tardis.io.atom_data.base module

class tardis.io.atom_data.base.AtomData(atom_data, ionization_data, levels=None, lines=None, macro_atom_data=None, macro_atom_references=None, zeta_data=None, collision_data=None, collision_data_temperatures=None, synpp_refs=None, photoionization_data=None, yg_data=None, two_photon_data=None, linelist_atoms=None, linelist_molecules=None, decay_radiation_data=None, molecule_data=None)

Bases: object

Class for storing atomic data

Parameters:

atom_datapandas.DataFrame

A DataFrame containing the *basic atomic data* with:

index : atomic_number columns : symbol, name, mass[u].

ionization_datapandas.DataFrame

A DataFrame containing the *ionization data* with:

index : atomic_number, ion_number columns : ionization_energy[eV].

It is important to note here is that `ion_number` describes the *final ion state*

e.g. H I - H II is described with ion=1

levelspandas.DataFrame

A DataFrame containing the *levels data* with:

index : numerical index columns : atomic_number, ion_number, level_number, energy[eV], g[1], metastable.

linespandas.DataFrame

A DataFrame containing the *lines data* with:

index : numerical index columns : line_id, atomic_number, ion_number, level_number_lower, level_number_upper, wavelength[angstrom], nu[Hz], f_lu[1], f_ul[1], B_ul[?], B_ul[?], A_ul[1/s].

macro_atom_data

A DataFrame containing the *macro atom data* with:

index : numerical index columns : atomic_number, ion_number, source_level_number, destination_level_number, transition_line_id, transition_type, transition_probability;

macro_atom_references

A DataFrame containing the *macro atom references* with:

index : numerical index columns : atomic_number, ion_number, source_level_number, count_down, count_up, count_total.

Refer to the docs: http://tardis.readthedocs.io/en/latest/physics/plasma/macroatom.html

collision_data(pandas.DataFrame, np.array)

A DataFrame containing the *electron collisions data* with:

index : atomic_number, ion_number, level_number_lower, level_number_upper columns : e_col_id, delta_e, g_ratio, c_ul;

collision_data_temperaturesnp.array

An array with the collision temperatures.

zeta_data

A DataFrame containing the *zeta data* for the

nebular ionization calculation

(i.e., the fraction of recombinations that go directly to the

ground state) with:

index : atomic_number, ion_charge columns : temperatures[K]

synpp_refs?

photoionization_datapandas.DataFrame

A DataFrame containing the *photoionization data* with:

index : numerical index columns : atomic_number, ion_number, level_number, nu[Hz], x_sect[cm^2]

two_photon_datapandas.DataFrame

A DataFrame containing the *two photon decay data* with:

index: atomic_number, ion_number, level_number_lower, level_number_upper columns: A_ul[1/s], nu0[Hz], alpha, beta, gamma

decay_radiation_datapandas.DataFrame

A dataframe containing the *decay radiation data* with:

index: Isotope names columns: atomic_number, element, Rad energy, Rad intensity decay mode. Curated from nndc

linelist_atomspandas.DataFrame

A DataFrame containing a linelist of input atoms

linelist_moleculespandas.DataFrame

A DataFrame containing a linelist of input molecules

molecule_dataMolecularData

A class containing the *molecular data* with:

equilibrium_constants, partition_functions, dissociation_energies

Notes

1. The units of some columns are given in the square brackets. They are NOT the parts of columns’ names!

Attributes:

preparedbool

atom_datapandas.DataFrame

ionization_datapandas.DataFrame

macro_atom_data_allpandas.DataFrame

macro_atom_references_allpandas.DataFrame

collision_datapandas.DataFrame

collision_data_temperaturesnumpy.array

zeta_datapandas.DataFrame

synpp_refspandas.DataFrame

photoionization_datapandas.DataFrame

two_photon_datapandas.DataFrame

decay_radiation_datapandas.DataFrame

linelist_atomspandas.DataFrame

linelist_moleculespandas.DataFrame

molecule_dataMolecularData

Methods

from_hdf:	Function to read the atom data from a TARDIS atom HDF Store
prepare_atom_data:	Prepares the atom data to set the lines, levels and if requested macro atom data. This function mainly cuts the levels and lines by discarding any data that is not needed (any data for atoms that are not needed

classmethod from_hdf(fname=None)

Function to read the atom data from a TARDIS atom HDF Store

Parameters:

fnamePath, optional

Path to the HDFStore file or name of known atom data file (default: None)

get_attributes_from_store(store_key)

Gets atom_data attributes, throws error and sets to None if they are not available.

Parameters:

storepd.HDFStore

Data source

store_keystr

HDFStore value to check

hdf_names = ['atom_data', 'ionization_data', 'levels', 'lines', 'macro_atom_data', 'macro_atom_references', 'zeta_data', 'collision_data', 'collision_data_temperatures', 'synpp_refs', 'photoionization_data', 'yg_data', 'two_photon_data', 'linelist_atoms', 'linelist_molecules', 'decay_radiation_data']

prepare_atom_data(selected_atomic_numbers, line_interaction_type, nlte_species, continuum_interaction_species)

Prepares the atom data to set the lines, levels and if requested macro atom data. This function mainly cuts the levels and lines by discarding any data that is not needed (any data for atoms that are not needed

Parameters:

selected_atomsset

set of selected atom numbers, e.g. set([14, 26])

line_interaction_typestr

can be ‘scatter’, ‘downbranch’ or ‘macroatom’

prepare_continuum_interaction_data(continuum_interaction_species)

Prepares the atom data for the continuum interaction

Parameters:

continuum_interactionContinuumInteraction

The continuum interaction object

prepare_line_level_indexes()

prepare_lines()

Prepare line data

prepare_macro_atom_data(line_interaction_type, tmp_lines_lower2level_idx, tmp_lines_upper2level_idx)

related_groups = [('macro_atom_data_all', 'macro_atom_references_all')]

exception tardis.io.atom_data.base.AtomDataMissingError

Bases: Exception

exception tardis.io.atom_data.base.AtomDataNotPreparedError

Bases: Exception

class tardis.io.atom_data.base.MoleculeData(equilibrium_constants: DataFrame, partition_functions: DataFrame, dissociation_energies: DataFrame)

Bases: object

Class to hold molecular data. Held by the AtomData object.

equilibrium_constants : pandas.DataFrame A DataFrame containing the molecular equilibrium constants with:

index: molecule columns: temperatures

partition_functions : pandas.DataFrame A DataFrame containing the molecular partition functions with:

index: molecule columns: temperatures

dissociation_energies : pandas.DataFrame A DataFrame containing the molecular dissociation energies with:

index: molecule

dissociation_energies: DataFrame

equilibrium_constants: DataFrame

partition_functions: DataFrame