mirror of
https://github.com/cosmo-sims/MUSIC.git
synced 2024-09-19 17:03:46 +02:00
513 lines
23 KiB
C++
513 lines
23 KiB
C++
/*
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output_enzo.cc - This file is part of MUSIC -
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a code to generate multi-scale initial conditions
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for cosmological simulations
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Copyright (C) 2010 Oliver Hahn
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*/
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#ifdef HAVE_HDF5
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#include <sys/types.h>
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#include <sys/stat.h>
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#include "output.hh"
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#include "HDF_IO.hh"
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#define MAX_SLAB_SIZE 268435456 // = 256 MBytes
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class enzo_output_plugin : public output_plugin
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{
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protected:
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struct patch_header{
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int component_rank;
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size_t component_size;
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std::vector<int> dimensions;
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int rank;
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std::vector<int> top_grid_dims;
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std::vector<int> top_grid_end;
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std::vector<int> top_grid_start;
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};
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struct sim_header{
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std::vector<int> dimensions;
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std::vector<int> offset;
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float a_start;
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float dx;
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float h0;
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float omega_b;
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float omega_m;
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float omega_v;
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float vfact;
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};
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sim_header the_sim_header;
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void write_sim_header( std::string fname, const sim_header& h )
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{
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HDFWriteGroupAttribute( fname, "/", "Dimensions", h.dimensions );
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HDFWriteGroupAttribute( fname, "/", "Offset", h.offset );
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HDFWriteGroupAttribute( fname, "/", "a_start", h.a_start );
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HDFWriteGroupAttribute( fname, "/", "dx", h.dx );
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HDFWriteGroupAttribute( fname, "/", "h0", h.h0 );
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HDFWriteGroupAttribute( fname, "/", "omega_b", h.omega_b );
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HDFWriteGroupAttribute( fname, "/", "omega_m", h.omega_m );
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HDFWriteGroupAttribute( fname, "/", "omega_v", h.omega_v );
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HDFWriteGroupAttribute( fname, "/", "vfact", h.vfact );
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}
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void write_patch_header( std::string fname, std::string dsetname, const patch_header& h )
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{
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HDFWriteDatasetAttribute( fname, dsetname, "Component_Rank", h.component_rank );
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HDFWriteDatasetAttribute( fname, dsetname, "Component_Size", h.component_size );
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HDFWriteDatasetAttribute( fname, dsetname, "Dimensions", h.dimensions );
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HDFWriteDatasetAttribute( fname, dsetname, "Rank", h.rank );
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HDFWriteDatasetAttribute( fname, dsetname, "TopGridDims", h.top_grid_dims );
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HDFWriteDatasetAttribute( fname, dsetname, "TopGridEnd", h.top_grid_end );
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HDFWriteDatasetAttribute( fname, dsetname, "TopGridStart", h.top_grid_start );
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}
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void dump_grid_data( std::string fieldname, const grid_hierarchy& gh, double factor = 1.0, double add = 0.0 )
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{
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char enzoname[256], filename[256];
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for(unsigned ilevel=levelmin_; ilevel<=levelmax_; ++ilevel )
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{
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std::vector<int> ng, ng_fortran;
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ng.push_back( gh.get_grid(ilevel)->size(0) );
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ng.push_back( gh.get_grid(ilevel)->size(1) );
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ng.push_back( gh.get_grid(ilevel)->size(2) );
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ng_fortran.push_back( gh.get_grid(ilevel)->size(2) );
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ng_fortran.push_back( gh.get_grid(ilevel)->size(1) );
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ng_fortran.push_back( gh.get_grid(ilevel)->size(0) );
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//... need to copy data because we need to get rid of the ghost zones
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//... write in slabs if data is more than MAX_SLAB_SIZE (default 128 MB)
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//... full 3D block size
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size_t all_data_size = (size_t)ng[0] * (size_t)ng[1] * (size_t)ng[2];
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//... write in slabs of MAX_SLAB_SIZE unless all_data_size is anyway smaller
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size_t max_slab_size = std::min((size_t)MAX_SLAB_SIZE/sizeof(double), all_data_size );
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//... but one slab hast to be at least the size of one slice
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max_slab_size = std::max(((size_t)ng[0] * (size_t)ng[1]), max_slab_size );
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//... number of slices in one slab
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size_t slices_in_slab = (size_t)((double)max_slab_size / ((size_t)ng[0] * (size_t)ng[1]));
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size_t nsz[3] = { ng[2], ng[1], ng[0] };
