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music-panphasia/main.cc

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First commit of original files.
2022-04-29 14:37:23 +02:00
/*
main.cc - This file is part of MUSIC -
a code to generate multi-scale initial conditions
for cosmological simulations
Copyright (C) 2010 Oliver Hahn
*/
#include <stdio.h>
#include <iostream>
#include <iomanip>
#include <math.h>
#include <gsl/gsl_rng.h>
#include <gsl/gsl_randist.h>
#include <gsl/gsl_integration.h>
#include "general.hh"
#include "defaults.hh"
#include "output.hh"
#include "config_file.hh"
#include "poisson.hh"
#include "mg_solver.hh"
#include "fd_schemes.hh"
#include "random.hh"
#include "densities.hh"
#include "convolution_kernel.hh"
#include "cosmology.hh"
#include "transfer_function.hh"
#define THE_CODE_NAME "music!"
#define THE_CODE_VERSION "1.6"
namespace music
{
struct framework
{
transfer_function *the_transfer_function;
//poisson_solver *the_poisson_solver;
config_file *the_config_file;
refinement_hierarchy *the_refinement_hierarchy;
};
}
//... declare static class members here
transfer_function *TransferFunction_real::ptf_ = NULL;
transfer_function *TransferFunction_k::ptf_ = NULL;
tf_type TransferFunction_k::type_;
tf_type TransferFunction_real::type_;
real_t TransferFunction_real::nspec_ = -1.0;
real_t TransferFunction_k::nspec_ = -1.0;
//... prototypes for routines used in main driver routine
void splash(void);
void modify_grid_for_TF( const refinement_hierarchy& rh_full, refinement_hierarchy& rh_TF, config_file& cf );
void print_hierarchy_stats( config_file& cf, const refinement_hierarchy& rh );
void store_grid_structure( config_file& cf, const refinement_hierarchy& rh );
double compute_finest_mean( grid_hierarchy& u );
double compute_finest_sigma( grid_hierarchy& u );
void splash(void)
{
std::cout
<< "\n __ __ __ __ ______ __ ______ \n"
<< " /\\ \"-./ \\ /\\ \\/\\ \\ /\\ ___\\ /\\ \\ /\\ ___\\ \n"
<< " \\ \\ \\-./\\ \\ \\ \\ \\_\\ \\ \\ \\___ \\ \\ \\ \\ \\ \\ \\____ \n"
<< " \\ \\_\\ \\ \\_\\ \\ \\_____\\ \\/\\_____\\ \\ \\_\\ \\ \\_____\\ \n"
<< " \\/_/ \\/_/ \\/_____/ \\/_____/ \\/_/ \\/_____/ \n\n"
<< " this is " << THE_CODE_NAME << " version " << THE_CODE_VERSION << "\n\n\n";
}
void modify_grid_for_TF( const refinement_hierarchy& rh_full, refinement_hierarchy& rh_TF, config_file& cf )
{
unsigned lbase, lbaseTF, lmax, overlap;
lbase = cf.getValue<unsigned>( "setup", "levelmin" );
lmax = cf.getValue<unsigned>( "setup", "levelmax" );
lbaseTF = cf.getValueSafe<unsigned>( "setup", "levelmin_TF", lbase );
overlap = cf.getValueSafe<unsigned>( "setup", "overlap", 4 );
rh_TF = rh_full;
unsigned pad = overlap;
for( unsigned i=lbase+1; i<=lmax; ++i )
{
int x0[3], lx[3], lxmax = 0;
for( int j=0; j<3; ++j )
{
lx[j] = rh_TF.size(i,j)+2*pad;
x0[j] = rh_TF.offset_abs(i,j)-pad;
if( lx[j] > lxmax )
lxmax = lx[j];
}
//... make sure that grids are divisible by 4 for convolution.
lxmax += lxmax%4;
for( int j=0; j<3; ++j )
{
double dl = 0.5*((double)(lxmax-lx[j]));
int add_left = (int)ceil(dl);
lx[j] = lxmax;
x0[j] -= add_left;
x0[j] += x0[j]%2;
}
rh_TF.adjust_level(i, lx[0], lx[1], lx[2], x0[0], x0[1], x0[2] );
}
if( lbaseTF > lbase )
{
std::cout << " - Will use levelmin = " << lbaseTF << " to compute density field...\n";
for( unsigned i=lbase; i<=lbaseTF; ++i )
{
unsigned nfull = (unsigned)pow(2,i);
rh_TF.adjust_level(i, nfull, nfull, nfull, 0, 0, 0);
}
}
}
void print_hierarchy_stats( config_file& cf, const refinement_hierarchy& rh )
{
double omegam = cf.getValue<double>("cosmology","Omega_m");
double omegab = cf.getValue<double>("cosmology","Omega_b");
bool bbaryons = cf.getValue<bool>("setup","baryons");
double boxlength = cf.getValue<double>("setup","boxlength");
unsigned levelmin = rh.levelmin();
double dx = boxlength/(double)(1<<levelmin), dx3=dx*dx*dx;
double rhom = 2.77519737e11; // h-1 M_o / (h-1 Mpc)**3
double cmass, bmass(0.0), mtotgrid;
if( bbaryons )
{
cmass = (omegam-omegab)*rhom*dx3;
bmass = omegab*rhom*dx3;
}else
cmass = omegam*rhom*dx3;
std::cout << "-------------------------------------------------------------\n";
if( rh.get_shift(0)!=0||rh.get_shift(1)!=0||rh.get_shift(2)!=0 )
std::cout << " - Domain will be shifted by (" << rh.get_shift(0) << ", " << rh.get_shift(1) << ", " << rh.get_shift(2) << ")\n" << std::endl;
std::cout << " - Grid structure:\n";
for( unsigned ilevel=rh.levelmin(); ilevel<=rh.levelmax(); ++ilevel )
{
double rfac = 1.0/(1<<(ilevel-rh.levelmin())), rfac3=rfac*rfac*rfac;
mtotgrid = omegam*rhom*dx3*rfac3*rh.size(ilevel, 0)*rh.size(ilevel, 1)*rh.size(ilevel, 2);
std::cout
<< " Level " << std::setw(3) << ilevel << " : offset = (" << std::setw(5) << rh.offset(ilevel,0) << ", " << std::setw(5) << rh.offset(ilevel,1) << ", " << std::setw(5) << rh.offset(ilevel,2) << ")\n"
<< " size = (" << std::setw(5) << rh.size(ilevel,0) << ", " << std::setw(5) << rh.size(ilevel,1) << ", " << std::setw(5) << rh.size(ilevel,2) << ")\n";
if( ilevel == rh.levelmax() )
{
std::cout << "-------------------------------------------------------------\n";
std::cout << " - Finest level :\n";
