WarpX.H

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/* Copyright 2016-2020 Andrew Myers, Ann Almgren, Aurore Blelly
 *                     Axel Huebl, Burlen Loring, David Grote
 *                     Glenn Richardson, Junmin Gu, Luca Fedeli
 *                     Mathieu Lobet, Maxence Thevenet, Michael Rowan
 *                     Remi Lehe, Revathi Jambunathan, Weiqun Zhang
 *                     Yinjian Zhao
 *
 * This file is part of WarpX.
 *
 * License: BSD-3-Clause-LBNL
 */
#ifndef WARPX_H_
#define WARPX_H_

#include "BoundaryConditions/PML_fwd.H"
#include "Diagnostics/BackTransformedDiagnostic_fwd.H"
#include "Diagnostics/MultiDiagnostics_fwd.H"
#include "Diagnostics/ReducedDiags/MultiReducedDiags_fwd.H"
#include "EmbeddedBoundary/WarpXFaceInfoBox_fwd.H"
#include "FieldSolver/FiniteDifferenceSolver/FiniteDifferenceSolver_fwd.H"
#include "FieldSolver/FiniteDifferenceSolver/MacroscopicProperties/MacroscopicProperties_fwd.H"
#include "Filter/NCIGodfreyFilter_fwd.H"
#include "Particles/ParticleBoundaryBuffer_fwd.H"
#include "Particles/MultiParticleContainer_fwd.H"
#include "Particles/WarpXParticleContainer_fwd.H"
#ifdef WARPX_USE_PSATD
#   ifdef WARPX_DIM_RZ
#       include "FieldSolver/SpectralSolver/SpectralSolverRZ_fwd.H"
#       include "BoundaryConditions/PML_RZ_fwd.H"
#   else
#       include "FieldSolver/SpectralSolver/SpectralSolver_fwd.H"
#   endif
#endif
#include "Evolve/WarpXDtType.H"
#include "FieldSolver/ElectrostaticSolver.H"
#include "Filter/BilinearFilter.H"
#include "Parallelization/GuardCellManager.H"
#include "Utils/Parser/IntervalsParser.H"
#include "Utils/WarpXAlgorithmSelection.H"

#include <AMReX.H>
#include <AMReX_AmrCore.H>
#include <AMReX_Array.H>
#include <AMReX_Config.H>
#ifdef AMREX_USE_EB
#   include <AMReX_EBFabFactory.H>
#endif
#include <AMReX_GpuContainers.H>
#include <AMReX_IntVect.H>
#include <AMReX_LayoutData.H>
#include <AMReX_Parser.H>
#include <AMReX_REAL.H>
#include <AMReX_RealBox.H>
#include <AMReX_RealVect.H>
#include <AMReX_Vector.H>
#include <AMReX_VisMF.H>

#include <AMReX_BaseFwd.H>
#include <AMReX_AmrCoreFwd.H>

#include <array>
#include <iostream>
#include <limits>
#include <memory>
#include <optional>
#include <string>
#include <vector>

enum struct PatchType : int
{
    fine,
    coarse
};

class WarpX
    : public amrex::AmrCore
{
public:

    friend class PML;

    static WarpX& GetInstance ();
    static void ResetInstance ();

    WarpX ();
    ~WarpX ();

    static std::string Version (); 
    static std::string PicsarVersion (); 

    int Verbose () const { return verbose; }

    void InitData ();

    void Evolve (int numsteps = -1);

    MultiParticleContainer& GetPartContainer () { return *mypc; }
    MacroscopicProperties& GetMacroscopicProperties () { return *m_macroscopic_properties; }

    ParticleBoundaryBuffer& GetParticleBoundaryBuffer () { return *m_particle_boundary_buffer; }

    static void shiftMF (amrex::MultiFab& mf, const amrex::Geometry& geom,
                         int num_shift, int dir, const int lev, bool update_cost_flag,
                         amrex::Real external_field=0.0, bool useparser = false,
                         amrex::ParserExecutor<3> const& field_parser={});

    static void GotoNextLine (std::istream& is);

    static std::string authors;

    static amrex::Vector<amrex::Real> E_external_grid;
    static amrex::Vector<amrex::Real> B_external_grid;

    static std::string B_ext_grid_s;
    static std::string E_ext_grid_s;

    static std::string str_Bx_ext_grid_function;
    static std::string str_By_ext_grid_function;
    static std::string str_Bz_ext_grid_function;
    static std::string str_Ex_ext_grid_function;
    static std::string str_Ey_ext_grid_function;
    static std::string str_Ez_ext_grid_function;

    std::unique_ptr<amrex::Parser> Bxfield_parser;
    std::unique_ptr<amrex::Parser> Byfield_parser;
    std::unique_ptr<amrex::Parser> Bzfield_parser;
    std::unique_ptr<amrex::Parser> Exfield_parser;
    std::unique_ptr<amrex::Parser> Eyfield_parser;
    std::unique_ptr<amrex::Parser> Ezfield_parser;

    // Algorithms
    static short current_deposition_algo;
    static short charge_deposition_algo;
    static short field_gathering_algo;
    static short particle_pusher_algo;
    static short maxwell_solver_id;
    static short load_balance_costs_update_algo;
    static int em_solver_medium;
    static int macroscopic_solver_algo;
    static amrex::Vector<int> field_boundary_lo;
    static amrex::Vector<int> field_boundary_hi;
    static amrex::Vector<ParticleBoundaryType> particle_boundary_lo;
    static amrex::Vector<ParticleBoundaryType> particle_boundary_hi;

    static short J_in_time;
    static short rho_in_time;

    static bool do_current_centering;

