atomicdataMB¶

atomicdataMB provides support for the Neutral Cloud and Exospheres Model (nexoclom) and can be used as a standalone package.

atomicmass¶

atomicmass - Return the atomic mass of an atom or molecule.

This is really just a wrapper for periodictable but returns the mass as an astropy quantity.

atomicdataMB.atomicmass.atomicmass(species)[source]¶

Return the atomic mass of an atom or molecule.

Parameters

species: Chemical formula requested species. See periodictable for formatting options.

Returns

The atomicmass of species as an astropy quantity with units = AMU $(1\, \mathrm{AMU} = 1.660539 \times 10^{-27}\, \mathrm{kg})$. If periodictable returns a ValueError, None is returned.

Examples

>>> from atomicdataMB import atomicmass
>>> print(atomicmass('Na'))
22.98977 u
>>> print(atomicmass('H2O'))
18.01528 u
>>> print(atomicmass('X'))
WARNING: mathMB.atomicmass: X not found
None

g_values¶

g_values - Routines related to g-values and radiation pressure The g-value is the the product of the solar flux at the dopler-shifted emission wavelength and the scattering probability per atom. See Killen, R.M. et al., Icarus 209, 75–87, 2009. for details on calculating g-values for important species in Mercury’s atmosphere.

The radiation acceleration is given by $a_{rad} = h g/m \lambda$, where h is Plank’s constant, g is the g-value as a function of radial velocity, m is the mass of the accelerated species, and λ is the wavelength of the absorbed photon.

class atomicdataMB.g_values.RadPresConst(sp, aplanet)[source]¶

Class containing radial acceleration vs. velocity for a specified atom.

Parameters

sp: atomic species
aplanet: Distance from the Sun. Can be given as an astropy quantity with distance units or as a float assumed to be in AU. Default = 1 AU
database: Database containing solar system information. Default = thesolarsystem which probably shouldn’t be overridden.

Class Attributes

species: The input species
aplanet: The input distance from the Sun
velocity: Radial velocity deviation relative to the Sun in km/s. Positive values indicate motion away from the Sun. Given as a numpy array of astropy quantities
accel: Radial acceleration vs. velocity with units km/s**2.

class atomicdataMB.g_values.gValue(sp, wavelength=None, aplanet=<Quantity 1. AU>)[source]¶

Class containing g-value vs. velocity for a specified atom and transition.

Parameters

sp: atomic species
wavelength: Wavelength of the transition. Default=None.
aplanet: Distance from the Sun. Can be given as an astropy quantity with distance units or as a float assumed to be in AU. Default = 1 AU

Class Attributes

species: The input species
wavelength: The input wavelength
aplanet: The input aplanet
velocity: Radial velocity deviation relative to the Sun in km/s. Positive values indicate motion away from the Sun. Given as a numpy array of astropy quantities
g: g-value as function of velocity in units 1/s.

atomicdataMB.g_values.make_gvalue_table()[source]¶

Creates and populates gvalues database table. Creates a database table called gvalues. Fields in the table:

filename: Filename in project tree containing the data; used only for populating the database
reference: Source of the g-values
species: Atomic species
refpt: Distance from Sun in AU for which the g-values were calculated.
wavelength: At-rest wavelength for the g-values in Å.
velocity: $\Delta \mathrm{v}$ from rest in km/s.
g: g-values in photons/s as a fucntion of velocity.

Parameters

None

Returns

No Output

photolossrates¶

photolossrates - Determine photoionization and photodissociation rates

class atomicdataMB.photolossrates.PhotoRate(species, aplanet_=<Quantity 1. AU>)[source]¶

Determine photoreactions and photorates for a species.

Parameters

species: Species to compute rates for.
aplanet: Distance from the Sun. Default is 1 AU. Given as either a numeric type or an astropy quantity with length units.

