Update NUOPC cap and externals to match CAM

[nusbaume]

This PR updates the NUOPC cap to match the version used in cam6_3_160, as well as the externals. Additional clean-up was also performed, including the removal of the now deprecated MCT cap.

Resolves #146

Tests run:

Ran Kessler and Held-Suarez snapshot comparison runs on Derecho with GNU.

Ran official regression tests (test_driver.sh) with both GNU and Intel on Derecho.

[nusbaume]

@cacraigucar @peverwhee when reviewing the src/cpl/nuopc/* files I would avoid trying to review them on Github, and instead just diff them against the same files that are currently in the CAM development branch to see what the differences currently are between SIMA and CAM. Of course if you have any questions or concerns with those files just let me know. Thanks!

[cacraigucar]

To find my comments, I did a mixture of xxdiff cam6_3_037 vs cam6_3_161 and xxdiff cam6_3_161 vs your cam-sima fork.

[cacraigucar]

In this routine, I see:

• use_cslam was instituted as a replacement for fv_nphys>0
• line 256 no longer had =thermodynamic_active_species_num+3, but simply has =3
• at line 400, the GLL grid no longer has the 'area' attribute, just 'np' and 'ne'
• fvm_aerawt and physgrid_areawt were added in a number of places

[nusbaume]

Yep all of those changes will be coming in with my future SE dycore update PR (as each one of them will require non-trivial changes to the dycore code itself).

[cacraigucar]

Leaving this unresolved, just so I can find it again, but agree to deferring

[cacraigucar]

Leaving this unresolved, just so I can find it again, but agree to deferring

[peverwhee]

A few small things!

I also think someone recently added a "SHOULD" to the CAM Fortran coding standard to keep use statements at the lowest scope - something to consider.

Thanks @nusbaume !

[nusbaume]

@peverwhee Just FYI I also did some use statement re-arrangement to try and better match the Fortran coding standards for CAM-SIMA. I didn't completely finish the effort though, mostly to avoid making comparisons with the original CAM code overly difficult.

[peverwhee]

thanks @nusbaume !