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