From 9f6e8ba253e142cb6d07847cb3acee353c63dbdc Mon Sep 17 00:00:00 2001
From: "jian.kuang" <Jian.Kuang@noaa.gov>
Date: Thu, 10 Sep 2020 14:13:57 -0500
Subject: [PATCH 1/9] CICE6 adoption

---
 sorc/build_fv3_coupled.sh | 2 +-
 sorc/checkout.sh          | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/sorc/build_fv3_coupled.sh b/sorc/build_fv3_coupled.sh
index d33992c74c..5aee3e911e 100755
--- a/sorc/build_fv3_coupled.sh
+++ b/sorc/build_fv3_coupled.sh
@@ -22,6 +22,6 @@ if [ $target = orion ]; then target=orion.intel ; fi
 cd fv3_coupled.fd/
 FV3=$( pwd -P )/FV3
 cd tests/
-./compile.sh "$FV3" "$target" "CCPP=Y SUITES=FV3_GFS_2017_coupled,FV3_GFS_2017_satmedmf_coupled,FV3_GFS_v15p2_coupled MOM6=Y CICE=Y WW3=Y CMEPS=Y" 1
+./compile.sh "$FV3" "$target" "CCPP=Y SUITES=FV3_GFS_2017_coupled,FV3_GFS_2017_satmedmf_coupled,FV3_GFS_v15p2_coupled MOM6=Y CICE6=Y WW3=Y CMEPS=Y" 1
 mv -f fcst_1.exe ../NEMS/exe/nems_fv3_ccpp_mom6_cice5_ww3.x
 
diff --git a/sorc/checkout.sh b/sorc/checkout.sh
index 3a6707ba33..431a3afba8 100755
--- a/sorc/checkout.sh
+++ b/sorc/checkout.sh
@@ -16,7 +16,7 @@ rm -f ${topdir}/checkout-fv3_coupled.log
 if [[ ! -d fv3_coupled.fd ]] ; then
     git clone https://github.com/ufs-community/ufs-s2s-model fv3_coupled.fd >> ${topdir}/checkout-fv3_coupled.log 2>&1
     cd fv3_coupled.fd
-    git checkout ufss2s_cmeps_v0.7 
+    git checkout s2s_prototype5.0
     git submodule update --init --recursive
     cd ${topdir}
 else

From ba4dd520bdfd8f8b2a74bd8864e8171a63d63db8 Mon Sep 17 00:00:00 2001
From: "jian.kuang" <Jian.Kuang@noaa.gov>
Date: Thu, 10 Sep 2020 19:21:44 -0500
Subject: [PATCH 2/9] configuration and workflow update

---
 modulefiles/module_base.orion | 2 +-
 ush/parsing_namelists_CICE.sh | 5 ++---
 workflow/config/fcst.yaml     | 6 ++++++
 3 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/modulefiles/module_base.orion b/modulefiles/module_base.orion
index 4c790db468..2f78059706 100644
--- a/modulefiles/module_base.orion
+++ b/modulefiles/module_base.orion
@@ -50,7 +50,7 @@ module load prod_util/1.2.0
 ##
 module use /apps/contrib/NCEPLIBS/lib/modulefiles
 module load netcdfp/4.7.4.release
-module load esmflocal/8.1.0.21bs.release
+module load esmflocal/8.1.0.27bs.release
 module load post-intel-sandybridge/8.0.5
 
 module load wgrib/2.0.8
diff --git a/ush/parsing_namelists_CICE.sh b/ush/parsing_namelists_CICE.sh
index f80eeecfbf..5b0ee6d3b5 100644
--- a/ush/parsing_namelists_CICE.sh
+++ b/ush/parsing_namelists_CICE.sh
@@ -149,7 +149,6 @@ cat > ice_in <<eof
   , hs1             = 0.03
   , dpscale         = 1.0e-3
   , frzpnd          = 'hlid'
-  , snowinfil       = .true.
   , rfracmin        = 0.15
   , rfracmax        = 1.
   , pndaspect       = 0.8
@@ -197,8 +196,8 @@ cat > ice_in <<eof
     nprocs = $ICEPETS
   , nx_global         = $NX_GLB
   , ny_global         = $NY_GLB
-  , block_size_x      = `expr 2 * $NX_GLB / $ICEPETS`
-  , block_size_y      = `expr $NY_GLB / 2`
+  , block_size_x      = $(( 2 * ( $NX_GLB / $ICEPETS ) ))
+  , block_size_y      = $(( $NY_GLB / 2 ))
   , max_blocks        = -1
   , processor_shape   = 'slenderX2'
   , distribution_type = 'cartesian'
diff --git a/workflow/config/fcst.yaml b/workflow/config/fcst.yaml
index 76543bdf87..7e3af1f4a5 100644
--- a/workflow/config/fcst.yaml
+++ b/workflow/config/fcst.yaml
@@ -64,6 +64,12 @@ config_fcst:
     export NTHREADS_FV3="{doc.fv3_gfs_settings.layout.nth}"
     export memory_fcst="1024M"
 
+    #######################################################################
+    # COUPLING COMPONENTS
+    export OCN_model="{doc.ocn_settings.MOD}"
+    export ICE_model="{doc.ice_settings.MOD}"
+    export WAV_model="{doc.wave_settings.MOD}"
+
     #######################################################################
     # PE Mapping
     export ATMPETS="{doc.fv3_gfs_settings.ATMPETS}"

From f623ddb6091aa7f0029b9e39dc4cb788d22e500a Mon Sep 17 00:00:00 2001
From: "jian.kuang" <Jian.Kuang@noaa.gov>
Date: Fri, 11 Sep 2020 09:59:53 -0500
Subject: [PATCH 3/9] MESHICE file linking

---
 ush/forecast_postdet.sh   | 1 +
 ush/nems_configure.sh     | 2 ++
 workflow/config/fcst.yaml | 1 +
 3 files changed, 4 insertions(+)

diff --git a/ush/forecast_postdet.sh b/ush/forecast_postdet.sh
index a991d28590..3b4acb0e26 100755
--- a/ush/forecast_postdet.sh
+++ b/ush/forecast_postdet.sh
@@ -746,6 +746,7 @@ CICE_postdet()
         echo "Link CICE fixed files"
         $NLN -sf $FIXcice/${ice_grid_file} $DATA/
         $NLN -sf $FIXcice/${ice_kmt_file} $DATA/
+        $NLN -sf $FIXcice/$MESHICE $DATA/
 }
 
 CICE_nml()
diff --git a/ush/nems_configure.sh b/ush/nems_configure.sh
index 840cb685d7..d6ed6a5e5f 100755
--- a/ush/nems_configure.sh
+++ b/ush/nems_configure.sh
@@ -74,6 +74,8 @@ fi
 if [ $cplice = .true. ]; then
 	sed -i -e "s;@\[ice_model\];$ICE_model;g" tmp1
 	sed -i -e "s;@\[ice_petlist_bounds\];$ice_petlist_bounds;g" tmp1
+        sed -i -e "s;@\[MESHICE\];$MESHICE;g" tmp1
+        sed -i -e "s;@\[FHMAX\];$FHMAX_GFS;g" tmp1
 fi
 if [ $cplchem = .true. ]; then
 	sed -i -e "s;@\[chem_model\];gsd;g" tmp1
diff --git a/workflow/config/fcst.yaml b/workflow/config/fcst.yaml
index 7e3af1f4a5..3bc3ce55d8 100644
--- a/workflow/config/fcst.yaml
+++ b/workflow/config/fcst.yaml
@@ -82,6 +82,7 @@ config_fcst:
     # CICE parameters
     export NX_GLB="{doc.ice_settings.NX_GLB}"
     export NY_GLB="{doc.ice_settings.NY_GLB}"
+    export MESHICE="mesh.mx${doc.ice_settings.ICERES}.nc"
 
     if [[ "$machine" == "WCOSS_C" ]]; then
         export memory_fcst="1024M"

