radis.lbl.loader module

Summary

Module to host the databank loading / database initialisation parts of SpectrumFactory. This is done through SpectrumFactory inheritance of the DatabankLoader class defined here

Routine Listings

PUBLIC METHODS

• radis.lbl.loader.DatabankLoader.load_databank() >>> load line database

• radis.lbl.loader.DatabankLoader.init_databank() >>> load loader

• radis.lbl.loader.DatabankLoader.fetch_databank() >>> fetch from HITRAN online

• radis.lbl.loader.DatabankLoader.init_database() >>> to interact / generate a SpectrumDatabase

• radis.lbl.loader.DatabankLoader.get_conditions()

• radis.lbl.loader.DatabankLoader.get_partition_function_interpolator()

• radis.lbl.loader.DatabankLoader.get_partition_function_calculator()

PRIVATE METHODS - DATABASE LOADING

• radis.lbl.loader.DatabankLoader._load_databank()

• radis.lbl.loader.DatabankLoader._reload_databank()

• radis.lbl.loader.DatabankLoader._check_line_databank()

• radis.lbl.loader.DatabankLoader._retrieve_from_database()

• radis.lbl.loader.DatabankLoader._build_partition_function_interpolator()

• radis.lbl.loader.DatabankLoader._build_partition_function_calculator()

Most methods are written in inherited class with the following inheritance scheme:

DatabankLoader > BaseFactory > BroadenFactory > BandFactory > SpectrumFactory .. inheritance-diagram:: radis.lbl.factory.SpectrumFactory

parts:

1

Notes

RADIS includes automatic rebuilding of Deprecated cache files + a global variable to force regenerating them after a given version. See "OLDEST_COMPATIBLE_VERSION" key in radis.config

class ConditionDict

Bases: dict

A class to hold Spectrum calculation input conditions (Input), computation parameters (Parameters), or miscellaneous parameters (MiscParams). Works like a dict except you can also access attribute with:

v = a.key   # equivalent to v = a[key]

Also can be copied, deepcopied, and parallelized in multiprocessing

Notes

for developers: Parameters and Input could also have simply derived from the (object) class, but it may have missed some convenient functions implemented for dict. For instance, how to be picked / unpickled.

See also

Input, Parameters, MiscParams

copy()

Return a shallow copy of the dict.

get_params()

Returns the variables (and their values) contained in the dictionary, minus some based on their type. Numpy array, dictionaries and pandas DataFrame are removed. None is removed in general, except for some keys (‘cutoff’, ‘truncation’) Tuples are converted to string

class DatabankLoader

Bases: object

digraph inheritanceb7d785f131 { bgcolor=transparent; rankdir=LR; size="8.0, 12.0"; "BandFactory" [URL="radis.lbl.bands.html#radis.lbl.bands.BandFactory",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="See Also"]; "BroadenFactory" -> "BandFactory" [arrowsize=0.5,style="setlinewidth(0.5)"]; "BaseFactory" [URL="radis.lbl.base.html#radis.lbl.base.BaseFactory",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top"]; "DatabankLoader" -> "BaseFactory" [arrowsize=0.5,style="setlinewidth(0.5)"]; "BroadenFactory" [URL="radis.lbl.broadening.html#radis.lbl.broadening.BroadenFactory",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="A class that holds all broadening methods."]; "BaseFactory" -> "BroadenFactory" [arrowsize=0.5,style="setlinewidth(0.5)"]; "DatabankLoader" [URL="#radis.lbl.loader.DatabankLoader",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip=".. inheritance-diagram:: radis.lbl.factory.SpectrumFactory"]; "SpectrumFactory" [URL="radis.lbl.factory.html#radis.lbl.factory.SpectrumFactory",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="A class to put together all functions related to loading CDSD and HITRAN"]; "BandFactory" -> "SpectrumFactory" [arrowsize=0.5,style="setlinewidth(0.5)"]; }

See also

SpectrumFactory

NwG

NwL

SpecDatabase

autoretrievedatabase

autoupdatedatabase

columns_list_to_load(load_columns_type)

cond_units

database

dataframe_engine

dataframe_type

df0

initial line database after loading. If for any reason, you want to manipulate the line database manually (for instance, keeping only lines emitting by a particular level), you need to access the df0 attribute of SpectrumFactory.

