[PIdx::uy].dataPtr(); + ParticleReal* AMREX_RESTRICT uzp = attribs[PIdx::uz].dataPtr(); + const auto np = pti.numParticles(); const auto lev = pti.GetLevel(); const auto index = pti.GetPairIndex(); - Real* AMREX_RESTRICT xpold = tmp_particle_data[lev][index][TmpIdx::xold ].dataPtr(); - Real* AMREX_RESTRICT ypold = tmp_particle_data[lev][index][TmpIdx::yold ].dataPtr(); - Real* AMREX_RESTRICT zpold = tmp_particle_data[lev][index][TmpIdx::zold ].dataPtr(); - Real* AMREX_RESTRICT uxpold = tmp_particle_data[lev][index][TmpIdx::uxold].dataPtr(); - Real* AMREX_RESTRICT uypold = tmp_particle_data[lev][index][TmpIdx::uyold].dataPtr(); - Real* AMREX_RESTRICT uzpold = tmp_particle_data[lev][index][TmpIdx::uzold].dataPtr(); + ParticleReal* AMREX_RESTRICT xpold = tmp_particle_data[lev][index][TmpIdx::xold ].dataPtr(); + ParticleReal* AMREX_RESTRICT ypold = tmp_particle_data[lev][index][TmpIdx::yold ].dataPtr(); + ParticleReal* AMREX_RESTRICT zpold = tmp_particle_data[lev][index][TmpIdx::zold ].dataPtr(); + ParticleReal* AMREX_RESTRICT uxpold = tmp_particle_data[lev][index][TmpIdx::uxold].dataPtr(); + ParticleReal* AMREX_RESTRICT uypold = tmp_particle_data[lev][index][TmpIdx::uyold].dataPtr(); + ParticleReal* AMREX_RESTRICT uzpold = tmp_particle_data[lev][index][TmpIdx::uzold].dataPtr(); ParallelFor( np, [=] AMREX_GPU_DEVICE (long i) { xpold[i]=xp[i]; ypold[i]=yp[i]; zpold[i]=zp[i]; - + uxpold[i]=uxp[i]; uypold[i]=uyp[i]; uzpold[i]=uzp[i]; @@ -1753,7 +1677,7 @@ void PhysicalParticleContainer::GetParticleSlice(const int direction, const Real slice_box.setHi(direction, z_max); diagnostic_particles.resize(finestLevel()+1); - + for (int lev = 0; lev < nlevs; ++lev) { const Real* dx = Geom(lev).CellSize(); @@ -1800,7 +1724,7 @@ void PhysicalParticleContainer::GetParticleSlice(const int direction, const Real auto& uzp_old = tmp_particle_data[lev][index][TmpIdx::uzold]; const long np = pti.numParticles(); - + Real uzfrm = -WarpX::gamma_boost*WarpX::beta_boost*PhysConst::c; Real inv_c2 = 1.0/PhysConst::c/PhysConst::c; @@ -1835,7 +1759,7 @@ void PhysicalParticleContainer::GetParticleSlice(const int direction, const Real Real uzp = uz_old_p *weight_old + uz_new_p *weight_new; diagnostic_particles[lev][index].GetRealData(DiagIdx::w).push_back(wp[i]); - + diagnostic_particles[lev][index].GetRealData(DiagIdx::x).push_back(xp); diagnostic_particles[lev][index].GetRealData(DiagIdx::y).push_back(yp); diagnostic_particles[lev][index].GetRealData(DiagIdx::z).push_back(zp); @@ -1860,7 +1784,7 @@ PhysicalParticleContainer::ContinuousInjection(const RealBox& injection_box) AddPlasma(lev, injection_box); } -/* \brief Gather fields from FArrayBox exfab, eyfab, ezfab, bxfab, byfab, +/* \brief Gather fields from FArrayBox exfab, eyfab, ezfab, bxfab, byfab, * bzfab into arrays of fields on particles Exp, Eyp, Ezp, Bxp, Byp, Bzp. * \param Exp-Bzp: fields on particles. * \param exfab-bzfab: FAB of electric and magnetic fields for particles in pti @@ -1870,7 +1794,7 @@ PhysicalParticleContainer::ContinuousInjection(const RealBox& injection_box) * \param np_to_gather: number of particles onto which fields are gathered * \param thread_num: if using OpenMP, thread number * \param lev: level on which particles are located - * \param gather_lev: level from which particles gather fields (lev-1) for + * \param gather_lev: level from which particles gather fields (lev-1) for particles in buffers. */ void @@ -1897,14 +1821,14 @@ PhysicalParticleContainer::FieldGather (WarpXParIter& pti, AMREX_ALWAYS_ASSERT_WITH_MESSAGE((gather_lev==(lev-1)) || (gather_lev==(lev )), "Gather buffers only work for lev-1"); - + // If no particles, do not do anything if (np_to_gather == 0) return; // Get cell size on gather_lev const std::array<Real,3>& dx = WarpX::CellSize(std::max(gather_lev,0)); // Set staggering shift depending on e_is_nodal const Real stagger_shift = e_is_nodal ? 