monofonIC/include/particle_generator.hh

/*******************************************************************\
 particle_generator.hh - This file is part of MUSIC2 -
 a code to generate initial conditions for cosmological simulations 
 
 CHANGELOG (only majors, for details see repo):
    10/2019 - Oliver Hahn - first implementation
\*******************************************************************/
#pragma once

#include <math/vec3.hh>
#include <grid_interpolate.hh>

#if defined(USE_HDF5)
#include "HDF_IO.hh"
#endif

namespace particle {

enum lattice{
    lattice_glass = -1,
    lattice_sc  = 0, // SC : simple cubic
    lattice_bcc = 1, // BCC: body-centered cubic
    lattice_fcc = 2, // FCC: face-centered cubic
    lattice_rsc = 3, // RSC: refined simple cubic
};

const std::vector< std::vector<vec3_t<real_t>> > lattice_shifts = 
{   
    // first shift must always be zero! (otherwise set_positions and set_velocities break)
    /* SC : */ {{0.0,0.0,0.0}},
    /* BCC: */ {{0.0,0.0,0.0},{0.5,0.5,0.5}},
    /* FCC: */ {{0.0,0.0,0.0},{0.0,0.5,0.5},{0.5,0.0,0.5},{0.5,0.5,0.0}},
    /* RSC: */ {{0.0,0.0,0.0},{0.0,0.0,0.5},{0.0,0.5,0.0},{0.0,0.5,0.5},{0.5,0.0,0.0},{0.5,0.0,0.5},{0.5,0.5,0.0},{0.5,0.5,0.5}},
};

const std::vector<vec3_t<real_t>> second_lattice_shift =
{
        /* SC : */ {0.5, 0.5, 0.5}, // this corresponds to CsCl lattice
        /* BCC: */ {0.5, 0.5, 0.0}, // is there a diatomic lattice with BCC base?!?
        /* FCC: */ {0.5, 0.5, 0.5}, // this corresponds to NaCl lattice
        // /* FCC: */ {0.25, 0.25, 0.25}, // this corresponds to Zincblende/GaAs lattice
        /* RSC: */ {0.25, 0.25, 0.25},
};

template<typename field_t>
void initialize_lattice( container& particles, lattice lattice_type, const bool b64reals, const bool b64ids, const size_t IDoffset, const field_t& field, config_file& cf ){
    if( lattice_type != lattice_glass )
    {
        // number of modes present in the field
        const size_t num_p_in_load = field.local_size();
        // unless SC lattice is used, particle number is a multiple of the number of modes (=num_p_in_load):
        const size_t overload = 1ull<<std::max<int>(0,lattice_type); // 1 for sc, 2 for bcc, 4 for fcc, 8 for rsc
        // allocate memory for all local particles
        particles.allocate( overload * num_p_in_load, b64reals, b64ids );
        // set particle IDs to the Lagrangian coordinate (1D encoded) with additionally the field shift encoded as well
        for( size_t i=0,ipcount=0; i<field.size(0); ++i ){
            for( size_t j=0; j<field.size(1); ++j){
                for( size_t k=0; k<field.size(2); ++k,++ipcount){
                    for( size_t iload=0; iload<overload; ++iload ){
                        if( b64ids ){
                            particles.set_id64( ipcount+iload*num_p_in_load, IDoffset + overload*field.get_cell_idx_1d(i,j,k)+iload );
                        }else{
                            particles.set_id32( ipcount+iload*num_p_in_load, IDoffset + overload*field.get_cell_idx_1d(i,j,k)+iload );
                        }
                    }
                }
            }
        }
    }
    else
    {
#if defined(USE_HDF5)
        std::string glass_fname = cf.get_value<std::string>("setup","GlassFileName");
        
        std::vector<int> glass_dims;
        HDFGetDatasetExtent( glass_fname, "/PartType1/Coordinates", glass_dims );
        music::ilog << "Glass file contains " << glass_dims[0] << " particles." << std::endl;
        
        size_t ntiles = cf.get_value<size_t>("setup","GlassTiles");
        size_t num_p = glass_dims[0] * ntiles*ntiles*ntiles / MPI::get_size();
        size_t off_p = MPI::get_rank() * num_p;

        particles.allocate( num_p, b64reals, b64ids );

        for( size_t i=0; i<num_p; ++i ){
            if( b64ids ){
                particles.set_id64( i, IDoffset + i + off_p );
            }else{
                particles.set_id32( i, IDoffset + i + off_p );
            }
        }
#else
        throw std::runtime_error("Class lattice requires HDF5 support. Enable and recompile.");
#endif
    }
}

