Panan updates

MOM_input

@@ -10,6 +10,10 @@ V_TRUNC_FILE = "V_velocity_truncations" ! default = ""
                                 ! velocity truncations are written. Undefine this for efficiency if this
                                 ! diagnostic is not needed.
 
+! === module MOM_file_parser ===
+FATAL_UNUSED_PARAMS = True      !   [Boolean] default = False
+                                ! If true, kill the run if there are any unused parameters.
+
 ! This section contains non default layout parameters which are set.
 ! ------------------------
 ! === module MOM_domains ===
@@ -91,7 +95,7 @@ GRID_CONFIG = "mosaic"          !
                                 !     cartesian - use a (flat) Cartesian grid.
                                 !     spherical - use a simple spherical grid.
                                 !     mercator - use a Mercator spherical grid.
-GRID_FILE = "ocean_hgrid_cropped.nc" !
+GRID_FILE = "ocean_hgrid.nc"    !
                                 ! Name of the file from which to read horizontal grid data.
 RAD_EARTH = 6.371229E+06        !   [m] default = 6.378E+06
                                 ! The radius of the Earth.
@@ -122,8 +126,6 @@ TOPO_CONFIG = "file"            !
                                 !     Phillips - ACC-like idealized topography used in the Phillips config.
                                 !     dense - Denmark Strait-like dense water formation and overflow.
                                 !     USER - call a user modified routine.
-TOPO_FILE = "topog_Charrassin_nocavity_cropped.nc" ! default = "topog.nc"
-                                ! The file from which the bathymetry is read.
 MAXIMUM_DEPTH = 6000.0          !   [m]
                                 ! The maximum depth of the ocean.
 
@@ -198,7 +200,7 @@ REGRIDDING_COORDINATE_MODE = "ZSTAR" ! default = "LAYER"
                                 !  HYCOM1 - HyCOM-like hybrid coordinate
                                 !  HYBGEN - Hybrid coordinate from the Hycom hybgen code
                                 !  ADAPTIVE - optimize for smooth neutral density surfaces
-ALE_COORDINATE_CONFIG = "FILE:ocean_vgrid_cropped.nc,interfaces=zeta" ! default = "UNIFORM"
+ALE_COORDINATE_CONFIG = "FILE:ocean_vgrid.nc,interfaces=zeta" ! default = "UNIFORM"
                                 ! Determines how to specify the coordinate resolution. Valid options are:
                                 !  PARAM       - use the vector-parameter ALE_RESOLUTION
                                 !  UNIFORM[:N] - uniformly distributed
@@ -239,7 +241,7 @@ INIT_LAYERS_FROM_Z_FILE = True  !   [Boolean] default = False
                                 ! Z-space file on a latitude-longitude grid.
 
 ! === module MOM_initialize_layers_from_Z ===
-TEMP_SALT_Z_INIT_FILE = "ACCESS-OM2_IC_bfilled_smoothedland.nc" ! default = "temp_salt_z.nc"
+TEMP_SALT_Z_INIT_FILE = "ocean_temp_salt.res.nc" ! default = "temp_salt_z.nc"
                                 ! The name of the z-space input file used to initialize temperatures (T) and
                                 ! salinities (S). If T and S are not in the same file, TEMP_Z_INIT_FILE and
                                 ! SALT_Z_INIT_FILE must be set.
@@ -254,7 +256,7 @@ TEMP_SALT_INIT_VERTICAL_REMAP_ONLY = True !   [Boolean] default = False
                                 ! If true, initial conditions are on the model horizontal grid. Extrapolation
                                 ! over missing ocean values is done using an ICE-9 procedure with vertical ALE
                                 ! remapping .
-OBC_SEGMENT_001_DATA = "U=file:forcing_access_yr2_8km_fill.nc(u),V=file:forcing_access_yr2_8km_fill.nc(v),SSH=file:forcing_access_yr2_8km_fill.nc(eta_t),TEMP=file:forcing_access_yr2_8km_fill.nc(pot_temp),SALT=file:forcing_access_yr2_8km_fill.nc(salt)" !
+OBC_SEGMENT_001_DATA = "U=file:OBC37S_forcing_access_yr2_4km.nc(u),V=file:OBC37S_forcing_access_yr2_4km.nc(v),SSH=file:OBC37S_forcing_access_yr2_4km.nc(eta_t),TEMP=file:OBC37S_forcing_access_yr2_4km.nc(pot_temp),SALT=file:OBC37S_forcing_access_yr2_4km.nc(salt)" !
                                 ! OBC segment docs
 