Warning

never overwrite the df0 attribute, else some metadata may be lost in the process. Only use inplace operations. If reducing the number of lines, add a df0.reset_index()

For instance:

from radis import SpectrumFactory
sf = SpectrumFactory(
    wavenum_min= 2150.4,
    wavenum_max=2151.4,
    pressure=1,
    isotope=1)
sf.load_databank('HITRAN-CO-TEST')
sf.df0.drop(sf.df0[sf.df0.vu!=1].index, inplace=True)   # keep lines emitted by v'=1 only
sf.eq_spectrum(Tgas=3000, name='vu=1').plot()

df0 contains the lines as they are loaded from the database. df1 is generated during the spectrum calculation, after the line database reduction steps, population calculation, and scaling of intensity and broadening parameters with the calculated conditions.

See also

df1

Type:

pd.DataFrame

df1

line database, scaled with populations + linestrength cutoff Never edit manually. See all comments about df0

See also

df0

Type:

pd.DataFrame

fetch_databank(source='hitran', database='default', parfunc=None, levels=None, levelsfmt='radis', load_energies=False, include_neighbouring_lines=True, parse_local_global_quanta=True, drop_non_numeric=True, db_use_cached=True, lvl_use_cached=True, memory_mapping_engine='default', load_columns='equilibrium', parallel=True, extra_params=None, **kwargs)

Fetch the latest files from [HITRAN-2020], [HITEMP-2010] (or newer), [ExoMol-2020] or [GEISA-2020] or [Kurucz-2017], and store them locally in memory-mapping formats for extremely fast access.

Parameters:

• source (str) – Which database to use. Options are 'hitran', 'hitemp', 'exomol', 'geisa', 'kurucz', 'nist'.

• database (str) – If fetching from HITRAN, 'full' downloads the full database and registers it, 'range' downloads only the lines in the range of the molecule. If fetching from HITEMP, Kurucz, or NIST, only 'full' is available. If fetching from ExoMol, use this parameter to choose which database to use. Keep 'default' to use the recommended one. Default is 'full'.

parfunc: str or None

Path to a tabulated partition function file to use. This argument only affects molecules.

levels: dict or None

Path to energy levels (needed for non-eq calculations). Format: {1:path_to_levels_iso_1, 3:path_to_levels_iso3}. This argument only affects molecules. Default is None.

levelsfmt: str or None

How to read the previous file. Known formats: 'cdsd-pc', 'radis' or any of KNOWN_LVLFORMAT. This argument only affects molecules. Default is 'radis'.

load_energies: bool

If False, don’t load energy levels. This means that nonequilibrium spectra cannot be calculated, but it saves some memory. This argument only affects molecules. Default is False.

include_neighbouring_lines: bool

If True, includes off-range, neighbouring lines that contribute because of lineshape broadening. Default is True.

parse_local_global_quanta: bool or 'auto'

If True, parses the HITRAN/HITEMP ‘glob’ and ‘loc’ columns to extract quanta identifying the lines. Default is True.

drop_non_numeric: bool

If True, non-numeric columns are dropped. This improves performance. Default is True.

db_use_cached: bool or 'regen'

Use cached database if available.

memory_mapping_engine: str

Which library to use to read HDF5 files. Options are 'pytables', 'vaex', 'feather'. Default is 'default'.

parallel: bool

If True, uses joblib.parallel to load database with multiple processes. Default is True.

load_columns: list, 'all', 'equilibrium', 'noneq', diluent

Columns names to load. Default is 'equilibrium'.

Notes

HITRAN is fetched with Astroquery or HAPI, and HITEMP with fetch_hitemp(). HITEMP files are generated in a ~/.radisdb database.

