mirror of
https://github.com/cosmo-sims/monofonIC.git
synced 2024-09-19 17:03:45 +02:00
Merged master into develop
This commit is contained in:
Oliver Hahn
commit
561c9ffa06
4 changed files with 373 additions and 121 deletions
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@ -17,7 +17,7 @@ Currently supported features (the list is growing, so check back):
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- Multiple Einstein-Boltzmann modules: direct interface with [CLASS](https://lesgourg.github.io/class_public/class.html), file input from CAMB, and fitting formulae (Eisenstein&Hu).
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- Multiple output modules for RAMSES, Arepo, Gadget-2/3, and HACC (courtesy M.Buehlmann) via plugins (Swift and Nyx are next).
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- Multiple output modules for RAMSES, Arepo, Gadget-2/3, SWIFT, and HACC (courtesy M.Buehlmann) via plugins (Nyx is next).
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- Multiple random number modules (MUSIC1,NGenIC,Panphasia,...) (A new MUSIC2 module is in development)
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@ -144,9 +144,12 @@ NumThreads = 8
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# format = genericio
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# filename = ics_hacc
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##> SWIFT compatible HDF5 format
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##> SWIFT compatible HDF5 format. Format broadly similar to gadget_hdf5 but in a single
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##> file even when using MPI. No h-factors for position and masses and no sqrt(a)-factor for the velocities.
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##> IDs are stored using 64-bits unless UseLongids is set to false.
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# format = SWIFT
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# filename = ics_swift.hdf5
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# UseLongids = true
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##> Generic HDF5 output format for testing or PT-based calculations
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# format = generic
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@ -886,6 +886,178 @@ inline void HDFWriteDatasetVector( const std::string Filename, const std::string
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H5Fclose( HDF_FileID );
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}
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template< typename T >
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inline void HDFCreateEmptyDataset( const std::string Filename, const std::string ObjName, const size_t num_particles, const bool filter = false)
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{
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hid_t
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HDF_FileID,
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HDF_DatasetID,
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HDF_DataspaceID,
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HDF_Type,
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HDF_Prop;
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hsize_t HDF_Dims;
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HDF_Prop = H5Pcreate(H5P_DATASET_CREATE);
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if (filter)
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{
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// 1MB chunking
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hsize_t HDF_Dims[1] = {1024 * 1024 / sizeof(T)};
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H5Pset_chunk(HDF_Prop, 1, HDF_Dims);
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// md5 checksum
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H5Pset_fletcher32(HDF_Prop);
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}
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HDF_FileID = H5Fopen( Filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT );
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HDF_Type = GetDataType<T>();
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HDF_Dims = (hsize_t) (num_particles);
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HDF_DataspaceID = H5Screate_simple(1, &HDF_Dims, NULL);
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HDF_DatasetID = H5Dcreate( HDF_FileID, ObjName.c_str(), HDF_Type,
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HDF_DataspaceID, HDF_Prop );
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H5Dclose( HDF_DatasetID );
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H5Sclose( HDF_DataspaceID );
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H5Pclose( HDF_Prop );
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H5Fclose( HDF_FileID );
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}
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template< typename T >
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inline void HDFCreateEmptyDatasetVector( const std::string Filename, const std::string ObjName, const size_t num_particles, const bool filter = false)
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{
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hid_t
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HDF_FileID,
