{"last_commit_sha":"7d12e4cf1f043abd30f8d2c4926132b2d9e187c9","persisted":true,"title":"Documentation","content":"Summary: - [Input file](#input-file) - [output_files](#output_files) - [target_parameters](#target_parameters) - [light_source_parameters](#light_source_parameters) - [atmosphere_parameters](#atmosphere_parameters) - [species_parameters](#species_parameters) - [spectrum_parameters](#spectrum_parameters) - [clouds_parameters](#clouds_parameters) - [retrieval_parameters](#retrieval_parameters) - [options](#options) - [paths](#paths) - [Output file (HDF5)](#output-file-hdf5) - [Code](#code) # Input file The input file format is [Fortran namelist](https://software.intel.com/content/www/us/en/develop/documentation/fortran-compiler-developer-guide-and-reference/top/language-reference/a-to-z-reference/m-to-n/namelist.html). All of the headers and variables must be present. If your input file does not work, start back with a working example. An input file, _example.nml_ is provided with any distributed version of *Exo-REM*, with a short description of each variables. Comments are handled with `!`. 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 directory is set with `path_outputs` (see [`paths`](#paths)). - `spectrum_file_prefix` - string - prefix of the spectrum files - e.g. with `spectrum_file_prefix = 'spectra'`, the spectrum file will be _spectra_XXX.dat_, where _XXX_ is the output files suffix. Has no influence if `ouput_hdf5` is `True`. - `temperature_profile_file_prefix` - string - prefix of the temperature profile files - e.g. with `temperature_profile_file_prefix = 'temperature_profile'`, the temperature file will be _temperature_profile_XXX.dat_, where _XXX_ is the output files suffix. Has no influence if `ouput_hdf5` is `True`. - `vmr_file_prefix` - string - prefix of the volume mixing ratio profiles files - e.g. with `vmr_file_prefix = 'vmr'`, the vmr file will be _vmr_XXX.dat_, where _XXX_ is the output files suffix. Has no influence if `ouput_hdf5` is `True`. - `output_files_suffix` - string - suffix of the output files - e.g. with `output_files_suffix = 'example'` and `ouput_hdf5 = False`, the output files will be _YYY_example.dat_, where _YYY_ are the output files prefix. If `ouput_hdf5` is `True`, the sole output file will be _example.h5_. ## 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 - e.g. `use_gravity = False`. In that case, the equatorial gravity at 1 bar is derived from `target_equatorial_radius` and `target_mass`. If `True`, the equatorial gravity at 1 bar is derived from `target_equatorial_gravity`. - `use_flattening` - boolean - if True, uses flattening instead of polar radius to calculate gravity - e.g. `use_flattening = True`. In that case, the gravity at 1 bar will be derived from `target_flattening`, `latitude` and the equatorial gravity. If `False`, the gravity at 1 bar will be derived from `target_polar_radius`, `target_equatorial_radius`, `latitude` and the equatorial gravity. - `target_mass` - float - (kg) mass of the target - e.g. `target_mass = 5e25`. Used to calculate gravity, only if `use_gravity` is `False`. - `target_equatorial_gravity` - float - (m.s-2) gravity at 1 bar of the target - e.g. `target_equatorial_gravity = 14.83`. Used only if `use_gravity` is `True`. - `target_equatorial_radius` - float - (m) equatorial radius at 1 bar of the target - e.g. `target_equatorial_radius = 15000e3`. - `target_polar_radius` - float - (m) polar radius at 1 bar of the target - e.g. `target_polar_radius = 15000e3`. Used only if `use_flattening` is `False`. - `target_flattening` - float - flattening of the target - e.g. `target_flattening = 0` for a perfect sphere. Used only if `use_flattening` is `True`. - `latitude` - float - (deg) latitude of observation on the target - e.g. `latitude = 0` to look at the equator. - `target_internal_temperature` - float - (K) internal (or intrinsic) temperature of the target - e.g. `target_internal_temperature = 500`. This is the temperature derived from the radiosity (upward flux) of the target (i.e. the radiosity corresponds to that of a black body at `target_internal_temperature`) if it was perfectly isolated (i.e. without any external light source/star). *Exo-REM* will change the temperature profile so that the calculated internal temperature is as close as possible to `target_internal_temperature`. - `emission_angle` [unused parameter] - float - (deg) emission angle - e.g. `emission_angle = 0.0` to look along the normal of the atmosphere. Could be used in the calculation of the emission spectrum. ## light_source_parameters The `light_source_parameters` section handles the light source (star) settings. - `add_light_source` - boolean - if True, add the light source - e.g. `add_light_source = True`. In that case, a light source/star will be added, and the atmosphere will be irradiated. If `False`, the other parameters in this section are not taken into. - `use_irradiation` - boolean - if True, use irradiation instead of range to calculate the light source spectrum - e.g. `use_irradiation = False`. In that case, the irradiation will be calculated using `light_source_range`. If `True`, the distance between the light source and the target will be calculated from `light_source_irradiation`. - `use_light_source_spectrum` - boolean - if True, use a spectrum for the light source instead of a black body - e.g. `use_light_source_spectrum = False`. In that case, the spectral irradiance of the target will be calculated from a black body. If `True`, the spectral irradiance is read from `light_source_spectrum_file` and re-adapted so that the light source radiosity correspond to `light_source_effective_temperature`. - `light_source_radius` - float - (m) radius of the light source - e.g. `light_source_radius = 100e6`. - `light_source_range` - float - (m) distance between the target and the light source - e.g. `light_source_range = 2e9`. Used to calculate the target/planet irradiance if `use_irradiation` is `False`. - `light_source_effective_temperature` - float - (K) light source effective temperature - e.g. `light_source_effective_temperature = 3450`. - `light_source_irradiation` - float - (W.m-2) light source irradiation - e.g. `light_source_irradiation = 20000`. Used to calculate the target/planet irradiance if `use_irradiation` is `True`. - `light_source_spectrum_file` - string - spectrum of the light source - e.g. with `light_source_spectrum_file = 'spectrum_BTSettl_3500K_logg5_met0.dat'`. The file must be placed in the `path_light_source_spectra` directory. Used only if `use_light_source_spectrum` is `True`. - `incidence_angle` [unused parameter] - float - (deg) incident light source light relative to the normal of the atmosphere - e.g. `incidence_angle = 0.0` if the light rays are have the same direction than the normal of the atmosphere. Could be used to calculate the temperature profile at a specific local hour on the target/planet. ## atmosphere_parameters The `atmosphere_parameters` section handles the atmospheric settings. - `use_metallicity` - boolean - if True, uses metallicity instead of H2, He and Z VMR to get the elemental abundances - e.g. `use_metallicity = True`. In that case, the elemental abundances are calculated from `metallicity`. If `False`, they are calculated from `h2_vmr`, `he_vmr` and `z_vmr`. - `use_pressure_grid` - boolean - if True, uses the pressure grid in the temperature profile file to generate the pressure grid - e.g. `use_pressure_grid = False`. In that case, the pressure grid will be equally spaced in the log-space between `pressure_min` and `pressure_max`. If `True`, it will be directly read from `temperature_profile_file` (see [`retrieval_parameters`](#retrieval_parameters)). - `h2_vmr` - float - H2 volume mixing ratio - e.g. `h2_vmr = 0.6`. `h2_vmr`, `he_vmr` and `z_vmr` will be automatically adjusted so that their sum is 1. - `he_vmr` - float - He volume mixing ratio - e.g. `he_vmr = 0.1`. `h2_vmr`, `he_vmr` and `z_vmr` will be automatically adjusted so that their sum is 1. - `z_vmr` - float - other species volume mixing ratio - e.g. `z_vmr = 0.3`. `h2_vmr`, `he_vmr` and `z_vmr` will be automatically adjusted so that their sum is 1. The heavy elements abundances are scaled from the solar abundance. - `metallicity` - float - (solar metallicity) atmospheric metallicity - e.g. `metallicity = 10.0`. The metallicity is a factor by which all the elemental abundances except H are multiplied compared to their solar abundances. The solar abundances are read in the _data/solar_abundances.dat_ file. - `n_levels` - integer - number of atmospheric levels - e.g. `n_levels = 81`. If `use_pressure_grid` is `False`, the bottom level has the pressure `pressure_max`, and the top level has the pressure `pressure_min`. `retrieval_level_top` must be lower or equal to this parameter. - `n_species` - integer - number of absorbing species - e.g. `n_species = 13`. This parameter must match the number of elements in `species_names` and `species_at_equilibrium` (see [`species_parameters`](#species_parameters)). - `n_cia` - integer - number of collision induced absorptions - e.g. `n_cia = 3`. This parameter must match the number of elements