diff options
Diffstat (limited to 'Source/Particles')
| -rwxr-xr-x | Source/Particles/Deposition/ChargeDeposition.H | 8 | ||||
| -rw-r--r-- | Source/Particles/Deposition/CurrentDeposition.H | 26 | ||||
| -rw-r--r-- | Source/Particles/Gather/FieldGather.H | 2 | ||||
| -rw-r--r-- | Source/Particles/MultiParticleContainer.H | 36 | ||||
| -rw-r--r-- | Source/Particles/MultiParticleContainer.cpp | 46 | ||||
| -rw-r--r-- | Source/Particles/PhysicalParticleContainer.H | 10 | ||||
| -rw-r--r-- | Source/Particles/PhysicalParticleContainer.cpp | 122 | ||||
| -rw-r--r-- | Source/Particles/RigidInjectedParticleContainer.H | 2 | ||||
| -rw-r--r-- | Source/Particles/ShapeFactors.H | 2 | ||||
| -rw-r--r-- | Source/Particles/WarpXParticleContainer.H | 72 | ||||
| -rw-r--r-- | Source/Particles/WarpXParticleContainer.cpp | 18 | ||||
| -rw-r--r-- | Source/Particles/deposit_cic.F90 | 4 | ||||
| -rw-r--r-- | Source/Particles/interpolate_cic.F90 | 34 | ||||
| -rw-r--r-- | Source/Particles/push_particles_ES.F90 | 22 |
14 files changed, 202 insertions, 202 deletions
diff --git a/Source/Particles/Deposition/ChargeDeposition.H b/Source/Particles/Deposition/ChargeDeposition.H index f02eb1033..b9210e67c 100755 --- a/Source/Particles/Deposition/ChargeDeposition.H +++ b/Source/Particles/Deposition/ChargeDeposition.H @@ -18,8 +18,8 @@ * /param q : species charge. */ template <int depos_order> -void doChargeDepositionShapeN(const amrex::Real * const xp, - const amrex::Real * const yp, +void doChargeDepositionShapeN(const amrex::Real * const xp, + const amrex::Real * const yp, const amrex::Real * const zp, const amrex::Real * const wp, const int * const ion_lev, @@ -69,7 +69,7 @@ void doChargeDepositionShapeN(const amrex::Real * const xp, amrex::Real sx[depos_order + 1]; // i: leftmost grid point (node-centered) that the particle touches const int i = compute_shape_factor<depos_order>(sx, x); - + #if (defined WARPX_DIM_3D) // y direction const amrex::Real y = (yp[ip] - ymin)*dyi; @@ -86,7 +86,7 @@ void doChargeDepositionShapeN(const amrex::Real * const xp, for (int iz=0; iz<=depos_order; iz++){ for (int ix=0; ix<=depos_order; ix++){ amrex::Gpu::Atomic::Add( - &rho_arr(lo.x+i+ix, lo.y+k+iz, 0), + &rho_arr(lo.x+i+ix, lo.y+k+iz, 0), sx[ix]*sz[iz]*wq); } } diff --git a/Source/Particles/Deposition/CurrentDeposition.H b/Source/Particles/Deposition/CurrentDeposition.H index c7dfde75a..7a96dab9a 100644 --- a/Source/Particles/Deposition/CurrentDeposition.H +++ b/Source/Particles/Deposition/CurrentDeposition.H @@ -24,8 +24,8 @@ * /param q : species charge. */ template <int depos_order> -void doDepositionShapeN(const amrex::Real * const xp, - const amrex::Real * const yp, +void doDepositionShapeN(const amrex::Real * const xp, + const amrex::Real * const yp, const amrex::Real * const zp, const amrex::Real * const wp, const amrex::Real * const uxp, @@ -39,7 +39,7 @@ void doDepositionShapeN(const amrex::Real * const xp, const std::array<amrex::Real,3>& dx, const std::array<amrex::Real, 3> xyzmin, const amrex::Dim3 lo, - const amrex::Real stagger_shift, + const amrex::Real stagger_shift, const amrex::Real q) { // Whether ion_lev is a null pointer (do_ionization=0) or a real pointer @@ -77,7 +77,7 @@ void doDepositionShapeN(const amrex::Real * const xp, const amrex::Real vx = uxp[ip]*gaminv; const amrex::Real vy = uyp[ip]*gaminv; const amrex::Real vz = uzp[ip]*gaminv; - // wqx, wqy wqz are particle current in each direction + // wqx, wqy wqz are particle current in each direction #if (defined WARPX_DIM_RZ) // In RZ, wqx is actually wqr, and wqy is wqtheta // Convert to cylinderical at the mid point @@ -117,7 +117,7 @@ void doDepositionShapeN(const amrex::Real * const xp, amrex::Real sx0[depos_order + 1]; // j0: leftmost grid point (cell-centered) that the particle touches const int j0 = compute_shape_factor<depos_order>(sx0, xmid-stagger_shift); - + #if (defined WARPX_DIM_3D) // y direction const amrex::Real ymid= (yp[ip]-ymin)*dyi-dts2dy*vy; @@ -138,13 +138,13 @@ void doDepositionShapeN(const amrex::Real * const xp, for (int iz=0; iz<=depos_order; iz++){ for (int ix=0; ix<=depos_order; ix++){ amrex::Gpu::Atomic::Add( - &jx_arr(lo.x+j0+ix, lo.y+l +iz, 0), + &jx_arr(lo.x+j0+ix, lo.y+l +iz, 0), sx0[ix]*sz [iz]*wqx); amrex::Gpu::Atomic::Add( - &jy_arr(lo.x+j +ix, lo.y+l +iz, 0), + &jy_arr(lo.x+j +ix, lo.y+l +iz, 0), sx [ix]*sz [iz]*wqy); amrex::Gpu::Atomic::Add( - &jz_arr(lo.x+j +ix, lo.y+l0+iz, 0), + &jz_arr(lo.x+j +ix, lo.y+l0+iz, 0), sx [ix]*sz0[iz]*wqz); } } @@ -156,7 +156,7 @@ void doDepositionShapeN(const amrex::Real * const xp, &jx_arr(lo.x+j0+ix, lo.y+k +iy, lo.z+l +iz), sx0[ix]*sy [iy]*sz [iz]*wqx); amrex::Gpu::Atomic::Add( - &jy_arr(lo.x+j +ix, lo.y+k0+iy, lo.z+l +iz), + &jy_arr(lo.x+j +ix, lo.y+k0+iy, lo.z+l +iz), sx [ix]*sy0[iy]*sz [iz]*wqy); amrex::Gpu::Atomic::Add( &jz_arr(lo.x+j +ix, lo.y+k +iy, lo.z+l0+iz), @@ -240,7 +240,7 @@ void doEsirkepovDepositionShapeN (const amrex::Real * const xp, const amrex::Real clightsq = 1.0/PhysConst::c/PhysConst::c; // Loop over particles and deposit into Jx_arr, Jy_arr and Jz_arr - amrex::ParallelFor( + amrex::ParallelFor( np_to_depose, [=] AMREX_GPU_DEVICE (long ip) { @@ -302,7 +302,7 @@ void doEsirkepovDepositionShapeN (const amrex::Real * const xp, const amrex::Real x_new = (xp[ip] - xmin)*dxi; const amrex::Real x_old = x_new - dtsdx0*uxp[ip]*gaminv; #endif -#if (defined WARPX_DIM_3D) +#if (defined WARPX_DIM_3D) const amrex::Real y_new = (yp[ip] - ymin)*dyi; const amrex::Real y_old = y_new - dtsdy0*uyp[ip]*gaminv; #endif @@ -336,7 +336,7 @@ void doEsirkepovDepositionShapeN (const amrex::Real * const xp, #if (defined WARPX_DIM_3D) const int j_new = compute_shape_factor<depos_order>(sy_new+1, y_new); const int j_old = compute_shifted_shape_factor<depos_order>(sy_old, y_old, j_new); -#endif +#endif const int k_new = compute_shape_factor<depos_order>(sz_new+1, z_new); const int k_old = compute_shifted_shape_factor<depos_order>(sz_old, z_old, k_new); @@ -418,7 +418,7 @@ void doEsirkepovDepositionShapeN (const amrex::Real * const xp, for (int imode=1 ; imode < n_rz_azimuthal_modes ; imode++) { // The factor 2 comes from the normalization of the modes // The minus sign comes from the different convention with respect to Davidson et al. - const Complex djt_cmplx = -2.*I*(i_new-1 + i + xmin*dxi)*wq*invdtdx/(double)imode* + const Complex djt_cmplx = -2.*I*(i_new-1 + i + xmin*dxi)*wq*invdtdx/(double)imode* (sx_new[i]*sz_new[k]*(xy_new - xy_mid) + sx_old[i]*sz_old[k]*(xy_mid - xy_old)); amrex::Gpu::Atomic::Add( &Jy_arr(lo.x+i_new-1+i, lo.y+k_new-1+k, 0, 2*imode-1), djt_cmplx.real()); amrex::Gpu::Atomic::Add( &Jy_arr(lo.x+i_new-1+i, lo.y+k_new-1+k, 0, 2*imode), djt_cmplx.imag()); diff --git a/Source/Particles/Gather/FieldGather.H b/Source/Particles/Gather/FieldGather.H index d8d1d78ef..6727b0aa9 100644 --- a/Source/Particles/Gather/FieldGather.H +++ b/Source/Particles/Gather/FieldGather.H @@ -97,7 +97,7 @@ void doGatherShapeN(const amrex::Real * const xp, Bxp[ip] = 0; Byp[ip] = 0; Bzp[ip] = 0; - // Each field is gathered in a separate block of + // Each field is gathered in a separate block of // AMREX_SPACEDIM nested loops because the deposition // order can differ for each component of each field // when lower_in_v is set to 1 diff --git a/Source/Particles/MultiParticleContainer.H b/Source/Particles/MultiParticleContainer.H index 305baf4ff..ac261b177 100644 --- a/Source/Particles/MultiParticleContainer.H +++ b/Source/Particles/MultiParticleContainer.H @@ -51,24 +51,24 @@ public: const amrex::Vector<std::unique_ptr<amrex::FabArray<amrex::BaseFab<int> > > >& masks); /// - /// This evolves all the particles by one PIC time step, including charge deposition, the + /// This evolves all the particles by one PIC time step, including charge deposition, the /// field solve, and pushing the particles, for all the species in the MultiParticleContainer. /// This is the electrostatic version. /// - void EvolveES (const amrex::Vector<std::array<std::unique_ptr<amrex::MultiFab>, 3> >& E, - amrex::Vector<std::unique_ptr<amrex::MultiFab> >& rho, + void EvolveES (const amrex::Vector<std::array<std::unique_ptr<amrex::MultiFab>, 3> >& E, + amrex::Vector<std::unique_ptr<amrex::MultiFab> >& rho, amrex::Real t, amrex::Real dt); /// - /// This pushes the particle positions by one half time step for all the species in the + /// This pushes the particle positions by one half time step for all the species in the /// MultiParticleContainer. It is used to desynchronize the particles after initializaton /// or when restarting from a checkpoint. This is the electrostatic version. - /// + /// void PushXES (amrex::Real dt); /// /// This deposits the particle charge onto rho, accumulating the value for all the species - /// in the MultiParticleContainer. rho is assumed to contain node-centered multifabs. + /// in the MultiParticleContainer. rho is assumed to contain node-centered multifabs. /// This version is hard-coded for CIC deposition. /// void DepositCharge(amrex::Vector<std::unique_ptr<amrex::MultiFab> >& rho, bool local = false); @@ -79,7 +79,7 @@ public: /// amrex::Real sumParticleCharge(bool local = false); #endif // WARPX_DO_ELECTROSTATIC - + /// /// Performs the field gather operation using the input fields E and B, for all the species /// in the MultiParticleContainer. This is the electromagnetic version of the field gather. @@ -87,7 +87,7 @@ public: void FieldGather (int lev, const amrex::MultiFab& Ex, const amrex::MultiFab& Ey, const amrex::MultiFab& Ez, const amrex::MultiFab& Bx, - const amrex::MultiFab& By, const amrex::MultiFab& Bz); + const amrex::MultiFab& By, const amrex::MultiFab& Bz); /// /// This evolves all the particles by one PIC time step, including current deposition, the @@ -97,8 +97,8 @@ public: void Evolve (int lev, const amrex::MultiFab& Ex, const