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HDF_DatasetID,
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HDF_DataspaceID,
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HDF_Type,
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HDF_Prop;
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hsize_t HDF_Dims[2];
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HDF_Prop = H5Pcreate(H5P_DATASET_CREATE);
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if (filter)
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{
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// ~1MB chunking
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hsize_t HDF_Dims[2] = {256 * 1024 / sizeof(T), 3};
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H5Pset_chunk(HDF_Prop, 2, HDF_Dims);
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// md5 checksum
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H5Pset_fletcher32(HDF_Prop);
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}
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HDF_FileID = H5Fopen( Filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT );
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HDF_Type = GetDataType<T>();
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HDF_Dims[0] = (hsize_t) (num_particles);
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HDF_Dims[1] = (hsize_t) 3;
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HDF_DataspaceID = H5Screate_simple(2, HDF_Dims, NULL);
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HDF_DatasetID = H5Dcreate( HDF_FileID, ObjName.c_str(), HDF_Type,
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HDF_DataspaceID, HDF_Prop );
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H5Dclose( HDF_DatasetID );
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H5Sclose( HDF_DataspaceID );
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H5Pclose( HDF_Prop );
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H5Fclose( HDF_FileID );
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}
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template< typename T >
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inline void HDFWriteDatasetChunk( const std::string Filename, const std::string ObjName, const std::vector<T> &Data, const size_t offset )
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{
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hid_t
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HDF_FileID,
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HDF_DatasetID,
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HDF_MemDataspaceID,
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HDF_FileDataspaceID,
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HDF_Type;
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hsize_t HDF_Dims,
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HDF_Shape,
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HDF_Offset;
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HDF_FileID = H5Fopen( Filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT );
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HDF_Type = GetDataType<T>();
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HDF_Dims = (hsize_t)Data.size();
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HDF_MemDataspaceID = H5Screate_simple(1, &HDF_Dims, NULL);
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HDF_Shape = (hsize_t)Data.size();
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HDF_Offset = (hsize_t)offset;
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HDF_DatasetID = H5Dopen( HDF_FileID, ObjName.c_str() );
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HDF_FileDataspaceID = H5Dget_space(HDF_DatasetID);
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H5Sselect_hyperslab(HDF_FileDataspaceID, H5S_SELECT_SET, &HDF_Offset, NULL, &HDF_Shape, NULL);
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H5Dwrite( HDF_DatasetID, HDF_Type, HDF_MemDataspaceID, HDF_FileDataspaceID, H5P_DEFAULT, &Data[0] );
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H5Dclose( HDF_DatasetID );
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H5Sclose( HDF_MemDataspaceID );
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H5Sclose( HDF_FileDataspaceID );
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H5Fclose( HDF_FileID );
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}
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template< typename T >
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inline void HDFWriteDatasetVectorChunk( const std::string Filename, const std::string ObjName, const std::vector<T> &Data, const size_t offset )
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{
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hid_t
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HDF_FileID,
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HDF_DatasetID,
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HDF_MemDataspaceID,
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HDF_FileDataspaceID,
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HDF_Type;
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hsize_t HDF_Dims[2],
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HDF_Shape[2],
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HDF_Offset[2];
