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MUSIC/plugins/output_grafic2.cc

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/*
output_grafic2.cc - This file is part of MUSIC -
a code to generate multi-scale initial conditions
for cosmological simulations
Copyright (C) 2010 Oliver Hahn
*/
#include <sys/types.h>
#include <sys/stat.h>
#include <fstream>
#include "output.hh"
//! Implementation of class grafic2_output_plugin
/*!
This class implements a grafic-2 (cf. Bertschinger 2001) compatible
output format. With some RAMSES extras.
*/
class grafic2_output_plugin : public output_plugin
{
protected:
typedef struct{
int n1, n2, n3;
float dxini0;
float xoff10,xoff20,xoff30;
float astart0,omega_m0,omega_l0,h00;
}header;
bool bhavehydro_;
//float metal_floor_;
int passive_variable_index_;
float passive_variable_value_;
void write_file_header( std::ofstream& ofs, unsigned ilevel, const grid_hierarchy& gh )
{
header loc_head;
double
boxlength = cf_.getValue<double>("setup","boxlength"),
H0 = cf_.getValue<double>("cosmology","H0"),
zstart = cf_.getValue<double>("setup","zstart"),
astart = 1.0/(1.0+zstart),
omegam = cf_.getValue<double>("cosmology","Omega_m"),
omegaL = cf_.getValue<double>("cosmology","Omega_L");
loc_head.n1 = gh.get_grid(ilevel)->size(0);
loc_head.n2 = gh.get_grid(ilevel)->size(1);
loc_head.n3 = gh.get_grid(ilevel)->size(2);
loc_head.dxini0 = boxlength / (H0*0.01) / pow(2.0,ilevel);
loc_head.xoff10 = gh.offset_abs(ilevel,0) * loc_head.dxini0;
loc_head.xoff20 = gh.offset_abs(ilevel,1) * loc_head.dxini0;
loc_head.xoff30 = gh.offset_abs(ilevel,2) * loc_head.dxini0;
loc_head.astart0 = astart;
loc_head.omega_m0 = omegam;
loc_head.omega_l0 = omegaL;
loc_head.h00 = H0;
int blksz = sizeof(header);
ofs.write( reinterpret_cast<char*> (&blksz), sizeof(int) );
ofs.write( reinterpret_cast<char*> (&loc_head), blksz );
ofs.write( reinterpret_cast<char*> (&blksz), sizeof(int) );
}
void write_sliced_array( std::ofstream& ofs, unsigned ilevel, const grid_hierarchy& gh, float fac = 1.0f )
{
unsigned n1,n2,n3;
n1 = gh.get_grid(ilevel)->size(0);
n2 = gh.get_grid(ilevel)->size(1);
n3 = gh.get_grid(ilevel)->size(2);
std::vector<float> data(n1*n2,0.0f);
for( unsigned i=0; i<n3; ++i )
{
data.clear();
for( unsigned j=0; j<n2; ++j )
for( unsigned k=0; k<n1; ++k )
data[j*n1+k] = (*gh.get_grid(ilevel))(k,j,i) * fac;
unsigned blksize = n1*n2*sizeof(float);
ofs.write( reinterpret_cast<char*> (&blksize), sizeof(unsigned) );
ofs.write( reinterpret_cast<char*> (&data[0]), blksize );
ofs.write( reinterpret_cast<char*> (&blksize), sizeof(unsigned) );
}
}
size_t restrict_mask( size_t n1, size_t n2, size_t n3, size_t o1, size_t o2, size_t o3,
size_t n1c, size_t n2c, size_t n3c, const float* finemask, float* coarsemask )
{
//unsigned n1p = n1/2, n2p = n2/2, n3p = n3/2;
for( size_t i=0; i<n1c*n2c*n3c; ++i )
coarsemask[i] = 0.0f;
for( size_t i=0; i<n1; ++i )
{
size_t ii=i/2+o1;
for( size_t j=0; j<n2; ++j )
{
size_t jj=j/2+o2;
for( size_t k=0; k<n3; ++k )
{
size_t kk=k/2+o3;
if( finemask[ (i*n2+j)*n3+k ] )
