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Update MEDUSA Guide some useful explanations authored by julpal's avatar julpal
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# MEDUSA Guide
......@@ -28,47 +27,65 @@ NEMO can use the BGC model's Chl or not. The different options can be set in NEM
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```
The different possibilities are :
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 : \
- 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 : \
- 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 : \
this option is to be found in MEDUSA's namelist : nammsa_ctl
```
&nammsa_ctl
ln_msa_carbchem = .true. !! activates Carbone cycle
ln_msa_avgqsr = .true. !! biology sees daily avg light
ln_msa_ccd = .false. !! reads ccd file to init ccd field.
ln_msa_preico2 = .false. !! atm co2 forced at pre-ind level
ln_msa_ukesm_cpl = .false. !! activate coupling in MEDUSA with UKESM.
ln_msa_omipdic = .false. !! 2 dic pre-ind and date-related
ln_msa_zmp = .false. !! switch to Tom's Oithona + 2 very fast detritus
ln_msa_noco2flux = .false. !! debug - cut sea-air co2 fluxes
ln_msa_debug = .false. !! add lots of debug print statements
ln_msa_nancheck = .false. !! checks if any nans in bio 3D fields
ln_msa_check_n_fix = .false. !! check and exceptionally fix crazy
!! values for DIC, ALK, T, and S.
!! avoids carb chem crashes
ln_msa_kill_medusa = .false. !! debug - no bio sources and sinks
ln_msa_no_detsink = .false. !! debug - poc don't sink
ln_msa_ice_frac = .true. !! mask light with ice fraction
ln_msa_nemo_qsr = .true. !! use 3D light field attenuated
!! from NEMO if TRUE
/
```
Set `ln_mas_qsr` to `.true.`
6. To couple light and chl without using NEMO's *all* *included* subroutine,
Simply do both 3. and 5. :
- set `ln_qsr_rgb` to `.true.`
- and `nn_chldta` to 3
- and `ln_msa_qsr` to `.true.`
\ No newline at end of file
1. NEMO sees a flat constant chl :
- set `ln_qsr_rgb` to `.true.`
- and `nn_chldta` to 0
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 :
- 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 :
this option is to be found in MEDUSA's namelist : nammsa_ctl
```
&nammsa_ctl
ln_msa_carbchem = .true. !! activates Carbone cycle
ln_msa_avgqsr = .true. !! biology sees daily avg light
ln_msa_ccd = .false. !! reads ccd file to init ccd field.
ln_msa_preico2 = .false. !! atm co2 forced at pre-ind level
ln_msa_ukesm_cpl = .false. !! activate coupling in MEDUSA with UKESM.
ln_msa_omipdic = .false. !! 2 dic pre-ind and date-related
ln_msa_zmp = .false. !! switch to Tom's Oithona + 2 very fast detritus
ln_msa_noco2flux = .false. !! debug - cut sea-air co2 fluxes
ln_msa_debug = .false. !! add lots of debug print statements
ln_msa_nancheck = .false. !! checks if any nans in bio 3D fields
ln_msa_check_n_fix = .false. !! check and exceptionally fix crazy
!! values for DIC, ALK, T, and S.
!! avoids carb chem crashes
ln_msa_kill_medusa = .false. !! debug - no bio sources and sinks
ln_msa_no_detsink = .false. !! debug - poc don't sink
ln_msa_ice_frac = .true. !! mask light with ice fraction
ln_msa_nemo_qsr = .true. !! use 3D light field attenuated
!! from NEMO if TRUE
/
```
Set `ln_mas_qsr` to `.true.`
6. To couple light and chl without using NEMO's *all* *included* subroutine,
Simply do both 3. and 5. :
- 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.`
\ No newline at end of file