path: root/Source/Initialization/WarpXInitData.cpp

/* Copyright 2019-2020 Andrew Myers, Ann Almgren, Aurore Blelly
 * Axel Huebl, Burlen Loring, Maxence Thevenet
 * Michael Rowan, Remi Lehe, Revathi Jambunathan
 * Weiqun Zhang
 *
 *
 * This file is part of WarpX.
 *
 * License: BSD-3-Clause-LBNL
 */
#include "WarpX.H"
#include "Filter/BilinearFilter.H"
#include "Filter/NCIGodfreyFilter.H"
#include "Parser/GpuParser.H"
#include "Utils/WarpXUtil.H"
#include "Utils/WarpXAlgorithmSelection.H"

#include <AMReX_ParallelDescriptor.H>
#include <AMReX_ParmParse.H>

#ifdef BL_USE_SENSEI_INSITU
#   include <AMReX_AmrMeshInSituBridge.H>
#endif

#include <memory>

using namespace amrex;

void
WarpX::PostProcessBaseGrids (BoxArray& ba0) const
{
    if (numprocs != 0) {
        const Box& dom = Geom(0).Domain();
        const IntVect& domlo = dom.smallEnd();
        const IntVect& domlen = dom.size();
        const IntVect sz = domlen / numprocs;
        const IntVect extra = domlen - sz*numprocs;
        BoxList bl;
#if (AMREX_SPACEDIM == 3)
        for (int k = 0; k < numprocs[2]; ++k) {
            // The first extra[2] blocks get one extra cell with a total of
            // sz[2]+1.  The rest get sz[2] cells.  The docomposition in y
            // and x directions are similar.
            int klo = (k < extra[2]) ? k*(sz[2]+1) : (k*sz[2]+extra[2]);
            int khi = (k < extra[2]) ? klo+(sz[2]+1)-1 : klo+sz[2]-1;
            klo += domlo[2];
            khi += domlo[2];
#endif
            for (int j = 0; j < numprocs[1]; ++j) {
                int jlo = (j < extra[1]) ? j*(sz[1]+1) : (j*sz[1]+extra[1]);
                int jhi = (j < extra[1]) ? jlo+(sz[1]+1)-1 : jlo+sz[1]-1;
                jlo += domlo[1];
                jhi += domlo[1];
                for (int i = 0; i < numprocs[0]; ++i) {
                    int ilo = (i < extra[0]) ? i*(sz[0]+1) : (i*sz[0]+extra[0]);
                    int ihi = (i < extra[0]) ? ilo+(sz[0]+1)-1 : ilo+sz[0]-1;
                    ilo += domlo[0];
                    ihi += domlo[0];
                    bl.push_back(Box(IntVect(AMREX_D_DECL(ilo,jlo,klo)),
                                     IntVect(AMREX_D_DECL(ihi,jhi,khi))));
        AMREX_D_TERM(},},})
        ba0 = BoxArray(std::move(bl));
    }
}

void
WarpX::InitData ()
{
    WARPX_PROFILE("WarpX::InitData()");

    if (restart_chkfile.empty())
    {
        ComputeDt();
        InitFromScratch();
    }
    else
    {
        InitFromCheckpoint();
        if (is_synchronized) {
            ComputeDt();
        }
        PostRestart();
    }

    ComputePMLFactors();

    if (WarpX::use_fdtd_nci_corr) {
        WarpX::InitNCICorrector();
    }

    if (WarpX::use_filter) {
        WarpX::InitFilter();
    }

    BuildBufferMasks();

    if (WarpX::em_solver_medium==1) {
        m_macroscopic_properties->InitData();
    }

    InitDiagnostics();

    if (ParallelDescriptor::IOProcessor()) {
        std::cout << "\nGrids Summary:\n";
        printGridSummary(std::cout, 0, finestLevel());
    }

    if (restart_chkfile.empty())
    {
        multi_diags->FilterComputePackFlush( -1, true );

        // Write reduced diagnostics before the first iteration.
        if (reduced_diags->m_plot_rd != 0)
        {
            reduced_diags->ComputeDiags(-1);
            reduced_diags->WriteToFile(-1);
        }
    }