From 7034e12d509cef3aba47113192cdd25f09d98ecf Mon Sep 17 00:00:00 2001
From: "jian.kuang" <Jian.Kuang@noaa.gov>
Date: Fri, 11 Sep 2020 10:17:05 -0500
Subject: [PATCH 4/9] update hera module

---
 modulefiles/module_base.hera | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modulefiles/module_base.hera b/modulefiles/module_base.hera
index 32d9c72d5a..6497b80a9d 100644
--- a/modulefiles/module_base.hera
+++ b/modulefiles/module_base.hera
@@ -36,4 +36,4 @@ module load z/1.2.11
 
 #Load from emc.nemspara
 module use -a /scratch1/NCEPDEV/nems/emc.nemspara/soft/modulefiles
-module load esmf/8.0.0
+module load esmflocal/8.1.0.27bs.release

From 20e65f0cd8abdadf4971d3f2ef9ac403f494e2eb Mon Sep 17 00:00:00 2001
From: "jian.kuang" <Jian.Kuang@noaa.gov>
Date: Fri, 11 Sep 2020 10:29:22 -0500
Subject: [PATCH 5/9] remove "," in front of every line of ice_in

---
 ush/parsing_namelists_CICE.sh | 1084 ++++++++++++++++-----------------
 1 file changed, 542 insertions(+), 542 deletions(-)

diff --git a/ush/parsing_namelists_CICE.sh b/ush/parsing_namelists_CICE.sh
index 5b0ee6d3b5..b4bd1b5a37 100644
--- a/ush/parsing_namelists_CICE.sh
+++ b/ush/parsing_namelists_CICE.sh
@@ -4,593 +4,593 @@ CICE_namelists(){
 
 cat > ice_in <<eof  
 &setup_nml
-    days_per_year  = 365
-  , use_leap_years = .true.
-  , year_init      = $year
-  , istep0         = $steps
-  , dt             = $ICETIM
-  , npt            = $npt
-  , ndtd           = 1
-  , runtype        = '$RUNTYPE' 
-  , runid          = 'cpcice' 
-  , ice_ic         = '$iceic'
-  , restart        = .true.
-  , restart_ext    = .false.
-  , use_restart_time = $USE_RESTART_TIME
-  , restart_format = 'nc'
-  , lcdf64         = .false.
-  , numin          = 21
-  , numax          = 89
-  , restart_dir    = './RESTART/'
-  , restart_file   = 'iced'
-  , pointer_file   = './ice.restart_file'
-  , dumpfreq       = '$dumpfreq'
-  , dumpfreq_n     =  $dumpfreq_n
-  , dump_last      = .false.  
-  , bfbflag        = 'off'
-  , diagfreq       = 6
-  , diag_type      = 'file'
-  , diag_file      = 'ice_diag.d'
-  , print_global   = .true.
-  , print_points   = .true.
-  , latpnt(1)      =  90.
-  , lonpnt(1)      =   0.
-  , latpnt(2)      = -65.
-  , lonpnt(2)      = -45.
-  , dbug           = .false.
-  , histfreq       = 'm','d','h','x','x'
-  , histfreq_n     =  0 , 0 , 6 , 1 , 1
-  , hist_avg       = $cice_hist_avg
-  , history_dir    = './history/'
-  , history_file   = 'iceh'
-  , write_ic       = .true.
-  , incond_dir     = './history/'
-  , incond_file    = 'iceh_ic'
-  , version_name   = 'CICE_6.0.2'
+   days_per_year  = 365
+   use_leap_years = .true.
+   year_init      = $year
+   istep0         = $steps
+   dt             = $ICETIM
+   npt            = $npt
+   ndtd           = 1
+   runtype        = '$RUNTYPE' 
+   runid          = 'cpcice' 
+   ice_ic         = '$iceic'
+   restart        = .true.
+   restart_ext    = .false.
+   use_restart_time = $USE_RESTART_TIME
+   restart_format = 'nc'
+   lcdf64         = .false.
+   numin          = 21
+   numax          = 89
+   restart_dir    = './RESTART/'
+   restart_file   = 'iced'
+   pointer_file   = './ice.restart_file'
+   dumpfreq       = '$dumpfreq'
+   dumpfreq_n     =  $dumpfreq_n
+   dump_last      = .false.  
+   bfbflag        = 'off'
+   diagfreq       = 6
+   diag_type      = 'file'
+   diag_file      = 'ice_diag.d'
+   print_global   = .true.
+   print_points   = .true.
+   latpnt(1)      =  90.
+   lonpnt(1)      =   0.
+   latpnt(2)      = -65.
+   lonpnt(2)      = -45.
+   dbug           = .false.
+   histfreq       = 'm','d','h','x','x'
+   histfreq_n     =  0 , 0 , 6 , 1 , 1
+   hist_avg       = $cice_hist_avg
+   history_dir    = './history/'
+   history_file   = 'iceh'
+   write_ic       = .true.
+   incond_dir     = './history/'
+   incond_file    = 'iceh_ic'
+   version_name   = 'CICE_6.0.2'
 /
 
 &grid_nml
-    grid_format  = 'nc'
-  , grid_type    = 'displaced_pole'
-  , grid_file    = '$ice_grid_file'
-  , kmt_file     = '$ice_kmt_file'
-  , use_bathymetry = .false.
-  , kcatbound    = 0
-  , ncat         = 5
-  , nfsd         = 1
-  , nilyr        = 7
-  , nslyr        = 1
-  , nblyr        = 1
-  , nfsd         = 1
+   grid_format  = 'nc'
+   grid_type    = 'displaced_pole'
+   grid_file    = '$ice_grid_file'
+   kmt_file     = '$ice_kmt_file'
+   use_bathymetry = .false.
+   kcatbound    = 0
+   ncat         = 5
+   nfsd         = 1
+   nilyr        = 7
+   nslyr        = 1
+   nblyr        = 1
+   nfsd         = 1
 /
 
 &tracer_nml
-    n_aero       = 1
-  , n_zaero      = 0
-  , n_algae      = 0
-  , n_doc        = 0
-  , n_dic        = 0
-  , n_don        = 0
-  , n_fed        = 0
-  , n_fep        = 0
-  , tr_iage      = .true.
-  , restart_age  = .false.
-  , tr_FY        = .true.
-  , restart_FY   = .false.
-  , tr_lvl       = .true.
-  , restart_lvl  = .false.
-  , tr_pond_cesm = .false.
-  , restart_pond_cesm = .false.
-  , tr_pond_topo = .false.
-  , restart_pond_topo = .false.
-  , tr_pond_lvl  = $tr_pond_lvl
-  , restart_pond_lvl  = $restart_pond_lvl
-  , tr_aero      = .false.
-  , restart_aero = .false.
-  , tr_fsd       = .false.
-  , restart_fsd  = .false.
+   n_aero       = 1
+   n_zaero      = 0
+   n_algae      = 0
+   n_doc        = 0
+   n_dic        = 0
+   n_don        = 0
+   n_fed        = 0
+   n_fep        = 0
+   tr_iage      = .true.
+   restart_age  = .false.
+   tr_FY        = .true.
+   restart_FY   = .false.
+   tr_lvl       = .true.
+   restart_lvl  = .false.
+   tr_pond_cesm = .false.
+   restart_pond_cesm = .false.
+   tr_pond_topo = .false.
+   restart_pond_topo = .false.
+   tr_pond_lvl  = $tr_pond_lvl
+   restart_pond_lvl  = $restart_pond_lvl
+   tr_aero      = .false.
+   restart_aero = .false.
+   tr_fsd       = .false.
+   restart_fsd  = .false.
 /
 
