MESA compress

nnaps-mesa compress [options]

-i, -inputdir (str) <input directory path>

The directory containing all mesa models. Each model in its own sub folder.

-f, -infofile (str) <info file path>

Path to a csv file containing a list of all the models that you want to extra, with potentially extra information to add to the individual models. This file needs to contain at least 1 column with the name of the folder containing the MESA model. This collumn needs to be called ‘path’. Example of such a file:

path,extra_info1, extra_info2
model_dir1,10,disk
model_dir2,20,halo

-o, -outputdir (str) <output directory path>

The path to the directory where you want the compressed hdf5 MESA files to be stored.

-s, -setup (str) <setup file path>

yaml file containing the settings the compress action.

If not setup file is give, nnaps-mesa will look for one in the current directory or in the <user>/.nnaps directory. In that case the filename of the setup file needs to be defaults_compress.yaml.

If no setup file can be found anywhere, nnaps-mesa will use the defaults stored in the mesa.defaults module.

--skip

When provided, nnaps-mesa will only compress models that are not yet present in the output folder. Models that already have a compressed hdf5 version in the output folder will be ignored.

Basic usage

The most simple way to use the compress tool is to provide the folder where all MESA models are located, and the folder where you want the compressed files to be stored:

nnaps-mesa compress -i <input folder> -o <output folder>

compress will use standard settings assuming the following file structure for a MESA run:

MESA model
├── LOGS
│   ├── binary_history.data
│   ├── history1.data
│   ├── history2.data
│   ├── profile1.profile
│   ├── profile2.profile
│   └── profile3.profile
├── inlist_project
├── inlist1
├── inlist2
└── log.txt

The binary and stellar history files are located in the LOGS directory together with any potential profiles. The terminal output of the MESA run is stored in the log.txt file. By default the binary and stellar history will be compressed together with all profiles found. compress will also extract the stopping condition from the terminal output if possible. The compressed hdf5 file has the following structure.

MESA model
├── extra_info
│   └── termination_code
├── history
│   ├── binary
│   ├── star1
│   └── star2
├── profile_legend
└── profiles
    ├── profile1
    ├── profile1
    └── profile3

profile_legend is an array containing the model_number when the profile is taken together with the profile name. Both for profiles and history files, only the actual data is saved, not the header info!

Setup file

By using a custom setup file you can specify exactly what should be included in the hdf5 archive and what the exact structure of the MESA model directory is.

The setup file has to be structured in yaml format, and can be provided using the -s option.

star_columns: []
binary_columns: []
profile_columns: []
input_path_kw: 'path'
input_path_prefix: ''
star1_history_file: 'LOGS/history1.data'
star2_history_file: 'LOGS/history2.data'
binary_history_file: 'LOGS/binary_history.data'
log_file: 'log.txt'
add_stopping_condition: True
profile_files: []
profiles_path: 'LOGS'
profile_pattern: 'profile_*.data'

star_columns (list)

A list of all columns in the star history file to include. When empty or not included all columns will be kept.

binary_columns (list)

A list of all columns in the binary history file to include. When empty or not included all columns will be kept.

profile_columns (list)

A list of all columns in profiles to include. When empty or not included all columns will be kept.

input_path_kw (str)

If nnaps-mesa compress is called with a file_list.csv and a model_directory, then this keyword indicates the name of the column in the file_list.csv that contains the path of the directory containing the MESA model relative to the working directory. The default is ‘path’.

input_path_prefix (str)

If nnaps-mesa compress is called with a file_list.csv and a model_directory, then this keyword indicates the optional prefix to be added in front of the directory given in the file_list.csv by the input_path_kw. The full path relative to the current working directory is then:

input_path_prefix + file_list.csv[input_path_kw]

star1_history_file (str)

The path of the history file of the first star relative to the model directory.

star2_history_file (str)

The path of the history file of the second star relative to the model directory.

binary_history_file (str)

The path of the binary history file relative to the model directory.

log_file (str)

The path of the logging output of MESA relative to the model directory.

add_stopping_condition (boolean)

When true, the stopping criteria of MESA will be extracted from the log_file and included in the hdf5 file.

profile_files (list)

A list of which profile files to include. If empty or not included all profile files that can be identified using the profile_pattern keyword will be included.

profiles_path (str)

The path of the directory containing the profiles relative to the model directory

profile_pattern (str)

The pattern of the profiles to include. Will only be used when profile_files is empty or not included.

Reading compressed files

NNaPS provides two methods to easily read the compressed files. The read_hdf5() function will read any hdf5 formatted file and return the content as a python dictionary, while the read_compressed_track() reads hdf5 files created by NNaPS and returns the result in a more directly usable way. read_compressed_track() returns the combined stellar and binary history in one array, dealing automatically with inequalities in time steps in the different history files. It also returns a dictionary with other info, and if requested a dictionary containing the profiles.