mirror of
https://github.com/cosmo-sims/MUSIC.git
synced 2024-09-19 17:03:46 +02:00
modified directory structure, fixed compiler warnings in g++ 9
This commit is contained in:
Oliver Hahn
parent
6ad3934f23
commit
b77fedd700
71 changed files with 4308 additions and 4349 deletions
26
Makefile
26
Makefile
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@ -9,11 +9,11 @@ BOXLIB_HOME = ${HOME}/nyx_tot_sterben/BoxLib
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##############################################################################
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### compiler and path settings
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CC = g++
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CC = g++-9
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OPT = -Wall -Wno-unknown-pragmas -O3 -g -mtune=native
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CFLAGS =
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LFLAGS = -lgsl -lgslcblas
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CPATHS = -I. -I$(HOME)/local/include -I/opt/local/include -I/usr/local/include
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CPATHS = -I./src -I$(HOME)/local/include -I/opt/local/include -I/usr/local/include
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LPATHS = -L$(HOME)/local/lib -L/opt/local/lib -L/usr/local/lib
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##############################################################################
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@ -78,20 +78,20 @@ TARGET = MUSIC
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OBJS = output.o transfer_function.o Numerics.o defaults.o constraints.o random.o\
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convolution_kernel.o region_generator.o densities.o cosmology.o poisson.o\
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densities.o cosmology.o poisson.o log.o main.o \
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$(patsubst plugins/%.cc,plugins/%.o,$(wildcard plugins/*.cc))
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$(patsubst src/plugins/%.cc,src/plugins/%.o,$(wildcard src/plugins/*.cc))
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##############################################################################
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# stuff for BoxLib
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BLOBJS = ""
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ifeq ($(strip $(HAVEBOXLIB)), yes)
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IN_MUSIC = YES
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TOP = ${PWD}/plugins/nyx_plugin
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TOP = ${PWD}/src/plugins/nyx_plugin
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CCbla := $(CC)
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include plugins/nyx_plugin/Make.ic
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include src/plugins/nyx_plugin/Make.ic
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CC := $(CCbla)
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CPATHS += $(INCLUDE_LOCATIONS)
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LPATHS += -L$(objEXETempDir)
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BLOBJS = $(foreach obj,$(objForExecs),plugins/boxlib_stuff/$(obj))
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BLOBJS = $(foreach obj,$(objForExecs),src/plugins/boxlib_stuff/$(obj))
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#
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endif
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@ -102,23 +102,29 @@ all: $(OBJS) $(TARGET) Makefile
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bla:
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echo $(BLOBJS)
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blabla:
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echo $(OBJS)
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ifeq ($(strip $(HAVEBOXLIB)), yes)
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$(TARGET): $(OBJS) plugins/nyx_plugin/*.cpp
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cd plugins/nyx_plugin; make BOXLIB_HOME=$(BOXLIB_HOME) FFTW3=$(FFTW3) SINGLE=$(SINGLEPRECISION)
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$(TARGET): $(OBJS) src/plugins/nyx_plugin/*.cpp
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cd src/plugins/nyx_plugin; make BOXLIB_HOME=$(BOXLIB_HOME) FFTW3=$(FFTW3) SINGLE=$(SINGLEPRECISION)
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$(CC) $(LPATHS) -o $@ $^ $(LFLAGS) $(BLOBJS) -lifcore
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else
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$(TARGET): $(OBJS)
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$(CC) $(LPATHS) -o $@ $^ $(LFLAGS)
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endif
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%.o: %.cc *.hh Makefile
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%.o: src/%.cc src/*.hh Makefile
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$(CC) $(CFLAGS) $(CPATHS) -c $< -o $@
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src/plugins/%.o: src/plugins/%.cc src/*.hh Makefile
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$(CC) $(CFLAGS) $(CPATHS) -c $< -o $@
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clean:
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rm -rf $(OBJS)
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ifeq ($(strip $(HAVEBOXLIB)), yes)
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oldpath=`pwd`
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cd plugins/nyx_plugin; make realclean BOXLIB_HOME=$(BOXLIB_HOME)
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cd src/plugins/nyx_plugin; make realclean BOXLIB_HOME=$(BOXLIB_HOME)
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endif
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cd $(oldpath)
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@ -1,803 +0,0 @@
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/*
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* output_arepo.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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*
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* Copyright (C) 2010 Oliver Hahn
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*
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* Plugin: Dylan Nelson (dnelson@cfa.harvard.edu)
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*/
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#ifdef HAVE_HDF5
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#define GAS_PARTTYPE 0
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#define HIGHRES_DM_PARTTYPE 1
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#define COARSE_DM_DEFAULT_PARTTYPE 2
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#define STAR_PARTTYPE 4
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#define NTYPES 6
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#include <sstream>
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#include <string>
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#include <algorithm>
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#include "output.hh"
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#include "HDF_IO.hh"
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class arepo_output_plugin : public output_plugin
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{
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protected:
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// header/config
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std::vector< std::vector<unsigned int> > nPart;
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std::vector<long long> nPartTotal;
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std::vector<double> massTable;
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double time, redshift, boxSize;
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unsigned int numFiles, coarsePartType;
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double omega0, omega_L, hubbleParam;
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// configuration
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double UnitLength_in_cm, UnitMass_in_g, UnitVelocity_in_cm_per_s;
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double omega_b, rhoCrit;
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double posFac, velFac;
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long long nPartTotAllTypes;
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bool doBaryons, useLongIDs, doublePrec;
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size_t npfine, npart, npcoarse;
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std::vector<size_t> levelcounts;
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// parameter file hints
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int pmgrid, gridboost;
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float softening, Tini;
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using output_plugin::cf_;
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// Nx1 vector (e.g. masses,particleids)
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template< typename T >
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void writeHDF5_a( std::string fieldName, int partTypeNum, const std::vector<T> &data )
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{
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hid_t HDF_FileID, HDF_GroupID, HDF_DatasetID, HDF_DataspaceID, HDF_Type;
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hsize_t HDF_Dims, offset = 0;
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std::stringstream GrpName;
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GrpName << "PartType" << partTypeNum;
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for( unsigned i=0; i < numFiles; i++ )
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{
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std::string filename = fname_;
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HDF_Dims = data.size();
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// modify local filename and write size
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if( numFiles > 1 )
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{
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std::stringstream s;
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s << "." << i << ".hdf5";
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filename.replace(filename.find(".hdf5"), 5, s.str());
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HDF_Dims = ceil( data.size() / numFiles );
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if( i == numFiles-1 )
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HDF_Dims = data.size() - offset;
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}
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HDF_FileID = H5Fopen( filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT );
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HDF_GroupID = H5Gopen( HDF_FileID, GrpName.str().c_str() );
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HDF_Type = GetDataType<T>();
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HDF_DataspaceID = H5Screate_simple(1, &HDF_Dims, NULL);
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HDF_DatasetID = H5Dcreate(HDF_GroupID, fieldName.c_str(), HDF_Type, HDF_DataspaceID, H5P_DEFAULT);
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// write and close
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H5Dwrite( HDF_DatasetID, HDF_Type, H5S_ALL, H5S_ALL, H5P_DEFAULT, &data[offset] );
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H5Dclose( HDF_DatasetID );
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H5Sclose( HDF_DataspaceID );
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H5Gclose( HDF_GroupID );
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H5Fclose( HDF_FileID );
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offset += HDF_Dims;
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}
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}
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// Nx3 vector (e.g. pos,vel), where coord = index of the second dimension (written one at a time)
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template<typename T>
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void writeHDF5_b( std::string fieldName, int coord, int partTypeNum, std::vector<T> &data, bool readFlag = false )
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{
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hid_t HDF_FileID, HDF_GroupID, HDF_DatasetID, HDF_DataspaceID, HDF_Type;
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hsize_t HDF_Dims[2], HDF_DimsMem[2], w_offset = 0;
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std::stringstream GrpName;
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GrpName << "PartType" << partTypeNum;
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for( unsigned i=0; i < numFiles; i++ )
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{
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std::string filename = fname_;
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HDF_Dims[0] = data.size();
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// modify local filename and write size
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if( numFiles > 1 )
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{
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std::stringstream s;
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s << "." << i << ".hdf5";
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filename.replace(filename.find(".hdf5"), 5, s.str());
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HDF_Dims[0] = ceil( data.size() / numFiles );
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if( i == numFiles-1 )
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HDF_Dims[0] = data.size() - w_offset;
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}
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HDF_FileID = H5Fopen( filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT );
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HDF_GroupID = H5Gopen( HDF_FileID, GrpName.str().c_str() );
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HDF_Type = GetDataType<T>();
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HDF_Dims[1] = 3;
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// if dataset does not yet exist, create it (on first coord call)
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if( !(H5Lexists(HDF_GroupID, fieldName.c_str(), H5P_DEFAULT)) )
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{
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HDF_DataspaceID = H5Screate_simple(2, HDF_Dims, NULL);
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HDF_DatasetID = H5Dcreate( HDF_GroupID, fieldName.c_str(), HDF_Type, HDF_DataspaceID, H5P_DEFAULT );
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H5Sclose( HDF_DataspaceID );
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H5Dclose( HDF_DatasetID );
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}
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// make memory space (just indicates the size/shape of data)
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HDF_DimsMem[0] = HDF_Dims[0];
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HDF_DimsMem[1] = 1;
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hid_t HDF_MemoryspaceID = H5Screate_simple(2, HDF_DimsMem, NULL);
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// open hyperslab
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hsize_t count[2]={1,1}, stride[2]={1,1}, offset[2]={0,0};
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offset[1] = coord; // set where in the second dimension to write
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count[0] = HDF_Dims[0]; // set size in the first dimension (num particles of this type)
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HDF_DatasetID = H5Dopen(HDF_GroupID, fieldName.c_str());
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HDF_DataspaceID = H5Dget_space(HDF_DatasetID);
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H5Sselect_hyperslab(HDF_DataspaceID, H5S_SELECT_SET, offset, stride, count, NULL);
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// write (or read) and close
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if( readFlag )
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H5Dread( HDF_DatasetID, HDF_Type, HDF_MemoryspaceID, HDF_DataspaceID, H5P_DEFAULT,
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&data[w_offset] );
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else
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H5Dwrite( HDF_DatasetID, HDF_Type, HDF_MemoryspaceID, HDF_DataspaceID, H5P_DEFAULT,
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&data[w_offset] );
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H5Dclose( HDF_DatasetID );
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H5Gclose( HDF_GroupID );
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H5Fclose( HDF_FileID );
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w_offset += HDF_Dims[0];
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}
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}
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// called from finalize()
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void generateAndWriteIDs( void )
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{
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long long offset = 1; // don't use ID==0
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nPartTotAllTypes = 0;
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for( size_t i=0; i < nPartTotal.size(); i++ )
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{
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if( !nPartTotal[i] )
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continue;
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nPartTotAllTypes += nPartTotal[i];
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if( !useLongIDs )
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{
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std::vector<int> ids = std::vector<int>(nPartTotal[i]);
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for( int j=0; j < nPartTotal[i]; j++ )
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ids[j] = offset + j;
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writeHDF5_a( "ParticleIDs", i, ids );
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}
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else
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{
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std::vector<long long> ids = std::vector<long long>(nPartTotal[i]);
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for( long long j=0; j < nPartTotal[i]; j++ )
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ids[j] = offset + j;
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writeHDF5_a( "ParticleIDs", i, ids );
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}
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// make IDs of all particle types sequential (unique) = unnecessary, but consistent with gadget output format
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offset += nPartTotal[i];
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}
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}
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void countLeafCells( const grid_hierarchy& gh )
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{
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npfine = 0; npart = 0; npcoarse = 0;
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npfine = gh.count_leaf_cells(gh.levelmax(), gh.levelmax());
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npart = gh.count_leaf_cells(gh.levelmin(), gh.levelmax());
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if( levelmax_ != levelmin_ ) // multimass
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npcoarse = gh.count_leaf_cells(gh.levelmin(), gh.levelmax()-1);
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}
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template< typename T >
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void __write_dm_mass( const grid_hierarchy& gh )
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{
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countLeafCells(gh);
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// fill levelcount for header
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levelcounts = std::vector<size_t>(levelmax_-levelmin_+1);
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for( int ilevel=gh.levelmax(); ilevel>=(int)gh.levelmin(); --ilevel )
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levelcounts[gh.levelmax()-ilevel] = gh.count_leaf_cells(ilevel, ilevel);
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if( levelmax_ > levelmin_ +1 ) // morethan2bnd
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{
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// DM particles will have variable masses
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size_t count = 0;
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std::vector<T> data(npcoarse);
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for( int ilevel=gh.levelmax()-1; ilevel>=(int)gh.levelmin(); --ilevel )
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{
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// baryon particles live only on finest grid, these particles here are total matter particles
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T pmass = omega0 * rhoCrit * pow(boxSize*posFac,3.0)/pow(2,3*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_in_mask(ilevel,i,j,k) && !gh.is_refined(ilevel,i,j,k) )
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{
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data[count++] = pmass;
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}
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}
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if( count != npcoarse )
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throw std::runtime_error("Internal consistency error while writing masses");
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writeHDF5_a( "Masses", coarsePartType, data ); // write DM
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}
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else
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{
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// DM particles will all have the same mass, just write to massTable
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if( levelmax_ != levelmin_ ) // multimass
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massTable[coarsePartType] = omega0 * rhoCrit * pow(boxSize*posFac,3.0)/pow(2,3*levelmin_);
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}
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}
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template< typename T >
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void __write_dm_position( int coord, const grid_hierarchy& gh )
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{
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countLeafCells(gh);
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// update header
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hsize_t offset_fine = 0, offset_coarse = 0;
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for( unsigned i=0; i < numFiles; i++ ) {
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hsize_t dims_fine = ceil( npfine / numFiles );
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hsize_t dims_coarse = ceil( npcoarse / numFiles );
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if( i == numFiles-1 ) {
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dims_fine = npfine - offset_fine;
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dims_coarse = npcoarse - offset_coarse;
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}
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nPart[i][HIGHRES_DM_PARTTYPE] = dims_fine;
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nPart[i][coarsePartType] = dims_coarse;
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offset_fine += dims_fine;
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offset_coarse += dims_coarse;
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}
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nPartTotal[HIGHRES_DM_PARTTYPE] = npfine;
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nPartTotal[coarsePartType] = npcoarse;
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// FINE: collect displacements and convert to absolute coordinates with correct units
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int ilevel = gh.levelmax();
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std::vector<T> data(npfine);
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size_t count = 0;
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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_in_mask(ilevel,i,j,k) && !gh.is_refined(ilevel,i,j,k) )
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{
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double xx[3];
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gh.cell_pos(ilevel, i, j, k, xx);
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xx[coord] = (xx[coord] + (*gh.get_grid(ilevel))(i,j,k)) * boxSize;
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xx[coord] = fmod( xx[coord] + boxSize,boxSize );
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data[count++] = (T) (xx[coord] * posFac);
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}
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writeHDF5_b( "Coordinates", coord, HIGHRES_DM_PARTTYPE, data ); // write fine DM
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if( count != npfine )
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throw std::runtime_error("Internal consistency error while writing fine DM pos");
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// COARSE: collect displacements and convert to absolute coordinates with correct units
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if( levelmax_ != levelmin_ ) // multimass
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{
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data = std::vector<T> (npcoarse,0.0);
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count = 0;
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for( int ilevel=gh.levelmax()-1; 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_in_mask(ilevel,i,j,k) && !gh.is_refined(ilevel,i,j,k) )
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{
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double xx[3];
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gh.cell_pos(ilevel, i, j, k, xx);
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xx[coord] = (xx[coord] + (*gh.get_grid(ilevel))(i,j,k)) * boxSize;
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if ( !doBaryons ) // if so, we will handle the mod in write_gas_position
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xx[coord] = fmod( xx[coord] + boxSize,boxSize ) * posFac;
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data[count++] = (T) xx[coord];
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}
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if( count != npcoarse )
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throw std::runtime_error("Internal consistency error while writing coarse DM pos");
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writeHDF5_b( "Coordinates", coord, coarsePartType, data ); // write coarse DM
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}
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}
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template< typename T >
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void __write_dm_velocity( int coord, const grid_hierarchy& gh )
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{
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countLeafCells(gh);
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// FINE: collect velocities and convert to correct units
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int ilevel = gh.levelmax();
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||||
|
||||
std::vector<T> data(npfine);
|
||||
size_t count = 0;
|
||||
|
||||
for( unsigned i=0; i<gh.get_grid(ilevel)->size(0); ++i )
|
||||
for( unsigned j=0; j<gh.get_grid(ilevel)->size(1); ++j )
|
||||
for( unsigned k=0; k<gh.get_grid(ilevel)->size(2); ++k )
|
||||
if( gh.is_in_mask(ilevel,i,j,k) && !gh.is_refined(ilevel,i,j,k) )
|
||||
{
|
||||
data[count++] = (T) (*gh.get_grid(ilevel))(i,j,k) * velFac;
|
||||
}
|
||||
|
||||
writeHDF5_b( "Velocities", coord, HIGHRES_DM_PARTTYPE, data ); // write fine DM
|
||||
|
||||
if( count != npfine )
|
||||
throw std::runtime_error("Internal consistency error while writing fine DM pos");
|
||||
|
||||
// COARSE: collect velocities and convert to correct units
|
||||
if( levelmax_ != levelmin_ ) // multimass
|
||||
{
|
||||
data = std::vector<T> (npcoarse,0.0);
|
||||
count = 0;
|
||||
|
||||
for( int ilevel=gh.levelmax()-1; ilevel>=(int)gh.levelmin(); --ilevel )
|
||||
for( unsigned i=0; i<gh.get_grid(ilevel)->size(0); ++i )
|
||||
for( unsigned j=0; j<gh.get_grid(ilevel)->size(1); ++j )
|
||||
for( unsigned k=0; k<gh.get_grid(ilevel)->size(2); ++k )
|
||||
if( gh.is_in_mask(ilevel,i,j,k) && !gh.is_refined(ilevel,i,j,k) )
|
||||
{
|
||||
data[count++] = (T) (*gh.get_grid(ilevel))(i,j,k) * velFac;
|
||||
}
|
||||
|
||||
if( count != npcoarse )
|
||||
throw std::runtime_error("Internal consistency error while writing coarse DM pos");
|
||||
|
||||
writeHDF5_b( "Velocities", coord, coarsePartType, data ); // write coarse DM
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
template< typename T >
|
||||
void __write_gas_velocity( int coord, const grid_hierarchy& gh )
|
||||
{
|
||||
