Deprecate skl BGC option without removing code yet

Refactor bgc_tracer_type initialization in CICE ice_init_column.F90,
subroutine init_zbgc, fixes implementation bug

cicecore/shared/ice_init_column.F90

@@ -55,27 +55,6 @@ module ice_init_column
          nitratetype        , ammoniumtype       , silicatetype,  &
          dmspptype          , dmspdtype          , humtype
 
-      real (kind=dbl_kind), dimension(icepack_max_dic) :: &
-         dictype
-
-      real (kind=dbl_kind), dimension(icepack_max_algae) :: &
-         algaltype   ! tau_min for both retention and release
-
-      real (kind=dbl_kind), dimension(icepack_max_doc) :: &
-         doctype
-
-      real (kind=dbl_kind), dimension(icepack_max_don) :: &
-         dontype
-
-      real (kind=dbl_kind), dimension(icepack_max_fe) :: &
-         fedtype
-
-      real (kind=dbl_kind), dimension(icepack_max_fe) :: &
-         feptype
-
-      real (kind=dbl_kind), dimension(icepack_max_aero) :: &
-         zaerotype
-
       real (kind=dbl_kind) :: &
           grid_o, l_sk, grid_o_t, initbio_frac, &
           frazil_scav, grid_oS, l_skS, &
@@ -1419,6 +1398,16 @@ subroutine input_zbgc
       ! biogeochemistry
       !-----------------------------------------------------------------
 
+      ! deprecate skl bgc (Aug 2024)
+      ! no skl code removed yet
+      if (skl_bgc) then
+         if (my_task == master_task) then
+            write(nu_diag,*) 'ERROR: skl_bgc is not validate and temporarily DEPRECATED'
+            write(nu_diag,*) 'ERROR: if you would like to use skl_bgc, please contact the Consortium'
+            abort_flag = 102
+         endif
+      endif
+
       if (.not. tr_brine) then
          if (solve_zbgc) then
             if (my_task == master_task) then
@@ -2399,6 +2388,27 @@ subroutine init_zbgc
          tr_bgc_DON,    tr_bgc_Fe,    tr_zaero,     &
          tr_bgc_hum
 
+      real (kind=dbl_kind), dimension(icepack_max_dic) :: &
+         dictype
+
+      real (kind=dbl_kind), dimension(icepack_max_algae) :: &
+         algaltype   ! tau_min for both retention and release
+
+      real (kind=dbl_kind), dimension(icepack_max_doc) :: &
+         doctype
+
+      real (kind=dbl_kind), dimension(icepack_max_don) :: &
+         dontype
+
+      real (kind=dbl_kind), dimension(icepack_max_fe) :: &
+         fedtype
+
+      real (kind=dbl_kind), dimension(icepack_max_fe) :: &
+         feptype
+
+      real (kind=dbl_kind), dimension(icepack_max_aero) :: &
+         zaerotype
+
       real (kind=dbl_kind) :: &
          initbio_frac, &
          frazil_scav
@@ -2501,13 +2511,29 @@ subroutine init_zbgc
          stat=ierr)
       if (ierr/=0) call abort_ice(subname//' Out of Memory')
 
-      R_C2N(1) = ratio_C2N_diatoms
-      R_C2N(2) = ratio_C2N_sp
-      R_C2N(3) = ratio_C2N_phaeo
-
-      R_chl2N(1) = ratio_chl2N_diatoms
-      R_chl2N(2) = ratio_chl2N_sp
-      R_chl2N(3) = ratio_chl2N_phaeo
+      R_C2N(1)     = ratio_C2N_diatoms
+      R_C2N(2)     = ratio_C2N_sp
+      R_C2N(3)     = ratio_C2N_phaeo
+
+      R_chl2N(1)   = ratio_chl2N_diatoms
+      R_chl2N(2)   = ratio_chl2N_sp
+      R_chl2N(3)   = ratio_chl2N_phaeo
+
+      algaltype(1) = algaltype_diatoms
+      algaltype(2) = algaltype_sp
+      algaltype(3) = algaltype_phaeo
+      dictype(:)   = -c1
+      doctype(1)   = doctype_s
+      doctype(2)   = doctype_l
+      dontype(1)   = dontype_protein
+      fedtype(1)   = fedtype_1
+      feptype(1)   = feptype_1
+      zaerotype(1) = zaerotype_bc1
+      zaerotype(2) = zaerotype_bc2
+      zaerotype(3) = zaerotype_dust1
+      zaerotype(4) = zaerotype_dust2
+      zaerotype(5) = zaerotype_dust3
+      zaerotype(6) = zaerotype_dust4
 
       !-----------------------------------------------------------------
       ! assign tracer dependencies
@@ -2837,6 +2863,7 @@ subroutine init_zbgc
          write(nu_diag,1000) ' frazil_scav               = ', frazil_scav
 
       endif  ! skl_bgc or solve_bgc
+      call flush_fileunit(nu_diag)
       endif  ! master_task
 