 &thermo_nml
-    kitd              = 1
-  , ktherm            = 1
-  , conduct           = 'MU71'
-  , a_rapid_mode      =  0.5e-3
-  , Rac_rapid_mode    =    10.0
-  , aspect_rapid_mode =     1.0
-  , dSdt_slow_mode    = -5.0e-8
-  , phi_c_slow_mode   =    0.05
-  , phi_i_mushy       =    0.85
-  , sw_redist         = .true.
+   kitd              = 1
+   ktherm            = 1
+   conduct           = 'MU71'
+   a_rapid_mode      =  0.5e-3
+   Rac_rapid_mode    =    10.0
+   aspect_rapid_mode =     1.0
+   dSdt_slow_mode    = -5.0e-8
+   phi_c_slow_mode   =    0.05
+   phi_i_mushy       =    0.85
+   sw_redist         = .true.
 /
 
 &dynamics_nml
-    kdyn            = 1
-  , ndte            = 120
-  , revised_evp     = .false.
-  , kevp_kernel     = 0
-  , brlx            = 300.0
-  , arlx            = 300.0
-  , ssh_stress      = 'coupled'
-  , advection       = 'remap'
-  , kstrength       = 1
-  , krdg_partic     = 1
-  , krdg_redist     = 1
-  , mu_rdg          = 3
-  , Cf              = 17.
-  , Ktens           = 0.
-  , e_ratio         = 2.
-  , basalstress     = .false.
-  , k1              = 8.
-  , coriolis        = 'latitude'
-  , kridge          = 1
-  , ktransport      = 1
+   kdyn            = 1
+   ndte            = 120
+   revised_evp     = .false.
+   kevp_kernel     = 0
+   brlx            = 300.0
+   arlx            = 300.0
+   ssh_stress      = 'coupled'
+   advection       = 'remap'
+   kstrength       = 1
+   krdg_partic     = 1
+   krdg_redist     = 1
+   mu_rdg          = 3
+   Cf              = 17.
+   Ktens           = 0.
+   e_ratio         = 2.
+   basalstress     = .false.
+   k1              = 8.
+   coriolis        = 'latitude'
+   kridge          = 1
+   ktransport      = 1
 /
 
 &shortwave_nml
-    shortwave       = 'dEdd'
-  , albedo_type     = 'default'
-  , albicev         = 0.78
-  , albicei         = 0.36
-  , albsnowv        = 0.98
-  , albsnowi        = 0.70 
-  , ahmax           = 0.3
-  , R_ice           = 0.
-  , R_pnd           = 0.
-  , R_snw           = 1.5
-  , dT_mlt          = 1.5
-  , rsnw_mlt        = 1500.
-  , kalg            = 0.0
+   shortwave       = 'dEdd'
+   albedo_type     = 'default'
+   albicev         = 0.78
+   albicei         = 0.36
+   albsnowv        = 0.98
+   albsnowi        = 0.70 
+   ahmax           = 0.3
+   R_ice           = 0.
+   R_pnd           = 0.
+   R_snw           = 1.5
+   dT_mlt          = 1.5
+   rsnw_mlt        = 1500.
+   kalg            = 0.0
 /
 
 &ponds_nml
-    hp1             = 0.01
-  , hs0             = 0.
-  , hs1             = 0.03
-  , dpscale         = 1.0e-3
-  , frzpnd          = 'hlid'
-  , rfracmin        = 0.15
-  , rfracmax        = 1.
-  , pndaspect       = 0.8
+   hp1             = 0.01
+   hs0             = 0.
+   hs1             = 0.03
+   dpscale         = 1.0e-3
+   frzpnd          = 'hlid'
+   rfracmin        = 0.15
+   rfracmax        = 1.
+   pndaspect       = 0.8
 /
 
 &forcing_nml
-    formdrag        = .false.
-  , atmbndy         = 'default'
-  , calc_strair     = .true.
-  , calc_Tsfc       = .true.
-  , highfreq        = .false.
-  , natmiter        = 5
-  , ustar_min       = 0.0005
-  , emissivity      = 0.95
-  , fbot_xfer_type  = 'constant'
-  , update_ocn_f    = $FRAZIL_FWSALT
-  , l_mpond_fresh   = .false.
-  , tfrz_option     = 'linear_salt'
-  , restart_coszen  = .true.
-  , oceanmixed_ice  = .false.
-  , wave_spec_type  = 'none'
-  , wave_spec_file  = 'unknown_wave_spec_file'
-  , nfreq           = 25
-  , restore_ice     = .false.
-  , restore_ocn     = .false.
-  , trestore        =  90
-  , precip_units    = 'mm_per_month'
-  , default_season  = 'winter'
-  , atm_data_type   = 'ncar'
-  , ocn_data_type   = 'default'
-  , bgc_data_type   = 'default'
-  , fe_data_type    = 'default'
-  , ice_data_type   = 'default'
-  , fyear_init      = 1997
-  , ycycle          = 1
-  , atm_data_format = 'nc'
-  , atm_data_dir    = './INPUT/gx3_forcing_fields.nc'
-  , bgc_data_dir    = 'unknown_bgc_data_dir'
-  , ocn_data_format = 'bin'
-  , ocn_data_dir    = '/unknown_ocn_data_dir'
-  , oceanmixed_file = 'unknown_oceanmixed_file'
+   formdrag        = .false.
+   atmbndy         = 'default'
+   calc_strair     = .true.
+   calc_Tsfc       = .true.
+   highfreq        = .false.
+   natmiter        = 5
+   ustar_min       = 0.0005
+   emissivity      = 0.95
+   fbot_xfer_type  = 'constant'
+   update_ocn_f    = $FRAZIL_FWSALT
+   l_mpond_fresh   = .false.
+   tfrz_option     = 'linear_salt'
+   restart_coszen  = .true.
+   oceanmixed_ice  = .false.
+   wave_spec_type  = 'none'
+   wave_spec_file  = 'unknown_wave_spec_file'
+   nfreq           = 25
+   restore_ice     = .false.
+   restore_ocn     = .false.
+   trestore        =  90
+   precip_units    = 'mm_per_month'
+   default_season  = 'winter'
+   atm_data_type   = 'ncar'
+   ocn_data_type   = 'default'
+   bgc_data_type   = 'default'
+   fe_data_type    = 'default'
+   ice_data_type   = 'default'
+   fyear_init      = 1997
+   ycycle          = 1
+   atm_data_format = 'nc'
+   atm_data_dir    = './INPUT/gx3_forcing_fields.nc'
+   bgc_data_dir    = 'unknown_bgc_data_dir'
+   ocn_data_format = 'bin'
+   ocn_data_dir    = '/unknown_ocn_data_dir'
+   oceanmixed_file = 'unknown_oceanmixed_file'
 /
 
 &domain_nml
-    nprocs = $ICEPETS
-  , nx_global         = $NX_GLB
-  , ny_global         = $NY_GLB
-  , block_size_x      = $(( 2 * ( $NX_GLB / $ICEPETS ) ))
-  , block_size_y      = $(( $NY_GLB / 2 ))
-  , max_blocks        = -1
-  , processor_shape   = 'slenderX2'
-  , distribution_type = 'cartesian'
-  , distribution_wght = 'latitude'
-  , ew_boundary_type  = 'cyclic'
-  , ns_boundary_type  = 'tripole'
-  , maskhalo_dyn      = .false.
-  , maskhalo_remap    = .false.
-  , maskhalo_bound    = .false.
+   nprocs = $ICEPETS
+   nx_global         = $NX_GLB
+   ny_global         = $NY_GLB
+   block_size_x      = $(( 2 * ( $NX_GLB / $ICEPETS ) ))
+   block_size_y      = $(( $NY_GLB / 2 ))
+   max_blocks        = -1
+   processor_shape   = 'slenderX2'
+   distribution_type = 'cartesian'
+   distribution_wght = 'latitude'
+   ew_boundary_type  = 'cyclic'
+   ns_boundary_type  = 'tripole'
+   maskhalo_dyn      = .false.
+   maskhalo_remap    = .false.
+   maskhalo_bound    = .false.
 /
 