// invalidates field, phase shifted to unspecified position after return
template<typename field_t>
void set_positions( container& particles, const lattice lattice_type, bool is_second_lattice, int idim, real_t lunit, const bool b64reals, field_t& field, config_file& cf )
{
    // works only for Bravais types
    if( lattice_type >= 0 ){
        const size_t num_p_in_load = field.local_size();
        for( int ishift=0; ishift<(1<<lattice_type); ++ishift ){
            // if we are dealing with the secondary lattice, apply a global shift
            if( ishift==0 && is_second_lattice ){
                field.shift_field( second_lattice_shift[lattice_type] );
            }

            // can omit first shift since zero by convention, unless shifted already above, otherwise apply relative phase shift
            if( ishift>0 ){
                field.shift_field( lattice_shifts[lattice_type][ishift] - lattice_shifts[lattice_type][ishift-1] );
            }
            // read out values from phase shifted field and set assoc. particle's value
            const auto ipcount0 = ishift * num_p_in_load;
            for( size_t i=0,ipcount=ipcount0; i<field.size(0); ++i ){
                for( size_t j=0; j<field.size(1); ++j){
                    for( size_t k=0; k<field.size(2); ++k){
                        auto pos = field.template get_unit_r_shifted<real_t>(i,j,k,lattice_shifts[lattice_type][ishift] 
                            + (is_second_lattice? second_lattice_shift[lattice_type] : vec3_t<real_t>{0.,0.,0.}) );
                        if( b64reals ){
                            particles.set_pos64( ipcount++, idim, pos[idim]*lunit + field.relem(i,j,k) );
                        }else{
                            particles.set_pos32( ipcount++, idim, pos[idim]*lunit + field.relem(i,j,k) );
                        }
                    }
                }
            }
        }
    }else{
#if defined(USE_HDF5)
        std::string glass_fname = cf.get_value<std::string>("setup","GlassFileName");
        size_t ntiles = cf.get_value<size_t>("setup","GlassTiles");
        
        real_t lglassbox = 1.0;
        HDFReadGroupAttribute( glass_fname, "Header", "BoxSize", lglassbox );

        std::vector<real_t> glass_pos;
        HDFReadDataset( glass_fname, "/PartType1/Coordinates", glass_pos );
        size_t np_in_file = glass_pos.size()/3;
        size_t num_p = np_in_file * ntiles*ntiles*ntiles / MPI::get_size();
        size_t off_p = num_p * MPI::get_rank();
        
        std::vector< std::array<real_t,3> > glass_posr(num_p,{0.0,0.0,0.0});

        std::array<real_t,3> ng({field.n_[0],field.n_[1],field.n_[2]});

        for( size_t i=0; i<num_p; ++i ){
            size_t idxpart = off_p+i;
            size_t idx_in_glass = idxpart%np_in_file;
            size_t idxtile = idxpart / np_in_file;
            size_t tile_z = idxtile%(ntiles*ntiles);
            size_t tile_y = ((idxtile-tile_z)/ntiles)%ntiles;
            size_t tile_x = (((idxtile-tile_z)/ntiles)-tile_y)/ntiles;
            glass_posr[i][0] = std::fmod((glass_pos[3*idx_in_glass+0]/lglassbox + real_t(tile_x)) / ntiles * ng[0] + ng[0], ng[0]);
            glass_posr[i][1] = std::fmod((glass_pos[3*idx_in_glass+1]/lglassbox + real_t(tile_y)) / ntiles * ng[1] + ng[1], ng[1]);
            glass_posr[i][2] = std::fmod((glass_pos[3*idx_in_glass+2]/lglassbox + real_t(tile_z)) / ntiles * ng[2] + ng[2], ng[2]);
        }
        
        grid_interpolate<1,field_t> interp( field );

        interp.domain_decompose_pos( glass_posr );

        for( size_t i=0; i<num_p; ++i ){
            auto pos = glass_posr[i];
            real_t disp = interp.get_cic_at( pos );
            if( b64reals ){
                particles.set_pos64( i, idim, pos[idim]/ng[idim]*lunit + disp );
            }else{
                particles.set_pos32( i, idim, pos[idim]/ng[idim]*lunit + disp );
            }
        }
        