countLeafCells(gh);
|
||||
|
||||
std::vector<T> gas_data(npart); // read/write gas at all levels from the gh
|
||||
size_t count = 0;
|
||||
|
||||
for( int ilevel=levelmax_; ilevel>=(int)levelmin_; --ilevel )
|
||||
for( unsigned i=0; i<gh.get_grid(ilevel)->size(0); ++i )
|
||||
for( unsigned j=0; j<gh.get_grid(ilevel)->size(1); ++j )
|
||||
for( unsigned k=0; k<gh.get_grid(ilevel)->size(2); ++k )
|
||||
if( gh.is_in_mask(ilevel,i,j,k) && !gh.is_refined(ilevel,i,j,k) )
|
||||
{
|
||||
gas_data[count++] = (T) (*gh.get_grid(ilevel))(i,j,k) * velFac;
|
||||
}
|
||||
|
||||
if( count != npart )
|
||||
throw std::runtime_error("Internal consistency error while writing GAS pos");
|
||||
|
||||
// calculate modified DM velocities if: multimass and baryons present
|
||||
if( doBaryons && npcoarse )
|
||||
{
|
||||
double facb = omega_b / omega0;
|
||||
double facc = (omega0 - omega_b) / omega0;
|
||||
|
||||
std::vector<T> dm_data(npcoarse);
|
||||
|
||||
writeHDF5_b( "Velocities", coord, coarsePartType, dm_data, true ); // read coarse DM vels
|
||||
|
||||
// overwrite
|
||||
for( size_t i=0; i < npcoarse; i++ )
|
||||
dm_data[i] = facc*dm_data[i] + facb*gas_data[npfine + i];
|
||||
|
||||
writeHDF5_b( "Velocities", coord, coarsePartType, dm_data ); // overwrite coarse DM vels
|
||||
} // dm_data deallocated
|
||||
|
||||
// restrict gas_data to fine only and request write
|
||||
std::vector<T> data( gas_data.begin() + 0, gas_data.begin() + npfine );
|
||||
|
||||
std::vector<T>().swap( gas_data ); // deallocate
|
||||
|
||||
writeHDF5_b( "Velocities", coord, GAS_PARTTYPE, data ); // write highres gas
|
||||
}
|
||||
|
||||
template< typename T >
|
||||
void __write_gas_position( int coord, const grid_hierarchy& gh )
|
||||
{
|
||||
countLeafCells(gh);
|
||||
|
||||
// update header (will actually write only gas at levelmax)
|
||||
hsize_t offset = 0;
|
||||
|
||||
for( unsigned i=0; i < numFiles; i++ ) {
|
||||
hsize_t dims = ceil( npfine / numFiles );
|
||||
if( i == numFiles-1 )
|
||||
dims = npfine - offset;
|
||||
|
||||
nPart[i][GAS_PARTTYPE] = dims;
|
||||
offset += dims;
|
||||
}
|
||||
|
||||
nPartTotal[GAS_PARTTYPE] = npfine;
|
||||
|
||||
std::vector<double> gas_data(npart); // read/write gas at all levels from the gh
|
||||
size_t count = 0;
|
||||
|
||||
double h = 1.0/(1ul<<gh.levelmax());
|
||||
|
||||
for( int ilevel=gh.levelmax(); ilevel>=(int)gh.levelmin(); --ilevel )
|
||||
for( unsigned i=0; i<gh.get_grid(ilevel)->size(0); ++i )
|
||||
for( unsigned j=0; j<gh.get_grid(ilevel)->size(1); ++j )
|
||||
for( unsigned k=0; k<gh.get_grid(ilevel)->size(2); ++k )
|
||||
if( gh.is_in_mask(ilevel,i,j,k) && !gh.is_refined(ilevel,i,j,k) )
|
||||
{
|
||||
double xx[3];
|
||||
gh.cell_pos(ilevel, i, j, k, xx);
|
||||
|
||||
// shift particle positions (this has to be done as the same shift
|
||||
// is used when computing the convolution kernel for SPH baryons)
|
||||
xx[coord] += 0.5*h;
|
||||
|
||||
xx[coord] = (xx[coord] + (*gh.get_grid(ilevel))(i,j,k)) * boxSize;
|
||||
|
||||
gas_data[count++] = xx[coord];
|
||||
}
|
||||
|
||||
if( count != npart )
|
||||
throw std::runtime_error("Internal consistency error while writing coarse DM pos");
|
||||
|
||||
// calculate modified DM coordinates if: multimass and baryons present
|
||||
if( doBaryons && npcoarse )
|
||||
{
|
||||
double facb = omega_b / omega0;
|
||||
double facc = (omega0 - omega_b) / omega0;
|
||||
|
||||
std::vector<T> dm_data(npcoarse);
|
||||
|
||||
writeHDF5_b( "Coordinates", coord, coarsePartType, dm_data, true ); // read coarse DM vels
|
||||
|
||||
// overwrite
|
||||
for( size_t i=0; i < npcoarse; i++ ) {
|
||||
dm_data[i] = facc*dm_data[i] + facb*gas_data[npfine + i];
|
||||
dm_data[i] = fmod( dm_data[i] + boxSize, boxSize ) * posFac;
|
||||
}
|
||||
|
||||
writeHDF5_b( "Coordinates", coord, coarsePartType, dm_data ); // overwrite coarse DM vels
|
||||
}
|
||||
|
||||
// restrict gas_data to fine only and request write
|
||||
//std::vector<float> data( gas_data.begin() + 0, gas_data.begin() + npfine );
|
||||
|
||||
std::vector<T> data(npfine);
|
||||
|
||||
for( size_t i = 0; i < npfine; i++ )
|
||||
data[i] = (T) ( fmod( gas_data[i] + boxSize, boxSize ) * posFac );
|
||||
|
||||
std::vector<double>().swap( gas_data ); // deallocate
|
||||
|
||||
writeHDF5_b( "Coordinates", coord, GAS_PARTTYPE, data ); // write highres gas
|
||||
|
||||
}
|
||||
|
||||
public:
|
||||
arepo_output_plugin( config_file& cf ) : output_plugin( cf )
|
||||
{
|
||||
// ensure that everyone knows we want to do SPH, implies: bsph=1, bbshift=1, decic_baryons=1
|
||||
// -> instead of just writing gas densities (which are here ignored), the gas displacements are also written
|
||||
cf.insertValue("setup","do_SPH","yes");
|
||||
|
||||
// init header and config parameters
|
||||
nPartTotal = std::vector<long long>(NTYPES,0);
|
||||
massTable = std::vector<double>(NTYPES,0.0);
|
||||
|
||||
coarsePartType = cf.getValueSafe<unsigned>("output","arepo_coarsetype",COARSE_DM_DEFAULT_PARTTYPE);
|
||||
UnitLength_in_cm = cf.getValueSafe<double>("output","arepo_unitlength",3.085678e21); // 1.0 kpc
|
||||
UnitMass_in_g = cf.getValueSafe<double>("output","arepo_unitmass",1.989e43); // 1.0e10 solar masses
|
||||
UnitVelocity_in_cm_per_s = cf.getValueSafe<double>("output","arepo_unitvel",1e5); // 1 km/sec
|
||||
|
||||
omega0 = cf.getValue<double>("cosmology","Omega_m");
|
||||
omega_b = cf.getValue<double>("cosmology","Omega_b");
|
||||
omega_L = cf.getValue<double>("cosmology","Omega_L");
|
||||
redshift = cf.getValue<double>("setup","zstart");
|
||||
boxSize = cf.getValue<double>("setup","boxlength");
|
||||
doBaryons = cf.getValueSafe<bool>("setup","baryons",false);
|
||||
useLongIDs = cf.getValueSafe<bool>("output","arepo_longids",false);
|
||||
numFiles = cf.getValueSafe<unsigned>("output","arepo_num_files",1);
|
||||
doublePrec = cf.getValueSafe<bool>("output","arepo_doubleprec",0);
|
||||
|
||||
for( unsigned i=0; i < numFiles; i++ )
|
||||
nPart.push_back( std::vector<unsigned int>(NTYPES,0) );
|
||||
|
||||
// factors which multiply positions and velocities
|
||||
time = 1.0/(1.0+redshift);
|
||||
posFac = 3.085678e24 / UnitLength_in_cm; // MUSIC uses Mpc internally, i.e. posFac=1e3 for kpc output
|
||||
velFac = ( 1.0f / sqrt(time) ) * boxSize;
|
||||
|
||||
// critical density
|
||||
rhoCrit = 27.7519737e-9; // in h^2 1e10 M_sol / kpc^3
|
||||
rhoCrit *= pow(UnitLength_in_cm/3.085678e21, 3.0);
|
||||
rhoCrit *= (1.989e43/UnitMass_in_g);
|
||||
|
||||
// calculate PMGRID suggestion
|
||||
pmgrid = pow(2,levelmin_) * 2; // unigrid
|
||||
gridboost = 1;
|
||||
|
||||
if( levelmin_ != levelmax_ )
|
||||
{
|
||||
double lxref[3], x0ref[3], x1ref[3];
|
||||
double pmgrid_new;
|
||||
|
||||
the_region_generator->get_AABB(x0ref,x1ref,levelmax_); // generalized beyond box
|
||||
for (int i=0; i < 3; i++)
|
||||
lxref[i] = x1ref[i] - x0ref[i];
|
||||
|
||||
// fraction box length of the zoom region
|
||||
lxref[0] = pow( (lxref[0]*lxref[1]*lxref[2]),0.333 );
|
||||
|
||||
pmgrid_new = pow(2,levelmax_) * 2; // to cover entire box at highest resolution
|
||||
pmgrid_new *= lxref[0]; // only need to cover a fraction
|
||||
|
||||
if( (gridboost=round(pmgrid_new/pmgrid)) > 1 )
|
||||
gridboost = pow(2, ceil(log(gridboost)/log(2.0))); // round to nearest, higher power of 2
|
||||
if( gridboost == 0 )
|
||||
gridboost = 1;
|
||||
}
|
||||
|
||||
// calculate Tini for gas
|
||||
hubbleParam = cf.getValue<double>("cosmology","H0")/100.0;
|
||||
|
||||
double astart = 1.0/(1.0+redshift);
|
||||
double h2 = hubbleParam*hubbleParam;
|
||||
double adec = 1.0/( 160.0*pow(omega_b*h2/0.022,2.0/5.0) );
|
||||
double Tcmb0 = 2.726;
|
||||
|
||||
Tini = astart<adec? Tcmb0/astart : Tcmb0/astart/astart*adec;
|
||||
|
||||
// calculate softening suggestion
|
||||
softening = (boxSize * posFac) / pow(2,levelmax_) / 40.0;
|
||||
|
||||
// header and sanity checks
|
||||
if ( !doBaryons )
|
||||
massTable[HIGHRES_DM_PARTTYPE] = omega0 * rhoCrit * pow(boxSize*posFac,3.0)/pow(2,3*levelmax_);
|
||||
else
|
||||
massTable[HIGHRES_DM_PARTTYPE] = (omega0-omega_b) * rhoCrit * pow(boxSize*posFac,3.0)/pow(2,3*levelmax_);
|
||||
|
||||
if ( coarsePartType == GAS_PARTTYPE || coarsePartType == HIGHRES_DM_PARTTYPE)
|
||||
throw std::runtime_error("Error: Specified illegal Arepo particle type for coarse particles.");
|
||||
if ( coarsePartType == STAR_PARTTYPE )
|
||||
LOGWARN("WARNING: Specified coarse particle type will collide with stars if USE_SFR enabled.");
|
||||
|
||||
// create file(s)
|
||||
for( unsigned i=0; i < numFiles; i++ )
|
||||
{
|
||||
std::string filename = fname_;
|
||||
if( numFiles > 1 )
|
||||
{
|
||||
size_t pos = filename.find(".hdf5");
|
||||
if( pos != filename.length()-5 )
|
||||
throw std::runtime_error("Error: Unexpected output filename (doesn't end in .hdf5).");
|
||||
|
||||
std::stringstream s;
|
||||
s << "." << i << ".hdf5";
|
||||
filename.replace(pos, 5, s.str());
|
||||
}
|
||||
|
||||
HDFCreateFile(filename);
|
||||
|
||||
// create particle type groups
|
||||
std::stringstream GrpName;
|
||||
GrpName << "PartType" << HIGHRES_DM_PARTTYPE;
|
||||
|
||||
HDFCreateGroup(filename, GrpName.str().c_str()); // highres or unigrid DM
|
||||
|
||||
if( doBaryons )
|
||||
{
|
||||
GrpName.str("");
|
||||
GrpName << "PartType" << GAS_PARTTYPE;
|
||||
HDFCreateGroup(filename, GrpName.str().c_str()); // gas
|
||||
}
|
||||
|
||||
if( levelmax_ != levelmin_ ) // multimass
|
||||
{
|
||||
GrpName.str("");
|
||||
GrpName << "PartType" << coarsePartType;
|
||||
HDFCreateGroup(filename, GrpName.str().c_str()); // coarse DM
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
~arepo_output_plugin()
|
||||
{ }
|
||||
|
||||
/* ------------------------------------------------------------------------------- */
|
||||
void write_dm_mass( const grid_hierarchy& gh )
|
||||
{
|
||||
if(!doublePrec)
|
||||
__write_dm_mass<float>(gh);
|
||||
else
|
||||
__write_dm_mass<double>(gh);
|
||||
}
|
||||
|
||||
void write_dm_position( int coord, const grid_hierarchy& gh )
|
||||
{
|
||||
if(!doublePrec)
|
||||
__write_dm_position<float>(coord, gh);
|
||||
else
|
||||
__write_dm_position<double>(coord, gh);
|
||||
}
|
||||
|
||||
void write_dm_velocity( int coord, const grid_hierarchy& gh )
|
||||
{
|
||||
if(!doublePrec)
|
||||
__write_dm_velocity<float>(coord, gh);
|
||||
else
|
||||
__write_dm_velocity<double>(coord, gh);
|
||||
}
|
||||
|
||||
void write_dm_density( const grid_hierarchy& gh )
|
||||
{ /* skip */ }
|
||||
|
||||
void write_dm_potential( const grid_hierarchy& gh )
|
||||
{ /* skip */ }
|
||||
|
||||
/* ------------------------------------------------------------------------------- */
|
||||
void write_gas_velocity( int coord, const grid_hierarchy& gh )
|
||||
{
|
||||
if(!doublePrec)
|
||||
__write_gas_velocity<float>(coord, gh);
|
||||
else
|
||||
__write_gas_velocity<double>(coord, gh);
|
||||
}
|
||||
|
||||
void write_gas_position( int coord, const grid_hierarchy& gh )
|
||||
{
|
||||
if(!doublePrec)
|
||||
__write_gas_position<float>(coord, gh);
|
||||
else
|
||||
__write_gas_position<double>(coord, gh);
|
||||
}
|
||||
|
||||
void write_gas_density( const grid_hierarchy& gh )
|
||||
{
|
||||
// if only saving highres gas, then all gas cells have the same initial mass
|
||||
// do not write out densities as we write out displacements
|
||||
if( doBaryons )
|
||||
massTable[GAS_PARTTYPE] = omega_b * rhoCrit * pow(boxSize*posFac,3.0)/pow(2,3*levelmax_);
|
||||
}
|
||||
|
||||
void write_gas_potential( const grid_hierarchy& gh )
|
||||
{ /* skip */ }
|
||||
|
||||
void finalize( void )
|
||||
{
|
||||
// generate and add contiguous IDs for each particle type we have written
|
||||
generateAndWriteIDs();
|
||||
|
||||
std::vector<unsigned int> nPartTotalLW(nPartTotal.size());
|
||||
std::vector<unsigned int> nPartTotalHW(nPartTotal.size());
|
||||
for( size_t i=0; i < nPartTotalHW.size(); i++ ) {
|
||||
nPartTotalHW[i] = (unsigned)( (size_t)nPartTotal[i] >> 32 );
|
||||
nPartTotalLW[i] = (unsigned int)( (size_t)nPartTotal[i] );
|
||||
}
|
||||
|
||||
// output particle counts
|
||||
std::cout << " - Arepo : wrote " << nPartTotAllTypes << " particles..." << std::endl;
|
||||
for( size_t i=0; i < nPartTotal.size(); i++ )
|
||||
std::cout << " type [" << i << "] : " << std::setw(12) << nPartTotal[i] << std::endl;
|
||||
std::cout << std::endl;
|
||||
|
||||
// write final header (some of these fields are required, others are extra info)
|
||||
for( unsigned i=0; i < numFiles; i++ )
|
||||
{
|
||||
std::string filename = fname_;
|
||||
if( numFiles > 1 )
|
||||
{
|
||||
std::stringstream s;
|
||||
s << "." << i << ".hdf5";
|
||||
filename.replace(filename.find(".hdf5"), 5, s.str());
|
||||
|
||||
std::cout << " " << filename;
|
||||
for( size_t j=0; j < nPart[i].size(); j++ )
|
||||
std::cout << " " << std::setw(10) << nPart[i][j];
|
||||
std::cout << std::endl;
|
||||
}
|
||||
|
||||
HDFCreateGroup(filename, "Header");
|
||||
|
||||
HDFWriteGroupAttribute(filename, "Header", "NumPart_ThisFile", nPart[i] );
|
||||
HDFWriteGroupAttribute(filename, "Header", "NumPart_Total", nPartTotalLW );
|
||||
HDFWriteGroupAttribute(filename, "Header", "NumPart_Total_HighWord", nPartTotalHW );
|
||||
HDFWriteGroupAttribute(filename, "Header", "MassTable", massTable );
|
||||
HDFWriteGroupAttribute(filename, "Header", "BoxSize", boxSize );
|
||||
HDFWriteGroupAttribute(filename, "Header", "NumFilesPerSnapshot", numFiles );
|
||||
HDFWriteGroupAttribute(filename, "Header", "Time", time );
|
||||
HDFWriteGroupAttribute(filename, "Header", "Redshift", redshift );
|
||||
HDFWriteGroupAttribute(filename, "Header", "Omega0", omega0 );
|
||||
HDFWriteGroupAttribute(filename, "Header", "OmegaLambda", omega_L );
|
||||
HDFWriteGroupAttribute(filename, "Header", "OmegaBaryon", omega_b );
|
||||
HDFWriteGroupAttribute(filename, "Header", "HubbleParam", hubbleParam );
|
||||
HDFWriteGroupAttribute(filename, "Header", "Flag_Sfr", 0 );
|
||||
HDFWriteGroupAttribute(filename, "Header", "Flag_Cooling", 0 );
|
||||
HDFWriteGroupAttribute(filename, "Header", "Flag_StellarAge", 0 );
|
||||
HDFWriteGroupAttribute(filename, "Header", "Flag_Metals", 0 );
|
||||
HDFWriteGroupAttribute(filename, "Header", "Flag_Feedback", 0 );
|
||||
HDFWriteGroupAttribute(filename, "Header", "Flag_DoublePrecision", (int)doublePrec );
|
||||
HDFWriteGroupAttribute(filename, "Header", "Music_levelmin", levelmin_ );
|
||||
HDFWriteGroupAttribute(filename, "Header", "Music_levelmax", levelmax_ );
|
||||
HDFWriteGroupAttribute(filename, "Header", "Music_levelcounts", levelcounts );
|
||||
HDFWriteGroupAttribute(filename, "Header", "haveBaryons", (int)doBaryons );
|
||||
HDFWriteGroupAttribute(filename, "Header", "longIDs", (int)useLongIDs );
|
||||
HDFWriteGroupAttribute(filename, "Header", "suggested_pmgrid", pmgrid );
|
||||
HDFWriteGroupAttribute(filename, "Header", "suggested_gridboost", gridboost );
|
||||
HDFWriteGroupAttribute(filename, "Header", "suggested_highressoft", softening );
|
||||
HDFWriteGroupAttribute(filename, "Header", "suggested_gas_Tinit", Tini );
|
||||
}
|
||||
|
||||
// give config/parameter file hints
|
||||
if( useLongIDs )
|
||||
std::cout << " - Arepo: Wrote 64bit IDs, enable LONGIDS." << std::endl;
|
||||
if( doublePrec )
|
||||
std::cout << " - Arepo: Double precision ICs, set INPUT_IN_DOUBLEPRECISION." << std::endl;
|
||||
if( NTYPES != 6 )
|
||||
std::cout << " - Arepo: Using [" << NTYPES << "] particle types, set NTYPES to match." << std::endl;
|
||||
if( doBaryons )
|
||||
std::cout << " - Arepo: Wrote high-res gas (only), set REFINEMENT_HIGH_RES_GAS and GENERATE_GAS_IN_ICS with "
|
||||
<< "SPLIT_PARTICLE_TYPE=" << pow(2,coarsePartType) << "." << std::endl;
|
||||
if( levelmax_ != levelmin_ )
|
||||
std::cout << " - Arepo: Have zoom type ICs, set PLACEHIGHRESREGION=" << pow(2,HIGHRES_DM_PARTTYPE)
|
||||
<< " (suggest PMGRID=" << pmgrid << " with GRIDBOOST=" << gridboost << ")." << std::endl;
|
||||
else
|
||||
std::cout << " - Arepo: Have unigrid type ICs (suggest PMGRID=" << pmgrid << ")." << std::endl;
|
||||
if( levelmax_ > levelmin_ + 1 )
|
||||
std::cout << " - Arepo: More than one coarse DM mass using same type, set INDIVIDUAL_GRAVITY_SOFTENING="
|
||||
<< pow(2,coarsePartType) << " (+" << pow(2,STAR_PARTTYPE) << " if including stars)." << std::endl;
|
||||
if( doBaryons )
|
||||
std::cout << " - Arepo: Set initial gas temperature to " << std::fixed << std::setprecision(3) << Tini << " K." << std::endl;
|
||||
std::cout << " - Arepo: Suggest grav softening = " << std::setprecision(3) << softening << " for high res DM." << std::endl;
|
||||
|
||||
}
|
||||
|
||||
};
|
||||
|
||||
namespace{
|
||||
output_plugin_creator_concrete< arepo_output_plugin > creator("arepo");
|
||||
}
|
||||
|
||||
#endif // HAVE_HDF5
|
||||
|
|
@ -1,912 +0,0 @@
|
|||
/*
|
||||
|
||||
output_art.cc - This file is part of MUSIC -
|
||||
a code to generate multi-scale initial conditions
|
||||
for cosmological simulations
|
||||
|
||||
Copyright (C) 2012 Jose Onorbe & Oliver Hahn
|
||||
|
||||
*/
|
||||
#include <stdio.h>
|
||||
#include <unistd.h>
|
||||
#include <string.h>
|
||||
#include <sys/types.h>
|
||||
#include <sys/stat.h>
|
||||
#include <vector>
|
||||
|
||||
#include "output.hh"
|
||||
|
||||
template<typename T>
|
||||
inline T bytereorder(T v )
|
||||
{
|
||||
T rval;
|
||||
(reinterpret_cast<unsigned char*>(&rval))[3] = (reinterpret_cast<unsigned char*>(&v))[0];
|
||||
(reinterpret_cast<unsigned char*>(&rval))[2] = (reinterpret_cast<unsigned char*>(&v))[1];
|
||||
(reinterpret_cast<unsigned char*>(&rval))[1] = (reinterpret_cast<unsigned char*>(&v))[2];
|
||||
(reinterpret_cast<unsigned char*>(&rval))[0] = (reinterpret_cast<unsigned char*>(&v))[3];
|
||||
return rval;
|
||||
}
|
||||
|
||||
|
||||
template< typename T_store=float >
|
||||
class art_output_plugin : public output_plugin
|
||||
{
|
||||
public:
|
||||
bool do_baryons_;
|
||||
bool swap_endianness_;
|
||||
double omegab_, omegam_;
|
||||
double gamma_;
|
||||
double astart_;
|
||||
double zstart_;
|
||||
size_t npcdm_;
|
||||
int hsize_;
|
||||
|
||||
protected:
|
||||
|
||||
enum iofields {
|
||||
id_dm_pos, id_dm_vel, id_gas_pos, id_gas_vel
|
||||
};
|
||||
|
||||
struct header
|
||||
{
|
||||
char head[45];
|
||||
float aexpN; // current expansion factor
|
||||
float aexp0; // initial expansion factor
|
||||
float amplt; // Amplitude of density fluctuations
|
||||
float astep; // Delta a -> time step.
|
||||
// This value is also stored in pt.dat (binary 1 float)
|
||||
// It is recalculated by art for the next steps so just a small value should work
|
||||
int istep; // step (=0 in IC)
|
||||
float partw; // mass of highest res particle.
|
||||
float TINTG; //=0 in IC
|
||||
float EKIN; //SUM 0.5 * m_i*(v_i**2) in code units
|
||||
float EKIN1; //=0 in IC
|
||||
float EKIN2; //=0 in IC
|
||||
float AU0; //=0 in IC
|
||||
float AEU0; //=0 in IC
|
||||
int NROWC; // Number of particles in 1 dim (number of particles per page = NROW**2)
|
||||
int NGRIDC; // Number of cells in 1 dim
|
||||
int nspecies; // number of dm species
|
||||
int Nseed; // random number used ( 0 for MUSIC? or set the random number used in the lowest level?)
|
||||
float Om0; //Omega_m
|
||||
float Oml0; //Omega_L
|
||||
float hubble; //hubble constant h=H/100
|
||||
float Wp5; //
|
||||
float Ocurv; //Omega_k
|
||||
float Omb0; // this parameter only appears in header in hydro runs
|
||||
float wpart[10]; // extras[0-9] particle masses from high res to low res (normalized to low res particle)
|
||||
// Mass of smallest particle=wpart[0]*0m0*2.746e+11*(Box/NGRID)**3 -> Msun/h
|
||||
// Mass of largest particle=wpart[nspecies-1]*0m0*2.746e+11*(Box/NGRID)**3 -> Msun/h
|
||||
int lpart[10]; // extras[10-19] number of particles from high res to low res cumulative!!!
|
||||
//(i.e., lpart[0]=Nhigh res particles; lpart[1]=lpart[0]+N_this_level; etc) so lpart[nspecies-1]=N total
|
||||
float extras[80]; //extras[20-99]
|
||||
//extras[9]=iLblock ->0 in IC
|
||||
//extras[10]=LevMin ->0 in IC
|
||||
//extras[11]=LevSmall ->0 in IC
|
||||
//extras[12]=LevLarge ->0 in IC
|
||||
//extras[13]=Omegab ->0 in IC; fix it?
|
||||
//extras[14]=sig8 ->0 in IC; fix it?
|
||||
//extras[15]=Spslope ->0 in IC; fix it? Slope of the Power spectrum
|
||||
//extras[16]=iDEswtch ->0 in IC; DE Flag=0:LCDM 1:w 2:RP 3:SUGRA
|
||||
//extras[17]=DEw0 ->0 in IC; w0 for DE z=0
|
||||
//extras[18]=DEwprime ->0 in IC; DE parameter
|
||||
//extras[59]= 0 or 1; is used as switch for random numbers generators [do not apply in music use 0?]
|
||||
//extras[60]= lux - level of luxury [do not apply in music use 0?]
|
||||
//extras[79]=Lbox (Mpc/h)
|
||||
|
||||
};
|
||||
|
||||
struct ptf
|
||||
{
|
||||
float astep;
|
||||
};
|
||||
|
||||
header header_;
|
||||
ptf ptf_;
|
||||
std::string fname;
|
||||
size_t np_fine_gas_, np_fine_dm_, np_coarse_dm_;
|
||||
size_t block_buf_size_;
|
||||
size_t npartmax_;
|
||||
|
||||
double YHe_;
|
||||
|
||||
|
||||
// helper class to read temp files
|
||||
class pistream : public std::ifstream
|
||||
{
|
||||
public:
|
||||
pistream (std::string fname, size_t npart )
|
||||
: std::ifstream( fname.c_str(), std::ios::binary )
|
||||
{
|
||||
size_t blk;
|
||||
|
||||
if( !this->good() )
|
||||
{
|
||||
LOGERR("Could not open buffer file in ART output plug-in");
|
||||
throw std::runtime_error("Could not open buffer file in ART output plug-in");
|
||||
}
|
||||
|
||||
this->read( (char*)&blk, sizeof(size_t) );
|
||||
|
||||
if( blk != (size_t)(npart*sizeof(T_store)) )
|
||||
{
|
||||
LOGERR("Internal consistency error in ART output plug-in");
|
||||
LOGERR("Expected %d bytes in temp file but found %d",npart*(unsigned)sizeof(T_store),blk);
|
||||
throw std::runtime_error("Internal consistency error in ART output plug-in");
|
||||
}
|
||||
}
|
||||
|
||||
pistream ()
|
||||
{
|
||||
|
||||
}
|
||||
|
||||
void open(std::string fname, size_t npart )
|
||||
{
|
||||
std::ifstream::open( fname.c_str(), std::ios::binary );
|
||||
size_t blk;
|
||||
|
||||
if( !this->good() )
|
||||
{
|
||||
LOGERR("Could not open buffer file \'%s\' in ART output plug-in",fname.c_str());
|
||||
throw std::runtime_error("Could not open buffer file in ART output plug-in");
|
||||
}
|
||||
|
||||
this->read( (char*)&blk, sizeof(size_t) );
|
||||
|
||||
if( blk != (size_t)(npart*sizeof(T_store)) )
|
||||
{
|
||||
LOGERR("Internal consistency error in ART output plug-in");
|
||||
LOGERR("Expected %d bytes in temp file but found %d",npart*(unsigned)sizeof(T_store),blk);
|
||||
throw std::runtime_error("Internal consistency error in ART output plug-in");
|
||||
}
|
||||
}
|
||||
};
|
||||
|
||||
|
||||
// non-public member functions
|
||||
void write_header_file( void ) //PMcrd.DAT
|
||||
{
|
||||
|
||||
std::string fout;
|
||||
if(do_baryons_)
|
||||
fout = "/PMcrdIC.DAT";
|
||||
else
|
||||
fout = "/PMcrd.DAT";
|
||||
std::string partfname = fname_ + fout;
|
||||
std::ofstream ofs( partfname.c_str(), std::ios::trunc );
|
||||
//ofs.open(fname_.c_str(), std::ios::binary|std::ios::trunc );
|
||||
header this_header(header_);
|
||||
//Should be 529 in a dm only run; 533 in a baryon run
|
||||
//but not working for alignment so it must be written one by one:
|
||||
int blksize = hsize_;
|
||||
if( swap_endianness_ )
|
||||
{
|
||||
LOGINFO("ART : swap_endianness option enabled");
|
||||
blksize = bytereorder( blksize );
|
||||
this_header.aexpN = bytereorder( this_header.aexpN );
|
||||
this_header.aexp0 = bytereorder( this_header.aexp0 );
|
||||
this_header.amplt = bytereorder( this_header.amplt );
|
||||
this_header.astep = bytereorder( this_header.astep );
|
||||
this_header.istep = bytereorder( this_header.istep );
|
||||
this_header.partw = bytereorder( this_header.partw );
|
||||
this_header.TINTG = bytereorder( this_header.TINTG );
|
||||
this_header.EKIN = bytereorder( this_header.EKIN );
|
||||
this_header.EKIN1 = bytereorder( this_header.EKIN1 );
|
||||
this_header.EKIN2 = bytereorder( this_header.EKIN2 );
|
||||
this_header.AEU0 = bytereorder( this_header.AEU0 );
|
||||
this_header.AEU0 = bytereorder( this_header.AEU0 );
|
||||
this_header.NROWC = bytereorder( this_header.NROWC );
|
||||
this_header.NGRIDC = bytereorder( this_header.NGRIDC );
|
||||
this_header.nspecies = bytereorder( this_header.nspecies );
|
||||
this_header.Nseed = bytereorder( this_header.Nseed );
|
||||
this_header.Om0 = bytereorder( this_header.Om0);
|
||||
this_header.Oml0 = bytereorder( this_header.Oml0 );
|
||||
this_header.hubble = bytereorder( this_header.hubble );
|
||||
this_header.Wp5 = bytereorder( this_header.Wp5 );
|
||||
this_header.Ocurv = bytereorder( this_header.Ocurv );
|
||||
this_header.Omb0 = bytereorder( this_header.Omb0 );
|
||||
for( int i=0; i<10; ++i )
|
||||
{
|
||||
this_header.wpart[i] = bytereorder( this_header.wpart[i] );
|
||||
this_header.lpart[i] = bytereorder( this_header.lpart[i] );
|
||||
}
|
||||
for( int i=0; i<80; ++i )
|
||||
{
|
||||
this_header.extras[i] = bytereorder( this_header.extras[i] );
|
||||
}
|
||||
}
|
||||
ofs.write( (char *)&blksize, sizeof(int) );
|
||||
//ofs.write( (char *)&this_header,sizeof(header)); //Not working because struct aligment, so:
|
||||
ofs.write( (char *)&this_header.head,sizeof(this_header.head));
|
||||
ofs.write( (char *)&this_header.aexpN,sizeof(this_header.aexpN));
|
||||
ofs.write( (char *)&this_header.aexp0,sizeof(this_header.aexp0));
|
||||
ofs.write( (char *)&this_header.amplt,sizeof(this_header.amplt));
|
||||
ofs.write( (char *)&this_header.astep,sizeof(this_header.astep));
|
||||
ofs.write( (char *)&this_header.istep,sizeof(this_header.istep));
|
||||
ofs.write( (char *)&this_header.partw,sizeof(this_header.partw));
|
||||
ofs.write( (char *)&this_header.TINTG,sizeof(this_header.TINTG));
|
||||
ofs.write( (char *)&this_header.EKIN,sizeof(this_header.EKIN));
|
||||
ofs.write( (char *)&this_header.EKIN1,sizeof(this_header.EKIN1));
|
||||
ofs.write( (char *)&this_header.EKIN2,sizeof(this_header.EKIN2));
|
||||
ofs.write( (char *)&this_header.AEU0,sizeof(this_header.AEU0));
|
||||
ofs.write( (char *)&this_header.AEU0,sizeof(this_header.AEU0));
|
||||
ofs.write( (char *)&this_header.NROWC,sizeof(this_header.NROWC));
|
||||
ofs.write( (char *)&this_header.NGRIDC,sizeof(this_header.NGRIDC));
|
||||
ofs.write( (char *)&this_header.nspecies,sizeof(this_header.nspecies));
|
||||
ofs.write( (char *)&this_header.Nseed,sizeof(this_header.Nseed));
|
||||
ofs.write( (char *)&this_header.Om0,sizeof(this_header.Om0));
|
||||
ofs.write( (char *)&this_header.Oml0,sizeof(this_header.Oml0));
|
||||
ofs.write( (char *)&this_header.hubble,sizeof(this_header.hubble));
|
||||
ofs.write( (char *)&this_header.Wp5,sizeof(this_header.Wp5));
|
||||
ofs.write( (char *)&this_header.Ocurv,sizeof(this_header.Ocurv));
|
||||
ofs.write( (char *)&this_header.wpart,sizeof(this_header.wpart));
|
||||
ofs.write( (char *)&this_header.lpart,sizeof(this_header.lpart));
|
||||
ofs.write( (char *)&this_header.extras,sizeof(this_header.extras));
|
||||
ofs.write( (char *)&blksize, sizeof(int) );
|
||||
ofs.close();
|
||||
LOGINFO("ART : done writing header file.");
|
||||
}
|
||||
|
||||
void write_pt_file( void ) //pt.dat
|
||||
{
|
||||
std::string partfname = fname_ + "/pt.dat";
|
||||
std::ofstream ofs( partfname.c_str(), std::ios::trunc );
|
||||
//ofs.open(fname_.c_str(), std::ios::binary|std::ios::trunc );
|
||||
ptf this_ptf(ptf_);
|
||||
int blksize = sizeof(ptf); //4
|
||||
if( swap_endianness_ )
|
||||
{
|
||||
blksize = bytereorder( blksize );
|
||||
this_ptf = bytereorder( this_ptf );
|
||||
}
|
||||
ofs.write( (char *)&blksize, sizeof(int) );
|
||||
ofs.write( (char *)&this_ptf,sizeof(ptf));
|
||||
ofs.write( (char *)&blksize, sizeof(int) );
|
||||
ofs.close();
|
||||
LOGINFO("ART : done writing pt file.");
|
||||
}
|
||||
|
||||
|
||||
void adjust_buf_endianness( T_store* buf )
|
||||
{
|
||||
if( swap_endianness_ )
|
||||
{
|
||||
for( size_t i=0; i<block_buf_size_; ++i )
|
||||
buf[i] = bytereorder<T_store>( buf[i] );
|
||||
}
|
||||
}
|
||||
|
||||
/*
|
||||
The direct format write the particle data in pages. Each page of particles is read into a common block,
|
||||
which has the structure: X(Npage),Y(Npage),Z(Npage),Vx(Npage),Vy(Npage),Vz(Npage).
|
||||
There are NO Fortran size blocks pre or after these blocks!!
|
||||
|
||||
The number of particles in each page (Npage) is Npage = Nrow**2; Npages = (N_particles -1)/NPAGE +1
|
||||
so in last page sometimes can be tricky (zooms): N_in_last=N_particles -NPAGE*(Npages-1)
|
||||
But keep in mind that ART expects all pages to be written in full regarding of the actual number of particles
|
||||
you care about.
|
||||
|
||||
*/
|
||||
void assemble_DM_file( void ) //PMcrs0.DAT
|
||||
{
|
||||
// file name
|
||||
|
||||
std::string fout;
|
||||
if(do_baryons_)
|
||||
fout = "/PMcrs0IC.DAT";
|
||||
else
|
||||
fout = "/PMcrs0.DAT";
|
||||
|
||||
std::string partfname = fname_ + fout;
|
||||
std::ofstream ofs( partfname.c_str(), std::ios::trunc );
|
||||
|
||||
// generate all temp file names
|
||||
char fnx[256],fny[256],fnz[256],fnvx[256],fnvy[256],fnvz[256];
|
||||
sprintf( fnx, "___ic_temp_%05d.bin", 100*id_dm_pos+0 );
|
||||
sprintf( fny, "___ic_temp_%05d.bin", 100*id_dm_pos+1 );
|
||||
sprintf( fnz, "___ic_temp_%05d.bin", 100*id_dm_pos+2 );
|
||||
sprintf( fnvx, "___ic_temp_%05d.bin", 100*id_dm_vel+0 );
|
||||
sprintf( fnvy, "___ic_temp_%05d.bin", 100*id_dm_vel+1 );
|
||||
sprintf( fnvz, "___ic_temp_%05d.bin", 100*id_dm_vel+2 );
|
||||
|
||||
// create buffers for temporary data
|
||||
T_store *tmp1, *tmp2, *tmp3, *tmp4, *tmp5, *tmp6;
|
||||
|
||||
tmp1 = new T_store[block_buf_size_];
|
||||
tmp2 = new T_store[block_buf_size_];
|
||||
tmp3 = new T_store[block_buf_size_];
|
||||
tmp4 = new T_store[block_buf_size_];
|
||||
tmp5 = new T_store[block_buf_size_];
|
||||
tmp6 = new T_store[block_buf_size_];
|
||||
|
||||
|
||||
// read in the data from the temporary files in slabs and write it to the output file
|
||||
size_t npleft, n2read;
|
||||
size_t npcdm = npcdm_;
|
||||
|
||||
LOGINFO("writing DM data to ART format file");
|
||||
//ofs.open(fname_.c_str(), std::ios::binary|std::ios::trunc );
|
||||
|
||||
pistream ifs_x, ifs_y, ifs_z, ifs_vx, ifs_vy, ifs_vz;
|
||||
|
||||
ifs_x.open( fnx, npcdm );
|
||||
ifs_y.open( fny, npcdm );
|
||||
ifs_z.open( fnz, npcdm );
|
||||
ifs_vx.open( fnvx, npcdm );
|
||||
ifs_vy.open( fnvy, npcdm );
|
||||
ifs_vz.open( fnvz, npcdm );
|
||||
|
||||
npleft = npcdm;
|
||||
n2read = std::min(block_buf_size_,npleft);
|
||||
while( n2read > 0 )
|
||||
{
|
||||
// To make sure last page in zooms have 0s in non-relevant values
|
||||
// NOT MANDATORY. Can be commented if makes things slow
|
||||
// but I do not like the idea of writting data in the file
|
||||
// that could be interpreted as real.