 ! === module MOM_diag_mediator ===
@@ -265,7 +267,7 @@ DIAG_COORDS = "z Z ZSTAR", "rho2 RHO2 RHO" !
                                 ! A list of string tuples associating diag_table modules to a coordinate
                                 ! definition used for diagnostics. Each string is of the form
                                 ! "MODULE_SUFFIX,PARAMETER_SUFFIX,COORDINATE_NAME".
-DIAG_COORD_DEF_Z = "FILE:ocean_vgrid_cropped.nc,interfaces=zeta" ! default = "WOA09"
+DIAG_COORD_DEF_Z = "FILE:ocean_vgrid.nc,interfaces=zeta" ! default = "WOA09"
                                 ! Determines how to specify the coordinate resolution. Valid options are:
                                 !  PARAM       - use the vector-parameter DIAG_COORD_RES_Z
                                 !  UNIFORM[:N] - uniformly distributed
@@ -516,10 +518,7 @@ TKE_ITIDE_MAX = 0.1             !   [W m-2] default = 1000.0
 READ_TIDEAMP = True             !   [Boolean] default = False
                                 ! If true, read a file (given by TIDEAMP_FILE) containing the tidal amplitude
                                 ! with INT_TIDE_DISSIPATION.
-TIDEAMP_FILE = "tideamp_Charrassin_nocavity_cropped.nc" ! default = "tideamp.nc"
-                                ! The path to the file containing the spatially varying tidal amplitudes with
-                                ! INT_TIDE_DISSIPATION.
-H2_FILE = "bottom_roughness_Charrassin_nocavity_cropped.nc" !
+H2_FILE = "bottom_roughness.nc" !
                                 ! The path to the file containing the sub-grid-scale topographic roughness
                                 ! amplitude with INT_TIDE_DISSIPATION.
 BBL_EFFIC = 0.01                !   [nondim] default = 0.2
@@ -592,6 +591,14 @@ USE_RIVER_HEAT_CONTENT = True   !   [Boolean] default = False
 USE_CALVING_HEAT_CONTENT = True !   [Boolean] default = False
                                 ! If true, use the fluxes%calving_Hflx field to set the heat carried by runoff,
                                 ! instead of using SST*CP*froz_runoff.
+VAR_PEN_SW = True               !   [Boolean] default = False
+                                ! If true, use one of the CHL_A schemes specified by OPACITY_SCHEME to determine
+                                ! the e-folding depth of incoming short wave radiation.
+CHL_FILE = "chl_globcolour_monthly_clim.nc" !
+                                ! CHL_FILE is the file containing chl_a concentrations in the variable CHL_A. It
+                                ! is used when VAR_PEN_SW and CHL_FROM_FILE are true.
+CHL_VARNAME = "CHL"             ! default = "CHL_A"
+                                ! Name of CHL_A variable in CHL_FILE.
 
 ! === module MOM_energetic_PBL ===
 ML_OMEGA_FRAC = 0.001           !   [nondim] default = 0.0
@@ -655,11 +662,8 @@ LT_MOD_LAC5 = 0.22              !   [nondim] default = 0.95
                                 ! unstable Obukhov depth.
 
 ! === module MOM_opacity ===
-PEN_SW_SCALE = 15.0             !   [m] default = 0.0
-                                ! The vertical absorption e-folding depth of the penetrating shortwave
-                                ! radiation.
-PEN_SW_FRAC = 0.42              !   [nondim] default = 0.0
-                                ! The fraction of the shortwave radiation that penetrates below the surface.
+PEN_SW_NBANDS = 3               ! default = 1
+                                ! The number of bands of penetrating shortwave radiation.
 
