claireyung:dev-MC_4km_jra_ryf+regionalpanan. PR #3.

CITATION.cff

@@ -102,6 +102,34 @@ authors:
     family-names: Yang
     email: Luwei.Yang@anu.edu.au
     affiliation: Research School of Earth Sciences, Australian National University
+  - given-names: Claire
+    family-names: Yung
+    email: Claire.Yung@anu.edu.au
+    affiliation: Research School of Earth Sciences, Australian National University
+    orcid: 'https://orcid.org/0000-0002-0052-7668'
+  - given-names: Wilton
+    family-names: Aguiar
+    email: wilton.aguiar@anu.edu.au
+    affiliation: Research School of Earth Sciences, Australian National University
+    orcid: 'https://orcid.org/0000-0003-2453-9791'
+  - given-names: Helen
+    family-names: Macdonald
+    email: helen.macdonald@anu.edu.au
+    affiliation: ACCESS-NRI
+    orcid: 'https://orcid.org/0000-0003-4734-3150'
+  - given-names: Edward
+    family-names: Yang
+    email: edward.yang@anu.edu.au
+    affiliation: ACCESS-NRI
+  - given-names: David
+    family-names: Gwyther
+    email: d.gwyther@uq.edu.au
+    affiliation: School of the Environment, University of Queensland
+    orcid: 'https://orcid.org/0000-0002-7218-2785'
+  - given-names: Fabio
+    family-names: Boeira Dias
+    email: f.boeira_dias@unsw.edu.au
+    orcid: 'https://orcid.org/0000-0002-2965-2120'
 identifiers:
   - description: "The concept DOI of all ACCESS-OM3 configurations."
     type: doi

README.md

@@ -1,3 +1,7 @@
+## MOM6-CICE6 4km JRA55-do RYF regional pan-Antarctic ACCESS-OM3 configuration
+
+**WARNING: This configuration is still under development and should not be used for production.**
+
 See [`main` branch
 README](https://github.com/ACCESS-NRI/access-om3-configs/blob/main/README.md) for usage
 information.

config.yaml

@@ -2,9 +2,9 @@
 
 # If submitting to a different project to your default, uncomment line below 
 # and change project code as appropriate; also set shortpath below
-# project: x77
+# project: ol01
 # Force payu to always find, and save, files in this scratch project directory
-# shortpath: /scratch/v45
+# shortpath: /scratch/x77
 
 # Using payu sync is recommend to copy data from ephemeral scratch space to 
 # longer term storage
@@ -23,32 +23,33 @@ modules:
         - model-tools/mppnccombine-fast
 
 queue: normalsr
-ncpus: 1976
+ncpus: 1664
 jobfs: 10GB
-mem: 9500GB
-walltime: 6:00:00
-jobname: 25km_jra_ryf
+mem: 8000GB
+walltime: 4:00:00
+jobname: 4km_panAn_om3
 