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HDF_FileID = H5Fopen( Filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT );
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HDF_Type = GetDataType<T>();
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HDF_Dims[0] = (hsize_t)(Data.size()/3);
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HDF_Dims[1] = 3;
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HDF_MemDataspaceID = H5Screate_simple(2, HDF_Dims, NULL);
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if( Data.size() % 3 != 0 ){
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std::cerr << " - Warning: Trying to write vector data in HDFWriteDatasetVector\n"
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<< " but array length not divisible by 3!\n\n";
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}
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HDF_Shape[0] = (hsize_t)(Data.size()/3);
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HDF_Shape[1] = (hsize_t)3;
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HDF_Offset[0] = (hsize_t)offset;
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HDF_Offset[1] = (hsize_t)0;
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HDF_DatasetID = H5Dopen( HDF_FileID, ObjName.c_str() );
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HDF_FileDataspaceID = H5Dget_space(HDF_DatasetID);
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H5Sselect_hyperslab(HDF_FileDataspaceID, H5S_SELECT_SET, HDF_Offset, NULL, HDF_Shape, NULL);
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H5Dwrite( HDF_DatasetID, HDF_Type, HDF_MemDataspaceID, HDF_FileDataspaceID, H5P_DEFAULT, &Data[0] );
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H5Dclose( HDF_DatasetID );
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H5Sclose( HDF_MemDataspaceID );
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H5Sclose( HDF_FileDataspaceID );
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H5Fclose( HDF_FileID );
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}
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inline void HDFCreateGroup( const std::string Filename, const std::string GroupName )
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{
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hid_t HDF_FileID, HDF_GroupID;
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@ -38,29 +38,32 @@ class swift_output_plugin : public output_plugin
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{
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protected:
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int num_files_, num_simultaneous_writers_;
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int num_ranks_, this_rank_;
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int num_files_;
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real_t lunit_, vunit_, munit_;
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real_t boxsize_, hubble_param_, astart_, zstart_;
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bool blongids_, bdobaryons_;
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std::string this_fname_;
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std::array<uint32_t,7> npart_, npartTotal_, npartTotalHighWord_;
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std::array<uint64_t,7> npart_;
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std::array<uint32_t,7> npartTotal_, npartTotalHighWord_;
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std::array<double,7> mass_;
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double time_;
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double ceint_, h_;
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public:
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//! constructor
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explicit swift_output_plugin(config_file &cf, std::unique_ptr<cosmology::calculator> &pcc)
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: output_plugin(cf, pcc, "SWIFT")
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{
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// SWIFT uses a single file as IC */
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num_files_ = 1;
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#ifdef USE_MPI
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// use as many output files as we have MPI tasks
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MPI_Comm_size(MPI_COMM_WORLD, &num_files_);
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#endif
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this_rank_ = 0;
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num_ranks_ = 1;
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real_t astart = 1.0 / (1.0 + cf_.get_value<double>("setup", "zstart"));
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const double rhoc = 27.7519737; // in h^2 1e10 M_sol / Mpc^3
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const double rhoc = 27.7536609198; // in h^2 1e10 M_sol / Mpc^3 assuming SWIFT's internal constants
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hubble_param_ = pcc->cosmo_param_["h"];
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zstart_ = cf_.get_value<double>("setup","zstart");
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@ -71,7 +74,7 @@ public:
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vunit_ = boxsize_; // final units will be in km/s
