radis.io.exomol module

Created on Sun May 22 18:11:23 2022

@author: erwan

fetch_exomol(molecule, database=None, local_databases=None, databank_name='EXOMOL-{molecule}', isotope='1', load_wavenum_min=None, load_wavenum_max=None, columns=None, cache=True, verbose=True, clean_cache_files=True, return_local_path=False, return_partition_function=False, engine='default', output='pandas', skip_optional_data=True, **kwargs)

Stream ExoMol file from EXOMOL website. Unzip and build a HDF5 file directly.

Returns a Pandas DataFrame containing all lines.

Parameters:

• molecule (str) – ExoMol molecule

• database (str) – database name. Ex: POKAZATEL or BT2 for H2O. See KNOWN_EXOMOL_DATABASE_NAMES. If None and there is only one database available, use it.

• local_databases (str) – where to create the RADIS HDF5 files. Default "~/.radisdb/exomol". Can be changed in radis.config["DEFAULT_DOWNLOAD_PATH"] or in ~/radis.json config file

• databank_name (str) – name of the databank in RADIS Configuration file Default "EXOMOL-{molecule}"

• isotope (str or int) – load only certain isotopes, sorted by terrestrial abundances : '1', '2', etc. Default 1.

  Note

  In RADIS, isotope abundance is included in the line intensity calculation. However, the terrestrial abundances used may not be relevant to non-terrestrial applications. By default, the abundance is given reading HITRAN data. If the molecule does not exist in the HITRAN database, the abundance is read from the radis/radis_default.json configuration file, which can be modified by editing radis.config after import or directly by editing the user ~/radis.json user configuration file (overwrites radis_default.json). In the radis/radis_default.json file, values were calculated with a simple model based on the terrestrial isotopic abundance of each element.

• load_wavenum_min, load_wavenum_max (float (cm-1)) – load only specific wavenumbers.

• columns (list of str) – list of columns to load. If None, returns all columns in the file.

Other Parameters:

• cache (bool, or 'regen' or 'force') – if True, use existing HDF5 file. If False or 'regen', rebuild it. If 'force', crash if not cache file found. Default True.

• verbose (bool)

• clean_cache_files (bool) – if True clean downloaded cache files after HDF5 are created.

• return_local_path (bool) – if True, also returns the path of the local database file.

• return_partition_function (bool) – if True, also returns a PartFuncExoMol object.

• engine (‘vaex’, ‘feather’) – which memory-mapping library to use. If ‘default’ use the value from ~/radis.json

• output (‘pandas’, ‘vaex’, ‘jax’) – format of the output DataFrame. If 'jax', returns a dictionary of jax arrays. If 'vaex', output is a vaex.dataframe.DataFrameLocal

  Note

  Vaex DataFrames are memory-mapped. They do not take any space in RAM and are extremely useful to deal with the largest databases.

• skip_optional_data (bool) – If False, fetch all fields which are marked as available in the ExoMol definition file. If True, load only the first 4 columns of the states file (“i”, “E”, “g”, “J”). The structure of the columns above 5 depend on the the definitions file (*.def) and the Exomol version. If skip_optional_data=False, two errors may occur:

  • a field is marked as present/absent in the *.def field but is absent/present in the *.states file (ie both files are inconsistent).

  • in the updated version of Exomol, new fields have been added in the states file of some species. But it has not been done for all species, so both structures exist. For instance, the states file of https://exomol.com/data/molecules/HCl/1H-35Cl/HITRAN-HCl/ follows the structure described in [1], unlike the states file of https://exomol.com/data/molecules/NO/14N-16O/XABC/ which follows the structure described in [2].

Returns:

• df (pd.DataFrame or vaex.dataframe.DataFrameLocal) – Line list A HDF5 file is also created in local_databases and referenced in the RADIS config file with name databank_name

• local_path (str) – path of local database file if return_local_path

Examples

Calculate a spectrum from ExoMol

Calculate a spectrum from ExoMol

Notes

if using load_only_wavenum_above/below or isotope, the whole database is anyway downloaded and uncompressed to local_databases fast access .HDF5 files (which will take a long time on first call). Only the expected wavenumber range & isotopes are returned. The .HFD5 parsing uses hdf2df()

References

[1]

Tennyson, J., Yurchenko, S. N., Al-Refaie, A. F., Barton, E. J., Chubb, K. L., Coles, P. A., … Zak, E. (2016). The ExoMol database: molecular line lists for exoplanet and other hot atmospheres. https://doi.org/10.1016/j.jms.2016.05.002

[2]

Tennyson, J., Yurchenko, S. N., Al-Refaie, A. F., Clark, V. H. J., Chubb, K. L., Conway, E. K., … Yurchenko, O. P. (2020). The 2020 release of the ExoMol database: Molecular line lists for exoplanet and other hot atmospheres. Journal of Quantitative Spectroscopy and Radiative Transfer, 255, 107228. https://doi.org/10.1016/j.jqsrt.2020.107228

See also

fetch_hitran(), fetch_hitemp(), fetch_kurucz(), hdf2df()