amrex::MultiFab& Ey, const amrex::MultiFab& Ez, const amrex::MultiFab& Bx, const amrex::MultiFab& By, const amrex::MultiFab& Bz, - amrex::MultiFab& jx, amrex::MultiFab& jy, amrex::MultiFab& jz, - amrex::MultiFab* cjx, amrex::MultiFab* cjy, amrex::MultiFab* cjz, + amrex::MultiFab& jx, amrex::MultiFab& jy, amrex::MultiFab& jz, + amrex::MultiFab* cjx, amrex::MultiFab* cjy, amrex::MultiFab* cjz, amrex::MultiFab* rho, amrex::MultiFab* crho, const amrex::MultiFab* cEx, const amrex::MultiFab* cEy, const amrex::MultiFab* cEz, const amrex::MultiFab* cBx, const amrex::MultiFab* cBy, const amrex::MultiFab* cBz, @@ -108,7 +108,7 @@ public: /// This pushes the particle positions by one half time step for all the species in the /// MultiParticleContainer. It is used to desynchronize the particles after initializaton /// or when restarting from a checkpoint. This is the electromagnetic version. - /// + /// void PushX (amrex::Real dt); /// @@ -116,7 +116,7 @@ public: /// MultiParticleContainer. It is used to desynchronize the particles after initializaton /// or when restarting from a checkpoint. It is also used to synchronize particles at the /// the end of the run. This is the electromagnetic version. - /// + /// void PushP (int lev, amrex::Real dt, const amrex::MultiFab& Ex, const amrex::MultiFab& Ey, const amrex::MultiFab& Ez, const amrex::MultiFab& Bx, const amrex::MultiFab& By, const amrex::MultiFab& Bz); @@ -124,7 +124,7 @@ public: /// /// This deposits the particle charge onto a node-centered MultiFab and returns a unique ptr /// to it. The charge density is accumulated over all the particles in the MultiParticleContainer - /// + /// std::unique_ptr<amrex::MultiFab> GetChargeDensity(int lev, bool local = false); void doFieldIonization (); @@ -132,7 +132,7 @@ public: void Checkpoint (const std::string& dir) const; void WritePlotFile (const std::string& dir) const; - + void Restart (const std::string& dir); void PostRestart (); @@ -178,7 +178,7 @@ public: const amrex::Real t_boost, const amrex::Real t_lab, const amrex::Real dt, amrex::Vector<WarpXParticleContainer::DiagnosticParticleData>& parts) const; - // Inject particles during the simulation (for particles entering the + // Inject particles during the simulation (for particles entering the // simulation domain after some iterations, due to flowing plasma and/or // moving window). void ContinuousInjection(const amrex::RealBox& injection_box) const; @@ -189,7 +189,7 @@ public: std::vector<std::string> GetSpeciesNames() const { return species_names; } PhysicalParticleContainer& GetPCtmp () { return *pc_tmp; } - + protected: // Particle container types @@ -218,10 +218,10 @@ private: void mapSpeciesProduct (); int getSpeciesID (std::string product_str); - + // Number of species dumped in BoostedFrameDiagnostics int nspecies_boosted_frame_diags = 0; - // map_species_boosted_frame_diags[i] is the species ID in + // map_species_boosted_frame_diags[i] is the species ID in // MultiParticleContainer for 0<i<nspecies_boosted_frame_diags std::vector<int> map_species_boosted_frame_diags; int do_boosted_frame_diags = 0; diff --git a/Source/Particles/MultiParticleContainer.cpp b/Source/Particles/MultiParticleContainer.cpp index 640439337..612583e2f 100644 --- a/Source/Particles/MultiParticleContainer.cpp +++ b/Source/Particles/MultiParticleContainer.cpp @@ -23,7 +23,7 @@ MultiParticleContainer::MultiParticleContainer (AmrCore* amr_core) allcontainers[i]->m_deposit_on_main_grid = m_deposit_on_main_grid[i]; allcontainers[i]->m_gather_from_main_grid = m_gather_from_main_grid[i]; } - + for (int i = nspecies; i < nspecies+nlasers; ++i) { allcontainers[i].reset(new LaserParticleContainer(amr_core, i, lasers_names[i-nspecies])); } @@ -359,7 +359,7 @@ MultiParticleContainer { BL_PROFILE("MultiParticleContainer::GetLabFrameData"); - + // Loop over particle species for (int i = 0; i < nspecies_boosted_frame_diags; ++i){ int isp = map_species_boosted_frame_diags[i]; @@ -368,41 +368,41 @@ MultiParticleContainer pc->GetParticleSlice(direction, z_old, z_new, t_boost, t_lab, dt, diagnostic_particles); // Here, diagnostic_particles[lev][index] is a WarpXParticleContainer::DiagnosticParticleData // where "lev" is the AMR level and "index" is a [grid index][tile index] pair. - + // Loop over AMR levels for (int lev = 0; lev <= pc->finestLevel(); ++lev){ - // Loop over [grid index][tile index] pairs - // and Fills parts[species number i] with particle data from all grids and - // tiles in diagnostic_particles. parts contains particles from all + // Loop over [grid index][tile index] pairs + // and Fills parts[species number i] with particle data from all grids and + // tiles in diagnostic_particles. parts contains particles from all // AMR levels indistinctly. for (auto it = diagnostic_particles[lev].begin(); it != diagnostic_particles[lev].end(); ++it){ // it->first is the [grid index][tile index] key - // it->second is the