mirror of
https://github.com/cosmo-sims/monofonIC.git
synced 2024-09-19 17:03:45 +02:00
first commit of the masked particle load for the upcoming Virgo consortium simulations
This commit is contained in:
Oliver Hahn
parent
762bef3aa2
commit
9ea23ea581
3 changed files with 263 additions and 20 deletions
|
|
@ -20,7 +20,8 @@ DoFixing = no # do mode fixing à la Angulo&Pontzen (https://arxiv.o
|
|||
DoInversion = no # invert phases (for paired simulations)
|
||||
|
||||
ParticleLoad = sc # particle load, can be 'sc' (1x), 'bcc' (2x) or 'fcc' (4x)
|
||||
# (increases number of particles by given factor!), or 'glass'
|
||||
# (increases number of particles by given factor!),
|
||||
# or 'glass' or 'masked'
|
||||
|
||||
## if `ParticleLoad = glass' then specify here where to load the glass distribution from
|
||||
# GlassFileName = glass128.hdf5
|
||||
|
|
|
|||
|
|
@ -29,13 +29,20 @@ namespace particle
|
|||
|
||||
enum lattice
|
||||
{
|
||||
lattice_glass = -1,
|
||||
lattice_masked = -2, // masked lattices are SC lattices with a specifiable mask leaving out particles
|
||||
lattice_glass = -1, // glass: needs a glass file
|
||||
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<bool>> lattice_masks =
|
||||
{
|
||||
// mask from Richings et al. https://arxiv.org/pdf/2005.14495.pdf
|
||||
{true,true,true,true,true,true,true,false},
|
||||
};
|
||||
|
||||
const std::vector<std::vector<vec3_t<real_t>>> lattice_shifts =
|
||||
{
|
||||
// first shift must always be zero! (otherwise set_positions and set_velocities break)
|
||||
|
|
@ -149,11 +156,40 @@ namespace particle
|
|||
|
||||
private:
|
||||
particle::container particles_;
|
||||
size_t global_num_particles_;
|
||||
|
||||
static constexpr int masksize_ = 2;
|
||||
std::array<int, masksize_*masksize_*masksize_> particle_type_mask_;
|
||||
|
||||
inline int get_mask_value( const vec3_t<size_t>& global_idx_3d ) const
|
||||
{
|
||||
int sig = ((global_idx_3d[0]%masksize_)*masksize_
|
||||
+global_idx_3d[1]%masksize_)*masksize_
|
||||
+global_idx_3d[2]%masksize_;
|
||||
return particle_type_mask_[sig];
|
||||
}
|
||||
|
||||
public:
|
||||
lattice_generator(lattice lattice_type, const bool b64reals, const bool b64ids, const bool bwithmasses, size_t IDoffset, const field_t &field, config_file &cf)
|
||||
/**
|
||||
* @brief Construct a new lattice generator object
|
||||
*
|
||||
* @param lattice_type Type of the lattice (currently: 0=SC, 1=BCC, 2=FCC, 3=double SC, -1=glass, -2=masked SC)
|
||||
* @param lattice_index Index of the 'atom type', i.e. whether CDM, baryons, ... (currently only supports 0 or 1)
|
||||
* @param b64reals Boolean whether 64bit floating point shall be used to store positions/velocities/masses
|
||||
* @param b64ids Boolean whether 64bit integers should be used for IDS
|
||||
* @param bwithmasses Boolean whether distinct masses for each particle shall be stored
|
||||
* @param IDoffset The global ID offset to be applied to this generation of particles
|
||||
* @param field Reference to the field from which particles shall be generated (used only to set dimensions)
|
||||
* @param cf Reference to the config_file object
|
||||
*/
|
||||
|
||||
lattice_generator(lattice lattice_type, int lattice_index, const bool b64reals, const bool b64ids, const bool bwithmasses, size_t IDoffset, const field_t &field, config_file &cf)
|
||||
: global_num_particles_(0)
|
||||
{
|
||||
if (lattice_type != lattice_glass)
|
||||
// initialise the particle mask with zeros (only used if lattice_type==lattice_masked)
|
||||
for( auto& m : particle_type_mask_) m = 0;
