Cherry-pick 0.4.0 release related changes into 0.25deg ryf configuration (#169)

* License file

* Update incorrect note in MOM_override

See https://github.com/COSIMA/access-om3/issues/251

Co-authored-by: minghangli-uni <[email protected]>

* Add non-default from MOM_parameter_doc.layout in the middle

reorder MOM_input to follow MOM_parameter_doc.short

Put non-default values from MOM_parameter_doc.debugging at the top

Co-authored-by: Dougie Squire <[email protected]>

* Add WIND_STAGGER to MOM_INPUT for clarity

This only affects the logging, the actual value is hardcoded through a #ifdef CESMCOUPLED

* Change atm and ice mesh from 1deg -> 025deg
Change ice_ntasks to be 96

Remove unused components

payu-org/payu#496 Removed some checks in Payu which required unused components to be present in the nuopc.runconfig file.

Co-authored-by: Dougie Squire <[email protected]>

* Update to ACCESS-NRI/ACCESS-OM3 deployment 25.01.0

* Update field dictionary with latest from CMEPS

* add_gusts parameter needed for 0.4.0 build

* Update nuopc.runconfig to turn-off dates in restart_pointers

* Turn on netcdf4 per https://github.com/COSIMA/access-om3/issues/81

The new build uses openmpi4.1.7, which fixes some bugs preventing parallel reads over symlinks. This allows use of parallelio netcdf4 option, even though at this resolution for most components we will still only use one PE for IO.

* Use .d and .m in CICE history output filenames

Per https://github.com/COSIMA/access-om3/issues/201

* Turn off extra cice restarts and remove non functioning write_restart_at_endofrun

per https://github.com/COSIMA/access-om3/issues/175

* Set Earth radius the same as the UM

* Update MOM6 parameters and docs

See https://github.com/COSIMA/access-om3/issues/274

---------

Co-authored-by: anton-seaice <[email protected]>
Co-authored-by: Dougie Squire <[email protected]>
Co-authored-by: Anton Steketee <[email protected]>
Co-authored-by: dougiesquire <[email protected]>

Author: 3 people

LICENSE

@@ -1,5 +1,2 @@
-! WARNING: DO NOT EDIT this file! Any user change made in this file will be
-!          overriden. This file is automatically generated. MOM6 parameter
-!          changes may be made via SourceMods or user_nl_mom.
-!-------------------------------------------------------------------------
-
+! NOTE: User made changes to this file override the settings in MOM_input
+!       This provides a clear record of how your configuration differs from the standard

MOM_input

@@ -46,7 +46,7 @@ modules:
     use:
         - /g/data/vk83/modules
     load:
-        - access-om3/2024.09.0
+        - access-om3/2025.01.0
         - nco/5.0.5
 
-payu_minimum_version: 1.1.4
+payu_minimum_version: 1.1.6

MOM_override

@@ -77,6 +77,9 @@ DEBUG_BT = False                !   [Boolean] default = False
 ! The following parameters are used for diabatic processes.
 DEBUG_CONSERVATION = False      !   [Boolean] default = False
                                 ! If true, monitor conservation and extrema.
+WRITE_TRACER_MIN_MAX = False    !   [Boolean] default = False
+                                ! If true, write the maximum and minimum values of temperature, salinity and
+                                ! some tracer concentrations to stdout when the energy files are written.
 
 ! === module MOM_file_parser ===
 REPORT_UNUSED_PARAMS = True     !   [Boolean] default = True

config.yaml

@@ -7,7 +7,7 @@ GLOBAL_INDEXING = False         !   [Boolean] default = False
                                 ! static memory.
 
 ! === module MOM_domains ===
-!SYMMETRIC_MEMORY_ = False      !   [Boolean]
+!SYMMETRIC_MEMORY_ = True       !   [Boolean]
                                 ! If defined, the velocity point data domain includes every face of the
                                 ! thickness points. In other words, some arrays are larger than others,
                                 ! depending on where they are on the staggered grid.  Also, the starting index
@@ -25,7 +25,7 @@ THIN_HALO_UPDATES = True        !   [Boolean] default = True
                                 ! the PE count to be changed at run time.  This can only be set at compile time.
 AUTO_MASKTABLE = True           !   [Boolean] default = False
                                 ! Turn on automatic mask table generation to eliminate land blocks.
-MASKTABLE = "MOM_auto_mask_table"    ! default = "MOM_mask_table"
+MASKTABLE = "MOM_auto_mask_table" ! default = "MOM_mask_table"
                                 ! A text file to specify n_mask, layout and mask_list. This feature masks out
                                 ! processors that contain only land points. The first line of mask_table is the
                                 ! number of regions to be masked out. The second line is the layout of the model
@@ -38,19 +38,19 @@ MASKTABLE = "MOM_auto_mask_table"    ! default = "MOM_mask_table"
                                 !  4,6
                                 !  1,2
                                 !  3,6
-NIPROC = 36                     !
+NIPROC = 31                     !
                                 ! The number of processors in the x-direction. With STATIC_MEMORY_ this is set
                                 ! in MOM_memory.h at compile time.
-NJPROC = 30                     !
+NJPROC = 56                     !
                                 ! The number of processors in the y-direction. With STATIC_MEMORY_ this is set
                                 ! in MOM_memory.h at compile time.
-LAYOUT = 36, 30                 !
+LAYOUT = 31, 56                 !
                                 ! The processor layout that was actually used.
 AUTO_IO_LAYOUT_FAC = 0          ! default = 0
                                 ! When AUTO_MASKTABLE is enabled, io layout is calculated by performing integer
                                 ! division of the runtime-determined domain layout with this factor. If the
                                 ! factor is set to 0 (default), the io layout is set to 1,1.
-IO_LAYOUT = 1, 1                ! default = 1
+IO_LAYOUT = 1, 1                !
                                 ! The processor layout to be used, or 0,0 to automatically set the io_layout to
                                 ! be the same as the layout.