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munit_ = rhoc * std::pow(boxsize_, 3) / hubble_param_; // final units will be in 1e10 M_sol
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blongids_ = cf_.get_value_safe<bool>("output", "UseLongids", false);
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blongids_ = cf_.get_value_safe<bool>("output", "UseLongids", true);
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bdobaryons_ = cf_.get_value<bool>("setup","DoBaryons");
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for (int i = 0; i < 7; ++i)
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@ -84,31 +87,49 @@ public:
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time_ = astart;
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this_fname_ = fname_;
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#ifdef USE_MPI
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int thisrank = 0;
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MPI_Comm_rank(MPI_COMM_WORLD, &thisrank);
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if (num_files_ > 1)
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this_fname_ += "." + std::to_string(thisrank);
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MPI_Comm_rank(MPI_COMM_WORLD, &this_rank_);
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MPI_Comm_size(MPI_COMM_WORLD, &num_ranks_);
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#endif
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// Now that we modified the filename for MPI support, propagate the change to the super-class
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// as it does operations on the file behind our back.
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fname_ = this_fname_;
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if (bdobaryons_) {
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const double gamma = cf_.get_value_safe<double>("cosmology", "gamma", 5.0 / 3.0);
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const double YHe = pcc_->cosmo_param_["YHe"];
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const double omegab = pcc_->cosmo_param_["Omega_b"];
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const double Tcmb0 = pcc_->cosmo_param_["Tcmb"];
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// compute gas internal energy
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const double npol = (fabs(1.0 - gamma) > 1e-7) ? 1.0 / (gamma - 1.) : 1.0;
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const double unitv = 1e5;
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const double adec = 1.0 / (160. * std::pow(omegab * hubble_param_ * hubble_param_ / 0.022, 2.0 / 5.0));
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const double Tini = astart_ < adec ? Tcmb0 / astart_ : Tcmb0 / astart_ / astart_ * adec;
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const double mu = (Tini > 1.e4) ? 4.0 / (8. - 5. * YHe) : 4.0 / (1. + 3. * (1. - YHe));
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ceint_ = 1.3806e-16 / 1.6726e-24 * Tini * npol / mu / unitv / unitv;
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music::ilog.Print("Swift : Calculated initial gas temperature: %.2f K/mu", Tini / mu);
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music::ilog.Print("Swift : set initial internal energy to %.2e km^2/s^2", ceint_);
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h_ = boxsize_ / hubble_param_ / cf_.get_value<double>("setup","GridRes");
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music::ilog.Print("Swift : set initial smoothing length to mean inter-part separation: %.2f Mpc", h_);
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}
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// Only ranks 0 writes the header
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if (this_rank_ != 0) return;
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// delete output file if it exists
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unlink(this_fname_.c_str());
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unlink(fname_.c_str());
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// create output HDF5 file
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HDFCreateFile(this_fname_);
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HDFCreateFile(fname_);
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// Write UNITS header using the physical constants assumed internally by SWIFT
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HDFCreateGroup(this_fname_, "Units");
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HDFWriteGroupAttribute(this_fname_, "Units", "Unit mass in cgs (U_M)", 1.98841e43); // 10^10 Msun in grams
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HDFWriteGroupAttribute(this_fname_, "Units", "Unit length in cgs (U_L)", 3.08567758149e24); // 1 Mpc in cm
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HDFWriteGroupAttribute(this_fname_, "Units", "Unit time in cgs (U_t)", 3.08567758149e19); // so that unit vel is 1 km/s
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HDFWriteGroupAttribute(this_fname_, "Units", "Unit current in cgs (U_I)", 1.0); // 1 Ampere
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HDFWriteGroupAttribute(this_fname_, "Units", "Unit temperature in cgs (U_T)", 1.0); // 1 Kelvin