    PerformanceHints();
}

void
WarpX::InitDiagnostics () {
    multi_diags->InitData();
    if (do_back_transformed_diagnostics) {
        const Real* current_lo = geom[0].ProbLo();
        const Real* current_hi = geom[0].ProbHi();
        Real dt_boost = dt[0];
        // Find the positions of the lab-frame box that corresponds to the boosted-frame box at t=0
        Real zmin_lab = static_cast<Real>(
            current_lo[moving_window_dir]/( (1.+beta_boost)*gamma_boost ));
        Real zmax_lab = static_cast<Real>(
            current_hi[moving_window_dir]/( (1.+beta_boost)*gamma_boost ));
        myBFD = std::make_unique<BackTransformedDiagnostic>(
                                               zmin_lab,
                                               zmax_lab,
                                               moving_window_v, dt_snapshots_lab,
                                               num_snapshots_lab,
                                               dt_slice_snapshots_lab,
                                               num_slice_snapshots_lab,
                                               gamma_boost, t_new[0], dt_boost,
                                               moving_window_dir, geom[0],
                                               slice_realbox,
                                               particle_slice_width_lab);
    }
}

void
WarpX::InitFromScratch ()
{
    const Real time = 0.0;

    AmrCore::InitFromScratch(time);  // This will call MakeNewLevelFromScratch

    mypc->AllocData();
    mypc->InitData();

    // Loop through species and calculate their space-charge field
    bool const reset_fields = false; // Do not erase previous user-specified values on the grid
    ComputeSpaceChargeField(reset_fields);

    InitPML();
}

void
WarpX::InitPML ()
{
    if (do_pml)
    {
        amrex::IntVect do_pml_Lo_corrected = do_pml_Lo;

#ifdef WARPX_DIM_RZ
        do_pml_Lo_corrected[0] = 0; // no PML at r=0, in cylindrical geometry
#endif
        pml[0] = std::make_unique<PML>(boxArray(0), DistributionMap(0), &Geom(0), nullptr,
                             pml_ncell, pml_delta, amrex::IntVect::TheZeroVector(),
                             dt[0], nox_fft, noy_fft, noz_fft, do_nodal,
                             do_dive_cleaning, do_moving_window,
                             pml_has_particles, do_pml_in_domain,
                             do_pml_Lo_corrected, do_pml_Hi);
        for (int lev = 1; lev <= finest_level; ++lev)
        {
            amrex::IntVect do_pml_Lo_MR = amrex::IntVect::TheUnitVector();
#ifdef WARPX_DIM_RZ
            //In cylindrical geometry, if the edge of the patch is at r=0, do not add PML
            if ((max_level > 0) && (fine_tag_lo[0]==0.)) {
                do_pml_Lo_MR[0] = 0;
            }
#endif
            pml[lev] = std::make_unique<PML>(boxArray(lev), DistributionMap(lev),
                                   &Geom(lev), &Geom(lev-1),
                                   pml_ncell, pml_delta, refRatio(lev-1),
                                   dt[lev], nox_fft, noy_fft, noz_fft, do_nodal,
                                   do_dive_cleaning, do_moving_window,
                                   pml_has_particles, do_pml_in_domain,
                                   do_pml_Lo_MR, amrex::IntVect::TheUnitVector());
        }
    }
}

void
WarpX::ComputePMLFactors ()
{
    if (do_pml)
    {
        for (int lev = 0; lev <= finest_level; ++lev)
        {
            pml[lev]->ComputePMLFactors(dt[lev]);
        }
    }
}

void
WarpX::InitNCICorrector ()
{
    if (WarpX::use_fdtd_nci_corr)
    {
        for (int lev = 0; lev <= max_level; ++lev)
        {
            const Geometry& gm = Geom(lev);
            const Real* dx = gm.CellSize();
            amrex::Real dz, cdtodz;
            if (AMREX_SPACEDIM == 3){
                dz = dx[2];
            }else{
                dz = dx[1];
            }
            cdtodz = PhysConst::c * dt[lev] / dz;