|
||||
|
||||
if (lattice_type >= 0) // These are the Bravais lattices
|
||||
{
|
||||
music::wlog << "Glass ICs will currently be incorrect due to disabled ghost zone updates! ";
|
||||
|
||||
|
|
@ -163,6 +199,9 @@ namespace particle
|
|||
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, bwithmasses);
|
||||
// set the global number of particles for this lattice_type and lattice_index
|
||||
global_num_particles_ = field.global_size() * overload;
|
||||
|
||||
// set particle IDs to the Lagrangian coordinate (1D encoded) with additionally the field shift encoded as well
|
||||
|
||||
IDoffset = IDoffset * overload * field.global_size();
|
||||
|
|
@ -188,7 +227,82 @@ namespace particle
|
|||
}
|
||||
}
|
||||
}
|
||||
else if( lattice_type == lattice_masked )
|
||||
{
|
||||
if( field.global_size()%8 != 0 ){
|
||||
music::elog << "For masked lattice type, linear field resolution must be a multiple of two." << std::endl;
|
||||
abort();
|
||||
}
|
||||
|
||||
if( lattice_index > 1 || lattice_index < 0 ){
|
||||
music::elog << "For masked lattice type, lattice index must be 0 or 1." << std::endl;
|
||||
abort();
|
||||
}
|
||||
|
||||
// set the particle mask
|
||||
if( cf.get_value_safe("setup","DoBaryons",false) )
|
||||
{
|
||||
// mask everywehere 0, except the last element
|
||||
for( auto& m : particle_type_mask_) m = 0;
|
||||
particle_type_mask_[7] = 1;
|
||||
}else{
|
||||
// mask everywehere 0
|
||||
for( auto& m : particle_type_mask_) m = 0;
|
||||
}
|
||||
|
||||
// count number of particles taking into account masking
|
||||
size_t ipcount = 0;
|
||||
for (size_t i = 0; i < field.rsize(0); ++i)
|
||||
{
|
||||
for (size_t j = 0; j < field.rsize(1); ++j)
|
||||
{
|
||||
for (size_t k = 0; k < field.rsize(2); ++k)
|
||||
{
|
||||
if( this->get_mask_value(field.get_cell_idx_3d(i,j,k)) != lattice_index ) continue;
|
||||
++ipcount;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// set global number of particles
|
||||
#if defined(USE_MPI)
|
||||
MPI_Allreduce( &ipcount, &global_num_particles_, 1, MPI_UNSIGNED_LONG_LONG, MPI_SUM, MPI_COMM_WORLD );
|
||||
#else
|
||||
global_num_particles_ = ipcount;
|
||||
#endif
|
||||
|
||||
// number of modes present in the field
|
||||
const size_t num_p_in_load = ipcount;
|
||||
|
||||
// allocate memory for all local particles
|
||||
particles_.allocate(num_p_in_load, b64reals, b64ids, bwithmasses);
|
||||
|
||||
// set particle IDs to the Lagrangian coordinate (1D encoded) with additionally the field shift encoded as well
|
||||
IDoffset = IDoffset * field.global_size();
|
||||
|
||||
for (size_t i = 0, ipcount = 0; i < field.rsize(0); ++i)
|
||||
{
|
||||
for (size_t j = 0; j < field.rsize(1); ++j)
|
||||
{
|
||||
for (size_t k = 0; k < field.rsize(2); ++k)
|
||||
{
|
||||
if( this->get_mask_value(field.get_cell_idx_3d(i,j,k)) != lattice_index ) continue;
|
||||
|
||||
if (b64ids)
|
||||
{
|
||||
particles_.set_id64(ipcount, IDoffset + field.get_cell_idx_1d(i, j, k));
|
||||
}
|
||||
else
|
||||
{
|
||||
particles_.set_id32(ipcount, IDoffset + field.get_cell_idx_1d(i, j, k));
|
||||
}
|
||||
++ipcount;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
else if( lattice_type == lattice_glass )
|
||||
{
|
||||
glass_ptr_ = std::make_unique<glass>( cf, field );
|
||||
particles_.allocate(glass_ptr_->size(), b64reals, b64ids, false);
|
||||
|
|
@ -206,14 +320,24 @@ namespace particle
|
|||
}
|
||||
}
|
||||
}
|
||||
|
||||
music::ilog << "Created Particles [" << lattice_index << "] : " << global_num_particles_ << std::endl;