See also

load_databank(), init_databank()

References

[1]

Astroquery

get_abundance(molecule, isotope)

Get isotopic abundance

Parameters:

• molecule (str)

• isotope (int, or list) – isotope number, sorted in terrestrial abundance

Examples

Use it from SpectrumFactory:

sf.get_abundance("H2O", 1)
sf.get_abundance("CH4", [1,2,3])

Examples using radis.lbl.loader.DatabankLoader.get_abundance

Use Custom Abundances

Use Custom Abundances

See also

set_abundance()

get_conditions(ignore_misc=False, add_config=False)

Get all parameters defined in the SpectrumFactory.

Other Parameters:

ignore_misc (boolean) – if True, then all attributes considered as Factory ‘descriptive’ parameters, as defined in get_conditions() are ignored when comparing the database to current factory conditions. It should obviously only be attributes that have no impact on the Spectrum produced by the factory. Default False

get_partition_function_calculator(molecule, isotope, elec_state)

Retrieve Partition Function Calculator.

Parameters:

• molecule (str)

• isotope (int)

• elec_state (str)

get_partition_function_interpolator(molecule, isotope, elec_state)

Retrieve Partition Function Interpolator.

Parameters:

• molecule (str)

• isotope (int)

• elec_state (str)

get_partition_function_molecule(molecule)

Retrieve Partition Function for Molecule.

Parameters:

molecule (str)

init_databank(*args, **kwargs)

Method to init databank parameters but only load them when needed.

Databank is reloaded by _check_line_databank() Same inputs Parameters as load_databank():

Parameters:

name (a section name specified in your ~/radis.json) – .radis has to be created in your HOME (Unix) / User (Windows). If not None, all other arguments are discarded. Note that all files in database will be loaded and it may takes some time. Better limit the database size if you already know what range you need. See Configuration file and DBFORMAT for expected ~/radis.json format

Other Parameters:

• path (str, list of str, None) – list of database files, or name of a predefined database in the Configuration file (json) Accepts wildcards * to select multiple files

• format ('hitran', 'cdsd-hitemp', 'cdsd-4000', or any of KNOWN_DBFORMAT) – database type. 'hitran' for HITRAN/HITEMP, 'cdsd-hitemp' and 'cdsd-4000' for the different CDSD versions. Default 'hitran'

  format to read tabulated partition function file. If hapi, then HAPI (HITRAN Python interface) [1]_ is used to retrieve them (valid if your database is HITRAN data). HAPI is embedded into RADIS. Check the version. If partfuncfmt is None then it is inferred from format (e.g. hapi for hitran, exomol for exomol). Default None.

• parfunc (filename or None) – path to tabulated partition function to use.

  hapi.py file. If not given, then the hapi.py embedded in RADIS is used (check version)

• levels (dict of str or None) – path to energy levels (needed for non-eq calculations). Format: {1:path_to_levels_iso_1, 3:path_to_levels_iso3}. Default None

• levelsfmt (‘cdsd-pc’, ‘radis’ (or any of KNOWN_LVLFORMAT) or None) – how to read the previous file. Known formats: (see KNOWN_LVLFORMAT). If radis, energies are calculated using the diatomic constants in radis.db database if available for given molecule. Look up references there. If None, non equilibrium calculations are not possible. Default 'radis'.

• db_use_cached (boolean, or None) – if True, a pandas-readable csv file is generated on first access, and later used. This saves on the datatype cast and conversion and improves performances a lot. But! … be sure to delete these files to regenerate them if you happen to change the database. If 'regen', existing cached files are removed and regenerated. It is also used to load energy levels from .h5 cache file if exist. If None, the value given on Factory creation is used. Default None

• load_energies (boolean) – if False, dont load energy levels. This means that nonequilibrium spectra cannot be calculated, but it saves some memory. Default True

• include_neighbouring_lines (bool) – True, includes off-range, neighbouring lines that contribute because of lineshape broadening. The neighbour_lines parameter is used to determine the limit. Default True.