 model: access-om3
 exe: access-om3-MOM6-CICE6
 input:
-    - /g/data/vk83/configurations/inputs/access-om3/cice/grids/global.25km/2025.11.27/kmt.nc
-    - /g/data/vk83/configurations/inputs/access-om3/mom/grids/mosaic/global.25km/2025.09.02/ocean_hgrid.nc
-    - /g/data/vk83/configurations/inputs/access-om3/mom/grids/vertical/global.25km/2025.03.12/ocean_vgrid.nc
-    - /g/data/vk83/configurations/inputs/access-om3/mom/initial_conditions/global.25km/2025.10.24/woa23_ts_01_mom.nc
-    - /g/data/vk83/configurations/inputs/access-om3/mom/surface_salt_restoring/global.25km/2025.10.24/salt_sfc_restore.nc
-    - /g/data/vk83/configurations/inputs/access-om3/mom/tidal_external_files/global.25km/2025.09.03/bottom_roughness.nc
-    - /g/data/vk83/configurations/inputs/access-om3/mom/tidal_external_files/global.25km/2025.09.03/tideamp.nc
-    - /g/data/vk83/configurations/inputs/access-om3/share/grids/global.25km/2025.11.27/topog.nc
-    - /g/data/vk83/configurations/inputs/access-om3/mom/chlorophyll/global.25km/2025.11.21/chl_globcolour_monthly_clim.nc
-    - /g/data/vk83/configurations/inputs/access-om3/share/meshes/global.25km/2025.11.27/access-om3-25km-ESMFmesh.nc
-    - /g/data/vk83/configurations/inputs/access-om3/share/meshes/global.25km/2025.11.27/access-om3-25km-nomask-ESMFmesh.nc
+    - /g/data/tm70/cy8964/mom6/input/input-8km/kmt_Charrassin_nocavity_cropped.nc
+    - /g/data/tm70/cy8964/mom6/input/input-8km/ocean_hgrid_cropped.nc
+    - /g/data/tm70/cy8964/mom6/input/input-8km/ocean_vgrid_cropped.nc
+    - /g/data/tm70/cy8964/mom6/input/input-8km/ACCESS-OM2_IC_bfilled_smoothedland.nc
+    - /g/data/tm70/cy8964/mom6/input/input-8km/salt_restore_interpolated_nearest.nc
+    - /g/data/tm70/cy8964/mom6/input/input-8km/bottom_roughness_Charrassin_nocavity_cropped.nc
+    - /g/data/tm70/cy8964/mom6/input/input-8km/tideamp_Charrassin_nocavity_cropped.nc
+    - /g/data/tm70/cy8964/mom6/input/input-8km/topog_Charrassin_nocavity_cropped.nc
+    - /g/data/tm70/cy8964/mom6/input/input-8km/access-om3-8km-ESMFmesh_Charrassin_nocavity_cropped.nc
+    - /g/data/tm70/cy8964/mom6/input/input-8km/access-om3-8km-nomask-ESMFmesh_Charrassin_nocavity_cropped.nc
     - /g/data/vk83/prerelease/configurations/inputs/access-om3/share/meshes/share/2026.01.21/JRA55do-datm-ESMFmesh.nc
     - /g/data/vk83/prerelease/configurations/inputs/access-om3/share/meshes/share/2026.01.21/JRA55do-drof-ESMFmesh.nc
-    - /g/data/vk83/configurations/inputs/access-om3/cmeps/remap_weights/global.25km/2025.11.27/access-om3-25km-rof-remap-weights.nc
+    - /g/data/tm70/cy8964/mom6/input/input-8km/access-om3-8km-rof-remap-weights_Charrassin_nocavity_cropped.nc
     - /g/data/vk83/configurations/inputs/JRA-55/RYF/v1-6/data
+    - /g/data/tm70/cy8964/mom6/input/input-8km/forcing_access_yr2_8km_fill.nc
+    - /g/data/tm70/cy8964/mom6/input/input-8km/diag_rho2.nc
 
-runlog: true
+runlog: True
 metadata: 
     enable: true
 manifest:
@@ -63,9 +64,9 @@ platform:
 collate:
   restart: true
   mpi: true
-  walltime: 4:00:00
-  mem: 30GB
-  ncpus: 4
+  walltime: 1:00:00
+  mem: 80GB
+  ncpus: 16
   queue: normalsr
   exe: mppnccombine-fast
 

datm.streams.xml

@@ -67,7 +67,7 @@
   </stream_info>
   <stream_info name="JRA55do.SWDN">
     <taxmode>cycle</taxmode>
-    <dtlimit>1.0</dtlimit>
+    <dtlimit>2</dtlimit>
     <readmode>single</readmode>
     <mapalgo>bilinear</mapalgo>
     <year_first>1900</year_first>

datm_in

@@ -8,10 +8,10 @@
   flds_preso3 = .false.
   flds_wiso = .false.
   iradsw = 1
-  model_maskfile = "./INPUT/access-om3-25km-nomask-ESMFmesh.nc"
-  model_meshfile = "./INPUT/access-om3-25km-nomask-ESMFmesh.nc"
-  nx_global = 1440
-  ny_global = 1152
+  model_maskfile = "./INPUT/access-om3-8km-nomask-ESMFmesh_Charrassin_nocavity_cropped.nc"
+  model_meshfile = "./INPUT/access-om3-8km-nomask-ESMFmesh_Charrassin_nocavity_cropped.nc"
+  nx_global = 4320
+  ny_global = 1442
   restfilm = "null"
   skip_restart_read = .false.
 /

diag_table

@@ -49,9 +49,6 @@ ACCESS-OM3
 "access-om3.mom6.3d.agessc+z.1mon.mean.%4yr", 1, "months", 1, "days", "time", 1, "years"
 "ocean_model_z", "agessc", "agessc", "access-om3.mom6.3d.agessc+z.1mon.mean.%4yr", "all", "average", "none", 2
 
