README.md

Optab opacity database

This directory stores opacity databases used in Optab.

Notes

• Keep the directory structure as is because Optab programs use the relative paths.
• As for molecular line lists, we recommend to start with HITRAN/HITEMP since Exomol database is gigantic.

---

1016620_Supplementary_Data/

• This directory stores free-free Gaunt factor data by van Hoof et al. (2014).
• Extract their supplementary data in this directory.

Karzas_Latter_1961.tsv

• This file is "Table I" (bound-free Gaunt factors) in Karzas and Latter (1961) (© AAS. Reproduced with permission).

photo/

• This directory contains Verner's photoionization cross sections data.
• Copy all files in https://www.pa.uky.edu/~verner/dima/photo/ into this directory.

TOPbase/

• This directory is a workspace for TOPbase: photoionization cross sections.

1. Execute get_topbase.sh to retrieve the cross section data:

   % bash ../fetch/get_topbase.sh
   

2. Execute convert_topbase_h5 to store the data in the specific HDF5 format for Optab:

   % ../src/convert_topbase_h5
   

NIST/

• This directory is a workspace for NIST Atomic Weights and Isotopic Compositions with Relative Atomic Masses and Atomic Spectra Database Levels.

1. Execte get_nist_atomic.sh and get_nist_levels.sh to retrieve the data, respectively:

   % bash ../fetch/get_nist_atomic.sh
   % bash ../fetch/get_nist_levels.sh
   

2. Execute convert_nist_h5 to store the data in the specifice HDF5 format for Optab:

   % ../src/convert_nist_h5
   

HITRAN/

• This directory is a workspace for HITRAN molecular linelists.

1. Execulte get_hitran_meta.sh to retrieve HITRAN Isotopologue Metadata:

   % bash ../fetch/get_hitran_meta.sh
   

The following procedure is for H₂O in HITRAN. Repeat it for other species.

2. Get linelists (.par files):
   1. Goto Line-by-Line Search.
   2. "Select Molecules" → check 1. H2O
   3. "Select Isotopologues" → check all isotopologues
   4. "Select Wavenumber / Wavelength Range" → leave blank for ν_max
   5. "Select or Create Output Format" → do nothing
   6. "Start Data Search> Search Results" → download the "Output transitions data (160-character .par format)" as original/01_HITRAN.par. Here, "01" is the two digits molecule ID of H₂O.
3. Break down the downloaded .par file to make separate .par files for different isotoplogue:

   $ ../src/preproc_hitran original/01_HITRAN.par

4. Convert each isotopologue .par file to an HDF5 file in the specific format for Optab:

   $ ../src/convert_lines_h5

The following procedure is for H₂O in HITEMP. Repeat it for other species.

2. Get linelists (.par files):

   1. Goto https://hitran.org/hitemp/data/HITEMP-2010/H2O_line_list/.
   2. Download all zipped files and unzip them.
   3. Concatenate all unzipped files into a single file, original/01_HITEMP2010.par.

3. Break down the downloaded .par file to make separate .par files for different isotoplogue:

   $ ../src/preproc_hitran original/01_HITEMP2010.par

4. Convert each isotopologue .par file to an HDF5 file in the specific format for Optab:

   $ ../src/convert_lines_h5

Exomol/

• This directory is a workspace for Exomol molecular linelists.

The following procedure is for 1H2-16O__POKAZATEL. Repeat it for other species.

1. Get a set of data files (.def, .pf, .states, .trans files) from https://www.exomol.com/data/molecules/H2O/1H2-16O/POKAZATEL/ and place them in the subdirectory 1H2-16O__POKAZATEL/.
2. Get .broad files from https://www.exomol.com/data/molecules/H2O/, and place them in this directory. Note that the .broad files are provided only for limited species; if not provided, ignore this step.
3. Here is the list of the data files:

   1H2-16O__H2.broad
   1H2-16O__He.broad
   1H2-16O__POKAZATEL/1H2-16O__POKAZATEL.def
   1H2-16O__POKAZATEL/1H2-16O__POKAZATEL.pf
   1H2-16O__POKAZATEL/1H2-16O__POKAZATEL.states
   1H2-16O__POKAZATEL/1H2-16O__POKAZATEL__00000-00100.trans
   1H2-16O__POKAZATEL/1H2-16O__POKAZATEL__00100-00200.trans
   1H2-16O__POKAZATEL/1H2-16O__POKAZATEL__00200-00300.trans
   ...
   

4. Edit list_convert.txt to list the relative paths of the .trans files, and convert them into a n HDF5 file in the specific format for Optab:

   $ cat list_convert.txt
   1H2-16O__POKAZATEL/1H2-16O__POKAZATEL__00000-00100.trans
   1H2-16O__POKAZATEL/1H2-16O__POKAZATEL__00100-00200.trans
   1H2-16O__POKAZATEL/1H2-16O__POKAZATEL__00200-00300.trans
   ...
   $ ../src/convert_lines_h5

Kurucz/

• This directory is a workspace for Kurucz atomic linelinsts

1. Execute get_kurucz_linelists.sh, which retrieves two linelists, gfall08oct17.dat and gfpred26apr18.dat, from Kurucz database and puts them in the subdirectory linelists/. Edit list_convert.txt to list the relative paths of the linelists, and execute convert_lines_h5 to generate HDF5 files for Optab:

   $ bash ../fetch/get_kurucz_linelists.sh
   $ ls linelists/*.dat > list_convert.txt
   $ ../src/convert_lines_h5

2. Execute get_kurucz_gfgam.sh to get the level data file gf????.gam for all species available, and execute convert_gfgam_h5 to generate an HDF5 file for Optab:

   $ bash ../fetch/get_kurucz_gfgam.sh
   $ ../src/convert_gfgam_h5

h5/

• This directory is the storage for the files in the HDF5 format made for Optab.