coarsemask[(ii*n2c+jj)*n3c+kk] += 1.0f;
}
}
}
size_t count_ref = 0;
for( size_t i=0; i<n1c*n2c*n3c; ++i )
if( coarsemask[i] > 0.1f )
{
coarsemask[i] = 1.0f;
++count_ref;
}
return count_ref;
}
void write_refinement_mask( const grid_hierarchy& gh )
{
// generate mask for highest level
char ff[256];
size_t n1,n2,n3;
n1 = gh.get_grid(gh.levelmax())->size(0);
n2 = gh.get_grid(gh.levelmax())->size(1);
n3 = gh.get_grid(gh.levelmax())->size(2);
std::vector<float> data(n1*n2*n3,0.0f);
// do finest level
{
// get mask for levelmax
for( size_t i=0; i<n1; ++i )
for( size_t j=0; j<n2; ++j )
for( size_t k=0; k<n3; ++k )
if( !gh.is_refined(gh.levelmax(),i,j,k) )
data[(i*n2+j)*n3+k] = 1.0;
else
data[(i*n2+j)*n3+k] = 0.0;
// write mask
sprintf(ff,"%s/level_%03d/ic_refmap",fname_.c_str(), gh.levelmax() );
std::ofstream ofs(ff,std::ios::binary|std::ios::trunc);
write_file_header( ofs, gh.levelmax(), gh );
std::ofstream ofs_metals;
if( passive_variable_value_ > 0.0f )
{
sprintf(ff,"%s/level_%03d/ic_pvar_%05d",fname_.c_str(), gh.levelmax(), passive_variable_index_ );
ofs_metals.open(ff,std::ios::binary|std::ios::trunc);
write_file_header( ofs_metals, gh.levelmax(), gh );
}
std::vector<float> block(n1*n2,0.0f);
for( unsigned k=0; k<n3; ++k )
{
for( unsigned j=0; j<n2; ++j )
for( unsigned i=0; i<n1; ++i )
block[j*n1+i] = data[(i*n2+j)*n3+k];
unsigned blksize = n1*n2*sizeof(float);
ofs.write( reinterpret_cast<char*> (&blksize), sizeof(unsigned) );
ofs.write( reinterpret_cast<char*> (&block[0]), blksize );
ofs.write( reinterpret_cast<char*> (&blksize), sizeof(unsigned) );
if( passive_variable_value_ > 0.0f ){
for( unsigned j=0; j<n2; ++j )
for( unsigned i=0; i<n1; ++i )
block[j*n1+i] = data[(i*n2+j)*n3+k] * passive_variable_value_;
unsigned blksize = n1*n2*sizeof(float);
ofs_metals.write( reinterpret_cast<char*> (&blksize), sizeof(unsigned) );
ofs_metals.write( reinterpret_cast<char*> (&block[0]), blksize );
ofs_metals.write( reinterpret_cast<char*> (&blksize), sizeof(unsigned) );
}
}
}
// do all coarser levels
for( unsigned ilevel=levelmax_-1; ilevel>=levelmin_; --ilevel )
{
size_t n1c,n2c,n3c,o1,o2,o3;
n1c = gh.get_grid(ilevel)->size(0);
n2c = gh.get_grid(ilevel)->size(1);
n3c = gh.get_grid(ilevel)->size(2);
n1 = gh.get_grid(ilevel+1)->size(0);
n2 = gh.get_grid(ilevel+1)->size(1);
n3 = gh.get_grid(ilevel+1)->size(2);
o1 = gh.get_grid(ilevel+1)->offset(0);
o2 = gh.get_grid(ilevel+1)->offset(1);
o3 = gh.get_grid(ilevel+1)->offset(2);
std::vector<float> data_coarse( n1c*n2c*n3c, 0.0f );
/*if( ilevel <= levelmax_-2 )
{
for( size_t i=0; i<n1*n2*n3; ++i )
data[i] = 0.0;
for( unsigned i=2; i<n1-2; ++i )
for( unsigned j=2; j<n2-2; ++j )
for( unsigned k=2; k<n3-2; ++k )
data[(i*n2+j)*n3+k] = 1.0;
}*/
size_t nref;
nref = restrict_mask( n1, n2, n3, o1, o2, o3, n1c, n2c, n3c, &data[0], &data_coarse[0] );
LOGINFO("%f of cells on level %d are refined",(double)nref/(n1c*n2c*n3c),ilevel);
sprintf(ff,"%s/level_%03d/ic_refmap",fname_.c_str(), ilevel );
std::ofstream ofs(ff,std::ios::binary|std::ios::trunc);
