update doc - see COSIMA/access-om3#224

ACCESS-NRI · Sep 3, 2024 · 7de31c4 · 7de31c4
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diff --git a/doc/MOM_input b/doc/MOM_input
@@ -71,7 +71,7 @@ NJGLOBAL = 300                  !
                                 ! domain. With STATIC_MEMORY_ this is set in MOM_memory.h at compile time.
 
 ! === module MOM_fixed_initialization ===
-INPUTDIR = "./input/"           ! default = "."
+INPUTDIR = "./INPUT/"           ! default = "."
                                 ! The directory in which input files are found.
 
 ! === module MOM_grid_init ===
@@ -141,6 +141,12 @@ DTFREEZE_DP = -7.75E-08         !   [deg C Pa-1] default = 0.0
                                 ! When TFREEZE_FORM=LINEAR, this is the derivative of the freezing potential
                                 ! temperature with pressure.
 
+EPS_OMESH = 1e-13
+                                ! "default = 0.0001
+                                ! An float which sets the allowable error (in degrees) between
+                                ! grid angle defined in the ESMF mesh file used by CMEPS
+                                ! and the ocean_hgrid file used by mom
+
 ! === module MOM_tracer_flow_control ===
 USE_IDEAL_AGE_TRACER = True     !   [Boolean] default = False
                                 ! If true, use the ideal_age_example tracer package.
@@ -201,6 +207,9 @@ Z_INIT_FILE_PTEMP_VAR = "temp"  ! default = "ptemp"
                                 ! The name of the potential temperature variable in TEMP_Z_INIT_FILE.
 Z_INIT_ALE_REMAPPING = True     !   [Boolean] default = False
                                 ! If True, then remap straight to model coordinate from file.
+Z_INIT_REMAP_GENERAL = True     !   [Boolean] default = False
+                                ! If false, only initializes to z* coordinates. If true, allows initialization
+                                ! directly to general coordinates.
 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
@@ -620,8 +629,6 @@ SALT_RESTORE_FILE = "salt_sfc_restore.nc" ! default = "salt_restore.nc"
 SRESTORE_AS_SFLUX = True        !   [Boolean] default = False
                                 ! If true, the restoring of salinity is applied as a salt flux instead of as a
                                 ! freshwater flux.
-MAX_DELTA_SRESTORE = 0.5        !   [PSU or g kg-1] default = 999.0
-                                ! The maximum salinity difference used in restoring terms.
 GUST_CONST = 0.02               !   [Pa] default = 0.0
                                 ! The background gustiness in the winds.
 

diff --git a/doc/README_doc.md b/doc/README_doc.md
@@ -7,3 +7,4 @@ The files in here should be the minimum required to support code search from lin
 ## Update history
 1. Updated Mon 12 Feb 2024 14:22:51 AEDT from branch [1deg_jra55do_ryf](https://github.com/ACCESS-NRI/access-om3-configs/tree/1deg_jra55do_ryf) commit [a6829f9](https://github.com/ACCESS-NRI/access-om3-configs/tree/a6829f9)
 1. Updated Wed 27 Mar 2024 12:59:33 AEDT from branch [1deg_jra55do_ryf](https://github.com/ACCESS-NRI/access-om3-configs/tree/1deg_jra55do_ryf) commit [c2585c7](https://github.com/ACCESS-NRI/access-om3-configs/tree/c2585c7)
+1. Updated Mon  2 Sep 2024 16:14:36 AEST from branch [1deg_jra55do_ryf](https://github.com/ACCESS-NRI/access-om3-configs/tree/1deg_jra55do_ryf) commit [2bc6107](https://github.com/ACCESS-NRI/access-om3-configs/tree/2bc6107)
diff --git a/doc/config.yaml b/doc/config.yaml
@@ -2,41 +2,50 @@
 