 &zbgc_nml
-    tr_brine        = .false.
-  , restart_hbrine  = .false.
-  , tr_zaero        = .false.
-  , modal_aero      = .false.
-  , skl_bgc         = .false.
-  , z_tracers       = .false.
-  , dEdd_algae      = .false.
-  , solve_zbgc      = .false.
-  , bgc_flux_type   = 'Jin2006'
-  , restore_bgc     = .false.
-  , restart_bgc     = .false.
-  , scale_bgc       = .false.
-  , solve_zsal      = .false.
-  , restart_zsal    = .false.
-  , tr_bgc_Nit      = .true.
-  , tr_bgc_C        = .true.
-  , tr_bgc_chl      = .false.
-  , tr_bgc_Am       = .true.
-  , tr_bgc_Sil      = .true.
-  , tr_bgc_DMS      = .false.
-  , tr_bgc_PON      = .true.
-  , tr_bgc_hum      = .true.
-  , tr_bgc_DON      = .false.
-  , tr_bgc_Fe       = .true. 
-  , grid_o          = 0.006
-  , grid_o_t        = 0.006
-  , l_sk            = 0.024
-  , grid_oS         = 0.0
-  , l_skS           = 0.028
-  , phi_snow        = -0.3
-  , initbio_frac    = 0.8
-  , frazil_scav     = 0.8  
-  , ratio_Si2N_diatoms = 1.8                         
-  , ratio_Si2N_sp      = 0.0
-  , ratio_Si2N_phaeo   = 0.0
-  , ratio_S2N_diatoms  = 0.03  
-  , ratio_S2N_sp       = 0.03 
-  , ratio_S2N_phaeo    = 0.03
-  , ratio_Fe2C_diatoms = 0.0033
-  , ratio_Fe2C_sp      = 0.0033
-  , ratio_Fe2C_phaeo   = 0.1
-  , ratio_Fe2N_diatoms = 0.023 
-  , ratio_Fe2N_sp      = 0.023
-  , ratio_Fe2N_phaeo   = 0.7
-  , ratio_Fe2DON       = 0.023
-  , ratio_Fe2DOC_s     = 0.1
-  , ratio_Fe2DOC_l     = 0.033
-  , fr_resp            = 0.05
-  , tau_min            = 5200.0
-  , tau_max            = 173000.0
-  , algal_vel          = 0.0000000111
-  , R_dFe2dust         = 0.035
-  , dustFe_sol         = 0.005
-  , chlabs_diatoms     = 0.03
-  , chlabs_sp          = 0.01
-  , chlabs_phaeo       = 0.05
-  , alpha2max_low_diatoms = 0.8
-  , alpha2max_low_sp      = 0.67
-  , alpha2max_low_phaeo   = 0.67
-  , beta2max_diatoms   = 0.018
-  , beta2max_sp        = 0.0025
-  , beta2max_phaeo     = 0.01
-  , mu_max_diatoms     = 1.44
-  , mu_max_sp          = 0.851
-  , mu_max_phaeo       = 0.851
-  , grow_Tdep_diatoms  = 0.06
-  , grow_Tdep_sp       = 0.06
-  , grow_Tdep_phaeo    = 0.06
-  , fr_graze_diatoms   = 0.0
-  , fr_graze_sp        = 0.1
-  , fr_graze_phaeo     = 0.1
-  , mort_pre_diatoms   = 0.007
-  , mort_pre_sp        = 0.007
-  , mort_pre_phaeo     = 0.007
-  , mort_Tdep_diatoms  = 0.03
-  , mort_Tdep_sp       = 0.03
-  , mort_Tdep_phaeo    = 0.03
-  , k_exude_diatoms    = 0.0
-  , k_exude_sp         = 0.0
-  , k_exude_phaeo      = 0.0
-  , K_Nit_diatoms      = 1.0
-  , K_Nit_sp           = 1.0
-  , K_Nit_phaeo        = 1.0
-  , K_Am_diatoms       = 0.3
-  , K_Am_sp            = 0.3
-  , K_Am_phaeo         = 0.3
-  , K_Sil_diatoms      = 4.0
-  , K_Sil_sp           = 0.0
-  , K_Sil_phaeo        = 0.0
-  , K_Fe_diatoms       = 1.0
-  , K_Fe_sp            = 0.2
-  , K_Fe_phaeo         = 0.1
-  , f_don_protein      = 0.6
-  , kn_bac_protein     = 0.03
-  , f_don_Am_protein   = 0.25
-  , f_doc_s            = 0.4
-  , f_doc_l            = 0.4
-  , f_exude_s          = 1.0
-  , f_exude_l          = 1.0
-  , k_bac_s            = 0.03
-  , k_bac_l            = 0.03
-  , T_max              = 0.0
-  , fsal               = 1.0
-  , op_dep_min         = 0.1
-  , fr_graze_s         = 0.5
-  , fr_graze_e         = 0.5
-  , fr_mort2min        = 0.5
-  , fr_dFe             = 0.3
-  , k_nitrif           = 0.0
-  , t_iron_conv        = 3065.0
-  , max_loss           = 0.9
-  , max_dfe_doc1       = 0.2
-  , fr_resp_s          = 0.75
-  , y_sk_DMS           = 0.5
-  , t_sk_conv          = 3.0
-  , t_sk_ox            = 10.0
-  , algaltype_diatoms  = 0.0
-  , algaltype_sp       = 0.5
-  , algaltype_phaeo    = 0.5
-  , nitratetype        = -1.0
-  , ammoniumtype       = 1.0
-  , silicatetype       = -1.0
-  , dmspptype          = 0.5
-  , dmspdtype          = -1.0
-  , humtype            = 1.0
-  , doctype_s          = 0.5
-  , doctype_l          = 0.5
-  , dontype_protein    = 0.5
-  , fedtype_1          = 0.5
-  , feptype_1          = 0.5
-  , zaerotype_bc1      = 1.0
-  , zaerotype_bc2      = 1.0
-  , zaerotype_dust1    = 1.0
-  , zaerotype_dust2    = 1.0
-  , zaerotype_dust3    = 1.0
-  , zaerotype_dust4    = 1.0
-  , ratio_C2N_diatoms  = 7.0
-  , ratio_C2N_sp       = 7.0
-  , ratio_C2N_phaeo    = 7.0
-  , ratio_chl2N_diatoms= 2.1
-  , ratio_chl2N_sp     = 1.1
-  , ratio_chl2N_phaeo  = 0.84
-  , F_abs_chl_diatoms  = 2.0
-  , F_abs_chl_sp       = 4.0
-  , F_abs_chl_phaeo    = 5.0
-  , ratio_C2N_proteins = 7.0
+   tr_brine        = .false.
+   restart_hbrine  = .false.
+   tr_zaero        = .false.
+   modal_aero      = .false.
+   skl_bgc         = .false.
+   z_tracers       = .false.
+   dEdd_algae      = .false.
+   solve_zbgc      = .false.
+   bgc_flux_type   = 'Jin2006'
+   restore_bgc     = .false.
+   restart_bgc     = .false.
+   scale_bgc       = .false.
+   solve_zsal      = .false.
+   restart_zsal    = .false.
+   tr_bgc_Nit      = .true.
+   tr_bgc_C        = .true.
+   tr_bgc_chl      = .false.
+   tr_bgc_Am       = .true.
+   tr_bgc_Sil      = .true.
+   tr_bgc_DMS      = .false.
+   tr_bgc_PON      = .true.
+   tr_bgc_hum      = .true.
+   tr_bgc_DON      = .false.
+   tr_bgc_Fe       = .true. 
+   grid_o          = 0.006
+   grid_o_t        = 0.006
+   l_sk            = 0.024
+   grid_oS         = 0.0
+   l_skS           = 0.028
+   phi_snow        = -0.3
+   initbio_frac    = 0.8
+   frazil_scav     = 0.8  
+   ratio_Si2N_diatoms = 1.8                         
+   ratio_Si2N_sp      = 0.0
+   ratio_Si2N_phaeo   = 0.0
+   ratio_S2N_diatoms  = 0.03  
+   ratio_S2N_sp       = 0.03 
+   ratio_S2N_phaeo    = 0.03
+   ratio_Fe2C_diatoms = 0.0033
+   ratio_Fe2C_sp      = 0.0033
+   ratio_Fe2C_phaeo   = 0.1
+   ratio_Fe2N_diatoms = 0.023 
+   ratio_Fe2N_sp      = 0.023
+   ratio_Fe2N_phaeo   = 0.7
+   ratio_Fe2DON       = 0.023
+   ratio_Fe2DOC_s     = 0.1
+   ratio_Fe2DOC_l     = 0.033
+   fr_resp            = 0.05
+   tau_min            = 5200.0
+   tau_max            = 173000.0
+   algal_vel          = 0.0000000111
+   R_dFe2dust         = 0.035
+   dustFe_sol         = 0.005
+   chlabs_diatoms     = 0.03
+   chlabs_sp          = 0.01
+   chlabs_phaeo       = 0.05
+   alpha2max_low_diatoms = 0.8
+   alpha2max_low_sp      = 0.67
+   alpha2max_low_phaeo   = 0.67
+   beta2max_diatoms   = 0.018
+   beta2max_sp        = 0.0025
+   beta2max_phaeo     = 0.01
+   mu_max_diatoms     = 1.44
+   mu_max_sp          = 0.851
+   mu_max_phaeo       = 0.851
+   grow_Tdep_diatoms  = 0.06
+   grow_Tdep_sp       = 0.06
+   grow_Tdep_phaeo    = 0.06
+   fr_graze_diatoms   = 0.0
+   fr_graze_sp        = 0.1
+   fr_graze_phaeo     = 0.1
+   mort_pre_diatoms   = 0.007
+   mort_pre_sp        = 0.007
+   mort_pre_phaeo     = 0.007
+   mort_Tdep_diatoms  = 0.03
+   mort_Tdep_sp       = 0.03
+   mort_Tdep_phaeo    = 0.03
+   k_exude_diatoms    = 0.0
+   k_exude_sp         = 0.0
+   k_exude_phaeo      = 0.0
+   K_Nit_diatoms      = 1.0
+   K_Nit_sp           = 1.0
+   K_Nit_phaeo        = 1.0
+   K_Am_diatoms       = 0.3
+   K_Am_sp            = 0.3
+   K_Am_phaeo         = 0.3
+   K_Sil_diatoms      = 4.0
+   K_Sil_sp           = 0.0
+   K_Sil_phaeo        = 0.0
+   K_Fe_diatoms       = 1.0
+   K_Fe_sp            = 0.2
+   K_Fe_phaeo         = 0.1
+   f_don_protein      = 0.6
+   kn_bac_protein     = 0.03
+   f_don_Am_protein   = 0.25
+   f_doc_s            = 0.4
+   f_doc_l            = 0.4
+   f_exude_s          = 1.0
+   f_exude_l          = 1.0
+   k_bac_s            = 0.03
+   k_bac_l            = 0.03
+   T_max              = 0.0
+   fsal               = 1.0
+   op_dep_min         = 0.1
+   fr_graze_s         = 0.5
+   fr_graze_e         = 0.5
+   fr_mort2min        = 0.5
+   fr_dFe             = 0.3
+   k_nitrif           = 0.0
+   t_iron_conv        = 3065.0
+   max_loss           = 0.9
+   max_dfe_doc1       = 0.2
+   fr_resp_s          = 0.75
+   y_sk_DMS           = 0.5
+   t_sk_conv          = 3.0
+   t_sk_ox            = 10.0
+   algaltype_diatoms  = 0.0
+   algaltype_sp       = 0.5
+   algaltype_phaeo    = 0.5
+   nitratetype        = -1.0
+   ammoniumtype       = 1.0
+   silicatetype       = -1.0
+   dmspptype          = 0.5
+   dmspdtype          = -1.0
+   humtype            = 1.0
+   doctype_s          = 0.5
+   doctype_l          = 0.5
+   dontype_protein    = 0.5
+   fedtype_1          = 0.5
+   feptype_1          = 0.5
+   zaerotype_bc1      = 1.0
+   zaerotype_bc2      = 1.0
+   zaerotype_dust1    = 1.0
+   zaerotype_dust2    = 1.0
+   zaerotype_dust3    = 1.0
+   zaerotype_dust4    = 1.0
+   ratio_C2N_diatoms  = 7.0
+   ratio_C2N_sp       = 7.0
+   ratio_C2N_phaeo    = 7.0
+   ratio_chl2N_diatoms= 2.1
+   ratio_chl2N_sp     = 1.1
+   ratio_chl2N_phaeo  = 0.84
+   F_abs_chl_diatoms  = 2.0
+   F_abs_chl_sp       = 4.0
+   F_abs_chl_phaeo    = 5.0
+   ratio_C2N_proteins = 7.0
 /
 