Class Attributes

species: Species
aplanet: Distance from the Sun; astropy quantity with units AU
rate: Reaction rate; astropy quantity with units s^{-1}. Rate is the sum of all possible reactions for the species.
reactions: Pandas dataframe with columns for reaction and rate (in s^{-1}) for each reaction for the species. This can be used to determine the products produced by photolysis and photoionization.

Example

>>> from atomicdataMB import PhotoRate
>>> kappa = PhotoRate('Na', 0.33)
>>> print(kappa)
Species = Na
Distance = 0.33 AU
Rate = 6.666666666666666e-05 1 / s
>>> print(kappa.rate)
6.666666666666666e-05 1 / s
>>> print(kappa.reactions)
               reaction                  kappa
0  Na, photon -> Na+, e  6.666666666666666e-05
>>> kappa = PhotoRate('H_2O')
>>> print(kappa)
Species = H_2O
Distance = 1.0 AU
Rate = 1.2056349999999999e-05 1 / s
>>> print(kappa.reactions)
                     reaction     kappa
0      H_2O, photon -> H_2, O  5.97e-07
1       H_2O, photon -> OH, H  1.03e-05
2     H_2O, photon -> H, H, O  7.54e-07
3   H_2O, photon -> H, OH+, e  5.54e-08
4   H_2O, photon -> OH, H+, e  1.31e-08
5    H_2O, photon -> H_2O+, e  3.31e-07
6  H_2O, photon -> H_2, O+, e  5.85e-09

atomicdataMB.photolossrates.make_photo_table()[source]¶

Creates and populates photorates database table. Creates a database table called photorates. Fields in the table:

filename: Filename in project tree containing the data; used only for populating the database
reference: Source of the photoionization or photodissociation rate
species: Atomic or molecular species
reaction: Photoionization or photodissociation reaction

If multiple reaction rates are found for a reaction, user is prompted to choose the best one. Most of the reactions are in: Huebner & Mukherjee (2015), Astrophys. Space Sci., 195, 1-294.

Parameters

None

Returns

No output

initialize_atomicdata¶

Populate the database with the available atomic data. Currently populates g-values and photoionization rates. If the database does not exist, it will be created. By default, the tables will only be created if

atomicdataMB.initialize_atomicdata.initialize_atomicdata(force=False)[source]¶

Populate the database with available atomic data if nececssary.

Parameters

force: By default, the database tables are only created if they do not already exist. Set force to True to force the tables to be remade. This would be necessary if there are updates to the atomic data.

Output

No output.

database_connect¶

database_connect - Return a database connection to saved atomic data

atomicdataMB.database_connect.database_connect(database=None, port=None, return_con=True)[source]¶

Return a database connection to saved atomic data Wrapper for psycopg2.connect() that determines database and port to use.

Parameters

database: Database to connect to. If not given, it must be supplied in the $HOME/.nexoclom configuration file.
port: Port the database server uses. If not given, it must be supplied in the $HOME/.nexoclom configuration file.
return_con: False to return database name and port instead of connection. Default = True

Returns

Database connection with autocommit = True unless return_con = False

Examples

>>> from atomicdataMB import database_connect
>>> database, port = database_connect(return_con=False)
>>> print(f'database = {database}; port = {port}')
database = thesolarsystemmb; port = 5432
>>> with database_connect() as con:
...     cur = con.cursor()
...     cur.execute('SELECT DISTINCT species from gvalues')
...     species = cur.fetchall()
>>> species = [s[0] for s in species]
>>> print(species)
['Ca', 'OH', 'O', 'Ti', 'C', 'Mg+', 'Na', 'Mg', 'H', 'Mn', 'He',
 'Ca+', 'K', 'S']

Installation¶

atomicdataMB can be installed with pip:

$ pip install atomicdataMB

Reporting Issues¶

This project is hosted on github at atomicdataMB. Please report bugs or make comments there.

Contributing¶

Please let me know if you would like to make contributions.

Authors: Matthew Burger
License: LICENSE