if( dx*rfac > 0.1 )
std::cout << " extent = " << dx*rfac*rh.size(ilevel,0) << " x " << dx*rfac*rh.size(ilevel,1) << " x " << dx*rfac * rh.size(ilevel,2) << " h-3 Mpc**3\n";
else if( dx*rfac > 1e-4 )
std::cout << " extent = " << dx*rfac*1000.0*rh.size(ilevel,0) << " x " << dx*rfac*1000.0*rh.size(ilevel,1) << " x " << dx*rfac*1000.0*rh.size(ilevel,2) << " h-3 kpc**3\n";
else
std::cout << " extent = " << dx*rfac*1.e6*rh.size(ilevel,0) << " x " << dx*rfac*1.e6*rh.size(ilevel,1) << " x " << dx*rfac*1.e6 * rh.size(ilevel,2) << " h-3 pc**3\n";
std::cout << " mtotgrid = " << mtotgrid << " h-1 M_o\n";
std::cout << " particle mass = " << cmass*rfac3 << " h-1 M_o\n";
if( bbaryons )
std::cout << " baryon mass/cell = " << bmass*rfac3 << " h-1 M_o\n";
if( dx*rfac > 0.1 )
std::cout << " dx = " << dx*rfac << " h-1 Mpc\n";
else if( dx*rfac > 1e-4 )
std::cout << " dx = " << dx*rfac*1000.0 << " h-1 kpc\n";
else
std::cout << " dx = " << dx*rfac*1.e6 << " h-1 pc\n";
}
}
std::cout << "-------------------------------------------------------------\n";
}
void store_grid_structure( config_file& cf, const refinement_hierarchy& rh )
{
char str1[128], str2[128];
for( unsigned i=rh.levelmin(); i<=rh.levelmax(); ++i )
{
for( int j=0; j<3; ++j )
{
sprintf(str1,"offset(%d,%d)",i,j);
sprintf(str2,"%d",rh.offset(i,j));
cf.insertValue("setup",str1,str2);
sprintf(str1,"size(%d,%d)",i,j);
sprintf(str2,"%ld",rh.size(i,j));
cf.insertValue("setup",str1,str2);
}
}
}
double compute_finest_mean( grid_hierarchy& u )
{
double sum = 0.0;
size_t count = 0;
for( int ix = 0; ix < (int)(*u.get_grid(u.levelmax())).size(0); ++ix )
for( int iy = 0; iy < (int)(*u.get_grid(u.levelmax())).size(1); ++iy )
for( int iz = 0; iz < (int)(*u.get_grid(u.levelmax())).size(2); ++iz )
if( ! u.is_refined(u.levelmax(),ix,iy,iz) )
{
sum += (*u.get_grid(u.levelmax()))(ix,iy,iz);
++count;
}
sum /= count;
return sum;
}
double compute_finest_sigma( grid_hierarchy& u )
{
double sum = 0.0, sum2 = 0.0;
for( int ix = 0; ix < (int)(*u.get_grid(u.levelmax())).size(0); ++ix )
for( int iy = 0; iy < (int)(*u.get_grid(u.levelmax())).size(1); ++iy )
for( int iz = 0; iz < (int)(*u.get_grid(u.levelmax())).size(2); ++iz )
{
sum += (*u.get_grid(u.levelmax()))(ix,iy,iz);
sum2 += (*u.get_grid(u.levelmax()))(ix,iy,iz)* (*u.get_grid(u.levelmax()))(ix,iy,iz);
}
size_t N = (size_t)(*u.get_grid(u.levelmax())).size(0)
* (size_t)(*u.get_grid(u.levelmax())).size(1)
* (size_t)(*u.get_grid(u.levelmax())).size(2);
sum /= N;
sum2 /= N;
return sqrt(sum2-sum*sum);
}
double compute_finest_max( grid_hierarchy& u )
{
double valmax = 0.0;
for( int ix = 0; ix < (int)(*u.get_grid(u.levelmax())).size(0); ++ix )
for( int iy = 0; iy < (int)(*u.get_grid(u.levelmax())).size(1); ++iy )
for( int iz = 0; iz < (int)(*u.get_grid(u.levelmax())).size(2); ++iz )
{
if( fabs((*u.get_grid(u.levelmax()))(ix,iy,iz)) > fabs(valmax) )
valmax = (*u.get_grid(u.levelmax()))(ix,iy,iz);
}
return valmax;
}
/*****************************************************************************************************/
/*****************************************************************************************************/
/*****************************************************************************************************/
region_generator_plugin *the_region_generator;
//RNG_plugin *the_random_number_generator;
int main (int argc, const char * argv[])
{
const unsigned nbnd = 4;
unsigned lbase, lmax, lbaseTF;
//------------------------------------------------------------------------------
//... parse command line options
//------------------------------------------------------------------------------
splash();
if( argc != 2 ){
std::cout << " This version is compiled with the following plug-ins:\n";
print_region_generator_plugins();
print_transfer_function_plugins();
print_RNG_plugins();
print_output_plugins();
std::cerr << "\n In order to run, you need to specify a parameter file!\n\n";
exit(0);
}
//------------------------------------------------------------------------------
//... open log file
//------------------------------------------------------------------------------
char logfname[128];
sprintf(logfname,"%s_log.txt",argv[1]);
MUSIC::log::setOutput(logfname);
time_t ltime=time(NULL);
LOGINFO("Opening log file \'%s\'.",logfname);
LOGUSER("Running %s, version %s",THE_CODE_NAME,THE_CODE_VERSION);
LOGUSER("Log is for run started %s",asctime( localtime(&ltime) ));
#ifdef FFTW3
LOGUSER("Code was compiled using FFTW version 3.x");
#else
LOGUSER("Code was compiled using FFTW version 2.x");
#endif
#ifdef SINGLETHREAD_FFTW
LOGUSER("Code was compiled for single-threaded FFTW");
#else
LOGUSER("Code was compiled for multi-threaded FFTW");
#endif
#ifdef _OPENMP
LOGUSER("Running with a maximum of %d OpenMP threads", omp_get_max_threads() );
#else
LOGUSER("MUSIC is running internally in single-thread mode");
#endif
#ifdef SINGLE_PRECISION
LOGUSER("Code was compiled for single precision.");
#else
LOGUSER("Code was compiled for double precision.");
#endif
//------------------------------------------------------------------------------
//... read and interpret config file
