Documentation.md

@@ -268,10 +268,22 @@ The `clouds_parameters` section handles the clouds settings. The cloud optical c
     - 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.
@@ -311,6 +323,10 @@ The `retrieval_parameters` section handles the retrieval/inversion settings.
     - 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)
@@ -330,6 +346,10 @@ The `retrieval_parameters` section handles the retrieval/inversion settings.
 
 ## 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
@@ -342,6 +362,10 @@ The `options` section handles the output options settings.
     - 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
@@ -503,7 +527,7 @@ Structure of the file:
     |           ├── ...
     |           └── gasn
     ├── levels
-    |   ├── altitude                    <- (array float) atltitude in 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
@@ -516,6 +540,12 @@ Structure of the file:
     |   ├── 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 chi2 and the 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