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MEDUSA Guide some useful explanations

MEDUSA Guide
- Chlorophyll and light

MEDUSA Guide

Here are some explanations on how to use some functionalities of MEDUSA.

Chlorophyll and light

The different light settings of MEDUSA

NEMO-MEDUSA enables you to use different light-Chl configurations.
NEMO can use the BGC model's Chl or not. The different options can be set in NEMO's namelist_cfg : namtra_qsr

!-----------------------------------------------------------------------
&namtra_qsr    !   penetrative solar radiation                          (ln_traqsr =T)
!-----------------------------------------------------------------------
   !                       !  type of penetration                        (default: NO selection)
   ln_qsr_rgb  = .true.      !  RGB light penetration (Red-Green-Blue)
   ln_qsr_2bd  = .false.      !  2BD light penetration (two bands)
   ln_qsr_bio  = .false.      !  bio-model light penetration
   !                       !  RGB & 2BD choices:
   nn_chldta   =      3       !  RGB : Chl data (=1) or cst value (=0)
   cn_dir      = '/work/n01/shared/julpal/ANCIL4.2/'      !  root directory for the chlorophyl data location
   !___________!_________________________!___________________!___________!_____________!________!___________!__________________!__________!_______________!
   !           !  file name                           ! frequency (hours) ! variable  ! time interp.!  clim  ! 'yearly'/ ! weights filename                  ! rotation ! land/sea mask !
   !           !                                      !  (if <0  months)  !   name    !   (logical) !  (T/F) ! 'monthly' !                  ! pairing  !    filename   !
   sn_chl      ='merged_ESACCI_BIOMER4V1R1_CHL_REG05' , -1.              , 'CHLA'     , .true.     , .true.     , 'yearly'  , 'weights_reg05_2_eorca1_bilinear.nc'  , ''       , ''
/

The different possibilities are :

NEMO sees a flat constant chl :
- set ln_qsr_rgb to .true.
- and nn_chldta to 0
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.
For NEMO to see MEDUSA's chl :
- set ln_qsr_rgb to .true.
- and nn_chldta to 3
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.

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.

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 :

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.
The light the model phytoplankton sees in the partially ice-covered regions is an average of ice-free and ice-covered light; whereas, in reality, the phytoplankton should 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.

Daily cycle or Daily averaged light

By Default, MEDUSA should be run with Daily averaged light.
All chl and Production paramaters are tuned for an averaged light.
You can double check it's done this way by making sure that ln_msa_avgqsr in nammsa_ctl is set to .true.

If you use the fully coupled chl-light scheme, make also sure that ln_trcdc2dm is set to .true. (dc2dm for "Daily Cycle to Daily Mean"
ln_trcdc2dm can be found in namtrc_dcy in the namelist_top

!-----------------------------------------------------------------------
&namtrc_dcy      !  Diurnal cycle
!-----------------------------------------------------------------------
   ln_trcdc2dm   =  .true.   !  Diurnal cycle for TOP
/

If, for some reason you need the light daily cycle, set ln_msa_avgqsr and ln_trcdc2dm to .false. (ln_trcdc2dm, should not be necessary, but, i mention it just for good measure - can't be too prudent)