|
||||
|
||||
}
|
||||
|
||||
// invalidates field, phase shifted to unspecified position after return
|
||||
void set_masses(const lattice lattice_type, bool is_second_lattice, const real_t munit, const bool b64reals, field_t &field, config_file &cf)
|
||||
void set_masses(const lattice lattice_type, int lattice_index, const real_t munit, const bool b64reals, field_t &field, config_file &cf)
|
||||
{
|
||||
// works only for Bravais types
|
||||
if (lattice_type >= 0)
|
||||
// works only for Bravais types and masked type
|
||||
assert( lattice_type>=0 || lattice_type==lattice_masked );
|
||||
|
||||
if (lattice_type >= 0) // Bravais lattices
|
||||
{
|
||||
if( lattice_index > 1 || lattice_index < 0 ){
|
||||
music::elog << "For Bravais lattice type, lattice index must be 0 or 1." << std::endl;
|
||||
abort();
|
||||
}
|
||||
|
||||
const size_t overload = 1ull << std::max<int>(0, lattice_type); // 1 for sc, 2 for bcc, 4 for fcc, 8 for rsc
|
||||
const size_t num_p_in_load = field.local_size();
|
||||
const real_t pmeanmass = munit / real_t(field.global_size()* overload);
|
||||
|
|
@ -225,7 +349,7 @@ namespace particle
|
|||
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)
|
||||
if (ishift == 0 && lattice_index > 0)
|
||||
{
|
||||
field.shift_field(second_lattice_shift[lattice_type]);
|
||||
}
|
||||
|
|
@ -261,7 +385,49 @@ namespace particle
|
|||
music::ilog << "Particle Mass : mean/munit = " << mean_pm/munit << " ; fractional RMS = " << std_pm / mean_pm * 100.0 << "%" << std::endl;
|
||||
if(std_pm / mean_pm > 0.1 ) music::wlog << "Particle mass perturbation larger than 10%, consider decreasing \n\t the starting redshift or disabling baryon decaying modes." << std::endl;
|
||||
if(bmass_negative) music::elog << "Negative particle mass produced! Decrease the starting \n\t redshift or disable baryon decaying modes!" << std::endl;
|
||||
} else if( lattice_type == lattice_masked ) {
|
||||
if( field.global_size()%8 != 0 ){
|
||||
music::elog << "For masked lattice type, linear field resolution must be a multiple of two." << std::endl;
|
||||
abort();
|
||||
}
|
||||
|
||||
if( lattice_index > 1 || lattice_index < 0 ){
|
||||
music::elog << "For masked lattice type, lattice index must be 0 or 1." << std::endl;
|
||||
abort();
|
||||
}
|
||||
|
||||
const real_t pmeanmass = munit / global_num_particles_;
|
||||
|
||||
bool bmass_negative = false;
|
||||
auto mean_pm = field.mean() * pmeanmass;
|
||||
auto std_pm = field.std() * pmeanmass;
|
||||
|
||||
// read out values from phase shifted field and set assoc. particle's value
|
||||
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)
|
||||
{
|
||||
if( this->get_mask_value(field.get_cell_idx_3d(i,j,k)) != lattice_index ) continue;
|
||||
|
||||
// get
|
||||
const auto pmass = pmeanmass * field.relem(i, j, k);
|
||||
|
||||
// check for negative mass
|
||||
bmass_negative |= pmass<0.0;
|
||||
|
||||
// set
|
||||
if (b64reals) particles_.set_mass64(ipcount++, pmass);
|
||||
else particles_.set_mass32(ipcount++, pmass);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// diagnostics
|
||||
music::ilog << "Particle Mass : mean/munit = " << mean_pm/munit << " ; fractional RMS = " << std_pm / mean_pm * 100.0 << "%" << std::endl;
|
||||
if(std_pm / mean_pm > 0.1 ) music::wlog << "Particle mass perturbation larger than 10%, consider decreasing \n\t the starting redshift or disabling baryon decaying modes." << std::endl;
|
||||
if(bmass_negative) music::elog << "Negative particle mass produced! Decrease the starting \n\t redshift or disable baryon decaying modes!" << std::endl;