            // Initialize Godfrey filters
            // Same filter for fields Ex, Ey and Bz
            const bool nodal_gather = !galerkin_interpolation;
            nci_godfrey_filter_exeybz[lev] = std::make_unique<NCIGodfreyFilter>(
                godfrey_coeff_set::Ex_Ey_Bz, cdtodz, nodal_gather);
            // Same filter for fields Bx, By and Ez
            nci_godfrey_filter_bxbyez[lev] = std::make_unique<NCIGodfreyFilter>(
                godfrey_coeff_set::Bx_By_Ez, cdtodz, nodal_gather);
            // Compute Godfrey filters stencils
            nci_godfrey_filter_exeybz[lev]->ComputeStencils();
            nci_godfrey_filter_bxbyez[lev]->ComputeStencils();
        }
    }
}

void
WarpX::InitFilter (){
    if (WarpX::use_filter){
        WarpX::bilinear_filter.npass_each_dir = WarpX::filter_npass_each_dir.toArray<unsigned int>();
        WarpX::bilinear_filter.ComputeStencils();
    }
}

void
WarpX::PostRestart ()
{
    if (WarpX::maxwell_solver_id == MaxwellSolverAlgo::PSATD) {
        amrex::Abort("WarpX::PostRestart: TODO for PSATD");
    }
    mypc->PostRestart();
}


void
WarpX::InitLevelData (int lev, Real /*time*/)
{

    ParmParse pp("warpx");

    // default values of E_external_grid and B_external_grid
    // are used to set the E and B field when "constant" or
    // "parser" is not explicitly used in the input.
    pp.query("B_ext_grid_init_style", B_ext_grid_s);
    std::transform(B_ext_grid_s.begin(),
                   B_ext_grid_s.end(),
                   B_ext_grid_s.begin(),
                   ::tolower);

    pp.query("E_ext_grid_init_style", E_ext_grid_s);
    std::transform(E_ext_grid_s.begin(),
                   E_ext_grid_s.end(),
                   E_ext_grid_s.begin(),
                   ::tolower);

    // if the input string is "constant", the values for the
    // external grid must be provided in the input.
    if (B_ext_grid_s == "constant")
        pp.getarr("B_external_grid", B_external_grid);

    // if the input string is "constant", the values for the
    // external grid must be provided in the input.
    if (E_ext_grid_s == "constant")
        pp.getarr("E_external_grid", E_external_grid);

    // initialize the averaged fields only if the averaged algorithm
    // is activated ('psatd.do_time_averaging=1')
    ParmParse ppsatd("psatd");
    ppsatd.query("do_time_averaging", fft_do_time_averaging );

    for (int i = 0; i < 3; ++i) {
        current_fp[lev][i]->setVal(0.0);
        if (lev > 0)
           current_cp[lev][i]->setVal(0.0);

        // Initialize aux MultiFabs on level 0
        if (lev == 0) {
            Bfield_aux[lev][i]->setVal(0.0);
            Efield_aux[lev][i]->setVal(0.0);
            if (fft_do_time_averaging) {
                Bfield_avg_aux[lev][i]->setVal(0.0);
                Efield_avg_aux[lev][i]->setVal(0.0);
            }
        }

        if (B_ext_grid_s == "constant" || B_ext_grid_s == "default") {
           Bfield_fp[lev][i]->setVal(B_external_grid[i]);
           if (fft_do_time_averaging) {
                Bfield_avg_fp[lev][i]->setVal(B_external_grid[i]);
           }

           if (lev > 0) {
              Bfield_aux[lev][i]->setVal(B_external_grid[i]);
              Bfield_cp[lev][i]->setVal(B_external_grid[i]);
              if (fft_do_time_averaging) {
                  Bfield_avg_aux[lev][i]->setVal(B_external_grid[i]);
                  Bfield_avg_cp[lev][i]->setVal(B_external_grid[i]);
              }
           }
        }
        if (E_ext_grid_s == "constant" || E_ext_grid_s == "default") {
           Efield_fp[lev][i]->setVal(E_external_grid[i]);
           if (fft_do_time_averaging) {
               Efield_avg_fp[lev][i]->setVal(E_external_grid[i]);
            }

           if (lev > 0) {
              Efield_aux[lev][i]->setVal(E_external_grid[i]);
              Efield_cp[lev][i]->setVal(E_external_grid[i]);
              if (fft_do_time_averaging) {
                  Efield_avg_aux[lev][i]->setVal(E_external_grid[i]);
                  Efield_avg_cp[lev][i]->setVal(E_external_grid[i]);
              }
           }
        }
    }