 &icefields_nml
-    f_tmask         = .true.
-  , f_blkmask       = .true.
-  , f_tarea         = .true.
-  , f_uarea         = .true.
-  , f_dxt           = .false.
-  , f_dyt           = .false.
-  , f_dxu           = .false.
-  , f_dyu           = .false.
-  , f_HTN           = .false.
-  , f_HTE           = .false.
-  , f_ANGLE         = .true.
-  , f_ANGLET        = .true.
-  , f_NCAT          = .true.
-  , f_VGRDi         = .false.
-  , f_VGRDs         = .false.
-  , f_VGRDb         = .false.
-  , f_VGRDa         = .true.
-  , f_bounds        = .false.
-  , f_aice          = 'mdhxx' 
-  , f_hi            = 'mdhxx'
-  , f_hs            = 'mdhxx' 
-  , f_Tsfc          = 'mdhxx' 
-  , f_sice          = 'mdhxx' 
-  , f_uvel          = 'mdhxx' 
-  , f_vvel          = 'mdhxx'
-  , f_uatm          = 'mdhxx'
-  , f_vatm          = 'mdhxx'
-  , f_fswdn         = 'mdhxx' 
-  , f_flwdn         = 'mdhxx'
-  , f_snowfrac      = 'x'
-  , f_snow          = 'mdhxx' 
-  , f_snow_ai       = 'x' 
-  , f_rain          = 'mdhxx' 
-  , f_rain_ai       = 'x' 
-  , f_sst           = 'mdhxx' 
-  , f_sss           = 'mdhxx' 
-  , f_uocn          = 'mdhxx' 
-  , f_vocn          = 'mdhxx' 
-  , f_frzmlt        = 'mdhxx'
-  , f_fswfac        = 'mdhxx'
-  , f_fswint_ai     = 'x'
-  , f_fswabs        = 'mdhxx' 
-  , f_fswabs_ai     = 'x' 
-  , f_albsni        = 'mdhxx' 
-  , f_alvdr         = 'mdhxx'
-  , f_alidr         = 'mdhxx'
-  , f_alvdf         = 'mdhxx'
-  , f_alidf         = 'mdhxx'
-  , f_alvdr_ai      = 'x'
-  , f_alidr_ai      = 'x'
-  , f_alvdf_ai      = 'x'
-  , f_alidf_ai      = 'x'
-  , f_albice        = 'mdhxx'
-  , f_albsno        = 'mdhxx'
-  , f_albpnd        = 'mdhxx'
-  , f_coszen        = 'mdhxx'
-  , f_flat          = 'mdhxx' 
-  , f_flat_ai       = 'x' 
-  , f_fsens         = 'mdhxx' 
-  , f_fsens_ai      = 'x' 
-  , f_fswup         = 'x'
-  , f_flwup         = 'mdhxx' 
-  , f_flwup_ai      = 'x' 
-  , f_evap          = 'mdhxx' 
-  , f_evap_ai       = 'x' 
-  , f_Tair          = 'mdhxx' 
-  , f_Tref          = 'mdhxx' 
-  , f_Qref          = 'mdhxx'
-  , f_congel        = 'mdhxx' 
-  , f_frazil        = 'mdhxx' 
-  , f_snoice        = 'mdhxx' 
-  , f_dsnow         = 'mdhxx' 
-  , f_melts         = 'mdhxx'
-  , f_meltt         = 'mdhxx'
-  , f_meltb         = 'mdhxx'
-  , f_meltl         = 'mdhxx'
-  , f_fresh         = 'mdhxx'
-  , f_fresh_ai      = 'x'
-  , f_fsalt         = 'mdhxx'
-  , f_fsalt_ai      = 'x'
-  , f_fbot          = 'mdhxx'
-  , f_fhocn         = 'mdhxx' 
-  , f_fhocn_ai      = 'x' 
-  , f_fswthru       = 'mdhxx' 
-  , f_fswthru_ai    = 'x' 
-  , f_fsurf_ai      = 'x'
-  , f_fcondtop_ai   = 'x'
-  , f_fmeltt_ai     = 'x' 
-  , f_strairx       = 'mdhxx' 
-  , f_strairy       = 'mdhxx' 
-  , f_strtltx       = 'x' 
-  , f_strtlty       = 'x' 
-  , f_strcorx       = 'x' 
-  , f_strcory       = 'x' 
-  , f_strocnx       = 'mdhxx' 
-  , f_strocny       = 'mdhxx' 
-  , f_strintx       = 'x' 
-  , f_strinty       = 'x'
-  , f_taubx         = 'x'
-  , f_tauby         = 'x'
-  , f_strength      = 'x'
-  , f_divu          = 'mdhxx'
-  , f_shear         = 'mdhxx'
-  , f_sig1          = 'x' 
-  , f_sig2          = 'x'
-  , f_sigP          = 'x' 
-  , f_dvidtt        = 'mdhxx' 
-  , f_dvidtd        = 'mdhxx' 
-  , f_daidtt        = 'mdhxx'
-  , f_daidtd        = 'mdhxx' 
-  , f_dagedtt       = 'x'
-  , f_dagedtd       = 'x'
-  , f_mlt_onset     = 'mdhxx'
-  , f_frz_onset     = 'mdhxx'
-  , f_hisnap        = 'x'
-  , f_aisnap        = 'x'
-  , f_trsig         = 'x'
-  , f_icepresent    = 'x'
-  , f_iage          = 'x'
-  , f_FY            = 'x'
-  , f_aicen         = 'x'
-  , f_vicen         = 'x'
-  , f_vsnon         = 'x'
-  , f_snowfracn     = 'x'
-  , f_keffn_top     = 'x'
-  , f_Tinz          = 'x'
-  , f_Sinz          = 'x'
-  , f_Tsnz          = 'x'
-  , f_fsurfn_ai     = 'x'
-  , f_fcondtopn_ai  = 'x'
-  , f_fmelttn_ai    = 'x'
-  , f_flatn_ai      = 'x'
-  , f_fsensn_ai     = 'x'
+   f_tmask         = .true.
+   f_blkmask       = .true.
+   f_tarea         = .true.
+   f_uarea         = .true.
+   f_dxt           = .false.
+   f_dyt           = .false.
+   f_dxu           = .false.
+   f_dyu           = .false.
+   f_HTN           = .false.
+   f_HTE           = .false.
+   f_ANGLE         = .true.
+   f_ANGLET        = .true.
+   f_NCAT          = .true.
+   f_VGRDi         = .false.
+   f_VGRDs         = .false.
+   f_VGRDb         = .false.
+   f_VGRDa         = .true.
+   f_bounds        = .false.
+   f_aice          = 'mdhxx' 
+   f_hi            = 'mdhxx'
+   f_hs            = 'mdhxx' 
+   f_Tsfc          = 'mdhxx' 
+   f_sice          = 'mdhxx' 
+   f_uvel          = 'mdhxx' 
+   f_vvel          = 'mdhxx'
+   f_uatm          = 'mdhxx'
+   f_vatm          = 'mdhxx'
+   f_fswdn         = 'mdhxx' 
+   f_flwdn         = 'mdhxx'
+   f_snowfrac      = 'x'
+   f_snow          = 'mdhxx' 
+   f_snow_ai       = 'x' 
+   f_rain          = 'mdhxx' 
+   f_rain_ai       = 'x' 
+   f_sst           = 'mdhxx' 
+   f_sss           = 'mdhxx' 
+   f_uocn          = 'mdhxx' 
+   f_vocn          = 'mdhxx' 
+   f_frzmlt        = 'mdhxx'
+   f_fswfac        = 'mdhxx'
+   f_fswint_ai     = 'x'
+   f_fswabs        = 'mdhxx' 
+   f_fswabs_ai     = 'x' 
+   f_albsni        = 'mdhxx' 
+   f_alvdr         = 'mdhxx'
+   f_alidr         = 'mdhxx'
+   f_alvdf         = 'mdhxx'
+   f_alidf         = 'mdhxx'
+   f_alvdr_ai      = 'x'
+   f_alidr_ai      = 'x'
+   f_alvdf_ai      = 'x'
+   f_alidf_ai      = 'x'
+   f_albice        = 'mdhxx'
+   f_albsno        = 'mdhxx'
+   f_albpnd        = 'mdhxx'
+   f_coszen        = 'mdhxx'
+   f_flat          = 'mdhxx' 
+   f_flat_ai       = 'x' 
+   f_fsens         = 'mdhxx' 
+   f_fsens_ai      = 'x' 
+   f_fswup         = 'x'
+   f_flwup         = 'mdhxx' 
+   f_flwup_ai      = 'x' 
+   f_evap          = 'mdhxx' 
+   f_evap_ai       = 'x' 
+   f_Tair          = 'mdhxx' 
+   f_Tref          = 'mdhxx' 
+   f_Qref          = 'mdhxx'
+   f_congel        = 'mdhxx' 
+   f_frazil        = 'mdhxx' 
+   f_snoice        = 'mdhxx' 
+   f_dsnow         = 'mdhxx' 
+   f_melts         = 'mdhxx'
+   f_meltt         = 'mdhxx'
+   f_meltb         = 'mdhxx'
+   f_meltl         = 'mdhxx'
+   f_fresh         = 'mdhxx'
+   f_fresh_ai      = 'x'
+   f_fsalt         = 'mdhxx'
+   f_fsalt_ai      = 'x'
+   f_fbot          = 'mdhxx'
+   f_fhocn         = 'mdhxx' 
+   f_fhocn_ai      = 'x' 
+   f_fswthru       = 'mdhxx' 
+   f_fswthru_ai    = 'x' 
+   f_fsurf_ai      = 'x'
+   f_fcondtop_ai   = 'x'
+   f_fmeltt_ai     = 'x' 
+   f_strairx       = 'mdhxx' 
+   f_strairy       = 'mdhxx' 
+   f_strtltx       = 'x' 
+   f_strtlty       = 'x' 
+   f_strcorx       = 'x' 
+   f_strcory       = 'x' 
+   f_strocnx       = 'mdhxx' 
+   f_strocny       = 'mdhxx' 
+   f_strintx       = 'x' 
+   f_strinty       = 'x'
+   f_taubx         = 'x'
+   f_tauby         = 'x'
+   f_strength      = 'x'
+   f_divu          = 'mdhxx'
+   f_shear         = 'mdhxx'
+   f_sig1          = 'x' 
+   f_sig2          = 'x'
+   f_sigP          = 'x' 
+   f_dvidtt        = 'mdhxx' 
+   f_dvidtd        = 'mdhxx' 
+   f_daidtt        = 'mdhxx'
+   f_daidtd        = 'mdhxx' 
+   f_dagedtt       = 'x'
+   f_dagedtd       = 'x'
+   f_mlt_onset     = 'mdhxx'
+   f_frz_onset     = 'mdhxx'
+   f_hisnap        = 'x'
+   f_aisnap        = 'x'
+   f_trsig         = 'x'
+   f_icepresent    = 'x'
+   f_iage          = 'x'
+   f_FY            = 'x'
+   f_aicen         = 'x'
+   f_vicen         = 'x'
+   f_vsnon         = 'x'
+   f_snowfracn     = 'x'
+   f_keffn_top     = 'x'
+   f_Tinz          = 'x'
+   f_Sinz          = 'x'
+   f_Tsnz          = 'x'
+   f_fsurfn_ai     = 'x'
+   f_fcondtopn_ai  = 'x'
+   f_fmelttn_ai    = 'x'
+   f_flatn_ai      = 'x'
+   f_fsensn_ai     = 'x'
 /
 