//------------------------------------------------------------------------------
config_file cf(argv[1]);
std::string tfname,randfname,temp;
bool force_shift(false);
double boxlength;
//------------------------------------------------------------------------------
//... initialize some parameters about grid set-up
//------------------------------------------------------------------------------
boxlength = cf.getValue<double>( "setup", "boxlength" );
lbase = cf.getValue<unsigned>( "setup", "levelmin" );
lmax = cf.getValue<unsigned>( "setup", "levelmax" );
lbaseTF = cf.getValueSafe<unsigned>( "setup", "levelmin_TF", lbase );
if( lbase == lmax && !force_shift )
cf.insertValue("setup","no_shift","yes");
if( lbaseTF < lbase )
{
std::cout << " - WARNING: levelminTF < levelmin. This is not good!\n"
<< " I will set levelminTF = levelmin.\n";
LOGUSER("levelminTF < levelmin. set levelminTF = levelmin.");
lbaseTF = lbase;
cf.insertValue("setup","levelmin_TF",cf.getValue<std::string>("setup","levelmin"));
}
// .. determine if spectral sampling should be used
if( !cf.containsKey( "setup", "kspace_TF" ))
cf.insertValue( "setup", "kspace_TF", "yes");
bool bspectral_sampling = cf.getValue<bool>( "setup", "kspace_TF" );
if( bspectral_sampling )
LOGINFO("Using k-space sampled transfer functions...");
else
LOGINFO("Using real space sampled transfer functions...");
//------------------------------------------------------------------------------
//... initialize multithread FFTW
//------------------------------------------------------------------------------
#if not defined(SINGLETHREAD_FFTW)
int nthreads = 1;
#ifdef _OPENMP
nthreads = omp_get_max_threads();
#endif
#ifdef FFTW3
#ifdef SINGLE_PRECISION
fftwf_init_threads();
fftwf_plan_with_nthreads(nthreads);
#else
fftw_init_threads();
fftw_plan_with_nthreads(nthreads);
#endif
#else
fftw_threads_init();
#endif
#endif
//------------------------------------------------------------------------------
//... initialize cosmology
//------------------------------------------------------------------------------
bool
do_baryons = cf.getValue<bool>("setup","baryons"),
do_2LPT = cf.getValueSafe<bool>("setup","use_2LPT",false),
do_LLA = cf.getValueSafe<bool>("setup","use_LLA",false);
transfer_function_plugin *the_transfer_function_plugin
= select_transfer_function_plugin( cf );
cosmology cosmo( cf );
std::cout << " - starting at a=" << cosmo.astart << std::endl;
CosmoCalc ccalc(cosmo,the_transfer_function_plugin);
cosmo.pnorm = ccalc.ComputePNorm( 2.0*M_PI/boxlength );
cosmo.dplus = ccalc.CalcGrowthFactor( cosmo.astart )/ccalc.CalcGrowthFactor( 1.0 );
cosmo.vfact = ccalc.CalcVFact( cosmo.astart );
if( !the_transfer_function_plugin->tf_has_total0() )
cosmo.pnorm *= cosmo.dplus*cosmo.dplus;
//... directly use the normalisation via a parameter rather than the calculated one
cosmo.pnorm = cf.getValueSafe<double>("setup","force_pnorm",cosmo.pnorm);
double vfac2lpt = 1.0;
if( the_transfer_function_plugin->tf_velocity_units() && do_baryons )
{
vfac2lpt = cosmo.vfact; // if the velocities are in velocity units, we need to divide by vfact for the 2lPT term
cosmo.vfact = 1.0;
}
//
{
char tmpstr[128];
sprintf(tmpstr,"%.12g",cosmo.pnorm);
cf.insertValue("cosmology","pnorm",tmpstr);
sprintf(tmpstr,"%.12g",cosmo.dplus);
cf.insertValue("cosmology","dplus",tmpstr);
sprintf(tmpstr,"%.12g",cosmo.vfact);
cf.insertValue("cosmology","vfact",tmpstr);
}
the_region_generator = select_region_generator_plugin( cf );
//------------------------------------------------------------------------------
//... determine run parameters
//------------------------------------------------------------------------------
if( !the_transfer_function_plugin->tf_is_distinct() && do_baryons )
std::cout << " - WARNING: The selected transfer function does not support\n"
<< " distinct amplitudes for baryon and DM fields!\n"
<< " Perturbation amplitudes will be identical!" << std::endl;
//------------------------------------------------------------------------------
//... start up the random number generator plugin
//... see if we need to set some grid building constraints
noise_generator rand( cf, the_transfer_function_plugin );
//------------------------------------------------------------------------------
//... determine the refinement hierarchy
//------------------------------------------------------------------------------
refinement_hierarchy rh_Poisson( cf );
store_grid_structure(cf, rh_Poisson);
//rh_Poisson.output();
print_hierarchy_stats( cf, rh_Poisson );
refinement_hierarchy rh_TF( rh_Poisson );
modify_grid_for_TF( rh_Poisson, rh_TF, cf );
//rh_TF.output();
LOGUSER("Grid structure for Poisson solver:");
rh_Poisson.output_log();
LOGUSER("Grid structure for density convolution:");
rh_TF.output_log();
//------------------------------------------------------------------------------
//... initialize the output plug-in
//------------------------------------------------------------------------------
std::string outformat, outfname;
outformat = cf.getValue<std::string>( "output", "format" );
outfname = cf.getValue<std::string>( "output", "filename" );