|
||||
if(n2read<block_buf_size_)
|
||||
{
|
||||
for (int i = 0; i < int(block_buf_size_); i++)
|
||||
{
|
||||
tmp1[i]=0.0;tmp2[i]=0.0;tmp3[i]=0.0;tmp4[i]=0.0;
|
||||
tmp5[i]=0.0;tmp6[i]=0.0;
|
||||
}
|
||||
}
|
||||
ifs_x.read( reinterpret_cast<char*>(&tmp1[0]), n2read*sizeof(T_store) );
|
||||
ifs_y.read( reinterpret_cast<char*>(&tmp2[0]), n2read*sizeof(T_store) );
|
||||
ifs_z.read( reinterpret_cast<char*>(&tmp3[0]), n2read*sizeof(T_store) );
|
||||
ifs_vx.read( reinterpret_cast<char*>(&tmp4[0]), n2read*sizeof(T_store) );
|
||||
ifs_vy.read( reinterpret_cast<char*>(&tmp5[0]), n2read*sizeof(T_store) );
|
||||
ifs_vz.read( reinterpret_cast<char*>(&tmp6[0]), n2read*sizeof(T_store) );
|
||||
|
||||
adjust_buf_endianness( tmp1 );
|
||||
adjust_buf_endianness( tmp2 );
|
||||
adjust_buf_endianness( tmp3 );
|
||||
adjust_buf_endianness( tmp4 );
|
||||
adjust_buf_endianness( tmp5 );
|
||||
adjust_buf_endianness( tmp6 );
|
||||
|
||||
ofs.write( reinterpret_cast<char*>(&tmp1[0]), block_buf_size_*sizeof(T_store) );
|
||||
ofs.write( reinterpret_cast<char*>(&tmp2[0]), block_buf_size_*sizeof(T_store) );
|
||||
ofs.write( reinterpret_cast<char*>(&tmp3[0]), block_buf_size_*sizeof(T_store) );
|
||||
ofs.write( reinterpret_cast<char*>(&tmp4[0]), block_buf_size_*sizeof(T_store) );
|
||||
ofs.write( reinterpret_cast<char*>(&tmp5[0]), block_buf_size_*sizeof(T_store) );
|
||||
ofs.write( reinterpret_cast<char*>(&tmp6[0]), block_buf_size_*sizeof(T_store) );
|
||||
|
||||
npleft -= n2read;
|
||||
n2read = std::min( block_buf_size_,npleft );
|
||||
}
|
||||
|
||||
ifs_x.close();
|
||||
ifs_y.close();
|
||||
ifs_z.close();
|
||||
ifs_vx.close();
|
||||
ifs_vy.close();
|
||||
ifs_vz.close();
|
||||
ofs.close();
|
||||
|
||||
// clean up temp files
|
||||
unlink(fnx);
|
||||
unlink(fny);
|
||||
unlink(fnz);
|
||||
unlink(fnvx);
|
||||
unlink(fnvy);
|
||||
unlink(fnvz);
|
||||
|
||||
delete[] tmp1;
|
||||
delete[] tmp2;
|
||||
delete[] tmp3;
|
||||
delete[] tmp4;
|
||||
delete[] tmp5;
|
||||
delete[] tmp6;
|
||||
|
||||
LOGINFO("ART : done writing DM file.");
|
||||
|
||||
}
|
||||
|
||||
|
||||
/*
|
||||
ART users currently create the baryon grid structure from the dark matter data file.
|
||||
Therefore they have decided that the best way to implement baryons for ART in MUSIC was
|
||||
by creating a file with the same dm format but using the baryon displacements and velocities.
|
||||
From this file they will create the actual grid suign their tools.
|
||||
|
||||
So here we have just to re-create the dark matter file format but using the baryon data.
|
||||
*/
|
||||
void assemble_gas_file( void ) //PMcrs0_GAS.DAT
|
||||
{
|
||||
// file name
|
||||
std::string partfname = fname_ + "/PMcrs0_GAS.DAT";
|
||||
std::ofstream ofs( partfname.c_str(), std::ios::trunc );
|
||||
|
||||
// generate all temp file names
|
||||
char fnx[256],fny[256],fnz[256],fnvx[256],fnvy[256],fnvz[256];
|
||||
sprintf( fnx, "___ic_temp_%05d.bin", 100*id_gas_pos+0 );
|
||||
sprintf( fny, "___ic_temp_%05d.bin", 100*id_gas_pos+1 );
|
||||
sprintf( fnz, "___ic_temp_%05d.bin", 100*id_gas_pos+2 );
|
||||
sprintf( fnvx, "___ic_temp_%05d.bin", 100*id_gas_vel+0 );
|
||||
sprintf( fnvy, "___ic_temp_%05d.bin", 100*id_gas_vel+1 );
|
||||
sprintf( fnvz, "___ic_temp_%05d.bin", 100*id_gas_vel+2 );
|
||||
|
||||
// create buffers for temporary data
|
||||
T_store *tmp1, *tmp2, *tmp3, *tmp4, *tmp5, *tmp6;
|
||||
|
||||
tmp1 = new T_store[block_buf_size_];
|
||||
tmp2 = new T_store[block_buf_size_];
|
||||
tmp3 = new T_store[block_buf_size_];
|
||||
tmp4 = new T_store[block_buf_size_];
|
||||
tmp5 = new T_store[block_buf_size_];
|
||||
tmp6 = new T_store[block_buf_size_];
|
||||
|
||||
|
||||
// read in the data from the temporary files in slabs and write it to the output file
|
||||
size_t npleft, n2read;
|
||||
size_t npcgas = npcdm_; // # of gas elemets should be equal to # of dm elements
|
||||
|
||||
LOGINFO("writing gas data to ART format file");
|
||||
//ofs.open(fname_.c_str(), std::ios::binary|std::ios::trunc );
|
||||
|
||||
pistream ifs_x, ifs_y, ifs_z, ifs_vx, ifs_vy, ifs_vz;
|
||||
|
||||
|
||||
ifs_x.open( fnx, npcgas );
|
||||
ifs_y.open( fny, npcgas );
|
||||
ifs_z.open( fnz, npcgas );
|
||||
ifs_vx.open( fnvx, npcgas );
|
||||
ifs_vy.open( fnvy, npcgas );
|
||||
ifs_vz.open( fnvz, npcgas );
|
||||
|
||||
npleft = npcgas;
|
||||
n2read = std::min(block_buf_size_,npleft);
|
||||
while( n2read > 0 )
|
||||
{
|
||||
// To make sure last page in zooms have 0s in non-relevant values
|
||||
// NOT MANDATORY. Can be commented if makes things slow
|
||||
// but I do not like the idea of writting data in the file
|
||||
// that could be interpreted as real.
|
||||
if(n2read<block_buf_size_)
|
||||
{
|
||||
for (int i = 0; i < int(block_buf_size_); i++)
|
||||
{
|
||||
tmp1[i]=0.0;tmp2[i]=0.0;tmp3[i]=0.0;tmp4[i]=0.0;
|
||||
tmp5[i]=0.0;tmp6[i]=0.0;
|
||||
}
|
||||
}
|
||||
ifs_x.read( reinterpret_cast<char*>(&tmp1[0]), n2read*sizeof(T_store) );
|
||||
ifs_y.read( reinterpret_cast<char*>(&tmp2[0]), n2read*sizeof(T_store) );
|
||||
ifs_z.read( reinterpret_cast<char*>(&tmp3[0]), n2read*sizeof(T_store) );
|
||||
ifs_vx.read( reinterpret_cast<char*>(&tmp4[0]), n2read*sizeof(T_store) );
|
||||
ifs_vy.read( reinterpret_cast<char*>(&tmp5[0]), n2read*sizeof(T_store) );
|
||||
ifs_vz.read( reinterpret_cast<char*>(&tmp6[0]), n2read*sizeof(T_store) );
|
||||
|
||||
adjust_buf_endianness( tmp1 );
|
||||
adjust_buf_endianness( tmp2 );
|
||||
adjust_buf_endianness( tmp3 );
|
||||
adjust_buf_endianness( tmp4 );
|
||||
adjust_buf_endianness( tmp5 );
|
||||
adjust_buf_endianness( tmp6 );
|
||||
|
||||
ofs.write( reinterpret_cast<char*>(&tmp1[0]), block_buf_size_*sizeof(T_store) );
|
||||
ofs.write( reinterpret_cast<char*>(&tmp2[0]), block_buf_size_*sizeof(T_store) );
|
||||
ofs.write( reinterpret_cast<char*>(&tmp3[0]), block_buf_size_*sizeof(T_store) );
|
||||
ofs.write( reinterpret_cast<char*>(&tmp4[0]), block_buf_size_*sizeof(T_store) );
|
||||
ofs.write( reinterpret_cast<char*>(&tmp5[0]), block_buf_size_*sizeof(T_store) );
|
||||
ofs.write( reinterpret_cast<char*>(&tmp6[0]), block_buf_size_*sizeof(T_store) );
|
||||
|
||||
npleft -= n2read;
|
||||
n2read = std::min( block_buf_size_,npleft );
|
||||
}
|
||||
|
||||
ifs_x.close();
|
||||
ifs_y.close();
|
||||
ifs_z.close();
|
||||
ifs_vx.close();
|
||||
ifs_vy.close();
|
||||
ifs_vz.close();
|
||||
ofs.close();
|
||||
|
||||
// clean up temp files
|
||||
unlink(fnx);
|
||||
unlink(fny);
|
||||
unlink(fnz);
|
||||
unlink(fnvx);
|
||||
unlink(fnvy);
|
||||
unlink(fnvz);
|
||||
|
||||
delete[] tmp1;
|
||||
delete[] tmp2;
|
||||
delete[] tmp3;
|
||||
delete[] tmp4;
|
||||
delete[] tmp5;
|
||||
delete[] tmp6;
|
||||
|
||||
LOGINFO("ART : done writing gas file.");
|
||||
// Temperature
|
||||
const double Tcmb0 = 2.726;
|
||||
const double h2 = header_.hubble*header_.hubble;
|
||||
const double adec = 1.0/(160.*pow(omegab_*h2/0.022,2.0/5.0));
|
||||
const double Tini = astart_<adec? Tcmb0/astart_ : Tcmb0/astart_/astart_*adec;
|
||||
const double mu = (Tini>1.e4) ? 4.0/(8.-5.*YHe_) : 4.0/(1.+3.*(1.-YHe_));
|
||||
LOGINFO("ART : set initial gas temperature to %.3f K (%.3f K/mu)",Tini, Tini/mu);
|
||||
|
||||
|
||||
}
|
||||
|
||||
public:
|
||||
|
||||
|
||||
explicit art_output_plugin ( config_file& cf )
|
||||
: output_plugin( cf )
|
||||
{
|
||||
if( mkdir( fname_.c_str(), 0777 ) );
|
||||
|
||||
do_baryons_ = cf.getValueSafe<bool>("setup","baryons",false);
|
||||
// We need to say that we want to do SPH for baryons
|
||||
// because if not MUSIC does not calculate/write gas positions
|
||||
cf.insertValue("setup","do_SPH","yes");
|
||||
// header size (alignment problem)
|
||||
hsize_ = 529; // dm & hydro run
|
||||
|
||||
omegab_ = cf.getValueSafe<double>("cosmology","Omega_b",0.0);
|
||||
omegam_ = cf.getValue<double>("cosmology","Omega_m");
|
||||
zstart_ = cf.getValue<double>("setup","zstart");
|
||||
astart_ = 1.0/(1.0+zstart_);
|
||||
|
||||
|
||||
swap_endianness_ = cf.getValueSafe<bool>("output","art_swap_endian",true);
|
||||
|
||||
int levelmin = cf.getValue<unsigned>("setup","levelmin");
|
||||
int levelmax = cf.getValue<unsigned>("setup","levelmax");
|
||||
block_buf_size_ = (size_t) (pow(pow(2,levelmax),2)); //Npage=nrow^2; Number of particles in each page
|
||||
|
||||
YHe_ = cf.getValueSafe<double>("cosmology","YHe",0.248);
|
||||
gamma_ = cf.getValueSafe<double>("cosmology","gamma",5.0/3.0);
|
||||
// Set header
|
||||
std::string thead;
|
||||
thead=cf.getValueSafe<std::string>("output","header","ICs generated using MUSIC");
|
||||
strcpy(header_.head,thead.c_str()); // text for the header; any easy way to add also the version?
|
||||
std::string ws = " "; // Filling with blanks. Any better way?
|
||||
for (int i=thead.size(); i<45;i++)
|
||||
{
|
||||
header_.head[i]=ws[0];
|
||||
}
|
||||
header_.aexpN = astart_;
|
||||
header_.aexp0 = header_.aexpN;
|
||||
header_.amplt = 0.0; // Amplitude of density fluctuations
|
||||
header_.astep = cf.getValue<double>("output","astep"); // Seems that this must also be in the config file
|
||||
ptf_.astep=header_.astep; // to write pt file
|
||||
header_.istep = 0; // step (=0 in IC)
|
||||
header_.partw = 0.0; // mass of highest res particle. SEE BELOW
|
||||
header_.TINTG = 0; //=0 in IC
|
||||
header_.EKIN = 0.0; //SUM 0.5 * m_i*(v_i**2) in code units. Seems that 0 is ok for ICs
|
||||
header_.EKIN1 = 0; //=0 in IC
|
||||
header_.EKIN2 = 0; //=0 in IC
|
||||
header_.AU0 = 0; //=0 in IC
|
||||
header_.AEU0 = 0; //=0 in IC
|
||||
header_.NROWC = (int) pow(2,levelmax); // Number of particles in 1 dim (number of particles per page = NROW**2)
|
||||
header_.NGRIDC = (int) pow(2,levelmin); // Number of cells in 1 dim
|
||||
header_.nspecies = 0; // number of dm species
|
||||
for( int ilevel=levelmax; ilevel>=(int)levelmin; --ilevel )
|
||||
{
|
||||
header_.nspecies+=1;
|
||||
}
|
||||
//header_.partw SEE BELOW
|
||||
|
||||
header_.Nseed = 0; // random number used ( 0 for MUSIC? or set the random number used in the lowest level?)
|
||||
header_.Om0 = cf.getValue<double>("cosmology","Omega_m"); //Omega_m
|
||||
header_.Oml0 = cf.getValue<double>("cosmology","Omega_L"); //Omega_L
|
||||
header_.hubble = cf.getValue<double>("cosmology","H0")/100; //hubble constant h=H/100
|
||||
header_.Wp5 = 0.0; // 0.0
|
||||
header_.Ocurv = 1.0 - header_.Oml0 - header_.Om0; //
|
||||
header_.Omb0 = cf.getValue<double>("cosmology","Omega_b");; // this parameter only appears in header in hydro runs
|
||||
for (int i=0;i<10;i++)
|
||||
{
|
||||
header_.wpart[i] = 0.0; // extras[0-9] part. masses from high res to low res (normalized to low res particle)
|
||||
header_.lpart[i] = 0; // extras[10-19] # particles from high res to low res cumulative!!!
|
||||
}
|
||||
for (int i=0;i<header_.nspecies;i++)
|
||||
{
|
||||
header_.wpart[i] = 1.0/pow(8.0,(header_.nspecies-i-1)); //from high res to lo res // 8 should be changed for internal variable?
|
||||
}
|
||||
header_.partw = header_.wpart[0]; // mass of highest res particle.
|
||||
for (int i=0;i<80;i++)
|
||||
{
|
||||
header_.extras[i] = 0.0; //extras[20-99]
|
||||
}
|
||||
header_.extras[13] = cf.getValueSafe<double>("cosmology","Omega_b",0.0);
|
||||
header_.extras[14] = cf.getValue<double>("cosmology","sigma_8");
|
||||
header_.extras[15] = cf.getValue<double>("cosmology","nspec"); //Slope of the Power spectrum
|
||||
header_.extras[79] = cf.getValue<double>("setup","boxlength");
|
||||
|
||||
LOGINFO("ART : done header info.");
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
void write_dm_mass( const grid_hierarchy& gh )
|
||||
{
|
||||
|
||||
//... write data for dark matter mass......
|
||||
// This is not needed for ART
|
||||
}
|
||||
|
||||
void write_dm_position( int coord, const grid_hierarchy& gh )
|
||||
{
|
||||
size_t nptot = gh.count_leaf_cells(gh.levelmin(), gh.levelmax());
|
||||
//... store all the meta data about the grid hierarchy in header variables
|
||||
npcdm_ = nptot;
|
||||
for (int i=0;i<header_.nspecies;i++)
|
||||
{
|
||||
header_.lpart[i] = gh.count_leaf_cells(gh.levelmax()-i, gh.levelmax()); //cumulative!!
|
||||
}
|
||||
|
||||
// Now, let us write the dm particle info
|
||||
std::vector<T_store> temp_data;
|
||||
temp_data.reserve( block_buf_size_ );
|
||||
|
||||
|
||||
//coordinates are in the range 1 - (NGRID+1)
|
||||
// so scale factor is scaleX = Box/NGRID -> to Mpc/h (Box in Mpc/h)
|
||||
double xfac = (double) header_.NGRIDC;
|
||||
|
||||
char temp_fname[256];
|
||||
sprintf( temp_fname, "___ic_temp_%05d.bin", 100*id_dm_pos+coord );
|
||||
std::ofstream ofs_temp( temp_fname, std::ios::binary|std::ios::trunc );
|
||||
|
||||
size_t blksize = sizeof(T_store)*nptot;
|
||||
ofs_temp.write( (char *)&blksize, sizeof(size_t) );
|
||||
|
||||
size_t nwritten = 0;
|
||||
for( int ilevel=gh.levelmax(); ilevel>=(int)gh.levelmin(); --ilevel )
|
||||
for( unsigned i=0; i<gh.get_grid(ilevel)->size(0); ++i )
|
||||
for( unsigned j=0; j<gh.get_grid(ilevel)->size(1); ++j )
|
||||
for( unsigned k=0; k<gh.get_grid(ilevel)->size(2); ++k )
|
||||
if( gh.is_in_mask(ilevel,i,j,k) && !gh.is_refined(ilevel,i,j,k) )
|
||||
{
|
||||
double xx[3];
|
||||
gh.cell_pos(ilevel, i, j, k, xx);
|
||||
|
||||
xx[coord] = fmod( (xx[coord]+(*gh.get_grid(ilevel))(i,j,k)) + 1.0, 1.0 ) ;
|
||||
xx[coord] = (xx[coord]*xfac)+1.0;
|
||||
//xx[coord] = ((xx[coord]+(*gh.get_grid(ilevel))(i,j,k)));
|
||||
|
||||
if( temp_data.size() < block_buf_size_ )
|
||||
temp_data.push_back( xx[coord] );
|
||||
else
|
||||
{
|
||||
ofs_temp.write( (char*)&temp_data[0], sizeof(T_store)*block_buf_size_ );
|
||||
nwritten += block_buf_size_;
|
||||
temp_data.clear();
|
||||
temp_data.push_back( xx[coord] );
|
||||
}
|
||||
}
|
||||
|
||||
if( temp_data.size() > 0 )
|
||||
{
|
||||
ofs_temp.write( (char*)&temp_data[0], sizeof(T_store)*temp_data.size() );
|
||||
nwritten += temp_data.size();
|
||||
}
|
||||
|
||||
if( nwritten != nptot )
|
||||
throw std::runtime_error("Internal consistency error while writing temporary file for positions");
|
||||
|
||||
//... dump to temporary file
|
||||
ofs_temp.write( (char *)&blksize, sizeof(size_t) );
|
||||
|
||||
if( ofs_temp.bad() )
|
||||
throw std::runtime_error("I/O error while writing temporary file for positions");
|
||||
|
||||
ofs_temp.close();
|
||||
}
|
||||
|
||||
void write_dm_velocity( int coord, const grid_hierarchy& gh )
|
||||
{
|
||||
size_t nptot = gh.count_leaf_cells(gh.levelmin(), gh.levelmax());
|
||||
|
||||
std::vector<T_store> temp_data;
|
||||
temp_data.reserve( block_buf_size_ );
|
||||
|
||||
//In ART velocities are P = a_expansion*V_pec/(x_0H_0)
|
||||
// where x_0 = comoving cell_size=Box/Ngrid;H_0 = Hubble at z=0
|
||||
// so scale factor to physical km/s is convV= BoxV/AEXPN/NGRID
|
||||
// (BoxV is Box*100; aexpn=current expansion factor)
|
||||
//internal units of MUSIC: To km/s just multiply by Lbox
|
||||
double vfac = (header_.aexpN*header_.NGRIDC)/(100.0);
|
||||
|
||||
char temp_fname[256];
|
||||
sprintf( temp_fname, "___ic_temp_%05d.bin", 100*id_dm_vel+coord );
|
||||
std::ofstream ofs_temp( temp_fname, std::ios::binary|std::ios::trunc );
|
||||
|
||||
size_t blksize = sizeof(T_store)*nptot;
|
||||
ofs_temp.write( (char *)&blksize, sizeof(size_t) );
|
||||
|
||||
size_t nwritten = 0;
|
||||
for( int ilevel=gh.levelmax(); ilevel>=(int)gh.levelmin(); --ilevel )
|
||||
for( unsigned i=0; i<gh.get_grid(ilevel)->size(0); ++i )
|
||||
for( unsigned j=0; j<gh.get_grid(ilevel)->size(1); ++j )
|
||||
for( unsigned k=0; k<gh.get_grid(ilevel)->size(2); ++k )
|
||||
if( gh.is_in_mask(ilevel,i,j,k) && !gh.is_refined(ilevel,i,j,k) )
|
||||
{
|
||||
if( temp_data.size() < block_buf_size_ )
|
||||
temp_data.push_back( (*gh.get_grid(ilevel))(i,j,k) * vfac );
|
||||
else
|
||||
{
|
||||
ofs_temp.write( (char*)&temp_data[0], sizeof(T_store)*block_buf_size_ );
|
||||
nwritten += block_buf_size_;
|
||||
temp_data.clear();
|
||||
temp_data.push_back( (*gh.get_grid(ilevel))(i,j,k) * vfac );
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
if( temp_data.size() > 0 )
|
||||
{
|
||||
ofs_temp.write( (char*)&temp_data[0], sizeof(T_store)*temp_data.size() );
|
||||
nwritten += temp_data.size();
|
||||
}
|
||||
|
||||
if( nwritten != nptot )
|
||||
throw std::runtime_error("Internal consistency error while writing temporary file for DM velocities");
|
||||
|
||||
//... dump to temporary file
|
||||
ofs_temp.write( (char *)&blksize, sizeof(size_t) );
|
||||
|
||||
if( ofs_temp.bad() )
|
||||
throw std::runtime_error("I/O error while writing temporary file for DM velocities");
|
||||
|
||||
ofs_temp.close();
|
||||
}
|
||||
|
||||
void write_dm_density( const grid_hierarchy& gh )
|
||||
{
|
||||
//... we don't care about DM density for art
|
||||
}
|
||||
|
||||
void write_dm_potential( const grid_hierarchy& gh )
|
||||
{ }
|
||||
|
||||
|
||||
|
||||
void write_gas_position( int coord, const grid_hierarchy& gh )
|
||||
{
|
||||
|
||||
size_t nptot = gh.count_leaf_cells(gh.levelmin(), gh.levelmax());
|
||||
|
||||
std::vector<T_store> temp_data;
|
||||
temp_data.reserve( block_buf_size_ );
|
||||
|
||||
|
||||
//ART coordinates are in the range 1 - (NGRID+1)
|
||||
double xfac = (double) header_.NGRIDC;
|
||||
|
||||
char temp_fname[256];
|
||||
sprintf( temp_fname, "___ic_temp_%05d.bin", 100*id_gas_pos+coord );
|
||||
std::ofstream ofs_temp( temp_fname, std::ios::binary|std::ios::trunc );
|
||||
|
||||
size_t blksize = sizeof(T_store)*nptot;
|
||||
ofs_temp.write( (char *)&blksize, sizeof(size_t) );
|
||||
|
||||
size_t nwritten = 0;
|
||||
for( int ilevel=gh.levelmax(); ilevel>=(int)gh.levelmin(); --ilevel )
|
||||
for( unsigned i=0; i<gh.get_grid(ilevel)->size(0); ++i )
|
||||
for( unsigned j=0; j<gh.get_grid(ilevel)->size(1); ++j )
|
||||
for( unsigned k=0; k<gh.get_grid(ilevel)->size(2); ++k )
|
||||
if( gh.is_in_mask(ilevel,i,j,k) && !gh.is_refined(ilevel,i,j,k) )
|
||||
{
|
||||
double xx[3];
|
||||
gh.cell_pos(ilevel, i, j, k, xx);
|
||||
|
||||
xx[coord] = fmod( (xx[coord]+(*gh.get_grid(ilevel))(i,j,k)) + 1.0, 1.0 ) ;
|
||||
xx[coord] = (xx[coord]*xfac)+1.0;
|
||||
|
||||
if( temp_data.size() < block_buf_size_ )
|
||||
temp_data.push_back( xx[coord] );
|
||||
else
|
||||
{
|
||||
ofs_temp.write( (char*)&temp_data[0], sizeof(T_store)*block_buf_size_ );
|
||||
nwritten += block_buf_size_;
|
||||
temp_data.clear();
|
||||
temp_data.push_back( xx[coord] );
|
||||
}
|
||||
}
|
||||
|
||||
if( temp_data.size() > 0 )
|
||||
{
|
||||
ofs_temp.write( (char*)&temp_data[0], sizeof(T_store)*temp_data.size() );
|
||||
nwritten += temp_data.size();
|
||||
}
|
||||
|
||||
if( nwritten != nptot )
|
||||
throw std::runtime_error("Internal consistency error while writing temporary file for gas positions");
|
||||
|
||||
//... dump to temporary file
|
||||
ofs_temp.write( (char *)&blksize, sizeof(size_t) );
|
||||
|
||||
if( ofs_temp.bad() )
|
||||
throw std::runtime_error("I/O error while writing temporary file for gas positions");
|
||||
|
||||
ofs_temp.close();
|
||||
|
||||
}
|
||||
|
||||
void write_gas_velocity( int coord, const grid_hierarchy& gh )
|
||||
{
|
||||
|
||||
size_t nptot = gh.count_leaf_cells(gh.levelmin(), gh.levelmax());
|
||||
|
||||
std::vector<T_store> temp_data;
|
||||
temp_data.reserve( block_buf_size_ );
|
||||
|
||||
//In ART velocities are P = a_expansion*V_pec/(x_0H_0)
|
||||
// where x_0 = comoving cell_size=Box/Ngrid;H_0 = Hubble at z=0
|
||||
// so scale factor to physical km/s is convV= BoxV/AEXPN/NGRID
|
||||
// (BoxV is Box*100; aexpn=current expansion factor)
|
||||
//internal units of MUSIC: To km/s just multiply by Lbox
|
||||
double vfac = (header_.aexpN*header_.NGRIDC)/(100.0);
|
||||
|
||||
char temp_fname[256];
|
||||
sprintf( temp_fname, "___ic_temp_%05d.bin", 100*id_gas_vel+coord );
|
||||
std::ofstream ofs_temp( temp_fname, std::ios::binary|std::ios::trunc );
|
||||
|
||||
size_t blksize = sizeof(T_store)*nptot;
|
||||
ofs_temp.write( (char *)&blksize, sizeof(size_t) );
|
||||
|
||||
size_t nwritten = 0;
|
||||
for( int ilevel=gh.levelmax(); ilevel>=(int)gh.levelmin(); --ilevel )
|
||||
for( unsigned i=0; i<gh.get_grid(ilevel)->size(0); ++i )
|
||||
for( unsigned j=0; j<gh.get_grid(ilevel)->size(1); ++j )
|
||||
for( unsigned k=0; k<gh.get_grid(ilevel)->size(2); ++k )
|
||||
if( gh.is_in_mask(ilevel,i,j,k) && !gh.is_refined(ilevel,i,j,k) )
|
||||
{
|
||||
if( temp_data.size() < block_buf_size_ )
|
||||
temp_data.push_back( (*gh.get_grid(ilevel))(i,j,k) * vfac );
|
||||
else
|
||||
{
|
||||
ofs_temp.write( (char*)&temp_data[0], sizeof(T_store)*block_buf_size_ );
|
||||
nwritten += block_buf_size_;
|
||||
temp_data.clear();
|
||||
temp_data.push_back( (*gh.get_grid(ilevel))(i,j,k) * vfac );
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
if( temp_data.size() > 0 )
|
||||
{
|
||||
ofs_temp.write( (char*)&temp_data[0], sizeof(T_store)*temp_data.size() );
|
||||
nwritten += temp_data.size();
|
||||
}
|
||||
|
||||
if( nwritten != nptot )
|
||||
throw std::runtime_error("Internal consistency error while writing temporary file for gas velocities");
|
||||
|
||||
//... dump to temporary file
|
||||
ofs_temp.write( (char *)&blksize, sizeof(size_t) );
|
||||
|
||||
if( ofs_temp.bad() )
|
||||
throw std::runtime_error("I/O error while writing temporary file for gas velocities");
|
||||
|
||||
ofs_temp.close();
|
||||
}
|
||||
|
||||
void write_gas_density( const grid_hierarchy& gh )
|
||||
{ }
|
||||
void write_gas_potential( const grid_hierarchy& gh )
|
||||
{ }
|
||||
|
||||
void finalize( void )
|
||||
{
|
||||
this->write_header_file();
|
||||
this->write_pt_file();
|
||||
this->assemble_DM_file();
|
||||
if(do_baryons_)
|
||||
{
|
||||
this->assemble_gas_file();
|
||||
}
|
||||
}
|
||||
};
|
||||
|
||||
namespace{
|
||||
output_plugin_creator_concrete<art_output_plugin<float> > creator("art");