-"access-om3.mom6.3d.rhopot0+z.1mon.mean.%4yr", 1, "months", 1, "days", "time", 1, "years"
-"ocean_model_z", "rhopot0", "rhopot0", "access-om3.mom6.3d.rhopot0+z.1mon.mean.%4yr", "all", "average", "none", 2
-
 "access-om3.mom6.3d.rhopot2+z.1mon.mean.%4yr", 1, "months", 1, "days", "time", 1, "years"
 "ocean_model_z", "rhopot2", "rhopot2", "access-om3.mom6.3d.rhopot2+z.1mon.mean.%4yr", "all", "average", "none", 2
 
@@ -70,12 +67,6 @@ ACCESS-OM3
 "access-om3.mom6.3d.KE+z.1mon.mean.%4yr", 1, "months", 1, "days", "time", 1, "years"
 "ocean_model_z", "KE", "KE", "access-om3.mom6.3d.KE+z.1mon.mean.%4yr", "all", "average", "none", 2
 
-"access-om3.mom6.3d.Kd_Itidal_Work+z.1mon.mean.%4yr", 1, "months", 1, "days", "time", 1, "years"
-"ocean_model_z", "Kd_Itidal_Work", "Kd_Itidal_Work", "access-om3.mom6.3d.Kd_Itidal_Work+z.1mon.mean.%4yr", "all", "average", "none", 2
-
-"access-om3.mom6.3d.rsdoabsorb+z.1mon.mean.%4yr", 1, "months", 1, "days", "time", 1, "years"
-"ocean_model_z", "rsdoabsorb", "rsdoabsorb", "access-om3.mom6.3d.rsdoabsorb+z.1mon.mean.%4yr", "all", "average", "none", 2
-
 
 # monthly 3d fields on rho2
 
@@ -91,30 +82,6 @@ ACCESS-OM3
 "access-om3.mom6.3d.vmo+rho2.1mon.mean.%4yr", 1, "months", 1, "days", "time", 1, "years"
 "ocean_model_rho2", "vmo", "vmo", "access-om3.mom6.3d.vmo+rho2.1mon.mean.%4yr", "all", "average", "none", 2
 
-"access-om3.mom6.3d.uhGM+rho2.1mon.mean.%4yr", 1, "months", 1, "days", "time", 1, "years"
-"ocean_model_rho2", "uhGM", "uhGM", "access-om3.mom6.3d.uhGM+rho2.1mon.mean.%4yr", "all", "average", "none", 2
-
-"access-om3.mom6.3d.vhGM+rho2.1mon.mean.%4yr", 1, "months", 1, "days", "time", 1, "years"
-"ocean_model_rho2", "vhGM", "vhGM", "access-om3.mom6.3d.vhGM+rho2.1mon.mean.%4yr", "all", "average", "none", 2
-
-"access-om3.mom6.3d.GM_sfn_y+rho2.1mon.mean.%4yr", 1, "months", 1, "days", "time", 1, "years"
-"ocean_model_rho2", "GM_sfn_y", "GM_sfn_y", "access-om3.mom6.3d.GM_sfn_y+rho2.1mon.mean.%4yr", "all", "average", "none", 2
-
-
-# monthly 3d fields on native
-
-"access-om3.mom6.3d.e.1mon.mean.%4yr", 1, "months", 1, "days", "time", 1, "years"
-"ocean_model", "e", "e", "access-om3.mom6.3d.e.1mon.mean.%4yr", "all", "average", "none", 2
-
-"access-om3.mom6.3d.thkcello.1mon.mean.%4yr", 1, "months", 1, "days", "time", 1, "years"
-"ocean_model", "thkcello", "thkcello", "access-om3.mom6.3d.thkcello.1mon.mean.%4yr", "all", "average", "none", 2
-
-"access-om3.mom6.3d.Kd_interface.1mon.mean.%4yr", 1, "months", 1, "days", "time", 1, "years"
-"ocean_model", "Kd_interface", "Kd_interface", "access-om3.mom6.3d.Kd_interface.1mon.mean.%4yr", "all", "average", "none", 2
-
-"access-om3.mom6.3d.Kd_ePBL.1mon.mean.%4yr", 1, "months", 1, "days", "time", 1, "years"
-"ocean_model", "Kd_ePBL", "Kd_ePBL", "access-om3.mom6.3d.Kd_ePBL.1mon.mean.%4yr", "all", "average", "none", 2
-
 