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if( levelmin_ != levelmax_ )
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sprintf( enzoname, "%s.%d", fieldname.c_str(), ilevel-levelmin_ );
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else
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sprintf( enzoname, "%s", fieldname.c_str() );
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sprintf( filename, "%s/%s", fname_.c_str(), enzoname );
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HDFCreateFile( filename );
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write_sim_header( filename, the_sim_header );
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#ifdef SINGLE_PRECISION
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//... create full array in file
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HDFHyperslabWriter3Ds<float> *slab_writer = new HDFHyperslabWriter3Ds<float>( filename, enzoname, nsz );
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//... create buffer
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float *data_buf = new float[ slices_in_slab * (size_t)ng[0] * (size_t)ng[1] ];
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#else
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//... create full array in file
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HDFHyperslabWriter3Ds<double> *slab_writer = new HDFHyperslabWriter3Ds<double>( filename, enzoname, nsz );
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//... create buffer
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double *data_buf = new double[ slices_in_slab * (size_t)ng[0] * (size_t)ng[1] ];
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#endif
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//... write slice by slice
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size_t slices_written = 0;
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while( slices_written < (size_t)ng[2] )
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{
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slices_in_slab = std::min( (size_t)ng[2]-slices_written, slices_in_slab );
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#pragma omp parallel for
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for( int k=0; k<(int)slices_in_slab; ++k )
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for( int j=0; j<ng[1]; ++j )
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for( int i=0; i<ng[0]; ++i )
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data_buf[ (size_t)(k*ng[1]+j)*(size_t)ng[0]+(size_t)i ] =
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(add+(*gh.get_grid(ilevel))(i,j,k+slices_written))*factor;
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size_t count[3], offset[3];
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count[0] = slices_in_slab;
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count[1] = ng[1];
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count[2] = ng[0];
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offset[0] = slices_written;;
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offset[1] = 0;
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offset[2] = 0;
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slab_writer->write_slab( data_buf, count, offset );
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slices_written += slices_in_slab;
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}
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//... free buffer
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delete[] data_buf;
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//... finalize writing and close dataset
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delete slab_writer;
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//... header data for the patch
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patch_header ph;
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ph.component_rank = 1;
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ph.component_size = (size_t)ng[0]*(size_t)ng[1]*(size_t)ng[2];
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ph.dimensions = ng;
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ph.rank = 3;
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ph.top_grid_dims.assign(3, 1<<levelmin_);
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//... offset_abs is in units of the current level cell size
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double rfac = 1.0/(1<<(ilevel-levelmin_));
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ph.top_grid_start.push_back( (int)(gh.offset_abs(ilevel, 0)*rfac) );
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ph.top_grid_start.push_back( (int)(gh.offset_abs(ilevel, 1)*rfac) );
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ph.top_grid_start.push_back( (int)(gh.offset_abs(ilevel, 2)*rfac) );
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ph.top_grid_end.push_back( ph.top_grid_start[0] + (int)(ng[0]*rfac) );
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ph.top_grid_end.push_back( ph.top_grid_start[1] + (int)(ng[1]*rfac) );
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ph.top_grid_end.push_back( ph.top_grid_start[2] + (int)(ng[2]*rfac) );
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write_patch_header( filename, enzoname, ph );
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}
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}
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public:
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enzo_output_plugin( config_file& cf )
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: output_plugin( cf )
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{
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if( mkdir( fname_.c_str(), 0777 ) )
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{
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perror( fname_.c_str() );
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throw std::runtime_error("Error in enzo_output_plugin!");
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}
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bool bhave_hydro = cf_.getValue<bool>("setup","baryons");
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bool align_top = cf.getValueSafe<bool>( "setup", "align_top", false );
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if( !align_top )
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LOGWARN("Old ENZO versions may require \'align_top=true\'!");
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the_sim_header.dimensions.push_back( 1<<levelmin_ );
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the_sim_header.dimensions.push_back( 1<<levelmin_ );
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the_sim_header.dimensions.push_back( 1<<levelmin_ );
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the_sim_header.offset.push_back( 0 );
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the_sim_header.offset.push_back( 0 );
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the_sim_header.offset.push_back( 0 );
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the_sim_header.a_start = 1.0/(1.0+cf.getValue<double>("setup","zstart"));
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the_sim_header.dx = cf.getValue<double>("setup","boxlength")/the_sim_header.dimensions[0]/(cf.getValue<double>("cosmology","H0")*0.01); // not sure?!?