|
||||
}else{
|
||||
// should not happen
|
||||
music::elog << "Cannot have individual particle masses for glasses!" << std::endl;
|
||||
|
|
@ -270,15 +436,21 @@ namespace particle
|
|||
}
|
||||
|
||||
// invalidates field, phase shifted to unspecified position after return
|
||||
void set_positions(const lattice lattice_type, bool is_second_lattice, int idim, real_t lunit, const bool b64reals, field_t &field, config_file &cf)
|
||||
void set_positions(const lattice lattice_type, int lattice_index, int idim, real_t lunit, const bool b64reals, field_t &field, config_file &cf)
|
||||
{
|
||||
if (lattice_type >= 0)
|
||||
|
||||
if (lattice_type >= 0) // Bravais lattice
|
||||
{
|
||||
if( lattice_index > 1 || lattice_index < 0 ){
|
||||
music::elog << "For Bravais lattice type, lattice index must be 0 or 1." << std::endl;
|
||||
abort();
|
||||
}
|
||||
|
||||
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)
|
||||
if (ishift == 0 && lattice_index==1)
|
||||
{
|
||||
field.shift_field(second_lattice_shift[lattice_type]);
|
||||
}
|
||||
|
|
@ -296,7 +468,7 @@ namespace particle
|
|||
{
|
||||
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>{real_t(0.), real_t(0.), real_t(0.)}));
|
||||
auto pos = field.template get_unit_r_shifted<real_t>(i, j, k, lattice_shifts[lattice_type][ishift] + (lattice_index==1 ? second_lattice_shift[lattice_type] : vec3_t<real_t>{real_t(0.), real_t(0.), real_t(0.)}));
|
||||
if (b64reals)
|
||||
{
|
||||
particles_.set_pos64(ipcount++, idim, pos[idim] * lunit + field.relem(i, j, k));
|
||||
|
|
@ -310,6 +482,38 @@ namespace particle
|
|||
}
|
||||
}
|
||||
}
|
||||
else if( lattice_type == lattice_masked )
|
||||
{
|
||||
if( field.global_size()%8 != 0 ){
|
||||
music::elog << "For masked lattice type, linear field resolution must be a multiple of two." << std::endl;
|
||||
abort();
|
||||
}
|
||||
|
||||
if( lattice_index > 1 || lattice_index < 0 ){
|
||||
music::elog << "For masked lattice type, lattice index must be 0 or 1." << std::endl;
|
||||
abort();
|
||||
}
|
||||
|
||||
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)
|
||||
{
|
||||
if( this->get_mask_value(field.get_cell_idx_3d(i,j,k)) != lattice_index ) continue;
|
||||
|
||||
// get position (in box units) of the current cell of 3d array 'field'
|
||||
auto pos = field.template get_unit_r<real_t>(i, j, k);
|
||||
// add the displacement to get the particle position
|
||||
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
|
||||
{
|
||||
glass_ptr_->update_ghosts( field );
|
||||
|
|
@ -330,15 +534,20 @@ namespace particle
|
|||
}
|
||||
}
|
||||
|
||||
void set_velocities(lattice lattice_type, bool is_second_lattice, int idim, const bool b64reals, field_t &field, config_file &cf)
|
||||
void set_velocities(lattice lattice_type, int lattice_index, int idim, const bool b64reals, field_t &field, config_file &cf)
|
||||
{
|
||||
if (lattice_type >= 0)
|
||||
if (lattice_type >= 0) // Bravais lattice
|
||||
{
|
||||
if( lattice_index > 1 || lattice_index < 0 ){
|
||||
music::elog << "For Bravais lattice type, lattice index must be 0 or 1." << std::endl;
|
||||
abort();
|
||||
}
|
||||
|
||||
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)
|
||||
if (ishift == 0 && lattice_index==1)
|
||||
{
|
||||
field.shift_field(second_lattice_shift[lattice_type]);
|
||||
}
|
||||
|
|
@ -368,6 +577,35 @@ namespace particle
|
|||
}
|
||||
}
|
||||
}
|
||||
else if( lattice_type == lattice_masked )
|
||||
{
|
||||
if( field.global_size()%8 != 0 ){
|
||||