    // if the input string for the B-field is "parse_b_ext_grid_function",
    // then the analytical expression or function must be
    // provided in the input file.
    if (B_ext_grid_s == "parse_b_ext_grid_function") {

#ifdef WARPX_DIM_RZ
       amrex::Abort("E and B parser for external fields does not work with RZ -- TO DO");
#endif
       Store_parserString(pp, "Bx_external_grid_function(x,y,z)",
                                                    str_Bx_ext_grid_function);
       Store_parserString(pp, "By_external_grid_function(x,y,z)",
                                                    str_By_ext_grid_function);
       Store_parserString(pp, "Bz_external_grid_function(x,y,z)",
                                                    str_Bz_ext_grid_function);
       Bxfield_parser = std::make_unique<ParserWrapper<3>>(
                                makeParser(str_Bx_ext_grid_function,{"x","y","z"}));
       Byfield_parser = std::make_unique<ParserWrapper<3>>(
                                makeParser(str_By_ext_grid_function,{"x","y","z"}));
       Bzfield_parser = std::make_unique<ParserWrapper<3>>(
                                makeParser(str_Bz_ext_grid_function,{"x","y","z"}));

       // Initialize Bfield_fp with external function
       InitializeExternalFieldsOnGridUsingParser(Bfield_fp[lev][0].get(),
                                                 Bfield_fp[lev][1].get(),
                                                 Bfield_fp[lev][2].get(),
                                                 getParser(Bxfield_parser),
                                                 getParser(Byfield_parser),
                                                 getParser(Bzfield_parser),
                                                 lev);
       if (lev > 0) {
          InitializeExternalFieldsOnGridUsingParser(Bfield_aux[lev][0].get(),
                                                    Bfield_aux[lev][1].get(),
                                                    Bfield_aux[lev][2].get(),
                                                    getParser(Bxfield_parser),
                                                    getParser(Byfield_parser),
                                                    getParser(Bzfield_parser),
                                                    lev);

          InitializeExternalFieldsOnGridUsingParser(Bfield_cp[lev][0].get(),
                                                    Bfield_cp[lev][1].get(),
                                                    Bfield_cp[lev][2].get(),
                                                    getParser(Bxfield_parser),
                                                    getParser(Byfield_parser),
                                                    getParser(Bzfield_parser),
                                                    lev);
       }
    }

    // if the input string for the E-field is "parse_e_ext_grid_function",
    // then the analytical expression or function must be
    // provided in the input file.
    if (E_ext_grid_s == "parse_e_ext_grid_function") {

#ifdef WARPX_DIM_RZ
       amrex::Abort("E and B parser for external fields does not work with RZ -- TO DO");
#endif
       Store_parserString(pp, "Ex_external_grid_function(x,y,z)",
                                                    str_Ex_ext_grid_function);
       Store_parserString(pp, "Ey_external_grid_function(x,y,z)",
                                                    str_Ey_ext_grid_function);
       Store_parserString(pp, "Ez_external_grid_function(x,y,z)",
                                                    str_Ez_ext_grid_function);

       Exfield_parser = std::make_unique<ParserWrapper<3>>(
                                makeParser(str_Ex_ext_grid_function,{"x","y","z"}));
       Eyfield_parser = std::make_unique<ParserWrapper<3>>(
                                makeParser(str_Ey_ext_grid_function,{"x","y","z"}));
       Ezfield_parser = std::make_unique<ParserWrapper<3>>(
                                makeParser(str_Ez_ext_grid_function,{"x","y","z"}));

