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Below is the complete list of headers and variables as well as an extended description. The units are indicated in parenthesis:
## output_files
The `output_files` section allows you to personalize the names of the output files.
The `output_files` section allows you to personalize the names of the output files. The output directory is set with `path_outputs` (see [`paths`](#paths)).
- `spectrum_file_prefix`
- string
- prefix of the spectrum files
......@@ -40,7 +40,6 @@ The `output_files` section allows you to personalize the names of the output fil
## target_parameters
The `target_parameters` section handles the target (planet) settings.
- `use_gravity`
- boolean
- if True, uses equatorial gravity instead of mass to calculate gravity
......@@ -199,17 +198,17 @@ The `species_parameters` section handles the atmospheric elemental abundances, w
- elements listed here won't have the atmospheric metallicity if use_atmospheric_metallicity is False (atmosphere_parameters/metallicity)
- e.g. `elements_names = 'He', 'Ne', 'Ar', 'Kr', 'Xe'` to set the elemental abundances of the noble gases at a different value than `metallicity`.
- `elements_h_ratio`
- list of float
- <element>/H ratio of the elements listed above (only used if both use_atmospheric_metallicity and use_elements_metallicity are False)
- list of floats
- element over hydrogen ratio of the elements listed above (only used if both use_atmospheric_metallicity and use_elements_metallicity are False)
- e.g. `elements_h_ratio = 8.395e-2, 1e-30, 1e-30, 1e-30, 1e-30`, in combination with the example above for `elements_names`, `use_elements_metallicity = False`, `use_atmospheric_metallicity = False`, to set He/H = 8.395e-2, Ne/H = 1e-30, ...
- `elements_metallicity`
- list of float
- list of floats
- (solar metallicity) elemental metallicity of the elements listed above
- e.g. `elements_metallicity = 1, 1, 1, 1, 1`, in combination with the example above for `elements_names`, `use_elements_metallicity = True`, `use_atmospheric_metallicity = False`, to set elemental abundances of the noble gases to 1 time their solar value.
- `species_names`
- list of strings
- absorbing species in atmosphere
- e.g. `species_names = 'CH4', 'CO', 'CO2', 'FeH', 'H2O', 'H2S', 'HCN', 'K', 'Na', 'NH3', 'PH3', 'TiO', 'VO'`. The number of elements must match `n_species` (see [`atmosphere_parameters`](#atmosphere_parameters)).
- e.g. `species_names = 'CH4', 'CO', 'CO2', 'FeH', 'H2O', 'H2S', 'HCN', 'K', 'Na', 'NH3', 'PH3', 'TiO', 'VO'`. The number of elements must match `n_species` (see [`atmosphere_parameters`](#atmosphere_parameters)). The k-coefficients of these species must be within the `path_k_coefficients` directory (see [`paths`](#paths)).
- `species_at_equilibrium`
- list of booleans
- if True, the species is at thermochemical equilibrium, else it is out of equilibrium
......@@ -217,7 +216,7 @@ The `species_parameters` section handles the atmospheric elemental abundances, w
- `cia_names`
- list of strings
- collision induced absorptions to be included
- e.g. `cia_names = 'H2-H2', 'H2-He', 'H2O-H2O'`. The number of elements must match `n_cia` (see [`atmosphere_parameters`](#atmosphere_parameters)).
- e.g. `cia_names = 'H2-H2', 'H2-He', 'H2O-H2O'`. The number of elements must match `n_cia` (see [`atmosphere_parameters`](#atmosphere_parameters)). The CIA files must be within the `path_cia` directory (see [`paths`](#paths)).
- `load_vmr_profiles`
- boolean
- if True, load VMR profiles from a file (can be useful only if chemistry is deactivated)
......@@ -243,17 +242,148 @@ The `spectrum_parameters` section handles the spectral range and resolution of t
- e.g. `wavenumber_min = 200`.
## clouds_parameters
The `clouds_parameters` section handles the clouds settings.
The `clouds_parameters` section handles the clouds settings. The cloud optical constants must be within the `path_clouds` directory (see [`paths`](#paths)).
