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Changing the bathymetry, land-sea mask and OASIS remapping weights

This tutorial describes the process to follow when changing the bathymetry and land-sea mask for the purposes of, say, opening a strait or simulating a paleo-oceanographic situation.

1. Make your changes to the MOM topog.nc file

All changes to the bathymetry are made by creating a custom version of the topog.nc located in the MOM folder of the input (e.g. /short/public/access-om2/input_236a3011/mom_1deg for the 1-degree model). Any locations with a depth greater than 0 will be considered sea points subsequently for mask creation, while anything that has depth 0 (or negative depth) will be considered land. Place the new topography file in your own input folder (e.g. /short/e14/rmh561/access-om2/input/custom_topog_test/mom_1deg/). This new input folder needs to be refered to in your config.yaml in the mom submodule section above the default input folder (a similar line is needed to include the other custom input files below):

    - name: ocean
      model: mom
      exe: /short/e14/rmh561/access-om2/bin/fms_ACCESS-OM_1c1f23e_libaccessom2_b6caeab.x
      input:
         - /short/e14/rmh561/access-om2/input/custom_topog_test/mom_1deg
         - /short/public/access-om2/input_236a3011/mom_1deg

2. Changing the associated land–sea masks

Since the input topog.nc file has been changed, MOM's & CICE's land-sea masks will also need to be changed to match the new topography. The topog2mask script will create the corresponding CICE mask file (kmt.nc) and MOM mask file (ocean_grid.nc).

Download topogtools via:

git clone https://github.com/COSIMA/topogtools.git

This repository contains a simple python script (topog2mask.py) that will create the matching land–sea masks through the command: ./topog2mask.py topog.nc kmt.nc ocean_mask.nc

Place the new files in your input folder, referring to them in config.yaml above the public inputs (kmt.nc in the cice submodule).

3. Changing the OASIS remapping files

The OASIS coupler is in charge of feeding CICE with the correct atmospheric forcings. To do this, OASIS remaps the atmosphere grid into the corresponding CICE grid according to the remapping weights files specified for each field in the ATMOSPHERE --->>> ICE section of namcouple. The default remapping weights files (rmp_jra55_cice_conserve.nc and rmp_jra55_cice_smooth.nc) mask out the atmospheric forcings over land. If they are not remade then OASIS will feed the model 0's over every land point, which can result in a variety of errors (e.g. a division-by-zero runtime error associated with the air temperature, or problems with the air-sea heat flux, see Issue 173.

To remake the mapping files using the new land-sea masks use the script make_remap_weights.py in the access-om2/tools/ directory. This script needs the ocean_mask.nc and ocean_hgrid.nc input files from mom, as well as the JRA55 data directories and the yatm_1deg directory (not sure why for this last one?). I used the following command from a qsub script (executed from my custom_topog_test input directory) to get this working (I'm not on x77 so couldn't use Nic's directories):

../../tools/make_remap_weights.py ./ /g/data1/ua8/JRA55-do/RYF/v1-3/ ../yatm_1deg/ --atm JRA55 --ocean MOM1 --npes 16

(the ocean_mask.nc and ocean_hgrid.nc files must be in the ./mom_1deg folder). Note that the 1/4-degree and 1/10-degree models likely require more resources and a longer processing time (see the tools/make_remap_weights.sh qsub script).

This command produces the JRA55_MOM1_conserve.nc and JRA55_MOM1_patch.nc remapping weights files that should be copied into a commmon_1deg_jra55/ input directory and then referenced in config.yaml under the common inputs:

model: access-om2
input:
     - /short/e14/rmh561/access-om2/input/custom_topog_test/common_1deg_jra55
     - /short/public/access-om2/input_236a3011/common_1deg_jra55

Finally, the ATMOSPHERE --->>> ICE section of namcouple needs to be changed to refer to these new remap weights files. Replace all appearances of rmp_jra55_cice_conserve.nc with JRA55_MOM1_conserve.nc and rmp_jra55_cice_smooth.nc with JRA55_MOM1_patch.nc.

4. Checks

You should now be good to go. It is worth doing a payu setup to check that all input folders' paths are correct. Note that some of the problems won't neccessarily result in a error being thrown by the model (e.g. incorrect conserve remapping weights - see Issue 173). A useful field to look at to check that things are working is the net surface heat flux net_sfc_heating.