 &icefields_mechred_nml
-    f_alvl         = 'x'
-  , f_vlvl         = 'x'
-  , f_ardg         = 'x'
-  , f_vrdg         = 'x'
-  , f_dardg1dt     = 'x'
-  , f_dardg2dt     = 'x'
-  , f_dvirdgdt     = 'x'
-  , f_opening      = 'x'
-  , f_ardgn        = 'x'
-  , f_vrdgn        = 'x'
-  , f_dardg1ndt    = 'x'
-  , f_dardg2ndt    = 'x'
-  , f_dvirdgndt    = 'x'
-  , f_krdgn        = 'x'
-  , f_aparticn     = 'x'
-  , f_aredistn     = 'x'
-  , f_vredistn     = 'x'
-  , f_araftn       = 'x'
-  , f_vraftn       = 'x'
+   f_alvl         = 'x'
+   f_vlvl         = 'x'
+   f_ardg         = 'x'
+   f_vrdg         = 'x'
+   f_dardg1dt     = 'x'
+   f_dardg2dt     = 'x'
+   f_dvirdgdt     = 'x'
+   f_opening      = 'x'
+   f_ardgn        = 'x'
+   f_vrdgn        = 'x'
+   f_dardg1ndt    = 'x'
+   f_dardg2ndt    = 'x'
+   f_dvirdgndt    = 'x'
+   f_krdgn        = 'x'
+   f_aparticn     = 'x'
+   f_aredistn     = 'x'
+   f_vredistn     = 'x'
+   f_araftn       = 'x'
+   f_vraftn       = 'x'
 /
 