 # 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: x77
 
 # Force payu to always find, and save, files in this scratch project directory
 # (you may need to add the corresponding PBS -l storage flag in sync_data.sh)
-shortpath: /scratch/v45
+# shortpath: /scratch/v45
 
 queue: normal
-ncpus: 48
+ncpus: 240
 jobfs: 10GB
-mem: 192GB
+mem: 960GB
 
 walltime: 01:00:00
 jobname: 1deg_jra55do_ryf
 
 model: access-om3
 
-exe: /g/data/ik11/spack/0.20.1/opt/linux-rocky8-cascadelake/intel-2021.6.0/access-om3-main-lxbeca7/bin/access-om3-MOM6-CICE6
-input: 
-    - /g/data/ik11/inputs/access-om3/0.x.0/1deg/share # shared grids and topography
-    - /g/data/ik11/inputs/access-om3/0.x.0/1deg/mom # grids, ICs etc
-    - /g/data/ik11/inputs/access-om3/0.x.0/1deg/cice # grids, ICs etc
-    - /g/data/ik11/inputs/access-om3/0.x.0/share/meshes/JRA55do-ESMFmesh.nc # mesh for JRA55-do stream
-    - /g/data/ik11/inputs/JRA-55/RYF/v1-4 # datm and drof JRA55-do streams data
+exe: access-om3-MOM6-CICE6
+input:
+    - /g/data/vk83/experiments/inputs/access-om3/share/meshes/global.1deg/2024.01.25/access-om2-1deg-ESMFmesh.nc
+    - /g/data/vk83/experiments/inputs/access-om3/share/meshes/global.1deg/2024.01.25/access-om2-1deg-nomask-ESMFmesh.nc
+    - /g/data/vk83/experiments/inputs/access-om3/share/meshes/share/2024.01.25/JRA55do-ESMFmesh.nc
+    - /g/data/vk83/experiments/inputs/access-om3/share/grids/global.1deg/2020.10.22/topog.nc
+    - /g/data/vk83/experiments/inputs/access-om3/mom/grids/mosaic/global.1deg/2020.05.30/ocean_hgrid.nc
+    - /g/data/vk83/experiments/inputs/access-om3/mom/grids/vertical/global.1deg/2023.07.28/ocean_vgrid.nc
+    - /g/data/vk83/experiments/inputs/access-om3/mom/initial_conditions/global.1deg/2020.10.22/ocean_temp_salt.res.nc
+    - /g/data/vk83/experiments/inputs/access-om3/mom/surface_salt_restoring/global.1deg/2020.05.30/salt_sfc_restore.nc
+    - /g/data/vk83/experiments/inputs/access-om3/cice/grids/global.1deg/2024.05.14/grid.nc
+    - /g/data/vk83/experiments/inputs/access-om3/cice/grids/global.1deg/2024.05.14/kmt.nc
+    - /g/data/vk83/experiments/inputs/access-om3/cice/initial_conditions/global.1deg/2023.07.28/iced.1900-01-01-10800.nc
+    - /g/data/vk83/experiments/inputs/JRA-55/RYF/v1-4/data
 
 collate: false
 runlog: false
+metadata: 
+    enable: false
 
 userscripts:
-    setup: ./setup_cice_restarts.sh
-    archive: ./archive_cice_restarts.sh
+    setup: /usr/bin/bash /g/data/vk83/apps/om3-scripts/payu_config/setup.sh
+    archive: /usr/bin/bash /g/data/vk83/apps/om3-scripts/payu_config/archive.sh
 
