Add PBS job and submission wrapper for bottom roughness generation on Gadi

[minghangli-uni]

closes #116

[minghangli-uni]

Below is the help message of submit_bottom_roughness.sh

$ ./submit_bottom_roughness.sh -h

Submit bottom roughness generation PBS job (Gadi).

./submit_bottom_roughness.sh -s PATH_TO_SAVE -r RESOLUTION -p true|false -g HGRID -t TOPOG -j PBS_SCRIPT

Note:
  Reusing PATH_TO_SAVE across resolutions is recommended. The WOA intermediate
  file (depth variance on the WOA grid) is resolution-independent and can be
  reused. After the first run, subsequent runs in the same directory will
  typically skip the intermediate step and only perform regridding much faster.

  However the final output filename is always 'bottom_roughness.nc'.
  Please run one resolution at a time and move or rename the output file
  (e.g. to /g/data/vk83/) before running the next resolution to avoid
  overwriting previous results.

  -h   Show this help message

Required arguments:
  -s   Path to save intermediate and final outputs
  -r   Resolution is one of: 100km, 25km, 8km, panan_4km.
  -p   Periodic mode: true (periodic longitude); false (aperiodic longitude) is not supported yet.
       (Sets BOTH PERIODIC_REGRID and PERIODIC_LON_LAPLACE as a bundle)
  -g   Path to ocean_hgrid.nc
  -t   Path to ocean_topog.nc
  -j   Path to PBS script

Examples:
  # periodic longitude
  ./submit_bottom_roughness.sh -s /path/to/save -r 25km -p true -g /path/to/hgrid.nc -t /path/to/topog.nc -j /path/to/pbs_bottom_roughness.pbs
  # aperiodic longitude (not supported yet)

Hence for 25km configs, one can do,

$ ./submit_bottom_roughness.sh \
-s . \
-p true \
-g /g/data/vk83/configurations/inputs/access-om3/mom/grids/mosaic/global.25km/2025.09.02/ocean_hgrid.nc \
-t /g/data/vk83/configurations/inputs/access-om3/share/grids/global.25km/2025.11.27/topog.nc \
-r 25km \
-j pbs_bottom_roughness.pbs

[minghangli-uni]

Hi @aekiss would you mind reviewing this?

[aekiss]

LGTM, thanks @minghangli-uni - I assume you've tested it?

[minghangli-uni]

LGTM, thanks @minghangli-uni - I assume you've tested it?

Yep I've tested it. Could you please approve this again?