Optab opacity database

February 17, 2026 · View on GitHub

This directory houses the opacity databases utilized by Optab.

Notes

Retain the current directory structure, as Optab relies on relative path references.

We recommend starting with the HITRAN/HITEMP database for molecular line lists, as the Exomol database's extensive size may be overwhelming for initial exploration.

Please be aware that the scripts provided for downloading the databases may become obsolete if there are changes in the database formats. If you encounter such issues, kindly inform the author (shirose@jamstec.go.jp).

`h5/`

This directory serves as the repository for HDF5-formatted files created for optab.

`1016620_Supplementary_Data/`

This directory contains the free-free Gaunt factor data authored by van Hoof et al. (2014), sourced from data.nublado.org.
```
cd 1016620_Supplementary_Data/
bash get_gauntff.sh
```

`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 stores Verner's photoionization cross sections data.

Copy photo.dat and table1.dat from the site.
```
cd photo/
bash get_photo.sh
```

`TOPbase/`

This directory serves as a workspace for TOPbase: photoionization cross sections.
```
cd TOPbase/
```

Execute get_topbase.py to retrieve the cross section data files and convert them to a specific HDF5 format for Optab:
```
python3 get_topbase.py
```

`NIST/`

This directory functions as a workspace for the NIST databases on Atomic Weights and Isotopic Compositions with Relative Atomic Masses and Atomic Spectra Database Levels.
```
cd NIST/
```

Execute get_nist_parallel.py to retrieve the level/atomic data and convert them to a specific HDF5 format for Optab:
```
python3 get_nist_parallel.py
```
or try get_nist.py (slower) if you encounter a network issue.

`HITRAN/`

This directory is a workspace for HITRAN molecular linelists.
```
cd HITRAN/
```

HITRAN Isotopologue Metadata and the partition function files (REQUIREMENT: w3m):
```
python3 get_hitran_meta.py
```
Linelists (.par files):
1. LBL (REQUIREMENT: Google Chrome, selenium (Python package), webdriver_manager (Python package)):
```
python3 get_hitran_lines.py "/Users/shirose/Library/Application\ Support/Google/Chrome/Default"
```
  The required argument is your Chrome user profile directory. To find this, visit chrome://version in Chrome..
  NOTE:
  - If you are redirected to the registration page, register or log in. Then, exit Chrome and restart the process.
  - Alternatively, you can download the linelists manually; refer to the instructions provided within the code.
2. HITEMP (REQUIREMENT: Google Chrome, selenium (Python package), webdriver_manager (Python package)):
```
python3 get_hitemp_lines.py "/Users/shirose/Library/Application\ Support/Google/Chrome/Default"
```
  The required argument is your Chrome user profile directory. To find this, visit chrome://version in Chrome. Available molecules: H2O, CO2, N2O, CO, CH4, NO, NO2, OH.
  NOTE:
  - If you are redirected to the registration page, register or log in. Then, exit Chrome and restart the process.
Create individual .par files for each isotopologue and convert them to HDF5 files ready for optab:
```
bash preproc_and_convert_HITRAN.sh
bash preproc_and_convert_HITEMP.sh
```

`Kurucz/`

This directory serves as a workspace for Kurucz atomic linelinsts
```
cd Kurucz/
```

Execute get_kurucz_linelists.sh to retrieve two linelists, gfall08oct17.dat and gfpred26apr18.dat, from Kurucz database and convert them to HDF5 files for Optab:
```
bash get_kurucz_lines.sh
```
Execute get_kurucz_gfgam.sh to get the level data files gf????.gam for all species available (ignore Not Found errors) and convert them to an HDF5 file for Optab:
```
python3 get_kurucz_gfgam.py
```

`Exomol/`

This directory is a workspace for Exomol molecular linelists.

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

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/.
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.

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
...

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