• drop_columns (list) – columns names to drop from Line DataFrame after loading the file. Not recommended to use, unless you explicitly want to drop information (for instance if dealing with too large databases). If [], nothing is dropped. If 'auto', parameters considered unnecessary are dropped. See drop_auto_columns_for_dbformat and drop_auto_columns_for_levelsfmt. Default 'auto'.

• load_columns (list, 'all', 'equilibrium', 'noneq') – columns names to load. If 'equilibrium', only load the columns required for equilibrium calculations. If 'noneq', also load the columns required for non-LTE calculations. See drop_all_but_these. If 'all', load everything. Note that for performances, it is better to load only certain columns rather than loading them all and dropping them with drop_columns. Default 'equilibrium'.

  Warning

  if using 'equilibrium', not all parameters will be available for a Spectrum line_survey().

• **Other arguments are related to how to open the files (****)

Notes

Useful in conjunction with init_database() when dealing with large line databanks when some of the spectra may have been precomputed in a spectrum database (SpecDatabase) Note that any previously loaded databank is discarded on the method call

See also

-, -, -

init_database(path, autoretrieve=True, autoupdate=True, add_info=['Tvib', 'Trot'], add_date='%Y%m%d', compress=True, **kwargs)

Init a SpecDatabase folder in path to later store our spectra. Spectra can also be automatically retrieved from the database instead of being calculated.

Parameters:

• path (str) – path to database folder. If it doesnt exist, create it Accepts wildcards * to select multiple files

• autoretrieve (boolean, or 'force') – if True, a database lookup is performed whenever a new spectrum is calculated. If the spectrum already exists then it is retrieved from the database instead of being calculated. Spectra are considered the same if all the stored conditions fit. If set to 'force', an error is raised if the spectrum is not found in the database (use it for debugging). Default True

• autoupdate (boolean) – if True, all spectra calculated by this Factory are automatically exported in database. Default True (but only if init_database is explicitly called by user)

• add_info (list, or None/False) – append these parameters and their values if they are in conditions. Default ['Tvib', 'Trot']

• add_date (str, or None/False) – adds date in strftime format to the beginning of the filename. Default ‘%Y%m%d’

• compress (boolean, or 2) – if True, Spectrum are read and written in binary format. This is faster, and takes less memory space. Default True. If 2, additionally remove all redundant quantities.

Other Parameters:

**kwargs (**dict) – arguments sent to SpecDatabase initialization.

Returns:

db – the database where spectra will be stored or retrieved

Return type:

SpecDatabase

Example #7: Database fitting using SpecDatabase.fit_spectrum

Example #7: Database fitting using SpecDatabase.fit_spectrum

Spectrum Database

Spectrum Database

input

input_wunit

interactive_params

levels

levelspath

load_databank(name=None, path=None, format: ['hitran', 'hitemp', 'cdsd-hitemp', 'cdsd-4000', 'hitemp-radisdb', 'hdf5-radisdb', 'geisa'] = None, parfunc=None, levels=None, levelsfmt: ['radis', 'cdsd-pc', 'cdsd-pcN', 'cdsd-hamil', None] = None, db_use_cached=True, lvl_use_cached=True, load_energies=False, include_neighbouring_lines=True, drop_columns='auto', load_columns='equilibrium')

Loads databank from shortname in the Configuration file. (json), or by manually setting all attributes.

Databank includes: - lines - partition function & format (tabulated or calculated) - (optional) energy levels, format

Parameters:

name (a section name specified in your ~/radis.json) – .radis has to be created in your HOME (Unix) / User (Windows). If not None, all other arguments are discarded. Note that all files in database will be loaded and it may takes some time. Better limit the database size if you already know what range you need. See Configuration file and DBFORMAT for expected ~/radis.json format

Other Parameters:

• path (str, list of str, None) – list of database files, or name of a predefined database in the Configuration file (json) Accepts wildcards * to select multiple files

• format ('hitran', 'cdsd-hitemp', 'cdsd-4000', or any of KNOWN_DBFORMAT) – database type. 'hitran' for HITRAN/HITEMP, 'cdsd-hitemp' and 'cdsd-4000' for the different CDSD versions. Default 'hitran'

• parfunc (filename or None) – path to tabulated partition function to use.