output_plugin *the_output_plugin = select_output_plugin( cf );
//------------------------------------------------------------------------------
//... initialize the random numbers
//------------------------------------------------------------------------------
std::cout << "=============================================================\n";
std::cout << " GENERATING WHITE NOISE\n";
std::cout << "-------------------------------------------------------------\n";
LOGUSER("Computing white noise...");
rand.initialize_for_grid_structure( rh_TF );
//------------------------------------------------------------------------------
//... initialize the Poisson solver
//------------------------------------------------------------------------------
bool bdefd = cf.getValueSafe<bool> ( "poisson" , "fft_fine", true );
bool bglass = cf.getValueSafe<bool>("output","glass", false);
bool bsph = cf.getValueSafe<bool>("setup","do_SPH",false) && do_baryons;
bool bbshift= bsph && !bglass;
bool kspace = cf.getValueSafe<bool>( "poisson", "kspace", false );
bool kspace2LPT = kspace;
bool decic_DM = cf.getValueSafe<bool>( "output", "glass_cicdeconvolve", false );
bool decic_baryons = cf.getValueSafe<bool>( "output", "glass_cicdeconvolve", false ) & bsph;
//... if in unigrid mode, use k-space instead of hybrid
if(bdefd && (lbase==lmax))
{
kspace=true;
bdefd=false;
kspace2LPT=false;
}
std::string poisson_solver_name;
if( kspace )
poisson_solver_name = std::string("fft_poisson");
else
poisson_solver_name = std::string("mg_poisson");
unsigned grad_order = cf.getValueSafe<unsigned> ( "poisson" , "grad_order", 4 );
//... switch off if using kspace anyway
//bdefd &= !kspace;
poisson_plugin_creator *the_poisson_plugin_creator = get_poisson_plugin_map()[ poisson_solver_name ];
poisson_plugin *the_poisson_solver = the_poisson_plugin_creator->create( cf );
//---------------------------------------------------------------------------------
//... THIS IS THE MAIN DRIVER BRANCHING TREE RUNNING THE VARIOUS PARTS OF THE CODE
//---------------------------------------------------------------------------------
bool bfatal = false;
try{
if( ! do_2LPT )
{
LOGUSER("Entering 1LPT branch");
//------------------------------------------------------------------------------
//... cdm density and displacements
//------------------------------------------------------------------------------
std::cout << "=============================================================\n";
std::cout << " COMPUTING DARK MATTER DISPLACEMENTS\n";
std::cout << "-------------------------------------------------------------\n";
LOGUSER("Computing dark matter displacements...");
grid_hierarchy f( nbnd );//, u(nbnd);
tf_type my_tf_type = cdm;
if( !do_baryons || !the_transfer_function_plugin->tf_is_distinct() )
my_tf_type = total;
GenerateDensityHierarchy( cf, the_transfer_function_plugin, my_tf_type , rh_TF, rand, f, false, false );
coarsen_density(rh_Poisson, f, bspectral_sampling);
f.add_refinement_mask( rh_Poisson.get_coord_shift() );
normalize_density(f);
LOGUSER("Writing CDM data");
the_output_plugin->write_dm_mass(f);
the_output_plugin->write_dm_density(f);
grid_hierarchy u( f ); u.zero();
the_poisson_solver->solve(f, u);
if(!bdefd)
f.deallocate();
LOGUSER("Writing CDM potential");
the_output_plugin->write_dm_potential(u);
//------------------------------------------------------------------------------
//... DM displacements
//------------------------------------------------------------------------------
{
grid_hierarchy data_forIO(u);
for( int icoord = 0; icoord < 3; ++icoord )
{
if( bdefd )
{
data_forIO.zero();
*data_forIO.get_grid(data_forIO.levelmax()) = *f.get_grid(f.levelmax());
poisson_hybrid(*data_forIO.get_grid(data_forIO.levelmax()), icoord, grad_order,
data_forIO.levelmin()==data_forIO.levelmax(), decic_DM );
*data_forIO.get_grid(data_forIO.levelmax()) /= 1<<f.levelmax();
the_poisson_solver->gradient_add(icoord, u, data_forIO );
}
else
//... displacement
the_poisson_solver->gradient(icoord, u, data_forIO );
double dispmax = compute_finest_max( data_forIO );
LOGINFO("max. %c-displacement of HR particles is %f [mean dx]",'x'+icoord, dispmax*(double)(1ll<<data_forIO.levelmax()));
coarsen_density( rh_Poisson, data_forIO, false );
LOGUSER("Writing CDM displacements");
the_output_plugin->write_dm_position(icoord, data_forIO );
}
if( do_baryons )
u.deallocate();
data_forIO.deallocate();
}
//------------------------------------------------------------------------------
//... gas density
//------------------------------------------------------------------------------
if( do_baryons )
{
std::cout << "=============================================================\n";
std::cout << " COMPUTING BARYON DENSITY\n";
std::cout << "-------------------------------------------------------------\n";
adapted Swift output to include masses, smoothing lengths, and internal energies as gas particle properties
2022-07-04 17:02:46 +02:00
if( outformat == "swift"){
LOGUSER("Writing baryon data as particle attributes...");
the_output_plugin->write_gas_properties(f);
}
First commit of original files.
