radis.io.exomol module¶

Molecular database (MDB) class

MdbExomol is the MDB for ExoMol

Initial code borrowed from the Exojax code (which you should also have a look at !), by @HajimeKawahara, under MIT License.

class MdbExomol(path, molecule, database=None, local_databases=None, name='EXOMOL-{molecule}', nurange=[0.0, inf], margin=1.0, crit=-inf, bkgdatm='Air', broadf=True, engine='vaex', verbose=True, cache=True, skip_optional_data=True)[source]¶

Bases: DatabaseManager

molecular database of ExoMol

MdbExomol is a class for ExoMol.

Parameters

path (str) – path for Exomol data directory/tag. For instance, “/home/CO/12C-16O/Li2015”
nurange (array) – wavenumber range list (cm-1) or wavenumber array
margin (float) – margin for nurange (cm-1)
crit (float) – line strength lower limit for extraction
bkgdatm (str) – background atmosphere for broadening. e.g. H2, He,
broadf (bool) – if False, the default broadening parameters in .def file is used

Other Parameters

engine (str) – which memory mapping engine to use : ‘vaex’, ‘pytables’ (HDF5), ‘feather’
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]_.

Notes

The trans/states files can be very large. For the first time to read it, we convert it to the feather or hdf5-format. After the second-time, we use the feather/hdf5 format instead.

Examples

# Init database, download files if needed.
mdb = MdbExomol(
    local_path,
    molecule=molecule,
    name=databank_name,
    local_databases=local_databases,
    # nurange=[load_wavenum_min, load_wavenum_max],
    engine="vaex",
)

# Get cache files to load :
mgr = mdb.get_datafile_manager()
local_files = [mgr.cache_file(f) for f in mdb.trans_file]

# Load files
df = mdb.load(
    local_files,
    columns=columns_exomol,
    lower_bound=([('nu_lines', load_wavenum_min)] if load_wavenum_min else []) + ([("Sij0", mdb.crit)] if not np.isneginf(mdb.crit) else []),
    upper_bound=([('nu_lines', load_wavenum_max)] if load_wavenum_max else []),
    output="jax", # or "pytables", "vaex"
)

Calculate a spectrum from ExoMol

Compare CO xsections from the ExoMol and HITEMP database

nu_lines (nd array): line center (cm-1) Sij0 (nd array): line strength at T=Tref (cm) dev_nu_lines (np array): line center in device (cm-1) logsij0 (np array): log line strength at T=Tref A (np array): Einstein A coefficient elower (np array): the lower state energy (cm-1) gpp (np array): statistical weight jlower (np array): J_lower jupper (np array): J_upper n_Tref (np array): temperature exponent alpha_ref (np array): alpha_ref (gamma0) n_Tref_def: default temperature exponent in .def file, used for jlower not given in .broad alpha_ref_def: default alpha_ref (gamma0) in .def file, used for jlower not given in .broad

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

QT_interp(T)[source]¶

interpolated partition function

Parameters: T (temperature)
Return type: Q(T) interpolated in jnp.array

download(molec, extension, numtag=None)[source]¶

Downloading Exomol files

Parameters

molec (like “12C-16O__Li2015”)
extension (extension list e.g. [“.pf”,”.def”,”.trans.bz2”,”.states.bz2”,”.broad”])
numtag (number tag of transition file if exists. e.g. “11100-11200”)

Notes

The download URL is written in exojax.utils.url.

qr_interp(T)[source]¶

interpolated partition function ratio

Parameters: T (temperature)
Return type: qr(T)=Q(T)/Q(Tref) interpolated in jnp.array

set_broadening(df, alpha_ref_def=None, n_Texp_def=None, output=None)[source]¶

setting broadening parameters

Parameters

alpha_ref (set default alpha_ref and apply it. None=use self.alpha_ref_def)
n_Texp_def (set default n_Texp and apply it. None=use self.n_Texp_def)

Return type

None. Updates df with alpha_ref, n_Texp_def

to_partition_function_tabulator()[source]¶: Generate a PartFuncExoMol object

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)[source]¶

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 extremelly 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) – 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

Compare CO xsections from the ExoMol and HITEMP database

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

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radis.io.exomol module¶