  If not given, then the hapi.py embedded in RADIS is used (check version). This argument only affects molecules.

• levels (dict of str or None) – path to energy levels (needed for non-eq calculations). Format: {1:path_to_levels_iso_1, 3:path_to_levels_iso3}. Default None. This argument only affects molecules.

• levelsfmt (‘cdsd-pc’, ‘radis’ (or any of KNOWN_LVLFORMAT) or None) – how to read the previous file. Known formats: (see KNOWN_LVLFORMAT). If radis, energies are calculated using the diatomic constants in radis.db database if available for given molecule. Look up references there. If None, non equilibrium calculations are not possible. Default 'radis'. This argument only affects molecules.

• db_use_cached (boolean, or None) – if True, a pandas-readable csv file is generated on first access, and later used. This saves on the datatype cast and conversion and improves performances a lot. But! … be sure to delete these files to regenerate them if you happen to change the database. If 'regen', existing cached files are removed and regenerated. It is also used to load energy levels from .h5 cache file if exist. If None, the value given on Factory creation is used. Default True

• load_energies (boolean) – if False, dont load energy levels. This means that nonequilibrium spectra cannot be calculated, but it saves some memory. Default True This argument only affects molecules.

• include_neighbouring_lines (bool) – True, includes off-range, neighbouring lines that contribute because of lineshape broadening. The neighbour_lines parameter is used to determine the limit. Default True.

• **Other arguments are related to how to open the files (****)

• drop_columns (list) – columns names to drop from Line DataFrame after loading the file. Not recommended to use, unless you explicitly want to drop information (for instance if dealing with too large databases). If [], nothing is dropped. If 'auto', parameters considered useless are dropped. See drop_auto_columns_for_dbformat and drop_auto_columns_for_levelsfmt. If 'all', parameters considered unnecessary for equilibrium calculations are dropped, including all information about lines that could be otherwise available in Spectrum() method. Warning: nonequilibrium calculations are not possible in this mode. Default 'auto'.

• load_columns (list, 'all', 'equilibrium', 'noneq') – columns names to load. If 'equilibrium', only load the columns required for equilibrium calculations. If 'noneq', also load the columns required for non-LTE calculations. See drop_all_but_these. If 'all', load everything. Note that for performances, it is better to load only certain columns rather than loading them all and dropping them with drop_columns. Default 'equilibrium'.

  Warning

  if using 'equilibrium', not all parameters will be available for a Spectrum line_survey().

See also

• Only load when needed: init_databank()

• Download from HITRAN: fetch_databank()

Configuration file with: - all line database formats: DBFORMAT - all energy levels database formats: LVLFORMAT

References

[1]

HAPI: The HITRAN Application Programming Interface

min_width

misc

Miscellaneous parameters (MiscParams) params that cannot change the output of calculations (ex: number of CPU, etc.)

molparam

contains information about molar mass; isotopic abundance.

See MolParams

Type:

MolParam

params

Parameters they may change the output of calculations (ex: threshold, cutoff, broadening methods, etc.)

Type:

Computational parameters

parsum

parsum_calc

store all partition function calculators, per isotope

Type:

dict

parsum_tab

store all partition function tabulators, per isotope

Type:

dict

profiler

reftracker

save_memory

if True, tries to save RAM memory (but may take a little for time, saving stuff to files instead of RAM for instance)

Type:

bool

set_abundance(molecule, isotope, abundance)

Set isotopic abundance

Parameters:

• molecule (str)

• isotope (int, or list) – isotope number, sorted in terrestrial abundance

• abundance (float, or list)

