Documentation.md

+# 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.
+
+- `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.
+- `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.
+- `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.
+- `output_files_suffix`
+    - string
+    - suffix of the output files
+    - e.g. with `output_files_suffix = 'example'`, the output files will be _YYY_example.dat_, where _YYY_ are the output files prefix.
+
+## target_parameters
+The `target_parameters` 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 will be derived from `target_equatorial_radius` and `target_mass`. If True, the equatorial gravity at 1 bar will be 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 temperature of the target
+    - e.g. `target_internal_temperature = 500`. This is the temperature derived from the radiosity 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.
+
+# 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 docstrings in the source code.
\ No newline at end of file