#else
        throw std::runtime_error("Class lattice requires HDF5 support. Enable and recompile.");
#endif
    }
}

template <typename field_t>
void set_velocities(container &particles, lattice lattice_type, bool is_second_lattice, int idim, const bool b64reals, field_t &field, config_file& cf)
{
    // works only for Bravais types
    if( lattice_type >= 0 ){
        const size_t num_p_in_load = field.local_size();
        for( int ishift=0; ishift<(1<<lattice_type); ++ishift ){
            // if we are dealing with the secondary lattice, apply a global shift
            if (ishift == 0 && is_second_lattice){
                field.shift_field(second_lattice_shift[lattice_type]);
            }
            // can omit first shift since zero by convention, unless shifted already above, otherwise apply relative phase shift
            if (ishift > 0){
                field.shift_field( lattice_shifts[lattice_type][ishift]-lattice_shifts[lattice_type][ishift-1] );
            }
            // read out values from phase shifted field and set assoc. particle's value
            const auto ipcount0 = ishift * num_p_in_load;
            for( size_t i=0,ipcount=ipcount0; i<field.size(0); ++i ){
                for( size_t j=0; j<field.size(1); ++j){
                    for( size_t k=0; k<field.size(2); ++k){
                        if( b64reals ){
                            particles.set_vel64( ipcount++, idim, field.relem(i,j,k) );
                        }else{
                            particles.set_vel32( ipcount++, idim, field.relem(i,j,k) );
                        }
                    }
                }
            }
        }
    }else{
#if defined(USE_HDF5)
        std::string glass_fname = cf.get_value<std::string>("setup","GlassFileName");
        size_t ntiles = cf.get_value<size_t>("setup","GlassTiles");
        
        real_t lglassbox = 1.0;
        HDFReadGroupAttribute( glass_fname, "Header", "BoxSize", lglassbox );

        std::vector<real_t> glass_pos;
        HDFReadDataset( glass_fname, "/PartType1/Coordinates", glass_pos );
        size_t np_in_file = glass_pos.size()/3;
        size_t num_p = np_in_file * ntiles*ntiles*ntiles / MPI::get_size();
        size_t off_p = num_p * MPI::get_rank();
        
        std::vector< std::array<real_t,3> > glass_posr(num_p,{0.0,0.0,0.0});

        std::array<real_t,3> ng({field.n_[0],field.n_[1],field.n_[2]});

        for( size_t i=0; i<num_p; ++i ){
            size_t idxpart = off_p+i;
            size_t idx_in_glass = idxpart%np_in_file;
            size_t idxtile = idxpart / np_in_file;
            size_t tile_z = idxtile%(ntiles*ntiles);
            size_t tile_y = ((idxtile-tile_z)/ntiles)%ntiles;
            size_t tile_x = (((idxtile-tile_z)/ntiles)-tile_y)/ntiles;
            glass_posr[i][0] = std::fmod((glass_pos[3*idx_in_glass+0]/lglassbox + real_t(tile_x)) / ntiles * ng[0] + ng[0], ng[0]);
            glass_posr[i][1] = std::fmod((glass_pos[3*idx_in_glass+1]/lglassbox + real_t(tile_y)) / ntiles * ng[1] + ng[1], ng[1]);
            glass_posr[i][2] = std::fmod((glass_pos[3*idx_in_glass+2]/lglassbox + real_t(tile_z)) / ntiles * ng[2] + ng[2], ng[2]);
        }
        
        grid_interpolate<1,field_t> interp( field );

        interp.domain_decompose_pos( glass_posr );

        for( size_t i=0; i<num_p; ++i ){
            auto pos = glass_posr[i];
            real_t vel = interp.get_cic_at( pos );
            if( b64reals ){
                particles.set_vel64( i, idim, vel );
            }else{
                particles.set_vel32( i, idim, vel );
            }
        }
        
#else
        throw std::runtime_error("Class lattice requires HDF5 support. Enable and recompile.");
#endif
    }
}


} // end namespace particles