 &icefields_pond_nml
-    f_apondn       = 'x'
-  , f_apeffn       = 'x'
-  , f_hpondn       = 'x'
-  , f_apond        = 'mdhxx'
-  , f_hpond        = 'mdhxx'
-  , f_ipond        = 'mdhxx'
-  , f_apeff        = 'mdhxx'
-  , f_apond_ai     = 'x'
-  , f_hpond_ai     = 'x'
-  , f_ipond_ai     = 'x'
-  , f_apeff_ai     = 'x'
+   f_apondn       = 'x'
+   f_apeffn       = 'x'
+   f_hpondn       = 'x'
+   f_apond        = 'mdhxx'
+   f_hpond        = 'mdhxx'
+   f_ipond        = 'mdhxx'
+   f_apeff        = 'mdhxx'
+   f_apond_ai     = 'x'
+   f_hpond_ai     = 'x'
+   f_ipond_ai     = 'x'
+   f_apeff_ai     = 'x'
 /
 
 &icefields_bgc_nml
-    f_faero_atm    = 'x'
-  , f_faero_ocn    = 'x'
-  , f_aero         = 'x'
-  , f_fbio         = 'x'
-  , f_fbio_ai      = 'x'
-  , f_zaero        = 'x'
-  , f_bgc_S        = 'x'
-  , f_bgc_N        = 'x'
-  , f_bgc_C        = 'x'
-  , f_bgc_DOC      = 'x'
-  , f_bgc_DIC      = 'x'
-  , f_bgc_chl      = 'x'
-  , f_bgc_Nit      = 'x'
-  , f_bgc_Am       = 'x'
-  , f_bgc_Sil      = 'x'
-  , f_bgc_DMSPp    = 'x'
-  , f_bgc_DMSPd    = 'x'
-  , f_bgc_DMS      = 'x'
-  , f_bgc_DON      = 'x'
-  , f_bgc_Fe       = 'x'
-  , f_bgc_hum      = 'x'
-  , f_bgc_PON      = 'x'
-  , f_bgc_ml       = 'x'
-  , f_upNO         = 'x'
-  , f_upNH         = 'x'
-  , f_bTin         = 'x'
-  , f_bphi         = 'x'
-  , f_iDi          = 'x'
-  , f_iki          = 'x'
-  , f_fbri         = 'x'
-  , f_hbri         = 'x'
-  , f_zfswin       = 'x'
-  , f_bionet       = 'x'
-  , f_biosnow      = 'x'
-  , f_grownet      = 'x'
-  , f_PPnet        = 'x'
-  , f_algalpeak    = 'x'
-  , f_zbgc_frac    = 'x'
+   f_faero_atm    = 'x'
+   f_faero_ocn    = 'x'
+   f_aero         = 'x'
+   f_fbio         = 'x'
+   f_fbio_ai      = 'x'
+   f_zaero        = 'x'
+   f_bgc_S        = 'x'
+   f_bgc_N        = 'x'
+   f_bgc_C        = 'x'
+   f_bgc_DOC      = 'x'
+   f_bgc_DIC      = 'x'
+   f_bgc_chl      = 'x'
+   f_bgc_Nit      = 'x'
+   f_bgc_Am       = 'x'
+   f_bgc_Sil      = 'x'
+   f_bgc_DMSPp    = 'x'
+   f_bgc_DMSPd    = 'x'
+   f_bgc_DMS      = 'x'
+   f_bgc_DON      = 'x'
+   f_bgc_Fe       = 'x'
+   f_bgc_hum      = 'x'
+   f_bgc_PON      = 'x'
+   f_bgc_ml       = 'x'
+   f_upNO         = 'x'
+   f_upNH         = 'x'
+   f_bTin         = 'x'
+   f_bphi         = 'x'
+   f_iDi          = 'x'
+   f_iki          = 'x'
+   f_fbri         = 'x'
+   f_hbri         = 'x'
+   f_zfswin       = 'x'
+   f_bionet       = 'x'
+   f_biosnow      = 'x'
+   f_grownet      = 'x'
+   f_PPnet        = 'x'
+   f_algalpeak    = 'x'
+   f_zbgc_frac    = 'x'
 /
 