    //  to satisfy the continuity equation and charge conservation
    bool current_correction;

    bool update_with_rho = false;

    static bool do_single_precision_comms;

    static amrex::IntVect m_fill_guards_fields;

    static amrex::IntVect m_fill_guards_current;

    static bool do_dive_cleaning;
    static bool do_divb_cleaning;

    static int nox;
    static int noy;
    static int noz;

    static int field_centering_nox;
    static int field_centering_noy;
    static int field_centering_noz;

    static int current_centering_nox;
    static int current_centering_noy;
    static int current_centering_noz;

    static int n_rz_azimuthal_modes;
    static int ncomps;

    static bool use_fdtd_nci_corr;
    static bool galerkin_interpolation;

    static bool use_filter;
    static bool use_kspace_filter;
    static bool use_filter_compensation;

    static bool serialize_initial_conditions;

    static bool do_back_transformed_diagnostics;
    static std::string lab_data_directory;
    static int  num_snapshots_lab;
    static amrex::Real dt_snapshots_lab;
    static bool do_back_transformed_fields;
    static bool do_back_transformed_particles;

    static amrex::Real gamma_boost;
    static amrex::Real beta_boost;
    static amrex::Vector<int> boost_direction;
    static amrex::Real zmax_plasma_to_compute_max_step;
    static bool do_compute_max_step_from_zmax;

    static bool do_dynamic_scheduling;
    static bool refine_plasma;

    static utils::parser::IntervalsParser sort_intervals;
    static amrex::IntVect sort_bin_size;

    static bool do_subcycling;
    static bool do_multi_J;
    static int do_multi_J_n_depositions;

    static bool do_device_synchronize;
    static bool safe_guard_cells;

    static int n_field_gather_buffer;
    static int n_current_deposition_buffer;

    static bool do_nodal;

    // Global rho nodal flag to know about rho index type when rho MultiFab is not allocated
    amrex::IntVect m_rho_nodal_flag;

    std::array<const amrex::MultiFab* const, 3>
    get_array_Bfield_aux  (const int lev) const {
        return {
            Bfield_aux[lev][0].get(),
            Bfield_aux[lev][1].get(),
            Bfield_aux[lev][2].get()
        };
    }
    std::array<const amrex::MultiFab* const, 3>
    get_array_Efield_aux  (const int lev) const {
        return {
            Efield_aux[lev][0].get(),
            Efield_aux[lev][1].get(),
            Efield_aux[lev][2].get()
        };
    }

    amrex::MultiFab * get_pointer_Efield_aux  (int lev, int direction) const { return Efield_aux[lev][direction].get(); }
    amrex::MultiFab * get_pointer_Bfield_aux  (int lev, int direction) const { return Bfield_aux[lev][direction].get(); }

    amrex::MultiFab * get_pointer_Efield_fp  (int lev, int direction) const { return Efield_fp[lev][direction].get(); }
    amrex::MultiFab * get_pointer_Bfield_fp  (int lev, int direction) const { return Bfield_fp[lev][direction].get(); }
    amrex::MultiFab * get_pointer_current_fp  (int lev, int direction) const { return current_fp[lev][direction].get(); }
    amrex::MultiFab * get_pointer_rho_fp  (int lev) const { return rho_fp[lev].get(); }
    amrex::MultiFab * get_pointer_F_fp  (int lev) const { return F_fp[lev].get(); }
    amrex::MultiFab * get_pointer_G_fp  (int lev) const { return G_fp[lev].get(); }
    amrex::MultiFab * get_pointer_phi_fp  (int lev) const { return phi_fp[lev].get(); }

    amrex::MultiFab * get_pointer_Efield_cp  (int lev, int direction) const { return Efield_cp[lev][direction].get(); }
    amrex::MultiFab * get_pointer_Bfield_cp  (int lev, int direction) const { return Bfield_cp[lev][direction].get(); }
    amrex::MultiFab * get_pointer_current_cp  (int lev, int direction) const { return current_cp[lev][direction].get(); }
    amrex::MultiFab * get_pointer_rho_cp  (int lev) const { return rho_cp[lev].get(); }
    amrex::MultiFab * get_pointer_F_cp  (int lev) const { return F_cp[lev].get(); }
    amrex::MultiFab * get_pointer_G_cp  (int lev) const { return G_cp[lev].get(); }

    amrex::MultiFab * get_pointer_edge_lengths  (int lev, int direction) const { return m_edge_lengths[lev][direction].get(); }
    amrex::MultiFab * get_pointer_face_areas  (int lev, int direction) const { return m_face_areas[lev][direction].get(); }

    const amrex::MultiFab& getEfield  (int lev, int direction) {return *Efield_aux[lev][direction];}
    const amrex::MultiFab& getBfield  (int lev, int direction) {return *Bfield_aux[lev][direction];}

    const amrex::MultiFab& getcurrent_cp (int lev, int direction) {return *current_cp[lev][direction];}
    const amrex::MultiFab& getEfield_cp  (int lev, int direction) {return  *Efield_cp[lev][direction];}
    const amrex::MultiFab& getBfield_cp  (int lev, int direction) {return  *Bfield_cp[lev][direction];}
    const amrex::MultiFab& getrho_cp (int lev) {return  *rho_cp[lev];}
    const amrex::MultiFab& getF_cp (int lev) {return *F_cp[lev];}
    const amrex::MultiFab& getG_cp (int lev) {return *G_cp[lev];}

    const amrex::MultiFab& getcurrent_fp (int lev, int direction) {return *current_fp[lev][direction];}
    const amrex::MultiFab& getEfield_fp  (int lev, int direction) {return *Efield_fp[lev][direction];}
    const amrex::MultiFab& getBfield_fp  (int lev, int direction) {return *Bfield_fp[lev][direction];}
    const amrex::MultiFab& getrho_fp (int lev) {return *rho_fp[lev];}
    const amrex::MultiFab& getphi_fp (int lev) {return *phi_fp[lev];}
    const amrex::MultiFab& getF_fp (int lev) {return *F_fp[lev];}
    const amrex::MultiFab& getG_fp (int lev) {return *G_fp[lev];}

    const amrex::MultiFab& getEfield_avg_fp (int lev, int direction) {return *Efield_avg_fp[lev][direction];}
    const amrex::MultiFab& getBfield_avg_fp (int lev, int direction) {return *Bfield_avg_fp[lev][direction];}
    const amrex::MultiFab& getEfield_avg_cp (int lev, int direction) {return *Efield_avg_cp[lev][direction];}
    const amrex::MultiFab& getBfield_avg_cp (int lev, int direction) {return *Bfield_avg_cp[lev][direction];}

    bool DoPML () const {return do_pml;}

#if (defined WARPX_DIM_RZ) && (defined WARPX_USE_PSATD)
    const PML_RZ* getPMLRZ() {return pml_rz[0].get();}
#endif

    std::vector<bool> getPMLdirections() const;

    static amrex::LayoutData<amrex::Real>* getCosts (int lev);

    void setLoadBalanceEfficiency (const int lev, const amrex::Real efficiency)
    {
        if (m_instance)
        {
            m_instance->load_balance_efficiency[lev] = efficiency;
        } else
        {
            return;
        }
    }