write_file_header( ofs, ilevel, gh );
std::ofstream ofs_metals;
if( passive_variable_value_ > 0.0f )
{
sprintf(ff,"%s/level_%03d/ic_pvar_%05d",fname_.c_str(), ilevel, passive_variable_index_ );
ofs_metals.open(ff,std::ios::binary|std::ios::trunc);
write_file_header( ofs_metals, ilevel, gh );
}
std::vector<float> block(n1c*n2c,0.0f);
for( unsigned i=0; i<n3c; ++i )
{
for( unsigned j=0; j<n2c; ++j )
for( unsigned k=0; k<n1c; ++k )
block[j*n1c+k] = data_coarse[(k*n2c+j)*n3c+i];
unsigned blksize = n1c*n2c*sizeof(float);
ofs.write( reinterpret_cast<char*> (&blksize), sizeof(unsigned) );
ofs.write( reinterpret_cast<char*> (&block[0]), blksize );
ofs.write( reinterpret_cast<char*> (&blksize), sizeof(unsigned) );
if( passive_variable_value_ > 0.0f ){
for( unsigned j=0; j<n2c; ++j )
for( unsigned k=0; k<n1c; ++k )
block[j*n1c+k] = data_coarse[(k*n2c+j)*n3c+i] * passive_variable_value_;
unsigned blksize = n1c*n2c*sizeof(float);
ofs_metals.write( reinterpret_cast<char*> (&blksize), sizeof(unsigned) );
ofs_metals.write( reinterpret_cast<char*> (&block[0]), blksize );
ofs_metals.write( reinterpret_cast<char*> (&blksize), sizeof(unsigned) );
}
}
data.swap( data_coarse );
}
}
void write_ramses_namelist( const grid_hierarchy& gh )
{
//... also write the refinement options to a dummy namelist file
char ff[256];
sprintf(ff,"%s/ramses.nml",fname_.c_str() );
std::ofstream ofst(ff,std::ios::trunc);
// -- RUN_PARAMS -- //
ofst
<< "&RUN_PARAMS\n"
<< "cosmo=.true.\n"
<< "pic=.true.\n"
<< "poisson=.true.\n";
if( bhavehydro_ )
ofst << "hydro=.true.\n";
else
ofst << "hydro=.false.\n";
ofst
<< "nrestart=0\n"
<< "nremap=1\n"
<< "nsubcycle=";
for( unsigned ilevel=gh.levelmin(); ilevel<=gh.levelmax(); ++ilevel )
ofst << "1,";
ofst << "1,2\n";
ofst
<< "ncontrol=1\n"
<< "verbose=.false.\n/\n\n";
// -- INIT_PARAMS -- //
ofst
<< "&INIT_PARAMS\n"
<< "filetype=\'grafic\'\n";
for( unsigned i=gh.levelmin();i<=gh.levelmax(); ++i)
{
sprintf(ff,"initfile(%d)=\'%s/level_%03d\'\n",i-gh.levelmin()+1,fname_.c_str(), i );
ofst << std::string(ff);
}
ofst << "/\n\n";
unsigned naddref = 8; // initialize with settings for 10 additional levels of refinement
unsigned nexpand = (cf_.getValue<unsigned>("setup","padding")-1)/2;
// -- AMR_PARAMS -- //
ofst << "&AMR_PARAMS\n"
<< "levelmin=" << gh.levelmin() << "\n"
<< "levelmax=" << gh.levelmax()+naddref << "\n"
<< "nexpand=";
if( gh.levelmax() == gh.levelmin() )
ofst << "1";
else
{
for( unsigned ilevel=gh.levelmin(); ilevel<gh.levelmax()-1; ++ilevel )
ofst << nexpand << ",";
ofst << "1,1";
}
ofst << "\n"
<< "ngridtot=2000000\n"
<< "nparttot=3000000\n"
<< "/\n\n";
ofst << "&REFINE_PARAMS\n"
<< "m_refine=" << gh.levelmax()-gh.levelmin()+1+naddref << "*8.,\n";
if( bhavehydro_ )
ofst << "ivar_refine=" << 5+passive_variable_index_ << "\n"
<< "var_cut_refine=" << passive_variable_value_*0.01 << "\n";
else
ofst << "ivar_refine=0\n";
ofst << "mass_cut_refine=" << 2.0/pow(2,3*gh.levelmax()) << "\n"
<< "interpol_var=1\n"
<< "interpol_type=0\n"
<< "/\n\n";
LOGINFO("The grafic2 output plug-in wrote the grid data to a partial");