in `cia_names` (see [`species_parameters`](#species_parameters)). - `n_clouds` - integer - number of clouds in atmosphere - e.g. `n_clouds = 2`. This parameter must match the number of elements in `cloud_names`, `cloud_particle_radius`, `sedimentation_parameter`, `cloud_particle_density`, `cloud_molar_mass` and `reference_wavenumber` (see [`clouds_parameters`](#clouds_parameters)). - `eddy_mode` - string - eddy diffusion coefficient (Kzz) mode ('constant'|'Ackerman'|'AckermanConvective'|'infinity') - e.g. `eddy_mode = 'AckermanConvective'`. `'constant'` mean that the Kzz is constant within the pressure grid, set to the value of `eddy_diffusion_coefficient`. `'Ackerman'` mean that Kzz is calculated using the method from Ackerman et al. `'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). - `eddy_diffusion_coefficient` - float - (cm2.s-1) eddy diffusion coefficient - e.g. `eddy_diffusion_coefficient = 1e8`. Used if `eddy_mode = 'constant'`. - `pressure_min` - float - (Pa) pressure at the top of the atmospheric grid - e.g. `pressure_min = 1e-1`. Used only if `use_pressure_grid` is `False`. - `pressure_max` - float - (Pa) pressure at the bottom of the atmospheric grid - e.g. `pressure_min = 1e7`. Used only if `use_pressure_grid` is `False`. ## species_parameters The `species_parameters` section handles the atmospheric elemental abundances, which absorbing species to include and the chemical mode (equilibrium or out-of-equilibrium). - `use_atmospheric_metallicity` - boolean - if True, use the atmospheric metallicity instead of the element/H ratios or the elements metallicity to get the elemental abundances - e.g. `use_atmospheric_metallicity = False`. In that case, the elemental abundances are calculated from `elements_h_ratio` if `use_elements_metallicity` is `False`, or else from `elements_metallicity`. If `True`, the elemental abundances are calculated only from `metallicity` (see [`atmosphere_parameters`](#atmosphere_parameters)). - Example: - `use_atmospheric_metallicity = True`, `metallicity = 10`: He/H, C/H, O/H, N/H ... are set to 10 times their solar value. - `use_atmospheric_metallicity = False`, `metallicity = 10`, `use_elements_metallicity = False`, `elements_names = 'He', 'C'`, `elements_h_ratio = 8e-2, 1e-30`: He/H = 8e-2, C/H = 1e-30. O/H, N/H, ... are set to 10 times their solar value. - `use_atmospheric_metallicity = False`, `metallicity = 10`, `use_elements_metallicity = True`, `elements_names = 'He', 'C'`, `elements_metallicity = 1, 5`: He/H is set to 1 times its solar value. C/H is set to 5 times its solar value. O/H, N/H, ... are set to 10 times their solar value. - `use_elements_metallicity` - boolean - if True, use the atmospheric metallicity instead of the element/H ratios or the elements metallicity to get the elemental abundances - e.g. `use_atmospheric_metallicity = False`. In that case, the elemental abundances are calculated from `elements_h_ratio` if `use_elements_metallicity` is `False`, or else from `elements_metallicity`. If `True`, the elemental abundances are calculated only from `metallicity` (see [`atmosphere_parameters`](#atmosphere_parameters)). - `elements_names` - list of strings - 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 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 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)). 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 - e.g. `species_at_equilibrium = False, False, False, False, False, False, False, False, False, False, False, False, False` To set all the absorbing species in out-of-equilibrium mode. The number of elements must match `n_species` (see [`atmosphere_parameters`](#atmosphere_parameters)). - `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)). 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) - e.g. `load_vmr_profiles = False`. In that case, the VMR are initialized by *Exo-REM*. If `True`, the VMR are read from `vmr_profiles_file`. This has no impact if `n_iterations` (see [`retrieval_parameters`](#retrieval_parameters)) is greater than 0. - `vmr_profiles_file` - string - VMR profiles file, ignored if load_vmr_profiles is False - e.g. `vmr_profiles_file = 'vmr_example_ref.dat'`. The file must be in the `path_vmr_profiles` directory. ## spectrum_parameters The `spectrum_parameters` section handles the spectral range and resolution of the calculated spectrum. - `wavenumber_min` - float - (cm-1) first wavenumber of the calculated spectrum - e.g. `wavenumber_min = 130`. - `wavenumber_max` - float - (cm-1) last wavenumber of the calculated spectrum - e.g. `wavenumber_min = 