corresponding + // it->second is the corresponding // WarpXParticleContainer::DiagnosticParticleData value parts[i].GetRealData(DiagIdx::w).insert( parts[i].GetRealData(DiagIdx::w ).end(), it->second.GetRealData(DiagIdx::w ).begin(), it->second.GetRealData(DiagIdx::w ).end()); - + parts[i].GetRealData(DiagIdx::x).insert( parts[i].GetRealData(DiagIdx::x ).end(), it->second.GetRealData(DiagIdx::x ).begin(), it->second.GetRealData(DiagIdx::x ).end()); - + parts[i].GetRealData(DiagIdx::y).insert( parts[i].GetRealData(DiagIdx::y ).end(), it->second.GetRealData(DiagIdx::y ).begin(), it->second.GetRealData(DiagIdx::y ).end()); - + parts[i].GetRealData(DiagIdx::z).insert( parts[i].GetRealData(DiagIdx::z ).end(), it->second.GetRealData(DiagIdx::z ).begin(), it->second.GetRealData(DiagIdx::z ).end()); - + parts[i].GetRealData(DiagIdx::ux).insert( parts[i].GetRealData(DiagIdx::ux).end(), it->second.GetRealData(DiagIdx::ux).begin(), it->second.GetRealData(DiagIdx::ux).end()); - + parts[i].GetRealData(DiagIdx::uy).insert( parts[i].GetRealData(DiagIdx::uy).end(), it->second.GetRealData(DiagIdx::uy).begin(), it->second.GetRealData(DiagIdx::uy).end()); - + parts[i].GetRealData(DiagIdx::uz).insert( parts[i].GetRealData(DiagIdx::uz).end(), it->second.GetRealData(DiagIdx::uz).begin(), it->second.GetRealData(DiagIdx::uz).end()); @@ -413,7 +413,7 @@ MultiParticleContainer /* \brief Continuous injection for particles initially outside of the domain. * \param injection_box: Domain where new particles should be injected. - * Loop over all WarpXParticleContainer in MultiParticleContainer and + * Loop over all WarpXParticleContainer in MultiParticleContainer and * calls virtual function ContinuousInjection. */ void @@ -429,7 +429,7 @@ MultiParticleContainer::ContinuousInjection(const RealBox& injection_box) const /* \brief Update position of continuous injection parameters. * \param dt: simulation time step (level 0) - * All classes inherited from WarpXParticleContainer do not have + * All classes inherited from WarpXParticleContainer do not have * a position to update (PhysicalParticleContainer does not do anything). */ void @@ -457,7 +457,7 @@ MultiParticleContainer::doContinuousInjection () const } /* \brief Get ID of product species of each species. - * The users specifies the name of the product species, + * The users specifies the name of the product species, * this routine get its ID. */ void @@ -465,8 +465,8 @@ MultiParticleContainer::mapSpeciesProduct () { for (int i=0; i<nspecies; i++){ auto& pc = allcontainers[i]; - // If species pc has ionization on, find species with name - // pc->ionization_product_name and store its ID into + // If species pc has ionization on, find species with name + // pc->ionization_product_name and store its ID into // pc->ionization_product. if (pc->do_field_ionization){ int i_product = getSpeciesID(pc->ionization_product_name); @@ -577,7 +577,7 @@ namespace } // --- product runtime attribs GpuArray<Real*,6> runtime_attribs_product; - bool do_boosted_product = WarpX::do_boosted_frame_diagnostic + bool do_boosted_product = WarpX::do_boosted_frame_diagnostic && pc_product->DoBoostedFrameDiags(); if (do_boosted_product) { std::map<std::string, int> comps_product = pc_product->getParticleComps(); @@ -624,7 +624,7 @@ namespace attribs_product[ia][ip] = attribs_source[ia][is]; } // Update xold etc. if boosted frame diagnostics required - // for product species. Fill runtime attribs with a copy of + // for product species. Fill runtime attribs with a copy of // current properties (xold = x etc.). if (do_boosted_product) { runtime_attribs_product[0][ip] = p_source.pos(0); @@ -647,7 +647,7 @@ MultiParticleContainer::doFieldIonization () // Loop over all species. // Ionized particles in pc_source create particles in pc_product for (auto& pc_source : allcontainers){ - + // Skip if not ionizable if (!pc_source->do_field_ionization){ continue; } @@ -661,7 +661,7 @@ MultiParticleContainer::doFieldIonization () // they do not exist (or if they were defined by default, i.e., // without runtime component). #ifdef _OPENMP - // Touch all tiles of source species in serial if runtime attribs + // Touch all tiles of source species in serial if runtime attribs for (MFIter mfi = pc_source->MakeMFIter(lev); mfi.isValid(); ++mfi) { const int grid_id = mfi.index(); const int tile_id = mfi.LocalTileIndex(); @@ -683,7 +683,7 @@ MultiParticleContainer::doFieldIonization () MFItInfo info; if (pc_source->do_tiling && Gpu::notInLaunchRegion()) { AMREX_ALWAYS_ASSERT_WITH_MESSAGE( - pc_product->do_tiling, + pc_product->do_tiling, "For ionization, either all or none of the " "particle species must use tiling."); info.EnableTiling(pc_source->tile_size); diff --git a/Source/Particles/PhysicalParticleContainer.H b/Source/Particles/PhysicalParticleContainer.H index c7494fbdf..7946b4650 100644 --- a/Source/Particles/PhysicalParticleContainer.H +++ b/Source/Particles/PhysicalParticleContainer.H @@ -24,7 +24,7 @@ public: void InitIonizationModule (); -#ifdef WARPX_DO_ELECTROSTATIC +#ifdef WARPX_DO_ELECTROSTATIC virtual void FieldGatherES(const amrex::Vector<std::array<std::unique_ptr<amrex::MultiFab>, 3> >& E, const amrex::Vector<std::unique_ptr<amrex::FabArray<amrex::BaseFab<int> > > >& masks) override; @@ -32,7 +32,7 @@ public: amrex::Vector<std::unique_ptr<amrex::MultiFab> >& rho, amrex::Real t, amrex::Real dt) override; #endif // WARPX_DO_ELECTROSTATIC - + virtual void FieldGather (int lev, const amrex::MultiFab& Ex, const amrex::MultiFab& Ey, @@ -99,14 +99,14 @@ public: const amrex::MultiFab& Bx, const amrex::MultiFab& By, const amrex::MultiFab& Bz) override; - + void copy_attribs(WarpXParIter& pti,const amrex::Real* xp, const amrex::Real* yp, const amrex::Real* zp); virtual void PostRestart () final {} void SplitParticles(int lev); - + virtual void buildIonizationMask (const amrex::MFIter& mfi, const int lev, amrex::Gpu::ManagedDeviceVector<int>& ionization_mask) override; @@ -125,7 +125,7 @@ public: std::array<amrex::Real, 3> u, amrex::Real weight); virtual void GetParticleSlice(const int direction, const amrex::Real z_old, - const amrex::Real z_new, const amrex::Real t_boost, + const amrex::Real z_new, const amrex::Real t_boost, const amrex::Real t_lab, const amrex::Real dt, DiagnosticParticles& diagnostic_particles) final; 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 diff --git a/Source/Particles/RigidInjectedParticleContainer.H b/Source/Particles/RigidInjectedParticleContainer.H index b920ece0a..a635e9aa0 100644 --- a/Source/Particles/RigidInjectedParticleContainer.H +++ b/Source/Particles/RigidInjectedParticleContainer.H @@ -60,7 +60,7 @@ public: virtual void ReadHeader (std::istream& is) override; virtual void WriteHeader (std::ostream& os) const override; - + private: // User input quantities diff --git a/Source/Particles/ShapeFactors.H b/Source/Particles/ShapeFactors.H index 9d185714a..be79a4871 100644 --- a/Source/Particles/ShapeFactors.H +++ b/Source/Particles/ShapeFactors.H @@ -1,7 +1,7 @@ #ifndef SHAPEFACTORS_H_ #define SHAPEFACTORS_H_ -// Compute shape factor and return index of leftmost cell where +// Compute shape factor and return index of leftmost cell where // particle writes. // Specialized templates are defined below for orders 0 to 3. template <int depos_order> diff --git a/Source/Particles/WarpXParticleContainer.H b/Source/Particles/WarpXParticleContainer.H index f7e46b2d3..06540871b 100644 --- a/Source/Particles/WarpXParticleContainer.H +++ b/Source/Particles/WarpXParticleContainer.H @@ -73,19 +73,19 @@ public: const amrex::Cuda::ManagedDeviceVector<amrex::Real>& y, const amrex::Cuda::ManagedDeviceVector<amrex::Real>& z); #endif - const std::array<RealVector, PIdx::nattribs>& GetAttribs () const { - return GetStructOfArrays().GetRealData(); + const std::array<RealVector, PIdx::nattribs>& GetAttribs () const { + return GetStructOfArrays().GetRealData(); } - - std::array<RealVector, PIdx::nattribs>& GetAttribs () { - return GetStructOfArrays().GetRealData(); + + std::array<RealVector, PIdx::nattribs>& GetAttribs () { + return GetStructOfArrays().GetRealData(); } - const RealVector& GetAttribs (int comp) const { + const RealVector& GetAttribs (int comp) const { return GetStructOfArrays().GetRealData(comp); } - - RealVector& GetAttribs (int comp) { + + RealVector& GetAttribs (int comp) { return GetStructOfArrays().GetRealData(comp); } @@ -102,15 +102,15 @@ class WarpXParticleContainer public: friend MultiParticleContainer; - // amrex::StructOfArrays with DiagIdx::nattribs amrex::Real components + // amrex::StructOfArrays with DiagIdx::nattribs amrex::Real components // and 0 int components for the particle data. using DiagnosticParticleData = amrex::StructOfArrays<DiagIdx::nattribs, 0>; // DiagnosticParticles is a vector, with one element per MR level. - // DiagnosticParticles[lev] is typically a key-value pair where the key is - // a pair [grid_index, tile_index], and the value is the corresponding + // DiagnosticParticles[lev] is typically a key-value pair where the key is + // a pair [grid_index, tile_index], and the value is the corresponding // DiagnosticParticleData (see above) on this tile. using DiagnosticParticles = amrex::Vector<std::map<std::pair<int, int>, DiagnosticParticleData> >; - + WarpXParticleContainer (amrex::AmrCore* amr_core, int ispecies); virtual ~WarpXParticleContainer() {} @@ -124,12 +124,12 @@ public: const amrex::MultiFab& Ez, const amrex::MultiFab& Bx, const amrex::MultiFab& By, const amrex::MultiFab& Bz) {} -#ifdef WARPX_DO_ELECTROSTATIC +#ifdef WARPX_DO_ELECTROSTATIC virtual void EvolveES (const amrex::Vector<std::array<std::unique_ptr<amrex::MultiFab>, 3> >& E, - amrex::Vector<std::unique_ptr<amrex::MultiFab> >& rho, + amrex::Vector<std::unique_ptr<amrex::MultiFab> >& rho, amrex::Real t, amrex::Real dt) = 0; #endif // WARPX_DO_ELECTROSTATIC - + virtual void Evolve (int lev, const amrex::MultiFab& Ex, const amrex::MultiFab& Ey, const amrex::MultiFab& Ez, const amrex::MultiFab& Bx, const amrex::MultiFab& By, const amrex::MultiFab& Bz, @@ -143,10 +143,10 @@ public: virtual void PostRestart () = 0; virtual void GetParticleSlice(const int direction, const amrex::Real z_old, - const amrex::Real z_new, const amrex::Real t_boost, + const amrex::Real z_new, const amrex::Real t_boost, const amrex::Real t_lab, const amrex::Real dt, DiagnosticParticles& diagnostic_particles) {} - + void AllocData (); /// @@ -154,7 +154,7 @@ public: /// It is used to desynchronize the particles after initializaton /// or when restarting from a checkpoint. /// This is the electrostatic version of the particle push. - /// + /// void PushXES (amrex::Real dt); /// @@ -162,13 +162,13 @@ public: /// It is used to desynchronize the particles after initializaton /// or when restarting from a checkpoint. /// This is the electromagnetic version of the particle push. - /// + /// void PushX ( amrex::Real dt); void PushX (int lev, amrex::Real dt); /// /// This pushes the particle momenta by dt. - /// + /// virtual void PushP (int lev, amrex::Real dt, const amrex::MultiFab& Ex, const amrex::MultiFab& Ey, @@ -208,9 +208,9 @@ public: int depos_lev, amrex::Real dt); - // If particles start outside of the domain, ContinuousInjection - // makes sure that they are initialized when they enter the domain, and - // NOT before. Virtual function, overriden by derived classes. + // If particles start outside of the domain, ContinuousInjection + // makes sure that they are initialized when they enter the domain, and + // NOT before. Virtual function, overriden by derived classes. // Current status: // PhysicalParticleContainer: implemented. // LaserParticleContainer: implemented. @@ -219,7 +219,7 @@ public: // Update optional sub-class-specific injection location. virtual void UpdateContinuousInjectionPosition(amrex::Real dt) {} - /// + /// /// This returns the total charge for all the particles in this ParticleContainer. /// This is needed when solving Poisson's equation with periodic boundary conditions. /// @@ -259,9 +259,9 @@ public: // split along axes (0) or diagonals (1) int split_type = 0; - using amrex::ParticleContainer<0, 0, PIdx::nattribs>::AddRealComp; + using amrex::ParticleContainer<0, 0, PIdx::nattribs>::AddRealComp; using amrex::ParticleContainer<0, 0, PIdx::nattribs>::AddIntComp; - + void AddRealComp (const std::string& name, bool comm=true) { particle_comps[name] = NumRealComps(); @@ -274,7 +274,7 @@ public: AddIntComp(comm); } - int DoBoostedFrameDiags () const { return do_boosted_frame_diags; } + int DoBoostedFrameDiags () const { return do_boosted_frame_diags; } virtual void buildIonizationMask (const amrex::MFIter& mfi, const int lev, amrex::Gpu::ManagedDeviceVector<int>& ionization_mask) @@ -286,7 +286,7 @@ protected: std::map<std::string, int> particle_comps; std::map<std::string, int> particle_icomps; - + int species_id; amrex::Real charge; @@ -300,9 +300,9 @@ protected: static int do_not_push; - // Whether to allow particles outside of the simulation domain to be + // Whether to allow particles outside of the simulation domain to be // initialized when they enter the domain. - // This is currently required because continuous injection does not + // This is currently required because continuous injection does not // support all features allowed by direct injection. int do_continuous_injection = 0; @@ -316,7 +316,7 @@ protected: amrex::Gpu::ManagedVector<amrex::Real> adk_prefactor; amrex::Gpu::ManagedVector<amrex::Real> adk_exp_prefactor; std::string physical_element; - + int do_boosted_frame_diags = 1; amrex::Vector<amrex::FArrayBox> local_rho; @@ -326,20 +326,20 @@ protected: using DataContainer = amrex::Gpu::ManagedDeviceVector<amrex::Real>; using PairIndex = std::pair<int, int>; - + amrex::Vector<DataContainer> m_xp, m_yp, m_zp, m_giv; - // Whether to dump particle quantities. + // Whether to dump particle quantities. // If true, particle position is always dumped. int plot_species = 1; - // For all particle attribs (execept position), whether or not + // For all particle attribs (execept position), whether or not // to dump to file. amrex::Vector<int> plot_flags; // list of names of attributes to dump. amrex::Vector<std::string> plot_vars; - + amrex::Vector<std::map<PairIndex, std::array<DataContainer, TmpIdx::nattribs> > > tmp_particle_data; - + private: virtual void particlePostLocate(ParticleType& p, const amrex::ParticleLocData& pld, const int lev) override; diff --git a/Source/Particles/WarpXParticleContainer.cpp b/Source/Particles/WarpXParticleContainer.cpp index 4e80374d8..83de9fb0e 100644 --- a/Source/Particles/WarpXParticleContainer.cpp +++ b/Source/Particles/WarpXParticleContainer.cpp @@ -228,7 +228,7 @@ WarpXParticleContainer::AddNParticles (int lev, #endif