0.0 : 0.5; - + // Get box from which field is gathered. // If not gathering from the finest level, the box is coarsened. Box box; @@ -1914,26 +1838,26 @@ PhysicalParticleContainer::FieldGather (WarpXParIter& pti, const IntVect& ref_ratio = WarpX::RefRatio(gather_lev); box = amrex::coarsen(pti.tilebox(),ref_ratio); } - + // Add guard cells to the box. box.grow(ngE); - + const Array4<const Real>& ex_arr = exfab->array(); const Array4<const Real>& ey_arr = eyfab->array(); const Array4<const Real>& ez_arr = ezfab->array(); const Array4<const Real>& bx_arr = bxfab->array(); const Array4<const Real>& by_arr = byfab->array(); const Array4<const Real>& bz_arr = bzfab->array(); - - const Real * const AMREX_RESTRICT xp = m_xp[thread_num].dataPtr() + offset; - const Real * const AMREX_RESTRICT zp = m_zp[thread_num].dataPtr() + offset; - const Real * const AMREX_RESTRICT yp = m_yp[thread_num].dataPtr() + offset; - + + const ParticleReal * const AMREX_RESTRICT xp = m_xp[thread_num].dataPtr() + offset; + const ParticleReal * const AMREX_RESTRICT zp = m_zp[thread_num].dataPtr() + offset; + const ParticleReal * const AMREX_RESTRICT yp = m_yp[thread_num].dataPtr() + offset; + // Lower corner of tile box physical domain const std::array<Real, 3>& xyzmin = WarpX::LowerCorner(box, gather_lev); - + const Dim3 lo = lbound(box); - + // Depending on l_lower_in_v and WarpX::nox, call // different versions of template function doGatherShapeN if (WarpX::l_lower_order_in_v){ @@ -2016,10 +1940,10 @@ void PhysicalParticleContainer::InitIonizationModule () } // Compute ADK prefactors (See Chen, JCP 236 (2013), equation (2)) // For now, we assume l=0 and m=0. - // The approximate expressions are used, + // The approximate expressions are used, // without Gamma function Real wa = std::pow(PhysConst::alpha,3) * PhysConst::c / PhysConst::r_e; - Real Ea = PhysConst::m_e * PhysConst::c*PhysConst::c /PhysConst::q_e * + Real Ea = PhysConst::m_e * PhysConst::c*PhysConst::c /PhysConst::q_e * std::pow(PhysConst::alpha,4)/PhysConst::r_e; Real UH = table_ionization_energies[0]; Real l_eff = std::sqrt(UH/ionization_energies[0]) - 1.; @@ -2034,18 +1958,18 @@ void PhysicalParticleContainer::InitIonizationModule () Real C2 = std::pow(2,2*n_eff)/(n_eff*tgamma(n_eff+l_eff+1)*tgamma(n_eff-l_eff)); adk_power[i] = -(2*n_eff - 1); Real Uion = ionization_energies[i]; - adk_prefactor[i] = dt * wa * C2 * ( Uion/(2*UH) ) + adk_prefactor[i] = dt * wa * C2 * ( Uion/(2*UH) ) * std::pow(2*std::pow((Uion/UH),3./2)*Ea,2*n_eff - 1); adk_exp_prefactor[i] = -2./3 * std::pow( Uion/UH,3./2) * Ea; } } /* \brief create mask of ionized particles (1 if ionized, 0 otherwise) - * + * * \param mfi: tile or grid * \param lev: MR level * \param ionization_mask: Array with as many elements as particles in mfi. - * This function initialized the array, and set each element to 1 or 0 + * This function initialized the array, and set each element to 1 or 0 * depending on whether the particle is ionized or not. */ void @@ -2074,15 +1998,15 @@ PhysicalParticleContainer::buildIonizationMask (const amrex::MFIter& mfi, const // Otherwise, resize ionization_mask, and get poiters to attribs arrays. ionization_mask.resize(np); int * const AMREX_RESTRICT p_ionization_mask = ionization_mask.data(); - const Real * const AMREX_RESTRICT ux = soa.GetRealData(PIdx::ux).data(); - const Real * const AMREX_RESTRICT uy = soa.GetRealData(PIdx::uy).data(); - const Real * const AMREX_RESTRICT uz = soa.GetRealData(PIdx::uz).data(); - const Real * const AMREX_RESTRICT ex = soa.GetRealData(PIdx::Ex).data(); - const Real * const AMREX_RESTRICT ey = soa.GetRealData(PIdx::Ey).data(); - const Real * const AMREX_RESTRICT ez = soa.GetRealData(PIdx::Ez).data(); - const Real * const AMREX_RESTRICT bx = soa.GetRealData(PIdx::Bx).data(); - const Real * const AMREX_RESTRICT by = soa.GetRealData(PIdx::By).data(); - const Real * const AMREX_RESTRICT bz = soa.GetRealData(PIdx::Bz).data(); + const ParticleReal * const AMREX_RESTRICT ux = soa.GetRealData(PIdx::ux).data(); + const ParticleReal * const AMREX_RESTRICT uy = soa.GetRealData(PIdx::uy).data(); + const ParticleReal * const AMREX_RESTRICT uz = soa.GetRealData(PIdx::uz).data(); + const ParticleReal * const AMREX_RESTRICT ex = soa.GetRealData(PIdx::Ex).data(); + const ParticleReal * const AMREX_RESTRICT ey = soa.GetRealData(PIdx::Ey).data(); + const ParticleReal * const AMREX_RESTRICT ez = soa.GetRealData(PIdx::Ez).data(); + const ParticleReal * const AMREX_RESTRICT bx = soa.GetRealData(PIdx::Bx).data(); + const ParticleReal * const AMREX_RESTRICT by = soa.GetRealData(PIdx::By).data(); + const ParticleReal * const AMREX_RESTRICT bz = soa.GetRealData(PIdx::Bz).data(); int* ion_lev = soa.GetIntData(particle_icomps["ionization_level"]).data(); Real c = PhysConst::c; @@ -2091,7 +2015,7 @@ PhysicalParticleContainer::buildIonizationMask (const amrex::MFIter& mfi, const // Loop over all particles in grid/tile. If ionized, set mask to 1 // and increment ionization level. - ParallelFor( + ParallelFor( np, [=] AMREX_GPU_DEVICE (long i) { // Get index of ionization_level |