2022-04-29 14:37:23 +02:00
LOGUSER("Computing baryon density...");
GenerateDensityHierarchy( cf, the_transfer_function_plugin, baryon , rh_TF, rand, f, false, bbshift );
coarsen_density(rh_Poisson, f, bspectral_sampling);
f.add_refinement_mask( rh_Poisson.get_coord_shift() );
normalize_density(f);
if( !do_LLA )
{
LOGUSER("Writing baryon density");
the_output_plugin->write_gas_density(f);
}
if( bsph )
{
u = f; u.zero();
the_poisson_solver->solve(f, u);
if(!bdefd)
f.deallocate();
grid_hierarchy data_forIO(u);
for( int icoord = 0; icoord < 3; ++icoord )
{
if( bdefd )
{
data_forIO.zero();
*data_forIO.get_grid(data_forIO.levelmax()) = *f.get_grid(f.levelmax());
poisson_hybrid(*data_forIO.get_grid(data_forIO.levelmax()), icoord, grad_order,
data_forIO.levelmin()==data_forIO.levelmax(), decic_baryons);
*data_forIO.get_grid(data_forIO.levelmax()) /= 1<<f.levelmax();
the_poisson_solver->gradient_add(icoord, u, data_forIO );
}
else
//... displacement
the_poisson_solver->gradient(icoord, u, data_forIO );
coarsen_density( rh_Poisson, data_forIO, false );
LOGUSER("Writing baryon displacements");
the_output_plugin->write_gas_position(icoord, data_forIO );
}
u.deallocate();
data_forIO.deallocate();
if( bdefd )
f.deallocate();
}
else if( do_LLA )
{
u = f; u.zero();
the_poisson_solver->solve(f, u);
compute_LLA_density( u, f,grad_order );
u.deallocate();
normalize_density(f);
LOGUSER("Writing baryon density");
the_output_plugin->write_gas_density(f);
}
f.deallocate();
}
//------------------------------------------------------------------------------
//... velocities
//------------------------------------------------------------------------------
if( (!the_transfer_function_plugin->tf_has_velocities() || !do_baryons) && !bsph )
{
std::cout << "=============================================================\n";
std::cout << " COMPUTING VELOCITIES\n";
std::cout << "-------------------------------------------------------------\n";
LOGUSER("Computing velocitites...");
if( do_baryons || the_transfer_function_plugin->tf_has_velocities() )
{
LOGUSER("Generating velocity perturbations...");
GenerateDensityHierarchy( cf, the_transfer_function_plugin, vtotal , rh_TF, rand, f, false, false );
coarsen_density(rh_Poisson, f, bspectral_sampling);
f.add_refinement_mask( rh_Poisson.get_coord_shift() );
normalize_density(f);
u = f;
u.zero();
the_poisson_solver->solve(f, u);
if(!bdefd)
f.deallocate();
}
grid_hierarchy data_forIO(u);
for( int icoord = 0; icoord < 3; ++icoord )
{
//... displacement
if(bdefd)
{
data_forIO.zero();
*data_forIO.get_grid(data_forIO.levelmax()) = *f.get_grid(f.levelmax());
poisson_hybrid(*data_forIO.get_grid(data_forIO.levelmax()), icoord, grad_order,
data_forIO.levelmin()==data_forIO.levelmax(), decic_baryons );
*data_forIO.get_grid(data_forIO.levelmax()) /= 1<<f.levelmax();
the_poisson_solver->gradient_add(icoord, u, data_forIO );
}
else
the_poisson_solver->gradient(icoord, u, data_forIO );
//... multiply to get velocity
data_forIO *= cosmo.vfact;
//... velocity kick to keep refined region centered?
double sigv = compute_finest_sigma( data_forIO );
LOGINFO("sigma of %c-velocity of high-res particles is %f",'x'+icoord, sigv);
coarsen_density( rh_Poisson, data_forIO, false );
LOGUSER("Writing CDM velocities");
the_output_plugin->write_dm_velocity(icoord, data_forIO);
if( do_baryons )
{
LOGUSER("Writing baryon velocities");
the_output_plugin->write_gas_velocity(icoord, data_forIO);
}
}
u.deallocate();
data_forIO.deallocate();
}
else
{
LOGINFO("Computing separate velocities for CDM and baryons:");
std::cout << "=============================================================\n";
std::cout << " COMPUTING DARK MATTER VELOCITIES\n";
std::cout << "-------------------------------------------------------------\n";
LOGUSER("Computing dark matter velocitites...");
//... we do baryons and have velocity transfer functions, or we do SPH and not to shift
//... do DM first
GenerateDensityHierarchy( cf, the_transfer_function_plugin, vcdm , rh_TF, rand, f, false, false );
coarsen_density(rh_Poisson, f, bspectral_sampling);
f.add_refinement_mask( rh_Poisson.get_coord_shift() );
normalize_density(f);
u = f; u.zero();
the_poisson_solver->solve(f, u);
if(!bdefd)
f.deallocate();
grid_hierarchy data_forIO(u);
for( int icoord = 0; icoord < 3; ++icoord )
{
//... displacement
if(bdefd)
{
data_forIO.zero();
*data_forIO.get_grid(data_forIO.levelmax()) = *f.get_grid(f.levelmax());
poisson_hybrid(*data_forIO.get_grid(data_forIO.levelmax()), icoord, grad_order,
data_forIO.levelmin()==data_forIO.levelmax(), decic_DM );
*data_forIO.get_grid(data_forIO.levelmax()) /= 1<<f.levelmax();
the_poisson_solver->gradient_add(icoord, u, data_forIO );
}
else
the_poisson_solver->gradient(icoord, u, data_forIO );
//... multiply to get velocity
data_forIO *= cosmo.vfact;
double sigv = compute_finest_sigma( data_forIO );
LOGINFO("sigma of %c-velocity of high-res DM is %f",'x'+icoord, sigv);
coarsen_density( rh_Poisson, data_forIO, false );
LOGUSER("Writing CDM velocities");
the_output_plugin->write_dm_velocity(icoord, data_forIO);
}
u.deallocate();
data_forIO.deallocate();
f.deallocate();
std::cout << "=============================================================\n";
std::cout << " COMPUTING BARYON VELOCITIES\n";
std::cout << "-------------------------------------------------------------\n";
LOGUSER("Computing baryon velocitites...");
//... do baryons
GenerateDensityHierarchy( cf, the_transfer_function_plugin, vbaryon , rh_TF, rand, f, false, bbshift );
coarsen_density(rh_Poisson, f, bspectral_sampling);
f.add_refinement_mask( rh_Poisson.get_coord_shift() );
normalize_density(f);
u = f; u.zero();
the_poisson_solver->solve(f, u);
if(!bdefd)
f.deallocate();
data_forIO = u;
for( int icoord = 0; icoord < 3; ++icoord )
{
//... displacement
if(bdefd)
{
data_forIO.zero();
*data_forIO.get_grid(data_forIO.levelmax()) = *f.get_grid(f.levelmax());
poisson_hybrid(*data_forIO.get_grid(data_forIO.levelmax()), icoord, grad_order,
data_forIO.levelmin()==data_forIO.levelmax(), decic_baryons );
*data_forIO.get_grid(data_forIO.levelmax()) /= 1<<f.levelmax();
the_poisson_solver->gradient_add(icoord, u, data_forIO );
}
else
the_poisson_solver->gradient(icoord, u, data_forIO );
//... multiply to get velocity
data_forIO *= cosmo.vfact;
double sigv = compute_finest_sigma( data_forIO );
LOGINFO("sigma of %c-velocity of high-res baryons is %f",'x'+icoord, sigv);
coarsen_density( rh_Poisson, data_forIO, false );
LOGUSER("Writing baryon velocities");
the_output_plugin->write_gas_velocity(icoord, data_forIO);
}
u.deallocate();
f.deallocate();
data_forIO.deallocate();
}
/*********************************************************************************************/
/*********************************************************************************************/
/*** 2LPT ************************************************************************************/
/*********************************************************************************************/
}else {
//.. use 2LPT ...
LOGUSER("Entering 2LPT branch");
grid_hierarchy f( nbnd ), u1(nbnd), u2LPT(nbnd), f2LPT( nbnd );
tf_type my_tf_type = vcdm;
bool dm_only = !do_baryons;
if( !do_baryons || !the_transfer_function_plugin->tf_has_velocities() )
my_tf_type = total;
std::cout << "=============================================================\n";
if( my_tf_type == total )
{
std::cout << " COMPUTING VELOCITIES\n";
LOGUSER("Computing velocities...");
}else{
std::cout << " COMPUTING DARK MATTER VELOCITIES\n";
LOGUSER("Computing dark matter velocities...");
}
std::cout << "-------------------------------------------------------------\n";
GenerateDensityHierarchy( cf, the_transfer_function_plugin, my_tf_type , rh_TF, rand, f, false, false );
coarsen_density(rh_Poisson, f, bspectral_sampling);
f.add_refinement_mask( rh_Poisson.get_coord_shift() );
normalize_density(f);
if( dm_only )
{
the_output_plugin->write_dm_density(f);
the_output_plugin->write_dm_mass(f);
}
adapted Swift output to include masses, smoothing lengths, and internal energies as gas particle properties
2022-07-04 17:02:46 +02:00
// //For our current use with Richings, this is unnecessary here. Only leaving it b/c we might need it everywhere we also write_dm_mass.
// if( do_baryons && outformat == "swift"){
// LOGUSER("Writing baryon data as particle attributes...");
// the_output_plugin->write_gas_properties(f);
// }
First commit of original files.
