MOM6 assimilate script for CESM

[hkershaw-brown]

Description:

assimilate.sh for MOM6 Draft pull request for initial review.

To do:

• inflation file movement
• CESM archiver - restart files need stashing for the next step (what to do here)
• sensible default filter options for MOM6

Fixes issue

fixes #451

Types of changes

• [ ] Bug fix (non-breaking change which fixes an issue)
• [x] New feature (non-breaking change which adds functionality)
• [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
• [ ] Documentation update

Documentation changes needed?

• [x] My change requires a change to the documentation.
  • [ ] I have updated the documentation accordingly.

Tests

Please describe any tests you ran to verify your changes.

Run on Derecho

Edit DART/models/MOM6/cesm_scripts/assimilate.sh:
   dart_build_dir=/path/to/DART/models/MOM6/work

Edit DART/models/MOM6/work/input.nml with assimilation options.  (this gets copied to the CESM run dir)

Get CESM 
git clone -b cesm2_3_alpha16g https://github.com/ESCOMP/CESM.git 
cd CESM

./manage_externals/checkout_externals -o

cime/scripts/create_newcase --run-unsupported --res T62_g16 --compset CMOM_JRA --case 
CMOM_JRA.T62_g16.ens3.alpha15g --ninst 3 --project P93300012 --multi-driver

Run CESM without DART: (default is 5 days)
cd CMOM_JRA.T62_g16.ens3.alpha15g
./case.setup 
./xmlchange DOUT_S=FALSE
./xmlchange CALENDAR=GREGORIAN
./xmlchange RUN_STARTDATE=2015-01-01
./case.build
./case.submit

Run with data assimilation:
./xmlchange CONTINUE_RUN=TRUE
./xmlchange DATA_ASSIMILATION_OCN=TRUE

./xmlchange DATA_ASSIMILATION_SCRIPT=/path/to/DART/models/MOM6/cesm_scripts/assimilate.sh

./xmlquery STOP_OPTION
./xmlchange STOP_N=1
./xmlquery DATA_ASSIMILATION_CYCLES

Edit user_nl_mom_000X 
   RESTART_CHECKSUMS_REQUIRED = False
./case.submit

Checklist for merging

• [ ] Updated changelog entry
• [ ] Documentation updated
• [ ] Update conf.py

Checklist for release

• [ ] Merge into main
• [ ] Create release from the main branch with appropriate tag
• [ ] Delete feature-branch

Testing Datasets

• [ ] Dataset needed for testing available upon request
• [ ] Dataset download instructions included
• [ ] No dataset needed

[hkershaw-brown]

closing, will reopen this or python+cime version based on needs of CROCODILE (regional MOM6 CESM).