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the_sim_header.h0 = cf.getValue<double>("cosmology","H0")*0.01;
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if( bhave_hydro )
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the_sim_header.omega_b = cf.getValue<double>("cosmology","Omega_b");
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else
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the_sim_header.omega_b = 0.0;
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the_sim_header.omega_m = cf.getValue<double>("cosmology","Omega_m");
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the_sim_header.omega_v = cf.getValue<double>("cosmology","Omega_L");
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the_sim_header.vfact = cf.getValue<double>("cosmology","vfact")*the_sim_header.h0; //.. need to multiply by h, ENZO wants this factor for non h-1 units
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}
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~enzo_output_plugin()
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{ }
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void write_dm_mass( const grid_hierarchy& gh )
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{ /* do nothing, not needed */ }
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void write_dm_density( const grid_hierarchy& gh )
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{ /* write the parameter file data */
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bool bhave_hydro = cf_.getValue<bool>("setup","baryons");
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double refine_region_fraction = cf_.getValueSafe<double>( "output", "enzo_refine_region_fraction", 0.8 );
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char filename[256];
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unsigned nbase = (unsigned)pow(2,levelmin_);
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sprintf( filename, "%s/parameter_file.txt", fname_.c_str() );
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std::ofstream ofs( filename, std::ios::trunc );
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ofs
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<< "# Relevant Section of Enzo Paramter File (NOT COMPLETE!) \n"
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<< "ProblemType = 30 // cosmology simulation\n"
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<< "TopGridRank = 3\n"
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<< "TopGridDimensions = " << nbase << " " << nbase << " " << nbase << "\n"
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<< "SelfGravity = 1 // gravity on\n"
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<< "TopGridGravityBoundary = 0 // Periodic BC for gravity\n"
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<< "LeftFaceBoundaryCondition = 3 3 3 // same for fluid\n"
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<< "RightFaceBoundaryCondition = 3 3 3\n"
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<< "RefineBy = 2\n"
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<< "\n"
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<< "#\n";
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if( bhave_hydro )
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ofs
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<< "CosmologySimulationOmegaBaryonNow = " << the_sim_header.omega_b << "\n"
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<< "CosmologySimulationOmegaCDMNow = " << the_sim_header.omega_m-the_sim_header.omega_b << "\n";
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else
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ofs
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<< "CosmologySimulationOmegaBaryonNow = " << 0.0 << "\n"
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<< "CosmologySimulationOmegaCDMNow = " << the_sim_header.omega_m << "\n";
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if( bhave_hydro )
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ofs
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<< "CosmologySimulationDensityName = GridDensity\n"
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<< "CosmologySimulationVelocity1Name = GridVelocities_x\n"
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<< "CosmologySimulationVelocity2Name = GridVelocities_y\n"
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<< "CosmologySimulationVelocity3Name = GridVelocities_z\n";
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ofs
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<< "CosmologySimulationCalculatePositions = 1\n"