|
||||
}
|
||||
|
|
@ -1,634 +0,0 @@
|
|||
/*
|
||||
|
||||
output_enzo.cc - This file is part of MUSIC -
|
||||
a code to generate multi-scale initial conditions
|
||||
for cosmological simulations
|
||||
|
||||
Copyright (C) 2010 Oliver Hahn
|
||||
|
||||
*/
|
||||
|
||||
#ifdef HAVE_HDF5
|
||||
|
||||
#include <sys/types.h>
|
||||
#include <sys/stat.h>
|
||||
|
||||
#include "output.hh"
|
||||
|
||||
#include "HDF_IO.hh"
|
||||
|
||||
#define MAX_SLAB_SIZE 268435456 // = 256 MBytes
|
||||
|
||||
|
||||
class enzo_output_plugin : public output_plugin
|
||||
{
|
||||
protected:
|
||||
|
||||
struct patch_header{
|
||||
int component_rank;
|
||||
size_t component_size;
|
||||
std::vector<int> dimensions;
|
||||
int rank;
|
||||
std::vector<int> top_grid_dims;
|
||||
std::vector<int> top_grid_end;
|
||||
std::vector<int> top_grid_start;
|
||||
};
|
||||
|
||||
struct sim_header{
|
||||
std::vector<int> dimensions;
|
||||
std::vector<int> offset;
|
||||
float a_start;
|
||||
float dx;
|
||||
float h0;
|
||||
float omega_b;
|
||||
float omega_m;
|
||||
float omega_v;
|
||||
float vfact;
|
||||
};
|
||||
|
||||
|
||||
sim_header the_sim_header;
|
||||
|
||||
void write_sim_header( std::string fname, const sim_header& h )
|
||||
{
|
||||
HDFWriteGroupAttribute( fname, "/", "Dimensions", h.dimensions );
|
||||
HDFWriteGroupAttribute( fname, "/", "Offset", h.offset );
|
||||
HDFWriteGroupAttribute( fname, "/", "a_start", h.a_start );
|
||||
HDFWriteGroupAttribute( fname, "/", "dx", h.dx );
|
||||
HDFWriteGroupAttribute( fname, "/", "h0", h.h0 );
|
||||
HDFWriteGroupAttribute( fname, "/", "omega_b", h.omega_b );
|
||||
HDFWriteGroupAttribute( fname, "/", "omega_m", h.omega_m );
|
||||
HDFWriteGroupAttribute( fname, "/", "omega_v", h.omega_v );
|
||||
HDFWriteGroupAttribute( fname, "/", "vfact", h.vfact );
|
||||
}
|
||||
|
||||
void write_patch_header( std::string fname, std::string dsetname, const patch_header& h )
|
||||
{
|
||||
HDFWriteDatasetAttribute( fname, dsetname, "Component_Rank", h.component_rank );
|
||||
HDFWriteDatasetAttribute( fname, dsetname, "Component_Size", h.component_size );
|
||||
HDFWriteDatasetAttribute( fname, dsetname, "Dimensions", h.dimensions );
|
||||
HDFWriteDatasetAttribute( fname, dsetname, "Rank", h.rank );
|
||||
HDFWriteDatasetAttribute( fname, dsetname, "TopGridDims", h.top_grid_dims );
|
||||
HDFWriteDatasetAttribute( fname, dsetname, "TopGridEnd", h.top_grid_end );
|
||||
HDFWriteDatasetAttribute( fname, dsetname, "TopGridStart", h.top_grid_start );
|
||||
}
|
||||
|
||||
void dump_mask( const grid_hierarchy& gh )
|
||||
{
|
||||
char enzoname[256], filename[256];
|
||||
std::string fieldname("RefinementMask");
|
||||
|
||||
for(unsigned ilevel=levelmin_; ilevel<=levelmax_; ++ilevel )
|
||||
{
|
||||
std::vector<int> ng, ng_fortran;
|
||||
ng.push_back( gh.get_grid(ilevel)->size(0) );
|
||||
ng.push_back( gh.get_grid(ilevel)->size(1) );
|
||||
ng.push_back( gh.get_grid(ilevel)->size(2) );
|
||||
|
||||
ng_fortran.push_back( gh.get_grid(ilevel)->size(2) );
|
||||
ng_fortran.push_back( gh.get_grid(ilevel)->size(1) );
|
||||
ng_fortran.push_back( gh.get_grid(ilevel)->size(0) );
|
||||
|
||||
//... need to copy data because we need to get rid of the ghost zones
|
||||
//... write in slabs if data is more than MAX_SLAB_SIZE (default 128 MB)
|
||||
|
||||
//... full 3D block size
|
||||
size_t all_data_size = (size_t)ng[0] * (size_t)ng[1] * (size_t)ng[2];
|
||||
|
||||
//... write in slabs of MAX_SLAB_SIZE unless all_data_size is anyway smaller
|
||||
size_t max_slab_size = std::min((size_t)MAX_SLAB_SIZE/sizeof(double), all_data_size );
|
||||
|
||||
//... but one slab hast to be at least the size of one slice
|
||||
max_slab_size = std::max(((size_t)ng[0] * (size_t)ng[1]), max_slab_size );
|
||||
|
||||
//... number of slices in one slab
|
||||
size_t slices_in_slab = (size_t)((double)max_slab_size / ((size_t)ng[0] * (size_t)ng[1]));
|
||||
|
||||
size_t nsz[3] = { ng[2], ng[1], ng[0] };
|
||||
|
||||
if( levelmin_ != levelmax_ )
|
||||
sprintf( enzoname, "%s.%d", fieldname.c_str(), ilevel-levelmin_ );
|
||||
else
|
||||
sprintf( enzoname, "%s", fieldname.c_str() );
|
||||
|
||||
sprintf( filename, "%s/%s", fname_.c_str(), enzoname );
|
||||
|
||||
HDFCreateFile( filename );
|
||||
write_sim_header( filename, the_sim_header );
|
||||
|
||||
//... create full array in file
|
||||
HDFHyperslabWriter3Ds<int> *slab_writer = new HDFHyperslabWriter3Ds<int>( filename, enzoname, nsz );
|
||||
|
||||
//... create buffer
|
||||
int *data_buf = new int[ slices_in_slab * (size_t)ng[0] * (size_t)ng[1] ];
|
||||
|
||||
//... write slice by slice
|
||||
size_t slices_written = 0;
|
||||
while( slices_written < (size_t)ng[2] )
|
||||
{
|
||||
slices_in_slab = std::min( (size_t)ng[2]-slices_written, slices_in_slab );
|
||||
|
||||
#pragma omp parallel for
|
||||
for( int k=0; k<(int)slices_in_slab; ++k )
|
||||
for( int j=0; j<ng[1]; ++j )
|
||||
for( int i=0; i<ng[0]; ++i )
|
||||
{
|
||||
int mask_val = -1;
|
||||
|
||||
if( gh.is_in_mask(ilevel,i,j,k+slices_written) )
|
||||
{
|
||||
if( gh.is_refined(ilevel,i,j,k+slices_written) )
|
||||
mask_val = 1;
|
||||
else
|
||||
mask_val = 0;
|
||||
}
|
||||
data_buf[ (size_t)(k*ng[1]+j)*(size_t)ng[0]+(size_t)i ] = mask_val;
|
||||
}
|
||||
|
||||
size_t count[3], offset[3];
|
||||
|
||||
count[0] = slices_in_slab;
|
||||
count[1] = ng[1];
|
||||
count[2] = ng[0];
|
||||
|
||||
offset[0] = slices_written;;
|
||||
offset[1] = 0;
|
||||
offset[2] = 0;
|
||||
|
||||
slab_writer->write_slab( data_buf, count, offset );
|
||||
slices_written += slices_in_slab;
|
||||
|
||||
}
|
||||
|
||||
|
||||
delete[] data_buf;
|
||||
delete slab_writer;
|
||||
|
||||
//... header data for the patch
|
||||
patch_header ph;
|
||||
|
||||
ph.component_rank = 1;
|
||||
ph.component_size = (size_t)ng[0]*(size_t)ng[1]*(size_t)ng[2];
|
||||
ph.dimensions = ng;
|
||||
ph.rank = 3;
|
||||
|
||||
ph.top_grid_dims.assign(3, 1<<levelmin_);
|
||||
|
||||
//... offset_abs is in units of the current level cell size
|
||||
|
||||
double rfac = 1.0/(1<<(ilevel-levelmin_));
|
||||
|
||||
ph.top_grid_start.push_back( (int)(gh.offset_abs(ilevel, 0)*rfac) );
|
||||
ph.top_grid_start.push_back( (int)(gh.offset_abs(ilevel, 1)*rfac) );
|
||||
ph.top_grid_start.push_back( (int)(gh.offset_abs(ilevel, 2)*rfac) );
|
||||
|
||||
ph.top_grid_end.push_back( ph.top_grid_start[0] + (int)(ng[0]*rfac) );
|
||||
ph.top_grid_end.push_back( ph.top_grid_start[1] + (int)(ng[1]*rfac) );
|
||||
ph.top_grid_end.push_back( ph.top_grid_start[2] + (int)(ng[2]*rfac) );
|
||||
|
||||
write_patch_header( filename, enzoname, ph );
|
||||
}
|
||||
}
|
||||
|
||||
void dump_grid_data( std::string fieldname, const grid_hierarchy& gh, double factor = 1.0, double add = 0.0 )
|
||||
{
|
||||
char enzoname[256], filename[256];
|
||||
|
||||
for(unsigned ilevel=levelmin_; ilevel<=levelmax_; ++ilevel )
|
||||
{
|
||||
std::vector<int> ng, ng_fortran;
|
||||
ng.push_back( gh.get_grid(ilevel)->size(0) );
|
||||
ng.push_back( gh.get_grid(ilevel)->size(1) );
|
||||
ng.push_back( gh.get_grid(ilevel)->size(2) );
|
||||
|
||||
ng_fortran.push_back( gh.get_grid(ilevel)->size(2) );
|
||||
ng_fortran.push_back( gh.get_grid(ilevel)->size(1) );
|
||||
ng_fortran.push_back( gh.get_grid(ilevel)->size(0) );
|
||||
|
||||
|
||||
//... need to copy data because we need to get rid of the ghost zones
|
||||
//... write in slabs if data is more than MAX_SLAB_SIZE (default 128 MB)
|
||||
|
||||
//... full 3D block size
|
||||
size_t all_data_size = (size_t)ng[0] * (size_t)ng[1] * (size_t)ng[2];
|
||||
|
||||
//... write in slabs of MAX_SLAB_SIZE unless all_data_size is anyway smaller
|
||||
size_t max_slab_size = std::min((size_t)MAX_SLAB_SIZE/sizeof(double), all_data_size );
|
||||
|
||||
//... but one slab hast to be at least the size of one slice
|
||||
max_slab_size = std::max(((size_t)ng[0] * (size_t)ng[1]), max_slab_size );
|
||||
|
||||
//... number of slices in one slab
|
||||
size_t slices_in_slab = (size_t)((double)max_slab_size / ((size_t)ng[0] * (size_t)ng[1]));
|
||||
|
||||
size_t nsz[3] = { ng[2], ng[1], ng[0] };
|
||||
|
||||
if( levelmin_ != levelmax_ )
|
||||
sprintf( enzoname, "%s.%d", fieldname.c_str(), ilevel-levelmin_ );
|
||||
else
|
||||
sprintf( enzoname, "%s", fieldname.c_str() );
|
||||
|
||||
sprintf( filename, "%s/%s", fname_.c_str(), enzoname );
|
||||
|
||||
HDFCreateFile( filename );
|
||||
write_sim_header( filename, the_sim_header );
|
||||
|
||||
#ifdef SINGLE_PRECISION
|
||||
//... create full array in file
|
||||
HDFHyperslabWriter3Ds<float> *slab_writer = new HDFHyperslabWriter3Ds<float>( filename, enzoname, nsz );
|
||||
|
||||
//... create buffer
|
||||
float *data_buf = new float[ slices_in_slab * (size_t)ng[0] * (size_t)ng[1] ];
|
||||
#else
|
||||
//... create full array in file
|
||||
HDFHyperslabWriter3Ds<double> *slab_writer = new HDFHyperslabWriter3Ds<double>( filename, enzoname, nsz );
|
||||
|
||||
//... create buffer
|
||||
double *data_buf = new double[ slices_in_slab * (size_t)ng[0] * (size_t)ng[1] ];
|
||||
#endif
|
||||
|
||||
//... write slice by slice
|
||||
size_t slices_written = 0;
|
||||
while( slices_written < (size_t)ng[2] )
|
||||
{
|
||||
slices_in_slab = std::min( (size_t)ng[2]-slices_written, slices_in_slab );
|
||||
|
||||
#pragma omp parallel for
|
||||
for( int k=0; k<(int)slices_in_slab; ++k )
|
||||
for( int j=0; j<ng[1]; ++j )
|
||||
for( int i=0; i<ng[0]; ++i )
|
||||
data_buf[ (size_t)(k*ng[1]+j)*(size_t)ng[0]+(size_t)i ] =
|
||||
(add+(*gh.get_grid(ilevel))(i,j,k+slices_written))*factor;
|
||||
|
||||
size_t count[3], offset[3];
|
||||
|
||||
count[0] = slices_in_slab;
|
||||
count[1] = ng[1];
|
||||
count[2] = ng[0];
|
||||
|
||||
offset[0] = slices_written;;
|
||||
offset[1] = 0;
|
||||
offset[2] = 0;
|
||||
|
||||
slab_writer->write_slab( data_buf, count, offset );
|
||||
slices_written += slices_in_slab;
|
||||
|
||||
}
|
||||
|
||||
//... free buffer
|
||||
delete[] data_buf;
|
||||
|
||||
//... finalize writing and close dataset
|
||||
delete slab_writer;
|
||||
|
||||
|
||||
//... header data for the patch
|
||||
patch_header ph;
|
||||
|
||||
ph.component_rank = 1;
|
||||
ph.component_size = (size_t)ng[0]*(size_t)ng[1]*(size_t)ng[2];
|
||||
ph.dimensions = ng;
|
||||
ph.rank = 3;
|
||||
|
||||
ph.top_grid_dims.assign(3, 1<<levelmin_);
|
||||
|
||||
//... offset_abs is in units of the current level cell size
|
||||
|
||||
double rfac = 1.0/(1<<(ilevel-levelmin_));
|
||||
|
||||
ph.top_grid_start.push_back( (int)(gh.offset_abs(ilevel, 0)*rfac) );
|
||||
ph.top_grid_start.push_back( (int)(gh.offset_abs(ilevel, 1)*rfac) );
|
||||
ph.top_grid_start.push_back( (int)(gh.offset_abs(ilevel, 2)*rfac) );
|
||||
|
||||
ph.top_grid_end.push_back( ph.top_grid_start[0] + (int)(ng[0]*rfac) );
|
||||
ph.top_grid_end.push_back( ph.top_grid_start[1] + (int)(ng[1]*rfac) );
|
||||
ph.top_grid_end.push_back( ph.top_grid_start[2] + (int)(ng[2]*rfac) );
|
||||
|
||||
write_patch_header( filename, enzoname, ph );
|
||||
}
|
||||
}
|
||||
|
||||
public:
|
||||
|
||||
enzo_output_plugin( config_file& cf )
|
||||
: output_plugin( cf )
|
||||
{
|
||||
if( mkdir( fname_.c_str(), 0777 ) )
|
||||
{
|
||||
perror( fname_.c_str() );
|
||||
throw std::runtime_error("Error in enzo_output_plugin!");
|
||||
}
|
||||
|
||||
bool bhave_hydro = cf_.getValue<bool>("setup","baryons");
|
||||
bool align_top = cf.getValueSafe<bool>( "setup", "align_top", false );
|
||||
|
||||
if( !align_top )
|
||||
LOGWARN("Old ENZO versions may require \'align_top=true\'!");
|
||||
|
||||
the_sim_header.dimensions.push_back( 1<<levelmin_ );
|
||||
the_sim_header.dimensions.push_back( 1<<levelmin_ );
|
||||
the_sim_header.dimensions.push_back( 1<<levelmin_ );
|
||||
|
||||
the_sim_header.offset.push_back( 0 );
|
||||
the_sim_header.offset.push_back( 0 );
|
||||
the_sim_header.offset.push_back( 0 );
|
||||
|
||||
the_sim_header.a_start = 1.0/(1.0+cf.getValue<double>("setup","zstart"));
|
||||
the_sim_header.dx = cf.getValue<double>("setup","boxlength")/the_sim_header.dimensions[0]/(cf.getValue<double>("cosmology","H0")*0.01); // not sure?!?
|
||||
the_sim_header.h0 = cf.getValue<double>("cosmology","H0")*0.01;
|
||||
|
||||
if( bhave_hydro )
|
||||
the_sim_header.omega_b = cf.getValue<double>("cosmology","Omega_b");
|
||||
else
|
||||
the_sim_header.omega_b = 0.0;
|
||||
|
||||
the_sim_header.omega_m = cf.getValue<double>("cosmology","Omega_m");
|
||||
the_sim_header.omega_v = cf.getValue<double>("cosmology","Omega_L");
|
||||
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
|
||||
|
||||
}
|
||||
|
||||
~enzo_output_plugin()
|
||||
{ }
|
||||
|
||||
void write_dm_mass( const grid_hierarchy& gh )
|
||||
{ /* do nothing, not needed */ }
|
||||
|
||||
|
||||
void write_dm_density( const grid_hierarchy& gh )
|
||||
{ /* write the parameter file data */
|
||||
|
||||
bool bhave_hydro = cf_.getValue<bool>("setup","baryons");
|
||||
double refine_region_fraction = cf_.getValueSafe<double>( "output", "enzo_refine_region_fraction", 0.8 );
|
||||
char filename[256];
|
||||
unsigned nbase = (unsigned)pow(2,levelmin_);
|
||||
|
||||
// write out the refinement masks
|
||||
dump_mask( gh );
|
||||
|
||||
// write out a parameter file
|
||||
|
||||
sprintf( filename, "%s/parameter_file.txt", fname_.c_str() );
|
||||
|
||||
std::ofstream ofs( filename, std::ios::trunc );
|
||||
|
||||
ofs
|
||||
<< "# Relevant Section of Enzo Paramter File (NOT COMPLETE!) \n"
|
||||
<< "ProblemType = 30 // cosmology simulation\n"
|
||||
<< "TopGridRank = 3\n"
|
||||
<< "TopGridDimensions = " << nbase << " " << nbase << " " << nbase << "\n"
|
||||
<< "SelfGravity = 1 // gravity on\n"
|
||||
<< "TopGridGravityBoundary = 0 // Periodic BC for gravity\n"
|
||||
<< "LeftFaceBoundaryCondition = 3 3 3 // same for fluid\n"
|
||||
<< "RightFaceBoundaryCondition = 3 3 3\n"
|
||||
<< "RefineBy = 2\n"
|
||||
<< "\n"
|
||||
<< "#\n";
|
||||
|
||||
if( bhave_hydro )
|
||||
ofs
|
||||
<< "CosmologySimulationOmegaBaryonNow = " << the_sim_header.omega_b << "\n"
|
||||
<< "CosmologySimulationOmegaCDMNow = " << the_sim_header.omega_m-the_sim_header.omega_b << "\n";
|
||||
else
|
||||
ofs
|
||||
<< "CosmologySimulationOmegaBaryonNow = " << 0.0 << "\n"
|
||||
<< "CosmologySimulationOmegaCDMNow = " << the_sim_header.omega_m << "\n";
|
||||
|
||||
if( bhave_hydro )
|
||||
ofs
|
||||
<< "CosmologySimulationDensityName = GridDensity\n"
|
||||
<< "CosmologySimulationVelocity1Name = GridVelocities_x\n"
|
||||
<< "CosmologySimulationVelocity2Name = GridVelocities_y\n"
|
||||
<< "CosmologySimulationVelocity3Name = GridVelocities_z\n";
|
||||
|
||||
ofs
|
||||
<< "CosmologySimulationCalculatePositions = 1\n"
|
||||
<< "CosmologySimulationParticleVelocity1Name = ParticleVelocities_x\n"
|
||||
<< "CosmologySimulationParticleVelocity2Name = ParticleVelocities_y\n"
|
||||
<< "CosmologySimulationParticleVelocity3Name = ParticleVelocities_z\n"
|
||||
<< "CosmologySimulationParticleDisplacement1Name = ParticleDisplacements_x\n"
|
||||
<< "CosmologySimulationParticleDisplacement2Name = ParticleDisplacements_y\n"
|
||||
<< "CosmologySimulationParticleDisplacement3Name = ParticleDisplacements_z\n"
|
||||
<< "\n"
|
||||
<< "#\n"
|
||||
<< "# define cosmology parameters\n"
|
||||
<< "#\n"
|
||||
<< "ComovingCoordinates = 1 // Expansion ON\n"
|
||||
<< "CosmologyOmegaMatterNow = " << the_sim_header.omega_m << "\n"
|
||||
<< "CosmologyOmegaLambdaNow = " << the_sim_header.omega_v << "\n"
|
||||
<< "CosmologyHubbleConstantNow = " << the_sim_header.h0 << " // in 100 km/s/Mpc\n"
|
||||
<< "CosmologyComovingBoxSize = " << cf_.getValue<double>("setup","boxlength") << " // in Mpc/h\n"
|
||||
<< "CosmologyMaxExpansionRate = 0.015 // maximum allowed delta(a)/a\n"
|
||||
<< "CosmologyInitialRedshift = " << cf_.getValue<double>("setup","zstart") << " //\n"
|
||||
<< "CosmologyFinalRedshift = 0 //\n"
|
||||
<< "GravitationalConstant = 1 // this must be true for cosmology\n"
|
||||
<< "#\n"
|
||||
<< "#\n"
|
||||
<< "ParallelRootGridIO = 1\n"
|
||||
<< "ParallelParticleIO = 1\n"
|
||||
<< "PartitionNestedGrids = 1\n"
|
||||
<< "CosmologySimulationNumberOfInitialGrids = " << 1+levelmax_-levelmin_ << "\n";
|
||||
|
||||
|
||||
int num_prec = 10;
|
||||
|
||||
if( levelmax_ > 15 )
|
||||
num_prec = 17;
|
||||
|
||||
//... only for additionally refined grids
|
||||
for( unsigned ilevel = 0; ilevel< levelmax_-levelmin_; ++ilevel )
|
||||
{
|
||||
double h = 1.0/(1<<(levelmin_+1+ilevel));
|
||||
|
||||
ofs
|
||||
|
||||
<< "CosmologySimulationGridDimension[" << 1+ilevel << "] = "
|
||||
<< std::setw(16) << gh.size( levelmin_+ilevel+1, 0 ) << " "
|
||||
<< std::setw(16) << gh.size( levelmin_+ilevel+1, 1 ) << " "
|
||||
<< std::setw(16) << gh.size( levelmin_+ilevel+1, 2 ) << "\n"
|
||||
|
||||
<< "CosmologySimulationGridLeftEdge[" << 1+ilevel << "] = "
|
||||
<< std::setw(num_prec+6) << std::setprecision(num_prec) << h*gh.offset_abs(levelmin_+ilevel+1, 0) << " "
|
||||
<< std::setw(num_prec+6) << std::setprecision(num_prec) << h*gh.offset_abs(levelmin_+ilevel+1, 1) << " "
|
||||
<< std::setw(num_prec+6) << std::setprecision(num_prec) << h*gh.offset_abs(levelmin_+ilevel+1, 2) << "\n"
|
||||
|
||||
<< "CosmologySimulationGridRightEdge[" << 1+ilevel << "] = "
|
||||
<< std::setw(num_prec+6) << std::setprecision(num_prec) << h*(gh.offset_abs(levelmin_+ilevel+1, 0)+gh.size( levelmin_+ilevel+1, 0 )) << " "
|
||||
<< std::setw(num_prec+6) << std::setprecision(num_prec) << h*(gh.offset_abs(levelmin_+ilevel+1, 1)+gh.size( levelmin_+ilevel+1, 1 )) << " "
|
||||
<< std::setw(num_prec+6) << std::setprecision(num_prec) << h*(gh.offset_abs(levelmin_+ilevel+1, 2)+gh.size( levelmin_+ilevel+1, 2 )) << "\n"
|
||||
|
||||
<< "CosmologySimulationGridLevel[" << 1+ilevel << "] = " << 1+ilevel << "\n";
|
||||
}
|
||||
|
||||
if( levelmin_ != levelmax_ )
|
||||
{
|
||||
double h = 1.0/(1<<levelmax_);
|
||||
|
||||
|
||||
double cen[3],le[3],re[3];
|
||||
for (int i=0;i<3;i++)
|
||||
{
|
||||
cen[i] = gh.offset_abs(levelmax_, i)+gh.size( levelmax_, i )/2;
|
||||
le[i] = cen[i]-refine_region_fraction*gh.size( levelmax_,i)/2;
|
||||
re[i] = le[i] +refine_region_fraction*gh.size( levelmax_, i);
|
||||
}
|
||||
|
||||
|
||||
ofs
|
||||
<< "#\n"
|
||||
<< "# region allowed for further refinement\n"
|
||||
<< "#\n"
|
||||
// << "RefineRegionAutoAdjust = 1\n"
|
||||
<< "RefineRegionLeftEdge = "
|
||||
<< std::setw(num_prec+6) << std::setprecision(num_prec) << h*le[0] << " "
|
||||
<< std::setw(num_prec+6) << std::setprecision(num_prec) << h*le[1] << " "
|
||||
<< std::setw(num_prec+6) << std::setprecision(num_prec) << h*le[2] << "\n"
|
||||
<< "RefineRegionRightEdge = "
|
||||
<< std::setw(num_prec+6) << std::setprecision(num_prec) << h*re[0] << " "
|
||||
<< std::setw(num_prec+6) << std::setprecision(num_prec) << h*re[1] << " "
|
||||
<< std::setw(num_prec+6) << std::setprecision(num_prec) << h*re[2]<< "\n";
|
||||
}
|
||||
|
||||
|
||||
// determine density maximum and minimum location
|
||||
real_t rhomax = -1e30, rhomin = 1e30;
|
||||
double loc_rhomax[3] = {0.0,0.0,0.0}, loc_rhomin[3] = {0.0,0.0,0.0};
|
||||
int lvl_rhomax = 0, lvl_rhomin = 0;
|
||||
real_t rhomax_lm = -1e30, rhomin_lm = 1e30;
|
||||
double loc_rhomax_lm[3] = {0.0,0.0,0.0}, loc_rhomin_lm[3] = {0.0,0.0,0.0};
|
||||
|
||||
|
||||
for( int ilevel=gh.levelmax(); ilevel>=(int)gh.levelmin(); --ilevel )
|
||||
for( unsigned i=0; i<gh.get_grid(ilevel)->size(0); ++i )
|
||||
for( unsigned j=0; j<gh.get_grid(ilevel)->size(1); ++j )
|
||||
for( unsigned k=0; k<gh.get_grid(ilevel)->size(2); ++k )
|
||||
if( ! gh.is_refined(ilevel,i,j,k) )
|
||||
{
|
||||
real_t rho = (*gh.get_grid(ilevel))(i,j,k);
|
||||
|
||||
if( rho > rhomax )
|
||||
{
|
||||
rhomax = rho;
|
||||
lvl_rhomax = ilevel;
|
||||
gh.cell_pos(ilevel, i, j, k, loc_rhomax);
|
||||
}
|
||||
|
||||
if( rho < rhomin )
|
||||
{
|
||||
rhomin = rho;
|
||||
lvl_rhomin = ilevel;
|
||||
gh.cell_pos(ilevel, i, j, k, loc_rhomin);
|
||||
}
|
||||
|
||||
if( ilevel == (int)gh.levelmax() )
|
||||
{
|
||||
if( rho > rhomax_lm )
|
||||
{
|
||||
rhomax_lm = rho;
|
||||
gh.cell_pos(ilevel, i, j, k, loc_rhomax_lm);
|
||||
}
|
||||
|
||||
if( rho < rhomin_lm )
|
||||
{
|
||||
rhomin_lm = rho;
|
||||
gh.cell_pos(ilevel, i, j, k, loc_rhomin_lm);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
double h = 1.0/(1<<levelmin_);
|
||||
double shift[3];
|
||||
shift[0] = -(double)cf_.getValue<int>( "setup", "shift_x" )*h;
|
||||
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
|
||||
|
||||
|
||||
809
src/plugins/output_arepo.cc
Normal file
809
src/plugins/output_arepo.cc
Normal file
|
|
@ -0,0 +1,809 @@
|
|||
/*
|
||||
* output_arepo.cc - This file is part of MUSIC -
|
||||
* a code to generate multi-scale initial conditions
|
||||
* for cosmological simulations
|
||||
*
|
||||
* Copyright (C) 2010 Oliver Hahn
|
||||
*
|
||||
* Plugin: Dylan Nelson (dnelson@cfa.harvard.edu)
|
||||
*/
|
||||
|
||||
#ifdef HAVE_HDF5
|
||||
|
||||
#define GAS_PARTTYPE 0
|
||||
#define HIGHRES_DM_PARTTYPE 1
|
||||
#define COARSE_DM_DEFAULT_PARTTYPE 2
|
||||
#define STAR_PARTTYPE 4
|
||||
#define NTYPES 6
|
||||
|
||||
#include <sstream>
|
||||
#include <string>
|
||||
#include <algorithm>
|
||||
#include "output.hh"
|
||||
#include "HDF_IO.hh"
|
||||
|
||||
class arepo_output_plugin : public output_plugin
|
||||
{
|
||||
protected:
|
||||
// header/config
|
||||
std::vector<std::vector<unsigned int>> nPart;
|
||||
std::vector<long long> nPartTotal;
|
||||
std::vector<double> massTable;
|
||||
double time, redshift, boxSize;
|
||||
unsigned int numFiles, coarsePartType;
|
||||
|
||||
double omega0, omega_L, hubbleParam;
|
||||
|
||||
// configuration
|
||||
double UnitLength_in_cm, UnitMass_in_g, UnitVelocity_in_cm_per_s;
|
||||