30130`. - `wavenumber_step` - float - (cm-1) wavenumber step of the calculated spectrum - e.g. `wavenumber_min = 200`. ## clouds_parameters 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)). `'fixedRadiusCondensation'` is the same than `'fixedSedimentation'`, but the sedimentation radius is set constant two layers above the cloud condensation level. `'fixedRadiusTime'` mean that the mean cloud particle radius is calculated from the condensation timescale. - `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)). - `supersaturation_parameter` - list of floats - supersaturation parameter of the clouds - e.g. `supersaturation_parameter = 0.003, 0.003`. - `sticking_efficiency` - list of floats - sticking efficiency of the clouds - e.g. `sticking_efficiency = 1.0, 1.0`. - `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)). - `load_cloud_profiles` - boolean - if True, use initial cloud profile defined in vmr_profiles_file - e.g. `load_cloud_profiles = False`. ## retrieval_parameters The `retrieval_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. - `n_burn_iterations` - integer - number of iterations before the end where all the physics is calculated at every iterations - e.g. `n_burn_iterations = 99`. - `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_transmission_spectra` - boolean - if True, output the transmission spectra - e.g. `output_transmission_spectra = True`. This enable the output of the transmission spectrum, plus the contributions to the transmission spectrum if the output contribution options are set to True (see below). - `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. - `output_fluxes` - boolean - if True, output the radiosities without the effect of irradiance - e.g. `output_fluxes = True`. This enable the output of the fluxes (i.e. the radiosities without light source). - `output_hdf5` - boolean - if True, set the output format to HDF5 - e.g. `output_hdf5 = True`. This enable the output in HDF5, this is recommended as the HDF5 output is more complete. ## 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/'`. # Output file (HDF5) The units of each dataset are indicated under the `units` attribute. Structure of the file: ``` . ├── model_parameters <- parameters used in the model | ├── atmosphere | | └── eddy_mode <- (scalar string) model eddy mode | ├── clouds | | ├── fraction <- (scalar float) model cloud fraction | | ├── mode <- (scalar string) model cloud mode | | ├── particle_density | | | ├── cloud1 <- (scalar float) cloud 1 particle density | | | ├── ... | | | └── cloudn | | ├── particle_radius | | | ├── cloud1 <- (scalar float) cloud 1 particle radius | | | ├── ... | | | └── cloudn | | ├── reference_wavenumber | | | ├── cloud1 <- (scalar float) cloud 1 reference wavenumber | | | ├── ... | | | └── cloudn | | └── sedimentation_parameter | | ├── cloud1 <- (scalar float) cloud 1 sedimentation param. | | ├── ... | | └── cloudn | ├── light_source | | ├── effective_temperature <- (scalar float) light source T_eff | | ├── radius <- (scalar float) light source radius | | ├── range <- (scalar float) light source range | | └── spectral_irradiance <- (scalar float) light source irradiance | ├── retrieval | | ├── chemistry_iteration_interval <- (scalar integer) | | ├── cloud_iteration_interval <- (scalar integer) | | ├── flux_error_bottom <- (scalar float) | | ├── flux_error_top <- (scalar float) | | ├── level_bottom <- (scalar integer) lowest level of retrieval | | ├── level_top <- (scalar integer) highest level of retrieval | | ├── n_burn_iterations <- (scalar integer) | | ├── n_iterations <- (scalar integer) | | ├── n_non_adiabatic_iterations <- (scalar integer) | | ├── pressure_apriori <- (array float) pressures used in a-priori | | ├── smoothing_bottom <- (scalar float) | | ├── smoothing_top <- (scalar float) | | ├── temperature_apriori <- (array float) temperatures used in a-priori | | ├── tolerance <- (scalar float) | | └── weight_apriori <- (scalar float) | ├── species | | ├── absorber_is_at_equilibrium | | | ├── abs1 <- (scalar string) (T|F) if T, abs1 is at eq. | | | ├── ... | | | └── absn | | ├── collision_induced_absorptions <- (scalar string) CIAs in model | | ├── elemental_abundances | | | ├── Al <- (scalar float) Al/H ratio in model | | | ├── ... | | | └── Zn | | └── solar_elemental_abundances | | ├── Al <- (scalar float) Al/H solar ratio | | ├── ... | | └── Zn | └── target | ├── equatorial_radius_1e5Pa <- (scalar float) r_eq at 10^5 Pa | ├── internal_temperature <- (scalar float) | ├── latitude <- (scalar float) | ├── mass <- (scalar float) | ├── polar_radius_1e5Pa <- (scalar float) r_pol at 10^5 Pa | └── radius_1e5Pa <- (scalar float) radius at 10^5 Pa └── outputs <- model output ├── layers | ├── clouds | | ├── opacity | | | ├── cloud1 <- (array float) cloud 1 tau at reference_wavenumber | | | ├── ... | | | └── cloudn | | ├── particle_radius | | | ├── cloud1 <- (array float) cloud 1 particle radius | | | ├── ... | | | └── cloudn | | └── volume_mixing_ratio | | | ├── cloud1 <- (array float) cloud 1 vmr | | | ├── ... | | | └── cloudn | ├── condensates | | ├── pressure_condensation | | | ├── cond1 <- (scalar float) pressure of condensation of condensate 1 | | | ├── ... | | | └── condn | | ├── volume_mixing_ratio_condensation | | | ├── cond1 <- (scalar float) vmr at condensation of condensate 1 | | | ├── ... | | | └── condn | | └── volume_mixing_ratio_saturation | | ├── cond1 <- (array float) saturation vmr of condensate 1 | | ├── ... | | └── condn | ├── eddy_diffusion_coefficient <- (array float) Kzz in layers | ├── gravity <- (array float) gravity in layers | ├── isobaric_molar_heat_capacity<- (array float) C_p in layers | ├── molar_mass <- (array float) molar mass in layers | ├── pressure <- (array float) pressure in layers | ├── temperature <- (array float) temperature in layers | └── volume_mixing_ratios | ├── absorbers | | ├── abs1 <- (array float) vmr of absorbing gas 1 | | ├── ... | | └── absn | ├── elements_gas_phase | | ├── Al <- (array float) weighted sum of the vmr of all gases containing element Al (ex. 0.7 H2, 0.1 H = 1.4 + 0.1 H) | | ├── ... | | └── Zn | └── gases | ├── gas1 <- (array float) vmr of non-absorbing gas 1 | ├── ... | └── gasn ├── levels | ├── altitude <- (array float) altitude in levels | ├── delta_temperature_convection<- (array float) difference of temperature due to convection | ├── gradiant_temperature <- (array float) T gradiant | ├── is_convective <- (array integer) (0|1) if 1, convection is occurring at the level | ├── kernel_temperature <- (2D-array float) matrix K of retrieval | ├── pressure <- (array float) pressure in levels | ├── radiosity_convective <- (array float) radiosity due to convection | ├── radiosity_error <- (array float) error on radiosity | ├── radiosity_internal <- (array float) internal radiosity | ├── temperature <- (array float) temperature in levels | ├── temperature_adiabatic <- (array float) adiabatic temperature in levels | ├── temperature_uncertainty <- (array float) uncertainty on temperatures | └── temperature_uncertainty_b <- (array float) variant of the uncertainty on temperatures ├── run_quality | ├── actual_internal_temperature <- (scalar float) actual T_int of the planet at the end of the run | ├── chi2_retrieval <- (scalar float) reduced chi2 of the retrieval | ├── delta_chi2_retrieval <- (scalar float) relative difference between the red. chi2 and the red. chi2 at the previous iteration | ├── delta_temperature <- (array float) difference between the temperature and the temperature at the previous iteration | └── radiosity_actual_target_ratio <- (scalar float) ratio of the actual radiosity of the planet at the end of the run and the targeted radiosity (calculated with internal_temperature in input) └── spectra ├── emission | ├── contributions | | ├── abs1 <- (array float) contribution of absorbing gas 1 + CIA + Rayleigh | | ├── ... | | ├── absn | | ├── cia_rayleigh <- (array float) contribution of CIA + Rayleigh | | └── thermal <- (array float) thermal contribution + CIA + Rayleigh | └── spectral_radiosity <- (array float) total spectral radiosity ├── flux | ├── spectral_flux <- (array float) spectral flux | ├── spectral_flux_clear <- (array float) spectral flux without clouds | └── spectral_flux_cloud <- (array float) spectral flux with full cloud coverage ├── transmission | ├── contributions | | ├── abs1 <- (array float) contribution of absorbing gas 1 + CIA + Rayleigh | | ├── ... | | ├── absn | | ├── cia_rayleigh <- (array float) contribution of CIA + Rayleigh | | └── clouds <- (array float) cloud contribution + CIA + Rayleigh | ├── derivative <- (2D-array float) derivative of the transmission spectrum | ├── transit_depth <- (array float) | ├── transit_depth_clear <- (array float) transit depth without clouds | ├── transit_depth_full_cover<- (array float) transit depth with full coverage | └── spectral_radiosity <- (array float) total spectral radiosity └── wavenumber <- (array float) wavenumber ``` # Code **This page is a work in progress** In order to have information on the different functions used in the code and their parameters, we you can look at the 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