TauREx-FastChem plugin

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

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 a valid C/C++ compiler must be present. You can compile it by doing:

git clone https://github.com/ucl-exoplanets/FastChem.git
cd 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 taurex_fastchem 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]])