Merge branch 'master+bgc' into 01deg_jra55v140_iaf_cycle4

resolved conflicts:
	config.yaml
	manifests/exe.yaml
	manifests/input.yaml
	metadata.yaml
	ocean/diag_table
	ocean/diag_table_source.yaml

Author: aekiss

README.md

@@ -1,5 +1,9 @@
-# 01deg_jra55_iaf
-Standard configuration for 0.1 degree [ACCESS-OM2](https://github.com/COSIMA/access-om2) experiment (ACCESS-OM2-01) with JRA55-do interannual forcing (IAF).
+# 01deg_jra55_iaf with BGC
+Standard configuration for 0.1 degree [ACCESS-OM2](https://github.com/COSIMA/access-om2) experiment (ACCESS-OM2-01) with JRA55-do interannual forcing (IAF) and coupled biogeochemistry in the ocean and sea ice.
+
+This is the BGC version, on the `master+bgc` branch. For the physics-only version (no BGC), use the `master` branch.
+
+This BGC setup includes both ocean and sea ice BGC. To turn off the sea ice BGC and have BGC only in the ocean, set `skl_bgc = .false.` in `ice/cice_input.nml`.
 
 For usage instructions, see the [ACCESS-OM2 wiki](https://github.com/COSIMA/access-om2/wiki).
 

accessom2.nml

@@ -19,5 +19,5 @@
 
     ! Runtime for a single segment/job/submit, format is years, months, seconds,
     ! two of which must be zero.
-    restart_period = 0, 3, 0
+    restart_period = 0, 1, 0
 &end

config.yaml

@@ -19,7 +19,7 @@ input: /g/data/ik11/inputs/access-om2/input_20201102/common_01deg_jra55
 submodels:
     - name: atmosphere
       model: yatm
-      exe: /g/data/ik11/inputs/access-om2/bin/yatm_44e8821.exe
+      exe: /g/data/ik11/inputs/access-om2/bin/yatm_0ab7295.exe
       input:
             - /g/data/ik11/inputs/access-om2/input_20201102/yatm_01deg
             - /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/atmos/3hr/rsds/gr/v20190429
@@ -37,17 +37,20 @@ submodels:
 
     - name: ocean
       model: mom
-      exe: /g/data/ik11/inputs/access-om2/bin/fms_ACCESS-OM-BGC_af3a94d_libaccessom2_44e8821.x
+      exe: /g/data/ik11/inputs/access-om2/bin/fms_ACCESS-OM-BGC_1d9af9d_libaccessom2_0ab7295.x
       input:
+            - /g/data/ik11/inputs/access-om2/input_bgc_20211105/01deg-cycle4
             - /g/data/ik11/inputs/access-om2/input_20201120/mom_01deg_150x100
             - /g/data/ik11/inputs/access-om2/input_20201102/mom_01deg
             - /g/data/ik11/inputs/access-om2/passive4-2020-11-13
       ncpus: 10461
 
     - name: ice
       model: cice5
-      exe: /g/data/ik11/inputs/access-om2/bin/cice_auscom_18x15.3600x2700_1682p_9864af2_libaccessom2_44e8821.exe
-      input: /g/data/ik11/inputs/access-om2/input_20201102/cice_01deg
+      exe: /g/data/ik11/inputs/access-om2/bin/cice_auscom_18x15.3600x2700_1682p_3a5d05f_libaccessom2_0ab7295.exe
+      input:
+            - /g/data/ik11/inputs/access-om2/input_bgc_20211105/01deg-cycle4
+            - /g/data/ik11/inputs/access-om2/input_20201102/cice_01deg
       ncpus: 1682
 
 # Collation
@@ -66,6 +69,8 @@ stacksize: unlimited
 restart_freq: 1  # use tidy_restarts.py instead
 mpirun: --mca io ompio --mca io_ompio_num_aggregators 1
 qsub_flags: -W umask=027
+env:
+    UCX_LOG_LEVEL: 'error'
 # set number of cores per node (28 for normalbw, 48 for normal on gadi)
 platform:
     nodesize: 48

ice/cice_in.nml

@@ -141,15 +141,15 @@
     restart_hbrine    = .false.
     restore_bgc       = .false.
     sil_data_type     = 'default'
-    skl_bgc           = .false.
+    skl_bgc           = .true.
     tr_bgc_am_sk      = .false.
     tr_bgc_c_sk       = .false.
     tr_bgc_chl_sk     = .false.
     tr_bgc_dms_sk     = .false.
     tr_bgc_dmspd_sk   = .false.
     tr_bgc_dmspp_sk   = .false.
     tr_bgc_sil_sk     = .false.
-    tr_brine          = .false.
+    tr_brine          = .true.
 /
 
