LTE Molecule Model

There is a tool for modeling the full LTE spectrum of a molecule. It uses the CDMS / VAMDC database (http://portal.vamdc.eu/vamdc_portal/home.seam) and the vamdclib (http://vamdclib.readthedocs.io) python library to compute the partition function of a molecule. It uses astroquery.splatalogue (http://astroquery.readthedocs.io/en/latest/splatalogue/splatalogue.html) to identify the line frequencies and energy levels.

A very simple example looks like this:

freqs, aij, deg, EU, partfunc = get_molecular_parameters('CH3OH',
                                                         fmin=90*u.GHz,
                                                         fmax=100*u.GHz)
def modfunc(xarr, vcen, width, tex, column):
    return generate_model(xarr, vcen, width, tex, column, freqs=freqs, aij=aij,
                          deg=deg, EU=EU, partfunc=partfunc)

fitter = generate_fitter(modfunc, name="CH3OH")

The molecular parameter lookup stage is often slow and may be a bottleneck.

Details can be found in the API documentation:

LTE Molecule Modeling Tool

Uses astroquery & vamdclib to obtain molecular parameters. http://astroquery.readthedocs.io/en/latest/splatalogue/splatalogue.html

Equations are based on Mangum & Shirley 2015 (2015PASP..127..266M)

Module API

pyspeckit.spectrum.models.lte_molecule.Jnu(nu, T)

RJ equivalent temperature (MS15 eqn 24)

pyspeckit.spectrum.models.lte_molecule.Jnu_cgs(nu, T)

RJ equivalent temperature (MS15 eqn 24) (use cgs constants for speed)

pyspeckit.spectrum.models.lte_molecule.generate_fitter(model_func, name)

Generator for hnco fitter class

pyspeckit.spectrum.models.lte_molecule.generate_model(xarr, vcen, width, tex, column, freqs, aij, deg, EU, partfunc, background=None, tbg=2.73)

Model Generator

pyspeckit.spectrum.models.lte_molecule.get_molecular_parameters(molecule_name, molecule_name_vamdc=None, tex=50, fmin=<Quantity 1.0 GHz>, fmax=<Quantity 1.0 THz>, line_lists=['SLAIM'], chem_re_flags=0, **kwargs)

Get the molecular parameters for a molecule from the CDMS database using vamdclib

Parameters:

molecule_name : string

The string name of the molecule (normal name, like CH3OH or CH3CH2OH)

molecule_name_vamdc : string or None

If specified, gives this name to vamdc instead of the normal name. Needed for some molecules, like CH3CH2OH -> C2H5OH.

tex : float

Optional excitation temperature (basically checks if the partition function calculator works)

fmin : quantity with frequency units

fmax : quantity with frequency units

The minimum and maximum frequency to search over

line_lists : list

A list of Splatalogue line list catalogs to search. Valid options include SLAIM, CDMS, JPL. Only a single catalog should be used to avoid repetition of transitions and species

chem_re_flags : int

An integer flag to be passed to splatalogue’s chemical name matching tool

Examples

>>> freqs, aij, deg, EU, partfunc = get_molecular_parameters(molecule_name='CH2CHCN',
...                                                          fmin=220*u.GHz,
...                                                          fmax=222*u.GHz,
...                                                          molecule_name_vamdc='C2H3CN')
>>> freqs, aij, deg, EU, partfunc = get_molecular_parameters('CH3OH',
...                                                          fmin=90*u.GHz,
...                                                          fmax=100*u.GHz)

pyspeckit.spectrum.models.lte_molecule.line_tau(tex, total_column, partition_function, degeneracy, frequency, energy_upper, einstein_A=None)

Given the excitation temperature of the state, total column density of the molecule, the partition function, the degeneracy of the state, the frequency of the state, and the upper-state energy level, return the optical depth of that transition.

This is a helper function for the LTE molecule calculations. It implements the equations

\[\tau_\nu = \frac{c^2}{8 \pi \nu^2} A_{ij} N_u \exp\left( \frac{h \nu}{k_B T_{ex}}\right)\]

\[N_{u} = N_{tot} \frac{g_u}{Q} \exp\left(\frac{-E_u}{k_B T_{ex}} \right)\]

based on Equation 29 of Mangum & Shirley 2015 (2015PASP..127..266M)

pyspeckit.spectrum.models.lte_molecule.line_tau_cgs(tex, total_column, partition_function, degeneracy, frequency, energy_upper, einstein_A)

Given the excitation temperature of the state, total column density of the molecule, the partition function, the degeneracy of the state, the frequency of the state, and the upper-state energy level, return the optical depth of that transition.

Unlike line_tau(), this function requires inputs in CGS units.

This is a helper function for the LTE molecule calculations. It implements the equations

\[\tau_\nu = \frac{c^2}{8 \pi \nu^2} A_{ij} N_u \exp\left( \frac{h \nu}{k_B T_{ex}}\right)\]

\[N_{u} = N_{tot} \frac{g_u}{Q} \exp\left(\frac{-E_u}{k_B T_{ex}} \right)\]

based on Equations 11 and 29 of Mangum & Shirley 2015 (2015PASP..127..266M)

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