taurex-ggchem 1.0.0.dev0

Python Wrapper for GGchem chemical scheme

TauREx-GGchem plugin

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

Installation

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

pip install taurex_ggchem

Installing from source

To install from source a valid C/C++ and FORTRAN compiler must be present. You can compile it by doing:

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

Running in TauREx

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

[Chemistry]
chemistry_type = ggchem
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
equilibrium_condensation = 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:

Argument	Description	Type	Default	Required
dispol_files	Path to thermochemical data	list of strings	Built-in (BarklemCollet,StockKitzmann_withoutTsuji, WoitkeRefit )
abundance_profile	Initial abundance profile. Either solar, meteor, ocean or earth	string	'solar'
selected_elements	List of elements to include	list of string	All elements in GGchem
ratio_elements	List of elements to set the ratio	list of string
ratios_to_O	ratio of each 'ratio_element' relative to oxygen	array
he_h_ratio	He/H ratio	float	0.083
metallicity	Metallicity relative to initial abundance	float	1.0
include_charge	Include ions	bool	False
equilibrium_condensation	Include condenstation	bool	False
dustchem_file	Dust chemistry file	string	Built-in (DustChem.dat)
Tfast	Lowest temperature (K) to use faster method	float	1000
new_back_it		integer	6
new_back_fac		float	1e5
new_pre_method		integer	2
new_full_it		bool	False
new_fast_level		integer	1

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
C_O_ratio	C/O ratio
N_O_ratio	N/O ratio
Na_O_ratio	Na/O ratio
Mg_O_ratio	Mg/O ratio
Si_O_ratio	Si/O ratio
Fe_O_ratio	Fe/O ratio
Al_O_ratio	Al/O ratio
Ca_O_ratio	Ca/O ratio
Ti_O_ratio	Ti/O ratio
S_O_ratio	S/O ratio
Cl_O_ratio	Cl/O ratio
K_O_ratio	K/O ratio
Li_O_ratio	Li/O ratio
F_O_ratio	F/O ratio
P_O_ratio	P/O ratio
V_O_ratio	V/O ratio
Cr_O_ratio	Cr/O ratio
Mn_O_ratio	Mn/O ratio
Ni_O_ratio	Ni/O ratio
Zr_O_ratio	Zr/O ratio
W_O_ratio	W/O ratio

Running in Python

You can import the chemistry scheme in Python pretty easily

>>> from taurex_ggchem import GGChem
>>> gg = GGChem(metallicity=1.0,  
         selected_elements=['H','He','C','O','N','K'], 
         abundance_profile='earthcrust', 
         equilibrium_condensation=True) 

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

>>> tm = TransmissionModel(chemistry=gg)

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

>>> nlayers = 100
>>> T = numpy.linspace(400,1000,nlayers)
>>> P = numpy.logspace(1,5, nlayers)
>>> gg.initialize_chemistry(nlayers=nlayers, temperature_profile=T, pressure_profile=P)
>>> gg.gases
['H', 'He', 'C', 'O', 'N',..., 'N3', 'O3', 'C3H']
>>> gg.mixProfile
array([[4.75989782e-04, 4.93144149e-04, 5.10561665e-04, ...,
        2.89575385e-05, 2.47386006e-05, 2.10241059e-05],
       ...,
       [2.49670621e-16, 1.44224904e-16, 8.29805526e-17, ...,
        9.48249338e-42, 4.75884162e-42, 2.37999459e-42]])
>>> gg.condensates
['C[s]', 'H2O[s]', 'H2O[l]', 'NH3[s]', 'CH4[s]', 'CO[s]', 'CO2[s]']
>>> gg.condensateMixProfile
array([[0.00000000e+00, 0.00000000e+00, 0.00000000e+00,...,
        0.00000000e+00, 0.00000000e+00],
       [0.00000000e+00, 0.00000000e+00, 0.00000000e+00, ...,
        0.00000000e+00, 9.82922802e-10, 1.88551848e-10, 2.88471985e-11,
        4.40651877e-12, 6.95597887e-13],
        ...,
        [0.00000000e+00, 0.00000000e+00, 0.00000000e+00, ...,
        0.00000000e+00, 0.00000000e+00]])

Bibliography

If you use the plugin please cite the relevant articles. TauREx will output it at program end. You can get the citation from Python like so:

from taurex import __citations__
print(__citations__)
print(gg.nice_citation())

Which gives:

TauREx III: A fast, dynamic and extendable framework for retrievals
Al-Refaie, Ahmed F., Changeat, Quentin, Waldmann, Ingo P., Tinetti, Giovanna
arXiv, 1912.07759, 2019

Equilibrium chemistry down to 100 K - Impact of silicates and phyllosilicates on the carbon to oxygen ratio
Woitke, P., Helling, Ch., Hunter, G. H., Millard, J. D., Turner, G. E., Worters, M., Blecic, J., Stock, J. W.
A&A, 614, A1, 2018

You can also generate bibtex from the input file like so:

taurex -i myinput.par --bibtex mybib.bib