Examples

from radis import SpectrumFactory

sf = SpectrumFactory(
    2284.2,
    2284.6,
    wstep=0.001,  # cm-1
    pressure=20 * 1e-3,  # bar
    mole_fraction=400e-6,
    molecule="CO2",
    isotope="1,2",
    verbose=False
)
sf.load_databank("HITEMP-CO2-TEST")
print("Abundance of CO2[1,2]", sf.get_abundance("CO2", [1, 2]))
sf.eq_spectrum(2000).plot("abscoeff")

#%% Set the abundance of CO2(626) to 0.8; and the abundance of CO2(636) to 0.2 (arbitrary):
sf.set_abundance("CO2", [1, 2], [0.8, 0.2])
print("New abundance of CO2[1,2]", sf.get_abundance("CO2", [1, 2]))

sf.eq_spectrum(2000).plot("abscoeff", nfig="same")

Use Custom Abundances

Use Custom Abundances

See also

get_abundance()

set_atomic_partition_functions(pfsource=None)

Construct an interpolator or calculator for atomic partition functions and store it in the parsum attribute

Parameters:

pfsource (string) – The source for the partition function tables for an interpolator or energy level tables for a calculator. Sources implemented so far are ‘barklem’ and ‘kurucz’ for the former, and ‘nist’ for the latter. ‘default’ is currently ‘nist’.

truncation

units

verbose

increase verbose level. 0, 1, 2 supported at the moment

Type:

bool, or int

warn(message, category='default', level=0)

Trigger a warning, an error or just ignore based on the value defined in the warnings dictionary. The warnings can thus be deactivated selectively by setting the SpectrumFactory

warnings attribute

Parameters:

• message (str) – what to print

• category (str) – one of the keys of self.warnings. See warnings

• level (int) – warning level. Only print warnings when verbose level is higher than the warning levels. i.e., warnings of level 1 appear only if verbose==True, warnings of level 2 appear only for verbose>=2, etc.. Warnings of level 0 appear only the time. Default 0

Examples

::

if not ((df.Erotu > tol).all() and (df.Erotl > tol).all()):

self.warn(

“There are negative rotational energies in the database”, “NegativeEnergiesWarning”,

)

Notes

All warnings in the SpectrumFactory should call to this method rather than the default warnings.warn() method, because it allows easier runtime modification of how to deal with warnings

See also

warnings

warnings

Default warnings for SpectrumFactory. See default_warning_status

Type:

dict

wavenumber

wavenumber_calc

wbroad_centered

woutrange

class Input

Bases: ConditionDict

Holds Spectrum calculation input conditions, under the attribute input of SpectrumFactory. Works like a dict except you can also access attribute with:

v = sf.input.key   # equivalent to v = sf.input[key]

See also

params, misc

Telec

Tgas

Tref

Trot

Tvib

isatom

isneutral

isotope

medium

mole_fraction

molecule

overpopulation

path_length

pfsource

potential_lowering

pressure

rot_distribution

self_absorption

species

state

vib_distribution

wavelength_max

wavelength_min

wavenum_max

wavenum_min

KNOWN_DBFORMAT = ['hitran', 'hitemp', 'cdsd-hitemp', 'cdsd-4000', 'hitemp-radisdb', 'hdf5-radisdb', 'geisa']

Known formats for Line Databases:

• 'hitran' : [HITRAN-2020] original .par format.

• 'hitemp' : [HITEMP-2010] original format (same format as ‘hitran’).

• 'cdsd-hitemp' : CDSD-HITEMP original format (CO2 only, same lines as HITEMP-2010).

• 'cdsd-4000' : [CDSD-4000] original format (CO2 only).

• 'hitemp-radisdb' : HITEMP under RADISDB format (pytables-HDF5 with RADIS column names).

• 'hdf5-radisdb' : arbitrary HDF5 file with RADIS column names.

• 'geisa' : [GEISA-2020] original .par format.

To install all databases manually see the Configuration file and the list of databases .