music::elog << "For masked lattice type, linear field resolution must be a multiple of two." << std::endl;
|
||||
abort();
|
||||
}
|
||||
|
||||
if( lattice_index > 1 || lattice_index < 0 ){
|
||||
music::elog << "For masked lattice type, lattice index must be 0 or 1." << std::endl;
|
||||
abort();
|
||||
}
|
||||
|
||||
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)
|
||||
{
|
||||
if( this->get_mask_value(field.get_cell_idx_3d(i,j,k)) != lattice_index ) continue;
|
||||
|
||||
if (b64reals){
|
||||
particles_.set_vel64(ipcount++, idim, field.relem(i, j, k));
|
||||
}else{
|
||||
particles_.set_vel32(ipcount++, idim, field.relem(i, j, k));
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
else
|
||||
{
|
||||
glass_ptr_->update_ghosts( field );
|
||||
|
|
|
|||
|
|
@ -116,7 +116,8 @@ int run( config_file& the_config )
|
|||
: ((lattice_str=="fcc")? particle::lattice_fcc
|
||||
: ((lattice_str=="rsc")? particle::lattice_rsc
|
||||
: ((lattice_str=="glass")? particle::lattice_glass
|
||||
: particle::lattice_sc))));
|
||||
: ((lattice_str=="masked")? particle::lattice_masked
|
||||
: particle::lattice_sc)))));
|
||||
|
||||
//--------------------------------------------------------------------------------------------------------
|
||||
//! apply fixing of the complex mode amplitude following Angulo & Pontzen (2016) [https://arxiv.org/abs/1603.05253]
|
||||
|
|
@ -536,8 +537,11 @@ int run( config_file& the_config )
|
|||
size_t IDoffset = (this_species == cosmo_species::baryon)? ((the_output_plugin->has_64bit_ids())? 1 : 1): 0 ;
|
||||
|
||||
// allocate particle structure and generate particle IDs
|
||||
bool secondary_lattice = (this_species == cosmo_species::baryon &&
|
||||
the_output_plugin->write_species_as(this_species) == output_type::particles) ? true : false;
|
||||
|
||||
particle_lattice_generator_ptr =
|
||||
std::make_unique<particle::lattice_generator<Grid_FFT<real_t>>>( lattice_type, the_output_plugin->has_64bit_reals(), the_output_plugin->has_64bit_ids(),
|
||||
std::make_unique<particle::lattice_generator<Grid_FFT<real_t>>>( lattice_type, secondary_lattice, the_output_plugin->has_64bit_reals(), the_output_plugin->has_64bit_ids(),
|
||||
bDoBaryons, IDoffset, tmp, the_config );
|
||||
}
|
||||
|
||||
|
|
@ -545,7 +549,7 @@ int run( config_file& the_config )
|
|||
if( bDoBaryons && (the_output_plugin->write_species_as( this_species ) == output_type::particles
|
||||
|| the_output_plugin->write_species_as( this_species ) == output_type::field_lagrangian) )
|
||||
{
|
||||
bool shifted_lattice = (this_species == cosmo_species::baryon &&
|
||||
bool secondary_lattice = (this_species == cosmo_species::baryon &&
|
||||
the_output_plugin->write_species_as(this_species) == output_type::particles) ? true : false;
|
||||
|
||||
const real_t munit = the_output_plugin->mass_unit();
|
||||
|
|
@ -568,7 +572,7 @@ int run( config_file& the_config )
|
|||
});
|
||||
|
||||
if( the_output_plugin->write_species_as( this_species ) == output_type::particles ){
|
||||
particle_lattice_generator_ptr->set_masses( lattice_type, shifted_lattice, 1.0, the_output_plugin->has_64bit_reals(), rho, the_config );
|
||||
particle_lattice_generator_ptr->set_masses( lattice_type, secondary_lattice, 1.0, the_output_plugin->has_64bit_reals(), rho, the_config );
|
||||
}else if( the_output_plugin->write_species_as( this_species ) == output_type::field_lagrangian ){
|
||||
the_output_plugin->write_grid_data( rho, this_species, fluid_component::mass );
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in a new issue