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<< "CosmologySimulationParticleVelocity1Name = ParticleVelocities_x\n"
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<< "CosmologySimulationParticleVelocity2Name = ParticleVelocities_y\n"
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<< "CosmologySimulationParticleVelocity3Name = ParticleVelocities_z\n"
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<< "CosmologySimulationParticleDisplacement1Name = ParticleDisplacements_x\n"
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<< "CosmologySimulationParticleDisplacement2Name = ParticleDisplacements_y\n"
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<< "CosmologySimulationParticleDisplacement3Name = ParticleDisplacements_z\n"
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<< "\n"
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<< "#\n"
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<< "# define cosmology parameters\n"
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<< "#\n"
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<< "ComovingCoordinates = 1 // Expansion ON\n"
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<< "CosmologyOmegaMatterNow = " << the_sim_header.omega_m << "\n"
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<< "CosmologyOmegaLambdaNow = " << the_sim_header.omega_v << "\n"
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<< "CosmologyHubbleConstantNow = " << the_sim_header.h0 << " // in 100 km/s/Mpc\n"
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<< "CosmologyComovingBoxSize = " << cf_.getValue<double>("setup","boxlength") << " // in Mpc/h\n"
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<< "CosmologyMaxExpansionRate = 0.015 // maximum allowed delta(a)/a\n"
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<< "CosmologyInitialRedshift = " << cf_.getValue<double>("setup","zstart") << " //\n"
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<< "CosmologyFinalRedshift = 0 //\n"
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<< "GravitationalConstant = 1 // this must be true for cosmology\n"
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<< "#\n"
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<< "#\n"
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<< "ParallelRootGridIO = 1\n"
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<< "ParallelParticleIO = 1\n"
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<< "PartitionNestedGrids = 1\n"
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<< "CosmologySimulationNumberOfInitialGrids = " << 1+levelmax_-levelmin_ << "\n";
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int num_prec = 10;
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if( levelmax_ > 15 )
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num_prec = 17;
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//... only for additionally refined grids
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for( unsigned ilevel = 0; ilevel< levelmax_-levelmin_; ++ilevel )
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{
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double h = 1.0/(1<<(levelmin_+1+ilevel));
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ofs
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<< "CosmologySimulationGridDimension[" << 1+ilevel << "] = "
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<< std::setw(16) << gh.size( levelmin_+ilevel+1, 0 ) << " "
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<< std::setw(16) << gh.size( levelmin_+ilevel+1, 1 ) << " "
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<< std::setw(16) << gh.size( levelmin_+ilevel+1, 2 ) << "\n"
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<< "CosmologySimulationGridLeftEdge[" << 1+ilevel << "] = "
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<< std::setw(num_prec+6) << std::setprecision(num_prec) << h*gh.offset_abs(levelmin_+ilevel+1, 0) << " "
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<< std::setw(num_prec+6) << std::setprecision(num_prec) << h*gh.offset_abs(levelmin_+ilevel+1, 1) << " "
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<< std::setw(num_prec+6) << std::setprecision(num_prec) << h*gh.offset_abs(levelmin_+ilevel+1, 2) << "\n"
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<< "CosmologySimulationGridRightEdge[" << 1+ilevel << "] = "
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<< std::setw(num_prec+6) << std::setprecision(num_prec) << h*(gh.offset_abs(levelmin_+ilevel+1, 0)+gh.size( levelmin_+ilevel+1, 0 )) << " "
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<< std::setw(num_prec+6) << std::setprecision(num_prec) << h*(gh.offset_abs(levelmin_+ilevel+1, 1)+gh.size( levelmin_+ilevel+1, 1 )) << " "
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<< std::setw(num_prec+6) << std::setprecision(num_prec) << h*(gh.offset_abs(levelmin_+ilevel+1, 2)+gh.size( levelmin_+ilevel+1, 2 )) << "\n"
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<< "CosmologySimulationGridLevel[" << 1+ilevel << "] = " << 1+ilevel << "\n";
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}
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if( levelmin_ != levelmax_ )
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{
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double h = 1.0/(1<<levelmax_);
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double cen[3],le[3],re[3];
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for (int i=0;i<3;i++)
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{
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cen[i] = gh.offset_abs(levelmax_, i)+gh.size( levelmax_, i )/2;
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le[i] = cen[i]-refine_region_fraction*gh.size( levelmax_,i)/2;
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re[i] = le[i] +refine_region_fraction*gh.size( levelmax_, i);
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}
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ofs
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<< "#\n"
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<< "# region allowed for further refinement\n"
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<< "#\n"
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// << "RefineRegionAutoAdjust = 1\n"
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<< "RefineRegionLeftEdge = "
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<< std::setw(num_prec+6) << std::setprecision(num_prec) << h*le[0] << " "
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<< std::setw(num_prec+6) << std::setprecision(num_prec) << h*le[1] << " "
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<< std::setw(num_prec+6) << std::setprecision(num_prec) << h*le[2] << "\n"
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<< "RefineRegionRightEdge = "
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<< std::setw(num_prec+6) << std::setprecision(num_prec) << h*re[0] << " "
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<< std::setw(num_prec+6) << std::setprecision(num_prec) << h*re[1] << " "
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<< std::setw(num_prec+6) << std::setprecision(num_prec) << h*re[2]<< "\n";
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}
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// determine density maximum and minimum location
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real_t rhomax = -1e30, rhomin = 1e30;
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double loc_rhomax[3] = {0.0,0.0,0.0}, loc_rhomin[3] = {0.0,0.0,0.0};
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int lvl_rhomax = 0, lvl_rhomin = 0;
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real_t rhomax_lm = -1e30, rhomin_lm = 1e30;
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double loc_rhomax_lm[3] = {0.0,0.0,0.0}, loc_rhomin_lm[3] = {0.0,0.0,0.0};
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for( int ilevel=gh.levelmax(); ilevel>=(int)gh.levelmin(); --ilevel )
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for( unsigned i=0; i<gh.get_grid(ilevel)->size(0); ++i )
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for( unsigned j=0; j<gh.get_grid(ilevel)->size(1); ++j )
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for( unsigned k=0; k<gh.get_grid(ilevel)->size(2); ++k )
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if( ! gh.is_refined(ilevel,i,j,k) )
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{
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real_t rho = (*gh.get_grid(ilevel))(i,j,k);
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if( rho > rhomax )
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{
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rhomax = rho;
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lvl_rhomax = ilevel;
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gh.cell_pos(ilevel, i, j, k, loc_rhomax);
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}
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if( rho < rhomin )
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{
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rhomin = rho;