    amrex::Real getLoadBalanceEfficiency (const int lev)
    {
        if (m_instance)
        {
            return m_instance->load_balance_efficiency[lev];
        } else
        {
            return -1;
        }
    }

    static amrex::IntVect filter_npass_each_dir;
    BilinearFilter bilinear_filter;
    amrex::Vector< std::unique_ptr<NCIGodfreyFilter> > nci_godfrey_filter_exeybz;
    amrex::Vector< std::unique_ptr<NCIGodfreyFilter> > nci_godfrey_filter_bxbyez;

    amrex::Real time_of_last_gal_shift = 0;
    amrex::Vector<amrex::Real> m_v_galilean = amrex::Vector<amrex::Real>(3, amrex::Real(0.));
    amrex::Array<amrex::Real,3> m_galilean_shift = {{0}};

    amrex::Vector<amrex::Real> m_v_comoving = amrex::Vector<amrex::Real>(3, amrex::Real(0.));

    static int num_mirrors;
    amrex::Vector<amrex::Real> mirror_z;
    amrex::Vector<amrex::Real> mirror_z_width;
    amrex::Vector<int> mirror_z_npoints;

    std::unique_ptr<MultiReducedDiags> reduced_diags;

    void applyMirrors(amrex::Real time);

    void ComputeDt ();

    void PrintMainPICparameters ();

    void WriteUsedInputsFile () const;

    void PrintDtDxDyDz ();

    void ComputeMaxStep ();
    // Compute max_step automatically for simulations in a boosted frame.
    void computeMaxStepBoostAccelerator(const amrex::Geometry& geom);

    int  MoveWindow (const int step, bool move_j);

    void ShiftGalileanBoundary ();
    void UpdatePlasmaInjectionPosition (amrex::Real dt);
    void ResetProbDomain (const amrex::RealBox& rb);
    void EvolveE (         amrex::Real dt);
    void EvolveE (int lev, amrex::Real dt);
    void EvolveB (         amrex::Real dt, DtType dt_type);
    void EvolveB (int lev, amrex::Real dt, DtType dt_type);
    void EvolveF (         amrex::Real dt, DtType dt_type);
    void EvolveF (int lev, amrex::Real dt, DtType dt_type);
    void EvolveG (         amrex::Real dt, DtType dt_type);
    void EvolveG (int lev, amrex::Real dt, DtType dt_type);
    void EvolveB (int lev, PatchType patch_type, amrex::Real dt, DtType dt_type);
    void EvolveE (int lev, PatchType patch_type, amrex::Real dt);
    void EvolveF (int lev, PatchType patch_type, amrex::Real dt, DtType dt_type);
    void EvolveG (int lev, PatchType patch_type, amrex::Real dt, DtType dt_type);

    void MacroscopicEvolveE (         amrex::Real dt);
    void MacroscopicEvolveE (int lev, amrex::Real dt);
    void MacroscopicEvolveE (int lev, PatchType patch_type, amrex::Real dt);

    void Hybrid_QED_Push (         amrex::Vector<amrex::Real> dt);

    void Hybrid_QED_Push (int lev, amrex::Real dt);

    void Hybrid_QED_Push (int lev, PatchType patch_type, amrex::Real dt);

    static amrex::Real quantum_xi_c2;

    void LoadBalance ();
    void ResetCosts ();

    utils::parser::IntervalsParser get_load_balance_intervals () const
    {
        return load_balance_intervals;
    }

    void DampFieldsInGuards (const int lev,
                             const std::array<std::unique_ptr<amrex::MultiFab>,3>& Efield,
                             const std::array<std::unique_ptr<amrex::MultiFab>,3>& Bfield);

    void DampFieldsInGuards (const int lev, std::unique_ptr<amrex::MultiFab>& mf);

#ifdef WARPX_DIM_RZ
    void ApplyInverseVolumeScalingToCurrentDensity(amrex::MultiFab* Jx,
                                                   amrex::MultiFab* Jy,
                                                   amrex::MultiFab* Jz,
                                                   int lev);

    void ApplyInverseVolumeScalingToChargeDensity(amrex::MultiFab* Rho,
                                                  int lev);
#endif

    void ApplyEfieldBoundary (const int lev, PatchType patch_type);
    void ApplyBfieldBoundary (const int lev, PatchType patch_type, DtType dt_type);

    void DampPML ();
    void DampPML (const int lev);
    void DampPML (const int lev, PatchType patch_type);
    void DampPML_Cartesian (const int lev, PatchType patch_type);

    void DampJPML ();
    void DampJPML (int lev);
    void DampJPML (int lev, PatchType patch_type);

    void CopyJPML ();
    bool isAnyBoundaryPML();

    void NodalSyncPML ();

    void NodalSyncPML (int lev);

    void NodalSyncPML (int lev, PatchType patch_type);

    PML* GetPML (int lev);
#if (defined WARPX_DIM_RZ) && (defined WARPX_USE_PSATD)
    PML_RZ* GetPML_RZ (int lev);
#endif

    void doFieldIonization ();
    void doFieldIonization (int lev);

#ifdef WARPX_QED

    void doQEDEvents ();
    void doQEDEvents (int lev);
#endif

    void PushParticlesandDepose (int lev, amrex::Real cur_time, DtType a_dt_type=DtType::Full, bool skip_current=false);
    void PushParticlesandDepose (         amrex::Real cur_time, bool skip_current=false);

    // This function does aux(lev) = fp(lev) + I(aux(lev-1)-cp(lev)).
    // Caller must make sure fp and cp have ghost cells filled.
    void UpdateAuxilaryData ();
    void UpdateAuxilaryDataStagToNodal ();
    void UpdateAuxilaryDataSameType ();

    void UpdateCurrentNodalToStag (amrex::MultiFab& dst, amrex::MultiFab const& src);

    // Fill boundary cells including coarse/fine boundaries
    void FillBoundaryB   (amrex::IntVect ng, std::optional<bool> nodal_sync = std::nullopt);
    void FillBoundaryE   (amrex::IntVect ng, std::optional<bool> nodal_sync = std::nullopt);
    void FillBoundaryB_avg   (amrex::IntVect ng);
    void FillBoundaryE_avg   (amrex::IntVect ng);

    void FillBoundaryF   (amrex::IntVect ng, std::optional<bool> nodal_sync = std::nullopt);
    void FillBoundaryG   (amrex::IntVect ng, std::optional<bool> nodal_sync = std::nullopt);
    void FillBoundaryAux (amrex::IntVect ng);
    void FillBoundaryE   (int lev, amrex::IntVect ng, std::optional<bool> nodal_sync = std::nullopt);
    void FillBoundaryB   (int lev, amrex::IntVect ng, std::optional<bool> nodal_sync = std::nullopt);
    void FillBoundaryE_avg   (int lev, amrex::IntVect ng);
    void FillBoundaryB_avg   (int lev, amrex::IntVect ng);

    void FillBoundaryF   (int lev, amrex::IntVect ng, std::optional<bool> nodal_sync = std::nullopt);
    void FillBoundaryG   (int lev, amrex::IntVect ng, std::optional<bool> nodal_sync = std::nullopt);
    void FillBoundaryAux (int lev, amrex::IntVect ng);

    void SyncCurrentAndRho ();

    void SyncCurrent (
        const amrex::Vector<std::array<std::unique_ptr<amrex::MultiFab>,3>>& J_fp,
        const amrex::Vector<std::array<std::unique_ptr<amrex::MultiFab>,3>>& J_cp);

    void SyncRho ();

    amrex::Vector<int> getnsubsteps () const {return nsubsteps;}
    int getnsubsteps (int lev) const {return nsubsteps[lev];}
    amrex::Vector<int> getistep () const {return istep;}
    int getistep (int lev) const {return istep[lev];}
    void setistep (int lev, int ii) {istep[lev] = ii;}
    amrex::Vector<amrex::Real> gett_old () const {return t_old;}
    amrex::Real gett_old (int lev) const {return t_old[lev];}
    amrex::Vector<amrex::Real> gett_new () const {return t_new;}
    amrex::Real gett_new (int lev) const {return t_new[lev];}
    void sett_new (int lev, amrex::Real time) {t_new[lev] = time;}
    amrex::Vector<amrex::Real> getdt () const {return dt;}
    amrex::Real getdt (int lev) const {return dt[lev];}
    int getdo_moving_window() const {return do_moving_window;}
    amrex::Real getmoving_window_x() const {return moving_window_x;}
    amrex::Real getcurrent_injection_position () const {return current_injection_position;}
    bool getis_synchronized() const {return is_synchronized;}

    int maxStep () const {return max_step;}
    amrex::Real stopTime () const {return stop_time;}

    void AverageAndPackFields( amrex::Vector<std::string>& varnames,
        amrex::Vector<amrex::MultiFab>& mf_avg, const amrex::IntVect ngrow) const;

    void prepareFields( int const step, amrex::Vector<std::string>& varnames,
        amrex::Vector<amrex::MultiFab>& mf_avg,
        amrex::Vector<const amrex::MultiFab*>& output_mf,
        amrex::Vector<amrex::Geometry>& output_geom ) const;

    static std::array<amrex::Real,3> CellSize (int lev);
    static amrex::RealBox getRealBox(const amrex::Box& bx, int lev);

    static std::array<amrex::Real,3> LowerCorner (const amrex::Box& bx, const int lev, const amrex::Real time_shift_delta);
    static std::array<amrex::Real,3> UpperCorner (const amrex::Box& bx, const int lev, const amrex::Real time_shift_delta);

    static amrex::IntVect RefRatio (int lev);

    static const amrex::iMultiFab* CurrentBufferMasks (int lev);
    static const amrex::iMultiFab* GatherBufferMasks (int lev);

    static int do_electrostatic;

    // Parameters for lab frame electrostatic
    static amrex::Real self_fields_required_precision;
    static amrex::Real self_fields_absolute_tolerance;
    static int self_fields_max_iters;
    static int self_fields_verbosity;

    static int do_moving_window; // boolean
    static int start_moving_window_step; // the first step to move window
    static int end_moving_window_step; // the last step to move window
    static int moving_window_active (int const step) {
        bool const step_before_end = (step < end_moving_window_step) || (end_moving_window_step < 0);
        bool const step_after_start = (step >= start_moving_window_step);
        return do_moving_window && step_before_end && step_after_start;
    }
    static int moving_window_dir;
    static amrex::Real moving_window_v;
    static bool fft_do_time_averaging;

    // slice generation //
    static int num_slice_snapshots_lab;
    static amrex::Real dt_slice_snapshots_lab;
    static amrex::Real particle_slice_width_lab;
    amrex::RealBox getSliceRealBox() const {return slice_realbox;}

    // these should be private, but can't due to Cuda limitations
    static void ComputeDivB (amrex::MultiFab& divB, int const dcomp,
                             const std::array<const amrex::MultiFab* const, 3>& B,
                             const std::array<amrex::Real,3>& dx);

    static void ComputeDivB (amrex::MultiFab& divB, int const dcomp,
                             const std::array<const amrex::MultiFab* const, 3>& B,
                             const std::array<amrex::Real,3>& dx, amrex::IntVect const ngrow);

    void ComputeDivE(amrex::MultiFab& divE, const int lev);

    const amrex::IntVect getngEB() const { return guard_cells.ng_alloc_EB; }
    const amrex::IntVect getngF() const { return guard_cells.ng_alloc_F; }
    const amrex::IntVect getngUpdateAux() const { return guard_cells.ng_UpdateAux; }
    const amrex::IntVect get_ng_depos_J() const {return guard_cells.ng_depos_J;}
    const amrex::IntVect get_ng_depos_rho() const {return guard_cells.ng_depos_rho;}
    const amrex::IntVect get_ng_fieldgather () const {return guard_cells.ng_FieldGather;}

    const amrex::IntVect get_numprocs() const {return numprocs;}

    ElectrostaticSolver::PoissonBoundaryHandler m_poisson_boundary_handler;
    void ComputeSpaceChargeField (bool const reset_fields);
    void AddBoundaryField ();
    void AddSpaceChargeField (WarpXParticleContainer& pc);
    void AddSpaceChargeFieldLabFrame ();
    void computePhi (const amrex::Vector<std::unique_ptr<amrex::MultiFab> >& rho,
                     amrex::Vector<std::unique_ptr<amrex::MultiFab> >& phi,
                     std::array<amrex::Real, 3> const beta = {{0,0,0}},
                     amrex::Real const required_precision=amrex::Real(1.e-11),
                     amrex::Real absolute_tolerance=amrex::Real(0.0),
                     const int max_iters=200,
                     const int verbosity=2) const;