if ( (NumRuntimeRealComps()>0) || (NumRuntimeIntComps()>0) ){ - auto& ptile = DefineAndReturnParticleTile(0, 0, 0); + auto& ptile = DefineAndReturnParticleTile(0, 0, 0); } particle_tile.push_back(p); @@ -242,7 +242,7 @@ WarpXParticleContainer::AddNParticles (int lev, particle_tile.push_back_real(PIdx::uz, vz + ibegin, vz + iend); if ( (NumRuntimeRealComps()>0) || (NumRuntimeIntComps()>0) ){ - auto& ptile = DefineAndReturnParticleTile(0, 0, 0); + auto& ptile = DefineAndReturnParticleTile(0, 0, 0); } for (int comp = PIdx::uz+1; comp < PIdx::nattribs; ++comp) @@ -289,7 +289,7 @@ WarpXParticleContainer::DepositCurrent(WarpXParIter& pti, const long offset, const long np_to_depose, int thread_num, int lev, int depos_lev, Real dt) -{ +{ AMREX_ALWAYS_ASSERT_WITH_MESSAGE((depos_lev==(lev-1)) || (depos_lev==(lev )), "Deposition buffers only work for lev-1"); @@ -316,7 +316,7 @@ WarpXParticleContainer::DepositCurrent(WarpXParIter& pti, const IntVect& ref_ratio = WarpX::RefRatio(depos_lev); tilebox = amrex::coarsen(pti.tilebox(),ref_ratio); } - + // Staggered tile boxes (different in each direction) Box tbx = convert(tilebox, WarpX::jx_nodal_flag); Box tby = convert(tilebox, WarpX::jy_nodal_flag); @@ -360,11 +360,11 @@ WarpXParticleContainer::DepositCurrent(WarpXParIter& pti, // Lower corner of tile box physical domain // Note that this includes guard cells since it is after tilebox.ngrow const std::array<Real, 3>& xyzmin = WarpX::LowerCorner(tilebox, depos_lev); - // xyzmin is built on pti.tilebox(), so it does + // xyzmin is built on pti.tilebox(), so it does // not include staggering, so the stagger_shift has to be done by hand. - // Alternatively, we could define xyzminx from tbx (and the same for 3 + // Alternatively, we could define xyzminx from tbx (and the same for 3 // directions and for jx, jy, jz). This way, sx0 would not be needed. - // Better for memory? worth trying? + // Better for memory? worth trying? const Dim3 lo = lbound(tilebox); BL_PROFILE_VAR_START(blp_deposit); @@ -431,7 +431,7 @@ WarpXParticleContainer::DepositCurrent(WarpXParIter& pti, ion_lev is a null pointer. * \param rho : Full array of charge density * \param icomp : Component of rho into which charge is deposited. - 0: old value (before particle push). + 0: old value (before particle push). 1: new value (after particle push). * \param offset : Index of first particle for which charge is deposited * \param np_to_depose: Number of particles for which charge is deposited. @@ -471,7 +471,7 @@ WarpXParticleContainer::DepositCharge (WarpXParIter& pti, RealVector& wp, const IntVect& ref_ratio = WarpX::RefRatio(depos_lev); tilebox = amrex::coarsen(pti.tilebox(),ref_ratio); } - + tilebox.grow(ngRho); const int nc = (rho->nComp() == 1 ? 1 : rho->nComp()/2); diff --git a/Source/Particles/deposit_cic.F90 b/Source/Particles/deposit_cic.F90 index e4e1ace03..1fe80016f 100644 --- a/Source/Particles/deposit_cic.F90 +++ b/Source/Particles/deposit_cic.F90 @@ -7,11 +7,11 @@ module warpx_ES_deposit_cic contains -! This routine computes the charge density due to the particles using cloud-in-cell +! This routine computes the charge density due to the particles using cloud-in-cell ! deposition. The Fab rho is assumed to be node-centered. ! ! Arguments: -! particles : a pointer to the particle array-of-structs +! particles : a pointer to the particle array-of-structs ! ns : the stride length of particle struct (the size of the struct in number of reals) ! np : the number of particles ! weights : the particle weights diff --git a/Source/Particles/interpolate_cic.F90 b/Source/Particles/interpolate_cic.F90 index bc2c4f37e..005ab35f4 100644 --- a/Source/Particles/interpolate_cic.F90 +++ b/Source/Particles/interpolate_cic.F90 @@ -12,7 +12,7 @@ contains ! node-centered. ! ! Arguments: -! particles : a pointer to the particle array-of-structs +! particles : a pointer to the particle array-of-structs ! ns : the stride length of particle struct (the size of the struct in number of reals) ! np : the number of particles ! Ex_p : the electric field in the x-direction at the particle positions (output) @@ -91,7 +91,7 @@ contains wx_hi*wy_lo*wz_hi*Ez(i+1, j, k+1) + & wx_hi*wy_hi*wz_lo*Ez(i+1, j+1, k ) + & wx_hi*wy_hi*wz_hi*Ez(i+1, j+1, k+1) - + end do end subroutine warpx_interpolate_cic_3d @@ -184,7 +184,7 @@ contains lx = (particles(1, n) - plo(1))*inv_dx(1) ly = (particles(2, n) - plo(2))*inv_dx(2) lz = (particles(3, n) - plo(3))*inv_dx(3) - + i = floor(lx) j = floor(ly) k = floor(lz) @@ -203,11 +203,11 @@ contains wx_hi = lx - i wy_hi = ly - j wz_hi = lz - k - + wx_lo = 1.0d0 - wx_hi wy_lo = 1.0d0 - wy_hi wz_lo = 1.0d0 - wz_hi - + Ex_p(n) = wx_lo*wy_lo*wz_lo*cEx(i, j, k ) + & wx_lo*wy_lo*wz_hi*cEx(i, j, k+1) + & wx_lo*wy_hi*wz_lo*cEx(i, j+1, k ) + & @@ -225,7 +225,7 @@ contains wx_hi*wy_lo*wz_hi*cEy(i+1, j, k+1) + & wx_hi*wy_hi*wz_lo*cEy(i+1, j+1, k ) + & wx_hi*wy_hi*wz_hi*cEy(i+1, j+1, k+1) - + Ez_p(n) = wx_lo*wy_lo*wz_lo*cEz(i, j, k ) + & wx_lo*wy_lo*wz_hi*cEz(i, j, k+1) + & wx_lo*wy_hi*wz_lo*cEz(i, j+1, k ) + & @@ -234,14 +234,14 @@ contains wx_hi*wy_lo*wz_hi*cEz(i+1, j, k+1) + & wx_hi*wy_hi*wz_lo*cEz(i+1, j+1, k ) + & wx_hi*wy_hi*wz_hi*cEz(i+1, j+1, k+1) - + ! otherwise use the fine else wx_hi = lx - i wy_hi = ly - j wz_hi = lz - k - + wx_lo = 1.0d0 - wx_hi wy_lo = 1.0d0 - wy_hi wz_lo = 1.0d0 - wz_hi @@ -254,7 +254,7 @@ contains wx_hi*wy_lo*wz_hi*Ex(i+1, j, k+1) + & wx_hi*wy_hi*wz_lo*Ex(i+1, j+1, k ) + & wx_hi*wy_hi*wz_hi*Ex(i+1, j+1, k+1) - + Ey_p(n) = wx_lo*wy_lo*wz_lo*Ey(i, j, k ) + & wx_lo*wy_lo*wz_hi*Ey(i, j, k+1) + & wx_lo*wy_hi*wz_lo*Ey(i, j+1, k ) + & @@ -263,7 +263,7 @@ contains wx_hi*wy_lo*wz_hi*Ey(i+1, j, k+1) + & wx_hi*wy_hi*wz_lo*Ey(i+1, j+1, k ) + & wx_hi*wy_hi*wz_hi*Ey(i+1, j+1, k+1) - + Ez_p(n) = wx_lo*wy_lo*wz_lo*Ez(i, j, k ) + & wx_lo*wy_lo*wz_hi*Ez(i, j, k+1) + & wx_lo*wy_hi*wz_lo*Ez(i, j+1, k ) + & @@ -272,7 +272,7 @@ contains wx_hi*wy_lo*wz_hi*Ez(i+1, j, k+1) + & wx_hi*wy_hi*wz_lo*Ez(i+1, j+1, k ) + & wx_hi*wy_hi*wz_hi*Ez(i+1, j+1, k+1) - + end if end do @@ -314,7 +314,7 @@ contains lx = (particles(1, n) - plo(1))*inv_dx(1) ly = (particles(2, n) - plo(2))*inv_dx(2) - + i = floor(lx) j = floor(ly) @@ -329,10 +329,10 @@ contains wx_hi = lx - i wy_hi = ly - j - + wx_lo = 1.0d0 - wx_hi wy_lo = 1.0d0 - wy_hi - + Ex_p(n) = wx_lo*wy_lo*cEx(i, j ) + & wx_lo*wy_hi*cEx(i, j+1) + & wx_hi*wy_lo*cEx(i+1, j ) + & @@ -342,13 +342,13 @@ contains wx_lo*wy_hi*cEy(i, j+1) + & wx_hi*wy_lo*cEy(i+1, j ) + & wx_hi*wy_hi*cEy(i+1, j+1) - + ! otherwise use the fine else wx_hi = lx - i wy_hi = ly - j - + wx_lo = 1.0d0 - wx_hi wy_lo = 1.0d0 - wy_hi @@ -356,7 +356,7 @@ contains wx_lo*wy_hi*Ex(i, j+1) + & wx_hi*wy_lo*Ex(i+1, j ) + & wx_hi*wy_hi*Ex(i+1, j+1) - + Ey_p(n) = wx_lo*wy_lo*Ey(i, j ) + & wx_lo*wy_hi*Ey(i, j+1) + & wx_hi*wy_lo*Ey(i+1, j ) + & diff --git a/Source/Particles/push_particles_ES.F90 b/Source/Particles/push_particles_ES.F90 index 9c7bd9e92..53dd3c181 100644 --- a/Source/Particles/push_particles_ES.F90 +++ b/Source/Particles/push_particles_ES.F90 @@ -8,13 +8,13 @@ module warpx_ES_push_particles contains ! -! This routine updates the particle positions and velocities using the +! This routine updates the particle positions and velocities using the ! leapfrog time integration algorithm, given the electric fields at the ! particle positions. It also enforces specular reflection off the domain ! walls. ! ! Arguments: -! particles : a pointer to the particle array-of-structs +! particles : a pointer to the particle array-of-structs ! ns : the stride length of particle struct (the size of the struct in number of reals) ! np : the number of particles ! vx_p : the particle x-velocities @@ -30,7 +30,7 @@ contains ! prob_hi : the right-hand corner of the problem domain ! subroutine warpx_push_leapfrog_3d(particles, ns, np, & - vx_p, vy_p, vz_p, & + vx_p, vy_p, vz_p, & Ex_p, Ey_p, Ez_p, & charge, mass, dt, & prob_lo, prob_hi) & @@ -43,7 +43,7 @@ contains real(amrex_real), intent(in) :: mass real(amrex_real), intent(in) :: dt real(amrex_real), intent(in) :: prob_lo(3), prob_hi(3) - + integer n real(amrex_real) fac @@ -69,7 +69,7 @@ contains vx_p(n) = -vx_p(n) end do -! ... y... +! ... y... do while (particles(2, n) .lt. prob_lo(2) .or. particles(2, n) .gt. prob_hi(2)) if (particles(2, n) .lt. prob_lo(2)) then particles(2, n) = 2.d0*prob_lo(2) - particles(2, n) @@ -107,7 +107,7 @@ contains real(amrex_real), intent(in) :: mass real(amrex_real), intent(in) :: dt real(amrex_real), intent(in) :: prob_lo(2), prob_hi(2) - + integer n real(amrex_real) fac @@ -131,7 +131,7 @@ contains vx_p(n) = -vx_p(n) end do -! ... y... +! ... y... do while (particles(2, n) .lt. prob_lo(2) .or. particles(2, n) .gt. prob_hi(2)) if (particles(2, n) .lt. prob_lo(2)) then particles(2, n) = 2.d0*prob_lo(2) - particles(2, n) @@ -152,7 +152,7 @@ contains ! from the velocities after particle initialization. ! ! Arguments: -! particles : a pointer to the particle array-of-structs +! particles : a pointer to the particle array-of-structs ! ns : the stride length of particle struct (the size of the struct in number of reals) ! np : the number of particles ! xx_p : the electric field in the x-direction at the particle positions @@ -190,7 +190,7 @@ contains vx_p(n) = -vx_p(n) end do -! ... y... +! ... y... do while (particles(2, n) .lt. prob_lo(2) .or. particles(2, n) .gt. prob_hi(2)) if (particles(2, n) .lt. prob_lo(2)) then particles(2, n) = 2.d0*prob_lo(2) - particles(2, n) @@ -209,7 +209,7 @@ contains end if vz_p(n) = -vz_p(n) end do - + end do end subroutine warpx_push_leapfrog_positions_3d @@ -241,7 +241,7 @@ contains vx_p(n) = -vx_p(n) end do -! ... y... +! ... y... do while (particles(2, n) .lt. prob_lo(2) .or. particles(2, n) .gt. prob_hi(2)) if (particles(2, n) .lt. prob_lo(2)) then particles(2, n) = 2.d0*prob_lo(2) - particles(2, n) |