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HDFCreateGroup(fname_, "Units");
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HDFWriteGroupAttribute(fname_, "Units", "Unit mass in cgs (U_M)", 1.98841e43); // 10^10 Msun in grams
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HDFWriteGroupAttribute(fname_, "Units", "Unit length in cgs (U_L)", 3.08567758149e24); // 1 Mpc in cm
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HDFWriteGroupAttribute(fname_, "Units", "Unit time in cgs (U_t)", 3.08567758149e19); // so that unit vel is 1 km/s
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HDFWriteGroupAttribute(fname_, "Units", "Unit current in cgs (U_I)", 1.0); // 1 Ampere
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HDFWriteGroupAttribute(fname_, "Units", "Unit temperature in cgs (U_T)", 1.0); // 1 Kelvin
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// Write MUSIC configuration header
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int order = cf_.get_value<int>("setup", "LPTorder");
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@ -122,32 +143,32 @@ public:
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int do_baryonsVrel = cf_.get_value<bool>("setup", "DoBaryonVrel");
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int L = cf_.get_value<int>("setup", "GridRes");
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HDFCreateGroup(this_fname_, "ICs_parameters");
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HDFWriteGroupAttribute(this_fname_, "ICs_parameters", "Code", std::string("MUSIC2 - monofonIC"));
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HDFWriteGroupAttribute(this_fname_, "ICs_parameters", "Git Revision", std::string(GIT_REV));
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HDFWriteGroupAttribute(this_fname_, "ICs_parameters", "Git Tag", std::string(GIT_TAG));
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HDFWriteGroupAttribute(this_fname_, "ICs_parameters", "Git Branch", std::string(GIT_BRANCH));
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HDFWriteGroupAttribute(this_fname_, "ICs_parameters", "Precision", std::string(CMAKE_PRECISION_STR));
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HDFWriteGroupAttribute(this_fname_, "ICs_parameters", "Convolutions", std::string(CMAKE_CONVOLVER_STR));
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HDFWriteGroupAttribute(this_fname_, "ICs_parameters", "PLT", std::string(CMAKE_PLT_STR));
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HDFWriteGroupAttribute(this_fname_, "ICs_parameters", "LPT Order", order);
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HDFWriteGroupAttribute(this_fname_, "ICs_parameters", "Particle Load", load);
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HDFWriteGroupAttribute(this_fname_, "ICs_parameters", "Transfer Function", tf);
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HDFWriteGroupAttribute(this_fname_, "ICs_parameters", "Cosmology Parameter Set", cosmo_set);
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HDFWriteGroupAttribute(this_fname_, "ICs_parameters", "Random Generator", rng);
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HDFWriteGroupAttribute(this_fname_, "ICs_parameters", "Mode Fixing", do_fixing);
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HDFWriteGroupAttribute(this_fname_, "ICs_parameters", "Mode inversion", do_invert);
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HDFWriteGroupAttribute(this_fname_, "ICs_parameters", "Baryons", do_baryons);
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HDFWriteGroupAttribute(this_fname_, "ICs_parameters", "Baryons Relative Velocity", do_baryonsVrel);
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HDFWriteGroupAttribute(this_fname_, "ICs_parameters", "Grid Resolution", L);
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HDFCreateGroup(fname_, "ICs_parameters");
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HDFWriteGroupAttribute(fname_, "ICs_parameters", "Code", std::string("MUSIC2 - monofonIC"));
|
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HDFWriteGroupAttribute(fname_, "ICs_parameters", "Git Revision", std::string(GIT_REV));
|
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HDFWriteGroupAttribute(fname_, "ICs_parameters", "Git Tag", std::string(GIT_TAG));
|
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HDFWriteGroupAttribute(fname_, "ICs_parameters", "Git Branch", std::string(GIT_BRANCH));
|
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HDFWriteGroupAttribute(fname_, "ICs_parameters", "Precision", std::string(CMAKE_PRECISION_STR));
|
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HDFWriteGroupAttribute(fname_, "ICs_parameters", "Convolutions", std::string(CMAKE_CONVOLVER_STR));
|
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HDFWriteGroupAttribute(fname_, "ICs_parameters", "PLT", std::string(CMAKE_PLT_STR));
|
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HDFWriteGroupAttribute(fname_, "ICs_parameters", "LPT Order", order);
|
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HDFWriteGroupAttribute(fname_, "ICs_parameters", "Particle Load", load);
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HDFWriteGroupAttribute(fname_, "ICs_parameters", "Transfer Function", tf);
|
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HDFWriteGroupAttribute(fname_, "ICs_parameters", "Cosmology Parameter Set", cosmo_set);