 ! === module MOM_tracer_advect ===
 TRACER_ADVECTION_SCHEME = "PPM:H3" ! default = "PLM"
@@ -715,7 +719,7 @@ ENTHALPY_FROM_COUPLER = True    !   [Boolean] default = False
 FLUXCONST = 0.11                !   [m day-1] default = 0.0
                                 ! The constant that relates the restoring surface fluxes to the relative surface
                                 ! anomalies (akin to a piston velocity).  Note the non-MKS units.
-SALT_RESTORE_FILE = "salt_restore_interpolated_nearest.nc" ! default = "salt_restore.nc"
+SALT_RESTORE_FILE = "salt_sfc_restore.nc" ! default = "salt_restore.nc"
                                 ! A file in which to find the surface salinity to use for restoring.
 SRESTORE_AS_SFLUX = True        !   [Boolean] default = False
                                 ! If true, the restoring of salinity is applied as a salt flux instead of as a

config.yaml

@@ -32,22 +32,23 @@ jobname: 4km_panAn_om3
 model: access-om3
 exe: access-om3-MOM6-CICE6
 input:
-    - /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/panan.4km/2026.01.08/kmt.nc
+    - /g/data/vk83/prerelease/configurations/inputs/access-om3/panan.4km/2026.01.08/ocean_hgrid.nc
+    - /g/data/vk83/prerelease/configurations/inputs/access-om3/panan.4km/2026.01.08/ocean_vgrid.nc
+    - /g/data/vk83/prerelease/configurations/inputs/access-om3/panan.4km/2026.01.08/ocean_temp_salt.res.nc
+    - /g/data/vk83/prerelease/configurations/inputs/access-om3/panan.4km/2026.01.08/salt_sfc_restore.nc
+    - /g/data/vk83/prerelease/configurations/inputs/access-om3/panan.4km/2026.01.08/bottom_roughness.nc
+    - /g/data/vk83/prerelease/configurations/inputs/access-om3/panan.4km/2026.01.08/tideamp.nc
+    - /g/data/vk83/prerelease/configurations/inputs/access-om3/panan.4km/2026.01.08/topog.nc
+    - /g/data/vk83/prerelease/configurations/inputs/access-om3/panan.4km/2026.02.11/chl_globcolour_monthly_clim.nc
+    - /g/data/vk83/prerelease/configurations/inputs/access-om3/panan.4km/2026.01.08/access-om3-4km-ESMFmesh.nc
+    - /g/data/vk83/prerelease/configurations/inputs/access-om3/panan.4km/2026.01.08/access-om3-4km-nomask-ESMFmesh.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/tm70/cy8964/mom6/input/input-8km/access-om3-8km-rof-remap-weights_Charrassin_nocavity_cropped.nc
+    - /g/data/vk83/prerelease/configurations/inputs/access-om3/panan.4km/2026.01.08/access-om3-4km-rof-remap-weights.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
+    - /g/data/vk83/prerelease/configurations/inputs/access-om3/panan.4km/2026.01.08/OBC37S_forcing_access_yr2_4km.nc
+    - /g/data/vk83/prerelease/configurations/inputs/access-om3/panan.4km/2026.01.08/diag_rho2.nc
 
 runlog: true
 metadata: 
@@ -61,6 +62,10 @@ platform:
     nodesize: 104
     nodemem: 512
 
+mpi:
+  flags:
+    - --mca pml ucx --mca coll ^ucc -x UCX_RNDV_THRESH=inf
+
 collate:
   restart: true
   mpi: true

datm_in

@@ -8,8 +8,8 @@
   flds_preso3 = .false.
   flds_wiso = .false.
   iradsw = 1
-  model_maskfile = "./INPUT/access-om3-8km-nomask-ESMFmesh_Charrassin_nocavity_cropped.nc"
-  model_meshfile = "./INPUT/access-om3-8km-nomask-ESMFmesh_Charrassin_nocavity_cropped.nc"
+  model_maskfile = "./INPUT/access-om3-4km-nomask-ESMFmesh.nc"
+  model_meshfile = "./INPUT/access-om3-4km-nomask-ESMFmesh.nc"
   nx_global = 4320
   ny_global = 1442
   restfilm = "null"