Documentation.md

@@ -7,7 +7,6 @@ Below is the complete list of headers and variables as well as an extended descr
 
 ## 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
@@ -26,7 +25,7 @@ The `output_files` section allows you to personalize the names of the output fil
     - 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.
+The `target_parameters` section handles the target (planet) settings.
 
 - `use_gravity`
     - boolean
@@ -62,13 +61,63 @@ The `target_parameters` handles the target (planet) settings.
     - 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`.
+    - (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 directly calculated from `use_light_source_spectrum`.
+- `use_irradiation`
+    - 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 will be 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`]()).
+
 # Code
 **This page is a work in progress**