- `cloud_mode`
- string
- cloud mode ('fixedRadius'|'fixedSedimentation'|'fixedRadiusCondensation'|'fixedRadiusTime')
- e.g. `eddy_mode = 'fixedSedimentation'`. `'fixedRadius'` mean that the mean cloud particle radius is constant within the pressure grid, set to the value of `cloud_particle_radius`. `'fixedSedimentation'` mean that mean cloud particle is calculated based on the value of `sedimentation_parameter` (see [Ackerman and Marley 2001](https://iopscience.iop.org/article/10.1086/321540/fulltext/52911.text.html)). `'AckermanConvective'` mean that Kzz is calculated using the method from Ackerman et al, but taking into account the convective flux. `'infinity'` is the same than AckermanConvective, but if `cloud_mode = 'fixedRadius'` (see [`clouds_parameters`](#clouds_parameters)), the cloud will extend to the top of the atmosphere (no sedimentation).
- e.g. `eddy_mode = 'fixedSedimentation'`. `'fixedRadius'` mean that the mean cloud particle radius is constant within the pressure grid, set to the value of `cloud_particle_radius`. `'fixedSedimentation'` mean that mean cloud particle is calculated based on the value of `sedimentation_parameter` (see [Ackerman and Marley 2001](https://iopscience.iop.org/article/10.1086/321540/fulltext/52911.text.html)). `'fixedRadiusCondensation'` is the same than `'fixedSedimentation'`, but the sedimentation radius is set constant two layers above the cloud condensation level.
- `cloud_fraction`
- float
- cloud cover fraction
- e.g. `cloud_fraction = 0.15` mean that 15% of the atmosphere is covered by clouds. The flux with clouds is calculated as `(1 - cloud_fraction) * flux_clear + cloud_fraction * flux_full_cover`.
- `cloud_names`
- list of strings
- condensing species forming the clouds
- e.g. `cloud_names = 'H2O', 'KCl'`. The number of elements must match `n_clouds` (see [`atmosphere_parameters`](#atmosphere_parameters)).
- `cloud_particle_radius`
- list of floats
- (m) mean radius of the cloud particles (fixed radius modes)
- e.g. `cloud_particle_radius = 50e-6, 5e-6`. Used only with `cloud_mode = 'fixedRadius'`. The number of elements must match `n_clouds` (see [`atmosphere_parameters`](#atmosphere_parameters)).
- `sedimentation_parameter`
- list of floats
- sedimentation parameter of the clouds
- e.g. `sedimentation_parameter = 2, 2`. Used only in the `'fixedSedimentation'` and `'fixedRadiusCondensation'` modes. The number of elements must match `n_clouds` (see [`atmosphere_parameters`](#atmosphere_parameters)).
- `cloud_particle_density`
- list of floats
- (kg.m-3) density of the clouds particles
- e.g. `cloud_particle_density = 917, 1980`. The number of elements must match `n_clouds` (see [`atmosphere_parameters`](#atmosphere_parameters)).
- `cloud_molar_mass `
- list of floats
- (kg.mol-1) molar mass of the clouds particles
- e.g. `cloud_molar_mass = 18.01528e-3, 74.5513e-3`. The number of elements must match `n_clouds` (see [`atmosphere_parameters`](#atmosphere_parameters)).
- `reference_wavenumber`
- list of floats
- (cm-1) [for diagnostic] wavenumber for cloud optical depth output
- e.g. `reference_wavenumber = 1e4, 1e4`. Output the cloud opacities at this wavenumber. The number of elements must match `n_clouds` (see [`atmosphere_parameters`](#atmosphere_parameters)).
## retrieval_parameters
The `clouds_parameters` section handles the retrieval/inversion settings.
- `temperature_profile_file`
- string
- a-priori temperature profile file
- e.g. `temperature_profile_file = 'temperature_profile_example_ref.dat' `. The file must be in the `path_temperature_profile` directory.
- `retrieval_level_bottom`
- integer
- min level for flux retrieval
- e.g. `retrieval_level_bottom = 2` mean that the retrieval will not take into account levels below the 2nd one. A value greater than 1 is strongly recommended.
- `retrieval_level_top`
- integer
- max level for flux retrieval
- e.g. `retrieval_level_top = 81` mean that the retrieval will not take into account levels above the 81st one. This value must be between `retrieval_level_bottom` and `n_levels`.
- `retrieval_flux_error_bottom`
- float
- relative flux error at the bottom of the atmospheric grid
- e.g. `retrieval_flux_error_bottom = 1e-3`. This represents the tolerance of the retrieval at the bottom of the atmosphere. A value between `1e-2` and `1e-15` is recommended.