 &forcing_nml
@@ -337,27 +337,27 @@
     f_bgc_dmsp_ml     = 'x'
     f_bgc_dmspd_sk    = 'x'
     f_bgc_dmspp_sk    = 'x'
-    f_bgc_n_sk        = 'x'
-    f_bgc_nit_ml      = 'x'
-    f_bgc_nit_sk      = 'x'
+    f_bgc_n_sk        = 'm'
+    f_bgc_nit_ml      = 'm'
+    f_bgc_nit_sk      = 'm'
     f_bgc_sil_ml      = 'x'
     f_bgc_sil_sk      = 'x'
     f_bphi            = 'x'
     f_btin            = 'x'
     f_faero_atm       = 'x'
     f_faero_ocn       = 'x'
-    f_fbri            = 'x'
+    f_fbri            = 'm'
     f_fn              = 'x'
-    f_fn_ai           = 'x'
+    f_fn_ai           = 'm'
     f_fnh             = 'x'
     f_fnh_ai          = 'x'
     f_fno             = 'x'
-    f_fno_ai          = 'x'
+    f_fno_ai          = 'm'
     f_fsil            = 'x'
     f_fsil_ai         = 'x'
     f_grownet         = 'x'
-    f_hbri            = 'x'
-    f_ppnet           = 'x'
+    f_hbri            = 'm'
+    f_ppnet           = 'm'
 /
 
 &icefields_drag_nml

ice/input_ice.nml

@@ -10,11 +10,11 @@
                         'runof_i', 'tair_i', 'qair_i', 'uwnd_i', 'vwnd_i',
                         'licalvf_i'
     fields_from_ocn   = 'sst_i', 'sss_i', 'ssu_i', 'ssv_i', 'sslx_i', 'ssly_i',
-                        'pfmice_i'
+                        'pfmice_i', 'ssn_i', 'ssalg_i'
     fields_to_ocn     = 'strsu_io', 'strsv_io', 'rain_io', 'snow_io', 'stflx_io',
                         'htflx_io', 'swflx_io', 'qflux_io', 'shflx_io',
                         'lwflx_io', 'runof_io', 'press_io', 'aice_io', 'melt_io',
-                        'form_io', 'licefw_io', 'licefh_io'
+                        'form_io', 'licefw_io', 'licefh_io', 'wnd10_io', 'nit_io', 'alg_io'
     gfdl_surface_flux = .true.
     ice_fwflux        = .true.
     ice_pressure_on   = .true.

manifests/exe.yaml

@@ -1,8 +1,8 @@
 format: yamanifest
 version: 1.0
 ---
-work/atmosphere/yatm_44e8821.exe:
-  fullpath: /g/data/ik11/inputs/access-om2/bin/yatm_44e8821.exe
+work/atmosphere/yatm_0ab7295.exe:
+  fullpath: /g/data/ik11/inputs/access-om2/bin/yatm_0ab7295.exe
   hashes:
     binhash: c34913cd8082c0e45124f648197ad8e1
     md5: cdcd9dd20f690bb874cdf392085857cf
@@ -14,5 +14,5 @@ work/ice/cice_auscom_18x15.3600x2700_1682p_9864af2_libaccessom2_44e8821.exe:
 work/ocean/fms_ACCESS-OM-BGC_af3a94d_libaccessom2_44e8821.x:
   fullpath: /g/data/ik11/inputs/access-om2/bin/fms_ACCESS-OM-BGC_af3a94d_libaccessom2_44e8821.x
   hashes:
-    binhash: 5bfc6828685f392eeb74a457f07498dd
-    md5: cc91484411d0d34e371bf4807652b4da
+    binhash: f066d7e29cd0fb7347720c4d29588caf
+    md5: 1c88bb1ea053b34db4c2d4e2b59ce500

