• MEDUSA Guide
  • Chlorophyll and light -- the different light settings of MEDUSA

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.