 # monthly 2d fields
 
@@ -169,78 +136,21 @@ ACCESS-OM3
 "access-om3.mom6.2d.pbo.1mon.mean.%4yr", 1, "months", 1, "days", "time", 1, "years"
 "ocean_model", "pbo", "pbo", "access-om3.mom6.2d.pbo.1mon.mean.%4yr", "all", "average", "none", 2
 
-"access-om3.mom6.2d.Chl_opac.1mon.mean.%4yr", 1, "months", 1, "days", "time", 1, "years"
-"ocean_model", "Chl_opac", "Chl_opac", "access-om3.mom6.2d.Chl_opac.1mon.mean.%4yr", "all", "average", "none", 2
-
-"access-om3.mom6.2d.SW_pen.1mon.mean.%4yr", 1, "months", 1, "days", "time", 1, "years"
-"ocean_model", "SW_pen", "SW_pen", "access-om3.mom6.2d.SW_pen.1mon.mean.%4yr", "all", "average", "none", 2
-
-"access-om3.mom6.2d.T_adx_2d.1mon.mean.%4yr", 1, "months", 1, "days", "time", 1, "years"
-"ocean_model", "T_adx_2d", "T_adx_2d", "access-om3.mom6.2d.T_adx_2d.1mon.mean.%4yr", "all", "average", "none", 2
-
-"access-om3.mom6.2d.T_ady_2d.1mon.mean.%4yr", 1, "months", 1, "days", "time", 1, "years"
-"ocean_model", "T_ady_2d", "T_ady_2d", "access-om3.mom6.2d.T_ady_2d.1mon.mean.%4yr", "all", "average", "none", 2
-
-"access-om3.mom6.2d.T_diffx_2d.1mon.mean.%4yr", 1, "months", 1, "days", "time", 1, "years"
-"ocean_model", "T_diffx_2d", "T_diffx_2d", "access-om3.mom6.2d.T_diffx_2d.1mon.mean.%4yr", "all", "average", "none", 2
-
-"access-om3.mom6.2d.T_diffy_2d.1mon.mean.%4yr", 1, "months", 1, "days", "time", 1, "years"
-"ocean_model", "T_diffy_2d", "T_diffy_2d", "access-om3.mom6.2d.T_diffy_2d.1mon.mean.%4yr", "all", "average", "none", 2
-
-"access-om3.mom6.2d.T_hbd_diffx_2d.1mon.mean.%4yr", 1, "months", 1, "days", "time", 1, "years"
-"ocean_model", "T_hbd_diffx_2d", "T_hbd_diffx_2d", "access-om3.mom6.2d.T_hbd_diffx_2d.1mon.mean.%4yr", "all", "average", "none", 2
-
-"access-om3.mom6.2d.T_hbd_diffy_2d.1mon.mean.%4yr", 1, "months", 1, "days", "time", 1, "years"
-"ocean_model", "T_hbd_diffy_2d", "T_hbd_diffy_2d", "access-om3.mom6.2d.T_hbd_diffy_2d.1mon.mean.%4yr", "all", "average", "none", 2
-
 "access-om3.mom6.2d.friver.1mon.mean.%4yr", 1, "months", 1, "days", "time", 1, "years"
 "ocean_model", "friver", "friver", "access-om3.mom6.2d.friver.1mon.mean.%4yr", "all", "average", "none", 2
 
-"access-om3.mom6.2d.ficeberg.1mon.mean.%4yr", 1, "months", 1, "days", "time", 1, "years"
-"ocean_model", "ficeberg", "ficeberg", "access-om3.mom6.2d.ficeberg.1mon.mean.%4yr", "all", "average", "none", 2
-
-"access-om3.mom6.2d.ePBL_h_ML.1mon.mean.%4yr", 1, "months", 1, "days", "time", 1, "years"
-"ocean_model", "ePBL_h_ML", "ePBL_h_ML", "access-om3.mom6.2d.ePBL_h_ML.1mon.mean.%4yr", "all", "average", "none", 2
+"access-om3.mom6.2d.fsitherm.1mon.mean.%4yr", 1, "months", 1, "days", "time", 1, "years"
+"ocean_model", "fsitherm", "fsitherm", "access-om3.mom6.2d.fsitherm.1mon.mean.%4yr", "all", "average", "none", 2
 