manifests/input.yaml

@@ -3441,11 +3441,41 @@ work/ocean/INPUT/chl.nc:
   hashes:
     binhash: c33b83b1f3f3b92ab7390b4c9888820f
     md5: 8cc506303102f2faad01b8ffb5268bf5
+work/ocean/INPUT/co2_iaf.nc:
+  fullpath: /g/data/ik11/inputs/access-om2/input_bgc_20211105/01deg/co2_iaf.nc
+  hashes:
+    binhash: 257ec39836576d3255fa1d8dc4bc4fec
+    md5: ca541da7d8e941a8adc02e6ea91b490b
+work/ocean/INPUT/co2_ryf.nc:
+  fullpath: /g/data/ik11/inputs/access-om2/input_bgc_20211105/01deg/co2_ryf.nc
+  hashes:
+    binhash: 0f6b961bd5b0049a93b8d4f5a8bca39e
+    md5: 6a9007d7cae9b700548bb59424e8c93e
+work/ocean/INPUT/csiro_bgc.res.nc:
+  fullpath: /g/data/ik11/inputs/access-om2/input_bgc_20211105/01deg/csiro_bgc.res.nc
+  hashes:
+    binhash: d7c90202768a175bee13a555d262a00b
+    md5: c2967270f16992eef0a4b53c6ebd3019
+work/ocean/INPUT/csiro_bgc_sediment.res.nc:
+  fullpath: /g/data/ik11/inputs/access-om2/input_bgc_20211105/01deg/csiro_bgc_sediment.res.nc
+  hashes:
+    binhash: 1a7e58ffc5db0e73ae5ee84bd9453a8b
+    md5: 2a55893f7c161780c54b94005ddd8330
+work/ocean/INPUT/dust.nc:
+  fullpath: /g/data/ik11/inputs/access-om2/input_bgc_20211105/01deg/dust.nc
+  hashes:
+    binhash: ad893e6167113e5a0bd07e573a6e52f6
+    md5: 4dc7c1b541f4dbf842541a4ff605ad00
 work/ocean/INPUT/grid_spec.nc:
   fullpath: /g/data/ik11/inputs/access-om2/input_20201102/mom_01deg/grid_spec.nc
   hashes:
     binhash: 22d51e6d15b1247123786da5e0672578
     md5: cb5674cf1d2be64b3c5c1eac948e51d7
+work/ocean/INPUT/i2o.nc:
+  fullpath: /g/data/ik11/inputs/access-om2/input_bgc_20211105/01deg/i2o.nc
+  hashes:
+    binhash: d0905db6c1d49557841d2fad17af0262
+    md5: 10dc60770024d5e71564ec120c4ba16c
 work/ocean/INPUT/mask_table.1642.80x75:
   fullpath: /g/data/ik11/inputs/access-om2/input_20201102/mom_01deg/mask_table.1642.80x75
   hashes:

metadata.yaml

@@ -4,11 +4,14 @@ created: 2021-03-25
 description: >-
   0.1 degree ACCESS-OM2 global model configuration under interannual forcing.
   The configuration is based on that described in Kiss et al. (2020),
-  https://doi.org/10.5194/gmd-13-401-2020, but with many improvements.
+  https://doi.org/10.5194/gmd-13-401-2020, but with many improvements and
+  coupled biogeochemistry in the ocean and sea ice.
   This is cycle 4 of the IAF spinup. 
   Configuration physics is identical to 01deg_jra55v140_iaf_cycle3 but executables and
-  diagnostics have changed, and ice-ocean coupled BGC is included.
+  diagnostics have changed, and sea ice and ocean coupled BGC is included.
   Initial conditions are from final 1 Jan 2019 restart from 01deg_jra55v140_iaf_cycle3.
+  and BGC tracers as in https://github.com/COSIMA/input_om2-bgc/tree/6aee4a4
+  with my_choice == '01deg_jra55v140_iaf_cycle4'.
   Run with JRA55-do v1.4.0 interannually-varying forcing with all solid runoff 
   converted to liquid runoff with no heat transfer.
   61-year spin up, from 1 Jan 1958 to 1 Jan 2019.
@@ -32,3 +35,5 @@ keywords:
   - access-om2-01
   - jra55-do-v1.4.0
   - iaf
+  - bgc
+  

namcouple

@@ -16,7 +16,7 @@
 ### 11 fields  atm -> ice
 ### 17 fields  ice -> ocn
 ###  7 fields  ocn -> ice
-   35
+   40
  $END
 #########################################################################
 # $JOBNAME
@@ -265,6 +265,21 @@ NA NA
 ##########
 licefh_io liceht -1 -1 0 i2o.nc IGNORED
 NA NA
+##########
+# Field 29 : 10 m winds
+########## 
+wnd10_io wnd_io -1 -1 0 i2o.nc IGNORED
+NA NA
+##########
+# Field 30 : ice-to-ocean nitrate flux [mmol m-2 s-1]
+##########
+nit_io iof_nit -1 -1 0 i2o.nc IGNORED
+NA NA
+##########
+# Field 31 : ice-to-ocean algae/phyto flux in nitrogen content [mmol m-2 s-1]
+##########
+alg_io iof_alg -1 -1 0 i2o.nc IGNORED
+NA NA
 ############################################################################
 #
 #                      OCEAN --->>> ICE
@@ -303,5 +318,15 @@ NA NA
 # Field 35 :  sea surface slope _y_ (m/m)
 ##########
 dssldy ssly_i -1 -1 0 o2i.nc IGNORED
+NA NA
+##########
+# Field 36 :  sea surface nitrate (mmol/m^3)
+##########
+n_surf ssn_i -1 -1 0 o2i.nc IGNORED
+NA NA
+##########
+# Field 37 :  sea surface algae/phytoplankton in nitrogen (mmol/m^3)
+##########
+alg_surf ssalg_i -1 -1 0 o2i.nc IGNORED
 NA NA
  $END