    void setPhiBC (amrex::Vector<std::unique_ptr<amrex::MultiFab> >& phi ) const;

    void computeE (amrex::Vector<std::array<std::unique_ptr<amrex::MultiFab>, 3> >& E,
                   const amrex::Vector<std::unique_ptr<amrex::MultiFab> >& phi,
                   std::array<amrex::Real, 3> const beta = {{0,0,0}} ) const;
    void computeB (amrex::Vector<std::array<std::unique_ptr<amrex::MultiFab>, 3> >& B,
                   const amrex::Vector<std::unique_ptr<amrex::MultiFab> >& phi,
                   std::array<amrex::Real, 3> const beta = {{0,0,0}} ) const;
    void computePhiTriDiagonal (const amrex::Vector<std::unique_ptr<amrex::MultiFab> >& rho,
                                      amrex::Vector<std::unique_ptr<amrex::MultiFab> >& phi) const;

    void InitializeExternalFieldsOnGridUsingParser (
         amrex::MultiFab *mfx, amrex::MultiFab *mfy, amrex::MultiFab *mfz,
         amrex::ParserExecutor<3> const& xfield_parser,
         amrex::ParserExecutor<3> const& yfield_parser,
         amrex::ParserExecutor<3> const& zfield_parser,
         std::array< std::unique_ptr<amrex::MultiFab>, 3 > const& edge_lengths,
         std::array< std::unique_ptr<amrex::MultiFab>, 3 > const& face_areas,
         const char field,
         const int lev);

    void InitializeEBGridData(int lev);

    void ComputeCostsHeuristic (amrex::Vector<std::unique_ptr<amrex::LayoutData<amrex::Real> > >& costs);

    void ApplyFilterandSumBoundaryRho (int lev, int glev, amrex::MultiFab& rho, int icomp, int ncomp);

    static amrex::Vector<amrex::Real> getFornbergStencilCoefficients(const int n_order, const bool nodal);

    // Device vectors of stencil coefficients used for finite-order centering of fields
    amrex::Gpu::DeviceVector<amrex::Real> device_field_centering_stencil_coeffs_x;
    amrex::Gpu::DeviceVector<amrex::Real> device_field_centering_stencil_coeffs_y;
    amrex::Gpu::DeviceVector<amrex::Real> device_field_centering_stencil_coeffs_z;

    // Device vectors of stencil coefficients used for finite-order centering of currents
    amrex::Gpu::DeviceVector<amrex::Real> device_current_centering_stencil_coeffs_x;
    amrex::Gpu::DeviceVector<amrex::Real> device_current_centering_stencil_coeffs_y;
    amrex::Gpu::DeviceVector<amrex::Real> device_current_centering_stencil_coeffs_z;

    // This needs to be public for CUDA.
    virtual void ErrorEst (int lev, amrex::TagBoxArray& tags, amrex::Real time, int /*ngrow*/) final;

protected:

    void InitLevelData (int lev, amrex::Real time);

    virtual void PostProcessBaseGrids (amrex::BoxArray& ba0) const final;

    virtual void MakeNewLevelFromScratch (int lev, amrex::Real time, const amrex::BoxArray& ba,
                                          const amrex::DistributionMapping& dm) final;

    virtual void MakeNewLevelFromCoarse (int /*lev*/, amrex::Real /*time*/, const amrex::BoxArray& /*ba*/,
                                         const amrex::DistributionMapping& /*dm*/) final;

    virtual void RemakeLevel (int lev, amrex::Real time, const amrex::BoxArray& ba,
                              const amrex::DistributionMapping& dm) final;

    virtual void ClearLevel (int lev) final;

private:

    // Singleton is used when the code is run from python
    static WarpX* m_instance;

    static void CheckSignals ();
    void HandleSignals ();

    void EvolveEM(int numsteps);

    void FillBoundaryB (const int lev, const PatchType patch_type, const amrex::IntVect ng, std::optional<bool> nodal_sync = std::nullopt);
    void FillBoundaryE (const int lev, const PatchType patch_type, const amrex::IntVect ng, std::optional<bool> nodal_sync = std::nullopt);
    void FillBoundaryF (int lev, PatchType patch_type, amrex::IntVect ng, std::optional<bool> nodal_sync = std::nullopt);
    void FillBoundaryG (int lev, PatchType patch_type, amrex::IntVect ng, std::optional<bool> nodal_sync = std::nullopt);

    void FillBoundaryB_avg (int lev, PatchType patch_type, amrex::IntVect ng);
    void FillBoundaryE_avg (int lev, PatchType patch_type, amrex::IntVect ng);

    void OneStep_nosub (amrex::Real t);
    void OneStep_sub1 (amrex::Real t);

    void OneStep_multiJ (const amrex::Real t);

    void RestrictCurrentFromFineToCoarsePatch (
        const amrex::Vector<std::array<std::unique_ptr<amrex::MultiFab>,3>>& J_fp,
        const amrex::Vector<std::array<std::unique_ptr<amrex::MultiFab>,3>>& J_cp,
        const int lev);
    void AddCurrentFromFineLevelandSumBoundary (
        const amrex::Vector<std::array<std::unique_ptr<amrex::MultiFab>,3>>& J_fp,
        const amrex::Vector<std::array<std::unique_ptr<amrex::MultiFab>,3>>& J_cp,
        const int lev);
    void StoreCurrent (const int lev);
    void RestoreCurrent (const int lev);
    void ApplyFilterJ (
        const amrex::Vector<std::array<std::unique_ptr<amrex::MultiFab>,3>>& current,
        const int lev,
        const int idim);
    void ApplyFilterJ (
        const amrex::Vector<std::array<std::unique_ptr<amrex::MultiFab>,3>>& current,
        const int lev);
    void SumBoundaryJ (
        const amrex::Vector<std::array<std::unique_ptr<amrex::MultiFab>,3>>& current,
        const int lev,
        const int idim,
        const amrex::Periodicity& period);
    void SumBoundaryJ (
        const amrex::Vector<std::array<std::unique_ptr<amrex::MultiFab>,3>>& current,
        const int lev,
        const amrex::Periodicity& period);
    void NodalSyncJ (
        const amrex::Vector<std::array<std::unique_ptr<amrex::MultiFab>,3>>& J_fp,
        const amrex::Vector<std::array<std::unique_ptr<amrex::MultiFab>,3>>& J_cp,
        const int lev,
        PatchType patch_type);

