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        "author": "Patricio Cubillos",
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        "description": "# repack\nRepack and Compress Line-transition Data for Radiative-tranfer Calculations\n\n[![Build Status](https://travis-ci.com/pcubillos/repack.svg?branch=master)](https://travis-ci.com/pcubillos/repack)\n[![PyPI](https://img.shields.io/pypi/v/lbl-repack.svg)](https://pypi.org/project/lbl-repack)\n[![GitHub](https://img.shields.io/github/license/pcubillos/repack.svg?color=blue)](https://github.com/pcubillos/repack/blob/master/LICENSE)\n\nThis code identifies the strong lines that dominate the spectrum from\nthe large-majority of weaker lines.  The code returns a binary\nline-by-line (LBL) file with the strong lines info (wavenumber, Elow,\ngf, and isotope ID), and an ascii file with the combined contribution\nof the weaker lines compressed into a continuum extinction coefficient\n(in cm-1 amagat-1) as function of wavenumber and temperature.\n\nCurrently available databases:\n* ExoMol (http://www.exomol.com/)\n* HITRAN (https://www.cfa.harvard.edu/hitran/)\n* Kurucz's TiO (http://kurucz.harvard.edu/molecules/tio)\n\n### Team Members\n* [Patricio Cubillos](https://github.com/pcubillos/) (IWF) <patricio.cubillos@oeaw.ac.at>\n\n### Install\n``repack`` has been [tested](https://travis-ci.com/pcubillos/repack) to work on Python 2.7, 3.6, and 3.7; and runs (at least) in both Linux and OSX.  You can install ``repack`` from the terminal with pip:\n\n```shell\n# Note that on PyPI ``repack``is indexed as ``lbl-repack``:\npip install lbl-repack\n```\n\nAlternative (for conda users or for developers), you can directly\ndowload the source code and install to your local machine with the\nfollowing terminal commands:\n\n```shell\ngit clone https://github.com/pcubillos/repack/\ncd repack\npython setup.py install\n```\n\n### Getting Started\n\nThe following example compresses the Exomol HCN line-transition data.  First, download the ExoMol HCN dataset (there is no need to unzip the files):\n\n```shell\n# Download ExoMol HCN data:\nwget http://exomol.com/db/HCN/1H-12C-14N/Harris/1H-12C-14N__Harris.states.bz2\nwget http://exomol.com/db/HCN/1H-12C-14N/Harris/1H-12C-14N__Harris.trans.bz2\nwget http://exomol.com/db/HCN/1H-12C-14N/Harris/1H-12C-14N__Harris.pf\nwget http://exomol.com/db/HCN/1H-13C-14N/Larner/1H-13C-14N__Larner.states.bz2\nwget http://exomol.com/db/HCN/1H-13C-14N/Larner/1H-13C-14N__Larner.trans.bz2\nwget http://exomol.com/db/HCN/1H-13C-14N/Larner/1H-13C-14N__Larner.pf\n```\n\nThen create a repack configuration file ('*repack_HCN.cfg*') like this below:\n\n```shell\n[REPACK]\n\n# Line-transition files:\nlblfiles = 1H-12C-14N__Harris.trans.bz2\n           1H-13C-14N__Larner.trans.bz2\n\n# Database type [exomol, hitran, or kurucz]:\ndbtype = exomol\n\n# Output file name (without file extension):\noutfile = HCN_exomol_0.3-33um_500-3000K\n\n# Wavenumber boundaries and sampling rate (in cm-1):\nwnmin =   303.0\nwnmax = 33334.0\ndwn   =     1.0\n\n# Temperature sampling:\ntmin  =  500.0\ntmax  = 3000.0\ndtemp =  100.0\n\n# Line-intensity threshold for strong/weak lines:\nsthresh = 0.1\n\n# Maximum chunk size of lines to handle at a time:\nchunksize = 15000000\n```\n\nAnd run ``repack``, which will produce the following screen output:\n```shell\n# Call the repack command-line executable for the HCN demo config file:\nrepack repack_HCN.cfg\n\n::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::\n  repack: line-transition data compression.\n  Version 1.2.8.\n  Copyright (c) 2017-2019 Patricio Cubillos.\n  repack is open-source software under the MIT license.\n::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::\n\n\nStarting: Sun Jul  7 19:52:28 2019\nUnzipping: '1H-12C-14N__Harris.trans.bz2'.\nUnzipping: '1H-13C-14N__Larner.trans.bz2'.\nReading: '1H-12C-14N__Harris.trans.bz2'.\nReading: '1H-13C-14N__Larner.trans.bz2'.\n  Flagging lines at  500 K (chunk 1/5):\n  Compression rate:       98.13%,    247,715/13,241,389 lines.\n  Flagging lines at 3000 K:\n  Compression rate:       96.17%,    506,751/13,241,389 lines.\n  Total compression rate: 95.11%,    648,132/13,241,389 lines.\n\n...\n\n  Flagging lines at  500 K (chunk 5/5):\n  Compression rate:       96.94%,    401,033/13,089,891 lines.\n  Flagging lines at 3000 K:\n  Compression rate:       93.09%,    904,262/13,089,891 lines.\n  Total compression rate: 91.42%,  1,122,911/13,089,891 lines.\n\nWith a threshold strength factor of 0.1,\nkept a total of 3,009,610 line transitions out of 65,586,274 lines.\n\nSuccessfully rewriten exomol line-transition info into:\n  'HCN_exomol_0.3-33um_500-3000K_lbl.dat' and\n  'HCN_exomol_0.3-33um_500-3000K_continuum.dat'.\nEnd: Sun Jul  7 19:59:59 2019\n```\n\nThe output binary file '*HCN_exomol_0.3-33um_500-3000K_lbl.dat*'\ncontains the line-by-line opacity information for HCN, which represent\nmost of the opacity contribution into the spectrum.  The information\nis encoded as a sequence of three doubles and an integer containing\nthe wavenumber (in cm-1), lower-state energy (in cm-1 units),\ngf value, and isotope index, respectively, for each transition.  This\ninfo can be easily read with the following python script:\n\n```python\nimport repack.utils as u\nwn, elow, gf, iiso = u.read_lbl('HCN_exomol_0.3-33um_500-3000K_lbl.dat')\n```\n\nThe output ascii file '*HCN_exomol_0.3-33um_500-3000K_continuum.dat*'\ncontains the remaining opacity contribution of the weak lines (in cm-1\namagat-1 units) as function of wavenumber and temperature.  This is a\nminor contribution compared to that of the LBL output file.\n\n\n### Be Kind\n\nPlease, be kind and acknowledge the effort of the authors by citing the article asociated to this project:  \n\n  [Cubillos (2017): An Algorithm to Compress Line-transition Data for Radiative-transfer Calculations](http://adsabs.harvard.edu/abs/2017ApJ...850...32C), ApJ 850, 32.  \n\n\n### License\n\nCopyright (c) 2017-2019 Patricio Cubillos and contributors.\n``repack`` is open-source software under the MIT license (see [LICENSE](https://github.com/pcubillos/repack/blob/master/LICENSE)).",
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