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MEDUSA Guide some useful explanations

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 :

  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.

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.
  2. 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.