-"access-om3.mom6.2d.h_ML.1mon.mean.%4yr", 1, "months", 1, "days", "time", 1, "years"
-"ocean_model", "h_ML", "h_ML", "access-om3.mom6.2d.h_ML.1mon.mean.%4yr", "all", "average", "none", 2
+"access-om3.mom6.2d.precip.1mon.mean.%4yr", 1, "months", 1, "days", "time", 1, "years"
+"ocean_model", "precip", "precip", "access-om3.mom6.2d.precip.1mon.mean.%4yr", "all", "average", "none", 2
 
 
 # monthly 2d max fields
 
 "access-om3.mom6.2d.mlotst.1mon.max.%4yr", 1, "months", 1, "days", "time", 1, "years"
 "ocean_model", "mlotst", "mlotst", "access-om3.mom6.2d.mlotst.1mon.max.%4yr", "all", "max", "none", 2
 
-"access-om3.mom6.2d.speed.1mon.max.%4yr", 1, "months", 1, "days", "time", 1, "years"
-"ocean_model", "speed", "speed", "access-om3.mom6.2d.speed.1mon.max.%4yr", "all", "max", "none", 2
-
-"access-om3.mom6.2d.zos.1mon.max.%4yr", 1, "months", 1, "days", "time", 1, "years"
-"ocean_model", "zos", "zos", "access-om3.mom6.2d.zos.1mon.max.%4yr", "all", "max", "none", 2
-
-"access-om3.mom6.2d.tos.1mon.max.%4yr", 1, "months", 1, "days", "time", 1, "years"
-"ocean_model", "tos", "tos", "access-om3.mom6.2d.tos.1mon.max.%4yr", "all", "max", "none", 2
-
-"access-om3.mom6.2d.sos.1mon.max.%4yr", 1, "months", 1, "days", "time", 1, "years"
-"ocean_model", "sos", "sos", "access-om3.mom6.2d.sos.1mon.max.%4yr", "all", "max", "none", 2
-
-"access-om3.mom6.2d.ePBL_h_ML.1mon.max.%4yr", 1, "months", 1, "days", "time", 1, "years"
-"ocean_model", "ePBL_h_ML", "ePBL_h_ML", "access-om3.mom6.2d.ePBL_h_ML.1mon.max.%4yr", "all", "max", "none", 2
-
-"access-om3.mom6.2d.h_ML.1mon.max.%4yr", 1, "months", 1, "days", "time", 1, "years"
-"ocean_model", "h_ML", "h_ML", "access-om3.mom6.2d.h_ML.1mon.max.%4yr", "all", "max", "none", 2
-
-
-# monthly 2d min fields
-
-"access-om3.mom6.2d.zos.1mon.min.%4yr", 1, "months", 1, "days", "time", 1, "years"
-"ocean_model", "zos", "zos", "access-om3.mom6.2d.zos.1mon.min.%4yr", "all", "min", "none", 2
-
-"access-om3.mom6.2d.tos.1mon.min.%4yr", 1, "months", 1, "days", "time", 1, "years"
-"ocean_model", "tos", "tos", "access-om3.mom6.2d.tos.1mon.min.%4yr", "all", "min", "none", 2
-
-"access-om3.mom6.2d.sos.1mon.min.%4yr", 1, "months", 1, "days", "time", 1, "years"
-"ocean_model", "sos", "sos", "access-om3.mom6.2d.sos.1mon.min.%4yr", "all", "min", "none", 2
-
 
 # daily 2D fields
 
@@ -259,32 +169,13 @@ ACCESS-OM3
 "access-om3.mom6.2d.speed.1day.mean.%4yr", 1, "days", 1, "days", "time", 1, "years"
 "ocean_model", "speed", "speed", "access-om3.mom6.2d.speed.1day.mean.%4yr", "all", "average", "none", 2
 