double omega_b, rhoCrit;
|
||||
double posFac, velFac;
|
||||
long long nPartTotAllTypes;
|
||||
bool doBaryons, useLongIDs, doublePrec;
|
||||
|
||||
size_t npfine, npart, npcoarse;
|
||||
std::vector<size_t> levelcounts;
|
||||
|
||||
// parameter file hints
|
||||
int pmgrid, gridboost;
|
||||
float softening, Tini;
|
||||
|
||||
using output_plugin::cf_;
|
||||
|
||||
// Nx1 vector (e.g. masses,particleids)
|
||||
template <typename T>
|
||||
void writeHDF5_a(std::string fieldName, int partTypeNum, const std::vector<T> &data)
|
||||
{
|
||||
hid_t HDF_FileID, HDF_GroupID, HDF_DatasetID, HDF_DataspaceID, HDF_Type;
|
||||
hsize_t HDF_Dims, offset = 0;
|
||||
|
||||
std::stringstream GrpName;
|
||||
GrpName << "PartType" << partTypeNum;
|
||||
|
||||
for (unsigned i = 0; i < numFiles; i++)
|
||||
{
|
||||
std::string filename = fname_;
|
||||
HDF_Dims = data.size();
|
||||
|
||||
// modify local filename and write size
|
||||
if (numFiles > 1)
|
||||
{
|
||||
std::stringstream s;
|
||||
s << "." << i << ".hdf5";
|
||||
filename.replace(filename.find(".hdf5"), 5, s.str());
|
||||
|
||||
HDF_Dims = ceil(data.size() / numFiles);
|
||||
if (i == numFiles - 1)
|
||||
HDF_Dims = data.size() - offset;
|
||||
}
|
||||
|
||||
HDF_FileID = H5Fopen(filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT);
|
||||
HDF_GroupID = H5Gopen(HDF_FileID, GrpName.str().c_str());
|
||||
|
||||
HDF_Type = GetDataType<T>();
|
||||
HDF_DataspaceID = H5Screate_simple(1, &HDF_Dims, NULL);
|
||||
HDF_DatasetID = H5Dcreate(HDF_GroupID, fieldName.c_str(), HDF_Type, HDF_DataspaceID, H5P_DEFAULT);
|
||||
|
||||
// write and close
|
||||
H5Dwrite(HDF_DatasetID, HDF_Type, H5S_ALL, H5S_ALL, H5P_DEFAULT, &data[offset]);
|
||||
|
||||
H5Dclose(HDF_DatasetID);
|
||||
H5Sclose(HDF_DataspaceID);
|
||||
|
||||
H5Gclose(HDF_GroupID);
|
||||
H5Fclose(HDF_FileID);
|
||||
|
||||
offset += HDF_Dims;
|
||||
}
|
||||
}
|
||||
|
||||
// Nx3 vector (e.g. pos,vel), where coord = index of the second dimension (written one at a time)
|
||||
template <typename T>
|
||||
void writeHDF5_b(std::string fieldName, int coord, int partTypeNum, std::vector<T> &data, bool readFlag = false)
|
||||
{
|
||||
hid_t HDF_FileID, HDF_GroupID, HDF_DatasetID, HDF_DataspaceID, HDF_Type;
|
||||
hsize_t HDF_Dims[2], HDF_DimsMem[2], w_offset = 0;
|
||||
|
||||
std::stringstream GrpName;
|
||||
GrpName << "PartType" << partTypeNum;
|
||||
|
||||
for (unsigned i = 0; i < numFiles; i++)
|
||||
{
|
||||
std::string filename = fname_;
|
||||
HDF_Dims[0] = data.size();
|
||||
|
||||
// modify local filename and write size
|
||||
if (numFiles > 1)
|
||||
{
|
||||
std::stringstream s;
|
||||
s << "." << i << ".hdf5";
|
||||
filename.replace(filename.find(".hdf5"), 5, s.str());
|
||||
|
||||
HDF_Dims[0] = ceil(data.size() / numFiles);
|
||||
if (i == numFiles - 1)
|
||||
HDF_Dims[0] = data.size() - w_offset;
|
||||
}
|
||||
|
||||
HDF_FileID = H5Fopen(filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT);
|
||||
HDF_GroupID = H5Gopen(HDF_FileID, GrpName.str().c_str());
|
||||
|
||||
HDF_Type = GetDataType<T>();
|
||||
HDF_Dims[1] = 3;
|
||||
|
||||
// if dataset does not yet exist, create it (on first coord call)
|
||||
if (!(H5Lexists(HDF_GroupID, fieldName.c_str(), H5P_DEFAULT)))
|
||||
{
|
||||
HDF_DataspaceID = H5Screate_simple(2, HDF_Dims, NULL);
|
||||
HDF_DatasetID = H5Dcreate(HDF_GroupID, fieldName.c_str(), HDF_Type, HDF_DataspaceID, H5P_DEFAULT);
|
||||
|
||||
H5Sclose(HDF_DataspaceID);
|
||||
H5Dclose(HDF_DatasetID);
|
||||
}
|
||||
|
||||
// make memory space (just indicates the size/shape of data)
|
||||
HDF_DimsMem[0] = HDF_Dims[0];
|
||||
HDF_DimsMem[1] = 1;
|
||||
hid_t HDF_MemoryspaceID = H5Screate_simple(2, HDF_DimsMem, NULL);
|
||||
|
||||
// open hyperslab
|
||||
hsize_t count[2] = {1, 1}, stride[2] = {1, 1}, offset[2] = {0, 0};
|
||||
|
||||
offset[1] = coord; // set where in the second dimension to write
|
||||
count[0] = HDF_Dims[0]; // set size in the first dimension (num particles of this type)
|
||||
|
||||
HDF_DatasetID = H5Dopen(HDF_GroupID, fieldName.c_str());
|
||||
HDF_DataspaceID = H5Dget_space(HDF_DatasetID);
|
||||
|
||||
H5Sselect_hyperslab(HDF_DataspaceID, H5S_SELECT_SET, offset, stride, count, NULL);
|
||||
|
||||
// write (or read) and close
|
||||
if (readFlag)
|
||||
H5Dread(HDF_DatasetID, HDF_Type, HDF_MemoryspaceID, HDF_DataspaceID, H5P_DEFAULT,
|
||||
&data[w_offset]);
|
||||
else
|
||||
H5Dwrite(HDF_DatasetID, HDF_Type, HDF_MemoryspaceID, HDF_DataspaceID, H5P_DEFAULT,
|
||||
&data[w_offset]);
|
||||
|
||||
H5Dclose(HDF_DatasetID);
|
||||
H5Gclose(HDF_GroupID);
|
||||
H5Fclose(HDF_FileID);
|
||||
|
||||
w_offset += HDF_Dims[0];
|
||||
}
|
||||
}
|
||||
|
||||
// called from finalize()
|
||||
void generateAndWriteIDs(void)
|
||||
{
|
||||
long long offset = 1; // don't use ID==0
|
||||
nPartTotAllTypes = 0;
|
||||
|
||||
for (size_t i = 0; i < nPartTotal.size(); i++)
|
||||
{
|
||||
if (!nPartTotal[i])
|
||||
continue;
|
||||
|
||||
nPartTotAllTypes += nPartTotal[i];
|
||||
|
||||
if (!useLongIDs)
|
||||
{
|
||||
std::vector<int> ids = std::vector<int>(nPartTotal[i]);
|
||||
for (int j = 0; j < nPartTotal[i]; j++)
|
||||
ids[j] = offset + j;
|
||||
|
||||
writeHDF5_a("ParticleIDs", i, ids);
|
||||
}
|
||||
else
|
||||
{
|
||||
std::vector<long long> ids = std::vector<long long>(nPartTotal[i]);
|
||||
for (long long j = 0; j < nPartTotal[i]; j++)
|
||||
ids[j] = offset + j;
|
||||
|
||||
writeHDF5_a("ParticleIDs", i, ids);
|
||||
}
|
||||
|
||||
// make IDs of all particle types sequential (unique) = unnecessary, but consistent with gadget output format
|
||||
offset += nPartTotal[i];
|
||||
}
|
||||
}
|
||||
|
||||
void countLeafCells(const grid_hierarchy &gh)
|
||||
{
|
||||
npfine = 0;
|
||||
npart = 0;
|
||||
npcoarse = 0;
|
||||
|
||||
npfine = gh.count_leaf_cells(gh.levelmax(), gh.levelmax());
|
||||
npart = gh.count_leaf_cells(gh.levelmin(), gh.levelmax());
|
||||
|
||||
if (levelmax_ != levelmin_) // multimass
|
||||
npcoarse = gh.count_leaf_cells(gh.levelmin(), gh.levelmax() - 1);
|
||||
}
|
||||
|
||||
template <typename T>
|
||||
void __write_dm_mass(const grid_hierarchy &gh)
|
||||
{
|
||||
countLeafCells(gh);
|
||||
|
||||
// fill levelcount for header
|
||||
levelcounts = std::vector<size_t>(levelmax_ - levelmin_ + 1);
|
||||
for (int ilevel = gh.levelmax(); ilevel >= (int)gh.levelmin(); --ilevel)
|
||||
levelcounts[gh.levelmax() - ilevel] = gh.count_leaf_cells(ilevel, ilevel);
|
||||
|
||||
if (levelmax_ > levelmin_ + 1) // morethan2bnd
|
||||
{
|
||||
// DM particles will have variable masses
|
||||
size_t count = 0;
|
||||
|
||||
std::vector<T> data(npcoarse);
|
||||
|
||||
for (int ilevel = gh.levelmax() - 1; ilevel >= (int)gh.levelmin(); --ilevel)
|
||||
{
|
||||
// baryon particles live only on finest grid, these particles here are total matter particles
|
||||
T pmass = omega0 * rhoCrit * pow(boxSize * posFac, 3.0) / pow(2, 3 * ilevel);
|
||||
|
||||
for (unsigned i = 0; i < gh.get_grid(ilevel)->size(0); ++i)
|
||||
for (unsigned j = 0; j < gh.get_grid(ilevel)->size(1); ++j)
|
||||
for (unsigned k = 0; k < gh.get_grid(ilevel)->size(2); ++k)
|
||||
if (gh.is_in_mask(ilevel, i, j, k) && !gh.is_refined(ilevel, i, j, k))
|
||||
{
|
||||
data[count++] = pmass;
|
||||
}
|
||||
}
|
||||
|
||||
if (count != npcoarse)
|
||||
throw std::runtime_error("Internal consistency error while writing masses");
|
||||
|
||||
writeHDF5_a("Masses", coarsePartType, data); // write DM
|
||||
}
|
||||
else
|
||||
{
|
||||
// DM particles will all have the same mass, just write to massTable
|
||||
if (levelmax_ != levelmin_) // multimass
|
||||
massTable[coarsePartType] = omega0 * rhoCrit * pow(boxSize * posFac, 3.0) / pow(2, 3 * levelmin_);
|
||||
}
|
||||
}
|
||||
|
||||
template <typename T>
|
||||
void __write_dm_position(int coord, const grid_hierarchy &gh)
|
||||
{
|
||||
countLeafCells(gh);
|
||||
|
||||
// update header
|
||||
hsize_t offset_fine = 0, offset_coarse = 0;
|
||||
|
||||
for (unsigned i = 0; i < numFiles; i++)
|
||||
{
|
||||
hsize_t dims_fine = ceil(npfine / numFiles);
|
||||
hsize_t dims_coarse = ceil(npcoarse / numFiles);
|
||||
|
||||
if (i == numFiles - 1)
|
||||
{
|
||||
dims_fine = npfine - offset_fine;
|
||||
dims_coarse = npcoarse - offset_coarse;
|
||||
}
|
||||
|
||||
nPart[i][HIGHRES_DM_PARTTYPE] = dims_fine;
|
||||
nPart[i][coarsePartType] = dims_coarse;
|
||||
|
||||
offset_fine += dims_fine;
|
||||
offset_coarse += dims_coarse;
|
||||
}
|
||||
|
||||
nPartTotal[HIGHRES_DM_PARTTYPE] = npfine;
|
||||
nPartTotal[coarsePartType] = npcoarse;
|
||||
|
||||
// FINE: collect displacements and convert to absolute coordinates with correct units
|
||||
int ilevel = gh.levelmax();
|
||||
|
||||
std::vector<T> data(npfine);
|
||||
size_t count = 0;
|
||||
|
||||
for (unsigned i = 0; i < gh.get_grid(ilevel)->size(0); ++i)
|
||||
for (unsigned j = 0; j < gh.get_grid(ilevel)->size(1); ++j)
|
||||
for (unsigned k = 0; k < gh.get_grid(ilevel)->size(2); ++k)
|
||||
if (gh.is_in_mask(ilevel, i, j, k) && !gh.is_refined(ilevel, i, j, k))
|
||||
{
|
||||
double xx[3];
|
||||
gh.cell_pos(ilevel, i, j, k, xx);
|
||||
|
||||
xx[coord] = (xx[coord] + (*gh.get_grid(ilevel))(i, j, k)) * boxSize;
|
||||
xx[coord] = fmod(xx[coord] + boxSize, boxSize);
|
||||
|
||||
data[count++] = (T)(xx[coord] * posFac);
|
||||
}
|
||||
|
||||
writeHDF5_b("Coordinates", coord, HIGHRES_DM_PARTTYPE, data); // write fine DM
|
||||
|
||||
if (count != npfine)
|
||||
throw std::runtime_error("Internal consistency error while writing fine DM pos");
|
||||
|
||||
// COARSE: collect displacements and convert to absolute coordinates with correct units
|
||||
if (levelmax_ != levelmin_) // multimass
|
||||
{
|
||||
data = std::vector<T>(npcoarse, 0.0);
|
||||
count = 0;
|
||||
|
||||
for (int ilevel = gh.levelmax() - 1; ilevel >= (int)gh.levelmin(); --ilevel)
|
||||
for (unsigned i = 0; i < gh.get_grid(ilevel)->size(0); ++i)
|
||||
for (unsigned j = 0; j < gh.get_grid(ilevel)->size(1); ++j)
|
||||
for (unsigned k = 0; k < gh.get_grid(ilevel)->size(2); ++k)
|
||||
if (gh.is_in_mask(ilevel, i, j, k) && !gh.is_refined(ilevel, i, j, k))
|
||||
{
|
||||
double xx[3];
|
||||
gh.cell_pos(ilevel, i, j, k, xx);
|
||||
|
||||
xx[coord] = (xx[coord] + (*gh.get_grid(ilevel))(i, j, k)) * boxSize;
|
||||
|
||||
if (!doBaryons) // if so, we will handle the mod in write_gas_position
|
||||
xx[coord] = fmod(xx[coord] + boxSize, boxSize) * posFac;
|
||||
|
||||
data[count++] = (T)xx[coord];
|
||||
}
|
||||
|
||||
if (count != npcoarse)
|
||||
throw std::runtime_error("Internal consistency error while writing coarse DM pos");
|
||||
|
||||
writeHDF5_b("Coordinates", coord, coarsePartType, data); // write coarse DM
|
||||
}
|
||||
}
|
||||
|
||||
template <typename T>
|
||||
void __write_dm_velocity(int coord, const grid_hierarchy &gh)
|
||||
{
|
||||
countLeafCells(gh);
|
||||
|
||||
// FINE: collect velocities and convert to correct units
|
||||
int ilevel = gh.levelmax();
|
||||
|
||||
std::vector<T> data(npfine);
|
||||
size_t count = 0;
|
||||
|
||||
for (unsigned i = 0; i < gh.get_grid(ilevel)->size(0); ++i)
|
||||
for (unsigned j = 0; j < gh.get_grid(ilevel)->size(1); ++j)
|
||||
for (unsigned k = 0; k < gh.get_grid(ilevel)->size(2); ++k)
|
||||
if (gh.is_in_mask(ilevel, i, j, k) && !gh.is_refined(ilevel, i, j, k))
|
||||
{
|
||||
data[count++] = (T)(*gh.get_grid(ilevel))(i, j, k) * velFac;
|
||||
}
|
||||
|
||||
writeHDF5_b("Velocities", coord, HIGHRES_DM_PARTTYPE, data); // write fine DM
|
||||
|
||||
if (count != npfine)
|
||||
throw std::runtime_error("Internal consistency error while writing fine DM pos");
|
||||
|
||||
// COARSE: collect velocities and convert to correct units
|
||||
if (levelmax_ != levelmin_) // multimass
|
||||
{
|
||||
data = std::vector<T>(npcoarse, 0.0);
|
||||
count = 0;
|
||||
|
||||
for (int ilevel = gh.levelmax() - 1; ilevel >= (int)gh.levelmin(); --ilevel)
|
||||
for (unsigned i = 0; i < gh.get_grid(ilevel)->size(0); ++i)
|
||||
for (unsigned j = 0; j < gh.get_grid(ilevel)->size(1); ++j)
|
||||
for (unsigned k = 0; k < gh.get_grid(ilevel)->size(2); ++k)
|
||||
if (gh.is_in_mask(ilevel, i, j, k) && !gh.is_refined(ilevel, i, j, k))
|
||||
{
|
||||
data[count++] = (T)(*gh.get_grid(ilevel))(i, j, k) * velFac;
|
||||
}
|
||||
|
||||
if (count != npcoarse)
|
||||
throw std::runtime_error("Internal consistency error while writing coarse DM pos");
|
||||
|
||||
writeHDF5_b("Velocities", coord, coarsePartType, data); // write coarse DM
|
||||
}
|
||||
}
|
||||
|
||||
template <typename T>
|
||||
void __write_gas_velocity(int coord, const grid_hierarchy &gh)
|
||||
{
|
||||
countLeafCells(gh);
|
||||
|
||||
std::vector<T> gas_data(npart); // read/write gas at all levels from the gh
|
||||
size_t count = 0;
|
||||
|
||||
for (int ilevel = levelmax_; ilevel >= (int)levelmin_; --ilevel)
|
||||
for (unsigned i = 0; i < gh.get_grid(ilevel)->size(0); ++i)
|
||||
for (unsigned j = 0; j < gh.get_grid(ilevel)->size(1); ++j)
|
||||
for (unsigned k = 0; k < gh.get_grid(ilevel)->size(2); ++k)
|
||||
if (gh.is_in_mask(ilevel, i, j, k) && !gh.is_refined(ilevel, i, j, k))
|
||||
{
|
||||
gas_data[count++] = (T)(*gh.get_grid(ilevel))(i, j, k) * velFac;
|
||||
}
|
||||
|
||||
if (count != npart)
|
||||
throw std::runtime_error("Internal consistency error while writing GAS pos");
|
||||
|
||||
// calculate modified DM velocities if: multimass and baryons present
|
||||
if (doBaryons && npcoarse)
|
||||
{
|
||||
double facb = omega_b / omega0;
|
||||
double facc = (omega0 - omega_b) / omega0;
|
||||
|
||||
std::vector<T> dm_data(npcoarse);
|
||||
|
||||
writeHDF5_b("Velocities", coord, coarsePartType, dm_data, true); // read coarse DM vels
|
||||
|
||||
// overwrite
|
||||
for (size_t i = 0; i < npcoarse; i++)
|
||||
dm_data[i] = facc * dm_data[i] + facb * gas_data[npfine + i];
|
||||
|
||||
writeHDF5_b("Velocities", coord, coarsePartType, dm_data); // overwrite coarse DM vels
|
||||
} // dm_data deallocated
|
||||
|
||||
// restrict gas_data to fine only and request write
|
||||
std::vector<T> data(gas_data.begin() + 0, gas_data.begin() + npfine);
|
||||
|
||||
std::vector<T>().swap(gas_data); // deallocate
|
||||
|
||||
writeHDF5_b("Velocities", coord, GAS_PARTTYPE, data); // write highres gas
|
||||
}
|
||||
|
||||
template <typename T>
|
||||
void __write_gas_position(int coord, const grid_hierarchy &gh)
|
||||
{
|
||||
countLeafCells(gh);
|
||||
|
||||
// update header (will actually write only gas at levelmax)
|
||||
hsize_t offset = 0;
|
||||
|
||||
for (unsigned i = 0; i < numFiles; i++)
|
||||
{
|
||||
hsize_t dims = ceil(npfine / numFiles);
|
||||
if (i == numFiles - 1)
|
||||
dims = npfine - offset;
|
||||
|
||||
nPart[i][GAS_PARTTYPE] = dims;
|
||||
offset += dims;
|
||||
}
|
||||
|
||||
nPartTotal[GAS_PARTTYPE] = npfine;
|
||||
|
||||
std::vector<double> gas_data(npart); // read/write gas at all levels from the gh
|
||||
size_t count = 0;
|
||||
|
||||
double h = 1.0 / (1ul << gh.levelmax());
|
||||
|
||||
for (int ilevel = gh.levelmax(); ilevel >= (int)gh.levelmin(); --ilevel)
|
||||
for (unsigned i = 0; i < gh.get_grid(ilevel)->size(0); ++i)
|
||||
for (unsigned j = 0; j < gh.get_grid(ilevel)->size(1); ++j)
|
||||
for (unsigned k = 0; k < gh.get_grid(ilevel)->size(2); ++k)
|
||||
if (gh.is_in_mask(ilevel, i, j, k) && !gh.is_refined(ilevel, i, j, k))
|
||||
{
|
||||
double xx[3];
|
||||
gh.cell_pos(ilevel, i, j, k, xx);
|
||||
|
||||
// shift particle positions (this has to be done as the same shift
|
||||
// is used when computing the convolution kernel for SPH baryons)
|
||||
xx[coord] += 0.5 * h;
|
||||
|
||||
xx[coord] = (xx[coord] + (*gh.get_grid(ilevel))(i, j, k)) * boxSize;
|
||||
|
||||
gas_data[count++] = xx[coord];
|
||||
}
|
||||
|
||||
if (count != npart)
|
||||
throw std::runtime_error("Internal consistency error while writing coarse DM pos");
|
||||
|
||||
// calculate modified DM coordinates if: multimass and baryons present
|
||||
if (doBaryons && npcoarse)
|
||||
{
|
||||
double facb = omega_b / omega0;
|
||||
double facc = (omega0 - omega_b) / omega0;
|
||||
|
||||
std::vector<T> dm_data(npcoarse);
|
||||
|
||||
writeHDF5_b("Coordinates", coord, coarsePartType, dm_data, true); // read coarse DM vels
|
||||
|
||||
// overwrite
|
||||
for (size_t i = 0; i < npcoarse; i++)
|
||||
{
|
||||
dm_data[i] = facc * dm_data[i] + facb * gas_data[npfine + i];
|
||||
dm_data[i] = fmod(dm_data[i] + boxSize, boxSize) * posFac;
|
||||
}
|
||||
|
||||
writeHDF5_b("Coordinates", coord, coarsePartType, dm_data); // overwrite coarse DM vels
|
||||
}
|
||||
|
||||
// restrict gas_data to fine only and request write
|
||||
//std::vector<float> data( gas_data.begin() + 0, gas_data.begin() + npfine );
|
||||
|
||||
std::vector<T> data(npfine);
|
||||
|
||||
for (size_t i = 0; i < npfine; i++)
|
||||
data[i] = (T)(fmod(gas_data[i] + boxSize, boxSize) * posFac);
|
||||
|
||||
std::vector<double>().swap(gas_data); // deallocate
|
||||
|
||||
writeHDF5_b("Coordinates", coord, GAS_PARTTYPE, data); // write highres gas
|
||||
}
|
||||
|
||||
public:
|
||||
arepo_output_plugin(config_file &cf) : output_plugin(cf)
|
||||
{
|
||||
// ensure that everyone knows we want to do SPH, implies: bsph=1, bbshift=1, decic_baryons=1
|
||||
// -> instead of just writing gas densities (which are here ignored), the gas displacements are also written
|
||||
cf.insertValue("setup", "do_SPH", "yes");
|
||||
|
||||
// init header and config parameters
|
||||
nPartTotal = std::vector<long long>(NTYPES, 0);
|
||||
massTable = std::vector<double>(NTYPES, 0.0);
|
||||
|
||||
coarsePartType = cf.getValueSafe<unsigned>("output", "arepo_coarsetype", COARSE_DM_DEFAULT_PARTTYPE);
|
||||
UnitLength_in_cm = cf.getValueSafe<double>("output", "arepo_unitlength", 3.085678e21); // 1.0 kpc
|
||||
UnitMass_in_g = cf.getValueSafe<double>("output", "arepo_unitmass", 1.989e43); // 1.0e10 solar masses
|
||||
UnitVelocity_in_cm_per_s = cf.getValueSafe<double>("output", "arepo_unitvel", 1e5); // 1 km/sec
|
||||
|
||||
omega0 = cf.getValue<double>("cosmology", "Omega_m");
|
||||
omega_b = cf.getValue<double>("cosmology", "Omega_b");
|
||||
omega_L = cf.getValue<double>("cosmology", "Omega_L");
|
||||
redshift = cf.getValue<double>("setup", "zstart");
|
||||
boxSize = cf.getValue<double>("setup", "boxlength");
|
||||
doBaryons = cf.getValueSafe<bool>("setup", "baryons", false);
|
||||
useLongIDs = cf.getValueSafe<bool>("output", "arepo_longids", false);
|
||||
numFiles = cf.getValueSafe<unsigned>("output", "arepo_num_files", 1);
|
||||
doublePrec = cf.getValueSafe<bool>("output", "arepo_doubleprec", 0);
|
||||
|
||||
for (unsigned i = 0; i < numFiles; i++)
|
||||
nPart.push_back(std::vector<unsigned int>(NTYPES, 0));
|
||||
|
||||
// factors which multiply positions and velocities
|
||||
time = 1.0 / (1.0 + redshift);
|
||||
posFac = 3.085678e24 / UnitLength_in_cm; // MUSIC uses Mpc internally, i.e. posFac=1e3 for kpc output
|
||||
velFac = (1.0f / sqrt(time)) * boxSize;
|
||||
|
||||
// critical density
|
||||
rhoCrit = 27.7519737e-9; // in h^2 1e10 M_sol / kpc^3
|
||||
rhoCrit *= pow(UnitLength_in_cm / 3.085678e21, 3.0);
|
||||
rhoCrit *= (1.989e43 / UnitMass_in_g);
|
||||
|
||||
// calculate PMGRID suggestion
|
||||
pmgrid = pow(2, levelmin_) * 2; // unigrid
|
||||
gridboost = 1;
|
||||
|
||||
if (levelmin_ != levelmax_)
|
||||
{
|
||||
double lxref[3], x0ref[3], x1ref[3];
|
||||
double pmgrid_new;
|
||||
|
||||
the_region_generator->get_AABB(x0ref, x1ref, levelmax_); // generalized beyond box
|
||||
for (int i = 0; i < 3; i++)
|
||||
lxref[i] = x1ref[i] - x0ref[i];
|
||||
|
||||
// fraction box length of the zoom region
|
||||
lxref[0] = pow((lxref[0] * lxref[1] * lxref[2]), 0.333);
|
||||
|
||||
pmgrid_new = pow(2, levelmax_) * 2; // to cover entire box at highest resolution
|
||||
pmgrid_new *= lxref[0]; // only need to cover a fraction
|
||||
|
||||
if ((gridboost = round(pmgrid_new / pmgrid)) > 1)
|
||||
gridboost = pow(2, ceil(log(gridboost) / log(2.0))); // round to nearest, higher power of 2
|
||||
if (gridboost == 0)
|
||||
gridboost = 1;
|
||||
}
|
||||
|
||||
// calculate Tini for gas
|
||||
hubbleParam = cf.getValue<double>("cosmology", "H0") / 100.0;
|
||||
|
||||
double astart = 1.0 / (1.0 + redshift);
|
||||
double h2 = hubbleParam * hubbleParam;
|
||||
double adec = 1.0 / (160.0 * pow(omega_b * h2 / 0.022, 2.0 / 5.0));
|
||||
double Tcmb0 = 2.726;
|
||||
|
||||
Tini = astart < adec ? Tcmb0 / astart : Tcmb0 / astart / astart * adec;
|
||||
|
||||
// calculate softening suggestion
|
||||
softening = (boxSize * posFac) / pow(2, levelmax_) / 40.0;
|
||||
|
||||
// header and sanity checks
|
||||
if (!doBaryons)
|
||||
massTable[HIGHRES_DM_PARTTYPE] = omega0 * rhoCrit * pow(boxSize * posFac, 3.0) / pow(2, 3 * levelmax_);
|
||||
else
|
||||
massTable[HIGHRES_DM_PARTTYPE] = (omega0 - omega_b) * rhoCrit * pow(boxSize * posFac, 3.0) / pow(2, 3 * levelmax_);
|
||||
|
||||
if (coarsePartType == GAS_PARTTYPE || coarsePartType == HIGHRES_DM_PARTTYPE)
|
||||
throw std::runtime_error("Error: Specified illegal Arepo particle type for coarse particles.");
|
||||
if (coarsePartType == STAR_PARTTYPE)
|
||||
LOGWARN("WARNING: Specified coarse particle type will collide with stars if USE_SFR enabled.");
|
||||
|
||||
// create file(s)
|
||||
for (unsigned i = 0; i < numFiles; i++)
|
||||
{
|
||||
std::string filename = fname_;
|
||||
if (numFiles > 1)
|
||||
{
|
||||
size_t pos = filename.find(".hdf5");
|
||||
if (pos != filename.length() - 5)
|
||||
throw std::runtime_error("Error: Unexpected output filename (doesn't end in .hdf5).");
|
||||
|
||||
std::stringstream s;
|
||||
s << "." << i << ".hdf5";
|
||||
filename.replace(pos, 5, s.str());
|
||||
}
|
||||
|
||||
HDFCreateFile(filename);
|
||||
|
||||
// create particle type groups
