BGC included 1deg_jra55_iaf

accessom2.nml

@@ -16,5 +16,5 @@
 
     ! Runtime for a single segment/job/submit, format is years, months, seconds,
     ! two of which must be zero.
-    restart_period = 5, 0, 0
+    restart_period = 1, 0, 0
 &end

config.yaml

@@ -9,10 +9,12 @@
 # shortpath: /scratch/v45
 
 queue: normal
-walltime: 3:00:00
+walltime: 1:00:00
 jobname: 1deg_jra55_iaf
 mem: 1000GB
-
+storage:
+        gdata:
+                - v45
 # Model configuration
 name: common
 model: access-om2
@@ -38,14 +40,18 @@ submodels:
 
     - name: ocean
       model: mom
-      exe: /g/data/ik11/inputs/access-om2/bin/fms_ACCESS-OM-BGC_af3a94d_libaccessom2_44e8821.x
-      input: /g/data/ik11/inputs/access-om2/input_20201102/mom_1deg
+      exe: /home/581/hh0162/scratch/access-om2-iamip2/bin/fms_ACCESS-OM-BGC_09931a0_libaccessom2_44e8821-modified.x
+      input: 
+      - /g/data/v45/hh0162/projects/icebgc/prep_omip2/input_om2-bgc/1deg
+      - /g/data/ik11/inputs/access-om2/input_20201102/mom_1deg
       ncpus: 216
 
     - name: ice
       model: cice5
-      exe: /g/data/ik11/inputs/access-om2/bin/cice_auscom_360x300_24p_dfb833a_libaccessom2_44e8821.exe
-      input: /g/data/ik11/inputs/access-om2/input_20201102/cice_1deg
+      exe: /home/581/hh0162/scratch/access-om2-iamip2/bin/cice_auscom_360x300_24p_30ba0cc-modified_libaccessom2_44e8821-modified.exe
+      input: 
+      - /g/data/v45/hh0162/projects/icebgc/prep_omip2/input_om2-bgc/1deg
+      - /g/data/ik11/inputs/access-om2/input_20201102/cice_1deg
       ncpus: 24
 
 # Collation

ice/cice_in.nml

@@ -141,7 +141,7 @@
     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.
@@ -150,6 +150,7 @@
     tr_bgc_dmspp_sk   = .false.
     tr_bgc_sil_sk     = .false.
     tr_brine          = .false.
+    dz_ocean1         = 2.3035
 /
 
 &forcing_nml
@@ -337,16 +338,16 @@
     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_fnh             = 'x'
@@ -356,8 +357,8 @@
     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

@@ -6,13 +6,13 @@ work/atmosphere/yatm_44e8821.exe:
   hashes:
     binhash: c34913cd8082c0e45124f648197ad8e1
     md5: cdcd9dd20f690bb874cdf392085857cf
-work/ice/cice_auscom_360x300_24p_16fcc6d_libaccessom2_44e8821.exe:
-  fullpath: /g/data/ik11/inputs/access-om2/bin/cice_auscom_360x300_24p_16fcc6d_libaccessom2_44e8821.exe
+work/ice/cice_auscom_360x300_24p_30ba0cc-modified_libaccessom2_44e8821-modified.exe:
+  fullpath: /home/581/hh0162/scratch/access-om2-iamip2/bin/cice_auscom_360x300_24p_30ba0cc-modified_libaccessom2_44e8821-modified.exe
   hashes:
-    binhash: 1ad702212bad17e13b63b82892efa9f5
-    md5: f26186f285a91cca933f6123525de172
-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
+    binhash: 83d14294051ff90aceb4e175b72bcd32
+    md5: 9f05fd65329a8f611727ad2a781575e3
+work/ocean/fms_ACCESS-OM-BGC_09931a0_libaccessom2_44e8821-modified.x:
+  fullpath: /home/581/hh0162/scratch/access-om2-iamip2/bin/fms_ACCESS-OM-BGC_09931a0_libaccessom2_44e8821-modified.x
   hashes:
-    binhash: 5bfc6828685f392eeb74a457f07498dd
-    md5: cc91484411d0d34e371bf4807652b4da
+    binhash: 8720b8c6e0ece3d70904bc9bee67e5b6
+    md5: 222d62240c3670ccd14218f99203c645