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HDFWriteGroupAttribute(fname_, "ICs_parameters", "Random Generator", rng);
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HDFWriteGroupAttribute(fname_, "ICs_parameters", "Mode Fixing", do_fixing);
|
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HDFWriteGroupAttribute(fname_, "ICs_parameters", "Mode inversion", do_invert);
|
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HDFWriteGroupAttribute(fname_, "ICs_parameters", "Baryons", do_baryons);
|
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HDFWriteGroupAttribute(fname_, "ICs_parameters", "Baryons Relative Velocity", do_baryonsVrel);
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HDFWriteGroupAttribute(fname_, "ICs_parameters", "Grid Resolution", L);
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if (tf == "CLASS") {
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double ztarget = cf_.get_value<double>("cosmology", "ztarget");
|
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HDFWriteGroupAttribute(this_fname_, "ICs_parameters", "Target Redshift", ztarget);
|
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HDFWriteGroupAttribute(fname_, "ICs_parameters", "Target Redshift", ztarget);
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}
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if (rng == "PANPHASIA") {
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std::string desc = cf_.get_value<std::string>("random", "descriptor");
|
||||
HDFWriteGroupAttribute(this_fname_, "ICs_parameters", "Descriptor", desc);
|
||||
HDFWriteGroupAttribute(fname_, "ICs_parameters", "Descriptor", desc);
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -156,55 +177,28 @@ public:
|
|||
{
|
||||
if (!std::uncaught_exception())
|
||||
{
|
||||
HDFCreateGroup(this_fname_, "Header");
|
||||
if (this_rank_ == 0) {
|
||||
|
||||
// Write Standard Gadget / SWIFT hdf5 header
|
||||
HDFCreateGroup(fname_, "Header");
|
||||
HDFWriteGroupAttribute(fname_, "Header", "Dimension", 3);
|
||||
HDFWriteGroupAttribute(fname_, "Header", "BoxSize", boxsize_ / hubble_param_); // in Mpc, not Mpc/h
|
||||
|
||||
HDFWriteGroupAttribute(this_fname_, "Header", "NumPart_Total", from_7array<unsigned>(npartTotal_));
|
||||
HDFWriteGroupAttribute(this_fname_, "Header", "NumPart_Total_HighWord", from_7array<unsigned>(npartTotalHighWord_));
|
||||
HDFWriteGroupAttribute(this_fname_, "Header", "NumPart_ThisFile", from_7array<unsigned>(npart_));
|
||||
HDFWriteGroupAttribute(this_fname_, "Header", "MassTable", from_7array<double>(mass_));
|
||||
HDFWriteGroupAttribute(fname_, "Header", "NumPart_Total", from_7array<unsigned>(npartTotal_));
|
||||
HDFWriteGroupAttribute(fname_, "Header", "NumPart_Total_HighWord", from_7array<unsigned>(npartTotalHighWord_));
|
||||
HDFWriteGroupAttribute(fname_, "Header", "NumPart_ThisFile", from_7array<uint64_t>(npart_));
|
||||
HDFWriteGroupAttribute(fname_, "Header", "MassTable", from_7array<double>(mass_));
|
||||
|
||||
HDFWriteGroupAttribute(this_fname_, "Header", "Time", from_value<double>(time_));
|
||||
HDFWriteGroupAttribute(this_fname_, "Header", "Redshift", from_value<double>(zstart_));
|
||||
HDFWriteGroupAttribute(this_fname_, "Header", "Flag_Entropy_ICs", from_value<int>(0));
|
||||
HDFWriteGroupAttribute(fname_, "Header", "Time", from_value<double>(time_));
|
||||
HDFWriteGroupAttribute(fname_, "Header", "Redshift", from_value<double>(zstart_));
|
||||
HDFWriteGroupAttribute(fname_, "Header", "Flag_Entropy_ICs", from_value<int>(0));
|
||||
|
||||
HDFWriteGroupAttribute(this_fname_, "Header", "NumFilesPerSnapshot", from_value<int>(num_files_));
|
||||
|
||||
// write GAS internal energy and smoothing length if baryons are enabled
|
||||
if( bdobaryons_ )
|
||||
{
|
||||
const double gamma = cf_.get_value_safe<double>("cosmology", "gamma", 5.0 / 3.0);
|
||||
const double YHe = pcc_->cosmo_param_["YHe"];
|
||||
//const double Omega0 = cf_.get_value<double>("cosmology", "Omega_m");
|
||||
const double omegab = pcc_->cosmo_param_["Omega_b"];
|
||||
const double Tcmb0 = pcc_->cosmo_param_["Tcmb"];
|
||||
|
||||
|
||||
// compute gas internal energy
|
||||
const double npol = (fabs(1.0 - gamma) > 1e-7) ? 1.0 / (gamma - 1.) : 1.0;
|
||||
const double unitv = 1e5;
|
||||
const double adec = 1.0 / (160. * std::pow(omegab * hubble_param_ * hubble_param_ / 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));
|
||||
const double ceint = 1.3806e-16 / 1.6726e-24 * Tini * npol / mu / unitv / unitv;
|
||||
|
||||
music::ilog.Print("Swift : Calculated initial gas temperature: %.2f K/mu", Tini / mu);
|
||||
music::ilog.Print("Swift : set initial internal energy to %.2e km^2/s^2", ceint);
|
||||
|
||||
std::vector<write_real_t> data( npart_[0], ceint );
|
||||
HDFWriteDataset(this_fname_, "PartType0/InternalEnergy", data);
|
||||
|
||||
const double h = boxsize_ / hubble_param_ / cf_.get_value<double>("setup","GridRes");
|
||||
|
||||
music::ilog.Print("Swift : set initial smoothing length to mean inter-part separation: %.2f Mpc", h);
|
||||
|
||||
data.assign( npart_[0], h);
|
||||
HDFWriteDataset(this_fname_, "PartType0/SmoothingLength", data);
|
||||
HDFWriteGroupAttribute(fname_, "Header", "NumFilesPerSnapshot", from_value<int>(num_files_));
|
||||
|
||||
music::ilog << "Done writing SWIFT IC file to " << fname_ << std::endl;
|
||||
music::ilog << "Note that the IC file does not contain any h-factors nor any extra sqrt(a)-factors for the velocities" << std::endl;
|
||||
