taurex-fastchem 1.0.0.dev0

Python Wrapper for FastChem chemical scheme

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.

Argument	Description	Type	Default	Required
H_He_ratio	He/H ratio	float	0.083
selected_elements	List of elements to include in model	list of string	All elements in FastChem
ratio_elements	List of elements to set the ratio	list of string
ratios_to_O	ratio of each 'ratio_element' relative to oxygen	array
elements_abundance_file	Path to file that defines initial abundances (in dex)	string	Builtin (solar)
metallicity	Metallicity relative to initial abundance	float	1.0
elements_datafile	Path to file containing elements and their masses	string	Built-in (chemical_abundances.dat)
species_datafile	Path to file containing species and thermochemical data	string	Built-in (logK.dat)
chem_accuracy
with_ions	Include ions	bool	False
pressure_accuracy
newton_error
max_chem_iter
max_press_iter
max_nedler_iter
longdouble	Use 80 bit floats for faster convergence	bool	False

Retrieval Parameters:

Fitting Parameter	Description
metallicity	Metallicity relative to solar

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:

Fitting Parameter	Description
Al_O_ratio	Al/O ratio
Ar_O_ratio	Ar/O ratio
C_O_ratio	C/O ratio
Ca_O_ratio	Ca/O ratio
Cl_O_ratio	Cl/O ratio
Co_O_ratio	Co/O ratio
Cr_O_ratio	Cr/O ratio
Cu_O_ratio	Cu/O ratio
F_O_ratio	F/O ratio
Fe_O_ratio	Fe/O ratio
Ge_O_ratio	Ge/O ratio
K_O_ratio	K/O ratio
Mg_O_ratio	Mg/O ratio
Mn_O_ratio	Mn/O ratio
N_O_ratio	N/O ratio
Na_O_ratio	Na/O ratio
Ne_O_ratio	Ne/O ratio
Ni_O_ratio	Ni/O ratio
P_O_ratio	P/O ratio
S_O_ratio	S/O ratio
Si_O_ratio	Si/O ratio
Ti_O_ratio	Ti/O ratio
V_O_ratio	V/O ratio
Zn_O_ratio	Zn/O ratio

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]])