diff options
Diffstat (limited to 'Source/Particles/PhysicalParticleContainer.cpp')
| -rw-r--r-- | Source/Particles/PhysicalParticleContainer.cpp | 122 |
1 files changed, 61 insertions, 61 deletions
diff --git a/Source/Particles/PhysicalParticleContainer.cpp b/Source/Particles/PhysicalParticleContainer.cpp index 318ad4664..99c6973f9 100644 --- a/Source/Particles/PhysicalParticleContainer.cpp +++ b/Source/Particles/PhysicalParticleContainer.cpp @@ -34,7 +34,7 @@ PhysicalParticleContainer::PhysicalParticleContainer (AmrCore* amr_core, int isp 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 +51,7 @@ 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 +68,9 @@ 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 +142,7 @@ 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 +154,7 @@ 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; @@ -387,11 +387,11 @@ 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) @@ -446,7 +446,7 @@ 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), @@ -458,9 +458,9 @@ PhysicalParticleContainer::AddPlasma (int lev, RealBox part_realbox) 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 +627,7 @@ 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 +865,7 @@ PhysicalParticleContainer::FieldGather (int lev, MultiFab* cost = WarpX::getCosts(lev); #ifdef _OPENMP -#pragma omp parallel +#pragma omp parallel #endif { #ifdef _OPENMP @@ -915,7 +915,7 @@ 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); @@ -949,11 +949,11 @@ PhysicalParticleContainer::Evolve (int lev, 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; @@ -978,9 +978,9 @@ PhysicalParticleContainer::Evolve (int lev, tmp_particle_data[lev][index][i].resize(np); } } - + #ifdef _OPENMP -#pragma omp parallel +#pragma omp parallel #endif { #ifdef _OPENMP @@ -1183,7 +1183,7 @@ PhysicalParticleContainer::Evolve (int lev, } const long np_current = (cjx) ? nfine_current : np; - + // // copy data from particle container to temp arrays // @@ -1199,14 +1199,14 @@ 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; @@ -1218,7 +1218,7 @@ 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); @@ -1234,7 +1234,7 @@ 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) @@ -1272,13 +1272,13 @@ PhysicalParticleContainer::Evolve (int lev, 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(); @@ -1286,14 +1286,14 @@ PhysicalParticleContainer::Evolve (int lev, cbzfab = &filtered_Bz; #endif } - + // 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); } @@ -1303,7 +1303,7 @@ 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], + PushPX(pti, m_xp[thread_num], m_yp[thread_num], m_zp[thread_num], m_giv[thread_num], dt); BL_PROFILE_VAR_STOP(blp_ppc_pp); @@ -1317,7 +1317,7 @@ 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, @@ -1337,7 +1337,7 @@ 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; @@ -1406,7 +1406,7 @@ 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) @@ -1503,11 +1503,11 @@ 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 + // 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, + pctmp_split.AddNParticles(lev, np_split_to_add, psplit_x.dataPtr(), psplit_y.dataPtr(), @@ -1559,12 +1559,12 @@ 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; @@ -1613,7 +1613,7 @@ 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(); @@ -1653,7 +1653,7 @@ 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); @@ -1701,7 +1701,7 @@ void PhysicalParticleContainer::copy_attribs(WarpXParIter& pti,const Real* xp, Real* AMREX_RESTRICT uxp = attribs[PIdx::ux].dataPtr(); Real* AMREX_RESTRICT uyp = attribs[PIdx::uy].dataPtr(); Real* AMREX_RESTRICT uzp = attribs[PIdx::uz].dataPtr(); - + const auto np = pti.numParticles(); const auto lev = pti.GetLevel(); const auto index = pti.GetPairIndex(); @@ -1717,7 +1717,7 @@ void PhysicalParticleContainer::copy_attribs(WarpXParIter& pti,const Real* xp, xpold[i]=xp[i]; ypold[i]=yp[i]; zpold[i]=zp[i]; - + uxpold[i]=uxp[i]; uypold[i]=uyp[i]; uzpold[i]=uzp[i]; @@ -1757,7 +1757,7 @@ 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(); @@ -1804,7 +1804,7 @@ 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; @@ -1839,7 +1839,7 @@ 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); @@ -1864,7 +1864,7 @@ 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 @@ -1874,7 +1874,7 @@ 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 @@ -1901,14 +1901,14 @@ 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; @@ -1918,26 +1918,26 @@ 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; - + // 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){ @@ -2020,10 +2020,10 @@ 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.; @@ -2038,18 +2038,18 @@ 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 @@ -2095,7 +2095,7 @@ 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 |