music::ilog << "The SWIFT parameters 'InitialConditions:cleanup_h_factors' and 'InitialConditions:cleanup_velocity_factors' should hence *NOT* be set!" << std::endl;
|
||||
}
|
||||
|
||||
music::ilog << "Wrote SWIFT IC file(s) to " << this_fname_ << std::endl;
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -247,52 +241,135 @@ public:
|
|||
void write_particle_data(const particle::container &pc, const cosmo_species &s, double Omega_species)
|
||||
{
|
||||
int sid = get_species_idx(s);
|
||||
|
||||
assert(sid != -1);
|
||||
|
||||
npart_[sid] = (pc.get_local_num_particles());
|
||||
npart_[sid] = (pc.get_global_num_particles());
|
||||
npartTotal_[sid] = (uint32_t)(pc.get_global_num_particles());
|
||||
npartTotalHighWord_[sid] = (uint32_t)((pc.get_global_num_particles()) >> 32);
|
||||
|
||||
std::array<double,7> particle_masses;
|
||||
if( pc.bhas_individual_masses_ )
|
||||
mass_[sid] = 0.0;
|
||||
particle_masses[sid] = 0.0;
|
||||
else
|
||||
mass_[sid] = Omega_species * munit_ / pc.get_global_num_particles();
|
||||
particle_masses[sid] = Omega_species * munit_ / pc.get_global_num_particles();
|
||||
|
||||
HDFCreateGroup(this_fname_, std::string("PartType") + std::to_string(sid));
|
||||
const size_t global_num_particles = pc.get_global_num_particles();
|
||||
|
||||
// start by creating the full empty datasets in the file
|
||||
if (this_rank_ == 0) {
|
||||
|
||||
HDFCreateGroup(fname_, std::string("PartType") + std::to_string(sid));
|
||||
|
||||
if (this->has_64bit_reals())
|
||||
{
|
||||
HDFCreateEmptyDatasetVector<double>(fname_, std::string("PartType") + std::to_string(sid) + std::string("/Coordinates"), global_num_particles, true);
|
||||
HDFCreateEmptyDatasetVector<double>(fname_, std::string("PartType") + std::to_string(sid) + std::string("/Velocities"), global_num_particles, true);
|
||||
}
|
||||
else
|
||||
{
|
||||
HDFCreateEmptyDatasetVector<float>(fname_, std::string("PartType") + std::to_string(sid) + std::string("/Coordinates"), global_num_particles, true);
|
||||
HDFCreateEmptyDatasetVector<float>(fname_, std::string("PartType") + std::to_string(sid) + std::string("/Velocities"), global_num_particles, true);
|
||||
}
|
||||
|
||||
if (this->has_64bit_ids())
|
||||
HDFCreateEmptyDataset<uint64_t>(fname_, std::string("PartType") + std::to_string(sid) + std::string("/ParticleIDs"), global_num_particles, true);
|
||||
else
|
||||
HDFCreateEmptyDataset<uint32_t>(fname_, std::string("PartType") + std::to_string(sid) + std::string("/ParticleIDs"), global_num_particles, true);
|
||||
|
||||
if (this->has_64bit_reals())
|
||||
HDFCreateEmptyDataset<double>(fname_, std::string("PartType") + std::to_string(sid) + std::string("/Masses"), global_num_particles, true);
|
||||
else
|
||||
HDFCreateEmptyDataset<float>(fname_, std::string("PartType") + std::to_string(sid) + std::string("/Masses"), global_num_particles, true);
|
||||
|
||||
if( bdobaryons_ && s == cosmo_species::baryon) {
|
||||
|
||||
// note: despite this being a constant array we still need to handle it in a distributed way
|
||||
HDFCreateEmptyDataset<write_real_t>(fname_, std::string("PartType") + std::to_string(sid) + std::string("/InternalEnergy"), global_num_particles, true);
|
||||
HDFCreateEmptyDataset<write_real_t>(fname_, std::string("PartType") + std::to_string(sid) + std::string("/SmoothingLength"), global_num_particles, true);
|
||||
}
|
||||
|
||||
music::ilog << "Created empty arrays for PartType" << std::to_string(sid) << " into file " << fname_ << "." << std::endl;
|
||||
}
|
||||
|
||||
// compute each rank's offset in the global array
|
||||
const size_t n_local = pc.get_local_num_particles();
|
||||
size_t offset = 0;
|
||||
#ifdef USE_MPI
|
||||
MPI_Exscan(&n_local, &offset, 1, MPI_UNSIGNED_LONG_LONG, MPI_SUM, MPI_COMM_WORLD);
|
||||
#endif
|
||||
|
||||
// now each node writes its own chunk in a round-robin fashion, appending at the end of the currently existing data
|
||||
for (int rank = 0; rank < num_ranks_; ++rank) {
|
||||
|
||||
#ifdef USE_MPI
|
||||
// wait until the initialisation or the previous rank in the loop is done
|
||||
MPI_Barrier(MPI_COMM_WORLD);
|
||||
#endif
|
||||
|
||||
if (rank == this_rank_) {
|
||||
|
||||
//... write positions and velocities.....
|
||||
if (this->has_64bit_reals())
|
||||
{
|
||||
HDFWriteDatasetVector(this_fname_, std::string("PartType") + std::to_string(sid) + std::string("/Coordinates"), pc.positions64_);
|
||||
HDFWriteDatasetVector(this_fname_, std::string("PartType") + std::to_string(sid) + std::string("/Velocities"), pc.velocities64_);
|
||||
HDFWriteDatasetVectorChunk(fname_, std::string("PartType") + std::to_string(sid) + std::string("/Coordinates"), pc.positions64_, offset);
|
||||
HDFWriteDatasetVectorChunk(fname_, std::string("PartType") + std::to_string(sid) + std::string("/Velocities"), pc.velocities64_, offset);
|
||||
}
|
||||
else
|
||||
{
|
||||
HDFWriteDatasetVector(this_fname_, std::string("PartType") + std::to_string(sid) + std::string("/Coordinates"), pc.positions32_);
|
||||
HDFWriteDatasetVector(this_fname_, std::string("PartType") + std::to_string(sid) + std::string("/Velocities"), pc.velocities32_);
|
||||
HDFWriteDatasetVectorChunk(fname_, std::string("PartType") + std::to_string(sid) + std::string("/Coordinates"), pc.positions32_, offset);
|
||||
HDFWriteDatasetVectorChunk(fname_, std::string("PartType") + std::to_string(sid) + std::string("/Velocities"), pc.velocities32_, offset);
|
||||
}
|
||||
|
||||
//... write ids.....