    void RestrictRhoFromFineToCoarsePatch (
        const amrex::Vector<std::unique_ptr<amrex::MultiFab>>& charge_fp,
        const amrex::Vector<std::unique_ptr<amrex::MultiFab>>& charge_cp,
        const int lev);
    void ApplyFilterandSumBoundaryRho (
        const amrex::Vector<std::unique_ptr<amrex::MultiFab>>& charge_fp,
        const amrex::Vector<std::unique_ptr<amrex::MultiFab>>& charge_cp,
        const int lev,
        PatchType patch_type,
        const int icomp,
        const int ncomp);
    void AddRhoFromFineLevelandSumBoundary (
        const amrex::Vector<std::unique_ptr<amrex::MultiFab>>& charge_fp,
        const amrex::Vector<std::unique_ptr<amrex::MultiFab>>& charge_cp,
        const int lev,
        const int icomp,
        const int ncomp);
    void NodalSyncRho (
        const amrex::Vector<std::unique_ptr<amrex::MultiFab>>& charge_fp,
        const amrex::Vector<std::unique_ptr<amrex::MultiFab>>& charge_cp,
        const int lev,
        PatchType patch_type,
        const int icomp,
        const int ncomp);

    void ReadParameters ();

    void BackwardCompatibility ();

    void InitFromScratch ();

    void AllocLevelData (int lev, const amrex::BoxArray& new_grids,
                         const amrex::DistributionMapping& new_dmap);

    amrex::DistributionMapping
    GetRestartDMap (const std::string& chkfile, const amrex::BoxArray& ba, int lev) const;

    void InitFromCheckpoint ();
    void PostRestart ();

    void InitPML ();
    void ComputePMLFactors ();

    void InitFilter ();

    void InitDiagnostics ();

    void InitNCICorrector ();

    void CheckGuardCells();

    void CheckGuardCells(amrex::MultiFab const& mf);

    void CheckKnownIssues();

    void PerformanceHints ();

    std::unique_ptr<amrex::MultiFab> GetCellCenteredData();

    void BuildBufferMasks ();
    void BuildBufferMasksInBox ( const amrex::Box tbx, amrex::IArrayBox &buffer_mask,
                                 const amrex::IArrayBox &guard_mask, const int ng );
    const amrex::iMultiFab* getCurrentBufferMasks (int lev) const {
        return current_buffer_masks[lev].get();
    }
    const amrex::iMultiFab* getGatherBufferMasks (int lev) const {
        return gather_buffer_masks[lev].get();
    }

    void ReorderFornbergCoefficients (amrex::Vector<amrex::Real>& ordered_coeffs,
                                      amrex::Vector<amrex::Real>& unordered_coeffs,
                                      const int order);
    void AllocateCenteringCoefficients (amrex::Gpu::DeviceVector<amrex::Real>& device_centering_stencil_coeffs_x,
                                        amrex::Gpu::DeviceVector<amrex::Real>& device_centering_stencil_coeffs_y,
                                        amrex::Gpu::DeviceVector<amrex::Real>& device_centering_stencil_coeffs_z,
                                        const int centering_nox,
                                        const int centering_noy,
                                        const int centering_noz);

    void AllocLevelMFs (int lev, const amrex::BoxArray& ba, const amrex::DistributionMapping& dm,
                        const amrex::IntVect& ngEB, amrex::IntVect& ngJ,
                        const amrex::IntVect& ngRho, const amrex::IntVect& ngF,
                        const amrex::IntVect& ngG, const bool aux_is_nodal);
#ifdef WARPX_USE_PSATD
#   ifdef WARPX_DIM_RZ
    void AllocLevelSpectralSolverRZ (amrex::Vector<std::unique_ptr<SpectralSolverRZ>>& spectral_solver,
                                     const int lev,
                                     const amrex::BoxArray& realspace_ba,
                                     const amrex::DistributionMapping& dm,
                                     const std::array<amrex::Real,3>& dx);
#   else
    void AllocLevelSpectralSolver (amrex::Vector<std::unique_ptr<SpectralSolver>>& spectral_solver,
                                   const int lev,
                                   const amrex::BoxArray& realspace_ba,
                                   const amrex::DistributionMapping& dm,
                                   const std::array<amrex::Real,3>& dx,
                                   const bool pml_flag=false);
#   endif
#endif

    amrex::Vector<int> istep;      // which step?
    amrex::Vector<int> nsubsteps;  // how many substeps on each level?

    amrex::Vector<amrex::Real> t_new;
    amrex::Vector<amrex::Real> t_old;
    amrex::Vector<amrex::Real> dt;

    // Particle container
    std::unique_ptr<MultiParticleContainer> mypc;
    std::unique_ptr<MultiDiagnostics> multi_diags;

    // Boosted Frame Diagnostics
    std::unique_ptr<BackTransformedDiagnostic> myBFD;

    //
    // Fields: First array for level, second for direction
    //

    // Full solution
    amrex::Vector<std::array< std::unique_ptr<amrex::MultiFab>, 3 > > Efield_aux;
    amrex::Vector<std::array< std::unique_ptr<amrex::MultiFab>, 3 > > Bfield_aux;

    // Fine patch
    amrex::Vector<            std::unique_ptr<amrex::MultiFab>      > F_fp;
    amrex::Vector<            std::unique_ptr<amrex::MultiFab>      > G_fp;
    amrex::Vector<            std::unique_ptr<amrex::MultiFab>      > rho_fp;
    amrex::Vector<            std::unique_ptr<amrex::MultiFab>      > phi_fp;
    amrex::Vector<std::array< std::unique_ptr<amrex::MultiFab>, 3 > > current_fp;
    amrex::Vector<std::array< std::unique_ptr<amrex::MultiFab>, 3 > > current_fp_vay;
    amrex::Vector<std::array< std::unique_ptr<amrex::MultiFab>, 3 > > Efield_fp;
    amrex::Vector<std::array< std::unique_ptr<amrex::MultiFab>, 3 > > Bfield_fp;
    amrex::Vector<std::array< std::unique_ptr<amrex::MultiFab>, 3 > > Efield_avg_fp;
    amrex::Vector<std::array< std::unique_ptr<amrex::MultiFab>, 3 > > Bfield_avg_fp;

    amrex::Vector<std::array< std::unique_ptr<amrex::MultiFab>, 3 > > m_edge_lengths;
    amrex::Vector<std::array< std::unique_ptr<amrex::MultiFab>, 3 > > m_face_areas;

    amrex::Vector<std::array< std::unique_ptr<amrex::iMultiFab>, 3 > > m_flag_info_face;
    amrex::Vector<std::array< std::unique_ptr<amrex::iMultiFab>, 3 > > m_flag_ext_face;
    amrex::Vector<std::array< std::unique_ptr<amrex::MultiFab>, 3 > > m_area_mod;
    amrex::Vector<std::array< std::unique_ptr<amrex::LayoutData<FaceInfoBox> >, 3 > > m_borrowing;

    amrex::Vector<std::array< std::unique_ptr<amrex::MultiFab>, 3 > > ECTRhofield;
    amrex::Vector<std::array< std::unique_ptr<amrex::MultiFab>, 3 > > Venl;

