TauREx-FastChem plugin

A Python wrapper built using the TauREx is available. The wrapper also installs all available datafiles included with FastChem

Note: This plugin does not support condensation yet but will do in future versions.

Installation

You can install one of the prebuilt binary wheels for Windows, macOS and manylinux through pip:

pip install taurex-fastchem

Installing from source

To install from source can be done so like this:

git clone https://github.com/ucl-exoplanets/taurex-fastchem
cd taurex-fastchem
pip install .

Running in TauREx

Once installed you can select the chemical model through the chemistry_type keyword under Chemistry.

[Chemistry]
chemistry_type = fastchem
metallicity = 1.0
selected_elements = H, He, C, N, O, Ti, V, S, K
ratio_elements = C, N, Ti
ratios_to_O = 0.5,0.001, 1e-4
with_ions = True

[Fitting]
Ti_O_ratio:fit = True
Ti_O_ratio:prior = "LogUniform(bounds=(-6,2))"
S_O_ratio:fit = True
S_O_ratio:prior = "LogUniform(bounds=(-6,2))"
metallicity:fit = True
metallicity:prior = "LogUniform(bounds=(-6,2))"

Input arguments:

These arguments apply to both the TauREx input file and python interface.

Retrieval Parameters:

The wrapper will generate oxygen retrieval parameters for all metallic elements within the chemical model. If Ti is present (either by default or specifing in selected_elements) then a Ti_O_ratio retrieval parameter will be available. Using the default selected_parameters will give access to:

Running in Python

You can import the chemistry scheme in Python pretty easily

>>> from pyfastchem import FastChem
>>> fc = FastChem(selected_elements=['H','He','C','O','N','K','e-'], 
                  with_ions=True, metallicity=1.0)

You can either pass it into a TauREx forward model like so:

>>> tm = TransmissionModel(chemistry=fc)

Or use it independently to compute volume mixing ratios by passing in temperature and pressure ( Pascal ) arrays:

>>> nlayers = 10
>>> temperature = np.linspace(300,100,nlayers)
>>> pressure = np.logspace(5,-3, nlayers) # Pa
>>> fc.initialize_chemistry(nlayers,temperature,pressure)
>>> fc.gases
['H', 'He', 'O', 'C', 'K', 'N', 'e-', ..., 'O+', 'O-', 'O2+', 'O2-']
>>> fc.mixProfile
array([[3.87435866e-036, 9.95149979e-039, 7.62616463e-042,
        1.23490910e-045, 2.58839801e-050, 3.41640407e-056,
        9.40930967e-064, 9.08433703e-074, 1.41255491e-087,
        1.38065040e-167],
        ...,
       [1.42400626e-001, 1.42400626e-001, 1.42400626e-001,
        1.42400626e-001, 1.42400626e-001, 1.42400791e-001,
        1.42398731e-001, 1.42398284e-001, 1.42367067e-001,
        9.96186945e-001]])