       // Initialize Efield_fp with external function
       InitializeExternalFieldsOnGridUsingParser(Efield_fp[lev][0].get(),
                                                 Efield_fp[lev][1].get(),
                                                 Efield_fp[lev][2].get(),
                                                 getParser(Exfield_parser),
                                                 getParser(Eyfield_parser),
                                                 getParser(Ezfield_parser),
                                                 lev);
       if (lev > 0) {
          InitializeExternalFieldsOnGridUsingParser(Efield_aux[lev][0].get(),
                                                    Efield_aux[lev][1].get(),
                                                    Efield_aux[lev][2].get(),
                                                    getParser(Exfield_parser),
                                                    getParser(Eyfield_parser),
                                                    getParser(Ezfield_parser),
                                                    lev);

          InitializeExternalFieldsOnGridUsingParser(Efield_cp[lev][0].get(),
                                                    Efield_cp[lev][1].get(),
                                                    Efield_cp[lev][2].get(),
                                                    getParser(Exfield_parser),
                                                    getParser(Eyfield_parser),
                                                    getParser(Ezfield_parser),
                                                    lev);
       }
    }

    if (F_fp[lev]) {
        F_fp[lev]->setVal(0.0);
    }

    if (rho_fp[lev]) {
        rho_fp[lev]->setVal(0.0);
    }

    if (F_cp[lev]) {
        F_cp[lev]->setVal(0.0);
    }

    if (rho_cp[lev]) {
        rho_cp[lev]->setVal(0.0);
    }

    if (costs[lev]) {
        for (int i : costs[lev]->IndexArray()) {
            (*costs[lev])[i] = 0.0;
            WarpX::setLoadBalanceEfficiency(lev, -1);
        }
    }
}

void
WarpX::InitializeExternalFieldsOnGridUsingParser (
       MultiFab *mfx, MultiFab *mfy, MultiFab *mfz,
       HostDeviceParser<3> const& xfield_parser, HostDeviceParser<3> const& yfield_parser,
       HostDeviceParser<3> const& zfield_parser, const int lev)
{

    const auto dx_lev = geom[lev].CellSizeArray();
    const RealBox& real_box = geom[lev].ProbDomain();
    amrex::IntVect x_nodal_flag = mfx->ixType().toIntVect();
    amrex::IntVect y_nodal_flag = mfy->ixType().toIntVect();
    amrex::IntVect z_nodal_flag = mfz->ixType().toIntVect();
    for ( MFIter mfi(*mfx, TilingIfNotGPU()); mfi.isValid(); ++mfi)
    {
       const amrex::Box& tbx = mfi.tilebox( x_nodal_flag, mfx->nGrowVect() );
       const amrex::Box& tby = mfi.tilebox( y_nodal_flag, mfy->nGrowVect() );
       const amrex::Box& tbz = mfi.tilebox( z_nodal_flag, mfz->nGrowVect() );

       auto const& mfxfab = mfx->array(mfi);
       auto const& mfyfab = mfy->array(mfi);
       auto const& mfzfab = mfz->array(mfi);