    //EB level set
    amrex::Vector<std::unique_ptr<amrex::MultiFab> > m_distance_to_eb;

    // store fine patch
    amrex::Vector<std::array< std::unique_ptr<amrex::MultiFab>, 3 > > current_store;

    // Nodal MultiFab for nodal current deposition if warpx.do_current_centering = 1
    amrex::Vector<std::array<std::unique_ptr<amrex::MultiFab>,3>> current_fp_nodal;

    // Coarse patch
    amrex::Vector<            std::unique_ptr<amrex::MultiFab>      > F_cp;
    amrex::Vector<            std::unique_ptr<amrex::MultiFab>      > G_cp;
    amrex::Vector<            std::unique_ptr<amrex::MultiFab>      > rho_cp;
    amrex::Vector<std::array< std::unique_ptr<amrex::MultiFab>, 3 > > current_cp;
    amrex::Vector<std::array< std::unique_ptr<amrex::MultiFab>, 3 > > Efield_cp;
    amrex::Vector<std::array< std::unique_ptr<amrex::MultiFab>, 3 > > Bfield_cp;
    amrex::Vector<std::array< std::unique_ptr<amrex::MultiFab>, 3 > > Efield_avg_cp;
    amrex::Vector<std::array< std::unique_ptr<amrex::MultiFab>, 3 > > Bfield_avg_cp;

    // Copy of the coarse aux
    amrex::Vector<std::array<std::unique_ptr<amrex::MultiFab>, 3 > > Efield_cax;
    amrex::Vector<std::array<std::unique_ptr<amrex::MultiFab>, 3 > > Bfield_cax;
    amrex::Vector<std::unique_ptr<amrex::iMultiFab> > current_buffer_masks;
    amrex::Vector<std::unique_ptr<amrex::iMultiFab> > gather_buffer_masks;

    // If charge/current deposition buffers are used
    amrex::Vector<std::array< std::unique_ptr<amrex::MultiFab>, 3 > > current_buf;
    amrex::Vector<std::unique_ptr<amrex::MultiFab> > charge_buf;

    // PML
    int do_pml = 0;
    int do_silver_mueller = 0;
    int pml_ncell = 10;
    int pml_delta = 10;
    int pml_has_particles = 0;
    int do_pml_j_damping = 0;
    int do_pml_in_domain = 0;
    static int do_similar_dm_pml;
    bool do_pml_dive_cleaning; // default set in WarpX.cpp
    bool do_pml_divb_cleaning; // default set in WarpX.cpp
    amrex::Vector<amrex::IntVect> do_pml_Lo;
    amrex::Vector<amrex::IntVect> do_pml_Hi;
    amrex::Vector<std::unique_ptr<PML> > pml;
#if (defined WARPX_DIM_RZ) && (defined WARPX_USE_PSATD)
    amrex::Vector<std::unique_ptr<PML_RZ> > pml_rz;
#endif
    amrex::Real v_particle_pml;

    amrex::Real moving_window_x = std::numeric_limits<amrex::Real>::max();
    amrex::Real current_injection_position = 0;

    // Plasma injection parameters
    int warpx_do_continuous_injection = 0;
    int num_injected_species = -1;
    amrex::Vector<int> injected_plasma_species;

    amrex::Real const_dt = amrex::Real(0.5e-11);

    // Macroscopic properties
    std::unique_ptr<MacroscopicProperties> m_macroscopic_properties;

    // Load balancing
    utils::parser::IntervalsParser load_balance_intervals;
    amrex::Vector<std::unique_ptr<amrex::LayoutData<amrex::Real> > > costs;
    int load_balance_with_sfc = 0;
    amrex::Real load_balance_knapsack_factor = amrex::Real(1.24);
    amrex::Real load_balance_efficiency_ratio_threshold = amrex::Real(1.1);
    amrex::Vector<amrex::Real> load_balance_efficiency;
    amrex::Real costs_heuristic_cells_wt = amrex::Real(0);
    amrex::Real costs_heuristic_particles_wt = amrex::Real(0);

    // Determines timesteps for override sync
    utils::parser::IntervalsParser override_sync_intervals;

    // Other runtime parameters
    int verbose = 1;

    bool use_hybrid_QED = 0;

    int max_step   = std::numeric_limits<int>::max();
    amrex::Real stop_time = std::numeric_limits<amrex::Real>::max();

    int regrid_int = -1;

    amrex::Real cfl = amrex::Real(0.999);

    std::string restart_chkfile;

    amrex::VisMF::Header::Version plotfile_headerversion  = amrex::VisMF::Header::Version_v1;
    amrex::VisMF::Header::Version slice_plotfile_headerversion  = amrex::VisMF::Header::Version_v1;

    bool use_single_read = true;
    bool use_single_write = true;
    int mffile_nstreams = 4;
    int field_io_nfiles = 1024;
    int particle_io_nfiles = 1024;

    amrex::RealVect fine_tag_lo;
    amrex::RealVect fine_tag_hi;

    bool is_synchronized = true;

    // Synchronization of nodal points
    const bool sync_nodal_points = true;

    guardCellManager guard_cells;