 modules:
-  use:
-      - /g/data/ik11/spack/0.20.1/modules/access-om3/0.x.0/linux-rocky8-cascadelake
-  load:
-      - intel-compiler/2021.6.0
-      - openmpi/4.1.4
-      - parallelio/2.5.10
+    use:
+        - /g/data/ik11/spack/0.21.2/modules/access-om3/0.x.0/linux-rocky8-cascadelake
+        - /g/data/hh5/public/modules
+    load:
+        - access-om3/63ed4a4777aeac0c62720ddbe7f85e4ed16f82eb_main
+        - conda/analysis3-24.01
diff --git a/doc/ice_in b/doc/ice_in
@@ -1,29 +1,32 @@
 &setup_nml
   bfbflag = "off" 
   conserv_check = .false.
-  debug_forcing = .true.
-  debug_model = .true.
   diagfreq = 960
   dumpfreq = "y"
   dump_last = .true.
   histfreq = "d", "m", "x", "x", "x"
+  hist_suffix = "", "m", "x", "x", "x" !limited to one character due to https://github.com/COSIMA/access-om3/issues/201
+  hist_time_axis = "middle"
+  history_deflate = 1
+  history_chunksize = 180, 150
   history_precision = 8
-  ice_ic = "./input/iced.1900-01-01-10800.nc"
+  restart_deflate = 1
+  ice_ic = "./INPUT/iced.1900-01-01-10800.nc"
   lcdf64 = .false.
   npt = 35040
   pointer_file      = './rpointer.ice'
   print_global      = .false.
 /
 &grid_nml
-  bathymetry_file = "./input/topog.nc"
+  bathymetry_file = "./INPUT/topog.nc"
   grid_atm = "A"
-  grid_file = "./input/grid.nc"
+  grid_file = "./INPUT/grid.nc"
   grid_format = "nc"
   grid_ice = "B"
   grid_ocn = "A"
   grid_type = "tripole"
   kcatbound = 0
-  kmt_file = "./input/kmt.nc"
+  kmt_file = "./INPUT/kmt.nc"
   nblyr = 1
   ncat = 5
   nfsd = 1
@@ -65,18 +68,18 @@
   ustar_min = 0.0005
 /
 &domain_nml
-  block_size_x = 16
-  block_size_y = 15
+  block_size_x = 15
+  block_size_y = 20
   distribution_type = "cartesian"
   distribution_wght = "latitude"
   maskhalo_bound = .true.
   maskhalo_dyn = .true.
   maskhalo_remap = .true.
-  max_blocks = 10
+  max_blocks = 15
   ns_boundary_type = "tripole"
   nx_global = 360
   ny_global = 300
-  processor_shape = "slenderX2"
+  processor_shape = "slenderX1"
 /
 &ice_prescribed_nml
 /
@@ -123,12 +126,26 @@
   f_fsurfn_ai = "m"
   f_hi = "md"
   f_hs = "md"
+  f_sifb = "md"
   f_snoice = "md"
   f_uvel = "md" , f_vvel = "md"
   f_vicen = "m"
   !-----------------------------------
   ! These fields are on by default (in ice_history_shared.F90) but lets turn them off
   !-----------------------------------
+  f_tlon         = .false. , f_tlat         = .false.
+  f_ulon         = .false. , f_ulat         = .false.
+  f_nlon         = .false. , f_nlat         = .false.
+  f_elon         = .false. , f_elat         = .false.
+  f_tmask        = .false. , f_umask        = .false.
+  f_nmask        = .false. , f_emask        = .false.
+  f_tarea        = .false. , f_uarea        = .false.
+  f_narea        = .false. , f_earea        = .false.
+  f_dxt          = .false. , f_dyt          = .false.
+  f_dxu          = .false. , f_dyu          = .false.
+  f_dxe          = .false. , f_dye          = .false.
+  f_dxn          = .false. , f_dyn          = .false.
+  f_HTN          = .false. , f_HTE          = .false.
   f_albpnd = 'x'
   f_atmdir = 'x' , f_atmspd = 'x'
   f_coszen = 'x'
@@ -157,4 +174,4 @@
   f_taubx = 'x' , f_tauby = 'x'
   f_Tref = 'x', f_Qref = 'x'
   f_uocn = 'x' , f_vocn = 'x'
-/
+/