  1000    format (a30,2x,f9.2)  ! a30 to align formatted, unformatted statements
@@ -2897,6 +2924,10 @@ subroutine init_bgc_trcr(nk,              nt_fbri,       &
 
       bgc_tracer_type(nlt_bgc) = bgctype
 
+      if (my_task == master_task) then
+         write(nu_diag,*) subname,'bgc_tracer_type',nlt_bgc,bgc_tracer_type(nlt_bgc)
+      endif
+
       if (nk > 1) then ! include vertical bgc in snow
          do k = nk, nk+1
             trcr_depend  (nt_bgc + k  ) = 2 ! snow volume

configuration/scripts/tests/base_suite.ts

@@ -57,9 +57,9 @@ restart        gx3     8x2        modal
 smoke          gx3     8x2        bgcz,diag1,run5day
 smoke          gx3     8x2        jra55do
 smoke          gx3     8x2        bgczm,diag1,debug
-smoke          gx3     8x1        bgcskl,diag1,debug
+#smoke          gx3     8x1        bgcskl,diag1,debug
 #smoke          gx3     4x1       bgcz,thread        smoke_gx3_8x2_bgcz
-restart        gx1     4x2        bgcsklclim,medium
+#restart        gx1     4x2        bgcsklclim,medium
 restart        gx1     8x1        bgczclim,medium
 smoke          gx1    24x1        medium,run90day,yi2008
 smoke          gx1    24x1        medium,run90day,yi2008,jra55do

configuration/scripts/tests/io_suite.ts

@@ -9,8 +9,8 @@ restart        gx3     8x4        gx3ncarbulk,alt04,histall,iobinary,precision8
 restart        gx3     4x4        gx3ncarbulk,alt05,histall,iobinary
 restart        gx3    14x2        gx3ncarbulk,alt06,histall,iobinary,precision8
 restart        gx3    14x2        gx3ncarbulk,alt07,histall,iobinary,precision8
-restart        gx3    32x1        gx3ncarbulk,bgcz,histall,iobinary,precision8
-restart        gx3    16x2        gx3ncarbulk,bgcskl,histall,iobinary
+#restart        gx3    32x1        gx3ncarbulk,bgcz,histall,iobinary,precision8
+#restart        gx3    16x2        gx3ncarbulk,bgczm,histall,iobinary
 restart        gx3    14x2        gx3ncarbulk,isotope,histall,iobinary,precision8
 restart        gx3    16x2        gx3ncarbulk,fsd12,histall,iobinary
 restart        gx3     8x4        gx3ncarbulk,debug,histall,iobinary,precision8,histinst
@@ -24,7 +24,7 @@ restart        gx3     8x4        alt05,histall,ionetcdf,iocdf2
 restart        gx3    16x2        alt06,histall,ionetcdf,iocdf5,precision8
 restart        gx3    16x2        alt07,histall,ionetcdf,iohdf5,precision8
 restart        gx3    30x1        bgczm,histall,ionetcdf,iocdf1
-restart        gx3    15x2        bgcskl,histall,ionetcdf,iocdf2,precision8
+restart        gx3    15x2        bgcz,histall,ionetcdf,iocdf2,precision8
 restart        gx3    31x1        isotope,histall,ionetcdf,iocdf5,precision8
 restart        gx3    14x2        fsd12,histall,ionetcdf,iohdf5
 restart        gx3    32x1        debug,histall,ionetcdf,iohdf5,histinst
@@ -39,7 +39,7 @@ restart        gx3     8x4        alt05,histall,iopio1,iopnetcdf5,precision8
 restart        gx3    32x1        alt06,histall,iopio1,iocdf1
 restart        gx3    32x1        alt07,histall,iopio1,iocdf2,precision8
 restart        gx3    16x2        bgczm,histall,iopio1,iocdf5,precision8
-restart        gx3    30x1        bgcskl,histall,iopio1,iohdf5,precision8
+restart        gx3    30x1        bgcz,histall,iopio1,iohdf5,precision8
 restart        gx3     8x4        isotope,histall,iopio1,iopnetcdf1
 restart        gx3    12x2        fsd12,histall,iopio1,iopnetcdf2
 restart        gx3    16x2        debug,histall,iopio1,iopnetcdf5,histinst
@@ -54,7 +54,7 @@ restart        gx3     8x4        alt05,histall,iopio2,iocdf5
 restart        gx3    16x2        alt06,histall,iopio2,iohdf5,iohdf5opts
 restart        gx3    16x2        alt07,histall,iopio2,iopnetcdf1
 restart        gx3    16x2        bgczm,histall,iopio2,iopnetcdf2
-restart        gx3    30x1        bgcskl,histall,iopio2,iopnetcdf5
+restart        gx3    30x1        bgcz,histall,iopio2,iopnetcdf5
 restart        gx3     8x4        isotope,histall,iopio2,iohdf5,precision8
 restart        gx3    12x2        fsd12,histall,iopio2,iocdf1,precision8
 restart        gx3    16x2        debug,histall,iopio2,iocdf2,histinst,precision8