LOGINFO(" RAMSES namelist file \'%s\'",fname_.c_str() );
}
void write_ramses_namelist_old( const grid_hierarchy& gh )
{
//... also write the refinement options to a dummy namelist file
char ff[256];
sprintf(ff,"%s/ramses.nml",fname_.c_str() );
std::ofstream ofst(ff,std::ios::trunc);
ofst
<< "&INIT_PARAMS\n"
<< "filetype=\'grafic\'\n";
for( unsigned i=gh.levelmin();i<=gh.levelmax(); ++i)
{
sprintf(ff,"initfile(%d)=\'%s/level_%03d\'\n",i-gh.levelmin()+1,fname_.c_str(), i );
ofst << std::string(ff);
}
ofst << "/\n\n";
double xc,yc,zc,l;
ofst
<< "&AMR_PARAMS\n"
<< "levelmin=" << gh.levelmin() << "\n"
<< "levelmax=" << gh.levelmax() << "\n"
<< "ngridtot=2000000\n"
<< "nparttot=3000000\n"
<< "nexpand=1\n/\n\n";
const size_t fprec = 12, fwid = 16;
if( gh.levelmax() > gh.levelmin() )
{
l = (double)(1l<<(gh.levelmin()+1));
xc = ((double)gh.offset_abs(gh.levelmin()+1,0)+0.5*(double)gh.size(gh.levelmin()+1,0))/l;
yc = ((double)gh.offset_abs(gh.levelmin()+1,1)+0.5*(double)gh.size(gh.levelmin()+1,1))/l;
zc = ((double)gh.offset_abs(gh.levelmin()+1,2)+0.5*(double)gh.size(gh.levelmin()+1,2))/l;
ofst << "&REFINE_PARAMS\n"
<< "m_refine= "<< std::setw(fwid) << std::setprecision(fprec) << 0.0;
for( unsigned i=gh.levelmin()+1;i<gh.levelmax(); ++i)
ofst << "," << std::setw(fwid) << std::setprecision(fprec) << 0.0;
ofst << "\nx_refine= "<< std::setw(fwid) << std::setprecision(fprec) << xc;
for( unsigned i=gh.levelmin()+1;i<gh.levelmax(); ++i)
{
l = (double)(1l<<(i+1));
xc = ((double)gh.offset_abs(i+1,0)+0.5*(double)gh.size(i+1,0))/l;
ofst << ","<< std::setw(fwid) << std::setprecision(fprec) << xc;
}
ofst << "\ny_refine= "<< std::setw(fwid) << std::setprecision(fprec) << yc;
for( unsigned i=gh.levelmin()+1;i<gh.levelmax(); ++i)
{
l = (double)(1l<<(i+1));
yc = ((double)gh.offset_abs(i+1,1)+0.5*(double)gh.size(i+1,1))/l;
ofst << ","<< std::setw(fwid) << std::setprecision(fprec) << yc;
}
ofst << "\nz_refine= "<< std::setw(fwid) << std::setprecision(fprec) << zc;
for( unsigned i=gh.levelmin()+1;i<gh.levelmax(); ++i)
{
l = (double)(1l<<(i+1));
zc = ((double)gh.offset_abs(i+1,2)+0.5*(double)gh.size(i+1,2))/l;
ofst << ","<< std::setw(fwid) << std::setprecision(fprec) << zc;
}
ofst << "\nr_refine= ";
for(unsigned i=gh.levelmin();i<gh.levelmax(); ++i )
{
size_t nmax = std::min(gh.size(i+1,0),std::min(gh.size(i+1,1),gh.size(i+1,2)));
double r = (nmax-4.0)/(double)(1l<<(i+1));
if( i==gh.levelmin() )
ofst << std::setw(fwid) << std::setprecision(fprec) << r;
else
ofst << "," << std::setw(fwid) << std::setprecision(fprec) << r;
}
ofst << "\nexp_refine=" << std::setw(fwid) << std::setprecision(fprec) << 10.0;
for( unsigned i=gh.levelmin()+1;i<gh.levelmax(); ++i)
ofst << "," << std::setw(fwid) << std::setprecision(fprec) << 10.0;
ofst << "\n/\n";
}
sprintf(ff,"%s/ramses.nml",fname_.c_str() );
std::cout << " - The grafic2 output plug-in wrote the grid data to a partial\n"
<< " RAMSES namelist file \'" << ff << "\'\n";
}
public:
grafic2_output_plugin( config_file& cf )
: output_plugin( cf )
{
// create directory structure