See also

Configuration file

Type:

list

KNOWN_LVLFORMAT = ['radis', 'cdsd-pc', 'cdsd-pcN', 'cdsd-hamil', None]

Known formats for Energy Level Databases (used in non-equilibrium calculations):

• 'radis': energies calculated with Dunham expansions by

  PartFunc_Dunham

• 'cdsd-pc': energies read from precomputed CDSD energies for CO2, with

  viblvl=(p,c) convention. See PartFuncCO2_CDSDcalc

• 'cdsd-pcN': energies read from precomputed CDSD energies for CO2, with

  viblvl=(p,c,N) convention. See PartFuncCO2_CDSDcalc

• 'cdsd-hamil': energies read from precomputed CDSD energies for CO2, with

  viblvl=(p,c,J,N) convention, i.e., a each rovibrational level can have a unique vibrational energy (this is needed when taking account Coupling terms) See PartFuncCO2_CDSDcalc

• None: means you can only do Equilibrium calculations.

See also

Configuration file

Type:

list

KNOWN_PARFUNCFORMAT = ['cdsd', 'hapi']

Known formats for partition function (tabulated files to read), or ‘hapi’ to fetch Partition Functions using HITRAN Python interface instead of reading a tabulated file.

See also

Configuration file

Type:

list

class MiscParams

Bases: ConditionDict

A class to hold Spectrum calculation descriptive parameters, under the attribute params of SpectrumFactory. Unlike Parameters, these parameters cannot influence the Spectrum output and will not be used when comparing Spectrum with existing, precomputed spectra in SpecDatabase Works like a dict except you can also access attribute with:

v = a.key

See also

input, params

add_at_used

chunksize

divide line database in chunks of lines

Type:

int

export_lines

export_populations

export_rovib_fraction

calculate nu_vib, nu_rot in lines

Type:

bool

load_energies

memory_mapping_engine

total_lines

number of lines in database.

Type:

int

warning_broadening_threshold

warning_linestrength_cutoff

raise a warning if the sum of linestrength cut is above that

Type:

float [0-1]

zero_padding

class Parameters

Bases: ConditionDict

Holds Spectrum calculation computation parameters, under the attribute params of SpectrumFactory. Works like a dict except you can also access attribute with:

v = sf.params.key    # equivalent to v = sf.params[key]

Also can be copied, deepcopied, and parallelized in multiprocessing

See also

input, misc

broadening_method

"voigt_poly", "convolve", "fft"

Type:

str

chunksize

cutoff

linestrength cutoff (molecule/cm)

Type:

float

db_use_cached

dbformat

format of Line Database. See KNOWN_DBFORMAT

Type:

str

dbpath

joined list of filepaths to Line Database

Type:

str

diluent

dxG

Gaussian step LDM lineshape database. Default _gaussian_step(0.01)

Type:

float

dxL

Lorentzian step for LDM lineshape database. Default _lorentzian_step(0.01)

Type:

float

export_lines

export_populations

folding_thresh

include_neighbouring_lines

if True, includes the contribution of off-range, neighbouring lines because of lineshape broadening. Default True.

Type:

bool

lbfunc

levelsfmt

format of Energy Database. See KNOWN_LVLFORMAT

Type:

str

lvl_use_cached

neighbour_lines

extra range (cm-1) on each side of the spectrum to account for neighbouring lines. Overwritten by SpectrumFactory

Type:

float

optimization

"simple", "min-RMS", None

Type:

str

parfuncpath

filepath to tabulated Partition Functions

Type:

str

parsum_mode

“full summation” or “tabulation” . calculation mode of partition function. See RovibParFuncCalculator

Type:

int

pseudo_continuum_threshold

threshold to assign lines in pseudo continuum. Overwritten in SpectrumFactory

Type:

float

sparse_ldm

“auto”, True, False . Sparse LDM calculation. See radis.lbl.broadening.BroadenFactory._apply_lineshape_LDM()

Type:

str

truncation

cutoff for half-width lineshape calculation (cm-1). Overwritten by SpectrumFactory

Type:

float

warning_broadening_threshold

warning_linestrength_cutoff

wavenum_max_calc

maximum calculated wavenumber (cm-1) initialized by SpectrumFactory

Type:

float

wavenum_min_calc

minimum calculated wavenumber (cm-1) initialized by SpectrumFactory

Type:

float

waveunit

should be cm-1.