       amrex::ParallelFor (tbx, tby, tbz,
            [=] AMREX_GPU_DEVICE (int i, int j, int k) {
                // Shift required in the x-, y-, or z- position
                // depending on the index type of the multifab
                amrex::Real fac_x = (1._rt - x_nodal_flag[0]) * dx_lev[0] * 0.5_rt;
                amrex::Real x = i*dx_lev[0] + real_box.lo(0) + fac_x;
#if (AMREX_SPACEDIM==2)
                amrex::Real y = 0._rt;
                amrex::Real fac_z = (1._rt - x_nodal_flag[1]) * dx_lev[1] * 0.5_rt;
                amrex::Real z = j*dx_lev[1] + real_box.lo(1) + fac_z;
#else
                amrex::Real fac_y = (1._rt - x_nodal_flag[1]) * dx_lev[1] * 0.5_rt;
                amrex::Real y = j*dx_lev[1] + real_box.lo(1) + fac_y;
                amrex::Real fac_z = (1._rt - x_nodal_flag[2]) * dx_lev[2] * 0.5_rt;
                amrex::Real z = k*dx_lev[2] + real_box.lo(2) + fac_z;
#endif
                // Initialize the x-component of the field.
                mfxfab(i,j,k) = xfield_parser(x,y,z);
            },
            [=] AMREX_GPU_DEVICE (int i, int j, int k) {
                amrex::Real fac_x = (1._rt - y_nodal_flag[0]) * dx_lev[0] * 0.5_rt;
                amrex::Real x = i*dx_lev[0] + real_box.lo(0) + fac_x;
#if (AMREX_SPACEDIM==2)
                amrex::Real y = 0._rt;
                amrex::Real fac_z = (1._rt - y_nodal_flag[1]) * dx_lev[1] * 0.5_rt;
                amrex::Real z = j*dx_lev[1] + real_box.lo(1) + fac_z;
#elif (AMREX_SPACEDIM==3)
                amrex::Real fac_y = (1._rt - y_nodal_flag[1]) * dx_lev[1] * 0.5_rt;
                amrex::Real y = j*dx_lev[1] + real_box.lo(1) + fac_y;
                amrex::Real fac_z = (1._rt - y_nodal_flag[2]) * dx_lev[2] * 0.5_rt;
                amrex::Real z = k*dx_lev[2] + real_box.lo(2) + fac_z;
#endif
                // Initialize the y-component of the field.
                mfyfab(i,j,k)  = yfield_parser(x,y,z);
            },
            [=] AMREX_GPU_DEVICE (int i, int j, int k) {
                amrex::Real fac_x = (1._rt - z_nodal_flag[0]) * dx_lev[0] * 0.5_rt;
                amrex::Real x = i*dx_lev[0] + real_box.lo(0) + fac_x;
#if (AMREX_SPACEDIM==2)
                amrex::Real y = 0._rt;
                amrex::Real fac_z = (1._rt - z_nodal_flag[1]) * dx_lev[1] * 0.5_rt;
                amrex::Real z = j*dx_lev[1] + real_box.lo(1) + fac_z;
#elif (AMREX_SPACEDIM==3)
                amrex::Real fac_y = (1._rt - z_nodal_flag[1]) * dx_lev[1] * 0.5_rt;
                amrex::Real y = j*dx_lev[1] + real_box.lo(1) + fac_y;
                amrex::Real fac_z = (1._rt - z_nodal_flag[2]) * dx_lev[2] * 0.5_rt;
                amrex::Real z = k*dx_lev[2] + real_box.lo(2) + fac_z;
#endif
                // Initialize the z-component of the field.
                mfzfab(i,j,k) = zfield_parser(x,y,z);
            }
        );
    }
}

void
WarpX::PerformanceHints ()
{
    // Check requested MPI ranks and available boxes
    amrex::Long total_nboxes = 0; // on all MPI ranks
    for (int ilev = 0; ilev <= finestLevel(); ++ilev) {
        total_nboxes += boxArray(ilev).size();
    }
    if (ParallelDescriptor::NProcs() > total_nboxes)
        amrex::Print() << "\n[Warning] [Performance] Too many resources / too little work!\n"
            << "  It looks like you requested more compute resources than "
            << "there are total number of boxes of cells available ("
            << total_nboxes << "). "
            << "You started with (" << ParallelDescriptor::NProcs()
            << ") MPI ranks, so (" << ParallelDescriptor::NProcs() - total_nboxes
            << ") rank(s) will have no work.\n"
#ifdef AMREX_USE_GPU
            << "  On GPUs, consider using 1-8 boxes per GPU that together fill "
            << "each GPU's memory sufficiently. If you do not rely on dynamic "
            << "load-balancing, then one large box per GPU is ideal.\n"
#endif
            << "  More information:\n"
            << "  https://warpx.readthedocs.io/en/latest/running_cpp/parallelization.html\n";

    // TODO: warn if some ranks have disproportionally more work than all others
    //       tricky: it can be ok to assign "vacuum" boxes to some ranks w/o slowing down
    //               all other ranks; we need to measure this with our load-balancing
    //               routines and issue a warning only of some ranks stall all other ranks
    // TODO: check MPI-rank to GPU ratio (should be 1:1)
    // TODO: check memory per MPI rank, especially if GPUs are underutilized
    // TODO: CPU tiling hints with OpenMP
}