[Chemistry]

This header describes the chemical composition of the atmosphere. The type of model used is defined by the chemistry_type variable.

The available chemistry_type are:

• ace

  • ACE equlibrium chemistry

  • Class: ACEChemistry

• taurex

  • Free chemistry

  • Class: TaurexChemistry

• custom

  • User-type chemistry. See Custom Types

---

ACE Equlibrium Chemistry

Warning

Since version 3.1 this has been removed from the base TauREx package. You can restore this chemical scheme by writing:

pip install acepython

chemistry_type = ace chemistry_type = equilibrium

Equilibrium chemistry using the ACE FORTRAN program. Fortran compiler required

Keywords

Variable	Type	Description	Default Value
metallicity	float	Stellar metallicity in solar units	1.0
co_ratio	float	C/O ratio	0.54951

Fitting Parameters

Parameter	Type	Description
ace_metallicity	float	Stellar metallicity in solar units
ace_co	float	C/O ratio

---

Taurex Chemistry

chemistry_type = taurex chemistry_type = free

This chemistry type allows you to define individual abundance profiles for each molecule. Molecules are either active or inactive depending on whats available. If no cross-sections are available then the moelcule is not actively absorbing.

Keywords

Variable	Type	Description	Default
fill_gases	str or list	Gas or gases to fill the atmosphere with	H2,He,
ratio	float or list	Ratio between first fill gas and every other fill gas	0.749

Fitting Parameters

On its own, this chemistry model provides fitting parameters relating to the fill gases used. These are only created when more than one fill gas is defined. Here, we use [Gas-0] to designate the first gas defined in the fill gas list and [Gas-(number)] to designate the nth gas after the main gas. If we have a gas list like:

fill_gases = H2,He,CO2,

then [Gas-1]_[Gas-0] == He_H2 and [Gas-2]_[Gas-0] == CO2_H2:

Parameter	Type	Description
[Gas-(n)]_[Gas-0]	float	Ratio of nth fill gas vs first fill gas

However molecules are defined as subheaders with the subheader being the name of the molecule. Each molecule can be assigned an abundance profile through the gas_type variable. For example, to describe a chemical profile with water in constant abundance in the atmosphere is simply done like so:

[Chemistry]
chemistry_type = taurex
fill_gases = H2,He,
ratio = 0.1524

    [[H2O]]
    gas_type = constant
    mix_ratio = 1e-4

For each molecule, the available gas_type are:

• constant

  • Constant abundance profile

  • Class: ConstantGas

• twopoint

  • Two Point abundance profile

  • Class: TwoPointGas

• twolayer

  • Two layer abundance profile

  • Class: TwoLayerGas

---

Gas Profiles

For these profiles, the fitting parameters generated have the name associated with the name of the molecule. For example: H2O_P, CH4_S etc. Because of this, we will use the moniker: [Mol]. Replacing this with the appropriate molecule will give you the correct fitting parameter name. e.g. [Mol]_surface should be H2O_surface for water etc.

Constant Profile

gas_type = constant

An abundance profile that is constant with height of the atmosphere

Keywords

Variable	Type	Description	Default
mix_ratio	float	Mixing ratio of molecule	1e-4

Fitting Parameters

Parameter	Type	Description
[Mol]	float	Mixing ratio of molecule

---

Two Layer Profile

gas_type = twolayer

An abundance profile where abundance is defined on the planet surface and top of the atmosphere with a pressure point determining the boundary between the layers. Smoothing is applied.

Keywords

Variable	Type	Description	Default
mix_ratio_surface	float	Mixing ratio at BOA	1e-4
mix_ratio_top	float	Mixing ratio at TOA	1e-8
mix_ratio_P	float	Pressure boundary (Pa)	1e3
mix_ratio_smoothing	int	Smoothing window	10

Fitting Parameters

Parameter	Type	Description
[Mol]_surface	float	Mixing ratio at BOA
[Mol]_top	float	Mixing ratio at TOA
[Mol]_P	float	Pressure boundary (Pa)

---

Chemsitry File

chemistry_type = file

Reads a multi-column text file. Order must be from BOA to TOA. Each column must represent a unique molecule.

Keywords

Variable	Type	Description	Default
filename	str	Path to chemistry file	None
gases	list	List of all molecules in column order	None