- `retrieval_flux_error_top`
- float
- relative flux error at the top of the atmospheric grid
- e.g. `retrieval_flux_error_top = 1e-5`. This represents the tolerance of the retrieval at the top of the atmosphere. A value between `1e-2` and `1e-15` is recommended.
- `n_iterations`
- integer
- number of iterations
- e.g. `n_iterations = 30`. Maximum number of iterations allowed.
- `n_non_adiabatic_iterations`
- integer
- number of iterations without including the adiabatic correction (necessary for convergence)
- e.g. `n_non_adiabatic_iterations = 15`. Maximum number of iterations without requiring an adiabatic temperature profile allowed. It is recommended to set this parameter `> 1` when far from convergence. It must be below `n_iterations`.
- `chemistry_iteration_interval`
- integer
- number of iterations between 2 calls the of the thermochemical equilibrium
- e.g. `chemistry_iteration_interval = 2` mean that the chemistry is calculated with an interval of 2 iterations, i.e. every 3 iterations.
- `cloud_iteration_interval`
- integer
- number of iterations between 2 calls of the cloud physics
- e.g. `cloud_iteration_interval = 4` mean that the cloud VMR is calculated with an interval of 4 iterations, i.e. every 5 iterations.
- `retrieval_tolerance`
- float
- tolerance for the flux convergence (0 to use the iterations limits)
- e.g. `retrieval_tolerance = 0.001` mean that if at iteration `i` the chi2 variation or the T/dT ratio is lower than 0.001, if `i < n_non_adiabatic_iterations`, the non-adiabatic runs end, else if `i > n_non_adiabatic_iterations`, the run end. A value of 0 for this parameter is recommended when far from convergence.
- `smoothing_bottom`
- float
- (height scale) vertical profile smoothing at the bottom of the atmosphere
- e.g. `smoothing_bottom = 0.5`.
- `smoothing_top`
- float
- (height scale) vertical profile smoothing at the top of the atmosphere
- e.g. `smoothing_top = 0.5`.
- `weight_apriori`
- float
- weight of the a priori, low weight means small variations
- e.g. `weight_apriori = 10`.
## options
The `options` section handles the output options settings.
- `output_species_spectral_contributions`
- boolean
- if True, output the absorbers spectral contribution
- e.g. `output_species_spectral_contributions = True`. This enable the output of each absorber (defined in `species_names`) + CIA + Rayleigh contributions, individually.
- `output_cia_spectral_contribution`
- boolean
- if True, output the CIA spectral contribution
- e.g. `output_cia_spectral_contribution = True`. This enable the output of the CIA + Rayleigh total contributions.
- `output_thermal_spectral_contribution`
- boolean
- if True, output the thermal spectral contribution
- e.g. `output_thermal_spectral_contribution = True`. This enable the output of the thermal contribution (i.e. without light source), which is useful to calculate e.g. the Bond albedo.
## paths
The `paths` section handles the output paths settings.
- `path_data`
- string
- path to molecular parameters files
- e.g. `path_data = '../data/'`.
- `path_cia`
- string
- path to collision induced absorption files
- e.g. `path_cia = '../cia/'`.
- `path_clouds`
- string
- path to the absorption cross sections files
- e.g. `path_clouds ='../data/cloud_optical_constants/'`.
- `path_k_coefficients`
- string
- path to the k coefficients files
- e.g. `path_k_coefficients = '../data/k_coefficients_tables/R50/'`.
- `path_temperature_profile`
- string
- path to the a-priori temperature profile file
- e.g. `path_temperature_profile = '../inputs/atmospheres/temperature_profiles/'`.
- `path_thermochemical_tables`
- string
- path to the thermochemical tables files
- e.g. `path_thermochemical_tables = '../data/thermochemical_tables/'`.
- `path_vmr_profiles`
- string
- path to the VMR profiles
- e.g. `path_vmr_profiles= '../inputs/atmospheres/vmr_profiles/'`.
- `path_light_source_spectra`
- string
- path to the stellar spectra
- e.g. `path_light_source_spectra = '../data/stellar_spectra/'`.
- `path_outputs`
- string
- path to molecular parameters files
- e.g. `path_outputs = '../outputs/exorem/'`.
# Code
**This page is a work in progress**
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