merge hot fixes from public release branch to develop branch

[junwang-noaa]

When public release branch is finalized, the hot fixes needs to be committed to develop branch.

Current we have following changes in fv3atm:
2. release/public-v1: bug fix for threading issue in stochastic physics (htps://github.com/NOAA-EMC/fv3atm/pull/62)
3. ufs_public_release: remove libxml2. (htps://github.com/NOAA-EMC/fv3atm/pull/55)
4. Fix dependencies for fv3cap library (htps://github.com/NOAA-EMC/fv3atm/pull/45)
5. make variables using filename_base consistant in length (htps://github.com/NOAA-EMC/fv3atm/pull/43)
6. Set default calendar to 'gregorian' (htps://github.com/NOAA-EMC/fv3atm/pull/34)
7. Remove unused and unsupported code (htps://github.com/NOAA-EMC/fv3atm/pull/31)

and following in NEMS:

1. fixes problem with MPI_Comm_Split in openmpi when hash is negative (fixes problem with MPI_Comm_Split in openmpi when hash is negative NOAA-EMC/NEMS#25)
2. Set default values for model_configure variables (Set default values for model_configure variables NOAA-EMC/NEMS#18)

more may come during the public release testing period.