remove( fname_.c_str() );
mkdir( fname_.c_str(), 0777 );
for(unsigned ilevel=levelmin_; ilevel<=levelmax_; ++ilevel )
{
char fp[256];
sprintf(fp,"%s/level_%03d",fname_.c_str(), ilevel );
mkdir( fp, 0777 );
}
bhavehydro_ = cf.getValue<bool>("setup","baryons");
//metal_floor_ = cf.getValueSafe<float>("output","ramses_metal_floor",1e-5);
passive_variable_index_ = cf.getValueSafe<int>("output","ramses_pvar_idx",1);
passive_variable_value_ = cf.getValueSafe<float>("output","ramses_pvar_val",1.0f);
}
/*~grafic2_output_plugin()
{ }*/
void write_dm_position( int coord, const grid_hierarchy& gh )
{
double
boxlength = cf_.getValue<double>("setup","boxlength");
for(unsigned ilevel=levelmin_; ilevel<=levelmax_; ++ilevel )
{
char ff[256];
sprintf(ff,"%s/level_%03d/ic_posc%c",fname_.c_str(), ilevel, (char)('x'+coord) );
std::ofstream ofs(ff,std::ios::binary|std::ios::trunc);
write_file_header( ofs, ilevel, gh );
write_sliced_array( ofs, ilevel, gh, boxlength );
}
}
void write_dm_velocity( int coord, const grid_hierarchy& gh )
{
double
boxlength = cf_.getValue<double>("setup","boxlength");
for(unsigned ilevel=levelmin_; ilevel<=levelmax_; ++ilevel )
{
char ff[256];
sprintf(ff,"%s/level_%03d/ic_velc%c",fname_.c_str(), ilevel, (char)('x'+coord) );
std::ofstream ofs(ff,std::ios::binary|std::ios::trunc);
write_file_header( ofs, ilevel, gh );
write_sliced_array( ofs, ilevel, gh, boxlength );
}
}
void write_gas_velocity( int coord, const grid_hierarchy& gh )
{
double
boxlength = cf_.getValue<double>("setup","boxlength");
for(unsigned ilevel=levelmin_; ilevel<=levelmax_; ++ilevel )
{
char ff[256];
sprintf(ff,"%s/level_%03d/ic_velb%c",fname_.c_str(), ilevel, (char)('x'+coord) );
std::ofstream ofs(ff,std::ios::binary|std::ios::trunc);
write_file_header( ofs, ilevel, gh );
write_sliced_array( ofs, ilevel, gh, boxlength );
}
}
void write_gas_density( const grid_hierarchy& gh )
{
for(unsigned ilevel=levelmin_; ilevel<=levelmax_; ++ilevel )
{
char ff[256];
sprintf(ff,"%s/level_%03d/ic_deltab",fname_.c_str(), ilevel );
std::ofstream ofs(ff,std::ios::binary|std::ios::trunc);
write_file_header( ofs, ilevel, gh );
write_sliced_array( ofs, ilevel, gh );
}
}
void write_dm_density( const grid_hierarchy& gh )
{
if(! bhavehydro_ )
write_gas_density(gh);
if( cf_.getValueSafe<bool>("output","ramses_nml",true) )
write_ramses_namelist(gh);
else if( cf_.getValueSafe<bool>("output","ramses_old_nml",false) )
write_ramses_namelist_old(gh);
if( gh.levelmin() != gh.levelmax() )
write_refinement_mask( gh );
}
void write_dm_mass( const grid_hierarchy& gh )
{ /* do nothing, not used... */ }
void write_dm_potential( const grid_hierarchy& gh )
{ /* do nothing, not used... */ }
void write_gas_potential( const grid_hierarchy& gh )
{ /* do nothing, not used... */ }
void write_gas_position( int coord, const grid_hierarchy& gh )
{ /* do nothing, not used... */ }
void finalize( void )
{ }
};
namespace{
output_plugin_creator_concrete<grafic2_output_plugin> creator("grafic2");
}
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