 &icefields_drag_nml
-    f_drag         = 'mdhxx'
-  , f_Cdn_atm      = 'mdhxx'
-  , f_Cdn_ocn      = 'mdhxx'
+   f_drag         = 'mdhxx'
+   f_Cdn_atm      = 'mdhxx'
+   f_Cdn_ocn      = 'mdhxx'
 /
 
 &icefields_fsd_nml
-  , f_fsdrad       = 'x'
-  , f_fsdperim     = 'x'
-  , f_afsd         = 'x'
-  , f_afsdn        = 'x'
-  , f_dafsd_newi   = 'x'
-  , f_dafsd_latg   = 'x'
-  , f_dafsd_latm   = 'x'
-  , f_dafsd_wave   = 'x'
-  , f_dafsd_weld   = 'x'
-  , f_wave_sig_ht  = 'x'
-  , f_aice_ww      = 'x'
-  , f_diam_ww      = 'x'
-  , f_hice_ww      = 'x'
+   f_fsdrad       = 'x'
+   f_fsdperim     = 'x'
+   f_afsd         = 'x'
+   f_afsdn        = 'x'
+   f_dafsd_newi   = 'x'
+   f_dafsd_latg   = 'x'
+   f_dafsd_latm   = 'x'
+   f_dafsd_wave   = 'x'
+   f_dafsd_weld   = 'x'
+   f_wave_sig_ht  = 'x'
+   f_aice_ww      = 'x'
+   f_diam_ww      = 'x'
+   f_hice_ww      = 'x'
 /
 eof
 

From 8ff46da4fc092391050a9bcb2fc2d0bd6e0e7822 Mon Sep 17 00:00:00 2001
From: "jian.kuang" <Jian.Kuang@noaa.gov>
Date: Fri, 11 Sep 2020 12:16:54 -0500
Subject: [PATCH 6/9] ice_in namelist correction

---
 ush/parsing_namelists_CICE.sh | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/ush/parsing_namelists_CICE.sh b/ush/parsing_namelists_CICE.sh
index b4bd1b5a37..66edff5251 100644
--- a/ush/parsing_namelists_CICE.sh
+++ b/ush/parsing_namelists_CICE.sh
@@ -51,7 +51,7 @@ cat > ice_in <<eof
 
 &grid_nml
    grid_format  = 'nc'
-   grid_type    = 'displaced_pole'
+   grid_type    = 'tripole'
    grid_file    = '$ice_grid_file'
    kmt_file     = '$ice_kmt_file'
    use_bathymetry = .false.
@@ -460,15 +460,15 @@ cat > ice_in <<eof
    f_taubx         = 'x'
    f_tauby         = 'x'
    f_strength      = 'x'
-   f_divu          = 'mdhxx'
-   f_shear         = 'mdhxx'
+   f_divu          = 'x'
+   f_shear         = 'x'
    f_sig1          = 'x' 
    f_sig2          = 'x'
    f_sigP          = 'x' 
-   f_dvidtt        = 'mdhxx' 
-   f_dvidtd        = 'mdhxx' 
-   f_daidtt        = 'mdhxx'
-   f_daidtd        = 'mdhxx' 
+   f_dvidtt        = 'x' 
+   f_dvidtd        = 'x' 
+   f_daidtt        = 'x'
+   f_daidtd        = 'x' 
    f_dagedtt       = 'x'
    f_dagedtd       = 'x'
    f_mlt_onset     = 'mdhxx'
@@ -572,9 +572,9 @@ cat > ice_in <<eof
 /
 
 &icefields_drag_nml
-   f_drag         = 'mdhxx'
-   f_Cdn_atm      = 'mdhxx'
-   f_Cdn_ocn      = 'mdhxx'
+   f_drag         = 'x'
+   f_Cdn_atm      = 'x'
+   f_Cdn_ocn      = 'x'
 /
 
 &icefields_fsd_nml

From 48b3a793ab831918387d735857701ce7e5ce8d34 Mon Sep 17 00:00:00 2001
From: "jian.kuang" <Jian.Kuang@noaa.gov>
Date: Fri, 11 Sep 2020 20:30:12 -0500
Subject: [PATCH 7/9] hera esmf module adjustment

---
 modulefiles/module_base.hera | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modulefiles/module_base.hera b/modulefiles/module_base.hera
index 6497b80a9d..be093f5650 100644
--- a/modulefiles/module_base.hera
+++ b/modulefiles/module_base.hera
@@ -36,4 +36,4 @@ module load z/1.2.11
 
 #Load from emc.nemspara
 module use -a /scratch1/NCEPDEV/nems/emc.nemspara/soft/modulefiles
-module load esmflocal/8.1.0.27bs.release
+module load esmf/8.0.1.08bs_ParallelNetCDF

From db14216be2a806786ad0547a0bbc91bbe2571fcd Mon Sep 17 00:00:00 2001
From: "jian.kuang" <Jian.Kuang@noaa.gov>
Date: Sun, 13 Sep 2020 20:59:10 -0500
Subject: [PATCH 8/9] update hera module bug fix in config.fcst

---
 modulefiles/module_base.hera | 7 +++++--
 workflow/config/fcst.yaml    | 2 +-
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/modulefiles/module_base.hera b/modulefiles/module_base.hera
index be093f5650..b406532b88 100644
--- a/modulefiles/module_base.hera
+++ b/modulefiles/module_base.hera
@@ -35,5 +35,8 @@ module load z/1.2.11
 
 
 #Load from emc.nemspara
-module use -a /scratch1/NCEPDEV/nems/emc.nemspara/soft/modulefiles
-module load esmf/8.0.1.08bs_ParallelNetCDF
+module -a /scratch1/NCEPDEV/nems/emc.nemspara/soft/modulefiles
+module load netcdf_parallel/4.7.4.release
+module load esmf/8.1.0bs27
+module load hdf5_parallel/1.10.6.release
+
diff --git a/workflow/config/fcst.yaml b/workflow/config/fcst.yaml
index 3bc3ce55d8..93975c6de6 100644
--- a/workflow/config/fcst.yaml
+++ b/workflow/config/fcst.yaml
@@ -82,7 +82,7 @@ config_fcst:
     # CICE parameters
     export NX_GLB="{doc.ice_settings.NX_GLB}"
     export NY_GLB="{doc.ice_settings.NY_GLB}"
-    export MESHICE="mesh.mx${doc.ice_settings.ICERES}.nc"
+    export MESHICE="mesh.mx{doc.ice_settings.ICERES}.nc"
 
     if [[ "$machine" == "WCOSS_C" ]]; then
         export memory_fcst="1024M"

From dd6b970232cc6048684f59477fb9c8573471be55 Mon Sep 17 00:00:00 2001
From: "jian.kuang" <Jian.Kuang@noaa.gov>
Date: Mon, 14 Sep 2020 14:03:22 -0500
Subject: [PATCH 9/9] fix typo

---
 modulefiles/module_base.hera | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modulefiles/module_base.hera b/modulefiles/module_base.hera
index b406532b88..b77fbe6e86 100644
--- a/modulefiles/module_base.hera
+++ b/modulefiles/module_base.hera
@@ -35,7 +35,7 @@ module load z/1.2.11
 
 
 #Load from emc.nemspara
-module -a /scratch1/NCEPDEV/nems/emc.nemspara/soft/modulefiles
+module use -a /scratch1/NCEPDEV/nems/emc.nemspara/soft/modulefiles
 module load netcdf_parallel/4.7.4.release
 module load esmf/8.1.0bs27
 module load hdf5_parallel/1.10.6.release