Type:

waverange unit

wstep

spectral resolution (cm-1)

Type:

float

broadening_coeff = ['gamma_co2', 'n_co2', 'gamma_h2o', 'n_h2o', 'gamma_he', 'n_he', 'gamma_h2', 'n_h2']

column names required for non-air diluent calculations.

Type:

list

df_metadata = ['molecule', 'iso', 'id', 'Ia', 'molar_mass', 'Qref', 'Qvib', 'Q', 'id', 'id', 'iso', 'iso', 'iso', 'iso', 'iso', 'iso', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'iso', 'id', 'id', 'id', 'id', 'iso', 'id', 'iso', 'id', 'id', 'id', 'id', 'id', 'id', 'iso', 'id', 'id', 'iso', 'id', 'iso', 'id', 'id', 'iso', 'id', 'id', 'iso', 'id', 'id', 'id', 'iso', 'id', 'id', 'id', 'id', 'iso', 'id']

metadata of line DataFrames df0, df1. @dev: when having only 1 molecule, 1 isotope, these parameters are constant for all rovibrational lines. Thus, it’s faster and much more memory efficient to transport them as attributes of the DataFrame rather than columns. The syntax is the same, thus the operations do not change, i.e:

k_b / df.molar_mass

will work whether molar_mass is a float or a column.

Warning

However, in the current Pandas implementation of DataFrame, attributes are lost whenever the DataFrame is recreated, transposed, pickled.

Thus, we use transfer_metadata() to keep the attributes after an operation, and expand_metadata() to make them columns before a Serializing operation (ex: multiprocessing) @dev: all of that is a high-end optimization. Users should not deal with internal DataFrames.

References

https://stackoverflow.com/q/13250499/5622825

Type:

list

drop_all_but_these = ['id', 'iso', 'wav', 'int', 'A', 'airbrd', 'selbrd', 'Tdpair', 'Tdpsel', 'Pshft', 'El', 'gp']

drop all columns but these if using drop_columns='all' in load_databank Note: nonequilibrium calculations wont be possible anymore and it wont be possible to identify lines with line_survey()

See also

-, -, -

Type:

list

drop_auto_columns_for_dbformat = {'cdsd-4000': ['wang2'], 'cdsd-hitemp': ['wang2', 'lsrc'], 'geisa': [], 'hdf5-radisdb': [], 'hitemp': ['ierr', 'iref', 'lmix', 'gpp'], 'hitemp-radisdb': [], 'hitran': ['ierr', 'iref', 'lmix', 'gpp']}

drop these columns if using drop_columns='auto' in load_databank Based on the value of dbformat=, some of these columns won’t be used.

See also

-, -, -, -

Type:

dict

drop_auto_columns_for_levelsfmt = {'cdsd-hamil': ['v1u', 'v2u', 'l2u', 'v3u', 'ru', 'v1l', 'v2l', 'l2l', 'v3l', 'rl'], 'cdsd-pc': ['v1u', 'v2u', 'l2u', 'v3u', 'ru', 'v1l', 'v2l', 'l2l', 'v3l', 'rl'], 'cdsd-pcN': ['v1u', 'v2u', 'l2u', 'v3u', 'ru', 'v1l', 'v2l', 'l2l', 'v3l', 'rl'], 'radis': [], None: []}

drop these columns if using drop_columns='auto' in load_databank Based on the value of lvlformat=, some of these columns won’t be used.

See also

-, -, -, -

Type:

dict

format_paths(s)

escape all special characters.

required_non_eq = ['branch', 'jl', 'vl', 'vu', 'v1l', 'v2l', 'l2l', 'v3l', 'v1u', 'v2u', 'l2u', 'v3u', 'polyl', 'wangl', 'rankl', 'polyu', 'wangu', 'ranku']

column names required for non-equilibrium calculations. See load_column= key of fetch_databank() and load_databank()

Type:

list