Documentation.md

@@ -10,7 +10,7 @@ Summary:
     - [retrieval_parameters](#retrieval_parameters)
     - [options](#options)
     - [paths](#paths)
-- [Output file (HDF5)](#output-file-(hdf5))
+- [Output file (HDF5)](#output-file-hdf5)
 - [Code](#code)
 
 # Input file
@@ -383,7 +383,61 @@ The `paths` section handles the output paths settings.
     - e.g. `path_outputs = '../outputs/exorem/'`.
 
 # Output file (HDF5)
+Struture 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
+└── outputs                     <- put here unformatted data
 
+```
 
 # Code
 **This page is a work in progress**