2022-04-29 14:37:23 +02:00
u1 = f; u1.zero();
//... compute 1LPT term
the_poisson_solver->solve(f, u1);
//... compute 2LPT term
if(bdefd)
f2LPT=f;
else
f.deallocate();
LOGINFO("Computing 2LPT term....");
if( !kspace2LPT )
compute_2LPT_source(u1, f2LPT, grad_order );
else{
LOGUSER("computing term using FFT");
compute_2LPT_source_FFT(cf, u1, f2LPT);
}
LOGINFO("Solving 2LPT Poisson equation");
u2LPT = u1; u2LPT.zero();
the_poisson_solver->solve(f2LPT, u2LPT);
//... if doing the hybrid step, we need a combined source term
if( bdefd )
{
f2LPT*=6.0/7.0/vfac2lpt;
f+=f2LPT;
if( !dm_only )
f2LPT.deallocate();
}
//... add the 2LPT contribution
u2LPT *= 6.0/7.0/vfac2lpt;
u1 += u2LPT;
grid_hierarchy data_forIO(u1);
for( int icoord = 0; icoord < 3; ++icoord )
{
if(bdefd)
{
data_forIO.zero();
*data_forIO.get_grid(data_forIO.levelmax()) = *f.get_grid(f.levelmax());
poisson_hybrid(*data_forIO.get_grid(data_forIO.levelmax()), icoord, grad_order,
data_forIO.levelmin()==data_forIO.levelmax(), decic_DM );
*data_forIO.get_grid(data_forIO.levelmax()) /= (1<<f.levelmax());
the_poisson_solver->gradient_add(icoord, u1, data_forIO );
}
else
the_poisson_solver->gradient(icoord, u1, data_forIO );
data_forIO *= cosmo.vfact;
double sigv = compute_finest_sigma( data_forIO );
std::cerr << " - velocity component " << icoord << " : sigma = " << sigv << std::endl;
coarsen_density( rh_Poisson, data_forIO, false );
LOGUSER("Writing CDM velocities");
the_output_plugin->write_dm_velocity(icoord, data_forIO);
if( do_baryons && !the_transfer_function_plugin->tf_has_velocities() && !bsph)
{
LOGUSER("Writing baryon velocities");
the_output_plugin->write_gas_velocity(icoord, data_forIO);
}
}
data_forIO.deallocate();
if( !dm_only )
u1.deallocate();
if( do_baryons && (the_transfer_function_plugin->tf_has_velocities() || bsph) )
{
std::cout << "=============================================================\n";
std::cout << " COMPUTING BARYON VELOCITIES\n";
std::cout << "-------------------------------------------------------------\n";
LOGUSER("Computing baryon displacements...");
GenerateDensityHierarchy( cf, the_transfer_function_plugin, vbaryon , rh_TF, rand, f, false, bbshift );
coarsen_density(rh_Poisson, f, bspectral_sampling);
f.add_refinement_mask( rh_Poisson.get_coord_shift() );
normalize_density(f);
u1 = f; u1.zero();
if(bdefd)
f2LPT=f;
//... compute 1LPT term
the_poisson_solver->solve(f, u1);
LOGINFO("Writing baryon potential");
the_output_plugin->write_gas_potential(u1);
//... compute 2LPT term
u2LPT = f; u2LPT.zero();
if( !kspace2LPT )
compute_2LPT_source(u1, f2LPT, grad_order );
else
compute_2LPT_source_FFT(cf, u1, f2LPT);
the_poisson_solver->solve(f2LPT, u2LPT);
//... if doing the hybrid step, we need a combined source term
if( bdefd )
{
f2LPT*=6.0/7.0/vfac2lpt;
f+=f2LPT;
f2LPT.deallocate();
}
//... add the 2LPT contribution
u2LPT *= 6.0/7.0/vfac2lpt;
u1 += u2LPT;
u2LPT.deallocate();
//grid_hierarchy data_forIO(u1);
data_forIO = u1;
for( int icoord = 0; icoord < 3; ++icoord )
{
if(bdefd)
{
data_forIO.zero();
*data_forIO.get_grid(data_forIO.levelmax()) = *f.get_grid(f.levelmax());
poisson_hybrid(*data_forIO.get_grid(data_forIO.levelmax()), icoord, grad_order,
data_forIO.levelmin()==data_forIO.levelmax(), decic_baryons );
*data_forIO.get_grid(data_forIO.levelmax()) /= (1<<f.levelmax());
the_poisson_solver->gradient_add(icoord, u1, data_forIO );
}
else
the_poisson_solver->gradient(icoord, u1, data_forIO );
data_forIO *= cosmo.vfact;
double sigv = compute_finest_sigma( data_forIO );
std::cerr << " - velocity component " << icoord << " : sigma = " << sigv << std::endl;
coarsen_density( rh_Poisson, data_forIO, false );
LOGUSER("Writing baryon velocities");
the_output_plugin->write_gas_velocity(icoord, data_forIO);
}
data_forIO.deallocate();
u1.deallocate();
}
std::cout << "=============================================================\n";
std::cout << " COMPUTING DARK MATTER DISPLACEMENTS\n";
std::cout << "-------------------------------------------------------------\n";
LOGUSER("Computing dark matter displacements...");
//... if baryons are enabled, the displacements have to be recomputed
//... otherwise we can compute them directly from the velocities
if( !dm_only )
{
// my_tf_type is cdm if do_baryons==true, total otherwise
my_tf_type = cdm;
if( !do_baryons || !the_transfer_function_plugin->tf_is_distinct() )
my_tf_type = total;
GenerateDensityHierarchy( cf, the_transfer_function_plugin, my_tf_type , rh_TF, rand, f, false, false );
coarsen_density(rh_Poisson, f, bspectral_sampling);
f.add_refinement_mask( rh_Poisson.get_coord_shift() );
normalize_density(f);
LOGUSER("Writing CDM data");
the_output_plugin->write_dm_density(f);
the_output_plugin->write_dm_mass(f);
u1 = f; u1.zero();
adapted Swift output to include masses, smoothing lengths, and internal energies as gas particle properties
2022-07-04 17:02:46 +02:00
if( do_baryons && outformat == "swift"){
LOGUSER("Writing baryon data as particle attributes...");
the_output_plugin->write_gas_properties(f);
}
First commit of original files.
