Refactor fv3atm history & restart to reduce redundant code. Add rrfs-sd and clm lake to quilt restart.

[SamuelTrahanNOAA]

Description

This is a major refactoring of the restart and history I/O code, which also adds CLM Lake and RRFS-SD to the quilting restart. It eliminates code duplication between read vs. write and quilt vs. non-quilt. Most notably, it merges the giant Sfcprop copy loops for sfc read, non-quilt write, and quilt write into a single function. With these changes, the code will be easier to maintain, and read vs. write bugs will be easier to find.

1. The code in FV3GFS_io.F90 and FV3GFS_restart.F90 has been split into several files, divided by purpose.
   • High-level API:
     • fv3atm_restart_io.F90 = code to read or write restart files, whether by quilt or not
     • fv3atm_history_io.F90 = code to write history files, whether by quilt or not
   • Low-level API, only accessed by those two files:
     • fv3atm_oro_io.F90 = code that reads oro files.
     • fv3atm_clm_lake_io.F90 = all clm lake restart I/O
     • fv3atm_rrfs_sd_io.F90 = all rrfs-sd restart I/O and emissions reading.
     • fv3atm_sfc_io.F90 = all other sfc file restart I/O
     • fv3atm_common_io.F90 = common utilities.
2. The quilt restart code can read and write CLM Lake and RRFS-SD scheme data.
3. FV3GFS has been changed to fv3atm everywhere in the fv3atm repository, except output file metadata.
4. The three massive loops that copy to and from Sfcprop are now a single subroutine, Sfc_io_transfer. This way, any differences between restart read and write will stand out prominently. (They're controlled by reading and warm_start flags.)
5. Data storage is now inside derived types, eliminating the numerous module-level arrays and indexes.
6. Quilt restart variables pass an axis index list instead of axis length (fix from @DusanJovic-NOAA)
7. An unused CLM Lake axis is gone. This is needed to get the quilt restart to match, since it can't output axis variables for axes that are never used. (fix from @DusanJovic-NOAA)
8. Comments for every subroutine, function, module, and derived type
9. Removed a large block of code guarded by #ifdef JUNK
10. Deleted unused variables.
11. Consistent indentation in fv3*io.F90 files (emacs f90-mode default)

Issue(s) addressed

• Closes Quilt Restart doesn't support the CLM Lake Model or RRFS-SD Scheme #658
• Closes Having three versions of Sfcprop grid copy routines for sfc restart is error-prone. #659

Testing

How were these changes tested?

New regression tests in ufs-community/ufs-weather-model#1769

What compilers / HPCs was it tested with?

Hera intel and gnu.

Are the changes covered by regression tests? (If not, why? Do new tests need to be added?)

Yes, there are new regression tests.

Have the ufs-weather-model regression test been run? On what platform?

Yes, on hera.intel and hera.gnu.

Will the code updates change regression test baseline? If yes, why? Please show the baseline directory below.

Any code that writes out CLM Lake restart data will change because I removed an unneeded axis variable. This is necessary due to a limitation of the quilt restart: it can't write axis information for axes that are never used.

Please commit the regression test log files in your ufs-weather-model branch

Done.

Dependencies

None.

[SamuelTrahanNOAA]

I'd like to ping:

• @haiqinli whose RRFS-SD code I refactored from FV3GFS_io.F90 into FV3GFS_rrfs_sd_io.F90.
• @tanyasmirnova, who is the other developer involved in CLM Lake.
• @junwang-noaa who asked me to add RRFS-SD and CLM Lake restart functionality to the quilt

[tanyasmirnova]

@SamuelTrahanNOAA Sam, thank you very much for your excellent work to make the I/O subroutine well-organized. It was the most confusing subroutine for me, and with your changes it would be easier to understand and add variables to I/O if needed.

[SamuelTrahanNOAA]

At the behest of @DusanJovic-NOAA, I have refactored a bit more. The fv3atm_history_io.F90 contains all history file routines, and fv3atm_restart_io.F90 contains all restart file routines.

[SamuelTrahanNOAA]

It would be great if @climbfuji reviewed this, since I'm refactoring code he wrote.

[zach1221]

@tanyasmirnova would you be able to review this PR again? It appears your approval from two weeks ago dropped after a change.

[SamuelTrahanNOAA]

would you be able to review this PR again? It appears your approval from two weeks ago dropped after a change.

No, github still shows it as being approved.

[SamuelTrahanNOAA]

I think it wants two approvals from people with reviewer access.

[zach1221]

@SamuelTrahanNOAA Yes, correct. We need one more approving review from a reviewer with write access.

[climbfuji]

This is great work @SamuelTrahanNOAA. Just one question for my understanding.

[FernandoAndrade-NOAA]

Regression tests for 1769 have completed successfully. This is ready for merging. @jkbk2004