manifests/input.yaml

@@ -3441,57 +3441,71 @@ work/atmosphere/INPUT/vas_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr
   hashes:
     binhash: 987ff85784eff1316d6929f631fe1426
     md5: b0e514bfac0d9dfbf538d36b8ecd17f9
-work/ice/RESTART/grid.nc:
-  copy: true
-  fullpath: /g/data/ik11/inputs/access-om2/input_20201102/cice_1deg/grid.nc
-  hashes:
-    binhash: e7108317ae28b1f9ae77711728925cb6
-    md5: 1213e346055ee073fe33dc12578d99c6
-work/ice/RESTART/i2o.nc:
-  copy: true
-  fullpath: /g/data/ik11/inputs/access-om2/input_20201102/cice_1deg/i2o.nc
-  hashes:
-    binhash: 527d494c80b2a3418645b962fd8706d0
-    md5: c96e06c3c80c0f680545db59ed3349e5
-work/ice/RESTART/kmt.nc:
-  copy: true
-  fullpath: /g/data/ik11/inputs/access-om2/input_20201102/cice_1deg/kmt.nc
-  hashes:
-    binhash: 13a23d6d9331abc9d677c6fd466a4433
-    md5: 1f9806c646a620378e5257e480bc9df7
-work/ice/RESTART/monthly_sstsss.nc:
-  copy: true
-  fullpath: /g/data/ik11/inputs/access-om2/input_20201102/cice_1deg/monthly_sstsss.nc
-  hashes:
-    binhash: 66f44d84fada351d4ebf05f196762d8c
-    md5: 323d4c605f83f4d7d3126da70153c2ed
-work/ice/RESTART/o2i.nc:
-  copy: true
-  fullpath: /g/data/ik11/inputs/access-om2/input_20201102/cice_1deg/o2i.nc
-  hashes:
-    binhash: 56f258e931a8eda2fc42b3a315d485eb
-    md5: 3498246dcd7da40d3b8c6b4a908b260f
-work/ice/RESTART/u_star.nc:
-  copy: true
-  fullpath: /g/data/ik11/inputs/access-om2/input_20201102/cice_1deg/u_star.nc
-  hashes:
-    binhash: f93a19930c5c59e03751e70a123ab01f
-    md5: 68cf0ef92576f96ef085cd7f243d0c39
+work/ocean/INPUT/bgc_param.nc:
+  fullpath: /g/data/v45/hh0162/projects/icebgc/prep_omip2/input_iamip2/bgc_param.nc
+  hashes:
+    binhash: 01dd023f892345a339a75c0f8def735e
+    md5: 9f55f5b4cb38960f394044eb6e2157dc
+work/ocean/INPUT/cfc_auscom.nc:
+  fullpath: /g/data/v45/hh0162/projects/icebgc/prep_omip2/input_iamip2/cfc_auscom.nc
+  hashes:
+    binhash: 0ef60fbcc83af2d6d33680b105527e0c
+    md5: 38660c8a5de3e3b63d2ae7ba5020d515
 work/ocean/INPUT/chl.nc:
   fullpath: /g/data/ik11/inputs/access-om2/input_20201102/mom_1deg/chl.nc
   hashes:
     binhash: 05b3313121bbb9825a20f0fb58901b21
     md5: a7aa5bcf4a3b9fa8102edd3b6b67c3a2
+work/ocean/INPUT/co2_obs.nc:
+  fullpath: /g/data/v45/hh0162/projects/icebgc/prep_omip2/input_iamip2/co2_obs.nc
+  hashes:
+    binhash: 0d42b3a70c19093494e3b20796f6a6fc
+    md5: 9958ce02abada0533a964b071dd3c26a
+work/ocean/INPUT/co2_obs_iamip2_con.nc:
+  fullpath: /g/data/v45/hh0162/projects/icebgc/prep_omip2/input_iamip2/co2_obs_iamip2_con.nc
+  hashes:
+    binhash: 2e99cdc6d56091658c5e20fb2a993364
+    md5: 6a3f17f1a034b777ac373266d5610789
+work/ocean/INPUT/co2_obs_omip2_1-3.nc:
+  fullpath: /g/data/v45/hh0162/projects/icebgc/prep_omip2/input_iamip2/co2_obs_omip2_1-3.nc
+  hashes:
+    binhash: a8cb6e3f4eb74200c1899c3f4fe7ff93
+    md5: a956460457c79590f018cad4efa4de3f
+work/ocean/INPUT/csiro_bgc.res.nc:
+  fullpath: /g/data/v45/hh0162/projects/icebgc/prep_omip2/input_iamip2/csiro_bgc.res.nc
+  hashes:
+    binhash: 4fc8b93f2d71ebafbd95b3ee8677d5f4
+    md5: a65da5e0413aa774c62cf596e8bd7271
+work/ocean/INPUT/csiro_bgc_sediment.res.nc:
+  fullpath: /g/data/v45/hh0162/projects/icebgc/prep_omip2/input_iamip2/csiro_bgc_sediment.res.nc
+  hashes:
+    binhash: 4bf4ff2cfc52f2d3fec82e2d770bfc18
+    md5: 47d3157c3fe17c8e3581350295c1413c
+work/ocean/INPUT/dust_om2.nc:
+  fullpath: /g/data/v45/hh0162/projects/icebgc/prep_omip2/input_iamip2/dust_om2.nc
+  hashes:
+    binhash: 7eb54e681b58ba9c484e9913d57337df
+    md5: e16438a05c180e8709d21ff880192b03
 work/ocean/INPUT/grid_spec.nc:
   fullpath: /g/data/ik11/inputs/access-om2/input_20201102/mom_1deg/grid_spec.nc
   hashes:
     binhash: 587ca8eb0cbc978232fe55a7bff054c9
     md5: 027d2f8fb1eda3ef1cf0a3f520a217f7
+work/ocean/INPUT/i2o.nc:
+  fullpath: /g/data/v45/hh0162/projects/icebgc/prep_omip2/input_iamip2/i2o.nc
+  hashes:
+    binhash: a3026b03b45556cb5a9ce4ae34603ffb
+    md5: 273fb9d25a2b9a7e4cbf158e3aea1e50
 work/ocean/INPUT/mask_table.24.16x15:
   fullpath: /g/data/ik11/inputs/access-om2/input_20201102/mom_1deg/mask_table.24.16x15
   hashes:
     binhash: 77b929b930cd4fca59f185b3222dde49
     md5: 2203b38758fb2b56a145ef16b7872af9
+work/ocean/INPUT/o2i.nc:
+  fullpath: /g/data/v45/hh0162/projects/icebgc/prep_omip2/input_iamip2/o2i.nc
+  hashes:
+    binhash: 11778d8b29e044047dd34b50922d9a21
+    md5: 0ce344f73b224f0809f31357fcdeba98
 work/ocean/INPUT/ocean_hgrid.nc:
   fullpath: /g/data/ik11/inputs/access-om2/input_20201102/mom_1deg/ocean_hgrid.nc
   hashes:
@@ -3522,6 +3536,26 @@ work/ocean/INPUT/ocean_vgrid.nc:
   hashes:
     binhash: cd9ef67b8cf6d4ea0c78554ac38e1bc3
     md5: 339ff716e3019a86fc861498e674250a
+work/ocean/INPUT/ocmip2_fice_monthly_om1p5_bc.nc:
+  fullpath: /g/data/v45/hh0162/projects/icebgc/prep_omip2/input_iamip2/ocmip2_fice_monthly_om1p5_bc.nc
+  hashes:
+    binhash: dca033091346f730c32d5357361ccee8
+    md5: c0ed75eef44962dbe6fc9f61dbd228a9
+work/ocean/INPUT/ocmip2_press_monthly_om2.nc:
+  fullpath: /g/data/v45/hh0162/projects/icebgc/prep_omip2/input_iamip2/ocmip2_press_monthly_om2.nc
+  hashes:
+    binhash: 814653bfaa6fad936ced1d862e8d6287
+    md5: fd7f6e66d09d9f6f87732290f0131b9d
+work/ocean/INPUT/ocmip2_xkw_monthly_om1p5_bc.nc:
+  fullpath: /g/data/v45/hh0162/projects/icebgc/prep_omip2/input_iamip2/ocmip2_xkw_monthly_om1p5_bc.nc
+  hashes:
+    binhash: 4592909e34c061a9e6aa3886c3d24609
+    md5: 348a035bed83e280bb0a1de0066947fc
+work/ocean/INPUT/ocmip2_xkw_monthly_om2.nc:
+  fullpath: /g/data/v45/hh0162/projects/icebgc/prep_omip2/input_iamip2/ocmip2_xkw_monthly_om2.nc
+  hashes:
+    binhash: 65728d3d89b4347544961058eb5c69c1
+    md5: fd87b17f01689105414865748f97b41b
 work/ocean/INPUT/roughness_amp.nc:
   fullpath: /g/data/ik11/inputs/access-om2/input_20201102/mom_1deg/roughness_amp.nc
   hashes: