MEDUSA-Guide-some-useful-explanations.md

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 # MEDUSA Guide 
@@ -28,21 +27,21 @@ NEMO can use the BGC model's Chl or not. The different options can be set in NEM
 /
 ``` 
 The different possibilities are :   
-1. NEMO sees a flat constant chl :  \
+1.  NEMO sees a flat constant chl :  
     - set `ln_qsr_rgb` to `.true.`
     - and `nn_chldta` to 0
-2. if you want NEMO to see a climatology :  \
+1.  If you want NEMO to see a climatology :  
     - set `ln_qsr_rgb` to `.true.`
     - and `nn_chldta` to 1 or 2 (1 for surface chl climatology; 2 for 3D chl climatology)
     - Fill `sn_chl` and `cn_dir` to point to the right chl climatology file.
-3. For NEMO to see MEDUSA's chl :  \
+3.  For NEMO to see MEDUSA's chl :  
     - set `ln_qsr_rgb` to `.true.`
     - and `nn_chldta` to 3 
 4.  For NEMO light and MEDUSA's Chl to be fully and properly coupled :
     - set `ln_qsr_bio` to `.true.` instead of `ln_qsr_rgb`.  
       That way, NEMO will use its own `trcopt` subroutine, and calculate the PAR carefully in 3 bands.  \
     {- ** WARNING ** -} : MEDUSA is not yet tuned for this option.
-5. If you want MEDUSA to use NEMO's attenuated light :  \ 
+5.  If you want MEDUSA to use NEMO's attenuated light :  
     this option is to be found in MEDUSA's namelist :  nammsa_ctl  
     ``` 
     &nammsa_ctl
@@ -72,3 +71,21 @@ The different possibilities are :
     - set `ln_qsr_rgb` to `.true.`
     - and `nn_chldta` to 3 
     - and `ln_msa_qsr` to `.true.`
+
+## Correcting light - chl and PP with the ice-fraction 
+
+Just to explain what this is about :\
+In MEDUSA II, the light (`qsr`) that NEMO and MEDUSA get at the surface already take into account the light attenuation for the sea-ice. It sounds reasonable to use this light without correction for the primary production calculations.  
+
+But :   
+1.  Some light manages to cross the fully ice-covered regions of the ocean, especially the Arctic, resulting in a significant chlorophyll concentration in these regions.
+1.  The light the phyto sees in the partially ice-covered regions is an average of ice-free and ice-covered light, whereas, the phyto plankton will grow in the ice-free parts, at full light. The ice-covered regions being assumed to be dark. 
+
+Here we managed to get the right chl and production at full light in partially ice-covered regions, that we then attenuate with the ice-fraction.
+The Arctic light-chl problem is solved in the process.
+
+To include this fix, 
+switch `ln_msa_ice_frac` in the namelist_medusa_cfg to `.true.`
+
+   
+ 
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