|
||||
if (this->has_64bit_ids())
|
||||
HDFWriteDataset(this_fname_, std::string("PartType") + std::to_string(sid) + std::string("/ParticleIDs"), pc.ids64_);
|
||||
HDFWriteDatasetChunk(fname_, std::string("PartType") + std::to_string(sid) + std::string("/ParticleIDs"), pc.ids64_, offset);
|
||||
else
|
||||
HDFWriteDataset(this_fname_, std::string("PartType") + std::to_string(sid) + std::string("/ParticleIDs"), pc.ids32_);
|
||||
HDFWriteDatasetChunk(fname_, std::string("PartType") + std::to_string(sid) + std::string("/ParticleIDs"), pc.ids32_, offset);
|
||||
|
||||
//... write masses.....
|
||||
if( pc.bhas_individual_masses_ ){
|
||||
if (this->has_64bit_reals()){
|
||||
HDFWriteDataset(this_fname_, std::string("PartType") + std::to_string(sid) + std::string("/Masses"), pc.mass64_);
|
||||
}else{
|
||||
HDFWriteDataset(this_fname_, std::string("PartType") + std::to_string(sid) + std::string("/Masses"), pc.mass32_);
|
||||
if( pc.bhas_individual_masses_ )
|
||||
{
|
||||
if (this->has_64bit_reals())
|
||||
HDFWriteDatasetChunk(fname_, std::string("PartType") + std::to_string(sid) + std::string("/Masses"), pc.mass64_, offset);
|
||||
else
|
||||
HDFWriteDatasetChunk(fname_, std::string("PartType") + std::to_string(sid) + std::string("/Masses"), pc.mass32_, offset);
|
||||
}
|
||||
else
|
||||
{
|
||||
std::vector<write_real_t> data( pc.get_local_num_particles(), particle_masses[sid]);
|
||||
|
||||
if (this->has_64bit_reals())
|
||||
HDFWriteDatasetChunk(fname_, std::string("PartType") + std::to_string(sid) + std::string("/Masses"), data, offset);
|
||||
else
|
||||
HDFWriteDatasetChunk(fname_, std::string("PartType") + std::to_string(sid) + std::string("/Masses"), data, offset);
|
||||
}
|
||||
|
||||
// write GAS internal energy and smoothing length if baryons are enabled
|
||||
if(bdobaryons_ && s == cosmo_species::baryon) {
|
||||
|
||||
std::vector<write_real_t> data( pc.get_local_num_particles(), ceint_ );
|
||||
HDFWriteDatasetChunk(fname_, std::string("PartType") + std::to_string(sid) + std::string("/InternalEnergy"), data, offset);
|
||||
|
||||
data.assign( pc.get_local_num_particles(), h_);
|
||||
HDFWriteDatasetChunk(fname_, std::string("PartType") + std::to_string(sid) + std::string("/SmoothingLength"), data, offset);
|
||||
}
|
||||
}
|
||||
|
||||
if (this_rank_ == 0) {
|
||||
music::ilog << "Rank " << rank << " wrote its PartType" << std::to_string(sid) << " data to the IC file." << std::endl;
|
||||
}
|
||||
}
|
||||
|
||||
#ifdef USE_MPI
|
||||
// end with a barrier to make sure everyone is done before the destructor does its job
|
||||
MPI_Barrier(MPI_COMM_WORLD);
|
||||
#endif
|
||||
}
|
||||
};
|
||||
|
||||
namespace
|
||||
{
|
||||
output_plugin_creator_concrete<swift_output_plugin<float>> creator1("SWIFT");
|
||||
output_plugin_creator_concrete<swift_output_plugin<double>> creator1("SWIFT");
|
||||
} // namespace
|
||||
|
||||
#endif
|
||||
|
|
|
|||
Loading…
Reference in a new issue