    //Slice Parameters
    int slice_max_grid_size;
    int slice_plot_int = -1;
    amrex::RealBox slice_realbox;
    amrex::IntVect slice_cr_ratio;
    amrex::Vector<            std::unique_ptr<amrex::MultiFab>      > F_slice;
    amrex::Vector<            std::unique_ptr<amrex::MultiFab>      > G_slice;
    amrex::Vector<            std::unique_ptr<amrex::MultiFab>      > rho_slice;
    amrex::Vector<std::array< std::unique_ptr<amrex::MultiFab>, 3 > > current_slice;
    amrex::Vector<std::array< std::unique_ptr<amrex::MultiFab>, 3 > > Efield_slice;
    amrex::Vector<std::array< std::unique_ptr<amrex::MultiFab>, 3 > > Bfield_slice;

    bool fft_periodic_single_box = false;
    int nox_fft = 16;
    int noy_fft = 16;
    int noz_fft = 16;

    amrex::IntVect numprocs{0};

    std::unique_ptr<ParticleBoundaryBuffer> m_particle_boundary_buffer;

    //
    // Embedded Boundary
    //

    // Factory for field data
    amrex::Vector<std::unique_ptr<amrex::FabFactory<amrex::FArrayBox> > > m_field_factory;

    amrex::FabFactory<amrex::FArrayBox> const& fieldFactory (int lev) const noexcept {
        return *m_field_factory[lev];
    }
#ifdef AMREX_USE_EB
    amrex::EBFArrayBoxFactory const& fieldEBFactory (int lev) const noexcept {
        return static_cast<amrex::EBFArrayBoxFactory const&>(*m_field_factory[lev]);
    }
#endif

public:
    void InitEB ();
public:
#ifdef AMREX_USE_EB
    static void ComputeEdgeLengths (std::array< std::unique_ptr<amrex::MultiFab>, 3 >& edge_lengths,
                                    const amrex::EBFArrayBoxFactory& eb_fact);
    static void ComputeFaceAreas (std::array< std::unique_ptr<amrex::MultiFab>, 3 >& face_areas,
                                  const amrex::EBFArrayBoxFactory& eb_fact);

    static void ScaleEdges (std::array< std::unique_ptr<amrex::MultiFab>, 3 >& edge_lengths,
                            const std::array<amrex::Real,3>& cell_size);
    static void ScaleAreas (std::array< std::unique_ptr<amrex::MultiFab>, 3 >& face_areas,
                            const std::array<amrex::Real,3>& cell_size);
    void MarkCells();
#endif
    void ComputeDistanceToEB ();
    amrex::Array1D<int, 0, 2> CountExtFaces();
    void ComputeFaceExtensions();
    void InitBorrowing();
    void ShrinkBorrowing();
    void ComputeOneWayExtensions();
    void ComputeEightWaysExtensions();
    void ApplyBCKCorrection(const int idim);

    void PSATDSubtractCurrentPartialSumsAvg ();

private:
    void ScrapeParticles ();

    void PushPSATD ();

#ifdef WARPX_USE_PSATD

    void PSATDForwardTransformEB (
        const amrex::Vector<std::array<std::unique_ptr<amrex::MultiFab>,3>>& E_fp,
        const amrex::Vector<std::array<std::unique_ptr<amrex::MultiFab>,3>>& B_fp,
        const amrex::Vector<std::array<std::unique_ptr<amrex::MultiFab>,3>>& E_cp,
        const amrex::Vector<std::array<std::unique_ptr<amrex::MultiFab>,3>>& B_cp);

    void PSATDBackwardTransformEB (
        const amrex::Vector<std::array<std::unique_ptr<amrex::MultiFab>,3>>& E_fp,
        const amrex::Vector<std::array<std::unique_ptr<amrex::MultiFab>,3>>& B_fp,
        const amrex::Vector<std::array<std::unique_ptr<amrex::MultiFab>,3>>& E_cp,
        const amrex::Vector<std::array<std::unique_ptr<amrex::MultiFab>,3>>& B_cp);

    void PSATDBackwardTransformEBavg (
        const amrex::Vector<std::array<std::unique_ptr<amrex::MultiFab>,3>>& E_avg_fp,
        const amrex::Vector<std::array<std::unique_ptr<amrex::MultiFab>,3>>& B_avg_fp,
        const amrex::Vector<std::array<std::unique_ptr<amrex::MultiFab>,3>>& E_avg_cp,
        const amrex::Vector<std::array<std::unique_ptr<amrex::MultiFab>,3>>& B_avg_cp);

    void PSATDForwardTransformJ (
        const amrex::Vector<std::array<std::unique_ptr<amrex::MultiFab>,3>>& J_fp,
        const amrex::Vector<std::array<std::unique_ptr<amrex::MultiFab>,3>>& J_cp,
        const bool apply_kspace_filter=true);

    void PSATDBackwardTransformJ (
        const amrex::Vector<std::array<std::unique_ptr<amrex::MultiFab>,3>>& J_fp,
        const amrex::Vector<std::array<std::unique_ptr<amrex::MultiFab>,3>>& J_cp);

    void PSATDForwardTransformRho (
        const amrex::Vector<std::unique_ptr<amrex::MultiFab>>& charge_fp,
        const amrex::Vector<std::unique_ptr<amrex::MultiFab>>& charge_cp,
        const int icomp, const int dcomp, const bool apply_kspace_filter=true);

    void PSATDMoveRhoNewToRhoOld ();

    void PSATDMoveJNewToJOld ();

    void PSATDForwardTransformF ();

    void PSATDBackwardTransformF ();

    void PSATDForwardTransformG ();

    void PSATDBackwardTransformG ();

    void PSATDCurrentCorrection ();

    void PSATDVayDeposition ();

    void PSATDPushSpectralFields ();

    void PSATDScaleAverageFields (const amrex::Real scale_factor);

    void PSATDEraseAverageFields ();

#   ifdef WARPX_DIM_RZ
        amrex::Vector<std::unique_ptr<SpectralSolverRZ>> spectral_solver_fp;
        amrex::Vector<std::unique_ptr<SpectralSolverRZ>> spectral_solver_cp;
#   else
        amrex::Vector<std::unique_ptr<SpectralSolver>> spectral_solver_fp;
        amrex::Vector<std::unique_ptr<SpectralSolver>> spectral_solver_cp;
#   endif

public:

#   ifdef WARPX_DIM_RZ
        SpectralSolverRZ&
#   else
        SpectralSolver&
#   endif
            get_spectral_solver_fp (int lev) {return *spectral_solver_fp[lev];}
#endif

private:
    amrex::Vector<std::unique_ptr<FiniteDifferenceSolver>> m_fdtd_solver_fp;
    amrex::Vector<std::unique_ptr<FiniteDifferenceSolver>> m_fdtd_solver_cp;
};

#endif