2022-04-29 14:37:23 +02:00
if(bdefd)
f2LPT=f;
//... compute 1LPT term
the_poisson_solver->solve(f, u1);
//... compute 2LPT term
u2LPT = f; u2LPT.zero();
if( !kspace2LPT )
compute_2LPT_source(u1, f2LPT, grad_order );
else
compute_2LPT_source_FFT(cf, u1, f2LPT);
the_poisson_solver->solve(f2LPT, u2LPT);
if( bdefd )
{
f2LPT*=3.0/7.0;
f+=f2LPT;
f2LPT.deallocate();
}
u2LPT *= 3.0/7.0;
u1 += u2LPT;
u2LPT.deallocate();
}else{
//... reuse prior data
/*f-=f2LPT;
the_output_plugin->write_dm_density(f);
the_output_plugin->write_dm_mass(f);
f+=f2LPT;*/
u2LPT *= 0.5;
u1 -= u2LPT;
u2LPT.deallocate();
if(bdefd)
{
f2LPT *= 0.5;
f-=f2LPT;
f2LPT.deallocate();
}
}
data_forIO = u1;
for( int icoord = 0; icoord < 3; ++icoord )
{
//... displacement
if(bdefd)
{
data_forIO.zero();
*data_forIO.get_grid(data_forIO.levelmax()) = *f.get_grid(f.levelmax());
poisson_hybrid(*data_forIO.get_grid(data_forIO.levelmax()), icoord, grad_order,
data_forIO.levelmin()==data_forIO.levelmax(), decic_DM );
*data_forIO.get_grid(data_forIO.levelmax()) /= 1<<f.levelmax();
the_poisson_solver->gradient_add(icoord, u1, data_forIO );
}
else
the_poisson_solver->gradient(icoord, u1, data_forIO );
double dispmax = compute_finest_max( data_forIO );
LOGINFO("max. %c-displacement of HR particles is %f [mean dx]",'x'+icoord, dispmax*(double)(1ll<<data_forIO.levelmax()));
coarsen_density( rh_Poisson, data_forIO, false );
LOGUSER("Writing CDM displacements");
the_output_plugin->write_dm_position(icoord, data_forIO );
}
data_forIO.deallocate();
u1.deallocate();
if( do_baryons && !bsph )
{
std::cout << "=============================================================\n";
std::cout << " COMPUTING BARYON DENSITY\n";
std::cout << "-------------------------------------------------------------\n";
LOGUSER("Computing baryon density...");
GenerateDensityHierarchy( cf, the_transfer_function_plugin, baryon , rh_TF, rand, f, true, false );
coarsen_density(rh_Poisson, f, bspectral_sampling);
f.add_refinement_mask( rh_Poisson.get_coord_shift() );
normalize_density(f);
if( !do_LLA )
the_output_plugin->write_gas_density(f);
else
{
u1 = f; u1.zero();
//... compute 1LPT term
the_poisson_solver->solve(f, u1);
//... compute 2LPT term
u2LPT = f; u2LPT.zero();
if( !kspace2LPT )
compute_2LPT_source(u1, f2LPT, grad_order );
else
compute_2LPT_source_FFT(cf, u1, f2LPT);
the_poisson_solver->solve(f2LPT, u2LPT);
u2LPT *= 3.0/7.0;
u1 += u2LPT;
u2LPT.deallocate();
compute_LLA_density( u1, f, grad_order );
normalize_density(f);
LOGUSER("Writing baryon density");
the_output_plugin->write_gas_density(f);
}
}
else if( do_baryons && bsph )
{
std::cout << "=============================================================\n";
std::cout << " COMPUTING BARYON DISPLACEMENTS\n";
std::cout << "-------------------------------------------------------------\n";
LOGUSER("Computing baryon displacements...");
GenerateDensityHierarchy( cf, the_transfer_function_plugin, baryon , rh_TF, rand, f, false, bbshift );
coarsen_density(rh_Poisson, f, bspectral_sampling);
f.add_refinement_mask( rh_Poisson.get_coord_shift() );
normalize_density(f);
LOGUSER("Writing baryon density");
the_output_plugin->write_gas_density(f);
u1 = f; u1.zero();
if(bdefd)
f2LPT=f;
//... compute 1LPT term
the_poisson_solver->solve(f, u1);
//... compute 2LPT term
u2LPT = f; u2LPT.zero();
if( !kspace2LPT )
compute_2LPT_source(u1, f2LPT, grad_order );
else
compute_2LPT_source_FFT(cf, u1, f2LPT);
the_poisson_solver->solve(f2LPT, u2LPT);
if( bdefd )
{
f2LPT*=3.0/7.0;
f+=f2LPT;
f2LPT.deallocate();
}
u2LPT *= 3.0/7.0;
u1 += u2LPT;
u2LPT.deallocate();
data_forIO = u1;
for( int icoord = 0; icoord < 3; ++icoord )
{
//... displacement
if(bdefd)
{
data_forIO.zero();
*data_forIO.get_grid(data_forIO.levelmax()) = *f.get_grid(f.levelmax());
poisson_hybrid(*data_forIO.get_grid(data_forIO.levelmax()), icoord, grad_order,
data_forIO.levelmin()==data_forIO.levelmax(), decic_baryons );
*data_forIO.get_grid(data_forIO.levelmax()) /= 1<<f.levelmax();
the_poisson_solver->gradient_add(icoord, u1, data_forIO );
}
else
the_poisson_solver->gradient(icoord, u1, data_forIO );
coarsen_density( rh_Poisson, data_forIO, false );
LOGUSER("Writing baryon displacements");
the_output_plugin->write_gas_position(icoord, data_forIO );
}
}
}
//------------------------------------------------------------------------------
//... finish output
//------------------------------------------------------------------------------
the_output_plugin->finalize();
delete the_output_plugin;
}catch(std::runtime_error& excp){
LOGERR("Fatal error occured. Code will exit:");
LOGERR("Exception: %s",excp.what());
std::cerr << " - " << excp.what() << std::endl;
std::cerr << " - A fatal error occured. We need to exit...\n";
bfatal = true;
}
std::cout << "=============================================================\n";
if( !bfatal )
{
std::cout << " - Wrote output file \'" << outfname << "\'\n using plugin \'" << outformat << "\'...\n";
LOGUSER("Wrote output file \'%s\'.",outfname.c_str());
}
//------------------------------------------------------------------------------
//... clean up
//------------------------------------------------------------------------------
delete the_transfer_function_plugin;
delete the_poisson_solver;
#if defined(FFTW3) and not defined(SINGLETHREAD_FFTW)
#ifdef SINGLE_PRECISION
fftwf_cleanup_threads();
#else
fftw_cleanup_threads();
#endif
#endif
//------------------------------------------------------------------------------
//... we are done !
//------------------------------------------------------------------------------
std::cout << " - Done!" << std::endl << std::endl;
ltime=time(NULL);
LOGUSER("Run finished succesfully on %s",asctime( localtime(&ltime) ));
cf.log_dump();
return 0;
}
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