update namelists and ancils -- still need to get the correct init con…

…d for MEDUSA. try with UKESM for a test

cfgs/GLOBAL_QCO_MEDUSA/eORCA1/namelist_medusa_cfg

@@ -1,13 +1,17 @@
 &nammsa_ctl
    ln_msa_carbchem     = .true.    !! activates Carbone cycle
    ln_msa_avgqsr       = .true.    !! biology sees daily avg light
-   ln_msa_ccd          = .false.   !! ?? - check
+   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
 /
@@ -30,7 +34,7 @@
    !___________!_________________________!___________________!___________!_____________!________!___________!__________________!__________!_______________!
    !           !  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_dust =       'mahowald.eORCA025_4.2.nc' ,  -1          , 'dust'    ,   .true.    , .true. , 'yearly'  ,    ''            ,    ''    ,    ''
+   sn_dust =       'mahowald.orca100_ext_nh.nc' ,  -1             , 'dust' ,   .true.    , .true. , 'yearly'  ,    ''            ,    ''    ,    ''
 /
 &nammsa_river        
    ln_read_rivn   = .true.
@@ -46,9 +50,9 @@
    !___________!_________________________!___________________!___________!_____________!________!___________!__________________!__________!_______________!
    !           !  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_riv_n  =  'river42_tot_N_flux_LS200km_SP10_5ITER_ORCA025.nc'    ,  -12 , 'RIV_N'   ,   .true.  , .true. , 'yearly'  ,    ''            ,    ''    ,    ''
-   sn_riv_s  =  'river42_tot_Si_flux_LS200km_SP10_5ITER_ORCA025.nc'   ,  -12 , 'RIV_Si'  ,   .true.  , .true. , 'yearly'  ,    ''            ,    ''    ,    ''
-   sn_riv_c  =  'river42_total_DIC_flux_LS200km_SP10_5ITER_ALIGN_ORCA025.nc',  -12 , 'RIV_C'   ,   .true.  , .true. , 'yearly'  ,    ''            ,    ''    ,    ''
-   sn_riv_a  =  'river42_total_ALK_flux_LS200km_SP10_5ITER_ALIGN_ORCA025.nc',  -12 , 'RIV_ALK' ,   .true.  , .true. , 'yearly'  ,    ''            ,    ''    ,    ''
+   sn_riv_n  =  'river_total_N_flux_IT03_SP10_eORCA100.nc'         ,  -12 , 'RIV_N'   ,   .false.  , .true. , 'yearly'  ,    ''            ,    ''    ,    ''
+   sn_riv_s  =  'river_inorg_Si_flux_IT03_SP10_eORCA100.nc'        ,  -12 , 'RIV_SI'  ,   .false.  , .true. , 'yearly'  ,    ''            ,    ''    ,    ''
+   sn_riv_c  =  'river_total_DIC_flux_IT03_SP10_OBfix_eORCA100.nc' ,  -12 , 'RIV_C' ,   .false.  , .true. , 'yearly'  ,    ''            ,    ''    ,    ''
+   sn_riv_a  =  'river_total_ALK_flux_IT03_SP10_OBfix_eORCA100.nc' ,  -12 , 'RIV_ALK' ,   .false.  , .true. , 'yearly'  ,    ''            ,    ''    ,    ''
 /
 

cfgs/GLOBAL_QCO_MEDUSA/eORCA1/namelist_top_cfg

@@ -46,12 +46,12 @@
 !
 !                !  file name               ! frequency (hours) ! variable   ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation !
 !                !                          !  (if <0  months)  !   name     !   (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  !
-   sn_trcdta(7)  = 'eORCA025_v4.2_DIN.nc' , -12       ,  'DIN'      ,  .false.    , .true. , 'yearly'  , '', '' ,  ''
-   sn_trcdta(8)  = 'eORCA025_v4.2_SIL.nc' , -12       ,  'SIL'      ,  .false.    , .true. , 'yearly'  , '', '' ,  ''
-   sn_trcdta(9)  = 'eORCA025_v4.2_FER.nc' , -12       ,  'FER'      ,  .false.    , .true. , 'yearly'  , '', '' ,  ''
-   sn_trcdta(13) = 'eORCA025_v4.2_DIC.nc' , -12       ,  'DIC'      ,  .false.    , .true. , 'yearly'  , '', '' ,  ''
-   sn_trcdta(14) = 'eORCA025_v4.2_ALK.nc' , -12       ,  'ALK'      ,  .false.    , .true. , 'yearly'  , '', '' ,  ''
-   sn_trcdta(15) = 'eORCA025_v4.2_OXY.nc' , -12       ,  'OXY'      ,  .false.    , .true. , 'yearly'  , '', '' ,  ''
+   sn_trcdta(7)  = 'NPD_ORCA1_MEDUSA_INIT.nc' , -12       ,  'TRNDIN'      ,  .false.    , .true. , 'yearly'  , '', '' ,  ''
+   sn_trcdta(8)  = 'NPD_ORCA1_MEDUSA_INIT.nc' , -12       ,  'TRNSIL'      ,  .false.    , .true. , 'yearly'  , '', '' ,  ''
+   sn_trcdta(9)  = 'NPD_ORCA1_MEDUSA_INIT.nc' , -12       ,  'TRNFER'      ,  .false.    , .true. , 'yearly'  , '', '' ,  ''
+   sn_trcdta(13) = 'NPD_ORCA1_MEDUSA_INIT.nc' , -12       ,  'TRNDiC'      ,  .false.    , .true. , 'yearly'  , '', '' ,  ''
+   sn_trcdta(14) = 'NPD_ORCA1_MEDUSA_INIT.nc' , -12       ,  'TRNALK'      ,  .false.    , .true. , 'yearly'  , '', '' ,  ''
+   sn_trcdta(15) = 'NPD_ORCA1_MEDUSA_INIT.nc' , -12       ,  'TRNOXY'      ,  .false.    , .true. , 'yearly'  , '', '' ,  ''
 !
   cn_dir        =  './INPUT/INIT_MEDUSA/' !  root directory for the location of the data files
   rn_trfac(7)   =   1.0      !  multiplicative factor

data/INPUT_eORCA1_Anemone/INIT_MEDUSA

@@ -0,0 +1 @@
+/dssgfs01/scratch/jpp1m13/ANCIL4.2/ORCA1/FILES/