-"access-om3.mom6.2d.evs.1day.mean.%4yr", 1, "days", 1, "days", "time", 1, "years"
-"ocean_model", "evs", "evs", "access-om3.mom6.2d.evs.1day.mean.%4yr", "all", "average", "none", 2
-
-"access-om3.mom6.2d.fsitherm.1day.mean.%4yr", 1, "days", 1, "days", "time", 1, "years"
-"ocean_model", "fsitherm", "fsitherm", "access-om3.mom6.2d.fsitherm.1day.mean.%4yr", "all", "average", "none", 2
-
-"access-om3.mom6.2d.precip.1day.mean.%4yr", 1, "days", 1, "days", "time", 1, "years"
-"ocean_model", "precip", "precip", "access-om3.mom6.2d.precip.1day.mean.%4yr", "all", "average", "none", 2
-
-"access-om3.mom6.2d.net_massout.1day.mean.%4yr", 1, "days", 1, "days", "time", 1, "years"
-"ocean_model", "net_massout", "net_massout", "access-om3.mom6.2d.net_massout.1day.mean.%4yr", "all", "average", "none", 2
-
-"access-om3.mom6.2d.net_massin.1day.mean.%4yr", 1, "days", 1, "days", "time", 1, "years"
-"ocean_model", "net_massin", "net_massin", "access-om3.mom6.2d.net_massin.1day.mean.%4yr", "all", "average", "none", 2
-
-"access-om3.mom6.2d.massout_flux.1day.mean.%4yr", 1, "days", 1, "days", "time", 1, "years"
-"ocean_model", "massout_flux", "massout_flux", "access-om3.mom6.2d.massout_flux.1day.mean.%4yr", "all", "average", "none", 2
-
-"access-om3.mom6.2d.massin_flux.1day.mean.%4yr", 1, "days", 1, "days", "time", 1, "years"
-"ocean_model", "massin_flux", "massin_flux", "access-om3.mom6.2d.massin_flux.1day.mean.%4yr", "all", "average", "none", 2
+"access-om3.mom6.2d.friver.1day.mean.%4yr", 1, "days", 1, "days", "time", 1, "years"
+"ocean_model", "friver", "friver", "access-om3.mom6.2d.friver.1day.mean.%4yr", "all", "average", "none", 2
 
 
 # daily scalar timeseries
 
 "access-om3.mom6.scalar.1day.snap.%4yr", 1, "days", 1, "days", "time", 1, "years"
-"ocean_model", "masso", "masso", "access-om3.mom6.scalar.1day.snap.%4yr", "all", "none", "none", 1
 "ocean_model", "soga", "soga", "access-om3.mom6.scalar.1day.snap.%4yr", "all", "none", "none", 1
 "ocean_model", "thetaoga", "thetaoga", "access-om3.mom6.scalar.1day.snap.%4yr", "all", "none", "none", 1
 "ocean_model", "tosga", "tosga", "access-om3.mom6.scalar.1day.snap.%4yr", "all", "none", "none", 1
@@ -304,8 +195,3 @@ ACCESS-OM3
 "ocean_model", "total_friver", "total_friver", "access-om3.mom6.scalar.1day.snap.%4yr", "all", "none", "none", 1
 "ocean_model", "total_net_massout", "total_net_massout", "access-om3.mom6.scalar.1day.snap.%4yr", "all", "none", "none", 1
 "ocean_model", "total_net_massin", "total_net_massin", "access-om3.mom6.scalar.1day.snap.%4yr", "all", "none", "none", 1
-"ocean_model", "total_PRCmE", "total_PRCmE", "access-om3.mom6.scalar.1day.snap.%4yr", "all", "none", "none", 1
-"ocean_model", "total_evap", "total_evap", "access-om3.mom6.scalar.1day.snap.%4yr", "all", "none", "none", 1
-"ocean_model", "total_icemelt", "total_icemelt", "access-om3.mom6.scalar.1day.snap.%4yr", "all", "none", "none", 1
-"ocean_model", "total_frunoff", "total_frunoff", "access-om3.mom6.scalar.1day.snap.%4yr", "all", "none", "none", 1
-"ocean_model", "total_lrunoff", "total_lrunoff", "access-om3.mom6.scalar.1day.snap.%4yr", "all", "none", "none", 1