|
||||
std::stringstream GrpName;
|
||||
GrpName << "PartType" << HIGHRES_DM_PARTTYPE;
|
||||
|
||||
HDFCreateGroup(filename, GrpName.str().c_str()); // highres or unigrid DM
|
||||
|
||||
if (doBaryons)
|
||||
{
|
||||
GrpName.str("");
|
||||
GrpName << "PartType" << GAS_PARTTYPE;
|
||||
HDFCreateGroup(filename, GrpName.str().c_str()); // gas
|
||||
}
|
||||
|
||||
if (levelmax_ != levelmin_) // multimass
|
||||
{
|
||||
GrpName.str("");
|
||||
GrpName << "PartType" << coarsePartType;
|
||||
HDFCreateGroup(filename, GrpName.str().c_str()); // coarse DM
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
~arepo_output_plugin()
|
||||
{
|
||||
}
|
||||
|
||||
/* ------------------------------------------------------------------------------- */
|
||||
void write_dm_mass(const grid_hierarchy &gh)
|
||||
{
|
||||
if (!doublePrec)
|
||||
__write_dm_mass<float>(gh);
|
||||
else
|
||||
__write_dm_mass<double>(gh);
|
||||
}
|
||||
|
||||
void write_dm_position(int coord, const grid_hierarchy &gh)
|
||||
{
|
||||
if (!doublePrec)
|
||||
__write_dm_position<float>(coord, gh);
|
||||
else
|
||||
__write_dm_position<double>(coord, gh);
|
||||
}
|
||||
|
||||
void write_dm_velocity(int coord, const grid_hierarchy &gh)
|
||||
{
|
||||
if (!doublePrec)
|
||||
__write_dm_velocity<float>(coord, gh);
|
||||
else
|
||||
__write_dm_velocity<double>(coord, gh);
|
||||
}
|
||||
|
||||
void write_dm_density(const grid_hierarchy &gh)
|
||||
{ /* skip */
|
||||
}
|
||||
|
||||
void write_dm_potential(const grid_hierarchy &gh)
|
||||
{ /* skip */
|
||||
}
|
||||
|
||||
/* ------------------------------------------------------------------------------- */
|
||||
void write_gas_velocity(int coord, const grid_hierarchy &gh)
|
||||
{
|
||||
if (!doublePrec)
|
||||
__write_gas_velocity<float>(coord, gh);
|
||||
else
|
||||
__write_gas_velocity<double>(coord, gh);
|
||||
}
|
||||
|
||||
void write_gas_position(int coord, const grid_hierarchy &gh)
|
||||
{
|
||||
if (!doublePrec)
|
||||
__write_gas_position<float>(coord, gh);
|
||||
else
|
||||
__write_gas_position<double>(coord, gh);
|
||||
}
|
||||
|
||||
void write_gas_density(const grid_hierarchy &gh)
|
||||
{
|
||||
// if only saving highres gas, then all gas cells have the same initial mass
|
||||
// do not write out densities as we write out displacements
|
||||
if (doBaryons)
|
||||
massTable[GAS_PARTTYPE] = omega_b * rhoCrit * pow(boxSize * posFac, 3.0) / pow(2, 3 * levelmax_);
|
||||
}
|
||||
|
||||
void write_gas_potential(const grid_hierarchy &gh)
|
||||
{ /* skip */
|
||||
}
|
||||
|
||||
void finalize(void)
|
||||
{
|
||||
// generate and add contiguous IDs for each particle type we have written
|
||||
generateAndWriteIDs();
|
||||
|
||||
std::vector<unsigned int> nPartTotalLW(nPartTotal.size());
|
||||
std::vector<unsigned int> nPartTotalHW(nPartTotal.size());
|
||||
for (size_t i = 0; i < nPartTotalHW.size(); i++)
|
||||
{
|
||||
nPartTotalHW[i] = (unsigned)((size_t)nPartTotal[i] >> 32);
|
||||
nPartTotalLW[i] = (unsigned int)((size_t)nPartTotal[i]);
|
||||
}
|
||||
|
||||
// output particle counts
|
||||
std::cout << " - Arepo : wrote " << nPartTotAllTypes << " particles..." << std::endl;
|
||||
for (size_t i = 0; i < nPartTotal.size(); i++)
|
||||
std::cout << " type [" << i << "] : " << std::setw(12) << nPartTotal[i] << std::endl;
|
||||
std::cout << std::endl;
|
||||
|
||||
// write final header (some of these fields are required, others are extra info)
|
||||
for (unsigned i = 0; i < numFiles; i++)
|
||||
{
|
||||
std::string filename = fname_;
|
||||
if (numFiles > 1)
|
||||
{
|
||||
std::stringstream s;
|
||||
s << "." << i << ".hdf5";
|
||||
filename.replace(filename.find(".hdf5"), 5, s.str());
|
||||
|
||||
std::cout << " " << filename;
|
||||
for (size_t j = 0; j < nPart[i].size(); j++)
|
||||
std::cout << " " << std::setw(10) << nPart[i][j];
|
||||
std::cout << std::endl;
|
||||
}
|
||||
|
||||
HDFCreateGroup(filename, "Header");
|
||||
|
||||
HDFWriteGroupAttribute(filename, "Header", "NumPart_ThisFile", nPart[i]);
|
||||
HDFWriteGroupAttribute(filename, "Header", "NumPart_Total", nPartTotalLW);
|
||||
HDFWriteGroupAttribute(filename, "Header", "NumPart_Total_HighWord", nPartTotalHW);
|
||||
HDFWriteGroupAttribute(filename, "Header", "MassTable", massTable);
|
||||
HDFWriteGroupAttribute(filename, "Header", "BoxSize", boxSize);
|
||||
HDFWriteGroupAttribute(filename, "Header", "NumFilesPerSnapshot", numFiles);
|
||||
HDFWriteGroupAttribute(filename, "Header", "Time", time);
|
||||
HDFWriteGroupAttribute(filename, "Header", "Redshift", redshift);
|
||||
HDFWriteGroupAttribute(filename, "Header", "Omega0", omega0);
|
||||
HDFWriteGroupAttribute(filename, "Header", "OmegaLambda", omega_L);
|
||||
HDFWriteGroupAttribute(filename, "Header", "OmegaBaryon", omega_b);
|
||||
HDFWriteGroupAttribute(filename, "Header", "HubbleParam", hubbleParam);
|
||||
HDFWriteGroupAttribute(filename, "Header", "Flag_Sfr", 0);
|
||||
HDFWriteGroupAttribute(filename, "Header", "Flag_Cooling", 0);
|
||||
HDFWriteGroupAttribute(filename, "Header", "Flag_StellarAge", 0);
|
||||
HDFWriteGroupAttribute(filename, "Header", "Flag_Metals", 0);
|
||||
HDFWriteGroupAttribute(filename, "Header", "Flag_Feedback", 0);
|
||||
HDFWriteGroupAttribute(filename, "Header", "Flag_DoublePrecision", (int)doublePrec);
|
||||
HDFWriteGroupAttribute(filename, "Header", "Music_levelmin", levelmin_);
|
||||
HDFWriteGroupAttribute(filename, "Header", "Music_levelmax", levelmax_);
|
||||
HDFWriteGroupAttribute(filename, "Header", "Music_levelcounts", levelcounts);
|
||||
HDFWriteGroupAttribute(filename, "Header", "haveBaryons", (int)doBaryons);
|
||||
HDFWriteGroupAttribute(filename, "Header", "longIDs", (int)useLongIDs);
|
||||
HDFWriteGroupAttribute(filename, "Header", "suggested_pmgrid", pmgrid);
|
||||
HDFWriteGroupAttribute(filename, "Header", "suggested_gridboost", gridboost);
|
||||
HDFWriteGroupAttribute(filename, "Header", "suggested_highressoft", softening);
|
||||
HDFWriteGroupAttribute(filename, "Header", "suggested_gas_Tinit", Tini);
|
||||
}
|
||||
|
||||
// give config/parameter file hints
|
||||
if (useLongIDs)
|
||||
std::cout << " - Arepo: Wrote 64bit IDs, enable LONGIDS." << std::endl;
|
||||
if (doublePrec)
|
||||
std::cout << " - Arepo: Double precision ICs, set INPUT_IN_DOUBLEPRECISION." << std::endl;
|
||||
if (NTYPES != 6)
|
||||
std::cout << " - Arepo: Using [" << NTYPES << "] particle types, set NTYPES to match." << std::endl;
|
||||
if (doBaryons)
|
||||
std::cout << " - Arepo: Wrote high-res gas (only), set REFINEMENT_HIGH_RES_GAS and GENERATE_GAS_IN_ICS with "
|
||||
<< "SPLIT_PARTICLE_TYPE=" << pow(2, coarsePartType) << "." << std::endl;
|
||||
if (levelmax_ != levelmin_)
|
||||
std::cout << " - Arepo: Have zoom type ICs, set PLACEHIGHRESREGION=" << pow(2, HIGHRES_DM_PARTTYPE)
|
||||
<< " (suggest PMGRID=" << pmgrid << " with GRIDBOOST=" << gridboost << ")." << std::endl;
|
||||
else
|
||||
std::cout << " - Arepo: Have unigrid type ICs (suggest PMGRID=" << pmgrid << ")." << std::endl;
|
||||
if (levelmax_ > levelmin_ + 1)
|
||||
std::cout << " - Arepo: More than one coarse DM mass using same type, set INDIVIDUAL_GRAVITY_SOFTENING="
|
||||
<< pow(2, coarsePartType) << " (+" << pow(2, STAR_PARTTYPE) << " if including stars)." << std::endl;
|
||||
if (doBaryons)
|
||||
std::cout << " - Arepo: Set initial gas temperature to " << std::fixed << std::setprecision(3) << Tini << " K." << std::endl;
|
||||
std::cout << " - Arepo: Suggest grav softening = " << std::setprecision(3) << softening << " for high res DM." << std::endl;
|
||||
}
|
||||
};
|
||||
|
||||
namespace
|
||||
{
|
||||
output_plugin_creator_concrete<arepo_output_plugin> creator("arepo");
|
||||
}
|
||||
|
||||
#endif // HAVE_HDF5
|
||||
903
src/plugins/output_art.cc
Normal file
903
src/plugins/output_art.cc
Normal file
|
|
@ -0,0 +1,903 @@
|
|||
/*
|
||||
|
||||
output_art.cc - This file is part of MUSIC -
|
||||
a code to generate multi-scale initial conditions
|
||||
for cosmological simulations
|
||||
|
||||
Copyright (C) 2012 Jose Onorbe & Oliver Hahn
|
||||
|
||||
*/
|
||||
#include <stdio.h>
|
||||
#include <unistd.h>
|
||||
#include <string.h>
|
||||
#include <sys/types.h>
|
||||
#include <sys/stat.h>
|
||||
#include <vector>
|
||||
|
||||
#include "output.hh"
|
||||
|
||||
template <typename T>
|
||||
inline T bytereorder(T v)
|
||||
{
|
||||
T rval;
|
||||
(reinterpret_cast<unsigned char *>(&rval))[3] = (reinterpret_cast<unsigned char *>(&v))[0];
|
||||
(reinterpret_cast<unsigned char *>(&rval))[2] = (reinterpret_cast<unsigned char *>(&v))[1];
|
||||
(reinterpret_cast<unsigned char *>(&rval))[1] = (reinterpret_cast<unsigned char *>(&v))[2];
|
||||
(reinterpret_cast<unsigned char *>(&rval))[0] = (reinterpret_cast<unsigned char *>(&v))[3];
|
||||
return rval;
|
||||
}
|
||||
|
||||
template <typename T_store = float>
|
||||
class art_output_plugin : public output_plugin
|
||||
{
|
||||
public:
|
||||
bool do_baryons_;
|
||||
bool swap_endianness_;
|
||||
double omegab_, omegam_;
|
||||
double gamma_;
|
||||
double astart_;
|
||||
double zstart_;
|
||||
size_t npcdm_;
|
||||
int hsize_;
|
||||
|
||||
protected:
|
||||
enum iofields
|
||||
{
|
||||
id_dm_pos,
|
||||
id_dm_vel,
|
||||
id_gas_pos,
|
||||
id_gas_vel
|
||||
};
|
||||
|
||||
struct header
|
||||
{
|
||||
char head[45];
|
||||
float aexpN; // current expansion factor
|
||||
float aexp0; // initial expansion factor
|
||||
float amplt; // Amplitude of density fluctuations
|
||||
float astep; // Delta a -> time step.
|
||||
// This value is also stored in pt.dat (binary 1 float)
|
||||
// It is recalculated by art for the next steps so just a small value should work
|
||||
int istep; // step (=0 in IC)
|
||||
float partw; // mass of highest res particle.
|
||||
float TINTG; //=0 in IC
|
||||
float EKIN; //SUM 0.5 * m_i*(v_i**2) in code units
|
||||
float EKIN1; //=0 in IC
|
||||
float EKIN2; //=0 in IC
|
||||
float AU0; //=0 in IC
|
||||
float AEU0; //=0 in IC
|
||||
int NROWC; // Number of particles in 1 dim (number of particles per page = NROW**2)
|
||||
int NGRIDC; // Number of cells in 1 dim
|
||||
int nspecies; // number of dm species
|
||||
int Nseed; // random number used ( 0 for MUSIC? or set the random number used in the lowest level?)
|
||||
float Om0; //Omega_m
|
||||
float Oml0; //Omega_L
|
||||
float hubble; //hubble constant h=H/100
|
||||
float Wp5; //
|
||||
float Ocurv; //Omega_k
|
||||
float Omb0; // this parameter only appears in header in hydro runs
|
||||
float wpart[10]; // extras[0-9] particle masses from high res to low res (normalized to low res particle)
|
||||
// Mass of smallest particle=wpart[0]*0m0*2.746e+11*(Box/NGRID)**3 -> Msun/h
|
||||
// Mass of largest particle=wpart[nspecies-1]*0m0*2.746e+11*(Box/NGRID)**3 -> Msun/h
|
||||
int lpart[10]; // extras[10-19] number of particles from high res to low res cumulative!!!
|
||||
//(i.e., lpart[0]=Nhigh res particles; lpart[1]=lpart[0]+N_this_level; etc) so lpart[nspecies-1]=N total
|
||||
float extras[80]; //extras[20-99]
|
||||
//extras[9]=iLblock ->0 in IC
|
||||
//extras[10]=LevMin ->0 in IC
|
||||
//extras[11]=LevSmall ->0 in IC
|
||||
//extras[12]=LevLarge ->0 in IC
|
||||
//extras[13]=Omegab ->0 in IC; fix it?
|
||||
//extras[14]=sig8 ->0 in IC; fix it?
|
||||
//extras[15]=Spslope ->0 in IC; fix it? Slope of the Power spectrum
|
||||
//extras[16]=iDEswtch ->0 in IC; DE Flag=0:LCDM 1:w 2:RP 3:SUGRA
|
||||
//extras[17]=DEw0 ->0 in IC; w0 for DE z=0
|
||||
//extras[18]=DEwprime ->0 in IC; DE parameter
|
||||
//extras[59]= 0 or 1; is used as switch for random numbers generators [do not apply in music use 0?]
|
||||
//extras[60]= lux - level of luxury [do not apply in music use 0?]
|
||||
//extras[79]=Lbox (Mpc/h)
|
||||
};
|
||||
|
||||
struct ptf
|
||||
{
|
||||
float astep;
|
||||
};
|
||||
|
||||
header header_;
|
||||
ptf ptf_;
|
||||
std::string fname;
|
||||
size_t np_fine_gas_, np_fine_dm_, np_coarse_dm_;
|
||||
size_t block_buf_size_;
|
||||
size_t npartmax_;
|
||||
|
||||
double YHe_;
|
||||
|
||||
// helper class to read temp files
|
||||
class pistream : public std::ifstream
|
||||
{
|
||||
public:
|
||||
pistream(std::string fname, size_t npart)
|
||||
: std::ifstream(fname.c_str(), std::ios::binary)
|
||||
{
|
||||
size_t blk;
|
||||
|
||||
if (!this->good())
|
||||
{
|
||||
LOGERR("Could not open buffer file in ART output plug-in");
|
||||
throw std::runtime_error("Could not open buffer file in ART output plug-in");
|
||||
}
|
||||
|
||||
this->read((char *)&blk, sizeof(size_t));
|
||||
|
||||
if (blk != (size_t)(npart * sizeof(T_store)))
|
||||
{
|
||||
LOGERR("Internal consistency error in ART output plug-in");
|
||||
LOGERR("Expected %d bytes in temp file but found %d", npart * (unsigned)sizeof(T_store), blk);
|
||||
throw std::runtime_error("Internal consistency error in ART output plug-in");
|
||||
}
|
||||
}
|
||||
|
||||
pistream()
|
||||
{
|
||||
}
|
||||
|
||||
void open(std::string fname, size_t npart)
|
||||
{
|
||||
std::ifstream::open(fname.c_str(), std::ios::binary);
|
||||
size_t blk;
|
||||
|
||||
if (!this->good())
|
||||
{
|
||||
LOGERR("Could not open buffer file \'%s\' in ART output plug-in", fname.c_str());
|
||||
throw std::runtime_error("Could not open buffer file in ART output plug-in");
|
||||
}
|
||||
|
||||
this->read((char *)&blk, sizeof(size_t));
|
||||
|
||||
if (blk != (size_t)(npart * sizeof(T_store)))
|
||||
{
|
||||
LOGERR("Internal consistency error in ART output plug-in");
|
||||
LOGERR("Expected %d bytes in temp file but found %d", npart * (unsigned)sizeof(T_store), blk);
|
||||
throw std::runtime_error("Internal consistency error in ART output plug-in");
|
||||
}
|
||||
}
|
||||
};
|
||||
|
||||
// non-public member functions
|
||||
void write_header_file(void) //PMcrd.DAT
|
||||
{
|
||||
|
||||
std::string fout;
|
||||
if (do_baryons_)
|
||||
fout = "/PMcrdIC.DAT";
|
||||
else
|
||||
fout = "/PMcrd.DAT";
|
||||
std::string partfname = fname_ + fout;
|
||||
std::ofstream ofs(partfname.c_str(), std::ios::trunc);
|
||||
//ofs.open(fname_.c_str(), std::ios::binary|std::ios::trunc );
|
||||
header this_header(header_);
|
||||
//Should be 529 in a dm only run; 533 in a baryon run
|
||||
//but not working for alignment so it must be written one by one:
|
||||
int blksize = hsize_;
|
||||
if (swap_endianness_)
|
||||
{
|
||||
LOGINFO("ART : swap_endianness option enabled");
|
||||
blksize = bytereorder(blksize);
|
||||
this_header.aexpN = bytereorder(this_header.aexpN);
|
||||
this_header.aexp0 = bytereorder(this_header.aexp0);
|
||||
this_header.amplt = bytereorder(this_header.amplt);
|
||||
this_header.astep = bytereorder(this_header.astep);
|
||||
this_header.istep = bytereorder(this_header.istep);
|
||||
this_header.partw = bytereorder(this_header.partw);
|
||||
this_header.TINTG = bytereorder(this_header.TINTG);
|
||||
this_header.EKIN = bytereorder(this_header.EKIN);
|
||||
this_header.EKIN1 = bytereorder(this_header.EKIN1);
|
||||
this_header.EKIN2 = bytereorder(this_header.EKIN2);
|
||||
this_header.AEU0 = bytereorder(this_header.AEU0);
|
||||
this_header.AEU0 = bytereorder(this_header.AEU0);
|
||||
this_header.NROWC = bytereorder(this_header.NROWC);
|
||||
this_header.NGRIDC = bytereorder(this_header.NGRIDC);
|
||||
this_header.nspecies = bytereorder(this_header.nspecies);
|
||||
this_header.Nseed = bytereorder(this_header.Nseed);
|
||||
this_header.Om0 = bytereorder(this_header.Om0);
|
||||
this_header.Oml0 = bytereorder(this_header.Oml0);
|
||||
this_header.hubble = bytereorder(this_header.hubble);
|
||||
this_header.Wp5 = bytereorder(this_header.Wp5);
|
||||
this_header.Ocurv = bytereorder(this_header.Ocurv);
|
||||
this_header.Omb0 = bytereorder(this_header.Omb0);
|
||||
for (int i = 0; i < 10; ++i)
|
||||
{
|
||||
this_header.wpart[i] = bytereorder(this_header.wpart[i]);
|
||||
this_header.lpart[i] = bytereorder(this_header.lpart[i]);
|
||||
}
|
||||
for (int i = 0; i < 80; ++i)
|
||||
{
|
||||
this_header.extras[i] = bytereorder(this_header.extras[i]);
|
||||
}
|
||||
}
|
||||
ofs.write((char *)&blksize, sizeof(int));
|
||||
//ofs.write( (char *)&this_header,sizeof(header)); //Not working because struct aligment, so:
|
||||
ofs.write((char *)&this_header.head, sizeof(this_header.head));
|
||||
ofs.write((char *)&this_header.aexpN, sizeof(this_header.aexpN));
|
||||
ofs.write((char *)&this_header.aexp0, sizeof(this_header.aexp0));
|
||||
ofs.write((char *)&this_header.amplt, sizeof(this_header.amplt));
|
||||
ofs.write((char *)&this_header.astep, sizeof(this_header.astep));
|
||||
ofs.write((char *)&this_header.istep, sizeof(this_header.istep));
|
||||
ofs.write((char *)&this_header.partw, sizeof(this_header.partw));
|
||||
ofs.write((char *)&this_header.TINTG, sizeof(this_header.TINTG));
|
||||
ofs.write((char *)&this_header.EKIN, sizeof(this_header.EKIN));
|
||||
ofs.write((char *)&this_header.EKIN1, sizeof(this_header.EKIN1));
|
||||
ofs.write((char *)&this_header.EKIN2, sizeof(this_header.EKIN2));
|
||||
ofs.write((char *)&this_header.AEU0, sizeof(this_header.AEU0));
|
||||
ofs.write((char *)&this_header.AEU0, sizeof(this_header.AEU0));
|
||||
ofs.write((char *)&this_header.NROWC, sizeof(this_header.NROWC));
|
||||
ofs.write((char *)&this_header.NGRIDC, sizeof(this_header.NGRIDC));
|
||||
ofs.write((char *)&this_header.nspecies, sizeof(this_header.nspecies));
|
||||
ofs.write((char *)&this_header.Nseed, sizeof(this_header.Nseed));
|
||||
ofs.write((char *)&this_header.Om0, sizeof(this_header.Om0));
|
||||
ofs.write((char *)&this_header.Oml0, sizeof(this_header.Oml0));
|
||||
ofs.write((char *)&this_header.hubble, sizeof(this_header.hubble));
|
||||
ofs.write((char *)&this_header.Wp5, sizeof(this_header.Wp5));
|
||||
ofs.write((char *)&this_header.Ocurv, sizeof(this_header.Ocurv));
|
||||
ofs.write((char *)&this_header.wpart, sizeof(this_header.wpart));
|
||||
ofs.write((char *)&this_header.lpart, sizeof(this_header.lpart));
|
||||
ofs.write((char *)&this_header.extras, sizeof(this_header.extras));
|
||||
ofs.write((char *)&blksize, sizeof(int));
|
||||
ofs.close();
|
||||
LOGINFO("ART : done writing header file.");
|
||||
}
|
||||
|
||||
void write_pt_file(void) //pt.dat
|
||||
{
|
||||
std::string partfname = fname_ + "/pt.dat";
|
||||
std::ofstream ofs(partfname.c_str(), std::ios::trunc);
|
||||
//ofs.open(fname_.c_str(), std::ios::binary|std::ios::trunc );
|
||||
ptf this_ptf(ptf_);
|
||||
int blksize = sizeof(ptf); //4
|
||||
if (swap_endianness_)
|
||||
{
|
||||
blksize = bytereorder(blksize);
|
||||
this_ptf = bytereorder(this_ptf);
|
||||
}
|
||||
ofs.write((char *)&blksize, sizeof(int));
|
||||
ofs.write((char *)&this_ptf, sizeof(ptf));
|
||||
ofs.write((char *)&blksize, sizeof(int));
|
||||
ofs.close();
|
||||
LOGINFO("ART : done writing pt file.");
|
||||
}
|
||||
|
||||
void adjust_buf_endianness(T_store *buf)
|
||||
{
|
||||
if (swap_endianness_)
|
||||
{
|
||||
for (size_t i = 0; i < block_buf_size_; ++i)
|
||||
buf[i] = bytereorder<T_store>(buf[i]);
|
||||
}
|
||||
}
|
||||
|
||||
/*
|
||||
The direct format write the particle data in pages. Each page of particles is read into a common block,
|
||||
which has the structure: X(Npage),Y(Npage),Z(Npage),Vx(Npage),Vy(Npage),Vz(Npage).
|
||||
There are NO Fortran size blocks pre or after these blocks!!
|
||||
|
||||
The number of particles in each page (Npage) is Npage = Nrow**2; Npages = (N_particles -1)/NPAGE +1
|
||||
so in last page sometimes can be tricky (zooms): N_in_last=N_particles -NPAGE*(Npages-1)
|
||||
But keep in mind that ART expects all pages to be written in full regarding of the actual number of particles
|
||||
you care about.
|
||||
|
||||
*/
|
||||
void assemble_DM_file(void) //PMcrs0.DAT
|
||||
{
|
||||
// file name
|
||||
|
||||
std::string fout;
|
||||
if (do_baryons_)
|
||||
fout = "/PMcrs0IC.DAT";
|
||||
else
|
||||
fout = "/PMcrs0.DAT";
|
||||
|
||||
std::string partfname = fname_ + fout;
|
||||
std::ofstream ofs(partfname.c_str(), std::ios::trunc);
|
||||
|
||||
// generate all temp file names
|
||||
char fnx[256], fny[256], fnz[256], fnvx[256], fnvy[256], fnvz[256];
|
||||
sprintf(fnx, "___ic_temp_%05d.bin", 100 * id_dm_pos + 0);
|
||||
sprintf(fny, "___ic_temp_%05d.bin", 100 * id_dm_pos + 1);
|
||||
sprintf(fnz, "___ic_temp_%05d.bin", 100 * id_dm_pos + 2);
|
||||
sprintf(fnvx, "___ic_temp_%05d.bin", 100 * id_dm_vel + 0);
|
||||
sprintf(fnvy, "___ic_temp_%05d.bin", 100 * id_dm_vel + 1);
|
||||
sprintf(fnvz, "___ic_temp_%05d.bin", 100 * id_dm_vel + 2);
|
||||
|
||||
// create buffers for temporary data
|
||||
T_store *tmp1, *tmp2, *tmp3, *tmp4, *tmp5, *tmp6;
|
||||
|
||||
tmp1 = new T_store[block_buf_size_];
|
||||
tmp2 = new T_store[block_buf_size_];
|
||||
tmp3 = new T_store[block_buf_size_];
|
||||
tmp4 = new T_store[block_buf_size_];
|
||||
tmp5 = new T_store[block_buf_size_];
|
||||
tmp6 = new T_store[block_buf_size_];
|
||||
|
||||
// read in the data from the temporary files in slabs and write it to the output file
|
||||
size_t npleft, n2read;
|
||||
size_t npcdm = npcdm_;
|
||||
|
||||
LOGINFO("writing DM data to ART format file");
|
||||
//ofs.open(fname_.c_str(), std::ios::binary|std::ios::trunc );
|
||||
|
||||
pistream ifs_x, ifs_y, ifs_z, ifs_vx, ifs_vy, ifs_vz;
|
||||
|
||||
ifs_x.open(fnx, npcdm);
|
||||
ifs_y.open(fny, npcdm);
|
||||
ifs_z.open(fnz, npcdm);
|
||||
ifs_vx.open(fnvx, npcdm);
|
||||
ifs_vy.open(fnvy, npcdm);
|
||||
ifs_vz.open(fnvz, npcdm);
|
||||
|
||||
npleft = npcdm;
|
||||
n2read = std::min(block_buf_size_, npleft);
|
||||
while (n2read > 0)
|
||||
{
|
||||
// To make sure last page in zooms have 0s in non-relevant values
|
||||
// NOT MANDATORY. Can be commented if makes things slow
|
||||
// but I do not like the idea of writting data in the file
|
||||
// that could be interpreted as real.
|
||||
if (n2read < block_buf_size_)
|
||||
{
|
||||
for (int i = 0; i < int(block_buf_size_); i++)
|
||||
{
|
||||
tmp1[i] = 0.0;
|
||||
tmp2[i] = 0.0;
|
||||
tmp3[i] = 0.0;
|
||||
tmp4[i] = 0.0;
|
||||
tmp5[i] = 0.0;
|
||||
tmp6[i] = 0.0;
|
||||
}
|
||||
}
|
||||
ifs_x.read(reinterpret_cast<char *>(&tmp1[0]), n2read * sizeof(T_store));
|
||||
ifs_y.read(reinterpret_cast<char *>(&tmp2[0]), n2read * sizeof(T_store));
|
||||
ifs_z.read(reinterpret_cast<char *>(&tmp3[0]), n2read * sizeof(T_store));
|
||||
ifs_vx.read(reinterpret_cast<char *>(&tmp4[0]), n2read * sizeof(T_store));
|
||||
ifs_vy.read(reinterpret_cast<char *>(&tmp5[0]), n2read * sizeof(T_store));
|
||||
ifs_vz.read(reinterpret_cast<char *>(&tmp6[0]), n2read * sizeof(T_store));
|
||||
|
||||
adjust_buf_endianness(tmp1);
|
||||
adjust_buf_endianness(tmp2);
|
||||
adjust_buf_endianness(tmp3);
|
||||
adjust_buf_endianness(tmp4);
|
||||
adjust_buf_endianness(tmp5);
|
||||
adjust_buf_endianness(tmp6);
|
||||
|
||||
ofs.write(reinterpret_cast<char *>(&tmp1[0]), block_buf_size_ * sizeof(T_store));
|
||||
ofs.write(reinterpret_cast<char *>(&tmp2[0]), block_buf_size_ * sizeof(T_store));
|
||||
ofs.write(reinterpret_cast<char *>(&tmp3[0]), block_buf_size_ * sizeof(T_store));
|
||||
ofs.write(reinterpret_cast<char *>(&tmp4[0]), block_buf_size_ * sizeof(T_store));
|
||||
ofs.write(reinterpret_cast<char *>(&tmp5[0]), block_buf_size_ * sizeof(T_store));
|
||||
ofs.write(reinterpret_cast<char *>(&tmp6[0]), block_buf_size_ * sizeof(T_store));
|
||||
|
||||
npleft -= n2read;
|
||||
n2read = std::min(block_buf_size_, npleft);
|
||||
}
|
||||
|
||||
ifs_x.close();
|
||||
ifs_y.close();
|
||||
ifs_z.close();
|
||||
ifs_vx.close();
|
||||
ifs_vy.close();
|
||||
ifs_vz.close();
|
||||
ofs.close();
|
||||
|
||||
// clean up temp files
|
||||
unlink(fnx);
|
||||
unlink(fny);
|
||||
unlink(fnz);
|
||||
unlink(fnvx);
|
||||
unlink(fnvy);
|
||||
unlink(fnvz);
|
||||
|
||||
delete[] tmp1;
|
||||
delete[] tmp2;
|
||||
delete[] tmp3;
|
||||
delete[] tmp4;
|
||||
delete[] tmp5;
|
||||
delete[] tmp6;
|
||||
|
||||
LOGINFO("ART : done writing DM file.");
|
||||
}
|
||||
|
||||
/*
|
||||
ART users currently create the baryon grid structure from the dark matter data file.
|
||||
Therefore they have decided that the best way to implement baryons for ART in MUSIC was
|
||||
by creating a file with the same dm format but using the baryon displacements and velocities.
|
||||
From this file they will create the actual grid suign their tools.
|
||||
|
||||
So here we have just to re-create the dark matter file format but using the baryon data.
|
||||
*/
|
||||
void assemble_gas_file(void) //PMcrs0_GAS.DAT
|
||||
{
|
||||
// file name
|
||||
std::string partfname = fname_ + "/PMcrs0_GAS.DAT";
|
||||
std::ofstream ofs(partfname.c_str(), std::ios::trunc);
|
||||
|
||||
// generate all temp file names
|
||||
char fnx[256], fny[256], fnz[256], fnvx[256], fnvy[256], fnvz[256];
|
||||
sprintf(fnx, "___ic_temp_%05d.bin", 100 * id_gas_pos + 0);
|
||||
sprintf(fny, "___ic_temp_%05d.bin", 100 * id_gas_pos + 1);
|
||||
sprintf(fnz, "___ic_temp_%05d.bin", 100 * id_gas_pos + 2);
|
||||
sprintf(fnvx, "___ic_temp_%05d.bin", 100 * id_gas_vel + 0);
|
||||
sprintf(fnvy, "___ic_temp_%05d.bin", 100 * id_gas_vel + 1);
|
||||
sprintf(fnvz, "___ic_temp_%05d.bin", 100 * id_gas_vel + 2);
|
||||
|
||||
// create buffers for temporary data
|
||||
T_store *tmp1, *tmp2, *tmp3, *tmp4, *tmp5, *tmp6;
|
||||
|
||||
tmp1 = new T_store[block_buf_size_];
|
||||
tmp2 = new T_store[block_buf_size_];
|
||||
tmp3 = new T_store[block_buf_size_];
|
||||
tmp4 = new T_store[block_buf_size_];
|
||||
tmp5 = new T_store[block_buf_size_];
|
||||
tmp6 = new T_store[block_buf_size_];
|
||||
|
||||
// read in the data from the temporary files in slabs and write it to the output file
|
||||
size_t npleft, n2read;
|
||||
size_t npcgas = npcdm_; // # of gas elemets should be equal to # of dm elements
|
||||
|
||||
LOGINFO("writing gas data to ART format file");
|
||||
//ofs.open(fname_.c_str(), std::ios::binary|std::ios::trunc );
|
||||
|
||||
pistream ifs_x, ifs_y, ifs_z, ifs_vx, ifs_vy, ifs_vz;
|
||||
|
||||
ifs_x.open(fnx, npcgas);
|
||||
ifs_y.open(fny, npcgas);
|
||||
ifs_z.open(fnz, npcgas);
|
||||
ifs_vx.open(fnvx, npcgas);
|
||||
ifs_vy.open(fnvy, npcgas);
|
||||
ifs_vz.open(fnvz, npcgas);
|
||||
|
||||
npleft = npcgas;
|
||||
n2read = std::min(block_buf_size_, npleft);
|
||||
while (n2read > 0)
|
||||
{
|
||||
// To make sure last page in zooms have 0s in non-relevant values
|
||||
// NOT MANDATORY. Can be commented if makes things slow
|
||||
// but I do not like the idea of writting data in the file
|
||||
// that could be interpreted as real.
|
||||
if (n2read < block_buf_size_)
|
||||
{
|
||||
for (int i = 0; i < int(block_buf_size_); i++)
|
||||
{
|
||||
tmp1[i] = 0.0;
|
||||
tmp2[i] = 0.0;
|
||||
tmp3[i] = 0.0;
|
||||
tmp4[i] = 0.0;
|
||||
tmp5[i] = 0.0;
|
||||
tmp6[i] = 0.0;
|
||||
}
|
||||
}
|
||||
ifs_x.read(reinterpret_cast<char *>(&tmp1[0]), n2read * sizeof(T_store));
|
||||
ifs_y.read(reinterpret_cast<char *>(&tmp2[0]), n2read * sizeof(T_store));
|
||||
ifs_z.read(reinterpret_cast<char *>(&tmp3[0]), n2read * sizeof(T_store));
|
||||
ifs_vx.read(reinterpret_cast<char *>(&tmp4[0]), n2read * sizeof(T_store));
|
||||
ifs_vy.read(reinterpret_cast<char *>(&tmp5[0]), n2read * sizeof(T_store));
|
||||
ifs_vz.read(reinterpret_cast<char *>(&tmp6[0]), n2read * sizeof(T_store));
|
||||
|
||||
adjust_buf_endianness(tmp1);
|
||||
adjust_buf_endianness(tmp2);
|
||||
adjust_buf_endianness(tmp3);
|
||||
adjust_buf_endianness(tmp4);
|
||||
adjust_buf_endianness(tmp5);
|
||||
adjust_buf_endianness(tmp6);
|
||||
|
||||
ofs.write(reinterpret_cast<char *>(&tmp1[0]), block_buf_size_ * sizeof(T_store));
|
||||
ofs.write(reinterpret_cast<char *>(&tmp2[0]), block_buf_size_ * sizeof(T_store));
|
||||
ofs.write(reinterpret_cast<char *>(&tmp3[0]), block_buf_size_ * sizeof(T_store));
|
||||
ofs.write(reinterpret_cast<char *>(&tmp4[0]), block_buf_size_ * sizeof(T_store));
|
||||
ofs.write(reinterpret_cast<char *>(&tmp5[0]), block_buf_size_ * sizeof(T_store));
|
||||
ofs.write(reinterpret_cast<char *>(&tmp6[0]), block_buf_size_ * sizeof(T_store));
|
||||
|
||||
npleft -= n2read;
|
||||
n2read = std::min(block_buf_size_, npleft);
|
||||
}
|
||||
|
||||
ifs_x.close();
|
||||
ifs_y.close();
|
||||
ifs_z.close();
|
||||
ifs_vx.close();
|
||||
ifs_vy.close();
|
||||
ifs_vz.close();
|
||||
ofs.close();
|
||||
|
||||
// clean up temp files
|
||||
unlink(fnx);
|
||||
unlink(fny);
|
||||
unlink(fnz);
|
||||
unlink(fnvx);
|
||||
unlink(fnvy);
|
||||
unlink(fnvz);
|
||||
|
||||
delete[] tmp1;
|
||||
delete[] tmp2;
|
||||
delete[] tmp3;
|
||||
delete[] tmp4;
|
||||
delete[] tmp5;
|
||||
delete[] tmp6;
|
||||
|
||||
LOGINFO("ART : done writing gas file.");
|
||||
// Temperature
|
||||
const double Tcmb0 = 2.726;
|
||||
const double h2 = header_.hubble * header_.hubble;
|
||||
const double adec = 1.0 / (160. * pow(omegab_ * h2 / 0.022, 2.0 / 5.0));
|
||||
const double Tini = astart_ < adec ? Tcmb0 / astart_ : Tcmb0 / astart_ / astart_ * adec;
|
||||
const double mu = (Tini > 1.e4) ? 4.0 / (8. - 5. * YHe_) : 4.0 / (1. + 3. * (1. - YHe_));
|
||||
LOGINFO("ART : set initial gas temperature to %.3f K (%.3f K/mu)", Tini, Tini / mu);
|
||||
}
|
||||
|
||||
public:
|
||||
explicit art_output_plugin(config_file &cf)
|
||||
: output_plugin(cf)
|
||||
{
|
||||
if (mkdir(fname_.c_str(), 0777))
|
||||
;
|
||||
|
||||
do_baryons_ = cf.getValueSafe<bool>("setup", "baryons", false);
|
||||
// We need to say that we want to do SPH for baryons
|
||||
// because if not MUSIC does not calculate/write gas positions
|
||||
cf.insertValue("setup", "do_SPH", "yes");
|
||||
// header size (alignment problem)
|
||||
hsize_ = 529; // dm & hydro run
|
||||
|
||||
omegab_ = cf.getValueSafe<double>("cosmology", "Omega_b", 0.0);
|
||||
omegam_ = cf.getValue<double>("cosmology", "Omega_m");
|
||||
zstart_ = cf.getValue<double>("setup", "zstart");
|
||||
astart_ = 1.0 / (1.0 + zstart_);
|
||||
|
||||
swap_endianness_ = cf.getValueSafe<bool>("output", "art_swap_endian", true);
|
||||
|
||||
int levelmin = cf.getValue<unsigned>("setup", "levelmin");
|
||||
int levelmax = cf.getValue<unsigned>("setup", "levelmax");
|
||||
block_buf_size_ = (size_t)(pow(pow(2, levelmax), 2)); //Npage=nrow^2; Number of particles in each page
|
||||
|
||||
YHe_ = cf.getValueSafe<double>("cosmology", "YHe", 0.248);
|
||||
gamma_ = cf.getValueSafe<double>("cosmology", "gamma", 5.0 / 3.0);
|
||||
// Set header
|
||||
std::string thead;
|
||||
thead = cf.getValueSafe<std::string>("output", "header", "ICs generated using MUSIC");
|
||||
strcpy(header_.head, thead.c_str()); // text for the header; any easy way to add also the version?
|
||||
std::string ws = " "; // Filling with blanks. Any better way?
|
||||
for (int i = thead.size(); i < 45; i++)
|
||||
{
|
||||
header_.head[i] = ws[0];
|
||||
}
|
||||
header_.aexpN = astart_;
|
||||
header_.aexp0 = header_.aexpN;
|
||||
header_.amplt = 0.0; // Amplitude of density fluctuations
|
||||
header_.astep = cf.getValue<double>("output", "astep"); // Seems that this must also be in the config file
|
||||
ptf_.astep = header_.astep; // to write pt file
|
||||
header_.istep = 0; // step (=0 in IC)
|
||||
header_.partw = 0.0; // mass of highest res particle. SEE BELOW
|
||||
header_.TINTG = 0; //=0 in IC
|
||||
header_.EKIN = 0.0; //SUM 0.5 * m_i*(v_i**2) in code units. Seems that 0 is ok for ICs
|
||||
header_.EKIN1 = 0; //=0 in IC
|
||||
header_.EKIN2 = 0; //=0 in IC
|
||||
header_.AU0 = 0; //=0 in IC
|
||||
header_.AEU0 = 0; //=0 in IC
|
||||
header_.NROWC = (int)pow(2, levelmax); // Number of particles in 1 dim (number of particles per page = NROW**2)
|
||||
header_.NGRIDC = (int)pow(2, levelmin); // Number of cells in 1 dim
|
||||
header_.nspecies = 0; // number of dm species
|
||||
for (int ilevel = levelmax; ilevel >= (int)levelmin; --ilevel)
|
||||
{
|
||||
header_.nspecies += 1;
|
||||
}
|
||||
//header_.partw SEE BELOW
|
||||
|
||||
header_.Nseed = 0; // random number used ( 0 for MUSIC? or set the random number used in the lowest level?)
|
||||
header_.Om0 = cf.getValue<double>("cosmology", "Omega_m"); //Omega_m
|
||||
header_.Oml0 = cf.getValue<double>("cosmology", "Omega_L"); //Omega_L
|
||||
header_.hubble = cf.getValue<double>("cosmology", "H0") / 100; //hubble constant h=H/100
|
||||
header_.Wp5 = 0.0; // 0.0
|
||||
header_.Ocurv = 1.0 - header_.Oml0 - header_.Om0; //
|
||||
header_.Omb0 = cf.getValue<double>("cosmology", "Omega_b");
|
||||
; // this parameter only appears in header in hydro runs
|
||||
for (int i = 0; i < 10; i++)
|
||||
{
|
||||
header_.wpart[i] = 0.0; // extras[0-9] part. masses from high res to low res (normalized to low res particle)
|
||||
header_.lpart[i] = 0; // extras[10-19] # particles from high res to low res cumulative!!!
|
||||
}
|
||||
for (int i = 0; i < header_.nspecies; i++)
|
||||
{
|
||||
header_.wpart[i] = 1.0 / pow(8.0, (header_.nspecies - i - 1)); //from high res to lo res // 8 should be changed for internal variable?
|
||||
}
|
||||
header_.partw = header_.wpart[0]; // mass of highest res particle.
|
||||
for (int i = 0; i < 80; i++)
|
||||
{
|
||||
header_.extras[i] = 0.0; //extras[20-99]
|
||||
}
|
||||
header_.extras[13] = cf.getValueSafe<double>("cosmology", "Omega_b", 0.0);
|
||||
header_.extras[14] = cf.getValue<double>("cosmology", "sigma_8");
|
||||
header_.extras[15] = cf.getValue<double>("cosmology", "nspec"); //Slope of the Power spectrum
|
||||
header_.extras[79] = cf.getValue<double>("setup", "boxlength");
|
||||
|
||||
LOGINFO("ART : done header info.");
|
||||
}
|
||||
|
||||
void write_dm_mass(const grid_hierarchy &gh)
|
||||
{
|
||||
|
||||
//... write data for dark matter mass......
|
||||
// This is not needed for ART
|
||||
}
|
||||
|
||||
void write_dm_position(int coord, const grid_hierarchy &gh)
|
||||
{
|
||||
size_t nptot = gh.count_leaf_cells(gh.levelmin(), gh.levelmax());
|
||||
//... store all the meta data about the grid hierarchy in header variables
|
||||
npcdm_ = nptot;
|
||||
for (int i = 0; i < header_.nspecies; i++)
|
||||
{
|
||||
header_.lpart[i] = gh.count_leaf_cells(gh.levelmax() - i, gh.levelmax()); //cumulative!!
|
||||
}
|
||||
|
||||
// Now, let us write the dm particle info
|
||||
std::vector<T_store> temp_data;
|
||||
temp_data.reserve(block_buf_size_);
|
||||
|
||||
//coordinates are in the range 1 - (NGRID+1)
|
||||
// so scale factor is scaleX = Box/NGRID -> to Mpc/h (Box in Mpc/h)
|
||||
double xfac = (double)header_.NGRIDC;
|
||||
|
||||
char temp_fname[256];
|
||||
sprintf(temp_fname, "___ic_temp_%05d.bin", 100 * id_dm_pos + coord);
|
||||
std::ofstream ofs_temp(temp_fname, std::ios::binary | std::ios::trunc);
|
||||
|
||||
size_t blksize = sizeof(T_store) * nptot;
|
||||
ofs_temp.write((char *)&blksize, sizeof(size_t));
|
||||
|
||||
size_t nwritten = 0;
|
||||
for (int ilevel = gh.levelmax(); ilevel >= (int)gh.levelmin(); --ilevel)
|
||||
for (unsigned i = 0; i < gh.get_grid(ilevel)->size(0); ++i)
|
||||
for (unsigned j = 0; j < gh.get_grid(ilevel)->size(1); ++j)
|
||||
for (unsigned k = 0; k < gh.get_grid(ilevel)->size(2); ++k)
|
||||
if (gh.is_in_mask(ilevel, i, j, k) && !gh.is_refined(ilevel, i, j, k))
|
||||
{
|
||||
double xx[3];
|
||||
gh.cell_pos(ilevel, i, j, k, xx);
|
||||
|
||||
xx[coord] = fmod((xx[coord] + (*gh.get_grid(ilevel))(i, j, k)) + 1.0, 1.0);
|
||||
xx[coord] = (xx[coord] * xfac) + 1.0;
|
||||
//xx[coord] = ((xx[coord]+(*gh.get_grid(ilevel))(i,j,k)));
|
||||
|
||||
if (temp_data.size() < block_buf_size_)
|
||||
temp_data.push_back(xx[coord]);
|
||||
else
|
||||
{
|
||||
ofs_temp.write((char *)&temp_data[0], sizeof(T_store) * block_buf_size_);
|
||||
nwritten += block_buf_size_;
|
||||
temp_data.clear();
|
||||
temp_data.push_back(xx[coord]);
|
||||
}
|
||||
}
|
||||
|
||||
if (temp_data.size() > 0)
|
||||
{
|
||||
ofs_temp.write((char *)&temp_data[0], sizeof(T_store) * temp_data.size());
|
||||
nwritten += temp_data.size();
|
||||
}
|
||||
|
||||
if (nwritten != nptot)
|
||||
throw std::runtime_error("Internal consistency error while writing temporary file for positions");
|
||||
|
||||
//... dump to temporary file
|
||||
ofs_temp.write((char *)&blksize, sizeof(size_t));
|
||||
|
||||
if (ofs_temp.bad())
|
||||
throw std::runtime_error("I/O error while writing temporary file for positions");
|
||||
|
||||
ofs_temp.close();
|
||||
}
|
||||
|
||||
void write_dm_velocity(int coord, const grid_hierarchy &gh)
|
||||
{
|
||||
size_t nptot = gh.count_leaf_cells(gh.levelmin(), gh.levelmax());
|
||||
|
||||
std::vector<T_store> temp_data;
|
||||
temp_data.reserve(block_buf_size_);
|
||||
|
||||
//In ART velocities are P = a_expansion*V_pec/(x_0H_0)
|
||||
// where x_0 = comoving cell_size=Box/Ngrid;H_0 = Hubble at z=0
|
||||
// so scale factor to physical km/s is convV= BoxV/AEXPN/NGRID
|
||||
// (BoxV is Box*100; aexpn=current expansion factor)
|
||||
//internal units of MUSIC: To km/s just multiply by Lbox
|
||||
double vfac = (header_.aexpN * header_.NGRIDC) / (100.0);
|
||||
|
||||
char temp_fname[256];
|
||||
sprintf(temp_fname, "___ic_temp_%05d.bin", 100 * id_dm_vel + coord);
|
||||
std::ofstream ofs_temp(temp_fname, std::ios::binary | std::ios::trunc);
|
||||
|
||||
size_t blksize = sizeof(T_store) * nptot;
|
||||
ofs_temp.write((char *)&blksize, sizeof(size_t));
|
||||
|
||||
size_t nwritten = 0;
|
||||
for (int ilevel = gh.levelmax(); ilevel >= (int)gh.levelmin(); --ilevel)
|
||||
for (unsigned i = 0; i < gh.get_grid(ilevel)->size(0); ++i)
|
||||
for (unsigned j = 0; j < gh.get_grid(ilevel)->size(1); ++j)
|
||||
for (unsigned k = 0; k < gh.get_grid(ilevel)->size(2); ++k)
|
||||
if (gh.is_in_mask(ilevel, i, j, k) && !gh.is_refined(ilevel, i, j, k))
|
||||
{
|
||||
if (temp_data.size() < block_buf_size_)
|
||||
temp_data.push_back((*gh.get_grid(ilevel))(i, j, k) * vfac);
|
||||
else
|
||||
{
|
||||
ofs_temp.write((char *)&temp_data[0], sizeof(T_store) * block_buf_size_);
|
||||
nwritten += block_buf_size_;
|
||||
temp_data.clear();
|
||||
temp_data.push_back((*gh.get_grid(ilevel))(i, j, k) * vfac);
|
||||
}
|
||||
}
|
||||
|
||||
if (temp_data.size() > 0)
|
||||
{
|
||||
ofs_temp.write((char *)&temp_data[0], sizeof(T_store) * temp_data.size());
|
||||
nwritten += temp_data.size();
|
||||
}
|
||||
|
||||
if (nwritten != nptot)
|
||||
throw std::runtime_error("Internal consistency error while writing temporary file for DM velocities");
|
||||
|
||||
//... dump to temporary file
|
||||
ofs_temp.write((char *)&blksize, sizeof(size_t));
|
||||
|
||||
if (ofs_temp.bad())
|
||||
throw std::runtime_error("I/O error while writing temporary file for DM velocities");
|
||||
|
||||
ofs_temp.close();
|
||||
}
|
||||
|
||||
void write_dm_density(const grid_hierarchy &gh)
|
||||
{
|
||||
//... we don't care about DM density for art
|
||||
}
|
||||
|
||||
void write_dm_potential(const grid_hierarchy &gh)
|
||||
{
|
||||
}
|
||||
|
||||
void write_gas_position(int coord, const grid_hierarchy &gh)
|
||||
{
|
||||
|
||||
size_t nptot = gh.count_leaf_cells(gh.levelmin(), gh.levelmax());
|
||||
|
||||
std::vector<T_store> temp_data;
|
||||
temp_data.reserve(block_buf_size_);
|
||||
|
||||
//ART coordinates are in the range 1 - (NGRID+1)
|
||||
double xfac = (double)header_.NGRIDC;
|
||||
|
||||
char temp_fname[256];
|
||||
sprintf(temp_fname, "___ic_temp_%05d.bin", 100 * id_gas_pos + coord);
|
||||
std::ofstream ofs_temp(temp_fname, std::ios::binary | std::ios::trunc);
|
||||
|
||||
size_t blksize = sizeof(T_store) * nptot;
|
||||
ofs_temp.write((char *)&blksize, sizeof(size_t));
|
||||
|
||||
size_t nwritten = 0;
|
||||
for (int ilevel = gh.levelmax(); ilevel >= (int)gh.levelmin(); --ilevel)
|
||||
for (unsigned i = 0; i < gh.get_grid(ilevel)->size(0); ++i)
|
||||
for (unsigned j = 0; j < gh.get_grid(ilevel)->size(1); ++j)
|
||||
for (unsigned k = 0; k < gh.get_grid(ilevel)->size(2); ++k)
|
||||
if (gh.is_in_mask(ilevel, i, j, k) && !gh.is_refined(ilevel, i, j, k))
|
||||
{
|
||||
double xx[3];
|
||||
gh.cell_pos(ilevel, i, j, k, xx);
|
||||
|
||||
xx[coord] = fmod((xx[coord] + (*gh.get_grid(ilevel))(i, j, k)) + 1.0, 1.0);
|
||||
xx[coord] = (xx[coord] * xfac) + 1.0;
|
||||
|
||||
if (temp_data.size() < block_buf_size_)
|
||||
temp_data.push_back(xx[coord]);
|
||||
else
|
||||
{
|
||||
ofs_temp.write((char *)&temp_data[0], sizeof(T_store) * block_buf_size_);
|
||||
nwritten += block_buf_size_;
|
||||
temp_data.clear();
|
||||
temp_data.push_back(xx[coord]);
|
||||
}
|
||||
}
|
||||
|
||||
if (temp_data.size() > 0)
|
||||
{
|
||||
ofs_temp.write((char *)&temp_data[0], sizeof(T_store) * temp_data.size());
|
||||
nwritten += temp_data.size();
|
||||
}
|
||||
|
||||
if (nwritten != nptot)
|
||||
throw std::runtime_error("Internal consistency error while writing temporary file for gas positions");
|
||||
|
||||
//... dump to temporary file
|
||||
ofs_temp.write((char *)&blksize, sizeof(size_t));
|
||||
|
||||
if (ofs_temp.bad())
|
||||
throw std::runtime_error("I/O error while writing temporary file for gas positions");
|
||||
|
||||
ofs_temp.close();
|
||||
}
|
||||
|
||||
void write_gas_velocity(int coord, const grid_hierarchy &gh)
|
||||
{
|
||||
|
||||
size_t nptot = gh.count_leaf_cells(gh.levelmin(), gh.levelmax());
|
||||
|
||||
std::vector<T_store> temp_data;
|
||||
temp_data.reserve(block_buf_size_);
|
||||
|
||||
//In ART velocities are P = a_expansion*V_pec/(x_0H_0)
|
||||
// where x_0 = comoving cell_size=Box/Ngrid;H_0 = Hubble at z=0
|
||||
// so scale factor to physical km/s is convV= BoxV/AEXPN/NGRID
|
||||
// (BoxV is Box*100; aexpn=current expansion factor)
|
||||
//internal units of MUSIC: To km/s just multiply by Lbox
|
||||
double vfac = (header_.aexpN * header_.NGRIDC) / (100.0);
|
||||
|
||||
char temp_fname[256];
|
||||
sprintf(temp_fname, "___ic_temp_%05d.bin", 100 * id_gas_vel + coord);
|
||||
std::ofstream ofs_temp(temp_fname, std::ios::binary | std::ios::trunc);
|
||||
|
||||
size_t blksize = sizeof(T_store) * nptot;
|
||||
ofs_temp.write((char *)&blksize, sizeof(size_t));
|
||||
|
||||
size_t nwritten = 0;
|
||||
for (int ilevel = gh.levelmax(); ilevel >= (int)gh.levelmin(); --ilevel)
|
||||
for (unsigned i = 0; i < gh.get_grid(ilevel)->size(0); ++i)
|
||||
for (unsigned j = 0; j < gh.get_grid(ilevel)->size(1); ++j)
|
||||
for (unsigned k = 0; k < gh.get_grid(ilevel)->size(2); ++k)
|
||||
if (gh.is_in_mask(ilevel, i, j, k) && !gh.is_refined(ilevel, i, j, k))
|
||||
{
|
||||
if (temp_data.size() < block_buf_size_)
|
||||
temp_data.push_back((*gh.get_grid(ilevel))(i, j, k) * vfac);
|
||||
else
|
||||
{
|
||||
ofs_temp.write((char *)&temp_data[0], sizeof(T_store) * block_buf_size_);
|
||||
nwritten += block_buf_size_;
|
||||
temp_data.clear();
|
||||
temp_data.push_back((*gh.get_grid(ilevel))(i, j, k) * vfac);
|
||||
}
|
||||
}
|
||||
|
||||
if (temp_data.size() > 0)
|
||||
{
|
||||
ofs_temp.write((char *)&temp_data[0], sizeof(T_store) * temp_data.size());
|
||||
nwritten += temp_data.size();
|
||||
}
|
||||
|
||||
if (nwritten != nptot)
|
||||
throw std::runtime_error("Internal consistency error while writing temporary file for gas velocities");
|
||||
|
||||
//... dump to temporary file
|
||||
ofs_temp.write((char *)&blksize, sizeof(size_t));
|
||||
|
||||
if (ofs_temp.bad())
|
||||
throw std::runtime_error("I/O error while writing temporary file for gas velocities");
|
||||
|
||||
ofs_temp.close();
|
||||
}
|
||||
|
||||
void write_gas_density(const grid_hierarchy &gh)
|
||||
{
|
||||
}
|
||||
void write_gas_potential(const grid_hierarchy &gh)
|
||||
{
|
||||
}
|
||||
|
||||
void finalize(void)
|
||||
{
|
||||
this->write_header_file();
|
||||
this->write_pt_file();
|
||||
this->assemble_DM_file();
|
||||
if (do_baryons_)
|
||||
{
|
||||
this->assemble_gas_file();
|
||||
}
|
||||
}
|
||||
};
|
||||
|
||||
namespace
|
||||
{
|
||||
output_plugin_creator_concrete<art_output_plugin<float>> creator("art");
|
||||
}
|
||||
617
src/plugins/output_enzo.cc
Normal file
617
src/plugins/output_enzo.cc
Normal file
|
|
@ -0,0 +1,617 @@
|
|||
/*
|
||||
|
||||
output_enzo.cc - This file is part of MUSIC -
|
||||
a code to generate multi-scale initial conditions
|
||||
for cosmological simulations
|
||||
|
||||
Copyright (C) 2010 Oliver Hahn
|
||||
|
||||
*/
|
||||
|
||||
#ifdef HAVE_HDF5
|
||||
|
||||
#include <sys/types.h>
|
||||
#include <sys/stat.h>
|
||||
|
||||
#include "output.hh"
|
||||
|
||||
#include "HDF_IO.hh"
|
||||
|
||||
#define MAX_SLAB_SIZE 268435456 // = 256 MBytes
|
||||
|
||||
class enzo_output_plugin : public output_plugin
|
||||
{
|
||||
protected:
|
||||
struct patch_header
|
||||
{
|
||||
int component_rank;
|
||||
size_t component_size;
|
||||
std::vector<int> dimensions;
|
||||
int rank;
|
||||
std::vector<int> top_grid_dims;
|
||||
std::vector<int> top_grid_end;
|
||||
std::vector<int> top_grid_start;
|
||||
};
|
||||
|
||||
struct sim_header
|
||||
{
|
||||
std::vector<int> dimensions;
|
||||
std::vector<int> offset;
|
||||
float a_start;
|
||||
float dx;
|
||||
float h0;
|
||||
float omega_b;
|
||||
float omega_m;
|
||||
float omega_v;
|
||||
float vfact;
|
||||
};
|
||||
|
||||
sim_header the_sim_header;
|
||||
|
||||
void write_sim_header(std::string fname, const sim_header &h)
|
||||
{
|
||||
HDFWriteGroupAttribute(fname, "/", "Dimensions", h.dimensions);
|
||||
HDFWriteGroupAttribute(fname, "/", "Offset", h.offset);
|
||||
HDFWriteGroupAttribute(fname, "/", "a_start", h.a_start);
|
||||
HDFWriteGroupAttribute(fname, "/", "dx", h.dx);
|
||||
HDFWriteGroupAttribute(fname, "/", "h0", h.h0);
|
||||
HDFWriteGroupAttribute(fname, "/", "omega_b", h.omega_b);
|
||||
HDFWriteGroupAttribute(fname, "/", "omega_m", h.omega_m);
|
||||
HDFWriteGroupAttribute(fname, "/", "omega_v", h.omega_v);
|
||||
HDFWriteGroupAttribute(fname, "/", "vfact", h.vfact);
|
||||
}
|
||||
|
||||
void write_patch_header(std::string fname, std::string dsetname, const patch_header &h)
|
||||
{
|
||||
HDFWriteDatasetAttribute(fname, dsetname, "Component_Rank", h.component_rank);
|
||||
HDFWriteDatasetAttribute(fname, dsetname, "Component_Size", h.component_size);
|
||||
HDFWriteDatasetAttribute(fname, dsetname, "Dimensions", h.dimensions);
|
||||
HDFWriteDatasetAttribute(fname, dsetname, "Rank", h.rank);
|
||||
HDFWriteDatasetAttribute(fname, dsetname, "TopGridDims", h.top_grid_dims);
|
||||
HDFWriteDatasetAttribute(fname, dsetname, "TopGridEnd", h.top_grid_end);
|
||||
HDFWriteDatasetAttribute(fname, dsetname, "TopGridStart", h.top_grid_start);
|
||||
}
|
||||
|
||||
void dump_mask(const grid_hierarchy &gh)
|
||||
{
|
||||
char enzoname[256], filename[512];
|
||||
std::string fieldname("RefinementMask");
|
||||
|
||||
for (unsigned ilevel = levelmin_; ilevel <= levelmax_; ++ilevel)
|
||||
{
|
||||
std::vector<int> ng, ng_fortran;
|
||||
ng.push_back(gh.get_grid(ilevel)->size(0));
|
||||
ng.push_back(gh.get_grid(ilevel)->size(1));
|
||||
ng.push_back(gh.get_grid(ilevel)->size(2));
|
||||
|
||||
ng_fortran.push_back(gh.get_grid(ilevel)->size(2));
|
||||
ng_fortran.push_back(gh.get_grid(ilevel)->size(1));
|
||||
ng_fortran.push_back(gh.get_grid(ilevel)->size(0));
|
||||
|
||||
//... need to copy data because we need to get rid of the ghost zones
|
||||
//... write in slabs if data is more than MAX_SLAB_SIZE (default 128 MB)
|
||||
|
||||
//... full 3D block size
|
||||
size_t all_data_size = (size_t)ng[0] * (size_t)ng[1] * (size_t)ng[2];
|
||||
|
||||
//... write in slabs of MAX_SLAB_SIZE unless all_data_size is anyway smaller
|
||||
size_t max_slab_size = std::min((size_t)MAX_SLAB_SIZE / sizeof(double), all_data_size);
|
||||
|
||||
//... but one slab hast to be at least the size of one slice
|
||||
max_slab_size = std::max(((size_t)ng[0] * (size_t)ng[1]), max_slab_size);
|
||||
|
||||
//... number of slices in one slab
|
||||
size_t slices_in_slab = (size_t)((double)max_slab_size / ((size_t)ng[0] * (size_t)ng[1]));
|
||||
|
||||
size_t nsz[3] = {size_t(ng[2]), size_t(ng[1]), size_t(ng[0])};
|
||||
|
||||
if (levelmin_ != levelmax_)
|
||||
sprintf(enzoname, "%s.%d", fieldname.c_str(), ilevel - levelmin_);
|
||||
else
|
||||
sprintf(enzoname, "%s", fieldname.c_str());
|
||||
|
||||
sprintf(filename, "%s/%s", fname_.c_str(), enzoname);
|
||||
|
||||
HDFCreateFile(filename);
|
||||
write_sim_header(filename, the_sim_header);
|
||||
|
||||
//... create full array in file
|
||||
HDFHyperslabWriter3Ds<int> *slab_writer = new HDFHyperslabWriter3Ds<int>(filename, enzoname, nsz);
|
||||
|
||||
//... create buffer
|
||||
int *data_buf = new int[slices_in_slab * (size_t)ng[0] * (size_t)ng[1]];
|
||||
|
||||
//... write slice by slice
|
||||
size_t slices_written = 0;
|
||||
while (slices_written < (size_t)ng[2])
|
||||
{
|
||||
slices_in_slab = std::min((size_t)ng[2] - slices_written, slices_in_slab);
|
||||
|
||||
#pragma omp parallel for
|
||||
for (int k = 0; k < (int)slices_in_slab; ++k)
|
||||
for (int j = 0; j < ng[1]; ++j)
|
||||
for (int i = 0; i < ng[0]; ++i)
|
||||
{
|
||||
int mask_val = -1;
|
||||
|
||||
if (gh.is_in_mask(ilevel, i, j, k + slices_written))
|
||||
{
|
||||
if (gh.is_refined(ilevel, i, j, k + slices_written))
|
||||
mask_val = 1;
|
||||
else
|
||||
mask_val = 0;
|
||||
}
|
||||
data_buf[(size_t)(k * ng[1] + j) * (size_t)ng[0] + (size_t)i] = mask_val;
|
||||
}
|
||||
|
||||
size_t count[3], offset[3];
|
||||
|
||||
count[0] = slices_in_slab;
|
||||
count[1] = ng[1];
|
||||
count[2] = ng[0];
|
||||
|
||||
offset[0] = slices_written;
|
||||
;
|
||||
offset[1] = 0;
|
||||
offset[2] = 0;
|
||||
|
||||
slab_writer->write_slab(data_buf, count, offset);
|
||||
slices_written += slices_in_slab;
|
||||
}
|
||||
|
||||
delete[] data_buf;
|
||||
delete slab_writer;
|
||||
|
||||
//... header data for the patch
|
||||
patch_header ph;
|
||||
|
||||
ph.component_rank = 1;
|
||||
ph.component_size = (size_t)ng[0] * (size_t)ng[1] * (size_t)ng[2];
|
||||
ph.dimensions = ng;
|
||||
ph.rank = 3;
|
||||
|
||||
ph.top_grid_dims.assign(3, 1 << levelmin_);
|
||||
|
||||
//... offset_abs is in units of the current level cell size
|
||||
|
||||
double rfac = 1.0 / (1 << (ilevel - levelmin_));
|
||||
|
||||
ph.top_grid_start.push_back((int)(gh.offset_abs(ilevel, 0) * rfac));
|
||||
ph.top_grid_start.push_back((int)(gh.offset_abs(ilevel, 1) * rfac));
|
||||
ph.top_grid_start.push_back((int)(gh.offset_abs(ilevel, 2) * rfac));
|
||||
|
||||
ph.top_grid_end.push_back(ph.top_grid_start[0] + (int)(ng[0] * rfac));
|
||||
ph.top_grid_end.push_back(ph.top_grid_start[1] + (int)(ng[1] * rfac));
|
||||
ph.top_grid_end.push_back(ph.top_grid_start[2] + (int)(ng[2] * rfac));
|
||||
|
||||
write_patch_header(filename, enzoname, ph);
|
||||
}
|
||||
}
|
||||
|
||||
void dump_grid_data(std::string fieldname, const grid_hierarchy &gh, double factor = 1.0, double add = 0.0)
|
||||
{
|
||||
char enzoname[256], filename[512];
|
||||
|
||||
for (unsigned ilevel = levelmin_; ilevel <= levelmax_; ++ilevel)
|
||||
{
|
||||
std::vector<int> ng, ng_fortran;
|
||||
ng.push_back(gh.get_grid(ilevel)->size(0));
|
||||
ng.push_back(gh.get_grid(ilevel)->size(1));
|
||||
ng.push_back(gh.get_grid(ilevel)->size(2));
|
||||
|
||||
ng_fortran.push_back(gh.get_grid(ilevel)->size(2));
|
||||
ng_fortran.push_back(gh.get_grid(ilevel)->size(1));
|
||||
ng_fortran.push_back(gh.get_grid(ilevel)->size(0));
|
||||
|
||||
//... need to copy data because we need to get rid of the ghost zones
|
||||
//... write in slabs if data is more than MAX_SLAB_SIZE (default 128 MB)
|
||||
|
||||
//... full 3D block size
|
||||
size_t all_data_size = (size_t)ng[0] * (size_t)ng[1] * (size_t)ng[2];
|
||||
|
||||
//... write in slabs of MAX_SLAB_SIZE unless all_data_size is anyway smaller
|
||||
size_t max_slab_size = std::min((size_t)MAX_SLAB_SIZE / sizeof(double), all_data_size);
|
||||
|
||||
//... but one slab hast to be at least the size of one slice
|
||||
max_slab_size = std::max(((size_t)ng[0] * (size_t)ng[1]), max_slab_size);
|
||||
|
||||
//... number of slices in one slab
|
||||
size_t slices_in_slab = (size_t)((double)max_slab_size / ((size_t)ng[0] * (size_t)ng[1]));
|
||||
|
||||
size_t nsz[3] = {size_t(ng[2]), size_t(ng[1]), size_t(ng[0])};
|
||||
|
||||
if (levelmin_ != levelmax_)
|
||||
sprintf(enzoname, "%s.%d", fieldname.c_str(), ilevel - levelmin_);
|
||||
else
|
||||
sprintf(enzoname, "%s", fieldname.c_str());
|
||||
|
||||
sprintf(filename, "%s/%s", fname_.c_str(), enzoname);
|
||||
|
||||
HDFCreateFile(filename);
|
||||
write_sim_header(filename, the_sim_header);
|
||||
|
||||
#ifdef SINGLE_PRECISION
|
||||
//... create full array in file
|
||||
HDFHyperslabWriter3Ds<float> *slab_writer = new HDFHyperslabWriter3Ds<float>(filename, enzoname, nsz);
|
||||
|
||||
//... create buffer
|
||||
float *data_buf = new float[slices_in_slab * (size_t)ng[0] * (size_t)ng[1]];
|
||||
#else
|
||||
//... create full array in file
|
||||
HDFHyperslabWriter3Ds<double> *slab_writer = new HDFHyperslabWriter3Ds<double>(filename, enzoname, nsz);
|
||||
|
||||
//... create buffer
|
||||
double *data_buf = new double[slices_in_slab * (size_t)ng[0] * (size_t)ng[1]];
|
||||
#endif
|
||||
|
||||
//... write slice by slice
|
||||
size_t slices_written = 0;
|
||||
while (slices_written < (size_t)ng[2])
|
||||
{
|
||||
slices_in_slab = std::min((size_t)ng[2] - slices_written, slices_in_slab);
|
||||
|
||||
#pragma omp parallel for
|
||||
for (int k = 0; k < (int)slices_in_slab; ++k)
|
||||
for (int j = 0; j < ng[1]; ++j)
|
||||
for (int i = 0; i < ng[0]; ++i)
|
||||
data_buf[(size_t)(k * ng[1] + j) * (size_t)ng[0] + (size_t)i] =
|
||||
(add + (*gh.get_grid(ilevel))(i, j, k + slices_written)) * factor;
|
||||
|
||||
size_t count[3], offset[3];
|
||||
|
||||
count[0] = slices_in_slab;
|
||||
count[1] = ng[1];
|
||||
count[2] = ng[0];
|
||||
|
||||
offset[0] = slices_written;
|
||||
;
|
||||
offset[1] = 0;
|
||||
offset[2] = 0;
|
||||
|
||||
slab_writer->write_slab(data_buf, count, offset);
|
||||
slices_written += slices_in_slab;
|
||||
}
|
||||
|
||||
//... free buffer
|
||||
delete[] data_buf;
|
||||
|
||||
//... finalize writing and close dataset
|
||||
delete slab_writer;
|
||||
|
||||
//... header data for the patch
|
||||
patch_header ph;
|
||||
|
||||
ph.component_rank = 1;
|
||||
ph.component_size = (size_t)ng[0] * (size_t)ng[1] * (size_t)ng[2];
|
||||
ph.dimensions = ng;
|
||||
ph.rank = 3;
|
||||
|
||||
ph.top_grid_dims.assign(3, 1 << levelmin_);
|
||||
|
||||
//... offset_abs is in units of the current level cell size
|
||||
|
||||
double rfac = 1.0 / (1 << (ilevel - levelmin_));
|
||||
|
||||
ph.top_grid_start.push_back((int)(gh.offset_abs(ilevel, 0) * rfac));
|
||||
ph.top_grid_start.push_back((int)(gh.offset_abs(ilevel, 1) * rfac));
|
||||
ph.top_grid_start.push_back((int)(gh.offset_abs(ilevel, 2) * rfac));
|
||||
|
||||
ph.top_grid_end.push_back(ph.top_grid_start[0] + (int)(ng[0] * rfac));
|
||||
ph.top_grid_end.push_back(ph.top_grid_start[1] + (int)(ng[1] * rfac));
|
||||
ph.top_grid_end.push_back(ph.top_grid_start[2] + (int)(ng[2] * rfac));
|
||||
|
||||
write_patch_header(filename, enzoname, ph);
|
||||
}
|
||||
}
|
||||
|
||||
public:
|
||||
enzo_output_plugin(config_file &cf)
|
||||
: output_plugin(cf)
|
||||
{
|
||||
if (mkdir(fname_.c_str(), 0777))
|
||||
{
|
||||
perror(fname_.c_str());
|
||||
throw std::runtime_error("Error in enzo_output_plugin!");
|
||||
}
|
||||
|
||||
bool bhave_hydro = cf_.getValue<bool>("setup", "baryons");
|
||||
bool align_top = cf.getValueSafe<bool>("setup", "align_top", false);
|
||||
|
||||
if (!align_top)
|
||||
LOGWARN("Old ENZO versions may require \'align_top=true\'!");
|
||||
|
||||
the_sim_header.dimensions.push_back(1 << levelmin_);
|
||||
the_sim_header.dimensions.push_back(1 << levelmin_);
|
||||
the_sim_header.dimensions.push_back(1 << levelmin_);
|
||||
|
||||
the_sim_header.offset.push_back(0);
|
||||
the_sim_header.offset.push_back(0);
|
||||
the_sim_header.offset.push_back(0);
|
||||
|
||||
the_sim_header.a_start = 1.0 / (1.0 + cf.getValue<double>("setup", "zstart"));
|
||||
the_sim_header.dx = cf.getValue<double>("setup", "boxlength") / the_sim_header.dimensions[0] / (cf.getValue<double>("cosmology", "H0") * 0.01); // not sure?!?
|
||||
the_sim_header.h0 = cf.getValue<double>("cosmology", "H0") * 0.01;
|
||||
|
||||
if (bhave_hydro)
|
||||
the_sim_header.omega_b = cf.getValue<double>("cosmology", "Omega_b");
|
||||
else
|
||||
the_sim_header.omega_b = 0.0;
|
||||
|
||||
the_sim_header.omega_m = cf.getValue<double>("cosmology", "Omega_m");
|
||||
the_sim_header.omega_v = cf.getValue<double>("cosmology", "Omega_L");
|
||||
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
|
||||
}
|
||||
|
||||
~enzo_output_plugin()
|
||||
{
|
||||
}
|
||||
|
||||
void write_dm_mass(const grid_hierarchy &gh)
|
||||
{ /* do nothing, not needed */
|
||||
}
|
||||
|
||||
void write_dm_density(const grid_hierarchy &gh)
|
||||
{ /* write the parameter file data */
|
||||
|
||||
bool bhave_hydro = cf_.getValue<bool>("setup", "baryons");
|
||||
double refine_region_fraction = cf_.getValueSafe<double>("output", "enzo_refine_region_fraction", 0.8);
|
||||
char filename[256];
|
||||
unsigned nbase = (unsigned)pow(2, levelmin_);
|
||||
|
||||
// write out the refinement masks
|
||||
dump_mask(gh);
|
||||
|
||||
// write out a parameter file
|
||||
|
||||
sprintf(filename, "%s/parameter_file.txt", fname_.c_str());
|
||||
|
||||
std::ofstream ofs(filename, std::ios::trunc);
|
||||
|
||||
ofs
|
||||
<< "# Relevant Section of Enzo Paramter File (NOT COMPLETE!) \n"
|
||||
<< "ProblemType = 30 // cosmology simulation\n"
|
||||
<< "TopGridRank = 3\n"
|
||||
<< "TopGridDimensions = " << nbase << " " << nbase << " " << nbase << "\n"
|
||||
<< "SelfGravity = 1 // gravity on\n"
|
||||
<< "TopGridGravityBoundary = 0 // Periodic BC for gravity\n"
|
||||
<< "LeftFaceBoundaryCondition = 3 3 3 // same for fluid\n"
|
||||
<< "RightFaceBoundaryCondition = 3 3 3\n"
|
||||
<< "RefineBy = 2\n"
|
||||
<< "\n"
|
||||
<< "#\n";
|
||||
|
||||
if (bhave_hydro)
|
||||
ofs
|
||||
<< "CosmologySimulationOmegaBaryonNow = " << the_sim_header.omega_b << "\n"
|
||||
<< "CosmologySimulationOmegaCDMNow = " << the_sim_header.omega_m - the_sim_header.omega_b << "\n";
|
||||
else
|
||||
ofs
|
||||
<< "CosmologySimulationOmegaBaryonNow = " << 0.0 << "\n"
|
||||
<< "CosmologySimulationOmegaCDMNow = " << the_sim_header.omega_m << "\n";
|
||||
|
||||
if (bhave_hydro)
|
||||
ofs
|
||||
<< "CosmologySimulationDensityName = GridDensity\n"
|
||||
<< "CosmologySimulationVelocity1Name = GridVelocities_x\n"
|
||||
<< "CosmologySimulationVelocity2Name = GridVelocities_y\n"
|
||||
<< "CosmologySimulationVelocity3Name = GridVelocities_z\n";
|
||||
|
||||
ofs
|
||||
<< "CosmologySimulationCalculatePositions = 1\n"
|
||||
<< "CosmologySimulationParticleVelocity1Name = ParticleVelocities_x\n"
|
||||
<< "CosmologySimulationParticleVelocity2Name = ParticleVelocities_y\n"
|
||||
<< "CosmologySimulationParticleVelocity3Name = ParticleVelocities_z\n"
|
||||
<< "CosmologySimulationParticleDisplacement1Name = ParticleDisplacements_x\n"
|
||||
<< "CosmologySimulationParticleDisplacement2Name = ParticleDisplacements_y\n"
|
||||
<< "CosmologySimulationParticleDisplacement3Name = ParticleDisplacements_z\n"
|
||||
<< "\n"
|
||||
<< "#\n"
|
||||
<< "# define cosmology parameters\n"
|
||||
<< "#\n"
|
||||
<< "ComovingCoordinates = 1 // Expansion ON\n"
|
||||
<< "CosmologyOmegaMatterNow = " << the_sim_header.omega_m << "\n"
|
||||
<< "CosmologyOmegaLambdaNow = " << the_sim_header.omega_v << "\n"
|
||||
<< "CosmologyHubbleConstantNow = " << the_sim_header.h0 << " // in 100 km/s/Mpc\n"
|
||||
<< "CosmologyComovingBoxSize = " << cf_.getValue<double>("setup", "boxlength") << " // in Mpc/h\n"
|
||||
<< "CosmologyMaxExpansionRate = 0.015 // maximum allowed delta(a)/a\n"
|
||||
<< "CosmologyInitialRedshift = " << cf_.getValue<double>("setup", "zstart") << " //\n"
|
||||
<< "CosmologyFinalRedshift = 0 //\n"
|
||||
<< "GravitationalConstant = 1 // this must be true for cosmology\n"
|
||||
<< "#\n"
|
||||
<< "#\n"
|
||||
<< "ParallelRootGridIO = 1\n"
|
||||
<< "ParallelParticleIO = 1\n"
|
||||
<< "PartitionNestedGrids = 1\n"
|
||||
<< "CosmologySimulationNumberOfInitialGrids = " << 1 + levelmax_ - levelmin_ << "\n";
|
||||
|
||||
int num_prec = 10;
|
||||
|
||||
if (levelmax_ > 15)
|
||||
num_prec = 17;
|
||||
|
||||
//... only for additionally refined grids
|
||||
for (unsigned ilevel = 0; ilevel < levelmax_ - levelmin_; ++ilevel)
|
||||
{
|
||||
double h = 1.0 / (1 << (levelmin_ + 1 + ilevel));
|
||||
|
||||
ofs
|
||||
|
||||
<< "CosmologySimulationGridDimension[" << 1 + ilevel << "] = "
|
||||
<< std::setw(16) << gh.size(levelmin_ + ilevel + 1, 0) << " "
|
||||
<< std::setw(16) << gh.size(levelmin_ + ilevel + 1, 1) << " "
|
||||
<< std::setw(16) << gh.size(levelmin_ + ilevel + 1, 2) << "\n"
|
||||
|
||||
<< "CosmologySimulationGridLeftEdge[" << 1 + ilevel << "] = "
|
||||
<< std::setw(num_prec + 6) << std::setprecision(num_prec) << h * gh.offset_abs(levelmin_ + ilevel + 1, 0) << " "
|
||||
<< std::setw(num_prec + 6) << std::setprecision(num_prec) << h * gh.offset_abs(levelmin_ + ilevel + 1, 1) << " "
|
||||
<< std::setw(num_prec + 6) << std::setprecision(num_prec) << h * gh.offset_abs(levelmin_ + ilevel + 1, 2) << "\n"
|
||||
|
||||
<< "CosmologySimulationGridRightEdge[" << 1 + ilevel << "] = "
|
||||
<< std::setw(num_prec + 6) << std::setprecision(num_prec) << h * (gh.offset_abs(levelmin_ + ilevel + 1, 0) + gh.size(levelmin_ + ilevel + 1, 0)) << " "
|
||||
<< std::setw(num_prec + 6) << std::setprecision(num_prec) << h * (gh.offset_abs(levelmin_ + ilevel + 1, 1) + gh.size(levelmin_ + ilevel + 1, 1)) << " "
|
||||
<< std::setw(num_prec + 6) << std::setprecision(num_prec) << h * (gh.offset_abs(levelmin_ + ilevel + 1, 2) + gh.size(levelmin_ + ilevel + 1, 2)) << "\n"
|
||||
|
||||
<< "CosmologySimulationGridLevel[" << 1 + ilevel << "] = " << 1 + ilevel << "\n";
|
||||
}
|
||||
|
||||
if (levelmin_ != levelmax_)
|
||||
{
|
||||
double h = 1.0 / (1 << levelmax_);
|
||||
|
||||
double cen[3], le[3], re[3];
|
||||
for (int i = 0; i < 3; i++)
|
||||
{
|
||||
cen[i] = gh.offset_abs(levelmax_, i) + gh.size(levelmax_, i) / 2;
|
||||
le[i] = cen[i] - refine_region_fraction * gh.size(levelmax_, i) / 2;
|
||||
re[i] = le[i] + refine_region_fraction * gh.size(levelmax_, i);
|
||||
}
|
||||
|
||||
ofs
|
||||
<< "#\n"
|
||||
<< "# region allowed for further refinement\n"
|
||||
<< "#\n"
|
||||
// << "RefineRegionAutoAdjust = 1\n"
|
||||
<< "RefineRegionLeftEdge = "
|
||||
<< std::setw(num_prec + 6) << std::setprecision(num_prec) << h * le[0] << " "
|
||||
<< std::setw(num_prec + 6) << std::setprecision(num_prec) << h * le[1] << " "
|
||||
<< std::setw(num_prec + 6) << std::setprecision(num_prec) << h * le[2] << "\n"
|
||||
<< "RefineRegionRightEdge = "
|
||||
<< std::setw(num_prec + 6) << std::setprecision(num_prec) << h * re[0] << " "
|
||||
<< std::setw(num_prec + 6) << std::setprecision(num_prec) << h * re[1] << " "
|
||||
<< std::setw(num_prec + 6) << std::setprecision(num_prec) << h * re[2] << "\n";
|
||||
}
|
||||
|
||||
// determine density maximum and minimum location
|
||||
real_t rhomax = -1e30, rhomin = 1e30;
|
||||
double loc_rhomax[3] = {0.0, 0.0, 0.0}, loc_rhomin[3] = {0.0, 0.0, 0.0};
|
||||
int lvl_rhomax = 0, lvl_rhomin = 0;
|
||||
real_t rhomax_lm = -1e30, rhomin_lm = 1e30;
|
||||
double loc_rhomax_lm[3] = {0.0, 0.0, 0.0}, loc_rhomin_lm[3] = {0.0, 0.0, 0.0};
|
||||
|
||||
for (int ilevel = gh.levelmax(); ilevel >= (int)gh.levelmin(); --ilevel)
|
||||
for (unsigned i = 0; i < gh.get_grid(ilevel)->size(0); ++i)
|
||||
for (unsigned j = 0; j < gh.get_grid(ilevel)->size(1); ++j)
|
||||
for (unsigned k = 0; k < gh.get_grid(ilevel)->size(2); ++k)
|
||||
if (!gh.is_refined(ilevel, i, j, k))
|
||||
{
|
||||
real_t rho = (*gh.get_grid(ilevel))(i, j, k);
|
||||
|
||||
if (rho > rhomax)
|
||||
{
|
||||
rhomax = rho;
|
||||
lvl_rhomax = ilevel;
|
||||
gh.cell_pos(ilevel, i, j, k, loc_rhomax);
|
||||
}
|
||||
|
||||
if (rho < rhomin)
|
||||
{
|
||||
rhomin = rho;
|
||||
lvl_rhomin = ilevel;
|
||||
gh.cell_pos(ilevel, i, j, k, loc_rhomin);
|
||||
}
|
||||
|
||||
if (ilevel == (int)gh.levelmax())
|
||||
{
|
||||
if (rho > rhomax_lm)
|
||||
{
|
||||
rhomax_lm = rho;
|
||||
gh.cell_pos(ilevel, i, j, k, loc_rhomax_lm);
|
||||
}
|
||||
|
||||
if (rho < rhomin_lm)
|
||||
{
|
||||
rhomin_lm = rho;
|
||||
gh.cell_pos(ilevel, i, j, k, loc_rhomin_lm);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
double h = 1.0 / (1 << levelmin_);
|
||||
double shift[3];
|
||||
shift[0] = -(double)cf_.getValue<int>("setup", "shift_x") * h;
|
||||
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
|
||||
1963
src/random.cc
Normal file
1963
src/random.cc
Normal file
File diff suppressed because it is too large
Load diff
Loading…
Reference in a new issue