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lvl_rhomin = ilevel;
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gh.cell_pos(ilevel, i, j, k, loc_rhomin);
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}
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if( ilevel == (int)gh.levelmax() )
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{
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if( rho > rhomax_lm )
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{
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rhomax_lm = rho;
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gh.cell_pos(ilevel, i, j, k, loc_rhomax_lm);
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}
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if( rho < rhomin_lm )
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{
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rhomin_lm = rho;
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gh.cell_pos(ilevel, i, j, k, loc_rhomin_lm);
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}
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}
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}
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double h = 1.0/(1<<levelmin_);
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double shift[3];
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shift[0] = -(double)cf_.getValue<int>( "setup", "shift_x" )*h;
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shift[1] = -(double)cf_.getValue<int>( "setup", "shift_y" )*h;
|
|
shift[2] = -(double)cf_.getValue<int>( "setup", "shift_z" )*h;
|
|
|
|
if( gh.levelmin() != gh.levelmax() )
|
|
{
|
|
LOGINFO("Global density extrema: ");
|
|
LOGINFO(" minimum: delta=%f at (%f,%f,%f) (level=%d)",rhomin,loc_rhomin[0],loc_rhomin[1],loc_rhomin[2],lvl_rhomin);
|
|
LOGINFO(" shifted back at (%f,%f,%f)",loc_rhomin[0]+shift[0],loc_rhomin[1]+shift[1],loc_rhomin[2]+shift[2]);
|
|
LOGINFO(" maximum: delta=%f at (%f,%f,%f) (level=%d)",rhomax,loc_rhomax[0],loc_rhomax[1],loc_rhomax[2],lvl_rhomax);
|
|
LOGINFO(" shifted back at (%f,%f,%f)",loc_rhomax[0]+shift[0],loc_rhomax[1]+shift[1],loc_rhomax[2]+shift[2]);
|
|
|
|
LOGINFO("Density extrema on finest level: ");
|
|
LOGINFO(" minimum: delta=%f at (%f,%f,%f)",rhomin_lm,loc_rhomin_lm[0],loc_rhomin_lm[1],loc_rhomin_lm[2]);
|
|
LOGINFO(" shifted back at (%f,%f,%f)",loc_rhomin_lm[0]+shift[0],loc_rhomin_lm[1]+shift[1],loc_rhomin_lm[2]+shift[2]);
|
|
LOGINFO(" maximum: delta=%f at (%f,%f,%f)",rhomax_lm,loc_rhomax_lm[0],loc_rhomax_lm[1],loc_rhomax_lm[2]);
|
|
LOGINFO(" shifted back at (%f,%f,%f)",loc_rhomax_lm[0]+shift[0],loc_rhomax_lm[1]+shift[1],loc_rhomax_lm[2]+shift[2]);
|
|
|
|
}else{
|
|
LOGINFO("Global density extrema: ");
|
|
LOGINFO(" minimum: delta=%f at (%f,%f,%f)",rhomin,loc_rhomin[0],loc_rhomin[1],loc_rhomin[2]);
|
|
LOGINFO(" shifted back at (%f,%f,%f)",loc_rhomin[0]+shift[0],loc_rhomin[1]+shift[1],loc_rhomin[2]+shift[2]);
|
|
LOGINFO(" maximum: delta=%f at (%f,%f,%f)",rhomax,loc_rhomax[0],loc_rhomax[1],loc_rhomax[2]);
|
|
LOGINFO(" shifted back at (%f,%f,%f)",loc_rhomax[0]+shift[0],loc_rhomax[1]+shift[1],loc_rhomax[2]+shift[2]);
|
|
|
|
}
|
|
|
|
}
|
|
|
|
|
|
void write_dm_velocity( int coord, const grid_hierarchy& gh )
|
|
{
|
|
char enzoname[256];
|
|
sprintf( enzoname, "ParticleVelocities_%c", (char)('x'+coord) );
|
|
|
|
double vunit = 1.0/(1.225e2*sqrt(the_sim_header.omega_m/the_sim_header.a_start));
|
|
|
|
dump_grid_data( enzoname, gh, vunit );
|
|
}
|
|
|
|
|
|
void write_dm_position( int coord, const grid_hierarchy& gh )
|
|
{
|
|
char enzoname[256];
|
|
sprintf( enzoname, "ParticleDisplacements_%c", (char)('x'+coord) );
|
|
|
|
dump_grid_data( enzoname, gh );
|
|
}
|
|
|
|
void write_dm_potential( const grid_hierarchy& gh )
|
|
{ }
|
|
|
|
void write_gas_potential( const grid_hierarchy& gh )
|
|
{ }
|
|
|
|
|
|
void write_gas_velocity( int coord, const grid_hierarchy& gh )
|
|
{
|
|
double vunit = 1.0/(1.225e2*sqrt(the_sim_header.omega_m/the_sim_header.a_start));
|
|
|
|
char enzoname[256];
|
|
sprintf( enzoname, "GridVelocities_%c", (char)('x'+coord) );
|
|
dump_grid_data( enzoname, gh, vunit );
|
|
}
|
|
|
|
|
|
void write_gas_position( int coord, const grid_hierarchy& gh )
|
|
{
|
|
/* do nothing, not needed */
|
|
}
|
|
|
|
|
|
void write_gas_density( const grid_hierarchy& gh )
|
|
{
|
|
|
|
char enzoname[256];
|
|
sprintf( enzoname, "GridDensity" );
|
|
dump_grid_data( enzoname, gh, the_sim_header.omega_b/the_sim_header.omega_m, 1.0 );
|
|
}
|
|
|
|
|
|
void finalize( void )
|
|
{ }
|
|
|
|
|
|
};
|
|
|
|
namespace{
|
|
output_plugin_creator_concrete<enzo_output_plugin> creator("enzo");
|
|
}
|
|
|
|
#endif
|
|
|
|
|